Whole-exome sequencing of non-BRCA1/BRCA2 mutation carrier cases at high-risk for hereditary breast/ovarian cancer

Abstract

The current study aimed to identify new breast and/or ovarian cancer predisposition genes. For that, whole-exome sequencing (WES) was performed in the germline DNA of 52 non-BRCA1/BRCA2/TP53 mutation carrier women at high-risk for hereditary breast and ovarian cancer (HBOC). All variants were classified using information from population and disease specific databases, in silico prediction tools and the American College of Medical Genetics and Genomics (ACMG) criteria. Loss of heterozygosity (LOH) of tumor samples and segregation analyses were performed whenever possible. The variants identified were investigated in a second, independent cohort of 17 BC cases. Pathogenic/Likely Pathogenic variants were identified in known cancer genes such as CHEK2, MUTYH, PMS2, and RAD51C. Rare and potentially pathogenic variants were identified in DNA repair genes (FAN1, POLQ, and RAD54L) and other cancer-related genes such as DROSHA and SLC34A2. Interestingly, the variant c.149T>G in the FAN1 gene was identified in two unrelated families, and exhibited LOH in the tumor tissue of one of them. In conclusion, this is the largest Brazilian WES study involving families at high-risk for HBOC which has brought novel insights into the role of potentially new genetic risk factors for hereditary breast and ovarian cancer.

Keywords: BRCAX; breast cancer predisposition; hereditary breast and ovarian cancer predisposition syndrome; hereditary cancer; whole-exome sequencing.

Figure 1

Variants selection workflow. Whole‐exome sequencing data from 52 unrelated Brazilian women at‐risk for HBOC, without germline pathogenic variants in BRCA1, BRCA2, and TP53 genes. Variants classified as “high‐impact” and “medium‐impact” by snpEFF/GEMINI were prioritized. Then, variants with base coverage more than or equal to 10× and variant allele frequency (VAF) more than or equal to 0.25 were selected, and those present in population databases with frequency less than or equal to 1% (MAF ≤ 0.01) were analyzed. The variants were also separated accordingly to ClinVar and ACMG classification. HBOC, hereditary breast and ovarian cancer

Figure 2

Likely pathogenic/pathogenic variants identified. In purple: frameshift variants; in blue: nonsense variants; in green: missense variants; in yellow: splice acceptor/donor variants. Information about tumor diagnosis: in light pink: breast cancer; in the dark pink: bilateral breast cancer; in greenish‐blue: ovarian cancer; in gray: melanoma. Information about age at diagnosis: in orange: diagnosis less than or equal to 30 years of age; in light yellow: 31–45 years of age; in blue: more than or equal to 46 years of age are represented

Figure 3

STRING pathway overview of DNA repair genes with pathogenic/likely pathogenic variants. Legends: in yellow: genes involved in homologous recombination, in light pink: genes involved Fanconi anemia, in blue: genes involved in mismatch repair, in green: genes involved in base excision repair, in orange: genes involved in nonhomologous end‐joining, and in gray: genes involved in nucleotide excision repair