DNA pooling is a potential tool for the efficient analysis of the large numbers of samples and DNA markers that are necessary for genome-wide association studies. A simple accurate method for measuring total allele differences 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 evaluated 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 different subjects. Pools were created from previously individually genotyped subjects and constructed so that the pool comparisons would provide real total allele differences varying from 0% to 55%. Calculated pool differences were then compared with the real total allele differences determined by individual genotyping results. Together over 200 comparisons demonstrated a correlation coefficient of 0.96, which compared favorably with other previous methods of analysis. This method could provide a rapid screen for total allele differences of greater than 10%, a threshold that should be applicable to detecting low relative risk genes in common diseases. Therefore, these studies suggest that DNA pooling could be a useful tool in association studies for the determination of candidate regions for a range of complex genetic diseases.
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