A Phase 2 Trial of Pembrolizumab in Metastatic Non-squamous NSCLC Examining Circulating Tumor DNA Levels as a Surrogate Biomarker of Response
Phase: PHASE2
Conditions: Metastatic Non-Squamous Non-Small Cell Lung Carcinoma
Sponsor: Joel Neal

A Phase II trial of pembrolizumab in metastatic NSCLC examining circulating tumor DNA levels as a s111Togate biomarker of response 
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A phase 2 trial of pembrolizumab in metastatic NSCLC examining 
circulating tumor DNA levels as a surrogate biomarker of response 
Coordinating Center 
Stanford Cancer hlstitute 
875 Blake Wilbur Dr 
Stanford, CA 94305 
Principal Investigator (Pl) 
Joel W Neal, MD, PhD 
Assistant Professor 
Dept of Medicine; Division of Oncology 
Stanford Cancer hlstitute 
875 Blake Wilbur Dr 
Stanford, CA 94305 
P: 650-725-3081; F: 650-498-5800 
jwneal@stanford.edu 
Co-Investigators 
Heather A Wakelee, MD 
Associate Professor 
Millie Das, MD 
Clinical Assistant Professor 
Dept of Medicine; Division of Oncology 
Stanford Cancer hlstitute 
875 Blake Wilbur Dr 
Stanford, CA 94305 
P: 650-736-7221; 
hwakelee@stanford.edu 
Kavitha Ramchandran, MD 
Clinical Assistant Professor 
Dept of Medicine; Division of Oncology 
Stanford Cancer Institute 
875 Blake Wilbur Dr 
Stanford, CA 94305 
P: 650-723-6750; F: 650-723-8596 
kavitha@stanford.edu 
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Dept of Medicine; Division of Oncology 
Stanford Cancer Institute 
875 Blake Wilbur Dr 
Stanford, CA 94305 
P: 650-498-6000· 
19 Feb1Ua1y 2021 
NCT02955758

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TABLE OF CONTENTS 
 
PROTOCOL SYNOPSIS ............................................................................................................. 5 
SCHEMA ..................................................................................................................................... 10 
LIST OF ABBREVIATIONS AND DEFINITION OF TERMS (EXAMPLE) .................... 11 
1. OBJECTIVES ...................................................................................................................... 12 
2. BACKGROUND .................................................................................................................. 13 
3. PARTICIPANT SELECTION AND ENROLLMENT PROCEDURES ....................... 30 
4. TREATMENT PLAN .......................................................................................................... 34 
5. INVESTIGATIONAL AGENT INFORMATION (PEMBROLIZUMAB) ................... 39 
6. DOSE MODIFICATIONS .................................................................................................. 41 
7. ADVERSE EVENTS AND REPORTING PROCEDURES ............................................ 45 
8. CORRELATIVE/SPECIAL STUDIES ............................................................................. 50 
9. STUDY CALENDAR (TABLE 4) ...................................................................................... 53 
10. MEASUREMENT.............................................................................................................. 56 
11. REGULATORY CONSIDERATIONS ........................................................................... 58 
12. STATISTICAL CONSIDERATIONS ............................................................................. 59 
13. REFERENCES ................................................................................................................... 61 
APPENDICES ............................................................................................................................. 65 
APPENDIX A:  ECOG PERFORMANCE STATUS ........................................................................ 65 
APPENDIX B:  RECIST VERSION 1.1 CRITERIA ...................................................................... 66  
 

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PROTOCOL SYNOPSIS 
TITLE 
A Phase 2 trial of pembrolizumab in metastatic NSCLC examining 
circulating tumor DNA levels as a surrogate biomarker of response 
STUDY PHASE 
2 
INDICATION 
Metastatic NSCLC  
INVESTIGATIONAL 
PRODUCT OR 
PROCEDURE 
Pembrolizumab 200 mg intravenous every 3 weeks for up to 
24 months of therapy  
PRIMARY 
OBJECTIVE(S) 
To correlate circulating tumor DNA (ctDNA) levels measured using 
Cancer Personalized Profiling by deep Sequencing (CAPP-Seq) 
with radiographic tumor assessments using RECIST v1.1 criteria in 
patients with metastatic NSCLC treated with pembrolizumab 
SECONDARY 
OBJECTIVE(S) 
• To determine the overall response rate (ORR) using 
RECIST v1.1 criteria in patients with metastatic NSCLC treated 
with pembrolizumab 
• To determine the progression-free survival (PFS) using 
RECIST v1.1 criteria in patients with metastatic NSCLC treated 
with pembrolizumab 
• To determine the safety and tolerability of pembrolizumab in 
patients with metastatic NSCLC 
EXPLORATORY 
OBJECTIVES 
 To correlate tumor immune leukocyte subpopulations identified 
using the CIBERSORT method alone and in conjunction with 
PD-L1 assessment on pre-treatment tumor samples with 
objective response using RECIST v1.1 criteria in patients with 
metastatic NSCLC treated with pembrolizumab 

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INCLUSION CRITERIA  
In order to be eligible for participation in this trial, the patient must 
meet ALL of the following criteria (ie, mark “yes” to all criteria): 
1. Has a pathologically proven recurrent or metastatic 
non-small cell lung cancer (non-squamous, squamous, 
mixed, and neuroendocrine histologies are allowed as of 
amendment 26 June 2018) 
2. (a) Previously received at least one line of prior systemic 
therapy for metastatic disease.  
i. 
If the patient has a known sensitizing EGFR mutation or 
ALK rearrangement, the patient must have received at least 
one prior targeted therapy for metastatic disease (ie, EGFR 
TKI therapy or ALK TKI therapy, respectively).   
ii. 
There is no limit on prior therapies allowed.  Patients must 
have completed previous treatment (including other 
investigational therapy) in greater than or equal to the 
following times prior to initiation of trial treatment: 
a. Anti-cancer monoclonal antibody (mAb) therapy must be 
completed ≥ 3 weeks prior to trial treatment  
b. Chemotherapy administered in a daily or weekly schedule 
must be completed ≥ 1 week prior to trial treatment 
c. Chemotherapy administered in an every 2-week schedule 
must be completed ≥ 2 weeks prior to trial treatment 
d. Chemotherapy administered in an every 3-week schedule 
must be completed ≥ 3 weeks prior to trial treatment 
e. Targeted small molecule therapy must be completed 
≥ 1 week prior to trial treatment 
OR 
(b) Have not received prior systemic therapy for their cancer in 
recurrent or metastatic setting, AND have a tumor with 
Tumor Proportion Score (TPS) ≥ 1% as measured by  
PD-L1 IHC, AND no evidence of a sensitizing 
EGFR mutation or ALK rearrangement if adenocarcinoma 
histology (molecular testing not required for other 
histologies). 
3. Prior radiation therapy allowed as long as completed in the 
following times prior to initiation of trial treatment: 
a. Definitive curative intent radiation ≥ 2 weeks prior to trial 
treatment 
b. Palliative body radiation ≥ 1 week prior to trial treatment 
c. Stereotactic brain radiation ≥ 1 week prior to trial treatment 
d. Whole brain radiation ≥ 2 weeks prior to trial treatment 
4. Patients with previously treated (with radiation or surgery) brain 
metastases are allowed.  Patients with untreated stable or 

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progressing metastases must have metastases ≤ 1.5 cm, be 
asymptomatic, and either not be on steroids or be on 10 mg 
prednisone equivalent or less.  
5. Has measurable disease based on RECIST v1.1 criteria.  
6. Is medically able and willing to undergo needle biopsy of a 
tumor lesion,  
-OR- 
Has known tumor PD-L1 expression and believed to have 
sufficient archival tumor available for genomic analysis (block 
or 10 unstained slides or Stanford STAMP NGS testing 
previously resulted or in process) 
7. Has life expectancy ≥ 3 months 
8. Ability to understand and the willingness to sign a written 
informed consent document.  
9. ≥ 18 years of age on day of signing informed consent 
10. ECOG performance status of 0, 1, or 2 (Appendix A) 
11. Adequate organ function: 
a. Absolute neutrophil count (ANC) ≥ 1,000/mcL 
b. Platelets ≥ 75,000/mcL 
c. Hemoglobin ≥ 8 g/dL 
d. Serum creatinine ≤ 1.5 X upper limit of normal (ULN) OR 
Measured or calculated creatinine clearance ≥ 30 mL/min 
for patient with creatinine levels > 1.5 X institutional ULN 
e. Serum total bilirubin ≤ 1.5 X ULN OR Direct bilirubin 
≤ ULN for patients with total bilirubin levels > 1.5 ULN 
f. AST (SGOT) and ALT (SGPT) ≤ 3 X ULN OR ≤ 5 X ULN 
for patients with liver metastases 
12. Female patients of childbearing potential must have a negative 
urine or serum pregnancy test prior to the first dose of trial 
treatment.  They must also agree to acceptable contraceptive 
methods (ie, combined estrogen progesterone hormonal 
contraception, progesterone only hormonal contraception, 
intrauterine device, have history of bilateral tubal ligation, or 
two barrier method) or agree to abstain from heterosexual 
activity, for the course of the study through 120 days after the 
last dose of trial treatment.   
-- Female patients are not considered to be of childbearing 
potential if (i) they have been surgically sterilized (such as 
hysterectomy plus bilateral salpingo-oophorectomy) or (ii) are 
free from menses for > 1 year (postmenopausal).  Female 
patients who have not had> 1 year of amenorrhea may have 
confirmation of postmenopausal state with two FSH 
measurements in postmenopausal range and should not be on 
hormonal contraception or hormonal replacement therapy 

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during testing. 
EXCLUSION CRITERIA 
In order to be eligible for participation in this trial, the patient must 
NOT meet the following criteria (ie, mark “no” to all criteria): 
1. Is currently receiving another investigational therapy 
2. Has received prior anti-PD-1 or anti-PD-L1 therapy 
3. Has clinically significant toxicities from previous anti-cancer 
therapy that have not resolved, or have not stabilized at a new 
baseline  
4. Has undergone a surgical procedure involving general 
anesthesia within 2 weeks of starting trial treatment, or has 
inadequate healing or recovery from complications of surgery 
prior to starting trial treatment.  This does not apply to low-risk 
procedures such as thoracentesis, paracentesis, chest 
tube/PleurX catheter placement, line placement, needle biopsy 
of tumor, and bronchoscopy.  
5. Is receiving high dose systemic steroid therapy or other 
immunosuppressive therapy within 3 days of trial treatment.  
Topical and intraarticular steroid injections are allowed, as are 
physiologic doses of systemic steroids (≤ 10 mg of prednisone 
equivalent daily).  
6. Has carcinomatous meningitis as determined by positive CSF 
cytology 
7. Has known additional malignancy that is undergoing active 
treatment.  
8. Has active autoimmune disease that has required systemic 
treatment in the past 2 years (ie, with use of disease modifying 
agents, supra-physiologic doses of systemic corticosteroids or 
immunosuppressive drugs).  Replacement therapy (eg, 
thyroxine, insulin, or physiologic corticosteroid replacement 
therapy for adrenal or pituitary insufficiency, etc.) is not 
considered a form of systemic treatment.  Asthma, 
type I diabetes mellitus, hypothyroidism, and vitiligo are 
allowed.  
9. Has a history or current evidence of any condition, therapy, or 
laboratory abnormality that might confound the results of the 
trial, interfere with the patient’s participation for the full 
duration of the trial, or is not in the best interest of the patient to 
participate, in the opinion of the treating investigator.  This 
includes known active tuberculosis; Grade 3 active infection; 
history of allogeneic bone marrow transplant or solid organ 
transplant; known history of Human Immunodeficiency Virus 
(HIV); known active Hepatitis B (eg, Hep B DNA positive in 
prior 3 months) or known active Hepatitis C (eg, HCV RNA 
[qualitative] is detected in prior 3 months).  
10. Known evidence of active, non-infectious, ≥ Grade 2 

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pneumonitis (ie, medical intervention indicated) in the last 
6 months 
11. Is pregnant or breastfeeding, or expecting to conceive children 
within the projected duration of the trial, starting with the 
screening visit through 120 days after the last dose of trial 
treatment 
TREATMENT 
SUMMARY 
All patients will receive pembrolizumab, 200 mg fixed-dose, 
30-minute intravenous infusion, every 3 weeks.  Trial treatment will 
be continued for up to 24 months of therapy, or until disease 
progression without clinical benefit, unacceptable toxicity, 
treatment consent withdrawal, or initiation of other cancer therapy.  
Dose-delays are permitted per protocol. 
SAMPLE SIZE  
25 patients with metastatic NSCLC 
STATISTICAL 
CONSIDERATIONS 
Statistical Plan 
The primary explanatory variables are percent ctDNA and ctDNA 
titer (a continuous variable in units pg/mL).  The correlation of 
percent ctDNA (and DNA titer) with sum of longest diameter of 
tumor target lesions (continuous variable in mm or cm, 
RECIST v1.1).  Correlations of two continuous variables will be 
made using Kendall correlation.  
Sample size justification:  
Clinically validated differences in ctDNA have not been established 
to date, but the variability over time does appear to closely follow 
tumor volume as demonstrated by previously published data1.  This 
may vary across tumor types.  25 patients would provide 80% 
power to detect a correlation of 0.64 with ctDNA and radiographic 
RECIST v1.1-based tumor assessments when using a Kendall 
correlation. 
 

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SCHEMA 
This is a prospective, open-label, non-randomized single-arm study that will enroll 
approximately 25 patients with metastatic NSCLC.  
 
 
 
 
 
 
 
BASELINE 
 
25 metastatic NSCLC 
patients without prior 
immunotherapy 
 
Tissue biopsy (optional) or 
archival tissue for 
CIBERSORT, DNA 
sequencing 
 
Plasma for baseline 
circulating tumor DNA 
(ctDNA) 
TREATMENT 
Pembrolizumab 200 mg iv 
every 3 weeks for up to 
24 months  (~35 cycles) 
Stage 1 cycle 1 
through 8 (approx. 
week 1 through 25): 
 ctDNA:  pre/post first 
dose, pre-cycle 2 
(~week 4) pre-cycle 3 
(~week 7), and then 
every 6 weeks 
Imaging every 6 weeks 
 
Stage 2 cycle 9 
through 17 (approx. 
week 25 through 52) 
 ctDNA and imaging 
every 9 weeks 
Stage 3 cycle 18 
through 35 (approx. 
week 52 through 105)  
 ctDNA and imaging 
every 12 weeks 
OUTCOMES 
Primary:  
-Correlate ctDNA levels 
(CAPP-Seq) with 
radiographic tumor 
assessments using 
RECIST v1.1 criteria 
Secondary:  
- Objective response rate 
- Progression-free 
survival 
-Safety/tolerability 
Exploratory: 
- CIBERSORT 

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LIST OF ABBREVIATIONS AND DEFINITION OF TERMS 
 
AE 
Adverse event 
BID 
Twice daily 
BSA 
Body surface area 
CBC 
Complete blood count 
CI 
Confidence interval 
CNS 
Central nervous system 
CRF 
Case report/Record form 
CR 
Complete response 
CTCAE 
Common Terminology Criteria for Adverse Events 
DSMB 
Data Safety Monitoring Board 
ECG 
Electrocardiogram 
HIV 
Human Immunodeficiency Virus 
HTN 
Hypertensions 
IRB 
Institutional Review Board 
IV 
Intravenous 
LLN 
Lower limit of normal  
OS 
Overall survival  
PD 
Progressive disease 
PFS 
Progression-free survival  
PR 
Partial response 
RECIST 
Response evaluation criteria in solid tumors 
RR 
Response rate 
SAE 
Serious adverse event 
SD 
Stable disease 
ULN 
Upper limit of normal 
WBC 
White blood cell 
 
 
  

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1. 
OBJECTIVES 
1.1 
Primary Objective  
To correlate circulating tumor DNA (ctDNA) levels measured using Cancer Personalized 
Profiling by deep Sequencing (CAPP-Seq) with radiographic tumor assessments using 
RECIST v1.1 criteria in patients with metastatic NSCLC treated with pembrolizumab  
• Hypothesis:  Circulating tumor DNA quantitative levels will serve as a surrogate 
biomarker of radiographic tumor measurements made using RECIST v1.1 criteria.  
1.2 
Secondary Objectives 
 
 To determine the overall response rate (ORR) using RECIST v1.1 criteria in patients with 
metastatic NSCLC treated with pembrolizumab 
 To determine the progression-free survival (PFS) using RECIST v1.1 in patients with 
metastatic NSCLC treated with pembrolizumab 
 To determine the safety and tolerability of pembrolizumab in patients with metastatic 
NSCLC 
1.3 Exploratory Objectives 
 To correlate tumor immune leukocyte subpopulations identified using the CIBERSORT 
method alone and in conjunction with PD-L1 assessment on pre-treatment tumor samples 
with overall response rate using RECIST v1.1 criteria in patients with metastatic NSCLC 
treated with pembrolizumab 

