Clinical trial NCT02292537
Conditions: Spinal Muscular Atrophy
Keywords: Spinal Muscular Atrophy SMA SMN SMNRx ISIS-SMNRx ISIS-SMN Rx ISIS 396443 CHERISH IONIS-SMNRx IONIS-SMN Rx
Sponsor: Biogen
Start date: 2014-11-24; Completion date: 2017-02-20
Enrollment: 126 participants; Allocation: RANDOMIZED; Intervention model: PARALLEL

Brief summary:
The primary objective of this study is to examine the clinical efficacy of nusinersen (ISIS 396443) administered intrathecally to participants with later-onset Spinal Muscular Atrophy (SMA). The secondary objective is to examine the safety and tolerability of nusinersen administered intrathecally to participants with later-onset SMA.

Detailed description:
This study was conducted and the protocol was registered by Ionis Pharmaceuticals, Inc.

In August 2016, sponsorship of the trial was transferred to Biogen.

Arms: arm 1: Nusinersen 12 mg solution via intrathecal (IT) injection on Days 1, 29, 85 and 274. arm 2: Sham comparator on Days 1, 29, 85 and 274.
Interventions: intervention 1: Nusinersen intervention 2: Sham procedure
Intervention descriptions: intervention 1: Administered by intrathecal (IT) lumbar puncture (LP) injection intervention 2: Small needle prick on the lower back at the location where the IT injection is normally made

Protocol documents:
Prot_001.pdf: 
IONIS PHARMACEUTICALS, INC. 
ISIS 396443-CS4 
A Phase 3, Randomized, Double-blind, Sham-Procedure Controlled 
Study to Assess the Clinical Efficacy and Safety of ISIS 396443 
Administered Intrathecally in Patients with Later-onset Spinal 
Muscular Atrophy 
 
Protocol Amendment 2 - 30 June 2016 
EudraCT No: 2014-001947-18 
Sponsor: 
Ionis Pharmaceuticals, Inc. 
2855 Gazelle Court 
Carlsbad, CA  92010 


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ISIS 396443-CS4 
CONFIDENTIAL 
Amendment 2 
Protocol 
 
30 June 2016 
 
4 
Protocol Signature Page 
 
Protocol Number: 
ISIS 396443-CS4 
Protocol Title: 
A Phase 3, Randomized, Double-blind, Sham-Procedure Controlled Study 
to Assess the Clinical Efficacy and Safety of ISIS 396443 Administered 
Intrathecally in Patients with Later-onset Spinal Muscular Atrophy 
Amendment: 
Amendment 2 
Date: 
30 June 2016 
 
I hereby acknowledge that I have read and understand the attached clinical protocol, entitled “A 
Phase 3, Randomized, Double-blind, Sham-Procedure Controlled Study to Assess the Clinical 
Efficacy and Safety of ISIS 396443 Administered Intrathecally in Patients with Later-onset 
Spinal Muscular Atrophy”, dated 30 June 2016, and agree to conduct the study as described 
herein. 
I agree to comply with the International Conference on Harmonization Tripartite Guideline on 
Good Clinical Practice (E6). 
I agree to ensure that the confidential information contained in this document will not be used for 
any purpose other than the evaluation or conduct of the clinical investigation without the prior 
written consent of Ionis Pharmaceuticals, Inc.  
 
 
 
 
 
 
Investigator’s Signature 
 
 
 
Investigator’s Name (please print) 
 
Date (DD Month YYYY) 
 


ISIS 396443-CS4 
CONFIDENTIAL 
Amendment 2 
Protocol 
 
30 June 2016 
 
5 
TABLE OF CONTENTS 
Page 
PROTOCOL AMENDMENT.......................................................................................................9 
PROTOCOL SYNOPSIS ............................................................................................................10 
STUDY GLOSSARY ...................................................................................................................14 
1. 
OBJECTIVES .....................................................................................................................16 
1.1 
Primary Objective ........................................................................................................16 
1.2 
Secondary Objective ....................................................................................................16 
1.3 
Tertiary Objective ........................................................................................................16 
2. 
BACKGROUND AND RATIONALE ..............................................................................16 
2.1 
Spinal Muscular Atrophy .............................................................................................16 
2.2 
Therapeutic Rationale ..................................................................................................17 
2.3 
ISIS 396443 .................................................................................................................18 
2.3.1 
Mechanism of Action .........................................................................................18 
2.3.2 
Chemistry ...........................................................................................................18 
2.3.3 
Preclinical Experience ........................................................................................18 
2.3.4 
Clinical Experience ............................................................................................19 
2.4 
Rationale for Dose and Schedule of Administration ...................................................20 
3. 
EXPERIMENTAL PLAN ..................................................................................................21 
3.1 
Study Design ................................................................................................................21 
3.2 
Number of Study Centers.............................................................................................21 
3.3 
Number of Subjects......................................................................................................21 
3.4 
Overall Study Duration and Follow-up........................................................................21 
3.4.1 
Screening ............................................................................................................22 
3.4.2 
Treatment ...........................................................................................................22 
3.4.3 
Post-Treatment Follow-up ..................................................................................22 
3.5 
End-of-Study ................................................................................................................22 
3.6 
Safety Monitoring and Data Safety Monitoring Board................................................22 
4. 
SUBJECT ENROLLMENT ...............................................................................................23 
4.1 
Screening......................................................................................................................23 
4.2 
Randomization .............................................................................................................23 
4.3 
Replacement of Subjects ..............................................................................................23 
4.4 
Unblinding of Treatment Assignment .........................................................................23 
5. 
SUBJECT ELIGIBILITY ..................................................................................................24 
5.1 
Inclusion Criteria .........................................................................................................24 
5.2 
Exclusion Criteria ........................................................................................................25 
6. 
STUDY PROCEDURES ....................................................................................................26 
6.1 
Study Schedule.............................................................................................................26 
6.2 
Study Assessments .......................................................................................................26 


ISIS 396443-CS4 
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Protocol 
 
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6.2.1 
Laboratory Analytes ...........................................................................................26 
6.2.2 
Neurological Examinations ................................................................................26 
6.2.3 
Pharmacokinetics Specimen Collection .............................................................26 
6.2.4 
Hammersmith Functional Motor Scale - Expanded ...........................................26 
6.2.5 
Motor Milestones ...............................................................................................27 
6.2.6 
PedsQL™ (Generic Core Scales and Neuromuscular Module) .........................27 
6.2.7 
Upper Limb Module Test ...................................................................................27 
6.2.8 
Assessment of Caregiver Experience with Neuromuscular Disease  
(ACEND) ...........................................................................................................27 
6.2.9 
Safety Evaluations ..............................................................................................27 
6.3 
Contraception Requirements ........................................................................................28 
7. 
STUDY DRUG ....................................................................................................................28 
7.1 
Study Drug Description ...............................................................................................28 
7.2 
Packaging and Labeling ...............................................................................................28 
7.3 
Study Drug Accountability ..........................................................................................28 
8. 
TREATMENT OF SUBJECTS .........................................................................................29 
8.1 
Study Drug Administration ..........................................................................................29 
8.2 
Sham Procedure ...........................................................................................................29 
8.3 
Other Protocol-Required Drugs ...................................................................................30 
8.4 
Other Protocol-Required Procedures ...........................................................................30 
8.5 
Treatment Precautions .................................................................................................30 
8.6 
Safety Monitoring Rules ..............................................................................................30 
8.7 
Stopping Rules .............................................................................................................30 
8.8 
Adjustment of Dose and/or Treatment Schedule .........................................................30 
8.9 
Discontinuation of Study Treatment ............................................................................31 
8.10 
Withdrawal of Subjects from the Study .......................................................................31 
8.11 
Concomitant Therapy and Procedures .........................................................................32 
8.11.1 
Concomitant Therapy .........................................................................................32 
8.11.2 
Concomitant Procedures ....................................................................................32 
9. 
SERIOUS AND NON-SERIOUS ADVERSE EVENT REPORTING ..........................32 
9.1 
Sponsor Review of Safety Information........................................................................32 
9.2 
Regulatory Requirements.............................................................................................32 
9.3 
Definitions....................................................................................................................33 
9.3.1 
Adverse Event ....................................................................................................33 
9.3.2 
Adverse Reaction and Suspected Adverse Reaction ..........................................33 
9.3.3 
Serious Adverse Event (SAE) ............................................................................33 
9.4 
Monitoring and Recording Adverse Events .................................................................34 
9.4.1 
Serious Adverse Events ......................................................................................34 
9.4.2 
Non-Serious Adverse Events .............................................................................34 
9.4.3 
Evaluation of Adverse Events (Serious and Non-Serious) ................................34 


ISIS 396443-CS4 
CONFIDENTIAL 
Amendment 2 
Protocol 
 
30 June 2016 
 
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9.4.3.1 
Relationship to the Study Drug ............................................................34 
9.4.3.2 
Severity ................................................................................................35 
9.4.3.3 
Action Taken with Study Drug ............................................................35 
9.4.3.4 
Treatment Given for Adverse Event ....................................................35 
9.4.3.5 
Outcome of the Adverse Event ............................................................35 
9.5 
Procedures for Handling Special Situations ................................................................36 
9.5.1 
Abnormalities of Laboratory Tests.....................................................................36 
9.5.2 
Prescheduled or Elective Procedures or Routinely Scheduled Treatments ........36 
9.5.3 
Dosing Errors .....................................................................................................37 
9.5.4 
Contraception and Pregnancy .............................................................................37 
10. STATISTICAL CONSIDERATIONS ..............................................................................37 
10.1 
Study Endpoints, Subsets, and Covariates ...................................................................37 
10.1.1 
Primary Efficacy Endpoint .................................................................................37 
10.1.2 
Secondary Efficacy Endpoints ...........................................................................37 
10.1.3 
Tertiary Efficacy Endpoints ...............................................................................38 
10.1.4 
Safety/Tolerability Endpoints.............................................................................38 
10.1.5 
Pharmacokinetic Endpoints ................................................................................38 
10.1.6 
Immunogenicity Endpoint ..................................................................................38 
10.2 
Sample Size Considerations .........................................................................................38 
10.3 
Populations ...................................................................................................................38 
10.4 
Definition of Baseline ..................................................................................................39 
10.5 
Interim Analysis ...........................................................................................................39 
10.6 
Planned Methods of Analysis ......................................................................................40 
10.6.1 
Demographic and Baseline Characteristics ........................................................40 
10.6.2 
Safety and Tolerability Analysis ........................................................................40 
10.6.3 
Efficacy Analysis ...............................................................................................40 
10.6.4 
Pharmacokinetic Analysis ..................................................................................41 
11. INVESTIGATOR’S REGULATORY OBLIGATIONS .................................................41 
11.1 
Informed Consent/Assent.............................................................................................41 
11.2 
Ethical Conduct of the Study .......................................................................................42 
11.3 
Institutional Review Board/Institutional Ethics Committee/Research Ethics Board ..42 
11.4 
Subject Confidentiality ................................................................................................42 
12. ADMINISTRATIVE AND LEGAL OBLIGATIONS ....................................................43 
12.1 
Protocol Amendments ..................................................................................................43 
12.2 
Study Termination .......................................................................................................43 
12.3 
Study Documentation and Storage ...............................................................................43 
12.4 
Study Monitoring .........................................................................................................44 
12.5 
Language ......................................................................................................................44 
12.6 
Compensation for Injury ..............................................................................................44 


ISIS 396443-CS4 
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13. REFERENCES ....................................................................................................................45 
14. APPENDICES .....................................................................................................................47 
Appendix A 
Schedule of Procedures ..............................................................................48 
Appendix B 
Laboratory Analytes...................................................................................51 
Appendix C 
Pharmacokinetic Sampling Schedule .........................................................53 
 
 
TABLE OF TABLES 
Page 
Table 1 
Study Drug Characteristics ................................................................................ 28 
Table 2 
ISIS 396443 Dose, Concentration, and Injection Volume................................. 29 
 
 
TABLE OF FIGURES 
Page 
Figure 1 
ASO Therapeutic Approach for Treatment of SMA ......................................... 17 
 
 


ISIS 396443-CS4 
CONFIDENTIAL 
Amendment 2 
Protocol 
 
30 June 2016 
 
9 
PROTOCOL AMENDMENT 
 
Protocol Number: 
 
ISIS 396443-CS4 
Protocol Title: 
A Phase 3, Randomized, Double-blind, Sham-Procedure 
Controlled Study to Assess the Clinical Efficacy and Safety of 
ISIS 396443 Administered Intrathecally in Patients with Later-
onset Spinal Muscular Atrophy 
Amendment Number: 
2 
Amendment Date: 
 
30 June 2016 
 
Modifications to the Protocol ISIS 396443-CS4 include clarifications of the interim analysis 
plan, specifically, its timing, subset of the total study population to be included, endpoints and 
the analytical methods to be utilized, as well as the potential changes to the study conduct that 
may occur on the basis of a positive benefit-risk assessment of the results of the interim analysis.  
In addition, minor administrative changes and clarifications (not included in the list of changes 
below) have also been made to correct errors and/or to improve the overall clarity of the original 
protocol but these changes do not impact subject safety, exposure, or the overall study design. 
The following table provides a summary list of major changes to the protocol: 
Protocol Section 
Description of Change 
Rationale 
Protocol Synopsis/ 
Study Design, 
Section 3.1 
Study Design 
Section 3.5 
End-of-Study 
Clarification is made related to the disposition 
of study subjects under the scenario of a 
premature study termination based on the 
result of a positive interim analysis 
Clarification is necessary to allow 
subjects who complete all study 
assessments to rollover into the long-
term extension study under the scenario 
of the current study being terminated 
early based on the assessment of risk-
benefit of ISIS 396443 as a result of the 
interim analysis 
Section 2.3.4 
Clinical Experience  
Updated to reflect the up-to-date information 
provided in the Investigator Brochure, 
Version 6, January 2016. 
Self-evident 
Section 4.4 
Unblinding of 
Treatment 
Assignment 
Statement added related to unblinding of 
certain representatives from the study 
Sponsor during the conduct of interim 
analysis, as detailed further in the Statistical 
Analysis Plan 
In order to conduct and review the 
results of an interim analysis, certain 
sponsor personnel will need to be 
unblinded to treatment assignment.  
Those personnel will no longer be 
involved in the conduct of the study after 
they’ve been unblinded 
Section 8.8 
Adjustment of Dose 
and/or Treatment 
Schedule 
Clarification made on the adjustment of visit 
schedule for subjects who experience 
dose/sham procedure delays as a result of an 
illness 
Approval of the new visit schedule by the 
study Medical Monitor is required in 
advance in order to ensure that adequate 
time elapses between 2 adjacent doses 
of Study Drug 
Section 10.5 
Interim Analysis 
Specific description of the timing and 
methodology for the interim analysis has been 
added 
Self-evident 
Section 10.6.3 
Efficacy Analysis 
Specific description of the methodology for 
the efficacy endpoints has been added 
Self-evident 


ISIS 396443-CS4 
CONFIDENTIAL 
Amendment 2 
Protocol 
 
30 June 2016 
 
10 
PROTOCOL SYNOPSIS 
Protocol Title 
A Phase 3, Randomized, Double-Blind, Sham Procedure Controlled Study to Assess 
the Clinical Efficacy and Safety of ISIS 396443 Administered Intrathecally in Patients 
with Later-onset  Spinal Muscular Atrophy 
Study Phase 
3 
Indication 
Later-onset Spinal Muscular Atrophy (SMA) 
Objectives 
Primary Objective: 
To examine the efficacy of ISIS 396443 administered intrathecally to patients with later-
onset SMA. 
Secondary Objective: 
To examine the safety and tolerability of ISIS 396443 administered intrathecally to 
patients with later-onset SMA. 
Tertiary Objective: 
To examine the CSF and plasma pharmacokinetics of ISIS 396443 administered 
intrathecally to patients with later-onset SMA. 
Number of Subjects 
Approximately 117 subjects will be enrolled into this study 
Treatment Groups 
12 mg ISIS 396443 or sham procedure control group 
Study Design  
This randomized, double-blind, sham-procedure controlled study will test the clinical 
efficacy, safety, tolerability, and pharmacokinetics of intrathecal ISIS 396443 over 
15 months.  Approximately 117 subjects will be randomized in a 2:1 ratio 
(78 ISIS 396443: 39 control) to receive ISIS 396443 by intrathecal lumbar puncture (LP) 
injection or to a sham-procedure control.  A dose of 12 mg ISIS 396443 will be given at 
each of 4 times over the 15 months (i.e., on Study Days 1, 29, 85, and 274). 
Randomization will be stratified based on: 
1. Age (< 6 years vs. ≥ 6 years at Screening) 
After Informed consent/assent is obtained, subjects will undergo a screening evaluation 
no greater than 28 days prior to first dose administration at which time their eligibility for 
the study will be examined.  Subjects who meet the eligibility criteria will be admitted to 
the study center on Study Day 1, undergo pre-dose evaluations, and then receive either 
an LP injection of Study Drug (ISIS 396443) or a sham procedure.  Subjects will return 
to the study center on Days 29, 85 and 274 for follow-up evaluations and subsequent 
injections/sham procedures.  Following the injection/sham procedure on Day 1, subjects 
will remain at the study center for at least 24 hours post-procedure for safety 
monitoring.  Following the injection/sham procedure on Day 29, 85, and 274 subjects 
will remain at the study center for at least 6 hours post-procedure for safety monitoring.  
Safety monitoring visits will occur on Days 30, 86, 92, 169, 275, 365, and 456 (through 
6 months following the last injection/sham procedure).  In addition, the study center will 
monitor the subject’s condition through telephone contact monthly throughout the study.  
For subjects receiving ISIS 396443, a CSF sample will be taken pre-dose on each 
injection day in a manner that maintains the blind. 
Following treatment and the final follow-up evaluation, all eligible subjects may elect to 
enroll in an open-label treatment extension study.  This will be done without unblinding 
to subject’s treatment group. 
In the event of a decision by the study Sponsor to terminate the study earlier on the 
grounds that conducting a sham-controlled study is no longer deemed ethical based on 
an updated risk-benefit assessment of ISIS 396443 from the planned interim analysis, 
all subjects will be invited for the end-of-double-blind-period (EODBP) study visit, during 
which all Day 456 assessments will be conducted.  After completing the EODBP visit, 
subjects will be considered study completers and will be allowed to enroll into the open-
label extension study. 


ISIS 396443-CS4 
CONFIDENTIAL 
Amendment 2 
Protocol 
 
30 June 2016 
 
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PROTOCOL SYNOPSIS Continued 
Study Design 
Continued 
If a subject terminates early from the study, they will be encouraged to complete safety 
assessments per the Day 456 visit.  If a subject is randomized but does not complete at 
least their first dose of ISIS 396443/undergo the first sham procedure, they will be 
replaced. 
Study Population and 
Main Criteria for 
Inclusion/ Exclusion 
Inclusion Criteria: 
Subjects must meet all of the following criteria at Screening to be eligible: 
1. 
Signed informed consent of parent or guardian.  Signed informed assent of 
subject, if indicated per subject’s age and institutional guidelines 
2. 
Genetic documentation of 5q SMA (homozygous gene deletion, mutation, or 
compound heterozygote) 
3. 
Onset of clinical signs and symptoms consistent with SMA at > 6 months of age 
4. 
Males and females 2 to 12 years of age 
5. 
Can sit independently, but has never had the ability to walk independently 
6. 
Motor Function Score (Hammersmith Functional Motor Scale – Expanded) 
≥ 10 and ≤ 54 at Screening 
7. 
Able to complete all study procedures, measurements and visits and parent or 
guardian/subject has adequately supportive psychosocial circumstances, in the 
opinion of the Investigator 
8. 
Estimated life expectancy > 2 years from Screening, in the opinion of the 
Investigator 
9. 
Meets age-appropriate institutional criteria for use of anesthesia/sedation, if use is 
planned for study procedures (as assessed by the Site Investigator and either 
anesthesiologist or pulmonologist) 
10. For subjects who, in the opinion of the Investigator,  have reached reproductive 
maturity, satisfy 1 of the following: 
Females:  have a negative pregnancy test at Screening and agrees to employ 
adequate contraceptive measures for the duration of the study.  Acceptable 
contraception methods are restricted to abstinence, barrier contraceptives, 
intrauterine contraceptive devices or licensed hormonal products. 
Males:  be abstinent for the duration of the study 
Exclusion Criteria: 
Subjects meeting any of the following criteria are not eligible for the study: 
1. 
Respiratory insufficiency, defined by the medical necessity for invasive or non-
invasive ventilation for > 6 hours during a 24 hour period, at Screening 
2. 
Medical necessity for a gastric feeding tube, where the majority of feeds are given 
by this route, as assessed by the Site Investigator 
3. 
Severe contractures or severe scoliosis evident on X-ray examination at Screening 
4. 
Hospitalization for surgery (i.e., scoliosis surgery, other surgery), pulmonary event, 
or nutritional support within 2 months of Screening or planned during the duration 
of the study 
5. 
Presence of an untreated or inadequately treated active infection requiring 
systemic antiviral or antimicrobial therapy at any time during the screening period 
6. 
History of brain or spinal cord disease, including tumors, or abnormalities by MRI 
or CT that would interfere with the LP procedures or CSF circulation 
7. 
Presence of an implanted shunt for the drainage of CSF or an implanted CNS 
catheter 
8. 
History of bacterial meningitis 
9. 
Dosing with ISIS 396443 in any previous clinical study 
10. Prior injury (e.g., upper or lower limb fracture) or surgical procedure which impacts 
the subject’s ability to perform any of the outcome measure testing required in the 
protocol and from which the subject has not fully recovered or achieved a stable 
baseline 


ISIS 396443-CS4 
CONFIDENTIAL 
Amendment 2 
Protocol 
 
30 June 2016 
 
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PROTOCOL SYNOPSIS Continued 
Study Population and 
Main Criteria for 
Inclusion/ Exclusion 
Continued 
Exclusion Criteria Continued: 
11. Clinically-significant abnormalities in hematology or clinical chemistry parameters 
or ECG, as assessed by the Site Investigator, at the Screening visit that would 
render the subject unsuitable for inclusion 
12. Treatment with another investigational drug (e.g., oral albuterol/salbutamol, 
riluzole, carnitine, creatine, sodium phenylbutyrate, etc.), biological agent, or 
device within 1-month of Screening or 5 half-lives of study agent, whichever is 
longer.  Treatment with valproate or hydroxyurea within 3-months of screening.  
Any history of gene therapy, antisense oligonucleotide therapy, or cell 
transplantation 
13. Ongoing medical condition that according to the Site Investigator would interfere 
with the conduct and assessments of the study.  Examples are medical disability 
(e.g., wasting or cachexia, severe anemia, etc.) that would interfere with the 
assessment of safety or would compromise the ability of the subject to undergo 
study procedures 
Study Drug and 
Administration 
ISIS 396443 (2.4 mg/mL) will be administered as an intrathecal LP injection.  The 
volume of the injection will be 5.0 mL.  Details regarding the LP dosing injection 
procedure and the sham procedure will be provided in the Dosing Administration 
Manual.  Details regarding the Study Drug will be provided in the Study Drug Manual. 
Per institutional guidelines, anesthesia/sedation may be used for the LP procedure. 
Criteria for Evaluation 
Primary Endpoint: 
• 
Change from baseline in HFMSE (Hammersmith Functional Motor Scale – 
Expanded) score at 15 months 
 
Secondary Endpoints:  
• 
Proportion of subjects who achieve a 3-point or greater increase from baseline in 
Hammersmith Functional Motor Scale – Expanded (HFMSE) score at 15 months 
• 
Proportion of subjects that achieve any new motor milestone at 15 months 
• 
Number of motor milestones achieved per subject at 15 months 
• 
Change from baseline in Upper Limb Module Test at 15 months 
• 
Proportion of subjects that achieve standing alone at 15 months 
• 
Proportion of subjects that achieve walking with assistance at 15 months 
 
Tertiary Endpoints:  
• 
Change from baseline in CSF SMN protein concentration  
• 
Clinical Global Impression of Change (Investigator and Caregiver assessment)  
• 
Change from baseline in PedsQL (Pediatric Quality of Life Inventory)  
• 
Change from baseline in Assessment of Caregiver Experience with Neuromuscular 
Disease (ACEND)  
• 
Disease-related hospitalizations and adverse events 
 
Safety/Tolerability Endpoints: 
• 
Adverse events 
• 
Vital signs and weight 
• 
Neurological examinations 
• 
Physical examinations  
• 
Clinical laboratory tests  
• 
ECGs 
• 
Use of concomitant medications 


ISIS 396443-CS4 
CONFIDENTIAL 
Amendment 2 
Protocol 
 
30 June 2016 
 
13 
PROTOCOL SYNOPSIS Continued 
Criteria for Evaluation 
Continued 
Pharmacokinetic Endpoints:  
• 
CSF levels of ISIS 396443 (sample taken pre-dose at each dosing) 
• 
Plasma levels of ISIS 396443 
 
Immunogenicity Endpoint:  
• 
Plasma antibodies to ISIS 396443 
Safety Monitoring  
Safety data will be reviewed on an ongoing basis by the Medical Monitor and by an 
Independent Data Safety and Monitoring Board (DSMB). 
Statistical 
Considerations  
The sample size for this study was estimated based on limited available natural history 
data for the target population and from the ISIS 396443-CS1 and CS2 clinical studies in 
children with SMA.  70 subjects in the treated group and 35 subjects in the control 
group will give at least 90% power to detect a 3-point difference between control and 
treated groups in change on the HFMSE with a standard deviation of 4.4, using a 
2-sided t-test with an alpha level of 0.05.  The sample size was obtained using the 
n-Query.  117 subjects will be enrolled to ensure that a small dropout rate will not affect 
the power of the primary efficacy analysis.  An interim analysis may take place when all 
subjects have completed the 6-month assessment and at least 39 subjects have 
completed the 15-month assessment. 
Sponsor 
Ionis Pharmaceuticals, Inc. 
 
 
 


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STUDY GLOSSARY 
Abbreviation/Acronym 
Definition 
ACEND 
Assessment of Caregiver Experience with Neuromuscular Disease 
AE 
Adverse event/experience 
ALT 
Alanine aminotransferase  
aPTT 
Activated partial thromboplastin time 
ASO 
Antisense oligonucleotide 
AST 
Aspartate aminotransferase 
BUN 
Blood urea nitrogen 
CGI 
Clinical Global Impressions of Change Rating Scale 
Cmax 
Maximum concentration 
CNS 
Central nervous system 
CPK 
Creatinine phosphokinase 
CRF 
Case report form 
CSF 
Cerebrospinal fluid 
DSMB 
Data and Safety Monitoring Board 
eCRF 
Electronic case report form 
ECG 
Electrocardiogram 
EODBP 
End-of-double-blind-period 
FL 
Full-length  
GCP 
Good Clinical Practice 
HFMSE 
Hammersmith Functional Motor Scale - Expanded 
hnRNP 
Heterogeneous nuclear ribonucleoproteins 
ICH 
International Conference on Harmonisation  
IEC 
Independent Ethics Committee 
INR 
International normalized ratio 
IRB 
Institutional Review Board 
IT 
Intrathecal 
IXRS 
Interactive Voice/Web-Response System 
LP 
Lumbar puncture 
MAD 
Multiple ascending-dose 
MedDRA 
Medical Dictionary for Regulatory Activities 


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miRNA 
Micro ribonucleic acid (RNA) 
MOE 
2′-O-(2-methoxyethyl)  
mRNA 
Messenger ribonucleic acid 
NCS 
Not clinically-significant 
OLE 
Open-label extension study 
PedsQL 
Pediatric Quality of Life Inventory 
PK 
Pharmacokinetic(s) 
PT 
Prothrombin Time 
SAE 
Serious adverse event 
SAP 
Statistical Analysis Plan 
SMA 
Spinal muscular atrophy 
SMN 
Survival motor neuron 
snRNA 
Small nuclear ribonucleic acid 
SUSARs 
Suspected unexpected serious adverse reactions 
Tmax 
Time to maximal concentration 
WMA 
World Medical Association 
 
 
 
 


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1. 
OBJECTIVES 
The objectives of this study are to evaulate the clinical efficacy, safety, tolerability, and 
pharmacokinetics (PK) of ISIS 396443 administered intrathecally to patients with later-onset 
Spinal Muscular Atrophy (SMA). 
1.1 
Primary Objective 
To examine the clinical efficacy of ISIS 396443 administered intrathecally to patients with 
later-onset SMA. 
1.2 
Secondary Objective 
To examine the safety and tolerability of ISIS 396443 administered intrathecally to patients with 
later-onset SMA. 
1.3 
Tertiary Objective 
To examine the cerebral spinal fluid and plasma PK of ISIS 396443 administered intrathecally to 
patients with later-onset SMA. 
2. 
BACKGROUND AND RATIONALE 
2.1 
Spinal Muscular Atrophy 
SMA is an autosomal recessive neuromuscular disease characterized by degeneration of the 
motor neurons in the anterior horn of the spinal cord, resulting in atrophy of the voluntary 
muscles of the limbs and trunk.  With an incidence of 1:6000 to 1:10,000 live births, it is the 
most common genetic cause of infant mortality, and a major cause of childhood morbidity due to 
weakness, in the U.S.  The natural history of SMA includes 4 major phenotypes that are 
recognized dependent on age of onset and achieved motor abilities.  The most severe form, 
Type 1 SMA (equivalent to infantile-onset SMA), has a disease onset within the first few months 
of life; these children are never able to sit or walk and usually die from respiratory failure by the 
age of 2 years.  Later-onset SMA can generally be divided into Type 2 and Type 3 SMA.  Type 2 
SMA patients are able to sit but never walk unaided, with symptoms presenting between  
6-18 months of age.  Type 3 SMA patients are able to sit and walk but individuals with this form 
may become severely and increasingly disabled.  Adult-onset SMA patients (Type 4) have an 
age of onset over 18 years of age and have normal life expectancies. 
In 95% of SMA patients, a deletion in the SMN1 gene on Chromosome 5q11-q13 is found; with 
the remaining 5% attributable to small mutations in the same gene (Lefebvre et al. 1995; 
Helmken et al. 2003).  SMN1 lies in the telomeric portion of an inverted duplication of a region 
of Chromosome 5.  The centromeric half of the duplication contains a homologous gene, named 
SMN2 that differs from SMN1 by 5 nucleotides.  The open reading frames for both genes encode 
for proteins with identical amino acid sequences.  Survival motor neuron (SMN) gene 
transcripts, similar to most mammalian transcripts, undergo alternative splicing in which certain 
exons are either included or excluded from the mature protein coding transcripts 
(Keren et al. 2010).  In particular, Exon 7 of the SMN1 gene is alternatively spliced with 90 to 
95% of the mature messenger ribonucleic acid (mRNA) transcripts derived from the SMN1 gene 
containing Exon 7, and 5 to 10% of transcripts missing Exon 7.  The transcripts missing Exon 7 
(often referred to as Δ7) produce a truncated protein which is defective and unstable 


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(Cho and Dreyfuss 2010).  One (1) of the 5 nucleotide differences between SMN1 and SMN2, a 
C to T substitution occurs in Exon 7 of the SMN2 gene resulting in an alternative splicing pattern 
that favors skipping of Exon 7.  The result is that as much as 90% of the transcripts produced 
from SMN2 are missing Exon 7.  The remainder, SMN2 transcripts containing Exon 7, produces 
a full-length (FL) protein product identical to the SMN1 protein, since the C to T substitution is 
silent.  Humans have a variable copy number of the SMN2 gene (0-8 copies) (Wirth et al. 2006).  
The number of SMN2 copies and the resulting amount of FL-SMN protein expressed in SMA 
patients (10-40% of normal SMN protein levels) correlates with SMA disease severity and thus 
SMN2 is a key modifier of disease phenotype (Coovert et al. 1997; Feldkotter et al. 2002; 
Lefebvre et al. 1997; Prior et al. 2004). 
2.2 
Therapeutic Rationale 
Since the number of SMN2 gene copies and resulting amount of SMN protein is correlated with 
disease onset and severity, a therapeutic approach predicted to benefit SMA patients is to 
increase the levels of full length SMN2 pre-mRNA by restoring the splicing pattern that gives 
rise to full length SMN2 mRNA.  Increasing inclusion of Exon 7 in the SMN2 transcript will 
increase FL-SMN protein levels and SMN protein activity.  A therapeutic strategy for promoting 
Exon 7 inclusion is through the use of antisense oligonucleotides (ASOs) (see Figure 1). 
 
Figure 1 
ASO Therapeutic Approach for Treatment of SMA 


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The known potential risks associated with ISIS 396443 are detailed in the Guidance to 
Investigator section of the Investigator’s Brochure.  Additional study associated risks related to 
the lumbar puncture (LP) procedure are also detailed in the Guidance to Investigator section of 
the Investigator’s Brochure. 
2.3 
ISIS 396443 
2.3.1 
Mechanism of Action 
ISIS 396443 is a fully modified, 2′-O-2-methoxyethyl (MOE), ASO drug designed to bind to a 
specific sequence in the intron downstream of Exon 7 of the SMN2 transcript.  The region of the 
pre-mRNA targeted by ISIS 396443 is normally occupied by heterogeneous nuclear 
ribonucleoproteins (hnRNP) A1/2 proteins, masking the U1 small nuclear ribonucleic acid 
(snRNA) binding site at the 5′-exon-intron junction of Exon 7, and is referred to as ISS-N1.  
U1 snRNA base pairs to the sequences that define the 5′-splice site, which is thought to be one of 
the first steps that initiate splicing of an intron.  ISIS 396443 displaces the hnRNP A1/2 proteins 
from the pre-mRNA binding site, allowing U1 snRNA to bind to the exon-intron junction and 
promote assembly of the spliceosomal complex, thus promoting inclusion of Exon 7 into the 
mRNA which results in production of FL-SMN protein. 
2.3.2 
Chemistry 
Chemically, ISIS 396443 is a synthetic oligomer of 18 nucleotides (i.e., an 18-mer) that are 
connected sequentially by phosphorothioate linkages.  Each of the 17 internucleotide linkages is 
a 3′-O to 5′-O phosphorothioate diester.  The 18 sugar residues are uniformly modified with 
2′-O-(2-methoxyethyl) (MOE).  These MOE-modified nucleotides confer (1) increased affinity 
to the target mRNA (McKay et al. 1999), (2) increased resistance to exonucleases and 
endonucleases (thereby increasing stability in tissue) (Geary et al. 2003), and (3) amelioration of 
some of the high dose toxicities associated with ASO containing only the phosphorothioate 
linkages (Henry et al. 2000). 
The sequence of ISIS 396443 is written as follows: 
5′ -MeUMeCAMeCMeUMeUMeUMeCAMeUAAMeUGMeCMeUGG- 3′ 
Where A and G are 2′-O-(2-methoxyethyl)nucleosides, MeC is 5-methyl-2′-O-(2-
methoxyethyl)cytidine and MeU designates 5-methyl-2′-O-(2-methoxyethyl)uridine. 
2.3.3 
Preclinical Experience 
Detailed information concerning the preclinical studies conducted with ISIS 396443 can be 
found in the Investigator’s Brochure.  A summary is included below. 
ISIS 396443 was identified after an extensive screen of greater than 500 2′-MOE 
oligonucleotides in in vitro splicing assays, reporter gene assays and in SMA patient fibroblasts 
(Hua et al. 2007; Hua et al. 2008).  Data have shown that ISIS 396443 promotes a concentration-
dependent increase in full-length transcripts (including Exon 7) in patient fibroblast cells, 
achieving greater than 90% full length SMN2 transcripts and forms nuclear structures, called 
gems, known to contain SMN protein.  In a mild mouse model of SMA, ISIS 396443 promoted 
inclusion of Exon 7 in the SMN2 transgene in a variety of peripheral tissues when dosed 


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systemically (Hua et al. 2008) and in central nervous system (CNS) tissue, including spinal cord, 
when injected into the lateral ventricle.  ISIS 396443 produced greater than 90% Exon 7 
inclusion in the transgenic mice and increased SMN protein production in motor neurons, 
resulting in the appearance of gems in motor neurons.  These studies were extended to a more 
severe mouse model of SMA (SMA Δ7) (Le et al. 2005), where the CNS delivery of drug 
produced a dose-dependent effect on SMN2 Exon 7 inclusion, SMN protein production, and 
survival.  These mice treated with ISIS 396443 demonstrated improved weight gain, 
improvements in muscle morphology, muscle strength, and motor coordination and improved 
morphology of the motor neuron junctions (Passini et al. 2011).  Further, ISIS 396443 was 
shown to distribute widely in the CNS following intrathecal (IT) administration in monkey 
(Passini et al. 2011). 
The pharmacokinetics and toxicity of ISIS 396443 were assessed following: 1) single intrathecal 
(IT) lumbar bolus injections (1 to 7 mg) in adult monkeys 2) following 14 weeks (with a 4-week 
interim sacrifice) of repeated IT lumbar bolus injections (0.3 to 3 mg/week or every other week) 
in juvenile monkeys and 3) following 53 weeks of repeated IT lumbar bolus injections in 
juvenile monkeys.  In addition, a dedicated pharmacokinetic study in adult monkeys was 
performed to assess the half-life of ISIS 396443 in CSF, tissues and plasma.  Detailed results 
from these preclinical studies conducted with ISIS 396443 can be found in the ISIS 396443 
Investigator’s Brochure. 
2.3.4 
Clinical Experience 
Excluding the current study ISIS 396443-CS4, 9 additional clinical studies with ISIS 396443 
have been initiated:  3 studies have been completed and 6 are ongoing.  Four (4) of the clinical 
studies are in patients with “later-onset SMA,” 2 trials are in “infantile-onset (Type I) SMA,” 
1 trial is in neonates and infants with genetically diagnosed and presymptomatic SMA, and 
2  trials are in both “infantile-onset” and “later-onset” populations.  The ISIS 396443 clinical 
studies are described in detail in the Investigator’s Brochure and listed here: 
• ISIS 396443-CS1 (completed):  an open-label, single ascending-dose (SAD) Phase 1 
study designed to assess the safety, tolerability and pharmacokinetics of ISIS 396443 in 
patients with SMA, aged 2 to 14 years 
• ISIS 396443-CS2 (completed):  an open-label, multiple ascending-dose (MAD) 
Phase 1/2a study designed to assess the safety, tolerability and pharmacokinetics of 
ISIS 396443 in patients with SMA, aged 2 to 15 years  
• ISIS 396443-CS10 (completed):  an open-label Phase 1 study to assess the safety and 
tolerability of a single IT dose (6 or 9 mg) of ISIS 396443 in patients with SMA who 
previously participated in ISIS 396443-CS1 
• ISIS 396443 CS12 (ongoing):  an open-label Phase 2 study to assess the safety and 
tolerability of a single IT dose (12 mg) of ISIS 396443 in patients with SMA who 
previously participated in either ISIS 396443 CS2 or ISIS 396443-CS10 
• ISIS 396443-CS3A (ongoing):  a multiple-dose Phase 2 study designed to assess the 
safety, tolerability, pharmacokinetics and efficacy of ISIS 396443 in patients with 
infantile-onset SMA (symptomatic SMA infants < 7 months of age) 


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• ISIS 396443-CS3B (ongoing):  a Phase 3 randomized, double-blind, sham-procedure 
controlled study to assess the clinical efficacy, safety, tolerability and pharmacokinetics 
of ISIS 396443 in patients with infantile-onset SMA 
• ISIS 396443-CS5 (232SM201:  ongoing):  an open-label Phase 2 study to assess the 
efficacy, safety, tolerability, and pharmacokinetics of multiple doses of ISIS 396443 
delivered intrathecally to subjects with genetically diagnosed and presymptomatic SMA 
• ISIS 396443-CS7 (232SM202:  ongoing):  a Phase 2, randomized, double-blind, 
sham-procedure controlled study to assess the safety and tolerability and explore the 
efficacy of ISIS 396443 administrated intrathecally in subjects with SMA who are not 
eligible to participate in the clinical studies ISIS 396443-CS3B or ISIS 396443-CS4 
• ISIS 396443-CS11 (ongoing):  an open-label Phase 3 extension study for patients with 
SMA who previously participated in investigational studies of ISIS 396443.  Safety and 
tolerability will be assessed in this study.  Up to 274 patients from ISIS 396443-CS3B, 
ISIS 396443-CS4, and ISIS 396443-CS12 are eligible to enroll 
2.4 
Rationale for Dose and Schedule of Administration 
The proposed study will test the clinical efficacy, safety, tolerability, and PK of multiple doses of 
ISIS 396443 administered as IT injections to subjects with later-onset SMA.  A single dose level 
of 12 mg ISIS 396443 will be evaulated, delivered as 4 doses administered over 9 months. 
ISIS 396443 will be administered using a loading regimen (dosings on Study Days 1, 29, 85) 
followed by maintenance dosing given 6 months thereafter (dosing on Study Day 274). 
The ISIS 396443-CS4 dose level and dose interval was selected based on preclinical toxicology 
and pharmacokinetic observations from monkey studies utilizing single-dose and repeat dosing 
IT administration, consideration of the target tissue concentration anticipated for drug 
pharmacology, and safety data in the completed and ongoing clinical studies of ISIS 396443 to 
date.  Based upon pharmacology and pharmacokinetic results in SMA transgenic mice, we 
estimate that the target tissue concentration to produce 50 to 90% SMN2 Exon 7 inclusion is 
between 1 and 10 μg/g spinal cord tissue.  Nonclinical studies in juvenile monkeys receiving IT 
doses of ISIS 396443 showed a resulting gradient of distribution of ISIS 396443 along the spinal 
cord, with mean lumbar spinal cord concentrations ranging from 1.6-2.3 fold and 2.0-3.5 fold 
higher than thoracic and cervical spinal cord levels, respectively.  The dose level selected for this 
multiple-dose clinical study (12 mg ISIS 396443) is predicted to achieve levels at the high end of 
this range (approximately 10 μg/g lumbar and 3 µg/g cervical spinal cord tissue concentrations), 
following the first dose.  The loading dose interval was selected based on the nonclinical 
pharmacokinetic and pharmacology data as the dose interval to achieve and maintain 
ISIS 396443 spinal cord tissue levels that are predicted to be within the upper end of the 
pharmacologically active range by Day 85 (predicted to be approximately 24 μg/g lumbar and 
8 μg/g cervical tissue concentration), while at the same time considering subject safety and 
convenience for repeated LP intrathecal injections.  The maintenance dose interval (once every 
6 months) was selected based on the estimated spinal tissue and CSF drug half-life (4-6 months) 
and was selected to maintain spinal cord tissue levels of ISIS 396443 at a steady-state level 
within the estimated pharmacologically active range. 


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Additional details on dose scaling and expected CSF and tissue concentrations are summarized 
in the Investigator’s Brochure. 
3. 
EXPERIMENTAL PLAN 
3.1 
Study Design 
This is a Phase 3 multicenter, double-blind, randomized, sham-procedure controlled study of 
ISIS 396443 in patients with later-onset SMA studied for 15 months.  Approximately 
117 subjects will be randomized 2:1 to receive 12 mg dose ISIS 396443 or a sham procedure 
control, respectively.  ISIS 396443 will be administered using a loading regime (dosings on 
Study Days 1, 29, and 85) followed by a maintenance dose 6 months thereafter (dosing on Study 
Day 274). 
Randomization will be stratified based on: 
1. Subject’s Age at Screening (< 6 years vs. ≥ 6 years) 
Following treatment and the Day 456 follow-up evaluation, all eligible subjects may elect to 
enroll in an open-label treatment extension study, pending study approval by the IRB or IEC and 
the appropriate regulatory authority.  This will be done without unblinding to subject’s treatment 
group. 
An interim analysis may take place when all subjects have completed the 6-month assessment 
and at least 39 subjects have completed the 15-month assessment.  In the event of a decision by 
the study Sponsor to terminate the study earlier on the grounds that conducting a sham-controlled 
study is no longer deemed ethical based on an updated risk benefit assessment of ISIS 396443 
from the planned interim analysis, all subjects will be invited for the end-of-double-blind-period 
(EODBP) study visit, during which all Day 456 assessments will be conducted.  After 
completing the EODBP visit, subjects will be considered study completers and will be allowed to 
enroll into the open-label extension study. 
3.2 
Number of Study Centers 
This study will be conducted at multiple centers worldwide. 
3.3 
Number of Subjects 
Approximately 117 subjects (2 ISIS 396443; 1 sham-procedure) will receive 12 mg dose of 
ISIS 396443 or a sham procedure control.  The total number of subjects randomized may be 
higher if some subjects do not receive their Day 1 dose/sham procedure.  The maximum number 
of subjects will not exceed 130. 
3.4 
Overall Study Duration and Follow-up 
The Study will consist of screening, treatment, and post-treatment follow-up-periods.  The total 
duration of participation in the study is approximately 16 months.  Please refer to the Schedule of 
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3.4.1 
Screening 
After informed consent/assent is obtained, subjects will undergo a screening evaluation no 
greater than 28 days prior to first dose administration at which their eligibility for the study will 
be examined. 
3.4.2 
Treatment 
Subjects who meet the eligibility criteria will be admitted to the study center on Study Day 1, 
undergo pre-dose evaluations, be randomized, and then receive either an LP injection of Study 
Drug (ISIS 396443) or a sham procedure.  Subjects will return to the study center on Days 29, 
85, and 274 for follow-up evaluations and subsequent injections/sham procedures.  Following the 
injection/sham procedure on Day 1, subjects will remain at the study center for at least 24 hours 
post-procedure for safety monitoring.  Following the injection/sham procedure on Day 29, 85, 
and 274 subjects will remain at the study center for at least 6 hours post-procedure for safety 
monitoring.  Safety monitoring visits will occur Study Days 30, 86, 92, 169, and 275 (through 
the last injection/sham procedure).  In addition, the study center will monitor the subject’s 
condition through telephone contact on a monthly basis. 
For subjects receiving ISIS 396443, a CSF sample for PK and SMN protein analyses will be 
taken pre-dose on each injection day in a manner that protects the blind. 
If a subject terminates early from the study, they will be encouraged to complete assessments per 
the Day 456 visit.  If a subject is randomized but does not successfully receive the first dose of 
ISIS 396443/undergo the first sham procedure, they will be replaced. 
3.4.3 
Post-Treatment Follow-up 
After completion of the Day 275 visit, subjects will enter the 6-month post-treatment evaluation 
period.  This period consists of Study Center visits on Day 365 and 456 and follow-up phone 
assessments on a monthly basis, as outlined in the Schedule of Procedures (Appendix A).  After 
completion of the Day 456 visit, subjects may be eligible to participate in an OLE study, pending 
study approval by the IRB or IEC and the appropriate regulatory authority. 
3.5 
End-of-Study 
The End-of-Study is last subject; last visit (either in-person visit or telephone contact).  In the 
event of a decision by the study Sponsor to terminate the study earlier on the grounds that 
conducting a sham-controlled study is no longer deemed ethical based on an updated risk-benefit 
assessment of ISIS 396443 from the planned interim analysis, all subjects will be invited for the 
EODBP study visit, during which all Day 456 assessments will be conducted.  The EODBP visit 
should occur no less than 2 weeks from the most recent dosing/sham procedure administered. 
After completing the EODBP visit, subjects will be considered study completers and will be 
allowed to enroll into the OLE study. 
3.6 
Safety Monitoring and Data Safety Monitoring Board 
Safety data will be reviewed on an ongoing basis by the Sponsor and the Medical Monitor.  
Safety data will also be reviewed on a quarterly basis by an independent data and safety 
monitoring board (DSMB).  The DSMB will be assembled to review safety, tolerability and 
efficacy (as needed) data collected on ISIS 396443 during this study.  Based on its ongoing 


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assessment of the data, the DSMB will provide recommendations to the Sponsor for modifying, 
stopping or continuing the study. 
4. 
SUBJECT ENROLLMENT 
4.1 
Screening 
Before subjects may be enrolled into the study, the Sponsor requires a copy of the Study Center’s 
written IRB or IEC approval of the protocol, informed consent form, informed assent form (if 
applicable) and all other subject information and/or recruitment material. 
Before a subject’s participation in the trial, the Investigator is responsible for obtaining written 
informed consent from the parent(s) or legal guardian(s) and, in cases where institutional 
guidelines and the patient’s age dictate, informed assent from the subject.  At the time of 
consent/assent, the subject will be considered enrolled into the study and will be assigned a 
unique screening number before any study procedures, including screening procedures, are 
performed.  The screening number must remain constant throughout the entire trial.  In the event 
the subject is re-consented and re-screened the subject must be given a new screening number.  
Screening numbers, once assigned, will not be re-used. 
4.2 
Randomization 
Subjects will be randomized after all screening assessments have been completed and after the 
Investigator and the Medical Monitor have verified that they are eligible per criteria in 
Sections 5.1 and 5.2.  No subject may begin treatment prior to randomization and assignment of 
a unique randomization number. 
Using an Interactive Voice/Web-Response System (IXRS), eligible subjects will be randomized 
2:1 to receive ISIS 396443 or sham-procedure control, respectively.  Randomization will be 
stratified for: 
• Subject’s Age at Screening (< 6 years vs. ≥ 6 years) 
The Sponsor Quality Assurance department or designee will hold a copy of the randomization 
lists generated by the IXRS vendor. 
4.3 
Replacement of Subjects 
If a subject does not successfully receive the first dose of ISIS 396443/undergo the first sham 
procedure, they will be replaced.  
4.4 
Unblinding of Treatment Assignment 
The Sponsor, parents, and key study site personnel will be blinded to subjects’ treatment 
assignment throughout the study.  The DSMB may be unblinded as described in the DSMB 
charter.  Representatives from the Sponsor may be unblinded at the interim analysis as described 
in the unblinding plan.  Those Sponsor representatives will no longer be involved in the conduct 
of the study after they have been unblinded. 
If a subject has experienced an SAE (as defined in Section 9.3.3), and/or when knowledge of the 
treatment assignment will impact the clinical management of the subject, the Investigator will 


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have the ability to unblind the treatment assignment for that subject using the IXRS.  However, 
prior to unblinding, the Investigator should attempt to contact the blinded Medical Monitor to 
discuss the emergency.  The Sponsor or designee will be informed of the unblinding of a subject 
within 24 hours.  Every reasonable attempt should be made to complete the Study Day 456 early 
termination procedures and observations (see Appendix A) prior to unblinding, as knowledge of 
the subject’s treatment assignment could influence subsequent assessments.  The Investigator 
must document the reasons for unblinding in the subject’s source documents.  The Investigator is 
strongly advised not to divulge the subject’s treatment assignment to any individual not directly 
involved in managing the medical emergency, nor to personnel involved with the analysis and 
conduct of the study.  In cases where there are ethical reasons to have a subject remain on study 
whose treatment assignment is unblinded for safety reasons, the Site Investigator must obtain 
specific approval from the Sponsor and the Medical Monitor for the subject to continue in the 
study. 
In addition, all suspected unexpected serious adverse reactions (SUSARs) will be unblinded by 
the Sponsor’s Drug Safety and Quality Assurance personnel for the purpose of regulatory 
reporting (Section 9.2). 
5. 
SUBJECT ELIGIBILITY 
5.1 
Inclusion Criteria  
Subjects must meet all of the following criteria at Screening to be eligible: 
1. Signed informed consent of parent or guardian.  Signed informed assent of subject, if 
indicated per subject’s age and institutional guidelines 
2. Genetic documentation of 5q SMA (homozygous gene deletion, mutation, or compound 
heterozygote) 
3. Onset of clinical signs and symptoms consistent with SMA at > 6 months of age 
4. Males and females 2 to 12 years of age 
5. Can sit independently, but has never had the ability to walk independently 
6. Motor Function Score (Hammersmith Functional Motor Scale – Expanded) ≥ 10 and ≤ 54 
at Screening 
7. Able to complete all study procedures, measurements and visits and parent or 
guardian/subject has adequately supportive psychosocial circumstances, in the opinion of 
the Investigator 
8. Estimated life expectancy > 2 years from screening, in the opinion of the Investigator 
9. Meets age-appropriate institutional criteria for use of anesthesia/sedation, if use is 
planned for study procedures (as assessed by the Site Investigator and either 
anesthesiologist or pulmonologist) 
10. For subjects who, in the opinion of the Investigator, have reached reproductive maturity, 
satisfy 1 of the following: 


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Females:  have a negative pregnancy test at Screening and agrees to employ adequate 
contraceptive measures for the duration of the study.  Acceptable contraception methods 
are restricted to abstinence, barrier contraceptives, intrauterine contraceptive devices or 
licensed hormonal products. 
Males:  be abstinent for the duration of the study 
5.2 
Exclusion Criteria 
Subjects meeting any of the following criteria are not eligible for the study: 
1. Respiratory insufficiency, defined by the medical necessity for invasive or non-invasive 
ventilation for > 6 hours during a 24 hour period, at Screening 
2. Medical necessity for a gastric feeding tube, where the majority of feeds are given by this 
route, as assessed by the Site Investigator 
3. Severe contractures or severe scoliosis evident on X-ray examination at Screening 
4. Hospitalization for surgery (i.e., scoliosis surgery, other surgery), pulmonary event, or 
nutritional support within 2 months of screening or planned during the duration of the 
study 
5. Presence of an untreated or inadequately treated active infection requiring systemic 
antiviral or antimicrobial therapy at any time during the screening period 
6. History of brain or spinal cord disease, including tumors, or abnormalities by MRI or CT 
that would interfere with the LP procedures or CSF circulation 
7. Presence of an implanted shunt for the drainage of CSF or an implanted CNS catheter 
8. History of bacterial meningitis 
9. Dosing with ISIS 396443 in any previous clinical study 
10. Prior injury (e.g., upper or lower limb fracture) or surgical procedure which impacts the 
subject’s ability to perform any of the outcome measure testing required in the protocol 
and from which the subject has not fully recovered or achieved a stable baseline 
11. Clinically-significant abnormalities in hematology or clinical chemistry parameters or 
ECG, as assessed by the Site Investigator, at the Screening visit that would render the 
subject unsuitable for inclusion 
12. Treatment with another investigational drug (e.g., oral albuterol/salbutamol, riluzole, 
carnitine, creatine, sodium phenylbutyrate, etc.), biological agent, or device within 
1-month of screening or 5 half-lives of study agent, whichever is longer.  Treatment with 
valproate or hydroxyurea within 3-months of screening.  Any history of gene therapy, 
antisense oligonucleotide therapy, or cell transplantation 
13. Ongoing medical condition that according to the Site Investigator would interfere with 
the conduct and assessments of the study.  Examples are medical disability (e.g., wasting 
or cachexia, severe anemia, etc.) that would interfere with the assessment of safety or 
would compromise the ability of the subject to undergo study procedures 


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6. 
STUDY PROCEDURES 
6.1 
Study Schedule 
All required study procedures are outlined in Appendices A, B and C. 
6.2 
Study Assessments 
6.2.1 
Laboratory Analytes 
Laboratory measurements of serum chemistry, hematology, urinalysis, coagulation parameters, 
and plasma antibodies to ISIS 396443 will be performed at the times shown in the Schedule of 
Procedures (Appendix A).  The analytes to be measured are shown in Appendix B. 
6.2.2 
Neurological Examinations 
Neurological examinations include assessment of mental status, level of consciousness, sensory 
function, motor function, cranial nerve function, and reflexes.  Neurological examinations will be 
performed at the times shown in the Schedule of Procedures (Appendix A). 
6.2.3 
Pharmacokinetics Specimen Collection 
Plasma and CSF specimens will be collected as shown in Appendix A (Schedule of Procedures) 
and Appendix C (Pharmacokinetic Sampling Schedule).  The following ISIS 396443 plasma PK 
parameters (though not necessarily limited to) will be derived when appropriate from the 
individual subject concentration vs. time profiles using noncompartmental-based methods and 
based on actual sampling times: 
• The maximal observed plasma drug concentration (Cmax) 
• The time to reach Cmax in plasma (Tmax) 
• The area under the plasma concentrations time curve from the time of the IT dose to the 
last collected sample 
• The apparent terminal elimination half-life (t½), if possible 
6.2.4 
Hammersmith Functional Motor Scale - Expanded 
Subjects will be evaluated using the Hammersmith Functional Motor Scale – Expanded 
(HFMSE) at the times shown in the Schedule of Procedures (Appendix A).  The HFMSE is a 
reliable and validated tool used to assess motor function in children with SMA.  The scale was 
originally developed with 20 scored activities and was devised for use in children with SMA 
Type 2 and Type 3 with limited ambulation to give objective information on motor ability and 
clinical progression (Main et al. 2003).  The expanded scale includes an additional module of 
13 items developed to allow for evaluation of ambulatory SMA patients (O’Hagen et al. 2007).  
The HFMSE has been shown to be highly correlated with other clinical assessments and shows 
good test-retest reliability.  The HFMSE is easy to use and quickly administered. 


