VERTRAULICH Eine Gewebeakquisitionsstudie zur Entwicklung

Transcrição

CONFIDENTIAL
A Tissue Acquisition Study for the Evaluation of a Methodology to Select TumorSpecific Neo-Antigens for the Treatment of NSCLC
Protocol Number:
GO-001
Indication Studied:
Non-Small Cell Lung Cancer
Sponsor Name and Address:
Gritstone Oncology, Inc.
5858 Horton Street, Suite 210
Emeryville, CA 94608 USA
88
M.D., Ph.D.
Responsible Medical Officer:
Compliance Statement:
This study will be conducted in accordance with
the ethical principles that have their origin in the
Declaration of Helsinki, clinical research
guidelines established by the Code of Federal
Regulations (Title 21, CFR Parts 50, 56, and 312),
and ICH GLP/GCP Guidelines. Essential study
documents will be archived in accordance with
applicable regulations.
Protocol Date:
Original: January 21, 2016
Amendment 1: September 8, 2016
CONFIDENTIALITY STATEMENT
The information in this document contains commercial information and trade secrets that
are privileged or confidential and may not be disclosed unless such disclosure is required
by applicable laws and regulations. In any event, persons to whom the information is
disclosed must be informed that the information is privileged or confidential and may not
be further disclosed by them. These restrictions on disclosure will apply equally to all
future information supplied to you which is indicated as privileged or confidential.
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Protocol No. GO-001
Amendment 1, dated September 8, 2016
Protocol Acceptance Form
Protocol:
GO-001
Title:
A Tissue Acquisition Study for the Evaluation of a Methodology to Select
Tumor-Specific Neo-Antigens for the Treatment of NSCLC
Date:
September 8, 2016 – Amendment 1
I have carefully read this protocol and agree that it contains all of the necessary information
required to conduct this study. I agree to conduct this study as described and according to the
Declaration of Helsinki, ICH Guidelines for GCP, and all applicable regulatory requirements.
Investigator’s Signature
Date
Name (printed)
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Protocol No. GO-001
TABLE OF CONTENTS
Description
1
Page
INTRODUCTION ........................................................................................................6
1.1
NSCLC and Tumor-Specific Neo-Antigens ..........................................................6
2
STUDY DESIGN ..........................................................................................................8
3
STUDY OBJECTIVES ..............................................................................................10
4
STUDY REQUIREMENTS ......................................................................................10
4.1
Patient Eligibility .................................................................................................10
4.1.1
4.1.2
4.2
4.2.1
4.2.2
4.3
Inclusion Criteria ..................................................................................................10
Exclusion Criteria.................................................................................................11
Study Procedures ..................................................................................................12
Patients Who Have Not Yet Initiated Anti-PD-(L)1 Therapy .............................12
Patients Who Have Already Initiated Anti-PD-(L)1 Therapy .............................12
Patient Withdrawal From The Study ...................................................................13
5
SPECIMEN COLLECTION AND MANAGEMENT............................................13
6
DATA COLLECTION ..............................................................................................14
6.1
6.2
6.3
6.4
7
8
Demographics ......................................................................................................14
Tumor History ......................................................................................................14
Treatment with Anti-PD-(L)1 Therapy ................................................................15
Specimen Collection ............................................................................................15
STATISTICAL AND BIOINFORMATICS ANALYSES......................................15
7.1
7.2
7.3
7.4
Primary Endpoints ................................................................................................15
Sequencing Analyses ...........................................................................................15
Handling of Samples and Data.............................................................................16
Statistical Analysis ...............................................................................................16
7.5
Sample Size ..........................................................................................................17
STUDY ADMINISTRATION ...................................................................................18
8.1
8.2
8.3
8.4
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Regulatory and Ethical Considerations ................................................................18
