The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

被引：3769

作者：

Ardlie, Kristin G.

DeLuca, David S. ^{[1
]}

Segre, Ayellet V. ^{[1
]}

Sullivan, Timothy J. ^{[1
]}

Young, Taylor R. ^{[1
]}

Gelfand, Ellen T. ^{[1
]}

Trowbridge, Casandra A. ^{[1
]}

Maller, Julian B. ^{[1
,2
]}

Tukiainen, Taru ^{[1
,2
]}

Lek, Monkol ^{[1
,2
]}

Ward, Lucas D. ^{[1
,3
]}

Kheradpour, Pouya ^{[1
,3
]}

Iriarte, Benjamin ^{[3
]}

Meng, Yan ^{[1
]}

Palmer, Cameron D. ^{[1
,4
,5
]}

Esko, Tonu ^{[1
,4
,5
,6
]}

Winckler, Wendy ^{[1
]}

Hirschhorn, Joel N. ^{[1
,4
,5
]}

Kellis, Manolis

MacArthur, Daniel G. ^{[1
,2
]}

Getz, Gad

Shabalin, Andrey A. ^{[7
]}

Li, Gen ^{[8
,9
]}

Zhou, Yi-Hui ^{[10
,11
,12
]}

Nobel, Andrew B. ^{[8
,9
]}

Rusyn, Ivan ^{[13
,14
]}

Wright, Fred A.

Lappalainen, Tuuli ^{[15
,16
,17
,18
,19
,20
]}

Ferreira, Pedro G. ^{[15
,16
,17
]}

Ongen, Halit ^{[15
,16
,17
]}

Rivas, Manuel A. ^{[21
]}

Battle, Alexis ^{[22
,23
]}

Mostafavi, Sara ^{[22
]}

Monlong, Jean ^{[24
,25
,26
]}

Sammeth, Michael ^{[24
,25
,27
]}

Mele, Marta ^{[24
,25
,28
]}

Reverter, Ferran ^{[24
,29
]}

Goldmann, Jakob M. ^{[24
,30
]}

Koller, Daphne ^{[22
]}

Guigo, Roderic ^{[24
,25
,31
]}

McCarthy, Mark I. ^{[21
,32
,33
]}

Dermitzakis, Emmanouil T.

Gamazon, Eric R. ^{[34
,35
,36
]}

Im, Hae Kyung ^{[34
,35
]}

Konkashbaev, Anuar ^{[34
,35
,36
]}

Nicolae, Dan L. ^{[34
,35
]}

Cox, Nancy J. ^{[34
,35
,36
]}

Flutre, Timothee ^{[37
,38
]}

Wen, Xiaoquan ^{[39
]}

Stephens, Matthew ^{[37
,40
]}

机构：

[1] Broad Inst MIT & Harvard, Cambridge, MA 02142 USA

[2] Massachusetts Gen Hosp, Analyt & Translat Genet Unit, Boston, MA 02114 USA

[3] MIT, MIT Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA

[4] Boston Childrens Hosp, Ctr Basic & Translat Obes Res, Boston, MA 02115 USA

[5] Boston Childrens Hosp, Div Endocrinol, Boston, MA 02115 USA

[6] Univ Tartu, Estonian Genome Ctr, EE-50090 Tartu, Estonia

[7] Virginia Commonwealth Univ, Ctr Biomarker Res & Personalized Med, Richmond, VA 23298 USA

[8] Univ N Carolina, Dept Stat & Operat Res, Chapel Hill, NC 27599 USA

[9] Univ N Carolina, Dept Biostat, Chapel Hill, NC 27599 USA

[10] N Carolina State Univ, Bioinformat Res Ctr, Raleigh, NC 27695 USA

[11] N Carolina State Univ, Dept Stat, Raleigh, NC 27695 USA

[12] N Carolina State Univ, Dept Biol Sci, Raleigh, NC 27695 USA

[13] Univ N Carolina, Dept Environm Sci & Engn, Chapel Hill, NC 27599 USA

[14] Texas A&M Univ, Dept Vet Integrat Biosci, College Stn, TX 77843 USA

[15] Univ Geneva, Sch Med, Dept Genet Med & Dev, CH-1211 Geneva, Switzerland

[16] Univ Geneva, Inst Genet & Genom Geneva iG3, CH-1211 Geneva, Switzerland

[17] Swiss Inst Bioinformat, CH-1211 Geneva, Switzerland

[18] Stanford Univ, Dept Genet, Stanford, CA 94305 USA

[19] New York Genome Ctr, New York, NY 10011 USA

[20] Columbia Univ, Med Ctr, Dept Syst Biol, New York, NY 10032 USA

[21] Univ Oxford, Nuffield Dept Clin Med, Wellcome Trust Ctr Human Genet Res, Oxford OX3 7BN, England

