An Open-Label, Multinational, Phase 1/2 Study of the Safety and Dose Escalation of SHP648, an Adeno-Associated Virus Serotype 8 (AAV8) Vector Expressing FIX Padua in Hemophilia B Subjects
Phase: PHASE1
Conditions: Hemophilia B
Sponsor: Baxalta now part of Shire

This document contains confidential and proprietary information of Shire and is disclosed pursuant to confidentiality 
and non-disclosure obligations. This information should be used solely for the purposes for which it was provided 
and should not be copied, shared with, or disclosed to any third party without the express written consent of Shire.
PROTOCOL: SHP648-101
TITLE:
An Open-Label, Multinational, Phase 1/2 Study of 
the Safety and Dose Escalation of SHP648, an 
Adeno-Associated Virus Serotype 8 (AAV8) Vector 
Expressing FIX Padua in Hemophilia B Subjects
SHORT TITLE:
A Phase 1/2 study of SHP648, an Adeno-Associated 
Viral Vector for Gene Transfer in Hemophilia B Subjects
STUDY PHASE:
Phase 1/2 
ACRONYM:
SHP648-101
DRUG:
SHP648i (AAV8.ss-3xCRM8-TTR-FIX_R338Lopt)
IND NUMBER:
19233
EUDRACT NUMBER:
2018-004024-11
OTHER NUMBER:
Not Applicable
SPONSOR:
Baxalta US Inc.*
300 Shire Way, Lexington, MA 02421 
AND 
Baxalta Innovations GmbH*
Industriestrasse 67, A-1221 Vienna 
* Baxalta is now part of Shire.
Shire is now part of Takeda
PRINCIPAL/COORDINATING
INVESTIGATOR:
TBD 
PROTOCOL HISTORY:
Amendment 1.0, 21 FEB 2020
Replaces: Original Protocol, 13 May 2019
                                                
i Also known as TAK748
For non-commercial use only

Shire
CONFIDENTIAL
Page 2
SHP648
Clinical Study Protocol: SHP648-101
21 FEB 2020
PROTOCOL SIGNATURE PAGE
Sponsor’s (Shire) Approval
Signature:
Date:
, MD
Investigator’s Acknowledgement
I have read this protocol for Study SHP648-101.
Title: An Open-Label, Multinational, Phase 1/2 Study of the Safety and Dose Escalation of 
SHP648, an Adeno-Associated Virus Serotype 8 (AAV8) Vector Expressing FIX Padua in 
Hemophilia B Subjects
I have fully discussed the objective(s) of this study and the contents of this protocol with the 
sponsor’s representative.
I understand that the information in this protocol is confidential and should not be disclosed, 
other than to those directly involved in the execution or the scientific/ethical review of the study, 
without written authorization from the sponsor. It is, however, permissible to provide the 
information contained herein to a subject in order to obtain their consent to participate.
I agree to conduct this study according to this protocol and to comply with its requirements, 
subject to ethical and safety considerations and guidelines, and to conduct the study in 
accordance with International Council for Harmonisation of Technical Requirements for 
Registration of Pharmaceuticals for Human Use guidelines on Good Clinical Practice and with 
the applicable regulatory requirements.
I understand that failure to comply with the requirements of the protocol may lead to the 
termination of my participation as an investigator for this study.
I understand that the sponsor may decide to suspend or prematurely terminate the study at any 
time for whatever reason; such a decision will be communicated to me in writing. Conversely, 
should I decide to withdraw from execution of the study I will communicate my intention 
immediately in writing to the sponsor.
Investigator Name and Address:
(please hand print or type)
Signature:
Date:
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Shire
CONFIDENTIAL
Page 3
SHP648
Clinical Study Protocol: SHP648-101
21 FEB 2020
SUMMARY OF CHANGES FROM PREVIOUS PROTOCOL VERSION
Protocol SHP648-101: Amendment 1, 21 FEB 2020
Replaces: Protocol SHP648-101: Original Protocol: 13 May 2019
Summary of Changes Since the Last Version of the Approved Protocol
Amendment Number
1.0
Amendment Date
21 FEB 2020
Global
Protocol Amendment Summary and Rationale:
Changes made in Protocol SHP648-101 Amendment 1 address the need for a higher number of subjects to be 
screened, for extension to a new region and introduction of a 6-week observational period between dosing of the 
first and the second subject of each cohort to comply with requests from the US Food and Drug Administration 
(FDA) and several Regulatory Agencies un Europe. 
Description of Each Change
Rationale
Section(s) Affected by Change
Minor grammatical and/or 
administrative changes and rewording 
for better readability have been made.
To improve the readability 
and/or clarity of the protocol
Throughout the document
Updated name of the Sponsor 
Signatory 
To be consistent with 
organizational changes 
Protocol Signature Page
Added IND number
To be consistent across study 
documentation
Protocol Cover Page
Updated study contact information
To be consistent with 
organizational changes 
Emergency Contact Information
Increased planned number of subjects 
to be screened to 60 subjects
To address the need for a higher 
number of subjects to be 
screened due to a high rate of 
screen failure
Synopsis: Subjects planned for 
screening
and throughout the protocol
Increased planned number of sites to 
be initiated to 30 sites
To address the need for a higher 
number of sites to be included
Synopsis: Site(s) and Region(s)
and throughout the protocol
Included the United States as one of 
the participating regions
To extend the study to a new 
region
Synopsis: Site(s) and Region(s)
Section 4.5
Changed the study period from 
2019 – 2023 to 2019 - 2024
To be consistent across study 
documentation
Synopsis: Study period (planned)
Updated the Study Rationale
Per a request from the German 
Regulatory Agency, PEI
Synopsis: Study Rationale
Section 2.3.
Added description of the safety follow 
up duration.
To improve clarity
Synopsis: Methodology
Section 4.4
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Shire
CONFIDENTIAL
Page 4
SHP648
Clinical Study Protocol: SHP648-101
21 FEB 2020
Summary of Changes Since the Last Version of the Approved Protocol
Amendment Number
1.0
Amendment Date
21 FEB 2020
Global
Protocol Amendment Summary and Rationale:
Changes made in Protocol SHP648-101 Amendment 1 address the need for a higher number of subjects to be 
screened, for extension to a new region and introduction of a 6-week observational period between dosing of the 
first and the second subject of each cohort to comply with requests from the US Food and Drug Administration 
(FDA) and several Regulatory Agencies un Europe. 
Description of Each Change
Rationale
Section(s) Affected by Change
Replaced internal Dose Escalation 
Committee by external Data 
Monitoring Committee
As per a request from the Central 
Ethics Committee of the Medical 
University in Vienna, Austria 
(Ethikkommision Medizinische 
Universität Wien)
Synopsis: Dose Escalation 
Section 6.2.1.1. and
throughout the document
Included an observational period of at 
least 6 weeks between the first three 
subjects in the first Cohort and first 
and second subjects in Cohort 2 and 
Cohort 3
As per a request from the US 
FDA and the German Regulatory 
Agency, PEI
Synopsis: Dose Escalation
Section 6.2.1.1
Clarified the schedule of data review 
by the DMC in case of dose cohort 
extension
To exclude any ambiguity and 
for consistency with the DMC 
Charter
Synopsis: Dose Escalation
Section 6.2.1.1
Updated options for DMC 
recommendation
To exclude any ambiguity for 
Dose Extension/Escalation
Synopsis: Dose Escalation
Section 6.2.1.1
Section 6.2.2
Updated duration of the observation 
period for the DMC decision
For improved clarity and to 
exclude any ambiguity regarding 
the decision criteria for Dose 
Extension/Escalation
Synopsis: Dose Escalation
Section 6.2.1.1
Revised Study Stopping Criterion #1 
for Enrollment and Dose Escalation 
For improved clarity on the risk 
of thrombosis
Synopsis: Stopping Criteria for 
Enrollment and Dose Escalation
Section 6.2.1.2
Added Study Stopping Criterion #2 for 
Enrollment and Dose Escalation to 
indicate that enrollment and escalation 
to next dose cohort must be paused if 
at week 14 a loss of endogenous FIX 
activity level >75% of the highest FIX 
activity level measured after SHP648 
administration occurs despite 
corticosteroid prophylaxis.
To exclude any ambiguity and 
clarify that a loss in gene 
expression impacting an efficacy 
endpoint is a criterion to pause 
enrollment/dose escalation
Synopsis: Stopping Criteria for 
Enrollment and Dose Escalation
Section 6.2.1.2
Study Stopping Criterion #9: Added to 
pause enrollment of additional subjects 
if any drug-related event occurs in 
SHP648 treated subjects that is 
deemed to pose an unacceptable risk to 
subjects by the investigator or medical 
monitor after further evaluation.
To prevent further dosing of the 
subjects until drug-related event 
deemed to pose unacceptable 
risk is fully evaluated by the 
DMC.
Synopsis: Stopping Criteria for 
Enrollment and Dose Escalation
Section 6.2.1.2
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Shire
CONFIDENTIAL
Page 5
SHP648
Clinical Study Protocol: SHP648-101
21 FEB 2020
Summary of Changes Since the Last Version of the Approved Protocol
Amendment Number
1.0
Amendment Date
21 FEB 2020
Global
Protocol Amendment Summary and Rationale:
Changes made in Protocol SHP648-101 Amendment 1 address the need for a higher number of subjects to be 
screened, for extension to a new region and introduction of a 6-week observational period between dosing of the 
first and the second subject of each cohort to comply with requests from the US Food and Drug Administration 
(FDA) and several Regulatory Agencies un Europe. 
Description of Each Change
Rationale
Section(s) Affected by Change
Specified the possibility for subjects to 
resume FIX prophylaxis regimen after 
week 14 when gene therapy treatment 
is insufficient to control or prevent 
spontaneous bleeds 
Per a request from the German 
Regulatory Agency, PEI.
Synopsis: FIX Utilization 
Section 6.6.3.1
Added section in Glucocorticoid Use 
in the Study:
“Notwithstanding the protocol 
language requiring that two subjects 
must first be eligible for reactive 
corticosteroid treatment, the Sponsor’s 
Medical Monitor with the concurrence 
of the Investigator, may permit the use 
of prophylactic steroids in any subject 
based on all available scientific 
evidence at the time of subject 
enrollment. Such evidence may include 
the clinical outcomes of others AAV-
based gene therapy studies as well as
nonclinical relevant data that may 
emerge. The possible use of 
corticosteroid will be communicated to 
potential subjects as part of the ICF 
process”
To exclude any ambiguity 
regarding the decision criteria to 
administer glucocorticoids 
during the study
Synopsis: Glucocorticoid Use in the 
Study
Section 6.6.3.2
Revised the criteria for employing 
glucocorticoid treatment to also list the 
criteria for implementing prophylactic 
glucocorticoid treatment
For improved clarity and to 
exclude any ambiguity regarding 
the decision criteria to administer 
glucocorticoids during the study
Synopsis: Glucocorticoid 
Treatment
Section 2.4.1 
Section 6.6.3.2
Revised the guidance for prednisolone 
dosing regimen to decrease the 
corticosteroid regimen duration
To closer align with current 
guidelines for the management 
of autoimmune hepatitis
Synopsis: Glucocorticoid 
Treatment 
Section 6.6.3.2, Table 4
Revised Inclusion Criterion #3
Per a request from the French 
Regulatory Agency ANSM and 
the German Regulatory 
Authority, PEI 
Synopsis: Inclusion Criteria
Section 5.1 
Revised Inclusion Criterion #4 
For improved clarity and to 
exclude any ambiguity
Synopsis: Inclusion Criteria 
Section 5.1 
Section 5.4.1
Appendix 4
For non-commercial use only

Shire
CONFIDENTIAL
Page 6
SHP648
Clinical Study Protocol: SHP648-101
21 FEB 2020
Summary of Changes Since the Last Version of the Approved Protocol
Amendment Number
1.0
Amendment Date
21 FEB 2020
Global
Protocol Amendment Summary and Rationale:
Changes made in Protocol SHP648-101 Amendment 1 address the need for a higher number of subjects to be 
screened, for extension to a new region and introduction of a 6-week observational period between dosing of the 
first and the second subject of each cohort to comply with requests from the US Food and Drug Administration 
(FDA) and several Regulatory Agencies un Europe. 
Description of Each Change
Rationale
Section(s) Affected by Change
Rearranged the order of the exclusions 
criteria 
For improved readability
Synopsis: Exclusion Criteria
Section 5.2
Revised Exclusion Criterion #4 
Added: “Subjects whose laboratory 
assessments are ≤1:10 may be re-
tested within the same Screening 
window and, if eligibility criterion is 
met on retest, may be enrolled after 
confirmation by the Sponsor’s Medical
Monitor.”
For improved clarity and to 
exclude any ambiguity
Synopsis: Exclusion Criteria 
Section 5.2
Revised Exclusion Criteria and 
numeration for Criteria #6, #7 #8, #9, 
#24, #30 (#8 became #7, #24 became 
#28, #26 became #30)
For improved clarity
Synopsis: Exclusion Criteria
Section 5.2
Revised Exclusion Criterion #15 to 
add preexisting diagnoses indicative of 
significant underlying liver disease, 
and tests to determine liver fibrosis 
status
For improved clarity and to 
exclude any ambiguity
Synopsis: Exclusion Criteria
Section 5.2
Divided the information in originally 
Exclusion Criterion #15 into Exclusion 
Criteria #15 to #18.
For improved readability
Synopsis: Exclusion Criteria
Section 5.2
Revised the threshold value provided 
for albumin level as a marker of liver 
disease in Exclusion Criterion #17 from 
“Albumin ≤ 3.5 g/dL to “. “Albumin 
below the central laboratory’s lower 
limit of normal” and albumin results 
are combined with FibroTest /
FibroSURE with a result > 0.48 
To increase specificity of the tests
Synopsis: Exclusion Criteria
Section 5.2
Added “Patients who do not consent to 
participate in SHP648 Extension Study
will be followed according to local 
safety regulations.”
For improved clarity on maximum 
duration of subject participation in 
Study SHP648-101 and planned 
safety follow-up.
Synopsis: Maximum Duration of 
Subject Participation 
Section 4.4
Revised the primary endpoint to not 
only cover incidence but also severity 
of AEs
Per request from German 
Regulatory Agency (PEI)
Synopsis: Primary Endpoint
Section 3.2., Table 3 
Section 9.5.1
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Shire
CONFIDENTIAL
Page 7
SHP648
Clinical Study Protocol: SHP648-101
21 FEB 2020
Summary of Changes Since the Last Version of the Approved Protocol
Amendment Number
1.0
Amendment Date
21 FEB 2020
Global
Protocol Amendment Summary and Rationale:
Changes made in Protocol SHP648-101 Amendment 1 address the need for a higher number of subjects to be 
screened, for extension to a new region and introduction of a 6-week observational period between dosing of the 
first and the second subject of each cohort to comply with requests from the US Food and Drug Administration 
(FDA) and several Regulatory Agencies un Europe. 
Description of Each Change
Rationale
Section(s) Affected by Change
Transferred all information regarding 
sample collection schedules from 
Table 1 to Table 2 
To be consistent with the current 
template for phase 2-4 clinical 
study protocols 
Section 1.3, Table 1 and Table 2
Added the sample blood collection 
schedule for transcriptome analysis 
and metabolomics, as well as related 
footnote “m”; adjusted footnote “c” 
accordingly
For consistency with assessment 
schedules and descriptions in 
Sections 8.1 and 8.2. 
Section 1.3.2, Table 2
Rearranged order of laboratory 
assessments to group similar 
parameters 
To improve the readability and 
clarity of the protocol
Section 1.3.2, Table 2
Shifted blood draw between week 4 
and week 14 for transcriptome and 
metabolomics from the clinic to the lab 
visit
To align with the back-up 
sampling schedule and to 
decrease the blood volume 
demand during the clinic visits
Section 1.3.2, Table 2
Section 8.1
Section 8.2
Specified time of Liver Function 
Testing
For clarity and consistency in 
assessment schedules
Section 1.3.2, Table 2
Added exome testing to the list of 
clinical laboratory assessments
For consistency with assessment 
schedules and descriptions in 
Sections 8.1 and 8.2. and 
Appendix 5
Section 1.3.2, Table 2
Added that back-up samples are to be  
collected also pre-infusion
To align with metabolomics 
schedule
Section 1.3.2, Table 2
Section 8.1.2
Added footnote “s”
To specify that whole exome 
sequencing, transcriptomics and 
metabolomics is optional
Section 1.3.2, Table 2
Updated current information on 
Hemophilia B
To provide most current 
information
Section 2
Inserted additional literature references
To accurately report literature 
sources
Section 2.3
Section 11
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Shire
CONFIDENTIAL
Page 8
SHP648
Clinical Study Protocol: SHP648-101
21 FEB 2020
Summary of Changes Since the Last Version of the Approved Protocol
Amendment Number
1.0
Amendment Date
21 FEB 2020
Global
Protocol Amendment Summary and Rationale:
Changes made in Protocol SHP648-101 Amendment 1 address the need for a higher number of subjects to be 
screened, for extension to a new region and introduction of a 6-week observational period between dosing of the 
first and the second subject of each cohort to comply with requests from the US Food and Drug Administration 
(FDA) and several Regulatory Agencies un Europe. 
Description of Each Change
Rationale
Section(s) Affected by Change
Inserted a cross-reference to 
Section 5.4.1
For improved readability of the 
document
Section 2.4.
Revised language to further clarify the 
benefit/risk balance 
Per a request from the German 
Regulatory Agency, PEI
Section 2.4.
Clarified the use of 
azathioprine/prednisone in subjects 
that do not tolerate corticosteroid 
therapy
For improved clarity and to 
exclude any ambiguity regarding 
the eligibility for combination 
treatment with azathioprine /
prednisolone
Section 2.4.1
Section 6.6.3.2
Deleted the short summary of the 
stopping/pausing criteria and kept a 
crosslink reference to the full list of 
criteria
To exclude any ambiguity
Section 2.4.1 
Added clarification regarding the use 
of immunomodulating drugs other than 
corticosteroids during the study period
Per a request from the German 
Regulatory Agency, PEI.
Section 6.6.3
Further clarified the language on the 
medications not permitted 30 days 
prior to therapy
Per a request from the German 
Regulatory Agency, PEI.
Section 6.6.4
Revised the reasons for 
discontinuation
Per a request from the German 
Regulatory Agency, PEI.
Section 7.2.
Revised wording regarding subject 
withdrawal. 
Per a request from the German 
Regulatory Agency, PEI.
Section 7.3.
Specified that transcriptome and 
metabolomics analyses may be 
performed if needed and if patient has 
provided informed consent
For improved clarity and to 
exclude any ambiguity
Section 8.1
Clarified the composition of the 
coagulation panel and the additional 
coagulation tests to be performed
For improved clarity and 
consistency with information in 
Table 2
Section 8.2.3.4.1
Added specifics of FibroSURE test
In alignment with Table 2, 
footnote “l”
Section 8.2.3.4.1
Clarified the process for 
communication of F9 gene mutation 
and HLA genotyping results
To avoid any ambiguity
Section 8.2.3.4.3
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Shire
CONFIDENTIAL
Page 9
SHP648
Clinical Study Protocol: SHP648-101
21 FEB 2020
Summary of Changes Since the Last Version of the Approved Protocol
Amendment Number
1.0
Amendment Date
21 FEB 2020
Global
Protocol Amendment Summary and Rationale:
Changes made in Protocol SHP648-101 Amendment 1 address the need for a higher number of subjects to be 
screened, for extension to a new region and introduction of a 6-week observational period between dosing of the 
first and the second subject of each cohort to comply with requests from the US Food and Drug Administration 
(FDA) and several Regulatory Agencies un Europe. 
Description of Each Change
Rationale
Section(s) Affected by Change
Specified that the genetic tests listed are 
mandatory and that voluntary genetic 
tests are listed in Section 8.2.4.3; added 
specifics of HLA test.
In alignment with Table 2, 
footnote “k”
Section 8.2.3.4.3
Streamlined the description of 
immunogenicity assays to be used in 
the study.
To provide only the information 
in scope for this document  
Section 8.2.3.4.4
Moved Additional Sample Collection 
from Section 8.2.3.4.1 to 
Section 8.2.3.4.6
To improve the readability and 
clarity of the protocol
Section 8.2.3.4.6
Changed duration of sample storage in
biorepositories to 5 years.
For consistency within protocol
Section 8.2.4.3
Appendix 5
Consolidated information of blood 
drawing and storage, previously in 
Section 8.2.3.4 and Section 8.2.3.5, in 
Section 8.2.5
To improve the readability and 
clarity of the protocol
Section 8.2.5
Moved paragraph describing patient 
diary from Section 8.2.4.4 to 
Section 8.2.6
To improve the readability and 
clarity of the protocol
Section 8.2.6
Inserted additional language to specify 
the source data from patient diaries 
that may be modified. 
For improved clarity and to 
exclude any ambiguity
Appendix 1.4
Moved paragraph describing treatment 
for subjects requiring urgent or 
emergency surgery after SHP648 
administration from Section 7.3 to 
Appendix 3.1
To improve the readability and 
clarity of the protocol
Appendix 3.1
Inserted additional language on 
follow-up and documentation of SAEs 
deemed related to the investigational 
drug
To fulfill a request by the safety 
board.
Appendix 3.5
Harmonized the general study stopping 
rules due to safety concerns with the 
pausing/stopping criteria specific to 
Study 201501
For consistency with the study 
design
Appendix 3.11
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CONFIDENTIAL
Page 10
SHP648
Clinical Study Protocol: SHP648-101
21 FEB 2020
Summary of Changes Since the Last Version of the Approved Protocol
Amendment Number
1.0
Amendment Date
21 FEB 2020
Global
Protocol Amendment Summary and Rationale:
Changes made in Protocol SHP648-101 Amendment 1 address the need for a higher number of subjects to be 
screened, for extension to a new region and introduction of a 6-week observational period between dosing of the 
first and the second subject of each cohort to comply with requests from the US Food and Drug Administration 
(FDA) and several Regulatory Agencies un Europe. 
Description of Each Change
Rationale
Section(s) Affected by Change
Revised guidance text
For consistency with Section 5.1 
and Section 5.4.1
Appendix 4
Updated Protocol History Table
To comply with the current 
template for phase 2-4 clinical 
study protocols and provide most 
current information
Appendix 8
See Appendix 8 for protocol history, including all amendments.
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CONFIDENTIAL
Page 11
SHP648
Clinical Study Protocol: SHP648-101
21 FEB 2020
EMERGENCY CONTACT INFORMATION
In the event of a serious adverse event (SAE), the investigator must fax or e-mail the “Shire 
Clinical Study Adverse Event Form for Serious Adverse Events (SAEs) and Non-serious 
Adverse Events (AEs) as Required by Protocol” within 24 hours to the Shire Global Drug Safety 
Department. The fax number and e-mail address are provided on the form (sent under separate 
cover). A copy of this form must also be sent to the Sponsor’s Medical Monitor using the details 
below.
Fax: 
email:
For protocol- or safety-related questions or concerns during normal business hours
(8:00 am-5:00 pm, Eastern Time), the investigator must contact the medical monitor:
 MD, PhD
 
e-mail: 
Mobile: 
For protocol- or safety-related questions or concerns outside of normal business hours, the 
investigator must contact:
Fax: 
email:
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CONFIDENTIAL
Page 12
SHP648
Clinical Study Protocol: SHP648-101
21 FEB 2020
PRODUCT QUALITY COMPLAINTS
Investigators are required to report investigational product quality complaints or non-medical 
complaints to Shire within 24 hours. If requested, defective product(s) will be returned to the 
sponsor for inspection and analysis.
A product quality complaint includes any instances where there is an allegation or report relating 
to Shire licensed or investigational products, received in writing, electronically, or orally, which 
indicates an impact to a product’s strength, identity, safety, purity, or quality, or which suggests 
that a product did not meet the criteria defined in the regulatory applications, licenses, or 
marketing authorizations for the product. Examples of investigational product quality complaints 
include, but are not limited to, the following:
Unit issues

Capsule fill empty or overage

Bottle/vial fill shortage or overage

Capsule/tablet damaged/broken

Syringe/vial cracked/broken

Syringe leakage

Missing components

Product discoloration

Device malfunction
Labeling

Label missing

Leaflet or Instructions For Use (IFU) 
missing 

Label illegible

Incomplete, inaccurate, or 
misleading labeling

Lot number or serial number 
missing
Packaging

Damaged packaging (e.g., secondary, 
primary, bag/pouch)

