Only the genotypes for those 311,226 SNPs that were typed in all 3,378 individuals were included in subsequent computational analyses. Closely related individuals were identified using estimation of the proportion of the genome shared identical by descent (IBD), and the relative with the lower call rate was removed. Inbreeding coefficient F was assessed in order to detect potential DNA contamination. SNPs found to be out of Hardy-Weinberg equilibrium at p<10−5, or missing more than 1% of genotypes, or with a minor allele frequency <0.01 were removed from the dataset [16]. The total rate of genotyping calls in the remaining individuals was 0.995. After QC, 273,454 SNPs remained (from 3,112 individuals), including 203 HapMap individuals that increased the overall sample size to 3,315. All QC procedures were conducted with Illumina's BeadStudio (www.illumina.com) and the PLINK software [7].
