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Integrated minimum-set primers and unique probe design algorithms for differential detection on symptom-related pathogens |
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| Authors: | Huang Yu-Cheng Chang Chun-Fan Chan Chen-Hsiung Yeh Tze-Jung Chang Ya-Chun Chen Chaur-Chin Kao Cheng-Yan |
| Affiliation: | 1Bioinformatics Laboratory, Department of Computer Science and Information Engineering, National Taiwan University Taipei, Taiwan 2Department of Plant Pathology and Microbiology, National Taiwan University Taipei, Taiwan 3Breed-Use-Special Laboratory, Center of Agriculture Hierarchical Utilization, Graduate Institute of Biotechnology, Chinese Culture University Taipei, Taiwan 4Department of Computer Science, National Tsing-Hua University Hsinchu, Taiwan 5Institute for Information Industry Taipei, Taiwan |
| Abstract: | Motivation: Differential detection on symptom-related pathogens(SRP) is critical for fast identification and accurate controlagainst epidemic diseases. Conventional polymerase chain reaction(PCR) requires a large number of unique primers to amplify selectedSRP target sequences. With multiple-use primers (mu-primers),multiple targets can be amplified and detected in one PCR experimentunder standard reaction condition and reduced detection complexity.However, the time complexity of designing mu-primers with thebest heuristic method available is too vast. We have formulatedminimum-set mu-primer design problem as a set covering problem(SCP), and used modified compact genetic algorithm (MCGA) tosolve this problem optimally and efficiently. We have also proposednew strategies of primer/probe design algorithm (PDA) on combiningboth minimum-set (MS) mu-primers and unique (UniQ) probes. Designedprimer/probe set by PDA-MS/UniQ can amplify multiple genes simultaneouslyupon physical presence with minimum-set mu-primer amplification(MMA) before intended differential detection with probes-arrayhybridization (PAH) on the selected target set of SRP. Results: The proposed PDA-MS/UniQ method pursues a much smallernumber of primers set compared with conventional PCR. In thesimulation experiment for amplifying 12 669 target sequences,the performance of our method with 68% reduction on requiredmu-primers number seems to be superior to the compared heuristicapproaches in both computation efficiency and reduction percentage.Our integrated PDA-MS/UniQ method is applied to the differentialdetection on 9 plant viruses from 4 genera with MMA and PAHof 11 mu-primers instead of 18 unique ones in conventional PCRwhile amplifying overall 9 target sequences. The results ofwet lab experiments with integrated MMA-PAH system have successfullyvalidated the specificity and sensitivity of the primers/probesdesigned with our integrated PDA-MS/UniQ method. Contact: cykao{at}csie.ntu.edu.tw Supplementary information: http://www.csie.ntu.edu.tw/~cykao/pda/ |
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