This analysis revealed that of the 1,535 amplified genes restricted to the HER2-negative components of our 12 HER2 heterogeneous breast cancers, 59 genes were statistically significantly copy number regulated in the luminal breast cancers of the TCGA dataset (Additional files 5 and 6), some of which were either recurrently amplified in the HER2-negative components of HER2 heterogeneous cases (for example, BRF2 in cases T2 and T4) or mutually exclusively amplified with HER2 in the TCGA luminal breast cancer dataset (for example, DSN1 in case T12) (Figure 3A,B; Additional file 6). Here, DSN1 is linked to breast carcinoma.