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Comprehensive prediction of mRNA splicing effects of BRCA1 and BRCA2 variants

Authors

  • Eliseos J. Mucaki,

    1. Department of Biochemistry, University of Western Ontario, London, Canada
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  • Peter Ainsworth,

    1. Department of Biochemistry, University of Western Ontario, London, Canada
    2. Health Sciences Center, London, Ontario, Canada
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  • Peter K. Rogan

    Corresponding author
    1. Department of Biochemistry, University of Western Ontario, London, Canada
    2. Department of Computer Science, University of Western Ontario, London, Canada
    • Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, N6A 5C1 Canada
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  • Communicated by Christophe Béroud

Abstract

Variants of uncertain significance (VUS) in the BRCA1 and BRCA2 genes potentially affecting coding sequence as well as normal splicing activity have confounded predisposition testing in breast cancer. Here, we apply information theory to analyze BRCA1/2 mRNA splicing mutations categorized as VUS. The method was validated for 31 of 36 mutations known to cause missplicing in BRCA1/2 and all 26 that do not alter splicing. All single-nucleotide variants in the Breast Cancer Information Resource (BIC; Breast Cancer Information Core Database; http://research.nhgri.nih.gov/bic; last access June 1, 2010) were then analyzed. Information analysis is similar in sensitivity to other predictive methods; however, the thermodynamic basis of the theory also enables splice-site affinity to be determined accurately, which is important for assessing mutations that render natural splice sites partially functional and competition between cryptic and natural splice sites. We report 299 of 2,071 single-nucleotide BIC mutations that are predicted to significantly weaken natural sites and/or strengthen cryptic splice sites, 171 of which are not designated as splicing mutations in the database. Splicing alterations are predicted for 68 of 690 BRCA1 and 60 of 958 BRCA2 mutations designated as VUS. These analyses should be useful in prioritizing suspected mutations for downstream expression studies and for predicting aberrantly spliced isoforms generated by these mutations. Hum Mutat 32:1–8, 2011. © 2011 Wiley-Liss, Inc.

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