Skip to main content

Table 5 Comparing accuracy of allele frequency estimates from different Hapmap reference samples for SNP6.0 platform.

From: Validation of pooled genotyping on the Affymetrix 500 k and SNP6.0 genotyping platforms using the polynomial-based probe-specific correction

Known AF compared with: Correlation MAD error (95% CI)
AF estimated from CEU Sample Set (90) Cases 0.889 0.097 (0.1095-0.1100)
  Controls 0.890 0.097 (0.1086-0.1090)
AF estimated from CHB Sample Set (45) Cases 0.989 0.035 (0.0364-0.0365)
  Controls 0.988 0.037 (0.0372-0.0374)
AF estimated from JPT Sample Set (45) Cases 0.984 0.040 (0.0426-0.0428)
  Controls 0.984 0.041 (0.0430-0.0432)
AF estimated from YRI Sample Set (90) Cases 0.780 0.125 (0.1567-0.1574)
  Controls 0.782 0.124 (0.1550-0.1557)
AF estimated from All Sample Sets (270) Cases 0.944 0.060 (0.0796-0.0799)
  Controls 0.945 0.059 (0.0789-0.0792)
  1. Known allele frequencies from each of the four Hapmap populations (CEU, CHB, JPT and YRI) as provided in the SNP6.0 Sample Data Set, and an average allele frequency across the four populations were compared with the estimated allele frequencies of the 160 case and 160 control samples genotyped on the SNP6.0 platform. The estimated allele frequencies were calculated using beta values obtained from the four individual Hapmap populations and their collated genotypes in the same data set.