An Open-Label, Phase II Study to Determine the Immunologic Correlates of Pembrolizumab-Mediated Tumor Regression in Subjects With Advanced Melanoma (KEYNOTE-161)
Phase: PHASE2
Conditions: Advanced Melanoma
Sponsor: Merck Sharp & Dohme LLC

Official Protocol Title: 
NCT number: 
NCT03407170
14-Jun-2019
Document Date: 
An Open-Label, Phase II Study to Determine the Immunologic 
Correlates of Pembrolizumab-Mediated Tumor Regression in 
Subjects with Advanced Melanoma (KEYNOTE-161).

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Title Page
THIS PROTOCOL AMENDMENT AND ALL OF THE INFORMATION RELATING 
TO IT ARE CONFIDENTIAL AND PROPRIETARY PROPERTY OF MERCK 
SHARP & DOHME CORP., A SUBSIDIARY OF MERCK & CO., INC., NJ, U.S.A.
(MSD).
This protocol amendment is applicable only to US.
Protocol Title: An Open-Label, Phase II Study to Determine the Immunologic Correlates 
of Pembrolizumab-Mediated Tumor Regression in Subjects with Advanced Melanoma 
(KEYNOTE-161).
Protocol Number: 161-04
Compound Number: MK-3475
Sponsor Name and Legal Registered Address: 
Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc. 
(hereafter referred to as the Sponsor or MSD)
One Merck Drive
P.O. Box 100
Whitehouse Station, New Jersey, 08889-0100, U.S.A.
Regulatory Agency Identifying Number(s):
IND NUMBER:   110080
EudraCT NUMBER: Not applicable
Approval Date:  14 June 2019
 
 
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Sponsor Signatory
Typed Name:
Title:
Date
Protocol-specific Sponsor contact information can be found in the Investigator Trial 
File Binder (or equivalent). 
Investigator Signatory
I agree to conduct this clinical study in accordance with the design outlined in this protocol 
and to abide by all provisions of this protocol.
Typed Name:
Title:
Date
 
 
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DOCUMENT HISTORY
Document
Date of Issue
Overall Rationale
Original Protocol
15-JUL-2015
Not applicable
MK3475-161-01
30-JUN-2016
To align the protocol with the current approved pembrolizumab risk 
language.
MK3475-161-02
13-NOV-2017
To align the protocol with the current approved pembrolizumab risk 
language and product label.
MK3475-161-03
23-FEB-2018
To correct the specific blood samples needed and total volume of blood 
collected during the study.
MK3475-161-04
14-JUN-2019
To clarify the timing of transfer of subjects to the planned pembrolizumab 
extension study (MK3475-587) because MK3475-161 is closing.
 
 
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PROTOCOL AMENDMENT SUMMARY OF CHANGES
Amendment 04
Overall Rationale for the Amendment:
To clarify the timing of transfer of subjects to the planned pembrolizumab extension study (MK3475-587) because MK3475-161 is 
closing.  
Summary of Changes Table:
Section # and Name
Description of Change
Brief Rationale
1.1 Synopsis
4.4 Beginning and End of 
Study Definition
8.1.7 Assignment of 
Treatment/Randomization 
Number
Added language to permit 
rollover into extension once 
the participant has achieved 
the study objective or the 
study has ended.
To clarify the timing of transfer of subjects to the planned 
pembrolizumb extension study (MK-3475-587) because MK-3475-161 
is closing.
5.1 Inclusion Criteria
10.3 Appendix 3:  
Contraceptive Guidance 
and Pregnancy Testing
Included contraceptive 
requirements for male 
participants.
To remain current with standard contraceptive language.
8.1.1.1 General Informed 
Consent
Added reconsent language for 
patients at initial radiographic 
disease progression.
To establish a mechanism for the patient to acknowledge their 
continued desire to be in the study when disease progression is 
determined by the study investigator.
10.7 Appendix 7:  
Abbreviations
Defined APaT
To update terminology
 
 
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Table of Contents
DOCUMENT HISTORY ........................................................................................................3
PROTOCOL AMENDMENT SUMMARY OF CHANGES...............................................4
1.
Protocol Summary .....................................................................................................14
Synopsis....................................................................................................................14
Schema .....................................................................................................................18
Schedule of Activities (SoA) ...................................................................................19
2.
Introduction................................................................................................................27
Study Rationale .......................................................................................................27
Background..............................................................................................................27
Pharmaceutical and Therapeutic Background .....................................................28
Inhibition of PD-1 as a Target for Cancer ....................................................28
Preclinical and Clinical Studies ...........................................................................28
Ongoing Clinical Studies .....................................................................................29
Benefit/Risk Assessment.........................................................................................29
3.
Objectives/Hypotheses and Endpoints.....................................................................29
4.
Study Design...............................................................................................................32
Overall Design .........................................................................................................32
Scientific Rationale for Study Design....................................................................33
Rationale for Endpoints .......................................................................................33
Efficacy Endpoints........................................................................................33
RECIST 1.1............................................................................................33
Modified RECIST 1.1 for Immune-based Therapeutics 
(iRECIST)..............................................................................................34
Safety Endpoints...........................................................................................34
Planned Exploratory Biomarker Research....................................................34
Future Biomedical Research.........................................................................36
Planned Genetic Analysis .............................................................................36
Justification for Dose ..............................................................................................36
 
 
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Beginning and End of Study Definition ................................................................37
Clinical Criteria for Early Study Termination .....................................................38
5.
Study Population........................................................................................................38
Inclusion Criteria....................................................................................................38
Exclusion Criteria ...................................................................................................41
Lifestyle Considerations .........................................................................................43
Meals and Dietary Restrictions............................................................................43
Contraception.......................................................................................................43
Pregnancy.............................................................................................................43
Use in Nursing Women........................................................................................43
Screen Failures ........................................................................................................44
Participant Replacement Strategy.........................................................................44
6.
Treatments..................................................................................................................44
Treatments Administered.......................................................................................44
Preparation/Handling/Storage/Accountability ....................................................44
Dose Preparation..................................................................................................44
Handling, Storage and Accountability.................................................................45
Measures to Minimize Bias: Randomization and Blinding.................................45
Method of Treatment Assignment .......................................................................45
Stratification..................................................................................................45
Blinding................................................................................................................45
Treatment Compliance...........................................................................................45
Concomitant Therapy.............................................................................................46
Acceptable Concomitant Therapy........................................................................46
Prohibited Concomitant Therapy.........................................................................46
Rescue Medications and Supportive Care ...........................................................47
Dose Modification ...................................................................................................48
Dose Modification and Toxicity Management for Immune-related AEs 
Associated With Pembrolizumab.........................................................................48
Dose Modification and Toxicity Management of Infusion-reactions 
Related to Pembrolizumab...................................................................................52
Other Allowed Dose Interruption for Pembrolizumab ........................................55
Treatment After the End of the Study ..................................................................55
 
 
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Clinical Supplies Disclosure...................................................................................55
7.
Discontinuation of Study Treatment and Participant Withdrawal ......................55
Discontinuation of Study Treatment.....................................................................55
Participant Withdrawal From the Study..............................................................56
Lost to Follow-up ....................................................................................................56
8.
Study Assessments and Procedures..........................................................................57
Administrative and General Procedures ..............................................................57
Informed Consent.................................................................................................57
General Informed Consent............................................................................57
Consent and Collection of Specimens for Future Biomedical 
Research........................................................................................................58
Inclusion/Exclusion Criteria ................................................................................58
Participant Identification Card.............................................................................58
Medical History ...................................................................................................58
Prior and Concomitant Medications Review .......................................................59
Prior Medications..........................................................................................59
Concomitant Medications.............................................................................59
Assignment of Screening Number.......................................................................59
Assignment of Treatment/Randomization Number.............................................59
Treatment Administration....................................................................................59
Timing of Dose Administration....................................................................59
Discontinuation and Withdrawal .........................................................................60
Withdrawal From Future Biomedical Research ...........................................60
Participant Blinding/Unblinding..........................................................................60
Calibration of Equipment.....................................................................................60
Efficacy Assessments...............................................................................................61
Tumor Imaging and Assessment of Disease........................................................61
Initial Tumor Imaging...................................................................................61
Tumor Imaging During the Study.................................................................61
End of Treatment and Follow-up Imaging....................................................62
RECIST 1.1 Assessment of Disease .............................................................62
iRECIST Assessment of Disease..................................................................63
 
 
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Photography for Cutaneous Lesions ....................................................................66
Safety Assessments..................................................................................................66
Physical Examinations.........................................................................................66
Complete Physical Examination...................................................................66
Directed Physical Examination.....................................................................66
Vital Signs............................................................................................................66
Electrocardiograms ..............................................................................................66
Eastern Cooperative Oncology Group Performance Scale..................................66
Clinical Safety Laboratory Assessments..............................................................67
Pregnancy Testing.........................................................................................67
Adverse Events (AEs), Serious Adverse Events (SAEs), and Other 
Reportable Safety Events .......................................................................................67
Time Period and Frequency for Collecting AE, SAE, and Other 
Reportable Safety Event Information ..................................................................68
Method of Detecting AEs, SAEs, and Other Reportable Safety Events..............70
Follow-up of AE, SAE and Other Reportable Safety Event Information............70
Regulatory Reporting Requirements for SAE .....................................................70
Disease-related Events and/or Disease-related Outcomes Not 
Qualifying as AEs or SAEs..................................................................................70
Pregnancy and Exposure During Breastfeeding ..................................................71
Events of Clinical Interest (ECIs) ........................................................................71
Treatment of Overdose...........................................................................................71
Pharmacokinetics....................................................................................................71
Blood Collection for Biomarker Analyses...........................................................71
Pharmacodynamics.................................................................................................72
Tumor Tissue Collection......................................................................................72
Biomarkers ..............................................................................................................72
Single Cell RNA Sequencing...............................................................................72
Planned Genetic Analysis Sample Collection......................................................73
Future Biomedical Research Sample Collection..................................................73
Visit Requirements..................................................................................................74
Screening..............................................................................................................74
Treatment Period..................................................................................................74
 
 
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Poststudy..............................................................................................................74
Safety Follow-up Visit..................................................................................74
Follow-up Visits............................................................................................75
Survival Follow-up .......................................................................................75
Survival Status ..............................................................................................75
9.
Statistical Analysis Plan ............................................................................................75
Statistical Analysis Plan Summary........................................................................76
Responsibility for Analyses/In-house Blinding.....................................................77
Hypotheses/Estimation ...........................................................................................77
Analysis Endpoints..................................................................................................77
Biomarker Endpoints ...........................................................................................77
Primary Biomarker Endpoints ......................................................................77
Secondary and Exploratory Biomarker Endpoints .......................................79
Efficacy Endpoints...............................................................................................79
Safety Endpoints ..................................................................................................79
Analysis Populations...............................................................................................79
Biomarker Analysis Population ...........................................................................79
Efficacy Analysis Population...............................................................................79
Safety Analysis Population..................................................................................79
Statistical Methods..................................................................................................80
Statistical Methods for Biomarker Analysis ........................................................80
Statistical Methods for Efficacy Analyses ...........................................................81
Statistical Methods for Safety Analyses ..............................................................83
Summaries of Baseline Characteristics, Demographics, and Other 
Analyses...............................................................................................................83
Interim Analyses .....................................................................................................83
Multiplicity ..............................................................................................................84
Sample Size and Power Calculations ....................................................................84
Sample Size and Power for Biomarker Analyses ................................................84
Sample Size and Power for Efficacy Analyses....................................................86
Sample Size and Power for Safety Analyses .......................................................86
Subgroup Analyses..................................................................................................86
Compliance (Medication Adherence)....................................................................86
 
 
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Extent of Exposure..................................................................................................86
10.
Supporting Documentation and Operational Considerations...............................87
Appendix 1:  Regulatory, Ethical and Study Oversight Considerations ...........87
Merck Code of Conduct for Clinical Trials .....................................................................87
Financial Disclosure.........................................................................................................89
Data Protection.................................................................................................................89
Confidentiality of Data ....................................................................................................89
Confidentiality of Participant Records.............................................................................89
Confidentiality of IRB/IEC Information..........................................................................90
Publication Policy............................................................................................................90
Compliance with Study Registration and Results Posting Requirements .......................90
Compliance with Law, Audit, and Debarment ................................................................90
Data Quality Assurance ...................................................................................................91
Source Documents ...........................................................................................................92
Study and Site Closure.....................................................................................................92
Appendix 2:  Collection and Management of Specimens for Future 
Biomedical Research...............................................................................................93
Appendix 3:  Contraceptive Guidance and Pregnancy Testing..........................97
Definitions........................................................................................................................97
Contraception Requirements............................................................................................98
Pregnancy Testing..........................................................................................................100
Appendix 4: Adverse Events:  Definitions and Procedures for 
Recording, Evaluating, Follow-up, and Reporting............................................101
Definition of AE ............................................................................................................101
Definition of SAE ..........................................................................................................102
Additional Events Reported in the Same Manner as SAE.............................................103
Recording AE and SAE .................................................................................................103
Reporting of AEs, SAEs, and Other Reportable Safety Events to the Sponsor.............107
Appendix 5:  Clinical Laboratory Tests..............................................................108
Appendix 6:  12.5 Description of the iRECIST Process for Assessment 
of Disease Progression ..........................................................................................110
Assessment at Screening and Prior to RECIST 1.1 Progression ...................................110
Assessment and Decision at RECIST 1.1 Progression ..................................................110
 
 
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Assessment at the Confirmatory Imaging......................................................................111
Confirmation of Progression..........................................................................................111
Persistent iUPD..............................................................................................................111
Resolution of iUPD........................................................................................................112
Management Following the Confirmatory Imaging ......................................................112
Detection of Progression at Visits After Pseudo-progression Resolves ........................112
Appendix 7:  Abbreviations .................................................................................114
11.
References.................................................................................................................116
 
 
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LIST OF TABLES
    
Table 1
Adequate Organ Function Laboratory Values......................................................40
Table 2
Study Treatment(s) ...............................................................................................44
Table 3
Dose Modification and Toxicity Management Guidelines for Immune-
related AEs Associated with Pembrolizumab.......................................................49
Table 4
Pembrolizumab Infusion Reaction Dose Modification and Treatment 
Guidelines.............................................................................................................53
Table 5
Imaging and Treatment After First Radiologic Evidence of Progressive 
Disease..................................................................................................................65
Table 6
Reporting Time Periods and Time Frames for Adverse Events and 
Other Reportable Safety Events............................................................................69
Table 7
Analysis Strategy for Efficacy Variables .............................................................82
Table 8
Analysis Strategy for Safety Parameters ..............................................................83
Table 9
Power for Baseline FCT .......................................................................................84
Table 10
Power for FCT Log Fold-Change From Baseline and ASCTFR .........................85
Table 11
Power for Other Biomarker Endpoints.................................................................85
Table 12
Highly Effective Contraception Methods.............................................................99
Table 13
Protocol-required Safety Laboratory Assessments.............................................108
 
 
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LIST OF FIGURES
          
Figure 1
Study Design.........................................................................................................18
Figure 2
Imaging and Treatment for Clinically Stable Participants Treated with 
Pembrolizumab After First Radiologic Evidence of PD by the 
Investigator ...........................................................................................................64
 
 
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1. Protocol Summary
Synopsis
Protocol Title:
An Open-Label, Phase II Study to Determine the Immunologic Correlates of 
Pembrolizumab-Mediated Tumor Regression in Subjects with Advanced 
Melanoma (KEYNOTE-161).
Short Title:
Immunologic determinants of response to pembrolizumab in advanced melanoma
Objectives/Hypotheses and Endpoints:
In all allocated participants receiving treatment for locally advanced or metastatic 
melanoma:
Objective/Hypothesis
Endpoint
Primary

Objective: To compare the baseline CD8+ 
tumor-infiltrating lymphocytes expressing 
a predefined single-cell RNA gene 
signature in participants with locally 
advanced or metastatic melanoma with 
primary response to pembrolizumab 
monotherapy (complete response 
[CR]/partial response [PR]) vs. those who 
do not respond (stable disease 
[SD]/progressive disease [PD]/Other) to
pembrolizumab monotherapy as 
determined by Response Evaluation 
Criteria in Solid Tumors (RECIST) 1.1.

Hypothesis: Participants who respond 
to pembrolizumab have a higher FCT 
at baseline compared to participants 
who do not respond to pembrolizumab.

The fraction of cytotoxic 
tumor-infiltrating T-lymphocytes 
(FCT), defined as the fraction of 
CD8+ T-cells expressing a 
predefined single-cell RNA gene 
signature to the total tumor 
infiltrating CD8+T-cells isolated 
from tumor biopsies.

Objective: To compare the changes from 
baseline in CD8+ tumor infiltrating 
lymphocytes expressing a predefined 
single-cell RNA gene signature in 
participants with locally advanced or 
metastatic melanoma with primary 
response (CR/PR) to pembrolizumab 

The fold-change from baseline in 
FCT.
 
 
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monotherapy vs. those who do not respond
(SD/PD/Other) to pembrolizumab 
monotherapy as determined by RECIST 
1.1.

Hypothesis: Participants who respond 
to pembrolizumab have a higher fold-
increase in FCT compared to baseline 
than participants who do not respond to 
pembrolizumab.

Objective: To compare the expansion of 
cytotoxic tumor-infiltrating T-cell clones 
between responders (CR/PR) and non-
responders (SD/PD/other) in participants 
with locally advanced or metastatic 
melanoma as determined by RECIST 1.1.

Hypothesis: Participants who respond 
to pembrolizumab have a higher 
Average Specific Cytotoxic T-
lymphocyte Frequency Ratio 
(ASCTFR) compared to participants 
who do not respond to pembrolizumab.

ASCTFR, defined as the arithmetic 
mean of log10 ratio of the 
frequency of individual, specific 
cytotoxic T-cell receptor (TCR)
clones on-treatment to pre-treatment
(baseline).  
Secondary

Objective:  To evaluate the objective
response rate (ORR), progression-free 
survival (PFS), and overall survival (OS) 
of participants with locally advanced or 
metastatic melanoma treated with 
pembrolizumab.

ORR, defined as the proportion of 
participants who have a best 
response as CR or PR per RECIST 
1.1 based on local site review

PFS, defined as the time from start 
of treatment until the first 
documented progressive disease 
(PD), based on local site review 
using RECIST 1.1, or death due to 
any cause, whichever occurs first.

OS, defined as the time from the 
start of treatment to date of death 
due to any cause

Objective:  To evaluate the safety and 
tolerability of pembrolizumab.

Number of participants with adverse 
events (AEs) and serious AEs
 
 
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
Number of participants 
discontinuing study treatment due 
to AEs.

Objective: To compare the tumor reactivity 
and antigenic determinants of CD8+ TCR 
clones in tumor tissue from participants 
who respond (CR/PR) to pembrolizumab 
compared to participants who do not 
respond (SD/PD/other) to pembrolizumab.

TCRs from CD8+ T-cell clones will 
be identified by single cell RNA 
sequencing (scRNAseq) and their 
killing function will be confirmed 
by TCR-transduced T-cells 
recognizing autologous tumor-
derived cell lines. 

Objective: To evaluate the relationship 
between neoepitope burden and 
clinical/immunological response to 
pembrolizumab.

Neoepitope sequencing will be 
generated based on scRNAseq, 
whole exome sequencing, and an 
epitope prediction algorithm to 
obtain neoepitope burden.
Overall Design:
Study Phase
Phase II
Clinical Indication
Advanced melanoma
Population
Patients with advanced melanoma
Study Type
Interventional
Type of Design
Multi-site, single arm
Type of Control
No treatment control
Study Blinding
Unblinded open-label
Estimated Duration 
of Study
The Sponsor estimates that the study will require 
approximately 30 months (or until the last survival data are 
available) from the time the first participant signs the 
informed consent until the last participant’s last study-related 
telephone call or visit. 
 
 
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Number of Participants:
Approximately 60 participants will be allocated.
Treatment Groups and Duration:
Treatment Groups
Pembrolizumab 200 mg every 3 weeks (Q3W)
Duration of 
Participation
Each participant will participate in the study from the time the 
participant signs the Informed Consent Form (ICF) through 
the final protocol-specified contact.
After a screening phase of 28 days, each participant will be 
assigned to receive study treatment until disease progression 
is radiographically documented and, when clinically 
appropriate, confirmed by the sites per immune-modified 
RECIST 1.1 for immune-based therapeutics (iRECIST), 
unacceptable adverse event(s) (AEs), intercurrent illness that 
prevents further administration of treatment, investigator’s 
decision to withdraw the participant, noncompliance with trial 
treatment or procedure requirements or administrative reasons 
requiring cessation of treatment, or until the participant has 
received 35 administrations of pembrolizumab (approximately 
2 years). After the end of treatment, each participant will be 
followed for the occurrence of AEs and spontaneously 
reported pregnancy as described under Section 8.4.1.
Participants who discontinue for reasons other than 
radiographic disease progression will have post-treatment 
follow-up imaging for disease status until disease progression 
is documented radiographically per RECIST 1.1, confirmed 
by the site per iRECIST, initiating a non-trial cancer 
treatment, withdrawing consent, or becoming lost to follow-
up. All participants will be followed by telephone for OS until 
death, withdrawal of consent, or the end of the study.
Once the participant has achieved the study objective or the 
study has ended, the participant is discontinued from this 
study and will be enrolled in a pembrolizumab extension 
study (MK3475-587) to continue protocol-defined 
assessments and treatment.
Study Governance:
Study Governance 
Committees
There are no governance committees in this study.
A list of abbreviations used in this document can be found in Appendix 7.
 
 
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Schema
The study design is depicted in Figure 1
Figure 1
Study Design
 
 
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Schedule of Activities (SoA)
Study Period:
Screenin
g Phase
Treatment Cycles
(3-week cycles)
EOT
Post-Treatment
Notes
Treatment Cycle/Title:
Screening 
(Visit 1)
Through Cycle 35
DC
Safety 
Follow-
up
Follow 
Up 
Visits
Survival 
Follow-
Up

Assessments and procedures are to be 
performed on Day 1 of each treatment cycle 
unless otherwise specified.

Results of a test performed prior to signing the 
ICF as part of routine clinical management are 
acceptable in lieu of a screening test if 
performed within the specified time frame 
(e.g., within 42 days prior to the first dose of 
study treatment).

If the DC visit occurs ≥30 days from last dose 
of study treatment, a Safety Follow-up Visit is 
not required.

For participants who DC for reasons other than 
confirmed PD, imaging continues until 
confirmed PD or initiation of a new anti-
neoplastic therapy. 

Follow-Up visits may be scheduled to coincide 
with Follow-Up imaging
1
2
3
4
5
6+
Scheduling Window (Days):
-28 to -1
+3
±3
±3
±3
±3
±3
At 
time 
of DC
30 days 
after last 
dose 
(±3 
days)
Every 
12 week
s post 
DC
(±7 
days) 
Every 
12 week
s
(±7 
days)
Administrative Procedures
ICF
X
Written ICF must be obtained prior to performing 
any protocol-specified procedure.  Screening 
number assigned at the time the ICF is signed.
FBR ICF
X
Participants can still participate in the study if they 
decline to sign the FBR ICF.
Inclusion/exclusion criteria
X
Participant identification card
X
Demographics and medical history
X
Prior and concomitant medication 
review
X
X
X
X
X
X
X
X
X
Record all medications taken within 30 days of the 
first dose of study treatment and all new 
medications started during the study, including 
medications for AEs.
Subsequent anti-neoplastic therapy
X
X
X
X
 
 
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Study Period:
Screenin
g Phase
Treatment Cycles
(3-week cycles)
EOT
Post-Treatment
Notes
Treatment Cycle/Title:
Screening 
(Visit 1)
Through Cycle 35
DC
Safety 
Follow-
up
Follow 
Up 
Visits
Survival 
Follow-
Up

Assessments and procedures are to be 
performed on Day 1 of each treatment cycle 
unless otherwise specified.

Results of a test performed prior to signing the 
ICF as part of routine clinical management are 
acceptable in lieu of a screening test if 
performed within the specified time frame 
(e.g., within 42 days prior to the first dose of 
study treatment).

If the DC visit occurs ≥30 days from last dose 
of study treatment, a Safety Follow-up Visit is 
not required.

For participants who DC for reasons other than 
confirmed PD, imaging continues until 
confirmed PD or initiation of a new anti-
neoplastic therapy. 

Follow-Up visits may be scheduled to coincide 
with Follow-Up imaging
1
2
3
4
5
6+
Scheduling Window (Days):
-28 to -1
+3
±3
±3
±3
±3
±3
At 
time 
of DC
30 days 
after last 
dose 
(±3 
days)
Every 
12 week
s post 
DC
(±7 
days) 
Every 
12 week
s
(±7 
days)
Survival status
X
After Investigator determined PD or start of new 
anticancer treatment. In addition, upon Sponsor 
request, participants may be contacted for survival 
status at any time during the course of the study.
Administration of Study 
Treatment
Pembrolizumab
X
X
X
X
X
X
200 mg Q3W
Study personnel will administer treatment in Cycle 
1 within 3 days of treatment allocation.
 
 
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Study Period:
Screenin
g Phase
Treatment Cycles
(3-week cycles)
EOT
Post-Treatment
Notes
Treatment Cycle/Title:
Screening 
(Visit 1)
Through Cycle 35
DC
Safety 
Follow-
up
Follow 
Up 
Visits
Survival 
Follow-
Up

Assessments and procedures are to be 
performed on Day 1 of each treatment cycle 
unless otherwise specified.

Results of a test performed prior to signing the 
ICF as part of routine clinical management are 
acceptable in lieu of a screening test if 
performed within the specified time frame 
(e.g., within 42 days prior to the first dose of 
study treatment).

If the DC visit occurs ≥30 days from last dose 
of study treatment, a Safety Follow-up Visit is 
not required.

For participants who DC for reasons other than 
confirmed PD, imaging continues until 
confirmed PD or initiation of a new anti-
neoplastic therapy. 

Follow-Up visits may be scheduled to coincide 
with Follow-Up imaging
1
2
3
4
5
6+
Scheduling Window (Days):
-28 to -1
+3
±3
±3
±3
±3
±3
At 
time 
of DC
30 days 
after last 
dose 
(±3 
days)
Every 
12 week
s post 
DC
(±7 
days) 
Every 
12 week
s
(±7 
days)
Efficacy Measurements
Scans performed as part of routine clinical 
management are acceptable for use as the 
screening scan if they are of diagnostic quality 
and performed within 28 days prior to the first 
dose of study treatment.
The same imaging technique should be used in a 
participant throughout the study.
Tumor imaging
X
X
X
X
X
The first on-study imaging will be performed at 
9 weeks (±7 days) after the date of allocation and 
then every 9 weeks (± 7 days) thereafter for the 
first year, or more frequently if clinically indicated.
After 52 weeks (12 months), imaging will be 
performed every 12 weeks (±7 days).
Imaging should be performed at the time of DC
(±4 weeks).  If imaging was obtained within 4 
weeks prior to DC, then imaging at DC is not 
mandatory.
Imaging timing should follow calendar days and 
should not be adjusted for delays in cycle starts of 
pembrolizumab.
 
