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10.4 data management and quality

The data will be entered into a HIPAA-compliant database. The Study Staff will be responsible for data processing, in accordance with procedural documentation. Database lock will occur once quality assurance procedures have been completed.  
All procedures for the handling and analysis of data will be conducted using good computing practices meeting FDA guidelines for the handling and analysis of data for clinical trials.
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10.5 data and safety monitoring

Adherence to the protocol, Good Clinical Practices (GCP) and institutional policy will be monitored by the PI during the course of the study through routine Disease Research Group (DRG) meetings (or equivalent). In addition, the SOCCI Cancer Clinical Trials Office (CCTO) Quality Management Core (QMC) will conduct internal monitoring visits and audits for data quality and protocol adherence. QMC reports will then be forwarded to the SOCCI Data and Safety Monitoring (DSMC). QMC will also conduct the following:
1. Central eligibility verification for all subjects enrolled as described in protocol Section 4.  
2. Central review of all eligibility waivers by a SOCCI Medical reviewer to assess appropriateness and risk to ensure quality data and ensure subject safety protections for investigator-initiated research
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10.5.2 safety monitoring high risk

Oversight of the progress and safety of the study will be provided by the PI. The PI will maintain continuous safety monitoring for the duration of the study by reviewing subject/study data. Adverse events and unanticipated problems are not expected, but if they occur they will be documented and reported according to CSMC IRB policies and procedures. If the PI becomes aware of any new safety information that may place subjects at increased risk than what was previously known the IRB will be promptly notified and if warranted, enrollment may be held until the PI determines whether a modification to the study is necessary and/or the informed consent documents are updated accordingly. In addition, this protocol will utilize the SOCCI Data and Safety Monitoring Committee will provide another layer of data and safety oversight. Committee membership includes experts in the field of oncology, nursing, pharmacy, and biostatistics in reviewing the over data, safety, quality, and study integrity of SOCCI interventional IITs. DSMC membership and responsibilities are governed by the committee charter. The DSMC findings and recommendations will be reported in writing to the Principal Investigator. A summary letter will be forwarded by the Principal Investigator or his/her designee to the CedarsSinai Medical Center IRB. .  
DSMC Medical Monitor: Ronald L. Paquette, MD The DSMC Medical Monitor appointed to this study is independent of the research team listed in this protocol. The DSMC Medical Monitor also assumes the specific duties and responsibilities of the Department of Defense (DoD) Research monitor as listed below.  
DSMC Monitors responsibilities include:
- Attend the DSMC meeting at which the submitted protocol is to be reviewed in order to present a brief synopsis of the reported study outcomes.  
- Assessment of DSM risk category and the proposed DSMP. Provide recommendation for PRMC's final determination. The Data and Safety Monitoring (DSM) Risk Category Worksheet may be used. The DSMP Reviewer Worksheet may be used.  
- Submit a written review summary to the DSMC Coordinator prior to the meeting. The DSMC medical/biostatistician monitor reviewer worksheet may be used. In the rare event the medical monitor or biostatistician are unable to attend and a substitute appointed DSMC Chair or Vice Chair, the monitor's written review summary may be read during the room. Proxy voting is not allowed.  
- Review of data and safety monitoring reports for each study is complete and accurate.  
DoD Research Monitor Duties, Authorities, and Responsibilities:
- Observe recruitment and enrollment procedures and the consent process for individuals, groups or units
- Oversee study interventions and interactions
- Review monitoring plans and UPIRSO reports
- Oversee data matching , data collection, and analysis
- At a minimum, the research monitor: may discuss the research protocol with the investigators, interview human subjects, and consult with others outside of the study about the research; shall have authority to stop a research protocol in progress, remove individual human subjects from a research protocol, and take whatever steps are necessary to protect the safety and well-being of human subjects until the IRB
can assess the monitor's report; shall have the responsibility to promptly report their observations and findings to the IRB or other designated official and the HRPO.
10.6 **Record Retention**
Study documentation includes all Case Report Forms, data correction forms or queries, source documents, monitoring/auditing logs/letters, and regulatory documents (e.g., protocol and amendments, IRB correspondence and approval, signed patient consent forms). Source documents include all recordings of observations or notations of clinical activities and all reports and records necessary for the evaluation and reconstruction of the clinical research study. Government agency regulations and directives require that the study investigator must retain all study documentation pertaining to the conduct of a clinical trial. Study documents should be kept on file per local guidelines.  
10.7 **Adherence to Protocol**
Except for an emergency situation in which proper care for the protection, safety, and well-being of the study patient requires alternative treatment, or a protocol exception request approved by the SOCCI Medical Director and CSMC IRB, the study shall be conducted exactly as described in the approved protocol.
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10.7.1 emergency modifications

