Each simulation began by generating genome-wide summary statistics for binary traits for 10 individual cohorts. We began with a series of simulations that specified a population prevalence of 1%, a liability-scale heritability of 15% in the population, cross-trait intercepts of 0 to reflect no sample overlap across the 10 cohorts, and a univariate intercept of 1.0 to reflect no uncontrolled for population stratification. Each cohort was specified to have a sample prevalence of either 10% (low ascertainment) or 50% (high ascertainment), with the balance of cohorts with low and high ascertainment varying across 11 simulation conditions (see Table 1 for details on each condition). Note that when liability-scale heritability is equal, but sample prevalence differs across cohorts, observed-scale heritability will differ across cohorts.
