Clinical trial NCT00924703
Conditions: Phenylketonuria
Sponsor: BioMarin Pharmaceutical
Start date: 2010-01-13; Completion date: 2019-01-31
Enrollment: 68 participants; Allocation: NA; Intervention model: SINGLE_GROUP

Brief summary:
This study is an extension of previous rAvPAL-PEG studies. Administration of rAvPAL-PEG will be continued to assess whether long-term dosing of rAvPAL-PEG is safe and can maintain reduced blood Phe concentrations in PKU subjects.

Detailed description:
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take rAvPAL-PEG. Subjects'previous rAvPAL-PEG dosing will continue in PAL-003. In PAL-003, each subject's dose will be adjusted as needed to attain or maintain blood Phe concentrations of 60-600 µmol/L. rAvPAL-PEG dose will be based on either a subject's weight or will be a fixed dose (subjects who have maintained blood Phe levels to 60-600 µmol/L for at least 2 consecutive weeks and who have maintained a stable rAvPAL-PEG dose for at least 2 consecutive weeks). Doses will be evaluated on an individual basis.

Arms: arm 1: rAvPAL-PEG in varying doses dependent on safety and efficacy.
Interventions: intervention 1: rAvPAL-PEG
Intervention descriptions: intervention 1: The doses are planned to be in the same range as those tested in PAL-002 or PAL-004 and then modified either by increasing or decreasing the dose, adhering to an upper limit up to 5.0 mg/kg per week or 375 mg/week, considering each subject's individual responses related to safety and efficacy.

Protocol documents:
Prot_000.pdf: 
 
 
 
 
    
 
 
 
 
 
 
Official Title: Long-term Extension of a Phase 2, Open-Label Dose-Finding Study to Evaluate the 
Safety, Efficacy, and Tolerability of Multiple Subcutaneous Doses of rAvPAL-PEG 
in Subjects with PKU 
 
NCT Number: NCT00924703 
 
Applicant/MAH: BioMarin Pharmaceutical Inc. 
 
Version Date: 31 March 2017  
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 




 
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2 
SYNOPSIS 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
TITLE OF STUDY: 
Long-term Extension of a Phase 2, Open-Label Dose-Finding Study to Evaluate the Safety, Efficacy, 
and Tolerability of Multiple Subcutaneous Doses of rAvPAL-PEG in Subjects with PKU 
PROTOCOL NUMBER:  PAL-003 
STUDY SITES:  Approximately 8 centers in the United States 
PHASE OF DEVELOPMENT:  Phase 2 
STUDY RATIONALE: 
The need exists for a treatment that will help individuals with phenylketonuria (PKU) safely achieve 
lifelong, reliable control of blood phenylalanine (Phe) concentrations and improve central nervous 
system developmental and functional outcomes. Phenylalanine ammonia lyase (rAvPAL-PEG) is a 
potential substitute for the phenylalanine hydroxylase (PAH) enzyme, which is defective in individuals 
with PKU. rAvPAL-PEG may control blood Phe concentrations, which may have additional clinical 
benefits. This study is an extension of the dose-finding study (Study PAL-002). Administration of 
rAvPAL-PEG will be continued to assess whether long-term dosing of rAvPAL-PEG is safe and can 
maintain reduced blood Phe concentrations in PKU subjects. 
OBJECTIVES: 
The primary objective of the study is: 
• 
To evaluate the effect of long-term administration of SC injections of rAvPAL-PEG on blood 
Phe concentrations in subjects with PKU. 
The secondary objectives of the study are: 
• 
To evaluate the safety and tolerability of long-term administration of subcutaneous (SC) 
injections of rAvPAL-PEG in subjects with PKU. 
• 
To evaluate the immune response to long-term administration of SC injections of 
rAvPAL-PEG in subjects with PKU who participated in Study PAL-002. 
• 
To evaluate steady-state PK of rAvPAL-PEG in subjects with PKU. 
STUDY DESIGN AND PLAN: 
This is a long-term extension of a Phase 2, open-label, dose-finding study (Study PAL-002) in 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
approximately 35 subjects with PKU. The doses are planned to be in the same range as those tested in 
PAL-002 (0.001 through 1.0 mg/kg per injection), provided no dose-limiting toxicity was observed in 
PAL-002. 
Only subjects who completed participation in PAL-002 will be enrolled into this study. Diet will not 
be altered during the course of this study, except as necessary for safety. 
Subjects will be evaluated for safety and for blood Phe concentrations throughout the study. Toxicity 
will be measured according to the National Cancer Institute (NCI) Common Terminology Criteria for 
Adverse Events (CTCAE), version 3. 
A Data Monitoring Committee will monitor the study. 
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take 
rAvPAL-PEG. PAL-002 participants’ rAvPAL-PEG dosing will continue in PAL-003 without 
interruption of weekly dosing. In PAL-003, each subject’s dose will be adjusted as needed to attain or 
maintain blood Phe concentrations below 480 µmol/L. Subjects will continue to receive injections in 
the clinic, administered by clinic staff, but may later be allowed to self-administer doses of study drug 
at home. Whether a subject may be allowed to self-administer study drug doses will be evaluated on an 
individual basis. 
The dose may be modified at any time for safety. 
Evaluations, observations, and procedures will be conducted at selected timepoints as shown in 
Table 2.1.1, Schedule of Events. After the subject’s blood Phe concentration has been controlled to 
within a target range (below 480 µmol/L), the subject may be asked to have additional blood draws for 
PK and blood Phe concentration analyses. 
A subject will continue in PAL-003 until one of the following occurs: 
1. The subject withdraws consent and discontinues from the study. 
2. The subject is discontinued from the study at the discretion of the Investigator. 
3. The drug becomes commercially available following the appropriate marketing approval. 
4. The study is terminated. 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
Dose Adjustment Methodology: 
Each subject’s dose may be modified based on the decision of the Investigator, in agreement with the 
Study Medical Officer. Depending upon the response to rAvPAL-PEG in PAL-002, a subject’s dose 
may be adjusted beginning on Day 1 of PAL-003 as follows. 
• 
The dose may be increased by increments of no more than 10-fold higher than the subject’s 
current dose. 
• 
The dose may be decreased as appropriate to achieve or maintain a favorable blood Phe 
concentration. 
• 
When adjusting the dose, a dose may be used that is between the dose cohort levels that were 
defined in the previous study (PAL-002). 
• 
The dose may be adjusted by increasing the frequency of injections per week, up to one dose 
per day, for a maximum total dose per week of 2 mg/kg. 
• 
When a dose is adjusted (either by changing the dose level or by changing the frequency of 
dosing), the subject must remain in the clinic for a minimum of 2 hours following the first 
modified dose administration, and an Investigator will remain on site during this time. 
Subjects must have blood Phe concentration tested 3 days after a dose adjustment. There must be a 
minimum of 2 weeks after each dose adjustment before any additional dose adjustments may be made, 
so that blood Phe concentrations can be assessed. 
Stopping Criteria: 
If an individual subject exhibits drug-related toxicity of CTCAE grade 3 or greater, that subject will 
have dosing halted until the toxicity resolves. The subject’s data will be evaluated by the Principal 
Investigator (PI) and the Study Medical Officer, and a decision will then be made whether to 
discontinue the subject from the study, restart dosing at the same dose level, or restart dosing at a 
lower dose level. 
In addition, if 2 or more subjects at a dose level exhibit drug-related toxicity of CTCAE grade 3 or 
greater, further dosing of subjects at that dose level and any higher dose levels will be halted until a 
safety assessment is completed. 
NUMBER OF SUBJECTS PLANNED:   
Approximately 35 subjects. 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
DIAGNOSIS AND ALL CRITERIA FOR INCLUSION AND EXCLUSION:  
Individuals eligible to participate in this study must meet all of the following criteria: 
• 
Must have completed participation in PAL-002. 
• 
Willing and able to provide written, signed informed consent, or, in the case of participants 
under the age of 18, provide written assent (if required) and written informed consent by a 
parent or legal guardian, after the nature of the study has been explained, and prior to any 
research-related procedures. 
• 
Willing and able to comply with all study procedures. 
• 
Females of childbearing potential must have a negative pregnancy test at Screening and be 
willing to have additional pregnancy tests during the study. Females considered not of 
childbearing potential include those who have been in menopause at least 2 years, or had tubal 
ligation at least 1 year prior to Screening, or who have had total hysterectomy. 
• 
Sexually active subjects must be willing to use an acceptable method of contraception while 
participating in the study. 
• 
Maintained a stable diet. 
• 
In generally good health as evidenced by physical examination, clinical laboratory evaluations 
(hematology, chemistry, and urinalysis), and electrocardiogram (ECG) at Screening. 
Individuals who meet any of the following exclusion criteria will not be eligible to participate in the 
study: 
• 
Use of any investigational product (with the exception of rAvPAL-PEG) or investigational 
medical device within 30 days prior to Screening, or requirement for any investigational agent 
prior to completion of all scheduled study assessments. 
• 
Use of any medication that is intended to treat PKU within 14 days prior to the administration 
of study drug. 
• 
Pregnant or breastfeeding at Screening or planning to become pregnant (self or partner) or to 
breastfeed at any time during the study. 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
• 
Concurrent disease or condition that would interfere with study participation or safety 
(eg, history or presence of clinically significant cardiovascular, pulmonary, hepatic, renal, 
hematologic, gastrointestinal, endocrine, immunologic, dermatologic, neurological, oncologic, 
or psychiatric disease). 
• 
Any condition that, in the view of the PI, places the subject at high risk of poor treatment 
compliance or of not completing the study. 
• 
Known hypersensitivity to rAvPAL-PEG or its excipients. 
• 
Alanine aminotransferase (ALT) concentration > 2 times the upper limit of normal. 
• 
Creatinine  > 1.5 times the upper limit of normal. 
INVESTIGATIONAL PRODUCT, DOSE, ROUTE AND REGIMEN: 
rAvPAL-PEG doses will be administered SC and the favorable dose (the dosage that provides control 
of blood Phe concentrations within the target range for a minimum of 2 weeks) will be determined for 
each subject by adjusting the dose level, dose frequency, or both, as agreed by the PI and the Study 
Medical Officer, based upon the subject’s response to doses. 
DURATION OF TREATMENT: 
Extension of multiple dosing will continue until one of the following occurs: 
1. The subject withdraws consent and discontinues from the study. 
2. The subject is discontinued from the study at the discretion of the Investigator. 
3. The drug becomes commercially available following the appropriate marketing approval. 
4. The study is terminated. 
REFERENCE THERAPY(IES), DOSE, ROUTE AND REGIMEN:  
None 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
CRITERIA FOR EVALUATION: 
Efficacy: 
Blood Phe concentrations will be measured. 
Safety: 
Safety will be evaluated on the incidence of adverse events (AEs) and clinically significant changes in 
vital signs or laboratory test results. 
Pharmacokinetic: 
Plasma concentrations of rAvPAL-PEG will be measured when steady-state levels of Phe are attained. 
STATISTICAL METHODS:  
Sample Size: 
Subjects who participated in PAL-002 may be enrolled into this study. No formal sample size 
calculation was conducted. 
Safety Analysis: 
All subjects who receive any amount of study drug in this study will be included in the safety analyses. 
Safety will be evaluated on the incidence of AEs, including serious AEs (SAEs), and clinically 
significant changes in vital signs and laboratory test results. 
Efficacy Analysis: 
Data from all subjects who receive any amount of study drug and who have any posttreatment efficacy 
data will be included in the efficacy analysis. 
Blood Phe concentration at each scheduled timepoint will be summarized using descriptive statistics 
(mean, standard deviation, median, minimum, and maximum). Change in blood Phe concentration 
from baseline to each scheduled timepoint will also be summarized. 
Pharmacokinetic Analysis: 
Data from all subjects who complete at least 2 weeks of the study will be included in the PK analysis. 
Steady-state PK (predose samples) of rAvPAL-PEG will be evaluated in PKU subjects after the 
subject has achieved and maintained target blood Phe concentration (below 480 µmol/L) for a 
minimum of 2 weeks (to allow assessment of blood Phe concentrations) and no further dose 
modification is planned. Once this target has been achieved, PK samples will be collected predose on 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
the same day each week for 3 consecutive weeks. 
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2.1 
Schedule of Events 
Table 2.1.1:  Schedule of Events 
Screeninga
Treatment Periodb,c 
Final F/U or 
ETV 
Week 1 
Weekly
Monthly (eg, 
Wk 4, 8, etc, 
Qrtly (eg, 
Wk 12, 24, 
etc) 
4 weeks after 
final dose 
Assessments and Events 
 
D 1 
 
 
 
 
Informed consent 
 
X 
 
 
 
 
 
Medical history and 
demographics 
 
X 
 
 
 
 
 
Physical examinationd 
 
X 
X 
 
 
X 
 
X 
Vital signs 
 
X 
X 
X 
X 
X 
 
X 
12-lead ECG 
 
X 
 
 
 
 
 
X 
Clinical laboratory testse 
 
X 
 
 
X 
X 
 
X 
Sedimentation rate 
 
X 
 
 
X 
 
X 
Urine pregnancy test 
 
X 
X 
 
X 
X 
 
X 
Injection-site inspectionf 
 
X 
(postdose)
X 
X 
X 
 
X 
Adverse eventsg 
 
XÅ------------------------------------------------------------------------Æ X 
Concomitant medications 
 
X 
X 
X 
X 
X 
 
X 
Diet query 
 
X 
X 
X 
X 
X 
 
X 
Serum rAvPAL-PEG 
antibodies 
 
X 
 
X 
X 
 
X 
Predose blood Phe and 
plasma tyrosineh 
 
X 
X 
X 
X 
X 
 
X 
Blood Phe (fingerstick)i 
 
 
3 days
postdos
e 
 
 
 
Predose PK samplej 
 
 
 
 
 
 
Administer IPk 
 
X 
X 
X 
X 
 
AE, adverse event; D, day; ECG, electrocardiogram; ETV, Early Termination Visit; F/U, Follow-up; IP, 
investigational product; PK, pharmacokinetics; Phe, phenylalanine; SAE, serious adverse event; Wk, week. 
a Screening assessments must be completed within 28 days from Day 1. These may be the same used for the 
Final Follow-up Visit of PAL-002, if they occur ≤ 28 days from Day 1. 
b Additional visits may occur if deemed necessary to monitor AEs or blood Phe, adjust dosing etc. 
c On days that a dose is given, all procedures should be performed predose, except where noted. 
d Complete physical examinations to include the evaluation of all major body systems, height (at Screening 
only), and weight. 
e Clinical laboratory tests to include hematology, chemistry, and urinalysis. 
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f If any injection site reaction is observed, the corresponding adverse event data must specify injection location 
(identify current vs. previous visit’s injection, e.g. right arm vs. left arm) 
g The reporting period for SAEs begins when informed consent is obtained and continues through 4 weeks after 
last dose or the final study visit. The reporting period for nonserious AEs is from the first administration of 
study drug to the final study visit. 
h Samples should be drawn in the morning, at least 2.5 hours after a meal. If dose is modified by increasing 
either dose frequency or dose level, additional blood Phe concentration testing should be done prior to each 
dose for the first 2 weeks following dose adjustment. 
i May be done by the subject at home. Samples should be taken in the morning, at least 2.5 hours after a meal. 
j. The PK blood samples will be collected after the subject has achieved and maintained target blood Phe 
concentration (below 480 µmol/L) for a minimum of 2 weeks. Once this target is achieved, predose PK 
samples will be collected on the same day each week for 3 consecutive weeks as specified in Section 9.7.3. 
k Dosing is up to 1.0 mg/kg per injection and up to one dose per day, for a total of up to 2.0 mg/kg/week. 
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3 TABLE OF CONTENTS 
1 
TITLE PAGE....................................................................................................................1 
2 SYNOPSIS...........................................................................................................................2 
2.1 
Schedule of Events.....................................................................................................9 
3 TABLE OF CONTENTS...................................................................................................11 
4 LIST OF ABBREVIATIONS AND DEFINITIONS OF TERMS....................................15 
5 ETHICS..............................................................................................................................19 
5.1 
Institutional Review Board or Ethics Committee ....................................................19 
5.2 
Ethical Conduct of Study .........................................................................................19 
5.3 
Subject Information and Informed Consent.............................................................20 
6 INVESTIGATORS AND STUDY ADMINISTRATIVE STRUCTURE ........................21 
7 INTRODUCTION .............................................................................................................22 
7.1 
Nonclinical Studies ..................................................................................................22 
7.2 
Previous Clinical Studies .........................................................................................23 
7.3 
Study Rationale ........................................................................................................23 
7.4 
Summary of Overall Risks and Benefits..................................................................24 
7.4.1 
Toxicity Due to Exposure to PEG...............................................................25 
7.4.2 
Toxicity Due to Immunologic Sensitization ...............................................25 
7.4.2.1 Management of Allergic Reactions .................................................26 
7.4.3 
Effects of Low Blood Phe ...........................................................................26 
8 STUDY OBJECTIVES......................................................................................................27 
9 INVESTIGATIONAL PLAN............................................................................................28 
9.1 
Overall Study Design and Plan ................................................................................28 
9.1.1 
Dose Adjustment Methodology...................................................................29 
9.1.2 
Stopping Criteria .........................................................................................29 
9.2 
Discussion of Study Design, Including Choice of Control Group...........................30 
9.3 
Selection of Study Population..................................................................................30 
9.3.1 
Inclusion Criteria.........................................................................................30 
9.3.2 
Exclusion Criteria........................................................................................31 
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9.3.3 
Removal of Subjects from Treatment or Assessment .................................31 
9.3.4 
Subject Identification and Replacement of Subjects...................................32 
9.4 
Treatments................................................................................................................33 
9.4.1 
Treatments Administered ............................................................................33 
9.4.2 
Identity of Investigational Product (IP).......................................................33 
9.4.2.1 Product Characteristics and Labeling..............................................33 
9.4.3 
Storage.........................................................................................................33 
9.4.4 
Directions for Administration .....................................................................33 
9.4.5 
Method of Assigning Subjects to Treatment Groups..................................34 
9.4.6 
Selection of Doses Used in the Study .........................................................34 
9.4.6.1 Selection of Timing of Dose for Each Subject................................34 
9.4.7 
Blinding.......................................................................................................34 
9.4.8 
Prior and Concomitant Medications............................................................34 
9.4.9 
Treatment Compliance ................................................................................35 
9.5 
Investigational Product Accountability....................................................................35 
9.5.1 
Return and Disposition of Clinical Supplies...............................................35 
9.6 
Dietary or Other Protocol Restrictions.....................................................................36 
9.7 
Efficacy and Safety Variables..................................................................................36 
9.7.1 
Efficacy and Safety Measurements Assessed .............................................36 
9.7.1.1 Demographic Data and Medical History .........................................36 
9.7.1.2 Physical Examination Findings .......................................................36 
9.7.1.3 Vital Sign Measurements.................................................................37 
9.7.1.4 Electrocardiography.........................................................................37 
9.7.2 
Efficacy Variable.........................................................................................37 
9.7.2.1 Blood Phenylalanine Concentrations...............................................37 
9.7.3 
Pharmacokinetic Variables..........................................................................37 
9.7.4 
Safety Variables ..........................................................................................37 
9.7.4.1 Pregnancy Testing ...........................................................................37 
9.7.4.2 rAvPAL-PEG-specific Antibodies ..................................................38 
9.7.5 
Clinical Laboratory Assessments ................................................................38 
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10 REPORTING ADVERSE EVENTS .................................................................................40 
10.1 Adverse Events.........................................................................................................40 
10.2 Serious Adverse Events............................................................................................42 
10.3 Pregnancy.................................................................................................................43 
10.4 BioMarin Pharmacovigilance Contact Information .................................................43 
11 APPROPRIATENESS OF MEASUREMENTS...............................................................44 
11.1 Pharmacokinetics .....................................................................................................44 
12 STUDY PROCEDURES ...................................................................................................45 
12.1 Prestudy....................................................................................................................45 
12.2 Screening Visit .........................................................................................................45 
12.3 Treatment Period......................................................................................................45 
12.3.1 Day 1 (Week 1) ...........................................................................................46 
12.3.2 Weekly Visits ..............................................................................................46 
12.3.3 Monthly Visits (Week 4, 8, 16, etc) ............................................................47 
12.3.4 Quarterly Visits (Week 12, 24, 36, etc).......................................................47 
12.4 Final Follow-up Visit (Day 113 [± 3 days]) /Early Termination Visit ....................48 
13 DATA QUALITY ASSURANCE.....................................................................................49 
14 STATISTICAL METHODS AND DETERMINATION OF SAMPLE SIZE..................50 
14.1 Statistical and Analytical Plans................................................................................50 
14.2 Safety Analysis.........................................................................................................50 
14.3 Pharmacokinetic Analysis........................................................................................50 
14.4 Efficacy Analysis .....................................................................................................50 
14.5 Determination of Sample Size..................................................................................51 
14.6 Handling of Missing Data ........................................................................................51 
14.7 Changes in the Conduct of the Study or Planned Analyses .....................................51 
15 DATA MONITORING COMMITTEE (DMC)................................................................52 
16 COMPENSATION, INSURANCE, AND INDEMNITY.................................................53 
17 CASE REPORT FORMS AND SOURCE DOCUMENTS..............................................54 
18 STUDY MONITORING AND AUDITING .....................................................................56 
19 RETENTION OF RECORDS ...........................................................................................57 
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20 USE OF INFORMATION AND PUBLICATION ...........................................................58 
21 REFERENCES ..................................................................................................................59 
22 INVESTIGATOR RESPONSIBILITIES ..........................................................................61 
22.1 Conduct of Study and Protection of Human Subjects..............................................61 
23 SIGNATURE PAGE .........................................................................................................62 
 
LIST OF TABLES 
Table 2.1.1:  Schedule of Events .............................................................................................. 9 
Table 9.7.1.1: Summary of Laboratory Assessments ............................................................. 36 
Table 9.7.5.1: Clinical Laboratory Tests ................................................................................ 39 
 
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4 
LIST OF ABBREVIATIONS AND DEFINITIONS OF TERMS 
Abbreviations 
ADR 
adverse drug reaction 
AE 
adverse event 
ALT 
alanine aminotransferase 
AST 
aspartate aminotransferase 
AUC 
area under the plasma concentration-time curve 
AUC0-7 days 
area under the plasma concentration-time curve from time zero on Day 1 to 
Day 8 
BUN 
blood urea nitrogen 
°C 
degree Celsius 
Ctrough 
predose concentration of rAvPAL-PEG 
CD 
Compact disk 
CFR 
Code of Federal Regulations 
CNS 
central nervous system 
CO2 
carbon dioxide 
CRA 
Clinical Research Associate 
CRF 
case report form 
CTCAE 
Common Terminal Criteria for Adverse Events 
CV 
cardiovascular 
DBP 
diastolic blood pressure 
DCF 
Data Clarification Form 
DMC 
Data Monitoring Committee 
ECG 
electrocardiogram 
ETV 
Early Termination Visit 
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FDA 
Food and Drug Administration 
f/u 
follow-up 
g 
gram 
GCP 
Good Clinical Practice 
GGT 
gamma-glutamyltransferase 
GI 
gastrointestinal 
IB 
Investigator’s Brochure 
IgG 
immunoglobulin G 
IgM 
immunoglobulin M 
ICF 
Informed Consent Form 
ICH 
International Conference on Harmonisation of Technical Requirements for 
Registration of Pharmaceuticals for Human Use 
IND 
Investigational New Drug 
IP 
investigational product 
IRB 
Institutional Review Board 
IV 
intravenous 
kg 
kilogram 
MedDRA 
Medical Dictionary for Regulatory Activities 
mg 
milligram 
mL 
milliliter 
mm Hg 
millimeter of mercury 
NAb 
neutralizing antibodies 
NCI 
National Cancer Institute 
OTC 
over the counter 
PAH 
phenylalanine hydroxylase 
PAL 
phenylalanine ammonia lyase 
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PEG 
methoxypolyethylene glycol 
Phe 
phenylalanine 
PI 
Principal Investigator 
PK 
pharmacokinetics 
PKU 
phenylketonuria 
rAvPAL-PEG phenylalanine ammonia lyase 
RBC 
red blood cell 
SAE 
serious adverse event 
SAP 
Statistical Analysis Plan 
SBP 
systolic blood pressure 
SC 
subcutaneous 
SD 
standard deviation 
SDV 
source data verified 
SGOT 
serum glutamic oxalo-acetic transaminase 
SGPT 
serum glutamic pyruvate transaminase 
US 
United States 
WBC 
white blood cell 
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Definition of Terms: 
Investigational Product (IP): 
“A pharmaceutical form of an active ingredient or placebo being tested or used as a reference 
in a clinical trial, including a product with a marketing authorization when used or assembled 
(formulated or packaged) in a way different from the approved form, or when used for an 
unapproved indication, or when used to gain further information about an approved use.” 
(from E6 ICH)  
The terms “IP” and “study drug” may be used interchangeably in the protocol. 
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5 
ETHICS 
5.1 
Institutional Review Board or Ethics Committee 
Prior to initiating the study, the Investigator will obtain written confirmation that the 
Institutional Review Board (IRB) is properly constituted and compliant with International 
Conference on Harmonisation of Technical Requirements for Registration of 
Pharmaceuticals for Human Use (ICH) and Good Clinical Practice (GCP) requirements, and 
applicable laws and local regulations. A copy of the confirmation from the IRB will be 
provided to BioMarin Pharmaceutical Inc. (BioMarin) or its designee. The Principal 
Investigator (PI) will provide the IRB with all appropriate material, including the protocol, 
Investigator’s Brochure (IB), the Informed Consent Form (ICF) including compensation 
procedures, and any other written information provided to the subjects, including all consent 
forms translated to a language other than the native language of the clinical site. The study 
will not be initiated and investigational product (IP) supplies will not be shipped to the site 
until appropriate documents from the IRB confirming unconditional approval of the protocol, 
the ICF and all subject recruitment materials are obtained in writing by the PI and copies are 
received at BioMarin or its designee. The approval document should refer to the study by 
protocol title and BioMarin protocol number (if possible), identify the documents reviewed, 
and include the date of the review and approval. BioMarin will ensure that the appropriate 
reports on the progress of the study were made to the IRB and BioMarin by the PI in 
accordance with applicable governmental regulations. 
5.2 
Ethical Conduct of Study 
This study will be conducted in accordance with the following: 
• United States (US) Code of Federal Regulations (CFR) sections that address clinical 
research studies, and/or other national and local regulations, as applicable 
• E6 ICH Guideline for GCP 
• The ethical principles established by the Declaration of Helsinki 
Specifically, this study is based on adequately performed laboratory and animal 
experimentation; the study will be conducted under a protocol reviewed and approved by an 
IRB; the study will be conducted by scientifically and medically qualified persons; the 
benefits of the study are in proportion to the risks; the rights and welfare of the subjects will 
be respected; the physicians conducting the study do not find the hazards to outweigh the 
potential benefits; and each subject, or his or her legally authorized representative will 
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provide written, informed consent before any study-related tests or evaluations are 
performed. 
5.3 
Subject Information and Informed Consent 
A properly written and executed ICF, in compliance with the Declaration of Helsinki, 
E6 ICH (GCP Guideline, Section 4.8) and 21 CFR §50 and other applicable local regulations, 
will be obtained for each subject prior to entering the subject into the study. The Investigator 
will prepare the ICF and provide the documents to BioMarin for approval prior to submission 
to the IRB. BioMarin and the IRB must approve the documents before they are implemented. 
A copy of the approved ICF, and if applicable, a copy of the approved subject information 
sheet, minor assent form, parental ICF for studies involving minors, and all ICFs translated to 
a language other than the native language of the clinical site must also be received by 
BioMarin or its designee prior to the delivery of study drug. 
Subjects under the age of 18 years will provide written assent (if required), and his/her 
legally authorized representative (parent or legal guardian) will provide written informed 
consent for such subjects. The Investigator will provide copies of the signed ICF to each 
subject (or the subject’s legally authorized representative) and will maintain the original in 
the subject’s record file. 
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6 
INVESTIGATORS AND STUDY ADMINISTRATIVE STRUCTURE 
Prior to beginning the study, the PI at each site must provide to BioMarin or its designee a 
fully executed and signed Form FDA (Food and Drug Administration) 1572 and a Financial 
Disclosure Form. All sub-Investigators must be listed on Form FDA 1572. Financial 
Disclosure Forms must also be completed for all sub-Investigators listed on the 
Form FDA 1572 who will be directly involved in the treatment or evaluation of research 
subjects in this study. 
The study will be administered by and monitored by employees or representatives of 
BioMarin. Clinical Research Associates (CRAs) or trained designees will monitor each site 
on a periodic basis and perform verification of source documentation for each subject as well 
as other required review processes. BioMarin’s Regulatory Affairs Department (or designee) 
will be responsible for the timely reporting of serious adverse events (SAEs) to appropriate 
regulatory authorities as required. 
Prior to database lock in multicenter studies, a Coordinating Investigator will be identified 
who will read the clinical study report and confirm that it accurately describes the conduct 
and results of the study, to the best of his or her knowledge. The Coordinating Investigator 
will be chosen on the basis of active participation in the study, ability to interpret data, and 
willingness to review and sign the report in a specified timeframe. 
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7 
INTRODUCTION 
A comprehensive review of phenylalanine ammonia lyase ( rAvPAL-PEG) is contained in 
the IB supplied by BioMarin; the Investigator should review this document prior to initiating 
this study. 
7.1 
Nonclinical Studies 
The murine model of phenylketonuria (PKU) BTBRPahenu2 (ENU2), a mouse line that is 
deficient in phenylalanine hydroxylase (PAH) activity (Shedlovsky, 1993, Genetics), was 
used for in vivo screening and pharmacodynamic studies. This mouse model exhibits 
characteristics similar to those seen in PKU patients, including hyperphenylalaninemia 
(baseline plasma phenylalanine [Phe] concentrations of 1000 to 2000 µM) and 
hypopigmentation. Weekly subcutaneous (SC) administration of 80 mg/kg of rAvPAL-PEG 
(approximately 4 IU/mouse) for greater than 3 months lowered blood Phe concentration from 
approximately 2000 µM to less than 200 µM. A similar profile of Phe reduction was also 
seen in ENU2 mice administered wild-type AvPAL-PEG (4 IU/mouse) over 8 weeks. In all 
these studies, regardless of the molecule, an attenuated Phe-lowering response was usually 
seen between Weeks 2 and 7. However, plasma Phe concentrations became stabilized at 
concentrations below 200 µM from Week 7 onward. In addition to the reduction of plasma 
Phe, a dose-related darkening in coat color occurred, indicating the biosynthesis of melanin, 
which was previously inhibited when plasma Phe could not be metabolized and plasma Phe 
concentrations were high. When administration of AvPAL-PEG was stopped for 2 to 7 weeks 
and then reinitiated with weekly administrations, no attenuated response was observed and 
Phe concentrations remained low throughout the week. 
The safety of rAvPAL-PEG was evaluated in safety pharmacology studies (respiratory, 
central nervous system [CNS] and cardiovascular [CV]) and toxicity with toxicokinetic 
studies (single and 28-day repeated dose) in rats and cynomolgus monkeys. Overall, in all 
toxicity studies no immune-related toxicities were seen either systemically or at the injection 
site. No specific methoxypolyethylene glycol (PEG)-related histological findings were 
observed during the 28-day repeated dose studies. 
Findings in cynomolgus monkeys dosed with a single administration of 
60 mg/kg rAvPAL-PEG included morbidity, decreased plasma Phe concentration, decreased 
protein synthesis, and gastrointestinal (GI) lesions. Plasma Phe concentrations were also 
reduced to below the level of detection in the lower dose groups, but without similar 
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toxicological consequence. Physiologically regulated Phe intake may have played a part in 
these morbidity results, although plasma Phe concentrations were low in all treated monkeys. 
The main finding in the 28-day study was the possible drug-related observation of minimal to 
slight degeneration of blood vessels of predominantly medium-sized muscular arteries with a 
non-dose-dependent involvement of different organs observed in 1 male in the 0.1 mg/kg and 
1 male and 1 female in the 1.0 mg/kg rAvPAL-PEG dose groups. 
The half-life of rAvPAL-PEG administered to normal rats at SC doses of 10, 25, and 
250 mg/kg, was 47, 33, and 44 hours, respectively, and exhibited modest area under the 
plasma concentration-time curve (AUC)-dose linearity. In the cynomolgus monkey after SC 
administration of rAvPAL-PEG, the half-life was 65 hours at 4 mg/kg, 71 hours at 12 mg/kg, 
and could not be determined at 60 mg/kg (the highest dose). Qualitatively, the kinetics of 
rAvPAL-PEG in the rat and monkey appear to have similar characteristics. The following 
findings were noted: (1) a 1-compartment model with first-order absorption appears to 
describe the plasma profiles of rAvPAL-PEG after single-dose administration, (2) absorption 
is slow and there is a long absorption period after SC administration to maximum plasma 
concentration, along with a long half-life, (3) elimination is slow and monophasic, (4) there 
does not appear to be a gender difference, and (5) AUC and the maximum plasma 
concentration (Cmax) are roughly linearly proportional. 
7.2 
Previous Clinical Studies 
This study is an extension of the second human clinical study with rAvPAL-PEG (Study 
PAL-002). Study PAL-001, the first-in-human clinical study of rAvPAL–PEG, was designed 
as a Phase 1, open-label, single-dose, dose-escalation study in approximately 35 subjects, 
16 to 50 years old, with PKU. The doses for this study are planned to be in the same range as 
those tested in PAL-001 and PAL-002 (0.001 through 1.0 mg/kg per injection), provided no 
dose-limiting toxicity was observed in those studies. 
7.3 
Study Rationale 
PKU is an autosomal, recessive, inherited disease characterized by deficiency in the enzyme 
PAH (Scriver CR, 2001, McGraw-Hill). Approximately 1 in every 10,000 infants in North 
America is born with PKU (Scriver CR, 2001, McGraw-Hill). Left untreated, PAH 
deficiency is associated with an abnormally elevated concentration of Phe, which is toxic to 
the brain (Kaufman, 1989, J Pediatr.) and can result in a variety of neuropathologic 
conditions, including mental retardation, microcephaly, delayed speech, seizures, and 
behavioral abnormalities (Scriver CR, 2001, McGraw-Hill). The brains of untreated patients 
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with PKU show evidence of hypomyelination and gliosis, arrest in cerebral development, 
and, in some cases, white matter degeneration (Huttenlocher, 2000, Eur.J Pediatr.). Elevated 
Phe during fetal development leads to severe mental retardation and can cause microcephaly, 
growth retardation, and congenital heart disease (Guttler, 2003, Pediatrics), (Koch, 2003, 
Pediatrics), (Lee, 2003, Pediatrics), (Levy, 2003, Pediatrics), (Matalon, 2003, Pediatrics), 
(Rouse, 2004, J.Pediatr.). 
For a subset of patients with residual enzyme activity, treatment with Kuvan® is an option. 
For all other patients, current management of PKU involves adherence to low-Phe medicinal 
diet formulas and dietary restriction of Phe-containing foods. Implementation of a 
Phe-restricted diet in infancy significantly reduces blood Phe concentrations and prevents 
many of the neuropathologic manifestations of PKU, including severe mental retardation. 
However, compliance with this restrictive diet can be difficult for older children, adolescents, 
and adults, and adherence may result in nutritional deficiencies due to the limitations of 
natural protein sources (Fisch, 2000, Eur.J.Pediatr.), (Walter, 2002, Lancet). 
The need exists for a treatment that will help individuals with phenylketonuria (PKU) safely 
achieve lifelong, reliable control of blood phenylalanine (Phe) concentrations and improve 
central nervous system developmental and functional outcomes. Phenylalanine ammonia 
lyase (rAvPAL-PEG) is a potential substitute for the phenylalanine hydroxylase (PAH) 
enzyme, which is defective in individuals with PKU. rAvPAL-PEG may control blood Phe 
concentrations, which may have additional clinical benefits. This study is an extension of the 
dose-finding study (PAL-002). Administration of rAvPAL-PEG will be continued to assess 
whether long-term dosing of rAvPAL-PEG is safe and can maintain reduced blood Phe 
concentrations in PKU subjects. 
7.4 
Summary of Overall Risks and Benefits 
It is not expected that data from PAL-001 and PAL-002 will change the assumption that 
rAvPAL-PEG has a toxicity profile similar to other recombinant PEGylated non-human 
enzymes currently in use. The toxicities of these drugs usually fall into 2 main categories: 
toxicity due to exposure to PEG, and toxicity due to immunologic sensitization. In addition, 
exaggerated pharmacological effects resulting in very low Phe concentrations could be 
observed. Other adverse events (AEs) that could occur with rAvPAL-PEG include 
injection-site reactions and other general symptoms. 
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7.4.1 Toxicity Due to Exposure to PEG 
Acute exposure to high doses of PEG can result in renal toxicity. There have been a few 
reports of PEG-related AEs in humans; cumulative intravenous (IV) PEG doses of 121 to 
240 g caused acute renal tubular necrosis, oliguria, and azotemia. The anticipated PEG 
exposure associated with the expected rAvPAL-PEG dose range (6 g per week) is at least 
80-fold lower than the reported toxic doses and comparable to exposures to PEG in widely 
used medicines and other compounds that are administered by the IV, oral, rectal, and topical 
routes (Webster, 2007, Drug Metab Dispos.). No indication of PEG-related toxicity at the 
ultrastructural level was observed in monkeys given up to 60 mg/kg of SC rAvPAL-PEG. 
In this study, subjects will be monitored closely with urine examinations and blood 
chemistries to follow kidney function. 
7.4.2 Toxicity Due to Immunologic Sensitization 
The active drug substance in rAvPAL-PEG is a bacterial protein, and as such, it is expected 
that it may elicit immune recognition and responses. In animal models, the immune response 
against the foreign protein PAL in rAvPAL-PEG has been mitigated by PEGylation. 
Epitopes that play a role in the immune response may be rendered inaccessible by PEG 
(Gamez, 2007, Mol.Genet.Metab). In vivo and in vitro experiments have shown that 
PEGylation of proteins and cells can attenuate the immunological response (Scott, 1997, 
Proc.Natl.Acad.Sci.U.S.A), (Chen, 2001, BioDrugs.). PEGylation has been effective in 
reducing anti-rAvPAL antibody titers in the mouse model, although PEGylation does not 
eliminate antibody formation. Although PEGylation of rAvPAL may have a significant effect 
on reducing the immunogenicity of the molecule, it is reasonable to expect that some 
individuals may exhibit immune responses upon exposure to the drug. These immune 
responses may be clinically irrelevant, cause symptoms of various degrees, or lead to 
neutralization of biological activity. Subjects participating in clinical trials will be monitored 
closely with specific antibody titers, sedimentation rates, and complete blood counts (CBCs). 
PEG itself is considered nonimmunogenic (Davis, 1981, Clin.Exp.Immunol.) (Harris, 2003, 
Nat.Rev.Drug Discov.), and antibodies against PEG seem to form only under special 
circumstances (Harris, 2003, Nat.Rev.Drug.Discov.) (Richter, 1983, Int.Arch.Allergy 
Appl.Immunol.) and may be of no clinical relevance in humans (Richter, 1984, 
Int.Arch.Allergy Appl.Immunol.). In some individuals, anti-PEG antibodies may be 
pre-existing due to previous exposure to PEG in other products. Anti-PEG antibodies have 
been associated with nonresponsiveness against therapy (Armstrong, 2007, Cancer), 
(Ganson, 2006, Arthritis Res.Ther.). 
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Allergic reactions to the SC injection of rAvPAL-PEG may be mild, moderate, or severe in 
intensity. Reactions may include pruritus, rash, shortness of breath, hypotension, or 
anaphylaxis. Clinical assessments should be conducted for a minimum of 2 hours after 
injection. Longer observations may be required at the discretion of the PI. The responsible 
physician should use all appropriate measures for the treatment of allergic reactions. Because 
of the small potential for anaphylaxis, equipment for emergency resuscitation (including 
epinephrine) should be within easy access during and after the rAvPAL-PEG injection. 
7.4.2.1 
Management of Allergic Reactions 
The following measures are recommended for the treatment of allergic symptoms: 
• Clearing the airway. 
• Vital sign check. 
• Administration of oral or IV diphenhydramine. 
• Administration of epinephrine if appropriate. 
• Administration of oxygen and IV fluids. 
• Administration of additional symptomatic treatment. 
• Transfer to an acute care facility of the study center. 
In addition, clinical judgment must be used in determining the appropriateness of 
corticosteroid administration. Acetaminophen or ibuprofen (5-10 mg/kg) may also be 
administered. An allergy and/or immunology consultation should be sought if necessary. 
7.4.3 Effects of Low Blood Phe 
Insufficient Phe intake or excessive rAvPAL-PEG exposure may cause blood Phe 
concentrations to be too low (eg, < 30 µmol/L). Prolonged low blood Phe concentrations can 
result in a catabolic state associated with poor growth and altered body functions, including 
mental and physical alterations, loss of appetite, anemia, rashes, and diarrhea. To ensure 
safety during this study, subjects will be monitored closely with frequent blood Phe 
concentration determinations. 
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8 
STUDY OBJECTIVES 
The primary objective of the study is: 
• To evaluate the effect of long-term administration of SC injections of rAvPAL-PEG 
on blood Phe concentrations in subjects with PKU. 
The secondary objectives of the study are: 
• To evaluate the safety and tolerability of long-term administration of subcutaneous 
(SC) injections of rAvPAL-PEG in subjects with PKU. 
• To evaluate the immune response to long-term administration of SC injections of 
rAvPAL-PEG in subjects with PKU who participated in Study PAL-002. 
• To evaluate steady-state PK of rAvPAL-PEG in subjects with PKU. 
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9 
INVESTIGATIONAL PLAN 
9.1 
Overall Study Design and Plan 
This is a long-term extension of a Phase 2, open-label, dose-finding study (PAL-002) in 
approximately 35 subjects with PKU. The doses are planned to be in the same range as those 
tested in PAL-002 (0.001 through 1.0 mg/kg per injection), provided no dose-limiting 
toxicity was observed in PAL-002. 
Only subjects who completed participation in PAL-002 will be enrolled into this study. Diet 
will not be altered during the course of this study, except as necessary for safety. 
Subjects will be evaluated for safety and for blood Phe concentrations throughout the study. 
Toxicity will be measured according to the National Cancer Institute (NCI) Common 
Terminology Criteria for Adverse Events (CTCAE), version 3. 
A Data Monitoring Committee will monitor the study. 
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take 
rAvPAL-PEG. PAL-002 participants’ rAvPAL-PEG dosing will continue in PAL-003 
without interruption of weekly dosing. In PAL-003, each subject’s dose will be adjusted as 
needed to attain or maintain blood Phe concentrations below 480 µmol/L based upon 
recommendations by the German Working Group for Metabolic Diseases (Burgard, 1999, 
Eur J Pediatr). Subjects will continue to receive injections in the clinic, administered by 
clinic staff, but may later be allowed to self-administer doses of study drug at home. Whether 
a subject may be allowed to self-administer study drug doses will be evaluated on an 
individual basis. All of the following criteria must be met before a subject may 
self-administer doses of the study drug: 
• The subject is willing and able to administer the study drug as directed. 
• The sponsor agrees that self-administration is appropriate. 
• The subject has achieved a favorable dose (ie, the dosage that provides control of 
blood Phe concentrations within the target range for a minimum of 2 weeks). 
• The subject has received appropriate training, including administering doses under 
supervision, until the subject and clinic staff both agree such training is no longer 
necessary. 
The dose may be modified at any time for safety. 
Evaluations, observations, and procedures will be conducted at selected timepoints as shown 
in Table 2.1.1, Schedule of Events. After the subject’s blood Phe concentration has been 
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controlled to within a target range (below 480 µmol/L), the subject may be asked to have 
additional blood draws for PK and blood Phe concentration analyses. 
A subject will continue in PAL-003 until one of the following occurs: 
1. The subject withdraws consent and discontinues from the study. 
2. The subject is discontinued from the study at the discretion of the Investigator. 
3. The drug becomes commercially available following the appropriate marketing 
approval. 
4. The study is terminated. 
9.1.1 Dose Adjustment Methodology 
Each subject’s dose may be modified based on the decision of the Investigator, in agreement 
with the Study Medical Officer. Depending upon the response to rAvPAL-PEG in PAL-002, 
a subject’s dose may be adjusted beginning on Day 1 of PAL-003 as follows. 
• The dose may be increased by increments of no more than 10-fold higher than the 
subject’s current dose. 
• The dose may be decreased as appropriate to achieve or maintain a favorable blood 
Phe concentration. 
• When adjusting the dose, a dose may be used that is between the dose cohort levels 
that were defined in the previous study (PAL-002). 
• The dose may be adjusted by increasing the frequency of injections per week, up to 
one dose per day, for a maximum total dose of 2 mg/kg/week. 
• When a dose is adjusted (either by changing the dose level or by changing the 
frequency of dosing), the subject must remain in the clinic for a minimum of 2 hours 
following the first modified dose administration, and an Investigator will remain on 
site during this time. 
Subjects must have blood Phe concentration tested 3 days after a dose adjustment. There 
must be a minimum of 2 weeks after each dose adjustment before any additional dose 
adjustments may be made so that blood Phe concentrations can be assessed. 
9.1.2 Stopping Criteria 
If an individual subject exhibits drug-related toxicity of CTCAE grade 3 or greater, that 
subject will have dosing halted until the toxicity resolves. The subject’s data will be 
evaluated by the Principle Investigator (PI) and the Study Medical Officer, and a decision 
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will then be made whether to discontinue the subject from the study, restart dosing at the 
same dose level, or restart dosing at a lower dose level. 
In addition, if 2 or more subjects at a dose level exhibit drug-related toxicity of CTCAE 
grade 3 or greater, further dosing of subjects at that dose level and any higher dose levels will 
be halted until a safety assessment is completed. 
9.2 
Discussion of Study Design, Including Choice of Control Group 
This open-label, Phase 2 trial was designed to be closely monitored with the goal of 
obtaining information about the efficacy, safety, tolerability, and PK of long-term 
administration of rAvPAL-PEG in subjects with PKU. There will be no control group in this 
study. 
9.3 
Selection of Study Population 
9.3.1 Inclusion Criteria 
Individuals eligible to participate in this study must meet all of the following criteria: 
• Must have completed participation in PAL-002. 
• Willing and able to provide written, signed informed consent, or in the case of 
subjects under the age of 18 years, provide written assent (if required) and written 
informed consent by a parent or legal guardian, after the nature of the study has been 
explained, and prior to any research-related procedures. 
• Willing and able to comply with all study procedures. 
• Females of childbearing potential must have a negative pregnancy test at Screening 
and be willing to have additional pregnancy tests during the study. Females 
considered not of childbearing potential include those who have been in menopause at 
least 2 years, or had tubal ligation at least 1 year prior to Screening, or who have had 
total hysterectomy. 
• Sexually active subjects must be willing to use an acceptable method of contraception 
while participating in the study. 
• Maintained a stable diet. 
• In generally good health as evidenced by physical examination, clinical laboratory 
evaluations (hematology, chemistry, and urinalysis), and electrocardiogram (ECG) at 
Screening. 
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9.3.2 Exclusion Criteria 
Individuals who meet any of the following exclusion criteria will not be eligible to participate 
in the study: 
• Use of any investigational product (with the exception of rAvPAL-PEG) or 
investigational medical device within 30 days prior to Screening, or requirement for 
any investigational agent prior to completion of all scheduled study assessments. 
• Use of any medication that is intended to treat PKU within 14 days prior to the 
administration of study drug. 
• Pregnant or breastfeeding at Screening or planning to become pregnant (self or 
partner) or to breastfeed at any time during the study. 
• Concurrent disease or condition that would interfere with study participation or safety 
(eg, history or presence of clinically significant cardiovascular, pulmonary, hepatic, 
renal, hematologic, gastrointestinal, endocrine, immunologic, dermatologic, 
neurological, oncologic, or psychiatric disease). 
• Any condition that, in the view of the PI, places the subject at high risk of poor 
treatment compliance or of not completing the study. 
• Known hypersensitivity to rAvPAL-PEG or its excipients. 
• Alanine aminotransferase (ALT) concentration > 2 times the upper limit of normal. 
• Creatinine > 1.5 times the upper limit of normal. 
9.3.3 Removal of Subjects from Treatment or Assessment 
Subjects (or their legally authorized representative) may withdraw their consent to participate 
in the study at any time without prejudice. The Investigator must withdraw from the study 
any subject who requests to be withdrawn. A subject’s participation in the study may be 
discontinued at any time at the discretion of the Investigator and in accordance with his/her 
clinical judgment. When possible, the tests and evaluations listed for the Early Termination 
Visit should be carried out (refer to Section 12.4). 
BioMarin must be notified of all subject withdrawals as soon as possible. BioMarin also 
reserves the right to discontinue the study at any time for either clinical or administrative 
reasons and to discontinue participation by an individual Investigator or site for poor 
enrollment or noncompliance. 
Reasons for which the Investigator or BioMarin may withdraw a subject from the study 
include, but are not limited to, the following: 
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• Subject experiences a serious or intolerable AE. 
• Subject develops a clinically significant laboratory abnormality. 
• Subject requires medication prohibited by the protocol. 
• Subject does not adhere to study requirements specified in the protocol. 
• Subject was erroneously admitted into the study or does not meet entry criteria. 
• Subject is lost to follow-up. 
• Subject becomes pregnant (refer to Section 10.3 for details on the reporting 
procedures to follow in the event of pregnancy). 
If a subject fails to return for scheduled visits, a documented effort must be made to 
determine the reason. If the subject cannot be reached by telephone within 7 days, a certified 
letter should be sent to the subject (or the subject’s legally authorized representative, if 
appropriate) requesting contact with the Investigator. This information should be recorded in 
the study records. 
The Investigator or designee must explain to each subject, before enrollment into the study, 
that for evaluation of study results, the subject’s protected health information obtained during 
the study may be shared with the study sponsor, regulatory agencies, and IRB. It is the 
Investigator’s (or designee’s) responsibility to obtain written permission to use protected 
health information per country-specific regulations, such as the Health Insurance Portability 
and Accountability Act (HIPAA) in the United States, from each subject, or if appropriate, 
the subject’s legally authorized representative. If permission to use protected health 
information is withdrawn, it is the Investigator’s responsibility to obtain a written request, to 
ensure that no further data will be collected from the subject and the subject will be removed 
from the study. 
9.3.4 Subject Identification and Replacement of Subjects 
Each subject was assigned a unique subject identifier in either PAL-001 or PAL-002. 
Subjects will retain the same subject number used in PAL-002. 
This unique identifier will be on all case report form (CRF) pages. In legal jurisdictions 
where use of initials is not permitted, a substitute identifier will be used.  
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9.4 
Treatments 
9.4.1 Treatments Administered 
BioMarin and/or its designee will provide the study site with a supply of IP sufficient for the 
completion of the study. 
9.4.2 Identity of Investigational Product (IP) 
9.4.2.1 
Product Characteristics and Labeling 
The rAvPAL-PEG drug product for SC injection is formulated and supplied as a sterile 
aqueous (colorless to pale yellow) solution in clear, single-use, type-1 borosilicate glass 
vials. Each 3 mL vial contains 1.5 ± 0.2 mL to deliver 10 mg of rAvPAL-PEG per 1 mL 
(10 mg/mL protein concentration). Each vial is filled with 1.5 ± 0.2 mL to allow the 
withdrawal and delivery of up to 1 mL of the drug product. 
Dilution instructions are provided in a separate instruction manual. 
The excipients in this drug product are tromethamine, tromethamine-hydrochloride, 
sodium chloride, L-phenylalanine, and water for injection. 
Drug product packaging will be identified with the lot number and expiration date, and will 
be provided in a box labeled with the study number. 
9.4.3 Storage 
At the study site, all IP must be stored at 5 ±3°C (41 ± 5°F) under the conditions specified in 
the IB in a secure area accessible only to the designated pharmacists and clinical site 
personnel. All IP must be stored and inventoried and the inventories must be carefully and 
accurately documented according to applicable state, federal and local regulations, ICH GCP, 
and study procedures. 
9.4.4 Directions for Administration 
Doses will be administered SC and the favorable dose will be determined for each subject by 
adjusting the dose level, dose frequency, or both, as agreed by the PI and the Study Medical 
Officer, based upon the subject’s response to doses. Dosing is up to a maximum dose per 
week of 2 mg/kg. 
Dosage is calculated by multiplying each subject’s weight in kilograms (kg) on Day 1 
(predose) by the assigned dose (in mg/kg). During the study, if the weight of a subject 
changes more than 10% from the measurement obtained at baseline or at a previous 
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measurement, the subject’s dose may be adjusted to accommodate the change. The change 
must be recorded. Refer to the Pharmacy Manual for additional information on calculating 
dosage. 
The injection sites should be alternated between doses, ie, upper left arm in Week 1, upper 
right arm in Week 2, etc. Doses may be administered in any of the common SC areas (upper 
arm, thigh, abdomen). If dose volume is such that a dose will be divided and given in more 
than 1 injection site, it is preferable to use both arms, both legs, or both sides of the abdomen. 
9.4.5 Method of Assigning Subjects to Treatment Groups 
This will be an open-label study; no randomization schedule will be generated. 
Subjects will retain the same subject number used in PAL-002. 
9.4.6 Selection of Doses Used in the Study 
This Phase 2 study aims to evaluate the efficacy, safety, tolerability, and PK parameters of 
multiple doses of rAvPAL-PEG after long-term administration in subjects with PKU. 
A favorable dose that produces a reduction in blood Phe concentration to below 480 µmol/L 
will be determined for each subject. Findings in cynomolgus monkeys dosed with a single 
administration of 60 mg/kg rAvPAL-PEG included severe morbidity, decreased plasma Phe 
concentration, decreased protein synthesis, and GI lesions. Plasma Phe concentrations were 
reduced to below the level of detection in the lower dose groups, without other findings. The 
doses for this study will be based upon the results of PAL-001 and PAL-002. 
9.4.6.1 
Selection of Timing of Dose for Each Subject 
Study drug will be administered in the morning by clinic staff or by the subject, if 
appropriate. 
9.4.7 Blinding 
This is an open-label study. 
9.4.8 Prior and Concomitant Medications 
All prescription and over-the-counter (OTC) medications taken by a subject for 30 days 
before Screening will be recorded on the designated CRF. The Investigator may prescribe 
additional medications during the study, as long as the prescribed medication is not 
prohibited by the protocol. In the event of an emergency, any needed medications may be 
prescribed without prior approval, but the medical monitor must be notified of the use of any 
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contraindicated medications immediately thereafter. Any concomitant medications added or 
discontinued during the study should be recorded on the CRF. 
Use of any investigational product (with the exception of rAvPAL-PEG used in PAL-002) or 
investigational medical device within 30 days before Screening, or requirement for any 
investigational agent prior to completion of all scheduled study assessments, is prohibited. 
Use of any medication that is intended to treat PKU within 14 days prior to the 
administration of study drug is prohibited. 
9.4.9 Treatment Compliance 
The date, time, volume, and concentration of each dose of study drug administered to each 
subject must be recorded in the dispensing log provided for the study, as well as on the 
appropriate CRF. This data will be used to assess treatment compliance. 
9.5 
Investigational Product Accountability 
The PI or designee is responsible for maintaining accurate records (including dates and 
quantities) of IP received, subjects to whom IP is dispensed (subject-by-subject dose specific 
accounting), and IP lost or accidentally or deliberately destroyed. The PI or designee must 
retain all unused or expired study supplies until the study monitor (on-site CRA) has 
confirmed the accountability data. 
9.5.1 Return and Disposition of Clinical Supplies 
Unused study drug must be kept in a secure location for accountability and reconciliation by 
the study monitor. The Investigator or designee must provide an explanation for any 
destroyed or missing study drug or study materials. 
Unused study drug may be destroyed on site, per the site’s standard operating procedures, but 
only after BioMarin has granted approval for drug destruction. The monitor must account for 
all study drug in a formal reconciliation process prior to study drug destruction. All study 
drug destroyed on site must be documented. Documentation must be provided to BioMarin 
and retained in the PIs study files. If a site is unable to destroy study drug appropriately, the 
site can return unused study drug to BioMarin upon request. The return of study drug or 
study drug materials must be accounted for on a Study Drug Return Form provided by 
BioMarin. 
All study drug and related materials should be stored, inventoried, reconciled, and destroyed 
or returned according to applicable state and federal regulations and study procedures. 
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9.6 
Dietary or Other Protocol Restrictions 
Subjects will be instructed that diet should not be altered during the course of the study 
except as necessary for safety. 
9.7 
Efficacy and Safety Variables 
9.7.1 Efficacy and Safety Measurements Assessed 
The Schedules of Events in the Synopsis (Section 2.1) describe the timing of required 
evaluations. 
For the laboratory assessments, the party responsible for performing the assessment and the 
pertinent protocol section describing the details of the test are listed in Table 9.7.1.1. 
Table 9.7.1.1: Summary of Laboratory Assessments 
Laboratory Assessment 
Party Responsible for 
Performing Test 
Section in Protocol for 
Details 
Clinical laboratory tests 
Central laboratory 
9.7.5 
rAvPAL-PEG-specific antibodies 
BioMarin 
9.7.4.2 
PK variables 
Central laboratory 
9.7.3 
Blood Phe concentrations 
Central laboratory 
9.7.2.1 
Phe, phenylalanine; PK, pharmacokinetic. 
9.7.1.1 
Demographic Data and Medical History 
Demographic data and a detailed medical history will be obtained at Screening. The medical 
history will include specific information concerning any prior or existing medical conditions 
that might interfere with study participation or safety. This medical history should elicit all 
major illnesses, diagnoses, and surgeries that the subject has ever had, and whether the 
subject has a history of alcohol and/or drug abuse. 
9.7.1.2 
Physical Examination Findings 
Physical examination will include assessment of weight; general appearance; CV; 
dermatologic; head, eyes, ears, nose, and throat; lymphatic; respiratory; GI; musculoskeletal; 
and neurological/psychological. Height will be measured at Screening only. Other body 
systems may be examined. Day 1 results will be the baseline values and clinically significant 
changes from baseline will be recorded as an AE. 
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9.7.1.3 
Vital Sign Measurements 
Vital signs will be measured after resting for 5 minutes, and include seated systolic blood 
pressure (SBP) and diastolic blood pressure (DBP) measured in millimeters of mercury 
(mm Hg), heart rate in beats per minute, respiration rate in breaths per minute, and 
temperature in degrees Celsius (°C). 
9.7.1.4 
Electrocardiography 
A standard 12-lead ECG will be recorded while the subject is resting, at Screening and at the 
final follow-up (F/U) Visit or Early Termination Visit (ETV). If clinically significant 
abnormalities are noted at Screening, the PI or designee is required to assess whether it is 
appropriate for the subject to enroll in the study. 
9.7.2 Efficacy Variable 
9.7.2.1 
Blood Phenylalanine Concentrations 
Blood samples for Phe concentration measurements will be drawn in the morning, at least 
2.5 hours after a meal, on the days and timepoints indicated in the Schedule of Events  
(Table 2.1.1). 
In addition, 3 days after each administration of study drug, the subject will have a blood Phe 
measurement by fingerstick. This may be done by the subject at home. 
A central laboratory will be used for blood Phe concentration analysis. 
9.7.3 Pharmacokinetic Variables 
Steady-state PK (predose samples) of rAvPAL-PEG will be evaluated in PKU subjects after 
the subject has achieved and maintained target blood Phe concentration (below 480 µmol/L) 
for a minimum of 2 weeks (to allow assessment of blood Phe concentrations) and no further 
dose modification is planned. Once this target has been achieved, PK samples will be 
collected predose on the same day each week for 3 consecutive weeks. 
BioMarin will perform the analysis. 
9.7.4 Safety Variables 
9.7.4.1 
Pregnancy Testing 
Female subjects of childbearing potential will have a urine pregnancy test at the timepoints 
specified in the Schedules of Events (Table 2.1.1). Female subjects with a positive pregnancy 
test at Screening do not meet eligibility criteria for enrollment. 
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Additional pregnancy tests will be performed at any visit in which pregnancy status is in 
question. Serum pregnancy tests will be performed in the event of a positive or equivocal 
urine pregnancy test results. 
Refer to Section 10.3 for details on the reporting procedures to follow in the event of 
pregnancy. 
9.7.4.2 
rAvPAL-PEG-specific Antibodies 
Immunoglobulin G (IgG) and M (IgM) antibodies and neutralizing antibodies (NAb) to 
rAvPAL-PEG will be measured using validated immunogenicity assays at the timepoints 
indicated in the Schedules of Events (Table 2.1.1). 
BioMarin will perform the analysis. 
9.7.5 Clinical Laboratory Assessments 
Any abnormal test results determined to be clinically significant by the Investigator should 
be repeated (at the Investigator’s discretion) until the cause of the abnormality is determined, 
the value returns to baseline or to within normal limits, or the Investigator determines that the 
abnormal value is no longer clinically significant. 
All clinical laboratory result pages should be initialed and dated by an Investigator, along 
with a comment regarding whether or not the result is clinically significant. 
The diagnosis, if known, associated with abnormalities in clinical laboratory tests that are 
considered clinically significant by the Investigator will be recorded on the AE CRF. 
Specific days for obtaining samples are provided in Table 2.1.1 and in Section 12. The 
scheduled clinical laboratory tests are listed in Table 9.7.5.1. A central laboratory will be 
used for analysis. 
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Table 9.7.5.1: Clinical Laboratory Tests 
Blood Chemistry 
Hematology 
Urine Tests 
Other 
Albumin  
Hemoglobin  
Appearance 
Alkaline 
Phosphatase  
Hematocrit  
Color 
Pregnancy test, if 
applicable 
ALT (SGPT)  
WBC count 
pH 
Pharmacokinetics 
AST (SGOT) 
RBC count 
Specific gravity 
Tyrosine 
Total bilirubin 
Platelet count 
Ketones 
BUN 
Differential cell count 
Protein 
Creatinine 
Sedimentation rate 
Glucose 
Serum rAvPAL-PEG-
specific antibodies 
(IgG, IgM, and NAb) 
GGT 
 
Bilirubin 
 
Total protein 
 
Nitrite 
 
Calcium 
 
Urobilinogen 
 
Sodium 
 
Hemoglobin 
 
Potassium 
 
 
 
Glucose 
 
 
 
Uric acid 
 
 
 
CO2 
 
 
 
Chloride 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
ALT, alanine aminotransferase; AST, aspartate aminotransferase; BUN, blood urea nitrogen; CO2, carbon 
dioxide; GGT, gamma-glutamyltransferase; IgG, immunoglobulin G; IgM, immunoglobulin M; NAb, 
neutralizing antibodies; RBC, red blood cell; SGOT, serum glutamic-oxaloacetic transaminase; SGPT, serum 
glutamic-pyruvic transaminase; WBC, white blood cell. 
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10 
REPORTING ADVERSE EVENTS 
10.1 
Adverse Events 
According to the ICH definition, an AE (or adverse experience) is “any untoward medical 
occurrence in a patient or clinical investigation subject administered a pharmaceutical 
product, and that does not necessarily have a causal relationship with this treatment. An AE 
can therefore be any unfavorable and unintended sign (including an abnormal laboratory 
finding), symptom, or disease temporally associated with the use of a medicinal 
(investigational) product, whether or not considered related to the IP.” 
An adverse drug reaction (ADR) is described by the ICH as “all noxious and unintended 
responses to a medicinal product related to any dose.” This means that a causal relationship 
between a medicinal product and an AE is at least a reasonable possibility, ie, the 
relationship cannot be ruled out. 
An AE may include intercurrent illnesses or injuries that represent an exacerbation (increase 
in frequency, severity, or specificity) of pre-existing conditions (eg, worsening of asthma). 
Whenever possible, it is preferable to record a diagnosis as the AE term rather than a series 
of terms relating to a diagnosis. 
The reporting period for non-serious AEs is the period from the first administration of study 
drug through the final F/U Visit or at the ETV. If a non-serious AE remains unresolved at the 
conclusion of the study, the PI and medical monitor will make a joint clinical assessment as 
to whether continued follow-up of the AE is warranted, and the results of this assessment 
must be documented. Resolution is defined as the return to baseline status or stabilization of 
the condition with the expectation that it will remain chronic. 
The Investigator will assess AEs for severity, for relationship to IP, and as to whether the 
event meets one or more of the definitions of an SAE (refer to Section 10.2). 
The Investigator will determine the severity of each AE and will record it on the source 
documents and AE CRF, using the categories defined below. 
Grade 
Description 
Mild 
No limitation of usual activities 
Moderate 
Some limitation of usual activities 
Severe 
Inability to carry out usual activities 
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The term “severe” is often used to describe the intensity (severity) of a specific event (as in 
mild, moderate, or severe myocardial infarction); the event itself, however, may be of 
relatively minor medical significance (such as severe headache). This is not the same as 
“serious,” which is based on subject/event outcome or action criteria usually associated with 
events that pose a threat to a subject’s life or functioning. Seriousness (not severity) serves as 
a guide for defining regulatory reporting obligations. 
The Investigator will determine the relationship of an AE to the IP and will record it on the 
source documents and AE CRF, using the categories defined below. 
Relationship 
Description 
Not Related 
Exposure to the IP has not occurred 
OR 
The administration of the IP and the occurrence of the AE are not 
reasonably related in time  
OR 
The AE is considered likely to be related to an etiology other than 
the use of the IP; that is, there are no facts [evidence] or arguments 
to suggest a causal relationship to the IP. 
Possibly 
Related 
The administration of the IP and the occurrence of the AE are 
reasonably related in time 
AND 
The AE could be explained equally well by factors or causes other 
than exposure to the IP. 
Probably 
Related 
The administration of IP and the occurrence of the AE are 
reasonably related in time  
AND 
The AE is more likely explained by exposure to the IP than by other 
factors or causes. 
In order to classify AEs and diseases, preferred terms will be assigned by the sponsor to the 
original terms entered on the CRF, using MedDRA (Medical Dictionary for Regulatory 
Activities terminology). 
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10.2 
Serious Adverse Events 
A SAE is defined as any AE that: 
• Results in death. 
• Is life threatening, that is, places the subject at immediate risk of death from the event 
as it occurred. This definition does not include a reaction that, had it occurred in a 
more severe form, might have caused death. 
• Requires in-patient hospitalization or prolongation of an existing in-patient 
hospitalization. Admission of a subject to the hospital as an in-patient as a result of an 
AE, even if the subject is released on the same day, qualifies as hospitalization. 
• Results in persistent or significant disability or incapacity. An event qualifies as 
resulting in a persistent or significant disability or incapacity if it involves a 
substantial disruption of the subject’s ability to carry out usual life functions. This 
definition is not intended to include experiences of relatively minor or temporary 
medical significance. 
• Is a congenital anomaly or birth defect, that is, an AE that occurs in the child or fetus 
of a subject exposed to IP prior to conception or during pregnancy. 
• Is an important medical event that does not meet any of the above criteria, but may 
jeopardize the subject or require medical or surgical intervention to prevent one of the 
outcomes listed above. Examples of such events are intensive treatment in the 
emergency room, allergic bronchospasm, blood dyscrasias or convulsions that do not 
result in hospitalization; or development of drug dependency or drug abuse. 
More than one of the above criteria may apply to any specific event. 
The reporting period for SAEs begins earlier than non-serious AEs and is the period from the 
time of signing of the ICF through 4 weeks after the last dose or at the ETV. SAEs reported 
to the Investigator outside of this reporting period will be reported to BioMarin if, in good 
medical judgment, the event has any bearing on the study data. SAEs must be followed by 
the Investigator until resolution, even if this extends beyond the study-reporting period. 
Resolution of an SAE is defined as the return to baseline status or stabilization of the 
condition with the expectation that it will remain chronic. 
Any SAE, whether or not considered related to study drug, will be reported immediately 
(within 24 hours) to BioMarin Pharmacovigilance by fax using the study-specific 
SAE Report Form. In addition to the outcome of the SAE, any medication or other 
therapeutic measures used to treat the event will be recorded on the appropriate CRF page(s). 
Investigators should not wait to collect additional information that fully documents the event 
before notifying BioMarin Pharmacovigilance of an SAE. BioMarin may be required to 
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report certain SAEs to regulatory authorities within 7 calendar days of being notified about 
the event; therefore, it is important that Investigators submit additional information requested 
by BioMarin as soon as it becomes available. 
Reporting of SAEs to the IRB will be done in compliance with the standard operating 
procedures and policies of the IRB and with applicable regulatory requirements. Adequate 
documentation must be obtained by BioMarin showing that the IRB was properly and 
promptly notified as required. 
10.3 
Pregnancy 
Pregnancy in a subject or partner should be reported immediately (within 24 hours) to 
BioMarin Pharmacovigilance by fax using the Pregnancy Form in the study reference 
materials. In addition, pregnancy in a subject is also reported on the End of Study CRF. The 
Investigator must make every effort to follow the subject through resolution of the pregnancy 
(delivery or termination) and to report the resolution on the Pregnancy Follow-up Form in the 
study reference materials. In the event of pregnancy in the partner of a study subject, the 
Investigator should make every reasonable attempt to obtain the woman’s consent for release 
of protected health information. 
10.4 
BioMarin Pharmacovigilance Contact Information 
Contact information for BioMarin Pharmacovigilance is as follows: 
BioMarin Pharmaceutical Inc. 
Address 
105 Digital Drive 
 
Novato, CA 94949 
Phone: 
(415) 506-6179 
Fax: 
(415) 532-3144 
E-mail: 
drugsafety@bmrn.com 
The Investigator is encouraged to discuss with the medical monitor any AEs for which the 
issue of seriousness is unclear or questioned. Contact information for the medical monitor is 
as follows: 
Name:  
, MD 
Address: 
105 Digital Drive 
 
 
Novato, CA 94949 USA 
Phone:  
 
Fax: 
 
 
E-mail: 
 
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11 
APPROPRIATENESS OF MEASUREMENTS 
11.1 
Pharmacokinetics 
The PK and safety assessments in this study are used widely and are generally recognized as 
reliable, accurate, and relevant. 
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12 
STUDY PROCEDURES 
12.1 
Prestudy 
An ICF must be signed and dated by the subject (or the subject’s legally authorized 
representative if the subject is less than 18 years of age), the PI or designee and witness 
(if required) before any study-related procedures are performed. 
12.2 
Screening Visit 
After subjects have signed an ICF, they will be screened for enrollment into the study. 
The following study activities will be performed at Screening: 
• Medical history and demographics 
• Physical examination and height 
• Vital signs 
• 12-lead ECG 
• Clinical laboratory tests (including hematology, chemistry, and urinalysis) 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• Assessment of SAEs 
• Concomitant medications 
• Diet query 
• Predose blood Phe and plasma tyrosine concentration 
For subjects who participated in PAL-002, these assessments may be the same used for the 
Final Follow-up Visit of PAL-002, if they occur within 28 days from Day 1. 
12.3 
Treatment Period 
During the Treatment Period, additional visits may occur if deemed necessary to monitor 
AEs or blood Phe concentrations. All study activities will occur on the first day of each week 
unless otherwise noted. On days that a dose is given, assessments will be done predose unless 
otherwise specified. 
If the dose is modified by increasing dose level, additional blood Phe concentration testing 
should be done on the third day following dose adjustment. If dose is modified by increasing 
either dose frequency or dose level, additional blood Phe concentration testing should be 
done prior to each dose for the first 2 weeks following dose adjustment. 
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12.3.1 Day 1 (Week 1) 
Within 28 days of completing screening assessments, the following study activities will be 
performed on Day 1: 
• Physical examination 
• Vital signs 
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• Injection-site inspection (postdose) 
• Assessment of SAEs (predose and postdose) and all AEs (postdose) 
• Concomitant medications 
• Diet query 
• Predose blood Phe and plasma tyrosine concentration 
• Serum rAvPAL-PEG antibodies 
• Administer study drug (study drug may be administered on additional days during the 
week [up to 1 dose per day] as determined by the Investigator, in agreement with the 
Study Medical Officer) 
12.3.2 Weekly Visits 
The following study activities will be performed at the weekly visits beginning with Week 2: 
• Vital signs 
• Injection-site inspection (previous and current injection site) 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• Predose blood Phe and plasm tyrosine concentration 
• Administer study drug (study drug may be administered on additional days during the 
week [up to 1 dose per day] as determined by the Investigator, in agreement with the 
Study Medical Officer) 
In addition, 3 days after each administration of study drug, the subject will have a blood Phe 
measurement by fingerstick. This may be done by the subject at home. 
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12.3.3 Monthly Visits (Week 4, 8, 16, etc) 
The following study activities will be performed at the monthly visits beginning with 
Week 4: 
• Vital signs 
• Clinical laboratory tests 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• Injection-site inspection (previous and current injection site) 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• Predose blood Phe and plasma tyrosine concentration 
• Serum rAvPAL-PEG antibodies 
• Administer study drug (study drug may be administered on additional days during the 
week [up to 1 dose per day] as determined by the Investigator, in agreement with the 
Study Medical Officer) 
12.3.4 Quarterly Visits (Week 12, 24, 36, etc) 
Quarterly visits consist of all monthly activities and include additional activities. The 
following study activities will be performed at the quarterly visits beginning with Week 12: 
• Physical examination 
• Vital signs 
• Clinical laboratory tests 
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• Injection-site inspection (previous and current injection site) 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• Predose blood Phe and plasma tyrosine concentration 
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• Serum rAvPAL-PEG antibodies 
• Administer study drug (study drug may be administered on additional days during the 
week [up to 1 dose per day] as determined by the Investigator, in agreement with the 
Study Medical Officer) 
12.4 
Final Follow-up Visit (Day 113 [± 3 days]) /Early Termination Visit 
The final follow-up (F/U) Visit or Early Termination Visit (ETV) will occur 4 weeks after 
the final dose of study drug. 
Any AE that caused a subject to withdraw from the study or any clinically significant 
abnormal laboratory value or vital sign measurement identified at the ETV will be followed 
by the Investigator.  
Every reasonable effort should be made to contact any subject who is lost to follow-up. 
The following study activities will be performed at the F/U Visit or ETV: 
• Physical examination and weight 
• Vital signs 
• 12-lead ECG 
• Clinical laboratory tests 
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• Injection-site inspection (previous injection site) 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• Predose blood Phe and plasma tyrosine concentration 
• Serum rAvPAL-PEG antibodies 
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13 
DATA QUALITY ASSURANCE 
BioMarin personnel or designees will visit the study site prior to initiation of the study to 
review with the site personnel information about the IP, protocol and other regulatory 
document requirements, any applicable randomization procedures, source document 
requirements, CRFs, monitoring requirements, and procedures for reporting AEs, including 
SAEs. 
At visits during and after the study, a CRA will monitor the site for compliance with 
regulatory documentation, with a focus on accurate and complete recording of data on CRFs 
from source documents, adherence to protocol, randomization (if applicable), SAE reporting 
and drug accountability records.  
The designated clinical data management group will enter or transfer CRF data into a study 
database. 
Data quality control and analysis will be performed by BioMarin or a designee, based on a 
predefined analysis plan. 
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14 
STATISTICAL METHODS AND DETERMINATION OF SAMPLE SIZE 
14.1 
Statistical and Analytical Plans 
Because of the small sample size, no formal statistical tests will be performed. Categorical 
data will be summarized using frequency and percent, while continuous data will be 
summarized using descriptive statistics (ie, number of observations, mean, median, standard 
deviation [SD], minimum, and maximum). 
The statistical analysis plan (SAP) will provide additional details about the planned statistical 
analysis. 
14.2 
Safety Analysis 
All subjects who receive any amount of study drug will be included in the safety analyses. 
Safety will be evaluated on the incidence of AEs and clinically significant changes in vital 
signs and laboratory test results. 
The verbatim terms reported on CRFs to identify AEs will be coded using MedDRA. 
Treatment-emergent AEs will be summarized for each treatment group by system organ 
class, preferred term, relationship to study drug, and severity. Changes from baseline in vital 
signs and laboratory test results will be summarized with descriptive statistics by dose group. 
14.3 
Pharmacokinetic Analysis 
Data from all subjects who complete at least 2 weeks of the study will be included in the PK 
analysis. 
Steady-state PK of rAvPAL-PEG will be evaluated in PKU subjects after the subject has 
achieved and maintained target blood Phe concentration (below 480 µmol/L) for a minimum 
of 2 weeks and no further dose modification is planned. 
14.4 
Efficacy Analysis 
Data from all subjects who receive any amount of study drug and who have any 
posttreatment efficacy data will be included in the efficacy analysis. 
Blood Phe concentration at each scheduled timepoint will be summarized using descriptive 
statistics (mean, SD, median, minimum, and maximum). Change in blood Phe concentration 
from baseline to each scheduled timepoint will also be summarized. 
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14.5 
Determination of Sample Size 
Subjects who participated in PAL-002 may be enrolled into this study. No formal sample size 
calculation was conducted. 
14.6 
Handling of Missing Data 
All analyses will be presented based on observed data only. Missing data will not be imputed 
for analyses unless sensitivity analyses are warranted. If imputations are used, detailed 
imputation methods will be described in the SAP before locking the database. 
14.7 
Changes in the Conduct of the Study or Planned Analyses 
Only BioMarin may modify the protocol. Any change in study conduct considered necessary 
by the PI will be made only after consultation with BioMarin, who will then issue a formal 
protocol amendment to implement the change. The only exception is when an Investigator 
considers that a subject’s safety is compromised without immediate action. In these 
circumstances, immediate approval of the chairman of the IRB must be sought, and the 
Investigator should inform BioMarin and the full IRB within 2 working days after the 
emergency occurs. 
With the exception of minor administrative or typographical changes, the IRB must review 
and approve all protocol amendments. Protocol amendments that have an impact on subject 
risk or the study objectives, or require revision of the ICF, must receive approval from the 
IRB prior to their implementation. 
When a protocol amendment substantially alters the study design or the potential risks or 
burden to subjects, the ICF will be amended and approved by BioMarin and the IRB, and all 
active subjects must again provide informed consent. 
Note: If discrepancies exist between the text of the statistical analysis as planned in the 
protocol, and the final SAP, a protocol amendment will not be issued and the SAP will 
prevail. 
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15 
DATA MONITORING COMMITTEE (DMC) 
The DMC will act in an advisory capacity to BioMarin to monitor subject safety and the 
efficacy of rAvPAL-PEG in subjects who participate in the study. Meetings of the DMC can 
be convened at any time at the discretion of the DMC Chair or the Study Medical Officer. 
The Chair will be notified by the Study Medical Officer of all SAEs and will receive 
summaries of other safety data as available. The DMC will review the study data as soon as it 
is available during the study and offer advice on whether or not to close the study on the 
basis of toxicity. Details regarding the DMC membership and safety data to be reviewed by 
members will be provided in a charter. 
The responsibilities of the DMC are to: 
• Review the study protocol, informed consent and assent documents, and plans for 
data monitoring. 
• Evaluate the progress of the trial, subjects’ risk versus benefit, and other factors that 
could affect the study outcome. 
• Consider relevant information that may have an impact on the safety of the 
participants or the ethics of the study. 
• Protect the safety of the study participants in accordance with the stopping rules as 
defined in study protocol. 
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16 
COMPENSATION, INSURANCE, AND INDEMNITY 
There will be no charge to study subjects to be in this study. BioMarin will pay all costs of 
tests, procedures, and treatments that are part of this study. In addition, after IRB approval, 
BioMarin may reimburse the cost of travel for study-related visits. BioMarin will not pay for 
any hospitalizations, tests, or treatments for medical problems of any sort, whether or not 
related to the study subject’s disease, that are not part of this study. Costs associated with 
hospitalizations, tests, and treatments should be billed and collected in the way that such 
costs are usually billed and collected. 
The Investigator should contact BioMarin immediately upon notification that a study subject 
has been injured by the IP or by procedures performed as part of the study. Any subject who 
experiences a study-related injury should be instructed by the Investigator to seek medical 
treatment at a pre-specified medical institution if possible, or at the closest medical treatment 
facility if necessary. The subject should be given the name of a person to contact to seek 
further information about, and assistance with, treatment for study-related injuries. The 
treating physician should bill the subject’s health insurance company or other third party 
payer for the cost of this medical treatment. If the subject has followed the Investigator’s 
instructions, BioMarin will pay for reasonable and necessary medical services to treat the 
injuries caused by the IP or study procedures, if these costs are not covered by health 
insurance or another third party that usually pays these costs. In some jurisdictions, BioMarin 
is obligated by law to pay for study-related injuries without prior recourse to third party 
payer billing. If this is the case, BioMarin will comply with the law. 
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17 
CASE REPORT FORMS AND SOURCE DOCUMENTS 
Electronic case report forms will be provided for each subject. The Investigator must review 
and electronically sign the completed CRF casebook to verify its accuracy. 
CRFs must be completed using a web–based application that has been validated. Study site 
personnel will be trained on the application and will enter the clinical data from source 
documentation. Unless explicitly allowed in the CRF instructions, blank data fields are not 
acceptable. 
In the event of an entry error, or if new information becomes available, the site personnel will 
correct the value by deselecting the erroneous response and then selecting or entering the 
factual response. In compliance with 21 CFR Part 11, the system will require the site 
personnel to enter a reason for changing the value. The documented audit trail will include 
the reason for the change, the original value, the new value, the time of the correction, and 
the identity of the operator. 
BioMarin’s policy is that study data on the CRFs must be verifiable to the source data, which 
necessitates access to all original recordings, laboratory reports, and subject records. 
In addition, all source data should be attributable (signed and dated). The Investigator must 
therefore agree to allow direct access to all source data. Subjects (or their legally authorized 
representative) must also allow access to their medical records, and subjects will be informed 
of this and will confirm their agreement when giving informed consent. If an Investigator or 
institution refuses to allow access to subject records because of confidentiality, arrangements 
must be made to allow an “interview” style of data verification. 
A CRA designated by BioMarin will compare the CRFs with the original source documents 
at the study site and evaluate them for completeness and accuracy before designating them as 
“source data verified” (SDV). If an error is discovered at any time or a clarification is 
needed, the CRA, or designee, will create an electronic query on the associated field. Site 
personnel will then answer the query by either correcting the data or responding to the query. 
The CRA will then review the response and determine either to close the query or re–query 
the site if the response does not fully address the question. This process is repeated until all 
open queries have been answered and closed. 
Before a subject’s CRF casebook can be locked, all data fields must be SDV and all queries 
closed. The Investigator will then electronically sign the casebook, specifying that the 
information on the CRFs is accurate and complete. The Data Manager, or designee, will then 
set the status of the forms, visits, and the entire casebook to locked. Upon completion of the 
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clinical study report for the entire study, an electronic copy of each site’s casebooks will be 
copied to a compact disk (CD) and sent to each site for retention with other study documents. 
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18 
STUDY MONITORING AND AUDITING 
Qualified individuals designated by BioMarin will monitor all aspects of the study according 
to GCP and standard operating procedures for compliance with applicable government 
regulations. The PI agrees to allow these monitors direct access to the clinical supplies, 
dispensing, and storage areas and to the clinical files, including original medical records, of 
the study subjects, and, if requested, agrees to assist the monitors. The PI and staff are 
responsible for being present or available for consultation during routinely scheduled site 
visits conducted by BioMarin or its designees. 
Members of BioMarin’s GCP Compliance Department or designees may conduct an audit of 
a clinical site at any time during or after completion of the study. The PI will be informed if 
an audit is to take place and advised as to the scope of the audit. Representatives of the FDA 
or other Regulatory Agencies may also conduct an audit of the study. If informed of such an 
inspection, the PI should notify BioMarin immediately. The PI will ensure that the auditors 
have access to the clinical supplies, study site facilities, original source documentation, and 
all study files. 
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19 
RETENTION OF RECORDS 
The PI must retain all study records required by BioMarin and by the applicable regulations 
in a secure and safe facility. The PI must consult a BioMarin representative before disposal 
of any study records, and must notify BioMarin of any change in the location, disposition or 
custody of the study files. The PI/institution must take measures to prevent accidental or 
premature destruction of essential documents, that is, documents that individually and 
collectively permit evaluation of the conduct of a study and the quality of the data produced, 
including paper copies of study records (eg, subject charts) as well as any original source 
documents that are electronic as required by applicable regulatory requirements.  
All study records must be retained for at least 2 years after the last approval of a marketing 
application in the U.S. or an ICH region and until (1) there are no pending or contemplated 
marketing applications in the United States or an ICH region or (2) at least 2 years have 
elapsed since the formal discontinuation of clinical development of the IP. The PI/institution 
should retain subject identifiers for at least 15 years after the completion or discontinuation 
of the study. Subject files and other source data must be kept for the maximum period of time 
permitted by the hospital, institution or private practice, but not less than 15 years. These 
documents should be retained for a longer period, however, if required by the applicable 
regulatory requirements or by a BioMarin agreement. BioMarin must be notified and will 
assist with retention should the PI/institution be unable to continue maintenance of subject 
files for the full 15 years. It is the responsibility of BioMarin to inform the PI/institution as to 
when these documents no longer need to be retained. 
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20 
USE OF INFORMATION AND PUBLICATION 
BioMarin recognizes the importance of communicating medical study data and therefore 
encourages their publication in reputable scientific journals and at seminars or conferences. 
The details of the processes of producing and reviewing reports, manuscripts, and 
presentations based on the data from this study will be described in the Clinical Study 
Agreement between BioMarin and the PI. 
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21 
REFERENCES 
Armstrong, Hempel, Koling, Chan, Fisher, Meiselman, Garratty. Antibody against 
poly(ethylene glycol) adversely affects PEG-asparaginase therapy in acute lymphoblastic 
leukemia patients. Cancer 110[1], 103-111. 2007.  
Burgard, Bremer, Bührdel, Clemens, Mönch, Przyrembel, Trefz, Ullrich. Rationale for the 
German recommendations for phenylalanine level control in phenylketonuria 1997. Eur J 
Pediatr 158, 46-54. 1999.  
Butterworth. Effects of hyperammonaemia on brain function. J Inherit Metab Dis 21 Suppl 1, 
6-20. 1998.  
Chen, Scott. Current and future applications of immunological attenuation via pegylation of 
cells and tissue. BioDrugs 15[12], 833-847. 2001.  
Davis, Abuchowski, Park, Davis. Alteration of the circulating life and antigenic properties of 
bovine adenosine deaminase in mice by attachment of polyethylene glycol. Clin Exp 
Immunol 46[3], 649-652. 1981.  
Fisch. Comments on diet and compliance in phenylketonuria. Eur J Pediatr 159 Suppl 2, 
S142-S144. 2000.  
Gamez, Wang, Sarkissian, Wendt, Fitzpatrick, Lemontt, Scriver, Stevens. Structure-based 
epitope and PEGylation sites mapping of phenylalanine ammonia-lyase for enzyme 
substitution treatment of phenylketonuria. Mol Genet Metab 91[4], 325-334. 2007.  
Ganson, Kelly, Scarlett, Sundy, Hershfield. Control of hyperuricemia in subjects with 
refractory gout, and induction of antibody against poly(ethylene glycol) (PEG), in a phase I 
trial of subcutaneous PEGylated urate oxidase. Arthritis Res Ther 8[1], R12. 2006.  
Guttler, Azen, Guldberg, Romstad, Hanley, Levy, Matalon, Rouse, Trefz, de la, Koch. 
Impact of the phenylalanine hydroxylase gene on maternal phenylketonuria outcome. 
Pediatrics 112[6 Pt 2], 1530-1533. 2003.  
Harris, Chess. Effect of pegylation on pharmaceuticals. Nat Rev Drug Discov 2[3], 214-221. 
2003.  
Huttenlocher. The neuropathology of phenylketonuria: human and animal studies. Eur J 
Pediatr 159 Suppl 2, S102-S106. 2000.  
Kaufman. An evaluation of the possible neurotoxicity of metabolites of phenylalanine. J 
Pediatr 114[5], 895-900. 1989.  
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Koch, Hanley, Levy, Matalon, Matalon, Rouse, Trefz, Guttler, Azen, Platt, Waisbren, 
Widaman, Ning, Friedman, de la. The Maternal Phenylketonuria International Study: 1984-
2002. Pediatrics 112[6 Pt 2], 1523-1529. 2003.  
Lee, Lilburn, Baudin. Maternal phenylketonuria: experiences from the United Kingdom. 
Pediatrics 112[6 Pt 2], 1553-1556. 2003.  
Levy. Historical background for the maternal PKU syndrome. Pediatrics 112[6 Pt 2], 1516-
1518. 2003.  
Matalon, Surendran, Matalon, Tyring, Quast, Jinga, Ezell, Szucs. Future role of large neutral 
amino acids in transport of phenylalanine into the brain. Pediatrics 112[6 Pt 2], 1570-1574. 
2003.  
Richter, Akerblom. Antibodies against polyethylene glycol produced in animals by 
immunization with monomethoxy polyethylene glycol modified proteins. Int Arch Allergy 
Appl Immunol 70[2], 124-131. 1983.  
Richter, Akerblom. Polyethylene glycol reactive antibodies in man: titer distribution in 
allergic patients treated with monomethoxy polyethylene glycol modified allergens or 
placebo, and in healthy blood donors. Int Arch Allergy Appl Immunol 74[1], 36-39. 1984.  
Rouse, Azen. Effect of high maternal blood phenylalanine on offspring congenital anomalies 
and developmental outcome at ages 4 and 6 years: the importance of strict dietary control 
preconception and throughout pregnancy. J Pediatr 144[2], 235-239. 2004.  
Scott, Murad, Koumpouras, Talbot, Eaton. Chemical camouflage of antigenic determinants: 
stealth erythrocytes. Proc Natl Acad Sci U S A 94[14], 7566-7571. 1997.  
Scriver CR, Kaufman S. Hyperphenylalaninemia: Phenylalanine Hydroxylase Deficiency. In: 
Beaudet AL, Sly WS, Valle D, editors. Metabolic and Molecular Bases of Inherited Disease. 
New York: McGraw-Hill, 2001: 1667-709.  
Shedlovsky, McDonald, Symula, Dove. Mouse models of human phenylketonuria. Genetics 
134[4], 1205-1210. 1993.  
Walter, White, Hall, MacDonald, Rylance, Boneh, Francis, Shortland, Schmidt, Vail. How 
practical are recommendations for dietary control in phenylketonuria? Lancet 360[9326], 55-
57. 2002.  
Webster, Didier, Harris, Siegel, Stadler, Tilbury, Smith. PEGylated proteins: evaluation of 
their safety in the absence of definitive metabolism studies. Drug Metab Dispos 35[1], 9-16. 
2007.  
 
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22 
INVESTIGATOR RESPONSIBILITIES 
22.1 
Conduct of Study and Protection of Human Subjects  
In accordance with FDA Form 1572, the Investigator will ensure that: 
• He or she will conduct the study in accordance with the relevant, current protocol and 
will only make changes in a protocol after notifying the sponsor, except when 
necessary to protect the safety, rights, or welfare of subjects. 
• He or she will personally conduct or supervise the study. 
• He or she will inform any potential subjects, or any persons used as controls, that the 
drugs are being used for investigational purposes and he or she will ensure that the 
requirements relating to obtaining informed consent in 21 Part 50 and institutional 
review board (IRB) review and approval in 21 CFR Part 56 are met.  
• He or she will report to the sponsor adverse experiences that occur in the course of 
the investigation in accordance with 21 CFR 312.64. 
• He or she has read and understands the information in the Investigator’s Brochure, 
including potential risks and side effects of the drug. 
• His or her staff and all persons who assist in the conduct of the study are informed 
about their obligations in meeting the above commitments. 
• He or she will ensure that adequate and accurate records in accordance with 
21 CFR 312.62 and to make those records available for inspection in accordance with 
21 CFR 312.68. 
• He or she will ensure that the IRB complies with the requirements of 21 CFR Part 56, 
and other applicable regulations, and conducts initial and ongoing reviews and 
approvals of the study. He or she will also ensure that any change in research activity 
and all problems involving risks to human subjects or others are reported to the IRB. 
Additionally, he or she will not make any changes in the research without IRB 
approval, except where necessary to eliminate apparent immediate hazards to human 
subjects. 
• He or she agrees to comply with all other requirements regarding the obligations of 
clinical Investigators and all other pertinent requirements in 21 CFR Part 312. 
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10. Made revisions to correct spelling, spacing, or punctuation, and/or made minor 
editorial revisions to improve clarity and consistency. 
11. PAL-001 and/or PAL-002 data may become available during this study and indicate 
the need for pharmacokinetic measurement of study drug accumulation (in addition to 
the current plan for analysis of study drug exposure).  If this is the case, the PAL-003 
protocol will be amended to require additional blood draws for PK analysis. 
 
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PROTOCOL AMENDMENT TEXT REVISIONS 
The following table summarizes the revisions made to the protocol and relates the changes to the appropriate rationale. Text that has been 
added or inserted is indicated by underlined font, and deleted text is indicated by strikethrough font. 
Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
Section 2 Synopsis 
(Study Rationale) 
STUDY RATIONALE: 
The need exists for a treatment that will help individuals with phenylketonuria 
(PKU) safely achieve lifelong, reliable control of blood phenylalanine (Phe) 
concentrations and improve central nervous system developmental and functional 
outcomes. Phenylalanine ammonia lyase (rAvPAL-PEG) is a potential substitute 
for the phenylalanine hydroxylase (PAH) enzyme, which is defective in individuals 
with PKU. rAvPAL-PEG may control blood Phe concentrations, which may have 
additional clinical benefits. This study will build upon the results of the first single-
dose pharmacokinetics (PK) study (Study PAL-001) and evaluate whether weekly 
injections of rAvPAL-PEG can reduce blood Phe concentrations in PKU subjects 
and whether repeated administration is safe. 
 
10 
Section 2 Synopsis 
(Diagnosis and All 
Criteria for Inclusion 
and Exclusion) 
Individuals who meet any of the following exclusion criteria will not be eligible to 
participate in the study: 
• Use of any investigational product (with the exception of rAvPAL-PEG) or 
investigational medical device within 30 days prior to Screening, or 
requirement for any investigational agent prior to completion of all 
scheduled study assessments. 
• Use of any medication that is intended to treat PKU within 14 days prior to 
the administration of study drug. 
 
1 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
• Use or planned use of any injectable drugs containing PEG (other than 
rAvPAL-PEG), including Depo-Provera, within 6 months prior to 
Screening and during study participation. 
• A prior reaction that included systemic symptoms (eg, generalized hives, 
respiratory or gastrointestinal problems, hypotension,  angioedema, 
anaphylaxis) to rAvPAL-PEG or a PEG-containing product. 
• Pregnant or breastfeeding at Screening or planning to become pregnant (self 
or partner) or to breastfeed at any time during the study.Concurrent disease 
or condition that would interfere with study participation or safety 
(eg, history or presence of clinically significant cardiovascular, pulmonary, 
hepatic, renal, hematologic, gastrointestinal, endocrine, immunologic, 
dermatologic, neurological, oncologic, or psychiatric disease). 
• Any condition that, in the view of the PI, places the subject at high risk of 
poor treatment compliance or of not completing the study. 
Table 2.1.1 Schedule 
of Events (footnote a) 
a It is preferable to perform PAL-003 Screening assessments the same day as PAL-002 
Final Follow-up Visit so there is no interruption of study drug. If performed on the same 
day, PAL-002 Final Follow-up Visit data may be used.  If not, PAL-003 Day 1 must occur  
≤ 28 days after PAL-003 Screening. 
 
8 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
Section 4 List of 
Abbreviations and 
Definitions of Terms 
IM 
intramuscular
Added new 
term 
10 
Section 4 List of 
Abbreviations and 
Definitions of Terms 
IVRS interactive voice response system
Added new 
term 
7 
Section 4 List of 
Abbreviations and 
Definitions of Terms 
PEG 
methoxypolyethylene glycol 
 
10 
Section 7.1 
Nonclinical Studies 
When administration of AvPAL-PEG was stopped for 2 to 7 weeks and then 
reinitiated with weekly administrations, no attenuated response was observed and 
Phe concentrations remained low and stable until the next administrationthroughout 
the week. 
Paragraph 1 
10 
Section 7.1 
Nonclinical Studies 
No specific methoxypolyethylene glycol (PEG)-related histological findings were 
observed during the 28-day repeated dose studies. 
Paragraph 2 
10 
Section 7.1 
Nonclinical Studies 
Findings in cynomolgus monkeys dosed with a single administration of 
60 mg/kg rAvPAL-PEG included morbidity,  reduced food consumption, 
dehydration, body weight loss, hypoactivity, hypothermia,decreased plasma Phe 
concentration, decreased protein synthesis, and gastrointestinal (GI) lesions. Plasma 
Phe concentrations were also reduced to below the level of detection in the lower 4 
and 12 mg/kg dose groups, but without similar toxicological consequence, 
implying that the physiological regulation of Phe levels may be an important factor 
for influencing morbidity. Physiologically regulated Phe intake may have played a 
Paragraphs 4 
and 5 
10 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
part in these morbidity results, although plasma Phe concentrations were low in all 
treated monkeys.
The main finding in the 28-day study was the possible drug-related observation of 
minimal to slight degeneration of blood vessels of predominantly medium-sized 
muscular arteries with a non-dose-dependent involvement of different organs 
observed in 1 male in the 0.1 mg/kg and 1 male and 1 female in the 1.0 mg/kg 
rAvPAL-PEG dose groups. No degeneration of the arteries was observed in 
animals administered 0 and 0.01 mg/kg rAvPAL-PEG.
Section 7.3 Study 
Rationale 
The need exists for a treatment that will help individuals with PKU safely achieve 
lifelong, reliable control of blood Phe concentrations and improve CNS 
developmental and functional outcomes. rAvPAL-PEG is a potential substitute for 
the PAH enzyme. rAvPAL-PEG may control blood Phe concentrations, which may 
have additional clinical benefits. This study will build upon the results of PAL-001 
and evaluate whether weekly injections of rAvPAL-PEG can reduce blood Phe 
concentrations in PKU subjects and whether repeated administration is safe. 
 
10 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
Section 7.4.2 Toxicity 
Due to an 
Immunologic Reaction 
PEG itself is considered nonimmunogenic (Davis, 1981, Clin.Exp.Immunol.) 
(Harris, 2003, Nat.Rev.Drug Discov.), and however, antibodies against PEG seem 
to form only under special circumstances may form when PEG is bound to 
compounds. (Harris, 2003, Nat.Rev.Drug.Discov.) (Richter, 1983, Int.Arch.Allergy 
Appl.Immunol.) and may be of no In some instances, development of such 
antibodies did not result in any significant clinical relevance effects in humans 
(Richter, 1984, Int.Arch.Allergy Appl.Immunol.). In some individuals, anti-PEG 
antibodies may be pre-existing due to previous exposure to PEG in other products. 
Anti-PEG antibodies have been associated with nonresponsiveness against therapy 
(Armstrong, 2007, Cancer), (Ganson, 2006, Arthritis Res.Ther.).
Two subjects enrolled in PAL-001 who had received one dose of rAvPAL-PEG 
experienced hypersensitivity reactions to intramuscular (IM) Depo-Provera, a 
contraceptive containing PEG 3350. Both subjects had previously received multiple 
IM Depo-Provera injections without complications. 
The first subject, a 
 year old 
, developed bruising at the injection site on 
Day 1 that resolved on Day 15. 
 developed hives and mild respiratory difficulty 
10 minutes after receiving IM Depo-Provera and 40 days after 
 rAvPAL-PEG 
injection. 
 was treated in the emergency room with 
 
. The events resolved the same 
day, and the subject had no further complications. The subject had no prior history 
of any reactions to Depo-Provera. Subsequently, while under the care of an 
allergist/immunologist, the subject had a mild reaction to a concentrated 
intradermal (1:10) exposure of Depo-Provera. 
 was later given a full dose of IM 
Depo-Provera without problems.
 
2, 3, 10 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
 
The second subject, an 
 year old 
, had a slightly raised, erythematic rash 
below the site of rAvPAL-PEG injection on Day 11 that resolved without treatment 
on Day 15. 
 developed generalized hives on 
arms and legs and mild 
difficulty breathing 20 minutes after receiving IM Depo-Provera (and 
 third dose 
of Gardasil) given 15 days after 
 rAvPAL-PEG injection. 
 symptoms 
subsided after 
 received 
 given by 
 mother. 
 did not visit the 
emergency room. The subject had no prior history of any reactions to Depo-Provera 
or Gardasil (Gardasil dose not contain PEG). 
 was subsequently seen by an 
allergist/immunologist, and the results are pending. 
Because Depo-Provera contains PEG 3350 as an excipient, it is possible that the 
administration of rAvPAL-PEG caused anti-PEG antibody formation that led to a 
cross-reaction with Depo-Provera in these subjects. Therefore, it is possible that 
prior exposure to rAvPAL-PEG might sensitize subjects to other PEG-containing 
injectable drugs. Alternatively, the presence of Depo-Provera could have led to 
antibody formation and cross-reaction with rAvPAL-PEG, leading to rAvPAL-PEG 
injection-site reactions. Since it is currently unknown whether Depo-Provera has a 
sensitizing effect to PEG and the exact basis for these reported events is not known, 
the use of PEG-containing injectable drugs prior to and during the study is 
prohibited as a precautionary measure (refer to the addendum and Sections 9.3.2 
and 9.4.8).
 
 
 
In the event of an allergic reaction, subjects may be asked to see an 
allergist/immunologist and/or provide up to 3 additional blood samples for 
antibody testing. This additional testing may occur up to 6 months following the 
final study visit.
 
 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
Section 9.1.1 
Management of Local 
and Systemic 
Reactions to rAvPAL-
PEG 
9.1.1     Management of Local and Systemic Reactions to rAvPAL-PEG 
9.1.1.1  Subjects Who Have Experienced Hypersensitivity Reactions to 
rAvPAL-PEG or a PEG-containing Product 
Subjects who had a previous reaction to rAvPAL-PEG or a PEG-containing 
product that warranted early termination from PAL-001 or PAL-002 are excluded 
from this study.  However, subjects may develop such reactions after enrollment in 
PAL-003.  Management of such reactions are described below. Refer to 
Figure 9.1.1.1.2.1:   for a flowchart for managing these subjects. 
9.1.1.2.1  Subjects with Local Reactions 
After enrollment in PAL-003, subjects who have a local reaction to rAvPAL-PEG 
or a PEG-containing product will be premedicated with acetaminophpen and 
antihistamines and/or oral steroids, 1 hour prior to study drug dosing. 
Recommended premedications are acetaminophen and antihistamine (Claritin is 
preferred). The dosage will be standard (eg, 1000 mg acetaminophen and 10 mg 
Claritin or 25 to 50 mg oral Benadryl; an example for steroids would be 70 mg oral 
prednisone). Because Benadryl can cause drowsiness, it should be administered 
only if the subject is accompanied by a designated driver. 
9.1.1.2.2  Subjects with Systemic Reactions 
After enrollment in PAL-003, subjects who have a systemic reaction that includes 
noncutaneous systemic symptoms, such as respiratory problems, hypotension, or 
angioedema, to rAvPAL-PEG or a PEG-containing product will be evaluated with 
a skin prick test. If the test is positive, the subject will be excluded from the study. 
Subjects with prior systemic reactions that included only skin manifestations to 
rAvPAL-PEG or a PEG-containing product after PAL-003 enrollment will be 
premedicated with acetaminophen and antihistamines and/or oral steroids (one hour 
prior to study drug dosing) and will continue to receive rAvPAL-PEG. 
Added new 
section 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
Reactions to skin prick testing or rAvPAL-PEG administered SC are defined as 
follows: 
Local reaction: 1 affected location, ie, hives, wheals, or swelling or an area of 
erythema or redness at or near the site of injection. 
Systemic reaction: more than 1 affected location, ie, cutaneous reaction in 
more than 1 area, and/or any other generalized symptoms, such as 
hypotension, angioedema or anaphylaxis or the involvement of other organ 
systems (eg, respiratory, cardiovascular, gastrointestinal). 
 
Section 9.1.1 
Management of Local 
and Systemic 
Reactions to rAvPAL-
PEG  
Figure 9.1.1.2.1  Management of Local and System Reactions to rAvPAL-PEG
Added new 
figure 
5 
Section 9.3.2 
Exclusion Criteria 
Individuals who meet any of the following exclusion criteria will not be eligible to 
participate in the study: 
• Use of any investigational product (with the exception of rAvPAL-PEG) or 
investigational medical device within 30 days prior to Screening, or 
requirement for any investigational agent prior to completion of all 
scheduled study assessments. 
• Use or planned use of any injectable drugs containing PEG (other than 
rAvPAL-PEG), including Depo-Provera, within 6 months prior to 
Screening and during study participation. 
 
1 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
• A prior reaction that included systemic symptoms (eg, generalized hives, 
respiratory or gastrointestinal problems, hypotension,  angioedema, 
anaphylaxis) to rAvPAL-PEG or a PEG-containing product. 
• Use of any medication that is intended to treat PKU within 14 days prior to 
the administration of study drug. 
• Pregnant or breastfeeding at Screening or planning to become pregnant (self 
or partner) or to breastfeed at any time during the study. 
• Concurrent disease or condition that would interfere with study participation 
or safety (eg, history or presence of clinically significant cardiovascular, 
pulmonary, hepatic, renal, hematologic, gastrointestinal, endocrine, 
immunologic, dermatologic, neurological, oncologic, or psychiatric 
disease). 
• Any condition that, in the view of the PI, places the subject at high risk of 
poor treatment compliance or of not completing the study. 
Section 9.3.4 Subject 
Identification and 
Replacement of 
Subjects 
After enrollment of 35 subjects, if any single cohort (identified during PAL-002) 
has less than 3 subjects due to early terminations, those subjects will be replaced. 
Replacement subjects will enter the study at the same dose cohort level as the 
subject they are replacing.
 
9 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
Section 9.4.4 
Directions for 
Administration 
Subjects may require more than 1 injection per dose, depending upon site policy 
(ie, some institutions do not permit a single SC injection of greater than 2 mL). The 
number of injections required for an individual weighing 80 kg (about 176 pounds) 
is provided in Table 9.4.4.1 as an example. Note this table is for example purposes 
only. Dosage calculations must be performed according to study drug preparation 
instructions provided in the PAL-003 Pharmacy Manual. 
Table 9.4.4.1:  Number of Injections Required For an Individual 
Weighing 80 kg
Dose Group 
(mg/kg)
Weight 
(kg)
Volume of Study Drug 
(mL)a
No. of 
Injectionsb
0.001
80
0.8
1
0.003
80
0.6
1
0.01
80
0.8
1
0.03
80
0.2
1
0.1
80
0.8
1
0.3
80
2.4
2
1.0
80
8.0
4
aStudy drug is supplied at a concentration of 10 mg/mL and is then diluted by differential amounts 
as specified in the PAL-003 Pharmacy Manual. Volume to be injected is calculated based on a 
starting volume attained following dilution. 
bNumber of injections per dose is dependent upon site policy for SC injections. The number of 
injections may vary at the discretion of the Investigator. 
 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
Section 9.4.5 Method 
of Assigning Subjects 
to Treatment Groups 
An interactive voice response system (IVRS) will be used to track subjects’ 
assigned dose and study drug inventory. 
 
7 
Section 9.4.6 Selection 
of Doses Used in the 
Study 
The doses for this study will be based upon the results of findings in PAL-001 and 
PAL-002. 
 
10 
Section 9.4.8 Prior and 
Concomitant 
Medications 
Use or planned use of any injectable drugs containing PEG (other than rAvPAL-
PEG), including Depo-Provera, is prohibited within 6 months prior to Screening 
and during study participation. A list of PEG-containing injectable drugs is 
provided in the study reference materials. Subjects who have had a prior reaction to 
rAvPAL-PEG or a PEG-containing product will be premedicated with 
acetaminophen and antihistamines and/or oral steroids (refer to Section 9.1.1). 
 
Subjects who have had a prior hypersensitivity reaction to rAvPAL-PEG or a 
PEG-containing product will be premedicated with acetaminophen and 
antihistamines and/or oral steroids (refer to Section 9.1.1). If the local or systemic 
reaction worsens with a repeat injection (as determined by the Investigator in 
consultation with the Study Medical Officer) even with premedication prior to 
study drug dosing, the subject must be withdrawn from the study.
 
1 
9.7.4.2 rAvPAL-PEG-
specific antibodies 
Antibody Testing
Anti-PEG antibodies will also be measured.
Re-named 
section 
10 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
Section 14.3 
Pharmacokinetic 
Analysis 
Should data become available from PAL-001 and/or PAL-002 which indicate study 
drug accumulation should also be measured, the protocol will be amended to 
require additional blood draws for PK analysis.
 
11 
Section 14.7 Interim 
Analyses 
At least one interim analysis may be performed by the sponsor during the study.
Added new 
section 
6 
 
 
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2 
SYNOPSIS 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
TITLE OF STUDY: 
Long-term Extension of a Phase 2, Open-Label Dose-Finding Study to Evaluate the Safety, Efficacy, 
and Tolerability of Multiple Subcutaneous Doses of rAvPAL-PEG in Subjects with PKU 
PROTOCOL NUMBER:  PAL-003 
STUDY SITES:  Approximately 8 centers in the United States 
PHASE OF DEVELOPMENT:  Phase 2 
STUDY RATIONALE: 
The need exists for a treatment that will help individuals with phenylketonuria (PKU) safely achieve 
lifelong, reliable control of blood phenylalanine (Phe) concentrations and improve functional 
outcomes. Phenylalanine ammonia lyase (rAvPAL-PEG) is a potential substitute for the phenylalanine 
hydroxylase (PAH) enzyme, which is defective in individuals with PKU. rAvPAL-PEG may control 
blood Phe concentrations, which may have additional clinical benefits. This study is an extension of 
the dose-finding study (Study PAL-002). Administration of rAvPAL-PEG will be continued to assess 
whether long-term dosing of rAvPAL-PEG is safe and can maintain reduced blood Phe concentrations 
in PKU subjects. 
OBJECTIVES: 
The primary objective of the study is: 
• 
To evaluate the effect of long-term administration of SC injections of rAvPAL-PEG on blood 
Phe concentrations in subjects with PKU. 
The secondary objectives of the study are: 
• 
To evaluate the safety and tolerability of long-term administration of subcutaneous (SC) 
injections of rAvPAL-PEG in subjects with PKU. 
• 
To evaluate the immune response to long-term administration of SC injections of 
rAvPAL-PEG in subjects with PKU who participated in Study PAL-002. 
• 
To evaluate steady-state PK of rAvPAL-PEG in subjects with PKU. 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
STUDY DESIGN AND PLAN: 
This is a long-term extension of a Phase 2, open-label, dose-finding study (Study PAL-002) in 
approximately 35 subjects with PKU. The doses are planned to be in the same range as those tested in 
PAL-002 (0.001 through 1.0 mg/kg per injection), provided no dose-limiting toxicity was observed in 
PAL-002. 
Only subjects who completed participation in PAL-002 will be enrolled into this study. Diet will not 
be altered during the course of this study, except as necessary for safety. 
Subjects will be evaluated for safety and for blood Phe concentrations throughout the study. Toxicity 
will be measured according to the National Cancer Institute (NCI) Common Terminology Criteria for 
Adverse Events (CTCAE), version 3. 
A Data Monitoring Committee will monitor the study. 
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take 
rAvPAL-PEG. PAL-002 participants’ rAvPAL-PEG dosing will continue in PAL-003 without 
interruption of weekly dosing. In PAL-003, each subject’s dose will be adjusted as needed to attain or 
maintain blood Phe concentrations below 480 µmol/L. Subjects will continue to receive injections in 
the clinic, administered by clinic staff, but may later be allowed to self-administer doses of study drug 
at home. Whether a subject may be allowed to self-administer study drug doses will be evaluated on an 
individual basis. 
The dose may be modified at any time for safety. 
Evaluations, observations, and procedures will be conducted at selected timepoints as shown in 
Table 2.1.1, Schedule of Events. After the subject’s blood Phe concentration has been controlled to 
within a target range (below 480 µmol/L), the subject may be asked to have additional blood draws for 
PK and blood Phe concentration analyses. 
A subject will continue in PAL-003 until one of the following occurs: 
1. The subject withdraws consent and discontinues from the study. 
2. The subject is discontinued from the study at the discretion of the Investigator. 
3. The drug becomes commercially available following the appropriate marketing approval. 
4. The study is terminated. 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
Dose Adjustment Methodology: 
Each subject’s dose may be modified based on the decision of the Investigator, in agreement with the 
Study Medical Officer. Depending upon the response to rAvPAL-PEG in PAL-002, a subject’s dose 
may be adjusted beginning on Day 1 of PAL-003 as follows. 
• 
The dose may be increased by increments of no more than 10-fold higher than the subject’s 
current dose. 
• 
The dose may be decreased as appropriate to achieve or maintain a favorable blood Phe 
concentration. 
• 
When adjusting the dose, a dose may be used that is between the dose cohort levels that were 
defined in the previous study (PAL-002). 
• 
The dose may be adjusted by increasing the frequency of injections per week, up to one dose 
per day, for a maximum total dose per week of 2 mg/kg. 
• 
When a dose is adjusted (either by changing the dose level or by changing the frequency of 
dosing), the subject must remain in the clinic for a minimum of 2 hours following the first 
modified dose administration, and an Investigator will remain on site during this time. 
Subjects must have blood Phe concentration tested 3 days after a dose adjustment. There must be a 
minimum of 2 weeks after each dose adjustment before any additional dose adjustments may be made, 
so that blood Phe concentrations can be assessed. 
Stopping Criteria: 
If an individual subject exhibits drug-related toxicity of CTCAE grade 3 or greater, that subject will 
have dosing halted until the toxicity resolves. The subject’s data will be evaluated by the Principal 
Investigator (PI) and the Study Medical Officer, and a decision will then be made whether to 
discontinue the subject from the study, restart dosing at the same dose level, or restart dosing at a 
lower dose level. 
In addition, if 2 or more subjects at a dose level exhibit drug-related toxicity of CTCAE grade 3 or 
greater, further dosing of subjects at that dose level and any higher dose levels will be halted until a 
safety assessment is completed. 
NUMBER OF SUBJECTS PLANNED:   
Approximately 35 subjects. 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
DIAGNOSIS AND ALL CRITERIA FOR INCLUSION AND EXCLUSION:  
Individuals eligible to participate in this study must meet all of the following criteria: 
• 
Must have completed participation in PAL-002. 
• 
Willing and able to provide written, signed informed consent, or, in the case of participants 
under the age of 18, provide written assent (if required) and written informed consent by a 
parent or legal guardian, after the nature of the study has been explained, and prior to any 
research-related procedures. 
• 
Willing and able to comply with all study procedures. 
• 
Females of childbearing potential must have a negative pregnancy test at Screening and be 
willing to have additional pregnancy tests during the study. Females considered not of 
childbearing potential include those who have been in menopause at least 2 years, or had tubal 
ligation at least 1 year prior to Screening, or who have had total hysterectomy. 
• 
Sexually active subjects must be willing to use an acceptable method of contraception while 
participating in the study. 
• 
Maintained a stable diet. 
• 
In generally good health as evidenced by physical examination, clinical laboratory evaluations 
(hematology, chemistry, and urinalysis), and electrocardiogram (ECG) at Screening. 
Individuals who meet any of the following exclusion criteria will not be eligible to participate in the 
study: 
• 
Use of any investigational product (with the exception of rAvPAL-PEG) or investigational 
medical device within 30 days prior to Screening, or requirement for any investigational agent 
prior to completion of all scheduled study assessments. 
• 
Use of any medication that is intended to treat PKU within 14 days prior to the administration 
of study drug. 
• 
Use or planned use of any injectable drugs containing PEG (other than rAvPAL-PEG), 
including Depo-Provera, within 6 months prior to Screening and during study 
participation. 
 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
• 
A prior reaction that included systemic symptoms (eg, generalized hives, respiratory or 
gastrointestinal problems, hypotension, angioedema, anaphylaxis) to rAvPAL-PEG or a 
PEG-containing product. 
• 
Pregnant or breastfeeding at Screening or planning to become pregnant (self or partner) or to 
breastfeed at any time during the study.Concurrent disease or condition that would interfere 
with study participation or safety (eg, history or presence of clinically significant 
cardiovascular, pulmonary, hepatic, renal, hematologic, gastrointestinal, endocrine, 
immunologic, dermatologic, neurological, oncologic, or psychiatric disease). 
• 
Any condition that, in the view of the PI, places the subject at high risk of poor treatment 
compliance or of not completing the study. 
• 
Known hypersensitivity to rAvPAL-PEG or its excipients, including hypersensitivity 
reactions that necessitated early termination from PAL-001 or PAL-002. 
• 
Alanine aminotransferase (ALT) concentration > 2 times the upper limit of normal. 
• 
Creatinine  > 1.5 times the upper limit of normal. 
INVESTIGATIONAL PRODUCT, DOSE, ROUTE AND REGIMEN: 
rAvPAL-PEG doses will be administered SC and the favorable dose (the dosage that provides control 
of blood Phe concentrations within the target range for a minimum of 2 weeks) will be determined for 
each subject by adjusting the dose level, dose frequency, or both, as agreed by the PI and the Study 
Medical Officer, based upon the subject’s response to doses. 
DURATION OF TREATMENT: 
Extension of multiple dosing will continue until one of the following occurs: 
1. The subject withdraws consent and discontinues from the study. 
2. The subject is discontinued from the study at the discretion of the Investigator. 
3. The drug becomes commercially available following the appropriate marketing approval. 
4. The study is terminated. 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
REFERENCE THERAPY(IES), DOSE, ROUTE AND REGIMEN:  
None 
CRITERIA FOR EVALUATION: 
Efficacy: 
Blood Phe concentrations will be measured. 
Safety: 
Safety will be evaluated on the incidence of adverse events (AEs) and clinically significant changes in 
vital signs or laboratory test results. 
Pharmacokinetic: 
Plasma concentrations of rAvPAL-PEG will be measured when steady-state levels of Phe are attained. 
STATISTICAL METHODS:  
Sample Size: 
Subjects who participated in PAL-002 may be enrolled into this study. No formal sample size 
calculation was conducted. 
Safety Analysis: 
All subjects who receive any amount of study drug in this study will be included in the safety analyses. 
Safety will be evaluated on the incidence of AEs, including serious AEs (SAEs), and clinically 
significant changes in vital signs and laboratory test results. 
Efficacy Analysis: 
Data from all subjects who receive any amount of study drug and who have any posttreatment efficacy 
data will be included in the efficacy analysis. 
Blood Phe concentration at each scheduled timepoint will be summarized using descriptive statistics 
(mean, standard deviation, median, minimum, and maximum). Change in blood Phe concentration 
from baseline to each scheduled timepoint will also be summarized. 
Pharmacokinetic Analysis: 
Data from all subjects who complete at least 2 weeks of the study will be included in the PK analysis. 
Steady-state PK (predose samples) of rAvPAL-PEG will be evaluated in PKU subjects after the 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
subject has achieved and maintained target blood Phe concentration (below 480 μmol/L) for a 
minimum of 2 weeks (to allow assessment of blood Phe concentrations) and no further dose 
modification is planned. Once this target has been achieved, PK samples will be collected predose on 
the same day each week for 3 consecutive weeks. 
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2.1 
Schedule of Events 
Table 2.1.1:  Schedule of Events 
Screeninga
Treatment Periodb,c
Final F/U or 
ETV 
Week 1 
Weekly
Monthly (eg, 
Wk 4, 8, etc, 
Qrtly (eg, 
Wk 12, 24, 
etc) 
4 weeks after 
final dose 
Assessments and Events 
 
D 1 
 
 
 
 
Informed consent 
 
X 
 
 
 
 
 
Medical history and 
demographics 
 
X 
 
 
 
 
 
Physical examinationd
 
X 
X 
 
 
X 
 
X 
Vital signs 
 
X 
X 
X 
X 
X 
 
X 
12-lead ECG 
 
X 
 
 
 
 
 
X 
Clinical laboratory testse
 
X 
 
 
X 
X 
 
X 
Sedimentation rate 
 
X 
 
 
X 
 
X 
Urine pregnancy test 
 
X 
X 
 
X 
X 
 
X 
Injection-site inspectionf 
 
X 
(postdose)
X 
X 
X 
 
X 
Adverse eventsg
 
XÅ------------------------------------------------------------------------Æ X 
Concomitant medications 
 
X 
X 
X 
X 
X 
 
X 
Diet query 
 
X 
X 
X 
X 
X 
 
X 
Serum rAvPAL-PEG 
antibodies 
 
X 
 
X 
X 
 
X 
Predose blood Phe and 
plasma tyrosineh
 
X 
X 
X 
X 
X 
 
X 
Blood Phe (fingerstick)i
 
 
3 days
postdos
e 
 
 
 
Predose PK samplej
 
 
 
 
 
 
Administer IPk
 
X 
X 
X 
X 
 
AE, adverse event; D, day; ECG, electrocardiogram; ETV, Early Termination Visit; F/U, Follow-up; IP, 
investigational product; PK, pharmacokinetics; Phe, phenylalanine; SAE, serious adverse event; Wk, week. 
a It is preferable to perform PAL-003 Screening assessments the same day as PAL-002 Final Follow-up 
Visit so there is no interruption of study drug. If performed on the same day, PAL-002 Final Follow-up 
Visit data may be used.  If not, PAL-003 Day 1 must occur  ≤ 28 days after PAL-003 Screening. 
b Additional visits may occur if deemed necessary to monitor AEs or blood Phe, adjust dosing etc. 
c On days that a dose is given, all procedures should be performed predose, except where noted. 
d Complete physical examinations to include the evaluation of all major body systems, height (at Screening 
only), and weight. 
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e Clinical laboratory tests to include hematology, chemistry, and urinalysis. 
f If any injection site reaction is observed, the corresponding adverse event data must specify injection location 
(identify current vs. previous visit’s injection, e.g. right arm vs. left arm) 
g The reporting period for SAEs begins when informed consent is obtained and continues through 4 weeks after 
last dose or the final study visit. The reporting period for nonserious AEs is from the first administration of 
study drug to the final study visit. 
h Samples should be drawn in the morning, at least 2.5 hours after a meal. If dose is modified by increasing 
either dose frequency or dose level, additional blood Phe concentration testing should be done prior to each 
dose for the first 2 weeks following dose adjustment. 
i May be done by the subject at home. Samples should be taken in the morning, at least 2.5 hours after a meal. 
j. The PK blood samples will be collected after the subject has achieved and maintained target blood Phe 
concentration (below 480 μmol/L) for a minimum of 2 weeks. Once this target is achieved, predose PK 
samples will be collected on the same day each week for 3 consecutive weeks as specified in Section 9.7.3. 
k Dosing is up to 1.0 mg/kg per injection and up to one dose per day, for a total of up to 2.0 mg/kg/week. 
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3 TABLE OF CONTENTS 
1 
TITLE PAGE....................................................................................................................1 
2 SYNOPSIS.........................................................................................................................16 
2.1 Schedule of Events....................................................................................................23 
3 TABLE OF CONTENTS...................................................................................................25 
4 LIST OF ABBREVIATIONS AND DEFINITIONS OF TERMS....................................29 
5 ETHICS..............................................................................................................................33 
5.1 Institutional Review Board or Ethics Committee .....................................................33 
5.2 Ethical Conduct of Study..........................................................................................33 
5.3 Subject Information and Informed Consent..............................................................34 
6 INVESTIGATORS AND STUDY ADMINISTRATIVE STRUCTURE ........................35 
7 INTRODUCTION .............................................................................................................36 
7.1 Nonclinical Studies ...................................................................................................36 
7.2 Previous Clinical Studies ..........................................................................................37 
7.3 Study Rationale.........................................................................................................37 
7.4 Summary of Overall Risks and Benefits...................................................................38 
7.4.1 
Toxicity Due to Exposure to PEG...............................................................39 
7.4.2 
Toxicity Due to an Immunologic Reaction.................................................39 
7.4.2.1 
Management of Allergic Reactions .............................................41 
7.4.3 
Effects of Low Blood Phe ...........................................................................41 
8 STUDY OBJECTIVES......................................................................................................42 
9 INVESTIGATIONAL PLAN............................................................................................43 
9.1 Overall Study Design and Plan.................................................................................43 
9.1.1 
Management of Local and Systemic Reactions to rAvPAL-PEG...............44 
9.1.1.1 
Subjects Who Have Experienced Hypersensitivity 
Reactions to rAvPAL-PEG or a PEG-containing Product...........44 
9.1.2 
Dose Adjustment Methodology...................................................................47 
9.1.3 
Stopping Criteria .........................................................................................47 
9.2 Discussion of Study Design, Including Choice of Control Group............................47 
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9.3 Selection of Study Population...................................................................................48 
9.3.1 
Inclusion Criteria.........................................................................................48 
9.3.2 
Exclusion Criteria........................................................................................48 
9.3.3 
Removal of Subjects from Treatment or Assessment .................................49 
9.3.4 
Subject Identification and Replacement of Subjects...................................50 
9.4 Treatments.................................................................................................................50 
9.4.1 
Treatments Administered ............................................................................50 
9.4.2 
Identity of Investigational Product (IP).......................................................51 
9.4.2.1 
Product Characteristics and Labeling ..........................................51 
9.4.3 
Storage.........................................................................................................51 
9.4.4 
Directions for Administration .....................................................................51 
9.4.5 
Method of Assigning Subjects to Treatment Groups ..................................52 
9.4.6 
Selection of Doses Used in the Study .........................................................52 
9.4.6.1 
Selection of Timing of Dose for Each Subject ............................53 
9.4.7 
Blinding.......................................................................................................53 
9.4.8 
Prior and Concomitant Medications............................................................53 
9.4.9 
Treatment Compliance ................................................................................54 
9.5 Investigational Product Accountability.....................................................................54 
9.5.1 
Return and Disposition of Clinical Supplies ...............................................54 
9.6 Dietary or Other Protocol Restrictions......................................................................54 
9.7 Efficacy and Safety Variables...................................................................................55 
9.7.1 
Efficacy and Safety Measurements Assessed .............................................55 
9.7.1.1 
Demographic Data and Medical History .....................................55 
9.7.1.2 
Physical Examination Findings....................................................55 
9.7.1.3 
Vital Sign Measurements.............................................................55 
9.7.1.4 
Electrocardiography.....................................................................56 
9.7.2 
Efficacy Variable.........................................................................................56 
9.7.2.1 
Blood Phenylalanine Concentrations...........................................56 
9.7.3 
Pharmacokinetic Variables..........................................................................56 
9.7.4 
Safety Variables ..........................................................................................56 
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9.7.4.1 
Pregnancy Testing........................................................................56 
9.7.4.2 
Antibody Testing .........................................................................57 
9.7.5 
Clinical Laboratory Assessments ................................................................57 
10 REPORTING ADVERSE EVENTS .................................................................................59 
10.1 Adverse Events .........................................................................................................59 
10.2 Serious Adverse Events ............................................................................................61 
10.3 Pregnancy..................................................................................................................62 
10.4 BioMarin Pharmacovigilance Contact Information..................................................62 
11 APPROPRIATENESS OF MEASUREMENTS...............................................................63 
11.1 Pharmacokinetics ......................................................................................................63 
12 STUDY PROCEDURES ...................................................................................................64 
12.1 Prestudy.....................................................................................................................64 
12.2 Screening Visit..........................................................................................................64 
12.3 Treatment Period.......................................................................................................65 
12.3.1 Day 1 (Week 1) ...........................................................................................65 
12.3.2 Weekly Visits ..............................................................................................66 
12.3.3 Monthly Visits (Week 4, 8, 16, etc) ............................................................66 
12.3.4 Quarterly Visits (Week 12, 24, 36, etc).......................................................67 
12.4 Final Follow-up Visit (Day 113 [± 3 days]) /Early Termination Visit.....................68 
13 DATA QUALITY ASSURANCE.....................................................................................69 
14 STATISTICAL METHODS AND DETERMINATION OF SAMPLE SIZE..................70 
14.1 Statistical and Analytical Plans.................................................................................70 
14.2 Safety Analysis .........................................................................................................70 
14.3 Pharmacokinetic Analysis.........................................................................................70 
14.4 Efficacy Analysis......................................................................................................70 
14.5 Determination of Sample Size ..................................................................................71 
14.6 Handling of Missing Data.........................................................................................71 
14.7 Interim Analyses .......................................................................................................71 
14.8 Changes in the Conduct of the Study or Planned Analyses......................................71 
15 DATA MONITORING COMMITTEE (DMC) ................................................................72 
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16 COMPENSATION, INSURANCE, AND INDEMNITY.................................................73 
17 CASE REPORT FORMS AND SOURCE DOCUMENTS..............................................74 
18 STUDY MONITORING AND AUDITING .....................................................................76 
19 RETENTION OF RECORDS............................................................................................77 
20 USE OF INFORMATION AND PUBLICATION............................................................78 
21 REFERENCES ..................................................................................................................79 
22 INVESTIGATOR RESPONSIBILITIES..........................................................................81 
22.1 Conduct of Study and Protection of Human Subjects...............................................81 
23 SIGNATURE PAGE .........................................................................................................82 
 
LIST OF TABLES 
Table 2.1.1:  Schedule of Events .............................................................................................23 
Table 9.4.4.1  Number of Injections Required For an Individual Weighing 80 kg.................52 
Table 9.7.1.1: Summary of Laboratory Assessments ..............................................................55 
Table 9.7.5.1: Clinical Laboratory Tests .................................................................................58 
 
LIST OF FIGURES 
Figure 9.1.1.1.2.1:  Management of Local and Systemic Reactions to rAvPAL-PEG............46 
 
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4 
LIST OF ABBREVIATIONS AND DEFINITIONS OF TERMS 
Abbreviations 
ADR 
adverse drug reaction 
AE 
adverse event 
ALT 
alanine aminotransferase 
AST 
aspartate aminotransferase 
AUC 
area under the plasma concentration-time curve 
AUC0-7 days
area under the plasma concentration-time curve from time zero on Day 1 
to Day 8 
BUN 
blood urea nitrogen 
°C 
degree Celsius 
Ctrough
predose concentration of rAvPAL-PEG 
CD 
Compact disk 
CFR 
Code of Federal Regulations 
CNS 
central nervous system 
CO2
carbon dioxide 
CRA 
Clinical Research Associate 
CRF 
case report form 
CTCAE 
Common Terminal Criteria for Adverse Events 
CV 
cardiovascular 
DBP 
diastolic blood pressure 
DCF 
Data Clarification Form 
DMC 
Data Monitoring Committee 
ECG 
electrocardiogram 
ETV 
Early Termination Visit 
FDA 
Food and Drug Administration 
f/u 
follow-up 
g 
gram 
GCP 
Good Clinical Practice 
GGT 
gamma-glutamyltransferase 
GI 
gastrointestinal 
IB 
Investigator’s Brochure 
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ICF 
Informed Consent Form 
ICH 
International Conference on Harmonisation of Technical Requirements for 
Registration of Pharmaceuticals for Human Use 
IgG 
immunoglobulin G 
IgM 
immunoglobulin M 
IND 
Investigational New Drug 
IP 
investigational product 
IRB 
Institutional Review Board 
IV 
intravenous 
IVRS 
interactive voice response system 
kg 
kilogram 
MedDRA 
Medical Dictionary for Regulatory Activities 
mg 
milligram 
mL 
milliliter 
mm Hg 
millimeter of mercury 
NAb 
neutralizing antibodies 
NCI 
National Cancer Institute 
OTC 
over the counter 
PAH 
phenylalanine hydroxylase 
PAL 
phenylalanine ammonia lyase 
PEG 
polyethylene glycol 
Phe 
phenylalanine 
PI 
Principal Investigator 
PK 
pharmacokinetics 
PKU 
phenylketonuria 
rAvPAL-PEG phenylalanine ammonia lyase 
RBC 
red blood cell 
SAE 
serious adverse event 
SAP 
Statistical Analysis Plan 
SBP 
systolic blood pressure 
SC 
subcutaneous 
SD 
standard deviation 
SDV 
source data verified 
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SGOT 
serum glutamic oxalo-acetic transaminase 
SGPT 
serum glutamic pyruvate transaminase 
US 
United States 
WBC 
white blood cell 
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Definition of Terms: 
Investigational Product (IP): 
“A pharmaceutical form of an active ingredient or placebo being tested or used as a reference 
in a clinical trial, including a product with a marketing authorization when used or assembled 
(formulated or packaged) in a way different from the approved form, or when used for an 
unapproved indication, or when used to gain further information about an approved use.” 
(from E6 ICH)  
The terms “IP” and “study drug” may be used interchangeably in the protocol. 
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5 
ETHICS 
5.1 
Institutional Review Board or Ethics Committee 
Prior to initiating the study, the Investigator will obtain written confirmation that the 
Institutional Review Board (IRB) is properly constituted and compliant with International 
Conference on Harmonisation of Technical Requirements for Registration of 
Pharmaceuticals for Human Use (ICH) and Good Clinical Practice (GCP) requirements, and 
applicable laws and local regulations. A copy of the confirmation from the IRB will be 
provided to BioMarin Pharmaceutical Inc. (BioMarin) or its designee. The Principal 
Investigator (PI) will provide the IRB with all appropriate material, including the protocol, 
Investigator’s Brochure (IB), the Informed Consent Form (ICF) including compensation 
procedures, and any other written information provided to the subjects, including all consent 
forms translated to a language other than the native language of the clinical site. The study 
will not be initiated and investigational product (IP) supplies will not be shipped to the site 
until appropriate documents from the IRB confirming unconditional approval of the protocol, 
the ICF and all subject recruitment materials are obtained in writing by the PI and copies are 
received at BioMarin or its designee. The approval document should refer to the study by 
protocol title and BioMarin protocol number (if possible), identify the documents reviewed, 
and include the date of the review and approval. BioMarin will ensure that the appropriate 
reports on the progress of the study were made to the IRB and BioMarin by the PI in 
accordance with applicable governmental regulations. 
5.2 
Ethical Conduct of Study 
This study will be conducted in accordance with the following: 
• United States (US) Code of Federal Regulations (CFR) sections that address clinical 
research studies, and/or other national and local regulations, as applicable 
• E6 ICH Guideline for GCP 
• The ethical principles established by the Declaration of Helsinki 
Specifically, this study is based on adequately performed laboratory and animal 
experimentation; the study will be conducted under a protocol reviewed and approved by an 
IRB; the study will be conducted by scientifically and medically qualified persons; the 
benefits of the study are in proportion to the risks; the rights and welfare of the subjects will 
be respected; the physicians conducting the study do not find the hazards to outweigh the 
potential benefits; and each subject, or his or her legally authorized representative will 
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provide written, informed consent before any study-related tests or evaluations are 
performed. 
5.3 
Subject Information and Informed Consent 
A properly written and executed ICF, in compliance with the Declaration of Helsinki, 
E6 ICH (GCP Guideline, Section 4.8) and 21 CFR §50 and other applicable local regulations, 
will be obtained for each subject prior to entering the subject into the study. The Investigator 
will prepare the ICF and provide the documents to BioMarin for approval prior to submission 
to the IRB. BioMarin and the IRB must approve the documents before they are implemented. 
A copy of the approved ICF, and if applicable, a copy of the approved subject information 
sheet, minor assent form, parental ICF for studies involving minors, and all ICFs translated to 
a language other than the native language of the clinical site must also be received by 
BioMarin or its designee prior to the delivery of study drug. 
Subjects under the age of 18 years will provide written assent (if required), and his/her 
legally authorized representative (parent or legal guardian) will provide written informed 
consent for such subjects. The Investigator will provide copies of the signed ICF to each 
subject (or the subject’s legally authorized representative) and will maintain the original in 
the subject’s record file. 
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6 
INVESTIGATORS AND STUDY ADMINISTRATIVE STRUCTURE 
Prior to beginning the study, the PI at each site must provide to BioMarin or its designee a 
fully executed and signed Form FDA (Food and Drug Administration) 1572 and a Financial 
Disclosure Form. All sub-Investigators must be listed on Form FDA 1572. Financial 
Disclosure Forms must also be completed for all sub-Investigators listed on the 
Form FDA 1572 who will be directly involved in the treatment or evaluation of research 
subjects in this study. 
The study will be administered by and monitored by employees or representatives of 
BioMarin. Clinical Research Associates (CRAs) or trained designees will monitor each site 
on a periodic basis and perform verification of source documentation for each subject as well 
as other required review processes. BioMarin’s Regulatory Affairs Department (or designee) 
will be responsible for the timely reporting of serious adverse events (SAEs) to appropriate 
regulatory authorities as required. 
Prior to database lock in multicenter studies, a Coordinating Investigator will be identified 
who will read the clinical study report and confirm that it accurately describes the conduct 
and results of the study, to the best of his or her knowledge. The Coordinating Investigator 
will be chosen on the basis of active participation in the study, ability to interpret data, and 
willingness to review and sign the report in a specified timeframe. 
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7 
INTRODUCTION 
A comprehensive review of phenylalanine ammonia lyase ( rAvPAL-PEG) is contained in 
the IB supplied by BioMarin; the Investigator should review this document prior to initiating 
this study. 
7.1 
Nonclinical Studies 
The murine model of phenylketonuria (PKU) BTBRPahenu2 (ENU2), a mouse line that is 
deficient in phenylalanine hydroxylase (PAH) activity (Shedlovsky, 1993, Genetics), was 
used for in vivo screening and pharmacodynamic studies. This mouse model exhibits 
characteristics similar to those seen in PKU patients, including hyperphenylalaninemia 
(baseline plasma phenylalanine [Phe] concentrations of 1000 to 2000 µM) and 
hypopigmentation. Weekly subcutaneous (SC) administration of 80 mg/kg of rAvPAL-PEG 
(approximately 4 IU/mouse) for greater than 3 months lowered blood Phe concentration from 
approximately 2000 µM to less than 200 µM. A similar profile of Phe reduction was also 
seen in ENU2 mice administered wild-type AvPAL-PEG (4 IU/mouse) over 8 weeks. In all 
these studies, regardless of the molecule, an attenuated Phe-lowering response was usually 
seen between Weeks 2 and 7. However, plasma Phe concentrations became stabilized at 
concentrations below 200 µM from Week 7 onward. In addition to the reduction of plasma 
Phe, a dose-related darkening in coat color occurred, indicating the biosynthesis of melanin, 
which was previously inhibited when plasma Phe could not be metabolized and plasma Phe 
concentrations were high. When administration of AvPAL-PEG was stopped for 2 to 7 weeks 
and then reinitiated with weekly administrations, no attenuated response was observed and 
Phe concentrations remained low and stable until the next administration. 
The safety of rAvPAL-PEG was evaluated in safety pharmacology studies (respiratory, 
central nervous system [CNS] and cardiovascular [CV]) and toxicity with toxicokinetic 
studies (single and 28-day repeated dose) in rats and cynomolgus monkeys. Overall, in all 
toxicity studies no immune-related toxicities were seen either systemically or at the injection 
site. No specific polyethylene glycol (PEG)-related histological findings were observed 
during the 28-day repeated dose studies. 
Findings in cynomolgus monkeys dosed with a single administration of 
60 mg/kg rAvPAL-PEG included reduced food consumption, dehydration, body weight 
loss, hypoactivity, hypothermia,decreased plasma Phe concentration, decreased protein 
synthesis, and gastrointestinal (GI) lesions. Plasma Phe concentrations were also reduced to 
below the level of detection in the 4 and 12 mg/kg dose groups, but without similar 
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toxicological consequence, implying that the physiological regulation of Phe levels may 
be an important factor for influencing morbidity.  
The main finding in the 28-day study was the possible drug-related observation of minimal to 
slight degeneration of blood vessels of predominantly medium-sized muscular arteries with a 
non-dose-dependent involvement of different organs observed in 1 male in the 0.1 mg/kg and 
1 male and 1 female in the 1.0 mg/kg rAvPAL-PEG dose groups. No degeneration of the 
arteries was observed in animals administered 0 and 0.01 mg/kg rAvPAL-PEG. 
The half-life of rAvPAL-PEG administered to normal rats at SC doses of 10, 25, and 
250 mg/kg, was 47, 33, and 44 hours, respectively, and exhibited modest area under the 
plasma concentration-time curve (AUC)-dose linearity. In the cynomolgus monkey after SC 
administration of rAvPAL-PEG, the half-life was 65 hours at 4 mg/kg, 71 hours at 12 mg/kg, 
and could not be determined at 60 mg/kg (the highest dose). Qualitatively, the kinetics of 
rAvPAL-PEG in the rat and monkey appear to have similar characteristics. The following 
findings were noted: (1) a 1-compartment model with first-order absorption appears to 
describe the plasma profiles of rAvPAL-PEG after single-dose administration, (2) absorption 
is slow and there is a long absorption period after SC administration to maximum plasma 
concentration, along with a long half-life, (3) elimination is slow and monophasic, (4) there 
does not appear to be a gender difference, and (5) AUC and the maximum plasma 
concentration (Cmax) are roughly linearly proportional. 
7.2 
Previous Clinical Studies 
This study is an extension of the second human clinical study with rAvPAL-PEG 
(Study PAL-002). Study PAL-001, the first-in-human clinical study of rAvPAL–PEG, was 
designed as a Phase 1, open-label, single-dose, dose-escalation study in approximately 
35 subjects, 16 to 50 years old, with PKU. The doses for this study are planned to be in the 
same range as those tested in PAL-001 and PAL-002 (0.001 through 1.0 mg/kg per 
injection), provided no dose-limiting toxicity was observed in those studies. 
7.3 
Study Rationale 
PKU is an autosomal, recessive, inherited disease characterized by deficiency in the enzyme 
PAH (Scriver CR, 2001, McGraw-Hill). Approximately 1 in every 10,000 infants in North 
America is born with PKU (Scriver CR, 2001, McGraw-Hill). Left untreated, PAH 
deficiency is associated with an abnormally elevated concentration of Phe, which is toxic to 
the brain (Kaufman, 1989, J Pediatr.) and can result in a variety of neuropathologic 
conditions, including mental retardation, microcephaly, delayed speech, seizures, and 
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behavioral abnormalities (Scriver CR, 2001, McGraw-Hill). The brains of untreated patients 
with PKU show evidence of hypomyelination and gliosis, arrest in cerebral development, 
and, in some cases, white matter degeneration (Huttenlocher, 2000, Eur.J Pediatr.). Elevated 
Phe during fetal development leads to severe mental retardation and can cause microcephaly, 
growth retardation, and congenital heart disease (Guttler, 2003, Pediatrics), (Koch, 2003, 
Pediatrics), (Lee, 2003, Pediatrics), (Levy, 2003, Pediatrics), (Matalon, 2003, Pediatrics), 
(Rouse, 2004, J.Pediatr.). 
For a subset of patients with residual enzyme activity, treatment with Kuvan® is an option. 
For all other patients, current management of PKU involves adherence to low-Phe medicinal 
diet formulas and dietary restriction of Phe-containing foods. Implementation of a 
Phe-restricted diet in infancy significantly reduces blood Phe concentrations and prevents 
many of the neuropathologic manifestations of PKU, including severe mental retardation. 
However, compliance with this restrictive diet can be difficult for older children, adolescents, 
and adults, and adherence may result in nutritional deficiencies due to the limitations of 
natural protein sources (Fisch, 2000, Eur.J.Pediatr.), (Walter, 2002, Lancet). 
The need exists for a treatment that will help individuals with phenylketonuria (PKU) safely 
achieve lifelong, reliable control of blood phenylalanine (Phe) concentrations and improve 
functional outcomes. Phenylalanine ammonia lyase (rAvPAL-PEG) is a potential substitute 
for the phenylalanine hydroxylase (PAH) enzyme, which is defective in individuals with 
PKU. rAvPAL-PEG may control blood Phe concentrations, which may have additional 
clinical benefits. This study is an extension of the dose-finding study (PAL-002). 
Administration of rAvPAL-PEG will be continued to assess whether long-term dosing of 
rAvPAL-PEG is safe and can maintain reduced blood Phe concentrations in PKU subjects. 
7.4 
Summary of Overall Risks and Benefits 
It is not expected that data from PAL-001 and PAL-002 will change the assumption that 
rAvPAL-PEG has a toxicity profile similar to other recombinant PEGylated non-human 
enzymes currently in use. The toxicities of these drugs usually fall into 2 main categories: 
toxicity due to exposure to PEG, and toxicity due to immunologic sensitization. In addition, 
exaggerated pharmacological effects resulting in very low Phe concentrations could be 
observed. Other adverse events (AEs) that could occur with rAvPAL-PEG include 
injection-site reactions and other general symptoms. 
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7.4.1 Toxicity Due to Exposure to PEG 
Acute exposure to high doses of PEG can result in renal toxicity. There have been a few 
reports of PEG-related AEs in humans; cumulative intravenous (IV) PEG doses of 121 to 
240 g caused acute renal tubular necrosis, oliguria, and azotemia. The anticipated PEG 
exposure associated with the expected rAvPAL-PEG dose range (6 g per week) is at least 
80-fold lower than the reported toxic doses and comparable to exposures to PEG in widely 
used medicines and other compounds that are administered by the IV, oral, rectal, and topical 
routes (Webster, 2007, Drug Metab Dispos.). No indication of PEG-related toxicity at the 
ultrastructural level was observed in monkeys given up to 60 mg/kg of SC rAvPAL-PEG. 
In this study, subjects will be monitored closely with urine examinations and blood 
chemistries to follow kidney function. 
7.4.2 Toxicity Due to an Immunologic Reaction 
The active drug substance in rAvPAL-PEG is a bacterial protein, and as such, it is expected 
that it may elicit immune recognition and responses. In animal models, the immune response 
against the foreign protein PAL in rAvPAL-PEG has been mitigated by PEGylation. 
Epitopes that play a role in the immune response may be rendered inaccessible by PEG 
(Gamez, 2007, Mol.Genet.Metab). In vivo and in vitro experiments have shown that 
PEGylation of proteins and cells can attenuate the immunological response (Scott, 1997, 
Proc.Natl.Acad.Sci.U.S.A), (Chen, 2001, BioDrugs.). PEGylation has been effective in 
reducing anti-rAvPAL antibody titers in the mouse model, although PEGylation does not 
eliminate antibody formation. Although PEGylation of rAvPAL may have a significant effect 
on reducing the immunogenicity of the molecule, it is reasonable to expect that some 
individuals may exhibit immune responses upon exposure to the drug. These immune 
responses may be clinically irrelevant, cause symptoms of various degrees, or lead to 
neutralization of biological activity. Subjects participating in clinical trials will be monitored 
closely with specific antibody titers, sedimentation rates, and complete blood counts (CBCs). 
PEG itself is considered nonimmunogenic (Davis, 1981, Clin.Exp.Immunol.) (Harris, 2003, 
Nat.Rev.Drug Discov.), however, antibodies against PEG may form when PEG is bound to 
compounds. (Harris, 2003, Nat.Rev.Drug.Discov.) (Richter, 1983, Int.Arch.Allergy 
Appl.Immunol.) In some instances, development of such antibodies did not result in any 
significant clinical effects in humans (Richter, 1984, Int.Arch.Allergy Appl.Immunol.). In 
some individuals, anti-PEG antibodies may be pre-existing due to previous exposure to PEG 
in other products. Anti-PEG antibodies have been associated with nonresponsiveness against 
therapy (Armstrong, 2007, Cancer), (Ganson, 2006, Arthritis Res.Ther.). 
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Two subjects enrolled in PAL-001 who had received one dose of rAvPAL-PEG 
experienced hypersensitivity reactions to intramuscular (IM) Depo-Provera, a 
contraceptive containing PEG 3350. Both subjects had previously received multiple IM 
Depo-Provera injections without complications. 
The first subject, a 
 year old 
, developed bruising at the injection site on Day 1 
that resolved on Day 15. 
 developed hives and mild respiratory difficulty 10 minutes 
after receiving IM Depo-Provera given 40 days after
 rAvPAL-PEG injection. 
 was treated in the emergency room with 
, and 
; and oral 
. The events resolved the same day, and the 
subject had no further complications. The subject had no prior history of any reactions 
to Depo-Provera. Subsequently, while under the care of an allergist/immunologist, 
the subject had a mild reaction to a concentrated intradermal (1:10) exposure of 
Depo-Provera. 
 was later given a full dose of IM Depo-Provera without problems. 
The second subject, an 
 year old 
, had a slightly raised, erythematic rash below 
the site of rAvPAL-PEG injection on Day 11 that resolved without treatment on Day 15. 
 developed generalized hives on 
 arms and legs and mild difficulty breathing 
20 minutes after receiving IM Depo-Provera (and 
 third dose of Gardasil) given 
15 days after 
 rAvPAL-PEG injection. 
 symptoms subsided after 
 received 
 given by 
 mother. 
 did not visit the emergency room. The subject 
had no prior history of any reactions to Depo-Provera or Gardasil (Gardasil dose not 
contain PEG). 
 was subsequently seen by an allergist/immunologist, and the results 
are pending. 
Because Depo-Provera contains PEG 3350 as an excipient, it is possible that the 
administration of rAvPAL-PEG caused anti-PEG antibody formation that led to a 
cross-reaction with Depo-Provera in these subjects. Therefore, it is possible that prior 
exposure to rAvPAL-PEG might sensitize subjects to other PEG-containing injectable 
drugs. Alternatively, the presence of Depo-Provera could have led to antibody 
formation and cross-reaction with rAvPAL-PEG, leading to rAvPAL-PEG 
injection-site reactions. Since it is currently unknown whether Depo-Provera has a 
sensitizing effect to PEG and the exact basis for these reported events is not known, the 
use of PEG-containing injectable drugs prior to and during the study is prohibited as a 
precautionary measure (refer to the addendum and Sections 9.3.2 and 9.4.8). 
Allergic reactions to the SC injection of rAvPAL-PEG may be mild, moderate or severe in 
intensity. Reactions may include pruritus, rash, shortness of breath, hypotension, or 
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anaphylaxis. Clinical assessments should be conducted for a minimum of 2 hours 
post-injection. Longer observations may be required at the discretion of the PI. The 
responsible physician should use all appropriate measures for the treatment of allergic 
reactions. Because of the small potential for anaphylaxis, equipment for emergency 
resuscitation (including epinephrine) should be within easy access during and after the 
rAvPAL-PEG injection. 
In the event of an allergic reaction, subjects may be asked to see an 
allergist/immunologist and/or provide up to 3 additional blood samples for antibody 
testing. This additional testing may occur up to 6 months following the final study visit. 
7.4.2.1 
Management of Allergic Reactions 
The following measures are recommended for the treatment of allergic symptoms: 
• Clearing the airway. 
• Vital sign check. 
• Administration of oral or IV diphenhydramine. 
• Administration of epinephrine if appropriate. 
• Administration of oxygen and IV fluids. 
• Administration of additional symptomatic treatment. 
• Transfer to an acute care facility of the study center. 
In addition, clinical judgment must be used in determining the appropriateness of 
corticosteroid administration. Acetaminophen or ibuprofen (5-10 mg/kg) may also be 
administered. An allergy and/or immunology consultation should be sought if necessary. 
7.4.3 Effects of Low Blood Phe 
Insufficient Phe intake or excessive rAvPAL-PEG exposure may cause blood Phe 
concentrations to be too low (eg, < 30 ˜m ol/L). Prolonged low blood Phe concentrations can 
result in a catabolic state associated with poor growth and altered body functions, including 
mental and physical alterations, loss of appetite, anemia, rashes, and diarrhea. To ensure 
safety during this study, subjects will be monitored closely with frequent blood Phe 
concentration determinations. 
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8 
STUDY OBJECTIVES 
The primary objective of the study is: 
• To evaluate the effect of long-term administration of SC injections of rAvPAL-PEG 
on blood Phe concentrations in subjects with PKU. 
The secondary objectives of the study are: 
• To evaluate the safety and tolerability of long-term administration of subcutaneous 
(SC) injections of rAvPAL-PEG in subjects with PKU. 
• To evaluate the immune response to long-term administration of SC injections of 
rAvPAL-PEG in subjects with PKU who participated in Study PAL-002. 
• To evaluate steady-state PK of rAvPAL-PEG in subjects with PKU. 
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9 
INVESTIGATIONAL PLAN 
9.1 
Overall Study Design and Plan 
This is a long-term extension of a Phase 2, open-label, dose-finding study (PAL-002) in 
approximately 35 subjects with PKU. The doses are planned to be in the same range as those 
tested in PAL-002 (0.001 through 1.0 mg/kg per injection), provided no dose-limiting 
toxicity was observed in PAL-002. 
Only subjects who completed participation in PAL-002 will be enrolled into this study. Diet 
will not be altered during the course of this study, except as necessary for safety. 
Subjects will be evaluated for safety and for blood Phe concentrations throughout the study. 
Toxicity will be measured according to the National Cancer Institute (NCI) Common 
Terminology Criteria for Adverse Events (CTCAE), version 3. 
A Data Monitoring Committee will monitor the study. 
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take 
rAvPAL-PEG. PAL-002 participants’ rAvPAL-PEG dosing will continue in PAL-003 
without interruption of weekly dosing. In PAL-003, each subject’s dose will be adjusted as 
needed to attain or maintain blood Phe concentrations below 480 µmol/L based upon 
recommendations by the German Working Group for Metabolic Diseases (Burgard, 1999, 
Eur J Pediatr). Subjects will continue to receive injections in the clinic, administered by 
clinic staff, but may later be allowed to self-administer doses of study drug at home. Whether 
a subject may be allowed to self-administer study drug doses will be evaluated on an 
individual basis. All of the following criteria must be met before a subject may 
self-administer doses of the study drug: 
• The subject is willing and able to administer the study drug as directed. 
• The sponsor agrees that self-administration is appropriate. 
• The subject has achieved a favorable dose (ie, the dosage that provides control of 
blood Phe concentrations within the target range for a minimum of 2 weeks). 
• The subject has received appropriate training, including administering doses under 
supervision, until the subject and clinic staff both agree such training is no longer 
necessary. 
The dose may be modified at any time for safety. 
Evaluations, observations, and procedures will be conducted at selected timepoints as shown 
in Table 2.1.1, Schedule of Events. After the subject’s blood Phe concentration has been 
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controlled to within a target range (below 480 µmol/L), the subject may be asked to have 
additional blood draws for PK and blood Phe concentration analyses. 
A subject will continue in PAL-003 until one of the following occurs: 
12. The subject withdraws consent and discontinues from the study. 
13. The subject is discontinued from the study at the discretion of the Investigator. 
14. The drug becomes commercially available following the appropriate marketing 
approval. 
15. The study is terminated. 
9.1.1 Management of Local and Systemic Reactions to rAvPAL-PEG 
9.1.1.1 
Subjects Who Have Experienced Hypersensitivity Reactions to 
rAvPAL-PEG or a PEG-containing Product 
Subjects who had a previous reaction to rAvPAL-PEG or a PEG-containing product 
that warranted early termination from PAL-001 or PAL-002 are excluded from this 
study.  However, subjects may develop such reactions after enrollment in PAL-003. 
Management of such reactions are described below. Refer to Figure 9.1.1.1.2.1 for a 
flowchart for managing these subjects. 
9.1.1.1.1 Subjects with Local Reactions 
After enrollment in PAL-003, subjects who have a local reaction to rAvPAL-PEG or a 
PEG-containing product will be premedicated with acetaminophpen and antihistamines 
and/or oral steroids, 1 hour prior to study drug dosing. Recommended premedications 
are acetaminophen and antihistamine (Claritin is preferred). The dosage will be 
standard (eg, 1000 mg acetaminophen and 10 mg Claritin or 25 to 50 mg oral Benadryl; 
an example for steroids would be 70 mg oral prednisone). Because Benadryl can cause 
drowsiness, it should be administered only if the subject is accompanied by a designated 
driver. 
9.1.1.1.2 Subjects with Systemic Reactions 
After enrollment in PAL-003, subjects who have a systemic reaction that includes 
noncutaneous systemic symptoms, such as respiratory problems, hypotension, or 
angioedema, to rAvPAL-PEG or a PEG-containing product will be evaluated with a 
skin prick test. If the test is positive, the subject will be excluded from the study. 
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Subjects with prior systemic reactions that included only skin manifestations to 
rAvPAL-PEG or a PEG-containing product after PAL-003 enrollment will be 
premedicated with acetaminophen and antihistamines and/or oral steroids (one hour 
prior to study drug dosing) and will continue to receive rAvPAL-PEG. 
Reactions to skin prick testing or rAvPAL-PEG administered SC are defined as 
follows: 
Local reaction: 1 affected location, ie, hives, wheals, or swelling or an area of erythema 
or redness at or near the site of injection. 
Systemic reaction: more than 1 affected location, ie, cutaneous reaction in more than 
1 area, and/or any other generalized symptoms, such as hypotension, angioedema or 
anaphylaxis or the involvement of other organ systems (eg, respiratory, cardiovascular, 
gastrointestinal). 
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Figure 9.1.1.1.2.1:  Management of Local and Systemic Reactions to rAvPAL-PEG 
 
Has the subject ever had a reaction 
to rAvPAL-PEG or a PEG-
containing product? 
• Administer rAvPAL-PEG 
• Observe for 2 hours 
NO 
Local 
reaction 
Systemic 
reaction 
• Premedicate 
• Administer rAvPAL-PEG 
• Observe for 2 hours 
• Obtain additional blood 
sample for antibody testing 
(according to regular study 
Schedule of Events) 
YES 
Systemic symptoms such 
as generalized hives, 
respiratory or 
gastrointestinal 
problems, hypotension, 
angioedema, or 
anaphylaxis 
Exclude subject 
from study 
 
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9.1.2 Dose Adjustment Methodology 
Each subject’s dose may be modified based on the decision of the Investigator, in agreement 
with the Study Medical Officer. Depending upon the response to rAvPAL-PEG in PAL-002, 
a subject’s dose may be adjusted beginning on Day 1 of PAL-003 as follows. 
• The dose may be increased by increments of no more than 10-fold higher than the 
subject’s current dose. 
• The dose may be decreased as appropriate to achieve or maintain a favorable blood 
Phe concentration. 
• When adjusting the dose, a dose may be used that is between the dose cohort levels 
that were defined in the previous study (PAL-002). 
• The dose may be adjusted by increasing the frequency of injections per week, up to 
one dose per day, for a maximum total dose of 2 mg/kg/week. 
• When a dose is adjusted (either by changing the dose level or by changing the 
frequency of dosing), the subject must remain in the clinic for a minimum of 2 hours 
following the first modified dose administration, and an Investigator will remain on 
site during this time. 
Subjects must have blood Phe concentration tested 3 days after a dose adjustment. There 
must be a minimum of 2 weeks after each dose adjustment before any additional dose 
adjustments may be made so that blood Phe concentrations can be assessed. 
9.1.3 Stopping Criteria 
If an individual subject exhibits drug-related toxicity of CTCAE grade 3 or greater, that 
subject will have dosing halted until the toxicity resolves. The subject’s data will be 
evaluated by the Principle Investigator (PI) and the Study Medical Officer, and a decision 
will then be made whether to discontinue the subject from the study, restart dosing at the 
same dose level, or restart dosing at a lower dose level. 
In addition, if 2 or more subjects at a dose level exhibit drug-related toxicity of CTCAE 
grade 3 or greater, further dosing of subjects at that dose level and any higher dose levels will 
be halted until a safety assessment is completed. 
9.2 
Discussion of Study Design, Including Choice of Control Group 
This open-label, Phase 2 trial was designed to be closely monitored with the goal of 
obtaining information about the efficacy, safety, tolerability, and PK of long-term 
administration of rAvPAL-PEG in subjects with PKU. There will be no control group in this 
study. 
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9.3 
Selection of Study Population 
9.3.1 Inclusion Criteria 
Individuals eligible to participate in this study must meet all of the following criteria: 
• Must have completed participation in PAL-002. 
• Willing and able to provide written, signed informed consent, or in the case of 
subjects under the age of 18 years, provide written assent (if required) and written 
informed consent by a parent or legal guardian, after the nature of the study has been 
explained, and prior to any research-related procedures. 
• Willing and able to comply with all study procedures. 
• Females of childbearing potential must have a negative pregnancy test at Screening 
and be willing to have additional pregnancy tests during the study. Females 
considered not of childbearing potential include those who have been in menopause at 
least 2 years, or had tubal ligation at least 1 year prior to Screening, or who have had 
total hysterectomy. 
• Sexually active subjects must be willing to use an acceptable method of contraception 
while participating in the study. 
• Maintained a stable diet. 
• In generally good health as evidenced by physical examination, clinical laboratory 
evaluations (hematology, chemistry, and urinalysis), and electrocardiogram (ECG) at 
Screening. 
9.3.2 Exclusion Criteria 
Individuals who meet any of the following exclusion criteria will not be eligible to participate 
in the study: 
• Use of any investigational product (with the exception of rAvPAL-PEG) or 
investigational medical device within 30 days prior to Screening, or requirement for 
any investigational agent prior to completion of all scheduled study assessments. 
• Use or planned use of any injectable drugs containing PEG (other than 
rAvPAL-PEG), including Depo-Provera, within 6 months prior to Screening and 
during study participation. 
• A prior reaction that included systemic symptoms (eg, generalized hives, 
respiratory or gastrointestinal problems, hypotension, angioedema, anaphylaxis) 
to rAvPAL-PEG or a PEG-containing product. 
• Use of any medication that is intended to treat PKU within 14 days prior to the 
administration of study drug. 
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• Pregnant or breastfeeding at Screening or planning to become pregnant (self or 
partner) or to breastfeed at any time during the study. 
• Concurrent disease or condition that would interfere with study participation or safety 
(eg, history or presence of clinically significant cardiovascular, pulmonary, hepatic, 
renal, hematologic, gastrointestinal, endocrine, immunologic, dermatologic, 
neurological, oncologic, or psychiatric disease). 
• Any condition that, in the view of the PI, places the subject at high risk of poor 
treatment compliance or of not completing the study. 
• Alanine aminotransferase (ALT) concentration > 2 times the upper limit of normal. 
• Creatinine > 1.5 times the upper limit of normal. 
9.3.3 Removal of Subjects from Treatment or Assessment 
Subjects (or their legally authorized representative) may withdraw their consent to participate 
in the study at any time without prejudice. The Investigator must withdraw from the study 
any subject who requests to be withdrawn. A subject’s participation in the study may be 
discontinued at any time at the discretion of the Investigator and in accordance with his/her 
clinical judgment. When possible, the tests and evaluations listed for the Early Termination 
Visit should be carried out (refer to Section 12.4). 
BioMarin must be notified of all subject withdrawals as soon as possible. BioMarin also 
reserves the right to discontinue the study at any time for either clinical or administrative 
reasons and to discontinue participation by an individual Investigator or site for poor 
enrollment or noncompliance. 
Reasons for which the Investigator or BioMarin may withdraw a subject from the study 
include, but are not limited to, the following: 
• Subject experiences a serious or intolerable AE. 
• Subject develops a clinically significant laboratory abnormality. 
• Subject requires medication prohibited by the protocol. 
• Subject does not adhere to study requirements specified in the protocol. 
• Subject was erroneously admitted into the study or does not meet entry criteria. 
• Subject is lost to follow-up. 
• Subject becomes pregnant (refer to Section 10.3 for details on the reporting 
procedures to follow in the event of pregnancy). 
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If a subject fails to return for scheduled visits, a documented effort must be made to 
determine the reason. If the subject cannot be reached by telephone within 7 days, a certified 
letter should be sent to the subject (or the subject’s legally authorized representative, if 
appropriate) requesting contact with the Investigator. This information should be recorded in 
the study records. 
The Investigator or designee must explain to each subject, before enrollment into the study, 
that for evaluation of study results, the subject’s protected health information obtained during 
the study may be shared with the study sponsor, regulatory agencies, and IRB. It is the 
Investigator’s (or designee’s) responsibility to obtain written permission to use protected 
health information per country-specific regulations, such as the Health Insurance Portability 
and Accountability Act (HIPAA) in the United States, from each subject, or if appropriate, 
the subject’s legally authorized representative. If permission to use protected health 
information is withdrawn, it is the Investigator’s responsibility to obtain a written request, to 
ensure that no further data will be collected from the subject and the subject will be removed 
from the study. 
9.3.4 Subject Identification and Replacement of Subjects 
Each subject was assigned a unique subject identifier in either PAL-001 or PAL-002. 
Subjects will retain the same subject number used in PAL-002. 
This unique identifier will be on all case report form (CRF) pages. In legal jurisdictions 
where use of initials is not permitted, a substitute identifier will be used.  
After enrollment of 35 subjects, if any single cohort (identified during PAL-002) has less 
than 3 subjects due to early terminations, those subjects will be replaced. Replacement 
subjects will enter the study at the same dose cohort level as the subject they are 
replacing. 
9.4 
Treatments 
9.4.1 Treatments Administered 
BioMarin and/or its designee will provide the study site with a supply of IP sufficient for the 
completion of the study. 
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9.4.2 Identity of Investigational Product (IP) 
9.4.2.1 
Product Characteristics and Labeling 
The rAvPAL-PEG drug product for SC injection is formulated and supplied as a sterile 
aqueous (colorless to pale yellow) solution in clear, single-use, type-1 borosilicate glass 
vials. Each 3 mL vial contains 1.5 ± 0.2 mL to deliver 10 mg of rAvPAL-PEG per 1 mL 
(10 mg/mL protein concentration). Each vial is filled with 1.5 ± 0.2 mL to allow the 
withdrawal and delivery of up to 1 mL of the drug product. 
Dilution instructions are provided in a separate instruction manual. 
The excipients in this drug product are tromethamine, tromethamine-hydrochloride, 
sodium chloride, L-phenylalanine, and water for injection. 
Drug product packaging will be identified with the lot number and expiration date, and will 
be provided in a box labeled with the study number. 
9.4.3 Storage 
At the study site, all IP must be stored at 5 ±3°C (41 ± 5°F) under the conditions specified in 
the IB in a secure area accessible only to the designated pharmacists and clinical site 
personnel. All IP must be stored and inventoried and the inventories must be carefully and 
accurately documented according to applicable state, federal and local regulations, ICH GCP, 
and study procedures. 
9.4.4 Directions for Administration 
Doses will be administered SC and the favorable dose will be determined for each subject by 
adjusting the dose level, dose frequency, or both, as agreed by the PI and the Study Medical 
Officer, based upon the subject’s response to doses. Dosing is up to a maximum dose per 
week of 2 mg/kg. 
Dosage is calculated by multiplying each subject’s weight in kilograms (kg) on Day 1 
(predose) by the assigned dose (in mg/kg). During the study, if the weight of a subject 
changes more than 10% from the measurement obtained at baseline or at a previous 
measurement, the subject’s dose may be adjusted to accommodate the change. The change 
must be recorded. Refer to the Pharmacy Manual for additional information on calculating 
dosage. 
The injection sites should be alternated between doses, ie, upper left arm in Week 1, upper 
right arm in Week 2, etc. Doses may be administered in any of the common SC areas (upper 
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arm, thigh, abdomen). If dose volume is such that a dose will be divided and given in more 
than 1 injection site, it is preferable to use both arms, both legs, or both sides of the abdomen. 
Subjects may require more than 1 injection per dose, depending upon site policy 
(ie, some institutions do not permit a single SC injection of greater than 2 mL). 
The number of injections required for an individual weighing 80 kg (about 176 pounds) 
is provided in Table 9.4.4.1 as an example, Note this table is for example purposes only. 
Dosage calculations must be performed according to study drug preparation 
instructions provided in the PAL-003 Pharmacy Manual. 
Table 9.4.4.1  Number of Injections Required For an Individual Weighing 80 kg 
Dose Group 
(mg/kg) 
Weight 
(kg) 
Volume of Study Drug
(mL)a
No. of 
Injectionsb
0.001 
80 
0.8 
1 
0.003 
80 
0.6 
1 
0.01 
80 
0.8 
1 
0.03 
80 
0.2 
1 
0.1 
80 
0.8 
1 
0.3 
80 
2.4 
2 
1.0 
80 
8.0 
4 
aStudy drug is supplied at a concentration of 10 mg/mL and is then diluted by differential 
amounts as specified in the PAL-003 Pharmacy Manual. Volume to be injected is calculated 
based on a starting volume attained following dilution. 
bNumber of injections per dose is dependent upon site policy for SC injections. The number of 
injections may vary at the discretion of the Investigator. 
9.4.5 Method of Assigning Subjects to Treatment Groups 
This will be an open-label study; no randomization schedule will be generated. 
Subjects will retain the same subject number used in PAL-002. 
An interactive voice response system (IVRS) will be used to track subjects’ assigned 
dose and study drug inventory. 
9.4.6 Selection of Doses Used in the Study 
This Phase 2 study aims to evaluate the efficacy, safety, tolerability, and PK parameters of 
multiple doses of rAvPAL-PEG after long-term administration in subjects with PKU. 
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A favorable dose that produces a reduction in blood Phe concentration to below 480 μmol/L 
will be determined for each subject. Findings in cynomolgus monkeys dosed with a single 
administration of 60 mg/kg rAvPAL-PEG included severe morbidity, decreased plasma Phe 
concentration, decreased protein synthesis, and GI lesions. Plasma Phe concentrations were 
reduced to below the level of detection in the lower dose groups, without other findings. The 
doses for this study will be based upon the findings in PAL-001 and PAL-002. 
9.4.6.1 
Selection of Timing of Dose for Each Subject 
Study drug will be administered in the morning by clinic staff or by the subject, if 
appropriate. 
9.4.7 Blinding 
This is an open-label study. 
9.4.8 Prior and Concomitant Medications 
All prescription and over-the-counter (OTC) medications taken by a subject for 30 days 
before Screening will be recorded on the designated CRF. The Investigator may prescribe 
additional medications during the study, as long as the prescribed medication is not 
prohibited by the protocol. In the event of an emergency, any needed medications may be 
prescribed without prior approval, but the medical monitor must be notified of the use of any 
contraindicated medications immediately thereafter. Any concomitant medications added or 
discontinued during the study should be recorded on the CRF. 
Use of any investigational product (with the exception of rAvPAL-PEG used in PAL-002) or 
investigational medical device within 30 days before Screening, or requirement for any 
investigational agent prior to completion of all scheduled study assessments, is prohibited. 
Use or planned use of any injectable drugs containing PEG (other than rAvPAL-PEG), 
including Depo-Provera, is prohibited within 6 months prior to Screening and during 
study participation. A list of PEG-containing injectable drugs is provided in the study 
reference materials. Subjects who have had a prior reaction to rAvPAL-PEG or a 
PEG-containing product will be premedicated with acetaminophen and antihistamines 
and/or oral steroids (refer to Section 9.1.1).
Subjects who have had a prior hypersensitivity reaction to rAvPAL-PEG or a 
PEG-containing product will be premedicated with acetaminophen and antihistamines 
and/or oral steroids (refer to Section 9.1.1). If the local or systemic reaction worsens 
with a repeat injection (as determined by the Investigator in consultation with the 
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Study Medical Officer) even with premedication prior to study drug dosing, the subject 
must be withdrawn from the study.
Use of any medication that is intended to treat PKU within 14 days prior to the 
administration of study drug is prohibited. 
9.4.9 Treatment Compliance 
The date, time, volume, and concentration of each dose of study drug administered to each 
subject must be recorded in the dispensing log provided for the study, as well as on the 
appropriate CRF. This data will be used to assess treatment compliance. 
9.5 
Investigational Product Accountability 
The PI or designee is responsible for maintaining accurate records (including dates and 
quantities) of IP received, subjects to whom IP is dispensed (subject-by-subject dose specific 
accounting), and IP lost or accidentally or deliberately destroyed. The PI or designee must 
retain all unused or expired study supplies until the study monitor (on-site CRA) has 
confirmed the accountability data. 
9.5.1 Return and Disposition of Clinical Supplies 
Unused study drug must be kept in a secure location for accountability and reconciliation by 
the study monitor. The Investigator or designee must provide an explanation for any 
destroyed or missing study drug or study materials. 
Unused study drug may be destroyed on site, per the site’s standard operating procedures, but 
only after BioMarin has granted approval for drug destruction. The monitor must account for 
all study drug in a formal reconciliation process prior to study drug destruction. All study 
drug destroyed on site must be documented. Documentation must be provided to BioMarin 
and retained in the PIs study files. If a site is unable to destroy study drug appropriately, the 
site can return unused study drug to BioMarin upon request. The return of study drug or 
study drug materials must be accounted for on a Study Drug Return Form provided by 
BioMarin. 
All study drug and related materials should be stored, inventoried, reconciled, and destroyed 
or returned according to applicable state and federal regulations and study procedures. 
9.6 
Dietary or Other Protocol Restrictions 
Subjects will be instructed that diet should not be altered during the course of the study 
except as necessary for safety. 
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9.7 
Efficacy and Safety Variables 
9.7.1 Efficacy and Safety Measurements Assessed 
The Schedules of Events in the Synopsis (Section 2.1) describe the timing of required 
evaluations. 
For the laboratory assessments, the party responsible for performing the assessment and the 
pertinent protocol section describing the details of the test are listed in Table 9.7.1.1. 
Table 9.7.1.1: Summary of Laboratory Assessments 
Laboratory Assessment 
Party Responsible for 
Performing Test 
Section in Protocol for 
Details 
Clinical laboratory tests 
Central laboratory 
9.7.5
Antibody testing 
BioMarin 
9.7.4.2
PK variables 
Central laboratory 
9.7.3
Blood Phe concentrations 
Central laboratory 
9.7.2.1
Phe, phenylalanine; PK, pharmacokinetic. 
9.7.1.1 
Demographic Data and Medical History 
Demographic data and a detailed medical history will be obtained at Screening. The medical 
history will include specific information concerning any prior or existing medical conditions 
that might interfere with study participation or safety. This medical history should elicit all 
major illnesses, diagnoses, and surgeries that the subject has ever had, and whether the 
subject has a history of alcohol and/or drug abuse. 
9.7.1.2 
Physical Examination Findings 
Physical examination will include assessment of weight; general appearance; CV; 
dermatologic; head, eyes, ears, nose, and throat; lymphatic; respiratory; GI; musculoskeletal; 
and neurological/psychological. Height will be measured at Screening only. Other body 
systems may be examined. Day 1 results will be the baseline values and clinically significant 
changes from baseline will be recorded as an AE. 
9.7.1.3 
Vital Sign Measurements 
Vital signs will be measured after resting for 5 minutes, and include seated systolic blood 
pressure (SBP) and diastolic blood pressure (DBP) measured in millimeters of mercury 
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(mm Hg), heart rate in beats per minute, respiration rate in breaths per minute, and 
temperature in degrees Celsius (°C). 
9.7.1.4 
Electrocardiography 
A standard 12-lead ECG will be recorded while the subject is resting, at Screening and at the 
final follow-up (F/U) Visit or Early Termination Visit (ETV). If clinically significant 
abnormalities are noted at Screening, the PI or designee is required to assess whether it is 
appropriate for the subject to enroll in the study. 
9.7.2 Efficacy Variable 
9.7.2.1 
Blood Phenylalanine Concentrations 
Blood samples for Phe concentration measurements will be drawn in the morning, at least 
2.5 hours after a meal, on the days and timepoints indicated in the Schedule of Events 
(Table 2.1.1). 
In addition, 3 days after each administration of study drug, the subject will have a blood Phe 
measurement by fingerstick. This may be done by the subject at home. 
A central laboratory will be used for blood Phe concentration analysis. 
9.7.3 Pharmacokinetic Variables 
Steady-state PK (predose samples) of rAvPAL-PEG will be evaluated in PKU subjects after 
the subject has achieved and maintained target blood Phe concentration (below 480 μmol/L) 
for a minimum of 2 weeks (to allow assessment of blood Phe concentrations) and no further 
dose modification is planned. Once this target has been achieved, PK samples will be 
collected predose on the same day each week for 3 consecutive weeks. 
BioMarin will perform the analysis. 
9.7.4 Safety Variables 
9.7.4.1 
Pregnancy Testing 
Female subjects of childbearing potential will have a urine pregnancy test at the timepoints 
specified in the Schedules of Events (Table 2.1.1). Female subjects with a positive pregnancy 
test at Screening do not meet eligibility criteria for enrollment. 
Additional pregnancy tests will be performed at any visit in which pregnancy status is in 
question. Serum pregnancy tests will be performed in the event of a positive or equivocal 
urine pregnancy test results. 
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Refer to Section 10.3 for details on the reporting procedures to follow in the event of 
pregnancy. 
9.7.4.2 
Antibody Testing 
Immunoglobulin G (IgG) and M (IgM) antibodies and neutralizing antibodies (NAb) to 
rAvPAL-PEG will be measured using validated immunogenicity assays at the timepoints 
indicated in the Schedule of Events (Table 2.1.1). Anti-PEG antibodies will also be 
measured. 
BioMarin will perform the analysis. 
9.7.5 Clinical Laboratory Assessments 
Any abnormal test results determined to be clinically significant by the Investigator should 
be repeated (at the Investigator’s discretion) until the cause of the abnormality is determined, 
the value returns to baseline or to within normal limits, or the Investigator determines that the 
abnormal value is no longer clinically significant. 
All clinical laboratory result pages should be initialed and dated by an Investigator, along 
with a comment regarding whether or not the result is clinically significant. 
The diagnosis, if known, associated with abnormalities in clinical laboratory tests that are 
considered clinically significant by the Investigator will be recorded on the AE CRF. 
Specific days for obtaining samples are provided in Table 2.1.1 and in Section 12. 
The scheduled clinical laboratory tests are listed in Table 9.7.5.1. A central laboratory will be 
used for analysis. 
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Table 9.7.5.1: Clinical Laboratory Tests 
Blood Chemistry 
Hematology 
Urine Tests 
Other 
Albumin  
Hemoglobin  
Appearance 
Alkaline 
Phosphatase  
Hematocrit  
Color 
Pregnancy test, if 
applicable 
ALT (SGPT)  
WBC count 
pH 
Pharmacokinetics 
AST (SGOT) 
RBC count 
Specific gravity 
Tyrosine 
Total bilirubin 
Platelet count 
Ketones 
BUN 
Differential cell count 
Protein 
Creatinine 
Sedimentation rate 
Glucose 
Serum rAvPAL-PEG-
specific antibodies 
(IgG, IgM, and NAb) 
GGT 
 
Bilirubin 
Phenylalanine 
Total protein 
 
Nitrite 
 
Calcium 
 
Urobilinogen 
 
Sodium 
 
Hemoglobin 
 
Potassium 
 
 
 
Glucose 
 
 
 
Uric acid 
 
 
 
CO2
 
 
 
Chloride 
 
 
 
ALT, alanine aminotransferase; AST, aspartate aminotransferase; BUN, blood urea nitrogen; CO2, carbon 
dioxide; GGT, gamma-glutamyltransferase; IgG, immunoglobulin G; IgM, immunoglobulin M; NAb, 
neutralizing antibodies; RBC, red blood cell; SGOT, serum glutamic-oxaloacetic transaminase; SGPT, serum 
glutamic-pyruvic transaminase; WBC, white blood cell. 
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10 
REPORTING ADVERSE EVENTS 
10.1 
Adverse Events 
According to the ICH definition, an AE (or adverse experience) is “any untoward medical 
occurrence in a patient or clinical investigation subject administered a pharmaceutical 
product, and that does not necessarily have a causal relationship with this treatment. An AE 
can therefore be any unfavorable and unintended sign (including an abnormal laboratory 
finding), symptom, or disease temporally associated with the use of a medicinal 
(investigational) product, whether or not considered related to the IP.” 
An adverse drug reaction (ADR) is described by the ICH as “all noxious and unintended 
responses to a medicinal product related to any dose.” This means that a causal relationship 
between a medicinal product and an AE is at least a reasonable possibility, ie, the 
relationship cannot be ruled out. 
An AE may include intercurrent illnesses or injuries that represent an exacerbation (increase 
in frequency, severity, or specificity) of pre-existing conditions (eg, worsening of asthma). 
Whenever possible, it is preferable to record a diagnosis as the AE term rather than a series 
of terms relating to a diagnosis. 
The reporting period for non-serious AEs is the period from the first administration of study 
drug through the final F/U Visit or at the ETV. If a non-serious AE remains unresolved at the 
conclusion of the study, the PI and medical monitor will make a joint clinical assessment as 
to whether continued follow-up of the AE is warranted, and the results of this assessment 
must be documented. Resolution is defined as the return to baseline status or stabilization of 
the condition with the expectation that it will remain chronic. 
The Investigator will assess AEs for severity, for relationship to IP, and as to whether the 
event meets one or more of the definitions of an SAE (refer to Section 10.2). 
The Investigator will determine the severity of each AE and will record it on the source 
documents and AE CRF, using the categories defined below. 
Grade 
Description 
Mild 
No limitation of usual activities 
Moderate 
Some limitation of usual activities 
Severe 
Inability to carry out usual activities 
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The term “severe” is often used to describe the intensity (severity) of a specific event (as in 
mild, moderate, or severe myocardial infarction); the event itself, however, may be of 
relatively minor medical significance (such as severe headache). This is not the same as 
“serious,” which is based on subject/event outcome or action criteria usually associated with 
events that pose a threat to a subject’s life or functioning. Seriousness (not severity) serves as 
a guide for defining regulatory reporting obligations. 
The Investigator will determine the relationship of an AE to the IP and will record it on the 
source documents and AE CRF, using the categories defined below. 
Relationship 
Description 
Not Related 
Exposure to the IP has not occurred 
OR 
The administration of the IP and the occurrence of the AE are not 
reasonably related in time  
OR 
The AE is considered likely to be related to an etiology other than 
the use of the IP; that is, there are no facts [evidence] or arguments 
to suggest a causal relationship to the IP. 
Possibly 
Related 
The administration of the IP and the occurrence of the AE are 
reasonably related in time 
AND 
The AE could be explained equally well by factors or causes other 
than exposure to the IP. 
Probably 
Related 
The administration of IP and the occurrence of the AE are 
reasonably related in time  
AND 
The AE is more likely explained by exposure to the IP than by other 
factors or causes. 
In order to classify AEs and diseases, preferred terms will be assigned by the sponsor to the 
original terms entered on the CRF, using MedDRA (Medical Dictionary for Regulatory 
Activities terminology). 
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10.2 
Serious Adverse Events 
A SAE is defined as any AE that: 
• Results in death. 
• Is life threatening, that is, places the subject at immediate risk of death from the event 
as it occurred. This definition does not include a reaction that, had it occurred in a 
more severe form, might have caused death. 
• Requires in-patient hospitalization or prolongation of an existing in-patient 
hospitalization. Admission of a subject to the hospital as an in-patient as a result of an 
AE, even if the subject is released on the same day, qualifies as hospitalization. 
• Results in persistent or significant disability or incapacity. An event qualifies as 
resulting in a persistent or significant disability or incapacity if it involves a 
substantial disruption of the subject’s ability to carry out usual life functions. 
This definition is not intended to include experiences of relatively minor or temporary 
medical significance. 
• Is a congenital anomaly or birth defect, that is, an AE that occurs in the child or fetus 
of a subject exposed to IP prior to conception or during pregnancy. 
• Is an important medical event that does not meet any of the above criteria, but may 
jeopardize the subject or require medical or surgical intervention to prevent one of the 
outcomes listed above. Examples of such events are intensive treatment in the 
emergency room, allergic bronchospasm, blood dyscrasias or convulsions that do not 
result in hospitalization; or development of drug dependency or drug abuse. 
More than one of the above criteria may apply to any specific event. 
The reporting period for SAEs begins earlier than non-serious AEs and is the period from the 
time of signing of the ICF through 4 weeks after the last dose or at the ETV. SAEs reported 
to the Investigator outside of this reporting period will be reported to BioMarin if, in good 
medical judgment, the event has any bearing on the study data. SAEs must be followed by 
the Investigator until resolution, even if this extends beyond the study-reporting period. 
Resolution of an SAE is defined as the return to baseline status or stabilization of the 
condition with the expectation that it will remain chronic. 
Any SAE, whether or not considered related to study drug, will be reported immediately 
(within 24 hours) to BioMarin Pharmacovigilance by fax using the study-specific 
SAE Report Form. In addition to the outcome of the SAE, any medication or other 
therapeutic measures used to treat the event will be recorded on the appropriate CRF page(s). 
Investigators should not wait to collect additional information that fully documents the event 
before notifying BioMarin Pharmacovigilance of an SAE. BioMarin may be required to 
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report certain SAEs to regulatory authorities within 7 calendar days of being notified about 
the event; therefore, it is important that Investigators submit additional information requested 
by BioMarin as soon as it becomes available. 
Reporting of SAEs to the IRB will be done in compliance with the standard operating 
procedures and policies of the IRB and with applicable regulatory requirements. Adequate 
documentation must be obtained by BioMarin showing that the IRB was properly and 
promptly notified as required. 
10.3 
Pregnancy 
Pregnancy in a subject or partner should be reported immediately (within 24 hours) to 
BioMarin Pharmacovigilance by fax using the Pregnancy Form in the study reference 
materials. In addition, pregnancy in a subject is also reported on the End of Study CRF. 
The Investigator must make every effort to follow the subject through resolution of the 
pregnancy (delivery or termination) and to report the resolution on the Pregnancy Follow-up 
Form in the study reference materials. In the event of pregnancy in the partner of a study 
subject, the Investigator should make every reasonable attempt to obtain the woman’s 
consent for release of protected health information. 
10.4 
BioMarin Pharmacovigilance Contact Information 
Contact information for BioMarin Pharmacovigilance is as follows: 
BioMarin Pharmaceutical Inc. 
Address 
105 Digital Drive 
 
 
Novato, CA 94949 
Phone:  
(415) 506-6179 
Fax: 
 
(415) 532-3144 
E-mail: 
drugsafety@bmrn.com 
The Investigator is encouraged to discuss with the medical monitor any AEs for which the 
issue of seriousness is unclear or questioned. Contact information for the medical monitor is 
as follows: 
Name:  
, MD 
Address: 
105 Digital Drive 
 
 
Novato, CA 94949 USA 
Phone:  
 
Fax: 
 
 
E-mail: 
 
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11 
APPROPRIATENESS OF MEASUREMENTS 
11.1 
Pharmacokinetics 
The PK and safety assessments in this study are used widely and are generally recognized as 
reliable, accurate, and relevant. 
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12 
STUDY PROCEDURES 
12.1 
Prestudy 
An ICF must be signed and dated by the subject (or the subject’s legally authorized 
representative if the subject is less than 18 years of age), the PI or designee and witness 
(if required) before any study-related procedures are performed. 
12.2 
Screening Visit 
After subjects have signed an ICF, they will be screened for enrollment into the study. 
The following study activities will be performed at Screening: 
• Medical history and demographics 
• Physical examination and height 
• Vital signs 
• 12-lead ECG 
• Clinical laboratory tests (including hematology, chemistry, and urinalysis) 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• Assessment of SAEs 
• Concomitant medications 
• Diet query 
• Predose blood Phe and plasma tyrosine concentration 
For subjects who participated in PAL-002, these assessments may be the same used for the 
Final Follow-up Visit of PAL-002, if they occur within 28 days from Day 1. 
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12.3 
Treatment Period 
During the Treatment Period, additional visits may occur if deemed necessary to monitor 
AEs or blood Phe concentrations. All study activities will occur on the first day of each week 
unless otherwise noted. On days that a dose is given, assessments will be done predose unless 
otherwise specified. 
If the dose is modified by increasing dose level, additional blood Phe concentration testing 
should be done on the third day following dose adjustment. If dose is modified by increasing 
either dose frequency or dose level, additional blood Phe concentration testing should be 
done prior to each dose for the first 2 weeks following dose adjustment. 
12.3.1 Day 1 (Week 1) 
Within 28 days of completing screening assessments, the following study activities will be 
performed on Day 1: 
• Physical examination 
• Vital signs 
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• Injection-site inspection (postdose) 
• Assessment of SAEs (predose and postdose) and all AEs (postdose) 
• Concomitant medications 
• Diet query 
• Predose blood Phe and plasma tyrosine concentration 
• Serum rAvPAL-PEG antibodies 
• Administer study drug (study drug may be administered on additional days during the 
week as determined by the Investigator, in agreement with the Study Medical Officer) 
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12.3.2 Weekly Visits 
The following study activities will be performed at the weekly visits beginning with Week 2: 
• Vital signs 
• Injection-site inspection (previous and current injection site) 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• Predose blood Phe and plasm tyrosine concentration 
• Administer study drug (study drug may be administered on additional days during the 
week as determined by the Investigator, in agreement with the Study Medical Officer) 
In addition, 3 days after each administration of study drug, the subject will have a blood Phe 
measurement by fingerstick. This may be done by the subject at home. 
12.3.3 Monthly Visits (Week 4, 8, 16, etc) 
The following study activities will be performed at the monthly visits beginning with 
Week 4: 
• Vital signs 
• Clinical laboratory tests 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• Injection-site inspection (previous and current injection site) 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• Predose blood Phe and plasma tyrosine concentration 
• Serum rAvPAL-PEG antibodies 
• Administer study drug (study drug may be administered on additional days during the 
week as determined by the Investigator, in agreement with the Study Medical Officer) 
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12.3.4 Quarterly Visits (Week 12, 24, 36, etc) 
Quarterly visits consist of all monthly activities and include additional activities. 
The following study activities will be performed at the quarterly visits beginning with 
Week 12: 
• Physical examination 
• Vital signs 
• Clinical laboratory tests 
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• Injection-site inspection (previous and current injection site) 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• Predose blood Phe and plasma tyrosine concentration 
• Serum rAvPAL-PEG antibodies 
• Administer study drug (study drug may be administered on additional days during the 
week as determined by the Investigator, in agreement with the Study Medical Officer) 
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12.4 
Final Follow-up Visit (Day 113 [± 3 days]) /Early Termination Visit 
The final follow-up (F/U) Visit or Early Termination Visit (ETV) will occur 4 weeks after 
the final dose of study drug. 
Any AE that caused a subject to withdraw from the study or any clinically significant 
abnormal laboratory value or vital sign measurement identified at the ETV will be followed 
by the Investigator.  
Every reasonable effort should be made to contact any subject who is lost to follow-up. 
The following study activities will be performed at the F/U Visit or ETV: 
• Physical examination and weight 
• Vital signs 
• 12-lead ECG 
• Clinical laboratory tests 
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• Injection-site inspection (previous injection site) 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• Predose blood Phe and plasma tyrosine concentration 
• Serum rAvPAL-PEG antibodies 
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13 
DATA QUALITY ASSURANCE 
BioMarin personnel or designees will visit the study site prior to initiation of the study to 
review with the site personnel information about the IP, protocol and other regulatory 
document requirements, any applicable randomization procedures, source document 
requirements, CRFs, monitoring requirements, and procedures for reporting AEs, including 
SAEs. 
At visits during and after the study, a CRA will monitor the site for compliance with 
regulatory documentation, with a focus on accurate and complete recording of data on CRFs 
from source documents, adherence to protocol, randomization (if applicable), SAE reporting 
and drug accountability records.  
The designated clinical data management group will enter or transfer CRF data into a study 
database. 
Data quality control and analysis will be performed by BioMarin or a designee, based on a 
predefined analysis plan. 
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14 
STATISTICAL METHODS AND DETERMINATION OF SAMPLE SIZE 
14.1 
Statistical and Analytical Plans 
Because of the small sample size, no formal statistical tests will be performed. Categorical 
data will be summarized using frequency and percent, while continuous data will be 
summarized using descriptive statistics (ie, number of observations, mean, median, standard 
deviation [SD], minimum, and maximum). 
The statistical analysis plan (SAP) will provide additional details about the planned statistical 
analysis. 
14.2 
Safety Analysis 
All subjects who receive any amount of study drug will be included in the safety analyses. 
Safety will be evaluated on the incidence of AEs and clinically significant changes in vital 
signs and laboratory test results. 
The verbatim terms reported on CRFs to identify AEs will be coded using MedDRA. 
Treatment-emergent AEs will be summarized for each treatment group by system organ 
class, preferred term, relationship to study drug, and severity. Changes from baseline in vital 
signs and laboratory test results will be summarized with descriptive statistics by dose group. 
14.3 
Pharmacokinetic Analysis 
Data from all subjects who complete at least 2 weeks of the study will be included in the PK 
analysis. 
Steady-state PK of rAvPAL-PEG will be evaluated in PKU subjects after the subject has 
achieved and maintained target blood Phe concentration (below 480 μmol/L) for a minimum 
of 2 weeks and no further dose modification is planned. 
Should data become available from PAL-001 and/or PAL-002 which indicate study 
drug accumulation should also be measured, the protocol will be amended to require 
additional blood draws for PK analysis. 
14.4 
Efficacy Analysis 
Data from all subjects who receive any amount of study drug and who have any 
posttreatment efficacy data will be included in the efficacy analysis. 
Blood Phe concentration at each scheduled timepoint will be summarized using descriptive 
statistics (mean, SD, median, minimum, and maximum). Change in blood Phe concentration 
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from baseline to each scheduled timepoint and presence/absence of antibodies will also be 
summarized. 
14.5 
Determination of Sample Size 
Subjects who participated in PAL-002 may be enrolled into this study. No formal sample size 
calculation was conducted. 
14.6 
Handling of Missing Data 
All analyses will be presented based on observed data only. Missing data will not be imputed 
for analyses unless sensitivity analyses are warranted. If imputations are used, detailed 
imputation methods will be described in the SAP before locking the database. 
14.7 
Interim Analyses 
At least one interim analysis may be performed by the sponsor during the study. 
14.8 
Changes in the Conduct of the Study or Planned Analyses 
Only BioMarin may modify the protocol. Any change in study conduct considered necessary 
by the PI will be made only after consultation with BioMarin, who will then issue a formal 
protocol amendment to implement the change. The only exception is when an Investigator 
considers that a subject’s safety is compromised without immediate action. In these 
circumstances, immediate approval of the chairman of the IRB must be sought, and the 
Investigator should inform BioMarin and the full IRB within 2 working days after the 
emergency occurs. 
With the exception of minor administrative or typographical changes, the IRB must review 
and approve all protocol amendments. Protocol amendments that have an impact on subject 
risk or the study objectives, or require revision of the ICF, must receive approval from the 
IRB prior to their implementation. 
When a protocol amendment substantially alters the study design or the potential risks or 
burden to subjects, the ICF will be amended and approved by BioMarin and the IRB, and all 
active subjects must again provide informed consent. 
Note: If discrepancies exist between the text of the statistical analysis as planned in the 
protocol, and the final SAP, a protocol amendment will not be issued and the SAP will 
prevail. 
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15 
DATA MONITORING COMMITTEE (DMC) 
The DMC will act in an advisory capacity to BioMarin to monitor subject safety and the 
efficacy of rAvPAL-PEG in subjects who participate in the study. Meetings of the DMC can 
be convened at any time at the discretion of the DMC Chair or the Study Medical Officer. 
The Chair will be notified by the Study Medical Officer of all SAEs and will receive 
summaries of other safety data as available. The DMC will review the study data as soon as it 
is available during the study, on a schedule defined in the DMC Charter, and offer advice on 
whether or not to proceed, modify or terminate study enrollment on the basis of toxicity. 
Details regarding the DMC membership and safety data to be reviewed by members will be 
provided in a charter. 
The responsibilities of the DMC are to: 
• Review the study protocol, informed consent and assent documents, and plans for 
data monitoring. 
• Evaluate the progress of the trial, subjects’ risk versus benefit, and other factors that 
could affect the study outcome. 
• Consider relevant information that may have an impact on the safety of the 
participants or the ethics of the study. 
• Protect the safety of the study participants in accordance with the stopping criteria as 
defined in study protocol Section 9.1.3. 
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16 
COMPENSATION, INSURANCE, AND INDEMNITY 
There will be no charge to study subjects to be in this study. BioMarin will pay all costs of 
tests, procedures, and treatments that are part of this study. In addition, after IRB approval, 
BioMarin may reimburse the cost of travel for study-related visits. BioMarin will not pay for 
any hospitalizations, tests, or treatments for medical problems of any sort, whether or not 
related to the study subject’s disease, that are not part of this study. Costs associated with 
hospitalizations, tests, and treatments should be billed and collected in the way that such 
costs are usually billed and collected. 
The Investigator should contact BioMarin immediately upon notification that a study subject 
has been injured by the IP or by procedures performed as part of the study. Any subject who 
experiences a study-related injury should be instructed by the Investigator to seek medical 
treatment at a pre-specified medical institution if possible, or at the closest medical treatment 
facility if necessary. The subject should be given the name of a person to contact to seek 
further information about, and assistance with, treatment for study-related injuries. 
The treating physician should bill the subject’s health insurance company or other third party 
payer for the cost of this medical treatment. If the subject has followed the Investigator’s 
instructions, BioMarin will pay for reasonable and necessary medical services to treat the 
injuries caused by the IP or study procedures, if these costs are not covered by health 
insurance or another third party that usually pays these costs. In some jurisdictions, BioMarin 
is obligated by law to pay for study-related injuries without prior recourse to third party 
payer billing. If this is the case, BioMarin will comply with the law. 
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17 
CASE REPORT FORMS AND SOURCE DOCUMENTS 
Electronic case report forms will be provided for each subject. The Investigator must review 
and electronically sign the completed CRF casebook to verify its accuracy. 
CRFs must be completed using a web–based application that has been validated. Study site 
personnel will be trained on the application and will enter the clinical data from source 
documentation. Unless explicitly allowed in the CRF instructions, blank data fields are not 
acceptable. 
In the event of an entry error, or if new information becomes available, the site personnel will 
correct the value by deselecting the erroneous response and then selecting or entering the 
factual response. In compliance with 21 CFR Part 11, the system will require the site 
personnel to enter a reason for changing the value. The documented audit trail will include 
the reason for the change, the original value, the new value, the time of the correction, and 
the identity of the operator. 
BioMarin’s policy is that study data on the CRFs must be verifiable to the source data, which 
necessitates access to all original recordings, laboratory reports, and subject records. 
In addition, all source data should be attributable (signed and dated). The Investigator must 
therefore agree to allow direct access to all source data. Subjects (or their legally authorized 
representative) must also allow access to their medical records, and subjects will be informed 
of this and will confirm their agreement when giving informed consent. If an Investigator or 
institution refuses to allow access to subject records because of confidentiality, arrangements 
must be made to allow an “interview” style of data verification. 
A CRA designated by BioMarin will compare the CRFs with the original source documents 
at the study site and evaluate them for completeness and accuracy before designating them as 
“source data verified” (SDV). If an error is discovered at any time or a clarification is 
needed, the CRA, or designee, will create an electronic query on the associated field. Site 
personnel will then answer the query by either correcting the data or responding to the query. 
The CRA will then review the response and determine either to close the query or re–query 
the site if the response does not fully address the question. This process is repeated until all 
open queries have been answered and closed. 
Before a subject’s CRF casebook can be locked, all data fields must be SDV and all queries 
closed. The Investigator will then electronically sign the casebook, specifying that the 
information on the CRFs is accurate and complete. The Data Manager, or designee, will then 
set the status of the forms, visits, and the entire casebook to locked. Upon completion of the 
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clinical study report for the entire study, an electronic copy of each site’s casebooks will be 
copied to a compact disk (CD) and sent to each site for retention with other study documents. 
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18 
STUDY MONITORING AND AUDITING 
Qualified individuals designated by BioMarin will monitor all aspects of the study according 
to GCP and standard operating procedures for compliance with applicable government 
regulations. The PI agrees to allow these monitors direct access to the clinical supplies, 
dispensing, and storage areas and to the clinical files, including original medical records, of 
the study subjects, and, if requested, agrees to assist the monitors. The PI and staff are 
responsible for being present or available for consultation during routinely scheduled site 
visits conducted by BioMarin or its designees. 
Members of BioMarin’s GCP Compliance Department or designees may conduct an audit of 
a clinical site at any time during or after completion of the study. The PI will be informed if 
an audit is to take place and advised as to the scope of the audit. Representatives of the FDA 
or other Regulatory Agencies may also conduct an audit of the study. If informed of such an 
inspection, the PI should notify BioMarin immediately. The PI will ensure that the auditors 
have access to the clinical supplies, study site facilities, original source documentation, and 
all study files. 
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19 
RETENTION OF RECORDS 
The PI must retain all study records required by BioMarin and by the applicable regulations 
in a secure and safe facility. The PI must consult a BioMarin representative before disposal 
of any study records, and must notify BioMarin of any change in the location, disposition or 
custody of the study files. The PI/institution must take measures to prevent accidental or 
premature destruction of essential documents, that is, documents that individually and 
collectively permit evaluation of the conduct of a study and the quality of the data produced, 
including paper copies of study records (eg, subject charts) as well as any original source 
documents that are electronic as required by applicable regulatory requirements. 
All study records must be retained for at least 2 years after the last approval of a marketing 
application in the U.S. or an ICH region and until (1) there are no pending or contemplated 
marketing applications in the United States or an ICH region or (2) at least 2 years have 
elapsed since the formal discontinuation of clinical development of the IP. The PI/institution 
should retain subject identifiers for at least 15 years after the completion or discontinuation 
of the study. Subject files and other source data must be kept for the maximum period of time 
permitted by the hospital, institution or private practice, but not less than 15 years. These 
documents should be retained for a longer period, however, if required by the applicable 
regulatory requirements or by a BioMarin agreement. BioMarin must be notified and will 
assist with retention should the PI/institution be unable to continue maintenance of subject 
files for the full 15 years. It is the responsibility of BioMarin to inform the PI/institution as to 
when these documents no longer need to be retained. 
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20 
USE OF INFORMATION AND PUBLICATION 
BioMarin recognizes the importance of communicating medical study data and therefore 
encourages their publication in reputable scientific journals and at seminars or conferences. 
The details of the processes of producing and reviewing reports, manuscripts, and 
presentations based on the data from this study will be described in the Clinical Study 
Agreement between BioMarin and the PI. 
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21 
REFERENCES 
Armstrong, Hempel, Koling, Chan, Fisher, Meiselman, Garratty. Antibody against 
poly(ethylene glycol) adversely affects PEG-asparaginase therapy in acute lymphoblastic 
leukemia patients. Cancer 110[1], 103-111. 2007.  
Burgard, Bremer, Bührdel, Clemens, Mönch, Przyrembel, Trefz, Ullrich. Rationale for the 
German recommendations for phenylalanine level control in phenylketonuria 1997. Eur J 
Pediatr 158, 46-54. 1999.  
Butterworth. Effects of hyperammonaemia on brain function. J Inherit Metab Dis 21 Suppl 1, 
6-20. 1998.  
Chen, Scott. Current and future applications of immunological attenuation via pegylation of 
cells and tissue. BioDrugs 15[12], 833-847. 2001.  
Davis, Abuchowski, Park, Davis. Alteration of the circulating life and antigenic properties of 
bovine adenosine deaminase in mice by attachment of polyethylene glycol. Clin Exp 
Immunol 46[3], 649-652. 1981.  
Fisch. Comments on diet and compliance in phenylketonuria. Eur J Pediatr 159 Suppl 2, 
S142-S144. 2000.  
Gamez, Wang, Sarkissian, Wendt, Fitzpatrick, Lemontt, Scriver, Stevens. Structure-based 
epitope and PEGylation sites mapping of phenylalanine ammonia-lyase for enzyme 
substitution treatment of phenylketonuria. Mol Genet Metab 91[4], 325-334. 2007.  
Ganson, Kelly, Scarlett, Sundy, Hershfield. Control of hyperuricemia in subjects with 
refractory gout, and induction of antibody against poly(ethylene glycol) (PEG), in a phase I 
trial of subcutaneous PEGylated urate oxidase. Arthritis Res Ther 8[1], R12. 2006.  
Guttler, Azen, Guldberg, Romstad, Hanley, Levy, Matalon, Rouse, Trefz, de la, Koch. 
Impact of the phenylalanine hydroxylase gene on maternal phenylketonuria outcome. 
Pediatrics 112[6 Pt 2], 1530-1533. 2003.  
Harris, Chess. Effect of pegylation on pharmaceuticals. Nat Rev Drug Discov 2[3], 214-221. 
2003.  
Huttenlocher. The neuropathology of phenylketonuria: human and animal studies. Eur J 
Pediatr 159 Suppl 2, S102-S106. 2000.  
Kaufman. An evaluation of the possible neurotoxicity of metabolites of phenylalanine. J 
Pediatr 114[5], 895-900. 1989.  
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Koch, Hanley, Levy, Matalon, Matalon, Rouse, Trefz, Guttler, Azen, Platt, Waisbren, 
Widaman, Ning, Friedman, de la. The Maternal Phenylketonuria International Study: 1984-
2002. Pediatrics 112[6 Pt 2], 1523-1529. 2003.  
Lee, Lilburn, Baudin. Maternal phenylketonuria: experiences from the United Kingdom. 
Pediatrics 112[6 Pt 2], 1553-1556. 2003.  
Levy. Historical background for the maternal PKU syndrome. Pediatrics 112[6 Pt 2], 1516-
1518. 2003.  
Matalon, Surendran, Matalon, Tyring, Quast, Jinga, Ezell, Szucs. Future role of large neutral 
amino acids in transport of phenylalanine into the brain. Pediatrics 112[6 Pt 2], 1570-1574. 
2003.  
Richter, Akerblom. Antibodies against polyethylene glycol produced in animals by 
immunization with monomethoxy polyethylene glycol modified proteins. Int Arch Allergy 
Appl Immunol 70[2], 124-131. 1983.  
Richter, Akerblom. Polyethylene glycol reactive antibodies in man: titer distribution in 
allergic patients treated with monomethoxy polyethylene glycol modified allergens or 
placebo, and in healthy blood donors. Int Arch Allergy Appl Immunol 74[1], 36-39. 1984.  
Rouse, Azen. Effect of high maternal blood phenylalanine on offspring congenital anomalies 
and developmental outcome at ages 4 and 6 years: the importance of strict dietary control 
preconception and throughout pregnancy. J Pediatr 144[2], 235-239. 2004.  
Scott, Murad, Koumpouras, Talbot, Eaton. Chemical camouflage of antigenic determinants: 
stealth erythrocytes. Proc Natl Acad Sci U S A 94[14], 7566-7571. 1997.  
Scriver CR, Kaufman S. Hyperphenylalaninemia: Phenylalanine Hydroxylase Deficiency. In: 
Beaudet AL, Sly WS, Valle D, editors. Metabolic and Molecular Bases of Inherited Disease. 
New York: McGraw-Hill, 2001: 1667-709.  
Shedlovsky, McDonald, Symula, Dove. Mouse models of human phenylketonuria. Genetics 
134[4], 1205-1210. 1993.  
Walter, White, Hall, MacDonald, Rylance, Boneh, Francis, Shortland, Schmidt, Vail. How 
practical are recommendations for dietary control in phenylketonuria? Lancet 360[9326], 55-
57. 2002.  
Webster, Didier, Harris, Siegel, Stadler, Tilbury, Smith. PEGylated proteins: evaluation of 
their safety in the absence of definitive metabolism studies. Drug Metab Dispos 35[1], 9-16. 
2007.  
 
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22 
INVESTIGATOR RESPONSIBILITIES 
22.1 
Conduct of Study and Protection of Human Subjects  
In accordance with FDA Form 1572, the Investigator will ensure that: 
• He or she will conduct the study in accordance with the relevant, current protocol and 
will only make changes in a protocol after notifying the sponsor, except when 
necessary to protect the safety, rights, or welfare of subjects. 
• He or she will personally conduct or supervise the study. 
• He or she will inform any potential subjects, or any persons used as controls, that the 
drugs are being used for investigational purposes and he or she will ensure that the 
requirements relating to obtaining informed consent in 21 Part 50 and institutional 
review board (IRB) review and approval in 21 CFR Part 56 are met.  
• He or she will report to the sponsor adverse experiences that occur in the course of 
the investigation in accordance with 21 CFR 312.64. 
• He or she has read and understands the information in the Investigator’s Brochure, 
including potential risks and side effects of the drug. 
• His or her staff and all persons who assist in the conduct of the study are informed 
about their obligations in meeting the above commitments. 
• He or she will ensure that adequate and accurate records in accordance with 
21 CFR 312.62 and to make those records available for inspection in accordance with 
21 CFR 312.68. 
• He or she will ensure that the IRB complies with the requirements of 21 CFR Part 56, 
and other applicable regulations, and conducts initial and ongoing reviews and 
approvals of the study. He or she will also ensure that any change in research activity 
and all problems involving risks to human subjects or others are reported to the IRB. 
Additionally, he or she will not make any changes in the research without IRB 
approval, except where necessary to eliminate apparent immediate hazards to human 
subjects. 
• He or she agrees to comply with all other requirements regarding the obligations of 
clinical Investigators and all other pertinent requirements in 21 CFR Part 312. 
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Proprietary and Confidential 
CLINICAL STUDY PROTOCOL AMENDMENT SUMMARY 
 
Amendment: 2 
Date: October 30, 2009 
 
RATIONALE AND SUMMARY OF CHANGES 
1. The primary objective of the study has been revised for clarity; multiple doses of SC 
injections of rAvPAL-PEG will be assessed for efficacy on blood Phe levels of 
subjects with phenylketonuria (PKU).  
2. Information regarding study drug dose adjustment (ie, allowable dose increases to 
achieve target Phe concentrations [ie, 120-600 µmol/L] and dose de-escalation for 
safety [ie, Phe concentration  < 120 µmol/L]) have been revised for clarity. 
Information regarding dose decreases relative to changes to subject diet has also been 
clarified. 
3. Additional pharmacokinetic (PK) sampling has been added to allow for additional 
assessment of study drug exposure and accumulation based on PK information from 
the Phase 1 study, PAL-001 (A Phase 1, Open-Label, Dose-Escalation Study to 
Evaluate the Safety, Tolerability, and Pharmacokinetics of Single, Subcutaneous 
Doses of rAvPAL-PEG in Subjects With Phenylketonuria). 
4. The information regarding the 2 subjects who reported serious adverse events in 
Study PAL-001 (A Phase 1, Open-Label, Dose-Escalation Study to Evaluate the 
Safety, Tolerability, and Pharmacokinetics of Single, Subcutaneous Doses of 
rAvPAL-PEG in Subjects With Phenylketonuria) has been updated. In addition, 
information regarding the future risk of using other PEG-containing or PEGylated 
injectable drugs has been added. 
5. The Nonclinical Studies section has been updated to include information regarding 
chronic repeat-dose toxicity and toxicokinetic studies in monkeys and rats. 
6. The stopping criteria have been revised for clarity. 
• The criterion for toxicity has been clarified; subjects who have a drug-related 
Common Terminology Criteria for Adverse Events (CTCAE) grade  ≥ 3 event that 
is treatment emergent will stop study drug until resolution of the event. 
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• The criterion for stopping dosing within a dose level has been clarified; if 2 or 
more subjects within a dose level have a drug-related CTCAE grade  ≥ 3 event that 
is treatment emergent, further dosing within that dose level will be stopped and no 
subjects in higher dose levels will be treated until a safety assessment is 
completed. The Food and Drug Administration (FDA) will also be notified. 
7. Information regarding the management of local and systemic reactions to 
rAvPAL-PEG has been revised for clarity and to incorporate safety measures based 
on information from the Phase 1 study, PAL-001, and recommendations from an 
allergy advisory board.  
• The definition of local skin reactions (at or near the injection site) has been 
revised for further clarity.  
• Definitions of large local skin reactions that are contiguous and are not contiguous 
to the study drug injection site have been added. 
• The definition of systemic reactions has been revised to include skin 
(eg, generalized skin reaction) and non-skin symptoms; the definition has also 
been broadened for further clarity. In addition, the skin prick test for subjects with 
systemic reactions has been removed. 
• Information regarding subjects who have a systemic reaction that includes skin 
symptoms (eg, generalized skin reaction) has been revised. Subjects who have a 
generalized skin reaction will complete an Unscheduled Hypersensitivity 
Reaction Visit and will then be terminated from the study.  
8. An Unscheduled Hypersensitivity Reaction Visit has been added for subjects who 
have a systemic reaction that includes skin symptoms (eg, generalized skin reaction) 
after administration of rAvPAL-PEG based on additional safety information from the 
Phase 1 study, PAL-001, and per the recommendation of an allergy advisory board.  
• The Unscheduled Hypersensitivity Reaction Visit includes clinical laboratory 
tests (urinalysis, hematology, chemistry) and tests for C-reactive protein (CRP), 
total hemolytic complement (CH50), complements C1 and C4, sedimentation rate, 
serum tryptase level, and serum anti-rAvPAL-PEG antibodies to be performed 
within 48 hours of the reaction. A PK sample will also be obtained.  
• Subjects who have a large local skin reaction that is not contiguous to the 
injection site and subjects who have a systemic reaction that does not include skin 
symptoms (generalized skin reaction) may also have the Unscheduled 
Hypersensitivity Reaction Visit assessments performed per Investigator discretion 
and in consultation with the Sponsor’s Medical Officer.  
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• All subjects who complete an Unscheduled Hypersensitivity Reaction Visit will 
be terminated from the study and will complete the Early Termination Visit 
assessments. 
9. Information regarding treatment of subjects with local skin reactions has been revised 
to incorporate recommendations made by an allergy advisory board. 
• For subjects who have had a prior local skin reaction to rAvPAL-PEG or 
PEG-containing product, pretreatment with oral steroids has been removed 
because long-term steroid use is not indicated for the study patient population. 
The preferred antihistamine has been changed from Claritin (loratadine) to Zyrtec 
(cetirizine). 
• Information regarding treatment of subjects who have a local skin reaction has 
been added. Subjects may be treated with non-sedating oral and/or topical 
antihistamines and/or topical steroids. 
10. Safety, PK, and blood Phe concentration assessments have been added for subjects 
who have their dose of rAvPAL-PEG increased in frequency to more than 1x/week. 
Subjects who have study drug frequency increased to 2x/week or daily should 
perform the Interim Dosing Visit assessments. 
11. Dosing information has been revised to incorporate the additional dose levels in 
PAL-002. In addition, information regarding self-administration of study drug by 
subjects has been removed; study drug will be administered by the study clinic staff 
or other qualified and trained study personnel only. 
12. Information regarding missed doses has been added. Subjects who miss more than 
2 scheduled doses will need to have their dose level and dose frequency re-evaluated. 
13. Information regarding the number of enrolled subjects has been revised to incorporate 
changes to Study PAL-002. In addition, information regarding replacement of 
subjects who do not complete the study has been removed. Only subjects who 
complete Study PAL-002 are eligible for participation in this study. 
14. Information regarding assessment for immunogenicity has been clarified; the specific 
antibody assessments have been clarified per FDA request.  
15. A 3-day diet diary has been added to the weekly visits. 
16. The severity grades for adverse event (AE) reporting have been revised; CTCAE 
grades 1-5 will now be used. 
17. The study duration has been revised; subjects will complete the study after 24 months 
of treatment with study drug. 
18. The target blood Phe concentration has been revised from 480 µmol/L to 
120-600 µmol/L for consistency with Study PAL-002. 
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19. The efficacy analysis has been revised to include assessment of subjects who 
maintain a target Phe concentration. Subjects to be included in the safety analysis 
population have been revised for clarity; subjects who have postdose safety 
information will be included in the safety analysis. 
20. PK, blood Phe, and tyrosine assessments have been revised for subjects who are on a 
stable dosing regimen for at least 3 months; subjects may have these assessments 
performed less frequently (ie, at the monthly versus weekly visits). 
21. The timing of the Early Termination visit has been revised from 1 week to 4 weeks 
after the final dose of study drug to allow for an assessment that was recommended 
by an allergy advisory board prior to study termination. 
22. Collection of subject’s allergy history has been added at the Screening visit.  
23. A chest X-ray has been added to the 12-month and 24-month visits. 
24. Information regarding an Interactive Voice Response System (IVRS) has been 
removed; study drug assignment will not be conducted using an IVRS. 
25. The Medical Monitor has been changed. 
26. The Schedule of Events and the Study Procedure section (Section 12.3) have been 
updated to reflect the changes to this amendment. In addition, assessment schedules 
have been added for subjects who increase their dose frequency to 2x/week and daily 
(Interim Dosing Visit). 
27. Administrative revisions have been made to improve clarity and consistency. 
 
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PROTOCOL AMENDMENT TEXT REVISIONS 
The following table summarizes the revisions made to the protocol and relates the changes to the appropriate rationale. Text that has been 
added or inserted is indicated by underlined font, and deleted text is indicated by strikethrough font. 
Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
Section 2/Synopsis 
(Objectives) 
The primary objective of the study is: 
• 
To evaluate the effect of long-term administration of multiple doses of SC 
injections of rAvPAL-PEG on blood Phe concentrations in subjects with PKU. 
The secondary objectives of the study are: 
• 
To evaluate the immune response to long-term administration of SC injections of 
rAvPAL-PEG in subjects with PKU who participated in Study PAL 002. 
 
1, 13, 27 
Section 2/Synopsis 
(Study Design and Plan) 
This is a long-term extension of a Phase 2, open-label, dose-finding study (Study 
PAL-002) in approximately 35-50 35 subjects with PKU. The doses are planned to be in 
the same range as those tested in PAL-002 (0.001 through 1.0 mg/kg per injection), 
provided no dose-limiting toxicity was observed in PAL-002. 
Only subjects who completed participation in PAL-002 will be enrolled into this study. 
Diet will not be altered during the course of this study, except as necessary for safety as 
determined by blood Phe concentrations. If a subject’s blood Phe concentration is 
 < 120 µmol/L, the subject’s diet may be adjusted to increase the amount of dietary Phe 
intake to maintain target blood Phe concentrations of 120-600 µmol/L. Changes to diet 
will be made per the discretion of the Investigator in consultation with the Sponsor’s 
Medical Officer. 
 
2, 13, 18, 27 
Section 2/Synopsis 
(Study Design and Plan) 
At least one interim analysis may be performed by the sponsor during the study. In 
addition to the Sponsor, aA Data Monitoring Committee (DMC) will monitor the study 
safety of subjects in the study. The DMC is an independent committee that will act in an 
advisory capacity to the Sponsor. 
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to 
 
11, 17, 18, 27 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
take rAvPAL-PEG. PAL-002 subjects’ participants’ rAvPAL-PEG dosing will continue 
in PAL-003 without interruption of weekly dosing. In PAL-003, each subject’s dose will 
be adjusted as needed to attain or maintain blood Phe concentrations of below 
120-600480 µmol/L. Subjects will continue to receive injections in the clinic, 
administered by clinic staff but may later be allowed to self administer doses of study 
drug at home. Whether a subject may be allowed to self administer study drug dDoses 
will be evaluated on an individual basis. 
The dose may be modified at any time for safety.  
Evaluations, observations, and procedures will be conducted at selected time points as 
shown in Table 2.1.1, Schedule of Events. After the subject’s blood Phe concentration 
has been controlled to within a target range (below 120-600480 µmol/L), the subject may 
be asked to have additional blood draws for PK and blood Phe concentration analyses as 
needed but not to exceed 3x/week (fingerstick tests may be performed more frequently). 
A subject will continue in PAL-003 until one of the following occurs: 
1. The subject withdraws consent and discontinues from the study. 
2. The subject is discontinued from the study at the discretion of the Investigator. 
3. The drug becomes commercially available following the appropriate marketing 
approval. The subject has completed the study through the Month 24 visit. 
4. The study is terminated. 
Section 2/Synopsis 
(Study Design and Plan) 
Dose Modifications: 
After any modifications (increases or decreases) to dose level or frequency, subjects 
should remain in the clinic for observation for at least 2 hours following the injection of 
study drug. The Investigator should remain at the site to assess the subject for safety. 
Dose Adjustment Increase Methodology: 
 
2, 11, 27 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
Each subject’s dose may be modified based on the decision of the Investigator, in 
agreement with the Study Medical Officer. Decisions regarding dose increases will 
depend on available blood Phe and drug concentrations.  
Blood Phe levels will be measured 3 days after each dose increase (fingerstick is 
acceptable); more frequent or daily blood Phe measurements may be performed. Subjects 
must have blood Phe concentration tested 3 days after a dose adjustment. There must be a 
minimum of 2 weeks after each dose adjustment before any additional dose adjustments 
may be made, so that blood Phe concentrations can be assessed. 
Depending upon the response to rAvPAL-PEG in PAL-002, an individual subject’s dose 
may be adjusted beginning on Day 1 of PAL-003 as follows. 
• 
The dose may be increased by increments of no more than 10-fold higher than 
the subject’s current dose. 
• 
When adjusting increasing the dose, a dose may be used that is between the dose 
cohort levels (0.001, 0.003, 0.01, 0.03, 0.06, 0.1, 0.3, 0.6, and 1.0 mg/kg) that 
were defined in the previous study (PAL-002). 
• 
The dose may be adjusted by increasing the frequency up to daily ofnumber of 
injections per week, up to one dose per day, for a maximum total weekly dose 
per week of not to exceed 2.0 mg/kg, including subjects who receive more than 
1 dose/week. Subjects who have increased their dose frequency will have 
additional assessments performed (Interim Dosing Visit). 
• 
When a dose is adjustedincreased (either by increasingchanging the dose level or 
by increasingchanging the frequency of dosing), the subject must remain in the 
clinic for a minimum of 2 hours following the first modified dose administration, 
and an Investigator will remain on site during this time. 
• 
Only 1 dose adjustment is allowed every 2 weeks. 
• 
Blood Phe levels will be measured 3 days after each dose increase (fingerstick is 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
acceptable); more frequent or daily blood Phe measurements may be performed. 
• 
The dose may be decreased as appropriate to achieve or maintain a favorable 
blood Phe concentration for safety. 
Dose Decrease Methodology 
A subject’s diet should be assessed prior to any dose decreases. Changes to diet should 
only be made if blood Phe concentrations are  < 120 µmol/L. If a subject’s blood Phe 
level is  < 120 µmol/L, the subject’s dietary Phe intake should be increased to achieve a 
stable blood Phe concentration of 120-600 µmol/L. If the subject’s blood Phe level is 
 < 120 µmol/L despite a high Phe diet, the rAvPAL-PEG dose will then be decreased. 
The subject will be asked about any changes to diet prior to any dose adjustments, and 
any changes to diet should be made per the discretion of the Investigator in consultation 
with the Sponsor’s Medical Officer. 
All dose decreases must be agreed to by both the Investigator and the Sponsor’s Medical 
Officer. Decisions regarding dose decreases will depend on available information 
regarding a subject’s blood Phe ( > 30% change from baseline) and drug concentrations, 
as well as toxicity (any hypersensitivity reaction). Dose decreases may occur for safety 
(ie, blood Phe concentration  < 120 µmol/L) or other toxicity that may be improved with a 
lower, more frequent dose. 
A dose should first be reduced by dose level (1.0, 0.6, 0.3, 0.1, 0.06, 0.03, 0.01, 0.003, 
0.001 mg/kg). It is also permitted to decrease dose in between these specified dose levels. 
If further dosing adjustments are required to attain the target Phe concentration, dosing 
frequency may be reduced.  
Section 2/Synopsis 
(Study Design and Plan) 
Stopping Criteria: 
If an individual subject exhibits drug related toxicity of a treatment-emergent CTCAE 
grade 3 or greater, that subject will have dosing halted until the toxicity resolves. 
 
