Genomic prediction of cognitive traits in childhood and adolescence

Abstract

Recent advances in genomics are producing powerful DNA predictors of complex traits, especially cognitive abilities. Here, we leveraged summary statistics from the most recent genome-wide association studies of intelligence and educational attainment, with highly genetically correlated traits, to build prediction models of general cognitive ability and educational achievement. To this end, we compared the performances of multi-trait genomic and polygenic scoring methods. In a representative UK sample of 7,026 children at ages 12 and 16, we show that we can now predict up to 11% of the variance in intelligence and 16% in educational achievement. We also show that predictive power increases from age 12 to age 16 and that genomic predictions do not differ for girls and boys. We found that multi-trait genomic methods were effective in boosting predictive power. Prediction accuracy varied across polygenic score approaches, however results were similar for different multi-trait and polygenic score methods. We discuss general caveats of multi-trait methods and polygenic score prediction, and conclude that polygenic scores for educational attainment and intelligence are currently the most powerful predictors in the behavioural sciences.

Figure 1.

Polygenic score prediction of intelligence (IQ) and educational achievement (EA) at age 12 and 16. Figure shows polygenic prediction accuracy across polygenic score methods. Error bars are bootstrapped 95% confidence intervals based on 1,000 replications.

Figure 2.

Within-trait and cross-trait polygenic score prediction of intelligence and educational achievement at age 16 across multi-trait methods. Note. MTAG = MTAG IQ3 (panel a)/ MTAG EA3 (panel b) polygenic scores constructed in Lassosum; SMTpred = IQ3 (panel a)/EA3 (panel b) wMT-SBLUP predictors; Genomic SEM = Common Factor polygenic score constructed in Lassosum (panel a and b). Error bars are bootstrapped 95% confidence intervals based on 1,000 replications.

Figure 3.

Mean intelligence scores (panel a) and mean educational achievement (panel b; GCSE grades) at age 16 by GPS deciles for the best polygenic predictors in the test set. Bars represent bootstrapped 95% confidence intervals. Coloured dots represent individual data points.