Affymetrix SNP array data (Oncoscan CNV) for Fudan University Shanghai Cancer Center Triple Negative Breast Cancer (FUSCCTNBC) project

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.

本研究对465例原发性三阴性乳腺癌（triple-negative breast cancer, TNBC）队列的临床、基因组及转录组数据进行了全面分析。本中国队列中，PIK3CA突变与22q11染色体拷贝数扩增的发生率高于癌症基因组图谱（The Cancer Genome Atlas, TCGA）队列。本研究将三阴性乳腺癌划分为四种基于转录组的亚型：1）腔面雄激素受体型（luminal androgen receptor, LAR）、2）免疫调节型（immunomodulatory, IM）、3）基底样免疫抑制型（basal-like immune-suppressed, BLIS）以及4）间质型（mesenchymal, MES）。各亚型均筛选出潜在治疗靶点或生物标志物。值得注意的是，腔面雄激素受体型亚型携带更多ERBB2体细胞突变，突变特征3发生率较低，且CDKN2A缺失更为常见。本研究提供的三阴性乳腺癌全景组学特征，可为进一步加深对三阴性乳腺癌的认识及推进其精准治疗提供参考依据。本研究对复旦大学附属肿瘤医院收治的401例原发性三阴性乳腺癌患者样本，开展了Affymetrix Oncoscan（Oncoscan CNV）单核苷酸多态性（single nucleotide polymorphism, SNP）芯片的拷贝数分析。本研究还纳入了上述患者中随机选取的23份白细胞样本，作为参照以排除潜在的重复性生殖系拷贝数变异及/或重复性假阳性检测结果。