untitled h1
8.0 statistical consideration and analysis

Assume the response rate for the platinum re-treatment therapy in platinum pre-treated ovarian, fallopian tube, and primary peritoneal cancer patients is 23%. One of the primary objectives of this phase I/II trial is to test whether a new combinatory therapy (platinum + anti-PD1 50 Protocol/Amendment No.: Version 5; 08/20/2018 antibody) can achieve a higher response rate (RR). We hypothesize that the true clinically  
 significant response rate for the new therapy is 40~50%. The following table shows the sample size required to have either 80% or 90% power to declare statistical significance at level 0.05 for a true response rate at 40%, 45%, or 50%. A sample size of 27 patients will be required to have 80% power when the true response rate of the new combinatorial therapy is around 50%.  
| Response Rate of the new Therapy   | Power 80%   | Power 90%   |
|------------------------------------|-------------|-------------|
| 40%                                | 66          | 88          |
| 45%                                | 41          | 54          |
| 50%                                | 27          | 37          |  
Furthermore, it is desirable to determine the response rate of the new combinatory therapy with sufficient precision. We can compute the standard error (SE) of the estimated response rates as the measure of precision for a range of true response rates. For the true response rate being in the range of 40%-50%, the SE does not vary much (0.07~0.09), and so there is adequate precision to detect the targeted response rate at 40-50%. The median progression-free survival time is another efficacy endpoint of interest. Suppose the median progression-free survival time is 17, 20, or 23, and for the target sample size 27, the power to detect a statistically significant improvement in median progression-free survival time assuming accrual time is 1 year and the follow-up time is 1 year is listed in the following table. This table shows that our targeted sample size provides good power to detect 40% or more improvement in median progression-free survival time.  
| 40% improvement in the                        | 60% improvement in   |      |
|-----------------------------------------------|----------------------|------|
| new therapy                                   | the new therapy      |      |
| The median PFS in historical control 17 weeks | 0.68                 | 0.89 |
| 0.66                                          | 0.88                 |      |  
| 20 weeks 23 weeks   | 0.65   | 0.89   |
|---------------------|--------|--------|
untitled h1
8.2 statistical analysis plan

Clinical characteristics of the study cohort at the time of initial diagnosis will be tabulated, including age, stage, surgical optimality, and disease status after initial platinum therapy. The clinical characteristics and outcome of platinum-resistant patients will be also tabulated when retreated with the combinatory therapy. The RR is the primary efficacy variable. The point estimate and the 95% exact confidence intervals will be reported for RR. The comparison with the historical control rate will be conducted by examining whether the 95% confidence internal covers the historical control rate. Additional analyses will be conducted to evaluate in logistic regression models the odds ratio of response rate on predictors such as platinum-free interval, time to progression after previous platinum treatment, number of prior platinum regimens etc. Other efficacy endpoints, which included progression free survival (PFS) and overall survival (OS), were also analyzed. Timeto-event variables were analyzed using the Kaplan-Meier method. Kaplan-Meier estimates of the survival function with 95% CIs at specific time points (using Greenwood's formula for the standard error) were computed. Comparisons with the historical control PFS and OS will be conducted by examining whether the 95% confidence internal covers the historical control proportions. The safety population included all patients who received at least one dose of study medication. The descriptions and grading scales found in the revised NCI Common Terminology Criteria for Adverse Events (CTCAE) version 4.0 will be utilized for adverse event reporting. (http://ctep.cancer.gov/reporting/ctc.html) The number and the percentage of patients who are removed from the study or altered dose regimen due to adverse effects will be reported.
untitled h1
9.0 labeling packaging storage and

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. Clinical Supplies will be provided by Merck as summarized in Table 7. Table 7 Product Descriptions  
| Product Name & Potency    | Dosage Form            |
|---------------------------|------------------------|
| Pembrolizumab 100 mg/ 4mL | Solution for Injection |
untitled h1
9.2 packaging and labeling information

