Researchers at the Mayo Clinic in Rochester, MN, combined validated functional assays with computer simulations to determine whether individual inherited mutations in the BRCA2 gene make women susceptible to developing breast or ovarian cancer.
The study, published in the American Journal of Human Genetics, describes a laboratory-based test called the homology-directed DNA repair (HDR) assay, which can establish which inherited mutations called variations of uncertain significance (VUS) in the BRCA2 gene are involved in cancer.
“Together, the results show that systematic functional assays in combination with in silico predictors of pathogenicity provide robust tools for clinical annotation of BRCA2 VUS,” wrote the investigators.
Genetic testing of women with a family history of breast or ovarian cancer has led to the identification of many unique BRCA2 VUS. Accurate classification of the pathogenicity of variants can help to identify individuals at risk for cancer and help with decisions regarding screening, preventative measures, and treatments.
In the study, a comprehensive assessment of VUS in the BRCA2 C-terminal DNA binding domain (DBD) was performed by using a validated functional assay of BRCA2 homologous recombination DNA-repair activity, and a classifier of variant pathogenicity was defined. Among 139 variants evaluated, 54 had ≥99% probability of pathogenicity, and 73 had ≥95% probability of neutrality.
Previously, only 13 BRCA2 VUS were established as pathogenic by multifactorial models and seven others were consistently identified as pathogenic. This study represents a substantial increase in the number of BRCA2 VUS annotated as likely pathogenic.
The investigators acknowledge possible limitations in the use of functional assays, either alone or in combination with in silico prediction methods for clinical VUS annotation. Currently, the sensitivity and specificity of the HDR assay are based on relatively small numbers of established pathogenic missense variants.
In addition, BRCA2 could have other functions that influence cancer risks but are not effectively measured by the HDR assay. Furthermore, it is not determined if the HDR assay, or other functional studies, can be applied to other regions of BRCA2.
“We have shown that the HDR functional assay is a robust tool for annotating BRCA2 VUS within the DBD of BRCA2 and exceeds the sensitivity and specificity requirements of most clinical tests,” concluded the authors.
They also note that functional studies combined with sequence-based predictors can contribute to clinical classification in the absence of family history information.
To read more about this study, click here.