Statistical Analysis
death, Tumour, primary malignant neoplasm, breast cancer
RECURRENCE, TUMOUR, EVENT, DISEASE, REGRESSION, PRIMARY MALIGNANT NEOPLASM
The criteria of the Reporting Recommendations for Tumour Marker Prognostic Studies (REMARK) guidelines were followed for this study.For pCR and EFS modeling, the iGES scores were analyzed as continuous variables. Stromal TILs were analyzed as continuous and discrete variables with different prespecified cutoffs (ie, 20%, 40%, and 60%). Immune-related gene expression signatures and TILs were also categorized by tertiles (ie, low, medium, and high) for visualization purposes.The association between TILs and iGESs was measured with Spearman correlation coefficients. For differential gene expression analysis, we performed a multiclass significance analysis of microarrays.The association of immune biomarkers with pCR was evaluated in the CALGB 40601 and PAMELA combined cohort by logistic regression models. In the CALGB 40601 trial, EFS was defined as the time from randomization to a breast cancer relapse after surgery, second primary malignant neoplasm, or death without recurrence for women who underwent surgery. For individuals who did not undergo surgery, the event was defined as death during clinical follow-up or noncompletion of neoadjuvant therapy due to progressive disease. The median follow-up was 9.1 years (IQR, 8.10-9.84). The association of immune biomarkers with EFS was evaluated with Cox regression models. All the analyses were based on the study clinical database frozen on June 10, 2021. All tests were 2-sided, and a .05 level of significance was used. All statistical analyses were performed with R version 3.5.2 (R Foundation for Statistical Computing) and Python version 3.6 (Python Software Foundation). Data analyses were performed from June 1, 2020, to January 1, 2022.