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SNPSplicer: systematic analysis of SNP-dependent splicing in genotyped cDNAs

Item Type:Article
Title:SNPSplicer: systematic analysis of SNP-dependent splicing in genotyped cDNAs
Creators Name:Elsharawy, A. and Manaster, C. and Teuber, M. and Rosenstiel, P. and Kwiatkowski, R. and Huse, K. and Platzer, M. and Becker, A. and Nuernberg, P. and Schreiber, S. and Hampe, J.
Abstract:Functional annotation of SNPs (as generated by HapMap (http://www.hapmap.org) for instance) is a major challenge. SNPs that lead to single amino acid substitutions, stop codons, or frameshift mutations can be readily interpreted, but these represent only a fraction of known SNPs. Many SNPs are located in sequences of splicing relevance-the canonical splice site consensus sequences, exonic and intronic splice enhancers or silencers (exonic splice enhancer [ESE], intronic splice enhancer [ISE], exonic splicing silencer [ESS], and intronic splicing silencer [ISS]), and others. We propose using sets of matching DNA and complementary DNA (cDNA) as a screening method to investigate the potential splice effects of SNPs in RT-PCR experiments with tissue material from genotyped sources. We have developed a software solution (SNPSplicer; http://www.ikmb.uni-kiel.de/snpsplicer) that aids in the rapid interpretation of such screening experiments. The utility of the approach is illustrated for SNPs affecting the donor splice sites (rs2076530:A>G, rs3816989:G>A) leading to the use of a cryptic splice site and exon skipping, respectively, and an exonic splice enhancer SNP (rs2274987:C/T), leading to inclusion of a new exon. We anticipate that this methodology may help in the functional annotation of SNPs in a more high-throughput fashion.
Keywords:SNP, Splicing, ESE, SNP-dependent splicing, HapMap
Source:Human Mutation
Page Range:1129-1134
Date:November 2006
Official Publication:https://doi.org/10.1002/humu.20377
PubMed:View item in PubMed

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