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Updated: Sep 7, 2025
Nanopore DNA Sequencing for Metagenomic Soil Analysis
Published on: December 14, 2017
Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing
Alicia Isabell Tüns1, Till Hartmann2, Simon Magin3
1Laboratory of Molecular Oncology, West German Cancer Center, Department of Medical Oncology, University Hospital Essen, Essen, Germany.
Abstract:
Occurrence of extra-chromosomal circular DNA is a phenomenon frequently observed in tumor cells, and the presence of such DNA has been recognized as a marker of adverse outcome across cancer types. We here describe a computational workflow for identification of DNA circles from long-read sequencing data. The workflow is implemented based on the Snakemake workflow management system. Its key step uses a graph-theoretic approach to identify putative circular fragments validated on simulated reads. We then demonstrate robustness of our approach using nanopore sequencing of selectively enriched circular DNA by highly sensitive and specific recovery of plasmids and the mitochondrial genome, which is the only circular DNA in normal human cells. Finally, we show that the workflow facilitates detection of larger circular DNA fragments containing extrachromosomal copies of the MYCN oncogene and the respective breakpoints, which is a potentially useful application in disease monitoring of several cancer types.
Insights
We developed a computational workflow to identify extra-chromosomal circular DNA (eccDNA) using long-read sequencing. This method accurately detects circular DNA, including oncogene fragments, aiding cancer research and monitoring.
Area of Science:
- Genomics
- Bioinformatics
- Cancer Biology
Background:
- Extra-chromosomal circular DNA (eccDNA) is prevalent in tumor cells and linked to poor prognosis.
- Identifying eccDNA is crucial for understanding cancer progression and developing therapeutic strategies.
Purpose of the Study:
- To present a computational workflow for detecting DNA circles from long-read sequencing data.
- To validate the workflow's accuracy and robustness in identifying various circular DNA elements.
Main Methods:
- Implementation of a Snakemake-based computational workflow.
- Utilizing a graph-theoretic approach for identifying circular DNA fragments.
- Validation using simulated reads and Nanopore sequencing of enriched circular DNA.
Main Results:
- The workflow demonstrated high sensitivity and specificity in recovering plasmids and mitochondrial DNA.
- Successfully detected larger circular DNA fragments, including extrachromosomal MYCN oncogene copies and breakpoints.
- The approach is robust and applicable to diverse circular DNA structures.
Conclusions:
- The developed workflow provides a reliable method for identifying eccDNA from long-read sequencing data.
- This tool has potential applications in cancer research, particularly for disease monitoring and understanding oncogene amplification.
