All genetic analyses were conducted using PLINK (18) versions 1.03 and 1.04. Our primary analyses tested the association of each SNP (coded additively) with BD using three distinct methods that control for genetic background heterogeneity (Table 1): (1) single locus, contingency table analysis with genomic control adjustment, (2) logistic regression using a LAMP-derived estimate of ancestry as a covariate, and (3) logistic regression using the top 4 MDS dimensions as covariates. Association analyses using these three methods were conducted within the EA and AA samples separately, as well as within the combined sample (see Table 1). For each analysis, the distribution of expected p-values under the null hypothesis (i.e., no association), and the genomic inflation value (λ) was calculated in PLINK using the adjust command (Figure S1). Genomic inflation values are reported as both uncorrected and corrected for a study size of 1,000 cases and 1,000 controls (19, 20).