 
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Confidential
Study Period:
Screenin
g Phase
Treatment Cycles
(3-week cycles)
EOT
Post-Treatment
Notes
Treatment Cycle/Title:
Screening 
(Visit 1)
Through Cycle 35
DC
Safety 
Follow-
up
Follow 
Up 
Visits
Survival 
Follow-
Up

Assessments and procedures are to be 
performed on Day 1 of each treatment cycle 
unless otherwise specified.

Results of a test performed prior to signing the 
ICF as part of routine clinical management are 
acceptable in lieu of a screening test if 
performed within the specified time frame 
(e.g., within 42 days prior to the first dose of 
study treatment).

If the DC visit occurs ≥30 days from last dose 
of study treatment, a Safety Follow-up Visit is 
not required.

For participants who DC for reasons other than 
confirmed PD, imaging continues until 
confirmed PD or initiation of a new anti-
neoplastic therapy. 

Follow-Up visits may be scheduled to coincide 
with Follow-Up imaging
1
2
3
4
5
6+
Scheduling Window (Days):
-28 to -1
+3
±3
±3
±3
±3
±3
At 
time 
of DC
30 days 
after last 
dose 
(±3 
days)
Every 
12 week
s post 
DC
(±7 
days) 
Every 
12 week
s
(±7 
days)
Digital photography: cutaneous 
lesions
X
X
X
X
X
Digital photography is recommended, but option 
for this study.
Safety Assessments
All on-treatment assessments should be 
performed prior to treatment administration.
Review AEs
X
X
X
X
X
X
X
X
X
X
All AEs and ECIs from the time of treatment 
allocation through 30 days following cessation of 
study treatment. 
All SAEs from the time of treatment allocation 
through 90 days following cessation of study 
treatment, or 30 days following cessation of study 
treatment if the participant initiates new anticancer 
therapy, whichever is earlier.
12-lead ECG
X
12-lead ECG performed using local standard 
procedures. Additional ECGs performed as 
clinically indicated.
Complete physical exam
X
Directed physical exam
X
X
X
X
X
X
X
Directed physical exam performed as clinically 
indicated.
Vital signs
X
X
X
X
X
X
X
X
X
X
Includes temperature, pulse, RR, DBP, SBP, and 
weight
 
 
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Study Period:
Screenin
g Phase
Treatment Cycles
(3-week cycles)
EOT
Post-Treatment
Notes
Treatment Cycle/Title:
Screening 
(Visit 1)
Through Cycle 35
DC
Safety 
Follow-
up
Follow 
Up 
Visits
Survival 
Follow-
Up

Assessments and procedures are to be 
performed on Day 1 of each treatment cycle 
unless otherwise specified.

Results of a test performed prior to signing the 
ICF as part of routine clinical management are 
acceptable in lieu of a screening test if 
performed within the specified time frame 
(e.g., within 42 days prior to the first dose of 
study treatment).

If the DC visit occurs ≥30 days from last dose 
of study treatment, a Safety Follow-up Visit is 
not required.

For participants who DC for reasons other than 
confirmed PD, imaging continues until 
confirmed PD or initiation of a new anti-
neoplastic therapy. 

Follow-Up visits may be scheduled to coincide 
with Follow-Up imaging
1
2
3
4
5
6+
Scheduling Window (Days):
-28 to -1
+3
±3
±3
±3
±3
±3
At 
time 
of DC
30 days 
after last 
dose 
(±3 
days)
Every 
12 week
s post 
DC
(±7 
days) 
Every 
12 week
s
(±7 
days)
Height
X
ECOG performance status
X
X
X
X
X
X
X
X
X
X
Screening assessment to be performed within 10 
days prior to treatment initiation.
Local Laboratory Procedures/ 
Assessments
All on-treatment samples should be collected on 
Day 1 of each cycle, prior to treatment 
administration but may be collected up to 
72 hours prior to the scheduled time point.
Urine or serum β-hCG pregnancy 
test – WOCBP only
X
WOCBP require a negative urine test within 72 
hours prior to the first dose of study treatment.
Serum test is only required if urine test is positive 
or is not evaluable.
Additional urine pregnancy testing can be 
conducted if required by local regulations or 
clinically indicated.
Serum FSH – WOCBP only
X
Only for women < 45 years old with no menses for 
≥1 year (12 months) and not currently on HRT or 
hormonal contraception.
 
 
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Study Period:
Screenin
g Phase
Treatment Cycles
(3-week cycles)
EOT
Post-Treatment
Notes
Treatment Cycle/Title:
Screening 
(Visit 1)
Through Cycle 35
DC
Safety 
Follow-
up
Follow 
Up 
Visits
Survival 
Follow-
Up

Assessments and procedures are to be 
performed on Day 1 of each treatment cycle 
unless otherwise specified.

Results of a test performed prior to signing the 
ICF as part of routine clinical management are 
acceptable in lieu of a screening test if 
performed within the specified time frame 
(e.g., within 42 days prior to the first dose of 
study treatment).

If the DC visit occurs ≥30 days from last dose 
of study treatment, a Safety Follow-up Visit is 
not required.

For participants who DC for reasons other than 
confirmed PD, imaging continues until 
confirmed PD or initiation of a new anti-
neoplastic therapy. 

Follow-Up visits may be scheduled to coincide 
with Follow-Up imaging
1
2
3
4
5
6+
Scheduling Window (Days):
-28 to -1
+3
±3
±3
±3
±3
±3
At 
time 
of DC
30 days 
after last 
dose 
(±3 
days)
Every 
12 week
s post 
DC
(±7 
days) 
Every 
12 week
s
(±7 
days)
PT, INR, aPTT
X
Screening samples are to be collected within 10 
days of treatment initiation.
Participants receiving anticoagulant therapy should 
have coagulation factors monitored closely 
throughout the study
CBC with differential
X
X
X
X
X
X
X
X
Screening samples are to be collected within 10 
days of treatment initiation.
For participants with a baseline estimated 
creatinine clearance below the normal institutional 
laboratory range, a baseline measured creatinine 
clearance should be performed.
Chemistry panel
X
X
X
X
X
X
X
X
LDH
X
Urinalysis
X
X
X
X
X
T3, FT4, TSH
X
X
X
X
X
Screening samples are to be collected within 10 
days of treatment initiation.
Thyroid function tests will be performed on Day 1 
of every 6 weeks (e.g., Cycles 2, 4, 6, etc.).
Free T3 is acceptable if T3 is not available.
BRAF testing
X
To be performed in participants without 
documented BRAF status
 
 
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Study Period:
Screenin
g Phase
Treatment Cycles
(3-week cycles)
EOT
Post-Treatment
Notes
Treatment Cycle/Title:
Screening 
(Visit 1)
Through Cycle 35
DC
Safety 
Follow-
up
Follow 
Up 
Visits
Survival 
Follow-
Up

Assessments and procedures are to be 
performed on Day 1 of each treatment cycle 
unless otherwise specified.

Results of a test performed prior to signing the 
ICF as part of routine clinical management are 
acceptable in lieu of a screening test if 
performed within the specified time frame 
(e.g., within 42 days prior to the first dose of 
study treatment).

If the DC visit occurs ≥30 days from last dose 
of study treatment, a Safety Follow-up Visit is 
not required.

For participants who DC for reasons other than 
confirmed PD, imaging continues until 
confirmed PD or initiation of a new anti-
neoplastic therapy. 

Follow-Up visits may be scheduled to coincide 
with Follow-Up imaging
1
2
3
4
5
6+
Scheduling Window (Days):
-28 to -1
+3
±3
±3
±3
±3
±3
At 
time 
of DC
30 days 
after last 
dose 
(±3 
days)
Every 
12 week
s post 
DC
(±7 
days) 
Every 
12 week
s
(±7 
days)
Central Laboratory Procedures/ 
Assessments
Blood for plasma biomarker 
analysis (EDTA tube)
X
X
X
X
Samples to be collected predose.
Additional samples should be collected at the time 
of initial documentation of radiographic response 
or progression and whenever a biopsy is 
performed.
Blood for serum biomarker analysis 
(serum tube)
X
X
X
X
Blood for RNA analysis (RNA 
PaxGene)
X
X
X
X
Blood for genetic analysis (DNA 
PaxGene)
X
Protocol-Specific Laboratory 
Assessments
PBMC collection (sodium heparin 
tube)
X
X
X
X
X
Samples to be collected predose.
Additional samples should be collected at the time 
of initial documentation of radiographic response 
or progression and whenever a biopsy is 
performed.
Blood for correlative DNA studies 
(EDTA tube)
X
 
 
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Protocol/Amendment No.: 161-04 
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Confidential
Study Period:
Screenin
g Phase
Treatment Cycles
(3-week cycles)
EOT
Post-Treatment
Notes
Treatment Cycle/Title:
Screening 
(Visit 1)
Through Cycle 35
DC
Safety 
Follow-
up
Follow 
Up 
Visits
Survival 
Follow-
Up

Assessments and procedures are to be 
performed on Day 1 of each treatment cycle 
unless otherwise specified.

Results of a test performed prior to signing the 
ICF as part of routine clinical management are 
acceptable in lieu of a screening test if 
performed within the specified time frame 
(e.g., within 42 days prior to the first dose of 
study treatment).

If the DC visit occurs ≥30 days from last dose 
of study treatment, a Safety Follow-up Visit is 
not required.

For participants who DC for reasons other than 
confirmed PD, imaging continues until 
confirmed PD or initiation of a new anti-
neoplastic therapy. 

Follow-Up visits may be scheduled to coincide 
with Follow-Up imaging
1
2
3
4
5
6+
Scheduling Window (Days):
-28 to -1
+3
±3
±3
±3
±3
±3
At 
time 
of DC
30 days 
after last 
dose 
(±3 
days)
Every 
12 week
s post 
DC
(±7 
days) 
Every 
12 week
s
(±7 
days)
Tumor Tissue Collection
Fresh tumor tissue collection
X
X
If a biopsy is obtained at Cycle 2 (Week 6; 42 days 
±3 days), then a second on-treatment biopsy 
obtained at an imaging visit that shows initial 
evidence of response or progression is optional.
Abbreviations: AE = adverse event; aPTT = activated partial thromboplastin time; CBC = complete blood count; DBP = diastolic blood pressure; DC = discontinuation; 
ECG = electrocardiogram; ECIs = events of clinical interest; ECOG = Easter Cooperative Oncology Group; EOT = end of treatment; FBR = future biomedical research; 
FSH = follicle stimulating hormone; FT4 = free thyroxine; hCG = human chorionic gonadotropin; HRT = hormone replacement therapy; ICF = informed consent form; 
INR = international normalized ratio; LDH = lactate dehydrogenase; PBMC = peripheral blood mononuclear cells; PD = progressive disease; PT = prothrombin time; 
Q3W = every 3 weeks; RNAseq = RNA sequencing; RR = respiratory rate; SAEs = serious adverse events; SBP = systolic blood pressure; T3 = triiodothyronine; TCR = T-
cell receptor; TSH = thyroid stimulating hormone; WOCBP = women of childbearing potential.
 
 
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2. Introduction
Study Rationale 
Pembrolizumab-mediated tumor regression is thought to be affected by tumor antigen-
specific T-cells that are quiescent in the setting of programmed cell death 1 (PD-1) receptor-
mediated inhibitory signaling, but are re-activated by PD-1 blockade to acquire cytolytic 
antitumor function [Disis, M. L. 2010].  However, these antitumor T-cells have not 
previously been directly studied in detail in participants with documented clinical response to 
PD-1 checkpoint blockade.   In participants with advanced melanoma, pembrolizumab has 
exhibited a high degree of clinical efficacy, with many participants achieving durable clinical 
response [Deschoolmeester, V. 2010] [Sasaki, A., et al 2008] [Shen, Z., et al 2010].  
However, a significant proportion of participants develop progressive disease despite 
pembrolizumab therapy.  Therefore, melanoma represents an ideal setting in which 
differences in clinical response patterns (e.g. response vs. progression) can be directly 
correlated with differences in antigen-specific T cell phenotype and function to gain deeper 
insights into the mechanistic determinants of tumor regression following checkpoint 
blockade.
In addition to the immunologic state of anti-tumor T-cells, the antigenic burden of the tumor 
may also be a critical determinant of pembrolizumab-mediated antitumor immunity.  
Emerging data suggest that neoepitopes created by tumor-specific mutations may serve as 
important targets of antitumor T-cell immunity in melanoma and other malignancies 
[Talmadge, J. E., et al 2007] [Thompson, R. H., et al 2007].  However, the relative 
contribution of neoepitopes vs. epitopes from common germline antigens, such as cancer-
testes antigens and tissue-specific differentiation antigens, has not previously been 
empirically determined.  Insights into this issue can be gained by evaluating the antigen 
specificity of dominant T-cell clones exhibiting significant cytotoxicity in the tumors of 
participants experiencing a clinical and radiographic response to pembrolizumab.  Melanoma 
represents an ideal setting because of both the high mutational burden of this tumor type 
from UV-related mutagenesis [Andersen, R. S., et al 2012] and the extensive characterization 
of dominant epitopes from common tumor-associated antigens [Deschoolmeester, V. 2010] 
[Sasaki, A., et al 2008] [Shen, Z., et al 2010] [Dudley, M. E., et al 2005].
In order to interrogate the biology of individual tumor-specific T-cells within the tumor 
microenvironment, a technical approach requiring dissociation of freshly-obtained tumor 
tissue is necessary to obtain and characterize viable tumor-infiltrating lymphocytes.  In 
addition, close observation is necessary to time on-treatment biopsies with clinical and/or 
radiographic evidence of response or progression.  A dedicated clinical trial will allow 
optimization of both clinical observation and tissue collection in order to obtain these data.
Background
Pembrolizumab is a potent humanized immunoglobulin G4 (IgG4) monoclonal antibody 
(mAb) with high specificity of binding to the PD-1 receptor, thus inhibiting its interaction 
with PD-1 ligand 1 (PD-L1) and PD-1 ligand 2 (PD-L2).  Based on preclinical in vitro data, 
pembrolizumab has high affinity and potent receptor blocking activity for PD-1.  
Pembrolizumab has an acceptable preclinical safety profile and is in clinical development as 
 
 
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an intravenous (IV) immunotherapy for advanced malignancies.  Keytruda® 
(pembrolizumab) is indicated for the treatment of patients across a number of indications.
Refer to the Investigator’s Brochure (IB)/approved labeling for detailed background 
information on pembrolizumab.
Pharmaceutical and Therapeutic Background
Inhibition of PD-1 as a Target for Cancer
The importance of intact immune surveillance function in controlling outgrowth of neoplastic 
transformations has been known for decades [Disis, M. L. 2010]. Accumulating evidence 
shows a correlation between tumor-infiltrating lymphocytes in cancer tissue and favorable 
prognosis in various malignancies.  In particular, the presence of cluster of differentiation 8 
positive (CD8+) T-cells and the ratio of CD8+ effector T-cells (Teff)/FoxP3+ regulatory T-
cells (Tregs) correlates with improved prognosis and long-term survival in solid 
malignancies, such as ovarian, colorectal, and pancreatic cancer; hepatocellular carcinoma; 
malignant melanoma; and renal cell carcinoma.  Tumor-infiltrating lymphocytes can be 
expanded ex vivo and reinfused, inducing durable objective tumor responses in cancers such 
as melanoma [Dudley, M. E., et al 2005] [Hunder, N. N., et al 2008].
The PD-1 receptor-ligand interaction is a major pathway hijacked by tumors to suppress 
immune control. The normal function of PD-1, expressed on the cell surface of activated 
T-cells under healthy conditions, is to down-modulate unwanted or excessive immune 
responses, including autoimmune reactions. PD-1 (encoded by the gene Pdcd1) is an Ig 
superfamily member related to CD28 and cytotoxic T-lymphocyte-associated protein 4 
(CTLA-4) that has been shown to negatively regulate antigen receptor signaling upon 
engagement of its ligands (PD L1 and/or PD-L2) [Greenwald, R. J., et al 2005] [Okazaki, T., 
et al 2001]. 
The structure of murine PD-1 has been resolved [Zhang, X., et al 2004]. PD-1 and its family 
members are type I transmembrane glycoproteins containing an Ig-variable–type (IgV type) 
domain responsible for ligand binding and a cytoplasmic tail responsible for the binding of 
signaling molecules.  The cytoplasmic tail of PD-1 contains 2 tyrosine-based signaling 
motifs, an immunoreceptor tyrosine-based inhibition motif, and an immunoreceptor tyrosine-
based switch motif.  Following T-cell stimulation, PD-1 recruits the tyrosine phosphatases, 
SHP-1 and SHP-2, to the immunoreceptor tyrosine-based switch motif within its cytoplasmic 
tail, leading to the dephosphorylation of effector molecules such as CD3 zeta (CD3ζ), protein 
kinase C-theta (PKCθ), and zeta-chain-associated protein kinase (ZAP70), which are 
involved in the CD3 T-cell signaling cascade [Chemnitz, J. M., et al 2004] [Sheppard, K-A, 
et al 2004] [Riley, J. L. 2009] [Okazaki, T., et al 2001].  The mechanism by which PD-1 
down-modulates T cell responses is similar to, but distinct from, that of CTLA-4, because 
both molecules regulate an overlapping set of signaling proteins [Parry, R. V., et al 2005] 
[Francisco, L. M., et al 2010].  As a consequence, the PD 1/PD-L1 pathway is an attractive 
target for therapeutic intervention in locally advanced or metastatic melanoma.
Preclinical and Clinical Studies
Refer to the pembrolizumab IB for preclinical and clinical study data.
 
 
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Ongoing Clinical Studies
Refer to the pembrolizumab IB for ongoing clinical study data.
Benefit/Risk Assessment
It cannot be guaranteed that participants in clinical studies will directly benefit from 
treatment during participation, as clinical studies are designed to provide information about 
the safety and effectiveness of an investigational medicine.
Additional details regarding specific benefits and risks for participants participating in this 
clinical study may be found in the accompanying IB and Informed Consent documents.
3. Objectives/Hypotheses and Endpoints
In all allocated participants receiving treatment for locally advanced or metastatic melanoma:
Objective/Hypothesis
Endpoint
Primary

Objective: To compare the baseline CD8+ 
tumor-infiltrating lymphocytes expressing a 
predefined single-cell RNA gene signature 
in participants with locally advanced or 
metastatic melanoma with primary response 
to pembrolizumab monotherapy (complete 
response [CR]/partial response [PR]) vs. 
those who do not respond (stable disease 
[SD]/progressive disease [PD]/other) to
pembrolizumab monotherapy as determined 
by Response Evaluation Criteria in Solid 
Tumors (RECIST) 1.1.

Hypothesis: Participants who respond to 
pembrolizumab have a higher FCT at 
baseline compared to participants who 
do not respond to pembrolizumab.

The fraction of cytotoxic 
tumor-infiltrating T-lymphocytes 
(FCT), defined as the fraction of 
CD8+ T-cells expressing a 
predefined single-cell RNA gene 
signature to the total tumor 
infiltrating CD8+ T-cells isolated 
from tumor biopsies.

Objective: To compare the changes from 
baseline in CD8+ tumor infiltrating 
lymphocytes expressing a predefined single-
cell RNA gene signature in participants with 
locally advanced or metastatic melanoma 
with primary response (CR/PR) to 
pembrolizumab monotherapy vs. those who 
do not respond (SD/PD/other) to
pembrolizumab monotherapy as determined 
by RECIST 1.1.

The fold-change from baseline in 
FCT.
 
 
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Objective/Hypothesis
Endpoint

Hypothesis: Participants who respond to 
pembrolizumab have a higher fold-
increase in FCT compared to baseline 
than participants who do not respond to 
pembrolizumab.

Objective: To compare the expansion of 
cytotoxic tumor-infiltrating T-cell clones 
between responders (CR/PR) and non-
responders (SD/PD/other) in participants 
with locally advanced or metastatic 
melanoma.

Hypothesis: Participants who respond to 
pembrolizumab have a higher Average 
Specific Cytotoxic T-lymphocyte 
Frequency Ratio (ASCTFR) compared to 
participants who do not respond to 
pembrolizumab.

ASCTFR, defined as the arithmetic 
mean of log10 ratio of the frequency 
of individual, specific cytotoxic T-
cell receptor (TCR) clones on-
treatment to pre-treatment (baseline).
Secondary

Objective:  To evaluate the objective
response rate (ORR), progression-free 
survival (PFS), and overall survival (OS) of 
participants with locally advanced or 
metastatic melanoma treated with 
pembrolizumab.

ORR, defined as the proportion of 
participants who have a best 
response as CR or PR per RECIST 
1.1 based on local site review.

PFS, defined as the time from start of 
treatment until the first documented 
progressive disease (PD), as 
determined by local site review using
RECIST 1.1, or death due to any 
cause, whichever occurs first.

OS, defined as the time from the start 
of treatment to date of death due to 
any cause.

Objective:  To evaluate the safety and 
tolerability of pembrolizumab.

Number of participants with adverse 
events (AEs) and serious AEs.

Number of participants discontinuing 
study treatment due to AEs.

Objective: To compare the tumor reactivity 
and antigenic determinants of CD8+ TCR 
clones in tumor tissue from participants 
who respond (CR/PR) to pembrolizumab 
compared to participants who do not 
respond (SD/PD/other) to pembrolizumab.

TCRs from CD8+ T-cell clones will 
be identified by single cell RNA 
sequencing (scRNAseq) and their 
killing function will be confirmed by 
TCR-transduced T-cells recognizing 
autologous tumor-derived cell lines.
 
 
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Objective/Hypothesis
Endpoint

Objective: To evaluate the relationship 
between neoepitope burden and 
clinical/immunological response to 
pembrolizumab.

Neoepitope sequencing will be 
generated based on scRNAseq, 
whole exome sequencing, and an 
epitope prediction algorithm to 
obtain neoepitope burden.
Exploratory

Objective: To evaluate ORR and PFS based 
on modified RECIST 1.1 for immune-based 
therapeutics (iRECIST).

ORR and PFS as determined by 
local site per iRECIST.

Objective: To characterize the gene 
expression profile of T-cells in participants 
who experience clinical benefit or 
nonclinical benefit.

scRNAseq of freshly sorted tumor-
infiltrating T-cells and the RNAseq 
profile of the whole tumor will be 
used to obtain a gene expression 
profile of T-cells.

Objective: To correlate the change in gene 
expression profile of CD8+ T-cell clones 
with proven tumor reactivity from 
participants with locally advanced or 
metastatic melanoma who do or do not 
experience tumor regression following 
treatment with pembrolizumab.

scRNAseq of freshly sorted tumor 
infiltrating T-lymphocytes and the 
RNAseq profile of the whole tumor 
from on-treatment tissue will be 
compared to baseline tissue.  CD8+ 
T-cell clone killing function will be 
confirmed by TCR-transduced T-
cells recognizing autologous tumor-
derived cell lines.

Objective: To evaluate the change in 
relative frequency of CD8+ T-cell clones 
with proven tumor reactivity in tumor tissue 
from participants with locally advanced or 
metastatic melanoma who do or do not 
experience tumor regression following 
treatment with pembrolizumab

TCRs from CD8+ T-cell clones with 
proven tumor reactivity will be 
evaluated for changes from 
pembrolizumab-treated tissue 
samples.

Objective: To compare the relative ratio of 
CD8+ effector T lymphocytes (Teff) to 
CD4+FOXP3+ regulatory T-cells (Tregs) in 
participants with locally advanced or 
metastatic melanoma who exhibit primary 
response vs. non-response.

The Teff/Treg ratio will be 
estimated by coupling scRNAseq 
with immunohistochemistry (IHC) 
staining data for markers (not 
funded by this proposal) as well as 
performing RNAseq of bulk 
samples.
 
 
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Objective/Hypothesis
Endpoint

Objective: To profile the intra-tumoral 
heterogeneity of malignant, immune, and 
stromal cells before and after treatment with 
pembrolizumab.

scRNAseq in combination with 
computational analysis will be used 
to reconstruct tumor circuits, 
immune circuits, and tumor-immune 
interactions from paired baseline 
and on-treatment samples.

Objective: To evaluate the correlation 
between intra-tumoral and peripheral blood 
dynamics of specific TCR T-cell clones in 
responders (PR/CR) and non-responders 
(SD/PD/Other) treated with pembrolizumab.

TCR data from blood and tumor 
will be generated from scRNAseq or 
adaptive TCR sequencing.

Objective: To explore the relationship 
between genetic variation and response to 
the treatment(s) administered

Variation across the human genome 
will be analyzed for association with 
clinical data collected in this study.
4. Study Design 
Overall Design 
This is a single-arm, open label, trial of pembrolizumab in participants with locally 
advanced/ or metastatic melanoma to be conducted in conformance with Good Clinical 
Practice (GCP). Approximately 60 participants with advanced/metastatic melanoma, 
RECIST 1.1-measureable disease, and lesions amenable to surgical resection or core biopsy 
will be enrolled.  Participants will undergo a baseline excisional, core, or punch biopsy. 
Blood samples for biomarker analysis will also be collected at the time of each biopsy. All 
participants will receive pembrolizumab at a dose of 200 mg every 3 weeks (Q3W). 
Participants will undergo one or more on-treatment excisional, core, or punch biopsies. 
Additional blood samples for biomarker analyses will be collected from all participants
during treatment and follow-up.
Participants will be evaluated with radiographic imaging to assess response to treatment at 
regular intervals. On study imaging will be assessed approximately every 9 weeks (63 days 
± 7 days) until verified progressive disease (PD) or initiation of a new anticancer regimen.
All imaging obtained on study will be reviewed by the Investigator using RECIST 1.1 for the 
determination of objective response rate (ORR) and progression-free survival (PFS). 
Treatment-based decisions may utilize site-assessed modified RECIST 1.1 for immune-based 
therapeutics (iRECIST) criteria (Section 8.2.1.5), which allows for participants with initial 
site-assessed PD to continue treatment until PD is confirmed by the site at least 4 weeks later.
Skin lesions and other superficial lesions that are only assessed by physical examination will 
be classified as non-target lesions and their assessment should follow the imaging assessment 
schedule. Skin lesions will be documented at baseline with qualitative digital photography, 
and followed for response assessment in the same way at each scheduled tumor assessment. 
 
