Literature DB >> 23708188

Combined sequence-based and genetic mapping analysis of complex traits in outbred rats.

Amelie Baud, Roel Hermsen, Victor Guryev, Pernilla Stridh, Delyth Graham, Martin W McBride, Tatiana Foroud, Sophie Calderari, Margarita Diez, Johan Ockinger, Amennai D Beyeen, Alan Gillett, Nada Abdelmagid, Andre Ortlieb Guerreiro-Cacais, Maja Jagodic, Jonatan Tuncel, Ulrika Norin, Elisabeth Beattie, Ngan Huynh, William H Miller, Daniel L Koller, Imranul Alam, Samreen Falak, Mary Osborne-Pellegrin, Esther Martinez-Membrives, Toni Canete, Gloria Blazquez, Elia Vicens-Costa, Carme Mont-Cardona, Sira Diaz-Moran, Adolf Tobena, Oliver Hummel, Diana Zelenika, Kathrin Saar, Giannino Patone, Anja Bauerfeind, Marie-Therese Bihoreau, Matthias Heinig, Young-Ae Lee, Carola Rintisch, Herbert Schulz, David A Wheeler, Kim C Worley, Donna M Muzny, Richard A Gibbs, Mark Lathrop, Nico Lansu, Pim Toonen, Frans Paul Ruzius, Ewart de Bruijn, Heidi Hauser, David J Adams, Thomas Keane, Santosh S Atanur, Tim J Aitman, Paul Flicek, Tomas Malinauskas, E Yvonne Jones, Diana Ekman, Regina Lopez-Aumatell, Anna F Dominiczak, Martina Johannesson, Rikard Holmdahl, Tomas Olsson, Dominique Gauguier, Norbert Hubner, Alberto Fernandez-Teruel, Edwin Cuppen, Richard Mott, Jonathan Flint.   

Abstract

Genetic mapping on fully sequenced individuals is transforming understanding of the relationship between molecular variation and variation in complex traits. Here we report a combined sequence and genetic mapping analysis in outbred rats that maps 355 quantitative trait loci for 122 phenotypes. We identify 35 causal genes involved in 31 phenotypes, implicating new genes in models of anxiety, heart disease and multiple sclerosis. The relationship between sequence and genetic variation is unexpectedly complex: at approximately 40% of quantitative trait loci, a single sequence variant cannot account for the phenotypic effect. Using comparable sequence and mapping data from mice, we show that the extent and spatial pattern of variation in inbred rats differ substantially from those of inbred mice and that the genetic variants in orthologous genes rarely contribute to the same phenotype in both species.

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Year:  2013        PMID: 23708188      PMCID: PMC3821058          DOI: 10.1038/ng.2644

Source DB:  PubMed          Journal:  Nat Genet        ISSN: 1061-4036            Impact factor:   38.330


  47 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  PLINK: a tool set for whole-genome association and population-based linkage analyses.

Authors:  Shaun Purcell; Benjamin Neale; Kathe Todd-Brown; Lori Thomas; Manuel A R Ferreira; David Bender; Julian Maller; Pamela Sklar; Paul I W de Bakker; Mark J Daly; Pak C Sham
Journal:  Am J Hum Genet       Date:  2007-07-25       Impact factor: 11.025

3.  KEGG: Kyoto Encyclopedia of Genes and Genomes.

Authors:  H Ogata; S Goto; K Sato; W Fujibuchi; H Bono; M Kanehisa
Journal:  Nucleic Acids Res       Date:  1999-01-01       Impact factor: 16.971

4.  A role for VAV1 in experimental autoimmune encephalomyelitis and multiple sclerosis.

Authors:  Maja Jagodic; Celine Colacios; Rita Nohra; Anne S Dejean; Amennai Daniel Beyeen; Mohsen Khademi; Audrey Casemayou; Lucille Lamouroux; Christine Duthoit; Olivier Papapietro; Louise Sjöholm; Isabelle Bernard; Dominique Lagrange; Ingrid Dahlman; Frida Lundmark; Annette B Oturai; Helle B Soendergaard; Anu Kemppinen; Janna Saarela; Pentti J Tienari; Hanne F Harbo; Anne Spurkland; Sreeram V Ramagopalan; Dessa A Sadovnick; George C Ebers; Maria Seddighzadeh; Lars Klareskog; Lars Alfredsson; Leonid Padyukov; Jan Hillert; Michel Clanet; Gilles Edan; Bertrand Fontaine; Gilbert J Fournié; Ingrid Kockum; Abdelhadi Saoudi; Tomas Olsson
Journal:  Sci Transl Med       Date:  2009-12-09       Impact factor: 17.956

5.  MHC2TA is associated with differential MHC molecule expression and susceptibility to rheumatoid arthritis, multiple sclerosis and myocardial infarction.

