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Genome-wide association study identifies 74 loci associated with educational attainment

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Okbay, Aysu, Beauchamp, Jonathan P., Fontana, Mark Alan, Lee, James J., Pers, Tune H., Rietveld, Cornelius A., Turley, Patrick, Chen, Guo-Bo +248 more·2016·Nature

Abstract

A genome-wide association study in 293,723 individuals identifies 74 genetic variants associated with educational attainment, which, although only explaining a small proportion of the variation in educational attainment, highlights candidate genes and pathways for further study. The level of educational attainment as measured by years of schooling completed, while strongly influenced by social and environmental factors, has also been shown to have a smaller genetic contribution. Philipp Koellinger, Peter Visscher and colleagues from the Social Science Genetic Association Consortium (SSGAC) now report a genome-wide association study in 293,723 individuals identifying 74 genetic variants associated with level of educational attainment. Although the genetic associations explain only a small proportion of the variation in educational attainment, they highlight candidate genes and pathways for further study. Educational attainment is strongly influenced by social and other environmental factors, but genetic factors are estimated to account for at least 20% of the variation across individuals1. Here we report the results of a genome-wide association study (GWAS) for educational attainment that extends our earlier discovery sample1,2 of 101,069 individuals to 293,723 individuals, and a replication study in an independent sample of 111,349 individuals from the UK Biobank. We identify 74 genome-wide significant loci associated with the number of years of schooling completed. Single-nucleotide polymorphisms associated with educational attainment are disproportionately found in genomic regions regulating gene expression in the fetal brain. Candidate genes are preferentially expressed in neural tissue, especially during the prenatal period, and enriched for biological pathways involved in neural development. Our findings demonstrate that, even for a behavioural phenotype that is mostly environmentally determined, a well-powered GWAS identifies replicable associated genetic variants that suggest biologically relevant pathways. Because educational attainment is measured in large numbers of individuals, it will continue to be useful as a proxy phenotype in efforts to characterize the genetic influences of related phenotypes, including cognition and neuropsychiatric diseases.

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  • Of the 162 lead SNPs identified at genome-wide significance in Okbay et al.'s pooled meta-analysis, 158 pass quality-control filters in our updated meta-analysis.

    “Of the 162 SNPs, 158 pass quality-control filters in our updated meta-analysis.”

    From Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals (2018) · cites this paper as Okbay et al. [10]

    The paper states that its meta-analysis identified 74 approximately independent genome-wide significant loci, with one lead SNP defined for each locus (Abstract; page unavailable). It does not report 162 lead SNPs. The statement that 158 passed filters in the citing authors’ updated meta-analysis describes their own analysis, not a result attributed to this source. (LLM, conf=0.88)

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  • Okbay et al. found positive genetic correlations between EduYears and intracranial volume, bipolar disorder, schizophrenia, cognitive performance, and height and negative genetic correlations between EduYears and Alzheimer's disease, neuroticism and body mass index in the EUR population.

    “Okbay et al. investigated the genetic correlation of EduYears with 14 traits and found positive genetic correlations between EduYears and intracranial volume, bipolar disorder, schizophrenia, cognitive performance, and height and negative genetic correlations between EduYears and Alzheimer’s disease, neuroticism and body mass index in the EUR population9.”

    From Shared genetic architectures of educational attainment in East Asian and European populations (2024) · cites this paper as [9]

    Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

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  • At the standard false discovery rate threshold of 5%, DEPICT prioritizes 1,838 genes, a tenfold increase relative to the earlier GWAS of EduYears.

    “At the standard false discovery rate (FDR) threshold of 5%, the bioinformatics tool DEPICT19 prioritizes 1,838 genes (Supplementary Table 7), a tenfold increase relative to the DEPICT results from an earlier GWAS of EduYears10.”

    From Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals (2018) · cites this paper as [10]

    Extended Data Figure 9 documents DEPICT-prioritized genes for EduYears, supporting the identification of this paper as an earlier DEPICT analysis. Our copy does not give the earlier gene count or establish the claimed tenfold comparison; the 1,838 genes are presented as the citing study’s result, not this source’s. (LLM, conf=0.78)

    Experimental — accuracy not yet measured
  • The 162 single-SNP associations from the largest previous study replicate in the subsample of our data (N = 726,808) at a rate closely matching theoretical projections from our Bayesian framework.