Investigators may implement a deviation from, or a change of, the protocol to eliminate an immediate hazard(s) to trial subjects without prior IRB approval. For any such emergency modification implemented, the IRB must be notified as soon as possible, but no more than 10 days from the investigator's awareness of the event.
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10.7.2 protocol exceptions and eligibility

An exception is an anticipated or planned deviation from the IRB-approved research protocol, as described in the IRB Policy*, Reporting Possible Unanticipated Problems* Involving Risks to Subject or Others (UPIRSO) Policy: Institutional Review Board/Research Compliance and Quality Improvement.  
A protocol exception most often involves a single subject and is not a permanent revision to the research protocol. Protocol exceptions that extend beyond a single subject should result in a protocol amendment to avoid serial violations.  
All exception requests must be reviewed by the SOCCI CCTO Medical Director and the Institutional Review Board prior to implementation. The PI or her/his designee is responsible for submitting a protocol exception and its supporting documents to the SOCCI Medical Director for review. Planned exceptions to the protocol that are more than logistical and/or have the potential to affect the subject's safety and/or study integrity may not be implemented without prior approval from the SOCCI Medical Director and IRB.
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special considerations for eligibility waivers

In general, subjects who do not meet the eligibility requirements should not be enrolled.  
In the rare event that it is appropriate for subject inclusion, the rationale/justification and subject case history should be forwarded to the SOCCI CCTO Medical Director for assessment **prior** to submission to the IRB for approval.  
The CCTO Medical Director will review the case and contact the PI if additional information is needed or further discussion is warranted. The CCTO Medical Director will provide a written assessment/recommended course of action. The CCTO Medical Director's assessment must be uploaded into CS-IRB with the waiver request for IRB
review and consideration. The CCTO Medical Director may recommend future protocol changes.
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eligibility waiver submission process

The PI and/or treating physician should provide written request for a waiver which includes case history and justification for prospective deviation from the study design to the SOCCI CCTO Medical Director.
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10.7.3 other protocol deviations

Logistical deviations from the protocol (e.g., minor changes to the study schedule for an individual subject) do not require prior IRB approval unless the deviation has the potential to affect the subject's safety. Such planned deviations that do meet this definition and do not affect the subject's safety should be noted in the subject's research record or deviation log as described in the SOCCI CCTO's Standard Operating Procedure 12:
Deviation and Noncompliance Reporting.  
Unintentional deviations from the protocol that might affect subject safety or study integrity should be reported to the IRB within 10 days from when the investigator becomes aware that such a deviation has occurred, as outlined in the SOCCI CCTO's Standard Operating Procedure 12: *Deviation and Noncompliance Reporting*. In this case, a Protocol Deviation report must be submitted in CS-IRB, per IRB policy, *Reporting* Possible Unanticipated Problems Involving Risks to Subject or Others (UPIRSO) Policy:
Institutional Review Board/Research Compliance and Quality Improvement. All submissions should include a description of the plan to avoid similar deviations or exceptions in the future.
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10.7.4 amendments to the protocol

Should amendments to the protocol be required, the amendments will be originated and documented by the PI. It should also be noted that when an amendment to the protocol substantially alters the study design or the potential risk to the patient, a revised consent form might be required.  
The written amendment, and if required the amended consent form, must be sent to the IRB for approval prior to implementation. Repeat exceptions or deviations to the protocol may suggest a protocol amendment is needed.  
10.8 **Obligations of Investigators**
The PI is responsible for the conduct of the clinical trial at the site in accordance with Title 21 of the Code of Federal Regulations and/or the Declaration of Helsinki. The PI is responsible for personally overseeing the treatment of all study patients. The PI must assure that all study site personnel, including co-investigators and other study staff members, adhere to the study protocol and all FDA/GCP/NCI regulations and guidelines regarding clinical trials both during and after study completion. The PI will be responsible for assuring that all the required data will be collected and entered onto the Case Report Forms and/or into a HIPAA-compliant study database. Periodically, monitoring visits will be conducted and the PI will provide access to his/her original records to permit verification of proper entry of data. At the completion of the study, all case report forms will be reviewed by the PI and will require her final signature to verify the accuracy of the data.
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12.0 references