6 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
The subject’s data will be evaluated by the Principal Investigator (PI) and the Study 
Medical Officer, and a decision will then be made whether to discontinue the subject 
from the study, restart dosing at the same dose level, or restart dosing at a lower dose 
level. 
In addition, if 2 or more subjects at a dose level exhibit drug related toxicity of a 
treatment-emergent CTCAE grade 3 or greater, further dosing of subjects at that dose 
level will be halted and no subjects will be treated at a any higher dose levels will be 
halted until a safety assessment is completed. In addition, the Food and Drug 
Administration (FDA) will be notified of this occurrence. 
Section 2/Synopsis 
(Number of Planned 
Subjects) 
35-5035 subjects. 
 
13, 27 
Section 2/Synopsis 
(Diagnosis and All 
Criteria for Inclusion and 
Exclusion) 
Numbering has been added to all of the criteria. 
 
27 
Section 2/Synopsis 
(Diagnosis and All 
Criteria for Inclusion and 
Exclusion) 
Individuals who meet any of the following exclusion criteria will not be eligible to 
participate in the study: 
3. 
Use or planned use of any injectable drugs containing PEG (other than 
rAvPAL-PEG), including Depo-Provera,within 6 months prior to Screening and 
during study participation. 
8. 
Known hypersensitivity to rAvPAL-PEG or its excipients, including 
hypersensitivity reactions that necessitated early termination from PAL 001 or 
PAL-002. 
 
27 
Section 2/Synopsis 
rAvPAL-PEG doses will be administered SC and the favorable dose (the dosage that 
provides control of blood Phe concentrations within the target range of 120-600 µmol/L 
 
18, 27 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
(Investigational Product, 
Dose, Route and 
Regimen) 
for a minimum of 2 weeks) will be determined for each subject by adjusting the dose 
level, dose frequency, or both, as agreed by the PI and the Study Medical Officer, based 
upon the subject’s response to doses. 
Section 2/Synopsis 
(Duration of Treatment) 
3. 
The drug becomes commercially available following the appropriate marketing 
approval. The subject has completed the study through the Month 24 visit. 
 
17 
Section 2/Synopsis 
(Criteria for Evaluation) 
Immunogenicity: 
The presence of antibodies will be assessed. 
 
27 
Section 2/Synopsis 
(Safety Analysis) 
All subjects who receive any amount of study drug in this study and have postdose safety 
information will be included in the safety analyses. 
 
19 
Section 2/Synopsis 
(Efficacy Analysis) 
Blood Phe concentration at each scheduled time point will be summarized using 
descriptive statistics (mean, standard deviation, median, minimum, and maximum). 
Change in blood Phe concentration from baseline to each scheduled time point and 
presence/absence of antibodies will also be summarized. In addition, the proportion of 
subjects who have maintained target Phe concentrations of 120-600 µmol/L will be 
summarized by each scheduled time point. 
 
19 
Section 2/Synopsis 
(Pharmacokinetic 
Analysis) 
Steady-state PK (predose samples) of rAvPAL-PEG will be evaluated in PKU subjects 
after the subject has achieved and maintained target blood Phe concentration (below 
120-600480 μmol/L) for a minimum of 2 weeks (to allow assessment of blood Phe 
concentrations) and no further dose modification is planned. Once this target has been 
achieved, PK samples will be collected predose on the same day each week for 
3 consecutive weeks. Should data become available from PAL-002 that indicate study 
drug accumulation should also be measured, additional blood draws may be added for PK 
analysis as needed but not to exceed 3x/week. 
 
3, 18 
Section 2.1/Schedule of 
Events (Table 2.1: 
The Schedule of Events has been revised to reflect changes to the study 
procedures. The Final F/U and Early Termination visits have been separated, and 
 
8, 10, 15, 20, 
21, 22, 23, 26 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
Schedule of Events) 
an Unscheduled Hypersensitivity Reaction Visit has also been added. 
Tables 2.1.2 (Interim Dosing Visit Schedule, Subjects Whose Dose Is Increased to 
2x/Week) and 2.1.3 (Interim Dosing Visit Schedule, Subjects Whose Dose Is 
Increased to Daily) have been added. 
Section 4/List of 
Abbreviations and 
Definition of Terms 
CBC complete blood count 
CH50 total hemolytic complement 
Cmax 
maximum plasma concentration 
CRP 
C-reactive protein  
CTCAE 
Common Terminoallogy Criteria for Adverse Events 
Ctrough predose concentration of rAvPAL PEG 
 DCF Data Clarification Form 
IND 
Investigational New Drug 
IVRS interactive voice response system 
IgE 
immunoglobulin E 
NOAEL 
no observable adverse effect level 
rAvPAL-PEG rAv phenylalanine ammonia lyase-PEG 
 
27 
Section 6/Investigators 
The study will be administered by and monitored by employees or representatives 
 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
and Study Administrative 
Structure 
of BioMarin. Clinical Research Associates (CRAs) or trained designees will 
monitor each site on a periodic basis and perform verification of source 
documentation for each subject as well as other required review processes. 
BioMarin’s Regulatory Affairs Department (or designee) will be responsible for 
the timely reporting of serious adverse events (SAEs) to appropriate regulatory 
authorities as required. Some study assessments, including administration of study 
drug, may be performed at the subject’s home. All assessments performed for this 
study will be administered by clinic staff or other qualified and trained study 
personnel. 
Section 7.1/Nonclinical 
Studies 
Weekly subcutaneous (SC) administration of 80 mg/kg of rAvPAL-PEG 
(approximately 4 IU/mouse) for greater than 2 to 3 months lowered and stabilized 
plasma blood Phe concentration from approximately 2000 µM to less than 
200 µM.  
The safety of rAvPAL-PEG was evaluated in safety pharmacology studies 
(respiratory, central nervous system [CNS] and cardiovascular [CV]) and toxicity 
with toxicokinetic studies (single and 28-day repeated dose) in rats and 
cynomolgus monkeys. Overall, in the nonclinical in all toxicity studies, no 
immune related toxicities anaphylactoid-like reactions or injection-site reactions 
were noted were seen either systemically or at the injection site. No specific 
polyethylene glycol (PEG)-related histological findings were observed during the 
28-day repeated dose studies. 
The main finding in the 28-day study was the possible drug-related observation of 
minimal to slight degeneration of blood vessels of predominantly medium-sized 
 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
muscular arteries with a non-dose-dependent involvement of different organs 
observed in 1 male in the 0.1 mg/kg and 1 male and 1 female in the 1.0 mg/kg 
rAvPAL-PEG dose groups. No degeneration of the arteries was observed in either 
the control or animals administered 0 and 0.01 mg/kg rAvPAL-PEG. 
Section 7.1/Nonclinical 
Studies 
Chronic repeat-dose toxicity and toxicokinetic studies were conducted in the rat 
(17/26 weeks) and monkey (39 weeks). In the 26-week study of rats, weight loss 
was observed in the rats given 25 mg/kg/dose of rAvPAL-PEG, SC; 
corresponding decreased food consumption was observed in the males. The main 
histological finding was focal-to-multifocal areas of vacuolar degeneration of 
renal tubule cells in the kidney of 3 males given 25 mg/kg and 3 females given 
 ≥ 8 mg/kg rAvPAL-PEG. This renal tubule finding persisted in the kidney of both 
sexes given  ≥ 8 mg/kg/dose at the end of the 12-week recovery phase without 
evidence of reversibility. Increased vacuolation was observed in histiocytic cells 
of the liver, spleen, mesenteric lymph node, mandibular lymph node, and adrenal 
cortex of males given 25 mg/kg/dose and females given  ≥ 8 mg/kg/dose; 
vacuolation of histiocytic cells in the testes were also observed in males given 
25 mg/kg/dose. Both renal tubule vacuolation and histiocytic cell vacuoles have 
been associated with PEG-related catabolism and administration of other 
PEGylated proteins. 
In the 39-week, chronic repeat-dose toxicity and toxicokinetic study in monkeys, 
dose levels of 7.0 and 5.0 mg/kg/dose rAvPAL-PEG were not tolerated in female 
monkeys and resulted in body weight loss, decreased food consumption, and 
 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
hypoactivity. The only adverse microscopic finding was arterial inflammation of 
small and mid-sized arteries in multiple organs and/or tissues in most animals that 
were given  ≥ 3 mg/kg/dose rAvPAL-PEG SC twice weekly at the end of the 
dosing phase. The inter-individual organ involvement was highly variable; some 
animals had findings in one organ and others had multiple organs with arterial 
inflammation. Additionally, not all arteries had signs of inflammation and arterial 
inflammation was resolved by the end of the 13-week recovery period. A full 
analysis of these findings including the involvement of the anti-drug antibodies, 
antibody isotypes, PEG distribution, and rAvPAL-PEG is ongoing. The no 
observable adverse effect level (NOAEL) for the 17-week and 39-week studies, in 
rat and monkey, respectively, is 1 mg/kg/dose.  The NOAEL from these studies 
represents greater than a 100-fold safety factor over the starting dose in PAL-002. 
Section 7.2/Previous 
Clinical Studies 
This study is an extension of the second human clinical study with rAvPAL-PEG 
(Study PAL-002). Study PAL-001, the first-in-human clinical study of 
rAvPAL-PEG, was designed as a Phase 1, open-label, single-dose, 
dose-escalation study in approximately 3525 subjects, 16 to 50 years old, with 
PKU. The doses for this study are based on data from nonclinical studies and 
PAL-001 and are planned to be in the same range as those tested in PAL-001 and 
PAL 002 (0.001 through 1.0 mg/kg per injection (not to exceed 2.0 mg/kg/week), 
provided no dose-limiting toxicity was observed in those studies Study PAL-002. 
 
27 
Section 7.4/Summary of 
Overall Risks and Benefits 
It is not expected that data from PAL 001 and PAL-002 will change the 
assumption that rAvPAL-PEG has a toxicity profile similar to other recombinant 
 
4, 27 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
PEGylated non-human enzymes currently in use.  
Section 7.4.1/Toxicity 
Due to Exposure to PEG 
No indication of PEG-related toxicity at the ultrastructural level was observed in 
monkeys given a single dose of up to 60 mg/kg of SC rAvPAL-PEG SC. 
 
27 
Section 7.4.2/Toxicity 
Due to an Immunologic 
Reaction 
This section has been reorganized to include updated safety information from 
Study PAL-001. Presentation of information in this section, including section 
numbers, has also been revised. 
 
27 
Section 7.4.2/Toxicity 
Due to an Immunologic 
Reaction 
The active drug substance in rAvPAL-PEG is a bacterial protein, and as such, it is 
expected that it may elicit immune recognition and responses. In animal models, 
the immune response against the foreign protein PAL in rAvPAL PEG has been 
mitigated by PEGylation. Epitopes that play a role in the immune response may 
be rendered inaccessible by PEG (Gamez, 2007, Mol.Genet.Metab). 
Administration of rAvPAL-PEG may lead to anti-PEG antibody formation, and 
the duration of this possible effect is not known. This may limit a subject’s future 
ability to be treated with other PEG-containing (eg, Depo-Provera) or PEGylated 
(eg, PEG-interferon) injectable drugs. It is therefore recommended that any 
PEG-containing injectable drug administered to subjects after completion of this 
study be done under medical observation. 
 
4, 27 
Section 7.4.2.1/ 
Reactions with 
Depo ProveraSystemic 
Skin Reactions 
Two subjects enrolled in PAL 001 who had received one dose of rAvPAL PEG 
experienced hypersensitivity reactions to intramuscular (IM) Depo Provera, 
a contraceptive containing PEG 3350. Both subjects had previously received 
multiple IM Depo Provera injections without complications. 
The first subject, a 
year old 
, developed bruising at the injection site on 
Day 1 that resolved on Day 15. 
 developed hives and mild respiratory 
 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
difficulty 10 minutes after receiving IM Depo-Provera given 40 days after 
 
rAvPAL PEG injection. 
 was treated in the emergency room with 
, 
, 
d, and 
; and oral 
 and 
. The events 
resolved the same day, and the subject had no further complications. The subject 
had no prior history of any reactions to Depo Provera. Subsequently, while under 
the care of an allergist/immunologist, the subject had a mild reaction to a 
concentrated intradermal (1:10) exposure of Depo Provera. 
 was later given a 
full dose of IM Depo Provera without problems. 
The second subject, an 
 year old 
, had a slightly raised, erythematic rash 
below the site of rAvPAL PEG injection on Day 11 that resolved without 
treatment on Day 15. 
 developed generalized hives on 
 arms and legs and 
mild difficulty breathing 20 minutes after receiving IM Depo Provera (and 
 
third dose of Gardasil) given 15 days after 
 rAvPAL PEG injection. 
 
symptoms subsided after 
 received oral 
 given by 
 mother. 
 did 
not visit the emergency room. The subject had no prior history of any reactions to 
Depo Provera or Gardasil (Gardasil dose not contain PEG). 
 was subsequently 
seen by an allergist/immunologist, and the results are pending.
Because Depo Provera contains PEG 3350 as an excipient, it is possible that the 
administration of rAvPAL PEG caused anti PEG antibody formation that led to a 
cross reaction with Depo Provera in these subjects. Therefore, it is possible that 
prior exposure to rAvPAL PEG might sensitize subjects to other PEG containing 
injectable drugs. Alternatively, the presence of Depo Provera could have led to 
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antibody formation and cross-reaction with rAvPAL-PEG, leading to rAvPAL-
PEG injection site reactions. Since it is currently unknown whether Depo Provera 
has a sensitizing effect to PEG and the exact basis for these reported events is not 
known, the use of PEG containing injectable drugs prior to and during the study is 
prohibited as a precautionary measure (refer to the addendum and Sections 9.3.2 
and 9.4.8). 
Two subjects who were enrolled in Study PAL-001 and received the 
protocol-defined single dose of rAvPAL-PEG reported systemic skin reactions 
(generalized skin rash) that were attributed to treatment with study drug. One 
subject received a single dose of 0.001 mg/kg rAvPAL-PEG, and the other subject 
received a single dose of 0.01 mg/kg rAvPAL-PEG. Both of these events were 
reported as serious and followed administration of Depo-Provera injections 
(medroxyprogesterone injection), an injectable contraception. These allergic 
reactions are thought to be related to the PEG molecules that are found in both the 
study drug, rAvPAL-PEG, and Depo-Provera. These reactions are not likely to be 
experienced concurrent with other birth control medications. 
The 2 subjects were administered study drug during PAL-001 and then 
experienced an allergic reaction following an injection of Depo-Provera. The 
symptoms of the reactions were hives on the arms and legs and difficulty 
breathing. The symptoms for both subjects resolved within 1 day following 
treatment with medication, including the 
 
. Both subjects were examined by an allergy specialist after 
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they completed participation in PAL-001. A skin prick test with Depo-Provera 
was administered as part of this examination. One subject had a mild allergic 
reaction to the test; however, no further reactions or complications were reported 
following subsequent administration of a full dose of Depo-Provera. The subject 
continues to receive regular doses (every 3 months) of Depo-Provera, and no 
further reactions have been reported to date (15OCT2009). The second subject 
also had a positive reaction to Depo-Provera following administration of the skin 
prick test. When a subsequent full dose of Depo-Provera was administered, 
 
developed hives, itching, and chills. The subject’s symptoms resolved within 
1 day of taking medication prescribed by an allergist. 
The active drug substance in rAvPAL-PEG is a bacterial protein that may elicit 
immune responses, such as urticaria, bronchospasm, itching, anaphylaxis, and 
others. It is possible that the physio-chemical properties of rAvPAL-PEG may 
induce immunologic sensitization to the protein rAvPAL and to PEG. Although 
results from nonclincal studies of rAvPAL-PEG conducted in rats and 
cynomolgus monkeys did not indicate signs of immune-mediated toxicities, it is 
possible that the physio-chemical properties of rAvPAL-PEG may induce 
immunologic sensitization to the protein rAvPAL and to PEG in humans. Since iIt 
is currently unknown whether administration of PEG-containing drugs, such as 
Depo-Provera, has a sensitizing effect to PEG in rAvPAL-PEG when 
administered in humans. Because and the exact basis for these reported events and 
their duration is not known, the use of PEG-containing injectable drugs prior to, 
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and during, and after this study is prohibited as a precautionary measure (refer to 
Sections 9.3.2 and 9.4.8.). 
Section 7.4.2.2/ 
Management of Allergic 
Reactions 
Information regarding the management of local skin, large local skin, and 
systemic reactions is provided in Section 9.1.1. Detailed instructions for the 
management of allergic reactions are provided in the Study Reference Manual. 
 
27 
Section 7.4.3/Effects of 
Low Blood Phe 
If a subject’s blood Phe concentration is too low, the subject’s diet, current dose 
of study drug, or both may be adjusted. 
 
1, 27 
Section 8/Study 
Objectives 
• 
To evaluate the effect of long-term administration of multiple doses of SC 
injections of rAvPAL-PEG on blood Phe concentrations in subjects with 
PKU. 
The secondary objectives of the study are: 
• 
To evaluate the immune response to long-term administration of SC 
injections of rAvPAL-PEG in subjects with PKU who participated in 
Study PAL 002. 
 
1, 13, 27 
Section 9.1/Overall Study 
Design and Plan 
This is a long-term extension of a Phase 2, open-label, dose-finding study 
(PAL-002) in approximately35-50 35 subjects with PKU. The doses are planned 
to be in the same range as those tested in PAL-002 (0.001 through 1.0 mg/kg per 
injection), provided no dose-limiting toxicity was observed in PAL-002. 
Only subjects who completed participation in PAL-002 will be enrolled into this 
study. Diet will not be altered during the course of this study, except as necessary 
for safety as determined by blood Phe concentrations. If a subject’s blood Phe 
 
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concentration is  < 120 µmol/L, the subject’s diet may be adjusted to increase the 
amount of dietary Phe intake to maintain target blood Phe concentrations of 
120-600 µmol/L. Changes to diet will be made per the discretion of the Investigator 
in consultation with the Sponsor’s Medical Officer. For information regarding 
changes to diet for safety and decreases in dose, refer to Section 9.1.2.2. 
Section 9.1/Overall Study 
Design and Plan 
At least one interim analysis may be performed by the sponsor during the study. 
In addition to the Sponsor, aA Data Monitoring Committee (DMC) will monitor 
the study safety of subjects in the study. The DMC is an independent committee 
that will act in an advisory capacity to the Sponsor. 
PAL-003 is designed to evaluate long-term treatment of subjects who are 
continuing to take rAvPAL-PEG. PAL-002 subjects’ participants’ rAvPAL-PEG 
dosing will continue in PAL-003 without interruption of weekly dosing. In PAL-
003, each subject’s dose will be adjusted as needed to attain or maintain blood 
Phe concentrations below of 120-600480 µmol/L based upon recommendations 
by the German Working Group for Metabolic Diseases (Burgard, 1999, Eur J 
Pediatr). Subjects will continue to receive injections in the clinic, administered by 
clinic staff., but may later be allowed to self administer doses of study drug at 
home. Whether a subject may be allowed to self administer study drug dDoses 
will be evaluated on an individual basis. All of the following criteria must be met 
before a subject may self administer doses of the study drug:
The subject is willing and able to administer the study drug as directed. 
 
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The sponsor agrees that self-administration is appropriate. 
The subject has achieved a favorable dose (ie, the dosage that provides control of 
blood Phe concentrations within the target range for a minimum of 2 weeks). 
The dose may be modified at any time for safety.
Evaluations, observations, and procedures will be conducted at selected time 
points as shown in Table 2.1.1, Schedule of Events. After the subject’s blood Phe 
concentration has been controlled to within a target range (below 
120-600480 µmol/L), the subject may be asked to have additional blood draws for 
PK and blood Phe concentration analyses as needed but not to exceed 3x/week 
(fingerstick tests may be performed more frequently). 
A subject will continue in PAL-003 until one of the following occurs: 
1. The subject withdraws consent and discontinues from the study. 
2. The subject is discontinued from the study at the discretion of the Investigator. 
3. The drug becomes commercially available following the appropriate marketing 
approval. The subject has completed the study through the Month 24 visit. 
4. The study is terminated. 
Section 9.1.1/ 
Management of Local 
and Systemic Reactions 
to rAvPAL-PEG 
Presentation of information in this section, including section numbers, has been 
revised. 
 
27 
Section 
9.1.1.1  
Subjects Who Have Had Experienced Previous Hypersensitivity  
 
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9.1.1/Management of 
Local and Systemic 
Reactions to 
rAvPAL-PEG 
 
 
Reactions to rAvPAL-PEG or a PEG-Containing Product 
Subjects who had a previous systemic reaction to rAvPAL-PEG or a 
PEG-containing product that warranted early termination from PAL 001 or 
PAL-002 are excluded from participation in this study. Subjects who experienced 
a generalized skin rash are included in this category. Subjects who have had a 
previous local skin reaction to rAvPAL-PEG in PAL-002 are eligible to 
participate in this study. However, sSubjects may develop such systemic, large 
local skin, or local skin reactions after enrollment in PAL-003. Management of 
such reactions described below. Refer to Figure 9 1.1.2.2.1  for a flowchart for 
managing these subjects. Refer to Section 9.1.1.2 for definitions of local skin, 
large local skin, and systemic skin reactions. For management of hypersensitivity 
reactions that occur during this study, refer to Section 9.1.1.3 and 
Figure 9.1.1.3.1. 
9.1.1.2  
Definition of Hypersensitivity Reactions to rAvPAL-PEG   
 
 
Administered Subcutaneously 
During Study PAL-003, subjects may experience hypersensitivity reactions to 
rAvPAL-PEG. The hypersensitivity reactions are defined as follows: 
Local skin reaction: 
• Skin signs or symptoms in 1 affected primary location, 1 affected location 
ie, hives, wheals, or swelling or an area of erythema, or redness, 
induration, pain, or itching at or near the site of injection. 
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9.1.1.3.1/Local Skin 
Reactions 
After enrollment in PAL 003, sSubjects who have had a local skin reaction (refer 
to Section 9.1.1.2 for definition) after administration ofto rAvPAL-PEG in 
PAL-001, PAL-002, or this study or a PEG containing product willmay be 
premedicated orally with acetaminophen and antihistamines and/or oral steroids, 
1 hour prior to study drug dosing. Recommended premedications are 
acetaminophen and antihistamine (Claritin Zyrtec [cetirizine] is preferred). 
The dosage will be standard (eg, 1000 mg acetaminophen and 10 mg Claritin 
Zyrtec or 25 to 50 mg Benadryl [diphenahydramine]; an example for steroids 
would be 70 mg oral prednisone). Because Benadryl can cause drowsiness, it may 
be administered only if the subject is accompanied by a designated driver.  
Symptoms of local reactions may be treated with local application of ice and 
non-sedating oral and/or topical antihistamines and/or topical steroids (refer to 
Section 7.4.2.2). 
If the local skin reaction worsens with a repeat injection (as determined by the 
Investigator in consultation with the Study Medical Officer) even with 
premedication prior to study drug dosing, the subject must be withdrawn from the 
study and complete an Early Termination Visit. 
9.1.1.3.2 
Large Local Skin Reactions 
If a subject has a local skin reaction, a digital photograph of the reaction should be 
 
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taken if possible. Large local skin reactions (refer to Section 9.1.1.2 for a 
definition) may or may not be contiguous to the rAvPAL-PEG injection site. 
The location of the large local skin reaction relative to the rAvPAL-PEG injection 
site will determine if a subject may remain in the study and continue to be 
administered rAvPAL-PEG. An example of a large local reaction that is not 
contiguous to the injection site is if an injection took place in the right upper arm 
and there are lesions beyond the elbow joint in the right forearm or lesions beyond 
the shoulder joint on the right trunk. 
Subjects who have large local skin reactions that are contiguous to the injection 
site may remain in the study. Subjects who have large local skin reactions that are 
not contiguous to the injection site may have additional assessments performed 
(Unscheduled Hypersensitivity Reaction Visit) per Investigator discretion and 
must then be terminated from the study. A decision to terminate a subject from 
the study must be agreed to by both the Investigator and the Sponsor’s Medical 
Officer. 
9.1.1.3.2.1 
Large Local Skin Reactions Contiguous to Injection Site 
Subjects who develop a large local skin reaction contiguous to the injection site 
after administration of rAvPAL-PEG or to rAvPAL-PEG or a PEG-containing 
product may remain in the study. Large local skin reactions that are contiguous to 
the injection site should be managed as local skin reactions (refer to 
Section 9.1.1.3.1). For the remainder of the study, subjects must be premedicated 
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orally with acetaminophen and antihistamines 1 hour prior to study drug dosing. 
Recommended premedications are acetaminophen and antihistamine (Zyrtec 
[cetirizine] is preferred). The dosage will be standard (eg, 1000 mg 
acetaminophen and 10 mg Zyrtec or 25 to 50 mg Benadryl [diphenahydramine]). 
Because Benadryl can cause drowsiness, it may be administered only if the 
subject is accompanied by a designated driver.  
Symptoms of large local skin reactions may be treated with local application of 
ice and topical, oral, or IV antihistamines and/or steroids as needed (refer to 
Section 7.4.2.2).  
9.1.1.3.2.2 
Large Local Skin Reactions Not Contiguous to Injection Site 
Large local skin reactions that are not contiguous to the injection site may be 
associated with a low risk of systemic symptoms or anaphylaxis upon re-exposure 
to rAvPAL-PEG and, therefore, will be managed as a systemic reaction. Subjects 
who develop large local skin reactions that are not contiguous to the injection site 
after administration of rAvPAL-PEG or to rAvPAL-PEG or a PEG-containing 
product may not continue to participate in the study. Subjects may have additional 
assessments performed (ie, Unscheduled Hypersensitivity Skin Reaction Visit) 
immediately after the reaction (within 48 hours): serum anti-rAvPAL-PEG 
antibodies (anti-PAL immunoglobulin G [IgG], anti-PAL immunoglobulin M 
[IgM], anti-PEG IgG, anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibody, 
and anti-rAvPAL-PEG immunoglobulin E [IgE]); serum tryptase level; 
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sedimentation rate; C-reactive protein (CRP), total hemolytic complement 
(CH50), and complements C1 and C4; and clinical laboratory tests (urinalysis, 
chemistry, hematology). Subjects will then be terminated from the study and 
should be scheduled to complete the Early Termination Visit (refer to 
Section 12.4). 
Symptoms of large local skin reactions may be treated with local application of 
ice and topical, oral, or IV antihistamines and/or steroids as needed (refer to 
Section 7.4.2.2).  
Section 9.1.1.3.3/ 
Systemic Reactions 
After enrollment in PAL 003, subjects who have a systemic reaction that includes 
noncutaneous systemic symptoms, such as respiratory problems, hypotension, or 
angioedema, to rAvPAL PEG or a PEG containing product will be evaluated with 
a skin prick test. If the test is positive, the subject will be excluded from the study. 
Subjects with prior systemic reactions that included only skin manifestations to 
rAvPAL PEG or a PEG containing product after PAL 003 enrollment will be 
premedicated with acetaminophen and antihistamines and/or oral steroids (one 
hour prior to study drug dosing) and will continue to receive rAvPAL PEG. 
Reactions to skin prick testing or rAvPAL PEG administered SC are defined as 
follows: 
Local reaction: 1 affected location, ie, hives, wheals, or swelling or an area of 
erythema or redness at or near the site of injection. 
 
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Systemic reaction: more than 1 affected location, ie, cutaneous reaction in more 
than 1 area, and/or any other generalized symptoms, such as hypotension, 
angioedema or anaphylaxis or the involvement of other organ systems (eg, 
respiratory, cardiovascular, gastrointestinal). 
Subjects who experience a systemic reaction (refer to Section 9.1.1.2 for a 
definition) after administration of rAvPAL-PEG will be terminated from the 
study. Subjects who experience generalized skin symptoms are included in this 
category. Immediately after the systemic reaction (within 48 hours), subjects with 
generalized skin symptoms must have additional assessments performed for 
safety (ie, Unscheduled Hypersensitivity Skin Reaction Visit): serum 
anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibody, and anti-rAvPAL-PEG 
IgE); serum tryptase level (optional; it is recommended that this sample be drawn 
immediately after reaction); sedimentation rate; CRP, CH50, C1, and C4; and 
clinical laboratory tests (urinalysis, chemistry, hematology; refer to 
Figure 9.1.1.3.1). Subjects who have a systemic reaction without generalized skin 
symptoms may have these assessments performed per Investigator discretion. 
Subjects will then be terminated from the study and should be scheduled to 
complete the Early Termination Visit (refer to Section 12.4). 
Section 9.1.2/Dose 
Modifications 
After any modifications (increases or decreases) to dose level or frequency, 
subjects should remain in the clinic for observation for at least 2 hours following 
the injection of study drug. The Investigator should remain at the site to assess the 
 
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subject for safety. 
Section 9.1.2.1/Dose 
Increase Methodology 
Each subject’s dose may be modified based on the decision of the Investigator, in 
agreement with the Study Medical Officer. Decisions regarding dose increases 
will depend on available blood Phe and drug concentrations. 
Depending upon the response to rAvPAL-PEG in PAL-002, an individual  
subject’s dose may be adjusted beginning on Day 1 of PAL-003 as follows: 
• 
The dose may be increased by increments of no more than 10-fold higher than 
the subject’s current dose. 
• 
When adjusting increasing the dose, a dose may be used that is between the 
dose cohort levels (0.001, 0.003, 0.01, 0.03, 0.06, 0.1, 0.3, 0.6, and 1.0 mg/kg) 
that were defined in the previous study (PAL-002). 
• 
The dose may be adjusted by increasing the frequency up to daily ofnumber of 
injections per week, up to one dose per day, for a maximum total weekly dose 
per week of not to exceed 2.0 mg/kg, including subjects who receive more 
than 1 dose/week. Subjects who increase their dose frequency should perform 
the Interim Dosing Visit assessments (refer to Section 12.3.5 and Tables 2.1.2 
and 2.1.3). 
• 
When a dose is adjustedincreased (either by increasingchanging the dose level 
or by increasingchanging the frequency of dosing), the subject must remain in 
the clinic for a minimum of 2 hours following the first modified dose 
administration, and an Investigator will remain on site during this time. 
Only 1 dose adjustment is allowed every 2 weeks.
• 
 
 
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• 
Blood Phe levels will be measured 3 days after each dose increase (fingerstick 
is acceptable); more frequent or daily blood Phe measurements may be 
performed. 
• 
The dose may be decreased as appropriate to achieve or maintain a favorable 
blood Phe concentration for safety. 
Subjects must have blood Phe concentration tested 3 days after a dose adjustment. 
There must be a minimum of 2 weeks after each dose adjustment before any 
additional dose adjustments may be made, so that blood Phe concentrations can 
be assessed. 
9.1.2.2  
Dose Decrease Methodology 
A subject’s diet should be assessed prior to any dose decreases. Changes to diet 
should only be made if blood Phe concentrations are  < 120 µmol/L. If a subject’s 
blood Phe level is  < 120 µmol/L, the subject’s dietary Phe intake should be 
increased to achieve a stable blood Phe concentration of 120-600 µmol/L. If the 
subject’s blood Phe level is  < 120 µmol/L despite a high Phe diet, the 
rAvPAL-PEG dose will then be decreased. The subject will be asked about any 
changes to diet prior to any dose adjustments, and any changes to diet should be 
made per the discretion of the Investigator in consultation with the Sponsor’s 
Medical Officer. 
All dose decreases must be agreed to by both the Investigator and the Sponsor’s 
Medical Officer. Decisions regarding dose decreases will depend on available 
information regarding a subject’s blood Phe (>30% change from baseline) and 
 
 
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drug concentrations, as well as toxicity (any hypersensitivity reaction as defined 
in Section 9.1.1.2). Dose decreases may occur for safety (ie, blood Phe 
concentration  < 120 µmol/L) or other toxicity that may be improved with a lower, 
more frequent dose. 
A dose should first be reduced by dose level (1.0, 0.6, 0.3, 0.1, 0.06, 0.03, 0.01, 
0.003, 0.001 mg/kg). It is also permitted to decrease dose in between these 
specified dose levels. If further dosing adjustments are required to attain the target 
Phe concentration, dosing frequency may be reduced.  
Section 9.1.3/Stopping 
Criteria 
If an individual subject exhibits drug related toxicity of a treatment-emergent 
ity 
 dose level exhibit drug
CTCAE grade 3 or greater, that subject will have dosing halted until the toxic
resolves. The subject’s data will be evaluated by the Principle Investigator (PI) 
and the Study Medical Officer, and a decision will then be made whether to 
discontinue the subject from the study, restart dosing at the same dose level, or 
restart dosing at a lower dose level. 
In addition, if 2 or more subjects at a
related toxicity of a 
treatment-emergent CTCAE grade 3 or greater, further dosing of subjects at that 
dose level will be halted and no subject will be treated at a any higher dose levels 
will be halted until a safety assessment is completed. In addition, the Food and 
Drug Administration (FDA) will be notified of this occurrence. 
 
6 
Section 9.3.2/Exclusion 
Criteria 
G (other than 
rAvPAL-PEG), including Depo-Provera, within 6
3. 
Use or planned use of any injectable drugs containing PE
 months prior to Screening and 
 
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during study participation. 
8.  
Known hypersensitivity to rAvPAL-PEG or its excipients, including 
hypersensitivity reactions that necessitated early termination from PAL-002. 
Section 9.3.4/Subject 
Identification and 
Replacement of Subjects 
After enrollment of 35 subjects, if any single cohort (identified during PAL 002) 
has less than 3 subjects due to early terminations, those subjects will be replaced. 
Replacement subjects will enter the study at the same dose cohort level as the 
subject they are replacing. 
Each subject was assigned a unique subject identifier in either PAL 001 or 
PAL 002. Subjects will retain the same subject number assigned used in 
s. In 
PAL-002. This unique identifier will be on all case report form (CRF) page
legal jurisdictions where use of initials is not permitted, a substitute identifier will 
be used.   
Subjects who do not complete the study will not be replaced. 
This unique identifier will be on all case report form (CRF) pages. In legal 
jurisdictions where use of initials is not permitted, a substitute identifier will be 
used.
 
13, 27 
Section 9.4.4/Directions 
for Administration 
y 
Study drug will be administered by clinic staff or other qualified and trained stud
personnel. 
Weighing 80 kg 
 
11, 27 
Table 9.4.4.1  Number of Injections Required For an Individual  
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Dos
b
e Group 
(mg/kg) 
Weight 
(kg) 
Volume of Study Drug 
(mL)a
No. of 
Injections
0.001 
80 
0.8 
1 
0.003 
80 
0.6 
1 
0.01 
80 
0.8 
1 
0.03 
80 
0.2 
1 
0.06 
80 
0.5 
1 
0.1 
80 
0.8 
1 
0.3 
80 
2.4 
2 
0.6 
80 
4.8 
2 or 3 
1.0 
80 
8.0 
4 
Every effort should be made to adhere 
inistration regimen. 
to the study drug adm
If a subject misses more than 2 scheduled doses of study drug, both dose level and 
dose fr
ncy will need
-evaluated.
eque
 to be re
 
Section 9.4.5/Method of 
Assigning Subjects to 
Treatment Groups 
An interactive voice response system (IVRS) will be used to track subjects’ 
assigned dose and study drug inventory.
 
24 
Section 9.4.6/Selection of
Doses Used in the Stud
 
y 
-PEG after long-term administration in 
subjects with PKU. A favorable
This Phase 2 study aims to evaluate the efficacy, safety, tolerability, and PK 
parameters of multiple doses of rAvPAL
 dose that produces a reduction in blood Phe 
concentrations to below 120-600480 μmol/L will be determined for each subject.  
1
7 
 
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The doses for this study are based upon the results of nonclinical studies and 
PAL-001. Findings in cynomolgus monkeys dosed with a single administration of 
60 mg/kg rAvPAL PEG included severe morbidity, decreased plasma Phe 
concentration, decreased protein synthesis, and GI lesions. Plasma Phe 
concentrations were reduced to below the level of detection in the lower dose 
groups, without other findings (refer to Section 7.1). The no observable adverse 
effect level (NOAELs) from nonclinical studies in rats and monkeys represents a 
greater than 100-fold safety factor over the starting dose administered in PAL-
002, (0.001 mg/kg). The doses for this study will be based upon the results of 
PAL 001 and PAL 002.
Section 9.4.6.1/Selection 
of Timing of Dose for 
Each Subject 
d 
Study drug will be administered in the morning by clinic staff or other qualifie
and trained study personnel or by the subject, if appropriate. 
 
11, 27 
Section 9.4.8/Prior and 
Concomitant Medications 
 6 months prior to 
Screening and during study participation. A list of PEG-containing injectable 
ad a prior 
Use or planned use of any injectable drugs containing PEG (other than 
rAvPAL-PEG), including Depo-Provera, is prohibited within
drugs is provided in the study reference materials. Subjects who have h
local skin reaction to rAvPAL-PEG or a PEG-containing product will be 
premedicated with acetaminophen and antihistamines and/or oral steroids (refe
Section 9.1.1). If the local skin reaction worsens with a repeat injection (as 
r to 
determined by the Investigator in consultation with the Study Medical Officer) 
even with premedication prior to study drug dosing, the subject must be 
 
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withdrawn from the study and complete an Early Termination Visit. 
Subjects who have had a prior systemic hypersensitivity reaction to rAvP
or a PEG-containing product are excluded from participation in this s
AL-PEG 
tudy will be 
premedicated with acetaminophen and antihistamines and/or oral steroids (refer to 
Section 9.1.1). If the local or systemic reaction worsens with a repeat injection (as 
determined by the Investigator in consultation with the Study Medical Officer) 
even with premedication prior to study drug dosing, the subject must be 
withdrawn from the study.
Section 9.6/Dietary or 
Other Protocol 
Restrictions 
se of the 
or safety. If a subject’s blood Phe concentration is 
Subjects will be instructed that diet should not be altered during the cour
study except as necessary f
 < 120 µmol/L, the subject’s diet will be adjusted to maintain blood Phe 
concentrations of 120-600 µmol/L. Changes to diet will be made per the 
discretion of the Investigator in consultation with the Sponsor’s Medical Officer. 
 to clinic 
A 3-day dietary record will be completed by subjects and will be brought
visits for review with clinic staff. It is preferable that subjects complete the 3-day 
record immediately prior to their next dose of study drug. The dietary record will 
be maintained with the study source documents.  
 
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Section No./Title 
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Comments 
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Change No. 
Section 9.7.1/Efficacy 
and Safety Measurements 
Assessed 
Table 9.7.1.1: Summary of Laboratory Assessments 
Laboratory Assessment 
Party Responsible 
for Performing Test 
Section in 
Protocol for 
Details 
Clinical laboratory tests 
Central laboratory 
9.7.5 
Antibody testing 
BioMarina
9.7.4.2 
PK variables 
Central 
laboratoryBioMarin 
9.7.3 
Blood Phe concentrations 
Central laboratory 
9.7.2.1 
Urinalysis, pregnancy test 
(urine), and sedimentation 
rate 
Local laboratory 
9.7.5, 9.7.4.1 
Phe, phenylalanine; PK, pharmacokinetic. 
aAnalysis of the anti-rAvPAL-PEG IgE assay will be performed by a Contract Research 
Organization. 
 
27 
Section 9.7.1.1/ 
Demographic Data and 
Medical History 
Demographic data and a detailed medical history, including allergy history, will 
be obtained at Screening.  
 
22 
Section 9.7.1.2/ 
Physical Examination 
Findings 
Physical examination will include assessment of weight; general appearance; CV; 
dermatologic; head, eyes, ears, nose, and throat; lymphatic; respiratory; GI; 
musculoskeletal; and neurological/psychological. Height will be measured at 
 
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Section No./Title 
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Comments 
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Screening only. 
Section 9.7.1.3/Vital Sign 
Measurements 
Vital signs will be measured after resting for 5 minutes, and include seated 
systolic blood pressure (SBP) and diastolic blood pressure (DBP) measured in 
millimeters of mercury (mm Hg), heart rate in beats per minute, respiration rate in 
breaths per minute, weight (kg), and temperature in degrees Celsius (°C). Height 
(cm) will be measured at Screening only. 
 
27 
Section 9.7.1.5/Chest 
X-Ray 
A chest X-ray will be performed at the Month 12 and Final Follow-Up (or Early 
Termination) visits to assess gross pulmonary health. 
 
23 
Section 9.7.2.1/Blood 
Phenylalanine 
Concentrations 
In addition, 3 days after each administration of study drug, the subject will have a 
blood Phe measurement by fingerstick as outlined in Table 2.1.1. This may be 
done by the subject at home. Subjects who have their dose frequency increased 
will have additional Phe assessments performed as outlined in Table 2.1.2 
and 2.1.3. 
 
27 
Section 9.7.3/ 
Pharmacokinetic 
Variables 
Steady-state PK (predose samples) of rAvPAL-PEG will be evaluated in PKU 
subjects after the subject has achieved and maintained target blood Phe 
concentrations (below 120-600480 μmol/L) for a minimum of 2 weeks (to allow 
assessment of blood Phe concentrations) and no further dose modification is 
planned. Once this target has been achieved, PK samples will be collected predose 
on the same day each week for 3 consecutive weeks. 
Subjects who have increased their dose frequency to twice weekly or daily will 
 
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Section No./Title 
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Comments 
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have additional PK assessments performed for 5 weeks after the change in dose 
regimen (refer to Section 12.3.5 and Tables 2.1.2 and 2.1.3).  
Section 9.7.4.1/ 
Pregnancy Testing 
Female subjects of childbearing potential will have a urine pregnancy test at the 
time points specified in the Schedules of Events (Table 2.1.1 and Table 2.1.2). 
Female subjects with a positive serum pregnancy test at Screening do not meet 
eligibility criteria for enrollment. 
 
27 
Section 9.7.4.2/ 
Antibody Testing 
Immunoglobulin G (IgG) and M (IgM) antibodies and neutralizing antibodies 
(NAb) to rAvPAL PEG will be measured using validated immunogeneticity 
assays at the timepoints indicated in the Schedule of Events (Table 2.1.1). Anti
PEG antibodies will also be measured. 
Immunogenicity will be assessed by determining antibody response and 
neutralizing activity with the following measurements: 1) anti-rAvPAL 
immunoglobulin G (IgG) antibodies, 2) anti-rAvPAL immunoglobulin M (IgM) 
antibodies, 3) anti-PEG IgG antibodies, 4) anti-PEG IgM antibodies, 
5) anti-rAvPAL-PEG immunoglobulin E (IgE) antibodies, and 6) 
anti-rAvPAL-PEG Enzyme Activity Neutralizing antibodies (NAb). Validated 
immunogenicity assays will be used per the time points indicated in the Schedule 
of Events (Table 2.1.1). 
BioMarin will perform the analysis except for anti-rAvPAL-PEG IgE antibodies, 
which will be assessed by a Contract Research Organization. 
 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
Section 9.7.5/Clinical 
Laboratory Assessments 
Table 9.7.5.1: Clinical Laboratory Tests has been revised to include tests for the 
Unscheduled Skin Reaction visits. In addition, information has been added to 
indicate that a local laboratory will perform sedimentation rate analysis and the 
other laboratory tests have been revised for accuracy. 
 
8, 27 
Section 10.1/Adverse 
Events 
The Investigator will determine the severity of each AE and will record it on the 
source documents and AE CRF, using the categories CTCAE v 3 grades defined 
below. Events that are CTCAE grades 4 and 5 are serious events and require 
completion of both an SAE form and AE eCRF. 
Grade 
Description 
1 
Mild 
2 
Moderate 
3 
Severe 
4 
Life threatening or debilitating 
5 
Death related 
Mild
No limitation of usual activities
Moderate
Some limitation of usual activities
Severe
Inability to carry out usual activities
 
 
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Section No./Title 
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Comments 
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Section 10.4/BioMarin 
Pharmacovigilance 
Contact Information 
Contact information for the Mmedical Mmonitor is as follows: 
Name:  
, MD 
Address: 
105 Digital Drive 
 
 
Novato, CA 94949 USA 
Phone:  
 
Fax: 
 
 
E-mail: 
 
 
25 
Section 12.2/Screening 
Visit 
• Medical history, including allergy history, and demographics 
• Physical examination and height 
• 
Vital signs, including height and weight  
• 
Predose bBlood Phe and plasma tyrosine concentration 
For subjects who participated in PAL-002, these assessments may be the same 
used for the Week 16 Final Follow up Visit of PAL-002, if they occur within 28 
days from Day 1. 
 
22, 27 
Section 12.3.1/Day 1 
(Week 1) 
• Vital signs, including weight 
• Predose PK sample  
• Serum rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG 
IgG, anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibody, and anti-
rAvPAL-PEG IgE) 
 
27 
Section 12.3.2/Weekly 
• Vital signs, including weight 
 
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Section No./Title 
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Comments 
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Visits 
• 3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the next dose of study drug.) 
• Predose PK sample  
o 
Per investigator discretion, once a subject is on a stable dosing 
regimen for at least 3 months (as evidenced by blood Phe levels of 
120-600 µmol/L for the majority of the 3 months), the predose PK 
assessment may be skipped at the weekly visits and performed at 
the monthly visits for the first year then 2-3 months thereafter. 
Weekly sampling should resume if the subject’s dosing regimen 
changes. 
• Predose blood Phe and plasma tyrosine concentration 
o 
Per investigator discretion, once a subject is on a stable dosing 
regimen for at least 3 months (as evidenced by blood Phe levels of 
120-600 µmol/L for the majority of the 3 months), the predose 
plasma Phe and tyrosine assessments may be skipped at the 
weekly visits and performed at the monthly visits for the first year 
then 2-3 months thereafter. The weekly plasma Phe assessment 
may be replaced with a Phe fingerstick test. Weekly testing should 
resume if the subject’s dosing regimen changes. 
Section 12.3.3/Monthly 
Visits 
Monthly visits consist of all weekly activities and include additional activities. 
The following study activities will be performed at the monthly visits beginning 
with Week 4: 
• Vital signs, including weight 
 
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Section No./Title 
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Comments 
Relates to 
Change No. 
• Chest x-ray (Month 12 visit only) 
• 3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the next dose of study drug.) 
• 
Predose PK sample (subjects who are on a stable dosing regimen for 
 ≥ 3 months only) 
o 
Per investigator discretion, once a subject is on a stable dosing 
regimen for at least 3 months (as evidenced by blood Phe levels of 
120-600 µmol/L for the majority of the 3 months), the predose PK 
assessment may be skipped at the weekly visits and performed at 
the monthly visits for the first year then 2-3 months thereafter. 
Weekly sampling should resume if the subject’s dosing regimen 
changes.  
• Predose blood Phe and plasma tyrosine concentration 
o 
Per investigator discretion, once a subject is on a stable dosing 
regimen for at least 3 months (as evidenced by blood Phe levels of 
120-600 µmol/L for the majority of the 3 months), the predose 
plasma Phe and tyrosine assessments may be skipped at the 
weekly visits and performed at the monthly visits for the first year 
then 2-3 months thereafter. The weekly plasma Phe assessment 
may be replaced with a Phe fingerstick test. Weekly testing should 
resume if the subject’s dosing regimen changes. 
• Serum rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG 
IgG, anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibody, and anti-
rAvPAL-PEG IgE) 
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Section No./Title 
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Comments 
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In addition, 3 days after each administration of study drug, the subject will have a 
blood Phe measurement by fingerstick. This may be done by the subject at home. 
Section 12.3.4/Quarterly 
Visits (Week 12, 24, 36, 
etc.) 
Quarterly visits consist of all weekly and monthly activities and include additional 
activities. The following study activities will be performed at the quarterly visits 
beginning with Week 12: 
• Vital signs, including weight 
• 3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the next dose of study drug.) 
• Predose PK sample (subjects who are on a stable dosing regimen for 
 ≥ 3 months only) 
o 
Per investigator discretion, once a subject is on a stable dosing 
regimen for at least 3 months (as evidenced by blood Phe levels of 
120-600 µmol/L for the majority of the 3 months), the predose PK 
assessment may be skipped at the weekly visits and performed at 
the monthly visits for the first year then 2-3 months thereafter. 
Weekly sampling should resume if the subject’s dosing regimen 
changes.   
• Serum rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG 
IgG, anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibody, and anti-
rAvPAL-PEG IgE) 
In addition, 3 days after each administration of study drug, the subject will have a 
blood Phe measurement by fingerstick. This may be done by the subject at home. 
 
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Section No./Title 
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Section 12.3.5/Interim 
Dosing Visit 
Subjects who increase their dose frequency from 1x/week to 2x/week or daily will 
have additional assessments performed for 5 weeks after the subject’s 
rAvPAL-PEG dose frequency has been increased. If the Interim Dosing Visit 
coincides with a weekly, monthly, or quarterly scheduled visit, the scheduled visit 
assessments should also be performed. The following study activities will be 
performed for the Interim Dosing Visit: 
• 
Vital signs, including weight 
• 
Injection-site inspection (previous and current injection site) 
• 
Assessment of AEs 
• 
Concomitant medications 
Blood Phe measurem
• 
ent by fingerstick 
e.
o This may be done by the subject at hom  
• 
PK sam le 
p
 
o 
Subjects who increase their dose frequency to 2x/week will have 
an additional predose PK sample obtained prior to administration 
of the first 4 doses (ie, for 2 weeks after the dose frequency 
increase). For the remaining 3 weeks after the dose frequency 
increase, a PK sample will be obtained weekly prior to the first 
dose. Refer to Table 2.1.2 for the Interim Dosing Visit schedule. 
o 
Subjects who have their dose frequency increased to daily will 
have additional PK samples obtained every day for the first week: 
12 hours after the first daily dose and predose every day for the 
 
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Section No./Title 
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Comments 
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rest of the week. After the first week of daily dosing, subjects will 
have weekly PK samples obtained for 4 additional weeks. Refer to 
Table 2.1.3 for the Interim Dosing Visit schedule. 
Section 12.3.6/ 
 Reaction 
Subjects who h
administration 
Unscheduled 
Hypersensitivity
Visit 
ave a generalized skin reaction after rAvPAL-PEG 
(refer to Section 9.1.1) will have assessments performed immediately following 
(within 48 hours) the reaction. Subjects who have other systemic symptoms or a 
large local skin reaction that is not contiguous to the injection site (refer to 
Section 9.1.1) may have these assessments performed per investigator discretion. 
• Injection-site inspection 
• Clinical laboratory tests 
• Sedimentation rate  
• CRP, CH50, C1, and C4 
ibodies 
• Serum rAvPAL-PEG ant
(anti-PAL IgG, anti-PAL IgM, 
anti-PEG IgG, anti-PEG IgM, anti-rAvPAL-PEG neutralizing 
antibody, and anti-rAvPAL-PEG IgE) 
Serum tryptase level 
• 
 
o
ely after reaction if possible.
 
Perform immediat
 
generalized skin 
o 
Assessment is optional for subjects who have a 
reaction per investigator discretion. 
sample
• PK 
 
 
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Section No./Title 
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Comments 
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• Assessment of AEs 
• Concomitant medications 
 
Subjects should then return to the clinic 4 weeks after their last dose of 
rAvPAL-PEG for the Early Termination Visit assessments (refer to Section 12.4). 
Section 12.4/Early 
Termination Visit 
12.4 
Final Follow up Visit (Day 113 [ ± 3 days])/Early Termination Visit 
The final follow up (F/U) Visit or Early Termination Visit (ETV) will occur 
4 weeks after the final dose of study drug. 
Subjects who complete an Unscheduled Hypersensitivity Reaction Visit (refer to 
Sections 12.3.6) will be terminated from the study. Subjects will then return 
4 weeks after the last dose of study drug for the Early Termination Visit. 
The following study activities will be performed at the F/U Visit or ETV: 
• Physical examination and weight 
• Vital signs, including weight 
• Chest x-ray  
• PK sample 
• Predose bBlood Phe and plasma tyrosine concentration 
• Serum rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG 
IgG, anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibody, and anti-
 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
rAvPAL-PEG IgE) 
Section 12.5/Final 
Follow-up Visit (Day 113 
[ ± 3 days])
12.54 Final Follow-up Visit (Day 113 [ ± 3 days]) /Early Termination Visit
Any AE that caused a subject to withdraw from the study or any clinically 
significant abnormal laboratory value or vital sign measurement identified at the 
ETV will be followed by the Investigator.  
Every reasonable effort should be made to contact any subject who is lost to 
follow up. 
The following study activities will be performed at the F/U Visit or ETV: 
• Vital signs, including weight 
• Chest x-ray  
• PK sample 
• Predose bBlood Phe and plasma tyrosine concentration 
• Serum rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG 
IgG, anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibody, and anti-
rAvPAL-PEG IgE) 
 
21, 27 
Section 14.2/Safety 
Analysis 
All subjects who receive any amount of study drug in this study and have 
postdose safety information will be included in the safety analyses. 
Safety will be evaluated on the incidence of AEs, including serious AEs (SAEs), 
and clinically significant changes in vital signs and laboratory test results. 
 
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Section No./Title 
Revision 
Comments 
Relates to 
Change No. 
The verbatim terms reported on CRFs to identify AEs will be coded using 
MedDRA. Treatment-emergent AEs will be summarized for each treatment group 
by system organ class, preferred term, relationship to study drug, and severity. 
Changes from baseline in vital signs and laboratory test results will be 
summarized with descriptive statistics by dose group. 
Section 14.3/ 
Pharmacokinetic 
Analysis 
Steady-state PK (predose samples) of rAvPAL-PEG will be evaluated in PKU 
subjects after the subject has achieved and maintained target blood Phe 
concentration (below 120-600480 μmol/L) for a minimum of 2 weeks and no 
further dose modification is planned. 
Should data become available from PAL 001 and/or PAL-002 which that indicate 
study drug accumulation should also be measured, the protocol will be amended 
to require additional blood draws may be added for PK analysis as needed but not 
to exceed 3x/week. 
 
18, 27 
Section 14.4/Efficacy 
Analysis 
In addition, the proportion of subjects who have maintained target Phe 
concentrations of 120-600 µmol/L will be summarized by each scheduled time 
point. 
 
19 
Section 14.7/Interim 
Analysis 
At least one interim analysis may be performed by the sponsor during the study. 
Safety will be assessed throughout the study on an ongoing basis (refer to 
Section 15 for information regarding the DMC). 
 
27 
Section 15/Data 
Monitoring Committee 
The DMC will act independently in an advisory capacity to BioMarin to monitor 
 
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Section No./Title 
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Comments 
Relates to 
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(DMC) 
the subjectsafety and the efficacy of rAvPAL-PEG in subjects who participate in 
the study. 
Section 21/References 
Burgard, Bremer, Bührdel, Clemens, Mönch, Przyrembel, Trefz, Ullrich. 
Rationale for the German recommendations for phenylalanine level control in 
phenylketonuria 1997. Eur J Pediatr 158, 46 54. 1999. 
Butterworth. Effects of hyperammonaemia on brain function. J Inherit Metab Dis 
21 Suppl 1, 6 20. 1998. 
 
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PAL-003 
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Proprietary and Confidential 
2 
SYNOPSIS 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
TITLE OF STUDY: 
Long-term Extension of a Phase 2, Open-Label Dose-Finding Study to Evaluate the Safety, Efficacy, 
and Tolerability of Multiple Subcutaneous Doses of rAvPAL-PEG in Subjects with PKU 
PROTOCOL NUMBER:  PAL-003 
STUDY SITES:  Approximately 8 centers in the United States 
PHASE OF DEVELOPMENT:  Phase 2 
STUDY RATIONALE: 
The need exists for a treatment that will help individuals with phenylketonuria (PKU) safely achieve 
lifelong, reliable control of blood phenylalanine (Phe) concentrations and improve functional 
outcomes. Phenylalanine ammonia lyase (rAvPAL-PEG) is a potential substitute for the phenylalanine 
hydroxylase (PAH) enzyme, which is defective in individuals with PKU. rAvPAL-PEG may control 
blood Phe concentrations, which may have additional clinical benefits. This study is an extension of 
the dose-finding study (Study PAL-002). Administration of rAvPAL-PEG will be continued to assess 
whether long-term dosing of rAvPAL-PEG is safe and can maintain reduced blood Phe concentrations 
in PKU subjects. 
OBJECTIVES: 
The primary objective of the study is: 
• 
To evaluate the effect of long-term administration of multiple doses of SC injections of 
rAvPAL-PEG on blood Phe concentrations in subjects with PKU. 
The secondary objectives of the study are: 
• 
To evaluate the safety and tolerability of long-term administration of subcutaneous (SC) 
injections of rAvPAL-PEG in subjects with PKU. 
• 
To evaluate the immune response to long-term administration of SC injections of 
rAvPAL-PEG in subjects with PKU. 
• 
To evaluate steady-state PK of rAvPAL-PEG in subjects with PKU. 
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PAL-003 
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Proprietary and Confidential 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
STUDY DESIGN AND PLAN: 
This is a long-term extension of a Phase 2, open-label, dose-finding study (Study PAL-002) in 
35-50 subjects with PKU. The doses are planned to be in the same range as those tested in PAL-002 
(0.001 through 1.0 mg/kg per injection), provided no dose-limiting toxicity was observed in PAL-002. 
Only subjects who completed participation in PAL-002 will be enrolled into this study. Diet will not 
be altered during the course of this study, except as necessary for safety as determined by blood Phe 
concentrations. If a subject’s blood Phe concentration is  < 120 µmol/L, the subject’s diet may be 
adjusted to increase the amount of dietary Phe intake to maintain target blood Phe 
concentrations of 120-600 µmol/L. Changes to diet will be made per the discretion of the 
Investigator in consultation with the Sponsor’s Medical Officer.  
Subjects will be evaluated for safety and for blood Phe concentrations throughout the study. Toxicity 
will be measured according to the National Cancer Institute (NCI) Common Terminology Criteria for 
Adverse Events (CTCAE), version 3. 
At least one interim analysis may be performed by the sponsor during the study. In addition to 
the Sponsor, a Data Monitoring Committee (DMC) will monitor the safety of subjects in the study. 
The DMC is an independent committee that will act in an advisory capacity to the Sponsor. 
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take 
rAvPAL-PEG. PAL-002 subjects’ rAvPAL-PEG dosing will continue in PAL-003 without 
interruption of dosing. In PAL-003, each subject’s dose will be adjusted as needed to attain or 
maintain blood Phe concentrations of 120-600 µmol/L. Doses will be evaluated on an individual basis. 
Evaluations, observations, and procedures will be conducted at selected time points. After the subject’s 
blood Phe concentration has been controlled to within a target range (120-600 µmol/L), the subject 
may be asked to have additional blood draws for PK and blood Phe concentration analyses as needed 
but not to exceed 3x/week (fingerstick tests may be performed more frequently). 
A subject will continue in PAL-003 until one of the following occurs: 
1. The subject withdraws consent and discontinues from the study. 
2. The subject is discontinued from the study at the discretion of the Investigator. 
3.  The subject has completed the study through the Month 24 visit. 
4.  The study is terminated. 
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PAL-003 
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Proprietary and Confidential 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
Dose Modifications: 
After any modifications (increases or decreases) to dose level or frequency, subjects should 
remain in the clinic for observation for at least 2 hours following the injection of study drug. 
The Investigator should remain at the site to assess the subject for safety. 
Dose Increase Methodology: 
Each subject’s dose may be modified based on the decision of the Investigator, in agreement with the 
Study Medical Officer. Decisions regarding dose increases will depend on blood Phe and drug 
concentrations.  
Blood Phe levels will be measured 3 days after each dose increase (fingerstick is acceptable); 
more frequent or daily blood Phe measurements may be performed.  
Depending upon the response to rAvPAL-PEG in PAL-002, an individual subject’s dose may be 
adjusted beginning on Day 1 of PAL-003 as follows. 
• The dose may be increased by increments of no more than 10-fold higher than the 
subject’s current dose. 
• When increasing the dose, a dose may be used that is between the dose levels (0.001, 
0.003, 0.01, 0.03, 0.06, 0.1, 0.3, 0.6, and 1.0 mg/kg) that were defined in the previous 
study (PAL-002). 
• The dose may be adjusted by increasing the frequency up to daily for a total weekly 
dose not to exceed 2.0 mg/kg, including subjects who receive more than 1 dose/week. 
Subjects who increase their dose frequency will have additional assessments 
performed (Interim Dosing Visit). 
• When a dose is increased (either by increasing the dose level or by increasing the 
frequency of dosing), the subject must remain in the clinic for a minimum of 2 hours 
following the first modified dose administration, and an Investigator will remain on site 
during this time. 
• Only 1 dose adjustment is allowed every 2 weeks. 
• Blood Phe levels will be measured 3 days after each dose increase (fingerstick is 
acceptable); more frequent or daily blood Phe measurements may be performed. 
Dose Decrease Methodology 
A subject’s diet should be assessed prior to any dose decreases. Changes to diet should only be 
made if a subject’s blood Phe concentrations  < 120 µmol/L. If a subject’s blood Phe level is 
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PAL-003 
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Proprietary and Confidential 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
 < 120 µmol/L, the subject’s dietary Phe intake should be increased to achieve a stable blood Phe 
concentration of 120-600 µmol/L. If the subject’s blood Phe level is  < 120 µmol/L despite a high 
Phe diet, the rAvPAL-PEG dose will then be decreased. The subject will be asked about any 
changes to diet prior to any dose adjustments, and any changes to diet should be made per the 
discretion of the Investigator in consultation with the Sponsor’s Medical Officer. 
All dose decreases must be agreed to by both the Investigator and the Sponsor’s Medical Officer. 
Decisions regarding dose decreases will depend on available information regarding a subject’s 
blood Phe ( > 30% change from baseline) and drug concentrations, as well as toxicity (any 
hypersensitivity reaction). Dose decreases may occur for safety (ie, blood Phe concentration 
 < 120 µmol/L) or other toxicity that may be improved with a lower, more frequent dose. 
A dose should first be reduced by dose level (1.0, 0.6, 0.3, 0.1, 0.06, 0.03, 0.01, 0.003, 0.001 
mg/kg). It is also permitted to decrease dose in between these specified dose levels. If further 
dosing adjustments are required to attain the target Phe concentration, dosing frequency may be 
reduced.  
Stopping Criteria: 
If an individual subject exhibits toxicity of a treatment-emergent CTCAE grade 3 or greater, that 
subject will have dosing halted until the toxicity resolves. The subject’s data will be evaluated by the 
Principal Investigator (PI) and the Study Medical Officer, and a decision will then be made whether to 
discontinue the subject from the study, restart dosing at the same dose level, or restart dosing at a 
lower dose level. 
In addition, if 2 or more subjects at a dose level exhibit toxicity of a treatment-emergent CTCAE 
grade 3 or greater, further dosing of subjects at that dose level will be halted and no subjects will be 
treated at a higher dose level until a safety assessment is completed. In addition, the Food and Drug 
Administration (FDA) will be notified of this occurrence. 
NUMBER OF SUBJECTS PLANNED: 
35-50 subjects. 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
DIAGNOSIS AND ALL CRITERIA FOR INCLUSION AND EXCLUSION:  
Individuals eligible to participate in this study must meet all of the following criteria: 
1. Must have completed participation in PAL-002. 
2. Willing and able to provide written, signed informed consent, or, in the case of 
participants under the age of 18, provide written assent (if required) and written informed 
consent by a parent or legal guardian, after the nature of the study has been explained, and 
prior to any research-related procedures. 
3. Willing and able to comply with all study procedures. 
4. Females of childbearing potential must have a negative pregnancy test at Screening and be 
willing to have additional pregnancy tests during the study. Females considered not of 
childbearing potential include those who have been in menopause at least 2 years, or had 
tubal ligation at least 1 year prior to Screening, or who have had total hysterectomy. 
5. Sexually active subjects must be willing to use an acceptable method of contraception 
while participating in the study. 
6. Maintained a stable diet. 
7. In generally good health as evidenced by physical examination, clinical laboratory 
evaluations (hematology, chemistry, and urinalysis), and electrocardiogram (ECG) at 
Screening. 
Individuals who meet any of the following exclusion criteria will not be eligible to participate in the 
study: 
1. Use of any investigational product (with the exception of rAvPAL-PEG) or investigational 
medical device within 30 days prior to Screening, or requirement for any investigational 
agent prior to completion of all scheduled study assessments. 
2. Use of any medication that is intended to treat PKU within 14 days prior to the 
administration of study drug. 
3. Use or planned use of any injectable drugs containing PEG (other than rAvPAL-PEG), 
including Depo-Provera, during study participation. 
 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
4. A prior reaction that included systemic symptoms (eg, generalized hives, respiratory or 
gastrointestinal problems, hypotension, angioedema, anaphylaxis) to rAvPAL-PEG or a 
PEG-containing product. 
5. Pregnant or breastfeeding at Screening or planning to become pregnant (self or partner) or 
to breastfeed at any time during the study.  
6. Concurrent disease or condition that would interfere with study participation or safety 
(eg, history or presence of clinically significant cardiovascular, pulmonary, hepatic, renal, 
hematologic, gastrointestinal, endocrine, immunologic, dermatologic, neurological, 
oncologic, or psychiatric disease). 
7. Any condition that, in the view of the PI, places the subject at high risk of poor treatment 
compliance or of not completing the study. 
8. Known hypersensitivity to rAvPAL-PEG or its excipients, including hypersensitivity 
reactions that necessitated early termination from PAL-002. 
9. Alanine aminotransferase (ALT) concentration > 2 times the upper limit of normal. 
10. Creatinine  > 1.5 times the upper limit of normal. 
INVESTIGATIONAL PRODUCT, DOSE, ROUTE AND REGIMEN: 
rAvPAL-PEG doses will be administered SC and the dosage that provides control of blood Phe 
concentrations within the target range of 120-600 µmol/L for a minimum of 2 weeks will be 
determined for each subject by adjusting the dose level, dose frequency, or both, as agreed by the PI 
and the Study Medical Officer, based upon the subject’s response to doses. 
DURATION OF TREATMENT: 
Extension of multiple dosing will continue until one of the following occurs: 
1. The subject withdraws consent and discontinues from the study. 
2. The subject is discontinued from the study at the discretion of the Investigator. 
3. The subject has completed the study through the Month 24 visit. 
4.  The study is terminated. 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
REFERENCE THERAPY(IES), DOSE, ROUTE AND REGIMEN:  
None 
CRITERIA FOR EVALUATION: 
Efficacy: 
Blood Phe concentrations will be measured. 
Immunogenicity: 
The presence of antibodies will be assessed. 
Safety: 
Safety will be evaluated on the incidence of adverse events (AEs) and clinically significant changes in 
vital signs or laboratory test results. 
Pharmacokinetic: 
Plasma concentrations of rAvPAL-PEG will be measured when steady-state levels of Phe are attained. 
STATISTICAL METHODS:  
Sample Size: 
Subjects who participated in PAL-002 may be enrolled into this study. No formal sample size 
calculation was conducted. 
Safety Analysis: 
All subjects who receive any amount of study drug in this study and have postdose safety 
information will be included in the safety analyses. 
Safety will be evaluated on the incidence of AEs, including serious AEs (SAEs), and clinically 
significant changes in vital signs and laboratory test results. 
Efficacy Analysis: 
Data from all subjects who receive any amount of study drug and who have any post-treatment 
efficacy data will be included in the efficacy analysis. 
Blood Phe concentration at each scheduled time point will be summarized using descriptive statistics 
(mean, standard deviation, median, minimum, and maximum). Change in blood Phe concentration 
from baseline to each scheduled time point and presence/absence of antibodies will also be 
summarized. In addition, the proportion of subjects who have maintained target Phe 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
concentrations of 120-600 µmol/L will be summarized by each scheduled time point. 
Pharmacokinetic Analysis: 
Data from all subjects who complete at least 2 weeks of the study will be included in the PK analysis. 
Steady-state PK (predose samples) of rAvPAL-PEG will be evaluated in PKU subjects after the 
subject has achieved and maintained target blood Phe concentration (120-600 μmol/L) for a minimum 
of 2 weeks (to allow assessment of blood Phe concentrations) and no further dose modification is 
planned. Should data become available from PAL-002 that indicate study drug accumulation 
should also be measured, additional blood draws may be added for PK analysis as needed but 
not to exceed 3x/week. 
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2.1 
Schedule of Events 
Table 2.1.1:  Schedule of Events 
Treatment Periodb,c
Week 1 
Weekly 
Monthly (eg, 
Wk 4, 8, etc.) 
Quarterly 
(eg, Wk 12, 
24, etc.) 
Final F/U Visit
Early Term. 
Visit 
Assessments and Events 
Screeninga
D 1 
Starting at 
Week 2 
Every 4th 
week; 
Perform in 
addition to 
weekly 
procedures 
Every 12th 
week. 
Perform in 
addition to 
monthly 
procedures 
1 week after 
final dose 
4 weeks after 
final dose 
Unsched. 
Hyper. 
Reaction Visit.d  
Perform within 
48 hours; then 
perform Early 
Term. 
procedures 
Informed consent 
 
X 
 
 
 
 
 
 
 
Medical history, including allergy history, 
and demographics 
 
X 
 
 
 
 
 
 
 
Physical examinatione
 
X 
X 
 
 
X 
X 
X 
 
Vital signs and weight 
 
X 
X 
X 
 
 
X 
X 
 
12-lead ECG 
 
X 
 
 
 
 
X 
X 
 
Clinical laboratory testsf
 
X 
 
 
X 
 
X 
X 
Xg
Sedimentation rate 
 
X 
 
 
X 
X 
X 
X 
Chest x-ray 
 
 
 
X  
(12-month 
visit only) 
 
X 
X 
 
Urine pregnancy testh
 
X 
X 
 
X 
 
X 
X 
 
Injection-site inspectioni
 
X 
(postdose)
X 
 
 
X 
X 
X 
Adverse eventsj
 
XÅ--------------------------------------------------------------------------------------ÆX 
X 
X 
Concomitant medications 
 
X 
X 
X 
 
 
 
X 
 
X 
X 
Diet query 
 
X 
X 
X 
 
 
 
X 
 
X 
 
3-Day diet diaryk
 
 
X 
 
 
 
 
 
Serum rAvPAL-PEG antibodies l
 
X 
 
X 
 
 
X 
 
X 
X 
Predose plasma Phe and plasma tyrosinem
 
X 
X 
Xn
 
 
X 
(postdose) 
X 
(postdose) 
 
Plasma Phe (fingerstick)o
 
 
 (3 days 
postdose) 
 
 
 
 
 
Plasma PK samplep
 
X 
Xn
 
 
X 
X 
X 
Administer IPq
 
X 
X 
 
 
 
 
 
Serum tryptase level r
 
 
 
 
 
 
 
X 
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AE, adverse event; CH50, total hemolytic complement; CRP, C-reactive protein; D, day; ECG, electrocardiogram; ETV, Early Termination Visit; F/U, Follow-up; 
Hyper, hypersensitivity; IgE, immunoglobulin E; IgG, immunoglobulin G; IgM, immunoglobulin M; IP, investigational product; PK, pharmacokinetics; Phe, 
phenylalanine; SAE, serious adverse event; Wk, week. 
a It is preferable to perform PAL-003 Screening assessments the same day as PAL-002 Week 16 visit so there is no interruption of study drug. If performed on the same 
day, PAL-002 Week 16 visit data may be used.  If not, PAL-003 Day 1 must occur  ≤ 28 days after PAL-003 Screening. 
b Additional visits may occur if deemed necessary to monitor AEs or blood Phe, adjust dosing etc. 
c On days that a dose is given, all procedures should be performed predose, except where noted. 
d Unscheduled hypersensitivity reaction assessments are mandatory for subjects who have a generalized skin reaction. Subjects who have other systemic 
symptoms or who have a large local skin reaction that is not contiguous to the injection site may have these assessments performed per investigator discretion. 
Assessments should be performed within 48 hours of the reaction. Subjects who complete an Unscheduled Hypersensitivity Reaction Visit must be terminated 
from the study and should complete an Early Termination Visit. 
e Complete physical examinations to include the evaluation of all major body systems. Height will be measured at Screening only. 
f Clinical laboratory tests to include hematology, chemistry, and urinalysis. 
g Subjects who have a generalized skin reaction should also be assessed for CRP, CH50, C1, and C4 within 48 hours of the reaction. Subjects who have other 
systemic symptoms or who have a large local skin reaction that is not contiguous to the injection site may have these assessments performed per investigator 
discretion. 
h If positive or equivocal, perform serum pregnancy test. 
i If any injection site reaction is observed, the corresponding adverse event data must specify injection location (identify current vs. previous visit’s injection, e.g. right 
arm vs. left arm). 
j The reporting period for SAEs begins when informed consent is obtained and continues through 4 weeks after last dose or the final study visit. The reporting period for 
nonserious AEs is from the first administration of study drug to the final study visit. 
k It is preferable that the subject complete the diary 3 days immediately prior to the next dose of study drug. 
l Includes testing for anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibody, and anti-rAvPAL-PEG IgE 
antibodies. 
m Samples should be drawn in the morning, at least 2.5 hours after a meal. If dose is modified by increasing dose level, additional blood Phe concentration testing 
should be done on the third day following dose adjustment. If dose is modified by increasing either dose frequency or dose level, additional blood Phe concentration 
testing should be done prior to each dose for the first 2 weeks following dose adjustment.  
n Per investigator discretion, once a subject is on a stable dosing regimen for at least 3 months (as evidenced by blood Phe levels of 120-600 µmol/L for the 
majority of the 3 months), the predose plasma Phe, tyrosine, and PK assessments may be skipped at the weekly visits and performed at the monthly visits for 
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the first year then 2-3 months thereafter. The weekly plasma Phe assessment may be replaced by a Phe fingerstick test. Weekly testing should resume if the 
subject’s dosing regimen changes. 
o May be done by the subject at home. Samples should be taken in the morning, at least 2.5 hours after a meal. 
p The PK blood samples will be collected after the subject has achieved and maintained target blood Phe concentrations (120-600 μmol/L) for a minimum of 2 weeks. 
Once this target is achieved, predose PK samples will be collected on the same day each week for 3 consecutive weeks.  
q Dosing is up to 1.0 mg/kg per injection and up to one dose per day, for a total not to exceed 2.0 mg/kg/week, including subjects who receive more than 1 dose/week. 
Every effort should be made to adhere to the study drug administration regimen. If a subject misses more than 2 scheduled doses of study drug, both dose level 
and dose frequency will need to be re-evaluated. 
r Mandatory for subjects who have a large local skin reaction that is not contiguous to the injection site or non-skin systemic symptoms. Optional for subjects 
who have a generalized skin reaction. Take sample immediately after reaction if possible. 
 
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Table 2.1.2:  Interim Dosing Visit Schedule, Subjects Whose Dose is Increased to 2x/Week 
Subjects Who Are Administered rAvPAL-PEG  2x/Week 
Treatment Perioda, b
First Week After Dose 
Adjustment 
Second Week After 
Dose Adjustment 
Third Week After Dose 
Adjustment 
Fourth Week After 
Dose Adjustment 
Fifth Week After Dose 
Adjustment 
Assessments and Events 
First Dose 
Second 
Dose 
First Dose 
Second 
Dose 
First Dose 
Second 
Dose 
First Dose 
Second 
Dose 
First Dose 
Second 
Dose 
Vital signs and weight 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Injection-site inspection 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Adverse eventsc
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Concomitant medications 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Plasma PK sample 
X 
X 
X 
X 
X 
 
X 
 
X 
 
Blood Phe (fingerstick)d
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
AE, adverse event; D, day; PK, pharmacokinetics; Phe, phenylalanine. 
a The additional Interim Dosing Visit assessments should be performed for 5 weeks after the subject’s rAvPAL-PEG dose frequency has been increased to 
2x/week. All assessments should be performed predose unless specified otherwise. 
b If the Interim Dosing Visit coincides with a regularly scheduled visit, the scheduled visit assessments should also be performed. 
c If any injection site reaction is observed, the corresponding AE data must specify injection location (identify current vs. previous visit’s injection, e.g,. right 
arm vs. left arm). 
d May be done by the subject at home. Samples should be taken in the morning, at least 2.5 hours after a meal. 
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Table 2.1.3:  Interim Dosing Visit Schedule, Subjects Whose Dose is Increased to Daily 
Subjects Who Are Administered rAvPAL-PEG Daily 
Treatment Perioda, b
First Day After 
Dose Adjustment 
First Week After 
Dose Adjustment 
Second Week After 
Dose Adjustment 
Third Week After 
Dose Adjustment 
Fourth Week After 
Dose Adjustment 
Fifth Week After 
Dose Adjustment 
Assessments and Events 
Dose 1 
Doses 2-7 
Doses 8-14 
Doses 15-21 
Doses 22-29 
Doses 30-36 
Vital signs and weight 
X 
X 
X 
X 
X 
X 
Injection-site inspection 
X 
X 
X 
X 
X 
X 
Adverse eventsc
X 
X 
X 
X 
X 
X 
Concomitant medications 
X 
X 
X 
X 
X 
X 
Plasma PK sample 
X  
(12 hours postdose) 
X 
(Daily) 
1x/week 
1x/week 
1x/week 
1x/week 
Blood Phe (fingerstick)d
X 
X 
X 
X 
X 
X 
AE, adverse event; D, day; PK, pharmacokinetics; Phe, phenylalanine. 
a The additional Interim Dosing Visit assessments should be performed for 5 weeks after the subject’s rAvPAL-PEG dose frequency has been increased to daily. 
All assessments should be performed predose unless specified otherwise. 
b the Interim Dosing Visit coincides with a regularly scheduled visit, the scheduled visit assessments should also be performed. 
c If any injection site reaction is observed, the corresponding AE data must specify injection location (identify current vs. previous visit’s injection, e.g,. right 
arm vs. left arm). 
d May be done by the subject at home. Samples should be taken in the morning, at least 2.5 hours after a meal. 
 
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3 TABLE OF CONTENTS 
1 TITLE PAGE .....................................................................................................................1 
2 SYNOPSIS...........................................................................................................................2 
2.1 Schedule of Events................................................................................................... 10 
3 TABLE OF CONTENTS...................................................................................................15 
4 LIST OF ABBREVIATIONS AND DEFINITIONS OF TERMS....................................19 
5 ETHICS..............................................................................................................................23 
5.1 Institutional Review Board or Ethics Committee.................................................... 23 
5.2 Ethical Conduct of Study......................................................................................... 23 
5.3 Subject Information and Informed Consent............................................................. 24 
6 INVESTIGATORS AND STUDY ADMINISTRATIVE STRUCTURE ........................25 
7 INTRODUCTION .............................................................................................................26 
7.1 Nonclinical Studies.................................................................................................. 26 
7.2 Previous Clinical Studies......................................................................................... 28 
7.3 Study Rationale........................................................................................................ 28 
7.4 Summary of Overall Risks and Benefits.................................................................. 29 
7.4.1 Toxicity Due to Exposure to PEG ...................................................................29 
7.4.2 Toxicity Due to an Immunologic Reaction......................................................30 
7.4.3 Effects of Low Blood Phe................................................................................33 
8 STUDY OBJECTIVES......................................................................................................34 
9 INVESTIGATIONAL PLAN............................................................................................35 
9.1 Overall Study Design and Plan................................................................................ 35 
9.1.1 Management of Local and Systemic Reactions to rAvPAL-PEG ...................36 
9.1.2 Dose Modifications..........................................................................................41 
9.1.3 Stopping Criteria..............................................................................................42 
9.2 Discussion of Study Design, Including Choice of Control Group .......................... 43 
9.3 Selection of Study Population ................................................................................. 43 
9.3.1 Inclusion Criteria .............................................................................................43 
9.3.2 Exclusion Criteria ............................................................................................43 
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9.3.3 Removal of Subjects from Treatment or Assessment......................................44 
9.3.4 Subject Identification and Replacement of Subjects .......................................45 
9.4 Treatments ............................................................................................................... 46 
9.4.1 Treatments Administered.................................................................................46 
9.4.2 Identity of Investigational Product (IP) ...........................................................46 
9.4.3 Storage .............................................................................................................46 
9.4.4 Directions for Administration..........................................................................46 
9.4.5 Method of Assigning Subjects to Treatment Groups.......................................48 
9.4.6 Selection of Doses Used in the Study..............................................................48 
9.4.7 Blinding............................................................................................................49 
9.4.8 Prior and Concomitant Medications ................................................................49 
9.4.9 Treatment Compliance.....................................................................................50 
9.5 Investigational Product Accountability ................................................................... 50 
9.5.1 Return and Disposition of Clinical Supplies....................................................50 
9.6 Dietary or Other Protocol Restrictions .................................................................... 50 
9.7 Efficacy and Safety Variables.................................................................................. 51 
9.7.1 Efficacy and Safety Measurements Assessed..................................................51 
9.7.2 Efficacy Variable .............................................................................................52 
9.7.3 Pharmacokinetic Variables ..............................................................................52 
9.7.4 Safety Variables...............................................................................................53 
9.7.5 Clinical Laboratory Assessments.....................................................................53 
10 REPORTING ADVERSE EVENTS .................................................................................56 
10.1 Adverse Events ........................................................................................................ 56 
10.2 Serious Adverse Events ........................................................................................... 59 
10.3 Pregnancy................................................................................................................. 60 
10.4 BioMarin Pharmacovigilance Contact Information................................................. 60 
11 APPROPRIATENESS OF MEASUREMENTS...............................................................61 
11.1 Safety and Pharmacokinetics................................................................................... 61 
12 STUDY PROCEDURES ...................................................................................................61 
12.1 Prestudy ................................................................................................................... 61 
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12.2 Screening Visit......................................................................................................... 61 
12.3 Treatment Period...................................................................................................... 62 
12.3.1 Day 1 (Week 1)................................................................................................62 
12.3.2 Weekly Visits...................................................................................................63 
12.3.3 Monthly Visits (Week 4, 8, 12, etc).................................................................63 
12.3.4 Quarterly Visits (Week 12, 24, 36, etc) ...........................................................65 
12.3.5 Interim Dosing Visit ........................................................................................66 
12.3.6 Unscheduled Hypersensitivity Reaction Visit .................................................66 
12.4 Early Termination Visit ........................................................................................... 68 
12.5 Final Follow-up Visit............................................................................................... 69 
13 DATA QUALITY ASSURANCE.....................................................................................70 
14 STATISTICAL METHODS AND DETERMINATION OF SAMPLE SIZE..................71 
14.1 Statistical and Analytical Plans ............................................................................... 71 
14.2 Safety Analysis ........................................................................................................ 71 
14.3 Pharmacokinetic Analysis........................................................................................ 71 
14.4 Efficacy Analysis..................................................................................................... 71 
14.5 Determination of Sample Size................................................................................. 72 
14.6 Handling of Missing Data........................................................................................ 72 
14.7 Interim Analyses...................................................................................................... 72 
14.8 Changes in the Conduct of the Study or Planned Analyses..................................... 72 
15 DATA MONITORING COMMITTEE (DMC) ................................................................74 
16 COMPENSATION, INSURANCE, AND INDEMNITY.................................................75 
17 CASE REPORT FORMS AND SOURCE DOCUMENTS..............................................76 
18 STUDY MONITORING AND AUDITING .....................................................................78 
19 RETENTION OF RECORDS............................................................................................79 
20 USE OF INFORMATION AND PUBLICATION............................................................80 
21 REFERENCES ..................................................................................................................81 
22 INVESTIGATOR RESPONSIBILITIES..........................................................................83 
22.1 Conduct of Study and Protection of Human Subjects ............................................. 83 
23 SIGNATURE PAGE .........................................................................................................84 
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4 
LIST OF ABBREVIATIONS AND DEFINITIONS OF TERMS 
Abbreviations 
ADR 
adverse drug reaction 
AE 
adverse event 
ALT 
alanine aminotransferase 
AST 
aspartate aminotransferase 
AUC 
area under the plasma concentration-time curve 
AUC0-7 days
area under the plasma concentration-time curve from time zero on Day 1 
to Day 8 
BUN 
blood urea nitrogen 
°C 
degree Celsius 
CBC 
complete blood count 
CD 
Compact disk 
CFR 
Code of Federal Regulations 
CH50 
total hemolytic complement 
Cmax
maximum plasma concentration 
CNS 
central nervous system 
CO2
carbon dioxide 
CRA 
Clinical Research Associate 
CRF 
case report form 
CRP 
C-reactive protein 
CTCAE 
Common Terminology Criteria for Adverse Events 
CV 
cardiovascular 
DBP 
diastolic blood pressure 
DMC 
Data Monitoring Committee 
ECG 
electrocardiogram 
ETV 
Early Termination Visit 
FDA 
Food and Drug Administration 
F/U 
follow-up 
g 
gram 
GCP 
Good Clinical Practice 
GGT 
gamma-glutamyltransferase 
GI 
gastrointestinal 
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IB 
Investigator’s Brochure 
ICF 
Informed Consent Form 
ICH 
International Conference on Harmonisation of Technical Requirements for 
Registration of Pharmaceuticals for Human Use 
IgE 
immunoglobulin E 
IgG 
immunoglobulin G 
IgM 
immunoglobulin M 
IP 
investigational product 
IRB 
Institutional Review Board 
IV 
intravenous 
kg 
kilogram 
MedDRA 
Medical Dictionary for Regulatory Activities 
mg 
milligram 
mL 
milliliter 
mm Hg 
millimeter of mercury 
NAb 
neutralizing antibodies 
NCI 
National Cancer Institute 
NOAEL 
no observable adverse effect level 
OTC 
over the counter 
PAH 
phenylalanine hydroxylase 
PAL 
phenylalanine ammonia lyase 
PEG 
polyethylene glycol 
Phe 
phenylalanine 
PI 
Principal Investigator 
PK 
pharmacokinetics 
PKU 
phenylketonuria 
rAvPAL-PEG rAv phenylalanine ammonia lyase-PEG 
RBC 
red blood cell 
SAE 
serious adverse event 
SAP 
Statistical Analysis Plan 
SBP 
systolic blood pressure 
SC 
subcutaneous 
SD 
standard deviation 
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SDV 
source data verified 
SGOT 
serum glutamic oxalo-acetic transaminase 
SGPT 
serum glutamic pyruvate transaminase 
US 
United States 
WBC 
white blood cell 
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Definition of Terms: 
Investigational Product (IP): 
“A pharmaceutical form of an active ingredient or placebo being tested or used as a reference 
in a clinical trial, including a product with a marketing authorization when used or assembled 
(formulated or packaged) in a way different from the approved form, or when used for an 
unapproved indication, or when used to gain further information about an approved use.” 
(from E6 ICH)  
The terms “IP” and “study drug” may be used interchangeably in the protocol. 
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5 
ETHICS 
5.1 
Institutional Review Board or Ethics Committee 
Prior to initiating the study, the Investigator will obtain written confirmation that the 
Institutional Review Board (IRB) is properly constituted and compliant with International 
Conference on Harmonisation of Technical Requirements for Registration of 
Pharmaceuticals for Human Use (ICH) and Good Clinical Practice (GCP) requirements, and 
applicable laws and local regulations. A copy of the confirmation from the IRB will be 
provided to BioMarin Pharmaceutical Inc. (BioMarin) or its designee. The Principal 
Investigator (PI) will provide the IRB with all appropriate material, including the protocol, 
Investigator’s Brochure (IB), the Informed Consent Form (ICF) including compensation 
procedures, and any other written information provided to the subjects, including all consent 
forms translated to a language other than the native language of the clinical site. The study 
will not be initiated and investigational product (IP) supplies will not be shipped to the site 
until appropriate documents from the IRB confirming unconditional approval of the protocol, 
the ICF and all subject recruitment materials are obtained in writing by the PI and copies are 
received at BioMarin or its designee. The approval document should refer to the study by 
protocol title and BioMarin protocol number (if possible), identify the documents reviewed, 
and include the date of the review and approval. BioMarin will ensure that the appropriate 
reports on the progress of the study were made to the IRB and BioMarin by the PI in 
accordance with applicable governmental regulations. 
5.2 
Ethical Conduct of Study 
This study will be conducted in accordance with the following: 
• 
United States (US) Code of Federal Regulations (CFR) sections that address clinical 
research studies, and/or other national and local regulations, as applicable 
• 
E6 ICH Guideline for GCP 
• 
The ethical principles established by the Declaration of Helsinki 
Specifically, this study is based on adequately performed laboratory and animal 
experimentation; the study will be conducted under a protocol reviewed and approved by an 
IRB; the study will be conducted by scientifically and medically qualified persons; the 
benefits of the study are in proportion to the risks; the rights and welfare of the subjects will 
be respected; the physicians conducting the study do not find the hazards to outweigh the 
potential benefits; and each subject, or his or her legally authorized representative will 
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provide written, informed consent before any study-related tests or evaluations are 
performed. 
5.3 
Subject Information and Informed Consent 
A properly written and executed ICF, in compliance with the Declaration of Helsinki, 
E6 ICH (GCP Guideline, Section 4.8) and 21 CFR §50 and other applicable local regulations, 
will be obtained for each subject prior to entering the subject into the study. The Investigator 
will prepare the ICF and provide the documents to BioMarin for approval prior to submission 
to the IRB. BioMarin and the IRB must approve the documents before they are implemented. 
A copy of the approved ICF, and if applicable, a copy of the approved subject information 
sheet, minor assent form, parental ICF for studies involving minors, and all ICFs translated to 
a language other than the native language of the clinical site must also be received by 
BioMarin or its designee prior to the delivery of study drug. 
Subjects under the age of 18 years will provide written assent (if required), and his/her 
legally authorized representative (parent or legal guardian) will provide written informed 
consent for such subjects. The Investigator will provide copies of the signed ICF to each 
subject (or the subject’s legally authorized representative) and will maintain the original in 
the subject’s record file. 
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6 
INVESTIGATORS AND STUDY ADMINISTRATIVE STRUCTURE 
Prior to beginning the study, the PI at each site must provide to BioMarin or its designee a 
fully executed and signed Form FDA (Food and Drug Administration) 1572 and a Financial 
Disclosure Form. All sub-Investigators must be listed on Form FDA 1572. Financial 
Disclosure Forms must also be completed for all sub-Investigators listed on the 
Form FDA 1572 who will be directly involved in the treatment or evaluation of research 
subjects in this study. 
The study will be administered by and monitored by employees or representatives of 
BioMarin. Clinical Research Associates (CRAs) or trained designees will monitor each site 
on a periodic basis and perform verification of source documentation for each subject as well 
as other required review processes. BioMarin’s Regulatory Affairs Department (or designee) 
will be responsible for the timely reporting of serious adverse events (SAEs) to appropriate 
regulatory authorities as required. Some study assessments, including administration of 
study drug, may be performed at the subject’s home. All assessments performed for 
this study will be administered by clinic staff or other qualified and trained study 
personnel. 
Prior to database lock in multicenter studies, a Coordinating Investigator will be identified 
who will read the clinical study report and confirm that it accurately describes the conduct 
and results of the study, to the best of his or her knowledge. The Coordinating Investigator 
will be chosen on the basis of active participation in the study, ability to interpret data, and 
willingness to review and sign the report in a specified timeframe. 
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7 
INTRODUCTION 
A comprehensive review of phenylalanine ammonia lyase ( rAvPAL-PEG) is contained in 
the IB supplied by BioMarin; the Investigator should review this document prior to initiating 
this study. 
7.1 
Nonclinical Studies 
The murine model of phenylketonuria (PKU) BTBRPahenu2 (ENU2), a mouse line that is 
deficient in phenylalanine hydroxylase (PAH) activity (Shedlovsky, 1993, Genetics), was 
used for in vivo screening and pharmacodynamic studies. This mouse model exhibits 
characteristics similar to those seen in PKU patients, including hyperphenylalaninemia 
(baseline plasma phenylalanine [Phe] concentrations of 1000 to 2000 µM) and 
hypopigmentation. Weekly subcutaneous (SC) administration of 80 mg/kg of rAvPAL-PEG 
(approximately 4 IU/mouse) for greater than 2 to 3 months lowered and stabilized plasma 
Phe concentration from approximately 2000 µM to less than 200 µM. A similar profile of 
Phe reduction was also seen in ENU2 mice administered wild-type AvPAL-PEG 
(4 IU/mouse) over 8 weeks. In all these studies, regardless of the molecule, an attenuated 
Phe-lowering response was usually seen between Weeks 2 and 7. However, plasma Phe 
concentrations became stable at concentrations below 200 µM from Week 7 onward. 
In addition to the reduction of plasma Phe, a dose-related darkening in coat color occurred, 
indicating the biosynthesis of melanin, which was previously inhibited when plasma Phe 
could not be metabolized and plasma Phe concentrations were high. When administration of 
AvPAL-PEG was stopped for 2 to 7 weeks and then reinitiated with weekly administrations, 
no attenuated response was observed and Phe concentrations remained low and stable until 
the next administration. 
The safety of rAvPAL-PEG was evaluated in safety pharmacology studies (respiratory, 
central nervous system [CNS] and cardiovascular [CV]) and toxicity with toxicokinetic 
studies (single and 28-day repeated dose) in rats and cynomolgus monkeys. Overall, in the 
nonclinical studies, no anaphylactoid-like reactions or injection-site reactions were 
noted. No specific polyethylene glycol (PEG)-related histological findings were observed 
during the 28-day repeated dose studies. 
Findings in cynomolgus monkeys dosed with a single administration of 
60 mg/kg rAvPAL-PEG included reduced food consumption, dehydration, body weight loss, 
hypoactivity, hypothermia,decreased plasma Phe concentration, decreased protein synthesis, 
and gastrointestinal (GI) lesions. Plasma Phe concentrations were also reduced to below the 
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level of detection in the 4 and 12 mg/kg dose groups, but without similar toxicological 
consequences, implying that the physiological regulation of Phe levels may be an important 
factor for influencing morbidity.  
The main finding in the 28-day study was the possible drug-related observation of minimal to 
slight degeneration of blood vessels of predominantly medium-sized muscular arteries with a 
non-dose-dependent involvement of different organs observed in 1 male in the 0.1 mg/kg and 
1 male and 1 female in the 1.0 mg/kg rAvPAL-PEG dose groups. No degeneration of the 
arteries was observed in either the control or animals administered 0.01 mg/kg 
rAvPAL-PEG. 
The half-life of rAvPAL-PEG administered to normal rats at SC doses of 10, 25, and 
250 mg/kg, was 47, 33, and 44 hours, respectively, and exhibited modest area under the 
plasma concentration-time curve (AUC)-dose linearity. In the cynomolgus monkey after SC 
administration of rAvPAL-PEG, the half-life was 65 hours at 4 mg/kg, 71 hours at 12 mg/kg, 
and could not be determined at 60 mg/kg (the highest dose). Qualitatively, the kinetics of 
rAvPAL-PEG in the rat and monkey appear to have similar characteristics. The following 
findings were noted: (1) a 1-compartment model with first-order absorption appears to 
describe the plasma profiles of rAvPAL-PEG after single-dose administration, (2) absorption 
is slow and there is a long absorption period after SC administration to maximum plasma 
concentration, along with a long half-life, (3) elimination is slow and monophasic, (4) there 
does not appear to be a gender difference, and (5) AUC and the maximum plasma 
concentration (Cmax) are roughly linearly proportional. 
Chronic repeat-dose toxicity and toxicokinetic studies were conducted in the rat 
(17/26 weeks) and monkey (39 weeks). In the 26-week study of rats, weight loss was 
observed in the rats given 25 mg/kg/dose of rAvPAL-PEG, SC; corresponding 
decreased food consumption was observed in the males. The main histological finding 
was focal-to-multifocal areas of vacuolar degeneration of renal tubule cells in the 
kidney of 3 males given 25 mg/kg and 3 females given  ≥ 8 mg/kg rAvPAL-PEG. 
This renal tubule finding persisted in the kidney of both sexes given  ≥ 8 mg/kg/dose at 
the end of the 12-week recovery phase without evidence of reversibility. Increased 
vacuolation was observed in histiocytic cells of the liver, spleen, mesenteric lymph node, 
mandibular lymph node, and adrenal cortex of males given 25 mg/kg/dose and females 
given  ≥ 8 mg/kg/dose; vacuolation of histiocytic cells in the testes were also observed in 
males given 25 mg/kg/dose. Both renal tubule vacuolation and histiocytic cell vacuoles 
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have been associated with PEG-related catabolism and administration of other 
PEGylated proteins. 
In the 39-week, chronic repeat-dose toxicity and toxicokinetic study in monkeys, dose 
levels of 7.0 and 5.0 mg/kg/dose rAvPAL-PEG were not tolerated in female monkeys 
and resulted in body weight loss, decreased food consumption, and hypoactivity. 
The only adverse microscopic finding was arterial inflammation of small and mid-sized 
arteries in multiple organs and/or tissues in most animals that were given  ≥ 3 
mg/kg/dose rAvPAL-PEG SC twice weekly at the end of the dosing phase. The 
inter-individual organ involvement was highly variable; some animals had findings in 
one organ and others had multiple organs with arterial inflammation. Additionally, not 
all arteries had signs of inflammation and arterial inflammation was resolved by the 
end of the 13-week recovery period. A full analysis of these findings including the 
involvement of the anti-drug antibodies, antibody isotypes, PEG distribution, and 
rAvPAL-PEG is ongoing. The no observable adverse effect level (NOAEL) for the 
17-week and 39-week studies, in rat and monkey, respectively, is 1 mg/kg/dose.  
The NOAEL from these studies represents greater than a 100-fold safety factor over the 
starting dose in PAL-002. 
7.2 
Previous Clinical Studies 
This study is an extension of the second human clinical study with rAvPAL-PEG 
(Study PAL-002). Study PAL-001, the first-in-human clinical study of rAvPAL–PEG, was 
designed as a Phase 1, open-label, single-dose, dose-escalation study in 25 subjects, 16 to 
50 years old, with PKU. The doses for this study are based on data from nonclinical 
studies and PAL-001 and are 0.001 through 1.0 mg/kg per injection (not to exceed 
2.0 mg/kg/week, provided no dose-limiting toxicity was observed in Study PAL-002. 
7.3 
Study Rationale 
PKU is an autosomal, recessive, inherited disease characterized by deficiency in the enzyme 
PAH (Scriver CR, 2001, McGraw-Hill). Approximately 1 in every 10,000 infants in North 
America is born with PKU (Scriver CR, 2001, McGraw-Hill). Left untreated, PAH 
deficiency is associated with an abnormally elevated concentration of Phe, which is toxic to 
the brain (Kaufman, 1989, J Pediatr.) and can result in a variety of neuropathologic 
conditions, including mental retardation, microcephaly, delayed speech, seizures, and 
behavioral abnormalities (Scriver CR, 2001, McGraw-Hill). The brains of untreated patients 
with PKU show evidence of hypomyelination and gliosis, arrest in cerebral development, 
and, in some cases, white matter degeneration (Huttenlocher, 2000, Eur.J Pediatr.). Elevated 
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Phe during fetal development leads to severe mental retardation and can cause microcephaly, 
growth retardation, and congenital heart disease (Guttler, 2003, Pediatrics), (Koch, 2003, 
Pediatrics), (Lee, 2003, Pediatrics), (Levy, 2003, Pediatrics), (Matalon, 2003, Pediatrics), 
(Rouse, 2004, J.Pediatr.). 
For a subset of patients with residual enzyme activity, treatment with Kuvan® is an option. 
For all other patients, current management of PKU involves adherence to low-Phe medicinal 
diet formulas and dietary restriction of Phe-containing foods. Implementation of a 
Phe-restricted diet in infancy significantly reduces blood Phe concentrations and prevents 
many of the neuropathologic manifestations of PKU, including severe mental retardation. 
However, compliance with this restrictive diet can be difficult for older children, adolescents, 
and adults, and adherence may result in nutritional deficiencies due to the limitations of 
natural protein sources (Fisch, 2000, Eur.J.Pediatr.), (Walter, 2002, Lancet). 
The need exists for a treatment that will help individuals with PKU safely achieve lifelong, 
reliable control of blood phenylalanine (Phe) concentrations and improve functional 
outcomes. Phenylalanine ammonia lyase (rAvPAL-PEG) is a potential substitute for the 
phenylalanine hydroxylase (PAH) enzyme, which is defective in individuals with PKU. 
rAvPAL-PEG may control blood Phe concentrations, which may have additional clinical 
benefits. This study is an extension of the dose-finding study (PAL-002). Administration of 
rAvPAL-PEG will be continued to assess whether long-term dosing of rAvPAL-PEG is safe 
and can maintain reduced blood Phe concentrations in PKU subjects. 
7.4 
Summary of Overall Risks and Benefits 
It is not expected that data from PAL-002 will change the assumption that rAvPAL-PEG has 
a toxicity profile similar to other recombinant PEGylated non-human enzymes currently in 
use. The toxicities of these drugs usually fall into 2 main categories: toxicity due to exposure 
to PEG, and toxicity due to immunologic sensitization. In addition, exaggerated 
pharmacological effects resulting in very low Phe concentrations could be observed. 
Other adverse events (AEs) that could occur with rAvPAL-PEG include injection-site 
reactions and other general symptoms. 
7.4.1 Toxicity Due to Exposure to PEG 
Acute exposure to high doses of PEG can result in renal toxicity. There have been a few 
reports of PEG-related AEs in humans; cumulative intravenous (IV) PEG doses of 121 to 
240 g caused acute renal tubular necrosis, oliguria, and azotemia. The anticipated PEG 
exposure associated with the expected rAvPAL-PEG dose range (6 g per week) is at least 
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80-fold lower than the reported toxic doses and comparable to exposures to PEG in widely 
used medicines and other compounds that are administered by the IV, oral, rectal, and topical 
routes (Webster, 2007, Drug Metab Dispos.). No indication of PEG-related toxicity at the 
ultrastructural level was observed in monkeys given a single dose of up to 60 mg/kg 
rAvPAL-PEG SC. 
In this study, subjects will be monitored closely with urine examinations and blood 
chemistries to follow kidney function. 
7.4.2 Toxicity Due to an Immunologic Reaction 
The active drug substance in rAvPAL-PEG is a bacterial protein, and as such, it is expected 
that it may elicit immune recognition and responses. Epitopes that play a role in the immune 
response may be rendered inaccessible by PEG (Gamez, 2007, Mol.Genet.Metab). In vivo 
and in vitro experiments have shown that PEGylation of proteins and cells can attenuate the 
immunological response (Scott, 1997, Proc.Natl.Acad.Sci.U.S.A), (Chen, 2001, BioDrugs.). 
PEGylation has been effective in reducing anti-rAvPAL antibody titers in the mouse model, 
although PEGylation does not eliminate antibody formation. Although PEGylation of 
rAvPAL may have a significant effect on reducing the immunogenicity of the molecule, it is 
reasonable to expect that some individuals may exhibit immune responses upon exposure to 
the drug. These immune responses may be clinically irrelevant, cause symptoms of various 
degrees, or lead to neutralization of biological activity. Subjects participating in clinical trials 
will be monitored closely with specific antibody titers, sedimentation rates, and complete 
blood counts (CBCs). 
PEG itself is considered nonimmunogenic (Davis, 1981, Clin.Exp.Immunol.) (Harris, 2003, 
Nat.Rev.Drug Discov.), however, antibodies against PEG may form when PEG is bound to 
compounds. (Harris, 2003, Nat.Rev.Drug.Discov.) (Richter, 1983, Int.Arch.Allergy 
Appl.Immunol.) In some instances, development of such antibodies did not result in any 
significant clinical effects in humans (Richter, 1984, Int.Arch.Allergy Appl.Immunol.). 
In some individuals, anti-PEG antibodies may be pre-existing due to previous exposure to 
PEG in other products. Anti-PEG antibodies have been associated with nonresponsiveness 
against therapy (Armstrong, 2007, Cancer), (Ganson, 2006, Arthritis Res.Ther.). 
Administration of rAvPAL-PEG may lead to anti-PEG antibody formation, and the 
duration of this possible effect is not known. This may limit a subject’s future ability to 
be treated with other PEG-containing (eg, Depo-Provera) or PEGylated 
(eg, PEG-interferon) injectable drugs. It is therefore recommended that any 
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PEG-containing injectable drug administered to subjects after completion of this study 
be done under medical observation. 
7.4.2.1 
Systemic Skin Reactions 
Two subjects who were enrolled in Study PAL-001 and received the protocol-defined 
single dose of rAvPAL-PEG reported systemic skin reactions (generalized skin rash) 
that were attributed to treatment with study drug. One subject received a single dose of 
0.001 mg/kg rAvPAL-PEG, and the other subject received a single dose of 0.01 mg/kg 
rAvPAL-PEG. Both of these events were reported as serious and followed 
administration of Depo-Provera injections (medroxyprogesterone injection), an 
injectable contraception. These allergic reactions are thought to be related to the PEG 
molecules that are found in both the study drug, rAvPAL-PEG, and Depo-Provera. 
These reactions are not likely to be experienced concurrent with other birth control 
medications. 
The 2 subjects were administered study drug during PAL-001 and then experienced an 
allergic reaction following an injection of Depo-Provera. The symptoms of the reactions 
were hives on the arms and legs and difficulty breathing. The symptoms for both 
subjects resolved within 1 day following treatment with medication, including the 
). Both subjects were examined by an allergy 
specialist after they completed participation in PAL-001. A skin prick test with Depo-
Provera was administered as part of this examination. One subject had a mild allergic 
reaction to the test; however, no further reactions or complications were reported 
following subsequent administration of a full dose of Depo-Provera. The subject 
continues to receive regular doses (every 3 months) of Depo-Provera, and no further 
reactions have been reported to date (15OCT2009). The second subject also had a 
positive reaction to Depo-Provera following administration of the skin prick test. When 
a subsequent full dose of Depo-Provera was administered, 
 developed hives, itching, 
and chills. The subject’s symptoms resolved within 1 day of taking medication 
prescribed by an allergist. 
The active drug substance in rAvPAL-PEG is a bacterial protein that may elicit 
immune responses, such as urticaria, bronchospasm, itching, anaphylaxis, and others. 
It is possible that the physio-chemical properties of rAvPAL-PEG may induce 
immunologic sensitization to the protein rAvPAL and to PEG. Although results from 
nonclincal studies of rAvPAL-PEG conducted in rats and cynomolgus monkeys did not 
indicate signs of immune-mediated toxicities, it is possible that the physio-chemical 
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properties of rAvPAL-PEG may induce immunologic sensitization to the protein 
rAvPAL and to PEG in humans.  It is currently unknown whether administration of 
PEG-containing drugs, such as Depo-Provera, has a sensitizing effect to PEG in 
rAvPAL-PEG when administered in humans. Because the exact basis for these reported 
events and their duration is not known, the use of PEG-containing injectable drugs prior to, 
during, and after this study is prohibited as a precautionary measure (refer to Sections 9.3.2 
and Section 9.4.8.). 
7.4.2.2 
Management of Allergic Reactions 
Allergic reactions to the SC injection of rAvPAL-PEG may be mild, moderate, or severe in 
intensity. Reactions may include pruritus, rash, shortness of breath, hypotension, or 
anaphylaxis. Clinical assessments should be conducted for a minimum of 2 hours 
post-injection. Longer observations may be required at the discretion of the PI. 
The responsible physician should use all appropriate measures for the treatment of allergic 
reactions. Because of the small potential for anaphylaxis, equipment for emergency 
resuscitation (including epinephrine) should be within easy access during and after the 
rAvPAL-PEG injection. 
In the event of an allergic reaction, subjects may be asked to see an allergist/immunologist 
and/or provide up to 3 additional blood samples for antibody testing. This additional testing 
may occur up to 6 months following the final study visit. 
The following measures are recommended for the treatment of allergic symptoms: 
• 
Clearing the airway. 
• 
Vital sign check. 
• 
Administration of oral or IV diphenhydramine. 
• 
Administration of epinephrine if appropriate. 
• 
Administration of oxygen and IV fluids. 
• 
Administration of additional symptomatic treatment. 
• 
Transfer to an acute care facility of the study center. 
In addition, clinical judgment must be used in determining the appropriateness of 
corticosteroid administration. Acetaminophen or ibuprofen (5-10 mg/kg) may also be 
administered. An allergy and/or immunology consultation should be sought if necessary. 
Information regarding the management of local skin, large local skin, and systemic 
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reactions is provided in Section 9.1.1. Detailed instructions for the management of 
allergic reactions are provided in the Study Reference Manual. 
7.4.3 Effects of Low Blood Phe 
Insufficient Phe intake or excessive rAvPAL-PEG exposure may cause blood Phe 
concentrations to be too low (eg, < 30 µmol/L). Prolonged low blood Phe concentrations can 
result in a catabolic state associated with poor growth and altered body functions, including 
mental and physical alterations, loss of appetite, anemia, rashes, and diarrhea. To ensure 
safety during this study, subjects will be monitored closely with frequent blood Phe 
concentration determinations. If a subject’s blood Phe concentration is too low, the 
subject’s diet, current dose of study drug, or both may be adjusted. 
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8 
STUDY OBJECTIVES 
The primary objective of the study is: 
• 
To evaluate the effect of long-term administration of multiple doses of SC injections 
of rAvPAL-PEG on blood Phe concentrations in subjects with PKU. 
The secondary objectives of the study are: 
• 
To evaluate the safety and tolerability of long-term administration of subcutaneous 
(SC) injections of rAvPAL-PEG in subjects with PKU. 
• 
To evaluate the immune response to long-term administration of SC injections of 
rAvPAL-PEG in subjects with PKU. 
• 
To evaluate steady-state PK of rAvPAL-PEG in subjects with PKU. 
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9 
INVESTIGATIONAL PLAN 
9.1 
Overall Study Design and Plan 
This is a long-term extension of a Phase 2, open-label, dose-finding study (PAL-002) in 
35-50 subjects with PKU. The doses are planned to be in the same range as those tested in 
PAL-002 (0.001 through 1.0 mg/kg per injection), provided no dose-limiting toxicity was 
observed in PAL-002. 
Only subjects who completed participation in PAL-002 will be enrolled into this study. 
Diet will not be altered during the course of this study, except as necessary for safety as 
determined by blood Phe concentrations. If a subject’s blood Phe concentration is 
 < 120 µmol/L, the subject’s diet may be adjusted to increase the amount of dietary Phe 
intake to maintain target blood Phe concentrations of 120-600 µmol/L. Changes to diet will 
be made per the discretion of the Investigator in consultation with the Sponsor’s 
Medical Officer. For information regarding changes to diet for safety and decreases in 
dose, refer to Section 9.1.2.2. 
Subjects will be evaluated for safety and for blood Phe concentrations throughout the study. 
Toxicity will be measured according to the National Cancer Institute (NCI) Common 
Terminology Criteria for Adverse Events (CTCAE), version 3. 
At least one interim analysis may be performed by the sponsor during the study. 
In addition to the Sponsor, a Data Monitoring Committee (DMC) will monitor the safety 
of subjects in the study. The DMC is an independent committee that will act in an 
advisory capacity to the Sponsor. 
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take 
rAvPAL-PEG. PAL-002 subjects’ rAvPAL-PEG dosing will continue in PAL-003 without 
interruption of dosing. In PAL-003, each subject’s dose will be adjusted as needed to attain 
or maintain blood Phe concentrations of 120-600 µmol/L. Doses will be evaluated on an 
individual basis.  
Evaluations, observations, and procedures will be conducted at selected time points as shown 
in Table 2.1.1, Schedule of Events. After the subject’s blood Phe concentration has been 
controlled to within a target range (120-600 µmol/L), the subject may be asked to have 
additional blood draws for PK and blood Phe concentration analyses as needed but not to 
exceed 3x/week (fingerstick tests may be performed more frequently). 
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A subject will continue in PAL-003 until one of the following occurs: 
1. The subject withdraws consent and discontinues from the study. 
2. The subject is discontinued from the study at the discretion of the Investigator. 
3. The subject has completed the study through the Month 24 visit. 
4. The study is terminated. 
9.1.1 Management of Local and Systemic Reactions to rAvPAL-PEG 
9.1.1.1 
Subjects Who Have Had Previous Hypersensitivity Reactions to 
rAvPAL-PEG or a PEG-containing Product 
Subjects who had a previous systemic reaction to rAvPAL-PEG or a PEG-containing product 
that warranted early termination from PAL-002 are excluded from participation in this 
study. Subjects who experienced a generalized skin rash are included in this category. 
Subjects who have had a previous local skin reaction to rAvPAL-PEG in PAL-002 are 
eligible to participate in this study. Subjects may develop systemic, large local skin, or 
local skin reactions after enrollment in PAL-003. Refer to Section 9.1.1.2 for definitions of 
systemic and local skin reactions. For management of hypersensitivity reactions that 
occur during this study, refer to Section 9.1.1.3 and Figure 9.1.1.3.1. 
9.1.1.2 
Definition of Hypersensitivity Reactions to rAvPAL-PEG Administered 
Subcutaneously 
During Study PAL-003, subjects may experience hypersensitivity reactions to 
rAvPAL-PEG. The hypersensitivity reactions are defined as follows: 
Local skin reaction: 
• Skin signs or symptoms in 1 affected primary location, ie, hives, wheals, or 
swelling or an area of erythema, redness, induration, pain, or itching at or near the 
site of injection. 
Large local skin reaction: 
• Skin signs or symptoms, ie, hives, wheals, or swelling or an area of erythema, 
redness, or induration with pain or itching that extends beyond the site of 
injection by approximately 6 inches (15 cm) and/or signs or symptoms that are 
not contiguous to the injection site. These may be associated with a low risk of 
systemic symptoms or anaphylaxis upon re-exposure and, therefore, will be 
managed as a systemic reaction when not contiguous to the injection site. 
Systemic reaction (including generalized skin symptoms): 
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9.1.1.3.1 Local Skin Reactions 
Subjects who have had a local skin reaction (refer to Section 9.1.1.2 for definition) after 
administration of rAvPAL-PEG in PAL-001, PAL-002, or this study may be premedicated 
with acetaminophen and antihistamines 1 hour prior to study drug dosing. Recommended 
premedications are acetaminophen and antihistamine (Zyrtec [cetirizine] is preferred). 
The dosage will be standard (eg, 1000 mg acetaminophen and 10 mg Zyrtec or 25 to 50 mg 
oral Benadryl [diphenahydramine]). Because Benadryl can cause drowsiness, it should be 
administered only if the subject is accompanied by a designated driver. 
Symptoms of local reactions may be treated with local application of ice and 
non-sedating oral and/or topical antihistamines and/or topical steroids (refer to 
Section 7.4.2.2). 
If the local skin reaction worsens with a repeat injection (as determined by the 
Investigator in consultation with the Study Medical Officer) even with premedication 
prior to study drug dosing, the subject must be withdrawn from the study and complete 
an Early Termination Visit. 
9.1.1.3.2 Large Local Skin Reactions 
Large local skin reactions (refer to Section 9.1.1.2 for a definition) may or may not be 
contiguous to the rAvPAL-PEG injection site. The location of the large local skin 
reaction relative to the rAvPAL-PEG injection site will determine if a subject may 
remain in the study and continue to be administered rAvPAL-PEG. An example of a 
large local reaction that is not contiguous to the injection site is if an injection took 
place in the right upper arm and there are lesions beyond the elbow joint in the right 
forearm or lesions beyond the shoulder joint on the right trunk.  
Subjects who have large local skin reactions that are contiguous to the injection site 
may remain in the study. Subjects who have large local skin reactions that are not 
contiguous to the injection site may have additional assessments performed 
(Unscheduled Hypersensitivity Reaction Visit) per Investigator discretion and must 
then be terminated from the study. A decision to terminate a subject from the study 
must be agreed to by both the Investigator and the Sponsor’s Medical Officer. 
9.1.1.3.2.1 
Large Local Skin Reactions Contiguous to Injection Site 
Subjects who develop a large local skin reaction contiguous to the injection site after 
administration of rAvPAL-PEG or to rAvPAL-PEG or a PEG-containing product may 
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remain in the study. Large local skin reactions that are contiguous to the injection site 
should be managed as local skin reactions (refer to Section 9.1.1.3.1). For the remainder 
of the study, subjects must be premedicated orally with acetaminophen and 
antihistamines 1 hour prior to study drug dosing. Recommended premedications are 
acetaminophen and antihistamine (Zyrtec [cetirizine] is preferred). The dosage will be 
standard (eg, 1000 mg acetaminophen and 10 mg Zyrtec or 25 to 50 mg Benadryl 
[diphenahydramine]). Because Benadryl can cause drowsiness, it may be administered 
only if the subject is accompanied by a designated driver.  
Symptoms of large local skin reactions may be treated with local application of ice and 
topical, oral, or IV antihistamines and/or steroids as needed (refer to Section 7.4.2.2).  
9.1.1.3.2.2 
Large Local Skin Reactions Not Contiguous to Injection Site 
Large local skin reactions that are not contiguous to the injection site may be associated 
with a low risk of systemic symptoms or anaphylaxis upon re-exposure to rAvPAL-PEG 
and, therefore, will be managed as a systemic reaction. Subjects who develop large local 
skin reactions that are not contiguous to the injection site after administration of 
rAvPAL-PEG or to rAvPAL-PEG or a PEG-containing product may not continue to 
participate in the study. Subjects may have additional assessments performed 
(ie, Unscheduled Hypersensitivity Skin Reaction Visit) immediately after the reaction 
(within 48 hours): serum anti-rAvPAL-PEG antibodies (anti-PAL immunoglobulin G 
[IgG], anti-PAL immunoglobulin M [IgM], anti-PEG IgG, anti-PEG IgM, anti-
rAvPAL-PEG neutralizing antibody, and anti-rAvPAL-PEG immunoglobulin E [IgE]); 
serum tryptase level; sedimentation rate; C-reactive protein (CRP), total hemolytic 
complement (CH50), and complements C1 and C4; and clinical laboratory tests 
(urinalysis, chemistry, hematology). Subjects will then be terminated from the study 
and should be scheduled to complete the Early Termination Visit (refer to Section 12.4).  
Symptoms of large local skin reactions may be treated with local application of ice and 
topical, oral, or IV antihistamines and/or steroids as needed (refer to Section 7.4.2.2). 
9.1.1.3.3 Systemic Reactions 
Subjects who experience a systemic reaction (refer to Section 9.1.1.2 for a definition) 
after administration of rAvPAL-PEG will be terminated from the study. Subjects who 
experience generalized skin symptoms are included in this category. Immediately after 
the systemic reaction (within 48 hours), subjects with generalized skin symptoms must 
have additional assessments performed for safety (ie, Unscheduled Hypersensitivity 
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Skin Reaction Visit): serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL 
IgM, anti-PEG IgG, anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibody, and 
anti-rAvPAL-PEG IgE); serum tryptase level (optional; it is recommended that this 
sample be drawn immediately after reaction); sedimentation rate; CRP, CH50, C1, and 
C4; and clinical laboratory tests (urinalysis, chemistry, hematology; refer to 
Figure 9.1.1.3.1). Subjects who have a systemic reaction without generalized skin 
symptoms may have these assessments performed per Investigator discretion. Subjects 
will then be terminated from the study and should be scheduled to complete the Early 
Termination Visit (refer to Section 12.4). 
9.1.2 Dose Modifications 
After any modifications (increases or decreases) to dose level or frequency, subjects 
should remain in the clinic for observation for at least 2 hours following the injection of 
study drug. The Investigator should remain at the site to assess the subject for safety. 
9.1.2.1 
Dose Increase Methodology 
Each subject’s dose may be modified based on the decision of the Investigator, in agreement 
with the Study Medical Officer. Decisions regarding dose increases will depend on blood 
Phe and drug concentrations. 
Depending upon the response to rAvPAL-PEG in PAL-002, an individual subject’s dose 
may be adjusted beginning on Day 1 of PAL-003 as follows: 
• 
The dose may be increased by increments of no more than 10-fold higher than the 
subject’s current dose. 
• 
When increasing the dose, a dose may be used that is between the dose levels (0.001, 
0.003, 0.01, 0.03, 0.06, 0.1, 0.3, 0.6, and 1.0 mg/kg) that were defined in the previous 
study (PAL-002). 
• 
The dose may be adjusted by increasing the frequency up to daily for a total weekly 
dose not to exceed 2.0 mg/kg, including subjects who receive more than 
1 dose/week. Subjects who increase their dose frequency should perform the 
Interim Dosing Visit assessments (refer to Section 12.3.5 and Table 2.1.2 and 
Table 2.1.3). 
• 
When a dose is increased (either by increasing the dose level or by increasing the 
frequency of dosing), the subject must remain in the clinic for a minimum of 2 hours 
following the first modified dose administration, and an Investigator will remain on 
site during this time. 
• 
Only 1 dose adjustment is allowed every 2 weeks. 
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• 
Blood Phe levels will be measured 3 days after each dose increase (fingerstick is 
acceptable); more frequent or daily blood Phe measurements may be performed. 
9.1.2.2 
Dose Decrease Methodology 
A subject’s diet should be assessed prior to any dose decreases. Changes to diet should 
only be made if blood Phe concentrations are  < 120 µmol/L. If a subject’s blood Phe 
level is  < 120 µmol/L, the subject’s dietary Phe intake should be increased to achieve a 
stable blood Phe concentration of 120-600 µmol/L. If the subject’s blood Phe level is 
 < 120 µmol/L despite a high Phe diet, the rAvPAL-PEG dose will then be decreased. 
The subject will be asked about any changes to diet prior to any dose adjustments, and 
any changes to diet should be made per the discretion of the Investigator in consultation 
with the Sponsor’s Medical Officer. 
All dose decreases must be agreed to by both the Investigator and the Sponsor’s 
Medical Officer. Decisions regarding dose decreases will depend on available 
information regarding a subject’s blood Phe ( > 30% change from baseline) and drug 
concentrations, as well as toxicity (any hypersensitivity reaction as defined in 
Section 9.1.1.2). Dose decreases may occur for safety (ie, blood Phe concentration 
 < 120 µmol/L) or other toxicity that may be improved with a lower, more frequent dose. 
A dose should first be reduced by dose level (1.0, 0.6, 0.3, 0.1, 0.06, 0.03, 0.01, 0.003, 
0.001 mg/kg). It is also permitted to decrease dose in between these specified dose levels. 
If further dosing adjustments are required to attain the target Phe concentration, 
dosing frequency may be reduced.  
9.1.3 Stopping Criteria 
If an individual subject exhibits toxicity of a treatment-emergent CTCAE grade 3 or 
greater, that subject will have dosing halted until the toxicity resolves. The subject’s data will 
be evaluated by the Principle Investigator (PI) and the Study Medical Officer, and a decision 
will then be made whether to discontinue the subject from the study, restart dosing at the 
same dose level, or restart dosing at a lower dose level. 
In addition, if 2 or more subjects at a dose level exhibit toxicity of a treatment-emergent 
CTCAE grade 3 or greater, further dosing of subjects at that dose level will be halted and no 
subject will be treated at a higher dose level until a safety assessment is completed. 
In addition, the Food and Drug Administration (FDA) will be notified of this 
occurrence. 
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9.2 
Discussion of Study Design, Including Choice of Control Group 
This open-label, Phase 2 trial was designed to be closely monitored with the goal of 
obtaining information about the efficacy, safety, tolerability, and PK of long-term 
administration of rAvPAL-PEG in subjects with PKU. There will be no control group in this 
study. 
9.3 
Selection of Study Population 
9.3.1 Inclusion Criteria 
Individuals eligible to participate in this study must meet all of the following criteria: 
1. Must have completed participation in PAL-002. 
2. Willing and able to provide written, signed informed consent, or in the case of 
subjects under the age of 18 years, provide written assent (if required) and written 
informed consent by a parent or legal guardian, after the nature of the study has been 
explained, and prior to any research-related procedures. 
3. Willing and able to comply with all study procedures. 
4. Females of childbearing potential must have a negative pregnancy test at Screening 
and be willing to have additional pregnancy tests during the study. Females 
considered not of childbearing potential include those who have been in menopause at 
least 2 years, or had tubal ligation at least 1 year prior to Screening, or who have had 
total hysterectomy. 
5. Sexually active subjects must be willing to use an acceptable method of contraception 
while participating in the study. 
6. Maintained a stable diet. 
7. In generally good health as evidenced by physical examination, clinical laboratory 
evaluations (hematology, chemistry, and urinalysis), and electrocardiogram (ECG) at 
Screening. 
9.3.2 Exclusion Criteria 
Individuals who meet any of the following exclusion criteria will not be eligible to participate 
in the study: 
1. Use of any investigational product (with the exception of rAvPAL-PEG) or 
investigational medical device within 30 days prior to Screening, or requirement for 
any investigational agent prior to completion of all scheduled study assessments. 
2. Use of any medication that is intended to treat PKU within 14 days prior to the 
administration of study drug. 
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3. Use or planned use of any injectable drugs containing PEG (other than 
rAvPAL-PEG), including Depo-Provera, during study participation. 
4. A prior reaction that included systemic symptoms (eg, generalized hives, respiratory 
or gastrointestinal problems, hypotension, angioedema, anaphylaxis) to rAvPAL-PEG 
or a PEG-containing product. 
5. Pregnant or breastfeeding at Screening or planning to become pregnant (self or 
partner) or to breastfeed at any time during the study. 
6. Concurrent disease or condition that would interfere with study participation or safety 
(eg, history or presence of clinically significant cardiovascular, pulmonary, hepatic, 
renal, hematologic, gastrointestinal, endocrine, immunologic, dermatologic, 
neurological, oncologic, or psychiatric disease). 
7. Any condition that, in the view of the PI, places the subject at high risk of poor 
treatment compliance or of not completing the study. 
8. Known hypersensitivity to rAvPAL-PEG or its excipients, including hypersensitivity 
reactions that necessitated early termination from PAL-002. 
9. Alanine aminotransferase (ALT) concentration > 2 times the upper limit of normal. 
10. Creatinine > 1.5 times the upper limit of normal. 
9.3.3 Removal of Subjects from Treatment or Assessment 
Subjects (or their legally authorized representative) may withdraw their consent to participate 
in the study at any time without prejudice. The Investigator must withdraw from the study 
any subject who requests to be withdrawn. A subject’s participation in the study may be 
discontinued at any time at the discretion of the Investigator and in accordance with his/her 
clinical judgment. When possible, the tests and evaluations listed for the Early Termination 
Visit should be carried out (refer to Section 12.4). 
BioMarin must be notified of all subject withdrawals as soon as possible. BioMarin also 
reserves the right to discontinue the study at any time for either clinical or administrative 
reasons and to discontinue participation by an individual Investigator or site for poor 
enrollment or noncompliance. 
Reasons for which the Investigator or BioMarin may withdraw a subject from the study 
include, but are not limited to, the following: 
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• 
Subject experiences a serious or intolerable adverse event (AE). 
• 
Subject develops a clinically significant laboratory abnormality. 
• 
Subject requires medication prohibited by the protocol. 
• 
Subject does not adhere to study requirements specified in the protocol. 
• 
Subject was erroneously admitted into the study or does not meet entry criteria. 
• 
Subject is lost to follow-up. 
• 
Subject becomes pregnant (refer to Section 10.3 for details on the reporting 
procedures to follow in the event of pregnancy). 
If a subject fails to return for scheduled visits, a documented effort must be made to 
determine the reason. If the subject cannot be reached by telephone within 7 days, a certified 
letter should be sent to the subject (or the subject’s legally authorized representative, if 
appropriate) requesting contact with the Investigator. This information should be recorded in 
the study records. 
The Investigator or designee must explain to each subject, before enrollment into the study, 
that for evaluation of study results, the subject’s protected health information obtained during 
the study may be shared with the study sponsor, regulatory agencies, and IRB. It is the 
Investigator’s (or designee’s) responsibility to obtain written permission to use protected 
health information per country-specific regulations, such as the Health Insurance Portability 
and Accountability Act (HIPAA) in the United States, from each subject, or if appropriate, 
the subject’s legally authorized representative. If permission to use protected health 
information is withdrawn, it is the Investigator’s responsibility to obtain a written request, to 
ensure that no further data will be collected from the subject and the subject will be removed 
from the study. 
9.3.4 Subject Identification and Replacement of Subjects 
Subjects will retain the same subject number assigned in PAL-002. This unique identifier 
will be on all case report form (CRF) pages. In legal jurisdictions where use of initials is 
not permitted, a substitute identifier will be used.  
Subjects who do not complete the study will not be replaced. 
 
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9.4 
Treatments 
9.4.1 Treatments Administered 
BioMarin and/or its designee will provide the study site with a supply of IP sufficient for the 
completion of the study. 
9.4.2 Identity of Investigational Product (IP) 
9.4.2.1 
Product Characteristics and Labeling 
The rAvPAL-PEG drug product for SC injection is formulated and supplied as a sterile 
aqueous (colorless to pale yellow) solution in clear, single-use, type-1 borosilicate glass 
vials. Each 3 mL vial contains 1.5 ± 0.2 mL to deliver 10 mg of rAvPAL-PEG per 1 mL 
(10 mg/mL protein concentration). Each vial is filled with 1.5 ± 0.2 mL to allow the 
withdrawal and delivery of up to 1 mL of the drug product. 
Dilution instructions are provided in a separate instruction manual. 
The excipients in this drug product are tromethamine, tromethamine-hydrochloride, 
sodium chloride, L-phenylalanine, and water for injection. 
Drug product packaging will be identified with the lot number and expiration date, and will 
be provided in a box labeled with the study number. 
9.4.3 Storage 
At the study site, all IP must be stored at 5 ±3°C (41 ± 5°F) under the conditions specified in 
the IB in a secure area accessible only to the designated pharmacists and clinical site 
personnel. All IP must be stored and inventoried and the inventories must be carefully and 
accurately documented according to applicable state, federal and local regulations, ICH GCP, 
and study procedures. 
9.4.4 Directions for Administration 
Doses will be administered SC and the favorable dose will be determined for each subject by 
adjusting the dose level, dose frequency, or both, as agreed by the PI and the Study Medical 
Officer, based upon the subject’s response to doses. Dosing is up to a maximum dose per 
week of 2 mg/kg. 
Dosage is calculated by multiplying each subject’s weight in kilograms (kg) on Day 1 
(predose) by the assigned dose (in mg/kg). During the study, if the weight of a subject 
changes more than 10% from the measurement obtained at baseline or at a previous 
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measurement, the subject’s dose may be adjusted to accommodate the change. The change 
must be recorded. Refer to the Pharmacy Manual for additional information on calculating 
dosage. 
The injection sites should be alternated between doses, ie, upper left arm in Week 1, upper 
right arm in Week 2, etc. Doses may be administered in any of the common SC areas (upper 
arm, thigh, abdomen). If dose volume is such that a dose will be divided and given in more 
than 1 injection site, it is preferable to use both arms, both legs, or both sides of the abdomen. 
Subjects may require more than 1 injection per dose, depending upon site policy (ie, some 
institutions do not permit a single SC injection of greater than 2 mL). The number of 
injections required for an individual weighing 80 kg (about 176 pounds) is provided in 
Table 9.4.4.1 as an example. Note this table is for example purposes only. Dosage calculations 
must be performed according to study drug preparation instructions provided in the PAL-003 
Pharmacy Manual. Study drug will be administered by clinic staff or other qualified and 
trained study personnel.  
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Table 9.4.4.1  Number of Injections Required For an Individual Weighing 80 kg 
Dose Group 
(mg/kg) 
Weight 
(kg) 
Volume of Study Drug
(mL)a
No. of 
Injectionsb
0.001 
80 
0.8 
1 
0.003 
80 
0.6 
1 
0.01 
80 
0.8 
1 
0.03 
80 
0.2 
1 
0.06 
80 
0.5 
1 
0.1 
80 
0.8 
1 
0.3 
80 
2.4 
2 
0.6 
80 
4.8 
2 or 3 
1.0 
80 
8.0 
4 
aStudy drug is supplied at a concentration of 10 mg/mL and is then diluted by differential amounts as specified 
in the PAL-003 Pharmacy Manual. Volume to be injected is calculated based on a starting volume attained 
following dilution. 
bNumber of injections per dose is dependent upon site policy for SC injections. The number of injections may 
vary at the discretion of the Investigator. 
 
Every effort should be made to adhere to the study drug administration regimen. If a 
subject misses more than 2 scheduled doses of study drug, both dose level and dose 
frequency will need to be re-evaluated. 
9.4.5 Method of Assigning Subjects to Treatment Groups 
This will be an open-label study; no randomization schedule will be generated. 
Subjects will retain the same subject number used in PAL-002. 
9.4.6 Selection of Doses Used in the Study 
This Phase 2 study aims to evaluate the efficacy, safety, tolerability, and PK parameters of 
multiple doses of rAvPAL-PEG after long-term administration in subjects with PKU. A dose 
that produces a reduction in blood Phe concentrations to 120-600 μmol/L will be determined 
for each subject.  
The doses for this study are based upon the results of nonclinical studies and PAL-001. 
The no observable adverse effect level (NOAELs) from nonclinical studies in rats and 
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monkeys represents a greater than 100-fold safety factor over the starting dose 
administered in PAL-002 (0.001 mg/kg). 
9.4.6.1 
Selection of Timing of Dose for Each Subject 
Study drug will be administered in the morning by clinic staff or other qualified and 
trained study personnel. 
9.4.7 Blinding 
This is an open-label study. 
9.4.8 Prior and Concomitant Medications 
All prescription and over-the-counter (OTC) medications taken by a subject for 30 days 
before Screening will be recorded on the designated CRF. The Investigator may prescribe 
additional medications during the study, as long as the prescribed medication is not 
prohibited by the protocol. In the event of an emergency, any needed medications may be 
prescribed without prior approval, but the medical monitor must be notified of the use of any 
contraindicated medications immediately thereafter. Any concomitant medications added or 
discontinued during the study should be recorded on the CRF. 
Use of any investigational product (with the exception of rAvPAL-PEG used in PAL-002) or 
investigational medical device within 30 days before Screening, or requirement for any 
investigational agent prior to completion of all scheduled study assessments, is prohibited. 
Use or planned use of any injectable drugs containing PEG (other than rAvPAL-PEG), 
including Depo-Provera, is prohibited within 6 months prior to Screening and during study 
participation. A list of PEG-containing injectable drugs is provided in the study reference 
materials. Subjects who have had a prior local skin reaction to rAvPAL-PEG or a 
PEG-containing product will be premedicated with acetaminophen and antihistamines (refer 
to Section 9.1.1). If the local skin reaction worsens with a repeat injection (as 
determined by the Investigator in consultation with the Study Medical Officer) even 
with premedication prior to study drug dosing, the subject must be withdrawn from the 
study and complete an Early Termination Visit. 
Subjects who have had a prior systemic reaction to rAvPAL-PEG or a PEG-containing 
product are excluded from participation in this study (refer to Section 9.1.1).  
Use of any medication that is intended to treat PKU within 14 days prior to the 
administration of study drug is prohibited. 
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9.4.9 Treatment Compliance 
The date, time, volume, and concentration of each dose of study drug administered to each 
subject must be recorded in the dispensing log provided for the study, as well as on the 
appropriate CRF. This data will be used to assess treatment compliance. 
9.5 
Investigational Product Accountability 
The PI or designee is responsible for maintaining accurate records (including dates and 
quantities) of IP received, subjects to whom IP is dispensed (subject-by-subject dose specific 
accounting), and IP lost or accidentally or deliberately destroyed. The PI or designee must 
retain all unused or expired study supplies until the study monitor (on-site CRA) has 
confirmed the accountability data. 
9.5.1 Return and Disposition of Clinical Supplies 
Unused study drug must be kept in a secure location for accountability and reconciliation by 
the study monitor. The Investigator or designee must provide an explanation for any 
destroyed or missing study drug or study materials. 
Unused study drug may be destroyed on site, per the site’s standard operating procedures, but 
only after BioMarin has granted approval for drug destruction. The monitor must account for 
all study drug in a formal reconciliation process prior to study drug destruction. All study 
drug destroyed on site must be documented. Documentation must be provided to BioMarin 
and retained in the PIs study files. If a site is unable to destroy study drug appropriately, the 
site can return unused study drug to BioMarin upon request. The return of study drug or 
study drug materials must be accounted for on a Study Drug Return Form provided by 
BioMarin. 
All study drug and related materials should be stored, inventoried, reconciled, and destroyed 
or returned according to applicable state and federal regulations and study procedures. 
9.6 
Dietary or Other Protocol Restrictions 
Subjects will be instructed that diet should not be altered during the course of the study 
except as necessary for safety. If a subject’s blood Phe concentration is  < 120 µmol/L, 
the subject’s diet will be adjusted to maintain blood Phe concentrations of 
120-600 µmol/L. Changes to diet will be made per the discretion of the Investigator in 
consultation with the Sponsor’s Medical Officer. 
A 3-day dietary record will be completed by subjects and will be brought to clinic visits 
for review with clinic staff. It is preferable that subjects complete the 3-day record 
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immediately prior to their next dose of study drug. The dietary record will be 
maintained with the study source documents.  
9.7 
Efficacy and Safety Variables 
9.7.1 Efficacy and Safety Measurements Assessed 
The Schedules of Events in the Synopsis (Section 2.1) describe the timing of required 
evaluations. 
For the laboratory assessments, the party responsible for performing the assessment and the 
pertinent protocol section describing the details of the test are listed in Table 9.7.1.1. 
Table 9.7.1.1: Summary of Laboratory Assessments 
Laboratory Assessment 
Party Responsible for 
Performing Test 
Section in Protocol for 
Details 
Clinical laboratory tests 
Central laboratory 
9.7.5
Antibody testing 
BioMarina
9.7.4.2
PK variables 
BioMarin 
9.7.3
Blood Phe concentrations 
Central laboratory 
9.7.2.1
Urinalysis, pregnancy test (urine), 
and sedimentation rate 
Local laboratory 
9.7.5, 9.7.4.1
Phe, phenylalanine; PK, pharmacokinetic. 
aAnalysis of the anti-rAvPAL-PEG IgE assay will be performed by a Contract Research Organization. 
9.7.1.1 
Demographic Data and Medical History 
Demographic data and a detailed medical history, including allergy history, will be obtained 
at Screening. The medical history will include specific information concerning any prior or 
existing medical conditions that might interfere with study participation or safety. 
This medical history should elicit all major illnesses, diagnoses, and surgeries that the subject 
has ever had, and whether the subject has a history of alcohol and/or drug abuse. 
9.7.1.2 
Physical Examination Findings 
Physical examination will include assessment of general appearance; CV; dermatologic; 
head, eyes, ears, nose, and throat; lymphatic; respiratory; GI; musculoskeletal; and 
neurological/psychological. Other body systems may be examined. Day 1 results will be the 
baseline values and clinically significant changes from baseline will be recorded as an AE. 
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9.7.1.3 
Vital Sign Measurements 
Vital signs will be measured after resting for 5 minutes, and include seated systolic blood 
pressure (SBP) and diastolic blood pressure (DBP) measured in millimeters of mercury 
(mm Hg), heart rate in beats per minute, respiration rate in breaths per minute, weight (kg), 
and temperature in degrees Celsius (°C). Height (cm) will be measured at Screening only. 
9.7.1.4 
Electrocardiography 
A standard 12-lead ECG will be recorded while the subject is resting, at Screening and at the 
final follow-up (F/U) Visit or Early Termination Visit (ETV). If clinically significant 
abnormalities are noted at Screening, the PI or designee is required to assess whether it is 
appropriate for the subject to enroll in the study. 
9.7.1.5 
Chest X-Ray 
A chest X-ray will be performed at the Month 12 and Final Follow-Up (or Early 
Termination) visits to assess gross pulmonary health.  
9.7.2 Efficacy Variable 
9.7.2.1 
Blood Phenylalanine Concentrations 
Blood samples for Phe concentration measurements will be drawn in the morning, at least 
2.5 hours after a meal, on the days and time points indicated in the Schedule of Events 
(Table 2.1.1). 
In addition, after each administration of study drug, the subject will have a blood Phe 
measurement by fingerstick as outlined in Table 2.1.1. This may be done by the subject at 
home. Subjects who have their dose frequency increased will have additional Phe 
assessments performed as outlined in Table 2.1.2 and Table 2.1.3. 
A central laboratory will be used for blood Phe concentration analysis. 
9.7.3 Pharmacokinetic Variables 
Steady-state PK (predose samples) of rAvPAL-PEG will be evaluated in PKU subjects after 
the subject has achieved and maintained target blood Phe concentration (120-600 μmol/L) for 
a minimum of 2 weeks (to allow assessment of blood Phe concentrations) and no further dose 
modification is planned. Once this target has been achieved, PK samples will be collected 
predose on the same day each week for 3 consecutive weeks. 
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Subjects who have increased their dose frequency to twice weekly or daily will have 
addition PK assessments performed for 5 weeks after the change in dose regimen (refer 
to Section 12.3.5 and Table 2.1.2 and Table 2.1.3). BioMarin will perform the analysis. 
9.7.4 Safety Variables 
9.7.4.1 
Pregnancy Testing 
Female subjects of childbearing potential will have a urine pregnancy test at the time points 
specified in the Schedules of Events (Table 2.1.1). Female subjects with a positive serum 
pregnancy test at Screening do not meet eligibility criteria for enrollment. 
Additional pregnancy tests will be performed at any visit in which pregnancy status is in 
question. Serum pregnancy tests will be performed in the event of a positive or equivocal 
urine pregnancy test result. 
Refer to Section 10.3 for details on the reporting procedures to follow in the event of 
pregnancy. 
9.7.4.2 
Antibody Testing 
Immunogenicity will be assessed by determining antibody response and neutralizing 
activity with the following measurements: 1) anti-rAvPAL immunoglobulin G (IgG) 
antibodies, 2) anti-rAvPAL immunoglobulin M (IgM) antibodies, 3) anti-PEG IgG 
antibodies, 4) anti-PEG IgM antibodies, 5) anti-rAvPAL-PEG immunoglobulin E (IgE) 
antibodies, and 6) anti-rAvPAL-PEG Enzyme Activity Neutralizing antibodies (NAb). 
Validated immunogenicity assays will be used per the time points indicated in the 
Schedule of Events (Table 2.1.1). 
BioMarin will perform the analysis except for anti-rAvPAL-PEG IgE antibodies, which 
will be assessed by a Contract Research Organization. 
9.7.5 Clinical Laboratory Assessments 
Any abnormal test results determined to be clinically significant by the Investigator should 
be repeated (at the Investigator’s discretion) until the cause of the abnormality is determined, 
the value returns to baseline or to within normal limits, or the Investigator determines that the 
abnormal value is no longer clinically significant. 
All clinical laboratory result pages should be initialed and dated by an Investigator, along 
with a comment regarding whether or not the result is clinically significant. 
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The diagnosis, if known, associated with abnormalities in clinical laboratory tests that are 
considered clinically significant by the Investigator will be recorded on the AE CRF. 
Specific days for obtaining samples are provided in Table 2.1.1 and in Section 12. 
The scheduled clinical laboratory tests are listed in Table 9.7.5.1. A central laboratory will be 
used for analysis. 
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Table 9.7.5.1: Clinical Laboratory Tests 
Blood Chemistry 
Hematology 
Urine Testsa
Other 
Albumin  
Hemoglobin  
Appearance 
Alkaline 
Phosphatase  
Hematocrit  
Color 
Pregnancy test, if 
applicablea
ALT (SGPT)  
WBC count 
pH 
 
AST (SGOT) 
RBC count 
Specific gravity 
Tyrosine 
Total bilirubin 
Platelet count 
Ketones 
BUN 
Differential cell count 
Protein 
Creatinine 
Sedimentation ratea
Glucose 
 
GGT 
CRPb
Bilirubin 
Phenylalanine 
Total protein 
 
Nitrite 
CH50 b
Calcium 
 
Urobilinogen 
C1
 b
Sodium 
 
Hemoglobin 
C4
 b
Potassium 
 
 
Serum tryptase level b,c
Glucose 
 
 
 
Uric acid 
 
 
 
CO2
 
 
 
Chloride 
 
 
 
ALT, alanine aminotransferase; AST, aspartate aminotransferase; BUN, blood urea nitrogen; CH50, total 
hemolytic complement; CO2, carbon dioxide; CRP, C-reactive protein; GGT, gamma-glutamyltransferase; 
RBC, red blood cell; SGOT, serum glutamic-oxaloacetic transaminase; SGPT, serum glutamic-pyruvic 
transaminase; WBC, white blood cell. 
a To be performed by local laboratory. 
b Perform for Unscheduled Skin Reaction visit only (within 48 hours of reaction).  
c Perform immediately after reaction if possible. 
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10 
REPORTING ADVERSE EVENTS 
10.1 
Adverse Events 
According to the ICH definition, an AE (or adverse experience) is “any untoward medical 
occurrence in a patient or clinical investigation subject administered a pharmaceutical 
product, and that does not necessarily have a causal relationship with this treatment. An AE 
can therefore be any unfavorable and unintended sign (including an abnormal laboratory 
finding), symptom, or disease temporally associated with the use of a medicinal 
(investigational) product, whether or not considered related to the IP.” 
An adverse drug reaction (ADR) is described by the ICH as “all noxious and unintended 
responses to a medicinal product related to any dose.” This means that a causal relationship 
between a medicinal product and an AE is at least a reasonable possibility, ie, the 
relationship cannot be ruled out. 
An AE may include intercurrent illnesses or injuries that represent an exacerbation (increase 
in frequency, severity, or specificity) of pre-existing conditions (eg, worsening of asthma). 
Whenever possible, it is preferable to record a diagnosis as the AE term rather than a series 
of terms relating to a diagnosis. 
The reporting period for non-serious AEs is the period from the first administration of study 
drug through the final F/U Visit or at the ETV. If a non-serious AE remains unresolved at the 
conclusion of the study, the PI and medical monitor will make a joint clinical assessment as 
to whether continued follow-up of the AE is warranted, and the results of this assessment 
must be documented. Resolution is defined as the return to baseline status or stabilization of 
the condition with the expectation that it will remain chronic. 
The Investigator will assess AEs for severity, for relationship to IP, and as to whether the 
event meets one or more of the definitions of a serious adverse event (SAE; refer to 
Section 10.2). 
The Investigator will determine the severity of each AE and will record it on the source 
documents and AE CRF, using the CTCAE v 3 grades defined below. Events that are 
CTCAE grades 4 and 5 are serious events and require completion of both an SAE form 
and AE eCRF. 
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Grade 
Description 
1 
Mild 
2 
Moderate 
3 
Severe 
4 
Life threatening or debilitating 
5 
Death related 
 
The term “severe” is often used to describe the intensity (severity) of a specific event (as in 
mild, moderate, or severe myocardial infarction); the event itself, however, may be of 
relatively minor medical significance (such as severe headache). This is not the same as 
“serious,” which is based on subject/event outcome or action criteria usually associated with 
events that pose a threat to a subject’s life or functioning. Seriousness (not severity) serves as 
a guide for defining regulatory reporting obligations. 
The Investigator will determine the relationship of an AE to the IP and will record it on the 
source documents and AE CRF, using the categories defined below. 
Relationship 
Description 
Not Related 
Exposure to the IP has not occurred 
OR 
The administration of the IP and the occurrence of the AE are not 
reasonably related in time  
OR 
The AE is considered likely to be related to an etiology other than 
the use of the IP; that is, there are no facts [evidence] or arguments 
to suggest a causal relationship to the IP. 
Possibly 
Related 
The administration of the IP and the occurrence of the AE are 
reasonably related in time 
AND 
The AE could be explained equally well by factors or causes other 
than exposure to the IP. 
Probably 
Related 
The administration of IP and the occurrence of the AE are 
reasonably related in time  
AND 
The AE is more likely explained by exposure to the IP than by other 
factors or causes. 
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In order to classify AEs and diseases, preferred terms will be assigned by the sponsor to the 
original terms entered on the CRF, using MedDRA (Medical Dictionary for Regulatory 
Activities terminology). 
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10.2 
Serious Adverse Events 
A SAE is defined as any AE that: 
• 
Results in death. 
• 
Is life threatening, that is, places the subject at immediate risk of death from the event 
as it occurred. This definition does not include a reaction that, had it occurred in a 
more severe form, might have caused death. 
• 
Requires in-patient hospitalization or prolongation of an existing in-patient 
hospitalization. Admission of a subject to the hospital as an in-patient as a result of an 
AE, even if the subject is released on the same day, qualifies as hospitalization. 
• 
Results in persistent or significant disability or incapacity. An event qualifies as 
resulting in a persistent or significant disability or incapacity if it involves a 
substantial disruption of the subject’s ability to carry out usual life functions. 
This definition is not intended to include experiences of relatively minor or temporary 
medical significance. 
• 
Is a congenital anomaly or birth defect, that is, an AE that occurs in the child or fetus 
of a subject exposed to IP prior to conception or during pregnancy. 
• 
Is an important medical event that does not meet any of the above criteria, but may 
jeopardize the subject or require medical or surgical intervention to prevent one of the 
outcomes listed above. Examples of such events are intensive treatment in the 
emergency room, allergic bronchospasm, blood dyscrasias or convulsions that do not 
result in hospitalization; or development of drug dependency or drug abuse. 
More than one of the above criteria may apply to any specific event. 
The reporting period for SAEs begins earlier than non-serious AEs and is the period from the 
time of signing of the ICF through 4 weeks after the last dose or at the ETV. SAEs reported 
to the Investigator outside of this reporting period will be reported to BioMarin if, in good 
medical judgment, the event has any bearing on the study data. SAEs must be followed by 
the Investigator until resolution, even if this extends beyond the study-reporting period. 
Resolution of an SAE is defined as the return to baseline status or stabilization of the 
condition with the expectation that it will remain chronic. 
Any SAE, whether or not considered related to study drug, will be reported immediately 
(within 24 hours) to BioMarin Pharmacovigilance by fax using the study-specific 
SAE Report Form. In addition to the outcome of the SAE, any medication or other 
therapeutic measures used to treat the event will be recorded on the appropriate CRF page(s). 
Investigators should not wait to collect additional information that fully documents the event 
before notifying BioMarin Pharmacovigilance of an SAE. BioMarin may be required to 
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report certain SAEs to regulatory authorities within 7 calendar days of being notified about 
the event; therefore, it is important that Investigators submit additional information requested 
by BioMarin as soon as it becomes available. 
Reporting of SAEs to the IRB will be done in compliance with the standard operating 
procedures and policies of the IRB and with applicable regulatory requirements. Adequate 
documentation must be obtained by BioMarin showing that the IRB was properly and 
promptly notified as required. 
10.3 
Pregnancy 
Pregnancy in a subject or partner should be reported immediately (within 24 hours) to 
BioMarin Pharmacovigilance by fax using the Pregnancy Form in the study reference 
materials. In addition, pregnancy in a subject is also reported on the End of Study CRF. 
The Investigator must make every effort to follow the subject through resolution of the 
pregnancy (delivery or termination) and to report the resolution on the Pregnancy Follow-up 
Form in the study reference materials. In the event of pregnancy in the partner of a study 
subject, the Investigator should make every reasonable attempt to obtain the woman’s 
consent for release of protected health information. 
10.4 
BioMarin Pharmacovigilance Contact Information 
Contact information for BioMarin Pharmacovigilance is as follows: 
BioMarin Pharmaceutical Inc. 
Address 
105 Digital Drive 
 
 
Novato, CA 94949 
Phone:  
(415) 506-6179 
Fax: 
 
(415) 532-3144 
E-mail: 
drugsafety@bmrn.com 
The Investigator is encouraged to discuss with the medical monitor any AEs for which the 
issue of seriousness is unclear or questioned. Contact information for the medical monitor is 
as follows: 
Name:  
, MD 
Address: 
105 Digital Drive 
 
 
Novato, CA 94949 USA 
Phone:  
 
Fax: 
 
 
E-mail: 
 
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11 
APPROPRIATENESS OF MEASUREMENTS 
11.1 
Safety and Pharmacokinetics 
The PK and safety assessments in this study are used widely and are generally recognized as 
reliable, accurate, and relevant. 
12 
STUDY PROCEDURES 
12.1 
Prestudy 
An ICF must be signed and dated by the subject (or the subject’s legally authorized 
representative if the subject is less than 18 years of age), the PI or designee and witness 
(if required) before any study-related procedures are performed. 
12.2 
Screening Visit 
After subjects have signed an ICF, they will be screened for enrollment into the study. 
The following study activities will be performed at Screening: 
• 
Medical history, including allergy history, and demographics 
• 
Physical examination  
• 
Vital signs, including height and weight 
• 
12-lead ECG 
• 
Clinical laboratory tests (including hematology, chemistry, and urinalysis) 
• 
Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• 
Assessment of SAEs 
• 
Concomitant medications 
• 
Diet query 
• 
Blood Phe and plasma tyrosine concentration 
For subjects who participated in PAL-002, these assessments may be the same used for the 
Week 16 Visit of PAL-002, if they occur within 28 days from Day 1. 
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•
ug may be administered on additional days during the 
12.3 
Treatment Period 
During the Treatment Period, additional visits may occur if deemed necessary to monitor 
AEs or blood Phe concentrations. All study activities will occur on the first day of each week 
unless otherwise noted. On days that a dose is given, assessments will be done predose unless 
otherwise specified. 
If the dose is modified by increasing dose level, additional blood Phe concentration testing 
should be done on the third day following dose adjustment. If dose is modified by increasing 
either dose frequency or dose level, additional blood Phe concentration testing should be 
done prior to each dose for the first 2 weeks following dose adjustment. 
12.3.1 Day 1 (Week 1) 
Within 28 days of completing screening assessments, the following study activities will be 
performed on Day 1: 
• 
Physical examination 
• 
Vital signs, including weight 
• 
Sedimentation rate 
• 
Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• 
Injection-site inspection (postdose) 
• 
Assessment of SAEs (predose and postdose) and all AEs (postdose) 
• 
Concomitant medications 
• 
Diet query 
• 
Predose PK sample 
• 
Predose blood Phe and plasma tyrosine concentration 
• 
Serum rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibody, and 
anti-rAvPAL-PEG IgE) 
Administer study drug (study dr
 
week as determined by the Investigator, in agreement with the Study Medical Officer) 
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12.3.2 Weekly Visits 
The following study activities will be performed at the weekly visits beginning with Week 2: 
• 
Vital signs, including weight 
• 
Injection-site inspection (previous and current injection site) 
• 
Assessment of AEs 
• 
Concomitant medications 
• 
Diet query 
• 
3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the next dose of study drug.) 
• 
Predose PK sample  
o 
Per investigator discretion, once a subject is on a stable dosing regimen for 
at least 3 months (as evidenced by blood Phe levels of 120-600 µmol/L for 
the majority of the 3 months), the predose PK assessment may be skipped at 
the weekly visits and performed at the monthly visits for the first year then 
2-3 months thereafter. Weekly sampling should resume if the subject’s 
dosing regimen changes. 
• 
Predose blood Phe and plasma tyrosine concentration 
o 
Per investigator discretion, once a subject is on a stable dosing regimen for 
at least 3 months (as evidenced by blood Phe levels of 120-600 µmol/L for 
the majority of the 3 months), the predose plasma Phe and tyrosine 
assessments may be skipped at the weekly visits and performed at the 
monthly visits for the first year then 2-3 months thereafter. The weekly 
plasma Phe assessment may be replaced with a Phe fingerstick test. Weekly 
testing should resume if the subject’s dosing regimen changes. 
• 
Administer study drug (study drug may be administered on additional days during the 
week as determined by the Investigator, in agreement with the Study Medical Officer) 
In addition, 3 days after each administration of study drug, the subject will have a blood Phe 
measurement by fingerstick. This may be done by the subject at home. 
12.3.3 Monthly Visits (Week 4, 8, 12, etc) 
Monthly visits consist of all weekly activities and include additional activities. 
The following study activities will be performed at the monthly visits beginning with 
Week 4: 
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• 
ug may be administered on additional days during the 
In addition,
• 
Vital signs, including weight 
• 
Clinical laboratory tests 
• 
Chest x-ray (Month 12 visit only) 
• 
Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• 
Injection-site inspection (previous and current injection site) 
• 
Assessment of AEs 
• 
Concomitant medications 
• 
Diet query 
• 
3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the next dose of study drug.) 
• 
Predose PK sample (subjects who are on a stable dosing regimen for  ≥ 3 months 
only) 
o 
Per investigator discretion, once a subject is on a stable dosing regimen for 
at least 3 months (as evidenced by blood Phe levels of 120-600 µmol/L for 
the majority of the 3 months), the predose PK assessment may be skipped at 
the weekly visits and performed at the monthly visits for the first year then 
2-3 months thereafter. Weekly sampling should resume if the subject’s 
dosing regimen changes.   
• 
Predose blood Phe and plasma tyrosine concentration 
o 
Per investigator discretion, once a subject is on a stable dosing regimen for 
at least 3 months (as evidenced by blood Phe levels of 120-600 µmol/L for 
the majority of the 3 months), the predose plasma Phe and tyrosine 
assessments may be skipped at the weekly visits and performed at the 
monthly visits for the first year then 2-3 months thereafter. The weekly 
plasma Phe assessment may be replaced with a Phe fingerstick test. Weekly 
testing should resume if the subject’s dosing regimen changes. 
• 
Serum rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibody, and 
anti-rAvPAL-PEG IgE) 
Administer study drug (study dr
week as determined by the Investigator, in agreement with the Study Medical Officer) 
 3 days after each administration of study drug, the subject will have a 
blood Phe measurement by fingerstick. This may be done by the subject at home. 
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•
Predose blood Phe and plasm
EG IgG, 
• 
ug may be administered on additional days during the 
In add
12.3.4 Quarterly Visits (Week 12, 24, 36, etc) 
Quarterly visits consist of all weekly and monthly activities and include additional activities. 
The following study activities will be performed at the quarterly visits beginning with 
Week 12: 
• 
Physical examination 
• 
Vital signs, including weight 
• 
Clinical laboratory tests 
• 
Sedimentation rate 
• 
Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• 
Injection-site inspection (previous and current injection site) 
• 
Assessment of AEs 
• 
Concomitant medications 
• 
Diet query 
• 
3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the next dose of study drug.) 
• 
Predose PK sample (subjects who are on a stable dosing regimen for  ≥ 3 months 
only) 
o 
Per investigator discretion, once a subject is on a stable dosing regimen for 
at least 3 months (as evidenced by blood Phe levels of 120-600 µmol/L for 
the majority of the 3 months), the predose PK assessment may be skipped at 
the weekly visits and performed at the monthly visits for the first year then 
2-3 months thereafter. Weekly sampling should resume if the subject’s 
dosing regimen changes.   
a tyrosine concentration 
 
• 
Serum rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-P
anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibody, and 
anti-rAvPAL-PEG IgE) 
Administer study drug (study dr
week as determined by the Investigator, in agreement with the Study Medical Officer) 
ition, 3 days after each administration of study drug, the subject will have a 
blood Phe measurement by fingerstick. This may be done by the subject at home. 
 
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2.3.5 Interim Dosing Visit 
ose frequency during the study from 1x/week to 2x/week 
des 
uding weight 
ious and current injection site) 
ations 
 fingerstick 
ect at home. 
• 
PK sam
e
 increase their dose frequency to 2x/week will have an additional 
 PK sample obtained prior to administration of the first 4 doses 
ng 
o 
amples obtained every day for the first week: 12 hours after 
ter the 
 
2.3.6  
Unscheduled Hypersensitivity Reaction Visit 
AL-PEG administration (refer 
to Section 9.1.1) will have assessments performed immediately following (within 
e 
1
Subjects who increase their d
or daily will have additional assessments performed for 5 weeks after the subject’s 
rAvPAL-PEG dose frequency has been increased. If the Interim Dosing Visit coinci
with a weekly, monthly, or quarterly scheduled visit, the scheduled visit assessments 
should also be performed. The following study activities will be performed for the 
Interim Dosing Visit: 
• 
Vital signs, incl
• 
Injection-site inspection (prev
• 
Assessment of AEs 
• 
Concomitant medic
• 
Blood Phe measurement by
o This may be done by the subj
pl   
o 
Subjects
predose
(ie, for 2 weeks after the dose frequency increase). For the remaining 
3 weeks after the dose frequency increase, a PK sample will be obtained 
weekly prior to the first dose. Refer to Table 2.1.2 for the Interim Dosi
Visit schedule. 
Subjects who have their dose frequency increased to daily will have 
additional PK s
the first daily dose and predose every day for the rest of the week. Af
first week of daily dosing, subjects will have weekly PK samples obtained 
for 4 additional weeks. Refer to Table 2.1.3 for the Interim Dosing Visit 
schedule. 
1
Subjects who have a generalized skin reaction after rAvP
48 hours) the reaction. Subjects who have other systemic symptoms or a large local skin 
reaction that is not contiguous to the injection site (refer to Section 9.1.1) may hav
these assessments performed per investigator discretion. 
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 antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
 neutralizing antibody, and 
ional for subjects who have a generalized skin reaction per 
 
• 
 s
• 
t medications 
 
Subjects should then return to the clinic 4 weeks after their last dose of rAvPAL-PEG 
r the Early Termination Visit assessments (refer to Section 12.4). 
• 
Injection-site inspection 
• 
Clinical laboratory tests 
• 
Sedimentation rate  
• 
CRP, CH50, C1, and C4 
• 
Serum rAvPAL-PEG
anti-PEG IgM, anti-rAvPAL-PEG
anti-rAvPAL-PEG IgE) 
• 
Serum tryptase level 
o 
Perform immediately after reaction if possible. 
o 
Assessment is opt
investigator discretion.
PK ample 
Assessment of AEs 
• 
Concomitan
fo
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•
a tyrosine concentration 
EG IgG, 
 
12.4 
Early Termination Visit 
The Early Termination Visit (ETV) will occur 4 weeks after the final dose of study drug. 
Subjects who complete an Unscheduled Hypersensitivity Reaction Visit (refer to 
Section 12.3.6) will be terminated from the study. Subjects will then return 4 weeks 
after the last dose of study drug for the Early Termination Visit. 
Any AE that caused a subject to withdraw from the study or any clinically significant 
abnormal laboratory value or vital sign measurement identified at the ETV will be followed 
by the Investigator.  
Every reasonable effort should be made to contact any subject who is lost to follow-up. 
The following study activities will be performed at the ETV: 
• 
Physical examination  
• 
Vital signs, including weight 
• 
12-lead ECG 
• 
Clinical laboratory tests 
• 
Chest x-ray  
• 
Sedimentation rate 
• 
Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• 
Injection-site inspection (previous injection site) 
• 
Assessment of AEs 
• 
Concomitant medications 
• 
Diet query 
PK sample 
 
• 
Blood Phe and plasm
• 
Serum rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-P
anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibody, and 
anti-rAvPAL-PEG IgE) 
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12.5 
Final Follow-up Visit 
The final follow-up (F/U) Visit will occur 1 week after the final dose of study drug. 
The following study activities will be performed at the F/U Visit: 
• Physical examination  
• Vital signs, including weight 
• 12-lead ECG 
• Clinical laboratory tests 
• Chest x-ray  
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• Injection-site inspection (previous injection site) 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• PK sample 
• Blood Phe and plasma tyrosine concentration 
• Serum rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibody, and 
anti-rAvPAL-PEG IgE) 
 
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13 
DATA QUALITY ASSURANCE 
BioMarin personnel or designees will visit the study site prior to initiation of the study to 
review with the site personnel information about the IP, protocol and other regulatory 
document requirements, any applicable randomization procedures, source document 
requirements, CRFs, monitoring requirements, and procedures for reporting AEs, including 
SAEs. 
At visits during and after the study, a CRA will monitor the site for compliance with 
regulatory documentation, with a focus on accurate and complete recording of data on CRFs 
from source documents, adherence to protocol, randomization (if applicable), SAE reporting 
and drug accountability records.  
The designated clinical data management group will enter or transfer CRF data into a study 
database. 
Data quality control and analysis will be performed by BioMarin or a designee, based on a 
predefined analysis plan. 
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14 
STATISTICAL METHODS AND DETERMINATION OF SAMPLE SIZE 
14.1 
Statistical and Analytical Plans 
Because of the small sample size, no formal statistical tests will be performed. Categorical 
data will be summarized using frequency and percent, while continuous data will be 
summarized using descriptive statistics (ie, number of observations, mean, median, standard 
deviation [SD], minimum, and maximum). 
The statistical analysis plan (SAP) will provide additional details about the planned statistical 
analysis. 
14.2 
Safety Analysis 
All subjects who receive any amount of study drug in this study and have postdose safety 
information will be included in the safety analyses. 
Safety will be evaluated on the incidence of AEs, including serious AEs (SAEs), and 
clinically significant changes in vital signs and laboratory test results. 
The verbatim terms reported on CRFs to identify AEs will be coded using MedDRA. 
Treatment-emergent AEs will be summarized by system organ class, preferred term, 
relationship to study drug, and severity. Changes from baseline in vital signs and laboratory 
test results will be summarized with descriptive statistics. 
14.3 
Pharmacokinetic Analysis 
Data from all subjects who complete at least 2 weeks of the study will be included in the PK 
analysis. 
Steady-state PK (predose samples) of rAvPAL-PEG will be evaluated in PKU subjects after 
the subject has achieved and maintained target blood Phe concentrations (120-600 μmol/L) 
for a minimum of 2 weeks and no further dose modification is planned. 
Should data become available from PAL-002 that indicate study drug accumulation should 
also be measured, additional blood draws may be added for PK analysis as needed but not 
to exceed 3x/week. 
14.4 
Efficacy Analysis 
Data from all subjects who receive any amount of study drug and who have any 
post-treatment efficacy data will be included in the efficacy analysis. 
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Blood Phe concentration at each scheduled time point will be summarized using descriptive 
statistics (mean, SD, median, minimum, and maximum). Change in blood Phe concentration 
from baseline to each scheduled time point and presence/absence of antibodies will also be 
summarized. In addition, the proportion of subjects who have maintained target Phe 
concentrations of 120-600 µmol/L will be summarized by each scheduled time point. 
14.5 
Determination of Sample Size 
Subjects who participated in PAL-002 may be enrolled into this study. No formal sample size 
calculation was conducted. 
14.6 
Handling of Missing Data 
All analyses will be presented based on observed data only. Missing data will not be imputed 
for analyses unless sensitivity analyses are warranted. If imputations are used, detailed 
imputation methods will be described in the SAP before locking the database. 
14.7 
Interim Analyses 
At least one interim analysis may be performed by the sponsor during the study. Safety will 
be assessed throughout the study on an ongoing basis (refer to Section 15 for 
information regarding the DMC). 
14.8 
Changes in the Conduct of the Study or Planned Analyses 
Only BioMarin may modify the protocol. Any change in study conduct considered necessary 
by the PI will be made only after consultation with BioMarin, who will then issue a formal 
protocol amendment to implement the change. The only exception is when an Investigator 
considers that a subject’s safety is compromised without immediate action. In these 
circumstances, immediate approval of the chairman of the IRB must be sought, and the 
Investigator should inform BioMarin and the full IRB within 2 working days after the 
emergency occurs. 
With the exception of minor administrative or typographical changes, the IRB must review 
and approve all protocol amendments. Protocol amendments that have an impact on subject 
risk or the study objectives, or require revision of the ICF, must receive approval from the 
IRB prior to their implementation. 
When a protocol amendment substantially alters the study design or the potential risks or 
burden to subjects, the ICF will be amended and approved by BioMarin and the IRB, and all 
active subjects must again provide informed consent. 
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Note: If discrepancies exist between the text of the statistical analysis as planned in the 
protocol, and the final SAP, a protocol amendment will not be issued and the SAP will 
prevail. 
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15 
DATA MONITORING COMMITTEE (DMC) 
The DMC will act independently in an advisory capacity to BioMarin to monitor the safety 
of rAvPAL-PEG in subjects who participate in the study. Meetings of the DMC can be 
convened at any time at the discretion of the DMC Chair or the Study Medical Officer. 
The Chair will be notified by the Study Medical Officer of all SAEs and will receive 
summaries of other safety data as available. The DMC will review the study data as soon as it 
is available during the study, on a schedule defined in the DMC Charter, and offer advice on 
whether or not to proceed, modify or terminate study enrollment on the basis of toxicity. 
Details regarding the DMC membership and safety data to be reviewed by members will be 
provided in a charter. 
The responsibilities of the DMC are to: 
• Review the study protocol, informed consent and assent documents, and plans for 
data monitoring. 
• Evaluate the progress of the trial, subjects’ risk versus benefit, and other factors that 
could affect the study outcome. 
• Consider relevant information that may have an impact on the safety of the 
participants or the ethics of the study. 
• Protect the safety of the study participants in accordance with the stopping criteria as 
defined in study protocol Section 9.1.3. 
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16 
COMPENSATION, INSURANCE, AND INDEMNITY 
There will be no charge to study subjects to be in this study. BioMarin will pay all costs of 
tests, procedures, and treatments that are part of this study. In addition, after IRB approval, 
BioMarin may reimburse the cost of travel for study-related visits. BioMarin will not pay for 
any hospitalizations, tests, or treatments for medical problems of any sort, whether or not 
related to the study subject’s disease, that are not part of this study. Costs associated with 
hospitalizations, tests, and treatments should be billed and collected in the way that such 
costs are usually billed and collected. 
The Investigator should contact BioMarin immediately upon notification that a study subject 
has been injured by the IP or by procedures performed as part of the study. Any subject who 
experiences a study-related injury should be instructed by the Investigator to seek medical 
treatment at a pre-specified medical institution if possible, or at the closest medical treatment 
facility if necessary. The subject should be given the name of a person to contact to seek 
further information about, and assistance with, treatment for study-related injuries. 
The treating physician should bill the subject’s health insurance company or other third party 
payer for the cost of this medical treatment. If the subject has followed the Investigator’s 
instructions, BioMarin will pay for reasonable and necessary medical services to treat the 
injuries caused by the IP or study procedures, if these costs are not covered by health 
insurance or another third party that usually pays these costs. In some jurisdictions, BioMarin 
is obligated by law to pay for study-related injuries without prior recourse to third party 
payer billing. If this is the case, BioMarin will comply with the law. 
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17 
CASE REPORT FORMS AND SOURCE DOCUMENTS 
Electronic case report forms will be provided for each subject. The Investigator must review 
and electronically sign the completed CRF casebook to verify its accuracy. 
CRFs must be completed using a web–based application that has been validated. Study site 
personnel will be trained on the application and will enter the clinical data from source 
documentation. Unless explicitly allowed in the CRF instructions, blank data fields are not 
acceptable. 
In the event of an entry error, or if new information becomes available, the site personnel will 
correct the value by deselecting the erroneous response and then selecting or entering the 
factual response. In compliance with 21 CFR Part 11, the system will require the site 
personnel to enter a reason for changing the value. The documented audit trail will include 
the reason for the change, the original value, the new value, the time of the correction, and 
the identity of the operator. 
BioMarin’s policy is that study data on the CRFs must be verifiable to the source data, which 
necessitates access to all original recordings, laboratory reports, and subject records. 
In addition, all source data should be attributable (signed and dated). The Investigator must 
therefore agree to allow direct access to all source data. Subjects (or their legally authorized 
representative) must also allow access to their medical records, and subjects will be informed 
of this and will confirm their agreement when giving informed consent. If an Investigator or 
institution refuses to allow access to subject records because of confidentiality, arrangements 
must be made to allow an “interview” style of data verification. 
A CRA designated by BioMarin will compare the CRFs with the original source documents 
at the study site and evaluate them for completeness and accuracy before designating them as 
“source data verified” (SDV). If an error is discovered at any time or a clarification is 
needed, the CRA, or designee, will create an electronic query on the associated field. Site 
personnel will then answer the query by either correcting the data or responding to the query. 
The CRA will then review the response and determine either to close the query or re–query 
the site if the response does not fully address the question. This process is repeated until all 
open queries have been answered and closed. 
Before a subject’s CRF casebook can be locked, all data fields must be SDV and all queries 
closed. The Investigator will then electronically sign the casebook, specifying that the 
information on the CRFs is accurate and complete. The Data Manager, or designee, will then 
set the status of the forms, visits, and the entire casebook to locked. Upon completion of the 
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clinical study report for the entire study, an electronic copy of each site’s casebooks will be 
copied to a compact disk (CD) and sent to each site for retention with other study documents. 
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18 
STUDY MONITORING AND AUDITING 
Qualified individuals designated by BioMarin will monitor all aspects of the study according 
to GCP and standard operating procedures for compliance with applicable government 
regulations. The PI agrees to allow these monitors direct access to the clinical supplies, 
dispensing, and storage areas and to the clinical files, including original medical records, of 
the study subjects, and, if requested, agrees to assist the monitors. The PI and staff are 
responsible for being present or available for consultation during routinely scheduled site 
visits conducted by BioMarin or its designees. 
Members of BioMarin’s GCP Compliance Department or designees may conduct an audit of 
a clinical site at any time during or after completion of the study. The PI will be informed if 
an audit is to take place and advised as to the scope of the audit. Representatives of the FDA 
or other Regulatory Agencies may also conduct an audit of the study. If informed of such an 
inspection, the PI should notify BioMarin immediately. The PI will ensure that the auditors 
have access to the clinical supplies, study site facilities, original source documentation, and 
all study files. 
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RETENTION OF RECORDS 
The PI must retain all study records required by BioMarin and by the applicable regulations 
in a secure and safe facility. The PI must consult a BioMarin representative before disposal 
of any study records, and must notify BioMarin of any change in the location, disposition or 
custody of the study files. The PI/institution must take measures to prevent accidental or 
premature destruction of essential documents, that is, documents that individually and 
collectively permit evaluation of the conduct of a study and the quality of the data produced, 
including paper copies of study records (eg, subject charts) as well as any original source 
documents that are electronic as required by applicable regulatory requirements. 
All study records must be retained for at least 2 years after the last approval of a marketing 
application in the U.S. or an ICH region and until (1) there are no pending or contemplated 
marketing applications in the United States or an ICH region or (2) at least 2 years have 
elapsed since the formal discontinuation of clinical development of the IP. The PI/institution 
should retain subject identifiers for at least 15 years after the completion or discontinuation 
of the study. Subject files and other source data must be kept for the maximum period of time 
permitted by the hospital, institution or private practice, but not less than 15 years. 
These documents should be retained for a longer period, however, if required by the 
applicable regulatory requirements or by a BioMarin agreement. BioMarin must be notified 
and will assist with retention should the PI/institution be unable to continue maintenance of 
subject files for the full 15 years. It is the responsibility of BioMarin to inform the 
PI/institution as to when these documents no longer need to be retained. 
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20 
USE OF INFORMATION AND PUBLICATION 
BioMarin recognizes the importance of communicating medical study data and therefore 
encourages their publication in reputable scientific journals and at seminars or conferences. 
The details of the processes of producing and reviewing reports, manuscripts, and 
presentations based on the data from this study will be described in the Clinical Study 
Agreement between BioMarin and the PI. 
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21 
REFERENCES 
Armstrong, Hempel, Koling, Chan, Fisher, Meiselman, Garratty. Antibody against 
poly(ethylene glycol) adversely affects PEG-asparaginase therapy in acute lymphoblastic 
leukemia patients. Cancer 110[1], 103-111. 2007.  
Chen, Scott. Current and future applications of immunological attenuation via pegylation of 
cells and tissue. BioDrugs 15[12], 833-847. 2001.  
Davis, Abuchowski, Park, Davis. Alteration of the circulating life and antigenic properties of 
bovine adenosine deaminase in mice by attachment of polyethylene glycol. Clin Exp 
Immunol 46[3], 649-652. 1981.  
Fisch. Comments on diet and compliance in phenylketonuria. Eur J Pediatr 159 Suppl 2, 
S142-S144. 2000.  
Gamez, Wang, Sarkissian, Wendt, Fitzpatrick, Lemontt, Scriver, Stevens. Structure-based 
epitope and PEGylation sites mapping of phenylalanine ammonia-lyase for enzyme 
substitution treatment of phenylketonuria. Mol Genet Metab 91[4], 325-334. 2007.  
Ganson, Kelly, Scarlett, Sundy, Hershfield. Control of hyperuricemia in subjects with 
refractory gout, and induction of antibody against poly(ethylene glycol) (PEG), in a phase I 
trial of subcutaneous PEGylated urate oxidase. Arthritis Res Ther 8[1], R12. 2006.  
Guttler, Azen, Guldberg, Romstad, Hanley, Levy, Matalon, Rouse, Trefz, de la, Koch. 
Impact of the phenylalanine hydroxylase gene on maternal phenylketonuria outcome. 
Pediatrics 112[6 Pt 2], 1530-1533. 2003.  
Harris, Chess. Effect of pegylation on pharmaceuticals. Nat Rev Drug Discov 2[3], 214-221. 
2003.  
Huttenlocher. The neuropathology of phenylketonuria: human and animal studies. Eur 
J Pediatr 159 Suppl 2, S102-S106. 2000.  
Kaufman. An evaluation of the possible neurotoxicity of metabolites of phenylalanine. 
J Pediatr 114[5], 895-900. 1989.  
Koch, Hanley, Levy, Matalon, Matalon, Rouse, Trefz, Guttler, Azen, Platt, Waisbren, 
Widaman, Ning, Friedman, de la. The Maternal Phenylketonuria International Study: 
1984-2002. Pediatrics 112[6 Pt 2], 1523-1529. 2003.  
Lee, Lilburn, Baudin. Maternal phenylketonuria: experiences from the United Kingdom. 
Pediatrics 112[6 Pt 2], 1553-1556. 2003.  
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Levy. Historical background for the maternal PKU syndrome. Pediatrics 112[6 Pt 2], 
1516-1518. 2003.  
Matalon, Surendran, Matalon, Tyring, Quast, Jinga, Ezell, Szucs. Future role of large neutral 
amino acids in transport of phenylalanine into the brain. Pediatrics 112[6 Pt 2], 1570-1574. 
2003.  
Richter, Akerblom. Antibodies against polyethylene glycol produced in animals by 
immunization with monomethoxy polyethylene glycol modified proteins. Int Arch Allergy 
Appl Immunol 70[2], 124-131. 1983.  
Richter, Akerblom. Polyethylene glycol reactive antibodies in man: titer distribution in 
allergic patients treated with monomethoxy polyethylene glycol modified allergens or 
placebo, and in healthy blood donors. Int Arch Allergy Appl Immunol 74[1], 36-39. 1984.  
Rouse, Azen. Effect of high maternal blood phenylalanine on offspring congenital anomalies 
and developmental outcome at ages 4 and 6 years: the importance of strict dietary control 
preconception and throughout pregnancy. J Pediatr 144[2], 235-239. 2004.  
Scott, Murad, Koumpouras, Talbot, Eaton. Chemical camouflage of antigenic determinants: 
stealth erythrocytes. Proc Natl Acad Sci U S A 94[14], 7566-7571. 1997.  
Scriver CR, Kaufman S. Hyperphenylalaninemia: Phenylalanine Hydroxylase Deficiency. 
In: Beaudet AL, Sly WS, Valle D, editors. Metabolic and Molecular Bases of Inherited 
Disease. New York: McGraw-Hill, 2001: 1667-709.  
Shedlovsky, McDonald, Symula, Dove. Mouse models of human phenylketonuria. Genetics 
134[4], 1205-1210. 1993.  
Walter, White, Hall, MacDonald, Rylance, Boneh, Francis, Shortland, Schmidt, Vail. How 
practical are recommendations for dietary control in phenylketonuria? Lancet 360[9326], 
55-57. 2002.  
Webster, Didier, Harris, Siegel, Stadler, Tilbury, Smith. PEGylated proteins: evaluation of 
their safety in the absence of definitive metabolism studies. Drug Metab Dispos 35[1], 9-16. 
2007.  
 
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22 
INVESTIGATOR RESPONSIBILITIES 
22.1 
Conduct of Study and Protection of Human Subjects  
In accordance with FDA Form 1572, the Investigator will ensure that: 
• He or she will conduct the study in accordance with the relevant, current protocol and 
will only make changes in a protocol after notifying the sponsor, except when 
necessary to protect the safety, rights, or welfare of subjects. 
• He or she will personally conduct or supervise the study. 
• He or she will inform any potential subjects, or any persons used as controls, that the 
drugs are being used for investigational purposes and he or she will ensure that the 
requirements relating to obtaining informed consent in 21 Part 50 and institutional 
review board (IRB) review and approval in 21 CFR Part 56 are met.  
• He or she will report to the sponsor adverse experiences that occur in the course of 
the investigation in accordance with 21 CFR 312.64. 
• He or she has read and understands the information in the Investigator’s Brochure, 
including potential risks and side effects of the drug. 
• His or her staff and all persons who assist in the conduct of the study are informed 
about their obligations in meeting the above commitments. 
• He or she will ensure that adequate and accurate records in accordance with 
21 CFR 312.62 and to make those records available for inspection in accordance with 
21 CFR 312.68. 
• He or she will ensure that the IRB complies with the requirements of 21 CFR Part 56, 
and other applicable regulations, and conducts initial and ongoing reviews and 
approvals of the study. He or she will also ensure that any change in research activity 
and all problems involving risks to human subjects or others are reported to the IRB. 
Additionally, he or she will not make any changes in the research without IRB 
approval, except where necessary to eliminate apparent immediate hazards to human 
subjects. 
• He or she agrees to comply with all other requirements regarding the obligations of 
clinical Investigators and all other pertinent requirements in 21 CFR Part 312. 
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CLINICAL STUDY PROTOCOL AMENDMENT SUMMARY 
 
Amendment: 3 
Date: May 04, 2011 
 
RATIONALE AND SUMMARY OF CHANGES 
The primary rationale for amending this protocol is to include a substudy to assess the safety, 
efficacy, pharmacokinetics (PK), and immune response when rAvPAL-PEG treatment is 
temporarily discontinued and then re-started in subjects.  
rAvPAL-PEG is being assessed as a long-term, chronic treatment for patients with PKU, and 
there is limited safety, efficacy, PK, and immune response information about the effects of a 
temporary dose interruption. Therefore, a Substudy has been added to this study to explore 
the effects of stopping and re-starting rAvPAL-PEG treatment. In this Substudy, up to 
10 subjects will stop dosing for a period of approximately 4 weeks. During this dosing 
interruption, subjects will be assessed for safety, efficacy, PK, and immune response and will 
continue to perform the scheduled study assessments. Subjects are eligible for participation 
in the Substudy if they are on a stable rAvPAL-PEG dosing regimen (ie, blood Phe levels 
have been reached at 60-600 µmol/L) for 4 weeks in this study, have not reported any serious 
adverse events (SAEs) during this study, and were not enrolled in Study PAL-004.  
Currently, there is no information regarding the PK profile of rAvPAL-PEG when blood Phe 
levels are at 60-600 µmol/L for subjects on a multiple-dose regimen. To address this lack of 
information, additional PK sampling will be performed prior to the dosing interruption. Upon 
restarting rAvPAL-PEG, PK sampling will also be performed to allow for collection of drug 
exposure data (area under the plasma concentration-time curve [AUC] and maximum plasma 
concentration [Cmax]), absorption rate, and clearance for subjects who have been previously 
exposed to rAvPAL-PEG in this Substudy. This information will allow for comparisons to be 
performed with subjects who were naïve to previous rAvPAL-PEG treatment from the Phase 
1 study, PAL-001. 
Following participation in the Substudy, subjects will return to the rAvPAL-PEG dose level 
and frequency that they were receiving prior to the dose interruption and will continue 
participation in the study until completion.  
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Because rAvPAL-PEG is a bacterial protein, an immune-mediated reaction and a reduction 
in efficacy (blood Phe reductions) are possible when rAvPAL-PEG dosing is re-introduced 
after the dose interruption of the Substudy. However, information from nonclinical studies, 
antibody results, and safety and efficacy results from the clinical studies to date (JAN2011) 
have shown that there is no added safety risk or risk of decreased efficacy when 
rAvPAL-PEG dosing is stopped and then re-started at the same dose level.  
• In nonclinical studies using the BTBR Pahenu2 (ENU2) mouse model, an animal 
model that exhibits characteristics similar to those of PKU patients, a 2-4 week 
dose-interruption was performed in animals administered 80 mg/kg/week. Following 
the dose interruption assessment, the animals re-started rAvPAL-PEG dosing at the 
same dose level (80 mg/kg/week). In this assessment, no safety issues were noted 
upon re-starting dosing with rAvPAL-PEG and there was an immediate return to 
stable blood Phe reductions.  
• There has not been any immediate immunoglobulin E (IgE)-mediated reactions to 
rAvPAL-PEG observed following administration of a rAvPAL-PEG injection. All 
reactions to rAvPAL-PEG have been reported approximately 12-24 hours following 
administration. To date, 1 out of 33 subjects has tested positive by serology to IgE 
antibodies without reporting any clinical symptoms to suggest anaphylaxis or a severe 
systemic reaction. Thus, it is not anticipated that reactions to rAvPAL-PEG are 
IgE-mediated.   
• To date (JAN2011), the clinical experience with re-starting rAvPAL-PEG dosing for 
subjects from Study PAL-001 who rolled over into Study PAL-002 does not indicate 
an increased safety risk or a decreased effect on reducing blood Phe levels upon 
re-introduction of drug.  
• Nine subjects who received a single dose of rAvPAL-PEG and completed the Phase 1 
study, PAL-001, rolled over into the multiple-dose, Phase 2 study, PAL-002. After a 
period of several months during which no drug was administered, these 9 subjects re-
started rAvPAL-PEG dosing in Study PAL-002 at the same starting doses as was 
administered in Study PAL-001. There has been no difference to date in the safety 
profile or efficacy profile of the subjects from Study PAL-001 who rolled over into 
Study PAL-002 (previously exposed to rAvPAL-PEG) when compared with subjects 
who were naive to rAvPAL-PEG dosing in Study PAL-002. Although previously 
exposed subjects had higher and a faster return of anti-PAL and anti-PEG 
immunoglobulin G (IgG) titers than those of naïve subjects, these results have not 
been associated with a higher safety risk or efficacy riskbased on information to date.  
o In Study PAL-002, 4 subjects to date have had a protocol-defined (per 
Protocol Amendment # 3 dated 30APR2010), 2-week washout (no dose 
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administered) following several weeks of a fixed dose of 0.06 mg/kg/week or 
0.1 mg/kg/week rAvPAL-PEG. Following the 2 weeks where no dose was 
administered, all 4 subjects re-started rAvPAL-PEG dosing at a higher dose 
with no safety issues reported to date. Blood Phe levels for these 4 subjects 
have not changed upon re-introduction of dosing. 
o Clinical experience with subjects who have had to temporarily halt dosing due 
to an adverse event also provides information that stopping and re-starting 
rAvPAL-PEG dosing does not appear to increase the risk to subject safety. To 
date, 10 subjects participating in either PAL-002 or PAL-003 have had to 
temporarily stop dosing due to an adverse event. All 10 subjects resumed 
dosing following resolution of the event or per determination by the 
Investigator that subject safety would not be jeopardized with re-starting 
dosing. These 10 subjects resumed dosing at a reduced dose level after 
approximately 1-7 weeks of no dosing. Upon re-starting dosing, none of these 
10 subjects have experienced additional safety issues. Eight subjects continue 
to receive dosing with rAvPAL-PEG (APR 2011) and have subsequently 
increased their dose level without additional reported adverse events that have 
resulted in a subsequent dosing interruption. 
 
In summary, because the risk to subject safety and efficacy is expected to be limited upon re-
starting rAvPAL-PEG, dosing will be re-started at the same dose level for subjects in the 
Substudy. Re-starting rAvPAL-PEG dosing must be performed in the clinic with 
post-administration observation performed to monitor subject safety. In addition, subjects 
will continue to be assessed per the safety assessment and stopping criteria defined in the 
protocol. Dose decreases for safety and increases also will continue to be performed relative 
to safety as defined in the protocol. In addition, the Substudy objectives have been added to 
assess the effect of stopping and re-starting rAvPAL-PEG dosing on safety and tolerability, 
efficacy (blood Phe concentration), PK, and immune response. The PK analysis has also been 
revised to accommodate for inclusion of the Substudy. 
Additional major changes implemented in this protocol amendment are as follows: 
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• The maximum allowable rAvPAL-PEG dose of 2.0 mg/kg/week has been increased 
to 5.0 mg/kg/week to allow for further dose increases. This change is based on 
available safety and blood Phe information to date (JAN2011) from this ongoing 
study and from the ongoing Phase 2 study, PAL-002. Experience from this study and 
Study PAL-002to date (JAN2011) indicates that rAvPAL-PEG administered in doses 
titrated up to a single administration of 2.0 mg/kg/week does not pose a clinically 
significant risk to subject safety. The most frequently reported AEs in this study and 
Study PAL-002 have been nonserious injection-site reactions and headache. The 
reported injection-site reactions have been self-limited and without sequelae. One 
SAE (dehydration and urticaria) has been reported to date; the event was reported as 
not related to treatment with rAvPAL-PEG and resolved. Two days after dosing with 
rAvPAL-PEG, the subject presented with upper respiratory infection symptoms.  The 
subject was started on 
 for the upper respiratory infection.  Twenty-four hours 
 after starting 
 and the third day after dosing with rAvPAL-PEG at 0.1mg/kg, 
the subject presented with a generalized skin reaction (urticaria).  Because the subject 
had no improvement while on 
, 
 went to the emergency room and was 
admitted to the hospital for intravenous fluid resuscitation and the 
 was 
stopped.  Since this event, this subject has remained in the study and and has 
continued dosing with rAvPAL-PEG, escalating the dose to 0.6 mg/kg with no 
additional events reported to date. Despite rAvPAL-PEG being well tolerated in doses 
up to 2.0 mg/kg/week, many of the subjects in Study PAL-003 have not yet been able 
to achieve and sustain blood Phe reductions to clinically significant levels 
(120-600 µmol/L; JAN2011). While some subjects who have been administered 
2.0 mg/kg/week rAvPAL-PEG have had > 50% reduction from baseline in blood Phe 
levels, they have not yet achieved the protocol-defined target blood Phe of 120-600 
µmol/L (JAN2011). It is hypothesized that administration of rAvPAL-PEG doses 
higher than 2.0 mg/kg/week will reduce the blood Phe levels further to within the 
protocol-defined range of clinical significance (60-600 µmol/L; target range revised 
per this protocol amendment) without jeopardizing subject safety. Dose increases up 
to 5.0 mg/kg/week may be implemented if none of the protocol-defined stopping 
safety criteria are met. Increases to 5.0 mg/kg/week must be performed in increments, 
every 2 weeks, per the dose increase instructions and safety assessment and stopping 
criteria outlined for the study. Upwards titration of dose to 5.0 mg/kg/week will be 
gradual to mitigate risk to subject safety. Also, subjects who increase dosing to up to 
5.0 mg/kg/week will continue to be monitored for safety, blood Phe, PK, and 
antibodies per the scheduled assessments and procedures. 
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• The study inclusion criteria have been modified to permit subjects who have 
completed Study PAL-004 (A Phase 2, Open-Label Study to Evaluate the Safety, 
Tolerability, and Efficacy of Subcutaneous Dose Levels of rAvPAL-PEG 
Administered Daily in Subjects with Phenylketonuria) to continue to receive 
rAvPAL-PEG in this study. Additionally, instruction regarding re-introduction of 
rAvPAL-PEG dosing has been added for subjects rolling over from Study PAL-004. 
rAvPAL-PEG treatment will be re-introduced at the same dose level and dosing 
frequency as was administered at the completion of Study PAL-004. Subjects will be 
monitored for safety when rAvPAL-PEG dosing is re-started in this study, and 
subjects will continue to be assessed per the safety assessment and stopping criteria 
defined in the protocol.  
• The target blood Phe level has been revised from 120-600 µmol/L to 60-600 µmol/L 
to allow for dosing that may provide greater clinical benefit to subjects. Blood Phe 
levels of approximately 60 ± 13 µmol/L are considered normal per the NIH 
Consensus Statement, 2000. 
• An exploratory objective has been added to assess the relationship of diet and change 
in blood Phe level in subjects with PKU. Information from a 3-day diet diary will be 
used to assess dietary Phe intake, as well as all other liquids and food. The study 
rationale has been revised to include information regarding the relationship of diet in 
blood Phe concentration following administration of rAvPAL-PEG in subjects with 
PKU. The study rationale and study outcome measures have also been revised to 
address this added study objective.  
• Information regarding self administration of rAvPAL-PEG has been added. 
Self-administration of study drug is now allowed by the subject but only if approved 
by both the Principal Investigator and the Sponsor’s Medical Officer and if adequate 
training is demonstrated. This change has been made to increase subject participation 
and to increase study completion given the long study duration.  
Specific revisions to the protocol, including the major changes presented and discussed 
above, are as follows: 
1. Information regarding the PAL-003 Substudy has been added. 
o Substudy objectives have been added for to assess for safety, efficacy, PK, 
and immune response (refer to the Synopsis [Section 2] and Section 8). 
o The secondary PK objective has been removed; the added PK objective 
for the Substudy will allow for analysis of PK profile, including clearance, 
when drug has been stopped and restarted in previously exposed subject 
who have been administered multiple doses of rAvPAL-PEG (refer to the 
Synopsis [Section 2] and Section 8), and the PK analysis has been 
modified to address the Substudy (Section 14.3).  
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o The Study Rationale has been revised to include information regarding the 
Substudy (refer to Section 7.3). The nonclinical section (Section 7.1) has 
also been updated with information regarding nonclinical results relative 
to stopping and re-starting dosing. 
o Information about the Substudy has been added to the Study Design 
section (refer to the Synopsis [Section 2] and Section 9.1).  
o Instruction regarding re-starting rAvPAL-PEG dosing following 
approximately 4 weeks of no dosing has been added (refer to Section 9.1). 
rAvPAL-PEG dosing will be re-started at the same dose level and dosing 
frequency as was administered prior to the dosing interruption. The first 
dose administered following the dose interruption must be performed in 
the clinic. A follow-up telephone call will be made to monitor subject 
safety 24 hours following the return to dosing. 
o Information regarding the risks of stopping and re-starting rAvPAL-PEG 
dosing has been added to the Overall Risks and Benefits section 
(Section 7.4.3). 
o Additional PK sampling has been added immediately prior to the dose 
interruption, during the dose interruption, and for the first week upon re-
starting rAvPAL-PEG. PK sampling timepoints have been added to 
Section 9.7.3. 
o The Study Procedures (Section 12.3.3) and have been modified to include 
the Substudy PK sampling, and a Substudy Schedule of Events 
(Table 2.1.2) has been added. 
2. The maximum weekly dose amount has been revised from 2.0 mg/kg to 5.0 mg/kg. 
o Information regarding dose increases has been revised; subjects may now 
increase their dose in increments up to 5.0 mg/kg/week (0.001, 0.003, 
0.01, 0.03, 0.06, 0.1, 0.2, 0.3, 0.4, 0.6, 0.8, 1.0, 2.0, 3.0, and 
4.0 mg/kg/week; refer to the Synopsis [Section 2] and Section 9.1.2.1) 
provided none of the safety assessment or stopping criteria are met. 
o Information regarding dose decreases has been revised to include 
decreases in increments for doses starting at 5.0 mg/kg/week (4.0, 3.0, 2.0, 
1.0, 0.8, 0.6, 0.4, 0.3, 0.2, 0.1, 0.06, 0.03, 0.01, 0.003, or 0.001 mg/kg; 
refer to the Synopsis [Section 2] and Section 9.1.2.2). 
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3. The target blood Phe level has been revised in this amendment from 120-600 µmol/L 
to 60-600 µmol/L. All subjects in this study may have their rAvPAL-PEG dose 
increased to achieve a blood Phe reduction to 60-600 µmol/L (refer to the Synopsis 
[Section 2], Section 9.1, Section 9.1.2, Section 9.4, Section 9.4.6, Section 9.7.3, 
Section 14.3, and Section 14.4) provided none of the safety assessment or stopping 
criteria are met. 
o Revisions to the criteria for blood Phe level and dosing modifications have 
been made to align with the target blood Phe level indicated in Study 
PAL-002 (60-600 µmol/L) and Study PAL-004 ( ≤ 60µmol/L). The 
individualized rAvPAL-PEG dosing will now be based on reductions in 
blood Phe level to within a range of 60-600 µmol/L. Previously, the 
individualized rAvPAL-PEG dosing was based on reductions in blood Phe 
levels to  ≥ 30% of baseline levels. 
4. Subjects who have completed Study PAL-004 are now eligible for enrollment into 
Study PAL-003.  
o The inclusion criterion #1 and exclusion criterion #8 have been revised to 
allow for inclusion of subjects who have completed Study PAL-004 (refer 
to the Synopsis [Section 2], Section 9.3.1, and Section 9.3.2). 
o Instruction regarding re-starting rAvPAL-PEG dosing has been added for 
subjects who completed Study PAL-004 and who are re-starting 
rAvPAL-PEG dosing in this study (refer to the Synopsis [Section 2]and 
Section 9.1) following approximately 4 weeks of no dosing. rAvPAL-PEG 
dosing will be re-started at the same dose level and frequency as was 
administered upon completion of PAL-004. A follow-up telephone call 
will be made to monitor subject safety 24 hours following the return to 
dosing. 
o The number of study sites and the number of participating subjects have 
been increased to accommodate for inclusion of subjects who completed 
Study PAL-004 (refer to Synopsis [Section 2] and Section 9.1). 
5. An exploratory objective has been added to assess the long-term effects of diet and 
change in blood Phe concentration following administration of rAvPAL-PEG (refer to 
Section 8). 
o Information regarding analysis of diet and change in blood Phe 
concentration has been added to the Study Rationale (Section 7.3), the 
Exploratory Efficacy Variable (Section 9.7.4), and the Statistical Analysis 
(Section 14.4) sections. 
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6. Information regarding diet has been revised. Subjects should no longer modify diet 
for blood Phe concentrations  ≤ 120  µmol/L. Diet should now remain stable during 
the study unless directed otherwise by the Investigator in consultation with the 
Sponsor’s Medical Officer (refer to Synopsis [Section 2], Section 9.1, and 
Section 9.6). 
7. Information regarding the allowed number of missed doses has been added to allow 
subjects who miss dosing due to reasons other than non-compliance to continue to 
participate in this long-term extension study. Subjects who miss more than 2 
consecutive weekly doses (subjects who are dosed weekly) or 3 consecutive daily 
doses (subjects who are dosed daily) are allowed to continue in the study (refer to 
Section 9.4.10). Subjects who miss doses due to subject decision, Sponsor decision, 
or Investigator decision may continue to participate in this study but must continue to 
perform the scheduled study assessments for blood Phe levels, pharmacokinetics 
(PK), antibodies, and safety.     
o Instructions have been added regarding how to re-start rAvPAL-PEG 
dosing following a dosing interruption that is not due to subject 
non-compliance. rAvPAL-PEG dosing will be re-started at the same dose 
level and frequency as was administered prior to the dosing interruption. 
o Subjects should continue to perform the scheduled study assessments 
during any dosing interruption. 
8. Information regarding the safety assessment criteria (referred to as the stopping 
criteria in the previous protocol amendment, A2) has been revised to align with the 
criteria in the other Phase 2 studies, PAL-002 and PAL-004.  
o The definition of the safety assessment criteria has been revised to better 
monitor subject safety. Dosing will be halted for subjects who have a 
Common Terminology Criteria for Adverse Events (CTCAE) grade  ≥ 3 
event, including a systemic reaction that is assessed by the Investigator as 
related to treatment with rAvPAL-PEG (Synopsis [Section 2] and 
Section 9.1.3).  
o The definition of the stopping criteria has been revised to better monitor 
subject safety. Dosing will be halted for the subjects at the same dose level 
until a safety evaluation has been completed if 2 or more subjects at a dose 
level have a Common Terminology Criteria for Adverse Events (CTCAE) 
grade  ≥ 3 event, including a systemic reaction that is assessed by the 
Investigator as related to treatment with rAvPAL-PEG (Synopsis 
[Section 2] and Section 9.1.4).  
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o Subjects who are discontinued from study treatment due to safety will now 
be asked to remain in the study and to continue to perform the remaining 
scheduled assessments to continue to collect information, including safety 
information, until study completion (refer to the Synopsis [Section 2] and 
Section 9.3.3).  
9. Based on clinical experience to date (JAN2011) from this ongoing study and ongoing 
Study PAL-002, reductions in blood Phe to normal levels (ie,  60± 13 µmol/L) have 
not had clinical consequences to subject safety. Therefore, information regarding the 
possible toxic effects of low blood Phe has been removed. 
o The Summary of Overall Risks and Benefits (Section 7.4) has been 
revised; information regarding the possible toxic effects of low blood Phe 
(Section 7.4.3) has been removed. 
10. The protocol is being amended to allow for self-administration of rAvPAL-PEG by 
subjects. This change is to facilitate subject recruitment and subject convenience in 
this long-term study. Subjects may self administer study drug at home only if the 
subject meets the protocol-specified requirements, per approval of both the Principal 
Investigator and the Sponsor’s Medical Officer, and if adequate training is 
demonstrated. Additional information will be provided in the PAL-003 Subject 
Self-Administration Training Materials (refer to the Synopsis [Section 2] and 
Section 9.4). 
11. Information regarding systemic reactions and large local reactions has been revised 
based on clinical experience from the ongoing Phase 2 study, PAL-002 (refer to 
Section 9.1.1) and to align with information in the protocols for the other Phase 2 
studies, PAL-002 and PAL-004.  
o Subjects who have had a systemic reaction or a large local reaction not 
contiguous to the injection site during the study are no longer required to 
discontinue from study treatment. Following the reaction, subjects will 
temporarily halt treatment and be required to complete the assessments of 
the Unscheduled Hypersensitivity Reaction visit, including assessment of 
immunoglobulin E (IgE). Subjects who do not have an IgE-mediated 
reaction may resume treatment with study drug per the discretion of the 
Investigator and the Sponsor’s Medical Officer with premedication and 
close monitoring. Subjects who have an IgE-mediated reaction should 
discontinue from further study treatment but continue to complete the 
remaining study assessments. Information for including these subjects in 
this study has been provided in Section 7.4.2.  
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o An additional assessment to monitor subject safety (ie, a drug-specific 
immunoglobulin E [IgE] assay) has been developed and validated for use 
during the study. Subjects who had a systemic reaction in Study PAL-002 
or Study PAL-004 must be premedicated with antihistamine and 
acetaminophen prior to each administration of rAvPAL-PEG in this study 
(Section 9.1.1.3.3). 
o The exclusion criterion (#4) has been revised to allow participation of 
subjects who have had a previous systemic reaction per the discretion of 
the Principal Investigator and the Sponsor’s Medical Officer (refer to the 
Synopsis [Section 2] and Section 9.3.2).  
o An optional skin biopsy of the affected and not affected area has been 
added to the Unscheduled Hypersensitivity Reaction Visit for subjects 
who have had a systemic reaction or a large local reaction not contiguous 
to the injection site. The biopsy is optional per subject consent and should 
be taken within 1 week of the reaction (refer to Section 9.1.1.3.3, Section 
12.3.7, and Table 2.1.1). The biopsy will allow for further monitoring of 
subject safety. 
12. To monitor for subject safety, assessments have been added for subjects who have 
rAvPAL-PEG dosing administered outside of a scheduled clinic visit, including 
subjects who are on a daily dosing regimen. AEs, concomitant medications, and an 
inspection of the injection site will be assessed (refer to Section 12 and Table 2.1.1).  
13. The safety assessments performed during the Unscheduled Hypersensitivity Reaction 
visit are now mandatory for subjects who have a systemic reaction or a large local 
reaction that is not contiguous with the injection site. This revision has been made to 
align with information in the protocols for the other Phase 2 studies, PAL-002 and 
PAL-004. Subjects who have been deemed appropriate to continue study treatment 
must perform the Unscheduled Hypersensitivity Reaction visit assessments prior to 
resuming dosing with rAvPAL-PEG (refer to Section 9.1.1, Section 12, and 
Table 2.1.1). 
14. The secondary objective regarding PK has been removed; rAvPAL-PEG drug 
exposure will be assessed per the objectives added for the Substudy [Section 2] and 
Section 8). In addition, the PK assessments for subjects who have reached target Phe 
levels for at least 2 weeks have been clarified; sampling will be performed once per 
week for 3 consecutive weeks (refer to Section 9.7.3). 
15. The Safety Reporting section has been revised for clarity and to align with 
information in the protocols for the other Phase 2 studies, PAL-002 and PAL-
004(refer to Section 10). 
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16. The required visits that must be performed in the clinic have been clarified; weekly 
visits are not required to be performed in the clinic if performed by a home healthcare 
professional. This change will allow for increased subject compliance (refer to 
Section 12 and Table 2.1.1). 
17. The duration of the study has been extended from 24 months to up to 60 months to 
allow for extended collection of long-term safety information from subjects who are 
administered rAvPAL-PEG (refer to the Synopsis [Section 2] and Section 9.1). 
18. The PK assessments have been removed from the Interim Dosing Visit for subjects 
who increase their dose frequency (refer to Section 12and Table 2.1.3and Table 2.1.4) 
because PK information will now be obtained from the Substudy. 
19. Information regarding the timing of dose administration and sampling for PK and 
blood Phe has been revised; dose administration and sampling no longer need to be 
performed in the morning but must be performed prior to dose administration. This 
change has been made to allow for feasibility of dosing for both sites and subjects 
(refer to Section 9.4.6.1, Section 9.7.2.1, and Section 9.4.6.1). 
20. Results from the completed Phase 1 study, PAL-001, have been added 
(Section 7.2.1). Information regarding Phase 2 Study PAL-002 has been updated and 
information regarding Phase 2 Study PAL-004 has been added to the Background 
section (refer to Section 7.2). 
21. Because the systemic allergic skin reactions reported in ongoing Study PAL-002 and 
this ongoing study to date (JAN2011) have been assessed as variants of delayed 
allergic reactions and do not typically occur until at least 12-24 hours after dose 
administration, the immediate post-dose observation period has been reduced. The 
post-administration observation period has been revised from 2 hours to 30-
60 minutes (refer to the Synopsis [Section 2], Section 7.4.2.2, Section 7.4.3, Section 
9.1, Section 9.1.1.3.3, Figure 9.1.1.3.1, Section 9.1.2.1, and Section 9.4.10). Subjects 
who have a systemic reaction regardless of when it occurs relative to dosing are still 
required to report to the clinic as soon as possible for assessment of safety and to have 
additional laboratory tests performed (ie, the Unscheduled Hypersensitivity Reaction 
Visit; refer to Section 12.3.7).  
o Subjects who increase their dosing frequency are no longer required to 
have the post-administration observation period if the increased frequency 
does not result in an increase in the total weekly dose amount administered 
(refer to the Synopsis [Section 2] and Section 9.1.2.1).  
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22. The maximum amount of dose allowed per injection of 1.0 mg/kg has been removed 
to align with information in the protocols for the other Phase 2 studies, PAL-002 and 
PAL-004; the dose amount and dosing frequency will be managed per the dose 
increases and dose decreases outlined per the revised information in this amendment 
(refer to the Synopsis [Section 2], Section 9.1, and Section 9.1.2).     
23. Phe (fingerstick) assessments have been added for subjects who modify their dose 
due to safety. These additional assessments will allow for blood Phe concentration to 
be assessed more frequently (daily for 3 days) following a change in dose (refer to 
Synopsis [Section 2], Section 9.1.2.1, and Section 12). 
24. A chest X-ray has been added to the Screening visit (refer to Section 12 and 
Table 2.1.1) to monitor for subject safety.  
25. Nonclinical information has been updated with results from the chronic, repeat-dose 
studies and updates made to the Investigators Brochure (version 4, 1MAR2011; refer 
to Section 7.1). 
26. The Schedule of Events (Table 2.1.1) and the Study Procedure section (Section 12) 
have been updated to reflect the changes to this amendment.  
27. Administrative revisions have been made to improve clarity and consistency. 
Specific revisions to the text of each section of the protocol (since the protocol amendment 
finalized on 30OCT2009), including the Synopsis, are outlined in Section 24. 
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2 
SYNOPSIS 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
TITLE OF STUDY: 
Long-term Extension of a Phase 2, Open-Label Dose-Finding Study to Evaluate the Safety, Efficacy, 
and Tolerability of Multiple Subcutaneous Doses of rAvPAL-PEG in Subjects with PKU 
PROTOCOL NUMBER:  PAL-003 
STUDY SITES:  Approximately 20 centers in the United States 
PHASE OF DEVELOPMENT:  Phase 2 
STUDY RATIONALE: 
The need exists for a treatment that will help individuals with phenylketonuria (PKU) safely achieve 
lifelong, reliable control of blood phenylalanine (Phe) concentrations and improve functional 
outcomes. PEGylated recombinant Anabaena variabilis phenylalanine ammonia lyase (rAvPAL-PEG) 
is a potential substitute for the phenylalanine hydroxylase (PAH) enzyme, which is defective in 
individuals with PKU. rAvPAL-PEG may control blood Phe concentrations, which may have 
additional clinical benefits. This study is an extension of the dose-finding studies (Study PAL-002 and 
Study PAL-004). Administration of rAvPAL-PEG will be continued to assess whether long-term 
dosing of rAvPAL-PEG is safe and can maintain reduced blood Phe concentrations in PKU subjects. 
Because rAvPAL-PEG is being assessed as a long-term chronic treatment for patients with PKU, there 
is a need to understand the effect of a temporary dosing interruption on the safety, efficacy (blood 
Phe), PK, and immune response. Therefore, a Substudy has been added to this study to assess the 
effects of stopping and re-starting rAvPAL-PEG treatment in subjects who are on a variety of 
rAvPAL-PEG dosing regimens (dose level and frequency). Up to 10 subjects who are on a variety of 
dosing regimens (dose level and frequency) in this study are eligible for participation in the Substudy 
and will stop dosing for a period of approximately 4 weeks. During this dosing interruption, subjects 
will be assessed for safety, efficacy, PK, and immune response and will continue to perform the 
scheduled study assessments.   
Blood Phe levels depend not only on the functional presence of the endogenous enzyme PAH but also 
on the dietary intake of Phe. It is important to understand the role of diet on blood Phe levels 
concurrent with the administration of rAvPAL-PEG treatment. Therefore, an exploratory objective has 
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May 04, 2011 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
been added to this study to assess the relationship of diet, rAvPAL-PEG administration, and blood Phe 
level. Changes to subject diet are not allowed in this study unless per the Investigator in consultation 
with the Sponsor’s Medical Officer. Diet will be monitored using a diet diary. 
OBJECTIVES: 
The primary objective of the study is: 
• 
To evaluate the effect of long-term administration of multiple doses of SC injections of 
rAvPAL-PEG on blood Phe concentrations in subjects with PKU. 
The secondary objectives of the study are: 
• 
To evaluate the safety and tolerability of long-term administration of subcutaneous (SC) 
injections of rAvPAL-PEG in subjects with PKU. 
• 
To evaluate the immune response to long-term administration of SC injections of 
rAvPAL-PEG in subjects with PKU. 
The exploratory objective of the study is as follows: 
• 
To assess the long-term relationship of diet and change in blood Phe concentration following 
administration with rAvPAL-PEG in subjects with PKU. 
The Substudy objectives are as follows: 
• 
To assess the safety and tolerability of stopping and re-starting rAvPAL-PEG dosing in a 
subset of subjects with PKU. 
• 
To evaluate the effect of stopping and re-starting rAvPAL-PEG dosing on blood Phe 
concentration in a subset of subjects with PKU. 
• 
To evaluate the effect of stopping and re-starting rAvPAL-PEG dosing on immune response in 
a subset of subjects with PKU.   
• 
To assess the effect of multiple doses of rAvPAL-PEG on the PK profile, in particular 
clearance of drug, when drug is stopped in a subset of subjects with PKU who have been 
previously exposed to rAvPAL-PEG.    
 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
STUDY DESIGN AND PLAN: 
This is a long-term extension of the Phase 2, open-label, dose-finding studies, PAL-002 and PAL-004, 
in approximately 100 subjects with PKU. The doses are planned to be in the same range as those tested 
in PAL-002 and PAL-004 (starting at 0.001 through 5.0 mg/kg/week), provided no dose-limiting 
toxicity is observed in PAL-002 or PAL-004. 
Only subjects who completed the protocol-defined study drug regimen in PAL-002 or PAL-004 will 
be enrolled into this study. Subjects who enroll from PAL-002 will either continue the dose regimen 
that was administered upon completion of PAL-002 or start dosing at a higher dose per the dose 
increase instructions. Subjects who enroll from PAL-002 may start this study at a higher dose level 
provided there was no interruption in dosing since completion of PAL-002 and enrollment into this 
study. Subjects who enroll from PAL-004 will re-start rAvPAL-PEG dosing in this study at the same 
dose level and frequency as was administered upon completion of PAL-004. The first dose will be 
administered in the clinic, and the subject must be observed for 30-60 minutes following 
administration due to restarting dosing in this study. A follow-up telephone call will be made to the 
subject to monitor subject safety 24 hours following the return to dosing.  
Diet should not be altered during the course of this study.Any decision to modify subject diet must be 
made per the Investigator in consultation with the Sponsor’s Medical Officer and must be performed 
under the supervision of the Investigaor in consultation with the Sponsor’s Medical Officer. To 
monitor for changes in subject diet, a diet diary will be issued to subjects for completion and will be 
reviewed with the clinical study staff.  
Subjects may self administer study drug at home if approved by the Investigator and the Sponsor’s 
Medical Officer and if adequate training is demonstrated. Subjects must meet a set of criteria to be 
considered appropriate for self administration.   
Subjects will be evaluated for safety throughout the study. Toxicity will be measured according to the 
National Cancer Institute (NCI) Common Terminology Criteria for Adverse Events (CTCAE), 
version 4. 
In addition to the Sponsor, a Data Monitoring Committee (DMC) will monitor the safety of subjects in 
the study. The DMC is an independent committee that will act in an advisory capacity to the Sponsor. 
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take 
rAvPAL-PEG. PAL-002 and PAL-004 subjects’ rAvPAL-PEG dosing will continue in PAL-003. In 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
PAL-003, each subject’s dose will be adjusted as needed to attain or maintain blood Phe 
concentrations of 60-600 µmol/L. Doses will be evaluated on an individual basis. 
Evaluations, observations, and procedures will be conducted at selected time points. After the subject’s 
blood Phe concentration has been controlled to within a target range (60-600 µmol/L), the subject may 
be asked to have additional blood draws for PK and blood Phe concentration analyses as needed per 
the discretion of the Investigator in consultation with the Sponsor’s Medical Officer.  
A subject will continue in PAL-003 until one of the following occurs: 
1. The subject withdraws consent and discontinues from the study. 
2. The subject is discontinued from the study at the discretion of the Investigator. 
3.  The subject has completed the study through the Month 60 visit. 
4.  The study is terminated. 
Subjects may withdraw from treatment with study drug at any time; however, subjects will be asked to 
continue to perform the study assessments until study completion. Subjects may also withdraw from 
study participation at any time. Because the completeness of the data affects the integrity, accuracy, 
and interpretation of study results, every effort should be made to retain subjects in the study and to 
have them complete the study assessments as scheduled as long as continued participation does not 
compromise subject safety. 
PAL-003 Substudy 
A subset of up to 10 subjects who are already enrolled and who have consented to participate in this 
study will be asked to participate in a Substudy to assess the effect that stopping and re-starting 
treatment with rAvPAL-PEG has on safety, efficacy, PK, and immune response. Subjects will be 
eligible for participation in the Substudy provided they also meet all of the PAL-003 eligibility criteria, 
have been on a stable dosing regimen for approximately 4 weeks during this study, have not had any 
serious adverse events reported during PAL-003, and were not enrolled in Study PAL-004. Subjects 
participating in the Substudy will have rAvPAL-PEG administration halted for approximately 4 weeks 
regardless of their dosing regimen (dose level and frequency). rAvPAL-PEG will not be administered 
during the dose interruption; however, subjects will continue to perform assessments for safety, blood 
Phe concentration, PK, and immune response. Subjects enrolled into the Substudy will also have 
additional PK sampling performed prior to the dosing interruption and during the dosing interruption. 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
To allow for PK sampling once dosing is stopped, subjects may be admitted to a research facility 
within 8 hours of stopping dosing where they will reside for at least 24 hours. After the dosing 
interruption, rAvPAL-PEG administration will be re-started at the same dose level and dosing 
frequency that was administered prior to the dosing interruption. Upon re-starting rAvPAL-PEG, the 
first dose must be administered in the clinic and the subject must be observed for 30-60 minutes 
following administration due to restarting dosing. A follow-up telephone call will be made to the 
subject to monitor subject safety 24 hours following the return to dosing. Additional PK sampling will 
also be performed for the first week after the dosing interruption. 
Dose Modifications: 
Dose Increase Methodology
Each subject’s dose may be modified based on the decision of the Investigator, in agreement with the 
Study Medical Officer. Decisions regarding dose increases will depend on a subject’s adverse event 
profile and blood Phe and drug concentrations.  
: 
 
For subjects from PAL-002 only, an individual subject’s dose may be adjusted beginning on Day 1 of 
PAL-003. For the duration of this study, an individual subject’s dose may be adjusted if warranted per 
a subject’s adverse event profile and blood Phe concentrations. Dose increases should be performed as 
follows. 
• The dose may be increased by increments of no more than 10-fold higher than the 
subject’s current dose. 
• When increasing the dose, a dose may be used that is between the dose levels (0.001, 
0.003, 0.01, 0.03, 0.06, 0.1, 0.2, 0.3, 0.4, 0.6, 0.8, 1.0, 2.0, 3.0, 4,0, and 5.0 mg/kg)) or per 
Investigator determination in consultation with the Sponsor’s Medical Officer based on 
available information regarding a subject’s blood Phe (60-600 µmol/L) as well as any 
adverse events (any hypersensitivity reaction) for an individual subject. 
• The dose may be adjusted by increasing the frequency up to dailyfor a total weekly dose 
not to exceed 5.0 mg/kg.Subjects who increase their dose frequency will have additional 
assessments performed (Interim Dosing Visit). 
• When a dose is increased, the subject must be observed for 30-60 minutes following the 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
first modified dose administration. Subjects who increase their dose frequency do not 
need to be observed following injection of study drug if the increase in frequency does not 
increase the overall weekly dose amount. 
• Only 1 dose (level or frequency) adjustment is allowed every 2 weeks. 
• Blood Phe levels will be measured daily for 3 days after each dose increase (fingerstick is 
acceptable); more frequent or daily blood Phe measurements may be performed. 
 