Tampered seals

Inadequate or faulty closure

Missing components within package
Foreign 
material

Contaminated product

Particulate in bottle/vial

Particulate in packaging
Please report the product quality complaint using the “Product Complaint Data Collection Form” 
via the email address:
Telephone number (provided for reference if needed):
Shire, Lexington, MA (USA)
For instructions on reporting AEs related to product complaints, see Appendix 3.4.
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CONFIDENTIAL
Page 13
SHP648
Clinical Study Protocol: SHP648-101
21 FEB 2020
TABLE OF CONTENTS
PROTOCOL SIGNATURE PAGE............................................................................................. 2
Sponsor’s (Shire) Approval...................................................................................................... 2
Investigator’s Acknowledgement ............................................................................................ 2
SUMMARY OF CHANGES FROM PREVIOUS PROTOCOL VERSION.......................... 3
EMERGENCY CONTACT INFORMATION ........................................................................ 11
PRODUCT QUALITY COMPLAINTS................................................................................... 12
TABLE OF CONTENTS ........................................................................................................... 13
1. PROTOCOL SUMMARY ..................................................................................................... 18
1.1 Synopsis.............................................................................................................................. 18
1.2 Schema ............................................................................................................................... 27
1.3 Schedules of Study Activities and Assessments.............................................................. 28
1.3.1 Study Activities .......................................................................................................... 28
1.3.2 Clinical Laboratory Assessments ............................................................................. 31
2. INTRODUCTION................................................................................................................... 36
2.1 Indication and Current Treatment Options................................................................... 37
2.1.1 Approved Therapies for Hemophilia B ................................................................... 37
2.2 Product Background and Clinical Information............................................................. 37
2.3 Study Rationale................................................................................................................. 38
2.4 Benefit/Risk Assessment of FIX Gene Therapy............................................................. 39
2.4.1 Evaluation of Anticipated Benefits and Risks of Using Prednisolone for 
Management of Presumptive Vector-Related Hepatitis ........................................ 42
2.5 Compliance Statement...................................................................................................... 44
3. OBJECTIVES AND ENDPOINTS ....................................................................................... 45
3.1 Study Objectives ............................................................................................................... 45
3.1.1 Primary Objective ..................................................................................................... 45
3.1.2 Secondary Objectives ................................................................................................ 45
3.1.3 Exploratory Objectives ............................................................................................. 45
3.2 Study Endpoints................................................................................................................ 46
4. STUDY DESIGN..................................................................................................................... 47
4.1 Overall Design................................................................................................................... 47
4.2 Scientific Rationale for Study Design.............................................................................. 47
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SHP648
Clinical Study Protocol: SHP648-101
21 FEB 2020
4.3 Justification for Dose........................................................................................................ 47
4.4 Duration of Subject Participation and Study Completion Definition.......................... 48
4.5 Sites and Regions .............................................................................................................. 48
5. STUDY POPULATION ......................................................................................................... 49
5.1 Inclusion Criteria.............................................................................................................. 49
5.2 Exclusion Criteria............................................................................................................. 49
5.3 Restrictions........................................................................................................................ 52
5.4 Reproductive Potential..................................................................................................... 52
5.4.1 Male Contraception................................................................................................... 52
6. STUDY INTERVENTION..................................................................................................... 53
6.1 Investigational Product .................................................................................................... 53
6.1.1 Identity of Investigational Product .......................................................................... 53
6.1.2 Blinding the Treatment Assignment ........................................................................ 53
6.2 Administration of Investigational Product..................................................................... 53
6.2.1 Dosing.......................................................................................................................... 53
6.2.1.1 Dose Escalation Plan........................................................................................... 54
6.2.1.2 Stopping Criteria for Enrollment and Dose Escalation.................................. 55
6.2.1.3 Data Monitoring Committee (DMC) ................................................................ 56
6.2.2 Dose Modification ...................................................................................................... 56
6.3 Labeling, Packaging, Storage, and Handling of Investigational Product.................... 57
6.3.1 Labeling ...................................................................................................................... 57
6.3.2 Packaging.................................................................................................................... 57
6.3.3 Storage ........................................................................................................................ 57
6.3.4 Special Handling........................................................................................................ 58
6.4 Drug Accountability ......................................................................................................... 58
6.5 Subject Compliance.......................................................................................................... 59
6.6 Prior and Concomitant Therapy..................................................................................... 59
6.6.1 Prior Treatment......................................................................................................... 59
6.6.2 Concomitant Treatment............................................................................................ 59
6.6.3 Permitted Treatment................................................................................................. 60
6.6.3.1 Use of Exogenous FIX throughout the Study................................................... 60
6.6.3.2 Glucocorticoid Use in the Study........................................................................ 61
6.6.4 Prohibited Treatment................................................................................................ 64
7. DISCONTINUATION OF STUDY INTERVENTION AND SUBJECT 
DISCONTINUATION/WITHDRAWAL............................................................................. 65
7.1 Discontinuation of Study Participation........................................................................... 65
7.2 Reasons for Discontinuation ............................................................................................ 65
7.3 Withdrawal from the Study............................................................................................. 65
7.4 Subjects “Lost to Follow-up” Prior to the Last Scheduled Visit.................................. 66
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8. STUDY ASSESSMENTS AND PROCEDURES................................................................. 67
8.1 Study Periods..................................................................................................................... 67
8.1.1 Screening Visit ........................................................................................................... 67
8.1.2 Treatment Period....................................................................................................... 69
8.1.2.1 Day 0 .................................................................................................................... 69
8.1.3 Follow-Up Period....................................................................................................... 70
8.1.3.1 Day 1 .................................................................................................................... 70
8.1.3.2 Week 1 to Week 3 ............................................................................................... 71
8.1.3.3 Week 4 to Week 14 ............................................................................................. 72
8.1.3.4 Week 15................................................................................................................ 73
8.1.3.5 Month 4 to Month 6 and Month 9..................................................................... 74
8.1.3.6 Study Completion Visit (Month 12).................................................................. 75
8.1.3.7 Unscheduled Visit ............................................................................................... 76
8.1.3.8 Early Study Termination Visit .......................................................................... 77
8.1.4 Additional Care of Subjects after the Study ........................................................... 78
8.2 Study Assessments ............................................................................................................ 78
8.2.1 Demographic and Other Baseline Characteristics ................................................. 78
8.2.1.1 Height and Weight.............................................................................................. 78
8.2.1.2 Medical and Medication History....................................................................... 78
8.2.2 Efficacy ....................................................................................................................... 79
8.2.2.1 Circulating Plasma FIX Activity and FIX Antigen Levels............................. 79
8.2.2.2 Number of Bleeding Episodes Post-SHP648 Infusion..................................... 79
8.2.2.3 Consumption of Exogenous FIX Compared to before Gene Transfer.......... 80
8.2.3 Safety........................................................................................................................... 80
8.2.3.1 Physical Examination......................................................................................... 80
8.2.3.2 Adverse Events.................................................................................................... 80
8.2.3.3 Vital Signs............................................................................................................ 81
8.2.3.4 Clinical Laboratory Tests .................................................................................. 81
8.2.3.5 Electrocardiogram.............................................................................................. 84
8.2.4 Other ........................................................................................................................... 85
8.2.4.2 Pharmacokinetics and Pharmacodynamics ..................................................... 85
8.2.4.3 Exploratory Assays............................................................................................. 85
8.2.4.5 Hemophilia Patient Experience with Gene Therapy Score ............................ 87
8.2.5 Volume of Blood to Be Drawn from Each Subject ................................................. 87
8.2.6 Subject Diary.............................................................................................................. 87
9. STATISTICAL CONSIDERATIONS .................................................................................. 89
9.1 Statistical Analysis Process .............................................................................................. 89
9.2 Data Monitoring Committee, Adaptive Design and Planned Interim Analysis.......... 89
9.3 Sample Size and Power Considerations.......................................................................... 89
9.4 Statistical Analysis Set(s).................................................................................................. 89
9.5 Methods of Analyses......................................................................................................... 90
9.5.1 Primary Endpoint...................................................................................................... 90
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9.5.2 Secondary Endpoints................................................................................................. 90
9.5.3 Exploratory Endpoints.............................................................................................. 91
9.6 Other Analyses .................................................................................................................. 91
10. SUPPORTING DOCUMENTATION AND OPERATIONAL CONSIDERATIONS .. 92
APPENDIX 1  REGULATORY, ETHICAL, AND STUDY OVERSIGHT 
CONSIDERATIONS........................................................................................................ 92
Appendix 1.1  Regulatory and Ethical Considerations ................................................... 92
Appendix 1.2  Sponsor’s Responsibilities ......................................................................... 92
Appendix 1.3  Investigator’s Responsibilities .................................................................. 93
Appendix 1.4  Data Management Considerations ........................................................... 96
Appendix 1.5  Ethical Considerations............................................................................... 97
APPENDIX 2  CLINICAL LABORATORY TESTS........................................................ 100
APPENDIX 3  ADVERSE EVENTS: DEFINITIONS AND PROCEDURES FOR 
RECORDING, EVALUATING, FOLLOW-UP, AND REPORTING...................... 101
Appendix 3.1  Adverse Event Definitions....................................................................... 101
Appendix 3.2  Collection of Adverse Events .................................................................. 105
Appendix 3.3  Assessment of Adverse Events ................................................................ 105
Appendix 3.4  Safety Reporting....................................................................................... 107
Appendix 3.5  Serious Adverse Event Collection Time Frame .................................... 107
Appendix 3.6  Serious Adverse Event Onset and Resolution Dates............................. 107
Appendix 3.7  Fatal Outcome .......................................................................................... 108
Appendix 3.8  Pregnancy ................................................................................................. 108
Appendix 3.9  Abuse, Misuse, Overdose and Medication Error.................................. 109
Appendix 3.10  Urgent Safety Measures......................................................................... 110
Appendix 3.11  Regulatory Agency, Institutional Review Board, Ethics Committee, 
Data Monitoring Committee and Site Reporting................................................. 110
APPENDIX 4  CONTRACEPTIVE GUIDANCE............................................................. 112
APPENDIX 5  GENETICS.................................................................................................. 113
APPENDIX 6  BLEED DEFINITIONS.............................................................................. 115
Appendix 6.1  Joint Bleeds............................................................................................... 115
Appendix 6.2  Muscle Bleeds ........................................................................................... 115
Appendix 6.3  Target Joints............................................................................................. 115
APPENDIX 7  ABBREVIATIONS ..................................................................................... 116
APPENDIX 8  PROTOCOL HISTORY ............................................................................ 119
11. REFERENCES.................................................................................................................... 120
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Tables
Table 1. Schedule of Activities..................................................................................................... 28
Table 2. Clinical Laboratory Assessments.................................................................................... 31
Table 3. Objectives and Endpoints ............................................................................................... 46
Table 4. Guidance for Prednisolone Dosing Regimen.................................................................. 63
Table 5. Common Excluded Treatments and Associated Washout Period .................................. 64
Table A1 Adverse Event Relationship Categorization
106
Figures
Figure 1. Study Schematic Diagram ............................................................................................. 27
Figure 2. Role of FIX in the Clotting Cascade ............................................................................. 36
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1. PROTOCOL SUMMARY
1.1 Synopsis
Protocol number: SHP648-101
Drug: SHP648 (AAV8.ss-3xCRM8-TTR-FIX_R338Lopt) 
Title of the study: An Open-Label, Multinational, Phase 1/2 Study of the Safety and Dose Escalation of SHP648, 
an Adeno-Associated Virus Serotype 8 (AAV8) Vector Expressing FIX Padua in Hemophilia B Subjects
Short title:
A Phase 1/2 study of SHP648, an Adeno-Associated Viral Vector for Gene Transfer in Hemophilia B Subjects
Study phase: Phase 1/2
Number of subjects (total and per treatment arm):
Subjects planned for screening: up to 60
Subjects planned for enrollment:  Up to 21 in total, with approximately 2-7 subjects per dose cohort and up to 
3 dose-cohorts
Investigator(s): Multicenter study
Site(s) and Region(s):
Up to 30 sites in the USA and several countries in and around Europe are planned. 
Study period (planned): 2019 – 2024
Clinical phase:
1/2
Objectives:
Primary:

Assess the safety of single, escalating, intravenous (IV) doses of SHP648.
Secondary:

Evaluate plasma FIX levels before and after SHP648 infusion and study the relationship between change in 
FIX activity and SHP648 dose.

Evaluate bleeding episodes post-SHP648 administration.

Assess humoral and cellular immune responses to FIX and the viral capsid (cp).

Determine the duration of SHP648 genomes present in bodily fluids.

Compare the consumption of exogenous FIX before and after gene transfer
Exploratory:
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Rationale:
SHP648 is a single-stranded (ss) adeno-associated viral (AAV) vector designed to deliver a functional copy of the 
human coagulation factor 9 (F9) Padua gene to the liver and drive endogenous hepatocyte-specific expression of 
the FIX protein in hemophilia B patients. There are currently no approved gene therapy products for patients with 
hemophilia B, who solely rely on infusions of exogenous FIX for disease management. The rationale for this 
study is 1) to evaluate the expression of the high specific activity Padua FIX variant driven by the transthyretin 
promoter and, a novel liver-specific cis-regulatory module (CRM8) enhancer element; 2) to determine the safety 
of SHP648 and the dose required to achieve FIX activity levels between 30-50% of normal in subjects with 
severe and moderately severe hemophilia B.
Investigational product, dose, and mode of administration: 

SHP648 (AAV8.ss-3xCRM8-TTR-FIX_R338Lopt)

Up to 3 dose cohorts

Single peripheral IV administration
Methodology:
This is a first-in-man, open label, multicenter, dose escalation study evaluating safety and FIX expression in up to 
a total of 21 adult hemophilia B subjects.
Subjects who provide signed informed consent will undergo screening for study participation which includes a 
physical exam, electrocardiogram (ECG), and laboratory assessments for baseline measurements and evaluation 
of pre-existing immunity to AAV8. Those meeting eligibility criteria will be sequentially assigned to a dose 
cohort. Each subject will be administered a single IV infusion of SHP648 on Day 0, and then followed for 
12 months in the primary study (see Figure 1, Study Schematic Diagram). Subjects will be asked to be followed 
up for at least 4 more years in a separate safety extension study to monitor long-term effects.
Dose Escalation:
Up to 3 doses will be evaluated in this study:

Cohort 1 dose:

4.0 x 1011 vector genome (vg)/kg body weight (BW)

Cohort 2 dose:

2-fold escalation of Cohort 1 dose:  8.0 x 1011 vg/kg BW
OR

3-fold escalation of Cohort 1 dose:  1.2 x 1012 vg/kg BW

Cohort 3 dose:

2-fold escalation of Cohort 2 dose 
-
1.6 x 1012 vg/kg BW (if cohort 2 dose was 8.0 x 1011 vg/kg BW) or 2.4 x 1012 vg/kg BW 
(if cohort 2 dose was 1.2 x 1012 vg/kg BW)
OR

3-fold escalation of Cohort 2 dose
-
2.4 x 1012 vg/kg BW (if cohort 2 dose was 8.0 x 1011 vg/kg BW) or 3.6 x 1012 vg/kg BW 
(if cohort 2 dose was 1.2 x 1012 vg/kg BW)
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Initially, one subject will be dosed in Cohort 1, followed by an observational period of at least 6 weeks. If no 
safety concern is observed in the first dosed subject, a second subject will be dosed. For each additional dose 
cohort, dosing of the second subject will be scheduled 6 weeks after dosing of the first subject at the earliest. 
If Cohort 1 is expanded, up to 7 subjects may be dosed in Cohort 1.
Decisions pertaining to cohort expansion, dose escalation, number of subjects to be dosed, as well as the exact 
dose for subsequent Cohort 2 and Cohort 3 will be made based on the recommendation provided by an external 
Data Monitoring Committee (DMC). The DMC will review data including the Week 14 visit of the second dosed 
subject in Cohort 1. The observation period for the DMC data cut in expanded Cohort 1 and for Cohorts 2 and 3 
may be adjusted to between 6 and 14 weeks based on Cohort 1 FIX expression peak data observed in the first two 
patients, as well as, other relevant study data and published literature.
After review of all safety and FIX activity data, the DMC will provide recommendations to pursue one of the 
following:
1.
Escalate to the next dosing cohort 
2.
Increase the number of subjects in the current dosing cohort 
3.
Cap enrollment at the current dosing cohort and complete the study
4.
Enroll additional subjects into a previous lower dose cohort in order to obtain additional safety 
information
5.
Enroll subjects into a modified dosing cohort that is intermediate between those into which subjects have 
been previously enrolled.
Stopping Criteria for Enrollment and Dose Escalation: 
Enrollment and escalation to next dose cohort will be paused until an independent DMC evaluates all available 
study data and makes a recommendation if any one of the following criteria are met:
1.
Achievement of vector-derived FIX activity level ≥ 150% in any subject at any time while on the study due 
to potential risk of thrombosis. The level of FIX activity is measured frequently throughout the study. Study 
enrollment will be paused based on the local laboratory results (Table 1 and Table 2) 
2.
First two subjects on corticosteroid prophylaxis experience, at week 14, a loss of endogenous FIX activity 
level >75% of the highest FIX activity level measured after SHP648 administration (based on one stage 
central laboratory). The level of FIX activity is assessed frequently throughout the study (Table 1 and 
Table 2).
3.
A value of 3 times the upper limit of normal (3 x ULN) or greater in ALT (alanine aminotransferase), AST 
(aspartate aminotransferase), or both in any subject after SHP648 administration that is not responsive after 
12 weeks of corticosteroid rescue treatment.
4.
A serious adverse event (SAE) that may be potentially related to SHP648 and which poses either an 
immediate risk to the subject’s health or is likely to adversely affect the subject’s health long term. This 
includes events classified as AEs qualifying for special notification (Brussels, 03/12/2009, ENTR/F/2/SF/dn 
D(2009) 35810; EMEA/CHMP/GTWP/60436/2007), if these are judged as potentially related to SHP648.
5.
The development in any subject of an inhibitor towards FIX (or FIX Padua) after having received SHP648. 
Further investigations of the characteristics and potential contributing factors and causal relationships of the 
observed FIX (or FIX Padua) inhibitor will be initiated.
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6.
Death of a subject, after having received SHP648, that is judged as, definitely, probably or possibly 
attributed to SHP648. Enrollment in the study and further dosing will be temporarily stopped in order to 
undergo review by the applicable regulatory authorities and the DMC.
7.
Occurrence of a malignancy at any point after gene transfer that is judged as probably or possibly related to 
SHP648.
8.
Occurrence of moderate or severe-drug-related AEs in 2 or more SHP648 treated subjects in a given cohort.
9.
If any other drug-related event occurs in SHP648 treated subjects and is deemed to pose an unacceptable 
risk to subjects by the investigator or medical monitor after further evaluation, additional subjects will not 
be enrolled or dosed until a decision is taken to stop or proceed with the study based on further evaluation of 
the available data by the DMC. Following a safety review of the event, study enrollment or dosing of 
subjects in the screening period may be restarted if the medical monitor and the investigator determine that 
it is safe to proceed with the study.
Study enrollment or dosing of currently enrolled subjects may be restarted if the DMC considers that it is safe to 
proceed with the study. All the applicable rules regarding DMC decisions are addressed in the DMC Charter.
FIX Assessment
FIX activity levels will be measured by both the central laboratory (one-stage clotting and chromogenic assays) 
and the site’s local laboratory (one-stage clotting or chromogenic assay) at all time points.  However, only central 
laboratory FIX activity values derived from the one-stage clotting assay will be utilized for determining subject 
eligibility, establishing baseline FIX activity levels, and informing study dose escalation decisions. Local 
laboratory FIX activity values, in addition to central laboratory FIX activity levels, may be used to inform the 
initiation of corticosteroid treatment (described below under “Glucocorticoid Treatment in the Event of Hepatic 
Inflammation” below).
FIX Utilization
During the course of the study, utilization of exogenous FIX for the prevention (prophylactic treatment in case of 
FIX activity levels <2% and other cases when necessary at the discretion of investigator and medical monitor) or 
episodic management (on-demand treatment) of hemorrhages will be at the discretion of the Investigator and/or 
local hemophilia physician in consultation with the study subject.  However, in order to measure FIX activity that 
is derived from the SHP648 transgene and not exogenous FIX products, subjects will be asked to refrain from 
prophylactic FIX usage between Weeks 3 to 14 post-SHP648 infusion and during the 3 weeks prior to Month 9. 
During these periods which are critical for the assessment of sustained vector-derived FIX expression (as both an 
efficacy and safety evaluation), on-demand treatment that is required for clinical bleeding should, if possible, be 
performed using a standard half-life FIX product rather than an extended half-life FIX concentrate. Whenever 
possible, a 5- day wash out period should be observed prior to any study visit with a FIX assessment, however, 
scheduled visits should not be missed in the case of a wash out of less than 5 days. 
Prophylactic regimen with exogenous FIX may be resumed after Week 14 in case of FIX activity levels <2% 
and/or at the discretion of the Investigator and in consultation with the Sponsor’s Medical Monitor, for subjects in 
whom gene therapy is insufficient to control or prevent spontaneous bleeds.
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Glucocorticoid Use in the Study
Should two subjects in any dosing cohort experience hepatic inflammation requiring reactive glucocorticosteroid
treatment, subjects who are subsequently dosed with SHP648 will receive prophylactic prednisolone (or 
prednisone) treatment starting at Day 8 after SHP648 infusion. Prophylactic treatment should follow the regimen
proposed in the Prednisolone Dosing Regimen table provided below. The corticosteroid regimen may be adjusted 
at the discretion of the Investigator in consultation with the Sponsor’s Medical Monitor depending on the 
subject’s tolerance of the regimen and the observed hepatic transaminase response Patients receiving 
corticosteroids may require additional visits to evaluate potential side effects of corticosteroid therapy and for 
dose adjustments, FVIII activity and liver function tests (LFTs) will be measured at these visits by local 
laboratories.
Notwithstanding the protocol language requiring that two subjects must first be eligible for reactive corticosteroid 
treatment, the Sponsor’s Medical Monitor with the concurrence of the investigator, may permit the use of 
prophylactic steroids in any subject based on all available scientific evidence at the time of subject enrollment. 
Such evidence may include the clinical outcomes of others AAV-based gene therapy studies as well as 
nonclinical relevant data that may emerge. The possible use of corticosteroid will be communicated to potential 
subjects as part of the ICF process.
Glucocorticoid Treatment 
A tapering course of glucocorticosteroid treatment initiated with 60 mg/day of prednisolone (or prednisone) will 
be employed:

Reactively, if any of the following criteria are met:  
a.
A subject demonstrates an apparent vector-associated FIX expression of greater than 3-fold baseline 
activity level 
(e.g., > 3-6% FIX activity level) followed by a loss of > 66% of any confirmed FIX activity value over a 
1- to 2-week period; 
AND/OR
b.
A subject demonstrates a clinically significant elevation in ALT defined as:

1.5x baseline value obtained at Screening Visit
OR

Above the ULN

Prophylactically at Day 8 after SHP648 infusion, if 2 subjects from the same dosing cohort experience 
hepatic inflammation requiring reactive glucocorticosteroid treatment.
A tapering course of corticosteroids (prednisolone or prednisone depending on which product is approved in the 
region) will be given to interrupt any evidence of clinical or subclinical hepatic inflammation and to support the 
potential for sustained transgenic FIX expression. The following is provided as guidance for the dosing regimen 
with corticosteroids and must be tailored to the individual subject depending on the tolerance of the regimen and 
the observed hepatic transaminase response at the discretion of the Investigator and in consultation with the 
Sponsor’s Medical Monitor.
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Guidance for Prednisolone Dosing Regimen 
Prednisolone Dose (mg/day)
Duration
60
1 week or more until AST/ALT decline is observed
40
1 week
30
1 week
25
1 week
20
1 week
15
1 week
12.5
2 weeks
10
2 weeks
5
1 week
Source: Terziroli Beretta-Piccoli et al., 2017
Note: Determine ALT and FIX activity weekly or twice weekly (as per study protocol).
Inclusion and Exclusion Criteria:
Inclusion Criteria:
1.
Male, aged 18 to 75 years at the time of screening.
2.
Established severe or moderately severe hemophilia B (plasma FIX activity ≤ 2% measured following 
≥5 half-lives of most recent exposure to exogenous FIX) and either ≥ 3 hemorrhages per year requiring 
treatment with exogenous FIX or use of prophylactic therapy.
3.
History of > 150 exposure days to exogenously administered FIX concentrates or cryoprecipitates.
4.
Sexually active man must agree to use a condom during sexual intercourse or limit sexual intercourse to 
post-menopausal, surgically sterilized, or contraception-practicing partners in the period from SHP648 
administration until AAV8 has been cleared from semen, as evidenced from negative analysis results for at 
least 2 consecutively collected semen samples assessed at the central laboratory (this criterion is applicable 
also for subjects who are surgically sterilized).
5.
Signed informed consent
Exclusion Criteria:
1.
Bleeding disorder(s) other than hemophilia B.
2.
Documented laboratory evidence of having developed inhibitors (≥ 0.6 Bethesda Units [BUs] on any single 
test) to FIX proteins at any time.
3.
Documented prior allergic reaction to any FIX product.
4.
Anti-AAV8 neutralizing antibody titer > 1:5. Subjects whose laboratory assessments are ≤1:10 may be 
re-tested within the same Screening window and, if eligibility criterion is met on retest, may be enrolled after 
confirmation by the Sponsor’s Medical Monitor.
5.
Known hypersensitivity to prednisolone or prednisone, or to any of the excipients.
6.
Having a disease in which treatment with prednisolone or prednisone is not tolerated (including, but not 
limited to osteoporosis with vertebral fractures, avascular necrosis, cataracts and glaucoma, difficult to 
control hypertension and diabetes as assessed by the treating physician).
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7.
Active Hepatitis C, as indicated by detectable Hepatitis C virus (HCV) ribonucleic acid (RNA) by reverse-
transcriptase polymerase chain reaction (rtPCR).
8.
Hepatitis B, as indicated by positive surface Hepatitis B virus (HBV) antigen test.
9.
Evidence of markers of potential underlying risk for autoimmune mediated hepatic disease:
a)
Anti-smooth muscle antibody (ASMA) titer ≥ 1:40. Values of 1:31 to 1:39 will be flagged as possibly 
abnormal and the Investigator and Medical Monitor will evaluate the subject for eligibility.
b)
Elevated anti-liver-kidney microsomal antibody type 1 (LKM1) titers.
c)
Total IgG > 1.5x ULN.
d)
Antinuclear antibody (ANA) titer > 1:320 OR ANA titer > 1:80 if demonstrated concurrently with ALT 
that is > ULN.
10. Receiving chronic systemic antiviral and/or interferon therapy within 4 weeks prior to enrollment.
11. Clinically significant infections (e.g., systemic fungal infections) requiring systemic treatment.
12. Known immune disorder (including myeloma and lymphoma).
13. Concurrent chemotherapy or biological therapy for treatment of neoplastic disease or other disorders.
14. An absolute neutrophil count < 1000 cells/mm3.
15. History of liver biopsy or imaging indicating moderate or severe fibrosis (Metavir fibrosis stage F2 or 
greater).
16. History of ascites, varices, variceal hemorrhage, or hepatic encephalopathy.
17. Any of the following pre-existing diagnoses, which are indicative of significant underlying liver disease, are 
present in the medical record: portal hypertension, splenomegaly.
a)
A subject is not eligible if the serum albumin level is below the central laboratory’s lower limit of 
normal; 
AND
b)
FibroTest/FibroSURE with a result > 0.48. Subjects with borderline Fibrosure assessments may be 
enrolled after confirmation by the Sponsor’s Medical Monitor. Of note, if a subject has a known history 
of Gilbert’s syndrome, A FibroTest cannot be used for fibrosis testing.
18. Markers of hepatic inflammation or cirrhosis as evidenced by 1 or more of the following:
a)
Platelet count < 150,000/µL.
b)
Total bilirubin > 1.5x ULN and direct bilirubin ≥ 0.5 mg/dL.
c)
ALT or AST > 1.0x ULN.
d)
Alkaline phosphatase > 2.0x ULN.
19. Prothrombin time international normalized ratio (INR) ≥ 1.4.
20. Serum creatinine > 1.5 mg/dL.
21. HIV if CD4+ cell count ≤200 mm3 and/or viral load >20 copies/ milliliter (mL)
22. Urine protein > 30 mg/dL.
23. Body mass index > 38.
24. Major surgery planned within 6 months after enrollment.
25. Acute or chronic disease that, in the opinion of the Investigator, would adversely affect subject safety or 
compliance or interpretation of study results.
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26. Received an AAV vector previously or any other gene transfer agent in the previous 12 months prior to 
Study Day 0.
27. Significant cardiovascular disease (such as New York Heart Association Class III or IV cardiac disease, 
congestive heart failure, myocardial infarction within the previous 6 months, unstable arrhythmias, or 
unstable angina) or significant pulmonary disease (including obstructive pulmonary disease).
28. History of arterial or venous thrombosis / thromboembolism, or a known pro-thrombotic condition.
29. Recent history of psychiatric illness or cognitive dysfunction (including drug or alcohol abuse) that, in the 
opinion of the Investigator, is likely to impair subject’s ability to comply with protocol mandated procedures.
30. Concurrent enrollment in another clinical study, unless it is an observational (non-interventional) clinical 
study that does not interfere with the requirements of the current protocol or have the potential to impact the 
evaluation of safety and efficacy of SHP648 and with prior consultation with the Sponsor’s Medical Monitor 
31. Subject is family member or employee of the Investigator.
Maximum duration of subject participation in the study:

Planned duration of screening period: up to 70 days prior to Day 0 for every subject
The planned enrollment period is about 45 days for each cohort to ensure sufficient subject enrollment

Planned duration of treatment period: 1 day for single infusion

Planned maximum duration of subject’s participation approximately 15 months. 