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6.2.5 
Motor Milestones 
Subjects will be evaluated for motor milestones at the times shown in the Schedule of Procedures 
(Appendix A).  Motor Milestones will be assessed using the WHO Motor Milestone criteria 
(WHO Multicentre Growth Reference Study Group 2006; Wijnhoven et al. 2004). 
6.2.6 
PedsQL™ (Generic Core Scales and Neuromuscular Module) 
Subjects will be evaluated using the Pediatric Quality of Life Inventory (PedsQL™) 
Measurement 4.0 Generic Core Scales and 3.0 Neuromuscular Module (Varni et al. 1999) at the 
times shown in the Schedule of Procedures (Appendix A).  This assessment has been validated 
by the American Spinal Muscular Atrophy Randomized Trials (AmSMART) group for use in 
SMA patients from age 2 to 18 years (Iannaccone et al. 2009). 
The PedsQL™ Measurement Model is a modular approach to measuring health-related quality of 
life (HRQOL) in children and adolescents.  The PedsQL consists of brief, practical, generic core 
scales as well as with condition-specific modules for use in designated clinical populations.  
Pediatric self-report is measured in children and adolescents ages 5-18 years, and parent proxy-
report of child HRQOL is measured for children and adolescents ages 2-18 years.  The 
PedsQL™ 4.0 Generic Core Scales include assessment of physical functioning, emotional 
functioning, social functioning, and school functioning.  The PedsQL 3.0 Neuromuscular 
Module was designed to measure HRQOL dimensions specific to children aged 2 to 18 years 
with neuromuscular disorders, including SMA. 
6.2.7 
Upper Limb Module Test 
Subjects will be evaluated using the Upper Limb Module Test (Mazzone et al. 2011) at the times 
shown in the Schedule of Procedures (Appendix A).  The Upper Limb Module Test is an 
outcome measure specifically developed to assess upper limb functional abilities in SMA 
patients, including young children and patients with severe contractures in the lower limbs in 
whom the possibility to detect functional changes, such as rolling or long sitting, is limited.  This 
test consists of upper limb performance items that are reflective of activities of daily living (i.e., 
raise a can to mouth as if drinking, take a coin and place it in a box, remove the lid of a 
container).  The Upper Limb Module Test is quickly administered and has been evaluated in 
SMA patients age 30 months to 27 years (Mazzone et al. 2011). 
6.2.8 
Assessment of Caregiver Experience with Neuromuscular Disease (ACEND) 
Parents of subjects will complete the Assessment of Caregiver Experience with Neuromuscular 
Disease (ACEND) questionnaire at the times shown in the Schedule of Procedures 
(Appendix A).  This assessment instrument has been designed to quantify the caregiver impact 
experienced by parents of children affected with severe neuromuscular diseases, including 
children with SMA (Matsumoto et al. 2011).  The ACEND includes domains assessing physical 
impact (including feeding/grooming/dressing, sitting/play, transfers, and mobility) and general 
caregiver impact (including time, emotion, and finance). 
6.2.9 
Safety Evaluations 
Safety will be evaluated by assessment of AEs including SAEs as described in Section 9.  
Additional safety evaluations include the following parameters: 


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• Vital signs and weight 
• Neurological examinations 
• Physical examinations  
• Clinical laboratory tests (serum chemistry, hematology, urinalysis) 
• Electrocardiograms (ECGs) 
• Use of concomitant medications 
6.3 
Contraception Requirements 
All male subjects must remain abstinent during the study. 
All female subjects of childbearing potential must either be abstinent or practice adequate 
contraception during the study.  For the purposes of this study, females of childbearing potential 
are defined as any female who has experienced menarche.  For the purposes of the study, 
acceptable contraception methods are abstinence, barrier contraceptives, intrauterine 
contraceptive devices or licensed hormonal products 
7. 
STUDY DRUG 
7.1 
Study Drug Description 
Study Drug (ISIS 396443 drug product) characteristics are listed under Table 1. 
The Study Drug is contained in 6 mL clear glass vials.  The Study Drug and its storage and 
preparation instructions will be provided by the Sponsor or designee.  The Study Drug must be 
stored securely at 2° to 8° C and protected from light. 
Table 1 
Study Drug Characteristics 
Study Drug 
ISIS 396443 Drug Product 
Strength 
2.4 mg/mL  
Volume/vial 
5.0 mL solution per vial 
Route of Administration 
IT injection 
 
7.2 
Packaging and Labeling 
The Sponsor will provide the Investigator with packaged Study Drug labeled in accordance with 
specific country regulatory requirements. 
7.3 
Study Drug Accountability 
The study staff is required to document receipt, dispensing and return of Study Drug supplies 
provided by the Sponsor.  Drug accountability documentation and all used and unused Study 
Drug vials must be returned to the Sponsor or designee. 


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8. 
TREATMENT OF SUBJECTS 
8.1 
Study Drug Administration 
Details regarding the LP dosing injection procedure will be provided in the Dosing 
Administration Manual.  ISIS 396443 will be administered by dedicated study personnel who are 
unblinded to treatment group; this cannot be any of the key study site personnel (i.e., the 
Principal Investigator, study coordinator, or outcomes assessors).  The Study Drug 
administration will be performed in a dedicated room and the key study personnel and the 
parents will not be present during the procedure to ensure blinding. 
ISIS 396443 will be administered as an intrathecal slow bolus (1-3 minute) LP injection.  
ISIS 396443 will be administered using a ‘spinal anesthesia’ needle and syringe.  A 22G to 25G 
spinal anesthesia needle is recommended, but a 21G may be used if indicated by subject size or 
clinical condition.  The target site for needle insertion is the L3/L4 space, but may be 1 segment 
above or 1-2 segments below this level, if needed.  The volume of the injection is 5 mL; prior to 
the injection 5 mL of CSF fluid is to be collected for analyses.  Depending on institutional 
guidelines, anesthesia or sedation may be used for the LP procedure, following institutional 
procedures.  Subjects will be encouraged to lie flat for 1-hour following dosing, if possible. 
Table 2 outlines the dose, ISIS 396443 concentration, and volume for administration of 
ISIS 396443. 
Table 2 
ISIS 396443 Dose, Concentration, and Injection Volume 
Dose 
(mg) 
Concentration 
(mg/mL) 
Injection Volume 
(mL) 
12 
2.4 
5.0 
 
Prior to each injection on Study Days 1, 29, 85, and 274, 5 mL of CSF fluid is to be collected for 
analyses.  CSF will be used for measurement of ISIS 396443 pharmacokinetic analyses and CSF 
SMN protein concentration.  Extra CSF may be stored for investigation of possible biomarkers 
of SMA disease or the pharmacodynamic effects of ISIS 396443 (e.g., CSF mRNA, CSF protein, 
CSF miRNA panel) or for profiling of drug binding proteins, bioanalytical method validation 
purposes, stability assessments, metabolite assessments, immunogenicity assessments (including 
assay development and validation purposes), or to assess other actions of ISIS 396443 with CSF 
constituents.  CSF analyses and data presentation will be conducted in a blinded manner. 
8.2 
Sham Procedure 
Subjects randomized to the sham-procedure control group will undergo a sham-procedure, rather 
than Study Drug administration, on Study Days 1, 29, 85, and 274.  Details regarding the sham 
procedure will be provided in the Dosing Administration Manual.  The sham procedure will be 
administered by dedicated study personnel who are unblinded to treatment group; this cannot be 
any of the key study site personnel (i.e., the Investigator, study coordinator, or outcomes 
assessors).  The sham procedure will be performed in a dedicated room and the key study 
personel and the parents will not be present during the procedure to ensure blinding. 


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In general, the sham procedure will consist of a small needle prick on the lower back at the 
location where the LP injection is normally made.  The needle will break the skin but no LP 
injection or needle insertion will occur.  The needle prick will be covered with the same bandage 
that is used to cover the LP injection normally, thus simulating the appearance of an LP 
injection.  If anesthesia or sedation is used for the LP procedure in ISIS 396443 treated subjects, 
then in order to maintain the blind, minimal sedation (i.e. a low dose of an anxiolytic) should be 
used for the sham procedure, following institutional procedures.  The study subject will be kept 
in the procedure room for the same amount of time that subjects administered Study Drug are 
kept, thus simulating the time period of a Study Drug administration procedure. 
Study Drug and sham kits will be packaged in a blinded fashion.  Blinded kits for sham 
procedure contain artificial CSF (5.0 mL solution per 6 mL vial) that will not be injected but will 
be used to simulate CSF samples for that subject.  
8.3 
Other Protocol-Required Drugs 
There are no other protocol required drugs. 
8.4 
Other Protocol-Required Procedures 
There are no other protocol-required treatment procedures. 
8.5 
Treatment Precautions 
There are no protocol-required treatment precautions. 
8.6 
Safety Monitoring Rules 
Please refer to the Guidance to Investigator section of the Investigator Brochure. 
8.7 
Stopping Rules 
There are no additional specific stopping rules for this study but the Investigator should discuss 
significant concerns relating to individual subjects with the Medical Monitor and the Sponsor to 
ensure that it is appropriate for the subject to continue Study Drug. 
8.8 
Adjustment of Dose and/or Treatment Schedule 
No adjustment of dose is permitted.  In the event of a concurrent illness that would prevent the 
dosing procedure from being performed safely, an adjustment in the dose schedule may be 
permitted, but must be approved by the Medical Monitor.  In general, each scheduled dose may 
be delayed by up to 4 weeks. 
If a delay from the initial study visit schedule occurs, the Medical Monitor must approve the 
subject-specific make-up schedule in advance.  In any schedule adjustments prescribed by the 
Medical Monitor, dose/sham procedures must occur at least 4 weeks apart with the goal of 
returning the subject to his/her initial study visit schedule.  Any subject whose dosing schedule 
changes as a result of such recommendations from the Medical Monitor (including skipping a 
dose/sham procedure) will still be considered as completing treatment and thus potentially 
eligible to participate in the open-label extension study. 


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8.9 
Discontinuation of Study Treatment 
A subject must permanently discontinue study treatment for any of the following: 
• The subject’s parents/guardians withdraw consent 
• The subject experiences an adverse event that necessitates permanent discontinuation of 
study treatment 
The reason for discontinuation of study treatment must be recorded in the Case Report Form 
(CRF) and source documentation. 
Subjects that discontinue treatment will continue follow-up unless consent is withdrawn 
(Appendix A). 
8.10 
Withdrawal of Subjects from the Study 
Subjects must be withdrawn from the study for any of the following: 
• Withdrawal of consent 
• The subject or the subject’s parents/guardians is/are unwilling or unable to comply with 
the protocol 
• The subject experiences a medical emergency that necessitates unblinding of the 
subject’s treatment assignment 
Other reasons for withdrawal of subjects from the study might include: 
• At the discretion of the Investigator for medical reasons 
• At the discretion of the Investigator or Sponsor for noncompliance 
• Significant protocol deviation 
• Decision by the Investigator or Sponsor 
All efforts will be made to complete and report the observations as thoroughly as possible up to 
the date of withdrawal.  All information, including the reason for withdrawal from Study, must 
be recorded in the CRF. 
Any subject for whom consent to participate in the study is withdrawn will be removed from 
further treatment and study observation immediately upon the date of request.  It should be 
encouraged that these subjects complete the early termination study procedures and observations 
at the time of withdrawal (Appendix A). 
For subjects withdrawn for reasons other than withdrawal of consent every effort should be made 
to complete the early termination study procedures and observations at the time of withdrawal 
(Appendix A). 


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8.11 
Concomitant Therapy and Procedures 
The use of concomitant therapies or procedures defined below must be recorded on the subject’s 
CRF.  AEs related to administration of these therapies or procedures must also be documented on 
the appropriate CRF. 
8.11.1 
Concomitant Therapy 
A concomitant therapy is any non-protocol specified drug or substance (including over-the-
counter medications, herbal medications and vitamin supplements) administered between the 
beginning of screening and last telephone contact or study visit. 
Subject’s parents/guardians should consult with the Site Investigator or qualified designee prior 
to initiating any new medication, including non-prescription compounds or any other non-drug 
therapy. 
Allowed Concomitant Therapy 
Throughout the study, Site Investigators or designated licensed physicians involved in the study 
may prescribe concomitant medications or treatments deemed necessary for adverse events or to 
provide adequate supportive care. 
Disallowed Concomitant Therapy 
Study subjects are prohibited from receiving other experimental agents during the study.  This 
includes marketed agents at experimental doses that are being tested for the treatment of SMA 
(e.g., oral albuterol/salbutamol, riluzole, carnitine, creatine, sodium phenylbutyrate, valproate, 
hydroxyurea). 
8.11.2 
Concomitant Procedures 
A concomitant procedure is any therapeutic intervention (e.g., surgery/biopsy) or diagnostic 
assessment (e.g., blood gas measurement, bacterial cultures) performed between the beginning of 
screening and last telephone contact or study visit. 
9. 
SERIOUS AND NON-SERIOUS ADVERSE EVENT REPORTING  
9.1 
Sponsor Review of Safety Information 
Safety information will be collected, reviewed, and evaluated by the Sponsor in accordance with 
the Safety Management Plan throughout the conduct of the clinical trial. 
9.2 
Regulatory Requirements 
The Sponsor is responsible for regulatory submissions and reporting to the Investigators of SAEs 
including suspected unexpected serious adverse reactions (SUSARs) per the International 
Conference on Harmonization (ICH) guidelines E2A and ICH E6.  Country-specific regulatory 
requirements will be followed in accordance with local country regulations and guidelines. 
IRBs/IECs will be notified of any serious adverse event (SAE) according to applicable 
regulations.  The DSMB will be notified of any SAE as specified in the DSMB charter. 


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9.3 
Definitions 
9.3.1 
Adverse Event 
An adverse event is any unfavorable and unintended sign (including a clinically-significant 
abnormal laboratory finding, for example), symptom, or disease temporally associated with the 
study or use of investigational drug product, whether or not the AE is considered related to the 
investigational drug product. 
9.3.2 
Adverse Reaction and Suspected Adverse Reaction 
An adverse reaction is any adverse event caused by the Study Drug. 
A suspected adverse reaction is any adverse event for which there is a reasonable possibility that 
the drug caused the adverse event.  A suspected adverse reaction implies a lesser degree of 
certainty about causality than an adverse reaction. 
9.3.3 
Serious Adverse Event (SAE) 
A serious adverse event is any adverse event that in the view of either the Investigator or 
Sponsor, meets any of the following criteria: 
• Results in death 
• Is life threatening: that is, poses an immediate risk of death at the time of the event 
An AE or suspected adverse reaction is considered “life-threatening” if, in the view of 
either the Investigator or Sponsor, its occurrence places the subject at immediate risk of 
death.  It does not include an AE or suspected adverse reaction that, had it occurred in a 
more severe form, might have caused death 
• Requires inpatient hospitalization or prolongation of existing hospitalization 
Hospitalization is defined as an admission of greater than 24 hours to a medical facility 
and does not always qualify as an AE 
• Results in a persistent or significant incapacity or substantial disruption of the ability to 
conduct normal life functions 
• Results in congenital anomaly or birth defect in the offspring of the subject (whether the 
subject is male or female) 
• Important medical events that may not result in death, are not life-threatening, or do not 
require hospitalization may also be considered serious when, based upon appropriate 
medical judgment, they may jeopardize the subject and may require medical or surgical 
intervention to prevent one of the outcomes listed in this definition.  Examples of such 
medical events include allergic bronchospasm requiring intensive treatment in an 
emergency room or at home, blood dyscrasias or convulsions that do not result in 
inpatient hospitalization, or the development of drug dependency or drug abuse 


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9.4 
Monitoring and Recording Adverse Events 
Any pre-existing conditions or signs and/or symptoms present in a subject prior to the start of the 
study (i.e., before informed consent) should be recorded as Medical History and not recorded as 
AEs unless the pre-existing condition worsened.  The Investigator should always group signs and 
symptoms into a single term that constitutes a single unifying diagnosis if possible. 
9.4.1 
Serious Adverse Events 
In the interest of subject safety, and in order to fulfill regulatory requirements, all SAEs 
(regardless of their relationship to Study Drug) should be reported to the Sponsor within 
24 hours of the Study Center’s first knowledge of the event.  The collection of SAEs will begin 
after the subject signs the informed consent form and stop at the end of the subject’s follow-up 
period which is defined as the subject’s last visit.  When the Investigator is reporting by 
telephone, it is important to speak to someone in person versus leaving a message.  An Initial 
Serious Adverse Event Form should be completed and a copy should be faxed to the Sponsor or 
designee. 
Detailed information should be actively sought and included on Follow-Up Serious Adverse 
Event Forms as soon as additional information becomes available.  All SAEs will be followed 
until resolution.  SAEs that remain ongoing past the subject’s last protocol-specified follow-up 
visit will be evaluated by the Investigator and Sponsor.  If the Investigator and Sponsor agree the 
subject’s condition is unlikely to resolve, the Investigator and Sponsor will determine the follow-
up requirement. 
9.4.2 
Non-Serious Adverse Events 
The recording of non-serious AEs will begin after the subject signs the informed consent form 
and will stop at the end of the subject’s follow-up period, which is defined as subject’s last visit.  
The Investigator will monitor each subject closely and record all observed or volunteered AEs on 
the Adverse Event Case Report Form. 
9.4.3 
Evaluation of Adverse Events (Serious and Non-Serious) 
The Investigator’s opinion of the following should be documented on the Adverse Event Case 
Report Form. 
9.4.3.1 
Relationship to the Study Drug 
The event’s relationship to the Study Drug is characterized by 1 of the following: 
• Related:  There is clear evidence that the event is related to the use of Study Drug, e.g., 
confirmation by positive re-challenge test 
• Possible:  The event cannot be explained by the subject’s medical condition, concomitant 
therapy, or other causes, and there is a plausible temporal relationship between the event 
and Study Drug administration 
• Unlikely/Remote:  An event for which an alternative explanation is more likely (e.g., 
concomitant medications or ongoing medical conditions) or the temporal relationship to 
Study Drug administration and/or exposure suggests that a causal relationship is unlikely 
(For reporting purposes, Unlikely/Remote will be grouped together with Not Related) 


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• Not Related:  The event can be readily explained by the subject’s underlying medical 
condition, concomitant therapy, or other causes, and therefore, the Investigator believes 
no relationship exists between the event and Study Drug 
9.4.3.2 
Severity 
The event’s severity is characterized by 1 of the following: 
• Mild:  The event is easily tolerated by the subject and does not affect the subject’s usual 
daily activities 
• Moderate:  The event causes the subject more discomfort and interrupts the subject’s 
usual daily activities 
• Severe:  The event is incapacitating and causes considerable interference with the 
subject’s usual daily activities 
If the event is an SAE, then all applicable seriousness criteria must be indicated (criteria listed in 
Section 9.3.3). 
9.4.3.3 
Action Taken with Study Drug 
Action taken with Study Drug due to the event is characterized by 1 of the following: 
• None:  No changes were made to Study Drug administration and dose 
• Permanently Discontinued:  Study drug was discontinued and not restarted 
• Temporarily Interrupted, restarted – same dose:  Dosing was temporarily interrupted 
or delayed due to the AE and restarted at the same dose without unblinding to treatment 
group 
9.4.3.4 
Treatment Given for Adverse Event 
Any treatment (e.g., medications or procedures) given for the AE should be recorded on the 
Adverse Event Case Report Form (treatment should also be recorded on the concomitant 
treatment or ancillary procedures CRF as appropriate). 
9.4.3.5 
Outcome of the Adverse Event 
If the event is a non-serious AE then the event’s outcome is characterized by 1 of the following: 
• AE Persists:  Subject terminates from the trial and the AE continues 
• Recovered:  Subject recovered completely from the AE 
• Became Serious:  The event became serious (the date that the event became serious 
should be recorded as the Resolution Date of that AE and the Onset Date of the 
corresponding SAE) 
• Change in Severity (if applicable):  AE severity changed 
If the event is a SAE then the event’s outcome is characterized by 1 of the following: 


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• Ongoing:  SAE continuing 
• Persists (as non-serious AE):  Subject has not fully recovered but the event no longer 
meets serious criteria and should be captured as an AE on the non-serious AE electronic 
case report form (eCRF) (the SAE resolution date should be entered as the date of onset 
of that AE) 
• Recovered:  Subject recovered completely from the SAE (the date of recovery should be 
entered as the SAE resolution date) 
• Fatal:  Subject died (the date of death should be entered as the SAE resolution date) 
9.5 
Procedures for Handling Special Situations 
9.5.1 
Abnormalities of Laboratory Tests 
Clinically-significant abnormal laboratory test results may, in the opinion of the Investigator, 
constitute or be associated with an AE.  Examples of these include abnormal laboratory results 
that are associated with symptoms, or require treatment, e.g., bleeding due to thrombocytopenia, 
tetany due to hypocalcemia, or cardiac arrhythmias due to hyperkalemia.  Whenever possible, the 
underlying diagnosis should be listed in preference to abnormal laboratory values as AEs.  
Clinically-significant abnormalities will be monitored by the Investigator until the parameter 
returns to its baseline value or until agreement is reached between the Investigator and Medical 
Monitor.  Laboratory abnormalities deemed not clinically-significant (NCS) by the Investigator 
should not be reported as AEs.  Similarly, laboratory abnormalities reported as AEs by the 
Investigator should not be deemed NCS on the laboratory sheet. 
The Investigator is responsible for reviewing and signing all laboratory reports.  The signed 
clinical laboratory reports will serve as source documents. 
9.5.2 
Prescheduled or Elective Procedures or Routinely Scheduled Treatments 
A prescheduled or elective procedure or a routinely scheduled treatment will not be considered 
an SAE, even if the subject is hospitalized; the Study Center must document all of the following: 
• The prescheduled or elective procedure or routinely scheduled treatment was scheduled 
(or was on a waiting list to be scheduled) prior to obtaining the subject’s consent to 
participate in the study 
• The condition that required the prescheduled or elective procedure or routinely scheduled 
treatment was present before and did not worsen or progress in the opinion of the 
Investigator between the subject’s consent to participate in the study and the timing of the 
procedure or treatment 
• The prescheduled or elective procedure or routinely scheduled treatment is the sole 
reason for the intervention or hospital admission 


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9.5.3 
Dosing Errors 
Study Drug errors defined as errors in administration or the administered dose should be 
documented as Protocol Deviations.  A brief description should be provided in the deviation, 
including whether the subject was symptomatic (list symptoms) or asymptomatic. 
Dosing details should be captured on the Dosing CRF. 
Should an overdose occur, the Investigator or designee should contact the Unblinded Medical 
Monitor within 24 hours. 
9.5.4 
Contraception and Pregnancy 
Female subjects that have reached reproductive maturity must have a negative pregnancy test at 
Screening and must not be able to become pregnant for the duration of the study, as described in 
Section 6.3. 
Male subjects must be abstinent during the duration of the study. 
If a subject becomes pregnant or a pregnancy is suspected, or if a male subject makes or believes 
that he has made someone pregnant during the study, then the site staff must be informed 
immediately.  An Initial Pregnancy Form should be submitted to the Sponsor or designee within 
24 hours of first learning of the occurrence of pregnancy.  Follow-up information including 
delivery or termination is reported on Follow-up Pregnancy Forms and reported within 24 hours. 
Payment for all aspects of obstetrical care, child or related care will be the subject’s 
responsibility. 
10. 
STATISTICAL CONSIDERATIONS 
10.1 
Study Endpoints, Subsets, and Covariates 
10.1.1 
Primary Efficacy Endpoint 
• Change from baseline in HFMSE (Hammersmith Functional Motor Scale – Expanded) 
score at 15 months 
10.1.2 
Secondary Efficacy Endpoints 
• Proportion of subjects who achieve a 3-point or greater increase from baseline in 
Hammersmith Functional Motor Scale – Expanded (HFMSE) score at 15 months 
• Proportion of subjects that achieve any new motor milestone at 15 months 
• Number of motor milestones achieved per subject at 15 months 
• Change from baseline in Upper Limb Module Test at 15 months 
• Proportion of subjects that achieve standing alone at 15 months 
• Proportion of subjects that achieve walking with assistance at 15 months 


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10.1.3 
Tertiary Efficacy Endpoints 
• Change from baseline in CSF SMN protein concentration 
• Clinical Global Impression of Change (Investigator and Caregiver assessment) 
• Change from baseline in PedsQL (Pediatric Quality of Life Inventory) 
• Change from baseline in Assessment of Caregiver Experience with Neuromuscular 
Disease (ACEND) 
• Disease-related hospitalizations and adverse events 
10.1.4 
Safety/Tolerability Endpoints 
• Adverse events 
• Vital signs and weight 
• Neurological examinations 
• Physical examinations  
• Clinical laboratory tests (serum chemistry, hematology, urinalysis) 
• Electrocardiograms (ECGs) 
• Use of concomitant medications 
10.1.5 
Pharmacokinetic Endpoints 
• CSF levels of ISIS 396443 
• Plasma levels of ISIS 396443 
10.1.6 
Immunogenicity Endpoint 
• Plasma antibodies to ISIS 396443 
10.2 
Sample Size Considerations 
The sample size for this study was estimated based on limited available natural history data for 
the target population and data from the ISIS 396443-CS1 and ISIS 396443-CS2 clinical studies.  
Seventy (70) patients in the treated group and 35 patients in the control group will give at least 
90% power to detect a 3-point difference between control and treated groups in change on the 
HFMSE with a standard deviation of 4.4, using a 2-sided t-test with an alpha level of 0.05.  The 
sample size was estimated using n-Query.  One hundred seventeen (117) patients enrolled will 
ensure that a small dropout rate will not affect the power of the primary efficacy analysis. 
10.3 
Populations 
Intent to Treat (ITT) Set:  All patients who are randomized and receive at least 1-dose of Study 
Drug/sham procedure. 


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Per-Protocol Set (PPS):  PPS will include the subset of the ITT who complete at least the initial 
3 doses of Study Drug/sham procedures, have baseline and Day 169 efficacy assessments and 
who have no significant protocol deviations that would be expected to affect efficacy 
assessments. 
Safety Set:  All patients who are randomized and receive at least 1-dose of Study Drug/sham 
procedure. 
Pharmacokinetic Population:  All patients who are randomized and for which there is at least 
1 evaluable post-dose/post-sham procedure pharmacokinetic sample. 
10.4 
Definition of Baseline 
The baseline is defined as the last non-missing assessment prior to the first dose of Study Drug. 
10.5 
Interim Analysis 
An interim analysis may take place when all subjects have completed the 6-month assessment 
and at least 39 subjects have completed the 15-month assessment.  At the time of the interim 
analysis, it is expected that approximately 52 subjects would have attended the Month 15 
assessment and all 126 subjects would have had the opportunity to attend the assessment at 
Month 6. 
At the interim analysis, the primary efficacy endpoint, change in HFMSE, will be tested at an 
alpha of 0.02.  For the interim analysis, the ITT Set will be used.  Since the Month 15 endpoint 
values will not be available for most of the patients, missing post-baseline HFMSE data will be 
handled using the multiple imputation method (Schafer 1997; Schafer 1999).  
To control the overall Type I error rate at 0.05 across interim and final analyses for the testing of 
primary and secondary endpoints, a stage-wise hierarchical strategy utilizing independent alpha 
spending functions for primary and secondary endpoints (Glimm et al. 2010) will be applied.  In 
the framework of the stage-wise hierarchical testing, at the final analysis alpha = 0.05 will be 
used in the sequential testing procedure for the secondary endpoints not tested at the interim, as 
detailed in the Statistical Analysis Plan (SAP).  
In the event that the primary endpoint is not statistically significant at the interim, at the final 
analysis, the primary endpoint will be tested at an alpha level determined based upon the 
resampling approach, as detailed in the SAP (Westfall and Young 1993). 
The analysis of safety data for the interim analysis will include all subjects who have received at 
least 1-dose of study treatment as of the targeted clinical cut-off date. 
A DSMB will review the interim analysis results and make recommendations on whether it is 
appropriate for the trial to continue.  During the interim analysis, subjects will continue in the 
study. 
Details of the analysis and controlled access to the unblinded data are contained in the SAP, the 
unblinding plan and the DSMB Charter.  


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10.6 
Planned Methods of Analysis 
Detailed description of the analysis methodology is provided in the SAP. 
Data collected on eCRF, lab data transfers, as well as any outcomes derived from the data, will 
be provided in the patient data listings.  Patient data listings will be presented for all patients 
enrolled into the study. 
Descriptive summary statistics including n, mean, median, standard deviation, standard error, 
interquartile range (25th percentile, 75th percentile), and range (minimum, maximum) for 
continuous variables, and counts and percentages for categorical variables will be used to 
summarize most data by treatment group. 
All primary, secondary and tertiary endpoints will be assessed in the ITT Set and PPS, with the 
former being the basis for the primary efficacy analysis.  All safety assessments will be 
performed on the Safety Set. PK endpoints will be assessed in the PK Set as applicable. 
10.6.1 
Demographic and Baseline Characteristics 
Demographic and baseline characteristics will be summarized using descriptive statistics by 
treatment group.  Patient disposition will be summarized by treatment group.  All patients 
enrolled will be included in a summary of patient disposition. 
10.6.2 
Safety and Tolerability Analysis 
Safety analyses will be conducted in the Safety Set. Treatment duration and amount of Study 
Drug received will be summarized by treatment group. 
All treatment-emergent adverse events and serious adverse events will be summarized for each 
treatment group using the MedDRATM coding system, by system organ class, preferred term, 
relationship to Study Drug, and severity.  Narratives of deaths, serious adverse events, including 
early withdrawals from Study Drug and from study due to adverse events, will also be provided. 
Laboratory tests including chemistry panel, complete blood count with differential, etc., will be 
summarized by study visit for each treatment group.  These safety variables will also be 
presented over time after Study Drug administration, as appropriate.  Vital sign results will be 
presented similarly. 
Physical and neurological examination findings and results from ECG will be listed for review.  
As appropriate, results will also be summarized descriptively for each treatment group.  
Concomitant medication usage for each subject will be listed for review. 
10.6.3 
Efficacy Analysis 
All statistical tests will be 2-sided with a Type 1 error rate of 5%, unless otherwise specified. 
The primary analysis of the primary endpoint is to compare the change from baseline in HFMSE 
score at Month 15 between treatment groups using the ITT Set.  The data will be analyzed using 
an analysis of covariance (ANCOVA) model with treatment group as a factor and age at 
screening and baseline HFMSE score as covariates.  The primary efficacy analysis will take 


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place after all patients have completed the Day 456/ET visit and the database has been locked.  
Missing data will be handled by the multiple imputation procedure. 
Several sensitivity analyses will also be conducted; the details of these analyses will be outlined 
in the SAP. 
In the framework of the stage wise hierarchical testing, since the secondary endpoints will not be 
tested at the interim (i.e., no alpha spending), at the final analysis alpha = 0.05 will be used in the 
sequential testing.  
The secondary endpoints will be tested in the following order: 
• Proportion of subjects with a 3-point or greater increase in HFMSE 
• Proportion of subjects achieving any new motor milestones at 15 months 
• Number of motor milestones achieved at 15 months 
• Change from baseline in upper limb module test at 15 months 
• Proportion of subjects achieving standing alone at 15 months 
• Proportion of subjects achieving walking with assistance at 15 months 
The primary analysis of each secondary endpoint will be based on the ITT Set.  Analyses based 
on the PPS are considered sensitivity analyses.  Missing data will be handled by the multiple 
imputation procedure.  Additional details of these analyses will be outlined in the SAP. 
10.6.4 
Pharmacokinetic Analysis 
Plasma pharmacokinetic parameters and ISIS 396443 concentrations in plasma and CSF for the 
Pharmacokinetic population will be summarized using descriptive statistics and, where 
warranted, presented graphically. 
11. 
INVESTIGATOR’S REGULATORY OBLIGATIONS 
11.1 
Informed Consent/Assent 
The written informed consent and assent documents should be prepared in the language(s) of the 
potential subject population, based on an English version provided by the Sponsor and should be 
easy to understand. 
Before a subject’s participation in the trial, the Investigator is responsible for obtaining written 
informed consent from the parent or legal guardian and, in cases where institutional guidelines 
and the subject’s age dictate, informed assent from the subject, after adequate explanation of the 
aims, methods, anticipated benefits, and potential hazards of the study and before any protocol-
specific screening procedures or any Study Drugs are administered.  Sufficient time must be 
given to consider whether to participate in the study. 
The acquisition of informed consent/assent and the parent/legal guardian’s/subject’s agreement 
or refusal of his/her notification of the primary care physician should be documented in the 
subject’s medical records, and the informed consent/assent form(s) should be signed and 


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personally dated by the parent/legal guardian/subject and by the study person who conducted the 
informed consent/assent discussion.  The original signed informed consent/assent form(s) should 
be retained in the Study Master File and in any other locations required by institutional policy, 
and a copy of the signed consent/assent form(s) should be provided to the parent or guardian. 
11.2 
Ethical Conduct of the Study 
The Guidelines of the World Medical Association (WMA) Declaration of Helsinki dated 
October 2002 the applicable regulations and guidelines of current Good Clinical Practice (GCP) 
as well as the demands of national drug and data protection laws and other applicable regulatory 
requirements will be strictly followed. 
11.3 
Institutional Review Board/Institutional Ethics Committee/Research Ethics Board 
A copy of the protocol, proposed informed consent form, proposed informed assent form (if 
applicable) other written subject information, and any proposed advertising material must be 
submitted to the IRB/IEC for written approval.  A copy of the written approval of the protocol 
and informed consent/assent forms must be received by the Sponsor before recruitment of 
subjects into the study and shipment of Study Drug.  A copy of the written approval of any other 
items/materials that must be approved by the Study Center or IRB/IEC must also be received by 
the Sponsor before recruitment of subjects into the study and shipment of Study Drug.  The 
Investigator’s Brochure must be submitted to the IRB/IEC for acknowledgement. 
The Investigator must submit to and, where necessary, obtain approval from the IRB/IEC for all 
subsequent protocol amendments and changes to the informed consent/assent documents.  The 
Investigator should notify the IRB/IEC of deviations from the protocol in accordance with ICH 
GCP Section 4.5.2.  The Investigator should also notify the IRB/IEC of serious adverse events 
occurring at the Study Center and other adverse event reports received from the Sponsor, in 
accordance with local procedures. 
The Investigator will be responsible for obtaining annual IRB/IEC approval/renewal throughout 
the duration of the study.  Copies of the Investigator’s reports, all IRB/IEC submissions and the 
IRB/IEC continuance of approval must be sent to the Sponsor. 
11.4 
Subject Confidentiality 
The Investigator must ensure that the subject’s confidentiality is maintained.  On the CRFs or 
other documents submitted to the Sponsor, subjects should be identified by unique, anonymous 
initials and a subject study number only.  Documents that are not for submission to the Sponsor 
(e.g., signed informed consent/assent forms) should be kept in strict confidence by the 
Investigator. 
In compliance with federal and local regulations/ICH GCP Guidelines, it is required that the 
Investigator and institution permit authorized representatives of the company, of the regulatory 
agency(s), and the IRB/IEC direct access to review the subject’s original medical records for 
verification of study-related procedures and data.  Direct access includes examining, analyzing, 
verifying, and reproducing any records and reports that are important to the evaluation of the 
study.  The Investigator is obligated to inform and obtain the consent of the subject’s parent or 
guardian to permit named representatives to have access to his/her study-related records without 
violating the confidentiality of the subject. 


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12. 
ADMINISTRATIVE AND LEGAL OBLIGATIONS 
12.1 
Protocol Amendments 
Agreement from the Investigator must be obtained for all protocol amendments and amendments 
to the informed consent/assent documents.  The regulatory authority and IRB/IEC must be 
informed of all amendments and give approval for any amendments likely to affect the safety of 
the subjects or the conduct of the trial.  The Investigator must send a copy of the approval letter 
from the IRB/IEC to the Sponsor. 
12.2 
Study Termination 
The Sponsor reserves the right to terminate the study.  The Investigator reserves the right to 
terminate their participation in the study, according to the terms of the site contract.  The 
Investigator/Sponsor should notify the IRB/IEC in writing of the trial’s completion or early 
termination and send a copy of the termination to the Sponsor. 
12.3 
Study Documentation and Storage 
The Investigator should ensure that all appropriately qualified persons to whom he/she has 
delegated trial duties are recorded on a Sponsor-approved Delegation of Site Responsibilities 
Form. 
Source documents are original documents, data, and records from which the subject’s CRF data 
are obtained.  These include but are not limited to hospital records, clinical and office charts, 
laboratory and pharmacy records, and correspondence.  In this study, CRFs may not be used as 
source documents. 
The Investigator and Study Center staff is responsible for maintaining a comprehensive and 
centralized filing system of all study-related (essential) documentation in accordance with 
Section 8 of the ICH Guidelines (E6), suitable for inspection at any time by representatives from 
the Sponsor and/or applicable regulatory authorities.  Elements should include: 
• Subject files containing completed CRFs, informed consents/assents, and supporting 
copies of source documentation 
• Study files containing the protocol with all amendments, Investigator’s Brochure, copies 
of pre-study documentation and all correspondence to and from the IRB and the Sponsor 
• If drug supplies are maintained at the Study Center, proof of receipt, Study Drug Product 
Accountability Record, Return of Study Drug Product for Destruction, and all drug-
related correspondence 
In addition, all original source documents supporting entries in the CRFs must be maintained and 
be readily available. 
No study document should be destroyed without prior written agreement between the Sponsor 
and the Investigator.  Should the Investigator wish to assign the study records to another party or 
move them to another location, he/she must notify the Sponsor. 


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12.4 
Study Monitoring 
The Sponsor representative and regulatory authority inspectors are responsible for contacting and 
visiting the Investigator for the purpose of inspecting the facilities and, upon request, inspecting 
the various records of the trial (e.g., CRFs and other pertinent data) provided that subject 
confidentiality is respected. 
The Sponsor monitor is responsible for inspecting the CRFs at regular intervals throughout the 
study to verify adherence to the protocol; completeness, accuracy, and consistency of the data; 
and adherence to local regulations on the conduct of clinical research.  The monitor should have 
access to subject medical records and other study-related records needed to verify the entries on 
the CRFs. 
The Investigator agrees to cooperate with the monitor to ensure that any problems detected in the 
course of these monitoring visits, including delays in completing CRFs, are resolved. 
In accordance with ICH GCP and the Sponsor’s audit plans, this study may be selected for audit 
by representatives from the Sponsor’s Clinical Quality Assurance Department.  Inspection of 
Study Center facilities (e.g., pharmacy, drug storage areas, laboratories) and review of study-
related records will occur to evaluate the trial conduct and compliance with the protocol, ICH 
GCP, and applicable regulatory requirements. 
To ensure the quality of clinical data a clinical data management review will be performed on 
subject data received by the Sponsor.  During this review, subject data will be checked for 
consistency, omissions, and any apparent discrepancies.  In addition, the data will be reviewed 
for adherence to the protocol and GCP.  To resolve any questions arising from the clinical data 
management review process, data queries and/or Study Center notifications will be sent to the 
Study Center for completion and return to Sponsor. 
The Principal Investigator will sign and date the indicated places on the CRF.  These signatures 
will indicate that the Principal Investigator inspected or reviewed the data on the CRF, the data 
queries, and the Study Center notifications, and agrees with the content. 
12.5 
Language 
CRFs must be completed in English.  Generic names for concomitant medications should be 
recorded in English if possible, unless it is a combination drug, then record the trade name in 
English. 
All written information and other material to be used by subjects and investigative staff must use 
vocabulary and language that are clearly understood. 
12.6 
Compensation for Injury 
The Sponsor maintains appropriate insurance coverage for clinical trials and will follow 
applicable local compensation laws.  Subjects will be treated and/or compensated for any study-
related illness/injury in accordance with the information provided in the Compensation for Injury 
section of the Informed Consent document. 
 


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13. 
REFERENCES 
Cho S and Dreyfuss G. A degron created by SMN2 Exon 7 skipping is a principal contributor to spinal muscular 
atrophy severity. Genes Dev 2010; 24: 438-442. 
Coovert DD, Le TT, McAndrew PE, et al. The survival motor neuron protein in spinal muscular atrophy. Hum Mol 
Genet 1997; 6: 1205-1214. 
Feldkotter M, Schwarzer V, Wirth R, et al. Quantitative analyses of SMN1 and SMN2 based on real-time light 
cycler PCR: fast and highly reliable carrier testing and prediction of severity of spinal muscular atrophy. Am J Hum 
Genet 2002; 70: 358-368. 
Geary RS, Yu RZ, Watanabe T, et al. Pharmacokinetics of a tumor necrosis factor-α phosphorothioate 2′-O-(2-
Methoxyethyl) modified antisense oligonucleotide: comparison across species. Drug Metab Disp 2003; 31: 
1419-1428. 
Glimm E, Maurer W, Bretz F. Hierarchical testing of multiple endpoints in group-sequential trials. Stat Med 2010; 
29 (2): 219-228. 
Helmken C, Hofmann Y, Schoenen F, et al. Evidence for a modifying pathway in SMA discordant families: reduced 
SMN level decreases the amount of its interacting partner and Htra2-beta1. Hum Genet 2003; 114: 11-21. 
Henry S, Stecker K, Brooks D, et al. Chemically modified oligonucleotides exhibit decreased immune stimulation in 
mice. J Pharmacol Exp Ther 2000; 292: 468-479. 
Hua Y, Vickers TA, Baker BF, et al. Enhancement of SMN2 Exon 7 inclusion by antisense oligonucleotides 
targeting the exon. PLoS Biol 2007; 5: e73. 
Hua Y, Vickers TA, Okunola HL, et al. Antisense masking of an HnRNP A1/A2 intronic splicing silencer corrects 
SMN2 splicing in transgenic mice. Am J Hum Genet 2008; 82: 834-848. Epub 2008 Mar 27. 
Iannaccone ST, Hynan LS, Morton A, et al; the AmSMART Group. The PedsQL in pediatric patients with spinal 
muscular atrophy: feasibility, reliability, and validity of the pediatric quality of life inventory generic core scales and 
neuromuscular module. Neuromuscul Disord 2009; 19: 805-812. 
Keren H, Lev-Maor G, Ast G. Alternative splicing and evolution: diversification, exon definition and function. 
Nat.Rev.Genet 2010; 11: 345-355. 
Le TT, Pham LT, Butchbach ME, et al. SMNΔ7, the major product of the centromeric survival motor neuron 
(SMN2) gene, extends survival in mice with spinal muscular atrophy and associates with full-length SMN. Hum 
Mol Genet 2005; 14: 845-857. 
Lefebvre S, Bürglen L, Reboullet S, et al. Identification and characterization of a spinal muscular atrophy-
determining gene. Cell 1995; 80: 155-165. 
Lefebvre S, Burlet P, Liu Q, et al. Correlation between severity and SMN protein level in spinal muscular atrophy. 
Nat Genet 1997; 16: 265-269. 
Main M, Kairon H, Mercuri E, Muntoni F. The Hammersmith functional motor scale for children with spinal 
muscular atrophy: a scale to test ability and monitor progress in children with limited ambulation. Eur J Paediatr 
Neurol 2003; 7(4): 155-159. 
Matsumoto H, Clayton-Krasinski DA, Klinge SA, et al. Development and initial validation of the assessment of 
caregiver experience with neuromuscular disease. J Pediatr Orthop 2011; 31: 284-292. 
Mazzone E, Bianco F, Martinelli D, et al. Assessing upper limb function in nonambulant SMA patients: 
development of a new module. Neuromuscul Disord 2011; 21: 406-412. 
McKay RA, Miraglia LJ, Cummins LL, et al. Characterization of a potent and specific class of antisense 
oligonucleotide inhibitor of human protein kinase C-α expression. J Bio Chem 1999; 274: 1715-1722. 
O’Hagen JM, Glanzman AM, McDermott MP, et al. An expanded version of the hammersmith functional motor 
scale for SMA II and III patients. Neuromuscular Disorders 2007; 17: 693-697. 


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Passini MA, Bu J, Richards AM, et al. Antisense oligonucleotides delivered to the mouse CNS ameliorate symptoms 
of severe spinal muscular atrophy. Science Trans Med 2011; 3: 1-12. 
Prior TW, Swoboda KJ, Scott HD, Hejmanowski AQ. Homozygous SMN1 deletions in unaffected family members 
and modification of the phenotype by SMN2 gene. Am J Med Genet 2004; 130A: 307-310. 
Schafer JL. Analysis of incomplete multivariate data. Boca Raton, FL. Chapman and Hall/CRC: 1997. 
Schafer JL. Multiple Imputation: A Primer. Statistical Methods in Medical Research 1999; 8: 3-15. 
Varni JW, Seid M, Rode CA. Measurement model for the pediatric quality of life inventory. Medical Care 1999; 37: 
126-139. 
Westfall PH and Young SS. Resampling-based multiple testing. New York; Wiley: 1993. 
WHO Multicentre Growth Reference Study Group. Assessment of sex differences and heterogeneity in motor 
milestone attainment among populations in the WHO Multicentre Growth Reference Study. Acta Pædiatrica, 2006; 
Suppl 450: 66/75. 
Wijnhoven T, de Onis M, Onyango A, et al. Assessment of gross motor development in the WHO Multicentre 
Growth Reference Study. Food Nutr Bull 2004; 21: S37-45. 
Wirth B, Brichta L, Schrank B, et al. Mildly affected patients with spinal muscular atrophy are partially protected by 
an increased SMN2 copy number. Hum Genet. 2006; 119(4): 422-428. 
 
 
 


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14. 
APPENDICES 
 
 
 
 
 


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Appendix A 
Schedule of Procedures 
 


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Appendix A Schedule of Procedures 
Subjects will also be monitored through phone contact on Study Days 8, 56, 113, 141, 204, 239, 302, 330, 393, 421 (all ± 2 days)9 
Study Period 
Screen 
Treatment/Follow-up 
Study Day 
D -28 
to 
D -1 
D1 
D2
D29 ( ± 1D) 
D30
D85 ( ± 2D) 
D86
D92
( ± 1D)
D169
( ± 2D) 
D274 ( ± 7D) 
D275
D365
( ± 7D) 
and 
D456
(+ 7D) 
and 
Early 
Term/ 
EODBP
Pre- 
dose 
LP/
SP 
Post-
dose
Pre-
dose
LP/
SP
Post-
dose
Pre-
dose
LP/
SP 
Post- 
dose 
Pre-
dose
LP/
SP
Post- 
dose
Informed Consent 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Inclusion/Exclusion 
Criteria 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Medical History 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Screening X-ray 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Urine Pregnancy 
Test11 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
X14 
SMN2 copy Number12 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Study Drug 
Injection/Sham 
Procedure 
 
 
X 
 
 
 
X7 
 
 
 
X7 
 
 
 
 
 
X7 
 
 
 
In-Patient Stay 
(24 hours) 
 
 
 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Vital Signs1 
X 
X 
 
4X2 
X3
X 
 
4X2 
X 
X 
 
4X2 
X 
X 
X 
X 
 
4X2 
X 
X 
Weight 
X 
X 
 
 
 
X 
 
 
 
X 
 
 
 
X 
X 
X 
 
 
 
X 
Height/ulnar length 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
X14 
Physical Examination 
X 
X 
 
 
 
X 
 
 
 
X 
 
 
 
X 
X 
X 
 
 
 
X 
Neurological 
Examination 
X 
X 
 
X4 
X3 
X 
 
X4 
X 
X 
 
X4 
X 
X 
X 
X 
 
X4 
X 
X 
ECG 
X 
 
 
 
X 
 
 
X 
 
 
 
 
 
X 
 
 
 
 
 
X14 
Safety Labs5 
X 
X 
 
 
X 
X 
 
 
 
X 
 
 
 
 
X 
X 
 
 
 
X14 
Coagulation Labs 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Immunogenicity  
 
X 
 
 
 
X 
 
 
 
X 
 
 
 
 
X 
X 
 
 
 
X14 


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Appendix A Schedule of Procedures Continued 
Study Period 
Screen 
Treatment/Follow-up 
Study Day 
D -28 
to 
D -1 
D1 
D2
D29 ( ± 1D) 
D30
D85 ( ± 2D) 
D86
D92
( ± 1D)
D169
( ± 2D)
D274 ( ± 7D) 
D275
D365
( ± 7D) 
and 
D456
(+ 7D) 
and 
Early 
Term/ 
EODBP
Pre- 
dose 
LP/
SP 
Post-
dose
Pre-
dose
LP/
SP
Post-
dose
Pre-
dose
LP/
SP 
Post- 
dose 
Pre-
dose
LP/
SP
Post-
dose
CSF PK8 
 
X 
 
 
 
X 
 
 
 
X 
 
 
 
 
 
X 
 
 
 
 
CSF SMN Protein 
 
X 
 
 
 
X 
 
 
 
X 
 
 
 
 
 
X 
 
 
 
 
Plasma PK8 
 
X 
 
3X 
X 
X 
 
 
 
X 
 
X 
 
 
X 
X 
 
 
 
X14 
HFMSE 
X10 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
WHO Motor Milestones 
X6, 10 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
Upper Limb 
X6, 10 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
PedsQL 
X6 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
ACEND 
X6 
 
 
 
 
 
 
 
 
 
 
 
 
 
X 
 
 
 
 
X14 
CGI 
 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
Con Med Recording9 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Adverse Event 
Collection9 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
1 
Resting blood pressure, pulse, respiratory rate, and temperature 
2 
Vital signs performed 1, 2, 4, 6 hours after dosing 
3 
Conducted within 20-24 hours after dosing 
4 
Neurological exams at 5 hours after dosing 
5 
Serum chemistry, hematology, urinalysis panels (Appendix B for analytes) 
6 
Efficacy assessments (with the exception of HFMSE) do not form part of the screening assessment or inclusion/exclusion criteria but are baseline 
measurements taken during the screening phase of the study 
7 
Overnight stay is optional on Day 29, Day 85, and Day 274  
8 
Refer to Appendix C for PK sampling schedule 
9 
At telephone contact, changes in concomitant medications and adverse events will be recorded  
10 To be performed 2 times during the screening period  
11 Urine pregnancy test performed for females of child-bearing potential, if positive to be confirmed by local serum test 
12 Only for those subjects who do not have documented evidence of SMN copy number from Athena Diagnostics 
13 These assessments may be performed up to 7 days prior to dosing, if necessary 
14 Assessed on Day 456 only 


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Appendix B 
Laboratory Analytes 
 
 
 


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Appendix B Laboratory Analytes 
CLINICAL SAFETY ASSESSMENTS 
(minimum requirements) 
OTHER ASSESSMENTS 
Clinical Chemistry 
Sodium 
Potassium 
Chloride 
Total protein 
Albumin 
Calcium 
Phosphorus 
Bicarbonate 
Glucose 
BUN 
Creatinine 
Cystatin C 
Total serum Bilirubin 
Alkaline phosphatase 
AST (SGOT) 
ALT (SGPT) 
CPK 
 
Coagulation 
aPTT 
PT 
INR 
Urinalysis  
Specific gravity 
pH 
Protein 
Glucose 
Ketones 
Bilirubin 
Blood 
Red blood cells 
White blood cells 
Epithelial cells 
Bacteria 
Casts 
Crystals 
 
Hematology 
Red blood cells 
Hemoglobin 
Hematocrit 
Platelets 
White blood cells 
WBC Differential 
• 
(% and absolute) 
• 
Neutrophils 
• 
Eosinophils 
• 
Basophils 
• 
Lymphocytes 
• 
Monocytes 
Pregnancy 
Urine hCG 
 
PK* 
Plasma ISIS 396443 levels 
CSF ISIS 396443 levels 
 
PD 
CSF SMN protein levels 
 
Immunogenicity Evaluation 
ISIS 396443 plasma Abs 
 
SMN Genetics 
SMN2 Copy Number 
* 
Any of the collected PK plasma and CSF samples from the study patients may also be used for investigation of 
possible biomarkers of SMA disease or the pharmacodynamic effects of ISIS 396443 (e.g., CSF mRNA, CSF 
protein, CSF miRNA panel) or for profiling of drug binding proteins, bioanalytical method validation purposes, 
stability assessments, metabolite assessments, immunogenicity assessments (including assay development and 
validation purposes), or to assess other actions of ISIS 396443 with plasma and CSF constituents. 
 
 


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Appendix C 
Pharmacokinetic Sampling Schedule 
 
 
 
 


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Appendix C Pharmacokinetic Sampling Schedule 
Treatment Period 
Study Day 
Timepoints 
Blood 
Collection  
CSF Collection  
Multiple Dose: 
LP Injection 
D1 
Pre-dose 
0.35 mL 
0.5 mL 
2 hr 
0.35  mL 
NA 
4 hr 
0.35  mL 
NA 
8 hr 
0.35  mL 
NA 
D2 
24 hr 
0.35  mL 
NA 
D29 
Pre-dose 
0.35  mL 
0.5 mL 
D85 
Pre-dose 
0.35  mL 
0.5 mL 
4 hr 
0.35  mL 
NA 
D169 
Anytime 
0.35  mL 
NA 
D274 
Pre-dose 
0.35  mL 
0.5 mL 
D456 
Anytime 
0.35  mL 
NA 
NA Not applicable (No Collection Scheduled) 
Details on sampling, preparation, and shipment are included in the study laboratory manual. 
Any of the collected PK plasma and CSF samples from the study patients may also be used for investigation of 
possible biomarkers of SMA disease or the pharmacodynamic effects of ISIS 396443 (e.g., CSF mRNA, CSF protein, 
CSF miRNA panel) or for profiling of drug binding proteins, bioanalytical method validation purposes, stability 
assessments, metabolite assessments, immunogenicity assessments (including assay development and validation 
purposes), or to assess other actions of ISIS 396443 with plasma and CSF constituents. 


I SI S 3 9 6 4 4 3 -C S 4  
C O N FI D E N TI A L  
 
Pr ot oc ol  
 
1 5 J ul y 2 0 1 6 
 
1  
Err at u m 
 
 
Pr ot oc ol N u m ber:  
I SI S 3 9 6 4 4 3-C S 4 
Pr ot oc ol Title:  
A P hase 3, Ra n d o mize d, D o u ble- bli n d, S ha m- Pr oce d ure C o ntr olle d St u d y 
t o Assess t he Cli nical Efficac y a n d Safet y of I SI S 3 9 6 4 4 3 A d mi nistere d 
I ntr at hecall y i n Patie nts wit h Later - o nset S pi nal M usc ular Atr o p h y 
A me n d me nt:  
1 5 J ul y 2 0 1 6 
 
I n cli nical pr ot oc ol I SI S 3 9 6 4 4 3- C S 4 A me n d me nt 2, A p pe n di x A ( Sc he d ule of Pr oce d ures), 
prese nts i n t he ta ble hea di n g Da y 4 5 6 visit as + 7 D.  Da y 4 5 6 s h o ul d ha ve prese nte d as  ± 7 D 
(see A p p e n di x A  i n t his Errat u m).  T his is a n a d mi nistrati ve err or o nl y.  
 