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2. 
BACKGROUND 
2.1 
Study Disease 
Background Lung Cancer and Immunotherapeutic Approaches 
In the United States, lung cancer is the number one cause of cancer-related deaths, with an 
estimated 221,200 new cases of lung cancer and 158,040 lung cancer-related deaths in 2015.2  
Non-small cell lung cancer (NSCLC) comprises 85% of new cases of lung cancer, and includes 
adenocarcinoma, squamous cell carcinoma, and large cell carcinoma.  In the first line setting, 
platinum-based chemotherapy improves overall survival when compared to best supportive 
care.3-7  Second line chemotherapeutics have more limited survival times, including single agent 
pemetrexed,8 docetaxel,8-11 and erlotinib.12  There has been significant progress in lung cancer 
care in the last two decades, with personalized treatment based on histology and genetic driver 
mutations such as EGFR and ALK.13-16  Chemotherapies and targeted therapies in the form of 
monoclonal antibodies and small molecule inhibitors have become the standard therapeutic 
classes used for the treatment of lung cancer.  
Historically, lung cancer was considered to be a non-immunogenic tumor, with a lack of clinical 
activity seen with previously attempted immunotherapeutic approaches such as vaccines and 
biologics (ie, interferon, tumor necrosis-factor-alpha).  However, as of March 4 2015, 
immunotherapy has become a new standard therapeutic approach for the treatment of lung 
cancer.  Nivolumab, a monoclonal antibody to immune checkpoint program death receptor-1 
(PD-1), marked the first FDA approval of immunotherapy for lung cancer.  The PD-L1/PD-1 
pathway is hijacked by the tumor and the interaction between the PD-L1 ligand on the tumor and 
PD-1 on the immune cell, inactivates the immune cell, resulting in tumor immune evasion, 
growth, and metastases.  Nivolumab outperformed docetaxel in a randomized phase 3 study in 
squamous cell NSCLC after first-line platinum-based chemotherapy (CHECKMATE-017), with 
an improvement in median overall survival of 9.2 months (95% CI, 7.3 to 13.3) vs 6.0 months 
(95% CI, 5.1 to 7.3), respectively (HR 0.59, 95% CI 0.44 to 0.79, P < 0.001).17  The randomized 
phase 3 study of nivolumab vs docetaxel in NSCLC of the lung after the first-line setting was 
also a positive trial, with a median improvement in overall survival of 12.2 vs 9.4 months, 
respectively (HR 0.73, 95% CI 0.59 to 0.89, P = 0.0015).18  Pembrolizumab was the 
2nd FDA-approved PD-1 inhibitor.  The clinical activity of pembrolizumab, the PD-1 inhibitor 
selected for examination in this trial, is described in Section 2.2.  There are several PD-1/PD-L1 
inhibitors in development for the treatment of NSCLC, all of which have demonstrated clinical 
activity. In this time durvalumab (PD-L1) has been approved as a consolidation therapy after 
concurrent chemotherapy and radiation for stage III NSCLC19 and atezolizumab (PD-L1) has 
been approved in the second line setting also outperforming docetaxel in survival.20  Despite 
responses seen in 15 to 20% of NSCLC patients with all PD-1/PD-L1 inhibitors, a robust 
predictive biomarker for response is not available.  

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Pembrolizumab 
2.2.1 Pembrolizumab Pharmaceutical and Therapeutic Background 
The importance of intact immune surveillance in controlling outgrowth of neoplastic 
transformation has been known for decades.  Accumulating evidence shows a correlation 
between tumor-infiltrating lymphocytes (TILs) in cancer tissue and favorable prognosis in 
various malignancies.  In particular, the presence of CD8+ T-cells and the ratio of CD8+ effector 
T-cells / FoxP3+ regulatory T-cells seems to correlate with improved prognosis and long-term 
survival in many solid tumors.  
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 CTLA-4 which has been shown to negatively regulate antigen receptor signaling 
upon engagement of its ligands (PD-L1 and/or PD-L2).  The structure of murine PD-1 has been 
resolved.  PD-1 and family members are type I transmembrane glycoproteins containing an Ig 
Variable-type (V-type) domain responsible for ligand binding and a cytoplasmic tail which is 
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 (ITIM) 
and an immunoreceptor tyrosine-based switch motif (ITSM).  Following T-cell stimulation, 
PD-1 recruits the tyrosine phosphatases SHP-1 and SHP-2 to the ITSM motif within its 
cytoplasmic tail, leading to the dephosphorylation of effector molecules such as CD3ζ, PKCθ 
and ZAP70 which are involved in the CD3 T-cell signaling cascade.  The mechanism by which 
PD-1 down modulates T-cell responses is similar to, but distinct from that of CTLA-4 as both 
molecules regulate an overlapping set of signaling proteins.  PD-1 was shown to be expressed on 
activated lymphocytes including peripheral CD4+ and CD8+ T-cells, B-cells, T regs and Natural 
Killer cells.  Expression has also been shown during thymic development on CD4-CD8- (double 
negative) T-cells as well as subsets of macrophages and dendritic cells.  The ligands for PD-1 
(PD-L1 and PD-L2) are constitutively expressed or can be induced in a variety of cell types, 
including non-hematopoietic tissues as well as in various tumors.  Both ligands are type I 
transmembrane receptors containing both IgV- and IgC-like domains in the extracellular region 
and contain short cytoplasmic regions with no known signaling motifs.  Binding of either PD-1 
ligand to PD-1 inhibits T-cell activation triggered through the T-cell receptor.  PD-L1 is 
expressed at low levels on various non-hematopoietic tissues, most notably on vascular 
endothelium, whereas PD-L2 protein is only detectably expressed on antigen-presenting cells 
found in lymphoid tissue or chronic inflammatory environments.  PD-L2 is thought to control 
immune T-cell activation in lymphoid organs, whereas PD-L1 serves to dampen unwarranted 
T-cell function in peripheral tissues.  Although healthy organs express little (if any) PD-L1, a 
variety of cancers were demonstrated to express abundant levels of this T-cell inhibitor.  This 
suggests that the PD-1/PD-L1 pathway plays a critical role in tumor immune evasion and should 
be considered as an attractive target for therapeutic intervention.  
2.2.2 Pembrolizumab Preclinical and Clinical Trial Data 
2.2.2.1 Mechanism of Action 
The programmed cell death 1 (PD-1) pathway represents a major immune control switch, which 
may be engaged by tumor cells to overcome active T-cell immune surveillance.  

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Pembrolizumab (KEYTRUDA, MK-3475; previously known as SCH 900475 and 
ORG 307488-0) is a potent and highly selective humanized monoclonal antibody (mAb) of the 
immunoglobulin G4 (IgG4)/kappa isotype designed to directly block the interaction between 
PD-1 and its ligands, programmed cell death ligand 1 (PD-L1) and programmed cell death 
ligand 2 (PD-L2).  This blockade enhances functional activity of the target lymphocytes to 
facilitate tumor regression and ultimately immune rejection.  Pembrolizumab has an acceptable 
preclinical safety profile and is in clinical development as an intravenous (IV) immunotherapy 
for advanced malignancies.  Keytruda (pembrolizumab) is indicated for the treatment of patients 
across a number of indications because of its mechanism of action to bind the PD-1 receptor on 
the T cell.  Keytruda (pembrolizumab) has been approved for lung cancer in the following 
indications: (i) single agent for first line treatment of patients with metastatic NSCLC whose 
tumors have high PD-L1 expression [tumor proportion score ≥ 50%] as determined by an 
FDA-approved test with no EGFR or ALK genomic tumor aberrations; (ii) single agent for 
treatment of patients with metastatic NSCLC whose tumors express PD-L1 [(tumor proportion 
score ≥ 1%] as determined by an FDA-approved test, with disease progression on or after 
platinum-containing chemotherapy (patients with EGFR or ALK genomic tumor aberrations 
should have disease progression on FDA-approved therapy for these aberrations prior to 
receiving pembrolizumab) (iii)  in combination with pemetrexed and carboplatin, as first-line 
treatment of patients with metastatic NSCLC (accelerated approval based on response rate and 
progression-free survival). For more details on specific indications refer to the most up to date 
Investigator Brochure.  
2.2.2.2 Animal Studies- Please refer to most up to date Investigator Brochure.  
2.2.2.2.1 Nonclinical Pharmacology- Please refer to most up to date Investigator Brochure. 
Pembrolizumab binds to human and Cynomolgus monkey PD-1 with comparable affinity and 
blocks the binding of human and Cynomolgus monkey PD-1 to PD-L1 and PD-L2 with 
comparable potency.  Pembrolizumab does not cross-react with dog, rat, or mouse PD-1.  
Pembrolizumab does not bind immunoglobulin superfamily members cluster of 
differentiation 28 (CD28), cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), or inducible 
T-cell costimulator (ICOS).  
Pembrolizumab strongly enhances T-lymphocyte immune responses in cultured blood cells from 
healthy human donors, cancer subjects, and nonhuman primates.  In T-cell activation assays 
using human donor blood cells, the half-maximal effective concentration (EC50) has been 
approximately 0.1 to 0.3 nM.  In addition to interleukin-2 (IL-2), tumor necrosis factor 
alpha (TNFα), interferon gamma (IFNγ), and levels of other cytokines were found to be 
modulated by pembrolizumab.  The antibody potentiates existing immune responses only in the 
presence of antigen and does not nonspecifically activate T-cells.  In the in vitro peripheral blood 
mononuclear cell (PBMC) and whole blood cytokine release assays, the cytokine levels induced 
by pembrolizumab were low and comparable to those induced by trastuzumab.  Pembrolizumab 
does not induce antibody-dependent cell-mediated cytotoxicity (ADCC) or 
complement-dependent cytotoxicity (CDC).  
Using anti–murine PD-1 surrogate antibodies, PD-1 blockade has been shown to significantly 
inhibit tumor growth in a variety of syngeneic murine tumor models.  In these experiments in 
mice, anti–PD-1 therapy is synergistic with chemotherapeutic agents such as gemcitabine and 
5-fluorouracil (5-FU), and combination therapy results in increased complete tumor regression 

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rates in vivo.  Studies also revealed that immunosuppressive doses of dexamethasone included in 
combination with agents used in standard-of-care treatment for NSCLC do not reduce the 
anti-tumor efficacy of an anti–murine PD-1 surrogate antibody.  
2.2.2.2.2 Nonclinical Pharmacokinetics- Please refer to most up to date Investigator Brochure. 
The pharmacokinetics (PK) of pembrolizumab were evaluated in a non–Good Laboratory 
Practices (GLP) single-dose PK study and two GLP repeat-dose toxicokinetic (TK) studies 
(1 month and 6 month) in Cynomolgus monkeys.  Pembrolizumab stability as a modified IgG4 
molecule was evaluated in vivo in mice. 
After single-dose IV administration at 0.3;  3;  or 30 mg/kg in Cynomolgus monkeys, decline of 
serum concentration followed multiphasic kinetics.  Anti–drug antibodies (ADAs) were detected 
in most of the treated animals.  Clearance (CL) and terminal half-life (t1/2) appeared to be 
dose-dependent in the dose range tested with t1/2 varying from 4 to 10 days.  In the 1-month 
repeat-dose (once weekly) GLP toxicity study at 6, 40, or 200 mg/kg in Cynomolgus monkeys, 
ADAs were detected in most of the low-dose (6 mg/kg) treated animals.  The systemic exposure 
over the 7-day dosing interval (AUC0-7 days) was sex-independent and increased with 
increasing dose.  The mean t1/2 values in individual ADA-negative animals ranged from 
15.7 to 22.3 days across doses. 
In the 6-month repeat-dose (every other week) GLP toxicity study at 6, 40, or 200 mg/kg in 
Cynomolgus monkeys, ADAs were detected in most of the low-dose (6 mg/kg) treated animals.  
The systemic exposure to pembrolizumab was independent of sex and was approximately 
dose-proportional across all doses.  The mean t1/2 values in individual ADA-negative animals 
ranged from 21 to 22 days across doses.  
IgG4 wild-type  molecule can undergo in vivo molecular rearrangement called Fab-arm (or half 
molecule) exchange by swapping their half molecule with other IgG4 half molecules, thereby 
generating bispecific or hybrid antibodies.  Pembrolizumab is a hinge mutated IgG4 (S228P), 
which prevents in vivo half-molecule swap (formation of hybrid).  An in vivo mice experiment 
has demonstrated that pembrolizumab did not form hybrid antibody with another wild-type IgG4 
molecule.  
2.2.2.2.3 Safety Pharmacology/Toxicology Please refer to most up to date Investigator Brochure. 
The safety of pembrolizumab was characterized in the 1-month repeat-dose toxicity study in 
Cynomolgus monkeys when administered as IV doses of 6, 40, or 200 mg/kg once-a-week (total 
of 5 doses) and in the 6-month repeat-dose toxicity study in Cynomolgus monkeys when 
administered as IV doses of 6, 40 or 200 mg/kg every other week (total of 12 doses).  
Pembrolizumab was well tolerated in Cynomolgus monkeys with a systemic exposure 
(AUC0-7 days) of up to approximately 170,000 μg day/mL over the course of the 1-month study, 
and with a systemic exposure (AUC0-14days) of up to approximately 67,500 μg day/mL over the 
course of the 6-month study. 
No findings of toxicological significance were observed in either the 1-month or 6-month 
toxicity studies with pembrolizumab and the no observed adverse effect level (NOAEL) was 
≥ 200 mg/kg (the highest dose evaluated).  In addition, no findings of toxicological relevance 
were observed in the in vitro tissue cross-reactivity studies with pembrolizumab using human 
and Cynomolgus monkey tissues or in immunotoxicology evaluation using the T-cell-dependent 
antibody response (TDAR) study in mice with antimurine PD-1 surrogate antibody muDX400. 

