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Unraveling the polygenic architecture of complex traits using blood eQTL metaanalysis

View ORCID ProfileUrmo Võsa, View ORCID ProfileAnnique Claringbould, Harm-Jan Westra, Marc Jan Bonder, Patrick Deelen, Biao Zeng, Holger Kirsten, Ashis Saha, Roman Kreuzhuber, Silva Kasela, Natalia Pervjakova, Isabel Alvaes, Marie-Julie Fave, Mawusse Agbessi, Mark Christiansen, Rick Jansen, Ilkka Seppälä, Lin Tong, Alexander Teumer, Katharina Schramm, Gibran Hemani, Joost Verlouw, Hanieh Yaghootkar, Reyhan Sönmez, Andrew Brown, Viktorija Kukushkina, Anette Kalnapenkis, Sina Rüeger, Eleonora Porcu, Jaanika Kronberg-Guzman, Johannes Kettunen, Joseph Powell, Bernett Lee, Futao Zhang, Wibowo Arindrarto, Frank Beutner, BIOS Consortium, Harm Brugge, i2QTL Consortium, Julia Dmitreva, Mahmoud Elansary, Benjamin P. Fairfax, Michel Georges, Bastiaan T. Heijmans, Mika Kähönen, Yungil Kim, Julian C. Knight, Peter Kovacs, Knut Krohn, Shuang Li, Markus Loeffler, Urko M. Marigorta, Hailang Mei, Yukihide Momozawa, Martina Müller-Nurasyid, Matthias Nauck, Michel Nivard, Brenda Penninx, Jonathan Pritchard, Olli Raitakari, Olaf Rotzchke, Eline P. Slagboom, Coen D.A. Stehouwer, Michael Stumvoll, Patrick Sullivan, Peter A.C. ‘t Hoen, Joachim Thiery, Anke Tönjes, Jenny van Dongen, Maarten van Iterson, Jan Veldink, Uwe Völker, Cisca Wijmenga, Morris Swertz, Anand Andiappan, Grant W. Montgomery, Samuli Ripatti, Markus Perola, Zoltan Kutalik, Emmanouil Dermitzakis, Sven Bergmann, Timothy Frayling, Joyce van Meurs, Holger Prokisch, Habibul Ahsan, Brandon Pierce, Terho Lehtimäki, Dorret Boomsma, Bruce M. Psaty, Sina A. Gharib, Philip Awadalla, Lili Milani, Willem Ouwehand, Kate Downes, Oliver Stegle, Alexis Battle, Jian Yang, Peter M. Visscher, Markus Scholz, Gregory Gibson, Tõnu Esko, View ORCID ProfileLude Franke
doi: https://doi.org/10.1101/447367
Urmo Võsa
1 Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
2 Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
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  • ORCID record for Urmo Võsa
  • For correspondence: urmo.vosa@gmail.com anniqueclaringbould@gmail.com ludefranke@gmail.com
Annique Claringbould
1 Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
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  • ORCID record for Annique Claringbould
  • For correspondence: urmo.vosa@gmail.com anniqueclaringbould@gmail.com ludefranke@gmail.com
Harm-Jan Westra
1 Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
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Marc Jan Bonder
1 Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
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Patrick Deelen
1 Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
3 Genomics Coordination Center, University Medical Centre Groningen, Groningen, The Netherlands
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Biao Zeng
4 School of Biological Sciences, Georgia Tech, Atlanta, United States of America
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Holger Kirsten
5 Institut für Medizinische InformatiK, Statistik und Epidemiologie, LIFE - Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany
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Ashis Saha
6 Department of Computer Science, Johns Hopkins University, Baltimore, United States of America
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Roman Kreuzhuber
7 Department of Haematology, University of Cambridge and NHS Blood and Transplant Cambridge Biomedical Campus, Cambridge, United Kingdom
8 European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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Silva Kasela
2 Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
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Natalia Pervjakova
2 Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
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Isabel Alvaes
9 Computational Biology, Ontario Institute for Cancer Research, Toronto, Canada
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Marie-Julie Fave
9 Computational Biology, Ontario Institute for Cancer Research, Toronto, Canada
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Mawusse Agbessi
9 Computational Biology, Ontario Institute for Cancer Research, Toronto, Canada
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Mark Christiansen
10 Cardiovascular Health Research Unit, University of Washington, Seattle, United States of America
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Rick Jansen
11 Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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Ilkka Seppälä
12 Department of Clinical Chemistry, Fimlab Laboratories and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
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Lin Tong
13 Department of Public Health Sciences, University of Chicago, Chicago, United States of America
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Alexander Teumer
14 Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
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Katharina Schramm
15 Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
16 Department of Medicine I, University Hospital Munich, Ludwig Maximilian’s University, München, Germany
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Gibran Hemani
17 MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
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Joost Verlouw
18 Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
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Hanieh Yaghootkar
19 Exeter Medical School, University of Exeter, Exeter, United Kingdom
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Reyhan Sönmez
20 Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
21 Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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Andrew Brown
22 Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
