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Updated: Jul 14, 2026

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

Published on: April 4, 2016

Circlehunter: a tool to identify extrachromosomal circular DNA from ATAC-Seq data.

Manqiu Yang¹, Shufan Zhang¹, Rong Jiang¹

¹School of Biology and Basic Medical Sciences, Soochow University, 215123, Suzhou, China.

|May 22, 2023

Summary

Extrachromosomal circular DNA (ecDNA) drives cancer evolution and heterogeneity. A new tool, CircleHunter, identifies ecDNA from ATAC-Seq data, revealing oncogene amplifications and therapeutic targets in lung cancer.

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Last Updated: Jul 14, 2026

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

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Published on: April 4, 2016

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

Area of Science:

Genomics
Cancer Biology
Bioinformatics

Background:

Extrachromosomal circular DNA (ecDNA) significantly contributes to cancer cell evolution and heterogeneity due to its non-Mendelian inheritance.
Understanding ecDNA's role is crucial for developing targeted cancer therapies.

Purpose of the Study:

To develop and validate a computational tool, CircleHunter, for identifying ecDNA from ATAC-Seq data.
To investigate the prevalence and characteristics of ecDNA-harboring oncogenes in various cancer types.

Main Methods:

CircleHunter utilizes the enhanced chromatin accessibility of ecDNA to identify it from ATAC-Seq data.
The tool's performance was evaluated using simulated data, achieving an F1 score of 0.93.
Analysis of 94 public ATAC-Seq datasets identified 1312 ecDNAs, including 37 amplified oncogenes.

Main Results:

CircleHunter accurately identifies ecDNA with high sensitivity and specificity, even with short read lengths.
The study identified numerous oncogenes within ecDNAs across diverse cancer datasets.
In small cell lung cancer, ecDNA-driven MYC amplification influenced NEUROD1 expression, suggesting sensitivity to Aurora kinase inhibitors.

Conclusions:

CircleHunter provides a valuable pipeline for ecDNA detection and analysis in cancer research.
The findings highlight ecDNA's role in oncogene amplification and provide insights into potential therapeutic strategies targeting ecDNA-driven cancers.