phenotype status using logistic regression with sample as a covariate. We selected the first four components and any others with a nominally significant correlation (p-value < 0.05) between the component and phenotype. We included these components in our GWAS. This process was done independently for all phenotype comparisons. Imputation was performed using the HapMap Phase3 CEU + TSI data and BEAGLE (21, 22) by sample on random subsets of 300 subjects. All analyses were performed using Plink (23).
