Conditions: Ornithine Transcarbamylase (OTC) Deficiency
Keywords: Gene Transfer OTC Deficiency Urea Cycle Disorder
Allocation: NON_RANDOMIZED | Intervention model: PARALLEL
Enrollment: 16
Healthy volunteers: no

Brief summary:
This is a Phase 1/2, open-label, single arm, multicenter, safety and dose finding study of DTX301 in adults with late-onset OTC deficiency. The primary objective of the study is to determine the safety of single intravenous (IV) doses of DTX301.

Detailed description:
Eligible participants will receive a single IV infusion of DTX301. Dose escalation will be conducted according to a model that uses the collected data to predict the safety profile of the dose in order to determine the optimal biological dose (OBD). The decision to proceed to the next dose cohort will be made after the data monitoring committee (DMC) has evaluated the safety data for all participants in a dosing cohort. Participants will be followed for 52 weeks after dosing. After completion of this study, participants will be asked to enroll in a 4-year extension study to evaluate the long term (a total of 5 years) safety and efficacy of DTX301.

This study was previously posted by Dimension Therapeutics, which has been acquired by Ultragenyx.

Arms:
arm 1: DTX301 (scAAV8OTC) 2.0 × 10\^12 GC/kg will be administered as a single peripheral IV infusion. A reactive corticosteroid taper regimen will be administered to control transient vector-induced hepatic effects. Sodium acetate will be used as a tracer to measure the rate of ureagenesis. arm 2: DTX301 (scAAV8OTC) 6.0 × 10\^12 GC/kg will be administered as a single peripheral IV infusion. A reactive corticosteroid taper regimen will be administered to control transient vector-induced hepatic effects. Sodium acetate will be used as a tracer to measure the rate of ureagenesis. arm 3: DTX301 (scAAV8OTC) 1.0 × 10\^13 GC/kg will be administered as a single peripheral IV infusion. A reactive corticosteroid taper regimen will be administered to control transient vector-induced hepatic effects. Sodium acetate will be used as a tracer to measure the rate of ureagenesis. arm 4: A prophylactic corticosteroid taper regimen (oral prednisone \[or prednisolone\], 60 mg tapered over 9 weeks) will be administered before dosing with DTX301 (scAAV8OTC) to prevent or minimize transient vector-induced hepatic effects. DTX301 (scAAV8OTC) 1.0x10\^13 GC/kg administered as a single peripheral IV infusion. Sodium acetate will be used as a tracer to measure the rate of ureagenesis.

Interventions: intervention 1: scAAV8OTC intervention 2: Reactive Corticosteroid Taper Regimen intervention 3: Prophylactic Corticosteroid Taper Regimen
Intervention descriptions: intervention 1: non-replicating, recombinant scAAV8 encoding human ornithine transcarbamylase (OTC) intervention 2: Oral prednisone \[or oral prednisolone\] 60 mg/day week 1, 40 mg/day Week 2, 30 mg/day Weeks 3 and 4, tapered by 5 mg/week Week 5 and beyond until liver enzymes return to baseline levels.

Corticosteroid treatment will be considered when a participant's alanine aminotransferase (ALT) level exceeded the upper limit of normal (ULN) and the ALT increase was considered by the Investigator to be related to DTX301. intervention 3: Oral prednisone \[or oral prednisolone\] 60 mg/day at least 5 days prior to DTX301 administration, tapered over 9 weeks.

A prophylactic corticosteroid taper regimen will be administered to prevent or minimize transient vector-induced hepatic effects.

Protocol document:
Prot_000.pdf: 
Confidential and Proprietary – Property of Ultragenyx Pharmaceutical Inc. 
CLINICAL STUDY PROTOCOL 
IND NUMBER: 17190 
EUDRACT NUMBER: 2016-001057-40 
 
A Phase 1/2, Open-Label Safety and Dose-Finding Study of Adeno-Associated Virus (AAV) 
Serotype 8 (AAV8)-Mediated Gene Transfer of Human Ornithine Transcarbamylase (OTC) in 
Adults with Late-Onset OTC Deficiency 
 
 
 
Protocol Number: 301OTC01 
 
Sponsor: 
Ultragenyx Pharmaceutical Inc. 
840 Memorial Drive 
Cambridge, MA 02139 
Sponsor Contact: 
Ana Cristina Puga, MD, PhD 
Vice President, Clinical Development 
Ultragenyx Pharmaceutical  
Telephone:
 
Medical Monitor: 
 
Medical Director, Pharmacovigilance 
PPD 
929 North Front Street 
Wilmington, NC 28401 
Telephone: 
 
Version of Protocol:  
06 
Date of Protocol:  
Amendment 5: 25 February 2020 
Amendment 4: 11 June 2019 
Amendment 3: 07 February 2017 
Amendment 2: 20 December 2016 
Amendment 1: 18 August 2016 
Original: 29 March 2016 
 
CONFIDENTIAL 
All financial and nonfinancial support for this study will be provided by Ultragenyx Pharmaceutical 
Inc. The concepts and information contained in this document or generated during the study are 
considered proprietary and may not be disclosed in whole or in part without the expressed, written 
consent of Ultragenyx Pharmaceutical. 
The study will be conducted according to the International Council for Harmonisation harmonised 
tripartite guideline E6(R2): Good Clinical Practice. 
 


Ultragenyx Pharmaceutical Inc. 
Protocol: 30 I OTCO I 
DTX301 
Protocol Approval 
Study Title 
A Phase 1/2, Open-Label Safety and Dose-Finding Study of Adeno-Associated 
Virus (AA V) Serotype 8 (AA V8)-Mediated Gene Transfer of Human 
Omithine Transcarbamylase (OTC) in Adults with Late-Onset OTC 
Deficiency 
Protocol Number 
3010TC01 
Protocol Version 
06 
Protocol Date 
Amendment 5: 25 February 2020 
Amendment 4: 11 June 2019 
Amendment 3: 07 February 2017 
Amendment 2: 20 December 2016 
Amendment 1: 18 August 2016 
Original: 
29 March 2016 
Protocol accepted and approved by: 
Sponsor Signatory 
Ana Cristina Puga, MD, PhD 
Date 
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Table of Contents 
Table of Contents ....................................................................................................................... 3 
List of Tables .............................................................................................................................. 8 
List of Figures ............................................................................................................................ 8 
Protocol Synopsis..................................................................................................................... 10 
List of Abbreviations................................................................................................................ 25 
1 
Introduction ...................................................................................................................... 27 
1.1 
Adeno-Associated Viral Vectors ............................................................................. 29 
1.2 
Selection of the AAV Clinical Candidate ................................................................ 30 
1.3 
Study Rationale ....................................................................................................... 31 
1.3.1 
Design Rationale ...................................................................................... 31 
1.3.2 
Dosing Rationale ..................................................................................... 34 
2 
Study Objectives and Endpoints ....................................................................................... 37 
3 
Investigational Plan .......................................................................................................... 39 
3.1 
Study Overview ...................................................................................................... 39 
3.2 
Overall Study Duration and Follow-Up .................................................................. 40 
3.2.1 
Screening Period ...................................................................................... 42 
3.2.2 
Baseline Period ........................................................................................ 43 
3.2.2.1 
Baseline Visit – Day 0 ............................................................................. 43 
3.2.2.2 
Baseline – Day 1 ...................................................................................... 43 
3.2.3 
Treatment Period ...................................................................................... 44 
3.2.3.1 
Home or Clinic Visits .............................................................................. 44 
3.2.3.2 
Outpatient Clinic or Home Health Service Visits .................................... 45 
3.2.3.3 
Inpatient Visits ......................................................................................... 45 
3.2.4 
Tapering of Ammonia Scavenger Therapy .............................................. 45 
3.2.5 
Modification of Dietary Restrictions ....................................................... 47 
3.2.6 
Occurrence of Hyperammonemia and Hyperammonemic Crisis (HAC) 48 
3.2.7 
Safety Stopping Criteria ........................................................................... 48 
3.2.8 
End of Study ............................................................................................ 49 
4 
Subject Selection .............................................................................................................. 49 


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4.1 
Inclusion Criteria .................................................................................................... 49 
4.2 
Exclusion Criteria ................................................................................................... 51 
5 
Screening and Randomization Procedures ....................................................................... 53 
5.1 
Subject Screening.................................................................................................... 53 
5.2 
Subject Randomization ........................................................................................... 53 
6 
Study Treatment ............................................................................................................... 54 
6.1 
Identity of DTX301 ................................................................................................ 54 
6.1.1 
Description of DTX301 ........................................................................... 54 
6.1.2 
Components Used for Manufacturing DTX301 ...................................... 54 
6.2 
Management of Clinical Supplies ........................................................................... 54 
6.2.1 
Packaging and Labeling ........................................................................... 54 
6.2.2 
Storage of Study Product ......................................................................... 55 
6.2.2.1 
Storage of DTX301 .................................................................................. 55 
6.2.3 
Study Product Accountability .................................................................. 55 
6.2.4 
Transmission of Infectious Agents ........................................................... 55 
6.2.5 
Exposure to Radiation .............................................................................. 55 
6.3 
Treatment Schedule and Administration ................................................................. 56 
6.3.1 
Administration of [1-13C]Sodium Acetate ............................................... 56 
6.3.2 
Administration of DTX301 ...................................................................... 56 
6.3.3 
Treatment Compliance ............................................................................. 57 
6.4 
Prior and Concomitant Therapy .............................................................................. 57 
6.4.1 
Permitted Medications ............................................................................. 57 
6.4.2 
Prohibited Medications ............................................................................ 58 
7 
Withdrawal of Subjects From the Study ........................................................................... 59 
7.1 
Study Withdrawal .................................................................................................... 59 
7.2 
Subject Replacement ............................................................................................... 59 
8 
Study Assessments and Procedures .................................................................................. 60 
8.1 
Efficacy Assessments .............................................................................................. 60 
8.1.1 
Ureagenesis .............................................................................................. 60 
8.1.2 
Plasma Ammonia Area Under the Curve from Time Zero to 24 Hours .. 60 
8.2 
Safety Assessments ................................................................................................. 60 


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8.2.1 
Physical Examination .............................................................................. 61 
8.2.2 
Vital Sign Measurements ......................................................................... 61 
8.2.3 
Electrocardiograms .................................................................................. 62 
8.2.4 
Clinical Laboratory Analyses................................................................... 62 
8.2.4.1 
Clinical Laboratory Parameters ............................................................... 63 
8.2.4.1.1 
Elevation of Liver Function Tests ................................................ 65 
8.2.4.1.2 
Treatment for Possible Vector-Induced Hepatitis ........................ 66 
8.2.5 
Other Laboratory Parameters ................................................................... 68 
8.2.5.1 
Neutralizing Antibodies to Adeno-Associated Virus Serotype 8 ............. 68 
8.2.5.2 
Adeno-Associated Virus Serotype 8 Binding Antibody Immunoglobulin 
G Assay .................................................................................................... 68 
8.2.5.3 
Anti-Ornithine Transcarbamylase Antibody Assay ................................. 68 
8.2.5.4 
Viral Shedding ......................................................................................... 68 
8.3 
Pharmacokinetics and Pharmacodynamic Assessments ......................................... 69 
8.3.1 
Ureagenesis .............................................................................................. 69 
8.3.2 
Plasma Ammonia Area Under the Curve from Time Zero to 24 Hours .. 69 
8.3.3 
Orotic Acid Excretion .............................................................................. 70 
8.4 
Quality-of-Life Assessment .................................................................................... 70 
8.4.1 
PROMIS Questionnaire ........................................................................... 70 
8.5 
Neuropsychological Tests ....................................................................................... 70 
8.5.1 
Intelligence .............................................................................................. 71 
8.5.2 
Motor Function ........................................................................................ 72 
8.5.2.1 
 ............................................................ 72 
8.5.3 
Executive Function .................................................................................. 72 
8.5.3.1 
................. 72 
8.5.4 
Memory .................................................................................................... 72 
8.5.4.1 
 
 ........................................ 72 
8.6 
Genotyping .............................................................................................................. 73 
8.6.1 
Ornithine Transcarbamylase Genotyping ................................................ 73 
8.7 
Other Assessments .................................................................................................. 73 
8.7.1 
Demographic, Medical, and Ornithine Transcarbamylase Deficiency 
History Assessments ................................................................................ 73 
8.7.2 
Ammonia Scavenger Use and Dietary Protein Intake ............................. 73 


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9 
Safety Monitoring and Reporting ..................................................................................... 74 
9.1 
Adverse Events and Serious Adverse Events ......................................................... 74 
9.1.1 
Definitions ............................................................................................... 74 
9.1.1.1 
Adverse Events ........................................................................................ 74 
9.1.1.2 
Serious Adverse Events ........................................................................... 75 
9.1.2 
Safety Reporting ...................................................................................... 75 
9.1.2.1 
Adverse Events ........................................................................................ 75 
9.1.2.2 
Serious Adverse Events ........................................................................... 76 
9.1.2.2.1 
Expedited Reporting .................................................................... 77 
9.1.3 
Assessment of Severity/Toxicity ............................................................. 77 
9.1.4 
Assessment of Causality .......................................................................... 78 
9.1.5 
Follow-Up of Subjects Reporting Adverse Events .................................. 79 
9.2 
Procedures for Handling Special Situations ........................................................... 79 
9.2.1 
Pregnancy ................................................................................................ 79 
9.2.2 
Treatment Noncompliance ....................................................................... 80 
9.2.2.1 
Overdose Management ............................................................................ 80 
9.2.2.2 
Medication Errors .................................................................................... 80 
9.3 
Data Monitoring Committee ................................................................................... 81 
10 Statistical and Analytical Plan .......................................................................................... 81 
10.1 Dose-Finding Algorithm and Process ..................................................................... 81 
10.2 Primary Endpoints .................................................................................................. 82 
10.3 Secondary Endpoints .............................................................................................. 82 
10.4 Exploratory Endpoints ............................................................................................ 82 
10.5 Statistical Analysis Methodology ........................................................................... 82 
10.5.1 
Determination of the Optimal Biological Dose ....................................... 83 
10.5.2 
Efficacy Analysis ..................................................................................... 85 
10.5.2.1 Ureagenesis .............................................................................................. 85 
10.5.2.2 Plasma Ammonia Area Under the Curve from Time Zero to 24 Hours .. 86 
10.5.3 
Safety Analyses ........................................................................................ 86 
10.5.3.1 Adverse Events ........................................................................................ 86 
10.5.3.2 Physical Examination Findings ............................................................... 86 
10.5.3.3 Vital Sign Measurements ......................................................................... 86 


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10.5.3.4 Electrocardiogram Results ....................................................................... 86 
10.5.3.5 Clinical Laboratory Assessment Results ................................................. 87 
10.5.3.6 Other Laboratory Results ......................................................................... 87 
10.5.4 
Neuropsychological Tests ........................................................................ 87 
10.5.5 
Quality-of-Life Assessment ..................................................................... 87 
10.5.6 
Other Analyses ......................................................................................... 87 
10.5.7 
Interim Analysis ....................................................................................... 87 
10.6 Data Quality Assurance........................................................................................... 88 
10.6.1 
Data Management .................................................................................... 88 
11 Ethics ................................................................................................................................ 89 
11.1 Institutional Review Board, Independent Ethics Committee, and Institutional 
Biosafety Committee ....................................................................................... 89 
11.2 Ethical Conduct of the Study .................................................................................. 90 
11.3 Subject Information and Consent ........................................................................... 90 
12 Investigator’s Obligations ................................................................................................ 90 
12.1 Confidentiality ........................................................................................................ 91 
12.2 Financial Disclosure and Obligations ..................................................................... 91 
12.3 Investigator Documentation .................................................................................... 91 
12.4 Study Conduct ......................................................................................................... 92 
12.5 Adherence to Protocol ............................................................................................ 92 
12.6 Adverse Events and Study Report Requirements ................................................... 92 
12.7 Investigator’s Final Report ..................................................................................... 93 
12.8 Record Retention .................................................................................................... 93 
12.9 Publications ............................................................................................................. 93 
13 Study Management ........................................................................................................... 93 
13.1 Monitoring .............................................................................................................. 93 
13.1.1 
Monitoring of the Study ........................................................................... 93 
13.1.2 
Inspection of Records .............................................................................. 94 
13.2 Management of Protocol Amendments and Deviations.......................................... 94 
13.2.1 
Modification of the Protocol .................................................................... 94 
13.2.2 
Protocol Deviations ................................................................................. 94 


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13.3 Study Termination ................................................................................................... 95 
13.4 Final Report ............................................................................................................ 95 
14 Reference List................................................................................................................... 97 
15 Appendices ..................................................................................................................... 103 
15.1 Appendix: Schedules of Events ............................................................................ 103 
15.2 Quality of Life Questionnaire ............................................................................... 112 
15.2.1 
PROMIS Questionnaire ......................................................................... 112 
15.3 Protocol Amendment History and Summary of Changes ..................................... 116 
15.3.1 
Amendment 1 (dated 18 August 2016) .................................................. 116 
15.3.2 
Amendment 2 (dated 20 December 2016) ............................................. 117 
15.3.3 
Amendment 3 (dated 07 February 2017) ............................................... 118 
15.3.4 
Amendment 4 (dated 11 June 2019) ...................................................... 119 
15.3.5 
Amendment 5 (dated 25 February 2020) ............................................... 121 
 
List of Tables 
Table 8-1 
Clinical Laboratory Parameters ...................................................................... 64 
Table 9-1 
PPD PVG Contact Information for SAE Reporting ....................................... 76 
Table 9-2 
General Guidelines for Grading Events not Captured by the CTCAE ........... 78 
Table 15-1 
Schedule of Events – Outpatient, Home Health Services, and Inpatient Clinic 
Visits ............................................................................................................. 104 
Table 15-2 
Schedule of Events – Clinic or Home Visits During the Initial 12-Week 
Treatment Period ............................................................................................ 111 
 
List of Figures 
Figure 1-1 
Overview of the Urea Cycle ........................................................................... 27 
Figure 3-1 
Study Design ................................................................................................... 41 
Figure 10-1 
 
 .................................................................... 84 


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Figure 10-2 
 
............................................................................................. 85 
 


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Protocol Synopsis 
Protocol Number: 
301OTC01 
Title: 
A Phase 1/2, Open-Label Safety and Dose-Finding Study of Adeno-Associated 
Virus (AAV) Serotype 8 (AAV8)-Mediated Gene Transfer of Human Ornithine 
Transcarbamylase (OTC) in Adults with Late-Onset OTC Deficiency 
Sponsor: 
Ultragenyx Pharmaceutical Inc. 
840 Memorial Drive 
Cambridge, MA 02139 
Study Phase: 
Phase 1/2 
Sample Size: 
The study is anticipated to enroll up to 18 subjects 
Study Sites: 
Approximately 20 global study sites 
Indication: 
OTC deficiency 
Primary Objective: 
• 
To determine the safety of single intravenous (IV) doses of DTX301 in 
adults with late-onset OTC deficiency. 
Secondary 
Objectives: 
• 
To establish a dose of DTX301 that has a meaningful increase in the rate of 
ureagenesis to allow further clinical development. 
• 
To evaluate the efficacy of single IV doses of DTX301 in adults with 
late-onset OTC deficiency, in the setting of tapering or discontinuing 
ammonia scavenger medications. 
Exploratory 
Objectives: 
• 
To assess the impact of DTX301, by dose, on the number of 
hyperammonemic crises during the study. 
• 
To evaluate the effect of DTX301, by dose, on urinary orotic acid levels. 
• 
To evaluate the effect of DTX301, by dose, on plasma glutamine and 
glutamate levels. 
• 
To assess the impact of DTX301, by dose, on the subject’s 
neuropsychological functioning. 
• 
To assess the impact of DTX301, by dose, on the subject’s quality of life 
(QoL). 
• 
To assess the impact of DTX301, by dose, on the use of ammonia 
scavengers. 
• 
To assess the impact of DTX301, by dose, on dietary protein restriction. 
• 
To describe the immune response to AAV8 capsid proteins after IV 
administration of DTX301. 
• 
To describe the immune response to OTC after IV administration of 
DTX301. 
Primary 
Endpoints: 
• 
The incidence of adverse events (AEs), treatment-emergent adverse events 
(TEAEs), and serious adverse events (SAEs) for each dosing cohort, 
assessed by severity and relationship to study product. 


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Secondary 
Endpoints: 
• 
The change from baseline in the rate of ureagenesis (as measured by the 
generation of [13C]urea over 4 hours) as determined by gas chromatography 
mass spectrometry over time to 52 weeks after the IV administration of 
DTX301. 
• 
The change from baseline (Day 0) in plasma ammonia area under the curve 
from time zero to 24 hours (AUC0-24) over time to 52 weeks after IV 
administration of DTX301 in the setting of tapering or discontinuing 
ammonia scavenger medications. 
Exploratory 
Endpoints: 
• 
The number of hyperammonemic crises observed for each dose over time to 
52 weeks after IV administration of DTX301. 
• 
The change from baseline in urinary orotic acid excretion over time to 
52 weeks after IV administration of DTX301. 
• 
The change from baseline in serum glutamine and glutamate over time to 
52 weeks after IV administration of DTX301. 
• 
Changes in responses to the 
 
 
 Working Memory Index (WMI), will be summarized by 
dose level of DTX301. 
• 
Responses to the Patient-Reported Outcomes Measurement Information 
System (PROMIS®) questionnaire, summarized by dose level of DTX301 
over time to Week 52. 
• 
Use of ammonia scavengers, summarized by dose level of DTX301. 
• 
Change in dietary protein intake, summarized by dose level of DTX301. 
• 
The development of neutralizing antibodies to AAV8 (as determined by a 
cell-based assay), summarized by time point and dose level of DTX301. 
• 
The development of anti-AAV8 binding antibodies (as determined by 
enzyme-linked immunosorbent assay [ELISA]), summarized by time point 
and dose level of DTX301. 
• 
The development of anti-OTC antibodies (as determined by ELISA), 
summarized by time point and dose level of DTX301. 
Subject 
Population: 
Inclusion Criteria 
Each subject must meet all of the following criteria at Screening to be enrolled in 
this study: 
1. Willing and able to provide written informed consent. 
2. Males and females ≥ 18 years of age with documented diagnosis of 
late-onset (defined as first manifestation of signs and symptoms at 
> 30 days of age) OTC deficiency, confirmed via enzymatic, biochemical, 
or molecular testing. This may include identification of a pathogenic 
mutation, pedigree analysis, liver OTC activity that is < 20% of normal 
activity, or elevated urinary orotate (> 20 µmol/mmol creatinine) after an 
allopurinol challenge test. 
3. Documented history of ≥ 1 symptomatic hyperammonemia event with 


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ammonia ≥ 100 µmol/L. 
4. Subject’s OTC deficiency is stable as evidenced by either a) no clinical 
symptoms of hyperammonemia OR b) plasma ammonia level 
< 100 µmol/L within the 4-week period preceding the Screening visit. 
5. Subject’s plasma ammonia level on Day 1 (predose) is < 100 µmol/L, for 
patients who historically maintain normal ammonia levels, and the subject 
is clinically stable; OR subject’s plasma ammonia level on Day 1 
(predose) is < 200 µmol/L, for patients who historically are not able to 
fully control ammonia levels with baseline management, and the subject is 
clinically stable. If the Day 1 (predose) ammonia level is inconsistent with 
the subject’s clinical status, the ammonia level may be repeated to ensure 
accurate results.  
6. On ongoing daily stable dose of ammonia scavenger therapy for 
≥ 4 weeks. 
7. No known allergic reaction to any component of DTX301. 
8. Willing and able to comply with study procedures and requirements, 
including periodic inpatient hospitalizations, frequent blood draws, and 
urine collections over a 24-hour period. 
9. Hematology and coagulation panel results are within the normal range or, 
if outside the normal range, deemed not clinically significant in the 
opinion of the investigator. 
10. Males and all females of childbearing potential must be willing to use 
effective contraception at the time of administration of gene transfer and 
for the 52 weeks following administration of DTX301 to prevent the 
potential transmission of the AAV vector. For male subjects, appropriate 
contraceptive methods include the use of a condom with spermicide. For 
female subjects, appropriate contraceptive methods include the use of a 
condom with spermicide plus at least 1 of the following: 
a. 
Oral contraceptives, other hormonal contraceptives (vaginal products, 
skin patches, or implanted or injectable products), or mechanical 
products such as an intrauterine device; 
b. Use of a diaphragm or cervical/vault cap; 
c. 
Previous female sterilization (surgical bilateral oophorectomy [with or 
without hysterectomy] or tubal ligation) at least 6 weeks prior to 
DTX301 administration. In case of an oophorectomy alone, the 
reproductive status of the subject must have been confirmed by 
follow-up hormone level assessment. 
NOTE: Abstinence is an acceptable form of birth control; however, appropriate 
contraception must be used if the subject becomes sexually active. Abstinence is 
defined as sexual inactivity consistent with the preferred and usual lifestyle of 
the subject. Periodic abstinence (calendar, symptothermal, post-ovulation 
methods), withdrawal (coitus interruptus), spermicides only, and lactational 
amenorrhea methods are not acceptable methods of contraception. A condom 
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in the study in order to prevent potential transmission of the vector via seminal 
fluid. 
 
NOTE: Females of childbearing potential are defined as all females 
physiologically capable of becoming pregnant, unless they are using highly 
effective methods of contraception for the duration of the study. 
Females are considered post-menopausal and not of childbearing potential if they 
have had 12 months of natural (spontaneous) amenorrhea with an appropriate 
clinical profile (eg, age appropriate, history of vasomotor symptoms) or have had 
surgical bilateral oophorectomy (with or without hysterectomy) or tubal ligation 
at least 6 weeks prior to enrollment. In the case of oophorectomy alone, only 
when the reproductive status of the woman has been confirmed by follow up 
hormone level assessment is she considered not of childbearing potential. 
Exclusion Criteria: 
Subjects meeting any of the following criteria at Screening will be excluded from 
the study: 
1. At Screening or Baseline (Day 0), plasma ammonia level ≥ 100 µmol/L 
for patients who historically maintain normal ammonia levels; OR plasma 
ammonia level ≥ 200 µmol/L for patients who historically are not able to 
fully control ammonia levels with baseline management; OR signs and 
symptoms of hyperammonemia, with documented elevated ammonia 
level, during the 4-week period preceding Day 0. If the ammonia level is 
inconsistent with the subject’s clinical status, the ammonia level may be 
repeated to ensure accurate results. 
2. Liver transplant, including hepatocyte cell therapy/transplant. 
3. History of liver disease as evidenced by any of the following: portal 
hypertension, ascites, splenomegaly, esophageal varices, hepatic 
encephalopathy, or a liver biopsy with evidence of stage 3 fibrosis. 
4. Significant hepatic inflammation or cirrhosis as evidenced by imaging or 
any of the following laboratory abnormalities: alanine aminotransferase 
(ALT) or aspartate aminotransferase (AST) > the upper limit of normal 
(ULN), total bilirubin > 1.5 × ULN, alkaline phosphatase > 2.5 × ULN. 
5. Serum creatinine > 2.0 mg/dL. 
6. Evidence of active hepatitis B virus (HBV) or hepatitis C virus (HCV) 
infection, documented by current use of antiviral therapy for HBV or HCV 
or by hepatitis B surface antigen (HBsAg) or HCV RNA positivity. 
NOTE: Subjects with a history of HCV infection must have 
documentation of 2 negative viral assays by polymerase chain reaction 
(PCR), collected at least 6 months apart, to be considered negative for 
HCV. Subjects with a history of HCV infection who test positive for HCV 
RNA at Screening can be rescreened once, after they have been treated 
and have documentation of at least 2 negative samples collected at least 
6 months apart. 
7. History of human immunodeficiency virus (HIV) infection AND any of 
the following: CD4+ cell count < 350 cells/mm3, change in antiretroviral 


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therapy regimen within 6 months prior to Day 0, or plasma viral load 
> 200 copies/mL, documented on 2 separate occasions, as measured by 
PCR. 
8. Active infection (viral or bacterial). 
9. Anti-AAV8 neutralizing antibody titer ≥ 1:5. 
10. Participation (current or previous) in another gene transfer study. 
11. Participation in another investigational medicine study within 3 months of 
Screening. 
12. History of a malignancy for which the subject has received treatment in 
the past 2 years except for prostate cancer treated with watchful waiting or 
surgically removed non-melanoma skin cancer. 
13. Has a positive serum pregnancy test at Screening (females of childbearing 
potential only), a positive urine pregnancy test at Baseline (Day 0; females 
of childbearing potential only), or is nursing. 
14. Has any other significant medical condition that the investigator feels 
would be a risk to the subject or would impede the study. 
Study Design: 
This is a Phase 1/2, open-label, single arm, multicenter, safety and dose-finding 
study of DTX301 in adults with late-onset OTC deficiency. The primary 
objective of the study is to determine the safety of single IV doses of DTX301. A 
key element of the study is the identification of the optimal biological dose 
(OBD) of DTX301. The secondary objectives of the study are the assessment of 
rate of ureagenesis, reflecting the direct in vivo efficiency of the urea cycle and 
the assessment of plasma ammonia (AUC0-24), reflecting clinical metabolic 
control. The target for DTX301 is to achieve a rate for ureagenesis of 
approximately 300 µmol/kg/hr (±10%), which is the approximate rate of 
ureagenesis in healthy adults.  
Eligible subjects will receive a single IV infusion of DTX301. Three subjects 
will be enrolled in Cohort 1 and a minimum of 2 to 3 subjects will be enrolled in 
each subsequent cohort. Dose escalation will be conducted according to a model 
that uses the collected data to predict the safety profile of the dose in order to 
determine the OBD. There will be a minimum of 12 weeks between the dosing 
of the last subject in one dosing cohort and the first subject in the next dosing 
cohort followed by data monitoring committee (DMC) review of a dosing cohort 
up to Cohort 3. Dosing of additional subjects as expansion of Cohort 3, and 
initiation of Cohort 4 (Dosing Process Optimization) may occur in parallel, 
following the DMC review of a minimum of 12 weeks of data from the initial 3 
subjects in Cohort 3. A continual reassessment method (CRM) will be used for 
dose finding to discover the OBD of DTX301. Cohort 4 is intended to dose at 
OBD. 
Subjects will be followed for 52 weeks after dosing. After completion of this 
study, subjects will be asked to enroll in a 4-year extension study to evaluate the 
long-term (a total of 5 years after dosing) safety and efficacy of DTX301. 
Study 
Methodology: 
Screening Period 
After a subject has provided written informed consent, the investigator or other 


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qualified study personnel will determine if the subject is eligible for the study. 
This will be accomplished by reviewing the inclusion and exclusion criteria and 
completing all of the screening assessments. Screening assessments may be 
performed on more than 1 day; all assessments must be completed and results 
available and reviewed prior to Day 0. 
Screening Assessments: Demographic data; OTC and general medical history; 
prior medications, therapies, and procedures; use of ammonia scavengers; dietary 
protein restrictions; vital sign measurements; height and weight will be recorded. 
A 12-lead electrocardiogram (ECG) and a complete physical examination will be 
performed. Blood samples will be collected for HBV, HCV, and HIV status; 
serum pregnancy test (females of childbearing potential only); AAV8 
neutralizing antibody testing; AAV8 binding antibody immunoglobulin G (IgG) 
testing, and clinical laboratory assessments (clinical chemistry, plasma ammonia 
[STAT sample], hematology, urinalysis, and coagulation panel). Adverse events 
and SAEs will be monitored after the subject has provided written informed 
consent. 
Subjects will be administered [1-13C]sodium acetate orally. Blood samples for 
determination of ureagenesis will be collected, via an indwelling catheter, before 
dosing (time 0) and at approximately 0.5, 1, 1.5, 2, 3, and 4 hours after dosing 
with [1-13C]sodium acetate. During Screening, assessment of rate of ureagenesis 
may be repeated if discrepant with subject’s clinical status and severity. 
Subjects participating in Cohort 4 (Dosing Process Optimization) will start the 
prophylactic corticosteroid regimen at least 5 days prior to dosing with DTX301. 
The subject must be assessed as clinically and metabolically stable, and 
intercurrent illnesses (eg, viral infection) or concomitant medications known to 
affects transaminases, be excluded. At any time after initiation of prophylactic 
corticosteroid regimen, additional assessments of plasma ammonia levels, amino 
acid profiles or any other biomarker to assess subject safety and clinical status 
may be performed, at the discretion of the investigator and as clinically 
indicated. 
Day 0 – Baseline Measurements 
Subjects will be admitted on Day 0 for the baseline determination of the 
following: plasma ammonia (AUC0-24) and urinary orotic acid levels over 
24 hours.  
Prior to the determination of plasma ammonia AUC0-24, blood samples will be 
collected for OTC genotyping, AAV8 neutralizing antibody testing, AAV8 
binding antibody IgG testing, anti-OTC antibody testing, amino acid panel, and 
clinical laboratory assessments (clinical chemistry, plasma ammonia [STAT 
sample], hematology, urinalysis, and coagulation panel). Saliva, urine, and stool 
samples will be collected to provide a baseline for assessment of viral shedding. 
A urine pregnancy test will be performed on all female subjects of childbearing 
potential. An ECG and a targeted physical examination will be performed. Vital 
sign measurements and weight will be recorded. Adverse events and SAEs will 
be monitored; concomitant medications, therapies, and procedures, use of 
ammonia scavengers and dietary protein restrictions will be recorded. 


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Subjects participating in Cohort 4 (Dosing Process Optimization) will start the 
prophylactic corticosteroid regimen at least 5 days prior to dosing with DTX301. 
The subject will complete the PROMIS questionnaire to evaluate QoL prior to 
the neuropsychological tests. 
The subject’s plasma ammonia level should be < 100 µmol/L or within the range 
of historical ammonia levels obtained when the subject was clinically stable in 
order to perform the neuropsychological tests. The study site may use the time 0 
(T 0) plasma ammonia sample (from AUC0-24 plasma ammonia) analyzed by the 
local laboratory (STAT sample) to determine the subject’s plasma ammonia 
level. The result must be available prior to initiating the tests. If the ammonia 
level is inconsistent with the subject’s clinical status, the ammonia level may be 
repeated to ensure accurate results. If the subject is deemed clinically unstable, 
the neuropsychological tests will be held. Subjects, in a nonfasted state, will 
complete the following neuropsychological tests: 
IQ: 
 
Motor Function: 
 
Executive Function: 
 
Memory: 
 
Blood samples will be collected for the determination of plasma ammonia 
(AUC0-24) at time 0 and at approximately 2, 4, 8, 12, 16, 20, and 24 hours. Urine 
will be collected for the determination of orotic acid at time 0 and at 
approximately 6, 12, 18, and 24 hours (relative to the start of plasma ammonia 
determination). Urine orotic acid concentration will be standardized to urine 
creatinine concentration.  
Day 1 – Determination of Plasma Ammonia, Ureagenesis, and DTX301 
Infusion 
The subject’s plasma ammonia level should be < 100 µmol/L or within the range 
of historical ammonia levels obtained when the subject was clinically stable in 
order to receive [1-13C]sodium acetate and DTX301. The 24-hour time point 
(T 24) from the local laboratory (STAT sample) for (AUC0-24) of plasma 
ammonia can be used and the result available prior to administering 
[1-13C]sodium acetate. If the ammonia level is inconsistent with the subject’s 
clinical status, the ammonia level may be repeated to ensure accurate results. If 
the subject is deemed clinically unstable, administration of [1-13C]sodium acetate 
will be held. Subjects will be administered [1-13C]sodium acetate orally 
(morning of Day 1). Blood samples for determination of ureagenesis will be 
collected, via an indwelling catheter, before dosing (time 0) and at approximately 
0.5, 1, 1.5, 2, 3, and 4 hours after dosing with [1-13C]sodium acetate. 
Prior to the preparation of DTX301, a blood sample will be collected for clinical 
chemistry (including liver function tests) and vital sign measurements will be 
recorded. Adverse events and SAEs will be monitored; concomitant medications, 
therapies, and procedures, use of ammonia scavengers and dietary protein 


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restrictions will be recorded. Prior to the start of DTX301 infusion, the study site 
must confirm that the subject’s plasma ammonia level on Day 1 (predose) is 
< 100 µmol/L for patients who historically maintain normal ammonia levels, and 
the subject is clinically stable; OR subject’s plasma ammonia level on Day 1 
(predose) is < 200 µmol/L, for patients who historically are not able to fully 
control ammonia levels with baseline management, and the subject is clinically 
stable. If the Day 1 (predose) ammonia level is inconsistent with the subject’s 
clinical status, the ammonia level may be repeated to ensure accurate results. 
NOTE: If the subject is deemed clinically unstable, dosing will be held, and the 
subject can be rescreened once the subject is determined to be clinically stable. 
The 24-hour time point (time 24) from local laboratory (STAT sample) for 
(AUC0-24) of plasma ammonia can serve as the DTX301 predose plasma 
ammonia result, if drawn within 12 hours of dosing with DTX301. If not, a new 
plasma ammonia (STAT sample) is to be collected prior to dosing with DTX301. 
Subjects will receive a single IV infusion of DTX301. The start of DTX301 
infusion should be after all samples and procedures specified for Day 0 and 
Day 1 (predose) have been completed. Subjects will be discharged after a 
24-hour observation period. 
After dosing with DTX301, a blood sample will be collected for clinical 
laboratory assessments (clinical chemistry [including liver function tests]) at 
approximately 0.5, 4, 8, and 22 hours after the start of infusion. A second sample 
for liver function tests only will be collected and sent to the local laboratory 
(STAT sample). Vital sign measurements will be recorded at 5 minutes after the 
start of infusion, and at approximately 0.5, 1, 2, 4, 6, 8, and 22 hours after the 
start of infusion. An ECG will be performed at 1 hour after the start of infusion. 
A single sample for plasma ammonia (STAT sample at local laboratory) will be 
collected and reviewed prior to discharging the subject. 
Subjects treated in Cohort 4 (Dosing Process Optimization) will utilize an 
alternative regimen of corticosteroids, aiming at prophylaxis of vector-induced 
hepatitis. Therefore, oral prednisone (or prednisolone) will be initiated before 
dosing with DTX301, sustained for 4 weeks, followed by tapering. At any time 
after initiation of prophylactic corticosteroid regimen, additional assessments of 
plasma ammonia levels, amino acid profiles or any other biomarker to assess 
subject safety and clinical status may be performed, at the discretion of the 
investigator and as clinically indicated. 
Clinic or Home Visits 
Subjects will be asked to provide samples for clinical chemistry approximately 
every 4 days through Week 12 of the study. One sample for LFTs is collected as 
part of clinical chemistry and sent to the central laboratory for analysis. A second 
sample for LFTs only is collected and sent to the local laboratory (STAT 
sample). Through Week 12, one sample for spot ammonia will be collected 
approximately once per week and sent to the local laboratory (STAT sample). If 
subjects cannot visit the study site in person, subjects may have the option of 
being visited by clinically trained and qualified personnel (if available) 
approximately every 4 days at their home through Week 12; the exception being 
required study site visits when the subject must visit the study site in person. At 
any point between scheduled visits, additional unscheduled assessment of LFTs, 


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plasma ammonia, or any other biomarker to assess subject safety and clinical 
status may be performed, at the discretion of the investigator.  
Weeks 2, 4, 10, 16, 20, and 36 (Outpatient Clinic Visit) (Table 15-1) 
Where available, agreed upon by the investigator and allowed by local 
regulation, an outpatient clinic visit may take place as home health services. 
Week 20 visit is a mandatory outpatient clinic visit for all subjects 
(Table 15-1). 
Weeks 6, 12, and 24 (Inpatient Visit) (Table 15-1) 
Subjects will be discharged following completion of all assessments, including 
plasma ammonia (AUC0-24), urinary orotic acid levels over 24 hours, and 
ureagenesis. Subjects will be housed for approximately 28 hours. 
End of Study (Week 52)/Early Withdrawal Visit (Inpatient Visit) 
A comprehensive visit will occur at Week 52 (Table 15-1). Subjects will be 
discharged following completion of all assessments, including plasma ammonia 
(AUC0-24), urinary orotic acid levels over 24 hours, ureagenesis, and 
neuropsychological tests. Subjects will be housed for approximately 28 hours. 
Following completion of the Week 52 visit, subjects will be asked to enroll in a 
4-year extension study to evaluate the long-term (a total of 5 years after dosing) 
safety and efficacy of DTX301.  


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Tapering of 
Ammonia 
Scavenger Therapy 
and Protein-
Restricted Diet: 
There are multiple types of ammonia scavenger medications available globally 
and patients with OTC deficiency typically have a personalized prescription of 
one or more ammonia scavenger medications to optimize the management of 
their disease. Adjustments to ammonia scavenger therapy may be considered 
following the Week 12 and Week 24 visits. Changes to baseline treatment (ie, 
ammonia scavenger therapy and protein-restricted diet) cannot occur until there 
is evidence of transgene expression reflected by continued evidence of metabolic 
stability with ammonia levels in the normal range or improved ammonia control 
if subjects have a history of ammonia levels above the upper limit of normal and 
supported by improvement in clinical signs and symptoms. The subject must be 
clinically stable and under good metabolic control before changes can be 
initiated or progressed. The risks of making adjustments to baseline treatment on 
their own, without express guidance from the site, will be reinforced with the 
subject at site visits. 
Changes to baseline treatment cannot occur while the subject is treated with 
corticosteroids or within a 2-week period of completing a corticosteroid taper.  
Modification of ammonia scavenger therapy cannot occur at the same time as 
changes in protein-restricted diet. Once medications or diet are adjusted or 
discontinued, the subject must demonstrate good metabolic control prior to 
adjustments in the other type of baseline treatment.  
Modification of baseline treatment will be individualized, dependent on the 
clinical judgment of the investigator, and based on review of the totality of 
longitudinal clinical and laboratory data for each subject, including spot plasma 
ammonia levels, plasma ammonia (AUC0-24), subject clinical 
stability/asymptomatic status, neurocognitive status, and subject-reported 
outcomes. Rate of ureagenesis cannot be used for decision-making in 
modification of ammonia scavenger therapy or protein-restricted diet and 
results will not be made available to the investigative sites until the end of 
the study. During periods of adjustment to baseline treatment, subjects will be 
closely monitored. 
At any time after modification and/or discontinuation of ammonia scavenger 
therapy, reinstitution of therapy may take place based on the subject’s clinical 
and metabolic status (elevated ammonia levels or signs and symptoms consistent 
with hyperammonemia), and under evaluation of the investigator.   