1. Demaria S, Volm MD, Shapiro RL, et al: Development of tumor-infiltrating lymphocytes in breast cancer after neoadjuvant paclitaxel chemotherapy. Clin Cancer Res 7:3025-30, 2001 2. Organization WH: World Cancer Report. Lyon, France, IARCPress, 2003 3. Berry DA, Cronin KA, Plevritis SK, et al: Effect of screening and adjuvant therapy on mortality from breast cancer. N Engl J Med 353:1784-92, 2005 4. Society AC: Cancer Facts and Figures. Atlanta, American Cancer Society, 2016 5. Perou CM, Sorlie T, Eisen MB, et al: Molecular portraits of human breast tumours. Nature 406:747-52, 2000 6. Dent R, Hanna WM, Trudeau M, et al: Pattern of metastatic spread in triplenegative breast cancer. Breast Cancer Res Treat 115:423-8, 2009 7. Adams S, Gray RJ, Demaria S, et al: Prognostic value of tumor-infiltrating lymphocytes in triple-negative breast cancers from two phase III randomized adjuvant breast cancer trials: ECOG 2197 and ECOG 1199. J Clin Oncol 32:2959-66, 2014 8. Dieci MV, Criscitiello C, Goubar A, et al: Prognostic value of tumor-infiltrating lymphocytes on residual disease after primary chemotherapy for triple-negative breast cancer: a retrospective multicenter study. Ann Oncol 26:1518, 2015 9. Jiang X, Ellison SJ, Alarid ET, et al: Interplay between the levels of estrogen and estrogen receptor controls the level of the granzyme inhibitor, proteinase inhibitor 9 and susceptibility to immune surveillance by natural killer cells. Oncogene 26:4106-14, 2007 10. Mostafa AA, Codner D, Hirasawa K, et al: Activation of ERalpha signaling differentially modulates IFN-gamma induced HLA-class II expression in breast cancer cells. PLoS One 9:e87377, 2014 11. Rakha EA, Reis-Filho JS, Ellis IO: Combinatorial biomarker expression in breast cancer. Breast Cancer Res Treat 120:293-308, 2010 12. Fisher B, Anderson S, Bryant J, et al: Twenty-year follow-up of a randomized trial comparing total mastectomy, lumpectomy, and lumpectomy plus irradiation for the treatment of invasive breast cancer. N Engl J Med 347:1233-41, 2002 13. Deng L, Liang H, Burnette B, et al: Irradiation and anti-PD-L1 treatment synergistically promote antitumor immunity in mice. J Clin Invest 124:687-95, 2014 14. Postow MA, Callahan MK, Barker CA, et al: Immunologic correlates of the abscopal effect in a patient with melanoma. N Engl J Med 366:925-31, 2012 15. Burnette BC, Liang H, Lee Y, et al: The efficacy of radiotherapy relies upon induction of type i interferon-dependent innate and adaptive immunity. Cancer Res 71:2488-96, 2011 16. Rugo H, Delord J-P, Im S-A, et al: Preliminary efficacy and safety of pembrolizumab (MK-3475) in patients with PD-L1–positive, estrogen receptor-positive
(ER+)/HER2-negative advanced breast cancer enrolled in KEYNOTE-028. Cancer Research 76:Abstract S5-07, 2016 17. Dirix L, Takacs I, Nikolinakos P, et al: Avelumab (MSB0010718C), an anti-PDL1 antibody, in patients with locally advanced or metastatic breast cancer: A phase Ib JAVELIN
solid tumor trial. Cancer research 76:Abstract S1-04, 2016 18. Nanda R, Chow LQ, Dees EC, et al: Pembrolizumab in Patients With Advanced Triple-Negative Breast Cancer: Phase Ib KEYNOTE-012 Study. J Clin Oncol 34:2460-7, 2016 19. Emens L, Braiteh F, Cassier P, et al: Inhibition of PD-L1 by MPDL3280A leads to clinical activity in patients with metastatic triple-negative breast cancer (TNBC). Cancer Research 75:Abstract 2859, 2015 20. Schmid P, Cruz C, Braiteh F, et al: Atezolizumab in metastatic TNBC (mTNBC):
Long-term clinical outcomes and biomarker analyses, AACR Annual Meeting 2017. Washington DC, 2017 21. Kachikwu EL, Iwamoto KS, Liao YP, et al: Radiation enhances regulatory T cell representation. Int J Radiat Oncol Biol Phys 81:1128-35, 2011 22. Jobling MF, Mott JD, Finnegan MT, et al: Isoform-specific activation of latent transforming growth factor beta (LTGF-beta) by reactive oxygen species. Radiat Res 166:83948, 2006 23. Demaria S, Kawashima N, Yang AM, et al: Immune-mediated inhibition of metastases after treatment with local radiation and CTLA-4 blockade in a mouse model of breast cancer. Clin Cancer Res 11:728-34, 2005 24. Dewan MZ, Galloway AE, Kawashima N, et al: Fractionated but not single-dose radiotherapy induces an immune-mediated abscopal effect when combined with anti-CTLA-4 antibody. Clin Cancer Res 15:5379-88, 2009 25. Verbrugge I, Hagekyriakou J, Sharp LL, et al: Radiotherapy increases the permissiveness of established mammary tumors to rejection by immunomodulatory antibodies. Cancer Res 72:3163-74, 2012 26. Ho A, Baker CA, Gucalp A, et al: Preliminary results from a single-arm, phase II
