All scores are based on results from a meta-analysis that excluded the prediction cohorts. Our first four scores were constructed from sets of LD-pruned SNPs associated with EduYears at various P-value thresholds: 5×10−8, 5×10−5, 5×10−3, and 1 (i.e., all SNPs). In both cohorts, the predictive power is greater for scores constructed with less stringent thresholds (Supplementary Figure 10). The sample-size-weighted mean incremental R2 increases from 3.2% at P < 5×10−8 to 9.4% at P ≤ 1. Our fifth score was generated from HapMap3 SNPs using the software LDpred25. Rather than dropping SNPs in LD with each other, LDpred is a Bayesian method which weights each SNP by (an approximation to) the posterior mean of its conditional effect, given other SNPs. This score was the most predictive in both cohorts, with an incremental R2 of 12.7% in AddHealth and 10.6% in HRS (and a sample-size weighted average of 11.4%).
