We have compared several genotyping methods to assess their applicability to single nucleotide polymorphism (SNP) allele frequency estimation in DNA pools. The accuracy of these methods (restriction fragment length polymorphism, real-time pyrophosphate DNA sequencing, single base extension with fluorescently labeled ddNTPs, homogeneous 5'-nuclease assay, and MALDI-TOF mass spectrometry) was tested by calculating the standard deviation among heterozygous individuals (which are natural DNA pools with 50% representation of each allele) and by estimating allele frequency in artificial pools. We show that although the methods differ in their accuracy, they can all serve for quantification of allele frequency in DNA pools with reasonable accuracy. We found that the influence of the error variance attributed to pool construction on quantification accuracy is insignificant and is SNP dependent.
The complex genetic nature of many common diseases makes the identification of the genes that predispose to these ailments a difficult task. Consequently, many factors have to be considered in choosing the optimal approach to be taken in gene discovery of susceptibility genes. The elements to be considered include the applicability of a family-based linkage paradigm versus a population-based association design and the effects of linkage disequilibrium (LD) and genotypic relative risk (GRR). In this review we discuss these various points and describe the impact on LD and GRR of studying an isolated (also termed 'founder' or 'homogeneous') population, such as Ashkenazi Jews, as compared to an outbred population, such as Caucasians.