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Tapering of 
Ammonia 
Scavenger Therapy 
and Protein-
Restricted Diet 
(continued): 
Reinstitution of ammonia scavenger therapy should be considered if: 
1.
Subjects demonstrate 2 or more documented consecutive laboratory
results of hyperammonemia (plasma ammonia level ≥ 100 µmol/L).
NOTE: If the subject is clinically stable, spot ammonia may be repeated
if discrepant with subject’s clinical status and severity, OR
2.
Subjects demonstrate upward trending plasma ammonia levels less than
100 µmol/L and associated with clinical signs or symptoms suggestive
of worsening underlying disease, OR
3.
Subjects experience a time of increased metabolic demand, such as
intercurrent viral infection, treatment with steroids, hyperammonemia,
or hyperammonemic crisis.
Learnings from this study will allow for the development of a more standardized 
protocol for tapering ammonia scavenger medications in future studies of 
DTX301. 
Occurrence of 
Hyperammonemia 
and 
Hyperammonemia 
Crisis (HAC) 
Consistent with the Urea Cycle Disorders Consortium (UCDC), we have defined 
hyperammonemic crisis (HAC) in this study as an episode of signs and 
symptoms associated with hyperammonemia (such as frequent vomiting, nausea, 
headache, lethargy, irritability, combativeness, and somnolence), with 
documented elevated ammonia levels (≥ 100 µmol/L) and requiring medical 
intervention [Kent and Holt 2017; Longo and Holt 2017; Diaz 2019]. 
On-study management of hyperammonemia plasma level or hyperammonemic 
crises may include, but is not limited to, intravenous hydration, discontinuation 
of all dietary protein intake, increase in ammonia scavenger therapy, 
hemodialysis in addition to treatment of underlying inciting illness or event (eg, 
acute infection, sepsis, bleeding, drug-related, etc.). Comprehensive, 
internationally accepted guidelines for management of urea cycle disorders are 
recommended [Häberle 2012; Häberle 2019]. 
Because there is a wide spectrum of presentation and severity of symptomatic 
hyperammonemia events, investigator judgment needs to be exercised and each 
subject’s management individualized (Section 3.2.4). 


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Treatment for 
Vector-Induced 
Hepatitis: 
The investigator, in conjunction with the Ultragenyx Pharmaceutical medical 
lead will consider starting oral steroid treatment, per protocol, for possible 
vector-induced hepatitis when a subject’s ALT is greater than the ULN and is 
considered by the investigator to be related to treatment with DTX301. The 
subject must be assessed as clinically and metabolically stable, and intercurrent 
illnesses (eg, viral infection) or concomitant medications known to affect 
transaminases, be excluded.   
Repeat liver function testing for confirmation of results should be considered to 
inform the use of steroid treatment. If repeat testing is deemed necessary, every 
effort should be made to repeat the testing within 24 hours from receipt of test 
results indicating elevated ALT. 
At any point between scheduled visits, additional, unscheduled assessments for 
LFTs, plasma ammonia or any other biomarker to assess subject safety and 
clinical status may be performed, at the discretion of the investigator.  
Changes to baseline treatment (ammonia scavenger medications and protein-
restricted diet) cannot occur while the subject is treated with corticosteroids or 
within a 2-week period of completing a corticosteroid taper.   
Based on available evidence, it is expected that vector-induced hepatitis will be 
self-limiting. Therefore, oral prednisone (or prednisolone) will be used per the 
American Association for the Study of Liver Disease guidelines in Cohorts 1 to 
3, with a slight modification: 
• 
Week 1: prednisone 60 mg/day 
• 
Week 2: prednisone 40 mg/day 
• 
Week 3 and Week 4: prednisone 30 mg/day 
• 
Week 5 and thereafter: Prednisone will be tapered by 5 mg/week until 
liver enzymes return to baseline levels. 
Cohort 4 (Dosing Process Optimization) will utilize an alternative regimen of 
corticosteroids, aiming at prophylaxis of vector-induced hepatitis. Therefore, oral 
prednisone (or prednisolone) will be initiated before dosing with DTX301, 
sustained for 4 weeks, followed by tapering as described below. Prophylactic 
corticosteroid regimens are in use for gene transfer therapies [Audentes 2017 
Clinicaltrials.gov identifier: NCT03223194; Abeona Therapeutics 2016 
ClinicalTrials.gov identifier: NCT02716246].  
• 
At least 5 days prior to administration of DTX301: prednisone 
60 mg/day 
• 
Study Day 1 (Week 1) through Week 4: prednisone 60 mg/day 
• 
Study Week 5 through Week 8, tapering every 5 days: 
• 
Prednisone 40 mg/day for 5 days, followed by prednisone 
30 mg/day for 5 days, prednisone 20 mg/day for 5 days, 
prednisone 10 mg/day for 5 days, prednisone 5 mg/day for 
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At any time after initiation of prophylactic corticosteroid regimen, additional 
assessments of plasma ammonia levels, amino acid profiles or any other 
biomarker to assess subject safety and clinical status may be performed, at the 
discretion of the investigator and as clinically indicated. 
Utilization of prednisone (or prednisolone) after dosing and after completion of 
the prophylactic regimen, remains available to all subjects when a subject’s ALT 
is greater than the ULN and is considered by the investigator to be related to 
treatment with DTX301. 
Safety Stopping 
Criteria: 
Enrollment will be stopped and the regulators will be notified if, at any time 
during the study, any of the following occur: 
• 
Death of a subject following administration of DTX301 
• 
An event with an intensity of ≥ Grade 3 (according to the Common 
Terminology Criteria for Adverse Events), but excluding 
hyperammonemic crises, develops following administration of DTX301 
• 
Occurrence of a hepatic malignancy following administration of 
DTX301 
Abnormal clinically significant laboratory values (clinical chemistry, plasma 
ammonia, hematology, urinalysis, and coagulation panel) as assessed by the 
investigator will be considered AEs. Laboratory values that meet any of the 
above criteria will result in a pause in enrollment until the DMC reviews the data 
and provides a recommendation for subsequent study conduct. 
Any event that meets any of the above criteria will be reported immediately and 
captured as an AE/SAE in the electronic case report form (eCRF), as appropriate. 
Enrollment and dosing will be temporarily suspended until the situation can be 
assessed and risks to the subjects mitigated. If an investigator reports an AE/SAE 
that meets any of the study stopping criteria, the DMC will meet on an ad hoc 
basis to review and assess the event. If study enrollment is suspended, all 
subjects who have been enrolled will remain in the study and will continue to be 
monitored through their completion or withdrawal from the study.  
All AEs will be graded according to the most current version of the National 
Cancer Institute Common Terminology Criteria for Adverse Events. 
Efficacy 
Assessments: 
Efficacy assessments include:  
The rate of ureagenesis, as measured by the generation of [13C]urea over 4 hours, 
will be determined by GCMS at Screening, on Day 1 and at 6, 12, 20, 24, and 
52 weeks after IV administration of DTX301. During Screening, assessment of 
rate of ureagenesis may be repeated if discrepant with subject’s clinical status 
and severity. 
The change from Baseline (Day 0) in AUC0-24 plasma ammonia at 6, 12, 24, and 
52 weeks after IV administration of DTX301. 


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Safety 
Assessments: 
Safety assessments will include the following: AEs, SAEs, complete and targeted 
physical examination findings, vital sign measurements, ECG results, clinical 
laboratory assessments (clinical chemistry, plasma ammonia, hematology, 
urinalysis, and coagulation panel), viral shedding, measurement of neutralizing 
antibody titer to AAV8, measurement of AAV8 binding antibodies, and 
measurement of anti-OTC antibodies. 
Pharmacokinetic/ 
Pharmacodynamic 
Assessments: 
Ureagenesis 
The conversion of the stable isotope [1-13C]sodium acetate to [13C]urea will be 
determined by GCMS. Blood samples will be collected in precooled heparinized 
tubes before dosing (time 0) and at approximately 0.5, 1, 1.5, 2, 3, and 4 hours 
after [1-13C]sodium acetate is administered orally at Screening, Baseline (Day 1), 
and over time to Week 52 after administration of DTX301. Blood samples will 
be immediately centrifuged to separate the plasma, which will be stored frozen 
at -70°C until shipped for analysis. During Screening, assessment of rate of 
ureagenesis may be repeated if discrepant with subject’s clinical status and 
severity. 
Plasma Ammonia 
The AUC0-24 of plasma ammonia will be determined at Baseline (Day 0) and 
over time to Week 52 after administration of DTX301. Two samples (one 
analyzed at the local laboratory [STAT sample], and the other analyzed at the 
central laboratory) will be collected at time 0 and at approximately 2, 4, 6, 8, 10, 
12, 16, 20, and 24 hours. 
Orotic Acid Excretion 
The excretion of orotic acid will be determined over a 24-hour period at Baseline 
(Day 0) and over time to Week 52 after administration of DTX301.  
Estimated Study 
Duration: 
The duration of the study is defined for each subject as the date signed written 
informed consent is provided through the visit at Week 52. Subjects will be in 
the study for approximately 56 weeks (including the screening period).  
After completion of this study, subjects will be asked to enroll in a 4-year 
extension study to evaluate the long-term (a total of 5 years after dosing) safety 
and efficacy of DTX301. 
Study Product, 
Dose, and Route of 
Administration: 
DTX301 will be administered as a single peripheral IV infusion.  
A continual reassessment method (CRM) will be used to determine the OBD. 
The following candidate doses may be evaluated to determine the OBD: 
• 
Dose 1: 2.0 × 1012 genome copies (GC)/kg 
• 
Dose 2: 6.0 × 1012 GC/kg  
• 
Dose 3: 1.0 × 1013 GC/kg 
Based on the results of the CRM, additional doses may be considered. 
Statistical 
Methods: 
Determination of the Optimal Biological Dose 
A CRM will be used for dose finding to discover the OBD of DTX301. The 
CRM uses the Bayesian method to model the probability of experiencing a 


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dose-limiting toxicity (DLT) for each given dose in order to determine the next 
dose. A DLT is defined as any AE/SAE ≥ Grade 3 that is considered related to 
DTX301 by the investigator. Noninformative as well as informative prior 
distributions (ie, historical data) for the model parameters can be used to help 
with the initial modeling of the probability of experiencing a DLT. The OBD is 
defined as the highest dose where the predicted probability of a DLT is less than 
the target toxicity level. Cohort 4 is intended to dose at the OBD. Subjects may 
be assigned in parallel to either expansion of Cohort 3 or Cohort 4, with at least 
1 male subject assigned to each. 
Interim Analysis 
An interim analysis may be conducted when 12-week data are available for all 
subjects from at least 2 cohorts. 
Safety Analyses 
All statistical analyses of safety outcomes will be descriptive. The incidence of 
AEs and TEAEs will be summarized for each dosing cohort by severity and 
relationship to study product. Serious AEs will be presented for each dosing 
cohort by relationship to study product. Summary tables will present incidence 
estimates and individual event rates by system organ class as well as within each 
system organ class. Subjects experiencing an event more than once with varying 
severity will be counted only once, in the maximum severity within each system 
organ class and preferred term. For incidence of relationship to study product, 
subjects will be counted only once, in the category of the strongest relationship 
to study product within each system organ class/preferred term. 


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List of Abbreviations 
Abbreviation 
Definition 
AAV 
adeno-associated virus 
AAV2 
adeno-associated virus serotype 2 
AAV8 
adeno-associated virus serotype 8 
AE 
adverse event 
ALT 
alanine aminotransferase 
AUC0-24 
area under the curve from time zero to 24 hours 
CFR 
Code of Federal Regulations 
CRA 
clinical research associate 
CRM 
continual reassessment method 
CTCAE 
Common Terminology Criteria for Adverse Events 
 
 
DLT 
dose-limiting toxicity 
DMC 
data monitoring committee 
ECG 
electrocardiogram 
eCRF 
electronic case report form 
EDC 
electronic data capture 
ELISA 
enzyme-linked immunosorbent assay 
FDA 
US Food and Drug Administration 
GC 
genome copies 
GCP 
Good Clinical Practice 
HAC 
hyperammonemic crisis 
HBV 
hepatitis B virus 
HCV 
hepatitis C virus 
IBC 
institutional biosafety committee 
ICF 
informed consent form 
ICH 
International Council for Harmonisation 
IEC 
independent ethics committee 
IgG 
immunoglobulin G 
IRB 
institutional review board 
IV 
intravenous 
MED 
minimal effective dose 
MedDRA 
Medical Dictionary for Regulatory Activities 


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Abbreviation 
Definition 
MTD 
maximum tolerated dose 
NCI 
National Cancer Institute 
OBD 
optimal biological dose 
OTC 
ornithine transcarbamylase 
PCR 
polymerase chain reaction 
PROMIS 
Patient-Reported Outcomes Measurement Information System 
PVG 
pharmacovigilance 
QoL 
quality of life 
 
 
SAE 
serious adverse event 
SAP 
statistical analysis plan 
SUSAR 
serious, unexpected, suspected adverse drug reaction 
UCD 
urea cycle disorder 
UCDC 
Urea Cycle Disorders Consortium 
ULN 
upper limit of normal 
WAIS-IV 
Wechsler Adult Intelligence Scale, Fourth Edition 
WASI-II 
Wechsler Abbreviated Scale of Intelligence, Second Edition 
WMI 
Working Memory Index 
 


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1 
Introduction 
The urea cycle is a series of biochemical reactions that is responsible for removing excess nitrogen, in 
the form of ammonia, from the body (Figure 1-1). In mammals, ammonia from the breakdown of 
dietary and endogenous protein is converted into urea in the liver; urea is nontoxic, water soluble, and 
easily excreted in the urine [Deignan 2008]. Urea cycle disorders (UCDs) result when there is a 
deficiency of any 1 of the 6 enzymes and 2 transporters that comprise the urea cycle: 
N-acetylglutamate synthase, carbamyl phosphate synthetase I, ornithine transcarbamylase (OTC), 
argininosuccinate synthetase, argininosuccinate lyase, arginase, citrin, or ornithine translocase 
[Jackson 1986]. Clinically, UCDs (which are estimated to affect approximately 1 in 
30,000 individuals worldwide) are characterized by excessive levels of plasma ammonia 
(hyperammonemia), which is a neurotoxin that can lead to irreversible cognitive impairment, coma, 
and death in the absence of immediate medical attention [Batshaw 1987; Krivitzky 2009]. 
Figure 1-1 
Overview of the Urea Cycle 
 
Abbreviations: AL, argininosuccinate lyase; ARG, arginase; AS, argininosuccinate synthetase; ATP, adenosine 
triphosphate; CoA, coenzyme A; CPSI, carbamyl phosphate synthetase I; HCO3, bicarbonate; 
NAG, N-acetylglutamate synthase; NH4+, ammonium ion; OTC, ornithine transcarbamylase. 


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Ornithine transcarbamylase deficiency, the most common of the UCDs, is currently estimated to 
occur in up to 1:62,000 live births [Lichter-Konecki 2013]. Ornithine transcarbamylase deficiency is 
an X-linked disorder that results from mutations in the OTC gene, affecting the expression or activity 
of the OTC protein [Caldovic 2015]. A deficiency in OTC activity prevents the normal flux of 
ammonia through the urea cycle and ultimately results in hyperammonemia. Ornithine 
transcarbamylase deficiency presents as a severe form (ie, complete OTC deficiency) in males shortly 
after birth (neonatal onset; ≤ 30 days of age) or later in life in both males and females (late onset; 
> 30 days of age) with disease that ranges from mild to severe depending on the residual activity of 
OTC [Tuchman 2008a].  
Males with neonatal-onset OTC deficiency, defined as the onset of signs and symptoms by 30 days of 
age, are typically normal at birth, but become symptomatic and critically ill within 2 to 3 days of 
initial presentation [Lichter-Konecki 2013]. Without treatment, these patients may fall into a 
hyperammonemic coma and develop severe neurologic abnormalities [Krivitzky 2009]. 
The prognosis of a newborn that falls into a hyperammonemic coma depends on the duration, rather 
than the magnitude, of the elevated ammonia level [Msall 1984]. Despite optimal management, a 
neonate with severe OTC deficiency may only tolerate as much as 1.5 g/kg/day of dietary protein, 
which is the minimum amount of dietary protein needed to grow. In contrast, males with partial OTC 
activity or heterozygous females can present with initial symptoms at any time from infancy through 
adulthood and are clinically classified as late-onset patients. 
Symptomatic hyperammonemic events, classified as hyperammonemic crises (HAC) are often 
triggered by acute stressors, most commonly concurrent infection, but can become a life-threatening 
event at any age [Lichter-Konecki 2013; Batshaw 2014]. For example, adults with late-onset OTC 
deficiency have become hyperammonemic after crush injury, following surgery, when on a 
high-protein diet, during the postpartum period, and when treated with chemotherapy, high-dose 
corticosteroids, valproate, or haloperidol [Lichter-Konecki 2013; Batshaw 2014]. Consistent with the 
Urea Cycle Disorders Consortium (UCDC), we have defined hyperammonemic crisis (HAC) in this 
study as an episode of signs and symptoms associated with hyperammonemia (such as frequent 
vomiting, nausea, headache, lethargy, irritability, combativeness, and somnolence), with documented 
elevated ammonia levels (≥ 100 µmol/L) and requiring medical intervention [Kent and Holt 2017; 
Longo and Holt 2017; Diaz 2019]. 
Successful rescue from an initial hyperammonemic crisis does not eliminate the chronic risk patients 
have for developing repeat episodes of hyperammonemia, which may present as lethargy, seizures, or 
coma. Regardless of the age of onset, neuropsychological complications for all individuals with OTC 


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deficiency typically include developmental delay, learning disabilities, intellectual disability, 
attention deficit hyperactivity disorder, and executive function deficits. 
The current standard of care for OTC deficiency is to limit dietary protein intake and supplement the 
diet with a high-energy source, such as glucose [Leonard 2001]. If plasma ammonia is not stabilized 
by dietary restriction alone, ammonia scavengers that promote an alternative pathway of nitrogen 
removal can be administered [Batshaw 2001; Häberle 2012; Lichter-Konecki 2013; Häberle 2019]. 
Ammonia scavengers cannot, however, completely prevent individuals from having 
hyperammonemic crises [Batshaw 2001]. Orthotopic liver transplantation can correct OTC 
deficiency; however, this is limited by donor availability and is associated with significant risk of 
morbidity and mortality [Leonard 2004].  
Thus, there remains a significant unmet medical need for a treatment that allows for sustained 
ammonia management and prevention of hyperammonemic crises associated with OTC deficiency. 
1.1 
Adeno-Associated Viral Vectors 
Adeno-associated virus (AAV) is a nonenveloped, icosahedral, single-stranded DNA virus. 
Given that wild-type AAV displays wide tissue tropism and is capable of persisting in tissues for long 
durations without pathogenic effects, the use of recombinant AAV vectors has become a popular tool 
for gene delivery. Additionally, recombinant AAV vectors are nonreplicating and the vector genomes 
exist as an episome following tissue transduction, minimizing the risk of insertional mutagenesis 
[Nakai 2001]. Since the first genetic engineering of wild-type AAV as a gene delivery vector in the 
early 1980s, recombinant AAV has shown great promise as an effective and safe gene delivery 
vehicle for treatment of diseases [Gao 2005]. 
Adeno-associated virus serotype 2 (AAV2) was the first AAV that was used for gene transfer 
applications and has been used in numerous studies for a variety of diseases such as 
alpha 1-antitrypsin deficiency, Batten disease, and cystic fibrosis [Mingozzi 2011]. In animal models, 
AAV-mediated gene transfer was shown to treat the underlying disease for many years [Snyder 1999; 
Mount 2002; Wang 2005; Nichols 2010]. However, in humans, AAV2-mediated delivery was either 
sub-therapeutic or only lasted a few months [Manno 2003; Manno 2006]. This was attributed to 
several limitations of AAV2 vectors including low transduction efficiency [Yan 2002], high 
seroprevalence of neutralizing antibodies against AAV2 in humans [Boutin 2010], and potentially 
destructive T-cell responses to capsids [Gao 2009; Vandenberghe 2006; Wang 2007]. 
Additionally, there has been evidence of B-cell responses against the transgene product in an animal 
model of hemophilia [Herzog 2001]. 


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1.2 
Selection of the AAV Clinical Candidate 
The host immune response (ie, neutralizing antibodies and T-cell responses) limiting the efficacy of 
AAV2-mediated gene transfer (Section 1.1) was not predicted in the initial animal studies, due to 
AAV2 not being endemic in the nonhuman animal species under investigation. Novel AAV 
serotypes, isolated from nonhuman primates, are divergent enough from endemic human serotypes to 
circumvent the neutralizing antibodies existing in most human subjects while retaining similar tissue 
tropism [Gao 2002].  
One of these serotypes, AAV serotype 8 (AAV8), displays strong tropism for the liver [Gao 2002] 
and has been tested extensively as a vector for gene transfer in nonclinical and clinical models of 
hemophilia [Davidoff 2005; Jiang 2006; Nathwani 2006; Nathwani 2007; Nathwani 2011a].  
These studies have shown that AAV8 has clear advantages over AAV2 that include the following: 
excellent transduction efficiency; liver-specific tropism; stable transgene expression; a lack of 
hepatotoxicity as measured by peak serum aminotransferases; a lack of liver histopathology findings; 
a lack of T-cell activation to the transgene product; and low levels of pre-existing neutralizing 
antibodies in human populations, minimizing their inhibition of in vivo transduction. Furthermore, in 
clinical studies, AAV8 has shown impressive efficacy and safety for the treatment of hemophilia B 
[Nathwani 2011a; Nathwani 2014] and is currently being studied for the treatment of glycogen 
storage disease type Ia (NCT03517085), hemophilia A (NCT03001830), hemophilia B 
(NCT00979238 and NCT01687608), X-linked retinoschisis (NCT02317887), human 
immunodeficiency virus-1 (NCT03374202), X-linked retinitis pigmentosa (NCT03116113), X-linked 
myotubular myopathy (NCT03199469), homozygous familial hypercholesterolemia (NCT02651675), 
Pompe disease (NCT03533673), mucopolysaccharidosis disease (NCT03173521), and achromatopsia 
(NCT03758404 and NCT03001310). 
The study product, DTX301, contains a codon-optimized human wild-type OTC gene with expression 
driven by both a liver-specific enhancer element and a liver-specific promoter encapsidated within a 
nonreplicating AAV8 vector. In spfash mice, which is an established nonclinical model of OTC 
deficiency that results from a missense mutation in exon 4 of the OTC gene [Hodges 1989], this 
vector showed a sustained, dose-dependent improvement in both OTC expression and activity 
following a single intravenous (IV) injection that was comparable to wild-type mice [Wang 2012]. 
These data provide support for the feasibility of this therapeutic approach in humans. 
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1. Adeno-associated virus is used as the vehicle for gene delivery. Unlike adenovirus, which had 
limited efficacy and significant toxicity at high doses in previous OTC gene transfer studies 
[Raper 2002; Raper 2003], AAV vectors have shown impressive safety and long-term 
efficacy in a number of diseases [Kay 2011; Nathwani 2011a; Nathwani 2014]; 
2. The liver is the natural site of ureagenesis. The AAV8 serotype demonstrates high liver 
tropism and can achieve efficient liver gene transfer following IV infusion [Gao 2002]; 
3. The AAV8 serotype is not thought to be endemic in the human population and, therefore, the 
prevalence of pre-existing neutralizing antibodies to AAV8 in patients with OTC deficiency 
is expected to be lower than other AAV serotypes, such as AAV2 [Calcedo 2013]. 
1.3 
Study Rationale 
Ornithine transcarbamylase gene transfer is expected to be effective for the treatment of OTC 
deficiency since the disease is caused by mutations within a single gene [Caldovic 2015]. Unlike 
current medical treatment options (dietary restriction and ammonia scavengers), OTC gene transfer 
offers the potential to correct the underlying deficiency for a prolonged period with a single IV 
infusion. Currently, no gene transfer product has been approved for the treatment of OTC deficiency. 
Increasing OTC activity and promoting the removal of ammonia through the urea cycle should allow 
patients with OTC deficiency to avoid hyperammonemic crises in the context of a well-controlled 
diet, while reducing or stopping ammonia scavenger therapy. Furthermore, depending on the level of 
OTC expression and activity achieved, patients may be able to loosen their dietary restrictions, which 
should greatly improve their quality of life (QoL). 
1.3.1 
Design Rationale 
The design of this study is consistent with global regulatory guidelines for protocol design, including: 
subject selection, dose estimation, precautions applied between dosing cohorts, risk mitigation, and 
study stopping criteria.  
Study 301OTC01 is a Phase 1/2, open-label, multicenter, safety and dose-finding study to determine 
the safety, tolerability, and preliminary efficacy of DTX301 in adults with late-onset OTC deficiency. 
The primary objective of the study is to determine the safety and tolerability of single doses of 
DTX301. A key element of the study is the identification of the optimal biological dose (OBD) of 
DTX301. The secondary objectives of the study are the assessment of rate of ureagenesis, reflecting 
the direct in vivo efficiency of the urea cycle and the assessment of plasma ammonia (AUC0-24), 
reflecting clinical metabolic control. The target for DTX301 is to achieve a rate for ureagenesis of 


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approximately 300 µmol/kg/hr (±10%), which is the approximate rate of ureagenesis in healthy adults 
[Matthews 1984; Jahoor 1987; Castillo 1996; Tuchman 2008b]. 
With regards to defining clinically meaningful hyperammonemia as ≥ 100 µmol/L in this study 
(Section 4), a plasma ammonia level of ≥ 100 µmol/L is widely accepted in both clinical practice and 
published literature as a clinically significant level where OTC patients are likely to be symptomatic 
(including neuropsychological impairments) due to hyperammonemia [Lichter-Konecki 2013]. 
Furthermore, plasma ammonia exceeding 100 µmol/L is identified by the United Kingdom National 
Metabolic Biochemistry Network as clinically elevated [Wright 2010] and is associated with an 
increased risk of death (odds ratio 1.5 or greater) in OTC patients [Ozanne 2012]. Published 
guidelines for the management of hyperammonemia in UCDs also recommend restarting enteral 
feeding once plasma ammonia is < 100 µmol/L [Häberle 2012; Häberle 2019]. 
Consistent with the UCDC, we have defined symptomatic hyperammonemic events, classified as 
hyperammonemic crisis (HAC) throughout the study, as an episode of signs and symptoms associated 
with hyperammonemia (such as frequent vomiting, nausea, headache, lethargy, irritability, 
combativeness, and somnolence) with documented elevated ammonia levels (≥ 100 µmol/L) and 
requiring medical intervention [Kent and Holt 2017; Longo and Holt 2017; Diaz 2019]. 
Eligible subjects will receive a single IV infusion of DTX301. Three subjects will be enrolled in 
Cohort 1 and a minimum of 2 to 3 subjects will be enrolled in each subsequent cohort; the number of 
subjects in each subsequent dosing cohort will be determined by subject results and availability of 
study product. Subjects in Cohorts 1 and 2 will be dosed at a minimum of 2 weeks (14 days) apart. 
The initial 3 subjects in Cohort 3 will be dosed at a minimum of 1 week apart (7 days). Additional 
subjects to Cohort 3 (Cohort Expansion) and subjects to Cohort 4 (Dosing Process Optimization) may 
be dosed less than 1 week apart. There will be a minimum of 12 weeks (84 days) followed by DMC 
review of a dosing cohort between the dosing of the last subject in one dosing cohort and the first 
subject in the next dosing cohort up to Cohort 3. Dosing of additional subjects as expansion of Cohort 
3, and initiation of Cohort 4 (Dosing Process Optimization) may occur in parallel, following the 
DMC review of a minimum of 12 weeks of data from the initial 3 subjects in Cohort 3. Subjects may 
be assigned to either expansion of Cohort 3 or Cohort 4, with at least 1 male subject assigned to each. 
A continual reassessment method (CRM) will be used for dose finding to discover the OBD of 
DTX301 (Section 10.5.1). Cohort 4 is intended to dose at the OBD. 
The proposed dosing interval of 14 days between subjects in the first and second dose cohorts, and 
7 days between each of the first 3 subjects in Cohort 3, followed by a shorter dosing interval in the 
expansion of Cohort 3 and Cohort 4, is supported by the safety profile and lack of serious adverse 


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reactions reported in AAV-mediated gene transfer in human subjects, including those using AAV8 
vector in a hemophilia B clinical study [Manno 2006; Nathwani 2011a; Nathwani 2014], and the 
ongoing safety review from this study, which includes DMC assessment [Diaz 2019; Ultragenyx 
Pharmaceutical, data on file]. Moreover, an ongoing Phase 1/2 clinical study in hemophilia B using 
AAV-mediated gene transfer at a starting dose of 5.0 × 1012 genome copies (GC)/kg (higher than the 
proposed DTX301 starting dose of 3.0 × 1012 GC/kg) at multiple European study sites is dosing 
subjects within a cohort at a minimum of only 1 day (24 hours) apart [uniQure 2014; 
Clinicaltrials.gov identifier: NCT02396342; EudraCT Number: 2013-005579-42]. 
The most common product-related AE observed in clinical studies with AAV-mediated gene transfer 
to subjects with moderate to severe hemophilia B has been an asymptomatic transient rise in liver 
aminotransferases (still within the normal reference range for these laboratory parameters) and 
concurrent decline in transgene expression approximately 7 to 10 weeks following vector 
administration [Manno 2006; Nathwani 2011a; Nathwani 2014]. In all cases, the transient rise in liver 
aminotransferases resolved without clinical sequelae. It has been hypothesized that this 
vector-induced hepatitis is due to the activation of capsid-specific cytotoxic T lymphocytes and 
destruction of transduced liver cells [Mingozzi 2007]. As this is the only identified AE with AAV 
gene transfer and, given that subjects in this study will be closely monitored for vector-induced 
hepatitis and treated with corticosteroids (Section 8.2.4.1.2), having an interval of more than 14 days 
between subjects within Cohorts 1 and 2 and 7 days between the first 3 subjects in Cohort 3 does not 
change either safety evaluations or the medical management of study subjects. To date, no infusion-
related or serious AEs (SAEs) have been reported with DTX301. Aligned with previous experience 
[Manno 2006; Nathwani 2011a; Nathwani 2014], only mild, transient, asymptomatic rises in liver 
enzymes have been observed in 6 subjects starting approximately 8 days to 7 weeks after vector 
administration that resolved with an oral corticosteroid taper regimen [Diaz 2019; Ultragenyx 
Pharmaceutical, data on file;]. To allow for refinement in management of asymptomatic transient 
rises in liver aminotransferases (vector-induced hepatitis) and concurrent decline in transgene 
expression following AAV vector administration, Cohort 4 (Dosing Process Optimization) will utilize 
an alternative regimen of oral corticosteroids. Based on available evidence, it is expected that 
vector-induced hepatitis will be self-limiting. Therefore, oral prednisone (or prednisolone) will be 
employed in a prophylactic regimen initiated before dosing with DTX301, sustained for 4 weeks, 
followed by tapering (Section 8.2.4.1.2). Prophylactic corticosteroid regimens are in use for gene 
transfer therapies [Audentes 2017 Clinicaltrials.gov identifier: NCT03223194; Abeona Therapeutics 
2016 ClinicalTrials.gov identifier: NCT02716246].  
Subject safety will be closely monitored throughout the study, including assessment of 
hyperammonemic crises, assessment of metabolic and clinical stability, frequent monitoring of liver 


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enzymes and plasma ammonia levels, and inpatient observation following dosing and at multiple time 
points throughout the 52-week study duration. 
After all subjects in Cohort 1 and Cohort 2, and the initial 3 subjects in Cohort 3 have completed 
Week 12, a data monitoring committee (DMC) will meet to review safety data (ie, AEs/SAEs, 
physical examination findings, vital sign measurements, electrocardiogram [ECG] results, and 
longitudinal clinical laboratory assessments [including assessment of liver function and plasma 
ammonia]) and provide a recommendation for progressing to the next dosing level, as applicable 
(Section 9.3), and enrollment of additional subjects to Cohort 3 (Cohort Expansion) and subjects to 
Cohort 4 (Dosing Process Optimization). If an investigator reports an AE/SAE that meets any of the 
study stopping criteria (Section 3.2.7), the DMC will meet on an ad hoc basis to review and assess the 
event. The DMC may, at any time, recommend modifying or pausing enrollment due to safety 
concerns based on these periodic data reviews. Additional DMC meetings may take place, as needed. 
The full scope of each review is outlined in the DMC charter.  
Subjects will be followed for 52 weeks after dosing. After completion of this study, subjects will be 
asked to enroll in a 4-year extension study to evaluate the long-term (a total of 5 years after dosing) 
safety and efficacy of DTX301.  
1.3.2 
Dosing Rationale 
The current working estimation to determine the clinical starting dose detailed below is based on 
available nonclinical data with DTX301, including the minimal effective dose (MED) and optimal 
effective dose of DTX301 in mice, clinical experience with other AAV8 products, and known 
limitations when scaling between species.  
Based on preliminary nonclinical study results of DTX301 
 
 
 
 
 
  
In order to estimate the allometric scaling needed for AAV8-mediated delivery of the OTC transgene 
in this study, two data sets using AAV-mediated transfer of human factor IX were examined: the 
uniQure (Amsterdam, The Netherlands) data set [uniQure 2015] and the Nathwani data set [Nathwani 
2007; Nathwani 2011a; Nathwani 2011b]. The AAV5 vector used in the uniQure studies was shown 
to have a 10-fold scaling between mouse and human [uniQure 2015]. The AAV8 vector used in the 


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Nathwani studies supports a 10-fold scaling from mouse to nonhuman primates and a 4-fold scaling 
between nonhuman primates and humans, for a total of 40-fold between mouse and human [Nathwani 
2007; Nathwani 2011a; Nathwani 2011b]. Therefore, when considering a clinical dosing rationale, in 
light of the available comparison data between mice and humans, it seems reasonable to consider a 
10-fold to 40-fold increase in dose from mice to humans to achieve similar target levels for the 
expression and activity of OTC. 
 
 
 
 
In comparison to the clinical development of traditional small molecule and biologic therapies, 
clinical studies for AAV-mediated gene transfer have an additional consideration; after initial dosing, 
it is expected that subjects who are administered DTX301 will develop neutralizing antibodies to 
AAV8 and will receive no benefit from subsequent dosing with this vector. Therefore, unlike classic 
dose-escalation studies, there is a greater focus on targeting efficacy in addition to safety.
 
 
 
 
 
 
 consistent with US Food 
and Drug Administration (FDA) Guidance for Industry on the Considerations for the Design of Early 
Phase Clinical Trials of Cellular and Gene Therapy Products [CBER 2015]. 
Another consideration is that the maximal feasible dose of vector that can be administered to mice in 
Good Laboratory Practice toxicology studies (based on dose volume and concentration of vector) is 
7.0 × 1013 GC/kg.
 
 
 
  
The starting dose for this study (2.0 × 1012 GC/kg) 
 
 
 which is anticipated to be the no observed 
adverse effect level. 
 
below the highest dose used in published nonhuman primate studies with AAV8 (2 × 1013 GC/kg) 
[Jiang 2006; McIntosh 2013] and is similar to the doses for other AAV-mediated gene transfer 


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products administered to humans of 2 × 1012 vector genomes/kg (AAV8) [Nathwani 2011a; 
Nathwani 2014] and 5 × 1012 GC/kg (AAV5) [uniQure 2014].
 
 GC/kg will provide a reasonable 
probability that all subjects in this study have the potential for a clinically substantial benefit from 
DTX301. 
An adaptive design for dose finding is being used in this study. The CRM will model the probability 
of experiencing a dose-limiting toxicity (DLT) in subsequent dosing cohorts using cumulative safety 
data (Section 10.5.1 and Figure 10-1). 
 
 
 
Additionally, depending on the results, additional subjects at the dose of interest may be 
recruited to confirm the OBD. 
Based on existing safety data from clinical studies using AAV-mediated gene transfer (including 
multiple hemophilia programs), substantial toxicity in the predicted therapeutic range is not 
anticipated. Ultragenyx Pharmaceutical is also taking into account the amount of DTX301 Chemistry, 
Manufacturing, and Controls material that can be produced over the anticipated timeline of this 
Phase 1/2 study. Assuming that a maximum tolerated dose (MTD) is not identified in nonclinical 
studies, the proposed dose-finding approach for this Phase 1/2 study is consistent with the FDA 
Guidance for Industry on the Considerations for the Design of Early Phase Clinical Trials of Cellular 
and Gene Therapy Products that achieving a specified target range of exposure is the focus of a 
cellular or gene therapy program when “there are significant practical limits of the dose of the product 
that can be produced or delivered” [CBER 2015]. 
For additional nonclinical information, please refer to the DTX301 investigator’s brochure. 


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2 
Study Objectives and Endpoints 
Objective 
Endpoint 
Primary 
To determine the safety of single IV doses of DTX301 
in adults with late-onset OTC deficiency. 
The incidence of AEs, TEAEs, and SAEs for each 
dosing cohort, assessed by severity and relationship to 
study product. 
Secondary 
To establish a dose of DTX301 that has a meaningful 
increase in the rate of ureagenesis to allow further 
clinical development. 
The change from baseline in the rate of ureagenesis 
(as measured by the generation of [13C]urea over 
4 hours) as determined by gas chromatography mass 
spectrometry over time to 52 weeks after the IV 
administration of DTX301. 
To evaluate the efficacy of single IV doses of 
DTX301 in adults with late-onset OTC deficiency in 
the setting of tapering or discontinuing ammonia 
scavenger medications. 
The change from baseline (Day 0) in plasma ammonia 
area under the curve from time zero to 24 hours 
(AUC0-24) over time to 52 weeks after IV 
administration of DTX301 in the setting of tapering or 
discontinuing ammonia scavenger medications. 
Exploratory 
To assess the impact of DTX301, by dose, on the 
number of hyperammonemic crises during the study. 
The number of hyperammonemic crises observed for 
each dose over time to 52 weeks after IV 
administration of DTX301. 
To evaluate the effect of DTX301, by dose, on urinary 
orotic acid levels. 
The change from baseline in urinary orotic acid 
excretion over time to 52 weeks after IV 
administration of DTX301. 
To evaluate the effect of DTX301, by dose, on plasma 
glutamine and glutamate levels. 
The change from baseline in serum glutamine and 
glutamate over time to 52 weeks after IV 
administration of DTX301 . 
To assess the impact of DTX301, by dose, on the 
subject’s neuropsychological functioning. 
Changes in responses to the following, summarized by 
dose level of DTX301:  
 
 
 
 
 
 
 
 
To assess the impact of DTX301, by dose, on the 
subject’s quality of life. 
Responses to the PROMIS questionnaire, summarized 
by dose level of DTX301 over time to Week 52. 
To assess the impact of DTX301, by dose, on the use 
of ammonia scavengers. 
Use of ammonia scavengers, summarized by dose 
level of DTX301. 
To assess the impact of DTX301, by dose, on dietary 
protein restriction. 
Change in dietary protein intake, summarized by dose 
level of DTX301. 
To describe the immune response to AAV8 capsid 
• The development of neutralizing antibodies to 


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Objective 
Endpoint 
proteins after IV administration of DTX301. 
AAV8 (as determined by a cell-based assay), 
summarized by time point and dose level of 
DTX301. 
• The development of anti-AAV8 binding antibodies 
(as determined by ELISA), summarized by time 
point and dose level of DTX301. 
To describe the immune response to OTC after IV 
administration of DTX301. 
• The development of anti-OTC antibodies (as 
determined by ELISA) summarized by time point 
and dose level of DTX301. 
Abbreviations: AAV8, adeno-associated virus serotype 8; AE, adverse event; AUC0-24, area under the curve from time zero 
to 24 hours; ELISA, enzyme-linked immunosorbent assay; IV, intravenous; OTC, ornithine transcarbamylase; 
PROMIS, Patient-Reported Outcomes Measurement Information System; SAE, serious adverse event; 
TEAE, treatment-emergent adverse event. 