Clinical supplies will be affixed with a clinical label in accordance with regulatory requirements.
untitled h1
9.3 clinical supplies disclosure

This trial is open-label; therefore, the subject, 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.
untitled h1
9.4 storage and handling requirements

Clinical supplies must be stored in a secure, limited-access location under the storage conditions specified on the label. Receipt and dispensing of trial medication must be recorded by an authorized person at the trial site. Clinical supplies may not be used for any purpose other than that stated in the protocol.
untitled h1
9.5 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 subjects 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.
untitled h1
10.0 administrative and regulatory details

In accordance with federal regulations, an Institutional Review Board that complies with the  
 regulations in 21 CFR 56 must review and approve this protocol and the informed consent form prior to initiation of the study.
untitled h1
10.2. study team roles and

Dr. Liao, the PI, will be responsible for the oversight of the research. Dr. Liao is responsible for ensuring that all information and documentation related to the conduct and safety of the study is disseminated to the proper agencies in the proper timeframe. In addition, Dr. Liao will delegate study responsibilities to qualified and trained research staff. Research physicians/sub-investigators will be responsible for conducting consent conferences. Research physicians/physician extenders may perform assessment as per the delegation log. Research Nurses/Coordinators will be responsible for initial screening and scheduling patient visits. The Research Coordinators will ensure that the clinical data is entered into the database in a timely manner, so as to have real time data to review and report any safety concerns trends. They will also be responsible for maintaining regulatory documentation to the various agencies involved with this research and ensure that all research team members are following the protocol and all regulations. All clinical research staff are required to complete the following training:
1. Human Subjects Protections 2. HIPAA 3. Good Clinical Practice New staff will also be required to review any existing standard operating procedures. This review will be documented that they understand the information. Existing staff will also be trained on new standard operating procedures and this training will also be documented on a Training Log for monitors to review at a site visit, if inclined.
untitled h1
10.3 confidentiality

All eligible patients will be assigned a UPN that will not contain any personally identifying information, such as name, initials, medical record number, social security number, etc. To maintain confidentiality, we protect the link between the patients' personal identifying information and UPN number by limiting who has access to the patients' chart documentation. Only delegated clinical research staff has access to the data, which remain locked at all times when not in use. All hard copy research records collected on potential and enrolled patients are stored in a locked filing cabinet that can only be accessed by approved clinical research staff when not in use. This staff includes: PI/study physician(s), and designated clinical research staff. These are also the only people that have access to the link between the patients' personal identifying information and their assigned UPN codes. In terms of the protections and security of electronic clinical data, it is being performed by the University of Washington Information Technology (UW IT) Services. The UW IT information 54 Protocol/Amendment No.: Version 5; 08/20/2018 security policy is to protect University of Washington (UW) information and information  
 systems. It also ensures compliance with UW policy and state and federal regulations.
untitled h1
10.4 compliance with financial disclosure

We will comply with the Financial Conflict of Interest Policy (GIM 10) mandated by the Office of Sponsored Programs of University of Washington. http://www.washington.edu/research/osp/gim/gim10.html
untitled h1
10.5 compliance with law audit

We will follow the terms of the signed contract and any subsequent amendments.
untitled h1
10.6 compliance with trial registration

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 subject to the requirements for submission to the Clinical Trials Data Bank, http://www.clinicaltrials.gov. Information posted will allow subjects 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.
untitled h1
10.7 quality management system

Our group has extensive experience running investigator initiated Phase I and II clinical trials. We have established collection materials and database which we are capable of entering, tracking and reporting clinical trial information, laboratory samples, and reporting requirements. We meet regularly to discuss active clinical trials in terms of recruitment, adverse events or any other issue that might arise. In addition, all clinical staff are trained in HIPAA, Human Subjects and GCP.
untitled h1
10.7.1 data management 10.7.2 collection