Authors:  Maria Swanberg; Olle Lidman; Leonid Padyukov; Per Eriksson; Eva Akesson; Maja Jagodic; Anna Lobell; Mohsen Khademi; Ola Börjesson; Cecilia M Lindgren; Pia Lundman; Anthony J Brookes; Juha Kere; Holger Luthman; Lars Alfredsson; Jan Hillert; Lars Klareskog; Anders Hamsten; Fredrik Piehl; Tomas Olsson
Journal:  Nat Genet       Date:  2005-04-10       Impact factor: 38.330

6.  T-bet dependent removal of Sin3A-histone deacetylase complexes at the Ifng locus drives Th1 differentiation.

Authors:  Shaojing Chang; Patrick L Collins; Thomas M Aune
Journal:  J Immunol       Date:  2008-12-15       Impact factor: 5.422

7.  Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

Authors:  Richard A Gibbs; George M Weinstock; Michael L Metzker; Donna M Muzny; Erica J Sodergren; Steven Scherer; Graham Scott; David Steffen; Kim C Worley; Paula E Burch; Geoffrey Okwuonu; Sandra Hines; Lora Lewis; Christine DeRamo; Oliver Delgado; Shannon Dugan-Rocha; George Miner; Margaret Morgan; Alicia Hawes; Rachel Gill; Robert A Holt; Mark D Adams; Peter G Amanatides; Holly Baden-Tillson; Mary Barnstead; Soo Chin; Cheryl A Evans; Steve Ferriera; Carl Fosler; Anna Glodek; Zhiping Gu; Don Jennings; Cheryl L Kraft; Trixie Nguyen; Cynthia M Pfannkoch; Cynthia Sitter; Granger G Sutton; J Craig Venter; Trevor Woodage; Douglas Smith; Hong-Mei Lee; Erik Gustafson; Patrick Cahill; Arnold Kana; Lynn Doucette-Stamm; Keith Weinstock; Kim Fechtel; Robert B Weiss; Diane M Dunn; Eric D Green; Robert W Blakesley; Gerard G Bouffard; Pieter J De Jong; Kazutoyo Osoegawa; Baoli Zhu; Marco Marra; Jacqueline Schein; Ian Bosdet; Chris Fjell; Steven Jones; Martin Krzywinski; Carrie Mathewson; Asim Siddiqui; Natasja Wye; John McPherson; Shaying Zhao; Claire M Fraser; Jyoti Shetty; Sofiya Shatsman; Keita Geer; Yixin Chen; Sofyia Abramzon; William C Nierman; Paul H Havlak; Rui Chen; K James Durbin; Amy Egan; Yanru Ren; Xing-Zhi Song; Bingshan Li; Yue Liu; Xiang Qin; Simon Cawley; Kim C Worley; A J Cooney; Lisa M D'Souza; Kirt Martin; Jia Qian Wu; Manuel L Gonzalez-Garay; Andrew R Jackson; Kenneth J Kalafus; Michael P McLeod; Aleksandar Milosavljevic; Davinder Virk; Andrei Volkov; David A Wheeler; Zhengdong Zhang; Jeffrey A Bailey; Evan E Eichler; Eray Tuzun; Ewan Birney; Emmanuel Mongin; Abel Ureta-Vidal; Cara Woodwark; Evgeny Zdobnov; Peer Bork; Mikita Suyama; David Torrents; Marina Alexandersson; Barbara J Trask; Janet M Young; Hui Huang; Huajun Wang; Heming Xing; Sue Daniels; Darryl Gietzen; Jeanette Schmidt; Kristian Stevens; Ursula Vitt; Jim Wingrove; Francisco Camara; M Mar Albà; Josep F Abril; Roderic Guigo; Arian Smit; Inna Dubchak; Edward M Rubin; Olivier Couronne; Alexander Poliakov; Norbert Hübner; Detlev Ganten; Claudia Goesele; Oliver Hummel; Thomas Kreitler; Young-Ae Lee; Jan Monti; Herbert Schulz; Heike Zimdahl; Heinz Himmelbauer; Hans Lehrach; Howard J Jacob; Susan Bromberg; Jo Gullings-Handley; Michael I Jensen-Seaman; Anne E Kwitek; Jozef Lazar; Dean Pasko; Peter J Tonellato; Simon Twigger; Chris P Ponting; Jose M Duarte; Stephen Rice; Leo Goodstadt; Scott A Beatson; Richard D Emes; Eitan E Winter; Caleb Webber; Petra Brandt; Gerald Nyakatura; Margaret Adetobi; Francesca Chiaromonte; Laura Elnitski; Pallavi Eswara; Ross C Hardison; Minmei Hou; Diana Kolbe; Kateryna Makova; Webb Miller; Anton Nekrutenko; Cathy Riemer; Scott Schwartz; James Taylor; Shan Yang; Yi Zhang; Klaus Lindpaintner; T Dan Andrews; Mario Caccamo; Michele Clamp; Laura Clarke; Valerie Curwen; Richard Durbin; Eduardo Eyras; Stephen M Searle; Gregory M Cooper; Serafim Batzoglou; Michael Brudno; Arend Sidow; Eric A Stone; J Craig Venter; Bret A Payseur; Guillaume Bourque; Carlos López-Otín; Xose S Puente; Kushal Chakrabarti; Sourav Chatterji; Colin Dewey; Lior Pachter; Nicolas Bray; Von Bing Yap; Anat Caspi; Glenn Tesler; Pavel A Pevzner; David Haussler; Krishna M Roskin; Robert Baertsch; Hiram Clawson; Terrence S Furey; Angie S Hinrichs; Donna Karolchik; William J Kent; Kate R Rosenbloom; Heather Trumbower; Matt Weirauch; David N Cooper; Peter D Stenson; Bin Ma; Michael Brent; Manimozhiyan Arumugam; David Shteynberg; Richard R Copley; Martin S Taylor; Harold Riethman; Uma Mudunuri; Jane Peterson; Mark Guyer; Adam Felsenfeld; Susan Old; Stephen Mockrin; Francis Collins
Journal:  Nature       Date:  2004-04-01       Impact factor: 49.962

