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The GTEx Consortium atlas of genetic regulatory effects across human tissues

View ORCID ProfileFrançois Aguet, Alvaro N Barbeira, Rodrigo Bonazzola, Andrew Brown, Stephane E Castel, Brian Jo, Silva Kasela, Sarah Kim-Hellmuth, Yanyu Liang, Meritxell Oliva, Princy E Parsana, Elise Flynn, Laure Fresard, Eric R Gaamzon, Andrew R Hamel, Yuan He, Farhad Hormozdiari, Pejman Mohammadi, Manuel Muñoz-Aguirre, YoSon Park, Ashis Saha, Ayellet V Segrć, Benjamin J Strober, Xiaoquan Wen, Valentin Wucher, Sayantan Das, Diego Garrido-Martín, Nicole R Gay, Robert E Handsaker, Paul J Hoffman, Seva Kashin, Alan Kwong, Xiao Li, Daniel MacArthur, John M Rouhana, Matthew Stephens, Ellen Todres, View ORCID ProfileAna Viñuela, Gao Wang, Yuxin Zou, The GTEx Consortium, Christopher D Brown, Nancy Cox, Emmanouil Dermitzakis, Barbara E Engelhardt, Gad Getz, Roderic Guigo, Stephen B Montgomery, Barbara E Stranger, Hae Kyung Im, Alexis Battle, View ORCID ProfileKristin G Ardlie, View ORCID ProfileTuuli Lappalainen
doi: https://doi.org/10.1101/787903
François Aguet
1The Broad Institute of MIT and Harvard, Cambridge, MA, USA
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  • ORCID record for François Aguet
  • For correspondence: francois@broadinstitute.org ana.vinuela@unige.ch kardlie@broadinstitute.org tlappalainen@nygenome.org
Alvaro N Barbeira
2Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
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Rodrigo Bonazzola
2Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
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Andrew Brown
3Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
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Stephane E Castel
4Population Health and Genomics, University of Dundee, Dundee, Scotland, UK
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Brian Jo
5New York Genome Center, New York, NY, USA
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Silva Kasela
4Population Health and Genomics, University of Dundee, Dundee, Scotland, UK
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Sarah Kim-Hellmuth
6Department of Systems Biology, Columbia University, New York, NY, USA
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Yanyu Liang
2Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
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Meritxell Oliva
2Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
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Princy E Parsana
7Department of Computer Science, Princeton University, Princeton, NJ, USA
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Elise Flynn
4Population Health and Genomics, University of Dundee, Dundee, Scotland, UK
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Laure Fresard
8Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, USA
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Eric R Gaamzon
9Statistical Genetics, Max Planck Institute of Psychiatry, Munich, Germany
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Andrew R Hamel
10Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
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Yuan He
7Department of Computer Science, Princeton University, Princeton, NJ, USA
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Farhad Hormozdiari
11Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
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Pejman Mohammadi
12Department of Pathology, Stanford University, Stanford, CA, USA
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Manuel Muñoz-Aguirre
13Data Science Institute, Vanderbilt University, Nashville, TN, USA
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YoSon Park
14Clare Hall, University of Cambridge, Cambridge, UK
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Ashis Saha
7Department of Computer Science, Princeton University, Princeton, NJ, USA
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Ayellet V Segrć
10Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
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Benjamin J Strober
7Department of Computer Science, Princeton University, Princeton, NJ, USA
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Xiaoquan Wen
15MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
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Valentin Wucher
13Data Science Institute, Vanderbilt University, Nashville, TN, USA
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Sayantan Das
15MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
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Diego Garrido-Martín
13Data Science Institute, Vanderbilt University, Nashville, TN, USA
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Nicole R Gay
8Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, USA
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Robert E Handsaker
16Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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Paul J Hoffman
17Ocular Genomics Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
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Seva Kashin
16Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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Alan Kwong
15MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
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Xiao Li
18Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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Daniel MacArthur
18Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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John M Rouhana
10Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
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Matthew Stephens
2Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
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Ellen Todres
1The Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Ana Viñuela
19Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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  • ORCID record for Ana Viñuela
  • For correspondence: francois@broadinstitute.org ana.vinuela@unige.ch kardlie@broadinstitute.org tlappalainen@nygenome.org
Gao Wang
20Scripps Research Translational Institute, La Jolla, CA, USA
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Yuxin Zou
20Scripps Research Translational Institute, La Jolla, CA, USA
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21Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
Christopher D Brown
14Clare Hall, University of Cambridge, Cambridge, UK
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Nancy Cox
9Statistical Genetics, Max Planck Institute of Psychiatry, Munich, Germany
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Emmanouil Dermitzakis
22Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
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Barbara E Engelhardt
5New York Genome Center, New York, NY, USA
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Gad Getz
18Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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Roderic Guigo
23Department of Statistics and Operations Research, Universitat Politècnica de Catalunya (UPC), Barcelona, Catalonia, Spain
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Stephen B Montgomery
24Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
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Barbara E Stranger
25Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
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Hae Kyung Im
2Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
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Alexis Battle
7Department of Computer Science, Princeton University, Princeton, NJ, USA
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Kristin G Ardlie
18Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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  • ORCID record for Kristin G Ardlie
  • For correspondence: francois@broadinstitute.org ana.vinuela@unige.ch kardlie@broadinstitute.org tlappalainen@nygenome.org
Tuuli Lappalainen
4Population Health and Genomics, University of Dundee, Dundee, Scotland, UK
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  • ORCID record for Tuuli Lappalainen
  • For correspondence: francois@broadinstitute.org ana.vinuela@unige.ch kardlie@broadinstitute.org tlappalainen@nygenome.org
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Abstract

