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

Autor: Cusin I; CALIPHO group, SIB Swiss Institute of Bioinformatics, 1211, Geneva 4, Switzerland., Teixeira D; CALIPHO group, SIB Swiss Institute of Bioinformatics, 1211, Geneva 4, Switzerland., Zahn-Zabal M; CALIPHO group, SIB Swiss Institute of Bioinformatics, 1211, Geneva 4, Switzerland., Rech de Laval V; CALIPHO group, SIB Swiss Institute of Bioinformatics, 1211, Geneva 4, Switzerland.; Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland., Gleizes A; CALIPHO group, SIB Swiss Institute of Bioinformatics, 1211, Geneva 4, Switzerland., Viassolo V; Oncogenetics and Cancer Prevention Unit, Division of Oncology, University Hospitals of Geneva, 1205, Geneva, Switzerland., Chappuis PO; Oncogenetics and Cancer Prevention Unit, Division of Oncology, University Hospitals of Geneva, 1205, Geneva, Switzerland.; Division of Genetic Medicine, University Hospitals of Geneva, 1205, Geneva, Switzerland., Hutter P; Sophia Genetics, Rue du Centre 172, 1025, Saint Sulpice, Switzerland., Bairoch A; CALIPHO group, SIB Swiss Institute of Bioinformatics, 1211, Geneva 4, Switzerland.; Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland., Gaudet P; CALIPHO group, SIB Swiss Institute of Bioinformatics, 1211, Geneva 4, Switzerland. pascale.gaudet@sib.swiss.; Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland. pascale.gaudet@sib.swiss.
Jazyk: angličtina
Zdroj: Human genomics [Hum Genomics] 2018 Jul 11; Vol. 12 (1), pp. 36. Date of Electronic Publication: 2018 Jul 11.
DOI: 10.1186/s40246-018-0168-0
Abstrakt: Background: Germline 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 Conclusion: We 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.
Databáze: MEDLINE
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