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Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing

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...

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Autores principales: Tüns, Alicia Isabell, Hartmann, Till, Magin, Simon, González, Rocío Chamorro, Henssen, Anton George, Rahmann, Sven, Schramm, Alexander, Köster, Johannes
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9195511/
https://www.ncbi.nlm.nih.gov/pubmed/35711922
http://dx.doi.org/10.3389/fgene.2022.867018
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author Tüns, Alicia Isabell
Hartmann, Till
Magin, Simon
González, Rocío Chamorro
Henssen, Anton George
Rahmann, Sven
Schramm, Alexander
Köster, Johannes
author_facet Tüns, Alicia Isabell
Hartmann, Till
Magin, Simon
González, Rocío Chamorro
Henssen, Anton George
Rahmann, Sven
Schramm, Alexander
Köster, Johannes
author_sort Tüns, Alicia Isabell
collection PubMed
description 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.
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spelling pubmed-91955112022-06-15 Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing Tüns, Alicia Isabell Hartmann, Till Magin, Simon González, Rocío Chamorro Henssen, Anton George Rahmann, Sven Schramm, Alexander Köster, Johannes Front Genet Genetics 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. Frontiers Media S.A. 2022-05-30 /pmc/articles/PMC9195511/ /pubmed/35711922 http://dx.doi.org/10.3389/fgene.2022.867018 Text en Copyright © 2022 Tüns, Hartmann, Magin, González, Henssen, Rahmann, Schramm and Köster. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Tüns, Alicia Isabell
Hartmann, Till
Magin, Simon
González, Rocío Chamorro
Henssen, Anton George
Rahmann, Sven
Schramm, Alexander
Köster, Johannes
Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing
title Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing
title_full Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing
title_fullStr Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing
title_full_unstemmed Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing
title_short Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing
title_sort detection and validation of circular dna fragments using nanopore sequencing
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9195511/
https://www.ncbi.nlm.nih.gov/pubmed/35711922
http://dx.doi.org/10.3389/fgene.2022.867018
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