Supervised analysis in luminal genomic subtypes. (a) Significant Genomic Identification of Significant Targets in Cancer (GISTIC) regions between BRCA2-mutated and non-BRCA2 tumors within the luminal-complex subtype. (b) Significant GISTIC regions between the luminal-complex and luminal-simple subtypes. (c) Distant metastasis-free survival (DMFS) for luminal A tumors stratified by classification as luminal-simple or non-luminal-simple in a combined Affymetrix gene-expression data set. Significant GISTIC regions were identified by Bonferroni-adjusted Student t test (P < 0.05); red indicates more-frequent gain, and green indicates more-frequent loss, in comparisons between GISTIC regions. Only significant regions with ≥20% CNA frequency are displayed.