Accuracy and sensitivity of DNA pooling with microsatellite repeats using capillary electrophoresis

Abstract DNA pooling is a genetic screening method that combines DNA from many individuals in a single polymerase chain reaction (PCR) reaction to generate a representation of allele frequencies. The substantial saving in effort with DNA pooling over individual genotyping facilitates linkage disequilibrium scanning of the human genome using many thousands of genetic markers, and is applicable to mapping of complex diseases such as schizophrenia. However, the literature to date has not addressed several crucial technical aspects of DNA pooling. These include: DNA quantification; the choice of electrophoresis methods; sensitivity (the minimum reliably detectable difference between pools); and methods of dealing with «plus-A» stutter. We have examined these points and make recommendations as to the best procedures to adopt as well as quantifying reproducibility and sensitivity. We conclude that, although allele frequencies derived from microsatellite pooling are distorted, differences of 5% or greater between pools can be reliably detected.