Dose Decrease Methodology 
All dose decreases must be agreed to by both the Investigator and the Sponsor’s Medical Officer. 
Decisions regarding dose decreases will depend on available information regarding a subject’s blood 
Phe (60-600 µmol/L), as well as any adverse events (any hypersensitivity reaction). Dose decreases 
may occur for safety (ie,   any adverse event that may be improved with a lower, more frequent dose).  
A dose should first be reduced by dose level (5.0, 4.0, 3.0, 2.0, 1.0, 0.8, 0.6, 0.4, 0.3, 0.2, 0.1, 0.06, 
0.03, 0.01, 0.003, 0.001 mg/kg). It is also permitted to decrease dose in between these specified dose 
levels. If further dosing adjustments are required to attain the target Phe concentration, dosing 
frequency may be reduced.  
Safety Assessment Criteria
If an individual subject exhibits toxicity of a treatment-emergent CTCAE grade 3 or greater or a 
systemic reaction that is assessed as related to treatment with study drug, that subject will have dosing 
halted until the toxicity resolves. The subject’s data will be evaluated by the Principal Investigator (PI) 
and the Study Medical Officer, and a decision will then be made whether to discontinue the subject 
from the study treatment, restart dosing at the same dose level, or restart dosing at a lower dose level. 
: 
Stopping Criteria: 
If 2 or more subjects at a dose level exhibit toxicity of a treatment-emergent CTCAE grade 3 or greater 
or a systemic reaction that is assessed as related to treatment with study drug, further dosing of 
subjects at that dose level will be evaluated  and  a safety assessment will be completed. In addition, 
the Food and Drug Administration (FDA) may be notified of this occurrence if appropriate. 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
NUMBER OF SUBJECTS PLANNED: 
Approximately 100 subjects. 
DIAGNOSIS AND ALL CRITERIA FOR INCLUSION AND EXCLUSION:  
Individuals eligible to participate in this study must meet all of the following criteria: 
1. Must have completed participation and all protocol-defined study drug in PAL-002 or 
PAL-004. 
2. Willing and able to provide written, signed informed consent, or, in the case of 
participants under the age of 18, provide written assent (if required) and written informed 
consent by a parent or legal guardian, after the nature of the study has been explained, and 
prior to any research-related procedures. 
3. Willing and able to comply with all study procedures. 
4. Females of childbearing potential must have a negative pregnancy test at Screening and be 
willing to have additional pregnancy tests during the study. Females considered not of 
childbearing potential include those who have been in menopause at least 2 years, or had 
tubal ligation at least 1 year prior to Screening, or who have had total hysterectomy. 
5. Sexually active subjects must be willing to use an acceptable method of contraception 
while participating in the study. 
6. Maintained a stable diet. 
7. In generally good health as evidenced by physical examination, clinical laboratory 
evaluations (hematology, chemistry, and urinalysis), and electrocardiogram (ECG) at 
Screening. 
Individuals who meet any of the following exclusion criteria will not be eligible to participate in the 
study: 
1. Use of any investigational product (with the exception of rAvPAL-PEG) or investigational 
medical device within 30 days prior to Screening, or requirement for any investigational 
agent prior to completion of all scheduled study assessments. 
2. Use of any medication other than rAvPAL-PEG that is intended to treat PKU within 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
14 days prior to the administration of study drug. 
3. Use or planned use of any injectable drugs containing PEG (other than rAvPAL-PEG), 
including Depo-Provera, within 6 months prior to Screening and during study 
participation. 
 
4. A prior reaction that included systemic symptoms (eg, generalized hives, respiratory or 
gastrointestinal problems, hypotension, angioedema, anaphylaxis) to rAvPAL-PEG or a 
PEG-containing product. Subjects with a prior systemic reaction of generalized rash may 
be eligible for participation per the discretion of the Principal Investigator in consultation 
with the Sponsor’s Medical Officer. However, subjects who discontinued from study 
treatment early due to a reaction are not eligible to enroll into this study.    
5. Pregnant or breastfeeding at Screening or planning to become pregnant (self or partner) or 
to breastfeed at any time during the study.  
6. Concurrent disease or condition that would interfere with study participation or safety 
(eg, history or presence of clinically significant cardiovascular, pulmonary, hepatic, renal, 
hematologic, gastrointestinal, endocrine, immunologic, dermatologic, neurological, 
oncologic, or psychiatric disease). 
7. Any condition that, in the view of the PI, places the subject at high risk of poor treatment 
compliance or of not completing the study. 
8. Known hypersensitivity to rAvPAL-PEG or its excipients, including hypersensitivity 
reactions that necessitated early termination from PAL-002 or PAL-004. 
9. Alanine aminotransferase (ALT) concentration > 2 times the upper limit of normal. 
10. Creatinine  > 1.5 times the upper limit of normal. 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
INVESTIGATIONAL PRODUCT, DOSE, ROUTE AND REGIMEN: 
rAvPAL-PEG   will be provided in 3 mL (milliliter) vials, each containing 1. 5 ± 0.2 mL to deliver 10 
mg of rAvPAL-PEG per 1 mL (10 mg/mL protein concentration). Each vial is filled with 1. 5 ± 0.2 
mL to allow the withdrawal and delivery of up to 1 mL of the drug product.  
Upon enrollment into this study, subjects from PAL-002 will be dosed with the same or higher dose 
than the dose that was administered upon completion of PAL-002. Subjects enrolling from PAL-004, 
will be administered the same dose that was administered upon completion of PAL-004. rAvPAL-PEG 
doses will be administered SC by either health care professionals or via self administration. The dose 
level may be increased per Investigator determination in consultation with the Sponsor’s Medical 
Officer based on on available information regarding a subject’s blood Phe level (60-600 µmol/L), as 
well as any adverse events (any hypersensitivity reaction) for an individual subject. The dosage that 
provides control of blood Phe concentrations within the target range of 6120-600 µmol/L for a 
minimum of 2 weeks will be determined for each subject by adjusting the dose level, dose frequency, 
or both, as agreed by the PI and the Study Medical Officer, based upon the subject’s response to doses. 
 
DURATION OF TREATMENT: 
Up to 60 months. 
REFERENCE THERAPY(IES), DOSE, ROUTE AND REGIMEN:  
None 
CRITERIA FOR EVALUATION: 
Efficacy: 
Blood Phe concentrations will be measured.  
Immunogenicity: 
The presence of antibodies (anti-PAL immunoglobulin G [IgG], anti-PAL IgM, anti-PEG IgG, anti-
PEG IgM, anti-rAvPAL-PEG neutralizing antibodies, and anti-PEG-PAL IgE) will be assessed. 
Safety: 
Safety will be evaluated on the incidence of adverse events (AEs) and clinically significant changes in 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
vital signs, ECG results, X-ray results, and laboratory test results. 
Pharmacokinetic: 
Plasma concentrations of rAvPAL-PEG will be measured for subjects participating in the Substudy. 
STATISTICAL METHODS:  
Sample Size: 
Subjects who participated in PAL-002 or PAL-004 may be enrolled into this study. No formal sample 
size calculation was conducted for this study or the PAL-003 Substudy. 
Safety Analysis: 
All subjects who receive any amount of study drug in this study and have postdose safety information 
will be included in the safety analyses. 
All AEs will be coded using the Medical Dictionary for Regulatory Activities (MedDRA). The 
incidence of AEs will be summarized by system organ class, preferred term, relationship to study drug, 
and severity. A by–subject listing will be provided for those subjects who experience a serious AE 
(SAE), including death, or experience an AE associated with early withdrawal from the study or study 
drug. Clinical laboratory data will be summarized by the type of laboratory test. Frequency and 
percentage of subjects who experience abnormal (ie, outside of reference range) and/or clinically 
significant abnormalities after study drug administration will be presented for each clinical laboratory 
test. For each clinical laboratory test, descriptive statistics will be provided for baseline and all 
subsequent post-treatment visits. Changes from baseline to the post-treatment visits will also be 
provided. Descriptive statistics, including clinically significant changes from baseline, of vital signs, 
ECG results, and X-ray results will also be provided. 
Efficacy Analysis: 
Data from all subjects who receive any amount of study drug and who have any post-treatment 
efficacy data will be included in the efficacy analysis. 
Blood Phe concentration at each scheduled time point will be summarized using descriptive statistics 
(mean, standard deviation, median, minimum, and maximum). Change in blood Phe concentration 
from baseline to each scheduled time point and presence/absence of antibodies will also be 
summarized. In addition, the proportion of subjects who have maintained target Phe concentrations of 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
60-600 µmol/L will be summarized by each scheduled time point. 
Exploratory Analysis: 
For subjects who have received any study drug in this study with any post-treatment blood Phe 
concentration measurements and diet diary information, the relationship of dietary Phe intake (per 
information reported on the subject diet diary) and blood Phe concentration will be explored.  
Substudy Analysis: 
For subjects who completed the Substudy, the effect of stopping and re-starting rAvPAL-PEG dosing 
on safety, blood Phe level, and immune response will be explored. 
Pharmacokinetic Analysis: 
Subjects who complete the Substudy will have the following PK parameters assessed: area under the 
plasma concentration-time curve (AUC), time to maximum plasma concentration (Tmax), maximum 
plasma concentration (Cmax), half life (t1/2), and clearance (CL/F).  
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2.1 
Schedule of Events 
Table 2.1.1:  Schedule of Events 
Assessments and Events 
Screeninga 
Treatment Periodb,c 
Final F/U 
Visit 
Early Term. 
Visit 
Unsched. 
Hyper. 
Reaction 
Visit.d  
Perform 
within 
48 hours; 
then 
perform 
Early Term. 
procedures 
Week 1 
Weekly 
Monthly 
(eg, Wk 4, 8, 
etc.) 
Quarterly  
(eg, Wk 12, 
24, etc.) 
D 1 
Starting at 
Week 2 
Every 4th 
week; 
Perform in 
addition to 
weekly 
procedures 
Every 12th 
week. 
Perform in 
addition to 
monthly 
procedures 1 week after 
final dose 
4 weeks after 
final dose 
Informed consent 
 
X 
 
 
 
 
 
 
 
Medical history, including allergy 
history, and demographics 
 
X 
 
 
 
 
 
 
 
Physical examinatione 
 
X 
X 
 
 
X 
X 
X 
 
Vital signs and weighte 
 
X 
X 
X 
 
 
X 
X 
 
12-lead ECG 
 
X 
 
 
 
 
X 
X 
 
Clinical laboratory testsf 
 
X 
 
 
X 
 
X 
X 
Xg 
Sedimentation rate 
 
X 
 
 
X 
X 
X 
X 
Chest x-ray 
X 
 
 
X  
(12-month 
visit only) 
 
X 
X 
 
Urine pregnancy testh 
 
X 
X 
 
X 
 
X 
X 
 
Injection-site inspectioni, k 
 
X 
(postdose) 
X 
 
 
X 
X 
X 
Adverse eventsj, k 
 
X--------------------------------------------------------------------------------------X 
X 
X 
Concomitant medicationsk 
 
X 
X 
X 
 
 
 
X 
 
X 
X 
Diet query 
 
X 
X 
X 
 
 
 
X 
 
X 
 
3-Day diet diaryl 
 
 
X 
 
 
X 
X 
 
Serum antibodies  
 
X 
 
X 
 
 
X 
 
X 
X 
Plasma Phe and plasma tyrosinem 
 
X 
X 
X 
 
 
X 
X 
 
Plasma Phe (fingerstick)n 
 
 
(3 days 
postdose) 
 
 
 
 
 
Plasma PK sampleo 
 
X 
X 
 
 
X 
X 
X 
Administer IPp 
 
X 
X 
 
 
 
 
 
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Assessments and Events 
Screeninga 
Treatment Periodb,c 
Final F/U 
Visit 
Early Term. 
Visit 
Unsched. 
Hyper. 
Reaction 
Visit.d  
Perform 
within 
48 hours; 
then 
perform 
Early Term. 
procedures 
Week 1 
Weekly 
Monthly 
(eg, Wk 4, 8, 
etc.) 
Quarterly  
(eg, Wk 12, 
24, etc.) 
D 1 
Starting at 
Week 2 
Every 4th 
week; 
Perform in 
addition to 
weekly 
procedures 
Every 12th 
week. 
Perform in 
addition to 
monthly 
procedures 1 week after 
final dose 
4 weeks after 
final dose 
Skin biopsy (optional; affected and 
not affected area) 
 
 
 
 
 
 
 
X 
Serum tryptase level q 
 
 
 
 
 
 
 
X 
AE, adverse event; C3, complement 3; C4, complement 4; CH50, total hemolytic complement; CRP, C-reactive protein; D, day; ECG, electrocardiogram; ETV, Early 
Termination Visit; F/U, Follow-up; Hyper, hypersensitivity; IgE, immunoglobulin E; IgG, immunoglobulin G; IgM, immunoglobulin M; IP, investigational product; PK, 
pharmacokinetics; Phe, phenylalanine; SAE, serious adverse event; Wk, week. 
a It is preferable to perform PAL-003 Screening assessments the same day as PAL-002 Week 16 visit or PAL-004 Week 16 visit so there is no interruption of study drug. 
If performed on the same day, PAL-002 Week 16 visit or PAL-004 Week 16 visit data may be used.  If not, PAL-003 Day 1 must occur  ≤ 28 days after PAL-003 
Screening. 
b Weekly visits do not require an in-clinic visit if conducted by a home healthcare professional. Monthly visits must be performed in the clinic. Dose modifications must 
be performed in the clinic. Additional visits may occur if deemed necessary to monitor AEs or blood Phe, adjust dosing etc. 
c On days that a dose is given, all procedures should be performed predose, except where noted. 
d Unscheduled hypersensitivity reaction assessments are mandatory for subjects who have a generalized skin reaction. Subjects who have other systemic symptoms or who 
have a large local skin reaction that is not contiguous to the injection site may have these assessments performed per investigator discretion. Assessments should be 
performed within 48 hours of the reaction Subjects who do not have an IgE-mediated reaction may resume study drug administration per the discretion of the Principal 
Investigator and the Sponsor’s Medical Officer with close monitoring. Subjects who remain in the study and continue study treatment must be premedicated. Refer to 
Section 9.1.1.3.3and Section 12.3.7. 
e Complete physical examinations to include the evaluation of all major body systems. Height will be measured at Screening only. 
f Clinical laboratory tests to include hematology, chemistry, and urinalysis. Refer to Table 9.7.6.1. 
g Subjects who have a systemic reaction or a large local reaction not contiguous with the injection site should be assessed for CRP, CH50, C1, C3, and C4 within 48 hours 
of the reaction.  
h If positive or equivocal, perform serum pregnancy test. 
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i If any injection site reaction is observed, the corresponding adverse event data must specify injection location (identify current vs. previous visit’s injection, eg, right arm 
vs. left arm). 
j The reporting period for SAEs begins when informed consent is obtained and continues through 4 weeks after last dose or the final study visit. The reporting period for 
nonserious AEs is from the first administration of study drug to the final study visit.  
k Subjects must have AEs and concomitant medications assessed and an injection-site inspection performed whenever dose is administered even if the administration does 
not coincide with a scheduled clinic visit.   
lIt is preferable that the subject complete the diary 3 days immediately prior to the next dose of study drug. 
m Samples should be drawn at least 2.5 hours after a meal. If dose is modified by increasing dose level, additional blood Phe concentration testing should be done on the 
third day following dose adjustment.  
n May be done by the subject at home. Samples should be taken at least 2.5 hours after a meal. Will be performed daily for 3 consecutive days after each dose increase. 
o The PK blood samples will be collected after the subject has achieved and maintained target blood Phe concentrations (60-600 μmol/L) for a minimum of 2 weeks. Once 
this target is achieved, once weekly predose PK samples will be collected for 3 consecutive weeks.   
p Dosing is up to 5.0 mg/kg/week, including subjects who receive more than 1 dose/week. Every effort should be made to adhere to the study drug administration regimen. 
If a subject misses more than 2 scheduled doses of study drug, both dose level and dose frequency will need to be re-evaluated.  
q Mandatory for subjects who have a systemic reaction or a large local skin reaction that is not contiguous to the injection site. Take sample immediately after reaction if 
possible. 
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Table 2.1.2:  Schedule of Events-Substudy 
Substudy 
Assessments and Events 
Substudy Perioda 
 
Final Dose 
(Day 1) 
Day 8 
Day 15 
Day 22 
Re-start Dose 
(Day 29) 
Physical examination b 
X 
X 
X 
X 
X 
Vital signs and weight 
X 
X 
X 
X 
X 
Clinical laboratory tests 
X 
X 
X 
X 
X 
Sedimentation rate 
X 
X 
X 
X 
X 
Urine pregnancy test c 
X 
X 
X 
X 
X 
Injection-site inspection d 
X 
(Pre & 
postdose) 
 
 
 
X 
(postdose) 
Adverse events  
X 
X 
X 
X 
X 
Concomitant medications 
X 
X 
X 
X 
X 
Diet query 
X 
X 
X 
X 
X 
3-Day diet diary e 
X 
X 
X 
X 
X 
Serum antibodies  
X 
X 
X 
X 
X 
Plasma Phe and plasma tyrosine 
X 
X 
(8, 12, and 16 hours/Day 1, 24 hours/Day 2, 48 hours/Day 
3, 72 hours/Day 4, 96 hours/Day 5, 144 hours/Day 7, 168 
hours/Day 8, 216 hours/Day 10 after Final Dose) 
X 
(Predose and 24 hours/Day 2, 48 
hours/Day 3, 72 hours/Day 4, 120 
hours/Day 6, 168 hours/Day 8 after Re-
start Dose 
Plasma PK sample 
 
X 
(Predose) 
X 
(8, 12, and 16 hours/Day 1, 24 hours/Day 2, 48 hours/Day 
3, 72 hours/Day 4, 96 hours/Day 5, 144 hours/Day 7, 168 
hours/Day 8, 216 hours/Day 10 after Final Dose) 
X 
(Predose and 24 hours/Day 2, 48 
hours/Day 3, 72 hours/Day 4, 120 
hours/Day 6, 168 hours/Day 8 after Re-
start Dose 
Administer IP 
X 
 
 
 
X 
AE, adverse event; IP, investigational product; PK, pharmacokinetics; Phe, phenylalanine. 
a On days that a dose is given, all procedures should be performed predose, except where noted. 
b Complete physical examinations to include the evaluation of all major body systems. 
c If positive or equivocal, perform serum pregnancy test. 
d If any injection site reaction is observed, the corresponding adverse event data must specify injection location (identify current vs. previous visit’s injection, eg, right arm 
vs. left arm). 
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eIt is preferable that the subject complete the diary 3 days immediately prior to the next dose of study drug on Substudy Days 1 and 29. On Substudy Days 8, 15, and 22, it 
is preferable that the subject complete the diary 3 days immediately prior to the next study visit. 
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Table 2.1.3:  Interim Dosing Visit Schedule, Subjects Whose Dose is Increased to 2x/Week 
Assessments and 
Events 
Subjects Who Are Administered rAvPAL-PEG  2x/Week 
Treatment Perioda, b 
First Week After 
Dose Adjustment 
Second Week After 
Dose Adjustment 
Third Week After 
Dose Adjustment 
Fourth Week After 
Dose Adjustment 
Fifth Week After 
Dose Adjustment 
First 
Dose 
Second 
Dose 
First 
Dose 
Second 
Dose 
First 
Dose 
Second 
Dose 
First 
Dose 
Second 
Dose 
First 
Dose 
Second 
Dose 
Vital signs and weight 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Injection-site 
inspection 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Adverse eventsc 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Concomitant 
medications 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Blood Phe 
(fingerstick)d 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
AE, adverse event; D, day; PK, pharmacokinetics; Phe, phenylalanine. 
a The additional Interim Dosing Visit assessments should be performed for 5 weeks after the subject’s rAvPAL-PEG dose frequency has been increased to 2x/week. All 
assessments should be performed predose unless specified otherwise. 
b If the Interim Dosing Visit coincides with a regularly scheduled visit, the scheduled visit assessments should also be performed.  
c If any injection site reaction is observed, the corresponding AE data must specify injection location (identify current vs. previous visit’s injection, e.g,. right arm vs. left 
arm). 
d May be done by the subject at home. Samples should be taken in the morning, at least 2.5 hours after a meal. 
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Table 2.1.4:  Interim Dosing Visit Schedule, Subjects Whose Dose is Increased to Daily 
Assessments and Events 
Subjects Who Are Administered rAvPAL-PEG Daily 
Treatment Perioda, b 
First Day After 
Dose Adjustment 
First Week After 
Dose Adjustment 
Second Week 
After Dose 
Adjustment 
Third Week After 
Dose Adjustment 
Fourth Week After 
Dose Adjustment 
Fifth Week After 
Dose Adjustment 
Dose 1 
Doses 2-7 
Doses 8-14 
Doses 15-21 
Doses 22-29 
Doses 30-36 
Vital signs and weight 
X 
X 
X 
X 
X 
X 
Injection-site inspection 
X 
X 
X 
X 
X 
X 
Adverse eventsc 
X 
X 
X 
X 
X 
X 
Concomitant 
medications 
X 
X 
X 
X 
X 
X 
Blood Phe (fingerstick)d 
X 
X 
X 
X 
X 
X 
AE, adverse event; D, day; PK, pharmacokinetics; Phe, phenylalanine. 
a The additional Interim Dosing Visit assessments should be performed for 5 weeks after the subject’s rAvPAL-PEG dose frequency has been increased to daily. All 
assessments should be performed predose unless specified otherwise. 
b the Interim Dosing Visit coincides with a regularly scheduled visit, the scheduled visit assessments should also be performed. 
c If any injection site reaction is observed, the corresponding AE data must specify injection location (identify current vs. previous visit’s injection, e.g,. right arm vs. left 
arm). 
d May be done by the subject at home. Samples should be taken in the morning, at least 2.5 hours after a meal. 
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3 
TABLE OF CONTENTS 
1 TITLE PAGE .......................................................................................................................1 
2 SYNOPSIS .........................................................................................................................14 
2.1 Schedule of Events ....................................................................................................25 
3 TABLE OF CONTENTS ...................................................................................................32 
4 LIST OF ABBREVIATIONS AND DEFINITIONS OF TERMS ....................................36 
5 ETHICS..............................................................................................................................39 
5.1 Institutional Review Board or Ethics Committee .....................................................39 
5.2 Ethical Conduct of Study ..........................................................................................39 
5.3 Subject Information and Informed Consent ..............................................................40 
6 INVESTIGATORS AND STUDY ADMINISTRATIVE STRUCTURE ........................41 
7 INTRODUCTION .............................................................................................................42 
7.1 Nonclinical Studies ...................................................................................................42 
7.2 Previous Clinical Studies ..........................................................................................44 
7.2.1 
Phase 1 Study PAL-001 ..............................................................................44 
7.2.2 
Phase 2 Studies PAL-002 and PAL-004 .....................................................45 
7.3 Study Rationale .........................................................................................................46 
7.4 Summary of Overall Risks and Benefits ...................................................................48 
7.4.1 
Toxicity Due to Exposure to PEG ...............................................................48 
7.4.2 
Toxicity Due to an Immunologic Reaction .................................................49 
7.4.3 
Effects of Stopping and Re-Starting rAvPAL-PEG Treatment ...................52 
8 STUDY OBJECTIVES ......................................................................................................55 
9 INVESTIGATIONAL PLAN ............................................................................................56 
9.1 Overall Study Design and Plan .................................................................................56 
9.1.1 
Management of Local and Systemic Reactions to rAvPAL-PEG ...............58 
9.1.2 
Dose Modifications .....................................................................................63 
9.1.3 
Safety Assessment Criteria ..........................................................................64 
9.1.4 
Stopping Criteria .........................................................................................64 
9.2 Discussion of Study Design, Including Choice of Control Group ............................64 
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9.3 Selection of Study Population ...................................................................................65 
9.3.1 
Inclusion Criteria .........................................................................................65 
9.3.2 
Exclusion Criteria ........................................................................................65 
9.3.3 
Removal of Subjects from Treatment or Assessment .................................66 
9.3.4 
Subject Identification and Replacement of Subjects ...................................67 
9.4 Treatments .................................................................................................................68 
9.4.1 
Treatments Administered ............................................................................69 
9.4.2 
Identity of Investigational Product (IP) .......................................................70 
9.4.3 
Storage .........................................................................................................70 
9.4.4 
Directions for Administration .....................................................................70 
9.4.5 
Method of Assigning Subjects to Treatment Groups ..................................72 
9.4.6 
Selection of Doses Used in the Study .........................................................72 
9.4.7 
Blinding .......................................................................................................73 
9.4.8 
Prior and Concomitant Medications ............................................................73 
9.4.9 
Treatment Compliance ................................................................................74 
9.4.10 Dose Interruption and Missed Doses ...........................................................74 
9.5 Investigational Product Accountability .....................................................................74 
9.5.1 
Return and Disposition of Clinical Supplies ...............................................74 
9.6 Dietary or Other Protocol Restrictions......................................................................75 
9.7 Efficacy and Safety Variables ...................................................................................75 
9.7.1 
Efficacy and Safety Measurements Assessed .............................................75 
9.7.2 
Efficacy Variable .........................................................................................77 
9.7.3 
Pharmacokinetic Variables ..........................................................................77 
9.7.4 
Exploratory Efficacy Variable .....................................................................77 
9.7.5 
Safety Variables ..........................................................................................78 
9.7.6 
Clinical Laboratory Assessments ................................................................78 
10 REPORTING ADVERSE EVENTS .................................................................................80 
10.1 Adverse Events .........................................................................................................80 
10.2 Serious Adverse Events ............................................................................................83 
10.3 Pregnancy ..................................................................................................................84 
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10.4 Urgent Safety Measures ............................................................................................84 
10.5 BioMarin Pharmacovigilance Contact Information ..................................................86 
11 APPROPRIATENESS OF MEASUREMENTS ...............................................................87 
11.1 Safety and Pharmacokinetics ....................................................................................87 
11.2 Diet Diary ..................................................................................................................87 
12 STUDY PROCEDURES ...................................................................................................88 
12.1 Prestudy .....................................................................................................................88 
12.2 Screening Visit ..........................................................................................................88 
12.3 Treatment Period .......................................................................................................88 
12.3.1 Day 1 (Week 1) ...........................................................................................89 
12.3.2 Weekly Visits ..............................................................................................90 
12.3.3 Substudy Visits (Weekly) ............................................................................91 
12.3.4 Monthly Visits (Week 4, 8, 12, etc) ............................................................92 
12.3.5 Quarterly Visits (Week 12, 24, 36, etc) .......................................................93 
12.3.6 Interim Dosing Visit ....................................................................................94 
12.3.7 Unscheduled Hypersensitivity Reaction Visit .............................................94 
12.4 Early Termination Visit ............................................................................................95 
12.5 Final Follow-up Visit ................................................................................................96 
13 DATA QUALITY ASSURANCE .....................................................................................97 
14 STATISTICAL METHODS AND DETERMINATION OF SAMPLE SIZE ..................98 
14.1 Statistical and Analytical Plans .................................................................................98 
14.2 Safety Analysis .........................................................................................................98 
14.3 Pharmacokinetic Analysis .........................................................................................98 
14.4 Efficacy Analysis ......................................................................................................99 
14.5 Determination of Sample Size ..................................................................................99 
14.6 Handling of Missing Data .........................................................................................99 
14.7 Interim Analyses .......................................................................................................99 
14.8 Changes in the Conduct of the Study or Planned Analyses ......................................99 
15 DATA MONITORING COMMITTEE (DMC) ..............................................................101 
16 COMPENSATION, INSURANCE, AND INDEMNITY ...............................................102 
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4 
LIST OF ABBREVIATIONS AND DEFINITIONS OF TERMS 
ADR 
Abbreviations 
adverse drug reaction 
AE 
adverse event 
ALT 
alanine aminotransferase 
AST 
aspartate aminotransferase 
AUC 
area under the plasma concentration-time curve 
AUC0-7 days 
area under the plasma concentration-time curve from time zero on Day 1 
to Day 8 
BUN 
blood urea nitrogen 
°C 
degree Celsius 
C3 
complement 3 
C4 
complement 4 
CBC 
complete blood count 
CD 
Compact disk 
CFR 
Code of Federal Regulations 
CH50 
total hemolytic complement 
Cmax 
maximum plasma concentration 
CNS 
central nervous system 
CO2 
carbon dioxide 
CRA 
Clinical Research Associate 
CRF 
case report form 
CRP 
C-reactive protein 
CTCAE 
Common Terminology Criteria for Adverse Events 
CV 
cardiovascular 
DBP 
diastolic blood pressure 
DMC 
Data Monitoring Committee 
ECG 
electrocardiogram 
ETV 
Early Termination Visit 
FDA 
Food and Drug Administration 
F/U 
follow-up 
g 
gram 
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GCP 
Good Clinical Practice 
GGT 
gamma-glutamyltransferase 
GI 
gastrointestinal 
IB 
Investigator’s Brochure 
ICF 
Informed Consent Form 
ICH 
International Conference on Harmonisation of Technical Requirements for 
Registration of Pharmaceuticals for Human Use 
IgE 
immunoglobulin E 
IgG 
immunoglobulin G 
IgM 
immunoglobulin M 
IP 
investigational product 
IRB 
Institutional Review Board 
IV 
intravenous 
kg 
kilogram 
MedDRA 
Medical Dictionary for Regulatory Activities 
mg 
milligram 
mL 
milliliter 
mm Hg 
millimeter of mercury 
NAb 
neutralizing antibodies 
NCI 
National Cancer Institute 
NOAEL 
no observable adverse effect level 
OTC 
over the counter 
PAH 
phenylalanine hydroxylase 
PAL 
phenylalanine ammonia lyase 
PEG 
polyethylene glycol 
Phe 
phenylalanine 
PI 
Principal Investigator 
PK 
pharmacokinetics 
PKU 
phenylketonuria 
rAvPAL-PEG recombinant Anabaena variabilis phenylalanine ammonia lyase-PEG 
RBC 
red blood cell 
SAE 
serious adverse event 
SAP 
Statistical Analysis Plan 
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SBP 
systolic blood pressure 
SC 
subcutaneous 
SD 
standard deviation 
SDV 
source data verified 
SGOT 
serum glutamic oxalo-acetic transaminase 
SGPT 
serum glutamic pyruvate transaminase 
US 
United States 
WBC 
white blood cell 
Definition of Terms: 
Investigational Product (IP): 
“A pharmaceutical form of an active ingredient or placebo being tested or used as a reference 
in a clinical trial, including a product with a marketing authorization when used or assembled 
(formulated or packaged) in a way different from the approved form, or when used for an 
unapproved indication, or when used to gain further information about an approved use.” 
(from E6 ICH)  
The terms “IP” and “study drug” may be used interchangeably in the protocol. 
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5 
ETHICS 
5.1 
Institutional Review Board or Ethics Committee 
Prior to initiating the study, the Investigator will obtain written confirmation that the 
Institutional Review Board (IRB) is properly constituted and compliant with International 
Conference on Harmonisation of Technical Requirements for Registration of 
Pharmaceuticals for Human Use (ICH) and Good Clinical Practice (GCP) requirements, and 
applicable laws and local regulations. A copy of the confirmation from the IRB will be 
provided to BioMarin Pharmaceutical Inc. (BioMarin) or its designee. The Principal 
Investigator (PI) will provide the IRB with all appropriate material, including the protocol, 
Investigator’s Brochure (IB), the Informed Consent Form (ICF) including compensation 
procedures, and any other written information provided to the subjects, including all consent 
forms translated to a language other than the native language of the clinical site. The study 
will not be initiated and investigational product (IP) supplies will not be shipped to the site 
until appropriate documents from the IRB confirming unconditional approval of the protocol, 
the ICF and all subject recruitment materials are obtained in writing by the PI and copies are 
received at BioMarin or its designee. The approval document should refer to the study by 
protocol title and BioMarin protocol number (if possible), identify the documents reviewed, 
and include the date of the review and approval. BioMarin will ensure that the appropriate 
reports on the progress of the study were made to the IRB and BioMarin by the PI in 
accordance with applicable governmental regulations. 
5.2 
Ethical Conduct of Study 
This study will be conducted in accordance with the following: 
• United States (US) Code of Federal Regulations (CFR) sections that address clinical 
research studies, and/or other national and local regulations, as applicable 
• E6 ICH Guideline for GCP 
• The ethical principles established by the Declaration of Helsinki 
Specifically, this study is based on adequately performed laboratory and animal 
experimentation; the study will be conducted under a protocol reviewed and approved by an 
IRB; the study will be conducted by scientifically and medically qualified persons; the 
benefits of the study are in proportion to the risks; the rights and welfare of the subjects will 
be respected; the physicians conducting the study do not find the hazards to outweigh the 
potential benefits; and each subject, or his or her legally authorized representative will 
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provide written, informed consent before any study-related tests or evaluations are 
performed. 
5.3 
Subject Information and Informed Consent 
A properly written and executed ICF, in compliance with the Declaration of Helsinki, 
E6 ICH (GCP Guideline, Section 4.8) and 21 CFR Part 50 and other applicable local 
regulations, will be obtained for each subject prior to entering the subject into the study. The 
Investigator will prepare the ICF and provide the documents to BioMarin for approval prior 
to submission to the IRB. BioMarin and the IRB must approve the documents before they are 
implemented. A copy of the approved ICF, and if applicable, a copy of the approved subject 
information sheet, minor assent form, parental ICF for studies involving minors, and all ICFs 
translated to a language other than the native language of the clinical site must also be 
received by BioMarin or its designee prior to the delivery of study drug. 
Subjects under the age of 18 years will provide written assent (if required), and his/her 
legally authorized representative (parent or legal guardian) will provide written informed 
consent for such subjects. The Investigator will provide copies of the signed ICF to each 
subject (or the subject’s legally authorized representative) and will maintain the original in 
the subject’s record file. 
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6 
INVESTIGATORS AND STUDY ADMINISTRATIVE STRUCTURE 
Prior to beginning the study, the PI at each site must provide to BioMarin or its designee a 
fully executed and signed Form FDA (Food and Drug Administration) 1572 and a Financial 
Disclosure Form. All sub-Investigators must be listed on Form FDA 1572. Financial 
Disclosure Forms must also be completed for all sub-Investigators listed on the 
Form FDA 1572 who will be directly involved in the treatment or evaluation of research 
subjects in this study. 
The study will be administered by and monitored by employees or representatives of 
BioMarin. Clinical Research Associates (CRAs) or trained designees will monitor each site 
on a periodic basis and perform verification of source documentation for each subject as well 
as other required review processes. BioMarin’s Regulatory Affairs Department (or designee) 
will be responsible for the timely reporting of serious adverse events (SAEs) to appropriate 
regulatory authorities as required. Some study assessments, including administration of study 
drug, may be performed at the subject’s home. All assessments performed for this study will 
be administered by clinic staff or other qualified and trained study personnel. 
Anti-rAvPAL-PEG (recombinant Anabaena variabilis phenylalanine ammonia lyase 
polyethylene glycol) immunoglobulin E (IgE) antibody analysis will be performed by a 
vendor; other antibody analysis will be performed by BioMarin. Clinical laboratory tests, 
including serum pregnancy tests (if applicable), will be analyzed and processed by a central 
laboratory, with the exception of erythrocyte sedimentation rate (ESR), urinalysis, and urine 
pregnancy tests (if applicable), which will be analyzed by a local laboratory. A central 
laboratory will also be used to perform analysis of blood phenylalanine (Phe) concentrations. 
Pharmacokinetic (PK) analysis will be performed by BioMarin. 
Prior to database lock in multicenter studies, a Coordinating Investigator will be identified 
who will read the clinical study report and confirm that it accurately describes the conduct 
and results of the study, to the best of his or her knowledge. The Coordinating Investigator 
will be chosen on the basis of active participation in the study, ability to interpret data, and 
willingness to review and sign the report in a specified timeframe. 
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7 
INTRODUCTION 
A comprehensive review of PEGylated recombinant Anabaena variabilis phenylalanine 
ammonia lyase (rAvPAL-PEG) is contained in the IB supplied by BioMarin; the Investigator 
should review this document prior to initiating this study. 
7.1 
Nonclinical Studies 
The nonclinical program for rAvPAL-PEG has characterized the pharmacology, 
pharmacokinetics (PK), and toxicology of rAvPAL-PEG using the intended clinical SC route 
of administration. Pharmacology was assessed in the BTBR Pahenu2 (ENU2) mouse model of 
PKU. The ENU2 mouse model exhibits characteristics similar to those of PKU patients, 
including hyperphenylalaninemia (baseline plasma Phe concentrations of 1000 to 2000 µM) 
and hypopigmentation. Following weekly doses of rAvPAL-PEG administered to male 
ENU2 mice, plasma Phe concentrations decreased from approximately 2000 µM to 
< 200 µM after 2 dose administrations. An attenuated reduction of blood Phe was seen 
between Week 3 and Week 7 of dosing. After 7 weekly administrations of rAvPAL-PEG, 
pharmacological activity returned as evidenced by stabilized concentrations of plasma Phe 
< 200 µM over the entire week, which continued for a total of 15 weeks. 
In pharmacodynamic studies in the BTBR Pahenu2 (ENU2) mouse model administered 
80 mg/kg/week rAvPEG-PAL, two dose interruption assessments were performed:  a 
2-4 week dose interruption and an 11-week dose interruption. Following both dose 
interruption assessments, the animals re-started rAvPAL-PEG at a dose of 80 mg/kg/week. 
No attenuated Phe response was observed when rAvPAL-PEG injections were temporarily 
stopped for 2-4 weeks, and there was an immediate return to stable blood Phe reductions. A 
similar interim attenuated response was observed with the longer dose interruption of 
approximately 11 weeks.  In both of these assessments, no safety issues were noted upon 
re-starting dosing with rAvPAL-PEG (Lapis, 2007, ASHG 57th Annual Meeting). 
Safety pharmacology studies were conducted in rats and cynomolgus monkeys. No 
respiratory or central nervous system (CNS) effects were seen with SC administration of 
rAvPAL-PEG. No changes in cardiovascular (CV) parameters, including electrocardiogram 
(ECG) waveforms, were observed in telemetry-instrumented monkeys assessed for the CV 
effects of rAvPAL-PEG administered subcutaneously. 
Pharmacokinetic parameters were evaluated in single-dose and repeat-dose studies in rats and 
cynomolgus monkeys. The elimination half-life (t1/2) values of rAvPAL-PEG administered to 
normal rats at SC doses of 10, 25, and 250 mg/kg were 47, 33, and 44 hours, respectively, 
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and exhibited modest area under the plasma concentration-time curve (AUC)-dose. In the 
cynomolgus monkey after SC administration of rAvPAL-PEG, the t1/2 was 65 hours at 
4.0 mg/kg, 71 hours at 12 mg/kg, and could not be determined at 60 mg/kg (the highest 
dose). Qualitatively, the kinetics of rAvPAL-PEG in the rat and monkey appear to have 
similar characteristics. The following findings were noted: (1) a 1-compartment model with 
first-order absorption appears to describe the plasma profiles of rAvPAL-PEG after 
single-dose administration, (2) absorption is slow and there is a long absorption period after 
SC administration to maximum observed plasma concentration (Cmax), along with a long t1/2, 
(3) elimination is slow and monophasic, (4) there does not appear to be a gender difference, 
and (5) the AUC and the Cmax are roughly linearly proportional.  
Toxicology of rAvPAL-PEG was assessed in single-dose and repeat-dose studies in normal 
rats and cynomolgus monkeys. In the single-dose rat study, decreased body weight gain and 
Kupffer cell vacuolization at the high SC dose of 250 mg/kg was observed; however, the 
Kupffer cell finding was not seen in the single-dose study in cynomolgus monkeys. In a 
26-week repeat-dose toxicity and toxicokinetic (TK) rat study, decreased body weight gain, 
decreased food consumption, vacuolation/hypertrophy of the renal tubule cells, and 
vacuolation of the histiocytic cells were observed in rats administered 25 mg/kg/dose, twice 
weekly. In a 39-week repeat-dose study in monkeys, arterial inflammation, perivascular 
cellular infiltrates in the SC injection sites, thymic atrophy, and increased lymphoid nodules 
in bone marrow of the sternum were observed in monkeys given ≥ 3 mg/kg/dose, twice 
weekly. Of these findings, only the arterial inflammation was deemed adverse and this 
finding was completely reversed after 13-weeks of recovery. The 
no-observed-adverse-effect-level (NOAEL) of rAvPAL-PEG when administered 
subcutaneously twice weekly for 26 weeks and 39 weeks in the rat and monkey, respectively, 
was 1.0 mg/kg. These NOAELs were based on histological findings of 
vacuolation/hypertrophy of the renal tubule cells in the rat and arterial inflammation findings 
in the monkey.  
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7.2 
Previous Clinical Studies 
The rAvPAL-PEG clinical development program has been designed to demonstrate the 
safety and efficacy of rAvPAL-PEG in reducing blood Phe concentrations in PKU patients 
who do not respond to treatment with Kuvan® or are not compliant with Kuvan® treatment. 
This study is an extension of the ongoing human clinical studies with rAvPAL-PEG 
(Study PAL-002 and Study PAL-004) based on data from the completed clinical study, 
PAL-001, and clinical experience to date (JAN2011) from this ongoing study and the other 
ongoing Phase 2 study, PAL-002.  
7.2.1 Phase 1 Study PAL-001 
The first-in-human trial using rAvPAL-PEG, Study PAL-001, was a Phase 1, open-label, 
dose-escalation study in PKU subjects in the US. The primary objective was to assess the 
safety and tolerability of single SC injections of rAvPAL-PEG. Secondary objectives were to 
evaluate the PK of single, SC injections of rAvPAL-PEG administered at escalating doses in 
subjects with PKU and to evaluate the effect of rAvPAL-PEG on blood Phe concentrations. 
The effectiveness of rAvPAL-PEG in decreasing Phe concentrations in nonclinical studies of 
ENU2 mice was consistent with what was observed in PAL-001. PAL-001 enrolled 25 PKU 
subjects with a mean (standard deviation; SD) baseline blood Phe concentration of 
1310 µmol/L (405). The 25 subjects who enrolled into the study were assigned to receive a 
single administration of rAvPAL-PEG at 1 of 5 dose levels: 0.001, 0.003, 0.01, 0.03, and 
0.1 mg/kg. Five subjects each received 1 of the 5 dose levels of rAvPAL-PEG. 
Key safety, efficacy, and PK results of Study PAL-001 are summarized as follows: 
• rAvPAL-PEG was well tolerated and had a clinically significant blood-lowering 
effect on Phe concentration when administered at a dose of 0.1 mg/kg. 
• For the 5 subjects who were administered 0.1 mg/kg rAvPAL-PEG, clinically 
significant reductions in blood Phe level were observed, with the most clinically 
significant decreases from baseline values to Day 7, ranging from 33.8% to 97.3% 
(mean of 58.12%). The mean baseline blood Phe level for these 5 subjects was 
1113 µmol/L. 
• Overall, no clinically significant reductions in blood Phe level were observed in 
subjects who were administered rAvPAL-PEG at the lower doses of 0.001, 0.003, 
0.01, and 0.03 mg/kg. 
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• For subjects who were administered rAvPAL-PEG at the 3 higher dose levels (0.01, 
0.03, and 0.1 mg/kg) and who had measurable rAvPAL-PEG concentration levels, the 
calculated PK parameters were a mean Tmax of 89-106 hours, a t1/2 of 46-120 hours, 
and an AUC0-t, and Cmax that were proportional with dose. Drug exposure was slightly 
increased with increased dose. 
 
7.2.2 Phase 2 Studies PAL-002 and PAL-004 
Currently, rAvPAL-PEG is being investigated in two Phase 2 clinical trials (PAL-002 and 
PAL-004). To date (JAN2011), a total of 33 subjects have been administered rAvPAL-PEG 
in Study PAL-002 and initiation and recruitment of clinical sites is underway for Study 
PAL-004.   
In PAL-002 (A Phase 2, Open-Label, Dose-Finding Study to Evaluate the Safety, Efficacy, 
and Tolerability of Multiple Subcutaneous Doses of rAvPAL-PEG in Subjects with PKU), 
approximately 55 subjects will be enrolled and will be administered multiple doses of 
rAvPAL-PEG up to 5.0 mg/kg/week. PAL-002 is a 2-part study. In Part 1, subjects will be 
assigned to 1 of 4 rAvPAL-PEG dose cohorts (0.001, 0.003, 0.01, 0.1 mg/kg, or 1.0 mg/kg). 
rAvPAL-PEG will be administered at a fixed weekly dose of 0.001 mg/kg (Cohort 1), 
0.003 mg/kg (Cohort 2), 0.01 mg/kg (Cohort 3), 1.0 mg/kg (Cohort 4), or 0.1 mg/kg (Part 1 
Substudy) for 8 weeks. In Part 2, all subjects who complete Part 1 will be administered an 
adjustable dose of rAvPAL-PEG for up to an additional 8 weeks. The dose administered in 
Part 2 may be adjusted by dose level and/or dose frequency to reach a target blood Phe 
concentration of 60-600 µmol/L. Study PAL-003 (Long-Term Extension of a Phase 2, Open-
Label, Dose-Finding Study to Evaluate the Safety, Efficacy, and Tolerability of Multiple 
Subcutaneous Doses of rAvPAL-PEG in Subjects with PKU) is an extension study of PAL-
002 and PAL-004. Once subjects have completed Study PAL-002 or PAL-004, they have the 
option to enroll into PAL-003 and to continue to receive doses of rAvPAL-PEG for up to an 
additional 60 months. 
Study PAL-002 was initiated in September 2009 and is ongoing. The primary objective of 
this study is to evaluate the effect of multiple doses of rAvPAL-PEG on blood Phe 
concentrations in subjects with PKU for up to 16 weeks of treatment. The secondary 
objectives of the study are (1) to evaluate the safety and tolerability of SC injections of 
multiple dose levels of rAvPAL-PEG, (2) to evaluate the antibody response to rAvPAL-PEG, 
and (3) to evaluate the PK profile of rAvPAL-PEG in subjects with PKU. The study protocol 
was amended (30APR2010) to include a substudy of an additional rAvPAL-PEG dose level 
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(0.1 mg/kg/week) that reduced blood Phe concentrations to clinically significant levels in the 
Phase 1 study, PAL-001. The protocol was amended again (28MAR2011) to increase the 
starting dose for Cohort 4 from 0.03 mg/kg/week to 1.0 mg/kg/week. To date (JAN2011), 
33 subjects have been enrolled into the study and all 10 subjects of the substudy have been 
dosed with 0.1 mg/kg rAvPAL-PEG. Additional information about the safety reported to date 
(JAN2011) is provided in Section 7.4.2. 
Study PAL-004 is designed to determine if daily administration of rAvPAL-PEG at daily 
dose levels (0.06, 0.1, 0.2, 0.4, 0.6, and 0.8 mg/kg/day) is safe and effective in reducing and 
maintaining consistent blood Phe concentrations in subjects with PKU. It is hypothesized that 
a higher starting dose and frequency will reduce blood Phe concentrations to near-normal 
levels in a timely manner and will provide the greatest clinical benefit. Considering the 
concentration and volume of drug that is administered subcutaneously, the only way to 
increase the rAvPAL-PEG dose is via daily administration. Therefore, in Study PAL-004, a 
higher starting dose of 0.4 mg/kg will be administered 5 days a week (referred to as daily), a 
dosing regimen that has been observed to be tolerated and to reduce blood Phe concentrations 
to clinically meaningful levels in previously exposed subjects in this study. Following 
completion of Study PAL-004, subjects have the option to enroll into this study and to 
continue to receive doses of rAvPAL-PEG for up to an additional 60 months. 
In this study, subjects in PAL-002 and PAL-004 will continue to be administered the same 
rAvPAL-PEG that was administered in PAL-002 or PAL-004. If the safety, PK, and blood 
Phe concentration results from either PAL-002 or PAL-004 indicate that the appropriate level 
of PEGylation and dosing regimen differs from that administered in PAL-002 or PAL-004, 
the PEGylation and/or dosing regimen administered in this study may change.    
7.3 
Study Rationale 
PKU is an autosomal, recessive, inherited disease characterized by deficiency in the enzyme 
PAH. Approximately 1 in every 10,000 infants in North America is born with PKU (Scriver, 
2001, McGraw-Hill). Left untreated, PAH deficiency is associated with an abnormally 
elevated concentration of Phe, which is toxic to the brain (Kaufman, 1989, J Pediatr.) and can 
result in a variety of neuropathologic conditions, including mental retardation, microcephaly, 
delayed speech, seizures, and behavioral abnormalities (Scriver, 2001, McGraw-Hill). The 
brains of untreated patients with PKU show evidence of hypomyelination and gliosis, arrest 
in cerebral development, and, in some cases, white matter degeneration (Huttenlocher, 2000, 
Eur.J Pediatr.). Elevated Phe during fetal development leads to severe mental retardation and 
can cause microcephaly, growth retardation, and congenital heart disease (Guttler, 2003, 
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Pediatrics), (Koch, 2003, Pediatrics), (Lee, 2003, Pediatrics), (Levy, 2003, Pediatrics), 
(Matalon, 2003, Pediatrics), (Rouse, 2004, J.Pediatr.). 
For a subset of patients with residual enzyme activity, treatment with Kuvan® is an option. 
For all other patients, current management of PKU involves adherence to low-Phe medicinal 
diet formulas and dietary restriction of Phe-containing foods. Implementation of a 
Phe-restricted diet in infancy significantly reduces blood Phe concentrations and prevents 
many of the neuropathologic manifestations of PKU, including severe mental retardation. 
However, compliance with this restrictive diet can be difficult for older children, adolescents, 
and adults, and adherence may result in nutritional deficiencies due to the limitations of 
natural protein sources (Fisch, 2000, Eur.J.Pediatr.), (Walter, 2002, Lancet). 
The need exists for a treatment that will help individuals with PKU safely achieve lifelong, 
reliable control of blood phenylalanine (Phe) concentrations and improve functional 
outcomes. rAvPAL-PEG is a potential substitute for the phenylalanine hydroxylase (PAH) 
enzyme, which is defective in individuals with PKU. rAvPAL-PEG may control blood Phe 
concentrations, which may have additional clinical benefits.  
Because rAvPAL-PEG is being assessed as a long-term chronic treatment for patients with 
PKU, there is a need to understand the effect of a temporary dosing interruption on the 
safety, efficacy (blood Phe), PK, and immune response. To date (JAN2011), there is limited 
information on the effects of a rAvPAL-PEG dose interruption in subjects with PKU. 
Therefore, a Substudy has been added to this study to assess the effects of stopping and re-
starting rAvPAL-PEG treatment in subjects who are on a variety of rAvPAL-PEG dosing 
regimens (dose level and frequency). Up to 10 subjects who are on a variety of dosing 
regimens (dose level and frequency) in this study are eligible for participation in the 
Substudy and will stop dosing for a period of approximately 4 weeks. During this dosing 
interruption, subjects will be assessed for safety, efficacy, PK, and immune response and will 
continue to perform the scheduled study assessments. There is no information regarding the 
pharmacokinetic (PK) profile of rAvPAL-PEG when blood Phe levels are at 60-600 µmol/L 
for subjects on a multiple-dose regimen. To address this lack of information, additional PK 
sampling will be performed prior to the dosing interruption. Upon restarting rAvPAL-PEG, 
PK sampling will also be performed to allow for collection of drug exposure data (area under 
the plasma concentration-time curve [AUC] and maximum plasma concentration [Cmax]), 
absorption rate, and clearance for subjects who have been previously exposed to rAvPAL-
PEG in this Substudy. This information will allow for comparisons to be performed with 
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subjects who were naïve to previous rAvPAL-PEG treatment from the Phase 1 study, 
PAL-001. 
Blood Phe levels depend not only on the functional presence of the endogenous enzyme PAH 
but also on the dietary intake of Phe. It is important to understand the role of diet on blood 
Phe levels concurrent with the administration of rAvPAL-PEG treatment. Therefore, an 
exploratory objective has been added to this study to assess the relationship of diet, 
rAvPAL-PEG administration, and blood Phe level. Changes to subject diet are not allowed in 
this study unless per the Investigator in consultation with the Sponsor’s Medical Officer. 
Diet will be monitored using a diet diary.     
This study is an extension of the dose-finding studies (PAL-002 and PAL-004). 
Administration of rAvPAL-PEG will be continued to assess whether long-term dosing of 
rAvPAL-PEG is safe and can maintain reduced blood Phe concentrations in PKU subjects. 
7.4 
Summary of Overall Risks and Benefits 
It is not expected that data from PAL-002 or PAL-004 will change the assumption that rAvPAL-PEG 
has a toxicity profile similar to other recombinant PEGylated non-human enzymes currently in use. 
The toxicities of these drugs usually fall into 2 main categories: toxicity due to exposure to PEG, and 
toxicity due to immunologic sensitization. In addition, exaggerated pharmacological effects resulting 
in very low Phe concentrations could be observed. Other adverse events (AEs) that could occur with 
rAvPAL-PEG include injection-site reactions and other general symptoms. 
7.4.1 Toxicity Due to Exposure to PEG 
Acute exposure to high doses of PEG can result in renal toxicity. There have been a few 
reports of PEG-related AEs in humans; cumulative intravenous (IV) PEG doses of 121 to 
240 g caused acute renal tubular necrosis, oliguria, and azotemia. The anticipated PEG 
exposure associated with the expected rAvPAL-PEG dose range (6 g per week) is at least 
80-fold lower than the reported toxic doses and comparable to exposures to PEG in widely 
used medicines and other compounds that are administered by the IV, oral, rectal, and topical 
routes (Webster, 2007, Drug Metab Dispos.). No indication of PEG-related toxicity at the 
ultrastructural level was observed in monkeys given a single dose of up to 60 mg/kg 
rAvPAL-PEG SC. In rats, both renal tubule vacuolation and histiocytic cell vacuoles have 
been assocated with PEG-related catabolism and administration of other PEGylated proteins 
(refer to Section 7.1). 
In this study, subjects will be monitored closely with urine examinations and blood 
chemistries to follow kidney function. 
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7.4.2 Toxicity Due to an Immunologic Reaction 
The active drug substance in rAvPAL-PEG is a bacterial protein, and as such, it is expected 
that it may elicit immune recognition and responses. Epitopes that play a role in the immune 
response may be rendered inaccessible by PEG (Gamez, 2007, Mol.Genet.Metab). In vivo 
and in vitro experiments have shown that PEGylation of proteins and cells can attenuate the 
immunological response (Scott, 1997, Proc.Natl.Acad.Sci.U.S.A), (Chen, 2001, BioDrugs.). 
PEGylation has been effective in reducing anti-rAvPAL antibody titers in the mouse model, 
although PEGylation does not eliminate antibody formation. Although PEGylation of 
rAvPAL may have a significant effect on reducing the immunogenicity of the molecule, it is 
reasonable to expect that some individuals may exhibit immune responses upon exposure to 
the drug. These immune responses may be clinically irrelevant, cause symptoms of various 
degrees, or lead to neutralization of biological activity. Subjects participating in clinical trials 
will be monitored closely with specific antibody titers, sedimentation rates, and complete 
blood counts (CBCs). 
In Study PAL-001, there were 11 subjects (out of 25 subjects in the study) with skin-related 
reactions (injection-site bruising, erythema, pain, rash, swelling, and urticaria) that occurred 
following the single administration of rAvPAL-PEG. For all of these subjects, the reactions 
were generalized skin reactions or injection-site skin reactions that did not compromise other 
organs and were not life-threatening. These suspected antibody-mediated responses were 
nonserious and mild or moderate in severity. These subjects are not considered to be at 
significant risk for antibody-mediated reactions with injection of rAvPAL-PEG during 
PAL-002, PAL-004, or this study; however, specific precautions for these subjects will be 
taken during this study to monitor subject safety (refer to Section 9.1.1). 
In Study PAL-002, 33 subjects have been dosed to date (JAN2011), including at dose levels 
of 2.0 mg/kg/week (or 0.4 mg/kg/5 days a week). Most reactions reported in these subjects 
have been nonserious and mild or moderate in severity. There has been 1 SAE reported to 
date; the event was reported as not related to treatment with study drug. There have been no 
reports of anaphylaxis to date (JAN2011). Subjects who have a systemic reaction during this 
study will undergo a series of assessments to monitor safety, including assessment of IgE 
antibodies, prior to determining if dosing may resume. Additionally, subjects who have 
systemic reactions will be premedicated and will be monitored closely for safety (refer to 
Section 9.1.1.3.3 for additional information regarding continued treatment of subjects with 
systemic reactions during the study). 
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PEG itself is considered nonimmunogenic (Davis, 1981, Clin.Exp.Immunol.), (Harris, 2003, 
Nat.Rev.Drug Discov.), however, antibodies against PEG may form when PEG is bound to 
compounds. (Harris, 2003, Nat.Rev.Drug Discov.),(Richter, 1983, Int.Arch.Allergy 
Appl.Immunol.).  In some instances, development of such antibodies did not result in any 
significant clinical effects in humans (Richter, 1984, Int.Arch.Allergy Appl.Immunol.). 
In some individuals, anti-PEG antibodies may be pre-existing due to previous exposure to 
PEG in other products. Anti-PEG antibodies have been associated with nonresponsiveness 
against therapy (Armstrong, 2007, Cancer), (Ganson, 2006, Arthritis Res.Ther.) 
Administration of rAvPAL-PEG may lead to anti-PEG antibody formation, and the duration 
of this possible effect is not known. This may limit a subject’s future ability to be treated 
with other PEG-containing (eg, Depo-Provera) or PEGylated (eg, PEG-interferon) injectable 
drugs. It is therefore recommended that any PEG-containing injectable drug administered to 
subjects after completion of this study be done under medical observation. 
7.4.2.1 
Systemic Skin Reactions 
Two out of 25 subjects who were enrolled in Study PAL-001 and received the 
protocol-defined single dose of rAvPAL-PEG reported systemic skin reactions (generalized 
skin rash) that were attributed to treatment with study drug. One subject received a single 
dose of 0.001 mg/kg rAvPAL-PEG, and the other subject received a single dose of 
0.01 mg/kg rAvPAL-PEG. One of these events was reported as serious, and the other was 
reported as nonserious; both events were reported following administration of Depo-Provera 
injections (medroxyprogesterone injection), an injectable contraception. These allergic 
reactions are thought to be related to the PEG molecules that are found in both the study 
drug, rAvPAL-PEG, and Depo-Provera. These reactions are not likely to be experienced 
concurrent with other birth control medications. 
The 2 subjects were administered study drug during PAL-001 and then experienced an 
allergic reaction following an injection of Depo-Provera. The symptoms of the reactions 
were hives on the arms and legs and difficulty breathing. The symptoms for both subjects 
resolved within 1 day following treatment with medication, including the 
 
. Both subjects were examined by an allergy specialist after they 
completed participation in PAL-001. A skin prick test with Depo-Provera was administered 
as part of this examination. One subject had a mild allergic reaction to the test; however, no 
further reactions or complications were reported following subsequent administration of a 
full dose of Depo-Provera. Upon study completion, the subject continued to receive regular 
doses (every 3 months) of Depo-Provera, and no further reactions were reported. The second 
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subject also had a positive reaction to Depo-Provera following administration of the skin 
prick test. When a subsequent full dose of Depo-Provera was administered, 
 developed 
hives, itching, and chills. The subject’s symptoms resolved within 1 day of taking medication 
prescribed by an allergist. See Section 7.2.1 for the results from Study PAL-001. 
The active drug substance in rAvPAL-PEG is a bacterial protein that may elicit immune 
responses, such as urticaria, bronchospasm, itching, anaphylaxis, and others. The results from 
nonclinical studies of rAvPAL-PEG conducted in rats and cynomolgus monkeys indicated 
the formation of anti-rAvPAL antibody titers that did not correspond with observations of 
injection-site reactions. Quantitation of anti-PEG titers were not assessed in the chronic 
repeat-dose studies in the rat and monkey. Although results from nonclincal studies of 
rAvPAL-PEG conducted in rats and cynomolgus monkeys did not indicate signs of 
immune-mediated toxicities, it is possible that the physio-chemical properties of 
rAvPAL-PEG may induce immunologic sensitization to the protein rAvPAL and to PEG in 
humans. It is currently unknown whether administration of PEG-containing drugs, such as 
Depo-Provera, has a sensitizing effect to PEG in rAvPAL-PEG when administered in 
humans. Because the exact basis for these reported events and their duration is not known, 
the use of PEG-containing injectable drugs prior to, during, and after this study is prohibited 
as a precautionary measure (refer to Section 9.3.2 and Section 9.4.8.). 
7.4.2.2 
Management of Allergic Reactions 
Allergic reactions to the SC injection of rAvPAL-PEG may be mild, moderate, or severe in 
intensity. Reactions may include pruritus, rash, shortness of breath, hypotension, or 
anaphylaxis. Clinical assessments should be conducted for a minimum of 30-60 minutes 
post-injection. Longer observations may be required at the discretion of the PI. 
The responsible physician should use all appropriate measures for the treatment of allergic 
reactions. Because of the small potential for anaphylaxis, equipment for emergency 
resuscitation (including epinephrine) should be within easy access during and after the 
rAvPAL-PEG injection. Subjects who qualify for self administration of study drug will be 
provided with emergency resuscitation instructions (refer to Section 9.4 and the Subject 
Self-Administration Training Materials). 
In the event of an allergic reaction, subjects may be asked to see an allergist/immunologist 
and/or provide up to 3 additional blood samples for antibody testing. This additional testing 
may occur up to 6 months following the final study visit. 
The following measures are recommended for the treatment of allergic symptoms: 
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• Maintain the airway. 
• Vital sign check. 
• Administration of oral or IV diphenhydramine. 
• Administration of epinephrine if appropriate. 
• Administration of oxygen and IV fluids. 
• Administration of additional symptomatic treatment. 
• Transfer to an acute care facility of the study center. 
In addition, clinical judgment must be used in determining the appropriateness of 
corticosteroid administration. Acetaminophen or ibuprofen (5-10 mg/kg) may also be 
administered. An allergy and/or immunology consultation should be sought if necessary. 
Information regarding the management of local skin, large local skin, and systemic reactions 
is provided in Section 9.1.1. Detailed instructions for the management of allergic reactions 
are provided in the Study Reference Manual. 
7.4.3 Effects of Stopping and Re-Starting rAvPAL-PEG Treatment 
The effects of starting, stopping, and re-starting rAvPAL-PEG dosing on safety and blood 
Phe reductions previously achieved through rAvPAL-PEG dosing are not well defined, and 
there is limited clinical experience with rAvPAL-PEG. Allergic reactions are a common and 
expected clinical outcome of re-starting biologic drugs, such as rAvPAL-PEG, and may 
occur when subjects re-start rAvPAL-PEG dosing. However, no information reported from 
the ongoing clinical studies, including this study, or nonclinical results point to an increased 
safety risk or decreased efficacywhen rAvPAL-PEG dosing is stopped and then re-started at 
the same dose level. 
• Nonclinical experience in the BTBR Pahenu2 (ENU2) mouse model indicates that 
dosing interruptions of 2-4 weeks for mice administered rAvPAL-PEG 
80 mg/kg/week had no increased safety risk upon re-starting dosing and there was an 
immediate return to stable blood Phe reductions (refer to Section 7.1).  
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• Antibody results from the ongoing Phase 2 study, PAL-002, and this ongoing study to 
date (JAN2011) have not indicated an immune response that points to an increased 
safety risk or decreased efficacy upon re-introduction of drug. There has not been any 
immediate immunoglobulin E (IgE)-mediated reactions to rAvPAL-PEG observed 
following administration of a rAvPAL-PEG injection. All reactions to rAvPAL-PEG 
have been reported approximately 12-24 hours following administration. To date, 
1 out of 33 subjects has tested positive by serology to IgE antibodies without 
reporting any clinical symptoms to suggest anaphylaxis or a severe systemic reaction. 
Thus, it is not anticipated that reactions to rAvPAL-PEG are IgE-mediated.   
• To date (JAN2011), the clinical experience with re-starting rAvPAL-PEG dosing for 
subjects from Study PAL-001 who rolled over into Study PAL-002 does not indicate 
an increased safety risk or a decreased effect on reducing blood Phe levels upon 
re-introduction of drug.  
o Nine subjects who received a single dose of rAvPAL-PEG and completed the 
Phase 1 study, PAL-001, rolled over into the multiple-dose, Phase 2 study, 
PAL-002. After a period of several months during which no drug was 
administered, these 9 subjects re-started rAvPAL-PEG dosing in Study PAL-
002 at the same starting doses as was administered in Study PAL-001. There 
has been no difference to date in the safety profile or efficacy profile of the 
subjects from Study PAL-001 who rolled over into Study PAL-002 
(previously exposed to rAvPAL-PEG) when compared with subjects who 
were naive to rAvPAL-PEG dosing in Study PAL-002. Although previously 
exposed subjects had higher and a faster return of anti-PAL and anti-PEG IgG 
titers than those of naïve subjects, these results have not been associated with 
a higher safety risk or efficacy riskbased on information to date.  
o In Study PAL-002, 4 subjects to date have had a protocol-defined (per 
Protocol Amendment # 3 dated 30APR2010), 2-week washout (no dose 
administered) following several weeks of a fixed dose of 0.06 mg/kg/week or 
0.1 mg/kg/week rAvPAL-PEG. Following the 2 weeks where no dose was 
administered, all 4 subjects re-started rAvPAL-PEG dosing at a higher dose 
with no safety issues reported to date. Blood Phe levels for these 4 subjects 
have not changed upon re-introduction of dosing. 
o Clinical experience with subjects who have had to temporarily halt dosing due 
to an adverse event also provides information that stopping and re-starting 
rAvPAL-PEG dosing does not appear to increase the risk to subject safety. To 
date, 10 subjects participating in either PAL-002 or PAL-003 have had to 
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temporarily stop dosing due to an adverse event. All 10 subjects resumed 
dosing following resolution of the event or per determination by the 
Investigator that subject safety would not be jeopardized with re-starting 
dosing. These 10 subjects resumed dosing at a reduced dose level after 
approximately 1-7 weeks of no dosing. Upon re-starting dosing, none of these 
10 subjects have experienced additional safety issues. Eight subjects continue 
to receive dosing with rAvPAL-PEG (APR 2011) and have subsequently 
increased their dose level without additional reported adverse events that have 
resulted in a subsequent dosing interruption. 
In this study, measures will be taken to reduce the risk to subject safety upon re-starting 
rAvPAL-PEG dosing while still allowing for reductions in blood Phe level to clinical 
significance (blood Phe reduction to 60-600 µmol/L). To mitigate the possible safety risks 
upon re-starting rAvPAL-PEG dosing, re-introduction of dosing should be performed in the 
clinic, and the subject must be observed for 30-60 minutes following administration due to 
restarting dosing. A follow-up telephone call should be made to subjects 24 hours following 
re-starting of dosing to monitor subject safety. Subjects will also continue to be assessed per 
the safety assessment and stopping criteria defined in Section 9.1.3 and Section 9.1.4, and 
dose decreases will continue to be performed relative to safety as defined in Section 9.1.2.2. 
To mitigate the possible reduced effect on blood Phe level upon re-starting rAvPAL-PEG, 
subjects in this study who interrupt dosing whether per the protocol (ie, subjects participating 
in the Substudy; refer to Section 9.1) or for other reasons (refer to Section 9.4.10) will 
re-start rAvPAL-PEG dosing at the same dose level. 
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8 
STUDY OBJECTIVES 
The primary objective of the study is: 
• To evaluate the effect of long-term administration of multiple doses of SC injections 
of rAvPAL-PEG on blood Phe concentrations in subjects with PKU. 
The secondary objectives of the study are: 
• To evaluate the safety and tolerability of long-term administration of subcutaneous 
(SC) injections of rAvPAL-PEG in subjects with PKU. 
• To evaluate the immune response to long-term administration of SC injections of 
rAvPAL-PEG in subjects with PKU. 
The exploratory objective of the study is as follows: 
• To assess the long-term relationship of diet and change in blood Phe concentration 
following administration with rAvPAL-PEG in subjects with PKU. 
The Substudy objectives are as follows: 
• To assess the safety and tolerability of stopping and re-starting rAvPAL-PEG dosing 
in a subset of subjects with PKU.    
• To evaluate the effect of stopping and re-starting rAvPAL-PEG dosing on blood Phe 
concentration in a subset of subjects with PKU. 
• To evaluate the effect of stopping and re-starting rAvPAL-PEG dosing on immune 
response in a subset of subjects with PKU. 
• To assess the effect of multiple doses of rAvPAL-PEG on the PK profile, in particular 
clearance of drug, when drug is stopped in a subset of subjects with PKU who have 
been previously exposed to rAvPAL-PEG.   
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9 
INVESTIGATIONAL PLAN 
9.1 
Overall Study Design and Plan 
This is a long-term extension of the Phase 2, open-label, dose-finding studies, PAL-002 and 
PAL-004, in approximately 100 subjects with PKU. The doses are planned to be in the same 
range as those tested in PAL-002 and PAL-004 (starting at 0.001 through 5.0 mg/kg/week), 
provided no dose-limiting toxicity was observed in PAL-002 or PAL-004. 
Only subjects who completed the protocol-defined study drug regimen in PAL-002 or PAL-
004 will be enrolled into this study. Subjects who enroll from PAL-002 will either continue 
the dose regimen that was administered upon completion of PAL-002 or start dosing at a 
higher dose per the dose increase instructions. Subjects who enroll from PAL-002 may start 
this study at a higher dose level provided there was no interruption in dosing since 
completion of PAL-002 and enrollment into this study. Subjects who enroll from PAL-004 
will re-start rAvPAL-PEG dosing in this study at the same dose level and frequency as was 
administered upon completion of PAL-004. The first dose will be administered in the clinic, 
and the subject must be observed for 30-60 minutes following administration due to 
restarting dosing in this study. A follow-up telephone call will be made to the subject to 
monitor subject safety 24 hours following the return to dosing. 
Diet should not be altered during the course of this study. Any decision to modify subject 
diet must be made per the Investigator in consultation with the Sponsor’s Medical Officer 
and must be performed under the supervision of the Investigator in consultation with the 
Sponsor’s Medical Officer. To monitor for changes in subject diet, a diet diary will be issued 
to subjects for completion and will be brought to each clinic visit for review with the clinical 
study staff.  
Subjects may self administer study drug at home if approved by the Investigator and the 
Sponsor’s Medical Officer and if adequate training is demonstrated. Subjects must meet a set 
of criteria to be considered appropriate for self administration. Refer to Section 9.4 for the 
criteria for which subjects may qualify for self administration. Additional information is 
provided in the Subject Self-Administration Training Materials. 
Subjects will be evaluated for safety throughout the study. Toxicity will be measured 
according to the National Cancer Institute (NCI) Common Terminology Criteria for Adverse 
Events (CTCAE), version 4. 
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In addition to the Sponsor, a Data Monitoring Committee (DMC) will monitor the safety of 
subjects in the study. The DMC is an independent committee that will act in an advisory 
capacity to the Sponsor. 
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take 
rAvPAL-PEG. PAL-002 and PAL-004 subjects’ rAvPAL-PEG dosing will continue in PAL-
003. In PAL-003, each subject’s dose will be adjusted as needed to attain or maintain blood 
Phe concentrations of 60-600 µmol/L. Doses will be evaluated on an individual basis.  
Evaluations, observations, and procedures will be conducted at selected time points as shown 
in Table 2.1.1, Table 2.1.2, Table 2.1.3 and Table 2.1.4 (Schedule of Events). After the 
subject’s blood Phe concentration has been controlled to within a target range 
(60-600 µmol/L), the subject may be asked to have additional blood draws for PK and blood 
Phe concentration analyses as needed per the discretion of the Investigator in consultation 
with the Sponsor’s Medical Officer. 
A subject will continue in PAL-003 until one of the following occurs: 
1. The subject withdraws consent and discontinues from the study. 
2. The subject is discontinued from the study at the discretion of the Investigator. 
3. The subject has completed the study through the Month 60 visit. 
4. The study is terminated. 
Subjects may withdraw from treatment with study drug at any time; however, subjects will 
be asked to continue to perform the study assessments until study completion. Subjects may 
also withdraw from study participation at any time. Because the completeness of the data 
affects the integrity, accuracy, and interpretation of study results, every effort should be made 
to retain subjects in the study and to have them complete the study assessments as scheduled 
as long as continued participation does not compromise subject safety. 
A subset of up to 10 subjects who are already enrolled and who have consented to participate 
in this study will be asked to participate in a Substudy to assess the effect that stopping and 
re-starting treatment with rAvPAL-PEG has on safety, efficacy, PK, and immune response. 
Subjects will be eligible for participation in the Substudy provided they also meet all of the 
PAL-003 eligibility criteria, have been on a stable dosing regimen for approximately 4 weeks 
during this study, have not had any serious adverse events reported during PAL-003, and 
were not enrolled in Study PAL-004. Subjects participating in the Substudy will have 
rAvPAL-PEG administration halted for approximately 4 weeks regardless of their dosing 
regimen (dose level and frequency). rAvPAL-PEG will not be administered during the dose 
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interruption; however, subjects will continue to perform assessments for safety, blood Phe 
concentration, PK, and immune response. Subjects enrolled into the Substudy will also have 
additional PK sampling performed prior to the dosing interruption and during the dosing 
interruption. To allow for PK sampling once dosing is stopped, subjects may be admitted to a 
research facility within 8 hours of stopping dosing where they will reside for at least 24 
hours. After the dosing interruption, rAvPAL-PEG administration will be re-started at the 
same dose level and dosing frequency that was administered prior to the dosing interruption. 
Upon re-starting rAvPAL-PEG, the first dose must be administered in the clinic and the 
subject must be observed for 30-60 minutes following administration due to restarting 
dosing. A follow-up telephone call will be made to the subject to monitor subject safety 
24 hours following the return to dosing. Additional PK sampling will also be performed for 
the first week after the dosing interruption. 
9.1.1 Management of Local and Systemic Reactions to rAvPAL-PEG 
Subjects who qualify for self administration of study drug will be provided with information 
and instruction with regard to management of local and systemic reactions (refer to the 
Subject Self-Administration Training Materials). 
9.1.1.1 
Subjects Who Have Had Previous Hypersensitivity Reactions to 
rAvPAL-PEG or a PEG-containing Product 
Subjects who had a previous systemic reaction to rAvPAL-PEG or a PEG-containing product 
that warranted early termination from PAL-002 or PAL-004 are excluded from participation 
in this study. Subjects who experienced a generalized skin rash are included in this category. 
Subjects who have had a previous local skin reaction to rAvPAL-PEG in PAL-002 or 
PAL-004 are eligible to participate in this study. Subjects who have had a previous reaction 
and are deemed eligible for participation must be premedicated orally with acetaminophen 
and/or antihistamines 1 hour prior to study drug dosing for the remainder of the study. The 
premedication dosage will be standard. Because antihistamines can cause drowsiness, it may 
be administered only if the subject is accompanied by a designated driver (if applicable). 
Subjects may develop systemic, large local skin, or local skin reactions after enrollment in 
PAL-003. Refer to Section 9.1.1.2 for definitions of systemic and local skin reactions. For 
management of hypersensitivity reactions that occur during this study, refer to 
Section 9.1.1.3 and Figure 9.1.1.3.1. 
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9.1.1.2 
Definition of Hypersensitivity Reactions to rAvPAL-PEG Administered 
Subcutaneously 
During Study PAL-003, subjects may experience hypersensitivity reactions to rAvPAL-PEG. 
The hypersensitivity reactions are defined as follows: 
Local skin reaction: 
• Skin signs or symptoms in 1 affected primary location, ie, hives, wheals, or swelling 
or an area of erythema, redness, induration, pain, or itching at or near the site of 
injection. 
• Large local skin reaction: 
• Skin signs or symptoms, ie, hives, wheals, or swelling or an area of erythema, 
redness, or induration with pain or itching that extends beyond the site of injection by 
approximately 6 inches (15 cm) and/or signs or symptoms that are not contiguous to 
the injection site. These may be associated with a low risk of systemic symptoms or 
anaphylaxis upon re-exposure and, therefore, will be managed as a systemic reaction 
when not contiguous to the injection site. 
• Systemic reaction (including generalized skin symptoms): 
• Skin and non-skin signs or symptoms in more than 1 affected primary location, 
ie, cutaneous reaction in more than 1 area and/or anaphylaxis or any other generalized 
symptoms, such as hypotension, angioedema or the involvement of other organ 
systems, eg, respiratory, cardiovascular, gastrointestinal, neurological; and/or a fever 
attributed to treatment with rAvPAL-PEG ( ≥ 100.4°F or  ≥ 38°C). 
For management of hypersensitivity reactions that occur during this study, refer to 
Section 9.1.1.3 and Figure 9.1.1.3.1. 
 
 
 
 
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9.1.1.3.1 Local Skin Reactions 
Subjects who have had a local skin reaction (refer to Section 9.1.1.2 for definition) after 
administration of rAvPAL-PEG in this study may continue if the symptoms do not worsen 
and no other symptoms have developed but may be premedicated with acetaminophen and/or 
antihistamines (standard dosage per the package insert) 1 hour prior to the next dose of study 
drug dosing. Because antihistamines can cause drowsiness, it should be administered only if 
the subject is accompanied by a designated driver. 
Symptoms of local reactions may be treated with local application of ice and non-sedating 
oral and/or topical antihistamines and/or topical steroids (refer to Section 7.4.2.2). 
If the local skin reaction worsens with a repeat injection (as determined by the Investigator in 
consultation with the Study Medical Officer) even with premedication prior to study drug 
dosing, the subject must be withdrawn from study treatment. 
9.1.1.3.2 Large Local Skin Reactions 
Large local skin reactions (refer to Section 9.1.1.2 for a definition) may or may not be 
contiguous to the rAvPAL-PEG injection site, and subjects with either type of large local 
skin reaction may continue dosing if the skin symptoms have resolved and no other 
symptoms have developed. Subjects may be premedicated orally with acetaminophen and/or 
antihistamines (standard dosage per the package insert) 1 hour prior to study drug dosing.  
9.1.1.3.2.1 
Large Local Skin Reactions Contiguous to Injection Site 
Subjects who develop a large local skin reaction contiguous to the injection site after 
administration of rAvPAL-PEG or to rAvPAL-PEG or a PEG-containing product may 
remain in the study if the skin symptoms have resolved and no other symptoms have 
developed. For the remainder of the study, subjects may be premedicated orally with 
acetaminophen and/or antihistamines (standard dosage per the package insert) 1 hour prior to 
the next dose of study drug. Because antihistamines can cause drowsiness, it may be 
administered only if the subject is accompanied by a designated driver (if applicable).  
Symptoms of large local skin reactions may be treated with local application of ice and 
topical, oral, or IV antihistamines and/or steroids as needed (refer to Section 7.4.2.2).  
9.1.1.3.2.2 
Large Local Skin Reactions Not Contiguous to Injection Site 
Large local skin reactions that are not contiguous to the injection site may be associated with 
a low risk of systemic symptoms or anaphylaxis upon re-exposure to rAvPAL-PEG and, 
therefore, will be managed as a systemic reaction (refer to Section 9.1.1.3.3). An example of 
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a large local reaction that is not contiguous to the injection site is if an injection took place in 
the right upper arm and there are lesions beyond the elbow joint in the right forearm or 
lesions beyond the shoulder joint on the right trunk. 
Symptoms of large local skin reactions may be treated with local application of ice and 
topical, oral, or IV antihistamines and/or steroids as needed (refer to Section 7.4.2.2). 
9.1.1.3.3 Systemic Reactions 
Subjects who experience a systemic reaction (refer to Section 9.1.1.2 for a definition) after 
administration of rAvPAL-PEG must stop further administrations of rAvPAL-PEG and must 
immediately return to the clinic for safety assessments . Subjects who experience generalized 
skin symptoms are included in this category. Immediately after the systemic reaction (within 
48 hours), subjects with generalized skin symptoms must have additional assessments 
performed for safety (ie, Unscheduled Hypersensitivity Reaction Visit): serum antibodies 
(anti--PAL IgG, anti-PAL IgM, anti-PEG IgG, anti-PEG IgM, anti rAvPAL-PEG IgE, 
anti-rAvPAL-PEG neutralizing antibodies); serum tryptase level (it is recommended that this 
sample be drawn immediately after reaction); sedimentation rate; CRP, CH50, C1, C3, and 
C4; skin biopsy (optional; affected and not affected area; to be performed within 1 week of 
reaction); and clinical laboratory tests (urinalysis, chemistry, hematology; refer to 
Figure 9.1.1.3.1).  
Following completion of the Unscheduled Systemic Reaction Visit, administration of 
rAvPAL-PEG may resume up to 1 week following the onset of the reaction if the systemic 
reaction is not IgE-mediated and the subject’s safety will not be further compromised with 
resumed dosing. rAvPAL-PEG administration will resume at the next lowest dose level. 
Restarting of rAvPAL-PEG administration following a systemic reaction must be performed 
in the clinic for the first week of resumed dosing. Subjects must be premedicated orally with 
acetaminophen and/or antihistamines (standard dosage per the package insert) 1 hour prior to 
study drug dosing for the remainder of the study. Additionally, subjects must be closely 
monitored for 30-60 minutes following every administration of study drug. Because 
antihistamines may cause drowsiness, the subject must be accompanied by a designated 
driver (if applicable). 
If blood Phe concentrations are not 60-600 µmol/L following 1 week of daily administration 
at the lowered dose cohort and there is no further evidence of toxicity (ie, another systemic 
reaction attributed to rAvPAL-PEG administration or clinically significant abnormal 
laboratory test results), the subject may be administered the next highest dose level in the 
clinic per the allowable dose increases outlined in Section 9.1.2. Subjects must be 
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premedicated orally with acetaminophen and/or antihistamines (standard dosage per the 
package insert) 1 hour prior to study drug dosing for the remainder of the study. 
Additionally, subjects must be closely monitored for 30-60 minutes following every study 
drug administration. Because antihistamines may cause drowsiness, the subject must be 
accompanied by a designated driver (if applicable). 
9.1.2 Dose Modifications 
9.1.2.1 
Dose Increase Methodology 
Each subject’s dose may be modified based on the decision of the Investigator, in agreement 
with the Study Medical Officer. Decisions regarding dose increases will depend on a 
subject’s adverse event profile and blood Phe and drug concentrations. 
For subjects from PAL-002, an individual subject’s dose may be adjusted beginning on Day 
1 of PAL-003. For the duration of this study, an individual subject’s dose may be adjusted if 
warranted per a subject’s adverse event profile and blood Phe concentrations. Dose increases 
should be performed as follows: 
• The dose may be increased by increments of no more than 10-fold higher than the 
subject’s current dose. 
• When increasing the dose, a dose may be used that is between the dose levels (0.001, 
0.003, 0.01, 0.03, 0.06, 0.1, 0.2, 0.3, 0.4, 0.6, 0.8,  1.0, 2.0, 3.0, 4.0, and 5.0 mg/kg)  
or per Investigator determination in consultation with the Sponsor’s Medical Officer 
based on available information regarding a subject’s blood Phe (60-600 µmol/L) as 
well as any adverse events (any hypersensitivity reaction) for an individual subject. 
• The dose may be adjusted by increasing the frequency up to daily for a total weekly 
dose not to exceed 5.0 mg/kg.Subjects who increase their dose frequency should 
perform the Interim Dosing Visit assessments (refer to Section 12.3.6 and Table 2.1.3 
and Table 2.1.4). 
• When a dose is increased, the subject must be observed for 30-60 minutes following 
the first modified dose administration. Subjects who increase their dose frequency do 
not need to be observed following injection of study drug if the increase in frequency 
does not increase the overall weekly dose amount. 
• Only 1 dose (level or frequency) adjustment is allowed every 2 weeks. 
• Blood Phe levels will be measured daily for 3 days after each dose increase 
(fingerstick is acceptable); more frequent or daily blood Phe measurements may be 
performed. 
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9.1.2.2 
Dose Decrease Methodology 
All dose decreases must be agreed to by both the Investigator and the Sponsor’s Medical 
Officer. Decisions regarding dose decreases will depend on available information regarding a 
subject’s blood Phe (60-600 µmol/L), as well as any adverse event (any hypersensitivity 
reaction as defined in Section 9.1.1.2). Dose decreases may occur for safety (ie,  any adverse 
event that may be improved with a lower, more frequent dose). 
A dose should first be reduced by dose level (5.0, 4.0, 3.0, 2.0, 1.0, 0.8, 0.6, 0.4, 0.3, 0.2, 0.1, 
0.06, 0.03, 0.01, 0.003, 0.001 mg/kg). It is also permitted to decrease dose in between these 
specified dose levels. If further dosing adjustments are required to attain the target Phe 
concentration, dosing frequency may be reduced.  
9.1.3 Safety Assessment Criteria 
If an individual subject exhibits toxicity of a treatment-emergent CTCAE grade 3 or greater 
or a systemic reaction that is assessed as related to treatment with study drug, that subject 
will have dosing halted until the toxicity resolves. The subject’s data will be evaluated by the 
Principle Investigator (PI) and the Study Medical Officer, and a decision will then be made 
whether to discontinue the subject from the study treatment, restart dosing at the same dose 
level, or restart dosing at a lower dose level. 
9.1.4 Stopping Criteria 
If 2 or more subjects at a dose level exhibit toxicity of a treatment-emergent CTCAE grade 3 
or greater or a systemic reaction that is assessed as related to treatment with study drug, 
further dosing of subjects at that dose level will evaluated and a safety assessment will be 
completed. In addition, the Food and Drug Administration (FDA) may be notified of this 
occurrence if appropriate. 
9.2 
Discussion of Study Design, Including Choice of Control Group 
This open-label, Phase 2 trial was designed to be closely monitored with the goal of 
obtaining information about the efficacy, safety, tolerability, and PK of long-term 
administration of rAvPAL-PEG in subjects with PKU. There will be no control group in this 
study. 
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9.3 
Selection of Study Population 
9.3.1 Inclusion Criteria 
Individuals eligible to participate in this study must meet all of the following criteria: 
1. Must have completed participation and all protocol-defined study drug in PAL-002 or 
PAL-004. 
2. Willing and able to provide written, signed informed consent, or in the case of 
subjects under the age of 18 years, provide written assent (if required) and written 
informed consent by a parent or legal guardian, after the nature of the study has been 
explained, and prior to any research-related procedures. 
3. Willing and able to comply with all study procedures. 
4. Females of childbearing potential must have a negative pregnancy test at Screening 
and be willing to have additional pregnancy tests during the study. Females 
considered not of childbearing potential include those who have been in menopause at 
least 2 years, or had tubal ligation at least 1 year prior to Screening, or who have had 
total hysterectomy. 
5. Sexually active subjects must be willing to use an acceptable method of contraception 
while participating in the study. 
6. Maintained a stable diet. 
7. In generally good health as evidenced by physical examination, clinical laboratory 
evaluations (hematology, chemistry, and urinalysis), and electrocardiogram (ECG) at 
Screening. 
9.3.2 Exclusion Criteria 
Individuals who meet any of the following exclusion criteria will not be eligible to participate 
in the study: 
1. Use of any investigational product (with the exception of rAvPAL-PEG) or 
investigational medical device within 30 days prior to Screening, or requirement for 
any investigational agent prior to completion of all scheduled study assessments. 
2. Use of any medication other than rAvPAL-PEG that is intended to treat PKU within 
14 days prior to the administration of study drug. 
3. Use or planned use of any injectable drugs containing PEG (other than 
rAvPAL-PEG), including Depo-Provera, within 6 months prior to Screening and 
during study participation. 
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4. A prior reaction that included systemic symptoms (eg, generalized hives, respiratory 
or gastrointestinal problems, hypotension, angioedema, anaphylaxis) to rAvPAL-PEG 
or a PEG-containing product. Subjects with a prior systemic reaction of generalized 
rash may be eligible for participation per the discretion of the Principal Investigator in 
consultation with the Sponsor’s Medical Officer. However, subjects who 
discontinued from study treatment early due to a reaction are not eligible to enroll 
into this study.      
5. Pregnant or breastfeeding at Screening or planning to become pregnant (self or 
partner) or to breastfeed at any time during the study. 
6. Concurrent disease or condition that would interfere with study participation or safety 
(eg, history or presence of clinically significant cardiovascular, pulmonary, hepatic, 
renal, hematologic, gastrointestinal, endocrine, immunologic, dermatologic, 
neurological, oncologic, or psychiatric disease). 
7. Any condition that, in the view of the PI, places the subject at high risk of poor 
treatment compliance or of not completing the study. 
8. Known hypersensitivity to rAvPAL-PEG or its excipients, including hypersensitivity 
reactions that necessitated early termination fro PAL-002 or PAL-004. 
9. Alanine aminotransferase (ALT) concentration > 2 times the upper limit of normal. 
10. Creatinine > 1.5 times the upper limit of normal. 
9.3.3 Removal of Subjects from Treatment or Assessment 
Subjects (or their legally authorized representative) may withdraw their consent to participate 
in the study or to receive study drug at any time without prejudice. The Investigator must 
withdraw from the study or study drug treatment any subject who requests to be withdrawn. 
A subject’s participation in the study may be discontinued at any time at the discretion of the 
Investigator and in accordance with his/her clinical judgment. When possible, a subject who 
is discontinued from study treatment should continue to perform the study tests and 
evaluations until study completion. For subjects who discontinue from the study, the tests 
and evaluations listed for the Early Termination Visit should be carried out (refer to 
Section 12.4). 
BioMarin must be notified of all subject withdrawals as soon as possible. BioMarin also 
reserves the right to discontinue the study at any time for either clinical or administrative 
reasons and to discontinue participation by an individual Investigator or site for poor 
enrollment or noncompliance. 
Reasons for which the Investigator or BioMarin may withdraw a subject from the study 
treatment include, but are not limited to, the following: 
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• Subject experiences a serious or intolerable adverse event (AE). 
• Subject develops a clinically significant laboratory abnormality. 
• Subject requires medication prohibited by the protocol. 
• Subject becomes pregnant (refer to Section 10.3 for details on the reporting 
procedures to follow in the event of pregnancy). 
Reasons for which the Investigator or BioMarin may withdraw a subject from the study 
include, but are not limited to, the following: 
• Subject does not adhere to study requirements specified in the protocol. 
• Subject was erroneously admitted into the study or does not meet entry criteria. 
• Subject is lost to follow-up. 
If a subject fails to return for scheduled visits, a documented effort must be made to 
determine the reason. If the subject cannot be reached by telephone within 7 days, a certified 
letter should be sent to the subject (or the subject’s legally authorized representative, if 
appropriate) requesting contact with the Investigator. This information should be recorded in 
the study records. 
The Investigator or designee must explain to each subject, before enrollment into the study, 
that for evaluation of study results, the subject’s protected health information obtained during 
the study may be shared with the study sponsor, regulatory agencies, and IRB. It is the 
Investigator’s (or designee’s) responsibility to obtain written permission to use protected 
health information per country-specific regulations, such as the Health Insurance Portability 
and Accountability Act (HIPAA) in the United States, from each subject, or if appropriate, 
the subject’s legally authorized representative. If permission to use protected health 
information is withdrawn, it is the Investigator’s responsibility to obtain a written request, to 
ensure that no further data will be collected from the subject and the subject will be removed 
from the study. 
9.3.4 Subject Identification and Replacement of Subjects 
Subjects will retain the same subject number assigned in PAL-002 or PAL-004. This unique 
identifier will be on all case report form (CRF) pages. In legal jurisdictions where use of 
initials is not permitted, a substitute identifier will be used.  
Subjects who do not complete the study will not be replaced. 
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9.4 
Treatments 
Upon enrollment into this study, subjects from PAL-002 will be dosed with the same or 
higher dose that was administered upon completion of PAL-002. Subjects enrolling from 
PAL-004, will be administered the same dose that was administered upon completion of 
PAL-004. rAvPAL-PEG doses will be administered SC by either health care professionals or 
via self administration. The dose level may be increased per Investigator determination in 
consultation with the Sponsor’s Medical Officer based on on available information regarding 
a subject’s blood Phe level (60-600 µmol/L), as well as any adverse events (any 
hypersensitivity reaction) for an individual subject. The dosage that provides control of blood 
Phe concentrations within the target range of 60-600 µmol/L for a minimum of 2 weeks will 
be determined for each subject by adjusting the dose level, dose frequency, or both, as agreed 
to by the PI and the Study Medical Officer, based upon the subject’s response to doses.  
Subjects may self administer study drug at home if approved by the Investigator and the 
Sponsor’s Medical Officer and if adequate training is demonstrated. Subjects may be eligible 
to self administer study drug if he or she meets the following criteria:  
• The subject is on a stable dosing regimen for 2 weeks. 
• The subject has not experienced any CTCAE Grade 3 or higher adverse event.  
• The subject has not experienced any hypersensitivity reaction to rAvPAL-PEG for at 
least 4 weeks. 
• The subject has no cognitive impairments that may increase the safety risk of self 
administration per the assessment of the PI.  
• The subject has been approved for self administration of study drug by the Sponsor’s 
Medical Officer. 
• The subject has completed the Self-Administration Training conducted by qualified 
study site personnel and has been observed by the study site personnel to be able to 
adequately prepare the proper dose and perform the injections safely.  
• The subject has been provided with epinephrine and has been trained on when and 
how to administer it.  
 
Qualified study site personnel will train each eligible subject on all procedures for self 
administration of study drug under the supervision of the PI. Qualified study site personnel 
will also be required to observe the subject prepare and perform at least 1 injection prior to 
allowing the subject to self administer a dose at home. The patient will see a study site nurse 
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or home healthcare nurse in person every week to ensure that the subject continues to 
perform all self-administration procedures correctly, to assess of adverse events, and to 
answer questions throughout the duration of the study. The study site nurse or home 
healthcare nurse will also perform the regularly scheduled assessments and procedures as 
outlined in Table 2.1.1 and Section 12; the subject must perform a clinic visit monthly at 
minimum. Training materials and other information specific to the study site personnel are 
provided in the Subject Self-Administration Training Materials.     
Subjects who are eligible for self administration will be provided with a Subject Study 
Manual. Self-administration training materials will be provided in the Subject Study Manual 
to supplement the in-person training provided by the qualified study site personnel. The 
Subject Study Manual will include step-by-step instruction on the following: 
• How to prepare and perform the injections of study drug safely. 
• How to receive, track, store, prepare, and return both used and unused study drug.   
• How to safely use and dispose of syringes used for injections of study drug. 
• How to use a new syringe and vial every time drug is administered. 
• How to care for their injection site after an injection of study drug.  
• How to identify an adverse reaction and how to report this reaction to the study site.  
• How and when to use epinephrine. 
• Who to contact at the study site in case of an emergency.  
The PI or the Sponsor’s Medical Officer may request that self administration be halted at any 
time and that the subject resume injections performed by the study site personnel or home 
healthcare nurse. 
9.4.1 Treatments Administered 
BioMarin and/or its designee will provide the study site or subject with a supply of IP 
sufficient for the completion of the study. BioMarin is responsible for shipping study drug to 
the clinical sites. The clinical site is responsible for supplyingthe study drug to subjects who 
qualify for self administration. Refer to the PAL-003 Pharmacy Manual for information 
pertaining to the distribution of study drug from sites.   
Information regarding supplying study drug to subjects who qualify for self administration is 
provided in the Subject Self-Administration Training Materials. 
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9.4.2 Identity of Investigational Product (IP) 
9.4.2.1 
Product Characteristics and Labeling 
The rAvPAL-PEG drug product for SC injection is formulated and supplied as a sterile 
aqueous (colorless to pale yellow) solution in clear, single-use, type-1 borosilicate glass 
vials. Each 3 mL vial contains 1.5 ± 0.2 mL to deliver 10 mg of rAvPAL-PEG per 1 mL 
(10 mg/mL protein concentration). Each vial is filled with 1.5 ± 0.2 mL to allow the 
withdrawal and delivery of up to 1 mL of the drug product. 
Dilution instructions are provided in a separate instruction manual. 
The excipients in this drug product are tromethamine, tromethamine-hydrochloride, 
sodium chloride, L-phenylalanine, and water for injection. 
Drug product packaging will be identified with the lot number and expiration date, and will 
be provided in a box labeled with the study number. 
9.4.3 Storage 
IP must be stored at 5 ±3°C (41 ± 5°F) under the conditions specified in the IB. At the site, 
the IP will be stored in a secure area accessible only to the designated pharmacists and 
clinical site personnel. All IP must be stored and inventoried and the inventories must be 
carefully and accurately documented according to applicable state, federal and local 
regulations, ICH GCP, and study procedures. 
Specific instructions for storage of study drug for subjects who qualify for self administration 
are provided in the Subject Self-Administration Training Materials.  
9.4.4 Directions for Administration 
Doses will be administered SC and the favorable dose will be determined for each subject by 
adjusting the dose level, dose frequency, or both, as agreed by the PI and the Study Medical 
Officer, based upon the subject’s response to doses. Dosing is up to a maximum dose per 
week of 5.0 mg/kg.  
Dosage is calculated by multiplying each subject’s weight in kilograms (kg) on Day 1 
(predose) by the assigned dose (in mg/kg). During the study, if the weight of a subject 
changes more than 10% from the measurement obtained at baseline or at a previous 
measurement, the subject’s dose may be adjusted to accommodate the change. The change 
must be recorded. Refer to the Pharmacy Manual for additional information on calculating 
dosage. 
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The injection sites should be alternated between doses, ie, upper left arm in Week 1, upper 
right arm in Week 2, etc. Doses may be administered in any of the common SC areas (upper 
arm, thigh, abdomen). If dose volume is such that a dose will be divided and given in more 
than 1 injection site, it is preferable to use both arms, both legs, or both sides of the abdomen. 
Subjects may require more than 1 injection per dose, depending upon site policy (ie, some 
institutions do not permit a single SC injection of greater than 2 mL). The number of 
injections required for an individual weighing 80 kg (about 176 pounds) is provided in 
Table 9.4.4.1 as an example. Note this table is for example purposes only. Dosage 
calculations must be performed according to study drug preparation instructions provided in 
the PAL-003 Pharmacy Manual. Study drug will be administered by clinic staff or other 
qualified and trained study personnel.  
Information for subjects who are participating in the Substudy and re-start rAvPAL-PEG 
dosing is provided in Section 9.1. Information for dosing of subjects who enroll into this 
study after completing Study PAL-004 is provided in Section 9.1. Instructions for subjects 
who re-start rAvPAL-PEG dosing due to unplanned missed doses are provided in 
Section 9.4.10.  
Instructions for administration of study drug for subjects who qualify for self administration 
are provided in the Subject Self-Administration Training Materials. 
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Table 9.4.4.1:  Number of Injections Required For an Individual Weighing 80 kg 
Dose Group 
(mg/kg) 
Weight 
(kg) 
Volume of Study Drug 
(mL)a 
No. of 
Injectionsb 
0.001 
80 
0.8 
1 
0.003 
80 
0.6 
1 
0.01 
80 
0.8 
1 
0.03 
80 
0.2 
1 
0.06 
80 
0.5 
1 
0.1 
80 
0.8 
1 
0.3 
80 
2.4 
2 
0.6 
80 
4.8 
2 or 3 
1.0 
80 
8.0 
4 
aStudy drug is supplied at a concentration of 10 mg/mL and is then diluted by differential amounts as specified 
in the PAL-003 Pharmacy Manual. Volume to be injected is calculated based on a starting volume. 
bNumber of injections per dose is dependent upon site policy for SC injections. The number of injections may 
vary at the discretion of the Investigator. 
 
Every effort should be made to adhere to the study drug administration regimen. If a subject 
misses more than 2 scheduled doses of study drug, both dose level and dose frequency may 
need to be re-evaluated (refer to Section 9.4.10). 
9.4.5 Method of Assigning Subjects to Treatment Groups 
This will be an open-label study; no randomization schedule will be generated. 
Subjects will retain the same subject number used in PAL-002 or PAL-004. 
9.4.6 Selection of Doses Used in the Study 
This Phase 2 study aims to evaluate the efficacy, safety, tolerability, and PK parameters of 
multiple doses of rAvPAL-PEG after long-term administration in subjects with PKU. A dose 
that produces a reduction in blood Phe concentrations to 60-600 μmol/L will be determined 
for each subject based on preliminary safety, antibody, and efficacy data from this ongoing 
study and the ongoing study, PAL-002, to date (JAN2011).  
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9.4.6.1 
Selection of Timing of Dose for Each Subject 
Study drug will be administered by clinic staff or other qualified and trained study personnel. 
Subjects may self administer study drug at home if approved by the Sponsor’s Medical 
Officer and if adequate training is provided (refer to Section 9.4). 
9.4.7 Blinding 
This is an open-label study. 
9.4.8 Prior and Concomitant Medications 
All prescription and over-the-counter (OTC) medications taken by a subject for 30 days 
before Screening will be recorded on the designated CRF. The Investigator may prescribe 
additional medications during the study, as long as the prescribed medication is not 
prohibited by the protocol. In the event of an emergency, any needed medications may be 
prescribed without prior approval, but the medical monitor must be notified of the use of any 
contraindicated medications immediately thereafter. Any concomitant medications added or 
discontinued during the study should be recorded on the CRF. 
Use of any investigational product (with the exception of rAvPAL-PEG used in PAL-002 or 
PAL-004) or investigational medical device within 30 days before Screening, or requirement 
for any investigational agent prior to completion of all scheduled study assessments, is 
prohibited. 
Use or planned use of any injectable drugs containing PEG (other than rAvPAL-PEG), 
including Depo-Provera, is prohibited within 6 months prior to Screening and during study 
participation. A list of PEG-containing injectable drugs is provided in the study reference 
materials. Subjects who have had a prior local skin reaction to rAvPAL-PEG or a 
PEG-containing product will be premedicated with acetaminophen and/or antihistamines 
(refer to Section 9.1.1). If the local skin reaction worsens with a repeat injection (as 
determined by the Investigator in consultation with the Study Medical Officer) even with 
premedication prior to study drug dosing, the subject must be withdrawn from the study and 
complete an Early Termination Visit. 
Subjects who have had a prior systemic reaction to rAvPAL-PEG or a PEG-containing 
product may participate in this study (refer to Section 9.1.1).  
Use of any medication that is intended to treat PKU within 14 days prior to the 
administration of study drug is prohibited. 
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9.4.9 Treatment Compliance 
The date, time, volume, and concentration of each dose of study drug administered to each 
subject must be recorded in the dispensing log provided for the study, as well as on the 
appropriate CRF. This data will be used to assess treatment compliance. 
9.4.10 Dose Interruption and Missed Doses  
Information for subjects who are participating in the Substudy and re-start rAvPAL-PEG 
dosing is provided in Section 9.1. Information for dosing of subjects who enroll into this 
study after completing Study PAL-002 or Study PAL-004 is provided in Section 9.1.  
During this long-term extension study, interruption of rAvPAL-PEG dosing may occur per 
subject decision or per the Investigator in consultation with the Sponsor’s Medical Officer. 
Subjects who miss more than 2 consecutive weekly doses (weekly dosing schedule) or 3 
consecutive daily doses (daily dosing schedule) for whatever reason may continue 
participation in this study. After a dosing interruption, rAvPAL-PEG administration should 
be re-started at the same dose level and dosing frequency that was administered prior to the 
dosing interruption. The first dose of rAvPAL-PEG following a dose interruption should be 
administered in a clinic setting, and the subject must be observed for 30-60 minutes 
following administration due to restarting dosing. A follow-up telephone call will be made to 
the subject to monitor subject safety 24 hours following the return to dosing. Subjects should 
continue to perform the study assessments as outlined in the Schedule of Events (refer to 
Table 2.1.1, Table 2.1.2, Table 2.1.3 and Table 2.1.4) during any dosing interruption.  
Subjects who miss rAvPAL-PEG dosing due to poor compliance may be discontinued from 
further study treatment per discretion of the Sponsor or Investigator (refer to Section 9.3.3).  
9.5 
Investigational Product Accountability 
The PI or designee is responsible for maintaining accurate records (including dates and 
quantities) of IP received, subjects to whom IP is dispensed (subject-by-subject dose specific 
accounting), IP returned, and IP lost or accidentally or deliberately destroyed. The PI or 
designee must retain all unused or expired study supplies until the study monitor (on-site 
CRA) has confirmed the accountability data. 
9.5.1 Return and Disposition of Clinical Supplies 
Unused study drug must be kept in a secure location for accountability and reconciliation by 
the study monitor. The Investigator or designee must provide an explanation for any 
destroyed or missing study drug or study materials. 
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Unused study drug may be destroyed on site, per the site’s standard operating procedures, but 
only after BioMarin has granted approval for drug destruction. The monitor must account for 
all study drug in a formal reconciliation process prior to study drug destruction. All study 
drug destroyed on site must be documented. Documentation must be provided to BioMarin 
and retained in the PIs study files. If a site is unable to destroy study drug appropriately, the 
site can return unused study drug to BioMarin upon request. The return of study drug or 
study drug materials must be accounted for on a Study Drug Return Form provided by 
BioMarin. 
Subjects who qualify for self administration of study drug will be provided with instructions 
for returning used and unused study drug and the proper disposal of any study drug materials 
(refer to the Subject Self-Administration Training Materials). 
All study drug and related materials should be stored, inventoried, reconciled, and destroyed 
or returned according to applicable state and federal regulations and study procedures. 
9.6 
Dietary or Other Protocol Restrictions 
Subjects will be instructed that diet should not be altered during the course of the study.   
Any decision to modify subject diet must be made per the Investigator in consultation with 
the Sponsor’s Medical Officer and must be performed under the supervision of the 
Investigaor in consultation with the Sponsor’s Medical Officer. 
A 3-day dietary record will be completed by subjects and will be brought to clinic visits for 
review with clinic staff. It is preferable that subjects complete the 3-day record immediately 
prior to their next dose of study drug. The dietary record will be maintained with the study 
source documents. Information regarding a subject diet diary is provided in Section 9.7.4. 
9.7 
Efficacy and Safety Variables 
9.7.1 Efficacy and Safety Measurements Assessed 
The Schedules of Events in the Synopsis (Section 2.1) describe the timing of required 
evaluations. 
For the laboratory assessments, the party responsible for performing the assessment and the 
pertinent protocol section describing the details of the test are listed in Table 9.7.1.1. 
 
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Table 9.7.1.1:  Summary of Laboratory Assessments 
Laboratory Assessment 
Party Responsible for 
Performing Test 
Section in Protocol for 
Details 
Clinical laboratory tests 
Central laboratory 
9.7.6 
Antibody testing 
BioMarina 
9.7.5.2 
PK variables 
BioMarin 
9.7.3 
Blood Phe concentrations 
Central laboratory 
9.7.2.1 
Urinalysis, pregnancy test (urine), 
and sedimentation rate 
Local laboratory 
9.7.6, 9.7.5.1 
Phe, phenylalanine; PK, pharmacokinetic. 
aAnalysis of the anti-rAvPAL-PEG IgE assay will be performed by a Contract Research Organization. 
 
9.7.1.1 
Demographic Data and Medical History 
Demographic data and a detailed medical history, including allergy history, will be obtained 
at Screening. The medical history will include specific information concerning any prior or 
existing medical conditions that might interfere with study participation or safety. 
This medical history should elicit all major illnesses, diagnoses, and surgeries that the subject 
has ever had, and whether the subject has a history of alcohol and/or drug abuse. 
9.7.1.2 
Physical Examination Findings 
Physical examination will include assessment of general appearance; CV; dermatologic; 
head, eyes, ears, nose, and throat; lymphatic; respiratory; GI; musculoskeletal; and 
neurological/psychological. Other body systems may be examined. Day 1 results will be the 
baseline values and clinically significant changes from baseline will be recorded as an AE. 
9.7.1.3 
Vital Sign Measurements 
Vital signs will be measured after resting for 5 minutes, and include seated systolic blood 
pressure (SBP) and diastolic blood pressure (DBP) measured in millimeters of mercury 
(mm Hg), heart rate in beats per minute, respiration rate in breaths per minute, weight (kg), 
and temperature in degrees Celsius (°C). Height (cm) will be measured at Screening only. 
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9.7.1.4 
Electrocardiography 
A standard 12-lead ECG will be recorded while the subject is resting, at Screening and at the 
Final Follow-Up (F/U) Visit or Early Termination Visit (ETV). If clinically significant 
abnormalities are noted at Screening, the PI or designee is required to assess whether it is 
appropriate for the subject to enroll in the study. 
9.7.1.5 
Chest X-Ray 
A chest X-ray will be performed at the Screening, Month 12, and Final Follow-Up (or Early 
Termination) visits to assess gross pulmonary health.  
9.7.2 Efficacy Variable 
9.7.2.1 
Blood Phenylalanine Concentrations 
Blood samples for Phe concentration measurements will be drawn at least 2.5 hours after a 
meal, on the days and time points indicated in the Schedule of Events (Table 2.1.1, 
Table 2.1.2, Table 2.1.3 and Table 2.1.4). 
In addition, after each administration of study drug, the subject will have a blood Phe 
measurement by fingerstick as outlined in Table 2.1.1, Table 2.1.2, Table 2.1.3 and 
Table 2.1.4. This may be done by the subject at home.  
A central laboratory will be used for blood Phe concentration analysis. 
9.7.3 Pharmacokinetic Variables 
Subjects enrolled in the Substudy will have additional PK sampling performed prior to the 
planned dosing interruption and upon re-introduction of rAvPAL-PEG. For subjects 
participating in the Substudy, PK sampling will be performed as follows: 
• When dosing is stopped, PK sampling will be performed prior to the final dose and 
then postdose at 8 hours, 12 hours, 16 hours, 24 hours, 48, hours, 72 hours, 96 hours, 
144 hours, 168 hours, and 216 hours. 
• When dosing is re-started, PK sampling will be performed predose and then postdose 
at 24 hours, 48 hours, 72 hours, 120 hours, and 168 hours. 
BioMarin will perform the anlaysis. 
9.7.4 Exploratory Efficacy Variable 
Diet will be assessed for its role in blood Phe reduction relative to rAvPAL-PEG dosing 
using a 3-day diet diary, which will be given to subjects to complete at home. Subjects will 
bring the completed diary with them to clinic visits. Subjects will be instructed to record all 
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food, beverages, special low-protein foods, and medical foods consumed for 3 consecutive 
days each week. If changes in diet are noted per the information on the diet diary, the subject 
will be instructed to maintain their diet as reported at the beginning of the study or as 
otherwise instructed by the Investigator. 
9.7.5 Safety Variables 
9.7.5.1 
Pregnancy Testing 
Female subjects of childbearing potential will have a urine pregnancy test at the time points 
specified in the Schedules of Events (Table 2.1.1 and Table 2.1.2). Female subjects with a 
positive serum pregnancy test at Screening do not meet eligibility criteria for enrollment. 
Additional pregnancy tests will be performed at any visit in which pregnancy status is in 
question. Serum pregnancy tests will be performed in the event of a positive or equivocal 
urine pregnancy test result. 
Refer to Section 10.3 for details on the reporting procedures to follow in the event of 
pregnancy. 
9.7.5.2 
Antibody Testing 
Immunogenicity will be assessed by determining immune response and neutralizing activity 
with the following measurements: anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, anti-PEG 
IgE, anti-PEG IgM, anti-rAvPAL-PEG IgE, and anti-rAvPAL-PEG neutralizing antibodies 
(refer to Section 9.1.1.3.3). Validated immunogenicity assays will be used per the time points 
indicated in the Schedule of Events (Table 2.1.1 and Table 2.1.2). 
BioMarin will perform the analysis except for IgE antibodies, which will be assessed by a 
Contract Research Organization. 
9.7.6 Clinical Laboratory Assessments 
Any abnormal test results determined to be clinically significant by the Investigator should 
be repeated (at the Investigator’s discretion) until the cause of the abnormality is determined, 
the value returns to baseline or to within normal limits, or the Investigator determines that the 
abnormal value is no longer clinically significant. 
All clinical laboratory result pages should be initialed and dated by an Investigator, along 
with a comment regarding whether or not any abnormal result is clinically significant. 
The diagnosis, if known, associated with abnormalities in clinical laboratory tests that are 
considered clinically significant by the Investigator will be recorded on the AE CRF. 
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Specific days for obtaining samples are provided in Table 2.1.1, Table 2.1.2, and in 
Section 12. The scheduled clinical laboratory tests are listed in Table 9.7.6.1. A central 
laboratory will be used for analysis. 
Table 9.7.6.1:  Clinical Laboratory Tests 
Blood Chemistry 
Hematology 
Urine Testsa 
Other 
Albumin  
Hemoglobin  
Appearance 
Pregnancy test, if 
applicablea 
Alkaline 
Phosphatase  
Hematocrit  
Color 
ALT (SGPT)  
WBC count 
pH 
 
AST (SGOT) 
RBC count 
Specific gravity 
Tyrosine 
Total bilirubin 
Platelet count 
Ketones 
 
BUN 
Differential cell count 
Protein 
Creatinine 
 
Glucose 
GGT 
 
Bilirubin 
Phenylalanine 
Total protein 
 
Nitrite 
CH50 b 
Calcium 
 
Urobilinogen 
C1
 b 
Sodium 
 
Hemoglobin 
C4
 b 
Potassium 
 
 
C3
 b  
Glucose 
 
 
Serum tryptase level b,c 
Uric acid 
 
 
Sedimentation ratea 
CO2 
 
 
CRPb 
Chloride 
 
 
 
ALT, alanine aminotransferase; AST, aspartate aminotransferase; BUN, blood urea nitrogen; C, complement; 
CH50, total hemolytic complement; CO2, carbon dioxide; CRP, C-reactive protein; GGT, 
gamma-glutamyltransferase; RBC, red blood cell; SGOT, serum glutamic-oxaloacetic transaminase; SGPT, 
serum glutamic-pyruvic transaminase; WBC, white blood cell. 
a To be performed by local laboratory. If urine pregnancy test is positive or equivocal, serum sample will be 
taken and assessed by a central laboratory. 
b Perform for Unscheduled Hypersensitivity Reaction visit only (within 48 hours of reaction).  
c Perform immediately after reaction if possible. 
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10 
REPORTING ADVERSE EVENTS 
10.1 
Adverse Events 
For this protocol, a reportable adverse event (AE) is any untoward medical occurrence (e.g., 
sign, symptom, illness, disease or injury) in a patient administered the study-drug or other 
protocol-imposed intervention, regardless of attribution. This includes the following: 
• AEs not previously observed in the subject that emerge during the course of the 
study. 
• Pre-existing medical conditions judged by the Investigator to have worsened in 
severity or frequency or changed in character during the study. 
• Complications that occur as a result of non-drug protocol-imposed interventions 
(eg, AEs related to screening procedures, medication washout, or no-treatment run-
in). 
An adverse drug reaction is any AE for which there is a reasonable possibility that the study 
drug caused the AE. “Reasonable possibility” means there is evidence to suggest a causal 
relationship between the study-drug and the AE. 
Whenever possible, it is preferable to record a diagnosis as the AE term rather than a series 
of terms relating to a diagnosis. 
The study period during which all non-serious AEs and SAEs will be reported begins after 
informed consent is obtained and the first adminstration of study drug  and continues until 
4 weeks following the last administration of study drug or the last visit of the treatment 
period (refer to Section 12). After informed consent but prior to initiation of study treatment, 
only SAEs associated with any protocol-imposed interventions will be reported. The criteria 
for determining, and the reporting of SAEs is provided in Section 10.2.   
The Investigator should follow all unresolved AEs until the events are resolved or stabilized, 
the subject is lost to follow-up, or it has been determined that the study treatment or study 
participation is not the cause of the AE. Resolution of AEs (with dates) should be 
documented on the appropriate CRF page(s) and in the subject’s medical record. 
The Investigator responsible for the care of the subject or qualified designee will assess AEs 
for severity, relationship to study-drug, and seriousness (see Section 10.2 for SAE 
definition). Severity (as in mild, moderate or severe headache) is not equivalent to 
seriousness, which is based on patient/event outcome or action criteria usually associated 
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with events that pose a threat to a patient’s life or functioning. Seriousness (not severity) 
serves as a guide for defining regulatory reporting obligations. 
The Investigator will determine the severity of each AE using the National Cancer Institute 
(NCI) Common Terminology Criteria for Adverse Events (CTCAE) v4. Adverse events that 
do not have a corresponding CTCAE term will be assessed according to the general 
guidelines for grading used in the CTCAE v4 as stated below. 
Grade 
Description 
1 
Mild: asymptomatic or mild symptoms; clinical or diagnostic 
observations only; intervention not indicated 
2 
Moderate: minimal, local or noninvasive intervention 
indicated; limiting age-appropriate instrumental activities of 
daily living (ADL)a 
3 
Severe or medically significant but not immediately life-
threatening: hospitalization or prolongation of hospitalization 
indicated; disabling; limiting self care activities of daily 
living (ADL) 
4 
Life threatening or debilitating: consequences; urgent 
intervention indicatedb 
5 
Death related to AE 
Grade 4 and 5 AEs should always be reported as SAEs. 
a Instrumental ADL refer to the following examples: preparing meals, shopping for groceries or clothes, using 
the telephone, managing money. 
b Self care ADL refer to the following examples: bathing, dressing and undressing, feeding oneself, using the 
toilet, taking medications, not bedridden. 
 
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The Investigator will determine the relationship of an AE to the study drug and will record it 
on the source documents and AE CRF, using the categories defined below. 
Relationship 
Description 
Not Related 
Exposure to the IP has not occurred 
OR 
The administration of the IP and the occurrence of the AE are not reasonably related in 
time  
OR 
The AE is considered likely to be related to an etiology other than the use of the IP; that 
is, there are no facts [evidence] or arguments to suggest a causal relationship to the IP. 
Possibly 
Related 
The administration of the IP and the occurrence of the AE are reasonably related in time 
AND 
The AE could be explained equally well by factors or causes other than exposure to the 
IP. 
Probably 
Related 
The administration of IP and the occurrence of the AE are reasonably related in time  
AND 
The AE is more likely explained by exposure to the IP than by other factors or causes. 
In order to classify AEs and diseases, preferred terms will be assigned by the sponsor to the original terms 
entered on the CRF, using MedDRA (Medical Dictionary for Regulatory Activities terminology). 
 
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10.2 
Serious Adverse Events 
A serious adverse event (SAE) is any untoward medical occurrence that at any dose meets 1 
or more of the following criteria: 
• Is fatal. 
• Is life threatening. 
• Note: Life-threatening refers to an event that places the patient at immediate risk of 
death. This definition does not include a reaction that, had it occurred in a more 
severe form, might have caused death. 
• Requires or prolongs inpatient hospitalization. 
• Results in persistent or significant disability or incapacity. 
• Is a congenital anomaly or birth defect in the child or fetus of a patient exposed to IP 
prior to conception or during pregnancy. 
• Is an important medical event or reaction. 
The reporting period for SAEs begins after informed consent is obtained, and continues until 
4 weeks following the last administration of study drug or End of Treatment Visit. 
All SAEs, whether or not considered related to study drug, must be reported within 24 hours 
of the site becoming aware of the event by faxing the study-specific SAE Report Form to 
BioMarin Pharmacovigilance (BPV). ). Each SAE must also be reported in the CRF 
Investigators should not wait to collect information that fully documents the event before 
notifying BPV of a SAE. BioMarin may be required to report certain SAEs to regulatory 
authorities within 7 calendar days of being notified about the event; therefore, it is important 
that Investigators submit any information requested by BioMarin as soon as it becomes 
available.The Investigator should follow all unresolved SAEs until the events are resolved or 
stabilized, the patient is lost to follow-up, or it has been determined that the study treatment 
or participation is not the cause of the AE. Resolution of AEs (with dates) should be 
documented in the CRF and in the patient’s medical record. 
For some SAEs, the Sponsor may follow up by telephone, fax, electronic mail, and/or a 
monitoring visit to obtain additional case details deemed necessary to appropriately evaluate 
the SAE report (e.g., hospital discharge summary, consultant report, or autopsy report). 
At the last scheduled visit, the Investigator should instruct each subject to report any 
subsequent SAEs that the subject’s personal physician(s) believes might be related to prior 
study treatment. 
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The Investigator should notify the study Sponsor of any death or SAE occurring at any time 
after a subject has discontinued or terminated study participation if felt to be related to prior 
study treatment. The Sponsor should also be notified if the Investigator should become aware 
of the development of cancer or of a congenital anomaly in a subsequently conceived 
offspring of a subject that participated in this study.  
Reporting of SAEs to the IRB will be done in compliance with the standard operating 
procedures and policies of the IRB and with applicable regulatory requirements. Adequate 
documentation must be obtained by BioMarin showing that the IRB was properly and 
promptly notified as required. 
10.3 
Pregnancy 
Pregnancy in a subject or partner should be reported within 24 hours of the site becoming 
aware of the pregnancy to BioMarin Pharmacovigilance by fax using the Pregnancy Form in 
the study reference materials. In addition, pregnancy in a subject is also reported on the End 
of Study CRF. The Investigator must make every effort to follow the subject through 
resolution of the pregnancy (delivery or termination) and to report the resolution on the 
Pregnancy Follow-up Form in the study reference materials. In the event of pregnancy in the 
partner of a study subject, the Investigator should make every reasonable attempt to obtain 
the woman’s consent for release of protected health information. 
10.4 
Urgent Safety Measures 
The regulations governing clinical trials state that the sponsor and Investigator are required to 
take appropriate urgent safety measures to protect subjects against any immediate hazards 
that may affect the safety of subjects, and that the appropriate regulatory bodies should be 
notified according to their respective regulations. According to the European Union (EU) 
Clinical Trial Directive 2001/20/EC, “…in the light of the circumstances, notably the 
occurrence of any new event relating to the conduct of the trial or the development of the 
investigational medicinal product where that new event is likely to affect the safety of the 
subjects, the sponsor and the Investigator shall take appropriate urgent safety measures to 
protect the subjects against any immediate hazard. The sponsor shall forthwith inform the 
competent authorities of those new events and the measures taken and shall ensure that the 
IRB/EC/REB is notified at the same time.” The reporting period for these events which may 
require the implementation of urgent safety measures is the period from the time of signing 
of the ICF through the completion of the last study visit or at the ETV. Investigators are 
required to report any events which may require the implementation of urgent safety 
measures to BioMarin with 24 hours. 
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Examples of situations that may require urgent safety measures include discovery of the 
following: 
• Immediate need to revise the IP administration (ie, modified dose amount or 
frequency not defined in protocol). 
• Lack of study scientific value, or detrimental study conduct or management. 
• Discovery that the quality or safety of the IP does not meet established safety 
requirements. 
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10.5 
BioMarin Pharmacovigilance Contact Information 
Contact information for BioMarin Pharmacovigilance is as follows: 
BioMarin Pharmaceutical Inc. 
Address 
105 Digital Drive 
 
 
Novato, CA 94949 
Phone:  
(415) 506-6179 
Fax: 
 
(415) 532-3144 
E-mail: 
drugsafety@bmrn.com 
The Investigator is encouraged to discuss with the medical monitor any AEs for which the 
issue of seriousness is unclear or questioned. Contact information for the medical monitor is 
as follows: 
Name:  
, MD 
Address: 
105 Digital Drive 
 
 
Novato, CA 94949 USA 
Phone:  
 
Fax: 
 
 
E-mail: 
 
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11 
APPROPRIATENESS OF MEASUREMENTS 
11.1 
Safety and Pharmacokinetics 
The PK and safety assessments in this study are used widely and are generally recognized as 
reliable, accurate, and relevant. 
11.2 
Diet Diary 
A 3-day diet diary will be issued to subjects for completion and will be brought to each clinic 
visit for review with the clinical study staff. Additional information regarding the diet diary 
is provided in Section 7.3, and information regarding administration of the diary is provided 
in Section 9.7.4. Additional information about diet is provided in Section 9.1 and Section 9.6. 
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12 
STUDY PROCEDURES 
12.1 
Prestudy 
An ICF must be signed and dated by the subject (or the subject’s legally authorized 
representative if the subject is less than 18 years of age), the PI or designee and witness 
(if required) before any study-related procedures are performed. 
12.2 
Screening Visit 
After subjects have signed an ICF, they will be screened for enrollment into the study. 
The following study activities will be performed at Screening: 
• Medical history, including allergy history, and demographics 
• Physical examination  
• Vital signs, including height and weight 
• Chest X-ray 
• 12-lead ECG 
• Clinical laboratory tests (including hematology, chemistry, and urinalysis) 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• Assessment of SAEs 
• Concomitant medications 
• Diet query 
• Blood Phe and plasma tyrosine concentration 
For subjects who participated in PAL-002 or PAL-004, these assessments may be the same 
as those used for the Week 16 Visit of PAL-002 or the Week 16 visit ofPAL-004, if they 
occur within 28 days from Day 1. 
12.3 
Treatment Period 
During the Treatment Period, additional visits may occur if deemed necessary to monitor 
AEs or blood Phe concentrations. All study activities will occur on the first day of each week 
unless otherwise noted. On days that a dose is given, assessments will be done predose unless 
otherwise specified. Subjects must have AEs and concomitant medications assessed and an 
injection-site inspection performed whenever dose is administered even if the administration 
does not coincide with a scheduled clinic visit.   
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If the dose is modified by increasing dose level, additional blood Phe concentration testing 
should be done daily for 3 days following dose adjustment. If dose is modified by increasing 
either dose frequency or dose level, additional blood Phe concentration testing should be 
done prior to each dose for the first 2 weeks following dose adjustment. 
12.3.1 Day 1 (Week 1) 
Within 28 days of completing screening assessments, the following study activities will be 
performed on Day 1: 
• Physical examination 
• Vital signs, including weight 
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• Injection-site inspection (postdose) 
• Assessment of SAEs (predose and postdose) and all AEs (postdose) 
• Concomitant medications 
• Diet query 
• PK sample 
• Blood Phe and plasma tyrosine concentration 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, and anti-rAvPAL-PEG neutralizing antibodies) 
• Administer study drug (study drug may be administered on additional days during the 
week as determined by the Investigator, in agreement with the Study Medical Officer) 
o For subjects enrolling into this study from Study PAL-004, first dose of 
rAvPAl-pEG must be given in the clinic setting and a telephone follow-up 
with the subject must be performed 24 hours later to assess safety issues. 
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12.3.2 Weekly Visits 
Weekly visits do not require an in-clinic visit if conducted by a home healthcare professional. 
However, dose modifications must be peformed in the clinic. Subjects must have AEs and 
concomitant medications assessed and an injection-site inspection performed whenever dose 
is administered even if the administration does not coincide with a scheduled clinic visit.   
The following study activities will be performed at the weekly visits beginning with Week 2: 
• Vital signs, including weight 
• Injection-site inspection (previous and current injection site) 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• 3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the next dose of study drug.) 
• PK sample  
• For subjects participating in the Substudy, refer to Section 12.3.3. 
• Blood Phe and plasma tyrosine concentration 
• Administer study drug (study drug may be administered on additional days during the 
week as determined by the Investigator, in agreement with the Study Medical Officer) 
o For subjects participating in the Substudy, refer to Section 12.3.3. 
In addition, 3 days after each administration of study drug, the subject will have a blood Phe 
measurement by fingerstick. This may be done by the subject at home. 
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12.3.3 Substudy Visits (Weekly) 
The following study activities will be performed on Day 1 of the Substudy (ie, final dose 
prior to interruption), Day 8, Day 15, Day 22, and Day 29 (ie, restart administration of study 
drug) for subjects participating in the Substudy: 
• Physical examination 
• Vital signs, including weight 
• Clinical laboratory tests 
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• Injection-site inspection (predose; postdose on Day 1; during weekly visit on Day 8, 
15, 22; and postdose on Day 29) 
• Assessment of AEs  
• Concomitant medications 
• Diet query 
• 3-day diet diary  
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, and anti-rAvPAL-PEG neutralizing antibodies,) 
• Blood Phe and plasma tyrosine concentration 
o When dosing is stopped, sampling for blood Phe assessment only will be 
performed prior to the final dose and then postdose at 8 hours, 12 hours, 
16 hours, 24 hours, 48, hours, 72 hours, 96 hours, 144 hours, 168 hours, 
and 216 hours. 
o When dosing is re-started, sampling for blood Phe assessment only will be 
performed predose and then postdose at 24 hours, 48 hours, 72 hours, 120 
hours, and 168 hours. 
• PK sample  
• For subjects participating in the Substudy, additional PK sampling will be performed 
upon the final dose prior to the planned dosing interruption and upon re-introduction 
of rAvPAL-PEG. Refer to Section 9.7.3 
• Administer study drug (Day 29 only) 
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o For subjects participating in the Substudy, administration of rAvPAL-PEG 
will not be performed for approximately 4 consecutive weeks regardless of 
their dosing regimen (dose level and frequency). After approximately 
4 weeks of no dosing, rAvPAL-PEG administration will be re-started at 
the same dose level and dosing frequency that was administered prior to 
the dosing interruption. The first dose of re-administration must be given 
in the clinic setting, and a telephone follow-up with the subject must be 
performed 24 hours later to assess safety issues. 
 
12.3.4 Monthly Visits (Week 4, 8, 12, etc) 
Subjects must have AEs and concomitant medications assessed and an injection-site 
inspection performed whenever dose is administered even if the administration does not 
coincide with a scheduled clinic visit.    
Monthly visits consist of all weekly activities and include additional activities and must be 
performed in the clinic. The following study activities will be performed at the monthly visits 
beginning with Week 4: 
• Vital signs, including weight 
• Clinical laboratory tests 
• Chest x-ray (Month 12 visit only) 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• Injection-site inspection (previous and current injection site) 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• 3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the next dose of study drug.) 
• PK sample  
• For subjects participating in the Substudy, refer to Section 12.3.3. 
• Blood Phe and plasma tyrosine concentration 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, and anti-rAvPAL-PEG neutralizing antibodies) 
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• Administer study drug (study drug may be administered on additional days during the 
week as determined by the Investigator, in agreement with the Study Medical Officer) 
o For subjects participating in the Substudy, refer to Section 12.3.3. 
In addition, 3 days after each administration of study drug, the subject will have a blood Phe 
measurement by fingerstick. This may be done by the subject at home. 
12.3.5 Quarterly Visits (Week 12, 24, 36, etc) 
Subjects must have AEs and concomitant medications assessed and an injection-site 
inspection performed whenever dose is administered even if the administration does not 
coincide with a scheduled clinic visit.    
Quarterly visits consist of all weekly and monthly activities and include additional activities. 
The following study activities will be performed at the quarterly visits beginning with 
Week 12: 
• Physical examination 
• Vital signs, including weight 
• Clinical laboratory tests 
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• Injection-site inspection (previous and current injection site) 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• 3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the next dose of study drug.) 
• PK sample  
o For subjects participating in the Substudy, refer to Section 12.3.3. 
• Blood Phe and plasma tyrosine concentration 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibodies)  
• Administer study drug (study drug may be administered on additional days during the 
week as determined by the Investigator, in agreement with the Study Medical Officer) 
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o For subjects participating in the Substudy, refer to Section 12.3.3. 
In addition, 3 days after each administration of study drug, the subject will have a blood Phe 
measurement by fingerstick. This may be done by the subject at home. 
12.3.6 Interim Dosing Visit 
Subjects who increase their dose frequency during the study from 1x/week to 2x/week or 
daily will have additional assessments performed for 5 weeks after the subject’s rAvPAL-
PEG dose frequency has been increased. If the Interim Dosing Visit coincides with a weekly, 
monthly, or quarterly scheduled visit, the scheduled visit assessments should also be 
performed. The following study activities will be performed for the Interim Dosing Visit: 
• Vital signs, including weight 
• Injection-site inspection (previous and current injection site) 
• Assessment of AEs 
• Concomitant medications 
• Blood Phe measurement by fingerstick 
o This may be done by the subject at home. 
12.3.7  
Unscheduled Hypersensitivity Reaction Visit 
Subjects who have a systemic reaction, including a generalized skin reaction, or a large local 
skin reaction that is not contiguous to the injection site after rAvPAL-PEG administration 
(refer to Section 9.1.1) will have assessments performed immediately following (within 
48 hours) the reaction.  
• Injection-site inspection 
• Clinical laboratory tests 
• Sedimentation rate  
• CRP, CH50, C1, C3, and C4 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG IgE, and anti-rAvPAL-PEG neutralizing 
antibodies) 
• Serum tryptase level 
• Perform immediately after reaction if possible. 
• Skin biopsy (optional; affected and not affected area; to be performed within 1 week 
of reaction) 
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• PK sample 
• Assessment of AEs 
• Concomitant medications 
Following completion of the Unscheduled Hypersensitivity Reaction Visit assessments, the 
subject may resume treatment with study drug per the discretion of the Investigator in 
consultation with the Sponsor’s Medical Officer. Subjects who have had an IgE-mediated 
reaction must be discontinued from further study drug administration. Subjects who do not 
have an IgE-mediated reaction may resume study drug administration under close 
monitoring; subjects must be premedicated orally with acetaminophen and/or antihistamines 
1 hour prior to study drug dosing for the remainder of the study (refer to Section 9.1.1.3.3). 
12.4 
Early Termination Visit 
The Early Termination Visit (ETV) will occur 4 weeks after the final dose of study drug. 
Subjects who terminate from study treatment early should continue to perform the remaining 
visit assessments in Section 12.3 as applicable until study completion. 
Any AE that caused a subject to withdraw from the study or any clinically significant 
abnormal laboratory value or vital sign measurement identified at the ETV will be followed 
by the Investigator.  
Every reasonable effort should be made to contact any subject who is lost to follow-up. 
The following study activities will be performed at the ETV: 
• Physical examination  
• Vital signs, including weight 
• 12-lead ECG 
• Clinical laboratory tests 
• Chest x-ray  
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• Injection-site inspection (previous injection site) 
• Assessment of AEs 
• Concomitant medications 
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• Diet query 
• 3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the Early Termination Visit.) 
• PK sample 
• Blood Phe and plasma tyrosine concentration 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibodies) 
 
12.5 
Final Follow-up Visit 
The final follow-up (F/U) Visit will occur 1 week after the final dose of study drug. 
The following study activities will be performed at the F/U Visit: 
• Physical examination  
• Vital signs, including weight 
• 12-lead ECG 
• Clinical laboratory tests 
• Chest x-ray  
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• Injection-site inspection (previous injection site) 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• 3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the Final Follow-up Visit.) 
• PK sample 
• Blood Phe and plasma tyrosine concentration 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibodies) 
 
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13 
DATA QUALITY ASSURANCE 
BioMarin personnel or designees will visit the study site prior to initiation of the study to 
review with the site personnel information about the IP, protocol and other regulatory 
document requirements, any applicable randomization procedures, source document 
requirements, CRFs, monitoring requirements, and procedures for reporting AEs, including 
SAEs. 
At visits during and after the study, a CRA will monitor the site for compliance with 
regulatory documentation, with a focus on accurate and complete recording of data on CRFs 
from source documents, adherence to protocol, randomization (if applicable), SAE reporting 
and drug accountability records.  
The designated clinical data management group will enter or transfer CRF data into a study 
database. 
Data quality control and analysis will be performed by BioMarin or a designee, based on a 
predefined analysis plan. 
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14 
STATISTICAL METHODS AND DETERMINATION OF SAMPLE SIZE 
14.1 
Statistical and Analytical Plans 
Because of the small sample size, no formal statistical tests will be performed. Categorical 
data will be summarized using frequency and percent, while continuous data will be 
summarized using descriptive statistics (ie, number of observations, mean, median, standard 
deviation [SD], minimum, and maximum). 
The statistical analysis plan (SAP) will provide additional details about the planned statistical 
analysis. 
14.2 
Safety Analysis 
All subjects who receive any amount of study drug in this study and have postdose safety 
information will be included in the safety analyses. 
All AEs will be coded using the Medical Dictionary for Regulatory Activities (MedDRA). 
The incidence of AEs will be summarized by system organ class, preferred term, relationship 
to study drug, and severity. A by–subject listing will be provided for those subjects who 
experience a serious AE (SAE), including death, or experience an AE associated with early 
withdrawal from the study or study drug. 
Clinical laboratory data will be summarized by the type of laboratory test. Frequency and 
percentage of subjects who experience abnormal (ie, outside of reference range) and/or 
clinically significant abnormalities after study drug administration will be presented for each 
clinical laboratory test. For each clinical laboratory test, descriptive statistics will be provided 
for baseline and all subsequent post-treatment visits. Changes from baseline to the post-
treatment visits will also be provided. Descriptive statistics, including clinically significant 
changes from baseine, of vital signs, ECG results, and X-ray results will also be provided. 
14.3 
Pharmacokinetic Analysis 
Subjects who complete the Substudy will have the following PK parameters assessed: area 
under the plasma concentration-time curve (AUC), time to maximum plasma concentration 
(Tmax), maximum plasma concentration (Cmax), half life (t1/2), and clearance (CL/F).Should 
data become available from PAL-002 or PAL-004 that indicate study drug accumulation 
should also be measured, additional blood draws may be added for PK analysis as needed per 
the discretion of the Investigator in consultation with the Sponsor’s Medical Officer. 
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14.4 
Efficacy Analysis 
Data from all subjects who receive any amount of study drug and who have any 
post-treatment efficacy data will be included in the efficacy analysis. 
Blood Phe concentration at each scheduled time point will be summarized using descriptive 
statistics (mean, SD, median, minimum, and maximum). Change in blood Phe concentration 
from baseline to each scheduled time point and presence/absence of antibodies will also be 
summarized. In addition, the proportion of subjects who have maintained target Phe 
concentrations of 60-600 µmol/L will be summarized by each scheduled time point. 
The relationship of dietary Phe intake (per information reported on the subject diet diary) and 
blood Phe concentration will also be explored. Subjects who received any amount of study 
drug with any post-treatment blood Phe concentration measurements and diet diary 
information will be included in this exploratory analysis. Information regarding this 
exploratory analysis will be provided in the Statistical Analyais Plan. 
For subjects who completed the Substudy, the effect of stopping and re-starting rAvPAL-
PEG dosing on safety, blood Phe level, and immune response will be explored. Information 
regarding the analysis will be provided in the Statistical Analyais Plan. 
14.5 
Determination of Sample Size 
Subjects who participated in PAL-002 or PAL-004 may be enrolled into this study. No 
formal sample size calculation was conducted for this study or the PAL-003 Substudy.   
14.6 
Handling of Missing Data 
All analyses will be presented based on observed data only. Missing data will not be imputed 
for analyses unless sensitivity analyses are warranted. If imputations are used, detailed 
imputation methods will be described in the SAP before locking the database. 
14.7 
Interim Analyses 
Safety will be assessed throughout the study on an ongoing basis (refer to Section 15 for 
information regarding the DMC). 
14.8 
Changes in the Conduct of the Study or Planned Analyses 
Only BioMarin may modify the protocol. Any change in study conduct considered necessary 
by the PI will be made only after consultation with BioMarin, who will then issue a formal 
protocol amendment to implement the change. The only exception is when an Investigator 
considers that a subject’s safety is compromised without immediate action. In these 
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circumstances, immediate approval of the chairman of the IRB must be sought, and the 
Investigator should inform BioMarin and the full IRB within 2 working days after the 
emergency occurs. 
With the exception of minor administrative or typographical changes, the IRB must review 
and approve all protocol amendments. Protocol amendments that have an impact on subject 
risk or the study objectives, or require revision of the ICF, must receive approval from the 
IRB prior to their implementation. 
When a protocol amendment substantially alters the study design or the potential risks or 
burden to subjects, the ICF will be amended and approved by BioMarin and the IRB, and all 
active subjects must again provide informed consent. 
Note: If discrepancies exist between the text of the statistical analysis as planned in the 
protocol, and the final SAP, a protocol amendment will not be issued and the SAP will 
prevail. 
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15 
DATA MONITORING COMMITTEE (DMC) 
The DMC will act independently in an advisory capacity to BioMarin to monitor the safety 
of rAvPAL-PEG in subjects who participate in the study. Meetings of the DMC can be 
convened at any time at the discretion of the DMC Chair or the Study Medical Officer. 
The Chair will be notified by the Study Medical Officer of all SAEs and will receive 
summaries of other safety data as available. The DMC will review the study data as soon as it 
is available during the study, on a schedule defined in the DMC Charter, and offer advice on 
whether or not to proceed, modify or terminate study enrollment on the basis of toxicity. 
Details regarding the DMC membership and safety data to be reviewed by members will be 
provided in a charter. 
The responsibilities of the DMC are to: 
• Review the study protocol, informed consent and assent documents, and plans for 
data monitoring. 
• Evaluate the progress of the trial, subjects’ risk versus benefit, and other factors that 
could affect the study outcome. 
• Consider relevant information that may have an impact on the safety of the 
participants or the ethics of the study. 
• Protect the safety of the study participants in accordance with the stopping criteria as 
defined in study protocol Section 9.1.3. 
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16 
COMPENSATION, INSURANCE, AND INDEMNITY 
There will be no charge to study subjects to be in this study. BioMarin will pay all costs of 
tests, procedures, and treatments that are part of this study. In addition, after IRB approval, 
BioMarin may reimburse the cost of travel for study-related visits. BioMarin will not pay for 
any hospitalizations, tests, or treatments for medical problems of any sort, whether or not 
related to the study subject’s disease, that are not part of this study. Costs associated with 
hospitalizations, tests, and treatments should be billed and collected in the way that such 
costs are usually billed and collected. 
The Investigator should contact BioMarin immediately upon notification that a study subject 
has been injured by the IP or by procedures performed as part of the study. Any subject who 
experiences a study-related injury should be instructed by the Investigator to seek medical 
treatment at a pre-specified medical institution if possible, or at the closest medical treatment 
facility if necessary. The subject should be given the name of a person to contact to seek 
further information about, and assistance with, treatment for study-related injuries. 
The treating physician should bill the subject’s health insurance company or other third party 
payer for the cost of this medical treatment. If the subject has followed the Investigator’s 
instructions, BioMarin will pay for reasonable and necessary medical services to treat the 
injuries caused by the IP or study procedures, if these costs are not covered by health 
insurance or another third party that usually pays these costs. In some jurisdictions, BioMarin 
is obligated by law to pay for study-related injuries without prior recourse to third party 
payer billing. If this is the case, BioMarin will comply with the law. 
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17 
CASE REPORT FORMS AND SOURCE DOCUMENTS 
Electronic case report forms will be provided for each subject. The Investigator must review 
and electronically sign the completed CRF casebook to verify its accuracy. 
CRFs must be completed using a web–based application that has been validated. Study site 
personnel will be trained on the application and will enter the clinical data from source 
documentation. Unless explicitly allowed in the CRF instructions, blank data fields are not 
acceptable. 
In the event of an entry error, or if new information becomes available, the site personnel will 
correct the value by deselecting the erroneous response and then selecting or entering the 
factual response. In compliance with 21 CFR Part 11, the system will require the site 
personnel to enter a reason for changing the value. The documented audit trail will include 
the reason for the change, the original value, the new value, the time of the correction, and 
the identity of the operator. 
BioMarin’s policy is that study data on the CRFs must be verifiable to the source data, which 
necessitates access to all original recordings, laboratory reports, and subject records. 
In addition, all source data should be attributable (signed and dated). The Investigator must 
therefore agree to allow direct access to all source data. Subjects (or their legally authorized 
representative) must also allow access to their medical records, and subjects will be informed 
of this and will confirm their agreement when giving informed consent. If an Investigator or 
institution refuses to allow access to subject records because of confidentiality, arrangements 
must be made to allow an “interview” style of data verification. 
A CRA designated by BioMarin will compare the CRFs with the original source documents 
at the study site and evaluate them for completeness and accuracy before designating them as 
“source data verified” (SDV). If an error is discovered at any time or a clarification is 
needed, the CRA, or designee, will create an electronic query on the associated field. Site 
personnel will then answer the query by either correcting the data or responding to the query. 
The CRA will then review the response and determine either to close the query or re–query 
the site if the response does not fully address the question. This process is repeated until all 
open queries have been answered and closed. 
Before a subject’s CRF casebook can be locked, all data fields must be SDV and all queries 
closed. The Investigator will then electronically sign the casebook, specifying that the 
information on the CRFs is accurate and complete. The Data Manager, or designee, will then 
set the status of the forms, visits, and the entire casebook to locked. Upon completion of the 
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clinical study report for the entire study, an electronic copy of each site’s casebooks will be 
copied to a compact disk (CD) and sent to each site for retention with other study documents. 
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18 
STUDY MONITORING AND AUDITING 
Qualified individuals designated by BioMarin will monitor all aspects of the study according 
to GCP and standard operating procedures for compliance with applicable government 
regulations. The PI agrees to allow these monitors direct access to the clinical supplies, 
dispensing, and storage areas and to the clinical files, including original medical records, of 
the study subjects, and, if requested, agrees to assist the monitors. The PI and staff are 
responsible for being present or available for consultation during routinely scheduled site 
visits conducted by BioMarin or its designees. 
Members of BioMarin’s GCP Compliance Department or designees may conduct an audit of 
a clinical site at any time during or after completion of the study. The PI will be informed if 
an audit is to take place and advised as to the scope of the audit. Representatives of the FDA 
or other Regulatory Agencies may also conduct an audit of the study. If informed of such an 
inspection, the PI should notify BioMarin immediately. The PI will ensure that the auditors 
have access to the clinical supplies, study site facilities, original source documentation, and 
all study files. 
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19 
RETENTION OF RECORDS 
The PI must retain all study records required by BioMarin and by the applicable regulations 
in a secure and safe facility. The PI must consult a BioMarin representative before disposal 
of any study records, and must notify BioMarin of any change in the location, disposition or 
custody of the study files. The PI/institution must take measures to prevent accidental or 
premature destruction of essential documents, that is, documents that individually and 
collectively permit evaluation of the conduct of a study and the quality of the data produced, 
including paper copies of study records (eg, subject charts) as well as any original source 
documents that are electronic as required by applicable regulatory requirements. 
All study records must be retained for at least 2 years after the last approval of a marketing 
application in the U.S. or an ICH region and until (1) there are no pending or contemplated 
marketing applications in the United States or an ICH region or (2) at least 2 years have 
elapsed since the formal discontinuation of clinical development of the IP. The PI/institution 
should retain subject identifiers for at least 15 years after the completion or discontinuation 
of the study. Subject files and other source data must be kept for the maximum period of time 
permitted by the hospital, institution or private practice, but not less than 15 years. 
These documents should be retained for a longer period, however, if required by the 
applicable regulatory requirements or by a BioMarin agreement. BioMarin must be notified 
and will assist with retention should the PI/institution be unable to continue maintenance of 
subject files for the full 15 years. It is the responsibility of BioMarin to inform the 
PI/institution as to when these documents no longer need to be retained. 
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20 
USE OF INFORMATION AND PUBLICATION 
BioMarin recognizes the importance of communicating medical study data and therefore 
encourages their publication in reputable scientific journals and at seminars or conferences. 
The details of the processes of producing and reviewing reports, manuscripts, and 
presentations based on the data from this study will be described in the Clinical Study 
Agreement between BioMarin and the PI. 
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21 
REFERENCES 
Armstrong, JK, Hempel, G, Koling, S, Chan, LS et. al. Antibody against poly(ethylene 
glycol) adversely affects PEG-asparaginase therapy in acute lymphoblastic leukemia patients. 
Cancer 110[1], 103-111. 2007.  
Chen, AM, Scott, MD. Current and future applications of immunological attenuation via 
pegylation of cells and tissue. BioDrugs 15[12], 833-847. 2001.  
Davis, S, Abuchowski, A, Park, YK, Davis, FF. Alteration of the circulating life and 
antigenic properties of bovine adenosine deaminase in mice by attachment of polyethylene 
glycol. Clin Exp Immunol 46[3], 649-652. 1981.  
Fisch, RO. Comments on diet and compliance in phenylketonuria. Eur J Pediatr 159 Suppl 2, 
S142-S144. 2000.  
Gamez, A, Wang, L, Sarkissian, CN, Wendt, D et. al. Structure-based epitope and 
PEGylation sites mapping of phenylalanine ammonia-lyase for enzyme substitution treatment 
of phenylketonuria. Mol Genet Metab 91[4], 325-334. 2007.  
Ganson, NJ, Kelly, SJ, Scarlett, E, Sundy, JS et. al. Control of hyperuricemia in subjects with 
refractory gout, and induction of antibody against poly(ethylene glycol) (PEG), in a phase I 
trial of subcutaneous PEGylated urate oxidase. Arthritis Res Ther 8[1], R12. 2006.  
Guttler, F, Azen, C, Guldberg, P, Romstad, A et. al. Impact of the phenylalanine hydroxylase 
gene on maternal phenylketonuria outcome. Pediatrics 112[6 Pt 2], 1530-1533. 2003.  
Harris, JM, Chess, RB. Effect of pegylation on pharmaceuticals. Nat Rev Drug Discov 2[3], 
214-221. 2003.  
Huttenlocher, PR. The neuropathology of phenylketonuria: human and animal studies. Eur J 
Pediatr 159 Suppl 2, S102-S106. 2000.  
Kaufman, S. An evaluation of the possible neurotoxicity of metabolites of phenylalanine. J 
Pediatr 114[5], 895-900. 1989.  
Koch, R, Hanley, W, Levy, H, Matalon, K et. al. The Maternal Phenylketonuria International 
Study: 1984-2002. Pediatrics 112[6 Pt 2], 1523-1529. 2003.  
Lapis. Long-term Correction of PKU in the Pahenu2 Mouse by Mutant and Chemically 
Modified Forms of Phenylalanine Ammonium Lyase. ASHG 57th Annual Meeting The 
American Society of Human Genetics)2007.  
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Lee, PJ, Lilburn, M, Baudin, J. Maternal phenylketonuria: experiences from the United 
Kingdom. Pediatrics 112[6 Pt 2], 1553-1556. 2003.  
Levy, HL. Historical background for the maternal PKU syndrome. Pediatrics 112[6 Pt 2], 
1516-1518. 2003.  
Matalon, R, Surendran, S, Matalon, KM, Tyring, S et. al. Future role of large neutral amino 
acids in transport of phenylalanine into the brain. Pediatrics 112[6 Pt 2], 1570-1574. 2003.  
Richter, AW, Akerblom, E. Antibodies against polyethylene glycol produced in animals by 
immunization with monomethoxy polyethylene glycol modified proteins. Int Arch Allergy 
Appl Immunol 70[2], 124-131. 1983.  
Richter, AW, Akerblom, E. Polyethylene glycol reactive antibodies in man: titer distribution 
in allergic patients treated with monomethoxy polyethylene glycol modified allergens or 
placebo, and in healthy blood donors. Int Arch Allergy Appl Immunol 74[1], 36-39. 1984.  
Rouse, B, Azen, C. Effect of high maternal blood phenylalanine on offspring congenital 
anomalies and developmental outcome at ages 4 and 6 years: the importance of strict dietary 
control preconception and throughout pregnancy. J Pediatr 144[2], 235-239. 2004.  
Scott, MD, Murad, KL, Koumpouras, F, Talbot, M et. al. Chemical camouflage of antigenic 
determinants: stealth erythrocytes. Proc Natl Acad Sci U S A 94[14], 7566-7571. 1997.  
Scriver, CR, Kaufman. Hyperphenylalaninemia: Phenylalanine Hydroxylase Deficiency. In: 
Beaudet AL, Sly WS, Valle D, editors. Metabolic and Molecular Bases of Inherited Disease. 
New York: McGraw-Hill, 2001: 1667-1724. 
Walter, JH, White, FJ, Hall, SK, MacDonald, A et. al. How practical are recommendations 
for dietary control in phenylketonuria? Lancet 360[9326], 55-57. 2002.  
Webster, R, Didier, E, Harris, P, Siegel, N et. al. PEGylated proteins: evaluation of their 
safety in the absence of definitive metabolism studies. Drug Metab Dispos 35[1], 9-16. 2007.  
 
 
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22 
INVESTIGATOR RESPONSIBILITIES 
22.1 
Conduct of Study and Protection of Human Subjects  
In accordance with FDA Form 1572, the Investigator will ensure that: 
• He or she will conduct the study in accordance with the relevant, current protocol and 
will only make changes in a protocol after notifying the sponsor, except when 
necessary to protect the safety, rights, or welfare of subjects. 
• He or she will personally conduct or supervise the study. 
• He or she will inform any potential subjects, or any persons used as controls, that the 
drugs are being used for investigational purposes and he or she will ensure that the 
requirements relating to obtaining informed consent in 21 CFR Part 50 and 
institutional review board (IRB) review and approval in 21 CFR Part 56 are met.  
• He or she will report to the sponsor adverse experiences that occur in the course of 
the investigation in accordance with 21 CFR 312.64. 
• He or she has read and understands the information in the Investigator’s Brochure, 
including potential risks and side effects of the drug. 
• His or her staff and all persons who assist in the conduct of the study are informed 
about their obligations in meeting the above commitments. 
• He or she will ensure that adequate and accurate records in accordance with 
21 CFR 312.62 and to make those records available for inspection in accordance with 
21 CFR 312.68. 
• He or she will ensure that the IRB complies with the requirements of 21 CFR Part 56, 
and other applicable regulations, and conducts initial and ongoing reviews and 
approvals of the study. He or she will also ensure that any change in research activity 
and all problems involving risks to human subjects or others are reported to the IRB. 
Additionally, he or she will not make any changes in the research without IRB 
approval, except where necessary to eliminate apparent immediate hazards to human 
subjects. 
• He or she agrees to comply with all other requirements regarding the obligations of 
clinical Investigators and all other pertinent requirements in 21 CFR Part 312. 
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24 
PROTOCOL AMENDMENT TEXT REVISIONS 
The following table summarizes the revisions made to the protocol and relates the changes to the appropriate rationale. Text that has been 
added or inserted is indicated by underlined font, and deleted text is indicated by strikethrough font. 
Section No./Title 
 
 
Section 2/Synopsis (Study 
Sites) 
Approximately 208 centers in the United States 
4 
Section 2/Synopsis (Study 
Rationale) 
The need exists for a treatment that will help individuals with phenylketonuria (PKU) safely 
achieve lifelong, reliable control of blood phenylalanine (Phe) concentrations and improve 
functional outcomes. Phenylalanine ammonia lyase (rAvPAL-PEG) is a potential substitute 
for the phenylalanine hydroxylase (PAH) enzyme, which is defective in individuals with 
PKU. rAvPAL-PEG may control blood Phe concentrations, which may have additional 
clinical benefits. This study is an extension of the dose-finding studiesy (Study PAL-002 
and Study PAL-004). Administration of rAvPAL-PEG will be continued to assess whether 
long-term dosing of rAvPAL-PEG is safe and can maintain reduced blood Phe 
concentrations in PKU subjects. 
Because rAvPAL-PEG is being assessed as a long-term chronic treatment for patients with 
PKU, there is a need to understand the effect of a temporary dosing interruption on the 
safety, efficacy (blood Phe), PK, and immune response. Therefore, a Substudy has been 
added to this study to assess the effects of stopping and re-starting rAvPAL-PEG treatment 
in subjects who are on a variety of rAvPAL-PEG dosing regimens (dose level and 
frequency). Up to 10 subjects who are on a variety of dosing regimens (dose level and 
frequency) in this study are eligible for participation in the Substudy and will stop dosing 
for a period of approximately 4 weeks. During this dosing interruption, subjects will be 
assessed for safety, efficacy, PK, and immune response and will continue to perform the 
scheduled study assessments. 
Blood Phe levels depend not only on the functional presence of the endogenous enzyme 
PAH but also on the dietary intake of Phe. It is important to understand the role of diet on 
blood Phe levels concurrent with the administration of rAvPAL-PEG treatment. Therefore, 
1, 5 
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Section No./Title 
 
 
an exploratory objective has been added to this study to assess the relationship of diet, 
rAvPAL-PEG administration, and blood Phe level. Changes to subject diet are not allowed 
in this study unless per the Investigator in consultation with the Sponsor’s Medical Officer. 
Diet will be monitored using a diet diary. 
Section 2/Synopsis 
(Objectives) 
The secondary objectives of the study are: 
• 
To evaluate the immune antibody response to long-term administration of SC 
injections of rAvPAL-PEG in subjects with PKU. 
• 
To evaluate steady state PK of rAvPAL PEG in subjects with PKU. 
The exploratory objective of the study is as follows: 
• 
To assess the long-term relationship of diet and change in blood Phe concentration 
following administration with rAvPAL-PEG in subjects with PKU. 
The Substudy objectives are as follows: 
• 
To assess the safety and tolerability of stopping and re-starting rAvPAL-PEG 
dosing in a subset of subjects with PKU. 
• 
To evaluate the effect of stopping and re-starting rAvPAL-PEG dosing on blood 
Phe concentration in a subset of subjects with PKU. 
• 
To evaluate the effect of stopping and re-starting rAvPAL-PEG dosing on immune 
response in a subset of subjects with PKU.   
• 
To assess the effect of multiple doses of rAvPAL-PEG on the PK profile, in 
particular clearance of drug, when drug is stopped in a subset of subjects with PKU 
who have been previously exposed to rAvPAL-PEG.    
 
1, 5, 14 
Section 2/Synopsis (Study 
Design and Plan) 
This is a long-term extension of athePhase 2, open-label, dose-finding studies,y (Study 
PAL-002 and PAL-004, in 35 50 approximately 100 subjects with PKU. The doses are 
planned to be in the same range as those tested in PAL-002 and PAL-004 (starting at 0.001 
through 51.0 mg/kg/weekper injection), provided no dose-limiting toxicity iwas observed in 
1-4, 6, 27  
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Section No./Title 
 
 
PAL-002 or PAL-004. 
Only subjects who completed the protocol-defined study drug regimen participation in 
PAL-002 or PAL-004 will be enrolled into this study. Subjects who enroll from PAL-002 
will either continue the dose regimen that was administered upon completion of PAL-002 
or start dosing at a higher dose per the dose increase instructions. Subjects who enroll from 
PAL-002 may start this study at a higher dose level provided there was no interruption in 
dosing since completion of PAL-002 and enrollment into this study. Subjects who enroll 
from PAL-004 will re-start rAvPAL-PEG dosing in this study at the same dose level and 
frequency as was administered upon completion of PAL-004. The first dose will be 
administered in the clinic, and the subject must be observed for 30-60 minutes following 
administration due to restarting dosing in this study. A follow-up telephone call will be 
made to the subject to monitor subject safety 24 hours following the return to dosing. 
Diet will should not be altered during the course of this study , except as necessary for 
safety as determined by blood Phe concentrations. If a subject’s blood Phe concentration is 
 < 120 µmol/L, the subject’s diet may be adjusted to increase the amount of dietary Phe 
intake to maintain target blood Phe concentrations of 120 600 µmol/L. Changes to diet will 
be made per the discretion of the Investigator in consultation with the Sponsor’s Medical 
Officer. Any decision to modify subject diet must be made per the Investigator in 
consultation with the Sponsor’s Medical Officer and must be performed under the 
supervision of the Investigaor in consultation with the Sponsor’s Medical Officer.To 
monitor for changes in subject diet, a diet diary will be issued to subjects for completion 
and will be reviewed with the clinical study staff.  
Subjects may self administer study drug at home if approved by the Investigator and the 
Sponsor’s Medical Officer and if adequate training is demonstrated. Subjects must meet a 
set of criteria to be considered appropriate for self administration.   
Subjects will be evaluated for safety and for blood Phe concentrations throughout the study. 
Toxicity will be measured according to the National Cancer Institute (NCI) Common 
Terminology Criteria for Adverse Events (CTCAE), version 43. 
At least one interim analysis may be performed by the sponsor during the study. In addition 
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Section No./Title 
 
 
to the Sponsor, a Data Monitoring Committee (DMC) will monitor the safety of subjects in 
the study. The DMC is an independent committee that will act in an advisory capacity to the 
Sponsor. 
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take 
rAvPAL-PEG. PAL-002 and PAL-004 subjects’ rAvPAL-PEG dosing will continue in 
PAL-003 without interruption of dosing. In PAL-003, each subject’s dose will be adjusted 
as needed to attain or maintain blood Phe concentrations of 6120-600 µmol/L. Doses will 
be evaluated on an individual basis. 
Evaluations, observations, and procedures will be conducted at selected time points. After 
the subject’s blood Phe concentration has been controlled to within a target range 
(6120-600 µmol/L), the subject may be asked to have additional blood draws for PK and 
blood Phe concentration analyses as needed per the discretion of the Investigator in 
consultation with the Sponsor’s Medical Officerbut not to exceed 3x/week (fingerstick tests 
may be performed more frequently).  
A subject will continue in PAL-003 until one of the following occurs: 
1. The subject withdraws consent and discontinues from the study. 
2. The subject is discontinued from the study at the discretion of the Investigator. 
3.  The subject has completed the study through the Month 2460 visit. 
4.  The study is terminated. 
Subjects may withdraw from treatment with study drug at any time; however, subjects will 
be asked to continue to perform the study assessments until study completion. Subjects may 
also withdraw from study participation at any time. Because the completeness of the data 
affects the integrity, accuracy, and interpretation of study results, every effort should be 
made to retain subjects in the study and to have them complete the study assessments as 
scheduled as long as continued participation does not compromise subject safety. 
PAL-003 Substudy 
A subset of up to 10 subjects who are already enrolled and who have consented to 
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participate in this study will be asked to participate in a Substudy to assess the effect that 
stopping and re-starting treatment with rAvPAL-PEG has on safety, efficacy, PK, and 
immune response. Subjects will be eligible for participation in the Substudy provided they 
also meet all of the PAL-003 eligibility criteria, have been on a stable dosing regimen for 
approximately 4 weeks during this study, have not had any serious adverse events reported 
during PAL-003, and were not enrolled in Study PAL-004. Subjects participating in the 
Substudy will have rAvPAL-PEG administration halted for approximately 4 weeks 
regardless of their dosing regimen (dose level and frequency). rAvPAL-PEG will not be 
administered during the dose interruption; however, subjects will continue to perform 
assessments for safety, blood Phe concentration, PK, and immune response. Subjects 
enrolled into the Substudy will also have additional PK sampling performed prior to the 
dosing interruption and during the dosing interruption. To allow for PK sampling once 
dosing is stopped, subjects may be admitted to a research facility within 8 hours of stopping 
dosing where they will reside for at least 24 hours. After the dosing interruption, rAvPAL-
PEG administration will be re-started at the same dose level and dosing frequency that was 
administered prior to the dosing interruption. Upon re-starting rAvPAL-PEG, the first dose 
must be administered in the clinic and the subject must be observed for 30-60 minutes 
following administration due to restarting dosing. A follow-up telephone call will be made 
to the subject to monitor subject safety 24 hours following the return to dosing. Additional 
PK sampling will also be performed for the first week after the dosing interruption. 
Section 2/Synopsis (Dose 
Modifications) 
Dose Modifications: 
After any modifications (increases or decreases) to dose level or frequency, subjects should 
remain in the clinic for observation for at least 2 hours following the injection of study 
drug. The Investigator should remain at the site to assess the subject for safety. 
Dose Increase Methodology: 
Each subject’s dose may be modified based on the decision of the Investigator, in 
agreement with the Study Medical Officer. Decisions regarding dose increases will depend 
on a subject’s adverse event profile and blood Phe and drug concentrations.  
Blood Phe levels will be measured 3 days after each dose increase (fingerstick is 
2, 3, 21, 22 
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acceptable); more frequent or daily blood Phe measurements may be performed.  
For subjects from PAL-002 onlyDepending upon the response to rAvPAL PEG in 
PAL 002, an individual subject’s dose may be adjusted beginning on Day 1 of PAL-003. 
For the duration of this study, an individual subject’s dose may be adjusted if warranted per 
a subject’s adverse event profile and blood Phe concentrations. Dose increases should be 
performed as follows. 
• The dose may be increased by increments of no more than 10-fold higher than 
the subject’s current dose. 
• When increasing the dose, a dose may be used that is between the dose levels 
(0.001, 0.003, 0.01, 0.03, 0.06, 0.1, 0.2, 0.3, 0.4, 0.6, 0.8, and 1.0, 2.0, 3.0, 4,0, 
and 5.0 mg/kg) that were defined in the previous study (PAL 002).or per 
Investigator determination in consultation with the Sponsor’s Medical Officer 
based on available information regarding a subject’s blood Phe 
(60-600 µmol/L) and drug concentrations, as well as any adverse events (any 
hypersensitivity reaction) for an individual subject. 
• The dose may be adjusted by increasing the frequency up to daily for a total 
weekly dose not to exceed 52.0 mg/kg, including subjects who receive more 
than 1 dose/week. Subjects who increase their dose frequency will have 
additional assessments performed (Interim Dosing Visit). 
• When a dose is increased (either by increasing the dose level or by increasing 
the frequency of dosing), the subject must remain in the clinicbe observed for a 
minimum of 30-60 minutes2 hours following the first modified dose 
administration, and an Investigator will remain on site during this 
time.Subjects who increase their dose frequency do not need to be observed 
following injection of study drug if the increase in frequency does not increase 
the overall weekly dose amount. 
• Only 1 dose (level or frequency) adjustment is allowed every 2 weeks. 
• Blood Phe levels will be measured daily for 3 days after each dose increase 
(fingerstick is acceptable); more frequent or daily blood Phe measurements 
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may be performed. 
Dose Decrease Methodology 
A subject’s diet should be assessed prior to any dose decreases. Changes to diet should only 
be made if a subject’s blood Phe concentrations  < 120 µmol/L. If a subject’s blood Phe 
level is  < 120 µmol/L, the subject’s dietary Phe intake should be increased to achieve a 
stable blood Phe concentration of 120 600 µmol/L. If the subject’s blood Phe level is 
 < 120 µmol/L despite a high Phe diet, the rAvPAL PEG dose will then be decreased. The 
subject will be asked about any changes to diet prior to any dose adjustments, and any 
changes to diet should be made per the discretion of the Investigator in consultation with 
the Sponsor’s Medical Officer. 
All dose decreases must be agreed to by both the Investigator and the Sponsor’s Medical 
Officer. Decisions regarding dose decreases will depend on available information regarding 
a subject’s blood Phe (60-600 µmol/L> 30% change from baseline) and drug 
concentrations, as well as any adverse eventstoxicity (any hypersensitivity reaction). Dose 
decreases may occur for safety (ie, blood Phe concentration  < 120 µmol/L) or other 
toxicityany adverse event that may be improved with a lower, more frequent dose).  
A dose should first be reduced by dose level (5.0, 4.0, 3.0, 2.0, 1.0, 0.8, 0.6, 0.4, 0.3, 0.2, 
0.1, 0.06, 0.03, 0.01, 0.003, 0.001 mg/kg). It is also permitted to decrease dose in between 
these specified dose levels. If further dosing adjustments are required to attain the target 
Phe concentration, dosing frequency may be reduced.  
 
Section 2/Synopsis 
(Stopping Safety 
Assessment Criteria) 
Safety AssessmentStopping Criteria: 
If an individual subject exhibits toxicity of a treatment-emergent CTCAE grade 3 or greater 
or a systemic reaction that is assessed as related to treatment with study drug, that subject 
will have dosing halted until the toxicity resolves. The subject’s data will be evaluated by 
the Principal Investigator (PI) and the Study Medical Officer, and a decision will then be 
made whether to discontinue the subject from the study treatment, restart dosing at the same 
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dose level, or restart dosing at a lower dose level. 
Stopping Criteria: 
In addition, if 2 or more subjects at a dose level exhibit toxicity of a treatment-emergent 
CTCAE grade 3 or greater or a systemic reaction that is assessed as related to treatment 
with study drug, further dosing of subjects at that dose level will be evaluated and halted 
and no subjects will be treated at a higher dose level until a safety assessment will be is 
completed. In addition, the Food and Drug Administration (FDA) will may be notified of 
this occurrence if appropriate. 
Section 2/Synopsis 
(Number of Subjects 
Planned) 
35 50Approximately 100 subjects. 
4 
Section 2/Synopsis 
(Diagnosis and All Criteria 
for Inclusion and 
Exclusion) 
Individuals eligible to participate in this study must meet all of the following criteria: 
1. Must have completed participation and all protocol-defined study drug in PAL-
002 or PAL-004. 
Individuals who meet any of the following exclusion criteria will not be eligible to 
participate in the study: 
1. Use of any investigational product (with the exception of rAvPAL-PEG) or 
investigational medical device within 30 days prior to Screening, or 
requirement for any investigational agent prior to completion of all scheduled 
study assessments. 
2. Use of any medication other than rAvPAL-PEG that is intended to treat PKU 
within 14 days prior to the administration of study drug. 
3. Use or planned use of any injectable drugs containing PEG (other than 
rAvPAL-PEG), including Depo-Provera, within 6 months prior to Screening 
and during study participation. 
4. A prior reaction that included systemic symptoms (eg, generalized hives, 
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respiratory or gastrointestinal problems, hypotension, angioedema, 
anaphylaxis) to rAvPAL-PEG or a PEG-containing product. Subjects with a 
prior systemic reaction of generalized rash may be eligible for participation per 
the discretion of the Principal Investigator in consultation with the Sponsor’s 
Medical Officer. However, subjects who discontinued from study treatment 
early due to a reaction are not eligible to enroll into this study.    
8. Known hypersensitivity to rAvPAL-PEG or its excipients, including 
hypersensitivity reactions that necessitated early termination from PAL-002 or 
PAL-004. 
 
Section 2/Synopsis 
(Investigational Product, 
Dose, Route, and 
Regimen) 
rAvPAL-PEG doses will be administered SC provided in 3 mL (milliliter) vials, each 
containing 1.5 ± 0.2 mL to deliver 10 mg of rAvPAL-PEG per 1 mL (10 mg/mL protein 
concentration). Each vial is filled with 1.5 ± 0.2 mL to allow the withdrawal and delivery of 
up to 1 mL of the drug product.  
Upon enrollment into this study, subjects from PAL-002 will be dosed with the same or 
higher dose than the dose that was administered upon completion of PAL-002. Subjects 
enrolling from PAL-004, will be administered the same dose that was administered upon 
completion of PAL-004. rAvPAL-PEG doses will be administered SC by either health care 
professionals or via self administration. The dose level may be increased per Investigator 
determination in consultation with the Sponsor’s Medical Officer based on on available 
information regarding a subject’s blood Phe level (60-600 µmol/L), as well as any adverse 
events (any hypersensitivity reaction) for an individual subject. tThe dosage that provides 
control of blood Phe concentrations within the target range of 6120-600 µmol/L for a 
minimum of 2 weeks will be determined for each subject by adjusting the dose level, dose 
frequency, or both, as agreed by the PI and the Study Medical Officer, based upon the 
subject’s response to doses. 
1, 3, 4, 27 
Section 2/Synopsis 
(Duration of Treatment) 
Up to 60 months.Extension of multiple dosing will continue until one of the following 
occurs: 
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1. The subject withdraws consent and discontinues from the study. 
2. The subject is discontinued from the study at the discretion of the Investigator. 
3. The subject has completed the study through the Month 24 visit. 
4. The study is terminated. 
 
Section 2/Synopsis 
(Criteria for Evaluation) 
Immunogenicity: 
The presence of antibodies (anti-PAL immunoglobulin G [IgG], anti-PAL IgM, anti-PEG 
IgG, anti-PEG IgM, anti-rAvPAL-PEG IgE, and anti-rAvPAL-PEG neutralizing antibodies) 
will be assessed. 
Safety: 
Safety will be evaluated on the incidence of adverse events (AEs) and clinically significant 
changes in vital signs, ECG results, X-ray results, andor laboratory test results. 
Pharmacokinetic: 
Plasma concentrations of rAvPAL-PEG will be measured when steady state levels of Phe 
are attainedfor subjects participating in the Substudy. 
22, 27 
Section 2/Synopsis 
(Statistical Methods) 
Sample Size: 
Subjects who participated in PAL-002 or PAL-004 may be enrolled into this study. 
No formal sample size calculation was conducted for this study or the PAL-003 Substudy. 
Safety Analysis: 
All subjects who receive any amount of study drug in this study and have postdose safety 
information will be included in the safety analyses. 
All AEs will be coded using the Medical Dictionary for Regulatory Activities (MedDRA). 
The incidence of AEs will be summarized by system organ class, preferred term, 
relationship to study drug, and severity. A by–subject listing will be provided for those 
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subjects who experience a serious AE (SAE), including death, or experience an AE 
associated with early withdrawal from the study or study drug.Safety will be evaluated on 
the incidence of AEs, including serious AEs (SAEs), and clinically significant changes in 
vital signs and laboratory test results.Clinical laboratory data will be summarized by the 
type of laboratory test. Frequency and percentage of subjects who experience abnormal (ie, 
outside of reference range) and/or clinically significant abnormalities after study drug 
administration will be presented for each clinical laboratory test. For each clinical 
laboratory test, descriptive statistics will be provided for baseline and all subsequent 
post-treatment visits. Changes from baseline to the post-treatment visits will also be 
provided. Descriptive statistics, including clinically significant changes from baseline, of 
vital signs, ECG results, and X-ray results will also be provided. 
Efficacy Analysis: 
Data from all subjects who receive any amount of study drug and who have any 
post-treatment efficacy data will be included in the efficacy analysis. 
Blood Phe concentration at each scheduled time point will be summarized using descriptive 
statistics (mean, standard deviation, median, minimum, and maximum). Change in blood 
Phe concentration from baseline to each scheduled time point and presence/absence of 
antibodies will also be summarized. In addition, the proportion of subjects who have 
maintained target Phe concentrations of 12060-600 µmol/L will be summarized by each 
scheduled time point. 
Exploratory Analysis: 
For subjects who have received any study drug in this study with any post-treatment blood 
Phe concentration measurements and diet diary information, the relationship of dietary Phe 
intake (per information reported on the subject diet diary) and blood Phe concentration will 
be explored.  
Substudy Analysis: 
For subjects who completed the Substudy, the effect of stopping and re-starting rAvPAL-
PEG dosing on safety, blood Phe level, and immune response will be explored. 
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Pharmacokinetic Analysis: 
Data from all subjects who complete at least 2 weeks of the study will be included in the PK 
analysis. 
Steady state PK (predose samples) of rAvPAL PEG will be evaluated in PKU subjects after 
the subject has achieved and maintained target blood Phe concentration (120 600 μmol/L) 
for a minimum of 2 weeks (to allow assessment of blood Phe concentrations) and no further 
dose modification is planned. Should data become available from PAL 002 that indicate 
study drug accumulation should also be measured, additional blood draws may be added for 
PK analysis as needed rbut not to exceed 3x/week. 
Subjects who complete the Substudy will have the following PK parameters assessed: area 
under the plasma concentration-time curve (AUC), time to maximum plasma concentration 
(Tmax), maximum plasma concentration (Cmax), half life (t1/2), and clearane (CL/F). 
Tables 2.1/Schedule of 
Events 
Table 2.1.1, Schedule of Events, has been revised to reflect change made to the study. 
Table 2.1.2, Schedule of Events-Substudy, has been added.  
Tables 2.1.23 and 2.1.34, Interim Dosing Visit Schdules, have been revised to remove the 
PK sampling. 
13, 16, 18, 
19, 22, 23, 
24, 26 
Section 4/List of 
Abbreviations and 
Definitions of Terms 
C3 
 
 
complement 3 
C4 
 
 
complement 4 
rAvPAL-PEG   
rAv recombinant Anabaena variabilis phenylalanine ammonia 
lyase-PEG 
27 
Section 6/Investigators and 
Administrative Structure  
Anti-rAvPAL-PEG (recombinant Anabaena variabilis phenylalanine ammonia lyase 
polyethylene glycol (rAvPAL and rAvPAL-PEG) IgE antibody analysis will be performed 
by a vendor; other antibody analysis will be performed by BioMarin. Clinical laboratory 
tests, including serum pregnancy tests (if applicable), will be analyzed and processed by a 
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central laboratory, with the exception of erythrocyte sedimentation rate (ESR), urinalysis, 
and urine pregnancy tests (if applicable), which will be analyzed by a local laboratory. A 
central laboratory will also be used to perform analysis of blood phenylalanine (Phe) 
concentrations. Pharmacokinetic (PK) analysis will be performed by BioMarin. 
 
Section 7.1/Nonclinical 
Studies 
The nonclinical program for rAvPAL-PEG has characterized the pharmacology, 
pharmacokinetics (PK), and toxicology of rAvPAL-PEG using the intended clinical SC 
route of administration. Pharmacology was assessed in the BTBR Pahenu2 (ENU2) mouse 
model of PKU. The ENU2 mouse model exhibits characteristics similar to those of PKU 
patients, including hyperphenylalaninemia (baseline plasma Phe concentrations of 1000 to 
2000 µM) and hypopigmentation. Following weekly doses of rAvPAL-PEG administered to 
male ENU2 mice, plasma Phe concentrations decreased from approximately 2000 µM to 
< 200 µM after 2 dose administrations. An attenuated reduction of blood Phe was seen 
between Week 3 and Week 7 of dosing. After 7 weekly administrations of rAvPAL-PEG, 
pharmacological activity returned as evidenced by stabilized concentrations of plasma Phe 
< 200 µM over the entire week, which continued for a total of 15 weeks. 
In pharmacodynamic studies in the BTBR Pahenu2 (ENU2) mouse model administered 
80 mg/kg/week rAvPEG-PAL, two dose interruption assessments were performed:  a 
2-4 week dose interruption and an 11-week dose interruption. Following both dose 
interruption assessments, the animals re-started rAvPAL-PEG at a dose of 80 mg/kg/week. 
No attenuated Phe response was observed when rAvPAL-PEG injections were temporarily 
stopped for 2-4 weeks, and there was an immediate return to stable blood Phe reductions. A 
similar interim attenuated response was observed with the longer dose interruption of 
approximately 11 weeks.  In both of these assessments, no safety issues were noted upon 
re-starting dosing with rAvPAL-PEG (Lapis et al., Long-term correction of PKU in the 
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Pahenu2 mouse by mutant and chemically modified forms of Phenylalanine Ammonium 
Lyase. The American Society of Human Genetics, 57th Annual Meeting, 2007). 
Safety pharmacology studies were conducted in rats and cynomolgus monkeys. No 
respiratory or central nervous system (CNS) effects were seen with SC administration of 
rAvPAL-PEG. No changes in cardiovascular (CV) parameters, including electrocardiogram 
(ECG) waveforms, were observed in telemetry-instrumented monkeys assessed for the CV 
effects of rAvPAL-PEG administered subcutaneously. 
Pharmacokinetic parameters were evaluated in single-dose and repeat-dose studies in rats 
and cynomolgus monkeys. The elimination half-life (t1/2) values of rAvPAL-PEG 
administered to normal rats at SC doses of 10, 25, and 250 mg/kg were 47, 33, and 
44 hours, respectively, and exhibited modest area under the plasma concentration-time 
curve (AUC)-dose. In the cynomolgus monkey after SC administration of rAvPAL-PEG, 
the t1/2 was 65 hours at 4.0 mg/kg, 71 hours at 12 mg/kg, and could not be determined at 60 
mg/kg (the highest dose). Qualitatively, the kinetics of rAvPAL-PEG in the rat and monkey 
appear to have similar characteristics. The following findings were noted: (1) a 
1-compartment model with first-order absorption appears to describe the plasma profiles of 
rAvPAL-PEG after single-dose administration, (2) absorption is slow and there is a long 
absorption period after SC administration to maximum observed plasma concentration 
(Cmax), along with a long t1/2, (3) elimination is slow and monophasic, (4) there does not 
appear to be a gender difference, and (5) the AUC and the Cmax are roughly linearly 
proportional.  
Toxicology of rAvPAL-PEG was assessed in single-dose and repeat-dose studies in normal 
rats and cynomolgus monkeys. In the single-dose rat study, decreased body weight gain and 
Kupffer cell vacuolization at the high SC dose of 250 mg/kg was observed; however, the 
Kupffer cell finding was not seen in the single-dose study in cynomolgus monkeys. In a 
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26-week repeat-dose toxicity and toxicokinetic (TK) rat study, decreased body weight gain, 
decreased food consumption, vacuolation/hypertrophy of the renal tubule cells, and 
vacuolation of the histiocytic cells were observed in rats administered 25 mg/kg/dose, twice 
weekly. In a 39-week repeat-dose study in monkeys, arterial inflammation, perivascular 
cellular infiltrates in the SC injection sites, thymic atrophy, and increased lymphoid nodules 
in bone marrow of the sternum were observed in monkeys given ≥ 3 mg/kg/dose, twice 
weekly. Of these findings, only the arterial inflammation was deemed adverse and this 
finding was completely reversed after 13-weeks of recovery. The 
no-observed-adverse-effect-level (NOAEL) of rAvPAL-PEG when administered 
subcutaneously twice weekly for 26 weeks and 39 weeks in the rat and monkey, 
respectively, was 1.0 mg/kg. These NOAELs were based on histological findings of 
vacuolation/hypertrophy of the renal tubule cells in the rat and arterial inflammation 
findings in the monkey.  
The murine model of phenylketonuria (PKU) BTBRPahenu2 (ENU2), a mouse line that is 
deficient in phenylalanine hydroxylase (PAH) activity (Shedlovsky, 1993, Genetics), was 
used for in vivo screening and pharmacodynamic studies. This mouse model exhibits 
characteristics similar to those seen in PKU patients, including hyperphenylalaninemia 
(baseline plasma phenylalanine [Phe] concentrations of 1000 to 2000 µM) and 
hypopigmentation. Weekly subcutaneous (SC) administration of 80 mg/kg of rAvPAL PEG 
(approximately 4 IU/mouse) for greater than 2 to 3 months lowered and stabilized plasma 
Phe concentration from approximately 2000 µM to less than 200 µM. A similar profile of 
Phe reduction was also seen in ENU2 mice administered wild type AvPAL PEG 
(4 IU/mouse) over 8 weeks. In all these studies, regardless of the molecule, an attenuated 
Phe lowering response was usually seen between Weeks 2 and 7. However, plasma Phe 
concentrations became stable at concentrations below 200 µM from Week 7 onward. 
In addition to the reduction of plasma Phe, a dose related darkening in coat color occurred, 
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indicating the biosynthesis of melanin, which was previously inhibited when plasma Phe 
could not be metabolized and plasma Phe concentrations were high. When administration of 
AvPAL PEG was stopped for 2 to 7 weeks and then reinitiated with weekly 
administrations, no attenuated response was observed and Phe concentrations remained low 
and stable until the next administration. 
The safety of rAvPAL PEG was evaluated in safety pharmacology studies (respiratory, 
central nervous system [CNS] and cardiovascular [CV]) and toxicity with toxicokinetic 
studies (single and 28 day repeated dose) in rats and cynomolgus monkeys. Overall, in the 
nonclinical studies, no anaphylactoid like reactions or injection site reactions were noted. 
No specific polyethylene glycol (PEG) related histological findings were observed during 
the 28 day repeated dose studies. 
Findings in cynomolgus monkeys dosed with a single administration of 
60 mg/kg rAvPAL PEG included reduced food consumption, dehydration, body weight 
loss, hypoactivity, hypothermia,decreased plasma Phe concentration, decreased protein 
synthesis, and gastrointestinal (GI) lesions. Plasma Phe concentrations were also reduced to 
below the level of detection in the 4 and 12 mg/kg dose groups, but without similar 
toxicological consequences, implying that the physiological regulation of Phe levels may be 
an important factor for influencing morbidity.  
The main finding in the 28 day study was the possible drug related observation of minimal 
to slight degeneration of blood vessels of predominantly medium sized muscular arteries 
with a non dose dependent involvement of different organs observed in 1 male in the 
0.1 mg/kg and 1 male and 1 female in the 1.0 mg/kg rAvPAL PEG dose groups. No 
degeneration of the arteries was observed in either the control or animals administered 0.01 
mg/kg rAvPAL PEG. 
The half life of rAvPAL PEG administered to normal rats at SC doses of 10, 25, and 
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250 mg/kg, was 47, 33, and 44 hours, respectively, and exhibited modest area under the 
plasma concentration time curve (AUC) dose linearity. In the cynomolgus monkey after SC 
administration of rAvPAL PEG, the half life was 65 hours at 4 mg/kg, 71 hours at 
12 mg/kg, and could not be determined at 60 mg/kg (the highest dose). Qualitatively, the 
kinetics of rAvPAL PEG in the rat and monkey appear to have similar characteristics. The 
following findings were noted: (1) a 1 compartment model with first order absorption 
appears to describe the plasma profiles of rAvPAL PEG after single dose administration, 
(2) absorption is slow and there is a long absorption period after SC administration to 
maximum plasma concentration, along with a long half life, (3) elimination is slow and 
monophasic, (4) there does not appear to be a gender difference, and (5) AUC and the 
maximum plasma concentration (Cmax) are roughly linearly proportional. 
Chronic repeat dose toxicity and toxicokinetic studies were conducted in the rat 
(17/26 weeks) and monkey (39 weeks). In the 26 week study of rats, weight loss was 
observed in the rats given 25 mg/kg/dose of rAvPAL PEG, SC; corresponding decreased 
food consumption was observed in the males. The main histological finding was 
focal to multifocal areas of vacuolar degeneration of renal tubule cells in the kidney of 
3 males given 25 mg/kg and 3 females given  ≥ 8 mg/kg rAvPAL PEG. This renal tubule 
finding persisted in the kidney of both sexes given  ≥ 8 mg/kg/dose at the end of the 
12 week recovery phase without evidence of reversibility. Increased vacuolation was 
observed in histiocytic cells of the liver, spleen, mesenteric lymph node, mandibular lymph 
node, and adrenal cortex of males given 25 mg/kg/dose and females given  ≥ 8 mg/kg/dose; 
vacuolation of histiocytic cells in the testes were also observed in males given 
25 mg/kg/dose. Both renal tubule vacuolation and histiocytic cell vacuoles have been 
associated with PEG related catabolism and administration of other PEGylated proteins. 
In the 39 week, chronic repeat dose toxicity and toxicokinetic study in monkeys, dose 
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levels of 7.0 and 5.0 mg/kg/dose rAvPAL PEG were not tolerated in female monkeys and 
resulted in body weight loss, decreased food consumption, and hypoactivity. The only 
adverse microscopic finding was arterial inflammation of small and mid sized arteries in 
multiple organs and/or tissues in most animals that were given  ≥ 3 mg/kg/dose rAvPAL
PEG SC twice weekly at the end of the dosing phase. The inter individual organ 
involvement was highly variable; some animals had findings in one organ and others had 
multiple organs with arterial inflammation. Additionally, not all arteries had signs of 
inflammation and arterial inflammation was resolved by the end of the 13 week recovery 
period. A full analysis of these findings including the involvement of the anti drug 
antibodies, antibody isotypes, PEG distribution, and rAvPAL PEG is ongoing. The no 
observable adverse effect level (NOAEL) for the 17 week and 39 week studies, in rat and 
monkey, respectively, is 1 mg/kg/dose. The NOAEL from these studies represents greater 
than a 100 fold safety factor over the starting dose in PAL 002. 
 
Section 7.2/Previous 
Clinical Studies 
This study is an extension of the second human clinical study with rAvPAL PEG 
(Study PAL 002). Study PAL 001, the first in human clinical study of rAvPAL PEG, was 
designed as a Phase 1, open label, single dose, dose escalation study in 25 subjects, 16 to 
50 years old, with PKU. The doses for this study are based on data from nonclinical studies 
and PAL 001 and are 0.001 through 1.0 mg/kg per injection (not to exceed 2.0 mg/kg/week, 
provided no dose limiting toxicity was observed in Study PAL 002. 
The rAvPAL-PEG clinical development program has been designed to demonstrate the 
safety and efficacy of rAvPAL-PEG in reducing blood Phe concentrations in PKU patients 
who do not respond to treatment with Kuvan® or are not compliant with Kuvan® treatment. 
This study is an extension of the ongoing human clinical studies with rAvPAL-PEG 
(Study PAL-002 and Study PAL-004) based on data from the completed clinical study, 
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PAL-001, and clinical experience to date (JAN2011) from this ongoing study and the other 
ongoing Phase 2 study, PAL-002, and are 0.001 through 5.0 mg/kg/week.  
 
Section 7.2.1/Phase 1 
Study: PAL-001 
The first-in-human trial using rAvPAL-PEG, Study PAL-001, was a Phase 1, open-label, 
dose-escalation study in PKU subjects in the US. The primary objective was to assess the 
safety and tolerability of single SC injections of rAvPAL-PEG. Secondary objectives were 
to evaluate the PK of single, SC injections of rAvPAL-PEG administered at escalating 
doses in subjects with PKU and to evaluate the effect of rAvPAL-PEG on blood Phe 
concentrations. 
The effectiveness of rAvPAL-PEG in decreasing Phe concentrations in nonclinical studies 
of ENU2 mice was consistent with what was observed in PAL-001. PAL-001 enrolled 
25 PKU subjects with a mean (standard deviation; SD) baseline blood Phe concentration of 
1310 µmol/L (405). The 25 subjects who enrolled into the study were assigned to receive a 
single administration of rAvPAL-PEG at 1 of 5 dose levels: 0.001, 0.003, 0.01, 0.03, and 
0.1 mg/kg. Five subjects each received 1 of the 5 dose levels of rAvPAL-PEG. 
Key safety, efficacy, and PK results of Study PAL-001 are summarized as follows: 
• 
rAvPAL-PEG was well tolerated and had a clinically significant blood-lowering 
effect on Phe concentration when administered at a dose of 0.1 mg/kg. 
• 
For the 5 subjects who were administered 0.1 mg/kg rAvPAL-PEG, clinically 
significant reductions in blood Phe level were observed, with the most clinically 
significant decreases from baseline values to Day 7, ranging from 33.8% to 97.3% 
(mean of 58.12%). The mean baseline blood Phe level for these 5 subjects was 
1113 µmol/L. 
• 
Overall, no clinically significant reductions in blood Phe level were observed in 
subjects who were administered rAvPAL-PEG at the lower doses of 0.001, 0.003, 
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0.01, and 0.03 mg/kg. 
• 
For subjects who were administered rAvPAL-PEG at the 3 higher dose levels (0.01, 
0.03, and 0.1 mg/kg) and who had measurable rAvPAL-PEG concentration levels, 
the calculated PK parameters were a mean Tmax of 89-106 hours, a t1/2 of 
46-120 hours, and an AUC0-t, and Cmax that were proportional with dose. Drug 
exposure was slightly increased with increased dose. 
 
Section 7.2.2/Phase 2 
Studies: PAL-002 and 
PAL-004 
Currently, rAvPAL-PEG is being investigated in two Phase 2 clinical trials (PAL-002 and 
PAL-004). To date (JAN2011), a total of 33 subjects have been administered rAvPAL-PEG 
in Study PAL-002 and initiation and recruitment of clinical sites is underway for Study 
PAL-004.   
In PAL-002 (A Phase 2, Open-Label, Dose-Finding Study to Evaluate the Safety, Efficacy, 
and Tolerability of Multiple Subcutaneous Doses of rAvPAL-PEG in Subjects with PKU), 
approximately 55 subjects will be enrolled and will be administered multiple doses of 
rAvPAL-PEG up to 5.0 mg/kg/week. PAL-002 is a 2-part study. In Part 1, subjects will be 
assigned to 1 of 4 rAvPAL-PEG dose cohorts (0.001, 0.003, 0.01, 0.1 mg/kg, or 1.0 mg/kg). 
rAvPAL-PEG will be administered at a fixed weekly dose of 0.001 mg/kg (Cohort 1), 
0.003 mg/kg (Cohort 2), 0.01 mg/kg (Cohort 3), 1.0 mg/kg (Cohort 4), or 0.1 mg/kg (Part 1 
Substudy) for 8 weeks. In Part 2, all subjects who complete Part 1 will be administered an 
adjustable dose of rAvPAL-PEG for up to an additional 8 weeks. The dose administered in 
Part 2 may be adjusted by dose level and/or dose frequency to reach a target blood Phe 
concentration of 60-600 µmol/L. Study PAL-003 (Long-Term Extension of a Phase 2, 
Open-Label, Dose-Finding Study to Evaluate the Safety, Efficacy, and Tolerability of 
Multiple Subcutaneous Doses of rAvPAL-PEG in Subjects with PKU) is an extension study 
of PAL-002 and PAL-004. Once subjects have completed Study PAL-002 or PAL-004, they 
have the option to enroll into PAL-003 and to continue to receive doses of rAvPAL-PEG 
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for up to an additional 60 months. 
Study PAL-002 was initiated in September 2009 and is ongoing. The primary objective of 
this study is to evaluate the effect of multiple doses of rAvPAL-PEG on blood Phe 
concentrations in subjects with PKU for up to 16 weeks of treatment. The secondary 
objectives of the study are (1) to evaluate the safety and tolerability of SC injections of 
multiple dose levels of rAvPAL-PEG, (2) to evaluate the antibody response to rAvPAL-
PEG, and (3) to evaluate the PK profile of rAvPAL-PEG in subjects with PKU. The study 
protocol was amended (30APR2010) to include a substudy of an additional rAvPAL-PEG 
dose level (0.1 mg/kg/week) that reduced blood Phe concentrations to clinically significant 
levels in the Phase 1 study, PAL-001. The protocol was amended again (28MAR2011) to 
increase the starting dose for Cohort 4 from 0.03 mg/kg/week to 1.0 mg/kg/week. To date 
(JAN2011), 33 subjects have been enrolled into the study and all 10 subjects of the 
substudy have been dosed with 0.1 mg/kg rAvPAL-PEG. Additional information about the 
safety reported to date (JAN2011) is provided in Section 7.4.2. 
Study PAL-004 is designed to determine if daily administration of rAvPAL-PEG at daily 
dose levels (0.06, 0.1, 0.2, 0.4, 0.6, and 0.8 mg/kg/day) is safe and effective in reducing and 
maintaining consistent blood Phe concentrations in subjects with PKU. It is hypothesized 
that a higher starting dose and frequency will reduce blood Phe concentrations to 
near-normal levels in a timely manner and will provide the greatest clinical benefit. 
Considering the concentration and volume of drug that is administered subcutaneously, the 
only way to increase the rAvPAL-PEG dose is via daily administration. Therefore, in Study 
PAL-004, a higher starting dose of 0.4 mg/kg will be administered 5 days a week (referred 
to as daily), a dosing regimen that has been observed to be tolerated and to reduce blood 
Phe concentrations to clinically meaningful levels in previously exposed subjects in this 
study. Following completion of Study PAL-004, subjects have the option to enroll into this 
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study and to continue to receive doses of rAvPAL-PEG for up to an additional 60 months. 
In this study, subjects in PAL-002 and PAL-004 will continue to be administered the same 
rAvPAL-PEG that was administered in PAL-002 or PAL-004. If the safety, PK, and blood 
Phe concentration results from either PAL-002 or PAL-004 indicate that the appropriate 
level of PEGylation and dosing regimen differs from that administered in PAL-002 or 
PAL-004, the PEGylation and/or dosing regimen administered in this study may change.    
 
Section 7.3/Study 
Rationale 
Because rAvPAL-PEG is being assessed as a long-term chronic treatment for patients with 
PKU, there is a need to understand the effect of a temporary dosing interruption on the 
safety, efficacy (blood Phe), PK, and immune response. To date (JAN2011), there is limited 
information on the effects of a rAvPAL-PEG dose interruption in subjects with PKU. 
Therefore, a Substudy has been added to this study to assess the effects of stopping and re-
starting rAvPAL-PEG treatment in subjects who are on a variety of rAvPAL-PEG dosing 
regimens (dose level and frequency). Up to 10 subjects who are on a variety of dosing 
regimens (dose level and frequency) in this study are eligible for participation in the 
Substudy and will stop dosing for a period of approximately 4 weeks. During this dosing 
interruption, subjects will be assessed for safety, efficacy, PK, and immune response and 
will continue to perform the scheduled study assessments. There is no information 
regarding the pharmacokinetic (PK) profile of rAvPAL-PEG when blood Phe levels are at 
60-600 µmol/L for subjects on a multiple-dose regimen. To address this lack of 
information, additional PK sampling will be performed prior to the dosing interruption. 
Upon restarting rAvPAL-PEG, PK sampling will also be performed to allow for collection 
of drug exposure data (area under the plasma concentration-time curve [AUC] and 
maximum plasma concentration [Cmax]), absorption rate, and clearance for subjects who 
have been previously exposed to rAvPAL-PEG in this Substudy. This information will 
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allow for comparisons to be performed with subjects who were naïve to previous rAvPAL-
PEG treatment from the Phase 1 study, PAL-001. 
Blood Phe levels depend not only on the functional presence of the endogenous enzyme 
PAH but also on the dietary intake of Phe. It is important to understand the role of diet on 
blood Phe levels concurrent with the administration of rAvPAL-PEG treatment. Therefore, 
an exploratory objective has been added to this study to assess the relationsihp of diet, 
rAvPAL-PEG administration, and blood Phe level. Changes to subject diet are not allowed 
in this study unless per the Investigator in consultation with the Sponsor’s Medical Officer. 
Diet will be monitored using a diet diary.   
This study is an extension of the dose-finding studiesy (PAL-002 and PAL-004). 
Administration of rAvPAL-PEG will be continued to assess whether long-term dosing of 
rAvPAL-PEG is safe and can maintain reduced blood Phe concentrations in PKU subjects. 
 
Section 7.4/Summary of 
Overall Risks and Benefits 
It is not expected that data from PAL-002 or PAL-004 will change the assumption that 
rAvPAL-PEG has a toxicity profile similar to other recombinant PEGylated non-human 
enzymes currently in use. 
4 
Section 7.4.1/Toxicitity 
Due to Exposure to PEG 
Acute exposure to high doses of PEG can result in renal toxicity. There have been a few 
reports of PEG-related AEs in humans; cumulative intravenous (IV) PEG doses of 121 to 
240 g caused acute renal tubular necrosis, oliguria, and azotemia. The anticipated PEG 
exposure associated with the expected rAvPAL-PEG dose range (6 g per week) is at least 
80-fold lower than the reported toxic doses and comparable to exposures to PEG in widely 
used medicines and other compounds that are administered by the IV, oral, rectal, and 
topical routes (Webster, 2007, Drug Metab Dispos.). No indication of PEG-related toxicity 
at the ultrastructural level was observed in monkeys given a single dose of up to 60 mg/kg 
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rAvPAL-PEG SC. In rats, both renal tubule vacuolation and histiocytic cell vacuoles have 
been assocated with PEG-related catabolism and administration of other PEGylated proteins 
(refer to Section 7.1). 
 
Section 7.4.2/Toxicity Due 
to an Immunologic 
Reactions 
In Study PAL-001, there were 11 subjects (out of 25 subjects in the study) with skin-related 
reactions (injection-site bruising, erythema, pain, rash, swelling, and urticaria) that occurred 
following the single administration of rAvPAL-PEG. For all of these subjects, the reactions 
were generalized skin reactions or injection-site skin reactions that did not compromise 
other organs and were not life-threatening. These suspected antibody-mediated responses 
were nonserious and mild or moderate in severity. These subjects are not considered to be at 
significant risk for antibody-mediated reactions with injection of rAvPAL-PEG during 
PAL-002, PAL-004, or this study; however, specific precautions for these subjects will be 
taken during this study to monitor subject safety (refer to Section 9.1.1). 
In Study PAL-002, 33 subjects have been dosed to date (JAN2011), including at dose levels 
of 2.0 mg/kg/week (or 0.4 mg/kg/5 days a week). Most reactions reported in these subjects 
have been nonserious and mild or moderate in severity. There has been 1 SAE reported to 
date; the event was reported as not related to treatment with study drug. There have been no 
reports of anaphylaxis to date (JAN2011). Subjects who have a systemic reaction during 
this study will undergo a series of assessments to monitor safety, including assessment of 
IgE antibodies, prior to determining if dosing may resume. Additionally, subjects who have 
systemic reactions will be premedicated and will be monitored closely for safety (refer to 
Section 9.1.6 for additional information regarding continued treatment of subjects with 
systemic reactions during the study). 
 
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Section 7.4.2.1/Systemic 
Skin Reactions 
Two out of 25 subjects who were enrolled in Study PAL-001 and received the 
protocol-defined single dose of rAvPAL-PEG reported systemic skin reactions (generalized 
skin rash) that were attributed to treatment with study drug. One subject received a single 
dose of 0.001 mg/kg rAvPAL-PEG, and the other subject received a single dose of 
0.01 mg/kg rAvPAL-PEG. Both of these events were reported as serious and followed 
administration One of these events was reported as serious, and the other was reported as 
nonserious; both events were reported following administration of Depo-Provera injections 
(medroxyprogesterone injection), an injectable contraception. These allergic reactions are 
thought to be related to the PEG molecules that are found in both the study drug, rAvPAL-
PEG, and Depo-Provera. These reactions are not likely to be experienced concurrent with 
other birth control medications. 
The 2 subjects were administered study drug during PAL-001 and then experienced an 
allergic reaction following an injection of Depo-Provera. The symptoms of the reactions 
were hives on the arms and legs and difficulty breathing. The symptoms for both subjects 
resolved within 1 day following treatment with medication, including the 
 
. Both subjects were examined by an allergy specialist after 
they completed participation in PAL-001. A skin prick test with Depo-Provera was 
administered as part of this examination. One subject had a mild allergic reaction to the test; 
however, no further reactions or complications were reported following subsequent 
administration of a full dose of Depo-Provera. The Upon study completion, the subject 
continueds to receive regular doses (every 3 months) of Depo-Provera, and no further 
reactions have beenwere reported to date (15OCT2009). The second subject also had a 
positive reaction to Depo-Provera following administration of the skin prick test. When a 
subsequent full dose of Depo-Provera was administered, 
developed hives, itching, and 
chills. The subject’s symptoms resolved within 1 day of taking medication prescribed by an 
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allergist. See Section 7.2.1 for the results from Study PAL-001. 
The active drug substance in rAvPAL-PEG is a bacterial protein that may elicit immune 
responses, such as urticaria, bronchospasm, itching, anaphylaxis, and others. It is possible 
that the physio chemical properties of rAvPAL PEG may induce immunologic sensitization 
to the protein rAvPAL and to PEG. The results from nonclinical studies of rAvPAL-PEG 
conducted in rats and cynomolgus monkeys indicated the formation of anti-rAvPAL 
antibody titers that did not correspond with observations of injection-site reactions. 
Quantitation of anti-PEG titers were not assessed in the chronic repeat-dose studies in the 
rat and monkey. Although results from nonclincal studies of rAvPAL-PEG conducted in 
rats and cynomolgus monkeys did not indicate signs of immune-mediated toxicities, it is 
possible that the physio-chemical properties of rAvPAL-PEG may induce immunologic 
sensitization to the protein rAvPAL and to PEG in humans. It is currently unknown whether 
administration of PEG-containing drugs, such as Depo-Provera, has a sensitizing effect to 
PEG in rAvPAL-PEG when administered in humans. Because the exact basis for these 
reported events and their duration is not known, the use of PEG-containing injectable drugs 
prior to, during, and after this study is prohibited as a precautionary measure (refer to 
Section 9.3.2 and Section 9.4.8.). 
 
Section 
7.4.2.2/Management of 
Allergic Reactions 
Allergic reactions to the SC injection of rAvPAL-PEG may be mild, moderate, or severe in 
intensity. Reactions may include pruritus, rash, shortness of breath, hypotension, or 
anaphylaxis. Clinical assessments should be conducted for a minimum of 230-60 
minuteshours post-injection. Longer observations may be required at the discretion of the 
PI. The responsible physician should use all appropriate measures for the treatment of 
allergic reactions. Because of the small potential for anaphylaxis, equipment for emergency 
resuscitation (including epinephrine) should be within easy access during and after the 
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rAvPAL-PEG injection. Subjects who qualify for self administration of study drug will be 
provided with emergency resuscitation instructions (refer to Section 9.4 and the Subject 
Self-Administration Training Materials). 
In the event of an allergic reaction, subjects may be asked to see an allergist/immunologist 
and/or provide up to 3 additional blood samples for antibody testing. This additional testing 
may occur up to 6 months following the final study visit. 
The following measures are recommended for the treatment of allergic symptoms: 
• 
ClearingMaintain the airway. 
 
Section 7.4.3/Effects of 
Stopping and Re-Starting 
rAvPAL-PEG Treatment 
The effects of starting, stopping, and re-starting rAvPAL-PEG dosing on safety and blood 
Phe reductions previously achieved through rAvPAL-PEG dosing are not well defined, and 
there is limited clinical experience with rAvPAL-PEG. Allergic reactions are a common 
and expected clinical outcome of re-starting biologic drugs, such as rAvPAL-PEG, and may 
occur when subjects re-start rAvPAL-PEG dosing. However, no information reported from 
the ongoing clinical studies, including this study, or nonclinical results point to an increased 
safety risk or decreased efficacy when rAvPAL-PEG dosing is stopped and then re-started 
at the same dose level: 
• 
Nonclinical experience in the the BTBR Pahenu2 (ENU2) mouse model indicates 
that dosing interruptions of 2-4 weeks for mice administered rAvPAL-PEG 
80 mg/kg/week had no increased safety risk upon re-starting dosing and there was 
an immediate return to stable blood Phe reductions (refer to Section 7.1).  
• 
Antibody results from the ongoing Phase 2 study, PAL-002, and this ongoing study 
to date (JAN2011) have not indicated an immune response that points to an 
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increased safety risk or decreased efficacy upon re-introduction of drug. There has 
not been any immediate immunoglobulin E (IgE)-mediated reactions to rAvPAL-
PEG observed following administration of a rAvPAL-PEG injection. All reactions 
to rAvPAL-PEG have been reported approximately 12-24 hours following 
administration. To date, 1 out of 33 subjects has tested positive by serology to IgE 
antibodies without reporting any clinical symptoms to suggest anaphylaxis or a 
severe systemic reaction. Thus, it is not anticipated that reactions to rAvPAL-PEG 
are IgE-mediated.   
• 
To date (JAN2011), the clinical experience with re-starting rAvPAL-PEG dosing 
for subjects from Study PAL-001 who rolled over into Study PAL-002 does not 
indicate an increased safety risk or a decreased effect on reducing blood Phe levels 
upon re-introduction of drug.  
o Nine subjects who received a single dose of rAvPAL-PEG and completed 
the Phase 1 study, PAL-001, rolled over into the multiple-dose, Phase 2 
study, PAL-002. After a period of several months during which no drug 
was administered, these 9 subjects re-started rAvPAL-PEG dosing in Study 
PAL-002 at the same starting doses as was administered in Study PAL-001. 
There has been no difference to date in the safety profile or efficacy profile 
of the subjects from Study PAL-001 who rolled over into Study PAL-002 
(previously exposed to rAvPAL-PEG) when compared with subjects who 
were naive to rAvPAL-PEG dosing in Study PAL-002. Although 
previously exposed subjects had higher and a faster return of anti-PAL and 
anti-PEG IgG titers than those of naïve subjects, these results have not been 
associated with a higher safety risk or efficacy riskbased on information to 
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o In Study PAL-002, 4 subjects to date have had a protocol-defined (per 
Protocol Amendment # 3 dated 30APR2010), 2-week washout (no dose 
administered) following several weeks of a fixed dose of 0.06 mg/kg/week 
or 0.1 mg/kg/week rAvPAL-PEG. Following the 2 weeks where no dose 
was administered, all 4 subjects re-started rAvPAL-PEG dosing at a higher 
dose with no safety issues reported to date. Blood Phe levels for these 4 
subjects have not changed upon re-introduction of dosing. 
o Clinical experience with subjects who have had to temporarily halt dosing 
due to an adverse event also provides information that stopping and 
re-starting rAvPAL-PEG dosing does not appear to increase the risk to 
subject safety. To date, 10 subjects participating in either PAL-002 or PAL-
003 have had to temporarily stop dosing due to an adverse event. All 10 
subjects resumed dosing following resolution of the event or per 
determination by the Investigator that subject safety would not be 
jeopardized with re-starting dosing. These 10 subjects resumed dosing at a 
reduced dose level after approximately 1-7 weeks of no dosing. Upon re-
starting dosing, none of these 10 subjects have experienced additional 
safety issues. Eight subjects continue to receive dosing with rAvPAL-PEG 
(APR 2011) and have subsequently increased their dose level without 
additional reported adverse events that have resulted in a subsequent dosing 
interruption. 
 
In this study, measures will be taken to reduce the risk to subject safety upon re-starting 
rAvPAL-PEG dosing while still allowing for reductions in blood Phe level to clinical 
significance (blood Phe reduction to 60-600 µmol/L). To mitigate the possible safety risks 
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upon re-starting rAvPAL-PEG dosing, re-introduction of dosing should be performed in the 
clinic, and the subject must be observed for 30-60 minutes following administration due to 
restarting dosing. A follow-up telephone call should be made to subjects 24 hours following 
re-starting of dosing to monitor subject safety. Subjects will also continue to be assessed per 
the safety assessment and stopping criteria defined in Section 9.1.3 and Section 9.1.4, and 
dose decreases will continue to be performed relative to safety as defined in Section 9.1.2.2. 
To mitigate the possible reduced effect on blood Phe level upon re-starting rAvPAL-PEG, 
subjects in this study who interrupt dosing whether per the protocol (ie, subjects 
participating in the Substudy; refer to Section 9.1) or for other reasons (refer to Section 
9.4.10) will re-start rAvPAL-PEG dosing at the same dose level.      
 
Section 7.4.3/Effects of 
Low Blood Phe 
Insufficient Phe intake or excessive rAvPAL PEG exposure may cause blood Phe 
concentrations to be too low (eg,  30 µmol/L). Prolonged low blood Phe concentrations 
can result in a catabolic state associated with poor growth and altered body functions, 
including mental and physical alterations, loss of appetite, anemia, rashes, and diarrhea. To 
ensure safety during this study, subjects will be monitored closely with frequent blood Phe 
concentration determinations. If a subject’s blood Phe concentration is too low, the 
subject’s diet, current dose of study drug, or both may be adjusted. 
 
9 
Section 8/Study Objectives 
The secondary objectives of the study are: 
• 
To evaluate the immune antibody response to long-term administration of SC 
injections of rAvPAL-PEG in subjects with PKU. 
• 
To evaluate steady state PK of rAvPAL PEG in subjects with PKU. 
The exploratory objective of the study is as follows: 
• 
To assess the long-term relationship of diet and change in blood Phe concentration 
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following administration with rAvPAL-PEG in subjects with PKU. 
The Substudy objectives are as follows: 
• 
To assess the safety and tolerability of stopping and re-starting rAvPAL-PEG 
dosing in a subset of subjects with PKU. 
• 
To evaluate the effect of stopping and re-starting rAvPAL-PEG dosing on blood 
Phe concentration in a subset of subjects with PKU. 
• 
To evaluate the effect of stopping and re-starting rAvPAL-PEG dosing on immune 
response in a subset of subjects with PKU.   
• 
To assess the effect of multiple doses of rAvPAL-PEG on the PK profile, in 
particular clearance of drug, when drug is stopped in a subset of subjects with PKU 
who have been previously exposed to rAvPAL-PEG.   
 
Section 9.1/Overall Study 
Design and Plan 
This is a long-term extension of athePhase 2, open-label, dose-finding studies,y (Study 
PAL-002 and PAL-004, in 35 50 approximately 1000 subjects with PKU. The doses are 
planned to be in the same range as those tested in PAL-002 and PAL-004 (starting at 0.001 
through 51.0 mg/kg/weekper injection), provided no dose-limiting toxicity iwas observed in 
PAL-002 or PAL-004. 
Only subjects who completed the protocol-defined study drug regimen participation in 
PAL-002 or PAL-004 will be enrolled into this study. Subjects who enroll from PAL-002 
will either continue the dose regimen that was administered upon completion of PAL-002 
or start dosing at a higher dose per the dose increase instructions. Subjects who enroll from 
PAL-002 may start this study at a higher dose level provided there was no interruption in 
dosing since completion of PAL-002 and enrollment into this study. Subjects who enroll 
from PAL-004 will re-start rAvPAL-PEG dosing in this study at the same dose level and 
frequency as was administered upon completion of PAL-004. The first dose will be 
administered in the clinic, and the subject must be observed for 30-60 minutes following 
administration due to restarting dosing in this study. A follow-up telephone call will be 
made to the subject to monitor subject safety 24 hours following the return to dosing. 
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Diet will should not be altered during the course of this study, except as necessary for safety 
as determined by blood Phe concentrations. If a subject’s blood Phe concentration is 
 < 120 µmol/L, the subject’s diet may be adjusted to increase the amount of dietary Phe 
intake to maintain target blood Phe concentrations of 120 600 µmol/L. Changes to diet will 
be made per the discretion of the Investigator in consultation with the Sponsor’s Medical 
Officer. For information regarding changes to diet for safety and decreases in dose, refer to 
Section 9.1.2.2. Any decision to modify subject diet must be made per the Investigator in 
consultation with the Sponsor’s Medical Officer and must be performed under the 
supervision of the Investigaor in consultation with the Sponsor’s Medical Officer. To 
monitor for changes in subject diet, a diet diary will be issued to subjects for completion 
and will be reviewed with the clinical study staff.  
Subjects may self administer study drug at home if approved by the Sponsor’s Medical 
Officer and if adequate training is provided. Subjects must meet a set of criteria to be 
considered appropriate for self administration. Refer to Section 9.4 for the criteria for which 
subjects may qualify for self administration. Additional information is provided in the 
Subject Self-Administration Training Materials. 
Subjects will be evaluated for safety and for blood Phe concentrations throughout the study. 
Toxicity will be measured according to the National Cancer Institute (NCI) Common 
Terminology Criteria for Adverse Events (CTCAE), version 43. 
At least one interim analysis may be performed by the sponsor during the study. In addition 
to the Sponsor, a Data Monitoring Committee (DMC) will monitor the safety of subjects in 
the study. The DMC is an independent committee that will act in an advisory capacity to the 
Sponsor. 
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take 
rAvPAL-PEG. PAL-002 and PAL-004 subjects’ rAvPAL-PEG dosing will continue in 
PAL-003without interruption of dosing. In PAL-003, each subject’s dose will be adjusted as 
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needed to attain or maintain blood Phe concentrations of 6120-600 µmol/L. Doses will be 
evaluated on an individual basis.  
Evaluations, observations, and procedures will be conducted at selected time points as 
shown in Table 2.1.1, Table 2.1.2, Table 2.1.3, and Table 2.1.4 (Schedule of Events). After 
the subject’s blood Phe concentration has been controlled to within a target range 
(6120-600 µmol/L), the subject may be asked to have additional blood draws for PK and 
blood Phe concentration analyses as needed per the discretion of the Investigator in 
consultation with the Sponsor’s Medical Officer.but not to exceed 3x/week (fingerstick tests 
may be performed more frequently). 
A subject will continue in PAL-003 until one of the following occurs: 
1. The subject withdraws consent and discontinues from the study. 
2. The subject is discontinued from the study at the discretion of the Investigator. 
3. The subject has completed the study through the Month 2460 visit. 
4. The study is terminated. 
Subjects may withdraw from treatment with study drug at any time; however, subjects will 
be asked to continue to perform the study assessments until study completion. Subjects may 
also withdraw from study participation at any time. Because the completeness of the data 
affects the integrity, accuracy, and interpretation of study results, every effort should be 
made to retain subjects in the study and to have them complete the study assessments as 
scheduled as long as continued participation does not compromise subject safety. 
A subset of up to 10 subjects who are already enrolled and who have consented to 
participate in this study will be asked to participate in a Substudy to assess the effect that 
stopping and re-starting treatment with rAvPAL-PEG has on safety, efficacy, PK, and 
immune response. Subjects will be eligible for participation in the Substudy provided they 
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also meet all of the PAL-003 eligibility criteria, have been on a stable dosing regimen for 
approximately 4 weeks during this study, have not had any serious adverse events reported 
during PAL-003, and were not enrolled in Study PAL-004. Subjects participating in the 
Substudy will have rAvPAL-PEG administration halted for approximately 4 weeks 
regardless of their dosing regimen (dose level and frequency). rAvPAL-PEG will not be 
administered during the dose interruption; however, subjects will continue to perform 
assessments for safety, blood Phe concentration, PK, and immune response. Subjects 
enrolled into the Substudy will also have additional PK sampling performed prior to the 
dosing interruption and during the dosing interruption. To allow for PK sampling once 
dosing is stopped, subjects may be admitted to a research facility within 8 hours of stopping 
dosing where they will reside for at least 24 hours. After the dosing interruption, rAvPAL-
PEG administration will be re-started at the same dose level and dosing frequency that was 
administered prior to the dosing interruption. Upon re-starting rAvPAL-PEG, the first dose 
must be administered in the clinic and the subject must be observed for 30-60 minutes 
following administration due to restarting dosing. A follow-up telephone call will be made 
to the subject to monitor subject safety 24 hours following the return to dosing. Additional 
PK sampling will also be performed for the first week after the dosing interruption. 
Section 9.1.1/Management 
of Local and Systemic 
Reactions to rAvPAL-PEG 
Subjects who qualify for self administration of study drug will be provided with 
information and instruction with regard to management of local and systemic reactions 
(refer to the Subject Self-Administration Training Materials). 
 
11, 13, 21 
Section 9.1.1.1/Subjects 
Who Have Had Previous 
Hypersensitivity Reactions 
to rAvPAL-PEG or a PEG-
Subjects who had a previous systemic reaction to rAvPAL-PEG or a PEG-containing 
product that warranted early termination from PAL-002 or PAL-004 are excluded from 
participation in this study. Subjects who experienced a generalized skin rash are included in 
this category. Subjects who have had a previous local skin reaction to rAvPAL-PEG in 
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containing Product 
PAL-002 or PAL-004are eligible to participate in this study. Subjects who have had a 
previous reaction and are deemed eligible for participation must be premedicated orally 
with acetaminophen and/or antihistamines 1 hour prior to study drug dosing for the 
remainder of the study. The premedication dosage will be standard. Because antihistamines 
can cause drowsiness, it may be administered only if the subject is accompanied by a 
designated driver (if applicable). Subjects may develop systemic, large local skin, or local 
skin reactions after enrollment in PAL-003. Refer to Section 9.1.1.2 for definitions of 
systemic and local skin reactions. For management of hypersensitivity reactions that occur 
during this study, refer to Section 9.1.1.3 and Figure 9.1.1.3.1. 
 
Section 9.1.1.2/Definitions 
of Hypersensitivity 
Reactions to rAvPAL-PEG 
Administered 
Subcutaneously 
• 
Skin and non-skin signs or symptoms in more than 1 affected primary location, 
ie, cutaneous reaction in more than 1 area and/or anaphylaxis or any other 
generalized symptoms, such as hypotension, angioedema or the involvement of 
other organ systems, eg, respiratory, cardiovascular, gastrointestinal, neurological; 
and/or a fever attributed to treatment with rAvPAL-PEG ( ≥ 100.4°F or  ≥ 38°C). 
 
11, 13, 21 
 
 
 
 
 
 
 
 
Section 9.1.3.3.1/Local 
Skin Reactions 
Subjects who have had a local skin reaction (refer to Section 9.1.1.2 for definition) after 
administration of rAvPAL-PEG in PAL 001, PAL 002,or this study may continue if the 
symptoms do not worsen and no other symptoms have developed but may be premedicated 
with acetaminophen and/or antihistamines (standard dosage per the package insert) 1 hour 
prior to the next dose of study drug dosing. Recommended premedications are 
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acetaminophen and antihistamine (Zyrtec [cetirizine] is preferred). The dosage will be 
standard (eg, 1000 mg acetaminophen and 10 mg Zyrtec or 25 to 50 mg oral Benadryl 
[diphenahydramine]). Because antihistamines Benadryl can cause drowsiness, it should be 
administered only if the subject is accompanied by a designated driver. 
Symptoms of local reactions may be treated with local application of ice and non-sedating 
oral and/or topical antihistamines and/or topical steroids (refer to Section 7.4.2.2). 
If the local skin reaction worsens with a repeat injection (as determined by the Investigator 
in consultation with the Study Medical Officer) even with premedication prior to study drug 
dosing, the subject must be withdrawn from the study treatmentand complete an Early 
Termination Visit. 
 
Figure 9.1.1.3.2/Large 
Local Skin Reactions 
Large local skin reactions (refer to Section 9.1.1.2 for a definition) may or may not be 
contiguous to the rAvPAL-PEG injection site, and subjects with either type of large local 
skin reaction may continue dosing if the skin symptoms have resolved and no other 
symptoms have developed. Subjects may be premedicated orally with acetaminophen 
and/or antihistamines (standard dosage per the package insert) 1 hour prior to study drug 
dosing. The location of the large local skin reaction relative to the rAvPAL PEG injection 
site will determine if a subject may remain in the study and continue to be administered 
rAvPAL PEG. An example of a large local reaction that is not contiguous to the injection 
site is if an injection took place in the right upper arm and there are lesions beyond the 
elbow joint in the right forearm or lesions beyond the shoulder joint on the right trunk.  
Subjects who have large local skin reactions that are contiguous to the injection site may 
remain in the study. Subjects who have large local skin reactions that are not contiguous to 
the injection site may have additional assessments performed (Unscheduled 
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Hypersensitivity Reaction Visit) per Investigator discretion and must then be terminated 
from the study. A decision to terminate a subject from the study must be agreed to by both 
the Investigator and the Sponsor’s Medical Officer. 
 
