Introduction. Next-generation sequencing (NGS) technologies offer the possibility to assess multiple genes for somatic mutations and may elucidate the driver genetic variations involved in carcinogenesis and disease progression. Among the different subtypes of breast cancer, the triple-negative subgroup (TNBC) is characterized by poor prognosis and a lack of reliable tumor markers. In particular, molecular profiling and the clinical observation that some patients with TNBC relapse early after surgery and show only poor responses to established therapies while others do not relapse at all, indicate the existence of major subgroups within the TNBC cohort. The aim of this study was to characterize somatic variants in breast cancer tumors obtained from a cohort of 147 Norwegian patients using a NGS panel with special emphasis on the TNBC subtype (57% of the patients).

Methods. Genomic DNA was extracted from paraffin embedded formalin fixed (FFPE) tissue obtained from 147 consecutive patients diagnosed with a primary BC at our hospital. The DNA samples were analyzed by next-generation sequencing (NGS) using Human Breast Cancer GeneRead DNAseq Targeted Panel V2 (Qiagen). The panel consists of a collection of PCR primers for targeted enrichment of the coding region of 44 genes commonly mutated in breast cancer. Target enrichment and library construction was performed according to the GeneReader workflow (Qiagen) and paired end sequencing was performed on a NextSeq 500 sequencer (Illumina) running 2 x 150 bp chemistry Version 2. Data analysis including alignment to the reference genome hg19 and variant calling was performed using Qiagen’s online Ingenuity Variant analysis.

Results. The ingenuity variant analysis classified the somatic mutations according to their clinical significance into four groups: pathogenic, likely pathogenic, benign and likely benign (as defined by the American College of Medical Genetics and Genomics). Focusing on the TNBC cases (n = 84), we observed that patients could be separated in two major subgroups, those with a combination of several mutations in pivotal genes (TP53, BRCA1/2, RB1, RET, PIK3CA etc.) and others, without any mutations in typical breast cancer related genes. Interestingly, the majority of tumors presenting with extremely low mutation rates were found to harbor a specific mutation in the EP300 gene (G211S). In fact, only 3 out of 29 TNBC carrying EP300-G211S had other pathogenic mutations. Breast cancer specific survival was significantly improved in EP300-G211S mut. positive patients.

Conclusion. Next generation sequencing of human triple-negative breast cancer samples suggests EP300 to be a pivotal player in breast cancer biology, potentially reflecting the overall mutational burden. These findings should be further investigated as the mutational status of EP300 might have significant implications for clinical decision making.

Note: This abstract was not presented at the meeting.

Citation Format: Vahid Bemanian, Torill Sauer, Joel Touma, Katja M. Vetvik, John C. Noone, Vessela N. Kristensen, Ida R. Bukholm, Jürgen Geisler. The EP300-G211S mutation is highly associated with a low mutational burden in triple-negative breast cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-027. doi:10.1158/1538-7445.AM2017-LB-027