Clinical trial NCT03796637
Conditions: Duchenne Muscular Dystrophy
Sponsor: PTC Therapeutics
Start date: 2019-04-11; Completion date: 2019-06-03
Enrollment: 6 participants; Allocation: NA; Intervention model: SINGLE_GROUP

Brief summary:
This study is designed to generate additional data on the effect of ataluren for producing dystrophin protein in nonsense mutation nmDMD participants. This study will evaluate dystrophin levels from participants with nmDMD who currently have been receiving ataluren for ≥9 months.

The study will have a single visit (Visit 1).

Detailed description:

Arms: arm 1: Participants who have been receiving ataluren, will be dosed daily 10 milligrams per kilogram (mg/kg) in the morning, 10 mg/kg at midday, and 20 mg/kg in the evening, for \>=9 months from ongoing PTC-sponsored nmDMD clinical trials.
Interventions: intervention 1: Ataluren
Intervention descriptions: intervention 1: Ataluren will be administered as per the dose and schedule specified in the arm.

Protocol documents:
Prot_000.pdf: 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 1 of 39 
CLINICAL PROTOCOL 
PHASE 2, NON-INTERVENTIONAL, CLINICAL STUDY TO ASSESS 
DYSTROPHIN LEVELS IN SUBJECTS WITH NONSENSE MUTATION 
DUCHENNE MUSCULAR DYSTROPHY WHO HAVE BEEN 
TREATED WITH ATALUREN FOR ≥9 MONTHS. 
PROTOCOL NUMBER:  PTC124-GD-046-DMD 
20 MARCH 2019 
VERSION 2.0 
PTC THERAPEUTICS, INC. 
100 CORPORATE COURT 
SOUTH PLAINFIELD, NJ 07080 USA 
Notice of Proprietary Information: This document contains confidential information owned by or in the 
possession/control of PTC Therapeutics, Inc.  Except as may otherwise be permitted in writing, by accepting or 
reviewing these materials, you agree that this information should not be disclosed to others (except where 
required by applicable law) and should not be used for unauthorized purposes.  In the event of an actual or 
suspected breach of this obligation, PTC Therapeutics, Inc. should be notified promptly.
NCT #NCT03796637


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 2 of 39 
PROTOCOL SYNOPSIS 
Name of Sponsor/Company: 
PTC Therapeutics 
Name of Investigational Product: 
Ataluren  
Title of Study:  
Phase 2, non-interventional, clinical study to assess dystrophin levels in subjects with nonsense 
mutation Duchenne muscular dystrophy who have been treated with ataluren for ≥9 months. 
Study Centers: 
The study will be performed at a single site at 
 
Phase of Development: Phase 2 
Objectives:  
Primary: 
• 
To assess the levels of dystrophin in ambulatory nonsense mutation Duchenne muscular 
dystrophy (nmDMD) subjects currently being treated with ataluren for ≥9 months using 
quantitative electrochemiluminescence (ECL) assay 
Secondary: 
• 
To assess dystrophin levels/intensity and protein localization by immunohistochemistry 
Pharmacokinetic: 
• 
To evaluate the steady state pharmacokinetics (PK) of ataluren    
Endpoints: 
Primary: 
• 
Mean dystrophin levels as measured by ECL 
Secondary: 
• 
Levels and localization of dystrophin protein as determined by immunohistochemistry 
Pharmacokinetic: 
• 
PK assessments using sparse sampling and population PK modeling in a separate report. 
The parameters include Cl/F, V/F, AUC0-24, Cmax, and Cave. 
Study Description and Methodology 
Single-site, non-interventional study to obtain additional data on the effect of ataluren on 
dystrophin protein production in nmDMD subjects who currently have been taking ataluren for ≥9 
months. 
Quantifying dystrophin levels from nmDMD subject muscle biopsies is challenging due to the 
difficulty of obtaining muscle samples that contain sufficient amounts of intact muscle cells for 
analysis. This study has been designed to mitigate these challenges, to the extent possible, by 
adherence to the following practice parameters: 
• 
Biopsies will be collected from ambulatory nmDMD subjects; a subject population that are 
more likely to have greater amounts of intact muscle cells compared with older, non-
ambulatory patients with nmDMD. 
• 
A total of no more than approximately 450 mg of muscle tissue (up to  cores per muscle) 
will be collected from the 
 and 
 
. If the 
 muscle 
is considered by the investigator to be too small for muscle biopsy sampling, the 
 
 muscle may be used. 
• 
Two validated, highly sensitive assays, ie, ECL and immunohistochemistry, will be used to 
measure dystrophin protein levels and to evaluate whether the protein localizes correctly to 
the muscle membrane. 
Study Population: Approximately 6 ataluren-treated subjects with nmDMD.  


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 3 of 39 
Main inclusion and exclusion criteria  
Inclusion criteria:  
1. Evidence of signed and dated informed consent/assent document(s) indicating that the 
patient (and/or his parent/legal guardian) has been informed of all pertinent aspects of the 
trial.   
2. Male sex. 
3. Ambulatory (ie, 10 m walk/run in <30seconds) and functional grade on the Brooke Upper 
Extremity Scale of a 1 or a 2. 
4. Currently being treated with ataluren 10, 10, 20 mg/kg for ≥9 months, with no gap in 
treatment of >1 month prior to study entry. 
5. Phenotypic evidence of DMD based on the onset of characteristic clinical symptoms or 
signs (eg, proximal muscle weakness, waddling gait, and Gowers’ maneuver) and an 
elevated serum creatine kinase (CK). Medical documentation of phenotypic evidence of 
DMD needs to be provided upon request by the PTC Therapeutics medical monitor. 
6. Willing to undergo muscle biopsy.  
Exclusion Criteria: 
1. Known contra-indication to muscle biopsy (ie, such as bleeding or clotting disorders). 
2. Exposure to another investigational drug within 2 months prior to enrollment in the study or 
ongoing participation in any non-ataluren interventional clinical trial.   
3. Requirement for daytime ventilator assistance or any use of invasive mechanical ventilation 
via tracheostomy. Note: Evening non-invasive mechanical ventilation such as use of bilevel 
positive airway pressure (Bi-PAP) therapy is allowed. 
4. Prior or ongoing medical condition (eg, concomitant illness, psychiatric condition, 
behavioral disorder, alcoholism, drug abuse), medical history, physical findings or 
laboratory abnormality that, in the Investigator’s opinion, could adversely affect the safety 
of the subject, makes it unlikely that the muscle biopsy or follow-up would be completed, or 
could impair the assessment of study results. 
Statistical analyses: 
Dystrophin levels will be summarized using descriptive statistics. 
 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 4 of 39 
SCHEDULE OF ASSESSMENTS 
Study Procedure 
Visit 1
1 
Follow-up 
(phone call) 
Notes 
Week 
(visit window) 
 
Week 1 
(± 3days) 
 
Informed Consent 
X 
 
A signed and dated informed consent must be obtained before conducting any study 
procedures. 
Inclusion/Exclusion 
X 
 
Demographics 
X 
 
Medical History 
X 
 
Physical Exam 
X 
 
Full physical exam will be performed. 
Clinical Labs 
X 
 
Biochemistry, hematology, and urinalysis laboratory assessments.  
Height/Weight/BMI 
X 
 
Vitals (HR & BP) 
X 
 
Vital signs will include systolic and diastolic blood pressure, pulse rate, and body 
temperature. The pulse rate and blood pressure determinations will be performed 
with the subject in a sitting position after a 5-minute rest. Blood pressure will be 
measured in triplicate and the average will be recorded.   
Timed function tests 
X 
 
Tests include time to climb 4 stairs, time to descend 4 stairs, time to rise from 
supine, and time to run/walk 10 meters. 
PK blood sampling 
X 
 
PK samples will be drawn pre-morning dose and 2 hours post-morning dose. 
Ataluren plasma concentrations will be analyzed in a population PK model for the 
estimation of key pharmacokinetic parameters including Cl/F, V/F, AUC0-24, Cmax, 
and Cave. 
Muscle biopsy 
X 
 
Muscle biopsy will be taken from the 
 and 
. If the 
 muscle is considered by the investigator to be too small for a muscle biopsy 
sample, the 
 muscle may be used 
AE/SAE Monitoring 
X 
X 
Concomitant 
medications 
X 
 
Treatments, including ataluren, taken one month prior to enrollment and during 
Visit 1 will be recorded. 
Abbreviations:  AE, adverse event; AUC0-24, area under the concentration curve from time 0 to 24 hours; BMI, body mass index; BP, blood pressure; 
Cl/F, clearance; Cave, average plasma concentration; Cmax, maximal plasma concentration; HR, heart rate; PK, pharmacokinetics; SAE, serious adverse 
event; V/F, volume of distribution 
1 
Subjects may have to return to the clinic for up to 3 days for completion of assessments and muscle biopsy. 
 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 5 of 39 
PROTOCOL IDENTIFIERS AND STUDY PERSONNEL 
Project Code 
PTC124-GD 
Therapeutic Area 
Genetic Disorders – Duchenne Muscular Dystrophy 
PTC Therapeutics Substance Identifier 
Ataluren (PTC124) 
IND Number 
068431 
Protocol Number  
PTC124-GD-046-DMD 
Protocol Version  
Version 2.0 
Protocol Version Date 
20 March 2019 
Protocol Phase  
Phase 2 
Protocol Title   
Phase 2, non-interventional, clinical study to assess 
dystrophin levels in subjects with nmDMD who have 
been treated with ataluren for ≥9 months 
 
PTC Clinical Lead  
PTC Therapeutics, Inc.  
100 Corporate Court 
South Plainfield, NJ  07080 USA 
Telephone (office):
Facsimile:
E-mail:
 
PTC Medical Monitor  
PTC Therapeutics, Inc. 
100 Corporate Court 
South Plainfield, NJ  07080 USA 
Telephone (office):
Facsimile:
E-mail:
 
PTC Biostatistician  
PTC Therapeutics, Inc.  
100 Corporate Court 
South Plainfield, NJ  07080 USA 
Telephone (office):
Facsimile: 
E-mail:
 
PTC Study Manager  
 
PTC Therapeutics, Inc.  
100 Corporate Court 
South Plainfield, NJ  07080 USA 
Telephone (office):
Facsimile:
E-mail: 
 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 6 of 39 
PTC THERAPEUTICS PROTOCOL APPROVAL SIGNATURES 
 
 
 
 
 
 
 
 
 
 
 
 
PTC Therapeutics, Inc. 
 
Date 
 
 
 
 
 
 
 
 
 
 
 
 
PTC Therapeutics, Inc. 
 
Date 
 
 
 
 
 
 
 
 
 
 
 
 
PTC Therapeutics, Inc. 
 
Date 
 
 
 
 
 
 
 
 
 
 
 
 
PTC Therapeutics, Inc. 
 
Date 
 
 
 
 
 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 7 of 39 
PRINCIPAL INVESTIGATOR AGREEMENT AND SIGNATURE 
 
I have read the protocol document and, on behalf of my institution, agree to comply with 
the protocol and all applicable regulations. 
 
