Single Nucleotide Polymorphisms Associated With Rat Expressed Sequences

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 ∼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 that result in the introduction of a premature stop codon and that could be confirmed experimentally. Two of these "in silico-identified knockouts" reside in interesting QTL regions. Data are publicly available via a Web interface (http://cascad.niob.knaw.nl), allowing simple and advanced search queries.[Supplemental material is available online at www.genome.org. The SNPs identified in this study can be found in the National Center of Biotechnology Information (NCBI) SNP database under submitter handle FGG_NIOB (ss12535137-ss12568440, ss12588074-ss12588105). The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: L.F.M. van Zutphen, B. Smits, M.B. Soares, T. Scheetz, and the Rat Genome Sequencing Consortium.]Single nucleotide polymorphisms (SNPs) are the most common type of DNA variation and the main source of phenotypic differences between individuals. Furthermore, SNPs have proven to be highly stable within populations and very useful as genetic markers in several applications including physical mapping, evolutionary studies, and association genetics. Although many experimental techniques for high-throughput SNP mining have been developed (for review, see Vignal et al. 2002), the generation of dense polymorphism maps is still a laborious and timeconsuming procedure. The alternative, in silico identification of SNPs using large data sets generated by sequencing projects, is a quick and cost-efficient approach for the generation of impressive amounts of candidate SNPs.Several candidate SNP detection pipelines based on EST data analysis have been described previously (Buetow et al. 1999;Marth et al. 1999;Picoult-Newberg et al. 1999;Brett et al. 2000). Application of computationally intensive BLAST search and/or Phrap fragment assembler, which ...

Genetic variation in the zebrafish

“…After clustering, 51,769 unique candidate SNPs were obtained. Although a similar amount of input EST sequences was used in this study compared with our previous analysis for the rat (Guryev et al 2004), we found 55% more candidate SNPs, suggesting a higher SNP frequency in zebrafish. Despite the high number of SNPs discovered in this effort, the CASCAD database currently contains only a small part of variation associated with expressed sequences.…”

“…We have developed a computational SNP discovery pipeline and candidate SNP database named CASCAD (Cascad Snp Candidate Database, http://cascad.niob.knaw.nl) (Guryev et al 2004(Guryev et al , 2005. Here, we report an application of this pipeline for construction and verification of a single-nucleotide variation database for zebrafish (D. rerio).…”

BN phenome: detailed characterization of the cardiovascular, renal, and pulmonary systems of the sequenced rat

“…These allele data are now being greatly supplemented by the addition of Ͼ45,000 single nucleotide polymorphisms (SNPs) identified across multiple rat strains (http://www.ncbi.nlm.nih.gov/SNP/snp_summary. cgi) (13,29). Furthermore, a growing number of rat strains are or will be resequenced for SNP discovery (1,5,24,29) by two major SNP discovery projects underway in Europe (the Functional Genomics Group in the Netherlands and the MaxDelbruck-Center for Molecular Medicine in Germany) and by Baylor College of Medicine (Houston, TX) via a recent National Human Genome Research Institute white paper to identify SNPs in an additional eight strains.…”

DNA Based Techniques for Studying Genetic Diversity

“…Other direct strategies include whole genome (WGSS) and reduced representation (RRSS) shotgun sequencing approaches. If comparative sequence data are available in public or other databases, various sequence comparison algorithms that identify nucleotide differences provide an alternative means to empirically discover SNPs (Guryev et al, 2005). In rice, for example, SNPs discovery on a genome wide basis was based on using either the genomicscale re-sequencing approaches or Sanger sequencing-based strategies.…”