We went on to perform a second set of simulations that aimed to systematically characterize the effect of different population generating parameters on liability-scale heritability estimates. For all conditions in this second set of simulations, the 10 cohorts consisted of 5 cohorts with 10% sample prevalence and 5 cohorts with 50% sample prevalence. The same population generating parameters from the first set of simulations were used (population prevalence = 1%; liability-scale heritability = 15%; cohort-level sample size = 5000; univariate LDSC intercept = 1) with the exception that one of these values was changed within each condition. This second set of simulations then consisted of 12 distinct conditions that examined the downstream consequences of changing the cohort-level sample size (1000, 10,000, 20,000, or 25,000), the liability-scale heritability (5%, 10%, 20%, or 25%), the population prevalence (1%, 5%, 10%, or 15%), or the LDSC univariate intercept (1.04) (see Table S1 in Supplement 2).