 
 
 
Principal Investigator 
 
Date 
 
 
 
Institution: 
 
Address: 
 
City: 
 
State/Province:  
Country: 
 
Phone: 
 
Fax: 
 
Email: 
 
 
 
 
 
 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 8 of 39 
TABLE OF CONTENTS 
PROTOCOL SYNOPSIS ........................................................................................................2 
SCHEDULE OF ASSESSMENTS .........................................................................................4 
PROTOCOL IDENTIFIERS AND STUDY PERSONNEL ................................................5 
PTC THERAPEUTICS PROTOCOL APPROVAL SIGNATURES .................................6 
PRINCIPAL INVESTIGATOR AGREEMENT AND SIGNATURE ...............................7 
TABLE OF CONTENTS ........................................................................................................8 
LIST OF TABLES .................................................................................................................10 
LIST OF ABBREVIATIONS AND DEFINITION OF TERMS .......................................11 
1 
INTRODUCTION .................................................................................................12 
1.1 
Disease Background ..............................................................................................12 
1.2 
Ataluren .................................................................................................................13 
1.2.1 
Ataluren-associated increased ribosomal readthrough of premature stop 
codons .....................................................................................................................13 
1.3 
Risk/Benefit Assessment .......................................................................................14 
2 
STUDY OBJECTIVE AND ENDPOINTS .........................................................15 
2.1 
Objectives ...............................................................................................................15 
2.1.1 
Primary Objective .................................................................................................15 
2.1.2 
Secondary Objectives ............................................................................................15 
2.1.3 
Pharmacokinetic: ..................................................................................................15 
2.2 
Endpoints ...............................................................................................................15 
2.2.1 
Primary Endpoint .................................................................................................15 
2.2.2 
Secondary Endpoints ............................................................................................15 
2.2.3 
Pharmacokinetic ....................................................................................................15 
3 
STUDY DESIGN ...................................................................................................16 
3.1 
Overall Design .......................................................................................................16 
3.1.1 
Muscle biopsy samples ..........................................................................................16 
3.1.2 
Evaluation of dystrophin levels ............................................................................16 
3.1.2.1 
Electrochemiluminescence assay ..........................................................................17 
3.1.2.2 
Immunohistochemistry assay .................................................................................17 
3.2 
Scientific Rationale for Study Design ..................................................................17 
3.3 
Justification of Dose ..............................................................................................18 
3.4 
End of Study Definition ........................................................................................18 
4 
STUDY POPULATION .......................................................................................19 
4.1 
Overview ................................................................................................................19 
4.2 
Inclusion Criteria ..................................................................................................19 
4.3 
Exclusion Criteria .................................................................................................19 
5 
ENROLLMENT PROCEDURES .......................................................................20 
5.1 
Source and Number of Subjects ..........................................................................20 
5.2 
Screening ................................................................................................................20 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 9 of 39 
6 
STUDY INTERVENTION ...................................................................................20 
6.1 
Study Intervention(s) Administration .................................................................20 
6.2 
Concomitant Therapy ...........................................................................................20 
6.3 
Discontinuation of Study Intervention ................................................................21 
6.4 
Participant Discontinuation/Withdrawal from the Study .................................21 
7 
STUDY ASSESSMENT AND PROCEDURES .................................................22 
7.1 
Schedule of Assessments and Study Parameters ................................................22 
7.2 
Safety Assessments and Other Assessments .......................................................23 
7.3 
Adverse Events and Serious Adverse Events .....................................................23 
7.3.1 
Definition of adverse events..................................................................................23 
7.3.2 
Definition of serious adverse events ....................................................................24 
7.3.3 
Eliciting adverse event information .....................................................................25 
7.3.4 
Recording Non‑serious AEs and SAEs ................................................................25 
7.3.5 
Describing adverse event relationship to muscle biopsy procedure .................26 
7.3.6 
Grading of severity of adverse event related to muscle biopsy procedure ......26 
7.3.7 
Adverse Event Reporting .....................................................................................27 
7.3.8 
Serious adverse event reporting ...........................................................................28 
7.3.9 
Reporting Pregnancy ............................................................................................28 
7.3.10 
PTC Therapeutics Adverse Event Reporting Requirement .............................29 
8 
STATISTICAL CONSIDERATIONS ................................................................29 
8.1 
Statistical Hypotheses ...........................................................................................29 
8.1.1 
Sample Size Determination ..................................................................................29 
8.2 
Population for Analyses ........................................................................................29 
8.2.1 
Intention-to-treat analysis set...............................................................................29 
8.3 
Safety Analysis Set ................................................................................................29 
8.4 
Statistical Analyses ................................................................................................29 
8.4.1 
General approach ..................................................................................................29 
8.4.2 
Analysis of primary efficacy endpoints ...............................................................30 
8.4.3 
Analysis of secondary efficacy endpoints ............................................................30 
8.4.4 
Safety analyses .......................................................................................................30 
8.4.5 
Planned interim analyses ......................................................................................30 
8.4.6 
Sub-group analyses ...............................................................................................30 
9 
SUPPORTING DOCUMENTATION AND OPERATIONAL 
CONSIDERATIONS ............................................................................................31 
9.1 
Regulatory, Ethical, and Study Oversight Considerations ...............................31 
9.1.1 
Informed consent process .....................................................................................31 
9.1.2 
Study discontinuation and closure .......................................................................31 
9.1.3 
Confidentiality and privacy ..................................................................................31 
9.1.4 
Future use of stored specimens and data ............................................................32 
9.1.5 
Clinical monitoring ...............................................................................................33 
9.1.6 
Quality assurance and quality control ................................................................33 
9.1.7 
Data handling and record keeping ......................................................................33 
9.1.8 
Protocol deviations ................................................................................................34 
9.1.9 
Publication and data sharing policy ....................................................................34 
9.2 
Additional Considerations ....................................................................................35 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 10 of 39 
9.3 
Protocol Amendment History ..............................................................................36 
10 
REFERENCES ......................................................................................................38 
 
LIST OF TABLES 
Table 1. 
Schedule of Assessments.....................................................................................22 
Table 2. 
Relationship of Study Muscle Biopsy Procedure to Adverse Event...............26 
Table 3. 
Grading of Adverse Event Severity Grade .......................................................27 
Table 4. 
Investigator Site Requirements for Reporting Adverse Events Not Related to 
Muscle Biopsy......................................................................................................27 
Table 5. 
Investigator Site Requirements for Reporting Muscle Biopsy-Related 
Adverse Events ....................................................................................................27 
  
 
 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 11 of 39 
LIST OF ABBREVIATIONS AND DEFINITION OF TERMS 
Term 
Definition 
AE 
Adverse event 
Bi-PAP 
Bilevel positive airway pressure  
BMD 
Becker muscular dystrophy 
BMI 
Body mass index 
BP 
Blood pressure 
CK 
Creatine kinase 
CRF 
Case report form 
CRO 
Contract research organization 
CTCAE 
Common Terminology Criteria for Adverse Events 
DMD 
Duchenne muscular dystrophy 
EC 
Ethics Committee 
ECL 
Electrochemiluminescence 
eCRF 
Electronic case report form 
FVC 
Forced vital capacity 
GCP 
Good Clinical Practice 
HR 
Heart rate 
ICF 
Informed consent form 
ICH 
International Councilfor Harmonisation 
IRB 
Institutional Review Board 
MedDRA 
Medical Dictionary for Regulatory Activities 
mRNA 
Messenger ribonucleic acid 
nmDMD 
Nonsense mutation Duchenne muscular dystrophy 
PK 
Pharmacokinetic 
RSI 
Reference Safety Information 
SAE 
Serious adverse event 
 
 
 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 12 of 39 
1 
INTRODUCTION 
1.1 
Disease Background 
Duchenne muscular dystrophy (DMD) is a rare, debilitating, progressive, and ultimately fatal 
childhood disease (Bushby 2010a, Bushby 2010b). It is an X-linked genetic muscle disorder 
that results from a mutation in the dystrophin gene. Dystrophin is a 427 kDa structural 
protein present at the muscle sarcolemma that provides stability to the muscle and is 
expressed in skeletal, respiratory, and cardiac muscle (Bushby 2010a, Mah 2016, Rae 2016). 
It is also expressed in neurons in specific parts of the brain, such as the hippocampus 
(Aartsma-Rus 2016).  
Dystrophin acts as a shock absorber during muscle contraction by linking the actin of the 
contractile apparatus to the layer of connective tissue that surrounds each fiber 
(Aartsma-Rus 2016). Consequently, dystrophin bears the mechanical stresses that occur 
during muscle contraction, stabilizing muscle cell membranes, and protecting muscles from 
injury (Petrof 1993). Dystrophin mutations disrupt the connection with the actin cytoskeleton 
and connective tissue resulting in chronic muscle damage, inflammation, and eventually 
replacement of muscle fibers by fat and fibrotic tissue resulting in progressive and 
irreversible loss of muscle function (Muntoni 2003). The culmination of muscle function loss 
leads to early death; the average life expectancy of DMD patients is about 25 years of age. 
Duchenne muscular dystrophy is noticeable in young children, who typically display 
underdeveloped or delayed development of motor skills relative to healthy boys 
(Bushby 2010a). Muscle function continues to deteriorate in pre-adolescence resulting in the 
loss of gross motor functions, including the ability to rise from the floor, to climb stairs, and 
to walk. Complete loss of ambulation typically occurs in the early teenage years. Loss of 
functional abilities occur sequentially, with the loss of one function preceding and predicting 
the loss of subsequent functions. Importantly, the age at loss of ambulation is predictive of 
the age of onset of severe respiratory insufficiency (forced vital capacity [FVC] <1 liter) 
requiring the need for ventilation assistance (Humbertclaude 2012), which in turn is 
predictive of death within 3 years (Phillips 2001). 
To date, no medications cure or reverse the effects of DMD. The goals of current 
interventions are to help slow or stabilize disease progression, prolong patients’ ability to 
manage activities of daily living, and delay the onset of subsequent deterioration. Recent 
clinical guidelines recommend treatment with glucocorticoids, which address the 
inflammatory component of the disease, and have beneficial effects on prolonging 
ambulation and muscle and respiratory function (Bushby 2010a, Bushby 2010b). Additional 
treatments are necessary, particularly those that treat the underlying cause of the disease. 
Because of the role of the dystrophin protein, dystrophin restoration therapy would be 
expected to stabilize or slow disease progression in patients with DMD. 
Approximately 10% to 15% of boys with DMD have the disease due to a nonsense mutation 
in the dystrophin gene (Aartsma-Rus 2006, Bladen 2015), resulting in a premature stop 
codon in the dystrophin mRNA (messenger ribonucleic acid). Consequently, ribosomal 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 13 of 39 
translation of nonsense codon containing mRNA results in premature termination of 
translation before a full-length, functional protein is generated. 
1.2 
Ataluren 
Ataluren is a small molecule being developed for the treatment of nonsense mutation 
Duchenne muscular dystrophy (nmDMD). Ataluren promotes ribosomal readthrough of 
premature stop codons enabling the formation of full-length, functional dystrophin protein 
(Welch 2007).   
The efficacy and safety of ataluren for the treatment of nmDMD were assessed in 
2 randomized, double-blind, placebo--controlled, 48-week trials (PTC124-GD-007-DMD 
[NCT00592553] [Study 007] and PTC124-GD-020-DMD [NCT01826487] [Study 020]). 
Data from these studies supported conditional marketing authorization of ataluren for the 
treatment of nmDMD in ambulatory patients aged ≥5 years in Europe and subsequently 
extended to ≥2 years of age based on pharmacokinetic extrapolation from study 
PTC124-GD 030-DMD.  
A detailed description of the chemistry, pharmacology, efficacy, and safety of ataluren is 
provided in the Investigator’s Brochure (IB). 
1.2.1 
Ataluren-associated increased ribosomal readthrough of premature stop 
codons 
The ability of ataluren to promote ribosomal readthrough of premature stop codons has been 
evaluated in a wide range of in vivo and in vitro preclinical experiments, including different 
organ and animal model systems, as well as cell-free and cell-based systems. In particular, 
preclinical studies in the mdx mouse and the sapje zebrafish nmDMD models and human 
myotubes consistently demonstrate that ataluren increases dystrophin production across key 
tissues, including skeletal muscle, heart, and diaphragm.  
Production of dystrophin from ataluren treatment was also investigated in nmDMD patients 
in the Phase 2a PTC124-GD-004-DMD study (Study 004) (Finkel 2013). In this trial, 
38 nmDMD patients received treatment with ataluren for 28 days. Results from the proof of 
concept study indicate that ataluren treatment leads to production of full-length dystrophin 
protein; post-treatment increases in dystrophin were quantified in 61% (23/38) of the 
patients. The mean change in muscle biopsy dystrophin expression from baseline to Day 28 
was 11% (p=0.008). In addition, immunohistochemistry experiments indicated the protein 
was correctly localized to membranes of muscle cells, suggesting functional activity. 
Myotubes derived from pre-treatment muscle biopsies were cultured in vitro in the presence 
of ataluren and 100% of the samples showed increases in dystrophin expression. Dystrophin 
expression was also evaluated in Study 007 in which nmDMD patients were treated with 
ataluren or placebo. Results from Study 007 were also supportive of an increase in 
dystrophin levels, consistent with Study 004 results. The increase in dystrophin levels in the 
two prior clinical studies are limited by the quality of muscle biopsy samples and the use of a 
non-validated immunofluorescence method of detecting dystrophin protein. 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 14 of 39 
1.3 
Risk/Benefit Assessment 
Under the current standard of care, nmDMD remains a disease with devastating 
consequences and bleak prognosis. The progressive and irreversible effects of nmDMD 
underscore the importance of early intervention with treatments that have the potential to 
slow physical deterioration and delay the natural course of this fatal disease. While treatment 
with corticosteroids target the inflammatory component of the disease, additional treatments 
are needed to address the loss of dystrophin, the underlying cause of the disease. 
The mechanism by which ataluren restores dystrophin has been established in comprehensive 
preclinical studies and supported in clinical evaluations. Moreover, the clinical benefit of 
ataluren has been demonstrated in two large randomized controlled trials Study 007 and 
Study 020. 
This study is designed to quantitatively evaluate dystrophin protein levels in muscle biopsies 
from boys with nmDMD who currently have been receiving ataluren for ≥9 months. The 
muscle biopsy technique to be used is less invasive than the standard muscle biopsy and is of 
relative low-risk to the subject. The use of two highly sensitive validated assays to evaluate 
dystrophin protein levels will increase the likelihood that each muscle biopsy sample will 
yield interpretable results. Hence, the study design and the importance of establishing the 
association of ataluren treatment with dystrophin expression results in a positive risk/benefit.  


