Literature DB >> 15060020

Integration of the rat recombination and EST maps in the rat genomic sequence and comparative mapping analysis with the mouse genome.

Steven P Wilder1, Marie-Thérèse Bihoreau, Karène Argoud, Takeshi K Watanabe, Mark Lathrop, Dominique Gauguier.   

Abstract

Inbred strains of the laboratory rat are widely used for identifying genetic regions involved in the control of complex quantitative phenotypes of biomedical importance. The draft genomic sequence of the rat now provides essential information for annotating rat quantitative trait locus (QTL) maps. Following the survey of unique rat microsatellite (11,585 including 1648 new markers) and EST (10,067) markers currently available, we have incorporated a selection of 7952 rat EST sequences in an improved version of the integrated linkage-radiation hybrid map of the rat containing 2058 microsatellite markers which provided over 10,000 potential anchor points between rat QTL and the genomic sequence of the rat. A total of 996 genetic positions were resolved (avg. spacing 1.77 cM) in a single large intercross and anchored in the rat genomic sequence (avg. spacing 1.62 Mb). Comparative genome maps between rat and mouse were constructed by successful computational alignment of 6108 mapped rat ESTs in the mouse genome. The integration of rat linkage maps in the draft genomic sequence of the rat and that of other species represents an essential step for translating rat QTL intervals into human chromosomal targets.

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Year:  2004        PMID： 15060020      PMCID： PMC383323          DOI： 10.1101/gr.2001604

Source DB:  PubMed          Journal:  Genome Res        ISSN： 1088-9051            Impact factor:   9.043


  30 in total

1.  Detailed comparative gene map of rat chromosome 1 with mouse and human genomes and physical mapping of an evolutionary chromosomal breakpoint.

Authors:  P J Kaisaki; M Rouard; P A Danoy; R H Wallis; S C Collins; M Rice; E R Levy; M Lathrop; M T Bihoreau; D Gauguier
Journal:  Genomics       Date:  2000-02-15       Impact factor: 5.736

2.  Initial sequencing and analysis of the human genome.

Authors:  E S Lander; L M Linton; B Birren; C Nusbaum; M C Zody; J Baldwin; K Devon; K Dewar; M Doyle; W FitzHugh; R Funke; D Gage; K Harris; A Heaford; J Howland; L Kann; J Lehoczky; R LeVine; P McEwan; K McKernan; J Meldrim; J P Mesirov; C Miranda; W Morris; J Naylor; C Raymond; M Rosetti; R Santos; A Sheridan; C Sougnez; Y Stange-Thomann; N Stojanovic; A Subramanian; D Wyman; J Rogers; J Sulston; R Ainscough; S Beck; D Bentley; J Burton; C Clee; N Carter; A Coulson; R Deadman; P Deloukas; A Dunham; I Dunham; R Durbin; L French; D Grafham; S Gregory; T Hubbard; S Humphray; A Hunt; M Jones; C Lloyd; A McMurray; L Matthews; S Mercer; S Milne; J C Mullikin; A Mungall; R Plumb; M Ross; R Shownkeen; S Sims; R H Waterston; R K Wilson; L W Hillier; J D McPherson; M A Marra; E R Mardis; L A Fulton; A T Chinwalla; K H Pepin; W R Gish; S L Chissoe; M C Wendl; K D Delehaunty; T L Miner; A Delehaunty; J B Kramer; L L Cook; R S Fulton; D L Johnson; P J Minx; S W Clifton; T Hawkins; E Branscomb; P Predki; P Richardson; S Wenning; T Slezak; N Doggett; J F Cheng; A Olsen; S Lucas; C Elkin; E Uberbacher; M Frazier; R A Gibbs; D M Muzny; S E Scherer; J B Bouck; E J Sodergren; K C Worley; C M Rives; J H Gorrell; M L Metzker; S L Naylor; R S Kucherlapati; D L Nelson; G M Weinstock; Y Sakaki; A Fujiyama; M Hattori; T Yada; A Toyoda; T Itoh; C Kawagoe; H Watanabe; Y Totoki; T Taylor; J Weissenbach; R Heilig; W Saurin; F Artiguenave; P Brottier; T Bruls; E Pelletier; C Robert; P Wincker; D R Smith; L Doucette-Stamm; M Rubenfield; K Weinstock; H M Lee; J Dubois; A Rosenthal; M Platzer; G Nyakatura; S Taudien; A Rump; H Yang; J Yu; J Wang; G Huang; J Gu; L Hood; L Rowen; A Madan; S Qin; R W Davis; N A Federspiel; A P Abola; M J Proctor; R M Myers; J Schmutz; M Dickson; J Grimwood; D R Cox; M V Olson; R Kaul; C Raymond; N Shimizu; K Kawasaki; S Minoshima; G A Evans; M Athanasiou; R Schultz; B A Roe; F Chen; H Pan; J Ramser; H Lehrach; R Reinhardt; W R McCombie; M de la Bastide; N Dedhia; H Blöcker; K Hornischer; G Nordsiek; R Agarwala; L Aravind; J A Bailey; A Bateman; S Batzoglou; E Birney; P Bork; D G Brown; C B Burge; L Cerutti; H C Chen; D Church; M Clamp; R R Copley; T Doerks; S R Eddy; E E Eichler; T S Furey; J Galagan; J G Gilbert; C Harmon; Y Hayashizaki; D Haussler; H Hermjakob; K Hokamp; W Jang; L S Johnson; T A Jones; S Kasif; A Kaspryzk; S Kennedy; W J Kent; P Kitts; E V Koonin; I Korf; D Kulp; D Lancet; T M Lowe; A McLysaght; T Mikkelsen; J V Moran; N Mulder; V J Pollara; C P Ponting; G Schuler; J Schultz; G Slater; A F Smit; E Stupka; J Szustakowki; D Thierry-Mieg; J Thierry-Mieg; L Wagner; J Wallis; R Wheeler; A Williams; Y I Wolf; K H Wolfe; S P Yang; R F Yeh; F Collins; M S Guyer; J Peterson; A Felsenfeld; K A Wetterstrand; A Patrinos; M J Morgan; P de Jong; J J Catanese; K Osoegawa; H Shizuya; S Choi; Y J Chen; J Szustakowki
Journal:  Nature       Date:  2001-02-15       Impact factor: 49.962

