Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression.


Journal

Nature genetics
ISSN: 1546-1718
Titre abrégé: Nat Genet
Pays: United States
ID NLM: 9216904

Informations de publication

Date de publication:
09 2021
Historique:
received: 20 05 2020
accepted: 12 07 2021
pubmed: 4 9 2021
medline: 15 10 2021
entrez: 3 9 2021
Statut: ppublish

Résumé

Trait-associated genetic variants affect complex phenotypes primarily via regulatory mechanisms on the transcriptome. To investigate the genetics of gene expression, we performed cis- and trans-expression quantitative trait locus (eQTL) analyses using blood-derived expression from 31,684 individuals through the eQTLGen Consortium. We detected cis-eQTL for 88% of genes, and these were replicable in numerous tissues. Distal trans-eQTL (detected for 37% of 10,317 trait-associated variants tested) showed lower replication rates, partially due to low replication power and confounding by cell type composition. However, replication analyses in single-cell RNA-seq data prioritized intracellular trans-eQTL. Trans-eQTL exerted their effects via several mechanisms, primarily through regulation by transcription factors. Expression of 13% of the genes correlated with polygenic scores for 1,263 phenotypes, pinpointing potential drivers for those traits. In summary, this work represents a large eQTL resource, and its results serve as a starting point for in-depth interpretation of complex phenotypes.

Identifiants

pubmed: 34475573
doi: 10.1038/s41588-021-00913-z
pii: 10.1038/s41588-021-00913-z
pmc: PMC8432599
mid: NIHMS1723987
doi:

Substances chimiques

Blood Proteins 0

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

1300-1310

Subventions

Organisme : NIMH NIH HHS
ID : R01 MH109905
Pays : United States
Organisme : NIEHS NIH HHS
ID : R01 ES023834
Pays : United States
Organisme : NIEHS NIH HHS
ID : R01 ES020506
Pays : United States
Organisme : Wellcome Trust
ID : 201488/Z/16/Z
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : R01 CA107431
Pays : United States
Organisme : NIEHS NIH HHS
ID : R21 ES024834
Pays : United States
Organisme : Medical Research Council
ID : G9815508
Pays : United Kingdom
Organisme : NIEHS NIH HHS
ID : R35 ES028379
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH101814
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM108711
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG008150
Pays : United States
Organisme : Medical Research Council
ID : MC_PC_19009
Pays : United Kingdom
Organisme : NHLBI NIH HHS
ID : R01 HL105756
Pays : United States
Organisme : Medical Research Council
ID : MC_PC_15018
Pays : United Kingdom

Investigateurs

Peter A C 't Hoen (PAC)
Joyce van Meurs (J)
Jenny van Dongen (J)
Maarten van Iterson (M)
Morris A Swertz (MA)
Marc Jan Bonder (M)

Informations de copyright

© 2021. The Author(s), under exclusive licence to Springer Nature America, Inc.

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Auteurs

Urmo Võsa (U)

Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands. urmo.vosa@gmail.com.
Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia. urmo.vosa@gmail.com.

Annique Claringbould (A)

Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands. anniqueclaringbould@gmail.com.
Oncode Institute, Amsterdam, the Netherlands. anniqueclaringbould@gmail.com.
Structural & Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. anniqueclaringbould@gmail.com.

Harm-Jan Westra (HJ)

Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
Oncode Institute, Amsterdam, the Netherlands.

Marc Jan Bonder (MJ)

Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

Patrick Deelen (P)

Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
Oncode Institute, Amsterdam, the Netherlands.
Genomics Coordination Center, University Medical Centre Groningen, Groningen, the Netherlands.
Department of Genetics, University Medical Centre Utrecht, Utrecht, the Netherlands.

Biao Zeng (B)

School of Biological Sciences, Georgia Tech, Atlanta, GA, USA.

Holger Kirsten (H)

Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.
LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany.

Ashis Saha (A)

Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.

Roman Kreuzhuber (R)

Department of Haematology, University of Cambridge, Cambridge, United Kingdom.
NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom.
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom.

Seyhan Yazar (S)

Garvan Institute of Medical Research, Garvan-Weizmann Centre for Cellular Genomics, Sydney, New South Wales, Australia.

Harm Brugge (H)

Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
Oncode Institute, Amsterdam, the Netherlands.

Roy Oelen (R)

Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
Oncode Institute, Amsterdam, the Netherlands.

Dylan H de Vries (DH)

Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
Oncode Institute, Amsterdam, the Netherlands.

