Intra-tumor genetic heterogeneity in breast cancers with heterogeneous HER2 gene amplification

We separately analyzed the HER2-negative and HER2-positive components of 12 HER2 heterogeneous breast cancers using gene copy number profiling and massively parallel sequencing, and identified potential driver genetic alterations restricted to the HER2-negative cells in each case. Our results indicate that even driver genetic alterations, such as HER2, can be heterogeneously distributed in a cancer, and that the HER2-negative components are likely driven by genetic alterations not present in the HER2-positive components, including BRF2 and DSN1 amplification. 13 breast cancers with heterogeneous HER2 protein overexpression and HER2 gene amplification by central immunohistochemistry and CISH were amenable to microdissection, as HER2-positive and HER2-negative areas were sufficiently discrete. The HER2-positive and HER2-negative components were microdissected either on a PixCell II laser capture microdissector (Arcturus) into separate tubes from 8um-thick representative tissue sections stained with HercepTest for guidance, or using a sterile needle under a stereomicroscope in selected cases.