 
 
 
1 5 J ul y 2 0 1 6 
 
Date ( D D M o nt h Y Y Y Y)  
Na me ( ple as e pri nt) 
 
Title  
 
 
P P D
 
P P D


ISIS 396443-CS4 
CONFIDENTIAL 
 
Protocol 
 
15 July 2016 
 
2 
Appendix A Schedule of Procedures 
Subjects will also be monitored through phone contact on Study Days 8, 56, 113, 141, 204, 239, 302, 330, 393, 421 (all ± 2 days)9 
Study Period 
Screen 
Treatment/Follow-up 
Study Day 
D -28 
to 
D -1 
D1 
D2 
D29 ( ± 1D) 
D30 
D85 ( ± 2D) 
D86 
D92 
( ± 1D) 
D169 
( ± 2D)  
D274 ( ± 7D) 
D275 
D365 
( ± 7D) 
and 
D456 
(±+ 7D) 
and 
Early 
Term/ 
EODBP 
Pre- 
dose 
LP/ 
SP 
Post- 
dose 
Pre- 
dose 
LP/ 
SP 
Post- 
dose 
Pre- 
dose 
LP/ 
SP 
Post- 
dose 
Pre- 
dose 
LP/ 
SP 
Post- 
dose 
Informed Consent 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Inclusion/Exclusion 
Criteria 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Medical History 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Screening X-ray 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Urine Pregnancy 
Test11 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
X14 
SMN2 copy Number12 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Study Drug 
Injection/Sham 
Procedure 
 
 
X 
 
 
 
X7 
 
 
 
X7 
 
 
 
 
 
X7 
 
 
 
In-Patient Stay 
(24 hours) 
 
 
 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Vital Signs1 
X 
X 
 
4X2 
X3 
X 
 
4X2 
X 
X 
 
4X2 
X 
X 
X 
X 
 
4X2 
X 
X 
Weight 
X 
X 
 
 
 
X 
 
 
 
X 
 
 
 
X 
X 
X 
 
 
 
X 
Height/ulnar length 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
X14 
Physical Examination 
X 
X 
 
 
 
X 
 
 
 
X 
 
 
 
X 
X 
X 
 
 
 
X 
Neurological 
Examination 
X 
X 
 
X4 
X3 
X 
 
X4 
X 
X 
 
X4 
X 
X 
X 
X 
 
X4 
X 
X 
ECG 
X 
 
 
 
X 
 
 
X 
 
 
 
 
 
X 
 
 
 
 
 
X14 
Safety Labs5 
X 
X 
 
 
X 
X 
 
 
 
X 
 
 
 
 
X 
X 
 
 
 
X14 
Coagulation Labs 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Immunogenicity  
 
X 
 
 
 
X 
 
 
 
X 
 
 
 
 
X 
X 
 
 
 
X14 


ISIS 396443-CS4 
CONFIDENTIAL 
 
Protocol 
 
15 July 2016 
 
3 
Appendix A Schedule of Procedures Continued 
Study Period 
Screen 
Treatment/Follow-up 
Study Day 
D -28 
to 
D -1 
D1 
D2 
D29 ( ± 1D) 
D30 
D85 ( ± 2D) 
D86 D92 
( ± 1D) 
D169 
( ± 2D) 
D274 ( ± 7D) 
D275 
D365 
( ± 7D) 
and 
D456 
(±+ 7D) 
and 
Early 
Term/ 
EODBP 
Pre- 
dose 
LP/ 
SP 
Post- 
dosD
ay 
456e 
Pre- 
dose 
LP/ 
SP 
Post- 
dose 
Pre- 
dose 
LP/ 
SP 
Post- 
dose 
Pre- 
dose 
LP/ 
SP 
Post- 
dose 
CSF PK8 
 
X 
 
 
 
X 
 
 
 
X 
 
 
 
 
 
X 
 
 
 
 
CSF SMN Protein 
 
X 
 
 
 
X 
 
 
 
X 
 
 
 
 
 
X 
 
 
 
 
Plasma PK8 
 
X 
 
3X 
X 
X 
 
 
 
X 
 
X 
 
 
X 
X 
 
 
 
X14 
HFMSE 
X10 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
WHO Motor Milestones 
X6, 10 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
Upper Limb 
X6, 10 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
PedsQL 
X6 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
ACEND 
X6 
 
 
 
 
 
 
 
 
 
 
 
 
 
X 
 
 
 
 
X14 
CGI 
 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
Con Med Recording9 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Adverse Event 
Collection9 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
1 
Resting blood pressure, pulse, respiratory rate, and temperature 
2 
Vital signs performed 1, 2, 4, 6 hours after dosing 
3 
Conducted within 20-24 hours after dosing 
4 
Neurological exams at 5 hours after dosing 
5 
Serum chemistry, hematology, urinalysis panels (Appendix B for analytes) 
6 
Efficacy assessments (with the exception of HFMSE) do not form part of the screening assessment or inclusion/exclusion criteria but are baseline 
measurements taken during the screening phase of the study 
7 
Overnight stay is optional on Day 29, Day 85, and Day 274  
8 
Refer to Appendix C for PK sampling schedule 
9 
At telephone contact, changes in concomitant medications and adverse events will be recorded  
10 To be performed 2 times during the screening period  
11 Urine pregnancy test performed for females of child-bearing potential, if positive to be confirmed by local serum test 
12 Only for those subjects who do not have documented evidence of SMN copy number from Athena Diagnostics 
13 These assessments may be performed up to 7 days prior to dosing, if necessary 
14 Assessed on Day 456 only 


 
 
 
 
ISIS PHARMACEUTICALS, INC. 
 
 
ISIS 396443-CS4 
 
A Phase 3, Randomized, Double-blind, Sham-Procedure Controlled 
Study to Assess the Clinical Efficacy and Safety of ISIS 396443 
Administered Intrathecally in Patients with Later-onset Spinal 
Muscular Atrophy 
 
Amendment 1 - 26 September 2014 
EudraCT No: 2014-001947-18 
 
 
 
 
Sponsor: 
Isis Pharmaceuticals, Inc. 
2855 Gazelle Court 
Carlsbad, CA  92010 


I SI S 3 9 6 4 4 3- C S 4 
Pr ot o c ol 
C O N FI D E N TI A L 
I SI S 3 9 6 4 4 3- C S 4 
A m e n d m e nt I 
2 6 S e pt e m b e r 2 0 14 
A P h as e 3, R a n d o mi z e d, D o u bl e- bli n d, S h a m- Pr o c e d ur e C o ntr oll e d 
St u d y t o Assess t h e Cli ni c al Effi c a c y a n d S af et y of I SI S 3 9 6 4 4 3 
A d mi nist er e d I ntr at h e c all y i n P ati e nts wit h L at er- o ns et S pi n al 
M us c ul ar Atr o p h y 
Pr ot o c ol A m e n d m e nt 1- 2 6 S e pt e m b er 2 0 1 4 
Pr ot o c ol Hist or y: 
Ori gi n al Pr ot oc ol: 
1 7 J ul y 2 0 1 4 
S p o ns or: 
Isis P h at m a c e uti c als, I nc. 
2 8 5 5 G a z ell e C o urt 
C ar ls b a d, C A 9 2 0 1 0 
P P D
2 


I SI S 3 9 6 4 4 3 -C S 4  
C O N FI D E N TI A L  
A me n d me nt 1  
Pr ot oc ol  
 
2 6  Se pte m ber 2 0 1 4  
 
3
 
 
I SI S 3 9 6 4 4 3  
Isis Pr ot o c ol N u m ber I SI S 3 9 6 4 4 3-C S 4 
Pr ot oc ol  A me n d me nt 1  
 
Cli nic al P h ase:   3 
A P h ase 3, R a n d o mi ze d, D o u ble -bli n d, S h a m -Pr oce d ure C o ntr olle d 
St u d y t o Assess t he Cli nic al Effic a c y a n d S afet y of I SI S 3 9 6 4 4 3  
A d mi nistere d I ntr at hec all y i n P ati e nts wit h L ater -o nset S pi n al 
M usc ul ar Atr o p h y  
 
Trial S p o ns or:  
Isis P har mace uticals,  I nc. 
2 8 5 5 Gazelle C o urt  
Carls ba d, C A  9 2 0 1 0  
P h o ne:  + 0 1 7 6 0 9 3 1 9 2 0 0  
Fa x:  
+ 0 1 7 6 0 6 0 3 2 7 0 0  
Ke y S p o ns or C o ntact:  
 
2 8 5 5 Gazelle C o urt  
Carls ba d, C A  9 2 0 1 0  
P h o ne:  + 
 
Fa x:  
+ 
 
 
 
Date:  
2 6  Se pte m ber  2 0 1 4  
 
 
C o nfi de nti alit y St ate me nt  
P P D
T his d oc u me nt c o ntai ns c o nfi de ntial i nf or mati o n of Isis P har mace uticals, I nc. t hat m ust n ot be 
discl ose d t o a n y o n e ot her t ha n t he reci pie nt st u d y staff a n d me m bers of t he i nstit uti o nal re vie w 
b oar d or a u t h orize d re gul at or y a ge n cies.  T his i nf or mati o n ca n n ot be use d f or a n y p ur p ose ot h er 
t ha n t he e val uati o n or c o n d uct of t he cli nical i n vesti gati o n wit h o ut t he pri or writte n c o nse nt of 
Isis P har mace uticals, I nc. 
P P D
P P D


ISIS 396443-CS4 
CONFIDENTIAL
Amendment 1
Protocol 
26 September 2014
 
4 
Protocol Signature Page 
 
Protocol Number: 
ISIS 396443-CS4 
Protocol Title: 
A Phase 3, Randomized, Double-blind, Sham-Procedure Controlled Study 
to Assess the Clinical Efficacy and Safety of ISIS 396443 Administered 
Intrathecally in Patients with Later-onset Spinal Muscular Atrophy 
Amendment: 
1 
Date: 
26 September 2014 
 
I hereby acknowledge that I have read and understand the attached clinical protocol, entitled “A 
Phase 3, Randomized, Double-blind, Sham-Procedure Controlled Study to Assess the Clinical 
Efficacy and Safety of ISIS 396443 Administered Intrathecally in Patients with Later-onset 
Spinal Muscular Atrophy”, dated 26 September 2014, and agree to conduct the study as 
described herein. 
I agree to comply with the International Conference on Harmonization Tripartite Guideline on 
Good Clinical Practice (E6). 
I agree to ensure that the confidential information contained in this document will not be used for 
any purpose other than the evaluation or conduct of the clinical investigation without the prior 
written consent of Isis Pharmaceuticals, Inc.  
 
 
 
 
 
 
Investigator’s Signature 
 
 
 
Investigator’s Name (please print) 
 
Date (DD Month YYYY) 
 


ISIS 396443-CS4 
CONFIDENTIAL
Amendment 1
Protocol 
26 September 2014
 
5 
TABLE OF CONTENTS 
Page 
PROTOCOL AMENDMENT.......................................................................................................9 
PROTOCOL SYNOPSIS ............................................................................................................10 
STUDY GLOSSARY ...................................................................................................................14 
1. 
OBJECTIVES .....................................................................................................................16 
1.1 
Primary Objective .....................................................................................................16 
1.2 
Secondary Objective .................................................................................................16 
1.3 
Tertiary Objective .....................................................................................................16 
2. 
BACKGROUND AND RATIONALE ..............................................................................16 
2.1 
Spinal Muscular Atrophy ..........................................................................................16 
2.2 
Therapeutic Rationale ...............................................................................................17 
2.3 
ISIS 396443 ..............................................................................................................18 
2.3.1 
Mechanism of Action ...............................................................................18 
2.3.2 
Chemistry .................................................................................................18 
2.3.3 
Preclinical Experience ..............................................................................18 
2.3.4 
Clinical Experience ..................................................................................19 
2.4 
Rationale for Dose and Schedule of Administration ................................................20 
3. 
EXPERIMENTAL PLAN ..................................................................................................20 
3.1 
Study Design .............................................................................................................20 
3.2 
Number of Study Centers ..........................................................................................21 
3.3 
Number of Subjects...................................................................................................21 
3.4 
Overall Study Duration and Follow-up .....................................................................21 
3.4.1 
Screening ..................................................................................................21 
3.4.2 
Treatment ..................................................................................................21 
3.4.3 
Post-Treatment Follow-up ........................................................................22 
3.5 
End of Study .............................................................................................................22 
3.6 
Safety Monitoring and Data Safety Monitoring Board .............................................22 
4. 
SUBJECT ENROLLMENT ...............................................................................................22 
4.1 
Screening...................................................................................................................22 
4.2 
Randomization ..........................................................................................................22 
4.3 
Replacement of Subjects ...........................................................................................23 
4.4 
Unblinding of Treatment Assignment ......................................................................23 
5. 
SUBJECT ELIGIBILITY ..................................................................................................23 
5.1 
Inclusion Criteria ......................................................................................................23 
5.2 
Exclusion Criteria .....................................................................................................24 
6. 
STUDY PROCEDURES ....................................................................................................25 
6.1 
Study Schedule..........................................................................................................25 
6.2 
Study Assessments ....................................................................................................25 


ISIS 396443-CS4 
CONFIDENTIAL
Amendment 1
Protocol 
26 September 2014
 
6 
6.2.1 
Laboratory Analytes .................................................................................25 
6.2.2 
Neurological Examinations ......................................................................25 
6.2.3 
Pharmacokinetics Specimen Collection ...................................................25 
6.2.4 
Hammersmith Functional Motor Scale - Expanded .................................26 
6.2.5 
Motor Milestones .....................................................................................26 
6.2.6 
PedsQL™ (Generic Core Scales and Neuromuscular Module) ...............26 
6.2.7 
Upper Limb Module Test .........................................................................26 
6.2.8 
Assessment of Caregiver Experience with Neuromuscular Disease 
(ACEND) ..................................................................................................27 
6.2.9 
Safety Evaluations ....................................................................................27 
6.3 
Contraception Requirements .....................................................................................27 
7. 
STUDY DRUG ....................................................................................................................27 
7.1 
Study Drug Description ............................................................................................27 
7.2 
Packaging and Labeling ............................................................................................28 
7.3 
Study Drug Accountability .......................................................................................28 
8. 
TREATMENT OF SUBJECTS .........................................................................................28 
8.1 
Study Drug Administration .......................................................................................28 
8.2 
Sham Procedure ........................................................................................................29 
8.3 
Other Protocol-Required Drugs ................................................................................29 
8.4 
Other Protocol-Required Procedures ........................................................................29 
8.5 
Treatment Precautions ..............................................................................................29 
8.6 
Safety Monitoring Rules ...........................................................................................29 
8.7 
Stopping Rules ..........................................................................................................30 
8.8 
Adjustment of Dose and/or Treatment Schedule ......................................................30 
8.9 
Discontinuation of Study Treatment .........................................................................30 
8.10 
Withdrawal of Subjects from the Study ....................................................................30 
8.11 
Concomitant Therapy and Procedures ......................................................................31 
8.11.1 
Concomitant Therapy ...............................................................................31 
8.11.2 
Concomitant Procedures ...........................................................................31 
9. 
SERIOUS AND NON-SERIOUS ADVERSE EVENT REPORTING ..........................31 
9.1 
Sponsor Review of Safety Information.....................................................................31 
9.2 
Regulatory Requirements ..........................................................................................32 
9.3 
Definitions.................................................................................................................32 
9.3.1 
Adverse Event ..........................................................................................32 
9.3.2 
Adverse Reaction and Suspected Adverse Reaction ................................32 
9.3.3 
Serious Adverse Event (SAE) ..................................................................32 
9.4 
Monitoring and Recording Adverse Events ..............................................................33 
9.4.1 
Serious Adverse Events ............................................................................33 
9.4.2 
Non-Serious Adverse Events ....................................................................33 
9.4.3 
Evaluation of Adverse Events (Serious and Non-Serious) ......................33 


ISIS 396443-CS4 
CONFIDENTIAL
Amendment 1
Protocol 
26 September 2014
 
7 
9.4.3.1 
Relationship to the Study Drug ...................................................34 
9.4.3.2 
Severity .......................................................................................34 
9.4.3.3 
Action Taken with Study Drug ...................................................34 
9.4.3.4 
Treatment Given for Adverse Event ...........................................34 
9.4.3.5 
Outcome of the Adverse Event ...................................................35 
9.5 
Procedures for Handling Special Situations .............................................................35 
9.5.1 
Abnormalities of Laboratory Tests ...........................................................35 
9.5.2 
Prescheduled or Elective Procedures or Routinely Scheduled 
Treatments ................................................................................................36 
9.5.3 
Dosing Errors ...........................................................................................36 
9.5.4 
Contraception and Pregnancy ...................................................................36 
10.  STATISTICAL CONSIDERATIONS ..............................................................................37 
10.1 
Study Endpoints, Subsets, and Covariates ................................................................37 
10.1.1 
Primary Endpoint .....................................................................................37 
10.1.2 
Secondary Efficacy Endpoints .................................................................37 
10.1.3 
Tertiary Efficacy Endpoints .....................................................................37 
10.1.4 
Safety/Tolerability Endpoints ...................................................................37 
10.1.5 
Pharmacokinetic Endpoints ......................................................................38 
10.1.6 
Immunogenicity Endpoint ........................................................................38 
10.2 
Sample Size Considerations ......................................................................................38 
10.3 
Populations ................................................................................................................38 
10.4 
Definition of Baseline ...............................................................................................38 
10.5 
Interim Analysis ........................................................................................................38 
10.6 
Planned Methods of Analysis ...................................................................................39 
10.6.1 
Demographic and Baseline Characteristics ..............................................39 
10.6.2 
Safety and Tolerability Analysis ..............................................................39 
10.6.3 
Efficacy Analysis .....................................................................................40 
10.6.4 
Pharmacokinetic Analysis ........................................................................41 
11.  INVESTIGATOR’S REGULATORY OBLIGATIONS .................................................41 
11.1 
Informed Consent/Assent .........................................................................................41 
11.2 
Ethical Conduct of the Study ....................................................................................42 
11.3 
Institutional Review Board/Institutional Ethics Committee/Research Ethics Board42 
11.4 
Subject Confidentiality .............................................................................................42 
12.  ADMINISTRATIVE AND LEGAL OBLIGATIONS ....................................................43 
12.1 
Protocol Amendments ...............................................................................................43 
12.2 
Study Termination ....................................................................................................43 
12.3 
Study Documentation and Storage............................................................................43 
12.4 
Study Monitoring ......................................................................................................44 
12.5 
Language ...................................................................................................................44 
12.6 
Compensation for Injury ...........................................................................................45 


ISIS 396443-CS4 
CONFIDENTIAL
Amendment 1
Protocol 
26 September 2014
 
8 
13.  REFERENCES ....................................................................................................................46 
14.  APPENDICES .....................................................................................................................48 
Appendix A 
Schedule of Procedures .....................................................................49 
Appendix B 
Laboratory Analytes .........................................................................52 
Appendix C 
Pharmacokinetic Sampling Schedule ................................................54 
 
 
TABLE OF TABLES 
Page 
Table 1 
Study Drug Characteristics ................................................................................ 28 
Table 2 
ISIS 396443 Dose, Concentration, and Injection Volume................................. 28 
 
 
TABLE OF FIGURES 
Page 
Figure 1 
ASO Therapeutic Approach for Treatment of SMA ......................................... 17 
 
 


ISIS 396443-CS4 
CONFIDENTIAL
Amendment 1
Protocol 
26 September 2014
 
9 
PROTOCOL AMENDMENT 
 
Protocol Number: 
ISIS 396443-CS4 
Protocol Title: 
A Phase 3, Randomized, Double-blind, Sham-Procedure Controlled Study 
to Assess the Clinical Efficacy and Safety of ISIS 396443 Administered 
Intrathecally in Patients with Later-onset Spinal Muscular Atrophy 
Amendment: 
1 
Amendment Date: 
26 September 2014 
 
 
Summary of Modifications: 
The purpose of this amendment is to revise the statistical method utilized to perform the interim 
analysis.  A typographical error in the protocol has also been fixed. 
The following table provides a summary list of changes to the protocol: 
Section 
Description of Change 
10.5 Interim Analysis 
The statistical method utilized to perform the interim 
analysis has been revised. 
 


ISIS 396443-CS4 
CONFIDENTIAL
Amendment 1
Protocol 
26 September 2014
 
10 
PROTOCOL SYNOPSIS 
Protocol Title 
A Phase 3, Randomized, Double-Blind, Sham Procedure Controlled Study to Assess 
the Clinical Efficacy and Safety of ISIS 396443 Administered Intrathecally in Patients 
with Later-onset  Spinal Muscular Atrophy 
Study Phase 
3 
Indication 
Later-onset Spinal Muscular Atrophy (SMA) 
Objectives 
Primary Objective: 
To examine the efficacy of ISIS 396443 administered intrathecally to patients with later-
onset SMA. 
Secondary Objective: 
To examine the safety and tolerability of ISIS 396443 administered intrathecally to 
patients with later-onset SMA. 
Tertiary Objective: 
To examine the CSF and plasma pharmacokinetics of ISIS 396443 administered 
intrathecally to patients with later-onset SMA. 
Number of Subjects 
Approximately 117 subjects will be enrolled into this study 
Treatment Groups 
12 mg ISIS 396443 or sham procedure control group 
Study Design  
This randomized, double-blind, sham-procedure controlled study will test the clinical 
efficacy, safety, tolerability, and pharmacokinetics of intrathecal ISIS 396443 over 
15 months.  Approximately 117 subjects will be randomized in a 2:1 ratio 
(78 ISIS 396443: 39 control) to receive ISIS 396443 by intrathecal lumbar puncture (LP) 
injection or to a sham-procedure control.  A dose of 12 mg ISIS 396443 will be given at 
each of 4 times over the 15 months (i.e., on Study Days 1, 29, 85, and 274). 
Randomization will be stratified based on: 
1) 
Age (< 6 years versus ≥ 6 years at Screening) 
After Informed consent/assent is obtained, subjects will undergo a screening evaluation 
no greater than 28 days prior to first dose administration at which time their eligibility for 
the study will be examined.  Subjects who meet the eligibility criteria will be admitted to 
the study center on Study Day 1, undergo pre-dose evaluations, and then receive either 
an LP injection of study drug (ISIS 396443) or a sham procedure.  Subjects will return 
to the study center on Days 29, 85 and 274 for follow-up evaluations and subsequent 
injections/sham procedures.  Following the injection/sham procedure on Day 1, subjects 
will remain at the study center for at least 24 hours post-procedure for safety 
monitoring.  Following the injection/sham procedure on Day 29, 85, and 274 subjects 
will remain at the study center for at least 6 hours post-procedure for safety monitoring.  
Safety monitoring visits will occur on Days 30, 86, 92, 169, 275, 365, and 456 (through 
6 months following the last injection/sham procedure).  In addition, the study center will 
monitor the subject’s condition through telephone contact monthly throughout the study.  
For subjects receiving ISIS 396443, a CSF sample will be taken pre-dose on each 
injection day in a manner that maintains the blind. 
Following treatment and the final follow-up evaluation, all eligible subjects may elect to 
enroll in an open-label treatment extension study.  This will be done without unblinding 
to subject’s treatment group. 
If a subject terminates early from the study, they will be encouraged to complete safety 
assessments per the Day 456 visit.  If a subject is randomized but does not complete at 
least their first dose of ISIS 396443/undergo the first sham procedure, they will be 
replaced. 
 


ISIS 396443-CS4 
CONFIDENTIAL
Amendment 1
Protocol 
26 September 2014
 
11 
Protocol Synopsis Continued 
Study Population and 
Main Criteria for 
Inclusion/ Exclusion 
Inclusion Criteria: 
Subjects must meet all of the following criteria at Screening to be eligible: 
1. 
Signed informed consent of parent or guardian.  Signed informed assent of 
subject, if indicated per subject’s age and institutional guidelines 
2. 
Genetic documentation of 5q SMA (homozygous gene deletion, mutation, or 
compound heterozygote) 
3. 
Onset of clinical signs and symptoms consistent with SMA at > 6 months of age 
4. 
Males and females 2 to 12 years of age 
5. 
Can sit independently, but has never had the ability to walk independently 
6. 
Motor Function Score (Hammersmith Functional Motor Scale – Expanded) 
≥ 10 and ≤ 54 at Screening 
7. 
Able to complete all study procedures, measurements and visits and parent or 
guardian/subject has adequately supportive psychosocial circumstances, in the 
opinion of the Investigator 
8. 
Estimated life expectancy > 2 years from Screening, in the opinion of the 
Investigator 
9. 
Meets age-appropriate institutional criteria for use of anesthesia/sedation, if use is 
planned for study procedures (as assessed by the Site Investigator and either 
anesthesiologist or pulmonologist) 
10. For subjects who, in the opinion of the Investigator,  have reached reproductive 
maturity, satisfy one of the following: 
Females:  have a negative pregnancy test at Screening and agrees to employ 
adequate contraceptive measures for the duration of the study.  Acceptable 
contraception methods are restricted to abstinence, barrier contraceptives, 
intrauterine contraceptive devices or licensed hormonal products. 
Males:  be abstinent for the duration of the study 
Exclusion Criteria: 
Subjects meeting any of the following criteria are not eligible for the study: 
1. 
Respiratory insufficiency, defined by the medical necessity for invasive or non-
invasive ventilation for > 6 hours during a 24 hour period, at Screening 
2. 
Medical necessity for a gastric feeding tube, where the majority of feeds are given 
by this route, as assessed by the Site Investigator 
3. 
Severe contractures or severe scoliosis evident on X-ray examination at Screening 
4. 
Hospitalization for surgery (i.e., scoliosis surgery, other surgery), pulmonary event, 
or nutritional support within 2 months of Screening or planned during the duration 
of the study 
5. 
Presence of an untreated or inadequately treated active infection requiring 
systemic antiviral or antimicrobial therapy at any time during the screening period 
6. 
History of brain or spinal cord disease, including tumors, or abnormalities by MRI 
or CT that would interfere with the LP procedures or CSF circulation 
7. 
Presence of an implanted shunt for the drainage of CSF or an implanted CNS 
catheter 
8. 
History of bacterial meningitis 
9. 
Dosing with ISIS 396443 in any previous clinical study 
10. Prior injury (e.g., upper or lower limb fracture) or surgical procedure which impacts 
the subject’s ability to perform any of the outcome measure testing required in the 
protocol and from which the subject has not fully recovered or achieved a stable 
baseline 


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Protocol Synopsis Continued 
Study Population and 
Main Criteria for 
Inclusion/ Exclusion 
Continued 
Exclusion Criteria Continued: 
11. Clinically significant abnormalities in hematology or clinical chemistry parameters 
or ECG, as assessed by the Site Investigator, at the Screening visit that would 
render the subject unsuitable for inclusion 
12. Treatment with another investigational drug (e.g., oral albuterol/salbutamol, 
riluzole, carnitine, creatine, sodium phenylbutyrate, etc.), biological agent, or 
device within 1-month of Screening or 5 half-lives of study agent, whichever is 
longer.  Treatment with valproate or hydroxyurea within 3-months of screening.  
Any history of gene therapy, antisense oligonucleotide therapy, or cell 
transplantation 
13. Ongoing medical condition that according to the Site Investigator would interfere 
with the conduct and assessments of the study.  Examples are medical disability 
(e.g., wasting or cachexia, severe anemia, etc.) that would interfere with the 
assessment of safety or would compromise the ability of the subject to undergo 
study procedures 
Study Drug and 
Administration 
ISIS 396443 (2.4 mg/mL) will be administered as an intrathecal LP injection.  The 
volume of the injection will be 5.0 mL.  Details regarding the LP dosing injection 
procedure and the sham procedure will be provided in the Dosing Administration 
Manual.  Details regarding the study drug will be provided in the Study Drug Manual. 
Per institutional guidelines, anesthesia/sedation may be used for the LP procedure. 
Criteria for Evaluation 
Primary Endpoint: 
• 
Change from baseline in HFMSE (Hammersmith Functional Motor Scale – 
Expanded) score at 15 months 
Secondary Endpoints:  
• 
Proportion of subjects who achieve a 3-point increase from baseline in 
Hammersmith Functional Motor Scale – Expanded (HFMSE) score at 15 months 
• 
Proportion of subjects that achieve any new motor milestone at 15 months 
• 
Number of motor milestones achieved per subject at 15 months 
• 
Change from baseline in Upper Limb Module Test at 15 months 
• 
Proportion of subjects that achieve standing alone at 15 months 
• 
Proportion of subjects that achieve walking with assistance at 15 months 
 
Tertiary Endpoints:  
• 
Change from baseline in CSF SMN protein concentration  
• 
Clinical Global Impression of Change (Investigator and Caregiver assessment)  
• 
Change from baseline in PedsQL (Pediatric Quality of Life Inventory)  
• 
Change from baseline in Assessment of Caregiver Experience with Neuromuscular 
Disease (ACEND)  
• 
Disease-related hospitalizations and adverse events 
 
Safety/Tolerability Endpoints: 
• 
Adverse events 
• 
Vital signs and weight 
• 
Neurological examinations 
• 
Physical examinations  
• 
Clinical laboratory tests  
• 
ECGs 
• 
Use of concomitant medications 


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Protocol Synopsis Continued 
Criteria for Evaluation 
Continued 
Pharmacokinetic Endpoints:  
• 
CSF levels of ISIS 396443 (sample taken pre-dose at each dosing) 
• 
Plasma levels of ISIS 396443 
Immunogenicity Endpoint:  
• 
Plasma antibodies to ISIS 396443 
Safety Monitoring  
Safety data will be reviewed on an ongoing basis by the Medical Monitor and by an 
Independent Data Safety and Monitoring Committee (DSMB). 
Statistical 
Considerations  
The sample size for this study was estimated based on limited available natural history 
data for the target population and from the ISIS 396443-CS1 and CS2 clinical studies in 
children with SMA.  70 subjects in the treated group and 35 subjects in the control 
group will give at least 90% power to detect a 3 point difference between control and 
treated groups in change on the HFMSE with a standard deviation of 4.4, using a two-
sided t-test with an alpha level of 0.05.  The sample size was obtained using the n-
Query.  117 subjects will be enrolled to ensure that a small dropout rate will not affect 
the power of the primary efficacy analysis.  An interim analysis may take place when all 
subjects have completed the 6 month assessment and at least 39 subjects have 
completed the 15 month assessment. 
Sponsor 
Isis Pharmaceuticals, Inc. 


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STUDY GLOSSARY 
Abbreviation/Acronym 
Definition 
ACEND 
Assessment of Caregiver Experience with Neuromuscular Disease 
AE 
Adverse event/experience 
ALT 
Alanine aminotransferase  
aPTT 
Activated partial thromboplastin time 
ASO 
Antisense oligonucleotide 
AST 
Aspartate aminotransferase 
BUN 
Blood urea nitrogen 
CGI 
Clinical Global Impressions of Change Rating Scale 
Cmax 
Maximum concentration 
CNS 
Central nervous system 
CPK 
Creatinine phosphokinase 
CRF 
Case report form 
CSF 
Cerebrospinal fluid 
DSMB 
Data and Safety Monitoring Board 
eCRF 
Electronic case report form 
ECG 
Electrocardiogram 
FL 
Full-length  
GCP 
Good Clinical Practice 
HFMSE 
Hammersmith Functional Motor Scale - Expanded 
hnRNP 
Heterogeneous nuclear ribonucleoproteins 
ICH 
International Conference on Harmonisation  
IEC 
Independent Ethics Committee 
INR 
International normalized ratio 
IRB 
Institutional Review Board 
IT 
Intrathecal 
IXRS 
Interactive Voice/Web-Response System 
LP 
Lumbar puncture 
MAD 
Multiple ascending-dose 
MedDRA 
Medical Dictionary for Regulatory Activities 
miRNA 
Micro ribonucleic acid (RNA) 


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MOE 
2′-O-(2-methoxyethyl)  
mRNA 
Messenger ribonucleic acid 
NCS 
Not clinically significant 
OLE 
Open-label extension study 
PedsQL 
Pediatric Quality of Life Inventory 
PK 
Pharmacokinetic(s) 
PT 
Prothrombin Time 
SAE 
Serious adverse event 
SAP 
Statistical Analysis Plan 
SMA 
Spinal muscular atrophy 
SMN 
Survival motor neuron 
snRNA 
Small nuclear ribonucleic acid 
SUSARs 
Suspected unexpected serious adverse reactions 
Tmax 
Time to maximal concentration 
WMA 
World Medical Association 
 


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1. 
OBJECTIVES 
The objectives of this study are to evaulate the clinical efficacy, safety, tolerability, and 
pharmacokinetics (PK) of ISIS 396443 administered intrathecally to patients with later-onset 
Spinal Muscular Atrophy (SMA). 
1.1 
Primary Objective 
To examine the clinical efficacy of ISIS 396443 administered intrathecally to patients with later-
onset SMA. 
1.2 
Secondary Objective 
To examine the safety and tolerability of ISIS 396443 administered intrathecally to patients with 
later-onset SMA. 
1.3 
Tertiary Objective 
To examine the cerebral spinal fluid and plasma PK of ISIS 396443 administered intrathecally to 
patients with later-onset SMA. 
2. 
BACKGROUND AND RATIONALE 
2.1 
Spinal Muscular Atrophy 
SMA is an autosomal recessive neuromuscular disease characterized by degeneration of the 
motor neurons in the anterior horn of the spinal cord, resulting in atrophy of the voluntary 
muscles of the limbs and trunk.  With an incidence of 1:6000 to 1:10,000 live births, it is the 
most common genetic cause of infant mortality, and a major cause of childhood morbidity due to 
weakness, in the U.S.  The natural history of SMA includes four major phenotypes that are 
recognized dependent on age of onset and achieved motor abilities.  The most severe form, 
Type 1 SMA (equivalent to infantile-onset SMA), has a disease onset within the first few months 
of life; these children are never able to sit or walk and usually die from respiratory failure by the 
age of 2 years.  Later-onset SMA can generally be divided into Type 2 and Type 3 SMA.  Type 2 
SMA patients are able to sit but never walk unaided, with symptoms presenting between  
6-18 months of age.  Type 3 SMA patients are able to sit and walk but individuals with this form 
may become severely and increasingly disabled.  Adult-onset SMA patients (Type 4) have an 
age of onset over 18 years of age and have normal life expectancies. 
In 95% of SMA patients, a deletion in the SMN1 gene on Chromosome 5q11-q13 is found; with 
the remaining 5% attributable to small mutations in the same gene (Lefebvre et al. 1995; 
Helmken et al. 2003).  SMN1 lies in the telomeric portion of an inverted duplication of a region 
of Chromosome 5.  The centromeric half of the duplication contains a homologous gene, named 
SMN2 that differs from SMN1 by 11 nucleotides.  The open reading frames for both genes 
encode for proteins with identical amino acid sequences.  Survival motor neuron (SMN) gene 
transcripts, similar to most mammalian transcripts, undergo alternative splicing in which certain 
exons are either included or excluded from the mature protein coding transcripts 
(Keren et al. 2010).  In particular, Exon 7 of the SMN1 gene is alternatively spliced with 90 to 
95% of the mature messenger ribonucleic acid (mRNA) transcripts derived from the SMN1 gene 
containing Exon 7, and 5 to 10% of transcripts missing Exon 7.  The transcripts missing Exon 7 
(often referred to as Δ7) produce a truncated protein which is defective and unstable 


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(Cho and Dreyfuss 2010).  One of the 11 nucleotide differences between SMN1 and SMN2, a C 
to T substitution occurs in Exon 7 of the SMN2 gene resulting in an alternative splicing pattern 
that favors skipping of Exon 7.  The result is that as much as 90% of the transcripts produced 
from SMN2 are missing Exon 7.  The remainder, SMN2 transcripts containing Exon 7, produces 
a full-length (FL) protein product identical to the SMN1 protein, since the C to T substitution is 
silent.  Humans have a variable copy number of the SMN2 gene (0-8 copies).  The number of 
SMN2 copies and the resulting amount of FL-SMN protein expressed in SMA patients (10-40% 
of normal SMN protein levels) correlates with SMA disease severity and thus SMN2 is a key 
modifier of disease phenotype (Coovert et al. 1997; Feldkotter et al. 2002; Lefebvre et al. 1997; 
Prior et al. 2004). 
2.2 
Therapeutic Rationale 
Since the number of SMN2 gene copies and resulting amount of SMN protein is correlated with 
disease onset and severity, a therapeutic approach predicted to benefit SMA patients is to 
increase the levels of full length SMN2 pre-mRNA by restoring the splicing pattern that gives 
rise to full length SMN2 mRNA.  Increasing inclusion of Exon 7 in the SMN2 transcript will 
increase FL-SMN protein levels and SMN protein activity.  A therapeutic strategy for promoting 
Exon 7 inclusion is through the use of antisense oligonucleotides (ASOs) (see Figure 1). 
 
Figure 1 
ASO Therapeutic Approach for Treatment of SMA 


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The known potential risks associated with ISIS 396443 are detailed in the Guidance to 
Investigator section of the Investigator’s Brochure.  Additional study associated risks related to 
the lumbar puncture (LP) procedure are also detailed in the Guidance to Investigator section of 
the Investigator’s Brochure. 
2.3 
ISIS 396443 
2.3.1 
Mechanism of Action 
ISIS 396443 is a fully modified, 2′-O-2-methoxyethyl (MOE), ASO drug designed to bind to a 
specific sequence in the intron downstream of Exon 7 of the SMN2 transcript.  The region of the 
pre-mRNA targeted by ISIS 396443 is normally occupied by heterogeneous nuclear 
ribonucleoproteins (hnRNP) A1/2 proteins, masking the U1 small nuclear ribonucleic acid 
(snRNA) binding site at the 5′-exon-intron junction of Exon 7, and is referred to as ISS-N1.  
U1 snRNA base pairs to the sequences that define the 5′-splice site, which is thought to be one of 
the first steps that initiate splicing of an intron.  ISIS 396443 displaces the hnRNP A1/2 proteins 
from the pre-mRNA binding site, allowing U1 snRNA to bind to the exon-intron junction and 
promote assembly of the spliceosomal complex, thus promoting inclusion of Exon 7 into the 
mRNA which results in production of FL-SMN protein. 
2.3.2 
Chemistry 
Chemically, ISIS 396443 is a synthetic oligomer of 18 nucleotides (i.e., an 18-mer) that are 
connected sequentially by phosphorothioate linkages.  Each of the 17 internucleotide linkages is 
a 3′-O to 5′-O phosphorothioate diester.  The 18 sugar residues are uniformly modified with 
2′-O-(2-methoxyethyl) (MOE).  These MOE-modified nucleotides confer (1) increased affinity 
to the target mRNA (McKay et al. 1999), (2) increased resistance to exonucleases and 
endonucleases (thereby increasing stability in tissue) (Geary et al. 2003), and (3) amelioration of 
some of the high dose toxicities associated with ASO containing only the phosphorothioate 
linkages (Henry et al. 2000). 
The sequence of ISIS 396443 is written as follows: 
5′ -MeUMeCAMeCMeUMeUMeUMeCAMeUAAMeUGMeCMeUGG- 3′ 
Where A and G are 2′-O-(2-methoxyethyl)nucleosides, MeC is 5-methyl-2′-O-(2-
methoxyethyl)cytidine and MeU designates 5-methyl-2′-O-(2-methoxyethyl)uridine. 
2.3.3 
Preclinical Experience 
Detailed information concerning the preclinical studies conducted with ISIS 396443 can be 
found in the Investigator’s Brochure.  A summary is included below. 
ISIS 396443 was identified after an extensive screen of greater than 500 2′-MOE 
oligonucleotides in in vitro splicing assays, reporter gene assays and in SMA patient fibroblasts 
(Hua et al. 2007; Hua et al. 2008).  Data have shown that ISIS 396443 promotes a concentration-
dependent increase in full-length transcripts (including Exon 7) in patient fibroblast cells, 
achieving greater than 90% full length SMN2 transcripts and forms nuclear structures, called 
gems, known to contain SMN protein.  In a mild mouse model of SMA, ISIS 396443 promoted 
inclusion of Exon 7 in the SMN2 transgene in a variety of peripheral tissues when dosed 
systemically (Hua et al. 2008) and in central nervous system (CNS) tissue, including spinal cord, 


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when injected into the lateral ventricle.  ISIS 396443 produced greater than 90% Exon 7 
inclusion in the transgenic mice and increased SMN protein production in motor neurons, 
resulting in the appearance of gems in motor neurons.  These studies were extended to a more 
severe mouse model of SMA (SMA Δ7) (Le et al. 2005), where the CNS delivery of drug 
produced a dose-dependent effect on SMN2 Exon 7 inclusion, SMN protein production, and 
survival.  These mice treated with ISIS 396443 demonstrated improved weight gain, 
improvements in muscle morphology, muscle strength, and motor coordination and improved 
morphology of the motor neuron junctions (Passini et al. 2011).  Further, ISIS 396443 was 
shown to distribute widely in the CNS following intrathecal (IT) administration in monkey 
(Passini et al. 2011). 
The pharmacokinetics and toxicity of ISIS 396443 were assessed following: 1) single intrathecal 
(IT) lumbar bolus injections (1 to 7 mg) in adult monkeys 2) following 14 weeks (with a 4-week 
interim sacrifice) of repeated IT lumbar bolus injections (0.3 to 3 mg/week or every other week) 
in juvenile monkeys and 3) following 53 weeks of repeated IT lumbar bolus injections in 
juvenile monkeys.  In addition, a dedicated pharmacokinetic study in adult monkeys was 
performed to assess the half-life of ISIS 396443 in CSF, tissues and plasma.  Detailed results 
from these preclinical studies conducted with ISIS 396443 can be found in the ISIS 396443 
Investigator’s Brochure. 
2.3.4 
Clinical Experience 
Detailed information concerning the clinical studies conducted with ISIS 396443 can be found in 
the Investigator’s Brochure.  A summary is included below. 
ISIS 396443 has been evaluated in a completed open-label, single ascending-dose (SAD) Phase 1 
study designed to assess the safety, tolerability and pharmacokinetics of ISIS 396443 in patients 
with SMA (ISIS 396443-CS1).  A single-dose of ISIS 396443 was administered by IT injection 
to SMA patients aged 2 to 14 years of age.  Four dose levels (1, 3, 6, and 9 mg) were evaluated 
sequentially.  Each dose level was studied in a cohort of 6 or 10 subjects, where all subjects 
received drug.  In this study all subjects completed dosing and the follow-up visits per protocol.  
Overall, ISIS 396443 was well-tolerated and no safety concerns were identified up to the 9.0 mg 
dose level, given as a single IT injection.  No serious adverse events (SAEs) or dose-limiting 
toxicities (DLTs) were reported in ISIS 396443-CS1.  Adverse events (AEs) reported were mild 
or moderate in severity and there was no relationship with ISIS 396443 dose level.  In addition, 
no ISIS 396443 related adverse changes in neurological exams were reported, despite intensive 
monitoring during the immediate post-dosing period.  CSF and plasma drug concentrations 
observed were generally consistent with predictions made from nonclinical monkey studies. 
ISIS 396443 is also being evaluated in four ongoing studies: ISIS 396443-CS2, 
ISIS 396443-CS10, ISIS 396443-CS12, and ISIS 396443-CS3A.  ISIS 396443-CS2 is an 
open-label, multiple ascending-dose (MAD) Phase 1/2a study designed to assess the safety, 
tolerability and pharmacokinetics of ISIS 396443 in patients with SMA.  Multiple doses of 
ISIS 396443, ranging from 3 mg to 12 mg, are being administered by intrathecal injection to 
SMA patients aged 2 to 15 years of age.  ISIS 396443-CS10 is an open-label, single dose, 
re-dosing study for SMA patients who previously participated in Cohorts 2, 3 and 4 in 
ISIS 396443-CS1.  ISIS 396443-CS12 is an ongoing open-label study to assess the safety and 
tolerability of a single (12 mg) intrathecal dose of ISIS 396443 in patients with spinal muscular 
atrophy who previously participated in ISIS 396443-CS2 or ISIS 396443-CS10.  


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ISIS 396443 CS3A is an open-label, multiple-dose study designed to assess the safety, 
tolerability and pharmacokinetics of ISIS 396443 in patients with infantile-onset SMA.  Multiple 
doses of ISIS 396443 are being administered by intrathecal injection to symptomatic SMA 
infants ≤ 7 months of age.  Two dose levels (6 and 12 mg dose equivalent scaled by CSF 
volume) are being evaluated sequentially. 
2.4 
Rationale for Dose and Schedule of Administration 
The proposed study will test the clinical efficacy, safety, tolerability, and PK of multiple doses of 
ISIS 396443 administered as IT injections to subjects with later-onset SMA.  A single dose level 
of 12 mg ISIS 396443 will be evaulated, delivered as 4 doses administered over 9 months. 
ISIS 396443 will be administered using a loading regimen (dosings on Study Days 1, 29, 85) 
followed by maintenance dosing given 6 months thereafter (dosing on Study Day 274). 
The ISIS 396443-CS4 dose level and dose interval was selected based on preclinical toxicology 
and pharmacokinetic observations from monkey studies utilizing single-dose and repeat dosing 
IT administration, consideration of the target tissue concentration anticipated for drug 
pharmacology, and safety data in the completed and ongoing clinical studies of ISIS 396443 to 
date.  Based upon pharmacology and pharmacokinetic results in SMA transgenic mice, we 
estimate that the target tissue concentration to produce 50 to 90% SMN2 Exon 7 inclusion is 
between 1 and 10 μg/g spinal cord tissue.  Nonclinical studies in juvenile monkeys receiving IT 
doses of ISIS 396443 showed a resulting gradient of distribution of ISIS 396443 along the spinal 
cord, with mean lumbar spinal cord concentrations ranging from 1.6-2.3 fold and 2.0-3.5 fold 
higher than thoracic and cervical spinal cord levels, respectively.  The dose level selected for this 
multiple-dose clinical study (12 mg ISIS 396443) is predicted to achieve levels at the high end of 
this range (approximately 10 μg/g lumbar and 3 ug/g cervical spinal cord tissue concentrations), 
following the first dose.  The loading dose interval was selected based on the nonclinical 
pharmacokinetic and pharmacology data as the dose interval to achieve and maintain 
ISIS 396443 spinal cord tissue levels that are predicted to be within the upper end of the 
pharmacologically active range by Day 85 (predicted to be approximately 24 μg/g lumbar and 
8 μg/g cervical tissue concentration), while at the same time considering subject safety and 
convenience for repeated LP intrathecal injections.  The maintenance dose interval (once every 
6 months) was selected based on the estimated spinal tissue and CSF drug half-life (4-6 months) 
and was selected to maintain spinal cord tissue levels of ISIS 396443 at a steady-state level 
within the estimated pharmacologically active range. 
Additional details on dose scaling and expected CSF and tissue concentrations are summarized 
in the Investigator’s Brochure. 
3. 
EXPERIMENTAL PLAN 
3.1 
Study Design 
This is a Phase 3 multicenter, double-blind, randomized, sham-procedure controlled study of 
ISIS 396443 in patients with later-onset SMA studied for 15 months.  Approximately 
117 subjects will be randomized 2:1 to receive 12 mg dose ISIS 396443 or a sham procedure 
control, respectively.  ISIS 396443 will be administered using a loading regime (dosings on 
Study Days 1, 29, and 85) followed by a maintenance dose 6 months thereafter (dosing on Study 
Day 274). 


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Randomization will be stratified based on: 
1) Subject’s Age at Screening (< 6 years versus ≥ 6 years) 
Following treatment and the Day 456 follow-up evaluation, all eligible subjects may elect to 
enroll in an open-label treatment extension study, pending study approval by the IRB or IEC and 
the appropriate regulatory authority.  This will be done without unblinding to subject’s treatment 
group. 
3.2 
Number of Study Centers 
This study will be conducted at multiple centers worldwide. 
3.3 
Number of Subjects 
Approximately 117 subjects (2 ISIS 396443; 1 sham-procedure) will receive 12 mg dose of 
ISIS 396443 or a sham procedure control.  The total number of subjects randomized may be 
higher if some subjects do not receive their Day 1 dose/sham procedure.  The maximum number 
of subjects will not exceed 130. 
3.4 
Overall Study Duration and Follow-up 
The Study will consist of screening, treatment, and post-treatment follow-up-periods.  The total 
duration of participation in the study is approximately 16 months.  Please refer to the Schedule of 
Procedures in Appendix A. 
3.4.1 
Screening 
After informed consent/assent is obtained, subjects will undergo a screening evaluation no 
greater than 28 days prior to first dose administration at which their eligibility for the study will 
be examined. 
3.4.2 
Treatment 
Subjects who meet the eligibility criteria will be admitted to the study center on Study Day 1, 
undergo pre-dose evaluations, be randomized, and then receive either an LP injection of study 
drug (ISIS 396443) or a sham procedure.  Subjects will return to the study center on Days 29, 85 
and 274 for follow-up evaluations and subsequent injections/sham procedures.  Following the 
injection/sham procedure on Day 1, subjects will remain at the study center for at least 24 hours 
post-procedure for safety monitoring.  Following the injection/sham procedure on Day 29, 85, 
and 274 subjects will remain at the study center for at least 6 hours post-procedure for safety 
monitoring.  Safety monitoring visits will occur Study Days 30, 86, 92, 169, and 275 (through 
the last injection/sham procedure).  In addition, the study center will monitor the subject’s 
condition through telephone contact on a monthly basis. 
For subjects receiving ISIS 396443, a CSF sample for PK and SMN protein analyses will be 
taken pre-dose on each injection day in a manner that protects the blind. 
If a subject terminates early from the study, they will be encouraged to complete assessments per 
the Day 456 visit.  If a subject is randomized but does not successfully receive the first dose of 
ISIS 396443/undergo the first sham procedure, they will be replaced. 


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3.4.3 
Post-Treatment Follow-up 
After completion of the Day 275 visit, subjects will enter the 6-month post-treatment evaluation 
period.  This period consists of Study Center visits on Day 365 and 456 and follow-up phone 
assessments on a monthly basis, as outlined in the Schedule of Procedures (Appendix A).  After 
completion of the Day 456 visit, subjects may be eligible to participate in an OLE study, pending 
study approval by the IRB or IEC and the appropriate regulatory authority. 
3.5 
End of Study 
The end of study is last subject; last visit (either in-person visit or telephone contact). 
3.6 
Safety Monitoring and Data Safety Monitoring Board 
Safety data will be reviewed on an ongoing basis by the Sponsor and the Medical Monitor.  
Safety data will also be reviewed on an ongoing basis by an independent DSMB.  The DSMB 
will be assembled to review safety, tolerability and efficacy (as needed) data collected on 
ISIS 396443 during this study.  Based on its ongoing assessment of the data, the DSMB will 
provide recommendations to the Sponsor for modifying, stopping or continuing the study. 
4. 
SUBJECT ENROLLMENT 
4.1 
Screening 
Before subjects may be enrolled into the study, the Sponsor requires a copy of the Study Center’s 
written IRB or IEC approval of the protocol, informed consent form, informed assent form (if 
applicable) and all other subject information and/or recruitment material. 
Before a subject’s participation in the trial, the Investigator is responsible for obtaining written 
informed consent from the parent(s) or legal guardian(s) and, in cases where institutional 
guidelines and the patient’s age dictate, informed assent from the subject.  At the time of 
consent/assent, the subject will be considered enrolled into the study and will be assigned a 
unique screening number before any study procedures, including screening procedures, are 
performed.  The screening number must remain constant throughout the entire trial.  In the event 
the subject is re-consented and re-screened the subject must be given a new screening number.  
Screening numbers, once assigned, will not be re-used. 
4.2 
Randomization 
Subjects will be randomized after all screening assessments have been completed and after the 
Investigator and the Medical Monitor have verified that they are eligible per criteria in 
Sections 5.1 and 5.2.  No subject may begin treatment prior to randomization and assignment of 
a unique randomization number. 
Using an Interactive Voice/Web-Response System (IXRS), eligible subjects will be randomized 
2:1 to receive ISIS 396443 or sham-procedure control, respectively.  Randomization will be 
stratified for: 
• Subject’s Age at Screening (< 6 years versus ≥ 6 years) 
The Sponsor Quality Assurance department or designee will hold a copy of the randomization 
lists generated by the IXRS vendor. 


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4.3 
Replacement of Subjects 
If a subject does not successfully receive the first dose of ISIS 396443/undergo the first sham 
procedure, they will be replaced.  
4.4 
Unblinding of Treatment Assignment 
The Sponsor, parents, and key study site personnel will be blinded to subjects’ treatment 
assignment throughout the study.  The DSMB may be unblinded as described in the DSMB 
charter. 
If a subject has experienced an SAE (as defined in Section 9.3.3), and/or when knowledge of the 
treatment assignment will impact the clinical management of the subject, the Investigator will 
have the ability to unblind the treatment assignment for that subject using the IXRS.  However, 
prior to unblinding, the Investigator should attempt to contact the blinded Medical Monitor to 
discuss the emergency.  The Sponsor or designee will be informed of the unblinding of a subject 
within 24 hours.  Every reasonable attempt should be made to complete the Study Day 456 early 
termination procedures and observations (see Appendix A) prior to unblinding, as knowledge of 
the subject’s treatment assignment could influence subsequent assessments.  The Investigator 
must document the reasons for unblinding in the subject’s source documents.  The Investigator is 
strongly advised not to divulge the subject’s treatment assignment to any individual not directly 
involved in managing the medical emergency, nor to personnel involved with the analysis and 
conduct of the study.  In cases where there are ethical reasons to have a subject remain on study 
whose treatment assignment is unblinded for safety reasons, the Site Investigator must obtain 
specific approval from the Sponsor and the Medical Monitor for the subject to continue in the 
study. 
In addition, all suspected unexpected serious adverse reactions (SUSARs) will be unblinded by 
the Sponsor’s Drug Safety and Quality Assurance personnel for the purpose of regulatory 
reporting (Section 9.2). 
5. 
SUBJECT ELIGIBILITY 
5.1 
Inclusion Criteria  
Subjects must meet all of the following criteria at Screening to be eligible: 
1. Signed informed consent of parent or guardian.  Signed informed assent of subject, if 
indicated per subject’s age and institutional guidelines 
2. Genetic documentation of 5q SMA (homozygous gene deletion, mutation, or compound 
heterozygote) 
3. Onset of clinical signs and symptoms consistent with SMA at > 6 months of age 
4. Males and females 2 to 12 years of age 
5. Can sit independently, but has never had the ability to walk independently 
6. Motor Function Score (Hammersmith Functional Motor Scale – Expanded) ≥ 10 and ≤ 54 
at Screening 


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7. Able to complete all study procedures, measurements and visits and parent or 
guardian/subject has adequately supportive psychosocial circumstances, in the opinion of 
the Investigator 
8. Estimated life expectancy > 2 years from screening, in the opinion of the Investigator 
9. Meets age-appropriate institutional criteria for use of anesthesia/sedation, if use is 
planned for study procedures (as assessed by the Site Investigator and either 
anesthesiologist or pulmonologist) 
10. For subjects who, in the opinion of the Investigator, have reached reproductive maturity, 
satisfy one of the following: 
Females:  have a negative pregnancy test at Screening and agrees to employ adequate 
contraceptive measures for the duration of the study.  Acceptable contraception methods 
are restricted to abstinence, barrier contraceptives, intrauterine contraceptive devices or 
licensed hormonal products. 
Males:  be abstinent for the duration of the study 
5.2 
Exclusion Criteria 
Subjects meeting any of the following criteria are not eligible for the study: 
1. Respiratory insufficiency, defined by the medical necessity for invasive or non-invasive 
ventilation for > 6 hours during a 24 hour period, at Screening 
2. Medical necessity for a gastric feeding tube, where the majority of feeds are given by this 
route, as assessed by the Site Investigator 
3. Severe contractures or severe scoliosis evident on X-ray examination at Screening 
4. Hospitalization for surgery (i.e., scoliosis surgery, other surgery), pulmonary event, or 
nutritional support within 2 months of screening or planned during the duration of the 
study 
5. Presence of an untreated or inadequately treated active infection requiring systemic 
antiviral or antimicrobial therapy at any time during the screening period 
6. History of brain or spinal cord disease, including tumors, or abnormalities by MRI or CT 
that would interfere with the LP procedures or CSF circulation 
7. Presence of an implanted shunt for the drainage of CSF or an implanted CNS catheter 
8. History of bacterial meningitis 
9. Dosing with ISIS 396443 in any previous clinical study 
10. Prior injury (e.g., upper or lower limb fracture) or surgical procedure which impacts the 
subject’s ability to perform any of the outcome measure testing required in the protocol 
and from which the subject has not fully recovered or achieved a stable baseline 
11. Clinically significant abnormalities in hematology or clinical chemistry parameters or 
ECG, as assessed by the Site Investigator, at the Screening visit that would render the 
subject unsuitable for inclusion 


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12. Treatment with another investigational drug (e.g., oral albuterol/salbutamol, riluzole, 
carnitine, creatine, sodium phenylbutyrate, etc.), biological agent, or device within 
1-month of screening or 5 half-lives of study agent, whichever is longer.  Treatment with 
valproate or hydroxyurea within 3-months of screening.  Any history of gene therapy, 
antisense oligonucleotide therapy, or cell transplantation 
13. Ongoing medical condition that according to the Site Investigator would interfere with 
the conduct and assessments of the study.  Examples are medical disability (e.g., wasting 
or cachexia, severe anemia, etc.) that would interfere with the assessment of safety or 
would compromise the ability of the subject to undergo study procedures 
6. 
STUDY PROCEDURES 
6.1 
Study Schedule 
All required study procedures are outlined in Appendices A, B and C. 
6.2 
Study Assessments 
6.2.1 
Laboratory Analytes 
Laboratory measurements of serum chemistry, hematology, urinalysis, coagulation parameters, 
and plasma antibodies to ISIS 396443 will be performed at the times shown in the Schedule of 
Procedures (Appendix A).  The analytes to be measured are shown in Appendix B. 
6.2.2 
Neurological Examinations 
Neurological examinations include assessment of mental status, level of consciousness, sensory 
function, motor function, cranial nerve function, and reflexes.  Neurological examinations will be 
performed at the times shown in the Schedule of Procedures (Appendix A). 
6.2.3 
Pharmacokinetics Specimen Collection 
Plasma and CSF specimens will be collected as shown in Appendix A (Schedule of Procedures) 
and Appendix C (Pharmacokinetic Sampling Schedule).  The following ISIS 396443 plasma PK 
parameters (though not necessarily limited to) will be derived when appropriate from the 
individual subject concentration vs. time profiles using noncompartmental-based methods and 
based on actual sampling times: 
• The maximal observed plasma drug concentration (Cmax) 
• The time to reach Cmax in plasma (Tmax) 
• The area under the plasma concentrations time curve from the time of the IT dose to the 
last collected sample 
• The apparent terminal elimination half-life (t½), if possible 
 
 


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6.2.4 
Hammersmith Functional Motor Scale - Expanded 
Subjects will be evaluated using the Hammersmith Functional Motor Scale – Expanded 
(HFMSE) at the times shown in the Schedule of Procedures (Appendix A).  The HFMSE is a 
reliable and validated tool used to assess motor function in children with SMA.  The scale was 
originally developed with 20 scored activities and was devised for use in children with SMA 
Type 2 and Type 3 with limited ambulation to give objective information on motor ability and 
clinical progression (Main et al. 2003).  The expanded scale includes an additional module of 
13 items developed to allow for evaluation of ambulatory SMA patients (O’Hagen et al. 2007).  
The HFMSE has been shown to be highly correlated with other clinical assessments and shows 
good test-retest reliability.  The HFMSE is easy to use and quickly administered. 
6.2.5 
Motor Milestones 
Subjects will be evaluated for motor milestones at the times shown in the Schedule of Procedures 
(Appendix A).  Motor Milestones will be assessed using the WHO Motor Milestone criteria 
(WHO Multicentre Growth Reference Study Group 2006; Wijnhoven et al. 2004). 
6.2.6 
PedsQL™ (Generic Core Scales and Neuromuscular Module) 
Subjects will be evaluated using the Pediatric Quality of Life Inventory (PedsQL™) 
Measurement 4.0 Generic Core Scales and 3.0 Neuromuscular Module (Varni et al. 1999) at the 
times shown in the Schedule of Procedures (Appendix A).  This assessment has been validated 
by the American Spinal Muscular Atrophy Randomized Trials (AmSMART) group for use in 
SMA patients from age 2 to 18 years (Iannaccone et al. 2009). 
The PedsQL™ Measurement Model is a modular approach to measuring health-related quality of 
life (HRQOL) in children and adolescents.  The PedsQL consists of brief, practical, generic core 
scales as well as with condition-specific modules for use in designated clinical populations.  
Pediatric self-report is measured in children and adolescents ages 5-18 years, and parent proxy-
report of child HRQOL is measured for children and adolescents ages 2-18 years.  The 
PedsQL™ 4.0 Generic Core Scales include assessment of physical functioning, emotional 
functioning, social functioning, and school functioning.  The PedsQL 3.0 Neuromuscular 
Module was designed to measure HRQOL dimensions specific to children aged 2 to 18 years 
with neuromuscular disorders, including SMA. 
6.2.7 
Upper Limb Module Test 
Subjects will be evaluated using the Upper Limb Module Test (Mazzone et al. 2011) at the times 
shown in the Schedule of Procedures (Appendix A).  The Upper Limb Module Test is an 
outcome measure specifically developed to assess upper limb functional abilities in SMA 
patients, including young children and patients with severe contractures in the lower limbs in 
whom the possibility to detect functional changes, such as rolling or long sitting, is limited.  This 
test consists of upper limb performance items that are reflective of activities of daily living (i.e., 
raise a can to mouth as if drinking, take a coin and place it in a box, remove the lid of a 
container).  The Upper Limb Module Test is quickly administered and has been evaluated in 
SMA patients age 30 months to 27 years (Mazzone et al. 2011). 


