All information measures need to be carefully considered in further analysis. In our study, by re-genotyping strongly associated SNPs, we found that an extremely tight inclusion threshold of our imputation quality measure RT2 greater than 0.98 was needed to achieve reliable results as shown in Figures 3 and 4; only 18 from the 89 top-ranking SNPs passed the post-analysis QC. These plots suggest that false positive findings are caused by imputation based on arrays of inferior quality, when cases and controls are not matched for genotyping platforms. Actually, in our GWAS for longevity we discarded the Affy500 data set because of the small number of reliable SNPs. It should be noted that 97K imputed SNPs remained in the analysis even for this stringent cutoff (Table 1). We also retyped the Affy500 cases with the Illumina 660K platform and recently published our GWAS.12
