SNP and haplotype mapping for genetic analysis in the rat

被引：139

作者：

Saar, Kathrin ^{[1
]}

Beck, Alfred ^{[2
]}

Bihoreau, Marie-Therese ^{[3
]}

Birney, Ewan ^{[4
]}

Brocklebank, Denise ^{[3
]}

Chen, Yuan ^{[4
]}

Cuppen, Edwin ^{[5
]}

Demonchy, Stephanie ^{[6
]}

Dopazo, Joaquin ^{[7
]}

Flicek, Paul ^{[4
]}

Foglio, Mario ^{[6
]}

Fujiyama, Asao ^{[8
,9
]}

Gut, Ivo G. ^{[6
]}

Gauguier, Dominique ^{[3
]}

Guigo, Roderic ^{[10
,11
]}

Guryev, Victor ^{[5
]}

Heinig, Matthias ^{[1
]}

Hummel, Oliver ^{[1
]}

Jahn, Niels ^{[12
]}

Klages, Sven ^{[2
]}

Kren, Vladimir ^{[13
,14
]}

Kube, Michael ^{[2
]}

Kuhl, Heiner ^{[2
]}

Kuramoto, Takashi ^{[15
]}

Kuroki, Yoko ^{[8
]}

Lechner, Doris ^{[6
]}

Lee, Young-Ae ^{[1
,16
]}

Lopez-Bigas, Nuria ^{[10
,11
]}

Lathrop, G. Mark ^{[6
]}

Mashimo, Tomoji ^{[15
]}

Medina, Ignacio ^{[7
]}

Mott, Richard ^{[2
,3
]}

Patone, Giannino ^{[1
]}

Perrier-Cornet, Jeanne-Antide ^{[6
]}

Platzer, Matthias ^{[12
]}

Pravenec, Michal ^{[13
,14
]}

Reinhardt, Richard

Sakaki, Yoshiyuki ^{[8
]}

Schilhabel, Markus ^{[12
]}

Schulz, Herbert ^{[1
]}

Serikawa, Tadao ^{[15
]}

Shikhagaie, Medya ^{[11
]}

Tatsumoto, Shouji ^{[8
]}

Taudien, Stefan ^{[12
]}

Toyoda, Atsushi ^{[8
]}

Voigt, Birger ^{[15
]}

Zelenika, Diana ^{[6
]}

Zimdahl, Heike ^{[1
]}

Hubner, Norbert ^{[1
]}

机构：

[1] Max Delbruck Ctr Mol Med, D-14195 Berlin, Germany

[2] Max Planck Inst Mol Genet, D-14195 Berlin, Germany

[3] Univ Oxford, Wellcome Trust Ctr Human Genet, Oxford OX3 7BN, England

[4] European Bioinformat Inst, Cambridge CB10 1SD, England

[5] Hubrecht Inst, NL-3584 CT Utrecht, Netherlands

[6] Ctr Natl Genotypage, Inst Genom, Commissariat Energie Atom, F-91057 Evry, France

[7] Ctr Invest Principe Felipe, Dept Bioinformat & Funct Genom Node, Valencia 46012, Spain

[8] RIKEN, Genom Sci Ctr, Tsurumi Ku, Kanagawa 2300045, Japan

[9] Res Org Informat & Syst, Natl Inst Informat, Chiyoda Ku, Tokyo 1018430, Japan

[10] Ctr Genom Regulat, Barcelona 08003, Catalonia, Spain

[11] Univ Pompeu Fabra, Expt & Hlth Sci Dept, Barcelona 08003, Catalonia, Spain

[12] Fritz Lipmann Inst, Leibniz Inst Age Res, D-07745 Jena, Germany

[13] Charles Univ Prague, Fac Med 1, Inst Biol & Med Genet, Prague 12800 2, Czech Republic

[14] Acad Sci Czech Republ, Inst Physiol, CR-14220 Prague 4, Czech Republic

[15] Kyoto Univ, Grad Sch Med, Inst Lab Anim, Sakyo Ku, Kyoto 6068501, Japan

[16] Charite, Pediat Pneumol & Immunol, D-13353 Berlin, Germany

来源：

NATURE GENETICS | 2008年 / 40卷 / 05期

基金：

英国惠康基金;

关键词：

D O I：

10.1038/ng.124

中图分类号：

Q3 [遗传学];

学科分类号：

071007 [遗传学]; 090102 [作物遗传育种];

摘要：

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 F-2 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.

