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 ε-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.
Keywords
- Local Search
- Multiobjective Optimization
- Multiplex Polymerase Chain Reaction
- Multiobjective Evolutionary Algorithm
- Partition Part
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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References
Cortez, A.L.L., Carvalho, A.C., Ikuno, A.A., Bürger, K.P., Vidal-Martins, A.M.C.: Identification of Salmonella spp. isolates from chicken abattoirs by multiplex-PCR. Research in Veterinary Science 81(3), 340–344 (2006)
Aquilante, C.L., Langaee, T.Y., Anderson, P.L., Zineh, I., Fletcher, C.V.: Multiplex PCR-pyrosequencing assay for genotyping CYP3A5 polymorphisms. Clinica Chimica Acta 372(1–2), 195–198 (2006)
Jääskeläinen, A.J., Piiparinen, H., Lappalainen, M., Koskiniemi, M., Antti, V.: Multiplex-PCR and oligonucleotide microarray for detection of eight different herpesviruses from clinical specimens. Journal of Clinical Virology 37(2), 83–90 (2006)
Nicodème, P., Steyaert, J.-M.: Selecting optimal oligonucleotide primers for multiplex PCR. In: Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, pp. 210–213 (1997)
Rouchka, E.C., Khalyfa, A., Cooper, N.G.F.: MPrime: efficient large scale multiple primer and oligonucleotide design for customized gene microarrays. BMC Bioinformatics 6(175) (2005)
Schoske, R., Vallone, P.M., Ruitberg, C.M., Butler, J.M.: Multiplex PCR design strategy used for the simultaneous amplification of 10 Y chromosome short tandem repeat (STR) loci. Analytical and Bioanalytical Chemistry 375, 333–343 (2003)
Liang, H.-L., Lee, C., Wu, J.-S.: Multiplex PCR primer design for gene family using genetic algorithm. In: GECCO ’05, Washington, DC, USA, pp. 67–74. ACM Press, New York (2005)
Lin, F.-M., Huang, H.-D., Huang, H.-Y., Horng, J.-T.: Primer design for multiplex PCR using a genetic algorithm. In: GECCO ’05, Washington, DC, USA, pp. 475–476. ACM Press, New York (2005)
Kaplinski, L., Andreson, P., Puurand, T., Remm, M.: MultiPLX: automatic grouping and evaluation of PCR primers. Bioinformatics 21(8), 1701–1702 (2005)
Rachlin, J., Ding, C., Cantor, C., Kasif, S.: MuPlex: multi-objective multiplex PCR assay design. Nucleic Acids Research 33, W544–W547 (2005)
Lee, C., Wu, J.-S., Shiue, Y.-L., Liang, H.-L.: MultiPrimer: Software for multiple primer design. Applied Bioinformatics 5(2), 99–109 (2006)
Yamada, T., Soma, H., Morishita, S.: PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genome. Nucleic Acids Research 34, W665–W669 (2006)
Rachlin, J., Ding, C., Cantor, C., Kasif, S.: Computational tradeoffs in multiplex PCR assay design for SNP genotyping. BMC Genomics 6(102) (2005)
Garey, M.R., Johnson, D.S.: Computers and Intractability: A Guide to the Theory of NP-completeness. W.H. Freeman and company, New York (1979)
Laumanns, M., Thiele, L., Deb, K., Zitzler, E.: Combining convergence and diversity in evolutionary multi-objective optimization. Evolutionary Computation 10(3), 263–282 (2002)
Shin, S.-Y., Lee, I.-H., Zhang, B.-T.: Multi-objective evolutionary optimization of DNA sequences for reliable DNA computing. IEEE Transactions on Evolutionary Computation 9(2), 143–158 (2005)
Rozen, S., Skaletsky, H.J.: Primer3 on the www for general users and for biologist programmers. In: Krawetz, S., Misener, S. (eds.) Bioinformatics Methods and Protocols: Methods in Molecular Biology, pp. 365–386. Humana Press, Totowa (2000), Source code available at, http://fokker.wi.mit.edu/primer3/
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Lee, IH., Shin, SY., Zhang, BT. (2007). Multiplex PCR Assay Design by Hybrid Multiobjective Evolutionary Algorithm. In: Obayashi, S., Deb, K., Poloni, C., Hiroyasu, T., Murata, T. (eds) Evolutionary Multi-Criterion Optimization. EMO 2007. Lecture Notes in Computer Science, vol 4403. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-70928-2_30
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DOI: https://doi.org/10.1007/978-3-540-70928-2_30
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-70927-5
Online ISBN: 978-3-540-70928-2
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