Exome Sequencing in BRCA1- and BRCA2-Negative Greek Families Identifies MDM1 and NBEAL1 as Candidate Risk Genes for Hereditary Breast Cancer

Abstract

Approximately 10% of breast cancer (BC) cases are hereditary BC (HBC), with HBC most commonly encountered in the context of hereditary breast and ovarian cancer (HBOC) syndrome. Although thousands of loss-of-function (LoF) alleles in over 20 genes have been associated with HBC susceptibility, the genetic etiology of approximately 50% of cases remains unexplained, even when polygenic risk models are considered. We focused on one of the least-studied European populations and applied whole-exome sequencing (WES) to 52 individuals from 17 Greek HBOC families, in which at least one patient was negative for known HBC risk variants. Initial screening revealed pathogenic variants in known cancer genes, including BARD1:p.Trp91* detected in a cancer-free individual, and MEN1:p.Glu260Lys detected in a BC patient. Gene- and variant-based approaches were applied to exome data to identify candidate risk variants outside of known risk genes. Findings were verified in a collection of Canadian HBOC patients of European ancestry (FBRCAX), in an independent group of Canadian BC patients (CHUM-BC) and controls (CARTaGENE), as well as in individuals from The Cancer Genome Atlas (TCGA) and the UK Biobank (UKB). Rare LoF variants were uncovered in MDM1 and NBEAL1 in Greek and Canadian HBOC patients. We also report prioritized missense variants SETBP1:c.4129G > C and C7orf34:c.248C > T. These variants comprise promising candidates whose role in cancer pathogenicity needs to be explored further.

Keywords: Greek population; MDM1; NBEAL1; candidate risk variants; exome sequencing; hereditary breast cancer.

Figure 1

Gene-based prioritization workflow. *For families where this was possible to be ascertained.

Figure 2

Principal component analysis (PCA) on 27,666 coding variant positions reveals that GRBC patients (one patient per family) map close to: (A) the EUR superpopulation, and (B) the IBS and TSI populations of 1000 Genomes. Abbreviations: GRBC, Greek Breast Cancer study; AFR, African; AMR, Admixed American; EAS, East Asian; EUR, European; SAS, South Asian; CEU, Central European; TSI, Tuscan; FIN, Finnish; GBR, British; IBS, Iberian.

Figure 3

(A) Segregation of MDM1:G394* in GRBC pedigree F25. Both mother (diagnosed with bilateral BC at 46 and 56 years of age) and daughter (diagnosed with BC at 44 years of age) were heterozygous carriers of the MDM1 stop-gain variant. (B) Genomic positions of MDM1 LoF variants detected in Greek (GRBC, MDM1:G394*) and French Canadian (FBRCAX and CHUM-BC, MDM1:p.R32fs) patients. Variants were experimentally validated using Ampliseq (GRBC) and Sanger sequencing (FBRCAX). CHUM-BC variants were detected using the iPLEX MassARRAY.

Figure 4

(A) Segregation of NBEAL1:E1155* in GRBC pedigree F22. Two sisters (diagnosed with BC at 59 and 60 years) were heterozygous carriers of the NBEAL1 stop-gain variant. Their niece, who was cancer-free at 40 years of age, was not a carrier of the variant. (B) Genomic positions of NBEAL1 LoF variants detected in GRBC (NBEAL1:E1155*) and FBRCAX (NBEAL1:p.R552*) patients. Variants were experimentally validated using Ampliseq (GRBC) and Sanger sequencing (FBRCAX).