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Detection and validation of circular DNA fragments using nanopore sequencing

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Item Type:Article
Title:Detection and validation of circular DNA fragments using nanopore sequencing
Creators Name:Tüns, A.I. and Hartmann, T. and Magin, S. and Chamorro González, R. and Henssen, A.G. and Rahmann, S. and Schramm, A. and Köster, J.
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.
Keywords:Cancer, Circular DNA, Nanopore Sequencing, Algorithm, Snakemake
Source:Frontiers in Genetics
Publisher:Frontiers Media SA
Page Range:867018
Date:30 May 2022
Official Publication:https://doi.org/10.3389/fgene.2022.867018
PubMed:View item in PubMed

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