Section 9.1.1.3.2.1/Large 
Local Skin Reactions 
Contiguous to Injection 
Site 
Subjects who develop a large local skin reaction contiguous to the injection site after 
administration of rAvPAL-PEG or to rAvPAL-PEG or a PEG-containing product may 
remain in the study if the skin symptoms have resolved and no other symptoms have 
developed. Large local skin reactions that are contiguous to the injection site should be 
managed as local skin reactions (refer to Section 9.1.1.3.1). For the remainder of the study, 
subjects must may be premedicated orally with acetaminophen and/or antihistamines 
(standard dosage per the package insert) 1 hour prior to the next dose of study drug dosing. 
Recommended premedications are acetaminophen and antihistamine (Zyrtec [cetirizine] is 
preferred). The dosage will be standard (eg, 1000 mg acetaminophen and 10 mg Zyrtec or 
25 to 50 mg Benadryl [diphenahydramine]). Because antihistaminesBenadryl can cause 
drowsiness, it may be administered only if the subject is accompanied by a designated 
driver (if applicable).  
 
11, 13, 21 
Section 9.1.1.3.2.2/Large 
Local Skin Reactions Not 
Contiguous to Injection 
Site 
Large local skin reactions that are not contiguous to the injection site may be associated 
with a low risk of systemic symptoms or anaphylaxis upon re-exposure to rAvPAL-PEG 
and, therefore, will be managed as a systemic reaction (refer to Section 9.1.1.3.3). An 
example of a large local reaction that is not contiguous to the injection site is if an injection 
took place in the right upper arm and there are lesions beyond the elbow joint in the right 
forearm or lesions beyond the shoulder joint on the right trunk. Subjects who develop large 
local skin reactions that are not contiguous to the injection site after administration of 
rAvPAL PEG or to rAvPAL PEG or a PEG containing product may not continue to 
11, 13, 21 
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participate in the study. Subjects may have additional assessments performed 
(ie, Unscheduled Hypersensitivity Skin Reaction Visit) immediately after the reaction 
(within 48 hours): serum anti rAvPAL PEG antibodies (anti PAL immunoglobulin G [IgG], 
anti PAL immunoglobulin M [IgM], anti PEG IgG, anti PEG IgM, anti rAvPAL PEG 
neutralizing antibody, and anti rAvPAL PEG immunoglobulin E [IgE]); serum tryptase 
level; sedimentation rate; C reactive protein (CRP), total hemolytic complement (CH50), 
and complements C1 and C4; and clinical laboratory tests (urinalysis, chemistry, 
hematology). Subjects will then be terminated from the study and should be scheduled to 
complete the Early Termination Visit (refer to Section 12.4).  
 
Section 9.1.1.3.3/Systemic 
Reactions 
Subjects who experience a systemic reaction (refer to Section 9.1.1.2 for a definition) after 
administration of rAvPAL-PEG must stop further administrations of rAvPAL-PEG and 
must immediately return to the clinic for safety assessments will be terminated from the 
study. Subjects who experience generalized skin symptoms are included in this category. 
Immediately after the systemic reaction (within 48 hours), subjects with generalized skin 
symptoms must have additional assessments performed for safety (ie, Unscheduled 
Hypersensitivity Skin Reaction Visit): serum anti-rAvPAL-PEG antibodies (anti-PAL 
immunoglobulin G [IgG], anti-PAL IgM, anti-PEG IgG, anti-PEG IgM, anti-rAvPAL-PEG 
IgE, and anti-rAvPAL-PEG neutralizing antibody)anti PAL IgG, anti PAL IgM, anti PEG 
IgG, anti PEG IgM, anti rAvPAL PEG neutralizing antibody, and anti rAvPAL PEG IgE); 
serum tryptase level (optional; it is recommended that this sample be drawn immediately 
after reaction); sedimentation rate; CRP, CH50, C1, C3, and C4; skin biopsy (optional; 
affected and not affected area; to be performed within 1 week of reaction); and clinical 
laboratory tests (urinalysis, chemistry, hematology; refer to Figure 9.1.1.3.1).  
Following completion of the Unscheduled Systemic Reaction Visit, administration of 
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rAvPAL-PEG may resume up to 1 week following the onset of the reaction if the systemic 
reaction is not IgE-mediated and the subject’s safety will not be further compromised with 
resumed dosing. rAvPAL-PEG administration will resume at the next lowest dose level. 
Restarting of rAvPAL-PEG administration following a systemic reaction must be 
performed in the clinic for the first week of resumed dosing. Subjects must be premedicated 
orally with acetaminophen and/or antihistamines (standard dosage per the package insert) 
1 hour prior to study drug dosing for the remainder of the study. Additionally, subjects must 
be closely monitored for 30-60 minutes following every administration of study drug. 
Because antihistamines may cause drowsiness, the subject must be accompanied by a 
designated driver (if applicable). 
If blood Phe concentrations are not 60-600 µmol/L following 1 week of daily 
administration at the lowered dose cohort and there is no further evidence of toxicity (ie,  
another systemic reaction attributed to rAvPAL-PEG administration or clinically significant 
abnormal laboratory test results), the subject may be administered the next highest dose 
level in the clinic per the allowable dose increases outlined in Section 9.1.2. Subjects must 
be premedicated orally with acetaminophen and/or antihistamines (standard dosage per the 
package insert) 1 hour prior to study drug dosing for the remainder of the study. 
Additionally, subjects must be closely monitored for 30-60 minutes following every study 
drug administration. Because antihistamines may cause drowsiness, the subject must be 
accompanied by a designated driver (if applicable). 
Subjects who have a systemic reaction without generalized skin symptoms may have these 
assessments performed per Investigator discretion. Subjects will then be terminated from 
the study and should be scheduled to complete the Early Termination Visit (refer to 
Section 12.4). 
 
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Section 9.1.2/Dose 
Modifications 
After any modifications (increases or decreases) to dose level or frequency, subjects should 
remain in the clinic for observation for at least 2 hours following the injection of study 
drug. The Investigator should remain at the site to assess the subject for safety. 
 
2, 3, 21, 22, 
23 
Section 9.1.2.1/Dose 
Increase Methodology 
Each subject’s dose may be modified based on the decision of the Investigator, in 
agreement with the Study Medical Officer. Decisions regarding dose increases will depend 
on a subject’s adverse event profile and blood Phe and drug concentrations.  
Blood Phe levels will be measured 3 days after each dose increase (fingerstick is 
acceptable); more frequent or daily blood Phe measurements may be performed.  
For subjects from PAL-002Depending upon the response to rAvPAL PEG in PAL 002, an 
individual subject’s dose may be adjusted beginning on Day 1 of PAL-003. For the duration 
of this study, an individual subject’s dose may be adjusted if warranted per a subject’s 
adverse event profile and blood Phe concentrations. Dose increases should be performed as 
follows. 
• The dose may be increased by increments of no more than 10-fold higher than 
the subject’s current dose. 
• When increasing the dose, a dose may be used that is between the dose levels 
(0.001, 0.003, 0.01, 0.03, 0.06, 0.1, 0.2, 0.3, 0.4, 0.6, 0.8, and 1.0, 2.0, 3.0, 4,0, 
and 5.0 mg/kg) that were defined in the previous study (PAL 002).or per 
Investigator determination in consultation with the Sponsor’s Medical Officer 
based on available information regarding a subject’s blood Phe 
(60-600 µmol/L) and drug concentrations, as well as any adverse events (any 
hypersensitivity reaction) for an individual subject. 
• The dose may be adjusted by increasing the frequency up to daily for a total 
weekly dose not to exceed 52.0 mg/kg, including subjects who receive more 
than 1 dose/week. Subjects who increase their dose frequency should perform 
the Interim Dosing Visit assessments (refer to Section 12.3.65 and Table 2.1.3 
Table 2.1.3:   and Table 2.1.4 Table 2.1.4:  ). 
2, 3, 21, 22, 
23 
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• When a dose is increased (either by increasing the dose level or by increasing 
the frequency of dosing), the subject must remain in the clinicbe observed for a 
minimum of 30-60 minutes2 hours following the first modified dose 
administration, and an Investigator will remain on site during this 
time.Subjects who increase their dose frequency do not need to be observed 
following injection of study drug if the increase in frequency does not increase 
the overall weekly dose amount. 
• Only 1 dose (level or frequency) adjustment is allowed every 2 weeks. 
• Blood Phe levels will be measured daily for 3 days after each dose increase 
(fingerstick is acceptable); more frequent or daily blood Phe measurements 
may be performed. 
 
Section 9.1.2.2/Dose 
Decrease Methodology 
A subject’s diet should be assessed prior to any dose decreases. Changes to diet should only 
be made if a subject’s blood Phe concentrations  < 120 µmol/L. If a subject’s blood Phe 
level is  < 120 µmol/L, the subject’s dietary Phe intake should be increased to achieve a 
stable blood Phe concentration of 120 600 µmol/L. If the subject’s blood Phe level is 
 < 120 µmol/L despite a high Phe diet, the rAvPAL PEG dose will then be decreased. The 
subject will be asked about any changes to diet prior to any dose adjustments, and any 
changes to diet should be made per the discretion of the Investigator in consultation with 
the Sponsor’s Medical Officer. 
All dose decreases must be agreed to by both the Investigator and the Sponsor’s Medical 
Officer. Decisions regarding dose decreases will depend on available information regarding 
a subject’s blood Phe (60-600 µmol/L> 30% change from baseline) and drug 
concentrations, as well as any adverse eventstoxicity (any hypersensitivity reaction as 
defined in Section 9.1.1.2). Dose decreases may occur for safety (ie, blood Phe 
concentration  < 120 µmol/L) or other toxicityany adverse event that may be improved with 
a lower, more frequent dose).  
A dose should first be reduced by dose level (5.0, 4.0, 3.0, 2.0, 1.0, 0.8, 0.6, 0.4, 0.3, 0.2, 
0.1, 0.06, 0.03, 0.01, 0.003, 0.001 mg/kg). It is also permitted to decrease dose in between 
2, 3, 21, 22, 
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these specified dose levels. If further dosing adjustments are required to attain the target 
Phe concentration, dosing frequency may be reduced.  
 
Section 9.1.3/Safety 
Assessment Stopping 
Criteria 
If an individual subject exhibits toxicity of a treatment-emergent CTCAE grade 3 or greater 
or a systemic reaction that is assessed as related to treatment with study drug, that subject 
will have dosing halted until the toxicity resolves. The subject’s data will be evaluated by 
the Principle Investigator (PI) and the Study Medical Officer, and a decision will then be 
made whether to discontinue the subject from the study treatment, restart dosing at the same 
dose level, or restart dosing at a lower dose level. 
 
8 
Section 9.1.4/Stopping 
Criteria 
Ifn addition, if 2 or more subjects at a dose level exhibit toxicity of a treatment-emergent 
CTCAE grade 3 or greater or a systemic reaction that is assessed as related to treatment 
with study drug, further dosing of subjects at that dose level will be evaluated and halted 
and no subject will be treated at a higher dose level until a safety assessment will be is 
completed. In addition, the Food and Drug Administration (FDA) may will be notified of 
this occurrence if appropriate. 
 
8 
Section 9.3.1/Inclusion 
Criteria 
Individuals eligible to participate in this study must meet all of the following criteria: 
1. Must have completed participation and all protocol-defined study drug in PAL-002 
or PAL-004. 
 
4 
Section 9.3.2/Exclusion 
Criteria 
Individuals who meet any of the following exclusion criteria will not be eligible to 
participate in the study: 
1. Use of any investigational product (with the exception of rAvPAL-PEG) or 
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investigational medical device within 30 days prior to Screening, or 
requirement for any investigational agent prior to completion of all scheduled 
study assessments. 
2. Use of any medication other than rAvPAL-PEG that is intended to treat PKU 
within 14 days prior to the administration of study drug. 
3. Use or planned use of any injectable drugs containing PEG (other than 
rAvPAL-PEG), including Depo-Provera, within 6 months prior to Screening 
and during study participation. 
4. A prior reaction that included systemic symptoms (eg, generalized hives, 
respiratory or gastrointestinal problems, hypotension, angioedema, 
anaphylaxis) to rAvPAL-PEG or a PEG-containing product. Subjects with a 
prior systemic reaction of generalized rash may be eligible for participation per 
the discretion of the Principal Investigator in consultation with the Sponsor’s 
Medical Officer. However, subjects who discontinued from study treatment 
early due to a reaction are not eligible to enroll into this study.        
9. Known hypersensitivity to rAvPAL-PEG or its excipients, including 
hypersensitivity reactions that necessitated early termination from PAL-002 or 
PAL-004. 
 
Section 9.3.3/Removal of 
Subjects from Treatment or 
Assessment 
Subjects (or their legally authorized representative) may withdraw their consent to 
participate in the study or to receive study drug at any time without prejudice. The 
Investigator must withdraw from the study or study drug treatment any subject who 
requests to be withdrawn. A subject’s participation in the study may be discontinued at any 
time at the discretion of the Investigator and in accordance with his/her clinical judgment. 
When possible, a subject who is discontinued from study treatment should continue to 
perform the study tests and evaluations until study completion. For subjects who 
discontinue from the study, the tests and evaluations listed for the Early Termination Visit 
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should be carried out (refer to Section 12.4). 
BioMarin must be notified of all subject withdrawals as soon as possible. BioMarin also 
reserves the right to discontinue the study at any time for either clinical or administrative 
reasons and to discontinue participation by an individual Investigator or site for poor 
enrollment or noncompliance. 
Reasons for which the Investigator or BioMarin may withdraw a subject from the study 
treatment include, but are not limited to, the following: 
• 
Subject experiences a serious or intolerable adverse event (AE). 
• 
Subject develops a clinically significant laboratory abnormality. 
• 
Subject requires medication prohibited by the protocol. 
• 
Subject becomes pregnant (refer to Section 10.3 for details on the reporting 
procedures to follow in the event of pregnancy). 
Reasons for which the Investigator or BioMarin may withdraw a subject from the study 
include, but are not limited to, the following: 
• 
Subject does not adhere to study requirements specified in the protocol. 
• 
Subject was erroneously admitted into the study or does not meet entry criteria. 
• 
Subject is lost to follow-up. 
• 
Subject becomes pregnant (refer to Section 10.3 for details on the reporting 
procedures to follow in the event of pregnancy). 
 
Section 9.3.4/Subject 
Identification and 
Subjects will retain the same subject number assigned in PAL-002 or PAL-004. 
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Replacement of Subjects 
Section 9. 4/Treatments 
Upon enrollment into this study, subjects from PAL-002 will be dosed with the same or 
higher dose that was administered upon completion of PAL-002. Subjects enrolling from 
PAL-004, will be administered the same dose that was administered upon completion of 
PAL-004. rAvPAL-PEG doses will be administered SC by either health care professionals 
or via self administration. The dose level may be increased per Investigator determination in 
consultation with the Sponsor’s Medical Officer based on on available information 
regarding a subject’s blood Phe level (60-600 µmol/L), as well as any adverse events (any 
hypersensitivity reaction) for an individual subject. The dosage that provides control of 
blood Phe concentrations within the target range of 60-600 µmol/L for a minimum of 2 
weeks will be determined for each subject by adjusting the dose level, dose frequency, or 
both, as agreed to by the PI and the Study Medical Officer, based upon the subject’s 
response to doses.  
Subjects may self administer study drug at home if approved by the Sponsor’s Medical 
Officer and if adequate training is provided. Subjects may be eligible to self administer 
study drug if he or she meets the following criteria:  
• 
The subject is on a stable dosing regimen for 2 weeks. 
• 
The subject has not experienced any CTCAE Grade 3 or higher adverse event.  
• 
The subject has not experienced any hypersensitivity reaction to rAvPAL-PEG for 
at least 4 weeks. 
• 
The subject has no cognitive impairments that may increase the safety risk of self 
administration per the assessment of the PI.  
• 
The subject has been approved for self administration of study drug by the 
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Sponsor’s Medical Officer. 
• 
The subject has completed the Self-Administration Training conducted by qualified 
study site personnel and has been observed by the study site personnel to be able to 
adequately prepare the proper dose and perform the injections safely.  
• 
The subject has been provided with epinephrine and has been trained on when and 
how to administer it.  
 
Qualified study site personnel will train each eligible subject on all procedures for self 
administration of study drug under the supervision of the PI. Qualified study site personnel 
will also be required to observe the subject prepare and perform at least 1 injection prior to 
allowing the subject to self administer a dose at home. The patient will see a study site 
nurse or home healthcare nurse in person every week to ensure that the subject continues to 
perform all self-administration procedures correctly, to assess for adverse events, and to 
answer questions throughout the duration of the study. The study site nurse or home 
healthcare nurse will also perform the regularly scheduled assessments and procedures as 
outlined in Table 2.1.1 and Section 12; the subject must perform a clinic visit monthly at 
minimum. Training materials and other information specific to the study site personnel are 
provided in the Subject Self-Administration Training Materials.     
Subjects who are eligible for self administration will be provided with a Subject Study 
Manual, Self-administration training materials will be provided in the Subject Study 
Manual to supplement the in-person training provided by the qualified study site personnel. 
The Subject Study Manual will include step-by-step instruction on the following: 
• 
How to prepare and perform the injections of study drug safely. 
• 
How to receive, track, store, prepare, and return both used and unused study drug.   
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• 
How to safely use and dispose of syringes used for injections of study drug. 
• 
How to care for their injection site after an injection of study drug.  
• 
How to identify an adverse reaction and how to report this reaction to the study site. 
• 
How and when to use epinephrine. 
• 
Who to contact at the study site in case of an emergency.  
 
The PI or the Sponsor’s Medical Officer may request that self administration be halted at 
any time and that the subject resume injections performed by the study site personnel or 
home healthcare nurse. 
 
Section 9.4.1/Treatments 
Administered 
BioMarin and/or its designee will provide the study site with a supply of IP sufficient for 
the completion of the study. BioMarin is responsible for shipping study drug to the clinical 
sites. The clinical site is responsible for supplyingthe study drug to subjects who qualify for 
self administration. Refer to the PAL-003 Pharmacy Manual for information pertaining to 
the distribution of study drug from sites.   
Information regarding supplying study drug to subjects who qualify for self administration 
is provided in the Subject Self-Administration Training Materials. 
 
10, 27 
Section 9.4.3/Storage 
At the study site, all IP must be stored at 5 ±3°C (41 ± 5°F) under the conditions specified 
in the IB. At the site, the IP will be stored in a secure area accessible only to the designated 
pharmacists and clinical site personnel. All IP must be stored and inventoried and the 
inventories must be carefully and accurately documented according to applicable state, 
federal and local regulations, ICH GCP, and study procedures. 
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Specific instructions for storage of study drug for subjects who qualify for self 
administration are provided in the Subject Self-Administration Training Materials. 
 
Section 9.4.4/Directions 
for Administration 
Doses will be administered SC and the favorable dose will be determined for each subject 
by adjusting the dose level, dose frequency, or both, as agreed by the PI and the Study 
Medical Officer, based upon the subject’s response to doses. Dosing is up to a maximum 
dose per week of 5.02 mg/kg.  
Information for subjects who are participating in the Substudy and re-start rAvPAL-PEG 
dosing is provided in Section 9.1. Information for dosing of subjects who enroll into this 
study after completing Study PAL-004 is provided in Section 9.1. Instructions for subjects 
who re-start rAvPAL-PEG dosing due to unplanned missed doses are provided in 
Section 9.4.10.  
Instructions for administration of study drug for subjects who qualify for self administration 
are provided in the Subject Self-Administration Training Materials. 
Every effort should be made to adhere to the study drug administration regimen. If a subject 
misses more than 2 scheduled doses of study drug, both dose level and dose frequency 
maywill need to be re-evaluated (refer to Section 9.4.10). 
 
2, 10, 27 
Section 9.4.5/Method of 
Assigning Subjects to 
Treatment Groups 
Subjects will retain the same subject number used in PAL-002 or PAL-004. 
 
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Section 9.4.6/Selection of 
Doses Used in the Study 
This Phase 2 study aims to evaluate the efficacy, safety, tolerability, and PK parameters of 
multiple doses of rAvPAL-PEG after long-term administration in subjects with PKU. 
A dose that produces a reduction in blood Phe concentrations to 6120-600 μmol/L will be 
determined for each subject based on preliminary safety, antibody, and efficacy data from 
this ongoing study and the ongoing study, PAL-002, to date (JAN2011).  
The doses for this study are based upon the results of nonclinical studies and PAL 001. The 
no observable adverse effect level (NOAELs) from nonclinical studies in rats and monkeys 
represents a greater than 100 fold safety factor over the starting dose administered in 
PAL 002 (0.001 mg/kg). 
 
3 
Section 9.4.6.1/Selection 
of Timing of Dose for 
Each Subject 
Study drug will be administered in the morning by clinic staff or other qualified and trained 
study personnel. 
Subjects may self administer study drug at home if approved by the Sponsor’s Medical 
Officer and if adequate training is provided (refer to Section 9.4). 
 
19 
Section 9.4.8/Prior and 
Concomitant Medications 
Use of any investigational product (with the exception of rAvPAL-PEG used in PAL-002 or 
PAL-004) or investigational medical device within 30 days before Screening, or 
requirement for any investigational agent prior to completion of all scheduled study 
assessments, is prohibited. 
Use or planned use of any injectable drugs containing PEG (other than rAvPAL-PEG), 
including Depo-Provera, is prohibited within 6 months prior to Screening and during study 
participation. A list of PEG-containing injectable drugs is provided in the study reference 
materials. Subjects who have had a prior local skin reaction to rAvPAL-PEG or a 
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PEG-containing product will be premedicated with acetaminophen and/or antihistamines 
(refer to Section 9.1.1). If the local skin reaction worsens with a repeat injection (as 
determined by the Investigator in consultation with the Study Medical Officer) even with 
premedication prior to study drug dosing, the subject must be withdrawn from the study and 
complete an Early Termination Visit. 
Subjects who have had a prior systemic reaction to rAvPAL-PEG or a PEG-containing 
product are excluded frommay participateion in this study (refer to Section 9.1.1).  
 
Section 9.4.10/Dose 
Interruption and Missed 
Doses 
Information for subjects who are participating in the Substudy and re-start rAvPAL-PEG 
dosing is provided in Section 9.1. Information for dosing of subjects who enroll into this 
study after completing Study PAL-002 or Study PAL-004 is provided in Section 9.1.  
During this long-term extension study, interruption of rAvPAL-PEG dosing may occur per 
subject decision or per the Investigator in consultation with the Sponsor’s Medical Officer. 
Subjects who miss more than 2 consecutive weekly doses (weekly dosing schedule) or 3 
consecutive daily doses (daily dosing schedule) for whatever reason may continue 
participation in this study. After a dosing interruption, rAvPAL-PEG administration should 
be re-started at the same dose level and dosing frequency that was administered prior to the 
dosing interruption. The first dose of rAvPAL-PEG following a dose interruption should be 
administered in a clinic setting, and the subject must be observed for 30-60 minutes 
following administration due to restarting dosing. A follow-up telephone call will be made 
to the subject to monitor subject safety 24 hours following the return to dosing. Subjects 
should continue to perform the study assessments as outlined in the Schedule of Events 
(refer to Table 2.1.1, Table 2.1.2, Table 2.1.3, and Table 2.1.4) during any dosing 
interruption.  
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Subjects who miss rAvPAL-PEG dosing due to poor compliance may be discontinued from 
further study treatment per discretion of the Sponsor or Investigator (refer to Section 9.3.3).  
 
Section 9.5/Investigational 
Product Accountability 
The PI or designee is responsible for maintaining accurate records (including dates and 
quantities) of IP received, subjects to whom IP is dispensed (subject-by-subject dose 
specific accounting), IP returned, and IP lost or accidentally or deliberately destroyed. The 
PI or designee must retain all unused or expired study supplies until the study monitor (on-
site CRA) has confirmed the accountability data. 
27 
Section 9.5.1/Return and 
Disposition of Clinical 
Supplies 
Subjects who qualify for self administration of study drug will be provided with instructions 
for returning used and unused study drug and the proper disposal of any study drug 
materials (refer to the Subject Self-Administration Training Materials). 
 
10 
Section 9.6/Dietary or 
Other Protocol Restrictions 
Subjects will be instructed that diet should not be altered during the course of the study. 
except as necessary for safety. If a subject’s blood Phe concentration is  < 120 µmol/L, 
the subject’s diet will be adjusted to maintain blood Phe concentrations of 120 600 µmol/L. 
Changes to diet will be made per the discretion of the Investigator in consultation with the 
Sponsor’s Medical Officer. Any decision to modify subject diet must be made per the 
Investigator in consultation with the Sponsor’s Medical Officer and must be performed 
under the supervision of the Investigaor in consultation with the Sponsor’s Medical Officer. 
A 3-day dietary record will be completed by subjects and will be brought to clinic visits for 
review with clinic staff. It is preferable that subjects complete the 3-day record immediately 
prior to their next dose of study drug. The dietary record will be maintained with the study 
source documents. Information regarding a subject diet diary is provided in Section 9.7.4. 
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Section 9.7.1.5/Chest X-
Ray 
A chest X-ray will be performed at the Screening, Month 12, and Final Follow-Up (or Early 
Termination) visits to assess gross pulmonary health.  
 
24 
Section 9.7.2.1/Blood 
Phenylalanine 
Concentrations  
Blood samples for Phe concentration measurements will be drawn in the morning, at least 
2.5 hours after a meal, on the days and time points indicated in the Schedule of Events 
(Table 2.1.1, Table 2.1.2, Table 2.1.3, and Table 2.1.4). 
In addition, after each administration of study drug, the subject will have a blood Phe 
measurement by fingerstick as outlined in Table 2.1.1, Table 2.1.2, Table 2.1.3, and Table 
2.1.4. This may be done by the subject at home. Subjects who have their dose frequency 
increased will have additional Phe assessments performed as outlined in Table 2.1.3:   and 
Table 2.1.4:  . 
 
19, 27 
Section 
9.7.3/Pharmacokinetic 
Variables 
Steady state PK (predose samples) of rAvPAL PEG will be evaluated in PKU subjects after 
the subject has achieved and maintained target blood Phe concentration (120 600 μmol/L) 
for a minimum of 2 weeks (to allow assessment of blood Phe concentrations) and no further 
dose modification is planned. Once this target has been achieved, PK samples will be 
collected predose on the same day each week for 3 consecutive weeks. 
Subjects enrolled in the Substudy will have additional PK sampling performed prior to the 
planned dosing interruption and upon re-introduction of rAvPAL-PEG. For subjects 
participating in the Substudy, PK sampling will be performed as follows: 
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• 
When dosing is stopped, PK sampling will be performed prior to the final dose and 
then postdose at 8 hours, 12 hours, 16, hours, 24 hours, 48, hours, 72 hours, 96 
hours, 144 hours, 168 hours, and 216 hours. 
• 
When dosing is re-started, PK sampling will be performed predose and then 
postdose at 24 hours, 48 hours, 72 hours, 120 hours, and 168 hours. 
 
Subjects who have increased their dose frequency to twice weekly or daily will have 
addition PK assessments performed for 5 weeks after the change in dose regimen (refer to 
Section 12.3.5 and Table 2.1.3:   and Table 2.1.4:  ). BioMarin will perform the analysis. 
Section 9.7.4/Exploratory 
Efficacy Variable 
Diet will be assessed for its role in blood Phe reduction relative to rAvPAL-PEG dosing 
using a 3-day diet diary, which will be given to subjects to complete at home. Subjects will 
bring the completed diary with them to clinic visits. Subjects will be instructed to record all 
food, beverages, special low-protein foods, and medical foods consumed for 3 consecutive 
days each week. If changes in diet are noted per the information on the diet diary, the 
subject will be instructed to maintain their diet as reported at the beginning of the study or 
as otherwise instructed by the Investigator. 
 
5 
Section 9.7.5.2/Antibody 
Testing 
Immunogenicity will be assessed by determining antibodyimmune response and 
neutralizing activity with the following measurements: anti-PAL IgG, anti-PAL IgM, 
anti-PEG IgG, anti-PEG IgM, anti-rAvPAL-PEG IgE, and anti-rAvPAL-PEG neutralizing 
antibodies ( refer to Section 9.1.1.3.3).1) anti rAvPAL immunoglobulin G (IgG) antibodies, 
2) anti rAvPAL immunoglobulin M (IgM) antibodies, 3) anti PEG IgG antibodies, 
4) anti PEG IgM antibodies, 5) anti rAvPAL PEG immunoglobulin E (IgE) antibodies, and 
6) anti rAvPAL PEG Enzyme Activity Neutralizing antibodies (NAb), and 7) rAvPAL
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PEG antibody clearing complexes (if needed). Validated immunogenicity assays will be 
used per the time points indicated in the Schedule of Events (Table 2.1.1 and Table 2.1.2). 
BioMarin will perform the analysis except for anti rAvPAL PEG IgE antibodies, which will 
be assessed by a Contract Research Organization. 
 
Section 9.7.6/Clninical 
Laboratory Assessments 
All clinical laboratory result pages should be initialed and dated by an Investigator, along 
with a comment regarding whether or not any abnormal the result is clinically significant. 
Table 9.7.6.1: Clinical Laboratory Tests has been revised to include information for 
subjects who have a positive result from the urine pregnancy test. 
27 
Section 10.1/ Adverse 
Events 
According to the ICH definition, an AE (or adverse experience) is “any untoward medical 
occurrence in a patient or clinical investigation subject administered a pharmaceutical 
product, and that does not necessarily have a causal relationship with this treatment. An AE 
can therefore be any unfavorable and unintended sign (including an abnormal laboratory 
finding), symptom, or disease temporally associated with the use of a medicinal 
(investigational) product, whether or not considered related to the IP.” For this protocol, a 
reportable adverse event (AE) is any untoward medical occurrence (e.g., sign, symptom, 
illness, disease or injury) in a patient administered the study-drug or other protocol-imposed 
intervention, regardless of attribution. This includes the following: 
• 
AEs not previously observed in the subject that emerge during the course of the 
study. 
• 
Pre-existing medical conditions judged by the Investigator to have worsened in 
severity or frequency or changed in character during the study. 
• 
Complications that occur as a result of non-drug protocol-imposed interventions 
(eg, AEs related to screening procedures, medication washout, or no-treatment run-
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in). 
An adverse drug reaction (ADR) is described by the ICH as “all noxious and unintended 
responses to a medicinal product related to any dose.” This means that a causal relationship 
between a medicinal product and an AE is at least a reasonable possibility, ie, the 
relationship cannot be ruled outAn adverse drug reaction is any AE for which there is a 
reasonable possibility that the study drug caused the AE. “Reasonable possibility” means 
there is evidence to suggest a causal relationship between the study-drug and the AE. 
An AE may include intercurrent illnesses or injuries that represent an exacerbation (increase 
in frequency, severity, or specificity) of pre existing conditions (eg, worsening of asthma). 
Whenever possible, it is preferable to record a diagnosis as the AE term rather than a series 
of terms relating to a diagnosis. 
The reporting period for non serious AEs is the period from the first administration of study 
drug through the final F/U Visit or at the ETV. If a non serious AE remains unresolved at 
the conclusion of the study, the PI and medical monitor will make a joint clinical 
assessment as to whether continued follow up of the AE is warranted, and the results of this 
assessment must be documented. Resolution is defined as the return to baseline status or 
stabilization of the condition with the expectation that it will remain chronic. 
The study period during which all non-serious AEs and SAEs will be reported begins after 
informed consent is obtained and the first adminstration of study drug  and continues until 
4 weeks following the last administration of study drug or the last visit of the treatment 
period (refer to Section 12). After informed consent but prior to initiation of study 
treatment, only SAEs associated with any protocol-imposed interventions will be reported. 
The criteria for determining, and the reporting of SAEs is provided inThe Investigator will 
assess AEs for severity, for relationship to IP, and as to whether the event meets one or 
more of the definitions of a serious adverse event (SAE; refer to Section 10.2). 
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The Investigator should follow all unresolved AEs until the events are resolved or 
stabilized, the subject is lost to follow-up, or it has been determined that the study treatment 
or study participation is not the cause of the AE. Resolution of AEs (with dates) should be 
documented on the appropriate CRF page(s) and in the subject’s medical record. 
The Investigator responsible for the care of the patient or qualified designee will assess AEs 
for severity, relationship to study-drug, and seriousness (see Section 10.2 for SAE 
definition). Severity (as in mild, moderate or severe headache) is not equivalent to 
seriousness, which is based on patient/event outcome or action criteria usually associated 
with events that pose a threat to a patient’s life or functioning. Seriousness (not severity) 
serves as a guide for defining regulatory reporting obligations. 
The Investigator will determine the severity of each AE using the National Cancer Institute 
(NCI) Common Terminology Criteria for Adverse Events (CTCAE) v4. Adverse events that 
do not have a corresponding CTCAE term will be assessed according to the general 
guidelines for grading used in the CTCAE v4 as stated below.and will record it on the 
source documents and AE CRF, using the CTCAE v 3 grades defined below. Events that 
are CTCAE grades 4 and 5 are serious events and require completion of both an SAE form 
and AE eCRF. 
Grade 
Description 
1 
Mild: asymptomatic or mild symptoms; clinical or 
diagnostic observations only; intervention not 
indicated 
2 
Moderate: minimal, local or noninvasive 
intervention indicated; limiting age-appropriate 
instrumental activities of daily living (ADL)a 
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3 
Severe or medically significant but not immediately 
life-threatening: hospitalization or prolongation of 
hospitalization indicated; disabling; limiting self 
care activities of daily living (ADL) 
4 
Life threatening or debilitating: consequences; 
urgent intervention indicatedb 
5 
Death related to AE 
Grade 4 and 5 AEs should always be reported as SAEs. 
a Instrumental ADL refer to the following examples: preparing meals, shopping for 
groceries or clothes, using the telephone, managing money. 
b Self care ADL refer to the following examples: bathing, dressing and undressing, feeding 
oneself, using the toilet, taking medications, not bedridden. 
 
The term “severe” is often used to describe the intensity (severity) of a specific event (as in 
mild, moderate, or severe myocardial infarction); the event itself, however, may be of 
relatively minor medical significance (such as severe headache). This is not the same as 
“serious,” which is based on subject/event outcome or action criteria usually associated 
with events that pose a threat to a subject’s life or functioning. Seriousness (not severity) 
serves as a guide for defining regulatory reporting obligations. 
The Investigator will determine the relationship of an AE to the IPstudy drug and will 
record it on the source documents and AE CRF, using the categories defined below. 
 
Section 10.2/Serious 
Adverse Events 
A serious adverse event (SAE) is any untoward medical occurrence that at any dose meets 1 
or more of the following criteria: 
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• 
Is fatal. 
• 
Is life threatening. 
Note: Life-threatening refers to an event that places the patient at immediate risk of 
death. This definition does not include a reaction that, had it occurred in a more 
severe form, might have caused death. 
• 
Requires or prolongs inpatient hospitalization. 
• 
Results in persistent or significant disability or incapacity. 
• 
Is a congenital anomaly or birth defect in the child or fetus of a patient exposed to 
IP prior to conception or during pregnancy. 
• 
Is an important medical event or reaction. 
A SAE is defined as any AE that: 
• 
Results in death. 
• 
Is life threatening, that is, places the subject at immediate risk of death from the 
event as it occurred. This definition does not include a reaction that, had it occurred 
in a more severe form, might have caused death. 
• 
Requires in patient hospitalization or prolongation of an existing in patient 
hospitalization. Admission of a subject to the hospital as an in patient as a result of 
an AE, even if the subject is released on the same day, qualifies as hospitalization. 
• 
Results in persistent or significant disability or incapacity. An event qualifies as 
resulting in a persistent or significant disability or incapacity if it involves a 
substantial disruption of the subject’s ability to carry out usual life functions. 
This definition is not intended to include experiences of relatively minor or 
temporary medical significance. 
• 
Is a congenital anomaly or birth defect, that is, an AE that occurs in the child or 
fetus of a subject exposed to IP prior to conception or during pregnancy. 
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• 
Is an important medical event that does not meet any of the above criteria, but may 
jeopardize the subject or require medical or surgical intervention to prevent one of 
the outcomes listed above. Examples of such events are intensive treatment in the 
emergency room, allergic bronchospasm, blood dyscrasias or convulsions that do 
not result in hospitalization; or development of drug dependency or drug abuse. 
More than one of the above criteria may apply to any specific event. 
The reporting period for SAEs begins after informed consent is obtained, and continues 
until 4 weeks following the last administration of study drug or End of Treatment Visit.The 
reporting period for SAEs begins earlier than non serious AEs and is the period from the 
time of signing of the ICF through 4 weeks after the last dose or at the ETV. SAEs reported 
to the Investigator outside of this reporting period will be reported to BioMarin if, in good 
medical judgment, the event has any bearing on the study data. SAEs must be followed by 
the Investigator until resolution, even if this extends beyond the study reporting period. 
Resolution of an SAE is defined as the return to baseline status or stabilization of the 
condition with the expectation that it will remain chronic. 
Any SAE, whether or not considered related to study drug, will be reported immediately 
(within 24 hours) to BioMarin Pharmacovigilance by fax using the study specific 
SAE Report Form. In addition to the outcome of the SAE, any medication or other 
therapeutic measures used to treat the event will be recorded on the appropriate CRF 
page(s). Investigators should not wait to collect additional information that fully documents 
the event before notifying BioMarin Pharmacovigilance of an SAE. BioMarin may be 
required to report certain SAEs to regulatory authorities within 7 calendar days of being 
notified about the event; therefore, it is important that Investigators submit additional 
information requested by BioMarin as soon as it becomes available. All SAEs, whether or 
not considered related to study drug, must be reported within 24 hours of the site becoming 
aware of the event by faxing the study-specific SAE Report Form to BioMarin 
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Pharmacovigilance (BPV). ). Each SAE must also be reported in the CRF Investigators 
should not wait to collect information that fully documents the event before notifying BPV 
of a SAE. BioMarin may be required to report certain SAEs to regulatory authorities within 
7 calendar days of being notified about the event; therefore, it is important that Investigators 
submit any information requested by BioMarin as soon as it becomes available. 
The Investigator should follow all unresolved SAEs until the events are resolved or 
stabilized, the patient is lost to follow-up, or it has been determined that the study treatment 
or participation is not the cause of the AE. Resolution of AEs (with dates) should be 
documented in the CRF and in the patient’s medical record. 
For some SAEs, the Sponsor may follow up by telephone, fax, electronic mail, and/or a 
monitoring visit to obtain additional case details deemed necessary to appropriately 
evaluate the SAE report (e.g., hospital discharge summary, consultant report, or autopsy 
report). 
At the last scheduled visit, the Investigator should instruct each subject to report any 
subsequent SAEs that the subject’s personal physician(s) believes might be related to prior 
study treatment. 
The investigator should notify the study Sponsor of any death or SAE occurring at any time 
after a subject has discontinued or terminated study participation if felt to be related to prior 
study treatment. The Sponsor should also be notified if the Investigator should become 
aware of the development of cancer or of a congenital anomaly in a subsequently conceived 
offspring of a subject that participated in this study. 
 
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Section 10.3/Pregnancy 
Pregnancy in a subject or partner should be reported immediately (within 24 hours of the 
site becoming aware of the pregnancy) to BioMarin Pharmacovigilance by fax using the 
Pregnancy Form in the study reference materials. In addition, pregnancy in a subject is also 
reported on the End of Study CRF. The Investigator must make every effort to follow the 
subject through resolution of the pregnancy (delivery or termination) and to report the 
resolution on the Pregnancy Follow-up Form in the study reference materials. In the event 
of pregnancy in the partner of a study subject, the Investigator should make every 
reasonable attempt to obtain the woman’s consent for release of protected health 
information. 
15 
Section 10.4/Urgent Safety 
Measures 
The regulations governing clinical trials state that the sponsor and Investigator are required 
to take appropriate urgent safety measures to protect subjects against any immediate 
hazards that may affect the safety of subjects, and that the appropriate regulatory bodies 
should be notified according to their respective regulations. According to the European 
Union (EU) Clinical Trial Directive 2001/20/EC, “…in the light of the circumstances, 
notably the occurrence of any new event relating to the conduct of the trial or the 
development of the investigational medicinal product where that new event is likely to 
affect the safety of the subjects, the sponsor and the Investigator shall take appropriate 
urgent safety measures to protect the subjects against any immediate hazard. The sponsor 
shall forthwith inform the competent authorities of those new events and the measures taken 
and shall ensure that the IRB/EC/REB is notified at the same time.” The reporting period 
for these events which may require the implementation of urgent safety measures is the 
period from the time of signing of the ICF through the completion of the last study visit or 
at the ETV. Investigators are required to report any events which may require the 
implementation of urgent safety measures to BioMarin with 24 hours. 
Examples of situations that may require urgent safety measures include discovery of the 
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following: 
• 
Immediate need to revise the IP administration (ie, modified dose amount or 
frequency not defined in protocol). 
• 
Lack of study scientific value, or detrimental study conduct or management. 
• 
Discovery that the quality or safety of the IP does not meet established safety 
requirements. 
 
 
Section 11.2/Diet Diary 
A 3-day diet diary will be issued to subjects for completion and will be brought to each 
clinic visit for review with the clinical study staff. Additional information regarding the diet 
diary is provided in Section 7.3, and information regarding administration of the diary is 
provided in Section 9.7.4. Additional information about diet is provided in Section 9.1 and 
Section 9.6. 
 
5 
Section 12.2/Screening 
Visit 
• 
Chest X-ray 
For subjects who participated in PAL-002 or PAL-004, these assessments may be the same 
as those used for the Week 16 Visit of PAL-002 or the Week 16 visit of PAL-004, if they 
occur within 28 days from Day 1. 
 
24, 26 
Section 12.3/Treatment 
Period 
During the Treatment Period, additional visits may occur if deemed necessary to monitor 
AEs or blood Phe concentrations. All study activities will occur on the first day of each 
week unless otherwise noted. On days that a dose is given, assessments will be done 
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predose unless otherwise specified. Subjects must have AEs and concomitant medications 
assessed and an injection-site inspection performed whenever dose is administered even if 
the administration does not coincide with a scheduled clinic visit.   
If the dose is modified by increasing dose level, additional blood Phe concentration testing 
should be done on the third daydaily for 3 days following dose adjustment. If dose is 
modified by increasing either dose frequency or dose level, additional blood Phe 
concentration testing should be done prior to each dose for the first 2 weeks following dose 
adjustment. 
 
Section 12.3.1/Day 1 
(Week 1) 
• 
3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the next dose of study drug.) 
• 
Predose PK sample 
• 
Predose bBlood Phe and plasma tyrosine concentration 
• 
Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, and anti-rAvPAL-PEG neutralizing antibodies) (anti PAL IgG, 
anti PAL IgM, anti PEG IgG, anti PEG IgM, anti rAvPAL PEG neutralizing 
antibody, and anti rAvPAL PEG IgE) 
• 
Administer study drug (study drug may be administered on additional days during 
the week as determined by the Investigator, in agreement with the Study Medical 
Officer) 
o For subjects enrolling into this study from Study PAL-004, first dose of 
rAvPAl-pEG must be given in the clinic setting and a telephone follow-
up with the subject must be performed 24 hours later to assess safety 
issues. 
 
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Section 12.3.2/Weekly 
Visits 
Weekly visits do not require an in-clinic visit if conducted by a home healthcare 
professional. However, dose modifications must be peformed in the clinic. Subjects must 
have AEs and concomitant medications assessed and an injection-site inspection performed 
whenever dose is administered even if the administration does not coincide with a 
scheduled clinic visit.  
• 
Predose PK sample  
o For subjects participating in the Substudy, refer to Section 12.3.3. 
o 
Per investigator discretion, once a subject is on a stable dosing regimen for at 
least 3 months (as evidenced by blood Phe levels of 120 600 µmol/L for the 
majority of the 3 months), the predose PK assessment may be skipped at the 
weekly visits and performed at the monthly visits for the first year then 2 3 
months thereafter. Weekly sampling should resume if the subject’s dosing 
regimen changes. 
• 
Predose bBlood Phe and plasma tyrosine concentration 
o 
Per investigator discretion, once a subject is on a stable dosing regimen for at 
least 3 months (as evidenced by blood Phe levels of 120 600 µmol/L for the 
majority of the 3 months), the predose plasma Phe and tyrosine assessments 
may be skipped at the weekly visits and performed at the monthly visits for 
the first year then 2 3 months thereafter. The weekly plasma Phe assessment 
may be replaced with a Phe fingerstick test. Weekly testing should resume if 
the subject’s dosing regimen changes. 
• 
Administer study drug (study drug may be administered on additional days during 
the week as determined by the Investigator, in agreement with the Study Medical 
Officer) 
o For subjects participating in the Substudy, refer to Section 12.3.3. 
 
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Section 12.3.3/Substudy 
Visits (Weekly) 
The following study activities will be performed on Day 1 of the Substudy (ie, final dose 
prior to interruption), Day 8, Day 15, Day 22, and Day 29 (ie, restart administration of 
study drug) for subjects participating in the Substudy: 
• 
Physical examination 
• 
Vital signs, including weight 
• 
Clinical laboratory tests 
• 
Sedimentation rate 
• 
Urine pregnancy test, if applicable (A serum pregnancy test will be performed in 
the event of any positive or equivocal urine pregnancy test result.) 
• 
Injection-site inspection (predose; postdose on Day 1; during weekly visit on Day 
8, 15, 22; and postdose on Day 29) 
• 
Assessment of AEs  
• 
Concomitant medications 
• 
Diet query 
• 
3-day diet diary  
• 
Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, and anti-rAvPAL-PEG neutralizing antibodies,) 
• 
Blood Phe and plasma tyrosine concentration 
o When dosing is stopped, sampling for blood Phe assessment only will 
be performed prior to the final dose and then postdose at 8 hours, 12 
hours, 16 hours, 24 hours, 48, hours, 72 hours, 96 hours, 144 hours, 
168 hours, and 216 hours. 
o When dosing is re-started, sampling for blood Phe assessment only will 
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be performed predose and then postdose at 24 hours, 48 hours, 72 
hours, 120 hours, and 168 hours. 
• 
PK sample  
o For subjects participating in the Substudy, additional PK sampling will 
be performed upon the final dose prior to the planned dosing 
interruption and upon re-introduction of rAvPAL-PEG. Refer to 
Section 9.7.3 
• 
Administer study drug (Day 29 only) 
o For subjects participating in the Substudy, administration of rAvPAL-
PEG will not be performed for approximately 4 consecutive weeks 
regardless of their dosing regimen (dose level and frequency). After 
approximately 4 weeks of no dosing, rAvPAL-PEG administration will 
be re-started at the same dose level and dosing frequency that was 
administered prior to the dosing interruption. The first dose of re-
administration must be given in the clinic setting, and a telephone 
follow-up with the subject must be performed 24 hours later to assess 
safety issues. 
 
Section 12.3.4/Monthly 
Visits (Week 4, 8, 12, etc) 
Subjects must have AEs and concomitant medications assessed and an injection-site 
inspection performed whenever dose is administered even if the administration does not 
coincide with a scheduled clinic visit.  
Monthly visits consist of all weekly activities and include additional activities and must be 
performed in the clinic. The following study activities will be performed at the monthly 
visits beginning with Week 4: 
• 
Predose PK sample (subjects who are on a stable dosing regimen for  ≥ 3 months 
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only) 
o For subjects participating in the Substudy, refer to Section 12.3.3. 
o 
Per investigator discretion, once a subject is on a stable dosing regimen for at 
least 3 months (as evidenced by blood Phe levels of 120 600 µmol/L for the 
majority of the 3 months), the predose PK assessment may be skipped at the 
weekly visits and performed at the monthly visits for the first year then 2 3 
months thereafter. Weekly sampling should resume if the subject’s dosing 
regimen changes.   
• 
Predose bBlood Phe and plasma tyrosine concentration 
o 
Per investigator discretion, once a subject is on a stable dosing regimen for at 
least 3 months (as evidenced by blood Phe levels of 120 600 µmol/L for the 
majority of the 3 months), the predose plasma Phe and tyrosine assessments 
may be skipped at the weekly visits and performed at the monthly visits for 
the first year then 2 3 months thereafter. The weekly plasma Phe assessment 
may be replaced with a Phe fingerstick test. Weekly testing should resume if 
the subject’s dosing regimen changes. 
• 
Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, and anti-rAvPAL-PEG neutralizing antibodies) (anti PAL IgG, 
anti PAL IgM, anti PEG IgG, anti PEG IgM, anti rAvPAL PEG neutralizing 
antibody, and anti rAvPAL PEG IgE) 
• 
Administer study drug (study drug may be administered on additional days during 
the week as determined by the Investigator, in agreement with the Study Medical 
Officer) 
o For subjects participating in the Substudy, refer to Section 12.3.3. 
 
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Section 12.3.5/Quarterly 
Visits (Week 12, 24, 36, 
etc) 
Subjects must have AEs and concomitant medications assessed and an injection-site 
inspection performed whenever dose is administered even if the administration does not 
coincide with a scheduled clinic visit.  
• 
Predose PK sample (subjects who are on a stable dosing regimen for  ≥ 3 months 
only) 
o For subjects participating in the Substudy, refer to Section 12.3.3. 
o 
Per investigator discretion, once a subject is on a stable dosing regimen for at 
least 3 months (as evidenced by blood Phe levels of 120 600 µmol/L for the 
majority of the 3 months), the predose PK assessment may be skipped at the 
weekly visits and performed at the monthly visits for the first year then 2 3 
months thereafter. Weekly sampling should resume if the subject’s dosing 
regimen changes.   
• 
Predose bBlood Phe and plasma tyrosine concentration 
• 
Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, and anti-rAvPAL-PEG neutralizing antibodies) (anti PAL IgG, 
anti PAL IgM, anti PEG IgG, anti PEG IgM, anti rAvPAL PEG neutralizing 
antibody, and anti rAvPAL PEG IgE) 
• 
Administer study drug (study drug may be administered on additional days during 
the week as determined by the Investigator, in agreement with the Study Medical 
Officer) 
o For subjects participating in the Substudy, refer to Section 12.3.3. 
 
26 
Section 12.3.65/Interim 
Dosing Visit 
• 
PK sample  
o 
Subjects increase their dose frequency to 2x/week will have an additional 
predose PK sample obtained prior to administration of the first 4 doses (ie, for 
2 weeks after the dose frequency increase). For the remaining 3 weeks after 
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the dose frequency increase, a PK sample will be obtained weekly prior to the 
first dose. Refer to Table 2.1.3:   for the Interim Dosing Visit schedule. 
o 
Subjects who have their dose frequency increased to daily will have additional 
PK samples obtained every day for the first week: 12 hours after the first daily 
dose and predose every day for the rest of the week. After the first week of 
daily dosing, subjects will have weekly PK samples obtained for 4 additional 
weeks. Refer to Table 2.1.4:   for the Interim Dosing Visit schedule. 
 
Section 
12.3.7/Unscheduled 
Hypersensitivity Reaction 
Visit 
Subjects who have a systemic reaction, including a generalized skin reaction, or a large 
local skin reaction that is not contiguous to the injection site after rAvPAL-PEG 
administration (refer to Section 9.1.1) will have assessments performed immediately 
following (within 48 hours) the reaction. Subjects who have other systemic symptoms or a 
large local skin reaction that is not contiguous to the injection site (refer to Section 9.1.1) 
may have these assessments performed per investigator discretion. 
• 
CRP, CH50, C1, C3, and C4 
• 
Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG IgE, and anti-rAvPAL-PEG neutralizing 
antibodies) (anti PAL IgG, anti PAL IgM, anti PEG IgG, anti PEG IgM, anti
rAvPAL PEG neutralizing antibody, and anti rAvPAL PEG IgE) 
• 
Serum tryptase level 
o 
Perform immediately after reaction if possible. 
o 
Assessment is optional for subjects who have a generalized skin reaction per 
investigator discretion. 
• 
Skin biopsy (optional; affected and not affected area; to be performed within 1 
week of reaction) 
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Following completion of the Unscheduled Hypersensitivity Reaction Visit assessments, the 
subject may resume treatment with study drug per the discretion of the Investigator in 
consultation with the Sponsor’s Medical Officer. Subjects who have had an IgE-mediated 
reaction must be discontinued from further study drug administration. Subjects who do not 
have an IgE-mediated reaction may resume study drug administration under close 
monitoring; subjects must be premedicated orally with acetaminophen and/or 
antihistamines 1 hour prior to study drug dosing for the remainder of the study (refer to 
Section 9.1.5.3.3). 
Subjects should then return to the clinic 4 weeks after their last dose of rAvPAL PEG 
for the Early Termination Visit assessments (refer to Section 12.4). 
Section 12.4/Early 
Termination Visit 
The Early Termination Visit (ETV) will occur 4 weeks after the final dose of study drug. 
Subjects who terminate from study treatment early should continue to perform the 
remaining visit assessments in Section 12.3 as applicable until study completion. 
Subjects who complete an Unscheduled Hypersensitivity Reaction Visit (refer to 
Section 12.3.6) will be terminated from the study. Subjects will then return 4 weeks after 
the last dose of study drug for the Early Termination Visit. 
• 
3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the Early Termination Visit.) 
• 
Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibodies) (anti PAL IgG, 
anti PAL IgM, anti PEG IgG, anti PEG IgM, anti rAvPAL PEG neutralizing 
antibody, and anti rAvPAL PEG IgE) 
 
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Section 12.5/Final Follow-
up Visit 
• 
3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the Final Follow-up Visit.) 
• 
Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibodies) (anti PAL IgG, 
anti PAL IgM, anti PEG IgG, anti PEG IgM, anti rAvPAL PEG neutralizing 
antibody, and anti rAvPAL PEG IgE) 
 
26 
Section 14.2/Safety 
Analysis 
All AEs will be coded using the Medical Dictionary for Regulatory Activities (MedDRA). 
The incidence of AEs will be summarized by system organ class, preferred term, 
relationship to study drug, and severity. A by–subject listing will be provided for those 
subjects who experience a serious AE (SAE), including death, or experience an AE 
associated with early withdrawal from the study or study drug.Safety will be evaluated on 
the incidence of AEs, including serious AEs (SAEs), and clinically significant changes in 
vital signs and laboratory test results. 
Clinical laboratory data will be summarized by the type of laboratory test. Frequency and 
percentage of subjects who experience abnormal (ie, outside of reference range) and/or 
clinically significant abnormalities after study drug administration will be presented for 
each clinical laboratory test. For each clinical laboratory test, descriptive statistics will be 
provided for baseline and all subsequent post-treatment visits. Changes from baseline to the 
post-treatment visits will also be provided. Descriptive statistics, including clinically 
significant changes from baseine, of vital signs, ECG results, and X-ray results will also be 
provided.The verbatim terms reported on CRFs to identify AEs will be coded using 
MedDRA. Treatment emergent AEs will be summarized by system organ class, preferred 
term, relationship to study drug, and severity. Changes from baseline in vital signs and 
laboratory test results will be summarized with descriptive statistics. 
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Section 
14.3/Pharmacokinetic 
Analysis 
Data from all subjects who complete at least 2 weeks of the study will be included in the PK 
analysis. 
Steady state PK (predose samples) of rAvPAL PEG will be evaluated in PKU subjects after 
the subject has achieved and maintained target blood Phe concentrations (12060 600 
μmol/L) for a minimum of 2 weeks and no further dose modification is planned. 
Subjects who complete the Substudy will have the following PK parameters assessed: area 
under the plasma concentration-time curve (AUC), time to maximum plasma concentration 
(Tmax), maximum plasma concentration (Cmax), half life (t1/2), and clearance (CL/F). 
Should data become available from PAL-002 or PAL-004 that indicate study drug 
accumulation should also be measured, additional blood draws may be added for PK 
analysis as needed per the discretion of the Investigator in consultation with the Sponsor’s 
Medical Officerbut not to exceed 3x/week. 
 
1 
Section 14.4/ Efficacy 
Analysis 
Data from all subjects who receive any amount of study drug and who have any 
post-treatment efficacy data will be included in the efficacy analysis. 
Blood Phe concentration at each scheduled time point will be summarized using descriptive 
statistics (mean, SD, median, minimum, and maximum). Change in blood Phe concentration 
from baseline to each scheduled time point and presence/absence of antibodies will also be 
summarized. In addition, the proportion of subjects who have maintained target Phe 
concentrations of 12060-600 µmol/L will be summarized by each scheduled time point. 
The relationship of dietary Phe intake (per information reported on the subject diet diary) 
1, 3, 5 
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and blood Phe concentration will also be explored. Subjects who received any amount of 
study drug with any post-treatment blood Phe concentration measurements and diet diary 
information will be included in this exploratory analysis. Information regarding this 
exploratory analysis will be provided in the Statistical Analyais Plan. 
For subjects who completed the Substudy, the effect of stopping and re-starting rAvPAL-
PEG dosing on safety, blood Phe level, and immune response will be explored. Information 
regarding the analysis will be provided in the Statistical Analyais Plan. 
 
Section 14.5/Determination 
of Sample Size 
Subjects who participated in PAL-002 or PAL-004 may be enrolled into this study. No 
formal sample size calculation was conducted for this study or the PAL-003 Substudy.   
 
1, 4 
Section 14.7/Interim 
Analyses 
At least one interim analysis may be performed by the sponsor during the study. Safety will 
be assessed throughout the study on an ongoing basis (refer to Section 15 for information 
regarding the DMC). 
 
27 
Section 20/References 
Lapis et al., Long-term correction of PKU in the Pahenu2 mouse by mutant and chemically 
modified forms of Phenylalanine Ammonium Lyase. The American Society of Human 
Genetics, 57th Annual Meeting, 2007 
27 
 
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BioMarin is a registered trademark of BioMarin Pharmaceutical Inc. 
CLINICAL STUDY PROTOCOL AMENDMENT SUMMARY 
Amendment: 4 
Date: June 7, 2012 
 
RATIONALE AND SUMMARY OF CHANGES 
The protocol for Study PAL-003 is being amended to make the following changes: 
1. Assessment of spot urine albumin/creatinine ratio has been added at study entry for 
newly enrolled subjects. In addition, all subjects will now have spot urine 
albumin/creatinine ratio assessed monthly after study entry. Complements (C3 and 
C4) will also be collected and assessed at study entry and every 3 months for all 
subjects; if complement levels are abnormal upon assessment, sampling will be 
performed monthly.   
Rationale for change:  The urine albumin/creatinine ratio and C3 and C4 tests have been 
added because they are measures of potential renal injury resulting from an immunologic 
reaction to rAvPAL-PEG. Several subjects currently being treated with rAvPAL-PEG have 
developed antibodies to rAvPAL-PEG and evidence of consumption of complement. While 
no subject in a rAvPAL-PEG study has had clinical laboratory evidence of renal injury as of 
May 2012, these tests have been added to increase detection of sensitivity to renal injury and 
to evaluate the potential for a clinically meaningful safety signal. 
2. 
Subjects who meet the criteria for blood Phe levels and rAvPAL-PEG dose will now 
have their blood Phe concentration collected monthly rather than weekly. 
Rationale for change:  Subjects will have their blood Phe concentration assessed monthly 
versus weekly if they have been on a stable dose of rAvPAL-PEG (ie, no dose change in the 
last 2 weeks) and have had a phenylalanine (Phe) level at or below target range 
(60-600 µmol/L) for 2 consecutive weeks, which is evidence that the dose-adjustment period 
has ended. For such subjects, assessment of blood Phe performed monthly is sufficient. 
However, if a subject’s blood Phe increases to  > 600 µmol/L or decreases to  ≤ 30 µmol/L for 
any of the monthly blood Phe draws, that subject should perform weekly blood Phe draws 
until the rAvPAL-PEG dose has been adjusted and the Phe level returns to within the 
protocol-defined target range for at least 2 weeks.  
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3. 
Information regarding hypersensitivity reactions and rAvPAL-PEG treatment, 
including how to treat hypersensitivity reactions, has been updated. 
Rationale for change:  As of May 2012, a total of 70 subjects have been administered 
rAvPAL-PEG in the Phase 1 (PAL-001) and Phase 2 (PAL-002 and -004) studies, including 
this extension study. With the information from these 70 subjects, there is a better 
understanding of the hypersensitivity reactions and rAvPAL-PEG treatment. Information 
regarding treatment with rAvPAL-PEG and subject care following a hypersensitivity reaction 
has been modified based on this additional information.  
4. 
A fixed dose of rAvPAL-PEG will be administered in this study. Additionally, a 
higher concentration of rAvPAL-PEG (15 mg/ml vs. 10 mg/ml) will be administered. 
Subjects who have demonstrated efficacy (ie, Phe within target range 60-600 µmol/L) 
for at least two consecutive Phe assessments may convert their weight-based 
rAvPAL-PEG dose to a fixed dose and may also divide their weekly dose into a 
7-days-a-week dosing regimen. 
Rationale for change:  The Phase 3 rAvPAL-PEG program will be conducted using a 
rAvPAL-PEG dosing concentration of 15 mg/ml, a fixed dose, and a 7-days-a-week dosing 
regimen. This extension study is being amended to incorporate the planned Phase 3 dosing 
regimen and concentration. Fixed dosing will simplify the dosing regimen to enable greater 
convenience for administration amongst the PKU patient population, especially for patients 
with significant neurocognitive dysfunction. The fixed doses proposed in this study are based 
on an average subject weight of 80 kg (based on the subjects in previous rAvPAL-PEG 
studies).  Efficacy information regarding the fixed doses will be collected in this study and 
the Phase 2 study, 165-205. Subjects who are on a fixed-dose regimen will be monitored for 
safety per the safety plan outlined in the protocol. The 15 mg/ml rAvPAL-PEG formulation 
is more concentrated than the 10 mg/ml formulation, allowing for fewer injections per dose. 
It is hypothesized that hypersensitivity reactions could be related to maximum plasma 
concentration (Cmax); therefore, subjects who qualify for home or self administration may 
divide their weekly dose for administration up to 7 days per week.   
5. 
A pharmacokinetics (PK) substudy has been added to evaluate the steady-state PK of 
rAvPAL-PEG in a minimum of 6 subjects who have achieved and maintained target 
blood Phe for at least 2 consecutive weeks and for whom no further dose 
modifications are planned. A corresponding PK substudy objective has been added. 
Rationale for change:  Subjects who are being treated with an efficacious dose of 
rAvPAL-PEG (ie, have received the same rAvPAL-PEG dose for at least 2 consecutive 
weeks) and for whom no further dose modifications are planned will qualify for the PK substudy. 
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Single-dose PK data have been collected from the Phase 1 study, PAL-001; however, there is 
little multiple-dose PK data when a stable dosing regimen has been implemented. With the 
PK substudy, multiple-dose PK data will be collected for subjects who have already achieved 
and maintained Phe reduction to within the protocol-defined target range.    
6. 
The previous PK substudy that required stopping and restarting rAvPAL-PEG dosing 
has been removed. No subjects were enrolled into this PK substudy. 
Rationale for change:  The previous PK substudy was designed to examine the effect of 
rAvPAL-PEG dosing interruptions on safety, efficacy, PK, and immune response.  This 
substudy has been discontinued because it requires subjects to discontinue treatment with 
rAvPAL-PEG, which would halt any Phe reduction benefits that may have occurred with 
treatment. The corresponding substudy objectives have been removed.  Unscheduled dose 
interruptions may still occur due to adverse events per the Investigator and the Sponsor’s 
Medical Officer. 
7. 
Finger stick Phe assessments have been removed. 
Rationale for change:  The plasma Phe samples currently implemented in the study provide 
sufficient assessment of blood Phe levels without subjecting subjects to the additional and 
painful finger stick procedure. The site staff may perform assessments of Phe levels at the 
local laboratory if needed. 
8. 
Guidance for treating subjects who develop hypophenylalaninemia has been added. 
Rationale for change:  Although there is no evidence in the literature that low Phe is of 
clinical significance in adults, it is hypothesized that sustained low blood Phe is a clinical 
concern because Phe is an essential amino acid.  Guidelines for treating subjects whose 
serum Phe levels reach ≤ 30 μmol/L for a minimum of 1 month have now been included in 
the study. 
9. 
A blood draw has been removed for subjects who enroll into PAL-003 from a 
previous rAvPAL-PEG study. Subjects who have performed a blood draw upon 
completion of a previous rAvPAL-PEG study do not need to perform another blood 
draw at the Screening Visit of this study if the blood draw was performed within 
28 days. Safety and efficacy information are not expected to change in the 28 days 
from completion of a previous rAvPAL-PEG study and the start of this study. 
Rationale for change:  Currently, subjects in Studies PAL-002 and PAL-004 immediately 
enroll  into the PAL-003 extension study (ie, do not stop rAvPAL-PEG dosing).  The 
PAL-003 protocol required a blood draw to be performed as part of screening that was 
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similar to the end-of-study blood draw performed for Studies PAL-002 and PAL-004.  When 
subjects enroll over into Study PAL-003 within 28 days of completing a previous 
rAvPAL-PEG study, the screening blood draw is not needed. Safety and efficacy information 
is not expected to change in the 28 days from completion of a previous rAvPAL-PEG study 
and the start of this study.   
10. 
Information regarding the management of allergic reactions has been updated. 
Rationale for change:  Administration of oral or IV glucocorticoids has been added as a 
recommended treatment. 
11. 
The inclusion criteria have been modified to allow enrollment of subjects from a 
Phase 2 rAvPAL-PEG study. 
Rationale for change:  This change will allow enrollment of subjects who complete Study 
165-205.    
12. 
Assessment of urinalysis test results has been moved from the local laboratory to the 
central laboratory. 
Rationale for change:  This change will help standardize test results across sites.    
13. 
Subject weight will now be measured monthly rather than weekly. 
Rationale for change:  Because the study is moving from weight-based dosing to a fixed 
dosing regimen (see amendment item #5 above), there is no need to obtain weight on a 
weekly basis.    
14. 
Subject diet diaries will be assessed monthly rather than weekly. 
Rationale for change:  Weekly diet diary assessment provides no added benefit to safety or 
efficacy when compared with monthly diet diaries. Monthly diet diary assessments will 
provide sufficient safety and efficacy information while increasing feasibility of completion 
for sites and subjects. 
15. 
Information regarding clinical rAvPAL-PEG studies has been updated. 
Rationale for change:  Information regarding Studies PAL-002 and -004 have been updated, 
and information regarding Study 165-205 has been added. 
16. 
Administrative revisions have been made to improve clarity and consistency. 
Specific revisions to the text of each section of the protocol (since the protocol amendment 
finalized on 4 May 2011), including the Synopsis, are outlined in Section 24. 
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2 
SYNOPSIS 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
TITLE OF STUDY: 
Long-term Extension of a Phase 2, Open-Label Dose-Finding Study to Evaluate the Safety, Efficacy, 
and Tolerability of Multiple Subcutaneous Doses of rAvPAL-PEG in Subjects with PKU 
PROTOCOL NUMBER:  PAL-003 
STUDY SITES:  Approximately 20 centers in the United States 
PHASE OF DEVELOPMENT:  Phase 2 
STUDY RATIONALE: 
The need exists for a treatment that will help individuals with phenylketonuria (PKU) safely achieve 
lifelong, reliable control of blood phenylalanine (Phe) concentrations and improve functional 
outcomes. PEGylated recombinant Anabaena variabilis phenylalanine ammonia lyase (rAvPAL-PEG) 
is a potential substitute for the phenylalanine hydroxylase (PAH) enzyme, which is defective in 
individuals with PKU. rAvPAL-PEG may control blood Phe concentrations, which may have 
additional clinical benefits. This study is an extension of the rAvPAL-PEG Phase 2 studies PAL-002, 
PAL-004, and 165-205. Administration of rAvPAL-PEG will be continued to assess whether long-
term dosing of rAvPAL-PEG is safe and can maintain reduced blood Phe concentrations in PKU 
subjects. 
Blood Phe levels depend not only on the functional presence of the endogenous enzyme PAH but also 
on the dietary intake of Phe. It is important to understand the role of diet on blood Phe levels 
concurrent with the administration of rAvPAL-PEG treatment. Therefore, an exploratory objective has 
been added to this study to assess the relationship of diet, rAvPAL-PEG administration, and blood Phe 
level. Changes to subject diet are not allowed in this study unless per the Investigator in consultation 
with the Sponsor’s Medical Officer. Diet will be monitored using a diet diary. 
A pharmacokinetic (PK) substudy has been added to evaluate the steady-state PK of rAvPAL-PEG in 
a minimum of 6 subjects who have achieved and maintained target blood Phe for at least 2 consecutive 
weeks and for whom no further dose modifications are planned. Single-dose PK data has been 
collected in the Phase 1 study, PAL-001. However, there is little multiple-dose PK data or data for 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
when subjects have reached and maintained a stable dosing regimen.  With the PK substudy, multiple-
dose PK data will be collected for subjects who have already achieved Phe reduction to within the 
protocol-defined target range. 
OBJECTIVES: 
The primary objective of the study is: 
• 
To evaluate the effect of long-term administration of multiple doses of SC injections of 
rAvPAL-PEG on blood Phe concentrations in subjects with PKU. 
The secondary objectives of the study are: 
• 
To evaluate the safety and tolerability of long-term administration of subcutaneous (SC) 
injections of rAvPAL-PEG in subjects with PKU. 
• 
To evaluate the immune response to long-term administration of SC injections of 
rAvPAL-PEG in subjects with PKU. 
The exploratory objective of the study is as follows: 
• 
To evaluate the long-term relationship of diet and change in blood Phe concentration 
following administration with rAvPAL-PEG in subjects with PKU. 
The Substudy objectives are as follows: 
• 
To evaluate steady-state PK of rAvPAL-PEG in subjects who have achieved and maintained 
target blood Phe concentration and for whom no further dose modifications are planned. 
 
STUDY DESIGN AND PLAN: 
This is a long-term extension of rAvPAL-PEG Phase 2 studies in approximately 100 subjects with 
PKU. The doses are planned to be in the same range as those tested in PAL-002 and PAL-004 (starting 
at 0.001 through 5.0 mg/kg/week), provided no dose-limiting toxicity is observed in a previous 
rAvPAL-PEG study. 
Only subjects who completed a previous rAvPAL-PEG study will be enrolled into this study. Subjects 
enrolling into PAL-003 with no interruption in dosing from a previous rAvPAL-PEG study may either 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
continue their previous dosing regimen or begin this study at a higher dose level. Subjects who have 
had dosing interruptions between the previous rAvPAL-PEG study and PAL-003 must have their 
starting dose determined per the Sponsor’s Medical Officer. The first dose will be administered in the 
clinic, and the subject must be observed for 30-60 minutes following administration. A follow-up 
telephone call will be made to the subject to monitor subject safety 24 hours following the return to 
dosing.  
Diet should not be altered during the course of this study.  Any decision to modify subject diet must be 
made per the Investigator in consultation with the Sponsor’s Medical Officer and must be performed 
under the supervision of the Investigator in consultation with the Sponsor’s Medical Officer. To 
monitor for changes in subject diet, a diet diary will be issued to subjects for completion and will be 
reviewed with the clinical study staff on a monthly basis.  
Subjects may self administer study drug at home if approved by the Investigator and the Sponsor’s 
Medical Officer and if adequate training is demonstrated. Subjects must meet a set of criteria to be 
considered appropriate for self administration.   
Subjects will be evaluated for safety throughout the study. Toxicity will be measured according to the 
National Cancer Institute (NCI) Common Terminology Criteria for Adverse Events (CTCAE), 
version 4. 
In addition to the Sponsor, a Data Monitoring Committee (DMC) will monitor the safety of subjects in 
the study. The DMC is an independent committee that will act in an advisory capacity to the Sponsor. 
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take 
rAvPAL-PEG. Subjects’ previous rAvPAL-PEG dosing will continue in PAL-003. In PAL-003, each 
subject’s dose will be adjusted as needed to attain or maintain blood Phe concentrations of 
60-600 µmol/L. rAvPAL-PEG dose will be based on either a subject’s weight or will be a fixed dose 
(subjects who have maintained blood Phe levels to 60-600 µmol/L for at least 2 consecutive weeks and 
who have maintained a stable rAvPAL-PEG dose for at least 2 consecutive weeks). Doses will be 
evaluated on an individual basis. 
Evaluations, observations, and procedures will be conducted at selected time points. After the subject’s 
blood Phe concentration has been controlled to within a target range (60-600 µmol/L), the subject may 
be asked to have additional blood draws for PK and blood Phe concentration analyses as needed per 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
the discretion of the Investigator in consultation with the Sponsor’s Medical Officer. 
• A subject will continue in PAL-003 until one of the following occurs: 
• 
The subject withdraws consent and discontinues from the study. 
• 
The subject is discontinued from the study at the discretion of the Investigator. 
• 
 The subject has completed the study through the Month 60 visit. 
• 
 The study is terminated. 
Subjects may withdraw from treatment with study drug at any time; however, subjects will be asked to 
continue to perform the study assessments until study completion. Subjects may also withdraw from 
study participation at any time. Because the completeness of the data affects the integrity, accuracy, 
and interpretation of study results, every effort should be made to retain subjects in the study and to 
have them complete the study assessments as scheduled as long as continued participation does not 
compromise subject safety. 
A PK substudy has been added to evaluate the steady-state PK of rAvPAL-PEG in a minimum of 6 
subjects who have achieved and maintained target blood Phe for at least 2 consecutive weeks and for 
whom no further dose modifications are planned.  Subjects enrolled into the substudy will have 
additional pre-dose PK sampling performed. 
PAL-003 Substudy 
Dose Modifications: 
Dose Increase Methodology
Each subject’s dose may be modified based on the decision of the Investigator, in agreement with the 
Sponsor’s Medical Officer. Decisions regarding dose increases will depend on a subject’s adverse 
event profile and blood Phe and drug concentrations.  
: 
An individual subject’s dose may be adjusted beginning on Day 1 of PAL-003. For the duration of this 
study, an individual subject’s dose may be adjusted if warranted per a subject’s adverse event profile 
and blood Phe concentrations. Dose increases should be performed as follows. 
• 
The dose may be increased by increments of no more than 10-fold higher than the subject’s 
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PAL-003 A4 
Page 10 
 
Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
current dose. 
• 
When increasing the dose, a dose may be used that is between the dose levels (0.001, 0.003, 
0.01, 0.03, 0.06, 0.1, 0.2, 0.3, 0.4, 0.6, 0.8, 1.0, 2.0, 3.0, 4,0, and 5.0 mg/kg)) or per 
Investigator determination in consultation with the Sponsor’s Medical Officer based on 
available information regarding a subject’s blood Phe (60-600 µmol/L) as well as any adverse 
events (any hypersensitivity reaction) for an individual subject. 
• 
The dose may be adjusted by increasing the frequency up to daily for a total weekly dose not 
to exceed 5.0 mg/kg.  Subjects who increase their dose frequency will have additional 
assessments performed (Interim Dosing Visit). 
• 
When a dose is increased, the subject must be observed for 30-60 minutes following the first 
modified dose administration. Subjects who increase their dose frequency do not need to be 
observed following injection of study drug if the increase in frequency does not increase the 
overall weekly dose amount. 
• 
Only 1 dose adjustment is allowed every 2 weeks. 
All dose decreases must be agreed to by both the Investigator and the Sponsor’s Medical Officer. 
Decisions regarding dose decreases will depend on available information regarding a subject’s blood 
Phe (60-600 µmol/L), as well as any adverse events (any hypersensitivity reaction). Dose decreases 
may occur for safety (ie, any adverse event that may be improved with a lower, more frequent dose).  
Dose Decrease Methodology 
A dose should first be reduced by dose level (5.0, 4.0, 3.0, 2.0, 1.0, 0.8, 0.6, 0.4, 0.3, 0.2, 0.1, 0.06, 
0.03, 0.01, 0.003, 0.001 mg/kg). It is also permitted to decrease dose in between these specified dose 
levels. If further dosing adjustments are required to attain the target Phe concentration, dosing 
frequency may be reduced. 
If the subject develops low blood Phe (as defined by a blood Phe level ≤ 30 µmol/L as measured by 
serum Phe levels for a minimum of 1 month), the subject’s rAvPAL-PEG dose should be decreased to 
the next lower dose. If the condition persists after another 1 month at the lower dose, the dose should 
be decreased again to the next lower level. If the subject continues to experience low blood Phe after 
two dose level reductions, the subject may be asked to consult the dietician to eliminate medical foods 
and/or formulas and to ensure a balanced and nutritious diet (as part of the routine standard of care for 
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PAL-003 A4 
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Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
PKU disease management, subject diet should be monitored by a dietician). 
Safety Assessment Criteria
If an individual subject exhibits toxicity of a treatment-emergent CTCAE grade 3 or greater or a 
systemic reaction that is assessed as related to treatment with study drug, that subject will have dosing 
halted until the toxicity resolves. The subject’s data will be evaluated by the Principal Investigator (PI) 
and the Sponsor’s Medical Officer, and a decision will then be made whether to discontinue the 
subject from the study treatment, restart dosing at the same dose level, or restart dosing at a lower dose 
level. 
: 
If 2 or more subjects at a dose level exhibit toxicity of a treatment-emergent CTCAE grade 3 or greater 
or a systemic reaction that is assessed as related to treatment with study drug, further dosing of 
subjects at that dose level will be evaluated and a safety assessment will be completed. In addition, the 
Food and Drug Administration (FDA) may be notified of this occurrence if appropriate. 
Stopping Criteria: 
NUMBER OF SUBJECTS PLANNED: 
Approximately 100 subjects. 
DIAGNOSIS AND ALL CRITERIA FOR INCLUSION AND EXCLUSION:  
Individuals eligible to participate in this study must meet all of the following criteria: 
1. Must have completed participation in a previous rAvPAL-PEG study. 
2. Willing and able to provide written, signed informed consent, or, in the case of participants 
under the age of 18, provide written assent (if required) and written informed consent by a 
parent or legal guardian, after the nature of the study has been explained, and prior to any 
research-related procedures. 
3. Willing and able to comply with all study procedures. 
4. Females of childbearing potential must have a negative pregnancy test at Screening and be 
willing to have additional pregnancy tests during the study. Females considered not of 
childbearing potential include those who have been in menopause at least 2 years, or had tubal 
ligation at least 1 year prior to Screening, or who have had total hysterectomy. 
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PAL-003 A4 
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Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
5. Sexually active subjects must be willing to use an acceptable method of contraception while 
participating in the study. 
6. Maintained a stable diet. 
7. In generally good health as evidenced by physical examination, clinical laboratory evaluations 
(hematology, chemistry, and urinalysis), and electrocardiogram (ECG) at Screening. 
Individuals who meet any of the following exclusion criteria will not be eligible to participate in the 
study: 
1. Use of any investigational product (with the exception of rAvPAL-PEG) or investigational 
medical device within 30 days prior to Screening, or requirement for any investigational agent 
prior to completion of all scheduled study assessments. 
2. Use of any medication other than rAvPAL-PEG that is intended to treat PKU within 14 days 
prior to the administration of study drug. 
3. Use or planned use of any injectable drugs containing PEG (other than rAvPAL-PEG), 
including Depo-Provera, within 6 months prior to Screening and during study participation.  
4. A prior reaction that included systemic symptoms (eg, generalized hives, respiratory or 
gastrointestinal problems, hypotension, angioedema, anaphylaxis) to rAvPAL-PEG or a 
PEG-containing product. Subjects with a prior systemic reaction may be eligible for 
participation per the discretion of the Principal Investigator in consultation with the Sponsor’s 
Medical Officer. However, subjects who discontinued from study treatment early due to a 
reaction are not eligible to enroll into this study.    
5. Pregnant or breastfeeding at Screening or planning to become pregnant (self or partner) or to 
breastfeed at any time during the study.  
6. Concurrent disease or condition that would interfere with study participation or safety 
(eg, history or presence of clinically significant cardiovascular, pulmonary, hepatic, renal, 
hematologic, gastrointestinal, endocrine, immunologic, dermatologic, neurological, oncologic, 
or psychiatric disease). 
7. Any condition that, in the view of the PI, places the subject at high risk of poor treatment 
compliance or of not completing the study. 
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PAL-003 A4 
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Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
8. Known hypersensitivity to rAvPAL-PEG or its excipients, including hypersensitivity reactions 
that necessitated early termination from a previous rAvPAL-PEG study. 
9. Alanine aminotransferase (ALT) concentration > 2 times the upper limit of normal. 
10. Creatinine  > 1.5 times the upper limit of normal. 
INVESTIGATIONAL PRODUCT, DOSE, ROUTE AND REGIMEN: 
rAvPAL-PEG will be provided in 3 mL (milliliter) vials, each containing 1.5 ± 0.2 mL to deliver either 
10 mg of rAvPAL-PEG per 1 mL (10 mg/mL protein concentration) or 15 mg or rAvPAL-PEG per 
1 mL (15 mg/mL protein concentration). Each vial is filled with 1.5 ± 0.2 mL to allow the withdrawal 
and delivery of up to 1 mL of the drug product.  
Upon enrollment into this study, subjects from previous rAvPAL-PEG studies will be dosed with the 
same or higher dose than the dose that was administered upon completion of that study provided that 
there was no interruption in dosing. Subjects who have had dosing interruptions between the previous 
rAvPAL-PEG study and PAL-003 must have their starting dose determined per the Sponsor’s Medical 
Officer. . rAvPAL-PEG doses will be administered SC by either health care professionals or via self 
administration. The dose level may be increased per Investigator determination in consultation with 
the Sponsor’s Medical Officer based on available information regarding a subject’s blood Phe level 
(60-600 µmol/L), as well as any adverse events (any hypersensitivity reaction) for an individual 
subject. The dosage that provides control of blood Phe concentrations within the target range of 
60-600 µmol/L for a minimum of 2 weeks will be determined for each subject by adjusting the dose 
level, dose frequency, or both, as agreed by the PI and the Sponsor’s Medical Officer, based upon the 
subject’s response to doses. 
Subjects who have demonstrated efficacy (ie, blood Phe within the target range of 60-600 µmol/L for 
at least 2 consecutive weeks) and who have maintained a stable rAvPAL-PEG dose for at least 
2 consecutive weeks may be eligible to transition from weight-based dosing to a fixed dosing regimen 
that would permit daily dosing (5- or 7-days-per-week). Subjects should convert their weight-based 
dose using the following table: 
Fixed Dosing 
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PAL-003 A4 
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Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
Weight-based dose 
(mg/kg) 
Equivalent 
fixed dose (mg) 
Vol for 10 mg/ml 
concentration (ml) 
Vol for 15 mg/ml 
concentration (ml) 
0.03 
2.5 
0.25 
0.17 
0.06 
5 
0.5 
0.33 
0.12 
10 
1 
0.67 
0.25 
20 
2 
1.33 
0.5 
40 
4 
2.67 
1.0 
75 
7.5 
5 
2.0 
150 
15 
10 
3.0 
225 
22.5 
15 
4.0 
300 
30 
20 
5.0 
375 
37.5 
25 
 
DURATION OF TREATMENT: 
Up to 60 months. 
REFERENCE THERAPY(IES), DOSE, ROUTE AND REGIMEN:  
None 
CRITERIA FOR EVALUATION: 
Efficacy
Blood Phe concentrations will be measured.  
: 
Immunogenicity
The presence of antibodies (anti-PAL immunoglobulin G [IgG], anti-PAL IgM, anti-PEG IgG, anti-
PEG IgM, anti-rAvPAL-PEG neutralizing antibodies, and anti-PEG-PAL IgE) will be assessed. 
: 
Safety: 
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PAL-003 A4 
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Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
Safety will be evaluated on the incidence of adverse events (AEs) and clinically significant changes in 
vital signs, ECG results, X-ray results, and laboratory test results. 
Pharmacokinetic
Plasma concentrations of rAvPAL-PEG will be measured for subjects participating in the Substudy. 
: 
STATISTICAL METHODS:  
Sample Size
Subjects who participated in a previous rAvPAL-PEG study may be enrolled into this study. 
No formal sample size calculation was conducted for this study or the PAL-003 Substudy. 
: 
Safety Analysis
All subjects who receive any amount of study drug in this study and have postdose safety information 
will be included in the safety analyses. 
: 
All AEs will be coded using the Medical Dictionary for Regulatory Activities (MedDRA). The 
incidence of AEs will be summarized by system organ class, preferred term, relationship to study drug, 
and severity. A by–subject listing will be provided for those subjects who experience a serious AE 
(SAE), including death, or experience an AE associated with early withdrawal from the study or study 
drug. Clinical laboratory data will be summarized by the type of laboratory test. Frequency and 
percentage of subjects who experience abnormal (ie, outside of reference range) and/or clinically 
significant abnormalities after study drug administration will be presented for each clinical laboratory 
test. For each clinical laboratory test, descriptive statistics will be provided for baseline and all 
subsequent post-treatment visits. Changes from baseline to the post-treatment visits will also be 
provided. Descriptive statistics, including clinically significant changes from baseline, of vital signs, 
ECG results, and X-ray results will also be provided. 
Efficacy Analysis
Data from all subjects who receive any amount of study drug and who have any post-treatment 
efficacy data will be included in the efficacy analysis. 
: 
Blood Phe concentration at each scheduled time point will be summarized using descriptive statistics 
(mean, standard deviation, median, minimum, and maximum). Change in blood Phe concentration 
from baseline to each scheduled time point and presence/absence of antibodies will also be 
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PAL-003 A4 
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Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
summarized. In addition, the proportion of subjects who have maintained target Phe concentrations of 
60-600 µmol/L will be summarized by each scheduled time point. 
Exploratory Analysis
For subjects who have received any study drug in this study with any post-treatment blood Phe 
concentration measurements and diet diary information, the relationship of dietary Phe intake (per 
information reported on the subject diet diary) and blood Phe concentration will be explored.  
: 
Substudy Analysis
For subjects who completed the Substudy, the steady-state PK of rAvPAL-PEG in subjects who have 
achieved and maintained target blood Phe will be explored. 
: 
Pharmacokinetic Analysis
Subjects who complete the Substudy will have the following PK parameters assessed: area under the 
plasma concentration-time curve (AUC), time to maximum plasma concentration (Tmax), maximum 
plasma concentration (Cmax), half life (t1/2), and clearance (CL/F).  
: 
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3 
TABLE OF CONTENTS 
1 TITLE PAGE .......................................................................................................................1 
2 SYNOPSIS ...........................................................................................................................6 
3 TABLE OF CONTENTS ...................................................................................................17 
4 LIST OF ABBREVIATIONS AND DEFINITIONS OF TERMS ....................................21 
5 ETHICS..............................................................................................................................25 
5.1 Institutional Review Board or Ethics Committee .....................................................25 
5.2 Ethical Conduct of Study ..........................................................................................25 
5.3 Subject Information and Informed Consent ..............................................................26 
6 INVESTIGATORS AND STUDY ADMINISTRATIVE STRUCTURE ........................27 
7 INTRODUCTION .............................................................................................................28 
7.1 Nonclinical Studies ...................................................................................................28 
7.2 Previous Clinical Studies ..........................................................................................30 
7.2.1 
Phase 1 Study PAL-001 ..............................................................................30 
7.2.2 
Phase 2 Studies PAL-002, PAL-004, and 165-205 .....................................31 
7.3 Study Rationale .........................................................................................................32 
7.4 Summary of Overall Risks and Benefits ...................................................................34 
7.4.1 
Toxicity Due to Exposure to PEG ...............................................................34 
7.4.2 
Toxicity Due to an Immunologic Reaction .................................................34 
8 STUDY OBJECTIVES ......................................................................................................39 
9 INVESTIGATIONAL PLAN ............................................................................................40 
9.1 Overall Study Design and Plan .................................................................................40 
9.1.1 
Management of Local and Systemic Reactions to rAvPAL-PEG ...............48 
9.1.2 
Dose Modifications .....................................................................................53 
9.1.3 
Safety Assessment Criteria ..........................................................................55 
9.1.4 
Stopping Criteria .........................................................................................55 
9.2 Discussion of Study Design, Including Choice of Control Group ............................55 
9.3 Selection of Study Population ...................................................................................55 
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9.3.1 
Inclusion Criteria .........................................................................................55 
9.3.2 
Exclusion Criteria ........................................................................................56 
9.3.3 
Removal of Subjects from Treatment or Assessment .................................57 
9.3.4 
Subject Identification and Replacement of Subjects ...................................58 
9.4 Treatments .................................................................................................................58 
9.4.1 
Treatments Administered ............................................................................60 
9.4.2 
Identity of Investigational Product (IP) .......................................................60 
9.4.3 
Storage .........................................................................................................61 
9.4.4 
Directions for Administration .....................................................................61 
9.4.5 
Method of Assigning Subjects to Treatment Groups ..................................63 
9.4.6 
Selection of Doses Used in the Study .........................................................64 
9.4.7 
Blinding .......................................................................................................64 
9.4.8 
Prior and Concomitant Medications ............................................................64 
9.4.9 
Treatment Compliance ................................................................................65 
9.4.10 Dose Interruption and Missed Doses ...........................................................65 
9.5 Investigational Product Accountability .....................................................................65 
9.5.1 
Return and Disposition of Clinical Supplies ...............................................66 
9.6 Dietary or Other Protocol Restrictions......................................................................66 
9.7 Efficacy and Safety Variables ...................................................................................67 
9.7.1 
Efficacy and Safety Measurements Assessed .............................................67 
9.7.2 
Efficacy Variable .........................................................................................68 
9.7.3 
Pharmacokinetic Variables ..........................................................................69 
9.7.4 
Exploratory Efficacy Variable .....................................................................69 
9.7.5 
Safety Variables ..........................................................................................69 
9.7.6 
Clinical Laboratory Assessments ................................................................70 
10 REPORTING ADVERSE EVENTS .................................................................................73 
10.1 Adverse Events .........................................................................................................73 
10.2 Serious Adverse Events ............................................................................................76 
10.3 Pregnancy ..................................................................................................................77 
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10.4 Urgent Safety Measures ............................................................................................77 
10.5 BioMarin Pharmacovigilance Contact Information ..................................................78 
11 APPROPRIATENESS OF MEASUREMENTS ...............................................................79 
11.1 Safety and Pharmacokinetics ....................................................................................79 
11.2 Diet Diary ..................................................................................................................79 
12 STUDY PROCEDURES ...................................................................................................80 
12.1 Prestudy .....................................................................................................................80 
12.2 Screening Visit ..........................................................................................................80 
12.3 Treatment Period .......................................................................................................80 
12.3.1 Day 1 (Week 1) ...........................................................................................81 
12.3.2 Weekly Visits ..............................................................................................81 
12.3.3 Substudy Visits ............................................................................................82 
12.3.4 Monthly Visits (Week 4, 8, 12, etc) ............................................................82 
12.3.5 Quarterly Visits (Week 12, 24, 36, etc) .......................................................83 
12.3.6 Interim Dosing Visit ....................................................................................83 
12.3.7 Weekly Telephone Visit ..............................................................................84 
12.3.8 Unscheduled Hypersensitivity Reaction Visit .............................................84 
12.4 Early Termination Visit ............................................................................................85 
12.5 Final Follow-up Visit ................................................................................................86 
13 DATA QUALITY ASSURANCE .....................................................................................87 
14 STATISTICAL METHODS AND DETERMINATION OF SAMPLE SIZE ..................88 
14.1 Statistical and Analytical Plans .................................................................................88 
14.2 Safety Analysis .........................................................................................................88 
14.3 Pharmacokinetic Analysis .........................................................................................88 
14.3.1 Pharmacokinetic Substudy Analysis ...........................................................89 
14.4 Efficacy Analysis ......................................................................................................89 
14.5 Determination of Sample Size ..................................................................................89 
14.6 Handling of Missing Data .........................................................................................89 
14.7 Interim Analyses .......................................................................................................89 
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4 
LIST OF ABBREVIATIONS AND DEFINITIONS OF TERMS 
ADR 
Abbreviations 
adverse drug reaction 
AE 
adverse event 
ALT 
alanine aminotransferase 
AST 
aspartate aminotransferase 
AUC 
area under the plasma concentration-time curve 
AUC0-7 days 
area under the plasma concentration-time curve from time zero on Day 1 
to Day 8 
BUN 
blood urea nitrogen 
°C 
degree Celsius 
C3 
complement 3 
C4 
complement 4 
CBC 
complete blood count 
CD 
Compact disk 
CFR 
Code of Federal Regulations 
CH50 
total hemolytic complement 
Cmax 
maximum plasma concentration 
CNS 
central nervous system 
CO2 
carbon dioxide 
CRA 
Clinical Research Associate 
CRF 
case report form 
CRP 
C-reactive protein 
CTCAE 
Common Terminology Criteria for Adverse Events 
CV 
cardiovascular 
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DBP 
diastolic blood pressure 
DMC 
Data Monitoring Committee 
ECG 
electrocardiogram 
ETV 
Early Termination Visit 
FDA 
Food and Drug Administration 
F/U 
follow-up 
g 
gram 
GCP 
Good Clinical Practice 
GGT 
gamma-glutamyltransferase 
GI 
gastrointestinal 
IB 
Investigator’s Brochure 
ICF 
Informed Consent Form 
ICH 
International Conference on Harmonisation of Technical Requirements for 
Registration of Pharmaceuticals for Human Use 
IgE 
immunoglobulin E 
IgG 
immunoglobulin G 
IgM 
immunoglobulin M 
IP 
investigational product 
IRB 
Institutional Review Board 
IV 
intravenous 
kg 
kilogram 
MedDRA 
Medical Dictionary for Regulatory Activities 
mg 
milligram 
mL 
milliliter 
mm Hg 
millimeter of mercury 
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NAb 
neutralizing antibodies 
NCI 
National Cancer Institute 
NOAEL 
no observable adverse effect level 
OTC 
over the counter 
PAH 
phenylalanine hydroxylase 
PAL 
phenylalanine ammonia lyase 
PEG 
polyethylene glycol 
Phe 
phenylalanine 
PI 
Principal Investigator 
PK 
pharmacokinetics 
PKU 
phenylketonuria 
rAvPAL-PEG recombinant Anabaena variabilis phenylalanine ammonia lyase-PEG 
RBC 
red blood cell 
SAE 
serious adverse event 
SAP 
Statistical Analysis Plan 
SBP 
systolic blood pressure 
SC 
subcutaneous 
SD 
standard deviation 
SDV 
source data verified 
SGOT 
serum glutamic oxalo-acetic transaminase 
SGPT 
serum glutamic pyruvate transaminase 
US 
United States 
WBC 
white blood cell 
 
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Definition of Terms: 
Investigational Product (IP): 
“A pharmaceutical form of an active ingredient or placebo being tested or used as a reference 
in a clinical trial, including a product with a marketing authorization when used or assembled 
(formulated or packaged) in a way different from the approved form, or when used for an 
unapproved indication, or when used to gain further information about an approved use.” 
(from E6 ICH)  
The terms “IP” and “study drug” may be used interchangeably in the protocol. 
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5 
ETHICS 
5.1 
Institutional Review Board or Ethics Committee 
Prior to initiating the study, the Investigator will obtain written confirmation that the 
Institutional Review Board (IRB) is properly constituted and compliant with International 
Conference on Harmonisation of Technical Requirements for Registration of 
Pharmaceuticals for Human Use (ICH) and Good Clinical Practice (GCP) requirements, and 
applicable laws and local regulations. A copy of the confirmation from the IRB will be 
provided to BioMarin Pharmaceutical Inc. (BioMarin) or its designee. The Principal 
Investigator (PI) will provide the IRB with all appropriate material, including the protocol, 
Investigator’s Brochure (IB), the Informed Consent Form (ICF) including compensation 
procedures, and any other written information provided to the subjects, including all consent 
forms translated to a language other than the native language of the clinical site. The study 
will not be initiated and investigational product (IP) supplies will not be shipped to the site 
until appropriate documents from the IRB confirming unconditional approval of the protocol, 
the ICF and all subject recruitment materials are obtained in writing by the PI and copies are 
received at BioMarin or its designee. The approval document should refer to the study by 
protocol title and BioMarin protocol number (if possible), identify the documents reviewed, 
and include the date of the review and approval. BioMarin will ensure that the appropriate 
reports on the progress of the study were made to the IRB and BioMarin by the PI in 
accordance with applicable governmental regulations. 
5.2 
Ethical Conduct of Study 
This study will be conducted in accordance with the following: 
• United States (US) Code of Federal Regulations (CFR) sections that address clinical 
research studies, and/or other national and local regulations, as applicable 
• E6 ICH Guideline for GCP 
• The ethical principles established by the Declaration of Helsinki 
Specifically, this study is based on adequately performed laboratory and animal 
experimentation; the study will be conducted under a protocol reviewed and approved by an 
IRB; the study will be conducted by scientifically and medically qualified persons; the 
benefits of the study are in proportion to the risks; the rights and welfare of the subjects will 
be respected; the physicians conducting the study do not find the hazards to outweigh the 
potential benefits; and each subject, or his or her legally authorized representative will 
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provide written, informed consent before any study-related tests or evaluations are 
performed. 
5.3 
Subject Information and Informed Consent 
A properly written and executed ICF, in compliance with the Declaration of Helsinki, 
E6 ICH (GCP Guideline, Section 4.8) and 21 CFR Part 50 and other applicable local 
regulations, will be obtained for each subject prior to entering the subject into the study. The 
Investigator will prepare the ICF and provide the documents to BioMarin for approval prior 
to submission to the IRB. BioMarin and the IRB must approve the documents before they are 
implemented. A copy of the approved ICF, and if applicable, a copy of the approved subject 
information sheet, minor assent form, parental ICF for studies involving minors, and all ICFs 
translated to a language other than the native language of the clinical site must also be 
received by BioMarin or its designee prior to the delivery of study drug. 
Subjects under the age of 18 years will provide written assent (if required), and his/her 
legally authorized representative (parent or legal guardian) will provide written informed 
consent for such subjects. The Investigator will provide copies of the signed ICF to each 
subject (or the subject’s legally authorized representative) and will maintain the original in 
the subject’s record file. 
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6 
INVESTIGATORS AND STUDY ADMINISTRATIVE STRUCTURE 
Prior to beginning the study, the PI at each site must provide to BioMarin or its designee a 
fully executed and signed Form FDA (Food and Drug Administration) 1572 and a Financial 
Disclosure Form. All sub-Investigators must be listed on Form FDA 1572. Financial 
Disclosure Forms must also be completed for all sub-Investigators listed on the 
Form FDA 1572 who will be directly involved in the treatment or evaluation of research 
subjects in this study. 
The study will be administered by and monitored by employees or representatives of 
BioMarin. Clinical Research Associates (CRAs) or trained designees will monitor each site 
on a periodic basis and perform verification of source documentation for each subject as well 
as other required review processes. BioMarin’s Regulatory Affairs Department (or designee) 
will be responsible for the timely reporting of serious adverse events (SAEs) to appropriate 
regulatory authorities as required. Some study assessments, including administration of study 
drug, may be performed at the subject’s home. All assessments performed for this study will 
be administered by clinic staff or other qualified and trained study personnel. 
Anti-rAvPAL-PEG (recombinant Anabaena variabilis phenylalanine ammonia lyase 
polyethylene glycol) immunoglobulin E (IgE) antibody analysis will be performed by a 
vendor; other antibody analysis will be performed by BioMarin. Clinical laboratory tests, 
including serum pregnancy tests (if applicable), will be analyzed and processed by a central 
laboratory, with the exception of erythrocyte sedimentation rate (ESR), and urine pregnancy 
tests (if applicable), which will be analyzed by a local laboratory. A central laboratory will 
also be used to perform analysis of blood phenylalanine (Phe) concentrations and urinalysis. 
Pharmacokinetic (PK) analysis will be performed by BioMarin. 
Prior to database lock in multicenter studies, a Coordinating Investigator will be identified 
who will read the clinical study report and confirm that it accurately describes the conduct 
and results of the study, to the best of his or her knowledge. The Coordinating Investigator 
will be chosen on the basis of active participation in the study, ability to interpret data, and 
willingness to review and sign the report in a specified timeframe. 
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7 
INTRODUCTION 
A comprehensive review of PEGylated recombinant Anabaena variabilis phenylalanine 
ammonia lyase (rAvPAL-PEG) is contained in the IB supplied by BioMarin; the Investigator 
should review this document prior to initiating this study. 
7.1 
Nonclinical Studies 
The nonclinical program for rAvPAL-PEG has characterized the pharmacology, 
pharmacokinetics (PK), and toxicology of rAvPAL-PEG using the intended clinical SC route 
of administration. Pharmacology was assessed in the BTBR Pahenu2 (ENU2) mouse model of 
PKU. The ENU2 mouse model exhibits characteristics similar to those of PKU patients, 
including hyperphenylalaninemia (baseline plasma Phe concentrations of 1000 to 2000 µM) 
and hypopigmentation. Following weekly doses of rAvPAL-PEG administered to male 
ENU2 mice, plasma Phe concentrations decreased from approximately 2000 µM to 
< 200 µM after 2 dose administrations. An attenuated reduction of blood Phe was seen 
between Week 3 and Week 7 of dosing. After 7 weekly administrations of rAvPAL-PEG, 
pharmacological activity returned as evidenced by stabilized concentrations of plasma Phe 
< 200 µM over the entire week, which continued for a total of 15 weeks. 
In pharmacodynamic studies in the BTBR Pahenu2 (ENU2) mouse model administered 
80 mg/kg/week rAvPEG-PAL, two dose interruption assessments were performed:  a 
2-4 week dose interruption and an 11-week dose interruption. Following both dose 
interruption assessments, the animals re-started rAvPAL-PEG at a dose of 80 mg/kg/week. 
No attenuated Phe response was observed when rAvPAL-PEG injections were temporarily 
stopped for 2-4 weeks, and there was an immediate return to stable blood Phe reductions. A 
similar interim attenuated response was observed with the longer dose interruption of 
approximately 11 weeks.  In both of these assessments, no safety issues were noted upon 
re-starting dosing with rAvPAL-PEG (Lapis, 2007, ASHG 57th Annual Meeting). 
Safety pharmacology studies were conducted in rats and cynomolgus monkeys. No 
respiratory or central nervous system (CNS) effects were seen with SC administration of 
rAvPAL-PEG. No changes in cardiovascular (CV) parameters, including electrocardiogram 
(ECG) waveforms, were observed in telemetry-instrumented monkeys assessed for the CV 
effects of rAvPAL-PEG administered subcutaneously. 
Pharmacokinetic parameters were evaluated in single-dose and repeat-dose studies in rats and 
cynomolgus monkeys. The elimination half-life (t1/2) values of rAvPAL-PEG administered to 
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normal rats at SC doses of 10, 25, and 250 mg/kg were 47, 33, and 44 hours, respectively, 
and exhibited modest area under the plasma concentration-time curve (AUC)-dose. In the 
cynomolgus monkey after SC administration of rAvPAL-PEG, the t1/2 was 65 hours at 
4.0 mg/kg, 71 hours at 12 mg/kg, and could not be determined at 60 mg/kg (the highest 
dose). Qualitatively, the kinetics of rAvPAL-PEG in the rat and monkey appear to have 
similar characteristics. The following findings were noted: (1) a 1-compartment model with 
first-order absorption appears to describe the plasma profiles of rAvPAL-PEG after 
single-dose administration, (2) absorption is slow and there is a long absorption period after 
SC administration to maximum observed plasma concentration (Cmax), along with a long t1/2, 
(3) elimination is slow and monophasic, (4) there does not appear to be a gender difference, 
and (5) the AUC and the Cmax are roughly linearly proportional.  
Toxicology of rAvPAL-PEG was assessed in single-dose and repeat-dose studies in normal 
rats and cynomolgus monkeys. In the single-dose rat study, decreased body weight gain and 
Kupffer cell vacuolization at the high SC dose of 250 mg/kg was observed; however, the 
Kupffer cell finding was not seen in the single-dose study in cynomolgus monkeys. In a 
26-week repeat-dose toxicity and toxicokinetic (TK) rat study, decreased body weight gain, 
decreased food consumption, vacuolation/hypertrophy of the renal tubule cells, and 
vacuolation of the histiocytic cells were observed in rats administered 25 mg/kg/dose, twice 
weekly. In a 39-week repeat-dose study in monkeys, arterial inflammation, perivascular 
cellular infiltrates in the SC injection sites, thymic atrophy, and increased lymphoid nodules 
in bone marrow of the sternum were observed in monkeys given ≥ 3 mg/kg/dose, twice 
weekly. Of these findings, only the arterial inflammation was deemed adverse and this 
finding was completely reversed after 13-weeks of recovery. The 
no-observed-adverse-effect-level (NOAEL) of rAvPAL-PEG when administered 
subcutaneously twice weekly for 26 weeks and 39 weeks in the rat and monkey, respectively, 
was 1.0 mg/kg. These NOAELs were based on histological findings of 
vacuolation/hypertrophy of the renal tubule cells in the rat and arterial inflammation findings 
in the monkey.  
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7.2 
Previous Clinical Studies 
The rAvPAL-PEG clinical development program has been designed to demonstrate the 
safety and efficacy of rAvPAL-PEG in reducing blood Phe concentrations in PKU subjects 
who do not respond to treatment with Kuvan® or are not compliant with Kuvan® treatment. 
This study is an extension of the ongoing human clinical studies with rAvPAL-PEG 
(Study PAL-002, Study PAL-004, and Study 165-205) based on data from the completed 
clinical study, PAL-001, and clinical experience as of JAN2011 from this ongoing study and 
the other ongoing Phase 2 studies, PAL-002 and PAL-004.  
7.2.1 Phase 1 Study PAL-001 
The first-in-human trial using rAvPAL-PEG, Study PAL-001, was a Phase 1, open-label, 
dose-escalation study in PKU subjects in the US. The primary objective was to assess the 
safety and tolerability of single SC injections of rAvPAL-PEG. Secondary objectives were to 
evaluate the PK of single, SC injections of rAvPAL-PEG administered at escalating doses in 
subjects with PKU and to evaluate the effect of rAvPAL-PEG on blood Phe concentrations. 
The effectiveness of rAvPAL-PEG in decreasing Phe concentrations in nonclinical studies of 
ENU2 mice was consistent with what was observed in PAL-001. PAL-001 enrolled 25 PKU 
subjects with a mean (standard deviation; SD) baseline blood Phe concentration of 
1310 µmol/L (405). The 25 subjects who enrolled into the study were assigned to receive a 
single administration of rAvPAL-PEG at 1 of 5 dose levels: 0.001, 0.003, 0.01, 0.03, and 
0.1 mg/kg. Five subjects each received 1 of the 5 dose levels of rAvPAL-PEG. 
Key safety, efficacy, and PK results of Study PAL-001 are summarized as follows: 
• rAvPAL-PEG was well tolerated and had a clinically significant blood-lowering 
effect on Phe concentration when administered at a dose of 0.1 mg/kg. 
• For the 5 subjects who were administered 0.1 mg/kg rAvPAL-PEG, clinically 
significant reductions in blood Phe level were observed, with the most clinically 
significant decreases from baseline values to Day 7, ranging from 33.8% to 97.3% 
(mean of 58.12%). The mean baseline blood Phe level for these 5 subjects was 
1113 µmol/L. 
• Overall, no clinically significant reductions in blood Phe level were observed in 
subjects who were administered rAvPAL-PEG at the lower doses of 0.001, 0.003, 
0.01, and 0.03 mg/kg. 
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• For subjects who were administered rAvPAL-PEG at the 3 higher dose levels (0.01, 
0.03, and 0.1 mg/kg) and who had measurable rAvPAL-PEG concentration levels, the 
calculated PK parameters were a mean Tmax of 89-106 hours, a t1/2 of 46-120 hours, 
and an AUC0-t, and Cmax that were proportional with dose. Drug exposure was slightly 
increased with increased dose. 
7.2.2 Phase 2 Studies PAL-002, PAL-004, and 165-205 
Currently, rAvPAL-PEG is being investigated in three Phase 2 clinical trials (PAL-002 and 
PAL-004). As of May 2012, a total of 70 subjects have been administered rAvPAL-PEG in a 
rAvPAL-PEG Phase 2 study.   
In PAL-002 (A Phase 2, Open-Label, Dose-Finding Study to Evaluate the Safety, Efficacy, 
and Tolerability of Multiple Subcutaneous Doses of rAvPAL-PEG in Subjects with PKU), 
approximately 55 subjects will be enrolled and will be administered multiple doses of 
rAvPAL-PEG up to 5.0 mg/kg/week. PAL-002 is a 2-part study. In Part 1, subjects will be 
assigned to 1 of 4 rAvPAL-PEG dose cohorts (0.001, 0.003, 0.01, 0.1 mg/kg, or 1.0 mg/kg). 
rAvPAL-PEG will be administered at a fixed weekly dose of 0.001 mg/kg (Cohort 1), 
0.003 mg/kg (Cohort 2), 0.01 mg/kg (Cohort 3), 1.0 mg/kg (Cohort 4), or 0.1 mg/kg (Part 1 
Substudy) for 8 weeks. In Part 2, all subjects who complete Part 1 will be administered an 
adjustable dose of rAvPAL-PEG for up to an additional 8 weeks. The dose administered in 
Part 2 may be adjusted by dose level and/or dose frequency to reach a target blood Phe 
concentration of 60-600 µmol/L.  
Study PAL-003 (Long-Term Extension of a Phase 2, Open-Label, Dose-Finding Study to 
Evaluate the Safety, Efficacy, and Tolerability of Multiple Subcutaneous Doses of rAvPAL-
PEG in Subjects with PKU) is an extension study of PAL-002, PAL-004 and 165-205 (A 
Phase 2, Multi-Center, Open-Label, Dose-Finding Study to Evaluate Safety, Efficacy and 
Tolerability of Subcutaneously Administered rAvPAL-PEG in Patients with PKU for 24 
Weeks). Once subjects have completed a previous rAvPAL-PEG study, they have the option 
to enroll into PAL-003 and to continue to receive doses of rAvPAL-PEG for up to an 
additional 60 months. 
Study PAL-002 was initiated in September 2009 and is ongoing. The primary objective of 
this study is to evaluate the effect of multiple doses of rAvPAL-PEG on blood Phe 
concentrations in subjects with PKU for up to 16 weeks of treatment. The secondary 
objectives of the study are (1) to evaluate the safety and tolerability of SC injections of 
multiple dose levels of rAvPAL-PEG, (2) to evaluate the antibody response to rAvPAL-PEG, 
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and (3) to evaluate the PK profile of rAvPAL-PEG in subjects with PKU. The study protocol 
was amended (30APR2010) to include a substudy of an additional rAvPAL-PEG dose level 
(0.1 mg/kg/week) that reduced blood Phe concentrations to clinically significant levels in the 
Phase 1 study, PAL-001. The protocol was amended again (28MAR2011) to increase the 
starting dose for Cohort 4 from 0.03 mg/kg/week to 1.0 mg/kg/week. As of JAN2011, 
33 subjects have been enrolled into the study and all 10 subjects of the substudy have been 
dosed with 0.1 mg/kg rAvPAL-PEG. Additional information about the safety reported as of 
JAN2011 is provided in Section 7.4.2. 
Study PAL-004 is designed to determine if daily administration of rAvPAL-PEG at daily 
dose levels (0.06, 0.1, 0.2, 0.4, 0.6, and 0.8 mg/kg/day) is safe and effective in reducing and 
maintaining consistent blood Phe concentrations in subjects with PKU. It is hypothesized that 
a higher starting dose and frequency will reduce blood Phe concentrations to near-normal 
levels in a timely manner and will provide the greatest clinical benefit. Considering the 
concentration and volume of drug that is administered subcutaneously, the only way to 
increase the rAvPAL-PEG dose is via daily administration. Therefore, in Study PAL-004, a 
higher starting dose of 0.4 mg/kg will be administered 5 days a week (referred to as daily), a 
dosing regimen that has been observed to be tolerated and to reduce blood Phe concentrations 
to clinically meaningful levels in previously exposed subjects in this study. Following 
completion of Study PAL-004, subjects have the option to enroll into this study and to 
continue to receive doses of rAvPAL-PEG for up to an additional 60 months. 
Study 165-205 is a Phase 2 study using a subject-driven dose modification schema to assess 
safety. In addition, fixed dosing at a drug concentration of 15 mg/mL rAvPAL-PEG will be 
assessed. As of May 2012, enrollment of subjects is underway for this study. 
In this study, subjects who completed a previous rAvPAL-PEG study will continue to be 
administered the same rAvPAL-PEG dose that was administered in the previous study. If the 
safety, PK, and blood Phe concentration results from the previous study indicate that the 
appropriate level of PEGylation and dosing regimen differs from that administered in the 
previous study, the PEGylation and/or dosing regimen administered in this study may 
change.    
7.3 
Study Rationale 
PKU is an autosomal, recessive, inherited disease characterized by deficiency in the enzyme 
PAH. Approximately 1 in every 10,000 infants in North America is born with PKU (Scriver, 
2001, McGraw-Hill). Left untreated, PAH deficiency is associated with an abnormally 
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elevated concentration of Phe, which is toxic to the brain (Kaufman, 1989, J Pediatr.) and can 
result in a variety of neuropathologic conditions, including mental retardation, microcephaly, 
delayed speech, seizures, and behavioral abnormalities (Scriver, 2001, McGraw-Hill). The 
brains of untreated patients with PKU show evidence of hypomyelination and gliosis, arrest 
in cerebral development, and, in some cases, white matter degeneration (Huttenlocher, 2000, 
Eur.J Pediatr.). Elevated Phe during fetal development leads to severe mental retardation and 
can cause microcephaly, growth retardation, and congenital heart disease (Guttler, 2003, 
Pediatrics), (Koch, 2003, Pediatrics), (Lee, 2003, Pediatrics), (Levy, 2003, Pediatrics), 
(Matalon, 2003, Pediatrics), (Rouse, 2004, J.Pediatr.). 
For a subset of patients with residual enzyme activity, treatment with Kuvan® is an option. 
For all other patients, current management of PKU involves adherence to low-Phe medicinal 
diet formulas and dietary restriction of Phe-containing foods. Implementation of a 
Phe-restricted diet in infancy significantly reduces blood Phe concentrations and prevents 
many of the neuropathologic manifestations of PKU, including severe mental retardation. 
However, compliance with this restrictive diet can be difficult for older children, adolescents, 
and adults, and adherence may result in nutritional deficiencies due to the limitations of 
natural protein sources (Fisch, 2000, Eur.J.Pediatr.), (Walter, 2002, Lancet). 
The need exists for a treatment that will help individuals with PKU safely achieve lifelong, 
reliable control of blood phenylalanine (Phe) concentrations and improve functional 
outcomes. rAvPAL-PEG is a potential substitute for the phenylalanine hydroxylase (PAH) 
enzyme, which is defective in individuals with PKU. rAvPAL-PEG may control blood Phe 
concentrations, which may have additional clinical benefits.  
Blood Phe levels depend not only on the functional presence of the endogenous enzyme PAH 
but also on the dietary intake of Phe. It is important to understand the role of diet on blood 
Phe levels concurrent with the administration of rAvPAL-PEG treatment. Therefore, an 
exploratory objective has been added to this study to assess the relationship of diet, 
rAvPAL-PEG administration, and blood Phe level. Changes to subject diet are not allowed in 
this study unless per the Investigator in consultation with the Sponsor’s Medical Officer. 
Diet will be monitored using a diet diary.     
A pharmacokinetic (PK) substudy has been added to evaluate the steady-state PK of 
rAvPAL-PEG in a minimum of 6 subjects who have achieved and maintained target blood 
Phe for at least 2 consecutive weeks and for whom no further dose modifications are planned. 
Single-dose PK data has been collected in the Phase 1 study, PAL-001. However, there is 
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little multiple-dose PK data or data for when subjects have reached and maintained a stable 
dosing regimen.  With the PK substudy, multiple-dose PK data will be collected for subjects 
who have already achieved Phe reduction to within the protocol-defined target range. 
This study is an extension of previous rAvPAL-PEG studies. Administration of 
rAvPAL-PEG will be continued to assess whether long-term dosing of rAvPAL-PEG is safe 
and can maintain reduced blood Phe concentrations in PKU subjects. 
7.4 
Summary of Overall Risks and Benefits 
It is not expected that data from previous rAvPAL-PEG studies will change the assumption 
that rAvPAL-PEG has a toxicity profile similar to other recombinant PEGylated non-human 
enzymes currently in use. The toxicities of these drugs usually fall into 2 main categories: 
toxicity due to exposure to PEG, and toxicity due to immunologic sensitization. In addition, 
exaggerated pharmacological effects resulting in very low Phe concentrations could be 
observed. Other adverse events (AEs) that could occur with rAvPAL-PEG include 
injection-site reactions and other general symptoms. 
7.4.1 Toxicity Due to Exposure to PEG 
Acute exposure to high doses of PEG can result in renal toxicity. There have been a few 
reports of PEG-related AEs in humans; cumulative intravenous (IV) PEG doses of 121 to 
240 g caused acute renal tubular necrosis, oliguria, and azotemia. The anticipated PEG 
exposure associated with the expected rAvPAL-PEG dose range (6 g per week) is at least 
80-fold lower than the reported toxic doses and comparable to exposures to PEG in widely 
used medicines and other compounds that are administered by the IV, oral, rectal, and topical 
routes (Webster, 2007, Drug Metab Dispos.). No indication of PEG-related toxicity at the 
ultrastructural level was observed in monkeys given a single dose of up to 60 mg/kg 
rAvPAL-PEG SC. In rats, both renal tubule vacuolation and histiocytic cell vacuoles have 
been assocated with PEG-related catabolism and administration of other PEGylated proteins 
(refer to Section 7.1). 
In this study, subjects will be monitored closely with urine examinations and blood 
chemistries to follow kidney function. 
7.4.2 Toxicity Due to an Immunologic Reaction 
The active drug substance in rAvPAL-PEG is a bacterial protein, and as such, it is expected 
that it may elicit immune recognition and responses. Epitopes that play a role in the immune 
response may be rendered inaccessible by PEG (Gamez, 2007, Mol.Genet.Metab). In vivo 
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and in vitro experiments have shown that PEGylation of proteins and cells can attenuate the 
immunological response (Scott, 1997, Proc.Natl.Acad.Sci.U.S.A), (Chen, 2001, BioDrugs.). 
PEGylation has been effective in reducing anti-rAvPAL antibody titers in the mouse model, 
although PEGylation does not eliminate antibody formation. Although PEGylation of 
rAvPAL may have a significant effect on reducing the immunogenicity of the molecule, it is 
reasonable to expect that some individuals may exhibit immune responses upon exposure to 
the drug. These immune responses may be clinically irrelevant, cause symptoms of various 
degrees, or lead to neutralization of biological activity. Subjects participating in clinical trials 
will be monitored closely with specific antibody titers, sedimentation rates, and complete 
blood counts (CBCs). 
As of May 2012, a total of 70 subjects have been administered rAvPAL-PEG in the single-
dose, Phase 1 study (PAL-001) and in the repeat -dosing Phase 2 studies (PAL-002, PAL-
004, and PAL-003). The dose levels in the repeat-dosing studies range from 0.001 to 5.0 
mg/kg/week administered in various frequencies (including 5 days a week). The most 
clinically significant AEs have been hypersensitivity reactions that have led to dosing 
interruptions and reductions. Most of the hypersensitivity reactions have been nonserious and 
mild-to-moderate in severity.  
A total of 4 SAEs have been reported in the previous rAvPAL-PEG studies.  Of these 4 
SAEs, 3 have been reported as related to rAvPAL-PEG. Two of the study-drug related SAEs 
occurred in Study PAL-001. Both of these SAEs occurred in subjects in the lower dose 
cohorts: an SAE of hypersensitivity reaction in a subject in the 0.001 mg/kg cohort and an 
SAE of anaphylactic reaction (urticaria) in a subject in the 0.01 mg/kg cohort. Neither SAE 
was severe or resulted in discontinuation from the study, and both of the SAEs resolved. 
There were no SAEs in subjects in the higher dose cohorts (0.03 mg/kg and 0.1mg/kg) in 
PAL-001. The third study drug-related SAE (angioedema) occurred in a subject in Study 
PAL-004. The fourth SAE (urticaria, dehydration) was reported as not related to study drug 
and occurred in a subject in Study PAL-002.  There have been no reports of anaphylaxis for 
any subject treated with rAvPEG-PAL (as of January 2012).  
Subjects who have a systemic clinical reaction at any time during this study may undergo a 
series of assessments to monitor safety, including assessment of complements, C-reactive 
protein (CRP), erythrocyte sedimentation rate (ESR), and IgE antibodies.  Reintroduction of 
rAvPAL-PEG dosing after a reaction will depend on clinical assessments and available 
laboratory data, such as chemistry and urine studies, to ensure that there has been no 
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end-organ damage prior to resuming treatment with rAvPAL-PEG. As of May 2012, 
antibody titers, including positive IgE titers, have not been predictive of future clinical 
reactions when dosing with rAvPAL-PEG.  Additionally, subjects will be premedicated to 
prevent or mitigate risk of hypersensitivity reactions (refer to Section 9.1.1.3.3). 
PEG itself is considered nonimmunogenic (Davis, 1981, Clin.Exp.Immunol.), (Harris, 2003, 
Nat.Rev.Drug Discov.), however, antibodies against PEG may form when PEG is bound to 
compounds. (Harris, 2003, Nat.Rev.Drug Discov.),(Richter, 1983, Int.Arch.Allergy 
Appl.Immunol.).  In some instances, development of such antibodies did not result in any 
significant clinical effects in humans (Richter, 1984, Int.Arch.Allergy Appl.Immunol.). 
In some individuals, anti-PEG antibodies may be pre-existing due to previous exposure to 
PEG in other products. Anti-PEG antibodies have been associated with nonresponsiveness 
against therapy (Armstrong, 2007, Cancer), (Ganson, 2006, Arthritis Res.Ther.).  
Administration of rAvPAL-PEG may lead to anti-PEG antibody formation, and the duration 
of this possible effect is not known. Subjects in the Phase 2 rAvPAL-PEG studies have 
developed both anti-PEG IgM and anti-PEG IgG antibodies. Antibody formation may limit a 
subject’s future ability to be treated with other PEG-containing (eg, Depo-Provera) or 
PEGylated (eg, PEG-interferon) injectable drugs. It is therefore recommended that any 
PEG-containing injectable drug administered to subjects after completion of this study be 
done under medical observation. 
7.4.2.1 
Systemic Skin Reactions 
Two out of 25 subjects who were enrolled in Study PAL-001 and received the 
protocol-defined single dose of rAvPAL-PEG reported systemic skin reactions (generalized 
skin rash) that were attributed to treatment with study drug. One subject received a single 
dose of 0.001 mg/kg rAvPAL-PEG, and the other subject received a single dose of 
0.01 mg/kg rAvPAL-PEG. One of these events was reported as serious, and the other was 
reported as nonserious; both events were reported following administration of Depo-Provera 
injections (medroxyprogesterone injection), an injectable contraception. These allergic 
reactions are thought to be related to the PEG molecules that are found in both the study 
drug, rAvPAL-PEG, and Depo-Provera. These reactions are not likely to be experienced 
concurrent with other birth control medications. 
The 2 subjects were administered study drug during PAL-001 and then experienced an 
allergic reaction following an injection of Depo-Provera. The symptoms of the reactions 
were hives on the arms and legs and difficulty breathing. The symptoms for both subjects 
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resolved within 1 day following treatment with medication, including the 
 
. Both subjects were examined by an allergy specialist after they 
completed participation in PAL-001. A skin prick test with Depo-Provera was administered 
as part of this examination. One subject had a mild allergic reaction to the test; however, no 
further reactions or complications were reported following subsequent administration of a 
full dose of Depo-Provera. Upon study completion, the subject continued to receive regular 
doses (every 3 months) of Depo-Provera, and no further reactions were reported. The second 
subject also had a positive reaction to Depo-Provera following administration of the skin 
prick test. When a subsequent full dose of Depo-Provera was administered, 
 developed 
hives, itching, and chills. The subject’s symptoms resolved within 1 day of taking medication 
prescribed by an allergist. See Section 7.2.1 for the results from Study PAL-001. 
The active drug substance in rAvPAL-PEG is a bacterial protein that may elicit immune 
responses, such as urticaria, bronchospasm, itching, anaphylaxis, and others. The results from 
nonclinical studies of rAvPAL-PEG conducted in rats and cynomolgus monkeys indicated 
the formation of anti-rAvPAL antibody titers that did not correspond with observations of 
injection-site reactions. Quantitation of anti-PEG titers were not assessed in the chronic 
repeat-dose studies in the rat and monkey. Although results from nonclincal studies of 
rAvPAL-PEG conducted in rats and cynomolgus monkeys did not indicate signs of 
immune-mediated toxicities, it is possible that the physio-chemical properties of 
rAvPAL-PEG may induce immunologic sensitization to the protein rAvPAL and to PEG in 
humans. It is currently unknown whether administration of PEG-containing drugs, such as 
Depo-Provera, has a sensitizing effect to PEG in rAvPAL-PEG when administered in 
humans. Because the exact basis for these reported events and their duration is not known, 
the use of PEG-containing injectable drugs prior to, during, and after this study is prohibited 
as a precautionary measure (refer to Section 9.3.2 and Section 9.4.8). 
7.4.2.2 
Management of Allergic Reactions 
Allergic reactions to the SC injection of rAvPAL-PEG may be mild, moderate, or severe in 
intensity. Reactions may include pruritus, rash, shortness of breath, hypotension, or 
anaphylaxis. Clinical assessments should be conducted for a minimum of 30-60 minutes 
post-injection. Longer observations may be required at the discretion of the PI. 
The responsible physician should use all appropriate measures for the treatment of allergic 
reactions. Because of the small potential for anaphylaxis, equipment for emergency 
resuscitation (including epinephrine) should be within easy access during and after the 
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rAvPAL-PEG injection. Subjects who qualify for self administration of study drug will be 
provided with emergency resuscitation instructions (refer to Section 9.4 and the Subject 
Self-Administration Training Materials). 
In the event of an allergic reaction, subjects may be asked to see an allergist/immunologist 
and/or provide up to 3 additional blood samples for immunology studies and complement 
testing. This additional testing may occur up to 6 months following the final study visit.   
The following measures are recommended for the treatment of allergic symptoms: 
• Maintain the airway. 
• Vital sign check. 
• Administration of oral or IV diphenhydramine. 
• Administration of epinephrine if appropriate. 
• Administration of oral or IV glucocorticoids. 
• Administration of oxygen and IV fluids. 
• Administration of additional symptomatic treatment (eg, acetaminiophen or 
ibuprofen). 
• Transfer to an acute care facility of the study center. 
In addition, clinical judgment must be used in determining the appropriateness of 
corticosteroid administration. An allergy and/or immunology consultation should be sought if 
necessary. Information regarding the management of local skin, large local skin, and 
systemic reactions is provided in Section 9.1.1. Detailed instructions for the management of 
allergic reactions are provided in the Study Reference Manual. 
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8 
STUDY OBJECTIVES 
The primary objective of the study is: 
• To evaluate the effect of long-term administration of multiple doses of SC injections 
of rAvPAL-PEG on blood Phe concentrations in subjects with PKU. 
The secondary objectives of the study are: 
• To evaluate the safety and tolerability of long-term administration of subcutaneous 
(SC) injections of rAvPAL-PEG in subjects with PKU. 
• To evaluate the immune response to long-term administration of SC injections of 
rAvPAL-PEG in subjects with PKU. 
The exploratory objective of the study is as follows: 
• To evaluate the long-term relationship of diet and change in blood Phe concentration 
following administration with rAvPAL-PEG in subjects with PKU. 
The Substudy objective is as follows: 
• To evaluate steady-state PK of rAvPAL-PEG in subjects who have achieved and 
maintained target blood Phe concentration and for whom no further dose 
modifications are planned. 
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9 
INVESTIGATIONAL PLAN 
9.1 
Overall Study Design and Plan 
This is a long-term extension of rAvPAL-PEG Phase 2 studies in approximately 100 subjects 
with PKU. The doses are planned to be in the same range as those tested in PAL-002 and 
PAL-004 (starting at 0.001 through 5.0 mg/kg/week), provided no dose-limiting toxicity was 
observed in a previous rAvPAL-PEG studies. 
Only subjects who completed a previous rAvPAL-PEG study will be enrolled into this study. 
Subjects enrolling into PAL-003 with no interruption in dosing from a previous rAvPAL-
PEG study may either continue their previous dosing regimen or begin this study at a higher 
dose level. Subjects who have had dosing interruptions between the previous rAvPAL-PEG 
study and PAL-003 must have their starting dose determined per the Sponsor’s Medical 
Officer.  The first dose will be administered in the clinic, and the subject must be observed 
for 30-60 minutes following administration. A follow-up telephone call will be made to the 
subject to monitor subject safety 24 hours following the return to dosing. 
Diet should not be altered during the course of this study. Any decision to modify subject 
diet must be made per the Investigator in consultation with the Sponsor’s Medical Officer 
and must be performed under the supervision of the Investigator in consultation with the 
Sponsor’s Medical Officer. To monitor for changes in subject diet, a diet diary will be issued 
to subjects for completion and will be brought to clinic monthly for review with the clinical 
study staff. 
Subjects may self administer study drug at home if approved by the Investigator and the 
Sponsor’s Medical Officer and if adequate training is demonstrated. Subjects must meet a set 
of criteria to be considered appropriate for self administration. Refer to Section 9.4 for the 
criteria for which subjects may qualify for self administration. Additional information is 
provided in the Subject Self-Administration Training Materials. 
Subjects will be evaluated for safety throughout the study. Toxicity will be measured 
according to the National Cancer Institute (NCI) Common Terminology Criteria for Adverse 
Events (CTCAE), version 4. 
In addition to the Sponsor, a Data Monitoring Committee (DMC) will monitor the safety of 
subjects in the study. The DMC is an independent committee that will act in an advisory 
capacity to the Sponsor. 
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PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take 
rAvPAL-PEG. Subjects’previous rAvPAL-PEG dosing will continue in PAL-003. In PAL-
003, each subject’s dose will be adjusted as needed to attain or maintain blood Phe 
concentrations of 60-600 µmol/L. rAvPAL-PEG dose will be based on either a subject’s 
weight or will be a fixed dose (subjects who have maintained blood Phe levels to 60-600 
µmol/L for at least 2 consecutive weeks and who have maintained a stable rAvPAL-PEG 
dose for at least 2 consecutive weeks; refer to Section 9.4.4). Doses will be evaluated on an 
individual basis.  
Evaluations, observations, and procedures will be conducted at selected time points as shown 
in Table 9.1.1 and Table 9.1.2.  After the subject’s blood Phe concentration has been 
controlled to within a target range (60-600 µmol/L), the subject may be asked to have 
additional blood draws for PK and blood Phe concentration analyses as needed per the 
discretion of the Investigator in consultation with the Sponsor’s Medical Officer. 
A subject will continue in PAL-003 until one of the following occurs: 
• The subject withdraws consent and discontinues from the study. 
• The subject is discontinued from the study at the discretion of the Investigator. 
• The subject has completed the study through the Month 60 visit. 
• The study is terminated. 
Subjects may withdraw from treatment with study drug at any time; however, subjects will 
be asked to continue to perform the study assessments until study completion. Subjects may 
also withdraw from study participation at any time. Because the completeness of the data 
affects the integrity, accuracy, and interpretation of study results, every effort should be made 
to retain subjects in the study and to have them complete the study assessments as scheduled 
as long as continued participation does not compromise subject safety. 
A PK substudy has been added to evaluate the steady-state PK of rAvPAL-PEG in a 
minimum of 6 subjects who have achieved and maintained target blood Phe for at least 2 
consecutive weeks and for whom no further dose modifications are planned.  Subjects 
enrolled into the substudy will have additional pre-dose PK sampling performed (refer to 
Table 9.1.2. 
The Schedule of Events and PK substudy collection schedules are presented below in 
Table 9.1.1 and Table 9.1.2  
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Table 9.1.1:  Schedule of Events 
Assessments and Events 
Screeninga 
Treatment Periodb,c 
Final F/U 
Visit 
Self 
Administra-
tion 
Early 
Term. 
Visit 
Unsched. 
Hyper. 
Reaction 
Visit.d  
Perform 
within 
48 hours 
Week 1 
Weeklyb 
Monthly 
(eg, Wk 4, 
8, etc.) 
Quarterly  
(eg, Wk 12, 
24, etc.) 
Interim 
Clinician 
Visit 
(HHRN or 
Site) 
D 1 
Starting 
at Week 2 
Every 4th 
week; 
Perform 
in 
addition 
to weekly 
procedure
s 
Every 12th 
week. 
Perform in 
addition to 
monthly 
procedures 
Up to daily 
1 week 
after final 
dose 
 
4 weeks 
after final 
dose 
Informed consent 
 
X 
 
 
 
 
 
 
 
 
 
Medical history, including 
allergy history, and 
demographics 
 
X 
 
 
 
 
 
 
 
 
 
Physical examinatione 
 
X 
X 
 
 
X 
 
X 
 
X 
 
Vital signse 
 
X 
X 
X 
 
 
X 
 
 
X 
X 
Weight 
X 
 
 
X 
 
 
 
 
 
 
12-lead ECG 
 
X 
 
 
 
 
 
X 
 
X 
 
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Assessments and Events 
Screeninga 
Treatment Periodb,c 
Final F/U 
Visit 
Self 
Administra-
tion 
Early 
Term. 
Visit 
Unsched. 
Hyper. 
Reaction 
Visit.d  
Perform 
within 
48 hours 
Week 1 
Weeklyb 
Monthly 
(eg, Wk 4, 
8, etc.) 
Quarterly  
(eg, Wk 12, 
24, etc.) 
Interim 
Clinician 
Visit 
(HHRN or 
Site) 
D 1 
Starting 
at Week 2 
Every 4th 
week; 
Perform 
in 
addition 
to weekly 
procedure
s 
Every 12th 
week. 
Perform in 
addition to 
monthly 
procedures 
Up to daily 
1 week 
after final 
dose 
 
4 weeks 
after final 
dose 
Clinical laboratory testsf 
 
X 
 
 
X 
 
 
X 
 
X 
Xg 
Complements C3 and C4
h 
X 
 
 
 
X 
 
 
 
 
X 
Sedimentation rate 
 
X 
 
 
X 
 
X 
 
X 
X 
Chest x-ray 
X 
 
 
X  
(Week 48 
visit only) 
 
 
X 
 
X 
 
Urine pregnancy testi 
 
X 
X 
 
X 
 
 
X 
 
X 
 
Injection-site inspectionji j 
 
X 
(postdose
) 
X 
 
 
X 
X 
X 
X 
X 
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Assessments and Events 
Screeninga 
Treatment Periodb,c 
Final F/U 
Visit 
Self 
Administra-
tion 
Early 
Term. 
Visit 
Unsched. 
Hyper. 
Reaction 
Visit.d  
Perform 
within 
48 hours 
Week 1 
Weeklyb 
Monthly 
(eg, Wk 4, 
8, etc.) 
Quarterly  
(eg, Wk 12, 
24, etc.) 
Interim 
Clinician 
Visit 
(HHRN or 
Site) 
D 1 
Starting 
at Week 2 
Every 4th 
week; 
Perform 
in 
addition 
to weekly 
procedure
s 
Every 12th 
week. 
Perform in 
addition to 
monthly 
procedures 
Up to daily 
1 week 
after final 
dose 
 
4 weeks 
after final 
dose 
Adverse eventsj, k 
X 
X 
X 
 
 
X 
X 
X 
X 
X 
Weekly phone call to self 
admin participants only (to 
assess AEs, Inj site reactions, 
concomitant medications) 
 
 
 
 
 
 
 
X 
X 
 
Concomitant medicationsj 
X 
X 
X 
 
 
X 
X 
X 
X 
X 
Diet query 
X 
X 
X 
 
 
 
X 
 
X 
 
3-Day diet diaryl 
 
 
 
X 
 
 
X 
 
X 
 
Serum antibodies  
 
X 
 
X 
 
 
X 
 
X 
X 
Plasma Phe and plasma 
X 
X 
X 
Xm 
 
 
X 
 
X 
 
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Assessments and Events 
Screeninga 
Treatment Periodb,c 
Final F/U 
Visit 
Self 
Administra-
tion 
Early 
Term. 
Visit 
Unsched. 
Hyper. 
Reaction 
Visit.d  
Perform 
within 
48 hours 
Week 1 
Weeklyb 
Monthly 
(eg, Wk 4, 
8, etc.) 
Quarterly  
(eg, Wk 12, 
24, etc.) 
Interim 
Clinician 
Visit 
(HHRN or 
Site) 
D 1 
Starting 
at Week 2 
Every 4th 
week; 
Perform 
in 
addition 
to weekly 
procedure
s 
Every 12th 
week. 
Perform in 
addition to 
monthly 
procedures 
Up to daily 
1 week 
after final 
dose 
 
4 weeks 
after final 
dose 
tyrosinem 
Plasma PK sample 
 
X 
Xo 
 
 
 
X 
 
X 
X 
Administer study drugn 
 
X 
X 
 
 
X 
 
X 
 
 
Skin biopsy (optional; affected 
and not affected area) 
 
 
 
 
 
 
 
 
 
X 
Serum tryptase level o 
 
 
 
 
 
 
 
 
 
X 
AE, adverse event; C3, complement 3; C4, complement 4; CH50, total hemolytic complement; CRP, C-reactive protein; D, day; ECG, electrocardiogram; ETV, 
Early Termination Visit; F/U, Follow-up; Hyper, hypersensitivity; IgE, immunoglobulin E; IgG, immunoglobulin G; IgM, immunoglobulin M; IP, 
investigational product; PK, pharmacokinetics; Phe, phenylalanine; SAE, serious adverse event; Wk, week. 
a A separate Screening visit for this study is required only if the time between completion of the previous rAvPAL-PEG study and enrollment into PAL-003 is 
greater than 28 days. 
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b Weekly visits do not require an in-clinic visit if conducted by a home healthcare professional. Monthly visits must be performed in the clinic. 
c On days that a dose is given, all procedures should be performed predose, except where noted. 
d Refer to Section 9.1.1.3.3 and Section 12.3.8. 
e Complete physical examinations to include the evaluation of all major body systems. Height will be measured at Screening only. 
f Clinical laboratory tests to include spot urine albumin/creatinine ratio, hematology, chemistry, and urinalysis. Urine microscopy will be performed if any 
urinalysis results are positive for hematuria.  Refer to Table 9.7.6.1. 
g Subjects who have a systemic reaction or a large local reaction not contiguous with the injection site should be assessed for CRP, CH50, C1, C3, and C4 within 
48 hours of the reaction.  
hComplement C3 and C4 will be collected at the Screening Visit and quarterly. Additional complement testing will be performed and as needed to resolve 
previous abnormal test results. 
i If positive or equivocal, perform serum pregnancy test. 
j If any injection site reaction is observed, the corresponding adverse event data must specify injection location (identify current vs. previous visit’s injection, eg, 
right arm vs. left arm). 
j Subjects must have AEs and concomitant medications assessed and an injection-site inspection performed whenever dose is administered even if the 
administration does not coincide with a scheduled clinic visit.   
k The reporting period for SAEs begins when informed consent is obtained and continues through 4 weeks after last dose or the final study visit. The reporting 
period for nonserious AEs is from the first administration of study drug to the final study visit.  
l  It is preferable that the subject complete the diary 3 days immediately prior to the next monthly visit. 
m Samples should be drawn at least 2.5 hours after a meal.  At the Investigator’s discretion, blood Phe may be collected monthly rather than weekly, provided the 
subject satisfies the criteria in Section 9.7.2.1. 
n Dosing is up to 5.0 mg/kg/week, including subjects who receive more than 1 dose/week. Every effort should be made to adhere to the study drug administration 
regimen. If a subject misses more than 2 scheduled doses of study drug, both dose level and dose frequency may be re-evaluated.  
o Mandatory for subjects who have a systemic reaction.  Take sample immediately after reaction if possible. 
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Table 9.1.2:  PK Substudy Dosing Regimens 
Treatment Frequency 
Plasma PK Sampling 
Example 
Subjects who are 
administered study drug 
once per week 
Pre-dose and every 24 hours 
thereafter (24, 48, 72, and 96 hours 
when possible), and pre-dose of the 
next weekly dose 
If dosed on Monday: 
Obtain PK sample pre-dose when possible – pre-dose Monday, Tuesday, Wednesday, 
Thursday, Friday, and pre-dose the following Monday. 
No further PK substudy draws. 
Subjects who are 
administered study drug two 
or three times per week 
Pre-dose and every 24 hours during 
the longest period between doses, 
when possible, and pre-dose of the 
next dose. 
If dosed on Monday, Thursday, and Friday: 
Obtain PK sample every 24 hours during the longest period between doses: Pre-dose 
Monday, Tuesday, Wednesday, and pre-dose Thursday. 
No further PK substudy draws. 
Subjects who are 
administered study drug four 
to seven times per week. 
Pre-dose and every 12 hours during 
the longest period between doses, 
when possible, then pre-dose of the 
next dose. 
If dosed Monday through Friday: 
Obtain PK sample every 12 hours during the longest period between doses (Friday to 
Monday): pre-dose Friday, 12 hours post-dose Friday, Saturday (24 and 36 hours post 
dose), Sunday (48 and 60 hours post-dose), and pre-dose the following Monday. 
No further PK substudy draws. 
 
 
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9.1.1 Management of Local and Systemic Reactions to rAvPAL-PEG 
Subjects who qualify for self administration of study drug will be provided with information 
and instruction with regard to management of local and systemic reactions (refer to the 
Subject Self-Administration Training Materials). 
9.1.1.1 
Subjects Who Have Had Previous Hypersensitivity Reactions to 
rAvPAL-PEG or a PEG-containing Product 
Subjects who had a previous systemic reaction to rAvPAL-PEG or a PEG-containing product 
that warranted early termination from a previous rAvPAL-PEG study are excluded from 
participation in this study. Subjects who experienced a generalized skin rash are included in 
this category. Subjects who have had a previous local skin reaction to rAvPAL-PEG in a 
previous rAvPAL-PEG study are eligible to participate in this study. Subjects who have had 
a previous reaction and are deemed eligible for participation must be premedicated orally 
with acetaminophen and/or non-sedating antihistamines 1-2 hours prior to study drug dosing 
for the remainder of the study. The premedication dosage will be standard. Because 
antihistamines can cause drowsiness, it may be administered only if the subject is 
accompanied by a designated driver (if applicable). Subjects may develop systemic, large 
local skin, or local skin reactions after enrollment in PAL-003. Refer to Section 9.1.1.2 for 
definitions of systemic and local skin reactions. For management of hypersensitivity 
reactions that occur during this study, refer to Section 9.1.1.3 and Figure 9.1.1.3.1 
9.1.1.2 
Definition of Reaction and Hypersensitivity Reactions to rAvPAL-PEG 
Administered Subcutaneously 
During Study PAL-003, subjects may experience hypersensitivity reactions to rAvPAL-PEG. 
The hypersensitivity reactions are defined as follows: 
Local skin reaction: 
• Skin signs or symptoms in 1 affected primary location, ie, hives, wheals, or swelling 
or an area of erythema, redness, induration, pain, or itching at or near the site of 
injection. 
Large local skin reaction: 
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• Skin signs or symptoms, ie, hives, wheals, or swelling or an area of erythema, 
redness, or induration with pain or itching that extends beyond the site of injection by 
approximately 6 inches (15 cm) and/or signs or symptoms that are not contiguous to 
the injection site. These may be associated with a low risk of systemic symptoms or 
anaphylaxis upon re-exposure and, therefore, will be managed as a systemic reaction 
when not contiguous to the injection site.  
Systemic reaction (including generalized skin symptoms): 
• Skin and non-skin signs or symptoms in more than 1 affected primary location, 
ie, cutaneous reaction in more than 1 area and/or anaphylaxis or any other generalized 
symptoms, such as hypotension, angioedema or the involvement of other organ 
systems, eg, respiratory, cardiovascular, gastrointestinal, neurological; and/or a fever 
attributed to treatment with rAvPAL-PEG ( ≥ 100.4°F or  ≥ 38°C). 
For management of hypersensitivity reactions that occur during this study, refer to 
Section 9.1.1.3 and Figure 9.1.1.3.1 
 
 
 
 
 
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9.1.1.3.1 Local Skin Reactions 
All subjects who experience a local skin reaction during this study may be premedicated 
orally with acetaminophen and/or non-sedating antihistamines 1-2 hours prior to study drug 
dosing (subjects may take non-sedating premedications prior to coming to clinic) for all 
future study doses. Recommended premedications are acetaminophen and/or non-sedating 
antihistamine. The dosage will be standard. Because antihistamines can cause drowsiness, 
sedating antihistamines may be administered only if the subject is accompanied by a 
designated driver. Symptoms of local reactions may be treated with local application of ice 
and non-sedating oral and/or topical antihistamines and/or topical steroids (refer to 
Section 7.4.2.2). 
If the local skin reaction worsens with a repeat injection (as determined by the Investigator in 
consultation with the Sponsor’s Medical Officer) even with premedication prior to study drug 
dosing, the subject must be withdrawn from study treatment. 
9.1.1.3.2 Large Local Skin Reactions 
Large local skin reactions (refer to Section 9.1.1.2 for a definition) may or may not be 
contiguous to the rAvPAL-PEG injection site, and subjects with either type of large local 
skin reaction may continue dosing if the skin symptoms have resolved and no other 
symptoms have developed. Subjects will be premedicated orally with acetaminophen and/or 
non-sedating antihistamines 1-2 hours prior to study drug dosing (subjects may take non-
sedating premedications prior to coming to clinic) for all future study doses. 
Symptoms of large local skin reactions may be treated with local application of ice and 
topical, oral, or IV antihistamines and/or steroids as needed (refer to Section 7.4.2.2). 
9.1.1.3.2.1 
Large Local Skin Reactions Contiguous to Injection Site 
Subjects who develop a large local skin reaction contiguous to the injection site after 
administration of rAvPAL-PEG or to rAvPAL-PEG or a PEG-containing product may 
remain in the study if the skin symptoms have resolved and no other symptoms have 
developed. For the remainder of the study, subjects will be premedicated orally with 
acetaminophen and/or non-sedating antihistamines 1-2 hours prior to study drug dosing 
(subjects may take non-sedating premedications prior to coming to clinic) for all future study 
doses. Because antihistamines can cause drowsiness, it may be administered only if the 
subject is accompanied by a designated driver (if applicable).  
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Symptoms of large local skin reactions may be treated with local application of ice and 
topical, oral, or IV antihistamines and/or steroids as needed (refer to Section 7.4.2.2).  
9.1.1.3.2.2 
Large Local Skin Reactions Not Contiguous to Injection Site 
Large local skin reactions that are not contiguous to the injection site may be associated with 
a low risk of systemic symptoms or anaphylaxis upon re-exposure to rAvPAL-PEG and, 
therefore, will be managed as a systemic reaction (refer to Section 9.1.1.3.3). An example of 
a large local reaction that is not contiguous to the injection site is if an injection took place in 
the right upper arm and there are lesions beyond the elbow joint in the right forearm or 
lesions beyond the shoulder joint on the right trunk. 
Symptoms of large local skin reactions may be treated with local application of ice and 
topical, oral, or IV antihistamines and/or steroids as needed (refer to Section 7.4.2.2). 
9.1.1.3.3 Systemic Reactions 
Subjects who experience a systemic reaction (refer to Section 9.1.1.2 for a definition) after 
administration of rAvPAL-PEG must stop further administrations of rAvPAL-PEG and must 
immediately return to the clinic for safety assessments. Subjects who experience generalized 
skin symptoms are included in this category. Immediately after the systemic reaction (within 
48 hours), subjects with generalized skin symptoms must have additional assessments 
performed for safety (ie, Unscheduled Hypersensitivity Reaction Visit): serum antibodies 
(anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, anti-PEG IgM, anti rAvPAL-PEG IgE, 
anti-rAvPAL-PEG neutralizing antibodies); serum tryptase level (it is recommended that this 
sample be drawn immediately after reaction); sedimentation rate; CRP, CH50, C1, C3, and 
C4; skin biopsy (optional; affected and not affected area; to be performed within 1 week of 
reaction); and clinical laboratory tests (urinalysis, chemistry, hematology; refer to 
Figure 9.1.1.3.1.  
Following the reaction, subjects will be required to complete the assessments of the 
Unscheduled Hypersensitivity Reaction visit, including assessment of IgE. If a subject 
presents with a clinical diagnosis of anaphylaxis, further dosing will be held while laboratory 
evaluation of IgE, as part of the Unscheduled Systemic Reaction Visit, is performed.  
Subjects who do not have an IgE-mediated reaction may resume study drug administration 
per the discretion of the Principal Investigator and the Sponsor’s Medical Officer; however, 
if subject was dosing at home, they will be required to come into the clinic for at least 1 
week. If laboratory data shows that the subject experienced an IgE-mediated reaction, dosing 
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will not resume until review of the case with the Investigator, Sponsor’s Medical Officer, and 
an allergist/immunologist.   
rAvPAL-PEG administration will resume at the next lowest dose level. Restarting of 
rAvPAL-PEG administration following a systemic reaction must be performed in the clinic 
for the first week of resumed dosing. Subjects must be premedicated orally with 
acetaminophen and/or antihistamines 1-2 hours prior to study drug dosing (subjects may take 
non-sedating premedications prior to coming to clinic) for all future study doses. 
Additionally, subjects must be closely monitored for 30-60 minutes following every 
administration of study drug. Because antihistamines may cause drowsiness, the subject must 
be accompanied by a designated driver (if applicable).   
If blood Phe concentrations are not 60-600 µmol/L following 1 week of daily administration 
at the lowered dose cohort and there is no further evidence of toxicity (ie, another systemic 
reaction attributed to rAvPAL-PEG administration or clinically significant abnormal 
laboratory test results), the subject may be administered the next highest dose level in the 
clinic per the allowable dose increases outlined in Section 9.1.2. Subjects must be 
premedicated orally with acetaminophen and/or antihistamines 1-2 hours prior to study drug 
dosing (subjects may take non-sedating premedications prior to coming to clinic) for all 
future study doses. Additionally, subjects must be closely monitored for 30-60 minutes 
following every study drug administration. Because antihistamines may cause drowsiness, 
the subject must be accompanied by a designated driver (if applicable). 
9.1.2 Dose Modifications 
9.1.2.1 
Dose Increase Methodology 
Each subject’s dose may be modified based on the decision of the Investigator, in agreement 
with the Sponsor’s Medical Officer. Decisions regarding dose increases will depend on a 
subject’s adverse event profile and blood Phe and drug concentrations. 
An individual subject’s dose may be adjusted beginning on Day 1 of PAL-003. For the 
duration of this study, an individual subject’s dose may be adjusted if warranted per a 
subject’s adverse event profile and blood Phe concentrations. Dose increases should be 
performed as follows: 
• The dose may be increased by increments of no more than 10-fold higher than the 
subject’s current dose. 
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• When increasing the dose, a dose may be used that is between the dose levels (0.001, 
0.003, 0.01, 0.03, 0.06, 0.1, 0.2, 0.3, 0.4, 0.6, 0.8,  1.0, 2.0, 3.0, 4.0, and 5.0 mg/kg)  
or per Investigator determination in consultation with the Sponsor’s Medical Officer 
based on available information regarding a subject’s blood Phe (60-600 µmol/L) as 
well as any adverse events (any hypersensitivity reaction) for an individual subject. 
• The dose may be adjusted by increasing the frequency up to daily for a total weekly 
dose not to exceed 5.0 mg/kg.  Subjects who increase their dose frequency should 
perform the Interim Dosing Visit assessments (refer to Section 12.3.6 and 
Table 9.1.1). 
• When a dose is increased, the subject must be observed for 30-60 minutes following 
the first modified dose administration. Subjects who increase their dose frequency do 
not need to be observed following injection of study drug if the increase in frequency 
does not increase the overall weekly dose amount. 
• Only 1 dose adjustment is allowed every 2 weeks. 
9.1.2.2 
Dose Decrease Methodology 
All dose decreases must be agreed to by both the Investigator and the Sponsor’s Medical 
Officer. Decisions regarding dose decreases will depend on available information regarding a 
subject’s blood Phe (60-600 µmol/L), as well as any adverse event (any hypersensitivity 
reaction as defined in Section 9.1.1.2). Dose decreases may occur for safety (ie, any adverse 
event that may be improved with a lower, more frequent dose). 
A dose should first be reduced by dose level (5.0, 4.0, 3.0, 2.0, 1.0, 0.8, 0.6, 0.4, 0.3, 0.2, 0.1, 
0.06, 0.03, 0.01, 0.003, 0.001 mg/kg). It is also permitted to decrease dose in between these 
specified dose levels. If further dosing adjustments are required to attain the target Phe 
concentration, dosing frequency may be reduced.  
If the subject develops low blood Phe (as defined by a blood Phe level ≤ 30 µmol/L as 
measured by serum Phe levels for a minimum of 1 month), the subject’s rAvPAL-PEG dose 
should be decreased to the next lower dose.  If the condition persists after another 1 month at 
the lower dose, the dose should be decreased again to the next lower level. If the subject 
continues to experience low blood Phe after two dose level reductions, the subject may be 
asked to consult the dietician to eliminate medical foods and/or formulas and to ensure a 
balanced and nutritious diet (as part of the routine standard of care for PKU disease 
management, subject diet should be monitored by a dietician). 
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9.1.3 Safety Assessment Criteria 
If an individual subject exhibits toxicity of a treatment-emergent CTCAE grade 3 or greater 
or a systemic reaction that is assessed as related to treatment with study drug, that subject 
will have dosing halted until the toxicity resolves. The subject’s data will be evaluated by the 
Principle Investigator (PI) and the Sponsor’s Medical Officer, and a decision will then be 
made whether to discontinue the subject from the study treatment, restart dosing at the same 
dose level, or restart dosing at a lower dose level. 
9.1.4 Stopping Criteria 
If 2 or more subjects at a dose level exhibit toxicity of a treatment-emergent CTCAE grade 3 
or greater or a systemic reaction that is assessed as related to treatment with study drug, 
further dosing of subjects at that dose level will evaluated and a safety assessment will be 
completed. In addition, the Food and Drug Administration (FDA) may be notified of this 
occurrence if appropriate. 
9.2 
Discussion of Study Design, Including Choice of Control Group 
This open-label, Phase 2 trial was designed to be closely monitored with the goal of 
obtaining information about the efficacy, safety, tolerability, and PK of long-term 
administration of rAvPAL-PEG in subjects with PKU. There will be no control group in this 
study. 
9.3 
Selection of Study Population 
9.3.1 Inclusion Criteria 
Individuals eligible to participate in this study must meet all of the following criteria: 
1. Must have completed participation in a previous rAvPAL-PEG study. 
2. Willing and able to provide written, signed informed consent, or in the case of 
subjects under the age of 18 years, provide written assent (if required) and written 
informed consent by a parent or legal guardian, after the nature of the study has been 
explained, and prior to any research-related procedures. 
3. Willing and able to comply with all study procedures. 
4. Females of childbearing potential must have a negative pregnancy test at Screening 
and be willing to have additional pregnancy tests during the study. Females 
considered not of childbearing potential include those who have been in menopause at 
least 2 years, or had tubal ligation at least 1 year prior to Screening, or who have had 
total hysterectomy. 
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5. Sexually active subjects must be willing to use an acceptable method of contraception 
while participating in the study. 
6. Maintained a stable diet. 
7. In generally good health as evidenced by physical examination, clinical laboratory 
evaluations (hematology, chemistry, and urinalysis), and electrocardiogram (ECG) at 
Screening. 
9.3.2 Exclusion Criteria 
Individuals who meet any of the following exclusion criteria will not be eligible to participate 
in the study: 
1. Use of any investigational product (with the exception of rAvPAL-PEG) or 
investigational medical device within 30 days prior to Screening, or requirement for 
any investigational agent prior to completion of all scheduled study assessments. 
2. Use of any medication other than rAvPAL-PEG that is intended to treat PKU within 
14 days prior to the administration of study drug. 
3. Use or planned use of any injectable drugs containing PEG (other than 
rAvPAL-PEG), including Depo-Provera, within 6 months prior to Screening and 
during study participation. 
4. A prior reaction that included systemic symptoms (eg, generalized hives, respiratory 
or gastrointestinal problems, hypotension, angioedema, anaphylaxis) to rAvPAL-PEG 
or a PEG-containing product. Subjects with a prior systemic reaction may be eligible 
for participation per the discretion of the Principal Investigator in consultation with 
the Sponsor’s Medical Officer. However, subjects who discontinued from study 
treatment early due to a reaction are not eligible to enroll into this study.      
5. Pregnant or breastfeeding at Screening or planning to become pregnant (self or 
partner) or to breastfeed at any time during the study. 
6. Concurrent disease or condition that would interfere with study participation or safety 
(eg, history or presence of clinically significant cardiovascular, pulmonary, hepatic, 
renal, hematologic, gastrointestinal, endocrine, immunologic, dermatologic, 
neurological, oncologic, or psychiatric disease). 
7. Any condition that, in the view of the PI, places the subject at high risk of poor 
treatment compliance or of not completing the study. 
8. Known hypersensitivity to rAvPAL-PEG or its excipients, including hypersensitivity 
reactions that necessitated early termination from a previous rAvPAL-PEG study. 
9. Alanine aminotransferase (ALT) concentration > 2 times the upper limit of normal. 
10. Creatinine > 1.5 times the upper limit of normal. 
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9.3.3 Removal of Subjects from Treatment or Assessment 
Subjects (or their legally authorized representative) may withdraw their consent to participate 
in the study or to receive study drug at any time without prejudice. The Investigator must 
withdraw from the study or study drug treatment any subject who requests to be withdrawn. 
A subject’s participation in the study may be discontinued at any time at the discretion of the 
Investigator and in accordance with his/her clinical judgment. When possible, a subject who 
is discontinued from study treatment should continue to perform the study tests and 
evaluations until study completion. For subjects who discontinue from the study, the tests 
and evaluations listed for the Early Termination Visit should be carried out (refer to 
Section 12.4). 
BioMarin must be notified of all subject withdrawals as soon as possible. BioMarin also 
reserves the right to discontinue the study at any time for either clinical or administrative 
reasons and to discontinue participation by an individual Investigator or site for poor 
enrollment or noncompliance. 
Reasons for which the Investigator or BioMarin may withdraw a subject from the study 
treatment include, but are not limited to, the following: 
• Subject experiences a serious or intolerable adverse event (AE). 
• Subject develops a clinically significant laboratory abnormality. 
• Subject requires medication prohibited by the protocol. 
• Subject becomes pregnant (refer to Section 10.3 for details on the reporting 
procedures to follow in the event of pregnancy). 
Reasons for which the Investigator or BioMarin may withdraw a subject from the study 
include, but are not limited to, the following: 
• Subject does not adhere to study requirements specified in the protocol. 
• Subject was erroneously admitted into the study or does not meet entry criteria. 
• Subject is lost to follow-up. 
If a subject fails to return for scheduled visits, a documented effort must be made to 
determine the reason. If the subject cannot be reached by telephone within 7 days, a certified 
letter should be sent to the subject (or the subject’s legally authorized representative, if 
appropriate) requesting contact with the Investigator. This information should be recorded in 
the study records. 
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The Investigator or designee must explain to each subject, before enrollment into the study, 
that for evaluation of study results, the subject’s protected health information obtained during 
the study may be shared with the study sponsor, regulatory agencies, and IRB. It is the 
Investigator’s (or designee’s) responsibility to obtain written permission to use protected 
health information per country-specific regulations, such as the Health Insurance Portability 
and Accountability Act (HIPAA) in the United States, from each subject, or if appropriate, 
the subject’s legally authorized representative. If permission to use protected health 
information is withdrawn, it is the Investigator’s responsibility to obtain a written request, to 
ensure that no further data will be collected from the subject and the subject will be removed 
from the study. 
9.3.4 Subject Identification and Replacement of Subjects 
Subjects will retain the same subject number assigned in their previous rAvPAL-PEG study. 
This unique identifier will be on all case report form (CRF) pages. In legal jurisdictions 
where use of initials is not permitted, a substitute identifier will be used.  
Subjects who do not complete the study will not be replaced. 
9.4 
Treatments 
Upon enrollment into this study, subjects from previous rAvPAL-PEG studies will be dosed 
with the same or higher dose that was administered upon completion of that study provided 
that there was no interruption in dosing.  rAvPAL-PEG doses will be administered SC by 
either health care professionals or via self administration. The dose level may be increased 
per Investigator determination in consultation with the Sponsor’s Medical Officer based on 
available information regarding a subject’s blood Phe level (60-600 µmol/L), as well as any 
adverse events (any hypersensitivity reaction) for an individual subject. The dosage that 
provides control of blood Phe concentrations within the target range of 60-600 µmol/L for a 
minimum of 2 weeks will be determined for each subject by adjusting the dose level, dose 
frequency, or both, as agreed to by the PI and the Sponsor’s Medical Officer, based upon the 
subject’s response to doses.  
Subjects may self administer study drug at home if approved by the Investigator and the 
Sponsor’s Medical Officer and if adequate training is demonstrated. Subjects may be eligible 
to self administer study drug if he or she meets the following criteria:  
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• The subject is on a stable dosing regimen for 2 weeks (ie, the subject has 
demonstrated a blood Phe level within 60-600 µmol/L for a minimum of 2 
consecutive weeks). 
• The subject has not experienced any CTCAE Grade 3 or higher adverse event.  
• The subject has not experienced any hypersensitivity reaction to rAvPAL-PEG for at 
least 4 weeks. 
• The subject has no cognitive impairments that may increase the safety risk of self 
administration per the assessment of the PI.  
• The subject has been approved for self administration of study drug by the Sponsor’s 
Medical Officer. 
• The subject has completed the Self-Administration Training conducted by qualified 
study site personnel and has been observed by the study site personnel to be able to 
adequately prepare the proper dose and perform the injections safely.  
• The subject has been provided with epinephrine and has been trained on when and 
how to administer it.  
Qualified study site personnel will train each eligible subject on all procedures for self 
administration of study drug under the supervision of the PI. Qualified study site personnel 
will also be required to observe the subject prepare and perform at least 1 injection prior to 
allowing the subject to self administer a dose at home. The subject will see a study site nurse 
or home healthcare nurse in person every week or receive a telephone call from site staff to 
ensure that the subject continues to perform all self-administration procedures correctly, to 
assess adverse events, and to answer questions throughout the duration of the study. The 
study site nurse or home healthcare nurse will also perform the regularly scheduled 
assessments and procedures as outlined in Table 9.1.1 and Section 12; the subject must 
perform a clinic visit monthly at minimum. Training materials and other information specific 
to the study site personnel are provided in the Subject Self-Administration Training 
Materials.     
Subjects who are eligible for self administration will be provided with a Subject Study 
Manual. Self-administration training materials will be provided in the Subject Study Manual 
to supplement the in-person training provided by the qualified study site personnel. The 
Subject Study Manual will include step-by-step instruction on the following: 
• How to prepare and perform the injections of study drug safely. 
• How to receive, track, store, prepare, and return both used and unused study drug.   
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• How to safely use and dispose of syringes used for injections of study drug. 
• How to use a new syringe and vial every time drug is administered. 
• How to care for their injection site after an injection of study drug.  
• How to identify an adverse reaction and how to report this reaction to the study site.  
• How and when to use epinephrine. 
• Who to contact at the study site in case of an emergency.  
The PI or the Sponsor’s Medical Officer may request that self administration be halted at any 
time and that the subject resume injections performed by the study site personnel or home 
healthcare nurse. 
Subjects who are within the target Phe range may also be permitted to convert from 
weight-based dosing to fixed dosing (refer to Section 9.4.4). 
9.4.1 Treatments Administered 
BioMarin and/or its designee will provide the study site or subject with a supply of IP 
sufficient for the completion of the study. BioMarin is responsible for shipping study drug to 
the clinical sites. The clinical site is responsible for supplying the study drug to subjects who 
qualify for self administration. Refer to the PAL-003 Pharmacy Manual for information 
pertaining to the distribution of study drug from sites.   
Information regarding supplying study drug to subjects who qualify for self administration is 
provided in the Subject Self-Administration Training Materials. 
9.4.2 Identity of Investigational Product (IP) 
9.4.2.1 
Product Characteristics and Labeling 
The rAvPAL-PEG drug product for SC injection is formulated and supplied as a sterile 
aqueous (colorless to pale yellow) solution in clear, single-use, type-1 borosilicate glass 
vials. Each 3 mL vial contains 1.5 ± 0.2 mL to deliver either 10 mg of rAvPAL-PEG per 
1 mL (10 mg/mL protein concentration) or 15 mg of rAvPAL-PEG per 1 mL (15 mg/mL 
protein concentration). Each vial is filled with 1.5 ± 0.2 mL to allow the withdrawal and 
delivery of up to 1 mL of the drug product. 
Dilution instructions are provided in a separate instruction manual. 
The excipients in this drug product are tromethamine, tromethamine-hydrochloride, 
sodium chloride, L-phenylalanine, and water for injection. 
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Drug product packaging will be identified with the lot number and expiration date, and will 
be provided in a box labeled with the study number. 
9.4.3 Storage 
IP must be stored at 5 ±3°C (41 ± 5°F) under the conditions specified in the IB. At the 
site, the IP will be stored in a secure area accessible only to the designated pharmacists and 
clinical site personnel. All IP must be stored and inventoried and the inventories must be 
carefully and accurately documented according to applicable state, federal and local 
regulations, ICH GCP, and study procedures. 
Specific instructions for storage of study drug for subjects who qualify for self administration 
are provided in the Subject Self-Administration Training Materials.  
9.4.4 Directions for Administration 
Doses will be administered SC and the favorable dose will be determined for each subject by 
adjusting the dose level, dose frequency, or both, as agreed by the PI and the Sponsor’s 
Medical Officer, based upon the subject’s response to doses. Dosing is up to a maximum 
dose per week of 5.0 mg/kg (or 375 mg for subjects receiving a fixed dose).  
For subjects receiving weight-based dosing, dosage is calculated by multiplying each 
subject’s weight in kilograms (kg) on Day 1 (predose) by the assigned dose (in mg/kg). 
During the study, if the weight of a subject changes more than 10% from the measurement 
obtained at baseline or at a previous measurement, the subject’s dose may be adjusted to 
accommodate the change. The change must be recorded. Refer to the Pharmacy Manual for 
additional information on calculating dosage. 
Subjects who have demonstrated efficacy (as measured by blood Phe within the target range 
of 60-600 µmol/L for at least 2 consecutive weeks) and who have maintained a stable 
rAvPAL-PEG dose for at least 2 consecutive weeks may be eligible to transition from 
weight-based dosing to a fixed dosing regimen that would permit daily dosing (5- or 7-days-
per-week).  Subjects who convert to a fixed-dosing regimen should convert their dose based 
upon the information presented in Table 9.4.4.1. 
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Table 9.4.4.1:  Fixed Doses for Subjects on Weight-Based Dose Regimen 
Weight-based 
dose (mg/kg) 
Equivalent 
fixed dose 
(mg) 
Vol for 10 
mg/ml 
concentration 
(ml) 
Vol for 15 
mg/ml 
concentration 
(ml) 
0.03 
2.5 
0.25 
0.17 
0.06 
5 
0.5 
0.33 
0.12 
10 
1 
0.67 
0.25 
20 
2 
1.33 
0.5 
40 
4 
2.67 
1.0 
75 
7.5 
5 
2.0 
150 
15 
10 
3.0 
225 
22.5 
15 
4.0 
300 
30 
20 
5.0 
375 
37.5 
25 
 
It is preferable that the injection sites should be alternated between doses, ie, upper left arm 
in Week 1, upper right arm in Week 2, etc. Doses may be administered in any of the common 
SC areas (upper arm, thigh, abdomen). If dose volume is such that a dose will be divided and 
given in more than 1 injection site, it is preferable to use both arms, both legs, or both sides 
of the abdomen. 
Subjects may require more than 1 injection per dose, depending upon site policy (ie, some 
institutions do not permit a single SC injection of greater than 2 mL). The number of 
injections required for an individual weighing 80 kg (about 176 pounds) is provided in 
Table 9.4.4.2 as an example. Note this table is for example purposes only. Dosage 
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calculations must be performed according to study drug preparation instructions provided in 
the PAL-003 Pharmacy Manual. Study drug will be administered by clinic staff, other 
qualified and trained study personnel, or qualified subjects. 
Information for dosing of subjects who enroll into this study after completing previous 
rAvPAL studies is provided in Section 9.1. Instructions for subjects who re-start rAvPAL-
PEG dosing due to unplanned missed doses are provided in Section 9.4.10.  
Instructions for administration of study drug for subjects who qualify for self administration 
are provided in the Subject Self-Administration Training Materials. 
Table 9.4.4.2:  Number of Injections Required For an Individual Weighing 80 kg 
Dose Group 
(mg/kg) 
Weight 
(kg) 
Volume of Study Drug 
(mL)a 
No. of 
Injectionsb 
0.001 
80 
0.8 
1 
0.003 
80 
0.6 
1 
0.01 
80 
0.8 
1 
0.03 
80 
0.2 
1 
0.06 
80 
0.5 
1 
0.1 
80 
0.8 
1 
0.3 
80 
2.4 
2 
0.6 
80 
4.8 
2 or 3 
1.0 
80 
8.0 
4 
aStudy drug is supplied at a concentration of 10 mg/mL and is then diluted by differential amounts as specified 
in the PAL-003 Pharmacy Manual. Volume to be injected is calculated based on a starting volume. 
bNumber of injections per dose is dependent upon site policy for SC injections. The number of injections may 
vary at the discretion of the Investigator. 
 
Every effort should be made to adhere to the study drug administration regimen. If a subject 
misses more than 2 scheduled doses of study drug, both dose level and dose frequency may 
need to be re-evaluated (refer to Section 9.4.10). 
9.4.5 Method of Assigning Subjects to Treatment Groups 
This will be an open-label study; no randomization schedule will be generated. 
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Subjects will retain the same subject number used in their previous rAvPAL-PEG study. 
9.4.6 Selection of Doses Used in the Study 
This Phase 2 study aims to evaluate the efficacy, safety, tolerability, and PK parameters of 
multiple doses of rAvPAL-PEG after long-term administration in subjects with PKU. A dose 
that produces a reduction in blood Phe concentrations to 60-600 μmol/L will be determined 
for each subject based on preliminary safety, antibody, and efficacy data from this ongoing 
study. 
9.4.6.1 
Selection of Timing of Dose for Each Subject 
Study drug will be administered by clinic staff or other qualified and trained study personnel. 
Subjects may self administer study drug at home if approved by the Sponsor’s Medical 
Officer and if adequate training is provided (refer to Section 9.4). 
9.4.7 Blinding 
This is an open-label study. 
9.4.8 Prior and Concomitant Medications 
All prescription and over-the-counter (OTC) medications taken by a subject for 30 days 
before Screening will be recorded on the designated CRF. The Investigator may prescribe 
additional medications during the study, as long as the prescribed medication is not 
prohibited by the protocol. In the event of an emergency, any needed medications may be 
prescribed without prior approval, but the Sponsor’s Medical Officer must be notified of the 
use of any contraindicated medications immediately thereafter. Any concomitant medications 
added or discontinued during the study should be recorded on the CRF. 
Use of any investigational product (with the exception of rAvPAL-PEG used in a previous 
rAvPAL-PEG study) or investigational medical device within 30 days before Screening, or 
requirement for any investigational agent prior to completion of all scheduled study 
assessments, is prohibited. 
Use or planned use of any injectable drugs containing PEG (other than rAvPAL-PEG), 
including Depo-Provera, is prohibited within 6 months prior to Screening and during study 
participation. A list of PEG-containing injectable drugs is provided in the study reference 
materials. Subjects who have had a prior local skin reaction to rAvPAL-PEG or a 
PEG-containing product will be premedicated with acetaminophen and/or non-sedating 
antihistamines (refer to Section 9.1.1). If the local skin reaction worsens with a repeat 
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injection (as determined by the Investigator in consultation with the Sponsor’s Medical 
Officer) even with premedication prior to study drug dosing, the subject must be withdrawn 
from the study and complete an Early Termination Visit. 
Subjects who have had a prior systemic reaction to rAvPAL-PEG or a PEG-containing 
product may participate in this study (refer to Section 9.1.1).  
Use of any medication that is intended to treat PKU within 14 days prior to the 
administration of study drug is prohibited. 
9.4.9 Treatment Compliance 
The date, time, volume, and concentration of each dose of study drug administered to each 
subject must be recorded in the dispensing log provided for the study, as well as on the 
appropriate CRF. This data will be used to assess treatment compliance. 
9.4.10 Dose Interruption and Missed Doses  
Information for dosing of subjects who enroll into this study after completing previous 
rAvPAL_PEG studies is provided in Section 9.1.  
During this long-term extension study, interruption of rAvPAL-PEG dosing may occur per 
subject decision or per the Investigator in consultation with the Sponsor’s Medical Officer. 
Subjects who miss more than 2 consecutive weekly doses (weekly dosing schedule) or 3 
consecutive daily doses (daily dosing schedule) for whatever reason may continue 
participation in this study. After a dosing interruption, rAvPAL-PEG administration should 
be re-started at the same dose level and dosing frequency that was administered prior to the 
dosing interruption. The first dose of rAvPAL-PEG following a dose interruption should be 
administered in a clinic setting, and the subject must be observed for 30-60 minutes 
following administration due to restarting dosing. A follow-up telephone call will be made to 
the subject to monitor subject safety 24 hours following the return to dosing. Subjects should 
continue to perform the study assessments as outlined in the Schedule of Events (refer to 
Table 9.1.1 during any dosing interruption.  
Subjects who miss rAvPAL-PEG dosing due to poor compliance may be discontinued from 
further study treatment per discretion of the Sponsor or Investigator (refer to Section 9.3.3).  
9.5 
Investigational Product Accountability 
The PI or designee is responsible for maintaining accurate records (including dates and 
quantities) of IP received, subjects to whom IP is dispensed (subject-by-subject dose specific 
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accounting), IP returned, and IP lost or accidentally or deliberately destroyed. The PI or 
designee must retain all unused or expired study supplies until the study monitor (on-site 
CRA) has confirmed the accountability data. 
9.5.1 Return and Disposition of Clinical Supplies 
Unused study drug must be kept in a secure location for accountability and reconciliation by 
the study monitor. The Investigator or designee must provide an explanation for any 
destroyed or missing study drug or study materials. 
Unused study drug may be destroyed on site, per the site’s standard operating procedures, but 
only after BioMarin has granted approval for drug destruction. The monitor must account for 
all study drug in a formal reconciliation process prior to study drug destruction. All study 
drug destroyed on site must be documented. Documentation must be provided to BioMarin 
and retained in the PIs study files. If a site is unable to destroy study drug appropriately, the 
site can return unused study drug to BioMarin upon request. The return of study drug or 
study drug materials must be accounted for on a Study Drug Return Form provided by 
BioMarin. 
Subjects who qualify for self administration of study drug will be provided with instructions 
for returning used and unused study drug and the proper disposal of any study drug materials 
(refer to the Subject Self-Administration Training Materials). 
All study drug and related materials should be stored, inventoried, reconciled, and destroyed 
or returned according to applicable state and federal regulations and study procedures. 
9.6 
Dietary or Other Protocol Restrictions 
Subjects will be instructed that diet should not be altered during the course of the study.   
Any decision to modify subject diet must be made per the Investigator in consultation with 
the Sponsor’s Medical Officer and must be performed under the supervision of the 
Investigator in consultation with the Sponsor’s Medical Officer. 
A 3-day dietary record will be completed by subjects and will be brought to clinic visits for 
review with clinic staff. It is preferable that subjects complete the 3-day record immediately 
prior to their next monthly study visit.The dietary record will be maintained with the study 
source documents. Information regarding a subject diet diary is provided in Section 9.7.4. 
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9.7 
Efficacy and Safety Variables 
9.7.1 Efficacy and Safety Measurements Assessed 
The Schedules of Events in the Synopsis describe the timing of required evaluations. 
For the laboratory assessments, the party responsible for performing the assessment and the 
pertinent protocol section describing the details of the test are listed in Table 9.7.1.1. 
Table 9.7.1.1:  Summary of Laboratory Assessments 
Laboratory Assessment 
Party Responsible for 
Performing Test 
Section in Protocol for 
Details 
Clinical laboratory tests 
Central laboratory 
9.7.6 
Antibody testing 
BioMarina 
9.7.5.2 
PK variables 
BioMarin 
9.7.3 
Blood Phe concentrations 
Central laboratory 
9.7.2.1 
Pregnancy test (urine) and 
sedimentation rate 
Local laboratory 
9.7.6, 9.7.5.1 
Urinalysis 
Central laboratory 
9.7.6 
Phe, phenylalanine; PK, pharmacokinetic. 
aAnalysis of the anti-rAvPAL-PEG IgE assay will be performed by a Contract Research Organization. 
 
9.7.1.1 
Demographic Data and Medical History 
Demographic data and a detailed medical history, including allergy history, will be obtained 
at Screening. The medical history will include specific information concerning any prior or 
existing medical conditions that might interfere with study participation or safety. 
This medical history should elicit all major illnesses, diagnoses, and surgeries that the subject 
has ever had, and whether the subject has a history of alcohol and/or drug abuse. 
9.7.1.2 
Physical Examination Findings 
Physical examination will include assessment of general appearance; CV; dermatologic; 
head, eyes, ears, nose, and throat; lymphatic; respiratory; GI; musculoskeletal; and 
neurological/psychological. Other body systems may be examined. Day 1 results will be the 
baseline values and clinically significant changes from baseline will be recorded as an AE. 
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9.7.1.3 
Vital Sign Measurements 
Vital signs will be measured after resting for 5 minutes, and include seated systolic blood 
pressure (SBP) and diastolic blood pressure (DBP) measured in millimeters of mercury 
(mm Hg), heart rate in beats per minute, respiration rate in breaths per minute, and 
temperature in degrees Celsius (°C). Height (cm) will be measured at Screening only.  
Weight will be measured at Screening and then monthly. 
9.7.1.4 
Electrocardiography 
A standard 12-lead ECG will be recorded while the subject is resting, at Screening and at the 
Final Follow-Up (F/U) Visit or Early Termination Visit (ETV). If clinically significant 
abnormalities are noted at Screening, the PI or designee is required to assess whether it is 
appropriate for the subject to enroll in the study. 
9.7.1.5 
Chest X-Ray 
A chest X-ray will be performed at the Screening, Week 48, and Final Follow-Up (or Early 
Termination) visits to assess gross pulmonary health.  
9.7.2 Efficacy Variable 
9.7.2.1 
Blood Phenylalanine Concentrations 
Blood samples for Phe concentration measurements will be drawn at least 2.5 hours after a 
meal, on the days and time points indicated in the Schedule of Events (Table 9.1.1).   
Blood Phe may be collected monthly, rather than weekly, at the discretion of the Investigator 
and provided that the subject meets the following criteria: 
• Is receiving a stable dose of rAvPAL-PEG (defined as no dose modifications or 
interruptions for at least the previous 2 weeks) 
• Has a stable blood Phe level (defined as Phe between 60-600 µmol/L for at least 2  
consecutive weeks) 
The subject may continue to have monthly, rather than weekly, blood Phe collection 
provided the following do not occur: 
• Blood Phe measurement > 600 µmol/L 
• Blood Phe measurement ≤  30 µmol/L 
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If either of these conditions occurs, then that subject should return to weekly blood Phe 
draws until the rAvPAL-PEG dose has been adjusted and the Phe level is again within the 
protocol-defined target range for at least 2 weeks. 
A central laboratory will be used for blood Phe concentration analysis. 
9.7.3 Pharmacokinetic Variables 
Subjects enrolled in the Substudy will have additional PK sampling performed. For subjects 
participating in the Substudy, PK sampling will be performed as follows: 
• For subjects who are administered rAvPAL-PEG once per week, plasma PK sampling 
will be performed pre-dose and every 24 hours thereafter (24, 48, 72, and 96 hours if 
possible), and then pre-dose of the next weekly dose. 
• For subjects who are administered rAvPAL-PEG two or three times per week, plasma 
PK sampling will be performed pre-dose and every 24 hours during the longest period 
between doses, when possible, and then pre-dose of the next dose.  
• For subjects who are administered rAvPAL-PEG four to seven times per week, 
plasma PK sampling will be performed pre-dose and every 12 hours during the 
longest period between doses, when possible, and then pre-dose of the next dose. 
See Table 9.1.2 for additional details. 
BioMarin will perform the analysis. 
9.7.4 Exploratory Efficacy Variable 
Diet will be assessed for its role in blood Phe reduction relative to rAvPAL-PEG dosing 
using a 3-day diet diary, which will be given to subjects to complete at home. Subjects will 
bring the completed diary with them to clinic visits on a monthly basis. Subjects will be 
instructed to record all food, beverages, special low-protein foods, and medical foods 
consumed for 3 consecutive days each month. If changes in diet are noted per the information 
on the diet diary, the subject will be instructed to maintain their diet as reported at the 
beginning of the study or as otherwise instructed by the Investigator. 
9.7.5 Safety Variables 
9.7.5.1 
Pregnancy Testing 
Female subjects of childbearing potential will have a urine pregnancy test at the time points 
specified in the Schedules of Events (Table 9.1.1). Female subjects with a positive serum 
pregnancy test at Screening do not meet eligibility criteria for enrollment. 
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Additional pregnancy tests will be performed at any visit in which pregnancy status is in 
question. Serum pregnancy tests will be performed in the event of a positive or equivocal 
urine pregnancy test result. 
Refer to Section 10.3 for details on the reporting procedures to follow in the event of 
pregnancy. 
9.7.5.2 
Antibody Testing 
Immunogenicity will be assessed by determining immune response and neutralizing activity 
with the following measurements: anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, anti-PAL 
IgE, anti-PEG IgM, anti-rAvPAL-PEG IgE, and anti-rAvPAL-PEG neutralizing antibodies 
(refer to Section 9.1.1.3.3). Immunogenicity assays will be performed at the time points 
indicated in the Schedule of Events (Table 9.1.1). 
BioMarin will perform all anti-body testing, except for IgE antibodies, which will be 
assessed by a Contract Research Organization. 
9.7.6 Clinical Laboratory Assessments 
Any abnormal test results determined to be clinically significant by the Investigator should 
be repeated (at the Investigator’s discretion) until the cause of the abnormality is determined, 
the value returns to baseline or to within normal limits, or the Investigator determines that the 
abnormal value is no longer clinically significant. 
All abnormal clinical laboratory result pages should be initialed and dated by an Investigator, 
along with a comment regarding whether or not the abnormal result is clinically significant. 
The diagnosis, if known, associated with abnormalities in clinical laboratory tests that are 
considered clinically significant by the Investigator will be recorded on the AE CRF. 
Specific days for obtaining samples are provided in Table 9.1.1 and in Section 12. 
The scheduled clinical laboratory tests are listed in Table 9.7.6.1. A central laboratory will be 
used for analysis. 
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Table 9.7.6.1:  Clinical Laboratory Tests 
Blood Chemistry 
Hematology 
Urine Testsa 
Other 
Albumin  
Hemoglobin  
Appearance 
Pregnancy test, if 
applicablea 
Alkaline 
Phosphatase  
Hematocrit  
Color 
ALT (SGPT)  
WBC count 
pH 
Phenylalanine 
AST (SGOT) 
RBC count 
Specific gravity 
Tyrosine 
Total bilirubin 
Platelet count 
Ketones 
Sedimentation ratea 
BUN 
Differential cell count 
Protein 
Creatinine 
 
Glucose 
GGT 
 
Spot urine 
albumin/creatinine 
ratio  
Additional 
Unscheduled 
Hypersensitivity 
Reaction Visit Testsb 
Total protein 
 
Nitrite 
CH50 
Calcium 
 
Urobilinogen 
C1, C3, C4
 
Sodium 
 
Hemoglobin 
Serum tryptase levelb  
Potassium 
 
Bilirubin 
CRP  
Glucose 
 
 
 
Uric acid 
 
 
Complement Testingc 
CO2 
 
 
C3 
Chloride 
 
 
C4 
ALT, alanine aminotransferase; AST, aspartate aminotransferase; BUN, blood urea nitrogen; C, complement; 
CH50, total hemolytic complement; CO2, carbon dioxide; CRP, C-reactive protein; GGT, 
gamma-glutamyltransferase; RBC, red blood cell; SGOT, serum glutamic-oxaloacetic transaminase; SGPT, 
serum glutamic-pyruvic transaminase; WBC, white blood cell. 
a To be performed by central laboratory. If urine pregnancy test is positive or equivocal, serum sample will be 
taken and assessed by a central laboratory. 
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b Perform immediately after reaction if possible. 
c  Complement C3 and C4 to be drawn at the Screening Visit and then quarterly or as needed to resolve abnormal 
test results. 
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10 
REPORTING ADVERSE EVENTS 
10.1 
Adverse Events 
For this protocol, a reportable adverse event (AE) is any untoward medical occurrence (e.g., 
sign, symptom, illness, disease or injury) in a subject administered the study-drug or other 
protocol-imposed intervention, regardless of attribution. This includes the following: 
• AEs not previously observed in the subject that emerge during the course of the 
study. 
• Pre-existing medical conditions judged by the Investigator to have worsened in 
severity or frequency or changed in character during the study. 
• Complications that occur as a result of non-drug protocol-imposed interventions 
(eg, AEs related to screening procedures, medication washout, or no-treatment run-
in). 
An adverse drug reaction is any AE for which there is a reasonable possibility that the study 
drug caused the AE. “Reasonable possibility” means there is evidence to suggest a causal 
relationship between the study-drug and the AE. 
Whenever possible, it is preferable to record a diagnosis as the AE term rather than a series 
of terms relating to a diagnosis. 
The study period during which all non-serious AEs and SAEs will be reported begins after 
informed consent is obtained and the first administration of study drug  and continues until 
4 weeks following the last administration of study drug or the last visit of the treatment 
period (refer to Section 12). After informed consent but prior to initiation of study treatment, 
only SAEs associated with any protocol-imposed interventions will be reported. The criteria 
for determining, and the reporting of SAEs is provided in Section 10.2.   
The Investigator should follow all unresolved AEs until the events are resolved or stabilized, 
the subject is lost to follow-up, or it has been determined that the study treatment or study 
participation is not the cause of the AE. Resolution of AEs (with dates) should be 
documented on the appropriate CRF page(s) and in the subject’s medical record. 
The Investigator responsible for the care of the subject or qualified designee will assess AEs 
for severity, relationship to study-drug, and seriousness (see Section 10.2 for SAE 
definition). Severity (as in mild, moderate or severe headache) is not equivalent to 
seriousness, which is based on subject/event outcome or action criteria usually associated 
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with events that pose a threat to a subject’s life or functioning. Seriousness (not severity) 
serves as a guide for defining regulatory reporting obligations. 
The Investigator will determine the severity of each AE using the National Cancer Institute 
(NCI) Common Terminology Criteria for Adverse Events (CTCAE) v4. Adverse events that 
do not have a corresponding CTCAE term will be assessed according to the general 
guidelines for grading used in the CTCAE v4 as stated below. 
Grade 
Description 
1 
Mild: asymptomatic or mild symptoms; clinical or diagnostic 
observations only; intervention not indicated 
2 
Moderate: minimal, local or noninvasive intervention 
indicated; limiting age-appropriate instrumental activities of 
daily living (ADL)a 
3 
Severe or medically significant but not immediately life-
threatening: hospitalization or prolongation of hospitalization 
indicated; disabling; limiting self care activities of daily 
living (ADL) 
4 
Life threatening or debilitating: consequences; urgent 
intervention indicatedb 
5 
Death related to AE 
Grade 4 and 5 AEs should always be reported as SAEs. 
a Instrumental ADL refer to the following examples: preparing meals, shopping for groceries or clothes, using 
the telephone, managing money. 
b Self care ADL refer to the following examples: bathing, dressing and undressing, feeding oneself, using the 
toilet, taking medications, not bedridden. 
 
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The Investigator will determine the relationship of an AE to the study drug and will record it 
on the source documents and AE CRF, using the categories defined below. 
Relationship 
Description 
Not Related 
Exposure to the IP has not occurred 
OR 
The administration of the IP and the occurrence of the AE are not 
reasonably related in time  
OR 
The AE is considered likely to be related to an etiology other than the use 
of the IP; that is, there are no facts [evidence] or arguments to suggest a 
causal relationship to the IP. 
Possibly 
Related 
The administration of the IP and the occurrence of the AE are reasonably 
related in time 
AND 
The AE could be explained equally well by factors or causes other than 
exposure to the IP. 
Probably 
Related 
The administration of IP and the occurrence of the AE are reasonably 
related in time  
AND 
The AE is more likely explained by exposure to the IP than by other factors 
or causes. 
In order to classify AEs and diseases, preferred terms will be assigned by the sponsor to the original terms 
entered on the CRF, using MedDRA (Medical Dictionary for Regulatory Activities terminology). 
 
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10.2 
Serious Adverse Events 
A serious adverse event (SAE) is any untoward medical occurrence that at any dose meets 1 
or more of the following criteria: 
• Is fatal. 
• Is life threatening. 
o Note: Life-threatening refers to an event that places the subject at 
immediate risk of death. This definition does not include a reaction that, 
had it occurred in a more severe form, might have caused death. 
• Requires or prolongs inpatient hospitalization. 
• Results in persistent or significant disability or incapacity. 
• Is a congenital anomaly or birth defect in the child or fetus of a subject exposed to IP 
prior to conception or during pregnancy. 
• Is an important medical event or reaction. 
The reporting period for SAEs begins after informed consent is obtained, and continues until 
4 weeks following the last administration of study drug or End of Treatment Visit. 
All SAEs, whether or not considered related to study drug, must be reported within 24 hours 
of the site becoming aware of the event by faxing the study-specific SAE Report Form to 
BioMarin Pharmacovigilance (BPV). ). Each SAE must also be reported in the CRF 
Investigators should not wait to collect information that fully documents the event before 
notifying BPV of a SAE. BioMarin may be required to report certain SAEs to regulatory 
authorities within 7 calendar days of being notified about the event; therefore, it is important 
that Investigators submit any information requested by BioMarin as soon as it becomes 
available.  The Investigator should follow all unresolved SAEs until the events are resolved 
or stabilized, the subject is lost to follow-up, or it has been determined that the study 
treatment or participation is not the cause of the AE. Resolution of AEs (with dates) should 
be documented in the CRF and in the subject’s medical record. 
For some SAEs, the Sponsor may follow up by telephone, fax, electronic mail, and/or a 
monitoring visit to obtain additional case details deemed necessary to appropriately evaluate 
the SAE report (e.g., hospital discharge summary, consultant report, or autopsy report). 
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At the last scheduled visit, the Investigator should instruct each subject to report any 
subsequent SAEs that the subject’s personal physician(s) believes might be related to prior 
study treatment. 
The Investigator should notify the study Sponsor of any death or SAE occurring at any time 
after a subject has discontinued or terminated study participation if felt to be related to prior 
study treatment. The Sponsor should also be notified if the Investigator should become aware 
of the development of cancer or of a congenital anomaly in a subsequently conceived 
offspring of a subject that participated in this study.  
Reporting of SAEs to the IRB will be done in compliance with the standard operating 
procedures and policies of the IRB and with applicable regulatory requirements. Adequate 
documentation must be obtained by BioMarin showing that the IRB was properly and 
promptly notified as required. 
10.3 
Pregnancy 
Pregnancy in a subject or partner should be reported within 24 hours of the site becoming 
aware of the pregnancy to BioMarin Pharmacovigilance by fax using the Pregnancy Form in 
the study reference materials. In addition, pregnancy in a subject is also reported on the End 
of Study CRF. The Investigator must make every effort to follow the subject through 
resolution of the pregnancy (delivery or termination) and to report the resolution on the 
Pregnancy Follow-up Form in the study reference materials. In the event of pregnancy in the 
partner of a study subject, the Investigator should make every reasonable attempt to obtain 
the woman’s consent for release of protected health information. 
10.4 
Urgent Safety Measures 
The regulations governing clinical trials state that the sponsor and Investigator are required to 
take appropriate urgent safety measures to protect subjects against any immediate hazards 
that may affect the safety of subjects, and that the appropriate regulatory bodies should be 
notified according to their respective regulations. According to the European Union (EU) 
Clinical Trial Directive 2001/20/EC, “…in the light of the circumstances, notably the 
occurrence of any new event relating to the conduct of the trial or the development of the 
investigational medicinal product where that new event is likely to affect the safety of the 
subjects, the sponsor and the Investigator shall take appropriate urgent safety measures to 
protect the subjects against any immediate hazard. The sponsor shall forthwith inform the 
competent authorities of those new events and the measures taken and shall ensure that the 
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IRB/EC/REB is notified at the same time.” The reporting period for these events which may 
require the implementation of urgent safety measures is the period from the time of signing 
of the ICF through the completion of the last study visit or at the ETV. Investigators are 
required to report any events which may require the implementation of urgent safety 
measures to BioMarin with 24 hours. 
Examples of situations that may require urgent safety measures include discovery of the 
following: 
• Immediate need to revise the IP administration (i.e., modified dose amount or 
frequency not defined in protocol). 
• Lack of study scientific value, or detrimental study conduct or management. 
• Discovery that the quality or safety of the IP does not meet established safety 
requirements. 
10.5 
BioMarin Pharmacovigilance Contact Information 
Contact information for BioMarin Pharmacovigilance is as follows: 
BioMarin Pharmaceutical Inc. 
Address 
105 Digital Drive 
 
 
Novato, CA 94949 
Phone:  
(415) 506-6179 
Fax: 
 
(415) 532-3144 
E-mail: 
drugsafety@bmrn.com 
The Investigator is encouraged to discuss with the Sponsor’s Medical Officer any AEs for 
which the issue of seriousness is unclear or questioned. Contact information for the 
Sponsor’s Medical Officer is as follows: 
Name:  
, MD 
Address: 
105 Digital Drive 
 
 
Novato, CA 94949 USA 
Phone:  
 
Fax: 
 
 
E-mail: 
 
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11 
APPROPRIATENESS OF MEASUREMENTS 
11.1 
Safety and Pharmacokinetics 
The PK and safety assessments in this study are used widely and are generally recognized as 
reliable, accurate, and relevant. 
11.2 
Diet Diary 
A 3-day diet diary will be issued to subjects for completion and will be brought to clinic on a 
monthly basis for review with the clinical study staff. Additional information regarding the 
diet diary is provided in Section 7.3, and information regarding administration of the diary is 
provided in Section 9.7.4. Additional information about diet is provided in Section 9.1 and 
Section 9.6. 
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12 
STUDY PROCEDURES 
12.1 
Prestudy 
An ICF must be signed and dated by the subject (or the subject’s legally authorized 
representative if the subject is less than 18 years of age), the PI or designee and witness 
(if required) before any study-related procedures are performed. 
12.2 
Screening Visit 
After subjects have signed an ICF, they will be screened for enrollment into the study. 
The following study activities will be performed at Screening: 
• Medical history, including allergy history, and demographics 
• Physical examination  
• Vital signs, including height and weight 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.).  For safety reasons, 
this test must be performed prior to the chest X-ray. 
• Chest X-ray 
• 12-lead ECG 
• Clinical laboratory tests (including spot urine albumin/creatinine ratio, hematology, 
chemistry, and urinalysis) 
• Complement C3 and C4 
• Assessment of SAEs 
• Concomitant medications 
• Diet query 
• Blood Phe and plasma tyrosine concentration 
For subjects who participated in a previous rAvPAL-PEG study, these assessments may be 
the same as those used for the last visit of the previous study, if they occur within 28 days 
from Day 1. 
12.3 
Treatment Period 
During the Treatment Period, additional visits may occur if deemed necessary to monitor 
AEs or blood Phe concentrations. All study activities will occur on the first day of each week 
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unless otherwise noted. On days that a dose is given, assessments will be done predose unless 
otherwise specified. Subjects must have AEs and concomitant medications assessed and an 
injection-site inspection performed whenever dose is administered even if the administration 
does not coincide with a scheduled clinic visit.   
If the dose is modified by increasing dose level, additional blood Phe concentration testing 
should be done daily for 3 days following dose adjustment. If dose is modified by increasing 
either dose frequency or dose level, additional blood Phe concentration testing should be 
done prior to each dose for the first 2 weeks following dose adjustment. 
12.3.1 Day 1 (Week 1) 
Within 28 days of completing screening assessments, the following study activities will be 
performed on Day 1: 
• Physical examination 
• Vital signs 
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• Injection-site inspection (postdose) 
• Assessment of SAEs (predose and postdose) and all AEs (postdose) 
• Concomitant medications 
• Diet query 
• PK sample 
• Blood Phe and plasma tyrosine concentration 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, and anti-rAvPAL-PEG neutralizing antibodies) 
• Administer study drug (study drug may be administered on additional days during the 
week as determined by the Investigator, in agreement with the Sponsor’s Medical 
Officer) 
12.3.2 Weekly Visits 
Weekly visits do not require an in-clinic visit if conducted by a home healthcare professional. 
However, dose modifications must be performed in the clinic. Subjects must have AEs and 
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concomitant medications assessed and an injection-site inspection performed whenever dose 
is administered even if the administration does not coincide with a scheduled clinic visit. For 
subjects on a stable dose of rAvPAL-PEG (ie, no dose change in the last 2 weeks) and have 
had a phenylalanine (Phe) level at or below target range (60-600 µmol/L) for 2 consecutive 
weeks   weekly visits may be waived and replaced by a telephone call per discretion of the 
Investigator but monthly visits are required. 
The following study activities will be performed at the weekly visits beginning with Week 2: 
• Vital signs 
• Injection-site inspection (previous and current injection site) 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• PK sample  
• Blood Phe and plasma tyrosine concentration 
o Blood Phe may be collected monthly, rather than weekly, if certain criteria 
are satisfied (refer to Section 9.7.2.1). 
• Administer study drug (study drug may be administered on additional days during the 
week as determined by the Investigator, in agreement with the Sponsor’s Medical 
Officer) 
• Weekly telephone call 
o For those subjects performing self administration and waiving (per 
Investigator discretion) the weekly visit (refer to Section 12.3.7). 
12.3.3 Substudy Visits 
For subjects participating in the PK substudy, refer to Section 9.7.3 and Table 9.1.2. 
12.3.4 Monthly Visits (Week 4, 8, 12, etc) 
Subjects must have AEs and concomitant medications assessed and an injection-site 
inspection performed whenever dose is administered even if the administration does not 
coincide with a scheduled clinic visit.    
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Beginning with Week 4, monthly visits must be performed in the clinic and consist of all 
weekly activities listed above in Section 12.3.2 as well as the additional study activities listed 
below: 
• Weight 
• Clinical laboratory tests 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) For safety reasons, this 
test must be performed prior to the chest X-ray. 
• Chest x-ray (Week 48 visit only) 
• 3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the next monthly visit.) 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, and anti-rAvPAL-PEG neutralizing antibodies) 
• Weekly telephone call 
o For those subjects performing self administration and waiving (per 
Investigator discretion) the weekly visit (refer to Section 12.3.7). 
12.3.5 Quarterly Visits (Week 12, 24, 36, etc) 
Subjects must have AEs and concomitant medications assessed and an injection-site 
inspection performed whenever dose is administered even if the administration does not 
coincide with a scheduled clinic visit.    
Beginning with Week 12, quarterly visits consist of all weekly (Section 12.3.2) and monthly 
(Section 12.3.4) activities listed above as well as the additional study activities listed below: 
• Physical examination 
• Complement C3 and C4 
• Sedimentation rate 
12.3.6 Interim Dosing Visit 
Subjects who increase their dose frequency during the study from 1x/week to 2x/week or 
daily will have additional assessments performed for 5 weeks after the subject’s rAvPAL-
PEG dose frequency has been increased. If the Interim Dosing Visit coincides with a weekly, 
monthly, or quarterly scheduled visit, the scheduled visit assessments should also be 
performed. The following study activities will be performed for the Interim Dosing Visit: 
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• Injection-site inspection (previous and current injection site) 
• Assessment of AEs 
• Concomitant medications 
• Administer study drug 
12.3.7 Weekly Telephone Visit 
Subjects who are administered rAvPAL-PEG at home and/or have been approved to self 
administered rAvPAL-PEG, should have a weekly telephone visit conducted. Subjects must 
still come into the clinic for the scheduled monthly visits per Table 9.1.1. The following 
should be discussed with the subject during the weekly telephone visit: 
• Injection-site self inspection (previous and current injection site) 
• Assessment of AEs 
• Concomitant medications 
• Confirmation of drug administration 
12.3.8 Unscheduled Hypersensitivity Reaction Visit 
Subjects who have a systemic reaction, including a generalized skin reaction, or a large local 
skin reaction that is not contiguous to the injection site after rAvPAL-PEG administration 
(refer to Section 9.1.1) will have assessments performed immediately following (within 
48 hours) the reaction.  
• Injection-site inspection 
• Clinical laboratory tests 
• Sedimentation rate  
• CRP, CH50, C1, C3, and C4 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG IgE, and anti-rAvPAL-PEG neutralizing 
antibodies) 
• Serum tryptase level 
• Skin biopsy (optional; affected and not affected area; to be performed within 1 week 
of reaction) 
• PK sample 
• Assessment of AEs 
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• Concomitant medications 
Following completion of the Unscheduled Hypersensitivity Reaction visit, subjects who do 
not have an IgE-mediated reaction may resume study drug administration per the discretion 
of the Principal Investigator and the Sponsor’s Medical Officer; however, if subject was 
dosing at home, they will be required to come into the clinic for at least 8 weeks. If 
laboratory data shows that the subject experienced an IgE-mediated reaction, dosing will not 
resume until review of the case with the Investigator, Sponsor’s Medical Officer and an 
allergist/immunologist (refer to Section 9.1.1.3.3). 
12.4 
Early Termination Visit 
The Early Termination Visit (ETV) will occur 4 weeks after the final dose of study drug. 
Subjects who terminate from study treatment early should continue to perform the remaining 
visit assessments in Section 12.3 as applicable until study completion. 
Any AE that caused a subject to withdraw from the study or any clinically significant 
abnormal laboratory value or vital sign measurement identified at the ETV will be followed 
by the Investigator.  
Every reasonable effort should be made to contact any subject who is lost to follow-up. 
The following study activities will be performed at the ETV: 
• Physical examination  
• Vital signs 
• 12-lead ECG 
• Clinical laboratory tests 
• Chest x-ray  
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.). For safety reasons, 
this test must be performed prior to the chest X-ray. 
• Injection-site inspection (previous injection site) 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
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• 3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the Early Termination Visit.) 
• PK sample 
• Blood Phe and plasma tyrosine concentration 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibodies) 
12.5 
Final Follow-up Visit 
The final follow-up (F/U) Visit will occur 1 week after the final dose of study drug. 
The following study activities will be performed at the F/U Visit: 
• Physical examination  
• Vital signs, including weight 
• 12-lead ECG 
• Clinical laboratory tests 
• Chest x-ray  
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.). For safety reasons, 
this test must be performed prior to the chest X-ray. 
• Injection-site inspection (previous injection site) 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• 3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the Final Follow-up Visit.) 
• PK sample 
• Blood Phe and plasma tyrosine concentration 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibodies) 
 
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13 
DATA QUALITY ASSURANCE 
BioMarin personnel or designees will visit the study site prior to initiation of the study to 
review with the site personnel information about the IP, protocol and other regulatory 
document requirements, any applicable randomization procedures, source document 
requirements, CRFs, monitoring requirements, and procedures for reporting AEs, including 
SAEs. 
At visits during and after the study, a CRA will monitor the site for compliance with 
regulatory documentation, with a focus on accurate and complete recording of data on CRFs 
from source documents, adherence to protocol, randomization (if applicable), SAE reporting 
and drug accountability records.  
The designated clinical data management group will enter or transfer CRF data into a study 
database. 
Data quality control and analysis will be performed by BioMarin or a designee, based on a 
predefined analysis plan. 
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14 
STATISTICAL METHODS AND DETERMINATION OF SAMPLE SIZE 
14.1 
Statistical and Analytical Plans 
Because of the small sample size, no formal statistical tests will be performed. Categorical 
data will be summarized using frequency and percent, while continuous data will be 
summarized using descriptive statistics (ie, number of observations, mean, median, standard 
deviation [SD], minimum, and maximum). 
The statistical analysis plan (SAP) will provide additional details about the planned statistical 
analysis. 
14.2 
Safety Analysis 
All subjects who receive any amount of study drug in this study and have postdose safety 
information will be included in the safety analyses. 
All AEs will be coded using the Medical Dictionary for Regulatory Activities (MedDRA). 
The incidence of AEs will be summarized by system organ class, preferred term, relationship 
to study drug, and severity. A by–subject listing will be provided for those subjects who 
experience a serious AE (SAE), including death, or experience an AE associated with early 
withdrawal from the study or study drug. 
Clinical laboratory data will be summarized by the type of laboratory test. Frequency and 
percentage of subjects who experience abnormal (ie, outside of reference range) and/or 
clinically significant abnormalities after study drug administration will be presented for each 
clinical laboratory test. For each clinical laboratory test, descriptive statistics will be provided 
for baseline and all subsequent post-treatment visits. Changes from baseline to the post-
treatment visits will also be provided. Descriptive statistics, including clinically significant 
changes from baseline, of vital signs, ECG results, and X-ray results will also be provided. 
14.3 
Pharmacokinetic Analysis 
Subjects who complete the Substudy will have the following PK parameters assessed: area 
under the plasma concentration-time curve (AUC), time to maximum plasma concentration 
(Tmax), maximum plasma concentration (Cmax), half life (t1/2), and clearance (CL/F).  Should 
data become available from previous rAvPAL-PEG studies that indicate study drug 
accumulation should also be measured, additional blood draws may be added for PK analysis 
as needed per the discretion of the Investigator in consultation with the Sponsor’s Medical 
Officer. 
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14.3.1 Pharmacokinetic Substudy Analysis 
For subjects who completed the Substudy, the steady-state PK of rAvPAL-PEG in subjects 
who have achieved and maintained target blood Phe will be explored. 
14.4 
Efficacy Analysis 
Data from all subjects who receive any amount of study drug and who have any 
post-treatment efficacy data will be included in the efficacy analysis. 
Blood Phe concentration at each scheduled time point will be summarized using descriptive 
statistics (mean, SD, median, minimum, and maximum). Change in blood Phe concentration 
from baseline to each scheduled time point and presence/absence of antibodies will also be 
summarized. In addition, the proportion of subjects who have maintained target Phe 
concentrations of 60-600 µmol/L will be summarized by each scheduled time point. 
The relationship of dietary Phe intake (per information reported on the subject diet diary) and 
blood Phe concentration will also be explored. Subjects who received any amount of study 
drug with any post-treatment blood Phe concentration measurements and diet diary 
information will be included in this exploratory analysis. Information regarding this 
exploratory analysis will be provided in the Statistical Analysis Plan. 
For subjects who completed the Substudy, the effect of stopping and re-starting rAvPAL-
PEG dosing on safety, blood Phe level, and immune response will be explored. Information 
regarding the analysis will be provided in the Statistical Analysis Plan. 
14.5 
Determination of Sample Size 
Subjects who participated in previous rAvPAL-PEG studies may be enrolled into this study. 
No formal sample size calculation was conducted for this study or the PAL-003 Substudy.   
14.6 
Handling of Missing Data 
All analyses will be presented based on observed data only. Missing data will not be imputed 
for analyses unless sensitivity analyses are warranted. If imputations are used, detailed 
imputation methods will be described in the SAP before locking the database. 
14.7 
Interim Analyses 
Safety will be assessed throughout the study on an ongoing basis (refer to Section 15 for 
information regarding the DMC). 
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14.8 
Changes in the Conduct of the Study or Planned Analyses 
Only BioMarin may modify the protocol. Any change in study conduct considered necessary 
by the PI will be made only after consultation with BioMarin, who will then issue a formal 
protocol amendment to implement the change. The only exception is when an Investigator 
considers that a subject’s safety is compromised without immediate action. In these 
circumstances, immediate approval of the chairman of the IRB must be sought, and the 
Investigator should inform BioMarin and the full IRB within 2 working days after the 
emergency occurs. 
With the exception of minor administrative or typographical changes, the IRB must review 
and approve all protocol amendments. Protocol amendments that have an impact on subject 
risk or the study objectives, or require revision of the ICF, must receive approval from the 
IRB prior to their implementation. 
When a protocol amendment substantially alters the study design or the potential risks or 
burden to subjects, the ICF will be amended and approved by BioMarin and the IRB, and all 
active subjects must again provide informed consent. 
Note: If discrepancies exist between the text of the statistical analysis as planned in the 
protocol, and the final SAP, a protocol amendment will not be issued and the SAP will 
prevail. 
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15 
DATA MONITORING COMMITTEE (DMC) 
The DMC will act independently in an advisory capacity to BioMarin to monitor the safety 
of rAvPAL-PEG in subjects who participate in the study. Meetings of the DMC can be 
convened at any time at the discretion of the DMC Chair or the Sponsor’s Medical Officer. 
The Chair will be notified by the Sponsor’s Medical Officer of all SAEs and will receive 
summaries of other safety data as available. The DMC will review the study data as soon as it 
is available during the study, on a schedule defined in the DMC Charter, and offer advice on 
whether or not to proceed, modify or terminate study enrollment on the basis of toxicity. 
Details regarding the DMC membership and safety data to be reviewed by members will be 
provided in a charter. 
The responsibilities of the DMC are to: 
• Review the study protocol, informed consent and assent documents, and plans for 
data monitoring. 
• Evaluate the progress of the trial, subjects’ risk versus benefit, and other factors that 
could affect the study outcome. 
• Consider relevant information that may have an impact on the safety of the 
participants or the ethics of the study. 
• Protect the safety of the study participants in accordance with the stopping criteria as 
defined in study protocol Section 9.1.4. 
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COMPENSATION, INSURANCE, AND INDEMNITY 
There will be no charge to study subjects to be in this study. BioMarin will pay all costs of 
tests, procedures, and treatments that are part of this study. In addition, after IRB approval, 
BioMarin may reimburse the cost of travel for study-related visits. BioMarin will not pay for 
any hospitalizations, tests, or treatments for medical problems of any sort, whether or not 
related to the study subject’s disease, that are not part of this study. Costs associated with 
hospitalizations, tests, and treatments should be billed and collected in the way that such 
costs are usually billed and collected. 
The Investigator should contact BioMarin immediately upon notification that a study subject 
has been injured by the IP or by procedures performed as part of the study. Any subject who 
experiences a study-related injury should be instructed by the Investigator to seek medical 
treatment at a pre-specified medical institution if possible, or at the closest medical treatment 
facility if necessary. The subject should be given the name of a person to contact to seek 
further information about, and assistance with, treatment for study-related injuries. 
The treating physician should bill the subject’s health insurance company or other third party 
payer for the cost of this medical treatment. If the subject has followed the Investigator’s 
instructions, BioMarin will pay for reasonable and necessary medical services to treat the 
injuries caused by the IP or study procedures, if these costs are not covered by health 
insurance or another third party that usually pays these costs. In some jurisdictions, BioMarin 
is obligated by law to pay for study-related injuries without prior recourse to third party 
payer billing. If this is the case, BioMarin will comply with the law. 
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CASE REPORT FORMS AND SOURCE DOCUMENTS 
Electronic case report forms will be provided for each subject. The Investigator must review 
and electronically sign the completed CRF casebook to verify its accuracy. 
CRFs must be completed using a web–based application that has been validated. Study site 
personnel will be trained on the application and will enter the clinical data from source 
documentation. Unless explicitly allowed in the CRF instructions, blank data fields are not 
acceptable. 
In the event of an entry error, or if new information becomes available, the site personnel will 
correct the value by deselecting the erroneous response and then selecting or entering the 
factual response. In compliance with 21 CFR Part 11, the system will require the site 
personnel to enter a reason for changing the value. The documented audit trail will include 
the reason for the change, the original value, the new value, the time of the correction, and 
the identity of the operator. 
BioMarin’s policy is that study data on the CRFs must be verifiable to the source data, which 
necessitates access to all original recordings, laboratory reports, and subject records. 
In addition, all source data should be attributable (signed and dated). The Investigator must 
therefore agree to allow direct access to all source data. Subjects (or their legally authorized 
representative) must also allow access to their medical records, and subjects will be informed 
of this and will confirm their agreement when giving informed consent. If an Investigator or 
institution refuses to allow access to subject records because of confidentiality, arrangements 
must be made to allow an “interview” style of data verification. 
A CRA designated by BioMarin will compare the CRFs with the original source documents 
at the study site and evaluate them for completeness and accuracy before designating them as 
“source data verified” (SDV). If an error is discovered at any time or a clarification is 
needed, the CRA, or designee, will create an electronic query on the associated field. Site 
personnel will then answer the query by either correcting the data or responding to the query. 
The CRA will then review the response and determine either to close the query or re–query 
the site if the response does not fully address the question. This process is repeated until all 
open queries have been answered and closed. 
Before a subject’s CRF casebook can be locked, all data fields must be SDV and all queries 
closed. The Investigator will then electronically sign the casebook, specifying that the 
information on the CRFs is accurate and complete. The Data Manager, or designee, will then 
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set the status of the forms, visits, and the entire casebook to locked. Upon completion of the 
clinical study report for the entire study, an electronic copy of each site’s casebooks will be 
copied to a compact disk (CD) and sent to each site for retention with other study documents. 
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STUDY MONITORING AND AUDITING 
Qualified individuals designated by BioMarin will monitor all aspects of the study according 
to GCP and standard operating procedures for compliance with applicable government 
regulations. The PI agrees to allow these monitors direct access to the clinical supplies, 
dispensing, and storage areas and to the clinical files, including original medical records, of 
the study subjects, and, if requested, agrees to assist the monitors. The PI and staff are 
responsible for being present or available for consultation during routinely scheduled site 
visits conducted by BioMarin or its designees. 
Members of BioMarin’s GCP Compliance Department or designees may conduct an audit of 
a clinical site at any time during or after completion of the study. The PI will be informed if 
an audit is to take place and advised as to the scope of the audit. Representatives of the FDA 
or other Regulatory Agencies may also conduct an audit of the study. If informed of such an 
inspection, the PI should notify BioMarin immediately. The PI will ensure that the auditors 
have access to the clinical supplies, study site facilities, original source documentation, and 
all study files. 
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RETENTION OF RECORDS 
The PI must retain all study records required by BioMarin and by the applicable regulations 
in a secure and safe facility. The PI must consult a BioMarin representative before disposal 
of any study records, and must notify BioMarin of any change in the location, disposition or 
custody of the study files. The PI/institution must take measures to prevent accidental or 
premature destruction of essential documents, that is, documents that individually and 
collectively permit evaluation of the conduct of a study and the quality of the data produced, 
including paper copies of study records (e.g., subject charts) as well as any original source 
documents that are electronic as required by applicable regulatory requirements. 
All study records must be retained for at least 2 years after the last approval of a marketing 
application in the U.S. or an ICH region and until (1) there are no pending or contemplated 
marketing applications in the United States or an ICH region or (2) at least 2 years have 
elapsed since the formal discontinuation of clinical development of the IP. The PI/institution 
should retain subject identifiers for at least 15 years after the completion or discontinuation 
of the study. Subject files and other source data must be kept for the maximum period of time 
permitted by the hospital, institution or private practice, but not less than 15 years. 
These documents should be retained for a longer period, however, if required by the 
applicable regulatory requirements or by a BioMarin agreement. BioMarin must be notified 
and will assist with retention should the PI/institution be unable to continue maintenance of 
subject files for the full 15 years. It is the responsibility of BioMarin to inform the 
PI/institution as to when these documents no longer need to be retained. 
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20 
USE OF INFORMATION AND PUBLICATION 
BioMarin recognizes the importance of communicating medical study data and therefore 
encourages their publication in reputable scientific journals and at seminars or conferences. 
The details of the processes of producing and reviewing reports, manuscripts, and 
presentations based on the data from this study will be described in the Clinical Study 
Agreement between BioMarin and the PI. 
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21 
REFERENCES 
Armstrong, JK, Hempel, G, Koling, S, Chan, LS et. al. Antibody against poly(ethylene 
glycol) adversely affects PEG-asparaginase therapy in acute lymphoblastic leukemia patients. 
Cancer 110[1], 103-111. 2007.  
Chen, AM, Scott, MD. Current and future applications of immunological attenuation via 
pegylation of cells and tissue. BioDrugs 15[12], 833-847. 2001.  
Davis, S, Abuchowski, A, Park, YK, Davis, FF. Alteration of the circulating life and 
antigenic properties of bovine adenosine deaminase in mice by attachment of polyethylene 
glycol. Clin Exp Immunol 46[3], 649-652. 1981.  
Fisch, RO. Comments on diet and compliance in phenylketonuria. Eur J Pediatr 159 Suppl 2, 
S142-S144. 2000.  
Gamez, A, Wang, L, Sarkissian, CN, Wendt, D et. al. Structure-based epitope and 
PEGylation sites mapping of phenylalanine ammonia-lyase for enzyme substitution treatment 
of phenylketonuria. Mol Genet Metab 91[4], 325-334. 2007.  
Ganson, NJ, Kelly, SJ, Scarlett, E, Sundy, JS et. al. Control of hyperuricemia in subjects with 
refractory gout, and induction of antibody against poly(ethylene glycol) (PEG), in a phase I 
trial of subcutaneous PEGylated urate oxidase. Arthritis Res Ther 8[1], R12. 2006.  
Guttler, F, Azen, C, Guldberg, P, Romstad, A et. al. Impact of the phenylalanine hydroxylase 
gene on maternal phenylketonuria outcome. Pediatrics 112[6 Pt 2], 1530-1533. 2003.  
Harris, JM, Chess, RB. Effect of pegylation on pharmaceuticals. Nat Rev Drug Discov 2[3], 
214-221. 2003.  
Huttenlocher, PR. The neuropathology of phenylketonuria: human and animal studies. Eur J 
Pediatr 159 Suppl 2, S102-S106. 2000.  
Kaufman, S. An evaluation of the possible neurotoxicity of metabolites of phenylalanine. J 
Pediatr 114[5], 895-900. 1989.  
Koch, R, Hanley, W, Levy, H, Matalon, K et. al. The Maternal Phenylketonuria International 
Study: 1984-2002. Pediatrics 112[6 Pt 2], 1523-1529. 2003.  
Lapis. Long-term Correction of PKU in the Pahenu2 Mouse by Mutant and Chemically 
Modified Forms of Phenylalanine Ammonium Lyase. ASHG 57th Annual Meeting The 
American Society of Human Genetics)2007.  
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Lee, PJ, Lilburn, M, Baudin, J. Maternal phenylketonuria: experiences from the United 
Kingdom. Pediatrics 112[6 Pt 2], 1553-1556. 2003.  
Levy, HL. Historical background for the maternal PKU syndrome. Pediatrics 112[6 Pt 2], 
1516-1518. 2003.  
Matalon, R, Surendran, S, Matalon, KM, Tyring, S et. al. Future role of large neutral amino 
acids in transport of phenylalanine into the brain. Pediatrics 112[6 Pt 2], 1570-1574. 2003.  
Richter, AW, Akerblom, E. Polyethylene glycol reactive antibodies in man: titer distribution 
in allergic patients treated with monomethoxy polyethylene glycol modified allergens or 
placebo, and in healthy blood donors. Int Arch Allergy Appl Immunol 74[1], 36-39. 1984.  
Richter, AW, Akerblom, E. Antibodies against polyethylene glycol produced in animals by 
immunization with monomethoxy polyethylene glycol modified proteins. Int Arch Allergy 
Appl Immunol 70[2], 124-131. 1983.  
Rouse, B, Azen, C. Effect of high maternal blood phenylalanine on offspring congenital 
anomalies and developmental outcome at ages 4 and 6 years: the importance of strict dietary 
control preconception and throughout pregnancy. J Pediatr 144[2], 235-239. 2004.  
Scott, MD, Murad, KL, Koumpouras, F, Talbot, M et. al. Chemical camouflage of antigenic 
determinants: stealth erythrocytes. Proc Natl Acad Sci U S A 94[14], 7566-7571. 1997.  
Scriver, CR, Kaufman. Hyperphenylalaninemia: Phenylalanine Hydroxylase Deficiency. In: 
Beaudet AL, Sly WS, Valle D, editors. Metabolic and Molecular Bases of Inherited Disease. 
New York: McGraw-Hill, 2001: 1667-1724. 
Walter, JH, White, FJ, Hall, SK, MacDonald, A et. al. How practical are recommendations 
for dietary control in phenylketonuria? Lancet 360[9326], 55-57. 2002.  
Webster, R, Didier, E, Harris, P, Siegel, N et. al. PEGylated proteins: evaluation of their 
safety in the absence of definitive metabolism studies. Drug Metab Dispos 35[1], 9-16. 2007.  
 
