Multiplex PCR Primer Design for Simultaneous Detection of Multiple Pathogens

2015 ◽  
pp. 91-101 ◽  
Author(s):  
Wenchao Yan
Keyword(s):  
Multiplex Pcr ◽  
Simultaneous Detection ◽  
Primer Design ◽  
Multiple Pathogens ◽  
Pcr Primer

Simultaneous detection of multiple pathogens by multiplex PCR coupled with DNA biochip hybridization

2017 ◽  
Vol 52 (2) ◽  
pp. 186-195 ◽  
Author(s):  
Hsiang-Yun Tung ◽  
Wei-Chen Chen ◽  
Bor-Rung Ou ◽  
Jan-Ying Yeh ◽  
Yeong-Hsiang Cheng ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Simultaneous Detection ◽  
Clinical Samples ◽  
Single Infection ◽  
Pcr Analysis ◽  
Enzyme Linked Immunosorbent Assay ◽  
Viral Pathogens ◽  
Single Target ◽  
Primer Sets ◽  
Multiple Pathogens

Traditional serological enzyme-linked immunosorbent assay (ELISA) is routinely used to monitor pathogens during quarantine in most animal facilities to prevent possible infection. However, the ELISA platform is a single-target assay, and screening all targeted pathogens is time-consuming and laborious. In this study, to increase sensitivity and to reduce diagnosis time for high-throughput processes, multiplex PCR and DNA biochip techniques were combined to develop a multi-pathogen diagnostic method for use instead of routine ELISA. Eight primer sets were designed for multiplex PCR to detect genes from seven targeted bacterial and viral pathogens. DNA–DNA hybridization was conducted on a biochip following the multiple PCR analysis. Using this method, a total of 24 clinical samples were tested, and the result showed that not only single infection but also co-infection by multi-pathogens can be detected. In conclusion, multiplex PCR coupled with a DNA biochip is an efficient method for detecting multi-pathogens in a reaction. This platform is a useful tool for quarantine services and disease prevention in animal facilities.

scholarly journals The web-based multiplex PCR primer design software Ultiplex and the associated experimental workflow: up to 100- plex multiplicity

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jie Yuan ◽  
Ji Yi ◽  
Meixiao Zhan ◽  
Qingqing Xie ◽  
Ting Ting Zhen ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Secondary Structures ◽  
Primer Design ◽  
Design Tool ◽  
Web Based ◽  
Tumour Diagnosis ◽  
Design Software ◽  
Nonspecific Amplification ◽  
User Friendly ◽  
Pcr Primer

Abstract Background A large number of variants have been employed in various medical applications, such as providing medication instructions, disease susceptibility testing, paternity testing, and tumour diagnosis. A high multiplicity PCR will outperform other technologies because of its lower cost, reaction time and sample consumption. To conduct a multiplex PCR with higher than 100 plex multiplicity, primers need to be carefully designed to avoid the formation of secondary structures and nonspecific amplification between primers, templates and products. Thus, a user-friendly, highly automated and highly user-defined web-based multiplex PCR primer design software is needed to minimize the work of primer design and experimental verification. Results Ultiplex was developed as a free online multiplex primer design tool with a user-friendly web-based interface (http://ultiplex.igenebook.cn). To evaluate the performance of Ultiplex, 294 out of 295 (99.7%) target primers were successfully designed. A total of 275 targets produced qualified primers after primer filtration, and 271 of those targets were successfully clustered into one compatible PCR group and could be covered by 108 primers. The designed primer group stably detected the rs28934573(C > T) mutation at lower than a 0.25% mutation rate in a series of samples with different ratios of HCT-15 and HaCaT cell line DNA. Conclusion Ultiplex is a web-based multiplex PCR primer tool that has several functions, including batch design and compatibility checking for the exclusion of mutual secondary structures and mutual false alignments across the whole genome. It offers flexible arguments for users to define their own references, primer Tm values, product lengths, plex numbers and tag oligos. With its user-friendly reports and web-based interface, Ultiplex will provide assistance for biological applications and research involving genomic variants.

scholarly journals MPprimer: a program for reliable multiplex PCR primer design

2010 ◽  
Vol 11 (1) ◽  
pp. 143 ◽  
Author(s):  
Zhiyong Shen ◽  
Wubin Qu ◽  
Wen Wang ◽  
Yiming Lu ◽  
Yonghong Wu ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Primer Design ◽  
Pcr Primer

A novel common primer multiplex PCR (CP-M-PCR) method for the simultaneous detection of meat species

Food Control ◽  
2009 ◽  
Vol 20 (4) ◽  
pp. 366-370 ◽  
Author(s):  
Weibin Bai ◽  
Wentao Xu ◽  
Kunlun Huang ◽  
Yanfang Yuan ◽  
Sishuo Cao ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Simultaneous Detection ◽  
Meat Species ◽  
Pcr Method

scholarly journals Degenerate PCR primer design for the specific identification of rhinovirus C

2015 ◽  
Vol 214 ◽  
pp. 15-24 ◽  
Author(s):  
Young Ran Nam ◽  
Uk Lee ◽  
Han Seok Choi ◽  
Kyoung Jin Lee ◽  
Nari Kim ◽  
...  
Keyword(s):  
Primer Design ◽  
Degenerate Pcr ◽  
Specific Identification ◽  
Rhinovirus C ◽  
Pcr Primer

scholarly journals VizPrimer: a web server for visualized PCR primer design based on known gene structure

2011 ◽  
Vol 27 (24) ◽  
pp. 3432-3434 ◽  
Author(s):  
Y. Zhou ◽  
W. Qu ◽  
Y. Lu ◽  
Y. Zhang ◽  
X. Wang ◽  
...  
Keyword(s):  
Gene Structure ◽  
Web Server ◽  
Primer Design ◽  
Pcr Primer

Use of a Multiplex PCR System for the Simultaneous Detection of Heat Labile Toxin I and Heat Stable Toxin II Genes of Enterotoxigenic Escherichia coli in Skim Milk and Porcine Stool

1998 ◽  
Vol 61 (2) ◽  
pp. 141-145 ◽  
Author(s):  
HAU-YANG TSEN ◽  
LIANG-ZHAO JIAN ◽  
WAN-RONG CHI
Keyword(s):  
Escherichia Coli ◽  
Multiplex Pcr ◽  
Simultaneous Detection ◽  
Skim Milk ◽  
Pcr Primers ◽  
Enterotoxigenic Escherichia Coli ◽  
Farm Animals ◽  
Target Cells ◽  
Heat Stable ◽  
Heat Labile

Enterotoxigenic Escherichia coli (ETEC) strains which produce heat labile and/or heat stable toxins (LT and ST) may cause diarrhea in humans and farm animals. Using PCR primers specific for the LT I and ST II genes, a multiplex PCR system which allows detection of LT I- and ST II-producing ETEC strains was developed. When skim milk was used for a PCR assay, it was found that if target cells in the sample were precultured in MacConkey broth for 8 h prior to PCR as few as 100 cells per ml of the sample could be detected. Without the preculture step, 104 CFU of target cells per 0.2 g of porcine stool specimen were required to generate visible PCR products. The multiplex PCR System can be used for rapid testing of fecal specimens, food and possibly environmental samples for the presence of ETEC strains.

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