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3 
Investigational Plan 
3.1 
Study Overview 
Study 301OTC01 is a Phase 1/2, open-label, multicenter, safety and dose-finding study to determine 
the safety, tolerability, and preliminary efficacy of DTX301 in adults with late-onset OTC deficiency. 
A key element of the study is the identification of the OBD for DTX301.The primary objective of the 
study is to determine the safety of single doses of DTX301. The secondary objectives of the study are 
the assessment of rate of ureagenesis, reflecting the direct in vivo efficiency of the urea cycle and the 
assessment of plasma ammonia (AUC0-24), reflecting clinical metabolic control. The target for 
DTX301 is to achieve a rate for ureagenesis of approximately 300 µmol/kg/hr (±10%), which is the 
approximate rate of ureagenesis in healthy adults [Matthews 1984; Jahoor 1987; Castillo 1996; 
Tuchman 2008b]. 
Eligible subjects will receive a single IV infusion of DTX301. Three subjects will be enrolled in 
Cohort 1 and a minimum of 2 to 3 subjects will be enrolled in each subsequent cohort. Dose 
escalation will be conducted according to a model that uses safety data to predict the OBD 
(Section 10.5.1, Figure 10-1, and Figure 10–2).  
The following candidate doses (per kilogram of body weight) will be used to determine the OBD 
(Section 10.5.1): 
• 
2.0 × 1012 GC/kg 
• 
6.0 × 1012 GC/kg 
• 
1.0 × 1013 GC/kg 
There will be a minimum of 14 days between dosing of each subject in Cohorts 1 and 2 and 7 days 
between dosing of the initial 3 subjects in Cohort 3. Additional subjects to Cohort 3 (Cohort 
Expansion) and subjects to Cohort 4 (Dosing Process Optimization) may be dosed less than 1 week 
apart.  
Dose escalation will be conducted according to a model that uses the collected data to predict the 
safety profile of the dose in order to determine the OBD. There will be a minimum of 12 weeks 
followed by data monitoring committee (DMC) review (Section 9.3) of a dosing cohort between the 
dosing of the last subject in one dosing cohort and the first subject in the next dosing cohort up to 
Cohort 3. Dosing of additional subjects as expansion of Cohort 3, and initiation of Cohort 4 (Dosing 
Process Optimization) may occur in parallel, following the DMC review of a minimum of 12 weeks 


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of data from the initial 3 subjects in Cohort 3. A CRM will be used for dose finding to discover the 
OBD of DTX301. Cohort 4 is intended to dose at OBD. There will be no intra-cohort dose 
escalations.  
Subjects treated in Cohort 4 (Dosing Process Optimization) will utilize an alternative regimen of 
corticosteroids, aiming at prophylaxis of vector-induced hepatitis. Therefore, oral prednisone (or 
prednisolone) will be initiated before dosing with DTX301, sustained for 4 weeks, followed by 
tapering (Section 8.2.4.1.2). 
Enrollment will be stopped, and the regulators will be notified if, at any time during the study, any of 
the safety stopping criteria are met (Section 3.2.7). 
Subjects will be followed for 52 weeks after dosing. After completion of this study, subjects will be 
asked to enroll in a 4-year extension study to evaluate the long-term (a total of 5 years after dosing) 
safety and efficacy of DTX301. 
3.2 
Overall Study Duration and Follow-Up 
The duration of the study is defined for each subject as the date that written informed consent is 
provided through the visit at Week 52. Subjects will be in the study for approximately 56 weeks 
(including the screening period). 
The study is anticipated to enroll up to 18 subjects at approximately 20 study sites globally.  
All study visits, clinic or home visits, and the timing of assessments are detailed in Table 15-1 and 
Table 15-2. Subjects will be asked to participate in 20 outpatient clinic or home visits (approximately 
1.5 to 5 hours in length depending on the assessments performed at the visit) and 5 inpatient clinic 
visits (approximately 24 to 48 hours in length). Where available, agreed upon by the investigator and 
allowed by local regulation, an outpatient clinic visit may take place as home health services. 
Investigators will be responsible for maintaining effective lines of communication between the 
investigator and the personnel who manage the subjects at home to guarantee that the 
investigator is constantly kept informed of subject safety, including metabolic and clinical 
status. 
A schematic of the study design is provided in Figure 3-1. 


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Figure 3-1 
Study Design 
Screening Period (Day –35 to Day –1) 
Determine subject eligibility 
Clinical and specialty labs and ECG 
Determine rate of ureagenesis (administer [1-13C]sodium acetate) 
Review ammonia scavenger use and dietary protein restrictions 
Subjects participating in Cohort 4 (Dosing Process Optimization) will start prophylactic corticosteroid regimen at least 5 days prior 
to dosing with DTX301 
Baseline (Day 0 through Day 1) – Inpatient 
Approximately 48-hour inpatient stay 
• 
Clinical and specialty labs and ECG 
• 
PROMIS questionnaire and neuropsychological tests, including a brief IQ test (WASI-II vocabulary and matrix reasoning 
subtests) 
• 
AUC0-24 plasma ammonia and 24-hour urinary orotic acid determination (Day 0) 
• 
Determine rate of ureagenesis (administer [1-13C]sodium acetate on Day 1) 
• 
Administer DTX301 (on Day 1 following completion of ureagenesis measurement) 
• 
Discharge (24 hours after DTX301 administration) 
Subjects participating in Cohort 4 (Dosing Process Optimization) will start prophylactic corticosteroid regimen at least 5 days prior 
to dosing with DTX301. 
Treatment Period 
Dose 
Cohort 
Outpatient Clinic Visits 
(Weeks 2, 4, 10, 16, 20, and 36) 
Inpatient Visits (approximately 28-hour) 
(Weeks 6, 12, and 24) 
1 to 3 
Clinical and specialty labs 
Clinical and specialty labs 
Viral shedding 
(saliva, urine, and stool) 
Viral shedding 
(saliva, urine, and stool) 
Vector genome sample (blood) 
Vector genome sample (blood) 
Orotic acid spot urine  
PROMIS questionnaire 
Rate of ureagenesis (administer  
[1-13C]sodium acetate at Week 20 only).   
Plasma ammonia AUC0-24 
Urinary orotic acid 
(every 6 hours over 24 hours) 
Determine rate of ureagenesis (administer  
[1-13C]sodium acetate) 
4 and 
expansion 
of 3 
Outpatient Clinic or Home Health Service Visits 
(Weeks 2, 4, 10, 16, and 36) 
Inpatient Visits (approximately 28-hour) 
(Weeks 6, 12, and 24) 
Clinical labs 
Clinical and specialty labs 
Orotic acid spot urine  
Viral shedding 
(saliva, urine, and stool) 
Outpatient Clinic or Home Health Service Visits 
(Weeks 10, 16, and 36) 
PROMIS questionnaire 
Viral shedding 
(saliva, urine, and stool) 
Plasma ammonia AUC0-24 
Outpatient Clinic  
(Weeks 20) 
Urinary orotic acid 
(every 6 hours over 24 hours) 
Rate of ureagenesis (administer  
[1-13C]sodium acetate); clinical labs, orotic acid spot 
urine, and viral shedding 
(saliva, urine, and stool) 
. 
 
 
• 
There will be a minimum of 14 days between subjects in Cohorts 1 and 2, and a minimum of 7 days between subjects between 
dosing of the initial 3 subjects in Cohort 3. Additional subjects to Cohort 3 (Cohort Expansion) and subjects to Cohort 4 
(Dosing Process Optimization) may be dosed less than 1 week apart. 
• 
There will be a minimum of 12 weeks followed by data monitoring committee (DMC) review of a dosing cohort between the 
dosing of the last subject in one dosing cohort and the first subject in the next dosing cohort up to Cohort 3.  
• 
Dosing of additional subjects as expansion of Cohort 3, and initiation of Cohort 4 (Dosing Process Optimization) may occur in 
parallel, following the DMC review of a minimum of 12 weeks of data from the initial 3 subjects in Cohort 3. 


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• 
Subjects treated in Cohort 4 (Dosing Process Optimization) will utilize an alternative regimen of corticosteroids, aiming at 
prophylaxis of vector-induced hepatitis. Therefore, oral prednisone (or prednisolone) will be initiated at least 5 days before 
dosing with DTX301, sustained for 4 weeks, followed by tapering. 
• 
Where available, agreed upon by the investigator, and allowed by local regulation, an outpatient clinic visit may take place as 
home health services.  
End of Study (Week 52)/Early Withdrawal – Inpatient 
Approximately 28-hour inpatient stay 
• 
Clinical and specialty labs and ECG 
• 
PROMIS questionnaire and neuropsychological tests 
• 
AUC0-24 plasma ammonia and 24-hour urinary orotic acid determination 
• 
Determine rate of ureagenesis (administer [1-13C]sodium acetate) 
• 
Discharge following completion of ureagenesis measurement 
• 
Subject will be asked to enroll in a long-term (4-year) extension study 
• 
Review ammonia scavenger use and dietary protein restrictions 
Abbreviations: AUC0-24, area under the curve from time zero to 24 hours; DMC, data monitoring committee; IQ, intelligence quotient; 
PROMIS, Patient-Reported Outcomes Measurement Information System; WASI-II, Wechsler Abbreviated Scale of Intelligence, 
Second Edition. 
3.2.1 
Screening Period 
After a subject has provided written informed consent, the investigator or other qualified study 
personnel will determine if the subject is eligible for the study. This will be accomplished by 
reviewing the inclusion and exclusion criteria (Section 4) and completing all of the screening 
assessments outlined with corresponding timeframe guidance in the Schedule of Events (Table 15-1). 
Screening should be concluded within 35 days before Day 0. NOTE: The screening assessments may 
be performed on more than 1 day; all assessments must be completed and results available and 
reviewed prior to Day 0. 
At Screening, blood and urine will be collected. Subjects will be administered [1-13C]sodium acetate 
orally for the determination of ureagenesis as outlined in Section 8.3.1. The assessment of rate of 
ureagenesis may be repeated during Screening if discrepant with subject’s clinical status and severity.  
The subject’s plasma ammonia level should be < 100 µmol/L or within the range of historical 
ammonia levels obtained when the subject was clinically stable in order to receive [1-13C]sodium 
acetate. If the ammonia level is inconsistent with a subject’s clinical status, the ammonia level may be 
repeated to ensure accurate results. If the subject is deemed clinically unstable, administration of 
[1-13C]sodium acetate dosing will be held. Blood samples for determination of ureagenesis will be 
collected, via an indwelling catheter, before dosing (time 0) and at approximately 0.5, 1, 1.5, 2, 3, and 
4 hours after dosing with [1-13C]sodium acetate. 
Subjects who screen fail due to one or more criteria that may potentially be resolved or reversed over 
time in the opinion of the investigator (for example, certain laboratory values or presence of active 
infection), or whose OTC deficiency is temporarily metabolically or clinically unstable, may be 


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rescreened one time. Subjects may be rescreened after being clinically and metabolically stable for at 
least 28 days. 
If rescreening is within 3 months of the original screening, the following must be repeated: 
hematology, coagulation and urinalysis, serum pregnancy test (if applicable), clinical chemistry, 
plasma ammonia, amino acid panel, AAV8 neutralizing antibody test, weight, and vital signs. 
Additional tests may be requested on a case-by-case basis, depending on the original reason for 
screen failure. The AAV8 screening neutralizing antibody results must be available and reviewed 
before IP administration. If the rescreening occurs more than 3 months after the original screening, all 
tests must be repeated except the following: OTC genotyping, HBV, HCV, and HIV. 
3.2.2 
Baseline Period 
Subjects will be admitted to the inpatient clinic on Day 0 and will be required to stay for 
approximately 48 hours. While the timing of assessments during the Baseline Visit outlined below 
reflects the most time efficient approach, individual centers may conduct alternate or extended timing 
and sequence of assessments that meet requirements, prior to dosing with DTX301. 
3.2.2.1 
Baseline Visit – Day 0 
The timing of all assessments and procedures for Day 0 is outlined in the Schedule of Events 
(Table 15-1). On Day 0, the baseline determination of plasma ammonia for area under the curve from 
time zero to 24 hours (AUC0-24) and urinary orotic acid levels (over 24 hours) will be performed. 
Samples for the determination of plasma ammonia (AUC0-24) and urinary orotic acid levels over 
24 hours will be collected prior to the oral administration of [1-13C]sodium acetate on Day 1. Blood 
and urine will be collected as outlined in Section 8.3.  
3.2.2.2 
Baseline – Day 1 
The timing of all assessments and procedures for Day 1 is outlined in the Schedule of Events 
(Table 15-1). The collection of samples for the determination of plasma ammonia (AUC0-24) and 
urinary orotic acid levels over 24 hours need to be completed prior to the determination of 
ureagenesis. Subjects will be administered [1-13C]sodium acetate orally for the determination of 
ureagenesis. Blood and urine will be collected as outlined in Section 8.3. 
Following completion of sampling for ureagenesis (ie, the 4-hour time point), subjects will then 
receive a single, peripheral IV infusion of DTX301. Safety (eg, vital sign measurements 
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[Section 9.1]) will be monitored for 24 hours following infusion of DTX301 (Table 15-1). Subjects 
will be discharged after a 24-hour observation period. Any AEs that occur during this 24-hour 
observation period will be treated with appropriate supportive and medical care deemed necessary for 
the well-being of the subject. 
Prior to the start of DTX301 infusion, the study site must confirm that the subject’s plasma ammonia 
level on Day 1 (predose) is < 100 µmol/L for patients who historically maintain normal ammonia 
levels, and the subject is clinically stable; OR subject’s plasma ammonia level on Day 1 (predose) is 
< 200 µmol/L, for patients who historically are not able to fully control ammonia levels with baseline 
management, and the subject is clinically stable. If the Day 1 (predose) ammonia level is inconsistent 
with the subject’s clinical status, the ammonia level may be repeated to ensure accurate results. The 
24-hour time point (T 24) from local laboratory (STAT sample) for (AUC0-24) of plasma ammonia can 
serve as the DTX301 predose plasma ammonia result, if drawn within 12 hours or less of dosing with 
DTX301. If not, a new plasma ammonia (STAT sample) is to be collected prior to dosing with 
DTX301. The predose plasma ammonia used to determine DTX301 dosing must be drawn 
within 12 hours or less of dosing. If the subject is deemed clinically unstable, dosing will be held, 
and the subject can be rescreened once the subject is determined to be clinically stable. Repeat of 
screening assessments or rescreen process may take place depending on timing and subject clinical 
status (Section 3.2.1 and Table 15-1). 
3.2.3 
Treatment Period 
Subjects will be evaluated approximately every 4 days through Week 12 at home, at outpatient clinic 
visits, or as inpatient visits (Table 15-1 and Table 15-2). Following the Week 12 visit, subjects will 
visit the study site once approximately every 4 weeks through Week 24, at Week 36, and at Week 52 
or their early withdrawal from the study (Table 15-1 and Table 15-2). Where available, agreed upon 
by the investigator and allowed by local regulation, an outpatient clinic visit may take place as home 
health services. Week 20 visit remains a mandatory outpatient clinic visit for all subjects. 
At any point between scheduled visits, additional unscheduled assessment of LFTs, plasma ammonia, 
or any other biomarker to assess subject safety and clinical status may be performed, at the discretion 
of the investigator. 
3.2.3.1 
Home or Clinic Visits 
Subjects will be asked to provide clinical laboratory samples approximately every 4 days through 
Week 12 of the study. Through Week 12, one sample for spot ammonia will be collected 


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approximately once a week, and sent to the local laboratory (STAT sample). If subjects cannot visit 
the study site in person, they may have the option of being visited by clinically trained and qualified 
personnel (if available) approximately every 4 days at their home through Week 12 (Table 15-2), the 
exception being required study site visits when the subject must visit the study site (Table 15-1). 
Saliva, urine, and stool samples will also be collected at these visits (through Week 12) for 
assessment of viral shedding (Table 15-2) and will continue to be collected until 3 consecutive 
negative results are obtained from each matrix (Section 8.2.5.3). 
3.2.3.2 
Outpatient Clinic or Home Health Service Visits 
Subjects will visit the study site on an outpatient basis at Weeks 2, 4, 10, 16, 20, and 36 for efficacy 
and safety assessments as well as the determination of ureagenesis (at Week 20 only) as outlined in 
the Schedule of Events (Table 15-1). Where available, agreed upon by the investigator and allowed 
by local regulation, an outpatient clinic visit may take place as home health Services. Week 20 visit 
remains a mandatory outpatient clinic visit for all subjects. 
3.2.3.3 
Inpatient Visits 
Subjects will be admitted to the study site at Weeks 6, 12, 24, and 52 for the determination of plasma 
ammonia (AUC0-24), urinary orotic acid levels, and ureagenesis. Samples for the determination of 
plasma ammonia (AUC0-24) and urinary orotic acid levels will be collected over the 24-hour period 
prior to the oral administration of [1-13C]sodium acetate. Blood and urine will be collected as outlined 
in Section 8.3. 
The timing of all assessments and procedures for each visit is outlined in the Schedule of Events 
(Table 15-1). Subjects will be discharged following the 4-hour time point for ureagenesis, after all 
assessments/samples have been completed/collected. Subjects will be housed for approximately 
28 hours. 
3.2.4 
Tapering of Ammonia Scavenger Therapy 
There are multiple types of ammonia scavenger medications available globally and patients with OTC 
deficiency typically have a personalized prescription of one more ammonia scavenger medications to 
optimize the management of their disease.  
Adjustments to ammonia scavenger therapy may be considered following the Week 12 and Week 24 
visits. Changes to baseline treatment (ie, ammonia scavenger therapy and protein-restricted diet) 


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cannot occur until there is evidence of transgene expression reflected by continued evidence of 
metabolic stability with ammonia levels in the normal range or improved ammonia control if subjects 
have a history of ammonia levels above the upper limit of normal and supported by improvement in 
clinical signs and symptoms. The subject must be clinically stable and under good metabolic control 
before changes can be initiated or progressed. The risks of making adjustments to baseline treatment 
on their own, without express guidance from the site, will be reinforced with the subject at site visits. 
Changes to baseline treatment cannot occur while the subject is treated with corticosteroids or within 
a 2-week period of completing a corticosteroid taper.  
Modification of ammonia scavenger therapy cannot occur at the same time as changes in 
protein-restricted diet. Once medications or diet are adjusted or discontinued, the subject must 
demonstrate good metabolic control prior to adjustments in the other type of baseline treatment.  
Modification of baseline treatment will be individualized, dependent on the clinical judgment of the 
investigator, and based on review of the totality of longitudinal clinical and laboratory data for each 
subject, including spot plasma ammonia levels, plasma ammonia (AUC0-24), subject clinical 
stability/asymptomatic status, neurocognitive status, and subject-reported outcomes. Rate of 
ureagenesis cannot be used for decision-making in modification of ammonia scavenger therapy 
or protein-restricted diet and results will not be made available to the investigative sites until 
the end of the study. During periods of adjustment to baseline treatment subjects will be closely 
monitored. 
At any time after modification and/or discontinuation of ammonia scavenger therapy, reinstitution of 
therapy may take place based on the subject’s clinical and metabolic status (elevated ammonia levels 
or signs and symptoms consistent with hyperammonemia), and under evaluation of the investigator.  
Reinstitution of ammonia scavenger therapy should be considered if: 
1. Subjects demonstrate 2 or more documented consecutive laboratory results of 
hyperammonemia (plasma ammonia level ≥ 100 µmol/L). NOTE: If the subject is clinically 
stable, spot ammonia may be repeated if discrepant with subject’s clinical status and severity, 
OR 
2. Subjects demonstrate upward trending plasma ammonia levels less than 100 µmol/L, 
associated with clinical signs or symptoms suggestive of worsening underlying disease, OR 


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3. Subjects experience a time of increased metabolic demand, such as intercurrent viral infection, 
treatment with steroids, hyperammonemia, or hyperammonemic crisis (Section 3.2.6). 
After reinstitution of ammonia scavenger therapy, once intercurrent illness is resolved (if applicable), 
and the subject is documented as clinically and metabolically stable, a second round of modification 
of baseline treatment can be considered. All provisions for stepwise reduction and disease monitoring 
as described above are to be followed. Additional assessments of plasma ammonia levels, amino acid 
profiles, or any other biomarker to assess subject safety and clinical status may be performed, at the 
discretion of the investigator and as clinically indicated. Learnings from this study will allow for the 
development of a more standardized protocol for tapering ammonia scavenger medications in future 
studies of DTX301. 
3.2.5 
Modification of Dietary Restrictions 
Patients with OTC deficiency typically have a personalized dietary regimen, which encompasses 
protein-restriction adapted to their metabolic and clinical status to optimize the management of their 
disease.  
Subjects will receive a prescribed diet (grams of protein per 24 hours) on Day 0 of the study and this 
diet will be reviewed at Weeks 6, 12, 24, and 52. Dietary protein intake by the subject between visits 
and dietary restrictions will be reviewed at each visit (Section 8.7.2 and Table 15-1).   
Modification of baseline protein-restricted diet cannot occur at the same time and/or visit as 
modification of baseline ammonia scavenger therapy. Once medications or diet are adjusted or 
discontinued, the subject must demonstrate good metabolic control prior to adjustments in the other 
type of baseline treatment. During periods of adjustment to baseline treatment, subjects will be 
closely monitored. 
Changes to baseline treatment cannot occur while the subject is treated with corticosteroids or within 
a 2-week period of completing a corticosteroid taper. 
At any time after protein-restricted diet has been modified or fully liberalized, reinstitution of 
restrictions may take place based on the subject’s clinical and metabolic status and under evaluation 
of the investigator. If a subject successfully discontinues alternate pathway medication or diet it may 
be necessary to restart standard of care therapy during a time of increased metabolic demand, such as 


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intercurrent viral infection, treatment with steroids, hyperammonemia, or hyperammonemic crisis 
(Section 3.2.6). 
3.2.6 
Occurrence of Hyperammonemia and Hyperammonemic Crisis (HAC) 
Consistent with the Urea Cycle Disorders Consortium (UCDC), we have defined hyperammonemic 
crisis (HAC) in this study as an episode of signs and symptoms associated with hyperammonemia 
(such as frequent vomiting, nausea, headache, lethargy, irritability, combativeness, and somnolence), 
with documented elevated ammonia levels (≥ 100 µmol/L) and requiring medical intervention [Kent 
and Holt 2017; Longo and Holt 2017; Diaz 2019]. 
On-study management of hyperammonemia plasma level or hyperammonemic crises may include, 
but is not limited to, intravenous hydration, discontinuation of all dietary protein intake, increase in 
ammonia scavenger therapy, hemodialysis in addition to treatment of underlying inciting illness or 
event (eg, acute infection, sepsis, bleeding, drug-related, etc.). Comprehensive, internationally 
accepted guidelines for management of urea cycle disorders are recommended [Häberle 2012; 
Häberle 2019].  
Because there is a wide spectrum of presentation and severity of symptomatic hyperammonemia 
events, investigator judgment needs to be exercised and each subject’s management individualized 
(Section 3.2.4, Section 8.3.2). 
3.2.7 
Safety Stopping Criteria 
Enrollment will be stopped, and the regulators will be notified if, at any time during the study, any of 
the following occur: 
• 
Death of a subject following administration of DTX301 
• 
An event with an intensity ≥ Grade 3 (according to the Common Terminology Criteria for 
Adverse Events (CTCAE) [Section 9.1.3]), but excluding hyperammonemic crises 
(Section 3.2.6), develops following administration of DTX301 
• 
Occurrence of a hepatic malignancy following administration of DTX301 
Following DMC review when a stopping rule is met, if the decision is to restart enrollment, a 
substantial amendment will need to be approved by the regulatory authority. 


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Abnormal clinically significant laboratory values (clinical chemistry, plasma ammonia, hematology, 
urinalysis, and coagulation panel) as assessed by the investigator will be considered AEs. Laboratory 
values that meet any of the above criteria will result in a pause in enrollment until the DMC reviews 
the data and provide a recommendation for subsequent study conduct. 
Any event that meets the above criteria will be reported immediately (within 24 hours) as outlined in 
Section 9.1.2.2 and the appropriate page(s) in the electronic case report form (eCRF) must be 
completed. Enrollment and dosing will be temporarily suspended until the situation can be assessed 
and risks to the subjects mitigated. The DMC will meet on an ad hoc basis if an investigator reports 
an AE/SAE that meets any of the study stopping criteria to review and assess the event. If study 
enrollment is suspended, all subjects who have been enrolled will remain in the study and will 
continue to be monitored through their completion or withdrawal from the study. 
3.2.8 
End of Study 
Subjects who complete all visits up to and including the Week 52 visit will have completed the study. 
Subjects who discontinue early will be asked to return for an early withdrawal visit, where all safety 
assessments should be performed (Table 15-1). Subjects with any ongoing AEs at this visit will 
continue to be monitored as outlined in Section 9.1.5. After completion of this study, subjects will be 
asked to enroll in a 4-year extension study to evaluate the long-term (a total of 5 years after dosing) 
safety and efficacy of DTX301. 
4 
Subject Selection 
Subjects will be assigned to study treatment only if they meet all of the inclusion criteria and none of 
the exclusion criteria. 
4.1 
Inclusion Criteria 
Each subject must meet all of the following criteria at Screening to be enrolled in this study: 
1. Willing and able to provide written informed consent. 


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2. Males and females ≥ 18 years of age with documented diagnosis of late-onset (defined as first 
manifestation of signs and symptoms at > 30 days of age) OTC deficiency, confirmed via 
enzymatic, biochemical, or molecular testing. This may include identification of a pathogenic 
mutation, via pedigree analysis, liver OTC activity that is < 20% of normal activity, or 
elevated urinary orotate (> 20 µmol/mmol creatinine) after an allopurinol challenge test 
[Tuchman 2008a]. 
3. Documented history of ≥ 1 symptomatic hyperammonemia event with ammonia 
≥ 100 µmol/L. 
4. Subject's OTC deficiency is stable as evidenced by either a) no clinical symptoms of 
hyperammonemia OR b) plasma ammonia level < 100 µmol/L within the 4-week period 
preceding the Screening visit. 
5. Subject’s plasma ammonia level on Day 1 (predose) is < 100 µmol/L, for patients who 
historically maintain normal ammonia levels, and the subject is clinically stable; OR subject’s 
plasma ammonia level on Day 1 (predose) is < 200 µmol/L, for patients who historically are 
not able to fully control ammonia levels with baseline management, and the subject is 
clinically stable. If the Day 1 (predose) ammonia level is inconsistent with the subject’s 
clinical status, the ammonia level may be repeated to ensure accurate results.  
6. On ongoing daily stable dose of ammonia scavenger therapy for ≥ 4 weeks. 
7. No known allergic reaction to any component of DTX301. 
8. Willing and able to comply with study procedures and requirements, including periodic 
inpatient hospitalizations, frequent blood draws, and urine collections over a 24-hour period. 
9. Hematology and coagulation panel results are within the normal range or, if outside the 
normal range, deemed not clinically significant in the opinion of the investigator. 
10. Males and all females of childbearing potential must be willing to use effective contraception 
at the time of administration of gene transfer and for the 52 weeks following administration of 
DTX301 to prevent the potential transmission of the AAV vector. For male subjects, 
appropriate contraceptive methods include the use of a condom with spermicide. For female 
subjects, appropriate contraceptive methods include the use of a condom with spermicide plus 
at least 1 of the following: 
a. 
Oral contraceptives, other hormonal contraceptives (vaginal products, skin patches, or 
implanted or injectable products), or mechanical products such as an intrauterine device; 
b. 
Use of a diaphragm or cervical/vault cap; 


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c. 
Previous female sterilization (surgical bilateral oophorectomy [with or without 
hysterectomy] or tubal ligation) at least 6 weeks prior to DTX301 administration. In case 
of an oophorectomy alone, the reproductive status of the subject must have been 
confirmed by follow-up hormone level assessment. 
NOTE: Abstinence is an acceptable form of birth control; however, appropriate contraception 
must be used if the subject becomes sexually active. Abstinence is defined as sexual inactivity 
consistent with the preferred and usual lifestyle of the subject. Periodic abstinence (calendar, 
symptothermal, post-ovulation methods), withdrawal (coitus interruptus), spermicides only, 
and lactational amenorrhea methods are not acceptable methods of contraception. A condom 
with spermicide is required to be used by all sexually active vasectomized males in the study 
in order to prevent potential transmission of the vector via seminal fluid. 
NOTE: Females of childbearing potential are defined as all females physiologically capable of 
becoming pregnant, unless they are using highly effective methods of contraception during for 
the duration of the study. 
Females are considered post-menopausal and not of childbearing potential if they have had 
12 months of natural (spontaneous) amenorrhea with an appropriate clinical profile (eg, age 
appropriate, history of vasomotor symptoms) or have had surgical bilateral oophorectomy 
(with or without hysterectomy) or tubal ligation at least 6 weeks prior to enrollment. In the 
case of oophorectomy alone, only when the reproductive status of the woman has been 
confirmed by follow up hormone level assessment is she considered not of childbearing 
potential. 
4.2 
Exclusion Criteria 
Subjects who meet any of the following criteria at Screening will be excluded from the study: 
1. At Screening or Baseline (Day 0), plasma ammonia level ≥ 100 µmol/L for patients who 
historically maintain normal ammonia levels; OR plasma ammonia level ≥ 200 µmol/L for 
patients who historically are not able to fully control ammonia levels with baseline 
management; OR signs and symptoms of hyperammonemia, with documented elevated 
ammonia level, during the 4-week period preceding Day 0. If the ammonia level is 
inconsistent with the subject’s clinical status, the ammonia level may be repeated to ensure 
accurate results. 
2. Liver transplant, including hepatocyte cell therapy/transplant. 


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3. History of liver disease as evidenced by any of the following: portal hypertension, ascites, 
splenomegaly, esophageal varices, hepatic encephalopathy, or a liver biopsy with evidence of 
stage 3 fibrosis. 
4. Significant hepatic inflammation or cirrhosis as evidenced by imaging or any of the following 
laboratory abnormalities: alanine aminotransferase (ALT) or aspartate aminotransferase > the 
upper limit of normal (ULN), total bilirubin > 1.5 × ULN, alkaline phosphatase > 2.5 × ULN. 
5. Serum creatinine > 2.0 mg/dL. 
6. Evidence of active hepatitis B virus (HBV) or hepatitis C virus (HCV) infection, documented 
by current use of antiviral therapy for HBV or HCV or by hepatitis B surface antigen (HBsAg) 
or HCV RNA positivity. NOTE: Subjects with a history of HCV infection must have 
documentation of 2 negative viral assays by polymerase chain reaction (PCR), collected at 
least 6 months apart, to be considered negative for HCV. Subjects with a history of HCV 
infection who test positive for HCV RNA at Screening can be rescreened once, after they have 
been treated and have documentation of at least 2 negative samples collected at least 6 months 
apart. 
7. History of human immunodeficiency virus (HIV) infection AND any of the following: 
CD4+ cell count < 350 cells/mm3, change in antiretroviral therapy regimen within 6 months 
prior to Day 0, or plasma viral load > 200 copies/mL, documented on 2 separate occasions, as 
measured by PCR. 
8. Active infection (viral or bacterial). 
9. Anti-AAV8 neutralizing antibody titer ≥ 1:5. 
10. Participation (current or previous) in another gene transfer study. 
11. Participation in another investigational medicine study within 3 months of Screening. 
12. History of a malignancy for which the subject has received treatment in the past 2 years except 
for prostate cancer treated with watchful waiting or surgically removed non-melanoma skin 
cancer. 
13. Has a positive serum pregnancy test at Screening (females of childbearing potential only), a 
positive urine pregnancy test at Baseline (Day 0; females of childbearing potential only), or is 
nursing. 
14. Has any other significant medical condition that the investigator feels would be a risk to the 
subject or would impede the study. 


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5 
Screening and Randomization Procedures 
5.1 
Subject Screening 
All potential subjects will sign an informed consent form (ICF) before any study procedures or 
assessments are performed or initiated (Section 11.3). Subjects will have the opportunity to have any 
questions answered before signing the ICF. All questions raised by the subject must be addressed 
before the investigator also signs the ICF. A copy of the signed ICF will be given to the subject. 
Subjects will be administered [1-13C]sodium acetate orally. Blood samples for determination of 
ureagenesis will be collected, via an indwelling catheter, before dosing (time 0) and at approximately 
0.5, 1, 1.5, 2, 3, and 4 hours after dosing with [1-13C]sodium acetate. During Screening, assessment of 
rate of ureagenesis may be repeated if discrepant with a subject’s clinical status and severity. 
Prior to the start of DTX301 infusion, the study site must confirm that the subject’s plasma ammonia 
level on Day 1 (predose) is < 100 µmol/L for patients who historically maintain normal ammonia 
levels, and the subject is clinically stable; OR the subject’s plasma ammonia level on Day 1 (predose) 
is < 200 µmol/L, for patients who historically are not able to fully control ammonia levels with 
baseline management, and the subject is clinically stable. If the subject is deemed clinically unstable, 
dosing with DTX301 will be held, and the subject can be rescreened once the subject is determined to 
be clinically stable, with repeat of relevant assessments or rescreened at a later date (Section 3.2.1). 
Subjects with a history of HCV infection who test positive for HCV RNA at Screening can be 
rescreened once, after they have been treated and have documentation of at least 2 negative samples 
collected at least 6 months apart. NOTE: To be eligible to participate in the study, subjects must have 
2 negative HCV viral assays by PCR at least 6 months apart. 
Study sites will maintain documentation of all potential subjects screened for inclusion in the study. If 
a subject is excluded from the study, the reasons for exclusion will be documented in the subject's 
source documents and on the screening log. 
5.2 
Subject Randomization 
This is an open-label study; 3 subjects will be enrolled into Cohort 1 and then, sequentially, into 
cohorts of a minimum of 2 to 3 subjects each, up to Cohort 3. Dosing of additional subjects in 
expansion of Cohort 3, and initiation of Cohort 4 (Dosing Process Optimization) may occur in 
parallel (Section 3.1) with at least 1 male subject assigned to each.  


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6 
Study Treatment 
6.1 
Identity of DTX301 
6.1.1 
Description of DTX301 
DTX301 is a nonreplicating, self-complementary, recombinant AAV8 vector that contains a 
codon-optimized, wild-type human OTC coding sequence. DTX301 demonstrates thermal stability, 
which is a general property of AAV and parvoviruses. DTX301 is supplied as a slightly 
 
 DTX301 is a 
homogeneous, monodisperse solution that is clear and colorless without visible particulates. 
6.1.2 
Components Used for Manufacturing DTX301 
 
  
 
 
 
 
 
 
 
. For additional information, 
please refer to the DTX301 investigator’s brochure. 
6.2 
Management of Clinical Supplies 
The study site will be provided supplies required for the infusion of DTX301. 
6.2.1 
Packaging and Labeling 
Each vial of study product provided to study sites will contain 1 mL of DTX301 frozen in 2 mL 
sterile glass vials with a primary label on the vial. Study product will have secondary packaging with 
a secondary label. The primary label meets all requirements for blister and small packaging units and 
will contain a unique identifier. The secondary label will contain required text for all countries 
participating in the study and will also contain a unique identifier. Secondary labeling will appear in 
the appropriate language for the country supplied. 


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6.2.2 
Storage of Study Product 
6.2.2.1 
Storage of DTX301 
DTX301 must be stored in a secure freezer at a controlled temperature at or below 
C. The study 
site is to maintain a daily log documenting the temperature. 
6.2.3 
Study Product Accountability 
The investigator or designated personnel will maintain accurate records of receipt of all study product 
(DTX301), including dates of receipt. In addition, accurate records will be kept regarding when and 
how much study product is dispensed and used by each subject in the study. Reasons for departure 
from the expected dispensing regimen must also be recorded. At the completion of the study, all study 
product will be reconciled and retained or destroyed according to instructions provided by the 
sponsor. 
6.2.4 
Transmission of Infectious Agents 
Recombinant AAV vectors are nonreplicative and are not expected to pose a risk of transmission. 
However, all sexually active subjects must use approved contraception from the time of DTX301 
dosing and for 52 weeks following administration (Section 4.1). All subjects enrolled in the study 
should be encouraged to discuss the use of approved contraception with his or her partner in order to 
prevent possible transmission of vector via seminal or vaginal fluid. The study product and 
posttreatment study samples should be handled using standard universal precautions. 
6.2.5 
Exposure to Radiation 
Carbon-13 is a naturally occurring, stable isotope of carbon that emits no radioactivity, has no known 
adverse biological effects, and is safe to use in children and adults [Koletzko 1997; Tuchman 2008b].  
Detailed instructions for dose preparation and administration of [1-13C]sodium acetate are provided in 
the ureagenesis manual. 
 


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6.3 
Treatment Schedule and Administration 
6.3.1 
Administration of [1-13C]Sodium Acetate 
Subjects will be administered 
 [1-13C]sodium acetate dissolved in 60 mL of 
water at the time points specified in the Schedule of Events (Table 15-1). 
The dose of [1-13C]sodium acetate administered will be calculated using the subject’s weight recorded 
at Screening. Prior to oral administration, calculations will be checked by the study site pharmacist 
and a member of medical personnel charged with administration of [1-13C]sodium acetate. 
The subject’s plasma ammonia level should be < 100 µmol/L or within the range of historical 
ammonia levels obtained when the subject was clinically stable in order to receive [1-13C]sodium 
acetate (Section 8.2.4.1; Section 4.1). If the ammonia level is inconsistent with the subject’s clinical 
status, the ammonia level may be repeated to ensure accurate results. If the subject is deemed 
clinically unstable, administration of [1-13C]sodium acetate will be held until the subject is 
determined to be clinically stable. 
Subjects may experience a temporary, mildly unpleasant salty and/or acidic taste from the sodium 
acetate component of the compound. The study site must be equipped with emergency resuscitation 
capabilities. Any event that is considered an AE associated with the administration of [1-13C]sodium 
acetate (Section 9.1.1) should be recorded in the appropriate page of the eCRF (Section 9.1.2). 
Sodium acetate is the sodium salt of acetic acid, a naturally occurring metabolite. Sodium acetate is a 
commonly used food additive (E 262).  
Detailed instructions for dose preparation and administration of [1-13C]sodium acetate are provided in 
the ureagenesis manual. 
6.3.2 
Administration of DTX301 
Subjects will receive a single, peripheral IV infusion of DTX301, administered by qualified study 
personnel as designated by the investigator (Table 15-1). The dose will be determined by the cohort 
and candidate dose (Section 3.1). 
The dose of DTX301 to be administered will be calculated using the subject’s weight recorded at 
Screening. The subject’s weight will be verified prior to administration of DTX301 to ensure that 
their current weight is within 10% of their screening weight. NOTE: Any subject weighing > 100 kg 
(> 220 lb) will be dosed as if his or her weight is 100 kg. Prior to infusion, all infusion bag labels will 


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be checked by the study site pharmacist and a minimum of 2 medical personnel charged with 
administration of DTX301. NOTE: Study product should not be prepared for infusion until the 
subject’s plasma ammonia level on Day 1 is confirmed to be less than 100 µmol/L or within the range 
of historical ammonia levels obtained when the subject was clinically stable (Section 4.1). 
The study site must be equipped with emergency resuscitation capabilities. On Day 1, an IV catheter 
will be inserted into a peripheral vein and flushed with saline.  
Detailed instructions for dose preparation and subsequent infusion of DTX301 are provided in the 
pharmacy manual. 
6.3.3 
Treatment Compliance 
[1-13C]sodium acetate will be administered orally at the study site and observed by qualified 
personnel. The dose and time of administration will be recorded in the subject’s eCRF. Adherence to 
baseline ammonia scavenger medication regimens and modifications to ammonia scavenger 
medication regimens (Section 3.2.4) and protein-restricted diet (Section 3.2.5) is also considered 
treatment compliance.  
DTX301 will be administered at the infusion center via a single IV infusion administered by qualified 
personnel. The dose, start time, stop time, and volume of infusion will be recorded in the subject’s 
eCRF. 
6.4 
Prior and Concomitant Therapy 
Use of all prior and concomitant medications will be recorded in the subject’s eCRF. The minimum 
requirement is that the drug name, the dates of administration, and the reason for use are to be 
recorded. This will include all prescription drugs, herbal products, vitamins, minerals, and 
over-the-counter medications. Any changes in concomitant medication use will also be recorded in 
the subject’s eCRF. 
6.4.1 
Permitted Medications 
The use of permitted medications (date, dosage, reason for therapy) will be recorded on the 
concomitant medication page in the eCRF. 
If a subject starts a new medication, including medications to alleviate complications associated with 
OTC deficiency and herbal supplements, it should be discussed with the investigator. 


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Any concomitant medication deemed necessary for the welfare of the subject during the study may be 
given. It is the responsibility of the investigator to ensure that details regarding the medication are 
recorded in full in the eCRF. 
6.4.2 
Prohibited Medications 
Use of any of the following medications is prohibited, unless the investigator feels these medications 
are medically indicated. If medically indicated, the use of prohibited medications (date, dosage, 
reason for therapy) will be recorded on the concomitant medication page in the eCRF: 
• 
Another investigational product to treat OTC deficiency; 
• 
Another gene therapy product; or 
• 
Any other medication currently under investigation. 


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7 
Withdrawal of Subjects From the Study 
7.1 
Study Withdrawal 
Subjects may withdraw from the study at any time and for any reason without prejudice to their future 
medical care by the investigator or at the study site. Any subject who withdraws consent to participate 
in the study will be removed from further treatment and/or study observation immediately upon the 
date of request. 
The investigator must record the reason for withdrawal on the relevant page in the eCRF. The reason 
for withdrawal may include the following:  
1. Withdrawal of consent 
2. Administrative decision by the investigator or the sponsor 
3. Ineligibility 
4. Significant protocol deviation 
5. Subject noncompliance 
6. Adverse event 
If a subject is withdrawn due to an AE, the investigator will arrange for the subject to have follow-up 
visits until the AE has resolved or stabilized (Section 9.1.5).  
If a subject requests or decides to withdraw from the study, all efforts will be made to complete and 
report the observations as thoroughly as possible up to the date of withdrawal, and an early 
withdrawal visit will be performed. 
7.2 
Subject Replacement 
If a subject withdraws from the study after receiving DTX301, the subject will not be replaced. 
Subjects who withdraw from the study after signing the ICF, but before receiving DTX301, will be 
replaced and the replacement subject will be sequentially assigned to treatment with a new subject 
identification number. 


