Abstract 5224: Next-generation sequencing of a panel of genes contributing to breast cancer risk
Authors: Uhrhammer Nancy A. , El Saghir Nagi , Bidet Yannick , Delahaye-Sourdeix Manon , Ponelle Flora , Ollier Marie , Viala Sandrine , Kreidieh Firas , Khoueiry-Zgheib Nathalie , Bignon Yves-Jean 
Published: July 2016

Abstract
BRCA mutations account for a minority of hereditary breast cancer risk families. Many other genes have been identified, with rare but highly penetrant mutations, or more frequent mutations giving modest breast cancer risk. Next generation sequencing has made it possible to explore a wide sample of genes for their contribution to breast cancer risk. We have sequenced gene panels in two populations of non-BRCA breast cancer families.
First, 47 French families were selected for triple-negative breast cancer in the index case and &gt;1 first degree relative with breast cancer. A panel of 33 genes involved in cancer risk, DNA repair, and/or partners of BRCA1 or BRCA2 was sequenced using DNA capture and GS-Flex sequencing. Second, a Lebanese cohort of 25 non-BRCA cases with Manchester scores &gt;18 was sequenced on a MiSeq after capture of a similar panel of 37 genes. BRCA1 and BRCA2 were included in both panels to confirm previously obtained results. Large rearrangements were detected using MLPA.
Sequence alignment and variant identification was performed using a combination of commercial software and an in-house GATK-based pipeline. Variants were described as neutral or likely neutral if the MAF in online databases exceeded 1%, if in silico analyses suggested neutrality, and if splicing prediction algorithms agreed on the absence of any significant effect.
NGS analysis confirmed the absence of BRCA mutations. Deleterious mutations were observed in three Lebanese cases: two with a deletion in PALB2 and one stop mutation in ATM. Nine additional Lebanese cases and four from the French TNBC group were found to carry variants of unknown significance (VUS) in one or more genes. Most cases were found to have one VUS; two TNBC cases had more than one VUS and one Lebanese case had a VUS and a PALB2 mutation.
The cases with deleterious mutations had Manchester scores of 56, 22 and 19. Scores for cases with VUSs ranged from 18 to 45 (average 23), and those with only neutral or likely neutral variants ranged from 18 to 27 (average 21.8). These differences are not significant, but additional cases are under study and will be presented. No difference was observed between French TNBC families with or without VUSs.
DNA capture of gene panels is a quick and efficient way of analyzing multiple genes involved in hereditary cancer risk. Our panels focused on a limited number of genes involved in DNA repair and/or direct interactions with the BRCA genes: the small number of genes allowed us to analyze a maximum number of patients per experiment on two relatively low-throughput machines. Although the two cohorts are small, they show that the number of variants requiring follow-up in non-BRCA genes is low. The absence of deleterious mutations in genes involved in homologous recombination repair in the TNBC cohort showed that although genes of this pathway are candidates for tumor sensitivity to PARP inhibitors, the candidates we tested may not be frequently constitutionally mutated.
Citation Format: Nancy A. Uhrhammer, Nagi El Saghir, Yannick Bidet, Manon Delahaye-Sourdeix, Flora Ponelle, Marie Ollier, Sandrine Viala, Firas Kreidieh, Nathalie Khoueiry-Zgheib, Yves-Jean Bignon. Next-generation sequencing of a panel of genes contributing to breast cancer risk. [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 5224.