Abstract
This paper presents a new program to design specific and reliable primers for amplification of exons in a multiplex PCR. The program is composed of two components: a data acquisition component and a data processing component. The data acquisition component automates time–consuming steps of preparing data for the primers design algorithms. It provides up-to-date information about selected genes including coding sequences and locations of SNPs. The data processing component automates the process of grouping candidate primers into an optimal set for the multiplex PCR by checking their specificity. It is an original and unconventional method that combines the hierarchical clustering and the separate-and-conquer strategy. The results obtained for various genes and presented in this paper prove that the proposed method is an effective way to design an optimal set of primers for the multiplex PCR.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Aggarwal, C.C., Yu, P.S.: Data Mining Techniques for Associations, Clustering and Classification. In: Zhong, N., Zhou, L. (eds.) PAKDD 1999. LNCS (LNAI), vol. 1574, pp. 13–23. Springer, Heidelberg (1999)
Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic local alignment search tool. J. Mol. Biol. 215(3), 403–410 (1990)
Chamberlain, J.S., Gibbs, R.A., Ranier, J.E., Nguyen, P.N., Caskey, C.T.: Deletion screening of the duchenne muscular dystrophy locus via multiplex dna amplification. Nucleic Acids Res. 16(23), 11141–11156 (1988)
Chen, et al.: Design of multiplex pcr primers using heuristic algorithm for sequential deletion applications. Comput. Biol. Chem. 33(2), 181–188 (2009)
Defays, D.: An efficient algorithm for a complete link method. The Computer Journal 20(4), 364–366 (1977)
Dieffenbach, C.W., Lowe, T.M., Dveksler, G.S.: General concepts for pcr primer design. PCR Methods Appl. 3(3), S30–S37 (1993)
Edwards, M.C., Gibbs, R.A.: Multiplex pcr: advantages, development, and applications. PCR Methods Appl. 3(4), S65–S75 (1994)
Ncbi-genbank flat file release, ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt
Fürnkranz, J.: Separate-and-conquer rule learning. Artificial Intelligence Review 13, 3–54 (1999)
Gervais, A.L., Marques, M., Gaudreau, L.: Pcrtiler: automated design of tiled and specific pcr primer pairs. Nucleic Acids Res. 38(Web Server issue), W308–W312 (2010)
Guberman, et al: Biomart central portal: an open database network for the biological community. Database (Oxford) 2011, bar041 (2011)
Henegariu, O., Heerema, N.A., Dlouhy, S.R., Vance, G.H., Vogt, P.H.: Multiplex PCR: critical parameters and step-by-step protocol. Biotechniques 23(3), 504–511 (1997)
dbsnp summary, http://www.ncbi.nlm.nih.gov/SNP/snp_summary.cgi
Huang, Y.C., Chang, C.F., Chan, C.H., Yeh, T.J., Chang, Y.C., Chen, C.C., Kao, C.Y.: Integrated minimum-set primers and unique probe design algorithms for differential detection on symptom-related pathogens. Bioinformatics 21(24), 4330–4337 (2005)
Jabado, O.J., Palacios, G., Kapoor, V., Hui, J., Renwick, N., Zhai, J., Briese, T., Lipkin, W.I.: Greene scprimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments. Nucleic Acids Res. 34(22), 6605–6611 (2006)
Kent, W.J.: Blat–the blast-like alignment tool. Genome Res. 12(4), 656–664 (2002)
Markoulatos, P., Siafakas, N., Moncany, M.: Multiplex polymerase chain reaction: a practical approach. J. Clin. Lab. Anal. 16(1), 47–51 (2002)
Qu, W., Shen, Z., Zhao, D., Yang, Y., Zhang, C.: Mfeprimer: multiple factor evaluation of the specificity of pcr primers. Bioinformatics 25(2), 276–278 (2009)
Rachlin, J., Ding, C., Cantor, C., Kasif, S.: Computational tradeoffs in multiplex pcr assay design for snp genotyping. BMC Genomics 6, 102 (2005)
Rachlin, J., Ding, C., Cantor, C., Kasif, S.: Muplex: multi-objective multiplex pcr assay design. Nucleic Acids Res. 33(Web Server issue), W544–W547 (2005)
Robertson, J.M., Walsh-Weller, J.: An introduction to pcr primer design and optimization of amplification reactions. Methods Mol. Biol. 98, 121–154 (1998)
Rozen, S., Skaletsky, H.: Primer3 on the www for general users and for biologist programmers. Methods Mol. Biol. 132, 365–386 (2000)
Shen, et al.: Mpprimer: a program for reliable multiplex pcr primer design. BMC Bioinformatics 11, 143 (2010)
Smith, T.F., Waterman, M.S.: Identification of common molecular subsequences. J. Mol. Biol. 147(1), 195–197 (1981)
Untergasser, A., Nijveen, H., Rao, X., Bisseling, T., Geurts, R., Leunissen, J.A.M.: Primer3plus, an enhanced web interface to primer3. Nucleic Acids Res. 35(Web Server issue), W71–W74 (2007)
Wang, J., Li, K.-B., Sung, W.-K.: G-primer: greedy algorithm for selecting minimal primer set. Bioinformatics 20(15), 2473–2475 (2004)
Yamada, T., Soma, H., Morishita, S.: Primerstation: a highly specific multiplex genomic pcr primer design server for the human genome. Nucleic Acids Res. 34(Web Server issue), W665–W669 (2006)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Skowron, A., Pokrzywa, R. (2013). An Automated Approach of Designing Multiplex PCR Primers for the Amplification of Exons. In: Morzy, T., Härder, T., Wrembel, R. (eds) Advances in Databases and Information Systems. Advances in Intelligent Systems and Computing, vol 186. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-32741-4_22
Download citation
DOI: https://doi.org/10.1007/978-3-642-32741-4_22
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-32740-7
Online ISBN: 978-3-642-32741-4
eBook Packages: EngineeringEngineering (R0)