The two-dimensional PCA plot of the remaining samples is shown in Figure 1. Dimensions above the second did not show any further significant population structure. We performed an independent association analysis of each SNP concordant between the Illumina 1M-Duo and 550Kv3 chips by comparing allele frequency. We used a Fisher’s exact test using Plink software [18] because of the small number of cases used. Due to the small sample size, we were powered only to find variants with strong effect.
