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Lee JJ, Wedow R, Okbay A, Kong E, Maghzian O, Zacher M, Nguyen-Viet TA, Bowers P, Sidorenko J, Karlsson Linnér R, Fontana MA, Kundu T, Lee C, Li H, Li R, Royer R, Timshel PN, Walters RK, Willoughby EA, Yengo L, Alver M, Bao Y, Clark DW, Day FR, Furlotte NA, Joshi PK, Kemper KE, Kleinman A, Langenberg C, Mägi R, Trampush JW, Verma SS, Wu Y, Lam M, Zhao JH, Zheng Z, Boardman JD, Campbell H, Freese J, Harris KM, Hayward C, Herd P, Kumari M, Lencz T, Luan J, Malhotra AK, Metspalu A, Milani L, Ong KK, Perry JRB, Porteous DJ, Ritchie MD, Smart MC, Smith BH, Tung JY, Wareham NJ, Wilson JF, Beauchamp JP, Conley DC, Esko T, Lehrer SF, Magnusson PKE, Oskarsson S, Pers TH, Robinson MR, Thom K, Watson C, Chabris CF, Meyer MN, Laibson DI, Yang J, Johannesson M, Koellinger PD, Turley P, Visscher PM, Benjamin DJ, Cesarini D. Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals. Nat Genet 2018; 50:1112-1121. [PMID: 30038396 PMCID: PMC6393768 DOI: 10.1038/s41588-018-0147-3] [Citation(s) in RCA: 1278] [Impact Index Per Article: 213.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 04/30/2018] [Indexed: 02/06/2023]
Abstract
Here we conducted a large-scale genetic association analysis of educational attainment in a sample of approximately 1.1 million individuals and identify 1,271 independent genome-wide-significant SNPs. For the SNPs taken together, we found evidence of heterogeneous effects across environments. The SNPs implicate genes involved in brain-development processes and neuron-to-neuron communication. In a separate analysis of the X chromosome, we identify 10 independent genome-wide-significant SNPs and estimate a SNP heritability of around 0.3% in both men and women, consistent with partial dosage compensation. A joint (multi-phenotype) analysis of educational attainment and three related cognitive phenotypes generates polygenic scores that explain 11-13% of the variance in educational attainment and 7-10% of the variance in cognitive performance. This prediction accuracy substantially increases the utility of polygenic scores as tools in research.
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Affiliation(s)
- James J Lee
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Robbee Wedow
- Department of Sociology, University of Colorado Boulder, Boulder, CO, USA
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Institute of Behavioral Science, University of Colorado Boulder, Boulder, CO, USA
| | - Aysu Okbay
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
- Department of Economics, School of Business and Economics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - Edward Kong
- Department of Economics, Harvard University, Cambridge, MA, USA
| | - Omeed Maghzian
- Department of Economics, Harvard University, Cambridge, MA, USA
| | - Meghan Zacher
- Department of Sociology, Harvard University, Cambridge, MA, USA
| | - Tuan Anh Nguyen-Viet
- Center for Economic and Social Research, University of Southern California, Los Angeles, CA, USA
| | - Peter Bowers
- Department of Economics, Harvard University, Cambridge, MA, USA
| | - Julia Sidorenko
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Richard Karlsson Linnér
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Economics, School of Business and Economics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Institute for Behavior and Biology, Erasmus University Rotterdam, Rotterdam, The Netherlands
| | - Mark Alan Fontana
- Center for Economic and Social Research, University of Southern California, Los Angeles, CA, USA
- Center for the Advancement of Value in Musculoskeletal Care, Hospital for Special Surgery, New York, NY, USA
| | - Tushar Kundu
- Center for Economic and Social Research, University of Southern California, Los Angeles, CA, USA
| | - Chanwook Lee
- Department of Economics, Harvard University, Cambridge, MA, USA
| | - Hui Li
- Department of Economics, Harvard University, Cambridge, MA, USA
| | - Ruoxi Li
- Center for Economic and Social Research, University of Southern California, Los Angeles, CA, USA
| | - Rebecca Royer
- Center for Economic and Social Research, University of Southern California, Los Angeles, CA, USA
| | - Pascal N Timshel
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen, Denmark
- Statens Serum Institut, Department of Epidemiology Research, Copenhagen, Denmark
| | - Raymond K Walters
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emily A Willoughby
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Loïc Yengo
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Maris Alver
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Yanchun Bao
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | - David W Clark
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Felix R Day
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | | | - Peter K Joshi
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- Institute of Social and Preventive Medicine, University Hospital of Lausanne, Lausanne, Switzerland
| | - Kathryn E Kemper
