However, among the 357,361 SNPs measured on Illumina and imputed on Affy (Figure 1b), we see an overall increase in λ to 1.6. We see an increase in the percentage of highly significant SNPs to 1.3% when using soft call genotypes, and to 2.1% when using hard call genotypes. Thus, when using hard call genotypes, 7,644 SNPs are being declared significant at the 5 ×10−8 level. These increases are most prominent among SNPs with low MAF, as shown in the Figure. The Type I error inflation is also apparent, though less dramatic, among the 458,034 SNPs measured on Affy and imputed on Illumina (Figure 1c) where λ = 1.3 overall, and where we are seeing 0.4% highly significant SNPs when using soft calls and 0.8% highly significant SNPs when using hard calls; we see similar numbers among the 1,392,682 SNPs imputed in both (Figure 1d). Results were largely unchanged when we first pooled the two groups and then imputed.
