Individual genotyping was conducted by Perlegen Sciences (Mountain View, CA, USA) using a set of four proprietary, high-density oligonucleotide arrays. The SNPs on these arrays were selected to tag common variation in the HapMap European and Asian panels using previously described genotype data (31), tagging approach (32), and methodology (33). At the beginning of GAIN, all HapMap (34) samples were genotyped with the Perlegen GWAS platform. Independent review of these data by the GAIN analysis group (19) showed 99.8% agreement with prior HapMap genotypes and the mean maximum r2 between the Perlegen SNPs and HapMap phase II SNPs (31) was 0.89 for single and 0.96 for multi-marker analyses. The genotyping procedures and genotyping calling algorithms are described in the Supplemental Methods and in prior reports (35, 36). Briefly, 40 × 96-well plates were sent to Perlegen for GWAS genotyping. Genotyping was conducted blind to case-control status. Cases and controls were randomly allocated to plates and to positions within plates. Each plate contained DNA samples from 93 Dutch subjects plus 3 quality control samples. The three quality control samples included: two
