In each fatSNP2 sample, SNPs had call rates in cases and controls ≥97% with the exception of rs12476147 in the UK (92% in cases ), rs12613195 in the Munich (96% in cases) and both rs1344706 (93% in cases) and rs17584522 in the Dublin sample (95% and 93% in cases and controls respectively) (supplemental table 4). In the UK samples, the more complete imputed genotypes for rs12476147 gave similar results to the array SNP. No marker in any of the populations studied had a HWE P-value <0.05. Of ~1300 genotype pairs (HapMap or duplicates) for the 8 independent markers genotyped in our follow-up study, we observed only 1 genotyping discrepancy. For rs17584522, which was genotyped by the Dublin group, the comparison of 72 duplicate samples and 83 HapMap samples revealed no discrepancies.
