open access: Prioritizing Variants in Complete Hereditary Breast and Ovarian Cancer Genes in Patients Lacking Known BRCA Mutations

Prioritizing Variants in Complete Hereditary Breast and Ovarian Cancer Genes in Patients Lacking Known BRCA Mutations - Caminsky - 2016 - Human Mutation

Introduction

Currently, the lifetime risk for a woman to develop breast cancer (BC) is 12.3% and 1.3% in the case of ovarian cancer (OC [Howlander et al., 2014]). Approximately 5–10% of all BC cases are hereditary in nature, versus 25% for OC, where relative risk (RR) of BC or OC with one affected first degree family member is estimated at 2.1 and 3.1, respectively [Stratton et al., 1998; Walsh et al., 2011]. Two highly penetrant genes, BRCA1 and BRCA2, are associated with a large proportion of hereditary breast and ovarian cancer (HBOC) cases. However, the estimated rate of linkage to these genes is significantly higher than the proportion of pathogenic mutations identified in HBOC families [Ford et al., 1998], suggesting unrecognized or unidentified variants in BRCA1/2.

Clinical BRCA1/2 testing is restricted primarily to coding regions. Limitations on how variants can be interpreted, lack of functional validation, and mutations in other genes contribute to uninformative results. The heritability that is not associated with BRCA genes is likely due to other genetic factors rather than environmental causes, specifically moderate- and low-risk susceptibility genes [Antoniou and Easton, 2006]. Hollestelle et al. [2010] point out the challenges in estimating increased risks associated with mutations in these genes, as the disease patterns are often incompletely penetrant, and require large pedigree studies to confidently assess pathogenicity.

Next-generation sequencing (NGS) of gene panels for large cohorts of affected and unaffected individuals has become an increasingly popular approach to confront these challenges. Numerous HBOC gene variants have been catalogued, including cases in which RR (risk ratio) has been determined; however, the literature is also flooded with variants lacking a clinical interpretation [Cassa et al., 2012]. It is not feasible to functionally evaluate the effects all of the variant(s) of uncertain significance (VUS) identified by NGS. Further, in silico assessment of protein coding variants has not been entirely reliable [Rogan and Zou, 2013; Vihinen, 2013]. Several approaches have been developed to better assess variants from exome and genome-wide NGS data [Duzkale et al., 2013; Kircher et al., 2014]. Nevertheless, there is an unmet need for other methods that quickly and accurately bridge variant identification and classification.

To begin to address this problem, we sought to provide potentially novel interpretations of noncoding sequence changes, based on disruption or acquisition of interactions with proteins that recognize nucleic acid binding sites. Information theory (IT) based analysis predicts changes in sequence binding affinity, and it has been applied and validated for use in the analysis of splice sites (SSs),......

 In the present study, we have sequenced 13 additional genes that have been deemed HBOC susceptibility loci (BARD1, EPCAM, MLH1, MRE11A, MSH2, MSH6, MUTYH, NBN, PMS2, PTEN, RAD51B, STK11, and XRCC2 [Minion et al., 2015]). These genes encode proteins with roles in DNA repair, surveillance, and cell cycle regulation (Fig. 1; for further evidence supporting this gene set see Supp. Table S1 [Apostolou and Fostira, 2013; Al Bakir and Gabra, 2014]), and are associated with specific disease syndromes that confer an increased risk of BC and OC, as well as many other types of cancer (Supp. Table S2). High-risk genes confer >4 times increased risk of BC compared to the general population. BRCA1 and BRCA2 are estimated to increase risk 20-fold [Antoniou et al., 2003]....

 Figure 1. (below) Common genomic pathways among 20 HBOC genes, including risk and relevant literature. The left, top, and right circles indicate sequenced genes that play important roles in the mismatch repair (MMR), Fanconi anemia, and DNA double-strand break repair pathways, respectively. The bottom circle contains genes involved in cell cycle control. Genes considered to present a high risk of breast and/or ovarian cancer when mutated are bolded, moderate-risk genes are underlined, and low-risk genes are in normal font. The estimated number of articles listing a gene's association with breast or ovarian cancer (based on a systematic search in PubMed [performed June 2015]) is indicated in superscript. **MUTYH is only high risk in the case of bi-allelic mutations. *EPCAM is not involved in any pathways, but is associated with hereditary nonpolyposis colorectal cancer (HNPCC) by virtue of the fact that 3′ deletions of EPCAM can cause epigenetic silencing of MSH2, causing Lynch syndrome protein. See Supp. Table S1 for citations and further evidence supporting this gene set.