Figure 2
Gene copy number alterations in HER2-positive and HER2-negative components of HER2 heterogeneous breast cancers. (A) Frequency plots of copy number gains and losses (top) and of amplifications (bottom) in HER2 non-amplified and HER2-amplified components of 12 HER2 heterogeneous breast cancers. The proportion of cases in which each bacterial artificial chromosome (BAC) clone is gained/amplified (green) or lost (red) is plotted (y-axis) for each BAC clone according to its genomic position (x-axis). Inverse Log10 values of the Fisher’s exact test P-values are plotted according to genomic location (x-axis) at the bottom of each graph. The only statistically significant difference identified between the genomic profiles of HER2 non-amplified and HER2-amplified components of 12 HER2 heterogeneous breast cancers was HER2 itself. (B) Hierarchical clustering of the genomic profiles of HER2-positive and HER2-negative components of 12 HER2 heterogeneous breast cancers. Hierarchical cluster analysis was performed with categorical states (that is, gains, losses, and amplifications) using Euclidean distance metric and the Wards algorithm. Amp, amplification; Del, deletion; NC, normal copy number.