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6.2.8 
Assessment of Caregiver Experience with Neuromuscular Disease (ACEND) 
Parents of subjects will complete the Assessment of Caregiver Experience with Neuromuscular 
Disease (ACEND) questionnaire at the times shown in the Schedule of Procedures 
(Appendix A).  This assessment instrument has been designed to quantify the caregiver impact 
experienced by parents of children affected with severe neuromuscular diseases, including 
children with SMA (Matsumoto et al. 2011).  The ACEND includes domains assessing physical 
impact (including feeding/grooming/dressing, sitting/play, transfers, and mobility) and general 
caregiver impact (including time, emotion, and finance). 
6.2.9 
Safety Evaluations 
Safety will be evaluated by assessment of AEs including SAEs as described in Section 9.  
Additional safety evaluations include the following parameters: 
• Vital signs and weight 
• Neurological examinations 
• Physical examinations  
• Clinical laboratory tests (serum chemistry, hematology, urinalysis) 
• Electrocardiograms (ECGs) 
• Use of concomitant medications 
6.3 
Contraception Requirements 
All male subjects must remain abstinent during the study. 
All female subjects of childbearing potential must either be abstinent or practice adequate 
contraception during the study.  For the purposes of this study, females of childbearing potential 
are defined as any female who has experienced menarche.  For the purposes of the study, 
acceptable contraception methods are abstinence, barrier contraceptives, intrauterine 
contraceptive devices or licensed hormonal products 
7. 
STUDY DRUG 
7.1 
Study Drug Description 
Study Drug (ISIS 396443 drug product) characteristics are listed under Table 1. 
The Study Drug is contained in 6 mL clear glass vials.  The Study Drug and its storage and 
preparation instructions will be provided by the Sponsor or designee.  The Study Drug must be 
stored securely at 2° to 8° C and protected from light. 
 
 


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Table 1 
Study Drug Characteristics 
Study Drug 
ISIS 396443 Drug Product 
Strength 
2.4 mg/mL  
Volume/vial 
5.0 mL solution per vial 
Route of Administration 
IT injection 
 
7.2 
Packaging and Labeling 
The Sponsor will provide the Investigator with packaged Study Drug labeled in accordance with 
specific country regulatory requirements. 
7.3 
Study Drug Accountability 
The study staff is required to document receipt, dispensing and return of Study Drug supplies 
provided by the Sponsor.  Drug accountability documentation and all used and unused Study 
Drug vials must be returned to the Sponsor or designee. 
8. 
TREATMENT OF SUBJECTS 
8.1 
Study Drug Administration 
Details regarding the LP dosing injection procedure will be provided in the Dosing 
Administration Manual.  ISIS 396443 will be administered by dedicated study personnel who are 
unblinded to treatment group; this cannot be any of the key study site personnel (i.e., the 
Principal Investigator, study coordinator, or outcomes assessors).  The study drug administration 
will be performed in a dedicated room and the key study personnel and the parents will not be 
present during the procedure to ensure blinding. 
ISIS 396443 will be administered as an intrathecal slow bolus (1-3 minute) LP injection.  
ISIS 396443 will be administered using a ‘spinal anesthesia’ needle and syringe.  A 22G to 25G 
spinal anesthesia needle is recommended, but a 21G may be used if indicated by subject size or 
clinical condition.  The target site for needle insertion is the L3/L4 space, but may be 1 segment 
above or 1-2 segments below this level, if needed.  The volume of the injection is 5 mL; prior to 
the injection 5 mL of CSF fluid is to be collected for analyses.  Depending on institutional 
guidelines, anesthesia or sedation may be used for the LP procedure, following institutional 
procedures.  Subjects will be encouraged to lie flat for 1 hour following dosing, if possible. 
Table 2 outlines the dose, ISIS 396443 concentration, and volume for administration of 
ISIS 396443. 
Table 2 
ISIS 396443 Dose, Concentration, and Injection Volume 
Dose 
(mg) 
Concentration 
(mg/mL) 
Injection Volume 
(mL) 
12 
2.4 
5.0 
 


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Prior to each injection on Study Days 1, 29, 85, and 274, 5 mL of CSF fluid is to be collected for 
analyses.  CSF will be used for measurement of ISIS 396443 pharmacokinetic analyses and CSF 
SMN protein concentration.  Extra CSF may be stored for investigation of possible biomarkers 
of SMA disease or the pharmacodynamic effects of ISIS 396443 (e.g., CSF mRNA, CSF protein, 
CSF miRNA panel) or for profiling of drug binding proteins, bioanalytical method validation 
purposes, stability assessments, metabolite assessments, immunogenicity assessments (including 
assay development and validation purposes), or to assess other actions of ISIS 396443 with CSF 
constituents.  CSF analyses and data presentation will be conducted in a blinded manner. 
8.2 
Sham Procedure 
Subjects randomized to the sham-procedure control group will undergo a sham-procedure, rather 
than study drug administration, on Study Days 1, 29, 85, and 274.  Details regarding the sham 
procedure will be provided in the Dosing Administration Manual.  The sham procedure will be 
administered by dedicated study personnel who are unblinded to treatment group; this cannot be 
any of the key study site personnel (i.e., the Investigator, study coordinator, or outcomes 
assessors).  The sham procedure will be performed in a dedicated room and the key study 
personel and the parents will not be present during the procedure to ensure blinding. 
In general, the sham procedure will consist of a small needle prick on the lower back at the 
location where the LP injection is normally made.  The needle will break the skin but no LP 
injection or needle insertion will occur.  The needle prick will be covered with the same bandage 
that is used to cover the LP injection normally, thus simulating the appearance of an LP 
injection.  If anesthesia or sedation is used for the LP procedure in ISIS 396443 treated subjects, 
then in order to maintain the blind, minimal sedation (i.e. a low dose of an anxiolytic) should be 
used for the sham procedure, following institutional procedures.  The study subject will be kept 
in the procedure room for the same amount of time that subjects administered study drug are 
kept, thus simulating the time period of a study drug administration procedure. 
Study drug and sham kits will be packaged in a blinded fashion.  Blinded kits for sham procedure 
contain artificial CSF (5.0 mL solution per 6 mL vial) that will not be injected but will be used to 
simulate CSF samples for that subject.  
8.3 
Other Protocol-Required Drugs 
There are no other protocol required drugs. 
8.4 
Other Protocol-Required Procedures 
There are no other protocol-required treatment procedures. 
8.5 
Treatment Precautions 
There are no protocol-required treatment precautions. 
8.6 
Safety Monitoring Rules 
Please refer to the Guidance to Investigator section of the Investigator Brochure. 


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8.7 
Stopping Rules 
There are no additional specific stopping rules for this study but the Investigator should discuss 
significant concerns relating to individual subjects with the Medical Monitor and the Sponsor to 
ensure that it is appropriate for the subject to continue Study Drug. 
8.8 
Adjustment of Dose and/or Treatment Schedule 
No adjustment of dose is permitted.  In the event of a concurrent illness that would prevent the 
dosing procedure from being performed safely, an adjustment in the dose schedule may be 
permitted, but must be approved by the Medical Monitor.  In general, each scheduled dose may 
be delayed by up to 4 weeks. 
8.9 
Discontinuation of Study Treatment 
A subject must permanently discontinue study treatment for any of the following: 
• The subject’s parents/guardians withdraw consent 
• The subject experiences an adverse event that necessitates permanent discontinuation of 
study treatment 
The reason for discontinuation of study treatment must be recorded in the Case Report Form 
(CRF) and source documentation. 
Subjects that discontinue treatment will continue follow-up unless consent is withdrawn 
(Appendix A). 
8.10 
Withdrawal of Subjects from the Study 
Subjects must be withdrawn from the study for any of the following: 
• Withdrawal of consent 
• The subject or the subject’s parents/guardians is/are unwilling or unable to comply with 
the protocol 
• The subject experiences a medical emergency that necessitates unblinding of the 
subject’s treatment assignment 
Other reasons for withdrawal of subjects from the study might include: 
• At the discretion of the Investigator for medical reasons 
• At the discretion of the Investigator or Sponsor for noncompliance 
• Significant protocol deviation 
• Decision by the Investigator or Sponsor 
All efforts will be made to complete and report the observations as thoroughly as possible up to 
the date of withdrawal.  All information, including the reason for withdrawal from Study, must 
be recorded in the CRF. 


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Any subject for whom consent to participate in the study is withdrawn will be removed from 
further treatment and study observation immediately upon the date of request.  It should be 
encouraged that these subjects complete the early termination study procedures and observations 
at the time of withdrawal (Appendix A). 
For subjects withdrawn for reasons other than withdrawal of consent every effort should be made 
to complete the early termination study procedures and observations at the time of withdrawal 
(Appendix A). 
8.11 
Concomitant Therapy and Procedures 
The use of concomitant therapies or procedures defined below must be recorded on the subject’s 
CRF.  AEs related to administration of these therapies or procedures must also be documented on 
the appropriate CRF. 
8.11.1 
Concomitant Therapy 
A concomitant therapy is any non-protocol specified drug or substance (including over-the-
counter medications, herbal medications and vitamin supplements) administered between the 
beginning of screening and last telephone contact or study visit. 
Subject’s parents/guardians should consult with the Site Investigator or qualified designee prior 
to initiating any new medication, including non-prescription compounds or any other non-drug 
therapy. 
Allowed Concomitant Therapy 
Throughout the study, Site Investigators or designated licensed physicians involved in the study 
may prescribe concomitant medications or treatments deemed necessary for adverse events or to 
provide adequate supportive care. 
Disallowed Concomitant Therapy 
Study subjects are prohibited from receiving other experimental agents during the study.  This 
includes marketed agents at experimental doses that are being tested for the treatment of SMA 
(e.g., oral albuterol/salbutamol, riluzole, carnitine, creatine, sodium phenylbutyrate, valproate, 
hydroxyurea). 
8.11.2 
Concomitant Procedures 
A concomitant procedure is any therapeutic intervention (e.g., surgery/biopsy) or diagnostic 
assessment (e.g., blood gas measurement, bacterial cultures) performed between the beginning of 
screening and last telephone contact or study visit. 
9. 
SERIOUS AND NON-SERIOUS ADVERSE EVENT REPORTING  
9.1 
Sponsor Review of Safety Information 
Safety information will be collected, reviewed, and evaluated by the Sponsor in accordance with 
the Safety Management Plan throughout the conduct of the clinical trial. 


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9.2 
Regulatory Requirements 
The Sponsor is responsible for regulatory submissions and reporting to the Investigators of SAEs 
including suspected unexpected serious adverse reactions (SUSARs) per the International 
Conference on Harmonization (ICH) guidelines E2A and ICH E6.  Country-specific regulatory 
requirements will be followed in accordance with local country regulations and guidelines. 
IRBs/IECs will be notified of any serious adverse event (SAE) according to applicable 
regulations.  The DSMB will be notified of any SAE as specified in the DSMB charter. 
9.3 
Definitions 
9.3.1 
Adverse Event 
An adverse event is any unfavorable and unintended sign (including a clinically significant 
abnormal laboratory finding, for example), symptom, or disease temporally associated with the 
study or use of investigational drug product, whether or not the AE is considered related to the 
investigational drug product. 
9.3.2 
Adverse Reaction and Suspected Adverse Reaction 
An adverse reaction is any adverse event caused by the Study Drug. 
A suspected adverse reaction is any adverse event for which there is a reasonable possibility that 
the drug caused the adverse event.  A suspected adverse reaction implies a lesser degree of 
certainty about causality than an adverse reaction. 
9.3.3 
Serious Adverse Event (SAE) 
A serious adverse event is any adverse event that in the view of either the Investigator or 
Sponsor, meets any of the following criteria: 
• Results in death 
• Is life threatening: that is, poses an immediate risk of death at the time of the event 
An AE or suspected adverse reaction is considered “life-threatening” if, in the view of 
either the Investigator or Sponsor, its occurrence places the subject at immediate risk of 
death.  It does not include an AE or suspected adverse reaction that, had it occurred in a 
more severe form, might have caused death 
• Requires inpatient hospitalization or prolongation of existing hospitalization 
Hospitalization is defined as an admission of greater than 24 hours to a medical facility 
and does not always qualify as an AE 
• Results in a persistent or significant incapacity or substantial disruption of the ability to 
conduct normal life functions 
• Results in congenital anomaly or birth defect in the offspring of the subject (whether the 
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• Important medical events that may not result in death, are not life-threatening, or do not 
require hospitalization may also be considered serious when, based upon appropriate 
medical judgment, they may jeopardize the subject and may require medical or surgical 
intervention to prevent one of the outcomes listed in this definition.  Examples of such 
medical events include allergic bronchospasm requiring intensive treatment in an 
emergency room or at home, blood dyscrasias or convulsions that do not result in 
inpatient hospitalization, or the development of drug dependency or drug abuse 
9.4 
Monitoring and Recording Adverse Events 
Any pre-existing conditions or signs and/or symptoms present in a subject prior to the start of the 
study (i.e., before informed consent) should be recorded as Medical History and not recorded as 
AEs unless the pre-existing condition worsened.  The Investigator should always group signs and 
symptoms into a single term that constitutes a single unifying diagnosis if possible. 
9.4.1 
Serious Adverse Events 
In the interest of subject safety, and in order to fulfill regulatory requirements, all SAEs 
(regardless of their relationship to Study Drug) should be reported to the Sponsor within 
24 hours of the Study Center’s first knowledge of the event.  The collection of SAEs will begin 
after the subject signs the informed consent form and stop at the end of the subject’s follow-up 
period which is defined as the subject’s last visit.  When the Investigator is reporting by 
telephone, it is important to speak to someone in person versus leaving a message.  An Initial 
Serious Adverse Event Form should be completed and a copy should be faxed to the Sponsor or 
designee. 
Detailed information should be actively sought and included on Follow-Up Serious Adverse 
Event Forms as soon as additional information becomes available.  All SAEs will be followed 
until resolution.  SAEs that remain ongoing past the subject’s last protocol-specified follow-up 
visit will be evaluated by the Investigator and Sponsor.  If the Investigator and Sponsor agree the 
subject’s condition is unlikely to resolve, the Investigator and Sponsor will determine the follow-
up requirement. 
9.4.2 
Non-Serious Adverse Events 
The recording of non-serious AEs will begin after the subject signs the informed consent form 
and will stop at the end of the subject’s follow-up period, which is defined as subject’s last visit.  
The Investigator will monitor each subject closely and record all observed or volunteered AEs on 
the Adverse Event Case Report Form. 
9.4.3 
Evaluation of Adverse Events (Serious and Non-Serious) 
The Investigator’s opinion of the following should be documented on the Adverse Event Case 
Report Form. 
 
 


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9.4.3.1 
Relationship to the Study Drug 
The event’s relationship to the Study Drug is characterized by one of the following: 
• Related:  There is clear evidence that the event is related to the use of Study Drug e.g., 
confirmation by positive re-challenge test 
• Possible:  The event cannot be explained by the subject’s medical condition, concomitant 
therapy, or other causes, and there is a plausible temporal relationship between the event 
and Study Drug administration 
• Unlikely/Remote:  An event for which an alternative explanation is more likely (e.g., 
concomitant medications or ongoing medical conditions) or the temporal relationship to 
Study Drug administration and/or exposure suggests that a causal relationship is unlikely 
(For reporting purposes, Unlikely/Remote will be grouped together with Not Related) 
• Not Related:  The event can be readily explained by the subject’s underlying medical 
condition, concomitant therapy, or other causes, and therefore, the Investigator believes 
no relationship exists between the event and Study Drug 
9.4.3.2 
Severity 
The event’s severity is characterized by one of the following: 
• Mild:  The event is easily tolerated by the subject and does not affect the subject’s usual 
daily activities 
• Moderate:  The event causes the subject more discomfort and interrupts the subject’s 
usual daily activities 
• Severe:  The event is incapacitating and causes considerable interference with the 
subject’s usual daily activities 
If the event is an SAE, then all applicable seriousness criteria must be indicated (criteria listed in 
Section 9.3.3). 
9.4.3.3 
Action Taken with Study Drug 
Action taken with Study Drug due to the event is characterized by one of the following: 
• None:  No changes were made to Study Drug administration and dose 
• Permanently Discontinued:  Study drug was discontinued and not restarted 
• Temporarily Interrupted, restarted – same dose:  Dosing was temporarily interrupted 
or delayed due to the AE and restarted at the same dose without unblinding to treatment 
group 
9.4.3.4 
Treatment Given for Adverse Event 
Any treatment (e.g., medications or procedures) given for the AE should be recorded on the 
Adverse Event Case Report Form (treatment should also be recorded on the concomitant 
treatment or ancillary procedures CRF as appropriate). 


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9.4.3.5 
Outcome of the Adverse Event 
If the event is a non-serious AE then the event’s outcome is characterized by one of the 
following: 
• AE Persists:  Subject terminates from the trial and the AE continues 
• Recovered:  Subject recovered completely from the AE 
• Became Serious:  The event became serious (the date that the event became serious 
should be recorded as the Resolution Date of that AE and the Onset Date of the 
corresponding SAE) 
• Change in Severity (if applicable):  AE severity changed 
If the event is a SAE then the event’s outcome is characterized by one of the following: 
• Ongoing:  SAE continuing 
• Persists (as non-serious AE):  Subject has not fully recovered but the event no longer 
meets serious criteria and should be captured as an AE on the non-serious AE electronic 
case report form (eCRF) (the SAE resolution date should be entered as the date of onset 
of that AE) 
• Recovered:  Subject recovered completely from the SAE (the date of recovery should be 
entered as the SAE resolution date) 
• Fatal:  Subject died (the date of death should be entered as the SAE resolution date) 
9.5 
Procedures for Handling Special Situations 
9.5.1 
Abnormalities of Laboratory Tests 
Clinically significant abnormal laboratory test results may, in the opinion of the Investigator, 
constitute or be associated with an AE.  Examples of these include abnormal laboratory results 
that are associated with symptoms, or require treatment, e.g., bleeding due to thrombocytopenia, 
tetany due to hypocalcemia, or cardiac arrhythmias due to hyperkalemia.  Whenever possible, the 
underlying diagnosis should be listed in preference to abnormal laboratory values as AEs.  
Clinically significant abnormalities will be monitored by the Investigator until the parameter 
returns to its baseline value or until agreement is reached between the Investigator and Medical 
Monitor.  Laboratory abnormalities deemed not clinically significant (NCS) by the Investigator 
should not be reported as AEs.  Similarly, laboratory abnormalities reported as AEs by the 
Investigator should not be deemed NCS on the laboratory sheet. 
The Investigator is responsible for reviewing and signing all laboratory reports.  The signed 
clinical laboratory reports will serve as source documents. 
 
 


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9.5.2 
Prescheduled or Elective Procedures or Routinely Scheduled Treatments 
A prescheduled or elective procedure or a routinely scheduled treatment will not be considered 
an SAE, even if the subject is hospitalized; the Study Center must document all of the following: 
• The prescheduled or elective procedure or routinely scheduled treatment was scheduled 
(or was on a waiting list to be scheduled) prior to obtaining the subject’s consent to 
participate in the study 
• The condition that required the prescheduled or elective procedure or routinely scheduled 
treatment was present before and did not worsen or progress in the opinion of the 
Investigator between the subject’s consent to participate in the study and the timing of the 
procedure or treatment 
• The prescheduled or elective procedure or routinely scheduled treatment is the sole 
reason for the intervention or hospital admission 
9.5.3 
Dosing Errors 
Study drug errors defined as errors in administration or the administered dose should be 
documented as Protocol Deviations.  A brief description should be provided in the deviation, 
including whether the subject was symptomatic (list symptoms) or asymptomatic. 
Dosing details should be captured on the Dosing CRF. 
Should an overdose occur, the Investigator or designee should contact the Unblinded Medical 
Monitor within 24 hours. 
9.5.4 
Contraception and Pregnancy 
Female subjects that have reached reproductive maturity must have a negative pregnancy test at 
Screening and must not be able to become pregnant for the duration of the study, as described in 
Section 6.3. 
Male subjects must be abstinent during the duration of the study. 
If a subject becomes pregnant or a pregnancy is suspected, or if a male subject makes or believes 
that he has made someone pregnant during the study, then the site staff must be informed 
immediately.  An Initial Pregnancy Form should be submitted to the Sponsor or designee within 
24 hours of first learning of the occurrence of pregnancy.  Follow-up information including 
delivery or termination is reported on Follow-up Pregnancy Forms and reported within 24 hours. 
Payment for all aspects of obstetrical care, child or related care will be the subject’s 
responsibility. 


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10. 
STATISTICAL CONSIDERATIONS 
10.1 
Study Endpoints, Subsets, and Covariates 
10.1.1 
Primary Endpoint 
• Change from baseline in HFMSE (Hammersmith Functional Motor Scale – Expanded) 
score at 15 months 
10.1.2 
Secondary Efficacy Endpoints 
• Proportion of subjects who achieve a 3-point increase from baseline in Hammersmith 
Functional Motor Scale – Expanded (HFMSE) score at 15 months 
• Proportion of subjects that achieve any new motor milestone at 15 months 
• Number of motor milestones achieved per subject at 15 months 
• Change from baseline in Upper Limb Module Test at 15 months 
• Proportion of subjects that achieve standing alone at 15 months 
• Proportion of subjects that achieve walking with assistance at 15 months 
10.1.3 
Tertiary Efficacy Endpoints 
• Change from baseline in CSF SMN protein concentration 
• Clinical Global Impression of Change (Investigator and Caregiver assessment) 
• Change from baseline in PedsQL (Pediatric Quality of Life Inventory) 
• Change from baseline in Assessment of Caregiver Experience with Neuromuscular 
Disease (ACEND) 
• Disease-related hospitalizations and adverse events 
10.1.4 
Safety/Tolerability Endpoints 
• Adverse events 
• Vital signs and weight 
• Neurological examinations 
• Physical examinations  
• Clinical laboratory tests (serum chemistry, hematology, urinalysis) 
• Electrocardiograms (ECGs) 
• Use of concomitant medications 


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10.1.5 
Pharmacokinetic Endpoints 
• CSF levels of ISIS 396443 
• Plasma levels of ISIS 396443 
10.1.6 
Immunogenicity Endpoint 
• Plasma antibodies to ISIS 396443 
10.2 
Sample Size Considerations 
The sample size for this study was estimated based on limited available natural history data for 
the target population and data from the ISIS 396443-CS1 and ISIS 396443-CS2 clinical studies.  
70 patients in the treated group and 35 patients in the control group will give at least 90% power 
to detect a 3 point difference between control and treated groups in change on the HFMSE with a 
standard deviation of 4.4, using a two-sided t-test with an alpha level of 0.05.  The sample size 
was estimated using n-Query.  117 patients enrolled will ensure that a small dropout rate will not 
affect the power of the primary efficacy analysis. 
10.3 
Populations 
Intent to Treat (ITT) Set:  All patients who are randomized, receive at least one dose of study 
drug/sham procedure, and have a baseline and at least one post baseline efficacy evaluation. 
Per-Protocol Set (PPS):  PPS will include the subset of the ITT who complete at least the initial 
3 doses of study drug/sham procedures, have baseline and Day 169 efficacy assessments and 
who have no significant protocol deviations that would be expected to affect efficacy 
assessments. 
Safety Set:  All patients who are randomized and receive at least one dose of study drug/sham 
procedure. 
Pharmacokinetic Population:  All patients who are randomized and for which there is at least one 
evaluable post-dose/post-sham procedure pharmacokinetic sample. 
10.4 
Definition of Baseline 
The baseline is defined as the last non-missing assessment prior to the first dose of Study Drug. 
10.5 
Interim Analysis 
An interim analysis may take place when all subjects have completed the 6 month assessment 
and at least 39 subjects have completed the 15 month assessment.  At the interim analysis and 
final analysis, the same Mixed Effects Repeated Measures (MMRM) model will be used in 
analyzing the same endpoint (change in Hammersmith Functional Motor Scale Expanded 
(HFMSE) at month 15 from baseline).  At the interim analysis, since the month 15 endpoint 
values are not available for most of the patients, missing post-baseline HFMSE data will be 
handled using the multiple imputation method (Schafer 1997; Schafer 1999). 
A DSMB will review the interim analysis results and make determinations on whether it is 
appropriate for the trial to continue.  During the interim analysis, subject accrual will continue.  


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Details of the analysis and controlled access to the unblinded data are contained in the Statistical 
Analysis Plan (SAP) and DSMB Charter. 
In order to control the Type 1 error, a sequential closed testing procedure will be employed with 
the sequence of the endpoints as defined in Sections 10.1.1 and 10.1.2 at the interim and final 
analyses. 
If the interim analysis is performed, it will be conducted at the significance level of 0.01.  The 
significance level for the final analysis will be determined using an alpha allocation with a 
multiplicity adjustment method that will increase the significance level for the final analysis 
above 0.04 by accounting for the correlation between the interim and final analyses.  The 
analyses of the secondary endpoints at the interim and the final analysis will be performed at the 
same significance level as that for the primary analysis. 
If the interim analysis is not performed, significance level for the final analysis will remain at 
0.05. 
10.6 
Planned Methods of Analysis 
Data collected on eCRF, lab data transfers, as well as any outcomes derived from the data, will be 
provided in the patient data listings.  Patient data listings will be presented for all patients enrolled 
into the study. 
Descriptive summary statistics including n, mean, median, standard deviation, standard error, 
interquartile range (25th percentile, 75th percentile), and range (minimum, maximum) for 
continuous variables, and counts and percentages for categorical variables will be used to 
summarize most data by treatment group. 
All primary, secondary and tertiary endpoints will be assessed in the ITT Set and PPS, with the 
former being the basis for the primary efficacy analysis.  All safety assessments will be 
performed on the Safety Set. PK endpoints will be assessed in the PK Set as applicable. 
10.6.1 
Demographic and Baseline Characteristics 
Demographic and baseline characteristics will be summarized using descriptive statistics by 
treatment group.  Patient disposition will be summarized by treatment group.  All patients 
enrolled will be included in a summary of patient disposition. 
10.6.2 
Safety and Tolerability Analysis 
Safety analyses will be conducted in the Safety Set. Treatment duration and amount of study 
drug received will be summarized by treatment group. 
All treatment-emergent adverse events and serious adverse events will be summarized for each 
treatment group using the MedDRATM coding system, by system organ class, preferred term, 
relationship to Study Drug, and severity.  Narratives of deaths, serious adverse events, including 
early withdrawals from study drug and from study due to adverse events, will also be provided. 
Laboratory tests including chemistry panel, complete blood count with differential, etc. will be 
summarized by study visit for each treatment group.  These safety variables will also be 
presented over time after study drug administration, as appropriate.  Vital sign results will be 
presented similarly. 


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Physical and neurological examination findings and results from ECG will be listed for review.  
As appropriate, results will also be summarized descriptively for each treatment group.  
Concomitant medication usage for each subject will be listed for review. 
10.6.3 
Efficacy Analysis 
All statistical tests will be 2-sided with a Type 1 error rate of 5%, unless otherwise specified. 
Secondary efficacy endpoints have been rank prioritized in the order shown in Section 10.1.2.  In 
order to control the Type 1 error, a sequential closed testing procedure will be employed with the 
sequence of endpoints defined as above.  Testing of secondary endpoints will be performed only 
if the treatment comparison of the primary endpoint is statistically significant (p < 0.050, unless 
interim analysis is performed).  Testing of the secondary endpoints will be conducted according 
to the sequence above: if the first secondary endpoint (proportion of patients that achieve a 
3-point increase from baseline in HFMSE at 15 months) is statistically significant (p < 0.050, 
unless interim analysis is performed) then the second secondary endpoint (proportion of subjects 
that achieve any new motor milestone at 15 months) will be tested at the same significance level.  
However, if the treatment comparison based on the first secondary endpoint is not statistically 
significant, then all endpoints of a lower rank will not be considered statistically significant.  
This process is repeated with each subsequent secondary endpoint. 
Analyses of tertiary efficacy endpoints will not include adjustments for multiplicity. 
The primary analysis of the primary endpoint is to compare the change from baseline in HFMSE 
score at Month 15 between treatment groups using the ITT Set.  The data will be analyzed using 
a Mixed Effects Model with Repeated Measures (MMRM) model where the treatment group, 
time, treatment by time interaction, and patient age at Screening will be included in the model as 
fixed effects; patient will be a random effect; the baseline HFMSE score will be included as a 
covariate.  No imputation for missing data will be made.  The unstructured covariance model 
will be used and test of fixed effects will be carried out.  The treatment contrast for Month 15 
will be estimated by the model.  The primary efficacy analysis will take place after all patients 
have completed the Day 456/ET visit and the database has been locked. 
The following sensitivity analyses will also be conducted, and details of the analyses will be 
outlined in the SAP:  
• The primary analysis will be repeated in the PPS. 
• The primary analysis will be repeated in the subset of ITT Set who have non-missing 
Month 15 HFMSE score. 
• The LOCF method will be used to impute missing Month 15 HFMSE score.  Stratified 
Wilcoxon Rank Sum test and ANCOVA with the stratification factor and baseline 
HFMSE score as covariates will be used to analyze the imputed data. 


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The primary analysis of each secondary endpoint will be based on the ITT Set.  Analyses based 
on the PPS are considered sensitivity analyses. 
• Comparison of proportion of subjects that achieve a 3-point increase from baseline in 
HFMSE score at Month 15 between the treatment groups.  The data will be analyzed 
using the logistic regression adjusting for each patient’s age at screening and baseline 
HFMSE score.  If a patient terminates study before Month 15 due to AE, lack of efficacy 
or other types of treatment failure, then the patient will be considered as a non-responder.  
If a patient terminates study before Month 15 or has missing HFMSE score at Month 15 
due to any other reason, then the patient will not be included in the analysis. 
• Comparison of proportion of subjects that achieve any new motor milestone at Month 15 
between the treatment groups.  The data will be analyzed using the logistic regression 
adjusting for each patient’s age at Screening and baseline number of motor milestones 
that a patient has achieved.  If a patient terminates study before Month 15 due to AE, lack 
of efficacy or other types of treatment failure, then the patient will be considered as a 
non-responder.  If a patient terminates study before Month 15 or has missing data at 
Month 15 due to any other reason, then the patient will not be included in the analysis. 
• Comparison of number of motor milestones achieved per subject at Month 15 between 
treatment groups.  The data will be analyzed in a similar way to the primary endpoint. 
• Comparison of change from baseline in Upper Limb Module Test at Month 15 between 
treatment groups.  The data will be analyzed in a similar way to the primary endpoint. 
• Comparison of proportion of subjects that achieve standing alone milestone at Month 15 
between the treatment groups.  The data will be analyzed in a similar way to the 
proportion of subjects that achieve any new motor milestone at Month 15. 
• Comparison of proportion of subjects that achieved walking with assistance milestone at 
Month 15 between the treatment groups.  The data will be analyzed in a similar way to 
the proportion of subjects that achieve any motor milestone at Month 15. 
10.6.4 
Pharmacokinetic Analysis 
Plasma pharmacokinetic parameters and ISIS 396443 concentrations in plasma and CSF for the 
Pharmacokinetic population will be summarized using descriptive statistics and, where 
warranted, presented graphically. 
11. 
INVESTIGATOR’S REGULATORY OBLIGATIONS 
11.1 
Informed Consent/Assent 
The written informed consent and assent documents should be prepared in the language(s) of the 
potential subject population, based on an English version provided by the Sponsor and should be 
easy to understand. 
Before a subject’s participation in the trial, the Investigator is responsible for obtaining written 
informed consent from the parent or legal guardian and, in cases where institutional guidelines 
and the subject’s age dictate, informed assent from the subject, after adequate explanation of the 


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aims, methods, anticipated benefits, and potential hazards of the study and before any protocol-
specific screening procedures or any study drugs are administered.  Sufficient time must be given 
to consider whether to participate in the study. 
The acquisition of informed consent/assent and the parent/legal guardian’s/subject’s agreement 
or refusal of his/her notification of the primary care physician should be documented in the 
subject’s medical records, and the informed consent/assent form(s) should be signed and 
personally dated by the parent/legal guardian/subject and by the study person who conducted the 
informed consent/assent discussion.  The original signed informed consent/assent form(s) should 
be retained in the Study Master File and in any other locations required by institutional policy, 
and a copy of the signed consent/assent form(s) should be provided to the parent or guardian. 
11.2 
Ethical Conduct of the Study 
The Guidelines of the World Medical Association (WMA) Declaration of Helsinki dated 
October 2002 the applicable regulations and guidelines of current Good Clinical Practice (GCP) 
as well as the demands of national drug and data protection laws and other applicable regulatory 
requirements will be strictly followed. 
11.3 
Institutional Review Board/Institutional Ethics Committee/Research Ethics Board 
A copy of the protocol, proposed informed consent form, proposed informed assent form (if 
applicable) other written subject information, and any proposed advertising material must be 
submitted to the IRB/IEC for written approval.  A copy of the written approval of the protocol 
and informed consent/assent forms must be received by the Sponsor before recruitment of 
subjects into the study and shipment of Study Drug.  A copy of the written approval of any other 
items/materials that must be approved by the Study Center or IRB/IEC must also be received by 
the Sponsor before recruitment of subjects into the study and shipment of Study Drug.  The 
Investigator’s Brochure must be submitted to the IRB/IEC for acknowledgement. 
The Investigator must submit to and, where necessary, obtain approval from the IRB/IEC for all 
subsequent protocol amendments and changes to the informed consent/assent documents.  The 
Investigator should notify the IRB/IEC of deviations from the protocol in accordance with ICH 
GCP Section 4.5.2.  The Investigator should also notify the IRB/IEC of serious adverse events 
occurring at the Study Center and other adverse event reports received from the Sponsor, in 
accordance with local procedures. 
The Investigator will be responsible for obtaining annual IRB/IEC approval/renewal throughout 
the duration of the study.  Copies of the Investigator’s reports, all IRB/IEC submissions and the 
IRB/IEC continuance of approval must be sent to the Sponsor. 
11.4 
Subject Confidentiality 
The Investigator must ensure that the subject’s confidentiality is maintained.  On the CRFs or 
other documents submitted to the Sponsor, subjects should be identified by unique, anonymous 
initials and a subject study number only.  Documents that are not for submission to the Sponsor 
(e.g., signed informed consent/assent forms) should be kept in strict confidence by the 
Investigator. 
In compliance with federal and local regulations/ICH GCP Guidelines, it is required that the 
Investigator and institution permit authorized representatives of the company, of the regulatory 


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agency(s), and the IRB/IEC direct access to review the subject’s original medical records for 
verification of study-related procedures and data.  Direct access includes examining, analyzing, 
verifying, and reproducing any records and reports that are important to the evaluation of the 
study.  The Investigator is obligated to inform and obtain the consent of the subject’s parent or 
guardian to permit named representatives to have access to his/her study-related records without 
violating the confidentiality of the subject. 
12. 
ADMINISTRATIVE AND LEGAL OBLIGATIONS 
12.1 
Protocol Amendments 
Agreement from the Investigator must be obtained for all protocol amendments and amendments 
to the informed consent/assent documents.  The regulatory authority and IRB/IEC must be 
informed of all amendments and give approval for any amendments likely to affect the safety of 
the subjects or the conduct of the trial.  The Investigator must send a copy of the approval letter 
from the IRB/IEC to the Sponsor. 
12.2 
Study Termination 
The Sponsor reserves the right to terminate the study.  The Investigator reserves the right to 
terminate their participation in the study, according to the terms of the site contract.  The 
Investigator/Sponsor should notify the IRB/IEC in writing of the trial’s completion or early 
termination and send a copy of the termination to the Sponsor. 
12.3 
Study Documentation and Storage 
The Investigator should ensure that all appropriately qualified persons to whom he/she has 
delegated trial duties are recorded on a Sponsor-approved Delegation of Site Responsibilities 
Form. 
Source documents are original documents, data, and records from which the subject’s CRF data 
are obtained.  These include but are not limited to hospital records, clinical and office charts, 
laboratory and pharmacy records, and correspondence.  In this study, CRFs may not be used as 
source documents. 
The Investigator and Study Center staff is responsible for maintaining a comprehensive and 
centralized filing system of all study-related (essential) documentation in accordance with 
Section 8 of the ICH Guidelines (E6), suitable for inspection at any time by representatives from 
the Sponsor and/or applicable regulatory authorities.  Elements should include: 
• Subject files containing completed CRFs, informed consents/assents, and supporting 
copies of source documentation 
• Study files containing the protocol with all amendments, Investigator’s Brochure, copies 
of pre-study documentation and all correspondence to and from the IRB and the Sponsor 
• If drug supplies are maintained at the Study Center, proof of receipt, Study Drug Product 
Accountability Record, Return of Study Drug Product for Destruction, and all drug-
related correspondence 


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In addition, all original source documents supporting entries in the CRFs must be maintained and 
be readily available. 
No study document should be destroyed without prior written agreement between the Sponsor 
and the Investigator.  Should the Investigator wish to assign the study records to another party or 
move them to another location, he/she must notify the Sponsor. 
12.4 
Study Monitoring 
The Sponsor representative and regulatory authority inspectors are responsible for contacting and 
visiting the Investigator for the purpose of inspecting the facilities and, upon request, inspecting 
the various records of the trial (e.g., CRFs and other pertinent data) provided that subject 
confidentiality is respected. 
The Sponsor monitor is responsible for inspecting the CRFs at regular intervals throughout the 
study to verify adherence to the protocol; completeness, accuracy, and consistency of the data; 
and adherence to local regulations on the conduct of clinical research.  The monitor should have 
access to subject medical records and other study-related records needed to verify the entries on 
the CRFs. 
The Investigator agrees to cooperate with the monitor to ensure that any problems detected in the 
course of these monitoring visits, including delays in completing CRFs, are resolved. 
In accordance with ICH GCP and the Sponsor’s audit plans, this study may be selected for audit 
by representatives from the Sponsor’s Clinical Quality Assurance Department.  Inspection of 
Study Center facilities (e.g., pharmacy, drug storage areas, laboratories) and review of study-
related records will occur to evaluate the trial conduct and compliance with the protocol, ICH 
GCP, and applicable regulatory requirements. 
To ensure the quality of clinical data a clinical data management review will be performed on 
subject data received by the Sponsor.  During this review, subject data will be checked for 
consistency, omissions, and any apparent discrepancies.  In addition, the data will be reviewed 
for adherence to the protocol and GCP.  To resolve any questions arising from the clinical data 
management review process, data queries and/or Study Center notifications will be sent to the 
Study Center for completion and return to Sponsor. 
The Principal Investigator will sign and date the indicated places on the CRF.  These signatures 
will indicate that the Principal Investigator inspected or reviewed the data on the CRF, the data 
queries, and the Study Center notifications, and agrees with the content. 
12.5 
Language 
CRFs must be completed in English.  Generic names for concomitant medications should be 
recorded in English if possible, unless it is a combination drug, then record the trade name in 
English. 
All written information and other material to be used by subjects and investigative staff must use 
vocabulary and language that are clearly understood. 


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12.6 
Compensation for Injury 
The Sponsor maintains appropriate insurance coverage for clinical trials and will follow 
applicable local compensation laws.  Subjects will be treated and/or compensated for any study-
related illness/injury in accordance with the information provided in the Compensation for Injury 
section of the Informed Consent document. 


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13. 
REFERENCES 
Cho S and Dreyfuss G. A degron created by SMN2 Exon 7 skipping is a principal contributor to spinal muscular 
atrophy severity. Genes Dev 2010; 24: 438-442. 
Coovert DD, Le TT, McAndrew PE, Strasswimmer J, Crawford TO, Mendell JR, Coulson SE, Androphy EJ, 
Prior TW, Burghes AH. The survival motor neuron protein in spinal muscular atrophy. Hum Mol Genet 1997; 6: 
1205-1214. 
Feldkotter M, Schwarzer V, Wirth R, Wienker TF, Wirth B. Quantitative analyses of SMN1 and SMN2 based on 
real-time light cycler PCR: fast and highly reliable carrier testing and prediction of severity of spinal muscular 
atrophy. Am J Hum Genet 2002; 70: 358-368. 
Geary RS, Yu RZ, Watanabe T, Henry SP, Hardee GE, Chappell A, Matson J, Sasmor H, Cummins L, Levin AA. 
Pharmacokinetics of a tumor necrosis factor-α phosphorothioate 2′-O-(2-Methoxyethyl) modified antisense 
oligonucleotide: comparison across species. Drug Metab Disp 2003; 31: 1419-1428. 
Helmken C, Hofmann Y, Schoenen F, Oprea G, Raschke H, Rudnik-Schöneborn S, Zerres K, Wirth B. Evidence for 
a modifying pathway in SMA discordant families: reduced SMN level decreases the amount of its interacting 
partner and Htra2-beta1. Hum Genet 2003; 114: 11-21. 
Henry S, Stecker K, Brooks D, Monteith D, Concklin B, Bennett CF. Chemically modified oligonucleotides exhibit 
decreased immune stimulation in mice. J Pharmacol Exp Ther 2000; 292: 468-479. 
Hua Y, Vickers TA, Baker BF, Bennett CF, Krainer AR. Enhancement of SMN2 Exon 7 inclusion by antisense 
oligonucleotides targeting the exon. PLoS Biol 2007; 5: e73. 
Hua Y, Vickers TA, Okunola HL, Bennett CF, Krainer AR. Antisense masking of an HnRNP A1/A2 intronic 
splicing silencer corrects SMN2 splicing in transgenic mice. Am J Hum Genet 2008; 82: 834-848. Epub 2008 
Mar 27. 
Iannaccone ST, Hynan LS, Morton A, Buchanan R, Limbers CA, Varni JW, the AmSMART Group. The PedsQL in 
pediatric patients with spinal muscular atrophy: feasibility, reliability, and validity of the pediatric quality of life 
inventory generic core scales and neuromuscular module. Neuromuscul Disord 2009; 19: 805-812. 
Keren H, Lev-Maor G, Ast G. Alternative splicing and evolution: diversification, exon definition and function. 
Nat.Rev.Genet 2010; 11: 345-355. 
Le TT, Pham LT, Butchbach ME, Zhang HL, Monani UR, Coovert DD, Gavrilina TO, Xing L, Bassell GJ, 
Burghes AH. SMNΔ7, the major product of the centromeric survival motor neuron (SMN2) gene, extends survival 
in mice with spinal muscular atrophy and associates with full-length SMN. Hum Mol Genet 2005; 14: 845-857. 
Epub 2005 Feb 9. 
Lefebvre S, Bürglen L, Reboullet S, Clermont O, Burlet P, Viollet L, Benichou B, Cruaud C, Millasseau P, 
Zeviani M, Le Paslier D, Frézal J, Cohen D, Weissenbach J, Munnich A, Melki J. Identification and characterization 
of a spinal muscular atrophy-determining gene. Cell 1995; 80: 155-165. 
Lefebvre S, Burlet P, Liu Q, Bertrandy S, Clermont O, Munnich A, Dreyfuss G, Melki J. Correlation between 
severity and SMN protein level in spinal muscular atrophy. Nat Genet 1997; 16: 265-269. 
Main M, Kairon H, Mercuri E, Muntoni F. The Hammersmith functional motor scale for children with spinal 
muscular atrophy: a scale to test ability and monitor progress in children with limited ambulation. Eur J Paediatr 
Neurol 2003; 7(4): 155-159. 
Matsumoto H, Clayton-Krasinski DA, Klinge SA, Gomex JA, Booker WA, Hman JE, Roye Jr. DP, Vitale MG. 
Development and initial validation of the assessment of caregiver experience with neuromuscular disease. J Pediatr 
Orthop 2011; 31: 284-292. 
Mazzone E, Bianco F, Martinelli D, Glanzman A, Messina S, De Sanctis R, Main M, Eagle M, Florence J, 
Krosschell K, Vasco G, Pelliccioni M, Lombardo M, Pane M, Finkel R, Muntoni F, Bertini E, Mercuri E. Assessing 
upper limb function in nonambulant SMA patients: development of a new module. Neuromuscul Disord 2011; 21: 
406-412. 


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McKay RA, Miraglia LJ, Cummins LL, Owens SR, Sasmor H, Dean NM. Characterization of a potent and specific 
class of antisense oligonucleotide inhibitor of human protein kinase C-α expression. J Bio Chem 1999; 274: 1715-
1722. 
O’Hagen JM, Glanzman AM, McDermott MP, Ryan PA, Flickinger J, Quigley J, Riley S, Sanborn E, Irvine C, 
Martens WB, Annis C, Tawil R, Oskoui M, Darras BT, Finkel RS, De Vivo DC. An expanded version of the 
hammersmith functional motor scale for SMA II and III patients. Neuromuscular Disorders 2007; 17: 693-697. 
Passini MA, Bu J, Richards AM, Kinnecom C, Sardi SP, Stanek LM, Hua Y, Rigo F, Matson J, Hung G, Kaye EM, 
Shihabuddin LS, Krainer AR, Bennett CF, Cheng SH. Antisense oligonucleotides delivered to the mouse CNS 
ameliorate symptoms of severe spinal muscular atrophy. Science Trans Med 2011; 3: 1-12. 
Prior TW, Swoboda KJ, Scott HD, Hejmanowski AQ. Homozygous SMN1 deletions in unaffected family members 
and modification of the phenotype by SMN2 gene. Am J Med Genet 2004; 130A: 307-310. 
Schafer JL. Analysis of incomplete multivariate data. Boca Raton, FL. Chapman and Hall/CRC: 1997. 
Schafer JL. Multiple Imputation: A Primer. Statistical Methods in Medical Research 1999; 8: 3-15. 
Varni JW, Seid M, Rode CA. Measurement model for the pediatric quality of life inventory. Medical Care 1999; 37: 
126-139. 
WHO Multicentre Growth Reference Study Group. Assessment of sex differences and heterogeneity in motor 
milestone attainment among populations in the WHO Multicentre Growth Reference Study. Acta Pædiatrica, 2006; 
Suppl 450: 66/75. 
Wijnhoven T, de Onis M, Onyango A, Wang T, Bjoerneboe G, Bhandari N, Lartey A, Al Rashidi B. Assessment of 
gross motor development in the WHO Multicentre Growth Reference Study. Food Nutr Bull 2004; 21: S37-45. 
 


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14. 
APPENDICES 
 


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Appendix A 
Schedule of Procedures 
 


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Appendix A Schedule of Procedures 
Subjects will also be monitored through phone contact on Study Days 8, 56, 113, 141, 204, 239, 302, 330, 393, 421 (all ± 2 days)9 
Study Period 
Screen 
Treatment/Follow-up 
Study Day 
D -28 
to 
D -1 
D1 
D2
D29 (±1D) 
D30
D85 (±2D) 
D86
D92
(±1D)
D169
(±2D) 
D274 (±7D) 
D275
D365
(±7D) 
and 
D456
(+ 7D) 
and 
Early 
Term 
Pre- 
dose 
LP/
SP 
Post-
dose
Pre-
dose
LP/
SP
Post-
dose
Pre-
dose
LP/
SP 
Post- 
dose 
Pre-
dose
LP/
SP
Post- 
dose
Informed Consent 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Inclusion/Exclusion 
Criteria 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Medical History 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Screening X-ray 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Urine Pregnancy 
Test11 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
X14 
SMN2 copy Number12 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Study Drug 
Injection/Sham 
Procedure 
 
 
X 
 
 
 
X7 
 
 
 
X7 
 
 
 
 
 
X7 
 
 
 
In-Patient Stay 
(24 hours) 
 
 
 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Vital Signs1 
X 
X 
 
4X2 
X3
X 
 
4X2 
X 
X 
 
4X2 
X 
X 
X 
X 
 
4X2 
X 
X 
Weight 
X 
X 
 
 
 
X 
 
 
 
X 
 
 
 
X 
X 
X 
 
 
 
X 
Height/ulnar length 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
X14 
Physical Examination 
X 
X 
 
 
 
X 
 
 
 
X 
 
 
 
X 
X 
X 
 
 
 
X 
Neurological 
Examination 
X 
X 
 
X4 
X3 
X 
 
X4 
X 
X 
 
X4 
X 
X 
X 
X 
 
X4 
X 
X 
ECG 
X 
 
 
 
X 
 
 
X 
 
 
 
 
 
X 
 
 
 
 
 
X14 
Safety Labs5 
X 
X 
 
 
X 
X 
 
 
 
X 
 
 
 
 
X 
X 
 
 
 
X14 
Coagulation Labs 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Immunogenicity  
 
X 
 
 
 
X 
 
 
 
X 
 
 
 
 
X 
X 
 
 
 
X14 


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Appendix A Schedule of Procedures Continued 
Study Period 
Screen 
Treatment/Follow-up 
Study Day 
D -28 
to 
D -1 
D1 
D2
D29 (±1D) 
D30
D85 (±2D) 
D86
D92
(±1D)
D169
(±2D) 
D274 (±7D) 
D275
D365
(±7D) 
and 
D456
(+ 7D) 
and 
Early 
Term 
Pre- 
dose 
LP/
SP 
Post-
dose
Pre-
dose
LP/
SP
Post-
dose
Pre-
dose
LP/
SP 
Post- 
dose 
Pre-
dose
LP/
SP
Post-
dose
CSF PK8 
 
X 
 
 
 
X 
 
 
 
X 
 
 
 
 
 
X 
 
 
 
 
CSF SMN Protein 
 
X 
 
 
 
X 
 
 
 
X 
 
 
 
 
 
X 
 
 
 
 
Plasma PK8 
 
X 
 
3X 
X 
X 
 
 
 
X 
 
X 
 
 
X 
X 
 
 
 
X14 
HFMSE 
X10 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
WHO Motor Milestones 
X6, 10 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
Upper Limb 
X6, 10 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
PedsQL 
X6 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
ACEND 
X6 
 
 
 
 
 
 
 
 
 
 
 
 
 
X 
 
 
 
 
X14 
CGI 
 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
Con Med Recording9 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Adverse Event 
Collection9 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
1 
Resting blood pressure, pulse, respiratory rate, and temperature 
2 
Vital signs performed 1, 2, 4, 6 hours after dosing 
3 
Conducted within 20-24 hours after dosing 
4 
Neurological exams at 5 hours after dosing 
5 
Serum chemistry, hematology, urinalysis panels (Appendix B for analytes) 
6 
Efficacy assessments (with the exception of HFMSE) do not form part of the screening assessment or inclusion/exclusion criteria but are baseline 
measurements taken during the screening phase of the study 
7 
Overnight stay is optional on Day 29, Day 85, and Day 274  
8 
Refer to Appendix C for PK sampling schedule 
9 
At telephone contact, changes in concomitant medications and adverse events will be recorded  
10 To be performed 2 times during the screening period  
11 Urine pregnancy test performed for females of child-bearing potential, if positive to be confirmed by local serum test 
12 Only for those subjects who do not have documented evidence of SMN copy number from Athena Diagnostics 
13 These assessments may be performed up to 7 days prior to dosing, if necessary 
14 Assessed on Day 456 only 


ISIS 396443-CS4 
CONFIDENTIAL
Amendment 1
Protocol 
26 September 2014
 
52 
 
 
 
 
 
 
 
Appendix B 
Laboratory Analytes 
 
 
 


ISIS 396443-CS4 
CONFIDENTIAL
Amendment 1
Protocol 
26 September 2014
 
53 
Appendix B Laboratory Analytes 
CLINICAL SAFETY ASSESSMENTS 
(minimum requirements) 
OTHER ASSESSMENTS 
Clinical Chemistry 
Sodium 
Potassium 
Chloride 
Total protein 
Albumin 
Calcium 
Phosphorus 
Bicarbonate 
Glucose 
BUN 
Creatinine 
Cystatin C 
Total serum Bilirubin 
Alkaline phosphatase 
AST (SGOT) 
ALT (SGPT) 
CPK 
 
Coagulation 
aPTT 
PT 
INR 
Urinalysis  
Specific gravity 
pH 
Protein 
Glucose 
Ketones 
Bilirubin 
Blood 
Red blood cells 
White blood cells 
Epithelial cells 
Bacteria 
Casts 
Crystals 
 
Hematology 
Red blood cells 
Hemoglobin 
Hematocrit 
Platelets 
White blood cells 
WBC Differential 
• 
(% and absolute) 
• 
Neutrophils 
• 
Eosinophils 
• 
Basophils 
• 
Lymphocytes 
• 
Monocytes 
Pregnancy 
Urine hCG 
 
PK* 
Plasma ISIS 396443 levels 
CSF ISIS 396443 levels 
 
PD 
CSF SMN protein levels 
 
Immunogenicity Evaluation 
ISIS 396443 plasma Abs 
 
SMN Genetics 
SMN2 Copy Number 
* 
Any of the collected PK plasma and CSF samples from the study patients may also be used for investigation of 
possible biomarkers of SMA disease or the pharmacodynamic effects of ISIS 396443 (e.g., CSF mRNA, CSF 
protein, CSF miRNA panel) or for profiling of drug binding proteins, bioanalytical method validation purposes, 
stability assessments, metabolite assessments, immunogenicity assessments (including assay development and 
validation purposes), or to assess other actions of ISIS 396443 with plasma and CSF constituents. 
 
 


ISIS 396443-CS4 
CONFIDENTIAL
Amendment 1
Protocol 
26 September 2014
 
54 
 
 
 
 
 
 
 
Appendix C 
Pharmacokinetic Sampling Schedule 
 
 


ISIS 396443-CS4 
CONFIDENTIAL 
Amendment 1 
Protocol 
 
26 September 2014 
 
55 
Appendix C Pharmacokinetic Sampling Schedule 
Treatment Period 
Study Day 
Timepoints 
Blood 
Collection  
CSF Collection  
Multiple Dose: 
LP Injection 
D1 
Predose 
0.35 mL 
0.5 mL 
2 hr 
0.35  mL 
NA 
4 hr 
0.35  mL 
NA 
8 hr 
0.35  mL 
NA 
D2 
24 hr 
0.35  mL 
NA 
D29 
Predose 
0.35  mL 
0.5 mL 
D85 
Predose 
0.35  mL 
0.5 mL 
4 hr 
0.35  mL 
NA 
D169 
Anytime 
0.35  mL 
NA 
D274 
Predose 
0.35  mL 
0.5 mL 
D456 
Anytime 
0.35  mL 
NA 
NA Not applicable (No Collection Scheduled) 
Details on sampling, preparation, and shipment are included in the study laboratory manual. 
Any of the collected PK plasma and CSF samples from the study patients may also be used for investigation of 
possible biomarkers of SMA disease or the pharmacodynamic effects of ISIS 396443 (e.g., CSF mRNA, CSF protein, 
CSF miRNA panel) or for profiling of drug binding proteins, bioanalytical method validation purposes, stability 
assessments, metabolite assessments, immunogenicity assessments (including assay development and validation 
purposes), or to assess other actions of ISIS 396443 with plasma and CSF constituents. 


