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Table 1 Data sets used in this study. Number of samples (n) for a given data set indicates those with support vector machine (SVM)-predicted BRCA1-like status based on copy number data

From: Molecular and epigenetic profiles of BRCA1-like hormone-receptor-positive breast tumors identified with development and application of a copy-number-based classifier

Data set (n) Percentage ER positivitya Percentage Predicted BRCA1-like Purpose Data types analyzed Accession (if applicable) Refs.
Joosse et al. (74) 42.9 (27/63) 47.3 (35/74) BRCA1-like classifier training Copy number GSE9021, GSE9114 [16, 17]
BRCAx (106) 70.7 (41/58) 19.8 (21/106) BRCA1-like classifier validation Copy number GSE18626 [33]
CCLE breast cancer cell lines (10) 10.0 (1/10) 60.0 (6/10) BRCA1-like classifier experimental validation Copy number, MLPA Additional file 1: Table S1; portals.broadinstitute.org/ccle [34, 35]
TCGA breast cancer (957) 77.1 (704/913) 32.2 (308/957) BRCA1-like differential analyses Copy number, mutation, gene expression, DNA methylation, clinical synapse.org ;
gdc.cancer.gov ;
gdac.broadinstitute.org ;
[2, 39,40,41]
METABRIC (1968) 76.3 (1501/1968) 17.4 (343/1968) BRCA1-like differential analyses Copy number, gene expression, clinical cbioportal.org [28, 29]
  1. ER estrogen receptor, TCGA The Cancer Genome Atlas, CCLE Cancer Cell Line Encyclopedia, METABRIC Molecular Taxonomy of Breast Cancer International Consortium
  2. aER status is not reported, is unknown, or is equivocal in a subset of Joosse et al., BRCAx and TCGA breast tumors. Such tumors were excluded from percentage ER positivity calculation