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The nonclinical profile supports the safe clinical use of pembrolizumab at the proposed doses.  
2.2.2.3 Clinical Activity in Non-Small Cell Lung Cancer 
Single Agent Activity 
Pembrolizumab, the PD-1 inhibitor used in this study, received initially FDA-accelerated 
approved in October 2015 followed by full approval as single agent for treatment of patients with 
metastatic NSCLC whose tumors express PD-L1 [tumor proportion score ≥ 1%] as determined 
by an FDA-approved test, with disease progression on or after platinum-containing 
chemotherapy (patients with EGFR or ALK genomic tumor aberrations should have disease 
progression on FDA-approved therapy for these aberrations prior to receiving pembrolizumab).22   
In the phase 1 study of pembrolizumab in 495 heavily pretreated patients with lung cancer, there 
was a response rate of 19.4%;  median duration of response (DOR) of 12.5 months;  median PFS 
of 3.7 months;  and median OS of 12.0 months.  In updated results from the KEYNOTE-001 
phase 1 study of treatment-naïve NSCLC patients administered pembrolizumab as first-line 
therapy, the ORR was 26.7% (95% CI 18.4 to 36.5), including one complete response, disease 
control rate (DCR) of 67.3% (95% CI 57.3 to 76.3), median PFS of 6.1 months (95% CI 
4.1 to 9.1), and median OS not reached (95% CI 16.2 months to NR).23  Based on this study, 
there were studies of pembrolizumab as first-line therapy in non-small cell lung cancer (NSCLC) 
including phase 3 KEYNOTE-02424 and KEYNOTE-04225 studies, the former of which has been 
resulted and is described below.26  Pembrolizumab is also noted to have activity in brain 
metastases of patients with NSCLC.27  Of the 11 patients treated and evaluable, there was one 
complete response and 4 partial responses in the brain for an overall RR of 45%.  Intracranial 
response duration for the 5 responders was between 12+ to 22+ weeks.  
The KEYNOTE-010 study, a randomized, open label, phase 2/3 study of pembrolizumab 
2 mg/kg, pembrolizumab 10 mg/kg, or docetaxel 75 mg/m² every 3 weeks in advanced non-small 
cell lung cancer patients with PDL-1 positivity was reported.28 The median overall survival was 
10.4 months (95% CI 9.4 to 11.9) with pembrolizumab 2 mg/kg, 12.7 months (95% CI 
10.0 to 17.3) with pembrolizumab 10 mg/kg, and 8.5 months (95% CI 7.5 to 9.8) with docetaxel.  
Overall survival was significantly longer for pembrolizumab at 2 mg/kg and at 10 mg/kg vs 
docetaxel (HR 0.71, 95% CI 0.58 to 0.88, P = 0.0008 and HR 0.61, 95% CI 0.49 to 0.75, 
P < 0.0001, respectively).  Median progression free survival was 3.9 months (95% CI 3.1 to 4.1) 
with pembrolizumab 2 mg/kg, 4.0 months (95% CI 2.7 to 4.3) with pembrolizumab 10 mg/kg, 
and 4.0 months (95% CI  3.1 to 4.2) with docetaxel, with no significant difference for 
pembrolizumab 2 mg/kg vs docetaxel (HR 0.88, 95% CI 0.74 to 1.05, P = 0.07) or for 
pembrolizumab 10 mg/kg vs docetaxel (HR 0.79, 95% CI 0.66 to 0.94, P = 0.004.)  The overall 
survival between pembrolizumab 2 mg/kg and 10 mg/kg was similar in the overall population 
(HR 1.17, 95% CI 0.94 to 1.45).  The progression-free survival was also similar at each 
pembrolizumab dose (HR 1.09, 95% CI 0.92 to 1.30).  There was a response rate of 18% 
(N = 62/344) in the 2 mg/kg pembrolizumab group, 18% (N = 64/346) in the pembrolizumab 
10 mg/kg group, and 9% (N = 32/343) in the docetaxel group.  All responses were partial, and 
median time to response was 9 weeks.  The response rate was statistically significantly higher for 
either pembrolizumab dose vs docetaxel.  The median duration of response was also longer in the 
pembrolizumab arm vs docetaxel, not reached vs 8 months, respectively.  
Pembrolizumab has also been approved as a single agent for first line treatment of patients with 
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as determined by an FDA-approved test with no EGFR or ALK genomic tumor aberrations. This 
was based on the KEYNOTE-02426 study (NCT02142738), which was a randomized, 
multicenter, open-label, active-controlled trial in patients with metastatic NSCLC, whose tumors 
had high PD-L1 expression [tumor proportion score (TPS) of 50% or greater] as determined by 
PD-L1 IHC 22C3 pharmDx Kit immunohistochemistry assay, and had not received prior 
systemic treatment for metastatic NSCLC.  Patients with EGFR or ALK genomic tumor 
aberrations; autoimmune disease that required systemic therapy within 2 years of treatment;  a 
medical condition that required immunosuppression;  or who had received more than 30 Gy of 
radiation in the thoracic region within the prior 26 weeks of initiation of study were ineligible.  
Randomization was stratified by ECOG performance status (0 vs 1); histology 
(squamous vs nonsquamous);  and geographic region (East Asia vs non-East Asia).  Patients 
were randomized 1:1 to receive pembrolizumab 200 mg intravenously every 3 weeks or 
investigator’s choice of multiple platinum-containing chemotherapy regimens for 4 to 6 cycles 
followed by optional pemetrexed maintenance (for nonsquamous histologies).  Treatment with 
pembrolizumab continued until RECIST v1.1-defined progression of disease as determined by an 
independent radiology committee;  unacceptable toxicity;  or for up to 24 months.  Treatment 
could continue beyond disease progression if the patient was clinically stable and was considered 
by the investigator to be deriving clinical benefit.  Patients randomized to chemotherapy were 
offered pembrolizumab at the time of disease progression.  Assessment of tumor status was 
performed every 9 weeks.  The main efficacy outcome measure was PFS as assessed by a 
blinded independent central radiologists’ (BICR) review according to RECIST v1.1.  Additional 
efficacy outcome measures were OS and ORR as assessed by the BICR according to 
RECIST v1.1. 
A total of 305 patients were randomized:  154 patients to the pembrolizumab arm and 151 to the 
chemotherapy arm.  The study population characteristics were:  median age of 65 years 
(range: 33 to 90);  54% age 65 or older;  61% male;  82% white and 15% Asian;  65% ECOG 
performance status of 1;  18% with squamous and 82% with nonsquamous histology;  and 9% 
with history of brain metastases.  A total of 66 patients in the chemotherapy arm received 
pembrolizumab at the time of disease progression.  The trial demonstrated a statistically-
significant improvement in PFS for patients randomized to pembrolizumab as compared with 
chemotherapy (10.3 months vs 6 months respectively;  HR 0.50;  95% CI 0.37 to 0.68;  
p < 0.001).  Additionally, a pre-specified interim OS analysis at 108 events (64% of the events 
needed for final analysis) also demonstrated statistically-significant improvement of OS for 
patients randomized to pembrolizumab as compared with chemotherapy (70% vs 54% of patients 
alive at 12 months, respectively;  HR 0.60;  95% CI 0.41 to 0.89;  p = 0.005). 
Combinations clinical activity 
Pembrolizumab is also being developed in combination strategies in NSCLC including in 
combination with chemotherapies, targeted therapies, radiation, and other immunotherapeutic 
approaches.  Most recently, pembrolizumab has received accelerated approval in combination 
with pemetrexed and carboplatin, as first-line treatment of patients with metastatic NSCLC 
(accelerated approval based on response rate and progression-free survival).  This was based on 
data from the randomized phase 2 cohort G of the Keynote 21 study performed in the US and 
Taiwan.29  Patients were eligible for this study if they had no prior treatment for non-squamous 
stage IIIB or IV non-small cell lung cancer and no evidence of EGFR or ALK alteration;  ECOG 

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performance status 0-1;  measurable disease per RECIST v 1.1;  and tumor biopsy sample 
available for assessment of PD-L1 expression.  Pertinent exclusion criteria included receiving 
more than 30 Gy of radiation to the lungs in the prior 6 months; autoimmune disease requiring 
systemic treatment in the previous 2 years;  untreated brain metastases (although stable treated 
metastases were allowed);  or active interstitial lung disease or pneumonitis that required 
steroids.  In the pembrolizumab plus chemotherapy group, pembrolizumab 200 mg IV, 
pemetrexed 500 mg/m², and carboplatin AUC 5 were given IV every 3 weeks followed by 
24 months of pembrolizumab and optional pemetrexed maintenance chemotherapy indefinitely.  
The chemotherapy group received carboplatin and pemetrexed with optional pemetrexed 
maintenance indefinitely.  Crossover was allowed for patients on the carboplatin and pemetrexed 
only group to pembrolizumab monotherapy.  Treatment was discontinued for intolerable toxicity 
or disease progression;  however, patients could be treated beyond disease progression if ongoing 
clinic benefit.  Tumor imaging by CT or MRI was done at baseline and every 6 weeks the first 
18 weeks, then every 9 weeks for the first 12 months and every 12 weeks thereafter.  The 
primary endpoint was objective response rate as defined by RECIST version 1.1). 
There were 123 patients randomized, 60 patients in the pembrolizumab plus chemotherapy arm 
vs 63 patients in the chemotherapy-alone arm.  Overall, baseline characteristics were well 
balanced, although there was a higher proportion of adenocarcinoma, never smokers, and stable 
brain metastases in the pembrolizumab plus chemotherapy arm.  Also, pemetrexed maintenance 
was given more commonly in the pembrolizumab plus chemotherapy arm vs the 
chemotherapy-alone arm (85% vs 69%, respectively).  The distribution of PD-L1 expression in 
the pembrolizumab plus chemotherapy arm was approximately one third each of the following 
tumor proportion score categories  < 1%;  1 to 49%, and ≥ 50%.  The study met its primary 
endpoint as there was a statistically significant improvement in objective response rate with the 
pembrolizumab plus chemotherapy arm versus chemotherapy-alone arm:  55% (95% CI 
42 to 68; n = 33/60) vs 29% (95% CI 18 to 41; n = 18/63), respectively, p = 0.0016.  The median 
time to response was also faster in the pembrolizumab plus chemotherapy arm:  1.5 months (IQR 
1.4 to 2.8) vs 2.7 months (IQR 1.4 to 2.8), respectively.  The median duration of response in both 
arms was not reached.  There was also less progressive disease seen in the pembrolizumab plus 
chemotherapy arm:  3% vs 17%, respectively.  32% of the 62 patients in the chemotherapy 
crossed over to pembrolizumab monotherapy.  The responses appeared to be independent of 
PD-L1 expression in the pembrolizumab plus chemotherapy arm, as the PD-L1 < 1% group had 
a response rate of 57% while the PD-L1 ≥ 1% group had a response rate of 54%.  However, in 
the PD-L1 high-expressers (≥ 50%), the objective response rate was 80% (n = 16/20). 
Progression-free survival was also longer with the pembrolizumab plus chemotherapy arm 
compared to the chemotherapy-alone arm [median 13.0 months (95% CI 8.3 to NR) vs 
8.9 months (4.4 to 10.3), respectively; HR 0.53, 95% CI 0.31 to 0.91; p = 0.010).  Most recent 
reports of overall survival show trend for benefit and the KEYNOTE189 randomized phase 3 
study has been reported as positive.  The rate of treatment related adverse events were similar in 
both arms.  The most common treatment-related events of any grade in the pembrolizumab plus 
chemotherapy arm were fatigue (64%), nausea (58%), and anemia (32%).  Rash (27%) and 
alopecia (14%) were more common in the pembrolizumab plus chemotherapy arm compared to 
the chemotherapy alone arm by greater than 10%.  Immune-related adverse events were of 
course higher in the pembrolizumab plus chemotherapy arm at 22% vs 11% in the chemotherapy 
arm.  The most common immune-mediate adverse events were hypothyroidism (15%), 

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hypothyroidism (8%), pneumonitis (5%).  These results were subsequently confirmed by data 
from the larger KEYNOTE-189 study in a similar patient population.30 
2.2.2.4 Clinical Pharmacokinetics – Please refer to most up to date Investigator Brochure 
and/or most up to date Package Insert. 
The pharmacokinetic profile of pembrolizumab, with low clearance and limited volume of 
distribution is typical for therapeutic antibodies.  Exposure to pembrolizumab is approximately 
linear in the dose range of clinical relevance (1 to 10 mg/kg).  Furthermore, pembrolizumab has a 
low potential of eliciting the formation of anti-drug antibodies.  No formal pharmacokinetic drug 
interaction studies have been conducted.  
The pharmacokinetics (PK) of pembrolizumab was characterized using a population PK analysis 
with concentration data collected from 2993 patients with various cancers who received 
pembrolizumab doses of 1 to 10 mg/kg every 2 weeks, 2 to 10 mg/kg every 3 weeks, or 200 mg 
every 3 weeks.  Pembrolizumab clearance (CV%) is approximately 23% lower [geometric mean, 
195 mL/day (40%)] at steady state than that after the first dose [252 mL/day (37%)]; this 
decrease in clearance with time is not considered clinically important.  The geometric mean 
value (CV%) for volume of distribution at steady state is 6.0 L (20%) and for terminal half-life 
(t1/2 ) is 22 days (32%).  Steady-state concentrations of pembrolizumab were reached by 
16 weeks of repeated dosing with an every 3-week regimen and the systemic accumulation was 
2.1-fold.  The peak concentration (Cmax), trough concentration (Cmin), and area under the 
plasma concentration versus time curve at steady state (AUCss) of pembrolizumab increased 
dose proportionally in the dose range of 2 to 10 mg/kg every 3 weeks.  
Specific Populations:  The following factors had no clinically important effect on the CL of 
pembrolizumab:  age (range:  15 to 94 years);  sex;  race (89% White);  renal impairment (eGFR 
greater than or equal to 15 mL/min/1.73 m2);  mild hepatic impairment (total bilirubin less than 
or equal to upper limit of normal (ULN) and AST greater than ULN or total bilirubin between 1 
and 1.5 times ULN and any AST);  or tumor burden.  There is insufficient information to 
determine whether there are clinically important differences in the CL of pembrolizumab in 
patients with moderate or severe hepatic impairment.  
2.2.2.5 Clinical Safety- Please refer to most up to date Investigator brochure. 
Safety data are presented for a total of 2799 subjects in ongoing, Merck-sponsored clinical trials.  
Tables from the most recent Investigator Brochure are provided below for reference:  

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Table:  Most Frequently Reported (≥ 5%) Adverse Events Presented by Decreasing Frequency 
and Considered Drug-Related by the Investigator in Subjects Treated with Pembrolizumab 
(ASaT Population) 
 
 

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Table:  Most Frequently Reported (≥0.2%) Serious Adverse Events Presented by Decreasing 
Frequency and Considered Drug-Related by the Investigator in Subjects Treated with 
Pembrolizumab (ASaT Population) 
 
 
2.2.3 Rationale for Dose Selection/Regimen/Modification  
The planned dose of pembrolizumab for this study is 200 mg every 3 weeks (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: 
• 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 

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settings (monotherapy and in combination with chemotherapy).  Five studies compared 
2 mg mg/kg Q3W versus 10 mg/kg Q2W (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. 
For clinicaltrials.gov compliance 
An IND application was submitted because patients being treated are not necessarily same as the 
same FDA approved indication.  
2.3 
Rationale 
2.3.1 Rationale for the Trial and Selected Subject Population 
Rationale for Selected Subject Population 
PD-1 and PD-L1 inhibition is an active therapy in lung cancer.  Pembrolizumab, the PD-1 
inhibitor in this study, is FDA approved for lung cancer as a monotherapy in the following 
indications:  (i) single agent for first-line treatment of patients with metastatic NSCLC whose 
tumors have high PD-L1 expression [tumor proportion score ≥ 50%] as determined by an 
FDA-approved test with no EGFR or ALK genomic tumor aberrations;  (ii) single agent for 
treatment of patients with metastatic NSCLC whose tumors express PD-L1 [(tumor proportion 
score ≥ 1%] as determined by an FDA-approved test, with disease progression on or after 
platinum-containing chemotherapy (patients with EGFR or ALK genomic tumor aberrations 
should have disease progression on FDA-approved therapy for these aberrations prior to 
receiving pembrolizumab).  As described in Section 2.2.2.3.  For this study, we plan to enroll 
patients in the approved frontline monotherapy indication for pembrolizumab (KEYNOTE-024 
study)26, and expand this slightly to include 1% or greater based on the KEYNOTE-042 data 

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(Lopes, ASCO 2018 LBA4).  However, in the second line setting and beyond we will enroll 
patients irrespective of expression of PD-L1.  The rationale for that is detailed below since 
responses have been in NSCLC even in absence of PD-L1 expression.  
In the 495 patients reported from the phase 1 study, there were a total of 401 (81%) 
non-squamous;  81 squamous;  7 adenosquamous;  and 2 unknown histologies.33  The ORR in 
patients with squamous histology was 23.5% (N=20/85) and was similar to that in patients with 
non-squamous histology, 18.7% (N=75/401).  Within the patients with squamous histology, there 
was a higher response rate in patients with the highest PD-L1 proportion score (PS ≥ 50%, 
PS1 to 49%, PS < 1%): 64.3% (N = 9/14) > 22.7% (N = 5/22) > 0% (N = 0/8).  In the 
non-squamous histologies, there was also a higher response rate in patients with the highest 
PD-L1 proportion score: 37.7% (N = 23/61) > 14.9% (N = 13/87) > 13.6% (N = 3/22).  The 
non-squamous histology cohort included in this report included patients that were naïve to 
systemic therapy and patients who had progressed after ≥ 2 previous regimens.  Patients had 
received a variety of prior treatments: 19% were treatment naïve, 14.9% had received 1 prior 
systemic therapy, 24% had received 2, 21.4% had received 3, and 20.6% had received ≥ 4.  In 
patients that were previously treated, there was a higher ORR in patients with high PD-L1 
proportion scores: 43.9% (N = 25/57) > 15.6% (N = 12/77) > 9.1% (N = 24/22).  In patients that 
were treatment naïve, this trend for improved ORR was also true in patients with high PD-L1 
proportion scores (PS ≥ 50%, PS1 to 49%, PS < 1%):  50% (N = 8/16) > 19.2% (N = 5/26) 
> 16.7% (N = 1/6).  PD-L1 proportion score ≥ 50% was seen in equal prevalence in patients who 
were previously treated or treatment naïve, 22.7% (N = 146/643) and 24.9% (N = 45/181).  
Both treatment-naïve (PD-L1 high-expressers with absence of ALK/EGFR alteration) and  
previously-treated (irrespective of PD-L1 expression) metastatic NSCLC patients will be 
enrolled in this trial.  
Rationale for The Trial 
Despite clinical activity seen with PD-1/PD-L1 inhibition, there is no robust predictive 
biomarker at this time.  Described below are the biomarkers currently being studied, including 
PD-L1 protein expression by immunohistochemistry, gene expression signatures, T-cell receptor 
repertoire, tumor-infiltrating lymphocytes, cytokines, and mutational burden.  This is not a 
comprehensive list, as this field is evolving rapidly. 
The purpose of our study is to examine potential surrogate and predictive biomarkers of 
response to PD-1 therapy, pembrolizumab, in metastatic NSCLC using Stanford 
technologies, including circulating tumor DNA (CAPP-Seq)1 and as an exploratory 
endpoint gene expression immune signatures (CIBERSORT)34.  
Biomarkers 
PD-L1 Protein Expression by Immunohistochemistry 
Many biomarkers are being developed to determine the subgroup of patients who benefit from 
these therapies since collectively, PD-1/PD-L1 inhibitors only appear to results in response in 
15 to 20% of patients with previously-treated unselected NSCLC and up to 50% in patients with 
high PD-L1 expression.  PD-L1 protein expression as determined by immunohistochemistry is 
emerging as the primary predictor of response.  In a study examining 7 clinical trials in 511 
patients treated with PD-1/PD-L1 inhibition in lung cancer, the ORR was 23.2% (95% CI, 
18.5 to 27.9) for PD-L1 positive patients and 14.5% (95% CI, 9.6-19.4) for PD-L1 negative 