We have developed collection methods (case report form and source documentation) to capture study specific data. This includes, but in not limited to the capture of a patients prior disease treatment, clinical laboratory values, adverse events, medications and post enrollment treatments.
untitled h1
10.7.3 database 10.7.3.1. deviation tracking

We have developed a deviation tracking tool within our database, which allows us to track the  
 deviation, reporting requirements and study and regulatory outcomes.  
This report can easily be pulled for reporting purposes.
untitled h1
10.7.3.2 auditing

We perform regular internal audits and track the results. By doing this we are able to determine a trend in data collection methods and allow for improvements in data collection instruments or training. The database incorporates a robust data auditing and tracking feature that documents any data change made to an existing record in the study database, who made the data changes, and when the update was made. The module also tracks the creation and deletion of any records in individual tables and the user who deleted or added the record
untitled h1
10.7.3.3 long term follow up

We have the ability to develop report(s) that allow us to determine when a subject is due to for a study procedure (i.e. imaging or survival data).
untitled h1
10.7.4 security

The database is password protected. Passwords are changed every 90 days. Access privileges are obtained when a new employee is hired. If something is developed or requires new privileges then access will be assessed at that time. If there is a change in a clinical research staff responsibilities access will reassessed at that time. However, once someone has access privileges they can maintain this until they leave their position.
untitled h1
10.7.5 systems backup

The database is stored on a HIPAA compliant secure server with access granted only to the Tumor Vaccine Group. The database is backed-up on tape and stored off-site and the tape is handled according to HIPAA regulations.
untitled h1
11.0 monitoring 12.0 plan 12.1

Institutional support of trial monitoring will be in accordance with the FHCRC/UW Cancer Consortium Institutional Data and Safety Monitoring Plan. Under the provisions of this plan, FHCRC Clinical Research Support (CRS) coordinates data and compliance monitoring 56 Protocol/Amendment No.: Version 5; 08/20/2018 conducted by consultants, contract research organizations, or Fred Hutch employees  
 unaffiliated with the conduct of the study. Independent monitoring visits occur at specified intervals determined by the assessed risk level of the study and the findings of previous visits per the institutional DSMP. In addition, protocols are reviewed at least annually and as needed by the Consortium Data and Safety Monitoring Committee (DSMC), FHCRC Scientific Review Committee (SRC) and the FHCRC/UW Cancer Consortium Institutional Review Board (IRB). The review committees evaluate accrual, adverse events, stopping rules, and adherence to the applicable data and safety monitoring plan for studies actively enrolling or treating patients. The IRB reviews the study progress and safety information to assess continued acceptability of the risk-benefit ratio for human subjects. Approval of committees as applicable is necessary to continue the study. The trial will comply with the standard guidelines set forth by these regulatory committees and other institutional, state and federal guidelines.
untitled h1
12.2 medical monitor

The Medical Monitor, Ron Swensen, M.D., will review data with the P.I., designee, and/or other members of the clinical team, approximately every 6 months. All patients are reviewed for adverse events. Conduct of the study is reviewed and changes/clarifications can be requested/discussed with the Medical Monitor
untitled h1
13.0 appendices 13.1 ecog performance

| Grade                                                                                                                                                                                                                                                                                                    | Description                                                                                                                                                                                     |
|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 0                                                                                                                                                                                                                                                                                                        | Normal activity. Fully active, able to carry on all pre-disease  performance without restriction. Symptoms, but ambulatory. Restricted in physically strenuous                                  |
| 1                                                                                                                                                                                                                                                                                                        | activity, but ambulatory and able to carry out work of a light or  sedentary nature (e.g., light housework, office work). In bed <50% of the time. Ambulatory and capable of all self-care, but |
| 2                                                                                                                                                                                                                                                                                                        | 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 |                                                                                                                                                                                                 |
untitled h1
13.2 common terminology criteria for

