Genotype data from the NIMH-BP, GAIN-MDD, and German samples were used to impute data on 2.1 million HapMap Phase 2 SNPs by use of the program Markov Chain Haplotyping (MACH), version 1.0 20. MACH uses Markov chain haplotyping to resolve haplotypes, and thereby missing genotypes, from observed genotypes in unrelated individuals. We used the “greedy” algorithm, as recommended by the authors. SNPs that were flagged as having different alleles than in HapMap CEU or as monomorphic were reviewed, after which they were either recoded for the reverse strand (flipped) or dropped. SNPs that were flagged for allele frequencies that were markedly different from HapMap CEU were also reviewed. Palindromic SNPs whose allele frequencies were consistent with reversed coding were flipped. Other SNPs with unexpected allele frequencies were dropped. PLINK21 (vers. 1.4) was used to flip and drop SNPs as necessary. After all allele-coding, monomorphism, and palindrome issues were resolved, imputation was run again. SNPs in the results files were dropped if the MAF in cases or controls was <0.05 or if the error rate (as reported in the .erate output file) was >0.01. Finally, the imputed data were formatted into PLINK binaries for analysis.
