Reanalysis of BRCA1/2 negative high risk ovarian cancer patients reveals novel germline risk loci and insights into missing heritability

Abstract

While up to 25% of ovarian cancer (OVCA) cases are thought to be due to inherited factors, the majority of genetic risk remains unexplained. To address this gap, we sought to identify previously undescribed OVCA risk variants through the whole exome sequencing (WES) and candidate gene analysis of 48 women with ovarian cancer and selected for high risk of genetic inheritance, yet negative for any known pathogenic variants in either BRCA1 or BRCA2. In silico SNP analysis was employed to identify suspect variants followed by validation using Sanger DNA sequencing. We identified five pathogenic variants in our sample, four of which are in two genes featured on current multi-gene panels; (RAD51D, ATM). In addition, we found a pathogenic FANCM variant (R1931*) which has been recently implicated in familial breast cancer risk. Numerous rare and predicted to be damaging variants of unknown significance were detected in genes on current commercial testing panels, most prominently in ATM (n = 6) and PALB2 (n = 5). The BRCA2 variant p.K3326*, resulting in a 93 amino acid truncation, was overrepresented in our sample (odds ratio = 4.95, p = 0.01) and coexisted in the germline of these women with other deleterious variants, suggesting a possible role as a modifier of genetic penetrance. Furthermore, we detected loss of function variants in non-panel genes involved in OVCA relevant pathways; DNA repair and cell cycle control, including CHEK1, TP53I3, REC8, HMMR, RAD52, RAD1, POLK, POLQ, and MCM4. In summary, our study implicates novel risk loci as well as highlights the clinical utility for retesting BRCA1/2 negative OVCA patients by genomic sequencing and analysis of genes in relevant pathways.

The identification of pathogenic variants in BRCA1/2 negative, high risk, hereditary breast and/or ovarian cancer patients: High frequency of FANCM pathogenic variants

“…Approximately 5–10% of all breast cancers and up to 25% of all ovarian cancers have a genetic predisposition. To date, about 25 genes have been identified to predispose for hereditary breast and ovarian cancer (HBOC, MIM #604370), mainly involving an autosomal dominant inheritance pattern with incomplete penetrance and variable expressivity . Most of these genes are coding for tumor suppressors that function in genome maintenance by promoting homologous recombination repair after DNA double‐strand breaks .…”

“…To date, about 25 genes have been identified to predispose for hereditary breast and ovarian cancer (HBOC, MIM #604370), mainly involving an autosomal dominant inheritance pattern with incomplete penetrance and variable expressivity. 1,[3][4][5][6] Most of these genes are coding for tumor suppressors that function in genome maintenance by promoting homologous recombination repair after DNA double-strand breaks. 1 Up to now, 25% of all HBOCs can be explained by the highly penetrant risk genes BRCA1 and BRCA2 and up to 15% by other HBOC risk genes (e.g.…”

Utilizing iVariantGuide for Variant Assessment of Next‐Generation Sequencing

“…The iVariantGuide application was used to find novel loci in the WES data of 48 high‐grade serous OVCA women. The initial study (Stafford et al., ) used the Illumina VariantStudio variant application for the purpose of re‐evaluating the cohort as a comparative analysis with iVariantGuide.…”

“…Many of the variants in the previous study (Stafford et al., ) were identified by limiting the scope of the variants to 210 DNA repair and cell‐cycle regulation genes. For a more comparative analysis, we applied the same 210 genes to our preset, described in step 23 of Basic Protocol 1, and were able to identify the same variants as the previous study (Stafford et al., ), as well as 14 additional truncation variants that were not identified by Illumina's VariantStudio. While these additional SNPs have not been verified by Sanger sequencing, the read depth was ≥10 and quality ≥63.66, suggesting the variants are likely valid.…”

“…To exemplify the utility of iVariantGuide, we used whole-exome sequencing data (WES) of germline DNA from 48 serous ovarian cancers (OVCA) found in high-risk female patients (Stafford et al, 2017).The tertiary data analysis tools provided by iVariantGuide include variant assessment (Basic Protocol 1), pathway analysis, and GO enrichment (Basic Protocol 2)…”