Selecting Optimal Oligonucleotide Primers for Multiplex PCR

Pierre Nicodème and Jean-Marc Steyaert

Fifth International Conference on Intelligent Systems for Molecular Biology ISMB97 , pages 210-213, 1997


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.

Key words and phrases Multiplex PCR, diagnostic, heuristic algorithms, NP-completeness.

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