Mean χ2 statistics were higher for the Genomic SEM-derived summary statistics of common factors relative to univariate indicators (Table 1). It is important to note here that, whereas Genomic SEM may boost power in many cases, this is not the primary purpose of the method. Rather, it is to identify the relationship between SNPs and observed phenotypes as meditated through a user-specified model and to concurrently evaluate the construct validity of said model. Inspecting the distribution of univariate p-values for the newly identified SNPs for the general factors indicated that these SNPs were generally characterized by relatively low p-values, albeit not low enough to cross the genome-wide significance threshold for any individual phenotype (Supplementary Figures 12–13).
