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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...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
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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. |
format | Online Article Text |
id | pubmed-9195511 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
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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