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 15 of 39 
2 
STUDY OBJECTIVE AND ENDPOINTS 
2.1 
Objectives 
2.1.1 
Primary Objective 
● 
To assess the levels of dystrophin in ambulatory nmDMD subjects currently being 
treated with ataluren for ≥9 months using a quantitative electrochemiluminescence 
(ECL) assay 
2.1.2 
Secondary Objectives 
● 
To assess dystrophin levels/intensity and protein localization by 
immunohistochemistry 
2.1.3 
Pharmacokinetic: 
● 
To evaluate the steady state pharmacokinetics (PK) of ataluren   
2.2 
Endpoints 
2.2.1 
Primary Endpoint  
The primary endpoint is: 
● 
Mean dystrophin levels as measured by ECL 
2.2.2 
Secondary Endpoints 
The secondary endpoint is: 
● 
Levels and localization of dystrophin protein levels as determined by 
immunohistochemistry 
2.2.3 
Pharmacokinetic 
● 
PK assessments using sparse sampling and population PK modeling in a separate 
report. The parameters include Cl/F, V/F, AUC0-24, Cmax, and Cave 
 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 16 of 39 
3 
STUDY DESIGN 
3.1 
Overall Design 
This is a single-site, non-interventional study designed to generate additional data on the 
effect of ataluren for producing dystrophin protein in nonsense mutation nmDMD subjects. 
This study will evaluate dystrophin levels from subjects with nmDMD who currently have 
been receiving ataluren for ≥9 months.  
Approximately, 6 ambulatory nmDMD male subjects who have been receiving ataluren, 
dosed daily 10 mg/kg in the morning, 10 mg/kg at midday, and 20 mg/kg in the evening 
(10, 10, 20 mg/kg), for ≥9 months.  
The study will have a single visit (Visit 1) which will occur that the site of 
 
. At this visit, inclusion/exclusion 
criteria, demographics and medical history will be assessed. In addition, blood will be drawn 
for clinical labs and PK analysis pre-morning ataluren dose. A second blood sample for PK 
will also be taken 2 hours after morning ataluren dose. The muscle biopsy will also be 
performed at this visit. Adverse events will be monitored at Visit 1 and by a follow-up phone 
call approximately 1-week post Visit 1. 
3.1.1 
Muscle biopsy samples 
Muscle biopsies will be performed by appropriately trained staff at 
 All subjects will 
have a physical exam and a history taken and recorded prior to the procedure to assess 
muscle biopsy locations and determine if there is any intercurrent illness that places a subject 
at higher risk.  
Muscle biopsy of the 
 and right gastrocnemius 
 will be performed using an 
established core muscle biopsy procedure (Gallo 2018). If the 
 muscle is considered by 
the investigator to be too small for a muscle biopsy sample, the 
 muscle 
may be used. A total of no more than approximately 450 mg of muscle tissue (up to  cores 
per muscle) will be obtained. Vacuum needle muscle biopsy will be performed using local 
anesthesia or mild sedation, if needed. All biopsies will be preserved/frozen using standard 
protocol for ECL and immunohistochemistry (see Section 3.1.2).  
The need for conscious sedation will be evaluated on a case by case basis and will be 
provided by physicians who are credentialed to monitor and provide sedation in an outpatient 
setting. Following sedation, vital signs will be monitored until the subject returns to pre-
sedation baseline values. These techniques are standard of care at 
 for minor 
procedures on young patients. 
3.1.2 
Evaluation of dystrophin levels 
Two validated assays, ie, ECL and immunohistochemistry, will be used to assess dystrophin 
levels. The assays provide slightly different information, and together give a robust analysis.  


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 17 of 39 
3.1.2.1 
Electrochemiluminescence assay 
 
Electrochemiluminescence technology provides high sensitivity with a low background. The 
assay will be optimized and validated by an external contract research organization (CRO). 
Subject muscle biopsy samples will be shipped to and analyzed for dystrophin levels by a 
CRO.  
3.1.2.2 
Immunohistochemistry assay 
Immunohistochemistry will semi-quantitatively assess dystrophin protein levels and evaluate 
whether the dystrophin protein is correctly localized to the membrane of the muscle cell, 
consistent with a functional protein. Dystrophin measured using this assay will be the 
secondary endpoint. 
 
 Subject muscle biopsy samples will be shipped to and analyzed for 
dystrophin levels by a CRO. 
3.2 
Scientific Rationale for Study Design  
The study is designed to generate additional data on the effect of ataluren on promoting the 
production of dystrophin protein in nmDMD subjects. It is known that even small increases 
in dystrophin levels can result in milder disease phenotype in nmDMD patients. The levels of 
dystrophin in patients with Becker muscular dystrophy (BMD) have been reported to be 
higher than that observed in patients with Duchenne muscular dystrophy (DMD) 
(Anthony 2014). Consequently, patients with BMD generally have less severe disease 
compared with those with DMD; BMD patients often show a later onset of disease and 
slower disease progression (Muntoni 2003, Aartsma-Rus 2006). 
As described in Section 1.2.1, the ability of ataluren to promote ribosomal readthrough of 
premature stop codons has been demonstrated in a range of in vivo and in vitro preclinical 
assays. In addition, ataluren-associated increases in dystrophin protein levels was assessed in 
a prior clinical study. Of patients treated with ataluren 10, 10, 20 mg/kg, 55% (8/20) had an 
increase in dystrophin expression post-ataluren treatment (Finkel 2013). The findings from 
this study were consistent with ataluren treatment increasing dystrophin levels and indicated 
that the protein correctly localized to the muscle cell membranes, suggesting functional 
activity (Finkel 2013).  
Assessing dystrophin levels in patients with nmDMD can be challenging due to inherent 
difficulty in obtaining muscle samples that contain sufficient amounts of intact muscle cells 
for analysis, as nmDMD muscle, particularly in older patients, are often heterogenous with 
respect to fibrofatty replacement of muscle.  
From prior clinical trial experience, it is anticipated that although levels or dystrophin may 
increase in nmDMD muscle from baseline following ataluren therapy, the amount of 
dystrophin will still be low; hence, sensitive assays with good specificity are necessary to 
evaluate change in dystrophin levels with treatment.  


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 18 of 39 
Method of muscle biopsy sampling can also impact results. For example, variability can be 
introduced by assessing a bilateral muscle sampled from one side of the body before 
treatment and from the other side after treatment. 
This current study is designed to mitigate some of these difficulties.  
● 
Biopsies will be collected from ambulatory nmDMD subjects who have grade 1 or 
2 of the Brook Upper Extremity Scale (Brooke 1989, Connolly 2015) to increase 
the chance of collecting less heterogenous muscle tissue. 
● 
A total of no more than approximately 450 mg of muscle tissue (up to  cores per 
muscle) will be collected from the 
 and 
 
. If 
the 
 muscle is considered by the investigator to be too small for muscle 
biopsy sampling, the 
 muscle may be used. 
● 
Two validated, highly sensitive assays will be employed to measure ataluren-
associated increases in dystrophin protein levels and to evaluate whether the 
protein localizes correctly to the muscle membrane. 
3.3 
Justification of Dose 
Not applicable  
3.4 
End of Study Definition 
The end of the study is defined as completion of the follow-up phone call to assess adverse 
events (AEs) which occurs approximately 1 week (±3 days) following Visit 1.  
 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 19 of 39 
4 
STUDY POPULATION  
4.1 
Overview 
4.2 
Inclusion Criteria 
1. 
Evidence of signed and dated informed consent/assent document(s) indicating that 
the subject (and/or his parent/legal guardian) has been informed of all pertinent 
aspects of the trial.   
2. 
Male sex. 
3. 
Ambulatory (ie, 10m walk/run in <30seconds) and functional grade on the Brooke 
Upper Extremity Scale of a 1 or a 2. 
4. 
Currently being treated with ataluren 10, 10, 20 mg/kg for ≥9 months, with no gap 
in treatment of >1 month, prior to study entry. 
5. 
Phenotypic evidence of DMD based on the onset of characteristic clinical 
symptoms or signs (eg, proximal muscle weakness, waddling gait, and Gowers’ 
maneuver) by 6 years of age and an elevated serum creatine kinase (CK). Medical 
documentation of phenotypic evidence of DMD needs to be provided upon request 
by the PTC Therapeutics medical monitor. 
6. 
Willing to undergo muscle biopsy.  
4.3 
Exclusion Criteria 
1. 
Known contra-indication to muscle biopsy (ie. such as bleeding or clotting 
disorders). 
2. 
Exposure to another investigational drug within 2 months prior to study enrollment 
or ongoing participation in any non-ataluren interventional clinical trial.   
3. 
Requirement for daytime ventilator assistance or any use of invasive mechanical 
ventilation via tracheostomy. Note: Evening non-invasive mechanical ventilation 
such as use of bilevel positive airway pressure (Bi-PAP) therapy is allowed. 
4. 
Prior or ongoing medical condition (eg, concomitant illness, psychiatric condition, 
behavioral disorder), medical history, physical findings or laboratory abnormality 
that, in the investigator’s opinion, could adversely affect the safety of the subject, 
makes it unlikely that the course of treatment or follow-up would be completed, or 
could impair the assessment of study results. 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 20 of 39 
5 
ENROLLMENT PROCEDURES 
5.1 
Source and Number of Subjects 
Approximately 6 subjects will be enrolled. Subjects who currently have been receiving 
ataluren therapy for ≥9 months will be recruited. 
5.2 
Screening 
The Investigator must inform each subject and/or parent/legal guardian of the nature of the 
study, explain the potential risks, and obtain written informed consent/assent from the subject 
and/or parent(s)/legal guardian (as required by local regulations) prior to performing any 
study-related screening procedures. 
 
