Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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Comparison of digital PCR platforms using the molecular marker

  • Cherl-Joon Lee (Department of Bio-Convergence Engineering, Dankook University) ;
  • Wonseok Shin (NGS Clinical Laboratory, Dankook University Hospital) ;
  • Minsik Song (OPTOLANE Inc.) ;
  • Seung-Shick Shin (OPTOLANE Inc.) ;
  • Yujun Park (Department of Microbiology, College of Science & Technology, Dankook University) ;
  • Kornsorn Srikulnath (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Dong Hee Kim (Department of Anesthesiology and Pain Management, Dankook University College of Medicine) ;
  • Kyudong Han (Department of Bio-Convergence Engineering, Dankook University)
  • Received : 2023.02.02
  • Accepted : 2023.03.29
  • Published : 2023.06.30
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Abstract

Assays of clinical diagnosis and species identification using molecular markers are performed according to a quantitative method in consideration of sensitivity, cost, speed, convenience, and specificity. However, typical polymerase chain reaction (PCR) assay is difficult to quantify and have various limitations. In addition, to perform quantitative analysis with the quantitative real-time PCR (qRT-PCR) equipment, a standard curve or normalization using reference genes is essential. Within the last a decade, previous studies have reported that the digital PCR (dPCR) assay, a third-generation PCR, can be applied in various fields by overcoming the shortcomings of typical PCR and qRT-PCR assays. We selected Stilla Naica System (Stilla Technologies), Droplet Digital PCR Technology (Bio-Rad), and Lab on an Array Digital Real-Time PCR analyzer system (OPTOLANE) for comparative analysis among the various droplet digital PCR platforms currently in use commercially. Our previous study discovered a molecular marker that can distinguish Hanwoo species (Korean native cattle) using Hanwoo-specific genomic structural variation. Here, we report the pros and cons of the operation of each dPCR platform from various perspectives using this species identification marker. In conclusion, we hope that this study will help researchers to select suitable dPCR platforms according to their purpose and resources.

Keywords

Acknowledgement

The authors gratefully acknowledge the Bio-Medical Engineering Research Center at Dankook University. The research institute has been supported by the Department of Microbiology was supported through the Research-Focused Department Promotion & Interdisciplinary Convergence Research Project as a part of the Support Program for University Development for Dankook University in 2022.

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