For noteworthy associations, there were additional checks to ensure that an association was not due to experimental bias. These checks included: manual inspection of SNP cluster plots to ensure reasonable performance of the genotyping calling algorithm; evaluation of conformation to Hardy-Weinberg equilibrium in controls, cases, and overall (discussed in the Supplemental Methods); the checks for population stratification described above; evaluation of plate-specific association results to ensure that the overall association was not driven by one or a few plates; comparison of control MAFs to the HapMap EUR panel; and evaluation of the characteristics of a SNP in high linkage disequilibrium (“proxy association”) as a similar association with such a SNP decreases the chance of some forms of method artifacts.