 
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Adverse Event (AE) monitoring will be ongoing throughout the trial and graded in severity 
according to the guidelines outlined in the National Cancer Institute (NCI) Common 
Terminology Criteria for Adverse Events (CTCAE) version 4.0. Treatment with 
pembrolizumab will continue until 35 administrations of pembrolizumab (approximately 
2 years) of therapy have been completed, documented disease progression, unacceptable 
AE(s), intercurrent illness that prevents further administration of treatment, investigator’s 
decision to withdraw the participant, participant withdraws consent, pregnancy, 
noncompliance with trial treatment or procedure requirements, or administrative reasons.
After the end of treatment, each participant will be followed for a minimum of 30 days to 
monitor for AEs and Events of Clinical Interest (ECI). Serious AEs (SAEs) will be collected 
for up to 90 days after the end of treatment, or 30 days following cessation of treatment if the 
participant initiates new anticancer therapy, whichever is earlier. Participants will have 
post-treatment follow-up for disease status, including initiating a non-study cancer treatment 
and, experiencing disease progression, death, withdrawal of consent, or lost to follow-up.
The primary endpoints of the trial are based on the assessments of the frequency and 
clonality of cytotoxic tumor-infiltrating T-lymphocytes in participants with evidence of 
radiographic response versus progression, as assessed by RECIST 1.1.  Details of these 
correlative endpoints are described in Section 4.2.1.3.
Specific procedures to be performed during the study, as well as their prescribed times and 
associated visit windows, are outlined in the Schedule of Activities (SoA), Section 1.3. 
Details of each procedure are provided in Section 8.
Scientific Rationale for Study Design 
Rationale for Endpoints
Efficacy Endpoints
Clinical efficacy endpoints will include ORR, PFS and overall survival (OS). Response and 
progressive disease will be assessed by RECIST 1.1.  
Overall survival has been recognized as the gold standard for the demonstration of 
superiority of a new antineoplastic therapy in randomized clinical studies.
This trial will also use ORR and PFS based on RECIST 1.1 criteria as assessed by the 
investigator as secondary endpoints.  ORR and PFS are acceptable measures of clinical 
benefit for a late stage trial that demonstrates superiority of a new antineoplastic therapy, 
especially if the magnitude of the effect is large and the therapy has an acceptable 
risk/benefit profile.
Biomarker data will be assessed comparatively in responders and non-responders.
RECIST 1.1
RECIST 1.1 will be used by the local site when assessing images for efficacy measures and 
when determining eligibility (Section 8.2.1.4).  Although traditional RECIST 1.1 references a 
maximum of 5 target lesions in total and 2 per organ, this protocol has implemented a 
modification to RECIST 1.1 to allow a maximum of 10 target lesions in total and 5 per 
organ.
 
 
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Modified RECIST 1.1 for Immune-based Therapeutics (iRECIST)
RECIST 1.1 will be adapted to account for the unique tumor response characteristics seen 
following treatment with pembrolizumab (Section 8.2.1.5).  Immunotherapeutic agents such 
as pembrolizumab may produce antitumor effects by potentiating endogenous cancer-specific 
immune responses.  The response patterns seen with such an approach may extend beyond 
the typical time course of responses seen with cytotoxic agents, and patients treated with 
pembrolizumab may manifest a clinical response after an initial increase in tumor burden or 
even the appearance of new lesions. Thus, standard RECIST 1.1 may, not provide an 
accurate response assessment of immunotherapeutic agents such as pembrolizumab. Based 
on an analysis of participants with melanoma enrolled in KEYNOTE-001 (KN001), 7% of 
evaluable participants experienced delayed or early tumor pseudo-progression. Of note, 
participants who had progressive disease (PD) by RECIST 1.1 but not by the immune-related 
response criteria [Wolchok, J. D., et al 2009] had longer overall survival than participants 
with PD by both criteria [Hodi, F. S., et al 2014]. Additionally, the data suggest that RECIST 
1.1 may underestimate the benefit of pembrolizumab in approximately 15% of participants. 
These findings support the need to apply a modification to RECIST 1.1 that takes into 
account the unique patterns of atypical responses in immunotherapy and enables treatment 
beyond initial radiographic progression, if the participant is clinically stable. 
iRECIST assessment has been developed and published by the RECIST Working Group, 
with input from leading experts from industry and academia, along with participation from 
the US Food and Drug Administration and the European Medicines Agency [Seymour, L., et 
al 2017]. The unidimensional measurement of target lesions, qualitative assessment of non-
target lesions, and response categories are identical to RECIST 1.1, until progression is seen 
by RECIST 1.1. However, if a participant is clinically stable, additional imaging may be 
performed to confirm radiographic progression. iRECIST will be used by Investigators to 
assess tumor response and progression and make treatment decisions as well as for 
exploratory efficacy analyses where specified.
Safety Endpoints
Safety parameters commonly used for evaluating investigational systemic anticancer 
treatments are included as safety endpoints including, but not limited to, the incidence of, 
causality, and outcome of AEs/SAEs; and changes in vital signs and laboratory values. 
Adverse events will be assessed as defined by NCI CTCAE, Version 4.0.
Planned Exploratory Biomarker Research
Cancer immunotherapies represent an important and novel class of antitumor agents. 
However, the mechanism of action of these exciting new therapies is not completely 
understood and much remains to be learned regarding how best to leverage these new drugs 
in treating patients. Thus, to aid future patients, it is important to investigate the determinants 
of response or resistance to cancer immunotherapy and other treatments administered, as well 
as determinants of AEs in the course of our clinical studies. These efforts may identify novel 
predictive/PD biomarkers and generate information that may better guide single-agent and 
combination therapy with immuno-oncology drugs. To identify novel biomarkers, 
biospecimens (ie, blood components, tumor material) will be collected to support analyses of 
 
 
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cellular components (eg, protein, DNA, RNA, metabolites) and other circulating molecules. 
Investigations may include but are not limited to:
Germline (blood) genetic analyses (eg, SNP analyses, whole exome sequencing, whole 
genome sequencing)
This research may evaluate whether genetic variation within a clinical study population 
correlates with response to the treatment(s) under evaluation. If genetic variation is found to 
predict efficacy or adverse events, the data might inform optimal use of therapies in the 
patient population. Furthermore, it is important to evaluate germline DNA variation across 
the genome in order to interpret tumor-specific DNA mutations. Finally, microsatellite 
instability (MSI) may be evaluated as this is an important biomarker for some cancers (ie, 
colorectal cancer).
Genetic (DNA) analyses from tumor
The application of new technologies, such as next generation sequencing, has provided 
scientists the opportunity to identify tumor-specific DNA changes (ie, mutations, methylation 
status, microsatellite instability). Key molecular changes of interest to immuno-oncology 
drug development include the mutational burden of tumors and the clonality of T-cells in the 
tumor microenvironment. Increased mutational burden (sometimes referred to as a ‘hyper-
mutated’ state) may generate neo-antigen presentation in the tumor microenvironment. To 
conduct this type of research, it is important to identify tumor-specific mutations that occur 
across all genes in the tumor genome. Thus, genome-wide approaches may be used for this 
effort. Note that in order to understand tumor-specific mutations, it is necessary to compare 
the tumor genome with the germline genome. Microsatellite instability may also be evaluated 
as this is an important biomarker for some cancers (ie, colorectal cancer). Circulating tumor 
DNA and/or RNA may also be evaluated from blood samples.
Tumor and blood RNA analyses
Both genome-wide and targeted messenger RNA (mRNA) expression profiling and 
sequencing in tumor tissue and in blood may be performed to define gene signatures that 
correlate to clinical response to treatment with immunotherapies and/or other treatments 
administered. Immunotherapies induce a response in tumors that likely reflects an 
inflamed/immune phenotype. Specific immune-related gene sets (ie, those capturing 
interferon-gamma transcriptional pathways) may be evaluated and new signatures may be 
identified. Individual genes related to the immune system may also be evaluated (eg, IL-10). 
MicroRNA profiling may also be pursued as well as exosomal profiling.
Proteomics and immunohistochemistry (IHC) using blood or tumor
Tumor and blood samples from this study may undergo proteomic analyses (eg, PD-L1 IHC). 
PD L1 protein level in tumor sections, assessed by IHC, has been shown to correlate with 
response to immunotherapy in patients with NSCLC, and an in vitro diagnostic (IVD) device 
has been developed for use with immunotherapy in NSCLC. Preliminary data indicates that 
this association may also be true in additional cancer types (ie, triple negative breast cancer, 
head and neck, and gastric). Additional tumor or blood-derived proteins may also correlate 
with response to immunotherapy. Therefore, tumor tissue may be subjected to proteomic 
analyses using a variety of platforms that could include but are not limited to immunoassays 
 
 
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and liquid chromatography/mass spectrometry. This approach could identify novel protein 
biomarkers that could aid in patient selection for immunotherapy and/or treatments.
Other biomarkers
In addition to expression on the tumor tissue, PD-L1 and other tumor derived proteins can be 
shed from tumor and released into the blood. Assays such as enzyme-linked immunoassay 
(ELISA) that measure proteins may also be evaluated from blood samples. Correlation of 
these biomarkers with response to immunotherapy and/or treatments may identify new 
approaches for predictive biomarkers in blood, representing a major advance from today’s 
reliance on assessing tumor biomarkers. This research would serve to develop such assays for 
future clinical use. 
Other molecular changes of interest include the subtype of T-cells in the tumor 
microenvironment. The T-cell repertoire from tumor tissue and blood components may be 
evaluated.
Future Biomedical Research
The Sponsor will conduct future biomedical research on specimens for which consent was 
provided during this study. This research may include genetic analyses (DNA), gene 
expression profiling (ribonucleic acid [RNA]), proteomics, metabolomics (serum, plasma) 
and/or the measurement of other analytes, depending on which specimens are consented for 
future biomedical research.
Such research is for biomarker testing to address emergent questions not described elsewhere 
in the protocol (as part of the main study) and will only be conducted on specimens from 
appropriately consented participants. The objective of collecting/retaining specimens for 
future biomedical research is to explore and identify biomarkers that inform the scientific 
understanding of diseases and/or their therapeutic treatments. The overarching goal is to use 
such information to develop safer, more effective drugs/vaccines, and/or to ensure that 
participants receive the correct dose of the correct drug/vaccine at the correct time. The 
details of this future biomedical research substudy are presented in Appendix 2.
Planned Genetic Analysis
Understanding genetic determinants of drug response is an important endeavor during 
medical research. This research will evaluate whether genetic variation within a clinical trial 
population correlates with response to the treatment(s) under evaluation. If genetic variation 
is found to predict efficacy or adverse events, the data might inform optimal use of therapies 
in the patient population. This research contributes to understanding genetic determinants of 
efficacy and safety associated with the treatments in this study.
Justification for Dose 
The planned dose of pembrolizumab for this study is 200 mg Q3W.  Based on the totality of 
data generated in the Keytruda development program, 200 mg Q3W is the appropriate dose 
of pembrolizumab for adults across all indications and regardless of tumor type.  As outlined 
below, this dose is justified by:
 
 
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
Clinical data from 8 randomized studies demonstrating flat dose- and exposure-
efficacy relationships from 2 mg/kg Q3W to 10 mg/kg every 2 weeks (Q2W), 

Clinical data showing meaningful improvement in benefit-risk including overall 
survival at 200 mg Q3W across multiple indications, and

Pharmacology data showing full target saturation in both systemic circulation 
(inferred from pharmacokinetic [PK] data) and tumor (inferred from physiologically-
based PK [PBPK] analysis) at 200 mg Q3W
Among the 8 randomized dose-comparison studies, a total of 2262 participants were enrolled 
with melanoma and non-small cell lung cancer (NSCLC), covering different disease settings 
(treatment-naïve, previously treated, PD-L1 enriched, and all-comers) and different treatment 
settings (monotherapy and in combination with chemotherapy). Five studies compared 
2 mg/kg Q3W versus 10 mg/kg Q2W (KEYNOTE-001 [KN001] Cohort B2, KN001 
Cohort D, KN002, KN010, and KN021), and 3 studies compared 10 mg/kg Q3W versus 
10 mg/kg Q2W (KN001 Cohort B3, KN001 Cohort F2 and KN006). All of these studies 
demonstrated flat dose- and exposure-response relationships across the doses studied 
representing an approximate 5- to 7.5-fold difference in exposure. The 2 mg/kg (or 200 mg 
fixed-dose) Q3W provided similar responses to the highest doses studied. Subsequently, flat 
dose-exposure-response relationships were also observed in other tumor types including head 
and neck cancer, bladder cancer, gastric cancer and classical Hodgkin Lymphoma, 
confirming 200 mg Q3W as the appropriate dose independent of the tumor type. These 
findings are consistent with the mechanism of action of pembrolizumab, which acts by 
interaction with immune cells, and not via direct binding to cancer cells.
Additionally, pharmacology data clearly show target saturation at 200 mg Q3W. First, PK 
data in KN001 evaluating target-mediated drug disposition (TMDD) conclusively 
demonstrated saturation of PD-1 in systemic circulation at doses much lower than 200 mg 
Q3W. Second, a PBPK analysis was conducted to predict tumor PD-1 saturation over a wide 
range of tumor penetration and PD-1 expression. This evaluation concluded that 
pembrolizumab at 200 mg Q3W achieves full PD-1 saturation in both blood and tumor.
Finally, population PK analysis of pembrolizumab, which characterized the influence of 
body weight and other participant covariates on exposure, has shown that the fixed-dosing 
provides similar control of PK variability as weight based dosing, with considerable overlap 
in the distribution of exposures from the 200 mg Q3W fixed dose and 2 mg/kg Q3W dose. 
Supported by these PK characteristics, and given that fixed-dose has advantages of reduced 
dosing complexity and reduced potential of dosing errors, the 200 mg Q3W fixed-dose was 
selected for evaluation across all pembrolizumab protocols.
Beginning and End of Study Definition
The overall study begins when the first participant signs the Informed Consent Form (ICF). 
The overall study ends when the last participant completes the last study-related telephone-
call or visit, withdraws from the study or is lost to follow-up (ie, the participant is unable to 
be contacted by the investigator). Upon study completion, participants are discontinued and 
enrolled in a pembrolizumab extension study (ML3475-587).
 
 
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Clinical Criteria for Early Study Termination
There are no prespecified criteria for terminating the study early.
5. Study Population
Male/Female participants with a histologically-confirmed diagnosis of locally advanced or 
metastatic melanoma and who are at least 18 years of age on the day of signing the informed 
consent will be enrolled in this study.
Prospective approval of protocol deviations to recruitment and enrollment criteria, also 
known as protocol waivers or exemptions, is not permitted.
Inclusion Criteria
Participants are eligible to be included in the study only if all of the following criteria apply:
Type of Participant and Disease Characteristics
1. Male/female participants who are 18 years of age on the day of signing the informed 
consent with histologically confirmed diagnosis of unresectable stage III or metastatic 
melanoma not amenable to local therapy.

Participant may not have a diagnosis of uveal or ocular melanoma.

Participant who have not received prior systemic treatment (excluding adjuvant or 
neoadjuvant therapy) for melanoma or who have received one or more prior 
systemic treatments for melanoma are both eligible. 

Participant must have testing for a BRAF mutation prior to study entry. 
Participants with BRAF V600E mutant melanoma may have received prior BRAF 
inhibitor therapy as first-line systemic therapy and are eligible for this study as 
second-line treatment. Participants with BRAF V600E mutant melanoma who 
have NOT received a BRAF inhibitor are also eligible for this study as first-line 
treatment.
2. Have measurable disease per RECIST 1.1 as assessed by the local site 
investigator/radiology. Cutaneous lesions and other superficial lesions that are 
detectable only by physical examination are not considered measurable lesions for the 
purposes of this protocol, but may be considered as non-target lesions. Tumor lesions 
situated in a previously irradiated area are considered measurable if progression has 
been demonstrated in such lesions.
3. Be willing and able to undergo pre-treatment and on-treatment baseline excisional 
and/or image-guided core or punch biopsies, and have lesions that are amenable to 
excisional biopsy, high pass core needle, and/or punch biopsy.  Participants must 
have enough accessible lesions that, in the investigator's assessment, such biopsies 
can be performed both at baseline and at least 1 subsequent time point (i.e. at 6 weeks 
of treatment).
 
 
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4. Have resolution of toxic effect(s) of the most recent prior chemotherapy to Grade 1 or 
less (except alopecia). If the participant received major surgery or radiation therapy of 
>30 Gy, they must have recovered from the toxicity and/or complications from the 
intervention. 
Note:  Participants with ≤Grade 2 neuropathy or ≤Grade 2 alopecia are an exception 
to this criterion and may qualify for the study.
Note:  If the participant received major surgery, they must have recovered adequately 
from the toxicity and/or complications from the intervention prior to starting therapy.
Demographics
5. Have an Eastern Cooperative Oncology Group (ECOG) performance status of 0 or 1, 
as assessed within 10 days prior to treatment initiation
Male Participants
Contraceptive use by men should be consistent with local regulations regarding the methods
of contraception for those participating in clinical studies.
6. Male participants are eligible to participate if they agree to the following during the 
intervention period and for at least 120 days after the last dose of study intervention:
Refrain from donating sperm
PLUS either:
Be abstinent from heterosexual intercourse as their preferred and usual lifestyle 
(abstinent on a long term and persistent basis) and agree to remain abstinent
OR
Must agree to use contraception, unless confirmed to be azoospermic (vasectomized 
or secondary to medical cause [Appendix 3]), as detailed below:
Agree to use a male condom plus partner use of an additional contraceptive method 
when having penile-vaginal intercourse with a woman of child-bearing potential 
(WOCBP) who is not currently pregnant. Note: 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-vaginal penetration.
7. Male participants must agree to use male condom when engaging in any activity that 
allows for passage of ejaculate to another person of any sex.    
Female Participants
Contraceptive use by women should be consistent with local regulations regarding the 
methods of contraception for those participating in clinical studies.
8. A female participant is eligible to participate if she is not pregnant (see Appendix 3), 
not breastfeeding, and at least one of the following conditions applies: 
a.) Not a woman of childbearing potential (WOCBP) as defined in Appendix 3
OR 
b.) A WOCBP who agrees to follow the contraceptive guidance in Appendix 3 during 
the treatment period and for at least 120 days after the last dose of study treatment.
 
 
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Informed Consent
9. The participant (or legally acceptable representative if applicable) provides written 
informed consent/assent for the study. The participant may also provide 
consent/assent for future biomedical research. However the participant may 
participate in the main study without participating in future biomedical research.
Laboratory Values
10. Participant has adequate organ function as defined in Table 1; all screening laboratory 
tests should be performed within 10 days of treatment initiation.
Table 1
Adequate Organ Function Laboratory Values
System
Laboratory Value
Hematological
Absolute neutrophil count (ANC)
≥1500/µL
Platelets
≥100 000/µL
Hemoglobin
≥9.0 g/dL or ≥5.6 mmol/L1
Renal
Creatinine OR
Measured or calculated2 creatinine clearance
(GFR can also be used in place of creatinine or 
CrCl)
≤1.5 × ULN OR
≥30 mL/min for participant with creatinine levels 
>1.5 × institutional ULN
Hepatic
Total bilirubin
≤1.5 ×ULN OR direct bilirubin ≤ULN for 
participants with total bilirubin levels >1.5 × ULN
AST (SGOT) and ALT (SGPT)
≤2.5 × ULN (≤5 × ULN for participants with liver 
metastases)
Coagulation
International normalized ratio (INR) OR 
prothrombin time (PT)
Activated partial thromboplastin time (aPTT)
≤1.5 × ULN unless participant is receiving 
anticoagulant therapy as long as PT or aPTT is 
within therapeutic range of intended use of 
anticoagulants
Abbreviations: ALT (SGPT) = alanine aminotransferase (serum glutamic pyruvic transaminase); AST (SGOT) = 
aspartate aminotransferase (serum glutamic oxaloacetic transaminase); CrCl = creatinine clearance; GFR = 
glomerular filtration rate; ULN = upper limit of normal.
1.
Criteria must be met without erythropoietin dependency and without packed red blood cell (pRBC) transfusion 
within last 2 weeks.
2.
Creatinine clearance (CrCl) should be calculated per institutional standard.
Note: This table includes eligibility-defining laboratory value requirements for treatment; laboratory value requirements 
should be adapted according to local regulations and guidelines for the administration of specific chemotherapies.
 
 
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Exclusion Criteria 
Participants are excluded from the study if any of the following criteria apply:
Medical Conditions
1. Has disease that is suitable for local therapy administered with curative intent.
2. Has a history of interstitial lung disease.
3. A WOCBP who has a positive urine pregnancy test within 72 hours before the first 
dose of study treatment (see Appendix 3). If the urine test cannot be confirmed as 
negative, a serum pregnancy test is required. In such cases, the participant must be 
excluded from participation if the serum pregnancy result is positive.
Prior/Concomitant Therapy
4. Has received prior therapy with an anti-PD-1, anti-PD-L1, or anti-PD-L2 agent or 
with an agent directed to another stimulatory or co-inhibitory T-cell receptor 
(eg, CTLA-4, OX-40, CD137).
5. Has received prior systemic anti-cancer therapy including investigational agents 
within 4 weeks prior to allocation.
Note: Participants must have recovered from all AEs due to previous therapies to 
≤Grade 1 or baseline. Participants with ≤Grade 2 neuropathy may be eligible.
Note: If participant received major surgery, they must have recovered adequately 
from the toxicity and/or complications from the intervention prior to starting study 
treatment.
6. Has received prior radiotherapy within 2 weeks of start of study treatment.  
Participants must have recovered from all radiation-related toxicities, not require 
corticosteroids, and not have had radiation pneumonitis.  A 1-week washout is 
permitted for palliative radiation (≤2 weeks of radiotherapy) to non-CNS disease.
7. Has received a live vaccine within 30 days prior to the first dose of study drug.  
Examples of live vaccines include, but are not limited to, the following:  measles, 
mumps, rubella, varicella/zoster (chicken pox), yellow fever, rabies, Bacillus 
Calmette–Guérin (BCG), and typhoid vaccine.  Seasonal influenza vaccines for 
injection are generally killed virus vaccines and are allowed; however, intranasal 
influenza vaccines (eg, FluMist®) are live attenuated vaccines and are not allowed.
8. Has received transfusion of blood products (including platelets or red blood cells) or 
administration of colony stimulating factors (including granulocyte colony 
stimulating factor [G-CSF], granulocyte macrophage colony stimulating factor [GM-
CSF] or recombinant erythropoietin) within 4 weeks prior to study Day 1.
Prior/Concurrent Clinical Study Experience
9. Is currently participating in or has participated in a study of an investigational agent 
or has used an investigational device within 4 weeks prior to the first dose of study
treatment.
 
 
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Note:  Participants who have entered the follow-up phase of an investigational study 
may participate as long as it has been 4 weeks after the last dose of the previous 
investigational agent.
Diagnostic Assessments
10. Has a diagnosis of immunodeficiency or is receiving chronic systemic steroid therapy 
(in dosing exceeding 10 mg daily of prednisone equivalent) or any other form of 
immunosuppressive therapy within 7 days prior the first dose of study drug.
11. Has a known additional malignancy that is progressing or has required active 
treatment within the past 3 years.  
Note:  Participants with basal cell carcinoma of the skin, squamous cell carcinoma of 
the skin, transitional cell carcinoma of urothelial cancer, or carcinoma in situ (eg, 
breast carcinoma, cervical cancer in situ) that have undergone potentially curative 
therapy are not excluded.
12. Has known active CNS metastases and/or carcinomatous meningitis.  Participants 
with previously treated brain metastases may participate provided they are 
radiologically stable, ie, without evidence of progression for at least 4 weeks by 
repeat imaging (note that the repeat imaging should be performed during study 
screening), clinically stable and without requirement of steroid treatment for at least 
14 days prior to first dose of study treatment. 
13. Has severe hypersensitivity (≥Grade 3) to pembrolizumab and/or any of its 
excipients.
14. Has an active autoimmune disease that has required systemic treatment in past 2 years 
(ie, with use of disease modifying agents, corticosteroids or immunosuppressive 
drugs).  Replacement therapy (eg, thyroxine, insulin, or physiologic corticosteroid 
replacement therapy for adrenal or pituitary insufficiency) is not considered a form of 
systemic treatment and is allowed.
15. Has a history of (non-infectious) pneumonitis that required steroids or has current 
pneumonitis.
16. Has an active infection requiring systemic therapy.
17. Has a known history of human immunodeficiency virus (HIV) infection.  No HIV 
testing is required unless mandated by local health authority.
18. Has a known history of Hepatitis B (defined as Hepatitis B surface antigen [HBsAg] 
reactive) or known active Hepatitis C virus (defined as HCV RNA [qualitative] is 
detected) infection. 
Note: No testing for Hepatitis B and Hepatitis C is required unless mandated by local 
health authority.
19. Has a history or current evidence of any condition, therapy, or laboratory abnormality 
that might confound the results of the study, interfere with the participant's 
participation for the full duration of the study, or is not in the best interest of the 
participant to participate, in the opinion of the treating investigator.
 
 
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20. Has known psychiatric or substance abuse disorders that would interfere with 
cooperating with the requirements of the study.
Other Exclusions
21. Is pregnant or breastfeeding or expecting to conceive or father children within the 
projected duration of the study, starting with the screening visit through 120 days 
after the last dose of study treatment.
22. Is or has an immediate family member (eg, spouse, parent/legal guardian, sibling or 
child) who is investigational site or sponsor staff directly involved with this trial.
Lifestyle Considerations
Meals and Dietary Restrictions
Participants should maintain a normal diet unless modifications are required to manage an 
AE such as diarrhea, nausea, or vomiting.
Contraception
Pembrolizumab may have adverse effects on a fetus in utero.  Refer to Appendix 3 for 
approved methods of contraception.
Participants should be informed that taking the study medication may involve unknown risks 
to the fetus (unborn baby) if pregnancy were to occur during the study.  In order to 
participate in the study, participants of childbearing potential must adhere to the 
contraception requirement (Appendix 3) from the day of study medication initiation (or 
14 days prior to the initiation of study medication for oral contraception) throughout the 
study period up to 120 days after the last dose of study medication.  If there is any question 
that a participant of childbearing potential will not reliably comply with the requirements for 
contraception, that participant should not be entered into the study. 
Pregnancy
If a participant inadvertently becomes pregnant while on treatment with pembrolizumab, the 
participant will be immediately discontinued from study treatment.  The site will contact the 
participant at least monthly and document the participant’s status until the pregnancy has 
been completed or terminated.  The outcome of the pregnancy will be reported to the Sponsor 
without delay and within 24 hours if the outcome is an SAE (eg, death, abortion, congenital 
anomaly, or other disabling or life-threatening complication to the mother or newborn).  The 
study Investigator will make every effort to obtain permission to follow the outcome of the 
pregnancy and report the condition of the fetus or newborn to the Sponsor.  If a male 
participant impregnates his female partner, the study personnel at the site must be informed 
immediately and the pregnancy must be reported to the Sponsor and followed as described in 
Section 8.4.1.
Use in Nursing Women
It is unknown whether pembrolizumab is excreted in human milk.  Since many drugs are 
excreted in human milk, and because of the potential for serious adverse reactions in the 
nursing infant, participants who are breastfeeding are not eligible for enrollment.
 
