Investigation of monogenic causes of familial breast cancer: data from the BEACCON case-control study

Abstract

Breast cancer (BC) has a significant heritable component but the genetic contribution remains unresolved in the majority of high-risk BC families. This study aims to investigate the monogenic causes underlying the familial aggregation of BC beyond BRCA1 and BRCA2, including the identification of new predisposing genes. A total of 11,511 non-BRCA familial BC cases and population-matched cancer-free female controls in the BEACCON study were investigated in two sequencing phases: 1303 candidate genes in up to 3892 cases and controls, followed by validation of 145 shortlisted genes in an additional 7619 subjects. The coding regions and exon–intron boundaries of all candidate genes and 14 previously proposed BC genes were sequenced using custom designed sequencing panels. Pedigree and pathology data were analysed to identify genotype-specific associations. The contribution of ATM, PALB2 and CHEK2 to BC predisposition was confirmed, but not RAD50 and NBN. An overall excess of loss-of-function (LoF) (OR 1.27, p = 9.05 × 10−9) and missense (OR 1.27, p = 3.96 × 10−73) variants was observed in the cases for the 145 candidate genes. Leading candidates harbored LoF variants with observed ORs of 2–4 and individually accounted for no more than 0.79% of the cases. New genes proposed by this study include NTHL1, WRN, PARP2, CTH and CDK9. The new candidate BC predisposition genes identified in BEACCON indicate that much of the remaining genetic causes of high-risk BC families are due to genes in which pathogenic variants are both very rare and convey only low to moderate risk.

Contribution of large genomic rearrangements inPALB2to familial breast cancer: implications for genetic testing

“…One large deletion occurring in an intronic region in a case subject was considered of unknown significance. Although 4.3% of the patients in the familial breast cancer case cohort reported here were also affected with ovarian cancer (data published previously21), none were carriers of PALB2 LGRs and nor were the 14.8% patients with breast cancer with positive family history of ovarian cancer. However, the dataset is not big enough to be conclusive about genotype-phenotype correlations and larger studies are required for further investigation.…”

“…All cases previously tested negative for pathogenic variants in BRCA1 and BRCA2 , including LGRs. The subjects in this study were predominantly of European ancestry (95.3% cases and 98.8% controls) with a small proportion of Asian ancestry as reported previously 21. The average breast cancer diagnosis age of the cases was 49.7 years (range 19.0–94.8).…”

“…Index cases from 5770 families with hereditary breast cancer along with 5741 cancer-free women from the same population in the hereditary BrEAst Case CONtrol study21 were analysed for LGRs involving the PALB2 gene. The cases were female patients with breast and/or ovarian cancer (>95% breast cancer affected) in the Variants in Practice Study that were ascertained from the combined Victorian and Tasmanian Familial Cancer Centres, and Pathology North, NSW Health Pathology, Newcastle, Australia.…”

“…Cases and controls were sequenced using three custom-designed HaloPlex Targeted Enrichment Assay panels (Agilent Technologies, Santa Clara, California, USA). Library preparation was performed as described previously 21. Sequencing was performed at the Australian Genome Research Facility (North Melbourne, Victoria, Australia); library pools of 96 samples were sequenced on a HiSeq 2500 Genome Analyzer using 100 bp paired end reads (Illumina, San Diego, California, USA) with an average read depth target of >250×.…”

“…Sequencing BAM files were viewed in IGV, and all LoF variants in PALB2 were validated using Sanger sequencing. The total number of PALB2 LoF variants was published in a summary state21 and some individual LoF variants were previously published in detail in a tumour analysis paper 32…”