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

Table 2 Comparing estimated and known allele frequencies in pool replicates for SNP6.0 platform.

Known AF compared with:	Correlation	MAD error	(95% CI)
Case Pool Replicate 1	0.983	0.042	(0.0435-0.0437)
Case Pool Replicate 2	0.986	0.038	(0.0397-0.0399)
Case Pool Replicate 3	0.988	0.036	(0.0373-0.0375)
Average of Case Pools	0.989	0.035	(0.0363-0.0365)
Control Pool Replicate 1	0.985	0.042	(0.0423-0.0425)
Control Pool Replicate 2	0.984	0.041	(0.0421-0.0423)
Control Pool Replicate 3	0.985	0.040	(0.0415-0.0417)
Average of Control Pools	0.988	0.036	(0.0372-0.0374)

Known allele frequencies obtained from the SNP6.0 Sample Data Set of the Hapmap CHB population were compared with estimated allele frequencies from pooled genotyping of 160 case and 160 control samples. The comparison was carried out for samples in each of the replicate-pools, and for averaged allele frequencies across the 3 replicates.

ISSN: 2730-6844