Evaluation of HER2 status and characteristics by next-generation sequencing in breast cancer.

Although next-generation sequencing (NGS) has been widely used to provide comprehensive somatic mutational information for individualized therapy in breast cancer patients, whether or not it could reliably evaluate HER2 status to guide targeted therapy when compared to the current IHC/FISH standard criteria still lacks sufficient validations. We analyzed the clinicopathological and NGS somatic genomic data of 1,171 Chinese breast cancer patients. A commercial 520 gene panel was used to generate genomic variation data by NGS in breast cancer samples. We compared the concordance of HER2 status between NGS evaluation and IHC/FISH criteria. We further defined the amplification status of HER2 based on the length of amplification region beginning from ERBB2 and extending to adjacent genes by focal (<1 megabase) versus broad (>1 megabase) amplification and stratified the cohort accordingly to investigate its potential in predicting efficacy of trastuzumab-based neoadjuvant therapy. NGS showed high concordance with FISH/IHC-defined HER2 status with a sensitivity of 95.7%, specificity of 94.2%, and overall concordance rate of 94.9%. NGS characterized the genomic landscape of enrolled patients, identifying frequent mutations including TP53, ERBB2, PIK3CA, CDK12, MYC, and CCND1. The focal amplification subgroup exhibited significantly higher gene copy number (GCN) (31.7 vs 10.2, p < 0.001), greater HER2 positivity rates (98.3% vs. 78.3%, p < 0.001), higher IHC 3+ prevalence (91.7% vs. 48.5%, p < 0.001) and increased FISH + proportion (98.5% vs. 77.9%, p < 0.001). In patients receiving HER2-targeted neoadjuvant therapy, the focal amplification group had a higher pCR rate compared with broad amplification group (46.0% vs. 20.0%, p = 0.031). NGS demonstrates comparable capability to IHC/FISH in HER2 status interpretation and provides additional genomic information. Higher HER2 NGS copy numbers and focal amplification may be associated with a higher pCR rate.