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PMID: 21921910 Published · epublish English Comparative Study Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Mouse genomic variation and its effect on phenotypes and gene regulation.

Nature ·Vol. 477 ·No. 7364 ·2011-09-14 ·Pages 289-94

Keane TM, Goodstadt L, Danecek P, White MA, Wong K, Yalcin B, Heger A, Agam A, Slater G, Goodson M, Furlotte NA, Eskin E, Nellåker C, Whitley H, Cleak J, Janowitz D, Hernandez-Pliego P, Edwards A, Belgard TG, Oliver PL, McIntyre RE, Bhomra A, Nicod J, Gan X, Yuan W, van der Weyden L, Steward CA, Bala S, Stalker J, Mott R, Durbin R, Jackson IJ, Czechanski A, Guerra-Assunção JA, Donahue LR, Reinholdt LG, Payseur BA, Ponting CP, Birney E, Flint J, Adams DJ

Abstract

We report genome sequences of 17 inbred strains of laboratory mice and identify almost ten times more variants than previously known. We use these genomes to explore the phylogenetic history of the laboratory mouse and to examine the functional consequences of allele-specific variation on transcript abundance, revealing that at least 12% of transcripts show a significant tissue-specific expression bias. By identifying candidate functional variants at 718 quantitative trait loci we show that the molecular nature of functional variants and their position relative to genes vary according to the effect size of the locus. These sequences provide a starting point for a new era in the functional analysis of a key model organism.

MeSH Terms
Alleles Animals Animals, Laboratory/genetics Gene Expression Regulation/genetics Genetic Variation/genetics Genome/genetics Genomics Mice/classification,genetics Mice, Inbred C57BL/genetics Mice, Inbred Strains/genetics Phenotype Phylogeny Quantitative Trait Loci/genetics
Authors & Affiliations
41 authors, click to expand affiliations / ORCID
Keane Thomas M
The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK.
Goodstadt Leo
Danecek Petr
White Michael A
Wong Kim
Yalcin Binnaz
Heger Andreas
Agam Avigail
Slater Guy
Goodson Martin
Furlotte Nicholas A
Eskin Eleazar
Nellåker Christoffer
Whitley Helen
Cleak James
Janowitz Deborah
Hernandez-Pliego Polinka
Edwards Andrew
Belgard T Grant
Oliver Peter L
McIntyre Rebecca E
Bhomra Amarjit
Nicod Jérôme
Gan Xiangchao
Yuan Wei
van der Weyden Louise
Steward Charles A
Bala Sendu
Stalker Jim
Mott Richard
Durbin Richard
Jackson Ian J
Czechanski Anne
Guerra-Assunção José Afonso
Donahue Leah Rae
Reinholdt Laura G
Payseur Bret A
Ponting Chris P
Birney Ewan
Flint Jonathan
Adams David J
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Article Info
Journal
Nature
Abbr.
Nature
ISSN
1476-4687
DOI
10.1038/nature10413
Published
2011-09-14
Epub
2011-00-14
Pages
289-94
Language
English
Region
England
NLM ID
0410462
PMCID
PMC3276836
Subset
IM
Grants
Wellcome Trust · 077192 · United Kingdom
NIAID NIH HHS · N01AI15416 · United States
Medical Research Council · MC_U127561112 · United Kingdom
Medical Research Council · MC_U137761446 · United Kingdom
NHLBI NIH HHS · K25 HL080079 · United States
NLM NIH HHS · T15 LM007359 · United States
Wellcome Trust · 090532 · United Kingdom
Wellcome Trust · 079912 · United Kingdom
Wellcome Trust · 085906/Z/08/Z · United Kingdom
Medical Research Council · G0800024 · United Kingdom
Wellcome Trust · 083573/Z/07/Z · United Kingdom
Wellcome Trust · 082356 · United Kingdom
Wellcome Trust · 083573 · United Kingdom
Biotechnology and Biological Sciences Research Council · BB/F022697/1 · United Kingdom
Medical Research Council · MC_EX_G0802457 · United Kingdom
NHGRI NIH HHS · T32 HG002536 · United States
Cancer Research UK · A6997 · United Kingdom
Wellcome Trust · 085906 · United Kingdom
NLM NIH HHS · 2T15LM007359 · United States
Corrections
CommentIn
PMID: 22224210
External Links
PubMed source DOI: 10.1038/nature10413 PMC Full Text View journal details
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