In completely denaturing HPLC analysis, the PE products can be quantified by their absorbance at 260 nm. If the starting test sample is a mixture prepared by pooling many DNA samples in equal amounts (a process known as DNA pooling), the relative allele frequencies of a SNP in the DNA pool can be estimated by measuring the relative signal intensities of the two extension products of the DNA pool with reference to those of a heterozygote sample.
Note that a SNP only has two alleles and their relative allele frequencies sum up to 1. This provides a very cost-effective method for estimating the relative allele frequencies of a large number of different samples. Conventionally, estimation of allele frequencies is achieved by genotyping all samples individually, and this approach is of course very expensive and time-consuming if the number of samples is very large (in the range of several hundreds, or more preferably over 1,000 in genetic association studies, see the following).