Yang et al. proposed an adjustment to account for the incomplete coverage of genotyping platforms10. We applied this approach in the CARe data (see Supplementary Table 3), and observed an increase in hg2 of less than 1% in all phenotypes. We include genome-wide ancestry proportion as a fixed effect in our mixed model. If there exists an environmental factor that affects phenotype and is correlated with ancestry, our heritability estimates will discount this environmental effect leading to higher estimates of heritability. Specifically, it will remove the variance of the environmental factor that can be explained by ancestry from the environmental component ( σe2) in the denominator of the heritability estimate h2=σg2σg2+σe2 (see Online Methods).