Planned duration of follow-up after treatment: 12 months of monitoring post-SHP648 dosing in 
Study SHP648-101 followed by at least 4 years of long-term observation in a separate SHP648 Extension 
Study. Patients who do not consent to participate in SHP648 Extension Study will be followed according to 
local safety regulations.
Endpoints and Statistical analysis:
Analysis sets:
The Safety Analysis Set will consist of all subjects who receive any amount of investigational product (IP).
The Full Analysis Set (FAS) will consist of all subjects in the Safety Analysis Set who have at least 1 post-
baseline FIX activity assessment.
Primary Endpoints

Incidence and severity of AEs (serious or non-serious) related to IP that include development of FIX 
inhibitory antibodies, ECG findings, and clinically significant changes in standard laboratory parameters and 
in vital signs
Secondary Endpoints

Circulating plasma FIX activity and FIX antigen levels 

Annualized bleed rate (ABR) in comparison to before gene transfer

Neutralizing and binding antibody titers to AAV8

T-cell response to AAV8 and FIX transgene products

Presence of SHP648 genome by type of bodily fluid

Percentage of change in consumption of exogenous FIX before and after gene transfer
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Exploratory Endpoints
Statistical Analysis
All safety analyses will be performed using the Safety Analysis Set. All efficacy analysis will be performed over 
the FAS.
In general, descriptive summaries will be presented.  Continuous variables will be summarized using mean, 
standard deviation, maximum, minimum, median, and other percentiles as appropriate.  Categorical variables will 
be summarized using frequency counts and percentages.  Analyses will be performed within each cohort 
separately and overall when appropriate.
Adverse events (AEs) will be coded using the MedDRA. Treatment-emergent AEs (TEAEs) are defined as AEs 
with start dates at the time of or following the first exposure to IP. The number of events and percentage of 
TEAEs and AEs related to IP will be tabulated by system organ class, by preferred term, and by treatment cohort. 
TEAEs and AEs related to IP will be further summarized by severity. AEs leading to withdrawal, SAEs and 
deaths will be listed.
Clinical laboratory tests, vital signs, and ECG findings will be summarized by treatment cohort and visit. Criteria 
for clinically significant changes in laboratory parameters will be specified in the statistical analysis plan (SAP), 
with number and percent of subjects with such changes tabulated by cohort.
Development of inhibitory and total binding antibodies to FIX and vector-derived FIX will be descriptively 
summarized.
FIX activity and FIX antigen levels will be summarized by visit. ABR and exogenous FIX consumption data will 
also be descriptively summarized.
More detailed information about summarization of data, graphical representation, and analysis conventions will 
be provided in the SAP.
In addition to safety data reviews by the DMC, additional interim analyses on efficacy and safety data may be 
performed at study milestones (e.g., when the first two subjects in the first cohort finish the Week 14 visit, or 
when the first 2 subjects in the last cohort finish the Week 14 visit), or otherwise up to 2 times every year for the 
duration of the study. Analyses due to different trigger points may be waived or combined for efficiency.
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1.2 Schema
Figure 1. Study Schematic Diagram
Screening
(~2 months)
Post-SHP648 Infusion
(~12 months)
SHP648 Infusion
Day 0
Year 1
Safety
Dose response & FIX activity
Immune responses
Abs to AAV capsid and FIX
T-cell response to AAV capsid and FIX
Bleeding episodes
Consumption of exogenous FIX
Exploratory endpoints
*
* Safety and FIX activity data through Week 14 from at least 2 dosed subjects in a cohort will be utilized to 
inform cohort expansion and dose escalation decisions.
Abbreviations: FIX = coagulation FIX, Ab = antibody, AAV = adeno-associated virus
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1.3 Schedules of Study Activities and Assessments 
1.3.1 Study Activities
Table 1. Schedule of Activities
Procedures
Screeninga
Treatment Period
Follow-Up Period Visits
Day 0b
(SHP648 Dose)
Day 1
Weeks 1-3
Once
weekly
(Clinic only)
Weeks 4-14
Twice
weekly
(Clinic & Lab)c
Week 15
Once
weekly
(Clinic only)
Months 4, 5, 6, 9
Once
monthly
(Clinic only)
Month 12
Study 
Completion 
Visit
Unscheduled 
Visit
Early Study 
Termination 
Visitd
Time Window
Up to 70 days 
before Day 0
AND
at least 
5 days after 
last FIX dose
N/A
24 hours 
± 6 hours 
after 
infusion
±1 day
±1 day for 
Clinic Visits
Lab Visits: 
3-4 days after 
Clinic Visit
±1 day
±4 days
±7 days
NA
NA
Informed consente
Xe
Eligibility criteria review
X
X
Demographic 
information
X
Full physical 
examination including 
height and weight
X
X
X
Targeted physical 
examination
X
X
X
X
X
X
X
Target joint evaluation
X
X
X
Medical history
X
Laboratory assessments 
(see Table 2)
X
Pre- & post-
infusion
X
X
X
X
X
X
X
X
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Table 1. Schedule of Activities
Procedures
Screeninga
Treatment Period
Follow-Up Period Visits
Day 0b
(SHP648 Dose)
Day 1
Weeks 1-3
Once
weekly
(Clinic only)
Weeks 4-14
Twice
weekly
(Clinic & Lab)c
Week 15
Once
weekly
(Clinic only)
Months 4, 5, 6, 9
Once
monthly
(Clinic only)
Month 12
Study 
Completion 
Visit
Unscheduled 
Visit
Early Study 
Termination 
Visitd
Time Window
Up to 70 days 
before Day 0
AND
at least 
5 days after 
last FIX dose
N/A
24 hours 
± 6 hours 
after 
infusion
±1 day
±1 day for 
Clinic Visits
Lab Visits: 
3-4 days after 
Clinic Visit
±1 day
±4 days
±7 days
NA
NA
12-lead ECGf
Xf
Xf
Vital signs
X
Pre- & post-
infusiong
X
X
X
X
X
X
X
X
SHP648 treatment
X
AE review
=============================
Bleeding episodes
=============================
FIX utilization
X
=============================
Change in intensity of 
physical activity
X
=============================
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Table 1. Schedule of Activities
Procedures
Screeninga
Treatment Period
Follow-Up Period Visits
Day 0b
(SHP648 Dose)
Day 1
Weeks 1-3
Once
weekly
(Clinic only)
Weeks 4-14
Twice
weekly
(Clinic & Lab)c
Week 15
Once
weekly
(Clinic only)
Months 4, 5, 6, 9
Once
monthly
(Clinic only)
Month 12
Study 
Completion 
Visit
Unscheduled 
Visit
Early Study 
Termination 
Visitd
Time Window
Up to 70 days 
before Day 0
AND
at least 
5 days after 
last FIX dose
N/A
24 hours 
± 6 hours 
after 
infusion
±1 day
±1 day for 
Clinic Visits
Lab Visits: 
3-4 days after 
Clinic Visit
±1 day
±4 days
±7 days
NA
NA
Concomitant 
medications
X
=============================
Distribute/ review of 
patient diaryh
X
=============================h
Abbreviations: FIX = coagulation factor IX; 
; 12-lead ECG = 12-lead electrocardiogram; AE = adverse event; 
SHP648 = AAV-based FIX gene therapy product
a.
If the Screening Visit occurs >70 days prior to Day 0 visit, then the Screening Visit assessments must be repeated.
b.
At the discretion of the investigator, subjects will be monitored for the first 8 hours and may remain in the infusion center for 24 hours following infusion or return to the 
center for follow-up at 24 hours post-infusion (Day 1 Visit).
c.
Clinic Visits include: all indicated laboratory assessments; 
Lab Visits include: local laboratory Liver Function Test, FIX activity assessment, and backup sample collection ONLY. 
d.
In cases of withdrawn or discontinuation.
e.
If the 5-day wash out period is part of the site’s routine praxis, informed consent can be collected at the Screening Visit. Otherwise the informed consent must be collected 
beforehand to include a wash out period of 5 days as part of the study.
f.
12-lead ECG will be performed locally
g.
Up to 3 hours pre-infusion and at 5, 15, and 30 mins and 1, 2, 3, 4, 6, and 8 hours post-infusion
h. To be reviewed at every scheduled and unscheduled study visit
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1.3.2 Clinical Laboratory Assessments
Table 2. Clinical Laboratory Assessments
Laboratory
Assessments
Screeninga
Treatment 
Period
Follow-Up Period Visits
Day 0 b
(SHP648 
Dose)
Day 1
Weeks 1-3
Once
weekly
(Clinic only)
Weeks 4-14
Twice
weekly
(Clinic & Lab)c
Week 15
Once
weekly
(Clinic only)
Months 4, 5, 6, 9
Once
monthly
(Clinic only)
Month 12
Study 
Completion 
Visit
Unscheduled
Visit
Early Study 
Termination 
Visitd
Time Window
Up to 70 days 
before Day 0
AND
at least 5 days 
after last FIX 
dose
N/A
N/A
±1 day
±1 day for 
Clinic Visits
Lab Visits: 3-4 
days after Clinic 
Visit
±1 day
±4 days
±7 days
NA
NA
Hematologye
X
Xf
X
X
Weeksg 5, 7, 9, 
11, & 13
X
X
X
X
X
Coagulationh
X
Xf
X
X
Weeksg 5, 7, 9, 
11, & 13
X
X
X
X
X
aPTT
X
Pre-infusion
X
X
Xq
X
X
X
X
X
Clinical chemistriesi
X
Xf
X
X
Weeksg 5, 7, 9, 
11, & 13
X
X
X
X
X
Liver Function Testj
(Central and/or Local 
Laboratories)
Xg
Centralg: 
Weeks 4, 6, 8, 
10, 12, & 14
Local : twice 
weekly at Clin 
and Lab
FibroSUREl
X
X
X
X
X
Week 1
Week 6g
X
X
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Table 2. Clinical Laboratory Assessments
Laboratory
Assessments
Screeninga
Treatment 
Period
Follow-Up Period Visits
Day 0 b
(SHP648 
Dose)
Day 1
Weeks 1-3
Once
weekly
(Clinic only)
Weeks 4-14
Twice
weekly
(Clinic & Lab)c
Week 15
Once
weekly
(Clinic only)
Months 4, 5, 6, 9
Once
monthly
(Clinic only)
Month 12
Study 
Completion 
Visit
Unscheduled
Visit
Early Study 
Termination 
Visitd
Time Window
Up to 70 days 
before Day 0
AND
at least 5 days 
after last FIX 
dose
N/A
N/A
±1 day
±1 day for 
Clinic Visits
Lab Visits: 3-4 
days after Clinic 
Visit
±1 day
±4 days
±7 days
NA
NA
HIV serology
X
Hepatitis B surface 
antigen
X
Hepatitis C antibody
X
HCV RNA
X
Week 1
Week 6g
X
X
X
Markers of 
autoimmune-
mediated hepatitisn
X
Serum cytokineso
Xf
X
MHC haplotypek
X
FIX genotyping
X
FIX activity 
(one-stage and 
chromogenic assays; 
central and local 
laboratories)p
X
Pre-infusion
X
X
Xq
X
X
X
X
X
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Table 2. Clinical Laboratory Assessments
Laboratory
Assessments
Screeninga
Treatment 
Period
Follow-Up Period Visits
Day 0 b
(SHP648 
Dose)
Day 1
Weeks 1-3
Once
weekly
(Clinic only)
Weeks 4-14
Twice
weekly
(Clinic & Lab)c
Week 15
Once
weekly
(Clinic only)
Months 4, 5, 6, 9
Once
monthly
(Clinic only)
Month 12
Study 
Completion 
Visit
Unscheduled
Visit
Early Study 
Termination 
Visitd
Time Window
Up to 70 days 
before Day 0
AND
at least 5 days 
after last FIX 
dose
N/A
N/A
±1 day
±1 day for 
Clinic Visits
Lab Visits: 3-4 
days after Clinic 
Visit
±1 day
±4 days
±7 days
NA
NA
FIX antigen
X
Pre-infusion
X
Xg
X
X
X
X
X
FIX inhibitor 
(Bethesda assay; 
central laboratory)
X
X
Xg
X
X
X
X
X
Antibodies to FIX 
and FIX transgene 
product
X
Weeksg 6 & 8
Months 6 & 9
X
X
X
Neutralizing and 
binding antibodies to 
AAV8 and AAV2
X
Pre-infusion
Week 2
Weeksg 4, 8, & 
12
X
X
X
X
PBMCs for CMI 
response to AAV8 
and FIX transgene 
products
X
X
Xg
X
Months 4, 5 & 6
X
X
X
Vector genome 
shedding via PCR in 
blood, saliva, urine, 
stool, and semenr
X
X
Xr
Xg,r
Xr
Xr
X
X
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Table 2. Clinical Laboratory Assessments
Laboratory
Assessments
Screeninga
Treatment 
Period
Follow-Up Period Visits
Day 0 b
(SHP648 
Dose)
Day 1
Weeks 1-3
Once
weekly
(Clinic only)
Weeks 4-14
Twice
weekly
(Clinic & Lab)c
Week 15
Once
weekly
(Clinic only)
Months 4, 5, 6, 9
Once
monthly
(Clinic only)
Month 12
Study 
Completion 
Visit
Unscheduled
Visit
Early Study 
Termination 
Visitd
Time Window
Up to 70 days 
before Day 0
AND
at least 5 days 
after last FIX 
dose
N/A
N/A
±1 day
±1 day for 
Clinic Visits
Lab Visits: 3-4 
days after Clinic 
Visit
±1 day
±4 days
±7 days
NA
NA
Urine protein, total
X
Backup samples.
X
Pre- & 8h 
post-
infusion
X
X
Xt
X
X
X
X
X
Transcriptomics, and 
metabolomicsm,s
Pre- & 8h 
post-
infusion
X
X
Xt
X
X
X
X
X
Exome testings
X
Abbreviations: aPPT = activated partial thromboplastin time; RBC = red blood cells, FIX = coagulation factor IX, BUN = blood urea nitrogen; 
ALT = alanine aminotransferase, AST = aspartate aminotransferase, ALP = alkaline phosphatase, GGT = gamma-glutamyl-transpeptidase, 
and LDH = lactic dehydrogenase, CK = creatine kinase; LFT = Liver function test, ANA = antinuclear antibody; PCR = polymerase chain reaction; 
HIV = human immunodeficiency virus ; MHC = major histocompatibility complex ; HCV RNA = hepatitis C virus ribonucleic acid ; 
AAV8 and AAV2 =adeno associated virus serotype 8 and serotype 2; PBMCs = peripheral blood mononuclear cells; CMI = cell-mediated immunity.
a. If the Screening Visit occurs >70 days prior to Day 0 visit, then the Screening Visit assessments must be repeated.
b. At the discretion of the investigator, subjects will be monitored for the first 8 hours and may remain in the infusion center for 24 hours following infusion or return to the 
center for follow-up at 24 hours post-infusion (Day 1 Visit).
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Continued
c. Clinic Visits include: all indicated laboratory assessments; 
Lab Visits include: local laboratory Liver Function Test, FIX activity assessment, backup sample and voluntary whole blood collection for transcriptome ONLY.
d. In cases of withdrawn or discontinuation.
e. Hematology panel includes: complete blood count (hemoglobin, hematocrit, erythrocytes [i.e., RBC count], and leukocytes [i.e., white blood cell count]) with differential 
(i.e., basophils, eosinophils, lymphocytes, monocytes, neutrophils), platelet counts, RBC distribution width, mean corpuscular volume, and mean corpuscular hemoglobin 
concentration.
f
Time points for Day 0 sample collection: (a) pre-infusion: up to 3 hours prior to SHP648 infusion, and (b) post-infusion: 30 mins (±5 mins), 
4 hours (±10 mins), and 8 hours (±15 mins).
g. To be performed during Clinic Visits only, not during Lab Visits.
h. Coagulation panel includes: prothrombin time, international normalized ratio, thrombin time, D-dimer, fibrinogen activity. 
i.
Clinical chemistry panel includes: sodium, potassium, chloride, carbon dioxide, BUN, creatinine, glucose, calcium, phosphate, magnesium, albumin, total protein, CK, 
bilirubin (total & direct), ALT, AST, ALP, GGT, and LDH.
j.
Liver Function Tests (LFTs) include:  ALT, AST, and GGT;
- Local laboratory LFTs performed at screening, then twice weekly between Weeks 4-14 (at Clinic and Lab Visits). 
- Central laboratory LFTs performed at Weeks 4, 6, 8, 10, 12, & 14, at Clinic Visits only.
k. 4-digit analysis of the following loci:  HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRB1, and HLA-DRB3/4/5.
l.
FibroSURE Score provided based on an algorithm that includes following laboratory results: ALT, alpha-2-macroglobulin, apolipoprotein A1, total bilirubin, gamma 
glutamyl transferase.
m. The collection of whole blood for transcriptome analysis on Day 0 will occur at the pre-infusion and 8 hours post infusion time points and the plasma/serum sample for the 
metabolomics analysis will be obtained from the back-up sample at the same timepoints as for transcriptome
n. ANA, Total IgG, anti-smooth muscle antibody, anti-LKM1 titers.
o. Serum cytokines including IL-6 and TNFα
p. All samples collected for FIX activity assessment will be measured at the central laboratory with the one-stage assay and with the chromogenic assay. FIX activity will 
also be assessed by the local laboratory at all of the indicated time points and at the Clinic and Lab Visits (Weeks 4-14). The local laboratory may use either the one-stage 
or the chromogenic FIX. activity assay, depending upon which assay is the standard in the individual local laboratory and provides the most rapid result; however, the 
same assay must be used consistently throughout the study.
q. To be performed weekly at the Clinic and Lab Visits
r.
Vector shedding assessed at Screening, Day 1, weekly between Weeks 1-15 (at Clinic Visits), and at Months 4,5,6 & 9 as well as at Study Completion Visit (Month 12) 
until two consecutive negative results are obtained in the sample.
s. Whole exome sequencing, transcriptomics and metabolomics will be performed if subject provides consent
t.
Backup sample and transcriptomic collection to be performed between Weeks 4-14 during Lab Visits only.
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2. INTRODUCTION
Hemophilia B is a X-linked recessive bleeding disorder caused by mutations in the gene 
encoding clotting factor IX (FIX) that result in disruption of the normal clotting pathway. FIX is 
synthesized in the liver and circulates in the blood as a proenzyme. In the coagulation cascade, 
FIX is activated to FIXa by contact activation via factor XIa (FXIa) or as a consequence of 
vascular wall injury via tissue factor-FVIIa (TF/FVIIa) complex. FIXa forms a complex with 
activated factor VIII (FVIIIa), and this complex activates factor X (FX) to FXa, which ultimately 
leads to the formation of a stable fibrin clot, as depicted in Figure 2.
Figure 2. Role of FIX in the Clotting Cascade
Hemophilia B affects 1 in 20,000 male births. Disease severity correlates directly with the 
concentration of functional FIX protein in the plasma. Severe disease is characterized as having 
<1% of normal plasma levels of FIX (100% = 1 IU activity/mL or approximately 5000 ng 
protein/mL). Approximately 40% of all patients with hemophilia B have FIX activity levels 
lower than 1% which is associated with frequent soft tissue or intra-articular bleeds. Patients 
with moderate disease (1-5% FIX levels) may also require prophylaxis to treat traumatic and 
spontaneous bleeding. Chronic intra-articular bleeding leads to arthropathy with eventual joint 
degeneration, while intracranial and soft-tissue bleeds can be life threatening. Patients with mild 
disease maintain 5 to 40% of normal FIX levels. Patients with mild disease rarely have 
spontaneous bleeds, but they are at risk for trauma-induced bleeding (Schulman, 2012).
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2.1 Indication and Current Treatment Options 
2.1.1 Approved Therapies for Hemophilia B
Current treatment for hemophilia B is based on replacement of the deficient FIX with IV 
injections of recombinant FIX protein prophylactically or as needed to treat bleeding episodes. 
Factor IX replacement therapy has been shown to be effective in limiting bleeds and reducing 
mortality and morbidity (Löfqvist et al., 1997, Manco-Johnson et al., 1994). To prevent 
propagation of hemorrhage and extended morbidity, people with hemophilia and their families 
are taught to administer FIX concentrates at home at the first signs of bleeding. People with 
severe forms of the disease may need ongoing, preventive infusions (referred to as “prophylactic 
therapy” or “prophylaxis”).
Although FIX replacement therapy has improved the quality of life and prolonged the 
life expectancy of patients with hemophilia, there are several significant limitations associated 
with this therapy (Buckner et al., 2018). Because it is not curative, patients remain at risk for 
life-threatening bleeding episodes and chronic joint damage. In addition, FIX replacement 
therapy is constrained by the high cost, limited availability in some regions, and also short 
half-life of the clotting factors, about 18-24 hours for standard FIX concentrates up to 
86-115 hours for bioengineered recombinant FIX products with extended half-life 
(Oldenburg et al., 2018, Petrus et al., 2010, Roth et al., 2001, Santagostino et al., 2016).
Another important limitation of replacement therapy is that up to 2-3% of patients with 
hemophilia B develop neutralizing antibodies against the administered FIX protein (clinically 
referred to as inhibitors), which may make further replacement therapy ineffective and 
make bleeding episodes extremely difficult to manage (Fischer et al., 2015, Katz, 1996, 
Puetz et al., 2014). Depending on the specific genetic defect, the administered protein may 
present neoantigens to the immune system, inducing formation of antibodies or inhibitors 
(Fischer et al., 2015, Katz, 1996, Puetz et al., 2014).
2.2 Product Background and Clinical Information
The investigational product (IP) SHP648 is a gene therapy product engineered to induce the 
production of human factor FIX (FIX) protein in the liver cells of individuals with severe 
congenital FIX deficiency (hemophilia B) who currently rely on disease management with 
infusions of exogenous FIX. SHP648 is an AAV8-based vector designed to deliver a functional 
copy of the human F9 Padua gene to the liver and drive endogenous hepatocyte-specific 
expression of the FIX-Padua protein, a naturally-occurring FIX variant carrying the R338L 
amino acid substitution (Simioni et al., 2009). This amino acid alteration causes a gain-of-
function mutation, resulting in the expression of a FIX protein with increased specific activity 
compared to wild-type.
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The wild type AAV upon which the recombinant AAV vector is based, is a non-pathogenic, 
replication defective dependoparvovirus, which is not associated with human disease. During the 
manufacture of recombinant AAV gene delivery vectors, all viral genes are removed such that 
the only protein-coding deoxyribonucleic acid (DNA) sequence that is delivered in the SHP648 
vector is the F9-Padua gene along with DNA elements required for expression of the potentially 
therapeutic FIX Padua protein. The rationale for the choice of the serotype of 8 for the SHP648 
capsid is that, among the naturally occurring AAV serotypes, AAV8 is particularly efficient at 
infecting and directing gene expression in the human liver, with minimal “off-target” gene 
expression in other tissues (e.g., in antigen presenting cells). In addition, SHP648 incorporates a 
hepatocyte specific transthyretin enhancer / promoter to further restrict FIX-Padua expression to 
the target liver tissue and three tandem copies of a novel liver-specific cis-regulatory module 8 
(CRM8) element, to further enhance tissue-specific gene expression. 
SHP648 is intended to be given as a single one-time IV infusion by a healthcare provider, at a 
qualified Center. If successful transduction of hepatocytes is achieved, long-term hepatic 
expression and secretion of endogenous FIX into the blood stream may support hemostasis and 
in turn eliminate or reduce the prophylactic and/or on-demand use of exogenous FIX concentrate 
therapy in hemophilia B patients. In this initial Phase 1/2 clinical study up to 3 SHP648 doses 
will be investigated. A single dose based on observed therapeutic durability is to be determined 
from this Phase 1/2 study for further evaluation in future clinical studies.
See Section 6.1.1 for further information on SHP648 and its usage in this study.
Nonclinical dose response and toxicology studies with SHP648 have been completed. Data from 
these and additional nonclinical studies as well as a detailed description of SHP648 can be found 
in the SHP648 Investigator’s Brochure (IB). No prior study of SHP648 in humans has been 
performed.
2.3 Study Rationale
Results from in-human FIX gene therapy studies have demonstrated that therapeutic levels 
of functional FIX can be achieved in a dose dependent manner using AAV-based vectors, 
leading to amelioration of the disease phenotype and reduction or even discontinuation of FIX 
replacement therapy (George et al., 2017, Manno et al., 2006, Miesbach et al., 2018, Monahan et 
al., 2015b, Nathwani et al., 2014, Nathwani et al., 2011). However, the efficiency of vector 
transduction is hindered in patients with pre-existing neutralizing antibody to the AAV capsid. 
Furthermore, in some patients the duration of transgene expression may be limited by induction 
of a cell-mediated immune response to the AAV capsid which manifests itself clinically by a 
transient elevation of liver transaminases (Manno et al., 2006, Miesbach et al., 2018). 
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More recent trials have excluded subjects with neutralizing antibodies to the AAV capsid 
and have used gene therapy vectors based on AAV serotypes for which humans have 
reduced pre-existing immunity and with preferential hepatic tropism (e.g., AAV8, AAV5; 
(George et al., 2017, Miesbach et al., 2018, Monahan et al., 2015b, Nathwani et al., 2014, 
Nathwani et al., 2011)). AAV vectors with superior hepatic tropism can be administered 
systemically, which is less invasive than intrahepatic infusion. Current approaches aim to 
develop FIX gene therapy products that could potentially reduce the dose of vector required to 
achieve effective levels of FIX activity, thereby reducing the risk of vector-related hepatic 
inflammation (Arruda et al., 2018, Mingozzi and High, 2017).
SHP648 vector is based on the AAV8 technology and utilizes the liver-specific transthyretin 
(TTR) enhancer-promoter in combination with 3 copies of the liver-specific CRM8 element 
(Chuah et al., 2014, Nair et al., 2014) to further enhance hepatic expression. In addition, the 
codon-optimization of the human F9 transgene encoding a naturally-occurring variant of the 
coagulation FIX (FIX Padua, FIX_R338Lopt) protein has been revised resulting in a 5’ cytosine 
– phosphate – guanine 3' (CpG)-motif depleted (and thus potentially less immunogenic) 
nucleotide sequence, that nonetheless confers increased expression compared to the wild-type 
nucleotide sequence. Finally, the vector design has been changed from self-complementary to 
single-stranded to further reduce the potential immunogenicity of the vector.
There are currently no approved gene therapy products for patients with hemophilia B, who 
solely rely on infusions of exogenous FIX for disease management.  The rationale for this study 
is 1) to evaluate the expression of the high specific activity Padua FIX variant driven by the 
transthyretin promoter and, a novel liver-specific cis-regulatory module (CRM8) enhancer 
element; 2) to determine the safety of SHP648 and the dose required to achieve FIX activity 
levels between 30-50% of normal in subjects with severe and moderately severe hemophilia B.
2.4 Benefit/Risk Assessment of FIX Gene Therapy
Hemophilia B is a prime target disease for gene therapy, as it is caused by a single gene defect 
and has a broad therapeutic window. Furthermore, the F9 transcript has a suitable size for the 
DNA-cargo capacity of AAV vectors (Miesbach and Sawyer, 2018, Nathwani et al., 2004, 
Petrus et al., 2010). Since even a modest increase in the level of missing FIX can ameliorate the 
severe bleeding phenotype, it is anticipated that the successful development of a hemophilia B 
gene therapy product will lead to continuous endogenous expression of FIX and thereby address 
many of the current treatment limitations by achieving sustained greater than 1% circulating FIX 
activity at all times. Adherence to repeated venipuncture and infusions would not be needed to 
achieve this clinical goal if gene transfer is successful, wherein the goal is for the disease to be 
cured with a single intervention that effects durable gene expression.
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The investigational product SHP648 has not been tested in humans. The primary objective of the 
current study is to evaluate safety and to determine a dose of SHP648 that may lead to levels of 
FIX expression associated with freedom from spontaneous joint hemorrhage. As with all Phase 1 
trials, there is no expectation that study subjects will receive direct benefit. However, based on 
modelling of data from preclinical studies, a starting dose from Cohort 1 was chosen with the 
possibility that it may provide a clinically meaningful FIX level. SHP648 doses for the current 
Phase 1/2 trial have been chosen based upon preclinical research suggesting that all of the chosen 
doses may lead to FIX expression; however, there is no prior experience with SHP648 in 
humans. For this same reason, if a single injection of SHP648 directs FIX expression in humans, 
the anticipated length of persistence of expression following a single injection of SHP648 in 
humans is currently not known.
A dose of SHP648 could potentially result in a higher level of FIX activity than desired. As FIX 
activity increases beyond 100% of normal values, beginning at levels of approximately 150%, 
the blood may clot abnormally (a condition called hypercoagulation). The resultant clots or 
thrombin may lead to ischemia in one or more organs or to disseminated intravascular 
coagulation, a life- threatening condition. The risk of hypercoagulability is managed in the study 
through careful dose selection, cautious dose escalation and patient staggering and review of all 
available data by an external independent Data Monitoring Committee (DMC) prior to dose 
escalations. In the unlikely event that sustained supernormal elevations of FIX levels are 
observed in a study subject, this can be managed through the use of standard anticoagulant 
agents. Evaluation of Anticipated benefits and Risks of Using an AAV-based Gene Therapy 
Product
The AAV8 vector is predominantly a non-integrating virus, and so there is a potential for the 
loss of the episomally maintained AAV vector genomes with division of the transduced cells, 
which would result in a loss of expression of the therapeutic transgene over time. Targeting 
clotting factor expression to post-mitotic hepatocytes with a low cellular turnover rate may 
minimize dilutional effects resulting from new hepatocyte generation (Kattenhorn et al., 2016). 
AAV8 vectors expressing clotting factors have led to expression for greater than 10 years 
(and counting) in large animals and greater than 6 years (and counting) in one human trial 
(Nathwani A.C. et al., 2018, Nathwani et al., 2014, Nathwani et al., 2011).
The long-term safety of recombinant AAV (rAAV) vectors in humans is unknown; however, 
AAV vectors have been delivered to several hundred human subjects to date, in trials for cystic 
fibrosis, α1-antitrypsin deficiency, rheumatoid arthritis, congestive heart failure, lipoprotein 
lipase deficiency, as well as hemophilia, and have been remarkably free of vector-related AE 
(Chapin and Monahan, 2018, Colella et al., 2018). Several clinical trials have used naturally 
occurring or engineered AAV serotype vectors to achieve expression of FVIII or Factor IX 
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(FIX). The chief risk that has been observed in human clinical trials using systemic delivery of 
AAV vectors is that the subject’s immune system recognizes the AAV as an infectious agent and 
raises humoral (antibody-mediated) and potentially cell-mediated immune responses against the 
vector.
Wild-type AAV (WT AAV), the parent virus upon which rAAV vectors are based, is 
non-pathogenic, resulting in a milder immune response than would be expected for a
pathogenic virus. In addition, WT AAV is replication-defective and cannot produce an active 
infection without the coincident infection of a helper virus. Recombinant AAVs are further 
rendered non-pathogenic by having all of the gene sequences of WT AAV removed, resulting 
in extremely low environmental risk related to rAAV viral shedding (Baldo et al., 2013). 
The risk of vertical transmission is addressed in Section 5.4.1.
Nevertheless, at doses of rAAV gene therapy vectors used clinically, it is anticipated that all 
subjects will develop neutralizing antibodies against the capsid serotype. Although development 
of AAV-specific neutralizing antibodies is not associated with any symptoms or AEs, these 
antibodies would persist for years and prevent the repeat treatment with the same AAV vector 
until they are naturally cleared. Furthermore, the AAV serotype-specific neutralizing antibodies 
may or may not also cross-neutralize rAAV made using alternative AAV serotypes and diminish 
their efficiency. This consideration is relevant since the expected persistence of expression from 
a single injection of SHP648 is currently unknown.
In addition to the humoral response described above, a clinical laboratory complication of 
asymptomatic liver transaminase elevation (in particular the relatively liver-specific ALT) has 
been documented in some subjects on multiple hemophilia gene therapy and other AAV liver-
directed gene therapy trials (Manno et al., 2006, Miesbach et al., 2018, Nathwani et al., 2014).  
The systemic delivery of rAAV has been associated with a T lymphocyte response directed 
against the rAAV capsid that in many but not all cases has occurred coincident with the ALT 
elevations. This response has been ascribed to recall AAV-specific memory T cells previously 
generated following WT AAV natural infection in combination with a helper virus. Specifically, 
partial or complete loss of FIX expression following initial successful gene transfer has been 
observed in previous human clinical studies (Manno et al., 2006, Miesbach et al., 2018, 
Nathwani et al., 2014) utilizing liver-directed AAV vectors to correct hemophilia B. 
The loss of FIX expression could be demonstrated in some subjects to be associated with the 
expansion of AAV capsid-specific T effector lymphocytes in the peripheral blood, resulting 
in inflammatory signaling targeting the AAV transduced hepatocytes. This has been further 
noted clinically by observations of vector dose-dependent elevations of liver transaminase 
(serum ALT), which in all cases were within normal range and were asymptomatic.
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It remains unknown whether the capsid-directed immune response is the initiating phenomenon 
that leads to the loss of gene expression or whether other mechanisms are primary with the T cell 
signaling being a secondary phenomenon. In several of the clinical studies, the observed 
transaminitis and/or decrease in FIX levels was treated with weeks to months of high, tapering 
dose corticosteroids (prednisone / prednisolone), which have a broad but not T-cell specific 
immunosuppressive action. Corticosteroid therapy has in general been associated with 
normalizing liver transaminase levels, and in some (although not all) trials, with maintenance 
of some level of clotting factor activity.
Besides the primary T-cell mediated immune responses, innate immune responses to rAAV 
infection have been described in the preclinical setting. However, such responses have rarely 
been detected systemically in human clinical studies.
Neutralizing antibodies (“inhibitors”) to FIX or to FVIII have not developed in any 
AAV-directed trial of gene therapy for hemophilia (George et al., 2017, Manno et al., 2006, 
Miesbach et al., 2018, Nathwani et al., 2014, Rangarajan et al., 2017). The specific concern that 
expression of FIX after AAV gene transfer to hepatocytes might promote cellular stress via 
activation of the unfolded protein response (UPR) has recently been examined in a preclinical 
model, and a dose-dependent UPR could not be demonstrated, nor any negative effect upon liver 
pathology or FVIII immunogenicity (Zolotukhin et al., 2016). Moreover, data from large and 
small animal disease models suggests that liver-mediated expression of potentially immunogenic 
antigens, including FIX Padua variant protein, in the context of gene transfer, can mitigate the 
immune response to the transgenic protein, mediated in part by the induction of 
CD4+CD25+FoxP3+ regulatory T-cells (Crudele et al., 2015, Perrin et al., 2016).
AAV is a single-stranded, replication-deficient DNA parvovirus. The life cycle of the wild type 
AAV includes the potential to exist in a latent state following integration into the host cell 
genome. Integration of the wild type AAV is facilitated by the AAV replication (rep) proteins, 
encoded by the AAV rep genes. All coding sequences of the wild type AAV (including the 
sequences encoding AAV rep genes) are deleted during construction of rAAV expression 
cassettes and rAAV vectors.
2.4.1 Evaluation of Anticipated Benefits and Risks of Using Prednisolone for Management 
of Presumptive Vector-Related Hepatitis
Vector-derived factor expression that is followed by a decrease in factor levels has been 
observed in previous hemophilia gene therapy trials (Manno et al., 2006, Monahan et al., 2015a). 
The factor level decrease has been attributed to an immune response directed against the 
successfully transduced cells. The SHP648 vector design incorporates a single-stranded 
genome structure and an efficient codon optimization which greatly reduces the content of CpG 
repeats. These features minimize the appearance of Pathogen Associated Molecular Patterns 
(PAMPs) so as to minimize potential innate immune signaling via Toll-like Receptors. 
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However, a tapering course of glucocorticosteroid treatment initiated with 60 mg/day of 
prednisolone (or prednisone) will be employed:

