Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing

The Oxford Nanopore (ONT) platform provides portable and rapid genome sequencing, and its ability to natively profile DNA methylation without complex sample processing is attractive for point-of-care real-time sequencing. We recently demonstrated ONT shallow whole-genome sequencing to detect copy nu...

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Autores principales: Katsman, Efrat, Orlanski, Shari, Martignano, Filippo, Fox-Fisher, Ilana, Shemer, Ruth, Dor, Yuval, Zick, Aviad, Eden, Amir, Petrini, Iacopo, Conticello, Silvestro G., Berman, Benjamin P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9283844/
https://www.ncbi.nlm.nih.gov/pubmed/35841107
http://dx.doi.org/10.1186/s13059-022-02710-1
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author Katsman, Efrat
Orlanski, Shari
Martignano, Filippo
Fox-Fisher, Ilana
Shemer, Ruth
Dor, Yuval
Zick, Aviad
Eden, Amir
Petrini, Iacopo
Conticello, Silvestro G.
Berman, Benjamin P.
author_facet Katsman, Efrat
Orlanski, Shari
Martignano, Filippo
Fox-Fisher, Ilana
Shemer, Ruth
Dor, Yuval
Zick, Aviad
Eden, Amir
Petrini, Iacopo
Conticello, Silvestro G.
Berman, Benjamin P.
author_sort Katsman, Efrat
collection PubMed
description The Oxford Nanopore (ONT) platform provides portable and rapid genome sequencing, and its ability to natively profile DNA methylation without complex sample processing is attractive for point-of-care real-time sequencing. We recently demonstrated ONT shallow whole-genome sequencing to detect copy number alterations (CNAs) from the circulating tumor DNA (ctDNA) of cancer patients. Here, we show that cell type and cancer-specific methylation changes can also be detected, as well as cancer-associated fragmentation signatures. This feasibility study suggests that ONT shallow WGS could be a powerful tool for liquid biopsy. GRAPHICAL ABSTRACT: [Image: see text] SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02710-1.
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spelling pubmed-92838442022-07-15 Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing Katsman, Efrat Orlanski, Shari Martignano, Filippo Fox-Fisher, Ilana Shemer, Ruth Dor, Yuval Zick, Aviad Eden, Amir Petrini, Iacopo Conticello, Silvestro G. Berman, Benjamin P. Genome Biol Method The Oxford Nanopore (ONT) platform provides portable and rapid genome sequencing, and its ability to natively profile DNA methylation without complex sample processing is attractive for point-of-care real-time sequencing. We recently demonstrated ONT shallow whole-genome sequencing to detect copy number alterations (CNAs) from the circulating tumor DNA (ctDNA) of cancer patients. Here, we show that cell type and cancer-specific methylation changes can also be detected, as well as cancer-associated fragmentation signatures. This feasibility study suggests that ONT shallow WGS could be a powerful tool for liquid biopsy. GRAPHICAL ABSTRACT: [Image: see text] SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02710-1. BioMed Central 2022-07-15 /pmc/articles/PMC9283844/ /pubmed/35841107 http://dx.doi.org/10.1186/s13059-022-02710-1 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Katsman, Efrat
Orlanski, Shari
Martignano, Filippo
Fox-Fisher, Ilana
Shemer, Ruth
Dor, Yuval
Zick, Aviad
Eden, Amir
Petrini, Iacopo
Conticello, Silvestro G.
Berman, Benjamin P.
Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing
title Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing
title_full Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing
title_fullStr Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing
title_full_unstemmed Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing
title_short Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing
title_sort detecting cell-of-origin and cancer-specific methylation features of cell-free dna from nanopore sequencing
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9283844/
https://www.ncbi.nlm.nih.gov/pubmed/35841107
http://dx.doi.org/10.1186/s13059-022-02710-1
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