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patients.35  In the KEYNOTE-001 pembrolizumab data published for NSCLC, using a definition 
of PD-L1 positivity of expression in at least 50% of tumor cells, patients with PD-L1 positive 
tumors had a higher response rate at 45.2%, longer median PFS of 6.3 months, and median 
overall survival has not been reached.22 In updated results from the KEYNOTE-001 study, 
PD-L1 expression and its association with clinical benefit was evaluated in 91 patients who were 
treatment naïve and given pembrolizumab as first-line therapy.23  Of 91 patients with evaluable 
PD-L1 expression, 29.7% had a proportion score of ≥ 50%, 57.1% had a proportion score (PS) 
1 to 49%, and 13.2% had a proportion score < 1%.  The clinical activity of the groups were as 
follows based on PD-L1 expression:  1) PS ≥ 50%, ORR 51.9% / DCR 77.8% / 
mPFS 12.5 months / mOS not reached;  2) PS1-49%, ORR 17.3% / DCR 63.5% / 
mPFS 4.2 months / mOS 16.2 months;  and 3) PS < 1%, ORR 8.3% / DCR 66.7% / 
mPFS 3.5 months / mOS 10.4 months, respectively.  There is also a confirmatory phase 3 study 
(KEYNOTE-024) of pembrolizumab frontline for patients with PD-L1 PS ≥ 50% where the 
response rate was 45%.26 
The prototype PD-L1 immunohistochemistry assay of Merck PD-1 compound, pembrolizumab, 
was developed and validated at a single CLIA-certified laboratory site (QualTek Goleta, 
California).36 The 22C3 monoclonal mouse anti-human PD-L1 antibody clone was used along 
with commercially available reagents from the DAKO EnVision FLEX+ HRP-Polymer Kit 
(DAKO K8012, Carpinteria, California, USA).  The clinical trial immunohistochemistry assay 
has been developed as a companion diagnostic assay using a modified version of the prototype 
assay.  There were 4 standard scoring methods evaluated with the clinical trial assay:  
1) proportion score PS 0 to 100, the percentage of cells staining at any intensity;  2) proportion 
moderate/strong score P2S, 0-100, the percentage of cells staining at moderate or strong 
intensity;  3) proportion strong score, P3S, 0-100, the percentage of cells staining at strong 
intensity;  4) H-score, HS, sum of PS, P2S, and P3S.  In order to be an adequate sample in the 
prototype assay, ≥ 50 viable tumor cells or ≥ 5 viable PD-L1+ cells had to be present, and in the 
clinical trial assay, ≥ 100 viable tumor cells had to be present.  In the prototype assay, scoring 
accounted for tumor and immune cells demonstrating partial or complete membrane staining and 
in the clinical trial assay, only tumor cells were counted that demonstrated partial or complete 
membrane staining.  It is known that samples greater than 6 months resulted in deterioration 
PD-L1 expression by immunohistochemistry and the samples were excluded.  In the training set 
of 182 patients by all 4 scoring methods, the area under the ROC was similar, 0.74-0.77.  The cut 
off for the PS score chosen was 50%.  PD-L1 positivity based on this score resulted in an 
association with a significantly longer progression free survival by immune-related response 
criteria and a higher number of responders (odds ratio of 8.93).36   
The PD-L1 IHC 22C3 pharmDx is currently FDA-approved (BLA 125514, supplement 5, see 
package insert http://www.accessdata.fda.gov/drugsatfda_docs/label/2015/125514s005lbl.pdf) 
for pembrolizumab.  
Many other biomarkers are being examined since not all patients with PD-L1 expression 
have a response to these therapies, and responses are also seen in those patients without 
PD-L1 expression.  There are also several variables for the PD-L1 biomarker, including the 
definition of positivity from threshold percentage of cells staining positive to the types of 
cells staining (ie, tumor cells, tumor infiltrating immune cells, stroma).  The assays used 
also differ per company including the antibodies used for staining and also the IHC 
platform used.  The predictive ability of PD-L1 as a biomarker may also vary by line of 

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therapy.37  Tumor PD-L1 testing will be performed using standard of care FDA-approved 
PD-L1 testing for this trial.  
Biomarkers of PD-1/PD-L1 therapies 
Listed below are examples of biomarkers being explored for immunotherapy.  This is not an 
updated or comprehensive list, as this is a rapidly evolving field. 
Gene expression signatures 
Other biomarkers are being examined to help predict clinical activity to anti-PD-1/PD-L1 
therapy, and include RNA expression gene signatures.  For example, using the NanoString 
counter system, at least one of the following gene signatures that was enriched for 
interferon-gamma (6-gene), T-cell receptor (TCR) signaling (13-gene), expanded immune 
(18-gene), and de novo (33-gene) were predictive of response to pembrolizumab in gastric 
cancer38, bladder cancer39, and head and neck cancer40.  In melanoma patients treated with 
pembrolizumab, there were several immune-related gene signatures that were identified that 
were associated with clinical benefit to PD-1 therapy, including signatures describing interferon 
gamma signaling, antigen presentation, and T-cell specific markers.41  For example, there was a 
trend for improved response with the preliminary interferon gamma 10-gene signature and the 
preliminary expanded immune 28-gene signature in pembrolizumab-treated melanoma patients.  
For another inhibitor targeting the PD-1/PD-L1 axis, atezolizumab, T-helper type 1 (TH1) gene 
expression, CTLA4 expression and the absence of fractalkine (CX3CL1) in baseline specimens 
was associated with response.42  
T-cell receptor (TCR) repertoire, CD8+ T-cells, Cytokines, Others 
The heterogeneity of tumor infiltrating T-cell repertoire is also being examined as a potential 
predictor of clinical activity or lack thereof to PD-1 therapy.43  The TCR repertoire and cytokines 
have been explored in clinical trials with pembrolizumab in metastatic melanoma.44  Although 
there was no net expansion in unique TCR repertoire seen in patients treated with 
pembrolizumab, responders overall had more unique TCRs than nonresponders.  A more limited 
TCR repertoire in baseline tumor samples, suggestive of a clonal population of T cells, has also 
been associated with improved response.45  There was also a decrease in certain cytokines seen 
in responders but not in nonresponders with PD-1 therapy, including MCP-1, FGF-2, and IL-8.43  
Even peripheral blood count eosinophils have been correlated with long-term disease control in 
metastatic melanoma patients treated with pembrolizumab.46  In a study of 46 melanoma patients 
treated with pembrolizumab, it was suggested that an immunocompetent tumor, with pre-existing 
CD8+ T-cells, is required to achieve benefit to PD-1 therapy.45  The presence of CD8+ T cells at 
the invasive margin in baseline tumor samples was associated with response to pembrolizumab, 
and an increase in CD8+ T-cells at the invasive margin or in the center of the tumor was also 
associated with improved clinical benefit.  Overall, there were significantly higher numbers of 
CD8+;  PD-1+;  PD-L1+ cells at both the invasive margin and the tumor center in responders 
compared to nonresponders, suggesting an immunocompetent phenotype, is required for 
response to PD-1 therapy.  
Mutational Burden/Neoantigens 
It has been hypothesized that high somatic mutation burden with subsequent expression of 
immunogenic neoantigens explains why the main tumors (which are induced by mutagenic 
carcinogens, ie, UV light and cigarette smoking), melanoma and lung cancer, respond to immune 

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checkpoint inhibitors.  This hypothesis was corroborated by recent data in metastatic melanoma 
patients treated with ipilimumab, where whole exome sequencing was performed on tumors with 
matched blood samples.47  Mutational load was associated with clinical benefit in this study, but 
was not a sufficient predictive factor for benefit.  Identification of certain neoantigens via whole 
exome sequencing has also been reported as a potential predictor of response to 
immunotherapies in melanoma.  
Tumor mutation burden is being used to as a biomarker in ongoing large randomized studies 
with immunotherapy in lung cancer.  Somatic mutation burden and identification of neoantigens 
have also been associated with durable clinical benefit (DCB) in patients treated with 
pembrolizumab in metastatic NSCLC.48  Lung cancer is a notoriously heterogeneous group, with 
a large ranging mutation burden, particularly because some lung cancers are caused by cigarette 
smoke and others are not.  Whole exome sequencing was performed on two independent cohorts 
treated with pembrolizumab (n = 16 and n = 18, respectively).  There was a median of 200 
non-synonymous mutations per sample (11-1192) and a median number of 327 exonic mutations 
per sample (45-1732).  The number of nonsynonymous mutations correlated with DCB in 16 
patients in the discovery cohort; for example, there were 302 mutations in patients with DCB and 
148 in those without DCB (P=0.02).  Using a median of 209 mutations, patients whose tumor fell 
below the median had a 13% rate of DCB and those that fell above the median had a 73% rate of 
DCB (P = 0.04).  This differential benefit of high mutation burden was also seen for other 
clinical endpoints, including objective response rate (63% vs 0%, P = 0.03) and PFS 
(14.5 vs 3.7 months, P = 0.01, HR 0.19, 95% CI 0.05 to 0.70).  These findings were also seen in 
the validation cohort of 18 patients, who had similar baseline clinical characteristics (AUC 87%).  
Not surprisingly, since smoking increases the nonsynonymous mutation burden rate, smoking 
history is also associated with clinical benefit to pembrolizumab.  A molecular smoking 
signature, which is transversion high (TH) C-A, was associated with the highest overall 
response rate (56% vs 17% in transversion low (TL), P = 0.03) and the longest progression free 
survival (median not reached vs 3.5 months in TL, P = 0.0001).  In this study, neoantigens were 
also examined, with the quantity of neoantigens correlating with mutation burden of the tumor, 
and higher candidate neoantigen burden associated with DCB.  The predictive benefit of 
mutational burden also potentially explains why patients with EGFR mutations do not seem to 
derive as much benefit with the PD-1/PD-L1 inhibition, demonstrated across several large 
randomized studies.18 
2.4 
Study Design 
• This is a prospective open-label non-randomized single-arm treatment trial of 
pembrolizumab in metastatic NSCLC patients, with a primary endpoint of evaluation of 
pharmacodynamics minimally invasive surrogate biomarker of response, circulating 
tumor DNA.  
2.5 
Correlative Studies Background 
2.5.1 Detecting Tumor Mutations and Circulating Tumor DNA using Capp-Seq 
Beyond RECIST: Using circulating tumor DNA (ctDNA) levels as a surrogate biomarker of 
response to pembrolizumab 
While immune-related radiographic response criteria (ie, RECIST)49 have been developed for 
immunotherapy clinical trials, which allow for some degree of growth and the development of 

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new lesions, these criteria have not been fully validated and frequently are erroneous in 
separating responders from non-responders in real-time.50,51  Peripheral blood monitoring of 
cancer while on treatment is attractive.  CAncer Personalized Profiling by Deep Sequencing 
(CAPP-Seq) is a method to measure ctDNA using a selector of biotinylated DNA 
oligonucleotides that detect recurrent mutations in cancers.1  The initial design of the CAPP-Seq 
selector was created for NSCLC.  The initial selector targeted 521 exons and 13 introns from a 
total of 139 mutated genes, and could identify 96% of patients with NSCLC.  Using CAPP-Seq 
for noninvasive monitoring of cancer in the initial publication, had an impressive receiving 
operating characteristic (AUC 0.95), with a sensitivity of 85% and specificity of 96%.  The 
sensitivity was higher in tumors of more advanced stage; reaching 100% in Stage II-IV tumors.  
Newman et al (Diehn/Alizadeh labs, Stanford University, Stanford, CA) were able to correlate 
ctDNA levels with tumor volumes determined radiographically by PET and/or CT (R2 = 0.89, 
P = 0.0002).  ctDNA levels were also shown to fall dramatically in patients responding to 
chemotherapy and targeted therapeutics.  ctDNA was also helpful in determining if a patient had 
progressed after receiving definitive radiotherapy due to the difficulty in interpreting CT imaging 
after radiotherapy, and was also useful in surveillance monitoring after curative intent therapy for 
early-stage NSCLC.  Circulating tumor DNA as measured by CAPP-Seq has also been shown to 
identify molecular residual disease after definitive radiation treatment of locally advanced lung 
cancer:  (i) ctDNA was detectable in the first post-treatment blood sample in 94% of patients 
who subsequently experienced recurrence and (ii) ctDNA detected recurrence prior to 
radiographic progression in 72% of patients by a median of 5.2 months.52 
ctDNA as measured by CAPP-Seq technology may serve as a useful surrogate biomarker of 
clinical activity to pembrolizumab using baseline levels of ctDNA or change in levels of 
ctDNA longitudinally.  CAPP-Seq will be performed on baseline tumor samples when 
available to identify mutations.  In this trial, we will measure ctDNA levels as a surrogate 
biomarker of response, and correlate levels with radiographic response kinetics.  ctDNA 
may be superior to radiographic assessments in identifying responders to pembrolizumab 
from non-responders at an earlier time point.  
2.5.2 PD-L1 IHC 
PD-L1 immunohistochemistry will be performed using standard of care FDA-approved PD-L1 
testing and is performed as part of standard of care.  The prototype PD-L1 
immunohistochemistry assay of Merck PD-1 compound, pembrolizumab, was developed and 
validated at a single CLIA-certified laboratory site (QualTek; Goleta, California).36  The 22C3 
monoclonal mouse anti-human PDL 1 antibody clone was used along with commercially 
available reagents from the DAKO EnVision FLEX+ HRP-Polymer Kit (DAKO K8012, 
Carpinteria, California, USA).  The clinical trial immunohistochemistry assay has been 
developed as a companion diagnostic assay using a modified version of the prototype assay.  The 
PD-L1 IHC 22C3 pharmDx is currently FDA-approved for pembrolizumab as a qualitative 
immunohistochemical assay using Monoclonal Mouse Anti-PD-L1, Clone 22C3 intended for use 
in the detection of PD-L1 protein in formalin-fixed, paraffin-embedded (FFPE) non-small cell 
lung cancer (NSCLC) tissue using EnVision FLEX visualization system on Autostainer Link 48.  
PD-L1 protein expression is determined by using Tumor Proportion Score (TPS), which is the 
percentage of viable tumor cells showing partial or complete membrane staining.  The specimen 
is considered PD-L1 positive in the frontline setting if TPS ≥ 50% of the viable tumor cells 
exhibit membrane staining at any intensity.  PD-L1 IHC 22C3 pharmDx is indicated as an aid in 

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identifying NSCLC patients for treatment with pembrolizumab 
(http://www.fda.gov/MedicalDevices/ProductsandMedicalProcedures/InVitroDiagnostics/ucm30
1431.htm).  PD-L1 expression has been correlated with response and other clinical outcomes as 
described in Section 2.3.1.  
2.5.3 Immune gene expression signature using CIBERSORT 
Beyond PD-L1 protein expression:  Using CIBERSORT as a predictive biomarker of 
response to pembrolizumab  
While some studies have demonstrated a high proportion of response in patients with PD-L1 
expression on tumors and tumor-infiltrating cells35,53, there are still responses observed with 
pembrolizumab in PD-L1 negative patients.  The simple presence or absence of certain 
tumor-infiltrating immune cell subsets may also contribute to the likelihood of response.45  In 
solid tumors, it is challenging to profile individual immune cell infiltrates since methodologies 
such as FACS require large numbers of cells and dissolution of tumor stromal architecture.  
CIBERSORT has been used to illustrate the diversity of tumor immune cell infiltrate subsets in 
triple negative breast cancer54 and also overall survival outcomes of 18,000 human tumors across 
39 malignancies.55  In the triple-negative breast cancer cohort, following whole tumor gene 
expression microarray analysis, the Alizadeh/Diehn labs generated an algorithm (termed 
CIBERSORT) to identify individual infiltrative immune cell populations, and established an 
“immune score” based on this algorithm.54  The overall immune score and presence of activated 
CD4+ memory T cells in tumors both strongly correlated with pathological complete response 
(pCR) to chemotherapy plus a PARP inhibitor in breast cancer patients.  
CIBERSORT will be used in an exploratory analysis to examine baseline lung tumor tissue 
(when available) prior to anti-PD-1 treatment to identify the tumor infiltrating immune cell 
subtypes that may correlate with response to pembrolizumab.  This technique is potentially 
superior to conventional flow cytometry since it requires only a small amount of frozen 
tissue from biopsy as opposed to a larger amount of tissue with subsequent dissociation and 
manipulation.  

