Integrated minimum-set primers and unique probe design algorithms for differential detection on symptom-related pathogens

• Published in: Bioinformatics Vol. 21; no. 24; pp. 4330 - 4337
• Main Authors: Huang, Yu-Cheng, Chang, Chun-Fan, Chan, Chen-hsiung, Yeh, Tze-Jung, Chang, Ya-Chun, Chen, Chaur-Chin, Kao, Cheng-Yan
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 15.12.2005; Oxford Publishing Limited (England)
• Subjects: Algorithms; Base Sequence; Biological and medical sciences; Communicable Diseases - diagnosis; Computational Biology; DNA Primers; DNA Probes - genetics; Drug Design; Fundamental and applied biological sciences. Psychology; General aspects; Humans; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Models, Genetic; Plant Viruses - genetics; Plant Viruses - pathogenicity; Software Design; Thermodynamics; Virulence - genetics; Selection; Primer; Hybridization; Optimization; Amplification; Design; Polymerase chain reaction; Original document; Genetic algorithm; False negative; Pathogenic; Detection; Bioinformatics
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/bti730

Motivation: 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 method pursues a much smaller number of primers set compared with conventional PCR. In the simulation experiment for amplifying 12 669 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. Contact: cykao@csie.ntu.edu.tw Supplementary information: