Rare Germline Variants in DNA Repair Genes Detected in BRCA-Negative Finnish Patients with Early-Onset Breast Cancer

Abstract

Background: Breast cancer is the most common malignancy, with a mean age of onset of approximately 60 years. Only a minority of breast cancer patients present with an early onset at or before 40 years of age. An exceptionally young age at diagnosis hints at a possible genetic etiology. Currently, known pathogenic genetic variants only partially explain the disease burden of younger patients. Thus, new knowledge is warranted regarding additional risk variants. In this study, we analyzed DNA repair genes to identify additional variants to shed light on the etiology of early-onset breast cancer.

Methods: Germline whole-exome sequencing was conducted in a cohort of 63 patients diagnosed with breast cancer at or before 40 years of age (median 33, mean 33.02, range 23-40 years) with no known pathogenic variants in BRCA genes. After filtering, all detected rare variants were sorted by pathogenicity prediction scores (CADD score and REVEL) to identify the most damaging genetic changes. The remaining variants were then validated by comparison to a validation cohort of 121 breast cancer patients with no preselected age at cancer diagnosis (mean 51.4 years, range 28-80 years). Analysis of novel exonic variants was based on protein structure modeling.

Results: Five novel, deleterious variants in the genes WRN, RNF8, TOP3A, ERCC2, and TREX2 were found in addition to a splice acceptor variant in RNF4 and two frameshift variants in EXO1 and POLE genes, respectively. There were also multiple previously reported putative risk variants in other DNA repair genes.

Conclusions: Taken together, whole-exome sequencing yielded 72 deleterious variants, including 8 novel variants that may play a pivotal role in the development of early-onset breast cancer. Although more studies are warranted, we demonstrate that young breast cancer patients tend to carry multiple deleterious variants in one or more DNA repair genes.

Keywords: BRCA1/2 negative; Breast cancer; DNA repair genes; early onset; rare variants.

Figure 1

Flow chart describing variant calling and variant prioritization. Variants were called from whole-exome sequencing (WES) data obtained from 63 patients using the Genome Analysis Toolkit (GATK) and DeepVariant software after alignment using the Burrows–Wheeler Alignment Tool (BWA). Consensus variants were annotated using the Ensembl VEP 108. Annotated variants were initially filtered by the Combined Annotation Dependent Depletion (CADD) score and allele frequency (AF) obtained from the Genome Aggregation Database (gnomAD). After the prioritization step using variant consequences, non-synonymous variants were further filtered by REVEL score.

Figure 2

The Werner protein structure. The Werner helicase structure is shown by PYMOL in green color, and the red-color-highlighted variant is arginine, which is changed to proline at 732. (chr8:31111721, G/C) The arginine-732 (red) is bonded (red dotted lines) with Leucine-735, Asparagine-731, and proline-733. Mutation arginine-732-proline as a point mutated structure is shown in red color. Proline-732 is shown bonded with Leucine-735 and Phenylalanine-730. Variant in WRN is Arg732Pro (chr8:31111721, G/C). Superimposition is shown among the wild and mutated structure of Werner helicase by using Chimera software (https://www.cgl.ucsf.edu/chimerax/), accessed on 21 March 2022. The wild-type is shown in cyan color and mutated type is shown in green color.