Reactively, if any of the following criteria are met:
a.
A subject demonstrates an apparent vector-associated FIX expression of greater than 
3-fold baseline activity level 
(e.g., > 3-6% FIX activity level) followed by a loss of > 66% of any confirmed FIX 
activity value over a 1 to 2-week period;
AND/OR
b.
A subject demonstrates a clinically significant elevation in ALT defined as:

1.5x baseline value obtained at Screening Visit
OR

Above the ULN

Prophylactically at Day 8 after SHP648 infusion, if 2 subjects from the same dosing 
cohort experience hepatic inflammation requiring reactive glucocorticosteroid treatment.
For additional details and guidance on glucocorticoid treatment in Study SHP648-101 refer to 
Section 6.6.3.2.
The rationale to use corticosteroids in an attempt to interrupt the course of the apparent cytotoxic 
T-cell response (CTL) response includes: 1) to maintain the health of the gene-transduced liver 
and 2) to rescue transgenic clotting factor expression, with the understanding that rescue (if 
possible) of even modest amounts of sustained circulating factor activity is expected to improve 
the severe bleeding phenotype AND that repeat administration of the same gene therapy vector 
will not be possible due to expected development of high titer and long-lived AAV neutralizing 
antibodies. The rAAV-associated liver inflammation has in most individuals resolved rapidly 
(i.e. within 2 weeks) with the institution of high dose corticosteroid therapy, followed by taper 
over 8-12 weeks (George et al., 2017, Miesbach et al., 2018, Nathwani et al., 2014). Of note, 
based on data from three different AAV hemophilia B gene therapy trials, the response to 
supportive corticosteroids appears to be highly variable: sustained clotting factor expression has 
varied from 0% to 100% in individuals who received supportive corticosteroids in these trials 
(George et al., 2017, Miesbach et al., 2018, Nathwani et al., 2014).
Utilization of supportive corticosteroid treatment to interrupt ongoing transaminitis/loss of factor 
activity involves an initial systemic high dose of prednisolone followed by a conservative taper over 
5 to 8 weeks, patterned after the guidelines of the American Association for the Study of Liver 
Disease (AASLD) and the European Association for the Study of the Liver (EASL) for the 
treatment of autoimmune hepatitis (Manns et al., 2010, Nathwani et al., 2014, Soloway et al., 1972). 
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Chronic use of systemic steroids at doses of ≥5 mg daily is associated with a wide variety of AEs, 
although the risk for many of these AEs increases particularly with continuous use for greater than 
3-6 months. Should subjects receive a course of prednisolone therapy of <3 months (per protocol) 
the most important risks include: low bone mineral density (osteoporosis), osteonecrosis, adrenal 
suppression, hyperglycemia and diabetes; sleep and psychiatric disturbances. Loss of bone mineral 
density may occur with the planned doses, although in a meta-analysis of adult patients, the fracture 
risk rose with duration of therapy of 3-6 months or longer (Liu et al., 2013, van Staa et al., 2002).
Nevertheless, low bone mineral density and osteoporosis at baseline are prevalent in the hemophilia 
population, and understanding this risk is important. Osteonecrosis (most commonly at the femoral 
head) is greatest with courses longer than proposed in this protocol but has occurred with short-term 
glucocorticoid exposure. Adrenal suppression is expected after two weeks of prednisolone therapy 
(Liu et al., 2013) The protocol’s empiric prednisolone taper minimizes this risk, and screening 
for this outcome will be performed following tapering of prednisolone to a physiologic dose 
(Ahmet et al., 2011, Liu et al., 2013).  Although weight gain during the proposed course 
(<3 months) should be small, the development of Cushingoid features within 2 months of start 
of therapy is common (Fardet et al., 2007). Hyperglycemia may occur thus, glucose will be 
assayed regularly in all study subjects. Glucocorticoids use for even short periods of time may 
lead to psychiatric and cognitive disturbances including memory impairment, irritability, mood 
lability and sleep disturbance. If a subject does not tolerate corticosteroid therapy, Study Protocol 
SHP648-101 specifies the use of combination therapy with azathioprine/prednisone per the AASLD 
guidelines which allows lower cumulative glucocorticoid dose and risk.
The risks of the study will be managed by an external independent DMC based on pre-specified 
pausing/stopping criteria (refer to Section 6.2.1 for a full list of stopping/pausing criteria). 
A charter for the DMC will be separately provided.
Always refer to the latest version of the SHP648 investigator’s brochure (IB) for the overall 
benefit/risk assessment and the most accurate and current information regarding drug 
metabolism, pharmacokinetics, efficacy, and safety of SHP648.
2.5 Compliance Statement
This study will be conducted in accordance with this protocol, the International Council for 
Harmonisation Guideline for Good Clinical Practice E6 (Integrated Addendum to ICH E6[R1]: 
Guideline for Good Clinical Practice E6[R2] Current Step 4 version, 9 November 2016), Title 21 
of the US Code of Federal Regulations (US CFR), the EU Directives (2001/20/EC; 2005/28/EC), 
and applicable national and local regulatory requirements.
The responsibilities of the study sponsor and investigator(s) are described fully in Appendix 1.
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3. OBJECTIVES AND ENDPOINTS
3.1 Study Objectives
3.1.1 Primary Objective
The primary objective of the study is to assess the safety of single, escalating, IV doses of 
SHP648.
3.1.2 Secondary Objectives
The secondary objectives of the study are as follows:

Evaluate plasma FIX levels before and after SHP648 infusion and study the relationship 
between change in FIX activity and SHP648 dose.

Evaluate bleeding episodes post SHP648 administration.

Assess humoral and cellular immune responses to FIX and the viral capsid.

Determine the duration of SHP648 genomes present in bodily fluids.

Compare the consumption of exogenous FIX before and after gene transfer
3.1.3 Exploratory Objectives
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3.2 Study Endpoints
A summary of endpoints supporting the study objectives is presented in Table 3. 
Refer to Section 9 for a detailed description of endpoints and the planned statistical analysis. 
Table 3. Objectives and Endpoints
Objective
Endpoint(s)
Primary

Assess the safety of single, escalating, IV 
doses of SHP648.

Incidence and severity of AEs (serious or non-serious) 
related to IP that include development of FIX 
inhibitory antibodies, ECG findings, and clinically 
significant changes in standard laboratory parameters 
and in vital signs
Secondary

Evaluate plasma FIX levels before and after 
SHP648 infusion and study the relationship 
between change in FIX activity and SHP648 
dose.

Circulating plasma FIX activity and FIX antigen levels 

Evaluate bleeding episodes post SHP648 
administration.

ABR in comparison to before gene transfer

Assess humoral and cellular immune responses 
to FIX and the viral capsid.

Neutralizing and binding antibody titers to AAV8

T-cell response to AAV8 and FIX transgene products

Determine the duration of SHP648 genomes 
present in bodily fluids.  

Presence of SHP648 genome by type of bodily fluid

Compare the consumption of exogenous FIX 
before and after gene transfer

Percentage of change in consumption of exogenous 
FIX before and after gene transfer
Exploratory
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4. STUDY DESIGN
4.1 Overall Design 
Up to 21 adult male subjects with severe or moderately severe hemophilia B (FIX activity levels 
≤ 2%) will be dosed in this open-label, multinational, safety and dose escalation study. Subjects 
will be administered a single IV infusion of SHP648 in one of three ascending dose cohorts, and 
monitored for safety, FIX expression, and immune responses for 12 months post-SHP648 
infusion.
4.2 Scientific Rationale for Study Design
This study design will allow the study Sponsor and Regulatory Agencies to evaluate the safety 
and efficacy of an AAV8 Vector Expressing FIX Padua in Hemophilia B subjects as well as 
inform dosing decisions for a potential Phase 3 pivotal study. Safety and study progress will be 
monitored with a DMC that will provide a recommendation on further cohort size increase to 
collect additional data and dose modification based on data from previous cohorts.
4.3 Justification for Dose
SHP648-101 is to be initiated at a dose of 4.0×1011 vg/kg, which is expected to induce a FIX 
activity of 22% (according to results from nonclinical studies in mice) to 24% (according to 
results from nonclinical studies in rhesus monkeys). This clinical starting dose is 9.5 times lower 
than the “no observed adverse effect level” (NOAEL) of 3.8×1012 vg/kg (based on clinical 
release assay) determined during SHP648 non-clinical development. In term of AAV8 particle 
dose, the anticipated clinical starting dose (4.0×1011 vg/kg) is expected to reflect a particle titer 
dose of 5.5×1011 cp/kg. This represents an approximately 90-fold lower dose than the NOAEL 
for AAV 8 capsid particles (5.0×1013 cp/kg) determined during SHP648 non-clinical 
development. Similar to other gene therapy products, SHP648 is intended for single use only. 
Due to the demonstrated hepatic tropism of SHP648, it is to be administered by IV infusion (for 
further details refer to SHP648 Investigator’s Brochure).
A DMC is included in the study design to provide ongoing monitoring of safety and study 
progress. At each dose level, a decision must be made regarding the safety of increasing to a 
higher dose level. The DMC will provide a recommendation on whether to increase the number 
of subjects at a dose level to obtain additional safety information, cap enrollment at a dose level, 
or modify a dose at a subsequent dose level, taking into consideration data that are observed in 
other cohorts.
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4.4 Duration of Subject Participation and Study Completion Definition
The subject’s maximum duration of participation is expected to be approximately 15 months. 
Study SHP648-101 will last maximum 48 months from First Subject First Visit until Last 
Subject Last Visit. Afterwards all patients will be invited to participate in a separate safety 
extension study (SHP648 Extension Study) for an observation period of at least 4 more years to 
monitor long-term effects. Patients who do not consent to participate in SHP648 Extension Study
will be followed according to local safety regulations.
The Study Completion Date is defined as the date on which the last subject in the study 
completes the final protocol-defined assessment(s). This includes the follow-up visit or contact, 
whichever is later (refer to Section 8.1.3 for the defined follow-up period for this protocol).
4.5 Sites and Regions
Up to 60 subjects are planned to be screened for a total of up to 21 subjects enrolled. It is 
planned to have 2-7 subjects per dose cohort and up to 3 dose-cohorts.
Approximately 30 sites will be asked to participate, which will be located in the USA and several 
countries in and around the European region.
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5. STUDY POPULATION
Each subject must participate in the informed consent process and provide written informed 
consent before any procedures specified in the protocol are performed.
5.1 Inclusion Criteria
The subject will not be considered eligible for the study without meeting all of the criteria below.
1.
Male, aged 18 to 75 years at the time of screening.
2.
Established severe or moderately severe hemophilia B (plasma FIX activity 
≤2% measured following ≥ 5 half-lives of most recent exposure to exogenous FIX) 
and either ≥3 hemorrhages per year requiring treatment with exogenous FIX or use 
of prophylactic therapy.
3.
History of > 150 exposure days to exogenously administered FIX concentrates or 
cryoprecipitates.
4.
Sexually active man must agree to use a condom during sexual intercourse or limit sexual 
intercourse to post-menopausal, surgically sterilized, or contraception-practicing partners 
in the period from SHP648 administration until AAV8 has been cleared from semen, as 
evidenced from negative analysis results for at least 2 consecutively collected semen 
samples assessed at the central laboratory (this criterion is applicable also for subjects who 
are surgically sterilized).
5.
Signed informed consent
5.2 Exclusion Criteria
The subject will be excluded from the study if any of the following exclusion criteria are met.
1.
Bleeding disorder(s) other than hemophilia B.
2.
Documented laboratory evidence of having developed inhibitors (≥ 0.6 BU on any single 
test) to FIX proteins at any time.
3.
Documented prior allergic reaction to any FIX product.
4.
Anti-AAV8 neutralizing antibody titer > 1:5. Subjects whose laboratory assessments are 
≤1:10 may be re-tested within the same Screening window and, if eligibility criterion is 
met on retest, may be enrolled after confirmation by the Sponsor’s Medical Monitor.
5.
Known hypersensitivity to prednisolone or prednisone, or to any of the excipients.
6.
Having a disease in which treatment with prednisolone or prednisone is not tolerated 
(including, but not limited to osteoporosis with vertebral fractures, avascular necrosis, 
cataracts and glaucoma, difficult to control hypertension and diabetes as assessed by the 
treating physician).
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7.
Active Hepatitis C, as indicated by detectable Hepatitis C virus (HCV) ribonucleic acid 
(RNA) by reverse-transcriptase polymerase chain reaction (rtPCR).
8.
Hepatitis B, as indicated by positive surface Hepatitis B virus (HBV) antigen test.
9.
Evidence of markers of potential underlying risk for autoimmune mediated hepatic disease:
a.
Anti-smooth muscle antibody (ASMA) titer ≥ 1:40. Values of 1:31 to 1:39 will be 
flagged as possibly abnormal and the Investigator and Medical Monitor will evaluate 
the subject for eligibility.
b.
Elevated anti-liver-kidney microsomal antibody type 1 (LKM1) titers.
c.
Total IgG > 1.5x ULN.
d.
Antinuclear antibody (ANA) titer > 1:320 OR ANA titer > 1:80 if demonstrated 
concurrently with ALT that is > ULN.
10. Receiving chronic systemic antiviral and/or interferon therapy within 4 weeks prior to 
enrollment.
11. Clinically significant infections (e.g., systemic fungal infections) requiring systemic 
treatment.
12. Known immune disorder (including myeloma and lymphoma).
13. Concurrent chemotherapy or biological therapy for treatment of neoplastic disease or other 
disorders.
14. An absolute neutrophil count < 1000 cells/mm3.
15. History of liver biopsy or imaging indicating moderate or severe fibrosis (Metavir fibrosis 
stage F2 or greater).
16. History of ascites, varices, variceal hemorrhage, or hepatic encephalopathy.
17. Any of the following pre-existing diagnoses, which are indicative of significant underlying 
liver disease, are present in the medical record: portal hypertension, splenomegaly.
a.
A subject is not eligible if the serum albumin level is below the central laboratory’s 
lower limit of normal; 
AND
b.
FibroTest/FibroSURE with a result > 0.48. Subjects with borderline Fibrosure 
assessments may be enrolled after confirmation by the Sponsor’s Medical Monitor. 
Of note, if a subject has a known history of Gilbert’s syndrome, A FibroTest cannot be 
used for fibrosis testing.
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18. Markers of hepatic inflammation or cirrhosis as evidenced by 1 or more of the following:
a.
Platelet count < 150,000/µL.
b.
Total bilirubin > 1.5x ULN and direct bilirubin ≥ 0.5 mg/dL.
c.
ALT or AST > 1.0x ULN.
d.
Alkaline phosphatase > 2.0x ULN.
19. Prothrombin time INR ≥ 1.4.
20. Serum creatinine > 1.5 mg/dL.
21. HIV if CD4+ cell count ≤200 mm3 and/or viral load >20 copies/mL.
22. Urine protein > 30 mg/dL.
23. Body mass index > 38.
24. Major surgery planned within 6 months after enrollment.
25. Acute or chronic disease that, in the opinion of the Investigator, would adversely affect 
subject safety or compliance or interpretation of study results.
26. Received an AAV vector previously or any other gene transfer agent in the previous 
12 months prior to Study Day 0.
27. Significant cardiovascular disease (such as New York Heart Association Class III or IV 
cardiac disease, congestive heart failure, myocardial infarction within the previous 
6 months, unstable arrhythmias, or unstable angina) or significant pulmonary disease 
(including obstructive pulmonary disease).
28. History of arterial or venous thrombosis / thromboembolism, or a known pro-thrombotic 
condition.
29. Recent history of psychiatric illness or cognitive dysfunction (including drug or alcohol 
abuse) that, in the opinion of the Investigator, is likely to impair subject’s ability to comply 
with protocol mandated procedures.
30. Concurrent enrollment in another clinical study, unless it is an observational (non-
interventional) clinical study that does not interfere with the requirements of the current 
protocol or have the potential to impact the evaluation of safety and efficacy of SHP648 
and with prior consultation with the Sponsor’s Medical Monitor 
31. Subject is family member or employee of the Investigator.
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5.3 Restrictions 
Not applicable for this study.
5.4 Reproductive Potential
5.4.1 Male Contraception
The germline transmission of AAV8 and AAV2 was comparatively investigated in rabbits 
by Favaro et al., 2009. The results revealed a transient presence of AAV in the semen, which was 
vector dose-dependent but serotype-independent. Upon fractionation, the AAV was not present 
in motile sperm, greatly diminishing the risk of vertical transmission of vector DNA sequences. 
Furthermore, long-term follow-up showed that there was no recurrence of vector sequences in 
semen. The risk of transmission was also limited since infectious vector particles were detectable 
only up to Day 4 post injection. Moreover, since the ejaculate contains only 5% sperm and the 
AAV shedding into semen was comparable in vasectomized and non-vasectomized animals, the 
authors stated that the presence of AAV in semen does not necessarily imply transduction of 
germ cells and the associated risk of germline transmission (Favaro et al., 2009).
Based on the experience of Favaro et al., and others (Arruda et al., 2001, Couto et al., 2004, 
Favaro et al., 2009, Schuettrumpf et al., 2006) and the observed minimal distribution of SHP648 
to testes in mice during the nonclinical development program for SHP648, sexually active men 
participating in Study SHP648-101 must agree to use a condom during sexual intercourse or 
limit sexual intercourse to post-menopausal, surgically sterilized, or contraception-practicing 
partners in the period from SHP648 administration until AAV8 has been cleared from semen, as 
evidenced from negative analysis results for at least 2 consecutively collected semen samples 
assessed at the central laboratory (this is applicable also for subjects who are surgically 
sterilized).
Refer to Appendix 4 for further guidance.
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6. STUDY INTERVENTION
6.1 Investigational Product
6.1.1 Identity of Investigational Product
The IP is SHP648, which contains a single-stranded adeno-associated virus (ssAAV) genome 
consisting of liver-specific cis-regulatory modules (CRM8), a modified (truncated) murine 
transthyretin (pre-albumin) enhancer / promoter region, an intron derived from the minute virus 
of mice (MVM), a human codon-optimized coagulation factor 9 (F9) Padua transgene and a 
bovine growth hormone polyadenylation sequence (BGH polyA). The insert is flanked by 
adeno-associated virus serotype 2 (AAV2) inverted terminal repeat (ITR) sequences. The AAV 
serotype 8 (AAV8) capsid harboring the vector genome is composed of the viral structural 
proteins VP1, VP2, and VP3. 
SHP648 will be supplied as a 5 mL clear and sterile frozen aqueous solution in glass vials 
intended for IV infusion. The final product formulation consists of a solution of SHP648 in 
10 millimolar (mM) histidine, 100 mM NaCl, 50 mM glycine, 5% trehalose and 0.005% 
polysorbate (Tween®) 80. Additional information is provided in the most current 
SHP648 Investigator’s Brochure. 
The product is filled at a target (nominal) concentration of about 4.1 x 1012 vg/mL as described 
on the vial label and will be provided to the sites in 10R vials, which contains 5 mL of the IP. 
The dosing shall be calculated based on the actual concentration (to be retrieved from the 
certificate of analysis) and based on the subject’s body weight (BW).
6.1.2 Blinding the Treatment Assignment
Not Applicable as it is an open label study
6.2 Administration of Investigational Product
6.2.1 Dosing
Each patient will be assigned to one cohort only and will receive the respective assigned dose. 
This dose is to be administered once per patient as a peripheral intravenous infusion. For a 
detailed step by step guidance on handling and administration of the study drug, refer to the 
instructions in the SHP648 Pharmacy Manual.
Briefly, a qualified pharmacist and/or designee will thaw SHP648, pool the calculated 
amount into appropriate syringes, and provide the syringes to the investigator. The individual 
infusion volume will be based on the subject’s assigned dose, the actual concentration listed 
on the certificate of analysis for the used lot and BW determined at the Screening Visit. 
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Initially, approximately 10% of the SHP648 infusion volume will be administered by manual 
push followed by an observation period of 30 minutes to monitor for infusion reactions. The 
remaining product will then be administered as specified in the SHP648 Pharmacy Manual.
6.2.1.1 Dose Escalation Plan
Up to 3 SHP648 dose cohorts are planned to be evaluated in this study, where the dosing from 
one cohort to the next is increased based upon the results of the previous cohort.

