Abstract PD8-04: Ultra-deep multigene profiling of matched primary and metastatic hormone receptor positive breast cancer patients relapsed after adjuvant endocrine treatment reveals novel aberrations in the estrogen receptor pathway

Abstract

Abstract Introduction: Although recent large-scale efforts1,2 have examined the mutational landscape of hormone receptor positive (HR+) metastatic breast cancer (mBC), identifying enriched alterations in such context, most analyses have considered prevalently metastatic samples, comparing them with either unmatched primary cases from the same institutions or large early breast cancer (eBC) sequencing databases. Hence, the statistical power to identify de novo somatic mutations and copy number aberrations (sCNAs) and the biological interpretation of findings have been limited, as have the associations with specific adjuvant treatment subgroups. Patients and methods: We collected primary and metastatic formalin-fixed, paraffin-embedded (FFPE) samples, as well as a source of germline DNA, from 204 HR+ BC cases undergoing adjuvant endocrine treatment (ET) for their disease after chemotherapy when indicated, and relapsing at least six months after surgery, with complete clinical follow-up concerning therapy for the early stage of patients’ disease and first line treatment information. We sequenced samples with a bespoke NGS panel encompassing 134 BC-specific genes, comparing mBC with matched eBC samples after filtering for germline variants, and associating our findings with adjuvant therapy and first line treatment. We performed multi-color fluorescence in-situ hybridization (m-FISH) to validate selected sCNAs. Results: We retrieved and successfully sequenced matched eBC, mBC, and germline DNA samples for 132 HR+ BC patients with complete clinical annotation. Mean sequencing depth for somatic and germline sequenced samples was in excess of 3,000x and 1,000x, respectively. On top of confirming the enrichment of mBC in ESR1, as well as MAPK pathway and transcriptional factor somatic aberrations, we identified and validated the presence of de novo amplifications of ESR1 and CYP19A1, the gene encoding for the aromatase protein. To our knowledge, this is the first high-confidence report from an NGS cohort of eBC/mBC cases concerning de novo amplifications in the estrogen receptor pathway genes in HR+ patients relapsed after adjuvant ET, as well as the largest described matched HR+ eBC/mBC case set undergoing ultradeep multigene profiling with complete clinical annotation. Associations with treatment and outcome variables will be presented at the meeting.