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8 
Study Assessments and Procedures 
8.1 
Efficacy Assessments 
Planned time points for all efficacy measurements in the study are listed in Table 15-1.  
8.1.1 
Ureagenesis 
The change from baseline in the rate of ureagenesis will be assessed at specified time points 
(Table 15-1). Planned time points for the collection of blood samples to determine the rate of 
ureagenesis are provided in Section 8.3.1. Subjects will fast for at least 6 hours, including liquids 
containing protein, sugar or carbonate, prior to administration of [1-13C]sodium acetate. After dosing, 
subjects will continue to fast for at least 4 hours. Water is allowed ad libitum. During Screening, 
assessment of rate of ureagenesis may be repeated if discrepant with subject’s clinical status and 
severity. 
Details for the preparation and shipment of samples are included in the ureagenesis manual and the 
laboratory manual. 
8.1.2 
Plasma Ammonia Area Under the Curve from Time Zero to 24 Hours 
The change from baseline in plasma ammonia (AUC0-24) will be assessed at specified time points 
(Table 15-1). Planned time points for the collection of blood samples to determine plasma ammonia 
(AUC0-24) are provided in Section 8.3.2. Two samples will be collected at each time point for the 
plasma ammonia (AUC0-24) determination. One sample will be sent to the local laboratory and 
1 sample will be sent to the central laboratory. Details for the preparation and shipment of samples 
are included in the laboratory manual. 
8.2 
Safety Assessments 
Planned time points for all safety assessments are listed in the Schedules of Events (Table 15-1 and 
Table 15-2). Safety will be assessed based on AEs, SAEs, complete and targeted physical 
examination findings, vital sign measurements, ECG results, clinical laboratory assessments (clinical 
chemistry, plasma ammonia, hematology, urinalysis, and coagulation panel), viral shedding, 
measurement of neutralizing antibody titer to AAV8, measurement of AAV8 binding antibodies, and 
measurement of anti-OTC antibodies. 


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8.2.1 
Physical Examination 
A complete or targeted physical examination will be performed at the time points specified in the 
Schedule of Events (Table 15-1). 
A complete physical examination will include assessments of the head, eyes, ears, nose, and throat; 
skin; and the endocrine metabolic, neurological, respiratory, cardiovascular, gastrointestinal, and 
musculoskeletal systems. 
A targeted physical examination will include assessment of the skin and the respiratory, 
cardiovascular, and gastrointestinal systems. 
Physical examination findings will be captured on the appropriate page in the eCRF. 
8.2.2 
Vital Sign Measurements 
Vital sign measurements will be made at the time points specified in the Schedule of Events 
(Table 15-1). During the study, vital sign measurements are to be collected before any stimulating or 
anxiety-provoking procedures (eg, phlebotomy). Vital sign measurements will include heart rate, 
blood pressure (systolic and diastolic), and respiratory rate. Temperature will be included on days that 
the [1-13C] sodium acetate is administered (Screening, all inpatient visits and Week 20 outpatient 
visit. Height (at the Screening visit only) and weight will also be recorded.   
• 
On Day 0, weight will be measured to ensure that the weight is within 10% of the screening 
weight used to calculate the dose of DTX301. Subjects with a confirmed change in weight 
that is > 10% from Screening should be further evaluated to exclude the presence of an acute 
condition or illness; if a benign explanation for the weight change is identified and 
documented, DTX301 can be given and dosed using the weight obtained on Day 0. NOTE: 
Any subject weighing > 100 kg (> 220 lb) will be dosed as if his or her weight is 100 kg. 
• Vital signs should be measured with the subject having rested for at least 5 minutes 
beforehand. It is preferred that the measurement be late with the subject rested, rather than 
on-time with the subject not sufficiently rested. If the subject is not sufficiently rested, this 
needs to be stated in the source documents. 
• On Day 1, vital signs will be measured at predose, approximately 5 minutes, and 
0.5 (±5 minutes), 1 (±5 minutes), 2, 4, 6, and 8 hours (±15 minutes) after the start of DTX301 
infusion. Vital signs will also be measured at approximately 22 hours (±1 hour) after the start 
of infusion, prior to subject discharge. 


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• It is acceptable for heart rate to be captured from the 12-lead ECG (Section 8.2.3). 
Vital sign measurements will be recorded in the appropriate page in the eCRF. The medical monitor 
should be notified of any clinically significant changes or abnormal value in vital sign measurements 
(Section 9.1.2).  
8.2.3 
Electrocardiograms 
An ECG will be performed at the time points specified in the Schedule of Events (Table 15-1). 
• 
A single 12-lead ECG will be obtained at Screening, on Day 0 (baseline), at approximately 
1 hour (±15 minutes) after the start of infusion on Day 1, and at Week 52, using an ECG 
machine that automatically calculates the heart rate and measures PR, QRS, QT, and 
corrected QT intervals.  
Twelve-lead ECGs should be measured with the subject having rested for at least 5 minutes 
beforehand. It is preferred that the measurement be late with the subject rested, rather than on-time 
with the subject not sufficiently rested. If the subject is not sufficiently rested, this needs to be stated 
in the source documents. Electrocardiogram results will be recorded in the appropriate page in the 
eCRF. 
8.2.4 
Clinical Laboratory Analyses 
Laboratory tests, including LFTs and coagulation panel, will be closely monitored throughout the 
duration of the study. At any point between scheduled visits, additional, unscheduled assessment for 
LFTs, plasma ammonia, or any other biomarker to assess subject safety and clinical status may be 
performed, at the discretion of the investigator.  
Investigators will receive flagged notification of any laboratory values that are outside of the normal 
range. Any abnormal laboratory test results (clinical chemistry, plasma ammonia, hematology, 
urinalysis, coagulation panel, or other laboratory parameters), including those that worsen from 
baseline or are felt to be clinically significant in the medical and scientific judgment of the 
investigator, are to be recorded as AEs or SAEs (Section 9.1.2). 
However, any clinically significant safety assessments that are associated with OTC deficiency are 
not to be reported as AEs, unless they are judged by the investigator to be more severe than expected 
for the subject’s condition. 


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All laboratory tests with results that are significantly abnormal during participation in the study 
should be repeated until the values return to normal or baseline. If such values do not return to normal 
within a period judged reasonable by the investigator, the etiology should be identified, and the 
sponsor notified. 
Samples of blood, urine, saliva, and stool will be collected for study assessments. Any samples 
remaining at the end of the study may be stored for up to 15 years and analyzed to better understand 
the effect of DTX301 on OTC deficiency or other UCDs. The choice to allow retention and future 
analysis will be optional. 
8.2.4.1 
Clinical Laboratory Parameters 
The clinical laboratory parameters to be measured are listed in Table 8-1. Samples are to be collected 
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Table 8-1 
Clinical Laboratory Parameters 
Clinical chemistrya: 
Sodium, potassium, chloride, carbon dioxide, blood urea nitrogen, creatinine, glucose, 
calcium, phosphate, magnesium, albumin, total protein, creatine kinase, bilirubin (total, 
direct, and indirect), ALT, AST, ALP, gamma-glutamyltransferase, and lactate 
dehydrogenase 
Spot ammonia 
Plasma ammonia (STAT sample, local laboratory)b 
Hematology: 
Complete blood count with differential 
Urinalysis: 
Specific gravity, pH, glucose, protein, blood (by dipstick), ketones (by dipstick), and 
microscopic examination (if blood or protein is found) 
Urine chemistry: 
Orotic acid 
Coagulation panel: 
PT/INR, aPTT 
Amino acid panel: 
alanine, α-amino-butyric acid, arginine, asparagine, aspartic acid, citrulline, cystine, 
ethanolamine, glutamic acid, glutamine, glycine, histidine, homocysteine, 
hydroxyproline, isoleucine, leucine, lysine, methionine, ornithine, phenylalanine, proline, 
serine, taurine, threonine, tryptophan, tyrosine, and valine 
Otherc: 
HBV surface antigen (HBsAg), HCV RNA, HIV  
Abbreviations: ALP, alkaline phosphatase; ALT, alanine aminotransferase; aPTT, activated partial thromboplastin time; 
AST, aspartate aminotransferase; HBV, hepatitis B virus; HCV, hepatitis C virus; HIV, human immunodeficiency 
virus; LFT, liver function test; PT/INR, prothrombin time/international normalized ratio. 
a. 
Through Week 12, one sample for LFTs is collected as part of clinical chemistry and sent to the central laboratory for 
analysis. A second sample for LFTs only is collected and sent to the local laboratory (STAT sample). 
b. 
Special handling is required for plasma ammonia. At Screening, prior to neuropsychological testing and prior to dosing 
with [1-13C]sodium acetate, a sample will be collected to confirm the subject’s plasma ammonia level. The subject’s 
plasma ammonia level should be < 100 µmol/L or within the range of historical ammonia levels obtained when the 
subject was clinically stable (Section 4.1). If the ammonia level is inconsistent with the subject’s clinical status, the 
ammonia level may be repeated to ensure accurate results. If the subject is deemed clinically unstable, the assessments 
will be held until the subject is determined to be clinically stable. (Table 15-1). The study site may use the local 
laboratory sample from time 0 (prior to neuropsychological testing on Day 0 and at Week 52), and time 24 hour (prior 
to [1-13C]sodium acetate administration on Day 1 and at Weeks 6, 12, 24, and 52) from the plasma ammonia AUC0-24 
to confirm the subject’s plasma ammonia (Section 8.3.2). 
c. 
To be collected at Screening only. 
 
Details for the preparation and shipment of samples will be provided by the central or specialty 
laboratory. Reference ranges for all parameters will be provided to the study site by the central or 
specialty laboratory. 
A laboratory parameter may be repeated if there is any concern about the values obtained.  
At any time after initiation of a prophylactic corticosteroid regimen, additional assessments of plasma 
ammonia levels, amino acid profiles, or any other biomarker to assess subject safety and clinical 
status may be performed, at the discretion of the investigator and as clinically indicated. 
If additional nonprotocol-specified laboratory assessments are performed at the study site’s local 
laboratory and result in a change in subject management or the results are considered clinically 


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significant by the investigator (eg, SAE, AE, or dose modification), the results must be captured and 
sent to the sponsor along with other study data as defined in Section 9.1.2. 
8.2.4.1.1 
Elevation of Liver Function Tests 
In clinical studies with AAV-mediated gene transfer, a transient rise in liver aminotransferases and 
concurrent decline in transgene expression has been observed [Manno 2006; Nathwani 2011a; 
Nathwani 2014]. This has been hypothesized to be due to the activation of capsid-specific cytotoxic 
T lymphocytes and destruction of transduced liver cells [Mingozzi 2007]. However, in mice, T-cells 
activated against AAV capsid were not able to target and eliminate transduced hepatocytes 
[Wang 2007; Li C 2007; Li H 2007; Siders 2009] unless the transduced hepatocytes co-expressed the 
wild-type AAV capsid protein [Li C 2007].  
The inability to reproduce the observed effects in animal models has made it difficult to assess the 
validity of the hypothesis or to develop strategies to overcome or minimize aminotransferase 
elevations. Despite a lack of clear resolution that activation of cytotoxic T lymphocytes leads to a 
reduction in transgene expression from hepatocytes, appropriate precautions have been incorporated 
into this study. The use of oral steroids is allowed if a subject experiences elevations in liver 
aminotransferases.  
Liver function tests will be assessed as part of clinical chemistry (Section 8.2.4.1) at the time points 
specified in the Schedule of Events (Table 15-1 and Table 15-2). Liver function tests will be assessed 
at a central and local (STAT) laboratory approximately every 4 days through Week 12, which will 
allow for a rapid detection of any elevations following administration of DTX301. If a subject 
experiences an increase in liver function tests following treatment with DTX301, the investigator 
should consider the initiation of steroid treatment as outlined in Section 8.2.4.1.2, and taking into 
account dosing Cohort (Cohort 1-3). The event should be recorded as an AE or SAE, as defined in 
Section 9.1.2, on the appropriate pages in the eCRF if it is felt to be clinically significant in the 
medical and scientific judgment of the investigator. 
Cohort 4 (Dosing Process Optimization) will utilize an alternative regimen of corticosteroids, aiming 
at prophylaxis of AAV-mediated, transient rises in liver aminotransferases as outlined in 
Section 8.2.4.1.2. The subject must be assessed as clinically and metabolically stable to initiate the 
prophylactic corticosteroid regimen. 


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8.2.4.1.2 
Treatment for Possible Vector-Induced Hepatitis 
The investigator, in conjunction with the Ultragenyx Pharmaceutical Inc. medical lead will consider 
starting oral steroid treatment, per protocol, for possible vector-induced hepatitis when a subject’s 
ALT is greater than the ULN and is considered by the investigator to be related to treatment with 
DTX301. The subject must be assessed as clinically and metabolically stable, and intercurrent 
illnesses (eg, viral infection) or concomitant medications known to affect transaminases, be excluded.  
Repeat liver function testing for confirmation of results should be considered to inform the use of 
steroid treatment. If repeat testing is deemed necessary, every effort should be made to repeat the 
testing within 24 hours from receipt of test results indicating elevated ALT.  
At any point between scheduled visits, additional, unscheduled assessment for LFTs, plasma 
ammonia, or any other biomarker to assess subject safety and clinical status may be performed, at the 
discretion of the investigator. 
Changes to baseline treatment (ie, ammonia scavenger medications and protein-restricted diet) 
cannot occur while the subject is treated with corticosteroids or within a 2-week period of 
completing a corticosteroid taper. 
Based on available evidence, it is expected that vector-induced hepatitis will be self-limiting. 
Therefore, oral prednisone (or prednisolone) will be used per the American Association for the Study 
of Liver Disease guidelines, with a slight modification in Cohorts 1 to 3:  
• 
Week 1: prednisone 60 mg/day 
• 
Week 2: prednisone 40 mg/day 
• 
Week 3 and Week 4: prednisone 30 mg/day 
• 
Week 5 and thereafter: prednisone will be tapered by 5 mg/week until liver enzymes return to 
baseline levels. The use of prednisone will be recorded on the appropriate page in the eCRF. 


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Cohort 4 (Dosing Process Optimization) will utilize an alternative regimen of corticosteroids, aiming 
at prophylaxis of vector-induced hepatitis. Therefore, oral prednisone (or prednisolone) will be 
initiated before dosing with DTX301, sustained for 4 weeks, followed by tapering as described below. 
Prophylactic corticosteroid regimens are in use for gene transfer therapies [Audentes 2017 
Clinicaltrials.gov identifier: NCT03223194; Abeona Therapeutics 2016 ClinicalTrials.gov identifier: 
NCT02716246].  
• 
At least 5 days prior to dosing: prednisone 60 mg/day 
• 
Study Day 1 (Week 1) through Week 4: prednisone 60 mg/day 
• 
Study Week 5 through Week 8, tapering every 5 days: 
Taper Dose 
Duration 
40 mg/ day 
5 days 
30 mg/day 
5 days 
20 mg/day  
5 days 
10 mg/day 
5 days 
5 mg/day 
5 days 
5 mg every other day  
5 days 
 
At any time after initiation of prophylactic corticosteroid regimen, additional assessments of plasma 
ammonia levels, amino acid profiles, or any other biomarker to assess subject safety and clinical 
status may be performed, at the discretion of the investigator and as clinically indicated. 
Utilization of prednisone (or prednisolone) after dosing and after completion of the prophylactic 
regimen, remains available to all subjects when a subject’s ALT is greater than the ULN and is 
considered by the investigator to be related to treatment with DTX301.The use of prednisone (or 
prednisolone) will be recorded on the appropriate page in the eCRF. 


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8.2.5 
Other Laboratory Parameters 
Where applicable, details for the preparation and shipment of samples are included in the laboratory 
manual. 
8.2.5.1 
Neutralizing Antibodies to Adeno-Associated Virus Serotype 8 
Samples for neutralizing antibodies to AAV8 will be collected at the time points specified in the 
Schedule of Events (Table 15-1) to monitor for a humoral immune response to AAV8. The assay will 
be performed using a research method (a cell-based assay). 
8.2.5.2 
Adeno-Associated Virus Serotype 8 Binding Antibody 
Immunoglobulin G Assay 
Samples for the AAV8 binding antibody immunoglobulin G (IgG) assay will be collected at the time 
points specified in the Schedule of Events (Table 15-1) to monitor for circulating anti-AAV8 
antibodies. The assay will be performed using a research method (enzyme-linked immunosorbent 
assay [ELISA]). 
8.2.5.3 
Anti-Ornithine Transcarbamylase Antibody Assay 
Samples for the anti-OTC antibody assay will be collected at the time points specified in the Schedule 
of Events (Table 15-1) to monitor for circulating anti-OTC antibodies. The assay will be performed 
using a research method (ELISA). 
8.2.5.4 
Viral Shedding 
Saliva, urine, and stool will be collected at the time points specified in the Schedules of Events 
(Table 15-1 and Table 15-2) to monitor for the presence of shed virus. The presence of DTX301 will 
be determined 
. Subjects will be given an appropriate container to collect 
a stool sample at home. Samples for shedding analysis will be collected until the results are negative 
on 3 consecutive occasions for each matrix. 


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8.3 
Pharmacokinetics and Pharmacodynamic Assessments 
8.3.1 
Ureagenesis 
The conversion of the stable isotope [1-13C]sodium acetate to [13C]urea will be determined by gas 
chromatography mass spectrometry [Tuchman 2008b]. Blood samples will be collected in precooled 
heparinized tubes before dosing (time 0) and at approximately 0.5, 1, 1.5, 2, 3, and 4 hours 
(±5 minutes) after [1-13C]sodium acetate is administered orally at Screening, Baseline (Day 1), and 
over time to Week 52 after administration of DTX301 (Table 15-1).
 
. During Screening, 
assessment of rate of ureagenesis may be repeated if discrepant with subject’s clinical status and 
severity. Blood samples will be immediately centrifuged to separate the plasma, which will be stored 
frozen at –70°C until shipped for analysis. Details for the preparation and shipment of samples are 
included in the ureagenesis manual and the laboratory manual. 
8.3.2 
Plasma Ammonia Area Under the Curve from Time Zero to 24 Hours 
The AUC0-24 of plasma ammonia will be determined at Baseline (Day 0) and over time to Week 52 
after administration of DTX301 (Table 15-1). Two samples will be collected at time 0 and at 
approximately 2, 4, 8, 12, 16, 20, and 24 hours (±5 minutes). One sample will be sent to the local 
laboratory (STAT sample) and 1 sample will be sent to the central laboratory. If possible, ad hoc 
AUC0-24 plasma ammonia should be considered if a subject experiences symptomology deemed by 
the investigator to meet the definition of an HAC (Section 3.2.6), driven by the underlying disease or 
at a time of increased metabolic demand, such as intercurrent viral infection, or treatment with 
corticosteroids, and warranting inpatient monitoring based on investigator discretion.  
The subject’s plasma ammonia level should be < 100 µmol/L or within the range of historical 
ammonia levels obtained when the subject was clinically stable (Section 4.1) prior to administering 
the neuropsychological tests or [1-13C]sodium acetate and DTX301 (Day 1 only) (Table 15-1). If the 
ammonia level is inconsistent with the subject’s clinical status, the ammonia level may be repeated to 
ensure accurate results. If the subject is deemed clinically unstable, the assessments will be held until 
the subject is determined to be clinically stable. The study site may use the time 0 and time 24 hour 
plasma ammonia samples to confirm the subject’s plasma ammonia. The samples should be sent to 
the local laboratory (STAT sample) and results available prior to initiating the neuropsychological 
tests or administering [1-13C]sodium acetate and DTX301 (Day 1 only).  
Details for the preparation and shipment of samples are included in the laboratory manual. 


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8.3.3 
Orotic Acid Excretion 
The excretion of orotic acid will be determined over a 24-hour period. Urine samples will be collected 
approximately every 6 hours (× 4) at Baseline (Day 0) and over time to Week 52 after administration 
of DTX301 (Table 15-1). Details for the preparation and shipment of samples are included in the 
laboratory manual. 
8.4 
Quality-of-Life Assessment 
8.4.1 
PROMIS Questionnaire 
Subjects will be asked to complete the Patient-Reported Outcomes Measurement Information System 
(PROMIS) questionnaire (Appendix 15.2.1) on Day 0 (predose) and then at Weeks 6, 12, 24, and 52 
during the study (Table 15-1). NOTE: The PROMIS questionnaire should be completed prior to the 
neuropsychological tests on Day 0 and at Week 52.  
Patient-reported outcomes will be assessed by components of the PROMIS questionnaire, an 
instrument developed in collaboration with National Institutes of Health, which has been designed, 
calibrated, and validated using a large sample size of participants with chronic diseases for use in 
clinical care and research. PROMIS measures may be used as endpoints in clinical studies to assess 
the effectiveness of treatment. The UCD Consortium also uses the PROMIS questionnaire for the 
evaluation of QoL in their Longitudinal Study participants. 
Domains measured by PROMIS include physical, mental, and social well-being; versions of the 
PROMIS instrument include ones specific for adult and pediatric populations as well as for 
parent-proxy reporting for pediatric patients. The adult versions for the following self-reported 
domains will be included in this study [Reeve 2007; PROMIS 2009]: Cognitive Function, Anxiety, 
Depression, and Emotional/Behavioral Dyscontrol. 
8.5 
Neuropsychological Tests 
All neuropsychological tests will be administered to English speaking subjects (at a minimum) in a 
nonfasted state. All neuropsychological tests are to be administered by appropriately qualified 
individuals as determined by sponsor or representative. The subject’s plasma ammonia level should 
be < 100 µmol/L (Section 8.2.4.1) or within the range of historical ammonia levels obtained when the 
subject was clinically stable (Section 4.1) in order to perform the neuropsychological tests. If the 
ammonia level is inconsistent with the subject’s clinical status, the ammonia level may be repeated to 
ensure accurate results. The study site may use the time 0 (T 0) plasma ammonia sample (from 


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AUC0-24 plasma ammonia) analyzed by the local laboratory (STAT sample) to determine the subject’s 
plasma ammonia level. The result must be available prior to initiating the tests. If the subject is 
deemed clinically unstable, the neuropsychological tests will be held until the subject is determined to 
be clinically stable. Subjects may request pauses to rest during administration of the 
neuropsychological test battery, but the entire battery should be completed in 1 session. Additional 
details are provided in the neuropsychological section of the manual of operations. 
The neuropsychological assessments have been selected in close consultation with Dr. Susan 
Waisbren and are based on assessments where OTC participants in the UCD Consortium 
Longitudinal Study have shown cognitive deficits thus far (refer to the neuropsychological section of 
the manual of operations for further details). The most informative neuropsychological tests, as 
determined by these Phase 1/2 study data, may be included in further clinical studies with DTX301.  
Neuropsychological deficits, especially in memory and executive functioning, are considered to be 
important aspects of the OTC deficiency condition and have widespread effects on daily functioning 
and relationships. Improving or normalizing plasma ammonia and other blood biomarkers (glutamate 
and glutamine) is hypothesized to potentially improve neuropsychological functioning. Therefore, it 
is important to establish neuropsychological functioning prior to dosing with DTX301 as well as 
evaluate the trajectory of this functioning longitudinally, ideally over several years. During the 4-year 
extension study, subjects will take this same neuropsychological battery of tests every 2 years to 
assess changes over time in motor, executive, and memory function. 
8.5.1 
Intelligence 
Subjects will be asked to complete the Vocabulary and Matrix Reasoning subtests from the Wechsler 
Abbreviated Scale of Intelligence, Second Edition (WASI-II) at Baseline only (Table 15-1). The 
WASI-II provides general measure of cognitive function in subjects aged 6 to 89 years. The 
Vocabulary and Matrix Reasoning subtests provides an accurate, validated assessment of IQ that is 
highly correlated (r=0.86) with results from the Wechsler Adult Intelligence Scale, Fourth Edition 
(WAIS-IV) [Wechsler 2011]. The estimated time needed for completion of the WASI-II is 
30 minutes. 


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8.5.2 
Motor Function 
8.5.2.1 
 
 
 
 
 
 
 
 
8.5.3 
Executive Function 
8.5.3.1 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
8.5.4 
Memory 
8.5.4.1 
 
 
 
 
 
 
 
 
 


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8.6 
Genotyping 
8.6.1 
Ornithine Transcarbamylase Genotyping 
At Baseline, subjects will be asked to provide a single whole-blood sample for OTC genotyping. The 
objective of this research is to provide a background understanding to the etiology of the subject’s 
OTC deficiency and to investigate any relationship between genetic factors and the subject’s response 
to DTX301. The results do not need to be available prior to dosing with DTX301. 
8.7 
Other Assessments 
8.7.1 
Demographic, Medical, and Ornithine Transcarbamylase Deficiency 
History Assessments 
As allowed by local laws and regulations, the following demographic data may be captured on the 
appropriate page in the eCRF: date of birth, sex, race, and ethnicity. 
Medical, medication, and OTC deficiency medical history will be assessed as related to the eligibility 
criteria listed in Section 4.1 and Section 4.2. 
8.7.2 
Ammonia Scavenger Use and Dietary Protein Intake 
The use of ammonia scavenger therapy and dietary protein intake will be reviewed and recorded at 
each visit (Table 15-1).  
Changes to baseline treatment cannot occur until there is evidence of transgene expression reflected 
by continued evidence of metabolic stability with ammonia levels in the normal range or improved 
ammonia control if subjects have a history of ammonia levels above the upper limit of normal and 
supported by improvement in clinical signs and symptoms. The subject must be clinically stable and 
under good metabolic control before changes can be initiated or progressed. The risks of making 
adjustments to baseline treatment on their own, without express guidance from the site, will be 
reinforced with the subject at site visits. 
Changes to baseline treatment cannot occur while the subject is treated with corticosteroids or within 
a 2-week period of completing a corticosteroid taper.  


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Tapering or discontinuation of ammonia scavenger therapy cannot occur at the same time 
and/or visit as modification of protein-restricted diet. At any time after modification and/or 
discontinuation of ammonia scavenger therapy, reinstitution of therapy may take place based on the 
subject’s clinical and metabolic status (elevated ammonia levels, or signs and symptoms consistent 
with hyperammonemia ), and under evaluation of the investigator. 
Subjects will receive a prescribed diet (grams of protein per 24 hours) on Day 0 of the study and this 
diet will be reviewed at Weeks 6, 12, 24 and 52. Dietary protein intake by the subject between visits 
and dietary restrictions will be reviewed at each visit (Table 15-1) and recorded in the source 
documentation. Modification of baseline protein-restricted diet cannot occur at the same time 
and/or visit as modification of baseline ammonia scavenger therapy. At any time after 
protein-restricted diet has been modified or fully liberalized, reinstitution of restrictions may take 
place based on the subject’s clinical and metabolic status and under evaluation of the investigator.  
Once medications or diet are adjusted or discontinued, the subject must demonstrate good metabolic 
control prior to adjustments in the other type of baseline treatment. 
9 
Safety Monitoring and Reporting 
9.1 
Adverse Events and Serious Adverse Events 
Adverse events will be assessed from the time the subject signs the ICF through the end of study/early 
withdrawal visit. 
At every study visit, subjects will be asked a standard nonleading question to elicit any medically 
related changes in their well-being.  
In addition to subject observations, AEs identified from any study data (eg, laboratory values, 
physical examination findings, ECG changes) or identified from review of other documents (eg, 
subject diaries) that are relevant to subject safety will be documented on the AE page in the eCRF. 
9.1.1 
Definitions 
9.1.1.1 
Adverse Events 
The investigator is responsible for reporting all AEs that are observed or reported during the study, 
regardless of their relationship to study product or their clinical significance. 


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An AE is defined as any untoward medical occurrence in a subject enrolled into this study regardless 
of its causal relationship to study product. Subjects will be instructed to contact the investigator at any 
time after the subject signs the informed consent if any signs or symptoms develop. 
A treatment-emergent AE is defined as any event not present before exposure to study product or any 
event already present that worsens in either intensity or frequency after exposure to study product. 
9.1.1.2 
Serious Adverse Events 
An SAE is defined as any event that: 
• 
Results in death 
• 
Is immediately life-threatening 
• 
Requires inpatient hospitalization or prolongation of existing hospitalization.  
• 
NOTE: Hospitalization due to hyperammonemic crisis (HAC [Section 3.2.6]) will be 
considered an SAE. 
• 
NOTE: Nonemergent hospitalizations for subject monitoring in the setting of steroid 
administration for vector-induced hepatitis (Section 8.2.4.1.2) will not be considered an SAE. 
• 
Results in persistent or significant disability/incapacity 
• 
Results in a congenital anomaly/birth defect 
Additionally, important medical events that may not result in death, be life threatening, or require 
hospitalization may be considered SAEs when, based upon appropriate medical judgment, they may 
jeopardize the subject or may require medical or surgical intervention to prevent one of the outcomes 
listed in this definition. Examples of such medical events include allergic bronchospasm requiring 
intensive treatment in an emergency room or at home, blood dyscrasias or convulsions that do not 
result in inpatient hospitalization, or the development of drug dependency or drug abuse. 
9.1.2 
Safety Reporting 
9.1.2.1 
Adverse Events 
All AEs reported or observed during the study will be recorded on the AE page in the eCRF. 
Information to be collected includes drug treatment, dose, event term, time of onset, 
investigator-specified assessment of severity and relationship to study product, corticosteroid 


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regimen, [1-13C] sodium acetate, OTC deficiency, or hyperammonemia, time of resolution of the 
event, seriousness, any required treatment or evaluations, and outcome. Adverse events resulting from 
concurrent illnesses, reactions to concurrent illnesses, reactions to concurrent medications, or 
progression of disease states must also be reported. All AEs will be followed to adequate resolution. 
The Medical Dictionary for Regulatory Activities (MedDRA) will be used to code all AEs.  
Any medical condition that is present at the time that the subject is screened but does not deteriorate 
should not be reported as an AE. However, if the condition deteriorates at any time during the study, 
it should be recorded as an AE. 
9.1.2.2 
Serious Adverse Events 
Any AE that meets SAE criteria (Section 9.1.1.2) or any of the safety stopping criteria (Section 3.2.7) 
must be reported by the study site to PPD Pharmacovigilance (PVG) Department immediately (ie, 
within 24 hours) after the time study site personnel first learn about the event. The study site should 
record all SAE information in the SAE eCRF and submit the report via the electronic data capture 
(EDC) system. An event meeting any of the safety stopping criteria should only be reported as an 
SAE in the EDC system if it meets SAE criteria (Section 9.1.1.2). 
In the event of any fatal or life-threatening SAE, the investigator must immediately inform PPD 
PVG by telephone (Table 9-1) and report the SAE in the EDC system. If, for any reason, it is 
not possible to report the SAE in the EDC system (eg, the EDC system is unavailable), the study 
site should record the SAE on the paper SAE Reporting Form and fax it to PPD PVG 
(Table 9-1). As soon as it is possible, any SAE reported via fax must be entered into the EDC 
system. 
Table 9-1 
PPD PVG Contact Information for SAE Reporting 
Region 
Contact Information 
Rest of World 
Safety hotline: 
 
Safety faxa: 
 
North America 
Safety hotline: 
 
Safety faxa: 
 
Abbreviations: PVG, pharmacovigilance; SAE, serious adverse event. 
a. 
This is the preferred fax number for all regions. The toll-free fax number for North America can be provided upon 
request. 
 


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9.1.2.2.1 
Expedited Reporting 
The sponsor is responsible for reporting serious, unexpected, suspected adverse drug reactions 
(SUSARs) involving the study product(s) to all regulatory authorities and participating investigators 
in accordance with International Council for Harmonisation (ICH) guidelines and/or local regulatory 
requirements, as applicable. It is the responsibility of the investigator or designee to promptly notify 
the local institutional review board (IRB)/independent ethics committee (IEC)/institutional biosafety 
committee (IBC) of all SUSARs involving risk to human subjects.  
As there is no prior clinical experience with DTX301, reference safety information for assessing 
whether an AE is a SUSAR is currently not available. Therefore, any SAE considered related to 
DTX301 will be considered a SUSAR and reported immediately as detailed in Section 9.1.2. The 
SAE should be treated with appropriate supportive and medical care deemed necessary for the 
well-being of the subject. 
9.1.3 
Assessment of Severity/Toxicity 
The severity/toxicity, or intensity, of an AE refers to the extent to which an AE affects the subject’s 
daily activities. The intensity of the AE will be rated as Grade 1, 2, 3, 4, or 5 using the most current 
version of the National Cancer Institute (NCI) CTCAE [NCI CTCAE 2018]. The CTCAE provides 
descriptive terminology that can be used to standardize AE reporting. A severity/toxicity grade is 
provided for each AE term that is grouped by the highest level of MedDRA classification [NCI 
CTCAE 2018]. Specific symptoms and medical conditions have a clinical description for each level 
of severity/toxicity. In the event that an AE occurs during the study that is not captured by the 
CTCAE, the AE should be graded according to the general guidelines outlined in Table 9-2. 


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Table 9-2 
General Guidelines for Grading Events not Captured by the CTCAE 
Grade 
Criteria 
Grade 1: 
Mild; asymptomatic or mild symptoms; clinical or diagnostic observations only; intervention 
not indicated. 
Grade 2: 
Moderate; minimal, local, or noninvasive intervention indicated; limiting age-appropriate 
instrumental ADLa. 
Grade 3: 
Severe or medically significant but not immediately life-threatening; hospitalization or 
prolongation of hospitalization indicated; disabling; limiting self-care ADLb. 
Grade 4: 
Life-threatening consequences; urgent intervention indicated. 
Grade 5: 
Death related to AE. 
Abbreviations: ADL, activities of daily living; AE, adverse event. 
a. 
Instrumental ADL refers to preparing meals, shopping for groceries or clothes, using the telephone, managing money, 
etc. 
b. 
Self-care ADL refers to bathing, dressing and undressing, feeding self, using the toilet, taking medications, and not 
bedridden. 
 
Changes in the severity/toxicity of an AE should be documented to allow an assessment of the 
duration of the event at each level of intensity to be performed. Adverse events characterized as 
intermittent do not require documentation of onset and duration of each episode. 
9.1.4 
Assessment of Causality 
The investigator’s assessment of an AE’s relationship to study product is part of the documentation 
process, but it is not a factor in determining what is or is not reported in the study. If there is any 
doubt as to whether a clinical observation is an AE, the event should be reported. 


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The relationship or association of the study product in causing or contributing to the AE will be 
characterized using the following classification and criteria: 
Unrelated: 
This relationship suggests that there is no association between the study product and 
the reported event. 
Possible: 
This relationship suggests that treatment with the study product is causing or 
contributing to the AE; ie, the event follows a reasonable temporal sequence from the 
time of the study product administration or follows a known response pattern to the 
study product but could also be produced by other factors. 
Probable: 
This relationship suggests that a reasonable temporal sequence of the event with the 
study product administration exists and, based upon the known pharmacological action 
of the study product, known or previously reported adverse reactions to the drug or 
class of drugs, or judgment based on the investigator’s clinical experience, the 
association of the event with the study product seems likely. The event disappears or 
decreases on cessation or reduction of the dose of study product. 
Definite: 
This relationship suggests that a definite causal relationship exists between the study 
product administration and the AE, and other conditions (concurrent illness, 
progression/expression of disease state, or concurrent medication reaction) do not 
appear to explain the event. The event reappears or worsens if the study product is 
re-administered. 
 
The relationship or association of corticosteroid regimen, [1-13C] sodium acetate, OTC deficiency, or 
hyperammonemia in causing or contributing to the AE will also be characterized using the 
classification terms above. 
9.1.5 
Follow-Up of Subjects Reporting Adverse Events 
All AEs must be reported in detail on the appropriate page in the eCRF and followed to satisfactory 
resolution, until the investigator deems the event to be chronic or not clinically significant, or until the 
subject is considered to be stable. 
9.2 
Procedures for Handling Special Situations 
9.2.1 
Pregnancy 
A serum pregnancy test will be performed on all female study subjects of childbearing potential 
during Screening. A urine pregnancy test will be performed on all female study subjects of 
childbearing potential at each visit specified in the Schedule of Events (Table 15-1). 


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Pregnancy is not regarded as an AE unless there is a suspicion that a study drug may have interfered 
with the effectiveness of a contraceptive medication. Any pregnancy in a female study subject that 
occurs during study participation must be reported using the paper Pregnancy Report Form and fax it 
to PPD PVG (Table 9-1). To ensure subject safety, each pregnancy in a female study subject must be 
reported to PPD PVG Department (contact information in Section 9.1.2.2) within 2 weeks of learning 
of its occurrence.  
The pregnancy in a female study subject must be followed up to determine outcome (including 
spontaneous miscarriage, elective termination, normal birth, or congenital abnormality) and status of 
mother and child, even if the subject discontinued from the study. Pregnancy complications and 
elective terminations for medical reasons should not be reported as an AE or SAE. Spontaneous 
miscarriages must be reported as an SAE. All neonatal deaths that occur within 28 days of birth 
should be reported as an SAE. 
Any SAE occurring in association with a pregnancy in a female study subject brought to the 
investigator’s attention after the subject has completed the study and considered by the investigator as 
possibly related to the study product, must be promptly reported to Ultragenyx Pharmaceutical. 
9.2.2 
Treatment Noncompliance 
9.2.2.1 
Overdose Management 
An overdose is any dose of study product given to or taken by a subject that intentionally or 
unintentionally exceeds the dose, based on body weight (kg), described in Section 3.1. 
Overdoses without signs or symptoms do not need to be recorded as AEs; in case of any AEs 
associated with the overdose, these should be reported on the relevant AE or SAE section in the 
eCRF. The actual dose infused will be recorded on the appropriate page in the eCRF. 
There is no treatment for overdose. All subjects will be closely monitored at the time of infusion for 
any adverse effects and supportive care will be administered at the discretion of the investigator, as 
needed, should an overdose be suspected. 
9.2.2.2 
Medication Errors 
A medication error is defined as a mistake made in prescribing, dispensing, administration, or use of 
the study product. The treatment will be open-label and is to be administered by trained medical 
personnel at the study site. 


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9.3 
Data Monitoring Committee 
An independent DMC will be responsible for monitoring safety data from the study. The DMC will 
meet after all subjects in Cohort 1, all subjects in Cohort 2, and the initial 3 subjects in Cohort 3 have 
completed Week 12 of the study to review the safety data and to provide their recommendation for 
progressing to the next dosing cohort, or expansion of a dosing cohort. There will be no intra-cohort 
dose escalations. The DMC will also hold a meeting at completion of Week 12 for the first 3 subjects 
dosed in Cohort 4, and at the completion of Week 52 for all subjects. Additional DMC meetings may 
take place, as needed. 
The DMC will meet on an ad hoc basis if an investigator reports an AE/SAE that meets any of the 
safety stopping criteria (Section 3.2.7). The DMC may, at any time, recommend modifying or pausing 
enrollment due to safety concerns based on these periodic data reviews. Following DMC review when 
a stopping rule is met, if the decision is to restart enrollment, a substantial amendment will need to be 
approved by the regulatory authority. The full scope of each review will be outlined in the DMC 
charter. The DMC will comprise at least either 3 independent medical professionals or 2 independent 
medical professionals and an independent biostatistician who are qualified to review the data and 
provide recommendations for progressing to the next dosing level and progressing to the next dosing 
cohort and cohort expansion. The DMC charter details the members’ roles and responsibilities as part 
of the DMC as well as the process for each data review (ad hoc or scheduled). 
10 Statistical and Analytical Plan 
A statistical analysis plan (SAP) will be written and will provide a detailed description of the 
statistical methods and expand on the details provided in this protocol. Additional analyses may be 
added. 
10.1 Dose-Finding Algorithm and Process 
Dose finding for DTX301 will be accomplished through a CRM algorithm as described in 
Section 10.5.1. The operational process is as follows: 
• 
Data sources and methodologies used to determine the parameter values of the prior 
distributions of the toxicity model 
• 
Data elements and formats required in order to conduct modeling needed for producing 
dosing recommendation for the next dose 


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• 
Validation process of the modeling results and format and data to be provided to the DMC for 
dosing decisions 
10.2 Primary Endpoints 
The primary endpoint is the incidence of AEs, treatment-emergent AEs, and SAEs (Section 9.1). 
10.3 Secondary Endpoints 
The secondary endpoints are: 
• 
The change from baseline in the rate of ureagenesis (Section 8.1.1) 
• 
The change from baseline in AUC0-24 for plasma ammonia (Section 8.1.2) 
10.4 Exploratory Endpoints 
The exploratory endpoints are: 
• 
The number of hyperammonemic crises (HAC) (Section 8.2.4.1) 
• 
The change from baseline in urinary orotic acid secretion (Section 8.3.3) 
• 
The change from baseline in serum glutamine and glutamate (Section 8.2.4.1) 
• 
Changes in responses to neuropsychological tests (Section 8.4) 
• 
Responses to the PROMIS questionnaire (Section 8.4.1) 
• 
Use of ammonia scavenger therapy (Section 8.7.2) 
• 
Change in dietary protein intake (Section 8.7.2) 
• 
The development of neutralizing antibodies to AAV8 (Section 8.2.5.1) 
• 
The development of anti-AAV8 binding antibodies (Section 8.2.5.2) 
• 
The development of anti-OTC antibodies (Section 8.2.5.3) 
10.5 Statistical Analysis Methodology 
Dose-finding modeling will be conducted through specialized software that has been validated by 
PPD. SAS® software (SAS Institute, Inc., Cary, North Carolina, United States) Version 9.2 or later 


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will be used for general data manipulation and statistical analyses. Continuous variables will be 
summarized using the mean, the standard deviation, median, minimum value, and maximum value. 
Categorical variables will be summarized using frequency counts and percentages. Data will be listed 
in data listings. 
Details of the statistical analyses, methods, and data conventions are described in the SAP. 
10.5.1 
Determination of the Optimal Biological Dose 
The CRM uses the Bayesian method to model the probability of experiencing a DLT for each given 
dose in order to determine the next dose. A DLT is defined as any AE/SAE ≥ Grade 3 that is 
considered related to DTX301 by the investigator [NCI CTCAE 2018].
 
 
The OBD is defined as the highest dose 
where the predicted probability of experiencing a DLT is less than the target toxicity level.
 