[22] Stanford Univ, Dept Comp Sci, Stanford, CA 94305 USA

[23] Johns Hopkins Univ, Dept Comp Sci, Baltimore, MD 21218 USA

[24] CRG, Barcelona 08003, Catalonia, Spain

[25] Univ Pompeu Fabra, Barcelona 08003, Catalonia, Spain

[26] McGill Univ, Human Genet Dept, Montreal, PQ H3A 0G1, Canada

[27] Natl Inst Sci Comp, BR-25651075 Rio De Janeiro, Brazil

[28] Harvard Univ, Dept Stem Cell & Regenerat Biol, Cambridge, MA 02138 USA

[29] Univ Barcelona, E-08028 Barcelona, Spain

[30] Radboud Univ Nijmegen, NL-6525 ED Nijmegen, Netherlands

[31] Inst Hosp Mar Invest Med IMIM, Barcelona 08003, Spain

[32] Univ Oxford, Churchill Hosp, Oxford Ctr Diabet Endocrinol & Metab, Oxford OX3 7LJ, England

[33] Churchill Hosp, Oxford NIHR Biomed Res Ctr, Oxford OX3 7LJ, England

[34] Univ Chicago, Dept Med, Sect Genet Med, Chicago, IL 60637 USA

[35] Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA

[36] Vanderbilt Univ, Dept Med, Div Genet Med, Nashville, TN 37232 USA

[37] Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA

[38] INRA, Dept Plant Biol & Breeding, UMR 1334, AGAP, F-34060 Montpellier, France

[39] Univ Michigan, Dept Biostat, Ann Arbor, MI 48109 USA

[40] Univ Chicago, Dept Stat, Chicago, IL 60637 USA

[41] Stanford Univ, Dept Genet & Biol, Stanford, CA 94305 USA

[42] Univ Chicago, Howard Hughes Med Inst, Chicago, IL 60637 USA

[43] Icahn Sch Med Mt Sinai, Dept Genet & Genom Sci, New York, NY 10029 USA

[44] Icahn Sch Med Mt Sinai, Icahn Inst Genom & Multiscale Biol, New York, NY 10029 USA

[45] Harvard Univ, Dept Stat, Cambridge, MA 02138 USA

[46] Natl Dis Res Interchange, Philadelphia, PA 19103 USA

[47] Roswell Pk Canc Inst, Buffalo, NY 14263 USA

[48] Sci Care Inc, Phoenix, AZ USA

[49] Gift Life Donor Program, Philadelphia, PA 19103 USA

[50] LifeNet Hlth, Virginia Beach, VA 23453 USA

来源：

SCIENCE | 2015年 / 348卷 / 6235期

基金：

英国惠康基金; 欧洲研究理事会; 美国国家卫生研究院; 美国国家科学基金会; 瑞士国家科学基金会;

关键词：

GENOME-WIDE ASSOCIATION; VARIANTS; IDENTIFICATION; TRANSCRIPTOME; LOCI; ARCHITECTURE; RESOURCE; SYSTEMS;

D O I：

10.1126/science.1262110

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：

Understanding the functional consequences of genetic variation, and how it affects complex human disease and quantitative traits, remains a critical challenge for biomedicine. We present an analysis of RNA sequencing data from 1641 samples across 43 tissues from 175 individuals, generated as part of the pilot phase of the Genotype-Tissue Expression (GTEx) project. We describe the landscape of gene expression across tissues, catalog thousands of tissue-specific and shared regulatory expression quantitative trait loci (eQTL) variants, describe complex network relationships, and identify signals from genome-wide association studies explained by eQTLs. These findings provide a systematic understanding of the cellular and biological consequences of human genetic variation and of the heterogeneity of such effects among a diverse set of human tissues.