引用

页码：560 / 566

页数：7

共 41 条

[1]

[Anonymous], BIOTECHNIQUES S

[2]

Selective pressures at a codon-level predict deleterious mutations in human disease genes [J].

Arbiza, Leonardo ;

Duchi, Serena ;

Montaner, David ;

Burguet, Jordi ;

Pantoja-Uceda, David ;

Pineda-Lucena, Antonio ;

Dopazo, Joaquin ;

Dopazo, Hernan .

JOURNAL OF MOLECULAR BIOLOGY, 2006, 358 (05) :1390-1404

[3]

Haploview: analysis and visualization of LD and haplotype maps [J].

Barrett, JC ;

Fry, B ;

Maller, J ;

Daly, MJ .

BIOINFORMATICS, 2005, 21 (02) :263-265

[4]

A linkage map of the rat genome derived from three F-2 crosses [J].

Bihoreau, MT ;

Gauguier, D ;

Kato, N ;

Hyne, G ;

Lindpaintner, K ;

Rapp, JP ;

James, MR ;

Lathrop, GM .

GENOME RESEARCH, 1997, 7 (05) :434-440

[5]

Transcription factor map alignment of promoter regions [J].

Blanco, Enrique ;

Messeguer, Xavier ;

Smith, Temple F. ;

Guigo, Roderic .

PLOS COMPUTATIONAL BIOLOGY, 2006, 2 (05) :403-416

[6]

The genomes of recombinant inbred lines [J].

Broman, KW .

GENETICS, 2005, 169 (02) :1133-1146

[7]

Direct quantitative trait locus mapping of mammalian metabolic phenotypes in diabetic and normoglycemic rat models [J].

Dumas, Marc-Emmanuel ;

Wilder, Steven P. ;

Bihoreau, Marie-Therese ;

Barton, Richard H. ;

Fearnside, Jane F. ;

Argoud, Karene ;

D'Amato, Lisa ;

Wallis, Robert H. ;

Blancher, Christine ;

Keun, Hector C. ;

Baunsgaard, Dorrit ;

Scott, James ;

Sidelmann, Ulla Grove ;

Nicholson, Jeremy K. ;

Gauguier, Dominique .

NATURE GENETICS, 2007, 39 (05) :666-672

[8]

A sequence-based variation map of 8.27 million SNPs in inbred mouse strains [J].

Frazer, Kelly A. ;

Eskin, Eleazar ;

Kang, Hyun Min ;

Bogue, Molly A. ;

Hinds, David A. ;

Beilharz, Erica J. ;

Gupta, Robert V. ;

Montgomery, Julie ;

Morenzoni, Matt M. ;

Nilsen, Geoffrey B. ;

Pethiyagoda, Charit L. ;

Stuve, Laura L. ;

Johnson, Frank M. ;

Daly, Mark J. ;

Wade, Claire M. ;

Cox, David R. .

NATURE, 2007, 448 (7157) :1050-U8

[9]

Construction and analysis of a human-chimpanzee comparative clone map [J].

Fujiyama, A ;

Watanabe, H ;

Toyoda, A ;

Taylor, TD ;

Itoh, T ;

Tsai, SF ;

Park, HS ;

Yaspo, ML ;

Lehrach, H ;

Chen, Z ;

Fu, G ;

Saitou, N ;

Osoegawa, K ;

de Jong, PJ ;

Suto, Y ;

Hattori, M ;

Sakaki, Y .

SCIENCE, 2002, 295 (5552) :131-134

[10]

The structure of haplotype blocks in the human genome [J].

Gabriel, SB ;

Schaffner, SF ;

Nguyen, H ;

Moore, JM ;

Roy, J ;

Blumenstiel, B ;

Higgins, J ;

DeFelice, M ;

Lochner, A ;

Faggart, M ;

Liu-Cordero, SN ;

Rotimi, C ;

Adeyemo, A ;

Cooper, R ;

Ward, R ;

Lander, ES ;

Daly, MJ ;

Altshuler, D .

SCIENCE, 2002, 296 (5576) :2225-2229

← 1 2 3 4 5 →