We comprehensively analyzed clinical, genomic and transcriptomic data of a cohort of 465 primary triple-negative breast cancer (TNBC). PIK3CA mutations and copy number gains of chromosome 22q11 were more frequent in our Chinese cohort than in The Cancer Genome Atlas. We classified TNBCs into four transcriptome-based subtypes: 1) luminal androgen receptor (LAR), 2) immunomodulatory (IM), 3) basal-like immune-suppressed (BLIS), and 4) mesenchymal (MES). Putative therapeutic targets or biomarkers were identified among each subtype. Importantly, the LAR subtype showed more ERBB2 somatic mutations, infrequent mutational signature 3 and frequent CDKN2A loss. The comprehensive profile of TNBCs provided here will serve as a reference to further advance the understanding and precision treatment of TNBC.
Copy number analysis of Affymetrix Oncoscan (Oncoscan CNV) SNP arrays was performed for samples from 401 primary triple negative breast cancer patients treated at Fudan University Shanghai Cancer Center. There are also 23 randomly selected white blood cell samples from the mentioned patients, which were used as references for eliminating potential recurrent germline CNV and/or recurrent false positive calls.