Extract: Single nucleotide polymorphisms (SNPs) often represent allelic variants of genes. The differences between individuals within a species are mainly due to SNPs. SNPs are commonly used as genetic markers for genetic diseases and other phenotypic traits. Currently, throughput and accuracy are limiting factors in the widespread use of SNPs in diagnostics. A large number of both individuals and SNPs often have to be screened when searching for correlation between specific alleles and phenotypic traits. SNP genotyping analysis of one sample at a time is extremely costly and time consuming. Pooling DNA samples prior to quantitative SNP allele frequency determination in affected and control populations is an attractive way to increase throughput and reduce costs. Individual genotyping is only done when there is a significant discrepancy in allele frequencies between the affected and control populations. Despite extensive efforts, the technology to accurately quantify SNPs in sample pools is still lacking.