RGD Reference Report - Genetic variation in coding regions between and within commonly used inbred rat strains. - Rat Genome Database

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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.
RGD ID: 737878
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.

Annotation

Objects referenced in this article
Strain A2/Colle null Rattus norvegicus
Strain ACI/Kun null Rattus norvegicus
Strain ACI/SegHsd null Rattus norvegicus
Strain ACI/Ztm null Rattus norvegicus
Strain AGUS/OlaHsd null Rattus norvegicus
Strain ALC/Colle null Rattus norvegicus
Strain AMORAT/Wsl null Rattus norvegicus
Strain AO/OlaHsd null Rattus norvegicus
Strain ARISTORAT/Wsl null Rattus norvegicus
Strain AS/Ztm null Rattus norvegicus
Strain AUG/OlaHsd null Rattus norvegicus
Strain AVN/Orl null Rattus norvegicus
Strain BBWB/Mol null Rattus norvegicus
Strain BDE/Ztm null Rattus norvegicus
Strain BDII/Ztm null Rattus norvegicus
Strain BDIV/lfz null Rattus norvegicus
Strain BDIX/Orl null Rattus norvegicus
Strain BDVII/Cub null Rattus norvegicus
Strain BDX/Cub null Rattus norvegicus
Strain BH/Ztm null Rattus norvegicus
Strain BN/Crl null Rattus norvegicus
Strain BN/Cub null Rattus norvegicus
Strain BN/Gro null Rattus norvegicus
Strain BN/Gut null Rattus norvegicus
Strain BN/Han null Rattus norvegicus
Strain BN/Maas null Rattus norvegicus
Strain BN/Mol null Rattus norvegicus
Strain BN/NHsdCpb null Rattus norvegicus
Strain BN/OlaHsd null Rattus norvegicus
Strain BN/Orl null Rattus norvegicus
Strain BN/RijKun null Rattus norvegicus
Strain BN/RijN null Rattus norvegicus
Strain BN/SsN null Rattus norvegicus
Strain BP/Cub null Rattus norvegicus
Strain BS/Ztm null Rattus norvegicus
Strain BUF/Ztm null Rattus norvegicus
Strain CAP/Kuv null Rattus norvegicus
Strain CHOC/Cub null Rattus norvegicus
Strain COP/OlaHsd null Rattus norvegicus
Strain Crl:SD null Rattus norvegicus
Strain Crl:WI Wistar rats Rattus norvegicus
Strain DA/Ztm null Rattus norvegicus
Strain DZB/Gro null Rattus norvegicus
Strain E3/Ztm null Rattus norvegicus
Strain F344/NCrl null Rattus norvegicus
Strain F344/Ztm null Rattus norvegicus
Strain GC/Kun null Rattus norvegicus
Strain Hooded/Colle null Rattus norvegicus
Strain Hsd:SD Sprague Dawley Rattus norvegicus
Strain LE/Ztm null Rattus norvegicus
Strain LEP/Cub null Rattus norvegicus
Strain LEW/Crl Lewis Rattus norvegicus
Strain LEW/Cub null Rattus norvegicus
Strain LEW/Gut null Rattus norvegicus
Strain LEW/Han null Rattus norvegicus
Strain LEW/Ipcv null Rattus norvegicus
Strain LEW/Kuv null Rattus norvegicus
Strain LEW/Maas null Rattus norvegicus
Strain LEW/Nhg null Rattus norvegicus
Strain LEW/NHsdCpb null Rattus norvegicus
Strain LEW/Orl null Rattus norvegicus
Strain LEW/SsNHsd null Rattus norvegicus
Strain LEW/Ztm LEW/Ztm Rattus norvegicus
Strain LH/Ztu null Rattus norvegicus
Strain LOU/CHan Louvain Rattus norvegicus
Strain MHS/Gib Milan Hypertensive Strain Rattus norvegicus
Strain MNS/Gib Milan Normotensive Strain Rattus norvegicus
Strain MWF/Hsd Munich Wistar Fromter Rattus norvegicus
Strain NAR/SaU non-albumin rat Rattus norvegicus
Strain NEDH/K null Rattus norvegicus
Strain OKA/Wsl null Rattus norvegicus
Strain OM/Ztm Osborne-Mendel Rattus norvegicus
Strain PAR/Wsl null Rattus norvegicus
Strain PVG/OlaHsd null Rattus norvegicus
Strain R/A null Rattus norvegicus
Strain R/AEurRij null Rattus norvegicus
Strain R/AWa null Rattus norvegicus
Strain RHA/Kun Roman high avoidance Rattus norvegicus
Strain RNU/Mol null Rattus norvegicus
Strain SD/A null Rattus norvegicus
Strain SD/Rij null Rattus norvegicus
Strain SDH/Ztu null Rattus norvegicus
Strain SDL/Ipcv null Rattus norvegicus
Strain SHR/Maas null Rattus norvegicus
Strain SHRSP/Rivm null Rattus norvegicus
Strain SPRD/Ztm null Rattus norvegicus
Strain SR/JrIpcv null Rattus norvegicus
Strain SR/JrMol null Rattus norvegicus
Strain SS/JrIpcv null Rattus norvegicus
Strain U/A null Rattus norvegicus
Strain WAG/OlaHsd null Rattus norvegicus
Strain WAG/Rij null Rattus norvegicus
Strain WF/Gut null Rattus norvegicus
Strain WF/Mol null Rattus norvegicus
Strain WF/NHsd null Rattus norvegicus
Strain WF/Ztm null Rattus norvegicus
Strain WIST/Nhg Wistar Rattus norvegicus
Strain WKY/Ztm null Rattus norvegicus
Strain WOKA/K null Rattus norvegicus
Strain WOKW/K null Rattus norvegicus

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