Monique G P van der Wijst (MGP)

Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
Oncode Institute, Amsterdam, the Netherlands.

Silva Kasela (S)

Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia.

Natalia Pervjakova (N)

Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia.

Isabel Alves (I)

Computational Biology, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
L'institut du thorax, Université de Nantes, CHU Nantes, INSERM, CNRS, Nantes, France.

Marie-Julie Favé (MJ)

Computational Biology, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.

Mawussé Agbessi (M)

Computational Biology, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.

Mark W Christiansen (MW)

Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA.

Rick Jansen (R)

Department of Psychiatry, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Public Health Research Institute and Amsterdam Neuroscience, Amsterdam, the Netherlands.

Ilkka Seppälä (I)

Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.

Lin Tong (L)

Department of Public Health Sciences, University of Chicago, Chicago, IL, USA.

Alexander Teumer (A)

Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany.
DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany.

Katharina Schramm (K)

Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.
Department of Medicine I, University Hospital Munich, Ludwig Maximilian's University, Munich, Germany.

Gibran Hemani (G)

MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom.

Joost Verlouw (J)

Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands.

Hanieh Yaghootkar (H)

Genetics of Complex Traits, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, United Kingdom.
School of Life Sciences, College of Liberal Arts and Science, University of Westminster, London, United Kingdom.
Division of Medical Sciences, Department of Health Sciences, Luleå University of Technology, Luleå, Sweden.

Reyhan Sönmez Flitman (R)

Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
Swiss Institute of Bioinformatics, Lausanne, Switzerland.

Andrew Brown (A)

Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.
Population Health and Genomics, University of Dundee, Dundee, United Kingdom.

Viktorija Kukushkina (V)

Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia.

Anette Kalnapenkis (A)

Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia.

Sina Rüeger (S)

Lausanne University Hospital, Lausanne, Switzerland.

Eleonora Porcu (E)

Lausanne University Hospital, Lausanne, Switzerland.

Jaanika Kronberg (J)

Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia.

Johannes Kettunen (J)

Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland.
Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.
Biocenter Oulu, University of Oulu, Oulu, Finland.
Finnish Institute for Health and Welfare, Helsinki, Finland.

Bernett Lee (B)

Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore.

Futao Zhang (F)

Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.

Ting Qi (T)

Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.

Jose Alquicira Hernandez (JA)

Garvan Institute of Medical Research, Garvan-Weizmann Centre for Cellular Genomics, Sydney, New South Wales, Australia.

Wibowo Arindrarto (W)

Leiden University Medical Center, Leiden, the Netherlands.

Frank Beutner (F)

Heart Center Leipzig, Universität Leipzig, Leipzig, Germany.

Julia Dmitrieva (J)

Unit of Animal Genomics, WELBIO, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.

Mahmoud Elansary (M)

Unit of Animal Genomics, WELBIO, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.

Benjamin P Fairfax (BP)

Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.

Michel Georges (M)

Unit of Animal Genomics, WELBIO, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.

Bastiaan T Heijmans (BT)

Leiden University Medical Center, Leiden, the Netherlands.

Alex W Hewitt (AW)

Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Hobart, Tasmania, Australia.
Centre for Eye Research Australia, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia.

Mika Kähönen (M)

Department of Clinical Physiology, Tampere University Hospital and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.

Yungil Kim (Y)

Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
Genetics and Genomic Science Department, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

Julian C Knight (JC)

Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.

Peter Kovacs (P)

IFB Adiposity Diseases, Universität Leipzig, Leipzig, Germany.

Knut Krohn (K)

Interdisciplinary Center for Clinical Research, Faculty of Medicine, Universität Leipzig, Leipzig, Germany.

Shuang Li (S)

Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
Genomics Coordination Center, University Medical Centre Groningen, Groningen, the Netherlands.

Markus Loeffler (M)

Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.
LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany.

Urko M Marigorta (UM)

School of Biological Sciences, Georgia Tech, Atlanta, GA, USA.
Integrative Genomics Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, Derio, Spain.
IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.

Hailang Mei (H)

Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands.

Yukihide Momozawa (Y)

Unit of Animal Genomics, WELBIO, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan.

Martina Müller-Nurasyid (M)

Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.
Department of Medicine I, University Hospital Munich, Ludwig Maximilian's University, Munich, Germany.
IBE, Faculty of Medicine, LMU Munich, Munich, Germany.

Matthias Nauck (M)

DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany.
Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany.