23 Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
21 Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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Viktorija Kukushkina
2 Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
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Anette Kalnapenkis
2 Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
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Sina Rüeger
24 Lausanne University Hospital, Lausanne, Switzerland
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Eleonora Porcu
24 Lausanne University Hospital, Lausanne, Switzerland
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Jaanika Kronberg-Guzman
2 Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
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Johannes Kettunen
25 University of Helsinki, Helsinki, Finland
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Joseph Powell
26 Garvan Institute of Medical Research, Garvan-Weizmann Centre for Cellular Genomics, Sydney, Australia
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Bernett Lee
27 Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
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Futao Zhang
28 Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
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Wibowo Arindrarto
29 Leiden University Medical Center, Leiden, The Netherlands
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Frank Beutner
30 Heart Center Leipzig, Universität Leipzig, Leipzig, Germany
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Harm Brugge
1 Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
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Julia Dmitreva
31 Unit of Animal Genomics, WELBIO, GIGA-R & Faculty of Veterinary Medicine, University of Liege, 1 Avenue de l’Hôpital, Liège 4000, Belgium
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Mahmoud Elansary
31 Unit of Animal Genomics, WELBIO, GIGA-R & Faculty of Veterinary Medicine, University of Liege, 1 Avenue de l’Hôpital, Liège 4000, Belgium
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Benjamin P. Fairfax
32 Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
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Michel Georges
31 Unit of Animal Genomics, WELBIO, GIGA-R & Faculty of Veterinary Medicine, University of Liege, 1 Avenue de l’Hôpital, Liège 4000, Belgium
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Bastiaan T. Heijmans
29 Leiden University Medical Center, Leiden, The Netherlands
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Mika Kähönen
33 Department of Clinical Physiology, Tampere University Hospital and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
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Yungil Kim
34 Department of Computer Science, Johns Hopkins University, Baltimore, United States of America
35 Genetics and Genomic Science Department, Icahn School of Medicine at Mount Sinai, New York, United States of America
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Julian C. Knight
32 Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
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36 IFB Adiposity Diseases, Universität Leipzig, Leipzig, Germany
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37 Interdisciplinary Center for Clinical Research, Faculty of Medicine, Universität Leipzig, Leipzig, Germany
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Shuang Li
1 Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
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Markus Loeffler
5 Institut für Medizinische InformatiK, Statistik und Epidemiologie, LIFE - Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany
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4 School of Biological Sciences, Georgia Tech, Atlanta, United States of America
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38 Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
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Yukihide Momozawa
31 Unit of Animal Genomics, WELBIO, GIGA-R & Faculty of Veterinary Medicine, University of Liege, 1 Avenue de l’Hôpital, Liège 4000, Belgium
39 Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
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Martina Müller-Nurasyid
15 Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
16 Department of Medicine I, University Hospital Munich, Ludwig Maximilian’s University, München, Germany
40 DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
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41 Institute of Clinical Chemistry and Laboratory Medicine, Greifswald University Hospital, Greifswald, Germany
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42 Faculty of Genes, Behavior and Health, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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11 Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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43 Stanford University, Stanford, United States of America
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44 Turku University Hospital and University of Turku, Turku, Finland
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27 Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
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29 Leiden University Medical Center, Leiden, The Netherlands
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45 Department of Internal Medicine, Maastricht University Medical Centre, Maastricht, The Netherlands
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46 Department of Medicine, Universität Leipzig, Leipzig, Germany
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47 Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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Peter A.C. ‘t Hoen
48 Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen, Nijmegen, The Netherlands
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49 Institute for Laboratory Medicine, LIFE - Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany
