DNA was extracted from the same brain tissue samples used in the RNA analysis. Genotyping was performed on the Axiom™ Biobank Plus Genotyping Array (Catalog number: 000854). Initial QC was performed using PLINK (Purcell et al., 2007) to remove variants with: 1) no alternate alleles; 2) genotyping call rate ≤0.98; 3) Hardy-Weinberg Equilibrium p value <5E-5; and 4) samples with genotyping call rate <0.90. Phasing was performed on each chromosome using SHAPEIT2 (Delaneau et al., 2013) then imputation was done using IMPUTE2 (Marchini et al., 2007) with the 1,000 Genomes Phase 1 integrated reference panel excluding singleton variants. Analysis was performed on the imputed variants with imputation score (INFO) ≥0.8 and estimated MAF ≥0.05.