 
 
 
A high-level overview of the decision criteria to be used during dose finding are presented in 
Figure 10-1. Subjects (n=3) in the first cohort (Cohort 1) will be assigned to Dose 1. 
 
 
 
 
 Dose finding will continue in this manner 
until one of the following conditions is met:  
1. The MTD is reached. 
 
 
  
2. The OBD is found. 
 
 
3. All of the dosing cohorts have been enrolled. 


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Possible dosing paths during dose 
 
 
 
 
 
 
The protocol will also allow for adding an 
intermediate dose during either escalation or de-escalation, relative to the candidate doses outlined in 


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10.5.2 
Efficacy Analysis 
10.5.2.1 
Ureagenesis 
The change from baseline in the rate of ureagenesis (presented in µmol/kg/hr and the relative 
percentage to normal healthy adults [300 µmol/kg/hr]) will be determined for all subjects at Weeks 6, 
12, 20, 24, and 52 (Table 15-1). During Screening, assessment of rate of ureagenesis may be repeated 
if discrepant with subject’s clinical status and severity. Full details of the analysis will be provided in 
the SAP. 


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10.5.2.2 
Plasma Ammonia Area Under the Curve from Time Zero to 24 Hours 
The change from baseline in the plasma ammonia area under the curve (AUC0-24) and the 
time-normalized plasma ammonia, defined as plasma ammonia AUC0-24 divided by actual hours from 
zero to 24 hours, after IV administration of DTX301 will be determined for all subjects at Weeks 6, 
12, 24, and 52 (Table 15-1). Full details of the analysis will be provided in the SAP. 
10.5.3 
Safety Analyses 
All subjects who receive DTX301 will be included in the safety analysis. 
10.5.3.1 
Adverse Events 
All statistical analyses of safety outcomes will be descriptive. The incidence of AEs and 
treatment-emergent AEs will be summarized for each dosing cohort by severity and relationship to 
study product. Serious AEs will be presented for each dosing cohort by relationship to study product. 
Summary tables will present incidence estimates and individual event rates by system organ class as 
well as within each system organ class. Subjects experiencing an event more than once with varying 
severity will be counted only once, applying only the maximum severity observed within each system 
organ class and preferred term. For incidence of relationship to study product, subjects will be 
counted only once, in the category of the strongest relationship to study product within each system 
organ class and preferred term. 
10.5.3.2 
Physical Examination Findings 
Complete and targeted physical examination findings will be summarized by visit and dosing cohort. 
10.5.3.3 
Vital Sign Measurements 
Vital sign measurements (heart rate, blood pressure [systolic and diastolic], and respiratory rate) will 
be summarized over time in terms of absolute values and changes from baseline by visit and dosing 
cohort. Height and weight will be summarized. 
10.5.3.4 
Electrocardiogram Results 
Electrocardiogram data will be summarized by visit and dosing cohort. Each ECG will be classified 
as “abnormal” or “normal,” and the relevance of the abnormality will be summarized as “clinically 
significant” or “not clinically significant.” 


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10.5.3.5 
Clinical Laboratory Assessment Results 
For all laboratory assessments with continuous results, absolute values and changes from baseline 
will be summarized by visit and dosing cohort. For laboratory tests with categorical results, shifts 
from baseline will be summarized by visit and dosing cohort. Chemistry values from both the central 
laboratory and subjects’ local laboratories will be analyzed. 
10.5.3.6 
Other Laboratory Results 
Neutralizing antibodies (AAV8) and AAV8-binding antibody IgG assay results will be listed by time 
point and dosing cohort. Anti-OTC antibody assay and viral shedding results will be listed by time 
point and dosing cohort.  
10.5.4 
Neuropsychological Tests 
Changes in responses to the PROMIS mental health measurements and 
 
(Section 8.4) will be summarized by visit and dosing cohort as outlined in the SAP. Results of the 
other neuropsychological tests will be listed by visit and dosing cohort.  
10.5.5 
Quality-of-Life Assessment 
Associations between QoL and dose will be undertaken using tabular summaries and appropriate 
statistical methods as outlined in the SAP. 
10.5.6 
Other Analyses 
Summary statistical analyses will be provided for demographics, medical history, OTC deficiency 
medical history, prior and concomitant medications, use of ammonia scavengers, and dietary protein 
intake. A summary of subject disposition will be prepared. 
10.5.7 
Interim Analysis 
An interim analysis may be conducted when 12 weeks of data are available for all subjects from at 
least 2 dosing cohorts. Results and their dissemination will be at the sponsor’s discretion. A detailed 
plan for the analysis of the safety and efficacy data will be presented in the SAP. 


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10.6 Data Quality Assurance 
Study sites will maintain source documentation and enter subject data in the eCRF as accurately as 
possible and will rapidly respond to any reported discrepancies. The eCRFs are accessed through 
Medidata Rave® (New York, New York, United States). This EDC system is validated and compliant 
with US Title 21 Code of Federal Regulations (CFR) Part A1. Each person involved with the study 
will have an individual user name and password that allows for record traceability. Thus, the system, 
and subsequently any investigative reviews, can identify coordinators, investigators, and individuals 
who have entered or modified records, as well as the time and date of any modifications. A quality 
review of the data will be performed by the study site with additional reviews by the clinical monitor.  
Each eCRF is presented as an electronic copy, allowing data entry by study site personnel, who can 
add and edit data, add new subjects, identify and resolve discrepancies, and view records. This system 
provides immediate direct data transfer to the database, as well as immediate detection of 
discrepancies, enabling study site coordinators to resolve and manage discrepancies in a timely 
manner.  
Paper copies of the eCRFs and other database reports may be printed and signed by the investigator. 
This system provides study site personnel, monitors, and reviewers with access to hardcopy audits, 
discrepancy reviews, and investigator comment information.  
After all queries have been resolved, the SAP is approved and signed, and any summary/analysis 
populations are approved, the database will be locked. All summary and analysis of the data will be 
performed using SAS software Version 9.2 or later. 
10.6.1 
Data Management 
As part of the responsibilities assumed by participating in the study, the investigator agrees to 
maintain adequate case histories for the subjects treated as part of the research under this protocol. 
The investigator agrees to maintain accurate eCRFs and source documentation as part of the case 
histories. These source documents may include diary cards, laboratory reports, ECG strips, and other 
materials. 
The sponsor (or sponsor designee) will supply the eCRF. Study personnel must have documented 
training in the use of the EDC system before the system can be authorized.  
All eCRF information is to be completed. If an item is not available or is not applicable, this fact 
should be indicated. 


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Investigative study site personnel will enter subject data into the EDC system. The analysis data sets 
will be a combination of these data and data from other sources (eg, laboratory data). All entries and 
changes to the data in the eCRF will be recorded electronically with an audit trail specifying the date 
and time of entry or change and the name of the authorized person making the entry or change. The 
investigator will answer all queries issued, if applicable. Data queries and query correspondence will 
be included in the audit trail. 
Clinical data management will be performed in accordance with applicable sponsor (or sponsor 
designee) standards and data cleaning procedures to ensure the integrity of the data (eg, removing 
errors and inconsistencies in the data). Adverse events and concomitant medication terms will be 
coded using MedDRA and WHO Drug dictionary terminology, respectively. 
After database lock, each study site will receive an electronic copy of their study site-specific eCRF 
data as entered into the EDC system for the study, including full discrepancy and audit history. 
Additionally, an electronic copy of all of the study site’s data from the study will be created and sent 
to the sponsor for storage. The sponsor (or sponsor designee) will maintain a duplicate electronic 
copy for their records. In all cases, subject initials will not be collected or transmitted to the sponsor. 
11 Ethics 
11.1 Institutional Review Board, Independent Ethics Committee, and 
Institutional Biosafety Committee 
Federal regulations and the ICH guidelines require that approval be obtained from an IRB/IEC/IBC 
before participation of human subjects in research studies. Before study onset, the protocol, ICF, 
advertisements to be used for the recruitment of study subjects, and any other written information 
regarding this study to be provided to the subject or the subject’s legal guardian must be approved by 
an IRB/IEC/IBC. Documentation of all IRB/IEC/IBC approvals and of the IRB/IEC/IBC compliance 
with ICH harmonised tripartite guideline E6(R2): Good Clinical Practice (GCP) must be maintained 
by the study site and made available for review by the sponsor or its designee. 
All IRB/IEC/IBC approvals should be signed by the IRB/IEC/IBC chair or designee and must 
identify the IRB/IEC/IBC name and address, the clinical protocol by title or protocol number or both, 
and the date approval or a favorable opinion was granted. 
The investigator is responsible for providing written summaries of the progress and status of the study 
at intervals not exceeding 1 year or otherwise specified by the IRB/IEC/IBC. The investigator must 


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promptly supply the sponsor or its designee, the IRB/IEC/IBC, and, where applicable, the institution, 
with written reports on any changes significantly affecting the conduct of the study or increasing the 
risk to subjects. 
11.2 Ethical Conduct of the Study 
The study will be performed in accordance with the ethical principles that have their origin in the 
Declaration of Helsinki, ICH GCP, and all applicable local laws and regulations. 
11.3 Subject Information and Consent 
A written ICF in compliance with regulatory authority regulations and 21 CFR §50 shall be obtained 
from each subject before entering the study or performing any unusual or nonroutine procedure that 
involves risk to the subject. An ICF template may be provided by the sponsor to study sites. If any 
institution-specific modifications to study-related procedures are proposed or made by the study site, 
the ICF should be reviewed by the sponsor or its designee or both before IRB/IEC/IBC submission. 
Once reviewed, the ICF will be submitted by the investigator to his or her IRB/IEC/IBC for review 
and approval before the start of the study. If the ICF is revised during the course of the study, all 
active participating subjects must sign the revised form. 
Before recruitment and enrollment, each prospective subject or their legal guardian will be given a 
full explanation of the study and be given the opportunity to read the approved ICF. Once the 
investigator is assured that the subject or their legal guardian understands the implications of 
participating in the study, the subject or their legal guardian will be asked to give consent to 
participate in the study by signing the ICF. 
The investigator shall retain the signed original ICF(s) and must provide a copy of the signed original 
form to the subject or their legal guardian. 
12 Investigator’s Obligations 
The following administrative items are meant to guide the investigator in the conduct of the study but 
may be subject to change based on industry and government standard operating procedures, working 
practice documents, or guidelines. Any change will be reported to the IRB/IEC/IBC but will not 
require a protocol amendment. 


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12.1 Confidentiality 
All laboratory specimens, evaluation forms, reports, and other records will be identified in a manner 
designed to maintain subject confidentiality. All records will be kept in a secure storage area with 
limited access. Clinical information will not be released without the written permission of the subject 
(or the subject’s legal guardian), except as necessary for monitoring and auditing by the sponsor, its 
designee, the FDA, other applicable regulatory agencies, or the IRB/IEC/IBC. 
The investigator and all employees and coworkers involved with this study may not disclose or use 
for any purpose other than performance of the study any data, record, or other unpublished, 
confidential information disclosed to those individuals for the purpose of the study. Prior written 
agreement from the sponsor must be obtained for the disclosure of any said confidential information 
to other parties. 
12.2 Financial Disclosure and Obligations 
Investigators are required to provide financial disclosure information to allow the sponsor to submit 
the complete and accurate certification or disclosure statements required under 21 CFR §54. In 
addition, the investigator must provide to the sponsor a commitment to promptly update this 
information if any relevant changes occur during the course of the investigation and for 1 year 
following the completion of the study. 
Neither the sponsor nor PPD is financially responsible for further testing or treatment of any medical 
condition that may be detected during the screening process. In addition, in the absence of specific 
arrangements, neither the sponsor nor PPD is financially responsible for further treatment of the 
subject’s disease. 
12.3 Investigator Documentation 
Prior to beginning the study, the investigator will be asked to comply with ICH E6(R2) 8.2 and Title 
21 of the CFR by providing the following essential documents, including but not limited to: 
• 
IRB/IEC/IBC approvals; 
• 
Original investigator-signed investigator agreement page of the protocol; 
• 
Form FDA 1572 (or equivalent), fully executed, and all updates on a new fully executed 
Form FDA 1572 (or equivalent); 
• 
Curriculum vitae for the investigator and each subinvestigator; 


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• 
Financial disclosure information to allow the sponsor to submit complete and accurate 
certification or disclosure statements required under 21 CFR §54. In addition, the 
investigators must provide to the sponsor a commitment to promptly update this information 
if any relevant changes occur during the course of the investigation and for 1 year after the 
completion of the study; 
• 
IRB/IEC/IBC-approved ICF, samples of study site advertisements for recruitment for this 
study, and any other written information regarding this study that is to be provided to the 
subject or their legal guardian; and 
• 
Laboratory certifications and normal ranges for any local laboratories used by the study site, 
in accordance with 42 CFR §493. 
12.4 Study Conduct 
The investigator agrees that the study will be conducted according to the principles of ICH E6(R2). 
The investigator will conduct all aspects of this study in accordance with all national, state, and local 
laws or regulations. Study information from this protocol will be posted on publicly available clinical 
study registers before enrollment of subjects begins. 
Where available, agreed upon by the investigator and allowed by local regulation, an outpatient clinic 
visit may take place as home health services. Investigators will be responsible for maintaining 
effective lines of communication between the investigator and the personnel who manage the 
subjects at home to guarantee that the investigator is constantly kept informed of subject safety, 
including metabolic and clinical status. 
12.5 Adherence to Protocol 
The investigator agrees to conduct the study as outlined in this protocol in accordance with ICH 
E6(R2) and all applicable guidelines and regulations. 
12.6 Adverse Events and Study Report Requirements 
By participating in this study, the investigator agrees to submit reports of SAEs according to the time 
line and method outlined in the protocol. In addition, the investigator agrees to submit annual reports 
to the study site IRB/IEC/IBC as appropriate. 


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12.7 Investigator’s Final Report 
Upon completion of the study, the investigator, where applicable, should inform the institution; the 
investigator/institution should provide the IRB/IEC/IBC with a summary of the study’s outcome and 
the sponsor and regulatory authority(ies) with any reports required. 
12.8 Record Retention 
Essential documents should be retained until at least 2 years after the last approval of a marketing 
application in an ICH region and until there are no pending or contemplated marketing applications in 
an ICH region or at least 2 years have elapsed since the formal discontinuation of clinical 
development of the study product. These documents should be retained for a longer period, however, 
if required by the applicable regulatory requirements or by an agreement with the sponsor. It is the 
responsibility of the sponsor to inform the investigator/institution as to when these documents no 
longer need to be retained. 
12.9 Publications 
After completion of the study, the data may be considered for reporting at a scientific meeting or for 
publication in a scientific journal. In these cases, the sponsor will be responsible for these activities 
and will work with the investigators to determine how the manuscript is written and edited, the 
number and order of authors, the publication to which it will be submitted, and other related issues. 
The sponsor has final approval authority over all such issues. 
Data are the property of the sponsor and cannot be published without prior authorization from the 
sponsor, but data and publication thereof will not be unduly withheld. 
13 Study Management 
The administrative structure will include a DMC (Section 9.3). 
13.1 Monitoring 
13.1.1 
Monitoring of the Study 
The clinical monitor, as a representative of the sponsor, has the obligation to closely follow the 
progression of the study, ensuring that it is being conducted in compliance with the protocol, ICH 
E6(R2), all applicable local laws and regulations, and with current and applicable standard operating 


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procedures. In doing so, the monitor will visit the investigator and study site at periodic intervals, in 
addition to maintaining necessary telephone and written contact. The monitor will maintain current 
personal knowledge of the study through observation, review of study records and source 
documentation, and discussion of the conduct of the study with the investigator and study site 
personnel. 
13.1.2 
Inspection of Records 
Investigators and institutions involved in the study will permit study-related monitoring, audits, 
IRB/IEC/IBC review, and regulatory inspections by providing direct access to all study records. In 
the event of either an audit or inspection, the investigator agrees to allow the sponsor, representatives 
of the sponsor, or a regulatory agency (eg, FDA or other regulatory agency) access to all study 
records. 
The investigator should promptly notify the clinical research associate (CRA) of any audits or 
inspections scheduled by any regulatory authorities and promptly forward copies of any reports 
received to the CRA. The CRA will then inform and forward any reports to the sponsor. 
13.2 Management of Protocol Amendments and Deviations 
13.2.1 
Modification of the Protocol 
Any changes in this research activity, except those necessary to remove an apparent, immediate 
hazard to the subject, must be reviewed and approved by the sponsor or its designee. Amendments to 
the protocol must be submitted in writing to the investigator’s IRB/IEC/IBC for approval before 
subjects can be enrolled into an amended protocol. 
13.2.2 
Protocol Deviations 
A deviation from the protocol is a departure from the written procedures or processes. A significant 
deviation occurs when there is nonadherence to the protocol by the subject or investigator that 
results in a significant, additional risk to the subject or important change to the study design. 
Significant deviations can include nonadherence to inclusion or exclusion criteria, nonadherence to 
safety and efficacy-related assessments, or nonadherence to FDA regulations or ICH GCP guidelines, 
that could lead to the subject being withdrawn from the study (Section 7.1). Protocol waivers or 
exemptions are not permitted. Adherence to the study design requirements, including those specified 
in the Schedules of Events (Table 15-1 and Table 15-2), is essential for study conduct. 


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The investigator or designee must document and explain in the subject’s source documentation any 
deviation from the approved protocol. The investigator may implement a deviation from, or a change 
of, the protocol to eliminate an immediate hazard to study subjects without prior IRB/IEC/IBC 
approval. As soon as possible after such an occurrence, the implemented deviation or change, the 
reasons for it, and any proposed protocol amendments should be submitted to the IRB/IEC/IBC for 
review and approval, to the sponsor for agreement, and to the regulatory authorities, if required. 
Protocol deviations will be documented by the clinical monitor throughout the course of monitoring 
visits. Principal investigators will be notified in writing by the monitor of deviations. The 
IRB/IEC/IBC should be notified of all protocol deviations in a timely manner, as required. 
13.3 Study Termination 
Although the sponsor has every intention of completing the study, the sponsor reserves the right to 
discontinue the study at any time for clinical or administrative reasons. 
The end of the study is defined as the date on which the last subject completes the last visit (includes 
follow-up visit). 
13.4 Final Report 
Whether the study is completed or prematurely terminated, the sponsor will ensure that the clinical 
study reports are prepared and provided to the regulatory agency(ies) as required by the applicable 
regulatory requirement(s). The sponsor will also ensure that the clinical study reports in marketing 
applications meet the standards of the ICH harmonised tripartite guideline E3: Structure and content 
of clinical study reports. 
Where required by applicable regulatory requirements, an investigator signatory will be identified for 
the approval of the clinical study report. The investigator will be provided reasonable access to 
statistical tables, figures, and relevant reports and will have the opportunity to review the complete 
study results. 
Upon completion of the clinical study report, the sponsor will provide the investigator with a 
summary of the cumulative study results. The investigator is encouraged to share the cumulative 
summary results and will provide each subject with their individual data. The study results will be 
posted on publicly available clinical study registers, where required. 


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Declaration of Investigator 
I have read and understood all sections of the protocol titled “A Phase 1/2, Open-Label Safety and 
Dose-Finding Study of Adeno-Associated Virus (AAV) Serotype 8 (AAV8)-Mediated Gene Transfer 
of Human Ornithine Transcarbamylase (OTC) in Adults with Late-Onset OTC Deficiency.” 
I have read and agree to supervise all aspects of the protocol and to conduct the clinical investigation 
in accordance with the Final Protocol Version 06, dated 25 February 2020, the International Council 
for Harmonisation harmonised tripartite guideline E6(R2): Good Clinical Practice and all applicable 
government regulations and inform all who assist me in the conduct of this study of their 
responsibilities and obligations. 
 
 
 
Signature of Principal Investigator 
 
Date 
 
 
 
Printed Name of Principal Investigator 
 
 
 
 


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14 Reference List 
Batshaw ML, Monahan PS. Treatment of urea cycle disorders. Enzyme. 1987;38(1-4):242-50. 
Batshaw ML, MacArthur RB, Tuchman M. Alternative pathway therapy for urea cycle disorders: 
twenty years later. J Pediatr. 2001;138(1 Suppl):S46-54. 
Batshaw ML, Tuchman M, Summar M, et al. A longitudinal study of urea cycle disorders. Mol Genet 
Metab. 2014;113(1-2):127-30. 
Boutin S, Monteilhet V, Veron P, et al. Prevalence of serum IgG and neutralizing factors against 
adeno-associated virus (AAV) types 1, 2, 5, 6, 8, and 9 in the healthy population: implications for 
gene therapy using AAV vectors. Hum Gene Ther. 2010;21(6):704-12. 
Calcedo R, Wilson JM. Humoral immune response to AAV. Front Immunol. 2013;4:341. 
Caldovic L, Abdikarim I, Narain S, et al. Genotype-phenotype correlations in ornithine 
transcarbamylase deficiency: a mutation update. J Genet Genomics. 2015;42(5):181-94. 
Castillo L, Beaumier L, Ajami AM, et al. Whole body nitric oxide synthesis in healthy men 
determined from [15N]arginine-to[15N]citrulline labeling. Proc Nat Acad Sci U S A. 
1996;93(21):11460-5. 
Davidoff AM, Gray JT, Ng CY, et al. Comparison of the ability of adeno-associated viral vectors 
pseudotyped with serotype 2, 5, and 8 capsid proteins to mediate efficient transduction of the liver in 
murine and nonhuman primate models. Mol Ther. 2005;11(6):875-88. 
Deignan JL, Cederbaum SD, Grody WW. Contrasting features of urea cycle disorders in human 
patients and knockout mouse models. Mol Genet Metab. 2008;93(1):7-14. 
Delis DC, Kaplan E, Kramer JH. Delis-Kaplan Executive Function System (D-KEFS). San Antonio, 
TX: The Psychological Corporation. 2001. 
Diaz GA, Harding CO, Geberhiwot T, et al. Preliminary results from cohorts 1 and 2 of CAPtivate: a 
phase 1/2 clinical trial of AAV8-mediated liver-directed gene therapy in adults with late-onset OTC 
deficiency. Molecular Therapy. 2019;27(4S1):2-3. 


Ultragenyx Pharmaceutical Inc. 
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Protocol: 301OTC01 
 
Page 98 of 126 
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25 February 2020 
Diaz GA, Schulze A, Longo N, et al. Long-term safety and efficacy of glycerol phenylbutyrate for the 
management of urea cycle disorder patients. 2019;127(4):336-45. Doi: 
10.1016/j.ymgme.2019.07.004. Epub 2019 Jul 10. 
Gao GP, Alvira MR, Wang L, et al. Novel adeno-associated viruses from rhesus monkeys as vectors 
for human gene therapy. Proc Natl Acad Sci U S A. 2002;99(18):11854-9. 
Gao G, Vandenberghe LH, Wilson JM. New recombinant serotypes of AAV vectors. Curr Gene Ther. 
2005;5(3):285-97. 
Gao G, Wang Q, Calcedo R, et al. Adeno-associated virus-mediated gene transfer to nonhuman 
primate liver can elicit destructive transgene-specific T cell responses. Hum Gene Ther. 
2009;20(9):930-42. 
Guidance for industry: design of early-phase clinical trials for cellular and gene therapy products. 
CBER. June 2015. Available from: http://www.fda.gov/downloads/Biologi.../UCM359073.pdf.  
Häberle J, Boddaert N, Burlina A, et al. Suggested guidelines for the diagnosis and management of 
urea cycle disorders. Orphanet J Rare Dis. 2012;7:32. 
Häberle J, Burlina A, Chakrapani A, et al. Suggested guidelines for the diagnosis and management of 
urea cycle disorders: First revision. J Inherit Metab Dis. 2019;42(6):1192-1230. Doi: 
10.1002/jimd.12100. Epub 2019 May 15. 
Herzog RW, Mount JD, Arruda VR, et al. Muscle-directed gene transfer and transient immune 
suppression result in sustained partial correction of canine hemophilia B caused by a null mutation. 
Mol Ther. 2001;4(3):192-200. 
Hodges PE, Rosenberg LE. The spfash mouse: a missense mutation in the ornithine transcarbamylase 
gene also causes aberrant mRNA splicing. Proc Natl Acad Sci U S A. 1989;86(11):4142-6. 
Iasonos A, O’Quigley J. Adaptive dose-finding studies: a review of model-guided phase I trials. 
J Clin Oncol. 2014;32(23):2505-11. 
Jackson MJ, Beaudet AL, O’Brien WE. Mammalian urea cycle enzymes. Annu Rev Genet. 
1986;20:431-64. 
Jahoor F, Wolfe RR. Reassessment of primed constant-infusion tracer method to measure urea 
kinetics. Am J Physiol. 1987;252(4 Pt 1):E557-64. 


Ultragenyx Pharmaceutical Inc. 
DTX301 
Protocol: 301OTC01 
 
Page 99 of 126 
Version 06 
 
25 February 2020 
Jiang H, Couto LB, Patarroyo-White S, et al. Effects of transient immunosuppression on 
adeno-associated, virus-mediated, liver-directed gene transfer in rhesus macaques and implications 
for human gene therapy. Blood. 2006;108(10):3321-8. 
Kay MA. State-of-the-art gene-based therapies: the road ahead. Nat Rev Genet. 2011;12(5):316-28. 
Kent JD, Holt RJ. Hyperammonemic crises in patients with urea cycle disorders on chronic nitrogen 
scavenger therapy with either sodium phenylbutyrate or glycerol phenylbutyrate. Neuropsych. 
2017;7(2):131-6. 
Koletzko B, Sauerwald T, Demmelmair H. Safety of stable isotope use. Eur J Pediatr. 
1997;156(Suppl 1):S12-7. 
Krivitzky L, Babikian T, Lee HS, et al. Intellectual, adaptive, and behavioral functioning in children 
with urea cycle disorders. Pediatr Res. 2009;66(1):96-101. 
Leonard JV. The nutritional management of urea cycle disorders. J Pediatr. 2001;138(1 Suppl):S40-4. 
Leonard JV, McKiernan PJ. The role of liver transplantation in urea cycle disorders. Mol Genet 
Metab. 2004;81(Suppl 1):S74-8. 
Li C, Hirsch M, Asokan A, et al. Adeno-associated virus type 2 (AAV2) capsid-specific cytotoxic 
T lymphocytes eliminate only vector-transduced cells coexpressing the AAV capsid in vivo. J Virol. 
2007;81(14):7540-7. 
Li H, Murphy SL, Giles-Davis W, et al. Pre-existing AAV capsid-specific CD8+ T cells are unable to 
eliminate AAV-transduced hepatocytes. Mol Ther. 2007;15(4):792-800. 
Lichtenberger E, Kaufman A. Essentials of WAIS-IV Assessment, Second Edition. Hoboken, NJ: 
John C Wiley and Sons. 2009. 
Lichter-Konecki U, Caldovic L, Morizono H, Simpson K. Ornithine transcarbamylase deficiency. 
2013 Aug 29 [Updated 2016 Apr 14]. In: Pagon RA, Adam MP, Ardinger HH, et al, editors. 
GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2016. Available 
from: http://www.ncbi.nlm.nih.gov/books/NBK154378/. 
Longo N, Holt RJ. Glycerol phenylbutyrate for the maintenance treatment of patients with 
deficiencies in enzymes of the urea cycle. Expert Opin Orphan Drugs. 2017;5(12):999-1010. 


Ultragenyx Pharmaceutical Inc. 
DTX301 
Protocol: 301OTC01 
 
Page 100 of 126 
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25 February 2020 
Manno CS, Chew AJ, Hutchinson S, et al. AAV-mediated factor IX gene transfer to skeletal muscle 
in patients with severe hemophilia B. Blood. 2003;101(8):2963-72. 
Manno CS, Pierce GF, Arruda VR, et al. Successful transduction of liver in hemophilia by 
AAV-factor IX and limitations imposed by the host immune response. Nat Med. 2006;12(3):342-7. 
Matthews DE, Downey RS. Measurement of urea kinetics in humans: a validation of stable isotope 
tracer methods. Am J Physiol. 1984;246(6 Pt 1):E519-27. 
McIntosh J, Lenting PJ, Rosales C, et al. Therapeutic levels of FVIII following a single peripheral 
vein administration of rAAV vector encoding a novel human factor VIII variant. Blood. 
2013;121(17):3335-44. 
Mingozzi F, Maus MV, Hui DJ, et al. CD8+ T-cell responses to Adeno-associated virus capsid in 
humans. Nat Med. 2007;13(4):419-22. 
Mingozzi F, High KA. Therapeutic in vivo gene transfer for genetic disease using AAV: progress and 
challenges. Nat Rev Genet. 2011;12(5):341-55. 
Mount JD, Herzoq RW, Tillson DM, et al. Sustained phenotypic correction of hemophilia B with a 
factor IX null mutation by liver-directed gene therapy. Blood. 2002;99(8):2670-6. 
Msall M, Batshaw ML, Suss R, et al. Neurologic outcome in children with inborn errors of urea 
synthesis. Outcome of urea-cycle enzymopathies. N Engl J Med. 1984;310(23):1500-5. 
Nakai H, Yant SR, Storm TA, et al. Extrachromosomal recombinant adeno-associated virus vector 
genomes are primarily responsible for stable liver transduction in vivo. J Virol. 2001;75(15):6969-76. 
Nathwani AC, Gray JT, Ng CY, et al. Self-complementary adeno-associated virus vectors containing 
a novel liver-specific human factor IX expression cassette enable highly efficient transduction of 
murine and nonhuman primate liver. Blood. 2006;107(7):2653-61. 
Nathwani AC, Gray JT, McIntosh J, et al. Safe and efficient transduction of the liver after peripheral 
vein infusion of self-complementary AAV vector results in stable therapeutic expression of human 
FIX in nonhuman primates. Blood. 2007;109(4):1414-21. 
Nathwani AC, Tuddenham EG, Rangarajan S, et al., Adenovirus-associated virus vector-mediated 
gene transfer in hemophilia B. N Engl J Med. 2011a;365(25):2357-65. 


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Nathwani AC, Rosales C, McIntosh J, et al. Long-term safety and efficacy following systemic 
administration of a self-complementary AAV vector encoding human FIX pseudotyped with serotype 
5 and 8 capsid proteins. Mol Ther. 2011b;19:876-85. 
Nathwani AC, Reiss UM, Tuddenham EG, et al. Long-term safety and efficacy of factor IX gene 
therapy in hemophilia B. N Engl J Med. 2014;371(21):1994-2004. 
National Institutes of Health. National Cancer Institute (NCI). Common terminology criteria for 
adverse events (CTCAE). 01 March 2018. Available from: 
https://ctep.cancer.gov/protocolDevelopment/electronic_applications/ctc.htm#ctc_50 
National Institutes of Health’s The Patient Reported Outcomes Measurement Information System 
(PROMIS): A walk through the first four years. Jan 2009. Available from: 
www.nihpromis.org/Documents/PROMIS_The_First_Four_Years.pdf. 
Nichols TC, Raymer RA, Franck HW, et al. Prevention of spontaneous bleeding in dogs with 
haemophilia A and haemophilia B. Haemophilia. 2010;16(Suppl 3):19-23. 
Ozanne B, Nelson J, Cousineau J, et al. Threshold for toxicity from hyperammonemia in critically ill 
children. J Hepatol. 2012;56(1):123-8. 
Raper SE, Yudkoff M, Chirmule N, et al. A pilot study of in vivo liver-directed gene transfer with an 
adenoviral vector in partial ornithine transcarbamylase deficiency. Hum Gene Ther. 
2002;13(1):163-75. 
Raper SE, Chirmule N, Lee FS, et al. Fatal systemic inflammatory response syndrome in a ornithine 
transcarbamylase deficient patient following adenoviral gene transfer. Mol Genet Metab. 
2003;80(1-2):148-58. 
Reeve BB, Hays RD, Bjorner JB, et al. Psychometric evaluation and calibration of health-related 
quality of life item banks: plans for the Patient-Reported Outcomes Measurement Information System 
(PROMIS). Med Care. 2007;45(5 Suppl 1):S22-31. 
Siders WM, Shields J, Kaplan J, et al. Cytotoxic T lymphocyte responses to transgene product, not 
adeno-associated viral capsid protein, limit transgene expression in mice. Hum Gene Ther. 
2009;20(1):11-20. 
Snyder RO, Miao C, Meuse L, et al. Correction of hemophilia B in canine and murine models using 
recombinant adeno-associated viral vectors. Nat Med. 1999;5(1):64-70. 


Ultragenyx Pharmaceutical Inc. 
DTX301 
Protocol: 301OTC01 
 
Page 102 of 126 
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25 February 2020 
Tuchman M, Lee B, Lichter-Konecki U, et al. Cross-sectional multicenter study of patients with urea 
cycle disorders in the United States. Mol Genet Metab. 2008a;94(4):397-402. 
Tuchman M, Caldovic L, Daikhin Y, et al. N-carbamylglutamte markedly enhances ureagensis in 
N-acetyglutamate deficiency and propionic acidemia as measured by isotopic incorporation and blood 
biomarkers. Pediatr Res. 2008b;64(2):213-7. 
uniQure Investor Day Presentation Dec 1, 2014. uniQure: Hemophilia – the challenge for gene 
therapy. http://www.uniqure.com/uploads/presentations/3.%2020141201%20MBach%20FINAL.pdf.  
uniQure R&D Day presentation, Oct 15, 2015, uniQure R&D Day – New York City; Gene Therapy 
for Liver Disease and Metabolic Disorder; Deya Corzo, MD. 
http://www.uniqure.com/uploads/presentations/03%20Gene%20Therapy%20for%20Liver%20Diseas
e%20and%20Metabolic%20Disorder.pdf. 
Vandenberghe LH, Wang L, Somanathan S, et al. Heparin binding directs activation of T cells against 
adeno-associated virus serotype 2 capsid. Nat Med. 2006;12(8):967-71. 
Wang L, Calcedo R, Nichols TC, et al. Sustained correction of disease in naïve and AAV2 pretreated 
hemophilia B dogs: AAV2/8-mediated, liver-directed gene therapy. Blood. 2005;105(8):3079-86. 
Wang L, Figueredo J, Calcedo R, et al. Cross-presentation of adeno-associated virus serotype 2 
capsids activates cytotoxic T cells but does not render hepatocytes effective cytolytic targets. Hum 
Gene Ther. 2007;18(3):185-94. 
Wang L, Morizono H, Lin J, et al. Preclinical evaluation of a clinical candidate AAV8 vector for 
ornithine transcarbamylase (OTC) deficiency reveals functional enzyme from each persisting vector 
genome. Mol Genet Metab. 2012;105(2):203-11. 
Wechsler D. Wechsler Abbreviated Scale of Intelligence. San Antonio, TX: The Psychological 
Corporation. 2011. 
Wright K. UK National Metabolic Biochemistry Network: Guidelines for the Investigation of 
Hyperammonaemia. Version 02. 2010. Available from: http://www.metbio.net/docs/metbio-
guideline-amup100834-21-07-2010.pdf.  
Yan Z, Zak R, Luxton GW, et al. Ubiquitination of both adeno-associated virus type 2 and 5 capsid 
proteins affects the transduction efficiency of recombinant vectors. J Virol. 2002;76(5):2043-53. 


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15 Appendices 
15.1 Appendix: Schedules of Events 
 
 


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Table 15-1 
Schedule of Events – Outpatient, Home Health Services, and Inpatient Clinic Visits 
Procedure 
Screening 
Day 0 
(Baseline) 
Day 1 
(DTX301 Dosing) 
Treatment Period: Includes Inpatient Clinic (shaded gray) 
and Outpatient Clinic/HHS visits. For home visits, refer to 
Table 15-2. 
End of Study/ 
Early 
Withdrawal 
Visit Type 
OC 
IC 
IC 
OC/ 
HHS 
OC/ 
HHS 
IC 
OC/ 
HHS 
IC 
OC/ 
HHS 
OC (all 
subjects) IC 
OC/ 
HHS 
IC 
Prior to 
DTX301 
Infusion 
DTX301 
Dosing/ 
Postdose 
Week 
– 
- 
- 
– 
2 
4 
6 
10 
12 
16 
20 
24 
36 
52 
Day 
–35 to –1 
0 
1 
1 
14 
28 
42 
70 
84 
112 
140 
168 
252 
364 
Visit Window (Days) 
– 
– 
– 
 
±2 
±2 
±2 
±2 
±2 
±7 
±7 
±7 
±7 
±7 
Informed consent 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
Eligibility criteria 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
Demographics 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
OTC medical history 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
Medical history 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
Prior medication / therapies / 
procedures 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
HBV, HCV, HIV status 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
Serum pregnancy test 
(females of childbearing 
potential only) 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
Clinic admission 
 
Xa 
Xa 
 
 
 
Xb 
 
Xb 
 
 
Xb 
 
Xb 
Vital signs (HR, BP, RR) 
X 
X 
X 
Xd 
X 
X 
X 
X 
X 
X 
Xe 
X 
X 
X 
Temperature f 
X 
 
X 
 
 
 
X 
 
X 
 
X 
X 
 
X 
Height 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 


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Procedure 
Screening 
Day 0 
(Baseline) 
Day 1 
(DTX301 Dosing) 
Treatment Period: Includes Inpatient Clinic (shaded gray) 
and Outpatient Clinic/HHS visits. For home visits, refer to 
Table 15-2. 
End of Study/ 
Early 
Withdrawal 
Visit Type 
OC 
IC 
IC 
OC/ 
HHS 
OC/ 
HHS 
IC 
OC/ 
HHS 
IC 
OC/ 
HHS 
OC (all 
subjects) IC 
OC/ 
HHS 
IC 
Prior to 
DTX301 
Infusion 
DTX301 
Dosing/ 
Postdose 
Week 
– 
- 
- 
– 
2 
4 
6 
10 
12 
16 
20 
24 
36 
52 
Day 
–35 to –1 
0 
1 
1 
14 
28 
42 
70 
84 
112 
140 
168 
252 
364 
Visit Window (Days) 
– 
– 
– 
 
±2 
±2 
±2 
±2 
±2 
±7 
±7 
±7 
±7 
±7 
Weight 
X 
X 
 
 
 
 
 
 
 
 
 
 
 
X 
Urine pregnancy test 
(females of childbearing 
potential only) 
 
X 
 
 
X 
X 
X 
X 
X 
X 
Xe 
X 
X 
X 
Orotic acid spot urine 
 
 
 
 
X 
X 
 
X 
 
X 
Xe 
 
X 
 
24-hour urine orotic acidg, h 
 
X 
 
 
 
 
X 
 
X 
 
 
X 
 
X 
Sample for OTC genotyping 
 
Xc 
 
 
 
 
 
 
 
 
 
 
 
 
Clinical chemistry 
(including LFTs)i 
X 
Xc 
X 
Xj 
X 
X 
Xc 
X 
Xc 
X 
Xe 
Xc 
X 
Xc 
LFTs (STAT sample at local 
laboratory)i 
X 
X 
X 
Xj 
X 
X 
X 
X 
X 
 
 
X 
 
X 
Spot ammonia (STAT 
sample at local laboratory) 
X 
Xc 
X 
Xn 
X 
X 
Xc 
X 
Xc 
X 
Xe 
Xc 
X 
Xc 
Hematology / coagulation 
panel 
X 
X 
 
 
X 
 
X 
 
X 
 
 
X 
 
X 
Urinalysis 
X 
X 
 
 
 
 
X 
 
X 
 
 
X 
 
X 


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Procedure 
Screening 
Day 0 
(Baseline) 
Day 1 
(DTX301 Dosing) 
Treatment Period: Includes Inpatient Clinic (shaded gray) 
and Outpatient Clinic/HHS visits. For home visits, refer to 
Table 15-2. 
End of Study/ 
Early 
Withdrawal 
Visit Type 
OC 
IC 
IC 
OC/ 
HHS 
OC/ 
HHS 
IC 
OC/ 
HHS 
IC 
OC/ 
HHS 
OC (all 
subjects) IC 
OC/ 
HHS 
IC 
Prior to 
DTX301 
Infusion 
DTX301 
Dosing/ 
Postdose 
Week 
– 
- 
- 
– 
2 
4 
6 
10 
12 
16 
20 
24 
36 
52 
Day 
–35 to –1 
0 
1 
1 
14 
28 
42 
70 
84 
112 
140 
168 
252 
364 
Visit Window (Days) 
– 
– 
– 
 
±2 
±2 
±2 
±2 
±2 
±7 
±7 
±7 
±7 
±7 
Samples for plasma 
ammonia (AUC0-24)g,k 
 
Xl, m 
 
 
 
 
Xm 
 
Xm 
 
 
Xm 
 
Xl,m 
Amino acid panel 
 
Xc 
 
 
 
 
Xc 
 
Xc 
 
 
Xc 
 
Xc 
AAV8 neutralizing antibody 
test (cell-based assay) 
X 
Xc 
 
 
 
 
 
 
 
 
 
 
 
Xc 
AAV8 binding antibody IgG 
assay (ELISA) 
X 
Xc 
 
 
 
 
 
 
 
 
 
 
 
Xc 
Anti-OTC antibody assay 
(ELISA) 
 
X 
 
 
 
 
 
 
X 
 
 
 
 
X 
Saliva, urine, and stool for 
viral shedding 
 
 
Xc 
 
 
 
 
Xc 
X 
Xc 
X 
Xe 
Xc 
X 
Xc 
Complete PE 
X 
 
 
 
 
 
 
 
 
 
 
 
 
X 
Targeted PE 
 
X 
 
 
 
 
X 
 
X 
 
 
X 
 
 
12-Lead ECG 
X 
X 
 
Xp 
 
 
 
 
 
 
 
 
 
X 
PROMIS questionnaireq 
 
X 
 
 
 
 
X 
 
X 
 
 
X 
 
X 
WASI-II vocabulary and 
matrix reasoning subtests 
 
Xl 
 
 
 
 
 
 
 
 
 
 
 
 


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Procedure 
Screening 
Day 0 
(Baseline) 
Day 1 
(DTX301 Dosing) 
Treatment Period: Includes Inpatient Clinic (shaded gray) 
and Outpatient Clinic/HHS visits. For home visits, refer to 
Table 15-2. 
End of Study/ 
Early 
Withdrawal 
Visit Type 
OC 
IC 
IC 
OC/ 
HHS 
OC/ 
HHS 
IC 
OC/ 
HHS 
IC 
OC/ 
HHS 
OC (all 
subjects) IC 
OC/ 
HHS 
IC 
Prior to 
DTX301 
Infusion 
DTX301 
Dosing/ 
Postdose 
Week 
– 
- 
- 
– 
2 
4 
6 
10 
12 
16 
20 
24 
36 
52 
Day 
–35 to –1 
0 
1 
1 
14 
28 
42 
70 
84 
112 
140 
168 
252 
364 
Visit Window (Days) 
– 
– 
– 
 
±2 
±2 
±2 
±2 
±2 
±7 
±7 
±7 
±7 
±7 
 
 
 
Xl 
 
 
 
 
 
 
 
 
 
 
 
Xl 
 
 
Xl 
 
 
 
 
 
 
 
 
 
 
 
Xl 
 
 
 
 
Xl 
 
 
 
 
 
 
 
 
 
 
 
Xl 
Oral [1-13C]sodium acetater 
Xm 
 
Xm 
 
 
 
Xm 
 
Xm 
 
Xm 
Xm 
 
Xm 
Samples for ureagenesisg, s 
X 
 
X 
 
 
 
X 
 
X 
 
X 
X 
 
X 
IWRS 
Xt 
Xt 
 
 
 
 
 
 
 
 
 
 
 
 
DTX301 infusion 
 
 
 
Xm, u 
 
 
 
 
 
 
 
 
 
 
AE/SAE monitoring 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Concomitant medications / 
therapies / procedures 
 
X 
X 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Review personalized, 
prescribed diet 
 
X 
 
 
 
 
X 
 
X 
 
 
X 
 
X 
Review of dietary protein 
intake 
X 
X 
X 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 


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Procedure 
Screening 
Day 0 
(Baseline) 
Day 1 
(DTX301 Dosing) 
Treatment Period: Includes Inpatient Clinic (shaded gray) 
and Outpatient Clinic/HHS visits. For home visits, refer to 
Table 15-2. 
End of Study/ 
Early 
Withdrawal 
Visit Type 
OC 
IC 
IC 
OC/ 
HHS 
OC/ 
HHS 
IC 
OC/ 
HHS 
IC 
OC/ 
HHS 
OC (all 
subjects) IC 
OC/ 
HHS 
IC 
Prior to 
DTX301 
Infusion 
DTX301 
Dosing/ 
Postdose 
Week 
– 
- 
- 
– 
2 
4 
6 
10 
12 
16 
20 
24 
36 
52 
Day 
–35 to –1 
0 
1 
1 
14 
28 
42 
70 
84 
112 
140 
168 
252 
364 
Visit Window (Days) 
– 
– 
– 
 
±2 
±2 
±2 
±2 
±2 
±7 
±7 
±7 
±7 
±7 
Review of ammonia 
scavenger use 
X 
X 
X 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Consider tapering ammonia 
scavenger therapyv 
 
 
 
 
 
 
 
 
X 
 
 
X 
 
 
Abbreviations: AAV8, adeno-associated virus serotype 8; AE, adverse event; AUC0-24, area under the curve from time zero to 24 hours; BP, blood pressure; 
 ECG, electrocardiogram; ELISA, enzyme-linked immunosorbent assay; HBV, hepatitis B virus; HCV, hepatitis C virus; 
HHS, home health services; HIV, human immunodeficiency virus; HR, heart rate; IC, inpatient clinic; IgG, immunoglobulin G; IP, investigational product; IWRS, interactive 
web response system; LFT, liver function test; OC, outpatient clinic; OTC, ornithine transcarbamylase; PE, physical examination; PROMIS, Patient-Reported Outcomes 
Measurement Information System; 
 
 RR, respiratory rate; SAE, serious adverse event; WASI-II, Wechsler Abbreviated Scale of 
Intelligence, Second Edition; WAIS-IV, Wechsler Adult Intelligence Scale, Fourth Edition; WMI, Working Memory Index. 
Note 1: If rescreening is within 3 months of the original screening or if dosing is expected to occur more than 3 months after completion of original screening assessments, 
the following must be repeated: hematology, coagulation and urinalysis, serum pregnancy test (if applicable), clinical chemistry including LFTs, spot plasma ammonia, amino 
acid panel, AAV8 neutralizing antibody test, weight, and vital signs. Additional tests may be requested on a case-by-case basis, depending on the original reason for screen 
failure or delay in dosing. The AAV8 screening neutralizing antibody results must be available and reviewed before IP administration. If the rescreening occurs more 
than 3 months after the original screening, all tests must be repeated except the following: OTC genotyping, HBV, HCV, and HIV. 
Note 2: At any point between scheduled visits, additional, unscheduled assessment for LFTs, plasma ammonia, or any other biomarker to assess subject safety and clinical status 
may be performed, at the discretion of the investigator. 
Note 3: At any time after initiation of prophylactic corticosteroid regimen, additional assessments of plasma ammonia levels, amino acid profiles, or any other biomarker to assess 
subject safety and clinical status may be performed, at the discretion of the investigator and as clinically indicated. 
Note 4: Where available, agreed upon by the investigator and allowed by local regulation, an outpatient clinic visit may take place as home health services. Week 20 visit is a 
mandatory Outpatient clinic visit for all subjects. 