 
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Screen Failures
Screen failures are defined as participants who consent to participate in the clinical study but 
are not subsequently entered in the study. A minimal set of screen failure information is 
required to ensure transparent reporting of screen failure participants to meet the 
Consolidated Standards of Reporting Trials (CONSORT) publishing requirements and to 
respond to queries from regulatory authorities. Minimal information includes demography, 
screen failure details, eligibility criteria, and any adverse events (AEs) or serious adverse 
events (SAEs) meeting reporting requirements as outlined in the data entry guidelines.
Participant Replacement Strategy
A participant who discontinues from study treatment will not be replaced.
6. Treatments
Study treatment is defined as any investigational treatment(s), marketed product(s), placebo,
or medical device(s) intended to be administered to a study participant according to the study 
protocol.
Clinical supplies [study treatment(s) provided by the Sponsor] will be packaged to support 
enrollment. Clinical supplies will be affixed with a clinical label in accordance with 
regulatory requirements.
Treatments Administered
The study treatment(s) to be used in this study is outlined below in Table 2.
Table 2
Study Treatment(s)
Study 
Treatment 
Name
Dose 
Formulation
Unit Dose 
Strength(s)
Dosage 
Level(s)
Route of 
Administration
Use
Sourcing
Pembrolizumab
Solution for 
infusion
100 mg/vial
200 mg 
Q3W
IV infusion
Experi
mental
Provided 
centrally by the 
sponsor
Abbreviations: IV = intravenous; Q3W = every 3 weeks
All supplies indicated in Table 2 will be provided per the ‘Sourcing’ row depending upon 
local country operational requirements. Every attempt should be made to source these 
supplies from a single lot/batch number where possible (eg, not applicable in the case where 
multiple lots or batches may be required due to the length of the study etc.).
Refer to Section 8.1.8 for details regarding administration of the study treatment.
Preparation/Handling/Storage/Accountability
Dose Preparation
Details on preparation and administration of pembrolizumab are provided in the Pharmacy 
manual.
 
 
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Handling, Storage and Accountability
The investigator or designee must confirm appropriate temperature conditions have been 
maintained during transit for all study treatment received and any discrepancies are reported 
and resolved before use of the study treatment.
Only participants enrolled in the study may receive study treatment and only authorized site 
staff may supply or administer study treatment. All study treatments must be stored in a 
secure, environmentally controlled, and monitored (manual or automated) area in accordance 
with the labeled storage conditions with access limited to the investigator and authorized site 
staff.
The investigator, institution, or the head of the medical institution (where applicable) is 
responsible for study treatment accountability, reconciliation, and record maintenance (ie, 
receipt, reconciliation, and final disposition records).
For all study sites, the local country Sponsor personnel or designee will provide appropriate 
documentation that must be completed for drug accountability and return, or local discard
and destruction if appropriate. Where local discard and destruction is appropriate, the 
investigator is responsible for ensuring that a local discard/destruction procedure is 
documented.
The study site is responsible for recording the lot number, manufacturer, and expiry date for 
any locally purchased product as per local guidelines unless otherwise instructed by the 
Sponsor.
The investigator shall take responsibility for and shall take all steps to maintain appropriate 
records and ensure appropriate supply, storage, handling, distribution and usage of study 
treatments in accordance with the protocol and any applicable laws and regulations.
Measures to Minimize Bias: Randomization and Blinding
Method of Treatment Assignment 
Participants participating in this study will be allocated by nonrandom assignment.
Stratification
No stratification based on age, sex or other characteristics will be used in this study.
Blinding 
This study is an open-label study; therefore, the Sponsor, investigator and participant will 
know the treatment administered.
See Section 8.1.10 for a description of the method of unblinding a participant during the 
study, should such action be warranted.
Treatment Compliance
Interruptions from the protocol specified treatment plan for greater than 12 weeks between 
pembrolizumab doses require consultation between the investigator and the Sponsor and 
written documentation of the collaborative decision on participant management.
 
 
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Concomitant Therapy
Medications or vaccinations specifically prohibited in the exclusion criteria are not allowed 
during the ongoing study. If there is a clinical indication for any medication or vaccination
specifically prohibited, discontinuation from study treatment may be required. The 
investigator should discuss any questions regarding this with the Sponsor Clinical Director. 
The final decision on any supportive therapy or vaccination rests with the investigator and/or 
the participant's primary physician. However, the decision to continue the participant on 
study treatment requires the mutual agreement of the investigator, the Sponsor and the 
participant.
Acceptable Concomitant Therapy
All treatments that the investigator considers necessary for a participant’s welfare may be 
administered at the discretion of the investigator in keeping with the community standards of 
medical care.  All concomitant medication will be recorded on the case report form (CRF) 
including all prescription, over-the-counter (OTC), herbal supplements, and IV medications 
and fluids.  If changes occur during the trial period, documentation of drug dosage, 
frequency, route, and date may also be included on the CRF.
All concomitant medications received within 30 days before the first dose of trial treatment 
and 30 days after the last dose of trial treatment should be recorded.  Concomitant 
medications administered after 30 days after the last dose of trial treatment should be 
recorded for SAEs and ECIs as defined in Section 8.4.
Prohibited Concomitant Therapy
Participants are prohibited from receiving the following therapies during the Screening and 
Treatment Phase (including retreatment for post-complete response relapse) of this trial:

Antineoplastic systemic chemotherapy or biological therapy not specified in this 
protocol

Immunotherapy not specified in this protocol

Investigational agents other than pembrolizumab

Radiation therapy 
Note:  Radiation therapy to a symptomatic lesion or to the brain may be considered 
on an exceptional case by case basis after consultation with Sponsor.  The participant
must have clear measurable disease outside the radiated field.  Administration of 
palliative radiation therapy will be considered clinical progression for the purposes 
of determining PFS.

Live vaccines within 30 days prior to the first dose of trial treatment and while 
participating in the trial.  Examples of live vaccines include, but are not limited to, the 
following: measles, mumps, rubella, chickenpox, yellow fever, rabies, BCG, and 
typhoid (oral) vaccine. Seasonal influenza vaccines for injection are generally killed 
virus vaccines and are allowed. However, intranasal influenza vaccines (e.g. 
FluMist®) are live attenuated vaccines, and are not allowed.
 
 
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
Systemic glucocorticoids for any purpose other than to modulate symptoms from 
events of suspected immunologic etiology.  The use of glucocorticoids for AEs 
not attributed to pembrolizumab is allowed with approval from the Sponsor. 
Physiologic doses of corticosteroids (not exceeding 10 mg of prednisone 
equivalent daily) are allowed.
Note:  Inhaled steroids are allowed for management of asthma.
Participants who, in the assessment by the investigator, require the use of any of the 
aforementioned treatments for clinical management should be removed from the trial.  
Participants may receive other medications that the investigator deems to be medically 
necessary.
The Exclusion Criteria describe other medications that are prohibited in this trial.
There are no prohibited therapies during the Post-Treatment Follow-up Phase.
Rescue Medications and Supportive Care
Participants should receive appropriate supportive care measures as deemed necessary by the 
treating investigator.  Suggested supportive care measures for the management of AEs with 
potential immunologic etiology are outlined along with the dose modification guidelines in 
Section 6.6.1, Table 3.  Where appropriate, these guidelines include the use of oral or IV 
treatment with corticosteroids, as well as additional anti-inflammatory agents if symptoms do 
not improve with administration of corticosteroids.  Note that several courses of steroid 
tapering may be necessary as symptoms may worsen when the steroid dose is decreased.  For 
each disorder, attempts should be made to rule out other causes such as metastatic disease or
bacterial or viral infection, which might require additional supportive care.  The treatment 
guidelines are intended to be applied when the Investigator determines the events to be 
related to pembrolizumab. 
Note: If after the evaluation of the event, it is determined not to be related to pembrolizumab, 
the Investigator does not need to follow the treatment guidance.  Refer to Table 3 in 
Section 6.6.1 for guidelines regarding dose modification and supportive care. 
It may be necessary to perform conditional procedures such as bronchoscopy, endoscopy, or 
skin photography as part of evaluation of the event.
 
 
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Dose Modification  
Dose Modification and Toxicity Management for Immune-related AEs 
Associated With Pembrolizumab
AEs associated with pembrolizumab exposure may represent an immunologic etiology. 
These immune-related AEs (irAEs) may occur shortly after the first dose or several months 
after the last dose of pembrolizumab treatment and may affect more than one body system 
simultaneously. Therefore, early recognition and initiation of treatment is critical to reduce 
complications.  Based on existing clinical study data, most irAEs were reversible and could 
be managed with interruptions of pembrolizumab, administration of corticosteroids and/or 
other supportive care. For suspected irAEs, ensure adequate evaluation to confirm etiology or 
exclude other causes. Additional procedures or tests such as bronchoscopy, endoscopy, skin 
biopsy may be included as part of the evaluation. Based on the severity of irAEs, withhold or 
permanently discontinue pembrolizumab and administer corticosteroids. Dose modification 
and toxicity management guidelines for irAEs associated with pembrolizumab are provided 
in Table 3.
 
 
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Table 3
Dose Modification and Toxicity Management Guidelines for Immune-related AEs Associated with Pembrolizumab
General instructions:
1.
Corticosteroid taper should be initiated upon AE improving to Grade 1 or less and continue to taper over at least 4 weeks.
2.
For situations where pembrolizumab has been withheld, pembrolizumab can be resumed after AE has been reduced to Grade 1 or 0 and corticosteroid 
has been tapered. Pembrolizumab should be permanently discontinued if AE does not resolve within 12 weeks of last dose or corticosteroids cannot 
be reduced to ≤10 mg prednisone or equivalent per day within 12 weeks. 
3.
For severe and life-threatening irAEs, IV corticosteroid should be initiated first followed by oral steroid. Other immunosuppressive treatment should 
be initiated if irAEs cannot be controlled by corticosteroids.
irAEs
Toxicity grade or 
conditions (NCI 
CTCAE v4.0)
Action taken to 
pembrolizumab
irAE management with 
corticosteroid and/or other therapies 
Monitor and follow-up 
Pneumonitis 
Grade 2
Withhold 

Administer corticosteroids (initial 
dose of 1-2 mg/kg prednisone or 
equivalent) followed by taper

Monitor participants for signs and symptoms
of pneumonitis

Evaluate participants with suspected 
pneumonitis with radiographic imaging and 
initiate corticosteroid treatment

Add prophylactic antibiotics for opportunistic 
infections
Grade 3 or 4, or 
recurrent Grade 2
Permanently 
discontinue
Diarrhea / Colitis 
Grade 2 or 3
Withhold

Administer corticosteroids (initial 
dose of 1-2 mg/kg prednisone or 
equivalent) followed by taper

Monitor participants for signs and symptoms 
of enterocolitis (ie, diarrhea, abdominal pain, 
blood or mucus in stool with or without fever) 
and of bowel perforation (ie, peritoneal signs 
and ileus).

Participants with ≥Grade 2 diarrhea suspecting 
colitis should consider GI consultation and 
performing endoscopy to rule out colitis. 

Participants with diarrhea/colitis should be 
advised to drink liberal quantities of clear 
fluids.  If sufficient oral fluid intake is not 
feasible, fluid and electrolytes should be 
substituted via IV infusion.
Grade 4
Permanently 
discontinue
 
 
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irAEs
Toxicity grade or 
conditions (NCI 
CTCAE v4.0)
Action taken to 
pembrolizumab
irAE management with 
corticosteroid and/or other therapies 
Monitor and follow-up 
AST / ALT 
elevation or 
Increased 
bilirubin
Grade 2
Withhold

Administer corticosteroids (initial 
dose of 0.5-1 mg/kg prednisone or 
equivalent) followed by taper

Monitor with liver function tests (consider 
weekly or more frequently until liver enzyme 
value returned to baseline or is stable
Grade 3 or 4 
Permanently 
discontinue

Administer corticosteroids (initial 
dose of 1-2 mg/kg prednisone or 
equivalent) followed by taper
Type 1 diabetes 
mellitus (T1DM) 
or Hyperglycemia
Newly onset 
T1DM or 
Grade 3 or 4 
hyperglycemia 
associated with 
evidence of -cell 
failure
Withhold

Initiate insulin replacement therapy 
for participants with T1DM 

Administer anti-hyperglycemic in 
participants with hyperglycemia 

Monitor participants for hyperglycemia or 
other signs and symptoms of diabetes.
Hypophysitis
Grade 2
Withhold

Administer corticosteroids and 
initiate hormonal replacements as 
clinically indicated.  

Monitor for signs and symptoms of 
hypophysitis (including hypopituitarism and 
adrenal insufficiency)
Grade 3 or 4 
Withhold or 
permanently 
discontinue1
Hyperthyroidism 
Grade 2
Continue 

Treat with non-selective beta-
blockers (eg, propranolol) or 
thionamides as appropriate 

Monitor for signs and symptoms of thyroid 
disorders. 
Grade 3 or 4 
Withhold or 
permanently 
discontinue1
Hypothyroidism
Grade 2-4
Continue 

Initiate thyroid replacement 
hormones (eg, levothyroxine or 
liothyroinine) per standard of care

Monitor for signs and symptoms of thyroid 
disorders. 
 
 
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irAEs
Toxicity grade or 
conditions (NCI 
CTCAE v4.0)
Action taken to 
pembrolizumab
irAE management with 
corticosteroid and/or other therapies 
Monitor and follow-up 
Nephritis and 
Renal dysfunction
Grade 2
Withhold 

Administer corticosteroids 
(prednisone 1-2 mg/kg or 
equivalent) followed by taper.

Monitor changes of renal function
Grade 3 or 4 
Permanently 
discontinue
Myocarditis
Grade 1 or 2
Withhold

Based on severity of AE administer 
corticosteroids

Ensure adequate evaluation to confirm etiology 
and/or exclude other causes
Grade 3 or 4
Permanently 
discontinue
All other irAEs
Intolerable/ 
persistent Grade 2
Withhold

Based on type and severity of AE 
administer corticosteroids 

Ensure adequate evaluation to confirm etiology 
and/or exclude other causes
Grade 3
Withhold or 
discontinue based 
on the type of 
event.  Events that 
require 
discontinuation 
include and not 
limited to:  
Guillain-Barré
Syndrome, 
encephalitis
Grade 4 or 
recurrent Grade 3 
Permanently 
discontinue
Abbreviations: AE = adverse event; ALT = alanine aminotransferase; AST = aspartate aminotransferase; CTCAE = Common Terminology Criteria for Adverse Events; GI = 
gastrointestinal; irAE = immune-related adverse event; IV = intravenous; NCI = National Cancer Institute; T1DM = type 1 diabetes mellitus.
1.
Withhold or permanently discontinue pembrolizumab is at the discretion of the investigator or treating physician.  
NOTE: 
For participants with Grade 3 or 4 immune-related endocrinopathy where withhold of pembrolizumab is required, pembrolizumab may be resumed when AE resolves to ≤ 
Grade 2 and is controlled with hormonal replacement therapy or achieved metabolic control (in case of T1DM).  
 
 
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Dose Modification and Toxicity Management of Infusion-reactions Related to 
Pembrolizumab
Pembrolizumab may cause severe or life threatening infusion-reactions including severe 
hypersensitivity or anaphylaxis. Signs and symptoms usually develop during or shortly after 
drug infusion and generally resolve completely within 24 hours of completion of infusion. 
Dose modification and toxicity management guidelines on pembrolizumab associated 
infusion reaction are provided in Table 4.
 
 
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Table 4
Pembrolizumab Infusion Reaction Dose Modification and Treatment Guidelines
NCI CTCAE Grade
Treatment
Premedication at Subsequent Dosing
Grade 1
Mild reaction; infusion 
interruption not indicated; 
intervention not indicated
Increase monitoring of vital signs as medically indicated until the participant 
is deemed medically stable in the opinion of the investigator.
None
Grade 2
Requires therapy or infusion 
interruption but responds 
promptly to symptomatic 
treatment (e.g., antihistamines, 
NSAIDs, narcotics, IV fluids); 
prophylactic medications 
indicated for ≤24 hrs
Stop Infusion.
Additional appropriate medical therapy may include but is not limited to:
IV fluids
Antihistamines
NSAIDs
Acetaminophen
Narcotics
Increase monitoring of vital signs as medically indicated until the participant 
is deemed medically stable in the opinion of the investigator.
If symptoms resolve within 1 hour of stopping drug infusion, the infusion may 
be restarted at 50% of the original infusion rate (e.g. from 100 mL/hr to 50 
mL/hr).  Otherwise dosing will be held until symptoms resolve and the 
participant should be premedicated for the next scheduled dose.
Participants who develop Grade 2 toxicity despite adequate 
premedication should be permanently discontinued from further study 
drug treatment
Participant may be premedicated 1.5 h (± 
30 minutes) prior to infusion of 
pembrolizumab with:

Diphenhydramine 50 mg PO (or 
equivalent dose of antihistamine).

Acetaminophen 500-1000 mg PO (or 
equivalent dose of analgesic).
 
 
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NCI CTCAE Grade
Treatment
Premedication at Subsequent Dosing
Grades 3 or 4
Grade 3:
Prolonged (ie, not rapidly 
responsive to symptomatic 
medication and/or brief 
interruption of infusion); 
recurrence of symptoms 
following initial improvement; 
hospitalization indicated for 
other clinical sequelae (e.g., 
renal impairment, pulmonary 
infiltrates)
Grade 4:
Life-threatening; pressor or 
ventilatory support indicated
Stop Infusion.
Additional appropriate medical therapy may include but is not limited to:

Epinephrine**

IV fluids

Antihistamines

NSAIDs

Acetaminophen

Narcotics

Oxygen

Pressors

Corticosteroids
Increase monitoring of vital signs as medically indicated until the participant 
is deemed medically stable in the opinion of the investigator.
Hospitalization may be indicated.
**In cases of anaphylaxis, epinephrine should be used immediately.
Participant is permanently discontinued from further study drug 
treatment.
No subsequent dosing
Abbreviations: CTCAE = Common Terminology Criteria for Adverse Events; IV – intravenous; NCI – National Cancer Institute; NSAIDS = nonsteroidal anti-inflammatory 
drugs; PO = by mouth.
Appropriate resuscitation equipment should be available at the bedside and a physician readily available during the period of drug administration.
For further information, please refer to the CTCAE v4.0 at http://ctep.cancer.gov
 
 
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Other Allowed Dose Interruption for Pembrolizumab 
Pembrolizumab may be interrupted for situations other than treatment-related AEs such as 
medical / surgical events or logistical reasons not related to study therapy. Participants should 
be placed back on study therapy within 3 weeks of the scheduled interruption, unless 
otherwise discussed with the Sponsor. The reason for interruption should be documented in 
the participant's study record.
Treatment After the End of the Study 
There is no study-specified treatment following the end of the study.
Clinical Supplies Disclosure
This study is open-label; therefore, the participant, the study site personnel, the Sponsor 
and/or designee are not blinded. Study treatment (name, strength or potency) is included in 
the label text; random code/disclosure envelopes or lists are not provided.
7. Discontinuation of Study Treatment and Participant Withdrawal
Discontinuation of Study Treatment 
Discontinuation of study treatment does not represent withdrawal from the study.
As certain data on clinical events beyond study treatment discontinuation may be important 
to the study, they must be collected through the participant’s last scheduled follow-up, even 
if the participant has discontinued study treatment. Therefore, all participants who 
discontinue study treatment prior to completion of the protocol-specified treatment period 
will still continue to participate in the study as specified in Section 1.3 and Section 8.10.3.
Participants may discontinue study treatment at any time for any reason or be discontinued 
from the study treatment at the discretion of the investigator should any untoward effect 
occur. In addition, a participant may be discontinued from study treatment by the investigator 
or the Sponsor if study treatment is inappropriate, the study plan is violated, or for 
administrative and/or other safety reasons. Specific details regarding procedures to be 
performed at study treatment discontinuation are provided in Section 8.1.9.
A participant must be discontinued from study treatment but continue to be monitored in the 
study for any of the following reasons:
○
The participant or participant’s legally acceptable representative requests to discontinue 
study treatment.
o
Radiographic disease progression as determined by local/site assessment
Note: For unconfirmed radiographic disease progression, or confirmed progression with 
reduction in disease burden from baseline please see Section 8.2.1.4
o
Any progression or recurrence of any malignancy, or any occurrence of another 
malignancy that requires active treatment
o
Noncompliance with study treatment or procedure requirements
o
Recurrent Grade 2 pneumonitis
 
 
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o
Unacceptable AEs as described in Section 6.6
o
Intercurrent illness that prevents further administration of study treatment
o
The participant has a confirmed positive serum pregnancy test
o
Investigator’s decision to withdraw the participant
o
The participant is lost to follow-up (Section 7.3)
o
Completed 35 cycles (~2 years) of treatment with pembrolizumab
o
Administrative reasons
For participants who are discontinued from study treatment but continue to be monitored in 
the study, see Section 1.3 and Section 8.10.3 for those procedures to be completed at each 
specified visit.
Discontinuation from study treatment is “permanent.” Once a participant is discontinued, 
he/she shall not be allowed to restart study treatment. 
Participant Withdrawal From the Study
A participant must be withdrawn from the study if the participant or participant’s legally 
acceptable representative withdraws consent from the study.
If a participant withdraws from the study, they will no longer receive study treatment or be 
followed at scheduled protocol visits.
Specific details regarding procedures to be performed at the time of withdrawal from the 
study, as well as specific details regarding withdrawal from future biomedical research are 
outlined in Section 8.1.9. The procedures to be performed should a participant repeatedly fail 
to return for scheduled visits and/or if the study site is unable to contact the participant are 
outlined in Section 7.3.
Lost to Follow-up
If a participant fails to return to the clinic for a required study visit and/or if the site is unable 
to contact the participant, the following procedures are to be performed:
●
The site must attempt to contact the participant and reschedule the missed visit. If the 
participant is contacted, the participant should be counseled on the importance of 
maintaining the protocol-specified visit schedule.
●
The investigator or designee must make every effort to regain contact with the 
participant at each missed visit (eg, telephone calls and/or a certified letter to the 
participant’s last known mailing address or locally equivalent methods). These
contact attempts should be documented in the participant’s medical record.
●
Note:  A participant is not considered lost to follow-up until the last scheduled visit 
for the individual participant. The missing data for the participant will be managed 
via the prespecified statistical data handling and analysis guidelines.
 
 
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8. Study Assessments and Procedures

Study procedures and their timing are summarized in the SoA. 

Adherence to the study design requirements, including those specified in the SoA, 
is essential and required for study conduct.

The investigator is responsible for assuring that procedures are conducted by 
appropriately qualified or trained staff. Delegation of study site personnel 
responsibilities will be documented in the Investigator Trial File Binder (or 
equivalent).

All screening evaluations must be completed and reviewed to confirm that 
potential participants meet all eligibility criteria. The investigator will maintain a 
screening log to record details of all participants screened and to confirm 
eligibility or record reasons for screening failure, as applicable. 

Procedures conducted as part of the participant’s routine clinical management (eg, 
blood count) and obtained before signing of ICF may be utilized for screening or 
baseline purposes provided the procedure met the protocol-specified criteria and 
were performed within the time frame defined in the SoA.

Additional evaluations/testing may be deemed necessary by the investigator and 
or the Sponsor for reasons related to participant safety. In some cases, such 
evaluation/testing may be potentially sensitive in nature (eg, HIV, Hepatitis C, 
etc.), and thus local regulations may require that additional informed consent be 
obtained from the participant. In these cases, such evaluations/testing will be 
performed in accordance with those regulations.
Repeat or unscheduled samples may be taken for safety reasons or for technical issues with 
the samples.
Administrative and General Procedures
Informed Consent
The investigator or qualified designee must obtain documented consent from each potential 
participant or each participant’s legally acceptable representative prior to participating in a 
clinical study or future biomedical research. If there are changes to the participant’s status 
during the study (eg, health or age of majority requirements), the investigator or qualified 
designee must ensure the appropriate consent is in place. 
General Informed Consent
Consent must be documented by the participant’s dated signature or by the participant’s 
legally acceptable representative’s dated signature on a consent form along with the dated 
signature of the person conducting the consent discussion. 
A copy of the signed and dated consent form should be given to the participant before 
participation in the study.
 
 
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The initial ICF, any subsequent revised written ICF and any written information provided to 
the participant must receive the Institutional Review Board/Independent Ethics Committee’s
(IRB/IEC’s) approval/favorable opinion in advance of use. The participant or his/her legally 
acceptable representative should be informed in a timely manner if new information becomes 
available that may be relevant to the participant’s willingness to continue participation in the 
study. The communication of this information will be provided and documented via a revised 
consent form or addendum to the original consent form that captures the participant’s dated 
signature or by the participant’s legally acceptable representative’s dated signature.
The participant or his/her legally acceptable representative will be asked to sign consent at 
the point of initial radiographic disease progression.
Specifics about a study and the study population will be added to the consent form template 
at the protocol level. 
The informed consent will adhere to IRB/IEC requirements, applicable laws and regulations 
and Sponsor requirements.
Consent and Collection of Specimens for Future Biomedical Research
The investigator or qualified designee will explain the future biomedical research consent to 
the participant, answer all of his/her questions, and obtain written informed consent before 
performing any procedure related to the future biomedical research substudy. A copy of the 
informed consent will be given to the participant.
Inclusion/Exclusion Criteria
All inclusion and exclusion criteria will be reviewed by the investigator or qualified designee 
to ensure that the participant qualifies for the study.
Participant Identification Card
All participants will be given a Participant Identification Card identifying them as 
participants in a research study. The card will contain study site contact information 
(including direct telephone numbers) to be utilized in the event of an emergency. The 
investigator or qualified designee will provide the participant with a Participant Identification 
Card immediately after the participant provides written informed consent. At the time of 
treatment allocation/randomization, site personnel will add the treatment/randomization 
number to the Participant Identification Card.
The participant identification card also contains contact information for the emergency 
unblinding call center so that a health care provider can obtain information about study 
treatment in emergency situations where the investigator is not available.
Medical History
A medical history will be obtained by the investigator or qualified designee.
 
 
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Prior and Concomitant Medications Review
Prior Medications
The investigator or qualified designee will review prior medication use, including any 
protocol-specified washout requirement, and record prior medication taken by the participant 
within 30 days before the first dose of study medication.
Concomitant Medications
The investigator or qualified designee will record medication, if any, taken by the participant 
during the study.
Assignment of Screening Number
All consented participants will be given a unique screening number that will be used to 
identify the participant for all procedures that occur prior to treatment allocation. Each 
participant will be assigned only one screening number. Screening numbers must not be re-
used for different participants.
Any participant who is screened multiple times will retain the original screening number 
assigned at the initial screening visit.
Specific details on the screening visit requirements (screening/rescreening) are provided in 
Section 8.10.1. 
Assignment of Treatment/Randomization Number
All eligible participants will be allocated, by nonrandom assignment, and will receive a 
treatment/randomization number. The treatment/randomization number identifies the 
participant for all procedures occurring after treatment allocation/randomization. Once a 
treatment/randomization number is assigned to a participant, it can never be re-assigned to 
another participant.
A single participant cannot be assigned more than 1 treatment/randomization number.
In a situation where treatment reallocation of the participants is planned (eg, study extension 
periods), it will be based on a new allocation schedule; however, each participant will retain 
his/her original treatment/randomization number. Only the study intervention regimen 
associated with the treatment reallocation period or phase may change.
Treatment Administration
Administration of study medication will be witnessed by the investigator and/or study staff.
Study Treatment should begin within 3 days of treatment allocation.
Timing of Dose Administration
Pembrolizumab will be administered on Day 1 of each 3-week treatment cycle after all 
procedures and assessments have been completed as detailed in the SoA.
Pembrolizumab can be administered ±3 days of the targeted Day 1 for each cycle, except 
Cycle 1 where treatment can only be administered +3 days of the targeted Day 1.
 
