To identify genetic outliers and ascertain concordance with self-reported race, we completed a principal component (PC) analysis on SNPs common to the individual genotyping arrays (pruning by linkage disequilibrium (LD) r2 > 0.2) and the 1000 Genome phase 3 reference panels (African populations, AFR; Admixed American populations, AMR; East Asian populations, EAS; European populations, EUR; and South Asian populations, SAS) using EIGENSOFT (Patterson et al., 2006, Price et al., 2006). Samples 1 and 2 were analyzed separately. We then completed a second PC analysis using Asian populations from the 1000 Genome panels (EAS and SAS), now categorized by specific region, to investigate the fine-scale population structure of the included Thai samples (Supplemental Figure 1). A third PC analysis was done within the Thai samples, and the first 3 PCs were then used to correct for population stratification.
