Functional Analysis of a Large set of BRCA2 exon 7 Variants Highlights the Predictive Value of Hexamer Scores in Detecting Alterations of Exonic Splicing Regulatory Elements. Issue 11 (18th September 2013)

• Record Type: Journal Article
• Authors: Di Giacomo, Daniela; Gaildrat, Pascaline; Abuli, Anna; Abdat, Julie; Frébourg, Thierry; Tosi, Mario; Martins, Alexandra
• Is Part Of: Human mutation. Volume 34:Issue 11(2013:Nov.)
• Page Start: 1547
• Page End: 1557
• Publication Date: 2013-09-18
• Subjects: hereditary breast and ovarian cancer -- BRCA2 -- RNA splicing regulation -- bioinformatics predictions; Human chromosome abnormalities -- Periodicals; Mutation (Biology) -- Periodicals; 616.04205
• DOI: 10.1002/humu.22428
• Languages: English
• ISSNs: 1059-7794

Abstract

Abstract : Exonic variants can alter pre‐mRNA splicing not only by directly changing splice site sequences but also by modifying splicing regulatory elements, effects that are often difficult to predict. This work, based on minigene assays, revealed that 11 out of the 36 sequence variants identified in BRCA2 exon 7 are splicing regulatory mutations. We also found that the impact of these mutations could be efficiently predicted by a new in silico approach based on recently established hexamer scores. ABSTRACT: Exonic variants can alter pre‐mRNA splicing either by changing splice sites or by modifying splicing regulatory elements. Often these effects are difficult to predict and are only detected by performing RNA analyses. Here, we analyzed, in a minigene assay, 26 variants identified in the exon 7 of BRCA2, a cancer predisposition gene. Our results revealed eight new exon skipping mutations in this exon: one directly altering the 5′ splice site and seven affecting potential regulatory elements. This brings the number of splicing regulatory mutations detected in BRCA2 exon 7 to a total of 11, a remarkably high number considering the total number of variants reported in this exon ( n = 36), all tested in our minigene assay. We then exploited this large set of splicing data to test the predictive value of splicing regulator hexamers' scores recently established by Ke et al. (2011 ). Comparisons of hexamer‐based predictions with our experimental data revealed high sensitivity in detecting variants that increased exon skipping, an important feature for prescreening variants before RNA analysis. In conclusion, hexamer scores represent a promising tool for predicting the biological consequences of exonic variants and may have important applications for the interpretation of variants detected by high‐throughput sequencing.