Cohort 1 dose:
Starting dose: 4.0 x 1011 vg/kg BW

Cohort 2 dose:
2-fold escalation: 8.0 x 1011 vg/kg BW  
OR
3-fold escalation: 1.2 x 1012 vg/kg BW

Cohort 3 dose:
2-fold escalation of Cohort 2 dose 

1.6 x 1012 vg/kg BW (if cohort 2 dose was 8.0 x 1011 vg/kg BW) or 
2.4 x 1012 vg/kg BW (if cohort 2 dose was 1.2 x 1012 vg/kg BW)
OR
3-fold escalation of Cohort 2 dose

2.4 x 1012 vg/kg BW (if cohort 2 dose was 8.0 x 1011 vg/kg BW) or 
3.6 x 1012 vg/kg BW (if cohort 2 dose was 1.2 x 1012 vg/kg BW)
Initially, one subject will be dosed in Cohort 1, followed by an observational period of at least 
6 weeks. If no safety concern is observed in the first dosed subject, a second subject will be 
dosed. For each additional dose cohort, dosing of the second subject will be scheduled 6 weeks 
after dosing of the first subject at the earliest; up to 7 subjects may be dosed in Cohort 1, if 
Cohort 1 is expanded. 
Decisions pertaining to cohort expansion, dose escalation, number of subjects to be dosed, as 
well as the exact dose for subsequent Cohort 2 and Cohort 3 will be made based on the 
recommendation provided by an external Data Monitoring Committee (DMC). The DMC 
will review data including the Week 14 visit of the second dosed subject in Cohort 1. 
The observation period for the DMC data cut in expanded Cohort 1 and for Cohorts 2 and 3 may 
be adjusted to between 6 and 14 weeks based on Cohort 1 FIX expression peak data observed in 
the first two patients, as well as, other relevant study data and published literature.
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After review of all safety and FIX activity data, the DMC will provide recommendations to 
pursue one of the following:
1.
Escalate to the next dosing cohort 
2.
Increase the number of subjects in the current dosing cohort 
3.
Cap enrollment at the current dosing cohort and complete the study
4.
Enroll additional subjects into a previous lower dose cohort in order to obtain additional 
safety information
5.
Enroll subjects into a modified dosing cohort that is intermediate between those into which 
subjects have been previously enrolled.
6.2.1.2 Stopping Criteria for Enrollment and Dose Escalation
Enrollment and escalation to next dose cohort will be paused until an independent DMC 
evaluates all available study data and makes a recommendation if any one of the following 
criteria are met: 
1.
Achievement of vector-derived FIX activity level ≥ 150% in any subject at any time while 
on the study due to potential risk of thrombosis. The level of FIX activity is measured 
frequently throughout the study. Study enrollment will be paused based on the local 
laboratory results (Table 1 and Table 2).
2.
First two subjects on corticosteroid prophylaxis experience, at week 14, a loss of 
endogenous FIX activity level >75% of the highest FIX activity level measured after 
SHP648 administration (based on one stage central laboratory). The level of FIX activity is 
assessed frequently throughout the study (Table 1 and Table 2).
3.
A value of 3x ULN or greater in ALT, AST, or both in any subject after SHP648 
administration that is not responsive after 12 weeks of corticosteroid rescue treatment.
4.
A SAE that may be potentially related to SHP648 and which poses either an immediate 
risk to the subject’s health or is likely to adversely affect the subject’s health long term.  
This includes events classified as AEs qualifying for special notification (Brussels, 
03/12/2009, ENTR/F/2/SF/dn D(2009) 35810; EMEA/CHMP/GTWP/60436/2007), if 
these are judged as potentially related to SHP648.
5.
The development in any subject of an inhibitor towards FIX (or FIX Padua) after having 
received SHP648. Further investigations of the characteristics and potential contributing 
factors and causal relationships of the observed FIX (or FIX Padua) inhibitor will be 
initiated.
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6.
Death of subject after having received SHP648, that is judged as, definitely, probably or 
possibly attributed to SHP648. Enrollment in the study and further dosing will be 
temporarily stopped in order to undergo review by the applicable regulatory authorities and 
the DMC.
7.
Occurrence of a malignancy at any point after gene transfer that is judged as probably or 
possibly related to SHP648.
8.
Occurrence of moderate or severe-drug-related AEs in 2 or more SHP648 treated subjects 
in a given cohort.  
9.
If any other drug-related event occurs in SHP648 treated subjects and is deemed to pose an 
unacceptable risk to subjects by the investigator or medical monitor after further 
evaluation, additional subjects will not be enrolled or dosed until a decision is taken to stop 
or proceed with the study based on further evaluation of the available data by the DMC. 
Following a safety review of the event, study enrollment or dosing of subjects in the 
screening period may be restarted if the medical monitor and the investigator determine 
that it is safe to proceed with the study.
Study enrollment or dosing of currently enrolled subjects may be restarted if the DMC considers 
that it is safe to proceed with the study. All the applicable rules regarding DMC decisions are 
addressed in the DMC Charter.
6.2.1.3 Data Monitoring Committee (DMC)
The DMC is an external independent body that will consist of recognized medical experts in the 
fields of Hematology, Hepatology, Clinical Immunology and Gene Therapy. The DMC will act 
as an advisory body to the Sponsor that will monitor subject safety and recommend whether the 
study should continue, be modified or stopped.  Responsibilities of the DMC members and all 
the applicable rules regarding DMC decisions are addressed in the DMC Charter.
6.2.2 Dose Modification
The decision to proceed to the next dose level will be triggered after DMC review of safety, 
tolerability, and preliminary FIX expression data obtained in at least 2 participants at the prior 
dose level.
The DMC will monitor the safety during the study, and will have standing to approve or stop 
dose escalation, expand a dose cohort to obtain more safety data, cap enrollment at the current 
dosing cohort and complete the study, enroll additional subjects into a previous lower dose 
cohort in order to obtain additional safety information, modify or add a dose escalation in 
between planned dose cohort, and add a dose to a treatment regimen, modify observation period 
for the DMC data cut. (refer also to Section 6.2.1.1 and Section 6.2.1.2).
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6.3 Labeling, Packaging, Storage, and Handling of Investigational Product
6.3.1 Labeling
Labels containing study information and pack identification are applied to the IP container.
The IP is labeled with a minimum of the following: protocol number, product identification 
number, dosage form, directions for use, storage conditions, expiry date, lot number, the 
statements “For clinical trial use only” and “Contains genetically modified organisms” and the 
sponsor’s name and address. Any additional labeling requirements for participating countries
will also be included on the label.
Space is allocated on the label so that the site representative can record the Subject ID number.
Additional labels may not be added without the sponsor’s prior full agreement.
6.3.2 Packaging
The IP is filled in glass vials in volumes of 5mL with an approximate concentration of nominal 
4.1 x 1012 vg/mL. Each single vial is packed in a carton, which is labelled as well.
Changes to sponsor-supplied packaging prior to dosing may not occur without full agreement in 
advance by the sponsor.
6.3.3 Storage
SHP648 will be stored at -60°C or below. The investigator has overall responsibility for ensuring 
that investigational product is stored in a secure, limited-access location. Limited responsibility 
may be delegated to the pharmacy or member of the study team, but this delegation must be 
documented. The pharmacist/nominated team member will enter the unique subject identifier on 
the investigational product bottle label and the outer carton label as they are distributed.
The IP must be stored in accordance with labeled storage conditions. Temperature monitoring is 
required at the storage location to ensure that the investigational product is maintained within an 
established temperature range. The investigator is responsible for ensuring that the temperature is 
monitored throughout the duration of the study and that records are maintained; the temperature 
should be monitored continuously by using either an in-house system, a mechanical recording 
device such as a calibrated chart recorder, or by manual means, such that both minimum and 
maximum thermometric values over a specific time period can be recorded and retrieved as 
required. Such a device (i.e., certified min/max thermometer) would require manual resetting 
upon each recording. The sponsor must be notified immediately upon discovery of any 
excursion from the established range. Temperature excursions will require site investigation 
as to cause and remediation. The sponsor will determine the ultimate impact of excursions on 
the investigational product and will provide supportive documentation as necessary. 
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Under no circumstances should the product be dispensed to subjects until the impact has been 
determined and the product is deemed appropriate for use by the sponsor.
The sponsor should be notified immediately if there are any changes to the storage area of the IP, 
e.g., fumigation of a storage room.
6.3.4 Special Handling
Handling and disposal of SHP648 will comply with standards for Biosafety Level 1 Vectors as 
well as universal precautions.
6.4 Drug Accountability
Investigators will be provided with sufficient amounts of the investigational product to carry out 
this protocol for the agreed number of subjects. The investigator or designee will acknowledge 
receipt of the investigational product, documenting shipment content and condition. Accurate 
records of all investigational product dispensed, used, returned, and/or destroyed must be 
maintained as detailed further in this section.
The investigator has overall responsibility for administering/dispensing investigational product. 
Where permissible, tasks may be delegated to a qualified designee (e.g., a pharmacist) who is 
adequately trained in the protocol and who works under the direct supervision of the investigator. 
This delegation must be documented in the applicable study delegation of authority form.
The investigator or his/her designee (as documented by the investigator in the applicable study 
delegation of authority form) will administer/dispense the investigational product only to 
subjects included in this study following the procedures set out in the study protocol. Each 
subject will be given only the investigational product carrying his/her treatment assignment. 
All administered/dispensed medication will be documented in the subject’s source and/or other 
investigational product record. No investigational product stock or returned inventory from a 
Shire-sponsored study may be removed from the site where originally shipped without prior 
knowledge and consent by the sponsor. If such transfer is authorized by the sponsor, all 
applicable local, state, and national laws must be adhered to for the transfer.
The sponsor or its representatives must be permitted access to review the supplies storage and 
distribution procedures and records.
At the end of the study, or as instructed by the sponsor, all unused stock, are to be sent to a 
nominated contractor on behalf of the sponsor. Investigational products being returned to the 
sponsor’s designated contractors must be counted and verified by clinical site personnel and the 
sponsor (or designated CROW). For unused supplies where the original supplied tamper-evident 
feature is verified as intact, the tamper-evident feature must not be broken and the labeled 
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amount is to be documented in lieu of counting. Shipment return forms, when used, must be 
signed prior to shipment from the site. Returned investigational products must be packed in a 
tamper-evident manner to ensure product integrity. Contact the sponsor for authorization to 
return any investigational product prior to shipment. Shipment of all returned investigational 
product must comply with local, state, and national laws.
Based on entries in the site drug accountability forms, it must be possible to reconcile 
investigational products delivered with those used and returned. All investigational products 
must be accounted for and all discrepancies investigated and documented to the sponsor’s 
satisfaction.
6.5 Subject Compliance
All study procedures are to be performed under the direct supervision of the investigator/a 
licensed healthcare professional at the study site, and thus, no separate procedures will be used to 
monitor subject compliance.
6.6 Prior and Concomitant Therapy
All medications taken and non-drug therapies other than study treatment (including but 
not limited to FIX concentrates, herbal treatments, vitamins, behavioral treatment, 
non-pharmacological treatment, such as psychotherapy, as appropriate) received within 4 weeks 
prior to the Screening Visit (or pharmacokinetic equivalent of 5 half-lives, whichever is longer) 
and through the final study contact (including protocol-defined follow-up period) and the dose or 
amount taken must be recorded in the subject’s source document and on the concomitant 
medications and non-drug therapies electronic case report forms (eCRFs).
6.6.1 Prior Treatment
Prior treatment includes all treatment (including but not limited to FIX concentrates, herbal 
treatments, vitamins, non-pharmacological treatment such as psychotherapy as appropriate) 
received within 4 weeks prior to the Screening Visit. Prior treatment information must be 
recorded in the subject’s source document.
6.6.2 Concomitant Treatment 
Concomitant treatment refers to all treatment taken between the dates of the first dose of 
investigational product and the end of the follow-up period, inclusive. Concomitant treatment 
information must be recorded in the subject’s source document.
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6.6.3 Permitted Treatment
The following medications and non-drug therapies are permitted within 4 weeks before study 
entry and during the course of the study (refer also to Section 6.6.4, Table 5):

Medications:

Antiretroviral therapy.

Antihistamines, nonsteroidal anti-inflammatory drugs, acetaminophen, and 
corticosteroids by oral or parenteral route for the treatment of allergic reaction.

Hemostatic agents, such as tranexamic acid, are permitted, as indicated by the 
subject’s treating physician, to treat mucosal bleeding during the study.

FIX products (refer to Section 6.6.3.1).

Any medications deemed necessary by the subject’s physician to treat or prevent any 
medical condition (with the exception of any immunomodulating drug* other than 
anti-retroviral chemotherapy, and any investigational drug or device).

Any over-the-counter medication used by the subject to treat symptoms or signs of any 
medical condition.

Supplemental vitamins, minerals.

Non-drug therapies:

Any non-drug therapy (e.g., physiotherapy) deemed necessary by the subject’s 
physician to treat or prevent any medical condition.
* In general, it is the intention of the protocol to avoid the use immunomodulating drugs during the first 12 months 
following the SHP648 infusion as these may interfere with the evaluation of the immune response to SHP648. 
A clear exception is the use of corticosteroids, which has become recognized as a treatment element in gene 
therapy for patients exhibiting elevated liver enzymes. The risk-benefit of vaccination needs to be evaluated on the 
individual basis as the expected immune response to the vaccine may also confound the evaluation of the immune 
response to SHP648.
6.6.3.1 Use of Exogenous FIX throughout the Study
Clinical bleeding episodes will be managed with infusion of exogenous FIX. Usage of exogenous 
FIX for the prevention (prophylactic treatment in case of FIX activity levels <2% and other cases 
when necessary at the discretion of investigator and medical monitor) or episodic management 
(on-demand FIX treatment) of hemorrhages will be at the discretion of the investigator and/or 
local hemophilia physician, and in consultation with the study subject. However, in order to assess 
FIX activity levels derived specifically from the SHP648 transgene and not exogenous FIX 
products, subjects will be asked to refrain from prophylactic FIX usage between Week 3 to 
Week 14 post-SHP648 administration and during the 3 weeks prior to Month 9. 
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During these periods which are critical for the evaluation of sustained FIX expression from the 
vector (as both an efficacy and safety evaluation), on-demand treatment that is required for clinical 
bleeding should, if possible, be performed using a standard half-life FIX product (rather than an 
extended half-life FIX concentrate). Whenever possible, a 5- day wash out period should be 
observed prior to any study visit with a FIX assessment, however, scheduled visits should not be 
missed in the case of a wash out of less than 5 days. 
Prophylactic regimen with exogenous FIX may be resumed after Week 14 in case of FIX activity 
levels <2% and/or at the discretion of the Investigator in consultation with the Sponsor’s Medical 
Monitor, for subjects in whom gene therapy is insufficient to control or prevent spontaneous 
bleeds.
It is recognized and expected that suspected or evident bleeding episodes will be treated with 
infused FIX protein as per the standard of care. If possible, study visits should be scheduled at 
least 5 days after a FIX dose to minimize the chance that any FIX activity measured at the study 
visit results from exogenously administered FIX. However, with the exception of the Screening 
Visit, study visits should not be postponed if the study subject has infused FIX (e.g., for the 
treatment of bleeding) within 4 days of the scheduled study visit.
All use of exogenous FIX will be recorded in the source document and eCRF.
6.6.3.2 Glucocorticoid Use in the Study
Should two subjects in any dosing cohort, experience hepatic inflammation requiring reactive 
glucocorticosteroid treatment, subjects who are subsequently dosed with SHP648 will receive 
prophylactic prednisolone (or prednisone) treatment starting at Day 8 after SHP648 infusion. 
Prophylactic treatment should follow the regimen proposed below in Table 4. The corticosteroid 
regimen may be adjusted at the discretion of the Investigator in consultation with the Sponsor’s 
Medical Monitor depending on the subject’s tolerance of the regimen and the observed hepatic 
transaminase response. Patients receiving corticosteroids may require additional visits to 
evaluate potential side effects of corticosteroid therapy and for dose adjustments, FVIII activity 
and liver function tests (LFTs) will be measured at these visits by local laboratories. If a subject 
does not tolerate corticosteroid therapy, per the AASLD guidelines combination therapy with 
azathioprine/prednisone should be used. This combination therapy allows lower cumulative
glucocorticoid dose and risk.
Notwithstanding the protocol language requiring that two subjects must first be eligible 
for reactive corticosteroid treatment, the Sponsor Clinical Director with the concurrence 
of the investigator, may permit the use of prophylactic steroids in any subject based on 
all available scientific evidence at the time of subject enrollment. 
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Such evidence may include the clinical outcomes of others AAV-based gene therapy studies as 
well as nonclinical relevant data that may emerge. The possible use of corticosteroids will be 
communicated to potential subjects as part of the ICF process.
Glucocorticoid Treatment
A tapering course of glucocorticosteroid treatment initiated with 60 mg/day of prednisolone will 
be employed:

Reactively, if any of the following criteria are met:
a.
A subject demonstrates an apparent vector-associated FIX expression of greater than 
3-fold baseline activity level (e.g., > 3-6% FIX activity level) followed by a loss of 
> 66% of any confirmed FIX activity value over a 1- to 2-week period,
AND/OR
b.
A subject demonstrates a clinically significant ALT elevations defined as:

1.5 x baseline value at Screening Visit 
OR

above the upper limit of normal (ULN).

Prophylactically at Day 8 after SHP648 infusion, if two subjects from the same dosing 
cohort experience hepatic inflammation requiring reactive glucocorticosteroid treatment.
In geographies where prednisolone cannot be sourced at the strengths required for the specified 
dosing regimen (e.g. USA), prednisone will be provided. Prednisone is converted to the active 
metabolite prednisolone and is recommended by the AASLD and the EASL for the treatment of 
autoimmune hepatitis. Of note, in addition to central laboratory FIX activity levels, local 
laboratory FIX activity values may be used to inform the initiation of corticosteroid treatment 
(European Association for the Study of the Liver, 2015). 
A tapering course of corticosteroids (prednisolone or prednisone depending on which product is 
approved in the region) will be given to interrupt any evidence of clinical or subclinical hepatic 
inflammation and to support the potential for sustained transgenic FIX expression. It is 
imperative to begin dosing with prednisolone as soon as possible after either of the prednisolone-
triggering observations listed above has been made, preferably within 12-24 hours of the 
recognition of transaminitis or decreasing FIX activity. If a confirmatory blood sample can be
collected, this information will be useful in the management; however, the initiation of 
prednisolone therapy should not be delayed pending the opportunity for sample collection.
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The prednisolone dosing regimen described in Table 4 is provided as a guidance for the dosing 
regimen with corticosteroids and must be tailored to the individual subject depending on the 
tolerance of the regimen and the observed hepatic transaminase response at the discretion of the 
Investigator and in consultation with the Sponsor’s Medical Monitor.
Table 4. Guidance for Prednisolone Dosing Regimen 
Prednisolone Dose (mg/day)
Duration
60
1 week or more until AST/ALT decline is observed
40
1 week
30
1 week
25
1 week
20
1 week
15
1 week
12.5
2 weeks
10
2 weeks
5
1 week
Source: Terziroli Beretta-Piccoli et al., 2017
Note: Determine ALT and FIX activity weekly or twice weekly as per study protocol.
Careful monitoring for known side effects of prolonged exposure to Prednisolone should be 
maintained, including:

low bone mineral density (osteoporosis), 

osteonecrosis, 

adrenal suppression, 

hyperglycemia and diabetes; 

sleep and psychiatric disturbances.
If a subject does not tolerate corticosteroid therapy consideration should be given to combination 
therapy with azathioprine/corticosteroid per AASLD guidelines or other drug which allows 
lower cumulative glucocorticoid dose and risk as per standard of practice, in consultation with a 
hepatologist, so that the care can be individualized to the subject’s needs.
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6.6.4 Prohibited Treatment
The following medications and non-drug therapies are not permitted within 30 days before the 
SHP648 dose (unless stated otherwise):

Systemic antiviral and/or interferon therapy (with the exception of antiretroviral therapy).

Concurrent chemotherapy or biological therapy for treatment of neoplastic disease or other 
disorders.

An investigational intervention within 4 weeks prior to dosing or within 5 half-lives of the 
investigational drug administration, whichever is longer.
Received an AAV vector previously or any other gene transfer agent in the previous 
12 months prior to Study Day 0

Non-drug therapies:

Major surgery or an orthopedic surgical procedure planned within 6 months after 
dosing.
A subject who has taken any of these medications or anticipates receiving any of these non-drug 
therapies within the specified timeframe will be recorded as a protocol deviation.
The wash out periods of common prior treatments that are excluded medications in this study are 
presented in Table 5.
Table 5. Common Excluded Treatments and Associated Washout Period
Minimum Number of 
Days BEFORE First Dose
Minimum Number of 
Days AFTER First Dose
Treatment
30
365
180
Systemic antiviral therapy a
X
Interferon therapya
X
Concurrent chemotherapy or biological therapy for
treatment of neoplastic disease or other disorders
X
AAV vector or any other gene transfer agent
X
Investigational intervention b
X
Planned major surgery or an orthopedic surgical 
procedure
X
a. with the exception of antiretroviral therapy
b. or within 5 half-lives of the investigational drug administration, whichever is longer.
Treatments not listed above are considered allowable.
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7. DISCONTINUATION OF STUDY INTERVENTION AND SUBJECT 
DISCONTINUATION/WITHDRAWAL
7.1 Discontinuation of Study Participation
If study participation is discontinued (i.e., complete withdrawal from study participation), 
regardless of the reason, the evaluations listed for the Early Termination Visit should be 
performed as completely as possible.  Comments (spontaneous or elicited) or complaints made 
by the subject must be recorded in the source documents. The reason for discontinuation and date 
of discontinuation from study participation must be recorded in the source documents and the 
End of Study eCRF.
Subjects who received SHP648 and who then discontinue/withdraw will not be replaced.
7.2 Reasons for Discontinuation 
The reason for discontinuation must be determined by the investigator and recorded in the 
subject’s source document and on the End of Study eCRF. If a subject is discontinued for more 
than 1 reason, each reason should be documented in the source and the most clinically relevant 
reason should be indicated in the eCRF.
Reasons for discontinuation include, but are not limited to:

Adverse event (experienced prior to dosing that prevents further participation)

Withdrawal by subject

Lost to follow-up

Other - If “Other” is selected, the investigator must specify on the eCRF.
7.3 Withdrawal from the Study
Any subject may voluntarily withdraw (i.e., reduce the degree of participation in the study) 
consent for continued participation and data collection. A subject may withdraw from the study 
at any time and for any reason without prejudice to his/her future medical care by the physician 
or at the institution. The reason for withdrawal will be recorded on the End of Study eCRF. 
Assessments to be performed at the termination visit.
Subjects will also be withdrawn prior to SHP648 dosing for the following reasons:

The subject develops a confirmed FIX inhibitory antibody (≥0.6 Bethesda units (BU) by 
Nijmegen modification of the Bethesda assay).