6 
STUDY INTERVENTION 
6.1 
Study Intervention(s) Administration 
Not applicable as not an interventional study. 
6.2 
Concomitant Therapy 
Including ataluren, any treatments (ie, prescription and non-prescription drugs, health foods, 
herbal remedies, self-prescribed drugs, street drug, tobacco products, or alcohol) that are taken 
by a subject for one month prior to study enrollment and during Visit 1 are considered 
concomitant medications. Information regarding any concomitant medications will be 
collected and documented in the electronic case report form (eCRF) and in the source 
documents by the clinic staff.  
To the extent possible, administration of any prescription or over-the-counter drug products 
should be minimized during the study period. Subjects should be discouraged from use of 
“health supplements” (eg, creatine, glutamine, coenzyme Q), herbal remedies, growth 
hormone, self-prescribed drugs, at any time during clinical studies of ataluren.   
If considered necessary for the subject’s well-being, drugs for concomitant medical conditions 
or for symptom management may be given at the discretion of the investigator. The decision to 
authorize the use of any other drug(s) should consider the subject’s safety, the medical need, 
the potential for drug interactions, the possibility for masking symptoms of a more relevant 
underlying event, and whether use of a concomitant medication will compromise the 
outcome or integrity of the study.   
Subjects and parents/caregivers or legal guardian should be instructed about the importance 
of the need to inform the clinic staff of the use of any drugs or remedies (whether prescribed, 
over-the-counter, or illicit) before and during the course of the study.  


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 21 of 39 
The investigator is encouraged to consult the PTC medical monitor or designee with 
questions relating to specific drugs. 
6.3 
Discontinuation of Study Intervention 
Not applicable 
6.4 
Participant Discontinuation/Withdrawal from the Study 
The parent/caregiver or legal guardian has the right to withdraw consent and discontinue the 
study at any time. 
This study may be discontinued by the relevant regulatory authority, IRB/EC (Institutional 
Review Board/Ethics Committee), and/or PTC Therapeutics at any time. 
 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 22 of 39 
7 
STUDY ASSESSMENT AND PROCEDURES 
7.1 
Schedule of Assessments and Study Parameters 
Table 1. 
Schedule of Assessments 
Study Procedure 
Visit 1
1 
Follow-up 
(phone call) 
Notes 
Week 
(visit window) 
 
Week 1 
(± 3days) 
 
Informed Consent 
X 
 
A signed and dated informed consent must be obtained before conducting any study 
procedures. 
Inclusion/Exclusion 
X 
 
Demographics 
X 
 
Medical History 
X 
 
Physical Exam 
X 
 
Full physical exam will be performed. 
Clinical Labs 
X 
 
Biochemistry, hematology, and urinalysis laboratory assessments.  
Height/Weight/BMI 
X 
 
Vitals (HR & BP) 
X 
 
Vital signs will include systolic and diastolic blood pressure (BP), pulse rate, and body 
temperature. The pulse rate and BP determinations will be performed with the subject 
in a sitting position after a 5-minute rest. Blood pressure will be measured in triplicate 
and the average will be recorded.   
Timed function tests 
X 
 
Tests include time to climb 4 stairs, time to descend 4 stairs, time to rise from supine, 
and time to run/walk 10 meters. 
PK blood sampling 
X 
 
PK samples will be drawn pre-morning dose and 2 hours post-morning dose. Ataluren 
plasma concentrations will be analyzed in a population PK model for the estimation of 
key pharmacokinetic parameters including Cl/F, V/F, AUC0-24, Cmax, and Cave. 
Muscle biopsy 
X 
 
Muscle biopsy will be taken from the 
 and 
. If the 
 
muscle is considered by the investigator to be too small for a muscle biopsy sample, 
the 
 muscle may be used. 
AE/SAE Monitoring 
X 
X 
Concomitant 
medications 
X 
 
Treatments, including ataluren, taken one month prior to enrollment and during Visit 1 
will be recorded. 
Abbreviations:  AE, adverse event; AUC0-24, area under the concentration curve from time 0 to 24 hours; BMI, body mass index; BP, blood pressure; 
Cl/F, clearance; Cave, average plasma concentration; Cmax, maximal plasma concentration; HR, heart rate; PK, pharmacokinetics; SAE, serious adverse 
event; V/F, volume of distribution 
1 
Subjects may have to return to the clinic for up to 3 days for completion of assessments and muscle biopsy. 
 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 23 of 39 
7.2 
Safety Assessments and Other Assessments 
Subjects will be monitored closely for AEs and laboratory abnormalities during the study. 
For AEs and laboratory abnormalities, the investigator should use his/her judgment in 
determining whether the event or abnormality is clinically significant, whether diagnostic 
evaluation is warranted, and whether potential interruption of study drug therapy is 
appropriate. In general, life-threatening (Grade 4) or severe (Grade 3) AEs or laboratory 
abnormalities should be considered clinically significant, although recurrent or persistent 
moderate events (Grade 2) may also be considered clinically significant in certain 
circumstances. Reference should be made to the Common Terminology Criteria for Adverse 
Events (CTCAE) Version 5.0 for grading the severity of adverse events and laboratory 
abnormalities. 
While specific monitoring, diagnostic testing, and supportive care measures must be 
instituted based on the clinical judgment of the investigator, investigators should contact the 
PTC Therapeutics medical monitor to obtain guidance and to ascertain whether similar 
events are being seen at other sites. The PTC Therapeutics medical monitor should be 
notified of any AE or laboratory abnormality that leads to dose interruption and should be 
apprised of ancillary laboratory or other diagnostic findings and the evolving data from any 
work-up of the initial abnormality. The PTC Therapeutics medical monitor may suggest 
review of the case with gastroenterology, endocrinology, nephrology consultants or with 
other experts (either at the site or retained by PTC Therapeutics). 
7.3 
Adverse Events and Serious Adverse Events 
7.3.1 
Definition of adverse events 
An adverse event (AE) is any untoward medical occurrence associated with the use of a drug 
in humans, whether or not it is considered related to the drug. An AE can therefore be any 
unfavorable and unintended sign (including an abnormal laboratory finding), symptom, or 
disease in a study subject who is enrolled in this study. 
For this protocol, untoward medical occurrences that should be reported as AEs include the 
following: 
● 
All AEs relating to the muscle biopsy 
● 
Apparently unrelated illnesses, including worsening of a preexisting illness 
● 
Injury or accidents. Note that if a medical condition is known to have caused the 
injury or accident (a fall secondary to dizziness), the medical condition (dizziness) 
and the accident (fall) should be reported as 2 separate AEs. The outcome of the 
accident (hip fracture secondary to the fall) should be recorded in source 
documents. 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 24 of 39 
● 
Abnormalities in physiological testing or physical examination findings that 
require clinical intervention or further investigation (beyond ordering a repeat 
[confirmatory] test) 
● 
Laboratory that require clinical intervention or further investigation (beyond 
ordering a repeat [confirmatory] test) unless they are associated with an already 
reported clinical event. Laboratory abnormalities associated with a clinical event 
should be captured in the source documents. Laboratory abnormalities not 
requiring clinical intervention or further investigation will be captured as part of 
overall laboratory monitoring and should not be reported as AEs. 
● 
A preexisting condition (eg, allergic rhinitis) must be noted on the appropriate 
eCRF for Visit 1; however, it should not be reported as an AE unless the condition 
worsens or episodes increase in frequency during the AE reporting period. 
Diagnostic and therapeutic noninvasive and invasive procedures, such as surgery, 
should not be reported as AEs. However, the medical condition for which the 
procedure was performed should be reported if it meets the definition of an AE. 
For example, an acute appendicitis that occurs during the AE reporting period 
should be reported as the AE and the resulting appendectomy should be recorded 
in the source documents and eCRF. If a surgical procedure was planned prior to 
entry into the study, and the surgery is not performed because of a worsening of a 
baseline condition, this should not be reported as an AE. Note that, as described in 
Section 7.3.2 any hospitalization occurring as the consequence of an AE during 
the study period should be reported as a serious adverse event (SAE). 
Each AE is to be classified as serious or non-serious by the investigator using medical and 
scientific judgment. 
7.3.2 
Definition of serious adverse events  
An SAE is an untoward medical occurrence or effect associated with the use of a study drug 
at any dose, regardless of whether it is considered to be related to the study drug, which 
results in one of the following: 
● 
Results in death. This includes all deaths that occurred within 30 days of Visit 1, 
including deaths due to disease progression. Any death occurring later than 30 
days following Visit 1need not be reported as an SAE unless it is a result of an 
event that started within the period covered by the on-study definition. The 
reported AE should be the event that caused the death. In addition, any AE 
resulting in death that occurs subsequent to the AE reporting period and that the 
investigator assesses as possibly related to the muscle biopsy procedure should 
also be reported as serious. 
● 
Is life-threatening. This refers to an event in which the subject was at risk of death 
at the time of the event. It does not include an event that, had it occurred in a more 
severe form, hypothetically might have caused death. 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 25 of 39 
● 
Requires hospitalization or prolongation of existing hospitalization (excluding 
hospitalizations for administration of the study drug, procedures required by the 
study protocol, or treatment-related diagnostic procedures; other planned 
hospitalizations; or hospitalizations related only to progression of disease). 
Treatments in the emergency room for procedures such as hydration that do not 
require admitting the subject to the hospital and observational durations in the 
emergency room for less than 24 hours do not fall into this category. 
● 
Results in persistent or significant disability or incapacity or substantial disruption 
of the ability to conduct normal life functions, not related to cancer. 
● 
Any other medically important event that the investigator or the sponsor judges to 
be serious or which is defined as serious by the regulatory agency in the local 
country. These are AEs that might not be immediately life-threatening or result in 
death or hospitalization but might jeopardize the subject or might require 
intervention to prevent one of the other outcomes listed above. Medical judgment 
should be exercised in deciding whether an AE is serious based on above 
definition. Examples of such events are intensive treatment in an emergency room 
or at home for allergic bronchospasm, blood dyscrasias or convulsions that do not 
result in hospitalization, or development of drug dependency or drug abuse. 
7.3.3 
Eliciting adverse event information 
The investigator is to report all directly observed AEs and all AEs spontaneously reported by 
the study subject/parent(s)/legal guardian/legally acceptable representative. In addition, each 
study subject/parent(s)/legal guardian/legally acceptable representative will be questioned 
about AEs at each scheduled clinic visit after study drug administration or during any 
telephone contact with the subject/parent(s)/legal guardian/legally acceptable representative. 
The type of question asked should be open-ended, for example, “How have you been 
feeling?” or a similar type of query. 
7.3.4 
Recording Non‑serious AEs and SAEs 
All AEs (both serious and non-serious) which are not related to the muscle biopsy that occur 
in subjects during the AE reporting period must be recorded in the eCRF of the ataluren 
nmDMD trial in which the subject was recruited from. Those events considered related to the 
muscle biopsy should be reported to the Study 046. In addition, any known untoward event 
that occurs subsequent to the AE reporting period that the investigator assesses as related to 
the muscle biopsy procedure should also be recorded as an AE in Study 046. 
All AEs are to be recorded in the source documents and on the eCRF using concise medical 
terminology; whenever possible, terms contained in the Medical Dictionary for Regulatory 
Activities (MedDRA) should be employed. In addition, the following information should be 
recorded: 
● 
Indication of whether the event is serious or non-serious (see Section 7.3.2) 
● 
Relationship to study procedure (see Section 7.3.5) 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 26 of 39 
● 
Severity of the event (see Section 7.3.6) 
● 
Onset date 
● 
Resolution date, or date of death 
● 
Action taken 
● 
Outcome of the event 
Classification of the event as serious or non-serious determines the reporting procedures to 
be followed. 
7.3.5 
Describing adverse event relationship to muscle biopsy procedure 
The investigator should provide an assessment of the relationship of the AE to the study 
muscle biopsy, ie, whether there is a reasonable possibility that the muscle biopsy procedure 
caused the AE, using the considerations outlined in Table 2. 
Table 2. 
Relationship of Study Muscle Biopsy Procedure to Adverse Event  
 
