Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals

James J. Lee; Robbee Wedow; Aysu Okbay; Edward Kong; Omeed Maghzian; Meghan Zacher; Tuan Anh Nguyen-Viet; Peter Bowers; Julia Sidorenko; Richard Karlsson- Linnér; Mark Alan Fontana; Tushar Kundu; Chanwook Lee; Hui Li; Ruoxi Li; Rebecca Royer; Pascal N. Timshel; Raymond Walters; Emily A. Willoughby; Maris Alver; Yanchun Bao; David W. Clark; Felix R. Day; Nicholas A Furlotte; Peter K Joshi; Kathryn E. Kemper; Aaron Kleinman; Claudia Langenberg; Reedik Mägi; Joey W. Trampush; Shefali Setia Verma; Yang Wu; Max Lam; Jing Hua Zhao; Zhili Zheng; Jason D. Boardman; Harry Campbell; Jeremy Freese; Kathleen Mullan Harris; Caroline Hayward; Pamela Herd; Meena Kumari; Todd Lencz; Jian'an Luan; Anil K. Malhotra; Andres Metspalu; Lili Milani; Ken K Ong; John R B Perry; David J. Porteous; Marylyn D. Ritchie; Melissa C. Smart; Blair H. Smith; Joyce Y. Tung; Nicholas J Wareham; James F Wilson; Jonathan P Beauchamp; Dalton Conley; Tõnu Esko; Steven F. Lehrer; Patrik K. E. Magnusson; Sven Oskarsson; Tune H. Pers; Matthew R. Robinson; Kevin Thom; Chelsea Watson; Christopher F. Chabris; Michelle N Meyer; David Laibson; Jian Yang; Magnus Johannesson; Philipp D. Koellinger; Patrick Turley; Peter M. Visscher; Daniel J. Benjamin; David Cesarini; Loïc Yengo; 23Me Research Team; Cogent Cognitive Genomics Consorti; Social Science Genetic Association Consortium

doi:10.1038/s41588-018-0147-3

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Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals

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Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals

James J. Lee, Robbee Wedow, Aysu Okbay, Edward Kong, Omeed Maghzian, Meghan Zacher, Tuan Anh Nguyen-Viet, Peter Bowers, Julia Sidorenko, Richard Karlsson- Linnér, …

Nature Genetics, Vol.50(8), pp.1112-1121

2018-08

DOI: https://doi.org/10.1038/s41588-018-0147-3

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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Title: Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals
Creators - without role: James J. Lee - University of Minnesota Twin Cities (US)
Robbee Wedow - University of Colorado
Aysu Okbay - Vrije Universiteit Amsterdam (NL)
Edward Kong - Harvard University (US)
Omeed Maghzian - Harvard University (US)
Meghan Zacher - Harvard University (US)
Tuan Anh Nguyen-Viet - University of Southern California (US)
Peter Bowers - Harvard University (US)
Julia Sidorenko - University of Queensland (AU)
Richard Karlsson- Linnér - Erasmus University (NL)
Mark Alan Fontana - University of Southern California (US)
Tushar Kundu - University of Southern California (US)
Chanwook Lee - Harvard University (US)
Hui Li - Harvard University (US)
Ruoxi Li - University of Southern California (US)
Rebecca Royer - University of Southern California (US)
Pascal N. Timshel - Copenhagen University (DK)
Raymond Walters - Broad Institute
Emily A. Willoughby - University of Minnesota Twin Cities (US)
Maris Alver - University of Tartu
Yanchun Bao - University of Essex (GB)
David W. Clark - University of Edinburgh
Felix R. Day - Cambridge University (GB)
Nicholas A Furlotte - 23andMe
Peter K Joshi - University of Edinburgh
Kathryn E. Kemper - University of Queensland (AU)
Aaron Kleinman - 23andMe
Claudia Langenberg - Cambridge University (GB)
Reedik Mägi - University of Tartu
Joey W. Trampush - University of Southern California (US)
Shefali Setia Verma - Geisinger Health System
Yang Wu - University of Queensland (AU)
Max Lam - Institute of Mental Health
Jing Hua Zhao - University of Cambridge
Zhili Zheng - University of Queensland (AU)
Jason D. Boardman - University of Colorado
Harry Campbell - University of Edinburgh
Jeremy Freese - Stanford University (US)
Kathleen Mullan Harris - University of North Carolina
Caroline Hayward - University of Edinburgh
Pamela Herd - University of Essex (GB)
Meena Kumari - University of Essex (GB)
Todd Lencz - Hofstra Northwell School of Medicine
Jian'an Luan - Cambridge University (GB)
Anil K. Malhotra - Hofstra Northwell School of Medicine
Andres Metspalu - University of Tartu
Lili Milani - University of Tartu
Ken K Ong - University of Cambridge
John R B Perry - University of Cambridge
David J. Porteous - University of Edinburgh
Marylyn D. Ritchie - Geisinger Health System
Melissa C. Smart - University of Edinburgh
Blair H. Smith - University of Dundee
Joyce Y. Tung - 23andMe
Nicholas J Wareham - University of Cambridge
James F Wilson - University of Edinburgh
Jonathan P Beauchamp - University of Toronto (CA)
Dalton Conley - Princeton University (US)
Tõnu Esko - University of Tartu
Steven F. Lehrer - Queen's University
Patrik K. E. Magnusson - Karolinska Institutet (SE)
Sven Oskarsson - Uppsala University (SE)
Tune H. Pers - Copenhagen University (DK)
Matthew R. Robinson - University of Queensland (AU)
Kevin Thom - New York University
Chelsea Watson - University of Southern California (US)
Christopher F. Chabris - Geisinger Health System
Michelle N Meyer - Geisinger Health System
David Laibson - Harvard University (US)
Jian Yang - University of Queensland (AU)
Magnus Johannesson - Stockholm School of Economics, Department of Economics
Philipp D. Koellinger - Vrije Universiteit Amsterdam (NL)
Patrick Turley - Massachusetts General Hospital (US)
Peter M. Visscher - University of Queensland (AU)
Daniel J. Benjamin - University of Southern California (US)
David Cesarini - Center for Experimental Social Science
Loïc Yengo - University of Queensland (AU)
23Me Research Team
Cogent Cognitive Genomics Consorti
Social Science Genetic Association Consortium
Publication Details: Nature Genetics, Vol.50(8), pp.1112-1121
Publisher: Nature Research (part of Springer Nature)
Identifiers: 991001479407706056
Academic Unit: Department of Economics
Language: English
Resource Type: Journal article

Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals

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