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a. 
Subjects will be discharged 24 hours after the administration of DTX301 on Day 1. Subjects will be inpatient for approximately 48 consecutive hours. 
b. 
Subjects will be discharged after the administration of [1-13C]sodium acetate and after all samples for ureagenesis have been collected; subjects will be inpatient for 
approximately 28 hours. 
c. 
To be collected/performed before the start of plasma ammonia area under the curve from time zero to 24 hours (AUC0-24) determination. 
d. 
Vital signs to be measured at approximately 5 minutes after the start of DTX301 infusion, and at approximately 0.5 (±5 minutes), 1 (±5 minutes), 2, 4, 6, 8 (±15 minutes), and 
22 hours (±1 hour) after the start of DTX301 infusion. 
e. 
To be collected prior to the [1-13C]sodium acetate administration. 
f. 
Temperature will be measured prior to administration of [1-13C] sodium acetate. If the temperature is > 101°F or > 38°C, the procedure should not be initiated. 
g. 
Collection of samples for AUC0-24 of plasma ammonia and urine orotic acid determination is to be performed prior to administration of [1-13C]sodium acetate and sample 
collection for determination of the rate of ureagenesis. 
h. 
Urine samples to be collected at time 0 and at approximately 6, 12, 18, and 24 hours (relative to the start of plasma ammonia determination). Urinary orotic acid concentration 
will be standardized to urine creatinine concentration. 
i. 
Through Week 12, one sample for LFTs is collected as part of clinical chemistry and sent to the central laboratory for analysis. A second sample for LFTs only is collected 
and sent to the local laboratory (STAT sample). 
j. 
Samples for clinical chemistry to be collected at approximately 0.5, 4, 8, and 22 hours after the start of DTX301 infusion. 
k. 
Samples to be collected at time 0 and at approximately 2, 4, 8, 12, 16, 20, and 24 hours (relative to start of plasma ammonia determination). Two samples for plasma ammonia 
to be collected at each time point; 1 sample will be analyzed at the on-site local laboratory and the second sample will be processed and sent to the central laboratory.  
l. 
The subject’s plasma ammonia level should be < 100 µmol/L or within the range of historical ammonia levels obtained when the subject was clinically stable in order to 
perform the neuropsychological tests. The 0-hour plasma ammonia sample (for AUC0-24 of plasma ammonia) local laboratory result (STAT sample) may be used to confirm 
plasma ammonia levels. The results must be back prior to starting the neuropsychological tests.  
m. The subject’s plasma ammonia level should be < 100 µmol/L or within the range of historical ammonia levels obtained when the subject was clinically stable in order to 
receive [1-13C]sodium acetate and DTX301 (Day 1 only). If the ammonia level is inconsistent with the subject’s clinical status, the ammonia level may be repeated to ensure 
accurate results. If the subject is deemed clinically unstable, [1-13C]sodium acetate and DTX301 (Day 1 only) will be held until the subject is determined to be clinically 
stable. Rescreening procedures may apply (Screening and Day 1 only). On Day 1 and at Weeks 6, 12, 24, and 52, the 24-hour (T 24) plasma ammonia from the local (STAT 
sample) may be used. The result must be back prior to dosing with [1-13C]sodium acetate and DTX301 (Day 1 only). On Day 1, the same T 24 local laboratory (STAT 
sample) can serve as the DTX301 predose plasma ammonia result, if drawn within 12 hours or less of dosing with DTX301. If not, a new plasma ammonia (STAT sample) is 
to be collected prior to dosing with DTX301. 
n. 
A single sample for plasma ammonia (STAT sample at local laboratory) to be collected and reviewed prior to discharging the subject after DTX301 infusion. 


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o. 
Viral shedding determination in saliva, stool, and urine to be performed at Weeks 6, 10, and 12 and on Days 46, 58, 62, and 78 (Table 15-2). Samples will be collected until 
negative on 3 consecutive occasions. Subjects will be provided an appropriate container to collect a stool sample at home. 
p. 
12-Lead ECG to be performed at approximately 1 hour after the start of DTX301 infusion. 
q. 
PROMIS questionnaire to be completed prior to neuropsychological tests on Day 0 and at Week 52. 
r. 
At inpatient clinic visits, [1-13C]sodium acetate is to be administered orally on the second day of inpatient admission, after all samples for AUC0-24 plasma ammonia and orotic 
acid determination (over 24 hours) have been collected. Prior to administering [1-13C]sodium acetate, the site must confirm the subject’s plasma ammonia level. The 24-hour 
(T 24) plasma ammonia from the local laboratory (STAT sample) may be used. The subject’s plasma ammonia level should be < 100 µmol/L or within the range of historical 
ammonia levels obtained when the subject was clinically stable. If the ammonia level is inconsistent with the subject’s clinical status, the ammonia level may be repeated to 
ensure accurate results. If the subject is deemed clinically unstable, [1-13C]sodium acetate will be held until the subject is determined to be clinically stable. On Day 1, the 
same local laboratory (STAT sample) can serve as the DTX301 predose plasma ammonia used for this assessment should be drawn within 12 hours or less of dosing with 
DTX301. If not, a new plasma ammonia (STAT sample) is to be collected prior to dosing with DTX301. Subjects will fast for at least 6 hours, including liquids containing 
protein, sugar or carbonate, prior to administration of [1-13C]sodium acetate. After dosing, subjects will continue to fast for at least 4 hours. Water is allowed ad 
libitum. 
s. 
Samples to be collected before dosing with [1-13C]sodium acetate (time 0) and at approximately 0.5, 1, 1.5, 2, 3, and 4 hours after dosing with [1-13C]sodium acetate. Subjects 
will fast for at least 6 hours, including liquids containing protein, sugar or carbonate, prior to administration of [1-13C]sodium acetate. After dosing, subjects will continue to 
fast for at least 4 hours. Water is allowed ad libitum. During Screening, assessment of rate of ureagenesis may be repeated if discrepant with subject’s clinical status and 
severity. 
t. 
Once eligibility is confirmed, the study site should register the visit with IWRS. Study personnel must schedule the dosing visit in IWRS ideally 7 days but no less than 3 days 
prior to the actual visit date at the study site in order to allow for adequate shipment time and delivery of DTX301 to the study site. 
u. 
The start of DTX301 infusion should be after all samples for the determination of the rate of ureagenesis have been collected. Prior to the start of DTX301 infusion, the study 
site must confirm that the subject’s plasma ammonia level on Day 1 (predose) is < 100 µmol/L for patients who historically maintain normal ammonia levels, and the subject 
is clinically stable; OR the subject’s plasma ammonia level on Day 1 (predose) is < 200 µmol/L, for patients who historically are not able to fully control ammonia levels with 
baseline management, and the subject is clinically stable. If the Day 1 (predose) ammonia level is inconsistent with the subject’s clinical status, the ammonia level may be 
repeated to ensure accurate results. NOTE: If the subject is deemed clinically unstable, dosing will be held, and the subject can be rescreened once the subject is determined to 
be clinically stable. The same 24-h time point (T 24) from local laboratory (STAT sample) AUC0-24 of plasma ammonia can serve as the DTX301 predose plasma ammonia 
result, if drawn within 12 hours or less of dosing with DTX301. If not, a new plasma ammonia (STAT sample) is to be collected prior to dosing with DTX301. 
v. 
Adjustments to ammonia scavenger therapy may be considered following the Week 12 and Week 24 visits. The subject must be clinically stable and under good metabolic 
control before changes can be initiated or progressed. The risks of making adjustments to baseline treatment on their own, without express guidance from the site, will be 
reinforced with the subject at site visits. Modification of ammonia scavenger therapy cannot occur at the same time as changes in protein-restricted diet. Changes to baseline 
treatment cannot occur while the subject is treated with corticosteroids or within a 2-week period of completing a corticosteroid taper. Modification of baseline treatment will 
be individualized based on review of the totality of longitudinal clinical and laboratory data for each subject, including ammonia levels, plasma ammonia AUC0-24, subject 
clinical stability/asymptomatic status, neurocognitive status, and subject-reported outcomes. Rate of ureagenesis cannot be used for decision-making in modification of 
ammonia scavenger therapy or protein-restricted diet and results will not be made available to the investigative sites until the end of the study. 


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Table 15-2 
Schedule of Events – Clinic or Home Visits During the Initial 12-Week Treatment Period 
Procedure 
 
Treatment Period 
Week 
1 
2 
3 
4 
5 
6 
7 
8 
9 
10 
11 
12 
Day 
5 
9 
18 
22 
32 
36 
46 
50 
54 
58 
62 
66 
74 
78 
Visit Window 
(Days) 
±1 
±1 
±1 
±1 
±1 
±1 
±1 
±1 
±1 
±1 
±1 
±1 
±1 
±1 
Clinical chemistry (including LFTs)a 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
LFTs (local laboratory, STAT sample) a 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Spot ammonia (local laboratory STAT 
sample)b 
X 
X 
 
X 
 
X 
 
X 
 
X 
 
X 
X 
 
Saliva, urine, and stool for viral shedding 
 
 
 
 
 
 
 
X 
 
 
X 
X 
 
 
X 
Abbreviations: LFT, liver function test; 
 
. 
Note: At any time after initiation of prophylactic corticosteroid regimen, additional assessments of plasma ammonia levels, amino acid profiles, or any other biomarker 
to assess subject safety and clinical status may be performed, at the discretion of the investigator and as clinically indicated. 
a. 
Through Week 12, one sample for LTFs is collected as part of clinical chemistry and sent to the central laboratory for analysis. A second sample for LFTs only is collected 
and sent to the local laboratory (STAT sample). 
b. 
Through Week 12, one sample for spot ammonia is collected approximately once a week and sent to the local laboratory (STAT sample). 
c. 
Samples for viral shedding are to be collected at Weeks 6, 10, and 12 (see Table 15-1) and on Days 46, 58, 62, and 78 until negative on at least 3 consecutive occasions for 
each matrix. 
 


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15.2 Quality of Life Questionnaire 
15.2.1 
PROMIS Questionnaire 


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15.3 Protocol Amendment History and Summary of Changes 
15.3.1 
Amendment 1 (dated 18 August 2016) 
The primary objective of Amendment 1 of the protocol, 301OTC01, is to address feedback received 
from the US Food and Drug Administration, the Medicines and Healthcare Products Regulatory 
Agency, and the National Institutes of Health Recombinant DNA Advisory Committee. 
An overview of changes includes the following: 
• 
Section 1.3.1 (Design Rationale) has been updated to include rationale for defining 
hyperammonemia as ≥100 µmol/L. 
• 
The dosing interval between subjects within a cohort (14 days [Cohorts 1 and 2] and 7 days 
[subsequent cohorts]) has been revised. Additionally, Section 1.3.1 (Design Rationale) has been 
updated to include rationale for this change. 
• 
Section 1.3.2 (Dosing Rationale) has been revised to provide rationale for the new starting dose 
of 2.0 × 1012 genome copies (GC)/kg. 
• 
The rate of ureagenesis will now be the main efficacy parameter to identify the optimal biological 
dose (OBD) of DTX301. The AUC0-24 for serum ammonia will still be evaluated to help 
determine the efficacy of DTX301 (Section 2). 
• 
The candidate doses to determine the OBD of DTX301 have been revised as follows (Section 
3.1): 
• 
Dose 1: 2.0 × 1012 GC/kg (new starting dose) 
• 
Dose 2: 6.0 × 1012 GC/kg 
• 
Dose 3: 1.0 × 1013 GC/kg 
• 
The number of inpatient visits has been reduced from 8 to 5 to alleviate undue burden to subjects 
(Section 3.2.3). 
• 
The timing for tapering or discontinuing ammonia scavenger therapy has been revised. 
Investigators will now consider an adjustment to ammonia scavenger therapy following the visits 
at Week 12 and Week 24, after the most recent monitoring results are available (Section 3.2.4). 
• 
The study stopping criteria have been revised based on feedback received from regulatory 
authorities (Section 3.2.5). 


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• 
Inclusion criterion #2 has been updated to include specific examples of enzymatic, biochemical, 
or molecular testing that may be performed to confirm ornithine transcarbamylase (OTC) 
deficiency (Section 4.1). 
• 
Inclusion criterion #5 has been added to ensure that the subject's OTC deficiency is stable prior to 
receiving DTX301 (Section 4.1). 
• 
Inclusion criterion #10 was removed and incorporated into exclusion criterion #13 to have one 
cohesive criterion for excluding subjects that are pregnant (Section 4.2).  
• 
Due to reduction of inpatient visits, the rate of ureagenesis will now be measured at Screening, on 
Day 1, and at Weeks 6, 12, 20, 24, and 52 (Section 8.1.1). Additionally, if clinically indicated, the 
rate of ureagenesis can be measured at any outpatient visit (scheduled or unscheduled) 
• 
The decision criteria for determining whether to start steroids for suspected vector-induced 
hepatitis have been revised (Section 8.2.4.1.2).  
• 
The overall number of neuropsychological evaluations that will be performed has been reduced 
based on feedback from regulatory authorities (Section 8.5). 
• 
Weeks 18 and 22 have been added as a clinic or home visit to collect samples for clinical 
chemistry. 
• 
Specifying that subjects will receive a prescribed diet during each inpatient stay and that an 
adjustment may be made to the subject's prescribed diet has been removed from the protocol. 
• 
Minor editorial revisions. 
15.3.2 
Amendment 2 (dated 20 December 2016) 
The primary objective of Amendment 2 of the protocol, 301OTC01, is to address feedback received 
from the US Food and Drug Administration. 
An overview of changes includes the following: 
• 
Clarified that ammonia will be analyzed in plasma, not serum (global protocol revision). 
• 
Clarified that plasma ammonia levels must be <100 µmol/L prior to both administration of the 
neuropsychological tests (Section 8.5) and [1-13C]acetate administration (Section 6.3.1). 
• 
Revised the language regarding tapering of ammonia scavenger therapy following feedback from 
the FDA (Section 3.2.4). 


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• 
Added language regarding retesting of liver function tests in the event that possible vector-
induced hepatitis is suspected following feedback from the FDA (Section 8.2.4.1.2). 
• 
Added collection of samples to test for antibodies against ornithine transcarbamylase. 
• 
The schedule of events has been revised, as needed (Table 15-1). 
• 
Minor editorial revisions. 
15.3.3 
Amendment 3 (dated 07 February 2017) 
The primary objective of Amendment 3 of the protocol, 301OTC01, is to address feedback received 
from the United Kingdom (UK) Medicines and Healthcare Products Agency (MHRA) and the Gene 
Therapy Advisory Committee (GTAC). 
An overview of changes from Amendment 2 (20 December 2016) to Amendment 3 (07 February 
2017) includes the following: 
• 
Added UK MHRA-requested language around definition of abstinence as a form of birth control 
(Section 4.1). 
• 
Per UK MHRA request, added that following data monitoring committee (DMC) review when a 
stopping rule is met, if the decision is to restart enrollment, a substantial amendment will need to 
be approved by the regulatory authority (Sections 3.2.5 and 9.3). 
• 
Per GTAC request, provided further justification and clarification that the neuropsychological 
battery of testing is an important assessment for OTC deficiency patients and beyond this 52-
week study, it will be performed every 2 years during the 4-year extension study for each study 
subject (Section 8.5). 
• 
Per GTAC request, added language allowing study subjects to request rest time during 
administration of the neuropsychological battery (Section 8.5). 
• 
Per study sites’ request, clarified that the predose plasma ammonia used to determine DTX301 
dosing must be drawn within 12 hours or less of dosing (Section 3.2.2.2). 
• 
Per study sites’ request, clarified wording to reflect that flexibility in performing the ureagenesis 
test first is allowed so long as it does not overlap temporally with the plasma ammonia AUC0-24 
and urinary orotic acid levels over the 24-hour collection period (Section 3.2.2.1). 


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• 
Per Dimension Therapeutics (DMTX), deleted inclusion criterion #7 since there is no requirement 
to taper ammonia scavenger medications (Section 4.2). 
• 
Per DMTX, corrected the exclusion criterion (#9) for the anti-AAV8 neutralizing antibody titer to 
≥ 1:5 from > 1:5 (typographical error) (Section 4.2). 
• 
Per DMTX, clarified rescreening of patients (Section 3.2.1). 
• 
Per DMTX, changed the start of the DMC assessment for dose escalation from all subjects in a 
dose cohort having completed Week 6, to all subjects in a dose cohort having completed Week 12 
(Section 1.3.1). 
• 
Per DMTX, changed the alanine aminotransferase (ALT) threshold for considering starting 
steroid treatment from 2.5 × upper limit of normal (ULN), to greater than the ULN (Section 
8.2.4.1.2). Therefore, exclusion criterion #4 adjusted to ALT or aspartate aminotransferase > 
ULN from > 2.0 × ULN (Section 4.2). 
• 
Per DMTX, increased enzyme-linked immunospot assessments to approximately weekly during 
already scheduled visits through Week 12 for more frequent monitoring of immune response 
(Section 8.2.5.2 and Table 15–1). 
• 
Per DMTX, added liver function tests to be performed at local laboratory (STAT sample) during 
the  scheduled collections approximately every 4 days up through Week 12 in the interest of 
closer monitoring and faster turnaround of liver function testing results (Section 8.2.4.1.1, 
Table 8–1, and Table 15–1). 
15.3.4 
Amendment 4 (dated 11 June 2019) 
The primary objective of Amendment 4 of the protocol, 301OTC01, is to provide details on the 
inclusion of the additional subjects as expansion of Cohort 3, already foreseen in the original 
protocol, and to add Cohort 4 (Dosing Process Optimization). Subjects in Cohort 4 will receive 
DTX301 at the optimal biological dose and will receive a prophylactic corticosteroid regimen, 
intended to achieve prophylaxis of vector-induced hepatitis. 
An overview of changes from Amendment 3 (07 February 2017) to Amendment 4 (11 June 2019) 
includes the following: 


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• 
The sponsor name was updated globally from Dimension Therapeutics, Inc. to Ultragenyx 
Pharmaceutical Inc. 
• 
The sponsor signatory was updated globally to 
 MD, PhD.  
• 
The medical monitor was updated to 
 MD.  
• 
An ongoing AAV8 gene transfer clinical study in Crigler-Najjar syndrome, which uses a 
prophylactic steroid regimen, was added as a reference and cited as applicable (Sections 1.2, 
8.2.4.1.2).  
• 
The generation of fewer empty particles via a DTX301 manufacturing process, which was 
presented as a difference between this clinical study and previous gene transfer studies, was 
removed for accuracy (Section 1.2).  
• 
The changes detailed in Addendum A to Amendment 3 (dated 02 March 2017) were incorporated. 
The purpose of Addendum A was to align Figure 3–1 Study Design with the main text of the 
study protocol (Section 3.2). 
• 
The changes detailed in the country-specific Addendum B to Amendment 3 (dated 21 April 2017) 
for sites in the United Kingdom were incorporated. The purpose of the UK-specific Addendum B 
was to add the requirement that no subjects from UK sites can be dosed until at least 42 days after 
the first subject in the study (ie, first subject in Cohort 1) has been dosed. This change was made 
to address feedback received from the Gene Therapy Advisory Committee (GTAC) 
(Sections 1.3.1, 3.1, Figure 3–1). 
• 
The process for enrollment of additional subjects to Cohort 3 (Cohort Expansion) and an 
additional cohort (Cohort 4 [Dosing Process Optimization] was added (Sections 1.3.1, 3.1, 3.2, 
5.2, 10.5.1). 
• 
A reference to ongoing safety results from this study (Study 301OTC01) was added (Sections 
1.3.1, 14). 
• 
An ongoing AAV gene transfer clinical study in hemophilia B, which is dosing patients at a 
minimum of 1 day apart, was added as a reference and cited as applicable (Section 1.3.1).  
• 
The details of the prophylactic corticosteroid regimen to be implemented for Cohort 4 (Dosing 
Process Optimization) were added (Sections 1.3.1, 3.1, 8.2.4.1.1, 8.2.4.1.2). 


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• 
The screening period was extended and will begin at Day –35 (Sections 3.1, 3.2.1, 15.1, 
Table 15-1, Figure 3–1). 
• 
The decision to adjust or taper ammonia scavenger medications was updated to be made based on 
the investigator’s review of the totality of clinical and laboratory data (Sections 3.2.4, 15.1, 
Table 15-1 [footnote v]). 
• 
Instructions for dose preparation and administration of [1-13C] were updated according to the 
manufacturer and referenced to the ureagenesis manual (Sections 6.2.5, 6.3.1).  
• 
The duration of fasting before and after administration of [1-13C] sodium acetate was added 
(Sections 8.1.1, 15.1, Table 15-1 [footnotes r and s]).  
• 
The timing of DMC meetings was updated to account for additional subjects and 1 additional 
cohort (Sections 9.3, 10.5.1).  
• 
Text was removed that stated the statistical analysis plan will be finalized prior to the start of the 
study (Section 10).  
• 
The definition of the baseline rate of ureagenesis was updated (Section 10.5.2.1). 
• 
The presentation of other laboratory results and neuropsychological tests was updated to reflect 
the planned data presentation (Sections 10.5.3.6, 10.5.4) 
• 
Flexibility was added to the timing of the interim analysis. The statement that interim analyses 
would not bias the conduct of the study was removed (Section 10.5.7). 
15.3.5 
Amendment 5 (dated 25 February 2020) 
The primary objective of Amendment 5 of the protocol, 301OTC01, is to address written requests 
from the US Food and Drug Administration to provide more comprehensive guidance on monitoring 
of ammonia levels throughout the study, guidance to investigators on monitoring hyperammonemic 
crises, and more explicit guidance to investigators regarding tapering and discontinuation of ammonia 
scavenger medications and protein-restricted diet.  
An overview of changes from Amendment 4 (11 June 2019) to Amendment 5 (25 February 2020) 
includes the following: 


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• 
The medical monitor was updated to 
 MD to accurately reflect study personnel 
(Title Page). 
• 
The protocol amendment history and summary of changes were moved from the beginning of the 
protocol (ie, directly after the protocol approval page) to Appendix 15.3. This change was 
administrative in nature and does not change the content of the protocol (Section 15.3). 
• 
The age cutoff for presentation of disease signs and symptoms, which is used to delineate 
neonatal-onset from late-onset ornithine transcarbamylase (OTC) deficiency, was updated from 
≤ 1 month of age (neonatal onset) and ≥ 1 month of age (late onset) to ≤ 30 days of age (neonatal 
onset) and > 30 days of age (late onset). This change was made to align with the DTX301 clinical 
development documents and cited literature (Sections 1, 4.1). 
• 
The term hyperammonemic crisis (HAC) was introduced and defined explicitly to align with the 
Urea Cycle Disorders Consortium definition. This addition will ensure standardized monitoring 
of HACs throughout the remainder of this study (Sections 1, 1.3.1. 2, 3.2.6, 10.4). 
• 
The list of AAV8 clinical studies that are referenced in the introduction were updated to align 
with the Investigator’s Brochure and the most recent information (Section 1.3.1) 
• 
The timing of dosing for subjects in the United Kingdom in Cohort 1 was removed because 
Cohort 1 enrollment is now completed (Section 1.3.1, Figure 3-1). 
• 
The observed timing of elevations in liver enzymes following DTX301 administration was 
updated from “5 to 7 weeks” to “8 days to 7 weeks” after vector administration to reflect ongoing 
data from this Phase 1/2 study (301OTC01; Section 1.3.1).  
• 
An additional clinical trial (ClinicalTrials.gov identifier: NCT02716246) was referenced as 
justification for the prophylactic steroid regimen to be introduced in Cohort 4 (Dosing Process 
Optimization; Sections 1.3.1, 8.2.4.1.2).  
• 
The definition of baseline for the rate of ureagenesis was removed globally with the intent that 
baseline definitions will be presented in the statistical analysis plan (Sections 2, 10.5.2.1). 
• 
The text, “in the setting of tapering or discontinuing ammonia scavenger medications,” was 
removed from exploratory endpoints 2 and 3 (ie, urinary orotic acid excretion and glutamine and 
glutamate). The change was made because the intent is to assess these endpoints in all subjects, 
regardless of baseline treatment status (Section 2).  


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• 
The specified timing, “weekly,” was removed from the exploratory endpoint that evaluates use of 
ammonia scavengers. This change was made to reflect the manner by which the data are being 
captured and reported and to reflect subject management, which requires daily intake of 
scavengers at a prescribed dose (Sections 2, 8.7.2, 10.4). 
• 
The exploratory endpoints and corresponding assessments determined by the enzyme-linked 
immunospot [ELISPOT] assay and related to cell-mediated immune response to AAV8 and OTC 
were removed globally. These assays are exploratory in nature and to date have not revealed 
informative results, and require notable blood volume to be collected from subjects (Sections 2, 
8.2, 8.2.4.1.1, 10.4, 10.5.3.6, Table 15-1).  
• 
The sample size was updated from “approximately 6 to 18 subjects” to “up to 18 subjects” to 
reflect the current enrollment status of 9 subjects and plans to continue enrollment (Section 3.2).  
• 
It was added that “where available, agreed upon by the investigator and allowed by local 
regulation, an outpatient clinic visit may take place as home health services.” The Week 20 visit 
remains a mandatory outpatient clinic visit. This change was made to allow increased flexibility 
for protocol-specified abbreviated visits that may be performed as home health visits and have the 
potential to reduce subject burden in certain situations (Sections 3.2, 3.2.3, 3.2.3.2, 12.4, 
Figure 3-1, Table 15-1).  
• 
More comprehensive guidance and testing specifications were added to the rescreening procedure 
to ensure consistent testing and evaluations prior to enrollment and dosing (Section 3.2.1, 
Table 15-1). 
• 
The rules for administering [1-13C]sodium acetate and neuropsychological tests were updated as 
follows: The subject’s plasma ammonia level should be < 100 µmol/L or within the range of 
historical ammonia levels obtained when the subject was clinically stable in order to receive 
[1-13C]sodium acetate. If the ammonia level is inconsistent with a subject’s clinical status, the 
ammonia level may be repeated to ensure accurate results. This change was made to better reflect 
patient status with long-standing metabolic and clinical management (Sections 3.2.1, 6.3.1, 8.3.2, 
8.5, Table 8-1, Table 15-1). 
• 
Inclusion criterion #5 and globally affected text presenting the ammonia criteria prior to the start 
of DTX301 administration were updated as follows: Subject’s plasma ammonia level on Day 1 
(predose) is < 100 µmol/L, for patients who historically maintain normal ammonia levels, and the 
subject is clinically stable; OR the subject’s plasma ammonia level on Day 1 (predose) is 


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< 200 µmol/L, for patients who historically are not able to fully control ammonia levels with 
baseline management, and the subject is clinically stable. If the Day 1 (predose) ammonia level is 
inconsistent with the subject’s clinical status, the ammonia level may be repeated to ensure 
accurate results. This change was made to better reflect patient status with long-standing 
metabolic and clinical management (Sections 3.2.2.2, 4.1, 5.1, Table 15-1). 
• 
Exclusion criterion #1 was updated as follows: At Screening or Baseline (Day 0), plasma 
ammonia level ≥ 100 µmol/L for patients who historically maintain normal ammonia levels; OR 
plasma ammonia level ≥ 200 µmol/L for patients who historically are not able to fully control 
ammonia levels with baseline management; OR signs and symptoms of hyperammonemia, with 
documented elevated ammonia level, during the 4-week period preceding Day 0. If the ammonia 
level is inconsistent with the subject’s clinical status, the ammonia level may be repeated to 
ensure accurate results. This change was made to better reflect patient status with long-standing 
metabolic and clinical management (Section 4.2). 
• 
It was added that the assessment of rate of ureagenesis may be repeated during Screening if 
discrepant with subject’s clinical status and severity. The rate of ureagenesis is a direct in vivo 
assessment of the efficiency of the urea cycle and therefore should be compatible with patient 
severity given the understanding that neither ammonia scavenger therapy nor protein-restricted 
diet directly alters the cycle (Sections 3.2.1, 8.1.1, 8.3.1, 10.5.2.1, Table 15-1).  
• 
The details of obtaining spot plasma ammonia prior to dosing were clarified, and the requirement 
for a plasma ammonia (STAT sample) within 12 hours of DTX301 dosing was added explicitly 
(Section 3.2.2.2, Table 15-1).  
• 
It was added that at any point between scheduled visits (and after initiation of a prophylactic 
steroid regimen) additional testing of liver function tests, plasma ammonia, or other biomarkers to 
assess subject safety and clinical status may be performed, at the discretion of the investigator. 
This text was added to make it explicit that investigators have the flexibility to perform additional 
testing and that subject safety is being monitored closely throughout the study (Sections 3.2.3, 
3.2.4, 8.2.4, 8.2.4.1, 8.2.4.1.2, Table 15-1). 
• 
Spot ammonia testing was made explicit and added to additional visits to ensure ammonia is 
being monitored closely throughout the clinical study (Sections 3.2.3.1, 8.2, Table 15-1, 
Table 15-2). 


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• 
Text was added to explicitly state that subjects will be re-educated on the risks of making 
adjustments to baseline treatment on their own, without the clear guidance of the study site 
investigator (Sections 3.2.4, 8.7.2, Table 15-1). 
• 
Additional rules for changes to baseline treatment (ie, ammonia scavenger medication and 
protein-restricted diet) were added to ensure standardized implementation. The additional rules 
specify that changes to baseline treatment cannot occurring during or within 2 weeks of 
corticosteroid treatment. Changes to ammonia scavenger medication and protein-restricted diet 
must not occur at the same time (Sections 3.2.4, 3.2.5, 8.2.4.1.2, 8.7.2, Table 15-1). 
• 
Explicit text was added that rate of ureagenesis cannot be used for decision-making in 
modification of ammonia scavenger therapy or protein-restricted diet and results will not be made 
available to the investigative sites until the end of the study (Sections 3.2.4, Table 15-1). 
• 
Specific guidance was added for considering reinstitution of ammonia scavenger therapy and for 
implementing a second round of modification of baseline treatment. This guidance was added to 
ensure standardized modifications and assurance of subject safety (Sections 3.2.4). 
• 
Additional guidance was added for modification of protein-restricted diet. This guidance was 
added to ensure standardized modifications and assurance of subject safety (Section 3.2.5).  
• 
Inclusion criterion #6 was updated to specify that a stable dose of ammonia scavenger therapy 
must be “ongoing daily.” This text was added to ensure the intent of this criterion was explicitly 
stated (Section 4.1).  
• 
The number of medical personnel (in addition to the study site pharmacist) who must check the 
dosing calculations for [1-13C]sodium acetate was updated from “a minimum of 2 medical 
personnel” to “a member of medical personnel” (Section 6.3.1).  
• 
Treatment compliance was updated to include adherence to ammonia scavenger medication 
regimens and protein-restricted diet (Section 6.3.3).  
• 
The assessment of vector genome determination was removed globally. The results to date for 
this parameter, including the highest dose planned to be administered for the DTX301 program, 
have consistently demonstrated sequential reduction of blood viral load without rebound in 
values; therefore, based on medical consideration of results to date and to reduce subject burden, 
additional testing and collection of subject blood is not warranted (Sections 8.2, 10.5.3.6, 
Table 15-1). 


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• 
Electrocardiogram testing was removed from predose on Day 1 to reduce subject burden and 
based on medical evaluation of study results to date (Section 8.2.3). 
• 
It was added that prior to initiating the prophylactic steroid regimen (Cohort 4), the subject must 
be assessed as clinically and metabolically stable, and intercurrent illnesses (eg, viral infection) or 
concomitant medications known to affect transaminases, be excluded (Section 8.2.4.1.2). 
• 
Additional guidance was added to specify when ad hoc 24-hour plasma ammonia assessments 
should be considered to ensure subject safety is paramount (Section 8.3.2).  
• 
It was explicitly stated that hospitalization due to hyperammonemic crisis will be considered a 
serious adverse event (Section 9.1.1.2). 
• 
It was added that adverse events will be assessed in terms of the relationship to corticosteroid 
regimen, in addition to the previously included assessments of relationship (eg, study product, 
[1-13C] sodium acetate, OTC deficiency, or hyperammonemia). This update was made per a 
request from the Data Monitoring Committee (Sections 9.1.2.1, 9.1.4).  
• 
The version of the NCI CTCAE to be used was updated from Version 4.03 to the most current 
version (Sections 9.1.3, 14). 
• 
An Data Monitoring Committee meeting was introduced after completion of Week 12 for the first 
3 subjects dosed in Cohort 4. This meeting was adjusted per a request from the Data Monitoring 
Committee (Section 9.3).  
• 
The analysis of rate of ureagenesis was updated to include the relative percentage to normal 
healthy adults (Section 10.5.2.1).  
• 
The analysis of plasma ammonia was updated to include time-normalized plasma ammonia 
(Section 10.5.2.2).  
• 
Viral shedding, AAV8 neutralizing antibody, and AAV8 binding antibody IgG assay (ELISA) 
assessments were reduced based on medical consideration of results to date and to reduce subject 
burden (Table 15-1, Table 15-2).  
 