Description  
Probable  
A clinical event in which a relationship to the study muscle biopsy procedure seems 
probable because of such factors as consistency with known effects of the muscle 
biopsy procedure, a clear temporal association with the muscle biopsy procedure; or 
lack of alternative explanations for the event.  
Possible  
A clinical event occurring coincident with the muscle biopsy procedure and which may 
or may not be explained by concurrent disease or concomitant drugs or chemicals.  
Unlikely  
A clinical event with a temporal relationship to the study muscle biopsy procedure that 
does not preclude causality but for which there is a clear alternate cause that is more 
likely to have caused the adverse event than the procedure. Such alternatives include 
a concomitantly administered drug, the subject’s disease state, other medical 
conditions, or environmental factors.  
Unrelated  A clinical event, for which a relationship to the study muscle biopsy procedure seems 
improbable because of factors such as inconsistency with known effects of the muscle 
biopsy procedure, lack of a temporal association with the muscle biopsy procedure, 
and/or presence of alternative explanations for the event. Alternative explanations 
might include a known relationship of the adverse event to a concomitant drug, 
medical history of a similar event, the subject’s disease state, other medical conditions, 
or environmental factors.  
7.3.6 
Grading of severity of adverse event related to muscle biopsy procedure 
The severity of AE will be graded using the CTCAE Version 5.0. For each episode, the 
highest severity grade attained should be reported. 
If a CTCAE criterion does not exist, the investigator should use the grade or adjectives: 
Grade 1 (mild), Grade 2 (moderate), Grade 3 (severe), Grade 4 (life-threatening), or Grade 5 
(fatal) to describe the maximum intensity of the AE. For purposes of consistency with the 
CTCAE, these severity grades are defined in Table 3. 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 27 of 39 
Table 3. 
Grading of Adverse Event Severity Grade 
 
Adjective  
Description  
Grade 1  
Mild  
Sign or symptom is present, but it is easily tolerated, is not 
expected to have a clinically significant effect on the subject’s 
overall health and well-being, does not interfere with the subject’s 
usual function, and is not likely to require medical attention  
Grade 2  
Moderate  
Sign or symptom causes interference with usual activity or affects 
clinical status, and may require medical intervention  
Grade 3  
Severe  
Sign or symptom is incapacitating or significantly affects clinical 
status and likely requires medical intervention and/or close follow-up  
Grade 4  
Life-threatening  
Sign or symptom results in a potential threat to life  
Grade 5  
Fatal  
Sign or symptom results in death  
7.3.7 
Adverse Event Reporting 
Investigator site reporting requirements for AEs are summarized in Table 4 and Table 5. 
Table 4. 
Investigator Site Requirements for Reporting Adverse Events Not Related to 
Muscle Biopsy 
Event 
Recorded on the 
Parent Study eCRF 
Reported on the SAE Report Form to PTC 
Pharmacovigilance Within 24 Hours of Awareness 
Serious AE 
All  
All  
Non-Serious AE 
All  
None  
Abbreviations: AE, adverse event; eCRF, electronic case report form; SAE, serious adverse event 
Table 5. 
Investigator Site Requirements for Reporting Muscle Biopsy-Related Adverse 
Events 
Event 
Recorded on the 
Study 046 eCRF  
Reported on the SAE Report Form to PTC 
Pharmacovigilance Within 24 Hours of Awareness  
Serious AE 
All  
All  
Non-Serious AE 
All  
None  
Abbreviations: AE, adverse event; eCRF, electronic case report form; SAE, serious adverse event 
All AEs should be followed up by the investigator until they are resolved, or the investigator 
assesses them as chronic or stable. The investigator should consider protocol guidelines and 
use his/her discretion in ordering additional tests as necessary to monitor the resolution of 
such events. In the event of additional investigations, the PTC Therapeutics 
Pharmacovigilance Department or designee should be informed via e-mail or fax. A subject 
withdrawn from the study because of an AE must be followed by the investigator until 
clinical recovery is complete and laboratory results have returned to normal, or until 
progression has been stabilized. Follow up may need to continue after the subject has 
discontinued from the study, and additional investigations may be requested by the PTC 
Therapeutics medical monitoring team. 
The first day of AE reporting will coincide with the date of signing of Informed Consent and 
including a minimum of 30 calendar days after Visit 1. 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 28 of 39 
7.3.8 
Serious adverse event reporting 
All SAEs should be reported via the SAE report form to PTC Therapeutics within 24 hours 
of becoming aware of the event(s). In addition, the AE portion of the eCRF must also be 
completed. 
The SAE report form should be signed by the investigator; however, if the investigator is 
unable to sign at the time of the event or within 24 hours, the form should be signed by the 
clinical staff member reporting the SAE (eg, the study coordinator). The SAE report form 
must be faxed or e-mailed to the PTC Therapeutics Pharmacovigilance Department or 
designee and to the site IRB/EC (if required by local regulations) within 24 hours. 
Follow-up information to the SAE should be clearly documented as “follow-up” in the SAE 
report form and must also be faxed or e-mailed to the same party. All follow-up SAE report 
forms for the event must be signed by the investigator. Any source documents (eg, progress 
notes, nurses’ notes, laboratory and diagnostic test results, discharge summaries) provided to 
the sponsor should be redacted so that the subject’s name, address, and other personal 
identity information are obscured. Only the subject’s study number and initials are to be 
provided (in regions where the provision of such information is permitted). The information 
in the AE portion of the eCRF and the SAE report form(s) must match or be reconciled. 
Where the same data are collected, the forms must be completed in a consistent manner. For 
example, the same AE term should be used on both forms. 
In the rare event that the investigator does not become aware of the occurrence of an SAE 
immediately (for example, if a subject initially seeks treatment elsewhere), the investigator is 
to report the event within 24 hours after learning of it and to document his/her first awareness 
of the AE. 
The PTC Therapeutics Pharmacovigilance Department contact information for reporting 
SAEs is provided below. This information is also provided in the Study Manual and in the 
SAE report form. 
PTC Therapeutics Safety Department 
Attention: Pharmacovigilance 
E-mail:
Facsimile:
7.3.9 
Reporting Pregnancy 
Subjects enrolled in this trial will have not reached sexual maturity; therefore, there are 
no requirements for pregnancy avoidance for study participants. 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 29 of 39 
7.3.10 
PTC Therapeutics Adverse Event Reporting Requirement 
As the sponsor of the study, PTC Therapeutics is responsible for reporting certain safety 
information, particularly SAEs and subject deaths related to participation in the study, to 
each investigator in an expedited manner. If notification of an AE requiring expedited 
reporting to investigators is received, PTC Therapeutics or its designated representative will 
contact each investigational site participating in this study by e-mail, fax, and/or overnight 
mail such that the investigator can promptly notify the site IRB/EC per their local 
requirements. The initial expedited safety report will be provided as required according to 
local regulations (eg, within 15 days) after the earliest date PTC Therapeutics or an agent of 
PTC Therapeutics (eg, a site monitor) becomes aware of an AE. This awareness date is the 
date the regulatory reporting clock begins, and the date is considered Day 0. 
 
