We recommend that investigators who share down-sampled summary statistics generated with multivariate GWAS methods (e.g., Genomic SEM) report all six steps as supporting documentation, while steps 2–3 can be skipped when generating down-sampled univariate GWAS:What is the loss of genetic signal in down-sampled univariate GWASs (which may later be used as indicator phenotypes in Genomic SEM)?How do the factor loadings and factor model fit differ in multivariate Genomic SEM when the indicator phenotypes are down-sampled univariate GWASs?What is the loss of genetic signal at the factor level of multivariate GWAS when the indicator phenotypes are down-sampled univariate GWASs?How similar are gene-property analyses when using down-sampled GWASs?How similar is the pattern of genetic correlations with other traits when using down-sampled GWASs?How much explanatory power is lost when using polygenic scores (PGSs) constructed from down-sampled GWASs?
