In order to evaluate the ability of Genomic SEM to capture the genetic factor structure in the generating population, the GCTA package3 was used to generate 100 sets of 6 independent, 100% heritable phenotypes (“orthogonal genotypes”) to pair with genotypic data for 39,909 randomly selected, unrelated individuals of European descent from UKB data for the 1,209,498 SNPs present in HapMap3. The generating list of causal SNPs was set to 10,000 for all 600 genotypes, with the specific list of causal variants sampled with replacement from the 1,209,498 SNPs. One of the six orthogonal genotypes per set was designated an index of the general genetic factor and the remaining five were designated indices of domain-specific genetic factors. All of these orthogonal genotypes were scaled to M=0, SD=1. Five new correlated genotypes were then constructed, each as the weighted linear combination of the general genetic factor and one domain-specific genetic factor. Weights for contribution of the general genetic factor were λFg,k =.70, .60, .50, .40, and .30, for correlated genotypes 1–5, respectively. Weights for the domain-specific factors were (1−λFg,k2). Phenotypes were then