study assessing the efficacy of pembrolizumab plus radiotherapy in metastatic triple negative breast cancer. J Clin Oncol 35:abstract 95, 2017 27. von Minckwitz G, Schneeweiss A, Loibl S, et al: Neoadjuvant carboplatin in patients with triple-negative and HER2-positive early breast cancer (GeparSixto; GBG 66): a randomised phase 2 trial. Lancet Oncol 15:747-56, 2014 28. Schmid P, Adams S, Rugo HS, et al: Atezolizumab and Nab-Paclitaxel in Advanced Triple-Negative Breast Cancer. N Engl J Med 379:2108-2121, 2018 29. Holland R, Veling SH, Mravunac M, et al: Histologic multifocality of Tis, T1-2 breast carcinomas. Implications for clinical trials of breast-conserving surgery. Cancer 56:97990, 1985 30. Bartelink H, Maingon P, Poortmans P, et al: Whole-breast irradiation with or without a boost for patients treated with breast-conserving surgery for early breast cancer: 20year follow-up of a randomised phase 3 trial. Lancet Oncol 16:47-56, 2015 31. Polgar C, Fodor J, Orosz Z, et al: Electron and high-dose-rate brachytherapy boost in the conservative treatment of stage I-II breast cancer first results of the randomized Budapest boost trial. Strahlenther Onkol 178:615-23, 2002 32. Swedish Rectal Cancer T, Cedermark B, Dahlberg M, et al: Improved survival with preoperative radiotherapy in resectable rectal cancer. N Engl J Med 336:980-7, 1997 33. Tepper JE, Suit HD: Radiation therapy of soft tissue sarcomas. Cancer 55:2273-7, 1985 34. Horton JK, Blitzblau RC, Yoo S, et al: Preoperative Single-Fraction Partial Breast Radiation Therapy: A Novel Phase 1, Dose-Escalation Protocol With Radiation Response Biomarkers. Int J Radiat Oncol Biol Phys 92:846-55, 2015 35. Bondiau PY, Courdi A, Bahadoran P, et al: Phase 1 clinical trial of stereotactic body radiation therapy concomitant with neoadjuvant chemotherapy for breast cancer. Int J Radiat Oncol Biol Phys 85:1193-9, 2013 36. Lugade AA, Moran JP, Gerber SA, et al: Local radiation therapy of B16 melanoma tumors increases the generation of tumor antigen-specific effector cells that traffic to the tumor. J Immunol 174:7516-23, 2005 37. Gerber SA, Sedlacek AL, Cron KR, et al: IFN-gamma mediates the antitumor effects of radiation therapy in a murine colon tumor. Am J Pathol 182:2345-54, 2013 38. Lugade AA, Sorensen EW, Gerber SA, et al: Radiation-induced IFN-gamma production within the tumor microenvironment influences antitumor immunity. J Immunol 180:3132-9, 2008 39. Patnaik A, Kang SP, Rasco D, et al: Phase I Study of Pembrolizumab (MK-3475; Anti-PD-1 Monoclonal Antibody) in Patients with Advanced Solid Tumors. Clin Cancer Res 21:4286-93, 2015 40. Denkert C, Loibl S, Noske A, et al: Tumor-associated lymphocytes as an independent predictor of response to neoadjuvant chemotherapy in breast cancer. J Clin Oncol 28:105-13, 2010 41. Loi S, Sirtaine N, Piette F, et al: Prognostic and predictive value of tumorinfiltrating lymphocytes in a phase III randomized adjuvant breast cancer trial in node-positive breast cancer comparing the addition of docetaxel to doxorubicin with doxorubicin-based chemotherapy: BIG 02-98. J Clin Oncol 31:860-7, 2013 42. Zitvogel L, Galluzzi L, Kepp O, et al: Type I interferons in anticancer immunity.  
Nat Rev Immunol 15:405-14, 2015 43. Tan AH, Goh SY, Wong SC, et al: T helper cell-specific regulation of inducible costimulator expression via distinct mechanisms mediated by T-bet and GATA-3. J Biol Chem 283:128-36, 2008 44. Chen KH, Boettiger AN, Moffitt JR, et al: RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348:aaa6090, 2015 45. Iida N, Dzutsev A, Stewart CA, et al: Commensal bacteria control cancer response to therapy by modulating the tumor microenvironment. Science 342:967-70, 2013 46. Sivan A, Corrales L, Hubert N, et al: Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy. Science 350:1084-9, 2015 47. Stanton SE, Adams S, Disis ML: Variation in the Incidence and Magnitude of Tumor-Infiltrating Lymphocytes in Breast Cancer Subtypes: A Systematic Review. JAMA Oncol 2:1354-1360, 2016 48. Shah SP, Roth A, Goya R, et al: The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature 486:395-9, 2012 49. Wolff AC, Hammond ME, Hicks DG, et al: Recommendations for human epidermal growth factor receptor 2 testing in breast cancer: American Society of Clinical Oncology/College of American Pathologists clinical practice guideline update. J Clin Oncol 31:3997-4013, 2013 50. Zitvogel L, Apetoh L, Ghiringhelli F, et al: Immunological aspects of cancer chemotherapy. Nat Rev Immunol 8:59-73, 2008 51. Cortazar P, Zhang L, Untch M, et al: Pathological complete response and longterm clinical benefit in breast cancer: the CTNeoBC pooled analysis. Lancet 384:164-72, 2014 52. Toi M, Lee S-J, Lee E, et al: A phase III trial of adjuvant capecitabine in breast cancer patients with HER2-negative pathologic residual invasive disease after neoadjuvant chemotherapy (CREATE-X, JBCRG-04). Cancer Research 76:Abstract S1-07, 2016 53. Bleicher RJ, Ruth K, Sigurdson ER, et al: Time to Surgery and Breast Cancer Survival in the United States. JAMA Oncol 2:330-9, 2016 54. Chavez-MacGregor M, Clarke CA, Lichtensztajn DY, et al: Delayed Initiation of Adjuvant Chemotherapy Among Patients With Breast Cancer. JAMA Oncol 2:322-9, 2016 55. Morrow M, Jagsi R, Alderman AK, et al: Surgeon recommendations and receipt of mastectomy for treatment of breast cancer. JAMA 302:1551-6, 2009 56. Salgado R, Denkert C, Demaria S, et al: The evaluation of tumor-infiltrating lymphocytes (TILs) in breast cancer: recommendations by an International TILs Working Group 2014. Ann Oncol 26:259-71, 2015
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appendix a protocol summary of