Confidentiality of Information .............................................................................18
Monitoring of the Study .......................................................................................19
Termination of the Study .....................................................................................19
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Protocol No. GO-001
8.5
8.6
9
Record Retention ..................................................................................................19
Final Study Report and Publication .....................................................................20
REFERENCES ...........................................................................................................20
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Protocol No. GO-001
1
1.1
INTRODUCTION
NSCLC and Tumor-Specific Neo-Antigens
According to the American Cancer Society, lung cancer is the most common cancer
worldwide with approximately 1.35 million new cases annually, with non-small cell lung
cancer (NSCLC) accounting for almost 85 percent of all cases.(1) NSCLC progresses
rapidly with a five year survival rate in advanced NSCLC patients of less than 5%.
Recently, immune therapy has been approved for the treatment of NSCLC, with US FDA
approval of both nivolumab (Opdivo™) and pembrolizumab (Keytruda™) for the
treatment of metastatic NSCLC (both squamous and non-squamous histotypes) after
progression on platinum-based chemotherapy. Both drugs are monoclonal antibodies
(mAb) that inhibit the PD-1/PD-L1 immune checkpoint, and are therefore known as
checkpoint inhibitors (CPI). They prevent the deactivation of T cells by blocking the PD-1
receptor on T cells from binding its ligand (PD-L1) on tumor cells. It is believed that
inhibition of PD-1 leads to activation of pre-existing tumor-specific T cells followed by T
cell-mediated attack of tumor cells, leading in some cases to tumor shrinkage or even
complete response. There is optimism that some of the objective responses observed after
CPI therapy may be durable, as has been observed in metastatic melanoma, where
approved CPI include both anti-PD-1 and anti-CTLA-4 mAb. Several mAb that inhibit
PD-L1 are in late stage clinical development (e.g. atezolizumab, durvalumab) – data
suggest that their efficacy and toxicity are similar to those of anti-PD-1 mAb, and for most
clinical research purposes these reagents are regarded as equivalent.
With the advent of immune therapy in lung cancer, the identity of the antigens to which T
cells are responding has become a key question. Recent studies suggest that it is tumorspecific neo-antigens (TSNAs) which are the target of the therapeutic T cell responses
elicited by CPI therapy.
Tumors exhibit genetic instability as one of the “hallmarks of cancer”, and this leads to
frequent DNA mutations in tumor cells and their progeny. Some of these mutations occur
in functionally critical genes, leading to oncogenic constitutive gene activation (e.g.
activating mutations in the EGFR gene) or inhibition (e.g. defective BRCA1 or p53 tumor
suppressor genes). Many additional mutations occur in other genes unlikely to drive
cancer. When non-synonymous mutations, insertions, deletions, frameshift mutations, or
fusions occur in protein-encoding genes, they generate peptides of novel amino-acid
sequence, and these “altered-self” peptides can act as antigens for the immune system,
whether they arise from oncogenic or passenger mutations. It is important to note that these
so-called tumor-specific neo-antigens (TSNAs) are usually patient-unique – it is unlikely
that any two random patients will share a particular passenger tumor mutation.
Work by a group led by Tim Chan at Memorial Sloan Kettering Cancer Center (New York,
USA) demonstrated that patients with metastatic melanoma are more likely to respond to
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Protocol No. GO-001
CPI therapy (anti-CTLA-4 mAb) if their tumors contain large numbers of non-synonymous
exome mutations and large numbers of predicted TSNAs.(2) Prediction of TSNAs is
currently performed using DNA and RNA sequencing to identify the expressed subset of
non-synonymous exome mutations of a tumor specimen, and then predicting which
resulting mutant peptides (typically 9 amino acids in length) will bind with high affinity to
the class I HLA molecules of that particular patient. Furthermore, Chan’s team showed that
CD8+ T cells in the peripheral blood could be identified which recognized some of the
predicted TSNAs in the context of peripheral blood mononuclear cells (PBMCs) from the
same patient. These T cells were typically undetectable prior to CPI therapy, and then rose
in frequency alongside the emerging clinical response. Similar work was performed in the
setting of NSCLC patients receiving anti-PD-1 mAb therapy, and concordant observations
were made.(3)
Consequently, the hypothesis has arisen that a novel vaccination strategy could be
successfully deployed in NSCLC patients. This strategy would follow several steps:
