Mouse genomic variation and its effect on phenotypes and gene regulation

被引：1137

作者：

Keane, Thomas M. ^{[2
]}

Goodstadt, Leo ^{[1
]}

Danecek, Petr ^{[2
]}

White, Michael A. ^{[3
]}

Wong, Kim ^{[2
]}

Yalcin, Binnaz ^{[1
]}

Heger, Andreas ^{[4
]}

Agam, Avigail ^{[1
,4
]}

Slater, Guy ^{[2
]}

Goodson, Martin ^{[1
]}

Furlotte, Nicholas A. ^{[5
]}

Eskin, Eleazar ^{[5
]}

Nellaker, Christoffer ^{[4
]}

Whitley, Helen ^{[1
]}

Cleak, James ^{[1
]}

Janowitz, Deborah ^{[1
,6
]}

Hernandez-Pliego, Polinka ^{[1
]}

Edwards, Andrew ^{[1
]}

Belgard, T. Grant ^{[4
]}

Oliver, Peter L. ^{[4
]}

McIntyre, Rebecca E. ^{[2
]}

Bhomra, Amarjit ^{[1
]}

Nicod, Jerome ^{[1
]}

Gan, Xiangchao ^{[1
]}

Yuan, Wei ^{[1
]}

van der Weyden, Louise ^{[2
]}

Steward, Charles A. ^{[2
]}

Bala, Sendu ^{[2
]}

Stalker, Jim ^{[2
]}

Mott, Richard ^{[1
]}

Durbin, Richard ^{[2
]}

Jackson, Ian J. ^{[7
]}

Czechanski, Anne ^{[8
]}

Guerra-Assuncao, Jose Afonso ^{[9
]}

Donahue, Leah Rae ^{[8
]}

Reinholdt, Laura G. ^{[8
]}

Payseur, Bret A. ^{[3
]}

Ponting, Chris P. ^{[4
]}

Birney, Ewan ^{[9
]}

Flint, Jonathan ^{[1
]}

Adams, David J. ^{[2
]}

机构：

[1] Wellcome Trust Ctr Human Genet, Oxford OX3 7BN, England

[2] Wellcome Trust Sanger Inst, Cambridge CB10 1HH, England

[3] Univ Wisconsin, Genet Lab, Madison, WI 53706 USA

[4] Univ Oxford, Dept Physiol Anat & Genet, MRC Funct Genom Unit, Oxford OX1 3QX, England

[5] Univ Calif Los Angeles, Los Angeles, CA 90095 USA

[6] Ernst Moritz Arndt Univ Greifswald, Greifswald Klinikum Hansestadt Stralsund, Dept Psychiat & Psychotherapy, D-18437 Stralsund, Germany

[7] MRC, Human Genet Unit, Edinburgh EH4 2XU, Midlothian, Scotland

[8] Jackson Lab, Bar Harbor, ME 04609 USA

[9] European Bioinformat Inst, Cambridge CB10 1SD, England

来源：

NATURE | 2011年 / 477卷 / 7364期

基金：

英国惠康基金; 英国医学研究理事会; 英国生物技术与生命科学研究理事会; 美国国家科学基金会;

关键词：

COMPLEX TRAITS; INTELLECTUAL HISTORY; MICE; STRAINS; WIDE; ASSOCIATION; CONCORDANCE; TREES; ARCHITECTURE; DISSECTION;