 
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22 
INVESTIGATOR RESPONSIBILITIES 
22.1 
Conduct of Study and Protection of Human Subjects  
In accordance with FDA Form 1572, the Investigator will ensure that: 
• He or she will conduct the study in accordance with the relevant, current protocol and 
will only make changes in a protocol after notifying the sponsor, except when 
necessary to protect the safety, rights, or welfare of subjects. 
• He or she will personally conduct or supervise the study. 
• He or she will inform any potential subjects, or any persons used as controls, that the 
drugs are being used for investigational purposes and he or she will ensure that the 
requirements relating to obtaining informed consent in 21 CFR Part 50 and 
institutional review board (IRB) review and approval in 21 CFR Part 56 are met.  
• He or she will report to the sponsor adverse experiences that occur in the course of 
the investigation in accordance with 21 CFR 312.64. 
• He or she has read and understands the information in the Investigator’s Brochure, 
including potential risks and side effects of the drug. 
• His or her staff and all persons who assist in the conduct of the study are informed 
about their obligations in meeting the above commitments. 
• He or she will ensure that adequate and accurate records in accordance with 
21 CFR 312.62 and to make those records available for inspection in accordance with 
21 CFR 312.68. 
• He or she will ensure that the IRB complies with the requirements of 21 CFR Part 56, 
and other applicable regulations, and conducts initial and ongoing reviews and 
approvals of the study. He or she will also ensure that any change in research activity 
and all problems involving risks to human subjects or others are reported to the IRB. 
Additionally, he or she will not make any changes in the research without IRB 
approval, except where necessary to eliminate apparent immediate hazards to human 
subjects. 
• He or she agrees to comply with all other requirements regarding the obligations of 
clinical Investigators and all other pertinent requirements in 21 CFR Part 312. 
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24 
PROTOCOL AMENDMENT TEXT REVISIONS 
The following table summarizes the revisions made to the protocol and relates the changes to the appropriate rationale (see pages 2-4). Text 
that has been added or inserted is indicated by underlined font, and deleted text is indicated by strikethrough font. 
Section No./Title 
Revision 
Rationale 
Section 2/Synopsis, Study 
Rationale 
… This study is an extension of the rAvPAL-PEG Phase 2 studies PAL-002, PAL-004, and 165-205the dose finding 
studies (Study PAL 002 and Study PAL 004). Administration of rAvPAL-PEG will be continued to assess whether 
long-term dosing of rAvPAL-PEG is safe and can maintain reduced blood Phe concentrations in PKU subjects. 
Because rAvPAL PEG is being assessed as a long term chronic treatment for patients with PKU, there is a need to 
understand the effect of a temporary dosing interruption on the safety, efficacy (blood Phe), PK, and immune response. 
Therefore, a Substudy has been added to this study to assess the effects of stopping and re starting rAvPAL PEG 
treatment in subjects who are on a variety of rAvPAL PEG dosing regimens (dose level and frequency). Up to 
10 subjects who are on a variety of dosing regimens (dose level and frequency) in this study are eligible for participation 
in the Substudy and will stop dosing for a period of approximately 4 weeks. During this dosing interruption, subjects 
will be assessed for safety, efficacy, PK, and immune response and will continue to perform the scheduled study 
assessments.   
A pharmacokinetic (PK) substudy has been added to evaluate the steady-state PK of rAvPAL-PEG in a minimum of 6 
subjects who have achieved and maintained target blood Phe for at least 2 consecutive weeks and for whom no further 
dose modifications are planned. Single-dose PK data has been collected in the Phase 1 study, PAL-001. However, there 
is little multiple-dose PK data or data for when subjects have reached and maintained a stable dosing regimen.  With the 
PK substudy, multiple-dose PK data will be collected for subjects who have already achieved Phe reduction to within 
the protocol-defined target range. 
5, 6, 16 
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Section 2/Synopsis, Objectives 
The exploratory objective of the study is as follows: 
• 
To assess evaluate the long-term relationship of diet and change in blood Phe concentration following 
administration with rAvPAL-PEG in subjects with PKU. 
The Substudy objectives are as follows: 
• 
To evaluate steady-state PK of rAvPAL-PEG in subjects who have achieved and maintained target blood Phe 
concentration and for whom no further dose modifications are planned. 
• 
To assess the safety and tolerability of stopping and re starting rAvPAL PEG dosing in a subset of subjects 
with PKU. 
• 
To evaluate the effect of stopping and re starting rAvPAL PEG dosing on blood Phe concentration in a subset 
of subjects with PKU. 
• 
To evaluate the effect of stopping and re starting rAvPAL PEG dosing on immune response in a subset of 
subjects with PKU.   
• 
To assess the effect of multiple doses of rAvPAL PEG on the PK profile, in particular clearance of drug, when 
drug is stopped in a subset of subjects with PKU who have been previously exposed to rAvPAL PEG.    
5, 6, 16 
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Section 2/Synopsis, Study Design 
and Plan 
This is a long-term extension of rAvPAL-PEG Phase 2 studiesthe Phase 2, open label, dose finding studies, PAL 002 
and PAL 004, in approximately 100 subjects with PKU. The doses are planned to be in the same range as those tested in 
PAL-002 and PAL-004 (starting at 0.001 through 5.0 mg/kg/week), provided no dose-limiting toxicity is observed in a 
PAL 002 or PAL 004previous rAvPAL-PEG study004. 
Only subjects who completed the protocol defined study drug regimen in PAL 002 or PAL 004a previous rAvPAL-PEG 
study will be enrolled into this study. Subjects enrolling into PAL-003 with no interruption in dosing from a previous 
rAvPAL-PEG study may either continue their previous dosing regimen or begin this study at a higher dose level. 
Subjects who have had dosing interruptions between the previous rAvPAL-PEG study and PAL-003 must have their 
starting dose determined per the Sponsor’s Medical Officer.  Subjects who enroll from PAL 002 will either continue the 
dose regimen that was administered upon completion of PAL 002 or start dosing at a higher dose per the dose increase 
instructions. Subjects who enroll from PAL 002 may start this study at a higher dose level provided there was no 
interruption in dosing since completion of PAL 002 and enrollment into this study. Subjects who enroll from PAL 004 
will re start rAvPAL PEG dosing in this study at the same dose level and frequency as was administered upon 
completion of PAL 004. The first dose will be administered in the clinic, and the subject must be observed for 30-60 
minutes following administrationdue to restarting dosing in this study. A follow-up telephone call will be made to the 
subject to monitor subject safety 24 hours following the return to dosing.  
Diet should not be altered during the course of this study.  Any decision to modify subject diet must be made per the 
Investigator in consultation with the Sponsor’s Medical Officer and must be performed under the supervision of the 
InvestigaorInvestigator in consultation with the Sponsor’s Medical Officer. To monitor for changes in subject diet, a diet 
diary will be issued to subjects for completion and will be reviewed with the clinical study staff on a monthly basis.  
 
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take rAvPAL-PEG. PAL 002 
and PAL 004 Subjects’ previous subjects’ rAvPAL-PEG dosing will continue in PAL-003. In PAL-003, each subject’s 
dose will be adjusted as needed to attain or maintain blood Phe concentrations of 60-600 µmol/L. rAvPAL-PEG dose 
will be based on either a subject’s weight or will be a fixed dose (subjects who have maintained blood Phe levels to 
60-600 µmol/L for at least 2 consecutive weeks and who have maintained a stable rAvPAL-PEG dose for at least 2 
consecutive weeks). Doses will be evaluated on an individual basis. 
 
4, 6 
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Section 2/Synopsis, Study Design 
and Plan 
PAL-003 Substudy 
A PK substudy has been added to evaluate the steady-state PK of rAvPAL-PEG in a minimum of 6 subjects who have 
achieved and maintained target blood Phe for at least 2 consecutive weeks and for whom no further dose modifications 
are planned.  Subjects enrolled into the substudy will have additional pre-dose PK sampling performed.A subset of up to 
10 subjects who are already enrolled and who have consented to participate in this study will be asked to participate in a 
Substudy to assess the effect that stopping and re starting treatment with rAvPAL PEG has on safety, efficacy, PK, and 
immune response. Subjects will be eligible for participation in the Substudy provided they also meet all of the PAL 003 
eligibility criteria, have been on a stable dosing regimen for approximately 4 weeks during this study, have not had any 
serious adverse events reported during PAL 003, and were not enrolled in Study PAL 004. Subjects participating in the 
Substudy will have rAvPAL PEG administration halted for approximately 4 weeks regardless of their dosing regimen 
(dose level and frequency). rAvPAL PEG will not be administered during the dose interruption; however, subjects will 
continue to perform assessments for safety, blood Phe concentration, PK, and immune response. Subjects enrolled into 
the Substudy will also have additional PK sampling performed prior to the dosing interruption and during the dosing 
interruption. To allow for PK sampling once dosing is stopped, subjects may be admitted to a research facility within 8 
hours of stopping dosing where they will reside for at least 24 hours. After the dosing interruption, rAvPAL PEG 
administration will be re started at the same dose level and dosing frequency that was administered prior to the dosing 
interruption. Upon re starting rAvPAL PEG, the first dose must be administered in the clinic and the subject must be 
observed for 30 60 minutes following administration due to restarting dosing. A follow up telephone call will be made 
to the subject to monitor subject safety 24 hours following the return to dosing. Additional PK sampling will also be 
performed for the first week after the dosing interruption. 
5, 6 
Section 2/Synopsis, Dose Increase 
Methodology 
For subjects from PAL 002 only, Aan individual subject’s dose may be adjusted beginning on Day 1 of PAL-003. For 
the duration of this study, an individual subject’s dose may be adjusted if warranted per a subject’s adverse event profile 
and blood Phe concentrations. Dose increases should be performed as follows. 
• 
Only 1 dose (level or frequency) adjustment is allowed every 2 weeks. 
• 
Blood Phe levels will be measured daily for 3 days after each dose increase (fingerstick is acceptable); more 
frequent or daily blood Phe measurements may be performed. 
 
2, 7 
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Section 2/Synopsis, Dose 
Decrease Methodology 
If the subject develops low blood Phe (as defined by a blood Phe level ≤ 30 µmol/L as measured by serum Phe levels for 
a minimum of 1 month), the subject’s rAvPAL-PEG dose should be decreased to the next lower dose.  If the condition 
persists after another 1 month at the lower dose, the dose should be decreased again to the next lower level. If the subject 
continues to experience low blood Phe after two dose level reductions, the subject may be asked to consult the dietician 
to eliminate medical foods and/or formulas and to ensure a balanced and nutritious diet (as part of the routine standard 
of care for PKU disease management, subject diet should be monitored by a dietician). 
 
8 
Section 2/Synopsis, Diagnosis 
and All Criteria for Inclusion and 
Exclusion 
Individuals eligible to participate in this study must meet all of the following criteria: 
1. Must have completed participation and all protocol defined study drug in PAL 002 or PAL 004in a previous 
rAvPAL-PEG study. 
Individuals who meet any of the following exclusion criteria will not be eligible to participate in the study: 
4. A prior reaction that included systemic symptoms (eg, generalized hives, respiratory or gastrointestinal 
problems, hypotension, angioedema, anaphylaxis) to rAvPAL-PEG or a PEG-containing product. Subjects with 
a prior systemic reaction of generalized rash may be eligible for participation per the discretion of the Principal 
Investigator in consultation with the Sponsor’s Medical Officer. However, subjects who discontinued from 
study treatment early due to a reaction are not eligible to enroll into this study.    
8. Known hypersensitivity to rAvPAL-PEG or its excipients, including hypersensitivity reactions that necessitated 
early termination from PAL 002 or PAL a 004previous rAvPAL-PEG study004. 
 
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Section 2/Synopsis, 
Investigational Product, Dose, 
Route, and Regimen 
rAvPAL-PEG will be provided in 3 mL (milliliter) vials, each containing 1.5 ± 0.2 mL to deliver either 10 mg of 
rAvPAL-PEG per 1 mL (10 mg/mL protein concentration) or 15 mg or rAvPAL-PEG per 1 mL (15 mg/mL protein 
concentration). Each vial is filled with 1.5 ± 0.2 mL to allow the withdrawal and delivery of up to 1 mL of the drug 
product.  
Upon enrollment into this study, subjects from previous rAvPAL-PEG studies PAL 002 will be dosed with the same or 
higher dose than the dose that was administered upon completion of that study provided that there was no interruption in 
dosing. Subjects who have had dosing interruptions between the previous rAvPAL-PEG study and PAL-003 must have 
their starting dose determined per the Sponsor’s Medical Officer PAL 002. Subjects enrolling from PAL 004, will be 
administered the same dose that was administered upon completion of PAL 004. rAvPAL-PEG doses will be 
administered SC by either health care professionals or via self administration. The dose level may be increased per 
Investigator determination in consultation with the Sponsor’s Medical Officer based on onavailable information 
regarding a subject’s blood Phe level (60-600 µmol/L), as well as any adverse events (any hypersensitivity reaction) for 
an individual subject. The dosage that provides control of blood Phe concentrations within the target range of 
6120-600 µmol/L for a minimum of 2 weeks will be determined for each subject by adjusting the dose level, dose 
frequency, or both, as agreed by the PI and the Study Sponsor’s Medical Officer, based upon the subject’s response to 
doses. 
Fixed Dosing 
Subjects who have demonstrated efficacy (ie, blood Phe within the target range of 60-600 µmol/L for at least 2 
consecutive weeks) and who have maintained a stable rAvPAL-PEG dose for at least 2 consecutive weeks may be 
eligible to transition from weight-based dosing to a fixed dosing regimen that would permit daily dosing (5- or 7-days-
per-week).  Subjects should convert their weight-based dose using the following table: 
 
 
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Investigational Product, Dose, 
Route, and Regimen 
Weight-based 
dose (mg/kg) 
Equivalent 
fixed dose (mg) 
Vol for 10 mg/ml 
concentration (ml) 
Vol for 15 mg/ml 
concentration (ml) 
0.03 
2.5 
0.25 
0.17 
0.06 
5 
0.5 
0.33 
0.12 
10 
1 
0.67 
0.25 
20 
2 
1.33 
0.5 
40 
4 
2.67 
1.0 
75 
7.5 
5 
2.0 
150 
15 
10 
3.0 
225 
22.5 
15 
4.0 
300 
30 
20 
5.0 
375 
37.5 
25 
 
4 
Section 2/Synopsis, Sample Size 
Subjects who participated in PAL 002 or PAL 004a previous rAvPAL-PEG study may be enrolled into this study. 
No formal sample size calculation was conducted for this study or the PAL-003 Substudy. 
 
16 
Section 2/Synopsis, Substudy 
Analysis 
For subjects who completed the Substudy, the effect of stopping and re starting rAvPAL PEG dosing on safety, blood 
Phe level, and immune responsesteady-state PK of rAvPAL-PEG in subjects who have achieved and maintained target 
blood Phe will be explored. 
 
5, 6 
Section 6/Investigators and Study 
Administrative Structure 
Anti-rAvPAL-PEG (recombinant Anabaena variabilis phenylalanine ammonia lyase polyethylene glycol) 
immunoglobulin E (IgE) antibody analysis will be performed by a vendor; other antibody analysis will be performed by 
BioMarin. Clinical laboratory tests, including serum pregnancy tests (if applicable), will be analyzed and processed by a 
central laboratory, with the exception of erythrocyte sedimentation rate (ESR), [urinalysis], and urine pregnancy tests (if 
applicable), which will be analyzed by a local laboratory. A central laboratory will also be used to perform analysis of 
blood phenylalanine (Phe) concentrations and urinalysis. Pharmacokinetic (PK) analysis will be performed by BioMarin. 
 
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Section 7.2/Previous Clinical 
Studies 
The rAvPAL-PEG clinical development program has been designed to demonstrate the safety and efficacy of 
rAvPAL-PEG in reducing blood Phe concentrations in PKU subjects who do not respond to treatment with Kuvan® or 
are not compliant with Kuvan® treatment. This study is an extension of the ongoing human clinical studies with 
rAvPAL-PEG (Study PAL-002,andStudy PAL-004, and Study 165-205) based on data from the completed clinical 
study, PAL-001, and clinical experience to dateas of (JAN2011) from this ongoing study and the other ongoing Phase 2 
studiesy, PAL-002 and PAL-004.  
 
16 
Section 7.2.2/Phase 2 Studies 
PAL-002, PAL-004, and 165-205 
Currently, rAvPAL-PEG is being investigated in two three Phase 2 clinical trials (PAL-002 and PAL-004). To date 
(JAN2011)As of May 2012, a total of 7033 subjects have been administered rAvPAL-PEG in Study PAL 002a 
rAvPAL-PEG Phase 2 studyand initiation and recruitment of clinical sites is underway for Study PAL 004.   
Study PAL-003 (Long-Term Extension of a Phase 2, Open-Label, Dose-Finding Study to Evaluate the Safety, Efficacy, 
and Tolerability of Multiple Subcutaneous Doses of rAvPAL-PEG in Subjects with PKU) is an extension study of PAL-
002,and PAL-004, and 165-205 (A Phase 2, Multi-Center, Open-Label, Dose-Finding Study to Evaluate Safety, Efficacy 
and Tolerability of Subcutaneously Administered rAvPAL-PEG in Patients with PKU for 24 Weeks). Once subjects 
have completed Study PAL 002 or PAL a p004revious rAvPAL-PEG study004, they have the option to enroll into PAL-
003 and to continue to receive doses of rAvPAL-PEG for up to an additional 60 months. 
…. The protocol was amended again (28MAR2011) to increase the starting dose for Cohort 4 from 0.03 mg/kg/week to 
1.0 mg/kg/week. To date (As of JAN2011), 33 subjects have been enrolled into the study and all 10 subjects of the 
substudy have been dosed with 0.1 mg/kg rAvPAL-PEG. Additional information about the safety reported as of to date 
(JAN2011) is provided in Section 7.4.2. 
Study 165-205 is a Phase 2 study using a subject-driven dose modification schema to assess safety. In addition, fixed 
dosing at a drug concentration of 15 mg/mL rAvPAL-PEG will be assessed. As of May 2012, enrollment of subjects is 
underway for this study. 
In this study, subjects inwho completed a previous rAvPAL-PEG study PAL 002 and PAL 004 will continue to be 
administered the same rAvPAL-PEG dose that was administered in the previous studyPAL 002 or PAL 004. If the 
safety, PK, and blood Phe concentration results from the previous studyeither PAL 002 or PAL 004 indicate that the 
appropriate level of PEGylation and dosing regimen differs from that administered in the previous studyPAL 002 or 
PAL 004, the PEGylation and/or dosing regimen administered in this study may change.    
 
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Section 7.3/Study Rationale 
Because rAvPAL PEG is being assessed as a long term chronic treatment for patients with PKU, there is a need to 
understand the effect of a temporary dosing interruption on the safety, efficacy (blood Phe), PK, and immune response. 
To date (JAN2011), there is limited information on the effects of a rAvPAL PEG dose interruption in subjects with 
PKU. Therefore, a Substudy has been added to this study to assess the effects of stopping and re starting rAvPAL PEG 
treatment in subjects who are on a variety of rAvPAL PEG dosing regimens (dose level and frequency). Up to 
10 subjects who are on a variety of dosing regimens (dose level and frequency) in this study are eligible for participation 
in the Substudy and will stop dosing for a period of approximately 4 weeks. During this dosing interruption, subjects 
will be assessed for safety, efficacy, PK, and immune response and will continue to perform the scheduled study 
assessments. There is no information regarding the pharmacokinetic (PK) profile of rAvPAL PEG when blood Phe 
levels are at 60 600 µmol/L for subjects on a multiple dose regimen. To address this lack of information, additional PK 
sampling will be performed prior to the dosing interruption. Upon restarting rAvPAL PEG, PK sampling will also be 
performed to allow for collection of drug exposure data (area under the plasma concentration time curve [AUC] and 
maximum plasma concentration [Cmax]), absorption rate, and clearance for subjects who have been previously exposed 
to rAvPAL PEG in this Substudy. This information will allow for comparisons to be performed with subjects who were 
naïve to previous rAvPAL PEG treatment from the Phase 1 study, PAL 001. 
 
6, 15 
Section 7.3/Study Rationale 
A pharmacokinetic (PK) substudy has been added to evaluate the steady-state PK of rAvPAL-PEG in a minimum of 6 
subjects who have achieved and maintained target blood Phe for at least 2 consecutive weeks and for whom no further 
dose modifications are planned. Single-dose PK data has been collected in the Phase 1 study, PAL-001. However, there 
is little multiple-dose PK data or data for when subjects have reached and maintained a stable dosing regimen.  With the 
PK substudy, multiple-dose PK data will be collected for subjects who have already achieved Phe reduction to within 
the protocol-defined target range. 
This study is an extension of previous rAvPAL-PEGthethe dose finding studies(PAL 002 and PAL 004). 
Administration of rAvPAL-PEG will be continued to assess whether long-term dosing of rAvPAL-PEG is safe and can 
maintain reduced blood Phe concentrations in PKU subjects. 
 
5 
Section 7.4/Summary of Overall 
Risks and Benefits 
It is not expected that data from previous rAvPAL-PEG studies PAL 002 or PAL 004 will change the assumption that 
rAvPAL-PEG has a toxicity profile similar to other recombinant PEGylated non-human enzymes currently in use…. 
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Section 7.4.2/Toxicity Due to an 
Immunologic Reaction 
As of May 2012, a total of 70 subjects have been administered rAvPAL-PEG in the single-dose, Phase 1 study (PAL-
001) and in the repeat -dosing Phase 2 studies (PAL-002, PAL-004, and PAL-003).  The dose levels in the repeat-dosing 
studies range from 0.001 to 5.0 mg/kg/week administered in various frequencies (including 5 days a week).  The most 
clinically significant AEs have been hypersensitivity reactions that have led to dosing interruptions and reductions. Most 
of the hypersensitivity reactions have been nonserious and mild-to-moderate in severity.  
A total of 4 SAEs have been reported in the previous rAvPAL-PEG studies.  Of these 4 SAEs, 3 have been reported as 
related to rAvPAL-PEG.  Two of the study-drug related SAEs occurred in Study PAL-001.  Both of these SAEs 
occurred in subjects in the lower dose cohorts: an SAE of hypersensitivity reaction in a subject in the 0.001 mg/kg 
cohort and an SAE of anaphylactic reaction (urticaria) in a subject in the 0.01 mg/kg cohort.  Neither SAE was severe or 
resulted in discontinuation from the study, and both of the SAEs resolved.  There were no SAEs in subjects in the higher 
dose cohorts (0.03 mg/kg and 0.1mg/kg) in PAL-001.  The third study drug-related SAE (angioedema) occurred in a 
subject in Study PAL-004.  The fourth SAE (urticaria, dehydration) was reported as not related to study drug and 
occurred in a subject in Study PAL-002.  There have been no reports of anaphylaxis for any subject treated with 
rAvPEG-PAL (as of January 2012).  
 
15 
Section 7.4.2/Toxicity Due to an 
Immunologic Reaction 
Subjects who have a systemic clinical reaction at any time during this study may undergo a series of assessments to 
monitor safety, including assessment of complements, C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), 
and IgE antibodies.  Reintroduction of rAvPAL-PEG dosing after a reaction will depend on clinical assessments and 
available laboratory data, such as chemistry and urine studies, to ensure that there has been no end-organ damage prior 
to resuming treatment with rAvPAL-PEG. As of May 2012, antibody titers, including positive IgE titers, have not been 
predictive of future clinical reactions when dosing with rAvPAL-PEG.  Additionally, subjects will be premedicated to 
prevent or mitigate risk of hypersensitivity reactions (refer to Section 9.1.1.3.3). 
In Study PAL 001, there were 11 subjects (out of 25 subjects in the study) with skin related reactions (injection site 
bruising, erythema, pain, rash, swelling, and urticaria) that occurred following the single administration of rAvPAL
PEG. For all of these subjects, the reactions were generalized skin reactions or injection site skin reactions that did not 
compromise other organs and were not life threatening. These suspected antibody mediated responses were nonserious 
and mild or moderate in severity. These subjects are not considered to be at significant risk for antibody mediated 
reactions with injection of rAvPAL PEG during PAL 002, PAL 004, or this study; however, specific precautions for 
these subjects will be taken during this study to monitor subject safety (refer to Section 9.1.1). 
In Study PAL 002, 33 subjects have been dosed to date (JAN2011), including at dose levels of 2.0 mg/kg/week (or 0.4 
mg/kg/5 days a week). Most reactions reported in these subjects have been nonserious and mild or moderate in severity. 
There has been 1 SAE reported to date; the event was reported as not related to treatment with study drug. There have 
been no reports of anaphylaxis to date (JAN2011). Subjects who have a systemic reaction during this study will undergo 
a series of assessments to monitor safety, including assessment of IgE antibodies,  
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Section 7.4.2/Toxicity Due to an 
Immunologic Reaction 
, prior to determining if dosing may resume. Additionally, subjects who have systemic reactions will be premedicated 
and will be monitored closely for safety (refer to Section 9.1.1.3.3 for additional information regarding continued 
treatment of subjects with systemic reactions during the study). 
…. In some individuals, anti-PEG antibodies may be pre-existing due to previous exposure to PEG in other products. 
Anti-PEG antibodies have been associated with nonresponsiveness against therapy (Armstrong, 2007, Cancer), (Ganson, 
2006, Arthritis Res.Ther.).  Administration of rAvPAL-PEG may lead to anti-PEG antibody formation, and the duration 
of this possible effect is not known. Subjects in the Phase 2 rAvPAL-PEG studies have developed both anti-PEG IgM 
and anti-PEG IgG antibodies. Antibody formationThis may limit a subject’s future ability to be treated with other 
PEG-containing (eg, Depo-Provera) or PEGylated (eg, PEG-interferon) injectable drugs. It is therefore recommended 
that any PEG-containing injectable drug administered to subjects after completion of this study be done under medical 
observation. 
 
15 
Section 7.4.2.2/Management of 
Allergic Reactions 
In the event of an allergic reaction, subjects may be asked to see an allergist/immunologist and/or provide up to 
3 additional blood samples for antibody testingimmunology studies and complement testing. This additional testing may 
occur up to 6 months following the final study visit.   
The following measures are recommended for the treatment of allergic symptoms: 
• 
Administration of oral or IV glucocorticoids 
• 
Administration of oxygen and IV fluids. 
• 
Administration of additional symptomatic treatment (eg, acetaminiophen or ibuprofen). 
In addition, clinical judgment must be used in determining the appropriateness of corticosteroid administration. 
Acetaminophen or ibuprofen (5 10 mg/kg) may also be administered. An allergy and/or immunology consultation 
should be sought if necessary. Information regarding the management of local skin, large local skin, and systemic 
reactions is provided in Section 9.1.1. Detailed instructions for the management of allergic reactions are provided in the 
Study Reference Manual. 
 
1, 10, 16 
Section 7.4.3/Effects of Stopping 
and Re-Starting rAvPAL-PEG 
Treatment 
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Section 8/Study Objectives 
The exploratory objective of the study is as follows: 
• 
To assess evaluate the long-term relationship of diet and change in blood Phe concentration following 
administration with rAvPAL-PEG in subjects with PKU. 
The Substudy objectives are as follows: 
• 
To evaluate steady-state PK of rAvPAL-PEG in subjects who have achieved and maintained target blood Phe 
concentration and for whom no further dose modifications are planned. 
• 
To assess the safety and tolerability of stopping and re starting rAvPAL PEG dosing in a subset of subjects 
with PKU. 
• 
To evaluate the effect of stopping and re starting rAvPAL PEG dosing on blood Phe concentration in a subset 
of subjects with PKU. 
• 
To evaluate the effect of stopping and re starting rAvPAL PEG dosing on immune response in a subset of 
subjects with PKU.   
• 
To assess the effect of multiple doses of rAvPAL PEG on the PK profile, in particular clearance of drug, when 
drug is stopped in a subset of subjects with PKU who have been previously exposed to rAvPAL PEG.    
 
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Section 9.1/Overall Study Design 
and Plan 
This is a long-term extension of rAvPAL-PEG Phase 2 studiesthe Phase 2, open label, dose finding studies, PAL 002 
and PAL 004, in approximately 100 subjects with PKU. The doses are planned to be in the same range as those tested in 
PAL-002 and PAL-004 (starting at 0.001 through 5.0 mg/kg/week), provided no dose-limiting toxicity is observed in a 
PAL 002 or PAL 004previous rAvPAL-PEG study004. 
Only subjects who completed the protocol defined study drug regimen in PAL 002 or PAL 004a previous rAvPAL-PEG 
study will be enrolled into this study. Subjects enrolling into PAL-003 with no interruption in dosing from a previous 
rAvPAL-PEG study may either continue their previous dosing regimen or begin this study at a higher dose level. 
Subjects who have had dosing interruptions between the previous rAvPAL-PEG study and PAL-003 must have their 
starting dose determined per the Sponsor’s Medical Officer.  Subjects who enroll from PAL 002 will either continue the 
dose regimen that was administered upon completion of PAL 002 or start dosing at a higher dose per the dose increase 
instructions. Subjects who enroll from PAL 002 may start this study at a higher dose level provided there was no 
interruption in dosing since completion of PAL 002 and enrollment into this study. Subjects who enroll from PAL 004 
will re start rAvPAL PEG dosing in this study at the same dose level and frequency as was administered upon 
completion of PAL 004. The first dose will be administered in the clinic, and the subject must be observed for 30-60 
minutes following administrationdue to restarting dosing in this study. A follow-up telephone call will be made to the 
subject to monitor subject safety 24 hours following the return to dosing.  
Diet should not be altered during the course of this study. Any decision to modify subject diet must be made per the 
Investigator in consultation with the Sponsor’s Medical Officer and must be performed under the supervision of the 
Investigator in consultation with the Sponsor’s Medical Officer. To monitor for changes in subject diet, a diet diary will 
be issued to subjects for completion and will be brought to each clinic monthlyvisit for review with the clinical study 
staff. 
 
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take rAvPAL-PEG. 
Subjects’previous rAvPAL-PEG dosing will continue in PAL-003. In PAL-003, each subject’s dose will be adjusted as 
needed to attain or maintain blood Phe concentrations of 60-600 µmol/L. rAvPAL-PEG dose will be based on either a 
subject’s weight or will be a fixed dose (subjects who have maintained blood Phe levels to 60-600 µmol/L for at least 2 
consecutive weeks and who have maintained a stable rAvPAL-PEG dose for at least 2 consecutive weeks; refer to 
Section 9.4.4). Doses will be evaluated on an individual basis.  
 
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Section 9.1/Overall Study Design 
and Plan 
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take rAvPAL-PEG. PAL 002 
and PAL 004 sSubjects’previous rAvPAL-PEG dosing will continue in PAL-003. In PAL-003, each subject’s dose will 
be adjusted as needed to attain or maintain blood Phe concentrations of 60-600 µmol/L. rAvPAL-PEG dose will be 
based on either a subject’s weight or will be a fixed dose (subjects who have maintained blood Phe levels to 60-600 
µmol/L for at least 2 consecutive weeks and who have maintained a stable rAvPAL-PEG dose for at least 2 consecutive 
weeks; refer to Section 9.4.4). Doses will be evaluated on an individual basis.  
 
A PK substudy has been added to evaluate the steady-state PK of rAvPAL-PEG in a minimum of 6 subjects who have 
achieved and maintained target blood Phe for at least 2 consecutive weeks and for whom no further dose modifications 
are planned.  Subjects enrolled into the substudy will have additional pre-dose PK sampling performed (refer to Table 
9.1.2). 
 
A subset of up to 10 subjects who are already enrolled and who have consented to participate in this study will be asked 
to participate in a Substudy to assess the effect that stopping and re starting treatment with rAvPAL PEG has on safety, 
efficacy, PK, and immune response. Subjects will be eligible for participation in the Substudy provided they also meet 
all of the PAL 003 eligibility criteria, have been on a stable dosing regimen for approximately 4 weeks during this study, 
have not had any serious adverse events reported during PAL 003, and were not enrolled in Study PAL 004. Subjects 
participating in the Substudy will have rAvPAL PEG administration halted for approximately 4 weeks regardless of 
their dosing regimen (dose level and frequency). rAvPAL PEG will not be administered during the dose interruption; 
however, subjects will continue to perform assessments for safety, blood Phe concentration, PK, and immune response. 
Subjects enrolled into the Substudy will also have additional PK sampling performed prior to the dosing interruption and 
during the dosing interruption.  
4, 5 
Section 9.1/Overall Study Design 
and Plan 
To allow for PK sampling once dosing is stopped, subjects may be admitted to a research facility within 8 hours of 
stopping dosing where they will reside for at least 24 hours. After the dosing interruption, rAvPAL PEG administration 
will be re started at the same dose level and dosing frequency that was administered prior to the dosing interruption. 
Upon re starting rAvPAL PEG, the first dose must be administered in the clinic and the subject must be observed for 
30 60 minutes following administration due to restarting dosing. A follow up telephone call will be made to the subject 
to monitor subject safety 24 hours following the return to dosing. Additional PK sampling will also be performed for the 
first week after the dosing interruption. 
The Schedule of Events and interim dosingPK substudy collection schedules are presented below in Table 9.1.1 and 
Table 9.1.2:  , Table 9.1.3 and Table 9.1.4.  
 
4, 5   
Table 9.1.1/Schedule of Events 
This table has been updated to reflect changes in this amendment. 
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Table 9.1.2/PK Substudy Dosing 
Regimens 
This table has been added for the PK Substudy. The previous Table 9.1.2 regarding interim dosing in subjects w4rho 
increased dose to 2x/daily has been removed. 
5, 6 
Table 9.1.3/Interim Dosing Visit 
Schedule, Subjects Whose Dose 
is Increased to 2x/Week 
This table has been removed. 
16 
Section 9.1.1.1/Subjects Who 
Have Had Previous 
Hypersensitivity Reactions to 
rAvPAL-PEG or a PEG-
containing Product 
Subjects who had a previous systemic reaction to rAvPAL-PEG or a PEG-containing product that warranted early 
termination from a previous PAL 002 or PAL 004 rAvPAL-PEG study are excluded from participation in this study. 
Subjects who experienced a generalized skin rash are included in this category. Subjects who have had a previous local 
skin reaction to rAvPAL-PEG in PAL 002 or PAL 0a04 previous rAvPAL-PEG study are eligible to participate in this 
study. Subjects who have had a previous reaction and are deemed eligible for participation must be premedicated orally 
with acetaminophen and/or non-sedating antihistamines 1 hour1-2 hours prior to study drug dosing for the remainder of 
the study. The premedication dosage will be standard…. 
3 
Section 9.1.1.3.1/Local Skin 
Reactions 
All subjects who experience a local skin reaction during this study may be premedicated orally with acetaminophen 
and/or non-sedating antihistamines 1-2 hours prior to study drug dosing (subjects may take non-sedating premedications 
prior to coming to clinic) for all future study doses. Recommended premedications are acetaminophen and/or non-
sedating antihistamine. The dosage will be standard. Because antihistamines can cause drowsiness, sedating 
antihistamines may be administered only if the subject is accompanied by a designated driver. Subjects who have had a 
local skin reaction (refer to Section 9.1.1.2 for definition) after administration of rAvPAL PEG in this study may 
continue if the symptoms do not worsen and no other symptoms have developed but may be premedicated with 
acetaminophen and/or antihistamines (standard dosage per the package insert) 1 hour prior to the next dose of study drug 
dosing. Because antihistamines can cause drowsiness, it should be administered only if the subject is accompanied by a 
designated driver. 
 
3 
Section 9.1.1.3.2/Large Local 
Skin Reactions 
Large local skin reactions (refer to Section 9.1.1.2 for a definition) may or may not be contiguous to the rAvPAL-PEG 
injection site, and subjects with either type of large local skin reaction may continue dosing if the skin symptoms have 
resolved and no other symptoms have developed. Subjects will be premedicated orally with acetaminophen and/or non-
sedating antihistamines 1-2 hours prior to study drug dosing (subjects may take non-sedating premedications prior to 
coming to clinic) for all future study doses.may be premedicated orally with acetaminophen and/or antihistamines 
(standard dosage per the package insert) 1 hour prior to study drug dosing. 
Symptoms of large local skin reactions may be treated with local application of ice and topical, oral, or IV 
antihistamines and/or steroids as needed (refer to Section 7.4.2.2). 
 
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Section 9.1.1.3.2.1/Large Local 
Skin Reactions Contiguous to 
Injection Site 
…. For the remainder of the study, subjects will be premedicated orally with acetaminophen and/or non-sedating 
antihistamines 1-2 hours prior to study drug dosing (subjects may take non-sedating premedications prior to coming to 
clinic) for all future study dosesmay be premedicated orally with acetaminophen and/or antihistamines (standard dosage 
per the package insert) 1 hour prior to the next dose of study drug. Because antihistamines can cause drowsiness, it may 
be administered only if the subject is accompanied by a designated driver (if applicable).  
 
3 
Section 9.1.1.3.3/Systemic 
Reactions 
Following the reaction, subjects will be required to complete the assessments of the Unscheduled Hypersensitivity 
Reaction visit, including assessment of IgE. If a subject presents with a clinical diagnosis of anaphylaxis, further dosing 
will be held while laboratory evaluation of IgE, as part of the Unscheduled Systemic Reaction Visit, is performed.  
Subjects who do not have an IgE-mediated reaction may resume study drug administration per the discretion of the 
Principal Investigator and the Sponsor’s Medical Officer; however, if subject was dosing at home, they will be required 
to come into the clinic for at least 1 week. If laboratory data shows that the subject experienced an IgE-mediated 
reaction, dosing will not resume until review of the case with the Investigator, Sponsor Medical Officer, and an 
allergist/immunologist.   
 
Following completion of the Unscheduled Systemic Reaction Visit, administration of rAvPAL PEG may resume up to 1 
week following the onset of the reaction if the systemic reaction is not IgE mediated and the subject’s safety will not be 
further compromised with resumed dosing. rAvPAL-PEG administration will resume at the next lowest dose level. 
Restarting of rAvPAL-PEG administration following a systemic reaction must be performed in the clinic for the first 
week of resumed dosing. Subjects must be premedicated orally with acetaminophen and/or antihistamines 1-2 hours 
prior to study drug dosing (subjects may take non-sedating premedications prior to coming to clinic) for all future study 
dosespremedicated orally with acetaminophen and/or antihistamines (standard dosage per the package insert) 1 hour 
prior to study drug dosing for the remainder of the study. Additionally, subjects must be closely monitored for 
30-60 minutes following every administration of study drug. Because antihistamines may cause drowsiness, the subject 
must be accompanied by a designated driver (if applicable). 
 
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Section 9.1.1.3.3/Systemic 
Reactions 
If blood Phe concentrations are not 60-600 µmol/L following 1 week of daily administration at the lowered dose cohort 
and there is no further evidence of toxicity (ie, another systemic reaction attributed to rAvPAL-PEG administration or 
clinically significant abnormal laboratory test results), the subject may be administered the next highest dose level in the 
clinic per the allowable dose increases outlined in Section 9.1.2. Subjects must be premedicated orally with 
acetaminophen and/or antihistamines 1-2 hours prior to study drug dosing (subjects may take non-sedating 
premedications prior to coming to clinic) for all future study dosespremedicated orally with acetaminophen and/or 
antihistamines (standard dosage per the package insert) 1 hour prior to study drug dosing for the remainder of the study.  
Additionally, subjects must be closely monitored for 30-60 minutes following every study drug administration. Because 
antihistamines may cause drowsiness, the subject must be accompanied by a designated driver (if applicable). 
 
3 
Section 9.1.2.1/Dose Increase 
Methodology 
For subjects from PAL 002An individual subject’s dose may be adjusted beginning on Day 1 of PAL-003. For the 
duration of this study, an individual subject’s dose may be adjusted if warranted per a subject’s adverse event profile and 
blood Phe concentrations. Dose increases should be performed as follows: 
Only 1 dose (level or frequency) adjustment is allowed every 2 weeks. 
Blood Phe levels will be measured daily for 3 days after each dose increase (fingerstick is acceptable); more frequent or 
daily blood Phe measurements may be performed. 
 
2, 7 
Section 9.1.2.2/Dose Decrease 
Methodology 
If the subject develops low blood Phe (as defined by a blood Phe level ≤ 30 µmol/L as measured by serum Phe levels for 
a minimum of 1 month), the subject’s rAvPAL-PEG dose should be decreased to the next lower dose.  If the condition 
persists after another 1 month at the lower dose, the dose should be decreased again to the next lower level. If the subject 
continues to experience low blood Phe after two dose level reductions, the subject may be asked to consult the dietician 
to eliminate medical foods and/or formulas and to ensure a balanced and nutritious diet (as part of the routine standard 
of care for PKU disease management, subject diet should be monitored by a dietician). 
 
8 
Section 9.3.1/Inclusion Criteria 
1. Must have completed participation and all protocol defined study drug in PAL 002 or PAL 004in a previous 
rAvPAL-PEG study. 
 
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Section 9.3.2/Exclusion Criteria 
4. A prior reaction that included systemic symptoms (eg, generalized hives, respiratory or gastrointestinal 
problems, hypotension, angioedema, anaphylaxis) to rAvPAL-PEG or a PEG-containing product. Subjects with 
a prior systemic reaction of generalized rash may be eligible for participation per the discretion of the Principal 
Investigator in consultation with the Sponsor’s Medical Officer. However, subjects who discontinued from 
study treatment early due to a reaction are not eligible to enroll into this study.      
8. Known hypersensitivity to rAvPAL-PEG or its excipients, including hypersensitivity reactions that necessitated 
early termination from a PAL 002 or PAL previous rAvPAL-PEG study004. 
 
 
16 
Section 9.3.4/Subject 
Identification and Replacement of 
Subjects 
Subjects will retain the same subject number assigned in their previousPAL 002 or PAL rAvPAL-PEG study.004. This 
unique identifier will be on all case report form (CRF) pages. In legal jurisdictions where use of initials is not permitted, 
a substitute identifier will be used.  
 
16 
Section 9.4/Treatment 
Upon enrollment into this study, subjects from previous rAvPAL-PEG studies PAL 002 will be dosed with the same or 
higher dose that was administered upon completion of PAL 002that study provided that there was no interruption in 
dosing. Subjects enrolling from PAL 004, will be administered the same dose that was administered upon completion of 
PAL 004. rAvPAL-PEG doses will be administered SC by either health care professionals or via self administration…. 
Subjects may self administer study drug at home if approved by the Investigator and the Sponsor’s Medical Officer and 
if adequate training is demonstrated. Subjects may be eligible to self administer study drug if he or she meets the 
following criteria:  
• 
The subject is on a stable dosing regimen for 2 weeks (ie, the subject has demonstrated a blood Phe level within 
60-600 µmol/L for a minimum of 2 consecutive weeks). 
…. The patientsubject will see a study site nurse or home healthcare nurse in person every week or receive a telephone 
call from site staff to ensure that the subject continues to perform all self-administration procedures correctly, to assess 
of adverse events, and to answer questions throughout the duration of the study…. 
Subjects who are within the target Phe range may also be permitted to convert from weight-based dosing to fixed dosing 
(refer to Section 9.4.4). 
 
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Section 9.4.2.1/Product 
Characteristics and Labeling 
The rAvPAL-PEG drug product for SC injection is formulated and supplied as a sterile aqueous (colorless to pale 
yellow) solution in clear, single-use, type-1 borosilicate glass vials. Each 3 mL vial contains 1.5 ± 0.2 mL to deliver 
either 10 mg of rAvPAL-PEG per 1 mL (10 mg/mL protein concentration) or 15 mg of rAvPAL-PEG per 1 mL (15 
mg/mL protein concentration). Each vial is filled with 1.5 ± 0.2 mL to allow the withdrawal and delivery of up to 1 mL 
of the drug product. 
 
4 
Section 9.4.4/Directions for 
Administration 
Doses will be administered SC and the favorable dose will be determined for each subject by adjusting the dose level, 
dose frequency, or both, as agreed by the PI and the Study Sponsor’s Medical Officer, based upon the subject’s response 
to doses. Dosing is up to a maximum dose per week of 5.0 mg/kg (or 375 mg for subjects receiving a fixed dose).  
 
For subjects receiving weight-based dosing, dosageDosage is calculated by multiplying each subject’s weight in 
kilograms (kg) on Day 1 (predose) by the assigned dose (in mg/kg). During the study, if the weight of a subject changes 
more than 10% from the measurement obtained at baseline or at a previous measurement, the subject’s dose may be 
adjusted to accommodate the change. The change must be recorded. Refer to the Pharmacy Manual for additional 
information on calculating dosage. 
 
Subjects who have demonstrated efficacy (as measured by blood Phe within the target range of 60-600 µmol/L for at 
least 2 consecutive weeks) and who have maintained a stable rAvPAL-PEG dose for at least 2 consecutive weeks may 
be eligible to transition from weight-based dosing to a fixed dosing regimen that would permit daily dosing (5- or 7-
days-per-week).  Subjects who convert to a fixed-dosing regimen should convert their dose based upon the information 
presented in Table 9.4.4.1. 
Table 9.4.4.1:  Fixed Doses for Subjects on Weight-Based Dose Regimen 
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Table 9.4.4.1/ Directions for 
Administration 
Weight-based 
dose (mg/kg) 
Equivalent 
fixed dose (mg) 
Vol for 10 mg/ml 
concentration (ml) 
Vol for 15 mg/ml 
concentration (ml) 
0.03 
2.5 
0.25 
0.17 
0.06 
5 
0.5 
0.33 
0.12 
10 
1 
0.67 
0.25 
20 
2 
1.33 
0.5 
40 
4 
2.67 
1.0 
75 
7.5 
5 
2.0 
150 
15 
10 
3.0 
225 
22.5 
15 
4.0 
300 
30 
20 
5.0 
375 
37.5 
25 
 
It is preferable that theThe injection sites should be alternated between doses, ie, upper left arm in Week 1, upper right 
arm in Week 2, etc. Doses may be administered in any of the common SC areas (upper arm, thigh, abdomen). If dose 
volume is such that a dose will be divided and given in more than 1 injection site, it is preferable to use both arms, both 
legs, or both sides of the abdomen. 
 
4, 16 
Table 9.4.4.1/ Directions for 
Administration 
…. Study drug will be administered by clinic staff, or other qualified and trained study personnel, or qualified subjects. 
Information for subjects who are participating in the Substudy and re start rAvPAL PEG dosing is provided in Section 
9.1. Information for dosing of subjects who enroll into this study after completing Study PAL previous rAvPAL 
studies004 is provided in Section 9.1. Instructions for subjects who re-start rAvPAL-PEG dosing due to unplanned 
missed doses are provided in Section 9.4.10.  
 
16 
Section 9.4.5/Method of 
Assigning Subjects to Treatment 
Groups 
This will be an open-label study; no randomization schedule will be generated. 
Subjects will retain the same subject number used in PAL 002 or PAL 0 their previous 04 rAvPAL-PEG study. 
 
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Section 9.4.6/Selection of Doses 
Used in the Study 
This Phase 2 study aims to evaluate the efficacy, safety, tolerability, and PK parameters of multiple doses of 
rAvPAL-PEG after long-term administration in subjects with PKU. A dose that produces a reduction in blood Phe 
concentrations to 60-600 μmol/L will be determined for each subject based on preliminary safety, antibody, and efficacy 
data from this ongoing study.and the ongoing study, PAL 002, to date (JAN2011).  
 
16 
Section 9.4.8/Prior and 
Concomitant Medications 
Use of any investigational product (with the exception of rAvPAL-PEG used in PAL 002 or PAL 004a previous 
rAvPAL-PEG study) or investigational medical device within 30 days before Screening, or requirement for any 
investigational agent prior to completion of all scheduled study assessments, is prohibited. 
 
Use or planned use of any injectable drugs containing PEG (other than rAvPAL-PEG), including Depo-Provera, is 
prohibited within 6 months prior to Screening and during study participation. A list of PEG-containing injectable drugs 
is provided in the study reference materials. Subjects who have had a prior local skin reaction to rAvPAL-PEG or a 
PEG-containing product will be premedicated with acetaminophen and/or non-sedating antihistamines (refer to Section 
9.1.1)…. 
16 
Section 9.4.10/Dose Interruption 
and Missed Doses 
Information for subjects who are participating in the Substudy and re start rAvPAL PEG dosing is provided in Section 
9.1. Information for dosing of subjects who enroll into this study after completing Study PAL 002 or Study 
PALprevious rAvPAL PEG studies004 is provided in Section 9.1.  
 
6, 16 
Section 9.6/Dietary or Other 
Protocol Restrictions 
A 3-day dietary record will be completed by subjects and will be brought to clinic visits for review with clinic staff. It is 
preferable that subjects complete the 3-day record immediately prior to their next monthly dose of study drug study visit. 
The dietary record will be maintained with the study source documents. Information regarding a subject diet diary is 
provided in Section 9.7.4. 
14 
Table 9.7.1.1/Summary of 
Laboratory Assessments 
This table has been updated to reflect changes made to this protocol amendment. 
16 
Section 9.7.1.3/Vital Sign 
Measurements 
Vital signs will be measured after resting for 5 minutes, and include seated systolic blood pressure (SBP) and diastolic 
blood pressure (DBP) measured in millimeters of mercury (mm Hg), heart rate in beats per minute, respiration rate in 
breaths per minute, weight (kg), and temperature in degrees Celsius (°C). Height (cm) will be measured at Screening 
only.  Weight will be measured at Screening and then monthly. 
 
13 
Section 9.7.1.5/Chest X-Ray 
A chest X-ray will be performed at the Screening, Month 12Week 48, and Final Follow-Up (or Early Termination) visits 
to assess gross pulmonary health.  
 
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Section 9.7.2.1/Blood 
Phenylalanine Concentrations 
Blood samples for Phe concentration measurements will be drawn at least 2.5 hours after a meal, on the days and time 
points indicated in the Schedule of Events (Table 9.1.1, Table 9.1.2:   Table 9.1.3 and Table 9.1.4).   
Blood Phe may be collected monthly, rather than weekly, at the discretion of the Investigator and provided that the 
subject meets the following criteria: 
• 
Is receiving a stable dose of rAvPAL-PEG (defined as no dose modifications or interruptions for at least the 
previous 2 weeks) 
• 
Has a stable blood Phe level (defined as Phe between 60-600 µmol/L for at least 2 consecutive weeks) 
The subject may continue to have monthly, rather than weekly, blood Phe collection provided the following do not 
occur: 
• 
Blood Phe measurement > 600 µmol/L 
• 
Blood Phe measurement ≤  30 µmol/L 
If either of these conditions occurs, then that subject should return to weekly blood Phe draws until the rAvPAL-PEG 
dose has been adjusted and the Phe level is again within the protocol-defined target range for at least 2 weeks. 
In addition, after each administration of study drug, the subject will have a blood Phe measurement by fingerstick as 
outlined in Table 9.1.1, Table 9.1.2:  , Table 9.1.3 and Table 9.1.4 . This may be done by the subject at home.  
 
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Section 9.7.3/Pharmacokinetic 
Variables 
Subjects enrolled in the Substudy will have additional PK sampling performedprior to the planned dosing interruption 
and upon re introduction of rAvPAL PEG. For subjects participating in the Substudy, PK sampling will be performed as 
follows: 
• 
When dosing is stopped, PK sampling will be performed prior to the final dose and then postdose at 8 hours, 12 
hours, 16 hours, 24 hours, 48, hours, 72 hours, 96 hours, 144 hours, 168 hours, and 216 hours. 
• 
When dosing is re-started, PK sampling will be performed predose and then postdose at 24 hours, 48 hours, 72 
hours, 120 hours, and 168 hours.For subjects who are administered rAvPAL PEG once per week, plasma PK 
sampling will be performed pre dose and every 24 hours thereafter (24, 48, 72, and 96 hours if possible), and 
then pre dose of the next weekly dose. 
• 
For subjects who are administered rAvPAL-PEG two or three times per week, plasma PK sampling will be 
performed pre-dose and every 24 hours during the longest period between doses, when possible, and then pre-
dose of the next dose.  
• 
For subjects who are administered rAvPAL-PEG four to seven times per week, plasma PK sampling will be 
performed pre-dose and every 12 hours during the longest period between doses, when possible, and then pre-
dose of the next dose. 
See Table 9.1.2 for additional details. 
 
5, 6 
Section 9.7.4/Exploratory 
Efficacy Variables 
Diet will be assessed for its role in blood Phe reduction relative to rAvPAL-PEG dosing using a 3-day diet diary, which 
will be given to subjects to complete at home. Subjects will bring the completed diary with them to clinic visits on a 
monthly basis. Subjects will be instructed to record all food, beverages, special low-protein foods, and medical foods 
consumed for 3 consecutive days each weekmonth. If changes in diet are noted per the information on the diet diary, the 
subject will be instructed to maintain their diet as reported at the beginning of the study or as otherwise instructed by the 
Investigator. 
 
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Section 9.7.5.2/Antibody Testing 
Immunogenicity will be assessed by determining immune response and neutralizing activity with the following 
measurements: anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, anti PEG  anti-PEGPAL IgE, anti-PEG IgM, anti-rAvPAL-
PEG IgE, and anti-rAvPAL-PEG neutralizing antibodies (refer to Section 9.1.1.3.3). ValidatedI immunogenicity assays 
will be used perperformed at the time points indicated in the Schedule of Events (Table 9.1.1). 
 
BioMarin will perform theall antibody analysistesting, except for IgE antibodies, which will be assessed by a Contract 
Research Organization. 
 
16 
Section 9.7.6/Clinical Laboratory 
Assessments 
All abnormal clinical laboratory result pages should be initialed and dated by an Investigator, along with a comment 
regarding whether or not any the abnormal result is clinically significant. 
 
16 
Table 9.7.6.1/Clinical Laboratory 
Tests 
This table has been updated to reflect changes in this amendment. 
16 
Section 11.2/Diet Diary 
A 3-day diet diary will be issued to subjects for completion and will be brought to each clinic on a monthly basis visit 
for review with the clinical study staff. Additional information regarding the diet diary is provided in Section 7.3, and 
information regarding administration of the diary is provided in Section 9.7.4. Additional information about diet is 
provided in Section 9.1 and Section 9.6. 
 
14 
Section 12.2/Screening Visit 
• 
Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the event of any positive or 
equivocal urine pregnancy test result.).  For safety reasons, this test must be performed prior to the chest X-ray. 
• 
Clinical laboratory tests (including spot urine albumin/creatinine ratio, hematology, chemistry, and urinalysis) 
• 
Complement C3 and C4 
For subjects who participated in PAL 002 or PAL 004, these assessments may be the same as those used for the Week 
16 Visit of PAL 002 or the Week 16 visit ofPAL 004a previous rAvPAL-PEG study, these assessments may be the 
same as those used for the last visit of the previous study, if they occur within 28 days from Day 1. 
 
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Section 12.3.1/Day 1 (Week 1) 
• 
Vital signs, including weight 
• 
Administer study drug (study drug may be administered on additional days during the week as determined by 
the Investigator, in agreement with the Study Sponsor’s Medical Officer) 
o 
For subjects enrolling into this study from Study PAL 004, first dose of rAvPAL PEG must be 
given in the clinic setting and a telephone follow up with the subject must be performed 24 hours 
later to assess safety issues. 
 
13, 16 
Section 12.3.2/Weekly Visits 
Weekly visits do not require an in-clinic visit if conducted by a home healthcare professional. However, dose 
modifications must be performed in the clinic. Subjects must have AEs and concomitant medications assessed and an 
injection-site inspection performed whenever dose is administered even if the administration does not coincide with a 
scheduled clinic visit.  For subjects on a stable dose of rAvPAL-PEG (ie, no dose change in the last 2 weeks) and have 
had a phenylalanine (Phe) level at or below target range (60-600 µmol/L) for 2 consecutive weeks   weekly visits may 
be waived and replaced by a telephone call per discretion of the Investigator but monthly visits are required. 
• 
Vital signs, including weight 
• 
3 day diet diary (It is preferable that the subject complete the diary 3 days immediately prior to the next dose of 
study drug.) 
• 
For subjects participating in the Substudy, refer to Section 12.3.3. 
• 
Blood Phe and plasma tyrosine concentration 
o 
Blood Phe may be collected monthly, rather than weekly, if certain criteria are satisfied (refer to 
Section 9.7.2.1). 
• 
Weekly telephone call 
o 
For those subjects performing self administration and waiving (per Investigator discretion) the 
weekly visit (refer to Section 12.3.7). 
o 
For subjects participating in the Substudy, refer to Section 12.3.3. 
In addition, 3 days after each administration of study drug, the subject will have a blood Phe measurement by 
fingerstick. This may be done by the subject at home. 
 
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Section 12.3.3/Substudy Visits 
For subjects participating in the PK substudy, refer to Section 9.7.3 and Table 9.1.2:  .on Day 1 of the Substudy (ie, final 
dose prior to interruption), Day 8, Day 15, Day 22, and Day 29 (ie, restart administration of study drug) for subjects 
participating in the Substudy: 
• 
Physical examination 
• 
Vital signs, including weight 
• 
Clinical laboratory tests 
• 
Sedimentation rate 
• 
Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the event of any positive or 
equivocal urine pregnancy test result.) 
• 
Injection site inspection (predose; postdose on Day 1; during weekly visit on Day 8, 15, 22; and postdose on 
Day 29) 
• 
Assessment of AEs  
• 
Concomitant medications 
• 
Diet query 
• 
3 day diet diary  
• 
Serum anti rAvPAL PEG antibodies (anti PAL IgG, anti PAL IgM, anti PEG IgG, anti PEG IgM, and 
anti rAvPAL PEG neutralizing antibodies,) 
• 
Blood Phe and plasma tyrosine concentration 
o 
When dosing is stopped, sampling for blood Phe assessment only will be performed prior to the 
final dose and then postdose at 8 hours, 12 hours, 16 hours, 24 hours, 48, hours, 72 hours, 96 
hours, 144 hours, 168 hours, and 216 hours. 
 
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Section 12.3.3/Substudy Visits 
o 
When dosing is re started, sampling for blood Phe assessment only will be performed predose and 
then postdose at 24 hours, 48 hours, 72 hours, 120 hours, and 168 hours. 
• 
For subjects participating in the Substudy, additional PK sampling will be performed upon the final dose prior 
to the planned dosing interruption and upon re introduction of rAvPAL PEG. Refer to Section 9.7.3 
• 
Administer study drug (Day 29 only) 
o 
For subjects participating in the Substudy, administration of rAvPAL PEG will not be performed 
for approximately 4 consecutive weeks regardless of their dosing regimen (dose level and 
frequency). After approximately 4 weeks of no dosing, rAvPAL PEG administration will be re
started at the same dose level and dosing frequency that was administered prior to the dosing 
interruption. The first dose of re administration must be given in the clinic setting, and a 
telephone follow up with the subject must be performed 24 hours later to assess safety issues. 
 
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Section 12.3.4/Monthly Visits 
(Week 4, 8, 12, etc) 
Beginning with Week 4, Mmonthly visits must be performed in the clinic and consist of all weekly activitieslisted above 
in Section 12.3.2 as well as the additional and include additional activities and must be performed in the clinic. 
The following study activitieslisted belowwill be performed at the monthly visits beginning with Week 4: 
• 
Vital signsWeight, including weight 
• 
Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the event of any positive or 
equivocal urine pregnancy test result.) For safety reasons, this test must be performed prior to the chest X-ray. 
• 
Chest x-ray (Month 12Week 48 visit only) 
• 
Injection site inspection (previous and current injection site) 
• 
Assessment of AEs 
• 
Concomitant medications 
• 
Diet query 
• 
3-day diet diary (It is preferable that the subject complete the diary 3 days immediately prior to the next dose of 
study drugmonthly visit.) 
• 
PK sample  
• 
For subjects participating in the Substudy, refer to Section 12.3.3. 
• 
Blood Phe and plasma tyrosine concentration 
• 
Administer study drug (study drug may be administered on additional days during the week as determined by 
the Investigator, in agreement with the Study Medical Officer) 
• 
Weekly telephone call 
o 
For those subjects performing self administration and waiving (per Investigator discretion) the 
weekly visit (refer to Section 12.3.7). 
 
13, 14, 
16 
Section 12.3.4/Monthly Visits 
(Week 4, 8, 12, etc) 
o 
For subjects participating in the Substudy, refer to Section 12.3.3. 
• 
In addition, 3 days after each administration of study drug, the subject will have a blood Phe measurement by 
fingerstick. This may be done by the subject at home. 
 
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Section 12.3.5/Quarterly Visits 
(Week 12, 24, 35, etc) 
Beginning with Week 12, Qquarterlyuarterly visits consist of all weekly(Section 12.3.2) and monthly (Section 12.3.4) 
activities listed above as well as the additional study activities listed below and include additional activities. 
The following study activities will be performed at the quarterly visits beginning with Week 12: 
• 
Vital signs, including weight 
• 
Clinical laboratory tests 
• 
Complement C3 and C4 
• 
Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the event of any positive or 
equivocal urine pregnancy test result.) 
• 
Injection site inspection (previous and current injection site) 
• 
Assessment of AEs 
• 
Concomitant medications 
• 
Diet query 
• 
3 day diet diary (It is preferable that the subject complete the diary 3 days immediately prior to the next dose of 
study drug.) 
• 
PK sample  
o 
For subjects participating in the Substudy, refer to Section 12.3.3. 
• 
Blood Phe and plasma tyrosine concentration 
• 
Serum anti rAvPAL PEG antibodies (anti PAL IgG, anti PAL IgM, anti PEG IgG, anti PEG IgM, 
anti rAvPAL PEG neutralizing antibodies)  
• 
Administer study drug (study drug may be administered on additional days during the week as determined by 
the Investigator, in agreement with the Study Medical Officer) 
• 
For subjects participating in the Substudy, refer to Section 12.3.3. 
 
1, 16 
Section 12.3.5/Quarterly Visits 
(Week 12, 24, 35, etc) 
In addition, 3 days after each administration of study drug, the subject will have a blood Phe measurement by 
fingerstick. This may be done by the subject at home. 
 
 
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Section 12.3.6/Interim Dosing 
Visit 
• 
Vital signs, including weight 
• 
Administer study drug 
• 
Blood Phe measurement by fingerstick 
o 
This may be done by the subject at home. 
 
7, 16 
Section 12.3.7/Weekly Telephone 
Visit 
Subjects who are administered rAvPAL-PEG at home and/or have been approved to self administered rAvPAL-PEG, 
should have a weekly telephone visit conducted. Subjects must still come into the clinic for the scheduled monthly visits 
per Table 9.1.1. The following should be discussed with the subject during the weekly telephone visit: 
• 
Injection-site self inspection (previous and current injection site) 
• 
Assessment of AEs 
• 
Concomitant medications 
• 
Confirmation of drug administration 
 
16 
Section 12.3.8/Unscheduled 
Hypersensitivity Reaction Visit 
• 
Perform immediately after reaction if possible. 
 
3, 16 
Section 12.3.8/Unscheduled 
Hypersensitivity Reaction Visit 
Following completion of the Unscheduled Hypersensitivity Reaction visit, subjects who do not have an IgE-mediated 
reaction may resume study drug administration per the discretion of the Principal Investigator and the Sponsor’s 
Medical Officer; however, if subject was dosing at home, they will be required to come into the clinic for at least 8 
weeks. If laboratory data shows that the subject experienced an IgE-mediated reaction, dosing will not resume until 
review of the case with the Investigator, Sponsor Medical Officer and an allergist/immunologist Following completion 
of the Unscheduled Hypersensitivity Reaction Visit assessments, the subject may resume treatment with study drug per 
the discretion of the Investigator in consultation with the Sponsor’s Medical Officer. Subjects who have had an IgE
mediated reaction must be discontinued from further study drug administration. Subjects who do not have an IgE
mediated reaction may resume study drug administration under close monitoring; subjects must be premedicated orally 
with acetaminophen and/or antihistamines 1 hour prior to study drug dosing for the remainder of the study (refer to 
Section 9.1.1.3.3). 
 
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Section 12.4/Early Termination 
Visit 
• 
Vital signs, including weight 
• 
Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the event of any positive or 
equivocal urine pregnancy test result.). For safety reasons, this test must be performed prior to the chest X-ray. 
 
13, 16 
Section 12.5/Final Follow-up 
Visit 
• 
Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the event of any positive or 
equivocal urine pregnancy test result.). For safety reasons, this test must be performed prior to the chest X-ray. 
 
16 
Section 14.3/Pharmacokinetic 
Analysis 
Subjects who complete the Substudy will have the following PK parameters assessed: area under the plasma 
concentration-time curve (AUC), time to maximum plasma concentration (Tmax), maximum plasma concentration (Cmax), 
half life (t1/2), and clearance (CL/F).  Should data become available from PAL 002 or PAL 004 previous rAvPAL-PEG 
studies that indicate study drug accumulation should also be measured, additional blood draws may be added for PK 
analysis as needed per the discretion of the Investigator in consultation with the Sponsor’s Medical Officer. 
 
16 
Section 14.3.1/Pharmacokinetic 
Substudy Analysis 
For subjects who completed the Substudy, the steady-state PK of rAvPAL-PEG in subjects who have achieved and 
maintained target blood Phe will be explored. 
 
5 
Section 14.5/Determination of 
Sample Size 
Subjects who participated in PAL 002 or PAL 004 previous rAvPAL-PEG studies may be enrolled into this study. No 
formal sample size calculation was conducted for this study or the PAL-003 Substudy.   
 
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CLINICAL STUDY PROTOCOL AMENDMENT SUMMARY 
Amendment: 5 
 
Date: February 28, 2014 
 
RATIONALE AND SUMMARY OF CHANGES 
The protocol for Study PAL-003 is being amended to make the following changes: 
 
1. Study Duration: The PAL-003 study duration has been extended an additional 
26 months to allow continued access to rAvPAL-PEG for subjects who do not qualify 
for participation in Study 165-302 and to further characterize the long-term safety and 
tolerability of rAvPAL-PEG in this patient population. 
2. Subject Population: The study population has been revised to only include subjects 
who are on a stable rAvPAL-PEG dosing regimen of  < 70 mg/week or 
 > 350 mg/week. This study is intended to provide long-term access to rAvPAL-PEG 
until study termination or regulatory approval for subjects who are not eligible to 
transition into the pivotal, placebo-controlled, Phase 3 study, 165-302. Subjects who 
are on a stable rAvPAL-PEG dose regimen of  ≥ 70 mg/week to  ≤ 350 mg/week and 
do not transition to 165-302 will be withdrawn from this study. 
3. Consultation by Sponsor’s Medical Officer for Diet and Dose Modifications: Review 
and approval of diet and dose modifications by the sponsor’s medical officer is no 
longer required for this study, except for dose increases  > 350 mg/week. Significant 
modifications to dose and/or diet are not expected as subjects are generally on a stable 
maintenance rAvPAL-PEG dose regimen and are no longer performing dose titration.  
4. Observation Time following Dose Increases or Dose Interruption: The observation 
period following an increase in rAvPAL-PEG dose or re-introduction of 
rAvPAL-PEG following a dose interruption has been reduced to 30 minutes as longer 
periods of observation is have not proven to be useful. 
5. Clinic Visits: Clinic visits have been reduced from weekly to monthly because it is 
anticipated that rAvPAL-PEG dose adjustments will be infrequent (subjects are on a 
maintenance dose regimen) and to lessen patient burden. However, weekly telephone 
contacts will continue to be performed. Also, blood sampling for PK and 
immunogenicity assessments has been revised from monthly to every 12 weeks to 
better align with the long-term needs of this study and to lessen patient burden. 
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Proprietary and Confidential  
6. Unscheduled Hypersensitivity Reaction Visit: Assessments of urine/albumin 
creatinine ratio and urine N-methyl histamine have been added and sedimentation rate 
has been removed to align with the Hypersensitivity Reaction visit assessments 
performed in the Phase 3 studies. In addition, the window for the Hypersensitivity 
Reaction Visit has been changed to within 24 hours of event onset to enable timely 
assessment of hypersensitivity markers. 
7. Immunogenicity Testing: Antibody testing has been clarified. Anti-PAL 
immunoglobulin E (IgE) testing is no longer required for this study because there has 
been no observed association between anti-PAL IgE and hypersensitivity reactions. 
Anti-PAL-PEG IgE testing will continue to be performed as part of the 
Hypersensitivity Reaction Visit assessments. 
8. Safety Analysis: Details regarding analysis of hypersensitivity adverse events (AEs), 
including those that result in dose modification, have been added. Also, physical 
examination results and immunogenicity test results have been added to the safety 
analysis description. 
9. Adverse Event Reporting: The pregnancy reporting period has been clarified as the 
time from informed consent to 4 weeks after the last dose of study drug. Also, AE 
reporting for events that are not resolved at the time of study completion has been 
revised; AE outcomes with resolution dates if applicable should be reported on the 
appropriate Case Report Form (CRF). 
10. Premedication: Subjects who have a hypersensitivity reaction are no longer required 
to premedicate with acetaminophen and antihistamine for all subsequent doses of 
study drug. However, premedication prior to study drug administration is encouraged.  
11. Return to Dosing following Hypersensitivity Reactions: Return to dosing following a 
hypersensitivity reaction should be based on investigator assessment in consultation 
with the Sponsor’s Medical Officer.  
12. Pharmacokinetic Substudy: The sample size for the PK Substudy has been clarified as 
up to 6 subjects. 
13. Investigational Product: rAvPAL-PEG information has been updated to include 
information regarding the addition of 20-mg vials and prefilled syringes with 
rAvPAL-PEG. 
14. Clinical Background Information: Results from the Phase 2 studies PAL-002, 
PAL-004, and PAL 165-205 have been updated to align with information provided in 
the Phase 3 studies. 
15. Schedule of Events and Study Procedures: The Schedule of Events and the Study 
Procedures sections have been updated to reflect the changes to this amendment.   
16. Sponsor’s Medical Officer: The Medical Officer information has been updated. 
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17. Administrative Changes: Additional minor changes have been made to improve 
clarity and consistency. 
Specific revisions since the completion of the last protocol amendment (dated 07JUN2012) 
to the text of each section, including the Synopsis, are outlined in Section 24. 
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2 
SYNOPSIS 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
TITLE OF STUDY: 
Long-term Extension of a Phase 2, Open-Label Dose-Finding Study to Evaluate the Safety, Efficacy, 
and Tolerability of Multiple Subcutaneous Doses of rAvPAL-PEG in Subjects with PKU 
PROTOCOL NUMBER:  PAL-003 
STUDY SITES:  Approximately 20 centers in the United States 
PHASE OF DEVELOPMENT:  Phase 2 
STUDY RATIONALE: 
The need exists for a treatment that will help individuals with phenylketonuria (PKU) safely achieve 
lifelong, reliable control of blood phenylalanine (Phe) concentrations and improve functional 
outcomes. PEGylated recombinant Anabaena variabilis phenylalanine ammonia lyase (rAvPAL-PEG) 
is a potential substitute for the phenylalanine hydroxylase (PAH) enzyme, which is defective in 
individuals with PKU. rAvPAL-PEG may control blood Phe concentrations, which may have 
additional clinical benefits. This study is an extension of the rAvPAL-PEG Phase 2 studies PAL-002, 
PAL-004, and 165-205. Administration of rAvPAL-PEG will be continued to assess the long-term 
safety and efficacy of rAvPAL-PEG in PKU subjects. 
Blood Phe levels depend not only on the functional presence of the endogenous enzyme PAH but also 
on the dietary intake of Phe. It is important to understand the role of diet on blood Phe levels 
concurrent with the administration of rAvPAL-PEG treatment. Therefore, an exploratory objective has 
been added to this study to assess the relationship of diet, rAvPAL-PEG administration, and blood Phe 
level. Changes to subject diet are not allowed in this study unless per the Investigator. Diet will be 
monitored using a diet diary. 
A pharmacokinetic (PK) substudy has been added to evaluate the steady-state PK of rAvPAL-PEG in 
up to 6 subjects who have achieved and maintained target blood Phe for at least 2 consecutive 
measurements and for whom no further dose modifications are planned. Single-dose PK data has been 
collected in the Phase 1 study, PAL-001. However, there is little multiple-dose PK data or data for 
when subjects have reached and maintained a stable dosing regimen.  With the PK substudy, multiple-
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
dose PK data will be collected for subjects who have already achieved Phe reduction to within the 
protocol-defined target range. 
OBJECTIVES: 
The primary objective of the study is: 
• 
To evaluate the effect of long-term administration of multiple doses of SC injections of 
rAvPAL-PEG on blood Phe concentrations in subjects with PKU. 
The secondary objectives of the study are: 
• 
To evaluate the safety and tolerability of long-term administration of subcutaneous (SC) 
injections of rAvPAL-PEG in subjects with PKU. 
• 
To evaluate the immune response to long-term administration of SC injections of 
rAvPAL-PEG in subjects with PKU. 
The exploratory objective of the study is as follows: 
• 
To evaluate the long-term relationship of diet and change in blood Phe concentration 
following administration with rAvPAL-PEG in subjects with PKU. 
The Substudy objectives are as follows: 
• 
To evaluate steady-state PK of rAvPAL-PEG in subjects who have achieved and maintained 
target blood Phe concentration and for whom no further dose modifications are planned. 
 
STUDY DESIGN AND PLAN: 
This is a long-term extension of rAvPAL-PEG Phase 2 studies in up to 100 subjects with PKU. The 
doses are planned to be in the same range as those previously tested in the Phase 2 studies (starting at 
0.001 through 5.0 mg/kg/week or 2.5 mg through 375 mg/week), provided no dose-limiting toxicity is 
observed in a previous rAvPAL-PEG study. 
Only subjects who completed a previous rAvPAL-PEG study will be enrolled into this study. Subjects 
enrolling into PAL-003 with no interruption in dosing from a previous rAvPAL-PEG study may either 
continue their previous dosing regimen or begin this study at a higher dose level. Subjects who have 
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Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
had dosing interruptions between the previous rAvPAL-PEG study and PAL-003 must have their 
starting dose determined per the Sponsor’s Medical Officer. The first dose will be administered in the 
clinic, and the subject must be observed for 30 minutes following administration. A follow-up 
telephone call will be made to the subject to monitor subject safety 24 hours following the return to 
dosing.  
Diet should not be altered during the course of this study.  Any decision to modify subject diet must be 
made per the Investigator and must be performed under the supervision of the Investigator. To monitor 
for changes in subject diet, a diet diary will be issued to subjects for completion and will be reviewed 
with the clinical study staff on a monthly basis.  
Subjects may self administer study drug at home if approved by the Investigator and the Sponsor’s 
Medical Officer and if adequate training is demonstrated. Subjects must meet a set of criteria to be 
considered appropriate for self administration.   
Subjects will be evaluated for safety throughout the study. Toxicity will be measured according to the 
National Cancer Institute (NCI) Common Terminology Criteria for Adverse Events (CTCAE), 
version 4. 
In addition to the Sponsor, a Data Monitoring Committee (DMC) will monitor the safety of subjects in 
the study. The DMC is an independent committee that will act in an advisory capacity to the Sponsor. 
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take 
rAvPAL-PEG. Subjects’ previous rAvPAL-PEG dosing will generally continue in PAL-003. In 
PAL-003, each subject’s dose will be adjusted as needed to attempt to attain or maintain blood Phe 
concentrations of 60-600 µmol/L. rAvPAL-PEG dose will be based on either a subject’s weight or will 
be a fixed dose. Doses will be evaluated on an individual basis. 
Evaluations, observations, and procedures will be conducted at selected time points. After the subject’s 
blood Phe concentration has been controlled to within a target range (60-600 µmol/L), the subject may 
be asked to have additional blood draws for PK and blood Phe concentration analyses as needed per 
the discretion of the Investigator in consultation with the Sponsor’s Medical Officer. 
A subject will continue in PAL-003 until one of the following occurs: 
• 
The subject withdraws consent and discontinues from the study. 
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Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
• 
The subject is discontinued from the study at the discretion of the Investigator. 
• 
 The subject has completed the study through the Month 86 visit. 
• 
 The study is terminated. 
• 
The study drug receives marketing authorization. 
Subjects may withdraw from treatment with study drug at any time; however, subjects will be asked to 
continue to perform the study assessments until study completion. Subjects may also withdraw from 
study participation at any time. Because the completeness of the data affects the integrity, accuracy, 
and interpretation of study results, every effort should be made to retain subjects in the study and to 
have them complete the study assessments as scheduled as long as continued participation does not 
compromise subject safety. 
Subjects who participate in this study will be required to transition into a Phase 3 study (165-302) if 
weekly doses of rAvPAL-PEG are between 70 mg/week and 350 mg/week (inclusive) provided that 
doses of rAvPAL-PEG have been stable (ie, no major change in dose for at least 4 weeks). Subjects 
who meet these criteria must be transitioned from PAL-003 to Study 165-302 provided they meet the 
165-302 study eligibility criteria.  
Subjects who are eligible for Study 165-302 but do not transition into 165-302 will be withdrawn from 
this study. 
The PAL-003 study will continue until BMN-165 is approved by the Food and Drug Administration 
(FDA) for marketing in the United States or until the sponsor terminates further development of this 
drug for the treatment of PKU. 
PAL-003 Substudy 
A PK substudy has been added to evaluate the steady-state PK of rAvPAL-PEG in up to 6 subjects 
who have achieved and maintained target blood Phe for at least 2 consecutive measurements and for 
whom no further dose modifications are planned.  Subjects enrolled into the substudy will have 
additional pre-dose PK sampling performed. 
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PAL-003 A5 
Page 9 
 
Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
Dose Modifications: 
Dose Increase Methodology: 
Each subject’s dose may be modified based on the decision of the Investigator. Decisions regarding 
dose increases will depend on a subject’s adverse event profile and blood Phe and drug concentrations.  
An individual subject’s dose may be adjusted beginning on Day 1 of PAL-003. For the duration of this 
study, an individual subject’s dose may be adjusted if warranted per a subject’s adverse event profile 
and blood Phe concentrations. Dose increases should be performed as follows. 
• 
The dose may be increased by increments of no more than 10-fold higher than the subject’s 
current dose. 
• 
When increasing the dose, a dose may be used that is between the dose levels (0.001, 0.003, 
0.01, 0.03, 0.06, 0.1, 0.2, 0.3, 0.4, 0.6, 0.8, 1.0, 2.0, 3.0, 4,0, and 5.0 mg/kg or 2.5, 5, 10, 20, 
40, 75, 150, 225, 300, 375 mg/week) or per Investigator determination based on available 
information regarding a subject’s blood Phe (60-600 µmol/L) as well as any adverse events 
(any hypersensitivity reaction) for an individual subject. Dose increases  > 350 mg/week 
require consultation with the sponsor’s medical monitor. 
• 
The dose may be adjusted by increasing the frequency up to daily for a total weekly dose not 
to exceed 5.0 mg/kg or 375 mg/week. Dose increases  > 350 mg/week require consultation 
with the sponsor’s medical monitor. 
• 
When a dose is increased, the subject must be observed for 30 minutes following the first 
modified dose administration. Subjects who increase their dose frequency do not need to be 
observed following injection of study drug if the increase in frequency does not increase the 
overall weekly dose amount. 
• 
Only 1 dose adjustment is allowed every 2 weeks. 
Dose Decrease Methodology 
Decisions regarding dose decreases will depend on available information regarding a subject’s blood 
Phe (60-600 µmol/L), as well as any adverse events (any hypersensitivity reaction). Dose decreases 
may occur for hypophenylalanemia or any adverse event that may be improved with a lower, more 
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PAL-003 A5 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
frequent dose.  
A dose should first be reduced by dose level (5.0, 4.0, 3.0, 2.0, 1.0, 0.8, 0.6, 0.4, 0.3, 0.2, 0.1, 0.06, 
0.03, 0.01, 0.003, 0.001 mg/kg or 375, 300, 225, 150, 75, 40, 20, 10, 5, and 2.5 mg/week). It is also 
permitted to decrease dose in between these specified dose levels. If further dosing adjustments are 
required in response to safety, dosing frequency may also be reduced. 
If the subject develops low blood Phe (as defined by a blood Phe level ≤ 30 µmol/L), the subject’s 
rAvPAL-PEG dose should be decreased to the next lower dose. If the condition persists after another 
1 month at the lower dose, the dose should be decreased again to the next lower level. If the subject 
continues to experience low blood Phe after two dose level reductions, the subject may be asked to 
consult the dietician to eliminate medical foods and/or formulas and to ensure a balanced and 
nutritious diet (as part of the routine standard of care for PKU disease management, subject diet should 
be monitored by a dietician). 
Safety Assessment Criteria: 
If an individual subject exhibits toxicity of a treatment-emergent CTCAE grade 3 or greater or a 
systemic reaction that is assessed as related to treatment with study drug, that subject will have dosing 
halted until the toxicity resolves. The subject’s data will be evaluated by the Principal Investigator (PI) 
and the Sponsor’s Medical Officer, and a decision will then be made whether to discontinue the 
subject from the study treatment, restart dosing at the same dose level, or restart dosing at a lower dose 
level. 
Stopping Criteria: 
If 2 or more subjects at a dose level exhibit toxicity of a treatment-emergent CTCAE grade 3 or greater 
or a systemic reaction that is assessed as related to treatment with study drug, further dosing of 
subjects at that dose level will be evaluated and a safety assessment will be completed. In addition, the 
Food and Drug Administration (FDA) may be notified of this occurrence if appropriate. 
NUMBER OF SUBJECTS PLANNED: 
Up to 100 subjects. 
DIAGNOSIS AND ALL CRITERIA FOR INCLUSION AND EXCLUSION:  
Individuals eligible to participate in this study must meet all of the following criteria: 
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Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
1. Must have completed participation in a previous rAvPAL-PEG study. 
2. Willing and able to provide written, signed informed consent, or, in the case of participants 
under the age of 18, provide written assent (if required) and written informed consent by a 
parent or legal guardian, after the nature of the study has been explained, and prior to any 
research-related procedures. 
3. Willing and able to comply with all study procedures. 
4. Females of childbearing potential must have a negative pregnancy test at Screening and be 
willing to have additional pregnancy tests during the study. Females considered not of 
childbearing potential include those who have been in menopause at least 2 years, or had tubal 
ligation at least 1 year prior to Screening, or who have had total hysterectomy. 
5. Sexually active subjects must be willing to use an acceptable method of contraception while 
participating in the study. 
6. Maintained a stable diet. 
7. In generally good health as evidenced by physical examination, clinical laboratory evaluations 
(hematology, chemistry, and urinalysis), and electrocardiogram (ECG) at Screening. 
Individuals who meet any of the following exclusion criteria will not be eligible to participate in the 
study: 
1. Use of any investigational product (with the exception of rAvPAL-PEG) or investigational 
medical device within 30 days prior to Screening, or requirement for any investigational agent 
prior to completion of all scheduled study assessments. 
2. Use of any medication other than rAvPAL-PEG that is intended to treat PKU within 14 days 
prior to the administration of study drug. 
3. Use or planned use of any injectable drugs containing PEG (other than rAvPAL-PEG), 
including Depo-Provera, within 6 months prior to Screening and during study participation.  
4. A prior reaction that included systemic symptoms (eg, generalized hives, respiratory or 
gastrointestinal problems, hypotension, angioedema, anaphylaxis) to rAvPAL-PEG or a 
PEG-containing product. Subjects with a prior systemic reaction may be eligible for 
participation per the discretion of the Principal Investigator in consultation with the Sponsor’s 
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Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
Medical Officer. However, subjects who discontinued from study treatment early due to a 
reaction are not eligible to enroll into this study.    
5. Pregnant or breastfeeding at Screening or planning to become pregnant (self or partner) or to 
breastfeed at any time during the study.  
6. Concurrent disease or condition that would interfere with study participation or safety 
(eg, history or presence of clinically significant cardiovascular, pulmonary, hepatic, renal, 
hematologic, gastrointestinal, endocrine, immunologic, dermatologic, neurological, oncologic, 
or psychiatric disease). 
7. Any condition that, in the view of the PI, places the subject at high risk of poor treatment 
compliance or of not completing the study. 
8. Known hypersensitivity to rAvPAL-PEG or its excipients, including hypersensitivity reactions 
that necessitated early termination from a previous rAvPAL-PEG study. 
9. Alanine aminotransferase (ALT) concentration > 2 times the upper limit of normal. 
10. Creatinine  > 1.5 times the upper limit of normal. 
INVESTIGATIONAL PRODUCT, DOSE, ROUTE AND REGIMEN: 
The investigational product is rAvPAL-PEG (recombinant Anabaena variabilis phenylalanine 
ammonia lyase-PEG). rAvPAL-PEG will be provided in vials or prefilled syringes; subjects will be 
supplied with vials and syringes or prefilled syringes for administration in the clinic and self 
administration: 
• 
rAvPAL-PEG will be provided in 3 mL (milliliter) vials, each containing 1.5 ± 0.2 mL to 
deliver 15 mg of rAvPAL-PE per 1.0 mL (15 mg/mL protein concentration). Each vial is filled 
with 1.5 ± 0.2 mL to allow the withdrawal and delivery of up to 1.0 mL of the drug product. 
Or 
• 
rAvPAL-PEG will be provided in 3-mL vials, each containing 1.8 ±0.3 mL to deliver 20 mg of 
rAvPAL-PE per 1.3 mL (15 mg/mL protein concentration). Each vial is filled with 1.8 ± 
0.3 mL to allow withdrawal and delivery of up to 1.3 mL. 
 
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Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
Or 
• 
rAvPAL-PEG will be provided in prefilled syringes in three sizes that deliver up to 1 mL. 
Syringe sizes are 2.5 mg (5 mg/mL protein concentration), 10 mg (20 mg/mL protein 
concentration), and 20 mg (20 mg/mL protein concentration).  
 
Prefilled Syringe 
Volume 
Concentration 
Dose 
Sku #1 
0.5 mL 
5 mg/mL 
2.5 mg 
Sku #2 
0.5 mL 
20 mg/mL 
10 mg 
Sku #3 
1.0 mL 
20 mg/mL 
20 mg 
 
The excipients in this drug product are tromethamine, tromethamine-hydrochloride, sodium chloride, 
L-phenylalanine, and water for injection. 
rAvPAL-PEG doses will be administered SC by either health care professionals or via self 
administration. The dose level may be increased or decreased per Investigator determination based on 
available information regarding a subject’s blood Phe level (60-600 µmol/L), as well as any adverse 
events (any hypersensitivity reaction) for an individual subject. The dosage that provides control of 
blood Phe concentrations within the target range of 60-600 µmol/L for a minimum of 2 consecutive 
measurements will be determined for each subject by adjusting the dose level, dose frequency, or both, 
per the PI, based upon the subject’s response to doses. 
Fixed Dosing 
Subjects who have demonstrated efficacy (ie, blood Phe within the target range of 60-600 µmol/L for 
at least 2 consecutive measurements) and who have maintained a stable rAvPAL-PEG dose for at least 
2 consecutive measurements may be eligible to transition from weight-based dosing to a fixed dosing 
regimen that would permit daily dosing (5- or 7-days-per-week). Subjects should convert their 
weight-based dose using the following table: 
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PAL-003 A5 
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Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
 
Weight-based dose 
(mg/kg) 
Equivalent 
fixed dose (mg) 
Vol for 10 mg/ml 
concentration (ml) 
(vial) 
Vol for 15 mg/ml 
concentration (ml) 
(vial)a 
0.03 
2.5 
0.25 
0.17 
0.06 
5 
0.5 
0.33 
0.12 
10 
1 
0.67 
0.25 
20 
2 
1.33 
0.5 
40 
4 
2.67 
1.0 
75 
7.5 
5 
2.0 
150 
15 
10 
3.0 
225 
22.5 
15 
4.0 
300 
30 
20 
5.0 
375 
37.5 
25 
 a Applies to both 1.0 and 1.3 ml withdrawal. 
DURATION OF TREATMENT: 
Up to 86 months. 
REFERENCE THERAPY(IES), DOSE, ROUTE AND REGIMEN:  
None 
CRITERIA FOR EVALUATION: 
Efficacy: 
Blood Phe concentrations will be measured.  
Immunogenicity: 
The presence of antibodies (anti-PAL immunoglobulin G [IgG], anti-PAL IgM, anti-PEG IgG, 
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PAL-003 A5 
Page 15 
 
Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibodies, and anti-PEG-PAL IgE) will be assessed. 
Safety: 
Safety will be evaluated on the incidence of adverse events (AEs) and clinically significant changes in 
vital signs, ECG results, X-ray results, and laboratory test results. 
Pharmacokinetic: 
Plasma concentrations of rAvPAL-PEG will be measured for subjects participating in the Substudy. 
STATISTICAL METHODS:  
Sample Size: 
Subjects who participated in a previous rAvPAL-PEG study may be enrolled into this study. 
No formal sample size calculation was conducted for this study or the PAL-003 Substudy. 
Safety Analysis: 
All subjects who receive any amount of study drug in this study and have postdose safety information 
will be included in the safety analyses. 
The Medical Dictionary for Regulatory Activities terminology (MedDRA) will be used by the 
sponsor to assign system organ class and preferred term classification to events and diseases based 
on the original terms entered on the Case Report Form (CRF). The incidence of AEs will be 
summarized by system organ class, preferred term, relationship to study drug, and severity. A by–
subject listing will be provided for those subjects who experience a serious AE (SAE), including 
death, or experience an AE associated with early withdrawal from the study or study drug. 
Hypersensitivity AEs and AEs that result in dosing interruption or dose level reduction are of interest, 
and the percentage of subjects who report these AEs will be presented.  
Clinical laboratory data will be summarized by the type of laboratory test. Frequency and percentage 
of subjects who experience abnormal (ie, outside of reference range) and/or clinically significant 
abnormalities after study drug administration will be presented for each clinical laboratory test. For 
each clinical laboratory test, descriptive statistics will be provided for baseline and all subsequent 
post-treatment visits. Changes from baseline to the post-treatment visits will also be provided. 
Descriptive statistics for vital signs, physical examination results, ECG results, X-ray results, and 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
immunogenicity test results will also be provided. Additionally, antibodies and titers will be 
summarized by scheduled time point. 
 
Efficacy Analysis: 
Data from all subjects who receive any amount of study drug and who have any post-treatment 
efficacy data will be included in the efficacy analysis. 
Blood Phe concentration at each scheduled time point will be summarized using descriptive statistics 
(mean, standard deviation, median, minimum, and maximum). Change in blood Phe concentration 
from baseline (to be defined in the Statistical Analysis Plan [SAP]) to each scheduled time point and 
presence/absence of antibodies will also be summarized. In addition, the proportion of subjects who 
have maintained target Phe concentrations of 60-600 µmol/L will be summarized by each scheduled 
time point. 
Exploratory Analysis: 
Details regarding exploratory analyses will be provided in the SAP.  
Substudy Analysis: 
For subjects who completed the Substudy, the steady-state PK of rAvPAL-PEG in subjects who have 
achieved and maintained target blood Phe will be explored. 
Pharmacokinetic Analysis: 
Subjects who complete the Substudy will have the following PK parameters assessed: area under the 
plasma concentration-time curve (AUC), time to maximum plasma concentration (Tmax), maximum 
plasma concentration (Cmax), half life (t1/2), and clearance (CL/F).  
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3 
TABLE OF CONTENTS 
1 TITLE PAGE .......................................................................................................................1 
2 SYNOPSIS ...........................................................................................................................5 
3 TABLE OF CONTENTS ...................................................................................................17 
4 LIST OF ABBREVIATIONS AND DEFINITIONS OF TERMS ....................................21 
5 ETHICS..............................................................................................................................25 
5.1 Institutional Review Board or Ethics Committee .....................................................25 
5.2 Ethical Conduct of Study ..........................................................................................25 
5.3 Subject Information and Informed Consent ..............................................................26 
6 INVESTIGATORS AND STUDY ADMINISTRATIVE STRUCTURE ........................27 
7 INTRODUCTION .............................................................................................................28 
7.1 Nonclinical Studies ...................................................................................................28 
7.2 Previous Clinical Studies ..........................................................................................29 
7.2.1 
Phase 1 Study, PAL-001 .............................................................................30 
7.2.2 
Phase 2 Studies PAL-002, PAL-004, and 165-205 .....................................31 
7.3 Study Rationale .........................................................................................................34 
7.4 Summary of Overall Risks and Benefits ...................................................................35 
7.4.1 
Toxicity Due to Exposure to Polyethylene Glycol (PEG) ..........................36 
7.4.2 
Toxicity Due to an Immunologic Reaction .................................................36 
8 STUDY OBJECTIVES ......................................................................................................41 
9 INVESTIGATIONAL PLAN ............................................................................................42 
9.1 Overall Study Design and Plan .................................................................................42 
9.1.1 
Management of Local and Systemic Reactions to rAvPAL-PEG ...............50 
9.1.2 
Dose Modifications .....................................................................................55 
9.1.3 
Safety Assessment Criteria ..........................................................................57 
9.1.4 
Stopping Criteria .........................................................................................57 
9.2 Discussion of Study Design, Including Choice of Control Group ............................57 
9.3 Selection of Study Population ...................................................................................57 
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9.3.1 
Inclusion Criteria .........................................................................................57 
9.3.2 
Exclusion Criteria ........................................................................................58 
9.3.3 
Removal of Subjects from Treatment or Assessment .................................59 
9.3.4 
Subject Identification and Replacement of Subjects ...................................60 
9.4 Treatments .................................................................................................................60 
9.4.1 
Treatments Administered ............................................................................62 
9.4.2 
Identity of Investigational Product (IP) .......................................................62 
9.4.3 
Storage .........................................................................................................63 
9.4.4 
Directions for Administration .....................................................................63 
9.4.5 
Method of Assigning Subjects to Treatment Groups ..................................66 
9.4.6 
Selection of Doses Used in the Study .........................................................66 
9.4.7 
Blinding .......................................................................................................66 
9.4.8 
Prior and Concomitant Medications ............................................................66 
9.4.9 
Treatment Compliance ................................................................................67 
9.4.10 Dose Interruption and Missed Doses ...........................................................67 
9.5 Investigational Product Accountability .....................................................................68 
9.5.1 
Return and Disposition of Clinical Supplies ...............................................68 
9.6 Dietary or Other Protocol Restrictions......................................................................68 
9.7 Efficacy and Safety Variables ...................................................................................69 
9.7.1 
Efficacy and Safety Measurements Assessed .............................................69 
9.7.2 
Efficacy Variable .........................................................................................70 
9.7.3 
Pharmacokinetic Variables ..........................................................................70 
9.7.4 
Exploratory Efficacy Variable .....................................................................71 
9.7.5 
Safety Variables ..........................................................................................71 
9.7.6 
Clinical Laboratory Assessments ................................................................72 
10 REPORTING ADVERSE EVENTS .................................................................................74 
10.1 Adverse Events .........................................................................................................74 
10.2 Serious Adverse Events ............................................................................................77 
10.3 Pregnancy ..................................................................................................................78 
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10.4 Urgent Safety Measures ............................................................................................78 
10.5 BioMarin Pharmacovigilance Contact Information ..................................................79 
11 APPROPRIATENESS OF MEASUREMENTS ...............................................................80 
11.1 Safety and Pharmacokinetics ....................................................................................80 
11.2 Diet Diary ..................................................................................................................80 
12 STUDY PROCEDURES ...................................................................................................81 
12.1 Prestudy .....................................................................................................................81 
12.2 Screening Visit ..........................................................................................................81 
12.3 Treatment Period .......................................................................................................81 
12.3.1 Day 1 (Week 1) ...........................................................................................82 
12.3.2 Weekly Telephone Visit ..............................................................................83 
12.3.3 Substudy Visits ............................................................................................83 
12.3.4 Monthly Visits (Week 4, 8, 12, etc) ............................................................83 
12.3.5 Quarterly Visits (Week 12, 24, 36, etc) .......................................................84 
12.3.6 Unscheduled Hypersensitivity Reaction Visit .............................................84 
12.4 Early Termination Visit ............................................................................................85 
12.5 Final Follow-up Visit ................................................................................................86 
13 DATA QUALITY ASSURANCE .....................................................................................87 
14 STATISTICAL METHODS AND DETERMINATION OF SAMPLE SIZE ..................88 
14.1 Statistical and Analytical Plans .................................................................................88 
14.2 Safety Analysis .........................................................................................................88 
14.3 Pharmacokinetic Analysis .........................................................................................88 
14.3.1 Pharmacokinetic Substudy Analysis ...........................................................89 
14.4 Efficacy Analysis ......................................................................................................89 
14.5 Determination of Sample Size ..................................................................................89 
14.6 Handling of Missing Data .........................................................................................89 
14.7 Interim Analyses .......................................................................................................90 
14.8 Changes in the Conduct of the Study or Planned Analyses ......................................90 
15 DATA MONITORING COMMITTEE (DMC) ................................................................91 
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4 
LIST OF ABBREVIATIONS AND DEFINITIONS OF TERMS 
Abbreviations 
ADR 
adverse drug reaction 
AE 
adverse event 
ALT 
alanine aminotransferase 
AST 
aspartate aminotransferase 
AUC 
area under the plasma concentration-time curve 
AUC0-7 days 
area under the plasma concentration-time curve from time zero on Day 1 
to Day 8 
BUN 
blood urea nitrogen 
°C 
degree Celsius 
C3 
complement 3 
C4 
complement 4 
CBC 
complete blood count 
CD 
Compact disk 
CFR 
Code of Federal Regulations 
CH50 
total hemolytic complement 
Cmax 
maximum plasma concentration 
CNS 
central nervous system 
CO2 
carbon dioxide 
CRA 
Clinical Research Associate 
CRF 
case report form 
CRP 
C-reactive protein 
CTCAE 
Common Terminology Criteria for Adverse Events 
CV 
cardiovascular 
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DBP 
diastolic blood pressure 
DMC 
Data Monitoring Committee 
ECG 
electrocardiogram 
ETV 
Early Termination Visit 
FDA 
Food and Drug Administration 
F/U 
follow-up 
g 
gram 
GCP 
Good Clinical Practice 
GGT 
gamma-glutamyltransferase 
GI 
gastrointestinal 
IB 
Investigator’s Brochure 
ICF 
Informed Consent Form 
ICH 
International Conference on Harmonisation of Technical Requirements for 
Registration of Pharmaceuticals for Human Use 
IgE 
immunoglobulin E 
IgG 
immunoglobulin G 
IgM 
immunoglobulin M 
IP 
investigational product 
IRB 
Institutional Review Board 
IV 
intravenous 
kg 
kilogram 
MedDRA 
Medical Dictionary for Regulatory Activities 
mg 
milligram 
mL 
milliliter 
mm Hg 
millimeter of mercury 
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NAb 
neutralizing antibodies 
NCI 
National Cancer Institute 
NOAEL 
no observable adverse effect level 
OTC 
over the counter 
PAH 
phenylalanine hydroxylase 
PAL 
phenylalanine ammonia lyase 
PEG 
polyethylene glycol 
Phe 
phenylalanine 
PI 
Principal Investigator 
PK 
pharmacokinetics 
PKU 
phenylketonuria 
rAvPAL-PEG recombinant Anabaena variabilis phenylalanine ammonia lyase-PEG 
RBC 
red blood cell 
SAE 
serious adverse event 
SAP 
Statistical Analysis Plan 
SBP 
systolic blood pressure 
SC 
subcutaneous 
SD 
standard deviation 
SDV 
source data verified 
SGOT 
serum glutamic oxalo-acetic transaminase 
SGPT 
serum glutamic pyruvate transaminase 
US 
United States 
WBC 
white blood cell 
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Definition of Terms: 
Investigational Product (IP): 
“A pharmaceutical form of an active ingredient or placebo being tested or used as a reference 
in a clinical trial, including a product with a marketing authorization when used or assembled 
(formulated or packaged) in a way different from the approved form, or when used for an 
unapproved indication, or when used to gain further information about an approved use.” 
(from E6 ICH)  
The terms “IP” and “study drug” may be used interchangeably in the protocol. 
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5 
ETHICS 
5.1 
Institutional Review Board or Ethics Committee 
Prior to initiating the study, the Investigator will obtain written confirmation that the 
Institutional Review Board (IRB) is properly constituted and compliant with International 
Conference on Harmonisation of Technical Requirements for Registration of 
Pharmaceuticals for Human Use (ICH) and Good Clinical Practice (GCP) requirements, and 
applicable laws and local regulations. A copy of the confirmation from the IRB will be 
provided to BioMarin Pharmaceutical Inc. (BioMarin) or its designee. The Principal 
Investigator (PI) will provide the IRB with all appropriate material, including the protocol, 
Investigator’s Brochure (IB), the Informed Consent Form (ICF) including compensation 
procedures, and any other written information provided to the subjects, including all consent 
forms translated to a language other than the native language of the clinical site. The study 
will not be initiated and investigational product (IP) supplies will not be shipped to the site 
until appropriate documents from the IRB confirming unconditional approval of the protocol, 
the ICF and all subject recruitment materials are obtained in writing by the PI and copies are 
received at BioMarin or its designee. The approval document should refer to the study by 
protocol title and BioMarin protocol number (if possible), identify the documents reviewed, 
and include the date of the review and approval. BioMarin will ensure that the appropriate 
reports on the progress of the study were made to the IRB and BioMarin by the PI in 
accordance with applicable governmental regulations. 
5.2 
Ethical Conduct of Study 
This study will be conducted in accordance with the following: 
• United States (US) Code of Federal Regulations (CFR) sections that address clinical 
research studies, and/or other national and local regulations, as applicable 
• E6 ICH Guideline for GCP 
• The ethical principles established by the Declaration of Helsinki 
Specifically, this study is based on adequately performed laboratory and animal 
experimentation; the study will be conducted under a protocol reviewed and approved by an 
IRB; the study will be conducted by scientifically and medically qualified persons; the 
benefits of the study are in proportion to the risks; the rights and welfare of the subjects will 
be respected; the physicians conducting the study do not find the hazards to outweigh the 
potential benefits; and each subject, or his or her legally authorized representative will 
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provide written, informed consent before any study-related tests or evaluations are 
performed. 
5.3 
Subject Information and Informed Consent 
A properly written and executed ICF, in compliance with the Declaration of Helsinki, 
E6 ICH (GCP Guideline, Section 4.8) and 21 CFR Part 50 and other applicable local 
regulations, will be obtained for each subject prior to entering the subject into the study. The 
Investigator will prepare the ICF and provide the documents to BioMarin for approval prior 
to submission to the IRB. BioMarin and the IRB must approve the documents before they are 
implemented. A copy of the approved ICF, and if applicable, a copy of the approved subject 
information sheet, minor assent form, parental ICF for studies involving minors, and all ICFs 
translated to a language other than the native language of the clinical site must also be 
received by BioMarin or its designee prior to the delivery of study drug. 
Subjects under the age of 18 years will provide written assent (if required), and his/her 
legally authorized representative (parent or legal guardian) will provide written informed 
consent for such subjects. The Investigator will provide copies of the signed ICF to each 
subject (or the subject’s legally authorized representative) and will maintain the original in 
the subject’s record file. 
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6 
INVESTIGATORS AND STUDY ADMINISTRATIVE STRUCTURE 
Prior to beginning the study, the PI at each site must provide to BioMarin or its designee a 
fully executed and signed Form FDA (Food and Drug Administration) 1572 and a Financial 
Disclosure Form. All sub-Investigators must be listed on Form FDA 1572. Financial 
Disclosure Forms must also be completed for all sub-Investigators listed on the 
Form FDA 1572 who will be directly involved in the treatment or evaluation of research 
subjects in this study. 
The study will be administered by and monitored by employees or representatives of 
BioMarin. Clinical Research Associates (CRAs) or trained designees will monitor each site 
on a periodic basis and perform verification of source documentation for each subject as well 
as other required review processes. BioMarin’s Pharmacovigilance Department (or designee) 
will be responsible for the timely reporting of serious adverse events (SAEs) to appropriate 
regulatory authorities as required. Some study assessments, including administration of study 
drug, may be performed at the subject’s home. All assessments performed for this study will 
be administered by clinic staff or other qualified and trained study personnel. 
Anti-rAvPAL-PEG (recombinant Anabaena variabilis phenylalanine ammonia lyase 
polyethylene glycol) immunoglobulin E (IgE) antibody analysis will be performed by a 
vendor; other antibody analysis will be performed by BioMarin. Clinical laboratory tests, 
including serum pregnancy tests (if applicable), will be analyzed and processed by a central 
laboratory, with the exception of erythrocyte sedimentation rate (ESR), and urine pregnancy 
tests (if applicable), which will be analyzed by a local laboratory. A central laboratory will 
also be used to perform analysis of blood phenylalanine (Phe) concentrations and urinalysis. 
Pharmacokinetic (PK) analysis will be performed by BioMarin. 
Prior to database lock in multicenter studies, a Coordinating Investigator will be identified 
who will read the clinical study report and confirm that it accurately describes the conduct 
and results of the study, to the best of his or her knowledge. The Coordinating Investigator 
will be chosen on the basis of active participation in the study, ability to interpret data, and 
willingness to review and sign the report in a specified timeframe. 
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7 
INTRODUCTION 
A comprehensive review of PEGylated recombinant Anabaena variabilis phenylalanine 
ammonia lyase (rAvPAL-PEG) is contained in the IB supplied by BioMarin; the Investigator 
should review this document prior to initiating this study. 
7.1 
Nonclinical Studies 
The nonclinical program for rAvPAL-PEG has characterized the pharmacology, 
pharmacokinetics (PK), and toxicology of rAvPAL-PEG using the intended clinical SC route 
of administration. Pharmacology was assessed in the BTBR Pahenu2 (ENU2) mouse model of 
PKU. The ENU2 mouse model exhibits characteristics similar to those of PKU patients, 
including hyperphenylalaninemia (baseline plasma Phe concentrations of 1000 to 2000 µM) 
and hypopigmentation. Following weekly doses of rAvPAL-PEG administered to male 
ENU2 mice, plasma Phe concentrations decreased from approximately 2000 µM to 
< 200 µM after 2 dose administrations. An attenuated reduction of blood Phe was seen 
between Week 3 and Week 7 of dosing. After 7 weekly administrations of rAvPAL-PEG, 
pharmacological activity returned as evidenced by stabilized concentrations of plasma Phe 
< 200 µM over the entire week, which continued for a total of 15 weeks. 
In pharmacodynamic studies in the BTBR Pahenu2 (ENU2) mouse model administered 
80 mg/kg/week rAvPEG-PAL, two dose interruption assessments were performed:  a 
2-4 week dose interruption and an 11-week dose interruption. Following both dose 
interruption assessments, the animals re-started rAvPAL-PEG at a dose of 80 mg/kg/week. 
No attenuated Phe response was observed when rAvPAL-PEG injections were temporarily 
stopped for 2-4 weeks, and there was an immediate return to stable blood Phe reductions. A 
similar interim attenuated response was observed with the longer dose interruption of 
approximately 11 weeks.  In both of these assessments, no safety issues were noted upon 
re-starting dosing with rAvPAL-PEG (Lapis, 2007, ASHG 57th Annual Meeting). 
Safety pharmacology studies were conducted in rats and cynomolgus monkeys. No 
respiratory or central nervous system (CNS) effects were seen with SC administration of 
rAvPAL-PEG. No changes in cardiovascular (CV) parameters, including electrocardiogram 
(ECG) waveforms, were observed in telemetry-instrumented monkeys assessed for the CV 
effects of rAvPAL-PEG administered subcutaneously. 
Pharmacokinetic parameters were evaluated in single-dose and repeat-dose studies in rats and 
cynomolgus monkeys. The elimination half-life (t1/2) values of rAvPAL-PEG administered to 
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normal rats at SC doses of 10, 25, and 250 mg/kg were 47, 33, and 44 hours, respectively, 
and exhibited modest area under the plasma concentration-time curve (AUC)-dose. In the 
cynomolgus monkey after SC administration of rAvPAL-PEG, the t1/2 was 65 hours at 
4.0 mg/kg, 71 hours at 12 mg/kg, and could not be determined at 60 mg/kg (the highest 
dose). Qualitatively, the kinetics of rAvPAL-PEG in the rat and monkey appear to have 
similar characteristics. The following findings were noted: (1) a 1-compartment model with 
first-order absorption appears to describe the plasma profiles of rAvPAL-PEG after 
single-dose administration, (2) absorption is slow and there is a long absorption period after 
SC administration to maximum observed plasma concentration (Cmax), along with a long t1/2, 
(3) elimination is slow and monophasic, (4) there does not appear to be a gender difference, 
and (5) the AUC and the Cmax are roughly linearly proportional.  
Toxicology of rAvPAL-PEG was assessed in single-dose and repeat-dose studies in normal 
rats and cynomolgus monkeys. In the single-dose rat study, decreased body weight gain and 
Kupffer cell vacuolization at the high SC dose of 250 mg/kg was observed; however, the 
Kupffer cell finding was not seen in the single-dose study in cynomolgus monkeys. In a 
26-week repeat-dose toxicity and toxicokinetic (TK) rat study, decreased body weight gain, 
decreased food consumption, vacuolation/hypertrophy of the renal tubule cells, and 
vacuolation of the histiocytic cells were observed in rats administered 25 mg/kg/dose, twice 
weekly. In a 39-week repeat-dose study in monkeys, arterial inflammation, perivascular 
cellular infiltrates in the SC injection sites, thymic atrophy, and increased lymphoid nodules 
in bone marrow of the sternum were observed in monkeys given ≥ 3 mg/kg/dose, twice 
weekly. Of these findings, only the arterial inflammation was deemed adverse and this 
finding was completely reversed after 13-weeks of recovery. The 
no-observed-adverse-effect-level (NOAEL) of rAvPAL-PEG when administered 
subcutaneously twice weekly for 26 weeks and 39 weeks in the rat and monkey, respectively, 
was 1.0 mg/kg. These NOAELs were based on histological findings of 
vacuolation/hypertrophy of the renal tubule cells in the rat and arterial inflammation findings 
in the monkey.  
7.2 
Previous Clinical Studies 
The rAvPAL-PEG clinical development program has been designed to demonstrate the 
safety and efficacy of rAvPAL-PEG in reducing blood Phe concentrations in PKU subjects 
who do not respond to treatment with Kuvan® or are not compliant with Kuvan® treatment. 
This study is an extension of the ongoing human clinical studies with rAvPAL-PEG 
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(Study PAL-002, Study PAL-004, and Study 165-205) based on data from the completed 
clinical study, PAL-001, and clinical experience from this ongoing study and the other 
ongoing Phase 2 studies, PAL-002 and PAL-004.  
7.2.1 Phase 1 Study, PAL-001 
The first-in-human trial using rAvPAL-PEG, Study PAL-001, was a Phase 1, open-label, 
dose-escalation study in PKU subjects in the US. The primary objective was to assess the 
safety and tolerability of single SC injections of rAvPAL-PEG. Secondary objectives were to 
evaluate the PK of single, SC injections of rAvPAL-PEG administered at escalating doses in 
subjects with PKU and to evaluate the effect of rAvPAL-PEG on blood Phe concentrations. 
The effectiveness of rAvPAL-PEG in decreasing Phe concentrations in nonclinical studies of 
ENU2 mice was consistent with what was observed in PAL-001. PAL-001 enrolled 25 PKU 
subjects with a mean (standard deviation; SD) baseline blood Phe concentration of 
1310 µmol/L (405). The 25 subjects who enrolled into the study were assigned to receive a 
single administration of rAvPAL-PEG at 1 of 5 dose levels: 0.001, 0.003, 0.01, 0.03, and 
0.1 mg/kg. Five subjects each received 1 of the 5 dose levels of rAvPAL-PEG. 
Key safety, efficacy, and PK results of Study PAL-001 are summarized as follows: 
• rAvPAL-PEG was well tolerated and had a clinically significant blood-lowering 
effect on Phe concentration when administered at a dose of 0.1 mg/kg. 
• For the 5 subjects who were administered 0.1 mg/kg rAvPAL-PEG, clinically 
significant reductions in blood Phe level were observed, with the most clinically 
significant decreases from baseline values to Day 7, ranging from 33.8% to 97.3% 
(mean of 58.12%). The mean baseline blood Phe level for these 5 subjects was 
1113 µmol/L. 
• Overall, no clinically significant reductions in blood Phe level were observed in 
subjects who were administered rAvPAL-PEG at the lower doses of 0.001, 0.003, 
0.01, and 0.03 mg/kg. 
• For subjects who were administered rAvPAL-PEG at the 3 higher dose levels (0.01, 
0.03, and 0.1 mg/kg) and who had measurable rAvPAL-PEG concentration levels, the 
calculated PK parameters were a mean Tmax of 89-106 hours, a t1/2 of 46-120 hours, 
and an AUC0-t, and Cmax that were proportional with dose. Drug exposure was slightly 
increased with increased dose. 
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7.2.2 Phase 2 Studies PAL-002, PAL-004, and 165-205 
Based on results from the Phase 1, single-dose study, the Phase 2 studies have been designed 
to evaluate rAvPAL-PEG at various doses and dosing regimens to safely achieve and 
maintain blood Phe reductions in subjects with PKU. Currently, there are three ongoing 
Phase 2 studies (PAL-002, PAL-004, 165-205); an overview of each study is presented in 
Section 7.2.2.1 (PAL-002), Section 7.2.2.2 (PAL-004), and Section 7.2.2.3 (165-205).  
7.2.2.1 
Study PAL-002 
Study PAL-002 (A Phase 2, Open-Label, Dose-Finding Study to Evaluate the Safety, 
Efficacy, and Tolerability of Multiple Subcutaneous Doses of rAvPAL-PEG in Subjects With 
Phenylketonuria) was initiated in September 2009 and has completed enrollment. As of 
10 September 2012, 40 subjects have been enrolled and 37 have completed the study. 
PAL-002 enrolled 11 previously exposed subjects from the single-dose study, PAL-001, and 
29 subjects who were naïve to rAvPAL-PEG. Thirty-three of the 37 subjects who completed 
PAL-002 enrolled into this open-label extension study (PAL-003). Two subjects 
discontinued from the study due to lost to follow-up, relocation, or other reasons, and 
1 subject discontinued from the study due to an AE (skin reaction).  
The primary objective of this study was to evaluate the effect of multiple doses of 
rAvPAL-PEG (ranging from 0.001 mg/kg/week to 1.0 mg/kg/week) on blood Phe 
concentrations in subjects with PKU with up to 16 weeks of treatment. The secondary 
objectives of the study were to evaluate the safety and tolerability of SC injections of 
multiple doses of rAvPAL-PEG, to evaluate the immune response to rAvPAL-PEG, and to 
evaluate the PK profile of rAvPAL-PEG in subjects with PKU.  
The PAL-002 study design consists of two parts. In Part 1, rAvPAL-PEG was administered 
as a once weekly fixed, low-dose induction regimen for 8 weeks. In Part 2, the rAvPAL-PEG 
dose was titrated upwards; subjects received adjustable dose increases for up to 8 weeks to 
achieve a target blood Phe concentration of 600 µmol/L. The doses and dosing schedules 
were revised with a series of protocol amendments to incorporate the information gained 
during conduct of this early, open-label, multiple-dose study.  
A wide range of doses was planned for the PAL-002 study, beginning with doses as low as 
0.001mg/kg/week.  However, no substantial reductions in blood Phe level were observed in 
the majority of subjects who were administered rAvPAL-PEG in the initial four cohorts at 
doses of 0.001, 0.003, 0.01, and 0.03 mg/kg administered once per week. The absence of 
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appreciable Phe reduction after 16 weeks of treatment in this range of doses led to a decision 
to amend the study protocol to include a cohort with a higher starting dose of 0.1 
mg/kg/week, which had been previously shown to decrease blood Phe levels to 
approximately 600 µmol/L in the single-dose, Phase 1 study (PAL-001). After the first 
2 weeks of dosing at 0.1 mg/kg/week, transient Phe reduction was observed in this subset of 
subjects. However, this dosing regimen was accompanied by mild to moderate 
hypersensitivity reactions primarily after the second weekly dose, suggesting that additional 
exploration of dosing regimens would be required.  
In summary, preliminary results from PAL-002 demonstrated that doses below 0.1 g/kg 
administered once per week were not effective in reducing Phe levels.  While transient 
reduction of Phe was apparent at doses of at least 0.1 mg/kg given once per week, this dose 
regimen was associated with a high incidence of systemic hypersensitivity reactions, 
typically following the second weekly dose.  Further escalation above this dose of 
0.1 mg/kg/week would be required to sustain the effect on Phe levels over time.  Increased 
doses would require spreading dose administration over several days per week, as 
once-weekly administration of higher doses would not be practical due to the large volume of 
study drug.  Therefore, additional dosing regimens would need to be explored in a 
subsequent study (PAL-004). 
Once subjects completed Study PAL-002, they were eligible to enroll into this open-label 
extension study, PAL-003 to continue to receive rAvPAL-PEG up to a maximum dose of 
5.0 mg/kg/week or 375 mg/week. 
7.2.2.2 
Study PAL-004 
PAL-004 (An Open-Label Study to Evaluate the Safety, Tolerability, and Efficacy of 
Subcutaneous Dose Levels of rAvPAL-PEG Administered Daily in Subjects With 
Phenylketonuria) was initiated in April 2011 and has completed enrollment. As of 
10 September 2012, 16 subjects have been enrolled, 15 subjects have completed the study, 
and 15 subjects have enrolled into this study (PAL-003). One subject withdrew consent from 
continued participation prior to study completion. All subjects enrolled in this study were 
naïve to rAvPAL-PEG exposure. 
The objective of this study was to determine if daily administration (defined as 5days/week) 
of rAvPAL-PEG at dose levels of 0.06, 0.1, 0.2, 0.4, 0.6, and 0.8 mg/kg/day was safe and 
effective in reducing and maintaining blood Phe concentrations to 600 µmol/L in subjects 
with PKU. The starting dose was 0.4 mg/kg, administered 5 days/week. A total of 12 subjects 
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were added in sequence and were started on doses of 0.4, 0.2, 0.1, 0.06 mg, or 0.001/kg/day 
based on incoming safety data. Overall, subjects in PAL-004 who initiated treatment at 
higher daily doses of 0.1 to 0.4 mg/kg/day achieved immediate and substantial reduction of 
blood Phe levels, but dosing had to be temporarily reduced or interrupted due to the onset of 
systemic hypersensitivity reactions at approximately Day 10 of dosing. Phe reductions did 
not persist in the setting of temporary dose reduction or interruption, but Phe levels generally 
improved if higher dose levels were reinstated.  
To prevent the onset of hypersensitivity reactions that were temporally associated with the 
onset of anti-drug IgM responses, an additional dosing strategy was assessed in PAL-004; 
4 subjects initiated dosing at a low dose of 0.001mg/kg/day or 0.06mg/kg/day for 
5 consecutive days and then dosing was suspended for 2 weeks. Dosing was restarted on 
Day 21 at the initial dose followed by dose titration to target Phe levels. Subjects 
administered this dosing regimen had similar efficacy, but the incidence of hypersensitivity 
reactions appeared to be similar to that of subjects who did not have the planned dose 
interruption, suggesting little advantage with this alternate induction regimen.  
Experience from PAL-004 indicated that initiating daily rAvPAL-PEG dosing with relatively 
high daily doses was not sustainable due to the onset of hypersensitivity reactions that 
occurred approximately 9 to 12 days after the start of administration, nor was the alternate 
dosing regimen (2 week drug holiday) well tolerated or effective in Phe reduction. In 
addition, the daily treatment regimen did not reduce the time to achieve target blood Phe 
levels seen in previous studies. This study indicated that to improve tolerability, 
rAvPAL-PEG should be initiated with an induction period at doses substantially lower than 
0.4mg/kg, followed by upward dose titration toward target Phe levels.   
Once subjects completed Study PAL-004, they were eligible to enroll into this open-label 
extension study to continue to receive rAvPAL-PEG up to a maximum dose of 
5.0 mg/kg/week or 375 mg/week. 
7.2.2.3 
Study 165-205 
Study BMN 165-205 (A Phase 2, Multi-Center, Open-Label, Dose-Finding Study to Evaluate 
Safety, Efficacy, and Tolerability of Subcutaneously Administered rAvPAL-PEG in Subjects 
With PKU for 24 Weeks) was initiated in May 2012. Data from ongoing Studies PAL-002, 
PAL-004, and PAL-003 suggested that a 4-week treatment course with weekly dosing at a 
fixed low dose (induction), followed by a weekly 2-fold, upward titration of rAvPAL-PEG to 
approximately 10-fold higher than the initiation dose (maximum of 375 mg/week) is 
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effective and well tolerated. The objective of this study was to further assess this dosing 
regimen. Two rAvPAL-PEG dosing regimens were to be explored in this study:  weekly low-
dose induction (2.5 mg/week for 4 to 8 weeks), followed by a period of upward dose titration 
towards a target Phe level (600 µmol/L) followed by maintenance dosing at that level 
through the 24 week study duration (Group 1).  The other dosing regimen planned for this 
study (Group 2) involved administration of a single bolus dose of 8 mg, followed by a 
treatment holiday of at least 3 weeks duration followed by resumption and escalation of study 
drug administration following a pattern similar to that employed in Group 1. A total of 
24 subjects were enrolled into 165-205. In addition to confirming an effective, well-tolerated 
dose regimen, this study incorporated non-weight-based dosing, starting with dose 
administration once per week at a low dose (2.5mg) with gradual escalation and conversion 
of dose administration to 5x/week dosing for chronic maintenance therapy.  
Once subjects have completed Study 165-205, they are eligible to enroll into this study to 
continue to receive rAvPAL-PEG up to a maximum dose of 5.0 mg/kg/week or 
375 mg/week, or into the Phase 3 study, BMN 165-302. 
7.3 
Study Rationale 
PKU is an autosomal, recessive, inherited disease characterized by deficiency in the enzyme 
PAH. Approximately 1 in every 10,000 infants in North America is born with PKU  
Scriver, 2001, McGraw-Hill). Left untreated, PAH deficiency is associated with an abnormally 
elevated concentration of Phe, which is toxic to the brain (Kaufman, 1989, J Pediatr.) and can 
result in a variety of neuropathologic conditions, including mental retardation, microcephaly, 
delayed speech, seizures, and behavioral abnormalities (Scriver, 2001, McGraw-Hill). The 
brains of untreated patients with PKU show evidence of hypomyelination and gliosis, arrest 
in cerebral development, and, in some cases, white matter degeneration (Huttenlocher, 2000, 
Eur.J Pediatr.). Elevated Phe during fetal development leads to severe mental retardation and 
can cause microcephaly, growth retardation, and congenital heart disease (Guttler, 2003, 
Pediatrics), (Koch, 2003, Pediatrics), (Lee, 2003, Pediatrics), (Levy, 2003, Pediatrics), 
(Matalon, 2003, Pediatrics), (Rouse, 2004, J.Pediatr.). 
For a subset of patients with residual enzyme activity, treatment with Kuvan® is an option. 
For all other patients, current management of PKU involves adherence to low-Phe medicinal 
diet formulas and dietary restriction of Phe-containing foods. Implementation of a 
Phe-restricted diet in infancy significantly reduces blood Phe concentrations and prevents 
many of the neuropathologic manifestations of PKU, including severe mental retardation. 
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However, compliance with this restrictive diet can be difficult for older children, adolescents, 
and adults, and adherence may result in nutritional deficiencies due to the limitations of 
natural protein sources (Fisch, 2000, Eur.J.Pediatr.), (Walter, 2002, Lancet). 
The need exists for a treatment that will help individuals with PKU safely achieve lifelong, 
reliable control of blood phenylalanine (Phe) concentrations and improve functional 
outcomes. rAvPAL-PEG is a potential substitute for the phenylalanine hydroxylase (PAH) 
enzyme, which is defective in individuals with PKU. rAvPAL-PEG may control blood Phe 
concentrations, which may have additional clinical benefits.  
Blood Phe levels depend not only on the functional presence of the endogenous enzyme PAH 
but also on the dietary intake of Phe. It is important to understand the role of diet on blood 
Phe levels concurrent with the administration of rAvPAL-PEG treatment. Therefore, an 
exploratory objective has been added to this study to assess the relationship of diet, 
rAvPAL-PEG administration, and blood Phe level. Changes to subject diet are not allowed in 
this study unless per the Investigator. Diet will be monitored using a diet diary.     
A pharmacokinetic (PK) substudy has been added to evaluate the steady-state PK of 
rAvPAL-PEG in up to 6 subjects who have achieved and maintained target blood Phe for at 
least 2 consecutive measurements and for whom no further dose modifications are planned. 
Single-dose PK data has been collected in the Phase 1 study, PAL-001. However, there is 
little multiple-dose PK data or data for when subjects have reached and maintained a stable 
dosing regimen.  With the PK substudy, multiple-dose PK data will be collected for subjects 
who have already achieved Phe reduction to within the protocol-defined target range. 
This study is an extension of previous rAvPAL-PEG Phase 2 studies. Administration of 
rAvPAL-PEG will be continued to assess the long-term safety and efficacy of rAvPAL-PEG 
in PKU subjects. 
7.4 
Summary of Overall Risks and Benefits 
It is not expected that data from previous rAvPAL-PEG studies will change the assumption 
that rAvPAL-PEG has a toxicity profile similar to other recombinant PEGylated non-human 
enzymes currently in use. The toxicities of these drugs usually fall into 2 main categories: 
toxicity due to exposure to PEG, and toxicity due to immunologic sensitization. In addition, 
exaggerated pharmacological effects resulting in very low Phe concentrations could be 
observed. Other adverse events (AEs) that could occur with rAvPAL-PEG include 
injection-site reactions and other general symptoms. 
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7.4.1 Toxicity Due to Exposure to Polyethylene Glycol (PEG) 
Acute exposure to high doses of PEG can result in renal toxicity. There have been a few 
reports of PEG-related AEs in humans; cumulative intravenous (IV) PEG doses of 121 to 
240 g caused acute renal tubular necrosis, oliguria, and azotemia. The anticipated PEG 
exposure associated with the expected rAvPAL-PEG dose range (6 g per week) is at least 
80-fold lower than the reported toxic doses and comparable to exposures to PEG in widely 
used medicines and other compounds that are administered by the IV, oral, rectal, and topical 
routes (Webster, 2007, Drug Metab Dispos.). No indication of PEG-related toxicity at the 
ultrastructural level was observed in monkeys given a single dose of up to 60 mg/kg 
rAvPAL-PEG SC. In rats, both renal tubule vacuolation and histiocytic cell vacuoles have 
been assocated with PEG-related catabolism and administration of other PEGylated proteins 
(refer to Section 7.1). 
In this study, subjects will be monitored closely with urine examinations and blood 
chemistries to follow kidney function. 
7.4.2 Toxicity Due to an Immunologic Reaction 
The active drug substance in rAvPAL-PEG is a bacterial protein, and as such, it is expected 
that it may elicit immune recognition and responses. Epitopes that play a role in the immune 
response may be rendered inaccessible by PEG (Gamez, 2007, Mol.Genet.Metab). In vivo 
and in vitro experiments have shown that PEGylation of proteins and cells can attenuate the 
immunological response (Scott, 1997, Proc.Natl.Acad.Sci.U.S.A), (Chen, 2001, BioDrugs.). 
PEGylation has been effective in reducing anti-rAvPAL antibody titers in the mouse model, 
although PEGylation does not eliminate antibody formation. Although PEGylation of 
rAvPAL may have a significant effect on reducing the immunogenicity of the molecule, it is 
reasonable to expect that some individuals may exhibit immune responses upon exposure to 
the drug. These immune responses may be clinically irrelevant, cause symptoms of various 
degrees, or lead to neutralization of biological activity. Subjects participating in clinical trials 
will be monitored closely with specific antibody titers sedimentation rates, and complete 
blood counts (CBCs). 
As of May 2012, a total of 70 subjects have been administered rAvPAL-PEG in the single-
dose, Phase 1 study (PAL-001) and in the repeat -dosing Phase 2 studies (PAL-002, 
PAL-004, and PAL-003). The dose levels in the repeat-dosing studies range from 0.001 to 
5.0 mg/kg/week administered in various frequencies (including 5 days a week). The most 
clinically significant AEs have been hypersensitivity reactions that have led to dosing 
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interruptions and reductions. Most of the hypersensitivity reactions have been nonserious and 
mild-to-moderate in severity.  
A total of 4 SAEs have been reported in the previous rAvPAL-PEG studies.  Of these 
4 SAEs, 3 have been reported as related to rAvPAL-PEG. Two of the study-drug related 
SAEs occurred in Study PAL-001. Both of these SAEs occurred in subjects in the lower dose 
cohorts: an SAE of hypersensitivity reaction in a subject in the 0.001 mg/kg cohort and an 
SAE of anaphylactic reaction (urticaria) in a subject in the 0.01 mg/kg cohort. Neither SAE 
was severe or resulted in discontinuation from the study, and both of the SAEs resolved. 
There were no SAEs in subjects in the higher dose cohorts (0.03 mg/kg and 0.1mg/kg) in 
PAL-001. The third study drug-related SAE (angioedema) occurred in a subject in Study 
PAL-004. The fourth SAE (urticaria, dehydration) was reported as not related to study drug 
and occurred in a subject in Study PAL-002.  There have been no reports of anaphylaxis for 
any subject treated with rAvPEG-PAL (as of January 2012).  
Subjects who have a systemic clinical reaction at any time during this study may undergo a 
series of assessments to monitor safety, including assessment of complements, C-reactive 
protein (CRP), erythrocyte sedimentation rate (ESR), and IgE antibodies.  Reintroduction of 
rAvPAL-PEG dosing after a reaction will depend on clinical assessments and available 
laboratory data, such as chemistry and urine studies, to ensure that there has been no 
end-organ damage prior to resuming treatment with rAvPAL-PEG. As of May 2012, 
antibody titers, including positive IgE titers, have not been predictive of future clinical 
reactions when dosing with rAvPAL-PEG.  Additionally, subjects may be premedicated to 
prevent or mitigate risk of hypersensitivity reactions (refer to Section 9.1.1.3.3). 
PEG itself is considered nonimmunogenic (Davis, 1981, Clin.Exp.Immunol.), (Harris, 2003, 
Nat.Rev.Drug Discov.), however, antibodies against PEG may form when PEG is bound to 
compounds. (Harris, 2003, Nat.Rev.Drug Discov.),(Richter, 1983, Int.Arch.Allergy 
Appl.Immunol.).  In some instances, development of such antibodies did not result in any 
significant clinical effects in humans (Richter, 1984, Int.Arch.Allergy Appl.Immunol.). 
In some individuals, anti-PEG antibodies may be pre-existing due to previous exposure to 
PEG in other products. Anti-PEG antibodies have been associated with nonresponsiveness 
against therapy (Armstrong, 2007, Cancer), (Ganson, 2006, Arthritis Res.Ther.).  
Administration of rAvPAL-PEG may lead to anti-PEG antibody formation, and the duration 
of this possible effect is not known. Subjects in the Phase 2 rAvPAL-PEG studies have 
developed both anti-PEG IgM and anti-PEG IgG antibodies. Antibody formation may limit a 
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subject’s future ability to be treated with other PEG-containing (eg, Depo-Provera) or 
PEGylated (eg, PEG-interferon) injectable drugs. It is therefore recommended that any 
PEG-containing injectable drug administered to subjects after completion of this study be 
done under medical observation. 
7.4.2.1 
Systemic Skin Reactions 
Two out of 25 subjects who were enrolled in Study PAL-001 and received the 
protocol-defined single dose of rAvPAL-PEG reported systemic skin reactions (generalized 
skin rash) that were attributed to treatment with study drug. One subject received a single 
dose of 0.001 mg/kg rAvPAL-PEG, and the other subject received a single dose of 
0.01 mg/kg rAvPAL-PEG. One of these events was reported as serious, and the other was 
reported as nonserious; both events were reported following administration of Depo-Provera 
injections (medroxyprogesterone injection), an injectable contraception. These allergic 
reactions are thought to be related to the PEG molecules that are found in both the study 
drug, rAvPAL-PEG, and Depo-Provera. These reactions are not likely to be experienced 
concurrent with other birth control medications. 
The 2 subjects were administered study drug during PAL-001 and then experienced an 
allergic reaction following an injection of Depo-Provera. The symptoms of the reactions 
were hives on the arms and legs and difficulty breathing. The symptoms for both subjects 
resolved within 1 day following treatment with medication, including the 
 
. Both subjects were examined by an allergy specialist after they 
completed participation in PAL-001. A skin prick test with Depo-Provera was administered 
as part of this examination. One subject had a mild allergic reaction to the test; however, no 
further reactions or complications were reported following subsequent administration of a 
full dose of Depo-Provera. Upon study completion, the subject continued to receive regular 
doses (every 3 months) of Depo-Provera, and no further reactions were reported. The second 
subject also had a positive reaction to Depo-Provera following administration of the skin 
prick test. When a subsequent full dose of Depo-Provera was administered, 
 developed 
hives, itching, and chills. The subject’s symptoms resolved within 1 day of taking medication 
prescribed by an allergist. See Section 7.2.1 for the results from Study PAL-001. 
The active drug substance in rAvPAL-PEG is a bacterial protein that may elicit immune 
responses, such as urticaria, bronchospasm, itching, anaphylaxis, and others. The results from 
nonclinical studies of rAvPAL-PEG conducted in rats and cynomolgus monkeys indicated 
the formation of anti-rAvPAL antibody titers that did not correspond with observations of 
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the formation of anti-rAvPAL antibody titers that did not correspond with observations of 
injection-site reactions. Quantitation of anti-PEG titers were not assessed in the chronic 
repeat-dose studies in the rat and monkey. Although results from nonclincal studies of 
rAvPAL-PEG conducted in rats and cynomolgus monkeys did not indicate signs of 
immune-mediated toxicities, it is possible that the physio-chemical properties of 
rAvPAL-PEG may induce immunologic sensitization to the protein rAvPAL and to PEG in 
humans. It is currently unknown whether administration of PEG-containing drugs, such as 
Depo-Provera, has a sensitizing effect to PEG in rAvPAL-PEG when administered in 
humans. Because the exact basis for these reported events and their duration is not known, 
the use of PEG-containing injectable drugs prior to, during, and after this study is prohibited 
as a precautionary measure (refer to Section 9.3.2 and Section 9.4.8). 
7.4.2.2 
Management of Hypersensitivity Reactions 
Hypersensitivity reactions to the SC injection of rAvPAL-PEG may be mild, moderate, or 
severe in intensity. Reactions may include pruritus, rash, shortness of breath, hypotension, or 
anaphylaxis. Clinical assessments should be conducted for a minimum of 30minutes 
post-injection. Longer observations may be required at the discretion of the PI. 
The responsible physician should use all appropriate measures for the treatment of 
hypersensitivity reactions. Because of the small potential for anaphylaxis, equipment for 
emergency resuscitation (including epinephrine) should be within easy access during and 
after the rAvPAL-PEG injection. Subjects who qualify for self administration of study drug 
will be provided with emergency resuscitation instructions (refer to Section 9.4 and the 
Subject Self-Administration Training Materials). 
In the event of a hypersensitivity reaction, subjects may be asked to see an 
allergist/immunologist and/or provide up to 3 additional blood samples for immunology 
studies and complement testing. This additional testing may occur up to 6 months following 
the final study visit.   
The following measures are recommended for the treatment of hypersensitivity reaction 
symptoms: 
• Maintain the airway. 
• Vital sign check. 
• Administration of oral or IV diphenhydramine. 
• Administration of epinephrine if appropriate. 
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• Administration of oral or IV glucocorticoids. 
• Administration of oxygen and IV fluids. 
• Administration of additional symptomatic treatment (eg, acetaminiophen or 
ibuprofen). 
• Transfer to an acute care facility of the study center. 
 
In addition, clinical judgment must be used in determining the appropriateness of 
corticosteroid administration. An allergy and/or immunology consultation should be sought if 
necessary. Information regarding the management of local skin, large local skin, and 
systemic reactions is provided in Section 9.1.1. Detailed instructions for the management of 
hypersensitivity reactions are provided in the Study Reference Manual. 
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8 
STUDY OBJECTIVES 
The primary objective of the study is: 
• To evaluate the effect of long-term administration of multiple doses of SC injections 
of rAvPAL-PEG on blood Phe concentrations in subjects with PKU. 
The secondary objectives of the study are: 
• To evaluate the safety and tolerability of long-term administration of subcutaneous 
(SC) injections of rAvPAL-PEG in subjects with PKU. 
• To evaluate the immune response to long-term administration of SC injections of 
rAvPAL-PEG in subjects with PKU. 
The exploratory objective of the study is as follows: 
• To evaluate the long-term relationship of diet and change in blood Phe concentration 
following administration with rAvPAL-PEG in subjects with PKU. 
The Substudy objective is as follows: 
• To evaluate steady-state PK of rAvPAL-PEG in subjects who have achieved and 
maintained target blood Phe concentration and for whom no further dose 
modifications are planned. 
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9 
INVESTIGATIONAL PLAN 
9.1 
Overall Study Design and Plan 
This is a long-term extension of rAvPAL-PEG Phase 2 studies in up to 100 subjects with 
PKU. The doses are planned to be in the same range as those previously tested in the Phase 2 
studies (starting at 0.001 through 5.0 mg/kg/week or 2.5 mg through 375 mg/week), provided 
no dose-limiting toxicity was observed in a previous rAvPAL-PEG studies. 
Only subjects who completed a previous rAvPAL-PEG study will be enrolled into this study. 
Subjects enrolling into PAL-003 with no interruption in dosing from a previous 
rAvPAL-PEG study may either continue their previous dosing regimen or begin this study at 
a higher dose level. Subjects who have had dosing interruptions between the previous 
rAvPAL-PEG study and PAL-003 must have their starting dose determined per the Sponsor’s 
Medical Officer.  The first dose will be administered in the clinic, and the subject must be 
observed for 30 minutes following administration. A follow-up telephone call will be made 
to the subject to monitor subject safety 24 hours following the return to dosing. 
Diet should not be altered during the course of this study. Any decision to modify subject 
diet must be made per the Investigator and must be performed under the supervision of the 
Investigator. To monitor for changes in subject diet, a diet diary will be issued to subjects for 
completion and will be brought to clinic monthly for review with the clinical study staff. 
Subjects may self administer study drug at home if approved by the Investigator and the 
Sponsor’s Medical Officer and if adequate training is demonstrated. Subjects must meet a set 
of criteria to be considered appropriate for self administration. Refer to Section 9.4 for the 
criteria for which subjects may qualify for self administration. Additional information is 
provided in the Subject Self-Administration Training Materials. 
Subjects will be evaluated for safety throughout the study. Toxicity will be measured 
according to the National Cancer Institute (NCI) Common Terminology Criteria for Adverse 
Events (CTCAE), version 4. 
In addition to the Sponsor, a Data Monitoring Committee (DMC) will monitor the safety of 
subjects in the study. The DMC is an independent committee that will act in an advisory 
capacity to the Sponsor. 
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take 
rAvPAL-PEG. Subjects’previous rAvPAL-PEG dosing will generally continue in PAL-003. 
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In PAL-003, each subject’s dose will be adjusted as needed to attempt to attain or maintain 
blood Phe concentrations of 60-600 µmol/L. rAvPAL-PEG dose will be based on either a 
subject’s weight or will be a fixed dose. Doses will be evaluated on an individual basis.  
Evaluations, observations, and procedures will be conducted at selected time points as shown 
in Table 9.1.1 and Table 9.1.2.  After the subject’s blood Phe concentration has been 
controlled to within a target range (60-600 µmol/L), the subject may be asked to have 
additional blood draws for PK and blood Phe concentration analyses as needed per the 
discretion of the Investigator in consultation with the Sponsor’s Medical Officer. 
A subject will continue in PAL-003 until one of the following occurs: 
• The subject withdraws consent and discontinues from the study. 
• The subject is discontinued from the study at the discretion of the Investigator. 
• The subject has completed the study through the Month 86 visit. 
• The study is terminated. 
• 
The study drug receives marketing authorization. 
 
Subjects may withdraw from treatment with study drug at any time; however, subjects will 
be asked to continue to perform the study assessments until study completion. Subjects may 
also withdraw from study participation at any time. Because the completeness of the data 
affects the integrity, accuracy, and interpretation of study results, every effort should be made 
to retain subjects in the study and to have them complete the study assessments as scheduled 
as long as continued participation does not compromise subject safety. 
Subjects who participate in this study will be required to transition into a Phase 3 study 
(165-302) if weekly doses of rAvPAL-PEG are between 70 mg/week and 350 mg/week 
(inclusive) provided that doses of rAvPAL-PEG have been stable (ie, no major change in 
dose for at least 4 weeks). Subjects who meet these criteria must be transitioned from 
PAL-003 to Study 165-302 provided they meet the 165-302 study eligibility criteria.  
Subjects who are eligible for Study 165-302 but do not transition into 165-302 will be 
withdrawn from this study. 
The PAL-003 study will continue until BMN-165 is approved by the FDA for marketing in 
the United States or until the sponsor terminates further development of this drug for 
treatment of PKU. 
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A PK substudy has been added to evaluate the steady-state PK of rAvPAL-PEG in up to 
6 subjects who have achieved and maintained target blood Phe for at least 2 consecutive 
measurements and for whom no further dose modifications are planned.  Subjects enrolled 
into the substudy will have additional pre-dose PK sampling performed (refer to Table 9.1.2). 
The Schedule of Events and PK substudy collection schedules are presented below in 
Table 9.1.1 and Table 9.1.2  
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Table 9.1.1:  Schedule of Events 
Assessments and Events 
Screeninga 
Treatment Periodb,c 
Final F/U 
Visit 
Self 
Administration 
Early 
Term. 
Visit 
Unsched. 
Hyper. 
Reaction 
Visit.d  
Perform 
within 
24 hours 
Week 1 
Weekly 
Telephone 
Contacts 
Monthly b 
(eg, Wk 4, 
8, etc.) 
Quarterly  
(eg, 
Wk 12, 24, 
etc.) 
Interim 
Clinician 
Visit 
(HHRN 
or Site) 
D 1 
Starting at 
Week 2 
Every 4th 
week; 
Every 12th 
week. 
Perform in 
addition to 
monthly 
procedures 
Up to 
daily 
1 week 
after final 
dose 
 
4 weeks 
after 
final 
dose 
Informed consent 
X 
 
 
 
 
 
 
 
 
 
Medical history, including 
allergy history, and 
demographics 
X 
 
 
 
 
 
 
 
 
 
Physical examinatione 
X 
X 
 
 
X 
 
X 
 
X 
 
Vital signse 
X 
X 
 
X 
 
X 
 
 
X 
X 
Weight 
X 
 
 
X 
 
 
 
 
 
 
12-lead ECG 
X 
 
 
 
 
 
X 
 
X 
 
Clinical laboratory testsf 
X 
 
 
X 
 
 
X 
 
X 
Xg 
Complements C3 and C4
h 
X 
 
 
 
X 
 
 
 
 
X 
Sedimentation rate 
 
X 
 
 
X 
 
X 
 
X 
 
Chest x-ray 
X 
 
 
X  
(Week 48 
visit only) 
 
 
X 
 
X 
 
Urine pregnancy testi 
X 
X 
 
X 
 
 
X 
 
X 
 
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Assessments and Events 
Screeninga 
Treatment Periodb,c 
Final F/U 
Visit 
Self 
Administration 
Early 
Term. 
Visit 
Unsched. 
Hyper. 
Reaction 
Visit.d  
Perform 
within 
24 hours 
Week 1 
Weekly 
Telephone 
Contacts 
Monthly b 
(eg, Wk 4, 
8, etc.) 
Quarterly  
(eg, 
Wk 12, 24, 
etc.) 
Interim 
Clinician 
Visit 
(HHRN 
or Site) 
D 1 
Starting at 
Week 2 
Every 4th 
week; 
Every 12th 
week. 
Perform in 
addition to 
monthly 
procedures 
Up to 
daily 
1 week 
after final 
dose 
 
4 weeks 
after 
final 
dose 
Injection-site inspectionji j 
 
X 
(postdose) 
 
X 
 
X 
X 
X 
X 
X 
Adverse eventsj, k 
X 
X 
 
X 
 
X 
X 
X 
X 
X 
Weekly phone call to self 
admin participants only (to 
assess AEs, Inj site reactions, 
concomitant medications) 
 
 
X 
 
 
 
 
X 
X 
 
Concomitant medicationsj 
X 
X 
 
X 
 
X 
X 
X 
X 
X 
Diet query 
X 
X 
 
X 
 
 
X 
 
X 
 
3-Day diet diaryl 
 
 
 
X 
 
 
X 
 
X 
 
Serum antibodies m 
 
X 
 
 
X 
 
X 
 
X 
X 
Plasma Phe and plasma 
tyrosinen  
X 
X 
 
Xm 
 
 
X 
 
X 
 
Urine albumin/creatinine 
ratio 
 
 
 
 
 
 
 
 
 
X 
Urine N-methyl histamine 
 
 
 
 
 
 
 
 
 
X 
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Assessments and Events 
Screeninga 
Treatment Periodb,c 
Final F/U 
Visit 
Self 
Administration 
Early 
Term. 
Visit 
Unsched. 
Hyper. 
Reaction 
Visit.d  
Perform 
within 
24 hours 
Week 1 
Weekly 
Telephone 
Contacts 
Monthly b 
(eg, Wk 4, 
8, etc.) 
Quarterly  
(eg, 
Wk 12, 24, 
etc.) 
Interim 
Clinician 
Visit 
(HHRN 
or Site) 
D 1 
Starting at 
Week 2 
Every 4th 
week; 
Every 12th 
week. 
Perform in 
addition to 
monthly 
procedures 
Up to 
daily 
1 week 
after final 
dose 
 
4 weeks 
after 
final 
dose 
Plasma PK sample m 
 
X 
 
 
X 
 
X 
 
X 
 
Administer study drugo 
 
X 
 
X 
 
X 
 
X 
 
 
Skin biopsy (optional; 
affected and not affected 
area) 
 
 
 
 
 
 
 
 
 
X 
Serum tryptase level p 
 
 
 
 
 
 
 
 
 
X 
AE, adverse event; C3, complement 3; C4, complement 4; CH50, total hemolytic complement; CRP, C-reactive protein; D, day; ECG, electrocardiogram; ETV, 
Early Termination Visit; F/U, Follow-up; Hyper, hypersensitivity; IgE, immunoglobulin E; IgG, immunoglobulin G; IgM, immunoglobulin M; IP, 
investigational product; PK, pharmacokinetics; Phe, phenylalanine; SAE, serious adverse event; Wk, week. 
a A separate Screening visit for this study is required only if the time between completion of the previous rAvPAL-PEG study and enrollment into PAL-003 is 
greater than 28 days. 
b Monthly visits must be performed in the clinic. 
c On days that a dose is given, all procedures should be performed predose, except where noted. 
d Refer to Section 9.1.1.3.3 and Section 12.3.6. 
e Complete physical examinations to include the evaluation of all major body systems. Height will be measured at Screening only. 
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f Clinical laboratory tests to include spot urine albumin/creatinine ratio, hematology, chemistry, and urinalysis. Urine microscopy will be performed if any 
urinalysis results are positive for hematuria.  Refer to Table 9.7.6.1. 
g Subjects who have a systemic reaction or a large local reaction not contiguous with the injection site should be assessed for CRP, CH50, C1, C3, and C4 within 
24 hours of the reaction.  
hComplement C3 and C4 will be collected at the Screening Visit and quarterly. Additional complement testing will be performed and as needed to resolve 
previous abnormal test results. 
i If positive or equivocal, perform serum pregnancy test. 
j If any injection site reaction is observed, the corresponding adverse event data must specify injection location (identify current vs. previous visit’s injection, eg, 
right arm vs. left arm). 
j Subjects must have AEs and concomitant medications assessed and an injection-site inspection performed whenever dose is administered even if the 
administration does not coincide with a scheduled clinic visit.   
k The reporting period for SAEs begins when informed consent is obtained and continues through 4 weeks after last dose or the final study visit. The reporting 
period for nonserious AEs is from the first administration of study drug to the final study visit.  
l  It is preferable that the subject complete the diary 3 days immediately prior to the next monthly visit. 
m Sampling should be performed predose. 
n Samples should be drawn at least 2.5 hours after a meal.  At the Investigator’s discretion, blood Phe may be collected more often should more frequent 
monitoring of blood Phe levels be clinically warranted 
o Dosing is up to 5.0 mg/kg/week or 375 mg/week, including subjects who receive more than 1 dose/week. Every effort should be made to adhere to the study 
drug administration regimen. If a subject misses more than 2 scheduled doses of study drug, both dose level and dose frequency may be re-evaluated.  
p Mandatory for subjects who have a systemic reaction.  Take sample immediately after reaction if possible. 
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Table 9.1.2:  PK Substudy Dosing Regimens 
Treatment Frequency 
Plasma PK Sampling 
Example 
Subjects who are 
administered study drug 
once per week 
Pre-dose and every 24 hours 
thereafter (24, 48, 72, and 96 
hours when possible), and pre-
dose of the next weekly dose 
If dosed on Monday: 
Obtain PK sample pre-dose when possible – pre-dose Monday, Tuesday, 
Wednesday, Thursday, Friday, and pre-dose the following Monday. 
No further PK substudy draws. 
Subjects who are 
administered study drug 
two or three times per 
week 
Pre-dose and every 24 hours 
during the longest period 
between doses, when possible, 
and pre-dose of the next dose. 
If dosed on Monday, Thursday, and Friday: 
Obtain PK sample every 24 hours during the longest period between doses: Pre-
dose Monday, Tuesday, Wednesday, and pre-dose Thursday. 
No further PK substudy draws. 
Subjects who are 
administered study drug 
four to seven times per 
week. 
Pre-dose and every 12 hours 
during the longest period 
between doses, when possible, 
then pre-dose of the next dose. 
If dosed Monday through Friday: 
Obtain PK sample every 12 hours during the longest period between doses (Friday 
to Monday): pre-dose Friday, 12 hours post-dose Friday, Saturday (24 and 36 
hours post dose), Sunday (48 and 60 hours post-dose), and pre-dose the following 
Monday. 
No further PK substudy draws. 
 
 
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9.1.1 Management of Local and Systemic Reactions to rAvPAL-PEG 
Subjects who qualify for self administration of study drug will be provided with information 
and instruction with regard to management of local and systemic reactions (refer to the 
Subject Self-Administration Training Materials). 
9.1.1.1 
Subjects Who Have Had Previous Hypersensitivity Reactions to 
rAvPAL-PEG or a PEG-containing Product 
Subjects who had a previous systemic reaction to rAvPAL-PEG or a PEG-containing product 
that warranted early termination from a previous rAvPAL-PEG study are excluded from 
participation in this study. Subjects who have had a previous local skin reaction to 
rAvPAL-PEG in a previous rAvPAL-PEG study are eligible to participate in this study. 
Subjects who have had a previous reaction and are deemed eligible for participation must be 
premedicated orally with acetaminophen and/or non-sedating antihistamines 1-2 hours prior 
to study drug dosing for the remainder of the study. The premedication dosage will be 
standard. Because antihistamines can cause drowsiness, it may be administered only if the 
subject is accompanied by a designated driver (if applicable). Subjects may develop 
systemic, large local skin, or local skin reactions after enrollment in PAL-003. Refer to 
Section 9.1.1.2 for definitions of systemic and local skin reactions. For management of 
hypersensitivity reactions that occur during this study, refer to Section 9.1.1.3 and 
Figure 9.1.1.3.1. 
9.1.1.2 
Definition of Reaction and Hypersensitivity Reactions to rAvPAL-PEG 
Administered Subcutaneously 
During Study PAL-003, subjects may experience hypersensitivity reactions to rAvPAL-PEG. 
The hypersensitivity reactions are defined as follows: 
Local skin reaction: 
• Skin signs or symptoms in 1 affected primary location, ie, hives, wheals, or swelling 
or an area of erythema, redness, induration, pain, or itching at or near the site of 
injection. 
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Large local skin reaction: 
• Skin signs or symptoms, ie, hives, wheals, or swelling or an area of erythema, 
redness, or induration with pain or itching that extends beyond the site of injection by 
approximately 6 inches (15 cm) and/or signs or symptoms that are not contiguous to 
the injection site. These may be associated with a low risk of systemic symptoms or 
anaphylaxis upon re-exposure and, therefore, will be managed as a systemic reaction 
when not contiguous to the injection site.  
Systemic reaction (including generalized skin symptoms): 
• Skin and non-skin signs or symptoms in more than 1 affected primary location, 
ie, cutaneous reaction in more than 1 area and/or anaphylaxis or any other generalized 
symptoms, such as hypotension, angioedema or the involvement of other organ 
systems, eg, respiratory, cardiovascular, gastrointestinal, neurological; and/or a fever 
attributed to treatment with rAvPAL-PEG ( ≥ 100.4°F or  ≥ 38°C). 
For management of hypersensitivity reactions that occur during this study, refer to 
Section 9.1.1.3 and Figure 9.1.1.3.1.   
 
 
 
 
   
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9.1.1.3.1 Local Skin Reactions 
All subjects who experience a local skin reaction during this study may be premedicated 
orally with acetaminophen and/or non-sedating antihistamines 1-2 hours prior to study drug 
dosing (subjects may take non-sedating premedications prior to coming to clinic) for all 
future study doses. Recommended premedications are acetaminophen and/or non-sedating 
antihistamine. The dosage will be standard. Subjects must be accompanied by a designated 
driver (if applicable) because antihistamines can cause drowsiness. Symptoms of local 
reactions may be treated with local application of ice and non-sedating oral and/or topical 
antihistamines and/or topical steroids (refer to Section 7.4.2.2). 
If the local skin reaction worsens with a repeat injection (as determined by the Investigator in 
consultation with the Sponsor’s Medical Officer) even with premedication prior to study drug 
dosing, the subject must be withdrawn from study treatment. 
9.1.1.3.2 Large Local Skin Reactions 
Large local skin reactions (refer to Section 9.1.1.2 for a definition) may or may not be 
contiguous to the rAvPAL-PEG injection site, and subjects with either type of large local 
skin reaction may continue dosing if the skin symptoms have resolved and no other 
symptoms have developed. Subjects will be encouraged to premedicate orally with 
acetaminophen and/or non-sedating antihistamines 1-2 hours prior to study drug dosing 
(subjects may take non-sedating premedications prior to coming to clinic) for all future study 
doses. 
Symptoms of large local skin reactions may be treated with local application of ice and 
topical, oral, or IV antihistamines and/or steroids as needed (refer to Section 7.4.2.2). 
9.1.1.3.2.1 
Large Local Skin Reactions Contiguous to Injection Site 
Subjects who develop a large local skin reaction contiguous to the injection site after 
administration of rAvPAL-PEG or to rAvPAL-PEG or a PEG-containing product may 
remain in the study if the skin symptoms have resolved and no other symptoms have 
developed. For the remainder of the study, subjects will be encouraged to premedicate orally 
with acetaminophen and/or non-sedating antihistamines 1-2 hours prior to study drug dosing 
(subjects may take non-sedating premedications prior to coming to clinic) for all future study 
doses. Because antihistamines can cause drowsiness, it may be administered only if the 
subject is accompanied by a designated driver (if applicable).  
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Symptoms of large local skin reactions may be treated with local application of ice and 
topical, oral, or IV antihistamines and/or steroids as needed (refer to Section 7.4.2.2).  
9.1.1.3.2.2 
Large Local Skin Reactions Not Contiguous to Injection Site 
Large local skin reactions that are not contiguous to the injection site may be associated with 
a low risk of systemic symptoms or anaphylaxis upon re-exposure to rAvPAL-PEG and, 
therefore, will be managed as a systemic reaction (refer to Section 9.1.1.3.3). An example of 
a large local reaction that is not contiguous to the injection site is if an injection took place in 
the right upper arm and there are lesions beyond the elbow joint in the right forearm or 
lesions beyond the shoulder joint on the right trunk. 
Symptoms of large local skin reactions may be treated with local application of ice and 
topical, oral, or IV antihistamines and/or steroids as needed (refer to Section 7.4.2.2). 
9.1.1.3.3 Systemic Reactions 
Subjects who experience a systemic reaction (refer to Section 9.1.1.2 for a definition) after 
administration of rAvPAL-PEG must stop further administrations of rAvPAL-PEG and must 
immediately return to the clinic for safety assessments. Subjects who experience generalized 
skin symptoms are included in this category. Immediately after the systemic reaction (within 
24 hours), subjects with generalized skin symptoms must have additional assessments 
performed for safety (ie, Unscheduled Hypersensitivity Reaction Visit): serum antibodies 
(anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, anti-PEG IgM, anti rAvPAL-PEG IgE, 
anti-rAvPAL-PEG neutralizing antibodies); serum tryptase level (it is recommended that this 
sample be drawn immediately after reaction); urine albumin/creatinine ratio; urine N-methyl 
histamine; CRP, CH50, C1, C3, and C4; skin biopsy (optional; affected and not affected area; 
to be performed within 1 week of reaction); and clinical laboratory tests (urinalysis, 
chemistry, hematology; refer to Figure 9.1.1.3.1.  
Following the reaction, subjects will be required to complete the assessments of the 
Unscheduled Hypersensitivity Reaction visit, including assessment of IgE. If a subject 
presents with a clinical diagnosis of anaphylaxis, further dosing will be held while laboratory 
evaluation of IgE, as part of the Unscheduled Systemic Reaction Visit, is performed.  
Subjects may resume study drug administration per the discretion of the Principal 
Investigator and the Sponsor’s Medical Officer; however, if subject was dosing at home, they 
will be required to come into the clinic for at least 1 week.  
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rAvPAL-PEG administration will resume at the next lowest dose level. Restarting of 
rAvPAL-PEG administration following a systemic reaction must be performed in the clinic 
for the first week of resumed dosing. Subjects will be encouraged to premedicate orally with 
acetaminophen and/or antihistamines 1-2 hours prior to study drug dosing (subjects may take 
non-sedating premedications prior to coming to clinic) for all future study doses. 
Additionally, subjects must be closely monitored for 30 minutes following every 
administration of study drug. Because antihistamines may cause drowsiness, the subject must 
be accompanied by a designated driver (if applicable).   
If blood Phe concentrations are not 60-600 µmol/L following 1 week of daily administration 
at the lowered dose cohort and there is no further evidence of toxicity (ie, another systemic 
reaction attributed to rAvPAL-PEG administration or clinically significant abnormal 
laboratory test results), the subject may be administered the next highest dose level in the 
clinic per the allowable dose increases outlined in Section 9.1.2. Subjects will be encouraged 
to premedicate orally with acetaminophen and/or antihistamines 1-2 hours prior to study drug 
dosing (subjects may take non-sedating premedications prior to coming to clinic) for all 
future study doses. Additionally, subjects must be closely monitored for 30 minutes 
following every study drug administration. Because antihistamines may cause drowsiness, 
the subject must be accompanied by a designated driver (if applicable). 
9.1.2 Dose Modifications 
9.1.2.1 
Dose Increase Methodology 
Each subject’s dose may be modified based on the decision of the Investigator. Decisions 
regarding dose increases will depend on a subject’s adverse event profile and blood Phe and 
drug concentrations. 
An individual subject’s dose may be adjusted beginning on Day 1 of PAL-003. For the 
duration of this study, an individual subject’s dose may be adjusted if warranted per a 
subject’s adverse event profile and blood Phe concentrations. Dose increases should be 
performed as follows: 
• The dose may be increased by increments of no more than 10-fold higher than the 
subject’s current dose. 
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• When increasing the dose, a dose may be used that is between the dose levels (0.001, 
0.003, 0.01, 0.03, 0.06, 0.1, 0.2, 0.3, 0.4, 0.6, 0.8,  1.0, 2.0, 3.0, 4.0, and 5.0 mg/kg or 
2.5, 5, 10, 20, 40, 75, 150, 225, 300, 375 mg/week) or per Investigator determination 
based on available information regarding a subject’s blood Phe (60-600 µmol/L) as 
well as any adverse events for an individual subject. Dose increases  > 350 mg/week 
require consultation with the sponsor’s medical monitor. 
• The dose may be adjusted by increasing the frequency up to daily for a total weekly 
dose not to exceed 5.0 mg/kg or 375 mg/week.   Dose increases  > 350 mg/week require 
consultation with the sponsor’s medical monitor. 
• When a dose is increased, the subject must be observed for 30 minutes following the 
first modified dose administration. Subjects who increase their dose frequency do not 
need to be observed following injection of study drug if the increase in frequency 
does not increase the overall weekly dose amount. 
• Only 1 dose adjustment is allowed every 2 weeks. 
9.1.2.2 
Dose Decrease Methodology 
Decisions regarding dose decreases will depend on available information regarding a 
subject’s blood Phe (60-600 µmol/L), as well as any adverse event (any hypersensitivity 
reaction as defined in Section 9.1.1.2). Dose decreases may occur for hypophenylalanemia or 
any adverse event that may be improved with a lower, more frequent dose. 
A dose should first be reduced by dose level (5.0, 4.0, 3.0, 2.0, 1.0, 0.8, 0.6, 0.4, 0.3, 0.2, 0.1, 
0.06, 0.03, 0.01, 0.003, 0.001 mg/kg or 375, 300, 225, 150, 75, 40, 20, 10, 5, and 2.5 
mg/week). It is also permitted to decrease dose in between these specified dose levels. If 
further dosing adjustments are required in response to safety, dosing frequency may also be 
reduced.  
If the subject develops low blood Phe (as defined by a blood Phe level ≤ 30 µmol/L ), the 
subject’s rAvPAL-PEG dose should be decreased to the next lower dose.  If the condition 
persists after another 1 month at the lower dose, the dose should be decreased again to the 
next lower level. If the subject continues to experience low blood Phe after two dose level 
reductions, the subject may be asked to consult the dietician to eliminate medical foods 
and/or formulas and to ensure a balanced and nutritious diet (as part of the routine standard 
of care for PKU disease management, subject diet should be monitored by a dietician). 
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9.1.3 Safety Assessment Criteria 
If an individual subject exhibits toxicity of a treatment-emergent CTCAE grade 3 or greater 
or a systemic reaction that is assessed as related to treatment with study drug, that subject 
will have dosing halted until the toxicity resolves. The subject’s data will be evaluated by the 
Principal Investigator (PI) and the Sponsor’s Medical Officer, and a decision will then be 
made whether to discontinue the subject from the study treatment, restart dosing at the same 
dose level, or restart dosing at a lower dose level. 
9.1.4 Stopping Criteria 
If 2 or more subjects at a dose level exhibit toxicity of a treatment-emergent CTCAE grade 3 
or greater or a systemic reaction that is assessed as related to treatment with study drug, 
further dosing of subjects at that dose level will evaluated and a safety assessment will be 
completed. In addition, the Food and Drug Administration (FDA) may be notified of this 
occurrence if appropriate. 
9.2 
Discussion of Study Design, Including Choice of Control Group 
This open-label, Phase 2 trial was designed to be closely monitored with the goal of 
obtaining information about the efficacy, safety, tolerability, and PK of long-term 
administration of rAvPAL-PEG in subjects with PKU. There will be no control group in this 
study. 
9.3 
Selection of Study Population 
9.3.1 Inclusion Criteria 
Individuals eligible to participate in this study must meet all of the following criteria: 
1. Must have completed participation in a previous rAvPAL-PEG study. 
2. Willing and able to provide written, signed informed consent, or in the case of 
subjects under the age of 18 years, provide written assent (if required) and written 
informed consent by a parent or legal guardian, after the nature of the study has been 
explained, and prior to any research-related procedures. 
3. Willing and able to comply with all study procedures. 
4. Females of childbearing potential must have a negative pregnancy test at Screening 
and be willing to have additional pregnancy tests during the study. Females 
considered not of childbearing potential include those who have been in menopause at 
least 2 years, or had tubal ligation at least 1 year prior to Screening, or who have had 
total hysterectomy. 
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5. Sexually active subjects must be willing to use an acceptable method of contraception 
while participating in the study. 
6. Maintained a stable diet. 
7. In generally good health as evidenced by physical examination, clinical laboratory 
evaluations (hematology, chemistry, and urinalysis), and electrocardiogram (ECG) at 
Screening. 
9.3.2 Exclusion Criteria 
Individuals who meet any of the following exclusion criteria will not be eligible to participate 
in the study: 
1. Use of any investigational product (with the exception of rAvPAL-PEG) or 
investigational medical device within 30 days prior to Screening, or requirement for 
any investigational agent prior to completion of all scheduled study assessments. 
2. Use of any medication other than rAvPAL-PEG that is intended to treat PKU within 
14 days prior to the administration of study drug. 
3. Use or planned use of any injectable drugs containing PEG (other than 
rAvPAL-PEG), including Depo-Provera, within 6 months prior to Screening and 
during study participation. 
4. A prior reaction that included systemic symptoms (eg, generalized hives, respiratory 
or gastrointestinal problems, hypotension, angioedema, anaphylaxis) to rAvPAL-PEG 
or a PEG-containing product. Subjects with a prior systemic reaction may be eligible 
for participation per the discretion of the Principal Investigator in consultation with 
the Sponsor’s Medical Officer. However, subjects who discontinued from study 
treatment early due to a reaction are not eligible to enroll into this study.      
5. Pregnant or breastfeeding at Screening or planning to become pregnant (self or 
partner) or to breastfeed at any time during the study. 
6. Concurrent disease or condition that would interfere with study participation or safety 
(eg, history or presence of clinically significant cardiovascular, pulmonary, hepatic, 
renal, hematologic, gastrointestinal, endocrine, immunologic, dermatologic, 
neurological, oncologic, or psychiatric disease). 
7. Any condition that, in the view of the PI, places the subject at high risk of poor 
treatment compliance or of not completing the study. 
8. Known hypersensitivity to rAvPAL-PEG or its excipients, including hypersensitivity 
reactions that necessitated early termination from a previous rAvPAL-PEG study. 
9. Alanine aminotransferase (ALT) concentration > 2 times the upper limit of normal. 
10. Creatinine > 1.5 times the upper limit of normal. 
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9.3.3 Removal of Subjects from Treatment or Assessment 
Subjects (or their legally authorized representative) may withdraw their consent to participate 
in the study or to receive study drug at any time without prejudice. The Investigator must 
withdraw from the study or study drug treatment any subject who requests to be withdrawn. 
A subject’s participation in the study may be discontinued at any time at the discretion of the 
Investigator and in accordance with his/her clinical judgment. When possible, a subject who 
is discontinued from study treatment should continue to perform the study tests and 
evaluations until study completion. For subjects who discontinue from the study, the tests 
and evaluations listed for the Early Termination Visit should be carried out (refer to 
Section 12.4). 
BioMarin must be notified of all subject withdrawals as soon as possible. BioMarin also 
reserves the right to discontinue the study at any time for either clinical or administrative 
reasons and to discontinue participation by an individual Investigator or site for poor 
enrollment or noncompliance. 
Reasons for which the Investigator or BioMarin may withdraw a subject from the study 
treatment include, but are not limited to, the following: 
• Subject experiences a serious or intolerable adverse event (AE). 
• Subject develops a clinically significant laboratory abnormality. 
• Subject requires medication prohibited by the protocol. 
• Subject becomes pregnant (refer to Section 10.3 for details on the reporting 
procedures to follow in the event of pregnancy). 
Reasons for which the Investigator or BioMarin may withdraw a subject from the study 
include, but are not limited to, the following: 
• Subject does not adhere to study requirements specified in the protocol. 
• Subject was erroneously admitted into the study or does not meet entry criteria. 
• Subject is lost to follow-up. 
If a subject fails to return for scheduled visits, a documented effort must be made to 
determine the reason. If the subject cannot be reached by telephone within 7 days, a certified 
letter should be sent to the subject (or the subject’s legally authorized representative, if 
appropriate) requesting contact with the Investigator. This information should be recorded in 
the study records. 
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The Investigator or designee must explain to each subject, before enrollment into the study, 
that for evaluation of study results, the subject’s protected health information obtained during 
the study may be shared with the study sponsor, regulatory agencies, and IRB. It is the 
Investigator’s (or designee’s) responsibility to obtain written permission to use protected 
health information per country-specific regulations, such as the Health Insurance Portability 
and Accountability Act (HIPAA) in the United States, from each subject, or if appropriate, 
the subject’s legally authorized representative. If permission to use protected health 
information is withdrawn, it is the Investigator’s responsibility to obtain a written request, to 
ensure that no further data will be collected from the subject and the subject will be removed 
from the study. 
9.3.4 Subject Identification and Replacement of Subjects 
Subjects will retain the same subject number assigned in their previous rAvPAL-PEG study. 
This unique identifier will be on all case report form (CRF) pages. In legal jurisdictions 
where use of initials is not permitted, a substitute identifier will be used.  
Subjects who do not complete the study will not be replaced. 
9.4 
Treatments 
Upon enrollment into this study, subjects from previous rAvPAL-PEG studies will be dosed 
with the same or higher dose that was administered upon completion of that study provided 
that there was no interruption in dosing.  rAvPAL-PEG doses will be administered SC by 
either health care professionals or via self administration. The dose level may be increased 
per Investigator determination based on available information regarding a subject’s blood 
Phe level (60-600 µmol/L), as well as any adverse events (any hypersensitivity reaction) for 
an individual subject. The dosage that provides control of blood Phe concentrations within 
the target range of 60-600 µmol/L for a minimum of 2 weeks will be determined for each 
subject by adjusting the dose level, dose frequency, or both, per the PI, based upon the 
subject’s response to doses.  
Subjects may self administer study drug at home if approved by the Investigator and the 
Sponsor’s Medical Officer and if adequate training is demonstrated. Subjects may be eligible 
to self administer study drug if he or she meets the following criteria:  
• The subject is on a stable dosing regimen for 2 weeks (ie, the subject has 
demonstrated a blood Phe level within 60-600 µmol/L). 
• The subject has not experienced any CTCAE Grade 3 or higher adverse event.  
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• The subject has not experienced any hypersensitivity reaction to rAvPAL-PEG for at 
least 4 weeks. 
• The subject has no cognitive impairments that may increase the safety risk of self 
administration per the assessment of the PI.  
• The subject has been approved for self administration of study drug by the Sponsor’s 
Medical Officer. 
• The subject has completed the Self-Administration Training conducted by qualified 
study site personnel and has been observed by the study site personnel to be able to 
adequately prepare the proper dose and perform the injections safely.  
• The subject has been provided with epinephrine and has been trained on when and 
how to administer it.  
Qualified study site personnel will train each eligible subject on all procedures for self 
administration of study drug under the supervision of the PI. Qualified study site personnel 
will also be required to observe the subject prepare and perform at least 1 injection prior to 
allowing the subject to self administer a dose at home. The subject will see a study site nurse 
or home healthcare nurse in person every week or receive a telephone call from site staff to 
ensure that the subject continues to perform all self-administration procedures correctly, to 
assess adverse events, and to answer questions throughout the duration of the study. The 
study site nurse or home healthcare nurse will also perform the regularly scheduled 
assessments and procedures as outlined in Table 9.1.1 and Section 12; the subject must 
perform a clinic visit monthly at minimum. Training materials and other information specific 
to the study site personnel are provided in the Subject Self-Administration Training 
Materials.     
Subjects who are eligible for self administration will be provided with a Subject Study 
Manual. Self-administration training materials will be provided in the Subject Study Manual 
to supplement the in-person training provided by the qualified study site personnel. The 
Subject Study Manual will include step-by-step instruction on the following: 
• How to prepare and perform the injections of study drug safely. 
• How to receive, track, store, prepare, and return both used and unused study drug.   
• How to safely use and dispose of syringes used for injections of study drug. 
• How to use a new syringe and vial every time drug is administered. 
• How to care for their injection site after an injection of study drug.  
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• How to identify an adverse reaction and how to report this reaction to the study site.  
• How and when to use epinephrine. 
• Who to contact at the study site in case of an emergency.  
The PI or the Sponsor’s Medical Officer may request that self administration be halted at any 
time and that the subject resume injections performed by the study site personnel or home 
healthcare nurse. 
Subjects who are within the target Phe range may also be permitted to convert from 
weight-based dosing to fixed dosing (refer to Section 9.4.4). 
9.4.1 Treatments Administered 
BioMarin and/or its designee will provide the study site or subject with a supply of IP 
sufficient for the completion of the study. BioMarin is responsible for shipping study drug to 
the clinical sites. The clinical site is responsible for supplying the study drug to subjects who 
qualify for self administration. Refer to the PAL-003 Pharmacy Manual for information 
pertaining to the distribution of study drug from sites.   
Information regarding supplying study drug to subjects who qualify for self administration is 
provided in the Subject Self-Administration Training Materials. 
9.4.2 Identity of Investigational Product (IP) 
9.4.2.1 
Product Characteristics and Labeling 
The investigational product is rAvPAL-PEG (recombinant Anabaena variabilis phenylalanine 
ammonia lyase-PEG). rAvPAL-PEG will be provided in vials or prefilled syringes; subjects 
will be supplied with vials and syringes or prefilled syringes for administration in the clinic 
and self administration: 
• rAvPAL-PEG will be provided in 3 mL (milliliter) vials, each containing 1.5 ± 
0.2 mL to deliver 15 mg of rAvPAL-PEG per 1.0 mL (15 mg/mL protein 
concentration). Each vial is filled with 1.5 ± 0.2 mL to allow the withdrawal and 
delivery of up to 1.0 mL of the drug product. 
Or 
 
• 
rAvPAL-PEG will be provided in 3-mL vials, each containing 1.8 ±0.3 mL to deliver 20 mg 
of rAvPAL-PE per 1.3 mL (15 mg/mL protein concentration). Each vial is filled with 1.8 ± 
0.3 mL to allow withdrawal and delivery of up to 1.3 mL. 
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Or 
 
• rAvPAL-PEG will be provided in prefilled syringes in three sizes that deliver up to 
1 mL. Syringe sizes are 2.5 mg (5 mg/mL protein concentration), 10 mg (20 mg/mL 
protein concentration), and 20 mg (20 mg/mL protein concentration). 
 
Prefilled Syringe 
Volume 
Concentration 
Dose 
Sku #1 
0.5 mL 
5 mg/mL 
2.5 mg 
Sku #2 
0.5 mL 
20 mg/mL 
10 mg 
Sku #3 
1.0 mL 
20 mg/mL 
20 mg 
 
The excipients in this drug product are tromethamine, tromethamine-hydrochloride, sodium 
chloride, L-phenylalanine, and water for injection. 
Drug product packaging will be identified with the lot number and expiration date, and will 
be provided in a box labeled with the study number. 
9.4.3 Storage 
IP must be stored at 5 ±3°C (41 ± 5°F) under the conditions specified in the IB. At the 
site, the IP will be stored in a secure area accessible only to the designated pharmacists and 
clinical site personnel. All IP must be stored and inventoried and the inventories must be 
carefully and accurately documented according to applicable state, federal and local 
regulations, ICH GCP, and study procedures. 
Specific instructions for storage of study drug for subjects who qualify for self administration 
are provided in the Subject Self-Administration Training Materials.  
9.4.4 Directions for Administration 
Doses will be administered SC and the favorable dose will be determined for each subject by 
adjusting the dose level, dose frequency, or both, per the PI, based upon the subject’s 
response to doses. Dosing is up to a maximum dose per week of 5.0 mg/kg (or 375 mg for 
subjects receiving a fixed dose).  
For subjects receiving weight-based dosing, dosage is calculated by multiplying each 
subject’s weight in kilograms (kg) on Day 1 (predose) by the assigned dose (in mg/kg). 
During the study, if the weight of a subject changes more than 10% from the measurement 
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obtained at baseline or at a previous measurement, the subject’s dose may be adjusted to 
accommodate the change. The change must be recorded. Refer to the Pharmacy Manual for 
additional information on calculating dosage. 
Subjects who have demonstrated efficacy (as measured by blood Phe within the target range 
of 60-600 µmol/L for at least 2 consecutive measurements) and who have maintained a stable 
rAvPAL-PEG dose for at least 2 consecutive measurements may be eligible to transition 
from weight-based dosing to a fixed dosing regimen that would permit daily dosing (5- or 
7-days-per-week).  Subjects who convert to a fixed-dosing regimen should convert their dose 
based upon the information presented in Table 9.4.4.1. 
Table 9.4.4.1:  Fixed Doses for Subjects on Weight-Based Dose Regimen 
Weight-based 
dose (mg/kg) 
Equivalent 
fixed dose 
(mg) 
Vol for 10 
mg/ml 
concentration 
(ml) (vial) 
Vol for 15 
mg/ml 
concentration 
(ml) (vial)a 
0.03 
2.5 
0.25 
0.17 
0.06 
5 
0.5 
0.33 
0.12 
10 
1 
0.67 
0.25 
20 
2 
1.33 
0.5 
40 
4 
2.67 
1.0 
75 
7.5 
5 
2.0 
150 
15 
10 
3.0 
225 
22.5 
15 
4.0 
300 
30 
20 
5.0 
375 
37.5 
25 
a Applies to both 1.0 and 1.3 ml withdrawal. 
 
It is preferable that the injection sites should be alternated between doses, ie, upper left arm 
in Week 1, upper right arm in Week 2, etc. Doses may be administered in any of the common 
SC areas (upper arm, thigh, abdomen). If dose volume is such that a dose will be divided and 
given in more than 1 injection site, it is preferable to use both arms, both legs, or both sides 
of the abdomen. 
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Subjects may require more than 1 injection per dose, depending upon site policy (ie, some 
institutions do not permit a single SC injection of greater than 2 mL). The number of 
injections required for an individual weighing 80 kg (about 176 pounds) is provided in 
Table 9.4.4.2 as an example. Note this table is for example purposes only. Dosage 
calculations must be performed according to study drug preparation instructions provided in 
the PAL-003 Pharmacy Manual. Study drug will be administered by clinic staff, other 
qualified and trained study personnel, or qualified subjects. 
Information for dosing of subjects who enroll into this study after completing previous 
rAvPAL studies is provided in Section 9.1. Instructions for subjects who re-start 
rAvPAL-PEG dosing due to unplanned missed doses are provided in Section 9.4.10.  
Instructions for administration of study drug for subjects who qualify for self administration 
are provided in the Subject Self-Administration Training Materials. 
Table 9.4.4.2:  Example of Number of Injections Required For an Individual Weighing 
80 kg 
Dose Group 
(mg/kg) 
Weight 
(kg) 
Volume of Study Drug 
(mL)a 
No. of 
Injectionsb 
0.001 
80 
0.8 
1 
0.003 
80 
0.6 
1 
0.01 
80 
0.8 
1 
0.03 
80 
0.2 
1 
0.06 
80 
0.5 
1 
0.1 
80 
0.8 
1 
0.3 
80 
2.4 
2 
0.6 
80 
4.8 
2 or 3 
1.0 
80 
8.0 
4 
aStudy drug is supplied at a concentration of 10 mg/mL and is then diluted (where necessary for injection) by 
differential amounts as specified in the PAL-003 Pharmacy Manual. Volume to be injected is calculated based 
on a starting volume. 
bNumber of injections per dose is dependent upon site policy for SC injections. The number of injections may 
vary at the discretion of the Investigator. 
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Every effort should be made to adhere to the study drug administration regimen. If a subject 
misses more than 2 scheduled doses of study drug, both dose level and dose frequency may 
need to be re-evaluated (refer to Section 9.4.10). 
9.4.5 Method of Assigning Subjects to Treatment Groups 
This will be an open-label study; no randomization schedule will be generated. 
Subjects will retain the same subject number used in their previous rAvPAL-PEG study. 
9.4.6 Selection of Doses Used in the Study 
This Phase 2 study aims to evaluate the efficacy, safety, tolerability, and PK parameters of 
multiple doses of rAvPAL-PEG after long-term administration in subjects with PKU. A dose 
that produces a reduction in blood Phe concentrations to 60-600 μmol/L will be determined 
for each subject based on preliminary safety, antibody, and efficacy data from this ongoing 
study. 
9.4.6.1 
Selection of Timing of Dose for Each Subject 
Study drug will be administered by clinic staff or other qualified and trained study personnel. 
Subjects may self administer study drug at home if approved by the Sponsor’s Medical 
Officer and if adequate training is provided (refer to Section 9.4). 
9.4.7 Blinding 
This is an open-label study. 
9.4.8 Prior and Concomitant Medications 
All prescription and over-the-counter (OTC) medications taken by a subject for 30 days 
before Screening will be recorded on the designated CRF. The Investigator may prescribe 
additional medications during the study, as long as the prescribed medication is not 
prohibited by the protocol. In the event of an emergency, any needed medications may be 
prescribed without prior approval, but the Sponsor’s Medical Officer must be notified of the 
use of any contraindicated medications immediately thereafter. Any concomitant medications 
added or discontinued during the study should be recorded on the CRF. 
Use of any investigational product (with the exception of rAvPAL-PEG used in a previous 
rAvPAL-PEG study) or investigational medical device within 30 days before Screening, or 
requirement for any investigational agent prior to completion of all scheduled study 
assessments, is prohibited. 
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Use or planned use of any injectable drugs containing PEG (other than rAvPAL-PEG), 
including Depo-Provera, is prohibited within 6 months prior to Screening and during study 
participation. A list of PEG-containing injectable drugs is provided in the study reference 
materials. Subjects who have had a prior local skin reaction to rAvPAL-PEG or a 
PEG-containing product will be encouraged to be premedicate with acetaminophen and/or 
non-sedating antihistamines (refer to Section 9.1.1). If the local skin reaction worsens with a 
repeat injection (as determined by the Investigator in consultation with the Sponsor’s 
Medical Officer) even with premedication prior to study drug dosing, the subject must be 
withdrawn from the study and complete an Early Termination Visit. 
Subjects who have had a prior systemic reaction to rAvPAL-PEG or a PEG-containing 
product may participate in this study (refer to Section 9.1.1).  
Use of any medication that is intended to treat PKU within 14 days prior to the 
administration of study drug is prohibited. 
9.4.9 Treatment Compliance 
The date, time, volume, and concentration of each dose of study drug administered to each 
subject must be recorded in the dispensing log provided for the study, as well as on the 
appropriate CRF. This data will be used to assess treatment compliance. 
9.4.10 Dose Interruption and Missed Doses  
Information for dosing of subjects who enroll into this study after completing previous 
rAvPAL-PEG studies is provided in Section 9.1.  
During this long-term extension study, interruption of rAvPAL-PEG dosing may occur per 
subject decision or per the Investigator. Subjects who miss more than 2 consecutive weekly 
doses (weekly dosing schedule) or 3 consecutive daily doses (daily dosing schedule) for 
whatever reason may continue participation in this study. After a dosing interruption, 
rAvPAL-PEG administration should be re-started at the same dose level and dosing 
frequency that was administered prior to the dosing interruption. The first dose of 
rAvPAL-PEG following a dose interruption should be administered in a clinic setting, and 
the subject must be observed for 30 minutes following administration due to restarting 
dosing. A follow-up telephone call will be made to the subject to monitor subject safety 
24 hours following the return to dosing. Subjects should continue to perform the study 
assessments as outlined in the Schedule of Events (refer to Table 9.1.1 during any dosing 
interruption.  
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Subjects who miss rAvPAL-PEG dosing due to poor compliance may be discontinued from 
further study treatment per discretion of the Sponsor or Investigator (refer to Section 9.3.3).  
9.5 
Investigational Product Accountability 
The PI or designee is responsible for maintaining accurate records (including dates and 
quantities) of IP received, subjects to whom IP is dispensed (subject-by-subject dose specific 
accounting), IP returned, and IP lost or accidentally or deliberately destroyed. The PI or 
designee must retain all unused or expired study supplies until the study monitor (on-site 
CRA) has confirmed the accountability data. 
9.5.1 Return and Disposition of Clinical Supplies 
Unused study drug must be kept in a secure location for accountability and reconciliation by 
the study monitor. The Investigator or designee must provide an explanation for any 
destroyed or missing study drug or study materials. 
Unused study drug may be destroyed on site, per the site’s standard operating procedures, but 
only after BioMarin has granted approval for drug destruction. The monitor must account for 
all study drug in a formal reconciliation process prior to study drug destruction. All study 
drug destroyed on site must be documented. Documentation must be provided to BioMarin 
and retained in the PIs study files. If a site is unable to destroy study drug appropriately, the 
site can return unused study drug to BioMarin upon request. The return of study drug or 
study drug materials must be accounted for on a Study Drug Return Form provided by 
BioMarin. 
Subjects who qualify for self administration of study drug will be provided with instructions 
for returning used and unused study drug and the proper disposal of any study drug materials 
(refer to the Subject Self-Administration Training Materials). 
All study drug and related materials should be stored, inventoried, reconciled, and destroyed 
or returned according to applicable state and federal regulations and study procedures. 
9.6 
Dietary or Other Protocol Restrictions 
Subjects will be instructed that diet should not be altered during the course of the study. Any 
decision to modify subject diet must be made per the Investigator and must be performed 
under the supervision of the Investigator. 
A 3-day dietary record will be completed by subjects and will be brought to clinic visits for 
review with clinic staff. It is preferable that subjects complete the 3-day record immediately 
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prior to their next monthly study visit.The dietary record will be maintained with the study 
source documents. Information regarding a subject diet diary is provided in Section 9.7.4. 
9.7 
Efficacy and Safety Variables 
9.7.1 Efficacy and Safety Measurements Assessed 
The Schedules of Events in the Synopsis describe the timing of required evaluations. 
For the laboratory assessments, the party responsible for performing the assessment and the 
pertinent protocol section describing the details of the test are listed in Table 9.7.1.1. 
Table 9.7.1.1:  Summary of Laboratory Assessments 
Laboratory Assessment 
Party Responsible for 
Performing Test 
Section in Protocol for 
Details 
Clinical laboratory tests 
Central laboratory 
9.7.6 
Antibody testing 
BioMarina 
9.7.5.2 
PK variables 
BioMarin 
9.7.3 
Blood Phe concentrations 
Central laboratory 
9.7.2.1 
Pregnancy test (urine) and 
sedimentation rate 
Local laboratory 
9.7.6, 9.7.5.1 
Urinalysis 
Central laboratory 
9.7.6 
Phe, phenylalanine; PK, pharmacokinetic. 
aAnalysis of the anti-rAvPAL-PEG IgE assay will be performed by a Contract Research Organization. 
 
9.7.1.1 
Demographic Data and Medical History 
Demographic data and a detailed medical history, including allergy history, will be obtained 
at Screening. The medical history will include specific information concerning any prior or 
existing medical conditions that might interfere with study participation or safety. 
This medical history should elicit all major illnesses, diagnoses, and surgeries that the subject 
has ever had, and whether the subject has a history of alcohol and/or drug abuse. 
9.7.1.2 
Physical Examination Findings 
Physical examination will include assessment of general appearance; CV; dermatologic; 
head, eyes, ears, nose, and throat; lymphatic; respiratory; GI; musculoskeletal; and 
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neurological/psychological. Other body systems may be examined. Day 1 results will be the 
baseline values and clinically significant changes from baseline will be recorded as an AE. 
9.7.1.3 
Vital Sign Measurements 
Vital signs will be measured after resting for 5 minutes, and include seated systolic blood 
pressure (SBP) and diastolic blood pressure (DBP) measured in millimeters of mercury 
(mm Hg), heart rate in beats per minute, respiration rate in breaths per minute, and 
temperature in degrees Celsius (°C). Height (cm) will be measured at Screening only.  
Weight will be measured at Screening and then monthly. 
9.7.1.4 
Electrocardiography 
A standard 12-lead ECG will be recorded while the subject is resting, at Screening and at the 
Final Follow-Up (F/U) Visit or Early Termination Visit (ETV). If clinically significant 
abnormalities are noted at Screening, the PI or designee is required to assess whether it is 
appropriate for the subject to enroll in the study. 
9.7.1.5 
Chest X-Ray 
A chest X-ray will be performed at the Screening, Week 48, and Final Follow-Up (or Early 
Termination) visits to assess gross pulmonary health.  
9.7.2 Efficacy Variable 
9.7.2.1 
Blood Phenylalanine Concentrations 
Blood samples for Phe concentration measurements will be drawn monthly, at least 2.5 hours 
after a meal, on the days and time points indicated in the Schedule of Events (Table 9.1.1).   
Blood Phe may be collected more often than monthly at the discretion of the Investigator 
should more frequent monitoring of blood Phe levels be clinically required. 
A central laboratory will be used for blood Phe concentration analysis. 
9.7.3 Pharmacokinetic Variables 
Subjects enrolled in the Substudy will have additional PK sampling performed. For subjects 
participating in the Substudy, PK sampling will be performed as follows: 
• For subjects who are administered rAvPAL-PEG once per week, plasma PK sampling 
will be performed pre-dose and every 24 hours thereafter (24, 48, 72, and 96 hours if 
possible), and then pre-dose of the next weekly dose. 
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• For subjects who are administered rAvPAL-PEG two or three times per week, plasma 
PK sampling will be performed pre-dose and every 24 hours during the longest period 
between doses, when possible, and then pre-dose of the next dose.  
• For subjects who are administered rAvPAL-PEG four to seven times per week, 
plasma PK sampling will be performed pre-dose and every 12 hours during the 
longest period between doses, when possible, and then pre-dose of the next dose. 
See Table 9.1.2 for additional details. 
BioMarin will perform the analysis. 
9.7.4 Exploratory Efficacy Variable 
Diet will be assessed for its role in blood Phe reduction relative to rAvPAL-PEG dosing 
using a 3-day diet diary, which will be given to subjects to complete at home. Subjects will 
bring the completed diary with them to clinic visits on a monthly basis. Subjects will be 
instructed to record all food, beverages, special low-protein foods, and medical foods 
consumed for 3 consecutive days each month. If changes in diet are noted per the information 
on the diet diary, the subject will be instructed to maintain their diet as reported at the 
beginning of the study or as otherwise instructed by the Investigator. 
9.7.5 Safety Variables 
9.7.5.1 
Pregnancy Testing 
Female subjects of childbearing potential will have a urine pregnancy test at the time points 
specified in the Schedules of Events (Table 9.1.1). Female subjects with a positive serum 
pregnancy test at Screening do not meet eligibility criteria for enrollment. 
Additional pregnancy tests will be performed at any visit in which pregnancy status is in 
question. Serum pregnancy tests will be performed in the event of a positive or equivocal 
urine pregnancy test result. 
Refer to Section 10.4 for details on the reporting procedures to follow in the event of 
pregnancy. 
9.7.5.2 
Antibody Testing 
Immunogenicity will be assessed by determining immune response and neutralizing activity 
with the following measurements: anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, anti-PEG 
IgM, anti-rAvPAL-PEG IgE, and anti-rAvPAL-PEG neutralizing antibodies (refer to  
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Section 9.1.1.3.3). Immunogenicity assays will be performed at the time points indicated in the 
Schedule of Events (Table 9.1.1). 
BioMarin will perform all anti-body testing, except for IgE antibodies, which will be 
assessed by a Contract Research Organization. 
9.7.6 Clinical Laboratory Assessments 
Any abnormal test results determined to be clinically significant by the Investigator should 
be repeated (at the Investigator’s discretion) until the cause of the abnormality is determined, 
the value returns to baseline or to within normal limits, or the Investigator determines that the 
abnormal value is no longer clinically significant. 
All abnormal clinical laboratory result pages should be initialed and dated by an Investigator, 
along with a comment regarding whether or not the abnormal result is clinically significant. 
The diagnosis, if known, associated with abnormalities in clinical laboratory tests that are 
considered clinically significant by the Investigator will be recorded on the AE CRF. 
Table 9.7.6.1:  Clinical Laboratory Tests 
Blood Chemistry 
Hematology 
Urine Testsa 
Other 
Albumin  
Hemoglobin  
Appearance 
Pregnancy test, if 
applicablea 
Alkaline 
Phosphatase  
Hematocrit  
Color 
ALT (SGPT)  
WBC count 
pH 
Phenylalanine 
AST (SGOT) 
RBC count 
Specific gravity 
Tyrosine 
Total bilirubin 
Platelet count 
Ketones 
Sedimentation ratea 
BUN 
Differential cell count 
Protein 
Creatinine 
 
Glucose 
GGT 
 
Spot urine 
albumin/creatinine 
ratio  
Additional 
Unscheduled 
Hypersensitivity 
Reaction Visit Testsb 
Total protein 
 
Nitrite 
CH50 
Calcium 
 
Urobilinogen 
C1, C3, C4
 
Sodium 
 
Hemoglobin 
Serum tryptase levelb  
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Blood Chemistry 
Hematology 
Urine Testsa 
Other 
Potassium 
 
Bilirubin 
CRP  
Glucose 
 
 
Urine N-methyl 
histamine 
 
 
Urine albumin/creatinine 
ratio 
Uric acid 
 
 
Complement Testingc 
CO2 
 
 
C3 
Chloride 
 
 
C4 
ALT, alanine aminotransferase; AST, aspartate aminotransferase; BUN, blood urea nitrogen; C, complement; 
CH50, total hemolytic complement; CO2, carbon dioxide; CRP, C-reactive protein; GGT, 
gamma-glutamyltransferase; RBC, red blood cell; SGOT, serum glutamic-oxaloacetic transaminase; SGPT, 
serum glutamic-pyruvic transaminase; WBC, white blood cell. 
a To be performed by central laboratory. If urine pregnancy test is positive or equivocal, serum sample will be 
taken and assessed by a central laboratory. 
b Perform immediately after reaction if possible. 
c  Complement C3 and C4 to be drawn at the Screening Visit and then quarterly or as needed to resolve abnormal 
test results. 
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10 
REPORTING ADVERSE EVENTS 
10.1 
Adverse Events 
For this protocol, a reportable adverse event (AE) is any untoward medical occurrence (e.g., 
sign, symptom, illness, disease or injury) in a subject administered the study-drug or other 
protocol-imposed intervention, regardless of attribution. This includes the following: 
• AEs not previously observed in the subject that emerge during the course of the 
study. 
• Pre-existing medical conditions judged by the Investigator to have worsened in 
severity or frequency or changed in character during the study. 
• Complications that occur as a result of non-drug protocol-imposed interventions 
(eg, AEs related to screening procedures, medication washout, or no-treatment run-
in). 
An adverse drug reaction is any AE for which there is a reasonable possibility that the study 
drug caused the AE. “Reasonable possibility” means there is evidence to suggest a causal 
relationship between the study-drug and the AE. 
Whenever possible, it is preferable to record a diagnosis as the AE term rather than a series 
of terms relating to a diagnosis. 
The study period during which all non-serious AEs and SAEs will be reported begins after 
informed consent is obtained and the first administration of study drug  and continues until 
4 weeks following the last administration of study drug or the last visit of the treatment 
period (refer to Section 12). After informed consent but prior to initiation of study treatment, 
only SAEs associated with any protocol-imposed interventions will be reported. The criteria 
for determining, and the reporting of SAEs is provided in Section 10.2.   
The Investigator should follow all unresolved AEs until the events are resolved or stabilized, 
the subject is lost to follow-up, or it has been determined that the study treatment or study 
participation is not the cause of the AE. Outcome of AEs (and resolution dates) should be 
documented on the appropriate CRF page(s) and in the subject’s medical record unless the 
subject is lost to follow-up or it has been determined that the study treatment or study 
participation is not the cause of the AE. 
The Investigator responsible for the care of the subject or qualified designee will assess AEs 
for severity, relationship to study-drug, and seriousness (see Section 10.2 for SAE 
definition). Severity (as in mild, moderate or severe headache) is not equivalent to 
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seriousness, which is based on subject/event outcome or action criteria usually associated 
with events that pose a threat to a subject’s life or functioning. Seriousness (not severity) 
serves as a guide for defining regulatory reporting obligations. 
The Investigator will determine the severity of each AE using the National Cancer Institute 
(NCI) Common Terminology Criteria for Adverse Events (CTCAE) v4. Adverse events that 
do not have a corresponding CTCAE term will be assessed according to the general 
guidelines for grading used in the CTCAE v4 as stated below. 
Grade 
Description 
1 
Mild: asymptomatic or mild symptoms; clinical or diagnostic 
observations only; intervention not indicated 
2 
Moderate: minimal, local or noninvasive intervention 
indicated; limiting age-appropriate instrumental activities of 
daily living (ADL)a 
3 
Severe or medically significant but not immediately life-
threatening: hospitalization or prolongation of hospitalization 
indicated; disabling; limiting self care activities of daily 
living (ADL) 
4 
Life threatening or debilitating: consequences; urgent 
intervention indicatedb 
5 
Death related to AE 
Grade 4 and 5 AEs should always be reported as SAEs. 
a Instrumental ADL refer to the following examples: preparing meals, shopping for groceries or clothes, using 
the telephone, managing money. 
b Self care ADL refer to the following examples: bathing, dressing and undressing, feeding oneself, using the 
toilet, taking medications, not bedridden. 
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The Investigator will determine the relationship of an AE to the study drug and will record it 
on the source documents and AE CRF, using the categories defined below. 
Relationship 
Description 
Not Related 
Exposure to the IP has not occurred 
OR 
The administration of the IP and the occurrence of the AE are not 
reasonably related in time  
OR 
The AE is considered likely to be related to an etiology other than the use 
of the IP; that is, there are no facts [evidence] or arguments to suggest a 
causal relationship to the IP. 
Possibly 
Related 
The administration of the IP and the occurrence of the AE are reasonably 
related in time 
AND 
The AE could be explained equally well by factors or causes other than 
exposure to the IP. 
Probably 
Related 
The administration of IP and the occurrence of the AE are reasonably 
related in time  
AND 
The AE is more likely explained by exposure to the IP than by other factors 
or causes. 
In order to classify AEs and diseases, preferred terms will be assigned by the sponsor to the original terms 
entered on the CRF, using MedDRA (Medical Dictionary for Regulatory Activities terminology). 
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10.2 
Serious Adverse Events 
A serious adverse event (SAE) is any untoward medical occurrence that at any dose meets 1 
or more of the following criteria: 
• Is fatal. 
• Is life threatening. 
o Note: Life-threatening refers to an event that places the subject at 
immediate risk of death. This definition does not include a reaction that, 
had it occurred in a more severe form, might have caused death. 
• Requires or prolongs inpatient hospitalization. 
• Results in persistent or significant disability or incapacity. 
• Is a congenital anomaly or birth defect in the child or fetus of a subject exposed to IP 
prior to conception or during pregnancy. 
• Is an important medical event or reaction. 
The reporting period for SAEs begins after informed consent is obtained, and continues until 
4 weeks following the last administration of study drug or End of Treatment Visit. 
All SAEs, whether or not considered related to study drug, must be reported within 24 hours 
of the site becoming aware of the event by faxing the study-specific SAE Report Form to 
BioMarin Pharmacovigilance (BPV). Each SAE must also be reported in the CRF 
Investigators should not wait to collect information that fully documents the event before 
notifying BPV of a SAE. BioMarin may be required to report certain SAEs to regulatory 
authorities within 7 calendar days of being notified about the event; therefore, it is important 
that Investigators submit any information requested by BioMarin as soon as it becomes 
available.  The Investigator should follow all unresolved SAEs until the events are resolved 
or stabilized, the subject is lost to follow-up, or it has been determined that the study 
treatment or participation is not the cause of the AE. Resolution of AEs (with dates) should 
be documented in the CRF and in the subject’s medical record. 
For some SAEs, the Sponsor may follow up by telephone, fax, electronic mail, and/or a 
monitoring visit to obtain additional case details deemed necessary to appropriately evaluate 
the SAE report (e.g., hospital discharge summary, consultant report, or autopsy report). 
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At the last scheduled visit, the Investigator should instruct each subject to report any 
subsequent SAEs that the subject’s personal physician(s) believes might be related to prior 
study treatment. 
The Investigator should notify the study Sponsor of any death or SAE occurring at any time 
after a subject has discontinued or terminated study participation if felt to be related to prior 
study treatment. The Sponsor should also be notified if the Investigator should become aware 
of the development of cancer or of a congenital anomaly in a subsequently conceived 
offspring of a subject that participated in this study.  
Reporting of SAEs to the IRB will be done in compliance with the standard operating 
procedures and policies of the IRB and with applicable regulatory requirements. Adequate 
documentation must be obtained by BioMarin showing that the IRB was properly and 
promptly notified as required. 
10.3 
Pregnancy 
Pregnancy in a subject or partner should be reported within 24 hours of the site becoming 
aware of the pregnancy to BioMarin Pharmacovigilance by fax using the Pregnancy Form in 
the study reference materials. The reporting period for pregnancies begins with informed 
consent and continues until 4 weeks following the last study drug dose. In addition, 
pregnancy in a subject is also reported on the End of Study CRF. The Investigator must make 
every effort to follow the subject through resolution of the pregnancy (delivery or 
termination) and to report the resolution to BPV in the study reference materials. In the event 
of pregnancy in the partner of a study subject, the Investigator should make every reasonable 
attempt to obtain the woman’s consent for release of protected health information. 
10.4 
Urgent Safety Measures 
The regulations governing clinical trials state that the sponsor and Investigator are required to 
take appropriate urgent safety measures to protect subjects against any immediate hazards 
that may affect the safety of subjects, and that the appropriate regulatory bodies should be 
notified according to their respective regulations. According to the European Union (EU) 
Clinical Trial Directive 2001/20/EC, “…in the light of the circumstances, notably the 
occurrence of any new event relating to the conduct of the trial or the development of the 
investigational medicinal product where that new event is likely to affect the safety of the 
subjects, the sponsor and the Investigator shall take appropriate urgent safety measures to 
protect the subjects against any immediate hazard. The sponsor shall forthwith inform the 
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competent authorities of those new events and the measures taken and shall ensure that the 
IRB/EC/REB is notified at the same time.” The reporting period for these events which may 
require the implementation of urgent safety measures is the period from the time of signing 
of the ICF through the completion of the last study visit or at the ETV. Investigators are 
required to report any events which may require the implementation of urgent safety 
measures to BioMarin with 24 hours. 
Examples of situations that may require urgent safety measures include discovery of the 
following: 
• Immediate need to revise the IP administration (i.e., modified dose amount or 
frequency not defined in protocol). 
• Lack of study scientific value, or detrimental study conduct or management. 
• Discovery that the quality or safety of the IP does not meet established safety 
requirements. 
 
10.5 
BioMarin Pharmacovigilance Contact Information 
Contact information for BioMarin Pharmacovigilance is as follows: 
BioMarin Pharmaceutical Inc. 
Address 
105 Digital Drive 
 
 
Novato, CA 94949 
Phone:  
(415) 506-6179 
Fax: 
 
(415) 532-3144 
E-mail: 
drugsafety@bmrn.com 
The Investigator is encouraged to discuss with the Sponsor’s Medical Officer any AEs for 
which the issue of seriousness is unclear or questioned. Contact information for the 
Sponsor’s Medical Officer is as follows: 
Name:  
, MD 
Address: 
105 Digital Drive 
 
 
Novato, CA 94949 USA 
Phone:  
 
Fax: 
 
 
E-mail: 
 
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11 
APPROPRIATENESS OF MEASUREMENTS 
11.1 
Safety and Pharmacokinetics 
The PK and safety assessments in this study are used widely and are generally recognized as 
reliable, accurate, and relevant. 
11.2 
Diet Diary 
A 3-day diet diary will be issued to subjects for completion and will be brought to clinic on a 
monthly basis for review with the clinical study staff. Additional information regarding the 
diet diary is provided in Section 7.3, and information regarding administration of the diary is 
provided in Section 9.7.4. Additional information about diet is provided in Section 9.1 and 
Section 9.6. 
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12 
STUDY PROCEDURES 
12.1 
Prestudy 
An ICF must be signed and dated by the subject (or the subject’s legally authorized 
representative if the subject is less than 18 years of age), the PI or designee and witness 
(if required) before any study-related procedures are performed. 
12.2 
Screening Visit 
After subjects have signed an ICF, they will be screened for enrollment into the study. 
The following study activities will be performed at Screening: 
• Medical history, including allergy history, and demographics 
• Physical examination  
• Vital signs, including height and weight 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.).  For safety reasons, 
this test must be performed prior to the chest X-ray. 
• Chest X-ray 
• 12-lead ECG 
• Clinical laboratory tests (including spot urine albumin/creatinine ratio, hematology, 
chemistry, and urinalysis) 
• Complement C3 and C4 
• Assessment of SAEs 
• Concomitant medications 
• Diet query 
• Blood Phe and plasma tyrosine concentration 
For subjects who participated in a previous rAvPAL-PEG study, these assessments may be 
the same as those used for the last visit of the previous study, if they occur within 28 days 
from Day 1. 
12.3 
Treatment Period 
During the Treatment Period, additional visits may occur if deemed necessary to monitor 
AEs or blood Phe concentrations. All study activities will occur on the first day of each week 
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unless otherwise noted. On days that a dose is given, assessments will be done predose unless 
otherwise specified. Subjects must have AEs and concomitant medications assessed and an 
injection-site inspection performed whenever dose is administered even if the administration 
does not coincide with a scheduled clinic visit.   
If the dose is modified by increasing dose level, additional blood Phe concentration testing 
should be done daily for 3 days following dose adjustment. If dose is modified by increasing 
either dose frequency or dose level, additional blood Phe concentration testing should be 
done prior to each dose for the first 2 weeks following dose adjustment. 
12.3.1 Day 1 (Week 1) 
Within 28 days of completing screening assessments, the following study activities will be 
performed on Day 1: 
• Physical examination 
• Vital signs 
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• Injection-site inspection (postdose) 
• Assessment of SAEs (predose and postdose) and all AEs (postdose) 
• Concomitant medications 
• Diet query 
• PK sample 
• Blood Phe and plasma tyrosine concentration 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, and anti-rAvPAL-PEG neutralizing antibodies) 
• Administer study drug (study drug may be administered on additional days during the 
week as determined by the Investigator) 
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12.3.2 Weekly Telephone Visit 
Subjects should have a weekly telephone visit conducted. Subjects must still come into the 
clinic for the scheduled monthly visits per Table 9.1.1. The following should be discussed 
with the subject during the weekly telephone visit: 
• Injection-site self inspection (previous and current injection site) 
• Assessment of AEs 
• Concomitant medications 
• Confirmation of dose level, frequency, and study drug administration 
12.3.3 Substudy Visits 
For subjects participating in the PK substudy, refer to Section 9.7.3 and Table 9.1.2. 
12.3.4 Monthly Visits (Week 4, 8, 12, etc) 
Subjects must have AEs and concomitant medications assessed and an injection-site 
inspection performed whenever dose is administered even if the administration does not 
coincide with a scheduled clinic visit.    
Beginning with Week 4, monthly visits must be performed in the clinic. The following study 
activities will be performed: 
• Vital signs 
• Weight 
• Clinical laboratory tests 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) For safety reasons, this 
test must be performed prior to the chest X-ray. 
• Chest x-ray (Week 48 visit only) 
• Injection-site inspection (previous and current injection site) 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• Blood Phe and plasma tyrosine concentration 
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• 3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the next monthly visit.) 
 
12.3.5 Quarterly Visits (Week 12, 24, 36, etc) 
Subjects must have AEs and concomitant medications assessed and an injection-site 
inspection performed whenever dose is administered even if the administration does not 
coincide with a scheduled clinic visit.    
Beginning with Week 12, quarterly visits consist of all monthly (Section 12.3.4) activities 
listed above as well as the additional study activities listed below: 
• Physical examination 
• Complement C3 and C4 
• Sedimentation rate 
• PK sample 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, and anti-rAvPAL-PEG neutralizing antibodies) 
 
12.3.6 Unscheduled Hypersensitivity Reaction Visit 
Subjects who have a systemic reaction, including a generalized skin reaction, or a large local 
skin reaction that is not contiguous to the injection site after rAvPAL-PEG administration 
(refer to Section 9.1.1) will have assessments performed immediately following (within 
24 hours) the reaction.  
• Vital signs 
• Injection-site inspection 
• Clinical laboratory tests 
• Urine/albumin creatinine ratio 
• CRP, CH50, C1, C3, and C4 
• Urine N-methyl histamine 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG IgE, and anti-rAvPAL-PEG neutralizing 
antibodies) 
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• Serum tryptase level 
• Skin biopsy (optional; affected and not affected area; to be performed within 1 week 
of reaction) 
• Assessment of AEs 
• Concomitant medications 
Following completion of the Unscheduled Hypersensitivity Reaction visit, subjects may 
resume study drug administration per the discretion of the Principal Investigator and the 
Sponsor’s Medical Officer; however, if subject was dosing at home, they will be required to 
come into the clinic for at least 8 weeks.  
12.4 
Early Termination Visit 
The Early Termination Visit (ETV) will occur 4 weeks after the final dose of study drug. 
Subjects who terminate from study treatment early should continue to perform the remaining 
visit assessments in Section 12.3 as applicable until study completion. 
Any AE that caused a subject to withdraw from the study or any clinically significant 
abnormal laboratory value or vital sign measurement identified at the ETV will be followed 
by the Investigator.  
Every reasonable effort should be made to contact any subject who is lost to follow-up. 
The following study activities will be performed at the ETV: 
• Physical examination  
• Vital signs 
• 12-lead ECG 
• Clinical laboratory tests 
• Chest x-ray  
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.). For safety reasons, 
this test must be performed prior to the chest X-ray. 
• Injection-site inspection (previous injection site) 
• Assessment of AEs 
• Concomitant medications 
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• Diet query 
• 3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the Early Termination Visit.) 
• PK sample 
• Blood Phe and plasma tyrosine concentration 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibodies) 
12.5 
Final Follow-up Visit 
The final follow-up (F/U) Visit will occur 1 week after the final dose of study drug. 
The following study activities will be performed at the F/U Visit: 
• Physical examination  
• Vital signs, including weight 
• 12-lead ECG 
• Clinical laboratory tests 
• Chest x-ray  
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.). For safety reasons, 
this test must be performed prior to the chest X-ray. 
• Injection-site inspection (previous injection site) 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• 3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the Final Follow-up Visit.) 
• PK sample 
• Blood Phe and plasma tyrosine concentration 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibodies) 
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13 
DATA QUALITY ASSURANCE 
BioMarin personnel or designees will visit the study site prior to initiation of the study to 
review with the site personnel information about the IP, protocol and other regulatory 
document requirements, any applicable randomization procedures, source document 
requirements, CRFs, monitoring requirements, and procedures for reporting AEs, including 
SAEs. 
At visits during and after the study, a CRA will monitor the site for compliance with 
regulatory documentation, with a focus on accurate and complete recording of data on CRFs 
from source documents, adherence to protocol, randomization (if applicable), SAE reporting 
and drug accountability records.  
The designated clinical data management group will enter or transfer CRF data into a study 
database. 
Data quality control and analysis will be performed by BioMarin or a designee, based on a 
predefined analysis plan. 
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14 
STATISTICAL METHODS AND DETERMINATION OF SAMPLE SIZE 
14.1 
Statistical and Analytical Plans 
Because of the small sample size, no formal statistical tests will be performed. Categorical 
data will be summarized using frequency and percent, while continuous data will be 
summarized using descriptive statistics (ie, number of observations, mean, median, standard 
deviation [SD], minimum, and maximum). 
The statistical analysis plan (SAP) will provide additional details about the planned statistical 
analysis. 
14.2 
Safety Analysis 
All subjects who receive any amount of study drug in this study and have postdose safety 
information will be included in the safety analyses. 
The Medical Dictionary for Regulatory Activities terminology (MedDRA) will be used by 
the sponsor to assign system organ class and preferred term classification to events and 
diseases based on the original terms entered on the Case Report Form (CRF). 
The incidence of AEs will be summarized by system organ class, preferred term, relationship 
to study drug, and severity. A by–subject listing will be provided for those subjects who 
experience a serious AE (SAE), including death, or experience an AE associated with early 
withdrawal from the study or study drug. Hypersensitivity AEs and AEs that result in dosing 
interruption or dose level reduction are of interest, and the percentage of subjects who report 
these AEs will be presented. 
Clinical laboratory data will be summarized by the type of laboratory test. Frequency and 
percentage of subjects who experience abnormal (ie, outside of reference range) and/or 
clinically significant abnormalities after study drug administration will be presented for each 
clinical laboratory test. For each clinical laboratory test, descriptive statistics will be provided 
for baseline and all subsequent post-treatment visits. Changes from baseline to the post-
treatment visits will also be provided. Descriptive statisticsof vital signs, physical 
examination results, ECG results, and X-ray results, and immunogenicity test results will also 
be provided. Additionally, antibodies and titers will be summarized by scheduled time point. 
14.3 
Pharmacokinetic Analysis 
Subjects who complete the Substudy will have the following PK parameters assessed: area 
under the plasma concentration-time curve (AUC), time to maximum plasma concentration 
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(Tmax), maximum plasma concentration (Cmax), half life (t1/2), and clearance (CL/F).  Should 
data become available from previous rAvPAL-PEG studies that indicate study drug 
accumulation should also be measured, additional blood draws may be added for PK analysis 
as needed per the discretion of the Investigator in consultation with the Sponsor’s Medical 
Officer. 
14.3.1 Pharmacokinetic Substudy Analysis 
For subjects who completed the Substudy, the steady-state PK of rAvPAL-PEG in subjects 
who have achieved and maintained target blood Phe will be explored. 
14.4 
Efficacy Analysis 
Data from all subjects who receive any amount of study drug and who have any 
post-treatment efficacy data will be included in the efficacy analysis. 
Blood Phe concentration at each scheduled time point will be summarized using descriptive 
statistics (mean, SD, median, minimum, and maximum). Change in blood Phe concentration 
from baseline (to be defined in the SAP) to each scheduled time point and presence/absence 
of antibodies will also be summarized. In addition, the proportion of subjects who have 
maintained target Phe concentrations of 60-600 µmol/L will be summarized by each 
scheduled time point. 
The relationship of dietary Phe intake (per information reported on the subject diet diary) and 
blood Phe concentration will also be explored. Subjects who received any amount of study 
drug with any post-treatment blood Phe concentration measurements and diet diary 
information will be included in this exploratory analysis.  
Details regarding exploratory analyses will be provided in the Statistical Analysis Plan. 
14.5 
Determination of Sample Size 
Subjects who participated in previous rAvPAL-PEG studies may be enrolled into this study. 
No formal sample size calculation was conducted for this study or the PAL-003 Substudy.   
14.6 
Handling of Missing Data 
All analyses will be presented based on observed data only. Missing data will not be imputed 
for analyses unless sensitivity analyses are warranted. If imputations are used, detailed 
imputation methods will be described in the SAP before locking the database. 
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14.7 
Interim Analyses 
Safety will be assessed throughout the study on an ongoing basis (refer to Section 15 for 
information regarding the DMC). 
14.8 
Changes in the Conduct of the Study or Planned Analyses 
Only BioMarin may modify the protocol. Any change in study conduct considered necessary 
by the PI will be made only after consultation with BioMarin, who will then issue a formal 
protocol amendment to implement the change. The only exception is when an Investigator 
considers that a subject’s safety is compromised without immediate action. In these 
circumstances, immediate approval of the chairman of the IRB must be sought, and the 
Investigator should inform BioMarin and the full IRB within 2 working days after the 
emergency occurs. 
With the exception of minor administrative or typographical changes, the IRB must review 
and approve all protocol amendments. Protocol amendments that have an impact on subject 
risk or the study objectives, or require revision of the ICF, must receive approval from the 
IRB prior to their implementation. 
When a protocol amendment substantially alters the study design or the potential risks or 
burden to subjects, the ICF will be amended and approved by BioMarin and the IRB, and all 
active subjects must again provide informed consent. 
Note: If discrepancies exist between the text of the statistical analysis as planned in the 
protocol, and the final SAP, a protocol amendment will not be issued and the SAP will 
prevail. 
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15 
DATA MONITORING COMMITTEE (DMC) 
The DMC will act independently in an advisory capacity to BioMarin to monitor the safety 
of rAvPAL-PEG in subjects who participate in the study.  
The responsibilities of the DMC are to: 
• Review the study protocol, informed consent and assent documents, and plans for 
data monitoring. 
• Evaluate the progress of the trial, subjects’ risk versus benefit, and other factors that 
could affect the study outcome. 
• Assess the effect and relevance of new external evidence. 
• Consider relevant information that may have an impact on the safety of the 
participants or the ethics of the study. 
• Protect the safety of the study participants in accordance with the stopping criteria as 
defined in study protocol Section 9.1.4. 
• Make recommendations to the BioMarin concerning continuation or termination of 
the study or other study modifications based on observations. 
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16 
COMPENSATION, INSURANCE, AND INDEMNITY 
There will be no charge to study subjects to be in this study. BioMarin will pay all costs of 
tests, procedures, and treatments that are part of this study. In addition, after IRB approval, 
BioMarin may reimburse the cost of travel for study-related visits. BioMarin will not pay for 
any hospitalizations, tests, or treatments for medical problems of any sort, whether or not 
related to the study subject’s disease, that are not part of this study. Costs associated with 
hospitalizations, tests, and treatments should be billed and collected in the way that such 
costs are usually billed and collected. 
The Investigator should contact BioMarin immediately upon notification that a study subject 
has been injured by the IP or by procedures performed as part of the study. Any subject who 
experiences a study-related injury should be instructed by the Investigator to seek medical 
treatment at a pre-specified medical institution if possible, or at the closest medical treatment 
facility if necessary. The subject should be given the name of a person to contact to seek 
further information about, and assistance with, treatment for study-related injuries. 
The treating physician should bill the subject’s health insurance company or other third party 
payer for the cost of this medical treatment, unless the executed Clinical Trial Agreement 
between BioMarin and the institution of the investigator specifies otherwise. If the subject 
has followed the Investigator’s instructions, BioMarin may pay for reasonable and necessary 
medical services to treat the injuries caused by the IP or study procedures. In some 
jurisdictions, BioMarin is obligated by law to pay for study-related injuries without prior 
recourse to third party payer billing. If this is the case, BioMarin will comply with the law. 
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17 
CASE REPORT FORMS AND SOURCE DOCUMENTS 
Electronic case report forms will be provided for each subject. The Investigator must review 
and electronically sign the completed CRF casebook to verify its accuracy. 
CRFs must be completed using a web–based application that has been validated. Study site 
personnel will be trained on the application and will enter the clinical data from source 
documentation. Unless explicitly allowed in the CRF instructions, blank data fields are not 
acceptable. 
In the event of an entry error, or if new information becomes available, the site personnel will 
correct the value by deselecting the erroneous response and then selecting or entering the 
factual response. In compliance with 21 CFR Part 11, the system will require the site 
personnel to enter a reason for changing the value. The documented audit trail will include 
the reason for the change, the original value, the new value, the time of the correction, and 
the identity of the operator. 
BioMarin’s policy is that study data on the CRFs must be verifiable to the source data, which 
necessitates access to all original recordings, laboratory reports, and subject records. 
In addition, all source data should be attributable (signed and dated). The Investigator must 
therefore agree to allow direct access to all source data. Subjects (or their legally authorized 
representative) must also allow access to their medical records, and subjects will be informed 
of this and will confirm their agreement when giving informed consent.  
A CRA designated by BioMarin will compare the CRFs with the original source documents 
at the study site and evaluate them for completeness and accuracy before designating them as 
“source data verified” (SDV). If an error is discovered at any time or a clarification is 
needed, the CRA, or designee, will create an electronic query on the associated field. Site 
personnel will then answer the query by either correcting the data or responding to the query. 
The CRA will then review the response and determine either to close the query or re–query 
the site if the response does not fully address the question. This process is repeated until all 
open queries have been answered and closed. 
Before a subject’s CRF casebook can be locked, all data fields must be SDV and all queries 
closed. The Investigator will then electronically sign the casebook, specifying that the 
information on the CRFs is accurate and complete. The Data Manager, or designee, will then 
set the status of the forms, visits, and the entire casebook to locked. Upon completion of the 
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clinical study report for the entire study, an electronic copy of each site’s casebooks will be 
copied to a compact disk (CD) and sent to each site for retention with other study documents. 
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18 
STUDY MONITORING AND AUDITING 
Qualified individuals designated by BioMarin will monitor all aspects of the study according 
to GCP and standard operating procedures for compliance with applicable government 
regulations. The PI agrees to allow these monitors direct access to the clinical supplies, 
dispensing, and storage areas and to the clinical files, including original medical records, of 
the study subjects, and, if requested, agrees to assist the monitors. The PI and staff are 
responsible for being present or available for consultation during routinely scheduled site 
visits conducted by BioMarin or its designees. 
Members of BioMarin’s GCP Compliance Department or designees may conduct an audit of 
a clinical site at any time during or after completion of the study. The PI will be informed if 
an audit is to take place and advised as to the scope of the audit. Representatives of the FDA 
or other Regulatory Agencies may also conduct an audit of the study. If informed of such an 
inspection, the PI should notify BioMarin immediately. The PI will ensure that the auditors 
have access to the clinical supplies, study site facilities, original source documentation, and 
all study files. 
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19 
RETENTION OF RECORDS 
The PI must retain all study records required by BioMarin and by the applicable regulations 
in a secure and safe facility. The PI must consult a BioMarin representative before disposal 
of any study records, and must notify BioMarin of any change in the location, disposition or 
custody of the study files. The PI/institution must take measures to prevent accidental or 
premature destruction of essential documents, that is, documents that individually and 
collectively permit evaluation of the conduct of a study and the quality of the data produced, 
including paper copies of study records (e.g., subject charts) as well as any original source 
documents that are electronic as required by applicable regulatory requirements. 
All study records must be retained for at least 2 years after the last approval of a marketing 
application in the U.S. or an ICH region and until (1) there are no pending or contemplated 
marketing applications in the United States or an ICH region or (2) at least 2 years have 
elapsed since the formal discontinuation of clinical development of the IP. The PI/institution 
should retain subject identifiers for at least 15 years after the completion or discontinuation 
of the study. Subject files and other source data must be kept for the maximum period of time 
permitted by the hospital, institution or private practice, but not less than 15 years. 
These documents should be retained for a longer period, however, if required by the 
applicable regulatory requirements or by a BioMarin agreement. BioMarin must be notified 
and will assist with retention should the PI/institution be unable to continue maintenance of 
subject files for the full 15 years. It is the responsibility of BioMarin to inform the 
PI/institution as to when these documents no longer need to be retained. 
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20 
USE OF INFORMATION AND PUBLICATION 
BioMarin recognizes the importance of communicating medical study data and therefore 
encourages their publication in reputable scientific journals and at seminars or conferences. 
The details of the processes of producing and reviewing reports, manuscripts, and 
presentations based on the data from this study will be described in the Clinical Study 
Agreement between BioMarin and the PI. 
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21 
REFERENCES 
Armstrong, JK, Hempel, G, Koling, S, Chan, LS et. al. Antibody against poly(ethylene 
glycol) adversely affects PEG-asparaginase therapy in acute lymphoblastic leukemia patients. 
Cancer 110[1], 103-111. 2007.  
Chen, AM, Scott, MD. Current and future applications of immunological attenuation via 
pegylation of cells and tissue. BioDrugs 15[12], 833-847. 2001.  
Davis, S, Abuchowski, A, Park, YK, Davis, FF. Alteration of the circulating life and 
antigenic properties of bovine adenosine deaminase in mice by attachment of polyethylene 
glycol. Clin Exp Immunol 46[3], 649-652. 1981.  
Fisch, RO. Comments on diet and compliance in phenylketonuria. Eur J Pediatr 159 Suppl 2, 
S142-S144. 2000.  
Gamez, A, Wang, L, Sarkissian, CN, Wendt, D et. al. Structure-based epitope and 
PEGylation sites mapping of phenylalanine ammonia-lyase for enzyme substitution treatment 
of phenylketonuria. Mol Genet Metab 91[4], 325-334. 2007.  
Ganson, NJ, Kelly, SJ, Scarlett, E, Sundy, JS et. al. Control of hyperuricemia in subjects with 
refractory gout, and induction of antibody against poly(ethylene glycol) (PEG), in a phase I 
trial of subcutaneous PEGylated urate oxidase. Arthritis Res Ther 8[1], R12. 2006.  
Guttler, F, Azen, C, Guldberg, P, Romstad, A et. al. Impact of the phenylalanine hydroxylase 
gene on maternal phenylketonuria outcome. Pediatrics 112[6 Pt 2], 1530-1533. 2003.  
Harris, JM, Chess, RB. Effect of pegylation on pharmaceuticals. Nat Rev Drug Discov 2[3], 
214-221. 2003.  
Huttenlocher, PR. The neuropathology of phenylketonuria: human and animal studies. Eur J 
Pediatr 159 Suppl 2, S102-S106. 2000.  
Kaufman, S. An evaluation of the possible neurotoxicity of metabolites of phenylalanine. J 
Pediatr 114[5], 895-900. 1989.  
Koch, R, Hanley, W, Levy, H, Matalon, K et. al. The Maternal Phenylketonuria International 
Study: 1984-2002. Pediatrics 112[6 Pt 2], 1523-1529. 2003.  
Lapis. Long-term Correction of PKU in the Pahenu2 Mouse by Mutant and Chemically 
Modified Forms of Phenylalanine Ammonium Lyase. ASHG 57th Annual Meeting The 
American Society of Human Genetics)2007.  
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Lee, PJ, Lilburn, M, Baudin, J. Maternal phenylketonuria: experiences from the United 
Kingdom. Pediatrics 112[6 Pt 2], 1553-1556. 2003.  
Levy, HL. Historical background for the maternal PKU syndrome. Pediatrics 112[6 Pt 2], 
1516-1518. 2003.  
Matalon, R, Surendran, S, Matalon, KM, Tyring, S et. al. Future role of large neutral amino 
acids in transport of phenylalanine into the brain. Pediatrics 112[6 Pt 2], 1570-1574. 2003.  
Richter, AW, Akerblom, E. Antibodies against polyethylene glycol produced in animals by 
immunization with monomethoxy polyethylene glycol modified proteins. Int Arch Allergy 
Appl Immunol 70[2], 124-131. 1983.  
Richter, AW, Akerblom, E. Polyethylene glycol reactive antibodies in man: titer distribution 
in allergic patients treated with monomethoxy polyethylene glycol modified allergens or 
placebo, and in healthy blood donors. Int Arch Allergy Appl Immunol 74[1], 36-39. 1984.  
Rouse, B, Azen, C. Effect of high maternal blood phenylalanine on offspring congenital 
anomalies and developmental outcome at ages 4 and 6 years: the importance of strict dietary 
control preconception and throughout pregnancy. J Pediatr 144[2], 235-239. 2004.  
Scott, MD, Murad, KL, Koumpouras, F, Talbot, M et. al. Chemical camouflage of antigenic 
determinants: stealth erythrocytes. Proc Natl Acad Sci U S A 94[14], 7566-7571. 1997.  
Scriver, CR, Kaufman. Hyperphenylalaninemia: Phenylalanine Hydroxylase Deficiency. In: 
Beaudet AL, Sly WS, Valle D, editors. Metabolic and Molecular Bases of Inherited Disease. 
New York: McGraw-Hill, 2001: 1667-1724. 
Walter, JH, White, FJ, Hall, SK, MacDonald, A et. al. How practical are recommendations 
for dietary control in phenylketonuria? Lancet 360[9326], 55-57. 2002.  
Webster, R, Didier, E, Harris, P, Siegel, N et. al. PEGylated proteins: evaluation of their 
safety in the absence of definitive metabolism studies. Drug Metab Dispos 35[1], 9-16. 2007.  
 
