Clustering analysis. Unsupervised hierarchical clustering of 27 BRCA1-mutated tumors, 21 BLBCs, 17 luminal-J tumors and 31 luminal-H tumors. For each individual tumor, a KSE curve was calculated by smoothing each tumor profile with KC-SMART. A mean KSE value for was determined for all overlapping regions of gain and loss (shown in Table 2) between BLBCs (light blue) and BRCA1-mutated tumors (dark blue), and for the overlapping regions between the luminal-H (red) and luminal-J (pink) groups. We used two-dimensional Pearson correlation to perform complete linkage clustering over the mean KSE values and tumors.