to cryptic relatedness, strict relatedness filters were applied. For pairs with relatedness values > the negative of the smallest observed kinship (−0.014 for EUA and −0.045 for AFA, respectively), one subject was randomly removed. PC’s were then calculated in the remaining sets of unrelated subjects. Finally, to estimate h2SNP, an unweighted GRM was estimated without LD-pruning, and h2SNP was calculated on the liability scale using REML in LDAK, including 5 PC’s and dummy indicator variables for study (number of studies - 1) as covariates.