1. PI change from Alice Ho, MD to Stephen Shiao, MD, PhD
2. Revisions to study schema for clarification 3. Throughout document: research MRI has been removed 4. Formatting throughout document 5. Addition of Table 3: Dose Modification and Toxicity Management Guidelines for Immune-related AEs Associated with Pembrolizumab 6. Section 6.1.8: Research-Related Laboratory Evaluation Clarification that "Labs must be drawn, but do not require results to determine eligibility or treatment continuation."
7. Section 6.4: Time and Events Table o Clarification of Pathology review o Clarification of safety bloodwork and thyroid function panel (to be obtained at screening; additional specimens not required C1D1)
o Clarification of follow up schedule 8. Section 7.6: Reporting Requirements for Adverse Events o Change AE collection from within 30 days of last dose of pembrolizumab to 90 days o Updated expedited reporting contact and phone number
- 10. Section 11.0: Removal of reference 55
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amendment 2 (changes made in

1. List of abbreviations updated to include YR and SUSAR
2. Radiation treatment timing and dose clarified throughout document 3. Section 2.3: added new exploratory objective 2.3.5 to assess changes in breast cosmesis 4. Section 2.4: Safety evaluations clarified to include those related to both pembrolizumab and radiation therapy 5. Section 3.0: updated to clarify cohort number as 2 cohorts only 6. Section 4.1.17: WOCBP definition added to eligibility criteria regarding negative serum pregnancy test 7. Section 5.1.2: revisions to radiation treatment parameters that clarify total treatment dose 8. Section 5.1.2.3 - 5.1.2.9: radiation dosing constraints clarified 9. Section 5.4: Table 2 removed and replaced with table 3 (Table 3 relabeled as table 2).  
10. Section 6.1, 6.2 & 6.3: added directions and timing of cosmesis study procedures 11. Section 6.1: clarification of screening procedure timing within 14 days prior to C1D1 12. Section 6.2: clarification of adverse event collection for both pembrolizumab and radiation therapy 13. Section 6.4: Time and Events Table o Cosmesis study added to table o Clarification of adverse event collection o Clarification of pregnancy evaluations o Clarification of follow up scheduled, Q6Mo's post treatment 14. Section 7.3: clarification of adverse event collection timepoints 15. Section 7.6.4: addition of IND reporting guidelines 16. Appendix C: Harvard Four Tier Cosmesis Scale added to accompany breast cosmesis study 17. Formatting throughout document
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amendment 3 (changes made in

