Public SNP array data, expression data, and clinical annotation data was obtained for the TCGA ovarian (19 (link)) and breast cancer cohorts from the TCGA web site (41 ). BRCA1 and BRCA2 mutation status for the ovarian cancers was obtained from cBIO data portal (42 ). In the ovarian cohort, we identified 218 samples with SNP data that passed ASCAT (see below), BRCA mutation status, and interpretable clinical annotations for treatment and outcomes indicating initial treatment with adjuvant platinum-based chemotherapy, predominantly the combination of carboplatin and docetaxel. We classified “treatment sensitive” as those annotated as partial or complete response to initial treatment and no progression or recurrence within 6 months of initial treatment (n = 187); “treatment resistant” were those annotated as stable or progressive disease on initial therapy or disease recurrence or progression within 6 months (n = 31). In the breast cohort, we identified 78 samples with matched gene expression and SNP data that passed ASCAT, which were classified as ER−/HER2− based on clustering of the ESR1 and ERBB2 gene (see supplementary methods).