8 
STATISTICAL CONSIDERATIONS 
8.1 
Statistical Hypotheses 
Dystrophin levels will be summarized using descriptive statistics.  No statistical hypothesis 
testing will be performed. 
8.1.1 
Sample Size Determination 
No formal sample size calculation is performed for this study. 
8.2 
Population for Analyses 
8.2.1 
Intention-to-treat analysis set 
This analysis set will include all enrolled subjects with a valid assessment of dystrophin 
level, as measured by ECL. 
8.3 
Safety Analysis Set 
This analysis set will include all subjects who received at least one dose of ataluren and will 
be used for all summaries of safety. 
8.4 
Statistical Analyses 
8.4.1 
General approach 
In general, continuous variables will be summarized using descriptive statistics including 
mean, standard deviation, median, minimum, and maximum.  Categorical variables will be 
summarized using frequency count as number and percentage of subjects. 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 30 of 39 
8.4.2 
Analysis of primary efficacy endpoints 
The dystrophin level will be summarized by muscle biopsy locations using descriptive 
statistics based on ITT analysis set. 
8.4.3 
Analysis of secondary efficacy endpoints 
The secondary efficacy endpoints will be summarized in the same way as the primary 
efficacy endpoint. 
8.4.4 
Safety analyses 
Evaluations of safety will be performed using the safety analysis set. The incidence of AEs 
and SAEs will be tabulated using frequency count. 
8.4.5 
Planned interim analyses 
There are no planned interim analyses for this study. 
8.4.6 
Sub-group analyses 
Not Applicable 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 31 of 39 
9 
SUPPORTING DOCUMENTATION AND OPERATIONAL 
CONSIDERATIONS 
9.1 
Regulatory, Ethical, and Study Oversight Considerations 
9.1.1 
Informed consent process 
By signing the protocol, the investigator assures that informed consent/assent will be 
obtained from each parent/legal guardian prior to study entry and that the informed 
consent/assent will be obtained in accordance with current regulations. 
The investigator or sub-investigator will give each parent/legal guardian full and adequate 
verbal and written information regarding the objectives and procedures of the study and the 
possible risks involved. An informed consent/assent document will be provided to each 
parent/legal guardian in a language in which the parent/legal guardian is fluent. This 
information must be provided to the parent/legal guardian prior to undertaking any study 
related procedure. Adequate time should be provided for the parent/legal guardian to read the 
informed consent, to understand the risks and benefits of participating in the study, and to ask 
any questions that the parent/legal guardian may have about the study. The parent/legal 
guardian should be able to ask additional questions as and when needed during the conduct 
of the study. Where applicable, the subject will sign an age-appropriate assent form. 
Each parent/legal guardian will be given a copy of the signed consent/assent form. The 
original signed informed consent forms will be retained by the investigator with the study 
records. 
The written subject information must not be changed without prior approval by PTC 
Therapeutics and the IRB/EC. 
9.1.2 
Study discontinuation and closure 
PTC Therapeutics reserves the right to discontinue the study prior to inclusion of the 
intended number of subjects. The investigator, after consultation with the PTC Therapeutics 
medical monitor, reserves the right to discontinue the study at the investigator site for safety 
reasons at any time. 
After a decision to terminate the study, investigators must contact all subjects who are 
continuing their participation in the study and must do so within a time period set by PTC 
Therapeutics. As directed by PTC Therapeutics, all study materials must be collected, and all 
electronic data entry forms completed to the greatest extent possible. 
9.1.3 
Confidentiality and privacy 
Research records will be collected and stored in a manner that protects the confidentiality of 
subject information. The names and identities of all research subjects will be kept in strict 
confidence and will not appear on eCRFs, paper CRFs, or other records provided to or 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 32 of 39 
retained by PTC Therapeutics (or its authorized designee). The names and identities of the 
subjects need not be divulged; however, the records must nevertheless be inspected.  This 
will be accomplished by blanking out the subject’s name and replacing the name with the 
subject’s study identification number on any record provided to or retained by PTC 
Therapeutics. The informed consent form must include appropriate statements explaining 
these requirements. 
By signing this protocol, the investigator affirms to PTC Therapeutics that the investigator 
will maintain, in confidence, information furnished by PTC Therapeutics and will divulge 
such information to the IRB/IEC under an appropriate understanding of confidentiality with 
such board. 
9.1.4 
Future use of stored specimens and data 
As part of the current study, muscle tissue via biopsies will be collected to evaluate the effect 
of ataluren treatment on the expression of dystrophin protein as measured by ECL and 
immunohistochemistry. Sample processing will be performed by laboratories under the 
direction of the sponsor. Processing, analysis, and storage will be performed at a secure 
laboratory facility to protect the validity of the data and maintain subject privacy. 
The samples will be stored for 10-years. Only PTC Therapeutics and its representatives and 
agents will have access to muscle biopsy/extracts and they will not be shared with secondary 
researchers.  
These same samples will potentially be used to look at biochemical biomarkers that may be 
altered due to increased dystrophin levels and to generate new hypotheses (eg, identify 
factors involved in disease progression and identify possible new drug targets). No additional 
genetic testing will be performed or cell lines created. The results will be communicated to 
PTC Therapeutics.  
The subject/parent/caregiver will provide confirmation to allow any remaining specimens to 
be used for exploratory research work by PTC Therapeutics within the Informed Consent 
Form (ICF). The ICF will contain a separate authorization for the use of remaining tissue for 
exploratory research. Subjects/parents/caregivers will be told that participation in exploratory 
research is optional and that they can decline participation in this research. 
Subjects/parents/caregivers may withdraw their consent and request disposal of their stored 
samples at any time and for any reason during the storage period. 
No subject-identifying information (eg, initials, date of birth, government identifying 
number) will be associated with any of the biologic samples. All samples will be single 
coded and the sponsor will take steps to ensure that data are protected accordingly, and 
confidentiality is maintained to the extent possible.  
Given the research nature of the analysis, it will not be possible to return individual data to 
subjects. The results that may be generated are not currently anticipated to have clinical 
relevance to the patients or their family members. Therefore, these results will not be 
disclosed to the patients or their physicians. 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 33 of 39 
9.1.5 
Clinical monitoring 
In accordance with 21 Code of Federal Regulations Part 312.56 and/or relevant ICH 
International Council for Harmonisation) guidelines, PTC Therapeutics or a designee will 
periodically inspect all eCRFs, study documents, research facilities, and clinical laboratory 
facilities associated with this study at mutually convenient times, before, during, and after 
completion of the study. As required by applicable regulations (Responsibilities of Sponsors 
and Investigators), the monitoring visits provide PTC Therapeutics with the opportunity to 
evaluate the progress of the study; verify the accuracy and completeness of data in the 
eCRFs; ensure that all protocol requirements, relevant regulations, and investigator’s 
obligations are being fulfilled; and resolve any inconsistencies in the study records. This 
includes inspection of all documents and records required to be maintained by the 
Investigator, including but not limited to medical records (office, clinic, or hospital) for the 
subjects in this study. The names and identities of all research subjects will be kept in strict 
confidence and will not appear on eCRFs or other records provided to or retained by PTC 
Therapeutics. The investigator/institution guarantees direct access to source documents by 
PTC Therapeutics and appropriate regulatory authorities. 
It is important that the investigator and relevant institutional personnel are available during 
the monitoring visits and possible audits or inspections and that sufficient time is devoted to 
the process. 
9.1.6 
Quality assurance and quality control 
To ensure compliance with GCP (Good Clinical Practice) and all applicable regulatory 
requirements, PTC, PTC’s representatives, a regulatory authority or and Institutional Review 
board may conduct a quality assurance audit. Reasons for quality assurance audit may 
include but are not limited to: random selection, geographic proximity, suspected GCP 
violation, high enrolling site, recurring protocol deviations, etc. The purpose of a Sponsor 
audit or inspection is to systematically and independently examine all study-related activities 
and documents to determine whether these activities were conducted, and data were 
recorded, analyzed, and accurately reported according to the protocol, Good Clinical Practice 
guidelines of the International Council for Harmonisation, and any applicable regulatory 
requirements. The Investigator should contact the Sponsor immediately if contacted by a 
regulatory agency about an inspection. 
9.1.7 
Data handling and record keeping 
To enable evaluations and/or audits from regulatory authorities or PTC Therapeutics, the 
investigator agrees to keep accurate and complete records, including the identity of all 
participating subjects (sufficient information to link eCRFs and clinic records/source 
documents), all original signed informed consent forms, electronic copies (ie, CD-ROM, 
USB, etc.) or paper copies of the data that have been captured in the EDC for each subject 
(eCRFs), and detailed records of study drug disposition. All records and documents 
pertaining to the study will be maintained by the investigator until notification is received 
from PTC Therapeutics that the records no longer need to be retained. 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 34 of 39 
The investigator must obtain written permission from PTC Therapeutics before disposing of 
any records. The investigator will promptly notify PTC Therapeutics in the event of 
accidental loss or destruction of any study records. If the investigator relocates, retires, or for 
any reason withdraws from the study, the study records may be transferred to an acceptable 
designee, such as another investigator, another institution, or to PTC Therapeutics as 
applicable. 
9.1.8 
Protocol deviations 
A protocol deviation is defined as any intentional or unintentional change to, or 
noncompliance with, the approved protocol procedures or requirements. Deviations may 
result from the action or inaction of the subject, investigator, or site staff. Examples of 
deviations include, but are not limited to: 
● 
Failure to adhere to study exclusion and inclusion criteria 
● 
Use of medications that are specifically prohibited in the protocol 
● 
Missed or out-of-window visits 
● 
Failure to adhere to test requirements, including vital signs, laboratory tests, 
physical examinations, PK blood draws, medical history, etc. – either tests not 
done, incorrect tests done, or not done within the time frame specified in the 
protocol 
● 
Procedural deviations, failure to update the ICF when new risks become known, or 
failure to obtain IRB approvals for the protocol and ICF revisions 
Significant deviations are any deviations that impact subject eligibility (ie, protocol 
inclusion/exclusion violations), subject safety or a subject’s ability to continue in the clinical 
trial. 
At the outset of the study, a process for defining and handling protocol deviations will be 
established with the CRO. This will include determining which deviations will be designated 
significant; thus, requiring immediate notification to the PTC Therapeutics medical monitor 
and the sponsor. 
Prospective deviations (eg, protocol waivers) are prohibited per PTC policy. 
The investigator is responsible for seeing that any known protocol deviations are recorded 
handled as agreed. 
9.1.9 
Publication and data sharing policy 
The information developed during the conduct of this clinical study is considered 
confidential by PTC Therapeutics. This information may be disclosed as deemed necessary 
by PTC Therapeutics. 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 35 of 39 
PTC Therapeutics intends that the data from this study will be presented and published. The 
PTC Therapeutics staff under the direction of the PTC Therapeutics Chief Medical Officer or 
designee in collaboration with the investigator will be responsible for writing presentations 
and manuscripts for publication. Investigators will not be allowed to publish or present the 
data from this study without prior agreement with PTC Therapeutics. 
The investigator is obliged to provide the sponsor with complete test results and all data 
derived by the investigator from the study. During the study, only the sponsor may make 
study information available to other study Investigators or to regulatory agencies, except as 
required by law or regulation. Except as otherwise allowable in the clinical study site 
agreement, any public disclosure (including publicly accessible websites) related to the 
protocol or study results, other than study recruitment materials and/or advertisements, is the 
sole responsibility of the Sponsor. 
The sponsor may publish any data and information from the study (including data and 
information generated by the investigator) without the consent of the Investigator. 
Manuscript authorship for any peer-reviewed publication will appropriately reflect 
contributions to the production and review of the document. All publications and 
presentations must be prepared in accordance with this section and the Clinical Study Site 
Agreement. In the event of any discrepancy between the protocol and the Clinical Study Site 
Agreement, the Clinical Study Site Agreement will prevail. 
Data from all sites participating in the study will be pooled and analyzed by the sponsor or 
the sponsor’s designee. The first publication of the study results shall be made in conjunction 
with the results from other study sites as a multicenter publication. If a multicenter 
publication is not forthcoming within 24 months of completion of the study at all sites, the 
investigator may publish or present the results generated at his or her site. 
The investigator will provide the sponsor with a copy of any proposed publication or 
presentation for review and comment at least 60 days prior to such presentation or 
submission for publication. The sponsor shall inform the investigator in writing of any 
changes or deletions in such presentation or publication required to protect the sponsor’s 
confidential and proprietary technical information and to address inaccurate data or 
inappropriate interpretations in the context of any pooled multicenter results. At the 
expiration of such 60-day period, the investigator may proceed with the presentation or 
submission for publication unless the sponsor has notified the institution or the investigator 
in writing that such proposed publication or presentation discloses the sponsor’s confidential 
and proprietary technical information. Further, upon the request of the sponsor, the 
investigator will delay the publication or presentation for an additional 90 days to permit the 
sponsor to take necessary actions to protect its intellectual property interests. 
9.2 
Additional Considerations 
Not applicable 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 36 of 39 
9.3 
Protocol Amendment History 
 Original Protocol Issued:  12 Nov 2018 
Amendment 1 (20 Mar 2019) 
The overall reason for the amendment: The overall reason for the amendment was to 
ensure that sufficient muscle tissue for analysis was obtained from the biopsy procedure. 
Item 
No. 
Protocol 
Section 
Amendment/Update 
Reason/Rationale 
1 
Synopsis 
Changed from, “
 muscle biopsy samples will 
be collected from the 
 and 
 
.” to “A total of no more than 
approximately 450 mg of muscle tissue (up to 
 cores per muscle) will be obtained from the 
 
 and 
 
” 
To ensure 
sufficient muscle 
tissue for analysis 
2 
Synopsis 
Inclusion criteria #4 changed from, “Currently being 
treated with ataluren 10, 10, 20 mg/kg for 
≥9 months, with no gap in treatment of >1 month, in 
an ongoing PTC-sponsored nmDMD clinical trial  
prior to study entry.“ to “Currently being treated with 
ataluren 10, 10, 20 mg/kg for ≥9 months, with no 
gap in treatment of >1 month prior to study entry.” 
To allow IND 
subjects to be 
included 
3 
List of 
Abbreviations 
Changed from, “International Conferences on 
Harmonisation” to “International Council for 
Harmonisation” 
Correction 
4 
Section 3.1 
Changed from, ”Approximately, 6 ambulatory 
nmDMD male subjects who have been receiving 
ataluren, dosed daily 10 mg/kg in the morning, 
10 mg/kg at midday, and 20 mg/kg in the evening 
(10, 10, 20 mg/kg), for ≥9 months from ongoing 
PTC-sponsored nmDMD clinical trials.”to 
”Approximately, 6 ambulatory nmDMD male 
subjects who have been receiving ataluren, dosed 
daily 10 mg/kg in the morning, 10 mg/kg at midday, 
and 20 mg/kg in the evening (10, 10, 20 mg/kg), for 
≥9 months.” 
To allow IND 
subjects to be 
included 
5 
Section 3.1.1 
Changed from, “A total of  cores from each muscle 
will be obtained.” to “A total of no more than 
approximately 450 mg of muscle tissue (up to 
 cores per muscle) will be obtained.” 
To ensure 
sufficient muscle 
tissue for analysis 
6 
Section 3.2 
Changed from, “Three muscle biopsy samples will 
be collected from the 
 and 
 
