Identifying New Genes for Inherited Breast Cancer by Exome Sequencing

Abstract

Breast cancer is the most common cancer among American women and family history is an important risk factor for its occurrence. More than 20 genes have been identified with inherited mutations that lead to significantly increased risk of breast cancer. However, most familial breast cancer is not explained by mutations in these genes. The goal of this project was to identify additional breast cancer genes by exome sequencing. In order to select families for gene discovery, we first screened families for mutations in all known breast cancer genes using targeted capture and massively parallel sequencing (BROCA). Families that remained unsolved after screening with BROCA were evaluated by exome sequencing. Germline DNA of 144 subjects with breast cancer from 54 high incidence families was sequenced. All truncating mutations shared by at least two affected persons in a family were genotyped in all participating members of that family in order to evaluate co-segregation with cancer. Rare truncating mutations co-segregating with breast and ovarian cancer were detected in ATR, CHEK1, and GEN1, each in one of the 54 families. ATR is recruited to sites of DNA damage; ATR phosphorylates CHEK1 in response to DNA damage, leading to a halt in cell cycle progression; GEN1 is an endonuclease that resolves Holliday junctions. Like BRCA1 and BRCA2, all three candidate genes function in biological pathways related to homologous recombination repair. In order to identify additional mutations in these three genes, unrelated women with breast cancer or ovarian cancer and controls were evaluated with high-throughput targeted sequencing approaches including BROCA custom capture and Molecular Inversion Probes (MIPs). Public databases were also reviewed. In ATR, truncating mutations were identified in 4 of 2544 cases and 3 of 7652 controls (P = 0.049). In CHEK1 truncating mutations were identified in 5 of 2544 cases and 1 of 7652 controls (P = 0.004). In GEN1, truncating mutations were identified in 2 of 1717 cases and 3 of 7652 controls (P = 0.21). This study suggests new candidate genes for inherited predisposition to breast cancer while also demonstrating the challenges facing gene discovery for this complex disease.