引用

页码：648 / 660

页数：13

共 45 条

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← 1 2 3 4 5 →

共 45 条

[11] A Statistical Framework for Joint eQTL Analysis in Multiple Tissues [J].

Flutre, Timothee ;

Wen, Xiaoquan ;

Pritchard, Jonathan ;

Stephens, Matthew .

PLOS GENETICS, 2013, 9 (05)

[12] Dissecting the regulatory architecture of gene expression QTLs [J].

Gaffney, Daniel J. ;

Veyrieras, Jean-Baptiste ;

Degner, Jacob F. ;

Pique-Regi, Roger ;

Pai, Athma A. ;

Crawford, Gregory E. ;

Stephens, Matthew ;

Gilad, Yoav ;

Pritchard, Jonathan K. .

GENOME BIOLOGY, 2012, 13 (01)

[13] Architecture of the human regulatory network derived from ENCODE data [J].

Gerstein, Mark B. ;

Kundaje, Anshul ;

Hariharan, Manoj ;

Landt, Stephen G. ;

Yan, Koon-Kiu ;

Cheng, Chao ;

Mu, Xinmeng Jasmine ;

Khurana, Ekta ;

Rozowsky, Joel ;

Alexander, Roger ;

Min, Renqiang ;

Alves, Pedro ;

Abyzov, Alexej ;

Addleman, Nick ;

Bhardwaj, Nitin ;

Boyle, Alan P. ;

Cayting, Philip ;

Charos, Alexandra ;

Chen, David Z. ;

Cheng, Yong ;

Clarke, Declan ;

Eastman, Catharine ;

Euskirchen, Ghia ;

Frietze, Seth ;

Fu, Yao ;

Gertz, Jason ;

Grubert, Fabian ;

Harmanci, Arif ;

Jain, Preti ;

Kasowski, Maya ;

Lacroute, Phil ;

Leng, Jing ;

Lian, Jin ;

Monahan, Hannah ;

O'Geen, Henriette ;

Ouyang, Zhengqing ;

Partridge, E. Christopher ;

Patacsil, Dorrelyn ;

Pauli, Florencia ;

Raha, Debasish ;

Ramirez, Lucia ;

Reddy, Timothy E. ;

Reed, Brian ;

Shi, Minyi ;

Slifer, Teri ;

Wang, Jing ;

Wu, Linfeng ;

Yang, Xinqiong ;

Yip, Kevin Y. ;

Zilberman-Schapira, Gili .

NATURE, 2012, 489 (7414) :91-100

[14] Mapping cis- and trans-regulatory effects across multiple tissues in twins [J].

Grundberg, Elin ;

Small, Kerrin S. ;

Hedman, Asa K. ;

Nica, Alexandra C. ;

Buil, Alfonso ;

Keildson, Sarah ;

Bell, Jordana T. ;

Yang, Tsun-Po ;

Meduri, Eshwar ;

Barrett, Amy ;

Nisbett, James ;

Sekowska, Magdalena ;

Wilk, Alicja ;

Shin, So-Youn ;

Glass, Daniel ;

Travers, Mary ;

Min, Josine L. ;

Ring, Sue ;

Ho, Karen ;

Thorleifsson, Gudmar ;

Kong, Augustine ;

Thorsteindottir, Unnur ;

Ainali, Chrysanthi ;

Dimas, Antigone S. ;

Hassanali, Neelam ;

Ingle, Catherine ;

Knowles, David ;

Krestyaninova, Maria ;

Lowe, Christopher E. ;

Di Meglio, Paola ;

Montgomery, Stephen B. ;

Parts, Leopold ;

Potter, Simon ;

Surdulescu, Gabriela ;

Tsaprouni, Loukia ;

Tsoka, Sophia ;

Bataille, Veronique ;

Durbin, Richard ;

Nestle, Frank O. ;

O'Rahilly, Stephen ;

Soranzo, Nicole ;

Lindgren, Cecilia M. ;

Zondervan, Krina T. ;

Ahmadi, Kourosh R. ;

Schadt, Eric E. ;

Stefansson, Kari ;

Smith, George Davey ;

McCarthy, Mark I. ;

Deloukas, Panos ;

Dermitzakis, Emmanouil T. .