1. Obtain a tumor biopsy.
2. Sequence the tumor DNA and RNA to identify the expressed, non-synonymous
exome mutations
3. Test the patient’s HLA genes to determine their HLA type
4. Predict which of the mutant peptides are presented by the patient’s Class I HLA
alleles (in NSCLC, there are often several hundred candidate TSNAs).
Additionally, explore binding for Class II HLA alleles if feasible (considered more
challenging).
5. Assemble a prioritized list of TSNAs based on criteria such as predicted
presentation, expression level, or other parameters
6. Insert a subset of predicted TSNAs into a vaccine (multiple vector platforms could
be deployed – nucleic acid, peptide, viral or cellular, e.g. dendritic cell)
7. Immunize the patient with the patient-specific TSNA-containing vaccine, alongside
CPI adjunctive therapy
Gritstone Oncology (the sponsor) is pursuing this general strategy, and seeks to refine
steps 4 & 5 of the above workflow – namely, the prioritization of predicted TSNAs. This
step is critical because most vaccine vectors can accommodate only a limited number of
Class I TSNAs (typically 10-20) while a NSCLC patient can have several hundred
predicted TSNAs.(4) Selecting a small number of TSNAs from a pool of hundreds is thus a
challenge given that:
a) Most predicted high-affinity HLA-binding peptides are not present on the surface
of tumor cells due to other steps/factors in the processing pathway
b) The highest-affinity HLA-binding peptides may not be immunogenic
c) Expression of genes may be heterogeneous across biopsies from a single patient’s
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tumor mass – significant sampling error may be introduced by reliance on a single
biopsy
In order to evaluate and improve TSNA prediction for NSCLC patients, Gritstone
Oncology seeks to obtain tumor specimens and blood samples from patients with NSCLC
who have received CPI therapy with anti-PD-1 or anti-PD-L1 mAb (collectively termed
anti-PD-(L)1 treatment).
The goal of this study is to evaluate the immunogenicity of predicted neo-antigens in
NSCLC patients on anti-PD-(L)1 treatment by:
a) Estimating the fraction of predicted neo-antigens with pre-existing (recall) T cell
responses in both anti-PD-(L)1 responders and non-responders
b) Estimating the fraction of predicted neo-antigens to which T cells can respond
either through recall or in vitro de-novo priming
The dataset created will serve as a key pre-clinical proof-of-concept of the predicted
TSNA-based vaccine approach and create a wealth of integrated genomic and
immunologic data for exploratory research.
This is not an interventional study – typically only routine clinical samples will be
collected during routine clinic visits. There is an option for protocol-directed biopsy but it
is not mandatory. It is expected that by advancing our understanding of the nature of
TSNAs that drive therapeutically effective T cell responses, this study will ensure that
Gritstone Oncology’s future NSCLC vaccines comprise the optimized set of TSNAs
presented on the surface of each patient’s tumor cells and thus maximize chances of patient
benefit from vaccination.
2
STUDY DESIGN
This is a multi-center study conducted at cancer centers or hospitals located in the
Americas, Europe, and Asia designed to collect blood and tumor tissue from patients with
advanced (Stage IIIB, IV) NSCLC. Eligible patients will be appropriate candidates for
initiation of treatment with anti-PD-(L)1 therapy or will have already initiated anti-PD(L)1 therapy, and have signed an EC/IRB-approved informed consent form to provide
blood and tumor tissue specimens (core needle biopsy [CNB], resection) for exploratory
testing. All specimens will be collected according to standard institutional practices.
Formalin-fixed paraffin-embedded (FFPE) tumor specimens will be prepared locally as per
institutional procedures and sent to the sponsor’s designated laboratory for analysis.
Peripheral blood samples will be collected from all study patients for HLA typing,
germline exome sequencing, and isolation and cryopreservation of PBMCs for functional
T cell assays. In addition, patients enrolled at study centers in the United States will have
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peripheral blood samples collected for circulating cell-free DNA (cfDNA) and plasma
analysis. These patients will comprise a substudy aimed at understanding neo-antigen
DNA representation and evolution in plasma, and will inform potential development of
plasma-based neo-antigen assays. All blood samples will be prepared locally according to
instructions provided in the study Laboratory Manual and sent to the sponsor’s designated
laboratories for processing and analysis.
Tumor specimens will undergo DNA and RNA sequencing to determine predicted TSNAs
and assess tumor and infiltrating cells by expression analysis. They may also be analyzed
by immunohistochemistry/ immunofluorescence to assess immune cell infiltration into
tumors. Blood will be separated into plasma and cellular fractions. Plasma will be analyzed