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3. 
PARTICIPANT SELECTION AND ENROLLMENT PROCEDURES 
3.1 
Inclusion Criteria 
In order to be eligible for participation in this trial, the patient must meet ALL of the following 
criteria (ie, mark “yes” to all criteria): 
1. Has a pathologically-proven recurrent or metastatic non-small cell lung cancer 
(non-squamous;  squamous;  mixed;  and neuroendocrine histologies are allowed as of 
amendment 26 June 2018) 
2. Previously received at least one line of prior systemic therapy for metastatic disease.  
a. If the patient has a known sensitizing EGFR mutation or ALK rearrangement, the 
patient must have received at least 1 prior targeted therapy for metastatic disease 
(ie, EGFR TKI therapy or ALK TKI therapy, respectively).   
b. There is no limit on prior therapies allowed.  Patients must have completed previous 
treatment (including other investigational therapy) in greater than or equal to the 
following times prior to initiation of trial treatment:  
i. Anti-cancer monoclonal antibody (mAb) therapy must be completed ≥ 3 weeks 
prior to trial treatment  
ii. Chemotherapy administered in a daily or weekly schedule must be completed 
≥ 1 week prior to trial treatment 
iii. Chemotherapy administered in an every 2-week schedule must be completed 
≥ 2 weeks prior to trial treatment 
iv. Chemotherapy administered in an every 3-week schedule must be completed 
≥ 3 weeks prior to trial treatment 
v. Targeted small molecule therapy must be completed ≥ 1 week prior to trial 
treatment 
OR 
Has not received prior systemic therapy for their cancer in recurrent or metastatic setting, 
AND have a tumor with Tumor Proportion Score (TPS) ≥ 1% as measured by PD-L1 
IHC, AND no evidence of a sensitizing EGFR mutation or ALK rearrangement if 
adenocarcinoma histology (molecular testing not required for other histologies). 
3. Prior radiation therapy allowed as long as completed in the following times prior to 
initiation of trial treatment: 
a. Definitive curative intent radiation ≥ 2 weeks prior to trial treatment 
b. Palliative body radiation ≥ 1 week prior to trial treatment 
c. Stereotactic brain radiation ≥ 1 week prior to trial treatment 
d. Whole brain radiation ≥ 2 weeks prior to trial treatment 
4. Patients with previously-treated (with radiation or surgery) brain metastases are allowed.  
Patients with untreated stable or progressing metastases must have metastases ≤ 1.5 cm;  
be asymptomatic;  and either not be on steroids or be on 10 mg prednisone equivalent or 
less.  
5. Has measurable disease based on RECIST v1.1 criteria 

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6. Is medically able and willing to undergo needle biopsy of a tumor lesion, 
OR 
Has known tumor PD-L1 expression and believed to have sufficient archival tumor 
available for genomic analysis (block or 10 unstained slides or Stanford STAMP NGS 
testing previously resulted or in process)  
7. Has life expectancy ≥ 3 months 
8. Ability to understand and the willingness to sign a written informed consent document.  
9. ≥ 18 years of age on day of signing informed consent 
10. ECOG performance status of 0, 1, or 2 (Appendix A) 
11. Adequate organ function: 
a. Absolute neutrophil count (ANC) ≥ 1,000/mcL 
b. Platelets ≥ 75,000/mcL 
c. Hemoglobin ≥ 8 g/dL 
d. Serum creatinine ≤ 1.5 x upper limit of normal (ULN) OR measured or calculated 
creatinine clearance ≥ 30 mL/min for patient with creatinine levels 
> 1.5 x institutional ULN 
e. Serum total bilirubin ≤ 1.5 x ULN OR Direct bilirubin ≤ ULN for patients with total 
bilirubin levels > 1.5 ULN 
f. AST (SGOT) and ALT (SGPT) ≤ 3 x ULN OR ≤ 5 x ULN for patients with liver 
metastases 
12. Female patients of childbearing potential must have a negative urine or serum pregnancy 
test prior to the first dose of trial treatment.  They must also agree to acceptable 
contraceptive methods (ie, combined estrogen progesterone hormonal contraception;  
progesterone-only hormonal contraception;  intrauterine device;  have history of bilateral 
tubal ligation;  or 2-barrier method), or agree to abstain from heterosexual activity, for the 
course of the study through 120 days after the last dose of trial treatment.   
Female patients are not considered to be of childbearing potential if (i) they have been 
surgically-sterilized (such as hysterectomy plus bilateral salpingo-oophorectomy) or (ii) 
are free from menses for > 1 year (postmenopausal).  Female patients who have not 
had > 1 year of amenorrhea may have confirmation of postmenopausal state with 
2 FSH measurements in postmenopausal range and should not be on hormonal 
contraception or hormonal replacement therapy during testing. 
3.2 
Exclusion Criteria 
In order to be eligible for participation in this trial, the patient must NOT meet the following 
criteria (ie, mark “no” to all criteria): 
1. Is currently receiving another investigational therapy 
2. Has received prior anti-PD-1 or anti-PD-L1 therapy 
3. Has clinically-significant toxicities from previous anti-cancer therapy that have 
not resolved, or have not stabilized at a new baseline  
4. Has undergone a surgical procedure involving general anesthesia within 2 weeks of 
starting trial treatment, or has inadequate healing or recovery from complications of 
surgery prior to starting trial treatment.  This does not apply to low-risk procedures such 

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as thoracentesis;  paracentesis;  chest tube/PleurX catheter placement;  line placement;  
needle biopsy of tumor;  and bronchoscopy.  
5. Is receiving high-dose systemic steroid therapy or other immunosuppressive therapy 
within 3 days of trial treatment.  Topical and intraarticular steroid injections are allowed, 
as are physiologic doses of systemic steroids (≤ 10 mg of prednisone equivalent daily).  
6. Has carcinomatous meningitis as determined by positive CSF cytology 
7. Has known additional malignancy that is undergoing active treatment.  
8. Has active autoimmune disease that has required systemic treatment in the past 2 years 
(ie, with use of disease-modifying agents, supra-physiologic doses of systemic 
corticosteroids or immunosuppressive drugs).  Replacement therapy (eg, thyroxine, 
insulin;  or physiologic corticosteroid replacement therapy for adrenal or pituitary 
insufficiency, etc) is not considered a form of systemic treatment.  Asthma;  type I 
diabetes mellitus;  hypothyroidism;  and vitiligo are allowed.  
9. Has a history or current evidence of any condition;  therapy;  or laboratory abnormality 
that might confound the results of the trial, interfere with the patient’s participation for 
the full duration of the trial, or is not in the best interest of the patient to participate, in the 
opinion of the treating investigator.  This includes known active tuberculosis;  Grade 3 
active infection;  history of allogeneic bone marrow transplant or solid organ transplant;  
known history of human immunodeficiency virus (HIV);  known active Hepatitis B 
(eg, Hep B DNA-positive in prior 3 months) or known active Hepatitis C (eg, HCV RNA 
[qualitative] is detected in prior 3 months).  
10. Known current (non-infectious) pneumonitis or history of (non-infectious) pneumonitis 
that required oral steroids. 
11. Is pregnant or breastfeeding, or expecting to conceive children within the projected 
duration of the trial, starting with the screening visit through 120 days after the last dose 
of trial treatment 
 Statement of Eligibility 
By signing this form of this trial I verify that this patient is [
 eligible / 
 ineligible] for 
participation in the study.  This study is approved by the Stanford Cancer Institute Scientific 
Review Committee, the Stanford IRB, and has finalized financial and contractual agreements as 
required by Stanford School of Medicine’s Research Management Group (RMG).  

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Treating Physician Signature: 
Date: 
Printed Name: 
Secondary Reviewer Signature: 
Date: 
Printed Name: 
Study Coordinator Signature: 
Date: 
Printed Name: 
3.3 
Informed Consent Process 
All participants must be provided a consent form describing the study with sufficient information 
for participants to make an informed decision regarding their participation.  Participants must 
sign the IRB approved informed consent prior to participation in any study specific procedure.  
The participant must receive a copy of the signed and dated consent document.  The original 
signed copy of the consent document must be retained in the medical record or research file.  
3.4 
Randomization Procedures 
Patients in this study will not be randomized.  
3.5 
Study Timeline 
Primary Completion: 
The study will reach primary completion 24 months from the time the study opens to accrual.  
Study Completion: 
The study will reach study completion 48 months from the time the study opens to accrual.  

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4. 
TREATMENT PLAN 
Patients will initially be screened for eligibility.  If they are eligible for the trial and have signed 
informed consent, they will receive pembrolizumab.  There are 3 stages during the treatment 
phase of the study:  Stage I Cycle 1 through 8 (approximately Week 1 to 25), 
Stage II Cycle 9 through 17 (approximately Week 25 to 52), and Stage III Cycle 18 through 35 
(approximately Week 52 through 105).  The frequency of tumor imaging and correlative studies 
blood collection differs per stage of the treatment phase.  Screening, study visits, end of 
treatment visit, and follow-up will be conducted as outlined on the Study Calendar (Section 9).  
Details on Pembrolizumab Treatment:  
Dose Selection 
The rationale for selection of doses to be used in this trial is provided in Section 2.2.3 
Background and Rationale.  Details on preparation and administration of pembrolizumab are 
provided in the Pharmacy Manual.  
Timing of Dose Administration 
Trial treatment should be administered on Day 1 of each cycle after all procedures/assessments 
have been completed as detailed on the Study Calendar (Section 9) unless otherwise specified.  
Trial treatment may be administered up to 3 days before or after the scheduled Day 1 of each 
cycle.  
Pembrolizumab 200 mg will be administered as a 30 minute intravenous infusion every 
3 weeks.  Sites should make every effort to target infusion timing to be as close 30 minutes as 
possible.  However, given the variability of infusion pumps, a window is permitted (ie, infusion 
time is 30 minutes:  -5 min / +60 min).  
The Pharmacy Manual contains specific instructions for the preparation of the pembrolizumab 
infusion fluid and administration of infusion solution.  
Management of Infusion Reactions 
If an infusion reaction occurs, 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.  
Table 1 below shows treatment guidelines for patients who experience an infusion reaction 
associated with administration of pembrolizumab.  

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Table 1.  Treatment Guidelines for Infusion Reactions  
Associated with Administration of Pembrolizumab 
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 patient 
is deemed medically stable  
None 
Grade 2 
Requires infusion interruption 
but responds promptly to 
symptomatic treatment 
(eg, antihistamines, NSAIDS, 
narcotics, IV fluids); 
prophylactic medications 
indicated for ≤ 24 hrs 
Stop Infusion and monitor symptoms.  
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 patient 
is deemed medically stable.  
If symptoms resolve within one hour of stopping drug infusion, the 
infusion may be restarted at 50% of the original infusion rate (eg, from 
100 mL/hr to 50 mL/hr).  Otherwise dosing will be held until symptoms 
resolve and the patient should be premedicated for the next scheduled 
dose.  
For subjects who develop grade 2 toxicity despite adequate 
premedication, it is strongly recommended that the subject is 
permanently discontinued from further trial treatment 
administration.  In certain circumstances, rechallenge of drug may be 
allowed only with approval from the study PI 
Subject may be 
premedicated prior to 
infusion of 
pembrolizumab with: 
Diphenhydramine 50 mg 
po (or equivalent dose of 
antihistamine).  
Acetaminophen 
500 to 1000 mg po (or 
equivalent dose of 
antipyretic). 
Grade 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  
 
Grade 4: 
Life-threatening; pressor or 
ventilatory support indicated 
Stop Infusion.  
Additional appropriate medical therapy may include but is not limited to: 
IV fluids 
Antihistamines 
NSAIDS 
Acetaminophen 
Narcotics 
Oxygen 
Pressors 
Corticosteroids 
Epinephrine** in cases of anaphylaxis, use promptly 
Increase monitoring of vital signs as medically indicated until the patient 
is deemed medically stable.  
Hospitalization may be indicated.  
It is strongly recommended that the subject is permanently 
discontinued from further trial treatment administration.  In certain 
circumstances, rechallenge of drug may be allowed only with 
approval from the study PI  
No subsequent dosing 
4.1 
General Concomitant Medication and Supportive Care Guidelines 
Medications specifically prohibited in the exclusion criteria (with the exception of palliative 
radiation) are not allowed during the ongoing trial.  If there is a clinical indication for one of 
these or other medications specifically prohibited during the trial, discontinuation from trial 
therapy is usually appropriate, but exceptions can be granted with approval from the study PI.  

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4.1.1 Acceptable Concomitant Medications and other Supportive Therapies 
All treatments that the investigator considers necessary for a patient’s welfare may be 
administered at the discretion of the investigator in keeping with the community standards of 
medical care.  
Palliative radiation is allowed at the investigator’s discretion.  
4.1.2 Prohibited Concomitant Medications and other Supportive Therapies 
Subjects are prohibited from receiving the following therapies during the Screening and 
Treatment Phase of this trial: 
• Antineoplastic systemic anti-cancer chemotherapy or biological therapy  
• Immunotherapy not specified in this protocol 
• Investigational agents other than pembrolizumab  
• Systemic glucocorticoids (prednisone equivalent dose > 10 mg) for any purpose other 
than to modulate symptoms from an event of clinical interest of suspected immunologic 
etiology, unless permission is given from the study PI.  The use of physiologic doses of 
corticosteroids (prednisone equivalent dose ≤ 10 mg) is permitted throughout the study.  
• Patients who, in the assessment by the investigator, require the use of any of the 
aforementioned treatments for clinical management should be removed from trial 
treatment but should continue in the follow-up period if progression without clinical 
benefit has not yet occurred.  
There are no prohibited therapies during post-treatment follow-up.  
4.1.3  Blood draws 
The risks of blood draws include pain, bruising at the site where the blood is taken, redness and 
swelling of the vein and infection, and rare risk of fainting due to vasovagal syncope.  During the 
study, extra blood will be taken for correlative studies (ie, ctDNA).  
4.1.4 Tumor Biopsy 
This clinical trial has an optional tumor biopsy prior to enrollment.  The risks of the biopsy vary 
depending on the location of the biopsy or the procedure that is required to do the biopsy.  The 
risk of a lung biopsy includes some discomfort at the biopsy needle site, minor bleeding at the 
puncture site, hemoptysis, pneumothorax which may require placement of a chest tube; 
uncommon risks include infection and air embolism; rare risks include need for emergency 
surgery due to complications with procedure and death.  
4.1.5 Contraception  
Pembrolizumab may have adverse effects on a fetus in utero. Non-pregnant, non-breast-feeding 
women of childbearing potential may be enrolled if they are willing to use acceptable birth 
control (guidance below) or are women NOT of childbearing potential.  The following 
definitions are considered women NOT of childbearing potential1) surgically-sterilized, 
including one of the following: hysterectomy, bilateral salpingectomy, or bilateral 
oophorectomy;  2) postmenopausal, including a woman who has not had menses for greater than 
1 year OR in absence of 12 months of amenorrhea, a high follicle stimulating hormone level in 
postmenopausal range on two FSH measurements as long as woman is not using hormonal 

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contraception or hormonal replacement therapy;  or 3) not heterosexually active for the specified 
duration of the study.  
The following are considered highly effective contraceptive methods that are user dependent 
(failure rate of <1% per year when used consistently and correctly):  1) combined (estrogen- and 
progesterone- containing) hormonal contraception (i.e. oral, intravaginal, transdermal, 
injectable); and 2) progesterone-only hormonal contraception (i.e. oral, injectable). The 
following are considered highly effective contraceptive methods that have lower user 
dependency (failure rate of <1% per year when used consistently and correctly): 1) 
progesterone- only contraceptive implant; 2) intrauterine hormone-releasing system (IUS); 3) 
intrauterine device (IUD); 4) bilateral tubal occlusion; 5) vasectomized partner (i.e. provided that 
the partner is the sole male sexual partner of the women of childbearing potential and the 
absence of sperm has been confirmed; if not, an additional method of contraception should be 
used); 6) abstinence from heterosexual intercourse.  The acceptable alternative for the above 
highly effective contraceptive methods is 2 barrier methods including cervical cap, diaphragm;  
sponge,  condom (including by the partner);  or spermicide; or alternatively complete abstinence.   
Women subjects 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 they must adhere to the contraception requirement for the duration of 
the study and through 120 days after the last dose of trial treatment.  
There are no specific contraception requirements for male subjects with female partners of 
childbearing potential. 
 
