A Systematic Genetic Assessment of 1,433 Sequence Variants of Unknown Clinical Significance in the BRCA1 and BRCA2 Breast Cancer–Predisposition Genes

Abstract

Mutation screening of the breast and ovarian cancer-predisposition genes BRCA1 and BRCA2 is becoming an increasingly important part of clinical practice. Classification of rare nontruncating sequence variants in these genes is problematic, because it is not known whether these subtle changes alter function sufficiently to predispose cells to cancer development. Using data from the Myriad Genetic Laboratories database of nearly 70,000 full-sequence tests, we assessed the clinical significance of 1,433 sequence variants of unknown significance (VUSs) in the BRCA genes. Three independent measures were employed in the assessment: co-occurrence in trans of a VUS with known deleterious mutations; detailed analysis, by logistic regression, of personal and family history of cancer in VUS-carrying probands; and, in a subset of probands, an analysis of cosegregation with disease in pedigrees. For each of these factors, a likelihood ratio was computed under the hypothesis that the VUSs were equivalent to an "average" deleterious mutation, compared with neutral, with respect to risk. The likelihood ratios derived from each component were combined to provide an overall assessment for each VUS. A total of 133 VUSs had odds of at least 100 : 1 in favor of neutrality with respect to risk, whereas 43 had odds of at least 20 : 1 in favor of being deleterious. VUSs with evidence in favor of causality were those that were predicted to affect splicing, fell at positions that are highly conserved among BRCA orthologs, and were more likely to be located in specific domains of the proteins. In addition to their utility for improved genetics counseling of patients and their families, the global assessment reported here will be invaluable for validation of functional assays, structural models, and in silico analyses.

Contribution of bioinformatics predictions and functional splicing assays to the interpretation of unclassified variants of the BRCA genes

“…BRCA1 c.5194-12G4A had been predicted to be deleterious using a multifactorial LR model. 15 Here we show that it induces, in the minigene assay, the complete loss of the normal transcript and its replacement by an out-of-frame mRNA form (Figure 1b). After submission of this work, Whiley et al 17 have reported the same major splicing defect observed in a lymphoblastoid cell line from a patient carrying this mutation.…”

“…15 It was reported with no effect on splicing, 18 but another study 19 reported an effect in patient RNA. These discrepancies may reflect differences in RNA quality or stability of the relevant transcripts.…”

“…These models take into account multiple sources of data, including family data, tumor histopathology and co-occurrence with a deleterious mutation. [15][16][17] For previously not reported variants, or when family data had not been discussed in the publication of particular variants, we list in Tables 1 and 3 (last columns) the relevant features of patients in the corresponding families.…”

BRCA1 and BRCA2 mutations correlate with TP53 abnormalities and presence of immune cell infiltrates in ovarian high-grade serous carcinoma

“…BRCA1 and BRCA2 variants that were not considered pathogenic and/or were not recognized by the Breast Cancer Information Core (BIC) (http://research.nhgri.nih.gov/bic/) were not reported. 47 …”

Integrated analysis of unclassified variants in mismatch repair genes

“…For OR related to co-occurrence, we used the formula proposed by Easton et al 29 Co-occurrence was considered exclusively as the presence of a mutation in trans of the same gene, with the exception of cases with a recognizable biallelic phenotype. For families where the genetic test could be extended to at least one relative, OR of cosegregation of disease and variant were evaluated according to Thompson et al 30 For this analysis, we assumed the age-specific risks and penetrance estimated by Marroni et al 31 for the Italian population.…”