For the p-factor, neuroticism, and anthropometric traits, quality control (QC) procedures for producing the S and VS matrix followed the defaults in LDSC. We recommend using these defaults for multivariable LDSC, including removing SNPs with an MAF < 1%, information scores < .9, SNPs from the MHC region, and filtering SNPs to HapMap3. Quality control procedures for the multivariable regression example mirrored those used by Nieuwboer et al. (2016)23 for comparative purposes. More specifically, SNPs were excluded with MAFs < .05 as determined by the HapMap Consortium,57 and with information values less than 0.9 or greater than 1.1. SNPs were also filtered to HapMap3. The LD scores used for the analyses presented were estimated from 1000 Genomes Phase 3, but restricted to HapMap3 SNPs.