1. Formatting throughout document 2. Section 4.1.6: Clarified eligibility criteria to match study schema and current practices. TNBC
patients (defined as ER<10%, PR<10%, HER2-neu 0-1+ by IHC or FISH-negative; or as per MD
discretion).
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amendment 5 changes made in

1. Formatting changes throughout document 2. Addition of optional research breast MRI to the following sections:
a. Study schema and study summary updated b. 1.6 Correlative Studies c. Secondary Objective 2.3.6 added MRI to assess disease status d. Section 4.2.8: exclusion criteria added: For subjects who agree to the research breast MRI sub-study: Four or more previous gadolinium contrast scans in the past 12 months due to the risk of brain deposits following repeated use of gadolinium-based contrast agents.  
e. Study procedures 6.0 updated with correct MRI timepoints f. Section 6.4 Schedule of events updated to include MRI g. Optional MR Breast Imaging section added to 8.0 Correlatives/Special Studies
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amendment 6 changes made in

1. Formatting changes throughout document 2. Study objective 2.2.3 clarified safety/tolerability to feasibility throughout document 3. Addition of new study objective: To assess the pathological complete response (pCR) rates.  
a. Study summary updated b. Secondary Objective 2.3.7 added c. New study endpoint added to section 2.4 4. Clarification to section 3.0 to state that:
- If at least 80% of the **first** 10 subjects in the TNBC *cohort proceed with standard of care* therapy without delay, the combination will be deemed safe in the cohort, and enrollment in the HR+ cohort, as well as continued enrollment in the TNBC cohort (from 10 to 20 subjects), will occur at that time.  
5. Eligibility updates for inclusion criteria, section 4.1:
a. Addition of coagulation parameters b. Standard of care imaging criterion clarified 6. Eligibility updates for exclusion criteria, Section 4.2:
a. Addition of evidence of metastatic disease b. Addition of exclusion of immunodeficiencies
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amendment 4 (changes made in

2. Addition of 10 TNBC subjects throughout document:
a. Study Schema and Study Summary b. Section 3.0 Study Design c. Section 9.1 Sample Size 3. Radiation Therapy window updated to 5 business days throughout document 4. Section 5.8 Subject Replacement: Clarified subjects who fail to complete the study intervention or are not evaluable for the primary endpoint will be replaced.  
5. Section 6.0 Study Procedures: Screening window updated to 28 calendar days 6. Section 9.0 Statistics: Update to statistics to reflect enlarged sample size.  
c. Addition of exclusion of additional known malignancies progressing or receiving active treatment in past 3 years.  
d. Revised exclusion of concurrent diseases e. Revised exclusion of prohibited treatments and/or therapies f. Exclusion of WOCBP with positive pregnancy test within 72 hours prior to study start.  
7. Toxicity information updates from Merck added to section 5.4 Dosing a. Inclusion of Table 3 Pembrolizumab Infusion Reaction Dose modification and Treatment Guidelines; provided by Merck 8. Changed Section 10.5 to reflect the addition of the Data Safety and Monitoring Committee and revised risk categories and safety monitoring.
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amendment 7 changes made in