”. to “A total of no more than 
approximately 450 mg of muscle tissue (up to 
 cores per muscle) will be obtained from the 
 
 and 
.” 
To ensure 
sufficient muscle 
tissue for analysis 
7 
Section 4.2 
Inclusion criteria #4 changed from, “Currently being 
treated with ataluren 10, 10, 20 mg/kg for ≥9 
months, with no gap in treatment of >1 month, in an 
ongoing PTC-sponsored nmDMD clinical trial  prior 
to study entry.“ to “Currently being treated with 
ataluren 10, 10, 20 mg/kg for ≥9 months, with no 
gap in treatment of >1 month prior to study entry.“ 
To allow IND 
subjects to be 
included 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 37 of 39 
Item 
No. 
Protocol 
Section 
Amendment/Update 
Reason/Rationale 
8 
Section 5.1 
Changed from, “Subjects will be recruited from 
ongoing PTC sponsored nmDMD clinical trials who 
currently have been receiving ataluren therapy for 
≥9 months.” to “Subjects who currently have been 
receiving ataluren therapy for ≥9 months will be 
recruited.” 
To allow IND 
subjects to be 
included 
9 
Section 7.3.1 
Changed from, 
• “All AEs during the study visit and follow-up, 
including AEs related to the muscle biopsy” 
to 
• “All AEs relating to the muscle biopsy” 
Correction 
10 
Section 7.3.3 
Section deleted 
Reference Safety 
Information (RSI) 
in the ataluren IB 
does not apply to 
muscle biopsies 
11 
Section 8.4.2 
Changed from, “The dystrophin level will be 
summarized by muscle biopsy locations 
 
 using descriptive statistics 
based on ITT analysis set.” to “The dystrophin level 
will be summarized by muscle biopsy locations 
using descriptive statistics based on ITT analysis 
set.” 
To allow biopsy 
from the 
 
 
muscle if 
 
muscle is 
considered by the 
investigator to be 
too small for 
muscle biopsy 
sampling. 
12 
Section 9.1.5 
Changed from, “International Conferences on 
Harmonisation” to International Council for 
Harmonisation” 
Correction 
13 
Section 9.1.6 
Changed from, “International Council on 
Harmonisation” to “International Council for 
Harmonisation” 
Correction 
14 
Synopsis and 
Protocol 
Document date/version and TOC were updated. 
Update 
 
 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 38 of 39 
10 
REFERENCES 
Aartsma-Rus, A, Ginjaar, IB and Bushby, K. The importance of genetic diagnosis for 
duchenne muscular dystrophy. J Med Genet 2016;53(3):145-151. 
Aartsma-Rus, A, Van Deutekom, JC, Fokkema, IF, Van Ommen, GJ and Den Dunnen, JT. 
Entries in the leiden duchenne muscular dystrophy mutation database: An overview of 
mutation types and paradoxical cases that confirm the reading-frame rule. Muscle Nerve 
2006;34(2):135-144. 
Anthony, K, Arechavala-Gomeza, V, Ricotti, V, Torelli, S, Feng, L, Janghra, N, et al. 
Biochemical characterization of patients with in-frame or out-of-frame dmd deletions 
pertinent to exon 44 or 45 skipping. JAMA Neurol 2014;71(1):32-40. 
Bladen, CL, Salgado, D, Monges, S, Foncuberta, ME, Kekou, K, Kosma, K, et al. The treat-
nmd dmd global database: Analysis of more than 7,000 duchenne muscular dystrophy 
mutations. Hum Mutat 2015;36(4):395-402. 
Brooke, MH, Fenichel, GM, Griggs, RC, Mendell, JR, Moxley, R, Florence, J, et al. 
Duchenne muscular dystrophy: Patterns of clinical progression and effects of supportive 
therapy. Neurology 1989;39(4):475-481. 
Bushby, K, Finkel, R, Birnkrant, DJ, Case, LE, Clemens, PR, Cripe, L, et al. Diagnosis and 
management of duchenne muscular dystrophy, part 1: Diagnosis, and pharmacological and 
psychosocial management. Lancet Neurol 2010a;9(1):77-93. 
Bushby, K, Finkel, R, Birnkrant, DJ, Case, LE, Clemens, PR, Cripe, L, et al. Diagnosis and 
management of duchenne muscular dystrophy, part 2: Implementation of multidisciplinary 
care. Lancet Neurol 2010b;9(2):177-189. 
Connolly, AM, Malkus, EC, Mendell, JR, Flanigan, KM, Miller, JP, Schierbecker, JR, et al. 
Outcome reliability in non-ambulatory boys/men with duchenne muscular dystrophy. Muscle 
Nerve 2015;51(4):522-532. 
Finkel, RS, Flanigan, KM, Wong, B, Bonnemann, C, Sampson, J, Sweeney, HL, et al. Phase 
2a study of ataluren-mediated dystrophin production in patients with nonsense mutation 
duchenne muscular dystrophy. PLoS One 2013;8(12):e81302. 
Gallo, A, Abraham, A, Katzberg, HD, Ilaalagan, S, Bril, V and Breiner, A. Muscle biopsy 
technical safety and quality using a self-contained, vacuum-assisted muscle biopsy technique. 
Neuromuscul Disord 2018;28(5):450-453. 
Humbertclaude, V, Hamroun, D, Bezzou, K, Berard, C, Boespflug-Tanguy, O, Bommelaer, 
C, et al. Motor and respiratory heterogeneity in duchenne patients: Implication for clinical 
trials. Eur J Paediatr Neurol 2012;16(2):149-160. 
Mah, JK. Current and emerging treatment strategies for duchenne muscular dystrophy. 
Neuropsychiatr Dis Treat 2016;12:1795-1807. 


PTC124-GD-046-DMD 
Clinical Protocol 
V2.0 
PTC Therapeutics, Inc. - Confidential 
Page 39 of 39 
Muntoni, F, Torelli, S and Ferlini, A. Dystrophin and mutations: One gene, several proteins, 
multiple phenotypes. Lancet Neurol 2003;2(12):731-740. 
Petrof, BJ, Shrager, JB, Stedman, HH, Kelly, AM and Sweeney, HL. Dystrophin protects the 
sarcolemma from stresses developed during muscle contraction. Proc Natl Acad Sci U S A 
1993;90(8):3710-3714. 
Phillips, MF, Quinlivan, RC, Edwards, RH and Calverley, PM. Changes in spirometry over 
time as a prognostic marker in patients with duchenne muscular dystrophy. Am J Respir Crit 
Care Med 2001;164(12):2191-2194. 
Rae, MG and O'Malley, D. Cognitive dysfunction in duchenne muscular dystrophy: A 
possible role for neuromodulatory immune molecules. J Neurophysiol 2016;116(3):1304-
1315. 
Welch, EM, Barton, ER, Zhuo, J, Tomizawa, Y, Friesen, WJ, Trifillis, P, et al. Ptc124 targets 
genetic disorders caused by nonsense mutations. Nature 2007;447(7140):87-91. 
 

SAP_001.pdf: 
V1.0 
PTC Therapeutics, Inc. - Confidential 
Page 1 of 10 
STATISTICAL ANALYSIS PLAN 
 PHASE 2, NON-INTERVENTIONAL, CLINICAL STUDY TO ASSESS 
DYSTROPHIN LEVELS IN SUBJECTS WITH NONSENSE MUTATION 
DUCHENNE MUSCULAR DYSTROPHY WHO HAVE BEEN 
TREATED WITH ATALUREN FOR ≥9 MONTHS 
PTC124-GD-046-DMD 
VERSION 1.0 
12 FEBRUARY 2020 
PTC THERAPEUTICS, INC. 
100 CORPORATE COURT 
SOUTH PLAINFIELD, NJ 07080 USA 
Notice of Proprietary Information: This document contains confidential information owned by or in the 
possession/control of PTC Therapeutics, Inc.  Except as may otherwise be permitted in writing, by accepting or 
reviewing these materials, you agree that this information should not be disclosed to others (except where 
required by applicable law) and should not be used for unauthorized purposes.  In the event of an actual or 
suspected breach of this obligation, PTC Therapeutics, Inc. should be notified promptly.
NCT #NCT03796637


PTC124-GD-046-DMD 
Statistical Analysis Plan 
V1.0 
PTC Therapeutics, Inc. - Confidential 
Page 2 of 10 
APPROVAL SIGNATURES 
 
 
 
 
 
 
 
 
PTC Therapeutics, Inc. 
 
Date 
 
 
 
 
 
 
 
 
PTC Therapeutics, Inc. 
 
Date 
 
 
 
 
 
 
 
 
PTC Therapeutics, Inc. 
 
Date 
 


PTC124-GD-046-DMD 
Statistical Analysis Plan 
V1.0 
PTC Therapeutics, Inc. - Confidential 
Page 3 of 10 
TABLE OF CONTENTS 
APPROVAL SIGNATURES ..................................................................................................2 
TABLE OF CONTENTS ........................................................................................................3 
LIST OF ABBREVIATIONS AND DEFINITION OF TERMS .........................................5 
1 
INTRODUCTION .........................................................................................6 
2 
STUDY DESIGN ...........................................................................................6 
3 
STUDY OBJECTIVES AND ENDPOINTS ...............................................7 
3.1 
Study Objectives ................................................................................7 
3.1.1 
Primary Objective .................................................................7 
3.1.2 
Secondary Objective ..............................................................7 
3.1.3 
Pharmacokinetic ....................................................................7 
3.2 
Study Endpoints .................................................................................7 
3.2.1 
Primary Endpoint ..................................................................7 
3.2.2 
Secondary Endpoint ..............................................................7 
3.2.3 
Pharmacokinetic ....................................................................7 
3.3 
Sample Size .........................................................................................7 
4 
STUDY POPULATIONS ..............................................................................7 
4.1 
Screened Population ..........................................................................7 
4.2 
Enrolled Population ...........................................................................7 
4.3 
Intent to Treat (ITT) Population ......................................................7 
4.4 
Safety Population ...............................................................................8 
5 
GENERAL CONSIDERATIONS ................................................................8 
5.1 
Tables, Figures, and Listings ............................................................8 
5.2 
Missing Data Handling ......................................................................8 
6 
SUBJECT DATA ...........................................................................................8 
6.1 
Subject Disposition and Study Populations ....................................8 
6.2 
Treatment Exposure ..........................................................................8 
6.3 
Study Drug Compliance ....................................................................8 
6.4 
Demographic and Baseline Characteristics ....................................8 
6.5 
Concomitant Medications and Non-Drug Treatments ..................8 
6.6 
Medical History .................................................................................9 
7 
EFFICACY EVALUATION ........................................................................9 
7.1 
Muscle Biopsy ....................................................................................9 
7.1.1 
Electrochemiluminescence (ECL) ........................................9 
7.1.2 
Immunohistochemistry (IHC) ..............................................9 
7.2 
Timed Function Test .........................................................................9 
8 
SAFETY EVALUATION ...........................................................................10 
8.1 
Adverse Events .................................................................................10 
8.2 
Clinical Laboratory .........................................................................10 
8.3 
Vital Signs .........................................................................................10 
8.4 
Other Safety Assessments ...............................................................10 


PTC124-GD-046-DMD 
Statistical Analysis Plan 
V1.0 
PTC Therapeutics, Inc. - Confidential 
Page 4 of 10 
9 
PHARMACOKINETIC BLOOD SAMPLE .............................................10 
10 
CHANGES FROM THE PROTOCOL .....................................................10 
11 
BIBLIOGRAPHY ........................................................................................10 
 


