There were 6534 samples passing DNA and initial genotyping QC. Genotyping was performed at Rutgers University Cell and DNA Repository (RUCDR) using the Affymetrix BioBank array (653 k variants) which contains both common GWAS framework variants (296 k) for imputation and functional variants (357 k) including rare high impact exome variants (272 k), indels (18 k), eQTLs (16 k), and miscellaneous (51 k). QC excluded Off Target Variants found by SNPolisher, single nucleotide polymorphisms (SNPs) missing >5% of genotypes, samples missing >2% of genotypes, and SNPs missing >2% of genotypes after sample filtering, similar to the Psychiatric Genomics Consortium (PGC; Schizophrenia Working Group of the Psychiatric Genomics Consortium, 2014). This pre-imputation QC removed 209 samples, leaving 6,325 samples and 560,138 variants for imputation. Imputation was conducted using SHAPEIT2 (Delaneau et al., 2013)/IMPUTE2 (Howie et al., 2009) and the 1000 genomes phase 3 reference panel (n = 2,504) (1000 Genomes Project Consortium et al., 2015; Sudmant et al., 2015).
