In a TDT design, the number of observed transmissions of a given allele of a SNP is compared to the expected frequency under the assumption of no association (Spielman and Ewens 1996). Performing the TDT, the authors noted a highly significant imbalance in the number of major and minor allele over-transmissions. Given the large numbers of SNPs analyzed, these numbers would have been expected to be similar. Removing additional SNPs that had failed quality control in one of the other two GWAS based on the Perlegen microarray improved this imbalance partly, suggesting that genotyping error or missingness is (at least partly) responsible for this effect. Therefore, the authors repeated their analysis including a correction factor. Comparison of the presented tables listing the top-25 SNPs before and after correction shows that this resulted in the loss of half of the listed SNPs and a general downward correction of P values. Although, as the authors state, it might be (too) early to explore the biological relevance of the strongest observed associations, it is a fact that the list contains a number of
