Association analysis was performed in PLINK24. The basic association test was a transmission disequilibrium test (TDT), and the extra cases vs. controls analysis was performed by allelic association, after excluding cases that were not well-matched to the controls, based on multi-dimensional scaling (λ < 1.1). Combining the TDT and case-control tests was performed using expected and observed allele counts by the formula: Zmeta = (ΣEXP − ΣOBS)/√ΣVAR. Meta-analysis of AGRE/NIMH and replication data was performed using the statistic (ZAGRE/NIMH+Zreplication)/√2. Gene-set analysis was performed in PLINK using the set-based TDT. Imputation-based association was performed in PLINK with the proxy-tdt command, using the HapMap CEU parent samples as the reference panel and information score >0.8. Haplotype analysis in the linkage regions was performed using 5-SNP sliding windows, as implemented in PLINK hap-tdt. See Methods section for details of determination of genome-wide significance thresholds.
