title: Systematic evaluation of the effect of common SNPs on pre-mRNA splicing.
abstract: The evolutionary and biomedical importance of differential mRNA splicing is well established. Numerous studies have assessed patterns of differential splicing in different genes and correlated these patterns to the genotypes for adjacent single-nucleotide polymorphisms (SNPs). Here, we have chosen a reverse approach and screened dbSNP for common SNPs at either canonical splice sites or exonic splice enhancers (ESEs) that would be classified as putatively splicing-relevant by bioinformatic tools. The 223 candidate SNPs retrieved from dbSNP were experimentally tested using a previously established panel of 92 matching DNAs and cDNAs. For each SNP, 16 cDNAs providing a balanced representation of the genotypes at the respective SNP were investigated by nested RT-PCR and subsequent sequencing. Putative allele-dependent splicing was verified by the cloning of PCR products. The positive predictive value of the bioinformatics tools turned out to be low, ranging from 0% for ESEfinder to 9% (in the case of acceptor-site SNPs) for a recently reported neural network. The results highlight the need for a better understanding of the sequence characteristics of functional splice-sites to improve our ability to predict in silico the splicing relevance of empirically observed DNA sequence variants.
authors.affiliation: Institute of Clinical Molecular Biology, University Hospital Schleswig-Holstein, Kiel, Germany.
authors.forename: Abdou
authors.initials: A
authors.lastname: ElSharawy
authors.forename: Bernd
authors.initials: B
authors.lastname: Hundrieser
authors.forename: Mario
authors.initials: M
authors.lastname: Brosch
authors.forename: Michael
authors.initials: M
authors.lastname: Wittig
authors.forename: Klaus
authors.initials: K
authors.lastname: Huse
authors.forename: Matthias
authors.initials: M
authors.lastname: Platzer
authors.forename: Albert
authors.initials: A
authors.lastname: Becker
authors.forename: Matthias
authors.initials: M
authors.lastname: Simon
authors.forename: Philip
authors.initials: P
authors.lastname: Rosenstiel
authors.forename: Stefan
authors.initials: S
authors.lastname: Schreiber
authors.forename: Michael
authors.initials: M
authors.lastname: Krawczak
authors.forename: Jochen
authors.initials: J
authors.lastname: Hampe
mesh_terms: D004247:DNA / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D005838:Genotype; D006801:Humans; D016571:Neural Networks, Computer; D016133:Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D012322:RNA Precursors / Q000235:genetics*; D012326:RNA Splicing / Q000235:genetics*
chemical_list: D018076:DNA, Complementary; D012322:RNA Precursors; D004247:DNA