8.  DNase I sensitivity QTLs are a major determinant of human expression variation.

Authors:  Jacob F Degner; Athma A Pai; Roger Pique-Regi; Jean-Baptiste Veyrieras; Daniel J Gaffney; Joseph K Pickrell; Sherryl De Leon; Katelyn Michelini; Noah Lewellen; Gregory E Crawford; Matthew Stephens; Yoav Gilad; Jonathan K Pritchard
Journal:  Nature       Date:  2012-02-05       Impact factor: 49.962

9.  Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease.

Authors:  Gosia Trynka; Karen A Hunt; Nicholas A Bockett; Jihane Romanos; Vanisha Mistry; Agata Szperl; Sjoerd F Bakker; Maria Teresa Bardella; Leena Bhaw-Rosun; Gemma Castillejo; Emilio G de la Concha; Rodrigo Coutinho de Almeida; Kerith-Rae M Dias; Cleo C van Diemen; Patrick C A Dubois; Richard H Duerr; Sarah Edkins; Lude Franke; Karin Fransen; Javier Gutierrez; Graham A R Heap; Barbara Hrdlickova; Sarah Hunt; Leticia Plaza Izurieta; Valentina Izzo; Leo A B Joosten; Cordelia Langford; Maria Cristina Mazzilli; Charles A Mein; Vandana Midah; Mitja Mitrovic; Barbara Mora; Marinita Morelli; Sarah Nutland; Concepción Núñez; Suna Onengut-Gumuscu; Kerra Pearce; Mathieu Platteel; Isabel Polanco; Simon Potter; Carmen Ribes-Koninckx; Isis Ricaño-Ponce; Stephen S Rich; Anna Rybak; José Luis Santiago; Sabyasachi Senapati; Ajit Sood; Hania Szajewska; Riccardo Troncone; Jezabel Varadé; Chris Wallace; Victorien M Wolters; Alexandra Zhernakova; B K Thelma; Bozena Cukrowska; Elena Urcelay; Jose Ramon Bilbao; M Luisa Mearin; Donatella Barisani; Jeffrey C Barrett; Vincent Plagnol; Panos Deloukas; Cisca Wijmenga; David A van Heel
Journal:  Nat Genet       Date:  2011-11-06       Impact factor: 38.330

