From the simulated cohort-level GWAS z statistics, we computed logistic betas as follows: (10) blogitk,j=Zk,jnkvk(1−vk)σSNP,j2 where vk and nk reflects the cohort-specific sample prevalence and sample size, respectively, and σSNP,j2 reflects the variance of a given SNP j calculated as 2×MAF×(1−MAF), where MAF is the minor allele frequency. The logistic standard errors for a given SNP j and cohort k were then calculated as (11) SEblogitc,j=blogitk,jZk,j These logistic betas and standard errors were used to calculate the inverse-variance weighted meta-analytic beta across the 10 contributing cohorts as described in Supplement 1. This procedure then produced a single summary statistics file reflecting the meta-analyzed output across the 10 simulated cohorts. This summary statistics file was finally analyzed in LDSC in 1 of 2 ways, as described in the section below.
