Two recoded phenotype files were created each containing 2,938 control individuals (the combination of all the filtered 58C and NBS individuals) and the 1,963 T1D or the 1,924 T2D cases, respectively. Next, we performed the WTCCC standard case-control association analysis (χ2) to confirm the validity of the QC steps using PLINK [25]. Results of this analysis are outlined in Table 1.
