Genotyping of Pooled Microsatellite Markers by Combinatorial Optimization Techniques

An important everyday task for geneticists and molecular biologists is that of isolating and analyzing some particular DNA regions (markers), each drawn from a limited and known set of possible values (alleles). This procedure is called genotyp-ing and is based on DNA ampliication and size separation. In order to increase the throughput of genotyping, recently a new experiment has been proposed which tries to analyze many diierent markers of similar size at once. We study the mathematical problem corresponding to this model and give a branch and bound algorithm for its solution. We show that by using the techniques described in this paper, geno-typing of pooled markers can be computed eeectively, thus potentially achieving a considerable reduction in time and expense.