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 parents of one control on that plate (40 complete trios in total); and half the plates contained the same HapMap CEU sample (used for quality control in all GAIN projects) and half had a randomly-selected duplicate case sample. The total number of samples was 3,840 (=40 plates × 96 samples per plate) or 1,860 cases + 1,860 controls + 80 parents + 20 duplicate samples + 20 HapMap samples.