The subject is non-compliant with study procedures, in the opinion of the investigator. 
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7.4 Subjects “Lost to Follow-up” Prior to the Last Scheduled Visit
A minimum of 3 documented attempts must be made to contact any subject who is lost to 
follow-up at any time point prior to the last scheduled contact (office visit or telephone contact). 
At least 1 of these documented attempts must include a written communication sent to the 
subject’s last known address via courier or mail (with an acknowledgement of receipt request) 
asking that the subject return to the site for final safety evaluations.
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8. STUDY ASSESSMENTS AND PROCEDURES
8.1 Study Periods
Refer to Table 1 for the schedule of study activities. Study assessments are detailed in 
Section 8.2 and Table 2.
Any subject who provides informed consent (i.e., signs and dates the informed consent form 
[ICF]) is considered a subject in the study.
The written informed consent for all procedures and assessments for the conduct of the study 
must be obtained prior to any study related procedure. If the required 5-day wash out period falls 
into the routine praxis, the ICF can be signed at the Screening Visit, otherwise it has to be signed 
before wash-out.
Every single subject, who enters the study will get a unique subject identification code (SIC). 
Subjects who fail to meet eligibility criteria may be re-screened; they will be assigned a different 
SIC at re-screening.
8.1.1 Screening Visit 
Prior to the Screening Visit, all subjects will undergo a minimum wash out period of 5 days 
following their last FIX therapy (on-demand or prophylaxis), after which blood samples will be 
collected to determine eligibility. Subjects will undergo the screening visit (up to 70 days before 
Day 0) prior to dosing with SHP648 (Day 0). An enrollment period of 45 days is planned for 
each cohort.
FIX activity levels at the Screening Visit determined by the central laboratory with the one-stage 
clotting assay will be used as baseline FIX activity levels. 
The following procedures and assessments will be performed:

Availability of signed informed consent

Eligibility criteria checked

Demographic information

Full Physical exam (examination of general appearance, head and neck, eyes and ears, 
nose and throat, chest, lungs, heart, abdomen, extremities and joints, lymph nodes, skin, 
and neurological), including height and weight

Medical history including hemophilia history (confirmation of diagnosis and 
severity; presence of any target joints; historical annualized bleed rate (ABR) based 
on documented data within the last 12 months), and documentation of all FIX 
replacement therapies and other medications used within the last 12 months. 
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Medical history to also include any surgeries, hospitalizations within the last 12 months, 
exposure to mutagenic agents, recent malignancy(ies), recent incidence or exacerbation of 
a pre-existing neurologic disorder, recent incidence or exacerbation of a prior 
rheumatologic or other autoimmune disorder, recent incidence of hematologic disorder.

12-lead ECG

Vital signs

Blood, bodily fluids and stools for laboratory assessments (Table 2):

Hematology, coagulation and clinical chemistry panels

Activated partial thromboplastin time (aPTT)

Local Laboratory Liver Function Tests (LFTs) including ALT, AST, and GGT

Hepatitis B surface antigen, hepatitis C antibody, hepatitis C virus (HCV) RNA, 
markers of autoimmune-mediated hepatitis

FIX genotyping, FIX activity level (central and local laboratories), FIX antigen

FIX inhibitor 

Antibodies to FIX and FIX transgene product 

Neutralizing and binding antibodies to AAV8 and AAV2

Cell-mediated immune (CMI) response to AAV8 and FIX transgene products


FibroSURETM and urine protein

Saliva, urine, stool, and semen collected for PCR of vector genomes

Human leucocyte antigen (HLA) (MHC haplotype), human immunodeficiency 
virus (HIV) serology

Blood collected for backup

Blood collection for a possible whole exome sequencing if subject provides consent 

Distribute patient diaries (paper diary) to capture subject reported data including bleeding 
episodes and FIX usage



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A screen failure is a subject who has given informed consent and failed to meet the inclusion 
and/or met at least 1 of the exclusion criteria and has not been randomized or administered 
investigational product(s). The study site is responsible for maintaining an enrollment/screening 
log that includes all subjects enrolled. The log also will serve to document the reason for 
screening failure. If a subject does not satisfy all screening criteria, the same subject may be re-
screened at a later date. A complete or partial re-screen may also become necessary at the 
discretion of the investigator or sponsor.
All screening data will be collected and reported in eCRFs, regardless of screening outcome. For 
the purpose of analysis, only the data from the most recent screening outcome will be used. If a 
subject is re-screened after a prior screening failure, the End of Study eCRF should be 
completed, and a new ICF, new SIC and new eCRF are required for that subject. Exemptions 
may be granted for administrative reasons (e.g. delay in timely availability of laboratory results).
8.1.2 Treatment Period 
8.1.2.1 Day 0
On Day 0 visit, eligibility criteria will be reviewed. 
For subjects who meet all inclusion and exclusion criteria the following procedures and 
assessments will be performed:

Targeted physical exam (includes weight and examination of the liver and skin, and 
otherwise driven by signs, symptoms, and complaints)

Vital signs (up to 3 hours pre-infusion and at 5, 15, and 30 mins and 1, 2, 3, 4, 6, and 
8 hours post-infusion)

SHP648 administration (single infusion)

Blood collected for laboratory assessments

Hematology, coagulation and clinical chemistry panels

aPTT (pre-SHP648 infusion)

Serum cytokines (including IL-6 and TNF-α).

FIX activity (central and local laboratories) and FIX antigen (pre-infusion [up to 
3 hours prior to infusion])

Neutralizing and binding antibodies to AAV8 and AAV2 (up to 3 hours pre-infusion)

Blood collected for backup (up to 3 hours pre-infusion and 8 hours post-infusion)

If patient provided consent, sample collection for a possible transcriptome testing 
(up to 3 hours pre-infusion and 8 hours post-infusion) 
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
If patient provided consent, a possible metabolomics analysis can be done provided 
plasma / serum backup sample is available

Collect/ review patient diaries

Concomitant medications (including FIX usage)

Bleeding episodes, spontaneous and traumatic

AEs (i.e., Untoward Medical Occurrences at Day 0 Visit)

Changes in intensity of physical activity
8.1.3 Follow-Up Period 
The follow-up period for this protocol is 12 months after the dosing visit (Day 0 Visit). At the 
end of this period, there will be a study completion visit (refer to Section 8.1.3.6, Table 1 and 
Table 2).
All AEs and SAEs that are not resolved at the time of Study Completion will be followed to 
closure (see Section Appendix 3.2).
8.1.3.1 Day 1
The following procedures and assessments will be performed:

Targeted physical exam (examination of the liver and skin, and otherwise driven by signs, 
symptoms, and complaints)

Vital signs

Blood, bodily fluids and stools collected for laboratory assessments:

Hematology, coagulation and clinical chemistry panels

aPTT

Serum cytokines (including IL-6 and TNF-α) 

FIX activity (central and local laboratories)

Saliva, urine, stool, and semen collected for PCR of vector genomes

Blood collected for backup

If patient provided consent, sample collection for a possible transcriptome testing 

If patient provided consent, a possible metabolomics analysis can be done provided 
plasma / serum backup sample is available

12-lead ECG
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
Collect/ review patient diaries

Concomitant medications (including FIX usage)

Bleeding episodes, spontaneous and traumatic

AEs

Changes in intensity of physical activity
8.1.3.2 Week 1 to Week 3
The following procedures and assessments will be performed at the first visit of the week 
(Clinic Visit):

Targeted physical exam (examination of the liver and skin, and otherwise driven by signs, 
symptoms, and complaints)

Vital signs

Blood, bodily fluids and stools collected for laboratory assessments:

Hematology, coagulation and clinical chemistry panels 

aPTT

HCV RNA (Week 1 only) 

FIX activity (central and local laboratories) and FIX antigen

FIX inhibitor

neutralizing and binding antibodies to AAV8 and AAV2 (Week 2 only)

CMI response to AAV8 and FIX transgene products 


Saliva, urine, stool, and semen collected for PCR of vector genomes (until results 
are negative for 2 consecutive time points)

Blood collected for backup

If patient provided consent, sample collection for a possible transcriptome testing

If patient provided consent, a possible metabolomics analysis can be done provided 
plasma / serum backup sample is available

Collect/ review patient diaries

Concomitant medications (including FIX usage)

Bleeding episodes, spontaneous and traumatic
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
AEs

Changes in intensity of physical activity
8.1.3.3 Week 4 to Week 14
The following procedures and assessments will be performed at the Clinic Visit (first visit of the 
week):

Targeted physical exam (examination of the liver and skin, and otherwise driven by signs, 
symptoms, and complaints)

Vital signs

Blood, bodily fluids and stools collected for laboratory assessments:

Hematology (Weeks 5, 7, 9, 11, & 13)

Coagulation (Weeks 5, 7, 9, 11, & 13)

Clinical chemistry panels (Weeks 5, 7, 9, 11, & 13)

aPTT

LFTs 

Central Laboratory LFTs @ Clinic Visits during Weeks 4, 6, 8, 10, 12, and 14

Local Laboratory LFTs @ every Clinic Visits during Weeks 4-14.

HCV RNA (Week 6 only)

FIX activity (central and local laboratories), FIX antigen

FIX inhibitor

Antibodies to FIX and FIX transgene product (Weeks 6 and 8 only)

Neutralizing and binding antibodies to AAV8 and AAV2 (Weeks 4, 8, and 12 only)

CMI response to AAV8 and FIX transgene products


Saliva, urine, stool, and semen collected for PCR of vector genomes (until results 
are negative for 2 consecutive time points)

Collect/ review patient diaries (Week 4, then every 2 weeks)

Concomitant medications (including FIX usage)

Bleeding episodes, spontaneous and traumatic

AEs

Changes in intensity of physical activity
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The following assessments will be performed weekly at every Lab Visit (second visit of the 
week):

Blood collected for laboratory assessments:

aPTT

LFTs 

Local Laboratory LFTs 

FIX activity (central and local laboratories).

Blood collected for backup 

If patient provided consent, sample collection for a possible transcriptome testing

If patient provided consent, a possible metabolomics analysis can be done provided 
plasma / serum backup sample is available.
8.1.3.4 Week 15
The following procedures and assessments will be performed (Clinic Visit only):

Targeted physical exam (examination of the liver and skin, and otherwise driven by signs, 
symptoms, and complaints)

Vital signs

Blood, bodily fluids and stools collected for laboratory assessments

Hematology, coagulation and clinical chemistry panels

aPTT

FIX activity (central and local laboratories), FIX antigen

FIX inhibitor

CMI response to AAV8 and FIX transgene products

Saliva, urine, stool, and semen collected for PCR of vector genomes (until results 
are negative for 2 consecutive time points)

Blood collected for backup

If patient provided consent, sample collection for a possible transcriptome testing

If patient provided consent, a possible metabolomics analysis can be done provided 
plasma / serum backup sample is available

Collect/ review patient diaries

Concomitant medications (including FIX usage)
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
Bleeding episodes, spontaneous and traumatic

AEs

Changes in intensity of physical activity
8.1.3.5 Month 4 to Month 6 and Month 9
The following procedures and assessments will be performed monthly:

Targeted physical exam (examination of the liver and skin, and otherwise driven by signs, 
symptoms, and complaints)

Vital signs

Blood, bodily fluids and stools collected for laboratory assessments:

Hematology, coagulation and clinical chemistry panels 

aPTT

FIX activity (central and local laboratories) and FIX antigen

FIX inhibitor

Antibodies to FIX and FIX transgene product (Months 6 and Month 9 only)

Neutralizing and binding antibodies to AAV8 and AAV2

CMI response to AAV8 and FIX transgene products (Months 4, 5, and Month 6 
only)

Saliva, urine, stool, and semen collected for PCR of vector genomes (until results 
are negative for 2 consecutive time points)

Blood collected for backup

If patient provided consent, sample collection for a possible transcriptome testing

If patient provided consent, a possible metabolomics analysis can be done provided 
plasma / serum backup sample is available

Collect/ review patient diaries (to be reviewed every 2 weeks)

Concomitant medications (including FIX usage)

Bleeding episodes, spontaneous and traumatic

AEs

Changes in intensity of physical activity


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8.1.3.6 Study Completion Visit (Month 12)
The following procedures and assessments will be performed at the Study Completion Visit:

Full Physical exam (examination of general appearance, head and neck, eyes and ears, nose 
and throat, chest, lungs, heart, abdomen, extremities and joints, lymph nodes, skin, and 
neurological), including height and weight

Vital signs

Blood collected for laboratory assessments:

Hematology, coagulation and clinical chemistry panels

aPTT 

HCV RNA

FIX activity (central and local laboratories) and FIX antigen

FIX inhibitor

Antibodies to FIX and FIX transgene product

Neutralizing and binding antibodies to AAV8 and AAV2

CMI response to AAV8 and FIX transgene products


FibroSURE (Month 12 only)

Blood collected for backup

If patient provided consent, sample collection for a possible transcriptome testing

If patient provided consent, a possible metabolomics analysis can be done provided 
plasma / serum backup sample is available

Collect/ review patient diaries

Concomitant medications (including FIX usage)

Bleeding episodes, spontaneous and traumatic

AEs

Changes in intensity of physical activity



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For tabular summaries of activities and assessment to be performed at the Study Completion 
Visit refer to Table 1 and Table 2.
8.1.3.7 Unscheduled Visit
Unscheduled visits will be performed if a >50% decrease in FIX activity from that of the last 
visit is observed at any time after Week 14. FIX activity levels and liver enzyme levels will be 
assessed at these visits.
The following procedures and assessments will be performed:

Targeted physical exam (examination of the liver and skin, and otherwise driven by signs, 
symptoms, and complaints)

Vital signs

Blood collected for laboratory assessments:

Hematology, coagulation and clinical chemistry panels,

aPTT

HCV RNA

FIX activity (central and local laboratories) and FIX antigen

FIX inhibitor

Antibodies to FIX and FIX transgene product

Neutralizing and binding antibodies to AAV8 and AAV2

CMI response to AAV8 and FIX transgene products

Blood collected for backup

If patient provided consent, sample collection for a possible transcriptome analysis

If patient provided consent, a possible metabolomics analysis can be done provided 
plasma / serum backup sample is available

Collect/ review patient diaries.

Concomitant medications (including FIX usage)

Bleeding episodes, spontaneous and traumatic

AEs

Changes in intensity of physical activity
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8.1.3.8 Early Study Termination Visit
The following procedures and assessments will be performed at the Early Termination Visit 
(including in cases of withdrawal or discontinuation):

Full Physical exam (examination of general appearance, head and neck, eyes and ears, nose 
and throat, chest, lungs, heart, abdomen, extremities and joints, lymph nodes, skin, and 
neurological), including height and weight

Vital signs

Blood, bodily fluids and stools collected for laboratory assessments:

Hematology, coagulation and clinical chemistry panels

aPTT 

HCV RNA

FIX activity (central and local laboratories) and FIX antigen

FIX inhibitor

Antibodies to FIX and FIX transgene product

Neutralizing and binding antibodies to AAV8 and AAV2

CMI response to AAV8 and FIX transgene products


FibroSURE

Saliva, urine, stool, and semen collected for PCR of vector genomes (until results 
are negative for 2 consecutive time points)

Blood collected for backup

If patient provided consent, sample collection for a possible transcriptome testing

If patient provided consent, a possible metabolomics analysis can be done provided 
plasma / serum backup sample is available

Collect/ review patient diaries

Concomitant medications (including FIX usage)

Bleeding episodes, spontaneous and traumatic

AEs

Changes in intensity of physical activity

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

For tabular summaries of activities and assessment to be performed in case of early termination 
refer to Table 1 and Table 2.
8.1.4 Additional Care of Subjects after the Study
No aftercare is planned for this study. Subjects completing the current Phase 1/2 Study 
(SHP648-101) will be highly encouraged to enroll seamlessly into a follow-up interventional 
study (Extension Study), in which they will be observed for an additional 4 years. 
8.2 Study Assessments 
8.2.1 Demographic and Other Baseline Characteristics
Subject demographic information including gender, age, and race will be collected prior to the 
subject being administered the SHP648 infusion.
8.2.1.1 Height and Weight
Height (in or cm) and weight (lb or kg) will be measured and recorded in the physician’s source 
documents. 
8.2.1.2 Medical and Medication History
Medical and medication history will be collected and recorded in the physician’s source 
documents. At the Screening Visit, the subject’s medical history will be described for the 
following body systems including severity (defined in Appendix 3) or surgery and start and end 
dates, if known: eyes, ears, nose, and throat; respiratory; cardiovascular; gastrointestinal; 
musculoskeletal; neurological; endocrine; hematopoietic/lymphatic; dermatological; and 
genitourinary. History will also include hemophilia history (confirmation of diagnosis and 
severity; presence of any target joints; historical ABR based on documented data within the 
previous 12 months) and documentation of all FIX replacement therapies and other medications 
used within the last 12 months.
The historical ABR including treated and untreated bleeding episodes in the 12 months prior to 
study enrollment based on medical records should also be recorded in the eCRF.
Hospitalizations, exposure to mutagenic agents, recent malignancy(ies), recent incidence or 
exacerbation of a pre-existing neurologic disorder, recent incidence or exacerbation of a prior 
rheumatologic or other autoimmune disorder, and recent incidence of a hematologic disorder will 
be recorded from 4 months before providing informed consent up to study 
completion/discontinuation (refer to Table 1).
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All medications taken and non-drug therapies received, from 4 weeks before providing informed 
consent until completion/termination will be recorded on the concomitant medications and 
non-drug therapies eCRFs.
8.2.2 Efficacy
8.2.2.1 Circulating Plasma FIX Activity and FIX Antigen Levels 
The following assessments will be made at the time points presented in Table 1 and Table 2 as 
part of the analysis and interpretation of efficacy outcome measures:

FIX activity (Central Laboratory: one-stage clotting AND chromogenic assays; 
Local Laboratory: one-stage clotting OR chromogenic assay).

FIX antigen.
8.2.2.2 Number of Bleeding Episodes Post-SHP648 Infusion 
The number of bleeding episodes post-SHP648 administration will be assessed based upon each 
individual bleeding episode, spontaneous or traumatic, recorded in the subject’s paper diary, 
and/or recorded in the physician/nurse/study site notes. Documented bleeding episodes in the 
12 months prior to study enrollment will also be recorded in the eCRF
A bleed is defined as subjective (e.g., pain consistent with a joint bleed [see Appendix 6]) or 
objective evidence of bleeding which may or may not require treatment with FIX. Bleeding 
episodes occurring at the same anatomical location (e.g., right knee) with the same etiology 
(e.g., spontaneous vs. injury) within 72 hours of onset of the first episode will be considered a 
single bleeding episode. If a bleed occurs following resolution of the bleed, it will be considered 
to be a “new” bleed and recorded accordingly. Bleeding occurring at multiple locations related to 
the same injury (e.g., knee and ankle bleeds following a fall) will be counted as a single bleeding 
episode.
Adverse events (AEs) and the details of concomitant medication use coincident with the 
treatment of all acute bleeding episodes will be recorded. Note that bleeding episodes are not to 
be reported as AEs (Appendix 3).
Hemophilia-related events meeting the criteria for seriousness will be reported as SAEs and 
described on the serious adverse event report (SAER) form.
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8.2.2.3 Consumption of Exogenous FIX Compared to before Gene Transfer
Data pertaining to the consumption of exogenous FIX during the 12-month period prior to 
SHP648 infusion will be collected and recorded as part of the medical history. Post-gene transfer 
consumption of exogenous FIX will be measured at the time points indicated in Table 1.
Weight-adjusted consumption of exogenous FIX will be determined based upon the amount of 
exogenous FIX infused, as recorded in the subject’s paper diary and the subject’s weight, as 
measured at the study site.
8.2.3 Safety
8.2.3.1 Physical Examination
Physical examinations will be performed by the investigator. At the Screening Visit, the physical 
examination will be performed on all major organ systems (i.e., general appearance, head and 
neck, eyes and ears, nose and throat, chest, lungs, heart, abdomen, extremities and joints, lymph 
nodes, skin, and neurological and others as indicated). If an abnormal condition is detected at 
screening, the condition will be described on the medical history eCRF. 
At subsequent study visits (as described in Table 1), a targeted physical examination will be 
performed (i.e., examination of the liver and skin, and otherwise driven by signs, symptoms, and 
complaints). At study visits, if a new abnormal or worsened abnormal pre-existing condition is 
detected, the condition will be described on the AE eCRF. If the abnormal value was not deemed 
an AE because it was due to an error, due to a preexisting disease (described in Appendix 3), not 
clinically significant, a symptom of a new/worsened condition already recorded as an AE, or due 
to another issue that will be specified, the investigator will record the justification on the source 
record. 
Abnormalities identified at the Screening Visit and at subsequent study visits will be recorded in 
the physician’s source documents.
Patient Activity Level: In the event of a bleed, subjects will be asked to estimate their activity 
levels. Subjects will be asked whether there have been changes in the intensity of their physical 
activity.
8.2.3.2 Adverse Events
At each study visit, subjects will be questioned in a general way to ascertain if AEs have 
occurred since the previous visit (e.g., “Have you had any health problems since your last 
visit?”). Adverse events are collected from the time informed consent is signed. Refer to 
Appendix 3 for AE definitions, assessment, collection time frame, and reporting procedures.
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8.2.3.3 Vital Signs
Vital signs will include body temperature (°C or °F), respiratory rate (breaths/min), pulse rate 
(beats/min), and systolic and diastolic blood pressure (mmHg).
Vital signs will be measured at the Screening Visit, on Day 0 up to 3 hours before administration 
of IP and 5, 15, 30 minutes, 1, 2, 3, 4, 6, and 8 hours after administration of IP, at each 
subsequent study visit, and at study completion/discontinuation. Blood pressure will be measured 
when subjects are in the supine position.
Vital sign values are to be recorded on the eCRF. Additional tests and other evaluations required 
to establish the significance or etiology of an abnormal result or to monitor the course of an AE 
should be obtained when clinically indicated. Any abnormal value that persists should be 
followed at the discretion of the investigator. 
The investigator will assess whether a change from baseline (as determined at the Screening 
Visit) in vital signs may be deemed clinically significant and whether the change should be 
considered and recorded as an AE.
8.2.3.4 Clinical Laboratory Tests
All clinical laboratory assessments (refer to Table 2) will be performed at a central laboratory, 
according to the laboratory manual. In addition, Liver Function Tests (ALT, AST, GGT) and 
FIX activity assessment will be performed by the local laboratory. The schedule for sample 
collection for laboratory analysis is described in Table 1 and Table 2.
All clinical laboratory tests will be performed according to the laboratory’s standard procedures. 
Reference ranges will be supplied by the laboratory and used to assess the results for clinical 
significance and out-of-range changes which may be associated with, or constitute, an AE. The 
investigator should assess out-of-range clinical laboratory values for clinical significance, 
indicating if the value(s) is/are not clinically significant or clinically significant. The 
investigator’s assessment of each laboratory value will be recorded on the eCRF. 
Abnormal clinical laboratory values, which are unexpected or not explained by the subject’s 
clinical condition, may, at the discretion of the investigator or sponsor, be repeated as soon as 
possible until confirmed, explained, or resolved.
A complete list of the clinical laboratory tests to be performed is provided in the SHP648-101 
Laboratory Manual.
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8.2.3.4.1 Hematology, Coagulation, Clinical Chemistry, and Markers of Autoimmune 
Response
The hematology panel will consist of complete blood count (hemoglobin, hematocrit, 
erythrocytes [i.e., red blood cell {RBC} count], and leukocytes [i.e., white blood cell count]) 
with differential (i.e., basophils, eosinophils, lymphocytes, monocytes, neutrophils), platelet 
counts, RBC distribution width, mean corpuscular volume, and mean corpuscular hemoglobin 
concentration. 
The coagulation panel will consist of PT, international normalized ratio, thrombin time, D-dimer, 
and fibrinogen activity. In addition, activated partial thromboplastin time, FIX antigen, FIX 
activity (performed as one-stage assay and as chromogenic assay) will also be assessed. 
The clinical chemistry panel will consist of sodium, potassium, chloride, carbon dioxide, blood 
urea nitrogen (BUN), creatinine, glucose, calcium, phosphate, magnesium, albumin, total 
protein, creatine kinase (CK), bilirubin (total & direct), ALT, AST, alkaline phosphatase (ALP), 
gamma-glutamyl transpeptidase (GGT), and lactate dehydrogenase (LDH).
The FibroSURE™ (Laboratory Corporation of America, Raritan, NJ, United States) will be 
measured at the Screening Visit and at Month 12 (Study Completion Visit). This score is based 
on an algorithm that includes following laboratory results: ALT, alpha-2-macroglobulin, 
apolipoprotein A1, total bilirubin, gamma-glutamyl transferase.
Markers of autoimmune-mediated hepatitis will include ANA, total IgG, anti-smooth muscle 
antibody, and anti-LKM1 titers. Serum cytokines will also be measured.
 
Blood will be obtained for assessment of hematology and clinical chemistry parameters and 
markers of autoimmune response at the study visits presented in Table 2. Hematology and 
clinical chemistry assessments will be performed on ethylenediamine-tetraacetic 
acid-anticoagulated whole blood and serum, respectively, at the central laboratory. 
The FIX activity assay will be performed at both local and central laboratories. ALT (liver 
transaminases) will be performed at local laboratories at time points specified in Table 2
(i.e. Week 4 to Week 14).
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8.2.3.4.2 Viral Serology
Viral serology testing will include HIV-1 and HIV-2 antibody, Hepatitis B core antibody, 
Hepatitis B surface antigen (HBsAg), Hepatitis C virus antibody and HCV RNA. The HCV titer 
will be confirmed by PCR for all subjects reported as HCV positive. All assessments will be 
performed at the Screening Visit. HCV RNA will also be performed at Week 1 and Week 6, and 
at the Early Study Termination Visit. Any positive test in HBsAg will be repeated using a new 
blood sample (refer to Table 2).
8.2.3.4.3 Genetic tests
The following tests are mandatory:
Assessment of F9 gene mutations (FIX genotyping) and human leukocyte antigen (HLA) 
genotype (MHC haplotype) will be performed.  of the following loci:  HLA-A, HLA-B, HLA-C, 
HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRB1, and HLA-DRB3/4/5. 
Samples will be collected at the Screening Visit (refer to Table 2) and tested right away or at a 
later time. Analyses will be performed for the study at the central laboratory. 
The results will be provided to the sites. The investigator will be responsible for informing the 
subject of the test results. 
Further voluntary genetic tests are listed in Section 8.2.4.3. 
8.2.3.4.4 Immunogenicity
The presence of binding antibodies to FIX, Padua FIX (FIX transgene product), inhibitor assays 
to FIX and Padua FIX, binding and neutralizing antibodies to AAV8 and AAV2, and CMI 
response to AAV8 and FIX transgene products based on an ELISPOT assay will be determined 
at the time points presented in Table 2.
Immunogenicity assessments for the proposed study will be carried out using validated assays 
performed by a qualified laboratory.

Study subjects will be screened and monitored for the presence of AAV8 (vector used in 
this study) specific neutralizing antibodies and binding antibodies (IgG and IgM) at a 
central facility using a validated protocol.  Subjects will also be tested for binding and 
neutralizing antibodies against AAV2 that infects humans with high prevalence.