 
 
 
 
ISIS PHARMACEUTICALS, INC. 
 
 
ISIS 396443-CS4 
 
A Phase 3, Randomized, Double-blind, Sham-Procedure Controlled 
Study to Assess the Clinical Efficacy and Safety of ISIS 396443 
Administered Intrathecally in Patients with Later-onset Spinal 
Muscular Atrophy 
 
Original Protocol 17 July 2014 
EudraCT No: 2014-001947-18 
 
 
 
 
Sponsor: 
Isis Pharmaceuticals, Inc. 
2855 Gazelle Court 
Carlsbad, CA  92010 


I SI S 3 9 6 4 4 3- C S 4 
Pr ot o c ol 
C O N FI D E N TI A L 
I SI S 3 9 6 4 4 3- C S 4 
Ori gi n al 
1 7 . J ul y 2 0 1 4 
A P h as e 3, R a n d o mi z e d, D o u bl e- bli n d, S h a m- Pr o c e d ur e C o ntr oll e d 
St u d y t o Assess t h e Cli ni c al Effi c a c y a n d S af et y of I SI S 3 9 6 4 4 3 
A d mi nist er e d I ntr at h e c all y i n P ati e nts wit h L at er- o ns et S pi n al 
M us c ul ar Atr o p h y 
S p o ns or: 
Isis P h ar m a c e uti c als, I nc. 
2 8 5 5 G a z ell e C o urt 
C arls b a d, C A 9 2 0 1 0 
Ori gi n al Pr ot o c ol- 1 7 J ul y 2 0 1 4 
P P D
2 


I SI S 3 9 6 4 4 3 -C S 4  
C O N FI D E N TI A L  
Ori gi nal  
Pr ot oc ol  
 
1 7 J ul y 2 0 1 4  
 
3
 
 
I SI S 3 9 6 4 4 3  
Isis Pr ot o c ol N u m ber I SI S 3 9 6 4 4 3-C S 4 
Ori gi n al Pr ot oc ol 
 
Cli nic al P h ase:   3 
A P h ase 3, R a n d o mi ze d, D o u ble -bli n d, S h a m -Pr oce d ure C o ntr olle d 
St u d y t o Assess t he Cli nic al Effic a c y a n d S afet y of I SI S 3 9 6 4 4 3  
A d mi nistere d I ntr at hec all y i n P ati e nts wit h L ater -o nset S pi n al 
M usc ul ar Atr o p h y  
 
Trial S p o ns or:  
Isis P har mace uticals,  I nc. 
2 8 5 5 Gazelle C o urt  
Carls ba d, C A  9 2 0 1 0  
P h o ne:  + 0 1 7 6 0 9 3 1 9 2 0 0  
Fa x:  
+ 0 1 7 6 0 6 0 3 2 7 0 0  
Ke y S p o ns or  C o ntact:  
 
2 8 5 5 Gazelle C o urt  
Carls ba d, C A  9 2 0 1 0  
P h o ne:  + 
 
Fa x:  
+ 
 
 
 
Date:  
1 7  J ul y 2 0 1 4  
 
 
C o nfi de nti alit y St ate me nt  
P P D
T his d oc u me nt c o ntai ns c o nfi de ntial i nf or mati o n of Isis P har mace uticals, I nc. t hat m ust n ot be 
discl ose d t o a n y o n e ot her t ha n t he reci pie nt st u d y staff a n d me m bers of t he i nstit uti o nal re vie w 
b oar d or a ut h orize d r e gul at or y a ge n cies.  T his i nf or mati o n ca n n ot be use d f or a n y p ur p ose ot h er 
t ha n t he e val uati o n or c o n d uct of t he cli nical i n vesti gati o n wit h o ut t he pri or writte n c o nse nt of 
Isis P har mace uticals, I nc. 
P P D
P P D


ISIS 396443-CS4 
CONFIDENTIAL 
Original 
Protocol 
 
17 July 2014 
 
4 
Protocol Signature Page 
 
Protocol Number: 
ISIS 396443-CS4 
Protocol Title: 
A Phase 3, Randomized, Double-blind, Sham-Procedure Controlled Study 
to Assess the Clinical Efficacy and Safety of ISIS 396443 Administered 
Intrathecally in Patients with Later-onset Spinal Muscular Atrophy 
Amendment: 
Original Protocol 
Date: 
17 July 2014 
 
I hereby acknowledge that I have read and understand the attached clinical protocol, entitled “A 
Phase 3, Randomized, Double-blind, Sham-Procedure Controlled Study to Assess the Clinical 
Efficacy and Safety of ISIS 396443 Administered Intrathecally in Patients with Later-onset 
Spinal Muscular Atrophy”, dated 17 July 2014, and agree to conduct the study as described 
herein. 
I agree to comply with the International Conference on Harmonization Tripartite Guideline on 
Good Clinical Practice (E6). 
I agree to ensure that the confidential information contained in this document will not be used for 
any purpose other than the evaluation or conduct of the clinical investigation without the prior 
written consent of Isis Pharmaceuticals, Inc.  
 
 
 
 
 
 
Investigator’s Signature 
 
 
 
Investigator’s Name (please print) 
 
Date (DD Month YYYY) 
 


ISIS 396443-CS4 
CONFIDENTIAL 
Original 
Protocol 
 
17 July 2014 
 
5 
TABLE OF CONTENTS 
Page 
PROTOCOL SYNOPSIS ..............................................................................................................9 
STUDY GLOSSARY ...................................................................................................................13 
1. 
OBJECTIVES .....................................................................................................................15 
1.1 
Primary Objective .....................................................................................................15 
1.2 
Secondary Objective .................................................................................................15 
1.3 
Tertiary Objective .....................................................................................................15 
2. 
BACKGROUND AND RATIONALE ..............................................................................15 
2.1 
Spinal Muscular Atrophy ..........................................................................................15 
2.2 
Therapeutic Rationale ...............................................................................................16 
2.3 
ISIS 396443 ..............................................................................................................17 
2.3.1 
Mechanism of Action ...............................................................................17 
2.3.2 
Chemistry .................................................................................................17 
2.3.3 
Preclinical Experience ..............................................................................17 
2.3.4 
Clinical Experience ..................................................................................18 
2.4 
Rationale for Dose and Schedule of Administration ................................................19 
3. 
EXPERIMENTAL PLAN ..................................................................................................19 
3.1 
Study Design .............................................................................................................19 
3.2 
Number of Study Centers..........................................................................................20 
3.3 
Number of Subjects...................................................................................................20 
3.4 
Overall Study Duration and Follow-up.....................................................................20 
3.4.1 
Screening ..................................................................................................20 
3.4.2 
Treatment ..................................................................................................20 
3.4.3 
Post-Treatment Follow-up ........................................................................21 
3.5 
End of Study .............................................................................................................21 
3.6 
Safety Monitoring and Data Safety Monitoring Board.............................................21 
4. 
SUBJECT ENROLLMENT ...............................................................................................21 
4.1 
Screening...................................................................................................................21 
4.2 
Randomization ..........................................................................................................21 
4.3 
Replacement of Subjects ...........................................................................................22 
4.4 
Unblinding of Treatment Assignment ......................................................................22 
5. 
SUBJECT ELIGIBILITY ..................................................................................................22 
5.1 
Inclusion Criteria ......................................................................................................22 
5.2 
Exclusion Criteria .....................................................................................................23 
6. 
STUDY PROCEDURES ....................................................................................................24 
6.1 
Study Schedule..........................................................................................................24 
6.2 
Study Assessments ....................................................................................................24 
6.2.1 
Laboratory Analytes .................................................................................24 


ISIS 396443-CS4 
CONFIDENTIAL 
Original 
Protocol 
 
17 July 2014 
 
6 
6.2.2 
Neurological Examinations ......................................................................24 
6.2.3 
Pharmacokinetics Specimen Collection ...................................................24 
6.2.4 
Hammersmith Functional Motor Scale - Expanded .................................25 
6.2.5 
Motor Milestones .....................................................................................25 
6.2.6 
PedsQL™ (Generic Core Scales and Neuromuscular Module) ...............25 
6.2.7 
Upper Limb Module Test .........................................................................25 
6.2.8 
Assessment of Caregiver Experience with Neuromuscular Disease 
(ACEND) ..................................................................................................26 
6.2.9 
Safety Evaluations ....................................................................................26 
6.3 
Contraception Requirements .....................................................................................26 
7. 
STUDY DRUG ....................................................................................................................26 
7.1 
Study Drug Description ............................................................................................26 
7.2 
Packaging and Labeling ............................................................................................27 
7.3 
Study Drug Accountability .......................................................................................27 
8. 
TREATMENT OF SUBJECTS .........................................................................................27 
8.1 
Study Drug Administration .......................................................................................27 
8.2 
Sham Procedure ........................................................................................................28 
8.3 
Other Protocol-Required Drugs ................................................................................28 
8.4 
Other Protocol-Required Procedures ........................................................................28 
8.5 
Treatment Precautions ..............................................................................................28 
8.6 
Safety Monitoring Rules ...........................................................................................28 
8.7 
Stopping Rules ..........................................................................................................29 
8.8 
Adjustment of Dose and/or Treatment Schedule ......................................................29 
8.9 
Discontinuation of Study Treatment .........................................................................29 
8.10 
Withdrawal of Subjects from the Study ....................................................................29 
8.11 
Concomitant Therapy and Procedures ......................................................................30 
8.11.1 
Concomitant Therapy ...............................................................................30 
8.11.2 
Concomitant Procedures ...........................................................................30 
9. 
SERIOUS AND NON-SERIOUS ADVERSE EVENT REPORTING ..........................30 
9.1 
Sponsor Review of Safety Information.....................................................................30 
9.2 
Regulatory Requirements..........................................................................................31 
9.3 
Definitions.................................................................................................................31 
9.3.1 
Adverse Event ..........................................................................................31 
9.3.2 
Adverse Reaction and Suspected Adverse Reaction ................................31 
9.3.3 
Serious Adverse Event (SAE) ..................................................................31 
9.4 
Monitoring and Recording Adverse Events ..............................................................32 
9.4.1 
Serious Adverse Events ............................................................................32 
9.4.2 
Non-Serious Adverse Events ....................................................................32 
9.4.3 
Evaluation of Adverse Events (Serious and Non-Serious) ......................32 
9.4.3.1 
Relationship to the Study Drug ...................................................33 


ISIS 396443-CS4 
CONFIDENTIAL 
Original 
Protocol 
 
17 July 2014 
 
7 
9.4.3.2 
Severity .......................................................................................33 
9.4.3.3 
Action Taken with Study Drug ...................................................33 
9.4.3.4 
Treatment Given for Adverse Event ...........................................33 
9.4.3.5 
Outcome of the Adverse Event ...................................................34 
9.5 
Procedures for Handling Special Situations .............................................................34 
9.5.1 
Abnormalities of Laboratory Tests ...........................................................34 
9.5.2 
Prescheduled or Elective Procedures or Routinely Scheduled 
Treatments ................................................................................................35 
9.5.3 
Dosing Errors ...........................................................................................35 
9.5.4 
Contraception and Pregnancy ...................................................................35 
10. STATISTICAL CONSIDERATIONS ..............................................................................36 
10.1 
Study Endpoints, Subsets, and Covariates ................................................................36 
10.1.1 
Primary Endpoint .....................................................................................36 
10.1.2 
Secondary Efficacy Endpoints .................................................................36 
10.1.3 
Tertiary Efficacy Endpoints .....................................................................36 
10.1.4 
Safety/Tolerability Endpoints ...................................................................36 
10.1.5 
Pharmacokinetic Endpoints ......................................................................37 
10.1.6 
Immunogenicity Endpoint ........................................................................37 
10.2 
Sample Size Considerations ......................................................................................37 
10.3 
Populations ................................................................................................................37 
10.4 
Definition of Baseline ...............................................................................................37 
10.5 
Interim Analysis ........................................................................................................37 
10.6 
Planned Methods of Analysis ...................................................................................38 
10.6.1 
Demographic and Baseline Characteristics ..............................................38 
10.6.2 
Safety and Tolerability Analysis ..............................................................38 
10.6.3 
Efficacy Analysis .....................................................................................39 
10.6.4 
Pharmacokinetic Analysis ........................................................................40 
11. INVESTIGATOR’S REGULATORY OBLIGATIONS .................................................40 
11.1 
Informed Consent/Assent..........................................................................................40 
11.2 
Ethical Conduct of the Study ....................................................................................41 
11.3 
Institutional Review Board/Institutional Ethics Committee/Research Ethics Board41 
11.4 
Subject Confidentiality .............................................................................................41 
12. ADMINISTRATIVE AND LEGAL OBLIGATIONS ....................................................42 
12.1 
Protocol Amendments ...............................................................................................42 
12.2 
Study Termination ....................................................................................................42 
12.3 
Study Documentation and Storage ............................................................................42 
12.4 
Study Monitoring ......................................................................................................43 
12.5 
Language ...................................................................................................................43 
12.6 
Compensation for Injury ...........................................................................................43 


ISIS 396443-CS4 
CONFIDENTIAL 
Original 
Protocol 
 
17 July 2014 
 
8 
13. REFERENCES ....................................................................................................................44 
14. APPENDICES .....................................................................................................................46 
Appendix A 
Schedule of Procedures .....................................................................47 
Appendix B 
Laboratory Analytes .........................................................................50 
Appendix C 
Pharmacokinetic Sampling Schedule................................................52 
 
 
TABLE OF TABLES 
Page 
Table 1 
Study Drug Characteristics ................................................................................ 27 
Table 2 
ISIS 396443 Dose, Concentration, and Injection Volume................................. 27 
 
 
TABLE OF FIGURES 
Page 
Figure 1 
ASO Therapeutic Approach for Treatment of SMA ......................................... 16 
 
 


ISIS 396443-CS4 
CONFIDENTIAL 
Original 
Protocol 
 
17 July 2014 
 
9 
PROTOCOL SYNOPSIS 
Protocol Title 
A Phase 3, Randomized, Double-Blind, Sham Procedure Controlled Study to Assess 
the Clinical Efficacy and Safety of ISIS 396443 Administered Intrathecally in Patients 
with Later-onset  Spinal Muscular Atrophy 
Study Phase 
3 
Indication 
Later-onset Spinal Muscular Atrophy (SMA) 
Objectives 
Primary Objective: 
To examine the efficacy of ISIS 396443 administered intrathecally to patients with later-
onset SMA. 
Secondary Objective: 
To examine the safety and tolerability of ISIS 396443 administered intrathecally to 
patients with later-onset SMA. 
Tertiary Objective: 
To examine the CSF and plasma pharmacokinetics of ISIS 396443 administered 
intrathecally to patients with later-onset SMA. 
Number of Subjects 
Approximately 117 subjects will be enrolled into this study 
Treatment Groups 
12 mg ISIS 396443 or sham procedure control group 
Study Design  
This randomized, double-blind, sham-procedure controlled study will test the clinical 
efficacy, safety, tolerability, and pharmacokinetics of intrathecal ISIS 396443 over 
15 months.  Approximately 117 subjects will be randomized in a 2:1 ratio 
(78 ISIS 396443: 39 control) to receive ISIS 396443 by intrathecal lumbar puncture (LP) 
injection or to a sham-procedure control.  A dose of 12 mg ISIS 396443 will be given at 
each of 4 times over the 15 months (i.e., on Study Days 1, 29, 85, and 274). 
Randomization will be stratified based on: 
1) 
Age (<6 years versus ≥6 years at Screening) 
After Informed consent/assent is obtained, subjects will undergo a screening evaluation 
no greater than 28 days prior to first dose administration at which time their eligibility for 
the study will be examined.  Subjects who meet the eligibility criteria will be admitted to 
the study center on Study Day 1, undergo pre-dose evaluations, and then receive either 
an LP injection of study drug (ISIS 396443) or a sham procedure.  Subjects will return 
to the study center on Days 29, 85 and 274 for follow-up evaluations and subsequent 
injections/sham procedures.  Following the injection/sham procedure on Day 1, subjects 
will remain at the study center for at least 24 hours post-procedure for safety 
monitoring.  Following the injection/sham procedure on Day 29, 85, and 274 subjects 
will remain at the study center for at least 6 hours post-procedure for safety monitoring.  
Safety monitoring visits will occur on Days 30, 86, 92, 169, 275, 365, and 456 (through 
6 months following the last injection/sham procedure).  In addition, the study center will 
monitor the subject’s condition through telephone contact monthly throughout the study.  
For subjects receiving ISIS 396443, a CSF sample will be taken pre-dose on each 
injection day in a manner that maintains the blind. 
Following treatment and the final follow-up evaluation, all eligible subjects may elect to 
enroll in an open-label treatment extension study.  This will be done without unblinding 
to subject’s treatment group. 
If a subject terminates early from the study, they will be encouraged to complete safety 
assessments per the Day 456 visit.  If a subject is randomized but does not complete at 
least their first dose of ISIS 396443/undergo the first sham procedure, they will be 
replaced. 
 


ISIS 396443-CS4 
CONFIDENTIAL 
Original 
Protocol 
 
17 July 2014 
 
10 
Protocol Synopsis Continued 
Study Population and 
Main Criteria for 
Inclusion/ Exclusion 
Inclusion Criteria: 
Subjects must meet all of the following criteria at Screening to be eligible: 
1. 
Signed informed consent of parent or guardian.  Signed informed assent of 
subject, if indicated per subject’s age and institutional guidelines 
2. 
Genetic documentation of 5q SMA (homozygous gene deletion, mutation, or 
compound heterozygote) 
3. 
Onset of clinical signs and symptoms consistent with SMA at >6 months of age 
4. 
Males and females 2 to 12 years of age 
5. 
Can sit independently, but has never had the ability to walk independently 
6. 
Motor Function Score (Hammersmith Functional Motor Scale – Expanded) 
≥10 and ≤54 at Screening 
7. 
Able to complete all study procedures, measurements and visits and parent or 
guardian/subject has adequately supportive psychosocial circumstances, in the 
opinion of the Investigator 
8. 
Estimated life expectancy >2 years from Screening, in the opinion of the 
Investigator 
9. 
Meets age-appropriate institutional criteria for use of anesthesia/sedation, if use is 
planned for study procedures (as assessed by the Site Investigator and either 
anesthesiologist or pulmonologist) 
10. For subjects who, in the opinion of the Investigator,  have reached reproductive 
maturity, satisfy one of the following: 
Females:  have a negative pregnancy test at Screening and agrees to employ 
adequate contraceptive measures for the duration of the study.  Acceptable 
contraception methods are restricted to abstinence, barrier contraceptives, 
intrauterine contraceptive devices or licensed hormonal products. 
Males:  be abstinent for the duration of the study 
Exclusion Criteria: 
Subjects meeting any of the following criteria are not eligible for the study: 
1. 
Respiratory insufficiency, defined by the medical necessity for invasive or non-
invasive ventilation for >6 hours during a 24 hour period, at Screening 
2. 
Medical necessity for a gastric feeding tube, where the majority of feeds are given 
by this route, as assessed by the Site Investigator 
3. 
Severe contractures or severe scoliosis evident on X-ray examination at Screening 
4. 
Hospitalization for surgery (i.e., scoliosis surgery, other surgery), pulmonary event, 
or nutritional support within 2 months of Screening or planned during the duration 
of the study 
5. 
Presence of an untreated or inadequately treated active infection requiring 
systemic antiviral or antimicrobial therapy at any time during the screening period 
6. 
History of brain or spinal cord disease, including tumors, or abnormalities by MRI 
or CT that would interfere with the LP procedures or CSF circulation 
7. 
Presence of an implanted shunt for the drainage of CSF or an implanted CNS 
catheter 
8. 
History of bacterial meningitis 
9. 
Dosing with ISIS 396443 in any previous clinical study 
10. Prior injury (e.g., upper or lower limb fracture) or surgical procedure which impacts 
the subject’s ability to perform any of the outcome measure testing required in the 
protocol and from which the subject has not fully recovered or achieved a stable 
baseline 


ISIS 396443-CS4 
CONFIDENTIAL 
Original 
Protocol 
 
17 July 2014 
 
11 
Protocol Synopsis Continued 
Study Population and 
Main Criteria for 
Inclusion/ Exclusion 
Continued 
Exclusion Criteria Continued: 
11. Clinically significant abnormalities in hematology or clinical chemistry parameters 
or ECG, as assessed by the Site Investigator, at the Screening visit that would 
render the subject unsuitable for inclusion  
12. Treatment with another investigational drug (e.g., oral albuterol/salbutamol, 
riluzole, carnitine, creatine, sodium phenylbutyrate, etc.), biological agent, or 
device within 1-month of Screening or 5 half-lives of study agent, whichever is 
longer.  Treatment with valproate or hydroxyurea within 3-months of screening.  
Any history of gene therapy, antisense oligonucleotide therapy, or cell 
transplantation 
13. Ongoing medical condition that according to the Site Investigator would interfere 
with the conduct and assessments of the study.  Examples are medical disability 
(e.g., wasting or cachexia, severe anemia, etc.) that would interfere with the 
assessment of safety or would compromise the ability of the subject to undergo 
study procedures 
Study Drug and 
Administration 
ISIS 396443 (2.4 mg/mL) will be administered as an intrathecal LP injection.  The 
volume of the injection will be 5.0 mL.  Details regarding the LP dosing injection 
procedure and the sham procedure will be provided in the Dosing Administration 
Manual.  Details regarding the study drug will be provided in the Study Drug Manual. 
Per institutional guidelines, anesthesia/sedation may be used for the LP procedure. 
Criteria for Evaluation 
Primary Endpoint: 
• 
Change from baseline in HFMSE (Hammersmith Functional Motor Scale – 
Expanded) score at 15 months 
Secondary Endpoints:  
• 
Proportion of subjects who achieve a 3-point increase from baseline in 
Hammersmith Functional Motor Scale – Expanded (HFMSE) score at 15 months 
• 
Proportion of subjects that achieve any new motor milestone at 15 months 
• 
Number of motor milestones achieved per subject at 15 months 
• 
Change from baseline in Upper Limb Module Test at 15 months 
• 
Proportion of subjects that achieve standing alone at 15 months 
• 
Proportion of subjects that achieve walking with assistance at 15 months 
 
Tertiary Endpoints:  
• 
Change from baseline in CSF SMN protein concentration  
• 
Clinical Global Impression of Change (Investigator and Caregiver assessment)  
• 
Change from baseline in PedsQL (Pediatric Quality of Life Inventory)  
• 
Change from baseline in Assessment of Caregiver Experience with Neuromuscular 
Disease (ACEND)  
• 
Disease-related hospitalizations and adverse events 
 
Safety/Tolerability Endpoints: 
• 
Adverse events 
• 
Vital signs and weight 
• 
Neurological examinations 
• 
Physical examinations  
• 
Clinical laboratory tests  
• 
ECGs 
• 
Use of concomitant medications 


ISIS 396443-CS4 
CONFIDENTIAL 
Original 
Protocol 
 
17 July 2014 
 
12 
Protocol Synopsis Continued 
Criteria for Evaluation 
Continued 
Pharmacokinetic Endpoints:  
• 
CSF levels of ISIS 396443 (sample taken pre-dose at each dosing) 
• 
Plasma levels of ISIS 396443 
Immunogenicity Endpoint:  
• 
Plasma antibodies to ISIS 396443 
Safety Monitoring  
Safety data will be reviewed on an ongoing basis by the Medical Monitor and by an 
Independent Data Safety and Monitoring Committee (DSMB). 
Statistical 
Considerations  
The sample size for this study was estimated based on limited available natural history 
data for the target population and from the ISIS 396443-CS1 and CS2 clinical studies in 
children with SMA.  70 subjects in the treated group and 35 subjects in the control 
group will give at least 90% power to detect a 3 point difference between control and 
treated groups in change on the HFMSE with a standard deviation of 4.4, using a two-
sided t-test with an alpha level of 0.05.  The sample size was obtained using the n-
Query.  117 subjects will be enrolled to ensure that a small dropout rate will not affect 
the power of the primary efficacy analysis.  An interim analysis may take place when all 
subjects have completed the 6 month assessment and at least 39 subjects have 
completed the 15 month assessment. 
Sponsor 
Isis Pharmaceuticals, Inc. 
 
 


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STUDY GLOSSARY 
Abbreviation/Acronym 
Definition 
ACEND 
Assessment of Caregiver Experience with Neuromuscular Disease 
AE 
Adverse event/experience 
ALT 
Alanine aminotransferase  
aPTT 
Activated partial thromboplastin time 
ASO 
Antisense oligonucleotide 
AST 
Aspartate aminotransferase 
BUN 
Blood urea nitrogen 
CGI 
Clinical Global Impressions of Change Rating Scale 
Cmax 
Maximum concentration 
CNS 
Central nervous system 
CPK 
Creatinine phosphokinase 
CRF 
Case report form 
CSF 
Cerebrospinal fluid 
DSMB 
Data and Safety Monitoring Board 
eCRF 
Electronic case report form 
ECG 
Electrocardiogram 
FL 
Full-length  
GCP 
Good Clinical Practice 
HFMSE 
Hammersmith Functional Motor Scale - Expanded 
hnRNP 
Heterogeneous nuclear ribonucleoproteins 
ICH 
International Conference on Harmonisation  
IEC 
Independent Ethics Committee 
INR 
International normalized ratio 
IRB 
Institutional Review Board 
IT 
Intrathecal 
IXRS 
Interactive Voice/Web-Response System 
LP 
Lumbar puncture 
MAD 
Multiple ascending-dose 
MedDRA 
Medical Dictionary for Regulatory Activities 
miRNA 
Micro ribonucleic acid (RNA) 


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MOE 
2′-O-(2-methoxyethyl)  
mRNA 
Messenger ribonucleic acid 
NCS 
Not clinically significant 
OLE 
Open-label extension study 
PedsQL 
Pediatric Quality of Life Inventory 
PK 
Pharmacokinetic(s) 
PT 
Prothrombin Time 
SAE 
Serious adverse event 
SAP 
Statistical Analysis Plan 
SMA 
Spinal muscular atrophy 
SMN 
Survival motor neuron 
snRNA 
Small nuclear ribonucleic acid 
SUSARs 
Suspected unexpected serious adverse reactions 
Tmax 
Time to maximal concentration 
WMA 
World Medical Association 
 


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1. 
OBJECTIVES 
The objectives of this study are to evaulate the clinical efficacy, safety, tolerability, and 
pharmacokinetics (PK) of ISIS 396443 administered intrathecally to patients with later-onset 
Spinal Muscular Atrophy (SMA). 
1.1 
Primary Objective 
To examine the clinical efficacy of ISIS 396443 administered intrathecally to patients with later-
onset SMA. 
1.2 
Secondary Objective 
To examine the safety and tolerability of ISIS 396443 administered intrathecally to patients with 
later-onset SMA. 
1.3 
Tertiary Objective 
To examine the cerebral spinal fluid and plasma PK of ISIS 396443 administered intrathecally to 
patients with later-onset SMA. 
2. 
BACKGROUND AND RATIONALE 
2.1 
Spinal Muscular Atrophy 
SMA is an autosomal recessive neuromuscular disease characterized by degeneration of the 
motor neurons in the anterior horn of the spinal cord, resulting in atrophy of the voluntary 
muscles of the limbs and trunk.  With an incidence of 1:6000 to 1:10,000 live births, it is the 
most common genetic cause of infant mortality, and a major cause of childhood morbidity due to 
weakness, in the U.S.  The natural history of SMA includes four major phenotypes that are 
recognized dependent on age of onset and achieved motor abilities.  The most severe form, 
Type 1 SMA (equivalent to infantile-onset SMA), has a disease onset within the first few months 
of life; these children are never able to sit or walk and usually die from respiratory failure by the 
age of 2 years.  Later-onset SMA can generally be divided into Type 2 and Type 3 SMA.  Type 2 
SMA patients are able to sit but never walk unaided, with symptoms presenting between  
6-18 months of age.  Type 3 SMA patients are able to sit and walk but individuals with this form 
may become severely and increasingly disabled.  Adult-onset SMA patients (Type 4) have an 
age of onset over 18 years of age and have normal life expectancies. 
In 95% of SMA patients, a deletion in the SMN1 gene on Chromosome 5q11-q13 is found; with 
the remaining 5% attributable to small mutations in the same gene (Lefebvre et al. 1995; 
Helmken et al. 2003).  SMN1 lies in the telomeric portion of an inverted duplication of a region 
of Chromosome 5.  The centromeric half of the duplication contains a homologous gene, named 
SMN2 that differs from SMN1 by 11 nucleotides.  The open reading frames for both genes 
encode for proteins with identical amino acid sequences.  Survival motor neuron (SMN) gene 
transcripts, similar to most mammalian transcripts, undergo alternative splicing in which certain 
exons are either included or excluded from the mature protein coding transcripts 
(Keren et al. 2010).  In particular, Exon 7 of the SMN1 gene is alternatively spliced with 90 to 
95% of the mature messenger ribonucleic acid (mRNA) transcripts derived from the SMN1 gene 
containing Exon 7, and 5 to 10% of transcripts missing Exon 7.  The transcripts missing Exon 7 
(often referred to as Δ7) produce a truncated protein which is defective and unstable 


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(Cho and Dreyfuss 2010).  One of the 11 nucleotide differences between SMN1 and SMN2, a C 
to T substitution occurs in Exon 7 of the SMN2 gene resulting in an alternative splicing pattern 
that favors skipping of Exon 7.  The result is that as much as 90% of the transcripts produced 
from SMN2 are missing Exon 7.  The remainder, SMN2 transcripts containing Exon 7, produces 
a full-length (FL) protein product identical to the SMN1 protein, since the C to T substitution is 
silent.  Humans have a variable copy number of the SMN2 gene (0-8 copies).  The number of 
SMN2 copies and the resulting amount of FL-SMN protein expressed in SMA patients (10-40% 
of normal SMN protein levels) correlates with SMA disease severity and thus SMN2 is a key 
modifier of disease phenotype (Coovert et al. 1997; Feldkotter et al. 2002; Lefebvre et al. 1997; 
Prior et al. 2004). 
2.2 
Therapeutic Rationale 
Since the number of SMN2 gene copies and resulting amount of SMN protein is correlated with 
disease onset and severity, a therapeutic approach predicted to benefit SMA patients is to 
increase the levels of full length SMN2 pre-mRNA by restoring the splicing pattern that gives 
rise to full length SMN2 mRNA.  Increasing inclusion of Exon 7 in the SMN2 transcript will 
increase FL-SMN protein levels and SMN protein activity.  A therapeutic strategy for promoting 
Exon 7 inclusion is through the use of antisense oligonucleotides (ASOs) (see Figure 1). 
 
Figure 1 
ASO Therapeutic Approach for Treatment of SMA 


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The known potential risks associated with ISIS 396443 are detailed in the Guidance to 
Investigator section of the Investigator’s Brochure.  Additional study associated risks related to 
the lumbar puncture (LP) procedure are also detailed in the Guidance to Investigator section of 
the Investigator’s Brochure. 
2.3 
ISIS 396443 
2.3.1 
Mechanism of Action 
ISIS 396443 is a fully modified, 2′-O-2-methoxyethyl (MOE), ASO drug designed to bind to a 
specific sequence in the intron downstream of Exon 7 of the SMN2 transcript.  The region of the 
pre-mRNA targeted by ISIS 396443 is normally occupied by heterogeneous nuclear 
ribonucleoproteins (hnRNP) A1/2 proteins, masking the U1 small nuclear ribonucleic acid 
(snRNA) binding site at the 5′-exon-intron junction of Exon 7, and is referred to as ISS-N1.  
U1 snRNA base pairs to the sequences that define the 5′-splice site, which is thought to be one of 
the first steps that initiate splicing of an intron.  ISIS 396443 displaces the hnRNP A1/2 proteins 
from the pre-mRNA binding site, allowing U1 snRNA to bind to the exon-intron junction and 
promote assembly of the spliceosomal complex, thus promoting inclusion of Exon 7 into the 
mRNA which results in production of FL-SMN protein. 
2.3.2 
Chemistry 
Chemically, ISIS 396443 is a synthetic oligomer of 18 nucleotides (i.e., an 18-mer) that are 
connected sequentially by phosphorothioate linkages.  Each of the 17 internucleotide linkages is 
a 3′-O to 5′-O phosphorothioate diester.  The 18 sugar residues are uniformly modified with 
2′-O-(2-methoxyethyl) (MOE).  These MOE-modified nucleotides confer (1) increased affinity 
to the target mRNA (McKay et al. 1999), (2) increased resistance to exonucleases and 
endonucleases (thereby increasing stability in tissue) (Geary et al. 2003), and (3) amelioration of 
some of the high dose toxicities associated with ASO containing only the phosphorothioate 
linkages (Henry et al. 2000). 
The sequence of ISIS 396443 is written as follows: 
5′ -MeUMeCAMeCMeUMeUMeUMeCAMeUAAMeUGMeCMeUGG- 3′ 
Where A and G are 2′-O-(2-methoxyethyl)nucleosides, MeC is 5-methyl-2′-O-(2-
methoxyethyl)cytidine and MeU designates 5-methyl-2′-O-(2-methoxyethyl)uridine. 
2.3.3 
Preclinical Experience 
Detailed information concerning the preclinical studies conducted with ISIS 396443 can be 
found in the Investigator’s Brochure.  A summary is included below. 
ISIS 396443 was identified after an extensive screen of greater than 500 2′-MOE 
oligonucleotides in in vitro splicing assays, reporter gene assays and in SMA patient fibroblasts 
(Hua et al. 2007; Hua et al. 2008).  Data have shown that ISIS 396443 promotes a concentration-
dependent increase in full-length transcripts (including Exon 7) in patient fibroblast cells, 
achieving greater than 90% full length SMN2 transcripts and forms nuclear structures, called 
gems, known to contain SMN protein.  In a mild mouse model of SMA, ISIS 396443 promoted 
inclusion of Exon 7 in the SMN2 transgene in a variety of peripheral tissues when dosed 
systemically (Hua et al. 2008) and in central nervous system (CNS) tissue, including spinal cord, 


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when injected into the lateral ventricle.  ISIS 396443 produced greater than 90% Exon 7 
inclusion in the transgenic mice and increased SMN protein production in motor neurons, 
resulting in the appearance of gems in motor neurons.  These studies were extended to a more 
severe mouse model of SMA (SMA Δ7) (Le et al. 2005), where the CNS delivery of drug 
produced a dose-dependent effect on SMN2 Exon 7 inclusion, SMN protein production, and 
survival.  These mice treated with ISIS 396443 demonstrated improved weight gain, 
improvements in muscle morphology, muscle strength, and motor coordination and improved 
morphology of the motor neuron junctions (Passini et al. 2011).  Further, ISIS 396443 was 
shown to distribute widely in the CNS following intrathecal (IT) administration in monkey 
(Passini et al. 2011). 
The pharmacokinetics and toxicity of ISIS 396443 were assessed following: 1) single intrathecal 
(IT) lumbar bolus injections (1 to 7 mg) in adult monkeys 2) following 14 weeks (with a 4-week 
interim sacrifice) of repeated IT lumbar bolus injections (0.3 to 3 mg/week or every other week) 
in juvenile monkeys and 3) following 53 weeks of repeated IT lumbar bolus injections in 
juvenile monkeys.  In addition, a dedicated pharmacokinetic study in adult monkeys was 
performed to assess the half-life of ISIS 396443 in CSF, tissues and plasma.  Detailed results 
from these preclinical studies conducted with ISIS 396443 can be found in the ISIS 396443 
Investigator’s Brochure. 
2.3.4 
Clinical Experience 
Detailed information concerning the clinical studies conducted with ISIS 396443 can be found in 
the Investigator’s Brochure.  A summary is included below. 
ISIS 396443 has been evaluated in a completed open-label, single ascending-dose (SAD) Phase 1 
study designed to assess the safety, tolerability and pharmacokinetics of ISIS 396443 in patients 
with SMA (ISIS 396443-CS1).  A single-dose of ISIS 396443 was administered by IT injection 
to SMA patients aged 2 to 14 years of age.  Four dose levels (1, 3, 6, and 9 mg) were evaluated 
sequentially.  Each dose level was studied in a cohort of 6 or 10 subjects, where all subjects 
received drug.  In this study all subjects completed dosing and the follow-up visits per protocol.  
Overall, ISIS 396443 was well-tolerated and no safety concerns were identified up to the 9.0 mg 
dose level, given as a single IT injection.  No serious adverse events (SAEs) or dose-limiting 
toxicities (DLTs) were reported in ISIS 396443-CS1.  Adverse events (AEs) reported were mild 
or moderate in severity and there was no relationship with ISIS 396443 dose level.  In addition, 
no ISIS 396443 related adverse changes in neurological exams were reported, despite intensive 
monitoring during the immediate post-dosing period.  CSF and plasma drug concentrations 
observed were generally consistent with predictions made from nonclinical monkey studies. 
ISIS 396443 is also being evaluated in four ongoing studies: ISIS 396443-CS2, 
ISIS 396443-CS10, ISIS 396443-CS12, and ISIS 396443-CS3A.  ISIS 396443-CS2 is an 
open-label, multiple ascending-dose (MAD) Phase 1/2a study designed to assess the safety, 
tolerability and pharmacokinetics of ISIS 396443 in patients with SMA.  Multiple doses of 
ISIS 396443, ranging from 3 mg to 12 mg, are being administered by intrathecal injection to 
SMA patients aged 2 to 15 years of age.  ISIS 396443-CS10 is an open-label, single dose, 
re-dosing study for SMA patients who previously participated in Cohorts 2, 3 and 4 in 
ISIS 396443-CS1.  ISIS 396443-CS12 is an ongoing open-label study to assess the safety and 
tolerability of a single (12 mg) intrathecal dose of ISIS 396443 in patients with spinal muscular 
atrophy who previously participated in ISIS 396443-CS2 or ISIS 396443-CS10.  


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ISIS 396443 CS3A is an open-label, multiple-dose study designed to assess the safety, 
tolerability and pharmacokinetics of ISIS 396443 in patients with infantile-onset SMA.  Multiple 
doses of ISIS 396443 are being administered by intrathecal injection to symptomatic SMA 
infants ≤7 months of age.  Two dose levels (6 and 12 mg dose equivalent scaled by CSF volume) 
are being evaluated sequentially. 
2.4 
Rationale for Dose and Schedule of Administration 
The proposed study will test the clinical efficacy, safety, tolerability, and PK of multiple doses of 
ISIS 396443 administered as IT injections to subjects with later-onset SMA.  A single dose level 
of 12 mg ISIS 396443 will be evaulated, delivered as 4 doses administered over 9 months. 
ISIS 396443 will be administered using a loading regimen (dosings on Study Days 1, 29, 85) 
followed by maintenance dosing given 6 months thereafter (dosing on Study Day 274). 
The ISIS 396443-CS4 dose level and dose interval was selected based on preclinical toxicology 
and pharmacokinetic observations from monkey studies utilizing single-dose and repeat dosing 
IT administration, consideration of the target tissue concentration anticipated for drug 
pharmacology, and safety data in the completed and ongoing clinical studies of ISIS 396443 to 
date.  Based upon pharmacology and pharmacokinetic results in SMA transgenic mice, we 
estimate that the target tissue concentration to produce 50 to 90% SMN2 Exon 7 inclusion is 
between 1 and 10 μg/g spinal cord tissue.  Nonclinical studies in juvenile monkeys receiving IT 
doses of ISIS 396443 showed a resulting gradient of distribution of ISIS 396443 along the spinal 
cord, with mean lumbar spinal cord concentrations ranging from 1.6-2.3 fold and 2.0-3.5 fold 
higher than thoracic and cervical spinal cord levels, respectively.  The dose level selected for this 
multiple-dose clinical study (12 mg ISIS 396443) is predicted to achieve levels at the high end of 
this range (approximately 10 μg/g lumbar and 3 ug/g cervical spinal cord tissue concentrations), 
following the first dose.  The loading dose interval was selected based on the nonclinical 
pharmacokinetic and pharmacology data as the dose interval to achieve and maintain 
ISIS 396443 spinal cord tissue levels that are predicted to be within the upper end of the 
pharmacologically active range by Day 85 (predicted to be approximately 24 μg/g lumbar and 
8 μg/g cervical tissue concentration), while at the same time considering subject safety and 
convenience for repeated LP intrathecal injections.  The maintenance dose interval (once every 
6 months) was selected based on the estimated spinal tissue and CSF drug half-life (4-6 months) 
and was selected to maintain spinal cord tissue levels of ISIS 396443 at a steady-state level 
within the estimated pharmacologically active range. 
Additional details on dose scaling and expected CSF and tissue concentrations are summarized 
in the Investigator’s Brochure. 
3. 
EXPERIMENTAL PLAN 
3.1 
Study Design 
This is a Phase 3 multicenter, double-blind, randomized, sham-procedure controlled study of 
ISIS 396443 in patients with later-onset SMA studied for 15 months.  Approximately 
117 subjects will be randomized 2:1 to receive 12 mg dose ISIS 396443 or a sham procedure 
control, respectively.  ISIS 396443 will be administered using a loading regime (dosings on 
Study Days 1, 29, and 85) followed by a maintenance dose 6 months thereafter (dosing on Study 
Day 274). 


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Randomization will be stratified based on: 
1) Subject’s Age at Screening (<6 years versus ≥6 years) 
Following treatment and the Day 456 follow-up evaluation, all eligible subjects may elect to 
enroll in an open-label treatment extension study, pending study approval by the IRB or IEC and 
the appropriate regulatory authority.  This will be done without unblinding to subject’s treatment 
group. 
3.2 
Number of Study Centers 
This study will be conducted at multiple centers worldwide. 
3.3 
Number of Subjects 
Approximately 117 subjects (2 ISIS 396443; 1 sham-procedure) will receive 12 mg dose of 
ISIS 396443 or a sham procedure control.  The total number of subjects randomized may be 
higher if some subjects do not receive their Day 1 dose/sham procedure.  The maximum number 
of subjects will not exceed 130. 
3.4 
Overall Study Duration and Follow-up 
The Study will consist of screening, treatment, and post-treatment follow-up-periods.  The total 
duration of participation in the study is approximately 16 months.  Please refer to the Schedule of 
Procedures in Appendix A. 
3.4.1 
Screening 
After informed consent/assent is obtained, subjects will undergo a screening evaluation no 
greater than 28 days prior to first dose administration at which their eligibility for the study will 
be examined. 
3.4.2 
Treatment 
Subjects who meet the eligibility criteria will be admitted to the study center on Study Day 1, 
undergo pre-dose evaluations, be randomized, and then receive either an LP injection of study 
drug (ISIS 396443) or a sham procedure.  Subjects will return to the study center on Days 29, 85 
and 274 for follow-up evaluations and subsequent injections/sham procedures.  Following the 
injection/sham procedure on Day 1, subjects will remain at the study center for at least 24 hours 
post-procedure for safety monitoring.  Following the injection/sham procedure on Day 29, 85, 
and 274 subjects will remain at the study center for at least 6 hours post-procedure for safety 
monitoring.  Safety monitoring visits will occur Study Days 30, 86, 92, 169, and 275 (through 
the last injection/sham procedure).  In addition, the study center will monitor the subject’s 
condition through telephone contact on a monthly basis. 
For subjects receiving ISIS 396443, a CSF sample for PK and SMN protein analyses will be 
taken pre-dose on each injection day in a manner that protects the blind. 
If a subject terminates early from the study, they will be encouraged to complete assessments per 
the Day 456 visit.  If a subject is randomized but does not successfully receive the first dose of 
ISIS 396443/undergo the first sham procedure, they will be replaced. 


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3.4.3 
Post-Treatment Follow-up 
After completion of the Day 275 visit, subjects will enter the 6-month post-treatment evaluation 
period.  This period consists of Study Center visits on Day 365 and 456 and follow-up phone 
assessments on a monthly basis, as outlined in the Schedule of Procedures (Appendix A).  After 
completion of the Day 456 visit, subjects may be eligible to participate in an OLE study, pending 
study approval by the IRB or IEC and the appropriate regulatory authority. 
3.5 
End of Study 
The end of study is last subject; last visit (either in-person visit or telephone contact). 
3.6 
Safety Monitoring and Data Safety Monitoring Board 
Safety data will be reviewed on an ongoing basis by the Sponsor and the Medical Monitor.  
Safety data will also be reviewed on an ongoing basis by an independent DSMB.  The DSMB 
will be assembled to review safety, tolerability and efficacy (as needed) data collected on 
ISIS 396443 during this study.  Based on its ongoing assessment of the data, the DSMB will 
provide recommendations to the Sponsor for modifying, stopping or continuing the study. 
4. 
SUBJECT ENROLLMENT 
4.1 
Screening 
Before subjects may be enrolled into the study, the Sponsor requires a copy of the Study Center’s 
written IRB or IEC approval of the protocol, informed consent form, informed assent form (if 
applicable) and all other subject information and/or recruitment material. 
Before a subject’s participation in the trial, the Investigator is responsible for obtaining written 
informed consent from the parent(s) or legal guardian(s) and, in cases where institutional 
guidelines and the patient’s age dictate, informed assent from the subject.  At the time of 
consent/assent, the subject will be considered enrolled into the study and will be assigned a 
unique screening number before any study procedures, including screening procedures, are 
performed.  The screening number must remain constant throughout the entire trial.  In the event 
the subject is re-consented and re-screened the subject must be given a new screening number.  
Screening numbers, once assigned, will not be re-used. 
4.2 
Randomization 
Subjects will be randomized after all screening assessments have been completed and after the 
Investigator and the Medical Monitor have verified that they are eligible per criteria in 
Sections 5.1 and 5.2.  No subject may begin treatment prior to randomization and assignment of 
a unique randomization number. 
Using an Interactive Voice/Web-Response System (IXRS), eligible subjects will be randomized 
2:1 to receive ISIS 396443 or sham-procedure control, respectively.  Randomization will be 
stratified for: 
• Subject’s Age at Screening (<6 years versus ≥6 years) 
The Sponsor Quality Assurance department or designee will hold a copy of the randomization 
lists generated by the IXRS vendor. 


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The Sponsor Quality Assurance department or designee will hold a copy of the randomization 
lists generated by the IXRS vendor. 
4.3 
Replacement of Subjects 
If a subject does not successfully receive the first dose of ISIS 396443/undergo the first sham 
procedure, they will be replaced.  
4.4 
Unblinding of Treatment Assignment 
The Sponsor, parents, and key study site personnel will be blinded to subjects’ treatment 
assignment throughout the study.  The DSMB may be unblinded as described in the DSMB 
charter. 
If a subject has experienced an SAE (as defined in Section 9.3.3), and/or when knowledge of the 
treatment assignment will impact the clinical management of the subject, the Investigator will 
have the ability to unblind the treatment assignment for that subject using the IXRS.  However, 
prior to unblinding, the Investigator should attempt to contact the blinded Medical Monitor to 
discuss the emergency.  The Sponsor or designee will be informed of the unblinding of a subject 
within 24 hours.  Every reasonable attempt should be made to complete the Study Day 456 early 
termination procedures and observations (see Appendix A) prior to unblinding, as knowledge of 
the subject’s treatment assignment could influence subsequent assessments.  The Investigator 
must document the reasons for unblinding in the subject’s source documents.  The Investigator is 
strongly advised not to divulge the subject’s treatment assignment to any individual not directly 
involved in managing the medical emergency, nor to personnel involved with the analysis and 
conduct of the study.  In cases where there are ethical reasons to have a subject remain on study 
whose treatment assignment is unblinded for safety reasons, the Site Investigator must obtain 
specific approval from the Sponsor and the Medical Monitor for the subject to continue in the 
study. 
In addition, all suspected unexpected serious adverse reactions (SUSARs) will be unblinded by 
the Sponsor’s Drug Safety and Quality Assurance personnel for the purpose of regulatory 
reporting (Section 9.2). 
5. 
SUBJECT ELIGIBILITY 
5.1 
Inclusion Criteria  
Subjects must meet all of the following criteria at Screening to be eligible: 
1. Signed informed consent of parent or guardian.  Signed informed assent of subject, if 
indicated per subject’s age and institutional guidelines 
2. Genetic documentation of 5q SMA (homozygous gene deletion, mutation, or compound 
heterozygote) 
3. Onset of clinical signs and symptoms consistent with SMA at >6 months of age 
4. Males and females 2 to 12 years of age 
5. Can sit independently, but has never had the ability to walk independently 


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6. Motor Function Score (Hammersmith Functional Motor Scale – Expanded) ≥10 and ≤54 
at Screening 
7. Able to complete all study procedures, measurements and visits and parent or 
guardian/subject has adequately supportive psychosocial circumstances, in the opinion of 
the Investigator 
8. Estimated life expectancy >2 years from screening, in the opinion of the Investigator 
9. Meets age-appropriate institutional criteria for use of anesthesia/sedation, if use is 
planned for study procedures (as assessed by the Site Investigator and either 
anesthesiologist or pulmonologist) 
10. For subjects who, in the opinion of the Investigator, have reached reproductive maturity, 
satisfy one of the following: 
Females:  have a negative pregnancy test at Screening and agrees to employ adequate 
contraceptive measures for the duration of the study.  Acceptable contraception methods 
are restricted to abstinence, barrier contraceptives, intrauterine contraceptive devices or 
licensed hormonal products. 
Males:  be abstinent for the duration of the study 
5.2 
Exclusion Criteria 
Subjects meeting any of the following criteria are not eligible for the study: 
1. Respiratory insufficiency, defined by the medical necessity for invasive or non-invasive 
ventilation for >6 hours during a 24 hour period, at Screening 
2. Medical necessity for a gastric feeding tube, where the majority of feeds are given by this 
route, as assessed by the Site Investigator 
3. Severe contractures or severe scoliosis evident on X-ray examination at Screening 
4. Hospitalization for surgery (i.e., scoliosis surgery, other surgery), pulmonary event, or 
nutritional support within 2 months of screening or planned during the duration of the 
study 
5. Presence of an untreated or inadequately treated active infection requiring systemic 
antiviral or antimicrobial therapy at any time during the screening period 
6. History of brain or spinal cord disease, including tumors, or abnormalities by MRI or CT 
that would interfere with the LP procedures or CSF circulation 
7. Presence of an implanted shunt for the drainage of CSF or an implanted CNS catheter 
8. History of bacterial meningitis 
9. Dosing with ISIS 396443 in any previous clinical study 
10. Prior injury (e.g., upper or lower limb fracture) or surgical procedure which impacts the 
subject’s ability to perform any of the outcome measure testing required in the protocol 
and from which the subject has not fully recovered or achieved a stable baseline 


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11. Clinically significant abnormalities in hematology or clinical chemistry parameters or 
ECG, as assessed by the Site Investigator, at the Screening visit that would render the 
subject unsuitable for inclusion 
12. Treatment with another investigational drug (e.g., oral albuterol/salbutamol, riluzole, 
carnitine, creatine, sodium phenylbutyrate, etc.), biological agent, or device within 
1-month of screening or 5 half-lives of study agent, whichever is longer.  Treatment with 
valproate or hydroxyurea within 3-months of screening.  Any history of gene therapy, 
antisense oligonucleotide therapy, or cell transplantation 
13. Ongoing medical condition that according to the Site Investigator would interfere with 
the conduct and assessments of the study.  Examples are medical disability (e.g., wasting 
or cachexia, severe anemia, etc.) that would interfere with the assessment of safety or 
would compromise the ability of the subject to undergo study procedures 
6. 
STUDY PROCEDURES 
6.1 
Study Schedule 
All required study procedures are outlined in Appendices A, B and C. 
6.2 
Study Assessments 
6.2.1 
Laboratory Analytes 
Laboratory measurements of serum chemistry, hematology, urinalysis, coagulation parameters, 
and plasma antibodies to ISIS 396443 will be performed at the times shown in the Schedule of 
Procedures (Appendix A).  The analytes to be measured are shown in Appendix B. 
6.2.2 
Neurological Examinations 
Neurological examinations include assessment of mental status, level of consciousness, sensory 
function, motor function, cranial nerve function, and reflexes.  Neurological examinations will be 
performed at the times shown in the Schedule of Procedures (Appendix A). 
6.2.3 
Pharmacokinetics Specimen Collection 
Plasma and CSF specimens will be collected as shown in Appendix A (Schedule of Procedures) 
and Appendix C (Pharmacokinetic Sampling Schedule).  The following ISIS 396443 plasma PK 
parameters (though not necessarily limited to) will be derived when appropriate from the 
individual subject concentration vs. time profiles using noncompartmental-based methods and 
based on actual sampling times: 
• The maximal observed plasma drug concentration (Cmax) 
• The time to reach Cmax in plasma (Tmax) 
• The area under the plasma concentrations time curve from the time of the IT dose to the 
last collected sample 
• The apparent terminal elimination half-life (t½), if possible 
 
 


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6.2.4 
Hammersmith Functional Motor Scale - Expanded 
Subjects will be evaluated using the Hammersmith Functional Motor Scale – Expanded 
(HFMSE) at the times shown in the Schedule of Procedures (Appendix A).  The HFMSE is a 
reliable and validated tool used to assess motor function in children with SMA.  The scale was 
originally developed with 20 scored activities and was devised for use in children with SMA 
Type 2 and Type 3 with limited ambulation to give objective information on motor ability and 
clinical progression (Main et al. 2003).  The expanded scale includes an additional module of 
13 items developed to allow for evaluation of ambulatory SMA patients (O’Hagen et al. 2007).  
The HFMSE has been shown to be highly correlated with other clinical assessments and shows 
good test-retest reliability.  The HFMSE is easy to use and quickly administered. 
6.2.5 
Motor Milestones 
Subjects will be evaluated for motor milestones at the times shown in the Schedule of Procedures 
(Appendix A).  Motor Milestones will be assessed using the WHO Motor Milestone criteria 
(WHO Multicentre Growth Reference Study Group 2006; Wijnhoven et al. 2004). 
6.2.6 
PedsQL™ (Generic Core Scales and Neuromuscular Module) 
Subjects will be evaluated using the Pediatric Quality of Life Inventory (PedsQL™) 
Measurement 4.0 Generic Core Scales and 3.0 Neuromuscular Module (Varni et al. 1999) at the 
times shown in the Schedule of Procedures (Appendix A).  This assessment has been validated 
by the American Spinal Muscular Atrophy Randomized Trials (AmSMART) group for use in 
SMA patients from age 2 to 18 years (Iannaccone et al. 2009). 
The PedsQL™ Measurement Model is a modular approach to measuring health-related quality of 
life (HRQOL) in children and adolescents.  The PedsQL consists of brief, practical, generic core 
scales as well as with condition-specific modules for use in designated clinical populations.  
Pediatric self-report is measured in children and adolescents ages 5-18 years, and parent proxy-
report of child HRQOL is measured for children and adolescents ages 2-18 years.  The 
PedsQL™ 4.0 Generic Core Scales include assessment of physical functioning, emotional 
functioning, social functioning, and school functioning.  The PedsQL 3.0 Neuromuscular 
Module was designed to measure HRQOL dimensions specific to children aged 2 to 18 years 
with neuromuscular disorders, including SMA. 
6.2.7 
Upper Limb Module Test 
Subjects will be evaluated using the Upper Limb Module Test (Mazzone et al. 2011) at the times 
shown in the Schedule of Procedures (Appendix A).  The Upper Limb Module Test is an 
outcome measure specifically developed to assess upper limb functional abilities in SMA 
patients, including young children and patients with severe contractures in the lower limbs in 
whom the possibility to detect functional changes, such as rolling or long sitting, is limited.  This 
test consists of upper limb performance items that are reflective of activities of daily living (i.e., 
raise a can to mouth as if drinking, take a coin and place it in a box, remove the lid of a 
container).  The Upper Limb Module Test is quickly administered and has been evaluated in 
SMA patients age 30 months to 27 years (Mazzone et al. 2011). 


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6.2.8 
Assessment of Caregiver Experience with Neuromuscular Disease (ACEND) 
Parents of subjects will complete the Assessment of Caregiver Experience with Neuromuscular 
Disease (ACEND) questionnaire at the times shown in the Schedule of Procedures 
(Appendix A).  This assessment instrument has been designed to quantify the caregiver impact 
experienced by parents of children affected with severe neuromuscular diseases, including 
children with SMA (Matsumoto et al. 2011).  The ACEND includes domains assessing physical 
impact (including feeding/grooming/dressing, sitting/play, transfers, and mobility) and general 
caregiver impact (including time, emotion, and finance). 
6.2.9 
Safety Evaluations 
Safety will be evaluated by assessment of AEs including SAEs as described in Section 9.  
Additional safety evaluations include the following parameters: 
• Vital signs and weight 
• Neurological examinations 
• Physical examinations  
• Clinical laboratory tests (serum chemistry, hematology, urinalysis) 
• Electrocardiograms (ECGs) 
• Use of concomitant medications 
6.3 
Contraception Requirements 
All male subjects must remain abstinent during the study. 
All female subjects of childbearing potential must either be abstinent or practice adequate 
contraception during the study.  For the purposes of this study, females of childbearing potential 
are defined as any female who has experienced menarche.  For the purposes of the study, 
acceptable contraception methods are abstinence, barrier contraceptives, intrauterine 
contraceptive devices or licensed hormonal products 
7. 
STUDY DRUG 
7.1 
Study Drug Description 
Study Drug (ISIS 396443 drug product) characteristics are listed under Table 1. 
The Study Drug is contained in 6 mL clear glass vials.  The Study Drug and its storage and 
preparation instructions will be provided by the Sponsor or designee.  The Study Drug must be 
stored securely at 2° to 8° C and protected from light. 
 