    “In the subsample of our data (N = 726,808) that did not contribute to the earlier study’s analyses, the SNPs replicate at a rate that closely matches theoretical projections derived from our Bayesian framework (Supplementary Figure 3).”

    From Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals (2018) · cites this paper as [10]

    The paper’s replication discussion (page unavailable in our copy) reports that SNPs from a previous educational-attainment study replicated in new cohorts, and compares replication of its 74 lead SNPs with expected numbers. Extended Data Figure 4 gives a replication sample of N = 111,349. These passages do not support the claimed 162 associations, N = 726,808 subsample, or projections from the citing authors’ Bayesian framework. (LLM, conf=0.84)

    Experimental — accuracy not yet measured
  • The largest previous GWAS of educational attainment (N = 293,723) identified 74 approximately independent SNPs at genome-wide significance.

    “The largest (N = 293,723) GWAS of EA to date identified 74 approximately independent SNPs at genome-wide significance (hereafter, lead SNPs)”

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Okbay, A., Beauchamp, J. P., Fontana, M. A., Lee, J. J., Pers, T. H., Rietveld, C. A., Turley, P., Chen, G.-B., Emilsson, V., Meddens, S. F. W., Oskarsson, S., Pickrell, J. K., Thom, K., Timshel, P., de Vlaming, R., Abdellaoui, A., Ahluwalia, T. S., Bacelis, J., Baumbach, C., Bjornsdottir, G., Brandsma, J. H., Pina Concas, M., Derringer, J., Furlotte, N. A., Galesloot, T. E., Girotto, G., Gupta, R., Hall, L. M., Harris, S. E., Hofer, E., Horikoshi, M., Huffman, J. E., Kaasik, K., Kalafati, I. P., Karlsson, R., Kong, A., Lahti, J., Lee, S. J. V. D., deLeeuw, C., Lind, P. A., Lindgren, K.-O., Liu, T., Mangino, M., Marten, J., Mihailov, E., Miller, M. B., van der Most, P. J., Oldmeadow, C., Payton, A., Pervjakova, N., Peyrot, W. J., Qian, Y., Raitakari, O., Rueedi, R., Salvi, E., Schmidt, B., Schraut, K. E., Shi, J., Smith, A. V., Poot, R. A., St Pourcain, B., Teumer, A., Thorleifsson, G., Verweij, N., Vuckovic, D., Wellmann, J., Westra, H.-J., Yang, J., Zhao, W., Zhu, Z., Alizadeh, B. Z., Amin, N., Bakshi, A., Baumeister, S. E., Biino, G., Bønnelykke, K., Boyle, P. A., Campbell, H., Cappuccio, F. P., Davies, G., De Neve, J.-E., Deloukas, P., Demuth, I., Ding, J., Eibich, P., Eisele, L., Eklund, N., Evans, D. M., Faul, J. D., Feitosa, M. F., Forstner, A. J., Gandin, I., Gunnarsson, B., Halldórsson, B. V., Harris, T. B., Heath, A. C., Hocking, L. J., Holliday, E. G., Homuth, G., Horan, M. A., Hottenga, J.-J., de Jager, P. L., Joshi, P. K., Jugessur, A., Kaakinen, M. A., Kähönen, M., Kanoni, S., Keltigangas-Järvinen, L., Kiemeney, L. A. L. M., Kolcic, I., Koskinen, S., Kraja, A. T., Kroh, M., Kutalik, Z., Latvala, A., Launer, L. J., Lebreton, M. P., Levinson, D. F., Lichtenstein, P., Lichtner, P., Liewald, D. C. M., Cohort Study, L., Loukola, A., Madden, P. A., Mägi, R., Mäki-Opas, T., Marioni, R. E., Marques-Vidal, P., Meddens, G. A., McMahon, G., Meisinger, C., Meitinger, T., Milaneschi, Y., Milani, L., Montgomery, G. W., Myhre, R., Nelson, C. P., Nyholt, D. R., Ollier, W. E. R., Palotie, A., Paternoster, L., Pedersen, N. L., Petrovic, K. E., Porteous, D. J., Räikkönen, K., Ring, S. M., Robino, A., Rostapshova, O., Rudan, I., Rustichini, A., Salomaa, V., Sanders, A. R., Sarin, A.