CMI Assessment: the AAV8 and FIX specific cell mediated immunity will be assessed 
using validated IFN-γ ELISPOT assays at screening and throughout the study period.
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
Binding antibodies to FIX or Padua FIX, will be determined using validated FIX or 
Padua FIX specific enzyme-linked immunosorbent assay (ELISA). The assays will be 
performed at a qualified laboratory.

FIX Inhibitor Assay: Development of antibodies that inhibit FIX activity (FIX Inhibitors) 
and Padua FIX will be measured at a central laboratory using a validated, clot-based, 
method following the Nijmegen modification of the Bethesda assay.
Immunogenicity values are to be recorded on the eCRF. For each value, the investigator will 
determine whether the value is considered an AE (see definition in Appendix 3 and record the 
sign, symptom, or medical diagnosis on the AE eCRF).
Additional tests and other evaluations required to establish the significance or etiology of an 
abnormal result, or to monitor the course of an AE should be obtained when clinically indicated. 
Any abnormal value that persists should be followed at the discretion of the investigator.
8.2.3.4.5 Vector Genome Shedding
Blood and bodily excretions will be obtained at the time points presented in Table 1 and assessed 
for presence of SHP648 genome until 2 consecutive measurements are negative. Quantitative 
PCR assays will be used to detect SHP648 vector genome in blood, saliva, urine, stool, and 
semen.
An infectious center assay is used as a quality control and part of the characterization of the 
stocks of the investigational product. No viral growth-based assay is used in the evaluation of the 
body fluids of the treated subject.
8.2.3.5 Electrocardiogram
A standard 12-lead electrocardiogram (ECG) at rest will be performed at screening and at the 
Day 1 Visit and will be evaluated for medical significance by the investigator (refer to Table 1). 
12-lead ECG values are to be recorded on the eCRF. For each value, the investigator will 
determine whether the value is considered an AE (see definition in Appendix 3) and record the 
sign, symptom, or medical diagnosis on the AE eCRF. Additional tests and other evaluations 
required to establish the significance or etiology of an abnormal result or to monitor the course of 
an AE should be obtained when clinically indicated. Any abnormal value that persists should be 
followed at the discretion of the investigator. 
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8.2.4 Other
8.2.4.2 Pharmacokinetics and Pharmacodynamics 
The pharmacokinetic and pharmacodynamic activity of SHP648 will be evaluated using the 
following assessments:

FIX activity (central laboratory one-stage clotting assay) and FIX antigen (protein) levels 
in plasma

Antibodies to FIX and FIX transgene product

Neutralizing antibodies against AAV8 and AAV2

CMI response to AAV8 and FIX transgene product
Graphical displays over time may be used. Pharmacokinetic and pharmacodynamic analyses and 
modeling may be conducted to assess the timecourse of FIX and potential factors affecting the 
timecourse of FIX. Analyses and modeling may include, but are not limited to, FIX activity, FIX 
antigen concentration, clinical chemistry values, vector shedding values, subject demographics, 
antibody titers, concomitant drug use, clinical measures of effect, and AEs. This optional work 
will be reported separately. 
8.2.4.3 Exploratory Assays
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8.2.5 Volume of Blood to Be Drawn from Each Subject
Details of required blood sampling volumes for all mandatory and voluntary tests are presented 
in the Laboratory Manual and master ICF. 
Blood samples that remain after study testing is done may be stored and used to repeat testings, if 
the first testing does not provide a valid result. These samples will be destroyed at the latest 
when the final study report is written. 
In addition, mandatory backup samples in serum and plasma will be taken and stored short-term. 
These samples may be used primarily for re-testing and follow-up of an AE(s). Once it becomes 
apparent that these samples are no longer needed for the above-mentioned purposes, they will be 
destroyed once the final study report is written unless the patient provided consent that the 
samples may be used for further research. In this case, the remaining samples may be stored in a 
coded form for no more than 5 years after the final study report has been completed, and then the 
samples will be destroyed. 
8.2.6 Subject Diary
A paper diary will be provided to each subject at the Screening Visit to record the following 
information:
1.
Details of bleeding episodes.
2.
FIX consumption.
3.
Concomitant medications and non-drug therapies.
4.
Untoward medical occurrences.
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For each bleeding episode, the following information will be recorded by the subject or by 
authorized, qualified personnel at the participating site:

Location of bleed, e.g., joint, soft tissue, muscle, body cavity, intracranial, other.

Type of bleed, i.e., spontaneous (definitely no injury/trauma), injury (definitely due to 
injury/trauma), or unknown.

Severity of bleed:

Minor: Early hemarthrosis, mild muscle bleeding (refer to Appendix 6), or mild 
oral bleeding, including epistaxis.

Moderate: Moderate bleeding into muscles, bleeding into the oral cavity, 
definite/more extensive hemarthroses, and known trauma.

Major, life-/limb-threatening: Significant gastrointestinal bleeding, intracranial, 
intra-abdominal, or intrathoracic bleeding, central nervous system (CNS) bleeding, 
bleeding in the retropharyngeal or retroperitoneal spaces or iliopsoas sheath, 
fractures, head trauma.

Date and time of onset of bleed.

Date and time of resolution of bleeding episode.
Subjects will be trained on use of the diary. The diary will be provided in paper format and 
remain with the subject for the duration of the study. The investigator will review the diary for 
completeness and request missing information periodically and in a timely manner. Untoward 
events recorded in the paper diary will be reported as AEs according to the investigator’s 
discretion and clinical judgment. Subject entries in the paper diary will serve as source records.
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9. STATISTICAL CONSIDERATIONS
9.1 Statistical Analysis Process
All details regarding the statistical analysis and the preparation of tables, listings, and figures will 
be described in the statistical analysis plan (SAP). The SAP will provide the statistical methods 
and definitions for the analysis of the study outcomes, as well as describe the approaches to be 
taken for summarizing other study information such as subject disposition, demographics and 
baseline characteristics, investigational product exposure, and prior and concomitant 
medications. The SAP will also include a description of how missing, unused and spurious data 
will be addressed.
To preserve the integrity of the statistical analysis and study conclusions, the SAP will be 
finalized prior to database lock. All statistical analyses will be performed using SAS9.1 or 
later version (SAS Institute, Cary, NC 27513).
9.2 Data Monitoring Committee, Adaptive Design and Planned Interim Analysis 
An external Data Monitoring Committee (DMC) will be involved in the management of this 
study. The DMC will provide recommendation for dose escalation decisions as described in 
Section 6.2.1. Further details regarding the DMC can be found in the DMC charter, which will 
be available prior to the administration of investigational product.
In addition to safety data reviews by the DMC, additional interim analyses of efficacy and safety 
data may be performed at study milestones (e.g., when the first two subjects in the first cohort 
finish the Week 14 visit, or when the first 2 subjects in the last cohort finish the milestone week 
that will be determined by DMC once two patients in cohort 1 are evaluated for FIX peak 
expression), or otherwise up to 2 times every year for the duration of the study. Analyses due to 
different trigger points may be waived or combined for efficiency. 
9.3 Sample Size and Power Considerations
The sample size is expected to range from 2 to 21 evaluable subjects depending on the actual 
number of cohorts and the actual number of subjects in each cohort. This sample size was chosen 
to provide sufficient evidence of safety and exploration of signs of efficacy for this indication 
and is not based on formal statistical considerations. 
9.4 Statistical Analysis Set(s)
Classification into the Safety Analysis Set will be conducted prior to database lock. The Safety 
Analysis Set will consist of all subjects who receive any amount of IP. The Full Analysis Set 
(FAS) will consist of all subjects in the Safety Analysis Set who have at least 1 post-baseline 
FIX activity assessment. All safety analyses (including the primary analysis) will be performed 
on the Safety Analysis Set. All efficacy analyses will be performed on the FAS.
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9.5 Methods of Analyses
9.5.1 Primary Endpoint
The primary endpoint is the incidence and severity of AEs (serious and non-serious) related to 
SHP648 that include development of FIX inhibitory antibodies, ECG findings, and clinically 
significant changes in standard laboratory parameters and in vital signs.
AEs will be coded using the MedDRA. Treatment-emergent AEs (TEAEs) are defined as AEs 
with start dates at the time of or following the first exposure to IP.  The number of events and 
percentage of TEAEs and AEs related to IP will be tabulated by system organ class, by preferred 
term, and by treatment cohort. TEAEs and AEs related to IP will be further summarized by 
severity.  AEs leading to withdrawal, SAEs and deaths will be listed.
Clinical laboratory tests, vital signs, and ECG findings will be summarized by cohort and visit. 
Potentially clinically important findings will also be summarized or listed.
9.5.2 Secondary Endpoints
The secondary endpoints are: 

Circulating plasma FIX activity and FIX antigen levels 

ABR before in comparison to before gene transfer

Neutralizing and binding antibody titers to AAV8

T-cell response to AAV8 and FIX transgene products

Presence of SHP648 genome by type of bodily fluid  

Percentage of change in consumption of exogenous FIX before and after gene transfer
Plasma FIX levels, antigen levels, exogenous FIX consumption, and ABR will be summarized 
using descriptive statistics by cohort.
The number and proportion of subjects with positive neutralizing and binding antibodies too 
AAV8, of subjects with T-cell response to AAV8 and FIX transgene, and of those with SHP648 
genomes present in bodily fluids after the SHP 648 administration will be summarized by cohort 
and overall.
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9.5.3 Exploratory Endpoints
Exploratory endpoints include 
9.6 Other Analyses
No other analyses are planned in this study.
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10. SUPPORTING DOCUMENTATION AND OPERATIONAL CONSIDERATIONS
APPENDIX 1  REGULATORY, ETHICAL, AND STUDY OVERSIGHT
CONSIDERATIONS
Appendix 1.1  Regulatory and Ethical Considerations
This study is conducted in accordance with current applicable regulations including ICH E6, EU 
Directive 2001/20/EC, and all updates, as well as local ethical and legal requirements. 
Compliance with these regulations and guidelines also constitutes compliance with the ethical 
principles described in the Declaration of Helsinki.
The name and address of each third-party vendor (e.g., CRO) used in this study will be 
maintained in the investigator’s and sponsor’s files, as appropriate.
Appendix 1.2  Sponsor’s Responsibilities
Good Clinical Practice Compliance
The study sponsor and any third party to whom aspects of the study management or monitoring 
have been delegated will undertake their assigned roles for this study in compliance with all 
applicable industry regulations, current ICH Good Clinical Practice (GCP) Guidelines, as well as 
all applicable national and local laws and regulations.
Visits to sites are conducted by representatives of the study sponsor and/or the company 
organizing/managing the research on behalf of the sponsor to inspect study data, subjects’ 
medical records, and eCRFs in accordance with current GCP and the respective local and 
(inter)national government regulations and guidelines. Records and data may additionally be 
reviewed by auditors or by regulatory authorities.
The sponsor ensures that local regulatory authority requirements are met before the start of the 
study. The sponsor (or a nominated designee) is responsible for the preparation, submission, and 
confirmation of receipt of any regulatory authority approvals required prior to release of 
investigational product for shipment to the site.
Indemnity/Liability and Insurance
The sponsor of this research adheres to the recommendations of the Association of British 
Pharmaceutical Industry Guidelines. If appropriate, a copy of the indemnity document is 
supplied to the investigator before study initiation, per local country guidelines.
The sponsor ensures that suitable clinical study insurance coverage is in place prior to the start of 
the study. An insurance certificate is supplied to the CRO as necessary.
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Public Posting of Study Information
The sponsor is responsible for posting appropriate study information on applicable websites. 
Information included in clinical study registries may include participating investigators’ names 
and contact information.
The timing for study registration and results summary posting must be in accordance with 
applicable local and national requirements.
Submission of Summary of Clinical Study Report to Competent Authorities of Member 
States Concerned and Ethics Committees (ECs)
The sponsor will provide a summary of the clinical study report to the competent authority of the 
member state(s) concerned as required by regulatory requirement(s) and to comply with the 
Community guideline on GCP. This requirement will be fulfilled within 6 months of study 
completion date for pediatric studies and within 1 year for non-pediatric studies as per guidance. 
The sponsor will provide the ECs with a copy of the same summary.
Study Suspension, Termination, and Completion
The sponsor may suspend or terminate the study, or part of the study, at any time for any reason. 
If the study is suspended or terminated, the sponsor will ensure that applicable sites, regulatory 
agencies and IRBs/ECs are notified as appropriate. Additionally, the discontinuation of a 
registered clinical study which has been posted to a designated public website will be updated 
accordingly.
The sponsor will make an end-of-study declaration to the relevant competent authority as 
required by Article 10 (c) of Directive 2001/20/EC.
Appendix 1.3  Investigator’s Responsibilities
Good Clinical Practice Compliance
The investigator must undertake to perform the study in accordance with ICH GCP E6 R2 
(2016), EU Directive 2001/20/EC, and applicable regulatory requirements and guidelines.
It is the investigator’s responsibility to ensure that adequate time and appropriately trained 
resources are available at the site prior to commitment to participate in this study. The 
investigator should also be able to estimate or demonstrate a potential for recruiting the required 
number of suitable subjects within the agreed recruitment period.
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The investigator will maintain a list of appropriately qualified persons to whom the investigator 
has delegated significant study-related tasks, and shall, upon request of the sponsor, provide 
documented evidence of any licenses and certifications necessary to demonstrate such 
qualification. Curriculum vitae for investigators and sub-investigators are provided to the study 
sponsor (or designee) before starting the study.
If a potential research subject has a primary care physician, the investigator should, with the 
subject’s consent, inform them of the subject’s participation in the study.
A coordinating principal investigator is appointed to review the final clinical study report for 
multicenter studies. Agreement with the final clinical study report is documented by the signed 
and dated signature of the coordinating principal investigator, in compliance with Directive 
2001/83/EC as amended by Directive 2003/63/EC and ICH Guidance E3 (1995).
Protocol Adherence and Investigator Agreement
The investigator and any sub-investigators must adhere to the protocol as detailed in this 
document. The investigator is responsible for enrolling only those subjects who have met 
protocol eligibility criteria. Investigators are required to sign an investigator agreement to 
confirm acceptance and willingness to comply with the study protocol.
If the investigator suspends or terminates the study at their site, the investigator will promptly 
inform the sponsor and the IRB/EC and provide them with a detailed written explanation. The 
investigator will also return all investigational product, containers, and other study materials to 
the sponsor. Upon study completion, the investigator will provide the sponsor, IRB/EC 
(Institutional Review Board/Ethic Committee), and regulatory agency with final reports and 
summaries as required by (inter)national regulations.
Communication with local IRBs/ECs, to ensure accurate and timely information is provided at 
all phases during the study, may be done by the sponsor, applicable CRO, investigator, or for 
multicenter studies, the coordinating principal investigator according to national provisions and 
will be documented in the investigator agreement.
Documentation and Retention of Records
Case Report Forms
In this trial electronic Case Report Forms (eCRFs) will be used.
The investigator is responsible for maintaining adequate and accurate medical records from 
which accurate information is recorded onto CRFs, which have been designed to record all 
observations and other data pertinent to the clinical investigation. Case report forms must be 
completed by the investigator or designee as stated in the site delegation log.
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All data will have separate source documentation; no data will be recorded directly onto the 
CRF.
The CRA/study monitor will verify the contents against the source data per the monitoring plan. 
If the data are unclear or contradictory, queries are sent for corrections or verification of data.
Recording, Access, and Retention of Source Data and Study Documents
Original source data to be reviewed during this study will include, but are not limited to: 
subject’s medical file, Health Care Questionnaires, subject diary cards and original clinical 
laboratory reports.
All key data must be recorded in the subject’s source documents.
The investigator must permit authorized representatives of the sponsor; the respective national, 
local, or foreign regulatory authorities; the IRB/EC; and auditors to inspect facilities and to have 
direct access to original source records relevant to this study, regardless of media.
The CRA/study monitor (and auditors, IRB/EC or regulatory inspectors) may check the CRF 
entries against the source documents. The consent form includes a statement by which the 
subject agrees to the monitor/auditor from the sponsor or its representatives, national or local 
regulatory authorities, or the IRB/EC, having access to source data (e.g., subject’s medical file, 
appointment books, original laboratory reports, X-rays etc.).
These records must be made available within reasonable times for inspection and duplication, if 
required, by a properly authorized representative of any regulatory agency (e.g., the US FDA, 
European medicine agency (EMA), UK Medicines and Healthcare products Regulatory Agency) 
or an auditor.
Essential documents must be maintained according to ICH GCP requirements and may not be 
destroyed without written permission from the sponsor.
Audit/Inspection
To ensure compliance with relevant regulations, data generated by this study must be available 
for inspection upon request by representatives of, for example, the US FDA (as well as other US 
national and local regulatory authorities), the EMA, the Medicines and Healthcare products 
Regulatory Agency, other regulatory authorities, the sponsor or its representatives, and the 
IRB/EC for each site.
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Financial Disclosure
The investigator is required to disclose any financial arrangement during the study and for 1 year 
after, whereby the outcome of the study could be influenced by the value of the compensation for 
conducting the study, or other payments the investigator received from the sponsor. The 
following information is collected: any significant payments from the sponsor or subsidiaries 
such as a grant to fund ongoing research, compensation in the form of equipment, retainer for 
ongoing consultation or honoraria; any proprietary interest in investigational product; any 
significant equity interest in the sponsor or subsidiaries as defined in 21 CFR 54 2(b) (1998).
Appendix 1.4  Data Management Considerations
Data Collection
The study will be monitored according to GCP. The investigators’ authorized site personnel must 
enter the information required by the study CRF Completion Guidelines or similar for all data 
requiring transcription of the source. A study monitor will visit each site in accordance with the 
monitoring plan and review the CRF data against the source data for completeness and accuracy. 
Discrepancies between source data and data entered on the CRF will be addressed by qualified 
site personnel. When a data discrepancy warrants correction, the correction will be made by 
authorized site personnel. Data collection procedures will be discussed with the site at the site 
initiation visit and/or at the investigator’s meeting. 
Data Management
Data are to be entered into a clinical database. Quality control and data validation procedures are 
applied to ensure the validity and accuracy of the clinical database. No changes will be allowed 
to the source data from patient reported dairies except for the type of data listed below.
List of data that may be modified:

Demography 

Visit Labels\type 

Site-entered Data 

Data that can be verified through another source system like IRT
Data are to be reviewed and checked for omissions, errors, and values requiring further 
clarification using computerized and manual procedures. Data queries requiring clarification are 
to be communicated to the site for resolution. Only authorized personnel will make corrections to 
the clinical database, and all corrections are documented in an auditable manner.
Data Handling in blinded studies
This paragraph is not applicable to this study.
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Appendix 1.5  Ethical Considerations
Informed Consent
It is the responsibility of the investigator to obtain written informed consent from all study 
subjects prior to any study-related procedures including screening assessments. All consent 
documentation must be in accordance with applicable regulations and GCP. Each subject is 
requested to sign and date the subject informed consent form or a certified translation if 
applicable, after the subject has received and read the written subject information and received 
an explanation of what the study involves, including but not limited to: the objectives, potential 
benefits and risk, inconveniences, and the subject’s rights and responsibilities. A copy of the 
informed consent documentation (i.e., a complete set of subject information sheets and fully 
executed signature pages) must be given to the subject. This document requires translation into 
the local language. Signed consent forms must remain in each subject’s study file and must be 
available for verification at any time.
A copy of the IRB/EC’s written favorable opinion/approval of these documents must be 
provided to the sponsor prior to the start of the study unless it is agreed to and documented 
(abiding by regulatory guidelines and national provisions) prior to study start that another party 
(i.e., sponsor or coordinating principal investigator) is responsible for this action. Additionally, if 
the IRB/EC requires modification of the sample subject information and consent document 
provided by the sponsor, the documentation supporting this requirement must be provided to the 
sponsor.
Institutional Review Board or Ethics Committee
For sites outside the EU, it is the responsibility of the investigator to submit this protocol, the 
informed consent document (approved by the sponsor or their designee), relevant supporting 
information and all types of subject recruitment information to the IRB/EC for review, and all 
must be approved prior to site initiation.
The applicant for an EC opinion can be the sponsor or investigator for sites within the EU; for 
multicenter studies, the applicant can be the coordinating principal investigator or sponsor, 
according to national provisions.
Responsibility for coordinating with IRBs/ECs is defined in the investigator agreement. 
Investigational product supplies will not be released until the CRO has received written IRB/EC 
approval.
Prior to implementing changes in the study, the sponsor and the IRB/EC must approve any 
revisions of all informed consent documents and amendments to the protocol unless there is a 
subject safety issue. If required by local law, substantial amendments to the protocol must also 
be approved by the appropriate regulatory agency prior to implementation.
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For sites outside the EU, the investigator is responsible for keeping the IRB/EC apprised of the 
progress of the study and of any changes made to the protocol at least annually or more 
frequently in accordance with the requirements, policies, and procedures established by the 
IRB/EC. This can be the responsibility of the sponsor or investigator for sites within the EU; or 
for multicenter studies, the coordinating principal investigator, according to national provisions. 
The investigator must also keep the local IRB/EC informed of any serious and significant AEs as
required by IRB/EC procedures.
Privacy and Confidentiality
The confidentiality of records that may be able to identify subjects will be protected in 
accordance with applicable laws, regulations, and guidelines.
After subjects have consented to take part in the study, the sponsor and/or its representatives 
reviews their medical records and data collected during the study. These records and data may, in 
addition, be reviewed by others including the following: independent auditors who validate the 
data on behalf of the sponsor; third parties with whom the sponsor may develop, register, or 
market SHP648; national or local regulatory authorities; and the IRB(s)/EC(s) which gave 
approval for the study to proceed. The sponsor and/or its representatives accessing the records 
and data will take all reasonable precautions in accordance with applicable laws, regulations, and 
guidelines to maintain the confidentiality of subjects’ identities. Subjects are assigned a unique 
identifying number; however, their initials and date of birth may also be collected, if permitted 
under local laws governing privacy. 
The results of studies containing subjects’ unique identifying number, relevant medical records, 
and possibly initials and dates of birth, where allowed per local law, may be transferred to, and 
used in, other countries which may not afford the same level of protection that applies within the 
countries where this study is conducted. The purpose of any such transfer would include: to 
support regulatory submissions, to conduct new data analyses to publish or present the study 
results, or to answer questions asked by regulatory or health authorities.
Study Results/Publication Policy
The term “Publication” shall mean any paper, article, manuscript, report, poster, 
internet posting, presentation slides, abstract, outline, video, instructional material, 
presentation (in the form of a written summary), or other public disclosure of the study 
results, in printed, electronic, oral, or other form. The parties understand and agree that 
participation in the study may involve a commitment to publish the data from all sites 
participating in the study in a cooperative publication with other investigators prior to 
publication or oral presentations of the study results on an individual basis. 
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The site agrees not to publish or present the site’s study results until such time as either the 
aggregate multi-site study results are published in a cooperative publication or for a period of 
one (1) year after termination or completion of the study at all participating sites, whichever shall 
first occur. After that time, the site may publish the site’s study results in scientific journals or 
present the study results at symposia or other professional meetings in accordance with the 
following provisions:
If the study is part of a multicenter study, the first publication of the study results shall be made 
by the sponsor in conjunction with the sponsor’s presentation of a joint, multicenter publication 
of the compiled and analyzed study results. If such a multicenter publication is not submitted to a 
journal for publication by the sponsor within an 18-month period after conclusion, abandonment, 
or termination of the study at all sites, or after the sponsor confirms there shall be no multicenter 
study publication of the study results, an investigator may individually publish the study results 
from the specific site in accordance with this section. The investigator must, however, 
acknowledge in the publication the limitations of the single site data being presented.
At least sixty (60) days prior to submitting an abstract, manuscript, or other document for 
publication, a copy of the proposed publication will be provided to the sponsor by the site for 
review. Upon the sponsor’s request, the site agrees to remove any and all confidential 
information (expressly excluding study results) identified in the publication and to delay such 
submission or presentation for an additional sixty (60) day period in order to allow the sponsor 
time to file any patent application(s). All publications of the study results shall appropriately 
reference the multi-site study publication, if any, or the fact that the study results are a subset of 
data resulting from a larger multi-site study.
Shire is committed to transparent dissemination of all scientific, technical and medical 
manuscripts generated from Shire-supported research. Therefore, after January 1, 2018, Shire 
will require the submission of all Shire-supported research manuscripts to journals that offer 
public availability via Open Access (including publisher platforms/repositories and self-
archiving). Open Access refers to the free at point of entry, online availability of published 
research output with, where available, rights of re-use according to an End User License.
Unless otherwise required by the journal in which the publication appears, or the forum in which 
it is made, authorship will comply with the International Committee of Medical Journal Editors 
(ICMJE) Recommendation for the Conduct, Reporting, Editing and Publication of Scholarly 
Work in Medical journals. Participation as an investigator does not confer any rights to 
authorship of publications.
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APPENDIX 2  CLINICAL LABORATORY TESTS
For a list of the clinical laboratory tests that will be performed and special considerations 
regarding these laboratory tests, refer to the SHP648-101 Laboratory Manual.
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APPENDIX 3  ADVERSE EVENTS: DEFINITIONS AND PROCEDURES FOR 
RECORDING, EVALUATING, FOLLOW-UP, AND REPORTING
Appendix 3.1  Adverse Event Definitions
An adverse event (AE) is any untoward medical occurrence in a clinical investigation subject 
administered a pharmaceutical product and that does not necessarily have a causal relationship 
with this investigational product or medicinal product. An AE can therefore be any unfavorable 
and unintended sign (including a clinically significant laboratory finding), symptom, or disease 
temporally associated with the use of a medicinal (investigational) product, whether or not 
causality is suspected (ICH Guidance E2A 1995).
Treatment-emergent Adverse Event
A treatment-emergent adverse event (TEAE) is defined as any event emerging or manifesting at 
or after the initiation of treatment with an investigational product or medicinal product or any 
existing event that worsens in either intensity or frequency following exposure to the 
investigational product or medicinal product.
Serious Adverse Event
A serious adverse event (SAE) is any untoward clinical manifestation of signs, symptoms or 
outcomes (whether considered related to investigational product or not and at any dose:

Results in death

Is life-threatening. Note: The term “life-threatening” in the definition of “serious” refers to 
an event in which the subject was at risk of death at the time of the event; it does not refer 
to an event which hypothetically might have caused death if it was more severe.

Requires inpatient hospitalization or prolongation of hospitalization. Note: Hospitalizations 
that are the result of elective or previously scheduled investigations procedures or surgery 
for pre-existing conditions and have not worsened after initiation of treatment should not 
be classified as SAEs. 

For example, an admission for a previously scheduled ventral hernia repair would 
not be classified as an SAE; however, complication(s) resulting from a 
hospitalization for an elective or previously scheduled surgery that meet(s) serious 
criteria must be reported as SAE(s).

