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

Authors

  • Daniela Di Giacomo,

    1. Inserm U1079, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France
    2. Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Italy
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  • Pascaline Gaildrat,

    1. Inserm U1079, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France
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  • Anna Abuli,

    1. Inserm U1079, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France
    2. Cancer Research Program, Institut Hospital del Mar d'Investigacions Mèdiques, University of Barcelona, Spain
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  • Julie Abdat,

    1. Inserm U1079, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France
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  • Thierry Frébourg,

    1. Inserm U1079, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France
    2. Department of Genetics, University Hospital, Rouen, France
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  • Mario Tosi,

    1. Inserm U1079, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France
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  • Alexandra Martins

    Corresponding author
    1. Inserm U1079, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France
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  • Contract grant sponsors: French National Cancer Institute (INCa) and; Direction Générale de l'Offre des Soins (DGOS); Italian Ministry of Education, University and Research (MIUR); Spanish Institut Hospital del Mar d'Investigacions Mèdiques (IMIM); Spanish Secretaria d'Universitats i Recerca de la Generalitat de Catalunya (SUR); Departament d'Economia i Coneixement, Generalitat de Catalunya (2012 BE1 00172).

  • Communicated by Rachel Karchin

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.

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