The Genotype-Tissue Expression (GTEx) project was established to characterize genetic effects on the transcriptome across human tissues, and to link these regulatory mechanisms to trait and disease associations. Here, we present analyses of the v8 data, based on 17,382 RNA-sequencing samples from 54 tissues of 948 post-mortem donors. We comprehensively characterize genetic associations for gene expression and splicing in cis and trans, showing that regulatory associations are found for almost all genes, and describe the underlying molecular mechanisms and their contribution to allelic heterogeneity and pleiotropy of complex traits. Leveraging the large diversity of tissues, we provide insights into the tissue-specificity of genetic effects, and show that cell type composition is a key factor in understanding gene regulatory mechanisms in human tissues.

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  • https://www.gtexportal.com

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted October 03, 2019.
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The GTEx Consortium atlas of genetic regulatory effects across human tissues
François Aguet, Alvaro N Barbeira, Rodrigo Bonazzola, Andrew Brown, Stephane E Castel, Brian Jo, Silva Kasela, Sarah Kim-Hellmuth, Yanyu Liang, Meritxell Oliva, Princy E Parsana, Elise Flynn, Laure Fresard, Eric R Gaamzon, Andrew R Hamel, Yuan He, Farhad Hormozdiari, Pejman Mohammadi, Manuel Muñoz-Aguirre, YoSon Park, Ashis Saha, Ayellet V Segrć, Benjamin J Strober, Xiaoquan Wen, Valentin Wucher, Sayantan Das, Diego Garrido-Martín, Nicole R Gay, Robert E Handsaker, Paul J Hoffman, Seva Kashin, Alan Kwong, Xiao Li, Daniel MacArthur, John M Rouhana, Matthew Stephens, Ellen Todres, Ana Viñuela, Gao Wang, Yuxin Zou, The GTEx Consortium, Christopher D Brown, Nancy Cox, Emmanouil Dermitzakis, Barbara E Engelhardt, Gad Getz, Roderic Guigo, Stephen B Montgomery, Barbara E Stranger, Hae Kyung Im, Alexis Battle, Kristin G Ardlie, Tuuli Lappalainen
bioRxiv 787903; doi: https://doi.org/10.1101/787903
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The GTEx Consortium atlas of genetic regulatory effects across human tissues
François Aguet, Alvaro N Barbeira, Rodrigo Bonazzola, Andrew Brown, Stephane E Castel, Brian Jo, Silva Kasela, Sarah Kim-Hellmuth, Yanyu Liang, Meritxell Oliva, Princy E Parsana, Elise Flynn, Laure Fresard, Eric R Gaamzon, Andrew R Hamel, Yuan He, Farhad Hormozdiari, Pejman Mohammadi, Manuel Muñoz-Aguirre, YoSon Park, Ashis Saha, Ayellet V Segrć, Benjamin J Strober, Xiaoquan Wen, Valentin Wucher, Sayantan Das, Diego Garrido-Martín, Nicole R Gay, Robert E Handsaker, Paul J Hoffman, Seva Kashin, Alan Kwong, Xiao Li, Daniel MacArthur, John M Rouhana, Matthew Stephens, Ellen Todres, Ana Viñuela, Gao Wang, Yuxin Zou, The GTEx Consortium, Christopher D Brown, Nancy Cox, Emmanouil Dermitzakis, Barbara E Engelhardt, Gad Getz, Roderic Guigo, Stephen B Montgomery, Barbara E Stranger, Hae Kyung Im, Alexis Battle, Kristin G Ardlie, Tuuli Lappalainen
bioRxiv 787903; doi: https://doi.org/10.1101/787903

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