for circulating tumor DNA and may be analyzed for soluble HLA-peptide complexes (to
identify peptides bound to tumor-derived HLA molecules which are over-represented in
the plasma of cancer patients). T cells from the cellular fraction will be studied for
phenotype and functional response to predicted TSNAs. Non-T cells may (i) be examined
for circulating tumor cells, (ii) act as a source of autologous APCs, and (iii) allow
determination of the normal genome (aiding tumor mutational analysis and HLA typing).
Patient recruitment was initiated in April 2016, and is expected to last approximately 20
months to complete collection of specimens. Up to approximately 120 patients may be
enrolled to obtain blood and tumor specimens of sufficient quantity and quality to meet the
study goals.
If a patient has not yet initiated anti-PD-(L)1 therapy, blood will be collected and the
patient will provide an archival tumor specimen or, if no archival tumor specimen is
available, undergo a procedure (core needle biopsy [CNB], resection of a superficial tumor
lesion) to obtain a fresh tumor specimen prior to treatment. Patients who have already
initiated anti-PD-(L)1 therapy may also participate in this study. For these patients, a pretreatment archival tumor specimen is required for study entry.
All enrolled patients will have blood collected during routine clinical visits and following
the end of treatment with anti-PD-(L)1 therapy. Patients may elect to undergo a biopsy
following disease progression on anti-PD-(L)1 therapy, but this is an optional part of the
protocol and a separate consent must be obtained from the patient.
Anti-PD-(L)1 therapy should be administered per standard practice and is not considered a
part of this protocol.
If approved by the patient, tumor tissue and peripheral blood collected in excess of what is
required for testing will be stored at Gritstone Oncology (or a facility designated by
Gritstone Oncology) for future exploratory analyses to inform the diagnosis, prognosis, or
treatment of patients with NSCLC. Long-term storage of leftover patient tissue and blood
samples for future testing is optional and requires additional consent from the patient.
Limited clinical information on enrolled patients will be collected and is described in
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Section 5.
3
STUDY OBJECTIVES
The primary objective of this study is to evaluate the immunogenicity of predicted neoantigens in NSCLC patients receiving anti-PD-(L)1 treatment by:
a) Estimating the fraction of predicted neo-antigens with pre-existing (recall) T cell
b) Estimating the fraction of predicted neo-antigens to which T cells can respond
This data will serve as pre-clinical proof-of-concept of the predicted TSNA-based vaccine
approach and create an integrated genomic and immunologic dataset for exploratory
research in NSCLC immunotherapy.
4
4.1
STUDY REQUIREMENTS
Patient Eligibility
4.1.1 Inclusion Criteria
1. At least 18 years of age
2. Provide written consent on an EC/IRB-approved informed consent form prior to
any study-specific procedures
3. Have a confirmed diagnosis of locally advanced (Stage IIIB) or metastatic (Stage
IV) NSCLC
4. ECOG Performance Status 0-2
5. Either (a) a candidate for initiation of treatment with anti-PD-(L)1 therapy, or (b)
already initiated treatment with anti-PD-(L)1therapy
6. Have an archival tumor specimen available (from CNB or resection, and sufficient
to yield at least 10 sections of 5 micron thickness) for analysis, or able to undergo a
biopsy procedure for the purpose of obtaining tumor tissue and/or tumor cells
7. One or more tumor lesions detectable on a radiologic exam (CT scan, PET scan,
MRI or x-ray) prior to treatment with anti-PD-(L)1 therapy
8. Able to provide approximately 30-36 mL of peripheral blood at each study visit (at
baseline visit and serially during alternating standard of care visits) for research
purposes
9. For patients enrolled at a site participating in the collection of blood for
cfDNA/plasma analysis: Able to provide an additional 20 mL of peripheral blood
at each study visit (at baseline visit and serially during alternating standard of care
visits) as part of a substudy for research purposes
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4.1.2 Exclusion Criteria
1. Known EGFR activating mutations or ALK, RET, or ROS1 rearrangements, since
these patients may exhibit lower mutational burdens (and TSNA loads) and are less
likely to be informative for purposes of this protocol
2. Never smoker (patient has smoked fewer than 100 cigarettes in their lifetime)
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4.2
Study Procedures
Any procedure performed specifically for the purposes of this research study will be done
only after written informed consent has been obtained.
4.2.1 Patients Who Have Not Yet Initiated Anti-PD-(L)1 Therapy
Any patient entering this study prior to initiating anti-PD-(L)1 therapy will have the
following samples collected.
4.2.1.1 Before Anti-PD-(L) 1 Therapy
At any time following informed consent and before initiating anti-PD-(L)1 therapy, the
following samples will be collected once:




