SNP and haplotype mapping for genetic analysis in the rat.

K. Saar; A. Beck; M. Bihoreau; E. Birney; D. Brocklebank; Y. Chen; E. Cuppen; S. Demonchy; J. Dopazo; P. Flicek; M. Foglio; A. Fujiyama; I.G. Gut; D. Gauguier; R. Guigo; V. Guryev; M. Heinig; O. Hummel; N. Jahn; S. Klages; V. Kren; M. Kube; H. Kuhl; T. Kuramoto; Y. Kuroki; D. Lechner; Y.A. Lee; N. Lopez-Bigas; G.M. Lathrop; T. Mashimo; I. Medina; R. Mott; G. Patone; J.A. Perrier-Cornet; M. Platzer; M. Pravenec; R. Reinhardt; Y. Sakaki; M. Schilhabel; H. Schulz; T. Serikawa; M. Shikhagaie; S. Tatsumoto; S. Taudien; A. Toyoda; B. Voigt; D. Zelenika; H. Zimdahl; N. Hubner

doi:10.1038/ng.124

SNP and haplotype mapping for genetic analysis in the rat.

K. Saar, A. Beck, M. Bihoreau, E. Birney, D. Brocklebank, Y. Chen, E. Cuppen, S. Demonchy, J. Dopazo, P. Flicek, M. Foglio, A. Fujiyama, I.G. Gut, D. Gauguier, R. Guigo, V. Guryev, M. Heinig, O. Hummel, N. Jahn, S. KlagesV. Kren, M. Kube, H. Kuhl, T. Kuramoto, Y. Kuroki, D. Lechner, Y.A. Lee, N. Lopez-Bigas, G.M. Lathrop, T. Mashimo, I. Medina, R. Mott, G. Patone, J.A. Perrier-Cornet, M. Platzer, M. Pravenec, R. Reinhardt, Y. Sakaki, M. Schilhabel, H. Schulz, T. Serikawa, M. Shikhagaie, S. Tatsumoto, S. Taudien, A. Toyoda, B. Voigt, D. Zelenika, H. Zimdahl, N. Hubner

Hubrecht Institute

Research output: Contribution to journal/periodical › Article › Scientific › peer-review

145 Citations (Scopus)

Abstract

The laboratory rat is one of the most extensively studied model organisms. Inbred laboratory rat strains originated from limited Rattus norvegicus founder populations, and the inherited genetic variation provides an excellent resource for the correlation of genotype to phenotype. Here, we report a survey of genetic variation based on almost 3 million newly identified SNPs. We obtained accurate and complete genotypes for a subset of 20,238 SNPs across 167 distinct inbred rat strains, two rat recombinant inbred panels and an F2 intercross. Using 81% of these SNPs, we constructed high-density genetic maps, creating a large dataset of fully characterized SNPs for disease gene mapping. Our data characterize the population structure and illustrate the degree of linkage disequilibrium. We provide a detailed SNP map and demonstrate its utility for mapping of quantitative trait loci. This community resource is openly available and augments the genetic tools for this workhorse of physiological studies.

Original language	English
Pages (from-to)	560-566
Journal	Nature Genetics
Volume	40
Issue number	5
DOIs	https://doi.org/10.1038/ng.124
Publication status	Published - 2008

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Saar, K., Beck, A., Bihoreau, M., Birney, E., Brocklebank, D., Chen, Y., Cuppen, E., Demonchy, S., Dopazo, J., Flicek, P., Foglio, M., Fujiyama, A., Gut, I. G., Gauguier, D., Guigo, R., Guryev, V., Heinig, M., Hummel, O., Jahn, N., ... Hubner, N. (2008). SNP and haplotype mapping for genetic analysis in the rat. Nature Genetics, 40(5), 560-566. https://doi.org/10.1038/ng.124

@article{74720709267c4ea2a9010ac3e7447fff,

title = "SNP and haplotype mapping for genetic analysis in the rat.",

abstract = "The laboratory rat is one of the most extensively studied model organisms. Inbred laboratory rat strains originated from limited Rattus norvegicus founder populations, and the inherited genetic variation provides an excellent resource for the correlation of genotype to phenotype. Here, we report a survey of genetic variation based on almost 3 million newly identified SNPs. We obtained accurate and complete genotypes for a subset of 20,238 SNPs across 167 distinct inbred rat strains, two rat recombinant inbred panels and an F2 intercross. Using 81% of these SNPs, we constructed high-density genetic maps, creating a large dataset of fully characterized SNPs for disease gene mapping. Our data characterize the population structure and illustrate the degree of linkage disequilibrium. We provide a detailed SNP map and demonstrate its utility for mapping of quantitative trait loci. This community resource is openly available and augments the genetic tools for this workhorse of physiological studies.",

author = "K. Saar and A. Beck and M. Bihoreau and E. Birney and D. Brocklebank and Y. Chen and E. Cuppen and S. Demonchy and J. Dopazo and P. Flicek and M. Foglio and A. Fujiyama and I.G. Gut and D. Gauguier and R. Guigo and V. Guryev and M. Heinig and O. Hummel and N. Jahn and S. Klages and V. Kren and M. Kube and H. Kuhl and T. Kuramoto and Y. Kuroki and D. Lechner and Y.A. Lee and N. Lopez-Bigas and G.M. Lathrop and T. Mashimo and I. Medina and R. Mott and G. Patone and J.A. Perrier-Cornet and M. Platzer and M. Pravenec and R. Reinhardt and Y. Sakaki and M. Schilhabel and H. Schulz and T. Serikawa and M. Shikhagaie and S. Tatsumoto and S. Taudien and A. Toyoda and B. Voigt and D. Zelenika and H. Zimdahl and N. Hubner",