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | | | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Joey W Trampush
- BrainWorkup, LLC, Santa Monica, CA, USA
- Department of Psychiatry and Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shefali Setia Verma
- Department of Biomedical and Translational Informatics, Geisinger Health System, Danville, PA, USA
| | - Yang Wu
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Max Lam
- Institute of Mental Health, Singapore, Singapore
- Genome Institute, Singapore, Singapore
| | - Jing Hua Zhao
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Zhili Zheng
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
- The Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, China
| | - Jason D Boardman
- Department of Sociology, University of Colorado Boulder, Boulder, CO, USA
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Institute of Behavioral Science, University of Colorado Boulder, Boulder, CO, USA
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Jeremy Freese
- Department of Sociology, Stanford University, Stanford, CA, USA
| | - Kathleen Mullan Harris
- Department of Sociology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Pamela Herd
- Institute for Social and Economic Research, University of Essex, Colchester, UK
- La Follette School of Public Affairs, University of Wisconsin-Madison, Madison, WI, USA
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | - Todd Lencz
- Departments of Psychiatry and Molecular Medicine, Hofstra Northwell School of Medicine, Hempstead, NY, USA
- Center for Psychiatric Neuroscience, Feinstein Institute for Medical Research, Manhasset, NY, USA
- Psychiatry Research, The Zucker Hillside Hospital, Glen Oaks, CA, USA
| | - Jian'an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Anil K Malhotra
- Departments of Psychiatry and Molecular Medicine, Hofstra Northwell School of Medicine, Hempstead, NY, USA
- Center for Psychiatric Neuroscience, Feinstein Institute for Medical Research, Manhasset, NY, USA
- Psychiatry Research, The Zucker Hillside Hospital, Glen Oaks, CA, USA
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Ken K Ong
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - John R B Perry
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Marylyn D Ritchie
- Department of Biomedical and Translational Informatics, Geisinger Health System, Danville, PA, USA
| | - Melissa C Smart
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Blair H Smith
- Division of Population Health Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
- Medical Research Institute, University of Dundee, Dundee, UK
| | | | - Nicholas J Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - James F Wilson
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | | | - Dalton C Conley
- Department of Sociology, Princeton University, Princeton, NJ, USA
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Steven F Lehrer
- School of Policy Studies, Queen's University, Kingston, Ontario, Canada
- Department of Economics, New York University Shanghai, Pudong, Shanghai, China
- National Bureau of Economic Research, Cambridge, MA, USA
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Sven Oskarsson
- Department of Government, Uppsala University, Uppsala, Sweden
| | - Tune H Pers
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen, Denmark
- Statens Serum Institut, Department of Epidemiology Research, Copenhagen, Denmark
| | - Matthew R Robinson
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Kevin Thom
- Department of Economics, New York University, New York, NY, USA
| | - Chelsea Watson
- Center for Economic and Social Research, University of Southern California, Los Angeles, CA, USA
| | - Christopher F Chabris
- Autism and Developmental Medicine Institute, Geisinger Health System, Lewisburg, PA, USA
| | - Michelle N Meyer
- Center for Translational Bioethics and Health Care Policy, Geisinger Health System, Danville, PA, USA
| | - David I Laibson
- Department of Economics, Harvard University, Cambridge, MA, USA
| | - Jian Yang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Magnus Johannesson
- Department of Economics, Stockholm School of Economics, Stockholm, Sweden
| | - Philipp D Koellinger
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Economics, School of Business and Economics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Institute for Behavior and Biology, Erasmus University Rotterdam, Rotterdam, The Netherlands
| | - Patrick Turley
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia.
| | - Daniel J Benjamin
- Center for Economic and Social Research, University of Southern California, Los Angeles, CA, USA.
- National Bureau of Economic Research, Cambridge, MA, USA.
- Department of Economics, University of Southern California, Los Angeles, CA, USA.
| | - David Cesarini
- National Bureau of Economic Research, Cambridge, MA, USA
- Department of Economics, New York University, New York, NY, USA
- Center for Experimental Social Science, New York University, New York, NY, USA
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