-P., Schmidt, H., Scott, R. J., Smith, B. H., Smith, J. A., Staessen, J. A., Steinhagen-Thiessen, E., Strauch, K., Terracciano, A., Tobin, M. D., Ulivi, S., Vaccargiu, S., Quaye, L., van Rooij, F. J. A., Venturini, C., Vinkhuyzen, A. A. E., Völker, U., Völzke, H., Vonk, J. M., Vozzi, D., Waage, J., Ware, E. B., Willemsen, G., Attia, J. R., Bennett, D. A., Berger, K., Bertram, L., Bisgaard, H., Boomsma, D. I., Borecki, I. B., Bültmann, U., Chabris, C. F., Cucca, F., Cusi, D., Deary, I. J., Dedoussis, G. V., van Duijn, C. M., Eriksson, J. G., Franke, B., Franke, L., Gasparini, P., Gejman, P. V., Gieger, C., Grabe, H.-J., Gratten, J., Groenen, P. J. F., Gudnason, V., van der Harst, P., Hayward, C., Hinds, D. A., Hoffmann, W., Hyppönen, E., Iacono, W. G., Jacobsson, B., Järvelin, M.-R., Jöckel, K.-H., Kaprio, J., Kardia, S. L. R., Lehtimäki, T., Lehrer, S. F., Magnusson, P. K. E., Martin, N. G., McGue, M., Metspalu, A., Pendleton, N., Penninx, B. W. J. H., Perola, M., Pirastu, N., Pirastu, M., Polasek, O., Posthuma, D., Power, C., Province, M. A., Samani, N. J., Schlessinger, D., Schmidt, R., Sørensen, T. I. A., Spector, T. D., Stefansson, K., Thorsteinsdottir, U., Thurik, A. R., Timpson, N. J., Tiemeier, H., Tung, J. Y., Uitterlinden, A. G., Vitart, V., Vollenweider, P., Weir, D. R., Wilson, J. F., Wright, A. F., Conley, D. C., Krueger, R. F., Davey Smith, G., Hofman, A., Laibson, D. I., Medland, S. E., Meyer, M. N., Yang, J., Johannesson, M., Visscher, P. M., Esko, T., Koellinger, P. D., Cesarini, D., & Benjamin, D. J.
Affiliations
  • Erasmus MC (NL)
  • Harvard University (US)
  • University of Southern California (US)
  • University of Minnesota (US)
  • Statens Serum Institut (DK)
  • The University of Queensland (AU)
  • University of Iceland (IS)
  • Vrije Universiteit Amsterdam (NL)
  • Uppsala University (SE)
  • New York Genome Center (US)
  • New York University (US)
  • Broad Institute (US)
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  • Helmholtz Munich (DE)
  • University of Illinois Urbana-Champaign (US)
  • 23andMe (United States) (US)
  • Radboud University Medical Center (NL)
  • University of Trieste (IT)
  • University of Helsinki (FI)
  • University of Leicester (GB)
  • University of Edinburgh (GB)
  • Medical University of Graz (AT)
  • Centre for Human Genetics (GB)
  • Institute of Genetics and Cancer (GB)
  • Harokopio University of Athens (GR)
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  • Max Planck Institute for Human Development (DE)
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  • Finnish Institute for Health and Welfare (FI)
  • GGZ inGeest (NL)
  • National Institute on Aging (US)
  • University of Turku (FI)
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  • National Cancer Institute (US)
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  • Washington University in St. Louis (US)
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  • Stanford University (US)
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  • Endeavor Health (US)
  • University of Graz (AT)
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  • Institute for Integrative and Experimental Genomics (DE)
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  • Erasmus University Rotterdam (NL)
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  • Oulu University Hospital (FI)
  • Queen's University (CA)
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  • Union Graduate College (US)
  • Stockholm School of Economics (SE)
Corresponding author
  • Visscher, Peter M.
  • Koellinger, Philipp D.
  • Cesarini, David