 
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Pembrolizumab will be administered at a dose of 200mg using a 30-minute IV infusion. Sites 
should make every effort to target infusion timing to be as close to 30 minutes as possible. 
However, given the variability of infusion pumps from site to site, a window 
between -5 minutes and +10 minutes is permitted (i.e., the infusion time is 
30 minutes: -5 min/+10 min).
Discontinuation and Withdrawal
Participants who discontinue study treatment prior to completion of the treatment period
should be encouraged to continue to be followed for all remaining study visits.
When a participant withdraws from participation in the study, all applicable activities 
scheduled for the final study visit should be performed (at the time of withdrawal). Any AEs
which are present at the time of withdrawal should be followed in accordance with the safety 
requirements outlined in Section 8.4 .
Withdrawal From Future Biomedical Research
Participants may withdraw their consent for future biomedical research. Participants may 
withdraw consent at any time by contacting the principal investigator for the main study. If 
medical records for the main study are still available, the investigator will contact the 
Sponsor using the designated mailbox (clinical.specimen.management@merck.com). 
Subsequently, the participant's consent for future biomedical research will be withdrawn. A 
letter will be sent from the Sponsor to the investigator confirming the withdrawal. It is the 
responsibility of the investigator to inform the participant of completion of withdrawal. Any 
analyses in progress at the time of request for withdrawal or already performed prior to the 
request being received by the Sponsor will continue to be used as part of the overall research 
study data and results. No new analyses would be generated after the request is received.
In the event that the medical records for the main study are no longer available (eg, if the 
investigator is no longer required by regulatory authorities to retain the main study records) 
or the specimens have been completely anonymized, there will no longer be a link between 
the participant’s personal information and their specimens. In this situation, the request for 
specimen withdrawal cannot be processed.
Participant Blinding/Unblinding
This is an open label study; there is no blinding for this study.
Calibration of Equipment
The investigator or qualified designee has the responsibility to ensure that any device or 
instrument used for a clinical evaluation/test during a clinical study that provides information 
about inclusion/exclusion criteria and/or safety or efficacy parameters shall be suitably 
calibrated and/or maintained to ensure that the data obtained is reliable and/or reproducible. 
Documentation of equipment calibration must be retained as source documentation at the 
study site.
 
 
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Efficacy Assessments 
Tumor Imaging and Assessment of Disease
.  Tumor imaging is strongly preferred to be acquired by computed tomography (CT).  For 
the abdomen and pelvis, contrast-enhanced magnetic resonance imaging (MRI) may be used 
when CT with iodinated contrast is contraindicated, or when mandated by local practice.  
MRI is the strongly preferred modality for imaging the brain.  The same imaging technique 
regarding modality, ideally the same scanner, and the use of contrast should be used in a 
participant throughout the study to optimize the reproducibility of the assessment of existing 
and new tumor burden and improve the accuracy of the assessment of response or 
progression based on imaging.  Note: for the purposes of assessing tumor imaging, the term 
“Investigator” refers to the local investigator at the site and/or the radiological reviewer 
located at the site or at an offsite facility.
Participant eligibility will be determined using local assessment (Investigator assessment) 
based on RECIST 1.1.  In addition, images (including via other modalities) that are obtained 
at an unscheduled time point to determine disease progression, as well as imaging obtained 
for other reasons, but which demonstrate radiologic progression, should also be reviewed by 
the investigator.
If the Investigator considers the participant has progressed, but elects to implement iRECIST, 
the Investigator will assess for confirmation of progression by iRECIST at subsequent time 
points.
Initial Tumor Imaging
Initial tumor imaging must be performed within 28 days prior to the first dose of trial 
treatment.  The site study team must review screening images to confirm the participant has 
measurable disease per RECIST 1.1.
Tumor imaging performed as part of routine clinical management is acceptable for use as 
screening tumor imaging if it is of diagnostic quality and performed within 28 days prior to 
the date of allocation.
If brain imaging is performed to document the stability of existing metastases, MRI should 
be used if possible.  If MRI is medically contraindicated, CT with contrast is an acceptable 
alternative.
Tumor Imaging During the Study
The first on-study imaging assessment should be performed at 9 weeks (63 days ±7 days) 
from the date of allocation.  Subsequent imaging should be performed every 9 weeks 
(63 days ±7 days) or more frequently if clinically indicated.  After 12 months (52 weeks
±7 days), participants who remain on treatment will have imaging performed every 12 weeks 
(84 days ±7 days).  Imaging timing should follow calendar days and should not be adjusted 
for delayed for delays in cycle starts.  Imaging should continue to be performed until disease 
progression is identified by the Investigator (unless the Investigator elects to continue 
treatment and follow iRECIST), the start of new anticancer treatment, withdrawal of consent, 
death, or the end of the study, whichever occurs first.
 
 
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Imaging should continue to be performed until disease recurrence is assessed identified by 
the investigator (unless the Investigator elects to continue treatment and follow iRECIST), 
the start of new anti-cancer treatment, withdrawal of consent, death, or the end of the study, 
whichever occurs first.
Objective response should be confirmed by a repeat imaging assessment. Tumor imaging to 
confirm PR or CR should be performed at least 4 weeks after the first indication of a 
response is observed. Participants will then return to regular scheduled imaging, starting with 
the next scheduled imaging time point. Participants who receive additional imaging for 
confirmation do not need to undergo the next scheduled tumor imaging if it is less than 
4 weeks later; tumor imaging may resume at the subsequent scheduled imaging time point.
Per iRECIST (Section 8.2.1.5), disease progression should be confirmed by the site 4 to 
8 weeks after site-assessed first radiologic evidence of PD in clinically stable participants. 
Participants who have unconfirmed disease progression may continue on treatment at the 
discretion of the Investigator until progression is confirmed by the site, provided they have 
met the conditions detailed in Section 8.2.1.5. Participants who receive confirmatory imaging 
do not need to undergo the next scheduled tumor imaging if it is less than 4 weeks later; 
tumor imaging may resume at the subsequent scheduled imaging time point, if clinically 
stable. Participants who have confirmed disease progression by iRECIST, as assessed by the 
site, will discontinue study treatment. Exceptions are detailed in Section 8.2.1.5.
End of Treatment and Follow-up Imaging
For participants who discontinue study treatment, tumor imaging should be performed at the 
time of treatment discontinuation (±4 week window). If previous imaging was obtained 
within 4 weeks prior to the date of discontinuation, then imaging at treatment discontinuation 
is not mandatory. For participants who discontinue study treatment due to documented 
disease progression, this is the final required tumor imaging if the Investigator elects not to 
implement iRECIST.
For participants who discontinue study treatment without documented disease progression, 
every effort should be made to continue monitoring disease status by tumor imaging using 
the same imaging schedule used while on treatment (approximately every 9 weeks in Year 1 
or approximately every 12 weeks after Year 1) until the start of a new anticancer treatment, 
disease progression, pregnancy, death, withdrawal of consent, or the end of the study, 
whichever occurs first.
RECIST 1.1 Assessment of Disease
RECIST 1.1 will be used by the investigator as the primary measure for assessment of tumor 
response, date of disease progression, and as a basis for all protocol guidelines related to 
disease status (eg, discontinuation of study treatment). Although RECIST 1.1 references a 
maximum of 5 target lesions in total and 2 per organ, this protocol allows a maximum of 
10 target lesions in total and 5 per organ, if clinically relevant to enable a broader sampling 
of tumor burden.  Figure 2 illustrates the imaging flow involving verification of PD for 
clinically stable participants.
 
 
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iRECIST Assessment of Disease
iRECIST is based on RECIST 1.1, but adapted to account for the unique tumor response seen 
with immunotherapeutic drugs. iRECIST will be used by the Investigator to assess tumor 
response and progression, and make treatment decisions. When clinically stable, participants
should not be discontinued until progression is confirmed by the Investigator, working with 
local radiology, according to the rules outlined in Appendix 6. This allowance to continue 
treatment despite initial radiologic PD takes into account the observation that some 
participants can have a transient tumor flare in the first few months after the start of 
immunotherapy, and then experience subsequent disease response. This data will be captured 
in the clinical database.
Clinical stability is defined as the following: 

Absence of symptoms and signs indicating clinically significant progression of 
disease

No decline in ECOG performance status 

No requirements for intensified management, including increased analgesia, 
radiation, or other palliative care
Any participant deemed clinically unstable should be discontinued from study treatment at 
site-assessed first radiologic evidence of PD, and is not required to have repeat tumor 
imaging for confirmation of PD by iRECIST.
If the Investigator decides to continue treatment, the participant may continue to receive 
study treatment and the tumor assessment should be repeated 4 to 8 weeks later to confirm 
PD by iRECIST, per Investigator assessment. 
If repeat imaging does not confirm PD per iRECIST, as assessed by the Investigator, and the 
participant continues to be clinically stable, study treatment may continue and follow the 
regular imaging schedule.  If PD is confirmed, participants will be discontinued from study 
treatment.
If a participant has confirmed radiographic progression (iCPD) as defined in Appendix 6, 
study treatment should be discontinued; however, if the participant is achieving a clinically 
meaningful benefit, an exception to continue study treatment may be considered following 
consultation with the Sponsor.  In this case, if study treatment is continued, tumor imaging 
should continue to be performed following the intervals as outlined in Section 1.3. 
A description of the adaptations and iRECIST process is provided in Appendix 6, with 
additional details in the iRECIST publication [Seymour, L., et al 2017]. A summary of 
imaging and treatment requirements after first radiologic evidence of progression is provided 
in Table 5 and illustrated as a flowchart in Figure 2.
 
 
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Abbreviations:
iRECIST=modified Response Evaluation Criteria in Solid Tumors 1.1 for immune-based 
therapeutics; PD=progressive disease; RECIST 1.1=Response Evaluation Criteria in Solid Tumors 1.1.
Figure 2
Imaging and Treatment for Clinically Stable Participants Treated with 
Pembrolizumab After First Radiologic Evidence of PD by the Investigator
 
 
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Table 5
Imaging and Treatment After First Radiologic Evidence of Progressive Disease
Clinically Stable
Clinically Unstable
Imaging
Treatment
Imaging
Treatment
First radiologic evidence of 
PD by RECIST 1.1 
Repeat imaging at 4 to 
8 weeks to confirm PD.
May continue study treatment 
at the Investigator’s discretion 
while awaiting confirmatory 
tumor imaging by site by 
iRECIST.
Repeat imaging at 4 to 
8 weeks to confirm PD 
per Investigator’s 
discretion only.
Discontinue treatment
Repeat tumor imaging 
confirms PD (iCPD) by 
iRECIST per Investigator 
assessment
No additional imaging 
required.
Discontinue treatment 
(exception is possible upon 
consultation with Sponsor).
No additional imaging 
required.
Not applicable
Repeat tumor imaging 
shows iUPD by iRECIST 
per Investigator assessment
Repeat imaging at 4 to 
8 weeks to confirm PD.  
May occur at next 
regularly scheduled 
imaging visit.
Continue study treatment at the 
Investigator’s discretion.
Repeat imaging at 4 to 
8 weeks to confirm PD 
per Investigator’s 
discretion only.
Discontinue treatment
Repeat tumor imaging 
shows iSD, iPR, or iCR by 
iRECIST per Investigator 
assessment.
Continue regularly 
scheduled imaging 
assessments.
Continue study treatment at the 
Investigator’s discretion.
Continue regularly 
scheduled imaging 
assessments.
May restart study treatment if 
condition has improved and/or 
clinically stable per Investigator’s 
discretion.  Next tumor imaging 
should occur according to the 
regular imaging schedule.
Abbreviations:  iCPD=iRECIST confirmed progressive disease; iCR=iRECIST complete response; iRECIST=modified Response Evaluation Criteria in Solid Tumors 1.1 for 
immune-based therapeutics; iSD=iRECIST stable disease; iUPD=iRECIST unconfirmed progressive disease; PD=progressive disease; RECIST 1.1=Response Evaluation
Criteria in Solid Tumors 1.1.
Note: If progression has been verified, further management is by the site, based on iRECIST.  Any further imaging should still be reviewed by the investigator. If RECIST 1.1 
disease progression has not been verified, ideally the site should continue treatment. Whether or not treatment continues, imaging should be collected and by the Investigator 
until PD is verified 
 
 
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Photography for Cutaneous Lesions
Skin lesions will be classified as non-target lesions and their assessment should follow the 
imaging assessment schedule. Skin lesions will be documented at baseline with qualitative 
digital photography, and followed for response assessment in the same way at each scheduled 
tumor assessment. The timing for capturing cutaneous lesion photographs should follow the 
same schedule as the imaging scans.
Safety Assessments
Details regarding specific safety procedures/assessments to be performed in this study are 
provided below. The total amount of blood/tissue to be drawn/collected over the course of 
the study (from prestudy to poststudy visits), including approximate blood/tissue volumes 
drawn/collected by visit and by sample type per participant can be found in Section 8.
Planned time points for all safety assessments are provided in the SoA.
Physical Examinations
Complete Physical Examination
The investigator or qualified designee will perform a complete physical exam during 
screening, at Day 1 of each cycle, and during follow up, as specified in Section 1.3.  After the 
consent form is signed, new clinically significant abnormal physical examination findings 
should be recorded as AEs.
Directed Physical Examination
The investigator or qualified designee will perform a directed physical exam as per 
Section 1.3 and as clinically indicated.  New clinically significant abnormal findings should 
be recorded as AEs.
Vital Signs
The investigator or qualified designee will take vital signs as specified in the SoA
(Section 1.3).  Vital signs should include temperature, pulse, respiratory rate, and blood 
pressure. Weight will be recorded as specified in the SoA.  Height will be measured at 
screening only.
Electrocardiograms
A standard 12-lead ECG will be performed using local standard procedures at Screening.  
Clinically significant abnormal findings should be recorded as medical history.  Additional 
time points for standard 12-lead ECGs will be performed as per Section 1.3.  Clinically 
significant abnormal findings seen on the follow-up ECGs should be recorded as AEs.
Eastern Cooperative Oncology Group Performance Scale
The investigator or qualified designee will assess ECOG status at every visit.
 
 
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Clinical Safety Laboratory Assessments
Refer to Appendix 5 for the list of clinical laboratory tests to be performed and to the SoA for 
the timing and frequency. 
●
The investigator must review the laboratory report, document this review, and record 
any clinically relevant changes occurring during the study in the AE section of the 
case report form (CRF). The laboratory reports must be filed with the source 
documents. Clinically significant abnormal laboratory findings are those which are 
not associated with the underlying disease, unless judged by the investigator to be 
more severe than expected for the participant's condition.
●
All protocol-required laboratory assessments, as defined in Appendix 5, must be 
conducted in accordance with the laboratory manual and the SoA.
●
If laboratory values from nonprotocol specified laboratory assessments performed at 
the institution’s local laboratory require a change in study participant management or 
are considered clinically significant by the investigator (eg, SAE or AE or dose 
modification), then the results must be recorded in the appropriate CRF (eg, SLAB).
●
For any laboratory tests with values considered clinically significantly abnormal 
during participation in the study or within 30 days after the last dose of study 
treatment, every attempt should be made to perform repeat assessments until the 
values return to normal or baseline or if a new baseline is established as determined 
by the investigator. 
Pregnancy Testing
All women who are being considered for participation in the trial, and who are not surgically 
sterilized or postmenopausal, must be tested for pregnancy within 72 hours of each cycle of 
trial treatment and 30 days post-treatment.  If a urine test is positive or not evaluable, a serum 
test will be required.  Participants must be excluded/discontinued from the trial in the event 
of a positive or borderline-positive test result.
Adverse Events (AEs), Serious Adverse Events (SAEs), and Other Reportable 
Safety Events 
The definitions of an AE or SAE, as well as the method of recording, evaluating, and 
assessing causality of AE and SAE and the procedures for completing and transmitting AE, 
SAE, and other reportable safety event reports can be found in Appendix 4.
Progression of the cancer under study is not considered an AE as described in Section 8.4.5 
and Appendix 4.
AE, SAEs, and other reportable safety events will be reported by the participant (or, when 
appropriate, by a caregiver, surrogate, or the participant's legally authorized representative). 
The investigator, who is a qualified physician, and any designees are responsible for 
detecting, assessing, documenting, and reporting events that meet the definition of an AE or 
SAE as well as other reportable safety events. Investigators remain responsible for following 
up AE, SAEs, and other reportable safety events for outcome according to Section 8.4.3.
 
 
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Time Period and Frequency for Collecting AE, SAE, and Other Reportable 
Safety Event Information 
All AEs, SAEs, and other reportable safety events that occur after the consent form is signed 
but before treatment allocation/randomization must be reported by the investigator if the 
participant is receiving placebo run-in or other run-in treatment, if the event causes the 
participant to be excluded from the study, or is the result of a protocol-specified intervention, 
including but not limited to washout or discontinuation of usual therapy, diet, or a procedure. 

All AEs from the time of treatment allocation/randomization through 30 days 
following cessation of study treatment must be reported by the investigator. 

All AEs meeting serious criteria, from the time of treatment allocation/randomization 
through 90 days following cessation of study treatment, or 30 days following 
cessation of study treatment if the participant initiates new anticancer therapy, 
whichever is earlier must be reported by the investigator. 

All pregnancies and exposure during breastfeeding, from the time of treatment 
allocation/randomization through 120 days following cessation of study treatment, or 
30 days following cessation of study treatment if the participant initiates new 
anticancer therapy must be reported by the investigator. 

Additionally, any SAE brought to the attention of an investigator at any time outside 
of the time period specified above must be reported immediately to the Sponsor if the 
event is considered to be drug-related.
Investigators are not obligated to actively seek AE or SAE or other reportable safety events 
in former study participants. However, if the investigator learns of any SAE, including a 
death, at any time after a participant has been discharged from the study, and he/she 
considers the event to be reasonably related to the study treatment or study participation, the 
investigator must promptly notify the Sponsor.
All initial and follow-up AEs, SAEs and other reportable safety events will be recorded and 
reported to the Sponsor or designee within the time frames as indicated in Table 6.
 
 
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Table 6
Reporting Time Periods and Time Frames for Adverse Events and Other 
Reportable Safety Events
Type of Event
Time Period
Time
Frame to 
Report 
Event and 
Follow-up 
Informatio
n to 
SPONSOR:
Consent to 
Randomization
/ Allocation
Randomization
/ Allocation 
through 
Protocol-
Specified 
Follow-up 
Period
After the Protocol 
Specified Follow-up 
Period
Non-Serious 
Adverse Event 
(NSAE)
Report if:
- due to 
protocol-
specified 
intervention
- causes 
exclusion
- participant is 
receiving 
placebo run-in 
or other run-in 
treatment
Report all
Not required
Per data 
entry 
guidelines
Serious Adverse 
Event (SAE)
including Cancer 
and Overdose
Report if:
- due to 
protocol-
specified 
intervention
- causes 
exclusion
- participant is 
receiving 
placebo run-in 
or other run-in 
treatment
Report all
Report if:
- drug/vaccine related.
(Follow ongoing to 
outcome)
Within 24 
hours of 
learning of 
event
Pregnancy/Lactatio
n Exposure
Report if:
- due to 
intervention
- causes 
exclusion
Report all
Previously reported –
Follow to 
completion/termination
; report outcome
Within 24 
hours of 
learning of 
event
Event of Clinical 
Interest (require 
regulatory 
reporting)
Report if:
- due to 
intervention
- causes 
exclusion
Report
- Potential DILI
- Require 
regulatory 
reporting
Not required
Within 24 
hours of 
learning of 
event
Event of Clinical 
Interest (Do not 
require regulatory 
reporting)
Report if:
- due to 
intervention
- causes 
exclusion
Report
- non-DILI ECIs 
and those not 
requiring 
regulatory 
reporting
Not required
Within 5 
calendar 
days of 
learning of 
event
 
 
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Method of Detecting AEs, SAEs, and Other Reportable Safety Events
Care will be taken not to introduce bias when detecting AE and/or SAE and other reportable 
safety events. Open-ended and nonleading verbal questioning of the participant is the 
preferred method to inquire about AE occurrence.
Follow-up of AE, SAE and Other Reportable Safety Event Information 
After the initial AE/SAE report, the investigator is required to proactively follow each 
participant at subsequent visits/contacts. All AE, SAE, and other reportable safety events 
including pregnancy and exposure during breastfeeding, events of clinical interest (ECIs), 
Cancer and Overdose will be followed until resolution, stabilization, until the event is 
otherwise explained, or the participant is lost to follow-up (as defined in Section 7.3). In 
addition, the investigator will make every attempt to follow all nonserious AEs that occur in 
randomized participants for outcome. Further information on follow-up procedures is given 
in Appendix 4.
Regulatory Reporting Requirements for SAE
●
Prompt notification (within 24 hours) by the investigator to the Sponsor of SAE is 
essential so that legal obligations and ethical responsibilities towards the safety of 
participants and the safety of a study treatment under clinical investigation are met. 
●
The Sponsor has a legal responsibility to notify both the local regulatory authority 
and other regulatory agencies about the safety of a study treatment under clinical 
investigation. All AEs will be reported to regulatory authorities, IRB/IECs and 
investigators in accordance with all applicable global laws and regulations, ie, per 
ICH Topic E6 (R2) Guidelines for GCP.
●
Investigator safety reports must be prepared for suspected unexpected serious adverse 
reactions (SUSARs) according to local regulatory requirements and Sponsor policy 
and forwarded to investigators as necessary.
●
An investigator who receives an investigator safety report describing an SAE or other 
specific safety information (eg, summary or listing of SAE) from the Sponsor will file 
it along with the IB and will notify the IRB/IEC, if appropriate according to local 
requirements.
Disease-related Events and/or Disease-related Outcomes Not Qualifying as AEs 
or SAEs
Efficacy endpoints as outlined in this section will not be reported to the Sponsor as described 
in Section 8.4.1. 
Specifically, the suspected/actual events covered in this exception include any event that is 
disease progression of the cancer under study.
The Sponsor will monitor unblinded aggregated efficacy endpoint events and safety data to 
ensure the safety of the participants in the study. Any suspected endpoint which upon review 
is not progression of the cancer under study will be forwarded to Global Pharmacovigilance
as an SAE within 24 hours of determination that the event is not progression of the cancer 
under study.
 
 
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Pregnancy and Exposure During Breastfeeding
Although pregnancy and infant exposure during breastfeeding are not considered AEs, any 
pregnancy or infant exposure during breastfeeding in a participant (spontaneously reported to 
the investigator or their designee) that occurs during the study are reportable to the Sponsor.
All reported pregnancies must be followed to the completion/termination of the pregnancy. 
Pregnancy outcomes of spontaneous abortion, missed abortion, benign hydatidiform mole, 
blighted ovum, fetal death, intrauterine death, miscarriage and stillbirth must be reported as 
serious events (Important Medical Events). If the pregnancy continues to term, the outcome 
(health of infant) must also be reported.
Events of Clinical Interest (ECIs)
Selected nonserious and serious adverse events are also known as ECIs and must be reported 
to the Sponsor.
Events of clinical interest for this study include: 
1. an overdose of Sponsor's product, as defined in Section 8.5, that is not associated with 
clinical symptoms or abnormal laboratory results.
2. an elevated AST or ALT lab value that is greater than or equal to 3X the upper limit 
of normal and an elevated total bilirubin lab value that is greater than or equal to 2X 
the upper limit of normal and, at the same time, an alkaline phosphatase lab value that 
is less than 2X the upper limit of normal, as determined by way of protocol-specified 
laboratory testing or unscheduled laboratory testing.*
*Note: These criteria are based upon available regulatory guidance documents. The 
purpose of the criteria is to specify a threshold of abnormal hepatic tests that may 
require an additional evaluation for an underlying etiology. The study site 
guidance for assessment and follow-up of these criteria can be found in the 
Investigator Trial File Binder (or equivalent).
Treatment of Overdose
For this study, an overdose of pembrolizumab will be defined as any dose of 1000 mg or 
greater (≥5 times the indicated dose). 
No specific information is available on the treatment of overdose of pembrolizumab. In the 
event of overdose, the participant should be observed closely for signs of toxicity. 
Appropriate supportive treatment should be provided if clinically indicated.
Pharmacokinetics
PK parameters will not be evaluated in this study.
Blood Collection for Biomarker Analyses
Sample collection, storage and shipment instructions for blood and plasma samples will be 
provided in the procedures manual. 
 
 
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Pharmacodynamics
Tumor Tissue Collection
Fresh tumor tissue will be obtained at baseline (during the screening period) and on-
treatment.  On-treatment biopsies prior to radiographic determination of response or 
progression should be obtained at Week 6 (42 days ± 3 days) to evaluate pharmacodynamics 
in participants who subsequently respond, progress, or have SD.  If a biopsy is obtained at 
this time point, then a second on-treatment biopsy timed with response/progression is 
optional. Excisional biopsy, punch biopsy and high-pass core needle biopsy will be 
permitted.  Additional information on biopsy requirements and tissue handling can be found 
in the Procedures Manual.
Biomarkers
The following correlative blood samples will be collected:

PBMCs

Whole blood (for RNA analysis)

Whole blood (for DNA analysis)

Serum for biomarker analysis

Plasma for biomarker analysis
Please refer to the Procedures Manual for approximate blood volumes to be collected.
Single Cell RNA Sequencing
To ensure that high quality data is generated from scRNAseq, rigorous quality control (QC) 
efforts will be performed for this study for both the experimental procedures and 
computational analysis.
Experimental QC: Tissue dissociation will be performed using an optimized protocol to 
ensure a standardized procedure is followed for every participant-derived sample. Tissue will 
be processed in a rapid manner so that the profile of cellular RNA will remain as authentic as 
possible. By the end of the process, every sample will be assessed for cellular viability, the 
presence of ambient debris, and cell number. This QC test will determine if the sample is 
ready for further processing for sequencing or if additional steps are needed to improve the 
quality of the sample. If the quality of the sample needs to be improved, it will be treated 
with a magnetic bead-based method to enrich for viable cells, deplete debris, and reduce 
ambient RNA. If a second QC test confirms improvement in the quality of the sample, the 
cells will then be further processed.  Quality control measures will be included for library 
construction.  Bulk RNAseq will be performed on samples and the RNA integrity number 
(RIN) scores will be checked for the population.
Computational QC: scRNAseq data is noisy, and includes false negatives (“drop-outs”): 
genes expressed in the cell but not detected by the assay. The Klarman Cell Observatory
(KCO) at the Broad Institute has developed and leveraged state of the art tools, many 
 
 
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developed within the laboratory as well as from other groups, for pre-processing and QC of 
scRNAseq data.
The KCO pipeline uses RNAseq analysis tools such as Trinity, Tuxedo, and RSEM to align
reads, transcript reconstruction/annotation, abundance estimation, read quality trimming, and 
sample quality analysis. Library quality is scored based on alignment rates to the genome and 
transcriptome, the proportion of ribosomal (rRNA) reads, the uniformity of coverage, 3′ and 
5′ biases, biases associated with length or sequence composition, library complexity, 
reproducibility of expression estimates, and the relationship between single cell and bulk 
population profiles. The pipeline is optimized for plate, single nucleus sequencing 
(sNuc-Seq), Droplet-sequencing (Drop-Seq), DroNc-Seq, and 10x Genomics data, addressing 
each data type’s unique characteristics (e.g., unique molecular identifiers [UMIs], 3′-directed 
libraries, etc.). Tools will be incorporated that increase efficiency by pseudo-alignment, and 
address unique quality issues that arise at polymerase chain reaction, such as cell barcode 
chimeras. 
To calculate expression levels, alternatives to standard approaches that typically rely on 
assumptions that are violated in single cell profiles of heterogeneous cell populations will be 
considered. For example, in a population of T-cells, some may be active and others 
“quiescent” with the former having radically larger and more complex transcriptomes. This is
addressed by introducing a scaling factor reflecting the expected number of transcripts (or 
UMIs) in each condition and by revising differential expression tests, to account for the 
varying number of transcripts and genes in each condition. 
Planned Genetic Analysis Sample Collection
The sample for genetic analysis should be drawn for planned exploratory biomarker research. 
This sample will not be collected at the site if there is either a local law or regulation 
prohibiting collection, or if the IRB/IEC does not approve the collection of the sample for 
these purposes. If the sample is collected, leftover extracted DNA will be stored for future 
biomedical research if the participant signs the future biomedical research consent. If the 
genetic sample collection is not approved, but future biomedical research is approved and 
consent is given, this sample will be collected for the purpose of future biomedical research.
Future Biomedical Research Sample Collection 
If the participant signs the future biomedical research consent, the following specimens will 
be obtained as part of future biomedical research:

DNA for future research

Leftover plasma and serum from biomarker analyses

Leftover DNA and RNA

Leftover tumor tissue, including tumor cell lines

Leftover sorted single cells and PBMCs
 
 
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Visit Requirements
Visit requirements are outlined in Section 1.3. Specific procedure-related details are provided 
above in Section 8.
Screening
Written consent must be obtained prior to performing any protocol-specific procedure. 
Results of a test performed prior to the participant signing consent as part of routine clinical 
management are acceptable in lieu of a screening test if performed within the specified time 
frame. Screening procedures are to be completed within 28 days prior to the first dose of 
study treatment except for the following:

Consent Form signed within 42 days. The consent form must be signed prior to 
completing any protocol protocol-specified procedure.