4.2 Criteria for Removal from Trial Treatment 
A patient must be discontinued from trial treatment for any of the following reasons: 
• The patient withdraws consent (see below Section 4.2.1 for further details on type of 
consent withdrawn).  
• Confirmed radiographic disease progression (RECIST v1.1) without clinical benefit as 
determined by investigator 
o If the patient is having clinical benefit, patients may continue on therapy 
post-progression following approval from the PI before the second post-progression 
dose of therapy.  
• Unacceptable toxicity, including that which prevents further administration of trial 
treatment, or results in interruption of trial treatment greater than 12 weeks from the date 
of the scheduled interrupted dose  
• Reason other than treatment-related toxicity that results in interruption of trial treatment 
greater than 8 weeks from date of the scheduled interrupted dose.  
• Intercurrent illness that prevents further administration of trial treatment  
• Investigator’s decision to withdraw the patient 
• Pregnancy 
• Death 

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• Consistent and significant noncompliance with trial treatment or protocol-mandated 
procedures 
• The patient is lost to follow-up 
o Study personnel may use public records to check for mortality for any patients 
considered “lost to follow-up,” if permitted by applicable laws or regulations.  
• Completed 24 months of treatment (approximately 35 treatments) with pembrolizumab 
• Administrative reasons 
• The study is terminated by the investigator or Merck.  
o If the study is terminated by Merck, patients who are receiving clinical benefit from 
their participation in this study may continue to receive pembrolizumab from Merck.  
4.2.1 Withdrawal  
Patients may choose to discontinue the trial at any time, for any reason, and without prejudice to 
further treatment.  A patient who withdraws consent either in part or in whole of study 
participation will be asked to state the type (s) of withdrawal.  
• Treatment:  Withdrawal from treatment only; in this case, correlative research studies may 
be performed and follow up and outcomes data will continue as planned.  
• Treatment and correlative research:  Withdrawal from treatment with no further 
measurement of correlative research (note this will affect the primary endpoint but will not 
affect correlative research studies that have already been collected). 
• Treatment, correlative research, and follow-up:  Withdrawal from treatment, correlative 
research, and follow-up period (allowing no collection of off-study data, such as subsequent 
anti-cancer therapy, progression if not determined during study treatment, and survival).  
In the event of withdrawal of consent, the study staff and/or investigator must make every effort 
to ascertain the types(s) of consent withdrawn.  Full withdrawal of consent would include all 
3 types (treatment, correlative research, and follow up), and will be the default withdrawal unless 
otherwise affirmed by the subject.  
After discontinuation of treatment (unless there is full withdrawal of consent), the End of 
Treatment and Follow-up visit procedures should continue as described in Section 9 
(Study Calendar).  These patients will be followed up for efficacy outcomes until the end of the 
study.  They should be followed for safety until resolution or permanent sequelae of all toxicities 
attributable to the study drug.  
4.2.2 Discontinuation of Study Therapy after CR  
Discontinuation of study treatment may be considered for patients who have attained a 
confirmed CR that have been treated for at least 24 weeks with pembrolizumab and had at least 
2 treatments with pembrolizumab beyond the date when the initial CR was declared.  Future 
restarting of pembrolizumab would be expected to be administered as standard-of-care treatment, 
since pembrolizumab is FDA-approved for NSCLC. Assessments should proceed per section 9. 

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5. 
INVESTIGATIONAL AGENT INFORMATION (Pembrolizumab) 
5.1 
 Investigational Agent/Device/Procedure   
Refer to the most up-to-date Investigator’s Brochure (IB)/approved labeling for detailed 
background information on Pembrolizumab and see Section 2.2 for summary.  
Pembrolizumab 200 mg will be administered as a 30-minute intravenous infusion every 3 weeks 
for up to 24 months of therapy until disease progression without clinical benefit or unacceptable 
toxicity.  
For each individual trial, clinical supplies are to be stored in accordance with specific 
instructions on the label.  
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 
investigational product in accordance with the protocol and any applicable laws and regulations.  
Pembrolizumab will be provided by Merck as summarized in Table 2.  
Table 2 Product Descriptions 
Product Name & Potency 
Dosage Form 
Pembrolizumab 100 mg/ 4 mL 
Solution for Injection 
Packaging and Labeling Information 
Supplies will be labeled in accordance with regulatory requirements.  
Clinical Supplies Disclosure 
This trial is open-label; therefore, the patient, the trial site personnel, the Sponsor and/or 
designee are not blinded to treatment.  Drug identity (name, strength) is included in the label 
text; random code/disclosure envelopes or lists are not provided.  
5.2 
Availability 
Merck & Co (Kenilworth, NJ) is providing pembrolizumab.  
5.3 
Agent Ordering 
Refer to Merck order form for instructions to order drug or contact: 
Dana Gardener, Merck Research Laboratories 
351 N Sumneytown Pike UG2CD-30  
North Wales, PA  19454-2505 
Phone: 267-305-5403  |  Fax: 267-305 6534  |  Email: dana_gardner@merck.com.  
  
5.4 
Agent Accountability 
Storage and Handling Requirements 
Clinical supplies will be stored in a secure, limited-access location under the storage conditions 
specified on the label.  Receipt and dispensing of trial medication will be recorded by an 

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authorized person at the trial site.  Clinical supplies may not be used for any purpose other than 
that stated in the protocol.  
Returns and Reconciliation 
The investigator is responsible for keeping accurate records of the clinical supplies received from 
Merck or designee, the amount dispensed to and returned by the patients and the amount 
remaining at the conclusion of the trial.  
Upon completion or termination of the study, all unused and/or partially used investigational 
product will be destroyed at the site per institutional policy.  It is the Investigator’s responsibility 
to arrange for disposal of all empty containers, provided that procedures for proper disposal 
have been established according to applicable federal, state, local and institutional guidelines and 
procedures, and provided that appropriate records of disposal are kept.  

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6. 
DOSE MODIFICATIONS AND TOXICITY MANAGEMENT 
6.1 ADVERSE EVENT MANAGEMENT  
Adverse events (both non-serious and serious) associated with pembrolizumab exposure may 
represent an immunologic etiology.  These adverse events may occur shortly after the 1st dose or 
several months after the last dose of treatment and may affect more than one body system 
simultaneously.  Therefore, early recognition and initiation of treatment is critical to reduce 
complications.  For suspected irAEs, ensure adequate evaluation to confirm etiology or exclude 
other causes (i.e. disease progression or bacterial/viral infection).  Additional procedures or tests 
such as bronchoscopy, endoscopy, skin biopsy may be included as part of the evaluation.  It is 
generally recommended to involve other specialists for grade 3 and 4 events.  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.  Dose 
modification and toxicity management guidelines for irAEs associated with pembrolizumab are 
provided in Table 3 of section 6.2. 
Subjects should receive appropriate supportive care measures as deemed necessary by the 
treating investigator.  Suggested supportive care measures for the management of adverse events 
with potential immunologic etiology are outlined below.  Where appropriate, these guidelines 
include the use of oral or intravenous 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. The treatment guidelines are intended to be applied when the 
investigator determines the events to be related to pembrolizumab.  In cases in which 
intravenous steroids are suggested below, oral steroids may be administered instead, if clinically 
appropriate. Occasionally, more powerful immunosuppressants such as infliximab or 
mycophenolate mofetil may be necessary to control immune-related adverse events.  
6.2 Dose Modification Guidelines for Drug-Related Adverse Events 
Pembrolizumab should be withheld for severe or life-threatening AEs as per Table 3 below. 
These are considered guidelines, but drug administration can also be held for events not 
described below at the treating physician’s discretion.  If the recommendation is for trial 
treatment to be permanently discontinued, this should be strongly considered, but drug 
rechallenge may be allowed with prior approval from the PI. 

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7. 
ADVERSE EVENTS AND REPORTING PROCEDURES 
7.1 
Potential Adverse Events 
Refer to the most up-to-date Investigator’s Brochure (IB)/approved labeling for additional 
adverse event information on Pembrolizumab.  
Safety 
Refer to Section 2.2.2.5 Clinical Safety for further details.  
Important Safety Considerations- Refer to the most up-to-date Investigator’s Brochure (IB) 
There are no specific safety concerns based on the results of nonclinical studies.  Pembrolizumab 
has the same mechanism of action as other anti–PD-1 monoclonal antibodies.  Preclinical studies 
have suggested similar potency, and pharmacokinetic (PK) modeling has suggested similar 
human PK in the class.  Accordingly, the AEs observed with other anti–PD-1 antibodies may 
serve as an indicator for the AEs to expect in cancer subjects.  Furthermore, AEs from other 
immunotherapies for cancer were considered in the Pembrolizumab Program (MK-3475) Event 
of Clinical Interest Guidance Document.  
Pembrolizumab is generally well tolerated and demonstrates a favorable safety profile in 
comparison to chemotherapy.  Pembrolizumab is an immunomodulatory agent, and based on this 
mechanism of action, immune mediated adverse events are of primary concern.  Important 
identified risks for pembrolizumab are of an immune mediate nature, including:  pneumonitis;  
colitis;  hepatitis;  nephritis;  endocrinopathies that include hypophysitis (including 
hypopituitarism and secondary adrenal insufficiency);  thyroid disorder (hypothyroidism, 
hyperthyroidism);  and Type I diabetes mellitus; uveitis; myositis; Guillain-Barré syndrome;  
pancreatitis;  myocarditis;  severe skin reactions including Stevens-Johnson syndrome (SJS) and 
toxic epidermal necrolysis (TEN), some with fatal outcome;  and “solid organ transplant 
rejection following pembrolizumab treatment in donor organ recipients” (risk applicable to 
postmarketing setting only, as such patients are currently excluded from Merck clinical trials 
with pembrolizumab).  The risk profile for pembrolizumab also included 2 important potential 
risks – ie, myasthenic syndrome and increased risk of severe complications (such as early severe 
graft versus host disease and veno- occlusive disease) of allogeneic transplant in patients with 
hematologic malignancies who have previously been treated with PD-1 inhibitors.  Two new 
important identified risks also included “encephalitis” and “sarcoidosis.’  The majority of 
immunemediated adverse events were mild to moderate in severity, were manageable with 
appropriate care, and rarely required discontinuation of therapy.  Further details around 
frequency, reporting, and management of immune-related adverse events (irAEs) are described 
in other section of protocol and the most up-to-date Investigator’s Brochure.  In addition to the 
previously noted identified risks, infusion-related reactions are a risk but are not considered 
immune mediated; these are further described below.  
Infusion Reactions 
Infusion reactions have been reported with pembrolizumab at a rate of 2.5%; these were 
generally Grade 1 and 2 and the majority were considered related by the Investigator.  One event 
of Grade 4 anaphylaxis has been reported.  Infusion reactions may present as allergic reaction, 
serum sickness, infusion reaction, cytokine release syndrome, or anaphylaxis.  Mild infusion 
reactions can generally be treated with interruption of the infusion and medical intervention 
including IV fluids, antihistamines, nonsteroidal anti-inflammatory drugs, acetaminophen, and 

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narcotics as needed.  More severe or life threatening reactions may require pressors, 
corticosteroids, and epinephrine.  Please see Table 1 of Section 4:  Treatment Guidelines for 
Infusion Reactions Associated with Administration of Pembrolizumab. 
7.1.1 Assessing and Recording Adverse Events 
An adverse event is defined as any untoward medical occurrence in a patient administered trial 
treatment and which does not necessarily have to have a causal relationship with this treatment.  
An adverse event can therefore be any unfavorable and unintended sign (including an abnormal 
laboratory finding, for example), symptom, or disease temporally associated with the use of a 
medicinal product or protocol-specified procedure, whether or not considered related to the 
medicinal product or protocol-specified procedure.  Any worsening (ie, any clinically significant 
adverse change in frequency and/or intensity) of a preexisting condition that is temporally 
associated with the use of trial treatment, may also be considered an adverse event.  
Changes resulting from normal growth and development that do not vary significantly in 
frequency or severity from expected levels are not to be considered adverse events.  Examples of 
this may include onset of menopause occurring at a physiologically appropriate time.  
Adverse events may occur during the course of the use of Merck product in clinical trials, or as 
prescribed in clinical practice, from overdose (whether accidental or intentional), from abuse and 
from withdrawal.  
Progression of the cancer under study is not considered an adverse event.  
Adverse events may occur during the course of the use of trial treatment or within the follow-up 
period specified by the protocol.  
Adverse events may also occur in screened patients during any pre-allocation baseline period as 
a result of a protocol-specified intervention, including washout or discontinuation of usual 
therapy or a procedure.  
All adverse events should be recorded from the time the consent form is signed through the 
end of treatment, and at each examination on the Adverse Event CRFs.  The reporting 
timeframe for adverse events meeting any serious criteria is described in Section 7.2.  The 
investigator may follow subjects with non-serious adverse events for outcome.  
Adverse events may not be collected for subjects during the pre-screening period (for 
determination of archival tissue status) as long as that subject has not undergone any 
protocol-specified procedure or intervention.  If the subject requires a blood draw, fresh tumor 
biopsy, etc, the subject is first required to provide consent to the main study and AEs should be 
captured according to guidelines for standard AE reporting.  
7.1.2 Evaluating Adverse Events 
Adverse events will be graded according to CTCAE v4.03.  Both Serious and 
Non-Serious Adverse Events will be clearly noted in source documentation and listed on 
study specific Case Report Forms (CRFs).  The Protocol Director (PD) or designee will 
assess each Adverse Event (AE) to determine whether it is unexpected according to the 
Informed Consent, Protocol Document, or Investigator’s Brochure, and related to the 
investigation.  Toxicities should be characterized in terms regarding seriousness, 
causality, toxicity grading, duration, and action taken with regard to trial 
treatment.  All AEs of unknown etiology associated with pembrolizumab exposure 

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should be evaluated to determine if it is possibly an event of clinical interest (ECI) of a 
potentially immunologic etiology (termed immune-related adverse events, or irAEs).  
Patients with a trial treatment-related AE of Grade ≥ 1 and SAEs should be followed until 
the resolution of the AE to Grade 0 to 1, 30 days from last trial treatment, or until the 
beginning of a new anti-neoplastic therapy, whichever occurs first.  
7.1.2.2 Definition of an Overdose for This Protocol and Reporting of Overdose to the Sponsor 
and to Merck 
For purposes of this trial, an overdose of pembrolizumab is considered as any dose of 1,000 mg 
or greater (≥ 5-fold the indicated dose).  No specific information is available on the treatment of 
overdose of pembrolizumab.  Appropriate supportive treatment should be provided if clinically 
indicated.  In the event of overdose, the subject should be observed closely for signs of toxicity.  
Appropriate supportive treatment should be provided if clinically indicated.  
If an adverse event(s) is associated with (“results from”) the overdose of a Merck product, 
the adverse event(s) may be reported as a serious adverse event, even if no other seriousness 
criteria are met.  
If a dose of Merck’s product meeting the protocol definition of overdose is taken without any 
associated clinical symptoms or abnormal laboratory results, the overdose may be reported 
as a non-serious Event of Clinical Interest (ECI), using the terminology “accidental or 
intentional overdose without adverse effect.” 
A report of overdose with and without an adverse event should be reported to the Sponsor and to 
Merck Global Safety (Attn:  Worldwide Product Safety; FAX 215-661-6229). 
7.1.2.3 Reporting of Pregnancy and Lactation to the Sponsor and to Merck 
Although pregnancy and infant exposure during breast feeding are not considered adverse 
events, the investigators or their designees should report any pregnancy or lactation in a subject 
(spontaneously reported to them) that occurs during the trial.  
Pregnancies and lactations that occur after the consent form is signed but before treatment 
allocation should be reported by the investigator if they cause the subject to be excluded from the 
trial, or are the result of a protocol-specified intervention, including but not limited to washout or 
discontinuation of usual therapy or a procedure.    
Pregnancies and infant exposure during breast feeding that occur from the time of treatment 
allocation through the duration of trial treatment should be reported by the investigator.  All 
reported pregnancies may 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 should be 
reported as serious events (Important Medical Events).  If the pregnancy continues to term, 
the outcome (health of infant) may also be reported.  
Such events should be reported to the Sponsor and to Merck Global Safety  
(Attn: Worldwide Product Safety; FAX 215-661-6229) 

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7.1.3 Serious Adverse Events and Events of clinical interest 
A serious adverse event is any adverse event occurring at any dose or during any use of 
pembrolizumab that: 
• Results in death; 
• Is life threatening; 
• Results in persistent or significant disability/incapacity; 
• Results in or prolongs an existing inpatient hospitalization; Hospitalizations for elective 
medical or surgical procedures or treatments planned before enrollment in the treatment 
plan or routine check-ups are not SAEs by this criterion.  Admission to a palliative unit or 
hospice care facility is not considered to be a hospitalization.  
• Is a congenital anomaly/birth defect; 
• Is medically significant, may not result in death, not be life threatening, or not require 
hospitalization may be considered a serious adverse event when, based upon appropriate 
medical judgment, the event may jeopardize the patient and may require medical or 
surgical intervention to prevent one of the outcomes listed previously 
• Note: In addition to the above criteria, adverse events meeting either of the below 
criteria, although not serious per ICH definition, may be reportable to the Merck as SAEs 
to meet certain local requirements.  
● 
Is a new cancer (that is not a condition of the study); 
● 
Is associated with an overdose.  
Events of clinical interest (ECI) for this trial include: 
1. An overdose of Merck product, as defined in Section 7.1.2.2 - Definition of an Overdose for 
This Protocol and Reporting of Overdose to the Sponsor, 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 3 X ULN and an elevated 
total bilirubin lab value that is greater than or equal to 2 X ULN and, at the same time, an 
alkaline phosphatase lab value that is less than 2 X ULN, 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.  
Stanford Specific Reporting 
All Serious Adverse Events (SAEs) should be tracked until resolution of the SAE to 
Grade 0 to 1;  until 30 after the last dose of the study treatment;  or until the beginning of a new 
anti-neoplastic therapy, whichever comes earlier.  SAEs CTCAE Grade 3 and above (defined 
above), and all subsequent follow-up reports will be reported to the Stanford Cancer Institute 
Data and Safety Monitoring Committee (DSMC) using the study specific CRF regardless of the 
event’s relatedness to the investigation.  Following review by the DSMC, events meeting the 
IRB definition of ‘Unanticipated Problem’ will be reported to the IRB using eProtocol within 10 
working days of DSMC review, or within 5 working days for deaths or life-threatening 
experiences.  

