4.9.3 Data analysis The intention-to-treat (ITT) population will include all patients who were randomly assigned. ITT analysis will be performed with each randomized patient evaluated in the treatment arm to which randomized, regardless of actual treatment received. The per-protocol (PP) population is a subset of the ITT population. Patients may be excluded from the PP population for the following reasons and others as determined prior to database lock: violations of eligibility criteria, development of other malignancies, early recurrences occurring prior to completion of the entire PVS, receiving alternative disease-directed therapy without evidence of recurrence, or major deviation from prescribed vaccination schedule (to include boosters). Additionally, with the inclusion of HLA-A24 and/or A26-positive patients, the ITT and PP analysis will be performed with and without these patients. 4.9.3.1 Study patient characteristics Demographic characteristics of all patients in the ITT and PP populations will be summarized including age, race, disease histology, tumor size, estrogen receptor/progesterone receptor status, grade, nodal status, AJCC clinical stage, surgery extent, and other disease-directed therapies to include chemotherapy, radiation therapy, and hormonal therapy. Continuous variables will be summarized using the number of patients, mean, standard deviation, median, minimum, and maximum; and categorical variables will be summarized using the frequency count and the percentage of patients in each category. Differences between treatment groups will be determined using a chi-square test for categorical variables and a t-test for continuous variables. 4.9.3.2 Primary efficacy analysis The primary efficacy endpoint of the trial is invasive DFS. Invasive DFS will be defined as the time from the date of initiation of trastuzumab maintenance therapy to the date of invasive local, regional or distant recurrence, new primary, death due to any cause or last follow-up date if patient had no evidence of disease. Invasive DFS estimates will be determined using the Kaplan-Meier method and differences between treatment groups will be assessed using the 35 Protocol: 2014-0443 Version 2.1 Version Date: 11 April 2016 log-rank test. In addition, Cox proportional hazards regression models will be fit to determine the association between DFS and treatment group and covariates of interest. The primary efficacy analysis will be performed on the ITT population as primary and the PP population as secondary. Because it is anticipated that 50% of patients will be enrolled at MD Anderson, the primary efficacy analysis will also be conducted by site for the ITT and PP populations in order to explore the possibility of a treatment by investigative site interaction. Investigative sites that individually represent fewer than ten patients will be combined for this exploratory analysis; geographic region will be substituted if the average number of patients per site is fewer than ten. 4.9.3.3 Secondary efficacy analysis Safety The incidence of treatment-emergent AEs, SAEs, severe AEs, AEs related to study drug (defined as possibly, probably, or definitely related to study drug), and AEs which lead to study discontinuation will be summarized by treatment group. Differences between treatment groups will be determined using Fisher’s exact tests. A formal interim analysis for safety will be performed after the midpoint (50th patient) of enrollment and randomization. Time to AE onset will be estimated using the Kaplan-Meier method and treatment differences will be determined using the log-rank test. In addition, duration of any AE with >10% incidence, total number of AEs, SAEs, and related AEs will be summarized and treatment group differences assessed using a t-test or Wilcoxon rank sum test, depending on the distribution of the data. Immunologic response Immunologic responses will be determined using DTH reactions (in vivo) and dextramer assays (in vitro). With respect to the in vivo immunologic response as assessed by DTH reaction, the treatment groups will be compared with respect to the percentage with a positive post-vaccination DTH (defined as greater than pre-vaccination DTH) as well as absolute DTH reaction sizes within the groups. Expression percentages will be compared using a chi-square test while continuous outcomes such as mean DTH response will be compared using a paired t-test (within treatment group) and a two-sample t-test (between treatment groups). For the in vitro response evaluated by the dextramer assay, the number of peptide-specific CTL will be determined at multiple time points (see Section 4.4.4) during the trial. Changes from pre-vaccination levels to 36 Protocol: 2014-0443 Version 2.1 Version Date: 11 April 2016 each time point will be computed and evaluated using a repeated measures mixed-effects model with terms for treatment group, time point, and treatment group-by-time point interaction.