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

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

Jonathan P. Beauchamp | Gerardus A. Meddens | Joseph K. Pickrell | Steven F. Lehrer | M. P. Concas | Blair H. Smith | Bjarni V. Halldórsson | R. Marioni | C. Gieger | P. Visscher | I. Deary | R. Mägi | E. Mihailov | P. Deloukas | A. Auton | B. Halldórsson | L. Kiemeney | U. Thorsteinsdóttir | V. Vacic | A. Malhotra | C. Chabris | V. Salomaa | M. Perola | B. Alipanahi | K. Bryc | Z. Kutalik | M. Johannesson | K. Strauch | M. Mangino | J. Perry | N. Timpson | S. Shringarpure | V. Emilsson | David I. Laibson | I. Borecki | J. Vonk | T. Ahluwalia | J. Waage | K. Bønnelykke | G. Thorleifsson | S. Kardia | T. Meitinger | W. Iacono | G. Willemsen | A. Kraja | A. Metspalu | T. Esko | G. Montgomery | J. Tung | L. Milani | R. Rueedi | R. Poot | I. Rudan | D. Posthuma | D. Boomsma | N. Eklund | D. Porteous | D. Levinson | D. Nyholt | N. Wareham | M. Horikoshi | Antti-Pekka Sarin | J. Hottenga | H. Westra | P. Magnusson | T. Pers | L. Franke | N. Furlotte | G. Bjornsdottir | T. Lencz | M. 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