A new bioinformatics tool to help assess the significance of BRCA1 variants

Isabelle Cusin,Pierre Hutter,Monique Zahn-Zabal,Daniel Teixeira,Pascale Gaudet,Valeria Viassolo,Anne Gleizes,Amos Bairoch,Pierre O Chappuis,Valentine Rech De Laval

doi:10.1186/s40246-018-0168-0

Abstract

BackgroundGermline pathogenic variants in the breast cancer type 1 susceptibility gene BRCA1 are associated with a 60% lifetime risk for breast and ovarian cancer. This overall risk estimate is for all BRCA1 variants; obviously, not all variants confer the same risk of developing a disease. In cancer patients, loss of BRCA1 function in tumor tissue has been associated with an increased sensitivity to platinum agents and to poly-(ADP-ribose) polymerase (PARP) inhibitors. For clinical management of both at-risk individuals and cancer patients, it would be important that each identified genetic variant be associated with clinical significance. Unfortunately for the vast majority of variants, the clinical impact is unknown. The availability of results from studies assessing the impact of variants on protein function may provide insight of crucial importance.Results and conclusionWe have collected, curated, and structured the molecular and cellular phenotypic impact of 3654 distinct BRCA1 variants. The data was modeled in triple format, using the variant as a subject, the studied function as the object, and a predicate describing the relation between the two. Each annotation is supported by a fully traceable evidence. The data was captured using standard ontologies to ensure consistency, and enhance searchability and interoperability. We have assessed the extent to which functional defects at the molecular and cellular levels correlate with the clinical interpretation of variants by ClinVar submitters. Approximately 30% of the ClinVar BRCA1 missense variants have some molecular or cellular assay available in the literature. Pathogenic variants (as assigned by ClinVar) have at least some significant functional defect in 94% of testable cases. For benign variants, 77% of ClinVar benign variants, for which neXtProt Cancer variant portal has data, shows either no or mild experimental functional defects. While this does not provide evidence for clinical interpretation of variants, it may provide some guidance for variants of unknown significance, in the absence of more reliable data.The neXtProt Cancer variant portal (https://www.nextprot.org/portals/breast-cancer) contains over 6300 observations at the molecular and/or cellular level for BRCA1 variants.

Highlights

Germline pathogenic variants in the breast cancer type 1 susceptibility gene BRCA1 are associated with a 60% lifetime risk for breast and ovarian cancer
Two poly-(ADP-ribose) polymerase (PARP) inhibitors have been approved in the European Union and in the USA for the treatment of patients affected by advanced ovarian cancer with pathogenic or likely pathogenic BRCA1 or BRCA2 germline or somatic variants
Using the information derived from 100 publications, the functional impact of 3654 unique BRCA1 variants was captured: 431 natural variants and 3223 mutants generated by site-directed mutagenesis

Summary

Introduction

Germline pathogenic variants in the breast cancer type 1 susceptibility gene BRCA1 are associated with a 60% lifetime risk for breast and ovarian cancer. Inactivation of BRCA1 in tumor tissue, either due to BRCA1 germline or somatic pathogenic variants, epigenetic changes, or loss of wild-type alleles, is predictive for response to crosslinking chemotherapeutic agents, such as platinum-based drugs, and to PARP-inhibitors, leading to synthetic lethality in the presence of BRCA1/BRCA2 deficiency [13, 14]. Genetic variants are classified based on clinical assessment as pathogenic, likely pathogenic, variant of uncertain significance (VUS), likely benign, or benign This interpretation often takes into account co-segregation, the variant frequency in unaffected individuals, and the variant impact analyzed with prediction tools such as SIFT [16] and PolyPhen-2 [17]. Evidence from in vitro studies can provide insight of crucial importance for patient management

Results

Discussion

Conclusion