Figure 3

Identification of BRF2 and DSN1 amplification in HER2-negative components of HER2 heterogeneous breast cancers. (A) Gene copy number analysis of HER2-positive and HER2-negative components of HER2 heterogeneous breast cancers confirmed the presence and absence of HER2 amplification (genome plots, middle), respectively, and identified the presence of an 8p11-p12 amplification, including BRF2 and other breast cancer genes, in cases T2 and T4, and of a 20q11 amplification, encompassing DSN1, in case T12 restricted to the HER2-negative component of each case (chromosome plots, right). In the genome plots and chromosome plots, the genomic position is plotted along the x-axis and circular binary segmentation (cbs)-smoothed Log₂ ratio on the y-axis; amplifications are shown in bright green, gains in dark green, losses in dark red and normal copy number in black. (B) Selected amplified genes identified to be restricted to the HER2-negative components of HER2 heterogeneous breast cancers were assessed in luminal breast cancers from the TCGA dataset (for complete list of genes and data source, see Additional file 6).