Unsupervised analysis of Genomic Identification of Significant Targets in Cancer (GISTIC) regions identifies six CGH subgroups of breast cancer (BC) associated with different clinical and molecular characteristics. (a) Hierarchic clustering of 133 GISTIC regions identifies six subtypes with different clinical and molecular characteristics, and genomic aberrations. Horizontal dashed line for S-phase indicates the average across all samples. (b) Fraction of the genome altered (FGA) for genomic subtypes indicating that basal-complex samples are genomically unstable, whereas luminal-simple tumors are genomically stable. (c) Overall survival (OS) for 339 patients, for whom primary tumors were available, classified according to genomic subtypes, mirrors results obtained for the intrinsic gene-expression subtypes.