 


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Table 1 
Study Drug Characteristics 
Study Drug 
ISIS 396443 Drug Product 
Strength 
2.4 mg/mL  
Volume/vial 
5.0 mL solution per vial 
Route of Administration 
IT injection 
 
7.2 
Packaging and Labeling 
The Sponsor will provide the Investigator with packaged Study Drug labeled in accordance with 
specific country regulatory requirements. 
7.3 
Study Drug Accountability 
The study staff is required to document receipt, dispensing and return of Study Drug supplies 
provided by the Sponsor.  Drug accountability documentation and all used and unused Study 
Drug vials must be returned to the Sponsor or designee. 
8. 
TREATMENT OF SUBJECTS 
8.1 
Study Drug Administration 
Details regarding the LP dosing injection procedure will be provided in the Dosing 
Administration Manual.  ISIS 396443 will be administered by dedicated study personnel who are 
unblinded to treatment group; this cannot be any of the key study site personnel (i.e., the 
Principal Investigator, study coordinator, or outcomes assessors).  The study drug administration 
will be performed in a dedicated room and the key study personnel and the parents will not be 
present during the procedure to ensure blinding. 
ISIS 396443 will be administered as an intrathecal slow bolus (1-3 minute) LP injection.  
ISIS 396443 will be administered using a ‘spinal anesthesia’ needle and syringe.  A 22G to 25G 
spinal anesthesia needle is recommended, but a 21G may be used if indicated by subject size or 
clinical condition.  The target site for needle insertion is the L3/L4 space, but may be 1 segment 
above or 1-2 segments below this level, if needed.  The volume of the injection is 5 mL; prior to 
the injection 5 mL of CSF fluid is to be collected for analyses.  Depending on institutional 
guidelines, anesthesia or sedation may be used for the LP procedure, following institutional 
procedures.  Subjects will be encouraged to lie flat for 1 hour following dosing, if possible. 
Table 2 outlines the dose, ISIS 396443 concentration, and volume for administration of 
ISIS 396443. 
Table 2 
ISIS 396443 Dose, Concentration, and Injection Volume 
Dose 
(mg) 
Concentration 
(mg/mL) 
Injection Volume 
(mL) 
12 
2.4 
5.0 
 


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Prior to each injection on Study Days 1, 29, 85, and 274, 5 mL of CSF fluid is to be collected for 
analyses.  CSF will be used for measurement of ISIS 396443 pharmacokinetic analyses and CSF 
SMN protein concentration.  Extra CSF may be stored for investigation of possible biomarkers 
of SMA disease or the pharmacodynamic effects of ISIS 396443 (e.g., CSF mRNA, CSF protein, 
CSF miRNA panel) or for profiling of drug binding proteins, bioanalytical method validation 
purposes, stability assessments, metabolite assessments, immunogenicity assessments (including 
assay development and validation purposes), or to assess other actions of ISIS 396443 with CSF 
constituents.  CSF analyses and data presentation will be conducted in a blinded manner. 
8.2 
Sham Procedure 
Subjects randomized to the sham-procedure control group will undergo a sham-procedure, rather 
than study drug administration, on Study Days 1, 29, 85, and 274.  Details regarding the sham 
procedure will be provided in the Dosing Administration Manual.  The sham procedure will be 
administered by dedicated study personnel who are unblinded to treatment group; this cannot be 
any of the key study site personnel (i.e., the Investigator, study coordinator, or outcomes 
assessors).  The sham procedure will be performed in a dedicated room and the key study 
personel and the parents will not be present during the procedure to ensure blinding. 
In general, the sham procedure will consist of a small needle prick on the lower back at the 
location where the LP injection is normally made.  The needle will break the skin but no LP 
injection or needle insertion will occur.  The needle prick will be covered with the same bandage 
that is used to cover the LP injection normally, thus simulating the appearance of an LP 
injection.  If anesthesia or sedation is used for the LP procedure in ISIS 396443 treated subjects, 
then in order to maintain the blind, minimal sedation (i.e. a low dose of an anxiolytic) should be 
used for the sham procedure, following institutional procedures.  The study subject will be kept 
in the procedure room for the same amount of time that subjects administered study drug are 
kept, thus simulating the time period of a study drug administration procedure. 
Study drug and sham kits will be packaged in a blinded fashion.  Blinded kits for sham procedure 
contain artificial CSF (5.0 mL solution per 6 mL vial) that will not be injected but will be used to 
simulate CSF samples for that subject.  
8.3 
Other Protocol-Required Drugs 
There are no other protocol required drugs. 
8.4 
Other Protocol-Required Procedures 
There are no other protocol-required treatment procedures. 
8.5 
Treatment Precautions 
There are no protocol-required treatment precautions. 
8.6 
Safety Monitoring Rules 
Please refer to the Guidance to Investigator section of the Investigator Brochure. 


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8.7 
Stopping Rules 
There are no additional specific stopping rules for this study but the Investigator should discuss 
significant concerns relating to individual subjects with the Medical Monitor and the Sponsor to 
ensure that it is appropriate for the subject to continue Study Drug. 
8.8 
Adjustment of Dose and/or Treatment Schedule 
No adjustment of dose is permitted.  In the event of a concurrent illness that would prevent the 
dosing procedure from being performed safely, an adjustment in the dose schedule may be 
permitted, but must be approved by the Medical Monitor.  In general, each scheduled dose may 
be delayed by up to 4 weeks. 
8.9 
Discontinuation of Study Treatment 
A subject must permanently discontinue study treatment for any of the following: 
• The subject’s parents/guardians withdraw consent 
• The subject experiences an adverse event that necessitates permanent discontinuation of 
study treatment 
The reason for discontinuation of study treatment must be recorded in the Case Report Form 
(CRF) and source documentation. 
Subjects that discontinue treatment will continue follow-up unless consent is withdrawn 
(Appendix A). 
8.10 
Withdrawal of Subjects from the Study 
Subjects must be withdrawn from the study for any of the following: 
• Withdrawal of consent 
• The subject or the subject’s parents/guardians is/are unwilling or unable to comply with 
the protocol 
• The subject experiences a medical emergency that necessitates unblinding of the 
subject’s treatment assignment 
Other reasons for withdrawal of subjects from the study might include: 
• At the discretion of the Investigator for medical reasons 
• At the discretion of the Investigator or Sponsor for noncompliance 
• Significant protocol deviation 
• Decision by the Investigator or Sponsor 
All efforts will be made to complete and report the observations as thoroughly as possible up to 
the date of withdrawal.  All information, including the reason for withdrawal from Study, must 
be recorded in the CRF. 


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Any subject for whom consent to participate in the study is withdrawn will be removed from 
further treatment and study observation immediately upon the date of request.  It should be 
encouraged that these subjects complete the early termination study procedures and observations 
at the time of withdrawal (Appendix A). 
For subjects withdrawn for reasons other than withdrawal of consent every effort should be made 
to complete the early termination study procedures and observations at the time of withdrawal 
(Appendix A). 
8.11 
Concomitant Therapy and Procedures 
The use of concomitant therapies or procedures defined below must be recorded on the subject’s 
CRF.  AEs related to administration of these therapies or procedures must also be documented on 
the appropriate CRF. 
8.11.1 
Concomitant Therapy 
A concomitant therapy is any non-protocol specified drug or substance (including over-the-
counter medications, herbal medications and vitamin supplements) administered between the 
beginning of screening and last telephone contact or study visit. 
Subject’s parents/guardians should consult with the Site Investigator or qualified designee prior 
to initiating any new medication, including non-prescription compounds or any other non-drug 
therapy. 
Allowed Concomitant Therapy 
Throughout the study, Site Investigators or designated licensed physicians involved in the study 
may prescribe concomitant medications or treatments deemed necessary for adverse events or to 
provide adequate supportive care. 
Disallowed Concomitant Therapy 
Study subjects are prohibited from receiving other experimental agents during the study.  This 
includes marketed agents at experimental doses that are being tested for the treatment of SMA 
(e.g., oral albuterol/salbutamol, riluzole, carnitine, creatine, sodium phenylbutyrate, valproate, 
hydroxyurea). 
8.11.2 
Concomitant Procedures 
A concomitant procedure is any therapeutic intervention (e.g., surgery/biopsy) or diagnostic 
assessment (e.g., blood gas measurement, bacterial cultures) performed between the beginning of 
screening and last telephone contact or study visit. 
9. 
SERIOUS AND NON-SERIOUS ADVERSE EVENT REPORTING  
9.1 
Sponsor Review of Safety Information 
Safety information will be collected, reviewed, and evaluated by the Sponsor in accordance with 
the Safety Management Plan throughout the conduct of the clinical trial. 


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9.2 
Regulatory Requirements 
The Sponsor is responsible for regulatory submissions and reporting to the Investigators of SAEs 
including suspected unexpected serious adverse reactions (SUSARs) per the International 
Conference on Harmonization (ICH) guidelines E2A and ICH E6.  Country-specific regulatory 
requirements will be followed in accordance with local country regulations and guidelines. 
IRBs/IECs will be notified of any serious adverse event (SAE) according to applicable 
regulations.  The DSMB will be notified of any SAE as specified in the DSMB charter. 
9.3 
Definitions 
9.3.1 
Adverse Event 
An adverse event is any unfavorable and unintended sign (including a clinically significant 
abnormal laboratory finding, for example), symptom, or disease temporally associated with the 
study or use of investigational drug product, whether or not the AE is considered related to the 
investigational drug product. 
9.3.2 
Adverse Reaction and Suspected Adverse Reaction 
An adverse reaction is any adverse event caused by the Study Drug. 
A suspected adverse reaction is any adverse event for which there is a reasonable possibility that 
the drug caused the adverse event.  A suspected adverse reaction implies a lesser degree of 
certainty about causality than an adverse reaction. 
9.3.3 
Serious Adverse Event (SAE) 
A serious adverse event is any adverse event that in the view of either the Investigator or 
Sponsor, meets any of the following criteria: 
• Results in death 
• Is life threatening: that is, poses an immediate risk of death at the time of the event 
An AE or suspected adverse reaction is considered “life-threatening” if, in the view of 
either the Investigator or Sponsor, its occurrence places the subject at immediate risk of 
death.  It does not include an AE or suspected adverse reaction that, had it occurred in a 
more severe form, might have caused death 
• Requires inpatient hospitalization or prolongation of existing hospitalization 
Hospitalization is defined as an admission of greater than 24 hours to a medical facility 
and does not always qualify as an AE 
• Results in a persistent or significant incapacity or substantial disruption of the ability to 
conduct normal life functions 
• Results in congenital anomaly or birth defect in the offspring of the subject (whether the 
subject is male or female) 


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• Important medical events that may not result in death, are not life-threatening, or do not 
require hospitalization may also be considered serious when, based upon appropriate 
medical judgment, they may jeopardize the subject and may require medical or surgical 
intervention to prevent one of the outcomes listed in this definition.  Examples of such 
medical events include allergic bronchospasm requiring intensive treatment in an 
emergency room or at home, blood dyscrasias or convulsions that do not result in 
inpatient hospitalization, or the development of drug dependency or drug abuse 
9.4 
Monitoring and Recording Adverse Events 
Any pre-existing conditions or signs and/or symptoms present in a subject prior to the start of the 
study (i.e., before informed consent) should be recorded as Medical History and not recorded as 
AEs unless the pre-existing condition worsened.  The Investigator should always group signs and 
symptoms into a single term that constitutes a single unifying diagnosis if possible. 
9.4.1 
Serious Adverse Events 
In the interest of subject safety, and in order to fulfill regulatory requirements, all SAEs 
(regardless of their relationship to Study Drug) should be reported to the Sponsor within 
24 hours of the Study Center’s first knowledge of the event.  The collection of SAEs will begin 
after the subject signs the informed consent form and stop at the end of the subject’s follow-up 
period which is defined as the subject’s last visit.  When the Investigator is reporting by 
telephone, it is important to speak to someone in person versus leaving a message.  An Initial 
Serious Adverse Event Form should be completed and a copy should be faxed to the Sponsor or 
designee. 
Detailed information should be actively sought and included on Follow-Up Serious Adverse 
Event Forms as soon as additional information becomes available.  All SAEs will be followed 
until resolution.  SAEs that remain ongoing past the subject’s last protocol-specified follow-up 
visit will be evaluated by the Investigator and Sponsor.  If the Investigator and Sponsor agree the 
subject’s condition is unlikely to resolve, the Investigator and Sponsor will determine the follow-
up requirement. 
9.4.2 
Non-Serious Adverse Events 
The recording of non-serious AEs will begin after the subject signs the informed consent form 
and will stop at the end of the subject’s follow-up period, which is defined as subject’s last visit.  
The Investigator will monitor each subject closely and record all observed or volunteered AEs on 
the Adverse Event Case Report Form. 
9.4.3 
Evaluation of Adverse Events (Serious and Non-Serious) 
The Investigator’s opinion of the following should be documented on the Adverse Event Case 
Report Form. 
 
 


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9.4.3.1 
Relationship to the Study Drug 
The event’s relationship to the Study Drug is characterized by one of the following: 
• Related:  There is clear evidence that the event is related to the use of Study Drug e.g., 
confirmation by positive re-challenge test 
• Possible:  The event cannot be explained by the subject’s medical condition, concomitant 
therapy, or other causes, and there is a plausible temporal relationship between the event 
and Study Drug administration 
• Unlikely/Remote:  An event for which an alternative explanation is more likely (e.g., 
concomitant medications or ongoing medical conditions) or the temporal relationship to 
Study Drug administration and/or exposure suggests that a causal relationship is unlikely 
(For reporting purposes, Unlikely/Remote will be grouped together with Not Related) 
• Not Related:  The event can be readily explained by the subject’s underlying medical 
condition, concomitant therapy, or other causes, and therefore, the Investigator believes 
no relationship exists between the event and Study Drug 
9.4.3.2 
Severity 
The event’s severity is characterized by one of the following: 
• Mild:  The event is easily tolerated by the subject and does not affect the subject’s usual 
daily activities 
• Moderate:  The event causes the subject more discomfort and interrupts the subject’s 
usual daily activities 
• Severe:  The event is incapacitating and causes considerable interference with the 
subject’s usual daily activities 
If the event is an SAE, then all applicable seriousness criteria must be indicated (criteria listed in 
Section 9.3.3). 
9.4.3.3 
Action Taken with Study Drug 
Action taken with Study Drug due to the event is characterized by one of the following: 
• None:  No changes were made to Study Drug administration and dose 
• Permanently Discontinued:  Study drug was discontinued and not restarted 
• Temporarily Interrupted, restarted – same dose:  Dosing was temporarily interrupted 
or delayed due to the AE and restarted at the same dose without unblinding to treatment 
group 
9.4.3.4 
Treatment Given for Adverse Event 
Any treatment (e.g., medications or procedures) given for the AE should be recorded on the 
Adverse Event Case Report Form (treatment should also be recorded on the concomitant 
treatment or ancillary procedures CRF as appropriate). 


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9.4.3.5 
Outcome of the Adverse Event 
If the event is a non-serious AE then the event’s outcome is characterized by one of the 
following: 
• AE Persists:  Subject terminates from the trial and the AE continues 
• Recovered:  Subject recovered completely from the AE 
• Became Serious:  The event became serious (the date that the event became serious 
should be recorded as the Resolution Date of that AE and the Onset Date of the 
corresponding SAE) 
• Change in Severity (if applicable):  AE severity changed 
If the event is a SAE then the event’s outcome is characterized by one of the following: 
• Ongoing:  SAE continuing 
• Persists (as non-serious AE):  Subject has not fully recovered but the event no longer 
meets serious criteria and should be captured as an AE on the non-serious AE electronic 
case report form (eCRF) (the SAE resolution date should be entered as the date of onset 
of that AE) 
• Recovered:  Subject recovered completely from the SAE (the date of recovery should be 
entered as the SAE resolution date) 
• Fatal:  Subject died (the date of death should be entered as the SAE resolution date) 
9.5 
Procedures for Handling Special Situations 
9.5.1 
Abnormalities of Laboratory Tests 
Clinically significant abnormal laboratory test results may, in the opinion of the Investigator, 
constitute or be associated with an AE.  Examples of these include abnormal laboratory results 
that are associated with symptoms, or require treatment, e.g., bleeding due to thrombocytopenia, 
tetany due to hypocalcemia, or cardiac arrhythmias due to hyperkalemia.  Whenever possible, the 
underlying diagnosis should be listed in preference to abnormal laboratory values as AEs.  
Clinically significant abnormalities will be monitored by the Investigator until the parameter 
returns to its baseline value or until agreement is reached between the Investigator and Medical 
Monitor.  Laboratory abnormalities deemed not clinically significant (NCS) by the Investigator 
should not be reported as AEs.  Similarly, laboratory abnormalities reported as AEs by the 
Investigator should not be deemed NCS on the laboratory sheet. 
The Investigator is responsible for reviewing and signing all laboratory reports.  The signed 
clinical laboratory reports will serve as source documents. 
 
 


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9.5.2 
Prescheduled or Elective Procedures or Routinely Scheduled Treatments 
A prescheduled or elective procedure or a routinely scheduled treatment will not be considered 
an SAE, even if the subject is hospitalized; the Study Center must document all of the following: 
• The prescheduled or elective procedure or routinely scheduled treatment was scheduled 
(or was on a waiting list to be scheduled) prior to obtaining the subject’s consent to 
participate in the study 
• The condition that required the prescheduled or elective procedure or routinely scheduled 
treatment was present before and did not worsen or progress in the opinion of the 
Investigator between the subject’s consent to participate in the study and the timing of the 
procedure or treatment 
• The prescheduled or elective procedure or routinely scheduled treatment is the sole 
reason for the intervention or hospital admission 
9.5.3 
Dosing Errors 
Study drug errors defined as errors in administration or the administered dose should be 
documented as Protocol Deviations.  A brief description should be provided in the deviation, 
including whether the subject was symptomatic (list symptoms) or asymptomatic. 
Dosing details should be captured on the Dosing CRF. 
Should an overdose occur, the Investigator or designee should contact the Unblinded Medical 
Monitor within 24 hours. 
9.5.4 
Contraception and Pregnancy 
Female subjects that have reached reproductive maturity must have a negative pregnancy test at 
Screening and must not be able to become pregnant for the duration of the study, as described in 
Section 6.3. 
Male subjects must be abstinent during the duration of the study. 
If a subject becomes pregnant or a pregnancy is suspected, or if a male subject makes or believes 
that he has made someone pregnant during the study, then the site staff must be informed 
immediately.  An Initial Pregnancy Form should be submitted to the Sponsor or designee within 
24 hours of first learning of the occurrence of pregnancy.  Follow-up information including 
delivery or termination is reported on Follow-up Pregnancy Forms and reported within 24 hours. 
Payment for all aspects of obstetrical care, child or related care will be the subject’s 
responsibility. 


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10. 
STATISTICAL CONSIDERATIONS 
10.1 
Study Endpoints, Subsets, and Covariates 
10.1.1 
Primary Endpoint 
• Change from baseline in HFMSE (Hammersmith Functional Motor Scale – Expanded) 
score at 15 months 
10.1.2 
Secondary Efficacy Endpoints 
• Proportion of subjects who achieve a 3-point increase from baseline in Hammersmith 
Functional Motor Scale – Expanded (HFMSE) score at 15 months 
• Proportion of subjects that achieve any new motor milestone at 15 months 
• Number of motor milestones achieved per subject at 15 months 
• Change from baseline in Upper Limb Module Test at 15 months 
• Proportion of subjects that achieve standing alone at 15 months 
• Proportion of subjects that achieve walking with assistance at 15 months 
10.1.3 
Tertiary Efficacy Endpoints 
• Change from baseline in CSF SMN protein concentration 
• Clinical Global Impression of Change (Investigator and Caregiver assessment) 
• Change from baseline in PedsQL (Pediatric Quality of Life Inventory) 
• Change from baseline in Assessment of Caregiver Experience with Neuromuscular 
Disease (ACEND) 
• Disease-related hospitalizations and adverse events 
10.1.4 
Safety/Tolerability Endpoints 
• Adverse events 
• Vital signs and weight 
• Neurological examinations 
• Physical examinations  
• Clinical laboratory tests (serum chemistry, hematology, urinalysis) 
• Electrocardiograms (ECGs) 
• Use of concomitant medications 


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10.1.5 
Pharmacokinetic Endpoints 
• CSF levels of ISIS 396443 
• Plasma levels of ISIS 396443 
10.1.6 
Immunogenicity Endpoint 
• Plasma antibodies to ISIS 396443 
10.2 
Sample Size Considerations 
The sample size for this study was estimated based on limited available natural history data for 
the target population and data from the ISIS 396443-CS1 and ISIS 396443-CS2 clinical studies.  
70 patients in the treated group and 35 patients in the control group will give at least 90% power 
to detect a 3 point difference between control and treated groups in change on the HFMSE with a 
standard deviation of 4.4, using a two-sided t-test with an alpha level of 0.05.  The sample size 
was estimated using n-Query.  117 patients enrolled will ensure that a small dropout rate will not 
affect the power of the primary efficacy analysis. 
10.3 
Populations 
Intent to Treat (ITT) Set:  All patients who are randomized, receive at least one dose of study 
drug/sham procedure, and have a baseline and at least one post baseline efficacy evaluation. 
Per-Protocol Set (PPS):  PPS will include the subset of the ITT who complete at least the initial 
3 doses of study drug/sham procedures, have baseline and Day 169 efficacy assessments and 
who have no significant protocol deviations that would be expected to affect efficacy 
assessments. 
Safety Set:  All patients who are randomized and receive at least one dose of study drug/sham 
procedure. 
Pharmacokinetic Population:  All patients who are randomized and for which there is at least one 
evaluable post-dose/post-sham procedure pharmacokinetic sample. 
10.4 
Definition of Baseline 
The baseline is defined as the last non-missing assessment prior to the first dose of Study Drug. 
10.5 
Interim Analysis 
An interim analysis may take place when all subjects have completed the 6 month assessment 
and at least 39 subjects have completed the 15 month assessment.  At the interim analysis, the 
last recorded observation for each subject (i.e., at 6 to 15 months) will be used in the analysis.  
The data will be analyzed using ANCOVA with patient age at screening and baseline value as 
covariates. 
A DSMB will review the interim analysis results and make determinations on whether it is 
appropriate for the trial to continue.  During the interim analysis, subject accrual will continue. 
Details of the analysis and controlled access to the unblinded data are contained in the Statistical 
Analysis Plan (SAP) and DSMB Charter. 


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If the interim analysis is performed, based on the Lan-DeMets method for group sequential trials 
using O’Brien-Fleming boundaries (Reboussin et al. 2000), for a single interim analysis 
conducted using approximately 60% of the information, the levels of significance for the interim 
and final analyses are 0.01 and 0.0468, respectively.  In order to control the Type 1 error, a 
sequential closed testing procedure with significance level of 0.01 will be employed with the 
sequence of the endpoints as defined in Sections 10.1.1 and 10.1.2 at the interim analysis.  A 
significance level of 0.0468 will be used for sequential testing procedure at the final analysis.  
However, if the interim analysis is not performed, significance level for the final analysis will 
remain at 0.05. 
10.6 
Planned Methods of Analysis 
Data collected on eCRF, lab data transfers, as well as any outcomes derived from the data, will be 
provided in the patient data listings.  Patient data listings will be presented for all patients enrolled 
into the study. 
Descriptive summary statistics including n, mean, median, standard deviation, standard error, 
interquartile range (25th percentile, 75th percentile), and range (minimum, maximum) for 
continuous variables, and counts and percentages for categorical variables will be used to 
summarize most data by treatment group. 
All primary, secondary and tertiary endpoints will be assessed in the ITT Set and PPS, with the 
former being the basis for the primary efficacy analysis.  All safety assessments will be 
performed on the Safety Set. PK endpoints will be assessed in the PK Set as applicable. 
10.6.1 
Demographic and Baseline Characteristics 
Demographic and baseline characteristics will be summarized using descriptive statistics by 
treatment group.  Patient disposition will be summarized by treatment group.  All patients 
enrolled will be included in a summary of patient disposition. 
10.6.2 
Safety and Tolerability Analysis 
Safety analyses will be conducted in the Safety Set. Treatment duration and amount of study 
drug received will be summarized by treatment group. 
All treatment-emergent adverse events and serious adverse events will be summarized for each 
treatment group using the MedDRATM coding system, by system organ class, preferred term, 
relationship to Study Drug, and severity.  Narratives of deaths, serious adverse events, including 
early withdrawals from study drug and from study due to adverse events, will also be provided. 
Laboratory tests including chemistry panel, complete blood count with differential, etc. will be 
summarized by study visit for each treatment group.  These safety variables will also be 
presented over time after study drug administration, as appropriate.  Vital sign results will be 
presented similarly. 
Physical and neurological examination findings and results from ECG will be listed for review.  
As appropriate, results will also be summarized descriptively for each treatment group.  
Concomitant medication usage for each subject will be listed for review. 


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10.6.3 
Efficacy Analysis 
All statistical tests will be 2-sided with a Type 1 error rate of 5%, unless otherwise specified. 
Secondary efficacy endpoints have been rank prioritized in the order shown in Section 10.1.2.  In 
order to control the Type 1 error, a sequential closed testing procedure will be employed with the 
sequence of endpoints defined as above.  Testing of secondary endpoints will be performed only 
if the treatment comparison of the primary endpoint is statistically significant (p<0.050, unless 
interim analysis is performed).  Testing of the secondary endpoints will be conducted according 
to the sequence above: if the first secondary endpoint (proportion of patients that achieve a 
3-point increase from baseline in HFMSE at 15 months) is statistically significant (p<0.050, 
unless interim analysis is performed) then the second secondary endpoint (proportion of subjects 
that achieve any new motor milestone at 15 months) will be tested at the same significance level.  
However, if the treatment comparison based on the first secondary endpoint is not statistically 
significant, then all endpoints of a lower rank will not be considered statistically significant.  
This process is repeated with each subsequent secondary endpoint. 
Analyses of tertiary efficacy endpoints will not include adjustments for multiplicity. 
The primary analysis of the primary endpoint is to compare the change from baseline in HFMSE 
score at Month 15 between treatment groups using the ITT Set.  The data will be analyzed using 
a Mixed Effects Model with Repeated Measures (MMRM) model where the treatment group, 
time, treatment by time interaction, and patient age at Screening will be included in the model as 
fixed effects; patient will be a random effect; the baseline HFMSE score will be included as a 
covariate.  No imputation for missing data will be made.  The unstructured covariance model 
will be used and test of fixed effects will be carried out.  The treatment contrast for Month 15 
will be estimated by the model.  The primary efficacy analysis will take place after all patients 
have completed the Day 456/ET visit and the database has been locked. 
The following sensitivity analyses will also be conducted, and details of the analyses will be 
outlined in the SAP:  
• The primary analysis will be repeated in the PPS. 
• The primary analysis will be repeated in the subset of ITT Set who have non-missing 
Month 15 HFMSE score. 
• The LOCF method will be used to impute missing Month 15 HFMSE score.  Stratified 
Wilcoxon Rank Sum test and ANCOVA with the stratification factor and baseline 
HFMSE score as covariates will be used to analyze the imputed data. 
The primary analysis of each secondary endpoint will be based on the ITT Set.  Analyses based 
on the PPS are considered sensitivity analyses. 
• Comparison of proportion of subjects that achieve a 3-point increase from baseline in 
HFMSE score at Month 15 between the treatment groups.  The data will be analyzed 
using the logistic regression adjusting for each patient’s age at screening and baseline 
HFMSE score.  If a patient terminates study before Month 15 due to AE, lack of efficacy 
or other types of treatment failure, then the patient will be considered as a non-responder.  


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If a patient terminates study before Month 15 or has missing HFMSE score at Month 15 
due to any other reason, then the patient will not be included in the analysis. 
• Comparison of proportion of subjects that achieve any new motor milestone at Month 15 
between the treatment groups.  The data will be analyzed using the logistic regression 
adjusting for each patient’s age at Screening and baseline number of motor milestones 
that a patient has achieved.  If a patient terminates study before Month 15 due to AE, lack 
of efficacy or other types of treatment failure, then the patient will be considered as a 
non-responder.  If a patient terminates study before Month 15 or has missing data at 
Month 15 due to any other reason, then the patient will not be included in the analysis. 
• Comparison of number of motor milestones achieved per subject at Month 15 between 
treatment groups.  The data will be analyzed in a similar way to the primary endpoint. 
• Comparison of change from baseline in Upper Limb Module Test at Month 15 between 
treatment groups.  The data will be analyzed in a similar way to the primary endpoint. 
• Comparison of proportion of subjects that achieve standing alone milestone at Month 15 
between the treatment groups.  The data will be analyzed in a similar way to the 
proportion of subjects that achieve any new motor milestone at Month 15. 
• Comparison of proportion of subjects that achieved walking with assistance milestone at 
Month 15 between the treatment groups.  The data will be analyzed in a similar way to 
the proportion of subjects that achieve any motor milestone at Month 15. 
10.6.4 
Pharmacokinetic Analysis 
Plasma pharmacokinetic parameters and ISIS 396443 concentrations in plasma and CSF for the 
Pharmacokinetic population will be summarized using descriptive statistics and, where 
warranted, presented graphically. 
11. 
INVESTIGATOR’S REGULATORY OBLIGATIONS 
11.1 
Informed Consent/Assent 
The written informed consent and assent documents should be prepared in the language(s) of the 
potential subject population, based on an English version provided by the Sponsor and should be 
easy to understand. 
Before a subject’s participation in the trial, the Investigator is responsible for obtaining written 
informed consent from the parent or legal guardian and, in cases where institutional guidelines 
and the subject’s age dictate, informed assent from the subject, after adequate explanation of the 
aims, methods, anticipated benefits, and potential hazards of the study and before any protocol-
specific screening procedures or any study drugs are administered.  Sufficient time must be given 
to consider whether to participate in the study. 
The acquisition of informed consent/assent and the parent/legal guardian’s/subject’s agreement 
or refusal of his/her notification of the primary care physician should be documented in the 
subject’s medical records, and the informed consent/assent form(s) should be signed and 
personally dated by the parent/legal guardian/subject and by the study person who conducted the 


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informed consent/assent discussion.  The original signed informed consent/assent form(s) should 
be retained in the Study Master File and in any other locations required by institutional policy, 
and a copy of the signed consent/assent form(s) should be provided to the parent or guardian. 
11.2 
Ethical Conduct of the Study 
The Guidelines of the World Medical Association (WMA) Declaration of Helsinki dated 
October 2002 the applicable regulations and guidelines of current Good Clinical Practice (GCP) 
as well as the demands of national drug and data protection laws and other applicable regulatory 
requirements will be strictly followed. 
11.3 
Institutional Review Board/Institutional Ethics Committee/Research Ethics Board 
A copy of the protocol, proposed informed consent form, proposed informed assent form (if 
applicable) other written subject information, and any proposed advertising material must be 
submitted to the IRB/IEC for written approval.  A copy of the written approval of the protocol 
and informed consent/assent forms must be received by the Sponsor before recruitment of 
subjects into the study and shipment of Study Drug.  A copy of the written approval of any other 
items/materials that must be approved by the Study Center or IRB/IEC must also be received by 
the Sponsor before recruitment of subjects into the study and shipment of Study Drug.  The 
Investigator’s Brochure must be submitted to the IRB/IEC for acknowledgement. 
The Investigator must submit to and, where necessary, obtain approval from the IRB/IEC for all 
subsequent protocol amendments and changes to the informed consent/assent documents.  The 
Investigator should notify the IRB/IEC of deviations from the protocol in accordance with ICH 
GCP Section 4.5.2.  The Investigator should also notify the IRB/IEC of serious adverse events 
occurring at the Study Center and other adverse event reports received from the Sponsor, in 
accordance with local procedures. 
The Investigator will be responsible for obtaining annual IRB/IEC approval/renewal throughout 
the duration of the study.  Copies of the Investigator’s reports, all IRB/IEC submissions and the 
IRB/IEC continuance of approval must be sent to the Sponsor. 
11.4 
Subject Confidentiality 
The Investigator must ensure that the subject’s confidentiality is maintained.  On the CRFs or 
other documents submitted to the Sponsor, subjects should be identified by unique, anonymous 
initials and a subject study number only.  Documents that are not for submission to the Sponsor 
(e.g., signed informed consent/assent forms) should be kept in strict confidence by the 
Investigator. 
In compliance with federal and local regulations/ICH GCP Guidelines, it is required that the 
Investigator and institution permit authorized representatives of the company, of the regulatory 
agency(s), and the IRB/IEC direct access to review the subject’s original medical records for 
verification of study-related procedures and data.  Direct access includes examining, analyzing, 
verifying, and reproducing any records and reports that are important to the evaluation of the 
study.  The Investigator is obligated to inform and obtain the consent of the subject’s parent or 
guardian to permit named representatives to have access to his/her study-related records without 
violating the confidentiality of the subject. 


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12. 
ADMINISTRATIVE AND LEGAL OBLIGATIONS 
12.1 
Protocol Amendments 
Agreement from the Investigator must be obtained for all protocol amendments and amendments 
to the informed consent/assent documents.  The regulatory authority and IRB/IEC must be 
informed of all amendments and give approval for any amendments likely to affect the safety of 
the subjects or the conduct of the trial.  The Investigator must send a copy of the approval letter 
from the IRB/IEC to the Sponsor. 
12.2 
Study Termination 
The Sponsor reserves the right to terminate the study.  The Investigator reserves the right to 
terminate their participation in the study, according to the terms of the site contract.  The 
Investigator/Sponsor should notify the IRB/IEC in writing of the trial’s completion or early 
termination and send a copy of the termination to the Sponsor. 
12.3 
Study Documentation and Storage 
The Investigator should ensure that all appropriately qualified persons to whom he/she has 
delegated trial duties are recorded on a Sponsor-approved Delegation of Site Responsibilities 
Form. 
Source documents are original documents, data, and records from which the subject’s CRF data 
are obtained.  These include but are not limited to hospital records, clinical and office charts, 
laboratory and pharmacy records, and correspondence.  In this study, CRFs may not be used as 
source documents. 
The Investigator and Study Center staff is responsible for maintaining a comprehensive and 
centralized filing system of all study-related (essential) documentation in accordance with 
Section 8 of the ICH Guidelines (E6), suitable for inspection at any time by representatives from 
the Sponsor and/or applicable regulatory authorities.  Elements should include: 
• Subject files containing completed CRFs, informed consents/assents, and supporting 
copies of source documentation 
• Study files containing the protocol with all amendments, Investigator’s Brochure, copies 
of pre-study documentation and all correspondence to and from the IRB and the Sponsor 
• If drug supplies are maintained at the Study Center, proof of receipt, Study Drug Product 
Accountability Record, Return of Study Drug Product for Destruction, and all drug-
related correspondence 
In addition, all original source documents supporting entries in the CRFs must be maintained and 
be readily available. 
No study document should be destroyed without prior written agreement between the Sponsor 
and the Investigator.  Should the Investigator wish to assign the study records to another party or 
move them to another location, he/she must notify the Sponsor. 


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12.4 
Study Monitoring 
The Sponsor representative and regulatory authority inspectors are responsible for contacting and 
visiting the Investigator for the purpose of inspecting the facilities and, upon request, inspecting 
the various records of the trial (e.g., CRFs and other pertinent data) provided that subject 
confidentiality is respected. 
The Sponsor monitor is responsible for inspecting the CRFs at regular intervals throughout the 
study to verify adherence to the protocol; completeness, accuracy, and consistency of the data; 
and adherence to local regulations on the conduct of clinical research.  The monitor should have 
access to subject medical records and other study-related records needed to verify the entries on 
the CRFs. 
The Investigator agrees to cooperate with the monitor to ensure that any problems detected in the 
course of these monitoring visits, including delays in completing CRFs, are resolved. 
In accordance with ICH GCP and the Sponsor’s audit plans, this study may be selected for audit 
by representatives from the Sponsor’s Clinical Quality Assurance Department.  Inspection of 
Study Center facilities (e.g., pharmacy, drug storage areas, laboratories) and review of study-
related records will occur to evaluate the trial conduct and compliance with the protocol, ICH 
GCP, and applicable regulatory requirements. 
To ensure the quality of clinical data a clinical data management review will be performed on 
subject data received by the Sponsor.  During this review, subject data will be checked for 
consistency, omissions, and any apparent discrepancies.  In addition, the data will be reviewed 
for adherence to the protocol and GCP.  To resolve any questions arising from the clinical data 
management review process, data queries and/or Study Center notifications will be sent to the 
Study Center for completion and return to Sponsor. 
The Principal Investigator will sign and date the indicated places on the CRF.  These signatures 
will indicate that the Principal Investigator inspected or reviewed the data on the CRF, the data 
queries, and the Study Center notifications, and agrees with the content. 
12.5 
Language 
CRFs must be completed in English.  Generic names for concomitant medications should be 
recorded in English if possible, unless it is a combination drug, then record the trade name in 
English. 
All written information and other material to be used by subjects and investigative staff must use 
vocabulary and language that are clearly understood. 
12.6 
Compensation for Injury 
The Sponsor maintains appropriate insurance coverage for clinical trials and will follow 
applicable local compensation laws.  Subjects will be treated and/or compensated for any study-
related illness/injury in accordance with the information provided in the Compensation for Injury 
section of the Informed Consent document. 


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13. 
REFERENCES 
Cho S and Dreyfuss G. A degron created by SMN2 Exon 7 skipping is a principal contributor to spinal muscular 
atrophy severity. Genes Dev 2010; 24: 438-442. 
Coovert DD, Le TT, McAndrew PE, Strasswimmer J, Crawford TO, Mendell JR, Coulson SE, Androphy EJ, 
Prior TW, Burghes AH. The survival motor neuron protein in spinal muscular atrophy. Hum Mol Genet 1997; 6: 
1205-1214. 
Feldkotter M, Schwarzer V, Wirth R, Wienker TF, Wirth B. Quantitative analyses of SMN1 and SMN2 based on 
real-time light cycler PCR: fast and highly reliable carrier testing and prediction of severity of spinal muscular 
atrophy. Am J Hum Genet 2002; 70: 358-368. 
Geary RS, Yu RZ, Watanabe T, Henry SP, Hardee GE, Chappell A, Matson J, Sasmor H, Cummins L, Levin AA. 
Pharmacokinetics of a tumor necrosis factor-α phosphorothioate 2′-O-(2-Methoxyethyl) modified antisense 
oligonucleotide: comparison across species. Drug Metab Disp 2003; 31: 1419-1428. 
Helmken C, Hofmann Y, Schoenen F, Oprea G, Raschke H, Rudnik-Schöneborn S, Zerres K, Wirth B. Evidence for 
a modifying pathway in SMA discordant families: reduced SMN level decreases the amount of its interacting 
partner and Htra2-beta1. Hum Genet 2003; 114: 11-21. 
Henry S, Stecker K, Brooks D, Monteith D, Concklin B, Bennett CF. Chemically modified oligonucleotides exhibit 
decreased immune stimulation in mice. J Pharmacol Exp Ther 2000; 292: 468-479. 
Hua Y, Vickers TA, Baker BF, Bennett CF, Krainer AR. Enhancement of SMN2 Exon 7 inclusion by antisense 
oligonucleotides targeting the exon. PLoS Biol 2007; 5: e73. 
Hua Y, Vickers TA, Okunola HL, Bennett CF, Krainer AR. Antisense masking of an HnRNP A1/A2 intronic 
splicing silencer corrects SMN2 splicing in transgenic mice. Am J Hum Genet 2008; 82: 834-848. Epub 2008 
Mar 27. 
Iannaccone ST, Hynan LS, Morton A, Buchanan R, Limbers CA, Varni JW, the AmSMART Group. The PedsQL in 
pediatric patients with spinal muscular atrophy: feasibility, reliability, and validity of the pediatric quality of life 
inventory generic core scales and neuromuscular module. Neuromuscul Disord 2009; 19: 805-812. 
Keren H, Lev-Maor G, Ast G. Alternative splicing and evolution: diversification, exon definition and function. 
Nat.Rev.Genet 2010; 11: 345-355. 
Le TT, Pham LT, Butchbach ME, Zhang HL, Monani UR, Coovert DD, Gavrilina TO, Xing L, Bassell GJ, 
Burghes AH. SMNΔ7, the major product of the centromeric survival motor neuron (SMN2) gene, extends survival 
in mice with spinal muscular atrophy and associates with full-length SMN. Hum Mol Genet 2005; 14: 845-857. 
Epub 2005 Feb 9. 
Lefebvre S, Bürglen L, Reboullet S, Clermont O, Burlet P, Viollet L, Benichou B, Cruaud C, Millasseau P, 
Zeviani M, Le Paslier D, Frézal J, Cohen D, Weissenbach J, Munnich A, Melki J. Identification and characterization 
of a spinal muscular atrophy-determining gene. Cell 1995; 80: 155-165. 
Lefebvre S, Burlet P, Liu Q, Bertrandy S, Clermont O, Munnich A, Dreyfuss G, Melki J. Correlation between 
severity and SMN protein level in spinal muscular atrophy. Nat Genet 1997; 16: 265-269. 
Main M, Kairon H, Mercuri E, Muntoni F. The Hammersmith functional motor scale for children with spinal 
muscular atrophy: a scale to test ability and monitor progress in children with limited ambulation. Eur J Paediatr 
Neurol 2003; 7(4): 155-159. 
Matsumoto H, Clayton-Krasinski DA, Klinge SA, Gomex JA, Booker WA, Hman JE, Roye Jr. DP, Vitale MG. 
Development and initial validation of the assessment of caregiver experience with neuromuscular disease. J Pediatr 
Orthop 2011; 31: 284-292. 
Mazzone E, Bianco F, Martinelli D, Glanzman A, Messina S, De Sanctis R, Main M, Eagle M, Florence J, 
Krosschell K, Vasco G, Pelliccioni M, Lombardo M, Pane M, Finkel R, Muntoni F, Bertini E, Mercuri E. Assessing 
upper limb function in nonambulant SMA patients: development of a new module. Neuromuscul Disord 2011; 21: 
406-412. 


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McKay RA, Miraglia LJ, Cummins LL, Owens SR, Sasmor H, Dean NM. Characterization of a potent and specific 
class of antisense oligonucleotide inhibitor of human protein kinase C-α expression. J Bio Chem 1999; 274: 1715-
1722. 
O’Hagen JM, Glanzman AM, McDermott MP, Ryan PA, Flickinger J, Quigley J, Riley S, Sanborn E, Irvine C, 
Martens WB, Annis C, Tawil R, Oskoui M, Darras BT, Finkel RS, De Vivo DC. An expanded version of the 
hammersmith functional motor scale for SMA II and III patients. Neuromuscular Disorders 2007; 17: 693-697. 
Passini MA, Bu J, Richards AM, Kinnecom C, Sardi SP, Stanek LM, Hua Y, Rigo F, Matson J, Hung G, Kaye EM, 
Shihabuddin LS, Krainer AR, Bennett CF, Cheng SH. Antisense oligonucleotides delivered to the mouse CNS 
ameliorate symptoms of severe spinal muscular atrophy. Science Trans Med 2011; 3: 1-12. 
Prior TW, Swoboda KJ, Scott HD, Hejmanowski AQ. Homozygous SMN1 deletions in unaffected family members 
and modification of the phenotype by SMN2 gene. Am J Med Genet 2004; 130A: 307-310. 
Reboussin DM, DeMets DL, Kim K, Lan KKG. Computations for group sequential boundaries using the Lan-
DeMets spending function method. Controlled Clinical Trials 2000; 21: 190-207. 
Varni JW, Seid M, Rode CA. Measurement model for the pediatric quality of life inventory. Medical Care 1999; 37: 
126-139. 
WHO Multicentre Growth Reference Study Group. Assessment of sex differences and heterogeneity in motor 
milestone attainment among populations in the WHO Multicentre Growth Reference Study. Acta Pædiatrica, 2006; 
Suppl 450: 66/75. 
Wijnhoven T, de Onis M, Onyango A, Wang T, Bjoerneboe G, Bhandari N, Lartey A, Al Rashidi B. Assessment of 
gross motor development in the WHO Multicentre Growth Reference Study. Food Nutr Bull 2004; 21: S37-45. 
 


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14. 
APPENDICES 
 


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Appendix A 
Schedule of Procedures 
 


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Appendix A Schedule of Procedures 
Subjects will also be monitored through phone contact on Study Days 8, 56, 113, 141, 204, 239, 302, 330, 393, 421 (all ± 2 days)9 
Study Period 
Screen 
Treatment/Follow-up 
Study Day 
D -28 
to 
D -1 
D1 
D2 
D29 (±1D) 
D30 
D85 (±2D) 
D86 D92 
(±1D) 
D169 
(±2D)  
D274 (±7D) 
D275 
D365 
(±7D) 
and 
D456 
(+ 7D) 
and 
Early 
Term 
Pre- 
dose 
LP/ 
SP 
Post- 
dose 
Pre- 
dose 
LP/ 
SP 
Post- 
dose 
Pre- 
dose 
LP/ 
SP 
Post- 
dose 
Pre- 
dose 
LP/ 
SP 
Post- 
dose 
Informed Consent 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Inclusion/Exclusion 
Criteria 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Medical History 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Screening X-ray 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Urine Pregnancy 
Test11 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
X14 
SMN2 copy Number12 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Study Drug 
Injection/Sham 
Procedure 
 
 
X 
 
 
 
X7 
 
 
 
X7 
 
 
 
 
 
X7 
 
 
 
In-Patient Stay 
(24 hours) 
 
 
 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Vital Signs1 
X 
X 
 
4X2 
X3 
X 
 
4X2 
X 
X 
 
4X2 
X 
X 
X 
X 
 
4X2 
X 
X 
Weight 
X 
X 
 
 
 
X 
 
 
 
X 
 
 
 
X 
X 
X 
 
 
 
X 
Height/ulnar length 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
X14 
Physical Examination 
X 
X 
 
 
 
X 
 
 
 
X 
 
 
 
X 
X 
X 
 
 
 
X 
Neurological 
Examination 
X 
X 
 
X4 
X3 
X 
 
X4 
X 
X 
 
X4 
X 
X 
X 
X 
 
X4 
X 
X 
ECG 
X 
 
 
 
X 
 
 
X 
 
 
 
 
 
X 
 
 
 
 
 
X14 
Safety Labs5 
X 
X 
 
 
X 
X 
 
 
 
X 
 
 
 
 
X 
X 
 
 
 
X14 
Coagulation Labs 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Immunogenicity  
 
X 
 
 
 
X 
 
 
 
X 
 
 
 
 
X 
X 
 
 
 
X14 


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Appendix A Schedule of Procedures Continued 
Study Period 
Screen 
Treatment/Follow-up 
Study Day 
D -28 
to 
D -1 
D1 
D2 
D29 (±1D) 
D30 
D85 (±2D) 
D86 D92 
(±1D) 
D169 
(±2D) 
D274 (±7D) 
D275 
D365 
(±7D) 
and 
D456 
(+ 7D) 
and 
Early 
Term 
Pre- 
dose 
LP/ 
SP 
Post- 
dose 
Pre- 
dose 
LP/ 
SP 
Post- 
dose 
Pre- 
dose 
LP/ 
SP 
Post- 
dose 
Pre- 
dose 
LP/ 
SP 
Post- 
dose 
CSF PK8 
 
X 
 
 
 
X 
 
 
 
X 
 
 
 
 
 
X 
 
 
 
 
CSF SMN Protein 
 
X 
 
 
 
X 
 
 
 
X 
 
 
 
 
 
X 
 
 
 
 
Plasma PK8 
 
X 
 
3X 
X 
X 
 
 
 
X 
 
X 
 
 
X 
X 
 
 
 
X14 
HFMSE 
X10 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
WHO Motor Milestones 
X6, 10 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
Upper Limb 
X6, 10 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
PedsQL 
X6 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
ACEND 
X6 
 
 
 
 
 
 
 
 
 
 
 
 
 
X 
 
 
 
 
X14 
CGI 
 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
Con Med Recording9 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Adverse Event 
Collection9 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
1 
Resting blood pressure, pulse, respiratory rate, and temperature 
2 
Vital signs performed 1, 2, 4, 6 hours after dosing 
3 
Conducted within 20-24 hours after dosing 
4 
Neurological exams at 5 hours after dosing 
5 
Serum chemistry, hematology, urinalysis panels (Appendix B for analytes) 
6 
Efficacy assessments (with the exception of HFMSE) do not form part of the screening assessment or inclusion/exclusion criteria but are baseline 
measurements taken during the screening phase of the study 
7 
Overnight stay is optional on Day 29, Day 85, and Day 274  
8 
Refer to Appendix C for PK sampling schedule 
9 
At telephone contact, changes in concomitant medications and adverse events will be recorded  
10 To be performed 2 times during the screening period  
11 Urine pregnancy test performed for females of child-bearing potential, if positive to be confirmed by local serum test 
12 Only for those subjects who do not have documented evidence of SMN copy number from Athena Diagnostics 
13 These assessments may be performed up to 7 days prior to dosing, if necessary 
14 Assessed on Day 456 only 


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Appendix B 
Laboratory Analytes 
 
 
 


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Appendix B Laboratory Analytes 
CLINICAL SAFETY ASSESSMENTS 
(minimum requirements) 
OTHER ASSESSMENTS 
Clinical Chemistry 
Sodium 
Potassium 
Chloride 
Total protein 
Albumin 
Calcium 
Phosphorus 
Bicarbonate 
Glucose 
BUN 
Creatinine 
Cystatin C 
Total serum Bilirubin 
Alkaline phosphatase 
AST (SGOT) 
ALT (SGPT) 
CPK 
 
Coagulation 
aPTT 
PT 
INR 
Urinalysis  
Specific gravity 
pH 
Protein 
Glucose 
Ketones 
Bilirubin 
Blood 
Red blood cells 
White blood cells 
Epithelial cells 
Bacteria 
Casts 
Crystals 
 
Hematology 
Red blood cells 
Hemoglobin 
Hematocrit 
Platelets 
White blood cells 
WBC Differential 
• 
(% and absolute) 
• 
Neutrophils 
• 
Eosinophils 
• 
Basophils 
• 
Lymphocytes 
• 
Monocytes 
Pregnancy 
Urine hCG 
 
PK* 
Plasma ISIS 396443 levels 
CSF ISIS 396443 levels 
 
PD 
CSF SMN protein levels 
 
Immunogenicity Evaluation 
ISIS 396443 plasma Abs 
 
SMN Genetics 
SMN2 Copy Number 
* 
Any of the collected PK plasma and CSF samples from the study patients may also be used for investigation of 
possible biomarkers of SMA disease or the pharmacodynamic effects of ISIS 396443 (e.g., CSF mRNA, CSF 
protein, CSF miRNA panel) or for profiling of drug binding proteins, bioanalytical method validation purposes, 
stability assessments, metabolite assessments, immunogenicity assessments (including assay development and 
validation purposes), or to assess other actions of ISIS 396443 with plasma and CSF constituents. 
 
 


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Appendix C 
Pharmacokinetic Sampling Schedule 
 
 


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Appendix C Pharmacokinetic Sampling Schedule 
Treatment Period 
Study Day 
Timepoints 
Blood 
Collection  
CSF Collection  
Multiple Dose: 
LP Injection 
D1 
Predose 
0.35 mL 
0.5 mL 
2 hr 
0.35  mL 
NA 
4 hr 
0.35  mL 
NA 
8 hr 
0.35  mL 
NA 
D2 
24 hr 
0.35  mL 
NA 
D29 
Predose 
0.35  mL 
0.5 mL 
D85 
Predose 
0.35  mL 
0.5 mL 
4 hr 
0.35  mL 
NA 
D169 
Anytime 
0.35  mL 
NA 
D274 
Predose 
0.35  mL 
0.5 mL 
D456 
Anytime 
0.35  mL 
NA 
NA Not applicable (No Collection Scheduled) 
Details on sampling, preparation, and shipment are included in the study laboratory manual. 
Any of the collected PK plasma and CSF samples from the study patients may also be used for investigation of 
possible biomarkers of SMA disease or the pharmacodynamic effects of ISIS 396443 (e.g., CSF mRNA, CSF protein, 
CSF miRNA panel) or for profiling of drug binding proteins, bioanalytical method validation purposes, stability 
assessments, metabolite assessments, immunogenicity assessments (including assay development and validation 
purposes), or to assess other actions of ISIS 396443 with plasma and CSF constituents. 