Laboratory tests and evaluation of ECOG status are to be performed within 10 days 
prior to the first dose of study treatment

For women of reproductive potential, a urine pregnancy test will be performed within 
72 hours prior to the first dose of study treatment.  If urine pregnancy results cannot 
be confirmed as negative, a serum pregnancy test will be required (performed by the 
local study site laboratory)
Participants may be rescreened after initially failing to meet the inclusion/exclusion criteria. 
Results from assessments during the initial screening period are acceptable in lieu of a repeat 
screening test if performed within the specified time frame and the corresponding 
inclusion/exclusion criteria is met. Participants who are rescreened will retain their original 
screening number.
Treatment Period
Visit requirements are outlined in Section 1.3.  Specific procedure-related details are 
provided above in Section 8.1.
Poststudy
Safety Follow-up Visit
The mandatory Safety Follow-up Visit should be conducted approximately 30 days after the 
last dose of study treatment or before the initiation of a new anticancer treatment, whichever 
comes first. 
All AEs that occur prior to the Safety Follow-Up Visit should be recorded. Participants with 
an AE of Grade >1 will be followed until the resolution of the AE to Grade 0-1 or until the 
beginning of a new anticancer therapy, whichever occurs first. Serious AEs that occur within 
90 days of the end of treatment or before initiation of a new anticancer treatment should also 
be followed and recorded.
 
 
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Follow-up Visits
Participants who discontinue trial treatment for a reason other than disease progression will 
move into the Follow-Up Phase and should be assessed every 9 weeks (63 days ±7 days) 
during the first year (52 weeks) and every 12 weeks (84 days ±7 days) thereafter, by 
radiologic imaging to monitor disease status. Every effort should be made to collect 
information regarding disease status until the start of new anti-cancer therapy, disease 
progression, death, or end of study. Information regarding post-study anticancer treatment 
will be collected if new treatment is initiated.
Survival Follow-up
Participants who experience confirmed disease progression or start a new anticancer therapy, 
will move into the Survival Follow-Up Phase and should be contacted by telephone 
approximately every 12 weeks to assess for survival status until death, withdrawal of 
consent, or the end of the trial, whichever occurs first.
Survival Status
To ensure current and complete survival data is available at the time of database locks, 
updated survival status may be requested during the course of the study by the Sponsor.  For 
example, updated survival status may be requested prior to but not limited to an external Data 
Monitoring Committee (eDMC) review, interim and/or final analysis.  Upon Sponsor 
notification, all participants who do not/will not have a scheduled study visit or study contact 
during the Sponsor defined time period will be contacted for their survival status (excluding 
participants that have a previously recorded death event in the collection tool).
9. Statistical Analysis Plan 
This section outlines the statistical analysis strategy and procedures for the study.  Changes 
to analyses made after the protocol has been finalized, but prior to final database lock, will be 
documented in a supplemental statistical analysis plan (sSAP) and referenced in the Clinical 
Study Report (CSR) for the study.  Post hoc exploratory analyses will be clearly identified in 
the CSR.  Details around the analysis approach for biomarker endpoints related to the 
secondary and exploratory objectives are deemed out of scope for this SAP, but may be the 
subject of sSAPs.
 
 
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Statistical Analysis Plan Summary
Key elements of the statistical analysis plan are summarized below; the comprehensive plan 
is provided in Sections 9.2 through 9.12.
Study Design Overview
This is a single-arm, open label, trial of pembrolizumab in participants with 
advanced melanoma.
Treatment Assignment
All participants will receive pembrolizumab at a dose of 200 mg Q3W by non-
random assignment in an unblinded fashion.
Analysis Populations
Primary objectives: The All Participants as Treated (APaT) population will be 
used as the analyses population for primary objectives.  
Efficacy objective (secondary objective): APaT population.  
Safety: APaT population.
Primary Endpoints
1.
Fraction of cytotoxic tumor-infiltrating T-lymphocytes (FCT) at baseline.
2.
FCT fold change from baseline.
3.
Average Specific Cytotoxic T-lymphocyte Frequency Ratio (ASCTFR)
Key Secondary 
Endpoints / Variables
1.
Objective response rate (ORR) by RECIST 1.1 (investigator-assessed).
2.
Progression-free-survival (PFS) by RECIST 1.1 (investigator-assessed).
3.
Overall survival (OS). 
4.
Safety measures
Statistical Methods for 
Key Biomarker Analyses
The primary objectives will be evaluated by estimating the posterior distribution 
of the difference in means of the primary endpoints for responders vs. non-
responders via the Bayesian framework.
Statistical Methods for 
Key Efficacy Analyses
The secondary efficacy objective will be evaluated by reporting summary 
statistics and 95% confidence intervals for ORR (with Clopper-Pearson CI), PFS, 
and OS (via Kaplan-Meier method).
Statistical Methods for
Key Safety Analyses
Descriptive summary statistics will be provided as appropriate.
Interim Analyses
Interim analyses that will not change the conduct of the study may be performed 
during the course of the study. 
Final analyses: the final analyses will be carried out after all participants have 
had a 90-day follow-up after the end of treatment (unless lost to follow-up). If by 
that time the death rate is <70%, for OS and OS-related analyses, the final 
analyses will occur after death has occurred in approximately 70% of the subjects 
(~42 deaths). If the estimated interval between the 2 analyses is less than 3 
months, then the first analysis may be delayed and both analyses will be 
conducted at the later of the two.
Multiplicity
No multiplicity adjustment will be applied.
Sample Size and Power 
The study will enroll approximately 60 participants. If there are at least
10 responders, reasonable power supporting the primary objectives can be 
expected (~90% power for baseline FCT with a mean difference of 0.10; ~80% 
power for FCT fold-change from baseline with an effect size of 0.50 on natural 
log scale; and ~80% power for ASCTFR with an effect size of 0.50).  
 
 
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Responsibility for Analyses/In-house Blinding
The statistical analysis of the data obtained from this study will be conducted by, or under the 
direct auspices of, the Early Clinical Development Statistics Department in collaboration 
with Genetics and Pharmacogenomics Department of the Sponsor.
This trial is being conducted as an open-label study, i.e., participants, investigators, and 
Sponsor personnel will be aware of participant treatment assignments after each participant is 
enrolled and treatment is assigned.
Biomarker assays used to assess the primary, secondary and exploratory objectives in this 
study will be performed by personnel blinded to participants’ clinical outcome data, as 
appropriate, in order to preserve an objective evaluation of the study objectives. Separation 
between the generation of the biomarker data and knowledge of clinical outcome will permit 
a flexible assessment strategy for the complex biomarker data without impinging on the 
validity of the eventual comparison between responders and non-responders. If deemed 
appropriate, clinical outcome data of a subset of participants may be unblinded to certain 
biomarker personnel(s) and these data will be used as a testing dataset to generate specific 
hypotheses surrounding the biomarker data. These additional hypotheses will be tested in the 
corresponding validation dataset (i.e., participants not part of the testing dataset). If this 
testing and validation strategy is utilized, additional details will be provided in the sSAP 
prior to implementation.
Interim analyses and timing of the final analyses are described in Section 9.7.
Hypotheses/Estimation
Objectives of the study are stated in Section 3.
Analysis Endpoints
Biomarker, efficacy, and safety endpoints that will be evaluated are outlined in the following 
sections.
Biomarker Endpoints
Primary Biomarker Endpoints
The primary intra-tumoral biomarker measures that will be compared between responders 
and non-responders in evaluation of the primary objectives are 
1) FCT, defined as the fraction of cytotoxic CD8+ T-cells expressing a predefined single-
cell RNA gene signature to the total tumor infiltrating CD8+ T-cells isolated from tumor 
biopsies.
To quantify FCT based on scRNAseq data we will use a previously defined signature of 
cytotoxic T-cells [Tirosh, I., et al 2016]. RNAseq reads will be used to assemble TCR and B-
cell receptor sequences and then identify T-cell or B-cell clones.  Dimensionality reduction 
and graph clustering will then be used to partition cell types by their expression profiles and 
associate them with cell-specific signatures. Statistical scoring will be adapted for single cell 
data to identify key cell states and their respective signatures, within and across cell types 
(e.g., phases of the cell cycle, inflammation, activation states, “activation-independent 
 
 
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exhaustion, drug resistance signatures).  The cell type and state signatures will be compared 
to a large and diverse set of immune cells from various cancer cohorts [Tirosh, I., et al 2016] 
[Venteicher, A. S., et al 2017] [Zheng, C., et al 2017]. T-cells with an overall high expression 
of the cytotoxic signature will be defined as cytotoxic tumor-infiltrating T-lymphocytes. A 
cytotoxic score will be calculated for each cell to quantify the expression level of the 
cytotoxic signature (details in next paragraph). If the cells' cytotoxic score has a bimodal 
distribution, a natural cutoff will define highly cytotoxic T-cells. If it is not bimodal, we will 
define an “artificial” cutoff using the continuous scores (e.g., 90th percentile). The FCT will 
be calculated as the relative abundance of these cells compared to the overall number of 
sequenced CD8+ T-cells, i.e., the number of cytotoxic CD8+ T-cells (with high cytotoxic 
scores) divided by the number of total CD8+ T-cells that were sequenced in this tumor.
To calculate the cytotoxic score, genes will be binned into 50 expression bins according to 
their average expression across CD8+ T-cells. Let Tij be the normalized expression of gene i
in cell j. Let S be the gene signature of the cytotoxic T-cells, and S ̃ a random signature with 
the same distribution of genes across the expression bins as S. The cytotoxic score (CytS) of 
a cell is defined as:
2) FCT fold-change from baseline, and
3) Average Specific Cytotoxic T-lymphocyte Frequency Ratio (ASCTFR): defined as the 
arithmetic mean of log10 ratio of the frequency of individual specific cytotoxic TCR clones 
on-treatment to pre-treatment (baseline).  In this definition, pre-treatment frequencies of 
unique (as determined by TCR Vβ chain sequencing) specific cytotoxic clones will be used 
to normalize the on-treatment frequencies.  Each participant’s ASCTFR will then be 
calculated as the arithmetic mean of the log10 ratios of the on-treatment to pre-treatment 
frequencies across the unique specific cytotoxic clones identified within that participant.  For 
example, consider one participant who has two specific cytotoxic TCR clones, Clone A and 
Clone B, and for each of these two clones the participant has pre-treatment frequency 
measurements A0/B0 and on-treatment frequency measurements A1/B1, then the ASCTFR 
for this participant will be calculated as:
The specific TCR clones will be selected based on their frequency as well as the interferon-γ
signature. Here the frequency is in reference to the specific tumor-infiltrating lymphocyte 
TCR Vβ frequency distribution (obtained by TCR deep sequencing) in the pre-treatment and 
on-treatment biopsies. The cytolytic function of these TCR clones will be determined based 
on CytS obtained from the scRNAseq (as used in the definition of FCT). 
 
 
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Secondary and Exploratory Biomarker Endpoints
Details around other biomarker related endpoints associated with secondary and exploratory 
objectives,  including tumor-associated epitopes, the pipeline surrounding the identification 
of neoepitopes, what will define the response of T-cell clones to such epitopes, as well as 
details for the processing and normalization of the complex data sources to be generated by 
the set of methods described in Section 4.2.1.3 are deemed out of scope for this SAP, but will 
be described in the CSR and may be the subject of sSAPs.
Efficacy Endpoints
Secondary Efficacy Endpoints
1) ORR is defined as the proportion of the participants in the analysis population who 
have a best response as CR or PR. Responses are based on local site review using 
RECIST 1.1.
2) PFS is defined as the time from start of treatment to the first documented PD (based 
on local site review using RECIST 1.1) or death due to any cause, whichever occurs 
first.
3) OS is defined as the time from start of treatment to death due to any cause. 
Participants without documented death at the time of the analysis will be censored at 
the date of last follow-up. See Section 9.6.2 for the definition of censoring.
Safety Endpoints
Refer to Section 4.2.1.2 for the description of the safety measures.
Analysis Populations
Biomarker Analysis Population
The All Participants as Treated (APaT) population will be used for the analysis of biomarker 
endpoints.  The APaT population consists of all allocated participants who received at least 
one dose of study treatment.  For analysis related to post-baseline biomarker values, at least 
one post-baseline measurement is required for inclusion in the analysis of each specific 
biomarker endpoint.
Efficacy Analysis Population
The APaT population will be used for the analysis of ORR, PFS and OS. Details on the 
approach to handle missing data are provided in Section 9.6 Statistical Methods.
Safety Analysis Population
The APaT population will be used for the analysis of safety data in this study.  At least one 
laboratory or vital sign measurement obtained subsequent to at least one dose of study 
treatment is required for inclusion in the analysis of each specific parameter.  To assess 
change from baseline, a baseline measurement is also required.
 
 
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Statistical Methods
For the primary study objectives enumerated in Section 3, the overall analysis strategy is to 
formulate reasonable parametric models for the distributions of the measures describing the 
nature and frequency of cytotoxic tumor-infiltrating T-lymphocytes.  These models, 
formulated in a Bayesian framework, will be used to understand the differences for 
responders vs. non-responders by evaluating and comparing their posterior distributions of 
the model parameters.   Details are described in Section 9.6.1.
Analyses methods for efficacy and safety endpoints are described in Section 9.6.2 and 
Section 9.6.3, respectively.
Statistical Methods for Biomarker Analysis
This section describes the statistical methods that address the primary objectives.  Data will 
be examined for departures from the assumptions of the distribution model(s) as appropriate. 
Suitable data transformation may be applied if a serious departure from the assumptions of 
the model(s) is observed, or other suitable distributions may be used in the Bayesian models.
Methods related to secondary and/or exploratory biomarker related objectives may be 
described in sSAPs. 
Baseline FCT
To address the first primary objective, the difference in mean baseline FCT between 
responders and non-responders will be quantified by calculating the posterior probability that 
the mean baseline FCT for responders exceeds that of non-responders, under a Bayesian 
model assuming the participant FCTs arise from a Beta distribution.  Non-informative 
(vague) priors will be used: e.g., a Uniform (0, 1) prior for both the means of responders and 
non-responders.  The first primary hypothesis will be supported if the posterior probability 
that the mean baseline FCT for responders exceeds that of non-responders is greater than 
70%. The 95% posterior credible interval will also be provided for the difference in the mean 
baseline FCT between responders and non-responders.
Supportive analyses may be performed by comparing the average baseline CytS scores of the 
two populations by using a hierarchical linear model (HLM) that captures the hierarchical 
structure of the data. 
FCT Fold Change from Baseline
Individual FCT fold change from baseline values will be natural log transformed prior to 
statistical analysis. It is expected that the mean FCT log fold-change from baseline in 
responders is higher than that in non-responders.  The difference in mean FCT log 
fold-change from baseline between responders and non-responders will be quantified by 
calculating the posterior probability that the difference exceeds zero under the Bayesian 
framework.  The planned approach will be to assume that these participant-level FCT log 
fold-change from baseline values arise from normal distributions with means and variances 
that potentially differ for responders and non-responders. Non-informative (vague) priors 
will be used: e.g., a diffuse normal distribution centered at 0 with precision 1e-06 as prior for 
the mean, and a Gamma (1e-04, 1e-04) distribution as prior for the precision.  The same 
priors will be used for both responders and non-responders.  The second primary hypothesis 
 
 
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will be supported if the posterior probability that the mean FCT log fold-change from 
baseline of responders exceeds that of non-responders is greater than 70%.  The 95% 
posterior credible interval will also be provided for the difference in mean FCT log 
fold-change from baseline between responders and non-responders.  
Supportive analysis may be performed by adding to the hierarchical linear model a covariate 
time point to indicate whether the sample was taken before or after treatment, and an 
interaction term between the response and time point.
ASCTFR
Similarly, the third primary objective to compare the ASCTFR between responders and non-
responders will also be addressed using a Bayesian framework to compare means between 
the 2 groups of participants.  It is expected that on-treatment specific tumor-infiltrating 
cytotoxic T-lymphocytes represent a set of expanded, higher frequency clones among 
responders compared to non-responders.  The analysis method for ASCTFR will be similar to 
that for the FCT fold-change from baseline: we assume that these participant-level average 
log frequency ratios arise from normal distributions with means and variances that potentially 
differ for responders and non-responders.  The key quantity being estimated will be the 
posterior probability that the mean ASCTFR is larger in responders vs. non-responders.  
Non-informative (vague) priors will be used: e.g., a diffuse normal distribution centered at 0 
with precision 1e-06 as prior for the mean, and a Gamma (1e-04, 1e-04) distribution as prior 
for the precision.  The same priors will be used for both responders and non-responders.  The 
third primary hypothesis will be supported if the posterior probability that the mean ASCTFR 
for responders exceeds that of non-responders is greater than 70%. The 95% posterior 
credible interval will also be provided for the difference in mean ASCTFR between 
responders and non-responders.
Other Biomarker Endpoints
Details around the analysis approach for biomarker endpoints related to the secondary and 
exploratory objectives are deemed out of scope for this SAP, but may be the subject of 
sSAPs
Statistical Methods for Efficacy Analyses
The chief purpose of determining efficacy for this study is to define the appropriate subsets 
to be compared in the evaluation of the biology of intra-tumoral changes.  Participants will be 
separated as responder vs. non-responder, as assessed by RECIST 1.1 per investigator 
review.  
This section describes the statistical methods that address the secondary efficacy objective 
(ORR, PFS and OS).  
Objective response rate (ORR)
The ORR point estimate and its 95% Clopper-Pearson CI will be reported.  Participants
without disease assessment after the start of treatment will be considered as non-responders 
in ORR estimation.
 
 
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Progression-free-survival (PFS)
The Kaplan-Meier method will be used to estimate the PFS curve.  The median PFS and its 
associated two-sided 95% confidence interval (CI) will be estimated and reported.  The 
Kaplan-Meier estimates of the PFS rate at 6 months and other time points of interest will also 
be reported. Since disease progression is assessed periodically, PD can occur any time in the 
time interval between the last assessment where PD was not documented and the assessment 
when PD is documented.  For this analysis, for participants who have PD, the true date of 
disease progression will be approximated by the date of first assessment at which PD is 
objectively documented using RECIST 1.1, regardless of discontinuation of study drug.  
Death is always considered as a confirmed PD event.  Participants without documented 
PD/death will be censored at the last disease assessment date.  In the event that participants
without documented PD/death have new anticancer treatment initiated, the participants will 
be considered censored at last disease assessment before new anticancer treatment.
Overall Survival (OS)
The Kaplan-Meier method will be used to estimate the OS curve.  The median OS and its 
associated two-sided 95% CI will be estimated and reported.  The Kaplan-Meier estimates of 
the OS rate at 6 months and other time points of interest will also be reported. A sensitivity 
analysis of OS that censors participants at the time of initiation of new anticancer treatment 
will also be performed.  Table 7 summarizes the efficacy analyses.
Table 7
Analysis Strategy for Efficacy Variables
Endpoint/ 
Variable
(Description, 
Time Point)
Primary vs. 
Supportive 
Approach
Statistical Method
Analysis 
Populatio
n
Missing Data 
Approach
Secondary Objective
ORR
P
Point estimate with 95% 
Clopper-Pearson CI for ORR 
will be reported.
APaT
Participants with
missing data are
considered non-
responders
PFS
P
Kaplan-Meier method for PFS 
curve estimation, and summary 
statistics with 95% CIs will be 
reported.
APaT
Censored at last 
assessment (before 
new anticancer 
treatment)
OS
P
Kaplan-Meier method for OS 
curve estimation, and summary 
statistics with 95% CIs will be 
reported.
APaT
Censored at last 
date
OS
S
Kaplan-Meier method for OS 
curve estimation, and summary 
statistics with 95% CIs will be 
reported.
APaT
Censored at last 
date or initiation of 
new anticancer 
treatment
Abbreviations: APaT = All Participants as Treated; ORR = objective response rate; OS = overall survival; 
P = Primary approach; PFS = progression-free survival; S = Supportive approach.
 
 
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Statistical Methods for Safety Analyses
Safety and tolerability will be assessed by clinical review of all relevant parameters including 
AEs, laboratory tests, and vital signs.
Descriptive summary statistics will be provided for safety endpoints. See Table 8 for the list 
of safety endpoints to be summarized.  For continuous measures such as changes from 
baseline in laboratory tests and vital signs, summary statistics for baseline, on-treatment, and 
change from baseline values will be provided in table format.  Additional safety endpoints 
may also be summarized, as deemed clinically appropriate.
Table 8
Analysis Strategy for Safety Parameters
Safety Endpoint†
Descriptive Statistics
Any AE
Any Grade 3-5 AE
X
X
Any Serious AE
Onset and Duration of First Grade 3-5 AE
X
X
Any Drug-Related AE
X
Any Serious and Drug-Related AE
Any Grade 3-5 and Drug-Related AE
X
X
Discontinuation due to AE
Death
X
X
Specific AEs, SOCs
X
Change from Baseline Results (Labs, Vital Signs)
X
Abbreviations: AE = adverse event; SOC = system organ class
†Adverse events refer to both Clinical and Laboratory AEs.
Note: X = results will be provided.
Summaries of Baseline Characteristics, Demographics, and Other Analyses
The number and percentage of participants screened, allocated, the primary reasons for 
screen failure, and the primary reasons for discontinuation will be displayed.  Demographic 
variables (such as age), baseline characteristics, and prior and concomitant therapies will be 
summarized either by descriptive statistics or categorical tables.
Interim Analyses
During the course of the study, preliminary analyses of biomarker, efficacy and safety 
endpoints may be performed as data become available. The primary purpose of these 
analyses is to provide an early assessment of the study objectives. There is no intention to 
change the conduct of the current study based on the results of these analyses.
The final analyses will be carried out after all participants have had a 90-day follow-up after 
the end of treatment (unless lost to follow-up). If, by that time, the death rate is <70%, for OS 
and OS-related analyses, the final analyses will occur after death has occurred in 
 
 
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approximately 70% of the participants (~42 deaths). If the estimated interval between the 
2 analyses is less than 3 months, then the first analysis may be delayed and both analyses will 
be conducted at the later of the two.
Multiplicity
As all analyses are exploratory in nature, no multiplicity adjustments will be applied.
Sample Size and Power Calculations
Sample Size and Power for Biomarker Analyses
This study will enroll approximately 60 participants. Based on response rates observed 
previously for melanoma patients, it is assumed that the response rate is ~30%.  
For the endpoints of the primary objectives, there is no pre-specified difference in the means 
of prior interest.  Hence, the principal summary of results around the study objectives will be 
via the posterior probability that the mean difference exceeds 0 in the direction of responders 
showing the higher mean. For the primary objectives, the posterior probability threshold to 
claim statistical significance is set as 70% (or a ~2-to-1 odds), which is a reasonable level of 
certainty addressing these objectives.  
Table 9 shows the power to detect a difference in mean baseline FCT between responders 
and non-responders, assuming a few different sample sizes and true differences.  It is 
assumed that baseline FCT in non-responders follows a Beta distribution with alpha and beta 
parameters equal to 0.022 and 1, respectively, which puts ~95% of baseline FCT values 
below 0.10.  True mean differences shown were obtained by selecting higher values of the 
alpha parameter in the responders’ distribution, relative to non-responders, while keeping the 
beta parameter fixed at 1.  Bayesian models were fit allowing for different parameter values 
of responders and non-responders. The results suggest that for a true mean difference at or 
above 0.10 and at least 10 responders, we expect to observe ≥90% power (with the assumed 
Beta distributions).
Table 9
Power for Baseline FCT
N Responder
N Non-
Responder
True Mean Difference: δ a
% Powerb
10
50
0.05
68
0.10
90
15
45
0.05
80
0.10
96
20
40
0.05
83
0.10
98
a.
Assuming that baseline FCT in non-responders follows a Beta distribution with alpha and beta parameters equal to 
0.022 and 1, respectively, which puts 95% of baseline FCT values below 0.10.  Mean differences shown were 
obtained by selecting higher values of the alpha parameter in the responders’ distribution, relative to non-responders, 
while keeping the beta parameter fixed at 1.
b. Power is defined as Prob (PP(δ > 0) >70%); computed over 500 trial simulations.
 
 
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Table 10 below provides the power for detecting a difference in mean FCT log fold-change 
from baseline and ASCTFR between responders and non-responders.  A common standard 
deviation for the responders and non-responder was assumed for simplicity, although the 
Bayesian models were fit allowing for unique standard deviations.  It is shown that with at 
least 10 responders, for effect sizes at or above 0.50, we expect to observe ≥80% power.
Table 10
Power for FCT Log Fold-Change From Baseline and ASCTFR
N Responder
N Non-
Responder
True Mean Difference: δ a
% Power b
10
50
0.25
55
0.50
81
15
45
0.25
61
0.50
88
20
40
0.25
64
0.50
90
a.
Assuming standard deviation of 1 for each of the responder and non-responder groups, as would result if first 
dividing each of the non-responder and responder groups by their respective true (albeit unknown) standard 
deviations, and so this δ is essentially the effect size for this exercise.
b. Power is defined as Prob (PP(δ > 0) >70%); computed over 500 trial simulations.
As an illustration of precision associated with secondary and exploratory biomarker related 
objectives that may involve a large set of features being compared between responders and 
non-responders, Table 11 presents the power for comparing features between these 2 groups 
testing for significance at a false discovery rate (FDR) of 0.20.
Table 11
Power for Other Biomarker Endpoints
N Responder
N Non-Responder
Effect Sizea
% Powerb
10
50
0.50
12.3
0.75
30.7
1.00
59.0
1.50
95.4
15
45
0.50
16.7
0.75
44.3
1.00
75.4
1.50
98.7
20
40
0.50
20.9
0.75
54.7
1.00
82.7
1.50
99.7
a.
Standardized difference in the biomarker means between responders and non-responders.
b. Testing for significance at an FDR of 0.20 and assuming 90% of hypotheses are null and 10% have the given effect 
size.
 