Michel G Nivard (MG)

Department of Biological Psychology, Faculty of Behaviour and Movement Sciences, Vrije Universiteit, Amsterdam, the Netherlands.

Brenda W J H Penninx (BWJH)

Department of Psychiatry, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Public Health Research Institute and Amsterdam Neuroscience, Amsterdam, the Netherlands.

Jonathan K Pritchard (JK)

Department of Biology, Stanford University, Stanford, CA, USA.
Department of Genetics, Stanford University, Stanford, CA, USA.

Olli T Raitakari (OT)

Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland.
Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland.
Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland.

Olaf Rotzschke (O)

Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore.

Eline P Slagboom (EP)

Leiden University Medical Center, Leiden, the Netherlands.

Coen D A Stehouwer (CDA)

Department of Internal Medicine and School for Cardiovascular Diseases (CARIM), Maastricht University Medical Center, Maastricht, the Netherlands.

Michael Stumvoll (M)

Department of Medicine, Universität Leipzig, Leipzig, Germany.

Patrick Sullivan (P)

Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.

Peter A C 't Hoen (PAC)

Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen, Nijmegen, the Netherlands.

Joachim Thiery (J)

LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany.
Institute for Laboratory Medicine, LIFE-Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany.

Anke Tönjes (A)

Department of Medicine, Universität Leipzig, Leipzig, Germany.

Jenny van Dongen (J)

Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam Public Health Research Institute and Amsterdam Neuroscience, Amsterdam, the Netherlands.

Maarten van Iterson (M)

Leiden University Medical Center, Leiden, the Netherlands.

Jan H Veldink (JH)

UMC Utrecht Brain Center, University Medical Center Utrecht, Department of Neurology, Utrecht University, Utrecht, the Netherlands.

Uwe Völker (U)

Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.

Robert Warmerdam (R)

Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
Oncode Institute, Amsterdam, the Netherlands.

Cisca Wijmenga (C)

Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.

Morris Swertz (M)

Genomics Coordination Center, University Medical Centre Groningen, Groningen, the Netherlands.

Anand Andiappan (A)

Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore.

Grant W Montgomery (GW)

Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.

Samuli Ripatti (S)

Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
Broad Institute of MIT and Harvard, Cambridge, MA, USA.

Markus Perola (M)

National Institute for Health and Welfare, University of Helsinki, Helsinki, Finland.

Zoltan Kutalik (Z)

Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland.

Emmanouil Dermitzakis (E)

Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.
Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland.

Sven Bergmann (S)

Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
Swiss Institute of Bioinformatics, Lausanne, Switzerland.

Timothy Frayling (T)

Genetics of Complex Traits, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, United Kingdom.

Joyce van Meurs (J)

Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands.

Holger Prokisch (H)

Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany.
Institute of Human Genetics, Technical University Munich, Munich, Germany.

Habibul Ahsan (H)

Department of Public Health Sciences, University of Chicago, Chicago, IL, USA.

Brandon L Pierce (BL)

Department of Public Health Sciences, University of Chicago, Chicago, IL, USA.

Terho Lehtimäki (T)

Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.

Dorret I Boomsma (DI)

Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam Public Health Research Institute and Amsterdam Neuroscience, Amsterdam, the Netherlands.

Bruce M Psaty (BM)

Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA, USA.

Sina A Gharib (SA)

Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA.
Department of Medicine, University of Washington, Seattle, WA, USA.

Philip Awadalla (P)

Computational Biology, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.

Lili Milani (L)

Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia.

Willem H Ouwehand (WH)

Department of Haematology, University of Cambridge, Cambridge, United Kingdom.
NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom.
Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom.

Kate Downes (K)

Department of Haematology, University of Cambridge, Cambridge, United Kingdom.
NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom.

Oliver Stegle (O)

Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom.
Division of Computational Genomics and Systems Genetics, German Cancer Research Center, Heidelberg, Germany.

Alexis Battle (A)

Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.

Peter M Visscher (PM)

Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.

Jian Yang (J)

Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
School of Life Sciences, Westlake University, Hangzhou, China.
Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.

Markus Scholz (M)

Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.
LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany.

Joseph Powell (J)

Garvan Institute of Medical Research, Garvan-Weizmann Centre for Cellular Genomics, Sydney, New South Wales, Australia.
UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, New South Wales, Australia.

Greg Gibson (G)

School of Biological Sciences, Georgia Tech, Atlanta, GA, USA.

Tõnu Esko (T)

Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia.

Lude Franke (L)

Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands. lude@ludesign.nl.
Oncode Institute, Amsterdam, the Netherlands. lude@ludesign.nl.

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