Immune gene list and category information were obtained from IMMPORT (https://www.immport.org/). Transcripts per million (TPM) data and clinicopathological information of GSE163882 and GSE123845 datasets were obtained from Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/) and the literature (26 (link)). GSE163882 was sequenced on Illumina NextSeq 500 platform and served as a training set in this study. GSE123845 was sequenced on Illumina HiSeq 2500 platform and served as an independent external test set in this study. The detailed information on the training and test datasets was described in Table S1. Raw sequencing data of GSE163882 were downloaded from Sequence Read Archive (SRA, https://www.ncbi.nlm.nih.gov/sra, Accession: PRJNA688066). Raw data and clinicopathological information of GSE20271 profiled on a DNA microarray platform (Affymetrix Human Genome U133A 2.0 Array), were obtained from GEO. Samples in the datasets with incomplete pCR information were removed. Another RNA-seq dataset of BC patients was downloaded from The Cancer Genome Atlas (TCGA, https://portal.gdc.cancer.gov/, Accession: TCGA-BRCA), and the relevant mutation and immune microenvironment data were obtained from the literature (27 (link)). Hallmark and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway gene sets were collected from MSigDB (https://www.gsea-msigdb.org/).
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