After conducting a multivariate GWAS on the latent factors in down-sampled analyses with Genomic SEM, the loss of genetic signal at the factor level can be assessed by (i) examining the genetic correlation between the respective latent factors of the full and down-sampled summary statistics using bivariate LD Score regression (Bulik-Sullivan et al. 2015) and by (ii) estimating the decrease in genetic signal with key indicators (1), (3), and (4) from Step 1. Please note that key indicators (2) and (5) are not used to evaluate the genetic signal of the latent factor because they are not clearly defined (e.g., heritability is defined as a ratio with phenotypic variance as the denominator, which is absent in latent genetic factors).