 

SAP_001.pdf: 
 
Confidential 
 
 
 
 
Statistical Analysis Plan 
 
IND Number: 017190 
EUDRACT NUMBER: 2016-001057-40 
 
 
A Phase 1/2, Open-Label Safety and Dose-Finding Study of Adeno-Associated 
Virus (AAV) Serotype 8 (AAV8)-Mediated Gene Transfer of Human 
Ornithine Transcarbamylase (OTC) in Adults with Late-Onset OTC 
Deficiency 
 
Protocol Number: 301OTC01 
 
Sponsor: 
Ultragenyx Pharmaceutical Inc. 
840 Memorial Drive 
Cambridge, MA 02139 
Sponsor Contact: 
 
Senior Director, Biostatistics, Biometrics 
Ultragenyx Pharmaceutical Inc. 
PPD Contact: 
 
Senior Biostatistician, Biostatistics and Programming 
PPD 
Segreen Business Park, Via S. Bovio, 3, 
S. Felice, Segrate (MI), Italy, 20090 
 
Version of SAP:  
4.0 
Date of SAP:  
25 November 2021 
 
 
 
 
 


Statistical Analysis Plan 
 
301OTC01 
1 
Confidential 
Statistical Analysis Plan Amendment 
Summary of Changes 
The original 301OTC01 Statistical Analysis Plan (Version 1.0, dated 11 May 2017) was amended 3 times. Major changes in each SAP 
version are listed in Table 1. 
Table 1: 
Summary of SAP Versions (Original SAP Version 1.0, Dated 11 May 2017) 
Version 
(Version Date) 
Summary of Changes 
Version 2.0 
(10 November 2017) 
• 
Section 3.1, Overall Study Design and Plan: Clarified that DMC review of a cohort will occur following the collection of a 
minimum of 12 weeks (84 days) of safety data (with at least 6 weeks of supplementary efficacy data). 
• 
Section 3.2, Implementation of the N-CRM Model: Revised section to define the proposed N-CRM model for the study and to 
provide the details necessary for its implementation. 
• 
Section 4.1, Baseline and Change from Baseline: Added a rule for deriving the baseline value for absolute 13C-urea AUC0-240min 
percent of normal. 
• 
Section 4.15, Analysis Sets: Added the MTD Determining Set. 
• 
Section 8.1, Rate of Ureagenesis: Updated the method for estimating the rate of ureagenesis for individual subjects. For summary 
statistics and the longitudinal plot of change from Baseline, removed the time points 0.5, 1, 1.5, 2, and 3 hours relative to 
[1-13C]sodium acetate administration. 
• 
Section 8.3.1, Supplementary Ureagenesis Parameters: Removed absolute 13C-urea AUC0-240min from parameters to be derived. 
Removed units conversion factor for absolute 13C-urea AUC0-240min. For summary statistics, added absolute 13C-urea AUC0-240min 
percent of normal. 
• 
Section 9.1, Adverse Events: Removed summaries by System Organ Class and Preferred Term for the following categories: 
TEAEs leading to study discontinuation, serious TEAEs by relationship, and TEAEs with Grade ≥ 3. 
Version 3.0 
(08 July 2021) 
• 
Updated Sponsor name from Dimension Therapeutics, Inc. to Ultragenyx Pharmaceutical Inc. 
• 
Section 2, Objectives and Endpoints: Updated to align with Protocol Amendment 5. 
• 
Section 3.1, Overall Study Design and Plan: Updated to align with Protocol Amendment 5. 
• 
Section 3.2, Implementation of the N-CRM Model: Added the definition of DLT. Added that Cohort 3 expansion and Cohort 4 
will not be included in the dose-finding assessment. 
• 
Section 3.3, Treatments: Added Cohort 4 (1.0 × 1013 GC/kg plus prophylactic corticosteroids). Added that efficacy data will be 
modeled by dose level (ie, Cohorts 3 and 4 will be combined) and that other data will be summarized and reported by cohort. 
• 
Section 4.1.1, Ureagenesis Baseline: Updated the rules for deriving baseline values for ureagenesis parameters. Clarified that, 
when deriving baseline values for non-AUC supplementary ureagenesis parameters, Day 1 results will not be taken into 


Statistical Analysis Plan 
 
301OTC01 
2 
Confidential 
consideration if excluded per the rule for deriving the baseline value for the rate of ureagenesis. Added that derived and reported 
ureagenesis parameters will be summarized. 
• 
Section 4.1.2, Other Parameters Baseline: Added spot ammonia and urinary orotic acid AUC0-24hr. 
• 
Section 4.1.3, Change from Baseline: Updated the formula for calculating percent change from Baseline. 
• 
Section 4.9, Sample Size: Updated to align with Protocol Amendment 5. 
• 
Section 4.14, Unscheduled Visits: Added summaries of worst postbaseline value for hematology, chemistry, urinalysis, and amino 
acid parameters. Added that unscheduled visits will be included in figures for individual subjects. 
• 
Section 5.1, COVID-19: Added that no changes to planned analyses due to the impact of COVID-19 were made. Added pandemic 
start and end dates for participating countries. 
• 
Section 5.2, Disposition: Added that all disposition-related information for enrolled subjects will be listed. 
• 
Section 6.1, Demographics: Added that Screening and Baseline weight will be summarized. Added that the number of subjects by 
age category will be displayed. Added that all demographic data and baseline characteristics for subjects in the Safety Set will be 
listed. 
• 
Section 6.2, Medical History: Added that medical history data will be sorted in alphabetical order by System Organ Class and that 
Preferred Terms will be sorted in descending order by frequency within each System Organ Class. Added that medical history 
data will be listed. 
• 
Section 6.3, OTC Deficiency Medical History: Time since OTC deficiency became stable and time since stable dose of ammonia 
scavenger therapy will be reported in weeks instead of years. OTC deficiency medical history data for subjects in the Safety Set 
will be listed. 
• 
Section 7.1 Prior and Concomitant Medications: Prior and concomitant medications for subjects in the Safety Set will be listed. 
• 
Section 7.1.1, Prior Medications and Section 7.1.2, Concomitant Medications: Medications will be sorted in descending order by 
ATC level 4 term based on counts in the overall column.  
• 
Section 7.3, [1-13C]Sodium Acetate: Added section. Details related to [1-13C]sodium acetate administration for subjects in the 
Safety Set will be listed. 
• 
Section 8.1, Rate of Ureagenesis: Specified that MMRM outputs will include estimates for between-DTX301 dose (overall and by 
visit) comparisons. Removed summary statistics for rate of ureagenesis and longitudinal plot of change from Baseline to 4 hours 
postdose in rate of ureagenesis. Removed Yudkoff 2017 reference. 
• 
Section 8.2, Plasma Ammonia Area Under the Curve from Time 0 to 24 Hours: Summary statistics and listings will include time-
normalized plasma ammonia AUC0-24hr, which will be calculated by dividing AUC by the actual number of minutes between the 
0- and 24-hour time points and multiplying by 60. Added the geometric mean, CV%, and geometric CV% for plasma ammonia 
AUC0-24hr and time-normalized plasma ammonia AUC0-24hr by visit. Added the mean and standard deviation for the logarithmic 
transformation of plasma ammonia AUC0-24hr and time-normalized plasma ammonia AUC0-24hr. Added a linear MMRM to provide 
a comparison vs Baseline of the logarithmic transformation of plasma ammonia AUC0-24hr for each DTX301 dose. Updated the 
list of figures to be generated. 


Statistical Analysis Plan 
 
301OTC01 
3 
Confidential 
• 
Section 8.3.1, Supplementary Ureagenesis Parameters: Removed 13C-bicarbonate as a parameter to be derived. Added a linear 
MMRM to evaluate the association between change from Baseline in absolute 13C-urea AUC0-240min and DTX301 dose. Added a 
linear MMRM to provide a comparison vs Baseline of the logarithmic transformation of absolute 13C-urea AUC0-240min for each 
DTX301 dose. Added the geometric mean, CV%, and geometric CV% for absolute 13C-urea AUC0-240min and percent of normal 
absolute 13C-urea AUC0-240min by visit. Added the mean and standard deviation for the logarithmic transformation of absolute 
13C-urea AUC0-240min and percent of normal absolute 13C-urea AUC0-240min. Updated the list of figures to be generated. 
• 
Section 8.3.2, Hyperammonemic Crises: Revised summary statistics to be generated. The number of HACs and the number of 
patients with HAC will be summarized by DTX301 dose, overall and by occurrence period (predose vs postdose). Predose HAC 
is defined as a HAC that occurred within the 12 months before dosing. 
• 
Section 8.3.3, 24-Hour Urinary Orotic Acid Excretion and Spot Urinary Orotic Acid: Urinary orotic acid AUC0-24hr and time-
normalized urinary orotic acid AUC0-24hr will be derived following the same rules defined for plasma ammonia AUC0-24hr and 
time-normalized plasma ammonia AUC0-24hr. These parameters will be listed. Spot urinary orotic acid will be listed. 
• 
Sections 8.3.4, Neutralizing Antibodies to AAV8; Section 8.3.5, AAV8 Binding Antibodies; Section 8.3.6, Cell-mediated 
Immune Response to AAV8 and OTC: Removed summary table. Clarified that observed results and change from Baseline to each 
scheduled postbaseline time point will be presented for subjects in the Safety Set in a listing. 
• 
Section 8.3.7, Anti-OTC Antibodies: Added that results will be presented for subjects in the Safety set in a listing. 
• 
Section 8.3.8, Ammonia Scavenger Therapy: Removed summary table. Added that results will be presented in a listing. 
• 
Section 8.3.9, Dietary Protein Prescription: Added that details of dietary protein prescription for each subject will be presented in 
a listing. 
• 
Section 8.3.10.1, Vocabulary and Matrix Reasoning Subtests from the WASI-II: Removed listing of raw and scaled scores of the 
Vocabulary and Matrix Reasoning subtests and Full Scale IQ from the WASI-II based on the Safety Set. 
• 
Section 8.3.11, PROMIS Mental Health Measures: Removed summary of observed values and change from Baseline for 
PROMIS Mental Health Measures. 
• 
Section 8.3.13: Subgroup Analysis: Added subgroup analysis plots by gender. 
• 
Section 9, Safety Analysis: Updated the list of safety parameters. 
• 
Section 9.1, Adverse Events: Added that any events that occur after exposure to DTX301 and before the first visit of 
Study 301OTC02 will be considered TEAEs. For summaries by CTCAE grade, removed that AEs missing a CTCAE grade will 
be considered CTCAE Grade 3. Added that the Investigator will assess each AE for relationship to [1-13C]sodium acetate, OTC 
deficiency, hyperammonemia, and as of Protocol Amendment 5, corticosteroid regimen. Added a definition for HAC-related 
TEAE. Updated the AE summaries and listings to be generated. 
• 
Section 9.2, Death: Removed autopsy performed status because the data are not collected in eCRF. 
• 
Section 9.3, Clinical Laboratory Evaluations: Added spaghetti plots for ALT and AST levels over time. Added a box plot for 
ALT levels before and after DTX301 administration. Removed listing for ALT level and association with corticosteroid 
administration. 


Statistical Analysis Plan 
 
301OTC01 
4 
Confidential 
• 
Section 10, Statistical Considerations for Data Monitoring Committee Meeting: Updated timing of planned DMC data review 
meetings. 
• 
Section 11, Interim Analysis: Updated the details regarding a possible interim analysis. Added that no interim analysis was 
conducted. 
• 
Section 12, Changes from Analyses Planned in the Protocol: Removed details regarding rules for deriving baseline values for the 
rate of ureagenesis. Added potential exploratory analyses of time-normalized plasma ammonia and/or percent of normal 
ureagenesis activity by gender. Updated timing of planned DMC data review meetings. Added that no interim analysis was 
conducted. Added that the N-CRM model will be run after subjects in Cohort 4 complete Week 12 for submission to Health 
Canada. Added mixed models to compare the logarithmic transformation of plasma ammonia AUC0-24hr and absolute 13C-urea 
AUC0-240min vs Baseline. Added additional summary statistics for specific ammonia and ureagenesis parameters. 
• 
Section 13, References: Updated list of references. 
Version 4.0 
(25 November 2021) 
• 
Section 3.1, Overall Study Design and Plan: Updated the priority of enrollment for Cohort 4. 
• 
Section 8.1, Rate of Ureagenesis: Removed OTC genotype from the fixed effects in the MMRM model. 
• 
Section 8.2, Plasma Ammonia Area Under the Curve from Time 0 to 24 Hours: Geometric summary statistics will be provided 
overall, by cohort, and for Cohorts 3 and 4 combined. A linear MMRM will provide a comparison of the logarithmic 
transformation of plasma ammonia AUC0-24hr for each DTX301 dose vs the lowest dose and at each visit vs Baseline. Removed 
OTC genotype from the fixed effects and baseline results as a continuous covariate in the MMRM model. 
• 
Section 8.3.8, Baseline Disease Management: Added definitions of Responder and Complete Responder for future development. 
• 
Section 8.3.9, Dietary Protein Prescription: In addition to total daily dietary protein intake, intact food protein and medical food 
protein will be summarized. Counts and percentages of subjects with type of change and of subjects on unrestricted protein diet 
will be generated. 
• 
Section 9.4, DTX301 Vector Genome Determination and Viral Shedding: Baseline value, highest value/timepoint, and timepoint 
of third consecutive negative results will be provided for each subject and sample type. Median values over time by cohort and 
sample type will be presented in a figure. Longitudinal displays over time by cohort for each subject and sample type will be 
generated. 
• 
Section 13, References: Updated list of references. 
 


Ultragenyx Pharmaceutical Inc. 
 
 Statistical Analysis Plan, Version 4.0 
 
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Date Issued: 25 November 2021 
 
 
 
 
II
TABLE OF CONTENTS 
LIST OF ABBREVIATIONS ...................................................................................................... V 
1. 
INTRODUCTION ............................................................................................................ 7 
2. 
STUDY OBJECTIVES AND ENDPOINTS................................................................... 7 
3. 
INVESTIGATIONAL PLAN .......................................................................................... 9 
3.1. OVERALL STUDY DESIGN AND PLAN .................................................................................. 9 
3.2. IMPLEMENTATION OF THE N-CRM MODEL ......................................................................... 9 
3.2.1. 
CANDIDATE DOSES ........................................................................................................ 10 
3.2.2. 
DEFINITION OF A DOSE LIMITING TOXICITY .................................................................. 10 
3.2.3. 
DEFINITION OF THE MAXIMUM TOLERATED DOSE ........................................................ 10 
3.2.4. 
TARGET TOXICITY RATE ................................................................................................ 10 
3.2.5. 
ESCALATION RULE ........................................................................................................ 10 
3.2.6. 
N-CRM STOPPING RULES.............................................................................................. 10 
3.2.7. 
DOSE-TOXICITY MODEL ................................................................................................. 11 
3.2.8. 
NUMBER OF TOXICITIES REQUIRED BEFORE ALL DOSES ARE CONSIDERED UNSAFE ........ 11 
3.2.9. 
COHORT SIZE ................................................................................................................. 12 
3.2.10. 
OTHER CLARIFICATIONS............................................................................................. 12 
3.3. TREATMENTS .................................................................................................................... 12 
4. 
GENERAL STATISTICAL CONSIDERATIONS ..................................................... 13 
4.1. BASELINE AND CHANGE FROM BASELINE ......................................................................... 13 
4.1.1. 
UREAGENESIS BASELINE ............................................................................................... 13 
4.1.2. 
OTHER PARAMETERS BASELINE .................................................................................... 13 
4.1.3. 
CHANGE FROM BASELINE .............................................................................................. 13 
4.2. CONVERSION OF DAYS TO WEEKS OR MONTHS ................................................................ 14 
4.3. DURATION ........................................................................................................................ 14 
4.4. MISSING DATA ................................................................................................................. 14 
4.5. MULTIPLE TESTING .......................................................................................................... 14 
4.6. OUTPUT NUMBERING........................................................................................................ 14 
4.7. PRESENTATION OF CONTINUOUS AND CATEGORICAL VARIABLES .................................... 14 
4.8. RANDOMIZATION, STRATIFICATION, AND BLINDING ........................................................ 15 
4.9. SAMPLE SIZE .................................................................................................................... 15 
4.10. 
SIGNIFICANCE LEVEL .................................................................................................... 15 
4.11. 
SOFTWARE .................................................................................................................... 15 
4.12. 
STUDY DAY AND STUDY START DATE .......................................................................... 15 
4.13. 
SUBJECT IDENTIFICATION .............................................................................................. 15 
4.15. 
ANALYSIS SETS ............................................................................................................. 16 
4.15.1. 
SAFETY SET ............................................................................................................... 16 
4.15.2. 
MTD DETERMINING SET ........................................................................................... 16 
5. 
SUBJECT DISPOSITION ............................................................................................. 16 
5.1. COVID-19 ....................................................................................................................... 16 
5.2. DISPOSITION ..................................................................................................................... 17 
5.3. PROTOCOL DEVIATIONS ................................................................................................... 17 
5.4. DURATION OF STUDY PARTICIPATION .............................................................................. 17 


Ultragenyx Pharmaceutical Inc. 
 
 Statistical Analysis Plan, Version 4.0 
 
DTX301 
 
Date Issued: 25 November 2021 
 
 
 
 
III 
6. 
DEMOGRAPHICS AND BASELINE CHARACTERISTICS .................................. 17 
6.1. DEMOGRAPHICS ................................................................................................................ 17 
6.2. MEDICAL HISTORY ........................................................................................................... 18 
6.3. OTC DEFICIENCY MEDICAL HISTORY .............................................................................. 18 
6.4. OTC GENOTYPING ........................................................................................................... 18 
6.5. INCLUSION AND EXCLUSION CRITERIA ............................................................................. 18 
7. 
TREATMENTS AND MEDICATIONS ....................................................................... 19 
7.1. PRIOR AND CONCOMITANT MEDICATIONS ........................................................................ 19 
7.1.1. 
PRIOR MEDICATIONS ..................................................................................................... 19 
7.1.2. 
CONCOMITANT MEDICATIONS....................................................................................... 19 
7.2. STUDY DRUG .................................................................................................................... 19 
7.3. [1-13C] SODIUM ACETATE ................................................................................................. 20 
8. 
EFFICACY ANALYSIS................................................................................................. 20 
8.1. RATE OF UREAGENESIS..................................................................................................... 20 
8.2. PLASMA AMMONIA AREA UNDER THE CURVE FROM TIME ZERO TO 24 HOURS ............... 21 
8.3. EXPLORATORY ENDPOINTS ............................................................................................... 23 
8.3.1. 
SUPPLEMENTARY UREAGENESIS PARAMETERS ............................................................. 23 
8.3.2. 
HYPERAMMONEMIC CRISES (HAC) ............................................................................... 23 
8.3.3. 
24-HOUR URINARY OROTIC ACID EXCRETION AND SPOT URINARY OROTIC ACID ....... 24 
8.3.4. 
NEUTRALIZING ANTIBODIES TO AAV8 ......................................................................... 24 
8.3.5. 
AAV8 BINDING ANTIBODIES ........................................................................................ 24 
8.3.6. 
CELL-MEDIATED IMMUNE RESPONSE TO AAV8 AND OTC ........................................... 25 
8.3.7. 
ANTI-OTC ANTIBODIES ................................................................................................ 25 
8.3.8.1. 
AMMONIA SCAVENGER THERAPY .............................................................................. 25 
8.3.8.2. 
DIETARY PROTEIN PRESCRIPTION .............................................................................. 25 
8.3.9. 
NEUROPSYCHOLOGICAL TESTS ..................................................................................... 26 
8.3.9.1. 
VOCABULARY AND MATRIX REASONING SUBTESTS FROM THE WASI-II .................. 26 
8.3.9.2. 
 .................................................................... 26 
8.3.9.3. 
 ..... 26 
8.3.9.4. 
 
 
 
 
I ........................ 27 
8.3.10. 
PROMIS® MENTAL HEALTH MEASURES ................................................................. 27 
8.3.11. 
QUALITY OF LIFE IN NEUROLOGICAL DISORDERS MEASURES ................................... 27 
8.3.12. 
SUBGROUP ANALYSIS ................................................................................................. 28 
9. 
SAFETY ANALYSIS ..................................................................................................... 28 
9.1. ADVERSE EVENTS ............................................................................................................. 28 
9.2. DEATH .............................................................................................................................. 30 
9.3. CLINICAL LABORATORY EVALUATIONS ........................................................................... 30 
9.4. DTX301 VECTOR GENOME DETERMINATION AND VIRAL SHEDDING .............................. 31 
9.5. VITAL SIGN MEASUREMENTS ........................................................................................... 32 
9.6. ELECTROCARDIOGRAM RESULTS ...................................................................................... 32 
9.7. PHYSICAL EXAMINATION FINDINGS ................................................................................. 32 
10. 
STATISTICAL CONSIDERATIONS FOR DATA MONITORING COMMITTEE 
MEETING ....................................................................................................................... 33 


Ultragenyx Pharmaceutical Inc. 
 
 Statistical Analysis Plan, Version 4.0 
 
DTX301 
 
Date Issued: 25 November 2021 
 
 
 
 
IV 
11. 
INTERIM ANALYSIS ................................................................................................... 33 
12. 
CHANGES FROM ANALYSES PLANNED IN THE PROTOCOL ........................ 33 
13. 
REFERENCES ................................................................................................................ 34 
14. 
APPENDICES ................................................................................................................. 36 
 
 
 


Ultragenyx Pharmaceutical Inc. 
 
 Statistical Analysis Plan, Version 4.0 
 
DTX301 
 
Date Issued: 25 November 2021 
 
 
 
 
V
List of Abbreviations 
 
AAV8 
adeno-associated virus serotype 8 
AE 
adverse event 
ALP 
alkaline phosphatase 
ALT 
alanine aminotransferase 
aPTT 
activated partial thromboplastin time 
AST 
aspartate aminotransferase 
ATC 
anatomical therapeutic chemical  
AUC 
Area under the curve 
BUN 
blood urea nitrogen 
CDISC 
Clinical Data Interchange Standards Consortium 
CI 
confidence interval 
Cmax 
maximum concentration 
COVID-19 
Coronavirus Disease 2019 
CRM 
continual reassessment method 
CTMS 
clinical trial management system 
CV 
Coefficient of Variation 
 
 
DLT 
dose limiting toxicity 
DMC 
data monitoring committee 
ECG 
electrocardiogram 
eCRF  
electronic case report forms 
ELISA 
enzyme-linked immunosorbent assay 
ELISPOT 
enzyme-linked immunospot assay 
FACTS 
Fixed and Adaptive Clinical Trial Simulator 
GC 
genome copies 
GGT 
gamma-glutamyl transferase 
HAC 
hyperammonemic crises   
ICF 
informed consent form 
ICH 
International Council for Harmonisation 
IgG 
immunoglobulin G 
INR 
international normalized ratio 
IQ 
intelligence quotient 
IV 
intravenous 
LDH 
lactate dehydrogenase 
LLOQ 
lower limit of quantification 
LS 
Least Squares 
MCH 
erythrocyte mean corpuscular hemoglobin 
MCHC 
erythrocyte mean corpuscular hemoglobin concentration 
MCV 
erythrocyte mean corpuscular volume 


Ultragenyx Pharmaceutical Inc. 
 
 Statistical Analysis Plan, Version 4.0 
 
DTX301 
 
Date Issued: 25 November 2021 
 
 
 
 
VI 
MedDRA 
Medical Dictionary for Regulatory Activities 
MMRM 
mixed model for repeated measures 
MTD 
maximum tolerated dose 
N-CRM 
Neuenschwander’s continual reassessment method 
NCI-CTCAE 
National Cancer Institute Common Terminology Criteria for 
Adverse Events 
Neuro-QOL 
Quality of Life in Neurological Disorders 
OBD 
optimal biological dose 
OTC 
ornithine transcarbamylase 
PROMIS 
Patient-Reported Outcomes Measurement Information System® 
PT 
preferred term 
QTcB 
QTc using Bazett’s Correction 
QTcF 
QTc using Fridericia’s Correction 
RDW 
erythrocytes, erythrocytes distribution width 
SAE 
serious adverse event 
SAP 
statistical analysis plan 
SD 
standard deviation 
SE 
standard error 
SOC 
system organ class 
SS 
safety set 
TEAE 
treatment-emergent adverse event 
Tmax 
time to reach maximum concentration 
UCD 
urea cycle disorder 
UCDC 
Urea Cycle Disorders Consortium 
UK 
United Kingdom 
ULN 
upper limit of normal 
ULOQ 
upper limit of quantification 
USA 
United States of America 
WAIS-IV 
Weschler Adult Intelligence Scale, Fourth Edition 
WASI-II 
Weschler Abbreviated Scale of Intelligence, Second Edition 
WHO 
World Health Organization 
WMI 
Working Memory Index 
 
 
 


Ultragenyx Pharmaceutical Inc. 
 
 Statistical Analysis Plan, Version 4.0 
DTX301 
 
Date Issued: 25 November 2021 
 
 
 
7
1. Introduction 
 
Ornithine transcarbamylase (OTC) deficiency, the most common of the urea cycle 
disorders (UCDs), is currently estimated to occur in up to 1:62,000 live births [Lichter-
Konecki 2013]. OTC deficiency is an X-linked disorder that results from mutations in the 
OTC gene, affecting the expression or activity of the OTC protein [Caldovic 2015]. A 
deficiency in OTC activity prevents the normal flux of ammonia through the urea cycle 
and ultimately results in hyperammonemia. OTC deficiency presents as a severe form in 
males and rarely in females shortly after birth (neonatal onset; ≤ 30 days of age) or later in 
life for both males and females (late onset; > 30 days of age) with disease that ranges from 
mild to severe depending on the residual activity of OTC [Tuchman 2008a]. 
 
The current standard of care for OTC deficiency is to limit dietary protein intake and 
supplement the diet with a high-energy source, such as glucose [Leonard 2001]. If plasma 
ammonia is not stabilized by dietary restriction alone, ammonia scavengers that promote 
an alternative pathway of nitrogen removal can be administered [Batshaw 2001; Häberle 
2012; Lichter-Konecki 2013; Häberle 2019]. Ammonia scavengers cannot, however, 
completely prevent individuals from having hyperammonemic crises (HAC) [Batshaw 
2001]. Orthotopic liver transplantation can correct OTC deficiency; however, this is 
limited by donor availability and is associated with significant risk of morbidity and 
mortality [Leonard 2004]. 
 
Thus, there remains a significant unmet medical need for a treatment that allows for 
sustained ammonia management, prevention of HAC, and risk of neurological damage 
associated with OTC deficiency. 
 
This statistical analysis plan (SAP) is based on the clinical study protocol 301OTC01, 
Amendment 5 dated 25th of February 2020 and its associated electronic case report forms 
(eCRF). This document describes the rules and conventions to be used in the dose 
selection, analysis and representation of safety and efficacy data as presented in the clinical 
protocol.  
 
2. Study Objectives and Endpoints 
The study objectives and endpoints are presented in Table 2-1. 
Table 2–1 
Study Objectives and Endpoints 
Objective 
Endpoint 
Primary 
To determine the safety of single IV doses of 
DTX301 in adults with late-onset OTC deficiency. 
The incidence of AEs, TEAEs, and SAEs for each 
dosing cohort, assessed by severity and relationship 
to study product. 


Ultragenyx Pharmaceutical Inc. 
 
 Statistical Analysis Plan, Version 4.0 
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Date Issued: 25 November 2021 
 
 
 
8
Secondary 
To establish a dose of DTX301 that has a meaningful 
increase in the rate of ureagenesis to allow further 
clinical development. 
The change from baseline in the rate of ureagenesis 
(as measured by the generation of [13C]urea over 4 
hours) as determined by gas chromatography mass 
spectrometry over time to 52 weeks after the IV 
administration of DTX301. 
To evaluate the efficacy of single IV doses of 
DTX301 in adults with late-onset OTC deficiency in 
the setting of tapering or discontinuing ammonia 
scavenger medications. 
The change from baseline (Day 0) in plasma 
ammonia area under the curve from time zero to 24 
hours (AUC0-24) over time to 52 weeks after IV 
administration of DTX301 in the setting of tapering 
or discontinuing ammonia scavenger medications. 
Exploratory 
To assess the impact of DTX301, by dose, on the 
number of hyperammonemic crises during the study. 
The number of hyperammonemic crises observed for 
each dose over time to 52 weeks after IV 
administration of DTX301. 
To evaluate the effect of DTX301, by dose, on 
urinary orotic acid levels.  
The change from baseline in urinary orotic acid 
excretion over time to 52 weeks after IV 
administration of DTX301. 
To evaluate the effect of DTX301, by dose, on 
plasma glutamine and glutamate levels. 
The change from baseline in plasma glutamine and 
glutamate over time to 52 weeks after IV 
administration of DTX301. 
To assess the impact of DTX301, by dose, on the 
subject’s neuropsychological functioning. 
Changes in responses to the following, summarized 
by dose level of DTX301: 
 
 
 
 
 
 
 
To assess the impact of DTX301, by dose, on the 
subject’s quality of life. 
Responses to the PROMIS questionnaire, 
summarized by dose level of DTX301 over time to 
Week 52. 
To assess the impact of DTX301, by dose, on the use 
of ammonia scavengers. 
Use of ammonia scavengers, summarized by dose 
level of DTX301. 
To assess the impact of DTX301, by dose, on dietary 
protein restriction. 
Change in dietary protein intake, summarized by 
dose level of DTX301. 
To describe the immune response to AAV8 capsid 
proteins after IV administration of DTX301. 
• 
The development of neutralizing antibodies to 
AAV8 (as determined by a cell-based assay), 
summarized by time point and dose level of 
DTX301. 
• 
The development of anti-AAV8 binding 
antibodies (as determined by ELISA), 
summarized by time point and dose level of 
DTX301. 
To describe the immune response to OTC after IV 
administration of DTX301. 
The development of anti-OTC antibodies (as 
determined by ELISA) summarized by time point 
and dose level of DTX301. 
Abbreviations: AAV8, adeno-associated virus serotype 8; AE, adverse event; AUC0-24, area under the curve from time 
zero to 24 hours; ELISA, enzyme-linked immunosorbent assay; IV, intravenous; OTC, ornithine transcarbamylase; 
PROMIS, Patient-Reported Outcomes Measurement Information System; SAE, serious adverse event; TEAE, treatment-
emergent adverse event. 


Ultragenyx Pharmaceutical Inc. 
 
 Statistical Analysis Plan, Version 4.0 
DTX301 
 
Date Issued: 25 November 2021 
 
 
 
9
3. Investigational Plan 
3.1. Overall Study Design and Plan 
 
Study 301OTC01 is a Phase 1/2, open-label, single arm, multicenter, safety and dose-
finding study to determine the safety, tolerability, and preliminary efficacy of DTX301 in 
adults with late-onset OTC deficiency. A key element of the study is the identification of 
the optimal biological dose (OBD) for DTX301. The primary objective of the study is to 
determine the safety of single doses of DTX301. The secondary objectives are the 
assessment of rate of ureagenesis, reflecting the direct in vivo efficiency of the urea cycle 
and the assessment of plasma ammonia (area under the curve from 0 hours to 24 hours 
[AUC0-24]), reflecting clinical metabolic control. The target for DTX301 is to achieve a 
rate for ureagenesis of approximately 300 μmol/kg/hr (±10%), which is the approximate 
rate of ureagenesis in healthy adults as assessed by the ureagenesis assay employed 
[Matthews 1984; Jahoor 1987; Castillo 1996; Tuchman 2008b]. 
 
Eligible subjects will receive a single peripheral intravenous (IV) infusion of DTX301. 
Three subjects will be enrolled in cohort 1 and a minimum of 2 to 3 subjects will be 
enrolled in each subsequent cohort; the number of subjects in each subsequent dosing 
cohort will be determined by subject results and availability of study drug. Subjects in 
cohorts 1 and 2 will be dosed at a minimum of 2 weeks (14 days) apart. The initial 3 
subjects in cohort 3 will be dosed at a minimum of 1 week apart (7 days). Additional 
subjects to cohort 3 (cohort expansion) and subjects to cohort 4 (Dosing Process 
Optimization) may be dosed less than 1 week apart. Following the collection of a 
minimum of 12 weeks safety data, the data monitoring committee (DMC) will perform a 
review of a dosing cohort between the dosing of the last subject in one dosing cohort and 
the first subject in the next dosing cohort up to cohort 3. Dosing of additional subjects as 
expansion of cohort 3, and initiation of cohort 4 (Dosing Process Optimization) may occur 
in parallel, following the DMC review of a minimum of 12 weeks data from the initial 3 
subjects in cohort 3. A continual reassessment method (CRM) will be used for dose finding 
to discover the OBD of DTX301. Cohort 4 is intended to dose at the OBD. Cohort 4 was 
prioritized in enrollment as OBD had been declared with cohort 3. Enrollment in cohort 4 
was concluded after 2 patients enrolled as data on performance of prophylactic regimen, 
the focus of cohort 4, was evaluated and deemed sufficient. 
3.2. Implementation of the N-CRM model 
The purpose of this section is to define the proposed Neuenschwander’s continual 
reassessment method (N-CRM) model for this study and to provide the details necessary to 
allow its implementation. 
Where discrepancies exist between the text of this SAP and the study protocol document, 
the text in this SAP will prevail. 


Ultragenyx Pharmaceutical Inc. 
 
 Statistical Analysis Plan, Version 4.0 
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Date Issued: 25 November 2021 
 
 
 
10 
3.2.1. Candidate doses 
The candidate doses to be considered are as follows: 
Table 2 Candidate dose levels 
Candidate 
Dosing Level  
DTX301 
Dose 
(GC/kg) 
1 
2 x 1012 
2 
6 x 1012 
3 
1 x 1013 
GC=genome copies 
3.2.2. Definition of a Dose Limiting Toxicity 
A dose limiting toxicity (DLT) is defined as any Adverse Event (AE), with a toxicity grade 
of three or higher (AE ≥ Grade 3), that is considered related to the study drug by the 
investigator.  As the N-CRM will be performed after 12 weeks of data have accrued for the 
last open cohort, only DLTs that occur within 12 weeks will be considered. 
3.2.3. Definition of the Maximum Tolerated Dose 
The estimate of the maximum tolerated dose (MTD) will be that dose with p(DLT) nearest 
to the target toxicity rate, regardless of whether or not the estimated p(DLT) is above or 
below the target toxicity rate. 
3.2.4. Target toxicity rate 
The target toxicity rate is 0.25.  (Nota Bene: unlike the standard N-CRM model, this study 
will target a specific toxicity rate rather than a toxicity band.) 
3.2.5. Escalation rule 
The first cohort will receive 2x1012 GC/kg.  A dose is cleared once a single cohort has been 
assessed at that dose.  The maximum permitted dose escalation is 1 level relative to the 
highest cleared dose. Cohort 4 is not part of the cohorts included in the dose-escalation 
assessment as it is to be treated with the OBD defined with the assessment of the three 
previous dose cohorts. 
3.2.6. N-CRM Stopping rules  
The study will stop for success once results from six subjects treated at the current estimate 
of the MTD are available. Cohort 4 is not part of the assessment of the dose finding. 
The CRM model will recommend that the study is stopped for insufficient safety if the 
current estimate of the MTD is <2×1012 GC/kg. 


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3.2.7. Dose-toxicity model 
The relationship between dose and toxicity will be modelled using logistic regression with 
median dose as the reference dose and pseudo-dose levels (the x-hats) defined as 
log(dose/reference).  The minimum and maximum values for p(DLT) are 0 and 1 
respectively.   
 
Thus, we have 
𝑝𝑝(𝐷𝐷𝐷𝐷𝐷𝐷|𝑥𝑥ො, 𝛼𝛼, 𝛽𝛽) =
𝑒𝑒𝛼𝛼+𝛽𝛽𝑥𝑥ො
1 + 𝑒𝑒𝛼𝛼+𝛽𝛽𝑥𝑥ො 
 
Where the joint prior for α and β is given by 
 
ቀ𝛼𝛼
log 𝛽𝛽ቁ~𝑁𝑁ቆቀ
𝜇𝜇𝛼𝛼
𝜇𝜇𝛽𝛽ቁ, ൬
𝜎𝜎𝛼𝛼× 𝜎𝜎𝛼𝛼
𝜎𝜎𝛼𝛼× 𝜎𝜎𝛽𝛽× 𝜌𝜌
𝜎𝜎𝛼𝛼× 𝜎𝜎𝛽𝛽× 𝜌𝜌
𝜎𝜎𝛽𝛽× 𝜎𝜎𝛽𝛽
൰ቇ 
 
Initial values for μα, μβ, σα, σβ and ρ are based on the following assumptions for the 
distribution of p(DLT) at each dose: 
 
Dose 
2.5% 
centile 
Median 
(50% 
centile) 
97.5% 
centile 
2x1012 GC/kg 
0.006 
0.03 
0.65 
6x1012 GC/kg 
0.008 
0.06 
0.70 
1x1013 GC/kg 
0.012 
0.12 
0.80 
 
which lead to the following parameterization of the joint prior: 
 
Alpha 
Log(Beta) 
 
Mean 
SD 
Mean 
SD 
Rho 
-2.3097 
1.6604 
-0.4323 
0.0044 
-0.2405 
 
Thus, we set μα= -2.3097, logμβ = -0.4323, σα = 1.6604, logσβ = 0.0044 and ρ = -0.2405. 
 
Since the standard deviation (SD) of α is non-zero, the intercept is allowed to vary. 
3.2.8. Number of toxicities required before all doses are considered unsafe 
The CRM model will not recommend stopping for insufficient safety until at least two 
DLTs have been observed.  Note: this affects only the dose recommendation provided by 
the N-CRM model.  It does not prevent an earlier termination based on clinical review of 
data emerging from the study. 


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3.2.9. Cohort size 
The cohort size will be three evaluable patients in every case for cohorts 1 to 3 as the 
expansion of cohort 3 and cohort 4 is not part of the N-CRM assessment. A patient is 
classed as evaluable if the patient remained in the study for at least 12 weeks after dosing 
or a DLT was observed within 12 weeks of dosing.  Should a protocol amendment change 
the inclusion / exclusion criteria of the study for safety, then a decision will be taken and 
documented on which patients to include in the CRM model to recommend the next dose 
after the study resumes. The N-CRM model will not be modified to take into account any 
protocol amendment that may be developed after the first N-CRM model has been run. 
3.2.10. Other clarifications 
• The N-CRM model will not contribute to the identification of the OBD.  Estimation 
of the OBD will not influence the dose recommended by the CRM, but may be 
taken into account by the DMC when making the dosing decision for the next 
cohort. 
• A DMC recommendation to administer a dose other than the three doses listed in 
section 3.2.1 above will be implemented only after a protocol amendment. 
3.3. Treatments   
Subjects will receive a single, peripheral IV infusion of DTX301, administered by 
qualified study personnel as designated by the investigator. The dose will be determined by 
the cohort and candidate dose.  
Subjects in cohort 4 will be treated with the OBD defined with the assessment of the three 
previous dose cohorts. Subjects treated in cohort 4 (Dosing Process Optimization) will 
utilize an alternative regimen of corticosteroids, aiming at prophylaxis of vector-induced 
hepatitis. Therefore, prednisone (or prednisolone) will be initiated before dosing with 
DTX301, sustained for 4 weeks, followed by tapering. 
The dose of DTX301 to be administered will be calculated using the subject’s weight 
recorded at Screening. The subject’s weight will be verified prior to administration of 
DTX301 to ensure that their current weight is within 10% of their weight at Screening.  
The efficacy data will be modeled by dose (i.e. cohorts 3 and 4 will be combined, with 
OBD being determined as 1.0x1013 GC/kg). The other data will be summarized/reported by 
DTX301 dose/prophylactic corticosteroids (i.e. by cohort) and presented in the tables, 
figures and listings as follows: 
• 
DTX301 2.0x1012 GC/kg  
• DTX301 6.0x1012 GC/kg  
• DTX301 1.0x1013 GC/kg  
• DTX301 1.0x1013 GC/kg + Prophylactic corticosteroids  


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4. General Statistical Considerations 
4.1. Baseline and Change from Baseline 
4.1.1. 
Ureagenesis Baseline 
 
Samples for ureagenesis are collected over a 4 hour-period at Screening and Day 1 to 
assess baseline ureagenesis. The screening assessment can be repeated if discrepant with 
subject’s clinical status and severity.   
Baseline of ureagenesis is defined as the average of Screening and Day 1 results.  If the 
absolute difference of results between Screening and Day 1 is ≥ 25% of normal rate of 
ureagenesis, then the Screening value will become the Baseline for ureagenesis. 
If the Screening assessment has been repeated (i.e. unscheduled assessment) then the 
results from the unscheduled Screening visit will be used in lieu of the Screening results to 
determine the Baseline of ureagenesis.   
This rule will be used to determine the visits to be included in the baseline derivation for 
each of the ureagenesis parameters (derived and reported). 
 
For the non-AUC supplementary ureagenesis parameters, a baseline value is defined 
 
  
For AUC0-240min of absolute 13C-urea and AUC0-240min of 13C-Bicarbonate, the baseline 
value is defined
 
For percent of normal AUC0-240min of absolute 13C-urea,
 
 
 
4.1.2. 
Other Parameters Baseline 
 
For spot ammonia, plasma ammonia AUC0-24h and urinary orotic acid AUC0-24h the 
baseline value is defined 
. For urinary orotic acid, a baseline value is 
defined 
 For ammonia 
scavenger therapy usage, the baseline value is defined 
 
 For all other endpoints, the baseline value is 
 
 
 
4.1.3. 
Change from Baseline 
All explicit references to change from baseline in this SAP refer to absolute change from 
baseline. Change from baseline is defined 
 
 Percent change from baseline is defined 
 
 If either the baseline or 
post-baseline value is missing, then the change from baseline and percent change from 


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baseline value are set to missing. For each time point where change from baseline is 
evaluated for continuous variables, descriptive statistics will be displayed for the values at 
baseline, values at the given time point, and values for change from baseline at the given 
time point for those subjects who have data at both the baseline and the time point being 
evaluated.  
4.2. Conversion of Days to Weeks or Months 
The following conversion factors will be used to convert days into weeks or months: 1 
week = 7 days, 1 month = 30.4375 days. 
4.3. Duration 
Duration will be calculated as stop date – start date + 1, unless otherwise specified. 
Duration is calculated only when both dates are complete. Examples include duration of 
study participation, AE duration, and duration of oral steroid treatment. 
4.4. Missing Data 
Refer to the Appendices for imputation rules for partial and missing AE onset dates as well 
as partial and missing prior/concomitant medication start and end dates. For the adeno-
associated virus serotype 8 (AAV8) binding antibody immunoglobulin (IgG), neutralizing 
antibodies to AAV8, amino acid panel, cell-mediated immune Response to AAV8 and 
OTC, chemistry, hematology (including coagulation panel),  plasma ammonia (24 hours 
and spot), ureagenesis assay parameters, urinalysis, urinary orotic acid, vector genome 
determination (blood) and viral shedding (urine, saliva, and stool) laboratory data, 
quantitative results either below the lower limit of quantification (LLOQ) or above the 
upper limit of quantification (ULOQ) will be set to the LLOQ or ULOQ, respectively. 
Otherwise, no imputation of partial or missing values will be performed. 
4.5. Multiple Testing 
No formal adjustment for multiplicity will be performed. 
4.6. Output Numbering 
Numbering for tables, listings and figures will follow International Council for 
Harmonisation (ICH) E3 Guidelines. 
4.7. Presentation of Continuous and Categorical Variables 
Continuous data will be summarized using descriptive statistics (i.e., n, arithmetic mean, 
SD, median, minimum, and maximum). Categorical data will be summarized using 
event/subject count and percentage (n, %) in each category. Percentages will generally be 
reported to one decimal place. For descriptive statistics of all numeric variables, unless 
otherwise specified, the minimum and maximum will be displayed to the same level of 
precision as reported. Mean and median will be displayed to one level of precision greater 
than the data collected. SD will be displayed to two levels of precision greater than the data 
collected. P-values will be rounded to three decimal places. If a p-value is less than 0.001, 


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it will be reported as “<0.001.” If a p-value is greater than 0.999, it will be reported as 
“>0.999.” 
 