Blood for HLA typing and germline exome sequencing (6 mL)
Blood for isolation of PBMCs (30 mL)
Pre-treatment tumor biopsy (CNB or resection), if archival specimen is not
available
For substudy patients only: Blood for plasma/cfDNA analysis (20 mL)
4.2.1.2 During Anti-PD-(L) 1 Therapy
At alternating routine clinic visits where anti-PD-(L)1 therapy is administered, the
following blood samples will be collected for 6 months, or until disease progression, or
until discontinuation of anti-PD-(L)1 therapy, whichever is earliest:


4.2.1.3 After Disease Progression or Discontinuation of Anti-PD-(L)1 Therapy
Following disease progression or discontinuation of anti-PD-(L)1 therapy, the following
samples will be collected once:



Optional new tumor biopsy (CNB) or resection of the area of disease progression –
separate consent required
4.2.2 Patients Who Have Already Initiated Anti-PD-(L)1 Therapy
Any patient entering this study after already initiating anti-PD-(L)1 therapy must have an
archival FFPE tumor specimen available and submitted to the sponsor’s designated
laboratory for analysis. These patients will have the following samples collected.
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4.2.2.1 During Anti-PD-(L)1 Therapy
Following informed consent, patients will have the following blood samples collected at
alternating routine clinic visits where anti-PD-(L)1 therapy is administered, unless
otherwise specified, for 6 months, or until disease progression, or until discontinuation of
anti-PD-(L)1 therapy, whichever is earliest:



Blood for HLA typing and germline exome sequencing (6 mL) – only at the first
routine clinic visit following informed consent
4.2.2.2 After Disease Progression or Discontinuation of Anti-PD-(L)1 Therapy
Following disease progression or discontinuation of anti-PD-(L)1 therapy, the following
samples will be collected once:



4.3
Optional new tumor biopsy (CNB) or resection of the area of disease progression –
separate consent required
Patient Withdrawal From The Study
Patients may choose to discontinue their participation from the study at any time, for any
reason, and without prejudice to treatment.
In the event of a patient’s withdrawal from the study, the Investigator will promptly notify
the study sponsor. No blood or tumor specimen samples will be collected from the patient
subsequent to the patient’s withdrawal from the study. Any blood samples and tumor
specimen samples collected and not yet processed prior to the patient’s withdrawal from
the study may still be used, unless the patient requests otherwise. All processed samples
and clinical data obtained prior to patient withdrawal may still be used.
5
SPECIMEN COLLECTION AND MANAGEMENT
Tumor tissue derived from NSCLC (primary tumor, local or distant metastases) will be
collected and prepared locally as FFPE specimens according to standard institutional
procedures. For patients where archival specimens are available from both primary tumor
and distant metastases, both should be submitted if possible. FFPE blocks, unstained
slides, or tissue curls are acceptable specimen types to send to the sponsor for analysis.
FFPE blocks must be sufficient to yield, at minimum, 10 sections of 5 micron thickness
and are preferred over unstained slides. If only unstained slides are available, 10-20 slides
should be submitted. If possible, the unstained slides or tissue curls should be submitted
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with a H&E section confirming tumor content and surface area. Prepared tumor tissue
specimens will be sent to the sponsor’s designated laboratory for storage and analysis.
Peripheral blood samples will be collected according to standard institutional procedures,
prepared locally according to instructions provided in the study Laboratory Manual, and
sent to the sponsor’s designated laboratories for processing and analysis.
All specimens will be clearly labeled with the sponsor’s name, protocol number, patient
identification number, sample type and date of collection. No personally identifiable
information may be submitted with the samples.
Detailed sample handling instructions for tumor and blood specimens will be provided in a
separate study Laboratory Manual. Specimen collection kits, container labels, requisition
forms, shipping supplies and courier service will be provided by the Sponsor.
6
DATA COLLECTION
De-identified clinical information and tumor history will be collected on case report forms
and will include, but may not be limited to:
6.1
Demographics