SAP_000.pdf: 
 
ISIS 396443-CS4 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Statistical Analysis Plan 
 
 
 


ISIS 396443-CS4 
 
Statistical Analysis Plan Version 1.0 
 
2 
STATISTICAL ANALYSIS PLAN 
 
Product Studied: ISIS 396443 
 
Protocol Number(s): ISIS 396443-CS4 
 
 
A Phase 3, Randomized, Double-blind, Sham-Procedure Controlled Study  
to Assess the Clinical Efficacy and Safety of ISIS 396443 Administered Intrathecally  
in Patients with Later-onset Spinal Muscular Atrophy 
 
 
Date of Protocol: 30 June, 2016 
 
 
Date of Statistical Analysis Plan: 12 October, 2016 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 


----------
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ISIS 396443-CS4 
 
Statistical Analysis Plan Version 1.0 
 
4 
TABLE OF CONTENTS 
 
ABBREVIATIONS 
7 
1 
DESCRIPTION OF OBJECTIVES AND ENDPOINTS 
9 
1.1 
Primary objective, primary endpoint, secondary and tertiary efficacy endpoints 
9 
1.2 
Secondary objective and endpoints 
9 
1.3 
Tertiary objective 
9 
1.4 
Immunogenicity endpoint 
10 
2 
STUDY DESIGN 
10 
2.1 
Screening 
11 
2.2 
Treatment 
11 
2.3 
Post-treatment follow-up 
12 
2.4 
Schedule of procedures 
12 
3 
GENERAL CONSIDERATIONS 
16 
4 
STUDY SUBJECTS 
17 
4.1 
Subject accountability 
17 
4.2 
Demographic and baseline disease characteristics 
17 
4.3 
Extent of exposure 
18 
4.4 
Concomitant therapy 
19 
4.5 
Protocol deviations 
20 
5 
EFFICACY DATA 
21 
5.1 
Interim and final efficacy analyses 
21 
5.2 
Statistical testing procedures 
22 
5.3 
Multiple Imputation of missing data 
25 
Multiple imputation for HFMSE , upper limb module test endpoint, PedsQL and ACEND 
25 
Multiple imputation analysis methods 
26 


ISIS 396443-CS4 
 
Statistical Analysis Plan Version 1.0 
 
5 
5.4 
Baseline 
27 
5.5 
Analysis methods for the primary endpoint 
27 
5.5.1 
Final analysis of primary endpoint 
28 
5.5.2 
Interim analysis of primary endpoint 
29 
5.5.3 
Summary of analyses of the primary endpoint 
30 
5.6 
Analysis methods for the secondary endpoints 
31 
5.6.1 
Proportion of subjects who achieve a 3-point or greater increase from baseline in HFSME at 15 
months 31 
5.6.2 
Proportion of subjects who achieve any new motor milestones at 15 months 
32 
Imputation for motor milestones 
33 
5.6.3 
Number of new motor milestones achieved per subject at 15 months 
36 
5.6.4 
Change from baseline in Upper Limb Module Test at 15 months 
37 
5.6.5 
Proportion of subjects who achieve standing alone at 15 months 
39 
5.6.6 
Proportion of subjects who achieve walking with assistance at 15 months 
40 
5.6.7 
Interim Analysis 
41 
5.6.8 
Exploratory analysis 
41 
5.7 
Tertiary endpoints 
42 
5.7.1 
Change from baseline in CSF SMN protein concentration 
42 
5.7.2 
Clinical Global Impression of Change (Investigator and Caregiver assessments) 
42 
5.7.3 
Change from baseline in Pediatric Quality of Life Inventory 
43 
5.7.4 
Change from baseline in Assessment of Caregiver Experience with Neuromuscular Disease 
44 
5.7.5 
Disease-related hospitalizations and adverse events 
45 
5.8 
Subgroup analyses 
45 
5.9 
Unblinding Plan for the Interim Analysis 
46 
6 
SAFETY DATA 
47 
6.1 
Clinical adverse events 
47 
6.1.1 
Adverse events over time 
49 
6.1.2 
Adverse events by severity 
49 
6.1.3 
Adverse events by relationship to study treatment 
49 
6.1.4 
Serious adverse events 
49 
6.1.5 
Deaths 
49 
6.1.6 
Adverse events following dosing/sham procedure 
49 
6.1.7 
Adverse events by anti-ISIS 396443 antibody status 
50 
6.1.8 
Adverse Events Related to SMA 
50 
6.1.9 
Presentations 
50 
6.2 
Clinical laboratory data 
51 
6.3 
ECGs 
53 
6.3.1 
Qualitative analysis 
53 
6.3.2 
ECG outliers 
54 
6.4 
Vital signs 
54 
6.4.1 
Acute effects after dosing 
54 
6.4.2 
Chronic effects 
54 


ISIS 396443-CS4 
 
Statistical Analysis Plan Version 1.0 
 
6 
6.5 
Neurological examinations 
54 
6.5.1 
Acute effects after dosing 
55 
6.5.2 
Chronic effects 
55 
6.6 
Interim safety analyses 
55 
7 
PHARMACOKINETIC DATA 
55 
7.1 
CSF Concentration Data 
55 
7.2 
Plasma Pharmacokinetics 
56 
7.2.1 
Plasma Concentration Data 
56 
7.2.2 
Plasma Pharmacokinetic Parameters 
56 
8 
IMMUNOGENICITY DATA 
57 
9 
SAMPLE SIZE JUSTIFICATION 
58 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 


ISIS 396443-CS4 
 
Statistical Analysis Plan Version 1.0 
 
7 
 
Abbreviations 
AESTDT                     Start date of an adverse event 
ACEND 
 
Assessment of Caregiver Experience with Neuromuscular Disease 
ALT/SGPT 
 
alanine aminotransferase/serum glutamic pyruvic transaminase 
ANCOVA 
 
Analysis of Covariance 
AST/SGOT 
 
aspartate aminotransferase/serum glutamic-oxaloacetic transaminase 
ATC  
 
Anatomical Therapeutic Class  
AUC  
 
Are under the curve 
BLQ  
 
below the lower limit of quantification 
BUN  
 
blood urea nitrogen 
Cmax 
 
 
maximum observed drug concentration 
CGI 
 
 
Clinical Global Impression of Change Rating Scale 
CPK  
 
creatine phosphokinase 
CRF 
 
 
case report form 
CSF 
 
 
cerebrospinal fluid 
CV 
 
 
coefficient of variation 
DSMB  
 
Data Safety Monitoring Board 
EODBP 
 
End of Double Blind Period 
HFMSE 
 
Hammersmith Functional Motor Scale - Expanded 
IM 
 
 
immunogenicity 
IT 
 
 
intrathecal 
ITT 
 
 
intent-to-treat 
LLN 
 
 
lower limit of normal 
LLOQ  
 
lower limit of quantification 
LOCF  
 
Last observation carried forward 
LP 
 
 
lumbar-puncture 
MCMC 
 
Markov Chain Monte Carlo 
MedDRA 
 
Medical Dictionary for Regulatory Activities 
MI 
 
 
Multiple imputation 
MMRM 
 
Mixed effects Model for Repeated Measures 
OLE 
 
 
Open Label Extension 
PedsQL 
 
Pediatric Quality of Life Inventory 
PK 
 
 
pharmacokinetics 
PPS 
 
 
Per-protocol set 
PT 
 
 
Preferred term 
RBC  
 
red blood cell 
RE 
 
 
Relative Efficiency 
SD 
 
 
standard deviation 
SE 
 
 
standard error 
SMA  
 
Spinal Muscular Atrophy 
 
SMN  
 
Survival motor neuron 
SMQ  
 
Standardized MedDRA query 
SOC  
 
System Organ Class 
TRTSTDT  
 
Start date of study treatment/sham procedure 
Tmax 
 
 
time at which Cmax occurs 


ISIS 396443-CS4 
 
Statistical Analysis Plan Version 1.0 
 
8 
ULN  
 
upper limit of normal 
WBC  
 
white blood cell 
WHODrug 
 
World Health Organization drug dictionary 


ISIS 396443-CS4 
 
Statistical Analysis Plan Version 1.0 
 
9 
 
1 
Description of objectives and endpoints 
 
The objectives of this study are to evaulate the clinical efficacy, safety, tolerability, and 
pharmacokinetics (PK) of ISIS 396443 administered intrathecally to patients with later-onset 
Spinal Muscular Atrophy (SMA).  
 
1.1 
Primary objective, primary endpoint, secondary and tertiary efficacy endpoints 
The primary objective of the study is to examine the clinical efficacy of ISIS 396443 
administered intrathecally to patients with later-onset SMA.  
The primary endpoint is the change from baseline Hammersmith Functional Motor Scale – 
Expanded (HFMSE) score at 15 months. 
The secondary efficacy endpoints are 
• the proportion of subjects who achieve a 3-point or greater increase from baseline 
HFMSE score at 15 months 
• the proportion of subjects who achieve any new motor milestone at 15 months 
• the number of motor milestones achieved per subject at 15 months 
• the change from baseline in Upper Limb Module Test at 15 months 
• the proportion of subjects who achieve standing alone at 15 months 
• the proportion of subjects who achieve walking with assistance at 15 months. 
 
The tertiary efficacy endpoints are  
• the change from baseline in CSF SMN protein concentration 
• Clinical Global Impression of Change (investigator and caregiver assessments) 
• the change from baseline in Pediatric Quality of Life Inventory (PedsQL) 
• the change from baseline in Assessment of Caregiver Experience with Neuromuscular 
Disease (ACEND) 
• disease-related hospitalizations and adverse events. 
 
1.2 
Secondary objective and endpoints 
The secondary objective is to examine the safety and tolerability of ISIS 396443 administered 
intrathecally to patients with later-onset SMA.  
Safety/tolerability endpoints are adverse events, clinical laboratory tests (serum chemistry, 
hematology, urinalysis), ECGs, vital signs, weight, neurological examinations, use of 
concomitant medications and physical examinations.  
 
1.3 
Tertiary objective 
The tertiary objective is to examine the cerebral spinal fluid and plasma PK of ISIS 396443 
administered intrathecally to patients with later-onset SMA.  
The pharmacokinetic endpoints are 


ISIS 396443-CS4 
 
Statistical Analysis Plan Version 1.0 
 
10 
 
• CSF levels of ISIS 396443 
• plasma levels of ISIS 396443. 
 
1.4 
Immunogenicity endpoint 
The incidence and titer of plasma antibodies to ISIS 396443.  
 
 
2 
Study design 
 
This is a Phase 3, multicenter, double-blind, randomized, sham-procedure-controlled study of 
ISIS 396443 administered intrathecally over 15 months to patients with later-onset SMA.  
Approximately 117 subjects will be randomized 2:1 to receive a 12 mg dose of ISIS 396443 
or undergo a sham procedure as control, respectively.  Randomization will be stratified based 
on the subject’s age at screening: <6 years versus >6 years.  A separate randomization list will 
be used for Japan.  If a subject does not successfully receive the first dose of ISIS 396443 or 
undergo the first sham procedure, they will be replaced.  
ISIS 396443 will be administered using a loading regimen (dosing on Study Days 1, 29, and 
85) followed by a maintenance dosing 6 months thereafter (Day 274).  Subjects randomized to 
the sham-procedure control group will undergo a sham-procedure on Study Days 1, 29, 85, 
and 274.  
No adjustment of dose is permitted.  However, should a concurrent illness prevent the dosing 
procedure from being performed safely, each scheduled dose may be delayed by up to 4 
weeks.  
The study will consist of screening, treatment, and post-treatment follow-up-periods.  The 
total duration of participation in the study is approximately 16 months.  
Blinded safety data will be reviewed on an ongoing basis by the Sponsor and the Medical 
Monitor. Unblinded safety data will also be reviewed on an ongoing basis by an independent 
Data Safety Monitoring Board (DSMB) (Section 6.6). In the protocol it was planned that an 
interim analysis may be conducted when all subjects will have completed the month 6 
assessment and at least 39 will have completed the month 15 assessment. An interim efficacy 
analysis will be conducted using a targeted cut-off date of 31 August 2016 for the clinical 
data. At the time of the interim analysis, it is expected that approximately 52 subjects will 
have attended the Month 15 assessment and all 126 subjects will have had the opportunity to 
attend the assessment at Month 6 (Section 5.1).  
 
In the event of a decision by the study Sponsor to terminate the study earlier on the grounds 
that conducting a sham-controlled study is no longer deemed ethical based on an updated risk 
benefit assessment of ISIS 396443 from the planned interim analysis, all subjects will be 
invited for the end-of-double-blind-period (EODBP) study visit, during which all Day 456 
assessments will be conducted. After completing the EODBP visit, subjects will be 
considered study completers and will be allowed to enroll into the open-label extension study. 
 


ISIS 396443-CS4 
 
Statistical Analysis Plan Version 1.0 
 
11 
2.1 
Screening 
 
After informed consent is obtained, subjects will undergo a screening evaluation no greater 
than 28 days prior to administration of the first dose or first sham procedure at which their 
eligibility for the study will be examined.  
 
2.2 
Treatment 
Subjects who meet the eligibility criteria will be admitted to the study center on Day 1, 
undergo pre-dose evaluations, and then receive either an LP injection of ISIS 396443 or 
undergo a sham procedure.   
Both the sham procedure and ISIS 396443 will be administered by dedicated study personnel 
who are unblinded to treatment assignment (this will not be any of the key study site 
personnel such as the Principal Investigator, study coordinator, or outcomes assessors) in a 
dedicated room and the key study personnel and the parents will not be present during the 
procedure to ensure blinding of treatment assignment.   
ISIS 396443 will be administered as an intrathecal slow bolus (1-3 minute) LP injection.  ISIS 
396443 will be administered using a ‘spinal anesthesia’ needle and 5 mL syringe.  A 22G to 
25G spinal anesthesia needle is recommended.  The target site for needle insertion is the 
L3/L4 space, but may be 1 segment above or 1-2 segments below this level, if needed.  
General anesthesia or sedation may be used for the LP injection procedure depending on 
institutional guidelines.  
Subjects randomized to undergo a sham procedure will have a small needle prick on the lower 
back at the location where the LP injection would otherwise normally be made in subjects 
assigned to active treatment. The needle will break the skin but no LP injection or needle 
insertion into the deeper structures will occur. The needle puncture site will be covered with 
the same bandage that is used to cover the LP injection normally, thus simulating the 
appearance of an LP injection. If anesthesia or sedation is used for the LP procedure in ISIS 
396443-treated subjects, then in order to maintain the blind, minimal sedation should be used 
for the sham procedure, following institutional procedures. The study subject will be kept in 
the procedure room for the same amount of time that subjects administered study drug are 
kept, thus simulating the time period of a study drug administration procedure.  
Study drug and sham kits will be packaged in a blinded fashion.  Blinded kits for sham 
procedure contain artificial CSF (5.0 mL solution per 6 mL vial) that will not be injected but 
will be used to simulate CSF samples for that subject.  
Subjects will return to the study center on Days 29, 85, and 274 for follow-up evaluations and 
subsequent injections/sham procedures. Following the injection/sham procedure on Day 1, 
subjects will remain at the study center for at least 24 hours post-procedure for safety 
monitoring. Following the injection/sham procedure on Days 29, 85, and 274, subjects will 
remain at the study center for at least 6 hours post-procedure for safety monitoring. Safety 
monitoring visits will occur Study Days 30, 86, 92, 169, and 275 (through the last 
injection/sham procedure).  In addition, the study center will monitor the subject’s condition 
through telephone contact on a monthly basis. 


ISIS 396443-CS4 
 
Statistical Analysis Plan Version 1.0 
 
12 
For subjects receiving ISIS 396443, a CSF sample for PK analysis will be taken pre-dose on 
each injection day in a manner that protects the blind.  
Subjects who terminate early from the study will be encouraged to complete assessments per 
the Day 456 visit. Subjects who are randomized but do not successfully receive the first dose 
of ISIS 396443/undergo the first sham procedure will be replaced. Results from these subjects 
will be reported in the CSR as occurring before the start of treatment and will not be included 
in the formal analyses.  
 
2.3 
Post-treatment follow-up 
After completion of the Day 275 visit, subjects will enter the 6-month post-treatment 
evaluation period.  This period consists of two visits on Day 365 and 456 and follow-up 
phone assessments on a monthly basis. After completion of the Day 456 visit, subjects may be 
eligible to participate in an OLE study, pending study approval by the IRB or IEC and the 
appropriate regulatory authority. 
The end of study is last subject, last visit (either in-person visit or telephone contact).    
2.4 
Schedule of procedures 
Day 1 is considered to be the day when the first dose of ISIS 396443 is administered or when 
the first sham procedure is performed. Subjects are to return to the clinic 4 weeks later on Day 
29 (±1 day), 12 weeks later on Day 85 (±2 days), 13 weeks later on Day 92 (±1 day), 24 
weeks later on Day 169 (±2 days), 39 weeks later on Day 274 (±7 days), 12 months later on 
Day 365 (±7 days), and 15 months later on Day 456 (±7 days) for final follow-up.  
The schedule of events follows. 
 
 


ISIS 396443-CS4 
 
Statistical Analysis Plan Version 1.0 
 
 
 
 
13 
 
Subjects will also be monitored through phone contact on Study Days 8, 56, 113, 141, 204, 239, 302, 330, 393, 421 (all ± 2 days)9 
Study Period 
Screen 
Treatment/Follow-up 
Study Day 
D -28 
to 
D -1 
D1 
D2 
D29 ( ± 1D) 
D30 
D85 ( ± 2D) 
D86 
D92 
( ± 1D) 
D169 
( ± 2D)  
D274 ( ± 7D) 
D275 
D365 
( ± 7D) 
and 
D456 
(± 7D) 
and 
Early 
Term/ 
EODBP 
Pre- 
dose 
LP/ 
SP 
Post- 
dose 
Pre- 
dose 
LP/ 
SP 
Post- 
dose 
Pre- 
dose 
LP/ 
SP 
Post- 
dose 
Pre- 
dose 
LP/ 
SP 
Post- 
dose 
Informed Consent 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Inclusion/Exclusion 
Criteria 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Medical History 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Screening X-ray 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Urine Pregnancy 
Test11 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
X14 
SMN2 copy Number12 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Study Drug 
Injection/Sham 
Procedure 
 
 
X 
 
 
 
X7 
 
 
 
X7 
 
 
 
 
 
X7 
 
 
 
In-Patient Stay 
(24 hours) 
 
 
 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Vital Signs1 
X 
X 
 
4X2 
X3 
X 
 
4X2 
X 
X 
 
4X2 
X 
X 
X 
X 
 
4X2 
X 
X 
Weight 
X 
X 
 
 
 
X 
 
 
 
X 
 
 
 
X 
X 
X 
 
 
 
X 
Height/ulnar length 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
X14 
Physical Examination 
X 
X 
 
 
 
X 
 
 
 
X 
 
 
 
X 
X 
X 
 
 
 
X 
Neurological 
Examination 
X 
X 
 
X4 
X3 
X 
 
X4 
X 
X 
 
X4 
X 
X 
X 
X 
 
X4 
X 
X 
ECG 
X 
 
 
 
X 
 
 
X 
 
 
 
 
 
X 
 
 
 
 
 
X14 
Safety Labs5 
X 
X 
 
 
X 
X 
 
 
 
X 
 
 
 
 
X 
X 
 
 
 
X14 
Coagulation Labs 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Immunogenicity  
 
X 
 
 
 
X 
 
 
 
X 
 
 
 
 
X 
X 
 
 
 
X14 


ISIS 396443-CS4 
 
Statistical Analysis Plan Version 1.0 
 
 
14 
Appendix A Schedule of Procedures Continued 
Study Period 
Screen 
Treatment/Follow-up 
Study Day 
D -28 
to 
D -1 
D1 
D2 
D29 ( ± 1D) 
D30 
D85 ( ± 2D) 
D86 D92 
( ± 1D) 
D169 
( ± 2D) 
D274 ( ± 7D) 
D275 
D365 
( ± 7D) 
and 
D456 
(± 7D) 
and 
Early 
Term/ 
EODBP 
Pre- 
dose 
LP/ 
SP 
Post- 
dosD
ay 
456e 
Pre- 
dose 
LP/ 
SP 
Post- 
dose 
Pre- 
dose 
LP/ 
SP 
Post- 
dose 
Pre- 
dose 
LP/ 
SP 
Post- 
dose 
CSF PK8 
 
X 
 
 
 
X 
 
 
 
X 
 
 
 
 
 
X 
 
 
 
 
CSF SMN Protein 
 
X 
 
 
 
X 
 
 
 
X 
 
 
 
 
 
X 
 
 
 
 
Plasma PK8 
 
X 
 
3X 
X 
X 
 
 
 
X 
 
X 
 
 
X 
X 
 
 
 
X14 
HFMSE 
X10 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
WHO Motor Milestones 
X6, 10 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
Upper Limb 
X6, 10 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
PedsQL 
X6 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
ACEND 
X6 
 
 
 
 
 
 
 
 
 
 
 
 
 
X 
 
 
 
 
X14 
CGI 
 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 
X13 
 
 
 
X 
Con Med Recording9 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Adverse Event 
Collection9 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
1 
Resting blood pressure, pulse, respiratory rate, and temperature 
2 
Vital signs performed 1, 2, 4, 6 hours after dosing 
3 
Conducted within 20-24 hours after dosing 
4 
Neurological exams at 5 hours after dosing 
5 
Serum chemistry, hematology, urinalysis panels (Appendix B for analytes) 
6 
Efficacy assessments (with the exception of HFMSE) do not form part of the screening assessment or inclusion/exclusion criteria but are baseline 
measurements taken during the screening phase of the study 
7 
Overnight stay is optional on Day 29, Day 85, and Day 274  
8 
Refer to Appendix C for PK sampling schedule 
9 
At telephone contact, changes in concomitant medications and adverse events will be recorded  
10 To be performed 2 times during the screening period  
11 Urine pregnancy test performed for females of child-bearing potential, if positive to be confirmed by local serum test 
12 Only for those subjects who do not have documented evidence of SMN copy number from Athena Diagnostics 
13 These assessments may be performed up to 7 days prior to dosing, if necessary 


ISIS 396443-CS4 
 
Statistical Analysis Plan Version 1.0 
 
 
15 
14 Assessed on Day 456 only 


ISIS 396443-CS4 
 
Statistical Analysis Plan Version 1.0 
 
 
16 
3 
General considerations 
 
In this Statistical Analysis Plan, the terms “control” and “control group” refer to the set of 
subjects who were randomized to undergo the sham procedure, and the terms “treatment” and 
“dosed” are used interchangeably to describe those subjects in the ISIS 396443 group who 
received at least one intrathecal injection of ISIS 396443.  
In order to distinguish nominal visit names from duration defined in terms of days, visit 
names will be referred as “Day 29”, “Day 85,” etc., and “29 days” or “85 days,” etc. will be 
used to define time intervals. In the protocol definitions of the efficacy endpoints, and 
description of the interim analysis, “Month  6” is used to refer to “Day 169” and “Month 15” 
is used to refer to “Day 456” and this convention will be followed in this SAP. 
The Intent-to-treat (ITT) Set and the Per-protocol Set (PPS) will be used for the efficacy 
analyses.  The ITT Set is defined as all subjects who are randomized and received at least one 
dose of study drug/sham procedure.  Subjects will be analyzed in the treatment group to 
which they were randomized.  This will be the primary population for the analysis of efficacy 
endpoints.   
An Interim Efficacy Set will be defined for presentation of the WHO motor milestone 
endpoints in the event an interim analysis is performed.   The Interim Efficacy Set will be 
defined as the subset of subjects in the ITT Set who have the opportunity to be assessed at the 
Month 15 visit. Specifically, the Interim Efficacy Set will include all subjects with a Month 
15 visit and all subjects with time difference of at least 463 days (456 plus 7 day window) 
between date of first dose and the targeted clinical cut-off date for the interim analysis (i.e., 
dosed on or before May 27, 2015). However, a subject who has died or withdrawn will be 
included provided that there is a time difference of at least 449 days (456 minus 7 day 
window) between the date of first dose and the targeted clinical cut-off date of Aug 31, 2016 
for the interim analysis (i.e., dosed on or before June 10, 2015). 
In the event of the study being stopped early, an Efficacy Set will be similarly defined for the 
analysis of motor milestones.   If, however, the study continues to completion as planned, the 
ITT Set will be used for the final analysis of motor milestones. 
The PPS will include the subset of the ITT who complete at least the initial 3 doses of study 
drug/sham procedures, have baseline and Day 169 efficacy assessments and who have no 
significant protocol deviations that would be expected to affect efficacy assessments. 
Significant protocol deviations will be determined prior to database lock but will include 
subjects who had onset of signs and symptoms consistent with SMA at less than or equal to 6 
months of age, who cannot sit independently, whose HFMSE is <10 or >54 at screening, who 
had respiratory insufficiency at Screening (defined as medical necessity for invasive or non-
invasive ventilation for >6 hours during a 24-hour period), and subjects who took any 
medicines (such as valproate, riluzole, creatine, sodium phenylbutyrate, hydroxyurea, 
salbutamol, olesoxime) during the study for the treatment of SMA, shown to modulate SMN 
gene expression or SMA disease progression in humans or preclinical models. The Safety Set, 
comprised of all subjects who were randomized and received at least one dose of study drug 
or underwent one sham procedure, will be used for the analysis of safety data. Subjects 


ISIS 396443-CS4 
 
Statistical Analysis Plan Version 1.0 
 
 
17 
randomized to receive sham procedure, incorrectly treated with ISIS 396443 will be counted 
in the ISIS 396443 group from the first dose of ISIS 396443 received. 
The Pharmacokinetic Population is comprised of all subjects who were randomized and for 
which there is at least one evaluable post-dose/post-sham procedure pharmacokinetic sample.  
Analysis of immunogenicity data will also be based upon this population. 
A listing denoting inclusion/exclusion of patients in all the analysis populations will be 
provided.  
The individual sites in this multicenter study will be pooled for the purpose of statistical 
analysis.   
Summary statistics will be presented throughout.  For continuous endpoints, the summary 
statistics will generally include number of subjects with data, mean, standard deviation, 
median, minimum and maximum. For categorical endpoints, the summary statistics will 
generally include:  number of subjects randomized and/or dosed, number of subjects with 
data, and the percentage of those with data in each category.  Frequency distributions will be 
presented as appropriate.  
The statistical software, SAS® version 9.3 or above, will be used for all summaries and 
statistical analyses.  
4 
Study subjects 
 
4.1 
Subject accountability 
The number of subjects who were screened, who were randomized, who were dosed, and who 
completed treatment, along with reasons for discontinuing treatment and withdrawing from 
the study, will be presented by treatment group and overall.  In certain cases, CRF text 
detailing the reasons for discontinuation and/or withdrawal may suggest additional 
clarification of the reason provided on the CRF.  Therefore, additional information for subject 
accounting may be presented, utilizing reasons for discontinuing treatment and/or 
withdrawing from the study reclassified based on the detailed CRF text, prior to database 
lock.  Listings of those subjects who discontinued treatment and/or withdrew from the study 
and the reasons for discontinuation/withdrawal will be presented.  
4.2 
Demographic and baseline disease characteristics 
Baseline data (demography, medical history, SMA history, baseline disease characteristics, 
baseline quality of life) will be summarized.  
Demography includes age, sex, ethnicity and race.  Medical history will be coded in MedDRA 
and the number and percentage of subjects with each history by preferred term presented, 
including the presence of scoliosis and presence of contractures.  SMA history includes age of 
symptom onset, time from disease onset to enrollment, age at SMA diagnosis, time from 
diagnosis to enrollment, number of copies of the SMN2 gene, highest motor function 
achieved, current motor function, wheelchair use, and amount of physical therapy.   


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Baseline disease characteristics will be assessed by weight, height, ulnar length, weight for 
age, height for age, HFMSE, motor milestones, Upper Limb Module Test.  These assessments 
are further described in the next paragraph and Section 5. 
Weight for age and height for age will be summarized using the WHO child growth standards 
(WHO Child Growth Standards, 2006) for subjects aged up to 5 years and similarly the WHO 
growth reference data (WHO, 2007) for older subjects.  These standards comprise percentiles 
for weight and height for age by sex and are available on a website (www.who.int) in txt files. 
Subjects will be cross referenced with these files, given the age and sex of the subject to 
determine below which percentile they lie for each parameter.  The frequency and percentage 
will then be summarized for each of weight for age and height for age in the following 
categories:  ≤ 1st, ≤ 3rd, ≤5th, ≤15th, ≤25th, ≤50th and > 50th percentile.  The standards do not 
provide weight for age percentiles for subjects aged > 10 years since this is not an appropriate 
measure due to the confounding effect of the pubertal growth spurt. Therefore, subjects aged 
> 10 years at baseline will not be included in the summary for this parameter.     
Baseline quality of life and caregiver burden of SMA will be assessed by PedsQL and 
ACEND, respectively. 
Demographic, baseline disease characteristics, and baseline quality of life will be presented 
for the ITT Set, PPS and the Safety Set as appropriate.   
Formal statistical analyses will not be done to test for homogeneity between treatment groups.  
If there are apparent heterogeneities between the groups in any of the subject characteristics 
that are of clinical importance or could affect the treatment outcome, the impact of the 
imbalances will be investigated and, if appropriate, adjustments made in the efficacy and 
safety analyses.  
4.3 
Extent of exposure 
The number of doses received and the number of sham procedures performed will be 
displayed using frequency distributions. The amount of ISIS 396443 administered will be 
presented using summary statistics.  
Overall time on study will be defined as the total number of days a subject is known to be 
followed on study calculated as follows:  
 
Overall time on study =  
                     (Last date on study) – (Date of first dose or first sham procedure) + 1.  
The last date on study is defined as the latest visit or telephone contact or evaluation date or 
time of death from all available data for a given subject. 
Time on study will be categorized into the following intervals: 0 to <=90, 91 to <= 180, 181 
to <=270, 271 to <=360, 361 to <= 450, >450 days and summarized by treatment group and 
overall.  
Given the long half-life of ISIS 396443, subjects are considered to be exposed to study drug 
from the time the first dose was administered to the last day of follow-up.  Essentially, 
exposure is equivalent to time on study.   


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4.4 
Concomitant therapy 
Throughout the study concomitant medications or treatments deemed necessary for treatment 
of adverse events or to provide adequate supportive care may be prescribed.  A concomitant 
medication is any non-protocol specified drug or substance including over-the-counter 
medications, herbal medications and vitamin supplements.  Subjects are prohibited from 
receiving other experimental agents during the study including marketed agents at 
experimental doses that are being used for the treatment of SMA (e.g., oral 
albuterol/salbutamol, riluzole, carnitine, creatine, sodium phenylbutyrate, valproate, 
hydroxyurea).  All concomitant medications will be coded using the World Health 
Organization drug dictionary (WHODrug).   
A concomitant procedure is any therapeutic intervention (e.g., surgery/biopsy) or diagnostic 
assessment (e.g., X-ray) performed between screening and last visit.  All ancillary procedures 
will be coded using MedDRA.   
For the purposes of analysis, a concomitant therapy (including medication or ancillary 
procedure) is defined as any therapy that was taken on or after the first injection of ISIS 
396443 or first sham procedure.  This includes therapies that were started prior to the 
initiation of dosing/sham procedure if their use continued on or after the date of the first 
injection/first sham procedure.  In order to define concomitant therapies with missing start or 
stop dates, the following additional criteria will be used:  
• if both the start and stop dates of a particular therapy were missing, that therapy is 
considered concomitant; 
• if the start date of a therapy was missing and the stop date of that therapy fell on or 
after the date of dosing, that therapy is considered concomitant; 
• if the start date of a therapy was prior to the date of dosing and the stop date of that 
therapy was missing and the therapy was listed as continuing, that therapy is 
considered concomitant;  
• if the start date of a therapy was prior to the date of dosing and the stop date of that 
therapy was missing and the therapy was listed as not continuing, that therapy is 
considered concomitant; or 
• if the start/stop date of a therapy is partial then where it is not possible to rule out that 
it was not taken concomitantly it will be considered concomitant. 
 
Denote the end date of medication as CMENDT and the study treatment/sham procedure start 
date as TRTSTDT. The medication is classified concomitant provided any of the following is 
NOT true: 
• CMENDT is complete and CMENDT is less than TRTSTDT. 
• Day of CMENDT missing and year/month of CMENDT is strictly before year-month of 
TRTSTDT.  
• Month of CMENDT is missing and year of CMENDT is strictly before year of 
TRTSTDT. 


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The number and percentage of subjects taking each type of concomitant medication at 
baseline and during the study will be presented by preferred name for Safety Set.  The number 
and percentage of subjects who underwent each type of ancillary procedure during the study 
will be presented.   
Medications taken as part of the sham or lumbar puncture procedure are collected in the 
unblinded CRF and these will be presented separately.   
 
4.5 
Protocol deviations 
Protocol deviations identified during site monitoring will be captured in a protocol deviation 
log and categorized as major or minor deviations.  These deviations will be listed.  Major 
protocol deviations will be summarized including those that lead to exclusion from the Per-
protocol Set.  
 


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5 
Efficacy data 
 
The primary, secondary, and tertiary efficacy endpoints are listed in Section 1.1. 
 
5.1 
Interim and final efficacy analyses 
 
An interim analysis may take place when all subjects have completed the 6-month assessment 
and at least 39 subjects have completed the 15-month assessment with a targeted clinical cut-
off date of 31 August 2016. At the interim analysis, only the primary endpoint will be tested. 
The final efficacy analysis will take place when the last subject completes the 15-month 
assessment or earlier if the study is terminated on the grounds that conducting a sham-
controlled study is no longer deemed ethical based on the assessment of risk-benefit of ISIS 
396443. 
   
At the interim analysis and final analysis, the same analysis of covariance (ANCOVA) model 
will be used in analyzing the change from baseline in HFMSE score to month 15. At the 
interim analysis, the month 15 endpoint values will not be available for some patients, so a 
multiple imputation method will be used to estimate them (Section 5.3).  This method will 
also be used in the final analysis for the primary endpoint  
   
The interim analysis results will be reviewed by an independent Data Safety Monitoring 
Board (DSMB) and an Unblinded Senior Management Team from the Sponsor. 
Recommendation will be made on whether it is appropriate for the trial to continue according 
to the current protocol or whether the protocol needs to be modified. During the interim 
analysis, subjects will continue in the study. 
 
In the protocol it had been planned to conduct the interim efficacy analysis with an alpha of 
0.02, however in finalizing this statistical analysis plan it was decided to conduct the interim 
analysis at a significance level of 0.025.  If the study is not stopped at the interim analysis, the 
final analysis (test and confidence interval estimate procedures) will be conducted at a 
significance level determined by the resampling procedure as follows.   
 
Let T1 and T2 be the standardized test statistics at the interim and final analyses, respectively. 
In order to determine the alpha level for the final analysis, the correlation between T1 and T2 
is first estimated based on the resampling approach (Westfall and Young 1993): 
• Among the 126 subjects enrolled in the study, randomly assign 84 subjects to the ISIS 
396443 group and 42 subjects to the sham control group. 
•  Apply the re-randomized treatment assignment to the interim data and obtain the 
standardized test statistics T1.  
• Apply the re-randomized treatment assignment to the final data and obtain the 
standardized test statistics T2. 
Repeat the above procedure N times (N=10000) and obtain N pairs of test statistics T1 and T2. 
The correlation between T1 and T2 will then be estimated as the sample correlation of the N 
pairs.  
 


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Let c1  be the cut-off point for the interim two-sided test corresponding to an alpha of 0.025. 
Once the estimated correlation ρ is available, the cut-off point c2 for the final analysis is 
obtained by solving the nonlinear equation Pr(|T1| ≥ c1 or |T2| ≥ c2) =0.05, where  (T1, T2) 
follow a bivariate normal distribution with mean vector (0, 0), standard deviations of 1 and 
correlation ρ.  
 
5.2 
Statistical testing procedures 
 
Secondary efficacy endpoints have been rank prioritized: 
 
• the proportion of subjects who achieve a 3-point or greater increase from baseline 
HFMSE score at 15 months 
• the proportion of subjects who achieve any new motor milestone at 15 months 
• the number of motor milestones achieved per subject at 15 months 
• the change from baseline in Upper Limb Module Test at 15 months 
• the proportion of subjects who achieve standing alone at 15 months 
• the proportion of subjects who achieve walking with assistance at 15 months. 
 
In order to control the Type I error rate at 0.05 across interim and final analyses for the testing 
of primary and secondary efficacy endpoints, a stage wise hierarchical strategy utilizing 
independent alpha spending functions for primary and secondary endpoints (Glimm et al. 
2010) will be applied. In the framework of the stage wise hierarchical testing, since the 
secondary endpoints will not be tested at the interim (i.e., no alpha spending), at the final 
analysis alpha = 0.05 will be used in the sequential testing. The entire procedure is described 
below.    
 
At the interim analysis, the primary efficacy endpoint will be tested at an alpha of 0.025. If 
the primary efficacy endpoint is statistically significant at the interim analysis, then the 
secondary endpoints may be descriptively reported. No formal statistical comparison will be 
performed and no p-values will be calculated for statistical inference for these endpoints.  The 
only alpha spending proposed at the interim analysis is based on analysis of the primary 
efficacy endpoint, the only endpoint at the interim for which formal statistical testing will be 
conducted. 
 
In the event of a decision by the study Sponsor to terminate the study earlier on the grounds 
that conducting a sham-controlled study is no longer deemed ethical based on an updated 
risk-benefit assessment of ISIS 396443 from the planned interim analysis, all subjects will be 
invited for the EODBP study visit, during which all Day 456 assessments will be conducted.  
The EODBP visit should occur no less than 2 weeks from the most recent dosing/sham 
procedure administered. After completing the EODBP visit, subjects will be considered study 
completers and will be allowed to enroll into the OLE study.  Under this scenario, since 
patient participation and monitoring continue until the study is stopped, the final analysis that 
incorporates the accrued data will be conducted. At the final analysis, the primary efficacy 
endpoint will not be tested again since significance has already been achieved at the interim.  
The secondary endpoints will be tested at an alpha of 0.05 as shown in the diagram below.  
  


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In a scenario where the primary efficacy endpoint is not significant at the interim analysis, no 
additional data will be evaluated. In this case, at the final analysis, the primary endpoint will 
be tested at an alpha level determined based upon the resampling approach method. If the 
primary endpoint is not significant at the final analysis, then the testing of the secondary 
endpoints will be considered exploratory. If the primary endpoint is significant at the final 
analysis, then the secondary endpoints will be tested at an alpha of 0.05 as shown in the 
diagram below. 


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In the event that a secondary endpoint is not significant and formal testing is ended, the 
remaining endpoints will be tested but the results will be considered exploratory. 
 
Proportion of subjects 
achieving a 3-point or 
greater increase in HFMSE 
at 15 months 
Proportion of subjects 
achieving any new motor 
milestone at 15 months 
Sig. 
Not sig. 
Number of motor 
milestones achieved at 15 
months 
Change from baseline in 
Upper Limb Module Test at 
15 months 
End formal testing 
End formal testing 
End formal testing 
Not sig. 
Not sig. 
Sig. 
Sig. 
Proportion of subjects achieving 
standing alone at 15 months 
Proportion of subjects achieving 
walking with assistance at 15 
months 
Sig. 
End formal testing 
End formal testing 
Not sig. 
Not sig. 
Sig. 


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Analyses of tertiary efficacy endpoints will not include adjustments for multiplicity.  
 
The analysis of safety data for the interim analysis will include all subjects who have received 
at least one dose of study treatment as of the targeted clinical cut-off date. 
 
Although statistical stopping guidelines have been pre-specified for the interim analysis, a 
number of factors must be considered thoroughly as part of the decision to modify or stop the 
study. A recommendation to modify or stop the study will, therefore, not be based solely on 
statistical grounds. 
 
5.3 
Multiple Imputation of missing data 
 
In the protocol it was stated that the multiple imputation procedure would be used to impute 
missing values for all primary and secondary efficacy endpoints.  However in finalizing this 
statistical analysis plan it was decided that to handle the missing data in the WHO motor 
milestones, the multiple imputation procedure won’t be used because historical data showed 
that it’s very rare for non-ambulatory SMA patients to achieve certain milestones (such as 
walking alone).  Therefore, an imputation approach based upon multiple imputation would 
face challenges due to low or zero numbers of subjects in the sham arm achieving a response.  
The imputation rules and analyses for motor milestones are detailed in Section 5.6.2.      
Multiple imputation for HFMSE , upper limb module test endpoint, PedsQL and ACEND 
 
Since month 15 HFMSE score values will not be available for many of the patients at the 
interim analysis, missing data will be handled using the multiple imputation (MI) method 
(Schafer 1997; Schafer 1999).  The same method for imputation of missing values will be 
used at the final analysis. 
 
The imputations will be performed on total scores for baseline and post-baseline visits. The 
Markov Chain Monte Carlo (MCMC) method will be used under the multivariate normality 
assumption to impute the missing score by treatment group.  The treatment variable will be 
coded so that the ISIS 396443 group is the first in the sort order and therefore as the MI 
procedure is by treatment the imputation will be performed on ISIS 396443 subjects first. 
 Prior to the Proc MI step the dataset will be sorted by treatment and then ascending unique 
subject identifier (USUBJID).  The variable list for imputations will include the baseline total 
score, age at consent, as well as all available post-baseline total scores. A set of 100 complete 
imputed data sets will be generated and the relative efficiency (RE) parameter will be 
checked.  The RE is a very common parameter used in MI to determine the acceptability of 
the imputed results.  Regarding the number of imputations, since the sample size in this study 
is relatively small and proportion of missing information is large, it will be important to run a 
large number of imputations to get an RE that is close to 98% or higher.   
 
For PedsQL and ACEND the imputation will be performed independently on each dimension 
or summary score (constructed using all, or a subset of dimensions) separately, rather than at 
the item level.  
 
The following pseudo SAS code and seeds will be used to perform the multiple imputation.   


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proc mi data =in_data 
seed = x nimpute = 100 out= imp_data; 
mcmc chain = multiple; 
var base age D92 D169 D274 D365 D456; 
by treatment; 
run; 
 
 
 
Endpoint 
 
 
Seed 
 
HFMSE 
 
25980495 
Upper limb module test 
47886416 
PedsQL Core Parent   
   Physical functioning 
   Emotional functioning 
   Social functioning 
   School functioning 
   Psychosocial health summary 
   Total Score  
 
PedsQL Core Patient 
   About my health and activities 
   About my feelings 
   How I get along with others 
   About School 
   Total Score 
 
PedsQL Neuromuscular Parent 
   About my childs neuromuscular disease 
   Communication 
   About our family resources 
   Total Score 
 
PedsQL Neuromuscular Patient 
   About my neuromuscular disease 
   Communication 
   About our family resources 
   Total Score 
 
ACEND  
  Domain I – Feeding/Grooming/Dressing 
  Domain II – Sitting/playing 
  Domain III – Transfer 
  Domain IV – Mobility 
  Domain V – Time 
  Domain VI – Emotion 
  Domain VII - Finance 
  
 
12676424 
35764041 
85032085 
79256650 
74500750 
51407567 
 
 
48001267 
21787096 
95088062 
11511569 
13067474 
 
 
33325144 
27244614 
84519141 
49741400 
 
 
90156114 
62901627 
17014549 
76235199 
 
 
68757534 
14107127 
54836220 
96063155 
38462550 
85339274 
70873601 
 
 
 
Multiple imputation analysis methods 
 
For the HFMSE, PedsQL, ACEND, upper limb module the imputations will be performed on 
the ITT population.  In any sensitivity analyses using multiple imputation such as repeating 
the main analysis in the PPS the subset of subjects in the PPS will be selected from the 
multiple imputed datasets obtained from the ITT population. If the MI procedure imputes any 


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values outside the expected range for the scale e.g. from 0 to 66 for HFMS-E then values 
below 0 will be set to 0 and values above 66 will be set to be 66.   
 
For each of the 100 imputed datasets, the endpoint will be compared between treatment 
groups using an ANCOVA model for continuous endpoints or logistic regression for binary 
endpoints as described in the main analysis for each endpoint.  The estimates from the 100 
fitted models will be combined to provide an overall estimate with corresponding confidence 
intervals and p-value [Little et al, 2002]. 
 
For the continuous endpoints, the difference between treatments and the corresponding CI 
will be presented.  In addition, for each subject the median change from baseline to each visit 
will be calculated across the multiple datasets and summarized by treatment group.  For the 
analyses using logistic regression the odds ratio and corresponding CI will be presented.  In 
addition, the estimates of the binomial proportions in each treatment arm and the differences 
between treatments will be presented (Ratitch, 2013). 
 
If, due to a small sample size or other unforeseen scenario, the multiple imputation model 
does not converge or encounters computational difficulties, then the number of iterations will 
be increased.  If the model still fails then a Mixed Effects Model with Repeated Measures will 
be used as the primary analysis as described in Section 5.5.1.2.   
 
In the presentation of results from multiply imputed data, the number of subjects with missing 
data and the degree to which it is missing will be summarized.      
 
5.4 
Baseline 
In all efficacy analyses, baseline is defined as the last non-missing assessment prior to the first 
dose of ISIS 396443 or first sham procedure.  
5.5 
Analysis methods for the primary endpoint 
The HFMSE is a tool used to assess motor function in children with SMA. The scale was 
originally developed with 20 scored activities and was devised for use in children with Type 2 
and Type 3 SMA with limited ambulation to give objective information on motor ability and 
clinical progression. The expanded scale includes an additional module of 13 items developed 
to alleviate the ceiling effect and allow evaluation of higher functioning and ambulatory SMA 
patients. Each item is scored 0 (unable), 1(performs with modification or adaptation) or 2 
(able) and the total score is calculated by summing the 33 items and ranges from 0 to 66 with 
higher scores indicating greater motor function. If 6 or fewer items are missing, then these 
items will be imputed to be 0 when summing all 33 items. If greater than 6 items are missing, 
then the total score will be set to be missing. 
The primary endpoint is the change from baseline HFMSE score at 15 months.  
An interim analysis based on the primary endpoint may take place (Sections 5.1 and 5.2) and 
the analytical methods for the final (Section 5.5.1) and interim analyses (Section 5.5.2) are 
described. 


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5.5.1 
Final analysis of primary endpoint 
5.5.1.1 
Main analysis 
The main analysis is to compare the change from baseline HFMSE score at 15 months 
between the two treatment groups based on the ITT Set.  The data will be analyzed using an 
analysis of covariance (ANCOVA) model with treatment group as a factor and age at 
screening and baseline HFMSE score as covariates.  The null hypothesis is that ISIS 396443 
and sham procedure control groups have the same change from baseline HFSME score at 15 
months. Missing post-baseline HFMSE data will be handled using the multiple imputation 
method. 
5.5.1.2 
Sensitivity analyses 
Several sensitivity analyses will be performed for the final analysis of the primary endpoint.   
In the first, the main analysis will be repeated using the dataset from multiple imputation of 
the missing data in the ITT Set, to compare treatment groups using the PPS.  
In the second, the analysis will be performed using a Mixed Effects Model with Repeated 
Measures (MMRM) with an unstructured covariance matrix, where the treatment group, time 
(as a categorical variable), treatment by time interaction, and patient age at screening will be 
included in the model as fixed effects; patient will be a random effect; baseline HFMSE and 
baseline by time interaction will be included as a covariate. No imputation for missing visit 
data will be performed and the analysis will be performed on the ITT Set. 
In the third sensitivity analysis, only the subset of subjects in the ITT Set who have non-
missing values at 15 months will be analyzed using the same ANCOVA model as for the 
main analysis, in essence an analysis of ‘completers’. 
In the fourth sensitivity analysis the missing Month 15 values will be imputed by ‘last 
observation carried forward’.  This will be performed on the ITT set and data will be analyzed 
by analysis of covariance with treatment group as the factor and subject age at screening and 
baseline value as covariates.  
In the fifth sensitivity analysis the main analysis using multiple imputation will be repeated 
but for subjects who have a missing 15-month assessment and discontinue due to treatment 
failure or death the worst of the last observed value or the baseline value will be imputed.  
The reasons for treatment termination are captured in the CRF in several  categories as: 
‘Investigator judgment’, ‘Voluntary withdrawal’, ‘Pregnancy’, ’Ineligibility’, ’Protocol 
deviation’, ‘Adverse Event’ or ‘Other’, and a free text field captures further detail.  Therefore, 
a blinded medical review will be conducted, prior to unblinding to adjudicate if any are due to 
treatment failure.  This list will then be used in determining a subject’s response. 
From each imputation method, the data will be analyzed by analysis of covariance with 
treatment group as the factor and subject age at screening and baseline value as covariates.  
5.5.1.3 
 Exploratory analyses 
In order to further explore the change in HFMSE score during the study and the difference 
between treatment groups the change from baseline to each visit will be analyzed using an 
ANCOVA model and multiple imputation as described for the main analysis.  A plot of mean 


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change from baseline (based on the estimates from the ANCOVA model) over time will be 
provided by treatment group.  
The total HFMSE score and change from baseline to each visit will be presented using 
observed values. Individual items of the HFMSE and changes from baseline to each visit will 
be investigated to determine the pattern of shifts. 
Graphical representations to show each individuals response and Forest plots to summarize 
the primary endpoint and corresponding sensitivity analyses may be presented. 
Analyses will be conducted on the ITT Set and PPS. 
5.5.2 
Interim analysis of primary endpoint 
5.5.2.1 
Main analysis 
An interim analysis may take place as described in Section 5.1.  At the interim analysis, the 
primary endpoint will be analyzed using the same ANCOVA model as planned for the final 
analysis.  Endpoint values will not be available for many of the subjects at the interim analysis 
and the approach to handling missing post-baseline HFMSE data will also be the same as for 
the final analysis using the multiple imputation method (Section 5.3).  
Analyses will be conducted on the ITT Set. 
5.5.2.2 
Sensitivity analyses 
The sensitivity analyses planned for the final analysis of the primary endpoint will be repeated 
at the interim with the exception of the PPS analysis.  
The analysis of subjects with non-missing Month 15 values described for the primary 
endpoint will be performed at 15 months, but it is noted that since this is an interim analysis 
the number of subjects available will be small so this is included to explore the trend. 
One exploratory analysis using the same ANCOVA model as the primary analysis may be 
performed based upon the IES.  In the event a subject is in the IES but has a missing value at 
15 months then the median value for the subject at Month 15 across the 100 datasets from the 
multiply imputed data will be used in the imputation.   
The exploratory analyses outlined in Section 5.5.1.3 will be performed at the interim on the 
ITT Set using the imputed dataset from the main analysis.  
 
 
 
 
 
 
 
 
 


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5.5.3 
Summary of analyses of the primary endpoint 
 
Summary of analyses for the primary endpoint 
Analysis Method 
 
Final Analysis - Population: 
further notes 
Interim Analysis - Population: 
further notes 
Main analysis 
 
Analysis of covariance (treatment as fixed 
effect) with subject’s age at screening and 
baseline HFMSE value as covariates 
ITT; multiple imputation 
used to impute missing 15-
month values 
ITT Set; multiple imputation 
used to impute missing 15-
month values 
Sensitivity analyses 
 
 
 
Analysis of covariance (treatment as fixed 
effect) with subject’s age at screening and 
baseline HFMSE value as covariates 
 
PPS; multiple imputation 
used to impute missing 15-
month values 
 
  
  
 
MMRM model - treatment group, time (as 
a categorical covariate), treatment by time 
interaction, and patient age at screening 
will be included in the model as fixed 
effects; patient will be a random effect; 
baseline HFMSE and baseline HFMSE by 
time interaction will be included as a 
covariate. 
ITT: no imputation 
ITT Set, no imputation 
 
Analysis of covariance (treatment as fixed 
effect) with subject’s age at screening and 
baseline HFMSE value as covariates 
 
Subset of ITT with non-
missing 15-month values  
 
 
ITT Set; with non-missing 
15-month values  
 
 
Analysis of covariance (treatment as fixed 
effect) with subject’s age at screening and 
baseline HFMSE value as covariates 
 
ITT; last observation 
carried forward used to 
impute missing 15-month 
values 
 
ITT Set; last observation 
carried forward used to 
impute missing 15-month 
values 
 
Analysis of covariance (treatment as fixed 
effect) with subject’s age at screening and 
baseline HFMSE value as covariates 
 
ITT Set with Multiple 
imputation; worst of the 
baseline and last observed 
value for subjects who 
discontinue due to 
treatment failure or death.  
If missing for any other 
reason then use value from 
MI  
 
ITT Set with Multiple 
imputation; worst of the 
baseline and last observed 
value for subjects who 
discontinue due to treatment 
failure or death.  If missing 
for any other reason then 
use values from MI. 
 
 
 
 
 
 


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5.6 
Analysis methods for the secondary endpoints 
 
For many of the secondary endpoints, if a subject discontinues due to treatment failure or 
death then the subject will be defined to be a non-responder.  This will be determined as 
described in Section 5.5.1.2  
 
5.6.1 
Proportion of subjects who achieve a 3-point or greater increase from baseline in 
HFSME at 15 months 
5.6.1.1 
Final analysis 
Main analysis 
The multiple imputation datasets produced for the analysis of the primary endpoint will be 
utilized.  If a subject terminates the study prior to the 15-month assessment due to treatment 
failure or death, then the imputed value from the multiple imputation will be ignored and the 
subject will be considered a non-responder.  Any subject in the ITT Set who has an increase 
from baseline HFMSE score of 3 or more points at Month 15 will be defined as a responder; 
otherwise, a subject will be considered a non-responder. 
Treatment groups will be compared using logistic regression adjusting for each subject’s age 
at screening and baseline HFSME score.   
Sensitivity analysis 
Four sensitivity analyses will be performed.  In the first, the main analysis described above 
will be performed on the PPS.   
In the second, performed on the ITT Set without any imputation, any subject who has an 
increase from baseline in HFMSE score of 3 or more points at Month 15 will be defined as a 
responder.  If this was not achieved or the Month 15 value is missing, a subject will be 
defined as a non-responder.  
In the third, performed on the ITT Set without any imputation, if a subject terminates the 
study prior to the 15-month assessment due to treatment failure or death, then the subject will 
be considered as a non-responder, if the subject has missing Month 15 due to any other 
reason, he/she will not be included in the analysis.  
In the fourth sensitivity analysis, only the subset of subjects in the ITT Set who have non-
missing values at 15 months will be analyzed.  Any subject who has an increase from baseline 
in HFMSE of 3 or more points at Month 15 will be defined as a responder; otherwise, he/she 
will be considered a non-responder. 
Treatment groups will be compared using logistic regression adjusting for each subject’s age 
at screening and baseline score.      
 
 
 
 


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5.6.1.2 
Summary of analyses 
Summary of analyses for the secondary endpoint, proportion of subjects who achieve a 3-point or greater 
increase from baseline in HFMSE at 15 months 
Analysis Method 
 
Final Analysis - Population: 
further notes 
 
Main analysis 
Logistic regression adjusting for each 
subject’s age at screening and baseline 
HFSME score.  Subjects who terminate 
the study prior to the 15-month 
assessment due to treatment failure or 
death will be considered as a non-
responder 
ITT; multiple imputation used to 
impute missing 15-month values 
 
Sensitivity analyses 
 
 
Logistic regression adjusting for each 
subject’s age at screening and baseline 
HFSME score.  Subjects who terminate 
the study prior to the 15-month 
assessment due to treatment failure or 
death will be considered as a non-
responder 
 
 
PPS; multiple imputation used to 
impute missing 15-month values 
 
 
Logistic regression adjusting for each 
subject’s age at screening and baseline 
HFSME score. Subject with an increase of 
3 or more points will be considered a 
responder, else he/she will be considered 
a non-responder. 
 
ITT, no imputation 
 
 
Logistic regression adjusting for each 
subject’s age at screening and baseline 
HFSME score. Subjects who terminate the 
study prior to the 15-month assessment 
due to treatment failure or death will be 
considered non-responders 
 
Logistic regression adjusting for each 
subject’s age at screening and baseline 
HFSME score.   
ITT, subjects with missing Month 15 
not deemed due to treatment failure 
or death are excluded. 
 
 
 
 
ITT, with non-missing 15-month 
values  
 
 
 
 
 
5.6.2 
Proportion of subjects who achieve any new motor milestones at 15 months 
 
The WHO motor milestones are a set of six milestones in motor development, all of which 
would be expected to be attained by age 24 months in healthy children. The individual 
milestones are: 
 
• Sitting without support 
• Standing with assistance 


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• Hands and knees crawling 
• Walking with assistance 
• Standing alone 
• Walking alone 
 
Per the study inclusion criterion number 5, subjects would be expected to all have achieved 
and maintained at baseline the milestone ‘Sitting without support’ but none would have 
achieved the milestone of ‘Walking alone’.  The motor milestones are assessed at seven study 
visits using the WHO motor milestone criteria [WHO Multicentre Growth Reference Study 
Group 2006]. As part of the assessment, the examiner records an overall rating of the 
subject’s emotional state and then for each milestone one of the following four classifications: 
 
• No (inability) – Child tried but failed to perform the milestone    
• No (refusal) – Child refused to perform despite being calm and alert 
• Yes – Child was able to perform the milestone 
• Unable to test – Could not be tested because of irritability, drowsiness or sickness 
 
Imputation for motor milestones  
 
If for a milestone either ‘No (refusal)’ or ‘Unable to test’ are observed at a visit then the result 
will be first set to missing. Imputation will be performed for missing data considering each 
milestone separately using the following rules for scheduled visits. 
 
For baseline, the closest non-missing milestone prior to or at first dose will be selected.  If the 
motor milestone is still missing then the missing value will be imputed as the median of the 
non-missing values of the stratum to which the subject belongs to: Age at screening < 6 years 
or Age at screening >= 6 years.  In the event that the median at baseline is 0.5 then then the 
missing value will be imputed as 1.  If, for the subject with a missing value at a particular visit 
the corresponding visit is flanked by visits with non-missing milestones, the missing value 
will be imputed by using the worst result from the flanking visits.   Otherwise, if the 
imputation is the last visit, the missing value will be imputed as the lowest value observed 
across all subjects who have a non-missing value at this visit within the stratum: Age at 
screening < 6 years or Age at screening >= 6 years within the treatment group. Of note, only 
observed data will be utilized for imputation purposes and in a situation where unscheduled 
visit data is available these values will be utilized if these flank a missing visit.  Missing 
motor milestone items will be imputed first prior to any analysis.   
 
5.6.2.1 
Final analysis 
Main analysis 
Treatment groups will be compared using logistic regression adjusting for each subject’s age 
at screening and baseline number of milestones.  Missing data will be handled as described in 
Section 5.6.2.  If a subject terminates the study prior to the 15-month assessment due 
treatment failure or death then any imputed value will be ignored and the subject will be 
considered a non-responder. For the remaining subjects, the 15-month milestone data will be 


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assessed and if the baseline milestones achieved are still maintained at Month 15 and the 
subject has achieved at least one new milestone, he/she will be considered a responder. 
 
