SNPSplicer: systematic analysis of SNP-dependent splicing in genotyped cDNAs.
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.
ElSharawy
Abdou
A
Institute of Clinical Molecular Biology at the Christian-Albrechts-University, Kiel, Germany.
Manaster
Carl
C
Teuber
Markus
M
Rosenstiel
Philip
P
Kwiatkowski
Ruta
R
Huse
Klaus
K
Platzer
Matthias
M
Becker
Albert
A
Nürnberg
Peter
P
Schreiber
Stefan
S
Hampe
Jochen
J
D017398:Alternative Splicing / Q000502:physiology; D001483:Base Sequence; D001921:Brain / Q000166:cytology; D045744:Cell Line, Tumor; D004247:DNA / Q000097:blood; D004252:DNA Mutational Analysis / Q000379:methods; D018076:DNA, Complementary / Q000032:analysis*; D001330:Electronic Data Processing / Q000379:methods; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D022821:RNA Splice Sites / Q000235:genetics*; D012984:Software
D018076:DNA, Complementary; D022821:RNA Splice Sites; D004247:DNA