Single nucleotide polymorphisms associated with rat expressed sequences

Genome Research
Victor GuryevEdwin Cuppen

Abstract

Single nucleotide polymorphisms (SNPs) are the most common source of genetic variation in populations and are thus most likely to account for the majority of phenotypic and behavioral differences between individuals or strains. Although the rat is extensively studied for the latter, data on naturally occurring polymorphisms are mostly lacking. We have used publicly available sequences consisting of whole-genome shotgun (WGS), expressed sequence tag (EST), and mRNA data as a source for the in silico identification of SNPs in gene-coding regions and have identified a large collection of 33,305 high-quality candidate SNPs. Experimental verification of 471 candidate SNPs using a limited set of rat isolates revealed a confirmation rate of approximately 50%. Although the majority of SNPs were identified between Sprague-Dawley (EST data) and Brown Norway (WGS data) strains, we found that 66% of the verified variations are common among different rat strains. All SNPs were extensively annotated, including chromosomal and genetic map information, and nonsynonymous SNPs were analyzed by SIFT and PolyPhen prediction programs for their potential deleterious effect on protein function. Interestingly, we retrieved three SNPs from the database...Continue Reading

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Citations

Jul 25, 2007·Bioinformatics·Frank PanitzChristian Bendixen
Aug 16, 2005·Nucleic Acids Research·Eli EisenbergErez Y Levanon
Jun 13, 2012·Nucleic Acids Research·Ngak-Leng SimPauline C Ng
Mar 15, 2006·Genome Research·Victor GuryevEdwin Cuppen
Apr 28, 2006·Genome Biology·Loris MularoniM Mar Albà
Aug 10, 2006·PLoS Genetics·Victor GuryevEdwin Cuppen
Feb 18, 2010·Physiological Genomics·Kyoungmi KimJudith S Stern
Jan 18, 2006·Nature Genetics·Renae L MalekNorman H Lee
Apr 30, 2008·Nature Genetics·UNKNOWN STAR ConsortiumNorbert Hubner
Jun 15, 2007·Molecular and Biochemical Parasitology·Mariana SimõesGuilherme Oliveira
Oct 3, 2008·Animal Genetics·D M GorbachM F Rothschild

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