Confirmation of written informed consent

Confirmation of additional written informed consent for storage of remaining
specimens for exploratory analyses

Confirmation of additional written informed consent for optional biopsy following
disease progression on anti-PD-(L)1 therapy

Age

Gender

ECOG performance status at study entry

Race

Smoking history, including pack years and date discontinued
6.2
Tumor History

Date of initial diagnosis

Tumor stage (IIIB or IV)

Location of primary tumor, and metastases if present

Histological type

Date, site and type of biopsy at time of disease progression (if applicable)
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
Type(s), date(s), and duration of prior systemic NSCLC-directed therapies

Any other relevant clinical information
6.3
Treatment with Anti-PD-(L)1 Therapy

Indication for initiation of anti-PD-(L)1 therapy

Type and duration (dates) of treatment

Reason for discontinuation of treatment

Date of clinical response assessment(s), and substantiating lesion measurements

Date of clinical progression assessment
6.4
7
7.1
Specimen Collection

Site, date and type of biopsy procedure or tumor tissue collection (CNB or
resection)

Date of blood draw
STATISTICAL AND BIOINFORMATICS ANALYSES
Primary Endpoints
The primary objective of this study is to evaluate the immunogenicity of predicted neoantigens in NSCLC patients receiving anti-PD-(L)1 treatment. The primary endpoints are:
a) The estimated fraction of predicted neo-antigens with pre-existing (recall) T cell
b) The estimated fraction of predicted neo-antigens to which T cells can respond
7.2
Sequencing Analyses
Tumor and normal exomes will be sequenced on the Illumina HiSeq platform following
capture of all coding exons using IDT xGen® Lockdown® Probes targeting 39Mb or a
similar reagent. Tumor DNA will be sequenced at high average depth (~500x median
unique coverage), and corresponding normal samples will be sequenced at moderate
depth (50-100x median unique coverage). Tumor RNA will be extracted, converted to
cDNA and sequenced at high depth (~100 million read pairs). Discovered genomic
alterations may be confirmed by an additional targeted assay or sequencing method.
The goal of joint tumor and normal specimen analysis in the Gritstone process is to
accurately detect somatic (i.e., tumor-related) genomic alterations as candidate neoantigens and components of the neo-antigen prediction model. Tumor transcriptome
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(RNAseq) data will be used to prioritize expressed mutations as neo-antigens and as a
source of expression-based signatures for the neo-antigen prediction model. Normal
exome data is obtained primarily for the purpose of filtering germ-line variants and
artefactual variants from the tumor exome analysis. An additional use of germline
samples and data will be identification of patient HLA type (from normal exome
analysis or dedicated HLA typing on the MiSeq platform) and other polymorphisms
related to antigen processing, to be used in the neo-antigen prediction model. When
cfDNA specimens are available, cfDNA will be analyzed for presence and abundance of
somatic mutations and compared to results from tumor specimens.
Alignment of exome data to the human genome will use BWA-Mem or a similar method.
Detection of single-nucleotide mutations and short insertions and deletions will use one
or more of the following tools: VarScan, Mutect, FreeBayes, Platypus, Strelka,
SomaticSniper, VarDict. Detection of longer insertions and deletions will use one or
more of the following tools: Scalpel, Pindel-C. RNAseq data will be aligned to the
human genome using STAR, HISAT or a similar method. Non-reference splice junctions
will be recovered from alignments, and transcript assembly will use CLASS or a similar
method.
Mutations detected in exome sequencing will be queried in RNAseq alignments using
SNPiR. Allele-specific quantification from RNAseq alignments will use AlleleSeq,
ASEQ, Allele Workbench or a similar tool. HLA calling will use one or more of the
following tools: ATHLATES, neXtype, HLAminer, HLA-VBSeq, PHLAT, Optitype,
HLAreporter, seq2HLA. These methods may be complemented with methods developed
internally or additional methods available in the literature for the purpose of somatic
mutation detection and verification, transcript and expression analysis, or HLA type
determination.
7.3
Handling of Samples and Data
All patient data will be de-identified and reside in Gritstone’s secure, private Amazon
Web Services or internal file storage. Access to authorized personnel will be allowed
only for purposes of the study protocol. Patient specimens will be destroyed after the
study analyses have been completed, unless patient has provided consent for long-term
storage of leftover specimens for future research, in which case the patient specimens
will be kept indefinitely. Patients may request the destruction of their samples at any
time, if those samples have not yet been processed and analyzed. Processed samples and
study data cannot be discarded and may continue to be used per protocol.
7.4
Statistical Analysis
The primary endpoint fractions will be calculated as the average fraction of immunogenic
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TSNAs in the set of all tested TSNAs per patient, in each specified patient subgroup.
7.5
Sample Size
Sample size calculation for the study is based on achieving acceptable standard errors of
the estimate for the primary endpoints (i.e., immunogenic TSNA fractions). Assuming a 20
epitope/patient predicted TSNA set is tested, standard errors of the estimate (normal
approximation to the binomial distribution) are given in Figure 1 across a range of possible
immunogenic antigen fractions:
Figure 1
From Figure 1, we can see that given at least N=15 patients per subgroup, standard errors
of the estimate are <0.03 across all feasible fractions, and close to or less than 0.02 for
fractions 0.05-0.20, the expected fraction range.
The study thus targets enrollment of up to approximately N=120 patients:

Assuming 25% attrition due to inadequate tumor tissue, PBMCs, or other reasons,
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