PTC124-GD-046-DMD 
Statistical Analysis Plan 
V1.0 
PTC Therapeutics, Inc. - Confidential 
Page 5 of 10 
LIST OF ABBREVIATIONS AND DEFINITION OF TERMS 
Term 
Definition 
AE 
adverse event 
CRF 
Case Report Form 
DMD 
Duchenne muscular dystrophy 
ECL 
Electrochemiluminescence 
FDA 
Food and Drug Administration  
IHC 
immunohistochemistry 
ITT 
Intent to Treat 
MedDRA 
Medical Dictionary for Regulatory Activities 
nmDMD 
nonsense mutation Duchenne muscular dystrophy  
PK 
pharmacokinetics  
PT 
preferred term  
SAE 
serious adverse event 
SAP 
statistical analysis plan 
SOC 
system organ class  
TFT 
Timed Function Test 
WHODRUG 
World Health Organization Drug Dictionary 
 


PTC124-GD-046-DMD 
Statistical Analysis Plan 
V1.0 
PTC Therapeutics, Inc. - Confidential 
Page 6 of 10 
1 
INTRODUCTION 
Under the current standard of care, nonsense mutation Duchenne muscular dystrophy 
(nmDMD) remains a disease with devastating consequences and bleak prognosis.  
The progressive and irreversible effects of nmDMD underscore the importance of early 
intervention with treatments that have the potential to slow physical deterioration and delay 
the natural course of this fatal disease.  While treatment with corticosteroids target the 
inflammatory component of the disease, additional treatments are needed to address the loss 
of dystrophin, the underlying cause of the disease. 
The mechanism by which ataluren restores dystrophin has been established in comprehensive 
preclinical studies and supported in clinical evaluations.  Moreover, the clinical benefit of 
ataluren has been demonstrated in two large randomized controlled trials 
PTC124-GD-007-DMD (hereafter referred to as Study 007) and PTC124-GD-020-DMD 
(hereafter referred to as Study 020). 
The purpose of this statistical analysis plan (SAP) is to describe the procedures and the 
statistical methods that will be used in analyzing and reporting results for study 
PTC124-GD-046-DMD (hereafter referred to as Study 046).  This SAP is prepared based on 
the study protocol V2.0 (dated 08Mar2019). 
2 
STUDY DESIGN 
This is a single-site, non-interventional study designed to generate data on the effect of 
ataluren for producing dystrophin protein in nmDMD subjects.  This study will evaluate 
dystrophin levels from approximately 6 ambulatory nmDMD male subjects who have been 
receiving ataluren, dosed daily 10 mg/kg in the morning, 10 mg/kg at midday, and 20 mg/kg 
in the evening (10, 10, 20 mg/kg), for ≥9 months from ongoing PTC-sponsored nmDMD 
clinical trials.  
The study will have a single visit (Visit 1) which will occur that the site of 
 
.  At this visit, inclusion/exclusion 
criteria, demographics and medical history will be assessed. In addition, blood will be drawn 
for clinical labs and pharmacokinetics (PK) analysis pre-morning ataluren dose.  A second 
blood sample for PK will also be taken 2 hours after morning ataluren dose.  The muscle 
biopsy will also be performed at this visit. Adverse events will be monitored at Visit 1 and by 
a follow-up phone call approximately 1-week post Visit 1. 
Muscle biopsy of the 
 and 
 muscles will be performed using an 
established core muscle biopsy procedure.  If the 
 muscle is considered by the 
investigator to be too small for a muscle biopsy sample, the 
 muscle may 
be used.  A total of no more than approximately 450mg of muscle tissue (up to  cores per 
muscle) from each muscle will be obtained.  Vacuum needle muscle biopsy will be 
performed using local anesthesia or mild sedation, if needed.  All biopsies will be 
preserved/frozen using standard protocol for electrochemiluminescence (ECL) and 
immunohistochemistry (IHC). 


PTC124-GD-046-DMD 
Statistical Analysis Plan 
V1.0 
PTC Therapeutics, Inc. - Confidential 
Page 7 of 10 
3 
STUDY OBJECTIVES AND ENDPOINTS 
3.1 
Study Objectives 
3.1.1 
Primary Objective 
To assess the levels of dystrophin in ambulatory nmDMD subjects currently being treated 
with ataluren for ≥9 months using a quantitative electrochemiluminescence (ECL) assay. 
3.1.2 
Secondary Objective 
To assess dystrophin levels/intensity and protein localization by immunohistochemistry. 
3.1.3 
Pharmacokinetic 
To evaluate the steady state pharmacokinetics (PK) of ataluren. 
3.2 
Study Endpoints 
3.2.1 
Primary Endpoint 
Mean dystrophin levels as measured by ECL. 
3.2.2 
Secondary Endpoint 
Levels and localization of dystrophin protein levels as determined by immunohistochemistry. 
3.2.3 
Pharmacokinetic 
PK assessments using sparse sampling and population PK modeling in a separate report. 
The parameters include Cl/F, V/F, AUC0-24, Cmax, and Cave. 
3.3 
Sample Size 
No formal sample size calculation is performed for this study.  The sample size was 
determined empirically based on feasibility and subject availability. 
4 
STUDY POPULATIONS 
4.1 
Screened Population 
Screened population is defined as all patients who has signed informed consent. 
4.2 
Enrolled Population 
Enrolled population is defined as the subset of screen population who are not screen failures. 
4.3 
Intent to Treat (ITT) Population 
This analysis set will include all enrolled subjects with a valid assessment of dystrophin 
level, as measured by ECL. 


PTC124-GD-046-DMD 
Statistical Analysis Plan 
V1.0 
PTC Therapeutics, Inc. - Confidential 
Page 8 of 10 
4.4 
Safety Population 
This analysis set will include all subjects who received at least one dose of ataluren and will 
be used for all summaries of safety. 
5 
GENERAL CONSIDERATIONS 
5.1 
Tables, Figures, and Listings 
In general, continuous variables will be summarized using descriptive statistics including n 
(number of subjects), mean, standard deviation, median, minimum, and maximum.  
Categorical variables will be summarized using frequency count as number and percentage of 
subjects. 
Listings will be created for selected electronic case report form (CRF) domain sorted by 
subject and associated dates. 
5.2 
Missing Data Handling  
Observed data will be used for all analyses.  Missing data will not be imputed. 
6 
SUBJECT DATA 
6.1 
Subject Disposition and Study Populations 
The number of subjects in each analysis population will be summarized using frequency 
count. 
The number of subjects who completed or discontinued from the study and the reasons of 
discontinuation will be summarized based on the ITT populations. 
6.2 
Treatment Exposure 
Since this is a non-interventional study, treatment exposure summary is not applicable to this 
study.  The use of ataluren will be presented in the subject listings only. 
6.3 
Study Drug Compliance 
Since this is a non-interventional study, study drug compliance is not applicable to this study. 
6.4 
Demographic and Baseline Characteristics 
Demographic and baseline characteristics including age at biopsy date, ethnicity group, race, 
weight, height, and BMI at biopsy date will be summarized based on the ITT populations. 
6.5 
Concomitant Medications and Non-Drug Treatments 
Concomitant Medications  will be coded using the World Health Organization Drug 
Dictionary (WHODRUG), version March 1, 2019.  Non-drug treatments will be coded using 
Medical Dictionary for Regulatory Activities (MedDRA) version 22.1.  Prior medications 
and non-drug treatments are defined as those taken any time prior to biopsy date.  
Concomitant medications and non-drug treatments are defined as those taken any time on or 
after biopsy date. 


PTC124-GD-046-DMD 
Statistical Analysis Plan 
V1.0 
PTC Therapeutics, Inc. - Confidential 
Page 9 of 10 
The use of prior and concomitant medications and non-drug treatments will be presented in 
the subject listings only. 
6.6 
Medical History 
Medical history will be coded using MedDRA, version 22.1.  Medical history will be listed in 
the listings only. 
7 
EFFICACY EVALUATION 
All efficacy summaries will be generated based on the ITT population.  In addition to actual 
reported values, in case any measured dystrophin levels are below the lower limit of 
quantification (LLOQ), the levels will be set at 0.5*LLOQ for the statistical analysis. 
7.1 
Muscle Biopsy 
Muscle biopsies will be taken from several locations.  Multiple cores of muscles will be 
taken from each location and multiple samples will be prepared from each muscle cores.  
Dystrophin levels will be measured from each sample by both ECL and IHC.  The dystrophin 
levels measured by ECL will be considered as the primary efficacy endpoint.  The dystrophin 
levels measured by IHC will be considered as the secondary efficacy endpoint. 
7.1.1 
Electrochemiluminescence (ECL) 
Dystrophin levels will be summarized by muscle locations and across muscle locations.  
Within each muscle location, the best, the average and the median of dystrophin levels from 
each muscle cores for each subject will be summarized using descriptive statistics.  The same 
summary statistics will be presented across muscle locations.  In addition to dystrophin 
levels, the percent normal (defined as dystrophin level normalized to healthy subjects) 
measured by ECL will also be summarized using descriptive statistics. 
7.1.2 
Immunohistochemistry (IHC) 
The dystrophin levels measured by IHC will be summarized using descriptive statistics in the 
similar fashion as for ECL.  In addition to dystrophin levels (the mean staining intensity), the 
percentage of positive fibers will also be summarized using descriptive statistics. Within each 
muscle location, the best, the average and the median of dystrophin levels (the mean staining 
intensity) and the percentage of positive fibers from each muscle cores for each subject will 
be summarized using descriptive statistics.  The same summary statistics will be presented 
across muscle locations. 
7.2 
Timed Function Test 
Timed function tests (TFT) include the time taken to run/walk 10 meters, climb 4 stairs, 
descend 4 stairs, and stand from supine.  Since subjects only have one assessment in timed 
function test results.  The TFT assessments will be presented in the subject listings only. 


PTC124-GD-046-DMD 
Statistical Analysis Plan 
V1.0 
PTC Therapeutics, Inc. - Confidential 
Page 10 of 10 
8 
SAFETY EVALUATION 
All safety summaries will be generated based on the safety population. 
8.1 
Adverse Events  
Adverse events (AE) will be coded using the MedDRA version 22.1.  A treatment-emergent 
adverse event (TEAE) is defined as an adverse event that occurs on or after the biopsy date.  
Any AE with and end date prior to the biopsy date will not be considered as an TEAE. 
The following summaries will be provided for TEAEs: 
1. 
TEAE overview 
2. 
TEAEs by system organ class (SOC) and preferred term (PT) 
If a subject has multiple events under any given SOC and PT, the subject will be counted 
only once under that SOC and PT.  If a subject has the same AE on multiple occasions, the 
highest severity reported on the CRFs (“life-threatening”, “severe”, “moderate”, “mild”, 
“unknown”, and “not reported”) will be presented in the summaries. 
In addition, subjects experienced serious adverse events (SAE) will be presented in the 
subject listings only. 
8.2 
Clinical Laboratory 
Hematological, biochemistry, and urine evaluations (normal, abnormal - not clinically 
significant, and abnormal – clinically significant) collected at visit 1 will be presented in the 
subject listings only. 
8.3 
Vital Signs 
Vital signs including systolic blood pressure, diastolic blood pressure, pulse rate and oral 
temperature will be presented in the subject listings only. 
8.4 
Other Safety Assessments 
Other safety assessments including physician assessments will be presented in the subject 
listings only. 
9 
PHARMACOKINETIC BLOOD SAMPLE 
PK assessments using sparse sampling and population PK modeling will be presented in a 
separate report. Plasma concentration will be presented in the subject listings only. 
10 
CHANGES FROM THE PROTOCOL 
There are no major changes to the planned analyses from the protocol. 
11 
BIBLIOGRAPHY 
None