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46 Department of Medicine, Universität Leipzig, Leipzig, Germany
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11 Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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29 Leiden University Medical Center, Leiden, The Netherlands
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50 University Medical Center Utrecht, Utrecht, The Netherlands
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51 Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
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Cisca Wijmenga
1 Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
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3 Genomics Coordination Center, University Medical Centre Groningen, Groningen, The Netherlands
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27 Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
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52 Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
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Samuli Ripatti
53 Statistical and Translational Genetics, University of Helsinki, Helsinki, Finland
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54 National Institute for Health and Welfare, University of Helsinki, Helsinki, Finland
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Zoltan Kutalik
24 Lausanne University Hospital, Lausanne, Switzerland
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Emmanouil Dermitzakis
22 Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
23 Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
21 Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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Sven Bergmann
20 Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
21 Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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Timothy Frayling
19 Exeter Medical School, University of Exeter, Exeter, United Kingdom
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Joyce van Meurs
18 Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
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Holger Prokisch
55 Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
56 Institute of Human Genetics, Technical University Munich, Munich, Germany.
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Habibul Ahsan
13 Department of Public Health Sciences, University of Chicago, Chicago, United States of America
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Brandon Pierce
13 Department of Public Health Sciences, University of Chicago, Chicago, United States of America
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Terho Lehtimäki
12 Department of Clinical Chemistry, Fimlab Laboratories and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
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Dorret Boomsma
11 Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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Bruce M. Psaty
10 Cardiovascular Health Research Unit, University of Washington, Seattle, United States of America
57 Kaiser Permanente Washington Health Research Institute, Seattle, WA, United States of America
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Sina A. Gharib
58 Department of Medicine, University of Washington, Seattle, United States of America
10 Cardiovascular Health Research Unit, University of Washington, Seattle, United States of America
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Philip Awadalla
9 Computational Biology, Ontario Institute for Cancer Research, Toronto, Canada
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Lili Milani
2 Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
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Willem Ouwehand
7 Department of Haematology, University of Cambridge and NHS Blood and Transplant Cambridge Biomedical Campus, Cambridge, United Kingdom
59 Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton Cambridge, United Kingdom
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Kate Downes
7 Department of Haematology, University of Cambridge and NHS Blood and Transplant Cambridge Biomedical Campus, Cambridge, United Kingdom
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Oliver Stegle
8 European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
60 Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
61 Division of Computational Genomics and Systems Genetics, German Cancer Research Center, 69120 Heidelberg, Germany
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Alexis Battle
62 Departments of Biomedical Engineering and Computer Science, Johns Hopkins University, Baltimore, United States of America
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Jian Yang
28 Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
63 Institute for Advanced Research, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
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Peter M. Visscher
28 Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
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Markus Scholz
5 Institut für Medizinische InformatiK, Statistik und Epidemiologie, LIFE - Leipzig Research Center for Civilization Diseases, Universität Leipzig, Leipzig, Germany
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Gregory Gibson
4 School of Biological Sciences, Georgia Tech, Atlanta, United States of America
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Tõnu Esko
2 Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
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Lude Franke
1 Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
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  • ORCID record for Lude Franke
  • For correspondence: urmo.vosa@gmail.com anniqueclaringbould@gmail.com ludefranke@gmail.com
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Abstract

