Summary statistics are only restricted to HapMap3 SNPs for the estimation of the genetic covariance and sampling covariance matrix in LD-Score regression, whereas all SNPs passing QC filters are included for multivariate GWAS. To obtain summary statistics for multivariate GWAS, we recommend using QC procedures of removing SNPs with an MAF < .01 in the reference panel, and those SNPs with an INFO score < 0.6. MAFs were obtained for the current analyses using the 1000 Genomes Phase 3 reference panel. Using these QC steps, 1,979,881 SNPs were present across schizophrenia, bipolar disorder, MDD, PTSD, and anxiety. For neuroticism, there were 7,265,104 SNPs that were present across all phenotypes. These QC procedures are the defaults for the processing function within the GenomicSEM package. The regression effects for the univariate indicators of the p-factor were standardized using the procedure for logistic coefficients outlined above. Regression effects for neuroticism indicators were converted from linear probability to logistic coefficients and then standardized with respect to the variance in the outcome.