  • Benjamin, Daniel J.
ORCID
Venue
Nature
Published
2016-05-11
Volume
533
Issue
7604
Pages
539-542
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
OpenAlex
W2346626662
Cited by
1,297
References
16
Citations by year
2026: 44 · 2025: 81 · 2024: 88 · 2023: 110 · 2022: 119 · 2021: 130 · 2020: 190 · 2019: 170 · 2018: 176 · 2017: 140 · 2016: 48
FWCI
143.64
Type
journal article
Language
en
Open access
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Funders
  • Brigham and Women's Hospital
  • Massachusetts General Hospital
  • Florida State University
  • University of Minnesota
  • Helsingin Yliopisto
  • New York University Shanghai
  • University of Dundee
  • Queen Mary University of London
  • NorthShore University HealthSystem
  • QIMR Berghofer Medical Research Institute
  • Broad Institute
  • York University
  • National Institute for Health and Care Research (NF-SI-0514-10027)
  • University of Leicester
  • Imperial College London
  • University of Oxford
  • University of Manchester
  • University of Aberdeen
  • Hunter Medical Research Institute
  • Rijksuniversiteit Groningen
  • University of South Australia
  • Universiteit van Amsterdam
  • Erasmus Universiteit Rotterdam
  • Universiteit Maastricht
  • Erasmus Medisch Centrum
  • Queen's University
  • Lundbeckfonden (R163-2013-16235, R190 2014-3904)
  • King Abdulaziz University (21589)
  • Universität zu Lübeck
  • Vetenskapsrådet (421-2013-1061)
  • Tampereen Yliopisto
  • Consiglio Nazionale delle Ricerche
  • Universitair Medisch Centrum Groningen
  • Oulun Yliopisto
  • Centre Hospitalier Universitaire Vaudois
  • Rheinische Friedrich-Wilhelms-Universität Bonn
  • Tays
  • Terveyden ja hyvinvoinnin laitos
  • Háskólinn í Reykjavík
  • National Institutes of Health (AG042568)
  • School of Medicine, New York University
  • Stanley Center for Psychiatric Research, Broad Institute
  • Medical Research Council (MR/N01104X/1, MR/J012165/1, MR/K026992/1)
  • Biotechnology and Biological Sciences Research Council (BB/F022441/1)
  • Economic and Social Research Council (ES/M010341/1)
  • Helmholtz Zentrum München
  • Netherlands Heart Institute
  • School of Public Health, Imperial College London
  • Amsterdam Brain and Cognition
  • Biocenter, University of Oulu
  • Diamantina Institute, University of Queensland
  • Norwegian Institute of Public Health
  • National Institute on Aging (R01AG017917, R01AG015819, P30AG010161, T32AG000186, AG005842, RF1AG015819, R01AG042568, P01AG005842, P30AG012810, U01AG009740)
  • National Institute on Drug Abuse (R01DA036216, R37DA005147)
  • Eunice Kennedy Shriver National Institute of Child Health and Human Development (P2CHD047879)
  • Institute of Genetics
  • H2020 European Research Council (647648)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
  • Social Sciences › Psychology › Experimental and Cognitive Psychology › Cognitive Abilities and Testing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
Keywords
educational attainment, genetic variants, years of schooling, candidate genes, neural development, genetic architecture, cognitive characteristics, neuropsychiatric disorders
MeSH terms
Alzheimer Disease, Bipolar Disorder, Brain, Cognition, Educational Status, Fetus, Gene Expression Regulation, United Kingdom, Humans, Schizophrenia, Computational Biology, Polymorphism, Single Nucleotide, Genome-Wide Association Study, Molecular Sequence Annotation, Gene-Environment Interaction

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