title: A classification model for BRCA2 DNA binding domain missense variants based on homology-directed repair activity.
abstract: The relevance of many BRCA2 variants of uncertain significance (VUS) to breast cancer has not been determined due to limited genetic information from families carrying these alterations. Here, we classified six new variants as pathogenic or nonpathogenic by analysis of genetic information from families carrying 64 individual BRCA2 DNA binding domain (DBD) missense mutations using a multifactorial likelihood model of cancer causality. Next, we evaluated the use of a homology-directed DNA break repair (HDR) functional assay as a method for inferring the clinical relevance of VUS in the DBD of BRCA2 using 18 established nonpathogenic missense variants and all 13 established pathogenic missense mutations from the BRCA2 DBD. Compared with the known status of these variants based on the multifactorial likelihood model, the sensitivity of the HDR assay for pathogenic mutations was estimated at 100% [95% confidence interval (CI): 75.3%-100%] and specificity was estimated at 100% (95% CI: 81.5%-100%). A statistical classifier for predicting the probability of pathogenicity of BRCA2 DBD variants was developed using these functional results. When applied to 33 additional VUS, the classifier identified eight with 99% or more probability of nonpathogenicity and 18 with 99% or more probability of pathogenicity. Thus, in the absence of genetic evidence, a cell-based HDR assay can provide a probability of pathogenicity for all VUS in the BRCA2 DBD, suggesting that the assay can be used in combination with other information to determine the cancer relevance of BRCA2 VUS.
authors.affiliation: Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA.
authors.forename: Lucia
authors.initials: L
authors.lastname: Guidugli
authors.forename: Vernon S
authors.initials: VS
authors.lastname: Pankratz
authors.forename: Namit
authors.initials: N
authors.lastname: Singh
authors.forename: James
authors.initials: J
authors.lastname: Thompson
authors.forename: Catherine A
authors.initials: CA
authors.lastname: Erding
authors.forename: Christoph
authors.initials: C
authors.lastname: Engel
authors.forename: Rita
authors.initials: R
authors.lastname: Schmutzler
authors.forename: Susan
authors.initials: S
authors.lastname: Domchek
authors.forename: Katherine
authors.initials: K
authors.lastname: Nathanson
authors.forename: Paolo
authors.initials: P
authors.lastname: Radice
authors.forename: Christian
authors.initials: C
authors.lastname: Singer
authors.forename: Patricia N
authors.initials: PN
authors.lastname: Tonin
authors.forename: Noralane M
authors.initials: NM
authors.lastname: Lindor
authors.forename: David E
authors.initials: DE
authors.lastname: Goldgar
authors.forename: Fergus J
authors.initials: FJ
authors.lastname: Couch
mesh_terms: D024682:BRCA2 Protein / Q000235:genetics*; D001943:Breast Neoplasms / Q000145:classification* / Q000235:genetics*; D004260:DNA Repair / Q000235:genetics*; D005260:Female; D024522:Genes, BRCA2; D020022:Genetic Predisposition to Disease / Q000235:genetics; D014644:Genetic Variation; D006801:Humans; D015233:Models, Statistical; D020125:Mutation, Missense; D012372:ROC Curve; D012680:Sensitivity and Specificity
chemical_list: D024682:BRCA2 Protein