Genetic and Histopathologic Evaluation ofBRCA1andBRCA2DNA Sequence Variants of Unknown Clinical Significance

Abstract

Classification of rare missense variants as neutral or disease causing is a challenge and has important implications for genetic counseling. A multifactorial likelihood model for classification of unclassified variants in BRCA1 and BRCA2 has previously been developed, which uses data on cooccurrence of the unclassified variant with pathogenic mutations in the same gene, cosegregation of the unclassified variant with affected status, and Grantham analysis of the fit between the missense substitution and the evolutionary range of variation observed at its position in the protein. We have further developed this model to take into account relevant features of BRCA1-and BRCA2-associated tumors, such as the characteristic histopathology and immunochemical profiles associated with pathogenic mutations in BRCA1, and the fact that f80% of tumors from BRCA1 and BRCA2 carriers undergo inactivation of the wild-type allele by loss of heterozygosity. We examined 10 BRCA1 and 15 BRCA2 unclassified variants identified in Australian, multiple-case breast cancer families. By a combination of genetic, in silico, and histopathologic analyses, we were able to classify one BRCA1 variant as pathogenic and six BRCA1 and seven BRCA2 variants as neutral. Five of these neutral variants were also found in at least 1 of 180 healthy controls, suggesting that screening a large number of appropriate controls might be a useful adjunct to other methods for evaluation of unclassified

Intronic variants inBRCA1andBRCA2that affect RNA splicing can be reliably selected by splice-site prediction programs

“…However, alterations affecting the exon 3 of the BRCA2 gene should be interpret with caution since the Rad51 binding sites and nuclear localization signals in the 3 0 region of BRCA2 still remain [Diez et al, 2007]. Further research, such as the analysis of cosegregation in the family, frequency of the variant in cases and controls, and loss of heterozygosity (LOH) in tumors will be necessary to fully assess the clinical significance of this variant [Goldgar et al, 2004;Chenevix-Trench et al, 2006]. Given the high lifetime risk for breast cancer and ovarian cancer for BRCA1 and BRCA2 mutation carriers, it is essential that the clinical significance of the intronic variants is elucidated.…”

Basal-like breast cancer and the BRCA1 phenotype

“…More studies are required to examine whether the current screening criteria using family history are significantly enhanced by inclusion of pathological basal-like phenotype. Where the basal-like phenotype may already be currently useful is in the prediction of which BRCA gene is likely to be mutated in high-risk families, where a highrisk family with basal-like cancers is much more likely to have an underlying BRCA1 mutation than BRCA2 mutation, and also in the classification of BRCA1 variants of uncertain pathogenicity (Chenevix-Trench et al, 2006).…”

A recombination-based method to characterize human BRCA1 missense variants

“…However, in general, it is easier to conclude that a variant is non-pathogenic than pathogenic [25].…”