1. Revised study title 2. Clarification of Principal Investigators a. Stephen Shiao, MD, PhD as overall study PI
b. Reva Basho, MD as PI for ER+ cohort 3. Revisions to Study Schema for clarification of cohorts 4. Study Summary a. Number of subjects changed from 30 to 60 5. Background and Rationale a. Section 1.3.2 Clinical Data updated with recent observations to proceed with the phase II
portion of this trial 6. Study Objectives a. Section 2.1 Primary Objectives revised 7. Study Design Section 3.0 a. Updated description of study design to Phase Ib/II study b. Expansion of cohorts to 50 TNBC and 10 HR+ women c. Clarified safety assessment 8. Exclusion Criteria 4.2.8 minor correction to incomplete sentence 9. Exclusion Criteria a. Removed pregnancy testing within 72 hours prior to study start and moved as part of Study Procedures 10. Time and Events Table a. Added footnote regarding pregnancy testing for clarification on timepoints 11. Added Section 7.7 for Reporting to US Army Medical Research and Material Command Office
(USARMC) of Research Protections (ORP) Human Research Protection Office (HRPO)
12. Statistical Considerations a. Updated Section 9.1 Sample Size with description of Phase 1b and Phase II
b. Minor revision to Section 9.2.1 Efficacy Analysis for clarification and addition of Phase II
13. Registration Procedures Section 10.3 revised for new CCTO name 14. Safety Monitoring Section 10.5.2 a. Added details and reference to the DSMC Charter and appointed DSMC Medical Monitor for this study
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amendment 8 changes made in

1. Formatting changes throughout document 2. Inserted Protocol Signature Page 3. Study Schema: added procurement of fresh surgical tissue collection post neoadjuvant systemic therapy 4. Inclusion Criteria Clarification a. 4.1.7: minor revision to include acceptable assessment by clinical exam b. 4.1.12: minor revision to clarify that eligibility includes candidacy for breast-conserving therapy versus planned 5. Section 6.4: Time & Events Table a. Revised footnote \#10 to add option to procure fresh tissue specimen if surgery is after completion of SOC neoadjuvant systemic therapy 6. Section 6.5: minor corrections to subheading typos 7. Section 7.6.2: Expedited Reporting a. Added DSMC required language regarding expedited reporting for interventional cancer IITs 8. Section 8.1: Assay Methodology a. Correction of Appendix label in reference to the Salgado criteria b. Added description RCB value as a supplemental methodology for pCR assessment 9. Section 9.1 Sample Size: revised description to align with Section 3.0. 10. Addition of language to allow for fresh specimen collection at the time of SOC surgery if subject receives neoadjuvant systemic therapy after study treatment. The following sections incorporate this change:
a. Section 6.2.2: Prior to standard of care treatment or at the time of surgery if that is the planned standard of care treatment b. Section 6.4: Time and Events Table; Footnote \#10 c. Section 8.2: Sample Collection / Specimen Banking 11. Sections 10.5.2 and 10.7.3 updated with standard institutional language and required language by the Department of Defense. Removed references to the DSMC Charter as this is an internal document not to be released.
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amendment 9 changes made in

1. Section 6.3: Follow-up Procedures a. Added 6.3.5 description of endocrine toxicity assessment, including collection of full thyroid function panel and cortisol results at one year +/- 2 months post-treatment followup.  
b. Section 6.3.2: AE Assessment revised to clarify that AE collection may be completed via phone call for subjects who are receiving standard treatment at their local treating physician's office.  
2. Section 6.4: Time and Events Table a. Minor revision for additional timepoint for full thyroid function panel at one year posttreatment follow-up b. Added cortisol results collection at one year post-treatment follow-up as part of standard of care endocrine toxicity assessment c. Added Footnote \#16 for description of cortisol lab results along with full thyroid function panel at one year post-treatment follow-up (+/- 2 months).  
3. Section 7.0: Adverse Events a. Added note to clarify that AE collection may be done via phone call, usually around Weeks 7 - 25, for subjects receiving standard chemotherapy at their treating physician's office.
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amendment 10 changes made in

1. Section 4.1 Inclusion Criteria a. Inclusion criteria 4.1.17: Added note to clarify that in the setting of egg harvesting, patients are not required to take a pregnancy test within 72 hours of C1D1 due to the high likelihood of false positive results.  
2. Section 6.1 Study Procedures a. Study Procedures 6.1.10: Added note to clarify that in the setting of egg harvesting, patients are exempt from taking a pregnancy test within 72 hours of C1D1 due to the high likelihood of false positive results.  
3. Section 6.4 Time & Events Table a. Footnote \#8 clarifies pregnancy testing requirements in the setting of egg harvesting.
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amendment 11 changes made in