D O I：

10.1038/nature10413

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页码：289 / 294

页数：6

共 44 条

[1] Ané C, 2007, MOL BIOL EVOL, V24, P412
[2] Concordance trees, concordance factors, and the exploration of reticulate genealogy
Baum, David A.
[J]. TAXON, 2007, 56 (02) : 417 - 426
[3] A high-resolution association mapping panel for the dissection of complex traits in mice
Bennett, Brian J.
Farber, Charles R.
Orozco, Luz
Kang, Hyun Min
Ghazalpour, Anatole
Siemers, Nathan
Neubauer, Michael
Neuhaus, Isaac
Yordanova, Roumyana
Guan, Bo
Truong, Amy
Yang, Wen-pin
He, Aiqing
Kayne, Paul
Gargalovic, Peter
Kirchgessner, Todd
Pan, Calvin
Castellani, Lawrence W.
Kostem, Emrah
Furlotte, Nicholas
Drake, Thomas A.
Eskin, Eleazar
Lusis, Aldons J.
[J]. GENOME RESEARCH, 2010, 20 (02) : 281 - 290
[4] Accurate whole human genome sequencing using reversible terminator chemistry
Bentley, David R.
Balasubramanian, Shankar
Swerdlow, Harold P.
Smith, Geoffrey P.
Milton, John
Brown, Clive G.
Hall, Kevin P.
Evers, Dirk J.
Barnes, Colin L.
Bignell, Helen R.
Boutell, Jonathan M.
Bryant, Jason
Carter, Richard J.
Cheetham, R. Keira
Cox, Anthony J.
Ellis, Darren J.
Flatbush, Michael R.
Gormley, Niall A.
Humphray, Sean J.
Irving, Leslie J.
Karbelashvili, Mirian S.
Kirk, Scott M.
Li, Heng
Liu, Xiaohai
Maisinger, Klaus S.
Murray, Lisa J.
Obradovic, Bojan
Ost, Tobias
Parkinson, Michael L.
Pratt, Mark R.
Rasolonjatovo, Isabelle M. J.
Reed, Mark T.
Rigatti, Roberto
Rodighiero, Chiara
Ross, Mark T.
Sabot, Andrea
Sankar, Subramanian V.
Scally, Aylwyn
Schroth, Gary P.
Smith, Mark E.
Smith, Vincent P.
Spiridou, Anastassia
Torrance, Peta E.
Tzonev, Svilen S.
Vermaas, Eric H.
Walter, Klaudia
Wu, Xiaolin
Zhang, Lu
Alam, Mohammed D.
Anastasi, Carole
[J]. NATURE, 2008, 456 (7218) : 53 - 59
[5] Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse
Church, Deanna M.
Goodstadt, Leo
Hillier, LaDeana W.
Zody, Michael C.
Goldstein, Steve
She, Xinwe
Bult, Carol J.
Agarwala, Richa
Cherry, Joshua L.
DiCuccio, Michael
Hlavina, Wratko
Kapustin, Yuri
Meric, Peter
Maglott, Donna
Birtle, Zoe
Marques, Ana C.
Graves, Tina
Zhou, Shiguo
Teague, Brian
Potamousis, Konstantinos
Churas, Christopher
Place, Michael
Herschleb, Jill
Runnheim, Ron
Forrest, Daniel
Amos-Landgraf, James
Schwartz, David C.
Cheng, Ze
Lindblad-Toh, Kerstin
Eichler, Evan E.
Ponting, Chris P.
[J]. PLOS BIOLOGY, 2009, 7 (05):
[6] The Collaborative Cross, a community resource for the genetic analysis of complex traits
Churchill, G
Airey, DC
Allayee, H
Angel, JM
Attie, AD
Beatty, J
Beavis, WD
Belknap, JK
Bennett, B
Berrettini, W
Bleich, A
Bogue, M
Broman, KW
Buck, KJ
Buckler, E
Burmeister, M
Chesler, EJ
Cheverud, JM
Clapcote, S
Cook, MN
Cox, RD
Crabbe, JC
Crusio, WE
Darvasi, A
Deschnepper, CF
Doerge, RW
Farber, CR
Forejt, J
Gaile, D
Garlow, SJ
Geiger, H
Gershenfeld, H
Gordon, T
Gu, J
Gu, WK
de Haan, G
Hayes, NL
Heller, C
Himmelbauer, H
Hitzemann, R
Hunter, K
Hsu, HC
Iraqi, FA
Ivandic, B
Jacob, HJ
Jansen, RC
Jjepsen, KJ
Johnson, DK
Johnson, TE
Kempermann, G
[J]. NATURE GENETICS, 2004, 36 (11) : 1133 - 1137
[7] A genome-wide set of congenic mouse strains derived from DBA/2J on a C57BL/6J background
Davis, RC
Schadt, EE
Smith, DJ
Hsieh, EWY
Cervino, ACL
van Nas, A
Rosales, M
Doss, S
Meng, H
Allayee, H
Lusis, AJ
[J]. GENOMICS, 2005, 86 (03) : 259 - 270
[8] Break-Induced Replication Is Highly Inaccurate
Deem, Angela
Keszthelyi, Andrea
Blackgrove, Tiffany
Vayl, Alexandra
Coffey, Barbara
Mathur, Ruchi
Chabes, Andrei
Malkova, Anna
[J]. PLOS BIOLOGY, 2011, 9 (02)
[9] GENETIC IDENTIFICATION OF MOM-1, A MAJOR MODIFIER LOCUS AFFECTING MIN-INDUCED INTESTINAL NEOPLASIA IN THE MOUSE
DIETRICH, WF
LANDER, ES
SMITH, JS
MOSER, AR
GOULD, KA
LUONGO, C
BORENSTEIN, N
DOVE, W
[J]. CELL, 1993, 75 (04) : 631 - 639
[10] Genetic architecture of quantitative traits in mice, flies, and humans
Flint, Jonathan
Mackay, Trudy F. C.
[J]. GENOME RESEARCH, 2009, 19 (05) : 723 - 733

← 1 2 3 4 5 →