A simple and accurate method for determination of microsatellite total allele content differences between DNA pools

DNA pooling is a potential tool for the efficient analysis of the large num bers of samples and DNA markers that are necessary for genome-wide associat ion studies. A simple accurate method for measuring total allele difference s in comparisons between two pools containing large numbers of DNA samples is presented. This method compares relative peak height differences between electrophoretograms for each allele of a microsatellite. The method was ev aluated by the analysis of 11 microsatellite markers and DNA pooled sample sizes of 50, 100, and 200 individual DNA samples from the same number of di fferent subjects. Pools were created from previously individually genotyped subjects and constructed so that the pool comparisons would provide real t otal allele differences varying from 0% to 55%. Calculated pool differences were then compared with the real total allele differences determined by in dividual genotyping results, Together over 200 comparisons demonstrated a c orrelation coefficient of 0.96, which compared favorably with other previou s methods of analysis. This method could provide a rapid screen for total a llele differences of greater than 10%, a threshold that should be applicabl e to detecting low relative risk genes in common diseases. Therefore, these studies suggest that DNA pooling could be a useful tool in association stu dies for the determination of candidate regions for a range of complex gene tic diseases.