1. Study Summary a. For addition of survival status assessment for up to 5 years, study duration changed from
"Approx. 1 year" to "Approx. 5 years" 2. Section 4.1 Inclusion Criteria a. Inclusion criterion 4.1.17: Added note to incorporate language from Protocol Clarification Memo dated 30JUN2020 regarding pregnancy testing exemption for egg harvesting patients where due to false positive results lasting for at least two weeks (and therefore are exempt from pregnancy testing within 14 days of C1D1), these subjects may enroll only per investigator discretion.  
3. Section 6.1 Study Procedures a. Study Procedures 6.1.10: Added note to incorporate language from Protocol Clarification Memo dated 30JUN2020 regarding pregnancy testing exemption for egg harvesting patients where due to false positive results lasting for at least two weeks (and therefore are exempt from pregnancy testing within 14 days of C1D1), these subjects may enroll only per investigator discretion.  
b. Section 6.3.6: Added survival status assessment and any evidence of recurrence to be conducted every 6 months for up to 5 years c. Research blood tubes corrected to 3 CPT, 1 red-top tube, and 1 green-top tube of blood.  
4. Section 6.4 Time and Events Table a. Added timepoint for survival status assessment and documentation of recurrence for 5 years b. Research blood tubes corrected to 3 CPT, 1 red-top tube, and 1 green-top tube of blood.  
5. Section 8.0 Correlatives/Special Studies a. Added description of whole genome/exome sequencing from frozen or FFPE tumor samples.
iit2017-07-ho-pembrort preoperative combination of pembrolizumab
appendix b salgado criteria for

Recommendations for assessing tumor-infiltrating lymphocytes (TILs) in breast cancer  
1. TILs should be reported for the stromal compartment (=% stromal TILs). The denominator used to determine the % stromal TILs is the area of stromal tissue (i.e. area occupied by
mononuclear inflammatory cells over total intratumoral stromal area), not the number of stromal cells (i.e. fraction of total stromal nuclei that represent mononuclear inflammatory cell nuclei).  
2. TILs should be evaluated within the borders of the invasive tumor. 3. Exclude TILs outside of the tumor border and around DCIS and normal lobules.  
4. Exclude TILs in tumor zones with crush artifacts, necrosis, regressive hyalinization as well as in the previous core biopsy site.  
5. All mononuclear cells (including lymphocytes and plasma cells) should be scored, but polymorphonuclear leukocytes are excluded.  
6. One section (4–5 µm, magnification ×200–400) per patient is currently considered to be sufficient.  
7. Full sections are preferred over biopsies whenever possible. Cores can be used in the
pretherapeutic neoadjuvant setting; currently no validated methodology has been developed to score TILs after neoadjuvant treatment.  
8. A full assessment of average TILs in the tumor area by the pathologist should be used. Do not focus on hotspots.  
9. The working group's consensus is that TILs may provide more biological relevant information
when scored as a continuous variable, since this will allow more accurate statistical analyses, which can later be categorized around different thresholds. However, in daily practice, most pathologists will rarely report for example 13.5% and will round up to the nearest 5%–10%, in this example thus 15%. Pathologist should report their scores in as much detail as the pathologist feels comfortable with.  
10. TILs should be assessed as a continuous parameter. The percentage of stromal TILs is a semi quantitative parameter for this assessment, for example, 80% stromal TILs means that
80% of the stromal area shows a dense mononuclear infiltrate. For assessment of percentage values, the dissociated growth pattern of lymphocytes needs to be taken into account.  
Lymphocytes typically do not form solid cellular aggregates; therefore, the designation '100%
stromal TILs would still allow some empty tissue space between the individual lymphocytes.  
11. No formal recommendation for a clinically relevant TIL threshold(s) can be given at this stage.  
The consensus was that a valid methodology is currently more important than issues of thresholds for clinical use, which will be determined once a solid methodology is in place. lymphocyte-predominant breast cancer can be used as a descriptive term for tumors that contain more lymphocytes than tumor cells. However, the thresholds vary between 50% and 60% stromal lymphocytes.
iit2017-07-ho-pembrort preoperative combination of pembrolizumab
appendix c harvard four-tier cosmesis

| Score Excellent   | Treated breast nearly identical to untreated breast                                 |
|-------------------|-------------------------------------------------------------------------------------|
| Good              | Treated breast slightly different from untreated breast                             |
| Fair              | Treated breast clearly different from untreated breast but not  seriously distorted |
| Poor              | Treated breast seriously distorted                                                  |