Imputation was performed using IMPUTE v2.1.2 and the 1000 Genomes Project data as a reference panel. Only imputed SNPs that were in strong linkage disequilibrium (LD) (info>0.6) with genotyped SNPs and had a high certainty (>90%) of the predicted genotypes were retained. Imputed SNPs that showed significant genotyping platform effects were excluded. Imputed results were converted to MaCH format (i.e., .mldose, .mlinfo) using an in-house script. MaCH dosage data was used to create GRMs for each chromosome. Chromosome specific GRMs were then merged as needed for additional analyses. The total number of imputed SNPs after QC included 7,657,106 SNPs in both the TS and OCD samples.
