Introduction. Following the development of novel targeted therapies for selected breast cancer (BC) patients (like HER-2 pos. BC), the subgroup of triple-negative breast cancer (TNBC) patients is still characterized by a poor prognosis and a lack of reliable tumor markers that might guide medical therapy. Methods. Genomic DNA was extracted from paraffin embedded formalin fixed (FFPE) tissue obtained from 77 consecutive patients diagnosed with a TNBC 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 × 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 genetic mutations according to their clinical significance into four groups: pathogenic, likely pathogenic, benign and likely benign. We present only mutations in genes that are characterized as pathogenic or likely pathogenic, where the term “likely pathogenic” indicates greater than 90% certainty of the mutation being pathogenic (as defined by the American College of Medical Genetics and Genomics). Genetic variations were mostly observed in a subset of 44 genes included in the breast cancer panel. The tumor suppressor genes TP53 as well as BRCA1 and BRCA2 represented the highest mutation rates (>5%) among all TNBC samples. Interestingly, additional genes probably playing a pivotal role in breast cancer biology like EP300 and FGFR-1 were also found to be mutated at a high rate in TNBC. Conclusion. Next generation sequencing of samples obtained from primary TNBC patients confirmed a high level of pathogenic or likely pathogenic mutations in well-described key cancer genes like TP53, BRCA1/2, ATM, EGFR, RB1 and PIK3CA and frequently mutated additional genes (EP300, FGFR1) that will be further investigated.
Citation Format: Vahid Bemanian, Torill Sauer, Joel Touma, Katja Vetvik, Ying Chen, Vessela Kristensen, Ida Bukholm, Jürgen Geisler. Next generation sequencing (NGS) reveals high mutation rates in established and potentially novel cancer genes involved in triple-negative breast cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-246.