NATURE GENETICS, 2012, 44 (10) :1084-+

[15] GENCODE: The reference human genome annotation for The ENCODE Project [J].

Harrow, Jennifer ;

Frankish, Adam ;

Gonzalez, Jose M. ;

Tapanari, Electra ;

Diekhans, Mark ;

Kokocinski, Felix ;

Aken, Bronwen L. ;

Barrell, Daniel ;

Zadissa, Amonida ;

Searle, Stephen ;

Barnes, If ;

Bignell, Alexandra ;

Boychenko, Veronika ;

Hunt, Toby ;

Kay, Mike ;

Mukherjee, Gaurab ;

Rajan, Jeena ;

Despacio-Reyes, Gloria ;

Saunders, Gary ;

Steward, Charles ;

Harte, Rachel ;

Lin, Michael ;

Howald, Cedric ;

Tanzer, Andrea ;

Derrien, Thomas ;

Chrast, Jacqueline ;

Walters, Nathalie ;

Balasubramanian, Suganthi ;

Pei, Baikang ;

Tress, Michael ;

Manuel Rodriguez, Jose ;

Ezkurdia, Iakes ;

van Baren, Jeltje ;

Brent, Michael ;

Haussler, David ;

Kellis, Manolis ;

Valencia, Alfonso ;

Reymond, Alexandre ;

Gerstein, Mark ;

Guigo, Roderic ;

Hubbard, Tim J. .

GENOME RESEARCH, 2012, 22 (09) :1760-1774

[16] Potential etiologic and functional implications of genome-wide association loci for human diseases and traits [J].

Hindorff, Lucia A. ;

Sethupathy, Praveen ;

Junkins, Heather A. ;

Ramos, Erin M. ;

Mehta, Jayashri P. ;

Collins, Francis S. ;

Manolio, Teri A. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (23) :9362-9367

[17] Spatio-temporal transcriptome of the human brain [J].

Kang, Hyo Jung ;

Kawasawa, Yuka Imamura ;

Cheng, Feng ;

Zhu, Ying ;

Xu, Xuming ;

Li, Mingfeng ;

Sousa, Andre M. M. ;

Pletikos, Mihovil ;

Meyer, Kyle A. ;

Sedmak, Goran ;

Guennel, Tobias ;

Shin, Yurae ;

Johnson, Matthew B. ;

Krsnik, Zeljka ;

Mayer, Simone ;

Fertuzinhos, Sofia ;

Umlauf, Sheila ;

Lisgo, Steven N. ;

Vortmeyer, Alexander ;

Weinberger, Daniel R. ;

Mane, Shrikant ;

Hyde, Thomas M. ;

Huttner, Anita ;

Reimers, Mark ;

Kleinman, Joel E. ;

Sestan, Nenad .

NATURE, 2011, 478 (7370) :483-489

[18] Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics [J].

Khurana, Ekta ;

Fu, Yao ;

Colonna, Vincenza ;

Mu, Xinmeng Jasmine ;

Kang, Hyun Min ;

Lappalainen, Tuuli ;

Sboner, Andrea ;

Lochovsky, Lucas ;

Chen, Jieming ;

Harmanci, Arif ;

Das, Jishnu ;

Abyzov, Alexej ;

Balasubramanian, Suganthi ;

Beal, Kathryn ;

Chakravarty, Dimple ;

Challis, Daniel ;

Chen, Yuan ;

Clarke, Declan ;

Clarke, Laura ;

Cunningham, Fiona ;

Evani, Uday S. ;

Flicek, Paul ;

Fragoza, Robert ;

Garrison, Erik ;

Gibbs, Richard ;

Gumus, Zeynep H. ;

Herrero, Javier ;

Kitabayashi, Naoki ;

Kong, Yong ;

Lage, Kasper ;

Liluashvili, Vaja ;

Lipkin, Steven M. ;

MacArthur, Daniel G. ;

Marth, Gabor ;

Muzny, Donna ;

Pers, Tune H. ;

Ritchie, Graham R. S. ;

Rosenfeld, Jeffrey A. ;

Sisu, Cristina ;

Wei, Xiaomu ;

Wilson, Michael ;

Xue, Yali ;

Yu, Fuli ;

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