 
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Sample Size and Power for Efficacy Analyses
The estimation precision of efficacy analyses is illustrated with the expected precision for 
ORR.  Assuming a total of 60 participants included in the analysis with a 30% ORR, the 95% 
Clopper-Pearson CI for ORR will be (19%, 43%); assuming a total of 60 participants with a 
20% ORR, the 95% Clopper-Pearson CI for ORR will be (11%, 32%).
Sample Size and Power for Safety Analyses
For any specific AE, the probability of observing at least 1 AE in this study depends on the 
number of participants treated and the underlying percentage of participants with an AE in 
the study population.  Assuming a total of 60 participants included in the analysis, if the 
underlying incidence rate of a given type of AE is 1% or 3%, there is 45.3% or 83.9% chance 
of observing at least 1 AE among the 60 participants, respectively.  If no AE of a given type 
is observed among the 60 participants, this study will provide 95% confidence that the 
underlying percentage of participants with the AE is <4.9% in the study population treated 
with the study treatment.
Subgroup Analyses
No subgroup analyses are planned for this study.
Compliance (Medication Adherence)
Drug accountability data for trial treatment will be collected during the study. Compliance 
with trial treatment administration will be measured by participants: 1) receiving 
unscheduled study agent infusions/injections; 2) missing an infusion/injection. Numbers and 
percentages of participants and infusion/injection visits with any deviation in these measures 
will be reported for the APaT population.
Extent of Exposure
The Extent of Exposure to study treatment will be evaluated by summary statistics (e.g. N, 
mean, median, standard deviation etc.) for duration of treatment in cycles.
 
 
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10. Supporting Documentation and Operational Considerations
Appendix 1: Regulatory, Ethical and Study Oversight Considerations
Merck Code of Conduct for Clinical Trials
Merck*
Code of Conduct for Clinical Trials
I.
Introduction
A. Purpose
Merck, through its subsidiaries, conducts clinical trials worldwide to evaluate the safety and effectiveness of our 
products. As such, we are committed to designing, implementing, conducting, analyzing and reporting these trials in 
compliance with the highest ethical and scientific standards. Protection of participant safety is the overriding concern 
in the design of clinical trials. In all cases, Merck clinical trials will be conducted in compliance with local and/or 
national regulations and in accordance with the ethical principles that have their origin in the Declaration of Helsinki. 
B. Scope
Such standards shall be endorsed for all clinical interventional investigations sponsored by Merck irrespective of the 
party (parties) employed for their execution (eg, contract research organizations, collaborative research efforts). This 
Code is not intended to apply to trials which are observational in nature, or which are retrospective. Further, this Code 
does not apply to investigator-initiated trials which are not under the control of Merck.
II. Scientific Issues
A. Trial Conduct
1. Trial Design
Except for pilot or estimation trials, clinical trial protocols will be hypothesis-driven to assess safety, efficacy 
and/or pharmacokinetic or pharmacodynamic indices of Merck or comparator products. Alternatively, Merck may 
conduct outcomes research trials, trials to assess or validate various endpoint measures, or trials to determine 
participant preferences, etc. 
The design (ie, participant population, duration, statistical power) must be adequate to address the specific purpose 
of the trial. Research participants must meet protocol entry criteria to be enrolled in the trial. 
2. Site Selection
Merck selects investigative sites based on medical expertise, access to appropriate participants, adequacy of 
facilities and staff, previous performance in Merck trials, as well as budgetary considerations. Prior to trial 
initiation, sites are evaluated by Merck personnel to assess the ability to successfully conduct the trial.
3. Site Monitoring/Scientific Integrity
Trial sites are monitored to assess compliance with the trial protocol and general principles of Good Clinical 
Practice. Merck reviews clinical data for accuracy, completeness and consistency. Data are verified versus source 
documentation according to standard operating procedures. Per Merck policies and procedures, if fraud, 
misconduct or serious GCP-noncompliance are suspected, the issues are promptly investigated. When necessary, 
the clinical site will be closed, the responsible regulatory authorities and ethics review committees notified and 
data disclosed accordingly. 
B. Publication and Authorship
To the extent scientifically appropriate, Merck seeks to publish the results of trials it conducts. Some early phase or 
pilot trials are intended to be hypothesis-generating rather than hypothesis testing. In such cases, publication of results 
may not be appropriate since the trial may be underpowered and the analyses complicated by statistical issues of 
multiplicity.
Merck’s policy on authorship is consistent with the requirements outlined in the ICH-Good Clinical Practice 
guidelines. In summary, authorship should reflect significant contribution to the design and conduct of the trial, 
performance or interpretation of the analysis, and/or writing of the manuscript. All named authors must be able to 
defend the trial results and conclusions. Merck funding of a trial will be acknowledged in publications. 
 
 
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III. Participant Protection
A. IRB/IEC review
All clinical trials will be reviewed and approved by an independent IRB/IEC before being initiated at each site. 
Significant changes or revisions to the protocol will be approved by the IRB/IEC prior to implementation, except that 
changes required urgently to protect participant safety and well-being may be enacted in anticipation of IRB/IEC 
approval. For each site, the IRB/IEC and Merck will approve the participant informed consent form. 
B. Safety
The guiding principle in decision-making in clinical trials is that participant welfare is of primary importance. 
Potential participants will be informed of the risks and benefits of, as well as alternatives to, trial participation. At a 
minimum, trial designs will take into account the local standard of care. Participants are never denied access to 
appropriate medical care based on participation in a Merck clinical trial. 
All participation in Merck clinical trials is voluntary. Participants are enrolled only after providing informed consent 
for participation. Participants may withdraw from a Merck trial at any time, without any influence on their access to, 
or receipt of, medical care that may otherwise be available to them.
C. Confidentiality
Merck is committed to safeguarding participant confidentiality, to the greatest extent possible. Unless required by law, 
only the investigator, Sponsor (or representative) and/or regulatory authorities will have access to confidential medical 
records that might identify the research participant by name. 
D. Genomic Research
Genomic Research will only be conducted in accordance with informed consent and/or as specifically authorized by 
an Ethics Committee.
IV. Financial Considerations
A. Payments to Investigators
Clinical trials are time- and labor-intensive. It is Merck’s policy to compensate investigators (or the sponsoring 
institution) in a fair manner for the work performed in support of Merck trials. Merck does not pay incentives to 
enroll participants in its trials. However, when enrollment is particularly challenging, additional payments may be 
made to compensate for the time spent in extra recruiting efforts.
Merck does not pay for participant referrals. However, Merck may compensate referring physicians for time spent on 
chart review to identify potentially eligible participants.
B. Clinical Research Funding 
Informed consent forms will disclose that the trial is sponsored by Merck, and that the investigator or sponsoring 
institution is being paid or provided a grant for performing the trial. However, the local IRB/IEC may wish to alter 
the wording of the disclosure statement to be consistent with financial practices at that institution. As noted above, 
publications resulting from Merck trials will indicate Merck as a source of funding.
C. Funding for Travel and Other Requests
Funding of travel by investigators and support staff (eg, to scientific meetings, investigator meetings, etc.) will be 
consistent with local guidelines and practices including, in the U.S., those established by the American Medical 
Association (AMA). 
V. Investigator Commitment
Investigators will be expected to review Merck’s Code of Conduct as an appendix to the trial protocol, and in signing 
the protocol, agree to support these ethical and scientific standards.
* In this document, "Merck" refers to Merck Sharp & Dohme Corp. and Schering Corporation, each of which is a 
subsidiary of Merck & Co., Inc. Merck is known as MSD outside of the United States and Canada. As warranted by 
context, Merck also includes affiliates and subsidiaries of Merck & Co., Inc."
 
 
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Financial Disclosure
Financial Disclosure requirements are outlined in the US Food and Drug Administration 
Regulations, Financial Disclosure by Clinical Investigators (21 CFR Part 54). It is the 
Sponsor's responsibility to determine, based on these regulations, whether a request for 
Financial Disclosure information is required. It is the investigator's/subinvestigator's 
responsibility to comply with any such request. 
The investigator/subinvestigator(s) agree, if requested by the Sponsor in accordance with 21 
CFR Part 54, to provide his/her financial interests in and/or arrangements with the Sponsor to 
allow for the submission of complete and accurate certification and disclosure statements. 
The investigator/subinvestigator(s) further agree to provide this information on a 
Certification/Disclosure Form, commonly known as a financial disclosure form, provided by 
the Sponsor. The investigator/subinvestigator(s) also consent to the transmission of this 
information to the Sponsor in the United States for these purposes. This may involve the 
transmission of information to countries that do not have laws protecting personal data.
Data Protection
Participants will be assigned a unique identifier by the Sponsor. Any participant records or 
datasets that are transferred to the Sponsor will contain the identifier only; participant names 
or any information which would make the participant identifiable will not be transferred. 
The participant must be informed that his/her personal study-related data will be used by the 
Sponsor in accordance with local data protection law. The level of disclosure must also be 
explained to the participant. 
The participant must be informed that his/her medical records may be examined by Clinical 
Quality Assurance auditors or other authorized personnel appointed by the Sponsor, by 
appropriate IRB/IEC members, and by inspectors from regulatory authorities.
Confidentiality of Data
By signing this protocol, the investigator affirms to the Sponsor that information furnished to 
the investigator by the Sponsor will be maintained in confidence, and such information will 
be divulged to the IRB, IEC, or similar or expert committee; affiliated institution and 
employees, only under an appropriate understanding of confidentiality with such board or 
committee, affiliated institution and employees. Data generated by this study will be 
considered confidential by the investigator, except to the extent that it is included in a 
publication as provided in the Publications section of this protocol.
Confidentiality of Participant Records
By signing this protocol, the investigator agrees that the Sponsor (or Sponsor representative), 
IRB/IEC, or regulatory authority representatives may consult and/or copy study documents in 
order to verify worksheet/CRF data. By signing the consent form, the participant agrees to 
this process. If study documents will be photocopied during the process of verifying 
worksheet/CRF information, the participant will be identified by unique code only; full 
names/initials will be masked prior to transmission to the Sponsor.
 
 
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By signing this protocol, the investigator agrees to treat all participant data used and 
disclosed in connection with this study in accordance with all applicable privacy laws, rules 
and regulations.
Confidentiality of IRB/IEC Information
The Sponsor is required to record the name and address of each IRB/IEC that reviews and 
approves this study. The Sponsor is also required to document that each IRB/IEC meets 
regulatory and ICH GCP requirements by requesting and maintaining records of the names 
and qualifications of the IRB/IEC members and to make these records available for 
regulatory agency review upon request by those agencies.
Publication Policy
The results of this study may be published or presented at scientific meetings. The Sponsor 
will comply with the requirements for publication of study results. In accordance with 
standard editorial and ethical practice, the Sponsor will generally support publication of 
multicenter studies only in their entirety and not as individual site data. In this case, a 
coordinating investigator will be designated by mutual agreement.
If publication activity is not directed by the Sponsor, the investigator agrees to submit all 
manuscripts or abstracts to the Sponsor before submission. This allows the Sponsor to protect 
proprietary information and to provide comments. 
Authorship will be determined by mutual agreement and in line with International Committee 
of Medical Journal Editors authorship requirements.
Compliance with Study Registration and Results Posting Requirements
Under the terms of the Food and Drug Administration Amendments Act (FDAAA) of 2007 
and the European Medicines Agency (EMA) clinical trial Directive 2001/20/EC, the Sponsor 
of the study is solely responsible for determining whether the study and its results are subject
to the requirements for submission to http://www.clinicaltrials.gov, 
www.clinicaltrialsregister.eu or other local registries. MSD, as Sponsor of this study, will 
review this protocol and submit the information necessary to fulfill these requirements. MSD
entries are not limited to FDAAA or the EMA clinical trial directive mandated trials. 
Information posted will allow participants to identify potentially appropriate studies for their 
disease conditions and pursue participation by calling a central contact number for further 
information on appropriate study locations and site contact information. 
By signing this protocol, the investigator acknowledges that the statutory obligations under 
FDAAA, the EMA clinical trials directive or other locally mandated registries are that of the 
Sponsor and agrees not to submit any information about this study or its results to those 
registries.
Compliance with Law, Audit, and Debarment
By signing this protocol, the investigator agrees to conduct the study in an efficient and 
diligent manner and in conformance with this protocol; generally accepted standards of GCP
(eg, International Conference on Harmonization of Technical Requirements for Registration 
of Pharmaceuticals for Human Use Good Clinical Practice: Consolidated Guideline and other 
 
 
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generally accepted standards of GCP); and all applicable federal, state and local laws, rules 
and regulations relating to the conduct of the clinical study.
The Code of Conduct, a collection of goals and considerations that govern the ethical and 
scientific conduct of clinical investigations sponsored by MSD, is provided in this appendix 
under the Merck Code of Conduct for Clinical Trials.
The investigator agrees not to seek reimbursement from participants, their insurance 
providers or from government programs for procedures included as part of the study
reimbursed to the investigator by the Sponsor.
The investigator will promptly inform the Sponsor of any regulatory authority inspection 
conducted for this study.
The investigator agrees to provide the Sponsor with relevant information from inspection 
observations/findings to allow the Sponsor to assist in responding to any citations resulting 
from regulatory authority inspection, and will provide the Sponsor with a copy of the 
proposed response for consultation before submission to the regulatory authority. 
Persons debarred from conducting or working on clinical studies by any court or regulatory 
authority will not be allowed to conduct or work on this Sponsor’s studies. The investigator 
will immediately disclose in writing to the Sponsor if any person who is involved in 
conducting the study is debarred or if any proceeding for debarment is pending or, to the best 
of the investigator’s knowledge, threatened.
Data Quality Assurance
All participant data relating to the study will be recorded on printed or electronic CRF unless 
transmitted to the Sponsor or designee electronically (eg, laboratory data). The investigator 
or qualified designee is responsible for verifying that data entries are accurate and correct by 
physically or electronically signing the CRF. 
Detailed information regarding Data Management procedures for this protocol will be 
provided separately.
The investigator must maintain accurate documentation (source data) that supports the 
information entered in the CRF. 
The investigator must permit study-related monitoring, audits, IRB/IEC review, and 
regulatory agency inspections and provide direct access to source data documents. 
Study documentation will be promptly and fully disclosed to the Sponsor by the investigator 
upon request and also shall be made available at the study site upon request for inspection, 
copying, review and audit at reasonable times by representatives of the Sponsor or any 
regulatory authorities. The investigator agrees to promptly take any reasonable steps that are 
requested by the Sponsor or any regulatory authorities as a result of an audit or inspection to 
cure deficiencies in the study documentation and worksheets/CRFs.
The Sponsor or designee is responsible for the data management of this study including 
quality checking of the data. 
Study monitors will perform ongoing source data review and verification to confirm that data 
entered into the CRF by authorized site personnel are accurate, complete, and verifiable from 
 
 
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source documents; that the safety and rights of participants are being protected; and that the 
study is being conducted in accordance with the currently approved protocol and any other 
study agreements, ICH GCP, and all applicable regulatory requirements. 
Records and documents, including signed ICF, pertaining to the conduct of this study must 
be retained by the investigator for 15 years after study completion unless local regulations or 
institutional policies require a longer retention period. No records may be destroyed during 
the retention period without the written approval of the Sponsor. No records may be 
transferred to another location or party without written notification to the Sponsor. 
Source Documents
Source documents provide evidence for the existence of the participant and substantiate the 
integrity of the data collected. Source documents are filed at the investigator’s site.
Data reported on the CRF or entered in the eCRF that are transcribed from source documents 
must be consistent with the source documents or the discrepancies must be explained. The 
investigator may need to request previous medical records or transfer records, depending on 
the study. Also, current medical records must be available.
Study and Site Closure
The Sponsor or its designee may stop the study or study site participation in the study for 
medical, safety, regulatory, administrative, or other reasons consistent with applicable laws, 
regulations, and GCP. 
In the event the Sponsor prematurely terminates a particular study site, the Sponsor will 
promptly notify that study site’s IRB/IEC.
 
 
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Appendix 2: Collection and Management of Specimens for Future Biomedical 
Research
1. Definitions
a.
Biomarker:  A biological molecule found in blood, other body fluids, or tissues that is a 
sign of a normal or abnormal process or of a condition or disease. A biomarker may be 
used to see how well the body responds to a treatment for a disease or condition.1
b. Pharmacogenomics:  The investigation of variations of DNA and RNA characteristics as 
related to drug/vaccine response.2
c.
Pharmacogenetics:  A subset of pharmacogenomics, pharmacogenetics is the influence of 
variations in DNA sequence on drug/vaccine response.2
d. DNA:  Deoxyribonucleic acid.
e.
RNA:  Ribonucleic acid.
2. Scope of Future Biomedical Research
The specimens consented and/or collected in this study as outlined in Section 8.9 will be 
used in various experiments to understand:
o
The biology of how drugs/vaccines work
o
Biomarkers responsible for how a drug/vaccine enters and is removed by the body
o
Other pathways drugs/vaccines may interact with
o
The biology of disease
The specimen(s) may be used for future assay development and/or drug/vaccine 
development.
It is now well recognized that information obtained from studying and testing clinical 
specimens offers unique opportunities to enhance our understanding of how individuals 
respond to drugs/vaccines, enhance our understanding of human disease and ultimately 
improve public health through development of novel treatments targeted to populations 
with the greatest need. All specimens will be used by the Sponsor or those working for or 
with the Sponsor.
3. Summary of Procedures for Future Biomedical Research
a.
Participants for Enrollment
All participants enrolled in the clinical study will be considered for enrollment in the 
future biomedical research substudy.
b. Informed Consent
Informed consent for specimens (ie, DNA, RNA, protein, etc.) will be obtained 
during screening for protocol enrollment from all participants or legal guardians, at a 
study visit by the investigator or his or her designate. Informed consent for future 
biomedical research should be presented to the participants on the visit designated in 
the SoA. If delayed, present consent at next possible Participant Visit. Consent forms 
 
 
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signed by the participant will be kept at the clinical study site under secure storage for 
regulatory reasons. 
A template of each study site’s approved informed consent will be stored in the 
Sponsor’s clinical document repository.
c.
eCRF Documentation for Future Biomedical Research Specimens
Documentation of participant consent for future biomedical research will be captured 
in the eCRFs. Any specimens for which such an informed consent cannot be verified 
will be destroyed.
d. Future Biomedical Research Specimen(s)
Collection of specimens for future biomedical research will be performed as outlined 
in the SoA. In general, if additional blood specimens are being collected for future 
biomedical research, these will usually be obtained at a time when the participant is 
having blood drawn for other study purposes.
4. Confidential Participant Information for Future Biomedical Research 
In order to optimize the research that can be conducted with future biomedical research
specimens, it is critical to link participant' clinical information with future test results. In 
fact little or no research can be conducted without connecting the clinical study data to 
the specimen. The clinical data allow specific analyses to be conducted. Knowing 
participant characteristics like gender, age, medical history and treatment outcomes are 
critical to understanding clinical context of analytical results.
To maintain privacy of information collected from specimens obtained for future 
biomedical research, the Sponsor has developed secure policies and procedures. All 
specimens will be single-coded per ICH E15 guidelines as described below. 
At the clinical study site, unique codes will be placed on the future biomedical research
specimens. This code is a random number which does not contain any personally 
identifying information embedded within it. The link (or key) between participant 
identifiers and this unique code will be held at the study site. No personal identifiers will 
appear on the specimen tube. 
5. Biorepository Specimen Usage
Specimens obtained for the Sponsor will be used for analyses using good scientific 
practices. Analyses utilizing the future biomedical research specimens may be performed 
by the Sponsor, or an additional third party (eg, a university investigator) designated by 
the Sponsor. The investigator conducting the analysis will follow the Sponsor’s privacy 
and confidentiality requirements. Any contracted third party analyses will conform to the 
specific scope of analysis outlined in this substudy. Future biomedical research 
specimens remaining with the third party after specific analysis is performed will be 
reported to the Sponsor.
6. Withdrawal From Future Biomedical Research 
Participants may withdraw their consent for future biomedical research and ask that their 
biospecimens not be used for future biomedical research. Participants may withdraw 
consent at any time by contacting the principal investigator for the main study. If medical 
 
 
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records for the main study are still available, the investigator will contact the Sponsor 
using the designated mailbox (clinical.specimen.management@merck.com). 
Subsequently, the participant's specimens will be flagged in the biorepository and 
restricted to main study use only. If specimens were collected from study participants 
specifically for future biomedical research, these specimens will be removed from the 
biorepository and destroyed. Documentation will be sent to the investigator confirming 
withdrawal and/or destruction, if applicable. It is the responsibility of the investigator to 
inform the participant of completion of the withdrawal and/or destruction, if applicable. 
Any analyses in progress at the time of request for withdrawal/destruction or already 
performed prior to the request being received by the Sponsor will continue to be used as 
part of the overall research study data and results. No new analyses would be generated 
after the request is received.
In the event that the medical records for the main study are no longer available (eg, if the 
investigator is no longer required by regulatory authorities to retain the main study
records) or the specimens have been completely anonymized, there will no longer be a 
link between the participant’s personal information and their specimens. In this situation, 
the request for withdrawal of consent and/or destruction cannot be processed. 
7. Retention of Specimens 
Future biomedical research specimens will be stored in the biorepository for potential 
analysis for up to 20 years from the end of the main study. Specimens may be stored for 
longer if a regulatory or governmental authority has active questions that are being 
answered. In this special circumstance, specimens will be stored until these questions 
have been adequately addressed.
Specimens from the study site will be shipped to a central laboratory and then shipped to 
the Sponsor-designated biorepository. If a central laboratory is not utilized in a particular 
study, the study site will ship directly to the Sponsor-designated biorepository. The 
specimens will be stored under strict supervision in a limited access facility which 
operates to assure the integrity of the specimens. Specimens will be destroyed according 
to Sponsor policies and procedures and this destruction will be documented in the 
biorepository database.
8. Data Security
Databases containing specimen information and test results are accessible only to the 
authorized Sponsor representatives and the designated study administrator research 
personnel and/or collaborators. Database user authentication is highly secure, and is 
accomplished using network security policies and practices based on international 
standards to protect against unauthorized access.
9. Reporting of Future Biomedical Research Data to Participants
No information obtained from exploratory laboratory studies will be reported to the 
participant, family, or physicians. Principle reasons not to inform or return results to the 
participant include: Lack of relevance to participant health, limitations of predictive 
capability, and concerns regarding misinterpretation.
If important research findings are discovered, the Sponsor may publish results, present 
results in national meetings, and make results accessible on a public website in order to 
 
 
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rapidly report this information to doctors and participants. Participants will not be 
identified by name in any published reports about this study or in any other scientific 
publication or presentation.
10. Future Biomedical Research Study Population
Every effort will be made to recruit all participants diagnosed and treated on Sponsor 
clinical studies for future biomedical research.
11. Risks Versus Benefits of Future Biomedical Research 
For future biomedical research, risks to the participant have been minimized and are 
described in the future biomedical research informed consent.
The Sponsor has developed strict security, policies and procedures to address participant 
data privacy concerns. Data privacy risks are largely limited to rare situations involving 
possible breach of confidentiality. In this highly unlikely situation there is risk that the 
information, like all medical information, may be misused.
12. Questions
Any questions related to the future biomedical research should be e-mailed directly to 
clinical.specimen.management@merck.com.
13. References
1. National Cancer Institute [Internet]: Available from 
https://www.cancer.gov/publications/dictionaries/cancer-terms?cdrid=45618
2. International Conference on Harmonization [Internet]: E15: Definitions for Genomic 
Biomarkers, Pharmacogenomics, Pharmacogenetics, Genomic Data and Sample 
Coding Categories. Available from 
http://www.ich.org/products/guidelines/efficacy/efficacy-single/article/definitions-
for-genomic-biomarkers-pharmacogenomics-pharmacogenetics-genomic-data-and-
sample-cod.html
3. Industry Pharmacogenomics Working Group [Internet]: Understanding the Intent, 
Scope and Public Health Benefits of Exploratory Biomarker Research: A Guide for 
IRBs/IECs and Investigational Site Staff. Available at http://i-pwg.org/
4. Industry Pharmacogenomics Working Group [Internet]: Pharmacogenomics 
Informational Brochure for IRBs/IECs and Investigational Site Staff. Available at 
http://i-pwg.org/
 
 
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Appendix 3:  Contraceptive Guidance and Pregnancy Testing
Definitions 
Women of Childbearing Potential (WOCBP)
A woman is considered fertile following menarche and until becoming postmenopausal 
unless permanently sterile (see below) 
Women in the following categories are not considered WOCBP:
●
Premenarchal
●
Premenopausal female with 1 of the following:
○
Documented hysterectomy
○
Documented bilateral salpingectomy
○
Documented bilateral oophorectomy
Note:  Documentation can come from the site personnel’s review of the participant’s 
medical records, medical examination, or medical history interview.
●
Postmenopausal female
○
A postmenopausal state is defined as no menses for 12 months without an alternative 
medical cause. 
▪
A high follicle stimulating hormone (FSH) level in the postmenopausal range may 
be used to confirm a postmenopausal state in women not using hormonal 
contraception or hormone replacement therapy (HRT). However, in the absence 
of 12 months of amenorrhea, confirmation with two FSH measurements in the 
postmenopausal range is required. 
○
Females on HRT and whose menopausal status is in doubt will be required to use one 
of the nonhormonal highly effective contraception methods if they wish to continue 
their HRT during the study. Otherwise, they must discontinue HRT to allow 
confirmation of postmenopausal status before study enrollment.
 
 
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Contraception Requirements
Male Participants
Male participants with female partners of childbearing potential are eligible to participate if 
they agree to one of the following during the protocol defined time frame in section 5.1: 
●
Be abstinent from penile-vaginal intercourse as their usual and preferred lifestyle 
(abstinent on a long term and persistent basis) and agree to remain abstinent.
●
Use a male condom plus partner use of an additional contraceptive method when having 
penile-vaginal intercourse with a WOCBP who is not currently pregnant.
o
The following are not acceptable methods of contraception:
▪
Periodic abstinence (calendar, symptothermal, post-ovulation methods), 
withdrawal (coitus interruptus), spermicides only, and lactational amenorrhoea 
method (LAM).
▪
Male condom with cap, diaphragm or sponge with spermicide.
▪
Male and female condom cannot be used together.
○
Note: 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.
 
