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Related Experiment Video

Updated: Jul 11, 2025

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells
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FLED: a full-length eccDNA detector for long-reads sequencing data.

Fuyu Li1, Wenlong Ming2, Wenxiang Lu1

  • 1State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, P. R. China.

Briefings in Bioinformatics
|November 6, 2023
PubMed
Summary

A new algorithm, Full-Length eccDNA Detection (FLED), reconstructs extrachromosomal circular DNA (eccDNA) sequences using nanopore long-read sequencing. This method achieves high-throughput detection and reveals eccDNAs

Keywords:
extrachromosomal circular DNAfull-length detectionlong-read sequencing technology

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Reconstructing extrachromosomal circular DNA (eccDNA) sequences from short reads is difficult due to similarities with linear DNA.
  • Existing high-throughput methods for detecting full-length eccDNAs are limited.

Purpose of the Study:

  • To develop a novel algorithm for high-throughput, full-length eccDNA sequence reconstruction.
  • To investigate the role of eccDNAs in biological processes, particularly in cancer.

Main Methods:

  • Developed the Full-Length eccDNA Detection (FLED) algorithm.
  • Combined rolling circle amplification with nanopore long-read sequencing technology.
  • Validated eccDNA structures using Polymerase Chain Reaction (PCR) and Sanger sequencing.

Main Results:

  • Identified over 5000 full-length eccDNAs per sample in seven human cell lines.
  • FLED demonstrated higher sensitivity compared to existing nanopore-based eccDNA detectors.
  • Discovered eccDNAs overlapping cancer-related genes and cis-regulatory elements, with dysregulated expression in tumor cells.

Conclusions:

  • FLED enables unbiased, high-throughput reconstruction of full-length eccDNA sequences.
  • eccDNAs play a regulatory role in biological processes, including cancer development.
  • The FLED algorithm is freely available for research use.