If the subject requires urgent or emergency surgery after SHP648 administration, it 
is recognized and expected that during the surgery and in the post-surgical period, 
the subject can be treated with infused FIX concentrates to achieve FIX levels 
consistent with the standard of care at the subject institution.

Results in persistent or significant disability/incapacity
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
Results in a congenital abnormality/birth defect

Is an important medical event. Note: Important medical events that may not result in death, 
be life-threatening, or require hospitalization may be considered an SAE when, based upon 
appropriate medical judgment, they may jeopardize the subject and may require medical or 
surgical intervention to prevent 1 of the outcomes listed in this definition. Examples of 
such medical events include:

Bronchospasm associated with anaphylaxis 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.

Reviewed and confirmed seroconversion for human immunodeficiency virus (HIV), 
hepatitis A virus (HAV), hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis E 
virus (HEV), or parvovirus B19 (B19V)

Development of a confirmed inhibitor to FIX with an inhibitor level ≥0.6 BU using the 
Nijmegen modification of the Bethesda assay.

Severe hypersensitivity/anaphylactic reactions to SHP648.
Uncomplicated pregnancies, following paternal exposure to IP are not considered an (S)AE; 
however, any pregnancy complication or pregnancy termination by therapeutic, elective, or 
spontaneous abortion shall be considered an SAE. 
Any pregnancy that occurs in the partner of the father after administration of IP but prior to 
clearance of SHP648 genomes from the semen will be reported on a Pregnancy Report Form and 
followed-up at estimated date of delivery and 1 year post-delivery, if feasible.
For this protocol, bleeding events will not be collected as SAE(s):
Hospitalization for planned port placement or removal is not considered an SAE, however, 
any hospitalization required for an emergency port removal is considered an SAE.
Unexpected Adverse Event
An unexpected adverse event is an AE whose nature, severity, specificity, or outcome is not 
consistent with the term, representation, or description used in the Reference Safety Information 
(RSI). “Unexpected” also refers to the AEs that are mentioned in the IB as occurring with a class 
of drugs or as anticipated from the pharmacological properties of the product, but are not 
specifically mentioned as occurring with the particular product under investigation.
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The expectedness of AEs will be determined by the sponsor using the IB as the RSI. This 
determination will include considerations such as the number of AEs previously observed, but 
not on the basis of what might be anticipated form the pharmacological properties of a product.
Suspected Unexpected Serious Adverse Reaction 
A Suspected Unexpected Serious Adverse Reaction (SUSAR) is defined as any suspected 
adverse reaction to study treatment (i.e., including active comparators) that is both serious and 
unexpected. 
The event(s) must meet all of the following:

Suspected adverse reaction

Serious

Unexpected

Assessed as related to study treatment
Symptoms of the Disease under Study
Symptoms of the disease under study should not be classed as AEs as long as they are within the 
normal day-to-day fluctuation or expected disease progression and are part of the efficacy or 
effectiveness data collected in the study. Significant worsening of symptoms should be recorded 
as an AE.
For the purposes of this study, the following non-serious events experienced after the first IP 
exposure are to be collected under other study endpoints and thus are not reportable on the AE 
eCRF, nor will they be included in the analysis of AEs:
1.
Hospital or study site visits for administration of FIX.
2.
Hospitalization for routine bleeding episode management that could be managed in the 
clinic or home-setting but for which the subject was hospitalized.
3.
Hospitalizations for planned medical or surgical procedures, e.g., placement of a central 
venous line (however, when there is an increase in the severity, duration, or frequency of a 
preexisting disease, the event must be described on the AE eCRF).
4.
Seroconversion after documented HAV/HBV vaccination prior to or during the study 
period.
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5.
Bleeding episodes/hemophilia-related events: 
Bleeding episodes are part of the underlying disease and therefore are not AEs. If a 
bleeding episode was caused by an injury (e.g., a fall), the injury would not be reported as 
an AE, unless it resulted in a medical finding other than a bleeding episode (e.g., abrasion 
of skin; fractured tibia). Therefore, any hemophilia-related event (e.g., hemarthrosis, 
bruising, hemorrhage) will not be reported as an AE, but these events will be recorded 
on the bleeding event eCRF. However, hemophilia-related events meeting the criteria for 
seriousness (e.g., a gastrointestinal hemorrhage requiring hospitalization) will be reported 
as SAEs and described on the SAER form.
Preexisting conditions prior to randomization or initiation of study medication are described in 
the medical history, and those that manifest with the same severity, frequency, or duration after 
drug exposure, are not be recorded as AEs. However, when there is an increase in the severity, 
duration or frequency of a preexisting condition, the event must be described on the AE CRF.
Clinical Laboratory and Other Safety Assessment
A change in the value of a clinical laboratory parameter, vital sign measure, or ECG assessment 
can represent an AE if the change is clinically relevant or if, during administration of 
investigational product, a shift of a parameter is observed from a value in the normative range to 
a value that is outside the normal range and considered clinically significant, or a further waning 
of an already clinically significant value. When evaluating such changes, the extent of deviation 
from the reference range, the duration until return to the reference range, either while continuing 
administration or after the end of administration with the investigational product, and the range 
of variation of the respective parameter within its reference range, should also be considered.
If, at the end of the treatment phase, there are abnormal clinical laboratory (such as hematology 
panel or clinical chemistry panel), vital sign, or ECG values which were not present at the 
pretreatment evaluation observed closest to the start of study treatment, further investigations 
should be performed until the values return to within the reference range or until a plausible 
explanation (e.g., concomitant disease or expected disease evolution) is found for the abnormal 
values.
The investigator should assess, based on the above criteria and the clinical condition of the 
subject, whether a change in a clinical laboratory value, vital sign, or ECG parameter is clinically 
significant and represents an AE.
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Appendix 3.2  Collection of Adverse Events 
All AEs/SAEs are collected from the time the informed consent document is signed until the 
defined follow-up period stated in Section 8.1.3. This includes events occurring during the 
screening phase of the study, regardless of whether or not investigational product is 
administered. 
All AEs/SAEs must be followed to closure, regardless of whether the subject is still participating 
in the study. Closure indicates that an outcome is reached, or stabilization is achieved (the 
investigator does not expect any further improvement or worsening of the event). 
Recovering/resolving AEs will be followed until resolution, medically stabilized, or 4 weeks 
after the Study Completion/Termination Visit, whichever comes first, and the follow-up 
information is to be documented in the eCRF.
Appendix 3.3 Assessment of Adverse Events
Severity Categorization
The severity of AEs must be recorded during the course of the event including the start and stop 
dates for each change in severity. An event that changes in severity is captured as a new event. 
Worsening medical conditions, signs or symptoms present prior to initiation of investigational 
product, must be recorded as new AEs.
For example, if a subject reports mild intermittent dyspepsia prior to initiation of dosing with the 
investigational product and the dyspepsia becomes severe and more frequent after first dose, a 
new AE of severe dyspepsia (with the appropriate date of onset) should be documented in the 
source.
The medical assessment of severity is determined by using the following definitions:

Mild: A type of AE that is usually transient and may require only minimal treatment or 
therapeutic intervention. The event does not generally interfere with usual activities of 
daily living.

Moderate: A type of AE that is usually alleviated with specific therapeutic intervention. 
The event interferes with usual activities of daily living, causing discomfort but poses no 
significant or permanent risk of harm to the research subject.

Severe: A type of AE that interrupts usual activities of daily living, or significantly affects 
clinical status, or may require intensive therapeutic intervention.
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Relationship Categorization
A physician/investigator must make the assessment of relationship to investigational product for 
each AE. The investigator should decide whether, in his or her medical judgment, there is a 
reasonable possibility that the event may have been caused by the investigational product. If 
there is no valid reason for suggesting a relationship, then the AE should be classified as “not 
related”. Otherwise, if there is any valid reason, even if undetermined or untested, for suspecting 
a possible cause-and-effect relationship between the investigational product and the occurrence 
of the AE, then the AE should be considered “related”. The causality assessment must be 
documented in the source.
The following additional guidance may be helpful:
Table A1. Adverse Event Relationship Categorization
Related
The temporal relationship between the event and the administration of the investigational 
product is compelling enough and/or follows a known or suspected response pattern to that 
product, and the event cannot be explained by the subject’s medical condition, other therapies, 
or accident.
Not related
The event can be readily explained by other factors such as the subject’s underlying medical 
condition, concomitant therapy, or accident and no plausible temporal or biologic relationship 
exists between the investigational product and the event.
Outcome Categorization
The outcome of AEs must be documented in the source during the course of the study. Outcomes 
are as follows:

Fatal

Not Recovered/Not Resolved

Recovered/Resolved

Recovered/Resolved with Sequelae

Recovering/Resolving

Unknown
If applicable, action taken (i.e., dose increased, dose not changed, dose reduced, drug interrupted, 
drug withdrawn, not applicable, or unknown) will also be recorded on the AE CRF.
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Appendix 3.4  Safety Reporting
Reference Safety Information
The RSI for this study is the Investigator’s Brochure which the sponsor has provided under 
separate cover to all investigators.
Reporting Procedures
All initial and follow-up SAE reports must be reported by the investigator to the Shire Global 
Drug Safety Department and the CRO/Shire medical monitor within 24 hours of becoming aware 
of the event. Note: The 24-hour reporting requirement for SAEs does not apply to reports of 
abuse, misuse, overdose, or medication errors (see Appendix 3.9) unless they result in an SAE.
The investigator must complete, sign, and date the Shire “Clinical Study Adverse Event Form for 
Serious Adverse Events (SAEs) and Non-serious AEs as Required by Protocol”, verify the 
accuracy of the information recorded on the form with the corresponding source documents 
(Note: Source documents are not to be sent unless requested), and fax or e-mail the form to the 
Shire Global Drug Safety Department. A copy of the Shire Clinical Study Adverse Event Form 
for Serious Adverse Events (SAEs) and Non-serious AEs as Required by Protocol (and any 
applicable follow-up reports) must also be sent to the CRO/Shire medical monitor using the 
details specified in the emergency contact information section of the protocol.
Appendix 3.5  Serious Adverse Event Collection Time Frame
All SAEs (regardless of relationship to investigational product) are collected from the time the 
subject signs the informed consent until the defined follow-up period stated in Section 8.1.3 and 
must be reported to the Shire Global Drug Safety Department and the CRO/Shire medical 
monitor within 24 hours of the first awareness of the event.
In addition, any SAE(s) considered “related” to the investigational product and discovered by the 
investigator at any interval after the study has completed must be reported to the Shire Global 
Drug Safety Department within 24 hours of the reported first becoming aware of the event. 
Follow up and documentation of such SAE(s) will be conducted as per Shire's standard operating 
procedure.
Appendix 3.6  Serious Adverse Event Onset and Resolution Dates
The onset date of the SAE is defined as the date the event meets serious criteria. The resolution 
date is the date the event no longer meets serious criteria, the date the symptoms resolve, or the 
event is considered chronic. In the case of hospitalizations, the hospital admission and discharge 
dates are considered the onset and resolution dates, respectively.
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In addition, any signs or symptoms reported by the subject after signing the informed consent 
form, or leading up to the onset date of the SAE, or following the resolution date of the SAE, 
must be recorded as an AE, if appropriate.
Appendix 3.7  Fatal Outcome
Any SAE that results in the subject’s death (e.g., the SAE was noted as the primary cause of 
death) must have fatal checked as an outcome with the date of death recorded as the resolution 
date. For all other events ongoing at the time of death that did not contribute to the subject’s 
death, the outcome should be considered not resolved, without a resolution date recorded.
For any SAE that results in the subject’s death or any ongoing events at the time of death, unless 
another investigational product action was previously taken (e.g., drug interrupted, reduced, 
withdrawn), the action taken with the investigational product should be recorded as “dose not 
changed” or “not applicable” (if the subject never received investigational product). The 
investigational product action of withdrawn should not be selected solely as a result of the 
subject’s death.
Appendix 3.8  Pregnancy
All pregnancies are reported from the time informed consent is signed until the defined 
follow-up period stated in Section 8.1.3.
Any report of pregnancy for the partner of a male study participant must be reported within 
24 hours to the Shire Global Drug Safety Department using the Shire Investigational and 
Marketed Products Pregnancy Report Form. 
A copy of the Shire Investigational and Marketed Products Pregnancy Report Form (and any 
applicable follow-up reports) must also be sent to the CRO/Shire medical monitor using the 
details specified in the emergency contact information section of the protocol
Every effort should be made to gather information regarding the pregnancy outcome and 
condition of the infant. It is the responsibility of the investigator to obtain this information within 
30 calendar days after the initial notification and approximately 30 calendar days and 1 year 
post-partum.
Pregnancy complications such as spontaneous abortion/miscarriage, elective abortion or 
congenital abnormality are considered SAEs and must be reported using the Shire Clinical Study 
Serious Adverse Event and Non-serious AEs Required by the Protocol Form.
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In addition to the above, if the investigator determines that the pregnancy meets serious criteria, 
it must be reported as an SAE using the Shire Clinical Study Serious Adverse Event and 
Non-serious AEs Required by the Protocol Form as well as the Shire Investigational and 
Marketed Products Pregnancy Report Form. The test date of the first positive serum/urine -hCG 
test or ultrasound result will determine the pregnancy onset date.
Appendix 3.9  Abuse, Misuse, Overdose and Medication Error
Deviations from the protocol-specified dosage, including abuse, misuse, overdose, or 
withdrawal, medication error (as defined below), failures of expected pharmacological actions, 
and unexpected therapeutic or clinical benefits will be followed with regard to occurrence of 
AEs, lack of efficacy, and/or other observations because these events may be reportable to 
regulatory authorities.
Note: The 24-hour reporting requirement for SAEs does not apply to reports of abuse, misuse, 
overdose, or medication errors unless these result in an SAE.
The categories below are not mutually exclusive; the event can meet more than 1 category.

Abuse – Persistent or sporadic intentional intake of investigational product when used for a 
non-medical purpose (e.g., to alter one’s state of consciousness or get high) in a manner 
that may be detrimental to the individual and/or society

Misuse – Intentional use of investigational product other than as directed or indicated at 
any dose (Note: this includes a situation where the investigational product is not used as 
directed at the dose prescribed by the protocol)

Overdose – Intentional or unintentional intake of a dose of investigational product higher 
than the protocol-prescribed dose

Medication Error – An error made in prescribing, dispensing, administration, and/or use of 
an investigational product. For studies, medication errors are reportable to the sponsor only 
as defined below.
Medication errors should be collected/reported for all products under investigation.
The administration and/or use of an expired investigational product should be considered as a 
reportable medication error.
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Appendix 3.10  Urgent Safety Measures 
An urgent safety measure is an immediate action taken, which is not defined by the protocol, in 
order to protect subjects participating in a clinical trial from immediate harm, these do not 
constitute de facto deviation from the protocol. Urgent safety measures may be taken by the 
sponsor or clinical investigator, and may include any of the following:

Immediate change in study design or study procedures

Temporary or permanent halt of a given clinical trial or trials

Any other immediate action taken in order to protect clinical trial participants from 
immediate hazard to their health and safety
The investigator may implement urgent safety measures to protect study subjects from 
immediate hazard to their health or safety. The measures should implement immediately and 
does not require prior authorization from the sponsor. In the event(s) of an apparent direct hazard 
to the subject, the investigator will notify the sponsor immediately by phone and confirm 
notification to the sponsor in writing as soon as possible, and within 1 calendar day after the 
change is implemented. The sponsor will also ensure the responsible EC(s) and relevant 
competent authority(s) are notified of the urgent safety measures taken in such cases according to 
local regulations.
Appendix 3.11  Regulatory Agency, Institutional Review Board, Ethics Committee, Data 
Monitoring Committee and Site Reporting
The Sponsor and the clinical CRO are responsible for notifying the relevant regulatory 
authorities and central ECs of related, unexpected SAEs.
In addition, the sponsor is responsible for notifying active sites of all related, unexpected SAEs 
occurring during all interventional studies across the SHP648 program.
The investigator is responsible for notifying the local IRB/EC of SAEs or significant safety 
findings that occur at his or her site as required by IRB/EC procedures (see Appendix 1.5).
This study will be monitored by a DMC. Enrollment and escalation to the next dose cohort will 
be paused until an independent DMC evaluates all available study data and makes a 
recommendation if anyone of the following criteria is met:

A value of 3x ULN or greater in ALT, AST, or both in any subject after SHP648 
administration that is not responsive after 12 weeks of corticosteroid rescue treatment.
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
A SAE that may be potentially related to SHP648 and which poses either an immediate 
risk to the subject’s health or is likely to adversely affect the subject’s health long term. 
This includes events classified as AEs qualifying for special notification (Brussels, 
03/12/2009, ENTR/F/2/SF/dn D(2009) 35810; EMEA/CHMP/GTWP/60436/2007), if 
these are judged as potentially related to SHP648.

The development in any subject of an inhibitor towards FIX (or FIX Padua) after having 
received SHP648. Further investigations of the characteristics and potential contributing 
factors and causal relationships of the observed FIX (or FIX Padua) inhibitor will be 
initiated.

Death of subject after having received SHP648, that is judged as, definitely, probably or 
possibly attributed to SHP648.  Enrollment in the study and further dosing will be 
temporarily stopped in order to undergo review by the applicable regulatory authorities and 
the DMC.

Occurrence of a malignancy at any point after gene transfer that is judged as probably or 
possibly related to SHP648.

Occurrence of moderate or severe-drug-related AEs in 2 or more SHP648 treated subjects 
in a given cohort.  

If any other drug-related event occurs in SHP648 treated subjects and is deemed to pose an 
unacceptable risk to subjects by the investigator or medical monitor after further 
evaluation, additional subjects will not be enrolled or dosed until a decision is taken to stop 
or proceed with the study based on further evaluation of the available data by the DMC.
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APPENDIX 4  CONTRACEPTIVE GUIDANCE 
Male participants:
Male participants with female partners of childbearing potential are eligible to participate if they 
agree to ONE of the following in the period from SHP648 administration and until AAV8 has 
been cleared from semen, as evidenced from negative analysis results for at least two 
consecutive laboratory values for vector genome in semen samples are negative:

Are abstinent from penile-vaginal intercourse as their usual and preferred lifestyle 
(abstinent on a long term and persistent basis) and agree to remain abstinent

Agree to use a male condom plus partner use of a contraceptive method with a failure rate 
of <1% per year when having penile-vaginal intercourse with a partner of childbearing 
potential who is not currently pregnant
Men with a pregnant or breastfeeding partner must agree to remain abstinent from penile-vaginal 
intercourse or use a male condom during each episode of penile penetration in the period from 
SHP648 administration and until AAV8 has been cleared from semen, as evidenced from 
negative analysis results for at least two consecutive laboratory values for vector genome in 
semen samples are negative. 
Sexually active man must agree to use a condom during sexual intercourse or limit sexual 
intercourse to post-menopausal, surgically sterilized, or contraception-practicing partners in the 
period from SHP648 administration until AAV8 has been cleared from semen, as evidenced 
from negative analysis results for at least 2 consecutively collected semen samples assessed at 
the central laboratory (this criterion is applicable also for subjects who are surgically sterilized).
Refrain from donating sperm in the period from SHP648 administration and until AAV8 has 
been cleared from semen, as evidenced from negative analysis results for at least two 
consecutive laboratory values for vector genome in semen samples are negative.
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APPENDIX 5  GENETICS 
Shire intends to apply genetic research across the SHP648 development program to explore how 
genomic variations may affect the clinical parameters associated with and response to SHP648 
(and any background products, comparators, and concomitant medications), and potentially the 
basis of the indications under study in the protocol, in this case hemophilia B. Collection of 
appropriate samples from populations with well described clinical characteristics may lead to 
improvements in the design and interpretation of clinical studies, genetically guided treatment 
strategies, and a better understanding of disease etiology, which may lead to new therapeutic 
approaches.
Candidate genes which may be studied include those potentially related to the mechanism of 
action of SHP648 as well as those potentially responsible for absorption, disposition, 
metabolism, and excretion of SHP648. Future research may suggest other genes, gene categories, 
proteins, etc., as candidates for influencing not only response to SHP648 and, but also 
susceptibility to hemophilia B for which SHP648 may be evaluated. Thus, this additional 
genomic research may involve the future study of additional unnamed genes or gene categories, 
but only as they relate to hemophilia B disease susceptibility and drug action.
Samples will be drawn at the Screening Visit (3mL blood samples) for whole exome sequencing. 
Samples may only be collected from subjects who provide separate informed consent. 
Samples will be labeled with the study protocol number, the subject’s study identification 
number, and information related to the sample. No personal identifiers will be recorded on the 
sample labels.
Subjects terminating early from the study due to AE, tolerability, or drug-related issues should, 
where possible, be approached for their remaining protocol-defined samples at the earliest 
possible time. Unscheduled samples should be labeled with free text capturing study protocol 
number, subject’s study identification number, and information related to the sample (RNA or 
protein, sampling date, and time). Samples will be shipped to and stored at biorepositories as 
detailed in the laboratory manual. 
 
 
As an added level of security, the sample will be recoded with a new, unique number at the 
biorepository laboratory. This unique number is the only code used in any subsequent analysis 
and will be used to link a sample to a subject and to ensure that the subject’s identity remains 
confidential. 
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A link file linking the first and second codes will be kept in a secure place at the sponsor, with 
restricted access. This will be in a secure environment outside of the clinical study database and 
separate to any analysis results. This file will be used to identify the relevant samples for 
analysis, facilitate correlation of any results with clinical data, allow regulatory audit, and trace 
samples for destruction in the case of withdrawal of consent. No record of participation in this 
pharmacogenomics portion of the protocol, or any results derived from it, should be recorded in 
the subjects’ personal medical records. A record of participation in the pharmacogenomics 
portion of the protocol will, however, be captured in the study-specific source documentation 
records or CRF.
The sponsor, sponsor’s representatives, biorepositories, and any specialty laboratories will be 
blinded to the subject’s identity. The sample and/or extracted material will otherwise be stored 
for up to 5 years from the end of the study after which time it will be destroyed. Upon written 
request, subjects will be permitted to withdraw their sample from the analysis and have their 
sample and/or extracted material destroyed. The link will also be destroyed at the same time as 
any remaining sample(s) are destroyed. Any results already generated from the samples will not 
be removed from any analyses that have already been performed.
Participation in this portion of the study is optional and does not impact the subject’s eligibility 
for participation in the main clinical study. Subjects may continue to participate in the primary 
study if they refuse to provide a blood sample or if they withdraw their samples.
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APPENDIX 6  BLEED DEFINITIONS 
Appendix 6.1  Joint Bleeds
Features of an acute joint bleed include some or all of the following: ‘aura’, pain, swelling, 
warmth of the skin over the joint, decreased range of motion and difficulty in using the limb 
compared with baseline or loss of function.
The earliest clinical signs of a joint bleed are increased warmth over the area and discomfort with 
movement, particularly at the ends of range.
Later symptoms and signs include pain at rest, swelling, tenderness, and extreme loss of motion.
In patients with advanced arthropathy it may be difficult to distinguish pain-related arthritis from 
that associated with an acute bleed. Rapid resolution of pain following infusion of factor 
concentrates (typical of an acute hemarthrosis) or improvement of pain associated with activity 
soon after a period of rest (typical of chronic arthritis) can help distinguish between the two.
In infants and young children, reluctance to use the limb alone may be indicative of a 
joint/muscle bleed.
Appendix 6.2  Muscle Bleeds
Muscle bleeds can occur in any muscle of the body, usually from a direct blow or a sudden 
stretch. A muscle bleed is defined as an episode of bleeding into a muscle, determined clinically 
and/or by imaging studies, generally associated with pain and/or swelling and functional 
impairment over baseline.
For further definitions of central nervous system (CNS), gastrointestinal, and abdominal 
hemorrhages see the Guidelines for the Management of Hemophilia from the World Federation 
of Hemophilia (World Federation of Hemophilia Treatment Guidelines Working Group, 2012).
Appendix 6.3  Target Joints
A target joint is defined as a joint with three or more bleeds within a period of six consecutive 
months.
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APPENDIX 7  ABBREVIATIONS 
Abbreviation
Definition
AASLD
American Association for the Study of Liver Disease
AAV
Adeno-Associated Virus
AAV2
AAV of serotype 2
AAV8
AAV of serotype 8
AE
adverse event
ABR
Annualized bleed rate
ALT
alanine aminotransferase
ANA
Antinuclear antibody
AST
aspartate aminotransferase 
BU
Bethesda unit
BGH polyA
bovine growth hormone polyadenylation sequence
BW
body weight
CD4
cluster of differentiation 4
CMI
cell-mediated immune
CpG
5' cytosine – phosphate – guanine 3'
cp
capsid particles
CRM 8
liver-specific cis-regulatory module
CRO
contract research organization
DMC
Data Monitoring Committee
DNA
deoxyribonucleic acid
EASL
European Association for the Study of the Liver 
ECG
Electrocardiogram
EC
Ethic Committee
eCRF
electronic case report form
ELISA
enzyme-linked immunosorbent assay
EMA
European Medicine Agency
FAS
full analysis set
FDA
US Food and Drug Administration
F8
human gene encoding coagulation factor VIII
F9
human gene encoding coagulation factor IX 
FVIII
factor VIII
FIX
factor IX
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Abbreviation
Definition
FIX_R338L
factor IX with arginine at position 338 replaced by a lysine (Padua mutation)
GCP
good clinical practice
HAV
Hepatitis A Virus
HBV
Hepatitis B Virus
HCV
Hepatitis C Virus
HIV
Human Immunodeficiency Virus
ICH
International Council for Harmonisation of Technical Requirements for Pharmaceuticals 
for Human Use 
IB
Investigator’s Brochure
INR
international normalized ratio
IP
investigational product
IRB
institutional review board
ITR
inverted terminal repeat
IU
international Units
IV
intravenous(ly)
kg
kilogram
LKM1
anti-liver-kidney microsomal antibody type 1
mg
milligram
mL
milliliter 
mM
Millimolar 
MVM
Minute Virus of Mice
NOAEL
No observed adverse effect level 
PAMPs
Pathogen Associated Molecular Patterns
PCR
polymerase chain reaction
Q3
third year quartal
rAAV
recombinant AAV
rep 
replication 
RNA
ribonucleic acid
RSI
reference safety information
SAE
serious adverse event
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Abbreviation
Definition
SAP
statistical analysis plan
SHP648
Shire FIX gene therapy product (AAV8.ss-3xCRM8-TTR-FIX_R338Lopt), also known 
as TAK748
SIC
subject identification code
ss
single-stranded
SUSAR
suspected unexpected serious adverse reaction
TTR
transthyretin
ULN
upper limit of normal
vg
vector genome 
VP
viral structural protein
WT
wild type
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APPENDIX 8  PROTOCOL HISTORY 
Document
Date
Global/Country/Site Specific
Amendment 1.0
21 FEB 2020
Global
Original Protocol
13 MAY 2019
Global
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