The descriptions and grading scales found in the revised NCI Common Terminology Criteria for Adverse Events (CTCAE) version 4.0 will be utilized for adverse event reporting.  
(http://ctep.cancer.gov/reporting/ctc.html)
untitled h1
13.3 response evaluation criteria in

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. In addition, volumetric analysis will be explored by central review for response assessment.
untitled h1
13.4 carboplatin package insert http//www.fda.gov/ohrms/dockets/ac/05/briefing/20054180b0305carboplatin%20label%201-9-04%20fda.pdf

1. Cooke, S.L. and J.D. Brenton, Evolution of platinum resistance in high-grade serous ovarian cancer. The lancet oncology, 2011. 12(12): p. 1169-74.  
2. Colombo, N., et al., *Randomized, open-label, phase III study comparing patupilone*
(EPO906) with pegylated liposomal doxorubicin in platinum-refractory or -resistant patients with recurrent epithelial ovarian, primary fallopian tube, or primary peritoneal cancer. Journal of clinical oncology : official journal of the American Society of Clinical Oncology, 2012. 30(31): p. 3841-7.  
3. Luvero, D., A. Milani, and J.A. Ledermann, Treatment options in recurrent ovarian cancer: latest evidence and clinical potential. Therapeutic advances in medical oncology, 2014. 6(5): p. 229-39.  
4. Bryant, C.S., et al., Feasibility of extension of platinum-free interval with weekly bolus topotecan and subsequent platinum retreatment outcomes in recurrent ovarian cancer.  
Archives of gynecology and obstetrics, 2011. 283(2): p. 361-7.  
5. Zhang, L., et al., *Intratumoral T cells, recurrence, and survival in epithelial ovarian* cancer. The New England journal of medicine, 2003. 348(3): p. 203-13.  
6. Adams, S.F., et al., *Intraepithelial T cells and tumor proliferation: impact on the benefit* from surgical cytoreduction in advanced serous ovarian cancer. Cancer, 2009.  
115(13): p. 2891-902.  
7. Clarke, B., et al., *Intraepithelial T cells and prognosis in ovarian carcinoma: novel*  
  
associations with stage, tumor type, and BRCA1 loss. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc, 2009. 22(3): p.  
393-402.  
8. Hamanishi, J., et al., *Programmed cell death 1 ligand 1 and tumor-infiltrating CD8+*
T lymphocytes are prognostic factors of human ovarian cancer. Proc Natl Acad Sci U
S A, 2007. 104(9): p. 3360-5.  
9. Sato, E., et al., Intraepithelial CD8+ tumor-infiltrating lymphocytes and a high CD8+/regulatory T cell ratio are associated with favorable prognosis in ovarian cancer. Proc Natl Acad Sci U S A, 2005. 102(51): p. 18538-43.  
10. Shah, C.A., et al., *Intratumoral T cells, tumor-associated macrophages, and regulatory* T cells: association with p53 mutations, circulating tumor DNA and survival in women with ovarian cancer. Gynecologic oncology, 2008. 109(2): p. 215-9.  
11. Curiel, T.J., et al., Specific recruitment of regulatory T cells in ovarian carcinoma fosters immune privilege and predicts reduced survival. Nat Med, 2004. 10(9): p. 9429.  
12. Nielsen, J.S., et al., CD20+ tumor-infiltrating lymphocytes have an atypical CD27memory phenotype and together with CD8+ T cells promote favorable prognosis in ovarian cancer. Clinical cancer research : an official journal of the American Association for Cancer Research, 2012. 18(12): p. 3281-92.  
13. Hamanishi, J., et al., Programmed cell death 1 ligand 1 and tumor-infiltrating CD8+
T lymphocytes are prognostic factors of human ovarian cancer. Proceedings of the National Academy of Sciences of the United States of America, 2007. 104(9): p. 33605.  
14. Abiko, K., et al., PD-L1 on tumor cells is induced in ascites and promotes peritoneal dissemination of ovarian cancer through CTL dysfunction. Clin Cancer Res, 2013.  
19(6): p. 1363-74.  
15. Gatalica, Z., et al., *Programmed cell death 1 (PD-1) and its ligand (PD-L1) in common* cancers and their correlation with molecular cancer type. Cancer Epidemiol Biomarkers Prev, 2014. 23(12): p. 2965-70.  
16. Kandalaft, L.E., et al., The emergence of immunomodulation: combinatorial immunochemotherapy opportunities for the next decade. Gynecologic oncology, 2010.  
116(2): p. 222-33.  
17. Hato, S.V., et al., Molecular pathways: the immunogenic effects of platinum-based chemotherapeutics. Clinical cancer research : an official journal of the American Association for Cancer Research, 2014. 20(11): p. 2831-7.  
18. Lesterhuis, W.J., et al., *Platinum-based drugs disrupt STAT6-mediated suppression of* immune responses against cancer in humans and mice. The Journal of clinical investigation, 2011. 121(8): p. 3100-8.  
19. Hamanishi, J., et al., Efficacy and safety of anti-PD-1 antibody (Nivolumab: *BMS936558, ONO-4538) in patients with platinum-resistant ovarian cancer.* Journal of clinical oncology : official journal of the American Society of Clinical Oncology, 2014.  
32(5s): p. (suppl; abstr 5511).  
20. Chang, C.L., et al., Dose-dense chemotherapy improves mechanisms of antitumor immune response. Cancer research, 2013. 73(1): p. 119-27.  
21. Wei, H., et al., *Combinatorial PD-1 blockade and CD137 activation has therapeutic*  
  
