Characterization of Variants of Unknown Significance (VUS) in BRCA1
Approximately 3%-8% of breast cancer patients carry one defective BRCA1 or BRCA2 allele. While the rise of genetic testing have helped identify BRCA mutation carriers, the implication of certain mutations are still unknown. These comprise almost one third of all BRCA variants. These Variants of Unknown Significance (VUS) pose a challenge for clinicians and patients, since a VUS cannot guide treatment or prevention strategies. To solve this problem, our laboratory previously developed and validated a biological assay using gene expression data from EBV-transformed cell lines. This study adapted the previously validated assay for use in the clinic by converting to the NanoString nCounter platform and refining the classifier with k-TSP. The classifier was then applied to cell lines derived from individuals carrying novel BRCA1 variants to provide evidence for the pathogenicity of BRCA1 VUS. The overall accuracy of the resulting classifier was 92%. This classifier’s accuracy in the test set of samples derived from patients of KGH with known BRCA1 pathogenicity was 71%. This classifier provided potentially novel findings about two BRCA1 VUS: c.2050C>T and c.693G>A. All replicate samples tested from patient 43791 (c.2050C>T) and patient 43901 (c.693G>A) had a consensus prediction as not pathogenic. While these predictions provide new evidence towards better characterizing these BRCA1 VUS, they should remain as supplemental evidence that should be used in conjunction with evidence from other sources. Further validation incorporating additional samples is necessary to move this assay forward towards clinical implementation.