note = "Reporting year: 2008",

year = "2008",

doi = "10.1038/ng.124",

language = "English",

volume = "40",

pages = "560--566",

journal = "Nature Genetics",

issn = "1061-4036",

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Saar, K, Beck, A, Bihoreau, M, Birney, E, Brocklebank, D, Chen, Y, Cuppen, E, Demonchy, S, Dopazo, J, Flicek, P, Foglio, M, Fujiyama, A, Gut, IG, Gauguier, D, Guigo, R, Guryev, V, Heinig, M, Hummel, O, Jahn, N, Klages, S, Kren, V, Kube, M, Kuhl, H, Kuramoto, T, Kuroki, Y, Lechner, D, Lee, YA, Lopez-Bigas, N, Lathrop, GM, Mashimo, T, Medina, I, Mott, R, Patone, G, Perrier-Cornet, JA, Platzer, M, Pravenec, M, Reinhardt, R, Sakaki, Y, Schilhabel, M, Schulz, H, Serikawa, T, Shikhagaie, M, Tatsumoto, S, Taudien, S, Toyoda, A, Voigt, B, Zelenika, D, Zimdahl, H & Hubner, N 2008, 'SNP and haplotype mapping for genetic analysis in the rat.', Nature Genetics, vol. 40, no. 5, pp. 560-566. https://doi.org/10.1038/ng.124

TY - JOUR

T1 - SNP and haplotype mapping for genetic analysis in the rat.

AU - Saar, K.

AU - Beck, A.

AU - Bihoreau, M.

AU - Birney, E.

AU - Brocklebank, D.

AU - Chen, Y.

AU - Cuppen, E.

AU - Demonchy, S.

AU - Dopazo, J.

AU - Flicek, P.

AU - Foglio, M.

AU - Fujiyama, A.

AU - Gut, I.G.

AU - Gauguier, D.

AU - Guigo, R.

AU - Guryev, V.

AU - Heinig, M.

AU - Hummel, O.

AU - Jahn, N.

AU - Klages, S.

AU - Kren, V.

AU - Kube, M.

AU - Kuhl, H.

AU - Kuramoto, T.

AU - Kuroki, Y.

AU - Lechner, D.

AU - Lee, Y.A.

AU - Lopez-Bigas, N.

AU - Lathrop, G.M.

AU - Mashimo, T.

AU - Medina, I.

AU - Mott, R.

AU - Patone, G.

AU - Perrier-Cornet, J.A.

AU - Platzer, M.

AU - Pravenec, M.

AU - Reinhardt, R.

AU - Sakaki, Y.

AU - Schilhabel, M.

AU - Schulz, H.

AU - Serikawa, T.

AU - Shikhagaie, M.

AU - Tatsumoto, S.

AU - Taudien, S.

AU - Toyoda, A.

AU - Voigt, B.

AU - Zelenika, D.

AU - Zimdahl, H.

AU - Hubner, N.

N1 - Reporting year: 2008

PY - 2008

Y1 - 2008

N2 - The laboratory rat is one of the most extensively studied model organisms. Inbred laboratory rat strains originated from limited Rattus norvegicus founder populations, and the inherited genetic variation provides an excellent resource for the correlation of genotype to phenotype. Here, we report a survey of genetic variation based on almost 3 million newly identified SNPs. We obtained accurate and complete genotypes for a subset of 20,238 SNPs across 167 distinct inbred rat strains, two rat recombinant inbred panels and an F2 intercross. Using 81% of these SNPs, we constructed high-density genetic maps, creating a large dataset of fully characterized SNPs for disease gene mapping. Our data characterize the population structure and illustrate the degree of linkage disequilibrium. We provide a detailed SNP map and demonstrate its utility for mapping of quantitative trait loci. This community resource is openly available and augments the genetic tools for this workhorse of physiological studies.

AB - The laboratory rat is one of the most extensively studied model organisms. Inbred laboratory rat strains originated from limited Rattus norvegicus founder populations, and the inherited genetic variation provides an excellent resource for the correlation of genotype to phenotype. Here, we report a survey of genetic variation based on almost 3 million newly identified SNPs. We obtained accurate and complete genotypes for a subset of 20,238 SNPs across 167 distinct inbred rat strains, two rat recombinant inbred panels and an F2 intercross. Using 81% of these SNPs, we constructed high-density genetic maps, creating a large dataset of fully characterized SNPs for disease gene mapping. Our data characterize the population structure and illustrate the degree of linkage disequilibrium. We provide a detailed SNP map and demonstrate its utility for mapping of quantitative trait loci. This community resource is openly available and augments the genetic tools for this workhorse of physiological studies.

U2 - 10.1038/ng.124

DO - 10.1038/ng.124

M3 - Article

SN - 1061-4036

VL - 40

SP - 560

EP - 566

JO - Nature Genetics

JF - Nature Genetics

IS - 5

ER -

SNP and haplotype mapping for genetic analysis in the rat.

Abstract

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