OBJECTIVES 13 2.1 Primary objectives 13 2.2 Secondary objectives 13 3. STUDY DESIGN 14 3.1 Description of study 14 3.2 Rationale for study design 15 3.3 Outcome measures 16 3.3.1 Primary outcome measures 16 3.3.2 Secondary outcome measures 16 3.4 Safety considerations 17 3.4.1 Trastuzumab 17 3.4.2 Nelipepimut-S and GM-CSF 18 3.5 Compliance with laws and regulations 19 4. MATERIALS AND METHODS 19 4.1 Patients 19 4.1.1 Patient selection 19 4.1.2 Inclusion criteria 20 4.1.3 Exclusion criteria 23 4.2 Method of treatment assignment 23 4.3 Study treatment 23 4.3.1 Trastuzumab 24 4.3.2 Vaccine 24 4.3.2.1 Dosage and preparation 24 4.3.2.2 Storage 25 4.3.3 Inoculation series administration 25 4.3.4 Booster inoculations 26 4.4 Study assessments 26 4.4.1 Pretreatment assessments 26 4.4.2 Assessments during treatment 27 4.4.3 Follow-up assessments 27 4.4.4 Blood collection and processing 28 4.4.5 HLA-A2/A3/A24/A26 testing 29 4.4.6 Dextramer assay 29 4.4.7 Local reaction 29 4.4.8 DTH reaction 30 4.5 Discontinuation of protocol-specific therapy 30 4.6 Patient discontinuation 31 3 Protocol: 2014-0443 Version 2.1 Version Date: 11 April 2016 4.7 Study discontinuation 32 4.8 Data collection 32 4.9 Statistical methods 33 4.9.1 Rationale for study design 33 4.9.2 Sample size determination 33 4.9.3 Data analysis 34 4.9.3.1 Study patient characteristics 34 4.9.3.2 Primary efficacy analysis 34 4.9.3.3 Secondary efficacy analysis 35 4.9.4 Withdrawal 36 4.9.5 Missing data 36 4.9.6 Interim analysis 36 5. ADVERSE EVENTS 36 5.1 Adverse event and reporting definitions 36 5.2 Reporting of serious adverse events associated with 37 this study 5.2.1 MedWatch 3500A reporting guidelines 38 5.3 Reporting requirements for IND holders 39 6. INVESTIGATOR REQUIREMENTS 40 6.1 Study initiation 40 6.2 Study completion 40 6.3 Informed consent 41 6.4 Institutional review board or ethics committee approval 41 6.5 Study monitoring requirements 42 6.6 Data safety monitoring plan 42 6.7 Study medication accountability 42 6.8 Disclosure of data 43 6.9 Retention of records 43 6.10 Publications 43 6.11 Changes to protocol 43 Trial Appendices Appendix A Trial schema Appendix B Vaccination timeline Appendix C NCI Common Terminology Criteria for Adverse Events, v4.03 Appendix D E75 + GM-CSF and DTH Formulation Plan Appendix E Leukine package insert Appendix F ECOG performance status criteria Appendix G Data Safety Monitoring Plan (free standing document) Appendix H Adverse event reporting algorithm Appendix I MedWatch FDA form 3500 link Appendix J Study Flowchart Appendix K PI agreement and signature page 1.0 INTRODUCTION 4 Protocol: 2014-0443 Version 2.1 Version Date: 11 April 2016 1.1 Disease background Breast cancer is the most commonly diagnosed malignancy in women (excluding cancers of the skin) and is the second leading cause of cancer mortality. The American Cancer Society estimated that there will be over 230,000 new cases of breast cancer diagnosed in 2013, with an estimated 40,000 women expected to die from this disease annually.