Polygenic selection on educational attainment: a replication

Abstract

The genetic variants identified by three large genome-wide association studies (GWAS) of educational attainment were used to test a polygenic selection model. Average frequencies of alleles with positive (Beta) effect on the phenotype (polygenic scores) were compared across populations (N=26)using data from 1000 Genomes. Strong correlations between polygenic scores and population IQ were found. Moreover, the polygenic scores obtained from the three independent GWAS exhibited strong intercorrelations even after pruning for linkage disequilibrium. The method of correlated vectors revealed the presence of a Jensen effect of SNP p value on population IQ and factor from the two previous GWAS (r= -.25). Factor analysis produced similar estimates of polygenic selection strength for educational attainment across the three datasets. The SNPs from the largest GWAS were subset by p value (N= 7) and factor analyzed. An SNP set’s P value-rank correlated substantially (0.4) with a composite index including measures of predictive validity and reliability (r x population IQ, average factor loadings, r x factor scores from the 2 previous GWAS, SAC (spatial autocorrelation)-free effect on population IQ. Moreover, the composite index of factor reliability and validity was strongly correlated (r=0.96) to loadings on a factor extracted from the 7 factors (“meta-factor”). That is, the factors’ with stronger independent correlations to measures of accuracy had stronger loadings on the “meta-factor”. Nine hits were found to be in LD across publications. This produced replicated factor and polygenic scores with strong correlations to population IQ (0.89 and 0.82-0.9, respectively), surviving control for spatial autocorrelation (B= 0.69 and 0.35-0.79, respectively). The results together constitute a replication of preliminary findings and provide unequivocal evidence for recent diversifying polygenic selection on educational attainment and underlying cognitive ability.