3.  A genomic-systems biology map for cardiovascular function.

Authors:  M Stoll; A W Cowley; P J Tonellato; A S Greene; M L Kaldunski; R J Roman; P Dumas; N J Schork; Z Wang; H J Jacob
Journal:  Science       Date:  2001-11-23       Impact factor: 47.728

4.  Between rat and mouse zoo-FISH reveals 49 chromosomal segments that have been conserved in evolution.

Authors:  K Helou; A Walentinsson; G Levan; F Ståhl
Journal:  Mamm Genome       Date:  2001-10       Impact factor: 2.957

5.  Generation of a high-density rat EST map.

Authors:  T E Scheetz; M R Raymond; D Y Nishimura; A McClain; C Roberts; C Birkett; J Gardiner; J Zhang; N Butters; C Sun; A Kwitek-Black; H Jacob; T L Casavant; M B Soares; V C Sheffield
Journal:  Genome Res       Date:  2001-03       Impact factor: 9.043

6.  New target regions for human hypertension via comparative genomics.

Authors:  M Stoll; A E Kwitek-Black; A W Cowley; E L Harris; S B Harrap; J E Krieger; M P Printz; A P Provoost; J Sassard; H J Jacob
Journal:  Genome Res       Date:  2000-04       Impact factor: 9.043

7.  A high-resolution consensus linkage map of the rat, integrating radiation hybrid and genetic maps.

Authors:  M T Bihoreau; L Sebag-Montefiore; R F Godfrey; R H Wallis; J H Brown; P A Danoy; S C Collins; M Rouard; P J Kaisaki; M Lathrop; D Gauguier
Journal:  Genomics       Date:  2001-07       Impact factor: 5.736

8.  Automated construction of high-density comparative maps between rat, human, and mouse.

Authors:  A E Kwitek; P J Tonellato; D Chen; J Gullings-Handley; Y S Cheng; S Twigger; T E Scheetz; T L Casavant; M Stoll; M A Nobrega; M Shiozawa; M B Soares; V C Sheffield; H J Jacob
Journal:  Genome Res       Date:  2001-11       Impact factor: 9.043

9.  Insulin-degrading enzyme identified as a candidate diabetes susceptibility gene in GK rats.

Authors:  H Fakhrai-Rad; A Nikoshkov; A Kamel; M Fernström; J R Zierath; S Norgren; H Luthman; J Galli
Journal:  Hum Mol Genet       Date:  2000-09-01       Impact factor: 6.150

10.  A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat.

Authors:  R G Steen; A E Kwitek-Black; C Glenn; J Gullings-Handley; W Van Etten; O S Atkinson; D Appel; S Twigger; M Muir; T Mull; M Granados; M Kissebah; K Russo; R Crane; M Popp; M Peden; T Matise; D M Brown; J Lu; S Kingsmore; P J Tonellato; S Rozen; D Slonim; P Young; H J Jacob
Journal:  Genome Res       Date:  1999-06       Impact factor: 9.043
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  10 in total

