Call rates averaged over 97% for all samples, and most samples were called at 98% or better. Seven of 598 experiments failed to reach the 90% call rate threshold but only four participant samples failed to reach the 90% threshold in at least one experiment. These four participants were removed from further analysis. The concordance rate for the 34 repeated samples (36 experiments; two samples repeated three times) was 99.3%. Call rates for individual markers were established by the TGAS program for call rates over all cases and controls. Call rates were excellent, with an average call rate of 99.64% for the genotyped markers including all ancestrally informative markers (AIMs). Only one AIM failed to achieve a QC call rate of 90% and was removed from further analysis. Hardy Weinberg equilibrium (HWE) tests were carried out to reduce the likelihood of spurious genotype associations resulting from technical artifacts from the genotyping platform. All markers in controls were deemed to be in equilibrium (P > 0.01); tests were carried out within race groups.