10.  The HHpred interactive server for protein homology detection and structure prediction.

Authors:  Johannes Söding; Andreas Biegert; Andrei N Lupas
Journal:  Nucleic Acids Res       Date:  2005-07-01       Impact factor: 16.971

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  85 in total

1.  Fine mapping of bone structure and strength QTLs in heterogeneous stock rat.

Authors:  Imranul Alam; Daniel L Koller; Toni Cañete; Gloria Blázquez; Carme Mont-Cardona; Regina López-Aumatell; Esther Martínez-Membrives; Sira Díaz-Morán; Adolf Tobeña; Alberto Fernández-Teruel; Pernilla Stridh; Margarita Diez; Tomas Olsson; Martina Johannesson; Amelie Baud; Michael J Econs; Tatiana Foroud
Journal:  Bone       Date:  2015-08-19       Impact factor: 4.398

Review 2.  QTL mapping in outbred populations: successes and challenges.

Authors:  Leah C Solberg Woods
Journal:  Physiol Genomics       Date:  2013-12-10       Impact factor: 3.107

3.  Efficient set tests for the genetic analysis of correlated traits.

Authors:  Francesco Paolo Casale; Barbara Rakitsch; Christoph Lippert; Oliver Stegle
Journal:  Nat Methods       Date:  2015-06-15       Impact factor: 28.547

Review 4.  Dissecting the Genetics of Osteoporosis using Systems Approaches.

Authors:  Basel M Al-Barghouthi; Charles R Farber
Journal:  Trends Genet       Date:  2018-11-20       Impact factor: 11.639

Review 5.  Using Genetic and Species Diversity to Tackle Kidney Disease.

Authors:  Michael R Garrett; Ron Korstanje
Journal:  Trends Genet       Date:  2020-04-30       Impact factor: 11.639

6.  A statistical framework to guide sequencing choices in pedigrees.

Authors:  Charles Y K Cheung; Elizabeth Marchani Blue; Ellen M Wijsman
Journal:  Am J Hum Genet       Date:  2014-02-06       Impact factor: 11.025

7.  Propensity for social interaction predicts nicotine-reinforced behaviors in outbred rats.

Authors:  T Wang; W Han; B Wang; Q Jiang; L C Solberg-Woods; A A Palmer; H Chen
Journal:  Genes Brain Behav       Date:  2013-12-27       Impact factor: 3.449

8.  Genome-Wide Association Study in 3,173 Outbred Rats Identifies Multiple Loci for Body Weight, Adiposity, and Fasting Glucose.

Authors:  Apurva S Chitre; Oksana Polesskaya; Katie Holl; Jianjun Gao; Riyan Cheng; Hannah Bimschleger; Angel Garcia Martinez; Tony George; Alexander F Gileta; Wenyan Han; Aidan Horvath; Alesa Hughson; Keita Ishiwari; Christopher P King; Alexander Lamparelli; Cassandra L Versaggi; Connor Martin; Celine L St Pierre; Jordan A Tripi; Tengfei Wang; Hao Chen; Shelly B Flagel; Paul Meyer; Jerry Richards; Terry E Robinson; Abraham A Palmer; Leah C Solberg Woods
Journal:  Obesity (Silver Spring)       Date:  2020-08-29       Impact factor: 5.002

Review 9.  Systems genetics approaches to understand complex traits.

Authors:  Mete Civelek; Aldons J Lusis
Journal:  Nat Rev Genet       Date:  2013-12-03       Impact factor: 53.242

Review 10.  Rat models of human diseases and related phenotypes: a systematic inventory of the causative genes.

Authors:  Claude Szpirer
Journal:  J Biomed Sci       Date:  2020-08-02       Impact factor: 8.410

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