Huang, Yu-ChengYu-ChengHuangChang, Chun-FanChun-FanChangChan, Chen-hsiungChen-hsiungChanYeh, Tze-JungTze-JungYehYA-CHUN CHANGChen, Chaur-ChinChaur-ChinChenKao, Cheng-YanCheng-YanKao2018-09-102018-09-102005http://www.scopus.com/inward/record.url?eid=2-s2.0-28944447086&partnerID=MN8TOARShttp://scholars.lib.ntu.edu.tw/handle/123456789/314341Motivation: Differential detection on symptom-related pathogens (SRP) is critical for fast identification and accurate control against epidemic diseases. Conventional polymerase chain reaction (PCR) requires a large number of unique primers to amplify selected SRP target sequences. With multiple-use primers (mu-primers), multiple targets can be amplified and detected in one PCR experiment under standard reaction condition and reduced detection complexity. However, the time complexity of designing mu-primers with the best heuristic method available is too vast. We have formulated minimum-set mu-primer design problem as a set covering problem (SCP), and used modified compact genetic algorithm (MCGA) to solve this problem optimally and efficiently. We have also proposed new strategies of primer/probe design algorithm (PDA) on combining both minimum-set (MS) mu-primers and unique (UniQ) probes. Designed primer/ probe set by PDA-MS/UniQ can amplify multiple genes simultaneously upon physical presence with minimum-set mu-primer amplification (MMA) before intended differential detection with probes-array hybridization (PAH) on the selected target set of SRP. Results: The proposed PDA-MS/UniQ metho d pursues a much smaller number of primers set compared with conventional PCR. In the simulation experiment for amplifying 12669 target sequences, the performance of our method with 68% reduction on required mu-primers number seems to be superior to the compared heuristic approaches in both computation efficiency and reduction percentage. Our integrated PDA-MS/UniQ method is applied to the differential detection on 9 plant viruses from 4 genera with MMA and PAH of 11 mu-primers instead of 18 unique ones in conventional PCR while amplifying overall 9 target sequences. The results of wet lab experiments with integrated MMA-PAH system have successfully validated the specificity and sensitivity of the primers/ probes designed with our integrated PDA-MS/UniQ method. ? The Author 2005. Published by Oxford University Press. All rights reserved.application/pdf339087 bytesapplication/pdf[SDGs]SDG3article; computer system; DNA hybridization; DNA probe; gene amplification; gene targeting; genetic algorithm; genetic selection; genus; intermethod comparison; microbiological examination; molecular probe; nonhuman; pathogenesis; plant virus; polymerase chain reaction; priority journal; process design; sensitivity and specificity; validation process; Algorithms; Base Sequence; Communicable Diseases; Computational Biology; DNA Primers; DNA Probes; Drug Design; Humans; Models, Genetic; Plant Viruses; Software Design; Thermodynamics; Virulencejournal article10.1093/bioinformatics/bti730