data will be generated for N=90 patients.
Of N=90 total patients, specimens from 15 patients will be used to estimate the
fraction of predicted antigens to which T cells can respond either through recall or in
vitro de-novo priming, leaving N=75 for responder/non-responder analysis.
Assuming 20% RR in the N=75 remaining patients, the N=15 responders will be
used to estimate the fraction of predicted antigens with pre-existing (recall) T cell
responses in anti-PD(L)1 responders
Of the remaining N=60 non-responders, N=15 patients will be used to estimate the
fraction of predicted antigens with pre-existing (recall) T cell responses in antiPD(L)1 non-responders.
Samples from remaining non-responders (N=45) will be used to generate additional data in
either the de-novo priming or non-responder pre-existing T-cell analysis groups, or for
further exploratory assessments
8
8.1
STUDY ADMINISTRATION
Regulatory and Ethical Considerations
This study will be conducted in compliance with the protocol, GCPs, ICH, and FDA
regulatory requirements, and in accordance with the ethical principles of the Declaration of
Helsinki. U.S.-generated data will be handled in accordance with the Health Information
Portability and Accountability Act (HIPAA).
This protocol and any accompanying material will be submitted by the investigator to an
EC/IRB for review and approval, as required by institution policies. This also applies to
any protocol amendments that may be generated. Documentation of EC/IRB approval of
the protocol and informed consent form will be forwarded to the sponsor prior to patient
recruitment.
It is the responsibility of the investigator to ensure that a signed informed consent form
exists for each patient enrolled in this study.
The investigator will submit appropriate reports on the progress of the study to the
IEC/IRB in accordance with applicable national law and/or local regulations and in
agreement with the policy established by the IEC/IRB. The IEC/IRB must be informed by
the investigator of all subsequent study protocol amendments.
8.2
Confidentiality of Information
The investigator must assure that patients’ anonymity is strictly maintained and that their
identities are protected from unauthorized parties. Only a study identification code (i.e., not
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names) should be recorded on any form or specimen container submitted to the sponsor
and the EC/IRB.
The investigator agrees that this protocol remains the sole and exclusive property of
Gritstone Oncology. Information is not to be disclosed to any third party (except
employees or agents directly involved in the conduct of the study or as required by law)
without prior written consent from the sponsor. The investigator further agrees to take all
reasonable precautions to prevent the disclosure by any employee or agent of the study
institution to any third party or otherwise into the public domain.
8.3
Monitoring of the Study
A qualified individual designated by Gritstone Oncology may perform study monitoring at
individual sites to ensure satisfactory patient recruitment, data collection and protocol
adherence. The frequency of monitoring may vary depending on recruitment rate and
quality of data collected. Monitoring may also be performed remotely. The investigator
and staff are expected to cooperate and provide all relevant study documentation for the
