Genotyping was performed at Rutgers University Cell and DNA Repository using the Affymetrix BioBank array (653k) which contains both common GWAS framework variants (296k) for imputation and functional variants (357k) including rare high impact exome variants (272k), indels (18k), eQTLs (16k) and miscellaneous markers (51k). QC excluded Off Target Variants found by SNPolisher, high missingness SNPs (5%) and samples (2%), and post sample filtering high missingness SNPs (2%) similar to the Psychiatric Genomics Consortium (PGC).20 There were 6534 samples passing DNA and initial genotyping QC. An additional 209 samples were removed due to excessive relatedness (n = 194) and/or Pi_Hat > 0.1 (n = 180), leaving 6325 samples and 560138 variants for imputation. Imputation was conducted using SHAPEIT2,21 IMPUTE2,22 and the 1000 genomes phase 3 (1KGP) reference panel (n = 2504) which includes 81,706,022 variants.23,24 The post imputation and pre-GWAS filtering included excluding rare (MAF <0.005) and low quality (INFO<0.5) variants, SNPTEST v2.5.225 was used to calculate Hardy-Weinberg Equilibrium (HWE) which yielded 17,461,305 variants. Group (super-population or census race) GWAS filtering was performed using within grouping specific HWE (p-value>10−6) and
