Estimation of single nucleotide polymorphism allele frequency in DNA pools by using Pyrosequencing

Positional cloning of genes underlying complex diseases, such as type 2 diabetes mellitus (T2DM), typically follows a two-tiered process in which a chromosomal region is first identified by genome-wide linkage scanning, followed by association analyses using densely spaced single nucleotide polymorphic markers to identify the causal variant(s). The success of genome-wide single nucleotide polymorphism (SNP) detection has resulted in a vast number of potential markers available for use in the construction of such dense SNP maps. However, the cost of genotyping large numbers of SNPs in appropriately sized samples is nearly prohibitive. We have explored pooled DNA genotyping as a means of identifying differences in allele frequency between pools of individuals with T2DM and unaffected controls by using Pyrosequencing technology. We found that allele frequencies in pooled DNA were strongly correlated with those in individuals (r=0.99, P