 
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22 
INVESTIGATOR RESPONSIBILITIES 
22.1 
Conduct of Study and Protection of Human Subjects  
In accordance with FDA Form 1572, the Investigator will ensure that: 
• He or she will conduct the study in accordance with the relevant, current protocol and 
will only make changes in a protocol after notifying the sponsor, except when 
necessary to protect the safety, rights, or welfare of subjects. 
• He or she will personally conduct or supervise the study. 
• He or she will inform any potential subjects, or any persons used as controls, that the 
drugs are being used for investigational purposes and he or she will ensure that the 
requirements relating to obtaining informed consent in 21 CFR Part 50 and 
institutional review board (IRB) review and approval in 21 CFR Part 56 are met.  
• He or she will report to the sponsor adverse experiences that occur in the course of 
the investigation in accordance with 21 CFR 312.64. 
• He or she has read and understands the information in the Investigator’s Brochure, 
including potential risks and side effects of the drug. 
• His or her staff and all persons who assist in the conduct of the study are informed 
about their obligations in meeting the above commitments. 
• He or she will ensure that adequate and accurate records in accordance with 
21 CFR 312.62 and to make those records available for inspection in accordance with 
21 CFR 312.68. 
• He or she will ensure that the IRB complies with the requirements of 21 CFR Part 56, 
and other applicable regulations, and conducts initial and ongoing reviews and 
approvals of the study. He or she will also ensure that any change in research activity 
and all problems involving risks to human subjects or others are reported to the IRB. 
Additionally, he or she will not make any changes in the research without IRB 
approval, except where necessary to eliminate apparent immediate hazards to human 
subjects. 
• He or she agrees to comply with all other requirements regarding the obligations of 
clinical Investigators and all other pertinent requirements in 21 CFR Part 312. 
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24 
PROTOCOL AMENDMENT TEXT REVISIONS 
The following table summarizes the revisions made to the protocol and relates the changes to the appropriate rationale (see pages 2-4). Text 
that has been added or inserted is indicated by underlined font, and deleted text is indicated by strikethrough font. 
Section No./Title 
Revision 
Rationale 
Global change: Sponsor’s 
Medical Officer 
, MD 
 
16 
Section 2/Synopsis, Study 
Rationale 
….This study is an extension of the rAvPAL-PEG Phase 2 studies PAL-002, PAL-004, and 165-205. 
Administration of rAvPAL-PEG will be continued to assess whether long term dosingthe long-term safety 
and efficacy of rAvPAL-PEG is safe and can maintain reduced blood Phe concentrations in PKU subjects. 
….Therefore, an exploratory objective has been added to this study to assess the relationship of diet, 
rAvPAL-PEG administration, and blood Phe level. Changes to subject diet are not allowed in this study 
unless per the Investigatorin consultation with the Sponsor’s Medical Officer. Diet will be monitored using a 
diet diary. 
A pharmacokinetic (PK) substudy has been added to evaluate the steady-state PK of rAvPAL-PEG in a 
minimum ofup to 6 subjects who have achieved and maintained target blood Phe for at least 2 consecutive 
weeks measurements and for whom no further dose modifications are planned. Single-dose PK data has been 
collected in the Phase 1 study, PAL-001…. 
 
2, 3, 12 
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Section 2/Synopsis, 
Study Design and Plan 
This is a long-term extension of rAvPAL-PEG Phase 2 studies in approximately up to 100 subjects with PKU. The 
doses are planned to be in the same range as those previously tested in the Phase 2 studies PAL 002 and PAL 004 
(starting at 0.001 through 5.0 mg/kg/week or 2.5 mg through 375 mg/week), provided no dose-limiting toxicity is 
observed in a previous rAvPAL-PEG study. 
…. The first dose will be administered in the clinic, and the subject must be observed for 30 60 minutes following 
administration. A follow-up telephone call will be made to the subject to monitor subject safety 24 hours following 
the return to dosing.  
Diet should not be altered during the course of this study.  Any decision to modify subject diet must be made per 
the Investigator in consultation with the Sponsor’s Medical Officer and must be performed under the supervision 
of the Investigator in consultation with the Sponsor’s Medical Officer. To monitor for changes in subject diet, a 
diet diary will be issued to subjects for completion and will be reviewed with the clinical study staff on a monthly 
basis.  
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take rAvPAL-PEG. 
Subjects’ previous rAvPAL-PEG dosing will generally continue in PAL-003. In PAL-003, each subject’s dose will 
be adjusted as needed to attempt to attain or maintain blood Phe concentrations of 60-600 µmol/L. rAvPAL-PEG 
dose will be based on either a subject’s weight or will be a fixed dose (subjects who have maintained blood Phe 
levels to 60 600 µmol/L for at least 2 consecutive weeks and who have maintained a stable rAvPAL PEG dose for 
at least 2 consecutive weeks). Doses will be evaluated on an individual basis. 
A subject will continue in PAL-003 until one of the following occurs: 
• 
The subject has completed the study through the Month 860 visit. 
• 
 The study drug receives marketing authorization. 
 
2, 3, 4, 
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Section 2/Synopsis, 
Study Design and Plan 
Subjects who participate in this study will be required to transition into a Phase 3 study (165-302) if weekly 
doses of rAvPAL-PEG are between 70 mg/week and 350 mg/week (inclusive) provided that doses of rAvPAL-
PEG have been stable (ie, no major change in dose for at least 4 weeks). Subjects who meet these criteria must 
be transitioned from PAL-003 to Study 165-302 provided they meet the 165-302 study eligibility criteria.  
Subjects who are eligible for Study 165-302 but do not transition into 165-302 will be withdrawn from this 
study. 
The PAL-003 study will continue until BMN-165 is approved by the Food and Drug Administration (FDA) for 
marketing in the United States or until the sponsor terminates further development of this drug for the treatment 
of PKU. 
PAL-003 Substudy 
A PK substudy has been added to evaluate the steady-state PK of rAvPAL-PEG in a minimum ofup to 
6 subjects who have achieved and maintained target blood Phe for at least 2 consecutive weeksmeasurements 
and for whom no further dose modifications are planned.   
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Section 2/Synopsis, 
Dose Modifications 
Dose Increase Methodology: 
Each subject’s dose may be modified based on the decision of the Investigator, in agreement with the Sponsor’s 
Medical Officer. Decisions regarding dose increases will depend on a subject’s adverse event profile and blood 
Phe and drug concentrations.  
An individual subject’s dose may be adjusted beginning on Day 1 of PAL-003. For the duration of this study, an 
individual subject’s dose may be adjusted if warranted per a subject’s adverse event profile and blood Phe 
concentrations. Dose increases should be performed as follows. 
• 
When increasing the dose, a dose may be used that is between the dose levels (0.001, 0.003, 0.01, 0.03, 
0.06, 0.1, 0.2, 0.3, 0.4, 0.6, 0.8, 1.0, 2.0, 3.0, 4,0, and 5.0 mg/kg) or 2.5, 5, 10, 20, 40, 75, 150, 225, 300, 
375 mg/week) or per Investigator determination in consultation with the Sponsor’s Medical Officer 
based on available information regarding a subject’s blood Phe (60-600 µmol/L) as well as any adverse 
events (any hypersensitivity reaction) for an individual subject. Dose increases  > 350 mg/week require 
consultation with the sponsor’s medical monitor. 
• 
The dose may be adjusted by increasing the frequency up to daily for a total weekly dose not to exceed 
5.0 mg/kg Subjects who increase their dose frequency will have additional assessments performed 
(Interim Dosing Visit)or 375 mg/week. Dose increases  > 350 mg/week require consultation with the 
sponsor’s medical monitor. 
• 
When a dose is increased, the subject must be observed for 30 60 minutes following the first modified 
dose administration. Subjects who increase their dose frequency do not need to be observed following 
injection of study drug if the increase in frequency does not increase the overall weekly dose amount. 
 
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Section 2/Synopsis, 
Dose Modifications 
Dose Decrease Methodology 
All dose decreases must be agreed to by both the Investigator and the Sponsor’s Medical Officer. Decisions 
regarding dose decreases will depend on available information regarding a subject’s blood Phe (60-600 µmol/L), 
as well as any adverse events (any hypersensitivity reaction). Dose decreases may occur for safety (ie, 
hypophenylalanemia or any adverse event that may be improved with a lower, more frequent dose).  
A dose should first be reduced by dose level (5.0, 4.0, 3.0, 2.0, 1.0, 0.8, 0.6, 0.4, 0.3, 0.2, 0.1, 0.06, 0.03, 0.01, 
0.003, 0.001 mg/kg or 375, 300, 225, 150, 75, 40, 20, 10, 5, and 2.5 mg/week). It is also permitted to decrease 
dose in between these specified dose levels. If further dosing adjustments are required to attain the target Phe 
concentrationin response to safety, dosing frequency may also be reduced. 
If the subject develops low blood Phe (as defined by a blood Phe level ≤ 30 µmol/Las measured by serum Phe 
levels for a minimum of 1 month), the subject’s rAvPAL-PEG dose should be decreased to the next lower dose. 
If the condition persists after another 1 month at the lower dose, the dose should be decreased again to the next 
lower level. If the subject continues to experience low blood Phe after two dose level reductions, the subject 
may be asked to consult the dietician to eliminate medical foods and/or formulas and to ensure a balanced and 
nutritious diet (as part of the routine standard of care for PKU disease management, subject diet should be 
monitored by a dietician). 
 
2,3 
Section 2/Synopsis, 
Number of Subjects 
Planned 
ApproximatelyUp to 100 subjects. 
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Section 2/Synopsis, 
Investigational Product, 
Dose, Route and 
Regimen 
The investigational product is rAvPAL-PEG (recombinant Anabaena variabilis phenylalanine ammonia lyase-
PEG). rAvPAL-PEG will be provided in vials or prefilled syringes; subjects will be supplied with vials and 
syringes or prefilled syringes for administration in the clinic and self administration:rAvPAL PEG will be 
provided in 3 mL (milliliter) vials, each containing 1.5 ± 0.2 mL to deliver either 10 mg of rAvPAL PEG per 
1 mL (10 mg/mL protein concentration) or 15 mg or rAvPAL PEG per 1 mL (15 mg/mL protein concentration). 
Each vial is filled with 1.5 ± 0.2 mL to allow the withdrawal and delivery of up to 1 mL of the drug product.  
• 
rAvPAL-PEG will be provided in 3 mL (milliliter) vials, each containing 1.5 ± 0.2 mL to deliver 15 mg 
of rAvPAL-PE per 1.0 mL (15 mg/mL protein concentration). Each vial is filled with 1.5 ± 0.2 mL to 
allow the withdrawal and delivery of up to 1.0 mL of the drug product. 
Or 
• 
rAvPAL-PEG will be provided in 3-mL vials, each containing 1.8 ±0.3 mL to deliver 20 mg of 
rAvPAL-PE per 1.3 mL (15 mg/mL protein concentration). Each vial is filled with 1.8 ± 0.3 mL to 
allow withdrawal and delivery of up to 1.3 mL. 
Or 
• 
rAvPAL-PEG will be provided in prefilled syringes in three sizes that deliver up to 1 mL. Syringe sizes 
are 2.5 mg (5 mg/mL protein concentration), 10 mg (20 mg/mL protein concentration), and 20 mg 
(20 mg/mL protein concentration).  
Prefilled Syringe 
Volume 
Concentration 
Dose 
Sku #1 
0.5 mL 
5 mg/mL 
2.5 mg 
Sku #2 
0.5 mL 
20 mg/mL 
10 mg 
Sku #3 
1.0 mL 
20 mg/mL 
20 mg 
 
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Section 2/Synopsis, 
Investigational Product, 
Dose, Route and 
Regimen 
The excipients in this drug product are tromethamine, tromethamine-hydrochloride, sodium chloride, L-
phenylalanine, and water for injection. 
Upon enrollment into this study, subjects from previous rAvPAL PEG studies will be dosed with the same or 
higher dose than the dose that was administered upon completion of that study provided that there was no 
interruption in dosing. Subjects who have had dosing interruptions between the previous rAvPAL PEG study 
and PAL 003 must have their starting dose determined per the Sponsor’s Medical Officer. rAvPAL-PEG doses 
will be administered SC by either health care professionals or via self administration. The dose level may be 
increasedor decreased per Investigator determination in consultation with the Sponsor’s Medical Officer based 
on available information regarding a subject’s blood Phe level (60-600 µmol/L), as well as any adverse events 
(any hypersensitivity reaction) for an individual subject. The dosage that provides control of blood Phe 
concentrations within the target range of 60-600 µmol/L for a minimum of 2 weeks consecutive measurements 
will be determined for each subject by adjusting the dose level, dose frequency, or both, as agreed byper the PI 
and the Sponsor’s Medical Officer, based upon the subject’s response to doses. 
Fixed Dosing 
Subjects who have demonstrated efficacy (ie, blood Phe within the target range of 60-600 µmol/L for at least 
2 consecutive weeksmeasurements) and who have maintained a stable rAvPAL-PEG dose for at least 
2 consecutive weeks measurements may be eligible to transition from weight-based dosing to a fixed dosing 
regimen that would permit daily dosing (5- or 7-days-per-week). Subjects should convert their weight-based 
dose using the following table: 
Tabular information regarding fixed doses has been revised. 
3, 13 
Section 2/Synopsis, 
Duration of Treatment 
Up to 8660 months. 
1 
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Section 2/Synopsis, 
Statistical Methods 
Safety Analysis: 
The Medical Dictionary for Regulatory Activities terminology (MedDRA) will be used by the sponsor to assign 
system organ class and preferred term classification to events and diseases based on the original terms entered 
on the Case Report Form (CRF). All AEs will be coded using the Medical Dictionary for Regulatory Activities 
(MedDRA).The incidence of AEs will be summarized by system organ class, preferred term, relationship to 
study drug, and severity. A by–subject listing will be provided for those subjects who experience a serious AE 
(SAE), including death, or experience an AE associated with early withdrawal from the study or study drug. 
Hypersensitivity AEs and AEs that result in dosing interruption or dose level reduction are of interest, and the 
percentage of subjects who report these AEs will be presented.  
Clinical laboratory data will be summarized by the type of laboratory test. Frequency and percentage of subjects 
who experience abnormal (ie, outside of reference range) and/or clinically significant abnormalities after study 
drug administration will be presented for each clinical laboratory test. For each clinical laboratory test, 
descriptive statistics will be provided for baseline and all subsequent post-treatment visits. Changes from 
baseline to the post-treatment visits will also be provided. Descriptive statistics, including clinically significant 
changes from baseline, of for vital signs, physical examination results, ECG results, and X-ray results, and 
immunogenicity test results will also be provided. Additionally, antibodies and titers will be summarized by 
scheduled time point. 
Efficacy Analysis: 
Blood Phe concentration at each scheduled time point will be summarized using descriptive statistics (mean, 
standard deviation, median, minimum, and maximum). Change in blood Phe concentration from baseline (to be 
defined in the Statistical Analysis Plan [SAP]) to each scheduled time point and presence/absence of antibodies 
will also be summarized. In addition, the proportion of subjects who have maintained target Phe concentrations 
of 60-600 µmol/L will be summarized by each scheduled time point. 
Exploratory Analysis: 
For subjects who have received any study drug in this study with any post treatment blood Phe concentration 
measurements and diet diary information, the relationship of dietary Phe intake (per information reported on the 
subject diet diary), and blood Phe concentration will be exploredDetails regarding exploratory analyses will be 
provided in the SAP.  
 
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Section 6, Investigators 
and Study 
Administrative 
Structure 
The study will be administered by and monitored by employees or representatives of BioMarin. Clinical 
Research Associates (CRAs) or trained designees will monitor each site on a periodic basis and perform 
verification of source documentation for each subject as well as other required review processes. BioMarin’s 
Regulatory AffairsPharmacovigilance Department (or designee) will be responsible for the timely reporting of 
serious adverse events (SAEs) to appropriate regulatory authorities as required…. 
17 
Section 7.2, Previous 
Clinical Studies 
The rAvPAL-PEG clinical development program has been designed to demonstrate the safety and 
efficacy of rAvPAL-PEG in reducing blood Phe concentrations in PKU subjects who do not respond to 
treatment with Kuvan® or are not compliant with Kuvan® treatment. This study is an extension of the 
ongoing human clinical studies with rAvPAL-PEG (Study PAL-002, Study PAL-004, and Study 
165-205) based on data from the completed clinical study, PAL-001, and clinical experience as of 
JAN2011 from this ongoing study and the other ongoing Phase 2 studies, PAL-002 and PAL-004.  
 
17 
Section 7.2.2, Phase 2 
Studies PAL-002, 
PAL-004, and 165-205 
This section has been updated with results from Studies PAL-002, PAL-004, and PAL 165-205. 
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Section 7.3, Study 
Rationale 
Blood Phe levels depend not only on the functional presence of the endogenous enzyme PAH but also 
on the dietary intake of Phe. It is important to understand the role of diet on blood Phe levels 
concurrent with the administration of rAvPAL-PEG treatment. Therefore, an exploratory objective has 
been added to this study to assess the relationship of diet, rAvPAL-PEG administration, and blood Phe 
level. Changes to subject diet are not allowed in this study unless per the Investigator in consultation 
with the Sponsor’s Medical Officer. Diet will be monitored using a diet diary.     
A pharmacokinetic (PK) substudy has been added to evaluate the steady-state PK of rAvPAL-PEG in a 
minimum ofup to 6 subjects who have achieved and maintained target blood Phe for at least 2 
consecutive weeks measurements and for whom no further dose modifications are planned. Single-
dose PK data has been collected in the Phase 1 study, PAL-001. However, there is little multiple-dose 
PK data or data for when subjects have reached and maintained a stable dosing regimen.  With the PK 
substudy, multiple-dose PK data will be collected for subjects who have already achieved Phe 
reduction to within the protocol-defined target range. 
This study is an extension of previous rAvPAL-PEG Phase 2 studies. Administration of rAvPAL-PEG 
will be continued to assess whether long term dosingthe long-term safety and efficacy of 
rAvPAL-PEG is safe and can maintain reduced blood Phe concentrations in PKU subjects. 
 
2, 3, 12 
Section 7.4.2, Toxicity 
Due to an Immunologic 
Reaction 
….Additionally, subjects willmay be premedicated to prevent or mitigate risk of hypersensitivity 
reactions (refer to Section 9.1.1.3.3). 
 
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Section 7.4.2.2, 
Management of 
Allergic 
Hypersensitivity 
Reactions 
Allergic Hypersensitivity reactions to the SC injection of rAvPAL-PEG may be mild, moderate, or 
severe in intensity. Reactions may include pruritus, rash, shortness of breath, hypotension, or 
anaphylaxis. Clinical assessments should be conducted for a minimum of 30 60 minutes post-injection.  
 
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Section 9.1, Overall 
Study Design and Plan 
This is a long-term extension of rAvPAL-PEG Phase 2 studies in approximately up to 100 subjects with PKU. 
The doses are planned to be in the same range as those previously tested in the Phase 2 studies PAL 002 and 
PAL 004 (starting at 0.001 through 5.0 mg/kg/week or 2.5 mg through 375 mg/week), provided no 
dose-limiting toxicity is observed in a previous rAvPAL-PEG study. 
…. The first dose will be administered in the clinic, and the subject must be observed for 30 60 minutes 
following administration. A follow-up telephone call will be made to the subject to monitor subject safety 
24 hours following the return to dosing.  
Diet should not be altered during the course of this study.  Any decision to modify subject diet must be made per 
the Investigator in consultation with the Sponsor’s Medical Officer and must be performed under the 
supervision of the Investigator in consultation with the Sponsor’s Medical Officer. To monitor for changes in 
subject diet, a diet diary will be issued to subjects for completion and will be reviewed with the clinical study 
staff on a monthly basis.  
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take rAvPAL-PEG. 
Subjects’ previous rAvPAL-PEG dosing will generally continue in PAL-003. In PAL-003, each subject’s dose 
will be adjusted as needed to attempt to attain or maintain blood Phe concentrations of 60-600 µmol/L. 
rAvPAL-PEG dose will be based on either a subject’s weight or will be a fixed dose (subjects who have 
maintained blood Phe levels to 60 600 µmol/L for at least 2 consecutive weeks and who have maintained a 
stable rAvPAL PEG dose for at least 2 consecutive weeks). Doses will be evaluated on an individual basis. 
A subject will continue in PAL-003 until one of the following occurs: 
• 
The subject has completed the study through the Month 860 visit. 
• 
 The study drug receives marketing authorization. 
 
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Section 9.1, Overall 
Study Design and Plan 
Subjects who participate in this study will be required to transition into a Phase 3 study (165-302) if weekly 
doses of rAvPAL-PEG are between 70 mg/week and 350 mg/week (inclusive) provided that doses of rAvPAL-
PEG have been stable (ie, no major change in dose for at least 4 weeks). Subjects who meet these criteria must 
be transitioned from PAL-003 to Study 165-302 provided they meet the 165-302 study eligibility criteria.  
Subjects who are eligible for Study 165-302 but do not transition into 165-302 will be withdrawn from this 
study. 
The PAL-003 study will continue until BMN-165 is approved by the Food and Drug Administration (FDA) for 
marketing in the United States or until the sponsor terminates further development of this drug for the treatment 
of PKU. 
A PK substudy has been added to evaluate the steady-state PK of rAvPAL-PEG in a minimum ofup to 
6 subjects who have achieved and maintained target blood Phe for at least 2 consecutive weeksmeasurements 
and for whom no further dose modifications are planned…. 
2, 3, 4, 12 
Section 9.1, Table 
9.1.1, Schedule of 
Events 
This table has been revised to align with changes made within the amendment. 
15, 17 
Section 9.1.1.1, 
Subjects Who Have 
Had Previous 
Hypersensitivity 
Reactions to 
rAvPAL-PEG or a 
PEG-containing 
Product 
Subjects who had a previous systemic reaction to rAvPAL-PEG or a PEG-containing product that 
warranted early termination from a previous rAvPAL-PEG study are excluded from participation in 
this study. Subjects who experienced a generalized skin rash are included in this category. Subjects 
who have had a previous local skin reaction to rAvPAL-PEG in a previous rAvPAL-PEG study are 
eligible to participate in this study.  
 
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Section 9.1.1.3.2.1, 
Large Local Skin 
Reactions Contiguous 
to Injection Site 
Subjects who develop a large local skin reaction contiguous to the injection site after administration of 
rAvPAL-PEG or to rAvPAL-PEG or a PEG-containing product may remain in the study if the skin 
symptoms have resolved and no other symptoms have developed. For the remainder of the study, 
subjects will be encouraged to premedicated orally with acetaminophen and/or non-sedating 
antihistamines 1-2 hours prior to study drug dosing (subjects may take non-sedating premedications 
prior to coming to clinic) for all future study doses. Because antihistamines can cause drowsiness, it 
may be administered only if the subject is accompanied by a designated driver (if applicable).  
 
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Section 9.1.1.3.3, 
Systemic Reactions 
….Subjects who experience generalized skin symptoms are included in this category. Immediately 
after the systemic reaction (within 2448 hours), subjects with generalized skin symptoms must have 
additional assessments performed for safety (ie, Unscheduled Hypersensitivity Reaction Visit): serum 
antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, anti-PEG IgM, anti rAvPAL-PEG IgE, 
anti-rAvPAL-PEG neutralizing antibodies); serum tryptase level (it is recommended that this sample 
be drawn immediately after reaction); sedimentation rate;urine albumin/creatinine ratio; urine 
N-methyl histamine; CRP, CH50, C1, C3, and C4; skin biopsy (optional; affected and not affected area; 
to be performed within 1 week of reaction); and clinical laboratory tests (urinalysis, chemistry, 
hematology; refer to Figure 9.1.1.3.1.  
….  Subjects who do not have an IgE mediated reaction may resume study drug administration per the 
discretion of the Principal Investigator and the Sponsor’s Medical Officer; however, if subject was 
dosing at home, they will be required to come into the clinic for at least 1 week. If laboratory data 
shows that the subject experienced an IgE mediated reaction, dosing will not resume until review of 
the case with the Investigator, Sponsor’s Medical Officer, and an allergist/immunologist.   
rAvPAL-PEG administration will resume at the next lowest dose level. Restarting of rAvPAL-PEG 
administration following a systemic reaction must be performed in the clinic for the first week of 
resumed dosing. Subjects must will be encouraged to premedicated orally with acetaminophen and/or 
antihistamines 1-2 hours prior to study drug dosing (subjects may take non-sedating premedications 
prior to coming to clinic) for all future study doses. Additionally, subjects must be closely monitored 
for 30 60 minutes following every administration of study drug. Because antihistamines may cause 
drowsiness, the subject must be accompanied by a designated driver (if applicable).   
 
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Section 9.1.1.3.3, 
Systemic Reactions 
…. Subjects must will be encouraged to premedicated orally with acetaminophen and/or antihistamines 
1-2 hours prior to study drug dosing (subjects may take non-sedating premedications prior to coming 
to clinic) for all future study doses. Additionally, subjects must be closely monitored for 30 60 minutes 
following every study drug administration. Because antihistamines may cause drowsiness, the subject 
must be accompanied by a designated driver (if applicable). 
 
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Section 9.1.2.1, Dose 
Increase Methodology 
Dose Increase Methodology: 
Each subject’s dose may be modified based on the decision of the Investigator, in agreement with the Sponsor’s 
Medical Officer. Decisions regarding dose increases will depend on a subject’s adverse event profile and blood 
Phe and drug concentrations.  
An individual subject’s dose may be adjusted beginning on Day 1 of PAL-003. For the duration of this study, an 
individual subject’s dose may be adjusted if warranted per a subject’s adverse event profile and blood Phe 
concentrations. Dose increases should be performed as follows. 
• 
When increasing the dose, a dose may be used that is between the dose levels (0.001, 0.003, 0.01, 0.03, 
0.06, 0.1, 0.2, 0.3, 0.4, 0.6, 0.8, 1.0, 2.0, 3.0, 4,0, and 5.0 mg/kg) or 2.5, 5, 10, 20, 40, 75, 150, 225, 300, 
375 mg/week) or per Investigator determination in consultation with the Sponsor’s Medical Officer 
based on available information regarding a subject’s blood Phe (60-600 µmol/L) as well as any adverse 
events (any hypersensitivity reaction) for an individual subject. Dose increases  > 350 mg/week require 
consultation with the sponsor’s medical monitor. 
• 
The dose may be adjusted by increasing the frequency up to daily for a total weekly dose not to exceed 
5.0 mg/kg Subjects who increase their dose frequency will have additional assessments performed 
(Interim Dosing Visit)or 375 mg/week. Dose increases  > 350 mg/week require consultation with the 
sponsor’s medical monitor. 
• 
When a dose is increased, the subject must be observed for 30 60 minutes following the first modified 
dose administration. Subjects who increase their dose frequency do not need to be observed following 
injection of study drug if the increase in frequency does not increase the overall weekly dose amount. 
 
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Section 9.1.2.2, Dose 
Decrease Methodology 
Dose Decrease Methodology 
All dose decreases must be agreed to by both the Investigator and the Sponsor’s Medical Officer. Decisions 
regarding dose decreases will depend on available information regarding a subject’s blood Phe (60-600 µmol/L), 
as well as any adverse events (any hypersensitivity reaction). Dose decreases may occur for safety (ie, 
hypophenylalanemia or any adverse event that may be improved with a lower, more frequent dose).  
A dose should first be reduced by dose level (5.0, 4.0, 3.0, 2.0, 1.0, 0.8, 0.6, 0.4, 0.3, 0.2, 0.1, 0.06, 0.03, 0.01, 
0.003, 0.001 mg/kg or 375, 300, 225, 150, 75, 40, 20, 10, 5, and 2.5 mg/week). It is also permitted to decrease 
dose in between these specified dose levels. If further dosing adjustments are required to attain the target Phe 
concentrationin response to safety, dosing frequency may also be reduced. 
If the subject develops low blood Phe (as defined by a blood Phe level ≤ 30 µmol/Las measured by serum Phe 
levels for a minimum of 1 month), the subject’s rAvPAL-PEG dose should be decreased to the next lower dose. 
If the condition persists after another 1 month at the lower dose, the dose should be decreased again to the next 
lower level. If the subject continues to experience low blood Phe after two dose level reductions, the subject 
may be asked to consult the dietician to eliminate medical foods and/or formulas and to ensure a balanced and 
nutritious diet (as part of the routine standard of care for PKU disease management, subject diet should be 
monitored by a dietician). 
 
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Section 9.4, Treatments 
…. The dose level may be increased per Investigator determination in consultation with the Sponsor’s 
Medical Officer based on available information regarding a subject’s blood Phe level (60-600 µmol/L), 
as well as any adverse events (any hypersensitivity reaction) for an individual subject. The dosage that 
provides control of blood Phe concentrations within the target range of 60-600 µmol/L for a minimum 
of 2 weeks will be determined for each subject by adjusting the dose level, dose frequency, or both, as 
agreed to byper the PI and the Sponsor’s Medical Officer, based upon the subject’s response to doses.  
Subjects may self administer study drug at home if approved by the Investigator and the Sponsor’s 
Medical Officer and if adequate training is demonstrated. Subjects may be eligible to self administer 
study drug if he or she meets the following criteria:  
• The subject is on a stable dosing regimen for 2 weeks (ie, the subject has demonstrated a blood 
Phe level within 60-600 µmol/L for a minimum of 2 consecutive weeks). 
 
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Section 9.4.2.1, Product 
Characteristics and 
Labeling 
The investigational product is rAvPAL-PEG (recombinant Anabaena variabilis phenylalanine ammonia lyase-
PEG). rAvPAL-PEG will be provided in vials or prefilled syringes; subjects will be supplied with vials and 
syringes or prefilled syringes for administration in the clinic and self administration:rAvPAL PEG will be 
provided in 3 mL (milliliter) vials, each containing 1.5 ± 0.2 mL to deliver either 10 mg of rAvPAL PEG per 
1 mL (10 mg/mL protein concentration) or 15 mg or rAvPAL PEG per 1 mL (15 mg/mL protein concentration). 
Each vial is filled with 1.5 ± 0.2 mL to allow the withdrawal and delivery of up to 1 mL of the drug product.  
• 
rAvPAL-PEG will be provided in 3 mL (milliliter) vials, each containing 1.5 ± 0.2 mL to deliver 15 mg 
of rAvPAL-PE per 1.0 mL (15 mg/mL protein concentration). Each vial is filled with 1.5 ± 0.2 mL to 
allow the withdrawal and delivery of up to 1.0 mL of the drug product. 
Or 
• 
rAvPAL-PEG will be provided in 3-mL vials, each containing 1.8 ±0.3 mL to deliver 20 mg of 
rAvPAL-PE per 1.3 mL (15 mg/mL protein concentration). Each vial is filled with 1.8 ± 0.3 mL to 
allow withdrawal and delivery of up to 1.3 mL. 
Or 
• 
rAvPAL-PEG will be provided in prefilled syringes in three sizes that deliver up to 1 mL. Syringe sizes 
are 2.5 mg (5 mg/mL protein concentration), 10 mg (20 mg/mL protein concentration), and 20 mg (20 
mg/mL protein concentration).  
Prefilled Syringe 
Volume 
Concentration 
Dose 
Sku #1 
0.5 mL 
5 mg/mL 
2.5 mg 
Sku #2 
0.5 mL 
20 mg/mL 
10 mg 
Sku #3 
1.0 mL 
20 mg/mL 
20 mg 
 
 
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Section 9.4.2.1, Product 
Characteristics and 
Labeling 
The rAvPAL PEG drug product for SC injection is formulated and supplied as a sterile aqueous 
(colorless to pale yellow) solution in clear, single use, type 1 borosilicate glass vials. Each 3 mL vial 
contains 1.5 ± 0.2 mL to deliver either 10 mg of rAvPAL PEG per 1 mL (10 mg/mL protein 
concentration) or 15 mg of rAvPAL PEG per 1 mL (15 mg/mL protein concentration). Each vial is 
filled with 1.5 ± 0.2 mL to allow the withdrawal and delivery of up to 1 mL of the drug product. 
Dilution instructions are provided in a separate instruction manual. 
 
13 
Section 9.4.4, 
Directions for 
Administration 
Doses will be administered SC and the favorable dose will be determined for each subject by adjusting 
the dose level, dose frequency, or both, as agreed byper the PI and the Sponsor’s Medical Officer, 
based upon the subject’s response to doses. Dosing is up to a maximum dose per week of 5.0 mg/kg 
(or 375 mg for subjects receiving a fixed dose).  
Subjects who have demonstrated efficacy (as measured by blood Phe within the target range of 
60-600 µmol/L for at least 2 consecutive weeksmeasurements) and who have maintained a stable 
rAvPAL-PEG dose for at least 2 consecutive weeksmeasurements may be eligible to transition from 
weight-based dosing to a fixed dosing regimen that would permit daily dosing (5- or 7-days-per-week).  
Subjects who convert to a fixed-dosing regimen should convert their dose based upon the information 
presented in Table 9.4.4.1. 
Table 9.4.4.1 has been revised. 
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Section 9.4.8, Prior and 
Concomitant 
Medication 
….Subjects who have had a prior local skin reaction to rAvPAL-PEG or a PEG-containing product 
will be encouraged towill be premedicated with acetaminophen and/or non-sedating antihistamines 
(refer to Section 9.1.1). If the local skin reaction worsens with a repeat injection (as determined by the 
Investigator in consultation with the Sponsor’s Medical Officer) even with premedication prior to 
study drug dosing, the subject must be withdrawn from the study and complete an Early Termination 
Visit. 
 
10 
Section 9.4.10, Dose 
Interruption and Missed 
Doses 
During this long-term extension study, interruption of rAvPAL-PEG dosing may occur per subject 
decision or per the Investigator in consultation with the Sponsor’s Medical Officer. Subjects who miss 
more than 2 consecutive weekly doses (weekly dosing schedule) or 3 consecutive daily doses (daily 
dosing schedule) for whatever reason may continue participation in this study. After a dosing 
interruption, rAvPAL-PEG administration should be re-started at the same dose level and dosing 
frequency that was administered prior to the dosing interruption. The first dose of rAvPAL-PEG 
following a dose interruption should be administered in a clinic setting, and the subject must be 
observed for 30 60 minutes following administration due to restarting dosing. A follow-up telephone 
call will be made to the subject to monitor subject safety 24 hours following the return to dosing. 
Subjects should continue to perform the study assessments as outlined in the Schedule of Events (refer 
to Table 9.1.1 during any dosing interruption.  
 
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Section 9.6, Dietary or 
Other Protocol 
Restrictions 
Subjects will be instructed that diet should not be altered during the course of the study. Any decision 
to modify subject diet must be made per the Investigator in consultation with the Sponsor’s Medical 
Officer and must be performed under the supervision of the Investigator in consultation with the 
Sponsor’s Medical Officer. 
 
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Section 9.7.2.1, Blood 
Phenylalanine 
Concentration 
Blood samples for Phe concentration measurements will be drawn monthly, at least 2.5 hours after a 
meal, on the days and time points indicated in the Schedule of Events (Table 9.1.1:  ).   
Blood Phe may be collected more often than monthly, rather than weekly, at the discretion of the 
Investigator and provided that the subject meets the following criteriashould more frequent monitoring 
of blood Phe levels be clinically required. 
• Is receiving a stable dose of rAvPAL PEG (defined as no dose modifications or interruptions 
for at least the previous 2 weeks) 
• Has a stable blood Phe level (defined as Phe between 60 600 µmol/L for at least 2  consecutive 
weeks) 
The subject may continue to have monthly, rather than weekly, blood Phe collection provided the 
following do not occur: 
• Blood Phe measurement > 600 µmol/L 
• Blood Phe measurement ≤  30 µmol/L 
If either of these conditions occurs, then that subject should return to weekly blood Phe draws until the 
rAvPAL PEG dose has been adjusted and the Phe level is again within the protocol defined target 
range for at least 2 weeks. 
 
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Section 9.7.5.2, 
Antibody Testing 
Immunogenicity will be assessed by determining immune response and neutralizing activity with the 
following measurements: anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, anti PAL IgE, anti-PEG IgM, 
anti-rAvPAL-PEG IgE, and anti-rAvPAL-PEG neutralizing antibodies (refer to Section 9.1.1.3.3). 
Immunogenicity assays will be performed at the time points indicated in the Schedule of Events 
(Table 9.1.1:  ). 
 
7 
Section 9.7.6, Clinical 
Laboratory 
Assessments 
Table 9.7.6.1 has been updated to reflect changes made within this amendment. 
6, 17 
Section 10.1, Adverse 
Events 
The Investigator should follow all unresolved AEs until the events are resolved or stabilized, the 
subject is lost to follow-up, or it has been determined that the study treatment or study participation is 
not the cause of the AE. Resolution Outcome of AEs (and resolutionwith dates) should be documented 
on the appropriate CRF page(s) and in the subject’s medical record unless the subject is lost to follow-
up or it has been determined that the study treatment or study participation is not the cause of the AE. 
 
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Section 10.3, 
Pregnancy 
Pregnancy in a subject or partner should be reported within 24 hours of the site becoming aware of the 
pregnancy to BioMarin Pharmacovigilance by fax using the Pregnancy Form in the study reference 
materials. The reporting period for pregnancies begins with informed consent and continues until 
4 weeks following the last study drug dose. In addition, pregnancy in a subject is also reported on the 
End of Study CRF. The Investigator must make every effort to follow the subject through resolution of 
the pregnancy (delivery or termination) and to report the resolution to BPV on the Pregnancy Follow
up Formin the study reference materials. In the event of pregnancy in the partner of a study subject, the 
Investigator should make every reasonable attempt to obtain the woman’s consent for release of 
protected health information. 
 
9 
Section 10.5, BioMarin 
Pharmacovigilance 
Contact Information 
Name:  
, MD 
Address: 
105 Digital Drive 
 
 
Novato, CA 94949 USA 
Phone:  
 
Fax: 
 
 
E-mail: 
 
 
16 
Section 12.3.1, Day 1 
(Week 1) 
• Administer study drug (study drug may be administered on additional days during the week as 
determined by the Investigator, in agreement with the Sponsor’s Medical Officer) 
 
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Section 12.3.2, Weekly 
Telephone Visits 
Subjects should have a weekly telephone visit conducted. Subjects must still come into the clinic for the 
scheduled monthly visits per Table 9.1.1:  . The following should be discussed with the subject during the 
weekly telephone visit: 
• 
Injection-site self inspection (previous and current injection site) 
• 
Assessment of AEs 
• 
Concomitant medications 
• 
Confirmation of dose level, frequency, and study drug administration 
Weekly visits do not require an in clinic visit if conducted by a home healthcare professional. However, 
dose modifications must be performed in the clinic. Subjects must have AEs and concomitant medications 
assessed and an injection site inspection performed whenever dose is administered even if the 
administration does not coincide with a scheduled clinic visit. For subjects on a stable dose of 
rAvPAL PEG (ie, no dose change in the last 2 weeks) and have had a phenylalanine (Phe) level at or below 
target range (60 600 µmol/L) for 2 consecutive weeks   weekly visits may be waived and replaced by a 
telephone call per discretion of the Investigator but monthly visits are required. 
The following study activities will be performed at the weekly visits beginning with Week 2: 
• 
Vital signs 
• 
Injection site inspection (previous and current injection site) 
• 
Assessment of AEs 
• 
Concomitant medications 
• 
Diet query 
• 
PK sample  
 
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Section 12.3.2, Weekly 
Telephone Visits 
• Blood Phe and plasma tyrosine concentration 
o Blood Phe may be collected monthly, rather than weekly, if certain criteria are 
satisfied (refer to Section 9.7.2.1). 
• Administer study drug (study drug may be administered on additional days during the week as 
determined by the Investigator, in agreement with the Sponsor’s Medical Officer) 
• Weekly telephone call 
o For those subjects performing self administration and waiving (per Investigator 
discretion) the weekly visit (refer to Section 9.1.1.3.3). 
 
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Section 12.3.4, 
Monthly Visits (Week 
4, 8, 12, etc.) 
Beginning with Week 4, monthly visits must be performed in the clinic. The following study activities 
will be performedand consist of all weekly activities listed above in Section 12.3.2 as well as the 
additional study activities listed below: 
• Vital signs 
• Injection-site inspection (previous and current injection site) 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• Blood Phe and plasma tyrosine concentration 
• PK sample 
• Serum anti rAvPAL PEG antibodies (anti PAL IgG, anti PAL IgM, anti PEG IgG, anti PEG 
IgM, and anti rAvPAL PEG neutralizing antibodies) 
• Weekly telephone call 
o For those subjects performing self administration and waiving (per Investigator 
discretion) the weekly visit (refer to Section 12.3.6. 
 
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Section 12.3.5, 
Quarterly Visits (Week 
12, 24, 36, etc) 
Beginning with Week 12, quarterly visits consist of all weekly (Section 12.3.2) and monthly 
(Section 12.3.4) activities listed above as well as the additional study activities listed below: 
• PK sample 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, anti-PEG 
IgM, and anti-rAvPAL-PEG neutralizing antibodies) 
 
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Section 12.3.6, Interim 
Dosing Visit 
This visit has been removed 
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Section 12.3.7, 
Unscheduled 
Hypersensitivity 
Reaction Visit 
• Vital signs 
• Urine/albumin creatinine ratio 
• Sedimentation rate  
• Urine N-methyl histamine 
• PK sample 
 
Following completion of the Unscheduled Hypersensitivity Reaction visit, subjects who do not have an 
IgE mediated reaction may resume study drug administration per the discretion of the Principal 
Investigator and the Sponsor’s Medical Officer; however, if subject was dosing at home, they will be 
required to come into the clinic for at least 8 weeks. If laboratory data shows that the subject 
experienced an IgE mediated reaction, dosing will not resume until review of the case with the 
Investigator, Sponsor’s Medical Officer and an allergist/immunologist (refer to Section 9.1.1.3.3). 
 
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Section 14.2, Safety 
Analysis 
The Medical Dictionary for Regulatory Activities terminology (MedDRA) will be used by the sponsor 
to assign system organ class and preferred term classification to events and diseases based on the 
original terms entered on the Case Report Form (CRF). 
All AEs will be coded using the Medical Dictionary for Regulatory Activities (MedDRA). The 
incidence of AEs will be summarized by system organ class, preferred term, relationship to study drug, 
and severity. A by–subject listing will be provided for those subjects who experience a serious AE 
(SAE), including death, or experience an AE associated with early withdrawal from the study or study 
drug.Hypersensitivity AEs and AEs that result in dosing interruption or dose level reduction are of 
interest, and the percentage of subjects who report these AEs will be presented. 
Clinical laboratory data will be summarized by the type of laboratory test. Frequency and percentage 
of subjects who experience abnormal (ie, outside of reference range) and/or clinically significant 
abnormalities after study drug administration will be presented for each clinical laboratory test. For 
each clinical laboratory test, descriptive statistics will be provided for baseline and all subsequent 
post-treatment visits. Changes from baseline to the post-treatment visits will also be provided. 
Descriptive statistics, including clinically significant changes from baseline, of vital signs, physical 
examination results, ECG results, and X-ray results, and immunogenicity test results will also be 
provided. Additionally, antibodies and titers will be summarized by scheduled time point. 
 
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Section 14.4, Efficacy 
Analysis 
Change in blood Phe concentration from baseline (to be defined in the SAP) to each scheduled time 
point and presence/absence of antibodies will also be summarized.  
The relationship of dietary Phe intake (per information reported on the subject diet diary) and blood 
Phe concentration will also be explored. Subjects who received any amount of study drug with any 
post-treatment blood Phe concentration measurements and diet diary information will be included in 
this exploratory analysis. Information regarding this exploratory analysis will be provided in the 
Statistical Analysis Plan. 
For subjects who completed the Substudy, the effect of stopping and re starting rAvPAL PEG dosing 
on safety, blood Phe level, and immune response will be explored. Information regarding the 
analysisDetails regarding exploratory analyses will be provided in the SAP Statistical Analysis Plan. 
 
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Section 15, Data 
Monitoring Committee 
The DMC will act independently in an advisory capacity to BioMarin to monitor the safety of 
rAvPAL-PEG in subjects who participate in the study. Meetings of the DMC can be convened at any 
time at the discretion of the DMC Chair or the Sponsor’s Medical Officer. The Chair will be notified 
by the Sponsor’s Medical Officer of all SAEs and will receive summaries of other safety data as 
available. The DMC will review the study data as soon as it is available during the study, on a schedule 
defined in the DMC Charter, and offer advice on whether or not to proceed, modify or terminate study 
enrollment on the basis of toxicity. Details regarding the DMC membership and safety data to be 
reviewed by members will be provided in a charter. 
The responsibilities of the DMC are to: 
• Assess the effect and relevance of new external evidence. 
• Make recommendations to the BioMarin concerning continuation or termination of the study or 
other study modifications based on observations. 
 
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Section 16, 
Compensation, 
Insurance, and 
Indemnity 
….The treating physician should bill the subject’s health insurance company or other third party payer 
for the cost of this medical treatment, unless the executed Clinical Trial Agreement between BioMarin 
and the institution of the investigator specifies otherwise. If the subject has followed the Investigator’s 
instructions, BioMarin willmay pay for reasonable and necessary medical services to treat the injuries 
caused by the IP or study procedures, if these costs are not covered by health insurance or another third 
party that usually pays these costs. In some jurisdictions, BioMarin is obligated by law to pay for 
study-related injuries without prior recourse to third party payer billing. If this is the case, BioMarin 
will comply with the law. 
 
17 
Section 17, Case Report 
Forms and Source 
Documents 
BioMarin’s policy is that study data on the CRFs must be verifiable to the source data, which 
necessitates access to all original recordings, laboratory reports, and subject records. In addition, all 
source data should be attributable (signed and dated). The Investigator must therefore agree to allow 
direct access to all source data. Subjects (or their legally authorized representative) must also allow 
access to their medical records, and subjects will be informed of this and will confirm their agreement 
when giving informed consent. If an Investigator or institution refuses to allow access to subject 
records because of confidentiality, arrangements must be made to allow an “interview” style of data 
verification. 
 
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CLINICAL STUDY PROTOCOL AMENDMENT SUMMARY 
Amendment: 6 
Date: October 30, 2014 
 
RATIONALE AND SUMMARY OF CHANGES 
The protocol for Study PAL-003 is being amended to make the following changes: 
1. All subjects who are on stable doses of rAvPAL- PEG, including subjects on doses 
between 70 mg/week and 350 mg/week (inclusive) may remain in this study to 
continue open-label administration with rAvPAL-PEG. Subjects may be eligible for 
participation in the long-term, open-label extension portion of the Phase 3 study, 
165-302. These revisions align with changes being made to the BMN 165 Phase 3 
study, 165-302. 
2. The individual and study stopping criteria have been revised and reflect a better 
understanding of the risk/benefit with rAvPAL-PEG administration. Stopping criteria 
revisions are aligned with recommendations from an independent Data Monitoring 
Committee (DMC) and the Food and Drug Administration (FDA). 
a. If a severe or life-threatening National Cancer Institute Common Terminology 
Criteria for Adverse Events (NCI-CTCAE) grade  ≥ 3 hypersensitivity event 
occurs that is treatment-related and meets clinical criteria (Brown, 2004, 
J.Allergy Clin.Immunol.) for severe, an ad hoc independent DMC will 
convene within 7 days of the event to review and advise the sponsor on 
potential changes to the study conduct. 
b. Individual subjects who have an NCI-CTCAE grade  ≥ 3 hypersensitivity 
event that is treatment-related and is suspected to meet the clinical criteria 
(Brown, 2004, J.Allergy Clin.Immunol.) for severe in the judgment of the 
investigator and the sponsor’s medical monitor may be permanently 
discontinued from study drug. 
c. Anaphylaxis (per National Institute of Allergy and Infectious Disease/Food 
Allergy and Anaphylaxis Network [NIAID/FAAN] criteria) is an AE of 
special interest that should be reported to the sponsor within 24 hours to 
facilitate rapid reporting to sponsor for review. 
3. Instructions have been added for reintroducing study drug following anaphylaxis.  
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4. Safety precautions have been added:  
a. Premedications administered prior to study drug for subjects who have had a 
hypersensitivity AE have been revised based on a better understanding of the 
safety profile of rAvPAL-PEG. Changes are also consistent with 
recommendations from an independent immunologist. Should premedication 
be required, H1 antagonist, H2 antagonist, and non-steroidal 
anti-inflammatory medication (NSAIDs) should be administered 
approximately 2-3 hours prior to study drug per investigator determination. 
NSAIDs should be given with food and may be omitted if not tolerated. 
b. At least two epinephrine injectors will be issued to subjects for use in case of 
anaphylaxis. Subjects will receive training on self-administration and will be 
instructed to carry one epinephrine injector with them at all times. Sites will 
assess that the epinephrine injectors have not expired and that subjects are 
adhering to instructions.   
5. Information to track and categorize device (prefilled syringe) malfunction and 
failures, device-related injuries, and any medication errors attributed to device 
performance has been added.   
6. Anti-rAvPAL immunoglobulin E (IgE) antibody assessment has been added to the 
Hypersensitivity Reaction Visit to better assess IgE response. The anti-protein IgE 
test serves as a control to determine whether anti-rAvPAL IgE antibody positivity 
may be missed in anti-rAvPAL-PEG IgE assessment due to potential protein epitope 
masking by the extensive pegylation.  The collection and testing of serum anti-PAL 
IgG, anti-PAL IgM, anti-PEG IgG, anti-PEG IgM and anti-rAvPAL-PEG neutralizing 
antibodies for Unscheduled Hypersensitivity Visits are no longer necessary as all 
these antibodies are tested frequently (at routine study visits) and can provide results 
at or near the time of an hypersensitivity AE. 
7. rAvPAL-PEG dosing information has been revised to include instructions specific to 
prefilled syringe. Self-administration training for prefilled syringe drug product has 
been added. 
8. The study duration has been extended for another 12 months. The maximum study 
duration is now 98 months. 
9. The final follow-up visit schedule has been changed from 1 week to 4 weeks after the 
final dose to better monitor safety by collecting AEs and SAEs during this period, and 
to align with the Early Termination Visit as well as other BMN 165 protocols. 
10. The requirement for observed dosing in clinic following dose interruption has been 
extended from one day following the interruption to one week following interruption.  
This revision aligns the requirement for observed dosing following interruption in 
PAL-003 with that in the 165 phase 3 studies.  
11. The injection site inspection procedure has been discontinued. 
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Proprietary and Confidential  
12. The criteria for subject eligibility to self-administer study drug has been revised.  All 
subjects in PAL-003 have now been receiving home-based dosing for at least a year; 
in addition, all subjects in the ongoing Phase 3 BMN 165 studies are dosed at home.  
Safety data to date indicate that mild to moderate hypersensitivity adverse events 
commonly occur in subjects receiving BMN 165 but can generally be safely managed 
with continued home-based dosing.   Safety precautions including detailed guidance 
regarding response to hypersensitivity AEs are being added to all ongoing studies; 
this guidance supersedes previous PAL-003 instruction mandating return to 
clinic-based dosing for all hypersensitivity reactions or Grade 3 or higher adverse 
events.  In addition, PAL-003 experience has shown that dosing adjustments (either 
increase or decrease) are occasionally necessary to maintain optimal Phe control in 
the long term and can be safely made without return to clinic-based dosing. 
13. The rAvPAL-PEG immunogenicity profile has been revised and updated. Information 
that characterizes the specific antibody responses detected in subjects has been added.  
14. Additional minor changes have been made to improve clarity and consistency. 
Specific major revisions since the completion of the last protocol amendment (Amendment 5, 
dated 28FEB2014) to the text of each section are outlined in Section 24. 
 
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2 
SYNOPSIS 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
TITLE OF STUDY: 
Long-term Extension of a Phase 2, Open-Label Dose-Finding Study to Evaluate the Safety, Efficacy, 
and Tolerability of Multiple Subcutaneous Doses of rAvPAL-PEG in Subjects with PKU 
PROTOCOL NUMBER:  PAL-003 
STUDY SITES:  Approximately 20 centers in the United States 
PHASE OF DEVELOPMENT:  Phase 2 
STUDY RATIONALE: 
The need exists for a treatment that will help individuals with phenylketonuria (PKU) safely achieve 
lifelong, reliable control of blood phenylalanine (Phe) concentrations and improve functional 
outcomes. PEGylated recombinant Anabaena variabilis phenylalanine ammonia lyase (rAvPAL-PEG) 
is a potential substitute for the phenylalanine hydroxylase (PAH) enzyme, which is defective in 
individuals with PKU. rAvPAL-PEG may control blood Phe concentrations, which may have 
additional clinical benefits. This study is an extension of the rAvPAL-PEG Phase 2 studies PAL-002, 
PAL-004, and 165-205. Administration of rAvPAL-PEG will be continued to assess the long-term 
safety and efficacy of rAvPAL-PEG in PKU subjects. 
Blood Phe levels depend not only on the functional presence of the endogenous enzyme PAH but also 
on the dietary intake of Phe. It is important to understand the role of diet on blood Phe levels 
concurrent with the administration of rAvPAL-PEG treatment. Therefore, an exploratory objective has 
been added to this study to assess the relationship of diet, rAvPAL-PEG administration, and blood Phe 
level. Changes to subject diet are not allowed in this study unless per the Investigator. Diet will be 
monitored using a diet diary. 
A pharmacokinetic (PK) substudy has been added to evaluate the steady-state PK of rAvPAL-PEG in 
up to 6 subjects who have achieved and maintained target blood Phe for at least 2 consecutive 
measurements and for whom no further dose modifications are planned. Single-dose PK data has been 
collected in the Phase 1 study, PAL-001. However, there is little multiple-dose PK data or data for 
when subjects have reached and maintained a stable dosing regimen.  With the PK substudy, 
multiple-dose PK data were collected for subjects who have already achieved Phe reduction to within 
the protocol-defined target range.  This substudy has been completed as of 20 December 2013. 
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PAL-003 A6 
Page 6 
 
Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
OBJECTIVES: 
The primary objective of the study is: 
• 
To evaluate the effect of long-term administration of multiple doses of SC injections of 
rAvPAL-PEG on blood Phe concentrations in subjects with PKU. 
The secondary objectives of the study are: 
• 
To evaluate the safety and tolerability of long-term administration of subcutaneous (SC) 
injections of rAvPAL-PEG in subjects with PKU. 
• 
To evaluate the immune response to long-term administration of SC injections of 
rAvPAL-PEG in subjects with PKU. 
The exploratory objective of the study is as follows: 
• 
To evaluate the long-term relationship of diet and change in blood Phe concentration 
following administration with rAvPAL-PEG in subjects with PKU. 
The Substudy objectives are as follows: 
• 
To evaluate steady-state PK of rAvPAL-PEG in subjects who have achieved and maintained 
target blood Phe concentration and for whom no further dose modifications are planned. 
STUDY DESIGN AND PLAN: 
This is a long-term extension of rAvPAL-PEG Phase 2 studies in up to 100 subjects with PKU. The 
doses are planned to be in the same range as those previously tested in the Phase 2 studies (starting at 
0.001 through 5.0 mg/kg/week or 2.5 mg through 375 mg/week), provided no dose-limiting toxicity is 
observed in a previous rAvPAL-PEG study. Subjects’ doses will not exceed 375 mg/week. 
Only subjects who completed a previous rAvPAL-PEG study will be enrolled into this study. Subjects 
enrolling into PAL-003 with no interruption in dosing from a previous rAvPAL-PEG study may either 
continue their previous dosing regimen or begin this study at a higher dose level. Subjects who have 
had dosing interruptions between the previous rAvPAL-PEG study and PAL-003 must have their 
starting dose determined per the sponsor’s medical monitor. The first dose will be administered in the 
clinic, and the subject must be observed for 30 minutes following administration. Additionally, 
subjects will be given two epinephrine injectors and will be instructed to carry one epinephrine 
injector with them at all times (refer to Section 9.4). A follow-up telephone call will be made to the 
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Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
subject to monitor subject safety 24 hours following the return to dosing.  
Diet should not be altered during the course of this study.  Any decision to modify subject diet must be 
made per the Investigator and must be performed under the supervision of the Investigator. To monitor 
for changes in subject diet, a diet diary will be issued to subjects for completion and will be reviewed 
with the clinical study staff on a monthly basis.  
Subjects may self-administer study drug at home if approved by the Investigator and the sponsor’s 
medical monitor and if adequate training is demonstrated. Subjects must meet a set of criteria to be 
considered appropriate for self-administration.  Additional training will be provided to subjects and 
demonstration of competency required when prefilled syringe drug product is introduced, every 
24 weeks, and more often as needed. 
Subjects will be evaluated for safety throughout the study. Toxicity will be measured according to the 
National Cancer Institute (NCI) Common Terminology Criteria for Adverse Events (CTCAE), 
version 4. 
In addition to the Sponsor, a Data Monitoring Committee (DMC) will monitor the safety of subjects in 
the study. The DMC is an independent committee that will act in an advisory capacity to the Sponsor. 
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take 
rAvPAL-PEG. Subjects’ previous rAvPAL-PEG dosing will generally continue in PAL-003. In 
PAL-003, each subject’s dose will be adjusted as needed to attempt to attain or maintain blood Phe 
concentrations of 60-600 µmol/L. rAvPAL-PEG dose will be based on either a subject’s weight or will 
be a fixed dose. Doses will be evaluated on an individual basis. 
Evaluations, observations, and procedures will be conducted at selected time points. After the subject’s 
blood Phe concentration has been controlled to within a target range (60-600 µmol/L), the subject may 
be asked to have additional blood draws for PK and blood Phe concentration analyses as needed per 
the discretion of the Investigator in consultation with the sponsor’s medical monitor. 
A subject will continue in PAL-003 until one of the following occurs: 
• 
The subject withdraws consent and discontinues from the study. 
• 
The subject is discontinued from the study at the discretion of the Investigator or Sponsor. 
• 
 The subject has completed the study through the Month 98 visit. 
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PAL-003 A6 
Page 8 
 
Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
• 
 The study is terminated. 
• 
The study drug receives marketing authorization. 
Subjects may withdraw from treatment with study drug at any time; however, subjects will be asked to 
continue to perform the study assessments until study completion. Subjects may also withdraw from 
study participation at any time. Because the completeness of the data affects the integrity, accuracy, 
and interpretation of study results, every effort should be made to retain subjects in the study and to 
have them complete the study assessments as scheduled as long as continued participation does not 
compromise subject safety. 
A PK substudy has been added to evaluate the steady-state PK of rAvPAL-PEG in up to 6 subjects 
who have achieved and maintained target blood Phe for at least 2 consecutive measurements and for 
whom no further dose modifications are planned.  Subjects enrolled into the substudy will have 
additional pre-dose PK sampling performed.  This substudy has been completed as of 
20 December 2013 . 
PAL -003 Substudy 
Dose Modifications: 
Dose Increase Methodology
Each subject’s dose may be modified based on the decision of the Investigator. Decisions regarding 
dose increases will depend on a subject’s adverse event profile and blood Phe and drug concentrations.  
: 
An individual subject’s dose may be adjusted beginning on Day 1 of PAL-003. For the duration of this 
study, an individual subject’s dose may be adjusted if warranted per a subject’s adverse event profile 
and blood Phe concentrations. Dose increases should be performed as follows. 
• 
The dose may be increased by increments of no more than 10-fold higher than the subject’s 
current dose. 
• 
When increasing the dose, a dose may be used that is between the dose levels (0.001, 0.003, 
0.01, 0.03, 0.06, 0.1, 0.2, 0.3, 0.4, 0.6, 0.8, 1.0, 2.0, 3.0, 4,0, and 5.0 mg/kg or 2.5, 5, 10, 20, 
40, 75, 150, 225, 300, 375 mg/week) or per Investigator determination based on available 
information regarding a subject’s blood Phe (60-600 µmol/L) as well as any adverse events 
(any hypersensitivity reaction) for an individual subject. Dose increases  > 350 mg/week 
require consultation with the sponsor’s medical monitor. 
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PAL-003 A6 
Page 9 
 
Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
• 
The dose may be adjusted by increasing the frequency up to daily for a total weekly dose not 
to exceed 5.0 mg/kg or 375 mg/week.  Dose increases  > 350 mg/week require consultation 
with the sponsor’s medical monitor. 
• 
When a dose is increased, the subject must be observed for 30 minutes following the first 
modified dose administration. Subjects who increase their dose frequency do not need to be 
observed following injection of study drug if the increase in frequency does not increase the 
overall weekly dose amount. 
• 
Only 1 dose adjustment is allowed every 2 weeks. 
Decisions regarding dose decreases will depend on available information regarding a subject’s blood 
Phe (60-600 µmol/L), as well as any adverse events (any hypersensitivity reaction). Dose decreases 
may occur for hypophenylalanemia or any adverse event that may be improved with a lower dose.  
Dose Decrease Methodology 
A dose should first be reduced by dose level (5.0, 4.0, 3.0, 2.0, 1.0, 0.8, 0.6, 0.4, 0.3, 0.2, 0.1, 0.06, 
0.03, 0.01, 0.003, 0.001 mg/kg or 375, 300, 225, 150, 75, 40, 20, 10, 5, and 2.5 mg/week). It is also 
permitted to decrease dose in between these specified dose levels. If further dosing adjustments are 
required in response to safety, dosing frequency may also be adjusted. 
If the subject develops low blood Phe (as defined by a blood Phe level ≤ 30 µmol/L), the subject’s 
rAvPAL-PEG dose should be decreased to the next lower dose. If the condition persists after another 
1 month at the lower dose, the dose should be decreased again to the next lower level. If the subject 
continues to experience low blood Phe after two dose level reductions, the subject may be asked to 
consult the dietician to eliminate medical foods and/or formulas and to ensure a balanced and 
nutritious diet (as part of the routine standard of care for PKU disease management, subject diet should 
be monitored by a dietician). 
Safety Assessment Criteria: 
Subjects are evaluated for safety throughout the study and are trained to recognize potential 
hypersensitivity AEs (including anaphylaxis) and how to respond. Subjects are instructed to contact 
the investigator for any suspected hypersensitivity AE. The investigator may require further evaluation 
at the clinic. If a hypersensitivity AE (eg, injection-site reaction, rash, joint pain, itching) occurs, the 
subject may be advised to premedicate with H1 antagonist, H2 antagonist, and non-steroidal 
Response to Hypersensitivity Adverse Events  
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PAL-003 A6 
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Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
anti-inflammatory medication (NSAIDs) approximately 2-3 hours prior to  subsequent rAvPAL-PEG 
doses. NSAIDs should be given with food and may be omitted if not tolerated.  
Hypersensitivity AEs, including anaphylaxis, are expected with rAvPAL-PEG administration. 
rAvPAL-PEG dosing in response to a suspected hypersensitivity AE may be modified or halted 
depending on the severity of the event and suspected rAvPAL-PEG causality. Severity for 
hypersensitivity AEs will be per NCI-CTCAE grades. 
Subjects who have an NCI CTCAE grade  ≥ 3 hypersensitivity AE that is related to study drug and is 
suspected to meet Brown’s criteria for severe (grade 3) in the judgment of the investigator and the 
sponsor’s medical monitor may be permanently discontinued from study drug.  
Individual Stopping Criteria 
Dosing in response to a hypersensitivity AE depends on the NCI-CTCAE grade and suspected 
relationship to rAvPAL-PEG. Dosing instructions are presented in 
Dosing in Response to Hypersensitivity Adverse Events 
Table 9.1.1.2.1 and are regardless 
of previous occurrence. 
Once an AE (other than anaphylaxis) improves to grade 1 or resolves, study drug dose may be 
increased, maintained, or reduced. If dosing has been interrupted due to an AE (other than 
anaphylaxis) and the investigator determines it is safe for the subject to resume dosing, the first dose 
after improvement of the AE should be performed in the clinic. The subject must be observed for 
30 minutes following administration due to restarting dosing. The subject may be advised to 
premedicate with H1 antagonist, H2 antagonist, and NSAIDs approximately 2-3 hours prior to 
subsequent BMN 165 doses. NSAIDs should be given with food and may be omitted if not tolerated. 
If the investigator suspects that the event is anaphylaxis, the subject will be assessed in the clinic. 
Laboratory assessments for suspected anaphylaxis events should be performed prior to the next 
administration of study drug (if applicable) and include anti-rAvPAL IgE and anti-rAvPAL-PEG IgE 
(sampling must be performed >8 hours after event onset and before the next dose of study drug) and 
tryptase (within 24 hours of event onset). The investigator will consult with the sponsor’s medical 
monitor, and a decision will then be made whether to discontinue the subject from study drug, restart 
dosing at the same dose level, or restart dosing at a lower dose level. 
Response to Anaphylaxis  
For the first week of dosing after resolution of anaphylaxis, the study drug will be administered in a 
clinic setting with equipment for emergency resuscitation (including epinephrine) within easy access.  
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PAL-003 A6 
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Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
The subject must be observed for 30 minutes following administration due to restarting dosing. 
Additionally, the subject should be premedicated with H1 antagonist, H2 antagonist, and NSAIDs 
approximately 2-3 hours prior to each dose of study drug for one week upon return to dosing 
regardless of the duration of dose interruption. NSAIDs should be given with food and may be omitted 
if not tolerated.  
If an NCI-CTCAE grade  ≥ 3 hypersensitivity treatment-related event occurs and meets Brown’s 
criteria for severe (grade 3), an ad hoc independent DMC meeting will convene within 7 days of the 
event to review and advise the sponsor on potential changes to the study conduct. Clinically severe 
hypersensitivity is defined as significant hypoxia, hypotension or neurologic compromise that is 
life-threatening or required treatment to prevent a life-threatening event:  
Stopping Criteria: 
• 
Cyanosis or SpO2 ≤ 92%  
• 
Hypotension with SBP < 90 mm Hg (adults)  
• 
Neurologic alteration: loss of consciousness, collapse, incontinence 
Brown’s severity criteria are presented in Table 9.1.2.1.  
NUMBER OF SUBJECTS PLANNED: 
Up to 100 subjects. 
DIAGNOSIS AND ALL CRITERIA FOR INCLUSION AND EXCLUSION:  
Individuals eligible to participate in this study must meet all of the following criteria: 
1. Must have completed participation in a previous rAvPAL-PEG study. 
2. Willing and able to provide written, signed informed consent, or, in the case of participants 
under the age of 18, provide written assent (if required) and written informed consent by a 
parent or legal guardian, after the nature of the study has been explained, and prior to any 
research-related procedures. 
3. Willing and able to comply with all study procedures.  
4. Females of childbearing potential must have a negative pregnancy test at Screening and be 
willing to have additional pregnancy tests during the study. Females considered not of 
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PAL-003 A6 
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Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
childbearing potential include those who have been in menopause at least 2 years, or had tubal 
ligation at least 1 year prior to Screening, or who have had total hysterectomy. 
5. Sexually active subjects must be willing to use an acceptable method of contraception while 
participating in the study.  Males post vasectomy for 2 years with no known pregnancies do 
not need to use any other forms of contraception during the study. 
6. Maintained a stable diet. 
7. In generally good health as evidenced by physical examination, clinical laboratory evaluations 
(hematology, chemistry, and urinalysis), and electrocardiogram (ECG) at Screening. 
Individuals who meet any of the following exclusion criteria will not be eligible to participate in the 
study: 
1. Use of any investigational product (with the exception of rAvPAL-PEG) or investigational 
medical device within 30 days prior to Screening, or requirement for any investigational agent 
prior to completion of all scheduled study assessments. 
2. Use of any medication other than rAvPAL-PEG that is intended to treat PKU within 14 days 
prior to the administration of study drug. 
3. Use or planned use of any injectable drugs containing PEG (other than rAvPAL-PEG), 
including Depo-Provera, within 6 months prior to Screening and during study participation.  
4. A prior reaction that included systemic symptoms (eg, generalized hives, respiratory or 
gastrointestinal problems, hypotension, angioedema, anaphylaxis) to rAvPAL-PEG or a 
PEG-containing product. Subjects with a prior systemic reaction may be eligible for 
participation per the discretion of the Principal Investigator in consultation with the sponsor’s 
medical monitor. However, subjects who discontinued from study treatment early due to a 
reaction are not eligible to enroll into this study.    
5. Pregnant or breastfeeding at Screening or planning to become pregnant (self or partner) or to 
breastfeed at any time during the study.  
6. Concurrent disease or condition that would interfere with study participation or safety 
(eg, history or presence of clinically significant cardiovascular, pulmonary, hepatic, renal, 
hematologic, gastrointestinal, endocrine, immunologic, dermatologic, neurological, oncologic, 
or psychiatric disease). 
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PAL-003 A6 
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Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
7. Any condition that, in the view of the PI, places the subject at high risk of poor treatment 
compliance or of not completing the study. 
8. Known hypersensitivity to rAvPAL-PEG necessitating early termination from a previous 
rAvPAL-PEG study or known hypersensitivity to any of its excipients. 
9. Alanine aminotransferase (ALT) concentration > 2 times the upper limit of normal. 
10. Creatinine  > 1.5 times the upper limit of normal. 
INVESTIGATIONAL PRODUCT, DOSE, ROUTE AND REGIMEN: 
The investigational product is rAvPAL-PEG (recombinant Anabaena variabilis phenylalanine 
ammonia lyase-PEG). rAvPAL-PEG will be provided in vials or prefilled syringes; subjects will be 
supplied with vials and syringes or prefilled syringes for administration in the clinic and self-
administration: 
• 
rAvPAL-PEG will be provided in 3 mL (milliliter) vials, each containing 1.5 ± 0.2 mL to 
deliver 15 mg of rAvPAL-PEG per 1.0 mL (15 mg/mL protein concentration). Each vial is 
filled with 1.5 ± 0.2 mL to allow the withdrawal and delivery of up to 1.0 mL of the drug 
product. 
Or: 
• 
rAvPAL-PEG will be provided in 3-mL vials, each containing 1.8 ±0.3 mL to deliver 20 mg of 
rAvPAL-PEG per 1.3 mL (15 mg/mL protein concentration). Each vial is filled with 
1.8 ± 0.3 mL to allow withdrawal and delivery of up to 1.3 mL. 
Or: 
• 
rAvPAL-PEG will be provided in prefilled syringes in three sizes that deliver up to 1 mL. 
Syringe sizes are 2.5 mg (5 mg/mL protein concentration), 10 mg (20 mg/mL protein 
concentration), and 20 mg (20 mg/mL protein concentration).  
Refer to Table 9.4.2.1.1 for information on prefilled syringe volume, concentration, and dose. 
Subjects who have undergone training and who have demonstrated competency on the use of prefilled 
syringe in the study clinic may be eligible to transition from vial and syringe to prefilled syringe 
dosing. Additionally, regular refresher training on use of prefilled syringe will be provided in study 
clinic every 24 weeks, and more often as needed.  
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PAL-003 A6 
Page 14 
 
Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
Subjects should convert their vial and syringe dose to prefilled syringe dose using information 
presented in Table 9.4.2.1.2. 
The excipients in this drug product are tromethamine, tromethamine-hydrochloride, sodium chloride, 
L-phenylalanine, and water for injection. 
rAvPAL-PEG doses will be administered SC by either health care professionals or via 
self-administration. The dose level may be increased or decreased per Investigator determination based 
on available information regarding a subject’s blood Phe level (60-600 µmol/L), as well as any adverse 
events (any hypersensitivity reaction) for an individual subject. The dosage that provides control of 
blood Phe concentrations within the target range of 60-600 µmol/L for a minimum of 2 consecutive 
measurements will be determined for each subject by adjusting the dose level, dose frequency, or both, 
per the PI, based upon the subject’s response to doses. 
Subjects who have demonstrated efficacy (ie, blood Phe within the target range of 60-600 µmol/L for 
at least 2 consecutive measurements) and who have maintained a stable rAvPAL-PEG dose for at least 
2 consecutive measurements may be eligible to transition from weight-based dosing to a fixed dosing 
regimen that would permit daily dosing (5- or 7-days-per-week). Subjects should convert their 
weight-based dose using information presented in 
Fixed Dosing 
Table 9.4.4.1. 
DURATION OF TREATMENT: 
Up to 98 months. 
REFERENCE THERAPY(IES), DOSE, ROUTE AND REGIMEN:  
None 
CRITERIA FOR EVALUATION: 
Efficacy
Blood Phe concentrations will be measured.  
: 
Immunogenicity
The presence of antibodies (anti-PAL immunoglobulin G [IgG], anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibodies, anti-rAvPAL IgE, and anti-PEG-PAL IgE) 
will be assessed. 
: 
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PAL-003 A6 
Page 15 
 
Proprietary and Confidential  
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
Safety
Safety will be evaluated on the incidence of adverse events (AEs) and clinically significant changes in 
vital signs, ECG results, X-ray results, and laboratory test results. 
: 
Pharmacokinetic
Plasma concentrations of rAvPAL-PEG will be measured for subjects participating in the Substudy. 
: 
STATISTICAL METHODS:  
Sample Size
Subjects who participated in a previous rAvPAL-PEG study may be enrolled into this study. 
No formal sample size calculation was conducted for this study or the PAL-003 Substudy. 
: 
Safety Analysis
All subjects who receive any amount of study drug in this study and have postdose safety information 
will be included in the safety analyses. 
: 
The Medical Dictionary for Regulatory Activities terminology (MedDRA) will be used by the 
sponsor to assign system organ class and preferred term classification to events and diseases based 
on the original terms entered on the Case Report Form (CRF). The incidence of AEs will be 
summarized by system organ class, preferred term, relationship to study drug, and severity. A 
by-subject listing will be provided for those subjects who experience a serious AE (SAE), including 
death, or experience an AE associated with early withdrawal from the study or study drug. 
Hypersensitivity AEs and AEs that result in dosing interruption or dose level reduction are of interest, 
and the percentage of subjects who report these AEs will be presented.  
Clinical laboratory data will be summarized by the type of laboratory test. Frequency and percentage 
of subjects who experience abnormal (ie, outside of reference range) and/or clinically significant 
abnormalities after study drug administration will be presented for each clinical laboratory test. For 
each clinical laboratory test, descriptive statistics will be provided for baseline and all subsequent 
post-treatment visits. Changes from baseline to the post-treatment visits will also be provided. 
Descriptive statistics for vital signs, physical examination results, ECG results, X-ray results, and 
immunogenicity test results will also be provided. Additionally, antibodies and titers will be 
summarized by scheduled time point. 
 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
Efficacy Analysis
Data from all subjects who receive any amount of study drug and who have any post-treatment 
efficacy data will be included in the efficacy analysis. 
: 
Blood Phe concentration at each scheduled time point will be summarized using descriptive statistics 
(mean, standard deviation, median, minimum, and maximum). Change in blood Phe concentration 
from baseline (to be defined in the Statistical Analysis Plan [SAP]) to each scheduled time point and 
presence/absence of antibodies will also be summarized. In addition, the proportion of subjects who 
have maintained target Phe concentrations of 60-600 µmol/L will be summarized by each scheduled 
time point. 
Exploratory Analysis
Details regarding exploratory analyses will be provided in the SAP.  
: 
Substudy Analysis
For subjects who completed the Substudy, the steady-state PK of rAvPAL-PEG in subjects who have 
achieved and maintained target blood Phe will be explored. 
: 
Pharmacokinetic Analysis
Subjects who complete the Substudy will have the following PK parameters assessed: area under the 
plasma concentration-time curve (AUC), time to maximum plasma concentration (Tmax), maximum 
plasma concentration (Cmax), half life (t1/2), and clearance (CL/F).  
: 
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3 
TABLE OF CONTENTS 
1 TITLE PAGE .......................................................................................................................1 
2 SYNOPSIS ...........................................................................................................................5 
3 TABLE OF CONTENTS ...................................................................................................17 
4 LIST OF ABBREVIATIONS AND DEFINITIONS OF TERMS ....................................21 
5 ETHICS..............................................................................................................................25 
5.1 Institutional Review Board or Ethics Committee .....................................................25 
5.2 Ethical Conduct of Study ..........................................................................................25 
5.3 Subject Information and Informed Consent ..............................................................26 
6 INVESTIGATORS AND STUDY ADMINISTRATIVE STRUCTURE ........................27 
7 INTRODUCTION .............................................................................................................28 
7.1 Nonclinical Studies ...................................................................................................28 
7.2 Previous Clinical Studies ..........................................................................................29 
7.2.1 
Phase 1 Study, PAL-001 .............................................................................30 
7.2.2 
Phase 2 Studies PAL-002, PAL-004, and 165-205 .....................................30 
7.3 Study Rationale .........................................................................................................34 
7.4 Summary of Overall Risks and Benefits ...................................................................35 
7.4.1 
Toxicity Due to Exposure to Polyethylene Glycol (PEG) ..........................35 
7.4.2 
Immunologic Response ...............................................................................36 
7.4.3 
Management of Hypersensitivity Reactions ................................................37 
8 STUDY OBJECTIVES ......................................................................................................39 
9 INVESTIGATIONAL PLAN ............................................................................................40 
9.1 Overall Study Design and Plan .................................................................................40 
9.1.1 
Response to Hypersensitivity Adverse Events ............................................46 
9.1.2 
Study Stopping Criteria ...............................................................................48 
9.1.3 
Dose Modifications .....................................................................................49 
9.2 Discussion of Study Design, Including Choice of Control Group ............................50 
9.3 Selection of Study Population ...................................................................................50 
9.3.1 
Inclusion Criteria .........................................................................................50 
9.3.2 
Exclusion Criteria ........................................................................................51 
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9.3.3 
Removal of Subjects from Treatment or Assessment .................................52 
9.3.4 
Subject Identification and Replacement of Subjects ...................................53 
9.4 Treatments .................................................................................................................53 
9.4.1 
Treatments Administered ............................................................................55 
9.4.2 
Identity of Investigational Product (IP) .......................................................55 
9.4.3 
Storage .........................................................................................................58 
9.4.4 
Directions for Administration .....................................................................58 
9.4.5 
Method of Assigning Subjects to Treatment Groups ..................................59 
9.4.6 
Selection of Doses Used in the Study .........................................................60 
9.4.7 
Blinding .......................................................................................................60 
9.4.8 
Prior and Concomitant Medications ............................................................60 
9.4.9 
Treatment Compliance ................................................................................61 
9.4.10 Dose Interruption and Missed Doses ...........................................................61 
9.5 Investigational Product Accountability .....................................................................61 
9.5.1 
Return and Disposition of Clinical Supplies ...............................................62 
9.6 Dietary or Other Protocol Restrictions......................................................................62 
9.7 Efficacy and Safety Variables ...................................................................................62 
9.7.1 
Efficacy and Safety Measurements Assessed .............................................62 
9.7.2 
Efficacy Variable .........................................................................................64 
9.7.3 
Pharmacokinetic Variables ..........................................................................64 
9.7.4 
Exploratory Efficacy Variable .....................................................................64 
9.7.5 
Safety Variables ..........................................................................................65 
9.7.6 
Clinical Laboratory Assessments ................................................................65 
10 REPORTING ADVERSE EVENTS .................................................................................67 
10.1 Adverse Events .........................................................................................................67 
10.2 Serious Adverse Events ............................................................................................69 
10.3 Pregnancy ..................................................................................................................71 
10.4 Urgent Safety Measures ............................................................................................71 
10.5 BioMarin Pharmacovigilance Contact Information ..................................................72 
11 APPROPRIATENESS OF MEASUREMENTS ...............................................................73 
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11.1 Safety and Pharmacokinetics ....................................................................................73 
11.2 Diet Diary ..................................................................................................................73 
12 STUDY PROCEDURES ...................................................................................................74 
12.1 Prestudy .....................................................................................................................74 
12.2 Screening Visit ..........................................................................................................74 
12.3 Treatment Period .......................................................................................................74 
12.3.1 Day 1 (Week 1) ...........................................................................................75 
12.3.2 Weekly Telephone Visit ..............................................................................75 
12.3.3 Substudy Visits ............................................................................................76 
12.3.4 Monthly Visits (Week 4, 8, 12, etc) ............................................................76 
12.3.5 Quarterly Visits (Week 12, 24, 36, etc) .......................................................76 
12.3.6 Unscheduled Hypersensitivity Reaction Visit .............................................77 
12.4 Early Termination Visit ............................................................................................77 
12.5 Final Follow-up Visit ................................................................................................78 
13 DATA QUALITY ASSURANCE .....................................................................................80 
14 STATISTICAL METHODS AND DETERMINATION OF SAMPLE SIZE ..................81 
14.1 Statistical and Analytical Plans .................................................................................81 
14.2 Safety Analysis .........................................................................................................81 
14.3 Pharmacokinetic Analysis .........................................................................................81 
14.3.1 Pharmacokinetic Substudy Analysis ...........................................................82 
14.4 Efficacy Analysis ......................................................................................................82 
14.5 Determination of Sample Size ..................................................................................82 
14.6 Handling of Missing Data .........................................................................................82 
14.7 Interim Analyses .......................................................................................................83 
14.8 Changes in the Conduct of the Study or Planned Analyses ......................................83 
15 DATA MONITORING COMMITTEE (DMC) ................................................................84 
16 COMPENSATION, INSURANCE, AND INDEMNITY .................................................85 
17 CASE REPORT FORMS AND SOURCE DOCUMENTS ..............................................86 
18 STUDY MONITORING AND AUDITING .....................................................................87 
19 RETENTION OF RECORDS ...........................................................................................88 
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20 USE OF INFORMATION AND PUBLICATION ...........................................................89 
21 REFERENCES ..................................................................................................................90 
22 INVESTIGATOR RESPONSIBILITIES ..........................................................................92 
22.1 Conduct of Study and Protection of Human Subjects...............................................92 
23 SIGNATURE PAGE .........................................................................................................93 
24 PROTOCOL AMENDMENT MAJOR TEXT REVISIONS ............................................94 
 
LIST OF TABLES 
Table 9.1.1:  Schedule of Events .............................................................................................42 
Table 9.1.2:  PK Substudy Dosing Regimens ..........................................................................45 
Table 9.1.1.2.1:  Dosing Instructions in Response to Hypersensitivity Adverse Events .........47 
Table 9.1.2.1:  Brown’s Severity Criteria ................................................................................49 
Table 9.4.2.1.1:  Prefilled Syringe Volume, Concentration, and Dose ....................................56 
Table 9.4.2.1.2:  Conversion from Vial and Syringe Dose to Prefilled Syringe Dose ............56 
Table 9.4.4.1:  Fixed Doses for Subjects on Weight-Based Dose Regimen ............................59 
Table 9.7.1.1:  Summary of Laboratory Assessments .............................................................63 
Table 9.7.6.1:  Clinical Laboratory Tests ................................................................................66 
 
 
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4 
LIST OF ABBREVIATIONS AND DEFINITIONS OF TERMS 
ADR 
Abbreviations 
adverse drug reaction 
AE 
adverse event 
ALT 
alanine aminotransferase 
AST 
aspartate aminotransferase 
AUC 
area under the plasma concentration-time curve 
AUC0-7 days 
area under the plasma concentration-time curve from time zero on Day 1 
to Day 8 
BUN 
blood urea nitrogen 
°C 
degree Celsius 
C3 
complement 3 
C4 
complement 4 
CBC 
complete blood count 
CD 
Compact disk 
CFR 
Code of Federal Regulations 
CH50 
total hemolytic complement 
Cmax 
maximum plasma concentration 
CNS 
central nervous system 
CO2 
carbon dioxide 
CRA 
Clinical Research Associate 
CRF 
case report form 
CRP 
C-reactive protein 
CTCAE 
Common Terminology Criteria for Adverse Events 
CV 
cardiovascular 
DBP 
diastolic blood pressure 
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DMC 
Data Monitoring Committee 
ECG 
electrocardiogram 
ETV 
Early Termination Visit 
FDA 
Food and Drug Administration 
F/U 
follow-up 
g 
gram 
GCP 
Good Clinical Practice 
GGT 
gamma-glutamyltransferase 
GI 
gastrointestinal 
IB 
Investigator’s Brochure 
ICF 
Informed Consent Form 
ICH 
International Conference on Harmonisation of Technical Requirements for 
Registration of Pharmaceuticals for Human Use 
ID 
identification 
IgE 
immunoglobulin E 
IgG 
immunoglobulin G 
IgM 
immunoglobulin M 
IP 
investigational product 
IRB 
Institutional Review Board 
IV 
intravenous 
kg 
kilogram 
MedDRA 
Medical Dictionary for Regulatory Activities 
mg 
milligram 
mL 
milliliter 
mm Hg 
millimeter of mercury 
NAb 
neutralizing antibodies 
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NCI 
National Cancer Institute 
NIAID/FAAN National Institute of Allergy and Infectious Disease/Food Allergy and 
Anaphylaxis Network 
NOAEL 
no observable adverse effect level 
NSAID 
non-steroidal anti-inflammatory medication 
OTC 
over the counter 
PAH 
phenylalanine hydroxylase 
PAL 
phenylalanine ammonia lyase 
PEG 
polyethylene glycol 
Phe 
phenylalanine 
PI 
Principal Investigator 
PK 
pharmacokinetics 
PKU 
phenylketonuria 
rAvPAL-PEG 
recombinant Anabaena variabilis phenylalanine ammonia lyase-PEG 
RBC 
red blood cell 
SAE 
serious adverse event 
SAP 
Statistical Analysis Plan 
SBP 
systolic blood pressure 
SC 
subcutaneous 
SD 
standard deviation 
SDV 
source data verified 
SGOT 
serum glutamic oxalo-acetic transaminase 
SGPT 
serum glutamic pyruvate transaminase 
US 
United States 
WBC 
white blood cell 
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Definition of Terms: 
Investigational Product (IP): 
“A pharmaceutical form of an active ingredient or placebo being tested or used as a reference 
in a clinical trial, including a product with a marketing authorization when used or assembled 
(formulated or packaged) in a way different from the approved form, or when used for an 
unapproved indication, or when used to gain further information about an approved use.” 
(from E6 ICH)  
The terms “IP” and “study drug” may be used interchangeably in the protocol. 
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5 
ETHICS 
5.1 
Institutional Review Board or Ethics Committee 
Prior to initiating the study, the Investigator will obtain written confirmation that the 
Institutional Review Board (IRB) is properly constituted and compliant with International 
Conference on Harmonisation of Technical Requirements for Registration of 
Pharmaceuticals for Human Use (ICH) and Good Clinical Practice (GCP) requirements, and 
applicable laws and local regulations. A copy of the confirmation from the IRB will be 
provided to BioMarin Pharmaceutical Inc. (BioMarin) or its designee. The Principal 
Investigator (PI) will provide the IRB with all appropriate material, including the protocol, 
Investigator’s Brochure (IB), the Informed Consent Form (ICF) including compensation 
procedures, and any other written information provided to the subjects, including all consent 
forms translated to a language other than the native language of the clinical site. The study 
will not be initiated and investigational product (IP) supplies will not be shipped to the site 
until appropriate documents from the IRB confirming unconditional approval of the protocol, 
the ICF and all subject recruitment materials are obtained in writing by the PI and copies are 
received at BioMarin or its designee. The approval document should refer to the study by 
protocol title and BioMarin protocol number (if possible), identify the documents reviewed, 
and include the date of the review and approval. BioMarin will ensure that the appropriate 
reports on the progress of the study were made to the IRB and BioMarin by the PI in 
accordance with applicable governmental regulations. 
5.2 
Ethical Conduct of Study 
This study will be conducted in accordance with the following: 
• United States (US) Code of Federal Regulations (CFR) sections that address clinical 
research studies, and/or other national and local regulations, as applicable 
• E6 ICH Guideline for GCP 
• The ethical principles established by the Declaration of Helsinki 
Specifically, this study is based on adequately performed laboratory and animal 
experimentation; the study will be conducted under a protocol reviewed and approved by an 
IRB; the study will be conducted by scientifically and medically qualified persons; the 
benefits of the study are in proportion to the risks; the rights and welfare of the subjects will 
be respected; the physicians conducting the study do not find the hazards to outweigh the 
potential benefits; and each subject, or his or her legally authorized representative will 
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provide written, informed consent before any study-related tests or evaluations are 
performed. 
5.3 
Subject Information and Informed Consent 
A properly written and executed ICF, in compliance with the Declaration of Helsinki, 
E6 ICH (GCP Guideline, Section 4.8) and 21 CFR Part 50 and other applicable local 
regulations, will be obtained for each subject prior to entering the subject into the study. The 
Investigator will prepare the ICF and provide the documents to BioMarin for approval prior 
to submission to the IRB. BioMarin and the IRB must approve the documents before they are 
implemented. A copy of the approved ICF, and if applicable, a copy of the approved subject 
information sheet, minor assent form, parental ICF for studies involving minors, and all ICFs 
translated to a language other than the native language of the clinical site must also be 
received by BioMarin or its designee prior to the delivery of study drug. 
Subjects under the age of 18 years will provide written assent (if required), and his/her 
legally authorized representative (parent or legal guardian) will provide written informed 
consent for such subjects. The Investigator will provide copies of the signed ICF to each 
subject (or the subject’s legally authorized representative) and will maintain the original in 
the subject’s record file. 
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6 
INVESTIGATORS AND STUDY ADMINISTRATIVE STRUCTURE 
Prior to beginning the study, the PI at each site must provide to BioMarin or its designee a 
fully executed and signed Form FDA (Food and Drug Administration) 1572 and a Financial 
Disclosure Form. All sub-Investigators must be listed on Form FDA 1572. Financial 
Disclosure Forms must also be completed for all sub-Investigators listed on the 
Form FDA 1572 who will be directly involved in the treatment or evaluation of research 
subjects in this study. 
The study will be administered by and monitored by employees or representatives of 
BioMarin. Clinical Research Associates (CRAs) or trained designees will monitor each site 
on a periodic basis and perform verification of source documentation for each subject as well 
as other required review processes. BioMarin’s Pharmacovigilance Department (or designee) 
will be responsible for the timely reporting of serious adverse events (SAEs) to appropriate 
regulatory authorities as required. Some study assessments, including administration of study 
drug, may be performed at the subject’s home. All assessments performed for this study will 
be administered by clinic staff or other qualified and trained study personnel. 
Anti-rAvPAL-PEG (recombinant Anabaena variabilis phenylalanine ammonia lyase 
polyethylene glycol) immunoglobulin E (IgE) antibody analysis will be performed by a 
vendor; other antibody analysis will be performed by BioMarin. Clinical laboratory tests, 
including serum pregnancy tests (if applicable), will be analyzed and processed by a central 
laboratory, with the exception of erythrocyte sedimentation rate (ESR), and urine pregnancy 
tests (if applicable), which will be analyzed by a local laboratory. A central laboratory will 
also be used to perform analysis of blood phenylalanine (Phe) concentrations and urinalysis. 
Pharmacokinetic (PK) analysis will be performed by BioMarin. 
Prior to database lock in multicenter studies, a Coordinating Investigator will be identified 
who will read the clinical study report and confirm that it accurately describes the conduct 
and results of the study, to the best of his or her knowledge. The Coordinating Investigator 
will be chosen on the basis of active participation in the study, ability to interpret data, and 
willingness to review and sign the report in a specified timeframe. 
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7 
INTRODUCTION 
A comprehensive review of PEGylated recombinant Anabaena variabilis phenylalanine 
ammonia lyase (rAvPAL-PEG) is contained in the IB supplied by BioMarin; the Investigator 
should review this document prior to initiating this study. 
7.1 
Nonclinical Studies 
The nonclinical program for rAvPAL-PEG has characterized the pharmacology, 
pharmacokinetics (PK), and toxicology of rAvPAL-PEG using the intended clinical SC route 
of administration. Pharmacology was assessed in the BTBR Pahenu2 (ENU2) mouse model of 
PKU. The ENU2 mouse model exhibits characteristics similar to those of PKU patients, 
including hyperphenylalaninemia (baseline plasma Phe concentrations of 1000 to 2000 µM) 
and hypopigmentation. Following weekly doses of rAvPAL-PEG administered to male 
ENU2 mice, plasma Phe concentrations decreased from approximately 2000 µM to 
< 200 µM after 2 dose administrations. An attenuated reduction of blood Phe was seen 
between Week 3 and Week 7 of dosing. After 7 weekly administrations of rAvPAL-PEG, 
pharmacological activity returned as evidenced by stabilized concentrations of plasma Phe 
< 200 µM over the entire week, which continued for a total of 15 weeks. 
In pharmacodynamic studies in the BTBR Pahenu2 (ENU2) mouse model administered 
80 mg/kg/week rAvPEG-PAL, two dose interruption assessments were performed:  a 
2-4 week dose interruption and an 11-week dose interruption. Following both dose 
interruption assessments, the animals re-started rAvPAL-PEG at a dose of 80 mg/kg/week. 
No attenuated Phe response was observed when rAvPAL-PEG injections were temporarily 
stopped for 2-4 weeks, and there was an immediate return to stable blood Phe reductions. A 
similar interim attenuated response was observed with the longer dose interruption of 
approximately 11 weeks.  In both of these assessments, no safety issues were noted upon 
re-starting dosing with rAvPAL-PEG (Lapis, 2007, ASHG 57th Annual Meeting). 
Safety pharmacology studies were conducted in rats and cynomolgus monkeys. No 
respiratory or central nervous system (CNS) effects were seen with SC administration of 
rAvPAL-PEG. No changes in cardiovascular (CV) parameters, including electrocardiogram 
(ECG) waveforms, were observed in telemetry-instrumented monkeys assessed for the CV 
effects of rAvPAL-PEG administered subcutaneously. 
Pharmacokinetic parameters were evaluated in single-dose and repeat-dose studies in rats and 
cynomolgus monkeys. The elimination half-life (t1/2) values of rAvPAL-PEG administered to 
normal rats at SC doses of 10, 25, and 250 mg/kg were 47, 33, and 44 hours, respectively, 
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and exhibited modest area under the plasma concentration-time curve (AUC)-dose. In the 
cynomolgus monkey after SC administration of rAvPAL-PEG, the t1/2 was 65 hours at 
4.0 mg/kg, 71 hours at 12 mg/kg, and could not be determined at 60 mg/kg (the highest 
dose). Qualitatively, the kinetics of rAvPAL-PEG in the rat and monkey appear to have 
similar characteristics. The following findings were noted: (1) a 1-compartment model with 
first-order absorption appears to describe the plasma profiles of rAvPAL-PEG after 
single-dose administration, (2) absorption is slow and there is a long absorption period after 
SC administration to maximum observed plasma concentration (Cmax), along with a long t1/2, 
(3) elimination is slow and monophasic, (4) there does not appear to be a gender difference, 
and (5) the AUC and the Cmax are roughly linearly proportional.  
Toxicology of rAvPAL-PEG was assessed in single-dose and repeat-dose studies in normal 
rats and cynomolgus monkeys. In the single-dose rat study, decreased body weight gain and 
Kupffer cell vacuolization at the high SC dose of 250 mg/kg was observed; however, the 
Kupffer cell finding was not seen in the single-dose study in cynomolgus monkeys. In a 
26-week repeat-dose toxicity and toxicokinetic (TK) rat study, decreased body weight gain, 
decreased food consumption, vacuolation/hypertrophy of the renal tubule cells, and 
vacuolation of the histiocytic cells were observed in rats administered 25 mg/kg/dose, twice 
weekly. In a 39-week repeat-dose study in monkeys, arterial inflammation, perivascular 
cellular infiltrates in the SC injection sites, thymic atrophy, and increased lymphoid nodules 
in bone marrow of the sternum were observed in monkeys given ≥ 3 mg/kg/dose, twice 
weekly. Of these findings, only the arterial inflammation was deemed adverse and this 
finding was completely reversed after 13-weeks of recovery. The 
no-observed-adverse-effect-level (NOAEL) of rAvPAL-PEG when administered 
subcutaneously twice weekly for 26 weeks and 39 weeks in the rat and monkey, respectively, 
was 1.0 mg/kg. These NOAELs were based on histological findings of 
vacuolation/hypertrophy of the renal tubule cells in the rat and arterial inflammation findings 
in the monkey. 
7.2 
Previous Clinical Studies 
The rAvPAL-PEG clinical development program has been designed to demonstrate the 
safety and efficacy of rAvPAL-PEG in reducing blood Phe concentrations in PKU subjects 
who do not respond to treatment with Kuvan® or are not compliant with Kuvan® treatment. 
This study is an extension of the ongoing human clinical studies with rAvPAL-PEG 
(Study PAL-002, Study PAL-004, and Study 165-205) based on data from the completed 
clinical study, PAL-001, and clinical experience from this ongoing study and the other 
ongoing Phase 2 studies, PAL-002 and PAL-004.  
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7.2.1 Phase 1 Study, PAL-001 
The first-in-human trial using rAvPAL-PEG, Study PAL-001, was a Phase 1, open-label, 
dose-escalation study in PKU subjects in the US. The primary objective was to assess the 
safety and tolerability of single SC injections of rAvPAL-PEG. Secondary objectives were to 
evaluate the PK of single, SC injections of rAvPAL-PEG administered at escalating doses in 
subjects with PKU and to evaluate the effect of rAvPAL-PEG on blood Phe concentrations. 
The effectiveness of rAvPAL-PEG in decreasing Phe concentrations in nonclinical studies of 
ENU2 mice was consistent with what was observed in PAL-001. PAL-001 enrolled 25 PKU 
subjects with a mean (standard deviation; SD) baseline blood Phe concentration of 
1310 µmol/L (405). The 25 subjects who enrolled into the study were assigned to receive a 
single administration of rAvPAL-PEG at 1 of 5 dose levels: 0.001, 0.003, 0.01, 0.03, and 
0.1 mg/kg. Five subjects each received 1 of the 5 dose levels of rAvPAL-PEG. 
Key safety, efficacy, and PK results of Study PAL-001 are summarized as follows: 
• rAvPAL-PEG was well tolerated and had a clinically significant blood-lowering 
effect on Phe concentration when administered at a dose of 0.1 mg/kg. 
• For the 5 subjects who were administered 0.1 mg/kg rAvPAL-PEG, clinically 
significant reductions in blood Phe level were observed, with the most clinically 
significant decreases from baseline values to Day 7, ranging from 33.8% to 97.3% 
(mean of 58.12%). The mean baseline blood Phe level for these 5 subjects was 
1113 µmol/L. 
• Overall, no clinically significant reductions in blood Phe level were observed in 
subjects who were administered rAvPAL-PEG at the lower doses of 0.001, 0.003, 
0.01, and 0.03 mg/kg. 
• For subjects who were administered rAvPAL-PEG at the 3 higher dose levels (0.01, 
0.03, and 0.1 mg/kg) and who had measurable rAvPAL-PEG concentration levels, the 
calculated PK parameters were a mean Tmax of 89-106 hours, a t1/2 of 46-120 hours, 
and an AUC0-t, and Cmax that were proportional with dose. Drug exposure was slightly 
increased with increased dose. 
7.2.2 Phase 2 Studies PAL-002, PAL-004, and 165-205 
Based on results from the Phase 1, single-dose study, the Phase 2 studies have been designed 
to evaluate rAvPAL-PEG at various doses and dosing regimens to safely achieve and 
maintain blood Phe reductions in subjects with PKU. Currently, there are three ongoing 
Phase 2 studies (PAL-002, PAL-004, 165-205); an overview of each study is presented in 
Section 7.2.2.1 (PAL-002), Section 7.2.2.2 (PAL-004), and Section 7.2.2.3 (165-205).  
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7.2.2.1 
Study PAL-002 
Study PAL-002 (A Phase 2, Open-Label, Dose-Finding Study to Evaluate the Safety, 
Efficacy, and Tolerability of Multiple Subcutaneous Doses of rAvPAL-PEG in Subjects With 
Phenylketonuria) was initiated in September 2009 and has completed enrollment. As of 
10 September 2012, 40 subjects have been enrolled and 37 have completed the study. 
PAL-002 enrolled 11 previously exposed subjects from the single-dose study, PAL-001, and 
29 subjects who were naïve to rAvPAL-PEG. Thirty-three of the 37 subjects who completed 
PAL-002 enrolled into this open-label extension study (PAL-003). Two subjects 
discontinued from the study due to lost to follow-up, relocation, or other reasons, and 
1 subject discontinued from the study due to an AE (skin reaction).  
The primary objective of this study was to evaluate the effect of multiple doses of 
rAvPAL-PEG (ranging from 0.001 mg/kg/week to 1.0 mg/kg/week) on blood Phe 
concentrations in subjects with PKU with up to 16 weeks of treatment. The secondary 
objectives of the study were to evaluate the safety and tolerability of SC injections of 
multiple doses of rAvPAL-PEG, to evaluate the immune response to rAvPAL-PEG, and to 
evaluate the PK profile of rAvPAL-PEG in subjects with PKU.  
The PAL-002 study design consists of two parts. In Part 1, rAvPAL-PEG was administered 
as a once weekly fixed, low-dose induction regimen for 8 weeks. In Part 2, the rAvPAL-PEG 
dose was titrated upwards; subjects received adjustable dose increases for up to 8 weeks to 
achieve a target blood Phe concentration of 600 µmol/L. The doses and dosing schedules 
were revised with a series of protocol amendments to incorporate the information gained 
during conduct of this early, open-label, multiple-dose study.  
A wide range of doses was planned for the PAL-002 study, beginning with doses as low as 
0.001mg/kg/week.  However, no substantial reductions in blood Phe level were observed in 
the majority of subjects who were administered rAvPAL-PEG in the initial four cohorts at 
doses of 0.001, 0.003, 0.01, and 0.03 mg/kg administered once per week. The absence of 
appreciable Phe reduction after 16 weeks of treatment in this range of doses led to a decision 
to amend the study protocol to include a cohort with a higher starting dose of 
0.1 mg/kg/week, which had been previously shown to decrease blood Phe levels to 
approximately 600 µmol/L in the single-dose, Phase 1 study (PAL-001). After the first 
2 weeks of dosing at 0.1 mg/kg/week, transient Phe reduction was observed in this subset of 
subjects. However, this dosing regimen was accompanied by mild to moderate 
hypersensitivity reactions primarily after the second weekly dose, suggesting that additional 
exploration of dosing regimens would be required.  
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In summary, preliminary results from PAL-002 demonstrated that doses below 0.1 g/kg 
administered once per week were not effective in reducing Phe levels.  While transient 
reduction of Phe was apparent at doses of at least 0.1 mg/kg given once per week, this dose 
regimen was associated with a high incidence of systemic hypersensitivity reactions, 
typically following the second weekly dose.  Further escalation above this dose of 
0.1 mg/kg/week would be required to sustain the effect on Phe levels over time.  Increased 
doses would require spreading dose administration over several days per week, as 
once-weekly administration of higher doses would not be practical due to the large volume of 
study drug.  Therefore, additional dosing regimens would need to be explored in a 
subsequent study (PAL-004). 
Once subjects completed Study PAL-002, they were eligible to enroll into this open-label 
extension study, PAL-003 to continue to receive rAvPAL-PEG up to a maximum dose of 
5.0 mg/kg/week or 375 mg/week. 
7.2.2.2 
Study PAL-004 
PAL-004 (An Open-Label Study to Evaluate the Safety, Tolerability, and Efficacy of 
Subcutaneous Dose Levels of rAvPAL-PEG Administered Daily in Subjects With 
Phenylketonuria) was initiated in April 2011 and has completed enrollment. As of 
10 September 2012, 16 subjects have been enrolled, 15 subjects have completed the study, 
and 15 subjects have enrolled into this study (PAL-003). One subject withdrew consent from 
continued participation prior to study completion. All subjects enrolled in this study were 
naïve to rAvPAL-PEG exposure. 
The objective of this study was to determine if daily administration (defined as 5days/week) 
of rAvPAL-PEG at dose levels of 0.06, 0.1, 0.2, 0.4, 0.6, and 0.8 mg/kg/day was safe and 
effective in reducing and maintaining blood Phe concentrations to 600 µmol/L in subjects 
with PKU. The starting dose was 0.4 mg/kg, administered 5 days/week. A total of 12 subjects 
were added in sequence and were started on doses of 0.4, 0.2, 0.1, 0.06 mg, or 0.001/kg/day 
based on incoming safety data. Overall, subjects in PAL-004 who initiated treatment at 
higher daily doses of 0.1 to 0.4 mg/kg/day achieved immediate and substantial reduction of 
blood Phe levels, but dosing had to be temporarily reduced or interrupted due to the onset of 
systemic hypersensitivity reactions at approximately Day 10 of dosing. Phe reductions did 
not persist in the setting of temporary dose reduction or interruption, but Phe levels generally 
improved if higher dose levels were reinstated.  
To prevent the onset of hypersensitivity reactions that were temporally associated with the 
onset of anti-drug IgM responses, an additional dosing strategy was assessed in PAL-004; 
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4 subjects initiated dosing at a low dose of 0.001mg/kg/day or 0.06mg/kg/day for 
5 consecutive days and then dosing was suspended for 2 weeks. Dosing was restarted on 
Day 21 at the initial dose followed by dose titration to target Phe levels. Subjects 
administered this dosing regimen had similar efficacy, but the incidence of hypersensitivity 
reactions appeared to be similar to that of subjects who did not have the planned dose 
interruption, suggesting little advantage with this alternate induction regimen.  
Experience from PAL-004 indicated that initiating daily rAvPAL-PEG dosing with relatively 
high daily doses was not sustainable due to the onset of hypersensitivity reactions that 
occurred approximately 9 to 12 days after the start of administration, nor was the alternate 
dosing regimen (2 week drug holiday) well tolerated or effective in Phe reduction. In 
addition, the daily treatment regimen did not reduce the time to achieve target blood Phe 
levels seen in previous studies. This study indicated that to improve tolerability, 
rAvPAL-PEG should be initiated with an induction period at doses substantially lower than 
0.4mg/kg, followed by upward dose titration toward target Phe levels.   
Once subjects completed Study PAL-004, they were eligible to enroll into this open-label 
extension study to continue to receive rAvPAL-PEG up to a maximum dose of 
5.0 mg/kg/week or 375 mg/week. 
7.2.2.3 
Study 165-205 
Study BMN 165-205 (A Phase 2, Multi-Center, Open-Label, Dose-Finding Study to Evaluate 
Safety, Efficacy, and Tolerability of Subcutaneously Administered rAvPAL-PEG in Subjects 
With PKU for 24 Weeks) was initiated in May 2012. Data from ongoing Studies PAL-002, 
PAL-004, and PAL-003 suggested that a 4-week treatment course with weekly dosing at a 
fixed low dose (induction), followed by a weekly 2-fold, upward titration of rAvPAL-PEG to 
approximately 10-fold higher than the initiation dose (maximum of 375 mg/week) is 
effective and well tolerated. The objective of this study was to further assess this dosing 
regimen. Two rAvPAL-PEG dosing regimens were to be explored in this study:  weekly 
low-dose induction (2.5 mg/week for 4 to 8 weeks), followed by a period of upward dose 
titration towards a target Phe level (600 µmol/L) followed by maintenance dosing at that 
level through the 24 week study duration (Group 1).  The other dosing regimen planned for 
this study (Group 2) involved administration of a single bolus dose of 8 mg, followed by a 
treatment holiday of at least 3 weeks duration followed by resumption and escalation of study 
drug administration following a pattern similar to that employed in Group 1. A total of 
24 subjects were enrolled into 165-205. In addition to confirming an effective, well-tolerated 
dose regimen, this study incorporated non-weight-based dosing, starting with dose 
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administration once per week at a low dose (2.5mg) with gradual escalation and conversion 
of dose administration to 5x/week dosing for chronic maintenance therapy.  
Once subjects have completed Study 165-205, they are eligible to enroll into this study to 
continue to receive rAvPAL-PEG up to a maximum dose of 5.0 mg/kg/week or 
375 mg/week, or into the Phase 3 study, BMN 165-302. 
7.3 
Study Rationale 
PKU is an autosomal, recessive, inherited disease characterized by deficiency in the enzyme 
PAH. Approximately 1 in every 10,000 infants in North America is born with PKU 
(Scriver, 2001, McGraw-Hill). Left untreated, PAH deficiency is associated with an 
abnormally elevated concentration of Phe, which is toxic to the brain (Kaufman, 1989, J 
Pediatr.) and can result in a variety of neuropathologic conditions, including mental 
retardation, microcephaly, delayed speech, seizures, and behavioral abnormalities 
(Scriver, 2001, McGraw-Hill). The brains of untreated patients with PKU show evidence of 
hypomyelination and gliosis, arrest in cerebral development, and, in some cases, white matter 
degeneration (Huttenlocher, 2000, Eur.J Pediatr.). Elevated Phe during fetal development 
leads to severe mental retardation and can cause microcephaly, growth retardation, and 
congenital heart disease (Guttler, 2003, Pediatrics), (Koch, 2003, Pediatrics), (Lee, 2003, 
Pediatrics), (Levy, 2003, Pediatrics), (Matalon, 2003, Pediatrics), (Rouse, 2004, J.Pediatr.). 
For a subset of patients with residual enzyme activity, treatment with Kuvan® is an option. 
For all other patients, current management of PKU involves adherence to low-Phe medicinal 
diet formulas and dietary restriction of Phe-containing foods. Implementation of a 
Phe-restricted diet in infancy significantly reduces blood Phe concentrations and prevents 
many of the neuropathologic manifestations of PKU, including severe mental retardation. 
However, compliance with this restrictive diet can be difficult for older children, adolescents, 
and adults, and adherence may result in nutritional deficiencies due to the limitations of 
natural protein sources (Fisch, 2000, Eur.J.Pediatr.), (Walter, 2002, Lancet). 
The need exists for a treatment that will help individuals with PKU safely achieve lifelong, 
reliable control of blood phenylalanine (Phe) concentrations and improve functional 
outcomes. rAvPAL-PEG is a potential substitute for the phenylalanine hydroxylase (PAH) 
enzyme, which is defective in individuals with PKU. rAvPAL-PEG may control blood Phe 
concentrations, which may have additional clinical benefits.  
Blood Phe levels depend not only on the functional presence of the endogenous enzyme PAH 
but also on the dietary intake of Phe. It is important to understand the role of diet on blood 
Phe levels concurrent with the administration of rAvPAL-PEG treatment. Therefore, an 
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exploratory objective has been added to this study to assess the relationship of diet, 
rAvPAL-PEG administration, and blood Phe level. Changes to subject diet are not allowed in 
this study unless per the Investigator. Diet will be monitored using a diet diary.     
A pharmacokinetic (PK) substudy has been added to evaluate the steady-state PK of 
rAvPAL-PEG in up to 6 subjects who have achieved and maintained target blood Phe for at 
least 2 consecutive measurements and for whom no further dose modifications are planned. 
Single-dose PK data has been collected in the Phase 1 study, PAL-001. However, there is 
little multiple-dose PK data or data for when subjects have reached and maintained a stable 
dosing regimen.  With the PK substudy, multiple-dose PK data will be collected for subjects 
who have already achieved Phe reduction to within the protocol-defined target range. 
This study is an extension of previous rAvPAL-PEG Phase 2 studies. Administration of 
rAvPAL-PEG will be continued to assess the long-term safety and efficacy of rAvPAL-PEG 
in PKU subjects. 
7.4 
Summary of Overall Risks and Benefits 
It is not expected that data from previous rAvPAL-PEG studies will change the assumption 
that rAvPAL-PEG has a toxicity profile similar to other recombinant PEGylated non-human 
enzymes currently in use. The toxicities of these drugs usually fall into 2 main categories: 
toxicity due to exposure to PEG, and toxicity due to immunologic sensitization. In addition, 
exaggerated pharmacological effects resulting in very low Phe concentrations could be 
observed. Other adverse events (AEs) that could occur with rAvPAL-PEG include 
injection-site reactions and other general symptoms. 
7.4.1 Toxicity Due to Exposure to Polyethylene Glycol (PEG) 
Acute exposure to high doses of PEG can result in renal toxicity. There have been a few 
reports of PEG-related AEs in humans; cumulative intravenous (IV) PEG doses of 121 to 
240 g caused acute renal tubular necrosis, oliguria, and azotemia. The anticipated PEG 
exposure associated with the expected rAvPAL-PEG dose range (6 g per week) is at least 
80-fold lower than the reported toxic doses and comparable to exposures to PEG in widely 
used medicines and other compounds that are administered by the IV, oral, rectal, and topical 
routes (Webster, 2007, Drug Metab Dispos.). No indication of PEG-related toxicity at the 
ultrastructural level was observed in monkeys given a single dose of up to 60 mg/kg 
rAvPAL-PEG SC. In rats, both renal tubule vacuolation and histiocytic cell vacuoles have 
been assocated with PEG-related catabolism and administration of other PEGylated proteins 
(refer to Section 7.1). 
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In this study, subjects will be monitored closely with urine examinations and blood 
chemistries to follow kidney function. 
7.4.2 Immunologic Response 
The active drug substance in rAvPAL-PEG is a bacterial protein and elicits immune 
recognition and subsequent antibody responses. Antibody epitopes on the protein are 
expected to be rendered at least partially inaccessible by the extensive PEGylation on the 
drug (Gamez, 2007, Mol.Genet.Metab). In vivo and in vitro experiments have shown that 
PEGylation of proteins and cells can attenuate the immunological response (Scott, 1997, 
Proc.Natl.Acad.Sci.U.S.A), (Chen, 2001, BioDrugs.). PEGylation has been effective in 
reducing anti-rAvPAL antibody titers in the mouse model but does not eliminate antibody 
formation. Although PEGylation of rAvPAL likely reduces the antigenicity of the molecule, 
100% of individuals exposed to rAvPAL-PEG develop antibodies against rAvPAL.  
Drug-specific immune responses can range from clinical irrelevance to causing serious 
hypersensitivity AEs (such as anaphylaxis) and may reduce efficacy due to 
antibody-mediated drug clearance or antibody neutralization of enzymatic activity. 
Historically, PEG was thought to be nonimmunogenic (Davis, 1981, Clin.Exp.Immunol.), 
(Harris, 2003, Nat.Rev.Drug Discov.); however, repeated studies have found that 
subcutaneous (SC) and intravenous exposure to PEG can induce anti-PEG antibodies 
(Harris, 2003, Nat.Rev.Drug Discov.), (Richter, 1983, Int.Arch.Allergy Appl.Immunol.). In 
some instances, development of such antibodies did not result in significant clinical effects in 
humans (Richter, 1984, Int.Arch.Allergy Appl.Immunol.). However, PEG antibody responses 
were associated with hypersensitivity reactions to PEGylated liposomes (Judge, 2006, 
Mol.Ther.). Anti-PEG antibodies have also been associated with nonresponsiveness against 
therapy (Armstrong, 2007, Cancer), (Ganson, 2006, Arthritis Res.Ther.). 
Subjects participating in the Phase 2 clinical studies have been monitored closely for 
anti-drug immunogenicity (anti-rAvPAL immunoglobulin G [IgG], anti-rAvPAL IgM, 
anti-PEG IgM, anti-PEG IgG, neutralizing antibodies that inhibit PAL enzymatic activity, 
anti-rAvPAL IgE, and anti-rAvPAL-PEG IgE), complements, C-reactive protein (CRP), 
ESR, and complete chemistry. All subjects treated with rAvPAL-PEG in the Phase 2 clinical 
trials developed antibodies against the PAL protein. Anti-rAvPAL IgM antibodies were first 
detected within 2-3 weeks of treatment initiation and anti-rAvPAL IgG antibodies were 
detected within 2-3 months. The anti-rAvPAL IgG response generally peaked by 3-5 months 
and was sustained in all subjects. Neutralizing antibodies (NAb) capable of inhibiting 
enzymatic activity were detected in a minority of subjects 2-3 months after treatment 
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initiation. The timing of the NAb response suggests these antibodies may be a component of 
the anti-rAvPAL IgG response. It is expected that the centralized location of the PAL active 
site, within the tetrameric structure, makes it difficult for antibodies to bind and inhibit 
enzymatic activity. In addition, anti-PAL antibody binding is likely sterically hindered by the 
extensive PEGylation. The majority of treated subjects also developed a transient anti-PEG 
antibody response. The anti-PEG response was comprised of IgM and IgG isotypes. In 
general, anti-PEG antibodies were no longer detected after 5-6 months of treatment. This 
type of transient antibody response is typical of T cell-independent type 2 (TI-2) responses. 
The majority of immune-mediated AEs experienced in subjects treated with rAvPAL-PEG in 
the Phase 2 studies are believed to be the result of antibody-mediated hypersensitivity. The 
primary immune mediator is thought to be IgM immune complexes, as evidenced by the 
timing of onset prior to IgG development and the reduced occurrence over time. IgE positive 
test results have not been associated with hypersensitivity in any of the subjects thus far, and 
the majority of subjects have been safely rechallenged with rAvPAL-PEG following 
reactions. IgM immune complexes are known to be efficient activators of the classical 
complement pathway and can lead to the accumulation of complement component 
anaphylatoxins (C3a, C4a, C5a) that can induce hypersensitivity symptoms. Although IgG 
immune complexes can also activate the classical complement pathway, they do so with less 
efficiency than IgM. This is due, in part, to the requirement for multiple Fc regions in close 
proximity to activate the complement cascade, meaning that multiple monomeric IgG Abs 
are required to bind, whereas only one pentameric IgM Ab is needed to bind to activate 
complement. Also, in the case of rAvPAL-PEG, binding of anti-PAL IgG antibodies is likely 
compromised due to epitope masking by the PEGylation, which may reduce IgG-mediated 
complement activation in vivo. This complex dynamic between combined isotype-specific 
Ab responses and epitope accessibility is thought to be a major factor dictating the need for 
an induction and titration dose regimen in the treatment of rAvPAL-PEG to be implemented 
in this study. 
7.4.3 Management of Hypersensitivity Reactions 
Hypersensitivity reactions to the SC injection of rAvPAL-PEG may be mild, moderate, or 
severe in intensity. Reactions may include pruritus, rash, shortness of breath, hypotension, or 
anaphylaxis. Clinical assessments should be conducted for a minimum of 30 minutes 
post-injection. Longer observations may be required at the discretion of the PI. 
The responsible physician should use all appropriate measures for the treatment of 
hypersensitivity reactions. Because of the potential for anaphylaxis, equipment for 
emergency resuscitation (including epinephrine) should be within easy access during and 
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after the rAvPAL-PEG injection. Subject should be pre-medicated with H1 antagonist, H2 
antagonist, and NSAIDs approximately 2-3 hours prior to each dose of study drug for one 
week upon return to dosing regardless of the duration of dose interruption. NSAIDs should 
be given with food and may be omitted if not tolerated.  Subjects who qualify for self-
administration of study drug are trained to recognize a serious hypersensitivity AEs and how 
to respond. Additionally, subjects are given two epinephrine injectors and are instructed to 
carry one epinephrine injector with them at all times (Section 9.4). Refer to Section 9.1.1.3 
for instructions regarding resumption of study drug following resolution of symptoms 
consistent with a clinical diagnosis of anaphylaxis per National Institute of Allergy and 
Infectious Disease/Food Allergy and Anaphylaxis Network (NIAID/FAAN) criteria 
(Sampson, 2006, J.Allergy Clin.Immunol.).  
In the event of a hypersensitivity reaction, subjects may be asked to see an 
allergist/immunologist and/or provide up to 3 additional blood samples for immunology 
studies and complement testing. This additional testing may occur up to 6 months following 
the final study visit.   
The following measures are recommended for the treatment of hypersensitivity reaction 
symptoms: 
• Maintain the airway. 
• Vital sign check. 
• Administration of oral or IV diphenhydramine. 
• Administration of epinephrine if appropriate. 
• Administration of oral or IV glucocorticoids. 
• Administration of oxygen and IV fluids. 
• Administration of additional symptomatic treatment. 
• Transfer to an acute care facility of the study center. 
In addition, clinical judgment must be used in determining the appropriateness of 
corticosteroid administration. An allergy and/or immunology consultation should be sought if 
necessary. Detailed instructions for the management of hypersensitivity reactions are 
provided in the Study Reference Manual. 
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8 
STUDY OBJECTIVES 
The primary objective of the study is: 
• To evaluate the effect of long-term administration of multiple doses of SC injections 
of rAvPAL-PEG on blood Phe concentrations in subjects with PKU. 
The secondary objectives of the study are: 
• To evaluate the safety and tolerability of long-term administration of subcutaneous 
(SC) injections of rAvPAL-PEG in subjects with PKU. 
• To evaluate the immune response to long-term administration of SC injections of 
rAvPAL-PEG in subjects with PKU. 
The exploratory objective of the study is as follows: 
• To evaluate the long-term relationship of diet and change in blood Phe concentration 
following administration with rAvPAL-PEG in subjects with PKU. 
The Substudy objective is as follows: 
• To evaluate steady-state PK of rAvPAL-PEG in subjects who have achieved and 
maintained target blood Phe concentration and for whom no further dose 
modifications are planned. 
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9 
INVESTIGATIONAL PLAN 
9.1 
Overall Study Design and Plan 
This is a long-term extension of rAvPAL-PEG Phase 2 studies in up to 100 subjects with 
PKU. The doses are planned to be in the same range as those previously tested in the Phase 2 
studies (starting at 0.001 through 5.0 mg/kg/week or 2.5 mg through 375 mg/week), provided 
no dose-limiting toxicity was observed in a previous rAvPAL-PEG studies. Subjects’ doses 
will not exceed 375 mg/week. 
Only subjects who completed a previous rAvPAL-PEG study will be enrolled into this study. 
Subjects enrolling into PAL-003 with no interruption in dosing from a previous 
rAvPAL-PEG study may either continue their previous dosing regimen or begin this study at 
a higher dose level. Subjects who have had dosing interruptions between the previous 
rAvPAL-PEG study and PAL-003 must have their starting dose determined per the sponsor’s 
medical monitor.  The first week of dosing will be administered in the clinic, and the subject 
must be observed for 30 minutes following administration. Subjects are given two 
epinephrine injectors and are instructed to carry one epinephrine injector with them at all 
times (refer to Section 9.4). A follow-up telephone call will be made to the subject to monitor 
subject safety 24 hours following the return to dosing. 
Diet should not be altered during the course of this study. Any decision to modify subject 
diet must be made per the Investigator and must be performed under the supervision of the 
Investigator. To monitor for changes in subject diet, a diet diary will be issued to subjects for 
completion and will be brought to clinic monthly for review with the clinical study staff. 
Subjects may self-administer study drug at home if approved by the Investigator and the 
sponsor’s medical monitor and if adequate training is demonstrated. Subjects must meet a set 
of criteria to be considered appropriate for self-administration. Refer to Section 9.4 for the 
criteria for which subjects may qualify for self-administration. Additional information is 
provided in the Subject Self-Administration Training Materials. Additional training will be 
provided and demonstration of competency required when prefilled syringe drug product is 
introduced, every 24 weeks, and more often as needed. 
Subjects will be evaluated for safety throughout the study. Toxicity will be measured 
according to the National Cancer Institute (NCI) Common Terminology Criteria for Adverse 
Events (CTCAE), version 4. 
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In addition to the Sponsor, a Data Monitoring Committee (DMC) will monitor the safety of 
subjects in the study. The DMC is an independent committee that will act in an advisory 
capacity to the Sponsor. 
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take 
rAvPAL-PEG. Subjects’previous rAvPAL-PEG dosing will generally continue in PAL-003. 
In PAL-003, each subject’s dose will be adjusted as needed to attempt to attain or maintain 
blood Phe concentrations of 60-600 µmol/L. rAvPAL-PEG dose will be based on either a 
subject’s weight or will be a fixed dose. Doses will be evaluated on an individual basis.  
Evaluations, observations, and procedures will be conducted at selected time points as shown 
in Table 9.1.1 and Table 9.1.2.  After the subject’s blood Phe concentration has been 
controlled to within a target range (60-600 µmol/L), the subject may be asked to have 
additional blood draws for PK and blood Phe concentration analyses as needed per the 
discretion of the Investigator in consultation with the sponsor’s medical monitor. 
A subject will continue in PAL-003 until one of the following occurs: 
• The subject withdraws consent and discontinues from the study. 
• The subject is discontinued from the study at the discretion of the Investigator or 
Sponsor. 
• The subject has completed the study through the Month 98 visit. 
• The study is terminated. 
• The study drug receives marketing authorization. 
Subjects may withdraw from treatment with study drug at any time; however, subjects will 
be asked to continue to perform the study assessments until study completion. Subjects may 
also withdraw from study participation at any time. Because the completeness of the data 
affects the integrity, accuracy, and interpretation of study results, every effort should be made 
to retain subjects in the study and to have them complete the study assessments as scheduled 
as long as continued participation does not compromise subject safety.  
A PK substudy has been added to evaluate the steady-state PK of rAvPAL-PEG in up to 
6 subjects who have achieved and maintained target blood Phe for at least 2 consecutive 
measurements and for whom no further dose modifications are planned.  Subjects enrolled 
into the substudy will have additional pre-dose PK sampling performed (refer to Table 9.1.2). 
The Schedule of Events and PK substudy collection schedules are presented below in 
Table 9.1.1 and Table 9.1.2  
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Table 9.1.1:  Schedule of Events 
Assessments and Events 
Screeninga 
Treatment Periodb,c 
Final F/U 
Visit 
Self-
administration 
Early 
Term. 
Visit 
Unsched. 
Hyper. 
Reaction 
Visit.d  
Perform 
within 
24 hours 
Week 1 
Weekly 
Telephone 
Contacts 
Monthly b 
(eg, Wk 4, 
8, etc.) 
Quarterly  
(eg, Wk 12, 
24, etc.) 
Interim 
Clinician 
Visit (HHRN 
or Site) 
D 1 
Starting at 
Week 2 
Every 4th 
week; 
Every 12th 
week. 
Perform in 
addition to 
monthly 
procedures 
Up to daily 
4 weeks 
after final 
dose 
 
4 weeks 
after 
final 
dose 
Informed consent 
X 
 
 
 
 
 
 
 
 
 
Medical history, including 
allergy history, and 
demographics 
X 
 
 
 
 
 
 
 
 
 
Physical examinatione 
X 
X 
 
 
X 
 
X 
 
X 
 
Vital signse 
X 
X 
 
X 
 
X 
 
 
X 
X 
Weight 
X 
 
 
X 
 
 
 
 
 
 
12-lead ECG 
X 
 
 
 
 
 
X 
 
X 
 
Clinical laboratory testsf 
X 
 
 
X 
 
 
X 
 
X 
Xg 
Complements C3 and C4
h 
X 
 
 
 
X 
 
 
 
 
Xg 
Sedimentation rate 
 
X 
 
 
X 
 
X 
 
X 
 
Chest x-ray 
X 
 
 
X  
(Week 48 
visit only) 
 
 
X 
 
X 
 
Urine pregnancy testi 
X 
X 
 
X 
 
 
X 
 
X 
 
Adverse eventsj,k 
X 
X 
X 
X 
 
X 
X 
X 
X 
X 
Weekly phone call to self 
admin participants only (to 
assess AEs, Inj site reactions, 
concomitant medications) 
 
 
X 
 
 
 
 
X 
X 
 
Concomitant medications 
X 
X 
 X 
X 
 
X 
X 
X 
X 
X 
Diet query 
X 
X 
 
X 
 
 
X 
 
X 
 
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Assessments and Events 
Screeninga 
Treatment Periodb,c 
Final F/U 
Visit 
Self-
administration 
Early 
Term. 
Visit 
Unsched. 
Hyper. 
Reaction 
Visit.d  
Perform 
within 
24 hours 
Week 1 
Weekly 
Telephone 
Contacts 
Monthly b 
(eg, Wk 4, 
8, etc.) 
Quarterly  
(eg, Wk 12, 
24, etc.) 
Interim 
Clinician 
Visit (HHRN 
or Site) 
D 1 
Starting at 
Week 2 
Every 4th 
week; 
Every 12th 
week. 
Perform in 
addition to 
monthly 
procedures 
Up to daily 
4 weeks 
after final 
dose 
 
4 weeks 
after 
final 
dose 
3-Day diet diaryl 
 
 
 
X 
 
 
X 
 
X 
 
Serum antibodiesm 
 
X 
 
 
X 
 
X 
 
X 
X 
Plasma Phe and plasma 
tyrosinen  
X 
X 
 
Xm 
 
 
X 
 
X 
 
Urine albumin/creatinine ratio 
 
 
 
 
 
 
 
 
 
X 
Urine N-methyl histamine 
 
 
 
 
 
 
 
 
 
X 
Plasma PK sampleo 
 
X 
 
 
X 
 
X 
 
X 
 
Administer study drugp 
 
X 
 
X 
 
X 
 
X 
 
 
Training (prefilled syringe)q 
 
 
 
X 
Transition to 
prefilled 
syringe 
X 
Every 24 
weeks only 
 
 
 
 
 
Skin biopsy (optional; 
affected and not affected 
area) 
 
 
 
 
 
 
 
 
 
X 
Serum tryptase levelr 
 
 
 
 
 
 
 
 
 
X 
AE, adverse event; C3, complement 3; C4, complement 4; CH50, total hemolytic complement; CRP, C-reactive protein; D, day; ECG, electrocardiogram; ETV, Early 
Termination Visit; F/U, Follow-up; Hyper, hypersensitivity; IgE, immunoglobulin E; IgG, immunoglobulin G; IgM, immunoglobulin M; IP, investigational product; PK, 
pharmacokinetics; Phe, phenylalanine; SAE, serious adverse event; Wk, week. 
a A separate Screening visit for this study is required only if the time between completion of the previous rAvPAL-PEG study and enrollment into PAL-003 is greater than 
28 days. 
b Monthly visits must be performed in the clinic. 
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c On days that a dose is given, all procedures should be performed predose, except where noted. 
d Refer to Section 9.1.1 and Section 12.3.6. 
e Complete physical examinations to include the evaluation of all major body systems. Height will be measured at Screening only. 
f Clinical laboratory tests to include spot urine albumin/creatinine ratio, hematology, chemistry, and urinalysis. Urine microscopy will be performed if any urinalysis 
results are positive for hematuria.  Refer to Table 9.7.6.1. 
g Subjects who have a National Cancer Institute Common Terminology Criteria for Adverse Events (NCI-CTCAE) grade ≥ 3 hypersensitivity AE should be assessed for 
CRP, CH50, C1, C3, and C4 within 24 hours of the reaction.  
h Complement C3 and C4 will be collected at the Screening Visit and quarterly. Additional complement testing will be performed and as needed to resolve previous 
abnormal test results. 
i If positive or equivocal, perform serum pregnancy test. 
j If any injection site reaction is observed, the corresponding adverse event data must specify injection location (identify current vs. previous visit’s injection, eg, right arm 
vs. left arm). 
k The reporting period for SAEs begins when informed consent is obtained and continues through 4 weeks after last dose or the final study visit. The reporting period for 
nonserious AEs is from the first administration of study drug through 4 weeks after last dose or the early termination visit. The reporting period for device-related events 
begins with the first dose administered using prefilled syringe and ends with the last dose administered using prefilled syringe. 
l It is preferable that the subject complete the diary 3 days immediately prior to the next monthly visit. 
m For unscheduled hypersensitivity reaction visit, draw serum anti-rAvPAL IgE and anti-rAvPAL-PEG IgE only; sampling must be performed > 8 hours after event onset 
and before the next dose of study drug.  
n Samples should be drawn at least 2.5 hours after a meal.  At the Investigator’s discretion, blood Phe may be collected more often should more frequent monitoring of 
blood Phe levels be clinically warranted. 
o Sampling should be performed predose.   
p Dosing is up to 5.0 mg/kg/week or 375 mg/week, including subjects who receive more than 1 dose/week. Every effort should be made to adhere to the study drug 
administration regimen. If a subject misses more than 2 scheduled doses of study drug, both dose level and dose frequency may be re-evaluated.  
q Initial training on the use of prefilled syringe occurs at the next monthly visit and each subsequent day after transition until (in clinic or by HHRN) it has been 
determined the subject will switch to prefilled syringe. Once competency is documented, subjects can self-administer study drug using the prefilled syringe.  Regular 
refresher prefilled syringe training occurs in the study clinic every 24 weeks thereafter. 
r Mandatory for subjects who have a hypersensitivity AE.  Perform within 24 hours of event onset. 
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Table 9.1.2:  PK Substudy Dosing Regimens 
Treatment Frequency 
Plasma PK Sampling 
Example 
Subjects who are 
administered study drug 
once per week 
Pre-dose and every 24 hours 
thereafter (24, 48, 72, and 96 
hours when possible), and pre-
dose of the next weekly dose 
If dosed on Monday: 
Obtain PK sample pre-dose when possible – pre-dose Monday, Tuesday, 
Wednesday, Thursday, Friday, and pre-dose the following Monday. 
No further PK substudy draws. 
Subjects who are 
administered study drug 
two or three times per 
week 
Pre-dose and every 24 hours 
during the longest period 
between doses, when possible, 
and pre-dose of the next dose. 
If dosed on Monday, Thursday, and Friday: 
Obtain PK sample every 24 hours during the longest period between doses: Pre-
dose Monday, Tuesday, Wednesday, and pre-dose Thursday. 
No further PK substudy draws. 
Subjects who are 
administered study drug 
four to seven times per 
week. 
Pre-dose and every 12 hours 
during the longest period 
between doses, when possible, 
then pre-dose of the next dose. 
If dosed Monday through Friday: 
Obtain PK sample every 12 hours during the longest period between doses (Friday 
to Monday): pre-dose Friday, 12 hours post-dose Friday, Saturday (24 and 36 
hours post dose), Sunday (48 and 60 hours post-dose), and pre-dose the following 
Monday. 
No further PK substudy draws. 
 
 
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9.1.1 Response to Hypersensitivity Adverse Events 
Subjects are evaluated for safety throughout the study and are trained to recognize potential 
hypersensitivity AEs (including anaphylaxis) and how to respond. Subjects are instructed to 
contact the investigator for any suspected hypersensitivity AE. The investigator may require 
further evaluation at the clinic. If a hypersensitivity AE (eg, injection-site reaction, rash, joint 
pain, itching) occurs, the subject may be advised to premedicate with H1 antagonist, H2 
antagonist, and non-steroidal anti-inflammatory medication (NSAIDs) approximately 
2-3 hours prior to subsequent rAvPAL-PEG doses. NSAIDs should be given with food and 
may be omitted if not tolerated.  
Hypersensitivity AEs, including anaphylaxis, are expected with rAvPAL-PEG 
administration.  rAvPAL-PEG dosing in response to a suspected hypersensitivity AE may be 
modified or halted depending on the severity of the event and suspected rAvPAL-PEG 
causality (Section 9.1.1.3). Severity for hypersensitivity AEs will be per NCI-CTCAE 
grades. 
9.1.1.1 
Individual Stopping Criteria 
Subjects who have an NCI CTCAE grade ≥ 3 hypersensitivity AE that is related to study 
drug and is suspected to meet Brown’s criteria for severe (grade 3) in the judgment of the 
investigator and the sponsor’s medical monitor may be permanently discontinued from study 
drug. 
9.1.1.2 
Dosing in Response to Hypersensitivity Adverse Events 
Dosing in response to a hypersensitivity AE depends on the NCI-CTCAE grade and 
suspected relationship to rAvPAL-PEG. Dosing instructions are presented in Table 9.1.1.2.1 
and are regardless of previous occurrence: 
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Table 9.1.1.2.1:  Dosing Instructions in Response to Hypersensitivity Adverse Events 
NCI-
CTCAE 
Gradea 
Related to 
Study Drug 
Action with Study Drug 
 
HRV Assessmente 
Maintainb 
Reducec 
Interruptc 
Individual 
Stopping 
Criteria d 
1 
Yes or No 
X 
(X) 
Optional 
(X) 
Optional 
 
Investigator 
discretion 
2 
Yes or No 
X 
(X) 
Optional 
(X) 
Optional 
 
Investigator 
discretion 
3  
No 
X 
(X) 
Optional 
(X) 
Optional 
 
Investigator 
discretion 
3  
Yes  
X 
(X) 
Optional 
(X) 
Optional 
 
Yes 
3 
and is 
suspected to 
meet 
Brown’s 
criteria for 
severe d  
Yes  
 
 
 
X 
Consult with 
sponsor 
medical 
monitor 
Yes 
4 d 
Yes or No 
 
 
 
X 
Consult with 
sponsor 
medical 
monitor 
Yes 
AE, adverse event; CTCAE, Common Terminology Criteria for Adverse Events, version 4.03; HRV, 
Hypersensitivity Reaction Visit; NCI, National Cancer Institute. 
aNCI-CTCAE grade determination is performed by the investigator and may be done either via telephone or 
clinic visit. 
bThe investigator will instruct the subject to maintain the rAvPAL-PEG dose at the time of AE onset until 
improvement to grade 1 or resolution (per investigator assessment in the clinic or via telephone). 
cThe rAvPAL-PEG dose may be reduced or interrupted if necessary per investigator determination.  
d If a subject has an NCI-CTCAE grade  ≥ 3 hypersensitivity AE that is related to study drug and is suspected to 
meet Brown’s criteria for severe (grade 3) in the judgment of the investigator and the sponsor’s medical 
monitor, the subject may be permanently discontinued from study drug.  
eIf the investigator determines that the NCI-CTCAE grade  ≥ 3 hypersensitivity AE is related to administration 
with rAvPAL-PEG, the subject will be asked to return to the clinic within 24 hours of event onset for 
evaluation, including laboratory tests (chemistry, hematology, urinalysis, anti-rAvPAL IgE, 
anti-rAvPAL-PEG IgE [sampling must be performed >8 hours after event onset and before the next dose of 
study drug], urine albumin/creatinine ratio, urinary N-methyl histamine, CRP, C3, C4, and tryptase).  
 
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9.1.1.3 
Response to Anaphylaxis 
If the investigator suspects that the event is anaphylaxis, the subject will be assessed in the 
clinic. Laboratory assessments for suspected anaphylaxis events should be performed prior to 
the next administration of study drug (if applicable) and include anti-rAvPAL IgE and 
anti-rAvPAL-PEG IgE (sampling must be performed >8 hours after event onset and before 
the next dose of study drug) and tryptase (within 24 hours of event onset). The investigator 
will consult with the sponsor’s medical monitor, and a decision will then be made whether to 
discontinue the subject from study drug, restart dosing at the same dose level, or restart 
dosing at a lower dose level. 
For the first week of dosing after resolution of anaphylaxis, the study drug will be 
administered in a clinic setting with equipment for emergency resuscitation (including 
epinephrine) within easy access.  The subject must be observed for 30 minutes following 
administration due to restarting dosing. Additionally, the subject should be premedicated 
with H1 antagonist, H2 antagonist, and NSAIDs approximately 2-3 hours prior to each dose 
of study drug for one week upon return to dosing regardless of the duration of dose 
interruption. NSAIDs should be given with food and may be omitted if not tolerated.  
9.1.2 Study Stopping Criteria 
If an NCI-CTCAE grade ≥ 3 hypersensitivity treatment-related event occurs and meets 
Brown’s criteria for severe (grade 3), an ad hoc independent DMC meeting will convene 
within 7 days of the event to review and advise the sponsor on potential changes to the study 
conduct. Clinically severe hypersensitivity is defined as significant hypoxia, hypotension or 
neurologic compromise that is life-threatening or required treatment to prevent a 
life-threatening event:  
• Cyanosis or SpO2 ≤ 92%  
• Hypotension with SBP < 90 mm Hg (adults)  
• Neurologic alteration: loss of consciousness, collapse, incontinence 
Brown’s severity criteria are presented in Table 9.1.2.1. 
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Table 9.1.2.1:  Brown’s Severity Criteria 
Brown’s Criteria for 
Hypersensitivity Reactions 
Definition 
Mild (1) 
skin and subcutaneous tissue 
Generalized erythema, urticaria, periorbital edema, or angioedema 
Moderate (2) 
features suggested respiratory, 
cardiovascular, or 
gastrointestinal involvement 
Dyspnea, stridor, wheeze, nausea, vomiting, dizziness (pre-syncope), 
diaphoresis, chest or throat tightness, or abdominal pain  
 
Severe (3) 
hypoxia or neurologic 
compromise 
Cyanosis or SpO2 ≤ 92% at any stage, hypotension (SBP < 90 mm Hg in 
adults), confusion, collapse, loss of consciousness, or incontinence  
 
 
9.1.3 Dose Modifications 
9.1.3.1 
Dose Increase Methodology 
Each subject’s dose may be modified based on the decision of the Investigator. Decisions 
regarding dose increases will depend on a subject’s adverse event profile and blood Phe and 
drug concentrations. 
An individual subject’s dose may be adjusted beginning on Day 1 of PAL-003. For the 
duration of this study, an individual subject’s dose may be adjusted if warranted per a 
subject’s adverse event profile and blood Phe concentrations. Dose increases should be 
performed as follows: 
• The dose may be increased by increments of no more than 10-fold higher than the 
subject’s current dose. 
• When increasing the dose, a dose may be used that is between the dose levels (0.001, 
0.003, 0.01, 0.03, 0.06, 0.1, 0.2, 0.3, 0.4, 0.6, 0.8, 1.0, 2.0, 3.0, 4.0, and 5.0 mg/kg or 
2.5, 5, 10, 20, 40, 75, 150, 225, 300, 375 mg/week) or per Investigator determination 
based on available information regarding a subject’s blood Phe (60-600 µmol/L) as 
well as any adverse events for an individual subject. Dose increases  > 350 mg/week 
require consultation with the sponsor’s medical monitor. 
• The dose may be adjusted by increasing the frequency up to daily for a total weekly 
dose not to exceed 5.0 mg/kg or 375 mg/week. Dose increases  > 350 mg/week 
require consultation with the sponsor’s medical monitor. 
• When a dose is increased, the subject must be observed for 30 minutes following the 
first modified dose administration. Subjects who increase their dose frequency do not 
need to be observed following injection of study drug if the increase in frequency 
does not increase the overall weekly dose amount. 
• Only 1 dose adjustment is allowed every 2 weeks. 
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9.1.3.2 
Dose Decrease Methodology 
Decisions regarding dose decreases will depend on available information regarding a 
subject’s blood Phe (60-600 µmol/L), as well as any adverse event (any hypersensitivity 
reaction as defined in Section 9.1.1). Dose decreases may occur for hypophenylalanemia or 
any adverse event that may be improved with a lower dose. 
A dose should first be reduced by dose level (5.0, 4.0, 3.0, 2.0, 1.0, 0.8, 0.6, 0.4, 0.3, 0.2, 0.1, 
0.06, 0.03, 0.01, 0.003, 0.001 mg/kg or 375, 300, 225, 150, 75, 40, 20, 10, 5, and 2.5 
mg/week). It is also permitted to decrease dose in between these specified dose levels. If 
further dosing adjustments are required in response to safety, dosing frequency may also be 
adjusted.  
If the subject develops low blood Phe (as defined by a blood Phe level ≤ 30 µmol/L ), the 
subject’s rAvPAL-PEG dose should be decreased to the next lower dose.  If the condition 
persists after another 1 month at the lower dose, the dose should be decreased again to the 
next lower level. If the subject continues to experience low blood Phe after two dose level 
reductions, the subject may be asked to consult the dietician to eliminate medical foods 
and/or formulas and to ensure a balanced and nutritious diet (as part of the routine standard 
of care for PKU disease management, subject diet should be monitored by a dietician). 
9.2 
Discussion of Study Design, Including Choice of Control Group 
This open-label, Phase 2 trial was designed to be closely monitored with the goal of 
obtaining information about the efficacy, safety, tolerability, and PK of long-term 
administration of rAvPAL-PEG in subjects with PKU. There will be no control group in this 
study. 
9.3 
Selection of Study Population 
9.3.1 Inclusion Criteria 
Individuals eligible to participate in this study must meet all of the following criteria: 
1. Must have completed participation in a previous rAvPAL-PEG study. 
2. Willing and able to provide written, signed informed consent, or in the case of 
subjects under the age of 18 years, provide written assent (if required) and written 
informed consent by a parent or legal guardian, after the nature of the study has been 
explained, and prior to any research-related procedures. 
3. Willing and able to comply with all study procedures. 
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4. Females of childbearing potential must have a negative pregnancy test at Screening 
and be willing to have additional pregnancy tests during the study. Females 
considered not of childbearing potential include those who have been in menopause at 
least 2 years, or had tubal ligation at least 1 year prior to Screening, or who have had 
total hysterectomy. 
5. Sexually active subjects must be willing to use an acceptable method of contraception 
while participating in the study.  Males post vasectomy for 2 years with no known 
pregnancies do not need to use any other forms of contraception during the study. 
6. Maintained a stable diet. 
7. In generally good health as evidenced by physical examination, clinical laboratory 
evaluations (hematology, chemistry, and urinalysis), and electrocardiogram (ECG) at 
Screening. 
9.3.2 Exclusion Criteria 
Individuals who meet any of the following exclusion criteria will not be eligible to participate 
in the study: 
1. Use of any investigational product (with the exception of rAvPAL-PEG) or 
investigational medical device within 30 days prior to Screening, or requirement for 
any investigational agent prior to completion of all scheduled study assessments. 
2. Use of any medication other than rAvPAL-PEG that is intended to treat PKU within 
14 days prior to the administration of study drug. 
3. Use or planned use of any injectable drugs containing PEG (other than 
rAvPAL-PEG), including Depo-Provera, within 6 months prior to Screening and 
during study participation. 
4. A prior reaction that included systemic symptoms (eg, generalized hives, respiratory 
or gastrointestinal problems, hypotension, angioedema, anaphylaxis) to rAvPAL-PEG 
or a PEG-containing product. Subjects with a prior systemic reaction may be eligible 
for participation per the discretion of the Principal Investigator in consultation with 
the sponsor’s medical monitor. However, subjects who discontinued from study 
treatment early due to a reaction are not eligible to enroll into this study.      
5. Pregnant or breastfeeding at Screening or planning to become pregnant (self or 
partner) or to breastfeed at any time during the study. 
6. Concurrent disease or condition that would interfere with study participation or safety 
(eg, history or presence of clinically significant cardiovascular, pulmonary, hepatic, 
renal, hematologic, gastrointestinal, endocrine, immunologic, dermatologic, 
neurological, oncologic, or psychiatric disease). 
7. Any condition that, in the view of the PI, places the subject at high risk of poor 
treatment compliance or of not completing the study. 
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8. Known hypersensitivity to rAvPAL-PEG necessitating early termination from a 
previous rAvPAL-PEG study or known hypersensitivity to any of its excipients. 
9. Alanine aminotransferase (ALT) concentration > 2 times the upper limit of normal. 
10. Creatinine > 1.5 times the upper limit of normal. 
9.3.3 Removal of Subjects from Treatment or Assessment 
Subjects (or their legally authorized representative) may withdraw their consent to participate 
in the study or to receive study drug at any time without prejudice. The Investigator must 
withdraw from the study or study drug treatment any subject who requests to be withdrawn. 
A subject’s participation in the study may be discontinued at any time at the discretion of the 
Investigator and in accordance with his/her clinical judgment. When possible, a subject who 
is discontinued from study treatment should continue to perform the study tests and 
evaluations until study completion. For subjects who discontinue from the study, the tests 
and evaluations listed for the Early Termination Visit should be carried out (refer to 
Section 12.4). 
BioMarin must be notified of all subject withdrawals as soon as possible. BioMarin also 
reserves the right to discontinue the study at any time for either clinical or administrative 
reasons and to discontinue participation by an individual Investigator or site for poor 
enrollment or noncompliance. 
Reasons for which the Investigator or BioMarin may withdraw a subject from the study 
treatment include, but are not limited to, the following: 
• Subject experiences a serious or intolerable adverse event (AE). 
• Subject develops a clinically significant laboratory abnormality. 
• Subject requires medication prohibited by the protocol. 
• Subject becomes pregnant (refer to Section 10.3 for details on the reporting 
procedures to follow in the event of pregnancy). 
Reasons for which the Investigator or BioMarin may withdraw a subject from the study 
include, but are not limited to, the following: 
• Subject does not adhere to study requirements specified in the protocol. 
• Subject was erroneously admitted into the study or does not meet entry criteria. 
• Subject is lost to follow-up. 
If a subject fails to return for scheduled visits, a documented effort must be made to 
determine the reason. If the subject cannot be reached by telephone within 7 days, a certified 
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letter should be sent to the subject (or the subject’s legally authorized representative, if 
appropriate) requesting contact with the Investigator. This information should be recorded in 
the study records. 
The Investigator or designee must explain to each subject, before enrollment into the study, 
that for evaluation of study results, the subject’s protected health information obtained during 
the study may be shared with the study sponsor, regulatory agencies, and IRB. It is the 
Investigator’s (or designee’s) responsibility to obtain written permission to use protected 
health information per country-specific regulations, such as the Health Insurance Portability 
and Accountability Act (HIPAA) in the United States, from each subject, or if appropriate, 
the subject’s legally authorized representative. If permission to use protected health 
information is withdrawn, it is the Investigator’s responsibility to obtain a written request, to 
ensure that no further data will be collected from the subject and the subject will be removed 
from the study. 
9.3.4 Subject Identification and Replacement of Subjects 
Subjects will retain the same subject number assigned in their previous rAvPAL-PEG study. 
This unique identifier will be on all case report form (CRF) pages. In legal jurisdictions 
where use of initials is not permitted, a substitute identifier will be used.  
Subjects who do not complete the study will not be replaced. 
9.4 
Treatments 
Upon enrollment into this study, subjects from previous rAvPAL-PEG studies will be dosed 
with the same or higher dose that was administered upon completion of that study provided 
that there was no interruption in dosing.  rAvPAL-PEG doses will be administered SC by 
either health care professionals or via self-administration. The dose level may be adjusted per 
Investigator determination based on available information regarding a subject’s blood Phe 
level (60-600 µmol/L), as well as any adverse events (any hypersensitivity reaction) for an 
individual subject. The dosage that provides control of blood Phe concentrations within the 
target range of 60-600 µmol/L for a minimum of 2 weeks will be determined for each subject 
by adjusting the dose level, dose frequency, or both, per the PI, based upon the subject’s 
response to doses.  
Subjects may self-administer study drug at home if approved by the Investigator and the 
sponsor’s medical monitor and if adequate training is demonstrated. Subjects may be eligible 
to self-administer study drug if he or she meets the following criteria:  
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• The subject has no cognitive impairments that may increase the safety risk of 
self-administration per the assessment of the investigator.  
• The subject has been approved for self-administration of study drug by the sponsor’s 
medical monitor. 
• The subject has completed the Self-Administration Training conducted by qualified 
study site personnel and has been observed by the study site personnel to be able to 
adequately prepare the proper dose and perform the injections safely.  
• The subject has been provided with two epinephrine injectors and has been trained on 
when and how to administer it. The subject will be instructed to carry one epinephrine 
injector with them at all times. 
Qualified study site personnel will train each eligible subject on all procedures for 
self-administration of study drug (vial and syringe and prefilled syringe drug products) under 
the supervision of the PI. Qualified study site personnel will also be required to observe the 
subject prepare and perform at least 1 injection prior to allowing the subject to 
self-administer a dose at home. The subject will see a study site nurse or home healthcare 
nurse in person every week or receive a telephone call from site staff to ensure that the 
subject continues to perform all self-administration procedures correctly, to assess adverse 
events, and to answer questions throughout the duration of the study. The study site nurse or 
home healthcare nurse will also perform the regularly scheduled assessments and procedures 
as outlined in Table 9.1.1 and Section 12; the subject must perform a clinic visit monthly at 
minimum. Training materials and other information specific to the study site personnel are 
provided in the Subject Self-Administration Training Materials. Prefilled syringes are 
dispensed to subjects only
Subjects who are eligible for self-administration will be provided with a Subject Study 
Manual. Self-administration training materials will be provided in the Subject Study Manual 
to supplement the in-person training provided by the qualified study site personnel. The 
Subject Study Manual will include step-by-step instruction on the following: 
 after the subject (or caregiver) has completed training and 
competency is demonstrated in the clinic.  Additional regular refresher training occurs in the 
clinic, every 24 weeks, and more often as needed.  
• How to prepare and perform the injections of study drug safely. 
• How to receive, track, store, prepare, and return both used and unused study drug.   
• How to safely use and dispose of syringes, including prefilled syringes, used for 
injections of study drug. 
• How to use a new syringe and vial or new prefilled syringe every time drug is 
administered. 
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• How to care for their injection site after an injection of study drug.  
• How to identify an adverse reaction and how to report this reaction to the study site.  
• How and when to use epinephrine injectors. 
• Who to contact at the study site in case of an emergency.  
The PI or the sponsor’s medical monitor may request that self-administration be halted at any 
time and that the subject resume injections performed by the study site personnel or home 
healthcare nurse. 
Subjects who are within the target Phe range may also be permitted to convert from 
weight-based dosing to fixed dosing (refer to Section 9.4.4). 
9.4.1 Treatments Administered 
BioMarin and/or its designee will provide the study site or subject with a supply of IP 
sufficient for the completion of the study. BioMarin is responsible for shipping study drug to 
the clinical sites. The clinical site is responsible for supplying the study drug to subjects who 
qualify for self-administration. Refer to the PAL-003 Pharmacy Manual for information 
pertaining to the distribution of study drug from sites.   
Information regarding supplying study drug to subjects who qualify for self-administration is 
provided in the Subject Self-Administration Training Materials. 
9.4.2 Identity of Investigational Product (IP) 
9.4.2.1 
Product Characteristics and Labeling 
The investigational product is rAvPAL-PEG (recombinant Anabaena variabilis phenylalanine 
ammonia lyase-PEG). rAvPAL-PEG will be provided in vials or prefilled syringes; subjects 
will be supplied with vials and syringes or prefilled syringes for administration in the clinic 
and self-administration: 
• rAvPAL-PEG will be provided in 3 mL (milliliter) vials, each containing 1.5 ± 0.2 mL 
to deliver 15 mg of rAvPAL-PEG per 1.0 mL (15 mg/mL protein concentration). 
Each vial is filled with 1.5 ± 0.2 mL to allow the withdrawal and delivery of up to 
1.0 mL of the drug product. 
Or 
 
• rAvPAL-PEG will be provided in 3-mL vials, each containing 1.8 ± 0.3 mL to deliver 
20 mg of rAvPAL-PEG per 1.3 mL (15 mg/mL protein concentration). Each vial is 
filled with 1.8 ± 0.3 mL to allow withdrawal and delivery of up to 1.3 mL. 
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Or 
 
• rAvPAL-PEG will be provided in prefilled syringes in three sizes that deliver up to 
1 mL. Syringe sizes are 2.5 mg (5 mg/mL protein concentration), 10 mg (20 mg/mL 
protein concentration), and 20 mg (20 mg/mL protein concentration). 
Table 9.4.2.1.1:  Prefilled Syringe Volume, Concentration, and Dose 
Prefilled Syringe 
Volume 
Concentration 
Dose 
Sku #1 
0.5 mL 
5 mg/mL 
2.5 mg 
Sku #2 
0.5 mL 
20 mg/mL 
10 mg 
Sku #3 
1.0 mL 
20 mg/mL 
20 mg 
 
Subjects who have undergone training and who have demonstrated competency on the use of 
prefilled syringe in the study clinic may be eligible to transition from vial and syringe to 
prefilled syringe dosing. Additionally, regular refresher training on use of prefilled syringe 
will be provided in study clinic every 24 weeks, and more often as needed.  
Subjects should convert their vial and syringe dose to prefilled syringe dose using the 
following table: 
Table 9.4.2.1.2:  Conversion from Vial and Syringe Dose to Prefilled Syringe Dose 
Daily Dose (mg)  
Range 
Daily Dose (mg)  
Round Toa 
# of 2.5mg 
Prefilled Syringe 
Needed 
# of 10mg Prefilled 
Syringe Needed 
# of 20mg Prefilled 
Syringe Needed 
0 – 3.7 
2.5 
1 
0 
0 
3.8 – 6.2 
5 
2 
-- 
-- 
6.3 – 8.7 
7.5 
3 
-- 
-- 
8.8 – 11.2 
10 
-- 
1 
-- 
11.3 – 13.7 
12.5 
1 
1 
-- 
13.8 – 16.2 
15 
2 
1 
-- 
16.3 – 18.7 
17.5 
3 
1 
-- 
18.8 – 21.2 
20 
-- 
-- 
1 
21.3 – 23.7 
22.5 
1 
-- 
1 
23.8 – 26.2 
25 
2 
-- 
1 
26.3 – 28.7 
27.5 
3 
-- 
1 
28.8 – 31.2 
30 
-- 
1 
1 
31.3 – 33.7 
32.5 
1 
1 
1 
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Daily Dose (mg)  
Range 
Daily Dose (mg)  
Round Toa 
# of 2.5mg 
Prefilled Syringe 
Needed 
# of 10mg Prefilled 
Syringe Needed 
# of 20mg Prefilled 
Syringe Needed 
33.8 – 36.2 
35 
2 
1 
1 
36.3 – 38.7 
37.5 
3 
1 
1 
38.8 – 41.2 
40 
-- 
-- 
2 
41.3 – 44.9 
42.5 
1 
-- 
2 
45 – 54.9 
50 
-- 
1 
2 
55 – 64.9 
60 
-- 
-- 
3 
65 – 74.9 
70 
-- 
1 
3 
75 – 84.9 
80 
-- 
-- 
4 
85 – 94.9 
90 
-- 
1 
4 
95 – 104.9 
100 
-- 
-- 
5 
105 – 114.9 
110 
-- 
1 
5 
115 – 124.9 
120 
-- 
-- 
6 
125 – 134.9 
130 
-- 
1 
6 
135 – 144.9 
140 
-- 
-- 
7 
145 – 154.9 
150 
-- 
1 
7 
a For  < 45 mg/day, round to nearest 2.5 mg; for  ≥ 45 mg/day, round to nearest 10 mg. 
 
The excipients in this drug product are tromethamine, tromethamine-hydrochloride, sodium 
chloride, L-phenylalanine, and water for injection. 
rAvPAL PEG doses will be administered SC by either health care professionals or via 
self-administration. The dose level may be increased or decreased per Investigator 
determination based on available information regarding a subject’s blood Phe level 
(60 600 µmol/L), as well as any adverse events (any hypersensitivity AE) for an individual 
subject. The dosage that provides control of blood Phe concentrations within the target range 
of 60-600 µmol/L for a minimum of 2 consecutive measurements will be determined for each 
subject by adjusting the dose level, dose frequency, or both, per the PI, based upon the 
subject’s response to doses. 
For vial and syringe, drug product packaging will be identified with the lot number and 
expiration date and will be provided in a box labeled with the study number. 
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For prefilled syringe, drug product packaging will be identified with the size (2.5 mg, 10 mg, 
or 20 mg), lot number, and kit identification (ID). The expiration date will be available in a 
separate Certificate of Compliance issued for each lot. 
9.4.3 Storage 
IP must be stored at 5 ± 3°C (41 ± 5°F) under the conditions specified in the IB. At the 
site, the IP will be stored in a secure area accessible only to the designated pharmacists and 
clinical site personnel. All IP must be stored and inventoried and the inventories must be 
carefully and accurately documented according to applicable state, federal and local 
regulations, ICH GCP, and study procedures. 
Specific instructions for storage of study drug for subjects who qualify for self-administration 
are provided in the Subject Self-Administration Training Materials.  
9.4.4 Directions for Administration 
Doses will be administered SC and the favorable dose will be determined for each subject by 
adjusting the dose level, dose frequency, or both, per the PI, based upon the subject’s 
response to doses. Dosing is up to a maximum dose per week of 5.0 mg/kg (or 375 mg for 
subjects receiving a fixed dose).  
For subjects receiving weight-based dosing, dosage is calculated by multiplying each 
subject’s weight in kilograms (kg) on Day 1 (predose) by the assigned dose (in mg/kg). 
During the study, if the weight of a subject changes more than 10% from the measurement 
obtained at baseline or at a previous measurement, the subject’s dose may be adjusted to 
accommodate the change. The change must be recorded. Refer to the Pharmacy Manual for 
additional information on calculating dosage. 
Subjects who have demonstrated efficacy (as measured by blood Phe within the target range 
of 60-600 µmol/L for at least 2 consecutive measurements) and who have maintained a stable 
rAvPAL-PEG dose for at least 2 consecutive measurements may be eligible to transition 
from weight-based dosing to a fixed dosing regimen that would permit daily dosing (5- or 
7-days-per-week).  Subjects who convert to a fixed-dosing regimen should convert their dose 
based upon the information presented in Table 9.4.4.1. 
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Table 9.4.4.1:  Fixed Doses for Subjects on Weight-Based Dose Regimen  
Weight-based dose (mg/kg) 
Equivalent fixed dose 
(mg) 
Vol for 15 mg/ml 
concentration (ml) (vial)a 
0.03 
2.5 
0.17 
0.06 
5 
0.33 
0.12 
10 
0.67 
0.25 
20 
1.33 
0.5 
40 
2.67 
1.0 
75 
5 
2.0 
150 
10 
3.0 
225 
15 
4.0 
300 
20 
5.0 
375 
25 
a Applies to both 1.0 and 1.3 ml withdrawal. 
 
It is preferable that the injection sites should be alternated between doses, ie, upper left arm 
in Week 1, upper right arm in Week 2, etc. Doses may be administered in any of the common 
SC areas (upper arm, thigh, abdomen). If dose volume is such that a dose will be divided and 
given in more than 1 injection site, it is preferable to use both arms, both legs, or both sides 
of the abdomen. 
Subjects may require more than 1 injection per dose, depending upon site policy (ie, some 
institutions do not permit a single SC injection of greater than 2 mL).  Dosage calculations 
must be performed according to study drug preparation instructions provided in the PAL-003 
Pharmacy Manual. Study drug will be administered by clinic staff, other qualified and trained 
study personnel, or qualified subjects. 
Information for dosing of subjects who enroll into this study after completing previous 
rAvPAL studies is provided in Section 9.1. Instructions for subjects who re-start 
rAvPAL-PEG dosing due to unplanned missed doses are provided in Section 9.4.10.  
Instructions for administration of study drug for subjects who qualify for self-administration 
are provided in the Subject Self-Administration Training Materials. 
9.4.5 Method of Assigning Subjects to Treatment Groups 
This will be an open-label study; no randomization schedule will be generated. 
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Subjects will retain the same subject number used in their previous rAvPAL-PEG study. 
9.4.6 Selection of Doses Used in the Study 
This Phase 2 study aims to evaluate the efficacy, safety, tolerability, and PK parameters of 
multiple doses of rAvPAL-PEG after long-term administration in subjects with PKU. A dose 
that produces a reduction in blood Phe concentrations to 60-600 μmol/L will be determined 
for each subject based on preliminary safety, antibody, and efficacy data from this ongoing 
study. 
9.4.6.1 
Selection of Timing of Dose for Each Subject 
Study drug will be administered by clinic staff or other qualified and trained study personnel. 
Subjects may self-administer study drug at home if approved by the sponsor’s medical 
monitor and if adequate training is provided (refer to Section 9.4). 
9.4.7 Blinding 
This is an open-label study. 
9.4.8 Prior and Concomitant Medications 
All prescription and over-the-counter (OTC) medications taken by a subject for 30 days 
before Screening will be recorded on the designated CRF. The Investigator may prescribe 
additional medications during the study, as long as the prescribed medication is not 
prohibited by the protocol. In the event of an emergency, any needed medications may be 
prescribed without prior approval, but the sponsor’s medical monitor must be notified of the 
use of any contraindicated medications immediately thereafter. Any concomitant medications 
added or discontinued during the study should be recorded on the CRF. 
Use of any investigational product (with the exception of rAvPAL-PEG used in a previous 
rAvPAL-PEG study) or investigational medical device within 30 days before Screening, or 
requirement for any investigational agent prior to completion of all scheduled study 
assessments, is prohibited. 
Use or planned use of any injectable drugs containing PEG (other than rAvPAL-PEG), 
including Depo-Provera, is prohibited within 6 months prior to Screening and during study 
participation. A list of PEG-containing injectable drugs is provided in the study reference 
materials. Subjects who have had a prior hypersensitivity AE to rAvPAL-PEG or a 
PEG-containing product will be encouraged to be premedicate as outlined in Section 9.1.1. If 
the hypersensitivity AE worsens with a repeat injection (as determined by the Investigator in 
consultation with the sponsor’s medical monitor) even with premedication prior to study drug 
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dosing, the subject must be withdrawn from the study and complete an Early Termination 
Visit. 
Subjects who have had a prior hypersensitivity AE to rAvPAL-PEG or a PEG-containing 
product may participate in this study (refer to Section 9.3.2).  
Use of any medication that is intended to treat PKU within 14 days prior to the 
administration of study drug is prohibited. 
9.4.9 Treatment Compliance 
The date, time, volume, and concentration of each dose of study drug administered to each 
subject must be recorded in the dispensing log provided for the study, as well as on the 
appropriate CRF. This data will be used to assess treatment compliance. 
9.4.10 Dose Interruption and Missed Doses  
Information for dosing of subjects who enroll into this study after completing previous 
rAvPAL-PEG studies is provided in Section 9.1.  
During this long-term extension study, interruption of rAvPAL-PEG dosing may occur per 
subject decision or per the Investigator. After a dosing interruption of ≥ four consecutive 
doses, rAvPAL-PEG administration should be re-started at the same dose level and dosing 
frequency that was administered prior to the dosing interruption. The first week of dosing of 
rAvPAL-PEG following a dose interruption should be administered in a clinic setting, and 
the subject must be observed for 30 minutes following administration due to restarting 
dosing. Premedication with H1 antagonist, H2 antagonist, and non-steroidal anti-
inflammatory medication (NSAIDs) approximately 2-3 hours prior to study drug should be 
administered following any dose interruption of ≥ four consecutive doses. NSAIDs should be 
given with food and may be omitted if not tolerated. A follow-up telephone call will be made 
to the subject to monitor subject safety 24 hours following the return to dosing. Subjects 
should continue to perform the study assessments as outlined in the Schedule of Events (refer 
to Table 9.1.1) during any dosing interruption.  
Subjects who miss rAvPAL-PEG dosing due to poor compliance may be discontinued from 
further study treatment per discretion of the Sponsor or Investigator (refer to Section 9.3.3).  
9.5 
Investigational Product Accountability 
The PI or designee is responsible for maintaining accurate records (including dates and 
quantities) of IP received, subjects to whom IP is dispensed (subject-by-subject dose specific 
accounting), IP returned, and IP lost or accidentally or deliberately destroyed. The PI or 
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designee must retain all unused or expired study supplies until the study monitor (on-site 
CRA) has confirmed the accountability data. 
9.5.1 Return and Disposition of Clinical Supplies 
Unused study drug must be kept in a secure location for accountability and reconciliation by 
the study monitor. The Investigator or designee must provide an explanation for any 
destroyed or missing study drug or study materials. 
Unused study drug may be destroyed on site, per the site’s standard operating procedures, but 
only after BioMarin has granted approval for drug destruction. The monitor must account for 
all study drug in a formal reconciliation process prior to study drug destruction. All study 
drug destroyed on site must be documented. Documentation must be provided to BioMarin 
and retained in the PIs study files. If a site is unable to destroy study drug appropriately, the 
site can return unused study drug to BioMarin upon request. The return of study drug or 
study drug materials must be accounted for on a Study Drug Return Form provided by 
BioMarin. 
Subjects who qualify for self-administration of study drug will be provided with instructions 
for returning used and unused study drug and the proper disposal of any study drug materials 
(refer to the Subject Self-Administration Training Materials). 
All study drug and related materials should be stored, inventoried, reconciled, and destroyed 
or returned according to applicable state and federal regulations and study procedures. 
9.6 
Dietary or Other Protocol Restrictions 
Subjects will be instructed that diet should not be altered during the course of the study. Any 
decision to modify subject diet must be made per the Investigator and must be performed 
under the supervision of the Investigator. 
A 3-day dietary record will be completed by subjects and will be brought to clinic visits for 
review with clinic staff. It is preferable that subjects complete the 3-day record immediately 
prior to their next monthly study visit.  The dietary record will be maintained with the study 
source documents. Information regarding a subject diet diary is provided in Section 9.7.4. 
9.7 
Efficacy and Safety Variables 
9.7.1 Efficacy and Safety Measurements Assessed 
The Schedules of Events in the Synopsis describe the timing of required evaluations. 
For the laboratory assessments, the party responsible for performing the assessment and the 
pertinent protocol section describing the details of the test are listed in Table 9.7.1.1. 
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Table 9.7.1.1:  Summary of Laboratory Assessments 
Laboratory Assessment 
Party Responsible for 
Performing Test 
Section in Protocol for 
Details 
Clinical laboratory tests 
Central laboratory 
9.7.6 
Antibody testing 
BioMarina or CRO 
9.7.5.2 
PK variables 
BioMarin 
9.7.3 
Blood Phe concentrations 
Central laboratory 
9.7.2.1 
Pregnancy test (urine) and sedimentation rate 
Local laboratory 
9.7.6, 9.7.5.1 
Urinalysis 
Central laboratory 
9.7.6 
Phe, phenylalanine; PK, pharmacokinetic. 
aAnalysis of the anti-rAvPAL IgE and anti-rAvPAL-PEG IgE assay will be performed by a Contract Research 
Organization. 
 
9.7.1.1 
Demographic Data and Medical History 
Demographic data and a detailed medical history, including allergy history, will be obtained 
at Screening. The medical history will include specific information concerning any prior or 
existing medical conditions that might interfere with study participation or safety. 
This medical history should elicit all major illnesses, diagnoses, and surgeries that the subject 
has ever had, and whether the subject has a history of alcohol and/or drug abuse. 
9.7.1.2 
Physical Examination Findings 
Physical examination will include assessment of general appearance; CV; dermatologic; 
head, eyes, ears, nose, and throat; lymphatic; respiratory; GI; musculoskeletal; and 
neurological/psychological. Other body systems may be examined. Day 1 results will be the 
baseline values and clinically significant changes from baseline will be recorded as an AE. 
9.7.1.3 
Vital Sign Measurements 
Vital signs will be measured after resting for 5 minutes, and include seated systolic blood 
pressure (SBP) and diastolic blood pressure (DBP) measured in millimeters of mercury 
(mm Hg), heart rate in beats per minute, respiration rate in breaths per minute, and 
temperature in degrees Celsius (°C). Height (cm) will be measured at Screening only.  
Weight will be measured at Screening and then monthly. 
9.7.1.4 
Electrocardiography 
A standard 12-lead ECG will be recorded while the subject is resting, at Screening and at the 
Final Follow-Up (F/U) Visit or Early Termination Visit (ETV). If clinically significant 
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abnormalities are noted at Screening, the PI or designee is required to assess whether it is 
appropriate for the subject to enroll in the study. 
9.7.1.5 
Chest X-Ray 
A chest X-ray will be performed at the Screening, Week 48, and Final Follow-Up (or Early 
Termination) visits to assess gross pulmonary health.  
9.7.2 Efficacy Variable 
9.7.2.1 
Blood Phenylalanine Concentrations 
Blood samples for Phe concentration measurements will be drawn monthly, at least 2.5 hours 
after a meal, on the days and time points indicated in the Schedule of Events (Table 9.1.1).   
Blood Phe may be collected more often than monthly at the discretion of the Investigator 
should more frequent monitoring of blood Phe levels be clinically required. 
A central laboratory will be used for blood Phe concentration analysis. 
9.7.3 Pharmacokinetic Variables 
Subjects enrolled in the Substudy will have additional PK sampling performed. For subjects 
participating in the Substudy, PK sampling will be performed as follows: 
• For subjects who are administered rAvPAL-PEG once per week, plasma PK sampling 
will be performed pre-dose and every 24 hours thereafter (24, 48, 72, and 96 hours if 
possible), and then pre-dose of the next weekly dose. 
• For subjects who are administered rAvPAL-PEG two or three times per week, plasma 
PK sampling will be performed pre-dose and every 24 hours during the longest period 
between doses, when possible, and then pre-dose of the next dose.  
• For subjects who are administered rAvPAL-PEG four to seven times per week, 
plasma PK sampling will be performed pre-dose and every 12 hours during the 
longest period between doses, when possible, and then pre-dose of the next dose. 
See Table 9.1.2 for additional details. 
BioMarin will perform the analysis. 
9.7.4 Exploratory Efficacy Variable 
Diet will be assessed for its role in blood Phe reduction relative to rAvPAL-PEG dosing 
using a 3-day diet diary, which will be given to subjects to complete at home. Subjects will 
bring the completed diary with them to clinic visits on a monthly basis. Subjects will be 
instructed to record all food, beverages, special low-protein foods, and medical foods 
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consumed for 3 consecutive days each month. If changes in diet are noted per the information 
on the diet diary, the subject will be instructed to maintain their diet as reported at the 
beginning of the study or as otherwise instructed by the Investigator. 
9.7.5 Safety Variables 
9.7.5.1 
Pregnancy Testing 
Female subjects of childbearing potential will have a urine pregnancy test at the time points 
specified in the Schedules of Events (Table 9.1.1). Female subjects with a positive serum 
pregnancy test at Screening do not meet eligibility criteria for enrollment. 
Additional pregnancy tests will be performed at any visit in which pregnancy status is in 
question. Serum pregnancy tests will be performed in the event of a positive or equivocal 
urine pregnancy test result. 
Refer to Section 10.4 for details on the reporting procedures to follow in the event of 
pregnancy. 
9.7.5.2 
Antibody Testing 
Immunogenicity will be assessed by determining immune response and neutralizing activity 
with the following measurements: anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, anti-PEG 
IgM, anti-rAvPAL IgE, anti-rAvPAL-PEG IgE, and anti-rAvPAL-PEG neutralizing 
antibodies (refer to Section 9.1.1). Immunogenicity assays will be performed at the time 
points indicated in the Schedule of Events (Table 9.1.1). 
BioMarin or CRO will perform all anti-body testing, except for IgE antibodies, which will be 
assessed by a Contract Research Organization. 
9.7.6 Clinical Laboratory Assessments 
Any abnormal test results determined to be clinically significant by the Investigator should 
be repeated (at the Investigator’s discretion) until the cause of the abnormality is determined, 
the value returns to baseline or to within normal limits, or the Investigator determines that the 
abnormal value is no longer clinically significant. 
All abnormal clinical laboratory result pages should be initialed and dated by an Investigator, 
along with a comment regarding whether or not the abnormal result is clinically significant. 
The diagnosis, if known, associated with abnormalities in clinical laboratory tests that are 
considered clinically significant by the Investigator will be recorded on the AE CRF. 
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Table 9.7.6.1:  Clinical Laboratory Tests 
Blood Chemistry 
Hematology 
Urine Testsa 
Other 
Albumin  
Hemoglobin  
Appearance 
Pregnancy test, if applicablea 
Alkaline Phosphatase  
Hematocrit  
Color 
ALT (SGPT)  
WBC count 
pH 
Phenylalanine 
AST (SGOT) 
RBC count 
Specific gravity 
Tyrosine 
Total bilirubin 
Platelet count 
Ketones 
Sedimentation ratea 
BUN 
Differential cell count 
Protein 
Creatinine 
 
Glucose 
GGT 
 
Spot urine 
albumin/creatinine ratio  
Additional Unscheduled 
Hypersensitivity Reaction 
Visit Testsb 
Total protein 
 
Nitrite 
CH50 
Calcium 
 
Urobilinogen 
C1, C3, C4
 
Sodium 
 
Hemoglobin 
Serum tryptase levelb  
Potassium 
 
Bilirubin 
CRP  
Glucose 
 
 
Urine N-methyl histamine 
 
 
Urine albumin/creatinine ratio 
Uric acid 
 
 
Complement Testingc 
CO2 
 
 
C3 
Chloride 
 
 
C4 
ALT, alanine aminotransferase; AST, aspartate aminotransferase; BUN, blood urea nitrogen; C, complement; 
CH50, total hemolytic complement; CO2, carbon dioxide; CRP, C-reactive protein; GGT, 
gamma-glutamyltransferase; RBC, red blood cell; SGOT, serum glutamic-oxaloacetic transaminase; SGPT, 
serum glutamic-pyruvic transaminase; WBC, white blood cell. 
a To be performed by central laboratory. If urine pregnancy test is positive or equivocal, serum sample will be 
taken and assessed by a central laboratory. 
b Perform within 24 hours of event onset. 
c  Complement C3 and C4 to be drawn at the Screening Visit and then quarterly or as needed to resolve abnormal 
test results. 
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10 
REPORTING ADVERSE EVENTS 
10.1 
Adverse Events 
For this protocol, a reportable adverse event (AE) is any untoward medical occurrence 
(e.g., sign, symptom, illness, disease or injury) in a subject administered the study-drug or 
other protocol-imposed intervention, regardless of attribution. This includes the following: 
• AEs not previously observed in the subject that emerge during the course of the 
study. 
• Pre-existing medical conditions judged by the Investigator to have worsened in 
severity or frequency or changed in character during the study. 
• Complications that occur as a result of non-drug protocol-imposed interventions 
(eg, AEs related to screening procedures, medication washout, or no-treatment 
run-in). 
An adverse drug reaction is any AE for which there is a reasonable possibility that the study 
drug caused the AE. “Reasonable possibility” means there is evidence to suggest a causal 
relationship between the study-drug and the AE. 
Whenever possible, it is preferable to record a diagnosis as the AE term rather than a series 
of terms relating to a diagnosis. 
The study AE reporting period is as follows: After informed consent but prior to initiation of 
study treatment, only SAEs associated with any protocol-imposed interventions will be 
reported.  After informed consent is obtained and the first administration of study drug, all 
non-serious AEs and SAEs reporting period begins and continues until 4 weeks following the 
last administration of study drug or the early termination visit, whichever is longer (refer to 
Section 12). The criteria for determining, and the reporting of SAEs is provided in 
Section 10.2.   
For this study, a medical device is defined as the prefilled syringe and all of the component 
parts. The reporting period for device-related events begins with the first dose administered 
using prefilled syringe and ends with the last dose administered using prefilled syringe. 
Events assessed by the investigator as related to the device, including malfunction, injury, or 
medication error, will be captured into an electronic data capture system. All serious events 
related to the device will be reported to BioMarin Pharmacovigilance (BPV) within 24 hours 
using the device-related event report form and entered onto the appropriate eCRF page(s) as 
required.  
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The Investigator should follow all unresolved AEs until the events are resolved or stabilized, 
the subject is lost to follow-up, or it has been determined that the study treatment or study 
participation is not the cause of the AE. Outcome of AEs (and resolution dates) should be 
documented on the appropriate CRF page(s) and in the subject’s medical record unless the 
subject is lost to follow-up or it has been determined that the study treatment or study 
participation is not the cause of the AE. 
The Investigator responsible for the care of the subject or qualified designee will assess AEs 
for severity, relationship to study-drug, and seriousness (see Section 10.2 for SAE 
definition). Severity (as in mild, moderate or severe headache) is not equivalent to 
seriousness, which is based on subject/event outcome or action criteria usually associated 
with events that pose a threat to a subject’s life or functioning. Seriousness (not severity) 
serves as a guide for defining regulatory reporting obligations. 
The Investigator will determine the severity of each AE using the National Cancer Institute 
(NCI) Common Terminology Criteria for Adverse Events (CTCAE) v4. Adverse events that 
do not have a corresponding CTCAE term will be assessed according to the general 
guidelines for grading used in the CTCAE v4 as stated below. 
Grade 
Description 
1 
Mild: asymptomatic or mild symptoms; clinical or diagnostic 
observations only; intervention not indicated 
2 
Moderate: minimal, local or noninvasive intervention indicated; 
limiting age-appropriate instrumental activities of daily living (ADL)a 
3 
Severe or medically significant but not immediately life-threatening: 
hospitalization or prolongation of hospitalization indicated; disabling; 
limiting self care activities of daily living (ADL)b 
4 
Life threatening or debilitating: consequences; urgent intervention 
indicated 
5 
Death related to AE 
Grade 4 and 5 AEs should always be reported as SAEs. 
a Instrumental ADL refer to the following examples: preparing meals, shopping for groceries or clothes, using 
the telephone, managing money. 
b Self care ADL refer to the following examples: bathing, dressing and undressing, feeding oneself, using the 
toilet, taking medications, not bedridden. 
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The Investigator will determine the relationship of an AE to the study drug and will record it 
on the source documents and AE CRF, using the categories defined below. 
Relationship 
Description 
Not Related 
Exposure to the IP has not occurred 
OR 
The administration of the IP and the occurrence of the AE are not reasonably related in 
time  
OR 
The AE is considered likely to be related to an etiology other than the use of the IP; that is, 
there are no facts [evidence] or arguments to suggest a causal relationship to the IP. 
Possibly Related 
The administration of the IP and the occurrence of the AE are reasonably related in time 
AND 
The AE could be explained equally well by factors or causes other than exposure to the IP. 
Probably Related 
The administration of IP and the occurrence of the AE are reasonably related in time  
AND 
The AE is more likely explained by exposure to the IP than by other factors or causes. 
In order to classify AEs and diseases, preferred terms will be assigned by the sponsor to the original terms 
entered on the CRF, using MedDRA (Medical Dictionary for Regulatory Activities terminology). 
 
10.2 
Serious Adverse Events 
A serious adverse event (SAE) is any untoward medical occurrence that at any dose meets 
1 or more of the following criteria: 
• Is fatal. 
• Is life threatening. 
o Note: Life-threatening refers to an event that places the subject at 
immediate risk of death. This definition does not include a reaction that, 
had it occurred in a more severe form, might have caused death. 
• Requires or prolongs inpatient hospitalization. 
• Results in persistent or significant disability or incapacity. 
• Is a congenital anomaly or birth defect in the child or fetus of a subject exposed to IP 
prior to conception or during pregnancy. 
• Important medical events or reactions that may not be immediately life-threatening or 
result in death or hospitalization but may jeopardize the subject or may require 
intervention to prevent one of the other outcomes above should also usually be 
considered serious. 
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For this protocol, anaphylaxis per NIAID/FAAN criteria for the clinical diagnosis of 
anaphylaxis is designated as an AE of special interest (serious or nonserious and irrespective 
of severity) to facilitate rapid reporting and sponsor review. All occurrences of anaphylaxis 
per NIAID/FAAN criteria will be reported to the sponsor within 24 hours of the site 
becoming aware of the event using the SAE form. Severity and serious criteria (if applicable) 
should be reported on the SAE form. 
The reporting period for SAEs related to protocol imposed interventions begins after 
informed consent is obtained, the reporting period for all SAEs begins after first dose of 
study drug and continues until 4 weeks following the last administration of study drug or End 
of Treatment Visit. The reporting period for Serious Device Related Events begins after first 
dose of study drug and ends with the last administered dose. 
All SAEs (including serious device-related events), whether or not considered related to 
study drug, must be reported within 24 hours of the site becoming aware of the event by 
faxing the study-specific SAE Report Form or device Report Form to BioMarin 
Pharmacovigilance (BPV). Each SAE must also be reported in the CRF Investigators should 
not wait to collect information that fully documents the event before notifying BPV of a 
SAE. BioMarin may be required to report certain SAEs to regulatory authorities within 
7 calendar days of being notified about the event; therefore, it is important that Investigators 
submit any information requested by BioMarin as soon as it becomes available.  The 
Investigator should follow all unresolved SAEs until the events are resolved or stabilized, the 
subject is lost to follow-up, or it has been determined that the study treatment or participation 
is not the cause of the AE. Resolution of AEs (with dates) should be documented in the CRF 
and in the subject’s medical record. 
For some SAEs, the Sponsor may follow up by telephone, fax, electronic mail, and/or a 
monitoring visit to obtain additional case details deemed necessary to appropriately evaluate 
the SAE report (e.g., hospital discharge summary, consultant report, or autopsy report). 
At the last scheduled visit, the Investigator should instruct each subject to report any 
subsequent SAEs that the subject’s personal physician(s) believes might be related to prior 
study treatment. 
The Investigator should notify the study Sponsor of any death or SAE occurring at any time 
after a subject has discontinued or terminated study participation if felt to be related to prior 
study treatment. The Sponsor should also be notified if the Investigator should become aware 
of the development of cancer or of a congenital anomaly in a subsequently conceived 
offspring of a subject that participated in this study.  
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Reporting of SAEs to the IRB will be done in compliance with the standard operating 
procedures and policies of the IRB and with applicable regulatory requirements. Adequate 
documentation must be obtained by BioMarin showing that the IRB was properly and 
promptly notified as required. 
10.3 
Pregnancy 
Pregnancy in a subject or partner should be reported within 24 hours of the site becoming 
aware of the pregnancy to BioMarin Pharmacovigilance by fax using the Pregnancy Form in 
the study reference materials. The reporting period for pregnancies begins with informed 
consent and continues until 4 weeks following the last study drug dose. In addition, 
pregnancy in a subject is also reported on the End of Study CRF. The Investigator must make 
every effort to follow the subject through resolution of the pregnancy (delivery or 
termination) and to report the resolution to BPV in the study reference materials. In the event 
of pregnancy in the partner of a study subject, the Investigator should make every reasonable 
attempt to obtain the woman’s consent for release of protected health information. 
10.4 
Urgent Safety Measures 
The regulations governing clinical trials state that the sponsor and Investigator are required to 
take appropriate urgent safety measures to protect subjects against any immediate hazards 
that may affect the safety of subjects, and that the appropriate regulatory bodies should be 
notified according to their respective regulations. According to the European Union (EU) 
Clinical Trial Directive 2001/20/EC, “…in the light of the circumstances, notably the 
occurrence of any new event relating to the conduct of the trial or the development of the 
investigational medicinal product where that new event is likely to affect the safety of the 
subjects, the sponsor and the Investigator shall take appropriate urgent safety measures to 
protect the subjects against any immediate hazard. The sponsor shall forthwith inform the 
competent authorities of those new events and the measures taken and shall ensure that the 
IRB/EC/REB is notified at the same time.” The reporting period for these events which may 
require the implementation of urgent safety measures is the period from the time of signing 
of the ICF through the completion of the last study visit or at the ETV. Investigators are 
required to report any events which may require the implementation of urgent safety 
measures to BioMarin with 24 hours. 
Examples of situations that may require urgent safety measures include discovery of the 
following: 
• Immediate need to revise the IP administration (i.e., modified dose amount or 
frequency not defined in protocol). 
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• Lack of study scientific value, or detrimental study conduct or management. 
• Discovery that the quality or safety of the IP does not meet established safety 
requirements. 
10.5 
BioMarin Pharmacovigilance Contact Information 
Contact information for BioMarin Pharmacovigilance is as follows: 
BioMarin Pharmaceutical Inc. 
Address 
105 Digital Drive 
 
 
Novato, CA 94949 
Phone:  
(415) 506-6179 
Fax: 
 
(415) 532-3144 
E-mail: 
drugsafety@bmrn.com 
The Investigator is encouraged to discuss with the Sponsor’s Medical Office sponsor’s 
medical monitor r any AEs for which the issue of seriousness is unclear or questioned. 
Contact information for the sponsor’s medical monitor is as follows: 
Name:  
, MD 
Address: 
105 Digital Drive 
 
 
Novato, CA 94949 USA 
Phone:  
 
Fax: 
 
 
E-mail: 
 
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11 
APPROPRIATENESS OF MEASUREMENTS 
11.1 
Safety and Pharmacokinetics 
The PK and safety assessments in this study are used widely and are generally recognized as 
reliable, accurate, and relevant. 
11.2 
Diet Diary 
A 3-day diet diary will be issued to subjects for completion and will be brought to clinic on a 
monthly basis for review with the clinical study staff. Additional information regarding the 
diet diary is provided in Section 7.3, and information regarding administration of the diary is 
provided in Section 9.7.4. Additional information about diet is provided in Section 9.1 and 
Section 9.6. 
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12 
STUDY PROCEDURES 
12.1 
Prestudy 
An ICF must be signed and dated by the subject (or the subject’s legally authorized 
representative if the subject is less than 18 years of age), the PI or designee and witness 
(if required) before any study-related procedures are performed. 
12.2 
Screening Visit 
After subjects have signed an ICF, they will be screened for enrollment into the study. 
The following study activities will be performed at Screening: 
• Medical history, including allergy history, and demographics 
• Physical examination  
• Vital signs, including height and weight 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.).  For safety reasons, 
this test must be performed prior to the chest X-ray. 
• Chest X-ray 
• 12-lead ECG 
• Clinical laboratory tests (including spot urine albumin/creatinine ratio, hematology, 
chemistry, and urinalysis) 
• Complement C3 and C4 
• Assessment of SAEs 
• Concomitant medications 
• Diet query 
• Blood Phe and plasma tyrosine concentration 
For subjects who participated in a previous rAvPAL-PEG study, these assessments may be 
the same as those used for the last visit of the previous study, if they occur within 28 days 
from Day 1. 
12.3 
Treatment Period 
During the Treatment Period, additional visits may occur if deemed necessary to monitor 
AEs or blood Phe concentrations. All study activities will occur on the first day of each week 
unless otherwise noted. On days that a dose is given, assessments will be done predose unless 
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otherwise specified. Subjects must have AEs and concomitant medications assessed 
whenever dose is administered even if the administration does not coincide with a scheduled 
clinic visit.   
If the dose is modified by increasing dose level, additional blood Phe concentration testing 
should be done daily for 3 days following dose adjustment. If dose is modified by increasing 
either dose frequency or dose level, additional blood Phe concentration testing should be 
done prior to each dose for the first 2 weeks following dose adjustment. 
12.3.1 Day 1 (Week 1) 
Within 28 days of completing screening assessments, the following study activities will be 
performed on Day 1: 
• Physical examination 
• Vital signs 
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• Assessment of SAEs (predose and postdose) and all AEs (postdose) 
• Concomitant medications 
• Diet query 
• PK sample 
• Blood Phe and plasma tyrosine concentration 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, and anti-rAvPAL-PEG neutralizing antibodies) 
• Administer study drug (study drug may be administered on additional days during the 
week as determined by the Investigator) 
12.3.2 Weekly Telephone Visit 
Subjects should have a weekly telephone visit conducted. Subjects must still come into the 
clinic for the scheduled monthly visits per Table 9.1.1. The following should be discussed 
with the subject during the weekly telephone visit: 
• Injection-site self inspection (previous and current injection site) 
• Assessment of AEs 
• Concomitant medications 
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• Confirmation of dose level, frequency, and study drug administration 
12.3.3 Substudy Visits 
For subjects participating in the PK substudy, refer to Section 9.7.3 and Table 9.1.2. 
12.3.4 Monthly Visits (Week 4, 8, 12, etc) 
Subjects must have AEs and concomitant medications assessed whenever dose is 
administered even if the administration does not coincide with a scheduled clinic visit.    
Beginning with Week 4, monthly visits must be performed in the clinic. The following study 
activities will be performed: 
• Vital signs 
• Weight 
• Clinical laboratory tests 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) For safety reasons, this 
test must be performed prior to the chest X-ray. 
• Chest x-ray (Week 48 visit only) 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• Blood Phe and plasma tyrosine concentration 
• 3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the next monthly visit.) 
• Prefilled syringe self-administration training (to be performed prior to subjects 
transitioning from vial and syringe drug product to prefilled syringe drug product). 
• If additional training is needed on days subsequent to the monthly visit, additional 
clinic visit(s) or HHRN may be used. 
12.3.5 Quarterly Visits (Week 12, 24, 36, etc) 
Subjects must have AEs and concomitant medications assessed whenever dose is 
administered even if the administration does not coincide with a scheduled clinic visit.    
Beginning with Week 12, quarterly visits consist of all monthly (Section 12.3.4) activities 
listed above as well as the additional study activities listed below: 
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• Physical examination 
• Complement C3 and C4 
• Sedimentation rate 
• PK sample 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, and anti-rAvPAL-PEG neutralizing antibodies) 
• Prefilled syringe refresher training (every 24 weeks only) 
12.3.6 Unscheduled Hypersensitivity Reaction Visit 
Subjects who have an NCI-CTCAE grade ≥ 3 hypersensitivity reaction after rAvPAL-PEG 
administration (refer to Section 9.1.1) will have assessments performed immediately 
following (within 24 hours) the reaction.  
• Vital signs 
• Clinical laboratory tests 
• Urine/albumin creatinine ratio 
• CRP, CH50, C1, C3, and C4 
• Urine N-methyl histamine  
• Serum anti-rAvPAL IgE and anti-rAvPAL-PEG IgE only (performed > 8 hours after 
event onset) 
• Serum tryptase level 
• Skin biopsy (optional; affected and not affected area; to be performed within 1 week 
of the reaction) 
• Assessment of AEs 
• Concomitant medications 
Following completion of the Unscheduled Hypersensitivity Reaction visit, subjects may 
resume study drug administration per the discretion of the Principal Investigator and the 
sponsor’s medical monitor. 
12.4 
Early Termination Visit 
The Early Termination Visit (ETV) will occur 4 weeks after the final dose of study drug. 
Subjects who terminate from study treatment early should continue to perform the remaining 
visit assessments in Section 12.3 as applicable until study completion. 
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Any AE that caused a subject to withdraw from the study or any clinically significant 
abnormal laboratory value or vital sign measurement identified at the ETV will be followed 
by the Investigator.  
Every reasonable effort should be made to contact any subject who is lost to follow-up. 
The following study activities will be performed at the ETV: 
• Physical examination  
• Vital signs 
• 12-lead ECG 
• Clinical laboratory tests 
• Chest x-ray  
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.). For safety reasons, 
this test must be performed prior to the chest X-ray. 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• 3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the Early Termination Visit.) 
• PK sample 
• Blood Phe and plasma tyrosine concentration 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibodies) 
12.5 
Final Follow-up Visit 
The final follow-up (F/U) Visit will occur 4 weeks after the final dose of study drug. 
The following study activities will be performed at the F/U Visit: 
• Physical examination  
• Vital signs, including weight 
• 12-lead ECG 
• Clinical laboratory tests 
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• Chest x-ray  
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.). For safety reasons, 
this test must be performed prior to the chest X-ray. 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• 3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the Final Follow-up Visit.) 
• PK sample 
• Blood Phe and plasma tyrosine concentration 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibodies) 
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13 
DATA QUALITY ASSURANCE 
BioMarin personnel or designees will visit the study site prior to initiation of the study to 
review with the site personnel information about the IP, protocol and other regulatory 
document requirements, any applicable randomization procedures, source document 
requirements, CRFs, monitoring requirements, and procedures for reporting AEs, including 
SAEs. 
At visits during and after the study, a CRA will monitor the site for compliance with 
regulatory documentation, with a focus on accurate and complete recording of data on CRFs 
from source documents, adherence to protocol, randomization (if applicable), SAE reporting 
and drug accountability records.  
The designated clinical data management group will enter or transfer CRF data into a study 
database. 
Data quality control and analysis will be performed by BioMarin or a designee, based on a 
predefined analysis plan. 
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14 
STATISTICAL METHODS AND DETERMINATION OF SAMPLE SIZE 
14.1 
Statistical and Analytical Plans 
Because of the small sample size, no formal statistical tests will be performed. Categorical 
data will be summarized using frequency and percent, while continuous data will be 
summarized using descriptive statistics (ie, number of observations, mean, median, standard 
deviation [SD], minimum, and maximum). 
The statistical analysis plan (SAP) will provide additional details about the planned statistical 
analysis. 
14.2 
Safety Analysis 
All subjects who receive any amount of study drug in this study and have postdose safety 
information will be included in the safety analyses. 
The Medical Dictionary for Regulatory Activities terminology (MedDRA) will be used by 
the sponsor to assign system organ class and preferred term classification to events and 
diseases based on the original terms entered on the Case Report Form (CRF). 
The incidence of AEs will be summarized by system organ class, preferred term, relationship 
to study drug, and severity. A by–subject listing will be provided for those subjects who 
experience a serious AE (SAE), including death, or experience an AE associated with early 
withdrawal from the study or study drug. Hypersensitivity AEs and AEs that result in dosing 
interruption or dose level reduction are of interest, and the percentage of subjects who report 
these AEs will be presented. 
Clinical laboratory data will be summarized by the type of laboratory test. Frequency and 
percentage of subjects who experience abnormal (ie, outside of reference range) and/or 
clinically significant abnormalities after study drug administration will be presented for each 
clinical laboratory test. For each clinical laboratory test, descriptive statistics will be provided 
for baseline and all subsequent post-treatment visits. Changes from baseline to the 
post-treatment visits will also be provided. Descriptive statistics of vital signs, physical 
examination results, ECG results, and X-ray results, and immunogenicity test results will also 
be provided. Additionally, antibodies and titers will be summarized by scheduled time point. 
14.3 
Pharmacokinetic Analysis 
Subjects who complete the Substudy will have the following PK parameters assessed: area 
under the plasma concentration-time curve (AUC), time to maximum plasma concentration 
(Tmax), maximum plasma concentration (Cmax), half life (t1/2), and clearance (CL/F).  Should 
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data become available from previous rAvPAL-PEG studies that indicate study drug 
accumulation should also be measured, additional blood draws may be added for PK analysis 
as needed per the discretion of the Investigator in consultation with the sponsor’s medical 
monitor. 
14.3.1 Pharmacokinetic Substudy Analysis 
For subjects who completed the Substudy, the steady-state PK of rAvPAL-PEG in subjects 
who have achieved and maintained target blood Phe will be explored.  This substudy has 
been completed as of 20 December 2013. 
14.4 
Efficacy Analysis 
Data from all subjects who receive any amount of study drug and who have any 
post-treatment efficacy data will be included in the efficacy analysis. 
Blood Phe concentration at each scheduled time point will be summarized using descriptive 
statistics (mean, SD, median, minimum, and maximum). Change in blood Phe concentration 
from baseline (to be defined in the SAP) to each scheduled time point and presence/absence 
of antibodies will also be summarized. In addition, the proportion of subjects who have 
maintained target Phe concentrations of 60-600 µmol/L will be summarized by each 
scheduled time point. 
The relationship of dietary Phe intake (per information reported on the subject diet diary) and 
blood Phe concentration will also be explored. Subjects who received any amount of study 
drug with any post-treatment blood Phe concentration measurements and diet diary 
information will be included in this exploratory analysis.  
Details regarding exploratory analyses will be provided in the Statistical Analysis Plan. 
14.5 
Determination of Sample Size 
Subjects who participated in previous rAvPAL-PEG studies may be enrolled into this study. 
No formal sample size calculation was conducted for this study or the PAL-003 Substudy.   
14.6 
Handling of Missing Data 
All analyses will be presented based on observed data only. Missing data will not be imputed 
for analyses unless sensitivity analyses are warranted. If imputations are used, detailed 
imputation methods will be described in the SAP before locking the database. 
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14.7 
Interim Analyses 
Safety will be assessed throughout the study on an ongoing basis (refer to Section 15 for 
information regarding the DMC). 
14.8 
Changes in the Conduct of the Study or Planned Analyses 
Only BioMarin may modify the protocol. Any change in study conduct considered necessary 
by the PI will be made only after consultation with BioMarin, who will then issue a formal 
protocol amendment to implement the change. The only exception is when an Investigator 
considers that a subject’s safety is compromised without immediate action. In these 
circumstances, immediate approval of the chairman of the IRB must be sought, and the 
Investigator should inform BioMarin and the full IRB within 2 working days after the 
emergency occurs. 
With the exception of minor administrative or typographical changes, the IRB must review 
and approve all protocol amendments. Protocol amendments that have an impact on subject 
risk or the study objectives, or require revision of the ICF, must receive approval from the 
IRB prior to their implementation. 
When a protocol amendment substantially alters the study design or the potential risks or 
burden to subjects, the ICF will be amended and approved by BioMarin and the IRB, and all 
active subjects must again provide informed consent. 
Note: If discrepancies exist between the text of the statistical analysis as planned in the 
protocol, and the final SAP, a protocol amendment will not be issued and the SAP will 
prevail. 
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15 
DATA MONITORING COMMITTEE (DMC) 
The DMC will act independently in an advisory capacity to BioMarin to monitor the safety 
of rAvPAL-PEG in subjects who participate in the study.  
The responsibilities of the DMC are to: 
• Review the study protocol, informed consent and assent documents, and plans for 
data monitoring. 
• Evaluate the progress of the trial, subjects’ risk versus benefit, and other factors that 
could affect the study outcome. 
• Assess the effect and relevance of new external evidence. 
• Consider relevant information that may have an impact on the safety of the 
participants or the ethics of the study. 
• Protect the safety of the study participants in accordance with the stopping criteria as 
defined in study protocol Section 9.1.2. 
• Make recommendations to the BioMarin concerning continuation or termination of 
the study or other study modifications based on observations. 
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16 
COMPENSATION, INSURANCE, AND INDEMNITY 
There will be no charge to study subjects to be in this study. BioMarin will pay all costs of 
tests, procedures, and treatments that are part of this study. In addition, after IRB approval, 
BioMarin may reimburse the cost of travel for study-related visits. BioMarin will not pay for 
any hospitalizations, tests, or treatments for medical problems of any sort, whether or not 
related to the study subject’s disease, that are not part of this study. Costs associated with 
hospitalizations, tests, and treatments should be billed and collected in the way that such 
costs are usually billed and collected. 
The Investigator should contact BioMarin immediately upon notification that a study subject 
has been injured by the IP or by procedures performed as part of the study. Any subject who 
experiences a study-related injury should be instructed by the Investigator to seek medical 
treatment at a pre-specified medical institution if possible, or at the closest medical treatment 
facility if necessary. The subject should be given the name of a person to contact to seek 
further information about, and assistance with, treatment for study-related injuries. 
The treating physician should bill the subject’s health insurance company or other third party 
payer for the cost of this medical treatment, unless the executed Clinical Trial Agreement 
between BioMarin and the institution of the investigator specifies otherwise. If the subject 
has followed the Investigator’s instructions, BioMarin may pay for reasonable and necessary 
medical services to treat the injuries caused by the IP or study procedures. In some 
jurisdictions, BioMarin is obligated by law to pay for study-related injuries without prior 
recourse to third party payer billing. If this is the case, BioMarin will comply with the law. 
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17 
CASE REPORT FORMS AND SOURCE DOCUMENTS 
Electronic case report forms will be provided for each subject. The Investigator must review 
and electronically sign the completed CRF casebook to verify its accuracy. 
CRFs must be completed using a web–based application that has been validated. Study site 
personnel will be trained on the application and will enter the clinical data from source 
documentation. Unless explicitly allowed in the CRF instructions, blank data fields are not 
acceptable. 
In the event of an entry error, or if new information becomes available, the site personnel will 
correct the value by deselecting the erroneous response and then selecting or entering the 
factual response. In compliance with 21 CFR Part 11, the system will require the site 
personnel to enter a reason for changing the value. The documented audit trail will include 
the reason for the change, the original value, the new value, the time of the correction, and 
the identity of the operator. 
BioMarin’s policy is that study data on the CRFs must be verifiable to the source data, which 
necessitates access to all original recordings, laboratory reports, and subject records. 
In addition, all source data should be attributable (signed and dated). The Investigator must 
therefore agree to allow direct access to all source data. Subjects (or their legally authorized 
representative) must also allow access to their medical records, and subjects will be informed 
of this and will confirm their agreement when giving informed consent.  
A CRA designated by BioMarin will compare the CRFs with the original source documents 
at the study site and evaluate them for completeness and accuracy before designating them as 
“source data verified” (SDV). If an error is discovered at any time or a clarification is 
needed, the CRA, or designee, will create an electronic query on the associated field. Site 
personnel will then answer the query by either correcting the data or responding to the query. 
The CRA will then review the response and determine either to close the query or re–query 
the site if the response does not fully address the question. This process is repeated until all 
open queries have been answered and closed. 
Before a subject’s CRF casebook can be locked, all data fields must be SDV and all queries 
closed. The Investigator will then electronically sign the casebook, specifying that the 
information on the CRFs is accurate and complete. The Data Manager, or designee, will then 
set the status of the forms, visits, and the entire casebook to locked. Upon completion of the 
clinical study report for the entire study, an electronic copy of each site’s casebooks will be 
copied to a compact disk (CD) and sent to each site for retention with other study documents. 
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18 
STUDY MONITORING AND AUDITING 
Qualified individuals designated by BioMarin will monitor all aspects of the study according 
to GCP and standard operating procedures for compliance with applicable government 
regulations. The PI agrees to allow these monitors direct access to the clinical supplies, 
dispensing, and storage areas and to the clinical files, including original medical records, of 
the study subjects, and, if requested, agrees to assist the monitors. The PI and staff are 
responsible for being present or available for consultation during routinely scheduled site 
visits conducted by BioMarin or its designees. 
Members of BioMarin’s GCP Compliance Department or designees may conduct an audit of 
a clinical site at any time during or after completion of the study. The PI will be informed if 
an audit is to take place and advised as to the scope of the audit. Representatives of the FDA 
or other Regulatory Agencies may also conduct an audit of the study. If informed of such an 
inspection, the PI should notify BioMarin immediately. The PI will ensure that the auditors 
have access to the clinical supplies, study site facilities, original source documentation, and 
all study files. 
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19 
RETENTION OF RECORDS 
The PI must retain all study records required by BioMarin and by the applicable regulations 
in a secure and safe facility. The PI must consult a BioMarin representative before disposal 
of any study records, and must notify BioMarin of any change in the location, disposition or 
custody of the study files. The PI/institution must take measures to prevent accidental or 
premature destruction of essential documents, that is, documents that individually and 
collectively permit evaluation of the conduct of a study and the quality of the data produced, 
including paper copies of study records (e.g., subject charts) as well as any original source 
documents that are electronic as required by applicable regulatory requirements. 
All study records must be retained for at least 2 years after the last approval of a marketing 
application in the U.S. or an ICH region and until (1) there are no pending or contemplated 
marketing applications in the United States or an ICH region or (2) at least 2 years have 
elapsed since the formal discontinuation of clinical development of the IP. The PI/institution 
should retain subject identifiers for at least 15 years after the completion or discontinuation 
of the study. Subject files and other source data must be kept for the maximum period of time 
permitted by the hospital, institution or private practice, but not less than 15 years. 
These documents should be retained for a longer period, however, if required by the 
applicable regulatory requirements or by a BioMarin agreement. BioMarin must be notified 
and will assist with retention should the PI/institution be unable to continue maintenance of 
subject files for the full 15 years. It is the responsibility of BioMarin to inform the 
PI/institution as to when these documents no longer need to be retained. 
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20 
USE OF INFORMATION AND PUBLICATION 
BioMarin recognizes the importance of communicating medical study data and therefore 
encourages their publication in reputable scientific journals and at seminars or conferences. 
The details of the processes of producing and reviewing reports, manuscripts, and 
presentations based on the data from this study will be described in the Clinical Study 
Agreement between BioMarin and the PI. 
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21 
REFERENCES 
Armstrong, JK, Hempel, G, Koling, S, Chan, LS et. al. Antibody against poly(ethylene glycol) 
adversely affects PEG-asparaginase therapy in acute lymphoblastic leukemia patients. Cancer 110[1], 
103-111. 2007 
Brown, SG. Clinical features and severity grading of anaphylaxis. J Allergy Clin Immunol 114[2], 
371-376. 2004 
Chen, AM, Scott, MD. Current and future applications of immunological attenuation via pegylation 
of cells and tissue. BioDrugs 15[12], 833-847. 2001 
Davis, S, Abuchowski, A, Park, YK, Davis, FF. Alteration of the circulating life and antigenic 
properties of bovine adenosine deaminase in mice by attachment of polyethylene glycol. Clin Exp 
Immunol 46[3], 649-652. 1981 
Fisch, RO. Comments on diet and compliance in phenylketonuria. Eur J Pediatr 159 Suppl 2, S142-
S144. 2000 
Gamez, A, Wang, L, Sarkissian, CN, Wendt, D et. al. Structure-based epitope and PEGylation sites 
mapping of phenylalanine ammonia-lyase for enzyme substitution treatment of phenylketonuria. Mol 
Genet Metab 91[4], 325-334. 2007 
Ganson, NJ, Kelly, SJ, Scarlett, E, Sundy, JS et. al. Control of hyperuricemia in subjects with 
refractory gout, and induction of antibody against poly(ethylene glycol) (PEG), in a phase I trial of 
subcutaneous PEGylated urate oxidase. Arthritis Res Ther 8[1], R12. 2006 
Guttler, F, Azen, C, Guldberg, P, Romstad, A et. al. Impact of the phenylalanine hydroxylase gene on 
maternal phenylketonuria outcome. Pediatrics 112[6 Pt 2], 1530-1533. 2003 
Harris, JM, Chess, RB. Effect of pegylation on pharmaceuticals. Nat Rev Drug Discov 2[3], 214-221. 
2003 
Huttenlocher, PR. The neuropathology of phenylketonuria: human and animal studies. Eur J Pediatr 
159 Suppl 2, S102-S106. 2000 
Judge, A, McClintock, K, Phelps, JR, Maclachlan, I. Hypersensitivity and loss of disease site 
targeting caused by antibody responses to PEGylated liposomes. Mol Ther 13[2], 328-337. 2006 
Kaufman, S. An evaluation of the possible neurotoxicity of metabolites of phenylalanine. J Pediatr 
114[5], 895-900. 1989 
Koch, R, Hanley, W, Levy, H, Matalon, K et. al. The Maternal Phenylketonuria International Study: 
1984-2002. Pediatrics 112[6 Pt 2], 1523-1529. 2003 
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Lapis. Long-term Correction of PKU in the Pahenu2 Mouse by Mutant and Chemically Modified 
Forms of Phenylalanine Ammonium Lyase. ASHG 57th Annual Meeting The American Society of 
Human Genetics)2007.  
Lee, PJ, Lilburn, M, Baudin, J. Maternal phenylketonuria: experiences from the United Kingdom. 
Pediatrics 112[6 Pt 2], 1553-1556. 2003 
Levy, HL. Historical background for the maternal PKU syndrome. Pediatrics 112[6 Pt 2], 1516-1518. 
2003 
Matalon, R, Surendran, S, Matalon, KM, Tyring, S et. al. Future role of large neutral amino acids in 
transport of phenylalanine into the brain. Pediatrics 112[6 Pt 2], 1570-1574. 2003 
Richter, AW, Akerblom, E. Antibodies against polyethylene glycol produced in animals by 
immunization with monomethoxy polyethylene glycol modified proteins. Int Arch Allergy Appl 
Immunol 70[2], 124-131. 1983 
Richter, AW, Akerblom, E. Polyethylene glycol reactive antibodies in man: titer distribution in 
allergic patients treated with monomethoxy polyethylene glycol modified allergens or placebo, and in 
healthy blood donors. Int Arch Allergy Appl Immunol 74[1], 36-39. 1984 
Rouse, B, Azen, C. Effect of high maternal blood phenylalanine on offspring congenital anomalies 
and developmental outcome at ages 4 and 6 years: the importance of strict dietary control 
preconception and throughout pregnancy. J Pediatr 144[2], 235-239. 2004 
Sampson, HA, Munoz-Furlong, A, Campbell, RL, Adkinson, NF, Jr. et. al. Second symposium on the 
definition and management of anaphylaxis: summary report--Second National Institute of Allergy and 
Infectious Disease/Food Allergy and Anaphylaxis Network symposium. J Allergy Clin Immunol 
117[2], 391-397. 2006 
Scott, MD, Murad, KL, Koumpouras, F, Talbot, M et. al. Chemical camouflage of antigenic 
determinants: stealth erythrocytes. Proc Natl Acad Sci U S A 94[14], 7566-7571. 1997 
Scriver, CR, Kaufman. Hyperphenylalaninemia: Phenylalanine Hydroxylase Deficiency. In: Beaudet 
AL, Sly WS, Valle D, editors. Metabolic and Molecular Bases of Inherited Disease. New York: 
McGraw-Hill, 2001: 1667-1724. 
Walter, JH, White, FJ, Hall, SK, MacDonald, A et. al. How practical are recommendations for dietary 
control in phenylketonuria? Lancet 360[9326], 55-57. 2002 
Webster, R, Didier, E, Harris, P, Siegel, N et. al. PEGylated proteins: evaluation of their safety in the 
absence of definitive metabolism studies. Drug Metab Dispos 35[1], 9-16. 2007 
 
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22 
INVESTIGATOR RESPONSIBILITIES 
22.1 
Conduct of Study and Protection of Human Subjects  
In accordance with FDA Form 1572, the Investigator will ensure that: 
• He or she will conduct the study in accordance with the relevant, current protocol and 
will only make changes in a protocol after notifying the sponsor, except when 
necessary to protect the safety, rights, or welfare of subjects. 
• He or she will personally conduct or supervise the study. 
• He or she will inform any potential subjects, or any persons used as controls, that the 
drugs are being used for investigational purposes and he or she will ensure that the 
requirements relating to obtaining informed consent in 21 CFR Part 50 and 
institutional review board (IRB) review and approval in 21 CFR Part 56 are met.  
• He or she will report to the sponsor adverse experiences that occur in the course of 
the investigation in accordance with 21 CFR 312.64. 
• He or she has read and understands the information in the Investigator’s Brochure, 
including potential risks and side effects of the drug. 
• His or her staff and all persons who assist in the conduct of the study are informed 
about their obligations in meeting the above commitments. 
• He or she will ensure that adequate and accurate records in accordance with 
21 CFR 312.62 and to make those records available for inspection in accordance with 
21 CFR 312.68. 
• He or she will ensure that the IRB complies with the requirements of 21 CFR Part 56, 
and other applicable regulations, and conducts initial and ongoing reviews and 
approvals of the study. He or she will also ensure that any change in research activity 
and all problems involving risks to human subjects or others are reported to the IRB. 
Additionally, he or she will not make any changes in the research without IRB 
approval, except where necessary to eliminate apparent immediate hazards to human 
subjects. 
• He or she agrees to comply with all other requirements regarding the obligations of 
clinical Investigators and all other pertinent requirements in 21 CFR Part 312. 
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24 
PROTOCOL AMENDMENT MAJOR TEXT REVISIONS 
Section no./Title 
Text Revisions 
 
Rationale #1: 
Eligibility for receiving open-label drug in current or extension study 
9.1 Overall Study Design 
and Plan 
Subjects who participate in this study will be required to transition into a Phase 3 study (165 302) if weekly doses of rAvPAL PEG are 
between 70 mg/week and 350 mg/week (inclusive) provided that doses of rAvPAL PEG have been stable (ie, no major change in dose for 
at least 4 weeks). Subjects who meet these criteria must be transitioned from PAL 003 to Study 165 302 provided they meet the 165 302 
study eligibility criteria.  
Subjects who are eligible for Study 165 302 but do not transition into 165 302 will be withdrawn from this study. 
The PAL 003 study will continue until BMN 165 is approved by the FDA for marketing in the United States or until the sponsor 
terminates further development of this drug for treatment of PKU. 
 