monitor’s review, as requested. Routine communication with the site to keep abreast of
study updates and answer questions will occur by phone or email.
In addition to monitoring visits, the investigator and staff agree to accommodate studyrelated audits, EC/IRB review, and inspections by Food and Drug Administration (FDA)
and other regulatory agencies to the extent permitted by law, including providing direct
access to all relevant study documentation.
8.4
Termination of the Study
Both Gritstone Oncology and the investigator reserve the right to terminate the study at
any time. Should this be necessary, both parties will arrange discontinuation procedures. In
terminating the study, Gritstone Oncology and the investigator will assure that adequate
consideration is given to the protection of patient data and specimens already collected.
Except under exceptional circumstances, a 30-day written notification will be given.
8.5
Record Retention
The study site will maintain a study file, which should contain, at a minimum, the protocol
and any amendments, EC/IRB approvals and correspondence, any correspondence with
Gritstone Oncology, a signed informed consent form for each patient, and other studyrelated documents. The investigator shall retain appropriate records for 10 years after the
study finishes. However, these documents should be retained for a longer period if required
by the applicable regulatory requirement(s) or if needed by Gritstone Oncology. No data
should be destroyed without the agreement of Gritstone Oncology and the company will
inform the investigator in writing when the study-related records are no longer needed.
Should the investigator wish to assign the study records to another party or move them to
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Page 19 of 20
Protocol No. GO-001
another location, Gritstone Oncology must be notified in writing of the new responsible
person and/or the new location.
8.6
Final Study Report and Publication
A study report will be prepared by Gritstone Oncology. Data generated from this study are
the property of Gritstone Oncology and shall be held in strict confidence. Independent
analysis and/or publication of these data by the investigator(s) or any member of their staff
require prior written agreement with Gritstone Oncology. Permission is contingent on the
review by Gritstone Oncology of the statistical analysis and manuscript and will provide
for nondisclosure of Gritstone Oncology confidential or proprietary information. In all
cases, parties agree to submit all manuscripts or abstracts to all other parties 30 days prior
to submission. This will enable all parties to protect proprietary information and to provide
comments based on information that may not yet be available to other parties.
9
REFERENCES
1.
Herbst R, et al. Molecular Origins of Cancer: Lung Cancer. N Engl J Med 2008;
359:1367-80.
Snyder A, et al. Genetic basis for clinical response to CTLA-4 blockade in melanoma.
N Engl J Med 2014; 371:2189-99.
Rizvi N, et al. Mutational landscape determines sensitivity to PD-1 blockade in non–
small cell lung cancer. Science 2015; 348(6230):124-28.
Alexandrov LB, et al. Signatures of mutational processes in human cancer. Nature
2013; 500:415-21.
Tumeh PC, et al. PD-1 blockade induces responses by inhibiting adaptive immune
resistance. Nature 2014; 515:568-71.
2.
3.
4.
5.
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