1.  Mapping diabetes QTL in an intercross derived from a congenic strain of the Brown Norway and Goto-Kakizaki rats.

Authors:  Stephan C Collins; Robert H Wallis; Steven P Wilder; Karin J Wallace; Karène Argoud; Pamela J Kaisaki; Marie-Thérèse Bihoreau; Dominique Gauguier
Journal:  Mamm Genome       Date:  2006-06-12       Impact factor: 2.957

2.  Genetic control of plasma lipid levels in a cross derived from normoglycaemic Brown Norway and spontaneously diabetic Goto-Kakizaki rats.

Authors:  K Argoud; S P Wilder; M A McAteer; M T Bihoreau; F Ouali; P Y Woon; R H Wallis; A Ktorza; D Gauguier
Journal:  Diabetologia       Date:  2006-09-16       Impact factor: 10.122

3.  Chromosomal mapping of pancreatic islet morphological features and regulatory hormones in the spontaneously diabetic (Type 2) Goto-Kakizaki rat.

Authors:  Clare Finlay; Karène Argoud; Steven P Wilder; Fetta Ouali; Alain Ktorza; Pamela J Kaisaki; Dominique Gauguier
Journal:  Mamm Genome       Date:  2010-09-29       Impact factor: 2.957

4.  Linkage mapping bovine EST-based SNP.

Authors:  Warren M Snelling; Eduardo Casas; Roger T Stone; John W Keele; Gregory P Harhay; Gary L Bennett; Timothy P L Smith
Journal:  BMC Genomics       Date:  2005-05-19       Impact factor: 3.969

5.  Mutation patterns of amino acid tandem repeats in the human proteome.

Authors:  Loris Mularoni; Roderic Guigó; M Mar Albà
Journal:  Genome Biol       Date:  2006-04-26       Impact factor: 13.583

6.  Transcriptome Profiling in Rat Inbred Strains and Experimental Cross Reveals Discrepant Genetic Architecture of Genome-Wide Gene Expression.

Authors:  Pamela J Kaisaki; Georg W Otto; Karène Argoud; Stephan C Collins; Robert H Wallis; Steven P Wilder; Anthony C Y Yau; Christophe Hue; Sophie Calderari; Marie-Thérèse Bihoreau; Jean-Baptiste Cazier; Richard Mott; Dominique Gauguier
Journal:  G3 (Bethesda)       Date:  2016-11-08       Impact factor: 3.154

7.  Conserved properties of genetic architecture of renal and fat transcriptomes in rat models of insulin resistance.

Authors:  Georg W Otto; Pamela J Kaisaki; Francois Brial; Aurélie Le Lay; Jean-Baptiste Cazier; Richard Mott; Dominique Gauguier
Journal:  Dis Model Mech       Date:  2019-07-15       Impact factor: 5.758

8.  Functional annotations of diabetes nephropathy susceptibility loci through analysis of genome-wide renal gene expression in rat models of diabetes mellitus.

Authors:  Yaomin Hu; Pamela J Kaisaki; Karène Argoud; Steven P Wilder; Karin J Wallace; Peng Y Woon; Christine Blancher; Lise Tarnow; Per-Henrik Groop; Samy Hadjadj; Michel Marre; Hans-Henrik Parving; Martin Farrall; Roger D Cox; Mark Lathrop; Nathalie Vionnet; Marie-Thérèse Bihoreau; Dominique Gauguier
Journal:  BMC Med Genomics       Date:  2009-07-09       Impact factor: 3.063

9.  A set of highly informative rat simple sequence length polymorphism (SSLP) markers and genetically defined rat strains.

Authors:  Tomoji Mashimo; Birger Voigt; Toshiko Tsurumi; Kuniko Naoi; Satoshi Nakanishi; Ken-ichi Yamasaki; Takashi Kuramoto; Tadao Serikawa
Journal:  BMC Genet       Date:  2006-04-04       Impact factor: 2.797

10.  Integrating linkage and radiation hybrid mapping data for bovine chromosome 15.

Authors:  Warren M Snelling; Mathieu Gautier; John W Keele; Timothy P L Smith; Roger T Stone; Gregory P Harhay; Gary L Bennett; Naoya Ihara; Akiko Takasuga; Haruko Takeda; Yoshikazu Sugimoto; André Eggen
Journal:  BMC Genomics       Date:  2004-10-08       Impact factor: 3.969
  10 in total

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