Rationale #2a-c: 
Revisions to Stopping Criteria, AEs of special interest 
9.1.1.1 Individual Stopping 
Criteria 
9.1.1.1 Individual Stopping Criteria 
9.1.1.2 Dosing in Response 
to Hypersensitivity Adverse 
Events 
Subjects who have an NCI CTCAE grade  ≥ 3 hypersensitivity AE that is related to study drug and is suspected to meet Brown’s criteria 
for severe (grade 3) in the judgment of the investigator and the sponsor’s medical monitor may be permanently discontinued from study 
drug. 
9.1.1.2 Dosing in Response to Hypersensitivity Adverse Events 
Dosing in response to a hypersensitivity AE depends on the NCI-CTCAE grade and suspected relationship to rAvPAL-PEG. Dosing 
instructions are presented in Table 9.1.1.2.1 and are regardless of previous occurrence: 
 
PLEASE SEE TABLE 9.1.1.2.1 AT THE END OF SECTION 24 
9.1.2 Study Stopping Criteria 
If an NCI-CTCAE grade  ≥ 3 hypersensitivity treatment-related event occurs and meets Brown’s criteria for severe (grade 3), an ad hoc 
independent DMC meeting will convene within 7 days of the event to review and advise the sponsor on potential changes to the study 
conduct. Clinically severe hypersensitivity is defined as significant hypoxia, hypotension or neurologic compromise that is life-threatening 
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or required treatment to prevent a life-threatening event:  
• 
• 
Cyanosis or SpO2 ≤ 92%  
• 
Hypotension with SBP < 90 mm Hg (adults)  
Neurologic alteration: loss of consciousness, collapse, incontinence 
PLEASE SEE TABLE 9.1.2.1 AT THE END OF SECTION 24 
Brown’s severity criteria are presented in Table 9.1.2.1. 
9.1.3 Safety Assessment 
Criteria 
9.1.3 Safety Assessment Criteria 
If an individual subject exhibits toxicity of a treatment emergent CTCAE grade 3 or greater or a systemic reaction that is assessed as 
related to treatment with study drug, that subject will have dosing halted until the toxicity resolves. The subject’s data will be evaluated by 
the Principal Investigator (PI) and the Sponsor’s Medical Officer, and a decision will then be made whether to discontinue the subject from 
the study treatment, restart dosing at the same dose level, or restart dosing at a lower dose level. 
9.1.4 Stopping Criteria 
9.1.4 Stopping Criteria 
If 2 or more subjects at a dose level exhibit toxicity of a treatment emergent CTCAE grade 3 or greater or a systemic reaction that is 
assessed as related to treatment with study drug, further dosing of subjects at that dose level will evaluated and a safety assessment will be 
completed. In addition, the Food and Drug Administration (FDA) may be notified of this occurrence if appropriate. 
 
10.2 Serious Adverse 
Events 
 
For this protocol, anaphylaxis per NIAID/FAAN criteria for the clinical diagnosis of anaphylaxis is designated as an AE of special interest 
(serious or nonserious and irrespective of severity) to facilitate rapid reporting and sponsor review. All occurrences of anaphylaxis per 
NIAID/FAAN criteria will be reported to the sponsor within 24 hours of the site becoming aware of the event using the SAE form. Severity 
and serious criteria (if applicable) should be reported on the SAE form. 
Rationale #3: 
Resumption of drug after anaphylaxis 
9.1.1.3 Response to 
Anaphylaxis 
9.1.1.3 Response to Anaphylaxis 
If the investigator suspects that the event is anaphylaxis, the subject will be assessed in the clinic. Laboratory assessments for suspected 
anaphylaxis events should be performed prior to the next administration of study drug (if applicable) and include anti-rAvPAL IgE and 
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anti-rAvPAL-PEG IgE (sampling must be performed >8 hours after event onset and before the next dose of study drug) and tryptase 
(within 24 hours of event onset). The investigator will consult with the sponsor’s medical monitor, and a decision will then be made 
whether to discontinue the subject from study drug, restart dosing at the same dose level, or restart dosing at a lower dose level. 
 
For the first week of dosing after resolution of anaphylaxis, the study drug will be administered in a clinic setting with equipment for 
emergency resuscitation (including epinephrine) within easy access.  The subject must be observed for 30 minutes following administration 
due to restarting dosing. Additionally, the subject should be premedicated with H1 antagonist, H2 antagonist, and NSAIDs approximately 
2-3 hours prior to each dose of study drug for one week upon return to dosing regardless of the duration of dose interruption. NSAIDs 
should be given with food and may be omitted if not tolerated. 
Rationale # 4a, 4b: 
Safety precautions added regarding premedication and epinephrine injectors 
7.4.3 Management of 
Hypersensitivity Reactions 
 
…Because of the small potential for anaphylaxis, equipment for emergency resuscitation (including epinephrine) should be within easy 
access during and after the rAvPAL-PEG injection. Subject should be pre-medicated with H1 antagonist, H2 antagonist, and NSAIDs 
approximately 2-3 hours prior to each dose of study drug for one week upon return to dosing regardless of the duration of dose interruption. 
NSAIDs should be given with food and may be omitted if not tolerated.  Subjects who qualify for self-administration of study drug will be 
provided with emergency resuscitation are trained to recognize a serious hypersensitivity AEs and how to respond. Additionally, subjects 
are given two epinephrine injectors and are instructed to carry one epinephrine injector with them at all times (Section 9.4). Refer to 
Section 9.1.1.3 for instructions (refer to Section 9.4 and the Subject Self Administration Training Materials).regarding resumption of study 
drug following resolution of symptoms consistent with a clinical diagnosis of anaphylaxis per National Institute of Allergy and Infectious 
Disease/Food Allergy and Anaphylaxis Network (NIAID/FAAN) criteria (Sampson, H. A., et al, 2006, J Allergy Clin Immunol).
• 
Administration of additional symptomatic treatment (eg, acetaminiophen or ibuprofen). 
  
… An allergy and/or immunology consultation should be sought if necessary. Information regarding the management of local skin, large 
local skin, and systemic reactions is provided in Section 9.11. Detailed instructions… 
9.1.1 Response to 
Hypersensitivity Adverse 
Events 
9.1.1   Management of Local and Systemic Reactions to rAvPAL PEG 
Subjects who qualify for self administration of study drug will be provided with information and instruction with regard to management of 
local and systemic reactions (refer to the Subject Self Administration Training Materials). 
9.1.1  Response to Hypersensitivity Adverse Events 
Subjects are evaluated for safety throughout the study and are trained to recognize potential hypersensitivity AEs (including anaphylaxis) 
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and how to respond. Subjects are instructed to contact the investigator for any suspected hypersensitivity AE. The investigator may require 
further evaluation at the clinic. If a hypersensitivity AE (eg, injection-site reaction, rash, joint pain, itching) occurs, the subject may be 
advised to premedicate with H1 antagonist, H2 antagonist, and non-steroidal anti-inflammatory medication (NSAIDs) approximately 
2-3 hours prior to subsequent rAvPAL-PEG doses. NSAIDs should be given with food and may be omitted if not tolerated.  
9.1.1.1  Subjects Who Have Had Previous Hypersensitivity Reactions to rAvPAL PEG or a PEG containing Product 
Hypersensitivity AEs, including anaphylaxis, are expected with rAvPAL-PEG administration.  rAvPAL-PEG dosing in response to a 
suspected hypersensitivity AE may be modified or halted depending on the severity of the event and suspected rAvPAL-PEG causality 
(Section 9.1.1.3). Severity for hypersensitivity AEs will be per NCI-CTCAE grades. 
Subjects who had a previous systemic reaction to rAvPAL PEG or a PEG containing product that warranted early termination from a 
previous rAvPAL PEG study are excluded from participation in this study. Subjects who have had a previous local skin reaction to 
rAvPAL PEG in a previous rAvPAL PEG study are eligible to participate in this study. Subjects who have had a previous reaction and are 
deemed eligible for participation must be premedicated orally with acetaminophen and/or non sedating antihistamines 1 2 hours prior to 
study drug dosing for the remainder of the study. The premedication dosage will be standard. Because antihistamines can cause drowsiness, 
it may be administered only if the subject is accompanied by a designated driver (if applicable). Subjects may develop systemic, large local 
skin, or local skin reactions after enrollment in PAL 003. Refer to Section 9.1.1.2 for definitions of systemic and local skin reactions. For 
management of hypersensitivity reactions that occur during this study, refer to Section 9.1.1.3 and 9.1.1.3.1. 
9.1.1.2 Definition of Reaction and Hypersensitivity Reactions to rAvPAL PEG Administered Subcutaneously 
During Study PAL 003, subjects may experience hypersensitivity reactions to rAvPAL PEG. The hypersensitivity reactions are defined as 
follows: 
Local skin reaction: 
• 
Skin signs or symptoms in 1 affected primary location, ie, hives, wheals, or swelling or an area of erythema, redness, induration, 
pain, or itching at or near the site of injection. 
Large local skin reaction: 
• 
Skin signs or symptoms, ie, hives, wheals, or swelling or an area of erythema, redness, or induration with pain or itching that 
extends beyond the site of injection by approximately 6 inches (15 cm) and/or signs or symptoms that are not contiguous to the 
injection site. These may be associated with a low risk of systemic symptoms or anaphylaxis upon re exposure and, therefore, will 
be managed as a systemic reaction when not contiguous to the injection site.  
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Systemic reaction (including generalized skin symptoms): 
• 
Skin and non skin signs or symptoms in more than 1 affected primary location, ie, cutaneous reaction in more than 1 area and/or 
anaphylaxis or any other generalized symptoms, such as hypotension, angioedema or the involvement of other organ systems, eg, 
respiratory, cardiovascular, gastrointestinal, neurological; and/or a fever attributed to treatment with rAvPAL PEG ( ≥ 100.4°F or 
 ≥ 38°C). 
For management of hypersensitivity reactions that occur during this study, refer to Section 9.1.1.3 and Figure 9.1.1.3.1.  
 
 
 
 
9.1.1.3.1 Local Skin Reactions 
All subjects who experience a local skin reaction during this study may be premedicated orally with acetaminophen and/or non sedating 
antihistamines 1 2 hours prior to study drug dosing (subjects may take non sedating premedications prior to coming to clinic) for all future 
study doses. Recommended premedications are acetaminophen and/or non sedating antihistamine. The dosage will be standard. Subjects 
must be accompanied by a designated driver (if applicable) because antihistamines can cause drowsiness. Symptoms of local reactions may 
be treated with local application of ice and non sedating oral and/or topical antihistamines and/or topical steroids (refer to Section 7.4.3). 
If the local skin reaction worsens with a repeat injection (as determined by the Investigator in consultation with the Sponsor’s Medical 
Officer) even with premedication prior to study drug dosing, the subject must be withdrawn from study treatment. 
9.1.1.3.2 Large Local Skin Reactions 
Large local skin reactions (refer to Section 9.1.1.2 for a definition) may or may not be contiguous to the rAvPAL PEG injection site, and 
subjects with either type of large local skin reaction may continue dosing if the skin symptoms have resolved and no other symptoms have 
developed. Subjects will be encouraged to premedicate orally with acetaminophen and/or non sedating antihistamines 1 2 hours prior to 
study drug dosing (subjects may take non sedating premedications prior to coming to clinic) for all future study doses. 
Symptoms of large local skin reactions may be treated with local application of ice and topical, oral, or IV antihistamines and/or steroids as 
needed (refer to Section 7.4.3). 
9.1.1.3.2.1 Large Local Skin Reactions Contiguous to Injection Site 
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Subjects who develop a large local skin reaction contiguous to the injection site after administration of rAvPAL PEG or to rAvPAL PEG 
or a PEG containing product may remain in the study if the skin symptoms have resolved and no other symptoms have developed. For the 
remainder of the study, subjects will be encouraged to premedicate orally with acetaminophen and/or non sedating antihistamines 1 2 
hours prior to study drug dosing (subjects may take non sedating premedications prior to coming to clinic) for all future study doses. 
Because antihistamines can cause drowsiness, it may be administered only if the subject is accompanied by a designated driver (if 
applicable).  
Symptoms of large local skin reactions may be treated with local application of ice and topical, oral, or IV antihistamines and/or steroids as 
needed (refer to Section 7.4.3).  
9.1.1.3.2.2 Large Local Skin Reactions Not Contiguous to Injection Site 
Large local skin reactions that are not contiguous to the injection site may be associated with a low risk of systemic symptoms or 
anaphylaxis upon re exposure to rAvPAL PEG and, therefore, will be managed as a systemic reaction (refer to Section 9.1.1.3.3). An 
example of a large local reaction that is not contiguous to the injection site is if an injection took place in the right upper arm and there are 
lesions beyond the elbow joint in the right forearm or lesions beyond the shoulder joint on the right trunk. 
Symptoms of large local skin reactions may be treated with local application of ice and topical, oral, or IV antihistamines and/or steroids as 
needed (refer to Section 7.4.3). 
9.1.1.3.3 Systemic Reactions 
Subjects who experience a systemic reaction (refer to Section 9.1.1.2 for a definition) after administration of rAvPAL PEG must stop 
further administrations of rAvPAL PEG and must immediately return to the clinic for safety assessments. Subjects who experience 
generalized skin symptoms are included in this category. Immediately after the systemic reaction (within 24 hours), subjects with 
generalized skin symptoms must have additional assessments performed for safety (ie, Unscheduled Hypersensitivity Reaction Visit): 
serum antibodies (anti PAL IgG, anti PAL IgM, anti PEG IgG, anti PEG IgM, anti rAvPAL PEG IgE, anti rAvPAL PEG neutralizing 
antibodies); serum tryptase level (it is recommended that this sample be drawn immediately after reaction); urine albumin/creatinine ratio; 
urine N methyl histamine; CRP, CH50, C1, C3, and C4; skin biopsy (optional; affected and not affected area; to be performed within 1 week 
of reaction); and clinical laboratory tests (urinalysis, chemistry, hematology; refer to Figure 9.1.1.3.1.  
Following the reaction, subjects will be required to complete the assessments of the Unscheduled Hypersensitivity Reaction visit, including 
assessment of IgE. If a subject presents with a clinical diagnosis of anaphylaxis, further dosing will be held while laboratory evaluation of 
IgE, as part of the Unscheduled Systemic Reaction Visit, is performed.  Subjects may resume study drug administration per the discretion 
of the Principal Investigator and the Sponsor’s Medical Officer; however, if subject was dosing at home, they will be required to come into 
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the clinic for at least 1 week.  
rAvPAL PEG administration will resume at the next lowest dose level. Restarting of rAvPAL PEG administration following a systemic 
reaction must be performed in the clinic for the first week of resumed dosing. Subjects will be encouraged to premedicate orally with 
acetaminophen and/or antihistamines 1 2 hours prior to study drug dosing (subjects may take non sedating premedications prior to coming 
to clinic) for all future study doses. Additionally, subjects must be closely monitored for 30 minutes following every administration of 
study drug. Because antihistamines may cause drowsiness, the subject must be accompanied by a designated driver (if applicable).   
If blood Phe concentrations are not 60 600 µmol/L following 1 week of daily administration at the lowered dose cohort and there is no 
further evidence of toxicity (ie, another systemic reaction attributed to rAvPAL PEG administration or clinically significant abnormal 
laboratory test results), the subject may be administered the next highest dose level in the clinic per the allowable dose increases outlined in 
Section 8.1.2. Subjects will be encouraged to premedicate orally with acetaminophen and/or antihistamines 1 2 hours prior to study drug 
dosing (subjects may take non sedating premedications prior to coming to clinic) for all future study doses. Additionally, subjects must be 
closely monitored for 30 minutes following every study drug administration. Because antihistamines may cause drowsiness, the subject 
must be accompanied by a designated driver (if applicable).  
9.4.10 Dose Interruption 
and Missed Doses 
During this long-term extension study, interruption of rAvPAL-PEG dosing may occur per subject decision or per the Investigator. 
Subjects who miss more than 2 consecutive weekly doses (weekly dosing schedule) or 3 consecutive daily doses (daily dosing schedule) 
for whatever reason may continue participation in this study. After a dosing interruption After a dosing interruption of ≥ four consecutive 
doses, rAvPAL-PEG administration should be re-started at the same dose level and dosing frequency that was administered prior to the 
dosing interruption. The first dose of rAvPAL-PEG following a dose interruption should be administered in a clinic setting, and the subject 
must be observed for 30 minutes following administration due to restarting dosing. Premedication with H1 antagonist, H2 antagonist, and 
non-steroidal anti-inflammatory medication (NSAIDs) approximately 2-3 hours prior to study drug should be administered following any 
dose interruption of ≥ four consecutive doses. NSAIDs should be given with food and may be omitted if not tolerated. 
9.1 Overall Study Design 
and Plan 
A follow-up 
telephone call… 
9.4 Treatments 
Subjects are given two epinephrine injectors and are instructed to carry one epinephrine injector with them at all times (refer to 
Section 9.4). 
The subject has been provided with two epinephrine injectors and has been trained on when and how to administer it. 
 
The subject will be 
instructed to carry one epinephrine injector with them at all times. 
Rationale #5: 
Information tracking system for device malfunction 
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10.1 Adverse Events 
 
For this study, a medical device is defined as the prefilled syringe and all of the component parts. The reporting period for device-related 
events begins with the first dose administered using prefilled syringe and ends with the last dose administered using prefilled syringe. 
Events assessed by the investigator as related to the device, including malfunction, injury, or medication error, will be captured into an 
electronic data capture system. All serious events related to the device will be reported to BioMarin Pharmacovigilance (BPV) within 24 
hours using the device-related event report form and entered onto the appropriate eCRF page(s) as required.  
Rationale #6: 
Changes to antibody assessment  samples at Hypersensitivity Reaction Visit 
Table 9.1.1 footnote m 
9.1.1.3 Response to 
Anaphylaxis 
For unscheduled hypersensitivity reaction visit, draw serum anti-rAvPAL IgE and anti-rAvPAL-PEG IgE only; sampling must be 
performed > 8 hours after event onset and before the next dose of study drug. 
… Laboratory assessments for suspected anaphylaxis events should be performed prior to the next administration of study drug (if 
applicable) and include anti-rAvPAL IgE and anti-rAvPAL-PEG IgE (sampling must be performed >8 hours after event onset and before 
the next dose of study drug)
12.3.6 Unscheduled 
Hypersensitivity Visit 
… 
Serum anti-rAvPAL PEG antibodies (anti PAL IgG, anti PAL IgM, anti PEG IgG, anti PEG IgM, anti IgE and anti-rAvPAL-PEG IgE, 
and anti rAvPAL PEG neutralizing antibodies only (performed > 8 hours after event onset
 
) 
Rationale #7: 
Prefilled syringe instructions and training 
9.1 Overall Study Design 
and Plan 
… Additional information is provided in the Subject Self-Administration Training Materials. 
Table 9.1.1 footnote q 
Additional training will be provided and 
demonstration of competency required when prefilled syringe drug product is introduced, every 24 weeks, and more often as needed. 
9.4 Treatments 
Initial training on the use of prefilled syringe occurs at the next monthly visit and each subsequent day after transition until (in clinic or by 
HHRN) it has been determined the subject will switch to prefilled syringe. Once competency is documented, subjects can self-administer 
study drug using the prefilled syringe.  Regular refresher prefilled syringe training occurs in the study clinic every 24 weeks thereafter. 
9.4.2.1 Product 
Characteristics and 
Labeling 
Prefilled syringes are dispensed to subjects only after the subject (or caregiver) has completed training and competency is demonstrated in 
the clinic.  Additional regular refresher training occurs in the clinic, every 24 weeks, and more often as needed.  
Subjects who have undergone training and who have demonstrated competency on the use of prefilled syringe in the study clinic may be 
eligible to transition from vial and syringe to prefilled syringe dosing. Additionally, regular refresher training on use of prefilled syringe 
will be provided in study clinic every 24 weeks, and more often as needed.  
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PLEASE SEE THE DOSE CONVERSION TABLE AT THE END OF SECTION 24 
Subjects should convert their vial and syringe dose to prefilled syringe dose using the following table: 
9.4.2.1 Product 
Characteristics and 
Labeling 
Drug rAvPAL PEG doses will be administered SC by either health care professionals or via self-administration. The dose level may be 
increased or decreased per Investigator determination based on available information regarding a subject’s blood Phe level (60 600 
µmol/L), as well as any adverse events (any hypersensitivity AE) for an individual subject. The dosage that provides control of blood Phe 
concentrations within the target range of 60 -600 µmol/L for a minimum of 2 consecutive measurements will be determined for each 
subject by adjusting the dose level, dose frequency, or both, per the PI, based upon the subject’s response to doses. 
For vial and syringe, drug product packaging will be identified with the lot number and expiration date and will be provided in a box 
labeled with the study number. 
12.3.4 Monthly Visits 
For prefilled syringe, drug product packaging will be identified with the size (2.5 mg, 10 mg, or 20 mg), lot number, and kit identification 
(ID). The expiration date will be available in a separate Certificate of Compliance issued for each lot. 
• 
Prefilled syringe self-administration training (to be performed prior to subjects transitioning from vial and syringe drug product to 
prefilled syringe drug product). 
 
If additional training is needed on days subsequent to the monthly visit, additional clinic visit(s) or HHRN may be used. 
Rationale #8: 
Study duration extended 
Section 9.1 Overall Study 
Design and Plan 
The subject has completed the study through the Month 86 98
 
 visit. 
Rationale #9: 
Change to follow-up visit schedule 
Table 9.1.1 Schedule of 
Events 
12.5 Final Follow-up Visit 
Final F/U Visit:  1 week 4 weeks 
 
after final dose 
Rationale #10: 
Revision to length of observed dosing after dose interruption 
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Section 9.1 Overall Study 
Design and Plan 
Section 9.4.10 Dose 
Interruption and Missed 
Doses 
…The first dose week of dosing
 
 will be administered in the clinic… 
…The first dose week of dosing
 
 of rAvPAL‑ PEG following a dose interruption should be administered in a clinic setting… 
Rationale #11: 
Inspection of injection site procedure deleted 
Table 9.1.1 Schedule of 
Events and footnote 
 
Table: Injection site inspection 
Footnote: Subjects must have AEs and concomitant medications assessed and an injection site inspection performed whenever dose is 
administered even if the administration does not coincide with a scheduled clinic visit.   
12.3 Treatment period 
12.3.4 Monthly visits 
(Week 4, 8, 12, etc) 
12.3.5 Quarterly Visits 
(Week 12, 24, 36, etc) 
Subjects must have AEs and concomitant medications assessed and an injection site inspection performed whenever dose is administered 
even if the administration does not coincide with a scheduled clinic visit.   
12.3.4 Monthly visits 
(Week 4, 8, 12, etc) 
Injection site inspection (previous and current injection site) 
12.3.1 Day 1 (Week 1) 
12.3.6 Unscheduled 
Hypersensitivity Reaction 
Visit 
• 
Injection site inspection (postdose) 
Injection site inspection  
12.4 Early Termination 
Visit 
12.5 Final Follow-up Visit 
Injection site inspection (previous injection site) 
Table 9.1.1 Schedule of 
Table: Injection site inspection 
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Events and footnote 
 
Footnote: Subjects must have AEs and concomitant medications assessed and an injection site inspection performed whenever dose is 
administered even if the administration does not coincide with a scheduled clinic visit.   
 
Rationale #12: 
The criteria for subject eligibility to self-administer study drug has been revised 
9.4 Treatments 
• 
The subject is on a stable dosing regimen for 2 weeks (ie, the subject has demonstrated a blood Phe level within 60 600 µmol/L). 
• 
The subject has not experienced any CTCAE Grade 3 or higher adverse event.  
The subject has not experienced any hypersensitivity reaction to rAvPAL PEG for at least 4 weeks. 
 
Rationale #13: 
Revision and update to the rAvPAL-PEG immunogenicity profile; additional information characterizing specific antibody 
responses detected in subjects 
7.4.2 Immunologic 
Response 
7.4.2  Toxicity Due to an Immunologic Reaction Response 
The active drug substance in rAvPAL-PEG is a bacterial protein, and as such, it is expected that it may elicitelicits immune recognition and 
subsequent antibody responses. Epitopes that play a role inAntibody epitopes on the immune response mayprotein are expected to be rendered at 
least partially inaccessible by PEGthe extensive PEGylation on the drug (Gamez, 2007, Mol.Genet.Metab). In vivo and in vitro experiments have 
shown that PEGylation of proteins and cells can attenuate the immunological response (Scott, 1997, Proc.Natl.Acad.Sci.U.S.A), (Chen, 2001, 
BioDrugs.). PEGylation has been effective in reducing anti-rAvPAL antibody titers in the mouse model, although PEGylationbut does not 
eliminate antibody formation. Although PEGylation of rAvPAL may have a significant effect on reducinglikely reduces the 
immunogenicityantigenicity of the molecule, it is reasonable to expect that some 100% of individuals may exhibit exposed to rAvPAL-PEG 
develop antibodies against rAvPAL. 
Drug-specific immune responses upon exposure can range from clinical irrelevance to the causing serious hypersensitivity AEs (such as 
anaphylaxis) and may reduce efficacy due to antibody-mediated drug. These immune responses may be clinically irrelevant, cause symptoms of 
various degrees, clearance or lead to antibody neutralization of biological enzymatic
As of May 2012, a total of 70 subjects have been administered rAvPAL PEG in the single dose, Phase 1 study (PAL 001) and in the repeat 
dosing Phase 2 studies (PAL 002, PAL 004, and PAL 003). The dose levels in the repeat dosing studies range from 0.001 to 5.0 mg/kg/week 
administered in various frequencies (including 5 days a week). The most clinically significant AEs have been hypersensitivity reactions that have 
led to dosing interruptions and reductions. Most of the hypersensitivity reactions have been nonserious and mild to moderate in severity.  
 activity.  Subjects participating in clinical trials will be 
monitored closely with specific antibody titers sedimentation rates, and complete blood counts (CBCs). 
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A total of 4 SAEs have been reported in the previous rAvPAL PEG studies.  Of these 4 SAEs, 3 have been reported as related to rAvPAL PEG. 
Two of the study drug related SAEs occurred in Study PAL 001. Both of these SAEs occurred in subjects in the lower dose cohorts: an SAE of 
hypersensitivity reaction in a subject in the 0.001 mg/kg cohort and an SAE of anaphylactic reaction (urticaria) in a subject in the 0.01 mg/kg 
cohort. Neither SAE was severe or resulted in discontinuation from the study, and both of the SAEs resolved. There were no SAEs in subjects in 
the higher dose cohorts (0.03 mg/kg and 0.1mg/kg) in PAL 001. The third study drug related SAE (angioedema) occurred in a subject in Study 
PAL 004. The fourth SAE (urticaria, dehydration) was reported as not related to study drug and occurred in a subject in Study PAL 002.  There 
have been no reports of anaphylaxis for any subject treated with rAvPEG PAL (as of January 2012).  
Subjects who have a systemic clinical reaction at any time during this study may undergo a series of assessments to monitor safety, including 
assessment of complements, C reactive protein (CRP), erythrocyte sedimentation rate (ESR), and IgE antibodies.  Reintroduction of rAvPAL PEG 
dosing after a reaction will depend on clinical assessments and available laboratory data, such as chemistry and urine studies, to ensure that there 
has been no end organ damage prior to resuming treatment with rAvPAL PEG. As of May 2012, antibody titers, including positive IgE titers, have 
not been predictive of future clinical reactions when dosing with rAvPAL-PEG.  Additionally, subjects may be premedicated to prevent or 
mitigate risk of hypersensitivity reactions (refer to Section 9.1.1.3.3). 
PEG itself is considered nonimmunogenic Historically, PEG was thought to be nonimmunogenic (Davis, 1981, Clin.Exp.Immunol.), (Harris, 2003, 
Nat.Rev.Drug Discov.); however, repeated studies have found that subcutaneous (SC) and intravenous exposure to PEG can induce anti PEG 
antibodies (Harris, 2003, Nat.Rev.Drug Discov.) however, antibodies against PEG may form when PEG is bound to compounds. (Richter, 1983, 
Int.Arch.Allergy Appl.Immunol.). In some instances, development of such antibodies did not result in significant clinical effects in humans 
(Richter, 1984, Int.Arch.Allergy Appl.Immunol.) .  In some instances, development of such antibodies did not result in any significant clinical 
effects in humans . However, PEG antibody responses were associated with hypersensitivity reactions to PEGylated liposomes (Judge, 2006, 
Mol.Ther.).In some individuals, anti PEG antibodies may be pre existing due to previous exposure to PEG in other products. Anti PEG antibodies 
have also been associated with nonresponsiveness against therapy (Armstrong, 2007, Cancer), (Ganson, 2006, Arthritis Res.Ther.) .  
Administration of rAvPAL PEG may lead to anti PEG antibody formation, and the duration of this possible effect is not known. Subjects in the 
Phase 2 rAvPAL PEG studies have developed both anti PEG IgM and anti PEG IgG antibodies. Antibody formation may limit a subject’s future 
ability to be treated with other PEG containing (eg, Depo Provera) or PEGylated (eg, PEG interferon) injectable drugs. It is therefore 
recommended that any PEG containing injectable drug administered to subjects after completion of this study be done under medical observation. 
Systemic Skin Reactions 
Two out of 25 subjects who were enrolled in Study PAL 001 and received the protocol defined single dose of rAvPAL PEG reported systemic 
skin reactions (generalized skin rash) that were attributed to treatment with study drug. One subject received a single dose of 0.001 mg/kg 
rAvPAL PEG, and the other subject received a single dose of 0.01 mg/kg rAvPAL PEG. One of these events was reported as serious, and the 
other was reported as nonserious; both events were reported following administration of Depo-Provera injections (medroxyprogesterone injection), 
an injectable contraception. These allergic reactions are thought to be related to the PEG molecules that are found in both the study drug, rAvPAL
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PEG, and Depo Provera. These reactions are not likely to be experienced concurrent with other birth control medications. 
The 2 subjects were administered study drug during PAL 001 and then experienced an allergic reaction following an injection of Depo Provera. 
The symptoms of the reactions were hives on the arms and legs and difficulty breathing. The symptoms for both subjects resolved within 1 day 
following treatment with medication, including the antihistamine Benadryl (diphenhydramine). Both subjects were examined by an allergy 
specialist after they completed participation in PAL 001. A skin prick test with Depo Provera was administered as part of this examination. One 
subject had a mild allergic reaction to the test; however, no further reactions or complications were reported following subsequent administration 
of a full dose of Depo Provera. Upon study completion, the subject continued to receive regular doses (every 3 months) of Depo Provera, and no 
further reactions were reported. The second subject also had a positive reaction to Depo Provera following administration of the skin prick test. 
When a subsequent full dose of Depo Provera was administered, 
developed hives, itching, and chills. The subject’s symptoms resolved within 
1 day of taking medication prescribed by an allergist. See Section 7.2.1 for the results from Study PAL 001. 
The active drug substance in rAvPAL PEG is a bacterial protein that may elicit immune responses, such as urticaria, bronchospasm, itching, 
anaphylaxis, and others. The results from nonclinical studies of rAvPAL-PEG conducted in rats and cynomolgus monkeys indicated the formation 
of anti rAvPAL antibody titers that did not correspond with observations of injection site reactions. Quantitation of anti PEG titers were not 
assessed in the chronic repeat dose studies in the rat and monkey. Although results from nonclincal studies of rAvPAL PEG conducted in rats and 
cynomolgus monkeys did not indicate signs of immune mediated toxicities, it is possible that the physio chemical properties of rAvPAL PEG may 
induce immunologic sensitization to the protein rAvPAL and to PEG in humans. It is currently unknown whether administration of 
PEG containing drugs, such as Depo Provera, has a sensitizing effect to PEG in rAvPAL PEG when administered in humans. Because the exact 
basis for these reported events and their duration is not known, the use of PEG containing injectable drugs prior to, during, and after this study is 
prohibited as a precautionary measure (refer to Section 9.3.2 and Section 9.4.8). 
Subjects participating in the Phase 2 clinical studies have been monitored closely for anti-drug immunogenicity (anti-rAvPAL immunoglobulin G 
[IgG], anti-rAvPAL IgM, anti-PEG IgM, anti-PEG IgG, neutralizing antibodies that inhibit PAL enzymatic activity, anti-rAvPAL IgE, and anti-
rAvPAL-PEG IgE), complements, C-reactive protein (CRP), ESR, and complete chemistry. All subjects treated with rAvPAL-PEG in the Phase 2 
clinical trials developed antibodies against the PAL protein. Anti-rAvPAL IgM antibodies were first detected within 2-3 weeks of treatment 
initiation and anti-rAvPAL IgG antibodies were detected within 2-3 months. The anti-rAvPAL IgG response generally peaked by 3-5 months and 
was sustained in all subjects. Neutralizing antibodies (NAb) capable of inhibiting enzymatic activity were detected in a minority of subjects 2-3 
months after treatment initiation. The timing of the NAb response suggests these antibodies may be a component of the anti-rAvPAL IgG 
response. It is expected that the centralized location of the PAL active site, within the tetrameric structure, makes it difficult for antibodies to bind 
and inhibit enzymatic activity. In addition, anti-PAL antibody binding is likely sterically hindered by the extensive PEGylation. The majority of 
treated subjects also developed a transient anti-PEG antibody response. The anti-PEG response was comprised of IgM and IgG isotypes. In 
general, anti-PEG antibodies were no longer detected after 5-6 months of treatment. This type of transient antibody response is typical of T cell-
independent type 2 (TI-2) responses. 
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The majority of immune-mediated AEs experienced in subjects treated with rAvPAL-PEG in the Phase 2 studies are believed to be the result of 
antibody-mediated hypersensitivity. The primary immune mediator is thought to be IgM immune complexes, as evidenced by the timing of onset 
prior to IgG development and the reduced occurrence over time. IgE positive test results have not been associated with hypersensitivity in any of 
the subjects thus far, and the majority of subjects have been safely rechallenged with rAvPAL-PEG following reactions. IgM immune complexes 
are known to be efficient activators of the classical complement pathway and can lead to the accumulation of complement component 
anaphylatoxins (C3a, C4a, C5a) that can induce hypersensitivity symptoms. Although IgG immune complexes can also activate the classical 
complement pathway, they do so with less efficiency than IgM. This is due, in part, to the requirement for multiple Fc regions in close proximity 
to activate the complement cascade, meaning that multiple monomeric IgG Abs are required to bind, whereas only one pentameric IgM Ab is 
needed to bind to activate complement. Also, in the case of rAvPAL-PEG, binding of anti-PAL IgG antibodies is likely compromised due to 
epitope masking by the PEGylation, which may reduce IgG-mediated complement activation in vivo. This complex dynamic between combined 
isotype-specific Ab responses and epitope accessibility is thought to be a major factor dictating the need for an induction and titration dose 
regimen in the treatment of rAvPAL-PEG to be implemented in this study. 
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Table 9.1.1.2.1:  Dosing Instructions in Response to Hypersensitivity Adverse Events 
NCI-
CTCAE 
Gradea 
Related to 
Study Drug 
 
Action with Study Drug 
HRV 
Assessmente 
Maintainb 
Reducec 
Interruptc 
1 
Individual 
Stopping 
Criteria d 
X 
Yes or No 
(X) 
Optional 
 
(X) 
Optional 
2 
Investigator 
discretion 
X 
Yes or No 
(X) 
Optional 
 
(X) 
Optional 
Investigator 
discretion 
3  
X 
No 
(X) 
Optional 
 
(X) 
Optional 
Investigator 
discretion 
3  
X 
Yes  
(X) 
Optional 
 
(X) 
Optional 
Yes 
3 
and is 
suspected to 
meet 
Brown’s 
criteria for 
severe d  
 
Yes  
 
 
X 
Consult with 
sponsor 
medical 
monitor 
Yes 
4 d 
 
Yes or No 
 
 
X 
Consult with 
sponsor 
medical 
monitor 
a 
Yes 
b 
AE, adverse event; CTCAE, Common Terminology Criteria for Adverse Events, version 4.03; HRV, Hypersensitivity Reaction Visit; NCI, National Cancer Institute. 
c 
NCI-CTCAE grade determination is performed by the investigator and may be done either via telephone or clinic visit. 
d 
The investigator will instruct the subject to maintain the rAvPAL-PEG dose at the time of AE onset until improvement to grade 1 or resolution (per investigator assessment in the 
clinic or via telephone). 
e 
The rAvPAL-PEG dose may be reduced or interrupted if necessary per investigator determination.  
If a subject has an NCI-CTCAE grade  ≥ 3 hypersensitivity AE that is related to study drug and is suspected to meet Brown’s criteria for severe (grade 3) in the judgment of the 
investigator and the sponsor’s medical monitor, the subject may be permanently discontinued from study drug.  
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f 
 
If the investigator determines that the NCI-CTCAE grade  ≥ 3 hypersensitivity AE is related to administration with rAvPAL-PEG, the subject will be asked to return to the clinic 
within 24 hours of event onset for evaluation, including laboratory tests (chemistry, hematology, urinalysis, anti-rAvPAL IgE, anti-rAvPAL-PEG IgE [sampling must be performed 
>8 hours after event onset and before the next dose of study drug], urine albumin/creatinine ratio, urinary N-methyl histamine, CRP, C3, C4, and tryptase). 
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Table 9.1.2.1:  Brown’s Severity Criteria 
Brown’s Criteria for 
Hypersensitivity Reactions 
Definition 
Mild (1) 
skin and subcutaneous tissue 
Generalized erythema, urticaria, periorbital edema, or angioedema 
Moderate (2) 
features suggested 
respiratory, cardiovascular, 
or gastrointestinal 
involvement 
 
Dyspnea, stridor, wheeze, nausea, vomiting, dizziness (pre-syncope), 
diaphoresis, chest or throat tightness, or abdominal pain  
Severe (3) 
hypoxia or neurologic 
compromise 
 
Cyanosis or SpO2 ≤ 92% at any stage, hypotension (SBP < 90 mm Hg 
in adults), confusion, collapse, loss of consciousness, or incontinence  
 
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Vial and syringe dose to prefilled syringe dose conversion table: 
Daily Dose 
(mg)  
Range 
Daily Dose 
(mg)  
Round Toa 
# of 2.5mg 
Prefilled 
Syringe Needed 
# of 10mg 
Prefilled 
Syringe Needed 
# of 20mg 
Prefilled 
Syringe Needed 
0 – 3.7 
1 
2.5 
0 
0 
5 
3.8 – 6.2 
2 
-- 
-- 
6.3 – 8.7 
3 
7.5 
-- 
-- 
8.8 – 11.2 
10 
1 
-- 
-- 
11.3 – 13.7 
1 
12.5 
1 
-- 
13.8 – 16.2 
2 
15 
1 
-- 
16.3 – 18.7 
3 
17.5 
1 
-- 
18.8 – 21.2 
20 
-- 
1 
-- 
21.3 – 23.7 
1 
22.5 
1 
-- 
23.8 – 26.2 
2 
25 
1 
-- 
26.3 – 28.7 
3 
27.5 
1 
-- 
28.8 – 31.2 
30 
1 
-- 
1 
31.3 – 33.7 
1 
32.5 
1 
1 
33.8 – 36.2 
2 
35 
1 
1 
36.3 – 38.7 
3 
37.5 
1 
1 
38.8 – 41.2 
40 
-- 
2 
-- 
41.3 – 44.9 
1 
42.5 
2 
-- 
45 – 54.9 
50 
1 
-- 
2 
55 – 64.9 
60 
-- 
3 
-- 
65 – 74.9 
70 
1 
-- 
3 
75 – 84.9 
80 
-- 
4 
-- 
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Daily Dose 
(mg)  
Range 
Daily Dose 
(mg)  
Round Toa 
# of 2.5mg 
Prefilled 
Syringe Needed 
# of 10mg 
Prefilled 
Syringe Needed 
# of 20mg 
Prefilled 
Syringe Needed 
85 – 94.9 
90 
1 
-- 
4 
95 – 104.9 
100 
-- 
5 
-- 
105 – 114.9 
110 
1 
-- 
5 
115 – 124.9 
120 
-- 
6 
-- 
125 – 134.9 
130 
1 
-- 
6 
135 – 144.9 
140 
-- 
7 
-- 
145 – 154.9 
150 
1 
-- 
7 
 
a For  < 45 mg/day, round to nearest 2.5 mg; for  ≥ 45 mg/day, round to nearest 10 mg. 
 
 
 
 
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Amendment 7: 16 December 2015 
CLINICAL STUDY PROTOCOL AMENDMENT SUMMARY 
Amendment:  3 
Date: 16 December 2015 
 
RATIONALE AND SUMMARY OF CHANGES  
This section provides a numbered list of all significant changes and supporting rationale.  
1. Collection of skin reaction data is being added to aid in assessment of skin reaction 
adverse events (AEs). The Skin Reaction electronic Case Report Form (eCRF) should 
be completed for skin reactions that last 14 days or longer. Photographs of the skin 
reactions may also be collected. 
2. Additional information about subjects who are trying to conceive, are pregnant, 
and/or breastfeed during the study has been added. Subjects must stop study drug 
administration if trying to conceive, are pregnant, and/or are breastfeeding. Because 
of the long-term nature of this study, subjects may re-start study drug following birth 
and cessation of breastfeeding (if applicable) per the investigator and the sponsor. 
Information regarding contraception use has also been added. 
3. The inclusion criterion regarding contraception use for subjects who are sexually 
active has been revised. Subjects must now use two acceptable methods of 
contraception while participating in the study to align with the contraception 
requirements in the Phase 3 studies. 
4. The study duration has been extended from 98 months to 102 months. 
5. The AE reporting period has been clarified; nonserious AEs and serious AEs (SAEs) 
should continue to be reported through 4 weeks after the last dose of study drug or the 
Study Completion Visit/Early Termination Visit, whichever occurs last. 
6. Minor changes have been made to improve clarity and consistency. 
 
In addition, the Schedule of Events and Section 12 have been updated to reflect the changes 
in this amendment. Refer to Section 24 for a summary of the amendment revisions. 
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Amendment 7: 16 December 2015 
2 
SYNOPSIS 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
TITLE OF STUDY: 
Long-term Extension of a Phase 2, Open-Label Dose-Finding Study to Evaluate the Safety, Efficacy, 
and Tolerability of Multiple Subcutaneous Doses of rAvPAL-PEG in Subjects with PKU 
PROTOCOL NUMBER:  PAL-003 
STUDY SITES:  Approximately 20 centers in the United States 
PHASE OF DEVELOPMENT:  Phase 2 
STUDY RATIONALE: 
The need exists for a treatment that will help individuals with phenylketonuria (PKU) safely achieve 
lifelong, reliable control of blood phenylalanine (Phe) concentrations and improve functional 
outcomes. PEGylated recombinant Anabaena variabilis phenylalanine ammonia lyase (rAvPAL-PEG) 
is a potential substitute for the phenylalanine hydroxylase (PAH) enzyme, which is defective in 
individuals with PKU. rAvPAL-PEG may control blood Phe concentrations, which may have 
additional clinical benefits. This study is an extension of the rAvPAL-PEG Phase 2 studies PAL-002, 
PAL-004, and 165-205. Administration of rAvPAL-PEG will be continued to assess the long-term 
safety and efficacy of rAvPAL-PEG in PKU subjects. 
Blood Phe levels depend not only on the functional presence of the endogenous enzyme PAH but also 
on the dietary intake of Phe. It is important to understand the role of diet on blood Phe levels 
concurrent with the administration of rAvPAL-PEG treatment. Therefore, an exploratory objective has 
been added to this study to assess the relationship of diet, rAvPAL-PEG administration, and blood Phe 
level. Changes to subject diet are not allowed in this study unless per the Investigator. Diet will be 
monitored using a diet diary. 
A pharmacokinetic (PK) substudy has been added to evaluate the steady-state PK of rAvPAL-PEG in 
up to 6 subjects who have achieved and maintained target blood Phe for at least 2 consecutive 
measurements and for whom no further dose modifications are planned. Single-dose PK data has been 
collected in the Phase 1 study, PAL-001. However, there is little multiple-dose PK data or data for 
when subjects have reached and maintained a stable dosing regimen.  With the PK substudy, 
multiple-dose PK data were collected for subjects who have already achieved Phe reduction to within 
the protocol-defined target range.  This substudy has been completed as of 20 December 2013. 
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Amendment 7: 16 December 2015 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
OBJECTIVES: 
The primary objective of the study is: 
• 
To evaluate the effect of long-term administration of multiple doses of SC injections of 
rAvPAL-PEG on blood Phe concentrations in subjects with PKU. 
The secondary objectives of the study are: 
• 
To evaluate the safety and tolerability of long-term administration of subcutaneous (SC) 
injections of rAvPAL-PEG in subjects with PKU. 
• 
To evaluate the immune response to long-term administration of SC injections of 
rAvPAL-PEG in subjects with PKU. 
The exploratory objective of the study is as follows: 
• 
To evaluate the long-term relationship of diet and change in blood Phe concentration 
following administration with rAvPAL-PEG in subjects with PKU. 
The Substudy objectives are as follows: 
• 
To evaluate steady-state PK of rAvPAL-PEG in subjects who have achieved and maintained 
target blood Phe concentration and for whom no further dose modifications are planned. 
STUDY DESIGN AND PLAN: 
This is a long-term extension of rAvPAL-PEG Phase 2 studies in up to 100 subjects with PKU. The 
doses are planned to be in the same range as those previously tested in the Phase 2 studies (starting at 
0.001 through 5.0 mg/kg/week or 2.5 mg through 375 mg/week), provided no dose-limiting toxicity is 
observed in a previous rAvPAL-PEG study. Subjects’ doses will not exceed 375 mg/week. 
Only subjects who completed a previous rAvPAL-PEG study will be enrolled into this study. Subjects 
enrolling into PAL-003 with no interruption in dosing from a previous rAvPAL-PEG study may either 
continue their previous dosing regimen or begin this study at a higher dose level. Subjects who have 
had dosing interruptions between the previous rAvPAL-PEG study and PAL-003 must have their 
starting dose determined per the sponsor’s medical monitor. The first dose will be administered in the 
clinic, and the subject must be observed for 30 minutes following administration. Additionally, 
subjects will be given two epinephrine injectors and will be instructed to carry one epinephrine 
injector with them at all times. A follow-up telephone call will be made to the subject to monitor 
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Amendment 7: 16 December 2015 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
subject safety 24 hours following the return to dosing.  
Diet should not be altered during the course of this study.  Any decision to modify subject diet must be 
made per the Investigator and must be performed under the supervision of the Investigator. To monitor 
for changes in subject diet, a diet diary will be issued to subjects for completion and will be reviewed 
with the clinical study staff on a monthly basis.  
Subjects may self-administer study drug at home if approved by the Investigator and the sponsor’s 
medical monitor and if adequate training is demonstrated. Subjects must meet a set of criteria to be 
considered appropriate for self-administration.  Additional training will be provided to subjects and 
demonstration of competency required when prefilled syringe drug product is introduced, every 
24 weeks, and more often as needed. 
Subjects will be evaluated for safety throughout the study. Toxicity will be measured according to the 
National Cancer Institute (NCI) Common Terminology Criteria for Adverse Events (CTCAE), 
version 4. 
In addition to the Sponsor, a Data Monitoring Committee (DMC) will monitor the safety of subjects in 
the study. The DMC is an independent committee that will act in an advisory capacity to the Sponsor. 
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take 
rAvPAL-PEG. Subjects’ previous rAvPAL-PEG dosing will generally continue in PAL-003. In 
PAL-003, each subject’s dose will be adjusted as needed to attempt to attain or maintain blood Phe 
concentrations of 60-600 µmol/L. rAvPAL-PEG dose will be based on either a subject’s weight or will 
be a fixed dose. Doses will be evaluated on an individual basis. 
Evaluations, observations, and procedures will be conducted at selected time points. After the subject’s 
blood Phe concentration has been controlled to within a target range (60-600 µmol/L), the subject may 
be asked to have additional blood draws for PK and blood Phe concentration analyses as needed per 
the discretion of the Investigator in consultation with the sponsor’s medical monitor. 
A subject will continue in PAL-003 until one of the following occurs: 
• 
The subject withdraws consent and discontinues from the study. 
• 
The subject is discontinued from the study at the discretion of the Investigator or Sponsor. 
• 
 The subject has completed the study through the Month 98 visit. 
• 
 The study is terminated. 
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Amendment 7: 16 December 2015 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
• 
The study drug receives marketing authorization. 
Because the risks of taking rAvPAL-PEG during pregnancy and breastfeeding are unknown, subjects 
cannot take rAvPAL-PEG if they are trying to conceive, are pregnant, or are breastfeeding. Male 
subjects who are planning to impregnate a female partner and female subjects who are trying to 
become pregnant during the study will be discontinued immediately from study drug. Male subjects 
who have impregnated a female partner may re-start study drug after conception but must return to the 
study-required contraception use, which must include one barrier method. Subjects who remain in the 
study after discontinuation of study drug due to pregnancy may re-introduce rAvPAL-PEG dosing 
after the birth has been reported (or termination of the pregnancy) and breastfeeding has completed (if 
applicable) or after the subject is no longer actively trying to conceive. Re-starting rAvPAL-PEG 
dosing must be per investigator and sponsor agreement based on an assessment of the known risks and 
potential benefits while taking BMN 165. Female subjects must return to the study-required 
contraception use, which must include one barrier method, immediately after the birth (or termination 
of the pregnancy). 
Subjects may withdraw from treatment with study drug at any time; however, subjects will be asked to 
continue to perform the study assessments until study completion. Subjects may also withdraw from 
study participation at any time. Because the completeness of the data affects the integrity, accuracy, 
and interpretation of study results, every effort should be made to retain subjects in the study and to 
have them complete the study assessments as scheduled as long as continued participation does not 
compromise subject safety. 
PAL -003 Substudy 
A PK substudy has been added to evaluate the steady-state PK of rAvPAL-PEG in up to 6 subjects 
who have achieved and maintained target blood Phe for at least 2 consecutive measurements and for 
whom no further dose modifications are planned.  Subjects enrolled into the substudy will have 
additional pre-dose PK sampling performed.  This substudy has been completed as of 
20 December 2013. 
Dose Modifications: 
Dose Increase Methodology: 
Each subject’s dose may be modified based on the decision of the Investigator. Decisions regarding 
dose increases will depend on a subject’s adverse event profile and blood Phe and drug concentrations.  
An individual subject’s dose may be adjusted beginning on Day 1 of PAL-003. For the duration of this 
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PAL-003 A7 
Page 7 
 
Proprietary and Confidential  
Amendment 7: 16 December 2015 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
study, an individual subject’s dose may be adjusted if warranted per a subject’s adverse event profile 
and blood Phe concentrations. Dose increases should be performed as follows. 
• 
The dose may be increased by increments of no more than 10-fold higher than the subject’s 
current dose. 
• 
When increasing the dose, a dose may be used that is between the dose levels (0.001, 0.003, 
0.01, 0.03, 0.06, 0.1, 0.2, 0.3, 0.4, 0.6, 0.8, 1.0, 2.0, 3.0, 4,0, and 5.0 mg/kg or 2.5, 5, 10, 20, 
40, 75, 150, 225, 300, 375 mg/week) or per Investigator determination based on available 
information regarding a subject’s blood Phe (60-600 µmol/L) as well as any adverse events 
(any hypersensitivity reaction) for an individual subject. Dose increases  > 350 mg/week 
require consultation with the sponsor’s medical monitor. 
• 
The dose may be adjusted by increasing the frequency up to daily for a total weekly dose not 
to exceed 5.0 mg/kg or 375 mg/week.  Dose increases  > 350 mg/week require consultation 
with the sponsor’s medical monitor. 
• 
When a dose is increased, the subject must be observed for 30 minutes following the first 
modified dose administration. Subjects who increase their dose frequency do not need to be 
observed following injection of study drug if the increase in frequency does not increase the 
overall weekly dose amount. 
• 
Only 1 dose adjustment is allowed every 2 weeks. 
Dose Decrease Methodology 
Decisions regarding dose decreases will depend on available information regarding a subject’s blood 
Phe (60-600 µmol/L), as well as any adverse events (any hypersensitivity reaction). Dose decreases 
may occur for hypophenylalanemia or any adverse event that may be improved with a lower dose.  
A dose should first be reduced by dose level (5.0, 4.0, 3.0, 2.0, 1.0, 0.8, 0.6, 0.4, 0.3, 0.2, 0.1, 0.06, 
0.03, 0.01, 0.003, 0.001 mg/kg or 375, 300, 225, 150, 75, 40, 20, 10, 5, and 2.5 mg/week). It is also 
permitted to decrease dose in between these specified dose levels. If further dosing adjustments are 
required in response to safety, dosing frequency may also be adjusted. 
If the subject develops low blood Phe (as defined by a blood Phe level ≤ 30 µmol/L), the subject’s 
rAvPAL-PEG dose should be decreased to the next lower dose. If the condition persists after another 
1 month at the lower dose, the dose should be decreased again to the next lower level. If the subject 
continues to experience low blood Phe after two dose level reductions, the subject may be asked to 
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Proprietary and Confidential  
Amendment 7: 16 December 2015 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
consult the dietician to eliminate medical foods and/or formulas and to ensure a balanced and 
nutritious diet (as part of the routine standard of care for PKU disease management, subject diet should 
be monitored by a dietician). 
Safety Assessment Criteria: 
Response to Hypersensitivity Adverse Events  
Subjects are evaluated for safety throughout the study and are trained to recognize potential 
hypersensitivity AEs (including anaphylaxis) and how to respond. Subjects are instructed to contact 
the investigator for any suspected hypersensitivity AE. The investigator may require further evaluation 
at the clinic. If a hypersensitivity AE (eg, injection-site reaction, rash, joint pain, itching) occurs, the 
subject may be advised to premedicate with H1 antagonist, H2 antagonist, and non-steroidal 
anti-inflammatory medication (NSAIDs) approximately 2-3 hours prior to  subsequent rAvPAL-PEG 
doses. NSAIDs should be given with food and may be omitted if not tolerated.  
Hypersensitivity AEs, including anaphylaxis, are expected with rAvPAL-PEG administration. 
rAvPAL-PEG dosing in response to a suspected hypersensitivity AE may be modified or halted 
depending on the severity of the event and suspected rAvPAL-PEG causality. Severity for 
hypersensitivity AEs will be per NCI-CTCAE grades. 
Individual Stopping Criteria 
Subjects who have an NCI CTCAE grade  ≥ 3 hypersensitivity AE that is related to study drug and is 
suspected to meet Brown’s criteria for severe (grade 3) in the judgment of the investigator and the 
sponsor’s medical monitor may be permanently discontinued from study drug.  
Dosing in Response to Hypersensitivity Adverse Events 
Dosing in response to a hypersensitivity AE depends on the NCI-CTCAE grade and suspected 
relationship to rAvPAL-PEG.  
Once an AE (other than anaphylaxis) improves to grade 1 or resolves, study drug dose may be 
increased, maintained, or reduced. If dosing has been interrupted due to an AE (other than 
anaphylaxis) and the investigator determines it is safe for the subject to resume dosing, the first dose 
after improvement of the AE should be performed in the clinic. The subject must be observed for 
30 minutes following administration due to restarting dosing. The subject may be advised to 
premedicate with H1 antagonist, H2 antagonist, and NSAIDs approximately 2-3 hours prior to 
subsequent rAvPAL-PEG doses. NSAIDs should be given with food and may be omitted if not 
tolerated. 
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Proprietary and Confidential  
Amendment 7: 16 December 2015 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
Response to Anaphylaxis  
If the investigator suspects that the event is anaphylaxis, the subject will be assessed in the clinic. 
Laboratory assessments for suspected anaphylaxis events should be performed prior to the next 
administration of study drug (if applicable) and include anti-rAvPAL IgE and anti-rAvPAL-PEG IgE 
(sampling must be performed >8 hours after event onset and before the next dose of study drug) and 
tryptase (within 24 hours of event onset). The investigator will consult with the sponsor’s medical 
monitor, and a decision will then be made whether to discontinue the subject from study drug, restart 
dosing at the same dose level, or restart dosing at a lower dose level. 
For the first week of dosing after resolution of anaphylaxis, the study drug will be administered in a 
clinic setting with equipment for emergency resuscitation (including epinephrine) within easy access.  
The subject must be observed for 30 minutes following administration due to restarting dosing. 
Additionally, the subject should be premedicated with H1 antagonist, H2 antagonist, and NSAIDs 
approximately 2-3 hours prior to each dose of study drug for one week upon return to dosing 
regardless of the duration of dose interruption. NSAIDs should be given with food and may be omitted 
if not tolerated.  
Stopping Criteria: 
If an NCI-CTCAE grade  ≥ 3 hypersensitivity treatment-related event occurs and meets Brown’s 
criteria for severe (grade 3), an ad hoc independent DMC meeting will convene within 7 days of the 
event to review and advise the sponsor on potential changes to the study conduct. Clinically severe 
hypersensitivity is defined as significant hypoxia, hypotension or neurologic compromise that is 
life-threatening or required treatment to prevent a life-threatening event:  
• 
Cyanosis or SpO2 ≤ 92%  
• 
Hypotension with SBP < 90 mm Hg (adults)  
• 
Neurologic alteration: loss of consciousness, collapse, incontinence 
NUMBER OF SUBJECTS PLANNED: 
Up to 100 subjects. 
DIAGNOSIS AND ALL CRITERIA FOR INCLUSION AND EXCLUSION:  
Individuals eligible to participate in this study must meet all of the following criteria: 
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Proprietary and Confidential  
Amendment 7: 16 December 2015 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
• 
Must have completed participation in a previous rAvPAL-PEG study. 
• 
Willing and able to provide written, signed informed consent, or, in the case of participants 
under the age of 18, provide written assent (if required) and written informed consent by a 
parent or legal guardian, after the nature of the study has been explained, and prior to any 
research-related procedures. 
• 
Willing and able to comply with all study procedures.  
• 
Females of childbearing potential must have a negative pregnancy test at Screening and be 
willing to have additional pregnancy tests during the study. Females considered not of 
childbearing potential include those who have been in menopause at least 2 years, or had tubal 
ligation at least 1 year prior to Screening, or who have had total hysterectomy. 
• 
Sexually active subjects must be willing to use two acceptable methods of contraception while 
participating in the study.  Males post vasectomy for 2 years with no known pregnancies do 
not need to use any other forms of contraception during the study. 
• 
Maintained a stable diet. 
• 
In generally good health as evidenced by physical examination, clinical laboratory evaluations 
(hematology, chemistry, and urinalysis), and electrocardiogram (ECG) at Screening. 
Individuals who meet any of the following exclusion criteria will not be eligible to participate in the 
study: 
• 
Use of any investigational product (with the exception of rAvPAL-PEG) or investigational 
medical device within 30 days prior to Screening, or requirement for any investigational agent 
prior to completion of all scheduled study assessments. 
• 
Use of any medication other than rAvPAL-PEG that is intended to treat PKU within 14 days 
prior to the administration of study drug. 
• 
Use or planned use of any injectable drugs containing PEG (other than rAvPAL-PEG), 
including Depo-Provera, within 6 months prior to Screening and during study participation.  
• 
A prior reaction that included systemic symptoms (eg, generalized hives, respiratory or 
gastrointestinal problems, hypotension, angioedema, anaphylaxis) to rAvPAL-PEG or a 
PEG-containing product. Subjects with a prior systemic reaction may be eligible for 
participation per the discretion of the Principal Investigator in consultation with the sponsor’s 
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Proprietary and Confidential  
Amendment 7: 16 December 2015 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
medical monitor. However, subjects who discontinued from study drug early due to a reaction 
are not eligible to enroll into this study.    
• 
Pregnant or breastfeeding at Screening or planning to become pregnant (self or partner) or to 
breastfeed at any time during the study.  
• 
Concurrent disease or condition that would interfere with study participation or safety 
(eg, history or presence of clinically significant cardiovascular, pulmonary, hepatic, renal, 
hematologic, gastrointestinal, endocrine, immunologic, dermatologic, neurological, oncologic, 
or psychiatric disease). 
• 
Any condition that, in the view of the PI, places the subject at high risk of poor treatment 
compliance or of not completing the study. 
• 
Known hypersensitivity to rAvPAL-PEG necessitating early termination from a previous 
rAvPAL-PEG study or known hypersensitivity to any of its excipients. 
• 
Alanine aminotransferase (ALT) concentration > 2 times the upper limit of normal. 
• 
Creatinine  > 1.5 times the upper limit of normal. 
INVESTIGATIONAL PRODUCT, DOSE, ROUTE AND REGIMEN: 
The investigational product is rAvPAL-PEG (recombinant Anabaena variabilis phenylalanine 
ammonia lyase-PEG). rAvPAL-PEG will be provided in vials or prefilled syringes; subjects will be 
supplied with vials and syringes or prefilled syringes for administration in the clinic and self-
administration: 
• 
rAvPAL-PEG will be provided in 3 mL (milliliter) vials, each containing 1.5 ± 0.2 mL to 
deliver 15 mg of rAvPAL-PEG per 1.0 mL (15 mg/mL protein concentration). Each vial is 
filled with 1.5 ± 0.2 mL to allow the withdrawal and delivery of up to 1.0 mL of the drug 
product. 
Or: 
• 
rAvPAL-PEG will be provided in 3-mL vials, each containing 1.8 ±0.3 mL to deliver 20 mg of 
rAvPAL-PEG per 1.3 mL (15 mg/mL protein concentration). Each vial is filled with 
1.8 ± 0.3 mL to allow withdrawal and delivery of up to 1.3 mL. 
Or: 
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Proprietary and Confidential  
Amendment 7: 16 December 2015 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
• 
rAvPAL-PEG will be provided in prefilled syringes in three sizes that deliver up to 1 mL. 
Syringe sizes are 2.5 mg (5 mg/mL protein concentration), 10 mg (20 mg/mL protein 
concentration), and 20 mg (20 mg/mL protein concentration).  
Subjects who have undergone training and who have demonstrated competency on the use of prefilled 
syringe in the study clinic may be eligible to transition from vial and syringe to prefilled syringe 
dosing. Additionally, regular refresher training on use of prefilled syringe will be provided in study 
clinic every 24 weeks, and more often as needed.  
The excipients in this drug product are tromethamine, tromethamine-hydrochloride, sodium chloride, 
L-phenylalanine, and water for injection. 
rAvPAL-PEG doses will be administered SC by either health care professionals or via 
self-administration. The dose level may be increased or decreased per Investigator determination based 
on available information regarding a subject’s blood Phe level (60-600 µmol/L), as well as any adverse 
events (any hypersensitivity reaction) for an individual subject. The dosage that provides control of 
blood Phe concentrations within the target range of 60-600 µmol/L for a minimum of 2 consecutive 
measurements will be determined for each subject by adjusting the dose level, dose frequency, or both, 
per the PI, based upon the subject’s response to doses. 
Fixed Dosing 
Subjects who have demonstrated efficacy (ie, blood Phe within the target range of 60-600 µmol/L for 
at least 2 consecutive measurements) and who have maintained a stable rAvPAL-PEG dose for at least 
2 consecutive measurements may be eligible to transition from weight-based dosing to a fixed dosing 
regimen that would permit daily dosing (5- or 7-days-per-week).  
DURATION OF TREATMENT: 
Up to 102 months. 
REFERENCE THERAPY(IES), DOSE, ROUTE AND REGIMEN:  
None 
CRITERIA FOR EVALUATION: 
Efficacy: 
Blood Phe concentrations will be measured.  
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PAL-003 A7 
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Proprietary and Confidential  
Amendment 7: 16 December 2015 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
Immunogenicity: 
The presence of antibodies (anti-PAL immunoglobulin G [IgG], anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibodies, anti-rAvPAL IgE, and anti-PEG-PAL IgE) 
will be assessed. 
Safety: 
Safety will be evaluated on the incidence of adverse events (AEs) and clinically significant changes in 
vital signs, ECG results, X-ray results, and laboratory test results. 
Pharmacokinetic: 
Plasma concentrations of rAvPAL-PEG will be measured for subjects participating in the Substudy. 
STATISTICAL METHODS:  
Sample Size: 
Subjects who participated in a previous rAvPAL-PEG study may be enrolled into this study. 
No formal sample size calculation was conducted for this study or the PAL-003 Substudy. 
Safety Analysis: 
All subjects who receive any amount of study drug in this study and have postdose safety information 
will be included in the safety analyses. 
The Medical Dictionary for Regulatory Activities terminology (MedDRA) will be used by the 
sponsor to assign system organ class and preferred term classification to events and diseases based 
on the original terms entered on the Case Report Form (CRF). The incidence of AEs will be 
summarized by system organ class, preferred term, relationship to study drug, and severity. A 
by-subject listing will be provided for those subjects who experience a serious AE (SAE), including 
death, or experience an AE associated with early withdrawal from the study or study drug. 
Hypersensitivity AEs and AEs that result in dosing interruption or dose level reduction are of interest, 
and the percentage of subjects who report these AEs will be presented.  
Clinical laboratory data will be summarized by the type of laboratory test. Frequency and percentage 
of subjects who experience abnormal (ie, outside of reference range) and/or clinically significant 
abnormalities after study drug administration will be presented for each clinical laboratory test. For 
each clinical laboratory test, descriptive statistics will be provided for baseline and all subsequent 
post-treatment visits. Changes from baseline to the post-treatment visits will also be provided. 
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PAL-003 A7 
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Proprietary and Confidential  
Amendment 7: 16 December 2015 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
Descriptive statistics for vital signs, physical examination results, ECG results, X-ray results, and 
immunogenicity test results will also be provided. Additionally, antibodies and titers will be 
summarized by scheduled time point. 
Efficacy Analysis: 
Data from all subjects who receive any amount of study drug and who have any post-treatment 
efficacy data will be included in the efficacy analysis. 
Blood Phe concentration at each scheduled time point will be summarized using descriptive statistics 
(mean, standard deviation, median, minimum, and maximum). Change in blood Phe concentration 
from baseline (to be defined in the Statistical Analysis Plan [SAP]) to each scheduled time point and 
presence/absence of antibodies will also be summarized. In addition, the proportion of subjects who 
have maintained target Phe concentrations of 60-600 µmol/L will be summarized by each scheduled 
time point. 
Exploratory Analysis: 
Details regarding exploratory analyses will be provided in the SAP.  
Substudy Analysis: 
For subjects who completed the Substudy, the steady-state PK of rAvPAL-PEG in subjects who have 
achieved and maintained target blood Phe will be explored. 
Pharmacokinetic Analysis: 
Subjects who complete the Substudy will have the following PK parameters assessed: area under the 
plasma concentration-time curve (AUC), time to maximum plasma concentration (Tmax), maximum 
plasma concentration (Cmax), half life (t1/2), and clearance (CL/F).  
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3 
TABLE OF CONTENTS 
1 TITLE PAGE .......................................................................................................................1 
2 SYNOPSIS ...........................................................................................................................3 
3 TABLE OF CONTENTS ...................................................................................................15 
4 LIST OF ABBREVIATIONS AND DEFINITIONS OF TERMS ....................................19 
5 ETHICS..............................................................................................................................23 
5.1 Institutional Review Board or Ethics Committee .....................................................23 
5.2 Ethical Conduct of Study ..........................................................................................23 
5.3 Subject Information and Informed Consent ..............................................................24 
6 INVESTIGATORS AND STUDY ADMINISTRATIVE STRUCTURE ........................25 
7 INTRODUCTION .............................................................................................................26 
7.1 Nonclinical Studies ...................................................................................................26 
7.2 Previous Clinical Studies ..........................................................................................27 
7.2.1 
Phase 1 Study, PAL-001 .............................................................................28 
7.2.2 
Phase 2 Studies PAL-002, PAL-004, and 165-205 .....................................28 
7.3 Study Rationale .........................................................................................................32 
7.4 Summary of Overall Risks and Benefits ...................................................................33 
7.4.1 
Toxicity Due to Exposure to Polyethylene Glycol (PEG) ..........................33 
7.4.2 
Immunologic Response ...............................................................................34 
7.4.3 
Management of Hypersensitivity Reactions ................................................35 
8 STUDY OBJECTIVES ......................................................................................................37 
9 INVESTIGATIONAL PLAN ............................................................................................38 
9.1 Overall Study Design and Plan .................................................................................38 
9.1.1 
Response to Hypersensitivity Adverse Events ............................................45 
9.1.2 
Study Stopping Criteria ...............................................................................47 
9.1.3 
Dose Modifications .....................................................................................48 
9.2 Discussion of Study Design, Including Choice of Control Group ............................49 
9.3 Selection of Study Population ...................................................................................49 
9.3.1 
Inclusion Criteria .........................................................................................49 
9.3.2 
Exclusion Criteria ........................................................................................50 
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9.3.3 
Removal of Subjects from Treatment or Assessment .................................51 
9.3.4 
Subject Identification and Replacement of Subjects ...................................52 
9.4 Treatments .................................................................................................................52 
9.4.1 
Treatments Administered ............................................................................54 
9.4.2 
Identity of Investigational Product (IP) .......................................................54 
9.4.3 
Storage .........................................................................................................57 
9.4.4 
Directions for Administration .....................................................................57 
9.4.5 
Method of Assigning Subjects to Treatment Groups ..................................59 
9.4.6 
Selection of Doses Used in the Study .........................................................59 
9.4.7 
Blinding .......................................................................................................59 
9.4.8 
Prior and Concomitant Medications ............................................................59 
9.4.9 
Treatment Compliance ................................................................................60 
9.4.10 Dose Interruption and Missed Doses ...........................................................60 
9.5 Investigational Product Accountability .....................................................................61 
9.5.1 
Return and Disposition of Clinical Supplies ...............................................61 
9.6 Dietary or Other Protocol Restrictions......................................................................61 
9.7 Efficacy and Safety Variables ...................................................................................62 
9.7.1 
Efficacy and Safety Measurements Assessed .............................................62 
9.7.2 
Efficacy Variable .........................................................................................64 
9.7.3 
Pharmacokinetic Variables ..........................................................................64 
9.7.4 
Exploratory Efficacy Variable .....................................................................65 
9.7.5 
Safety Variables ..........................................................................................65 
9.7.6 
Clinical Laboratory Assessments ................................................................65 
10 REPORTING ADVERSE EVENTS .................................................................................68 
10.1 Adverse Events .........................................................................................................68 
10.2 Serious Adverse Events ............................................................................................70 
10.3 Pregnancy ..................................................................................................................72 
10.4 Urgent Safety Measures ............................................................................................72 
10.5 BioMarin Pharmacovigilance Contact Information ..................................................73 
11 APPROPRIATENESS OF MEASUREMENTS ...............................................................74 
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11.1 Safety and Pharmacokinetics ....................................................................................74 
11.2 Diet Diary ..................................................................................................................74 
12 STUDY PROCEDURES ...................................................................................................75 
12.1 Prestudy .....................................................................................................................75 
12.2 Screening Visit ..........................................................................................................75 
12.3 Treatment Period .......................................................................................................75 
12.3.1 Day 1 (Week 1) ...........................................................................................76 
12.3.2 Weekly Telephone Visit ..............................................................................76 
12.3.3 Substudy Visits ............................................................................................77 
12.3.4 Monthly Visits (Week 4, 8, 12, etc) ............................................................77 
12.3.5 Quarterly Visits (Week 12, 24, 36, etc) .......................................................77 
12.3.6 Unscheduled Hypersensitivity Reaction Visit .............................................78 
12.4 Study Completion/Early Termination Visit ..............................................................78 
13 DATA QUALITY ASSURANCE .....................................................................................80 
14 STATISTICAL METHODS AND DETERMINATION OF SAMPLE SIZE ..................81 
14.1 Statistical and Analytical Plans .................................................................................81 
14.2 Safety Analysis .........................................................................................................81 
14.3 Pharmacokinetic Analysis .........................................................................................81 
14.3.1 Pharmacokinetic Substudy Analysis ...........................................................82 
14.4 Efficacy Analysis ......................................................................................................82 
14.5 Determination of Sample Size ..................................................................................82 
14.6 Handling of Missing Data .........................................................................................82 
14.7 Interim Analyses .......................................................................................................83 
14.8 Changes in the Conduct of the Study or Planned Analyses ......................................83 
15 DATA MONITORING COMMITTEE (DMC) ................................................................84 
16 COMPENSATION, INSURANCE, AND INDEMNITY .................................................85 
17 CASE REPORT FORMS AND SOURCE DOCUMENTS ..............................................86 
18 STUDY MONITORING AND AUDITING .....................................................................87 
19 RETENTION OF RECORDS ...........................................................................................88 
20 USE OF INFORMATION AND PUBLICATION ...........................................................89 
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21 REFERENCES ..................................................................................................................90 
22 INVESTIGATOR RESPONSIBILITIES ..........................................................................92 
22.1 Conduct of Study and Protection of Human Subjects...............................................92 
23 SIGNATURE PAGE .........................................................................................................93 
24 PROTOCOL AMENDMENT TEXT REVISIONS ..........................................................94 
 
LIST OF TABLES 
Table 9.1.1:  Schedule of Events .............................................................................................41 
Table 9.1.2:  PK Substudy Dosing Regimens ..........................................................................44 
Table 9.1.1.2.1:  Dosing Instructions in Response to Hypersensitivity Adverse Events .........46 
Table 9.1.2.1:  Brown’s Severity Criteria ................................................................................48 
Table 9.4.2.1.1:  Prefilled Syringe Volume, Concentration, and Dose ....................................55 
Table 9.4.2.1.2:  Conversion from Vial and Syringe Dose to Prefilled Syringe Dose ............56 
Table 9.4.4.1:  Fixed Doses for Subjects on Weight-Based Dose Regimen ............................58 
Table 9.7.1.1:  Summary of Laboratory Assessments .............................................................63 
Table 9.7.6.1:  Clinical Laboratory Tests ................................................................................67 
 
 
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4 
LIST OF ABBREVIATIONS AND DEFINITIONS OF TERMS 
Abbreviations 
ADR 
adverse drug reaction 
AE 
adverse event 
ALT 
alanine aminotransferase 
AST 
aspartate aminotransferase 
AUC 
area under the plasma concentration-time curve 
AUC0-7 days 
area under the plasma concentration-time curve from time zero on Day 1 
to Day 8 
BUN 
blood urea nitrogen 
°C 
degree Celsius 
C3 
complement 3 
C4 
complement 4 
CBC 
complete blood count 
CD 
Compact disk 
CFR 
Code of Federal Regulations 
CH50 
total hemolytic complement 
Cmax 
maximum plasma concentration 
CNS 
central nervous system 
CO2 
carbon dioxide 
CRA 
Clinical Research Associate 
CRF 
case report form 
CRP 
C-reactive protein 
CTCAE 
Common Terminology Criteria for Adverse Events 
CV 
cardiovascular 
DBP 
diastolic blood pressure 
DMC 
Data Monitoring Committee 
ECG 
electrocardiogram 
ETV 
Early Termination Visit 
FDA 
Food and Drug Administration 
F/U 
follow-up 
g 
gram 
GCP 
Good Clinical Practice 
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GGT 
gamma-glutamyltransferase 
GI 
gastrointestinal 
IB 
Investigator’s Brochure 
ICF 
Informed Consent Form 
ICH 
International Conference on Harmonisation of Technical Requirements for 
Registration of Pharmaceuticals for Human Use 
ID 
identification 
IgE 
immunoglobulin E 
IgG 
immunoglobulin G 
IgM 
immunoglobulin M 
IP 
investigational product 
IRB 
Institutional Review Board 
IV 
intravenous 
kg 
kilogram 
MedDRA 
Medical Dictionary for Regulatory Activities 
mg 
milligram 
mL 
milliliter 
mm Hg 
millimeter of mercury 
NAb 
neutralizing antibodies 
NCI 
National Cancer Institute 
NIAID/FAAN National Institute of Allergy and Infectious Disease/Food Allergy and 
Anaphylaxis Network 
NOAEL 
no observable adverse effect level 
NSAID 
non-steroidal anti-inflammatory medication 
OTC 
over the counter 
PAH 
phenylalanine hydroxylase 
PAL 
phenylalanine ammonia lyase 
PEG 
polyethylene glycol 
Phe 
phenylalanine 
PI 
Principal Investigator 
PK 
pharmacokinetics 
PKU 
phenylketonuria 
rAvPAL-PEG 
recombinant Anabaena variabilis phenylalanine ammonia lyase-PEG 
RBC 
red blood cell 
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SAE 
serious adverse event 
SAP 
Statistical Analysis Plan 
SBP 
systolic blood pressure 
SC 
subcutaneous 
SD 
standard deviation 
SDV 
source data verified 
SGOT 
serum glutamic oxalo-acetic transaminase 
SGPT 
serum glutamic pyruvate transaminase 
US 
United States 
WBC 
white blood cell 
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Definition of Terms: 
Investigational Product (IP): 
“A pharmaceutical form of an active ingredient or placebo being tested or used as a reference 
in a clinical trial, including a product with a marketing authorization when used or assembled 
(formulated or packaged) in a way different from the approved form, or when used for an 
unapproved indication, or when used to gain further information about an approved use.” 
(from E6 ICH)  
The terms “IP” and “study drug” may be used interchangeably in the protocol. 
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5 
ETHICS 
5.1 
Institutional Review Board or Ethics Committee 
Prior to initiating the study, the Investigator will obtain written confirmation that the 
Institutional Review Board (IRB) is properly constituted and compliant with International 
Conference on Harmonisation of Technical Requirements for Registration of 
Pharmaceuticals for Human Use (ICH) and Good Clinical Practice (GCP) requirements, and 
applicable laws and local regulations. A copy of the confirmation from the IRB will be 
provided to BioMarin Pharmaceutical Inc. (BioMarin) or its designee. The Principal 
Investigator (PI) will provide the IRB with all appropriate material, including the protocol, 
Investigator’s Brochure (IB), the Informed Consent Form (ICF) including compensation 
procedures, and any other written information provided to the subjects, including all consent 
forms translated to a language other than the native language of the clinical site. The study 
will not be initiated and investigational product (IP) supplies will not be shipped to the site 
until appropriate documents from the IRB confirming unconditional approval of the protocol, 
the ICF and all subject recruitment materials are obtained in writing by the PI and copies are 
received at BioMarin or its designee. The approval document should refer to the study by 
protocol title and BioMarin protocol number (if possible), identify the documents reviewed, 
and include the date of the review and approval. BioMarin will ensure that the appropriate 
reports on the progress of the study were made to the IRB and BioMarin by the PI in 
accordance with applicable governmental regulations. 
5.2 
Ethical Conduct of Study 
This study will be conducted in accordance with the following: 
• United States (US) Code of Federal Regulations (CFR) sections that address clinical 
research studies, and/or other national and local regulations, as applicable 
• E6 ICH Guideline for GCP 
• The ethical principles established by the Declaration of Helsinki 
Specifically, this study is based on adequately performed laboratory and animal 
experimentation; the study will be conducted under a protocol reviewed and approved by an 
IRB; the study will be conducted by scientifically and medically qualified persons; the 
benefits of the study are in proportion to the risks; the rights and welfare of the subjects will 
be respected; the physicians conducting the study do not find the hazards to outweigh the 
potential benefits; and each subject, or his or her legally authorized representative will 
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provide written, informed consent before any study-related tests or evaluations are 
performed. 
5.3 
Subject Information and Informed Consent 
A properly written and executed ICF, in compliance with the Declaration of Helsinki, 
E6 ICH (GCP Guideline, Section 4.8) and 21 CFR Part 50 and other applicable local 
regulations, will be obtained for each subject prior to entering the subject into the study. The 
Investigator will prepare the ICF and provide the documents to BioMarin for approval prior 
to submission to the IRB. BioMarin and the IRB must approve the documents before they are 
implemented. A copy of the approved ICF, and if applicable, a copy of the approved subject 
information sheet, minor assent form, parental ICF for studies involving minors, and all ICFs 
translated to a language other than the native language of the clinical site must also be 
received by BioMarin or its designee prior to the delivery of study drug. 
Subjects under the age of 18 years will provide written assent (if required), and his/her 
legally authorized representative (parent or legal guardian) will provide written informed 
consent for such subjects. The Investigator will provide copies of the signed ICF to each 
subject (or the subject’s legally authorized representative) and will maintain the original in 
the subject’s record file. 
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6 
INVESTIGATORS AND STUDY ADMINISTRATIVE STRUCTURE 
Prior to beginning the study, the PI at each site must provide to BioMarin or its designee a 
fully executed and signed Form FDA (Food and Drug Administration) 1572 and a Financial 
Disclosure Form. All sub-Investigators must be listed on Form FDA 1572. Financial 
Disclosure Forms must also be completed for all sub-Investigators listed on the 
Form FDA 1572 who will be directly involved in the treatment or evaluation of research 
subjects in this study. 
The study will be administered by and monitored by employees or representatives of 
BioMarin. Clinical Research Associates (CRAs) or trained designees will monitor each site 
on a periodic basis and perform verification of source documentation for each subject as well 
as other required review processes. BioMarin’s Pharmacovigilance Department (or designee) 
will be responsible for the timely reporting of serious adverse events (SAEs) to appropriate 
regulatory authorities as required. Some study assessments, including administration of study 
drug, may be performed at the subject’s home. All assessments performed for this study will 
be administered by clinic staff or other qualified and trained study personnel. 
Anti-rAvPAL-PEG (recombinant Anabaena variabilis phenylalanine ammonia lyase 
polyethylene glycol) immunoglobulin E (IgE) antibody analysis will be performed by a 
vendor; other antibody analysis will be performed by BioMarin. Clinical laboratory tests, 
including serum pregnancy tests (if applicable), will be analyzed and processed by a central 
laboratory, with the exception of erythrocyte sedimentation rate (ESR), and urine pregnancy 
tests (if applicable), which will be analyzed by a local laboratory. A central laboratory will 
also be used to perform analysis of blood phenylalanine (Phe) concentrations and urinalysis. 
Pharmacokinetic (PK) analysis will be performed by BioMarin. 
Prior to database lock in multicenter studies, a Coordinating Investigator will be identified 
who will read the clinical study report and confirm that it accurately describes the conduct 
and results of the study, to the best of his or her knowledge. The Coordinating Investigator 
will be chosen on the basis of active participation in the study, ability to interpret data, and 
willingness to review and sign the report in a specified timeframe. 
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7 
INTRODUCTION 
A comprehensive review of PEGylated recombinant Anabaena variabilis phenylalanine 
ammonia lyase (rAvPAL-PEG) is contained in the IB supplied by BioMarin; the Investigator 
should review this document prior to initiating this study. 
7.1 
Nonclinical Studies 
The nonclinical program for rAvPAL-PEG has characterized the pharmacology, 
pharmacokinetics (PK), and toxicology of rAvPAL-PEG using the intended clinical SC route 
of administration. Pharmacology was assessed in the BTBR Pahenu2 (ENU2) mouse model of 
PKU. The ENU2 mouse model exhibits characteristics similar to those of PKU patients, 
including hyperphenylalaninemia (baseline plasma Phe concentrations of 1000 to 2000 µM) 
and hypopigmentation. Following weekly doses of rAvPAL-PEG administered to male 
ENU2 mice, plasma Phe concentrations decreased from approximately 2000 µM to 
< 200 µM after 2 dose administrations. An attenuated reduction of blood Phe was seen 
between Week 3 and Week 7 of dosing. After 7 weekly administrations of rAvPAL-PEG, 
pharmacological activity returned as evidenced by stabilized concentrations of plasma Phe 
< 200 µM over the entire week, which continued for a total of 15 weeks. 
In pharmacodynamic studies in the BTBR Pahenu2 (ENU2) mouse model administered 
80 mg/kg/week rAvPEG-PAL, two dose interruption assessments were performed:  a 
2-4 week dose interruption and an 11-week dose interruption. Following both dose 
interruption assessments, the animals re-started rAvPAL-PEG at a dose of 80 mg/kg/week. 
No attenuated Phe response was observed when rAvPAL-PEG injections were temporarily 
stopped for 2-4 weeks, and there was an immediate return to stable blood Phe reductions. A 
similar interim attenuated response was observed with the longer dose interruption of 
approximately 11 weeks.  In both of these assessments, no safety issues were noted upon 
re-starting dosing with rAvPAL-PEG (Lapis, 2007, ASHG 57th Annual Meeting). 
Safety pharmacology studies were conducted in rats and cynomolgus monkeys. No 
respiratory or central nervous system (CNS) effects were seen with SC administration of 
rAvPAL-PEG. No changes in cardiovascular (CV) parameters, including electrocardiogram 
(ECG) waveforms, were observed in telemetry-instrumented monkeys assessed for the CV 
effects of rAvPAL-PEG administered subcutaneously. 
Pharmacokinetic parameters were evaluated in single-dose and repeat-dose studies in rats and 
cynomolgus monkeys. The elimination half-life (t1/2) values of rAvPAL-PEG administered to 
normal rats at SC doses of 10, 25, and 250 mg/kg were 47, 33, and 44 hours, respectively, 
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and exhibited modest area under the plasma concentration-time curve (AUC)-dose. In the 
cynomolgus monkey after SC administration of rAvPAL-PEG, the t1/2 was 65 hours at 
4.0 mg/kg, 71 hours at 12 mg/kg, and could not be determined at 60 mg/kg (the highest 
dose). Qualitatively, the kinetics of rAvPAL-PEG in the rat and monkey appear to have 
similar characteristics. The following findings were noted: (1) a 1-compartment model with 
first-order absorption appears to describe the plasma profiles of rAvPAL-PEG after 
single-dose administration, (2) absorption is slow and there is a long absorption period after 
SC administration to maximum observed plasma concentration (Cmax), along with a long t1/2, 
(3) elimination is slow and monophasic, (4) there does not appear to be a gender difference, 
and (5) the AUC and the Cmax are roughly linearly proportional.  
Toxicology of rAvPAL-PEG was assessed in single-dose and repeat-dose studies in normal 
rats and cynomolgus monkeys. In the single-dose rat study, decreased body weight gain and 
Kupffer cell vacuolization at the high SC dose of 250 mg/kg was observed; however, the 
Kupffer cell finding was not seen in the single-dose study in cynomolgus monkeys. In a 
26-week repeat-dose toxicity and toxicokinetic (TK) rat study, decreased body weight gain, 
decreased food consumption, vacuolation/hypertrophy of the renal tubule cells, and 
vacuolation of the histiocytic cells were observed in rats administered 25 mg/kg/dose, twice 
weekly. In a 39-week repeat-dose study in monkeys, arterial inflammation, perivascular 
cellular infiltrates in the SC injection sites, thymic atrophy, and increased lymphoid nodules 
in bone marrow of the sternum were observed in monkeys given ≥ 3 mg/kg/dose, twice 
weekly. Of these findings, only the arterial inflammation was deemed adverse and this 
finding was completely reversed after 13-weeks of recovery. The 
no-observed-adverse-effect-level (NOAEL) of rAvPAL-PEG when administered 
subcutaneously twice weekly for 26 weeks and 39 weeks in the rat and monkey, respectively, 
was 1.0 mg/kg. These NOAELs were based on histological findings of 
vacuolation/hypertrophy of the renal tubule cells in the rat and arterial inflammation findings 
in the monkey. 
7.2 
Previous Clinical Studies 
The rAvPAL-PEG clinical development program has been designed to demonstrate the 
safety and efficacy of rAvPAL-PEG in reducing blood Phe concentrations in PKU subjects 
who do not respond to treatment with Kuvan® or are not compliant with Kuvan® treatment. 
This study is an extension of the ongoing human clinical studies with rAvPAL-PEG 
(Study PAL-002, Study PAL-004, and Study 165-205) based on data from the completed 
clinical study, PAL-001, and clinical experience from this ongoing study and the other 
ongoing Phase 2 studies, PAL-002 and PAL-004.  
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7.2.1 
Phase 1 Study, PAL-001 
The first-in-human trial using rAvPAL-PEG, Study PAL-001, was a Phase 1, open-label, 
dose-escalation study in PKU subjects in the US. The primary objective was to assess the 
safety and tolerability of single SC injections of rAvPAL-PEG. Secondary objectives were to 
evaluate the PK of single, SC injections of rAvPAL-PEG administered at escalating doses in 
subjects with PKU and to evaluate the effect of rAvPAL-PEG on blood Phe concentrations. 
The effectiveness of rAvPAL-PEG in decreasing Phe concentrations in nonclinical studies of 
ENU2 mice was consistent with what was observed in PAL-001. PAL-001 enrolled 25 PKU 
subjects with a mean (standard deviation; SD) baseline blood Phe concentration of 
1310 µmol/L (405). The 25 subjects who enrolled into the study were assigned to receive a 
single administration of rAvPAL-PEG at 1 of 5 dose levels: 0.001, 0.003, 0.01, 0.03, and 
0.1 mg/kg. Five subjects each received 1 of the 5 dose levels of rAvPAL-PEG. 
Key safety, efficacy, and PK results of Study PAL-001 are summarized as follows: 
•
rAvPAL-PEG was well tolerated and had a clinically significant blood-lowering
effect on Phe concentration when administered at a dose of 0.1 mg/kg.
•
For the 5 subjects who were administered 0.1 mg/kg rAvPAL-PEG, clinically
significant reductions in blood Phe level were observed, with the most clinically
significant decreases from baseline values to Day 7, ranging from 33.8% to 97.3%
(mean of 58.12%). The mean baseline blood Phe level for these 5 subjects was
1113 µmol/L.
•
Overall, no clinically significant reductions in blood Phe level were observed in
subjects who were administered rAvPAL-PEG at the lower doses of 0.001, 0.003,
0.01, and 0.03 mg/kg.
•
For subjects who were administered rAvPAL-PEG at the 3 higher dose levels (0.01,
0.03, and 0.1 mg/kg) and who had measurable rAvPAL-PEG concentration levels, the
calculated PK parameters were a mean Tmax of 89-106 hours, a t1/2 of 46-120 hours,
and an AUC0-t, and Cmax that were proportional with dose. Drug exposure was slightly
increased with increased dose.
7.2.2 
Phase 2 Studies PAL-002, PAL-004, and 165-205 
Based on results from the Phase 1, single-dose study, the Phase 2 studies have been designed 
to evaluate rAvPAL-PEG at various doses and dosing regimens to safely achieve and 
maintain blood Phe reductions in subjects with PKU. Currently, there are three ongoing 
Phase 2 studies (PAL-002, PAL-004, 165-205); an overview of each study is presented in 
Section 7.2.2.1 (PAL-002), Section 7.2.2.2 (PAL-004), and Section 7.2.2.3 (165-205).  
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7.2.2.1 
Study PAL-002 
Study PAL-002 (A Phase 2, Open-Label, Dose-Finding Study to Evaluate the Safety, 
Efficacy, and Tolerability of Multiple Subcutaneous Doses of rAvPAL-PEG in Subjects With 
Phenylketonuria) was initiated in September 2009 and has completed enrollment. As of 
10 September 2012, 40 subjects have been enrolled and 37 have completed the study. 
PAL-002 enrolled 11 previously exposed subjects from the single-dose study, PAL-001, and 
29 subjects who were naïve to rAvPAL-PEG. Thirty-three of the 37 subjects who completed 
PAL-002 enrolled into this open-label extension study (PAL-003). Two subjects 
discontinued from the study due to lost to follow-up, relocation, or other reasons, and 
1 subject discontinued from the study due to an AE (skin reaction).  
The primary objective of this study was to evaluate the effect of multiple doses of 
rAvPAL-PEG (ranging from 0.001 mg/kg/week to 1.0 mg/kg/week) on blood Phe 
concentrations in subjects with PKU with up to 16 weeks of treatment. The secondary 
objectives of the study were to evaluate the safety and tolerability of SC injections of 
multiple doses of rAvPAL-PEG, to evaluate the immune response to rAvPAL-PEG, and to 
evaluate the PK profile of rAvPAL-PEG in subjects with PKU.  
The PAL-002 study design consists of two parts. In Part 1, rAvPAL-PEG was administered 
as a once weekly fixed, low-dose induction regimen for 8 weeks. In Part 2, the rAvPAL-PEG 
dose was titrated upwards; subjects received adjustable dose increases for up to 8 weeks to 
achieve a target blood Phe concentration of 600 µmol/L. The doses and dosing schedules 
were revised with a series of protocol amendments to incorporate the information gained 
during conduct of this early, open-label, multiple-dose study.  
A wide range of doses was planned for the PAL-002 study, beginning with doses as low as 
0.001mg/kg/week.  However, no substantial reductions in blood Phe level were observed in 
the majority of subjects who were administered rAvPAL-PEG in the initial four cohorts at 
doses of 0.001, 0.003, 0.01, and 0.03 mg/kg administered once per week. The absence of 
appreciable Phe reduction after 16 weeks of treatment in this range of doses led to a decision 
to amend the study protocol to include a cohort with a higher starting dose of 
0.1 mg/kg/week, which had been previously shown to decrease blood Phe levels to 
approximately 600 µmol/L in the single-dose, Phase 1 study (PAL-001). After the first 
2 weeks of dosing at 0.1 mg/kg/week, transient Phe reduction was observed in this subset of 
subjects. However, this dosing regimen was accompanied by mild to moderate 
hypersensitivity reactions primarily after the second weekly dose, suggesting that additional 
exploration of dosing regimens would be required.  
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In summary, preliminary results from PAL-002 demonstrated that doses below 0.1 g/kg 
administered once per week were not effective in reducing Phe levels.  While transient 
reduction of Phe was apparent at doses of at least 0.1 mg/kg given once per week, this dose 
regimen was associated with a high incidence of systemic hypersensitivity reactions, 
typically following the second weekly dose.  Further escalation above this dose of 
0.1 mg/kg/week would be required to sustain the effect on Phe levels over time.  Increased 
doses would require spreading dose administration over several days per week, as 
once-weekly administration of higher doses would not be practical due to the large volume of 
study drug.  Therefore, additional dosing regimens would need to be explored in a 
subsequent study (PAL-004). 
Once subjects completed Study PAL-002, they were eligible to enroll into this open-label 
extension study, PAL-003 to continue to receive rAvPAL-PEG up to a maximum dose of 
5.0 mg/kg/week or 375 mg/week. 
7.2.2.2 
Study PAL-004 
PAL-004 (An Open-Label Study to Evaluate the Safety, Tolerability, and Efficacy of 
Subcutaneous Dose Levels of rAvPAL-PEG Administered Daily in Subjects With 
Phenylketonuria) was initiated in April 2011 and has completed enrollment. As of 
10 September 2012, 16 subjects have been enrolled, 15 subjects have completed the study, 
and 15 subjects have enrolled into this study (PAL-003). One subject withdrew consent from 
continued participation prior to study completion. All subjects enrolled in this study were 
naïve to rAvPAL-PEG exposure. 
The objective of this study was to determine if daily administration (defined as 5days/week) 
of rAvPAL-PEG at dose levels of 0.06, 0.1, 0.2, 0.4, 0.6, and 0.8 mg/kg/day was safe and 
effective in reducing and maintaining blood Phe concentrations to 600 µmol/L in subjects 
with PKU. The starting dose was 0.4 mg/kg, administered 5 days/week. A total of 12 subjects 
were added in sequence and were started on doses of 0.4, 0.2, 0.1, 0.06 mg, or 0.001/kg/day 
based on incoming safety data. Overall, subjects in PAL-004 who initiated treatment at 
higher daily doses of 0.1 to 0.4 mg/kg/day achieved immediate and substantial reduction of 
blood Phe levels, but dosing had to be temporarily reduced or interrupted due to the onset of 
systemic hypersensitivity reactions at approximately Day 10 of dosing. Phe reductions did 
not persist in the setting of temporary dose reduction or interruption, but Phe levels generally 
improved if higher dose levels were reinstated.  
To prevent the onset of hypersensitivity reactions that were temporally associated with the 
onset of anti-drug IgM responses, an additional dosing strategy was assessed in PAL-004; 
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4 subjects initiated dosing at a low dose of 0.001mg/kg/day or 0.06mg/kg/day for 
5 consecutive days and then dosing was suspended for 2 weeks. Dosing was restarted on 
Day 21 at the initial dose followed by dose titration to target Phe levels. Subjects 
administered this dosing regimen had similar efficacy, but the incidence of hypersensitivity 
reactions appeared to be similar to that of subjects who did not have the planned dose 
interruption, suggesting little advantage with this alternate induction regimen.  
Experience from PAL-004 indicated that initiating daily rAvPAL-PEG dosing with relatively 
high daily doses was not sustainable due to the onset of hypersensitivity reactions that 
occurred approximately 9 to 12 days after the start of administration, nor was the alternate 
dosing regimen (2 week drug holiday) well tolerated or effective in Phe reduction. In 
addition, the daily treatment regimen did not reduce the time to achieve target blood Phe 
levels seen in previous studies. This study indicated that to improve tolerability, 
rAvPAL-PEG should be initiated with an induction period at doses substantially lower than 
0.4mg/kg, followed by upward dose titration toward target Phe levels.   
Once subjects completed Study PAL-004, they were eligible to enroll into this open-label 
extension study to continue to receive rAvPAL-PEG up to a maximum dose of 
5.0 mg/kg/week or 375 mg/week. 
7.2.2.3 
Study 165-205 
Study 165-205 (A Phase 2, Multi-Center, Open-Label, Dose-Finding Study to Evaluate 
Safety, Efficacy, and Tolerability of Subcutaneously Administered rAvPAL-PEG in Subjects 
With PKU for 24 Weeks) was initiated in May 2012. Data from ongoing Studies PAL-002, 
PAL-004, and PAL-003 suggested that a 4-week treatment course with weekly dosing at a 
fixed low dose (induction), followed by a weekly 2-fold, upward titration of rAvPAL-PEG to 
approximately 10-fold higher than the initiation dose (maximum of 375 mg/week) is 
effective and well tolerated. The objective of this study was to further assess this dosing 
regimen. Two rAvPAL-PEG dosing regimens were to be explored in this study:  weekly 
low-dose induction (2.5 mg/week for 4 to 8 weeks), followed by a period of upward dose 
titration towards a target Phe level (600 µmol/L) followed by maintenance dosing at that 
level through the 24 week study duration (Group 1).  The other dosing regimen planned for 
this study (Group 2) involved administration of a single bolus dose of 8 mg, followed by a 
treatment holiday of at least 3 weeks duration followed by resumption and escalation of study 
drug administration following a pattern similar to that employed in Group 1. A total of 
24 subjects were enrolled into 165-205. In addition to confirming an effective, well-tolerated 
dose regimen, this study incorporated non-weight-based dosing, starting with dose 
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administration once per week at a low dose (2.5mg) with gradual escalation and conversion 
of dose administration to 5x/week dosing for chronic maintenance therapy.  
Once subjects have completed Study 165-205, they are eligible to enroll into this study to 
continue to receive rAvPAL-PEG up to a maximum dose of 5.0 mg/kg/week or 
375 mg/week, or into the Phase 3 study, 165-302. 
7.3 
Study Rationale 
PKU is an autosomal, recessive, inherited disease characterized by deficiency in the enzyme 
PAH. Approximately 1 in every 10,000 infants in North America is born with PKU 
(Scriver, 2001, McGraw-Hill). Left untreated, PAH deficiency is associated with an 
abnormally elevated concentration of Phe, which is toxic to the brain (Kaufman, 1989, J 
Pediatr.) and can result in a variety of neuropathologic conditions, including mental 
retardation, microcephaly, delayed speech, seizures, and behavioral abnormalities 
(Scriver, 2001, McGraw-Hill). The brains of untreated patients with PKU show evidence of 
hypomyelination and gliosis, arrest in cerebral development, and, in some cases, white matter 
degeneration (Huttenlocher, 2000, Eur.J Pediatr.). Elevated Phe during fetal development 
leads to severe mental retardation and can cause microcephaly, growth retardation, and 
congenital heart disease (Guttler, 2003, Pediatrics), (Koch, 2003, Pediatrics), (Lee, 2003, 
Pediatrics), (Levy, 2003, Pediatrics), (Matalon, 2003, Pediatrics), (Rouse, 2004, J.Pediatr.). 
For a subset of patients with residual enzyme activity, treatment with Kuvan® is an option. 
For all other patients, current management of PKU involves adherence to low-Phe medicinal 
diet formulas and dietary restriction of Phe-containing foods. Implementation of a 
Phe-restricted diet in infancy significantly reduces blood Phe concentrations and prevents 
many of the neuropathologic manifestations of PKU, including severe mental retardation. 
However, compliance with this restrictive diet can be difficult for older children, adolescents, 
and adults, and adherence may result in nutritional deficiencies due to the limitations of 
natural protein sources (Fisch, 2000, Eur.J.Pediatr.), (Walter, 2002, Lancet). 
The need exists for a treatment that will help individuals with PKU safely achieve lifelong, 
reliable control of blood phenylalanine (Phe) concentrations and improve functional 
outcomes. rAvPAL-PEG is a potential substitute for the phenylalanine hydroxylase (PAH) 
enzyme, which is defective in individuals with PKU. rAvPAL-PEG may control blood Phe 
concentrations, which may have additional clinical benefits.  
Blood Phe levels depend not only on the functional presence of the endogenous enzyme PAH 
but also on the dietary intake of Phe. It is important to understand the role of diet on blood 
Phe levels concurrent with the administration of rAvPAL-PEG treatment. Therefore, an 
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exploratory objective has been added to this study to assess the relationship of diet, 
rAvPAL-PEG administration, and blood Phe level. Changes to subject diet are not allowed in 
this study unless per the Investigator. Diet will be monitored using a diet diary.     
A pharmacokinetic (PK) substudy has been added to evaluate the steady-state PK of 
rAvPAL-PEG in up to 6 subjects who have achieved and maintained target blood Phe for at 
least 2 consecutive measurements and for whom no further dose modifications are planned. 
Single-dose PK data has been collected in the Phase 1 study, PAL-001. However, there is 
little multiple-dose PK data or data for when subjects have reached and maintained a stable 
dosing regimen.  With the PK substudy, multiple-dose PK data will be collected for subjects 
who have already achieved Phe reduction to within the protocol-defined target range. 
This study is an extension of previous rAvPAL-PEG Phase 2 studies. Administration of 
rAvPAL-PEG will be continued to assess the long-term safety and efficacy of rAvPAL-PEG 
in PKU subjects. 
7.4 
Summary of Overall Risks and Benefits 
It is not expected that data from previous rAvPAL-PEG studies will change the assumption 
that rAvPAL-PEG has a toxicity profile similar to other recombinant PEGylated non-human 
enzymes currently in use. The toxicities of these drugs usually fall into 2 main categories: 
toxicity due to exposure to PEG, and toxicity due to immunologic sensitization. In addition, 
exaggerated pharmacological effects resulting in very low Phe concentrations could be 
observed. Other adverse events (AEs) that could occur with rAvPAL-PEG include 
injection-site reactions and other general symptoms. 
7.4.1 
Toxicity Due to Exposure to Polyethylene Glycol (PEG) 
Acute exposure to high doses of PEG can result in renal toxicity. There have been a few 
reports of PEG-related AEs in humans; cumulative intravenous (IV) PEG doses of 121 to 
240 g caused acute renal tubular necrosis, oliguria, and azotemia. The anticipated PEG 
exposure associated with the expected rAvPAL-PEG dose range (6 g per week) is at least 
80-fold lower than the reported toxic doses and comparable to exposures to PEG in widely 
used medicines and other compounds that are administered by the IV, oral, rectal, and topical 
routes (Webster, 2007, Drug Metab Dispos.). No indication of PEG-related toxicity at the 
ultrastructural level was observed in monkeys given a single dose of up to 60 mg/kg 
rAvPAL-PEG SC. In rats, both renal tubule vacuolation and histiocytic cell vacuoles have 
been assocated with PEG-related catabolism and administration of other PEGylated proteins 
(refer to Section 7.1). 
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In this study, subjects will be monitored closely with urine examinations and blood 
chemistries to follow kidney function. 
7.4.2 
Immunologic Response 
The active drug substance in rAvPAL-PEG is a bacterial protein and elicits immune 
recognition and subsequent antibody responses. Antibody epitopes on the protein are 
expected to be rendered at least partially inaccessible by the extensive PEGylation on the 
drug (Gamez, 2007, Mol.Genet.Metab). In vivo and in vitro experiments have shown that 
PEGylation of proteins and cells can attenuate the immunological response (Scott, 1997, 
Proc.Natl.Acad.Sci.U.S.A), (Chen, 2001, BioDrugs.). PEGylation has been effective in 
reducing anti-rAvPAL antibody titers in the mouse model but does not eliminate antibody 
formation. Although PEGylation of rAvPAL likely reduces the antigenicity of the molecule, 
100% of individuals exposed to rAvPAL-PEG develop antibodies against rAvPAL.  
Drug-specific immune responses can range from clinical irrelevance to causing serious 
hypersensitivity AEs (such as anaphylaxis) and may reduce efficacy due to 
antibody-mediated drug clearance or antibody neutralization of enzymatic activity. 
Historically, PEG was thought to be nonimmunogenic (Davis, 1981, Clin.Exp.Immunol.), 
(Harris, 2003, Nat.Rev.Drug Discov.); however, repeated studies have found that 
subcutaneous (SC) and intravenous exposure to PEG can induce anti-PEG antibodies 
(Harris, 2003, Nat.Rev.Drug Discov.), (Richter, 1983, Int.Arch.Allergy Appl.Immunol.). In 
some instances, development of such antibodies did not result in significant clinical effects in 
humans (Richter, 1984, Int.Arch.Allergy Appl.Immunol.). However, PEG antibody responses 
were associated with hypersensitivity reactions to PEGylated liposomes (Judge, 2006, 
Mol.Ther.). Anti-PEG antibodies have also been associated with nonresponsiveness against 
therapy (Armstrong, 2007, Cancer), (Ganson, 2006, Arthritis Res.Ther.). 
Subjects participating in the Phase 2 clinical studies have been monitored closely for 
anti-drug immunogenicity (anti-rAvPAL immunoglobulin G [IgG], anti-rAvPAL IgM, 
anti-PEG IgM, anti-PEG IgG, neutralizing antibodies that inhibit PAL enzymatic activity, 
anti-rAvPAL IgE, and anti-rAvPAL-PEG IgE), complements, C-reactive protein (CRP), 
ESR, and complete chemistry. All subjects treated with rAvPAL-PEG in the Phase 2 clinical 
trials developed antibodies against the PAL protein. Anti-rAvPAL IgM antibodies were first 
detected within 2-3 weeks of treatment initiation and anti-rAvPAL IgG antibodies were 
detected within 2-3 months. The anti-rAvPAL IgG response generally peaked by 3-5 months 
and was sustained in all subjects. Neutralizing antibodies (NAb) capable of inhibiting 
enzymatic activity were detected in a minority of subjects 2-3 months after treatment 
initiation. The timing of the NAb response suggests these antibodies may be a component of 
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the anti-rAvPAL IgG response. It is expected that the centralized location of the PAL active 
site, within the tetrameric structure, makes it difficult for antibodies to bind and inhibit 
enzymatic activity. In addition, anti-PAL antibody binding is likely sterically hindered by the 
extensive PEGylation. The majority of treated subjects also developed a transient anti-PEG 
antibody response. The anti-PEG response was comprised of IgM and IgG isotypes. In 
general, anti-PEG antibodies were no longer detected after 5-6 months of treatment. This 
type of transient antibody response is typical of T cell-independent type 2 (TI-2) responses. 
The majority of immune-mediated AEs experienced in subjects treated with rAvPAL-PEG in 
the Phase 2 studies are believed to be the result of antibody-mediated hypersensitivity. The 
primary immune mediator is thought to be IgM immune complexes, as evidenced by the 
timing of onset prior to IgG development and the reduced occurrence over time. IgE positive 
test results have not been associated with hypersensitivity in any of the subjects thus far, and 
the majority of subjects have been safely rechallenged with rAvPAL-PEG following 
reactions. IgM immune complexes are known to be efficient activators of the classical 
complement pathway and can lead to the accumulation of complement component 
anaphylatoxins (C3a, C4a, C5a) that can induce hypersensitivity symptoms. Although IgG 
immune complexes can also activate the classical complement pathway, they do so with less 
efficiency than IgM. This is due, in part, to the requirement for multiple Fc regions in close 
proximity to activate the complement cascade, meaning that multiple monomeric IgG Abs 
are required to bind, whereas only one pentameric IgM Ab is needed to bind to activate 
complement. Also, in the case of rAvPAL-PEG, binding of anti-PAL IgG antibodies is likely 
compromised due to epitope masking by the PEGylation, which may reduce IgG-mediated 
complement activation in vivo. This complex dynamic between combined isotype-specific 
Ab responses and epitope accessibility is thought to be a major factor dictating the need for 
an induction and titration dose regimen in the treatment of rAvPAL-PEG to be implemented 
in this study. 
7.4.3 
Management of Hypersensitivity Reactions 
Hypersensitivity reactions to the SC injection of rAvPAL-PEG may be mild, moderate, or 
severe in intensity. Reactions may include pruritus, rash, shortness of breath, hypotension, or 
anaphylaxis. Clinical assessments should be conducted for a minimum of 30 minutes 
post-injection. Longer observations may be required at the discretion of the PI. 
The responsible physician should use all appropriate measures for the treatment of 
hypersensitivity reactions. Because of the potential for anaphylaxis, equipment for 
emergency resuscitation (including epinephrine) should be within easy access during and 
after the rAvPAL-PEG injection. Subject should be pre-medicated with H1 antagonist, H2 
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antagonist, and NSAIDs approximately 2-3 hours prior to each dose of study drug for one 
week upon return to dosing regardless of the duration of dose interruption. NSAIDs should 
be given with food and may be omitted if not tolerated.  Subjects who qualify for self-
administration of study drug are trained to recognize a serious hypersensitivity AEs and how 
to respond. Additionally, subjects are given two epinephrine injectors and are instructed to 
carry one epinephrine injector with them at all times (Section 9.4). Refer to Section 9.1.1.3 
for instructions regarding resumption of study drug following resolution of symptoms 
consistent with a clinical diagnosis of anaphylaxis per National Institute of Allergy and 
Infectious Disease/Food Allergy and Anaphylaxis Network (NIAID/FAAN) criteria 
(Sampson, 2006, J.Allergy Clin.Immunol.).  
In the event of a hypersensitivity reaction, subjects may be asked to see an 
allergist/immunologist and/or provide up to 3 additional blood samples for immunology 
studies and complement testing. This additional testing may occur up to 6 months following 
the final study visit.  
The following measures are recommended for the treatment of hypersensitivity reaction 
symptoms: 
• Maintain the airway. 
• Vital sign check. 
• Administration of oral or IV diphenhydramine. 
• Administration of epinephrine if appropriate. 
• Administration of oral or IV glucocorticoids. 
• Administration of oxygen and IV fluids. 
• Administration of additional symptomatic treatment. 
• Transfer to an acute care facility of the study center. 
In addition, clinical judgment must be used in determining the appropriateness of 
corticosteroid administration. An allergy and/or immunology consultation should be sought if 
necessary. Detailed instructions for the management of hypersensitivity reactions are 
provided in the Study Reference Manual. 
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8 
STUDY OBJECTIVES 
The primary objective of the study is: 
• To evaluate the effect of long-term administration of multiple doses of SC injections 
of rAvPAL-PEG on blood Phe concentrations in subjects with PKU. 
The secondary objectives of the study are: 
• To evaluate the safety and tolerability of long-term administration of subcutaneous 
(SC) injections of rAvPAL-PEG in subjects with PKU. 
• To evaluate the immune response to long-term administration of SC injections of 
rAvPAL-PEG in subjects with PKU. 
The exploratory objective of the study is as follows: 
• To evaluate the long-term relationship of diet and change in blood Phe concentration 
following administration with rAvPAL-PEG in subjects with PKU. 
The Substudy objective is as follows: 
• To evaluate steady-state PK of rAvPAL-PEG in subjects who have achieved and 
maintained target blood Phe concentration and for whom no further dose 
modifications are planned. 
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9 
INVESTIGATIONAL PLAN 
9.1 
Overall Study Design and Plan 
This is a long-term extension of rAvPAL-PEG Phase 2 studies in up to 100 subjects with 
PKU. The doses are planned to be in the same range as those previously tested in the Phase 2 
studies (starting at 0.001 through 5.0 mg/kg/week or 2.5 mg through 375 mg/week), provided 
no dose-limiting toxicity was observed in a previous rAvPAL-PEG studies. Subjects’ doses 
will not exceed 375 mg/week. 
Only subjects who completed a previous rAvPAL-PEG study will be enrolled into this study. 
Subjects enrolling into PAL-003 with no interruption in dosing from a previous 
rAvPAL-PEG study may either continue their previous dosing regimen or begin this study at 
a higher dose level. Subjects who have had dosing interruptions between the previous 
rAvPAL-PEG study and PAL-003 must have their starting dose determined per the sponsor’s 
medical monitor.  The first week of dosing will be administered in the clinic, and the subject 
must be observed for 30 minutes following administration. Subjects are given two 
epinephrine injectors and are instructed to carry one epinephrine injector with them at all 
times (refer to Section 9.4). A follow-up telephone call will be made to the subject to monitor 
subject safety 24 hours following the return to dosing. 
Diet should not be altered during the course of this study. Any decision to modify subject 
diet must be made per the Investigator and must be performed under the supervision of the 
Investigator. To monitor for changes in subject diet, a diet diary will be issued to subjects for 
completion and will be brought to clinic monthly for review with the clinical study staff. 
Subjects may self-administer study drug at home if approved by the Investigator and the 
sponsor’s medical monitor and if adequate training is demonstrated. Subjects must meet a set 
of criteria to be considered appropriate for self-administration. Refer to Section 9.4 for the 
criteria for which subjects may qualify for self-administration. Additional information is 
provided in the Subject Self-Administration Training Materials. Additional training will be 
provided and demonstration of competency required when prefilled syringe drug product is 
introduced, every 24 weeks, and more often as needed. 
Subjects will be evaluated for safety throughout the study. Toxicity will be measured 
according to the National Cancer Institute (NCI) Common Terminology Criteria for Adverse 
Events (CTCAE), version 4. 
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In addition to the Sponsor, a Data Monitoring Committee (DMC) will monitor the safety of 
subjects in the study. The DMC is an independent committee that will act in an advisory 
capacity to the Sponsor. 
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take 
rAvPAL-PEG. Subjects’previous rAvPAL-PEG dosing will generally continue in PAL-003. 
In PAL-003, each subject’s dose will be adjusted as needed to attempt to attain or maintain 
blood Phe concentrations of 60-600 µmol/L. rAvPAL-PEG dose will be based on either a 
subject’s weight or will be a fixed dose. Doses will be evaluated on an individual basis.  
Evaluations, observations, and procedures will be conducted at selected time points as shown 
in Table 9.1.1 and Table 9.1.2.  After the subject’s blood Phe concentration has been 
controlled to within a target range (60-600 µmol/L), the subject may be asked to have 
additional blood draws for PK and blood Phe concentration analyses as needed per the 
discretion of the Investigator in consultation with the sponsor’s medical monitor. 
A subject will continue in PAL-003 until one of the following occurs: 
• The subject withdraws consent and discontinues from the study. 
• The subject is discontinued from the study at the discretion of the Investigator or 
Sponsor. 
• The subject has completed the study through the Month 98 visit. 
• The study is terminated. 
• The study drug receives marketing authorization. 
Because the risks of taking rAvPAL-PEG during pregnancy and breastfeeding are unknown, 
subjects cannot take rAvPAL-PEG if they are trying to conceive, are pregnant, or are 
breastfeeding (refer to Section 9.3.2, Exclusion Criteria). Male subjects who are planning to 
impregnate a female partner and female subjects who are trying to become pregnant during 
the study will be discontinued immediately from study drug. Male subjects who have 
impregnated a female partner may re-start study drug after conception but must return to the 
study-required contraception use (refer to Section 9.3.1, Inclusion Criteria), which must 
include one barrier method. Subjects who remain in the study after discontinuation of study 
drug due to pregnancy may re-introduce rAvPAL-PEG dosing after the birth has been 
reported (or termination of the pregnancy) and breastfeeding has completed (if applicable) or 
after the subject is no longer actively trying to conceive. Re-starting rAvPAL-PEG dosing 
must be per investigator and sponsor agreement based on an assessment of the known risks 
and potential benefits while taking BMN 165. Female subjects must return to the 
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study-required contraception use (refer to Section 9.3.1), which must include one barrier 
method, immediately after the birth (or termination of the pregnancy).  
Subjects may withdraw from treatment with study drug at any time; however, subjects will 
be asked to continue to perform the study assessments until study completion. Subjects may 
also withdraw from study participation at any time. Because the completeness of the data 
affects the integrity, accuracy, and interpretation of study results, every effort should be made 
to retain subjects in the study and to have them complete the study assessments as scheduled 
as long as continued participation does not compromise subject safety.  
A PK substudy has been added to evaluate the steady-state PK of rAvPAL-PEG in up to 
6 subjects who have achieved and maintained target blood Phe for at least 2 consecutive 
measurements and for whom no further dose modifications are planned.  Subjects enrolled 
into the substudy will have additional pre-dose PK sampling performed (refer to Table 9.1.2). 
The Schedule of Events and PK substudy collection schedules are presented below in 
Table 9.1.1 and Table 9.1.2. 
 
 
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Table 9.1.1:  Schedule of Events 
Assessments and 
 Events 
Screeninga 
Treatment Periodb,c 
 
Self-
Administration 
Study 
Completion/Early 
Term. Visit 
Unsched. Hyper. 
Reaction Visit.d  
Perform within 
24 hours 
Week 
1 
Weekly 
Telephone 
Contacts 
Monthly b 
(eg, Wk 4, 
8, etc.) 
Quarterly  
(eg, Wk 12, 
24, etc.) 
 
D 1 
Starting at 
Week 2 
Every 4th 
week; 
Every 12th 
week. 
Perform in 
addition to 
monthly 
procedures 
 
 
 
4 weeks after 
final dose 
Informed consent 
X 
 
 
 
 
 
 
 
 
 
Medical history, including allergy 
history, and demographics 
X 
 
 
 
 
 
 
 
 
 
Physical examinatione 
X 
X 
 
 
X 
 
 
 
X 
 
Vital signse 
X 
X 
 
X 
 
 
 
 
X 
X 
Weight 
X 
 
 
X 
 
 
 
 
 
 
12-lead ECG 
X 
 
 
 
 
 
 
 
X 
 
Clinical laboratory testsf 
X 
 
 
X 
 
 
 
 
X 
Xg 
Complements C3 and C4h 
X 
 
 
 
X 
 
 
 
 
Xg 
Sedimentation rate 
 
X 
 
 
X 
 
 
 
X 
 
Chest x-ray 
X 
 
 
X  
(Week 48 
visit only) 
 
 
 
 
X 
 
Urine pregnancy testi 
X 
X 
 
X 
 
 
 
 
X 
 
Adverse eventsj,k 
X 
X 
X 
X 
 
 
 
X 
X 
X 
Weekly phone call to self admin 
participants only (to assess AEs, 
Inj site reactions, concomitant 
medications) 
 
 
X 
 
 
 
 
X 
 
 
Concomitant medications 
X 
X 
 X 
X 
 
 
 
X 
X 
X 
Diet query 
X 
X 
 
X 
 
 
 
 
X 
 
3-Day diet diaryl 
 
 
 
X 
 
 
 
 
X 
 
Serum antibodiesm 
 
X 
 
 
X 
 
 
 
X 
X 
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Assessments and 
 Events 
Screeninga 
Treatment Periodb,c 
 
Self-
Administration 
Study 
Completion/Early 
Term. Visit 
Unsched. Hyper. 
Reaction Visit.d  
Perform within 
24 hours 
Week 
1 
Weekly 
Telephone 
Contacts 
Monthly b 
(eg, Wk 4, 
8, etc.) 
Quarterly  
(eg, Wk 12, 
24, etc.) 
 
D 1 
Starting at 
Week 2 
Every 4th 
week; 
Every 12th 
week. 
Perform in 
addition to 
monthly 
procedures 
 
 
 
4 weeks after 
final dose 
Plasma Phe and plasma tyrosinen  
X 
X 
 
Xm 
 
 
 
 
X 
 
Urine albumin/creatinine ratio 
 
 
 
 
 
 
 
 
 
X 
Urine N-methyl histamine 
 
 
 
 
 
 
 
 
 
X 
Plasma PK sampleo 
 
X 
 
 
X 
 
 
 
X 
 
Administer study drugp 
 
X 
 
X 
 
 
 
X 
 
 
Training (prefilled syringe)q 
 
 
 
X 
Transition 
to prefilled 
syringe 
X 
Every 24 
weeks only 
 
 
 
 
 
Skin biopsy (optional; affected 
and not affected area) 
 
 
 
 
 
 
 
 
 
X 
Serum tryptase levelr 
 
 
 
 
 
 
 
 
 
X 
AE, adverse event; C3, complement 3; C4, complement 4; CH50, total hemolytic complement; CRP, C-reactive protein; D, day; ECG, electrocardiogram; eCRF, electronic 
Case Report Form; ETV, Early Termination Visit; F/U, Follow-up; Hyper, hypersensitivity; IgE, immunoglobulin E; IgG, immunoglobulin G; IgM, immunoglobulin M; 
IP, investigational product; PK, pharmacokinetics; Phe, phenylalanine; SAE, serious adverse event; Wk, week. 
a A separate Screening visit for this study is required only if the time between completion of the previous rAvPAL-PEG study and enrollment into PAL-003 is greater than 
28 days. 
b Monthly visits must be performed in the clinic. 
c On days that a dose is given, all procedures should be performed predose, except where noted. 
d Refer to Section 9.1.1 and Section 12.3.6. 
e Complete physical examinations to include the evaluation of all major body systems. Height will be measured at Screening only. 
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f Clinical laboratory tests to include spot urine albumin/creatinine ratio, hematology, chemistry, and urinalysis. Urine microscopy will be performed if any urinalysis 
results are positive for hematuria.  Refer to Table 9.7.6.1. 
g Subjects who have a National Cancer Institute Common Terminology Criteria for Adverse Events (NCI-CTCAE) grade ≥ 3 hypersensitivity AE should be assessed for 
CRP, CH50, C1, C3, and C4 within 24 hours of the reaction.  
h Complement C3 and C4 will be collected at the Screening Visit and quarterly. Additional complement testing will be performed and as needed to resolve previous 
abnormal test results. 
i If positive or equivocal, perform serum pregnancy test. Also refer to Section 9.1. 
j If any injection site reaction is observed, the corresponding adverse event data must specify injection location (identify current vs. previous visit’s injection, eg, right arm 
vs. left arm). If there is a skin reaction that lasts ≥ 14 days, the Skin Reaction eCRF should be completed. A photograph of the skin reaction may be taken by the subject 
or the site to help assess the event and may be collected by the sponsor. 
k The reporting period for SAEs begins when informed consent is obtained and continues through 4 weeks after last dose or completion of study participation, whichever 
occurs last. The reporting period for nonserious AEs is from the first administration of study drug through 4 weeks after last dose or the Study Completion Visit/Early 
Termination Visit, whichever occurs last. The reporting period for device-related events begins with the first dose administered using prefilled syringe and ends with the 
last dose administered using prefilled syringe. 
l It is preferable that the subject complete the diary 3 days immediately prior to the next monthly visit. 
m For unscheduled hypersensitivity reaction visit, draw serum anti-rAvPAL IgE and anti-rAvPAL-PEG IgE only; sampling must be performed > 8 hours after event onset 
and before the next dose of study drug.  
n Samples should be drawn at least 2.5 hours after a meal.  At the Investigator’s discretion, blood Phe may be collected more often should more frequent monitoring of 
blood Phe levels be clinically warranted. 
o Sampling should be performed predose.  
p Dosing is up to 5.0 mg/kg/week or 375 mg/week, including subjects who receive more than 1 dose/week. Every effort should be made to adhere to the study drug 
administration regimen. If a subject misses more than 2 scheduled doses of study drug, both dose level and dose frequency may be re-evaluated.  
q Initial training on the use of prefilled syringe occurs at the next monthly visit and each subsequent day after transition until (in clinic or by HHRN) it has been 
determined the subject will switch to prefilled syringe. Once competency is documented, subjects can self-administer study drug using the prefilled syringe.  Regular 
refresher prefilled syringe training occurs in the study clinic every 24 weeks thereafter. 
r Mandatory for subjects who have a hypersensitivity AE.  Perform within 24 hours of event onset. 
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Table 9.1.2:  PK Substudy Dosing Regimens 
Treatment Frequency 
Plasma PK Sampling 
Example 
Subjects who are 
administered study drug 
once per week 
Pre-dose and every 24 hours 
thereafter (24, 48, 72, and 96 
hours when possible), and 
pre-dose of the next weekly 
dose 
If dosed on Monday: 
Obtain PK sample pre-dose when possible – pre-dose Monday, Tuesday, 
Wednesday, Thursday, Friday, and pre-dose the following Monday. 
No further PK substudy draws. 
Subjects who are 
administered study drug 
two or three times per 
week 
Pre-dose and every 24 hours 
during the longest period 
between doses, when 
possible, and pre-dose of the 
next dose. 
If dosed on Monday, Thursday, and Friday: 
Obtain PK sample every 24 hours during the longest period between doses: 
Pre-dose Monday, Tuesday, Wednesday, and pre-dose Thursday. 
No further PK substudy draws. 
Subjects who are 
administered study drug 
four to seven times per 
week. 
Pre-dose and every 12 hours 
during the longest period 
between doses, when 
possible, then pre-dose of the 
next dose. 
If dosed Monday through Friday: 
Obtain PK sample every 12 hours during the longest period between doses 
(Friday to Monday): pre-dose Friday, 12 hours post-dose Friday, Saturday 
(24 and 36 hours post dose), Sunday (48 and 60 hours post-dose), and pre-
dose the following Monday. 
No further PK substudy draws. 
 
 
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9.1.1 
Response to Hypersensitivity Adverse Events 
Subjects are evaluated for safety throughout the study and are trained to recognize potential 
hypersensitivity AEs (including anaphylaxis) and how to respond. Subjects are instructed to 
contact the investigator for any suspected hypersensitivity AE. The investigator may require 
further evaluation at the clinic. If a hypersensitivity AE (eg, injection-site reaction, rash, joint 
pain, itching) occurs, the subject may be advised to premedicate with H1 antagonist, H2 
antagonist, and non-steroidal anti-inflammatory medication (NSAIDs) approximately 
2-3 hours prior to subsequent rAvPAL-PEG doses. NSAIDs should be given with food and 
may be omitted if not tolerated.  
Hypersensitivity AEs, including anaphylaxis, are expected with rAvPAL-PEG 
administration.  rAvPAL-PEG dosing in response to a suspected hypersensitivity AE may be 
modified or halted depending on the severity of the event and suspected rAvPAL-PEG 
causality (Section 9.1.1.3). Severity for hypersensitivity AEs will be per NCI-CTCAE 
grades. 
9.1.1.1 
Individual Stopping Criteria 
Subjects who have an NCI CTCAE grade ≥ 3 hypersensitivity AE that is related to study 
drug and is suspected to meet Brown’s criteria for severe (grade 3) in the judgment of the 
investigator and the sponsor’s medical monitor may be permanently discontinued from study 
drug. 
9.1.1.2 
Dosing in Response to Hypersensitivity Adverse Events 
Dosing in response to a hypersensitivity AE depends on the NCI-CTCAE grade and 
suspected relationship to rAvPAL-PEG. Dosing instructions are presented in Table 9.1.1.2.1 
and are regardless of previous occurrence: 
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Table 9.1.1.2.1:  Dosing Instructions in Response to Hypersensitivity Adverse Events 
NCI-CTCAE 
Gradea 
Related to 
Study Drug 
Action with Study Drug 
Individual 
Stopping 
Criteria d 
HRV  
Assessmente 
Maintainb 
Reducec 
Interruptc 
1 
Yes or No 
X 
(X) 
Optional 
(X) 
Optional 
 
Investigator 
discretion 
2 
Yes or No 
X 
(X) 
Optional 
(X) 
Optional 
 
Investigator 
discretion 
3  
No 
X 
(X) 
Optional 
(X) 
Optional 
 
Investigator 
discretion 
3  
Yes 
X 
(X) 
Optional 
(X) 
Optional 
 
Yes 
3 
and is suspected to 
meet Brown’s 
criteria for severe d  
Yes 
 
 
 
X 
Consult with 
sponsor 
medical 
monitor 
Yes 
4 d 
Yes or No 
 
 
 
X 
Consult with 
sponsor 
medical 
monitor 
Yes 
AE, adverse event; CTCAE, Common Terminology Criteria for Adverse Events, version 4.03; HRV, 
Hypersensitivity Reaction Visit; NCI, National Cancer Institute. 
a NCI-CTCAE grade determination is performed by the investigator and may be done either via telephone or 
clinic visit. 
b The investigator will instruct the subject to maintain the rAvPAL-PEG dose at the time of AE onset until 
improvement to grade 1 or resolution (per investigator assessment in the clinic or via telephone). 
cThe rAvPAL-PEG dose may be reduced or interrupted if necessary per investigator determination.  
d If a subject has an NCI-CTCAE grade  ≥ 3 hypersensitivity AE that is related to study drug and is suspected to 
meet Brown’s criteria for severe (grade 3) in the judgment of the investigator and the sponsor’s medical 
monitor, the subject may be permanently discontinued from study drug.  
e If the investigator determines that the NCI-CTCAE grade  ≥ 3 hypersensitivity AE is related to administration 
with rAvPAL-PEG, the subject will be asked to return to the clinic within 24 hours of event onset for 
evaluation, including laboratory tests (chemistry, hematology, urinalysis, anti-rAvPAL IgE, 
anti-rAvPAL-PEG IgE [sampling must be performed >8 hours after event onset and before the next dose of 
study drug], urine albumin/creatinine ratio, urinary N-methyl histamine, CRP, C3, C4, and tryptase).  
 
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9.1.1.3 
Response to Anaphylaxis 
If the investigator suspects that the event is anaphylaxis, the subject will be assessed in the 
clinic. Laboratory assessments for suspected anaphylaxis events should be performed prior to 
the next administration of study drug (if applicable) and include anti-rAvPAL IgE and 
anti-rAvPAL-PEG IgE (sampling must be performed >8 hours after event onset and before 
the next dose of study drug) and tryptase (within 24 hours of event onset). The investigator 
will consult with the sponsor’s medical monitor, and a decision will then be made whether to 
discontinue the subject from study drug, restart dosing at the same dose level, or restart 
dosing at a lower dose level. 
For the first week of dosing after resolution of anaphylaxis, the study drug will be 
administered in a clinic setting with equipment for emergency resuscitation (including 
epinephrine) within easy access.  The subject must be observed for 30 minutes following 
administration due to restarting dosing. Additionally, the subject should be premedicated 
with H1 antagonist, H2 antagonist, and NSAIDs approximately 2-3 hours prior to each dose 
of study drug for one week upon return to dosing regardless of the duration of dose 
interruption. NSAIDs should be given with food and may be omitted if not tolerated.  
9.1.2 
Study Stopping Criteria 
If an NCI-CTCAE grade ≥ 3 hypersensitivity treatment-related event occurs and meets 
Brown’s criteria for severe (grade 3), an ad hoc independent DMC meeting will convene 
within 7 days of the event to review and advise the sponsor on potential changes to the study 
conduct. Clinically severe hypersensitivity is defined as significant hypoxia, hypotension or 
neurologic compromise that is life-threatening or required treatment to prevent a 
life-threatening event:  
• Cyanosis or SpO2 ≤ 92%  
• Hypotension with SBP < 90 mm Hg (adults)  
• Neurologic alteration: loss of consciousness, collapse, incontinence 
Brown’s severity criteria are presented in Table 9.1.2.1. 
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Table 9.1.2.1:  Brown’s Severity Criteria 
Brown’s Criteria for 
Hypersensitivity Reactions 
Definition 
Mild (1) 
skin and subcutaneous tissue 
Generalized erythema, urticaria, periorbital edema, or angioedema 
Moderate (2) 
features suggested respiratory, 
cardiovascular, or 
gastrointestinal involvement 
Dyspnea, stridor, wheeze, nausea, vomiting, dizziness (pre-syncope), 
diaphoresis, chest or throat tightness, or abdominal pain  
 
Severe (3) 
hypoxia or neurologic 
compromise 
Cyanosis or SpO2 ≤ 92% at any stage, hypotension (SBP < 90 mm Hg in 
adults), confusion, collapse, loss of consciousness, or incontinence  
 
 
9.1.3 
Dose Modifications 
9.1.3.1 
Dose Increase Methodology 
Each subject’s dose may be modified based on the decision of the Investigator. Decisions 
regarding dose increases will depend on a subject’s adverse event profile and blood Phe and 
drug concentrations. 
An individual subject’s dose may be adjusted beginning on Day 1 of PAL-003. For the 
duration of this study, an individual subject’s dose may be adjusted if warranted per a 
subject’s adverse event profile and blood Phe concentrations. Dose increases should be 
performed as follows: 
• The dose may be increased by increments of no more than 10-fold higher than the 
subject’s current dose. 
• When increasing the dose, a dose may be used that is between the dose levels (0.001, 
0.003, 0.01, 0.03, 0.06, 0.1, 0.2, 0.3, 0.4, 0.6, 0.8, 1.0, 2.0, 3.0, 4.0, and 5.0 mg/kg or 
2.5, 5, 10, 20, 40, 75, 150, 225, 300, 375 mg/week) or per Investigator determination 
based on available information regarding a subject’s blood Phe (60-600 µmol/L) as 
well as any adverse events for an individual subject. Dose increases  > 350 mg/week 
require consultation with the sponsor’s medical monitor. 
• The dose may be adjusted by increasing the frequency up to daily for a total weekly 
dose not to exceed 5.0 mg/kg or 375 mg/week. Dose increases  > 350 mg/week 
require consultation with the sponsor’s medical monitor. 
• When a dose is increased, the subject must be observed for 30 minutes following the 
first modified dose administration. Subjects who increase their dose frequency do not 
need to be observed following injection of study drug if the increase in frequency 
does not increase the overall weekly dose amount. 
• Only 1 dose adjustment is allowed every 2 weeks. 
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9.1.3.2 
Dose Decrease Methodology 
Decisions regarding dose decreases will depend on available information regarding a 
subject’s blood Phe (60-600 µmol/L), as well as any adverse event (any hypersensitivity 
reaction as defined in Section 9.1.1). Dose decreases may occur for hypophenylalanemia or 
any adverse event that may be improved with a lower dose. 
A dose should first be reduced by dose level (5.0, 4.0, 3.0, 2.0, 1.0, 0.8, 0.6, 0.4, 0.3, 0.2, 0.1, 
0.06, 0.03, 0.01, 0.003, 0.001 mg/kg or 375, 300, 225, 150, 75, 40, 20, 10, 5, and 2.5 
mg/week). It is also permitted to decrease dose in between these specified dose levels. If 
further dosing adjustments are required in response to safety, dosing frequency may also be 
adjusted.  
If the subject develops low blood Phe (as defined by a blood Phe level ≤ 30 µmol/L ), the 
subject’s rAvPAL-PEG dose should be decreased to the next lower dose.  If the condition 
persists after another 1 month at the lower dose, the dose should be decreased again to the 
next lower level. If the subject continues to experience low blood Phe after two dose level 
reductions, the subject may be asked to consult the dietician to eliminate medical foods 
and/or formulas and to ensure a balanced and nutritious diet (as part of the routine standard 
of care for PKU disease management, subject diet should be monitored by a dietician). 
9.2 
Discussion of Study Design, Including Choice of Control Group 
This open-label, Phase 2 trial was designed to be closely monitored with the goal of 
obtaining information about the efficacy, safety, tolerability, and PK of long-term 
administration of rAvPAL-PEG in subjects with PKU. There will be no control group in this 
study. 
9.3 
Selection of Study Population 
9.3.1 
Inclusion Criteria 
Individuals eligible to participate in this study must meet all of the following criteria: 
1. Must have completed participation in a previous rAvPAL-PEG study. 
2. Willing and able to provide written, signed informed consent, or in the case of 
subjects under the age of 18 years, provide written assent (if required) and written 
informed consent by a parent or legal guardian, after the nature of the study has been 
explained, and prior to any research-related procedures. 
3. Willing and able to comply with all study procedures. 
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4. Females of childbearing potential must have a negative pregnancy test at Screening 
and be willing to have additional pregnancy tests during the study. Females 
considered not of childbearing potential include those who have been in menopause at 
least 2 years, or had tubal ligation at least 1 year prior to Screening, or who have had 
total hysterectomy. 
5. Sexually active subjects must be willing to use two acceptable methods of 
contraception while participating in the study.  Males post vasectomy for 2 years with 
no known pregnancies do not need to use any other forms of contraception during the 
study. 
6. Maintained a stable diet. 
7. In generally good health as evidenced by physical examination, clinical laboratory 
evaluations (hematology, chemistry, and urinalysis), and electrocardiogram (ECG) at 
Screening. 
9.3.2 
Exclusion Criteria 
Individuals who meet any of the following exclusion criteria will not be eligible to participate 
in the study: 
1. Use of any investigational product (with the exception of rAvPAL-PEG) or 
investigational medical device within 30 days prior to Screening, or requirement for 
any investigational agent prior to completion of all scheduled study assessments. 
2. Use of any medication other than rAvPAL-PEG that is intended to treat PKU within 
14 days prior to the administration of study drug. 
3. Use or planned use of any injectable drugs containing PEG (other than 
rAvPAL-PEG), including Depo-Provera, within 6 months prior to Screening and 
during study participation. 
4. A prior reaction that included systemic symptoms (eg, generalized hives, respiratory 
or gastrointestinal problems, hypotension, angioedema, anaphylaxis) to rAvPAL-PEG 
or a PEG-containing product. Subjects with a prior systemic reaction may be eligible 
for participation per the discretion of the Principal Investigator in consultation with 
the sponsor’s medical monitor. However, subjects who discontinued from study drug 
early due to a reaction are not eligible to enroll into this study.      
5. Pregnant or breastfeeding at Screening or planning to become pregnant (self or 
partner) or to breastfeed at any time during the study. 
6. Concurrent disease or condition that would interfere with study participation or safety 
(eg, history or presence of clinically significant cardiovascular, pulmonary, hepatic, 
renal, hematologic, gastrointestinal, endocrine, immunologic, dermatologic, 
neurological, oncologic, or psychiatric disease). 
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7. Any condition that, in the view of the PI, places the subject at high risk of poor 
treatment compliance or of not completing the study. 
8. Known hypersensitivity to rAvPAL-PEG necessitating early termination from a 
previous rAvPAL-PEG study or known hypersensitivity to any of its excipients. 
9. Alanine aminotransferase (ALT) concentration > 2 times the upper limit of normal. 
10. Creatinine > 1.5 times the upper limit of normal. 
9.3.3 
Removal of Subjects from Treatment or Assessment 
Subjects (or their legally authorized representative) may withdraw their consent to participate 
in the study or to receive study drug at any time without prejudice. The Investigator must 
withdraw from the study or study drug treatment any subject who requests to be withdrawn. 
A subject’s participation in the study may be discontinued at any time at the discretion of the 
Investigator and in accordance with his/her clinical judgment. When possible, a subject who 
is discontinued from study drug should continue to perform the study tests and evaluations 
until study completion. For subjects who discontinue from the study, the tests and 
evaluations listed for the Early Termination Visit should be carried out (refer to 
Section 12.4). 
BioMarin must be notified of all subject withdrawals as soon as possible. BioMarin also 
reserves the right to discontinue the study at any time for either clinical or administrative 
reasons and to discontinue participation by an individual Investigator or site for poor 
enrollment or noncompliance. 
Reasons for which the Investigator or BioMarin may withdraw a subject from the study drug 
include, but are not limited to, the following: 
• Subject experiences a serious or intolerable adverse event (AE). 
• Subject develops a clinically significant laboratory abnormality. 
• Subject requires medication prohibited by the protocol. 
• Subject becomes pregnant (refer to Section 10.3 for details on the reporting 
procedures to follow in the event of pregnancy and refer to Section 9.1 for details on 
re-introduction of study drug following pregnancy and breastfeeding). 
Reasons for which the Investigator or BioMarin may withdraw a subject from the study 
include, but are not limited to, the following: 
• Subject does not adhere to study requirements specified in the protocol. 
• Subject was erroneously admitted into the study or does not meet entry criteria. 
• Subject is lost to follow-up. 
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If a subject fails to return for scheduled visits, a documented effort must be made to 
determine the reason. If the subject cannot be reached by telephone within 7 days, a certified 
letter should be sent to the subject (or the subject’s legally authorized representative, if 
appropriate) requesting contact with the Investigator. This information should be recorded in 
the study records. 
The Investigator or designee must explain to each subject, before enrollment into the study, 
that for evaluation of study results, the subject’s protected health information obtained during 
the study may be shared with the study sponsor, regulatory agencies, and IRB. It is the 
Investigator’s (or designee’s) responsibility to obtain written permission to use protected 
health information per country-specific regulations, such as the Health Insurance Portability 
and Accountability Act (HIPAA) in the United States, from each subject, or if appropriate, 
the subject’s legally authorized representative. If permission to use protected health 
information is withdrawn, it is the Investigator’s responsibility to obtain a written request, to 
ensure that no further data will be collected from the subject and the subject will be removed 
from the study. 
9.3.4 
Subject Identification and Replacement of Subjects 
Subjects will retain the same subject number assigned in their previous rAvPAL-PEG study. 
This unique identifier will be on all case report form (CRF) pages. In legal jurisdictions 
where use of initials is not permitted, a substitute identifier will be used.  
Subjects who do not complete the study will not be replaced. 
9.4 
Treatments 
Upon enrollment into this study, subjects from previous rAvPAL-PEG studies will be dosed 
with the same or higher dose that was administered upon completion of that study provided 
that there was no interruption in dosing.  rAvPAL-PEG doses will be administered SC by 
either health care professionals or via self-administration. The dose level may be adjusted per 
Investigator determination based on available information regarding a subject’s blood Phe 
level (60-600 µmol/L), as well as any adverse events (any hypersensitivity reaction) for an 
individual subject. The dosage that provides control of blood Phe concentrations within the 
target range of 60-600 µmol/L for a minimum of 2 weeks will be determined for each subject 
by adjusting the dose level, dose frequency, or both, per the PI, based upon the subject’s 
response to doses.  
Subjects may self-administer study drug at home if approved by the Investigator and the 
sponsor’s medical monitor and if adequate training is demonstrated. Subjects may be eligible 
to self-administer study drug if he or she meets the following criteria:  
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• The subject has no cognitive impairments that may increase the safety risk of 
self-administration per the assessment of the investigator.  
• The subject has been approved for self-administration of study drug by the sponsor’s 
medical monitor. 
• The subject has completed the Self-Administration Training conducted by qualified 
study site personnel and has been observed by the study site personnel to be able to 
adequately prepare the proper dose and perform the injections safely.  
• The subject has been provided with two epinephrine injectors and has been trained on 
when and how to administer it. The subject will be instructed to carry one epinephrine 
injector with them at all times. 
Qualified study site personnel will train each eligible subject on all procedures for 
self-administration of study drug (vial and syringe and prefilled syringe drug products) under 
the supervision of the PI. Qualified study site personnel will also be required to observe the 
subject prepare and perform at least 1 injection prior to allowing the subject to 
self-administer a dose at home. The subject will see a study site nurse or home healthcare 
nurse in person every week or receive a telephone call from site staff to ensure that the 
subject continues to perform all self-administration procedures correctly, to assess adverse 
events, and to answer questions throughout the duration of the study. The study site nurse or 
home healthcare nurse will also perform the regularly scheduled assessments and procedures 
as outlined in Table 9.1.1 and Section 12; the subject must perform a clinic visit monthly at 
minimum. Training materials and other information specific to the study site personnel are 
provided in the Subject Self-Administration Training Materials. Prefilled syringes are 
dispensed to subjects only after the subject (or caregiver) has completed training and 
competency is demonstrated in the clinic.  Additional regular refresher training occurs in the 
clinic, every 24 weeks, and more often as needed.  
Subjects who are eligible for self-administration will be provided with a Subject Study 
Manual. Self-administration training materials will be provided in the Subject Study Manual 
to supplement the in-person training provided by the qualified study site personnel. The 
Subject Study Manual will include step-by-step instruction on the following: 
• How to prepare and perform the injections of study drug safely. 
• How to receive, track, store, prepare, and return both used and unused study drug.   
• How to safely use and dispose of syringes, including prefilled syringes, used for 
injections of study drug. 
• How to use a new syringe and vial or new prefilled syringe every time drug is 
administered. 
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• How to care for their injection site after an injection of study drug.  
• How to identify an adverse reaction and how to report this reaction to the study site.  
• How and when to use epinephrine injectors. 
• Who to contact at the study site in case of an emergency.  
The PI or the sponsor’s medical monitor may request that self-administration be halted at any 
time and that the subject resume injections performed by the study site personnel or home 
healthcare nurse. 
Subjects who are within the target Phe range may also be permitted to convert from 
weight-based dosing to fixed dosing (refer to Section 9.4.4). 
9.4.1 
Treatments Administered 
BioMarin and/or its designee will provide the study site or subject with a supply of IP 
sufficient for the completion of the study. BioMarin is responsible for shipping study drug to 
the clinical sites. The clinical site is responsible for supplying the study drug to subjects who 
qualify for self-administration. Refer to the PAL-003 Pharmacy Manual for information 
pertaining to the distribution of study drug from sites.  
Information regarding supplying study drug to subjects who qualify for self-administration is 
provided in the Subject Self-Administration Training Materials. 
9.4.2 
Identity of Investigational Product (IP) 
9.4.2.1 
Product Characteristics and Labeling 
The investigational product is rAvPAL-PEG (recombinant Anabaena variabilis phenylalanine 
ammonia lyase-PEG). rAvPAL-PEG will be provided in vials or prefilled syringes; subjects 
will be supplied with vials and syringes or prefilled syringes for administration in the clinic 
and self-administration: 
• rAvPAL-PEG will be provided in 3 mL (milliliter) vials, each containing 1.5 ± 0.2 mL 
to deliver 15 mg of rAvPAL-PEG per 1.0 mL (15 mg/mL protein concentration). 
Each vial is filled with 1.5 ± 0.2 mL to allow the withdrawal and delivery of up to 
1.0 mL of the drug product. 
Or 
• rAvPAL-PEG will be provided in 3-mL vials, each containing 1.8 ± 0.3 mL to deliver 
20 mg of rAvPAL-PEG per 1.3 mL (15 mg/mL protein concentration). Each vial is 
filled with 1.8 ± 0.3 mL to allow withdrawal and delivery of up to 1.3 mL. 
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Or 
 
• rAvPAL-PEG will be provided in prefilled syringes in three sizes that deliver up to 
1 mL. Syringe sizes are 2.5 mg (5 mg/mL protein concentration), 10 mg (20 mg/mL 
protein concentration), and 20 mg (20 mg/mL protein concentration). 
Table 9.4.2.1.1:  Prefilled Syringe Volume, Concentration, and Dose 
Prefilled Syringe 
Volume 
Concentration 
Dose 
Sku #1 
0.5 mL 
5 mg/mL 
2.5 mg 
Sku #2 
0.5 mL 
20 mg/mL 
10 mg 
Sku #3 
1.0 mL 
20 mg/mL 
20 mg 
 
Subjects who have undergone training and who have demonstrated competency on the use of 
prefilled syringe in the study clinic may be eligible to transition from vial and syringe to 
prefilled syringe dosing. Additionally, regular refresher training on use of prefilled syringe 
will be provided in study clinic every 24 weeks, and more often as needed.  
Subjects should convert their vial and syringe dose to prefilled syringe dose using the 
following table: 
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Table 9.4.2.1.2:  Conversion from Vial and Syringe Dose to Prefilled Syringe Dose 
Daily Dose (mg)  
Range 
Daily Dose (mg)  
Round Toa 
# of 2.5mg 
Prefilled Syringe 
Needed 
# of 10mg 
Prefilled Syringe 
Needed 
# of 20mg 
Prefilled Syringe 
Needed 
0 – 3.7 
2.5 
1 
0 
0 
3.8 – 6.2 
5 
2 
-- 
-- 
6.3 – 8.7 
7.5 
3 
-- 
-- 
8.8 – 11.2 
10 
-- 
1 
-- 
11.3 – 13.7 
12.5 
1 
1 
-- 
13.8 – 16.2 
15 
2 
1 
-- 
16.3 – 18.7 
17.5 
3 
1 
-- 
18.8 – 21.2 
20 
-- 
-- 
1 
21.3 – 23.7 
22.5 
1 
-- 
1 
23.8 – 26.2 
25 
2 
-- 
1 
26.3 – 28.7 
27.5 
3 
-- 
1 
28.8 – 31.2 
30 
-- 
1 
1 
31.3 – 33.7 
32.5 
1 
1 
1 
33.8 – 36.2 
35 
2 
1 
1 
36.3 – 38.7 
37.5 
3 
1 
1 
38.8 – 41.2 
40 
-- 
-- 
2 
41.3 – 44.9 
42.5 
1 
-- 
2 
45 – 54.9 
50 
-- 
1 
2 
55 – 64.9 
60 
-- 
-- 
3 
65 – 74.9 
70 
-- 
1 
3 
75 – 84.9 
80 
-- 
-- 
4 
85 – 94.9 
90 
-- 
1 
4 
95 – 104.9 
100 
-- 
-- 
5 
105 – 114.9 
110 
-- 
1 
5 
115 – 124.9 
120 
-- 
-- 
6 
125 – 134.9 
130 
-- 
1 
6 
135 – 144.9 
140 
-- 
-- 
7 
145 – 154.9 
150 
-- 
1 
7 
a For  < 45 mg/day, round to nearest 2.5 mg; for  ≥ 45 mg/day, round to nearest 10 mg. 
 
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The excipients in this drug product wre tromethamine, tromethamine-hydrochloride, sodium 
chloride, L-phenylalanine, and water for injection. 
rAvPAL PEG doses will be administered SC by either health care professionals or via 
self-administration. The dose level may be increased or decreased per Investigator 
determination based on available information regarding a subject’s blood Phe level 
(60 600 µmol/L), as well as any adverse events (any hypersensitivity AE) for an individual 
subject. The dosage that provides control of blood Phe concentrations within the target range 
of 60-600 µmol/L for a minimum of 2 consecutive measurements will be determined for each 
subject by adjusting the dose level, dose frequency, or both, per the PI, based upon the 
subject’s response to doses. 
For vial and syringe, drug product packaging will be identified with the lot number and 
expiration date and will be provided in a box labeled with the study number. 
For prefilled syringe, drug product packaging will be identified with the size (2.5 mg, 10 mg, 
or 20 mg), lot number, and kit identification (ID). The expiration date will be available in a 
separate Certificate of Compliance issued for each lot. 
9.4.3 
Storage 
IP must be stored at 5 ± 3°C (41 ± 5°F) under the conditions specified in the IB. At the site, 
the IP will be stored in a secure area accessible only to the designated pharmacists and 
clinical site personnel. All IP must be stored and inventoried and the inventories must be 
carefully and accurately documented according to applicable state, federal and local 
regulations, ICH GCP, and study procedures. 
Specific instructions for storage of study drug for subjects who qualify for self-administration 
are provided in the Subject Self-Administration Training Materials.  
9.4.4 
Directions for Administration 
Doses will be administered SC and the favorable dose will be determined for each subject by 
adjusting the dose level, dose frequency, or both, per the PI, based upon the subject’s 
response to doses. Dosing is up to a maximum dose per week of 5.0 mg/kg (or 375 mg for 
subjects receiving a fixed dose).  
For subjects receiving weight-based dosing, dosage is calculated by multiplying each 
subject’s weight in kilograms (kg) on Day 1 (predose) by the assigned dose (in mg/kg). 
During the study, if the weight of a subject changes more than 10% from the measurement 
obtained at baseline or at a previous measurement, the subject’s dose may be adjusted to 
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accommodate the change. The change must be recorded. Refer to the Pharmacy Manual for 
additional information on calculating dosage. 
Subjects who have demonstrated efficacy (as measured by blood Phe within the target range 
of 60-600 µmol/L for at least 2 consecutive measurements) and who have maintained a stable 
rAvPAL-PEG dose for at least 2 consecutive measurements may be eligible to transition 
from weight-based dosing to a fixed dosing regimen that would permit daily dosing (5- or 
7-days-per-week).  Subjects who convert to a fixed-dosing regimen should convert their dose 
based upon the information presented in Table 9.4.4.1. 
Table 9.4.4.1:  Fixed Doses for Subjects on Weight-Based Dose Regimen 
Weight-based dose (mg/kg) 
Equivalent fixed dose 
(mg) 
Vol for 15 mg/ml 
concentration (ml) (vial)a 
0.03 
2.5 
0.17 
0.06 
5 
0.33 
0.12 
10 
0.67 
0.25 
20 
1.33 
0.5 
40 
2.67 
1.0 
75 
5 
2.0 
150 
10 
3.0 
225 
15 
4.0 
300 
20 
5.0 
375 
25 
a Applies to both 1.0 and 1.3 ml withdrawal. 
It is preferable that the injection sites should be alternated between doses, ie, upper left arm 
in Week 1, upper right arm in Week 2, etc. Doses may be administered in any of the common 
SC areas (upper arm, thigh, abdomen). If dose volume is such that a dose will be divided and 
given in more than 1 injection site, it is preferable to use both arms, both legs, or both sides 
of the abdomen. 
Subjects may require more than 1 injection per dose, depending upon site policy (ie, some 
institutions do not permit a single SC injection of greater than 2 mL).  Dosage calculations 
must be performed according to study drug preparation instructions provided in the PAL-003 
Pharmacy Manual. Study drug will be administered by clinic staff, other qualified and trained 
study personnel, or qualified subjects. 
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Information for dosing of subjects who enroll into this study after completing previous 
rAvPAL studies is provided in Section 9.1. Instructions for subjects who re-start 
rAvPAL-PEG dosing due to unplanned missed doses are provided in Section 9.4.10.  
Instructions for administration of study drug for subjects who qualify for self-administration 
are provided in the Subject Self-Administration Training Materials. 
9.4.5 
Method of Assigning Subjects to Treatment Groups 
This will be an open-label study; no randomization schedule will be generated. 
Subjects will retain the same subject number used in their previous rAvPAL-PEG study. 
9.4.6 
Selection of Doses Used in the Study 
This Phase 2 study aims to evaluate the efficacy, safety, tolerability, and PK parameters of 
multiple doses of rAvPAL-PEG after long-term administration in subjects with PKU. A dose 
that produces a reduction in blood Phe concentrations to 60-600 μmol/L will be determined 
for each subject based on preliminary safety, antibody, and efficacy data from this ongoing 
study. 
9.4.6.1 
Selection of Timing of Dose for Each Subject 
Study drug will be administered by clinic staff or other qualified and trained study personnel. 
Subjects may self-administer study drug at home if approved by the sponsor’s medical 
monitor and if adequate training is provided (refer to Section 9.4). 
9.4.7 
Blinding 
This is an open-label study. 
9.4.8 
Prior and Concomitant Medications 
All prescription and over-the-counter (OTC) medications taken by a subject for 30 days 
before Screening will be recorded on the designated CRF. The Investigator may prescribe 
additional medications during the study, as long as the prescribed medication is not 
prohibited by the protocol. In the event of an emergency, any needed medications may be 
prescribed without prior approval, but the sponsor’s medical monitor must be notified of the 
use of any contraindicated medications immediately thereafter. Any concomitant medications 
added or discontinued during the study should be recorded on the CRF. 
Use of any investigational product (with the exception of rAvPAL-PEG used in a previous 
rAvPAL-PEG study) or investigational medical device within 30 days before Screening, or 
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requirement for any investigational agent prior to completion of all scheduled study 
assessments, is prohibited. 
Use or planned use of any injectable drugs containing PEG (other than rAvPAL-PEG), 
including Depo-Provera, is prohibited within 6 months prior to Screening and during study 
participation. A list of PEG-containing injectable drugs is provided in the study reference 
materials. Subjects who have had a prior hypersensitivity AE to rAvPAL-PEG or a 
PEG-containing product will be encouraged to be premedicate as outlined in Section 9.1.1. If 
the hypersensitivity AE worsens with a repeat injection (as determined by the Investigator in 
consultation with the sponsor’s medical monitor) even with premedication prior to study drug 
dosing, the subject must be withdrawn from the study and complete an Early Termination 
Visit. 
Subjects who have had a prior hypersensitivity AE to rAvPAL-PEG or a PEG-containing 
product may participate in this study (refer to Section 9.3.2).  
Use of any medication that is intended to treat PKU within 14 days prior to the 
administration of study drug is prohibited. 
9.4.9 
Treatment Compliance 
The date, time, volume, and concentration of each dose of study drug administered to each 
subject must be recorded in the dispensing log provided for the study, as well as on the 
appropriate CRF. This data will be used to assess treatment compliance. 
9.4.10 
Dose Interruption and Missed Doses  
Information for dosing of subjects who enroll into this study after completing previous 
rAvPAL-PEG studies is provided in Section 9.1.  
During this long-term extension study, interruption of rAvPAL-PEG dosing may occur per 
subject decision or per the Investigator. After a dosing interruption of ≥ four consecutive 
doses, rAvPAL-PEG administration should be re-started at the same dose level and dosing 
frequency that was administered prior to the dosing interruption. The first week of dosing of 
rAvPAL-PEG following a dose interruption should be administered in a clinic setting, and 
the subject must be observed for 30 minutes following administration due to restarting 
dosing. Premedication with H1 antagonist, H2 antagonist, and non-steroidal anti-
inflammatory medication (NSAIDs) approximately 2-3 hours prior to study drug should be 
administered following any dose interruption of ≥ four consecutive doses. NSAIDs should be 
given with food and may be omitted if not tolerated. A follow-up telephone call will be made 
to the subject to monitor subject safety 24 hours following the return to dosing. Subjects 
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should continue to perform the study assessments as outlined in the Schedule of Events (refer 
to Table 9.1.1) during any dosing interruption.  
Subjects who miss rAvPAL-PEG dosing due to poor compliance may be discontinued from 
further study drug per discretion of the Sponsor or Investigator (refer to Section 9.3.3).  
9.5 
Investigational Product Accountability 
The PI or designee is responsible for maintaining accurate records (including dates and 
quantities) of IP received, subjects to whom IP is dispensed (subject-by-subject dose specific 
accounting), IP returned, and IP lost or accidentally or deliberately destroyed. The PI or 
designee must retain all unused or expired study supplies until the study monitor (on-site 
CRA) has confirmed the accountability data. 
9.5.1 
Return and Disposition of Clinical Supplies 
Unused study drug must be kept in a secure location for accountability and reconciliation by 
the study monitor. The Investigator or designee must provide an explanation for any 
destroyed or missing study drug or study materials. 
Unused study drug may be destroyed on site, per the site’s standard operating procedures, but 
only after BioMarin has granted approval for drug destruction. The monitor must account for 
all study drug in a formal reconciliation process prior to study drug destruction. All study 
drug destroyed on site must be documented. Documentation must be provided to BioMarin 
and retained in the PIs study files. If a site is unable to destroy study drug appropriately, the 
site can return unused study drug to BioMarin upon request. The return of study drug or 
study drug materials must be accounted for on a Study Drug Return Form provided by 
BioMarin. 
Subjects who qualify for self-administration of study drug will be provided with instructions 
for returning used and unused study drug and the proper disposal of any study drug materials 
(refer to the Subject Self-Administration Training Materials). 
All study drug and related materials should be stored, inventoried, reconciled, and destroyed 
or returned according to applicable state and federal regulations and study procedures. 
9.6 
Dietary or Other Protocol Restrictions 
Subjects will be instructed that diet should not be altered during the course of the study. Any 
decision to modify subject diet must be made per the Investigator and must be performed 
under the supervision of the Investigator. 
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A 3-day dietary record will be completed by subjects and will be brought to clinic visits for 
review with clinic staff. It is preferable that subjects complete the 3-day record immediately 
prior to their next monthly study visit.  The dietary record will be maintained with the study 
source documents. Information regarding a subject diet diary is provided in Section 9.7.4. 
9.7 
Efficacy and Safety Variables 
9.7.1 
Efficacy and Safety Measurements Assessed 
The Schedules of Events in the Synopsis describe the timing of required evaluations. 
For the laboratory assessments, the party responsible for performing the assessment and the 
pertinent protocol section describing the details of the test are listed in Table 9.7.1.1. 
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Table 9.7.1.1:  Summary of Laboratory Assessments 
Laboratory Assessment 
Party Responsible for 
Performing Test 
Section in Protocol for 
Details 
Clinical laboratory tests 
Central laboratory 
9.7.6 
Antibody testing 
BioMarina or CRO 
9.7.5.2 
PK variables 
BioMarin 
9.7.3 
Blood Phe concentrations 
Central laboratory 
9.7.2.1 
Pregnancy test (urine) and 
sedimentation rate 
Local laboratory 
9.7.6,  
9.7.5.1 
Urinalysis 
Central laboratory 
9.7.6 
Phe, phenylalanine; PK, pharmacokinetic. 
aAnalysis of the anti-rAvPAL IgE and anti-rAvPAL-PEG IgE assay will be performed by a Contract Research 
Organization. 
 
9.7.1.1 
Demographic Data and Medical History 
Demographic data and a detailed medical history, including allergy history, will be obtained 
at Screening. The medical history will include specific information concerning any prior or 
existing medical conditions that might interfere with study participation or safety. 
This medical history should elicit all major illnesses, diagnoses, and surgeries that the subject 
has ever had, and whether the subject has a history of alcohol and/or drug abuse. 
9.7.1.2 
Physical Examination Findings 
Physical examination will include assessment of general appearance; CV; dermatologic; 
head, eyes, ears, nose, and throat; lymphatic; respiratory; GI; musculoskeletal; and 
neurological/psychological. Other body systems may be examined. Day 1 results will be the 
baseline values and clinically significant changes from baseline will be recorded as an AE. 
9.7.1.3 
Vital Sign Measurements 
Vital signs will be measured after resting for 5 minutes, and include seated systolic blood 
pressure (SBP) and diastolic blood pressure (DBP) measured in millimeters of mercury 
(mm Hg), heart rate in beats per minute, respiration rate in breaths per minute, and 
temperature in degrees Celsius (°C). Height (cm) will be measured at Screening only.  
Weight will be measured at Screening and then monthly. 
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9.7.1.4 
Electrocardiography 
A standard 12-lead ECG will be recorded while the subject is resting, at Screening and at the 
Final Follow-Up (F/U) Visit or Early Termination Visit (ETV). If clinically significant 
abnormalities are noted at Screening, the PI or designee is required to assess whether it is 
appropriate for the subject to enroll in the study. 
9.7.1.5 
Chest X-Ray 
A chest X-ray will be performed at the Screening, Week 48, and Final Follow-Up (or Early 
Termination) visits to assess gross pulmonary health.  
9.7.2 
Efficacy Variable 
9.7.2.1 
Blood Phenylalanine Concentrations 
Blood samples for Phe concentration measurements will be drawn monthly, at least 2.5 hours 
after a meal, on the days and time points indicated in the Schedule of Events (Table 9.1.1).  
Blood Phe may be collected more often than monthly at the discretion of the Investigator 
should more frequent monitoring of blood Phe levels be clinically required. 
A central laboratory will be used for blood Phe concentration analysis. 
9.7.3 
Pharmacokinetic Variables 
Subjects enrolled in the Substudy will have additional PK sampling performed. For subjects 
participating in the Substudy, PK sampling will be performed as follows: 
• For subjects who are administered rAvPAL-PEG once per week, plasma PK sampling 
will be performed pre-dose and every 24 hours thereafter (24, 48, 72, and 96 hours if 
possible), and then pre-dose of the next weekly dose. 
• For subjects who are administered rAvPAL-PEG two or three times per week, plasma 
PK sampling will be performed pre-dose and every 24 hours during the longest period 
between doses, when possible, and then pre-dose of the next dose.  
• For subjects who are administered rAvPAL-PEG four to seven times per week, 
plasma PK sampling will be performed pre-dose and every 12 hours during the 
longest period between doses, when possible, and then pre-dose of the next dose. 
See Table 9.1.2 for additional details. 
BioMarin will perform the analysis. 
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9.7.4 
Exploratory Efficacy Variable 
Diet will be assessed for its role in blood Phe reduction relative to rAvPAL-PEG dosing 
using a 3-day diet diary, which will be given to subjects to complete at home. Subjects will 
bring the completed diary with them to clinic visits on a monthly basis. Subjects will be 
instructed to record all food, beverages, special low-protein foods, and medical foods 
consumed for 3 consecutive days each month. If changes in diet are noted per the information 
on the diet diary, the subject will be instructed to maintain their diet as reported at the 
beginning of the study or as otherwise instructed by the Investigator. 
9.7.5 
Safety Variables 
9.7.5.1 
Pregnancy Testing 
Female subjects of childbearing potential will have a urine pregnancy test at the time points 
specified in the Schedules of Events (Table 9.1.1). Female subjects with a positive serum 
pregnancy test at Screening do not meet eligibility criteria for enrollment. 
Additional pregnancy tests will be performed at any visit in which pregnancy status is in 
question. Serum pregnancy tests will be performed in the event of a positive or equivocal 
urine pregnancy test result. 
Refer to Section 10.3 for details on the reporting procedures to follow in the event of 
pregnancy. 
9.7.5.2 
Antibody Testing 
Immunogenicity will be assessed by determining immune response and neutralizing activity 
with the following measurements: anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, anti-PEG 
IgM, anti-rAvPAL IgE, anti-rAvPAL-PEG IgE, and anti-rAvPAL-PEG neutralizing 
antibodies (refer to Section 9.1.1). Immunogenicity assays will be performed at the time 
points indicated in the Schedule of Events (Table 9.1.1). 
BioMarin or CRO will perform all anti-body testing, except for IgE antibodies, which will be 
assessed by a Contract Research Organization. 
9.7.6 
Clinical Laboratory Assessments 
Any abnormal test results determined to be clinically significant by the Investigator should 
be repeated (at the Investigator’s discretion) until the cause of the abnormality is determined, 
the value returns to baseline or to within normal limits, or the Investigator determines that the 
abnormal value is no longer clinically significant. 
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All abnormal clinical laboratory result pages should be initialed and dated by an Investigator, 
along with a comment regarding whether or not the abnormal result is clinically significant. 
The diagnosis, if known, associated with abnormalities in clinical laboratory tests that are 
considered clinically significant by the Investigator will be recorded on the AE CRF. 
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Table 9.7.6.1:  Clinical Laboratory Tests 
Blood Chemistry 
Hematology 
Urine Testsa 
Other 
Albumin  
Hemoglobin  
Appearance 
Pregnancy test, if 
applicablea 
Alkaline Phosphatase  
Hematocrit  
Color 
ALT (SGPT)  
WBC count 
pH 
Phenylalanine 
AST (SGOT) 
RBC count 
Specific gravity 
Tyrosine 
Total bilirubin 
Platelet count 
Ketones 
Sedimentation ratea 
BUN 
Differential cell count 
Protein 
Creatinine 
 
Glucose 
GGT 
 
Spot urine 
albumin/creatinine 
ratio  
Additional Unscheduled 
Hypersensitivity Reaction 
Visit Testsb 
Total protein 
 
Nitrite 
CH50 
Calcium 
 
Urobilinogen 
C1, C3, C4 
Sodium 
 
Hemoglobin 
Serum tryptase levelb  
Potassium 
 
Bilirubin 
CRP  
Glucose 
 
 
Urine N-methyl histamine 
 
 
Urine albumin/creatinine 
ratio 
Uric acid 
 
 
Complement Testingc 
CO2 
 
 
C3 
Chloride 
 
 
C4 
ALT, alanine aminotransferase; AST, aspartate aminotransferase; BUN, blood urea nitrogen; C, complement; 
CH50, total hemolytic complement; CO2, carbon dioxide; CRP, C-reactive protein; GGT, 
gamma-glutamyltransferase; RBC, red blood cell; SGOT, serum glutamic-oxaloacetic transaminase; SGPT, 
serum glutamic-pyruvic transaminase; WBC, white blood cell. 
a To be performed by central laboratory. If urine pregnancy test is positive or equivocal, serum sample will be 
taken and assessed by a central laboratory. 
b Perform within 24 hours of event onset. 
c Complement C3 and C4 to be drawn at the Screening Visit and then quarterly or as needed to resolve abnormal 
test results. 
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10 
REPORTING ADVERSE EVENTS 
10.1 
Adverse Events 
For this protocol, a reportable adverse event (AE) is any untoward medical occurrence 
(e.g., sign, symptom, illness, disease or injury) in a subject administered the study-drug or 
other protocol-imposed intervention, regardless of attribution. This includes the following: 
• AEs not previously observed in the subject that emerge during the course of the 
study. 
• Pre-existing medical conditions judged by the Investigator to have worsened in 
severity or frequency or changed in character during the study. 
• Complications that occur as a result of non-drug protocol-imposed interventions 
(eg, AEs related to screening procedures, medication washout, or no-treatment 
run-in). 
An adverse drug reaction is any AE for which there is a reasonable possibility that the study 
drug caused the AE. “Reasonable possibility” means there is evidence to suggest a causal 
relationship between the study-drug and the AE. 
Whenever possible, it is preferable to record a diagnosis as the AE term rather than a series 
of terms relating to a diagnosis. 
The study AE reporting period is as follows: After informed consent but prior to initiation of 
study drug, only SAEs associated with any protocol-imposed interventions will be reported.  
After informed consent is obtained and the first administration of study drug, all non-serious 
AEs and SAEs reporting period begins and continues until 4 weeks following the last 
administration of study drug or the Study Completion Visit/Early Termination Visit, 
whichever occurs last (refer to Section 12). The criteria for determining, and the reporting of 
SAEs is provided in Section 10.2.  
For this study, a medical device is defined as the prefilled syringe and all of the component 
parts. The reporting period for device-related events begins with the first dose administered 
using prefilled syringe and ends with the last dose administered using prefilled syringe. 
Events assessed by the investigator as related to the device, including malfunction, injury, or 
medication error, will be captured into an electronic data capture system. All serious events 
related to the device will be reported to BioMarin Pharmacovigilance (BPV) within 24 hours 
using the device-related event report form and entered onto the appropriate eCRF page(s) as 
required.  
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The Investigator should follow all unresolved AEs until the events are resolved or stabilized, 
the subject is lost to follow-up, or it has been determined that the study drug or study 
participation is not the cause of the AE. Outcome of AEs (and resolution dates) should be 
documented on the appropriate CRF page(s) and in the subject’s medical record unless the 
subject is lost to follow-up or it has been determined that the study drug or study 
participation is not the cause of the AE. 
The Investigator responsible for the care of the subject or qualified designee will assess AEs 
for severity, relationship to study-drug, and seriousness (see Section 10.2 for SAE 
definition). Severity (as in mild, moderate or severe headache) is not equivalent to 
seriousness, which is based on subject/event outcome or action criteria usually associated 
with events that pose a threat to a subject’s life or functioning. Seriousness (not severity) 
serves as a guide for defining regulatory reporting obligations. 
The Investigator will determine the severity of each AE using the National Cancer Institute 
(NCI) Common Terminology Criteria for Adverse Events (CTCAE) v4. Adverse events that 
do not have a corresponding CTCAE term will be assessed according to the general 
guidelines for grading used in the CTCAE v4 as stated below. 
Grade 
Description 
1 
Mild: asymptomatic or mild symptoms; clinical or diagnostic 
observations only; intervention not indicated 
2 
Moderate: minimal, local or noninvasive intervention indicated; limiting 
age-appropriate instrumental activities of daily living (ADL)a 
3 
Severe or medically significant but not immediately life-threatening: 
hospitalization or prolongation of hospitalization indicated; disabling; 
limiting self care activities of daily living (ADL)b 
4 
Life threatening or debilitating: consequences; urgent intervention 
indicated 
5 
Death related to AE 
Grade 4 and 5 AEs should always be reported as SAEs. 
a Instrumental ADL refer to the following examples: preparing meals, shopping for groceries or clothes, using 
the telephone, managing money. 
b Self care ADL refer to the following examples: bathing, dressing and undressing, feeding oneself, using the 
toilet, taking medications, not bedridden. 
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The Investigator will determine the relationship of an AE to the study drug and will record it 
on the source documents and AE CRF, using the categories defined below. 
Relationship 
Description 
Not Related 
Exposure to the IP has not occurred 
OR 
The administration of the IP and the occurrence of the AE are not reasonably related 
in time  
OR 
The AE is considered likely to be related to an etiology other than the use of the IP; 
that is, there are no facts [evidence] or arguments to suggest a causal relationship to 
the IP. 
Possibly 
Related 
The administration of the IP and the occurrence of the AE are reasonably related in 
time 
AND 
The AE could be explained equally well by factors or causes other than exposure to 
the IP. 
Probably 
Related 
The administration of IP and the occurrence of the AE are reasonably related in time  
AND 
The AE is more likely explained by exposure to the IP than by other factors or 
causes. 
In order to classify AEs and diseases, preferred terms will be assigned by the sponsor to the original terms 
entered on the CRF, using MedDRA (Medical Dictionary for Regulatory Activities terminology). 
 
10.2 
Serious Adverse Events 
A serious adverse event (SAE) is any untoward medical occurrence that at any dose meets 
1 or more of the following criteria: 
• Is fatal. 
• Is life threatening. 
o 
Note: Life-threatening refers to an event that places the subject at immediate 
risk of death. This definition does not include a reaction that, had it occurred 
in a more severe form, might have caused death. 
• Requires or prolongs inpatient hospitalization. 
• Results in persistent or significant disability or incapacity. 
• Is a congenital anomaly or birth defect in the child or fetus of a subject exposed to IP 
prior to conception or during pregnancy. 
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• Important medical events or reactions that may not be immediately life-threatening or 
result in death or hospitalization but may jeopardize the subject or may require 
intervention to prevent one of the other outcomes above should also usually be 
considered serious. 
For this protocol, anaphylaxis per NIAID/FAAN criteria for the clinical diagnosis of 
anaphylaxis is designated as an AE of special interest (serious or nonserious and irrespective 
of severity) to facilitate rapid reporting and sponsor review. All occurrences of anaphylaxis 
per NIAID/FAAN criteria will be reported to the sponsor within 24 hours of the site 
becoming aware of the event using the SAE form. Severity and serious criteria (if applicable) 
should be reported on the SAE form. 
The reporting period for SAEs related to protocol imposed interventions begins after 
informed consent is obtained, the reporting period for all SAEs begins after first dose of 
study drug and continues until 4 weeks following the last administration of study drug or End 
of Treatment Visit. The reporting period for Serious Device Related Events begins after first 
dose of study drug and ends with the last administered dose. 
All SAEs (including serious device-related events), whether or not considered related to 
study drug, must be reported within 24 hours of the site becoming aware of the event by 
faxing the study-specific SAE Report Form or device Report Form to BioMarin 
Pharmacovigilance (BPV). Each SAE must also be reported in the CRF Investigators should 
not wait to collect information that fully documents the event before notifying BPV of a 
SAE. BioMarin may be required to report certain SAEs to regulatory authorities within 
7 calendar days of being notified about the event; therefore, it is important that Investigators 
submit any information requested by BioMarin as soon as it becomes available.  The 
Investigator should follow all unresolved SAEs until the events are resolved or stabilized, the 
subject is lost to follow-up, or it has been determined that the study drug or participation is 
not the cause of the AE. Resolution of AEs (with dates) should be documented in the CRF 
and in the subject’s medical record. 
For some SAEs, the Sponsor may follow up by telephone, fax, electronic mail, and/or a 
monitoring visit to obtain additional case details deemed necessary to appropriately evaluate 
the SAE report (e.g., hospital discharge summary, consultant report, or autopsy report). 
At the last scheduled visit, the Investigator should instruct each subject to report any 
subsequent SAEs that the subject’s personal physician(s) believes might be related to prior 
study drug. 
The Investigator should notify the study Sponsor of any death or SAE occurring at any time 
after a subject has discontinued or terminated study participation if felt to be related to prior 
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study drug. The Sponsor should also be notified if the Investigator should become aware of 
the development of cancer or of a congenital anomaly in a subsequently conceived offspring 
of a subject that participated in this study.  
Reporting of SAEs to the IRB will be done in compliance with the standard operating 
procedures and policies of the IRB and with applicable regulatory requirements. Adequate 
documentation must be obtained by BioMarin showing that the IRB was properly and 
promptly notified as required. 
10.3 
Pregnancy 
Pregnancy in a subject or partner should be reported within 24 hours of the site becoming 
aware of the pregnancy to BioMarin Pharmacovigilance by fax using the Pregnancy Form in 
the study reference materials. The reporting period for pregnancies begins with informed 
consent and continues until 4 weeks following the last study drug dose. In addition, 
pregnancy in a subject is also reported on the End of Study CRF if the subject withdraws 
from the study due to pregnancy. The Investigator must make every effort to follow the 
subject through resolution of the pregnancy (delivery or termination) and to report the 
resolution to BPV in the study reference materials. In the event of pregnancy in the partner of 
a study subject, the Investigator should make every reasonable attempt to obtain the woman’s 
consent for release of protected health information. 
10.4 
Urgent Safety Measures 
The regulations governing clinical trials state that the sponsor and Investigator are required to 
take appropriate urgent safety measures to protect subjects against any immediate hazards 
that may affect the safety of subjects, and that the appropriate regulatory bodies should be 
notified according to their respective regulations. According to the European Union (EU) 
Clinical Trial Directive 2001/20/EC, “…in the light of the circumstances, notably the 
occurrence of any new event relating to the conduct of the trial or the development of the 
investigational medicinal product where that new event is likely to affect the safety of the 
subjects, the sponsor and the Investigator shall take appropriate urgent safety measures to 
protect the subjects against any immediate hazard. The sponsor shall forthwith inform the 
competent authorities of those new events and the measures taken and shall ensure that the 
IRB/EC/REB is notified at the same time.” The reporting period for these events which may 
require the implementation of urgent safety measures is the period from the time of signing 
of the ICF through the completion of the last study visit or at the ETV. Investigators are 
required to report any events which may require the implementation of urgent safety 
measures to BioMarin with 24 hours. 
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Examples of situations that may require urgent safety measures include discovery of the 
following: 
• Immediate need to revise the IP administration (i.e., modified dose amount or 
frequency not defined in protocol). 
• Lack of study scientific value, or detrimental study conduct or management. 
• Discovery that the quality or safety of the IP does not meet established safety 
requirements. 
10.5 
BioMarin Pharmacovigilance Contact Information 
Contact information for BioMarin Pharmacovigilance is as follows: 
BioMarin Pharmaceutical Inc. 
Address 
105 Digital Drive 
 
 
Novato, CA 94949 
Phone:  
(415) 506-6179 
Fax: 
 
(415) 532-3144 
E-mail: 
drugsafety@bmrn.com 
The Investigator is encouraged to discuss with the Sponsor’s Medical Office sponsor’s 
medical monitor r any AEs for which the issue of seriousness is unclear or questioned. 
Contact information for the sponsor’s medical monitor is as follows: 
Name:  
, MD 
Address: 
105 Digital Drive 
 
 
Novato, CA 94949 USA 
Phone:  
 
Fax: 
 
 
E-mail: 
 
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11 
APPROPRIATENESS OF MEASUREMENTS 
11.1 
Safety and Pharmacokinetics 
The PK and safety assessments in this study are used widely and are generally recognized as 
reliable, accurate, and relevant. 
11.2 
Diet Diary 
A 3-day diet diary will be issued to subjects for completion and will be brought to clinic on a 
monthly basis for review with the clinical study staff. Additional information regarding the 
diet diary is provided in Section 7.3, and information regarding administration of the diary is 
provided in Section 9.7.4. Additional information about diet is provided in Section 9.1 and 
Section 9.6. 
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12 
STUDY PROCEDURES 
12.1 
Prestudy 
An ICF must be signed and dated by the subject (or the subject’s legally authorized 
representative if the subject is less than 18 years of age), the PI or designee and witness 
(if required) before any study-related procedures are performed. 
12.2 
Screening Visit 
After subjects have signed an ICF, they will be screened for enrollment into the study. 
The following study activities will be performed at Screening: 
• Medical history, including allergy history, and demographics 
• Physical examination  
• Vital signs, including height and weight 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.).  For safety reasons, 
this test must be performed prior to the chest X-ray. 
• Chest X-ray 
• 12-lead ECG 
• Clinical laboratory tests (including spot urine albumin/creatinine ratio, hematology, 
chemistry, and urinalysis) 
• Complement C3 and C4 
• Assessment of SAEs 
• Concomitant medications 
• Diet query 
• Blood Phe and plasma tyrosine concentration 
For subjects who participated in a previous rAvPAL-PEG study, these assessments may be 
the same as those used for the last visit of the previous study, if they occur within 28 days 
from Day 1. 
12.3 
Treatment Period 
During the Treatment Period, additional visits may occur if deemed necessary to monitor 
AEs or blood Phe concentrations. On days that a dose is given, assessments will be done 
predose unless otherwise specified. Subjects must have AEs and concomitant medications 
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assessed whenever dose is administered even if the administration does not coincide with a 
scheduled clinic visit. If there is a skin reaction that lasts ≥ 14 days, the Skin Reaction eCRF 
should be completed. A photograph of the skin reaction may be taken by the subject or the 
site to help assess the event and may be collected by the sponsor.  
If the dose is modified by increasing dose level, additional blood Phe concentration testing 
should be done daily for 3 days following dose adjustment. If dose is modified by increasing 
either dose frequency or dose level, additional blood Phe concentration testing should be 
done prior to each dose for the first 2 weeks following dose adjustment. 
12.3.1 
Day 1 (Week 1) 
Within 28 days of completing screening assessments, the following study activities will be 
performed on Day 1: 
• Physical examination 
• Vital signs 
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• Assessment of SAEs (predose and postdose) and all AEs (postdose) 
• Concomitant medications 
• Diet query 
• PK sample 
• Blood Phe and plasma tyrosine concentration 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, and anti-rAvPAL-PEG neutralizing antibodies) 
• Administer study drug (study drug may be administered on additional days during the 
week as determined by the Investigator) 
12.3.2 
Weekly Telephone Visit 
Subjects should have a weekly telephone visit conducted. Subjects must still come into the 
clinic for the scheduled monthly visits per Table 9.1.1. The following should be discussed 
with the subject during the weekly telephone visit: 
• Injection-site self inspection (previous and current injection site) 
• Assessment of AEs 
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• Concomitant medications 
• Confirmation of dose level, frequency, and study drug administration 
12.3.3 
Substudy Visits 
For subjects participating in the PK substudy, refer to Section 9.7.3 and Table 9.1.2. 
12.3.4 
Monthly Visits (Week 4, 8, 12, etc) 
Subjects must have AEs and concomitant medications assessed whenever dose is 
administered even if the administration does not coincide with a scheduled clinic visit.    
Beginning with Week 4, monthly visits must be performed in the clinic. The following study 
activities will be performed: 
• Vital signs 
• Weight 
• Clinical laboratory tests 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) For safety reasons, this 
test must be performed prior to the chest X-ray. 
• Chest x-ray (Week 48 visit only) 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• Blood Phe and plasma tyrosine concentration 
• 3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the next monthly visit.) 
• Prefilled syringe self-administration training (to be performed prior to subjects 
transitioning from vial and syringe drug product to prefilled syringe drug product). 
• Administer study drug  
• If additional training is needed on days subsequent to the monthly visit, additional 
clinic visit(s) or HHRN may be used. 
12.3.5 
Quarterly Visits (Week 12, 24, 36, etc) 
Subjects must have AEs and concomitant medications assessed whenever dose is 
administered even if the administration does not coincide with a scheduled clinic visit.    
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Beginning with Week 12, quarterly visits consist of all monthly (Section 12.3.4) activities 
listed above as well as the additional study activities listed below: 
• Physical examination 
• Complement C3 and C4 
• Sedimentation rate 
• PK sample 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, and anti-rAvPAL-PEG neutralizing antibodies) 
• Prefilled syringe refresher training (every 24 weeks only) 
12.3.6 
Unscheduled Hypersensitivity Reaction Visit 
Subjects who have an NCI-CTCAE grade ≥ 3 hypersensitivity reaction after rAvPAL-PEG 
administration (refer to Section 9.1.1) will have assessments performed immediately 
following (within 24 hours) the reaction.  
• Vital signs 
• Clinical laboratory tests 
• Urine/albumin creatinine ratio 
• CRP, CH50, C1, C3, and C4 
• Urine N-methyl histamine  
• Serum anti-rAvPAL IgE and anti-rAvPAL-PEG IgE only (performed > 8 hours after 
event onset) 
• Serum tryptase level 
• Skin biopsy (optional; affected and not affected area; to be performed within 1 week 
of the reaction) 
• Assessment of AEs 
• Concomitant medications 
Following completion of the Unscheduled Hypersensitivity Reaction visit, subjects may 
resume study drug administration per the discretion of the Principal Investigator and the 
sponsor’s medical monitor. 
12.4 
Study Completion/Early Termination Visit 
Subjects should perform the Study Completion Visit 4 weeks after the last dose of study drug 
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or after completion of study participation, whichever occurs last.  
For subjects who terminate from the study early (refer to Section 9.3.3), the Early 
Termination Visit (ETV) will occur 4 weeks after the final dose of study drug or after 
withdrawal from study participation, whichever occurs last. Subjects who terminate from 
study drug early should continue to perform the remaining visit assessments in Section 12.3 
as applicable until study completion. 
Any AE that caused a subject to withdraw from the study or any clinically significant 
abnormal laboratory value or vital sign measurement identified at the ETV will be followed 
by the Investigator.  
Every reasonable effort should be made to contact any subject who is lost to follow-up. 
The following study activities will be performed at the ETV: 
• Physical examination  
• Vital signs 
• 12-lead ECG 
• Clinical laboratory tests 
• Chest x-ray  
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.). For safety reasons, 
this test must be performed prior to the chest X-ray. 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• 3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the Early Termination Visit.) 
• PK sample 
• Blood Phe and plasma tyrosine concentration 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibodies) 
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13 
DATA QUALITY ASSURANCE 
BioMarin personnel or designees will visit the study site prior to initiation of the study to 
review with the site personnel information about the IP, protocol and other regulatory 
document requirements, any applicable randomization procedures, source document 
requirements, CRFs, monitoring requirements, and procedures for reporting AEs, including 
SAEs. 
At visits during and after the study, a CRA will monitor the site for compliance with 
regulatory documentation, with a focus on accurate and complete recording of data on CRFs 
from source documents, adherence to protocol, randomization (if applicable), SAE reporting 
and drug accountability records.  
The designated clinical data management group will enter or transfer CRF data into a study 
database. 
Data quality control and analysis will be performed by BioMarin or a designee, based on a 
predefined analysis plan. 
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14 
STATISTICAL METHODS AND DETERMINATION OF SAMPLE SIZE 
14.1 
Statistical and Analytical Plans 
Because of the small sample size, no formal statistical tests will be performed. Categorical 
data will be summarized using frequency and percent, while continuous data will be 
summarized using descriptive statistics (ie, number of observations, mean, median, standard 
deviation [SD], minimum, and maximum). 
The statistical analysis plan (SAP) will provide additional details about the planned statistical 
analysis. 
14.2 
Safety Analysis 
All subjects who receive any amount of study drug in this study and have postdose safety 
information will be included in the safety analyses. 
The Medical Dictionary for Regulatory Activities terminology (MedDRA) will be used by 
the sponsor to assign system organ class and preferred term classification to events and 
diseases based on the original terms entered on the Case Report Form (CRF). 
The incidence of AEs will be summarized by system organ class, preferred term, relationship 
to study drug, and severity. A by–subject listing will be provided for those subjects who 
experience a serious AE (SAE), including death, or experience an AE associated with early 
withdrawal from the study or study drug. Hypersensitivity AEs and AEs that result in dosing 
interruption or dose level reduction are of interest, and the percentage of subjects who report 
these AEs will be presented. 
Clinical laboratory data will be summarized by the type of laboratory test. Frequency and 
percentage of subjects who experience abnormal (ie, outside of reference range) and/or 
clinically significant abnormalities after study drug administration will be presented for each 
clinical laboratory test. For each clinical laboratory test, descriptive statistics will be provided 
for baseline and all subsequent post-treatment visits. Changes from baseline to the 
post-treatment visits will also be provided. Descriptive statistics of vital signs, physical 
examination results, ECG results, and X-ray results, and immunogenicity test results will also 
be provided. Additionally, antibodies and titers will be summarized by scheduled time point. 
14.3 
Pharmacokinetic Analysis 
Subjects who complete the Substudy will have the following PK parameters assessed: area 
under the plasma concentration-time curve (AUC), time to maximum plasma concentration 
(Tmax), maximum plasma concentration (Cmax), half life (t1/2), and clearance (CL/F).  Should 
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data become available from previous rAvPAL-PEG studies that indicate study drug 
accumulation should also be measured, additional blood draws may be added for PK analysis 
as needed per the discretion of the Investigator in consultation with the sponsor’s medical 
monitor. 
14.3.1 
Pharmacokinetic Substudy Analysis 
For subjects who completed the Substudy, the steady-state PK of rAvPAL-PEG in subjects 
who have achieved and maintained target blood Phe will be explored.  This substudy has 
been completed as of 20 December 2013. 
14.4 
Efficacy Analysis 
Data from all subjects who receive any amount of study drug and who have any 
post-treatment efficacy data will be included in the efficacy analysis. 
Blood Phe concentration at each scheduled time point will be summarized using descriptive 
statistics (mean, SD, median, minimum, and maximum). Change in blood Phe concentration 
from baseline (to be defined in the SAP) to each scheduled time point and presence/absence 
of antibodies will also be summarized. In addition, the proportion of subjects who have 
maintained target Phe concentrations of 60-600 µmol/L will be summarized by each 
scheduled time point. 
The relationship of dietary Phe intake (per information reported on the subject diet diary) and 
blood Phe concentration will also be explored. Subjects who received any amount of study 
drug with any post-treatment blood Phe concentration measurements and diet diary 
information will be included in this exploratory analysis.  
Details regarding exploratory analyses will be provided in the Statistical Analysis Plan. 
14.5 
Determination of Sample Size 
Subjects who participated in previous rAvPAL-PEG studies may be enrolled into this study. 
No formal sample size calculation was conducted for this study or the PAL-003 Substudy.   
14.6 
Handling of Missing Data 
All analyses will be presented based on observed data only. Missing data will not be imputed 
for analyses unless sensitivity analyses are warranted. If imputations are used, detailed 
imputation methods will be described in the SAP before locking the database. 
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14.7 
Interim Analyses 
Safety will be assessed throughout the study on an ongoing basis (refer to Section 15 for 
information regarding the DMC). 
14.8 
Changes in the Conduct of the Study or Planned Analyses 
Only BioMarin may modify the protocol. Any change in study conduct considered necessary 
by the PI will be made only after consultation with BioMarin, who will then issue a formal 
protocol amendment to implement the change. The only exception is when an Investigator 
considers that a subject’s safety is compromised without immediate action. In these 
circumstances, immediate approval of the chairman of the IRB must be sought, and the 
Investigator should inform BioMarin and the full IRB within 2 working days after the 
emergency occurs. 
With the exception of minor administrative or typographical changes, the IRB must review 
and approve all protocol amendments. Protocol amendments that have an impact on subject 
risk or the study objectives, or require revision of the ICF, must receive approval from the 
IRB prior to their implementation. 
When a protocol amendment substantially alters the study design or the potential risks or 
burden to subjects, the ICF will be amended and approved by BioMarin and the IRB, and all 
active subjects must again provide informed consent. 
Note: If discrepancies exist between the text of the statistical analysis as planned in the 
protocol, and the final SAP, a protocol amendment will not be issued and the SAP will 
prevail. 
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15 
DATA MONITORING COMMITTEE (DMC) 
The DMC will act independently in an advisory capacity to BioMarin to monitor the safety 
of rAvPAL-PEG in subjects who participate in the study.  
The responsibilities of the DMC are to: 
• Review the study protocol, informed consent and assent documents, and plans for 
data monitoring. 
• Evaluate the progress of the trial, subjects’ risk versus benefit, and other factors that 
could affect the study outcome. 
• Assess the effect and relevance of new external evidence. 
• Consider relevant information that may have an impact on the safety of the 
participants or the ethics of the study. 
• Protect the safety of the study participants in accordance with the stopping criteria as 
defined in study protocol Section 9.1.2. 
• Make recommendations to the BioMarin concerning continuation or termination of 
the study or other study modifications based on observations. 
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16 
COMPENSATION, INSURANCE, AND INDEMNITY 
There will be no charge to study subjects to be in this study. BioMarin will pay all costs of 
tests, procedures, and treatments that are part of this study. In addition, after IRB approval, 
BioMarin may reimburse the cost of travel for study-related visits. BioMarin will not pay for 
any hospitalizations, tests, or treatments for medical problems of any sort, whether or not 
related to the study subject’s disease, that are not part of this study. Costs associated with 
hospitalizations, tests, and treatments should be billed and collected in the way that such 
costs are usually billed and collected. 
The Investigator should contact BioMarin immediately upon notification that a study subject 
has been injured by the IP or by procedures performed as part of the study. Any subject who 
experiences a study-related injury should be instructed by the Investigator to seek medical 
treatment at a pre-specified medical institution if possible, or at the closest medical treatment 
facility if necessary. The subject should be given the name of a person to contact to seek 
further information about, and assistance with, treatment for study-related injuries. 
The treating physician should bill the subject’s health insurance company or other third party 
payer for the cost of this medical treatment, unless the executed Clinical Trial Agreement 
between BioMarin and the institution of the investigator specifies otherwise. If the subject 
has followed the Investigator’s instructions, BioMarin may pay for reasonable and necessary 
medical services to treat the injuries caused by the IP or study procedures. In some 
jurisdictions, BioMarin is obligated by law to pay for study-related injuries without prior 
recourse to third party payer billing. If this is the case, BioMarin will comply with the law. 
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17 
CASE REPORT FORMS AND SOURCE DOCUMENTS 
Electronic case report forms will be provided for each subject. The Investigator must review 
and electronically sign the completed CRF casebook to verify its accuracy. 
CRFs must be completed using a web–based application that has been validated. Study site 
personnel will be trained on the application and will enter the clinical data from source 
documentation. Unless explicitly allowed in the CRF instructions, blank data fields are not 
acceptable. 
In the event of an entry error, or if new information becomes available, the site personnel will 
correct the value by deselecting the erroneous response and then selecting or entering the 
factual response. In compliance with 21 CFR Part 11, the system will require the site 
personnel to enter a reason for changing the value. The documented audit trail will include 
the reason for the change, the original value, the new value, the time of the correction, and 
the identity of the operator. 
BioMarin’s policy is that study data on the CRFs must be verifiable to the source data, which 
necessitates access to all original recordings, laboratory reports, and subject records. 
In addition, all source data should be attributable (signed and dated). The Investigator must 
therefore agree to allow direct access to all source data. Subjects (or their legally authorized 
representative) must also allow access to their medical records, and subjects will be informed 
of this and will confirm their agreement when giving informed consent.  
A CRA designated by BioMarin will compare the CRFs with the original source documents 
at the study site and evaluate them for completeness and accuracy before designating them as 
“source data verified” (SDV). If an error is discovered at any time or a clarification is 
needed, the CRA, or designee, will create an electronic query on the associated field. Site 
personnel will then answer the query by either correcting the data or responding to the query. 
The CRA will then review the response and determine either to close the query or re–query 
the site if the response does not fully address the question. This process is repeated until all 
open queries have been answered and closed. 
Before a subject’s CRF casebook can be locked, all data fields must be SDV and all queries 
closed. The Investigator will then electronically sign the casebook, specifying that the 
information on the CRFs is accurate and complete. The Data Manager, or designee, will then 
set the status of the forms, visits, and the entire casebook to locked. Upon completion of the 
clinical study report for the entire study, an electronic copy of each site’s casebooks will be 
copied to a compact disk (CD) and sent to each site for retention with other study documents. 
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18 
STUDY MONITORING AND AUDITING 
Qualified individuals designated by BioMarin will monitor all aspects of the study according 
to GCP and standard operating procedures for compliance with applicable government 
regulations. The PI agrees to allow these monitors direct access to the clinical supplies, 
dispensing, and storage areas and to the clinical files, including original medical records, of 
the study subjects, and, if requested, agrees to assist the monitors. The PI and staff are 
responsible for being present or available for consultation during routinely scheduled site 
visits conducted by BioMarin or its designees. 
Members of BioMarin’s GCP Compliance Department or designees may conduct an audit of 
a clinical site at any time during or after completion of the study. The PI will be informed if 
an audit is to take place and advised as to the scope of the audit. Representatives of the FDA 
or other Regulatory Agencies may also conduct an audit of the study. If informed of such an 
inspection, the PI should notify BioMarin immediately. The PI will ensure that the auditors 
have access to the clinical supplies, study site facilities, original source documentation, and 
all study files. 
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19 
RETENTION OF RECORDS 
The PI must retain all study records required by BioMarin and by the applicable regulations 
in a secure and safe facility. The PI must consult a BioMarin representative before disposal 
of any study records, and must notify BioMarin of any change in the location, disposition or 
custody of the study files. The PI/institution must take measures to prevent accidental or 
premature destruction of essential documents, that is, documents that individually and 
collectively permit evaluation of the conduct of a study and the quality of the data produced, 
including paper copies of study records (e.g., subject charts) as well as any original source 
documents that are electronic as required by applicable regulatory requirements. 
All study records must be retained for at least 2 years after the last approval of a marketing 
application in the U.S. or an ICH region and until (1) there are no pending or contemplated 
marketing applications in the United States or an ICH region or (2) at least 2 years have 
elapsed since the formal discontinuation of clinical development of the IP. The PI/institution 
should retain subject identifiers for at least 15 years after the completion or discontinuation 
of the study. Subject files and other source data must be kept for the maximum period of time 
permitted by the hospital, institution or private practice, but not less than 15 years. 
These documents should be retained for a longer period, however, if required by the 
applicable regulatory requirements or by a BioMarin agreement. BioMarin must be notified 
and will assist with retention should the PI/institution be unable to continue maintenance of 
subject files for the full 15 years. It is the responsibility of BioMarin to inform the 
PI/institution as to when these documents no longer need to be retained. 
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20 
USE OF INFORMATION AND PUBLICATION 
BioMarin recognizes the importance of communicating medical study data and therefore 
encourages the publication of these data in reputable scientific journals and at seminars or 
conferences. The details of the processes of producing and reviewing reports, manuscripts, 
and presentations based on the data from this study will be described in the Clinical Trial 
Agreement between BioMarin and the Investigator/Institution. Consideration for authorship 
of all publications will be based on compliance with the Uniform Requirements for 
Manuscripts Submitted to Biomedical Journals (“Uniform Requirements”) of the 
International Committee of Medical Journal Editors (ICMJE) 
(http://www.icmje.org/about-icmje/faqs/icmje-recommendations/) and good publication 
practices (GPP).  
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21 
REFERENCES 
Armstrong, JK, Hempel, G, Koling, S, Chan, LS et. al. Antibody against poly(ethylene glycol) 
adversely affects PEG-asparaginase therapy in acute lymphoblastic leukemia patients. Cancer 110[1], 
103-111. 2007 
Brown, SG. Clinical features and severity grading of anaphylaxis. J Allergy Clin Immunol 114[2], 
371-376. 2004 
Chen, AM, Scott, MD. Current and future applications of immunological attenuation via pegylation 
of cells and tissue. BioDrugs 15[12], 833-847. 2001 
Davis, S, Abuchowski, A, Park, YK, Davis, FF. Alteration of the circulating life and antigenic 
properties of bovine adenosine deaminase in mice by attachment of polyethylene glycol. Clin Exp 
Immunol 46[3], 649-652. 1981 
Fisch, RO. Comments on diet and compliance in phenylketonuria. Eur J Pediatr 159 Suppl 2, S142-
S144. 2000 
Gamez, A, Wang, L, Sarkissian, CN, Wendt, D et. al. Structure-based epitope and PEGylation sites 
mapping of phenylalanine ammonia-lyase for enzyme substitution treatment of phenylketonuria. Mol 
Genet Metab 91[4], 325-334. 2007 
Ganson, NJ, Kelly, SJ, Scarlett, E, Sundy, JS et. al. Control of hyperuricemia in subjects with 
refractory gout, and induction of antibody against poly(ethylene glycol) (PEG), in a phase I trial of 
subcutaneous PEGylated urate oxidase. Arthritis Res Ther 8[1], R12. 2006 
Guttler, F, Azen, C, Guldberg, P, Romstad, A et. al. Impact of the phenylalanine hydroxylase gene on 
maternal phenylketonuria outcome. Pediatrics 112[6 Pt 2], 1530-1533. 2003 
Harris, JM, Chess, RB. Effect of pegylation on pharmaceuticals. Nat Rev Drug Discov 2[3], 214-221. 
2003 
Huttenlocher, PR. The neuropathology of phenylketonuria: human and animal studies. Eur J Pediatr 
159 Suppl 2, S102-S106. 2000 
Judge, A, McClintock, K, Phelps, JR, Maclachlan, I. Hypersensitivity and loss of disease site 
targeting caused by antibody responses to PEGylated liposomes. Mol Ther 13[2], 328-337. 2006 
Kaufman, S. An evaluation of the possible neurotoxicity of metabolites of phenylalanine. J Pediatr 
114[5], 895-900. 1989 
Koch, R, Hanley, W, Levy, H, Matalon, K et. al. The Maternal Phenylketonuria International Study: 
1984-2002. Pediatrics 112[6 Pt 2], 1523-1529. 2003 
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Lapis. Long-term Correction of PKU in the Pahenu2 Mouse by Mutant and Chemically Modified 
Forms of Phenylalanine Ammonium Lyase. ASHG 57th Annual Meeting The American Society of 
Human Genetics) 2007.  
Lee, PJ, Lilburn, M, Baudin, J. Maternal phenylketonuria: experiences from the United Kingdom. 
Pediatrics 112[6 Pt 2], 1553-1556. 2003 
Levy, HL. Historical background for the maternal PKU syndrome. Pediatrics 112[6 Pt 2], 1516-1518. 
2003 
Matalon, R, Surendran, S, Matalon, KM, Tyring, S et. al. Future role of large neutral amino acids in 
transport of phenylalanine into the brain. Pediatrics 112[6 Pt 2], 1570-1574. 2003 
Richter, AW, Akerblom, E. Antibodies against polyethylene glycol produced in animals by 
immunization with monomethoxy polyethylene glycol modified proteins. Int Arch Allergy Appl 
Immunol 70[2], 124-131. 1983 
Richter, AW, Akerblom, E. Polyethylene glycol reactive antibodies in man: titer distribution in 
allergic patients treated with monomethoxy polyethylene glycol modified allergens or placebo, and in 
healthy blood donors. Int Arch Allergy Appl Immunol 74[1], 36-39. 1984 
Rouse, B, Azen, C. Effect of high maternal blood phenylalanine on offspring congenital anomalies 
and developmental outcome at ages 4 and 6 years: the importance of strict dietary control 
preconception and throughout pregnancy. J Pediatr 144[2], 235-239. 2004 
Sampson, HA, Munoz-Furlong, A, Campbell, RL, Adkinson, NF, Jr. et. al. Second symposium on the 
definition and management of anaphylaxis: summary report--Second National Institute of Allergy and 
Infectious Disease/Food Allergy and Anaphylaxis Network symposium. J Allergy Clin Immunol 
117[2], 391-397. 2006 
Scott, MD, Murad, KL, Koumpouras, F, Talbot, M et. al. Chemical camouflage of antigenic 
determinants: stealth erythrocytes. Proc Natl Acad Sci U S A 94[14], 7566-7571. 1997 
Scriver, CR, Kaufman. Hyperphenylalaninemia: Phenylalanine Hydroxylase Deficiency. In: Beaudet 
AL, Sly WS, Valle D, editors. Metabolic and Molecular Bases of Inherited Disease. New York: 
McGraw-Hill, 2001: 1667-1724. 
Walter, JH, White, FJ, Hall, SK, MacDonald, A et. al. How practical are recommendations for dietary 
control in phenylketonuria? Lancet 360[9326], 55-57. 2002 
Webster, R, Didier, E, Harris, P, Siegel, N et. al. PEGylated proteins: evaluation of their safety in the 
absence of definitive metabolism studies. Drug Metab Dispos 35[1], 9-16. 2007 
 
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22 
INVESTIGATOR RESPONSIBILITIES 
22.1 
Conduct of Study and Protection of Human Subjects  
In accordance with FDA Form 1572, the Investigator will ensure that: 
• He or she will conduct the study in accordance with the relevant, current protocol and 
will only make changes in a protocol after notifying the sponsor, except when 
necessary to protect the safety, rights, or welfare of subjects. 
• He or she will personally conduct or supervise the study. 
• He or she will inform any potential subjects, or any persons used as controls, that the 
drugs are being used for investigational purposes and he or she will ensure that the 
requirements relating to obtaining informed consent in 21 CFR Part 50 and 
institutional review board (IRB) review and approval in 21 CFR Part 56 are met.  
• He or she will report to the sponsor adverse experiences that occur in the course of 
the investigation in accordance with 21 CFR 312.64. 
• He or she has read and understands the information in the Investigator’s Brochure, 
including potential risks and side effects of the drug. 
• His or her staff and all persons who assist in the conduct of the study are informed 
about their obligations in meeting the above commitments. 
• He or she will ensure that adequate and accurate records in accordance with 
21 CFR 312.62 and to make those records available for inspection in accordance with 
21 CFR 312.68. 
• He or she will ensure that the IRB complies with the requirements of 21 CFR Part 56, 
and other applicable regulations, and conducts initial and ongoing reviews and 
approvals of the study. He or she will also ensure that any change in research activity 
and all problems involving risks to human subjects or others are reported to the IRB. 
Additionally, he or she will not make any changes in the research without IRB 
approval, except where necessary to eliminate apparent immediate hazards to human 
subjects. 
• He or she agrees to comply with all other requirements regarding the obligations of 
clinical Investigators and all other pertinent requirements in 21 CFR Part 312. 
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24 
PROTOCOL AMENDMENT TEXT REVISIONS 
The following is a summary of significant protocol revisions; added text is underlined and deleted text is struck. The study design schematic 
(Figure 9.1.1) and Schedule of Events (Table 9.1.1) were revised accordingly. Additional administrative changes have been made for 
consistency and clarity throughout this amendment and are reflected in the protocol body. Revisions made to the Synopsis (Section 2) are 
reflected in the corresponding protocol section as appropriate. Revisions to cross references to protocol tables, figures, sections, and 
references reside within the protocol body.  
Section 
Revision 
Rationale for 
Change 
Section 2, Section 9.1, 
Study Design 
Because the risks of taking rAvPAL-PEG during pregnancy and breastfeeding are unknown, subjects cannot 
take rAvPAL-PEG if they are trying to conceive, are pregnant, or are breastfeeding. Male subjects who are 
planning to impregnate a female partner and female subjects who are trying to become pregnant during the 
study will be discontinued immediately from study drug. Male subjects who have impregnated a female 
partner may re-start study drug after conception but must return to the study-required contraception use, 
which must include one barrier method. Subjects who remain in the study after discontinuation of study drug 
due to pregnancy may re-introduce rAvPAL-PEG dosing after the birth has been reported (or termination of 
the pregnancy) and breastfeeding has completed (if applicable) or after the subject is no longer actively 
trying to conceive. Re-starting rAvPAL-PEG dosing must be per investigator and sponsor agreement based 
on an assessment of the known risks and potential benefits while taking BMN 165. Female subjects must 
return to the study-required contraception use, which must include one barrier method, immediately after the 
birth (or termination of the pregnancy). 
2 
Section 2, Section 9.3.1, 
Inclusion Criteria 
Individuals eligible to participate in this study must meet all of the following criteria: 
• 
Sexually active subjects must be willing to use antwo acceptable methods of contraception while 
participating in the study.  Males post vasectomy for 2 years with no known pregnancies do not need 
to use any other forms of contraception during the study. 
3 
Section 2, Duration of 
Treatment 
Up to 10298 months. 
4 
Section 9.1, Study Design 
Because the risks of taking rAvPAL-PEG during pregnancy and breastfeeding are unknown, 
subjects cannot take rAvPAL-PEG if they are trying to conceive, are pregnant, or are breastfeeding 
(refer to Section 9.3.2, Exclusion Criteria). Male subjects who are planning to impregnate a female 
2 
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Section 
Revision 
Rationale for 
Change 
partner and female subjects who are trying to become pregnant during the study will be 
discontinued immediately from study drug. Male subjects who have impregnated a female partner 
may re-start study drug after conception but must return to the study-required contraception use 
(refer to Section 9.3.1, Inclusion Criteria), which must include one barrier method. Subjects who 
remain in the study after discontinuation of study drug due to pregnancy may re-introduce 
rAvPAL-PEG dosing after the birth has been reported (or termination of the pregnancy) and 
breastfeeding has completed (if applicable) or after the subject is no longer actively trying to 
conceive. Re-starting rAvPAL-PEG dosing must be per investigator and sponsor agreement based 
on an assessment of the known risks and potential benefits while taking BMN 165. Female subjects 
must return to the study-required contraception use (refer to Section 9.3.1), which must include one 
barrier method, immediately after the birth (or termination of the pregnancy). 
Table 9.1.1, Schedule of 
Events 
The table has been updated to reflect changes made with this amendment. 
1, 5, 6 
Section 9.3.3, Removal of 
Subjects from Treatment 
or Assessment 
Reasons for which the Investigator or BioMarin may withdraw a subject from the study treatment 
drug include, but are not limited to, the following: 
• Subject becomes pregnant (refer to Section 10.3 for details on the reporting procedures to 
follow in the event of pregnancy and refer to Section 9.1 for details on re-introduction of 
study drug following pregnancy and breastfeeding). 
2 
Section 10.1, Adverse 
Events 
….  After informed consent is obtained and the first administration of study drug, all non-serious 
AEs and SAEs reporting period begins and continues until 4 weeks following the last 
administration of study drug or the Study Completion Visit/Early Termination Visit, whichever is 
longeroccurs last (refer to Section 12). The criteria for determining, and the reporting of SAEs is 
provided in Section 10.2.   
5 
Section 10.3, Pregnancy 
Pregnancy in a subject or partner should be reported within 24 hours of the site becoming aware of 
the pregnancy to BioMarin Pharmacovigilance by fax using the Pregnancy Form in the study 
reference materials. The reporting period for pregnancies begins with informed consent and 
2 
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Section 
Revision 
Rationale for 
Change 
continues until 4 weeks following the last study drug dose. In addition, pregnancy in a subject is 
also reported on the End of Study CRF if the subject withdraws from the study due to pregnancy…. 
Section 12.3, Treatment 
Period 
During the Treatment Period, additional visits may occur if deemed necessary to monitor AEs or 
blood Phe concentrations. All study activities will occur on the first day of each week unless 
otherwise noted. On days that a dose is given, assessments will be done predose unless otherwise 
specified. Subjects must have AEs and concomitant medications assessed whenever dose is 
administered even if the administration does not coincide with a scheduled clinic visit. If there is a 
skin reaction that lasts ≥ 14 days, the Skin Reaction eCRF should be completed. A photograph of 
the skin reaction may be taken by the subject or the site to help assess the event and may be 
collected by the sponsor.  
1 
Section 12.4, Study 
Completion/Early 
Termination Visit 
Subjects should perform the Study Completion Visit 4 weeks after the last dose of study drug or 
after completion of study participation, whichever occurs last.  
For subjects who terminate from the study early (refer to Section 9.3.3), tThe Early Termination 
Visit (ETV) will occur 4 weeks after the final dose of study drug or after withdrawal from study 
participation, whichever occurs last. … 
5 
Section 20, Use of 
Information and 
Publication 
BioMarin recognizes the importance of communicating medical study data and therefore 
encourages the publication of these data in reputable scientific journals and at seminars or 
conferences. The details of the processes of producing and reviewing reports, manuscripts, and 
presentations based on the data from this study will be described in the Clinical Trial Agreement 
between BioMarin and the Investigator/Institution. Consideration for authorship of all publications 
will be based on compliance with the Uniform Requirements for Manuscripts Submitted to 
Biomedical Journals (“Uniform Requirements”) of the International Committee of Medical Journal 
Editors (ICMJE) (http://www.icmje.org/about-icmje/faqs/icmje-recommendations/) and good 
6 
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Rationale for 
Change 
publication practices (GPP).  
BioMarin recognizes the importance of communicating medical study data and therefore 
encourages their publication in reputable scientific journals and at seminars or conferences. The 
details of the processes of producing and reviewing reports, manuscripts, and presentations based 
on the data from this study will be described in the Clinical Trial Agreement between BioMarin and 
the institution of the investigator. 
 
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Proprietary and Confidential 
Amendment 8: 31 March 2017 
CLINICAL STUDY PROTOCOL 
Study Title: 
Long-term Extension of a Phase 2, Open-Label, Dose-Finding 
Study to Evaluate the Safety, Efficacy, and Tolerability of 
Multiple Subcutaneous Doses of rAvPAL-PEG in Subjects with 
PKU 
Protocol Number: 
PAL-003 
Investigational Product: 
rAvPAL-PEG (PEGylated recombinant Anabaena variabilis 
phenylalanine ammonia lyase) 
IND/EUDRACT Number: 
IND 076269 
Indication: 
Phenylketonuria (PKU) 
Sponsor: 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
Development Phase: 
Phase 2 
Sponsor's Responsible Medical 
Monitor: 
 MS 
 
Duration: 
Approximately 119 months   
Dose: 
0.001 to a maximum weekly dose of 5.0 mg/kg or 375 mg/week 
Date of Original Protocol: 
October 08, 2008 
Date of Amendment 1: 
February 09, 2009 
Date of Amendment 2: 
October 30, 2009 
Date of Amendment 3: 
May 04, 2011 
Date of Amendment 4: 
June 7, 2012 
Date of Amendment 5: 
February 28, 2014 
Date of Amendment 6: 
October 30, 2014 
Date of Amendment 7: 
December 16, 2015 
Date of Amendment 8: 
March 31, 2017  
 
Property of BioMarin 
CONFIDENTIAL 
May not be divulged, published, or otherwise disclosed to others without prior written approval from BioMarin. 
This study will be conducted according to the principles of Good Clinical Practice as described in the U.S. Code of Federal 
Regulations and the International Conference on Harmonisation Guidelines, including the archiving of essential documents. 
BioMarin is a registered trademark of BioMarin Pharmaceutical Inc. 
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CLINICAL STUDY PROTOCOL AMENDMENT SUMMARY 
Amendment:  8 
Date: 31 March 2017 
 
RATIONALE AND SUMMARY OF CHANGES  
This section provides a numbered list of all significant changes and supporting rationale:  
1. To monitor subject safety, a repeat urinalysis should be performed for subjects who 
have an abnormal or elevated proteinuria test result. Additionally, first or second 
morning void is being recommended for all urinalyses collected during the study. In 
addition, information regarding renal toxicity due to exposure to PEG has been 
updated in the background section (Section 7.4.1). 
2. Additional instruction has been added for subjects who are pregnant or are planning 
to become pregnant (or impregnate a female partner) during the study for clarity and 
to monitor subject safety.  
o Subjects who are planning to conceive must stop study drug at least 
4 weeks prior to trying to conceive and must use two forms of acceptable 
contraception prior to trying to conceive. 
o Subjects who are planning to become pregnant (or impregnate a female 
partner) during the study may modify their diet in consultation with the 
investigator and/or study dietician.  
o Subjects who are pregnant or are trying to conceive and have temporarily 
discontinued study drug are not required to perform the scheduled 
pharmacokinetic (PK) assessments.  
o Subjects who have been confirmed to be pregnant with a serum pregnancy 
test are not required to perform the urine pregnancy tests while pregnant. 
o Upon re-starting study drug following a pregnancy or breastfeeding, 
female subjects must have a confirmed negative urine pregnancy test 
result. 
3. Additional instruction regarding adverse event (AE) and serious AE (SAE) reporting 
has been added to provide clarity and to improve the quality of safety reporting. The 
following have been added: 
o Guidance on factors suggestive of a causal relationship to study drug to 
facilitate investigator assessments of AEs 
o Guidance on how to report AEs occurring secondary to other events  
o Guidance on reporting of persistent versus recurrent AEs  
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o Guidance on when abnormal laboratory test results should be reported as 
AEs  
o Guidance on how pre-existing conditions should be recorded  
o Guidance on where and how physician examination findings should be 
reported as AEs  
o Guidance on scenarios that do not require reporting hospitalization as an 
SAE  
o Guidance on how to report deaths  
o Guidance on how to report abortions 
o Guidance on reporting post-study SAEs  
o Guidance regarding sponsor request for additional case details for SAEs 
and AEs of special interest, including hospital discharge, consultant 
reports, and autopsy reports 
4. To monitor for subject safety, subjects who have an elevated urine/albumin creatinine 
ratio (defined as confirmed result of ≥  100 mg/g for subjects with results within 
normal range at baseline or a confirmed increase of 100-200 mg/g from baseline for 
subjects with elevated results at baseline) should be referred to a nephrologist for 
consultation. 
5. To monitor for subject safety, subjects who experience an injection-site skin reaction 
that lasts  ≥ 14 days should be referred for a dermatology consultation and may be 
asked to perform a skin biopsy. 
6. Instruction regarding the premedications to administer prior to injection of study drug 
has been revised to provide alternative medications to subjects who may not tolerate 
non-steroidal anti-inflammatory drugs (NSAIDS); subjects may alternatively be 
premedicated with antipyretics (eg, acetaminophen). 
7. Information regarding exploratory sample analysis (use of leftover blood and urine 
samples) during the study and after the subject completes the study has been added.  
8. The Schedule of Events has been modified; scheduled visits are to occur every 
8 weeks (rather than every 4 weeks and quarterly) to align with the visit schedule in 
the ongoing extension (Part 4) of the Phase 3 study, 165-302.  
9. The study duration has been extended from 102 months to approximately 
119 months.  
10. The responsible Medical Monitor has been changed. 
11. Minor changes were made to improve clarity and consistency and update protocol 
language to reflect more recent information and/or instruction regarding study 
conduct. 
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In addition, the Schedule of Events (Section 9.1) and Section 12 have been updated to reflect 
the changes in this amendment. Refer to Section 24 for a summary of the amendment 
revisions. 
 
