Using raw, individual-level genotype data simulation, we sought to validate the point estimates and standard errors (SEs) produced by Stratified Genomic SEM. We compare results for S0 and Sτ. We began by generating 100 sets of 45, 100% heritable phenotypes (“orthogonal genotypes”) using the GCTA package54. Each 100% heritable phenotype was specified to have 10,000 randomly selected causal variants from within a particular annotation. These phenotypes were paired with genotypic data for 100,000 randomly selected, unrelated individuals of European descent from UK Biobank data for the 1,209,498 SNPs present in HapMap3.