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Merck Specific Reporting 
For the time period beginning when the consent form is signed until treatment allocation, any 
serious adverse event or ECI, or follow-up to a serious adverse event or ECI, including death due 
to any cause other than progression of the cancer under study, that occurs to any subject should 
be reported to the Sponsor and to Merck Global Safety if it causes the subject to be excluded 
from the trial, or is the result of a protocol-specified intervention, including but not limited to 
washout or discontinuation of usual therapy or a procedure.  
For the time period beginning at treatment allocation through 30 days following cessation of 
treatment, any serious adverse event or ECI, or follow up to a serious adverse event or ECI 
including death due to any cause other than progression of the cancer under study whether or not 
related to the Merck product, should be reported to the Sponsor and Merck Global Safety.  
Any serious adverse event must be reported within 24 hours from the time the investigator 
is notified to the Sponsor and within 2 working days to Merck Global Safety.  
SAE reports should be forwarded to the Merck Global Safety facsimile number:  +1-
215-661-6229 
A copy of all 15-Day Reports and Annual Progress Reports is submitted as required by FDA, 
European Union (EU), Pharmaceutical and Medical Devices agency (PMDA) or other local 
regulators.  Investigators may cross reference this submission according to local regulations to 
the Merck Investigational Compound Number (IND, CSA, etc.) at the time of submission.  
Additionally investigators should submit a copy of these reports to Merck & Co., Inc (Attn: 
Worldwide Product Safety; FAX +1-215-661-6229) at the time of submission to FDA.  
8. 
CORRELATIVE/SPECIAL STUDIES  
Additional/alternative correlative research may be performed pending development of new 
technology and scientific advances.  
8.1 OPTIONAL TUMOR BIOPSY for Correlative Studies (CAPP-Seq, PD-L1 IHC, 
CIBERSORT) 
8.1.1 
Collection of Specimen(s) 
Patients may undergo an optional fresh tumor tissue biopsy prior to trial treatment to perform 
correlative studies including CAPP-Seq and CIBERSORT. Additional/alternative correlative 
research may be performed pending development of new technology and scientific advances.  If 
patient agrees to an optional fresh tumor biopsy, core biopsies (generally CT-guided or 
bronchoscopic) are preferred- if the patient needs a surgical approach or excisional approach for 
a standard of care related reason, this tissue can be used as long as the patient has already 
consented for the study.  
Fine needle aspiration, thoracentesis, or other specimens without tissue architecture preservation 
are generally not preferred but may be used if a core needle biopsy is contraindicated.  
At the point of the optional biopsy, a goal of at least 4 cores should be obtained once tumor yield 
is identified by a cytotechnologist.  The proceduralist may take additional cores if it is not felt to 
significantly increase the risk to the patient.  It is estimated that 2 cores will be snap-frozen, 

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separately, and 2 cores will be sent to pathology for formalin fixation and later recovery for 
correlative work.  If a patient undergoes an optional tumor biopsy, the following will be planned: 
• CAPP-Seq: Paraffin-embedded tissue will be sent for DNA sequencing to Stanford 
Molecular Pathology Laboratory (STAMP, Solid Tumor Actionable Panel, Stanford 
Hospital) or Diehn/Alizadeh labs (Stanford Campus) to establish patient specific 
mutational markers (> 95% of NSCLC patients have an identifiable marker in the panel).  
These can include single nucleotide variants and rearrangements such as ALK, ROS1, 
and RET.  
 
• CIBERSORT34: Fresh or snap frozen tissue will be sent to Alizadeh/Diehn labs 
(Stanford Campus) to undergo total RNA extraction and reverse transcription, then 
analyzed by microarray.  The data will be processed and scored using the CIBERSORT 
algorithm (CIBERSORT.stanford.edu).  A lung cancer population CIBERSORT 
algorithm will be established54, as the CIBERSORT algorithm can robustly identify an 
“unknown” new tumor type.  Individual populations of different subtypes of immune cell 
infiltrate subsets will be quantitated and an overall “immune score” will be generated.  

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• PD-L1 IHC33: Paraffin embedded tissue may be sent per standard protocol as standard of 
care FDA approved test if not already done.  This test does not have to be sent on the 
optional tumor biopsy as part of this study but could have been sent on archival tissue as 
per standard of care.  
8.1.2 
Handling of Specimens(s) 
• Once the biopsy is obtained it will be placed in a container with dry ice and transported to 
the Alizadeh/Diehn labs on the same day.  Part of the tissue will be sent to the Stanford 
Pathology Histology section in formalin for paraffin embedding.  PD-L1 IHC should 
have been sent previously on archival tumor as part of standard of care.  The rest of the 
tissue will be directly processed by Diehn/Alizadeh laboratories for Capp-Seq, 
CIBERSORT, and other studies that do not require paraffin embedding.  The samples 
will be stored in Diehn/Alizadeh laboratories.   
8.1.3 
Shipping of Specimen(s) 
• 
Biopsy will be transported on ice to the Diehn/Alizadeh lab on the same day.  
• 
PD-L1 testing will be performed per standard of care FDA approved test and may 
have been sent previously on archival tumor as part of standard of care.  
8.1.4  
Site(s) Performing Correlative Study 
Diehn/Alizadeh lab (Stanford Campus) will be performing CAPP-Seq and CIBERSORT.  If 
additional correlative work is proposed pending scientific advances, this may require the 
cooperation of other laboratories. 
8.1.5  Coding of specimens for privacy protection 
All specimens will be de-identified with a unique code identifier.  
8.2 BLOOD SAMPLES for Correlative Studies (CAPP-Seq ctDNA) 
8.2.1 Collection of Specimen(s) 
Blood will be drawn (goal of 30 to 50 mL whole blood at each timepoint) at the timepoints listed 
in Section 9 Study Calendar.  
The blood will be brought to the Diehn/Alizadeh labs as soon as possible, but always within 
4 hours of collection, for further processing.  
8.2.2 Handling of Specimens(s) 

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Blood samples will be hand-transported on ice to the Diehn/Alizadeh lab within 4 hours of draw.  
8.2.3 Shipping of Specimen(s) 
We do not anticipate shipping of specimens.   
8.2.4 Site(s) Performing Correlative Study 
CAPP-Seq will be performed by Diehn/Alizadeh labs (Stanford Campus).  CAPP-Seq result will 
be reported as circulating tumor DNA (ctDNA) as a percentage of total circulating free DNA and 
also as ctDNA titer (a continuous variable in units pg/mL).  The assay can identify less than 
0.005% ctDNA, though many advanced NSCLC tumors have greater than 1% ctDNA, resulting 
in a wide dynamic range for analysis. If additional correlative work is proposed pending 
scientific advances, this may require the cooperation of other laboratories. 
8.2.5 Coding of specimens for privacy protection 
All specimens will be de-identified with a unique code identifier.  
 

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• Treatment-Related Toxicity Delay: If a patient has a treatment delay due to treatment-related adverse event, the frequency of tumor imaging and correlative studies blood 
collection should continue to be performed at the frequency according to the stage of the study in which the cycle was interrupted, when feasible.  A dosing interruption for a 
treatment-related adverse event is allowed for 12 weeks from the date the scheduled dose was missed.  After approximately 21 days from date the scheduled dose was missed, 
the cycle should be recorded as completed at the initial "ideal" date and the next cycle initiated, even if drug is held and assessments were not performed to allow for ongoing 
scheduled correlatives.  
• Other delay: While the routine window for cycle is ± 3 days, a scheduled cycle (including drug administration, imaging, and correlative blood draw) may be additionally 
delayed for up to 21 days due to patient/physician preference or in the case of medical / surgical events or logistical reasons not related to trial treatment (eg, elective surgery, 
unrelated medical events, patient vacation, and/or holidays).  An interruption in this scenario is allowed for 21 days from date the scheduled cycle was missed.  Delay of cycles 
within Stage 1 of the trial is allowed but discouraged.  
• In order to minimize blood draws, if the patient had a dose interruption for any reason, the frequency of tumor imaging and correlative studies blood collection can be extended 
up to 21 days to allow these to coincide with other associated visit assessments/procedures.  This window can be further shortened/extended for unusual circumstances after 
discussion with the PI/co-PI.  
b Screening: Results of a test performed prior to the patient signing consent as part of routine clinical management are acceptable in lieu of a screening test if performed within 
the specified time frame (28 days).  Screening tests are allowable on day of first trial treatment as long as performed prior to trial treatment. 
c Written informed consent should be obtained prior to any study-specific procedure.  
d Medical history should be taken including details of prior cancer treatment.  
e The investigator or qualified designee should review medication use at screening, including any protocol-specified washout requirement, and should record medication, if any, 
taken by the patient during the trial.  
f Pembrolizumab 200 mg should be administered as a 30 minute IV infusion (± 3 days).  Trial treatment should be administered on Day 1 of each cycle after all 
procedures/assessments have been completed as detailed on the Study Calendar, except where noted.  
g The investigator or qualified designee should assess each patient to evaluate for potential new or worsening AEs at each cycle and more frequently if clinically indicated.  
Adverse events should be graded and recorded throughout the study according to NCI CTCAE v4.03.  
h The investigator or qualified designee should perform a physical exam at screening and prior to trial treatment administration.   
i 
Oxygen saturation should be measured at least at screening.  
k Perform either urine or serum pregnancy test on women of childbearing potential prior to first dose of trial treatment.  
m Safety Laboratory: After Cycle 1, safety lab samples (ie, CBC+diff, complete metabolic panel) can be collected up to 3 days prior to the scheduled time point.  Laboratory 
results should be known and acceptable prior to dosing (except for thyroid function tests, eg, T3, T4, TSH).  Complete blood count with differential (eg, Platelet, hemoglobin, 
white blood cell count and differential).  Chemistries include albumin;  alkaline phosphatase;  alanine aminotransferase;  aspartate aminotransferase;  carbon 
dioxide/bicarbonate;  calcium;  creatinine;  chloride;  glucose;   potassium;  sodium;  total bilirubin;  total protein.  
n Thyroid function tests should be performed at screening and then every 2 cycles (6 weeks) starting with Cycle 3 through Cycle 9.  They can be repeated as clinically indicated. 
o Body tumor imaging should be performed with computed tomography, with IV contrast when possible.  The initial tumor imaging should be performed within 30 days prior to 
the first dose of trial treatment.  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 trial treatment.  The same method of assessment should be used to characterize each identified and reported lesion at 
baseline and during follow-up.  For Stage I of treatment phase (Cycle 1 through 8), tumor imaging should be performed every 6 weeks ( ± 7 days).  For Stage II of treatment 
phase (Cycle 9 through 17), tumor imaging should be performed every 9 weeks (± 7 days).  For Stage III of treatment phase (≥ Cycle 18), tumor imaging should be performed 
every 12 weeks ( ± 7 days).  It is at the discretion of the investigator or qualified designee should more frequent imaging be clinically necessary.  Local reading (investigator 
assessment) should be used to determine eligibility and for patient management.  After the first documentation of progression (if the patient has clinical benefit) per RECIST 
v1.1, repeat imaging for confirmation is suggested given possibility of pseudo-progression.  Confirmatory imaging may be performed as early as 28 days later;  alternately, the 
scan performed at the next scheduled timepoint may be used as confirmation. 
p All patients must have a brain MRI (preferred) or head CT with contrast at baseline within 12 weeks prior to enrollment.  Patients with known brain metastases at baseline 
must have a brain MRI (preferred) or head CT within 28 days prior to enrollment.  Patients with known untreated brain metastases at baseline should have repeat imaging at the 
same interval as listed in footnote q for body tumor imaging.  

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q If the patient has consented to the optional tumor biopsy, this should be performed prior to first trial treatment.  Archival tissue may be retrieved when available.  Needle biopsy 
is preferred; cytology and fine needle aspiration is generally not sufficient but may be used.  Patients who initially receive clinical benefit from pembrolizumab but then come 
off study for progression may be offered a biopsy at the time of progression.  If the patient does consent to repeat biopsy at progression, this should ideally be performed within 
30 days of the end of treatment visit and prior to initiation of new anti-cancer systemic therapy. 
r Correlative blood study collection should be obtained in the following schedule (± 3 day window except where noted):  prior to first dose of trial treatment;  within 30 minutes 
(± 10 minutes) after completion of first dose of trial treatment;  pretreatment at Cycle 2 (~Week 4);  and Cycle 3 (~Week 7).  For the remaining part of Stage I of treatment 
phase, correlative studies blood collection should be collected every 6 weeks (± 3 days).  For Stage II of treatment phase (Cycle 9 through 17), correlative blood studies should 
be collected every 9 weeks (± 3 days).  For Stage III of treatment phase  (≥ Cycle 18), correlative blood studies should be collected every 12 weeks (± 3 days).  Correlative 
blood studies should be collected at the end of treatment visit (± 3 days).  All efforts should be made to have the correlative studies blood collection be performed at a similar 
time to imaging studies.  
s During the follow-up phase, all patients should be contacted every 12 weeks (± 2 weeks) to evaluate survival status from the time of the end of treatment visit until death, 
withdrawal of follow-up consent, or the end of the study, whichever occurs first.  For patients who came off-study for reasons other than disease progression, the following 
assessments/procedures should be strongly recommended every 12 weeks (± 2 weeks) until disease progression, initiating a cancer treatment, withdrawing consent or becoming 
lost to follow-up: tumor imaging and correlative studies blood collection.  In addition, anticancer therapy status, concomitant medication review, review of adverse events, 
directed physical exam, vital signs and weight, ECOG performance status may be performed if possible.  
t. End of treatment visit will be marked by confirmed radiographic disease progression without clinical benefit; unacceptable adverse events;  completion of 24 months of 
therapy;  or other event requiring trial treatment discontinuation.  Repeat imaging is recommended if patient has end of treatment visit for reason other than progression if 
imaging performed ≥ 6 weeks prior.  

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10. MEASUREMENTS 
Primary Outcome Measure:  To correlate circulating tumor DNA (ctDNA) levels measured 
using Cancer Personalized Profiling by deep Sequencing (CAPP-Seq) with radiographic 
tumor assessments using RECIST v1.1 criteria in patients with metastatic NSCLC treated 
with pembrolizumab 
Title: Circulating tumor DNA (CAPP-Seq)  
Time Frame:  See Study Calendar (Section 9) 
Safety Issue:  Is this outcome measure assessing a safety issue?  No 
10.1  Primary and Secondary Outcome measures 
10.1.1 Primary Outcome 
• To correlate circulating tumor DNA (ctDNA) levels measured using Cancer Personalized 
Profiling by deep Sequencing (CAPP-Seq) with radiographic tumor assessments using 
RECIST v1.1 criteria in patients with metastatic NSCLC treated with pembrolizumab  
• Relevant Subset: All patients treated with at least one dose of pembrolizumab, have at 
least one evaluable ctDNA measurement, and at least one follow-up imaging.  
• Measurement Definition  
o ctDNA measured as percentage of total circulating free DNA and also as ctDNA titer 
(continuous variable in units pg/mL) 
o Radiographic tumor assessments using RECIST v1.1 criteria (sum of 
longest diameters (SLD) of up to 5 target lesions, measured in mm or cm)  
• Measurement Methods 
o ctDNA levels measured using Cancer Personalized Profiling by deep Sequencing 
(CAPP-Seq)  
o Radiographic tumor assessments using RECIST v1.1 criteria (Appendix B)56 
• Measurement Timepoints 
o Refer to Study Calendar Section 9 
• Response Review 
o Investigators on the trial will perform tumor measurements based on 
RECIST v1.1 criteria.  There will be no independent review.  
10.2.1 Secondary Outcome 
10.2.1.1 
To determine the overall response rate using RECIST v1.1 criteria in 
patients with metastatic NSCLC treated with pembrolizumab 
• Relevant Subset: All patients treated with at least one dose of pembrolizumab.  
• Measurement Definition  
o Proportion of complete responses + partial responses as determined by RECIST v1.1 
criteria 
• Measurement Methods 
o RECIST version 1.1 criteria  (Appendix B) 

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• Measurement Timepoints 
o Refer to Study Calendar Section 9 for frequency of imaging 
10.2.1.2 
 To determine the progression-free survival using RECIST v1.1 criteria in 
patients with metastatic NSCLC treated with pembrolizumab 
• Relevant Subset: All patients treated with at least one dose of pembrolizumab.  
• Measurement Definition  
o Progression free survival measured from the time of first treatment with 
pembrolizumab to the time of radiographic progression, unequivocal clinical 
progression, or death from any cause, whichever comes earlier 
• Measurement Methods 
o RECIST v1.1 criteria  (Appendix B)56 
• Measurement Timepoints 
o Refer to Study Calendar Section 9 for frequency of imaging 
10.2.1.3 
To determine the safety and tolerability of pembrolizumab in patients with 
metastatic NSCLC 
• Relevant Subset: All patients enrolled on study who received trial treatment.  
• Measurement Definition  
o Incidence of adverse events 
• Measurement Methods 
o Common Terminology Criteria for Adverse Events (CTCAE v4.03) 
• Measurement Timepoints  
o From time of enrollment through the end-of-treatment visit.  Some patients will have 
adverse event collection during follow-up phase. 