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2 
SYNOPSIS 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
TITLE OF STUDY: 
Long-term Extension of a Phase 2, Open-Label Dose-Finding Study to Evaluate the Safety, Efficacy, 
and Tolerability of Multiple Subcutaneous Doses of rAvPAL-PEG in Subjects with PKU 
PROTOCOL NUMBER:  PAL-003 
STUDY SITES:  Approximately 20 centers in the United States 
PHASE OF DEVELOPMENT:  Phase 2 
STUDY RATIONALE: 
The need exists for a treatment that will help individuals with phenylketonuria (PKU) safely achieve 
lifelong, reliable control of blood phenylalanine (Phe) concentrations and improve functional 
outcomes. PEGylated recombinant Anabaena variabilis phenylalanine ammonia lyase (rAvPAL-PEG) 
is a potential substitute for the phenylalanine hydroxylase (PAH) enzyme, which is defective in 
individuals with PKU. rAvPAL-PEG may control blood Phe concentrations, which may have 
additional clinical benefits. This study is an extension of the rAvPAL-PEG Phase 2 studies PAL-002, 
PAL-004, and 165-205. Administration of rAvPAL-PEG will be continued to assess the long-term 
safety and efficacy of rAvPAL-PEG in PKU subjects. 
Blood Phe levels depend not only on the functional presence of the endogenous enzyme PAH but also 
on the dietary intake of Phe. It is important to understand the role of diet on blood Phe levels 
concurrent with the administration of rAvPAL-PEG treatment. Therefore, an exploratory objective has 
been added to this study to assess the relationship of diet, rAvPAL-PEG administration, and blood Phe 
level. Changes to subject diet are not allowed in this study unless per the Investigator. Diet will be 
monitored using a diet diary. 
A pharmacokinetic (PK) substudy has been added to evaluate the steady-state PK of rAvPAL-PEG in 
up to 6 subjects who have achieved and maintained target blood Phe for at least 2 consecutive 
measurements and for whom no further dose modifications are planned. Single-dose PK data has been 
collected in the Phase 1 study, PAL-001. However, there is little multiple-dose PK data or data for 
when subjects have reached and maintained a stable dosing regimen.  With the PK substudy, 
multiple-dose PK data were collected for subjects who have already achieved Phe reduction to within 
the protocol-defined target range.  This substudy has been completed as of 20 December 2013. 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
OBJECTIVES: 
The primary objective of the study is: 
• 
To evaluate the effect of long-term administration of multiple doses of SC injections of 
rAvPAL-PEG on blood Phe concentrations in subjects with PKU. 
The secondary objectives of the study are: 
• 
To evaluate the safety and tolerability of long-term administration of subcutaneous (SC) 
injections of rAvPAL-PEG in subjects with PKU. 
• 
To evaluate the immune response to long-term administration of SC injections of 
rAvPAL-PEG in subjects with PKU. 
The exploratory objective of the study is as follows: 
• 
To evaluate the long-term relationship of diet and change in blood Phe concentration 
following administration with rAvPAL-PEG in subjects with PKU. 
The Substudy objectives are as follows: 
• 
To evaluate steady-state PK of rAvPAL-PEG in subjects who have achieved and maintained 
target blood Phe concentration and for whom no further dose modifications are planned. 
STUDY DESIGN AND PLAN: 
This is a long-term extension of rAvPAL-PEG Phase 2 studies in up to 100 subjects with PKU. The 
doses are planned to be in the same range as those previously tested in the Phase 2 studies (starting at 
0.001 through 5.0 mg/kg/week or 2.5 mg through 375 mg/week), provided no dose-limiting toxicity is 
observed in a previous rAvPAL-PEG study. Subjects’ doses will not exceed 375 mg/week. 
Only subjects who completed a previous rAvPAL-PEG study will be enrolled into this study. Subjects 
enrolling into PAL-003 with no interruption in dosing from a previous rAvPAL-PEG study may either 
continue their previous dosing regimen or begin this study at a higher dose level. Subjects who have 
had dosing interruptions between the previous rAvPAL-PEG study and PAL-003 must have their 
starting dose determined per the sponsor’s medical monitor. The first dose will be administered in the 
clinic, and the subject must be observed for 30 minutes following administration. Additionally, 
subjects will be given two epinephrine injectors and will be instructed to carry one epinephrine 
injector with them at all times. A follow-up telephone call will be made to the subject to monitor 
subject safety 24 hours following the return to dosing.  
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
Diet should not be altered during the course of this study.  Any decision to modify subject diet must be 
made per the Investigator and must be performed under the supervision of the Investigator. To monitor 
for changes in subject diet, a diet diary will be issued to subjects for completion and will be reviewed 
with the clinical study staff on a monthly basis.  
Subjects may self-administer study drug at home if approved by the Investigator and the sponsor’s 
medical monitor and if adequate training is demonstrated. Subjects must meet a set of criteria to be 
considered appropriate for self-administration.  Additional training will be provided to subjects and 
demonstration of competency required when prefilled syringe drug product is introduced, every 
24 weeks, and more often as needed. 
Subjects will be evaluated for safety throughout the study. Toxicity will be measured according to the 
National Cancer Institute (NCI) Common Terminology Criteria for Adverse Events (CTCAE), 
version 4. 
In addition to the Sponsor, a Data Monitoring Committee (DMC) will monitor the safety of subjects in 
the study. The DMC is an independent committee that will act in an advisory capacity to the Sponsor. 
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take 
rAvPAL-PEG. Subjects’ previous rAvPAL-PEG dosing will generally continue in PAL-003. In 
PAL-003, each subject’s dose will be adjusted as needed to attempt to attain or maintain blood Phe 
concentrations of 60-600 µmol/L. rAvPAL-PEG dose will be based on either a subject’s weight or will 
be a fixed dose. Doses will be evaluated on an individual basis. 
Evaluations, observations, and procedures will be conducted at selected time points. After the subject’s 
blood Phe concentration has been controlled to within a target range (60-600 µmol/L), the subject may 
be asked to have additional blood draws for PK and blood Phe concentration analyses as needed per 
the discretion of the Investigator in consultation with the sponsor’s medical monitor. 
A subject will continue in PAL-003 until one of the following occurs: 
• 
The subject withdraws consent and discontinues from the study. 
• 
The subject is discontinued from the study at the discretion of the Investigator or Sponsor. 
• 
 The subject has completed the study through the Week 476 visit.  
• 
 The study is terminated. 
• 
The study drug receives marketing authorization.  
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
Because the risks of taking BMN 165 during pregnancy and breastfeeding are unknown, subjects 
cannot take BMN 165 if they are trying to conceive, are pregnant, or are breastfeeding (refer to 
Section 9.3.2 for Exclusion Criteria). Male subjects who are planning to impregnate a female partner 
and female subjects who are trying to become pregnant during the study must be temporarily 
discontinued from study drug for 4 weeks prior to trying to conceive. During that time, subjects must 
use two acceptable methods of contraception. Subjects who are planning to become pregnant (or 
impregnate a female partner) may modify their diet in consultation with the investigator and/or study 
dietician. Subjects who are confirmed to be pregnant per a serum pregnancy test and are temporarily 
off study drug are not required to perform the scheduled urine pregnancy tests. Subjects who are 
pregnant or are trying to conceive and have temporarily discontinued study drug should not perform 
the scheduled PK assessments. Male subjects who have impregnated a female partner may re-start 
study drug after conception following the investigator’s consultation with and approval by the medical 
monitor. Male subjects must return to the study-required contraception use, which must include one 
barrier method, prior to restarting study drug. Female subjects who remain in the study after temporary 
discontinuation of study drug due to pregnancy may restart BMN 165 dosing after a confirmed 
negative urine pregnancy test result, the birth has been reported (or termination of the pregnancy), and 
breastfeeding has completed (if applicable) or after the subject is no longer actively trying to conceive. 
Re-starting BMN 165 dosing requires the investigator’s prior consultation with and approval by the 
medical monitor. Female subjects must return to the study-required contraception use, which must 
include one barrier method, immediately after the birth (or termination of the pregnancy). 
Subjects may withdraw from treatment with study drug at any time; however, subjects will be asked to 
continue to perform the study assessments until study completion. Subjects may also withdraw from 
study participation at any time. Because the completeness of the data affects the integrity, accuracy, 
and interpretation of study results, every effort should be made to retain subjects in the study and to 
have them complete the study assessments as scheduled as long as continued participation does not 
compromise subject safety. 
PAL -003 Substudy 
A PK substudy has been added to evaluate the steady-state PK of rAvPAL-PEG in up to 6 subjects 
who have achieved and maintained target blood Phe for at least 2 consecutive measurements and for 
whom no further dose modifications are planned.  Subjects enrolled into the substudy will have 
additional pre-dose PK sampling performed.  This substudy has been completed as of 
20 December 2013. 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
Dose Modifications: 
Dose Increase Methodology: 
Each subject’s dose may be modified based on the decision of the Investigator. Decisions regarding 
dose increases will depend on a subject’s adverse event profile and blood Phe and drug concentrations.  
An individual subject’s dose may be adjusted beginning on Day 1 of PAL-003. For the duration of this 
study, an individual subject’s dose may be adjusted if warranted per a subject’s adverse event profile 
and blood Phe concentrations. Dose increases should be performed as follows: 
• 
The dose may be increased by increments of no more than 10-fold higher than the subject’s 
current dose. 
• 
When increasing the dose, a dose may be used that is between the dose levels (0.001, 0.003, 
0.01, 0.03, 0.06, 0.1, 0.2, 0.3, 0.4, 0.6, 0.8, 1.0, 2.0, 3.0, 4,0, and 5.0 mg/kg or 2.5, 5, 10, 20, 
40, 75, 150, 225, 300, 375 mg/week) or per Investigator determination based on available 
information regarding a subject’s blood Phe (60-600 µmol/L) as well as any adverse events 
(any hypersensitivity reaction) for an individual subject. Dose increases  > 350 mg/week 
require consultation with the sponsor’s medical monitor. 
• 
The dose may be adjusted by increasing the frequency up to daily for a total weekly dose not 
to exceed 5.0 mg/kg or 375 mg/week.  Dose increases  > 350 mg/week require consultation 
with the sponsor’s medical monitor. 
• 
When a dose is increased, the subject must be observed for 30 minutes following the first 
modified dose administration. Subjects who increase their dose frequency do not need to be 
observed following injection of study drug if the increase in frequency does not increase the 
overall weekly dose amount. 
• 
Only 1 dose adjustment is allowed every 2 weeks. 
Dose Decrease Methodology 
Decisions regarding dose decreases will depend on available information regarding a subject’s blood 
Phe (60-600 µmol/L), as well as any adverse events (any hypersensitivity reaction). Dose decreases 
may occur for hypophenylalanemia or any adverse event that may be improved with a lower dose.  
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
A dose should first be reduced by dose level (5.0, 4.0, 3.0, 2.0, 1.0, 0.8, 0.6, 0.4, 0.3, 0.2, 0.1, 0.06, 
0.03, 0.01, 0.003, 0.001 mg/kg or 375, 300, 225, 150, 75, 40, 20, 10, 5, and 2.5 mg/week). It is also 
permitted to decrease dose in between these specified dose levels. If further dosing adjustments are 
required in response to safety, dosing frequency may also be adjusted. 
If the subject develops low blood Phe (as defined by a blood Phe level ≤ 30 µmol/L), the subject’s 
rAvPAL-PEG dose should be decreased to the next lower dose. If the condition persists after another 
1 month at the lower dose, the dose should be decreased again to the next lower level. If the subject 
continues to experience low blood Phe after two dose level reductions, the subject may be asked to 
consult the dietician to eliminate medical foods and/or formulas and to ensure a balanced and 
nutritious diet (as part of the routine standard of care for PKU disease management, subject diet should 
be monitored by a dietician). 
Safety Assessment Criteria: 
Response to Hypersensitivity Adverse Events  
Subjects are evaluated for safety throughout the study and are trained to recognize potential 
hypersensitivity AEs (including anaphylaxis) and how to respond. Subjects are instructed to contact 
the investigator for any suspected hypersensitivity AE. The investigator may require further evaluation 
at the clinic. If a hypersensitivity AE (eg, injection-site reaction, rash, joint pain, itching) occurs, the 
subject may be advised to premedicate with H1 antagonist, H2 antagonist, and antipyretics 
(eg, acetaminophen) approximately 2-3 hours prior to subsequent rAvPAL-PEG doses. If non-steroidal 
anti-inflammatory medication (NSAIDs) is administered as a premedication, it should be given with 
food.  
Hypersensitivity AEs, including anaphylaxis, are expected with rAvPAL-PEG administration. 
rAvPAL-PEG dosing in response to a suspected hypersensitivity AE may be modified or halted 
depending on the severity of the event and suspected rAvPAL-PEG causality. Severity for 
hypersensitivity AEs will be per NCI-CTCAE grades. 
Individual Stopping Criteria 
Subjects who have an NCI CTCAE grade  ≥ 3 hypersensitivity AE that is related to study drug and is 
suspected to meet Brown’s criteria for severe (grade 3) in the judgment of the investigator and the 
sponsor’s medical monitor may be permanently discontinued from study drug.  
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Dosing in Response to Hypersensitivity Adverse Events 
Dosing in response to a hypersensitivity AE depends on the NCI-CTCAE grade and suspected 
relationship to rAvPAL-PEG.  
Once an AE (other than anaphylaxis) improves to grade 1 or resolves, study drug dose may be 
increased, maintained, or reduced. If dosing has been interrupted due to an AE (other than 
anaphylaxis) and the investigator determines it is safe for the subject to resume dosing, the first dose 
after improvement of the AE should be performed in the clinic. The subject must be observed for 
30 minutes following administration due to restarting dosing. The subject may be advised to 
premedicate with H1 antagonist, H2 antagonist, and antipyretics (eg, acetaminophen) approximately 
2-3 hours prior to subsequent rAvPAL-PEG doses. If NSAIDs are administered as a premedication, 
they should be given with food. 
Response to Anaphylaxis  
If the investigator suspects that the event is anaphylaxis, the subject will be assessed in the clinic. 
Laboratory assessments for suspected anaphylaxis events should be performed prior to the next 
administration of study drug (if applicable) and include anti-rAvPAL IgE and anti-rAvPAL-PEG IgE 
(sampling must be performed >8 hours after event onset and before the next dose of study drug) and 
tryptase (within 24 hours of event onset). The investigator will consult with the sponsor’s medical 
monitor, and a decision will then be made whether to discontinue the subject from study drug, restart 
dosing at the same dose level, or restart dosing at a lower dose level. 
For the first week of dosing after resolution of anaphylaxis, the study drug will be administered in a 
clinic setting with equipment for emergency resuscitation (including epinephrine) within easy access.  
The subject must be observed for 30 minutes following administration due to restarting dosing. 
Additionally, the subject should be premedicated with H1 antagonist, H2 antagonist, and antipyretics 
(eg, acetaminophen) approximately 2-3 hours prior to each dose of study drug for one week upon 
return to dosing regardless of the duration of dose interruption. If NSAIDs are administered as a 
premedication, they should be given with food.  
Stopping Criteria: 
If an NCI-CTCAE grade  ≥ 3 hypersensitivity treatment-related event occurs and meets Brown’s 
criteria for severe (grade 3), an ad hoc independent DMC meeting will convene within 7 days of the 
event to review and advise the sponsor on potential changes to the study conduct. Clinically severe 
hypersensitivity is defined as significant hypoxia, hypotension or neurologic compromise that is 
life-threatening or required treatment to prevent a life-threatening event:  
• 
Cyanosis or SpO2 ≤ 92%  
• 
Hypotension with SBP < 90 mm Hg (adults)  
• 
Neurologic alteration: loss of consciousness, collapse, incontinence 
NUMBER OF SUBJECTS PLANNED: 
Up to 100 subjects. 
DIAGNOSIS AND ALL CRITERIA FOR INCLUSION AND EXCLUSION:  
Individuals eligible to participate in this study must meet all of the following criteria: 
• 
Must have completed participation in a previous rAvPAL-PEG study. 
• 
Willing and able to provide written, signed informed consent, or, in the case of participants 
under the age of 18, provide written assent (if required) and written informed consent by a 
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Proprietary and Confidential  
Amendment 8: 31 March 2017 
NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
parent or legal guardian, after the nature of the study has been explained, and prior to any 
research-related procedures. 
• 
Willing and able to comply with all study procedures.  
• 
Females of childbearing potential must have a negative pregnancy test at Screening and be 
willing to have additional pregnancy tests during the study. Females considered not of 
childbearing potential include those who have been in menopause at least 2 years, or had tubal 
ligation at least 1 year prior to Screening, or who have had total hysterectomy. 
• 
Sexually active subjects must be willing to use two acceptable methods of contraception while 
participating in the study.  Males post vasectomy for 2 years with no known pregnancies do 
not need to use any other forms of contraception during the study. 
• 
Maintained a stable diet. 
• 
In generally good health as evidenced by physical examination, clinical laboratory evaluations 
(hematology, chemistry, and urinalysis), and electrocardiogram (ECG) at Screening. 
Individuals who meet any of the following exclusion criteria will not be eligible to participate in the 
study: 
• 
Use of any investigational product (with the exception of rAvPAL-PEG) or investigational 
medical device within 30 days prior to Screening, or requirement for any investigational agent 
prior to completion of all scheduled study assessments. 
• 
Use of any medication other than rAvPAL-PEG that is intended to treat PKU within 14 days 
prior to the administration of study drug. 
• 
Use or planned use of any injectable drugs containing PEG (other than rAvPAL-PEG), 
including Depo-Provera, within 6 months prior to Screening and during study participation.  
• 
A prior reaction that included systemic symptoms (eg, generalized hives, respiratory or 
gastrointestinal problems, hypotension, angioedema, anaphylaxis) to rAvPAL-PEG or a 
PEG-containing product. Subjects with a prior systemic reaction may be eligible for 
participation per the discretion of the Principal Investigator in consultation with the sponsor’s 
medical monitor. However, subjects who discontinued from study drug early due to a reaction 
are not eligible to enroll into this study.    
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
• 
Pregnant or breastfeeding at Screening or planning to become pregnant (self or partner) or to 
breastfeed at any time during the study.  
• 
Concurrent disease or condition that would interfere with study participation or safety 
(eg, history or presence of clinically significant cardiovascular, pulmonary, hepatic, renal, 
hematologic, gastrointestinal, endocrine, immunologic, dermatologic, neurological, oncologic, 
or psychiatric disease). 
• 
Any condition that, in the view of the PI, places the subject at high risk of poor treatment 
compliance or of not completing the study. 
• 
Known hypersensitivity to rAvPAL-PEG necessitating early termination from a previous 
rAvPAL-PEG study or known hypersensitivity to any of its excipients. 
• 
Alanine aminotransferase (ALT) concentration > 2 times the upper limit of normal. 
• 
Creatinine  > 1.5 times the upper limit of normal. 
INVESTIGATIONAL PRODUCT, DOSE, ROUTE AND REGIMEN: 
The investigational product is rAvPAL-PEG (recombinant Anabaena variabilis phenylalanine 
ammonia lyase-PEG). rAvPAL-PEG will be provided in vials or prefilled syringes; subjects will be 
supplied with vials and syringes or prefilled syringes for administration in the clinic and self-
administration: 
• 
rAvPAL-PEG will be provided in 3 mL (milliliter) vials, each containing 1.5 ± 0.2 mL to 
deliver 15 mg of rAvPAL-PEG per 1.0 mL (15 mg/mL protein concentration). Each vial is 
filled with 1.5 ± 0.2 mL to allow the withdrawal and delivery of up to 1.0 mL of the drug 
product. 
Or: 
• 
rAvPAL-PEG will be provided in 3-mL vials, each containing 1.8 ±0.3 mL to deliver 20 mg of 
rAvPAL-PEG per 1.3 mL (15 mg/mL protein concentration). Each vial is filled with 
1.8 ± 0.3 mL to allow withdrawal and delivery of up to 1.3 mL. 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
Or: 
• 
rAvPAL-PEG will be provided in prefilled syringes in three sizes that deliver up to 1 mL. 
Syringe sizes are 2.5 mg (5 mg/mL protein concentration), 10 mg (20 mg/mL protein 
concentration), and 20 mg (20 mg/mL protein concentration).  
Subjects who have undergone training and who have demonstrated competency on the use of prefilled 
syringe in the study clinic may be eligible to transition from vial and syringe to prefilled syringe 
dosing. Additionally, regular refresher training on use of prefilled syringe will be provided in study 
clinic every 24 weeks, and more often as needed.  
The excipients in this drug product are tromethamine, tromethamine-hydrochloride, sodium chloride, 
L-phenylalanine, and water for injection. 
rAvPAL-PEG doses will be administered SC by either health care professionals or via 
self-administration. The dose level may be increased or decreased per Investigator determination based 
on available information regarding a subject’s blood Phe level (60-600 µmol/L), as well as any adverse 
events (any hypersensitivity reaction) for an individual subject. The dosage that provides control of 
blood Phe concentrations within the target range of 60-600 µmol/L for a minimum of 2 consecutive 
measurements will be determined for each subject by adjusting the dose level, dose frequency, or both, 
per the PI, based upon the subject’s response to doses. 
Fixed Dosing 
Subjects who have demonstrated efficacy (ie, blood Phe within the target range of 60-600 µmol/L for 
at least 2 consecutive measurements) and who have maintained a stable rAvPAL-PEG dose for at least 
2 consecutive measurements may be eligible to transition from weight-based dosing to a fixed dosing 
regimen that would permit daily dosing (5- or 7-days-per-week).  
DURATION OF TREATMENT: 
Approximately 119 months  
REFERENCE THERAPY(IES), DOSE, ROUTE AND REGIMEN:  
None 
CRITERIA FOR EVALUATION: 
Efficacy: 
Blood Phe concentrations will be measured.  
Immunogenicity: 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
The presence of antibodies (anti-PAL immunoglobulin G [IgG], anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibodies, anti-rAvPAL IgE, and anti-PEG-PAL IgE) 
will be assessed. 
Safety: 
Safety will be evaluated on the incidence of adverse events (AEs) and clinically significant changes in 
vital signs, ECG results, X-ray results, and laboratory test results. 
Pharmacokinetic: 
Plasma concentrations of rAvPAL-PEG will be measured for subjects participating in the Substudy. 
STATISTICAL METHODS:  
Sample Size: 
Subjects who participated in a previous rAvPAL-PEG study may be enrolled into this study. 
No formal sample size calculation was conducted for this study or the PAL-003 Substudy. 
Safety Analysis: 
All subjects who receive any amount of study drug in this study and have postdose safety information 
will be included in the safety analyses. 
The Medical Dictionary for Regulatory Activities terminology (MedDRA) will be used by the 
sponsor to assign system organ class and preferred term classification to events and diseases based 
on the original terms entered on the Case Report Form (CRF). The incidence of AEs will be 
summarized by system organ class, preferred term, relationship to study drug, and severity. A 
by-subject listing will be provided for those subjects who experience a serious AE (SAE), including 
death, or experience an AE associated with early withdrawal from the study or study drug. 
Hypersensitivity AEs and AEs that result in dosing interruption or dose level reduction are of interest, 
and the percentage of subjects who report these AEs will be presented.  
Clinical laboratory data will be summarized by the type of laboratory test. Frequency and percentage 
of subjects who experience abnormal (ie, outside of reference range) and/or clinically significant 
abnormalities after study drug administration will be presented for each clinical laboratory test. For 
each clinical laboratory test, descriptive statistics will be provided for baseline and all subsequent 
post-treatment visits. Changes from baseline to the post-treatment visits will also be provided. 
Descriptive statistics for vital signs, physical examination results, ECG results, X-ray results, and 
immunogenicity test results will also be provided. Additionally, antibodies and titers will be 
summarized by scheduled time point. 
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NAME OF COMPANY 
BioMarin Pharmaceutical Inc. 
105 Digital Drive 
Novato, CA 94949 
 
NAME OF FINISHED PRODUCT: 
rAvPAL-PEG (PEGylated recombinant 
Anabaena variabilis phenylalanine ammonia 
lyase) 
 
NAME OF ACTIVE INGREDIENT: 
phenylalanine ammonia lyase 
SUMMARY TABLE 
Referring to Part of the 
Dossier: 
 
Volume: 
Page:  
Reference:  
FOR NATIONAL 
AUTHORITY USE 
ONLY: 
Efficacy Analysis: 
Data from all subjects who receive any amount of study drug and who have any post-treatment 
efficacy data will be included in the efficacy analysis. 
Blood Phe concentration at each scheduled time point will be summarized using descriptive statistics 
(mean, standard deviation, median, minimum, and maximum). Change in blood Phe concentration 
from baseline (to be defined in the Statistical Analysis Plan [SAP]) to each scheduled time point and 
presence/absence of antibodies will also be summarized. In addition, the proportion of subjects who 
have maintained target Phe concentrations of 60-600 µmol/L will be summarized by each scheduled 
time point. 
Exploratory Analysis: 
Details regarding exploratory analyses will be provided in the SAP.  
Substudy Analysis: 
For subjects who completed the Substudy, the steady-state PK of rAvPAL-PEG in subjects who have 
achieved and maintained target blood Phe will be explored. 
Pharmacokinetic Analysis: 
Subjects who complete the Substudy will have the following PK parameters assessed: area under the 
plasma concentration-time curve (AUC), time to maximum plasma concentration (Tmax), maximum 
plasma concentration (Cmax), half life (t1/2), and clearance (CL/F).  
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3 
TABLE OF CONTENTS 
1 TITLE PAGE .......................................................................................................................1 
2 SYNOPSIS ...........................................................................................................................5 
3 TABLE OF CONTENTS ...................................................................................................17 
4 LIST OF ABBREVIATIONS AND DEFINITIONS OF TERMS ....................................21 
5 ETHICS..............................................................................................................................24 
5.1 Institutional Review Board or Ethics Committee .....................................................24 
5.2 Ethical Conduct of Study ..........................................................................................24 
5.3 Subject Information and Informed Consent ..............................................................25 
6 INVESTIGATORS AND STUDY ADMINISTRATIVE STRUCTURE ........................26 
7 INTRODUCTION .............................................................................................................27 
7.1 Nonclinical Studies ...................................................................................................27 
7.2 Previous Clinical Studies ..........................................................................................28 
7.2.1 
Phase 1 Study, PAL-001 .............................................................................29 
7.2.2 
Phase 2 Studies PAL-002, PAL-004, and 165-205 .....................................29 
7.3 Study Rationale .........................................................................................................33 
7.4 Summary of Overall Risks and Benefits ...................................................................34 
7.4.1 
Toxicity Due to Exposure to Polyethylene Glycol (PEG) ..........................34 
7.4.2 
Immunologic Response ...............................................................................35 
7.4.3 
Management of Hypersensitivity Reactions ................................................37 
8 STUDY OBJECTIVES ......................................................................................................39 
9 INVESTIGATIONAL PLAN ............................................................................................40 
9.1 Overall Study Design and Plan .................................................................................40 
9.1.1 
Response to Hypersensitivity Adverse Events ............................................47 
9.1.2 
Study Stopping Criteria ...............................................................................49 
9.1.3 
Dose Modifications .....................................................................................50 
9.2 Discussion of Study Design, Including Choice of Control Group ............................51 
9.3 Selection of Study Population ...................................................................................51 
9.3.1 
Inclusion Criteria .........................................................................................51 
9.3.2 
Exclusion Criteria ........................................................................................52 
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9.3.3 
Removal of Subjects from Treatment or Assessment .................................53 
9.3.4 
Subject Identification and Replacement of Subjects ...................................54 
9.4 Treatments .................................................................................................................54 
9.4.1 
Treatments Administered ............................................................................56 
9.4.2 
Identity of Investigational Product (IP) .......................................................56 
9.4.3 
Storage .........................................................................................................59 
9.4.4 
Directions for Administration .....................................................................59 
9.4.5 
Method of Assigning Subjects to Treatment Groups ..................................61 
9.4.6 
Selection of Doses Used in the Study .........................................................61 
9.4.7 
Blinding .......................................................................................................61 
9.4.8 
Prior and Concomitant Medications ............................................................61 
9.4.9 
Treatment Compliance ................................................................................62 
9.4.10 Dose Interruption and Missed Doses ...........................................................62 
9.5 Investigational Product Accountability .....................................................................63 
9.5.1 
Return and Disposition of Clinical Supplies ...............................................63 
9.6 Dietary or Other Protocol Restrictions......................................................................63 
9.7 Efficacy and Safety Variables ...................................................................................64 
9.7.1 
Efficacy and Safety Measurements Assessed .............................................64 
9.7.2 
Efficacy Variable .........................................................................................65 
9.7.3 
Pharmacokinetic Variables ..........................................................................65 
9.7.4 
Exploratory Efficacy Variable .....................................................................66 
9.7.5 
Safety Variables ..........................................................................................66 
9.7.6 
Clinical Laboratory Assessments ................................................................67 
9.7.7 
Exploratory Sample Analyses .....................................................................69 
10 REPORTING ADVERSE EVENTS .................................................................................70 
10.1 Adverse Events .........................................................................................................70 
10.2 Serious Adverse Events ............................................................................................73 
10.3 Adverse Events Occurring Secondary to Other Events ............................................74 
10.4 Persistent or Recurrent Adverse Events ....................................................................74 
10.5 Abnormal Laboratory Values ....................................................................................74 
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10.6 Pre-existing Conditions .............................................................................................75 
10.7 General Physical Examination Findings ...................................................................75 
10.8 Hospitalization, Prolonged Hospitalization, or Surgery ...........................................76 
10.9 Deaths........................................................................................................................76 
10.10 Pregnancy..................................................................................................................76 
10.11 Follow-up of Subjects after Adverse Events ............................................................77 
10.12 Post-Study Adverse Events .......................................................................................77 
10.13 Urgent Safety Measures ............................................................................................77 
10.14 BioMarin Pharmacovigilance Contact Information ..................................................78 
11 APPROPRIATENESS OF MEASUREMENTS ...............................................................79 
11.1 Safety and Pharmacokinetics ....................................................................................79 
11.2 Diet Diary ..................................................................................................................79 
12 STUDY PROCEDURES ...................................................................................................80 
12.1 Prestudy .....................................................................................................................80 
12.2 Screening Visit ..........................................................................................................80 
12.3 Treatment Period .......................................................................................................80 
12.3.1 Day 1 (Week 1) ...........................................................................................81 
12.3.2 Weekly Telephone Visit ..............................................................................81 
12.3.3 Substudy Visits ............................................................................................82 
12.3.4 Every 8 Weeks .............................................................................................82 
12.3.5 Unscheduled Hypersensitivity Reaction Visit .............................................83 
12.4 Study Completion/Early Termination Visit ..............................................................83 
13 DATA QUALITY ASSURANCE .....................................................................................85 
14 STATISTICAL METHODS AND DETERMINATION OF SAMPLE SIZE ..................86 
14.1 Statistical and Analytical Plans .................................................................................86 
14.2 Safety Analysis .........................................................................................................86 
14.3 Pharmacokinetic Analysis .........................................................................................86 
14.3.1 Pharmacokinetic Substudy Analysis ...........................................................87 
14.4 Efficacy Analysis ......................................................................................................87 
14.5 Determination of Sample Size ..................................................................................87 
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14.6 Handling of Missing Data .........................................................................................87 
14.7 Interim Analyses .......................................................................................................88 
14.8 Changes in the Conduct of the Study or Planned Analyses ......................................88 
15 DATA MONITORING COMMITTEE (DMC) ................................................................89 
16 COMPENSATION, INSURANCE, AND INDEMNITY .................................................90 
17 CASE REPORT FORMS AND SOURCE DOCUMENTS ..............................................91 
18 STUDY MONITORING AND AUDITING .....................................................................92 
19 RETENTION OF RECORDS ...........................................................................................93 
20 USE OF INFORMATION AND PUBLICATION ...........................................................94 
21 REFERENCES ..................................................................................................................95 
22 INVESTIGATOR RESPONSIBILITIES ..........................................................................97 
22.1 Conduct of Study and Protection of Human Subjects...............................................97 
23 SIGNATURE PAGE .........................................................................................................98 
24 PROTOCOL AMENDMENT TEXT REVISIONS ..........................................................99 
 
LIST OF TABLES 
Table 9.1.1:  Schedule of Events .............................................................................................43 
Table 9.1.2:  PK Substudy Dosing Regimens ..........................................................................46 
Table 9.1.1.2.1:  Dosing Instructions in Response to Hypersensitivity Adverse Events .........48 
Table 9.1.2.1:  Brown’s Severity Criteria ................................................................................50 
Table 9.4.2.1.1:  Prefilled Syringe Volume, Concentration, and Dose ....................................57 
Table 9.4.2.1.2:  Conversion from Vial and Syringe Dose to Prefilled Syringe Dose ............58 
Table 9.4.4.1:  Fixed Doses for Subjects on Weight-Based Dose Regimen ............................60 
Table 9.7.1.1:  Summary of Laboratory Assessments .............................................................64 
Table 9.7.6.1:  Clinical Laboratory Tests ................................................................................68 
 
 
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4 
LIST OF ABBREVIATIONS AND DEFINITIONS OF TERMS 
Abbreviations 
ADR 
adverse drug reaction 
AE 
adverse event 
ALT 
alanine aminotransferase 
AST 
aspartate aminotransferase 
AUC 
area under the plasma concentration-time curve 
AUC0-7 days 
area under the plasma concentration-time curve from time zero on Day 1 to Day 
8 
BUN 
blood urea nitrogen 
°C 
degree Celsius 
C3 
complement 3 
C4 
complement 4 
CBC 
complete blood count 
CD 
Compact disk 
CFR 
Code of Federal Regulations 
CH50 
total hemolytic complement 
Cmax 
maximum plasma concentration 
CNS 
central nervous system 
CO2 
carbon dioxide 
CRA 
Clinical Research Associate 
CRF 
case report form 
CRP 
C-reactive protein 
CTCAE 
Common Terminology Criteria for Adverse Events 
CV 
cardiovascular 
DBP 
diastolic blood pressure 
DMC 
Data Monitoring Committee 
ECG 
electrocardiogram 
ETV 
Early Termination Visit 
FDA 
Food and Drug Administration 
F/U 
follow-up 
g 
gram 
GCP 
Good Clinical Practice 
GGT 
gamma-glutamyltransferase 
GI 
gastrointestinal 
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IB 
Investigator’s Brochure 
ICF 
Informed Consent Form 
ICH 
International Conference on Harmonisation of Technical Requirements for 
Registration of Pharmaceuticals for Human Use 
ID 
identification 
IgE 
immunoglobulin E 
IgG 
immunoglobulin G 
IgM 
immunoglobulin M 
IP 
investigational product 
IRB 
Institutional Review Board 
IV 
intravenous 
kg 
kilogram 
MedDRA 
Medical Dictionary for Regulatory Activities 
mg 
milligram 
mL 
milliliter 
mm Hg 
millimeter of mercury 
NAb 
neutralizing antibodies 
NCI 
National Cancer Institute 
NIAID/FAAN 
National Institute of Allergy and Infectious Disease/Food Allergy and 
Anaphylaxis Network 
NOAEL 
no observable adverse effect level 
NSAID 
non-steroidal anti-inflammatory medication 
OTC 
over the counter 
PAH 
phenylalanine hydroxylase 
PAL 
phenylalanine ammonia lyase 
PEG 
polyethylene glycol 
Phe 
phenylalanine 
PI 
Principal Investigator 
PK 
pharmacokinetics 
PKU 
phenylketonuria 
rAvPAL-PEG 
recombinant Anabaena variabilis phenylalanine ammonia lyase-PEG 
RBC 
red blood cell 
SAE 
serious adverse event 
SAP 
Statistical Analysis Plan 
SBP 
systolic blood pressure 
SC 
subcutaneous 
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SD 
standard deviation 
SDV 
source data verified 
SGOT 
serum glutamic oxalo-acetic transaminase 
SGPT 
serum glutamic pyruvate transaminase 
US 
United States 
WBC 
white blood cell 
 
Definition of Terms: 
Investigational Product (IP): 
“A pharmaceutical form of an active ingredient or placebo being tested or used as a reference 
in a clinical trial, including a product with a marketing authorization when used or assembled 
(formulated or packaged) in a way different from the approved form, or when used for an 
unapproved indication, or when used to gain further information about an approved use.” 
(from E6 ICH)  
The terms “IP” and “study drug” may be used interchangeably in the protocol. 
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5 
ETHICS 
5.1 
Institutional Review Board or Ethics Committee 
Prior to initiating the study, the Investigator will obtain written confirmation that the 
Institutional Review Board (IRB) is properly constituted and compliant with International 
Conference on Harmonisation of Technical Requirements for Registration of 
Pharmaceuticals for Human Use (ICH) and Good Clinical Practice (GCP) requirements, and 
applicable laws and local regulations. A copy of the confirmation from the IRB will be 
provided to BioMarin Pharmaceutical Inc. (BioMarin) or its designee. The Principal 
Investigator (PI) will provide the IRB with all appropriate material, including the protocol, 
Investigator’s Brochure (IB), the Informed Consent Form (ICF) including compensation 
procedures, and any other written information provided to the subjects, including all consent 
forms translated to a language other than the native language of the clinical site. The study 
will not be initiated and investigational product (IP) supplies will not be shipped to the site 
until appropriate documents from the IRB confirming unconditional approval of the protocol, 
the ICF and all subject recruitment materials are obtained in writing by the PI and copies are 
received at BioMarin or its designee. The approval document should refer to the study by 
protocol title and BioMarin protocol number (if possible), identify the documents reviewed, 
and include the date of the review and approval. BioMarin will ensure that the appropriate 
reports on the progress of the study were made to the IRB and BioMarin by the PI in 
accordance with applicable governmental regulations. 
5.2 
Ethical Conduct of Study 
This study will be conducted in accordance with the following: 
• United States (US) Code of Federal Regulations (CFR) sections that address clinical 
research studies, and/or other national and local regulations, as applicable 
• E6 ICH Guideline for GCP 
• The ethical principles established by the Declaration of Helsinki 
Specifically, this study is based on adequately performed laboratory and animal 
experimentation; the study will be conducted under a protocol reviewed and approved by an 
IRB; the study will be conducted by scientifically and medically qualified persons; the 
benefits of the study are in proportion to the risks; the rights and welfare of the subjects will 
be respected; the physicians conducting the study do not find the hazards to outweigh the 
potential benefits; and each subject, or his or her legally authorized representative will 
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provide written, informed consent before any study-related tests or evaluations are 
performed. 
5.3 
Subject Information and Informed Consent 
A properly written and executed ICF, in compliance with the Declaration of Helsinki, 
E6 ICH (GCP Guideline, Section 4.8) and 21 CFR Part 50 and other applicable local 
regulations, will be obtained for each subject prior to entering the subject into the study. The 
Investigator will prepare the ICF and provide the documents to BioMarin for approval prior 
to submission to the IRB. BioMarin and the IRB must approve the documents before they are 
implemented. A copy of the approved ICF, and if applicable, a copy of the approved subject 
information sheet, minor assent form, parental ICF for studies involving minors, and all ICFs 
translated to a language other than the native language of the clinical site must also be 
received by BioMarin or its designee prior to the delivery of study drug. 
Subjects under the age of 18 years will provide written assent (if required), and his/her 
legally authorized representative (parent or legal guardian) will provide written informed 
consent for such subjects. The Investigator will provide copies of the signed ICF to each 
subject (or the subject’s legally authorized representative) and will maintain the original in 
the subject’s record file. 
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6 
INVESTIGATORS AND STUDY ADMINISTRATIVE STRUCTURE 
Prior to beginning the study, the PI at each site must provide to BioMarin or its designee a 
fully executed and signed Form FDA (Food and Drug Administration) 1572 and a Financial 
Disclosure Form. All sub-Investigators must be listed on Form FDA 1572. Financial 
Disclosure Forms must also be completed for all sub-Investigators listed on the 
Form FDA 1572 who will be directly involved in the treatment or evaluation of research 
subjects in this study. 
The study will be administered by and monitored by employees or representatives of 
BioMarin. Clinical Research Associates (CRAs) or trained designees will monitor each site 
on a periodic basis and perform verification of source documentation for each subject as well 
as other required review processes. BioMarin’s Pharmacovigilance Department (or designee) 
will be responsible for the timely reporting of serious adverse events (SAEs) to appropriate 
regulatory authorities as required. Some study assessments, including administration of study 
drug, may be performed at the subject’s home. All assessments performed for this study will 
be administered by clinic staff or other qualified and trained study personnel. 
Anti-rAvPAL-PEG (recombinant Anabaena variabilis phenylalanine ammonia lyase 
polyethylene glycol) immunoglobulin E (IgE) antibody analysis will be performed by a 
vendor; other antibody analysis will be performed by BioMarin. Clinical laboratory tests, 
including serum pregnancy tests (if applicable), will be analyzed and processed by a central 
laboratory, with the exception of erythrocyte sedimentation rate (ESR), and urine pregnancy 
tests (if applicable), which will be analyzed by a local laboratory. A central laboratory will 
also be used to perform analysis of blood phenylalanine (Phe) concentrations and urinalysis. 
Pharmacokinetic (PK) analysis will be performed by BioMarin. 
Prior to database lock in multicenter studies, a Coordinating Investigator will be identified 
who will read the clinical study report and confirm that it accurately describes the conduct 
and results of the study, to the best of his or her knowledge. The Coordinating Investigator 
will be chosen on the basis of active participation in the study, ability to interpret data, and 
willingness to review and sign the report in a specified timeframe. 
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7 
INTRODUCTION 
A comprehensive review of PEGylated recombinant Anabaena variabilis phenylalanine 
ammonia lyase (rAvPAL-PEG) is contained in the IB supplied by BioMarin; the Investigator 
should review this document prior to initiating this study. 
7.1 
Nonclinical Studies 
The nonclinical program for rAvPAL-PEG has characterized the pharmacology, 
pharmacokinetics (PK), and toxicology of rAvPAL-PEG using the intended clinical SC route 
of administration. Pharmacology was assessed in the BTBR Pahenu2 (ENU2) mouse model of 
PKU. The ENU2 mouse model exhibits characteristics similar to those of PKU patients, 
including hyperphenylalaninemia (baseline plasma Phe concentrations of 1000 to 2000 µM) 
and hypopigmentation. Following weekly doses of rAvPAL-PEG administered to male 
ENU2 mice, plasma Phe concentrations decreased from approximately 2000 µM to 
< 200 µM after 2 dose administrations. An attenuated reduction of blood Phe was seen 
between Week 3 and Week 7 of dosing. After 7 weekly administrations of rAvPAL-PEG, 
pharmacological activity returned as evidenced by stabilized concentrations of plasma Phe 
< 200 µM over the entire week, which continued for a total of 15 weeks. 
In pharmacodynamic studies in the BTBR Pahenu2 (ENU2) mouse model administered 
80 mg/kg/week rAvPEG-PAL, two dose interruption assessments were performed: 
a 2-4 week dose interruption and an 11-week dose interruption. Following both dose 
interruption assessments, the animals re-started rAvPAL-PEG at a dose of 80 mg/kg/week. 
No attenuated Phe response was observed when rAvPAL-PEG injections were temporarily 
stopped for 2-4 weeks, and there was an immediate return to stable blood Phe reductions. 
A similar interim attenuated response was observed with the longer dose interruption of 
approximately 11 weeks. In both of these assessments, no safety issues were noted upon 
re-starting dosing with rAvPAL-PEG (Lapis, 2007, ASHG 57th Annual Meeting). 
Safety pharmacology studies were conducted in rats and cynomolgus monkeys. No 
respiratory or central nervous system (CNS) effects were seen with SC administration of 
rAvPAL-PEG. No changes in cardiovascular (CV) parameters, including electrocardiogram 
(ECG) waveforms, were observed in telemetry-instrumented monkeys assessed for the CV 
effects of rAvPAL-PEG administered subcutaneously. 
Pharmacokinetic parameters were evaluated in single-dose and repeat-dose studies in rats and 
cynomolgus monkeys. The elimination half-life (t1/2) values of rAvPAL-PEG administered to 
normal rats at SC doses of 10, 25, and 250 mg/kg were 47, 33, and 44 hours, respectively, 
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and exhibited modest area under the plasma concentration-time curve (AUC)-dose. In the 
cynomolgus monkey after SC administration of rAvPAL-PEG, the t1/2 was 65 hours at 
4.0 mg/kg, 71 hours at 12 mg/kg, and could not be determined at 60 mg/kg (the highest 
dose). Qualitatively, the kinetics of rAvPAL-PEG in the rat and monkey appear to have 
similar characteristics. The following findings were noted: (1) a 1-compartment model with 
first-order absorption appears to describe the plasma profiles of rAvPAL-PEG after 
single-dose administration, (2) absorption is slow and there is a long absorption period after 
SC administration to maximum observed plasma concentration (Cmax), along with a long t1/2, 
(3) elimination is slow and monophasic, (4) there does not appear to be a gender difference, 
and (5) the AUC and the Cmax are roughly linearly proportional.  
Toxicology of rAvPAL-PEG was assessed in single-dose and repeat-dose studies in normal 
rats and cynomolgus monkeys. In the single-dose rat study, decreased body weight gain and 
Kupffer cell vacuolization at the high SC dose of 250 mg/kg was observed; however, the 
Kupffer cell finding was not seen in the single-dose study in cynomolgus monkeys. In a 
26-week repeat-dose toxicity and toxicokinetic (TK) rat study, decreased body weight gain, 
decreased food consumption, vacuolation/hypertrophy of the renal tubule cells, and 
vacuolation of the histiocytic cells were observed in rats administered 25 mg/kg/dose, twice 
weekly. In a 39-week repeat-dose study in monkeys, arterial inflammation, perivascular 
cellular infiltrates in the SC injection sites, thymic atrophy, and increased lymphoid nodules 
in bone marrow of the sternum were observed in monkeys given ≥ 3 mg/kg/dose, twice 
weekly. Of these findings, only the arterial inflammation was deemed adverse and this 
finding was completely reversed after 13-weeks of recovery. The 
no-observed-adverse-effect-level (NOAEL) of rAvPAL-PEG when administered 
subcutaneously twice weekly for 26 weeks and 39 weeks in the rat and monkey, respectively, 
was 1.0 mg/kg. These NOAELs were based on histological findings of 
vacuolation/hypertrophy of the renal tubule cells in the rat and arterial inflammation findings 
in the monkey. 
7.2 
Previous Clinical Studies 
The rAvPAL-PEG clinical development program has been designed to demonstrate the 
safety and efficacy of rAvPAL-PEG in reducing blood Phe concentrations in PKU subjects 
who do not respond to treatment with Kuvan® or are not compliant with Kuvan® treatment. 
This study is an extension of the ongoing human clinical studies with rAvPAL-PEG 
(Study PAL-002, Study PAL-004, and Study 165-205) based on data from the completed 
clinical study, PAL-001, and clinical experience from this ongoing study and the other 
ongoing Phase 2 studies, PAL-002 and PAL-004.  
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7.2.1 Phase 1 Study, PAL-001 
The first-in-human trial using rAvPAL-PEG, Study PAL-001, was a Phase 1, open-label, 
dose-escalation study in PKU subjects in the US. The primary objective was to assess the 
safety and tolerability of single SC injections of rAvPAL-PEG. Secondary objectives were to 
evaluate the PK of single, SC injections of rAvPAL-PEG administered at escalating doses in 
subjects with PKU and to evaluate the effect of rAvPAL-PEG on blood Phe concentrations. 
The effectiveness of rAvPAL-PEG in decreasing Phe concentrations in nonclinical studies of 
ENU2 mice was consistent with what was observed in PAL-001. PAL-001 enrolled 25 PKU 
subjects with a mean (standard deviation; SD) baseline blood Phe concentration of 
1310 µmol/L (405). The 25 subjects who enrolled into the study were assigned to receive a 
single administration of rAvPAL-PEG at 1 of 5 dose levels: 0.001, 0.003, 0.01, 0.03, and 
0.1 mg/kg. Five subjects each received 1 of the 5 dose levels of rAvPAL-PEG. 
Key safety, efficacy, and PK results of Study PAL-001 are summarized as follows: 
• rAvPAL-PEG was well tolerated and had a clinically significant blood-lowering 
effect on Phe concentration when administered at a dose of 0.1 mg/kg. 
• For the 5 subjects who were administered 0.1 mg/kg rAvPAL-PEG, clinically 
significant reductions in blood Phe level were observed, with the most clinically 
significant decreases from baseline values to Day 7, ranging from 33.8% to 97.3% 
(mean of 58.12%). The mean baseline blood Phe level for these 5 subjects was 
1113 µmol/L. 
• Overall, no clinically significant reductions in blood Phe level were observed in 
subjects who were administered rAvPAL-PEG at the lower doses of 0.001, 0.003, 
0.01, and 0.03 mg/kg. 
• For subjects who were administered rAvPAL-PEG at the 3 higher dose levels 
(0.01, 0.03, and 0.1 mg/kg) and who had measurable rAvPAL-PEG concentration 
levels, the calculated PK parameters were a mean Tmax of 89-106 hours, a t1/2 of 
46-120 hours, and an AUC0-t, and Cmax that were proportional with dose. 
Drug exposure was slightly increased with increased dose. 
7.2.2 Phase 2 Studies PAL-002, PAL-004, and 165-205 
Based on results from the Phase 1, single-dose study, the Phase 2 studies have been designed 
to evaluate rAvPAL-PEG at various doses and dosing regimens to safely achieve and 
maintain blood Phe reductions in subjects with PKU. Currently, there are three ongoing 
Phase 2 studies (PAL-002, PAL-004, 165-205); an overview of each study is presented in 
Section 7.2.2.1 (PAL-002), Section 7.2.2.2 (PAL-004), and Section 7.2.2.3 (165-205).  
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7.2.2.1 
Study PAL-002 
Study PAL-002 (A Phase 2, Open-Label, Dose-Finding Study to Evaluate the Safety, 
Efficacy, and Tolerability of Multiple Subcutaneous Doses of rAvPAL-PEG in Subjects With 
Phenylketonuria) was initiated in September 2009 and has completed enrollment. As of 
10 September 2012, 40 subjects have been enrolled and 37 have completed the study. 
PAL-002 enrolled 11 previously exposed subjects from the single-dose study, PAL-001, and 
29 subjects who were naïve to rAvPAL-PEG. Thirty-three of the 37 subjects who completed 
PAL-002 enrolled into this open-label extension study (PAL-003). Two subjects 
discontinued from the study due to lost to follow-up, relocation, or other reasons, and 
1 subject discontinued from the study due to an AE (skin reaction).  
The primary objective of this study was to evaluate the effect of multiple doses of 
rAvPAL-PEG (ranging from 0.001 mg/kg/week to 1.0 mg/kg/week) on blood Phe 
concentrations in subjects with PKU with up to 16 weeks of treatment. The secondary 
objectives of the study were to evaluate the safety and tolerability of SC injections of 
multiple doses of rAvPAL-PEG, to evaluate the immune response to rAvPAL-PEG, and to 
evaluate the PK profile of rAvPAL-PEG in subjects with PKU.  
The PAL-002 study design consists of two parts. In Part 1, rAvPAL-PEG was administered 
as a once weekly fixed, low-dose induction regimen for 8 weeks. In Part 2, the rAvPAL-PEG 
dose was titrated upwards; subjects received adjustable dose increases for up to 8 weeks to 
achieve a target blood Phe concentration of 600 µmol/L. The doses and dosing schedules 
were revised with a series of protocol amendments to incorporate the information gained 
during conduct of this early, open-label, multiple-dose study.  
A wide range of doses was planned for the PAL-002 study, beginning with doses as low as 
0.001mg/kg/week.  However, no substantial reductions in blood Phe level were observed in 
the majority of subjects who were administered rAvPAL-PEG in the initial four cohorts at 
doses of 0.001, 0.003, 0.01, and 0.03 mg/kg administered once per week. The absence of 
appreciable Phe reduction after 16 weeks of treatment in this range of doses led to a decision 
to amend the study protocol to include a cohort with a higher starting dose of 
0.1 mg/kg/week, which had been previously shown to decrease blood Phe levels to 
approximately 600 µmol/L in the single-dose, Phase 1 study (PAL-001). After the first 
2 weeks of dosing at 0.1 mg/kg/week, transient Phe reduction was observed in this subset of 
subjects. However, this dosing regimen was accompanied by mild to moderate 
hypersensitivity reactions primarily after the second weekly dose, suggesting that additional 
exploration of dosing regimens would be required.  
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In summary, preliminary results from PAL-002 demonstrated that doses below 0.1 g/kg 
administered once per week were not effective in reducing Phe levels.  While transient 
reduction of Phe was apparent at doses of at least 0.1 mg/kg given once per week, this dose 
regimen was associated with a high incidence of systemic hypersensitivity reactions, 
typically following the second weekly dose.  Further escalation above this dose of 
0.1 mg/kg/week would be required to sustain the effect on Phe levels over time.  Increased 
doses would require spreading dose administration over several days per week, as 
once-weekly administration of higher doses would not be practical due to the large volume of 
study drug.  Therefore, additional dosing regimens would need to be explored in a 
subsequent study (PAL-004). 
Once subjects completed Study PAL-002, they were eligible to enroll into this open-label 
extension study, PAL-003 to continue to receive rAvPAL-PEG up to a maximum dose of 
5.0 mg/kg/week or 375 mg/week. 
7.2.2.2 
Study PAL-004 
PAL-004 (An Open-Label Study to Evaluate the Safety, Tolerability, and Efficacy of 
Subcutaneous Dose Levels of rAvPAL-PEG Administered Daily in Subjects With 
Phenylketonuria) was initiated in April 2011 and has completed enrollment. As of 
10 September 2012, 16 subjects have been enrolled, 15 subjects have completed the study, 
and 15 subjects have enrolled into this study (PAL-003). One subject withdrew consent from 
continued participation prior to study completion. All subjects enrolled in this study were 
naïve to rAvPAL-PEG exposure. 
The objective of this study was to determine if daily administration (defined as 5days/week) 
of rAvPAL-PEG at dose levels of 0.06, 0.1, 0.2, 0.4, 0.6, and 0.8 mg/kg/day was safe and 
effective in reducing and maintaining blood Phe concentrations to 600 µmol/L in subjects 
with PKU. The starting dose was 0.4 mg/kg, administered 5 days/week. A total of 12 subjects 
were added in sequence and were started on doses of 0.4, 0.2, 0.1, 0.06 mg, or 0.001/kg/day 
based on incoming safety data. Overall, subjects in PAL-004 who initiated treatment at 
higher daily doses of 0.1 to 0.4 mg/kg/day achieved immediate and substantial reduction of 
blood Phe levels, but dosing had to be temporarily reduced or interrupted due to the onset of 
systemic hypersensitivity reactions at approximately Day 10 of dosing. Phe reductions did 
not persist in the setting of temporary dose reduction or interruption, but Phe levels generally 
improved if higher dose levels were reinstated.  
To prevent the onset of hypersensitivity reactions that were temporally associated with the 
onset of anti-drug IgM responses, an additional dosing strategy was assessed in PAL-004; 
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administration once per week at a low dose (2.5mg) with gradual escalation and conversion 
of dose administration to 5x/week dosing for chronic maintenance therapy.  
Once subjects have completed Study 165-205, they are eligible to enroll into this study to 
continue to receive rAvPAL-PEG up to a maximum dose of 5.0 mg/kg/week or 
375 mg/week, or into the Phase 3 study, 165-302. 
7.3 
Study Rationale 
PKU is an autosomal, recessive, inherited disease characterized by deficiency in the enzyme 
PAH. Approximately 1 in every 10,000 infants in North America is born with PKU 
(Scriver, 2001, McGraw-Hill). Left untreated, PAH deficiency is associated with an 
abnormally elevated concentration of Phe, which is toxic to the brain (Kaufman, 1989, J 
Pediatr.) and can result in a variety of neuropathologic conditions, including mental 
retardation, microcephaly, delayed speech, seizures, and behavioral abnormalities 
(Scriver, 2001, McGraw-Hill). The brains of untreated patients with PKU show evidence of 
hypomyelination and gliosis, arrest in cerebral development, and, in some cases, white matter 
degeneration (Huttenlocher, 2000, Eur.J Pediatr.). Elevated Phe during fetal development 
leads to severe mental retardation and can cause microcephaly, growth retardation, and 
congenital heart disease (Guttler, 2003, Pediatrics), (Koch, 2003, Pediatrics), (Lee, 2003, 
Pediatrics), (Levy, 2003, Pediatrics), (Matalon, 2003, Pediatrics), (Rouse, 2004, J.Pediatr.). 
For a subset of patients with residual enzyme activity, treatment with Kuvan® is an option. 
For all other patients, current management of PKU involves adherence to low-Phe medicinal 
diet formulas and dietary restriction of Phe-containing foods. Implementation of a 
Phe-restricted diet in infancy significantly reduces blood Phe concentrations and prevents 
many of the neuropathologic manifestations of PKU, including severe mental retardation. 
However, compliance with this restrictive diet can be difficult for older children, adolescents, 
and adults, and adherence may result in nutritional deficiencies due to the limitations of 
natural protein sources (Fisch, 2000, Eur.J.Pediatr.), (Walter, 2002, Lancet). 
The need exists for a treatment that will help individuals with PKU safely achieve lifelong, 
reliable control of blood phenylalanine (Phe) concentrations and improve functional 
outcomes. rAvPAL-PEG is a potential substitute for the phenylalanine hydroxylase (PAH) 
enzyme, which is defective in individuals with PKU. rAvPAL-PEG may control blood Phe 
concentrations, which may have additional clinical benefits.  
Blood Phe levels depend not only on the functional presence of the endogenous enzyme PAH 
but also on the dietary intake of Phe. It is important to understand the role of diet on blood 
Phe levels concurrent with the administration of rAvPAL-PEG treatment. Therefore, an 
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exploratory objective has been added to this study to assess the relationship of diet, 
rAvPAL-PEG administration, and blood Phe level. Changes to subject diet are not allowed in 
this study unless per the Investigator. Diet will be monitored using a diet diary.     
A pharmacokinetic (PK) substudy has been added to evaluate the steady-state PK of 
rAvPAL-PEG in up to 6 subjects who have achieved and maintained target blood Phe for at 
least 2 consecutive measurements and for whom no further dose modifications are planned. 
Single-dose PK data has been collected in the Phase 1 study, PAL-001. However, there is 
little multiple-dose PK data or data for when subjects have reached and maintained a stable 
dosing regimen.  With the PK substudy, multiple-dose PK data will be collected for subjects 
who have already achieved Phe reduction to within the protocol-defined target range. 
This study is an extension of previous rAvPAL-PEG Phase 2 studies. Administration of 
rAvPAL-PEG will be continued to assess the long-term safety and efficacy of rAvPAL-PEG 
in PKU subjects. 
7.4 
Summary of Overall Risks and Benefits 
It is not expected that data from previous rAvPAL-PEG studies will change the assumption 
that rAvPAL-PEG has a toxicity profile similar to other recombinant PEGylated non-human 
enzymes currently in use. The toxicities of these drugs usually fall into 2 main categories: 
toxicity due to exposure to PEG, and toxicity due to immunologic sensitization. In addition, 
exaggerated pharmacological effects resulting in very low Phe concentrations could be 
observed. Other adverse events (AEs) that could occur with rAvPAL-PEG include 
injection-site reactions and other general symptoms. 
7.4.1 Toxicity Due to Exposure to Polyethylene Glycol (PEG) 
Acute exposure to high doses of PEG can result in renal toxicity. There have been a few 
reports of PEG-related AEs in humans; cumulative intravenous (IV) PEG doses of 121 to 
240 g caused acute renal tubular necrosis, oliguria, and azotemia. The anticipated PEG 
exposure associated with the expected rAvPAL-PEG dose range (6 g per week) is at least 
80-fold lower than the reported toxic doses and comparable to exposures to PEG in widely
used medicines and other compounds that are administered by the IV, oral, rectal, and topical
routes (Webster, 2007, Drug Metab Dispos.). No indication of PEG-related toxicity at the
ultrastructural level was observed in monkeys given a single dose of up to 60 mg/kg
rAvPAL-PEG SC. In rats, both renal tubule vacuolation and histiocytic cell vacuoles have
been assocated with PEG-related catabolism and administration of other PEGylated proteins
(refer to Section 7.1).
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Based on phase 3 data, as of 4MAR2016, there have been no reported events of 
glomerulonephritis or renal failure reported with pegvaliase administration. Of the 
10 subjects identified with UAC ratios  ≥ 3 mg/mmol on 3 or more consecutive 
measurements, values were generally in the microalbuminuria range and none had concurrent 
sustained hematuria. Seven of these 10 subjects had microalbuminuria at baseline prior to 
pegvaliase exposure, of which 2 events resolved while on pegvaliase treatment and 4 events 
did not progress while subjects remained on pegvaliase. One of these 7 subjects with baseline 
microalbuminuria (3.62 mg/mmol at baseline) had an increase in their UAC ratio during the 
study, which was more apparent after dose titration to 60 mg of pegvaliase (remaining in 
microalbuminuria range, with a most recent value of 20.36 mg/mmol), however evaluating 
relationship to pegvaliase treatment is confounded by a medical history of obesity, 
hypertension, and new onset pre-diabetes during the Phase 3 study that are conditions also 
associated with development of microalbuminuria. The subject continues on pegvaliase 
treatment with continued safety monitoring. 
Three of the 10 subjects developed new onset microalbuminuria for at least 3 consecutive 
measurements during the Phase 3 study, one of which resolved while continuing on 
pegvaliase treatment and 1 subject continues to have fluctuating low level microalbuminuria 
with intermittent values in the normal range. One subject discontinued from the Phase 3 study 
after a few intermittent elevations into the microalbuminuria range. The subject had a 
maximum UAC ratio of 175 mg/g on Day 8 on the study; at the time of study and study drug 
discontinuation (Day 36), UAC ratio was within the normal range at 19 mg/g. The final study 
visit recorded for this subject (Day 67) had a UAC ratio of 17 mg/g.  This subject reported a 
single concurrent grade 1 event of urticaria, which resolved in 2 days, and no other reported 
events suggestive of immune complex disease. None of the subjects described above have 
developed sustained elevations in serum creatinine or concurrent sustained hematuria. 
To monitor for renal toxicity, subjects participating in this study will undergo urinalysis, will 
be assessed for urine albumin/creatinine ratio, and will undergo blood chemistry tests to 
assess renal function. 
7.4.2 Immunologic Response 
The active drug substance in rAvPAL-PEG is a bacterial protein and elicits immune 
recognition and subsequent antibody responses. Antibody epitopes on the protein are 
expected to be rendered at least partially inaccessible by the extensive PEGylation on the 
drug (Gamez, 2007, Mol.Genet.Metab). In vivo and in vitro experiments have shown that 
PEGylation of proteins and cells can attenuate the immunological response (Scott, 1997, 
Proc.Natl.Acad.Sci.U.S.A), (Chen, 2001, BioDrugs.). PEGylation has been effective in 
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reducing anti-rAvPAL antibody titers in the mouse model but does not eliminate antibody 
formation. Although PEGylation of rAvPAL likely reduces the antigenicity of the molecule, 
100% of individuals exposed to rAvPAL-PEG develop antibodies against rAvPAL.  
Drug-specific immune responses can range from clinical irrelevance to causing serious 
hypersensitivity AEs (such as anaphylaxis) and may reduce efficacy due to 
antibody-mediated drug clearance or antibody neutralization of enzymatic activity. 
Historically, PEG was thought to be nonimmunogenic (Davis, 1981, Clin.Exp.Immunol.), 
(Harris, 2003, Nat.Rev.Drug Discov.); however, repeated studies have found that 
subcutaneous (SC) and intravenous exposure to PEG can induce anti-PEG antibodies 
(Harris, 2003, Nat.Rev.Drug Discov.), (Richter, 1983, Int.Arch.Allergy Appl.Immunol.). In 
some instances, development of such antibodies did not result in significant clinical effects in 
humans (Richter, 1984, Int.Arch.Allergy Appl.Immunol.). However, PEG antibody responses 
were associated with hypersensitivity reactions to PEGylated liposomes (Judge, 2006, 
Mol.Ther.). Anti-PEG antibodies have also been associated with nonresponsiveness against 
therapy (Armstrong, 2007, Cancer), (Ganson, 2006, Arthritis Res.Ther.). 
Subjects participating in the Phase 2 clinical studies have been monitored closely for 
anti-drug immunogenicity (anti-rAvPAL immunoglobulin G [IgG], anti-rAvPAL IgM, 
anti-PEG IgM, anti-PEG IgG, neutralizing antibodies that inhibit PAL enzymatic activity, 
anti-rAvPAL IgE, and anti-rAvPAL-PEG IgE), complements, C-reactive protein (CRP), 
ESR, and complete chemistry. All subjects treated with rAvPAL-PEG in the Phase 2 clinical 
trials developed antibodies against the PAL protein. Anti-rAvPAL IgM antibodies were first 
detected within 2-3 weeks of treatment initiation and anti-rAvPAL IgG antibodies were 
detected within 2-3 months. The anti-rAvPAL IgG response generally peaked by 3-5 months 
and was sustained in all subjects. Neutralizing antibodies (NAb) capable of inhibiting 
enzymatic activity were detected in a minority of subjects 2-3 months after treatment 
initiation. The timing of the NAb response suggests these antibodies may be a component of 
the anti-rAvPAL IgG response. It is expected that the centralized location of the PAL active 
site, within the tetrameric structure, makes it difficult for antibodies to bind and inhibit 
enzymatic activity. In addition, anti-PAL antibody binding is likely sterically hindered by the 
extensive PEGylation. The majority of treated subjects also developed a transient anti-PEG 
antibody response. The anti-PEG response was comprised of IgM and IgG isotypes. In 
general, anti-PEG antibodies were no longer detected after 5-6 months of treatment. This 
type of transient antibody response is typical of T cell-independent type 2 (TI-2) responses. 
The majority of immune-mediated AEs experienced in subjects treated with rAvPAL-PEG in 
the Phase 2 studies are believed to be the result of antibody-mediated hypersensitivity. The 
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primary immune mediator is thought to be IgM immune complexes, as evidenced by the 
timing of onset prior to IgG development and the reduced occurrence over time. IgE positive 
test results have not been associated with hypersensitivity in any of the subjects thus far, and 
the majority of subjects have been safely rechallenged with rAvPAL-PEG following 
reactions. IgM immune complexes are known to be efficient activators of the classical 
complement pathway and can lead to the accumulation of complement component 
anaphylatoxins (C3a, C4a, C5a) that can induce hypersensitivity symptoms. Although IgG 
immune complexes can also activate the classical complement pathway, they do so with less 
efficiency than IgM. This is due, in part, to the requirement for multiple Fc regions in close 
proximity to activate the complement cascade, meaning that multiple monomeric IgG Abs 
are required to bind, whereas only one pentameric IgM Ab is needed to bind to activate 
complement. Also, in the case of rAvPAL-PEG, binding of anti-PAL IgG antibodies is likely 
compromised due to epitope masking by the PEGylation, which may reduce IgG-mediated 
complement activation in vivo. This complex dynamic between combined isotype-specific 
Ab responses and epitope accessibility is thought to be a major factor dictating the need for 
an induction and titration dose regimen in the treatment of rAvPAL-PEG to be implemented 
in this study. 
7.4.3 Management of Hypersensitivity Reactions 
Hypersensitivity reactions to the SC injection of rAvPAL-PEG may be mild, moderate, or 
severe in intensity. Reactions may include pruritus, rash, shortness of breath, hypotension, or 
anaphylaxis. Clinical assessments should be conducted for a minimum of 30 minutes 
post-injection. Longer observations may be required at the discretion of the PI. 
The responsible physician should use all appropriate measures for the treatment of 
hypersensitivity reactions. Because of the potential for anaphylaxis, equipment for 
emergency resuscitation (including epinephrine) should be within easy access during and 
after the rAvPAL-PEG injection. Subject should be pre-medicated with H1 antagonist, H2 
antagonist, and antipyretics (eg, acetaminophen) approximately 2-3 hours prior to each dose 
of study drug for one week upon return to dosing regardless of the duration of dose 
interruption. If non-steroidal anti-inflammatory medication (NSAIDs) is administered as a 
premedication, it should be given with food.  Subjects who qualify for self-administration of 
study drug are trained to recognize a serious hypersensitivity AEs and how to respond. 
Additionally, subjects are given two epinephrine injectors and are instructed to carry one 
epinephrine injector with them at all times (Section 9.4). Refer to Section 9.1.1.3 for 
instructions regarding resumption of study drug following resolution of symptoms consistent 
with a clinical diagnosis of anaphylaxis per National Institute of Allergy and Infectious 
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Disease/Food Allergy and Anaphylaxis Network (NIAID/FAAN) criteria (Sampson, 2006, 
J.Allergy Clin.Immunol.).
In the event of a hypersensitivity reaction, subjects may be asked to see an 
allergist/immunologist and/or provide up to 3 additional blood samples for immunology 
studies and complement testing. This additional testing may occur up to 6 months following 
the final study visit.  
The following measures are recommended for the treatment of hypersensitivity reaction 
symptoms: 
•
Maintain the airway.
•
Vital sign check.
•
Administration of oral or IV diphenhydramine.
•
Administration of epinephrine if appropriate.
•
Administration of oral or IV glucocorticoids.
•
Administration of oxygen and IV fluids.
•
Administration of additional symptomatic treatment.
•
Transfer to an acute care facility of the study center.
In addition, clinical judgment must be used in determining the appropriateness of 
corticosteroid administration. An allergy and/or immunology consultation should be sought if 
necessary. Detailed instructions for the management of hypersensitivity reactions are 
provided in the Study Reference Manual. 
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8 
STUDY OBJECTIVES 
The primary objective of the study is: 
•
To evaluate the effect of long-term administration of multiple doses of SC injections
of rAvPAL-PEG on blood Phe concentrations in subjects with PKU.
The secondary objectives of the study are: 
•
To evaluate the safety and tolerability of long-term administration of subcutaneous
(SC) injections of rAvPAL-PEG in subjects with PKU.
•
To evaluate the immune response to long-term administration of SC injections of
rAvPAL-PEG in subjects with PKU.
The exploratory objective of the study is as follows: 
•
To evaluate the long-term relationship of diet and change in blood Phe concentration
following administration with rAvPAL-PEG in subjects with PKU.
The Substudy objective is as follows: 
•
To evaluate steady-state PK of rAvPAL-PEG in subjects who have achieved and
maintained target blood Phe concentration and for whom no further dose
modifications are planned.
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9 
INVESTIGATIONAL PLAN 
9.1 
Overall Study Design and Plan 
This is a long-term extension of rAvPAL-PEG Phase 2 studies in up to 100 subjects with 
PKU. The doses are planned to be in the same range as those previously tested in the Phase 2 
studies (starting at 0.001 through 5.0 mg/kg/week or 2.5 mg through 375 mg/week), provided 
no dose-limiting toxicity was observed in a previous rAvPAL-PEG studies. Subjects’ doses 
will not exceed 375 mg/week. 
Only subjects who completed a previous rAvPAL-PEG study will be enrolled into this study. 
Subjects enrolling into PAL-003 with no interruption in dosing from a previous 
rAvPAL-PEG study may either continue their previous dosing regimen or begin this study at 
a higher dose level. Subjects who have had dosing interruptions between the previous 
rAvPAL-PEG study and PAL-003 must have their starting dose determined per the sponsor’s 
medical monitor.  The first week of dosing will be administered in the clinic, and the subject 
must be observed for 30 minutes following administration. Subjects are given two 
epinephrine injectors and are instructed to carry one epinephrine injector with them at all 
times (refer to Section 9.4). A follow-up telephone call will be made to the subject to monitor 
subject safety 24 hours following the return to dosing. 
Diet should not be altered during the course of this study. Any decision to modify subject 
diet must be made per the Investigator and must be performed under the supervision of the 
Investigator. To monitor for changes in subject diet, a diet diary will be issued to subjects for 
completion and will be brought to clinic monthly for review with the clinical study staff. 
Subjects may self-administer study drug at home if approved by the Investigator and the 
sponsor’s medical monitor and if adequate training is demonstrated. Subjects must meet a set 
of criteria to be considered appropriate for self-administration. Refer to Section 9.4 for the 
criteria for which subjects may qualify for self-administration. Additional information is 
provided in the Subject Self-Administration Training Materials. Additional training will be 
provided and demonstration of competency required when prefilled syringe drug product is 
introduced, every 24 weeks, and more often as needed. 
Subjects will be evaluated for safety throughout the study. Toxicity will be measured 
according to the National Cancer Institute (NCI) Common Terminology Criteria for Adverse 
Events (CTCAE), version 4. 
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In addition to the Sponsor, a Data Monitoring Committee (DMC) will monitor the safety of 
subjects in the study. The DMC is an independent committee that will act in an advisory 
capacity to the Sponsor. 
PAL-003 is designed to evaluate long-term treatment of subjects who are continuing to take 
rAvPAL-PEG. Subjects’previous rAvPAL-PEG dosing will generally continue in PAL-003. 
In PAL-003, each subject’s dose will be adjusted as needed to attempt to attain or maintain 
blood Phe concentrations of 60-600 µmol/L. rAvPAL-PEG dose will be based on either a 
subject’s weight or will be a fixed dose. Doses will be evaluated on an individual basis.  
Evaluations, observations, and procedures will be conducted at selected time points as shown 
in Table 9.1.1 and Table 9.1.2.  After the subject’s blood Phe concentration has been 
controlled to within a target range (60-600 µmol/L), the subject may be asked to have 
additional blood draws for PK and blood Phe concentration analyses as needed per the 
discretion of the Investigator in consultation with the sponsor’s medical monitor. 
A subject will continue in PAL-003 until one of the following occurs: 
• The subject withdraws consent and discontinues from the study. 
• The subject is discontinued from the study at the discretion of the Investigator or 
Sponsor. 
• The subject has completed the study through the Week 476 visit.  
• The study is terminated. 
• The study drug receives marketing authorization.  
 
Because the risks of taking BMN 165 during pregnancy and breastfeeding are unknown, 
subjects cannot take BMN 165 if they are trying to conceive, are pregnant, or are 
breastfeeding (refer to Section 9.3.2 for Exclusion Criteria). Male subjects who are planning 
to impregnate a female partner and female subjects who are trying to become pregnant during 
the study must be temporarily discontinued from study drug for 4 weeks prior to trying to 
conceive. During that time, subjects must use two acceptable methods of contraception. 
Subjects who are planning to become pregnant (or impregnate a female partner) may modify 
their diet in consultation with the investigator and/or study dietician. Subjects who are 
confirmed to be pregnant per a serum pregnancy test and are temporarily off study drug are 
not required to perform the scheduled urine pregnancy tests. Subjects who are pregnant or are 
trying to conceive and have temporarily discontinued study drug should not perform the 
scheduled PK assessments. Male subjects who have impregnated a female partner may 
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re-start study drug after conception following the investigator’s consultation with and 
approval by the medical monitor. Male subjects must return to the study-required 
contraception use (refer to Section 9.3.1 for Inclusion Criteria), which must include one 
barrier method, prior to restarting study drug. Female subjects who remain in the study after 
temporary discontinuation of study drug due to pregnancy may restart BMN 165 dosing after 
a confirmed negative urine pregnancy test result, the birth has been reported (or termination 
of the pregnancy), and breastfeeding has completed (if applicable) or after the subject is no 
longer actively trying to conceive. Re-starting BMN 165 dosing requires the investigator’s 
prior consultation with and approval by the medical monitor. Female subjects must return to 
the study-required contraception use (refer to Section 9.3.1), which must include one barrier 
method, immediately after the birth (or termination of the pregnancy).  
Subjects may withdraw from treatment with study drug at any time; however, subjects will 
be asked to continue to perform the study assessments until study completion. Subjects may 
also withdraw from study participation at any time. Because the completeness of the data 
affects the integrity, accuracy, and interpretation of study results, every effort should be made 
to retain subjects in the study and to have them complete the study assessments as scheduled 
as long as continued participation does not compromise subject safety.  
A PK substudy has been added to evaluate the steady-state PK of rAvPAL-PEG in up to 
6 subjects who have achieved and maintained target blood Phe for at least 2 consecutive 
measurements and for whom no further dose modifications are planned.  Subjects enrolled 
into the substudy will have additional pre-dose PK sampling performed (refer to Table 9.1.2). 
The Schedule of Events and PK substudy collection schedules are presented below in 
Table 9.1.1 and Table 9.1.2. 
 
 
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Table 9.1.1:  Schedule of Events  
Assessments and 
 Events 
Screeninga 
Treatment Periodb,c 
Self-
Administration 
Study 
Completion/Early 
Term. Visit 
Unsched. Hyper. 
Reaction Visit.d  
Perform within 
24 hours 
Week 1 
Weekly 
Telephone 
Contacts 
Every 8 Weeksb 
D 1 
Starting at Week 
2 
 
 
4 weeks after final 
dose 
Informed consent 
X 
 
 
 
 
 
 
Medical history, including 
allergy history, and 
demographics 
X 
 
 
 
 
 
 
Physical examinatione 
X 
X 
 
X 
 
X 
 
Vital signse 
X 
X 
 
X 
 
X 
X 
Weight 
X 
 
 
X 
 
 
 
12-lead ECG 
X 
 
 
 
 
X 
 
Clinical laboratory testsf 
X 
 
 
X 
 
X 
Xg 
Complements C3 and C4h 
X 
 
 
X 
 
 
Xg 
Sedimentation rate 
 
X 
 
X 
 
X 
 
Chest x-ray 
X 
 
 
X  
(Week 48 visit 
only) 
 
X 
 
Urine pregnancy testi 
X 
X 
 
X 
 
X 
 
Adverse eventsj,k 
X 
X 
X 
X 
X 
X 
X 
Weekly phone call to self admin 
participants only (to assess AEs, 
Inj site reactions, concomitant 
medications) 
 
 
X 
 
X 
 
 
Concomitant medications 
X 
X 
 X 
X 
X 
X 
X 
Diet query 
X 
X 
 
X 
 
X 
 
3-Day diet diaryl 
 
 
 
X 
 
X 
 
Serum antibodiesm 
 
X 
 
X 
 
X 
X 
Plasma Phe and plasma 
tyrosinen  
X 
X 
 
Xm 
 
X 
 
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Assessments and 
 Events 
Screeninga 
Treatment Periodb,c 
Self-
Administration 
Study 
Completion/Early 
Term. Visit 
Unsched. Hyper. 
Reaction Visit.d  
Perform within 
24 hours 
Week 1 
Weekly 
Telephone 
Contacts 
Every 8 Weeksb 
D 1 
Starting at Week 
2 
 
 
4 weeks after final 
dose 
Urine albumin/creatinine ratio o 
 
 
 
 
 
 
X 
Urine N-methyl histamine 
 
 
 
 
 
 
X 
Plasma PK samplep 
 
X 
 
X 
 
X 
 
Administer study drugq 
 
X 
 
X 
X 
 
 
Training (prefilled syringe)r 
 
 
 
X 
Every 24 weeks 
only 
 
 
 
Skin biopsy (optional; affected 
and not affected area) 
 
 
 
 
 
 
X 
Serum tryptase levels 
 
 
 
 
 
 
X 
AE, adverse event; C3, complement 3; C4, complement 4; CH50, total hemolytic complement; CRP, C-reactive protein; D, day; ECG, electrocardiogram; eCRF, electronic 
Case Report Form; ETV, Early Termination Visit; F/U, Follow-up; Hyper, hypersensitivity; IgE, immunoglobulin E; IgG, immunoglobulin G; IgM, immunoglobulin M; 
IP, investigational product; PK, pharmacokinetics; Phe, phenylalanine; SAE, serious adverse event; Wk, week. 
a A separate Screening visit for this study is required only if the time between completion of the previous rAvPAL-PEG study and enrollment into PAL-003 is greater than 
28 days. 
b Visits must be performed in the clinic. 
c On days that a dose is given, all procedures should be performed predose, except where noted. 
d Refer to Section 9.1.1 and Section 12.3.6. 
e Complete physical examinations to include the evaluation of all major body systems. Height will be measured at Screening only. 
f Clinical laboratory tests to include spot urine albumin/creatinine ratio, hematology, chemistry, and urinalysis. Urine microscopy will be performed if any urinalysis 
results are positive for hematuria. It is recommended that urine samples are obtained as a first or second morning void. In the event of elevated urinary protein on a test 
result, a repeat urinalysis should be performed. This repeat urine sample must be performed in the morning at the first or second morning void to allow for accurate test 
results and may be performed by a home healthcare nurse. Refer to Table 9.7.6.1.  
g Subjects who have a National Cancer Institute Common Terminology Criteria for Adverse Events (NCI-CTCAE) grade ≥ 3 hypersensitivity AE should be assessed for 
CRP, CH50, C1, C3, and C4 within 24 hours of the reaction.  
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h Complement C3 and C4 will be collected at the Screening Visit and every 8 weeks. Additional complement testing may be performed as needed to resolve previous 
abnormal test results. 
i If positive or equivocal, perform serum pregnancy test. Subjects who are confirmed to be pregnant per a serum pregnancy test and are temporarily off study drug are not 
required to perform the scheduled urine pregnancy tests. Subjects who are planning to become pregnant (or impregnate a female partner) may modify their diet in 
consultation with the investigator and/or study dietician. Also refer to Section 9.1. 
j If any injection site reaction is observed, the corresponding adverse event data must specify injection location (identify current vs. previous visit’s injection, eg, right arm 
vs. left arm). If there is a skin reaction that lasts ≥ 14 days, the Skin Reaction eCRF should be completed. Subjects who experience an injection-site skin reaction that 
lasts  ≥ 14 days should be referred to a dermatologist for consultation and a skin biopsy. It is recommended that a photograph of the skin reaction be taken by the subject 
or the site to help assess the event; photographs may be collected by the sponsor. 
k The reporting period for SAEs begins when informed consent is obtained and continues through 4 weeks after last dose or completion of study participation, whichever 
occurs last. The reporting period for nonserious AEs is from the first administration of study drug through 4 weeks after last dose or the Study Completion Visit/Early 
Termination Visit, whichever occurs last. The reporting period for device-related events begins with the first dose administered using prefilled syringe and ends with the 
last dose administered using prefilled syringe. 
l It is preferable that the subject complete the diary 3 days immediately prior to the next monthly visit. 
m For unscheduled hypersensitivity reaction visit, draw serum anti-rAvPAL IgE and anti-rAvPAL-PEG IgE only; sampling must be performed > 8 hours after event onset 
and before the next dose of study drug.  
n Samples should be drawn at least 2.5 hours after a meal.  At the Investigator’s discretion, blood Phe may be collected more often should more frequent monitoring of 
blood Phe levels be clinically warranted. 
o It is recommended that urine samples are obtained as a first or second morning void. Subjects with a confirmed urine/albumin creatinine ratio of  ≥  100 mg/g should be 
referred to a nephrologist for consultation if results were within normal range at baseline. Subjects who had elevated results at baseline followed by a confirmed 
subsequent increase of 100-200 mg/g from baseline should also be referred to a nephrologist for consultation. 
po Sampling should be performed predose. Subjects who are pregnant or are trying to conceive and have temporarily discontinued study drug should not perform the 
scheduled PK assessments. 
q Dosing is up to 5.0 mg/kg/week or 375 mg/week, including subjects who receive more than 1 dose/week. Every effort should be made to adhere to the study drug 
administration regimen. If a subject misses more than 2 scheduled doses of study drug, both dose level and dose frequency may be re-evaluated.  
r Initial training on the use of prefilled syringe occurs at the next monthly visit and each subsequent day after transition until (in clinic or by HHRN) it has been 
determined the subject will switch to prefilled syringe. Once competency is documented, subjects can self-administer study drug using the prefilled syringe.  Regular 
refresher prefilled syringe training occurs in the study clinic every 24 weeks thereafter. 
s Mandatory for subjects who have a hypersensitivity AE. Perform within 24 hours of event onset. 
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Table 9.1.2:  PK Substudy Dosing Regimens 
Treatment Frequency 
Plasma PK Sampling 
Example 
Subjects who are 
administered study drug 
once per week 
Pre-dose and every 24 hours 
thereafter (24, 48, 72, and 96 hours 
when possible), and pre-dose of the 
next weekly dose 
If dosed on Monday: 
Obtain PK sample pre-dose when possible – pre-dose Monday, Tuesday, Wednesday, 
Thursday, Friday, and pre-dose the following Monday. 
No further PK substudy draws. 
Subjects who are 
administered study drug two 
or three times per week 
Pre-dose and every 24 hours during 
the longest period between doses, 
when possible, and pre-dose of the 
next dose. 
If dosed on Monday, Thursday, and Friday: 
Obtain PK sample every 24 hours during the longest period between doses: Pre-dose 
Monday, Tuesday, Wednesday, and pre-dose Thursday. 
No further PK substudy draws. 
Subjects who are 
administered study drug four 
to seven times per week. 
Pre-dose and every 12 hours during 
the longest period between doses, 
when possible, then pre-dose of the 
next dose. 
If dosed Monday through Friday: 
Obtain PK sample every 12 hours during the longest period between doses (Friday to 
Monday): pre-dose Friday, 12 hours post-dose Friday, Saturday (24 and 36 hours post 
dose), Sunday (48 and 60 hours post-dose), and pre-dose the following Monday. 
No further PK substudy draws. 
 
 
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9.1.1 Response to Hypersensitivity Adverse Events 
Subjects are evaluated for safety throughout the study and are trained to recognize potential 
hypersensitivity AEs (including anaphylaxis) and how to respond. Subjects are instructed to 
contact the investigator for any suspected hypersensitivity AE. The investigator may require 
further evaluation at the clinic. If a hypersensitivity AE (eg, injection-site reaction, rash, joint 
pain, itching) occurs, the subject may be advised to premedicate with H1 antagonist, H2 
antagonist, and antipyretics (eg, acetaminophen) approximately 2-3 hours prior to subsequent 
rAvPAL-PEG doses. If NSAIDs are administered as a premedication, they should be given 
with food. Subjects who experience an injection-site skin reaction that lasts  ≥ 14 days should 
be referred to a dermatologist for consultation and a skin biopsy. 
Hypersensitivity AEs, including anaphylaxis, are expected with rAvPAL-PEG 
administration.  rAvPAL-PEG dosing in response to a suspected hypersensitivity AE may be 
modified or halted depending on the severity of the event and suspected rAvPAL-PEG 
causality (Section 9.1.1.3). Severity for hypersensitivity AEs will be per NCI-CTCAE 
grades. 
9.1.1.1 
Individual Stopping Criteria 
Subjects who have an NCI CTCAE grade ≥ 3 hypersensitivity AE that is related to study 
drug and is suspected to meet Brown’s criteria for severe (grade 3) in the judgment of the 
investigator and the sponsor’s medical monitor may be permanently discontinued from study 
drug. 
9.1.1.2 
Dosing in Response to Hypersensitivity Adverse Events 
Dosing in response to a hypersensitivity AE depends on the NCI-CTCAE grade and 
suspected relationship to rAvPAL-PEG. Dosing instructions are presented in Table 9.1.1.2.1 
and are regardless of previous occurrence: 
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Table 9.1.1.2.1:  Dosing Instructions in Response to Hypersensitivity Adverse Events 
NCI-CTCAE 
Gradea 
Related to 
Study Drug 
Action with Study Drug 
Individual 
Stopping 
Criteria d 
HRV  
Assessmente 
Maintainb 
Reducec 
Interruptc 
1 
Yes or No 
X 
(X) 
Optional 
(X) 
Optional 
 
Investigator 
discretion 
2 
Yes or No 
X 
(X) 
Optional 
(X) 
Optional 
 
Investigator 
discretion 
3  
No 
X 
(X) 
Optional 
(X) 
Optional 
 
Investigator 
discretion 
3  
Yes 
X 
(X) 
Optional 
(X) 
Optional 
 
Yes 
3 
and is suspected to 
meet Brown’s 
criteria for severe d  
Yes 
 
 
 
X 
Consult with 
sponsor medical 
monitor 
Yes 
4 d 
Yes or No 
 
 
 
X 
Consult with 
sponsor medical 
monitor 
Yes 
AE, adverse event; CTCAE, Common Terminology Criteria for Adverse Events, version 4.03; HRV, 
Hypersensitivity Reaction Visit; NCI, National Cancer Institute. 
a NCI-CTCAE grade determination is performed by the investigator and may be done either via telephone or 
clinic visit. 
b The investigator will instruct the subject to maintain the rAvPAL-PEG dose at the time of AE onset until 
improvement to grade 1 or resolution (per investigator assessment in the clinic or via telephone). 
cThe rAvPAL-PEG dose may be reduced or interrupted if necessary per investigator determination.  
d If a subject has an NCI-CTCAE grade  ≥ 3 hypersensitivity AE that is related to study drug and is suspected to 
meet Brown’s criteria for severe (grade 3) in the judgment of the investigator and the sponsor’s medical 
monitor, the subject may be permanently discontinued from study drug.  
e If the investigator determines that the NCI-CTCAE grade  ≥ 3 hypersensitivity AE is related to administration 
with rAvPAL-PEG, the subject will be asked to return to the clinic within 24 hours of event onset for 
evaluation, including laboratory tests (chemistry, hematology, urinalysis, anti-rAvPAL IgE, 
anti-rAvPAL-PEG IgE [sampling must be performed >8 hours after event onset and before the next dose of 
study drug], urine albumin/creatinine ratio, urinary N-methyl histamine, CRP, C3, C4, and tryptase).  
 
9.1.1.3 
Response to Anaphylaxis 
If the investigator suspects that the event is anaphylaxis, the subject will be assessed in the 
clinic. Laboratory assessments for suspected anaphylaxis events should be performed prior to 
the next administration of study drug (if applicable) and include anti-rAvPAL IgE and 
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anti-rAvPAL-PEG IgE (sampling must be performed >8 hours after event onset and before 
the next dose of study drug) and tryptase (within 24 hours of event onset). The investigator 
will consult with the sponsor’s medical monitor, and a decision will then be made whether to 
discontinue the subject from study drug, restart dosing at the same dose level, or restart 
dosing at a lower dose level. 
For the first week of dosing after resolution of anaphylaxis, the study drug will be 
administered in a clinic setting with equipment for emergency resuscitation (including 
epinephrine) within easy access.  The subject must be observed for 30 minutes following 
administration due to restarting dosing. Additionally, the subject should be premedicated 
with H1 antagonist, H2 antagonist, and antipyretics (eg, acetaminophen) approximately 
2-3 hours prior to each dose of study drug for one week upon return to dosing regardless of 
the duration of dose interruption. If NSAIDs are administered as a premedication, they 
should be given with food.  
9.1.2 Study Stopping Criteria 
If an NCI-CTCAE grade ≥ 3 hypersensitivity treatment-related event occurs and meets 
Brown’s criteria for severe (grade 3), an ad hoc independent DMC meeting will convene 
within 7 days of the event to review and advise the sponsor on potential changes to the study 
conduct. Clinically severe hypersensitivity is defined as significant hypoxia, hypotension or 
neurologic compromise that is life-threatening or required treatment to prevent a 
life-threatening event:  
• Cyanosis or SpO2 ≤ 92%  
• Hypotension with SBP < 90 mm Hg (adults)  
• Neurologic alteration: loss of consciousness, collapse, incontinence 
Brown’s severity criteria are presented in Table 9.1.2.1. 
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Table 9.1.2.1:  Brown’s Severity Criteria 
Brown’s Criteria for 
Hypersensitivity Reactions 
Definition 
Mild (1) 
skin and subcutaneous tissue 
Generalized erythema, urticaria, periorbital edema, or angioedema 
Moderate (2) 
features suggested respiratory, 
cardiovascular, or gastrointestinal 
involvement 
Dyspnea, stridor, wheeze, nausea, vomiting, dizziness (pre-syncope), 
diaphoresis, chest or throat tightness, or abdominal pain 
Severe (3) 
hypoxia or neurologic compromise 
Cyanosis or SpO2 ≤ 92% at any stage, hypotension (SBP < 90 mm Hg 
in adults), confusion, collapse, loss of consciousness, or incontinence  
 
9.1.3 Dose Modifications 
9.1.3.1 
Dose Increase Methodology 
Each subject’s dose may be modified based on the decision of the Investigator. Decisions 
regarding dose increases will depend on a subject’s adverse event profile and blood Phe and 
drug concentrations. 
An individual subject’s dose may be adjusted beginning on Day 1 of PAL-003. For the 
duration of this study, an individual subject’s dose may be adjusted if warranted per a 
subject’s adverse event profile and blood Phe concentrations. Dose increases should be 
performed as follows: 
• The dose may be increased by increments of no more than 10-fold higher than the 
subject’s current dose. 
• When increasing the dose, a dose may be used that is between the dose levels (0.001, 
0.003, 0.01, 0.03, 0.06, 0.1, 0.2, 0.3, 0.4, 0.6, 0.8, 1.0, 2.0, 3.0, 4.0, and 5.0 mg/kg or 
2.5, 5, 10, 20, 40, 75, 150, 225, 300, 375 mg/week) or per Investigator determination 
based on available information regarding a subject’s blood Phe (60-600 µmol/L) as 
well as any adverse events for an individual subject. Dose increases  > 350 mg/week 
require consultation with the sponsor’s medical monitor. 
• The dose may be adjusted by increasing the frequency up to daily for a total weekly 
dose not to exceed 5.0 mg/kg or 375 mg/week. Dose increases  > 350 mg/week 
require consultation with the sponsor’s medical monitor. 
• When a dose is increased, the subject must be observed for 30 minutes following the 
first modified dose administration. Subjects who increase their dose frequency do not 
need to be observed following injection of study drug if the increase in frequency 
does not increase the overall weekly dose amount. 
• Only 1 dose adjustment is allowed every 2 weeks. 
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9.1.3.2 
Dose Decrease Methodology 
Decisions regarding dose decreases will depend on available information regarding a 
subject’s blood Phe (60-600 µmol/L), as well as any adverse event (any hypersensitivity 
reaction as defined in Section 9.1.1). Dose decreases may occur for hypophenylalanemia or 
any adverse event that may be improved with a lower dose. 
A dose should first be reduced by dose level (5.0, 4.0, 3.0, 2.0, 1.0, 0.8, 0.6, 0.4, 0.3, 0.2, 0.1, 
0.06, 0.03, 0.01, 0.003, 0.001 mg/kg or 375, 300, 225, 150, 75, 40, 20, 10, 5, and 2.5 
mg/week). It is also permitted to decrease dose in between these specified dose levels. If 
further dosing adjustments are required in response to safety, dosing frequency may also be 
adjusted.  
If the subject develops low blood Phe (as defined by a blood Phe level ≤ 30 µmol/L ), the 
subject’s rAvPAL-PEG dose should be decreased to the next lower dose.  If the condition 
persists after another 1 month at the lower dose, the dose should be decreased again to the 
next lower level. If the subject continues to experience low blood Phe after two dose level 
reductions, the subject may be asked to consult the dietician to eliminate medical foods 
and/or formulas and to ensure a balanced and nutritious diet (as part of the routine standard 
of care for PKU disease management, subject diet should be monitored by a dietician). 
9.2 
Discussion of Study Design, Including Choice of Control Group 
This open-label, Phase 2 trial was designed to be closely monitored with the goal of 
obtaining information about the efficacy, safety, tolerability, and PK of long-term 
administration of rAvPAL-PEG in subjects with PKU. There will be no control group in this 
study. 
9.3 
Selection of Study Population 
9.3.1 Inclusion Criteria 
Individuals eligible to participate in this study must meet all of the following criteria: 
1. Must have completed participation in a previous rAvPAL-PEG study. 
2. Willing and able to provide written, signed informed consent, or in the case of 
subjects under the age of 18 years, provide written assent (if required) and written 
informed consent by a parent or legal guardian, after the nature of the study has been 
explained, and prior to any research-related procedures. 
3. Willing and able to comply with all study procedures. 
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4. Females of childbearing potential must have a negative pregnancy test at Screening 
and be willing to have additional pregnancy tests during the study. Females 
considered not of childbearing potential include those who have been in menopause at 
least 2 years, or had tubal ligation at least 1 year prior to Screening, or who have had 
total hysterectomy. 
5. Sexually active subjects must be willing to use two acceptable methods of 
contraception while participating in the study.  Males post vasectomy for 2 years with 
no known pregnancies do not need to use any other forms of contraception during the 
study. 
6. Maintained a stable diet. 
7. In generally good health as evidenced by physical examination, clinical laboratory 
evaluations (hematology, chemistry, and urinalysis), and electrocardiogram (ECG) at 
Screening. 
9.3.2 Exclusion Criteria 
Individuals who meet any of the following exclusion criteria will not be eligible to participate 
in the study: 
1. Use of any investigational product (with the exception of rAvPAL-PEG) or 
investigational medical device within 30 days prior to Screening, or requirement for 
any investigational agent prior to completion of all scheduled study assessments. 
2. Use of any medication other than rAvPAL-PEG that is intended to treat PKU within 
14 days prior to the administration of study drug. 
3. Use or planned use of any injectable drugs containing PEG (other than 
rAvPAL-PEG), including Depo-Provera, within 6 months prior to Screening and 
during study participation. 
4. A prior reaction that included systemic symptoms (eg, generalized hives, respiratory 
or gastrointestinal problems, hypotension, angioedema, anaphylaxis) to rAvPAL-PEG 
or a PEG-containing product. Subjects with a prior systemic reaction may be eligible 
for participation per the discretion of the Principal Investigator in consultation with 
the sponsor’s medical monitor. However, subjects who discontinued from study drug 
early due to a reaction are not eligible to enroll into this study. 
5. Pregnant or breastfeeding at Screening or planning to become pregnant (self or 
partner) or to breastfeed at any time during the study. 
6. Concurrent disease or condition that would interfere with study participation or safety 
(eg, history or presence of clinically significant cardiovascular, pulmonary, hepatic, 
renal, hematologic, gastrointestinal, endocrine, immunologic, dermatologic, 
neurological, oncologic, or psychiatric disease). 
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7. Any condition that, in the view of the PI, places the subject at high risk of poor 
treatment compliance or of not completing the study. 
8. Known hypersensitivity to rAvPAL-PEG necessitating early termination from a 
previous rAvPAL-PEG study or known hypersensitivity to any of its excipients. 
9. Alanine aminotransferase (ALT) concentration > 2 times the upper limit of normal. 
10. Creatinine > 1.5 times the upper limit of normal. 
9.3.3 Removal of Subjects from Treatment or Assessment 
Subjects (or their legally authorized representative) may withdraw their consent to participate 
in the study or to receive study drug at any time without prejudice. The Investigator must 
withdraw from the study or study drug treatment any subject who requests to be withdrawn. 
A subject’s participation in the study may be discontinued at any time at the discretion of the 
Investigator and in accordance with his/her clinical judgment. When possible, a subject who 
is discontinued from study drug should continue to perform the study tests and evaluations 
until study completion. For subjects who discontinue from the study, the tests and 
evaluations listed for the Early Termination Visit should be carried out (refer to 
Section 12.4). 
BioMarin must be notified of all subject withdrawals as soon as possible. BioMarin also 
reserves the right to discontinue the study at any time for either clinical or administrative 
reasons and to discontinue participation by an individual Investigator or site for poor 
enrollment or noncompliance. 
Reasons for which the Investigator or BioMarin may withdraw a subject from the study drug 
include, but are not limited to, the following: 
• Subject experiences a serious or intolerable adverse event (AE). 
• Subject develops a clinically significant laboratory abnormality. 
• Subject requires medication prohibited by the protocol. 
• Subject becomes pregnant (refer to Section 10.3 for details on the reporting 
procedures to follow in the event of pregnancy and refer to Section 9.1 for details on 
re-introduction of study drug following pregnancy and breastfeeding). 
Reasons for which the Investigator or BioMarin may withdraw a subject from the study 
include, but are not limited to, the following: 
• Subject does not adhere to study requirements specified in the protocol. 
• Subject was erroneously admitted into the study or does not meet entry criteria. 
• Subject is lost to follow-up. 
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If a subject fails to return for scheduled visits, a documented effort must be made to 
determine the reason. If the subject cannot be reached by telephone within 7 days, a certified 
letter should be sent to the subject (or the subject’s legally authorized representative, if 
appropriate) requesting contact with the Investigator. This information should be recorded in 
the study records. 
The Investigator or designee must explain to each subject, before enrollment into the study, 
that for evaluation of study results, the subject’s protected health information obtained during 
the study may be shared with the study sponsor, regulatory agencies, and IRB. It is the 
Investigator’s (or designee’s) responsibility to obtain written permission to use protected 
health information per country-specific regulations, such as the Health Insurance Portability 
and Accountability Act (HIPAA) in the United States, from each subject, or if appropriate, 
the subject’s legally authorized representative. If permission to use protected health 
information is withdrawn, it is the Investigator’s responsibility to obtain a written request, to 
ensure that no further data will be collected from the subject and the subject will be removed 
from the study. 
9.3.4 Subject Identification and Replacement of Subjects 
Subjects will retain the same subject number assigned in their previous rAvPAL-PEG study. 
This unique identifier will be on all case report form (CRF) pages. In legal jurisdictions 
where use of initials is not permitted, a substitute identifier will be used.  
Subjects who do not complete the study will not be replaced. 
9.4 
Treatments 
Upon enrollment into this study, subjects from previous rAvPAL-PEG studies will be dosed 
with the same or higher dose that was administered upon completion of that study provided 
that there was no interruption in dosing.  rAvPAL-PEG doses will be administered SC by 
either health care professionals or via self-administration. The dose level may be adjusted per 
Investigator determination based on available information regarding a subject’s blood Phe 
level (60-600 µmol/L), as well as any adverse events (any hypersensitivity reaction) for an 
individual subject. The dosage that provides control of blood Phe concentrations within the 
target range of 60-600 µmol/L for a minimum of 2 weeks will be determined for each subject 
by adjusting the dose level, dose frequency, or both, per the PI, based upon the subject’s 
response to doses.  
Subjects may self-administer study drug at home if approved by the Investigator and the 
sponsor’s medical monitor and if adequate training is demonstrated. Subjects may be eligible 
to self-administer study drug if he or she meets the following criteria:  
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• The subject has no cognitive impairments that may increase the safety risk of 
self-administration per the assessment of the investigator.  
• The subject has been approved for self-administration of study drug by the sponsor’s 
medical monitor. 
• The subject has completed the Self-Administration Training conducted by qualified 
study site personnel and has been observed by the study site personnel to be able to 
adequately prepare the proper dose and perform the injections safely.  
• The subject has been provided with two epinephrine injectors and has been trained on 
when and how to administer it. The subject will be instructed to carry one epinephrine 
injector with them at all times. 
Qualified study site personnel will train each eligible subject on all procedures for 
self-administration of study drug (vial and syringe and prefilled syringe drug products) under 
the supervision of the PI. Qualified study site personnel will also be required to observe the 
subject prepare and perform at least 1 injection prior to allowing the subject to 
self-administer a dose at home. The subject will see a study site nurse or home healthcare 
nurse in person every week or receive a telephone call from site staff to ensure that the 
subject continues to perform all self-administration procedures correctly, to assess adverse 
events, and to answer questions throughout the duration of the study. The study site nurse or 
home healthcare nurse will also perform the regularly scheduled assessments and procedures 
as outlined in Table 9.1.1 and Section 12; the subject must perform a clinic visit monthly at 
minimum. Training materials and other information specific to the study site personnel are 
provided in the Subject Self-Administration Training Materials. Prefilled syringes are 
dispensed to subjects only after the subject (or caregiver) has completed training and 
competency is demonstrated in the clinic.  Additional regular refresher training occurs in the 
clinic, every 24 weeks, and more often as needed.  
Subjects who are eligible for self-administration will be provided with a Subject Study 
Manual. Self-administration training materials will be provided in the Subject Study Manual 
to supplement the in-person training provided by the qualified study site personnel. The 
Subject Study Manual will include step-by-step instruction on the following: 
• How to prepare and perform the injections of study drug safely. 
• How to receive, track, store, prepare, and return both used and unused study drug.   
• How to safely use and dispose of syringes, including prefilled syringes, used for 
injections of study drug. 
• How to use a new syringe and vial or new prefilled syringe every time drug is 
administered. 
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• How to care for their injection site after an injection of study drug.  
• How to identify an adverse reaction and how to report this reaction to the study site.  
• How and when to use epinephrine injectors. 
• Who to contact at the study site in case of an emergency.  
The PI or the sponsor’s medical monitor may request that self-administration be halted at any 
time and that the subject resume injections performed by the study site personnel or home 
healthcare nurse. 
Subjects who are within the target Phe range may also be permitted to convert from 
weight-based dosing to fixed dosing (refer to Section 9.4.4). 
9.4.1 Treatments Administered 
BioMarin and/or its designee will provide the study site or subject with a supply of IP 
sufficient for the completion of the study. BioMarin is responsible for shipping study drug to 
the clinical sites. The clinical site is responsible for supplying the study drug to subjects who 
qualify for self-administration. Refer to the PAL-003 Pharmacy Manual for information 
pertaining to the distribution of study drug from sites.  
Information regarding supplying study drug to subjects who qualify for self-administration is 
provided in the Subject Self-Administration Training Materials. 
9.4.2 Identity of Investigational Product (IP) 
9.4.2.1 
Product Characteristics and Labeling 
The investigational product is rAvPAL-PEG (recombinant Anabaena variabilis phenylalanine 
ammonia lyase-PEG). rAvPAL-PEG will be provided in vials or prefilled syringes; subjects 
will be supplied with vials and syringes or prefilled syringes for administration in the clinic 
and self-administration: 
• rAvPAL-PEG will be provided in 3 mL (milliliter) vials, each containing 1.5 ± 0.2 mL 
to deliver 15 mg of rAvPAL-PEG per 1.0 mL (15 mg/mL protein concentration). 
Each vial is filled with 1.5 ± 0.2 mL to allow the withdrawal and delivery of up to 
1.0 mL of the drug product. 
Or 
• rAvPAL-PEG will be provided in 3-mL vials, each containing 1.8 ± 0.3 mL to deliver 
20 mg of rAvPAL-PEG per 1.3 mL (15 mg/mL protein concentration). Each vial is 
filled with 1.8 ± 0.3 mL to allow withdrawal and delivery of up to 1.3 mL. 
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Or 
 
• rAvPAL-PEG will be provided in prefilled syringes in three sizes that deliver up to 
1 mL. Syringe sizes are 2.5 mg (5 mg/mL protein concentration), 10 mg (20 mg/mL 
protein concentration), and 20 mg (20 mg/mL protein concentration). 
Table 9.4.2.1.1:  Prefilled Syringe Volume, Concentration, and Dose 
Prefilled Syringe 
Volume 
Concentration 
Dose 
Sku #1 
0.5 mL 
5 mg/mL 
2.5 mg 
Sku #2 
0.5 mL 
20 mg/mL 
10 mg 
Sku #3 
1.0 mL 
20 mg/mL 
20 mg 
 
Subjects who have undergone training and who have demonstrated competency on the use of 
prefilled syringe in the study clinic may be eligible to transition from vial and syringe to 
prefilled syringe dosing. Additionally, regular refresher training on use of prefilled syringe 
will be provided in study clinic every 24 weeks, and more often as needed.  
Subjects should convert their vial and syringe dose to prefilled syringe dose using the 
following table: 
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Table 9.4.2.1.2:  Conversion from Vial and Syringe Dose to Prefilled Syringe Dose 
Daily Dose (mg)  
Range 
Daily Dose (mg)  
Round Toa 
# of 2.5mg 
Prefilled 
Syringe Needed 
# of 10mg 
Prefilled 
Syringe Needed 
# of 20mg 
Prefilled 
Syringe Needed 
0 – 3.7 
2.5 
1 
0 
0 
3.8 – 6.2 
5 
2 
-- 
-- 
6.3 – 8.7 
7.5 
3 
-- 
-- 
8.8 – 11.2 
10 
-- 
1 
-- 
11.3 – 13.7 
12.5 
1 
1 
-- 
13.8 – 16.2 
15 
2 
1 
-- 
16.3 – 18.7 
17.5 
3 
1 
-- 
18.8 – 21.2 
20 
-- 
-- 
1 
21.3 – 23.7 
22.5 
1 
-- 
1 
23.8 – 26.2 
25 
2 
-- 
1 
26.3 – 28.7 
27.5 
3 
-- 
1 
28.8 – 31.2 
30 
-- 
1 
1 
31.3 – 33.7 
32.5 
1 
1 
1 
33.8 – 36.2 
35 
2 
1 
1 
36.3 – 38.7 
37.5 
3 
1 
1 
38.8 – 41.2 
40 
-- 
-- 
2 
41.3 – 44.9 
42.5 
1 
-- 
2 
45 – 54.9 
50 
-- 
1 
2 
55 – 64.9 
60 
-- 
-- 
3 
65 – 74.9 
70 
-- 
1 
3 
75 – 84.9 
80 
-- 
-- 
4 
85 – 94.9 
90 
-- 
1 
4 
95 – 104.9 
100 
-- 
-- 
5 
105 – 114.9 
110 
-- 
1 
5 
115 – 124.9 
120 
-- 
-- 
6 
125 – 134.9 
130 
-- 
1 
6 
135 – 144.9 
140 
-- 
-- 
7 
145 – 154.9 
150 
-- 
1 
7 
a For  < 45 mg/day, round to nearest 2.5 mg; for  ≥ 45 mg/day, round to nearest 10 mg. 
 
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The excipients in this drug product are tromethamine, tromethamine-hydrochloride, sodium 
chloride, L-phenylalanine, and water for injection. 
rAvPAL PEG doses will be administered SC by either health care professionals or via 
self-administration. The dose level may be increased or decreased per Investigator 
determination based on available information regarding a subject’s blood Phe level 
(60 600 µmol/L), as well as any adverse events (any hypersensitivity AE) for an individual 
subject. The dosage that provides control of blood Phe concentrations within the target range 
of 60-600 µmol/L for a minimum of 2 consecutive measurements will be determined for each 
subject by adjusting the dose level, dose frequency, or both, per the PI, based upon the 
subject’s response to doses. 
For vial and syringe, drug product packaging will be identified with the lot number and 
expiration date and will be provided in a box labeled with the study number. 
For prefilled syringe, drug product packaging will be identified with the size (2.5 mg, 10 mg, 
or 20 mg), lot number, and kit identification (ID). The expiration date will be available in a 
separate Certificate of Compliance issued for each lot. 
9.4.3 Storage 
IP must be stored at 5 ± 3°C (41 ± 5°F) under the conditions specified in the IB. At the site, 
the IP will be stored in a secure area accessible only to the designated pharmacists and 
clinical site personnel. All IP must be stored and inventoried and the inventories must be 
carefully and accurately documented according to applicable state, federal and local 
regulations, ICH GCP, and study procedures. 
Specific instructions for storage of study drug for subjects who qualify for self-administration 
are provided in the Subject Self-Administration Training Materials.  
9.4.4 Directions for Administration 
Doses will be administered SC and the favorable dose will be determined for each subject by 
adjusting the dose level, dose frequency, or both, per the PI, based upon the subject’s 
response to doses. Dosing is up to a maximum dose per week of 5.0 mg/kg (or 375 mg for 
subjects receiving a fixed dose).  
For subjects receiving weight-based dosing, dosage is calculated by multiplying each 
subject’s weight in kilograms (kg) on Day 1 (predose) by the assigned dose (in mg/kg). 
During the study, if the weight of a subject changes more than 10% from the measurement 
obtained at baseline or at a previous measurement, the subject’s dose may be adjusted to 
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accommodate the change. The change must be recorded. Refer to the Pharmacy Manual for 
additional information on calculating dosage. 
Subjects who have demonstrated efficacy (as measured by blood Phe within the target range 
of 60-600 µmol/L for at least 2 consecutive measurements) and who have maintained a stable 
rAvPAL-PEG dose for at least 2 consecutive measurements may be eligible to transition 
from weight-based dosing to a fixed dosing regimen that would permit daily dosing (5- or 
7-days-per-week).  Subjects who convert to a fixed-dosing regimen should convert their dose 
based upon the information presented in Table 9.4.4.1. 
Table 9.4.4.1:  Fixed Doses for Subjects on Weight-Based Dose Regimen  
Weight-based dose 
(mg/kg) 
Equivalent fixed dose 
(mg) 
Vol for 15 mg/ml concentration 
(ml) (vial)a 
0.03 
2.5 
0.17 
0.06 
5 
0.33 
0.12 
10 
0.67 
0.25 
20 
1.33 
0.5 
40 
2.67 
1.0 
75 
5 
2.0 
150 
10 
3.0 
225 
15 
4.0 
300 
20 
5.0 
375 
25 
a Applies to both 1.0 and 1.3 ml withdrawal. 
 
It is preferable that the injection sites should be alternated between doses, ie, upper left arm 
in Week 1, upper right arm in Week 2, etc. Doses may be administered in any of the common 
SC areas (upper arm, thigh, abdomen). If dose volume is such that a dose will be divided and 
given in more than 1 injection site, it is preferable to use both arms, both legs, or both sides 
of the abdomen. 
Subjects may require more than 1 injection per dose, depending upon site policy (ie, some 
institutions do not permit a single SC injection of greater than 2 mL).  Dosage calculations 
must be performed according to study drug preparation instructions provided in the PAL-003 
Pharmacy Manual. Study drug will be administered by clinic staff, other qualified and trained 
study personnel, or qualified subjects. 
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Information for dosing of subjects who enroll into this study after completing previous 
rAvPAL studies is provided in Section 9.1. Instructions for subjects who re-start 
rAvPAL-PEG dosing due to unplanned missed doses are provided in Section 9.4.10.  
Instructions for administration of study drug for subjects who qualify for self-administration 
are provided in the Subject Self-Administration Training Materials. 
9.4.5 Method of Assigning Subjects to Treatment Groups 
This will be an open-label study; no randomization schedule will be generated. 
Subjects will retain the same subject number used in their previous rAvPAL-PEG study. 
9.4.6 Selection of Doses Used in the Study 
This Phase 2 study aims to evaluate the efficacy, safety, tolerability, and PK parameters of 
multiple doses of rAvPAL-PEG after long-term administration in subjects with PKU. A dose 
that produces a reduction in blood Phe concentrations to 60-600 μmol/L will be determined 
for each subject based on preliminary safety, antibody, and efficacy data from this ongoing 
study. 
9.4.6.1 
Selection of Timing of Dose for Each Subject 
Study drug will be administered by clinic staff or other qualified and trained study personnel. 
Subjects may self-administer study drug at home if approved by the sponsor’s medical 
monitor and if adequate training is provided (refer to Section 9.4). 
9.4.7 Blinding 
This is an open-label study. 
9.4.8 Prior and Concomitant Medications 
All prescription and over-the-counter (OTC) medications taken by a subject for 30 days 
before Screening will be recorded on the designated CRF. The Investigator may prescribe 
additional medications during the study, as long as the prescribed medication is not 
prohibited by the protocol. In the event of an emergency, any needed medications may be 
prescribed without prior approval, but the sponsor’s medical monitor must be notified of the 
use of any contraindicated medications immediately thereafter. Any concomitant medications 
added or discontinued during the study should be recorded on the CRF. 
Use of any investigational product (with the exception of rAvPAL-PEG used in a previous 
rAvPAL-PEG study) or investigational medical device within 30 days before Screening, or 
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requirement for any investigational agent prior to completion of all scheduled study 
assessments, is prohibited. 
Use or planned use of any injectable drugs containing PEG (other than rAvPAL-PEG), 
including Depo-Provera, is prohibited within 6 months prior to Screening and during study 
participation. A list of PEG-containing injectable drugs is provided in the study reference 
materials. Subjects who have had a prior hypersensitivity AE to rAvPAL-PEG or a 
PEG-containing product will be encouraged to be premedicate as outlined in Section 9.1.1. If 
the hypersensitivity AE worsens with a repeat injection (as determined by the Investigator in 
consultation with the sponsor’s medical monitor) even with premedication prior to study drug 
dosing, the subject must be withdrawn from the study and complete an Early Termination 
Visit. 
Subjects who have had a prior hypersensitivity AE to rAvPAL-PEG or a PEG-containing 
product may participate in this study (refer to Section 9.3.2).  
Use of any medication that is intended to treat PKU within 14 days prior to the 
administration of study drug is prohibited. 
9.4.9 Treatment Compliance 
The date, time, volume, and concentration of each dose of study drug administered to each 
subject must be recorded in the dispensing log provided for the study, as well as on the 
appropriate CRF. This data will be used to assess treatment compliance. 
9.4.10 Dose Interruption and Missed Doses  
Information for dosing of subjects who enroll into this study after completing previous 
rAvPAL-PEG studies is provided in Section 9.1.  
During this long-term extension study, interruption of rAvPAL-PEG dosing may occur per 
subject decision or per the Investigator. After a dosing interruption of ≥ four consecutive 
doses, rAvPAL-PEG administration should be re-started at the same dose level and dosing 
frequency that was administered prior to the dosing interruption. The first week of dosing of 
rAvPAL-PEG following a dose interruption should be administered in a clinic setting, and 
the subject must be observed for 30 minutes following administration due to restarting 
dosing. Premedication with H1 antagonist, H2 antagonist, and antipyretics 
(eg, acetaminophen) approximately 2-3 hours prior to study drug should be administered 
following any dose interruption of ≥ four consecutive doses. If NSAIDs are administered as a 
premedication, they should be given with food. A follow-up telephone call will be made to 
the subject to monitor subject safety 24 hours following the return to dosing. Subjects should 
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continue to perform the study assessments as outlined in the Schedule of Events (refer to 
Table 9.1.1) during any dosing interruption.  
Subjects who miss rAvPAL-PEG dosing due to poor compliance may be discontinued from 
further study drug per discretion of the Sponsor or Investigator (refer to Section 9.3.3).  
9.5 
Investigational Product Accountability 
The PI or designee is responsible for maintaining accurate records (including dates and 
quantities) of IP received, subjects to whom IP is dispensed (subject-by-subject dose specific 
accounting), IP returned, and IP lost or accidentally or deliberately destroyed. The PI or 
designee must retain all unused or expired study supplies until the study monitor (on-site 
CRA) has confirmed the accountability data. 
9.5.1 Return and Disposition of Clinical Supplies 
Unused study drug must be kept in a secure location for accountability and reconciliation by 
the study monitor. The Investigator or designee must provide an explanation for any 
destroyed or missing study drug or study materials. 
Unused study drug may be destroyed on site, per the site’s standard operating procedures, but 
only after BioMarin has granted approval for drug destruction. The monitor must account for 
all study drug in a formal reconciliation process prior to study drug destruction. All study 
drug destroyed on site must be documented. Documentation must be provided to BioMarin 
and retained in the PIs study files. If a site is unable to destroy study drug appropriately, the 
site can return unused study drug to BioMarin upon request. The return of study drug or 
study drug materials must be accounted for on a Study Drug Return Form provided by 
BioMarin. 
Subjects who qualify for self-administration of study drug will be provided with instructions 
for returning used and unused study drug and the proper disposal of any study drug materials 
(refer to the Subject Self-Administration Training Materials). 
All study drug and related materials should be stored, inventoried, reconciled, and destroyed 
or returned according to applicable state and federal regulations and study procedures. 
9.6 
Dietary or Other Protocol Restrictions 
Subjects will be instructed that diet should not be altered during the course of the study. 
Any decision to modify subject diet must be made per the Investigator and must be 
performed under the supervision of the Investigator. Subjects who are planning to become 
pregnant (or impregnate a female partner) may modify their diet in consultation with the 
investigator and/or study dietician. 
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A 3-day dietary record will be completed by subjects and will be brought to clinic visits for 
review with clinic staff. It is preferable that subjects complete the 3-day record immediately 
prior to their next monthly study visit.  The dietary record will be maintained with the study 
source documents. Information regarding a subject diet diary is provided in Section 9.7.4. 
9.7 
Efficacy and Safety Variables 
9.7.1 Efficacy and Safety Measurements Assessed 
The Schedules of Events in the Synopsis describe the timing of required evaluations. 
For the laboratory assessments, the party responsible for performing the assessment and the 
pertinent protocol section describing the details of the test are listed in Table 9.7.1.1. 
Table 9.7.1.1:  Summary of Laboratory Assessments 
Laboratory Assessment 
Party Responsible for 
Performing Test 
Section in Protocol for 
Details 
Clinical laboratory tests 
Central laboratory 
9.7.6 
Antibody testing 
BioMarina or CRO 
9.7.5.2 
PK variables 
BioMarin 
9.7.3 
Blood Phe concentrations 
Central laboratory 
9.7.2.1 
Pregnancy test (urine) and sedimentation 
rate 
Local laboratory 
9.7.6,  
9.7.5.1 
Urinalysis 
Central laboratory 
9.7.6 
Phe, phenylalanine; PK, pharmacokinetic. 
aAnalysis of the anti-rAvPAL IgE and anti-rAvPAL-PEG IgE assay will be performed by a Contract Research 
Organization. 
 
9.7.1.1 
Demographic Data and Medical History 
Demographic data and a detailed medical history, including allergy history, will be obtained 
at Screening. The medical history will include specific information concerning any prior or 
existing medical conditions that might interfere with study participation or safety. 
This medical history should elicit all major illnesses, diagnoses, and surgeries that the subject 
has ever had, and whether the subject has a history of alcohol and/or drug abuse. 
9.7.1.2 
Physical Examination Findings 
Physical examination will include assessment of general appearance; CV; dermatologic; 
head, eyes, ears, nose, and throat; lymphatic; respiratory; GI; musculoskeletal; and 
neurological/psychological. Other body systems may be examined. Day 1 results will be the 
baseline values and clinically significant changes from baseline will be recorded as an AE. 
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9.7.1.3 
Vital Sign Measurements 
Vital signs will be measured after resting for 5 minutes, and include seated systolic blood 
pressure (SBP) and diastolic blood pressure (DBP) measured in millimeters of mercury 
(mm Hg), heart rate in beats per minute, respiration rate in breaths per minute, and 
temperature in degrees Celsius (°C). Height (cm) will be measured at Screening only.  
Weight will be measured at Screening and then monthly. 
9.7.1.4 
Electrocardiography 
A standard 12-lead ECG will be recorded while the subject is resting, at Screening and at the 
Final Follow-Up (F/U) Visit or Early Termination Visit (ETV). If clinically significant 
abnormalities are noted at Screening, the PI or designee is required to assess whether it is 
appropriate for the subject to enroll in the study. 
9.7.1.5 
Chest X-Ray 
A chest X-ray will be performed at the Screening, Week 48, and Final Follow-Up (or 
Early Termination) visits to assess gross pulmonary health.  
9.7.2 Efficacy Variable 
9.7.2.1 
Blood Phenylalanine Concentrations 
Blood samples for Phe concentration measurements will be drawn monthly, at least 2.5 hours 
after a meal, on the days and time points indicated in the Schedule of Events (Table 9.1.1).  
Blood Phe may be collected more often than monthly at the discretion of the Investigator 
should more frequent monitoring of blood Phe levels be clinically required. 
A central laboratory will be used for blood Phe concentration analysis. 
9.7.3 Pharmacokinetic Variables 
Subjects enrolled in the Substudy will have additional PK sampling performed. For subjects 
participating in the Substudy, PK sampling will be performed as follows: 
• For subjects who are administered rAvPAL-PEG once per week, plasma PK sampling 
will be performed pre-dose and every 24 hours thereafter (24, 48, 72, and 96 hours if 
possible), and then pre-dose of the next weekly dose. 
• For subjects who are administered rAvPAL-PEG two or three times per week, plasma 
PK sampling will be performed pre-dose and every 24 hours during the longest period 
between doses, when possible, and then pre-dose of the next dose.  
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• For subjects who are administered rAvPAL-PEG four to seven times per week, 
plasma PK sampling will be performed pre-dose and every 12 hours during the 
longest period between doses, when possible, and then pre-dose of the next dose. 
See Table 9.1.2 for additional details. 
BioMarin will perform the analysis. 
9.7.4 Exploratory Efficacy Variable 
Diet will be assessed for its role in blood Phe reduction relative to rAvPAL-PEG dosing 
using a 3-day diet diary, which will be given to subjects to complete at home. Subjects will 
bring the completed diary with them to clinic visits on a monthly basis. Subjects will be 
instructed to record all food, beverages, special low-protein foods, and medical foods 
consumed for 3 consecutive days each month. If changes in diet are noted per the information 
on the diet diary, the subject will be instructed to maintain their diet as reported at the 
beginning of the study or as otherwise instructed by the Investigator. 
9.7.5 Safety Variables 
9.7.5.1 
Pregnancy Testing 
Female subjects of childbearing potential will have a urine pregnancy test at the time points 
specified in the Schedules of Events (Table 9.1.1). Subjects who are confirmed to be 
pregnant per a serum pregnancy test and are temporarily off study drug are not required to 
perform the scheduled urine pregnancy tests. Female subjects with a positive serum 
pregnancy test at Screening do not meet eligibility criteria for enrollment. 
Additional pregnancy tests will be performed at any visit in which pregnancy status is in 
question. Serum pregnancy tests will be performed in the event of a positive or equivocal 
urine pregnancy test result. 
Refer to Section 10.3 for details on the reporting procedures to follow in the event of 
pregnancy. 
9.7.5.2 
Antibody Testing 
Immunogenicity will be assessed by determining immune response and neutralizing activity 
with the following measurements: anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, anti-PEG 
IgM, anti-rAvPAL IgE, anti-rAvPAL-PEG IgE, and anti-rAvPAL-PEG neutralizing 
antibodies (refer to Section 9.1.1). Immunogenicity assays will be performed at the time 
points indicated in the Schedule of Events (Table 9.1.1). 
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BioMarin will perform all antibody testing, except for IgE antibodies, which will be assessed 
by a Contract Research Organization. 
9.7.6 Clinical Laboratory Assessments 
Any abnormal test results determined to be clinically significant by the Investigator should 
be repeated (at the Investigator’s discretion) until the cause of the abnormality is determined, 
the value returns to baseline or to within normal limits, or the Investigator determines that the 
abnormal value is no longer clinically significant. In the event of elevated urinary protein on 
a test result, a repeat urinalysis should be performed. This repeat urine sample must be 
performed in the morning at the first or second morning void to allow for accurate test results 
and may be performed by a home healthcare nurse. Subjects with a confirmed urine/albumin 
creatinine ratio of  ≥  100 mg/g should be referred to a nephrologist for consultation if results 
were within normal range at baseline. Subjects who had elevated results at baseline followed 
by a confirmed subsequent increase of 100-200 mg/g from baseline should also be referred to 
a nephrologist for consultation. 
All abnormal clinical laboratory result pages should be initialed and dated by an Investigator, 
along with a comment regarding whether or not the abnormal result is clinically significant. 
The diagnosis, if known, associated with abnormalities in clinical laboratory tests that are 
considered clinically significant by the Investigator will be recorded on the AE CRF. 
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Table 9.7.6.1:  Clinical Laboratory Tests 
Blood Chemistry 
Hematology 
Urine Testsa 
Other 
Albumin  
Hemoglobin  
Appearance 
Pregnancy test, if applicablea 
Alkaline Phosphatase  
Hematocrit  
Color 
ALT (SGPT)  
WBC count 
pH 
Phenylalanine 
AST (SGOT) 
RBC count 
Specific gravity 
Tyrosine 
Total bilirubin 
Platelet count 
Ketones 
Sedimentation ratea 
BUN 
Differential cell count 
Protein 
Creatinine 
 
Glucose 
GGT 
 
Spot urine 
albumin/creatinine ratio 
b 
Additional Unscheduled 
Hypersensitivity Reaction Visit 
Testsb 
Total protein 
 
Nitrite 
CH50 
Calcium 
 
Urobilinogen 
C1, C3, C4 
Sodium 
 
Hemoglobin 
Serum tryptase levelb  
Potassium 
 
Bilirubin 
CRP  
Glucose 
 
 
Urine N-methyl histamine 
 
 
Urine albumin/creatinine ratio c 
Uric acid 
 
 
Complement Testingd 
CO2 
 
 
C3 
Chloride 
 
 
C4 
ALT, alanine aminotransferase; AST, aspartate aminotransferase; BUN, blood urea nitrogen; C, complement; 
CH50, total hemolytic complement; CO2, carbon dioxide; CRP, C-reactive protein; GGT, 
gamma-glutamyltransferase; RBC, red blood cell; SGOT, serum glutamic-oxaloacetic transaminase; SGPT, 
serum glutamic-pyruvic transaminase; WBC, white blood cell. 
a To be performed by central laboratory. If urine pregnancy test is positive or equivocal, serum sample will be 
taken and assessed by a central laboratory. It is recommended that urine samples are obtained as a first or 
second morning void. In the event of elevated urinary protein on a test result, a repeat urinalysis should be 
performed. This repeat urine sample must be performed in the morning at the first or second morning void to 
allow for accurate test results and may be performed by a home healthcare nurse. 
b Perform within 24 hours of event onset. 
c It is recommended that urine samples are obtained as a first or second morning void. Subjects with a confirmed 
urine/albumin creatinine ratio of  ≥  100 mg/g should be referred to a nephrologist for consultation if results 
were within normal range at baseline. Subjects who had elevated results at baseline followed by a confirmed 
subsequent increase of 100-200 mg/g from baseline should also be referred to a nephrologist for consultation. 
d Complement C3 and C4 to be drawn at the Screening Visit and then every 8 weeks or as needed to resolve 
abnormal test results. 
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9.7.7 
Exploratory Sample Analyses  
Blood and urine samples will be collected to evaluate biochemical, molecular, and cellular 
aspects of PKU and to develop the assays used for these evaluations. For each portion of the 
blood and urine samples reserved for protocol-specified analyses, there may be multiple 
sample aliquots. Once samples have been successfully analyzed during the study, unused 
sample portions may be used during the study or after the subject’s study completion for 
assay development or other purposes.  
All samples collected in this study may be used for exploratory research. In addition, samples 
collected for other purposes may be used for exploratory research use once the primary use 
has been completed.  
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10 
REPORTING ADVERSE EVENTS  
10.1 
Adverse Events 
For this protocol, a reportable adverse event (AE) is any untoward medical occurrence 
(e.g., sign, symptom, illness, disease or injury) in a subject administered the study-drug or 
other protocol-imposed intervention, regardless of attribution. This includes the following: 
• AEs not previously observed in the subject that emerge during the course of the 
study. 
• Pre-existing medical conditions judged by the Investigator to have worsened in 
severity or frequency or changed in character during the study. 
• Complications that occur as a result of non-drug protocol-imposed interventions 
(eg, AEs related to screening procedures, medication washout, or no-treatment 
run-in). 
An adverse drug reaction is any AE for which there is a reasonable possibility that the study 
drug caused the AE. “Reasonable possibility” means there is evidence to suggest a causal 
relationship between the study-drug and the AE. 
Whenever possible, it is preferable to record a diagnosis as the AE term rather than a series 
of terms relating to a diagnosis. 
The study AE reporting period is as follows: After informed consent but prior to initiation of 
study drug, only SAEs associated with any protocol-imposed interventions will be reported.  
After informed consent is obtained and the first administration of study drug, all non-serious 
AEs and SAEs reporting period begins and continues until 4 weeks following the last 
administration of study drug or the Study Completion Visit/Early Termination Visit, 
whichever occurs last (refer to Section 12). The criteria for determining, and the reporting of 
SAEs is provided in Section 10.2.  
For this study, a medical device is defined as the prefilled syringe and all of the component 
parts. The reporting period for device-related events begins with the first dose administered 
using prefilled syringe and ends with the last dose administered using prefilled syringe. 
Events assessed by the investigator as related to the device, including malfunction, injury, or 
medication error, will be captured into an electronic data capture system. All serious events 
related to the device will be reported to BioMarin Pharmacovigilance (BPV) within 24 hours 
using the device-related event report form and entered onto the appropriate eCRF page(s) as 
required.  
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The Investigator should follow all unresolved AEs until the events are resolved or stabilized, 
the subject is lost to follow-up, or it has been determined that the study drug or study 
participation is not the cause of the AE. Outcome of AEs (and resolution dates) should be 
documented on the appropriate CRF page(s) and in the subject’s medical record unless the 
subject is lost to follow-up or it has been determined that the study drug or study 
participation is not the cause of the AE. 
The Investigator responsible for the care of the subject or qualified designee will assess AEs 
for severity, relationship to study-drug, and seriousness (see Section 10.2 for SAE 
definition). Severity (as in mild, moderate or severe headache) is not equivalent to 
seriousness, which is based on subject/event outcome or action criteria usually associated 
with events that pose a threat to a subject’s life or functioning. Seriousness (not severity) 
serves as a guide for defining regulatory reporting obligations. 
The Investigator will determine the severity of each AE using the National Cancer Institute 
(NCI) Common Terminology Criteria for Adverse Events (CTCAE) v4. Adverse events that 
do not have a corresponding CTCAE term will be assessed according to the general 
guidelines for grading used in the CTCAE v4 as stated below. 
Grade 
Description 
1 
Mild: asymptomatic or mild symptoms; clinical or diagnostic observations only; 
intervention not indicated 
2 
Moderate: minimal, local or noninvasive intervention indicated; limiting age-
appropriate instrumental activities of daily living (ADL)a 
3 
Severe or medically significant but not immediately life-threatening: hospitalization or 
prolongation of hospitalization indicated; disabling; limiting self care activities of 
daily living (ADL)b 
4 
Life threatening or debilitating: consequences; urgent intervention indicated 
5 
Death related to AE 
Grade 4 and 5 AEs should always be reported as SAEs. 
a Instrumental ADL refer to the following examples: preparing meals, shopping for groceries or clothes, using 
the telephone, managing money. 
b Self care ADL refer to the following examples: bathing, dressing and undressing, feeding oneself, using the 
toilet, taking medications, not bedridden. 
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The Investigator will determine the relationship of an AE to the study drug and will record it 
on the source documents and AE CRF, using the categories defined below. 
Relationship 
Description 
Not Related 
Exposure to the IP has not occurred 
OR 
The administration of the IP and the occurrence of the AE are not reasonably related in time  
OR 
The AE is considered likely to be related to an etiology other than the use of the IP; that is, 
there are no facts [evidence] or arguments to suggest a causal relationship to the IP. 
Possibly Related 
The administration of the IP and the occurrence of the AE are reasonably related in time 
AND 
The AE could be explained equally well by factors or causes other than exposure to the IP. 
Probably Related 
The administration of IP and the occurrence of the AE are reasonably related in time  
AND 
The AE is more likely explained by exposure to the IP than by other factors or causes. 
In order to classify AEs and diseases, preferred terms will be assigned by the sponsor to the original terms 
entered on the CRF, using MedDRA (Medical Dictionary for Regulatory Activities terminology). 
 
Factors suggestive of a causal relationship could include (but are not limited to) the 
following: 
• 
Plausible temporal relationship 
• 
Absence of alternative explanations 
• 
Rarity of event in a given patient or disease state 
• 
Absence of event prior to study drug exposure 
• 
Consistency with study product pharmacology 
• 
Known relationship to underlying mechanism of study drug action 
• 
Similarity to adverse reactions seen with related drug products 
• 
Abatement of AE with discontinuation of study drug, and/or recurrence of AE with 
reintroduction of study drug 
 
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10.2 
Serious Adverse Events 
A serious adverse event (SAE) is any untoward medical occurrence that at any dose meets 
1 or more of the following criteria: 
• Is fatal. 
• Is life threatening. 
o 
Note: Life-threatening refers to an event that places the subject at immediate 
risk of death. This definition does not include a reaction that, had it occurred 
in a more severe form, might have caused death. 
• Requires or prolongs inpatient hospitalization. 
• Results in persistent or significant disability or incapacity. 
• Is a congenital anomaly or birth defect in the child or fetus of a subject exposed to IP 
prior to conception or during pregnancy. 
• Important medical events or reactions that may not be immediately life-threatening or 
result in death or hospitalization but may jeopardize the subject or may require 
intervention to prevent one of the other outcomes above should also usually be 
considered serious. 
For this protocol, anaphylaxis per NIAID/FAAN criteria for the clinical diagnosis of 
anaphylaxis is designated as an AE of special interest (serious or nonserious and irrespective 
of severity) to facilitate rapid reporting and sponsor review. All occurrences of anaphylaxis 
per NIAID/FAAN criteria will be reported to the sponsor within 24 hours of the site 
becoming aware of the event using the SAE form. Severity and serious criteria (if applicable) 
should be reported on the SAE form. 
The reporting period for SAEs related to protocol imposed interventions begins after 
informed consent is obtained, the reporting period for all SAEs begins after first dose of 
study drug and continues until 4 weeks following the last administration of study drug or End 
of Treatment Visit. The reporting period for Serious Device Related Events begins after first 
dose of study drug and ends with the last administered dose. 
All SAEs (including serious device-related events), whether or not considered related to 
study drug, must be reported within 24 hours of the site becoming aware of the event by 
faxing the study-specific SAE Report Form or device Report Form to BioMarin 
Pharmacovigilance (BPV). Each SAE must also be reported in the CRF Investigators should 
not wait to collect information that fully documents the event before notifying BPV of a 
SAE. BioMarin may be required to report certain SAEs to regulatory authorities within 
7 calendar days of being notified about the event; therefore, it is important that Investigators 
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submit any information requested by BioMarin as soon as it becomes available.  The 
Investigator should follow all unresolved SAEs until the events are resolved or stabilized, the 
subject is lost to follow-up, or it has been determined that the study drug or participation is 
not the cause of the AE. Resolution of AEs (with dates) should be documented in the CRF 
and in the subject’s medical record. 
For some SAEs, the Sponsor may follow up by telephone, fax, electronic mail, and/or a 
monitoring visit to obtain additional case details deemed necessary to appropriately evaluate 
the SAE report (e.g., hospital discharge summary, consultant report, or autopsy report). 
Reporting of SAEs to the IRB will be done in compliance with the standard operating 
procedures and policies of the IRB and with applicable regulatory requirements. Adequate 
documentation must be obtained by BioMarin showing that the IRB was properly and 
promptly notified as required. 
10.3 
Adverse Events Occurring Secondary to Other Events 
In general, AEs occurring secondary to other events (eg, cascade events) should be identified 
by their primary cause. For example, if severe diarrhea is known to have resulted in 
dehydration, it is sufficient to record only diarrhea as an AE or SAE on the eCRF. However, 
medically important events that may be linked and/or separated in time should be recorded as 
independent events on the eCRF. For example, if severe hemorrhage leads to renal failure, 
both events should be recorded separately on the eCRF. 
10.4 
Persistent or Recurrent Adverse Events 
A persistent AE is one that extends continuously, without resolution, between subject 
evaluation time points. Such an event should be recorded only once on the eCRF unless its 
severity increases or decreases (in which case it should be recorded again on the AE eCRF). 
A recurrent AE is one that occurs and resolves between subject evaluation time points, but 
then subsequently recurs. All recurrences of the AE should be individually recorded as a 
separate event on the AE eCRF. 
10.5 
Abnormal Laboratory Values 
Laboratory test results will be recorded on the laboratory results pages of the eCRF, or 
appear on electronically produced laboratory reports submitted directly from the central 
laboratory, if applicable. 
Any laboratory result abnormality fulfilling the criteria for a SAE should be reported as such, 
in addition to being recorded as an AE in the eCRF. 
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A clinical laboratory abnormality should be documented as AE if it is not otherwise refuted 
by a repeat test to confirm the abnormality and any one or more of the following conditions 
is met: 
• Accompanied by clinical symptoms 
• Leading to a change in study medication (e.g. dose modification, interruption or 
permanent discontinuation)  
• Requiring a change in concomitant therapy (e.g. addition of, interruption of, 
discontinuation of, or any other change in a concomitant medication, therapy or 
treatment). 
• The abnormality suggests a disease and/or organ toxicity 
• The abnormality is of a degree that requires active management (eg, change of dose, 
discontinuation of study drug, more frequent follow-up assessments, further 
diagnostic investigation, etc.) 
This applies to any protocol and non-protocol specified safety and efficacy laboratory result 
from tests performed after the first dose of study medication that falls outside the laboratory 
reference range and meets the clinical significance criteria. 
This does not apply to any abnormal laboratory result that falls outside the laboratory 
reference range but that does not meet the clinical significance criteria (these will be 
analyzed and reported as laboratory abnormalities), those that are considered AEs of the type 
explicitly exempted by the protocol, or those which are a result of an AE that has already 
been reported.  
10.6 
Pre-existing Conditions 
A pre-existing condition is one that is present at the start of the study. Such conditions should 
be recorded as medical history on the appropriate eCRF. 
A pre-existing condition should be recorded as an AE or SAE during the study only if the 
frequency, intensity, or character of the condition worsens during the study period. It is 
important to convey the concept that a pre-existing condition has changed by including 
applicable language in the verbatim description of the event (eg, more frequent headaches). 
10.7 
General Physical Examination Findings 
At screening, any clinically significant abnormality should be recorded as a pre-existing 
condition (refer to Section 10.6). During the study, any new clinically significant findings 
and/or abnormalities discovered on physical examination that meet the definition of an AE 
(or an SAE) must be recorded and document as an AE or SAE on the AE eCRF. 
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10.8 
Hospitalization, Prolonged Hospitalization, or Surgery 
Any AE that results in hospitalization or prolonged hospitalization should be documented 
and reported as an SAE unless specifically instructed otherwise in this protocol (refer to 
Section 10.2). 
There are some hospitalization scenarios that do not require reporting as an SAE when there 
is no occurrence of an AE. These scenarios include planned hospitalizations or prolonged 
hospitalizations to the following: 
• Perform a protocol-mandated efficacy measurement 
• Undergo a diagnostic or elective surgical procedure for a pre-existing medical 
condition that has not changed in severity 
• Receive scheduled therapy (study drug or otherwise) for the study indication 
10.9 
Deaths 
All deaths that occur during the AE reporting period (refer to Section 10.1 for nonserious 
AEs and Section 10.2 for SAEs), regardless of attribution, will be recorded on the AE eCRF 
and expeditiously reported to the Sponsor as an SAE. 
When recording a death, the event or condition that caused or contributed to the fatal 
outcome should be recorded as the single medical concept on the eCRF. If the cause of death 
is unknown and cannot be ascertained at the time of reporting, record “Unexplained Death” 
or “Death of Unknown Cause” on the eCRF.   
10.10 Pregnancy 
Pregnancy in a subject or partner should be reported within 24 hours of the site becoming 
aware of the pregnancy to BioMarin Pharmacovigilance by fax using the Pregnancy Form in 
the study reference materials. The reporting period for pregnancies begins with informed 
consent and continues until 4 weeks following the last study drug dose. In addition, 
pregnancy in a subject is also reported on the Subject Disposition eCRF and the End of Study 
eCRF if the subject withdraws from the study due to pregnancy. The Investigator must make 
every effort to follow the subject through resolution of the pregnancy (delivery or 
termination) and to report the resolution to BPV in the study reference materials. In the event 
of pregnancy in the partner of a study subject, the Investigator should make every reasonable 
attempt to obtain the woman’s consent for release of protected health information. 
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Abortion, whether therapeutic or spontaneous, should always be classified as an SAE (as the 
Sponsor considers these to be medically significant), recorded on the eCRF, and 
expeditiously reported to the Sponsor as an SAE. 
10.11 Follow-up of Subjects after Adverse Events 
For some SAEs and AESIs, the sponsor may follow up by telephone, fax, electronic mail, 
and/or a monitoring visit to obtain additional case details (eg, hospital discharge summary, 
consultant report, or autopsy report) deemed necessary to appropriately evaluate the SAE 
report. 
10.12 Post-Study Adverse Events 
At the last scheduled visit, the investigator should instruct each subject to report to the 
investigator and/or to BPV directly any subsequent SAEs that the subject’s personal 
physician(s) believes might be related to prior study treatment. 
The investigator should notify the study sponsor of any death or SAE occurring at any time 
after a subject has discontinued or terminated study participation if the investigator believes 
that the death or SAE may have been related to prior study treatment. The sponsor should 
also be notified if the investigator should become aware of the development of cancer or of a 
congenital anomaly in a subsequently conceived offspring of a subject who participated in 
this study.  
10.13 Urgent Safety Measures 
The regulations governing clinical trials state that the sponsor and Investigator are required to 
take appropriate urgent safety measures to protect subjects against any immediate hazards 
that may affect the safety of subjects, and that the appropriate regulatory bodies should be 
notified according to their respective regulations. According to the European Union (EU) 
Clinical Trial Directive 2001/20/EC, “…in the light of the circumstances, notably the 
occurrence of any new event relating to the conduct of the trial or the development of the 
investigational medicinal product where that new event is likely to affect the safety of the 
subjects, the sponsor and the Investigator shall take appropriate urgent safety measures to 
protect the subjects against any immediate hazard. The sponsor shall forthwith inform the 
competent authorities of those new events and the measures taken and shall ensure that the 
IRB/EC/REB is notified at the same time.” The reporting period for these events which may 
require the implementation of urgent safety measures is the period from the time of signing 
of the ICF through the completion of the last study visit or at the ETV. Investigators are 
required to report any events which may require the implementation of urgent safety 
measures to BioMarin with 24 hours. 
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Examples of situations that may require urgent safety measures include discovery of the 
following: 
• Immediate need to revise the IP administration (i.e., modified dose amount or 
frequency not defined in protocol). 
• Lack of study scientific value, or detrimental study conduct or management. 
• Discovery that the quality or safety of the IP does not meet established safety 
requirements. 
10.14 BioMarin Pharmacovigilance Contact Information 
Contact information for BioMarin Pharmacovigilance is as follows: 
BioMarin Pharmaceutical Inc. 
Address 
105 Digital Drive 
 
 
Novato, CA 94949 
Phone:  
(415) 506-6179 
Fax: 
 
(415) 532-3144 
E-mail: 
drugsafety@bmrn.com 
The Investigator is encouraged to discuss with the Sponsor’s Medical Office sponsor’s 
medical monitor r any AEs for which the issue of seriousness is unclear or questioned. 
Contact information for the sponsor’s medical monitor is as follows: 
Name:  
 MS 
Address: 
105 Digital Drive 
 
 
Novato, CA 94949 USA 
Phone:  
 
Fax: 
 
 
E-mail: 
 
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11 
APPROPRIATENESS OF MEASUREMENTS 
11.1 
Safety and Pharmacokinetics 
The PK and safety assessments in this study are used widely and are generally recognized as 
reliable, accurate, and relevant. 
11.2 
Diet Diary 
A 3-day diet diary will be issued to subjects for completion and will be brought to clinic on a 
monthly basis for review with the clinical study staff. Additional information regarding the 
diet diary is provided in Section 7.3, and information regarding administration of the diary is 
provided in Section 9.7.4. Additional information about diet is provided in Section 9.1 and 
Section 9.6. 
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12 
STUDY PROCEDURES 
12.1 
Prestudy 
An ICF must be signed and dated by the subject (or the subject’s legally authorized 
representative if the subject is less than 18 years of age), the PI or designee and witness 
(if required) before any study-related procedures are performed. 
12.2 
Screening Visit 
After subjects have signed an ICF, they will be screened for enrollment into the study. 
The following study activities will be performed at Screening: 
• Medical history, including allergy history, and demographics 
• Physical examination  
• Vital signs, including height and weight 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.).  For safety reasons, 
this test must be performed prior to the chest X-ray. 
• Chest X-ray 
• 12-lead ECG 
• Clinical laboratory tests (including spot urine albumin/creatinine ratio, hematology, 
chemistry, and urinalysis) 
• Complement C3 and C4 
• Assessment of SAEs 
• Concomitant medications 
• Diet query 
• Blood Phe and plasma tyrosine concentration 
For subjects who participated in a previous rAvPAL-PEG study, these assessments may be 
the same as those used for the last visit of the previous study, if they occur within 28 days 
from Day 1. 
12.3 
Treatment Period 
During the Treatment Period, additional visits may occur if deemed necessary to monitor 
AEs or blood Phe concentrations. On days that a dose is given, assessments will be done 
predose unless otherwise specified. Subjects must have AEs and concomitant medications 
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assessed whenever dose is administered even if the administration does not coincide with a 
scheduled clinic visit. If there is a skin reaction that lasts ≥ 14 days, the Skin Reaction eCRF 
should be completed and the subject should be referred to a dermatologist for consultation 
and a skin biopsy. It is recommended that a photograph of the skin reaction may be taken by 
the subject or the site to help assess the event; photographs may be collected by the sponsor.  
If the dose is modified by increasing dose level, additional blood Phe concentration testing 
should be done daily for 3 days following dose adjustment. If dose is modified by increasing 
either dose frequency or dose level, additional blood Phe concentration testing should be 
done prior to each dose for the first 2 weeks following dose adjustment. 
12.3.1 Day 1 (Week 1) 
Within 28 days of completing screening assessments, the following study activities will be 
performed on Day 1: 
• Physical examination 
• Vital signs 
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) 
• Assessment of SAEs (predose and postdose) and all AEs (postdose) 
• Concomitant medications 
• Diet query 
• PK sample 
• Blood Phe and plasma tyrosine concentration 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, and anti-rAvPAL-PEG neutralizing antibodies) 
• Administer study drug (study drug may be administered on additional days during the 
week as determined by the Investigator) 
12.3.2 Weekly Telephone Visit 
Subjects should have a weekly telephone visit conducted. Subjects must still come into the 
clinic for the scheduled visits every 8 weeks per Table 9.1.1. The following should be 
discussed with the subject during the weekly telephone visit: 
• Injection-site self inspection (previous and current injection site) 
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• Assessment of AEs 
• Concomitant medications 
• Confirmation of dose level, frequency, and study drug administration 
12.3.3 Substudy Visits 
For subjects participating in the PK substudy, refer to Section 9.7.3 and Table 9.1.2. 
12.3.4 Every 8 Weeks   
Subjects must have AEs and concomitant medications assessed whenever dose is 
administered even if the administration does not coincide with a scheduled clinic visit.    
Visits must be performed in the clinic every 8 weeks. The following study activities will be 
performed: 
• Physical examination 
• Vital signs 
• Sedimentation rate 
• Weight 
• Clinical laboratory tests 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.) For safety reasons, this 
test must be performed prior to the chest X-ray. 
• Chest x-ray (Week 48 visit only) 
• Complement C3 and C4 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• PK sample 
• Blood Phe and plasma tyrosine concentration 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, and anti-rAvPAL-PEG neutralizing antibodies) 
• 3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the next monthly visit.) 
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• Prefilled syringe self-administration training (to be performed prior to subjects 
transitioning from vial and syringe drug product to prefilled syringe drug product). 
• Administer study drug  
• Prefilled syringe refresher training (every 24 weeks only) 
• If additional training is needed on days subsequent to the 8-week scheduled visit, 
additional clinic visit(s) or HHRN may be used. 
12.3.5 Unscheduled Hypersensitivity Reaction Visit 
Subjects who have an NCI-CTCAE grade ≥ 3 hypersensitivity reaction after rAvPAL-PEG 
administration (refer to Section 9.1.1) will have assessments performed immediately 
following (within 24 hours) the reaction.  
• Vital signs 
• Clinical laboratory tests 
• Urine/albumin creatinine ratio 
• CRP, CH50, C1, C3, and C4 
• Urine N-methyl histamine  
• Serum anti-rAvPAL IgE and anti-rAvPAL-PEG IgE only (performed > 8 hours after 
event onset) 
• Serum tryptase level 
• Skin biopsy (optional; affected and not affected area; to be performed within 1 week 
of the reaction) 
• Assessment of AEs 
• Concomitant medications 
Following completion of the Unscheduled Hypersensitivity Reaction visit, subjects may 
resume study drug administration per the discretion of the Principal Investigator and the 
sponsor’s medical monitor. 
12.4 
Study Completion/Early Termination Visit 
Subjects should perform the Study Completion Visit 4 weeks after the last dose of study drug 
or after completion of study participation, whichever occurs last.  
For subjects who terminate from the study early (refer to Section 9.3.3), the Early 
Termination Visit (ETV) will occur 4 weeks after the final dose of study drug or after 
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withdrawal from study participation, whichever occurs last. Subjects who terminate from 
study drug early should continue to perform the remaining visit assessments in Section 12.3 
as applicable until study completion. 
Any AE that caused a subject to withdraw from the study or any clinically significant 
abnormal laboratory value or vital sign measurement identified at the ETV will be followed 
by the Investigator.  
Every reasonable effort should be made to contact any subject who is lost to follow-up. 
The following study activities will be performed at the ETV: 
• Physical examination  
• Vital signs 
• 12-lead ECG 
• Clinical laboratory tests 
• Chest x-ray  
• Sedimentation rate 
• Urine pregnancy test, if applicable (A serum pregnancy test will be performed in the 
event of any positive or equivocal urine pregnancy test result.). For safety reasons, 
this test must be performed prior to the chest X-ray. 
• Assessment of AEs 
• Concomitant medications 
• Diet query 
• 3-day diet diary (It is preferable that the subject complete the diary 3 days 
immediately prior to the Early Termination Visit.) 
• PK sample 
• Blood Phe and plasma tyrosine concentration 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, anti-rAvPAL-PEG neutralizing antibodies) 
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13 
DATA QUALITY ASSURANCE 
BioMarin personnel or designees will visit the study site prior to initiation of the study to 
review with the site personnel information about the IP, protocol and other regulatory 
document requirements, any applicable randomization procedures, source document 
requirements, CRFs, monitoring requirements, and procedures for reporting AEs, including 
SAEs. 
At visits during and after the study, a CRA will monitor the site for compliance with 
regulatory documentation, with a focus on accurate and complete recording of data on CRFs 
from source documents, adherence to protocol, randomization (if applicable), SAE reporting 
and drug accountability records.  
The designated clinical data management group will enter or transfer CRF data into a study 
database. 
Data quality control and analysis will be performed by BioMarin or a designee, based on a 
predefined analysis plan. 
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14 
STATISTICAL METHODS AND DETERMINATION OF SAMPLE SIZE 
14.1 
Statistical and Analytical Plans 
Because of the small sample size, no formal statistical tests will be performed. Categorical 
data will be summarized using frequency and percent, while continuous data will be 
summarized using descriptive statistics (ie, number of observations, mean, median, standard 
deviation [SD], minimum, and maximum). 
The statistical analysis plan (SAP) will provide additional details about the planned statistical 
analysis. 
14.2 
Safety Analysis 
All subjects who receive any amount of study drug in this study and have postdose safety 
information will be included in the safety analyses. 
The Medical Dictionary for Regulatory Activities terminology (MedDRA) will be used by 
the sponsor to assign system organ class and preferred term classification to events and 
diseases based on the original terms entered on the Case Report Form (CRF). 
The incidence of AEs will be summarized by system organ class, preferred term, relationship 
to study drug, and severity. A by–subject listing will be provided for those subjects who 
experience a serious AE (SAE), including death, or experience an AE associated with early 
withdrawal from the study or study drug. Hypersensitivity AEs and AEs that result in dosing 
interruption or dose level reduction are of interest, and the percentage of subjects who report 
these AEs will be presented. 
Clinical laboratory data will be summarized by the type of laboratory test. Frequency and 
percentage of subjects who experience abnormal (ie, outside of reference range) and/or 
clinically significant abnormalities after study drug administration will be presented for each 
clinical laboratory test. For each clinical laboratory test, descriptive statistics will be provided 
for baseline and all subsequent post-treatment visits. Changes from baseline to the 
post-treatment visits will also be provided. Descriptive statistics of vital signs, physical 
examination results, ECG results, and X-ray results, and immunogenicity test results will also 
be provided. Additionally, antibodies and titers will be summarized by scheduled time point. 
14.3 
Pharmacokinetic Analysis 
Subjects who complete the Substudy will have the following PK parameters assessed: area 
under the plasma concentration-time curve (AUC), time to maximum plasma concentration 
(Tmax), maximum plasma concentration (Cmax), half life (t1/2), and clearance (CL/F).  Should 
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data become available from previous rAvPAL-PEG studies that indicate study drug 
accumulation should also be measured, additional blood draws may be added for PK analysis 
as needed per the discretion of the Investigator in consultation with the sponsor’s medical 
monitor. 
14.3.1 Pharmacokinetic Substudy Analysis 
For subjects who completed the Substudy, the steady-state PK of rAvPAL-PEG in subjects 
who have achieved and maintained target blood Phe will be explored.  This substudy has 
been completed as of 20 December 2013. 
14.4 
Efficacy Analysis 
Data from all subjects who receive any amount of study drug and who have any 
post-treatment efficacy data will be included in the efficacy analysis. 
Blood Phe concentration at each scheduled time point will be summarized using descriptive 
statistics (mean, SD, median, minimum, and maximum). Change in blood Phe concentration 
from baseline (to be defined in the SAP) to each scheduled time point and presence/absence 
of antibodies will also be summarized. In addition, the proportion of subjects who have 
maintained target Phe concentrations of 60-600 µmol/L will be summarized by each 
scheduled time point. 
The relationship of dietary Phe intake (per information reported on the subject diet diary) and 
blood Phe concentration will also be explored. Subjects who received any amount of study 
drug with any post-treatment blood Phe concentration measurements and diet diary 
information will be included in this exploratory analysis.  
Details regarding exploratory analyses will be provided in the Statistical Analysis Plan. 
14.5 
Determination of Sample Size 
Subjects who participated in previous rAvPAL-PEG studies may be enrolled into this study. 
No formal sample size calculation was conducted for this study or the PAL-003 Substudy.   
14.6 
Handling of Missing Data 
All analyses will be presented based on observed data only. Missing data will not be imputed 
for analyses unless sensitivity analyses are warranted. If imputations are used, detailed 
imputation methods will be described in the SAP before locking the database. 
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14.7 
Interim Analyses 
Safety will be assessed throughout the study on an ongoing basis (refer to Section 15 for 
information regarding the DMC). 
14.8 
Changes in the Conduct of the Study or Planned Analyses 
Only BioMarin may modify the protocol. Any change in study conduct considered necessary 
by the PI will be made only after consultation with BioMarin, who will then issue a formal 
protocol amendment to implement the change. The only exception is when an Investigator 
considers that a subject’s safety is compromised without immediate action. In these 
circumstances, immediate approval of the chairman of the IRB must be sought, and the 
Investigator should inform BioMarin and the full IRB within 2 working days after the 
emergency occurs. 
With the exception of minor administrative or typographical changes, the IRB must review 
and approve all protocol amendments. Protocol amendments that have an impact on subject 
risk or the study objectives, or require revision of the ICF, must receive approval from the 
IRB prior to their implementation. 
When a protocol amendment substantially alters the study design or the potential risks or 
burden to subjects, the ICF will be amended and approved by BioMarin and the IRB, and all 
active subjects must again provide informed consent. 
Note: If discrepancies exist between the text of the statistical analysis as planned in the 
protocol, and the final SAP, a protocol amendment will not be issued and the SAP will 
prevail. 
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15 
DATA MONITORING COMMITTEE (DMC) 
The DMC will act independently in an advisory capacity to BioMarin to monitor the safety 
of rAvPAL-PEG in subjects who participate in the study.  
The responsibilities of the DMC are to: 
• Review the study protocol, informed consent and assent documents, and plans for 
data monitoring. 
• Evaluate the progress of the trial, subjects’ risk versus benefit, and other factors that 
could affect the study outcome. 
• Assess the effect and relevance of new external evidence. 
• Consider relevant information that may have an impact on the safety of the 
participants or the ethics of the study. 
• Protect the safety of the study participants in accordance with the stopping criteria as 
defined in study protocol Section 9.1.2. 
• Make recommendations to the BioMarin concerning continuation or termination of 
the study or other study modifications based on observations. 
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16 
COMPENSATION, INSURANCE, AND INDEMNITY 
There will be no charge to study subjects to be in this study. BioMarin will pay all costs of 
tests, procedures, and treatments that are part of this study. In addition, after IRB approval, 
BioMarin may reimburse the cost of travel for study-related visits. BioMarin will not pay for 
any hospitalizations, tests, or treatments for medical problems of any sort, whether or not 
related to the study subject’s disease, that are not part of this study. Costs associated with 
hospitalizations, tests, and treatments should be billed and collected in the way that such 
costs are usually billed and collected. 
The Investigator should contact BioMarin immediately upon notification that a study subject 
has been injured by the IP or by procedures performed as part of the study. Any subject who 
experiences a study-related injury should be instructed by the Investigator to seek medical 
treatment at a pre-specified medical institution if possible, or at the closest medical treatment 
facility if necessary. The subject should be given the name of a person to contact to seek 
further information about, and assistance with, treatment for study-related injuries. 
The treating physician should bill the subject’s health insurance company or other third party 
payer for the cost of this medical treatment, unless the executed Clinical Trial Agreement 
between BioMarin and the institution of the investigator specifies otherwise. If the subject 
has followed the Investigator’s instructions, BioMarin may pay for reasonable and necessary 
medical services to treat the injuries caused by the IP or study procedures. In some 
jurisdictions, BioMarin is obligated by law to pay for study-related injuries without prior 
recourse to third party payer billing. If this is the case, BioMarin will comply with the law. 
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17 
CASE REPORT FORMS AND SOURCE DOCUMENTS 
Electronic case report forms will be provided for each subject. The Investigator must review 
and electronically sign the completed CRF casebook to verify its accuracy. 
CRFs must be completed using a web–based application that has been validated. Study site 
personnel will be trained on the application and will enter the clinical data from source 
documentation. Unless explicitly allowed in the CRF instructions, blank data fields are not 
acceptable. 
In the event of an entry error, or if new information becomes available, the site personnel will 
correct the value by deselecting the erroneous response and then selecting or entering the 
factual response. In compliance with 21 CFR Part 11, the system will require the site 
personnel to enter a reason for changing the value. The documented audit trail will include 
the reason for the change, the original value, the new value, the time of the correction, and 
the identity of the operator. 
BioMarin’s policy is that study data on the CRFs must be verifiable to the source data, which 
necessitates access to all original recordings, laboratory reports, and subject records. 
In addition, all source data should be attributable (signed and dated). The Investigator must 
therefore agree to allow direct access to all source data. Subjects (or their legally authorized 
representative) must also allow access to their medical records, and subjects will be informed 
of this and will confirm their agreement when giving informed consent.  
A CRA designated by BioMarin will compare the CRFs with the original source documents 
at the study site and evaluate them for completeness and accuracy before designating them as 
“source data verified” (SDV). If an error is discovered at any time or a clarification is 
needed, the CRA, or designee, will create an electronic query on the associated field. Site 
personnel will then answer the query by either correcting the data or responding to the query. 
The CRA will then review the response and determine either to close the query or re–query 
the site if the response does not fully address the question. This process is repeated until all 
open queries have been answered and closed. 
Before a subject’s CRF casebook can be locked, all data fields must be SDV and all queries 
closed. The Data Manager, or designee, will then set the status of the forms, visits, and the 
entire casebook to locked. The investigator will then electronically sign the casebook, 
specifying that the information on the CRFs is accurate and complete. Upon completion of 
the clinical study report for the entire study, an electronic copy of each site’s casebooks will 
be copied to a compact disk (CD) and sent to each site for retention with other study 
documents. 
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18 
STUDY MONITORING AND AUDITING 
Qualified individuals designated by BioMarin will monitor all aspects of the study according 
to GCP and standard operating procedures for compliance with applicable government 
regulations. The PI agrees to allow these monitors direct access to the clinical supplies, 
dispensing, and storage areas and to the clinical files, including original medical records, of 
the study subjects, and, if requested, agrees to assist the monitors. The PI and staff are 
responsible for being present or available for consultation during routinely scheduled site 
visits conducted by BioMarin or its designees. 
Members of BioMarin’s GCP Compliance Department or designees may conduct an audit of 
a clinical site at any time during or after completion of the study. The PI will be informed if 
an audit is to take place and advised as to the scope of the audit. Representatives of the FDA 
or other Regulatory Agencies may also conduct an audit of the study. If informed of such an 
inspection, the PI should notify BioMarin immediately. The PI will ensure that the auditors 
have access to the clinical supplies, study site facilities, original source documentation, and 
all study files. 
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RETENTION OF RECORDS 
The PI must retain all study records required by BioMarin and by the applicable regulations 
in a secure and safe facility. The PI must consult a BioMarin representative before disposal 
of any study records, and must notify BioMarin of any change in the location, disposition or 
custody of the study files. The PI/institution must take measures to prevent accidental or 
premature destruction of essential documents, that is, documents that individually and 
collectively permit evaluation of the conduct of a study and the quality of the data produced, 
including paper copies of study records (e.g., subject charts) as well as any original source 
documents that are electronic as required by applicable regulatory requirements. 
All study records must be retained for at least 2 years after the last approval of a marketing 
application in the U.S. or an ICH region and until (1) there are no pending or contemplated 
marketing applications in the United States or an ICH region or (2) at least 2 years have 
elapsed since the formal discontinuation of clinical development of the IP. The PI/institution 
should retain subject identifiers for at least 15 years after the completion or discontinuation 
of the study. Subject files and other source data must be kept for the maximum period of time 
permitted by the hospital, institution or private practice, but not less than 15 years. 
These documents should be retained for a longer period, however, if required by the 
applicable regulatory requirements or by a BioMarin agreement. BioMarin must be notified 
and will assist with retention should the PI/institution be unable to continue maintenance of 
subject files for the full 15 years. It is the responsibility of BioMarin to inform the 
PI/institution as to when these documents no longer need to be retained. 
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20 
USE OF INFORMATION AND PUBLICATION 
BioMarin recognizes the importance of communicating medical study data and therefore 
encourages the publication of these data in reputable scientific journals and at seminars or 
conferences. The details of the processes of producing and reviewing reports, manuscripts, 
and presentations based on the data from this study will be described in the Clinical Trial 
Agreement between BioMarin and the Investigator/Institution. Consideration for authorship 
of all publications will be based on compliance with the Uniform Requirements for 
Manuscripts Submitted to Biomedical Journals (“Uniform Requirements”) of the 
International Committee of Medical Journal Editors (ICMJE) 
(http://www.icmje.org/about-icmje/faqs/icmje-recommendations/) and good publication 
practices (GPP).  
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21 
REFERENCES 
Armstrong, JK, Hempel, G, Koling, S, Chan, LS et. al. Antibody against poly(ethylene glycol) 
adversely affects PEG-asparaginase therapy in acute lymphoblastic leukemia patients. Cancer 110[1], 
103-111. 2007 
Brown, SG. Clinical features and severity grading of anaphylaxis. J Allergy Clin Immunol 114[2], 
371-376. 2004 
Chen, AM, Scott, MD. Current and future applications of immunological attenuation via pegylation 
of cells and tissue. BioDrugs 15[12], 833-847. 2001 
Davis, S, Abuchowski, A, Park, YK, Davis, FF. Alteration of the circulating life and antigenic 
properties of bovine adenosine deaminase in mice by attachment of polyethylene glycol. Clin Exp 
Immunol 46[3], 649-652. 1981 
Fisch, RO. Comments on diet and compliance in phenylketonuria. Eur J Pediatr 159 Suppl 2, S142-
S144. 2000 
Gamez, A, Wang, L, Sarkissian, CN, Wendt, D et. al. Structure-based epitope and PEGylation sites 
mapping of phenylalanine ammonia-lyase for enzyme substitution treatment of phenylketonuria. Mol 
Genet Metab 91[4], 325-334. 2007 
Ganson, NJ, Kelly, SJ, Scarlett, E, Sundy, JS et. al. Control of hyperuricemia in subjects with 
refractory gout, and induction of antibody against poly(ethylene glycol) (PEG), in a phase I trial of 
subcutaneous PEGylated urate oxidase. Arthritis Res Ther 8[1], R12. 2006 
Guttler, F, Azen, C, Guldberg, P, Romstad, A et. al. Impact of the phenylalanine hydroxylase gene on 
maternal phenylketonuria outcome. Pediatrics 112[6 Pt 2], 1530-1533. 2003 
Harris, JM, Chess, RB. Effect of pegylation on pharmaceuticals. Nat Rev Drug Discov 2[3], 214-221. 
2003 
Huttenlocher, PR. The neuropathology of phenylketonuria: human and animal studies. Eur J Pediatr 
159 Suppl 2, S102-S106. 2000 
Judge, A, McClintock, K, Phelps, JR, Maclachlan, I. Hypersensitivity and loss of disease site 
targeting caused by antibody responses to PEGylated liposomes. Mol Ther 13[2], 328-337. 2006 
Kaufman, S. An evaluation of the possible neurotoxicity of metabolites of phenylalanine. J Pediatr 
114[5], 895-900. 1989 
Koch, R, Hanley, W, Levy, H, Matalon, K et. al. The Maternal Phenylketonuria International Study: 
1984-2002. Pediatrics 112[6 Pt 2], 1523-1529. 2003 
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Lapis. Long-term Correction of PKU in the Pahenu2 Mouse by Mutant and Chemically Modified 
Forms of Phenylalanine Ammonium Lyase. ASHG 57th Annual Meeting The American Society of 
Human Genetics) 2007.  
Lee, PJ, Lilburn, M, Baudin, J. Maternal phenylketonuria: experiences from the United Kingdom. 
Pediatrics 112[6 Pt 2], 1553-1556. 2003 
Levy, HL. Historical background for the maternal PKU syndrome. Pediatrics 112[6 Pt 2], 1516-1518. 
2003 
Matalon, R, Surendran, S, Matalon, KM, Tyring, S et. al. Future role of large neutral amino acids in 
transport of phenylalanine into the brain. Pediatrics 112[6 Pt 2], 1570-1574. 2003 
Richter, AW, Akerblom, E. Antibodies against polyethylene glycol produced in animals by 
immunization with monomethoxy polyethylene glycol modified proteins. Int Arch Allergy Appl 
Immunol 70[2], 124-131. 1983 
Richter, AW, Akerblom, E. Polyethylene glycol reactive antibodies in man: titer distribution in 
allergic patients treated with monomethoxy polyethylene glycol modified allergens or placebo, and in 
healthy blood donors. Int Arch Allergy Appl Immunol 74[1], 36-39. 1984 
Rouse, B, Azen, C. Effect of high maternal blood phenylalanine on offspring congenital anomalies 
and developmental outcome at ages 4 and 6 years: the importance of strict dietary control 
preconception and throughout pregnancy. J Pediatr 144[2], 235-239. 2004 
Sampson, HA, Munoz-Furlong, A, Campbell, RL, Adkinson, NF, Jr. et. al. Second symposium on the 
definition and management of anaphylaxis: summary report--Second National Institute of Allergy and 
Infectious Disease/Food Allergy and Anaphylaxis Network symposium. J Allergy Clin Immunol 
117[2], 391-397. 2006 
Scott, MD, Murad, KL, Koumpouras, F, Talbot, M et. al. Chemical camouflage of antigenic 
determinants: stealth erythrocytes. Proc Natl Acad Sci U S A 94[14], 7566-7571. 1997 
Scriver, CR, Kaufman. Hyperphenylalaninemia: Phenylalanine Hydroxylase Deficiency. In: Beaudet 
AL, Sly WS, Valle D, editors. Metabolic and Molecular Bases of Inherited Disease. New York: 
McGraw-Hill, 2001: 1667-1724. 
Walter, JH, White, FJ, Hall, SK, MacDonald, A et. al. How practical are recommendations for dietary 
control in phenylketonuria? Lancet 360[9326], 55-57. 2002 
Webster, R, Didier, E, Harris, P, Siegel, N et. al. PEGylated proteins: evaluation of their safety in the 
absence of definitive metabolism studies. Drug Metab Dispos 35[1], 9-16. 2007 
 
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22 
INVESTIGATOR RESPONSIBILITIES 
22.1 
Conduct of Study and Protection of Human Subjects  
In accordance with FDA Form 1572, the Investigator will ensure that: 
• He or she will conduct the study in accordance with the relevant, current protocol and 
will only make changes in a protocol after notifying the sponsor, except when 
necessary to protect the safety, rights, or welfare of subjects. 
• He or she will personally conduct or supervise the study. 
• He or she will inform any potential subjects, or any persons used as controls, that the 
drugs are being used for investigational purposes and he or she will ensure that the 
requirements relating to obtaining informed consent in 21 CFR Part 50 and 
institutional review board (IRB) review and approval in 21 CFR Part 56 are met.  
• He or she will report to the sponsor adverse experiences that occur in the course of 
the investigation in accordance with 21 CFR 312.64. 
• He or she has read and understands the information in the Investigator’s Brochure, 
including potential risks and side effects of the drug. 
• His or her staff and all persons who assist in the conduct of the study are informed 
about their obligations in meeting the above commitments. 
• He or she will ensure that adequate and accurate records in accordance with 
21 CFR 312.62 and to make those records available for inspection in accordance with 
21 CFR 312.68. 
• He or she will ensure that the IRB complies with the requirements of 21 CFR Part 56, 
and other applicable regulations, and conducts initial and ongoing reviews and 
approvals of the study. He or she will also ensure that any change in research activity 
and all problems involving risks to human subjects or others are reported to the IRB. 
Additionally, he or she will not make any changes in the research without IRB 
approval, except where necessary to eliminate apparent immediate hazards to human 
subjects. 
• He or she agrees to comply with all other requirements regarding the obligations of 
clinical Investigators and all other pertinent requirements in 21 CFR Part 312. 
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24 
PROTOCOL AMENDMENT TEXT REVISIONS  
The following is a summary of significant protocol revisions; added text is underlined and deleted text is struck. Additional administrative 
changes have been made for consistency and clarity throughout this amendment and are reflected in the protocol body. Revisions made to the 
Synopsis (Section 2) are reflected in the corresponding protocol section as appropriate. Revisions to cross references to protocol tables, 
figures, sections, and references reside within the protocol body.  
Section 
Revision 
Rationale for 
Change 
Global change 
Up to 102 Approximately 119 weeks 
9 
Global change 
Premedication with H1 antagonist, H2 antagonist, and non steroidal anti inflammatory medication 
(NSAIDs)antipyretics (eg, acetaminophen) approximately 2-3 hours prior to study drug should be 
administered for 1 week upon reintroduction of study drug at Part 3, Week 1 and Part 4, Week 1, 
as well as upon reintroduction of study drug after resolution of an AE, following any dose 
interruption of  ≥ 4 days, and for any dose increases in Part 4. If non-steroidal anti-inflammatory 
medication (NSAIDs) is administered as a premedication, it NSAIDs should be given with food 
and may be omitted if not tolerated. 
6 
Section 7.4.1, Toxicity 
Due to Exposure to 
Polyethylene Glycol 
(PEG) 
Based on phase 3 data, as of 4MAR2016, there have been no reported events of 
glomerulonephritis or renal failure reported with pegvaliase administration. Of the 10 subjects 
identified with UAC ratios  ≥ 3 mg/mmol on 3 or more consecutive measurements, values were 
generally in the microalbuminuria range and none had concurrent sustained hematuria. Seven of 
these 10 subjects had microalbuminuria at baseline prior to pegvaliase exposure, of which 2 
events resolved while on pegvaliase treatment and 4 events did not progress while subjects 
remained on pegvaliase. One of these 7 subjects with baseline microalbuminuria (3.62 mg/mmol 
at baseline) had an increase in their UAC ratio during the study, which was more apparent after 
dose titration to 60 mg of pegvaliase (remaining in microalbuminuria range, with a most recent 
value of 20.36 mg/mmol), however evaluating relationship to pegvaliase treatment is confounded 
1 
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Rationale for 
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by a medical history of obesity, hypertension, and new onset pre-diabetes during the Phase 3 
study that are conditions also associated with development of microalbuminuria. The subject 
continues on pegvaliase treatment with continued safety monitoring. 
Three of the 10 subjects developed new onset microalbuminuria for at least 3 consecutive 
measurements during the Phase 3 study, one of which resolved while continuing on pegvaliase 
treatment and 1 subject continues to have fluctuating low level microalbuminuria with intermittent 
values in the normal range. One subject discontinued from the Phase 3 study after a few 
intermittent elevations into the microalbuminuria range. The subject had a maximum UAC ratio of 
175 mg/g on Day 8 on the study; at the time of study and study drug discontinuation (Day 36), 
UAC ratio was within the normal range at 19 mg/g. The final study visit recorded for this subject 
(Day 67) had a UAC ratio of 17 mg/g.  This subject reported a single concurrent grade 1 event of 
urticaria, which resolved in 2 days, and no other reported events suggestive of immune complex 
disease. None of the subjects described above have developed sustained elevations in serum 
creatinine or concurrent sustained hematuria. 
To monitor for renal toxicity, subjects participating in this study will undergo urinalysis, will be 
assessed for urine albumin/creatinine ratio, and will undergo blood chemistry tests to assess renal 
function. In this study, subjects will be monitored closely with urine examinations and blood 
chemistries to follow kidney function. 
Section 9.1, Overall Study 
Design and Plan 
A subject will continue in PAL-003 until one of the following occurs: 
• The subject has completed the study through the Month 98Week 476 visit.  
9 
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Rationale for 
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Section 9.1, Overall Study 
Design and Plan 
Because the risks of taking BMN 165 during pregnancy and breastfeeding are unknown, subjects 
cannot take BMN 165 if they are trying to conceive, are pregnant, or are breastfeeding. Male 
subjects who are planning to impregnate a female partner and female subjects who are trying to 
become pregnant during the study will be discontinued immediately from study drug. Male 
subjects who have impregnated a female partner may re start study drug after conception but must 
return to the study required contraception use, which must include one barrier method. During 
Part 4 only, subjects who remain in the study after discontinuation of study drug due to pregnancy 
may re introduce BMN 165 dosing after the birth has been reported (or termination of the 
pregnancy) and breastfeeding has completed (if applicable) or after the subject is no longer 
actively trying to conceive. Re starting BMN 165 dosing must be per investigator and sponsor 
agreement based on an assessment of the known risks and potential benefits while taking BMN 
165. Female subjects must return to the study required contraception use, which must include one 
barrier method, immediately after the birth (or termination of the pregnancy). 
Because the risks of taking BMN 165 during pregnancy and breastfeeding are unknown, subjects cannot take BMN 
165 if they are trying to conceive, are pregnant, or are breastfeeding (refer to Section 9.3.2 for Exclusion Criteria). 
Male subjects who are planning to impregnate a female partner and female subjects who are trying to become 
pregnant during the study must be temporarily discontinued from study drug for 4 weeks prior to trying to conceive. 
During that time, subjects must use two acceptable methods of contraception. Subjects who are planning to become 
pregnant (or impregnate a female partner) may modify their diet in consultation with the investigator and/or study 
dietician. Subjects who are confirmed to be pregnant per a serum pregnancy test and are temporarily off study drug 
are not required to perform the scheduled urine pregnancy tests. Subjects who are pregnant or are trying to conceive 
and have temporarily discontinued study drug should not perform the scheduled PK assessments. Male subjects who 
have impregnated a female partner may re-start study drug after conception following the investigator’s consultation 
with and approval by the medical monitor. Male subjects must return to the study-required contraception use (refer to 
Section 9.3.1 for Inclusion Criteria), which must include one barrier method, prior to restarting study drug. Female 
subjects who remain in the study after temporary discontinuation of study drug due to pregnancy may restart BMN 
165 dosing after a confirmed negative urine pregnancy test result, the birth has been reported (or termination of the 
pregnancy), and breastfeeding has completed (if applicable) or after the subject is no longer actively trying to 
conceive. Re-starting BMN 165 dosing requires the investigator’s prior consultation with and approval by the medical 
monitor. Female subjects must return to the study-required contraception use (refer to Section 9.3.1), which must 
include one barrier method, immediately after the birth (or termination of the pregnancy). 
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Section 9.1, Table 9.1.1, 
Schedule of Events 
The Schedule of Event tables have been updated to reflect the changes in this amendment. 
Additionally, the monthly visits have been modified to occur every 8 weeks. 
8, 11 
Section 9.1.1, Response to 
Hypersensitivity Adverse 
Events 
Subjects who experience an injection-site skin reaction that lasts  ≥ 14 days should be referred to a 
dermatologist for consultation and a skin biopsy.  
5 
Section 9.6, Dietary or 
Other Protocol 
Restrictions 
Subjects will be instructed that diet should not be altered during the course of the study. Any 
decision to modify subject diet must be made per the Investigator and must be performed under 
the supervision of the Investigator. Subjects who are planning to become pregnant (or impregnate 
a female partner) may modify their diet in consultation with the investigator and/or study 
dietician. 
2 
Section 9.7.5.1, Pregnancy 
Testing 
Female subjects of childbearing potential will have a urine pregnancy test at the time points 
specified in the Schedules of Events (Table 9.1.1). Subjects who are confirmed to be pregnant per 
a serum pregnancy test and are temporarily off study drug are not required to perform the 
scheduled urine pregnancy tests. 
2 
Section 9.7.5.2, Antibody 
Testing 
BioMarin or CRO will perform all antibody testing, except for IgE antibodies, which will be 
assessed by a Contract Research Organization. 
11 
Section 9.7.6, Clinical 
Laboratory Assessments 
Any abnormal test results determined to be clinically significant by the investigator should be 
repeated (at the discretion of the investigator) until the cause of the abnormality is determined, the 
value returns to the level from Day 1 of Part 2 or to within normal limits, or the investigator 
determines that the abnormal value is no longer clinically significant. In the event of elevated 
urinary protein on a test result, a repeat urinalysis should be performed. This repeat urine sample 
must performed in the morning at the first or second morning void to allow for accurate test 
results and may be performed by a home healthcare nurse. Subjects with a confirmed 
urine/albumin creatinine ratio of  ≥  100 mg/g should be referred to a nephrologist for consultation 
1, 4 
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if results were within normal range at baseline. Subjects who had elevated results at baseline 
followed by a confirmed subsequent increase of 100-200 mg/g from baseline should also be 
referred to a nephrologist for consultation. 
Section 9.7.6.1, Table 
9.7.6.1.1 (Clinical 
Laboratory Tests) 
The table has been revised to add the following footnotes: 
a To be performed by central laboratory. If urine pregnancy test is positive or equivocal, serum 
sample will be taken and assessed by a central laboratory. It is recommended that urine samples 
are obtained as a first or second morning void. In the event of elevated urinary protein on a test 
result, a repeat urinalysis should be performed. This repeat urine sample must performed in the 
morning at the first or second morning void to allow for accurate test results and may be 
performed by a home healthcare nurse. 
c It is recommended that urine samples are obtained as a first or second morning void. Subjects 
with a confirmed urine/albumin creatinine ratio of  ≥  100 mg/g should be referred to a 
nephrologist for consultation if results were within normal range at baseline. Subjects who had 
elevated results at baseline followed by a confirmed subsequent increase of 100-200 mg/g from 
baseline should also be referred to a nephrologist for consultation. 
1, 4 
Section 9.7.7, Exploratory 
Sample Analyses 
Blood and urine samples will be collected to evaluate biochemical, molecular, and cellular aspects 
of PKU and to develop the assays used for these evaluations. For each portion of the blood and 
urine samples reserved for protocol-specified analyses, there may be multiple sample aliquots. 
Once samples have been successfully analyzed during the study, unused sample portions may be 
used during the study or after the subject’s study completion for assay development or other 
purposes.  
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All samples collected in this study may be used for exploratory research. In addition, samples 
collected for other purposes may be used for exploratory research use once the primary use has 
been completed.  
Section 10.1., Adverse 
Events 
Factors suggestive of a causal relationship could include (but are not limited to) the following: 
• 
Plausible temporal relationship 
• 
Absence of alternative explanations 
• 
Rarity of event in a given patient or disease state 
• 
Absence of event prior to study drug exposure 
• 
Consistency with study product pharmacology 
• 
Known relationship to underlying mechanism of study drug action 
• 
Similarity to adverse reactions seen with related drug products 
• 
Abatement of AE with discontinuation of study drug, and/or recurrence of AE with 
reintroduction of study drug 
3 
Section 10.3, Adverse 
Events Occurring 
Secondary to Other 
Events 
In general, AEs occurring secondary to other events (eg, cascade events) should be identified by 
their primary cause. For example, if severe diarrhea is known to have resulted in dehydration, it is 
sufficient to record only diarrhea as an AE or SAE on the eCRF. However, medically important 
events that may be linked and/or separated in time should be recorded as independent events on 
the eCRF. For example, if severe hemorrhage leads to renal failure, both events should be 
recorded separately on the eCRF. 
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Section 10.4, Persistent or 
Recurrent Adverse 
Events 
A persistent AE is one that extends continuously, without resolution, between subject evaluation 
time points. Such an event should be recorded only once on the eCRF unless its severity increases 
or decreases (in which case it should be recorded again on the AE eCRF). 
A recurrent AE is one that occurs and resolves between subject evaluation time points, but then 
subsequently recurs. All recurrences of the AE should be individually recorded as a separate event 
on the AE eCRF. 
3 
Section 10.5, Abnormal 
Laboratory Values 
Laboratory test results will be recorded on the laboratory results pages of the eCRF, or appear on 
electronically produced laboratory reports submitted directly from the central laboratory, if 
applicable. 
Any laboratory result abnormality fulfilling the criteria for a SAE should be reported as such, in 
addition to being recorded as an AE in the eCRF. 
A clinical laboratory abnormality should be documented as AE if it is not otherwise refuted by a 
repeat test to confirm the abnormality and any one or more of the following conditions is met: 
• Accompanied by clinical symptoms 
• Leading to a change in study medication (e.g. dose modification, interruption or 
permanent discontinuation)  
• Requiring a change in concomitant therapy (e.g. addition of, interruption of, 
discontinuation of, or any other change in a concomitant medication, therapy or 
treatment). 
• The abnormality suggests a disease and/or organ toxicity 
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• The abnormality is of a degree that requires active management (eg, change of dose, 
discontinuation of study drug, more frequent follow-up assessments, further diagnostic 
investigation, etc.) 
 
This applies to any protocol and non-protocol specified safety and efficacy laboratory result from 
tests performed after the first dose of study medication that falls outside the laboratory reference 
range and meets the clinical significance criteria. 
This does not apply to any abnormal laboratory result that falls outside the laboratory reference 
range but that does not meet the clinical significance criteria (these will be analyzed and reported 
as laboratory abnormalities), those that are considered AEs of the type explicitly exempted by the 
protocol, or those which are a result of an AE that has already been reported.  
Section 10.6, Pre-existing 
Conditions 
A pre-existing condition is one that is present at the start of the study. Such conditions should be 
recorded as medical history on the appropriate eCRF. 
A pre-existing condition should be recorded as an AE or SAE during the study only if the 
frequency, intensity, or character of the condition worsens during the study period. It is important 
to convey the concept that a pre-existing condition has changed by including applicable language 
in the verbatim description of the event (eg, more frequent headaches). 
3 
Section 10.7, General 
Physical Examination 
Findings 
At screening, any clinically significant abnormality should be recorded as a pre-existing condition 
(refer to Section 10.6). During the study, any new clinically significant findings and/or 
abnormalities discovered on physical examination that meet the definition of an AE (or an SAE) 
must be recorded and document as an AE or SAE on the AE eCRF. 
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Section 10.8, 
Hospitalization, 
Prolonged 
Hospitalization, or 
Surgery 
Any AE that results in hospitalization or prolonged hospitalization should be documented and 
reported as an SAE unless specifically instructed otherwise in this protocol (refer to Section 10.2). 
There are some hospitalization scenarios that do not require reporting as an SAE when there is no 
occurrence of an AE. These scenarios include planned hospitalizations or prolonged 
hospitalizations to the following: 
• Perform a protocol-mandated efficacy measurement 
• Undergo a diagnostic or elective surgical procedure for a pre-existing medical condition 
that has not changed 
• Receive scheduled therapy (study drug or otherwise) for the study indication 
3 
Section 10.9, Deaths 
All deaths that occur during the AE reporting period (refer to Section 10.1 for nonserious AEs and 
Section 10.2 for SAEs), regardless of attribution, will be recorded on the AE eCRF and 
expeditiously reported to the Sponsor as an SAE. 
When recording a death, the event or condition that caused or contributed to the fatal outcome 
should be recorded as the single medical concept on the eCRF. If the cause of death is unknown 
and cannot be ascertained at the time of reporting, record “Unexplained Death” or “Death of 
Unknown Cause” on the eCRF.   
3 
Section 10.10, Pregnancy 
Pregnancy in a subject or partner should be reported to BPV within 24 hours of the site becoming 
aware of the pregnancy by faxing the Pregnancy Form in the study reference materials. The 
reporting period for pregnancies begins with informed consent and continues until 4 weeks 
following the last study drug dose or the End of Treatment visit. In addition, pregnancy in a 
subject should also be reported on the End of Study eCRF and the Subject Disposition eCRF if the 
subject withdraws from the study due to pregnancy…. 
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Abortion, whether therapeutic or spontaneous, should always be classified as an SAE (as the 
Sponsor considers these to be medically significant), recorded on the eCRF, and expeditiously 
reported to the Sponsor as an SAE. 
Section 10.11, Follow-up 
of Subjects after Adverse 
Events 
For some SAEs and AESIs, the sponsor may follow up by telephone, fax, electronic mail, and/or a 
monitoring visit to obtain additional case details (eg, hospital discharge summary, consultant 
report, or autopsy report) deemed necessary to appropriately evaluate the SAE report. 
3 
Section 10.12, Post-Study 
Adverse Events 
At the last scheduled visit, the investigator should instruct each subject to report to the 
investigator and/or to BPV directly any subsequent SAEs that the subject’s personal physician(s) 
believes might be related to prior study treatment. 
The investigator should notify the study sponsor of any death or SAE occurring at any time after a 
subject has discontinued or terminated study participation if the investigator believes that the 
death or SAE may have been related to prior study treatment. The sponsor should also be notified 
if the investigator should become aware of the development of cancer or of a congenital anomaly 
in a subsequently conceived offspring of a subject who participated in this study.  
3 
Section 10.14, BioMarin 
Pharmacovigilance 
Contact Information 
Name:  
 
Address: 
105 Digital Drive 
 
 
Novato, CA 94949 USA 
Phone:  
 
Fax: 
 
  
E-mail: 
 
 
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Section 12.3, Treatment 
Period 
During the Treatment Period, additional visits may occur if deemed necessary to monitor AEs or 
blood Phe concentrations. On days that a dose is given, assessments will be done predose unless 
otherwise specified. Subjects must have AEs and concomitant medications assessed whenever 
dose is administered even if the administration does not coincide with a scheduled clinic visit. If 
there is a skin reaction that lasts ≥ 14 days, the Skin Reaction eCRF should be completed and the 
subject should be referred to a dermatologist for consultation and a skin biopsy. It is 
recommended that aA photograph of the skin reaction may be taken by the subject or the site to 
help assess the event; photographs and may be collected by the sponsor. 
5 
Section 12.3.2, Weekly 
Telephone Visit 
Subjects should have a weekly telephone visit conducted. Subjects must still come into the clinic 
for the scheduled monthly visits every 8 weeks per Table 9.1.1. The following should be 
discussed with the subject during the weekly telephone visit: 
8 
Section 12.3.4, Every 8 
Weeks 
Beginning with Week 4, monthly vVisits must be performed in the clinic every 8 weeks. The 
following study activities will be performed: 
• Physical examination 
• Sedimentation rate 
• Complement C3 and C4 
• PK sample 
• Serum anti-rAvPAL-PEG antibodies (anti-PAL IgG, anti-PAL IgM, anti-PEG IgG, 
anti-PEG IgM, and anti-rAvPAL-PEG neutralizing antibodies) 
• Prefilled syringe refresher training (every 24 weeks only) 
• If additional training is needed on days subsequent to the monthly 8-week scheduled visit, 
additional clinic visit(s) or HHRN may be used. 
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Section 12.3.5, Quarterly 
Visits 
This section has been deleted. 
8 
Section 17, Case Report 
Forms and Source 
Documents 
Before a CRF casebook can be locked, data fields must be source data verified and queries closed. 
The investigator will then electronically sign the casebook, specifying that the information on the 
CRFs is accurate and complete. The Data Manager (or designee) will then set the status of the 
forms, visits, and the entire casebook to Locked. The investigator will then electronically sign the 
casebook, specifying that the information on the CRFs is accurate and complete. Upon completion 
of the clinical study report, an electronic copy of each site’s casebooks will be copied to a 
compact disk and will be sent to each site for retention with other study documents. 
11 
 
 
 
 
 
 
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SAP_001.pdf: 
 
 
 
 
    
 
 
 
 
 
 
Official Title: Long-term Extension of a Phase 2, Open-Label Dose-Finding Study to Evaluate the 
Safety, Efficacy, and Tolerability of Multiple Subcutaneous Doses of rAvPAL-PEG 
in Subjects with PKU 
 
NCT Number: NCT00924703 
 
Applicant/MAH: BioMarin Pharmaceutical Inc. 
 
Version Date: 27 April 2016  
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 


 
Proprietary and Confidential 
 
 
 
105 Digital Drive 
Novato, CA 94949 
 
 
 
 
Statistical Analysis Plan  
 
PAL-003  
 
April 27, 2016 
 
 
 
 
The information in this document is considered privileged and confidential by BioMarin 
Pharmaceutical Inc., and may not be disclosed to others except to the extent necessary to obtain 
Institutional Review Board approval and informed consent, or as required by Federal and State Laws.  
Persons to whom this information is disclosed must be informed that this information is privileged 
and confidential and that it should not be further disclosed. 
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TABLE OF CONTENTS 
1 APPROVALS (SIGNATURE AND DATE) ......................................................................2 
2 INTRODUCTION ...............................................................................................................6 
2.1 Objectives of Study .....................................................................................................6 
2.2 Study Design ...............................................................................................................6 
2.3 Study Population .........................................................................................................7 
2.4 Study Dosage and Administration ..............................................................................7 
2.5 Sample Size Determination .........................................................................................7 
2.6 Blinding and Randomization Methods .......................................................................7 
2.7 Interim Analysis ..........................................................................................................8 
3 GENERAL ANALYSIS CONSIDERATION .....................................................................9 
3.1 Analysis Populations ...................................................................................................9 
3.1.1 
Efficacy .........................................................................................................9 
3.1.2 
Safety .............................................................................................................9 
3.1.3 
PK ..................................................................................................................9 
3.2 Treatment Group Presentation ....................................................................................9 
3.3 Pooling of Data from Sites with Small Enrollment ..................................................10 
3.4 Study Day Derivation................................................................................................10 
3.5 Visit Window for Analysis .......................................................................................10 
3.6 Handling of Dropouts and Missing Data ..................................................................12 
4 SUBJECT DISPOSITION .................................................................................................13 
5 END OF STUDY ...............................................................................................................14 
6 PROTOCOL EXEMPTIONS AND DEVIATIONS .........................................................15 
7 DEMOGRAPHICS AND BASELINE CHARACTERISTICS ........................................16 
8 MEDICAL HISTORY .......................................................................................................17 
9 PRIOR AND CONCOMITANT MEDICATIONS/PROCEDURES ................................18 
10 EXTENT OF EXPOSURE TO STUDY DRUG ...............................................................20 
11 EFFICACY EVALUATIONS ...........................................................................................21 
12 PHARMACOKINETIC EVALUATIONS ........................................................................23 
13 SAFETY EVALUATIONS ...............................................................................................24 
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13.1 Immunogenicity ........................................................................................................26 
13.2 Clinical Laboratory Tests ..........................................................................................26 
13.3 Vital Signs .................................................................................................................27 
13.4 12-lead Electrocardiogram ........................................................................................27 
13.5 Physical Examination ................................................................................................27 
13.6 Chest X-Ray ..............................................................................................................27 
13.7 Pregnancy Test ..........................................................................................................28 
13.8 Injection Site Inspection............................................................................................28 
14 REFERENCES ..................................................................................................................29 
15 SUMMARY OF CHANGES TO STUDY SAP ................................................................30 
16 APPENDICES ...................................................................................................................31 
 
LIST OF TABLES 
Table 1:  Visit Time Windows for the Treatment Period ........................................................11 
Table 2:  Visit Time Windows for the Treatment Period in PAL-003 ....................................12 
 
LIST OF APPENDICES 
Appendix 1: Searching Strategies for Adverse Event of Special Interest, and Sponsor 
Defined AEs of Significance .........................................................................31 
 
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2 
LIST OF ABBREVIATIONS 
Abbreviation 
Definition 
AE 
adverse event 
ALT 
alanine transaminase 
AST 
aspartate aminotransferase 
ATC 
Anatomical Therapeutic Chemical  
BMI 
body mass index 
BUN 
blood urea nitrogen 
CDF 
cumulative distribution function 
CSR 
CTCAE 
Clinical Study Report 
Common Terminology Criteria for Adverse Events 
DMC 
Data Monitoring Committee 
ECG 
electrocardiogram 
HAE 
hypersensitivity adverse event 
Hg 
mercury 
IgE 
immunoglobulin E 
IgG 
immunoglobulin G 
IgM 
immunoglobulin M 
LOCF 
last observation carried forward 
MedDRA 
Medical Dictionary for Regulatory Activities 
Nab 
neutralizing antibody 
NCI 
National Cancer Institute 
NIAID/FAAN 
National Institute of Allergy and Infectious Disease/Food Allergy and 
Anaphylaxis Network 
PAL 
phenylalanine 
PEG 
polyethylene glycol 
Phe 
phenylalanine 
PK 
pharmacokinetics 
PKU 
phenylketonuria 
PT 
preferred term 
rAvPAL-PEG  
recombinant Anabaena variabilis phenylalanine ammonia lyase-PEG 
SAP 
Statistical Analysis Plan 
SOC 
system organ class 
SMQ 
Standardized MedDRA Queries 
TEAE 
treatment-emergent adverse event 
Tab 
total antibody 
ULN 
upper limit of normal 
WHODrug 
World Health Organization Drug Dictionary 
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3 
INTRODUCTION 
This Statistical Analysis Plan (SAP) describes the statistical analysis methods and data 
presentations to be included in the Clinical Study Report (CSR) for PAL-003, Long-term 
Extension of a Phase 2, Open-Label, Dose-Finding Study to Evaluate the Safety, Efficacy, 
and Tolerability of Multiple Subcutaneous Doses of rAvPAL-PEG in Subjects with PKU. 
This SAP includes the data summary methodologies for analysis of safety, efficacy, and 
pharmacokinetics (PK) data. Results obtained from the analyses described in this document 
will provide the basis of the CSR for this study. Analysis methods specified in this document 
take precedence over those described in the protocol should there be any differences.   
3.1 
Objectives of Study 
The primary objective of the study is: 
• To evaluate the effect of long-term administration of multiple doses of subcutaneous 
(SC) injections of pegvaliase (also described as rAvPAL-PEG or pegvaliase) on 
blood Phe concentrations in subjects with phenylketonuria (PKU).  
The secondary objectives of the study are: 
• To evaluate the safety and tolerability of long-term administration of SC injections of 
pegvaliase in subjects with PKU.  
•  To evaluate the immune response to long-term administration of SC injections of 
pegvaliase in subjects with PKU.  
The exploratory objectives of the study are: 
• To evaluate the long-term relationship of diet and change in blood Phe concentration 
following administration with pegvaliase in subjects with PKU.  
The Substudy objectives are as follows:  
• To evaluate steady-state PK of pegvaliase in subjects who have achieved and 
maintained target blood Phe concentration and for whom no further dose 
modifications are planned.  
3.2 
Study Design 
This is a long-term extension of pegvaliase Phase 2 studies in subjects with PKU. The doses 
are planned to be in the same range as those tested in phase 2 (starting at 0.001 through 5.0 
mg/kg/week or 2.5 mg through 375 mg/week), provided no dose-limiting toxicity is observed 
in a previous pegvaliase study.  
Only subjects who completed a previous pegvaliase study will be enrolled into this study. 
Subjects enrolling into PAL-003 with no interruption in dosing from a previous pegvaliase 
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study may either continue their previous dosing regimen or begin this study at a higher dose 
level. Subjects who have had dosing interruptions between the previous pegvaliase study and 
PAL-003 must have their starting dose determined per the Sponsor’s Medical Officer. 
A PK substudy has been added to evaluate the steady-state PK of pegvaliase in up to 
6 subjects who have achieved and maintained target blood Phe for at least 2 consecutive 
measurements and for whom no further dose modifications are planned. Subjects enrolled 
into the substudy will have additional pre-dose PK sampling performed.  
3.3 
Study Population 
Only subjects who completed a previous pegvaliase study will be enrolled into this study. 
3.4 
Study Dosage and Administration 
Pegvaliase will be provided in vials or prefilled syringes; subjects will be supplied with vials 
and syringes or prefilled syringes for administration in the clinic and self administration: 
• Pegvaliase will be provided in 3 mL (milliliter) vials, each containing 1.5 ± 0.2 mL to 
deliver 15 mg of rAvPAL-PE per 1.0 mL (15 mg/mL protein concentration). Each 
vial is filled with 1.5 ± 0.2 mL to allow the withdrawal and delivery of up to 1.0 mL 
of the drug product. 
• Or 
• Pegvaliase will be provided in 3-mL vials, each containing 1.8 ±0.3 mL to deliver 
20 mg of rAvPAL-PE per 1.3 mL (15 mg/mL protein concentration). Each vial is 
filled with 1.8 ± 0.3 mL to allow withdrawal and delivery of up to 1.3 mL. 
• Or 
• Pegvaliase will be provided in prefilled syringes in three sizes that deliver up to 1 mL. 
Syringe sizes are 2.5 mg (5 mg/mL protein concentration), 10 mg (20 mg/mL protein 
concentration), and 20 mg (20 mg/mL protein concentration).  
Pegvaliase may be administered SC from 0.001 to a maximum weekly dose of 5.0 mg/kg or 
375 mg/week. 
3.5 
Sample Size Determination 
Subject who participated in a previous pegvaliase study may be enrolled into this study. No 
formal sample size calculation was conducted.  
3.6 
Blinding and Randomization Methods 
This is an open-label study. 
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3.7 
Interim Analysis  
There is no formal interim analysis planned. 
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4 
GENERAL ANALYSIS CONSIDERATION 
Descriptive summaries of continuous variables will include the number of subjects (n), mean, 
standard deviation, median, minimum, and maximum. Descriptive summaries of categorical 
variables will include n and percent.  Data from parent studies (PAL-002, PAL-004, 
165-205) will be integrated together with data in PAL-003 for long term safety and efficacy 
analysis. The baseline value of an assessment is defined as the last available measurement 
prior to first administration of study drug from parent studies (PAL-002, PAL-004, 165-205), 
unless otherwise specified. 
4.1 
Analysis Populations 
4.1.1 Efficacy 
The efficacy population will consist of all subjects who receive at least one dose of study 
drug and have post-treatment blood Phe concentration measurements in any of the phase 2 
studies (PAL-002, PAL-004, 165-205, PAL-003). 
4.1.2 Safety  
The safety population will consist of all subjects who receive at least one dose of study drug 
throughout the study duration of any of the phase 2 studies (PAL-002, PAL-004, 165-205, 
PAL-003). 
4.1.3 PK 
The PK population will consist of all subjects who receive any amount of study drug and 
have post-treatment plasma pegvaliase concentration measurements in any of the phase 2 
studies (PAL-002, PAL-004, 165-205, PAL-003). 
4.2 
Treatment Group Presentation 
Unless specified otherwise, analyses will be presented by parent Phase 2 studies (PAL-002, 
PAL-004, 165-205) combined, PAL-003, and all Phase 2 studies (PAL-002, PAL-004, 
165-205, PAL-003) combined. 
The following treatment groups may also be considered in the summary tables for 
corresponding assessments: 
For 
, analyses will be presented by current 
 
 
 at each assessment visit in both parent studies (PAL-002, PAL-004, 
165-205) and PAL-003. The weekly dose is defined as the 
 
prior to each assessment. 
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), analyses will be presented by daily 
 
 on or prior to AE onset date in both 
parent studies (PAL-002, PAL-004, 165-205) and PAL-003.  
4.3 
Pooling of Data from Sites with Small Enrollment 
Due to small sample sizes at each site, separate analyses by site or pooled site will not be 
performed. 
4.4 
Study Day Derivation 
Unless otherwise specified, the first study drug administration date for pegvaliase from 
parent studies (PAL-002, PAL-004, 165-205) is considered study day 1 and is used as the 
reference date for the derivation of study day in data displays. Study day is computed by 
subtracting study day 1 from a visit date plus 1 if the visit date occurs on or after the initial 
study drug start date.  Otherwise, the study day will be the visit date minus the study day 1. 
There is no Study Day 0. 
4.5 
Visit Window for Analysis 
An assessment for a subject will be classified according to the study day of the assessment 
where it falls within a visit window.  The windows are designated for each scheduled visit 
with a target day. If there are two or more assessments within a designated window, the 
assessment that is closest to the target day will be used for analyses.  If the two closest 
assessments to the target day are equidistant from the target day, then the average of the two 
assessments will be used for analyses. If the measurement is a laboratory categorical 
variable, however, then the worse of the 2 equidistant measurements will be used.  
Table 1 lists the visits assigned for the analyses of all assessments and the corresponding 
range of treatment days (window) during which a visit may have occurred by analysis 
parameter.  
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Table 1:  Visit Time Windows for the Treatment Period  
Scheduled Time Point 
Target Day 
Visit Window 
Baseline  
 
Last measurement prior to pegvaliase 
administration from parent studies (PAL-002, 
PAL-004, 165-205) 
Week 4 
Day 22 
Day 8 to Day 35 
Week 8 
Day 50 
Day 36 to Day 63 
Week 12 
Day 78 
Day 64 to Day 91 
Week 16 
Day 106 
Day 92 to Day 119 
Week 20 
Day 134 
Day 120 to Day 147 
Week 24 
Day 162 
Day 148 to Day 175 
… 
… 
… 
Week 388 
Day 2710 
Day 2696 to Day 2723 
Week 392 
Day 2738 
Day 2724 to Day 2751 
Week 396 
Day 2766 
Day 2752 to Day 2779 
Week 400 
Day 2794 
Day 2780 to Day 2807 
Week 404 
Day 2822 
Day 2808 to Day 2835 
Week 408 
Day 2850 
Day 2836 to Day 2863 
Week 412 
Day 2878 
Day 2864 to Day 2891 
Week 416 
Day 2906 
Day 2892 to Day 2919 
Every 4 weeks 
 
Blood Phe concentration will also be summarized based on the data collected in PAL-003 
and visits in Table 2. For this analysis, the first study drug administration date for pegvaliase 
from PAL-003 is considered as study day 1 and is used as the reference date for the 
derivation of study day in data displays.   
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Table 2:  Visit Time Windows for the Treatment Period in PAL-003 
Scheduled Time Point in 
PAL-003 
Target Day in 
PAL-003 
Visit Window in PAL-003 
PAL-003 Baseline  
 
Last measurement prior to pegvaliase 
administration from PAL-003 
Week 4 
Day 22 
Day 8 to Day 35 
Week 8 
Day 50 
Day 36 to Day 63 
Week 12 
Day 78 
Day 64 to Day 91 
Week 16 
Day 106 
Day 92 to Day 119 
Week 20 
Day 134 
Day 120 to Day 147 
Week 24 
Day 162 
Day 148 to Day 175 
Every 4 weeks 
 
4.6 
Handling of Dropouts and Missing Data 
Subjects who discontinued prematurely will not be replaced. To investigate the primary 
objective, last observation carry forward (LOCF) imputation approach will be used as 
sensitivity analyses.   
 
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5 
SUBJECT DISPOSITION 
The number of subjects enrolled, the number of subjects who received study drug, the 
number of subjects who completed study, and the number of subjects in each analysis 
population (efficacy, safety, PK) will be summarized. 
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6 
END OF STUDY 
For subjects who prematurely discontinued the study, the primary reason for discontinuation 
will be summarized. A subject listing of completion and early termination will be provided.  
 
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7 
PROTOCOL EXEMPTIONS AND DEVIATIONS 
A major protocol deviation is defined as a departure from the approved study protocol that 
may impact the rights, safety, or welfare of the subjects or the integrity of the data, which 
will be summarized by deviation category.  
A minor or administrative protocol deviation is defined as a departure from the approved 
study protocol that has minimum or no impact on the rights, safety, or welfare of the subjects 
or the integrity of the data. Minor protocol deviations will also be summarized by deviation 
category. For details regarding the classification of the deviations, please refer to the Study 
Specific Guideline for Managing Protocol Deviations. 
Major and minor protocol deviations occurring during the parent studies (PAL-002, 
PAL-004, 165-205) and PAL-003 study will be summarized.   
Subjects with protocol deviations during the parent studies (PAL-002, PAL-004, 165-205) 
and PAL-003 study will be provided in a listing. Subjects with inclusion or exclusion 
deviations during the parent studies (PAL-002, PAL-004, 165-205) and PAL-003 study will 
also be provided in a separate listing. 
  
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8 
DEMOGRAPHICS AND BASELINE CHARACTERISTICS 
Subject characteristics and demographic information before the first dose of parent studies 
(PAL-002, PAL-004, 165-205) and the first dose of PAL-003 will be summarized. The 
demographics including age, age group (16 to <18 years of age, 18 to <66 years of age, 
≥66 years of age), gender, race and ethnicity will be summarized using descriptive statistics. 
Subject characteristics will include height, weight, blood Phe concentration, intake of protein 
and dietary Phe, body mass index (BMI), BMI group (<25 kg/m2, ≥25 kg/m2 and <30 kg/m2, 
≥30 kg/m2), and immunogenicity status (positive, negative, or titer value). 
 
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9 
MEDICAL HISTORY 
Subject’s past medical history and surgeries prior to parent studies (PAL-002, PAL-004, 
165-205) and prior to PAL-003 were collected as general medical history. General medical 
history will be summarized by system organ class (SOC). A subject listing of each subject’s 
medical history collected at the Screening Visit will also be provided. 
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10 
PRIOR AND CONCOMITANT MEDICATIONS/PROCEDURES 
Prior and concomitant medications taken prior to, on or after the first dose of pegvaliase will 
be summarized for all enrolled subjects.  For analysis purposes, the following definitions will 
be used to determine prior and concomitant medications: 
• Prior medications: any medications taken within 30 days prior to the screening and 
prior to the initial pegvaliase administration date 
• Concomitant medications: any medications initially taken on or after the initial 
pegvaliase administration date 
• Prior and concomitant medications: any medications taken both prior to the initial 
pegvaliase administration date and on or after the initial pegvaliase administration 
date will be reported both as prior and concomitant medications. Therefore, any 
medications taken prior to the pegvaliase first dose date where the stop date is 
reported as “continuing” will be considered both as prior and concomitant 
medications. 
In the event the start date of a medication is completed missing, the start date will be imputed 
as the first dose date if the stop date is in the same year or later than the first dose date.  
In the event the start date of a medication is partial, the following imputation rules will be 
applied: 
• If only day is missing, then the start date will be imputed as the first day of the month, 
if the year and month is after the first dose year and month. If only day is missing, 
then the start date will be imputed as the last day of the month, if the year and month 
is prior to the first dose year and month. If month is the same as the month of first 
dose of pegvaliase then the start date will be imputed as the first dose date of 
pegvaliase.  
• If only year is non-missing, then the start date will be imputed as the first day of the 
year if the year is after the year of first dose. If year is the same as the year of first 
dose of pegvaliase then the start date will be imputed as the first dose date of 
pegvaliase. If year is before the year of first dose of study drug then the start date will 
be imputed to the first day of July of the year.  
In the event the stop date of a medication is partial, the following imputation rules will be 
applied: 
• If only day is missing, then the end date will be imputed as the last day of the month.  
• If only year is non-missing, then the end date will be imputed as the last day of the 
year.  
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All medications will be coded using the current version of the World Health Organization 
Drug (WHO Drug) dictionary (Sept. 2014). Prior and concomitant medication use will be 
summarized by Anatomical Therapeutic Chemical (ATC) medication class (Level 4) and 
preferred name (i.e., generic medication name) using descriptive statistics separately. A 
subject reporting the same medication more than once will be counted once when calculating 
the number and percentage of subjects who received that medication. A subject listing of 
prior and concomitant medications all subjects received will be provided. 
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11 
EXTENT OF EXPOSURE TO STUDY DRUG 
Exposure will be summarized using descriptive statistics such as n, mean, standard deviation, 
median, minimum, and maximum for the following variables: 
• Average of daily doses (mg/day) received 
• Average of dosing frequency (day) per week 
• Total amount of study drug (mg) received  
• Total duration of treatment in number of months, calculated by last dosing day minus 
first dosing day add 1 then divided by 30. 
• Number of patients who had duration in different categories: less than 12 months, 
between 12 months and 24 months, between 24 months and 36 months, between 36 
months and 48 months, longer than 48 months. 
• Number of patients which had average daily dose in different categories: <20 mg/day, 
≥20 mg/day to <40 mg/day, ≥40 mg/day to <60 mg/day, ≥60 mg/day. 
When calculating the total exposure duration on study drug, any dose interruption longer than 
28 days will be excluded from the calculation. 
 
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12 
EFFICACY EVALUATIONS 
Efficacy measurement (blood Phe concentration) from start of parent studies (PAL-002, 
PAL-004, 165-205) to 14 days after last dose of pegvaliase will be summarized using 
descriptive statistics for the CSR for PAL-003. Baseline blood Phe concentration is defined 
as the last available measurement prior to first administration of study drug from parent 
studies (PAL-002, PAL-004, 165-205). All efficacy data collected 14 days after the last dose 
in the study will not be included in the analysis. 
As the measure of efficacy, observed blood Phe concentration at scheduled time point, 
change from baseline and percentage change from baseline in blood Phe concentration at 
scheduled time point, daily dose at which subject first had blood Phe values ≤600 µmol/L, 
daily dose at which subject first had blood Phe values ≤360 µmol/L, daily dose at which 
subject first had at least 20% blood Phe reduction from baseline using the average of 
2 consecutive blood Phe assessments, time to when subject first had blood Phe values 
≤600 µmol/L, time to when subject first had blood Phe values ≤360 µmol/L, and time to 
when subject first had two consecutive Phe values with at least 20% blood Phe reduction will 
be summarized using descriptive statistics for the efficacy population. Percent of subjects 
with blood Phe concentration ≤ 360 µmol/L and percent of subjects with blood Phe 
concentration ≤ 600 µmol/L over time will also be summarized and plotted. 
To investigate the primary objective, last observation carry forward (LOCF) imputation 
approach will be used as sensitivity analyses.   
The distribution of responses in blood Phe concentration will be evaluated using the 
cumulative distribution function (CDF) (McLeod 2011). The percentage of subjects 
responding at the beginning of PAL-003, the end of first year of PAL-003 and the end of 
PAL-003 will be plotted against the continuous range of responses. Thus, the CDF will show 
a continuous plot of the proportion of subjects at each time point along the continuum of Phe 
levels, an approach that offers a visual comparison of the separation among the three 
timepoints across all levels of change so that a variety of responder definitions can be 
considered simultaneously. In a rare disease setting, such as with PKU, this approach is 
proposed over applying a categorical responder definition due to the limitations in sample 
size.  
A subject listing of blood Phe concentration will be provided. A summary table will be 
provided on the percent of subjects in each quartile of blood Phe concentration at each 
scheduled time point. Plots for mean blood Phe concentration, change from baseline and 
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percentage change from baseline in blood Phe concentration will also be generated for both 
observed values and values after LOCF imputation.  
For the diet diary, standard descriptive statistics will be presented for the observed, change 
from baseline and percent change from baseline values of the three-day average of dietary 
protein, tyrosine and dietary phenylalanine at each visit. The three-day average diet diary 
results will also be listed. To explore the change in blood Phe concentration with respect to 
changes in subject diet, plots will be generated for mean blood Phe concentration with mean 
dietary protein and mean dietary Phe, mean change from baseline blood Phe concentration 
with mean change from baseline of dietary protein and dietary Phe.  
 
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13 
PHARMACOKINETIC EVALUATIONS 
A subject listing of plasma pegvaliase concentration and a listing of PK parameters will be 
provided. Scatter plots of dose-normalized trough plasma pegvaliase concentration at the last 
visit of PAL-003 vs. antibody measurements will also be provided. The PK analysis plan will 
be detailed in a separate document. 
 
 
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14 
SAFETY EVALUATIONS 
Safety will be assessed by examining the incidence, exposure adjusted event rate, severity 
grade, and relationship to study drug of all treatment-emergent adverse events (TEAEs) 
reported during the study period.  In addition, changes in clinical laboratory results and vital 
signs from baseline values from parent studies (PAL-002, PAL-004, 165-205) will be 
assessed. All safety data collected 30 days after the last dose will not be included in the 
analysis. 
AEs will be coded in accordance with the MedDRA version 18.0.  Only treatment-emergent 
adverse events (TEAEs) occurring and reported during the study period will be included in 
the adverse event summaries.  A TEAE is defined as any AE that newly appeared or 
worsened in severity following initiation of the study drug administration till 30 days after 
last dose of the phase 2 studies (PAL-002, PAL-004, 165-205, PAL-003).  If the onset date of 
an AE is missing, the AE will be considered treatment-emergent. 
If the onset date or end date of an adverse event is partial, the same imputation rules 
described in section 10 will be applied: 
The incidence and frequency of all treatment-emergent AEs will be summarized by SOC, 
preferred term (PT), and severity grade.  For those AEs that occurred more than once during 
the study, the maximum severity will be used to summarize the AEs by severity. The SOCs 
and PTs will be displayed by descending order based on total population. 
The treatment-emergent AEs will be summarized in the following categories: 
• All AEs by SOC and preferred term 
• All AEs by SOC, preferred term, and severity 
• AEs assessed by the investigator as related to study drug by SOC and preferred term 
• AEs assessed by the investigator as related by SOC, preferred term and severity 
• Serious AEs (SAEs) by SOC and preferred term    
• SAEs assessed by the investigator as possibly or probably related to study drug by 
SOC and preferred term 
• All AEs by preferred term in descending frequency order  
• Hypersensitivity AE by SOC and PT 
• Hypersensitivity AE by SOC, PT and severity 
• Neuropsychiatric AE by SOC, PT and severity 
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      AE assessed by investigators as related to PFS/Device malfunction  
• AEs leading to dose interruption or reduction by SOC and preferred term 
• AEs leading to withdrawal from study by SOC and preferred term 
• AEs leading to study drug discontinuation by SOC and preferred term 
• Pregnancy 
• Death 
In addition to the standard summary tables and listings, the following information will also 
be summarized for AEs of special interest, and sponsor defined AEs of significance: 
• Time to event onset from most recent dose for Anaphylaxis per NIAID/FAAN criteria 
and Anaphylaxis per NIAID/FAAN criteria meeting Brown’s severe criteria 
• Time to first event onset per subject from first dose  
• Duration of the events 
• Patient characteristics for subjects with special types of  hypersensitivity AEs except 
for injection site reaction and arthralgia 
• Actions related to study drug 
• Common treatment 
• Incidence rate over time 
The AEs of special interest include: 
• Anaphylaxis per NIAID/FAAN criteria 
• Anaphylaxis per NIAID/FAAN criteria meeting Brown’s severe criteria 
The sponsor defined AEs of significance include:  
• Hypersensitivity AEs  
• Injection site reaction 
• Generalized skin reaction with ≥ 14 day duration 
• Injection site skin reaction with ≥ 14 day duration 
• Arthralgia 
The search strategy for AEs of special interest and sponsor defined AEs of significance is in 
Appendix 1. 
In addition to standard AE listings, by subject listings of injection site reaction AEs, AEs of 
special interest, sponsor defined AEs of significance, and psychiatric AEs under each 
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identification strategies will be provided. Study drug dose level at onset date of each of the 
AE will be presented on the listings. AEs will be sorted by onset date, preferred term, and 
dose of study drug at event onset date. Number of Hypersensitivity AE will be plotted over 
time (1-6 month, 6-12 month, and once each year after). 
Death information will also be displayed in a listing. 
14.1 
Immunogenicity 
Immunogenicity testing will be performed using validated immunogenicity assays. Blood 
samples for routine immunogenicity testing will be collected prior to dosing as indicated in 
the protocol. Routine immunogenicity testing will include assays for anti-rAvPAL 
immunoglobulin G (IgG), anti-rAvPAL IgM, anti-PEG IgM, anti-PEG IgG, and neutralizing 
antibodies (NAb). In the event of a Hypersensitivity Reaction visit, sampling and testing will 
be performed for anti-rAvPAL-PEG IgE and anti-rAvPAL IgE as well as other potentially-
related clinical laboratory tests, including CRP, C3/C4, and tryptase.  
For immunogenicity analysis, an incidence table will be provided for PAL IgG, PAL IgM, 
PEG IgG, PEG IgM, and NAb. Titer summary statistics will also be provided for PAL IgG 
and PEG IgG, including mean, median, standard deviation, and minimum/maximum titer 
values at each study visit. The mean titers for PAL IgG and PEG IgG and percent positivity 
for PAL IgM, PEG IgM and NAb will be plotted over time. A listing of anti-rAvPAL-PEG 
IgE and anti-rAvPAL IgE test results will be provided by subject. 
Anti-drug antibody impact on long-term safety will be evaluated. Plots and tables will be 
generated to explore the potential impact of anti-drug antibodies on hypersensitivity adverse 
event (HAE) frequency and severity. A listing will be provided of all hypersensitivity 
reaction visits with the most proximal antibody test result listed for each analyte, and when 
available, CRP, complement C3 and C4, and tryptase at the time of the event. 
Anti-drug antibody impact on long-term efficacy will be evaluated. Plots and tables will be 
generated to explore the potential impact of anti-drug antibodies on blood Phe levels 
14.2 
Clinical Laboratory Tests 
Standard descriptive statistics will be presented for clinical laboratory tests, including 
hematology, chemistry and urinalysis, at each scheduled visit and for change in laboratory 
values from baseline from parent studies (PAL-002, PAL-004, 165-205) to each scheduled 
visit. The proportion of subjects who experienced at least one laboratory test result with CTC 
grade as 3 or above and who experienced at least one laboratory test results outside the 
normal ranges will be presented for each measurement. Shift tables will be created for 
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selected laboratory parameters in clinical chemistry, hematology, and urinalysis (white blood 
cells [WBCs], neutrophils, eosinophils, basophils, erythrocyte sedimentation rate [ESR], 
serum creatinine, serum blood urea nitrogen [BUN], C3, C4, C-reactive protein [CRP], urine 
microalbumin, urine albumin/creatinine ratio, aspartate transaminase [AST], alanine 
transaminase [ALT], and total bilirubin, creatinine phosphokinase [CPK], hemoglobin 
decrease) to summarize the change in laboratory value from baseline to worst post-baseline 
value based on normal range (low, normal, and high) or National Cancer Institute (NCI) 
Common Terminology Criteria for Adverse Events (CTCAE) grading, where available. 
Results of complement 3, complement 4, C-reactive protein, micro albumin, urine 
albumin/creatinine ratio, aspartate aminotransferase (AST), alanine aminotransferase (ALT), 
bilirubin, serum creatinine, creatinine, and blood urea nitrogen (BUN) will be plotted 
overtime. A subject listing of laboratory test results for hematology, chemistry, urinalysis, 
and other laboratory tests will be provided separately. Values with CTC grade as 3 or above 
will be flagged in the listings. A listing of laboratory test results for subjects with ALT or 
AST ≥ 3x the upper limit of normal (ULN) and total bilirubin ≥ 2xULN will also be 
provided. 
14.3 
Vital Signs 
Vital signs will include seated systolic blood pressure and diastolic blood pressure measured 
in millimeters of mercury (mm Hg), heart rate in beats per minute, respiration rate in breaths 
per minute, and temperature in degrees Celsius (°C).  
Standard descriptive statistics will be presented for the observed and change from baseline 
values from parents studies (PAL-002, PAL-004, 165-205) at each visit. A subject listing will 
also be provided.  
14.4 
12-lead Electrocardiogram 
The frequency of abnormalities and clinically significant abnormalities in 12-lead 
electrocardiogram will be summarized at each visit. A subject listing of ECG findings will be 
provided. 
14.5 
Physical Examination 
A subject listing for clinically significant findings at each visit will be provided.  
14.6 
Chest X-Ray 
A subject listing for chest X-ray at each visit will be provided.  
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14.7 
Pregnancy Test 
A subject listing for pregnancy test at each visit will be provided.  
14.8 
Injection Site Inspection 
A subject listing for injection site inspection at each visit will be provided.  
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15 
REFERENCES 
McLeod LD, Coon CD, Martin SA, Fehnel SE, Hays RD. Interpreting patient-reported 
outcome results: US FDA guidance and emerging methods. Expert Rev Pharmacoecon 
Outcomes Res. 2011;11:163-9.  
 
 
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17 
APPENDICES 
Appendix 1: Searching Strategies for Adverse Event of Special Interest, and Sponsor 
Defined AEs of Significance 
MedDRA version 18.0 
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