ArticleGenome research2004
Single nucleotide polymorphisms associated with rat expressed sequences.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 46 citations in OpenAlex.
- Sex Influences Genetic Susceptibility to Depression-Like Behaviors in Chronic Unpredictable Mild Stress-Exposed Wistar Rats.Molecular neurobiology · 2025Article
- Identification of the genetic background of laboratory rats through amplicon-based next-generation sequencing for single-nucleotide polymorphism genotyping.BMC genomic data · 2024Article
- Single-Nucleotide Polymorphisms (SNP) Mining and Their Effect on the Tridimensional Protein Structure Prediction in a Set of Immunity-Related Expressed Sequence Tags (EST) in Atlantic Salmon (Frontiers in genetics · 2019Article
- Article
- High Variation in Single Nucleotide Polymorphisms (SNPs) and Insertions/Deletions (Indels) in the Highly Invasive Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) Middle East-Asia Minor 1 (MEAM1).Neotropical entomology · 2013Article
- Transcriptome-wide single nucleotide polymorphisms (SNPs) for abalone (Haliotis midae): validation and application using GoldenGate medium-throughput genotyping assays.International journal of molecular sciences · 2013Article
- SIFT web server: predicting effects of amino acid substitutions on proteins.Nucleic acids research · 2012Article
- Life or death? A physiogenomic approach to understand individual variation in responses to hemorrhagic shock.Current genomics · 2011Article
- Genes unlinked to the leptin receptor influence urinary albumin excretion in obese Zucker rats.Physiological genomics · 2010Article
- Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua).BMC genomics · 2010Article
- Multiplex microsatellite marker panels for genetic monitoring of common rat strains.Journal of the American Association for Laboratory Animal Science : JAALAS · 2008Article
- SNP and haplotype mapping for genetic analysis in the rat.Nature genetics · 2008Article
- Single nucleotide polymorphisms identification in expressed genes of Schistosoma mansoni.Molecular and biochemical parasitology · 2007Article
- Haplotype block structure is conserved across mammals.PLoS genetics · 2006Article
- A set of highly informative rat simple sequence length polymorphism (SSLP) markers and genetically defined rat strains.BMC genetics · 2006Article
- Genetic variation in the zebrafish.Genome research · 2006Article
- Mutation patterns of amino acid tandem repeats in the human proteome.Genome biology · 2006Article
- Efficient single nucleotide polymorphism discovery in laboratory rat strains using wild rat-derived SNP candidates.BMC genomics · 2005Article
- Identification of a rat model for usher syndrome type 1B by N-ethyl-N-nitrosourea mutagenesis-driven forward genetics.Genetics · 2005Article
- CASCAD: a database of annotated candidate single nucleotide polymorphisms associated with expressed sequences.BMC genomics · 2005Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.