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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...

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Related Experiment Video

Updated: Jun 5, 2026

CIRCLE-Seq for Interrogation of Off-Target Gene Editing
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Enhancing Next-Generation Sequencing Sensitivity with High-Recovery Adapter Ligation and Cas9-Mediated Dimer

Hwayeon Jeong1, Hana Kim1, Eunyoung Cho1

  • 1Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea.

Clinical Chemistry
|June 4, 2026
PubMed
Summary

PRIDE NGS enhances liquid biopsy sensitivity by improving adapter ligation efficiency and removing dimers, enabling earlier cancer detection and monitoring of minimal residual disease. This method lowers the detection limit for ultra-low-frequency variants without increasing sequencing costs.

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Enhanced Genome Editing with Cas9 Ribonucleoprotein in Diverse Cells and Organisms

Published on: May 25, 2018

Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • Detecting ultra-low-frequency variants (<0.1%) in circulating tumor DNA (ctDNA) is crucial for early cancer detection and minimal residual disease monitoring.
  • Sensitivity in liquid biopsy is limited by molecular recovery during library preparation, particularly adapter ligation.
  • Losses in early library preparation steps reduce analyzable molecules, which cannot be compensated by increased sequencing depth or bioinformatics.

Purpose of the Study:

  • To develop a novel library preparation strategy to improve the recovery and detection of ultra-low-frequency variants in liquid biopsy.
  • To enhance the sensitivity of next-generation sequencing (NGS) for clinical applications like early cancer detection.

Main Methods:

  • Developed Powerful Recovery and Improved Dimer Elimination (PRIDE) NGS, a library preparation method.
  • PRIDE NGS increases adapter ligation efficiency and utilizes CRISPR/Cas9 for adapter dimer removal.
  • The method is compatible with standard workflows, requiring no additional sequencing depth or bioinformatic changes.

Main Results:

  • PRIDE NGS significantly improved the recovery and detection of low-frequency variants compared to conventional methods.
  • More variants below 0.1% allele frequency were detected in reference standards using PRIDE NGS.
  • Clinical plasma samples showed increased variant detection, including those with functional impact, at comparable or lower sequencing depths.

Conclusions:

  • PRIDE NGS overcomes a key bottleneck in library preparation, lowering the detection threshold for ultra-low-frequency variants in liquid biopsy.
  • This clinically applicable approach enhances analytical sensitivity by improving molecular recovery, not by increasing sequencing burden.
  • PRIDE NGS supports routine clinical testing and longitudinal monitoring for cancer through improved liquid biopsy sensitivity.