on genotyped overlapping 60K SNPs with Affy500 (Sib 1), Illumina660 (Sib 2), and Illumina550 (control). In Figure 3c, the genomic control inflation factor is decreased from 1.16 to 1.06 as compared with Figure 3a and increased from 1.03 to 1.06 as compared with Figure 3b. This may suggest that there is a chip-effect, which was amplified by the imputation. Figure 3d shows that by applying a very stringent extra QC (RT2 >0.98, 60K genotyped and 97K imputed SNPs) inflation of test statistic could be dealt with (λGC=1.05). Therefore, the significantly biased results (Figure 3a) seem to be caused by the different chips from one of which is of low quality.
