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

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Item Type:	Article
Title:	SNPSplicer: systematic analysis of SNP-dependent splicing in genotyped cDNAs
Creators Name:	Elsharawy, A., Manaster, C., Teuber, M., Rosenstiel, P., Kwiatkowski, R., Huse, K., Platzer, M., Becker, A., Nuernberg, P., 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
ISSN:	1059-7794
Publisher:	Wiley
Volume:	27
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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