To estimate the proportion of phenotypic variance explained (‘chip heritability’; hg2), we used a genomic restricted maximum likelihood (GREML) method implemented in Genetic Complex Trait Analysis (GCTA; Yang, Lee, Goddard & Visscher 2011). The GREML method estimates the proportion of variation in a phenotype that is due to all SNPs, and exploits the fact that genotypic similarity (i.e., “relatedness”, measured using genotyped SNPs) will be correlated with phenotypic similarity for heritable traits. Individual-level quality control was implemented, and distantly related individuals with pair-wise relationships were filtered at two thresholds (KIBS < 0.05 and KIBS < 0.03). We included age (inverse-normalized), self-reported sex (male/female), genotyping platform and top four principal components as covariates. GREML analyses were run using only directly genotyped SNPs.
