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Efficient single nucleotide polymorphism discovery in laboratory rat strains using wild rat-derived SNP candidates

BACKGROUND: The laboratory rat (Rattus norvegicus) is an important model for studying many aspects of human health and disease. Detailed knowledge on genetic variation between strains is important from a biomedical, particularly pharmacogenetic point of view and useful for marker selection for genet...

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Autores principales: Smits, Bart MG, Guryev, Victor, Zeegers, Dimphy, Wedekind, Dirk, Hedrich, Hans J, Cuppen, Edwin
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2005
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1318490/
https://www.ncbi.nlm.nih.gov/pubmed/16316463
http://dx.doi.org/10.1186/1471-2164-6-170
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author Smits, Bart MG
Guryev, Victor
Zeegers, Dimphy
Wedekind, Dirk
Hedrich, Hans J
Cuppen, Edwin
author_facet Smits, Bart MG
Guryev, Victor
Zeegers, Dimphy
Wedekind, Dirk
Hedrich, Hans J
Cuppen, Edwin
author_sort Smits, Bart MG
collection PubMed
description BACKGROUND: The laboratory rat (Rattus norvegicus) is an important model for studying many aspects of human health and disease. Detailed knowledge on genetic variation between strains is important from a biomedical, particularly pharmacogenetic point of view and useful for marker selection for genetic cloning and association studies. RESULTS: We show that Single Nucleotide Polymorphisms (SNPs) in commonly used rat strains are surprisingly well represented in wild rat isolates. Shotgun sequencing of 814 Kbp in one wild rat resulted in the identification of 485 SNPs as compared with the Brown Norway genome sequence. Genotyping 36 commonly used inbred rat strains showed that 84% of these alleles are also polymorphic in a representative set of laboratory rat strains. CONCLUSION: We postulate that shotgun sequencing in a wild rat sample and subsequent genotyping in multiple laboratory or domesticated strains rather than direct shotgun sequencing of multiple strains, could be the most efficient SNP discovery approach. For the rat, laboratory strains still harbor a large portion of the haplotypes present in wild isolates, suggesting a relatively recent common origin and supporting the idea that rat inbred strains, in contrast to mouse inbred strains, originate from a single species, R. norvegicus.
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spelling pubmed-13184902005-12-22 Efficient single nucleotide polymorphism discovery in laboratory rat strains using wild rat-derived SNP candidates Smits, Bart MG Guryev, Victor Zeegers, Dimphy Wedekind, Dirk Hedrich, Hans J Cuppen, Edwin BMC Genomics Research Article BACKGROUND: The laboratory rat (Rattus norvegicus) is an important model for studying many aspects of human health and disease. Detailed knowledge on genetic variation between strains is important from a biomedical, particularly pharmacogenetic point of view and useful for marker selection for genetic cloning and association studies. RESULTS: We show that Single Nucleotide Polymorphisms (SNPs) in commonly used rat strains are surprisingly well represented in wild rat isolates. Shotgun sequencing of 814 Kbp in one wild rat resulted in the identification of 485 SNPs as compared with the Brown Norway genome sequence. Genotyping 36 commonly used inbred rat strains showed that 84% of these alleles are also polymorphic in a representative set of laboratory rat strains. CONCLUSION: We postulate that shotgun sequencing in a wild rat sample and subsequent genotyping in multiple laboratory or domesticated strains rather than direct shotgun sequencing of multiple strains, could be the most efficient SNP discovery approach. For the rat, laboratory strains still harbor a large portion of the haplotypes present in wild isolates, suggesting a relatively recent common origin and supporting the idea that rat inbred strains, in contrast to mouse inbred strains, originate from a single species, R. norvegicus. BioMed Central 2005-11-29 /pmc/articles/PMC1318490/ /pubmed/16316463 http://dx.doi.org/10.1186/1471-2164-6-170 Text en Copyright © 2005 Smits et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Smits, Bart MG
Guryev, Victor
Zeegers, Dimphy
Wedekind, Dirk
Hedrich, Hans J
Cuppen, Edwin
Efficient single nucleotide polymorphism discovery in laboratory rat strains using wild rat-derived SNP candidates
title Efficient single nucleotide polymorphism discovery in laboratory rat strains using wild rat-derived SNP candidates
title_full Efficient single nucleotide polymorphism discovery in laboratory rat strains using wild rat-derived SNP candidates
title_fullStr Efficient single nucleotide polymorphism discovery in laboratory rat strains using wild rat-derived SNP candidates
title_full_unstemmed Efficient single nucleotide polymorphism discovery in laboratory rat strains using wild rat-derived SNP candidates
title_short Efficient single nucleotide polymorphism discovery in laboratory rat strains using wild rat-derived SNP candidates
title_sort efficient single nucleotide polymorphism discovery in laboratory rat strains using wild rat-derived snp candidates
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1318490/
https://www.ncbi.nlm.nih.gov/pubmed/16316463
http://dx.doi.org/10.1186/1471-2164-6-170
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