Fig. 2

Landscape of gene copy number alterations in MBCs. a Hierarchical cluster analysis performed with SNP 6.0 defined copy number alterations (i.e., gains, losses, amplifications/high-level gains and deletions) using Euclidean distance metric and Ward’s algorithm. Histologic subtypes of MBCs are color-coded according to the legend. b Frequency plot of (top) copy number gains and losses and (bottom) amplifications/high-level gains and deletions in copy number cluster 1 and copy number cluster 2 identified by hierarchical clustering. The proportion of tumors in which each probe is gained/ amplified (green bars) or lost/ deleted (red bars) is plotted (y-axis) for each probe according to its genomic position (x-axis). Inverse Log₁₀ values of Fisher’s exact p value are plotted according to genomic position (x-axis) at the bottom of each graph