To assess the convergent and discriminant validity of down-sampled multivariate GWAS on latent factors, we can examine potential changes in the pattern of genetic correlation with other traits. If the down-sampled analysis tags the same genetic etiology, the confidence intervals of the point estimates should display considerable overlap. The overall pattern can be examined by estimating the rank correlation of the point estimates across traits, whereas significance of changes to individual genetic correlations can be assessed using a t-test.
