Selecting Optimal Oligonucleotide Primers for Multiplex PCR

Proceedings Of The Fifth International Conference On Intelligent Systems For Molecular Biology

Volume

Proceedings Of The Fifth International Conference On Intelligent Systems For Molecular Biology

Contents

We investigate the problem of designing efficient multiplex PCR for medical applications. We show that the problem is NP-complete by transformation to the Multiple Choice Matching problem and give an efficient approximation algorithm. We developed this algorithm in a computer program that predicts which genomic regions may be simultaneously amplified by PCR. Practical use of the software shows that the method can treat 250 non-polymorphic loci with less than 5 simultaneous experiments.