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Genetic variation in coding regions between and within commonly used inbred rat strains.

Authors: Smits, BM  Van Zutphen, BF  Plasterk, RH  Cuppen E.,  
Citation: Smits BM, etal., Genome Res. 2004 Jul;14(7):1285-90.
Pubmed: (View Article at PubMed) PMID:15231744
DOI: Full-text: DOI:10.1101/gr.2155004

Single nucleotide polymorphisms (SNPs) are the most common genetic variation in mammalian populations. Their significance is illustrated by their potential contribution to common disease but also by their potential for use in genetic association and mapping experiments. We have examined the genetic variation between commonly used inbred rat strains by using an efficient SNP discovery and typing assay based on enzyme-based (CEL I) heteroduplex cleavage. Screening of a panel of 96 different rat (sub-)strains for 100 genomic loci in 55 genes, whose human homologs are implicated in clinically relevant diseases like neurological disorder, cancer, schizophrenia, and obesity, resulted in the identification of 103 novel polymorphisms. As all strains are simultaneously genotyped in this setup, this allowed us to make an estimate of the genetic variation between and within commonly used rat inbred strains. Interestingly, we observed substantial genetic variation between colonies of the same inbred strain, maintained at different locations. Furthermore, we identified 17 non-synonymous SNPs that may have an effect on protein function and contribute to phenotypic differences between different laboratory strains.

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RGD Object Information
RGD ID: 737878
Created: 2004-03-24
Species: All species
Last Modified: 2004-07-15
Status: ACTIVE



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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.