When count data are presented, the percentage will be suppressed when the count is zero in 
order to draw attention to the non-zero counts. A row denoted “Missing” will be included 
in count tabulations where specified in the shells to account for dropouts and missing 
values. The denominator for all percentages will be the number of subjects within the 
analysis set of interest, unless otherwise specified. 
4.8. Randomization, Stratification, and Blinding 
This is an open label study, so there is no blinding of DTX301 dose, stratification, or 
randomization. 
4.9. Sample Size 
The study is expected to enroll up to 18 subjects. Three subjects will be enrolled into 
cohort 1 and then sequentially into cohorts of a minimum of 2 to 3 subjects. This sample 
size consideration is consistent with the sample size of other studies of similar design but is 
not based on a power calculation.  
4.10. 
Significance Level 
Unless otherwise specified, all testing of statistical significance will be 2-sided, and all p-
values less than or equal to 0.05 will be considered statistically significant. Similarly, all 
confidence intervals (CIs) will be two-sided with a significance level of 5%. 
4.11. 
Software 
Modelling to determine the OBD will be conducted 
 
 
 All other general data manipulation and statistical analyses will be 
conducted using SAS® Version 9.4 or higher (SAS® Institute, Inc., Cary, North Carolina, 
United States). 
4.12. 
Study Day and Study Start Date 
For assessments prior to DTX301 administration, study day will be defined as the 
assessment/event date minus date of DTX301 infusion (Day 1). For assessments on or after 
Day 1, study day will be defined as assessment/event date minus date of DTX301 infusion 
+ 1. Study start date is defined as the date the informed consent form (ICF) is signed. 
4.13. 
Subject Identification 
Subjects will be identified in data listings by subject identification number which consists 
of the subject number concatenated with the site number. Data listings will be sorted by 
subject identification number, visit, and parameter (where applicable). 


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4.14. 
Unscheduled Visits 
Unscheduled visits will not be included in by-visit summaries of data with the exception of 
worst post-baseline value in the shift from baseline summary of electrocardiogram (ECG) 
interpretation and summaries of worst post-baseline value for hematology, chemistry, 
urinalysis and amino-acid and summaries of newly notable laboratory abnormalities in 
chemistry relating to liver function test results. Moreover, unscheduled visits will be 
included into individual patient graphs.  
4.15. 
Analysis Sets 
4.15.1. Safety Set 
The Safety Set (SS) will include all subjects who receive DTX301. Subjects who receive a 
partial dose will be summarized or listed according to the nearest candidate dose (see Table 
3-1) based on the actual dose they received. The SS will be used to tabulate and list all of 
the safety endpoints, efficacy endpoints, and for the purpose of N-CRM modelling. 
 
4.15.2. MTD Determining Set 
See Section 3.2.8 for details. 
 
5. Subject Disposition 
5.1. COVID-19 
At the onset of the Coronavirus Disease 2019 (COVID-19) pandemic in Europe and North 
America, only 2 subjects in cohort 3 were ongoing 
 
 Due to the spacing of visits and number of 
ongoing subjects, it was decided to collect the impact of COVID-19 on the visits and/or 
assessments missed using a specific eCRF page and not to change the planned analysis. 
This data collection method was planned to be applied to patient 
 
 and, if applicable, to all patients of cohort 4 as well. All data collected on this 
page will be listed in a data listing. 
Table 5–1 
Pandemic Lock-down Restrictions Start/End Dates 
 
Country (region) 
Lock-down Start Date 
Lock-down Stop Date 
UK 
24-Mar-2020 
15-Jun-2020 
05-Nov-2020 
02-Dec-2020 
04-Jan-2021 
12-Apr-2021 
Spain 
14-Mar-2020 
11-May-2020 
France* 
17-Mar-2020 
11-May-2020 
30-Oct-2020 
14-Dec-2020 
Canada 
13-Mar-2020 
04-May-2020 


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USA (Massachusetts) 
24-Mar-2020 
25-May-2020 
USA (New York) 
20-Mar-2020 
10-June-20 
The start and stop dates correspond to the lock-down in each country/region, travel 
restriction may have been lifted at a later date in some country/regions. 
.  
 
5.2. Disposition 
Disposition will be summarized for all enrolled subjects (i.e. all subjects who signed the 
study informed consent and met all Screening Inclusion Criteria and did not meet any 
Screening Exclusion Criteria) by DTX301 dose/prophylactic corticosteroids and overall. 
The number and percentage of subjects who have been treated (i.e. SS), have completed 
the study, are ongoing or discontinued from the study, as well as the primary reason for 
study discontinuation (if applicable) will be tabulated. 
All disposition related information for enrolled subjects will be presented in a data listing. 
5.3. Protocol Deviations 
Protocol deviations will be recorded within the PPD Clinical Trial Management System 
(CTMS) and undergo cross-functional team review prior to database lock. The Deviation 
Guidance Document contains all potential protocol deviations, classified by CTMS 
subtype. In addition, protocol deviation classification (i.e. significant vs. not significant) as 
determined by Ultragenyx Pharmaceutical Inc. prior to database lock will be documented 
in CTMS. All protocol deviations will be presented in a data listing for the SS. 
5.4. Duration of Study Participation 
The duration of study participation will be summarized by DTX301 dose/prophylactic 
corticosteroids for all subjects based on the SS. The duration of study participation (days) 
is calculated as the date of the last visit (as recorded on the Study Completion/Early 
Withdrawal page) minus date of the first dose plus 1. If the date of the last visit on the 
Study Completion/Early Withdrawal eCRF page is missing or if a subject is lost to follow-
up, the latest available visit date will be used. The number of subjects in each of the 
following study participation duration categories will be displayed: ≤ 12 weeks (84 days), 
> 12 – 24 weeks (85 to 168 days), > 24 – 36 weeks (169 to 252 days), > 36 – 52 weeks 
(253 to 364 days), and > 52 weeks (365 days). 
6. Demographics and Baseline Characteristics 
6.1. Demographics 
Baseline demographics will be summarized by DTX301 dose/prophylactic corticosteroids 
and overall for all subjects in the SS. Baseline demographic data to be evaluated will 
include age, sex, race, ethnicity, height, and screening and baseline weight. The number of 
subjects in each of the following age categories will be displayed: 18 - < 30 years, 30 - < 
40 years, 40 - < 50 years, 50 - < 60 years, ≥ 60 years. 


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Descriptive statistics will be presented for age, height and weight. Age category, sex, race, 
and ethnicity will be summarized categorically. 
All demographic data and baseline characteristics, including contraception, for subjects in 
the SS will be listed. 
6.2. Medical History 
Medical history will be summarized by DTX301 dose/prophylactic corticosteroids for all 
subjects in the SS. Medical history data will be summarized by DTX301 dose/prophylactic 
corticosteroids and overall and by Medical Dictionary for Regulatory Activities 
(MedDRA) system organ class (SOC) and preferred term (PT).  Medical history data will 
be sorted in alphabetical order by SOC; PTs will be sorted in descending order by 
frequency within each SOC.  
Medical history data will be also listed. The dictionary version used for reporting the study 
will be described in the relevant table and listing footnotes. 
6.3. OTC Deficiency Medical History 
OTC deficiency medical history will be summarized by DTX301 dose/prophylactic 
corticosteroids for all subjects in the SS. The following OTC deficiency medical history 
items will be summarized: 
 
• Time since initial diagnosis of OTC deficiency (years) 
• Time since subject started therapy for OTC deficiency (years) 
• Family history of OTC deficiency (Yes/No) 
• OTC deficiency currently stable (Yes/No) 
• Time since OTC deficiency became stable (weeks) 
• Currently on stable dose of ammonia scavenger therapy (Yes/No) 
• Time since stable dose of ammonia scavenger therapy (weeks) 
 
The date of initial diagnosis of OTC deficiency and date the subject started therapy for 
OTC deficiency will be imputed as described in the Appendices. All time-related items 
will be calculated as the time from the date of interest to the date of Screening, inclusive. 
A subject data listing will be provided with all OTC deficiency medical history data for the 
SS. 
6.4. OTC Genotyping 
A listing will be provided with OTC genotype results for the SS. 
6.5. Inclusion and Exclusion Criteria 
All inclusion/exclusion criteria related information for enrolled subjects will be presented 
in a data listing. The listing will include the patients who failed inclusion/exclusion 
criteria. 


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7. Treatments and Medications 
7.1. Prior and Concomitant Medications 
Medications will be coded using the World Health Organization (WHO) Drug Dictionary. 
The WHO Drug Dictionary version used for reporting the study will be described in the 
relevant table and listing footnotes. If the medication start or end date is missing, it will be 
imputed before summary as described in the Appendices. If the start date of a medication is 
completely missing and the end date is before dosing of study drug on Day 1, it will be 
counted as a prior medication. If the start date of a medication is completely missing and 
the end date is after dosing of study drug on Day 1, it will be counted as both a prior and 
concomitant medication. If the start date of a medication is on or after the dose of study 
drug on Day 1 and the end date of the medication is completely missing, it will be counted 
as a concomitant medication. 
A subject data listing will be provided with medications data for the SS; a flag will be 
included to identify prior vs. concomitant medications. 
7.1.1. Prior Medications 
Prior medications are defined as those medications with a recorded end date before dosing 
of study drug on Day 1. The total number of prior medications will be summarized. The 
number and percentages of subjects with at least one prior medication will be summarized 
overall and by Anatomical Therapeutic Chemical (ATC) level 4 term and PT. Prior 
medications will be presented by DTX301 dose/prophylactic corticosteroids and overall 
using the SS. Medications will be sorted in descending order by ATC level 4 term based on 
counts in the overall column; PTs will be sorted in descending order of frequency within 
each ATC level 4 term based on counts in the overall column. 
7.1.2. Concomitant Medications 
Concomitant medications are defined as those medications that are taken on or after dosing 
of study drug on Day 1.  
 
The total number of concomitant medications will be summarized. The number and 
percentages of subjects with at least one concomitant medication will be summarized by 
ATC level 4 term and PT. Concomitant medications will be presented by DTX301 
dose/prophylactic corticosteroids  and overall using the SS. Medications will be sorted in 
descending order by ATC level 4 term based on counts in the overall column; PTs will be 
sorted in descending order of frequency within each ATC based on counts in the overall 
column.    
7.2. Study Drug 
The following details related to study drug administration on Day 1 will be listed for each 
subject in the SS: 
 
• Date of infusion 


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• Start time and End time 
• Planned dose 
• Dose administered 
• Dose interrupted status (Yes/No) and associated reason 
• Total volume infused 
• Dose adjusted status (Yes/No) and associated reason 
• Anatomical location of administration 
7.3. [1-13C] sodium acetate 
Details related to [1-13C] sodium acetate administration will be listed for each subject in 
the SS. 
8. Efficacy Analysis 
8.1. Rate of Ureagenesis 
This efficacy endpoint is defined as the change from baseline in rate of ureagenesis 
measured by the generation of 13C-urea over 4 hours as determined by isotope ratio mass 
spectrometry at Weeks 6, 12, 20, 24, Early Withdrawal, and End of Study (Week 52). The 
observed, change from baseline, and percent change from baseline in rate of ureagenesis 
will be summarized by DTX301 dose/prophylactic corticosteroids and visit based on the 
SS.  
 
Rate of ureagenesis (µmol*h/kg) for a given patient at a specific visit will be estimated 
using the following steps: 
 
 
 
 
 
 
 
  
 
 
 
 
 
 
The association between change from baseline in rate of ureagenesis and DTX301 dose 
(2.0x1012 GC/kg, 6.0x1012 GC/kg and 1.0x1013 GC/kg) will be evaluated 
 
 
 
 
 


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8.2. Plasma Ammonia Area Under the Curve from Time Zero to 24 Hours 
This efficacy endpoint is defined as change from baseline in the  
AUC0-24h of plasma ammonia at Weeks 6, 12, 24, Early Withdrawal, and End of Study 
(Week 52). Two samples will be collected at each visit and timepoint. One sample will 
be processed by the local laboratory and one sample will be processed by the central 
laboratory. The observed, change from baseline, and percent change from baseline in 
the AUC0-24h of plasma ammonia will be summarized by category (i.e. central laboratory 
vs. local laboratory), DTX301 dose/prophylactic corticosteroids , and visit based on the 
SS. Change from baseline in the AUC0-24h of plasma ammonia will be analyzed 
 
 used for change from baseline in rate of 
ureagenesis based on the SS. 
 
The baseline for the AUC0-24h measurement is based on the hourly plasma ammonia results 
beginning on Day 0 and ending on Day 1 prior to DTX301 administration. AUC0-24h will 
be calculated
 
 
)
c
 
 
 
 
 
   The 
rules for handling of missing data for the AUC0-24h calculation are described in the 
Appendices. 
The plasma ammonia listing and summary will also include the time-normalized AUC0-
24h, calculated 
 


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The following additional summary statistics will be provided (overall, by DTX301 
dose/prophylactic corticosteroids and for Cohorts 3 and 4 combined) for both AUC0-24h 
and time-normalized AUC0-24h of plasma ammonia by visit: geometric mean, 
coefficient of variation (CV) %, geometric CV%. The mean and the standard deviation 
will also be provided for the logarithmic transformation of both AUC0-24h and time-
normalized AUC0-24h of plasma ammonia. 
An additional linear mixed model for repeated measures will provide a comparison of the 
 
 
 
 
 
 
 
 
 
 
 
  
 
 
 
 
 
 
 
A longitudinal plot of plasma ammonia (as determined by central lab) will be provided 
by subject, including the display of the AUC0-24h for the subject alongside each plot.  
A longitudinal plot of plasma ammonia AUC0-24h (as determined by central lab), alanine 
aminotransferase (ALT) level (as determined by central lab for both scheduled and 
unscheduled visits), and corticosteroid regimen (prednisone/prednisolone) over time 
(each dose taken at the visit and possibly dose modifications in-between) will also be 
provided by subject.   
A plot displaying the rate of ureagenesis percentage of normal, the time-normalized 
plasma ammonia AUC0-24h (as determined by central laboratory) and corticosteroid 
regimen (prednisone/prednisolone)  over time (each dose taken at the visit and possibly 
dose modifications in-between) will be provided by subject. 
A panel plot displaying the time-normalized plasma ammonia AUC0-24h (as determined 
by central laboratory), spot ammonia (as determined by local lab), ALT level (as 
determined by central lab for both scheduled and unscheduled visits) and corticosteroid 


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regimen (prednisone/prednisolone) over time (each dose taken at the visit and possibly 
dose modifications in-between) will be provided by subject. 
Results from the spot ammonia samples collected as part of clinical chemistry will be 
reported alongside the 24-hour ammonia sample results and its derived parameters. 
8.3. Exploratory Endpoints 
8.3.1. Supplementary Ureagenesis Parameters 
The observed, change from baseline, and percent change from baseline for AUC0-240min of 
absolute 13C-urea, percent of normal AUC0-240min of absolute 13C-urea, AUC0-240min of 13C-
bicarbonate, and 13C-ureagenesis assay measures (e.g. total plasma urea [mmol/L], 
enrichment of 13C-bicarbonate (atom % excess), enrichment of 13C-urea [atom % excess], 
absolute 13C-urea concentration [µmol/L], Cmax 0-240min absolute 13C-urea [µmol/L], and 
Tmax 0-240min absolute 13C-urea [min]) will also be summarized by DTX301 
dose/prophylactic corticosteroids, visit at Weeks 6, 12, 20, 24, Early Withdrawal, and End 
of Study (Week 52), and time point (0, 1, 1.5, 2, 3, and 4 hours relative to dosing with [1-
13C]sodium acetate) where applicable based on the SS. 
 
 
 
 
 
 
 
The following additional summary statistics will be provided (overall, by DTX301 
dose/prophylactic corticosteroids and for Cohorts 3 and 4 combined) for AUC0-240min of 
absolute 13C-urea and percent of normal AUC0-240min of absolute 13C-urea by visit: 
 The mean and the standard deviation will also 
be provided 
 
 
 
8.3.2. Hyperammonemic crises (HAC) 
Following protocol amendment 5, HACs are specifically collected under the definition of 
the UCDCas an episode of signs and symptoms associated with hyperammonemia (such as 
frequent vomiting, nausea, headache, lethargy, irritability, combativeness, and 
somnolence),with documented elevated ammonia levels (≥ 100 µmol/L) and requiring 
medical intervention [Kent and Holt 2017; Longo and Holt 2017; Diaz 2019].  
 


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The number of HACs as well as the number of patients with HAC will be summarized by 
DTX301 dose/prophylactic corticosteroids, both overall and by occurrence period (pre-
dose vs. post-dose). Pre-dose hyperammonemic crises are defined as HACs occurred in the 
12 months before dosing. No further breakdown by visit will be provided as it is unlikely a 
patient has more than one crisis during the study.   
8.3.3. 24-hour Urinary Orotic Acid Excretion and Spot Urinary Orotic Acid 
The observed, change from baseline, and percent change from baseline in 24-hour 
urinary orotic acid excretion will be summarized by DTX301 dose/prophylactic 
corticosteroids , visit at Weeks 6, 12, 24, Early Withdrawal, and End of Study (Week 52), 
and time point (0, 6, 12, 18, and 24 hours relative to the start of plasma ammonia 
determination) based on the SS. Change from baseline and percent change from baseline 
will be calculated by matching time point (e.g. 0 hour results at each post-baseline visit 
will be compared to the 0 hour result at baseline). 
 
In addition, Urinary Orotic Acid AUC0-24h and its time-normalized version will be derived 
 
 
 These parameters will only be displayed in the listing.  
 
Spot Urinary Orotic Acid will be listed only. 
8.3.4. Neutralizing Antibodies to AAV8 
Samples for neutralizing antibodies to AAV8 will be collected at scheduled time points to 
monitor for a humoral immune response to AAV8. Observed results and change from 
baseline to each scheduled post-baseline time point will be presented for each subject in 
the SS in a listing. Observed results will also be presented over time along with AAV8 
binding antibody IgG results in a panel plot for each subject. 
 
From protocol amendment 5, AAV8 neutralizing antibody assessments were reduced based 
on medical consideration of results to date and to reduce subject burden. 
8.3.5. AAV8 Binding Antibodies 
Samples for AAV8 binding antibody IgG will be determined 
 
 Observed results and change from 
baseline to each scheduled post-baseline time point will be presented for each subject in 
the SS in a listing. Observed results will also be presented over time along with AAV8 
neutralizing antibody results in a panel plot for each subject. 
 
From protocol amendment 5, AAV8 binding antibody assessments were reduced based on 
medical consideration of results to date and to reduce subject burden. 


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8.3.6. Cell-mediated Immune Response to AAV8 and OTC 
The presence of T-cell specific response for AAV8 and OTC will be determined by an 
enzyme-linked immunospot assay (ELISPOT) at scheduled time points. Observed results 
and change from baseline to each scheduled post-baseline time point will be presented for 
each subject in the SS in a listing. Observed results will also be presented over time in a 
panel plot, split by DTX301 dose/prophylactic corticosteroids and by subject. 
 
Following protocol amendment 5, the assessment of cell-mediated immune response to 
AAV8 and OTC were removed globally. These assays are exploratory in nature and to date 
have not revealed informative results; moreover, require notable blood volume to be 
collected from subjects. 
 
The planned outputs will be still created, but patients enrolled under protocol amendment 5 
or a subsequent protocol amendment will not be included. 
8.3.7. Anti-OTC Antibodies 
The presence of circulating anti-OTC antibodies will be determined by ELISA at 
scheduled time points. The number and percentage of subjects will be presented by result 
category (i.e. Positive vs. Negative) and DTX301 dose/prophylactic corticosteroids in the 
SS at each scheduled post-baseline time point. 
Results (both categorical and continuous) will be displayed in a subject data listing for the 
SS.  
8.3.8. Baseline disease management 
Baseline disease management included ammonia-scavenging drugs and protein-restricted 
diet. 
Responder: A patient who has 50% reduction in baseline disease management. 
Complete responder: A patient who completely discontinues ammonia-scavenging drugs 
and protein-restricted diet. 
8.3.8.1. 
Ammonia Scavenger Therapy 
Ammonia scavenger therapy will be displayed in a subject data listing. 
8.3.8.2. 
Dietary Protein Prescription 
Total daily dose (g) of prescribed dietary protein intake, intact food protein and medical 
food protein will be summarized by DTX301 dose/prophylactic corticosteroids and visit 
based on the SS using the descriptive statistics. Counts and percentages of subjects with 
type of change will be summarized for total daily intact food protein and total daily 
medical food protein by DTX301 dose/prophylactic corticosteroids and visit.  
Counts and percentages of patients on unrestricted protein diet (i.e. unlimited intact food 
assumption and no medical food administration) at each visit will be provided. 
 


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Details of dietary protein prescription for each subject will be presented in a subject data 
listing. 
8.3.9. Neuropsychological Tests 
The observed and change from baseline for Patient-Reported Outcomes Measurement 
Information System® (PROMIS®) mental health measurements and the 
 
 will be summarized by DTX301 dose/prophylactic corticosteroids 
and visit at Early Withdrawal and End of Study (Week 52) unless otherwise noted based 
on the SS. All scoring will be performed by the study site psychologist or supervised 
designee and reviewed for inconsistencies or potential inaccuracies by a psychologist 
working as a consultant for Ultragenyx (CORE division). Both raw and 
scaled/standardized scores will be listed by subject and test type based on the SS for each 
of the following neuropsychological tests. 
8.3.9.1. 
Vocabulary and Matrix Reasoning Subtests from the WASI-II 
Subjects will be asked to complete the Vocabulary and Matrix Reasoning subtests from the 
Weschler Abbreviated Scale of Intelligence, Second Edition (WASI-II) at the Baseline 
Visit only. The WASI-II provides a general measure of cognitive functioning in subjects 
aged 6 to 89 years. The Vocabulary and Matrix Reasoning subtests provide an accurate, 
validated assessment of intelligence quotient (IQ) that is highly correlated (r=0.86) with 
results from the Wechsler Adult Intelligence Scale, Fourth Edition (WAIS-IV). Scaled 
scores for the Vocabulary and Matrix Reasoning subtests range from 20 to 80 whereas 
scaled scores for the Full Scale IQ range from 40 to 160. 
8.3.9.2. 
 
 
 
 
 
8.3.9.3. 
 
 
 
 
 


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8.3.9.4. 
 
 
 
 
 
8.3.10. PROMIS® Mental Health Measures 
Subjects will be asked to complete PROMIS® measures consisting of Anxiety (Adult 
Short Form 8a) and Depression (Adult Short Form 8a) at Day 0 (pre-dose) and at 
Weeks 6, 12, 24, and End of Study (Week 52). Higher scores indicate more of the 
concept being measured. Each measure consists of 8 items ranging from 1 to 5. Each 
measure can be scored as long as the subject answered at least 4 items. The formula for 
creating the total raw (or pro-rated) score is shown below: 
 
 
 
If the resulting total raw score is a fraction, round up to the nearest integer. Next, the total 
raw score is translated into a standardized score (T-score) using the applicable score 
conversion table (See Appendices). The T-score rescales the total raw score into a 
standardized score with a mean of 50 and a SD of 10. Therefore, a subject with a T-score 
of 40 is one SD below the mean. All scoring will be performed by the study site 
psychologist or supervised designee and reviewed for inconsistencies or potential 
inaccuracies by a psychologist working as a consultant for Ultragenyx (CORE division). 
All inconsistencies or potential inaccuracies will be queried and resolved appropriately 
prior to database lock. 
8.3.11. Quality of Life in Neurological Disorders Measures 
Subjects will be asked to complete the Quality of Life in Neurological Disorders 
(Neuro-QoL) Item Bank v2.0 measure of Cognitive Function – Short Form and Item 
Bank v1.0 measure of Emotional/Behavioral Dyscontrol – Short Form at Day 0 
(predose) and at Weeks 6, 12, 24, and End of Study (Week 52). Higher scores indicate 
more of the concept being measured. Each measure consists of 8 items ranging from 1 to 5. 
Each measure can be scored as long as the subject answered at least 4 items. The formula 
for creating the total raw (or pro-rated) score is shown below: 
 
 
 


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If the resulting total raw score is a fraction, round up to the nearest integer. Next, the total 
raw score is translated into a standardized score (T-score) using the applicable score 
conversion table (See Appendices). The T-score rescales the total raw score into a 
standardized score with a mean of 50 and a SD of 10. Therefore, a subject with a T-score 
of 40 is one SD below the mean. All scoring will be performed by the study site 
psychologist or supervised designee and reviewed for inconsistencies or potential 
inaccuracies by the psychologist at Ultragenyx. All inconsistencies or potential 
inaccuracies will be queried and resolved appropriately prior to database lock. 
8.3.12. Subgroup analysis 
Graphical displays of time-normalized ammonia and percent of normal ureagenesis activity 
over time will be provided by gender. 
9. Safety Analysis 
Safety will be assessed based on AEs, serious adverse event (SAEs), complete and targeted 
physical examination findings, vital sign measurements, ECG results, clinical laboratory 
evaluations (clinical chemistry, spot ammonia [included under efficacy section], 
hematology, urinalysis, and coagulation panel), blood for vector genome determination, 
measurement of neutralizing antibody to AAV8, measurement of AAV8 binding 
antibodies, and anti-OTC antibodies [the latter three included under efficacy section]. 
Assessment of any cell-mediated immune responses to AAV8 and OTC are collected prior 
to amendment 5. All safety analyses will be conducted for the SS. 
9.1. Adverse Events 
An AE is defined as any untoward medical occurrence in a subject enrolled into this study 
(from the time the subject signs the ICF until their exit from the study) regardless of its 
causal relationship to study drug. A treatment-emergent adverse event (TEAE) is defined 
as any event not present before exposure to study drug, or any event already present that 
worsens in intensity (i.e. severity) or frequency after exposure to study drug. Any events 
which occur after exposure to study drug and before the first visit of the extension study 
(301OTC02) will also be considered as TEAEs. 
 
AEs will be coded using MedDRA; the dictionary version used for reporting the study will 
be described in the relevant table and listing footnotes. Severity/toxicity grade will be 
defined according to the most current version of the National Cancer Institute Common 
Terminology Criteria for Adverse Events (NCI-CTCAE). 
 
There are four categories of relationship collected on the eCRF: “Unrelated”, “Possible”, 
“Probable”, or “Definite”. A related AE is an event where the investigator determined that 
the relationship to study drug was “Possible”, “Probable”, or “Definite”. For summaries by 
relationship, AEs with a missing relationship will be considered to be “Possible”. TEAEs 
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the AE is related to [1-13C] sodium acetate, OTC deficiency, hyperammonemia, and as of 
protocol amendment 5, to corticosteroid regimen.  
 
An HAC-related TEAE is defined as a TEAE which has been identified as associated with 
the crisis in the eCRF “Hyperammonemic Crisis” page.  
 
If AE start date is missing, it will be imputed as described in the Appendices. 
 
The incidence and the number and percentage of subjects will be summarized by DTX301 
dose/prophylactic corticosteroids and overall for each of the following: 
 
• All TEAEs 
• All serious TEAEs 
• All TEAEs with grade ≥3 
• All study drug related TEAEs 
• All study drug related serious TEAEs 
• All study drug related TEAEs ≥ grade 3 
• All TEAEs related to corticosteroid regimen (prednisone/prednisolone)  
• All HAC-related TEAEs 
• TEAEs leading to study discontinuation 
• Any AE leading to death 
 
The number and percentage of subjects with TEAEs will be summarized by DTX301 
dose/prophylactic corticosteroids, overall, SOC, and PT for each of the following: 
 
• TEAEs (including incidence) 
• TEAEs by relationship (including incidence) 
• TEAEs by severity (including incidence) 
• TEAEs by severity and relationship 
• TEAEs related to corticosteroid regimen (prednisone/prednisolone)  
• HAC-related TEAEs 
• Serious TEAEs 
• DLTs 
 
At each level of summarization, a subject will be counted only once for each TEAE he/she 
experiences within that level. Percentages will be calculated out of the number of subjects 
in the applicable analysis set. TEAEs will be sorted in alphabetical order by SOC. PTs will 
be sorted in descending order by frequency within each SOC.  
 
A data listing will be provided in the SS for each of the following: 
• All AEs 
• All SAEs 


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• DLTs 
• AEs leading to study discontinuation 
• AEs related to corticosteroid regimen 
9.2. Death 
All subjects who have an AE with an outcome of death will be presented in a listing. Date 
of death, and death certificate completion status will be included. 
9.3. Clinical Laboratory Evaluations 
Summary tables presenting observed values and changes from baseline to each scheduled 
post-baseline time point and minimum/maximum post-baseline value will be provided for 
clinical chemistry, hematology, urinalysis, and amino acids using standardized results.  
 
Results of clinical chemistry, hematology, and amino acid parameters will be categorized 
as low, normal, or high according to laboratory range specifications. Shifts from baseline 
to each scheduled post-baseline time point will be presented to show the number and 
percentage of subjects in each category by parameter. 
 
Results of urinalysis parameters will be categorized as normal or abnormal. Shifts from 
baseline to each scheduled post-baseline time point will be presented to show the number 
and percentage of subjects in each category by parameter. 
 
Spaghetti plots for both ALT and aspartate aminotransferase (AST) results separately, over 
time will be provided. 
A box plot of ALT results before and after gene transfer will be provided. 
 
Clinical Chemistry 
• ALT, albumin, alkaline phosphatase (ALP), AST, bilirubin (total and indirect), blood 
urea nitrogen (BUN), calcium, carbon dioxide, chloride, creatine kinase, creatinine, 
gamma-glutamyl transferase (GGT), glucose, magnesium, lactate dehydrogenase 
(LDH), phosphate, potassium, sodium, and total protein 
 
Hematology (including Coagulation Panel) 
• activated partial thromboplastin time (aPTT), basophils, basophils/leukocytes, 
eosinophils, eosinophils/leukocytes, erythrocyte mean corpuscular hemoglobin (MCH), 
erythrocyte mean corpuscular hemoglobin concentration (MCHC), erythrocyte mean 
corpuscular volume (MCV), erythrocytes, hematocrit, hemoglobin, leukocytes, 
lymphocytes, lymphocytes/leukocytes, monocytes, monocytes/leukocytes, neutrophils, 
neutrophils/leukocytes, platelets, international normalized ratio (INR), prothrombin 
time. 
 
 
 


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Urinalysis 
• blood, glucose, ketones, pH, protein, specific gravity, and microscopic examination (if 
blood or protein is found) 
 
Amino Acid Panel 
• Alanine, amino-butyric acid, arginine, asparagine, aspartic acid, , citrulline, cystine, 
ethanolamine, glutamic acid (aka “serum glutamate”), glutamine, glycine, histidine, 
homocysteine, hydroxyproline, isoleucine, leucine, lysine, methionine, ornithine, 
phenylalanine, proline, serine, taurine, threonine, tryptophan, tyrosine, and valine.  
 
Clinical chemistry measurements will be processed by both PPD Global Central 
Laboratory and local laboratories (liver function tests only) and summarized separately. 
Hematology and urinalysis measurements will be processed only by PPD Global Central 
Laboratory and summaries related to these laboratory categories will be limited to central 
lab results. 
Microscopic urinalysis results will be listed only. All laboratory data test results will be 
included by subject in applicable data listings. 
Newly notable laboratory abnormalities (i.e. abnormal post-baseline test results with 
corresponding normal baseline test results for a given parameter) in clinical chemistry, 
hematology, and urinalysis will be flagged in corresponding data listings. 
The number and percentage of subjects with ALT results greater than upper limit of normal 
(ULN) and also greater than or equal to 2.5×ULN using both local and central laboratory 
results will be summarized at each scheduled post-baseline time point and also 
corresponding to the maximum post-baseline value. If both central and local laboratory 
results are available for the same visit for a given subject, the highest result will be used 
for analysis purposes (regardless of the source). 
9.4. DTX301 Vector Genome Determination and Viral Shedding 
Saliva, stool, and urine samples will be collected at scheduled time points for viral 
shedding, while blood samples will be collected at scheduled time points for vector 
genome determination. The presence of DTX301 will be determined by 
 
 A summary table will be presented by sample type and 
DTX301 dose/prophylactic corticosteroids in the SS. Observed results and change from 
baseline to each scheduled post-baseline time point will be presented. Observed results will 
also be presented over time by sample type in a figure for each subject. Relevant individual 
vector shedding data (baseline value, highest value/timepoint, timepoint where the 3rd 
consecutive low value after peak) will be provided for each patient and sample type. 
Median values over time by cohort and sample type will be presented in a figure. 
Longitudinal displays of individuals data over time by cohort for each sample type will be 
presented. 
 


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Following protocol amendment 5, the assessment of vector genome determination was 
removed globally and viral shedding sampling was reduced based on medical 
consideration of results to date and to reduce subject burden. 
 
The planned outputs for vector genome determination will be still created, but patients 
enrolled under protocol amendment 5 or a subsequent protocol amendment will not be 
included.  
9.5. Vital Sign Measurements 
Summary tables will be presented by DTX301 dose/prophylactic corticosteroids for vital 
sign data, including weight (kg), pulse rate (beats/min), systolic blood pressure (mmHg), 
diastolic blood pressure (mmHg), respiratory rate (breaths/min), and temperature (C) 
regardless of body position for subjects in the SS. Observed results and change from 
baseline to each scheduled post-baseline time point will be presented in a data listing. 
9.6. Electrocardiogram Results 
An overall ECG interpretation (Normal, Abnormal – Not Clinically Significant, Abnormal 
– Clinically Significant) will be available based on local reading of ECG data. Shifts from 
baseline to each scheduled post-baseline time point and ‘worst post-baseline value’ will be 
presented to show the number and percentage of subjects in each category by DTX301 
dose/prophylactic corticosteroids for subjects in the SS. When considering ‘worst post-
baseline value’, interpretation is ordered as follows: Abnormal – Clinically Significant, 
Abnormal – Not Clinically Significant, and Normal.  
 
QTc using Bazett’s Correction (QTcB) and QTc using Fridericia’s Correction (QTcF) 
parameters will be computed using the following correction methods: 
 
Bazett: QTcB (msec) = QT (msec) / (RR/1000)1/2 
Fridericia: QTcF (msec) = QT (msec) / (RR/1000)1/3 
 
where RR is reported in milliseconds (msec). 
 
Results for Normal Sinus Rhythm, Ventricular Rate, P-R Interval, QRS Duration, QT 
Interval, QTcB Interval, and QTcF Interval will be listed only. 
9.7. Physical Examination Findings 
Complete and targeted physical examination findings will be classified by investigator as 
Normal, Abnormal – Not Clinically Significant, and Abnormal – Clinically Significant. 
Shifts from baseline to each post-baseline time point will be presented by body system to 
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10. Statistical Considerations for Data Monitoring Committee Meeting 
DMC members will meet after data from Week 12 are available for all subjects in cohort 1, 
cohort 2 and the first 3 subjects in cohort 3. The decision to proceed to the next dose 
cohort, expand a dosing cohort, and enroll subjects to cohort 4 (Dosing Process 
Optimization) will be made after each DMC meeting. The DMC will also hold a meeting 
at completion of Week 52 for all subjects. Additional DMC meetings may take place, as 
needed. The full scope of each review will be outlined in the DMC charter. 
11. Interim Analysis 
An interim analysis may be conducted when week 12 data are available from all subjects 
from at least 2 dosing cohorts. All tables/listings/figures for the full analysis will be 
produced for the interim analysis. No interim analysis has taken place.  
12. Changes from Analyses Planned in the Protocol 
 
Table 15-1 (Schedule of Events – Outpatient and Inpatient Clinic Visits) in the protocol 
defines the study day prior to DTX301 dosing as Day 0. However, in accordance with 
Clinical Data Interchange Standards Consortium (CDISC) conventions, the study day prior 
to DTX301 dosing will be defined as study day -1. 
 
Potential exploratory analyses of the time-normalized ammonia and/or percent of normal 
ureagenesis activity by gender has been added.   
 
The DMC will not hold a meeting at completion of Week 12 for the first 3 subjects in 
cohort 4. It has been agreed to have it only at the completion of Week 52 for all subjects. 
 
No interim analysis has taken place. 
 
 after patients in cohort 4 have completed the DLT 
window of 12 weeks or experienced a DLT prior to week 12 completion, in order to 
provide additional information for Health Canada submission. Patients from cohort 3 and 4 
will be pooled together in the N-CRM model.  
 
of AUC0-24h of 
plasma ammonia and of AUC0-240min of absolute 13C-urea vs. baseline have been added, 
along with other additional summary statistics for specific ureagenesis and ammonia 
parameters. 
 
 
 


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13. References 
Batshaw ML, MacArthur RB, Tuchman M. Alternative pathway therapy for urea cycle 
disorders: twenty years later. J Pediatr. 2001;138(1 Suppl):S46-54. 
 
Caldovic L, Abdikarim I, Narain S, et al. Genotype-phenotype correlations in ornithine 
transcarbamylase deficiency: a mutation update. J Genet Genomics. 2015;42(5):181-194. 
 
Castillo L, Beaumier L, Ajami AM, et al. Whole body nitric oxide synthesis in healthy 
men determined from [15N]arginine-to[15N]citrulline labeling. Proc Nat Acad Sci U S A. 
1996;93(21):11460-5. 
 
Feng, T. A Phase I/II Dose Finding Trial of Adeno-Associated Virus (AAV) Serotype 8-
Mediated Gene Transfer of Human Ornithine Transcarbamylase (OTC) in Adults with 
Late-Onset OTC Deficiency - Supplemental Information on Statistical Analyses: 
Simulation Report, Draft Version 3.0, August 2017. 
 
Häberle J, Boddaert N, Burlina A, et al. Suggested guidelines for the diagnosis and 
management of urea cycle disorders. Orphanet J Rare Dis. 2012;7:32.  
 
Häberle J, Burlina A, Chakrapani A, et al. Suggested guidelines for the diagnosis and 
management of urea cycle disorders: First revision. J Inherit Metab Dis. 2019; 42(6):1192-
1230. Doi: 10.1002/jimd.12100. Epub 2019 May 15. 
 
Jahoor F, Wolfe RR. Reassessment of primed constant-infusion tracer method to measure 
urea kinetics. Am J Physiol. 1987;252(4 Pt 1):E557-64. 
 
Kent JD, Holt RJ. Hyperammonemic crises in patients with urea cycle disorders on chronic 
nitrogen scavenger therapy with either sodium phenylbutyrate or glycerol phenylbutyrate. 
Neuropsych. 2017;7(2):131-6. 
 
Leonard JV. The nutritional management of urea cycle disorders. J Pediatr. 2001;138(1 
Suppl):S40-4. 
 
Leonard JV, McKiernan PJ. The role of liver transplantation in urea cycle disorders. Mol 
Genet Metab. 2004;81(Suppl 1):S74-8. 
 
Lichter-Konecki U, Caldovic L, Morizono H, Simpson K. Ornithine transcarbamylase 
deficiency. 2013 Aug 29 [Updated 2016 Apr 14]. In: Pagon RA, Adam MP, Ardinger HH, 
et al, editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 
1993-2016. Available from: http://www.ncbi.nlm.nih.gov/books/NBK154378/. 
 
Matthews DE, Downey RS. Measurement of urea kinetics in humans: a validation of stable 
isotope tracer methods. Am J Physiol. 1984;246(6 Pt 1):E519-27. 


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Neuenschwander B, Branson M, Gsponer T: Critical aspects of the Bayesian approach to 
phase I cancer trials, Statist. Med. 2008; 27: 2420–2439. 
 
Tuchman M, Lee B, Lichter-Konecki U, et al. Cross-sectional multicenter study of patients 
with urea cycle disorders in the United States. Mol Genet Metab. 2008a;94(4):397-402.  
 
Tuchman M, Caldovic L, Daikhin Y, et al. N-carbamylglutamte markedly enhances 
ureagensis in N-acetyglutamate deficiency and propionic acidemia as measured by isotopic 
incorporation and blood biomarkers. Pediatr Res. 2008b;64(2):213-7. 
 
Waisbren Susan. Neuropsychological Assessments for Psychologists and Study 
Coordinators. Protocol 301OTC01. Version 4.0, dated 01 May 2017.  
 
 
 
 


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14. Appendices 
Appendix A: Imputation Algorithm for Partial and Missing Dates 
AEs  
• If the onset date is completely missing, then the onset date is set to date of administration 
of study drug. 
• If year is present and month and day are missing: 
 If year = year  of administration of study drug, then set onset month and day 
to month and day of administration of study drug 
 If year < year of administration of study drug, then set onset month and day 
to December 31st. 
 If year > year   of administration of study drug, then set onset month and 
day to January 1st. 
• If month and year are present and day is missing: 
 If year=year  of administration of study drug and 
• If month = month of administration of study drug then set day to the 
day of administration of study drug 
• If month < month of administration of study drug then set day to the 
last day of the month 
• If month > month of administration of study drug then set day to the 
first day of the month 
 If year < year of administration of study drug then set day to the last day of 
the month 
 If year > year of administration of study drug then set day to first day of the 
month 
• If the imputed onset date created using the rules above comes after the complete stop date 
provided, then use the complete stop date 
 
Concomitant Medications 
• If start date is completely missing then start date will not be imputed. 
• If year is present and month and day are missing then set start month and start day to 
January 1. 
• If start year and start month are present and start day is missing then set start day to the 
first day of the month. 
• If end date is completely missing then end date will not be imputed. 
• If year is present and month and day are missing then set end month and end day to 
December 31. 
• If end year and end month are present and end day is missing then set end day to last day 
of the month. 
 
OTC Deficiency Medical History 
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• Month and day subject started therapy for OTC deficiency will be imputed as July 31st, 
respectively. 
 
Absolute 13C-Urea, AUC0-240min of 13C-Bicarbonate, AUC0-24h in Plasma Ammonia and 
urinary Orotic Acid AUC0-24h 
 
• For missing data at individual planned time points: 
o A single missing result between two planned time points that have non-missing 
results will be imputed by linear interpolation. 
o Two or more adjacent missing results will not be imputed and the AUCt1-t2 
measure will be set to missing 
o A single missing result at either the initial or final planned time point will be 
imputed by linear extrapolation using the first two or last two non-missing 
results, respectively. In the event that the extrapolated result is negative, the 
missing result will be set to zero. 
 
 
 
 
 
 


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Appendix B: Schedule of Events – Outpatient and Inpatient Clinic Visits 
 
 
 


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Appendix C: Schedule of Events – Clinic or Home Visits During the Treatment 
Period 
 
 
 
 
 
 
 
 
 


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