Summary While many disease-associated variants have been identified through genome-wide association studies, their downstream molecular consequences remain unclear.

To identify these effects, we performed cis- and trans-expression quantitative trait locus (eQTL) analysis in blood from 31,684 individuals through the eQTLGen Consortium.

We observed that cis-eQTLs can be detected for 88% of the studied genes, but that they have a different genetic architecture compared to disease-associated variants, limiting our ability to use cis-eQTLs to pinpoint causal genes within susceptibility loci.

In contrast, trans-eQTLs (detected for 37% of 10,317 studied trait-associated variants) were more informative. Multiple unlinked variants, associated to the same complex trait, often converged on trans-genes that are known to play central roles in disease etiology.

We observed the same when ascertaining the effect of polygenic scores calculated for 1,263 genome-wide association study (GWAS) traits. Expression levels of 13% of the studied genes correlated with polygenic scores, and many resulting genes are known to drive these traits.

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Posted October 19, 2018.
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Unraveling the polygenic architecture of complex traits using blood eQTL metaanalysis
Urmo Võsa, Annique Claringbould, Harm-Jan Westra, Marc Jan Bonder, Patrick Deelen, Biao Zeng, Holger Kirsten, Ashis Saha, Roman Kreuzhuber, Silva Kasela, Natalia Pervjakova, Isabel Alvaes, Marie-Julie Fave, Mawusse Agbessi, Mark Christiansen, Rick Jansen, Ilkka Seppälä, Lin Tong, Alexander Teumer, Katharina Schramm, Gibran Hemani, Joost Verlouw, Hanieh Yaghootkar, Reyhan Sönmez, Andrew Brown, Viktorija Kukushkina, Anette Kalnapenkis, Sina Rüeger, Eleonora Porcu, Jaanika Kronberg-Guzman, Johannes Kettunen, Joseph Powell, Bernett Lee, Futao Zhang, Wibowo Arindrarto, Frank Beutner, BIOS Consortium, Harm Brugge, i2QTL Consortium, Julia Dmitreva, Mahmoud Elansary, Benjamin P. Fairfax, Michel Georges, Bastiaan T. Heijmans, Mika Kähönen, Yungil Kim, Julian C. Knight, Peter Kovacs, Knut Krohn, Shuang Li, Markus Loeffler, Urko M. Marigorta, Hailang Mei, Yukihide Momozawa, Martina Müller-Nurasyid, Matthias Nauck, Michel Nivard, Brenda Penninx, Jonathan Pritchard, Olli Raitakari, Olaf Rotzchke, Eline P. Slagboom, Coen D.A. Stehouwer, Michael Stumvoll, Patrick Sullivan, Peter A.C. ‘t Hoen, Joachim Thiery, Anke Tönjes, Jenny van Dongen, Maarten van Iterson, Jan Veldink, Uwe Völker, Cisca Wijmenga, Morris Swertz, Anand Andiappan, Grant W. Montgomery, Samuli Ripatti, Markus Perola, Zoltan Kutalik, Emmanouil Dermitzakis, Sven Bergmann, Timothy Frayling, Joyce van Meurs, Holger Prokisch, Habibul Ahsan, Brandon Pierce, Terho Lehtimäki, Dorret Boomsma, Bruce M. Psaty, Sina A. Gharib, Philip Awadalla, Lili Milani, Willem Ouwehand, Kate Downes, Oliver Stegle, Alexis Battle, Jian Yang, Peter M. Visscher, Markus Scholz, Gregory Gibson, Tõnu Esko, Lude Franke
bioRxiv 447367; doi: https://doi.org/10.1101/447367
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Unraveling the polygenic architecture of complex traits using blood eQTL metaanalysis
Urmo Võsa, Annique Claringbould, Harm-Jan Westra, Marc Jan Bonder, Patrick Deelen, Biao Zeng, Holger Kirsten, Ashis Saha, Roman Kreuzhuber, Silva Kasela, Natalia Pervjakova, Isabel Alvaes, Marie-Julie Fave, Mawusse Agbessi, Mark Christiansen, Rick Jansen, Ilkka Seppälä, Lin Tong, Alexander Teumer, Katharina Schramm, Gibran Hemani, Joost Verlouw, Hanieh Yaghootkar, Reyhan Sönmez, Andrew Brown, Viktorija Kukushkina, Anette Kalnapenkis, Sina Rüeger, Eleonora Porcu, Jaanika Kronberg-Guzman, Johannes Kettunen, Joseph Powell, Bernett Lee, Futao Zhang, Wibowo Arindrarto, Frank Beutner, BIOS Consortium, Harm Brugge, i2QTL Consortium, Julia Dmitreva, Mahmoud Elansary, Benjamin P. Fairfax, Michel Georges, Bastiaan T. Heijmans, Mika Kähönen, Yungil Kim, Julian C. Knight, Peter Kovacs, Knut Krohn, Shuang Li, Markus Loeffler, Urko M. Marigorta, Hailang Mei, Yukihide Momozawa, Martina Müller-Nurasyid, Matthias Nauck, Michel Nivard, Brenda Penninx, Jonathan Pritchard, Olli Raitakari, Olaf Rotzchke, Eline P. Slagboom, Coen D.A. Stehouwer, Michael Stumvoll, Patrick Sullivan, Peter A.C. ‘t Hoen, Joachim Thiery, Anke Tönjes, Jenny van Dongen, Maarten van Iterson, Jan Veldink, Uwe Völker, Cisca Wijmenga, Morris Swertz, Anand Andiappan, Grant W. Montgomery, Samuli Ripatti, Markus Perola, Zoltan Kutalik, Emmanouil Dermitzakis, Sven Bergmann, Timothy Frayling, Joyce van Meurs, Holger Prokisch, Habibul Ahsan, Brandon Pierce, Terho Lehtimäki, Dorret Boomsma, Bruce M. Psaty, Sina A. Gharib, Philip Awadalla, Lili Milani, Willem Ouwehand, Kate Downes, Oliver Stegle, Alexis Battle, Jian Yang, Peter M. Visscher, Markus Scholz, Gregory Gibson, Tõnu Esko, Lude Franke
bioRxiv 447367; doi: https://doi.org/10.1101/447367

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