Genomics Inform.  2020 Mar;18(1):e4. 10.5808/GI.2020.18.1.e4.

Quantitative evaluation of the molecular marker using droplet digital PCR

Affiliations
  • 1Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea
  • 2Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea
  • 3Livestock Research Institute, Yeongju 36052, Korea
  • 4Department of Anesthesiology and Pain Management, Dankook University College of Medicine, Cheonan 31116, Korea

Abstract

Transposable elements (TEs) constitute approximately half of Bovine genome. They can be a powerful species-specific marker without regression mutations by the structure variation (SV) at the time of genomic evolution. In a previous study, we identified the Hanwoo-specific SV that was generated by a TE–association deletion event using traditional PCR method and Sanger sequencing validation. It could be used as a molecular marker to distinguish different cattle breeds (i.e., Hanwoo vs. Holstein). However, PCR is defective with various final copy quantifications from every sample. Thus, we applied to the droplet digital PCR (ddPCR) platform for accurate quantitative detection of the Hanwoo-specific SV. Although samples have low allele frequency variation within Hanwoo population, ddPCR could perform high sensitive detection with absolute quantification. We aimed to use ddPCR for more accurate quantification than PCR. We suggest that the ddPCR platform is applicable for the quantitative evaluation of molecular markers.

Keyword

droplet digital PCR; Hanwoo-specific marker; structure variation
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