An alternate version of the Aim 1 discovery analysis was conducted with COGA removed in order to facilitate PGS construction in the COGA sample. COGA was selected for PGS validation to maximize the remaining sample size in the meta-analytic GWAS. The residual variance parameterization, which includes the path from SNP to the common factor, was used for this component of the analysis plan to construct polygenic scores that are specific to developmental stages. The total number of SNPs in the analysis, included in the meta-analysis of ALSPAC and Add Health and the reference panel, was 6,071,632. Sample sizes for the gSEM GWAS analysis in adolescence, early adulthood, adulthood, and the common factor with COGA removed were 7,869.59, 7,070.74, 5,149, and 8230.73, respectively. A diagram of the gSEM GWAS model for residual genetic variance in adolescence is included in Figure S3.