Should the number of responders be less than 5 in either group, Fisher’s exact test will be 
used instead. If Fisher’s exact test is used, the unconditional confidence interval for the 
difference in response rates will be provided (Santner and Snell 1980). 
Sensitivity analysis 
Several sensitivity analyses will be performed.  In the first, the analysis described above will 
be performed on the PPS.  In the second, the analysis will be performed on the ITT Set and 
any subject who is missing all six milestone assessments at Month 15 will be considered a 
non-responder.  If 5 or fewer milestone assessments are missing at Month 15 then any missing 
individual milestones will be set to ‘Not (Inability)’ and for each subject the Month 15 
milestone data will then be assessed compared to baseline to determine response as in the 
main analysis.  In the third sensitivity analysis, performed on the ITT Set, any subject who is 
missing the Month 15 visit due to treatment failure or death will be considered to be a non-
responder.  Any subject who is missing all Month 15 milestone assessments for any other 
reason will be excluded from the analysis; otherwise, the analytical method will be the same 
as that for the previous analysis.  
In the fourth sensitivity analysis, only the subset of subjects in the ITT Set who have non-
missing values for all six milestones at 15 months will be analyzed.   If the baseline 
milestones achieved are still maintained at Month 15 and the subject has achieved at least one 
new milestone they will be considered as a responder.  Treatment groups will be compared 
using logistic regression adjusting for each subject’s age at screening and baseline score.       
Exploratory analysis 
 
Several additional analyses will be performed on the ITT Set (without any imputation) to 
further explore the consistency in achievement and maintenance of motor milestones during 
the course of the study.  In the first analysis, the proportion of subjects who achieve at least 
one new milestone compared to baseline and then maintain this milestone at successive visits 
will be assessed.  In order to be assessed as a responder, subjects would need to have 
completed the study and the following will also apply: 
• Milestones achieved at baseline are maintained across all study visits 
• The visit at which a subject first achieves at least one new milestone will be 
considered.  At least one of any new milestones achieved at this visit will then 
need to be maintained at subsequent visits 
•  At least two successive visits are required.  Thus, the first new milestone will 
need to be achieved at the latest by Month 12 in order to allow confirmation at 
Month 15 
 
In the second analysis, the proportion of subjects who achieve new milestones compared to 
baseline and maintain these milestones at successive visits will be assessed.  The definition 
will be similar to the first analysis but whenever a subject achieves any new milestone, this 
milestone will need to be maintained to Month 15.  Having first achieved any new milestone 


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compared to baseline, if a subject is unable to demonstrate maintenance of the milestone(s) at 
future visits, he/she will be defined as a non-responder.  
The proportion of subjects defined as responders under each definition will be analyzed by 
logistic regression adjusting for the subject’s age at screening and baseline number of 
milestones.   In addition, for each of these analyses, the number of visits at which a subject 
was judged to maintain the milestone as a responder will be summarized using counts and 
percentages. In this summary, non-responders will be presented as zero and 2, 3, 4 and 5 will 
be possible counts for responders. 
5.6.2.2 
Summary of analyses  
Summary of analyses for the secondary endpoint, proportion of subjects who achieve any new motor 
milestone at Month 15 
Analysis Method 
 
Final Analysis - Population: 
further notes 
 
Main analysis 
Logistic regression adjusting for each 
subject’s age at screening and baseline 
number of motor milestones.  Subjects 
who i) terminate the study prior to the 15-
month assessment due to treatment failure 
or death OR ii) for whom it cannot be 
confirmed they can still maintain the 
baseline milestone at Month 15 will be 
considered as a non-responders 
 
ITT; impute missing 15-
month values per Section 
5.6.2 
 
Sensitivity analyses 
 
 
Logistic regression adjusting for each 
subject’s age at screening and baseline 
number of motor milestones.  Subjects 
who i) terminate the study prior to the 15-
month assessment due to treatment failure 
or death OR ii ) for whom it cannot be 
confirmed they can still maintain the 
baseline milestone at Month 15 will be 
considered as a non-responders 
 
PPS; impute missing 15-
month values per Section 
5.6.2 
 
 
 
Logistic regression adjusting for each 
subject’s age at screening and baseline 
number of milestones.  Subjects missing 
<= 5, Month 15 milestones then impute 
each missing milestone as ‘Not, Inability’. 
Subjects who are i) missing all six 
assessments of motor milestones at Month 
15 OR ( ii) do not maintain the baseline 
milestone at Month 15 will be considered 
as a non-responders.  
 
 
 
ITT 
 
 
 
Logistic regression adjusting for each 
subject’s age at screening and baseline 
ITT: subjects with missing 
Month 15 not deemed due 
 
 


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number of milestones.  Subjects missing 
<= 5, Month 15 milestones then impute 
each missing milestone as ‘Not, Inability’. 
Subjects who are i) missing all six 
assessments of motor milestones at Month 
15 OR ii) do not maintain the baseline 
milestone at Month 15 will be considered 
as a non-responders 
 
to treatment failure or 
death are excluded. 
 
 
 
 
 
 
 
 
 
 
 
 
Logistic regression adjusting for each 
subject’s age at screening and baseline 
number of motor milestones.  Responder 
defined as at least one new milestone 
compared to baseline and maintained 
baseline milestones. 
 
 
ITT, with non-missing 15-
month values  
 
  
5.6.3 
Number of new motor milestones achieved per subject at 15 months 
5.6.3.1 
Final analysis 
Main analysis 
The main analysis is to compare the total number of new motor milestones achieved at 15 
months between the two treatment groups, based on the ITT Set.  Missing data will be 
handled as described in Section 5.6.2. and a total score for each visit calculated by summing 
the six milestones.   
For each milestone the Month 15 and baseline values will be compared and if the subject can 
achieve a new milestone compared to baseline then it will be counted +1, if the subject is 
unable to achieve the milestone then it will be scored -1 and if the milestone has been 
maintained then it will be scored 0.  These scores will then be summed to give a total score 
which could range between -6 (if a subject was able to perform all milestones at baseline but 
lost the ability and could not perform any milestones at Month 15) and + 6 (if a subject was 
unable to achieve any milestones at baseline but could achieve all at Month 15). 
The total number of new milestones achieved by each subject at Month 15 will be compared 
between treatment groups by analysis of covariance with treatment group as the factor and 
subject age at screening and baseline number of milestones as covariates. 
Sensitivity analysis 
Three sensitivity analyses will be performed.  In the first, the analysis described above will be 
performed on the PPS.   In the second, the same analysis will be repeated in the ITT, with an 
exception to assign the worst of last available observation and zero (0) new motor milestones 
achieved for subjects who terminate the study prior to the 15-month assessment the study 
prior to the 15-month assessment.  In the third sensitivity analysis, only the subset of subjects 
in the ITT Set who have non-missing values for all six milestones at 15 months will be 
analyzed. 
 


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5.6.3.2 
Summary of analyses 
Summary of analyses for the secondary endpoint, Number of motor milestones achieved per subject at 15 
months 
Analysis Method 
 
Final Analysis - Population: 
further notes 
 
Main analysis 
Analysis of covariance (treatment as fixed 
effect) with subject’s age at screening and 
baseline value as covariates 
ITT, impute missing 15-
month values per Section 
5.6.2 
 
Sensitivity analyses 
 
 
 
 
Analysis of covariance (treatment as fixed 
effect) with subject’s age at screening and 
baseline value as covariates 
 
 
PPS, impute missing 15-
month values per Section 
5.6.2 
 
 
 
Analysis of covariance (treatment as fixed 
effect) with subject’s age at screening and 
baseline value as covariates 
ITT, impute worst of last 
available observation and 
zero (0) new motor 
milestones achieved for 
subjects who discontinue 
prior to Month 15 
 
 
Analysis of covariance (treatment as fixed 
effect) with subject’s age at screening and 
baseline value as covariates 
 
 
ITT, with non-missing 15-
month values  
 
  
5.6.4 
Change from baseline in Upper Limb Module Test at 15 months 
 
The upper limb module test (Mazzone et al. 2011) referenced in the protocol was developed 
to assess the upper limb functional abilities in SMA patients using 9 items. However, a 
revised version of the upper limb module test developed by the Upper Limb Module Working 
Group will be performed in this study consisting of 20 items. The first item is assessed on a 
seven point scale ranging from 0 - ‘No useful function’ to 6 – ‘Can abduct both arms 
simultaneously elbows in extension in a full circle until they touch above the head’. This first 
item will not contribute to the total score. The remaining 19 items are assessed on a three 
point scale using the following criteria: 0 - Unable to achieve independently; 1 - Modified 
method but achieves goal independent of physical assistance from another person; 2 - Normal 
– achieves goal without any assistance. For each item, a score will be collected on the left and 
right side. A derived total score will be calculated by summing the scores from these 19 
individual items and ranges from 0 if the subject fails all activities to 38 if the subject 
achieves all activities. If, for an individual item, a response is recorded for both the left and 
right side the highest score will be used in calculating the total. If 3 or fewer items are still 
missing responses then it will be assumed that the score was 0. If greater than 3 items are 
missing, then the total score will be set to be missing.   


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5.6.4.1 
Final analysis 
Main analysis 
The main analysis is to compare the change from baseline upper limb module test total score 
at 15 months between the two treatment groups based on the ITT Set.  The method of multiple 
imputation will be used as described for the HFMSE. The change will be compared between 
treatment groups by analysis of covariance with treatment group as the factor and subject age 
at screening and baseline value as covariates.  
Sensitivity analysis 
Four sensitivity analyses will be performed.  In the first, the analysis described above will be 
performed on the PPS.  In the second, the analysis will be performed using a Mixed Effects 
Model with Repeated Measures (MMRM) with an unstructured covariance matrix, where the 
treatment group, time (as a categorical covariate), treatment by time interaction, and patient 
age at screening will be included in the model as fixed effects; patient will be a random effect; 
baseline upper limb score and baseline upper limb score by time interaction will be included 
as a covariate. No imputation for missing visit data will be performed and the analysis will be 
performed on the ITT Set.  In the third, the main analysis will be repeated but for subjects 
who terminate the study prior to the 15-month assessment due to treatment failure or death, 
the worst of the last observed value or the baseline value will be imputed.    In the fourth 
sensitivity analysis, only the subset of subjects in the ITT Set who have non-missing values at 
15 months will be analyzed.  For both of these treatment groups will be compared by analysis 
of covariance.  
5.6.4.2 
Summary of analyses 
Summary of analyses for the secondary endpoint, Change from baseline in upper limb module test at 15 
months 
Analysis Method 
 
Final Analysis - Population: 
further notes 
 
Main analysis 
Analysis of covariance (treatment as fixed 
effect) with subject’s age at screening and 
baseline value as covariates 
ITT, missing data handled 
using multiple imputation 
method 
 
Sensitivity analyses 
 
 
Analysis of covariance (treatment as fixed 
effect) with subject’s age at screening and 
baseline value as covariates 
 
MMRM model - treatment group, time (as 
a categorical covariate), treatment by time 
interaction, and patient age at screening 
will be included in the model as fixed 
effects; patient will be a random effect; 
baseline upper limb score and baseline 
upper limb score by time interaction will be 
included as a covariate. 
 
PPS, missing data handled 
using multiple imputation 
method 
 
 
ITT: no imputation for 
missing data 
 


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Analysis of covariance (treatment as fixed 
effect) with subject’s age at screening and 
baseline value as covariates 
 
ITT Set with Multiple 
imputation; worst of the 
baseline and last observed 
value for subjects who 
discontinue due to 
treatment failure or death.  
If missing for any other 
reason then use value from 
MI  
 
Analysis of covariance (treatment as fixed 
effect) with subject’s age at screening and 
baseline value as covariates 
 
ITT, with non-missing 15-
month values  
 
  
5.6.5 
Proportion of subjects who achieve standing alone at 15 months 
 
5.6.5.1 
Final analysis 
 
Main analysis 
The main analysis will be performed on the ITT Set and missing data will be imputed as 
described in Section 5.6.2.  If, a subject terminates the study prior to the 15-month assessment 
due to treatment failure or death then any imputed value will be ignored and the subject will 
be considered as a non-responder.  For the remaining subjects, if the subject was unable to 
achieve standing alone at baseline but could achieve this at Month 15 then they will be 
considered a responder.  Treatment groups will be compared using logistic regression 
adjusting for each subject’s age at screening and baseline ability to stand alone.  
Sensitivity analysis 
Four sensitivity analyses will be performed.  In the first, the analysis described above will be 
performed on the PPS.  In the second, performed on the ITT Set without any imputation, any 
subject who has no assessment of standing alone at Month 15 will be considered as a non-
responder; otherwise the analytical method is the same as that for the main analysis.   
In the third sensitivity analysis, performed on the ITT Set, any subject who is missing the 
Month 15 assessment due to treatment failure or death will be considered to be a non-
responder.  Any subject who is missing the Month 15 assessment for any other reason will be 
excluded from the analysis; otherwise the analytical method will be the same as that for the 
main analysis.  In the fourth sensitivity analysis, only the subset of subjects in the ITT Set 
who have non-missing values for standing alone at 15 months will be analyzed. 
 
 
 
 
 
 


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5.6.5.2 
Summary of analyses 
Summary of analyses for the secondary endpoint, Proportion of subjects who achieve standing alone at 
15 months 
Analysis Method 
 
Final Analysis - Population: 
further notes 
 
Main analysis 
Logistic regression adjusting for each 
subject’s age at screening and baseline 
ability to stand alone.  Subjects who 
terminate the study prior to the 15-month 
assessment due treatment failure or death 
will be considered as a non-responders 
 
ITT, impute missing 15-
month values per Section 
5.6.2 
 
Sensitivity analyses 
 
 
Logistic regression adjusting for each 
subject’s age at screening and baseline 
ability to stand alone.  Subjects who 
terminate the study prior to the 15-month 
assessment due treatment failure or death 
will be considered as a non-responders 
 
PPS, impute missing 15-
month values per Section 
5.6.2 
 
Logistic regression adjusting for each 
subject’s age at screening and baseline 
ability to stand alone.  Subjects who 
terminate the study prior to the 15-month 
assessment due to treatment failure or 
death will be considered as a non-
responders 
 
ITT 
 
Logistic regression adjusting for each 
subject’s age at screening and baseline 
ability to stand alone.  Subjects who 
terminate the study prior to the 15-month 
assessment due to treatment failure or 
death will be considered as a non-
responders 
 
ITT: completed/ discontinued 
subjects  with missing Month 
15 not deemed due to 
treatment failure or death are 
excluded 
 
Logistic regression adjusting for each 
subject’s age at screening and baseline 
ability to stand alone 
ITT, with non-missing 15-
month values  
 
 
 
 
  
 
5.6.6 
Proportion of subjects who achieve walking with assistance at 15 months 
 
This will be analyzed using the same main and sensitivity methods as described in Section 
5.6.5. 
 
 


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5.6.7 
Interim Analysis 
 
No testing of the secondary endpoints will be performed at the interim but summary statistics 
for each measure may be provided as follows.  For the HFMSE and upper limb endpoints the 
multiple imputation approach will be used as described in the main analysis, based on the ITT 
Set.  For the endpoints evaluating WHO motor milestones, the analysis will be performed as 
described but based on the IES.  To further explore the response in the cohort of subjects in 
the IES for the HFMSE and upper limb endpoint the main analysis will be repeated.  In these 
analyses if Month 15 is missing then the median of the MI values will be imputed.  For 
HFMSE if the reason for the missing Month 15 value is treatment failure or death then they 
would be set to be a non-responder and this would override any imputation.   
 
As an exploratory analysis for the WHO milestones the main analysis will be conducted based 
on data from Month 6, Month 9 and Month 12, separately. Specifically, let X denote Month 6, 
Month 9, or Month 12. The evaluable set at the interim analysis for the Day X visit is defined 
as the subset of subjects in the ITT Set who have the opportunity to be assessed at the Day X 
visit. Specifically, it will include all subjects with Day X visit and all subjects with time 
difference of at least X+7 days between the date of first dose and the targeted clinical cut-off 
date of Aug 31, 2016 for the interim analysis. However, a subject who has died or withdrawn 
will be included provided that there is a time difference of at least X-7 days between the date 
of first dose and the targeted clinical cut-off date of Aug 31, 2016 for the interim analysis.  
 
In a situation where an interim analysis is performed and a subject is in the evaluable set for a 
summary of WHO milestones but has missing data at this visit then this will be imputed using 
the rules in Section 5.6.2 up to the last visit at which a subject qualifies for inclusion in an 
evaluable set.  So a subject who is in the Month 12 evaluable set but not the IES and has a 
missing value at Month 12 then this will be imputed but a Month 15 value will not be 
imputed. 
 
In the event of a successful interim and subjects rolling over early to open label treatment, for 
the early final analysis the secondary endpoints will be evaluated as described for interim and 
evaluable sets for Month 6, Month 9, and Month 12 visits will be similarly defined as subsets 
of the ITT Set. 
 
5.6.8 
Exploratory analysis 
 
For each secondary endpoint in order to further explore the change over time, the change from 
baseline to each visit or the proportion responding in each group at each visit will be analyzed 
as described in the main analysis for the final analysis.  Summaries will be provided by 
treatment group.   
The following displays may be presented by visit using observed data with no imputations for 
missing total scores: 
• Thresholds of response in HFMSE, frequency and percentage 
• Change in total motor milestones 


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• Change in upper limb score   
Graphical representations to show each individuals response and Forest plots to summarize 
the primary endpoint and corresponding sensitivity analyses may also be presented. 
Analyses will be conducted on the ITT Set and PPS. 
 
5.7 
Tertiary endpoints 
5.7.1 
Change from baseline in CSF SMN protein concentration 
CSF SMN protein is collected pre-dose from subjects randomized to ISIS 396443 on Day 1 
(the baseline assessment) and pre-dose on Days 29, 85 and 274.   
The change and percentage change from baseline CSF will be presented by visit for subjects 
randomized to ISIS 396443.  A plot of the mean and percentage change from baseline over 
time will be presented.  
Scatter plots of change from baseline in HFMSE versus change from baseline in CSF SMN 
protein and corresponding Pearson’s correlation coefficient will be presented by visit.  
Analyses will be conducted on the ITT Set and PPS.   
5.7.2 
Clinical Global Impression of Change (Investigator and Caregiver assessments) 
The Clinical Global Impression of Change (CGI) is assessed at five visits post first dose on 
Days 92, 169, 274, 365 and 456.  At each visit the investigator and the subject’s caregiver 
each score how the subject has changed compared to ‘admission to the project’.  The 
assessment is scored on a 7- point ordinal scale (1= Very much improved, 2 = “Much 
improved”, 3 =”Minimally improved”, 4= “No change”, 5= “Minimally worse”, 6= “Much 
worse”, 7 = “Very much worse”).  
In order to investigate response on these scales, three definitions of responder will be defined:  
“Much improved”: Responder (<=2) versus Non-responder (>=3), “Any improvement”: 
Responder (<=3) versus Non-responder (>=4), “No worsening”: Responder (<=4) versus 
Non-responder (>=5).   
Main analysis 
The proportion of subjects who were responders  based on the “Much improved” definition of 
responder will be presented by visit. 
Exploratory analyses 
The main analysis will be repeated for the two alternative responder definitions of ‘Any 
improvement’ and ‘No worsening’.   
Agreement between investigator and caregiver 
The agreement in assessment between the investigator and the caregiver will be examined.  
For each visit the proportion of assessments which agree (have the same assessed value) will 
be presented.  In addition, at each visit the weighted Kappa coefficient will be calculated.  No 
statistical significance testing will be performed but the coefficient will be interpreted in line 
with the ranges suggested by Landis and Koch (1977) for strength of agreement.   


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The analyses will be presented by treatment group and overall for the ITT Set.  
Exploring the relationship between CGI and HFMSE 
The change in HFMSE from baseline for CGI responders/non-responder defined using the 
‘Much improved’ definition will be presented by treatment group, overall and by visit for both 
the investigator and caregiver assessment.  A similar analysis will also be performed 
presenting the proportion of subjects who achieve at least 2, 3 and 4 points improvement in 
HFMSE for CGI responder/non-responder by treatment group, overall and by visit for the ITT 
Set. 
5.7.3 
Change from baseline in Pediatric Quality of Life Inventory 
Subjects will be evaluated using the Pediatric Quality of Life Inventory (PedsQL™) 
Measurement 4.0 Generic Core Scales and 3.0 Neuromuscular Module (Varni et al. 1999) at 
screening (the baseline assessment) and on Days 92, 169, 274, 365 and 456.  
The questionnaires are specific to the age of the subject, and sites are instructed to get both 
subjects and caregivers to complete the same age specific questionnaire as was collected at 
baseline irrespective of whether or not the subjects cross an age boundary at a subsequent 
visit.   
The PedsQL parent questionnaire is collected for children in the following age categories: 2-
4, 5-7, 8-12 and 13-18 years.  Four dimensions are collected: Physical, Emotional, Social and 
School functioning and each item is scored on a 5 point ordinal scale (0= Never, 1 = Almost 
Never, 2= Sometimes, 3 = Often, 4 = Almost Always).  The PedsQL patient questionnaire is 
collected for children in the following categories: 5-7, 8-12 and 13-18.  Similar dimensions 
and 5-point ordinal scale are used as for the parents but for subjects aged 5 to 7 years a 3-
point ordinal scale is collected, omitting the response levels of 1 and 3.   
In the neuromuscular module, one parent questionnaire is collected for all subjects 
irrespective of age with three dimensions: ‘About my child’s neuromuscular disease’, 
Communication’ and ‘Family resources’.  The same 5-point ordinal scale is collected for each 
question.  The patient neuromuscular disease questionnaire is collected for subjects in the 
following age categories: 5-7, 8-12, 13 -18. The questionnaire for subjects aged 5-7 years uses 
the 3-point ordinal scale as above and has only one dimension - ‘About my Neuromuscular 
disease’.  The questionnaires for the remaining two age categories cover dimensions for 
‘Communication’ and ‘Family resources’ and use the 5-point ordinal scale.   
In scoring a dimension the first step is to reverse and linearly transform to a 0-100 scale (0 = 
100, 1 =75, 2=50, 3= 25, 4= 0), so a higher score is indicative of a better health related quality 
of life.  If greater than 50 percent of the items within a dimension are missing then the 
dimension score will not be computed, otherwise the mean score for the dimension will be 
calculated as the sum of items over the number of items answered. 
A psychosocial health summary score, constructed from three dimensions, will be calculated 
as the sum of items over the number of items answered in the emotional, social and school 
functioning scales. A total score will be calculated as the sum of all the items over the number 
of items answered on all the scales.  If greater than 50 percent of the items are missing, then 
the summary score or total score will be set to be missing.   


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For the neuromuscular module, a score for each dimension and then total score will be 
calculated in the same manner, no health summary scores are evaluated.   
For the generic PedsQL and neuromuscular module, the change and percentage change from 
baseline in the total score will be presented by visit and treatment group for both the parent 
and subject assessments.  Similarly, the changes in the individual dimensions and health 
summary score will also be presented.   
The change and percentage change from baseline score (each total score and parent/subject 
evaluation separately) to each visit will be analyzed using an ANCOVA model with treatment 
group as a factor and age at screening and baseline score as covariates.  A statistical test for a 
treatment effect will be performed at Days 92, 169, 274, 365 and 456.  
Multiple imputation as described in Section 5.3 will be used to impute missing post baseline 
values.  The imputation will be performed separately for each dimension and total and 
psychosocial summary scores.   Due to the age specific nature of these questionnaires, 
subjects aged 2-4 years would not be expected to complete the self-evaluation and if this is 
the case then imputations will not be performed and the subjects will be excluded from the 
analysis. 
A plot of mean change from baseline (each questionnaire and parent/subject separately) based 
on the estimates from the ANCOVA model over time will be provided by treatment group.   
Analyses will be conducted on the ITT Set and PPS. 
5.7.4 
Change from baseline in Assessment of Caregiver Experience with Neuromuscular 
Disease 
Parents of subjects will complete the Assessment of Caregiver Experience with 
Neuromuscular Disease (ACEND) questionnaire at screening and on Days 169 and 456.   This 
assessment instrument has been designed to quantify the caregiver impact experienced by 
parents of children affected with severe neuromuscular diseases, including children with SMA 
(Matsumoto et al. 2011).  
The ACEND includes a total of seven domains assessing physical impact (including 
feeding/grooming/dressing, sitting/play, transfers, and mobility) and general caregiver impact 
(including time, emotion, and finance) and each domain comprises several items.  The total 
score for a domain with n items, each item assessed on ordinal scale from 1 to z, is derived as 
follows: 100 multiplied by (Mean of the n items in the domain -1) divided by (z-1).  This total 
score will be on a scale of 0 to 100 with a higher score indicating a greater impact on the 
caregiver.  At least two items for the time domain and one item for the remaining domains 
need to be non-missing for a total to be calculated; else the total score will be set to be 
missing. 
The change and percentage change from baseline for each domain will be presented by visit 
and treatment group.  An ANCOVA model will be used to analyze the change and percentage 
change from baseline through to 15 months with missing data handled by multiple imputation 
as was described for PedsQL. Similarly, plots of the mean and percentage change from 
baseline over time, based on the ANCOVA model will be provided by treatment group. 
Analyses will be conducted on the ITT Set and PPS. 


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5.7.5 
Disease-related hospitalizations and adverse events 
A blinded medical review of the adverse events will be conducted in order to define those 
events which would be considered disease related.   The adverse event page in the CRF 
captures if an event is serious and one of the criteria of a serious event is if inpatient 
hospitalization required or hospitalization is prolonged. 
The number of disease related adverse events, and as a separate analysis the subset of these 
events which required hospitalization will be analyzed using the rate at which they occur.   
For descriptive purposes, the aggregate rate will be calculated for each treatment group by 
dividing the total number of events that occurred in a group by the total number of subject-
years on study.   
Annualized event rate will be calculated for each subject as the number of events that the 
subject experienced divided by the number of days on study and this ratio multiplied by 365. 
Although disease related adverse events occur as a stochastic process, and can be assumed to 
be from a Poisson distribution, studies in other therapeutic areas have shown that data of this 
type are typically over-dispersed, i.e., the variation seen is greater than that predicted by the 
Poisson model.  To account for over-dispersion in the annualized rate of events, the negative 
binomial distribution will be used.  Thus, on the basis of event rate, treatment groups will be 
compared using a negative binomial model adjusting for the stratification factor, age at 
screening.  An “offset” parameter, the logarithm of the time on study, will be included in the 
model.  If the data are underdispersed, or if the negative binomial regression model does not 
converge, a Poisson regression model with the same covariate will be used instead of the 
negative binomial regression model.  Dispersion will be evaluated from the Pearson chi-
squared statistic.    
Analyses will be performed on the ITT Set and PPS.  
5.8 
Subgroup analyses 
 
The main analysis for the primary endpoint and each secondary endpoint will be presented for 
the following subgroups: 
• geographic region (North America, Europe and Asia-Pacific).   
• below and above the stratification factor used in the randomization (Age at 
screening < 6 years versus >=6 years) 
• Disease duration (time from SMA onset to Screening in months) by tertiles 
 
The difference between treatments for continuous endpoints and the proportion of responders 
in each treatment group and the odds ratio for the binary endpoints will be presented. 
If the number of subjects in a subgroup is too small (e.g., < 15% of total number of subjects in 
the ITT population), the analysis in that subgroup may not be performed.  In the event an 
interim analysis is performed then subgroup analyses will be performed but the number of 
subjects with a Month 15 value within a  subgroup will be assessed and if <40% of subjects 
have a Month 15 value then these may not be presented . No statistical tests will be performed 
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It is anticipated that 8 subjects will be enrolled in Japan and a separate set of tables and listing 
will be presented for Japanese subjects. 
 
5.9 
Unblinding Plan for the Interim Analysis 
 
The interim analysis will be performed by a contract research organization (Parexel) and 
reviewed by an independent Data and Safety Monitoring Board (DSMB) overseeing the study 
and an Unblinded Senior Management Team from the sponsor.  The DSMB, in accordance 
with its Charter, will make a recommendation to the study Sponsor on whether or not the 
study should continue according to the protocol or any modifications are needed based on the 
emerging benefit/risk profile. 
 
After the review of the interim analysis results the Unblinded Senior Management Team will 
decide whether or not to proceed with regulatory submissions.  This decision will be based on 
totality of the data including the overall consistency of the data and the benefit/risk 
assessment.  If the Unblinded Senior Management Team decides to continue the study 
without regulatory submission, no additional personnel from the Sponsor will be unblinded to 
the interim data.  Should the Unblinded Senior Management Team decide to proceed with 
regulatory submissions, an internal filing team will be unblinded to the interim data.  The 
internal filing team will prepare and submit the marketing applications to the regulators.  
Members of both the Unblinded Senior Management Team and the internal filing team will 
not be involved with study management or operations after being unblinded to the interim 
data.  All internal individuals who had access to the unblinded interim data will no longer be 
involved in the conduct of the blinded study. 


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6 
Safety data 
Analyses of safety data will include adverse events and serious adverse events (Section 6.1), 
laboratory data (Section 6.2), ECGs (Section 6.3), vital signs (Section 6.4), and neurological 
examinations (Section 6.5).  Any worsening or new findings noted from the physical 
examinations will be reported as AEs. 
Analyses of safety data will be based on the Safety Set.  Baseline is defined as the last non-
missing result prior to the first dose of ISIS 396443 or the first sham procedure.  
6.1 
Clinical adverse events 
All adverse events (AEs) will be analyzed based on the principle of treatment emergence.  An 
adverse event will be regarded as treatment-emergent if it was present prior to receiving the 
first dose of ISIS 396443 or first sham procedure and subsequently worsened in severity, or 
was not present prior to receiving the first dose of ISIS 396443 or first sham procedure but 
subsequently appeared.   
In the situation where change in severity (but no change in seriousness) occurs for an adverse 
event, study sites are instructed to enter an end date and start a new record for the adverse 
event. In the new record, the changed severity is to be recorded and the start date will be set to 
be the end date of the previous record. Data linking those records are collected in the data 
base. Consider three scenarios: 
 
• The first AE record occurs prior to the first dose, the second AE record occurs on or 
after the first dose, and the severity increases: Only the second record will be counted 
as treatment-emergent. 
• The first AE record occurs prior to the first dose, the second AE record occurs on or 
after the first dose, and the severity decreases: Neither record will be counted as 
treatment-emergent. 
• Both records occur on or after the first dose: If the AE severity on the second record is 
worse than the severity on the first record, then count both records as treatment-
emergent.  But, if the severity improves, then only count the first record as treatment-
emergent. 
Of note, when counting the total number of treatment-emergent events, events linked through 
change in severity will still be counted as separate events. 
For events with missing start or stop dates, the following criteria will be used for the purpose 
of identifying treatment-emergent adverse events: 
• if both the start and stop dates for a particular event are missing, then the event is 
considered to have occurred on or after the first dose or sham procedure; 


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• if the start date for a particular event is missing and the stop date/time falls after the 
first dose or first sham procedure date/time, then the event is considered to have 
occurred on or after the first dose or sham procedure; 
• if the start time is missing and the start date is same as the first dosing or first sham 
procedure date, then the event is considered to have occurred on or after the first dose 
or sham procedure. 
• If it cannot be determined whether or not an event has occurred on or after dosing due 
to a missing or partial date, then the event will be assumed to have occurred on or after 
the first dose for the purpose of identifying treatment-emergent adverse events. 
Specifically, let AESTDT denote the start date of an adverse event and TRTSTDT be the start 
date of treatment/sham procedure. For the purpose of identifying treatment emergent adverse 
events, the following algorithm will be used for the imputation of missing or partial date: 
• If AESTDT is completely missing or the year is missing, then impute AESTDT to 
TRTSTDT. 
• If, in AESTDT, year is present and month/day are missing and year is equal to the 
year portion of TRTSTDT, then impute the month/day portion of AESTDT to the 
month/day portion of TRTSTDT. 
• If, in AESTDT, year is present and month/day are missing and year is not equal to the 
year portion of TRTSTDT, then impute the month/day portion of AESTDT to January 
01. 
• Consider the situation in AESTDT where year and month are present with only day 
missing. If the year and month are the same as those for TRTSTDT, then impute day 
in AESTDT with day in TRTSTDT. Otherwise, impute the day in AESTDT with the 
first day of the month. 
It is important to emphasize that the imputed date will not be used for calculations such as 
onset and duration of an adverse event.  
Due to the long half-life of ISIS 396443, analyses of treatment-emergent adverse events will 
include all events reported during the study. 
Adverse events will be coded using the MedDRA dictionary.  This coding system provides 
more than five levels to classify adverse events.  In general, adverse events will be presented 
by system organ class and preferred terms but other classifications may be used if warranted.   
The incidence of treatment-emergent adverse events will be summarized by treatment group 
and overall.  A subject having the same adverse event more than once will be counted only 
once in the incidence for that adverse event.  The summary tables will include incidence 
estimates for overall system organ class as well as for preferred terms within each system 
organ class.  Incidence will be presented by decreasing order by system organ class and by 
decreasing order by preferred term within each system organ class.  The most common 


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adverse events, i.e., those that occurred in at least 5% of subjects in either treatment group, 
will be presented.  In addition, adverse events that occurred with an incidence 5% or higher in 
the ISIS 396443 group than in the control group will be presented.  Upon examination of the 
actual data, different cut-offs may be used if it is deemed more appropriate.  
6.1.1 
Adverse events over time 
The incidence of AEs will be evaluated by time of onset by 90-day time intervals.  For a given 
time interval, the number of subjects who were followed for adverse events during that time 
interval will be presented along with the incidence of adverse events during that time interval.  
Therefore, for a given System Organ Class (SOC) or preferred term (PT), subjects will be 
counted only once for a given time interval but may be counted once across time intervals. 
The incidence of AEs will also be evaluated by treatment phase (loading phase: Day 1 to Day 
272, maintenance phase: Day 273 and beyond) using the same methodology as described 
above. 
 
For classifying adverse events into different time intervals, the algorithm in Section 6.1 for 
the imputation of missing or partial start dates will be used.  
 
6.1.2 
Adverse events by severity 
The investigator is to record the severity of each adverse event as mild, moderate, or severe.  
If a subject experiences the same adverse event multiple times, the event with the worst 
severity will be counted.  For each treatment group, the incidence within each category will be 
presented.  The incidence of severe events will be summarized by treatment group.  
6.1.3 
Adverse events by relationship to study treatment 
The investigator is to record the degree to which each adverse event is related to study drug 
(not related, unlikely or remotely related, possibly related, and related).  If a subject 
experiences the same adverse event multiple times, the event with the strongest relationship to 
study drug will be counted.  For each treatment group, the incidence within each category will 
be presented.  The incidence of drug-related events (those categorized as possibly related or 
related) will be summarized by treatment group.   
6.1.4 
Serious adverse events 
The incidence of treatment-emergent serious adverse events will be summarized by treatment 
group.  All serious adverse events will be listed including any that occurred prior to 
commencement of study treatment.  Similar tables will be generated for adverse events that 
led to discontinuation of study treatment and those that led to withdrawal from the study.  
6.1.5 
Deaths 
All adverse events which led to death will be listed. 
6.1.6 
Adverse events following dosing/sham procedure 
To examine the onset of any adverse events following dosing or the sham procedure the 
incidence of events that occur 0-6 hours, 6-24 hours, and 24-72 hours following dosing or 
sham procedure will be presented by treatment group.  In addition, presentations of events 


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that occurred in the first 24 hours and the first 72 hours following dosing or sham procedure 
will be provided.   
AEs potentially related to LP occurring within 7 days of dosing, such as the PTs headache and 
back pain will be summarized.   
 
For identifying adverse events following dosing or the sham procedure, the algorithm in 
Section 6.1 for the imputation of missing or partial start dates will be used. If time is missing 
and the event occurs on the same day as the day for dosing/sham procedure, the time for the 
dosing/sham procedure will be used as the imputed time.  
6.1.7 
Adverse events by anti-ISIS 396443 antibody status 
To determine the impact of the formation of anti-ISIS 396443 antibodies on the safety of ISIS 
396443, the incidence of adverse events in those ‘persistently’ positive, ‘transiently’ positive, 
and antibody negative will be presented.  The definition of persistence is given in Section 8.  
6.1.8 
Adverse Events Related to SMA 
The analysis of disease related events in Section 5.7.5 will present the overall incidence of 
events.  To further explore the nature of these events the following categories of event will be 
presented.   A blinded medical review prior to database lock will be conducted to ensure these 
proposed groupings are appropriate. 
• Respiratory events: events that are coded into the SOC of respiratory, thoracic, 
and mediastinal disorders, either as their primary SOC or their secondary SOC 
• Symptoms of gastric reflux: events identified by standardized MedDRA query 
(SMQ) for gastrointestinal nonspecific inflammations 
• Athralgia and other issues related to joints: events identified by SMQ for 
arthritis to initially identify terms.  The final set of terms will be refined by the 
medical review 
• Scoliosis: events identified by the PT Scoliosis 
• Contractures:  events identified using the PTs: Extremity contractures, joint 
contracture, muscle contracture and tendinous contracture 
6.1.9 
Presentations 
The following presentations will be shown:  
• 
an overall summary showing, for each treatment group, the number and percentage of 
subjects with an adverse event, a moderate or severe event, a severe event, a possibly 
or related event, a related event, a serious event, an event that led to discontinuation of 
study drug, and an event that led to withdrawal from the study 
• 
incidence by primary system organ class and preferred term 
• 
incidence, by preferred term, in at least 5% of subjects in either treatment group  
• 
incidence, by preferred term, of adverse events that occur with an incidence 5% or 
higher in any treated group (upon examining the actual data, different cut-off points 
may be used to examine the incidence of these adverse events if it is deemed more 
appropriate) 


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• 
incidence of mild, moderate and severe events by primary system organ class and 
preferred term   
• 
incidence of severe events by primary system organ class and preferred term 
• 
incidence of not related, unlikely to be related, possibly related, and related events by 
primary system organ class and preferred term 
• 
incidence of drug-related events by primary system organ class and preferred term   
• 
incidence of serious adverse events by primary system organ class and preferred term 
and a listing of serious adverse events 
• 
incidence of death and a listing of each death 
• 
incidence of events leading to discontinuation of study drug by primary system organ 
class and preferred term and a listing of such events  
• 
incidence of events leading to withdrawal from the study by primary system organ 
class and preferred term and a listing of such events 
• 
incidence of adverse events determined as following dosing/sham, by antibody status 
and events related to SMA  (each category presented separately) by primary system 
organ class and preferred term and a listing of such events. 
To avoid the potential for misleading interpretation of analysis of adverse events, no statistical 
testing will be performed.  
6.2 
Clinical laboratory data 
Blood is to be drawn and urine collected for laboratory analysis at screening, and on Day 1 
(pre-dose), 2, 29, 85, 169, 274 and 456.  The following clinical laboratory parameters are to 
be assessed:  
• Hematology: hemoglobin, hematocrit, red blood cell count, WBC count with 
differential both as absolute values and as a percentage (neutrophils, eosinophils, 
basophils, lymphocytes, and monocytes), and platelet count.   
• Blood chemistry: liver function (total bilirubin, alkaline phosphatase, ALT/SGPT, 
AST/SGOT,) kidney function and electrolytes (BUN, creatinine, sodium, potassium, 
chloride), total protein, albumin, calcium, phosphorous, bicarbonate, glucose, cystatin 
C, and CPK.  
• Urinalysis: specific gravity, pH, protein, glucose, ketones, bilirubin, blood, RBC, 
WBC, epithelial cells, bacteria, casts, and crystals.  
As described below, laboratory data will be examined using an analysis of “shifts”. However 
further analyses may be undertaken to more fully characterize potential laboratory safety 
signals, such as assessment of timing, recovery, reversibility, association with adverse events, 
etc.  
In the second approach, each subject’s laboratory values will be classified according to 
whether the test result is “low” (i.e., below the lower limit of normal [LLN]), “normal” 
(within the normal range), or “high” (i.e., above the upper limit of normal [ULN]).  If a 
subject is missing a baseline value but had a post-baseline value, then the baseline assessment 
is labeled as “unknown”.  Likewise, if a subject had a baseline value but had no post-baseline 
values, then the minimum and maximum are labeled as “unknown”.  Post-baseline laboratory 
results are defined as any assessment taken after the first dose, including data collected from 


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local laboratories.  The shifts (relative to the normal range) from baseline to the minimum and 
maximum post-baseline values will be presented.  Should a treatment affect a laboratory 
parameter, that parameter could be affected at different times for different subjects.  
Therefore, these analyses present the most extreme values for each subject.  For many 
laboratory parameters, the effect could be in either direction, (i.e., an increase or a decrease), 
so both the maximum and minimum values have been analyzed.  From these, the shifts 
(relative to the normal range) from baseline to low and high will be calculated.  If a subject's 
value shifts, it can change from normal to either low or high, from low to normal or high, 
from high to normal or low, or from unknown to low, normal, or high.  For each parameter, 
the incidence of shift to low will be summarized using the minimum post-baseline values.  
Shift to low includes subjects with a normal, high, or unknown baseline value and at least one 
post-baseline value of the given test.  Similarly, the incidence of shift to high will be 
summarized using the maximum post-baseline values.  Shift to high includes subjects with a 
low, normal, or unknown baseline value and at least one post-baseline value.  All blood and 
urine samples will be used in the shift analyses.  
Blood and urine samples for laboratory analysis are to be processed at a central laboratory.  
For many parameters, the laboratory has additional ranges, e.g., a notification to the site by 
telefacsimile that the subject’s result is outside the normal range significantly enough to 
warrant notification, and/or a panic alert involving a telephone call made to the investigational 
site to notify them that the subject’s result is outside of the normal range with potentially 
critical implications for the subject (see the table below).  For shift tables of lab parameters, 
those additional categories will be combined with the conventional categories. Specifically, 
• LT (Low – telefacsimile) and LP (Low panic) will be classified as L (Lower limit of 
normal) 
• HT (How – telefacsimile) and HP (How panic) will be classified as H (Upper limit of 
normal) 
For liver function tests, additional categories will be defined to present the baseline and post-
baseline values as within the upper limit of normal,  >1-<3 x ULN, ≥3-<5 x ULN, ≥ 5-<10 x 
ULN, ≥ 10 - <20 x ULN, >=20 x ULN for ALT/AST, >1-<2 x ULN, ≥ 2 x ULN for total 
bilirubin, and >1-1.5 x ULN and ≥ 1.5 x ULN for alkaline phosphatase.  
 
 
 
 
 
 
 
 
 
 
 
 
 


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LP 
 
LT 
L 
H 
HT 
HP 
HgB 
X 
X1 
X 
X 
X1 
X1 
HCT 
X 
X2 
X 
X 
X 
 
RBC 
 
X 
X 
X 
 
 
WBC 
X 
X 
X 
X 
X 
X 
  Neutrophils ct 
X3 
X 
X 
X 
X 
 
  Lymphocytes ct 
 
X4 
X 
X 
X4 
 
  Monocytes ct 
 
 
X 
X 
 
 
  Eosinophils ct 
- 
- 
- 
X 
 
 
  Basophils ct 
- 
- 
- 
X 
 
 
  Neutrophils % 
 
 
X 
X 
 
 
  Lymphocyte % 
 
 
X 
X 
 
 
  Monocytes % 
 
 
X 
X 
 
 
  Eosinophils % 
- 
- 
- 
X 
 
 
  Basophils % 
- 
- 
- 
X 
 
 
Platelets 
X 
X 
X 
X 
X 
 
 
 
 
 
 
 
 
Urea nitrogen 
 
 
X 
X 
X 
X 
Bicarbonate 
 
X 
X5 
X 
X 
 
Creatinine 
 
 
X 
X 
X 
X 
Glucose 
X 
X 
X 
X 
X 
X 
Calcium 
X 
X 
X 
X 
X 
X 
Phosphorus 
 
 
X 
X 
 
 
Total protein 
X 
X6 
X 
X 
 
X5 
Albumin 
 
 
X 
X 
 
 
CK 
 
 
X 
X 
X 
X 
Sodium 
X 
X 
X 
X 
X 
X 
Potassium 
X 
X 
X 
X 
X 
X 
Chloride 
 
 
X 
X 
 
 
Cystatin C 
 
 
X 
X 
X 
 
 
 
 
 
 
 
 
Total bilirubin 
 
 
X 
X 
X 
X 
Alkaline 
phosphatase 
 
 
X 
X 
X 
X 
ALT 
 
 
X 
X 
X 
X 
AST 
 
 
X 
X 
X 
X 
 
 
 
 
 
 
 
1 6Y-150Y only; 2 Female: 0 to 3Y only, Male 0Y to 6Y only, 3 7M-2Y and 6Y-59Y females and  
7M-59Y males only; 4 0Y to 6Y only; 5 4Y to 150Y only; 6 0Y to 4Y only. 
-;LLN is 0 
LP: low panic 
LT: Low – telefacsimile 
L: lower limit of normal 
H: upper limit of normal 
HT: high – telefacsimile 
HP: high - panic 
 
6.3 
ECGs 
ECGs are to be recorded at screening, and on Days 2, 29, 92 and 456 and will be quantified 
prior to the final database lock at a central reading laboratory.  ECG qualitative results include 
an overall interpretation of ‘normal’, ‘abnormal but not clinically significant’ or ‘abnormal 
and clinically significant’.  ECG quantitative parameters include heart rate, PR interval, QRS 
duration, uncorrected QT interval, and corrected QT interval.   
ECGs will be analyzed using two approaches.   
6.3.1 
Qualitative analysis 
Incidence tables will summarize both the number and percentage of subjects with an 
abnormal, clinically relevant baseline ECG and the number and percentage of subjects with 


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abnormal, clinically relevant worsening, defined as a post-baseline ECG interpreted as 
abnormal and clinically relevant, with a comparison with baseline value of deteriorated, not 
available, not required, or missing.  The incidence of clinically relevant worsening will be 
summarized at any time post-baseline and by visit post-baseline.  In addition, a summary of 
abnormality types and findings within abnormality types will be provided for subjects with an 
abnormal, clinically relevant baseline ECG and for subjects with abnormal, clinically relevant 
worsening.  
6.3.2 
ECG outliers 
Outlier analyses will be performed for the corrected Fridericia QT interval.  This will include 
summaries of the number and percentage of subjects with a post-baseline corrected QT 
interval greater than certain threshold values (e.g., >450 msec, >480 msec, and >500 msec) 
and the number and percentage of subjects with an increase from baseline in corrected QT 
interval in various categories (e.g., >30 msec and >60 msec).  These summaries will be 
performed on an overall basis, as well as separately for subjects whose baseline corrected QT 
intervals are normal (≤ 450 msec) and elevated (>450 msec).   
6.4 
Vital signs 
Vital signs are to be measured at screening, pre-dosing and at 1, 2, 4, 6, and 20-24 hours post-
dosing on dosing days (Days 1, 29, 85 and 274).  Additionally, assessments are made on Days 
92, 169, 365 and 456.  At each of these times, temperature, heart rate, respiratory rate, systolic 
and diastolic blood pressure will be measured.  
If multiple evaluations are on the same visit day and visit time, then the mean of these 
evaluations will be selected for inclusion in the analysis. 
The analysis of vital signs will be approached in two ways. 
6.4.1 
Acute effects after dosing 
On each dosing day, the change in each vital sign from pre-dosing on that day to post-dosing 
(i.e., from pre-dosing to 1 hour post-dosing, to 2 hours post-dosing, etc.) will be calculated.  
Summaries of actual values and change from pre-dosing for each dosing day will be 
presented.  
6.4.2 
Chronic effects 
To examine for possible chronic effects, the change from baseline (the pre-dosing value on 
Day 1) to the pre-dosing value on later dosing days and to Days 92, 169, 365 and 456 will be 
determined.  Summaries of actual values and change from baseline to each of these time 
points will be presented.  
6.5 
Neurological examinations 
Neurological examinations include assessment of mental status, level of consciousness, 
cranial nerves, reflexes, motor system, coordination/cerebellar function and sensation – 
temperature and vibration. These are to be assessed at screening, pre-dosing and at 5 and 20-
24 hours post-dosing on dosing days (Days 1, 29, 85 and 274) and on Day  92,169, 365 and 
456.  


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The result collected for the majority of the tests is ‘normal’ or ‘abnormal’, however the 
assessment of sensations is reported as ‘present’ or ‘absent’ and the assessment of reflexes is 
captured on an ordinal scale.  For each test it is recorded if secondary to SMA.  
6.5.1 
Acute effects after dosing 
On each dosing day, the shifts from pre-dosing assessment on that day to post-dosing (i.e., 
from pre-dosing to 5 hours post-dosing, to 24 hours post-dosing) will be determined.   
For each test and post dosing time point, the number and proportion of subjects who moved 
from ‘Normal’ to ‘Abnormal’ will be presented, for sensations the number and proportion 
who move from ‘Present’ to ‘Absent’ will be presented.  For the assessment of reflexes 
decreases (from pre-dosing 1 to post doing 0, 2 to1 etc) will be presented.  Only changes not 
deemed secondary to SMA will be presented. 
6.5.2 
Chronic effects 
To examine for possible chronic effects, changes from baseline (the pre-dosing value on Day 
1) to the pre-dosing value on later dosing days and to Day 92, 169, 365 and 456 will be 
determined.  Summaries will be presented in a similar manner to that described for the acute 
effects.  
6.6 
Interim safety analyses 
Safety data will be reviewed on an ongoing basis by the Sponsor and the Medical Monitor.  
Safety data will also be reviewed on an ongoing basis by the independent DSMB.  The DSMB 
will be assembled to review safety, tolerability and efficacy data collected on ISIS 396443 
during this study and to review the results of the predetermined interim efficacy analysis 
(Section 5.1).  Based on its ongoing assessment of the safety and tolerability of ISIS 396443, 
the DSMB will provide recommendations to the Sponsor for modifying, stopping or 
continuing the study as planned.  
Details on the safety assessments, frequency of review, meeting schedules and controlled 
access to unblinded data at the interim safety analyses are outlined in the DSMB Charter.  
 
7 
Pharmacokinetic data 
CSF and Plasma samples will be collected at protocol designated times for ISIS 396443 
pharmacokinetic assessments from both treatment groups in the Pharmacokinetic Population. 
The Pharmacokinetic Population includes all subjects who are randomized and for which 
there is at least one evaluable post-dose/post-sham procedure pharmacokinetic sample.  
7.1 
CSF Concentration Data 
CSF concentrations of ISIS 396443, along with the scheduled (nominal) and actual sampling 
times (i.e., time from IT dosing) will be listed (when applicable) for each patient, and day.  
Differences between scheduled and actual sampling days will also be listed for all patients.  
Percent differences between actual administered dose and nominal dose will also be listed.  
CSF concentrations below the lower limit of quantification (LLOQ) will be indicated by 
“BLQ”.  For the purpose of calculating typical descriptive statistics (n, mean, SD, %CV, 
geometric mean, geometric %CV, median, minimum, and maximum) for CSF concentrations, 
all BLQ values will be set to zero.  Mean CSF concentrations that are BLQ will be presented 


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as BLQ, and the SD and %CV will be reported as not applicable.  Summary statistics of the 
ISIS 396443 CSF concentrations will be tabulated by day.  At the discretion of the 
pharmacokineticist and/or biostatistician, samples may be excluded from descriptive statistics 
if there are large deviations between scheduled and actual sampling days or times, or large 
deviations between actual dose and nominal dose.  
Due to the limited CSF samples collected no CSF pharmacokinetic parameters will be 
calculated.  
7.2 
Plasma Pharmacokinetics 
7.2.1 
Plasma Concentration Data 
Plasma concentrations of ISIS 396443, along with the scheduled (nominal) and actual 
sampling times (i.e., time from IT dosing) will be listed (when applicable) for each patient, 
treatment group, and day.  Percentage differences between scheduled and actual sampling 
times will also be listed for all patients.  Percentage differences between actual administered 
dose and nominal dose will also be listed.  
Plasma concentrations below the lower limit of quantification (LLOQ) will be indicated by 
“BLQ”.  For the purpose of calculating typical descriptive statistics (n, mean, SD, %CV, 
geometric mean, geometric %CV, median, minimum, and maximum) for plasma 
concentrations, all BLQ values will be set to zero.  Mean plasma concentrations that are BLQ 
will be presented as BLQ, and the SD and %CV will be reported as not applicable.  Summary 
statistics of the ISIS 396443 plasma concentrations will be tabulated by day and scheduled 
time point.  At the discretion of the pharmacokineticist and/or biostatistician, samples may be 
excluded from descriptive statistics if there are large deviations between scheduled and actual 
sampling times, or large deviations between actual dose and nominal dose.  
ISIS 396443 plasma concentration versus time (actual) profiles from Day 1 to Day 29, for 
each patient, as well as the mean (±SD) plasma concentration versus time (scheduled) profiles 
for the applicable treatment group, will be presented graphically on linear and 
semilogarithmic scales. ISIS 396443 plasma concentration versus time (actual) profiles from 
Day 29 to Day 456, for each patient, as well as the mean (±SD) plasma concentration versus 
time (scheduled) profiles for the applicable treatment group, will be presented graphically on 
linear and semilogarithmic scales. Additionally, ISIS 396443 plasma concentration versus 
time (actual) profiles (Day 1) from 0 to 8 hours for all patients, as well as the mean (±SD) 
plasma concentration versus time (scheduled) profiles (0 to 8 hours) for the applicable 
treatment group will be presented graphically on linear and semilogarithmic scales. 
Additional plasma concentration versus time (actual) profiles, for all patients and for 
individual patients may also be generated, including but not necessarily limited to Day 1, 0 to 
24 hours; Day 85, 0 to 4 hours; and comparisons between Day 1 and Day 85, 0 to 8 hours.  
Samples may be excluded from the mean plots if there are large deviations between scheduled 
and actual sampling times, or large deviations between actual dose and nominal dose.  
7.2.2 
Plasma Pharmacokinetic Parameters 
Non-compartmental pharmacokinetic analysis of ISIS 396443 will be carried out on each 
individual subject data set using Phoenix WinNonlin version 6.0 or higher (Pharsight 
Corporation, Mountain View, CA).  Plasma pharmacokinetic parameters in each patient 
(when applicable) will be determined.  For calculation of PK parameters, all BLQ values will 


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be set to zero.  The following plasma PK parameters will be calculated (when applicable) and 
based on actual sampling times:  
• Cmax:  the maximum observed drug concentration in plasma, and  
• Tmax:  the time at which Cmax occurs.  
The following PK parameters may be calculated using actual sampling times where 
appropriate data exists at the discretion of the pharmacokinetic scientist:  
• AUC0-24h:  areas under the plasma concentration-time curve from zero time (pre-dose) 
to 24 hours after the IT administration will be calculated using the linear trapezoidal 
rule,  
• AUC0-8h:  areas under the plasma concentration-time curve from zero time (pre-dose) 
to 8 hours after the IT administration will be calculated using the linear trapezoidal 
rule, and  
Plasma pharmacokinetic parameters (if applicable) will be summarized using descriptive 
statistics (n, mean, SD, %CV, geometric mean, geometric %CV, median, minimum, and 
maximum) by treatment group, and day.   
Additional plasma pharmacokinetic parameters may be calculated (if applicable) at the 
discretion of the pharmacokineticist.  
Exposure-response relationships between selected pharmacodynamic (included but not 
limited to change in HFMSE) and pharmacokinetic measures (including but not limited to 
CSF concentrations, plasma AUC0-8hr, Cmax, and plasma trough concentrations) may also be 
explored (including with and without stratification by antibody status), where appropriate. 
 
8 
Immunogenicity data 
Immunogenicity (IM) testing (anti-ISIS 396443 antibody positivity), using designated plasma 
samples collected from each study subject, is planned to be conducted and reported.  
Immunogenicity plasma samples are to be collected pre-dosing on Days 1, 29, 85, and 274, 
and on Day 169 and 456.  Plasma samples collected at other time points for ISIS 396443 
concentration determinations may also be evaluated for IM testing if of further interest and 
deemed warranted by the pharmacokinetic scientist.  An individual sample result will be 
designated ‘antibody positive’ based on both positive screening and confirmation assay results 
(i.e., confirmed positive result), and otherwise will be deemed ‘antibody negative’.  A study 
subject will be given ‘antibody positive’ status if they have at least one confirmed positive 
sample result at any time during the treatment or post-treatment evaluation periods.  A study 
subject will be given ‘antibody negative’ status if all evaluated IM sample results are antibody 
negative and they have at least one evaluable IM result from Day 85 or later during the 
treatment and post-treatment evaluation periods.  Otherwise, a study subject will be given 
‘antibody inconclusive’ status.   
The IM incidence and IM incidence rate at each evaluated study time point, and for the 
overall treatment and post-treatment evaluation period, will be determined and appropriately 


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summarized, by treatment, as the number of and percentage of evaluated subjects with 
antibody negative, antibody positive, and antibody inconclusive status.  In addition, in 
antibody positive study subjects, antibody titers of any antibody positive samples will be 
reported (listed) and also appropriately summarized across subjects and by treatment (e.g., at 
each evaluated time point, or by observed peak titer values, etc.) at the discretion of the 
designated study pharmacokineticist and/or statistician.   
Antibody positivity in anti-ISIS 396443 antibody-positive subjects will also be designated 
(when possible) as being either ‘persistent’ or ‘transient’, but only for those subjects in which 
at least one confirmed antibody positive sample result is followed (>100 days later) by at least 
one additional IM sample assessment (which can be either a confirmed positive or negative 
result(s)).  Those study patients meeting the above criteria and with at least 2 confirmed 
positive IM results occurring greater than 100 days apart (~5 immunoglobulin half-lives) will 
be considered to have a ‘persistent’ antibody response.  All other subjects meeting the above 
criteria will be considered to have a ‘transient’ antibody response.  Those remaining anti-ISIS 
396443 antibody-positive subjects who do not meet the above criteria will not be classified as 
either ‘persistent’ or ‘transient’, and thus will be given the designation ‘ND’ (not 
determinable) for persistent/transient IM status.  
When and where warranted, PK (e.g., elevated plasma trough level) and selected safety and 
efficacy (e.g., HFMSE) results may be further summarized (stratified) by antibody status 
(antibody negative versus positive subjects) and treatment. In previous clinical trials, only 
minimal immunogenicity samples have confirmed positive for anti-ISIS 396443 antibodies, 
therefore, if no, or minimal, patients are designated ‘antibody positive’ stratification by 
antibody status will not be summarized.  
9 
Sample size justification 
 
The sample size for this study was estimated based on limited available natural history data 
for the target population and data from studies ISIS 396443-CS1 and ISIS 396443-CS2.  
Seventy patients in the treated group and 35 patients in the control group will give at least 
90% power to detect a 3-point difference between control and treated groups in the change 
from baseline HFMSE with a standard deviation of 4.4, using a two-sided test with an alpha 
level of 0.05.  117 patients enrolled will ensure that a small dropout rate will not affect the 
power of the primary efficacy analysis. 
 
 
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