Applying polynomial standard curve method to correct bias encountered in estimating allele frequencies using DNA pooling strategy

DNA pooling approach is a cost-saving strategy which is crucial for multiple-SNP association study and particularly for laboratories with limited budget. However, the biased allele frequency estimates cannot be completely abolished by κ correction. Using the SNaPshot™, we systematically examined the relations between actual minor allele frequencies (AMiAFs) levels and estimates obtained from the pooling process for all six types of SNPs. We applied principle of polynomial standard curves method (PSCM) to produce allele frequency estimates in pooled DNA samples and compared it with the κ method. The results showed that estimates derived from the PSCM were in general closer to AMiAFs than those from the κ method, particularly for C/G and G/T polymorphisms at the range of AMiAF between 20–40%. We demonstrated that applying PSCM in the SNaPshot™ platform is suitable for multiple-SNP association study using pooling strategy, due to its cost effectiveness and estimation accuracy.