engleski

In Silico Prediction of Potential Functional and Structural Effects of Novel BRCA1 and BRCA2 Unclassified Sequence Variants Found in Healthy Females in Croatia

BRCA1 (breast cancer 1 gene) and BRCA2 (breast cancer 2 gene) are the major hereditary breast/ovarian cancer predisposing genes and their mutations increase the risk of developing cancer. At present, almost half of all BRCA1 and BRCA2 sequence variants found are unclassified variants (UVs) so their clinical significance is unknown or uncertain. Interpretation of UVs is the major concern for BRCA genes, especially for risk assessment in genetic counseling. We have developed method (for the first time in Croatia) for detection of inherited predisposition to breast/ovarian cancer. We analyzed distribution and occurrence of all sequence variants in BRCA1 and BRCA2 genes on 200 healthy women in Croatia (more than 70 years old without any cancer affected family members). Those results could help us in assessing preliminary clinical significance of UVs once found in patients. The aim of this study is to predict the potential functional and structural effects of UVs using in silico methods. We used different publicly available web-based tools to identify UVs that may have deleterious effects with respect to different biomolecular functional categories (i.e. intronic and exonic splicing regulation, nonsynonymous amino acid SNP effect, interspecific amino acid conservation, belonging to known functional domain) so their clinical significance in cancer etiology could be assumed. Using straightforward physical and comparative considerations, we have found that two sequence variants with nonsynonymous amino acid changes and one amino acid deletion could have no impact on the structure and function of a BRCA1 and BRCA2 proteins. Two synonymous amino acid changes (silent mutations) could have impact on splicing regulation by disrupting and creating one exonic splicing enhancers. Our only intronic UV showed no potential impact on splicing because nucleotide changes at that position likely make no changes in consensus splice sites. All other exonic UVs do not lead to creation of potential cryptic splice sites. Predicting potential functional and structural effects of BRCA1 and BRCA2 UVs using in silico methods presents fast, easy and cheap method for assessing their preliminary clinical significance, especially in cases with low frequent and ethnic specific alleles, when it is difficult to make population based studies and when expensive in vitro functional assays must be performed.

BRCA1; BRCA2; in silico; UVs; mutations; polymorphisms; Croatia

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