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11. 
REGULATORY CONSIDERATIONS 
Compliance with Trial Registration and Results Posting Requirements 
Under the terms of the Food and Drug Administration Modernization Act (FDAMA) and the 
Food and Drug Administration Amendments Act (FDAAA), the Sponsor of the trial is solely 
responsible for determining whether the trial and its results are patient to the requirements for 
submission to the Clinical Trials Data Bank, http://www.clinicaltrials.gov.  Information posted 
will allow patients to identify potentially appropriate trials for their disease conditions and 
pursue participation by calling a central contact number for further information on appropriate 
trial locations and trial site contact information.  
11.1 
Institutional Review of Protocol 
The protocol, the proposed informed consent and all forms of participant information related to 
the study (eg, advertisements used to recruit participants) will be reviewed and approved by the 
Stanford IRB and Stanford Cancer Institute Scientific Review Committee (SRC).  Any changes 
made to the protocol will be submitted as a modification and will be approved by the IRB prior 
to implementation.  The Protocol Director will disseminate the protocol amendment information 
to all participating investigators.  
11.2 
Data and Safety Monitoring Plan:   
The Stanford Cancer Institute Data and Safety Monitoring Committee (DSMC) will be the 
monitoring entity for this study.  The DSMC will audit study-related activities to determine 
whether the study has been conducted in accordance with the protocol, local standard operating 
procedures, FDA regulations, and Good Clinical Practice (GCP).  This may include review of the 
following types of documents participating in the study: regulatory binders, case report forms, 
eligibility checklists, and source documents.  In addition, the DSMC will regularly review 
serious adverse events and protocol deviations associated with the research to ensure the 
protection of human patients.  Results of the DSMC audit will be communicated to the IRB and 
the appropriate regulatory authorities at the time of continuing review, or in an expedited 
fashion, as needed.  
11.3 
Data Management Plan 
Case Report Forms (CRFs) are printed or electronic documents designed to record all 
protocol-related information on each trial participant.  CRFs should summarize the clinical 
findings and observations necessary to ensure safety of participants on the study, and to 
document the study outcomes.  CRFs are required by the SRC for all Interventional studies.  
CRF design and creation must be completed prior to enrollment of the first participant.  The 
Protocol Director, or his/her designee, will prepare and maintain adequate and accurate 
participant case histories with observations and data pertinent to the study.  Study specific Case 
Report Forms (CRFs) will document treatment outcomes for data analysis.  Case report forms 
will be developed using the ONCORE_ database system and will be maintained by the research 
team.  CRFs will be kept in a locked office, only accessible to the research team.  

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12. 
STATISTICAL CONSIDERATIONS 
12.1 
Statistical Analysis Plan Summary 
This is an open-label non-randomized single-arm treatment trial of pembrolizumab in NSCLC 
patients, with a primary endpoint of evaluation of pharmacodynamics biomarker, circulating 
tumor DNA and its correlation with radiographic tumor assessments using RECIST v1.1 criteria.  
There is no statistical stopping rule is planned.  
12.2 Primary Analysis and Sample size justification 
The primary analysis will correlate circulating tumor DNA (ctDNA) levels measured using 
Cancer Personalized Profiling by deep Sequencing (CAPP-Seq) with radiographic tumor 
assessments using RECIST v1.1 criteria in patients with metastatic NSCLC treated with 
pembrolizumab.  The primary analysis population will include all patients treated with at least 
one dose of pembrolizumab, have at least one evaluable ctDNA measurement, and at least one 
follow-up imaging.  The primary explanatory variables are percent ctDNA and ctDNA titer (a 
continuous variable in units pg/mL).  The correlation of percent ctDNA (and DNA titer) with 
sum of longest diameter of tumor target lesions (continuous variable in mm or cm, RECIST 1.1) 
will be calculated using Kendall correlation.  The correlation of ctDNA (and DNA titer) with 
overall response category (RECIST v1.1) will be calculated using the Wilcoxon rank sum test.  
P-values will be reported without correction for multiple testing, however the number of 
statistical tests planned and/or performed will be included in reports of this study.  
12.2.1 Sample Size 
25 NSCLC patients 
Accrual estimate:  We estimate that we will enroll 25 eligible and evaluable metastatic NSCLC 
patients within an 18-month period.  
12.2.2 Sample size justification 
Clinically validated differences in ctDNA have not been established to date, but the variability 
over time does appear to closely follow tumor volume as demonstrated by previously-published 
data1.  This may vary across tumor types.  25 patients would provide 80% power to detect a 
correlation of 0.64 with ctDNA and radiographic RECIST 1.1-based tumor assessments when 
using a Kendall correlation.  
12.2.3 Effect size justification 
Clinically validated differences in ctDNA have not been established to date.  Previous studies 
have shown pretreatment ctDNA levels correlation with CT imaging in 9 patients (R2 = 0.89, 
p = 0.0002) and ctDNA levels correlation with CT imaging during therapy (R2 = 0.95 in a single 
patient and R2 = 0.85 in a single patient).1  Here, we aim for a slightly lower correlation given the 
larger sample size.  
12.3 Secondary Analysis Statistical Plan: 
12.3.1 Summary of Objectives 
 To determine the overall response rate using RECIST v1.1 criteria in patients with metastatic 
NSCLC treated with pembrolizumab 
 To determine the progression-free survival using RECIST v1.1 criteria in patients with 
metastatic NSCLC treated with pembrolizumab 

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 To determine the safety and tolerability of pembrolizumab in patients with metastatic 
NSCLC 
12.3.2 Populations Defined  
• See section 10.1.1 for primary endpoint population. 
• The safety population includes all patients enrolled on the study who receive 
pembrolizumab.  
• The efficacy population includes all patients treated with at least one dose of study drug.  
• The correlative study population (CIBERSORT, etc) includes all patients treated with 
at least one dose of pembrolizumab, have at least one evaluable correlative study 
assessment (ie, undergone optional tumor biopsy), and at least one follow-up imaging 
study.   
12.3.3 Statistics Defined (Descriptive and for Secondary Objectives) 
Demographic variables (such as age) and baseline tumor and treatment characteristics will be 
summarized by descriptive statistics.  The correlation of dichotomies will be assessed using 
Fisher's exact test.  The correlation of continuous or ordinal variables with a dichotomy will be 
made using Wilcoxon rank sum test.  The correlations of two continuous variables will be 
performed using Kendall correlation.  Adverse events will be tabulated by category and severity.  
Time-to-event categories will be calculated with Kaplan-Meier method.  Correlation involving a 
time-to-event variable with a dichotomy will be made using the log-rank test and displayed using 
Kaplan-Meier.  All analyses will use a two-sided significance level of 5%.  No adjustment for 
multiplicity will be carried out at this stage.  
12.4 Exploratory Objective 
To correlate tumor immune leukocyte subpopulations identified using the CIBERSORT method 
alone and in conjunction with PD-L1 assessment on pre-treatment tumor samples with objective 
response using RECIST v1.1 criteria in patients with metastatic NSCLC treated with 
pembrolizumab. 
For the exploratory data analysis that involves tumor immune leukocyte subpopulations 
identified by CIBERSORT, the data will be processed and scored using the CIBERSORT 
algorithm (CIBERSORT.stanford.edu).  A lung population CIBERSORT algorithm will be 
determined to generate an overall “immune score,” either as a categorical variable or a 
continuous variable.  This data may be correlated with response and other clinical outcome data.  
The correlation of CIBERSORT (or CIBERSORT in conjunction with PD-L1 ie, immune score 
high/PD-L1 positive) with response may be assessed using Fisher's exact test.  The correlations 
of continuous or ordinal variables with a dichotomy (ie, high immune score vs low score or high 
immune score/PD-L1 positive vs high immune score/PD-L1 negative) may be made using 
Wilcoxon rank sum test.  The correlations of two continuous variables will be performed using 
Kendall correlations.  
12.4 
Criteria for future studies 
If ctDNA appears promising as a surrogate biomarker of response to immunotherapy, we could 
design a trial stratified by this biomarker for further clinical validation.  

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response to immunotherapy: immune-related response criteria using unidimensional 
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in Localized Lung Cancer by Circulating Tumor DNA Profiling. Cancer Discov 7:1394-
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53. Taube JM, Klein A, Brahmer JR, et al: Association of PD-1, PD-1 ligands, and other features 
of the tumor immune microenvironment with response to anti-PD-1 therapy. Clin Cancer Res 
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54. Shaveta Vinayak RJG, Sylvia Adams, Kristin C. Jensen, Judith Manola, Anosheh Afghahi, 
Lori J. Goldstein, James M. Ford, Sunil S. Badve, Melinda L. Telli: Association of increased 
tumor-infiltrating lymphocytes (TILs) with immunomodulatory (IM) triple-negative breast 
cancer (TNBC) subtype and response to neoadjuvant platinum-based therapy in 
PrECOG0105. J Clin Oncol 32, 2014 
 
55. Gentles AJ, Newman AM, Liu CL, et al: The prognostic landscape of genes and infiltrating 
immune cells across human cancers. Nat Med 21:938-945, 2015 
 
56. Eisenhauer EA, Therasse P, Bogaerts J, et al: New response evaluation criteria in solid 
tumours: revised RECIST guideline (version 1.1). Eur J Cancer 45:228-47, 2009 

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Appendix A: ECOG Performance Status 
Grade 
Description 
0 
Normal activity.  Fully active, able to carry on all pre-disease 
performance without restriction. 
1 
Symptoms, but ambulatory.  Restricted in physically strenuous 
activity, but ambulatory and able to carry out work of a light or 
sedentary nature (eg, light housework, office work). 
2 
In bed < 50% of the time.  Ambulatory and capable of all self-care, 
but unable to carry out any work activities.  Up and about more than 
50% of waking hours. 
3 
In bed > 50% of the time.  Capable of only limited self-care, 
confined to bed or chair more than 50% of waking hours. 
4 
100% bedridden.  Completely disabled.  Cannot carry on any 
self-care.  Totally confined to bed or chair. 
5 
Dead. 
* As published in Am.  J Clin Oncol.:  Oken, M.M., Creech, R.H., Tormey, D.C., Horton, J., Davis, T.E., 
McFadden, E.T., Carbone, P.P.: Toxicity And Response Criteria Of The Eastern Cooperative 
Oncology Group. Am J Clin Oncol 5:649-655, 1982. The Eastern Cooperative Oncology Group, 
Robert Comis M.D., Group Chair.  

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Appendix B:  RECIST Version 1.1 Criteria  
Response Evaluation Criteria in Solid Tumors (RECIST) Version 1.1 for Evaluating 
Response in Solid Tumors 
RECIST version 1.1* will be used in this study for assessment of tumor response.  While either 
CT or MRI may be utilized, as per RECIST 1.1, CT is the preferred imaging technique in this 
study.  
* As published in the European Journal of Cancer: 
E.A. Eisenhauer, P. Therasse, J. Bogaerts, L.H. Schwartz, D. Sargent, R. Ford, J. Dancey, S. 
Arbuck, S. Gwyther, M. Mooney, L. Rubinstein, L. Shankar, L. Dodd, R. Kaplan, D. Lacombe, 
J. Verweij. New response evaluation criteria in solid tumors: Revised RECIST guideline 
(version 1.1).  Eur J Cancer.  2009 Jan;45(2):228-47.  
At baseline, tumor lesions/lymph nodes will be categorized measurable or non-measurable as 
follows: 
Measurable: 
• Tumor lesions: Must be accurately measured in at least one dimension (longest diameter in 
the plane of measurement is to be recorded) with a minimum size of: 
o 10 mm by CT, MRI or PET scan (slice thickness no greater than 5 mm) 
o 10 mm caliper measurement by clinical exam (lesions which cannot be accurately 
measured with calipers should be recorded as non-measurable) 
o 20 mm by chest X-ray 
• Malignant lymph nodes:  To be considered pathologically enlarged and measurable, a lymph 
node must be ≥ 15 mm in short axis when assessed by CT, MRI or PET scan (slice thickness 
recommended to be no greater than 5 mm).  At baseline and in follow-up, only the short axis 
will be measured and followed.  
Non-measurable: 
• All other lesions, including small lesions (longest diameter < 10 mm or pathological lymph 
nodes with ≥ 10 to < 15 mm short axis) as well as truly non-measurable lesions.  Lesions 
considered truly non-measurable include: leptomeningeal disease, ascites, pleural or 
pericardial effusion, inflammatory breast disease, lymphangitic involvement of skin or lung, 
abdominal masses/abdominal organomegaly identified by physical exam that is not 
measurable by reproducible imaging 
The same method of assessment and the same technique should be used to characterize each 
identified and reported lesion at baseline and during follow-up.  Imaging-based evaluation 
should always be done rather than clinical examination unless the lesion(s) being followed 
cannot be imaged but are assessable by clinical exam.  
• Clinical lesions: Clinical lesions will only be considered measurable when they are 
superficial and ≥ 10mm diameter as assessed using calipers (eg, skin nodules).  For the case 
of skin lesions, documentation by color photography including a ruler to estimate the size of 
the lesion is suggested.  As noted above, when lesions can be evaluated by both clinical exam 
and imaging, imaging evaluation should be undertaken since it is more objective and may 
also be reviewed at the end of the study.  

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• Chest X-ray: Chest CT is preferred over chest X-ray, particularly when progression is an 
important endpoint, since CT is more sensitive than X-ray, particularly in identifying new 
lesions.  However, lesions on chest X-ray may be considered measurable if they are clearly 
defined and surrounded by aerated lung.  
• CT, MRI: CT is the best currently available and reproducible method to measure lesions 
selected for response assessment.  This guideline has defined measurability of lesions on CT 
scan based on the assumption that CT slice thickness is 5mm or less.  
• Ultrasound: Ultrasound is not useful in assessment of lesion size and should not be used as a 
method of measurement.  
• Endoscopy, laparoscopy: The utilization of these techniques for objective tumor evaluation is 
not advised.  
• 
Tumor markers: Tumor markers alone cannot be used to assess objective tumor response.  If 
markers are initially above the upper normal limit, however, they must normalize for a 
patient to be considered in complete response.  
• Cytology, histology: These techniques can be used to differentiate between PR and CR in 
rare cases if required by protocol.  
Tumor Response Evaluation 
Baseline documentation of ‘target’ and ‘non-target’ lesions 
• When more than one measurable lesion is present at baseline all lesions up to a maximum of 
5 lesions total (and a maximum of 2 lesions per organ) representative of all involved organs 
should be identified as target lesions and will be recorded and measured at baseline.  
• Target lesions should be selected on the basis of their size (lesions with the longest diameter), 
be representative of all involved organs, but in addition should be those that lend themselves 
to reproducible repeated measurements.  
• A sum of the diameters (longest for non-nodal lesions, short axis for nodal lesions) for all 
target lesions will be calculated and reported as the baseline sum diameters. If lymph nodes 
are to be included in the sum, then as noted above, only the short axis is added into the sum.  
The baseline sum diameters will be used as reference to further characterize any objective 
tumor regression in the measurable dimension of the disease.  
Systemic Response Criteria 
Complete Response (CR) requires ALL of the following:  
• Disappearance of all target and non-target lesions 
• All pathological lymph nodes, whether target or non-target, must have reduction in short 
axis to < 10 mm.  
• No new lesion 
Partial Response (PR) requires ALL of the following: 
• At least 30% decrease in the sum of diameters of target lesions, taking as reference the 
baseline sum of diameters.  
• No unequivocal progression of existing non-target lesions 
• No new lesion 

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Progression of Disease (PD) requires ANY of the following: 
• At least 20% increase in the sum of diameters of target lesions, taking as reference the 
smallest sum on study (this includes the baseline sum if that is the smallest on study).  In 
addition to the relative increase of 20%, the sum must also demonstrate an absolute increase 
of at least 5 mm.  
• Unequivocal progression of existing non-target lesions 
• Appearance of one or more new lesions 
Stable Disease (SD) requires ALL of the following:  
• Not CR 
• Not PR 
• Not PD