Genomes and phenomes of a population of outbred rats and its progenitors

Amelie Baud, Victor Guryev, Oliver Hummel, Martina Johannesson, Jonathan Flint, Roel Hermsen, 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 NorinElisabeth 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, 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, Rikard Holmdahl, Tomas Olsson, Dominique Gauguier, Norbert Hubner, Alberto Fernandez-Teruel, Edwin Cuppen, Richard Mott

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14 Citations (Scopus)

Abstract

Finding genetic variants that contribute to phenotypic variation is one of the main challenges of modern genetics. We used an outbred population of rats (Heterogeneous Stock, HS) in a combined sequence-based and genetic mapping analysis to identify sequence variants and genes contributing to complex traits of biomedical relevance. Here we describe the sequences of the eight inbred progenitors of the HS and the variants that segregate between them. We report the genotyping of 1,407 HS rats, and the collection from 2,006 rats of 195 phenotypic measures that are relevant to models of anxiety, type 2 diabetes, hypertension and osteoporosis. We make available haplotype dosages for the 1,407 genotyped rats, since genetic mapping in the HS is best carried out by reconstructing each HS chromosome as a mosaic of the progenitor genomes. Finally, we have deposited an R object that makes it easy to incorporate our sequence data into any genetic study of HS rats. Our genetic data are available for both Rnor3.4 and Rnor5.0 rat assemblies.
Original languageEnglish
Article number140011
JournalScientific Data
Volume1
DOIs
Publication statusPublished - 10 Jun 2014

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    Baud, A., Guryev, V., Hummel, O., Johannesson, M., Flint, J., Hermsen, R., Stridh, P., Graham, D., McBride, M. W., Foroud, T., Calderari, S., Diez, M., Ockinger, J., Beyeen, A. D., Gillett, A., Abdelmagid, N., Guerreiro-Cacais, A. O., Jagodic, M., Tuncel, J., ... Mott, R. (2014). Genomes and phenomes of a population of outbred rats and its progenitors. Scientific Data, 1, [140011]. https://doi.org/10.1038/sdata.2014.11