 
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Female Participants
Female participants of childbearing potential are eligible to participate if they agree to use a 
highly effective method of contraception consistently and correctly as described in Table 12
during the protocol-defined time frame in Section 5.1. 
Table 12
Highly Effective Contraception Methods
Highly Effective Contraceptive Methods That Are User Dependent a
Failure rate of <1% per year when used consistently and correctly.
●
Combined (estrogen- and progestogen- containing ) hormonal contraception b
○
Oral 
○
Intravaginal 
○
Transdermal 
○
Injectable
●
Progestogen-only hormonal contraception b
○
Oral 
○
Injectable 
Highly Effective Methods That Have Low User Dependency 
Failure rate of <1% per year when used consistently and correctly.
●
Progestogen-only contraceptive implant b 
●
Intrauterine hormone-releasing system (IUS)
●
Intrauterine device (IUD)
●
Bilateral tubal occlusion
●
Vasectomized partner 
A vasectomized partner is a highly effective contraception method provided that the 
partner is the sole male sexual partner of the WOCBP and the absence of sperm has been 
confirmed. If not, an additional highly effective method of contraception should be used. 
●
Sexual abstinence 
Sexual abstinence is considered a highly effective method only if defined as refraining 
from heterosexual intercourse during the entire period of risk associated with the study
treatment. The reliability of sexual abstinence needs to be evaluated in relation to the 
duration of the study and the preferred and usual lifestyle of the participant.
Notes: 
Use should be consistent with local regulations regarding the use of contraceptive methods for participants of 
clinical studies. 
a) Typical use failure rates are higher than perfect-use failure rates (ie, when used consistently and 
correctly). 
b) If locally required, in accordance with Clinical Trial Facilitation Group (CTFG) guidelines, acceptable 
hormonal contraceptives are limited to those which inhibit ovulation. 
 
 
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Pregnancy Testing
WOCBP should only be included after a negative highly sensitive urine or serum pregnancy 
test. 
Following initiation of treatment additional pregnancy testing will be performed whenever an 
expected menstrual cycle is missed or when pregnancy is otherwise suspected, at the time 
points specified in the Schedule of Activities, and as required locally.
 
 
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Appendix 4: Adverse Events: Definitions and Procedures for Recording, 
Evaluating, Follow-up, and Reporting
Definition of AE
AE definition
●
An AE is any untoward medical occurrence in a patient or clinical study participant, 
temporally associated with the use of study treatment, whether or not considered 
related to the study treatment.
●
NOTE: An AE can therefore be any unfavorable and unintended sign (including an 
abnormal laboratory finding), symptom, or disease (new or exacerbated) temporally 
associated with the use of a study treatment.
●
NOTE: for purposes of AE definition, study treatment (also referred to as Sponsor’s 
product) includes any pharmaceutical product, biological product, vaccine, device, 
diagnostic agent or protocol specified procedure whether investigational (including 
placebo or active comparator product) or marketed, manufactured by, licensed by, 
provided by or distributed by the Sponsor for human use in this study.
Events meeting the AE definition
●
Any abnormal laboratory test results (hematology, clinical chemistry, or urinalysis) or 
other safety assessments (eg, ECG, radiological scans, vital signs measurements), 
including those that worsen from baseline, or are considered clinically significant in 
the medical and scientific judgment of the investigator.
●
Exacerbation of a chronic or intermittent pre-existing condition including either an 
increase in frequency and/or intensity of the condition.
●
New conditions detected or diagnosed after study treatment administration even 
though it may have been present before the start of the study.
●
Signs, symptoms, or the clinical sequelae of a suspected drug-drug interaction.
●
Signs, symptoms, or the clinical sequelae of a suspected overdose of either study 
treatment or a concomitant medication. 
●
For all reports of overdose (whether accidental or intentional) with an associated AE, 
the AE term should reflect the clinical symptoms or abnormal test result. An overdose 
of study treatment without any associated clinical symptoms or abnormal laboratory 
results is reported using the terminology “accidental or intentional overdose without
adverse effect.”
●
Any new cancer (that is not a condition of the study). 
Note: Progression of the cancer under study is not a reportable event. Refer to 
Section 8.4.5 for additional details.
 
 
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Events NOT meeting the AE definition 
●
Medical or surgical procedure (eg, endoscopy, appendectomy): the condition that 
leads to the procedure is the AE.
●
Situations in which an untoward medical occurrence did not occur (social and/or 
convenience admission to a hospital).
●
Anticipated day-to-day fluctuations of pre-existing disease(s) or condition(s) present 
or detected at the start of the study that do not worsen.
●
Surgery planned prior to informed consent to treat a pre-existing condition that has 
not worsened.
●
Refer to Section 8.4.5 for protocol specific exceptions
Definition of SAE
If an event is not an AE per definition above, then it cannot be an SAE even if serious 
conditions are met 
An SAE is defined as any untoward medical occurrence that, at any dose:
a.
Results in death
b. Is life-threatening
●
The term 'life-threatening' in the definition of 'serious' refers to an event in which the 
participant 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 were more severe.
c.
Requires inpatient hospitalization or prolongation of existing hospitalization
●
Hospitalization is defined as an inpatient admission, regardless of length of stay, even 
if the hospitalization is a precautionary measure for continued observation. (Note: 
Hospitalization for an elective procedure to treat a pre-existing condition that has not 
worsened is not an SAE. A pre-existing condition is a clinical condition that is diagnosed 
prior to the use of an MSD product and is documented in the patient’s medical history.
d. Results in persistent or significant disability/incapacity
●
The term disability means a substantial disruption of a person’s ability to conduct 
normal life functions.
●
This definition is not intended to include experiences of relatively minor medical 
significance such as uncomplicated headache, nausea, vomiting, diarrhea, influenza, and 
accidental trauma (eg, sprained ankle) which may interfere with or prevent everyday life 
functions but do not constitute a substantial disruption.
 
 
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e.
Is a congenital anomaly/birth defect
●
in offspring of participant taking the product regardless of time to diagnosis
f.
Other important medical events:
●
Medical or scientific judgment should be exercised in deciding whether SAE 
reporting is appropriate in other situations such as important medical events that may not 
be immediately life-threatening or result in death or hospitalization but may jeopardize 
the participant or may require medical or surgical intervention to prevent one of the other 
outcomes listed in the above definition. These events should usually be considered 
serious.
Examples of such events include invasive or malignant cancers, intensive treatment 
in an emergency room or at home for allergic bronchospasm, blood dyscrasias or
convulsions that do not result in hospitalization, or development of drug dependency 
or drug abuse.
Additional Events Reported in the Same Manner as SAE
Additional events which require reporting in the same manner as SAE
●
In addition to the above criteria, AEs meeting either of the below criteria, although 
not serious per ICH definition, are reportable to the Sponsor in the same time frame as 
SAEs to meet certain local requirements. Therefore, these events are considered serious 
by the Sponsor for collection purposes.
●
Is a new cancer (that is not a condition of the study);
●
Is associated with an overdose.
Recording AE and SAE
AE and SAE recording
●
When an AE/SAE occurs, it is the responsibility of the investigator to review all 
documentation (eg, hospital progress notes, laboratory, and diagnostics reports) 
related to the event.
●
The investigator will record all relevant AE/SAE information on the AE
CRFs/worksheets at each examination.
●
It is not acceptable for the investigator to send photocopies of the participant’s 
medical records to the Sponsor in lieu of completion of the AE CRF page.
●
There may be instances when copies of medical records for certain cases are 
requested by the Sponsor. In this case, all participant identifiers, with the exception of 
the participant number, will be blinded on the copies of the medical records before 
submission to the Sponsor.
 
 
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●
The investigator will attempt to establish a diagnosis of the event based on signs, 
symptoms, and/or other clinical information. In such cases, the diagnosis (not the 
individual signs/symptoms) will be documented as the AE/SAE.
Assessment of intensity
●
An event is defined as ‘serious’ when it meets at least 1 of the predefined outcomes as 
described in the definition of an SAE, NOT when it is rated as severe.
●
The investigator will make an assessment of intensity for each AE and SAE (and 
other reportable safety event) according to the NCI Common Terminology Criteria 
for Adverse Events (CTCAE), version 4.0. Any AE which changes CTCAE grade 
over the course of a given episode will have each change of grade recorded on the AE
CRFs/worksheets.
●
Grade 1: Mild; asymptomatic or mild symptoms; clinical or diagnostic 
observations only; intervention not indicated.
●
Grade 2: Moderate; minimal, local or noninvasive intervention indicated; limiting 
age-appropriate instrumental activities of daily living (ADL).
●
Grade 3: Severe or medically significant but not immediately life-threatening; 
hospitalization or prolongation of hospitalization indicated; disabling; limiting 
self-care ADL.
●
Grade 4: Life threatening consequences; urgent intervention indicated.
●
Grade 5: Death related to AE.
Assessment of causality
●
Did the Sponsor's product cause the AE?
●
The determination of the likelihood that the Sponsor's product caused the AE will 
be provided by an investigator who is a qualified physician. The investigator’s 
signed/dated initials on the source document or worksheet that supports the 
causality noted on the AE form, ensures that a medically qualified assessment of 
causality was done. This initialed document must be retained for the required 
regulatory time frame. The criteria below are intended as reference guidelines to 
assist the investigator in assessing the likelihood of a relationship between the test 
product and the AE based upon the available information
●
The following components are to be used to assess the relationship between 
the Sponsor's product and the AE; the greater the correlation with the 
components and their respective elements (in number and/or intensity), the more 
likely the Sponsor's product caused the AE:
●
Exposure:  Is there evidence that the participant was actually exposed to the 
Sponsor's product such as:  reliable history, acceptable compliance assessment 
(pill count, diary, etc.), expected pharmacologic effect, or measurement of 
drug/metabolite in bodily specimen?
 
 
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●
Time Course:  Did the AE follow in a reasonable temporal sequence from 
administration of the Sponsor's product? Is the time of onset of the AE 
compatible with a drug-induced effect (applies to studies with investigational 
medicinal product)?
●
Likely Cause:  Is the AE not reasonably explained by another etiology such 
as underlying disease, other drug(s)/vaccine(s), or other host or environmental 
factors
●
Dechallenge: Was the Sponsor's product discontinued or 
dose/exposure/frequency reduced?
●
If yes, did the AE resolve or improve?
●
If yes, this is a positive dechallenge. 
●
If no, this is a negative dechallenge.
(Note:  This criterion is not applicable if:  (1) the AE resulted in death or 
permanent disability; (2) the AE resolved/improved despite continuation of 
the Sponsor's product; (3) the study is a single-dose drug study); or (4) 
Sponsor's product(s) is/are only used one time.)
●
Rechallenge:  Was the participant re-exposed to the Sponsor's product in this 
study?
●
If yes, did the AE recur or worsen?
●
If yes, this is a positive rechallenge. 
●
If no, this is a negative rechallenge.
(Note:  This criterion is not applicable if:  (1) the initial AE resulted in death 
or permanent disability, or (2) the study is a single-dose drug study); or (3) 
Sponsor's product(s) is/are used only one time.)
NOTE:  IF A RECHALLENGE IS PLANNED FOR AN AE WHICH WAS SERIOUS 
AND WHICH MAY HAVE BEEN CAUSED BY THE SPONSOR'S PRODUCT, OR IF 
RE-EXPOSURE TO THE SPONSOR'S PRODUCT POSES ADDITIONAL 
POTENTIAL SIGNIFICANT RISK TO THE PARTICIPANT THEN THE 
RECHALLENGE MUST BE APPROVED IN ADVANCE BY THE SPONSOR 
CLINICAL DIRECTOR AS PER DOSE MODIFICATION GUIDELINES IN THE 
PROTOCOL, AND IF REQUIRED, THE INIRB/IEC.
●
Consistency with Study treatment Profile:Is the clinical/pathological 
presentation of the AE consistent with previous knowledge regarding the 
Sponsor's product or drug class pharmacology or toxicology?
●
The assessment of relationship will be reported on the CRFs/worksheets by an 
investigator who is a qualified physician according to his/her best clinical judgment, 
including consideration of the above elements.
●
Use the following scale of criteria as guidance (not all criteria must be present to be 
indicative of a Sponsor's product relationship).
 
 
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●
Yes, there is a reasonable possibility of Sponsor's product relationship:
There is evidence of exposure to the Sponsor's product. The temporal sequence of 
the AE onset relative to the administration of the Sponsor's product is reasonable. 
The AE is more likely explained by the Sponsor's product than by another cause. 
●
No, there is not a reasonable possibility of Sponsor's product relationship:
Participant did not receive the Sponsor's product OR temporal sequence of the AE 
onset relative to administration of the Sponsor's product is not reasonable OR the 
AE is more likely explained by another cause than the Sponsor’s product. (Also 
entered for a participant with overdose without an associated AE.)
●
For each AE/SAE, the investigator must document in the medical notes that he/she 
has reviewed the AE/SAE and has provided an assessment of causality.
●
There may be situations in which an SAE has occurred and the investigator has 
minimal information to include in the initial report to the Sponsor. However, it is very 
important that the investigator always make an assessment of causality for every event 
before the initial transmission of the SAE data to the Sponsor.
●
The investigator may change his/her opinion of causality in light of follow-up 
information and send an SAE follow-up report with the updated causality assessment.
●
The causality assessment is one of the criteria used when determining regulatory 
reporting requirements
Follow-up of AE and SAE
●
The investigator is obligated to perform or arrange for the conduct of supplemental 
measurements and/or evaluations as medically indicated or as requested by Sponsor 
to elucidate the nature and/or causality of the AE or SAE as fully as possible. This 
may include additional laboratory tests or investigations, histopathological 
examinations, or consultation with other health care professionals.
●
New or updated information will be recorded in the CRF.
●
The investigator will submit any updated SAE data to the Sponsor within 24 hours of 
receipt of the information.
 
 
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Reporting of AEs, SAEs, and Other Reportable Safety Events to the Sponsor 
AE, SAE, and other reportable safety event reporting to Sponsor via electronic data 
collection tool
●
The primary mechanism for reporting to the Sponsor will be the electronic data 
collection (EDC) tool. 
●
Electronic reporting procedures can be found in the EDC data entry guidelines (or 
equivalent).
●
If the electronic system is unavailable for more than 24 hours, then the site will 
use the paper AE Reporting form. 
●
Reference Section 8.4.1 for reporting time requirements 
●
The site will enter the SAE data into the electronic system as soon as it becomes 
available.
●
After the study is completed at a given site, the EDC tool will be taken off-line to 
prevent the entry of new data or changes to existing data.
●
If a site receives a report of a new SAE from a study participant or receives updated 
data on a previously reported SAE after the EDC tool has been taken off-line, then the 
site can report this information on a paper SAE form or by telephone (see next 
section).
●
Contacts for SAE reporting can be found in the Investigator Trial File Binder (or 
equivalent).
SAE reporting to the Sponsor via paper CRF
●
If the EDC tool is not operational, facsimile transmission or secure e-mail of the SAE 
paper CRF is the preferred method to transmit this information to the Sponsor.
●
In rare circumstances and in the absence of facsimile equipment, notification by 
telephone is acceptable with a copy of the SAE data collection tool sent by overnight 
mail or courier service.
●
Initial notification via telephone does not replace the need for the investigator to 
complete and sign the SAE CRF pages within the designated reporting time frames.
●
Contacts and instructions for SAE reporting and paper reporting procedures can be 
found in the Investigator Trial File Binder (or equivalent).
 
 
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Appendix 5: Clinical Laboratory Tests 

The tests detailed in Table 13 will be performed by the local laboratory. 

Protocol-specific requirements for inclusion or exclusion of participants are detailed 
in Section 5 of the protocol.

Additional tests may be performed at any time during the study as determined 
necessary by the investigator or required by local regulations.
Table 13
Protocol-required Safety Laboratory Assessments
Laboratory 
Assessments
Parameters
Hematology
Platelet Count 
RBC Indices:
MCV
MCH
%Reticulocytes
WBC count with 
Differential:
Neutrophils
Lymphocytes
Monocytes
Eosinophils
Basophils
RBC Count
Hemoglobin
Hematocrit
Chemistry
Blood Urea 
Nitrogen 
(BUN)
Potassium
Aspartate 
aminotransferase
(AST)/ Serum 
glutamic-
oxaloacetic 
transaminase 
(SGOT)
Total bilirubin 
(and direct 
bilirubin, if total 
bilirubin is 
elevated above 
the upper limit 
of normal)
Albumin
Bicarbonate
Chloride
Phosphorous
Creatinine
Sodium
Alanine 
aminotransferase
(ALT)/ Serum 
glutamic-pyruvic 
transaminase 
(SGPT)
Total protein
Glucose 
[fasting]
Calcium
Alkaline 
phosphatase
Magnesium
Uric acid
Thyroid 
stimulating 
hormone (TSH)
Triiodothyronine 
(T3)
Free thyroxine 
(FT4)
Routine 
Urinalysis
Specific gravity
pH, glucose, protein, blood, ketones, bilirubin, urobilinogen, nitrite, 
leukocyte esterase by dipstick
Microscopic examination (if blood or protein is abnormal)
 
 
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Laboratory 
Assessments
Parameters
Other 
Screening 
Tests

Follicle-stimulating hormone and estradiol (as needed in women of 
nonchildbearing potential only)

Serum or urine β human chorionic gonadotropin (β hCG) pregnancy 
test (as needed for WOCBP)

Serology (HIV antibody, hepatitis B surface antigen [HBsAg], and 
hepatitis C virus antibody) if applicable

Prothrombin time (PT), International normalized ratio (INR), activated 
partial thromboplastin time (aPTT)

BRAF mutational analysis

Lactate dehydrogenase

Blood for future biomedical research and planned genetic analysis.
Central 
Laboratory 
Samples

All study-required laboratory assessments will be performed by the 
local laboratory, with the exception of:

Blood for PBMCs
Blood for all correlative studies
NOTES: 
GFR (measured or calculated) or creatinine clearance (CrCl) can be used in place of creatinine
T3 is preferred but, if not available, free T3 may be tested.
Investigators must document their review of each laboratory safety report.
 
 
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Appendix 6:  12.5 Description of the iRECIST Process for Assessment of Disease 
Progression
Assessment at Screening and Prior to RECIST 1.1 Progression
Until radiographic disease progression based on RECIST 1.1, there is no distinct iRECIST 
assessment.
Assessment and Decision at RECIST 1.1 Progression
For participants who show evidence of radiological PD by RECIST 1.1 as determined by the 
Investigator, the Investigator will decide whether to continue a participant on study treatment 
until repeat imaging is obtained (using iRECIST for participant management (see Table 5
and Figure 2). This decision by the Investigator should be based on the participant’s overall 
clinical condition.
Clinical stability is defined as the following: 

Absence of symptoms and signs indicating clinically significant progression of
disease

No decline in ECOG performance status 

No requirements for intensified management, including increased analgesia, 
radiation, or other palliative care
Any participant deemed clinically unstable should be discontinued from study treatment at 
site-assessed first radiologic evidence of PD, and is not required to have repeat tumor 
imaging for confirmation of PD by iRECIST.
If the Investigator decides to continue treatment, the participant may continue to receive 
study treatment and the tumor assessment should be repeated 4 to 8 weeks later to confirm 
PD by iRECIST, per Investigator assessment.
Tumor flare may manifest as any factor causing radiographic progression per RECIST 1.1, 
including:

Increase in the sum of diameters of target lesion(s) identified at baseline to ≥20% and 
≥5 mm from nadir
o
Note: the iRECIST publication uses the terminology “sum of measurements”, but 
“sum of diameters” will be used in this protocol, consistent with the original 
RECIST 1.1 terminology.

Unequivocal progression of non-target lesion(s) identified at baseline

Development of new lesion(s)
iRECIST defines new response categories, including iUPD (unconfirmed progressive 
disease) and iCPD (confirmed progressive disease). For purposes of iRECIST assessment, 
the first visit showing progression according to RECIST 1.1 will be assigned a visit (overall) 
response of iUPD, regardless of which factors caused the progression.
 
 
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At this visit, target and non-target lesions identified at baseline by RECIST 1.1 will be 
assessed as usual.
New lesions will be classified as measurable or non-measurable, using the same size 
thresholds and rules as for baseline lesion assessment in RECIST 1.1. From measurable new 
lesions, up to 5 lesions total (up to 2 per organ), may be selected as New Lesions – Target.  
The sum of diameters of these lesions will be calculated, and kept distinct from the sum of 
diameters for target lesions at baseline.  All other new lesions will be followed qualitatively 
as New Lesions – Non-target.
Assessment at the Confirmatory Imaging
On the confirmatory imaging, the participant will be classified as progression confirmed 
(with an overall response of iCPD), or as showing persistent unconfirmed progression (with 
an overall response of iUPD), or as showing disease stability or response (iSD/iPR/iCR).
Confirmation of Progression
Progression is considered confirmed, and the overall response will be iCPD, if ANY of the 
following occurs:

Any of the factors that were the basis for the initial iUPD show worsening
o
For target lesions, worsening is a further increase in the sum of diameters of 
≥5 mm, compared to any prior iUPD time point
o
For non-target lesions, worsening is any significant growth in lesions overall, 
compared to a prior iUPD time point; this does not have to meet the 
“unequivocal” standard of RECIST 1.1
o
For new lesions, worsening is any of these:

An increase in the new lesion sum of diameters by ≥5 mm from a prior iUPD 
time point 

Visible growth of new non-target lesions 

The appearance of additional new lesions

Any new factor appears that would have triggered PD by RECIST 1.1
Persistent iUPD
Progression is considered not confirmed, and the overall response remains iUPD, if:

None of the progression-confirming factors identified above occurs AND

The target lesion sum of diameters (initial target lesions) remains above the initial PD 
threshold (by RECIST 1.1)
Additional imaging for confirmation should be scheduled 4 to 8 weeks from the imaging on 
which iUPD is seen. This may correspond to the next visit in the original visit schedule.  The 
assessment of the subsequent confirmation imaging proceeds in an identical manner, with 
possible outcomes of iCPD, iUPD, and iSD/iPR/iCR.
 
 
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Resolution of iUPD
Progression is considered not confirmed, and the overall response becomes iSD/iPR/iCR, if:

None of the progression-confirming factors identified above occurs, AND

The target lesion sum of diameters (initial target lesions) is not above the initial PD 
threshold. 
The response is classified as iSD or iPR (depending on the sum of diameters of the target 
lesions), or iCR if all lesions resolve.
In this case, the initial iUPD is considered to be pseudo-progression, and the level of 
suspicion for progression is “reset”. This means that the next visit that shows radiographic 
progression, whenever it occurs, is again classified as iUPD by iRECIST, and the 
confirmation process is repeated before a response of iCPD can be assigned.
Management Following the Confirmatory Imaging
If repeat imaging does not confirm PD per iRECIST, as assessed by the Investigator, and the 
participant continues to be clinically stable, study treatment may continue and follow the 
regular imaging schedule. If PD is confirmed, participants will be discontinued from study 
treatment.
NOTE: If a participant has confirmed radiographic progression (iCPD) as defined above, but 
the participant is achieving a clinically meaningful benefit, an exception to continue study 
treatment may be considered following consultation with the Sponsor. In this case, if study 
treatment is continued, tumor imaging should continue to be performed following the 
intervals as outlined in Section 6.
Detection of Progression at Visits After Pseudo-progression Resolves
After resolution of pseudo-progression (ie, achievement of iSD/iPR/iCR), iUPD is indicated 
by any of the following events:

Target lesions
o
Sum of diameters reaches the PD threshold (≥20% and ≥5 mm increase from 
nadir) either for the first time, or after resolution of previous pseudo-progression. 
The nadir is always the smallest sum of diameters seen during the entire trial, 
either before or after an instance of pseudo-progression.

Non-target lesions
o
If non-target lesions have never shown unequivocal progression, their doing so for 
the first time results in iUPD.
o
If non-target lesions have shown previous unequivocal progression, and this 
progression has not resolved, iUPD results from any significant further growth of 
non-target lesions, taken as a whole.

New lesions
o
New lesions appear for the first time
 
 
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o
Additional new lesions appear
o
Previously identified new target lesions show an increase of ≥5 mm in the new 
lesion sum of diameters, from the nadir value of that sum
o
Previously identified non-target lesions show any significant growth
If any of the events above occur, the overall response for that visit is iUPD, and the iUPD 
evaluation process (see Assessment at the Confirmatory Imaging above) is repeated. 
Progression must be confirmed before iCPD can occur.
The decision process is identical to the iUPD confirmation process for the initial PD, with 
one exception:  if new lesions occurred at a prior instance of iUPD, and at the confirmatory 
imaging the burden of new lesions has increased from its smallest value (for new target 
lesions, the sum of diameters is ≥5 mm increased from its nadir), then iUPD cannot resolve 
to iSD or iPR. It will remain iUPD until either a decrease in the new lesion burden allows 
resolution to iSD or iPR, or until a confirmatory factor causes iCPD.
Additional details about iRECIST are provided in the iRECIST publication [Seymour, L., et 
al 2017].
 
 
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Appendix 7: Abbreviations
Abbreviation
Definition
AE
Adverse Event
APaT
All Participants as Treated
CD
Cluster of Differentiation
CI
Confidence Interval
CNS
Central Nervous System
CR
Complete Response
CRF
Case Report Form
CSR
Clinical Study Report
CT
Computed Tomography
CTCAE
Common Terminology Criteria for Adverse Events
CTLA-4
Cytotoxic T-lymphocyte-associated Antigen 4
CyTOF
Time of Flight Mass Cytometry
CytS
Cytotoxic Score
ECG
Electrocardiogram
ECI
Events of Clinical Interest
ECOG
Eastern Cooperative Oncology Group
EDC
Electronic Data Capture
ERC
Ethics Review Committee
FCT
fraction of cytotoxic tumor-infiltrating T-lymphocytes
GCP
Good Clinical Practice
HIV
Human Immunodeficiency Virus
HLA
Human Leukocyte Antigen
IB
Investigator’s Brochure
ICH
International Council for Harmonisation
IEC
Independent Ethics Committee
Ig
Immunoglobulin
IHC
Immunohistochemistry
irAE
Immune-related Adverse Event
IRB
Institutional Review Board
iRECIST
Modified Response Evaluation Criteria in Solid Tumors 1.1 for 
Immune-based Therapeutics
IV
Intravenous(ly)
KCO
Klarman Cell Observatory
KN
KEYNOTE
LC MS/MS
Liquid chromatography tandem mass spectrometry
mAb
Monoclonal Antibody
MRI
Magnetic Resonance Imaging
NCI
National Cancer Institute
NSCLC
Non-small Cell Lung Cancer
ORR
Overall Response Rate
OS
overall survival
PBMCs
Peripheral Blood Mononuclear Cells
 
 
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Abbreviation
Definition
PBPK
Physiologically-based Pharmacokinetic
PD
progressive disease
PD-1
Programmed Cell Death 1
PD-L1
Programmed Cell Death 1 Ligand 1
PD-L2
Programmed Cell Death 1 Ligand 2
PFS
Progression-free Survival
PK
Pharmacokinetics
PR
Partial Response
Q2W
Every 2 Weeks
Q3W
Every 3 Weeks
QC
Quality Control
RECIST
Response Evaluation Criteria In Solid Tumors
RNASeq
RNA Sequencing
SAE
Serious Adverse Event
SAP
Statistical Analysis Plan
scRNAseq
Single Cell RNA-sequencing
SD
Stable Disease
sSAP
Supplemental Statistical Analysis Plan
TCR
T-cell Receptor
Teff
Effector T-lymphocytes
Tregs
Regulatory T-cells
UMI
Unique Molecular Identifiers
WOCBP
Woman of Childbearing Potential
 
 
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