Broad, hybrid capture-based next generation sequencing identified actionable genomic alterations in HER2-negative breast cancer.

e12544Background: Molecular profiling has revealed that breast cancer could at least be classified into 4 principle subtypes by status of estrogen receptor, progesterone receptor, and HER2. About 20% of all breast cancer patients harbored HER2 amplification and could benefit from anti-HER2 therapy. In this study, we set out to determine the frequency of potentially actionable genomic alterations via broad, hybrid capture-based next generation sequencing (NGS) in HER2 negative breast cancer tissues. Methods: 47 cases of HER2 negative combined with 14 cases of HER2 positive breast cancers previously determined by FISH testing were enrolled and all the patients signed the informed consent before assay. 7708 exons of 508 tumor related genes and 78 introns of 19 frequently rearranged genes were assessed for base substitutions, indels, copy number alterations, and gene fusions. The average median sequencing depth was about 400×. Results: 19 of 47 HER2 negative breast cancers harbored at least one genomic altera...