We considered two parameterizations of the gSEM GWAS model. The gSEM GWAS model for residual genetic variance in each developmental period was fit with paths from the SNP to both the residual and the common factor. This approach partitions the SNP effects into a component that is attributable to the common factor and a component that is directly associated with the residual genetic variance. An alternate approach models total genetic variance in each developmental period by omitting the path from the SNP to the common factor. A simulation supporting this distinction between the two model parameterizations is provided in the supplemental material. A diagram of the gSEM GWAS model for SNP effects on the total genetic variance in adolescence is included in Figure S1. A diagram of the gSEM GWAS model for SNP effects on the common factor is included in Figure S2.
