We conducted systematic quality control steps on the raw Illumina HumanHap300 genotyping data. Variants with a genotype call rate of less than 95% and also individuals where the overall genotype completion rate was less than 95% were excluded. We also conducted further exclusions where the genotype distribution clearly deviated from that expected by Hardy-Weinberg Equilibrium (HWE) among controls (p-value of less than 10−7) and where there were discrepancies between sex based genotype and reported sex, as well as individuals with unlikely heterozygosity rates across genetic variants on the X chromosome (Table S1). Those genotyped were restricted to individuals of self – reported European ethnicity. To further increase the ethnic homogeneity of the series, we used the program STRUCTURE [41] to identify individuals of mixed ethnicity. Using a subseries of 12,898 genetic variants from the HumanHap 300 BeadChip panel evenly distributed across the genome and in low linkage disequilibrium (LD) (r2<0.004) [42], we estimated the genetic profile of the study participants compared with individuals of known ethnic origins (the Caucasian, African and east-Asian individuals genotyped by the HapMap project). We excluded
