Usefulness of direct sequencing of pooled DNA for SNP identification and allele-frequency determination compatible with a common disease/common variant hypothesis

We examined the efficiency of direct sequencing of pooled DNA for developing common single nucleotide polymorphisms (SNPs) and its accuracy for estimating allele frequencies. A pool of 200 control DNAs was established and was used for developing SNPs and estimating minor allele frequencies (MAF). The sensitivity of the pooled DNA method for successfully detecting an SNP with an MAF >0.01 listed in the database was approximately 0.7; it was particularly efficient for detecting SNPs with MAF >0.1, which is compatible with the common disease/common variant hypothesis. The mean difference between the estimated and the observed MAFs was 0.03 ± 0.023. The pooled DNA method identified four additional SNPs, for which the allele frequency