Supplementary Note contains analyses and discussion of the possible causes of the remaining deflation we observe for EduYears. While the evidence is not conclusive, it suggests that the GWAS effect-size estimates may be biased upward by correlation between EA and a rearing environment conducive to EA. Consistent with this hypothesis, a recent paper15 reports that a polygenic score for EduYears based entirely on parents’ non-transmitted alleles is approximately 30% as predictive as a polygenic score based on transmitted alleles. (For height, the analogous estimate is only 6%.) The non-transmitted alleles affect parents’ EA but can only influence the child’s EA indirectly. If greater parental EA positively influences the rearing environment, then GWAS that control imperfectly for rearing environment will yield inflated estimates. The LD Score regression intercept does not capture this bias because the bias scales with the LD Score in the same way as a direct genetic effect.
