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 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; 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

doi:10.1038/sdata.2014.11

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

Research output: Contribution to journal › Article › Research › peer-review

18 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 language	English
Article number	140011
Journal	Scientific Data
Volume	1
DOIs	https://doi.org/10.1038/sdata.2014.11
Publication status	Published - 10 Jun 2014

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10.1038/sdata.2014.11

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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, Article 140011. https://doi.org/10.1038/sdata.2014.11

@article{f30d15dd3d484290be3a3059b76d6e32,

title = "Genomes and phenomes of a population of outbred rats and its progenitors",

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.",

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

year = "2014",

month = jun,

day = "10",

doi = "10.1038/sdata.2014.11",

language = "English",

volume = "1",

journal = "Scientific Data",

issn = "2052-4463",

publisher = "Nature Publishing Group",

}

Baud, A, Guryev, V, Hummel, O, Johannesson, M, Flint, J, Hermsen, R, Stridh, P, Graham, D, McBride, MW, Foroud, T, Calderari, S, Diez, M, Ockinger, J, Beyeen, AD, Gillett, A, Abdelmagid, N, Guerreiro-Cacais, AO, Jagodic, M, Tuncel, J, Norin, U, Beattie, E, Huynh, N, Miller, WH, Koller, DL, Alam, I, Falak, S, Osborne-Pellegrin, M, Martinez-Membrives, E, Canete, T, Blazquez, G, Vicens-Costa, E, Mont-Cardona, C, Diaz-Moran, S, Tobena, A, Zelenika, D, Saar, K, Patone, G, Bauerfeind, A, Bihoreau, MT, Heinig, M, Lee, YA, Rintisch, C, Schulz, H, Wheeler, DA, Worley, KC, Muzny, DM, Gibbs, RA, Lathrop, M, Lansu, N, Toonen, P, Ruzius, FP, De Bruijn, E, Hauser, H, Adams, DJ, Keane, T, Atanur, SS, Aitman, TJ, Flicek, P, Malinauskas, T, Jones, EY, Ekman, D, Lopez-Aumatell, R, Dominiczak, AF, Holmdahl, R, Olsson, T, Gauguier, D, Hubner, N, Fernandez-Teruel, A, Cuppen, E & Mott, R 2014, 'Genomes and phenomes of a population of outbred rats and its progenitors', Scientific Data, vol. 1, 140011. https://doi.org/10.1038/sdata.2014.11

TY - JOUR

T1 - Genomes and phenomes of a population of outbred rats and its progenitors

AU - Baud, Amelie

AU - Guryev, Victor

AU - Hummel, Oliver

AU - Johannesson, Martina

AU - Flint, Jonathan

AU - Hermsen, Roel

AU - Stridh, Pernilla

AU - Graham, Delyth

AU - McBride, Martin W.

AU - Foroud, Tatiana

AU - Calderari, Sophie

AU - Diez, Margarita

AU - Ockinger, Johan

AU - Beyeen, Amennai D.

AU - Gillett, Alan

AU - Abdelmagid, Nada

AU - Guerreiro-Cacais, Andre Ortlieb

AU - Jagodic, Maja

AU - Tuncel, Jonatan

AU - Norin, Ulrika

AU - Beattie, Elisabeth

AU - Huynh, Ngan

AU - Miller, William H.

AU - Koller, Daniel L.

AU - Alam, Imranul

AU - Falak, Samreen

AU - Osborne-Pellegrin, Mary

AU - Martinez-Membrives, Esther

AU - Canete, Toni

AU - Blazquez, Gloria

AU - Vicens-Costa, Elia

AU - Mont-Cardona, Carme

AU - Diaz-Moran, Sira

AU - Tobena, Adolf

AU - Zelenika, Diana

AU - Saar, Kathrin

AU - Patone, Giannino

AU - Bauerfeind, Anja

AU - Bihoreau, Marie Therese

AU - Heinig, Matthias

AU - Lee, Young Ae

AU - Rintisch, Carola

AU - Schulz, Herbert

AU - Wheeler, David A.

AU - Worley, Kim C.

AU - Muzny, Donna M.

AU - Gibbs, Richard A.

AU - Lathrop, Mark

AU - Lansu, Nico

AU - Toonen, Pim

AU - Ruzius, Frans Paul

AU - De Bruijn, Ewart

AU - Hauser, Heidi

AU - Adams, David J.

AU - Keane, Thomas

AU - Atanur, Santosh S.

AU - Aitman, Tim J.

AU - Flicek, Paul

AU - Malinauskas, Tomas

AU - Jones, E. Yvonne

AU - Ekman, Diana

AU - Lopez-Aumatell, Regina

AU - Dominiczak, Anna F.

AU - Holmdahl, Rikard

AU - Olsson, Tomas

AU - Gauguier, Dominique

AU - Hubner, Norbert

AU - Fernandez-Teruel, Alberto

AU - Cuppen, Edwin

AU - Mott, Richard

PY - 2014/6/10

Y1 - 2014/6/10

N2 - 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.

AB - 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.

U2 - 10.1038/sdata.2014.11

DO - 10.1038/sdata.2014.11

M3 - Article

SN - 2052-4463

VL - 1

JO - Scientific Data

JF - Scientific Data

M1 - 140011

ER -

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

Abstract

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