Multiplex PCR assay design by hybrid multiobjective evolutionary algorithm

Authors:
In-Hee Lee;Soo-Yong Shin;Byoung-Tak Zhang
Affiliations:
Biointelligence Laboratory, School of Computer Science and Engineering, Seoul National University, Seoul, Korea;Biointelligence Laboratory, School of Computer Science and Engineering, Seoul National University, Seoul, Korea;Biointelligence Laboratory, School of Computer Science and Engineering, Seoul National University, Seoul, Korea
Venue:
EMO'07 Proceedings of the 4th international conference on Evolutionary multi-criterion optimization
Year:
2007

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Abstract

Multiplex Polymerase Chain Reaction (PCR) assay is to amplify multiple target DNAs simultaneously using different primer pairs for each target DNA. Recently, it is widely used for various biology applications such as genotyping. For sucessful experiments, both the primer pairs for each target DNA and grouping of targets to be actually amplified in one tube should be optimized. This involves multiple conflicting objectives such as minimizing the interaction of primers in a group and minimizing the number of groups required for the assay. Therefore, a multiobjective evolutionary approach may be an appropriate approach. In this paper, a hybrid multiobjective evolutionary algorithm which combines ∈-multiobjective evolutionary algorithm with local search is proposed for multiplex PCR assay design. The proposed approach was compared with another multiobjective method, called MuPlex, and showed comparative performance by covering all of the given target sequences.