efficacy in murine cancer models and synergizes with cisplatin. PloS one, 2013. 8(12):
p. e84927.  
22. Pignata, S., et al., *Carboplatin plus paclitaxel once a week versus every 3 weeks in* patients with advanced ovarian cancer (MITO-7): a randomised, multicentre, openlabel, phase 3 trial. The Lancet. Oncology, 2014. 15(4): p. 396-405.  
23. Gore, M., et al., Randomized trial of dose-intensity with single-agent carboplatin in patients with epithelial ovarian cancer. London Gynaecological Oncology Group. J
Clin Oncol, 1998. 16(7): p. 2426-34.  
24. Herzog, T.J., et al., SGO guidance document *for clinical trial designs in ovarian* cancer: a changing paradigm. Gynecol Oncol, 2014. 135(1): p. 3-7.  
25. Wolchok, J.D., et al., Guidelines for the evaluation of immune therapy activity in solid tumors: immune-related response criteria. Clin Cancer Res, 2009. 15(23): p. 7412-20.  
26. Taube, J.M., 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, 2014.  
20(19): p. 5064-74.  
27. Robert, C., et al., *Anti-programmed-death-receptor-1 treatment with pembrolizumab* in ipilimumab-refractory advanced melanoma: a randomised dose-comparison cohort of a phase 1 trial. Lancet, 2014. 384(9948): p. 1109-17.  
28. Gustafson, M.P., et al., Immune monitoring using the predictive power of immune profiles. J Immunother Cancer, 2013. 1: p. 7.  
29. Curiel, T.J., et al., *Specific recruitment of regulatory T cells in ovarian carcinoma* fosters immune privilege and predicts reduced survival. Nature medicine, 2004. 10(9):
p. 942-9.  
30. Cui, T.X., et al., Myeloid-derived suppressor cells enhance stemness of cancer cells by inducing microRNA101 and suppressing the corepressor CtBP2. Immunity, 2013.  
39(3): p. 611-21.  
31. Park, H.J., et al., *PD-1 Upregulated on Regulatory T Cells during Chronic Virus* Infection Enhances the Suppression of CD8+ T Cell Immune Response via the Interaction with PD-L1 Expressed on CD8+ T Cells. J Immunol, 2015.