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

Efrat Katsman; Shari Orlanski; Filippo Martignano; Ilana Fox-Fisher; Ruth Shemer; Yuval Dor; Aviad Zick; Amir Eden; Iacopo Petrini; Silvestro G. Conticello; Benjamin P. Berman

doi:10.1186/s13059-022-02710-1

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

Efrat Katsman, Shari Orlanski, Filippo Martignano, Ilana Fox-Fisher, Ruth Shemer, Yuval Dor, Aviad Zick, Amir Eden, Iacopo Petrini, Silvestro G. Conticello^*, Benjamin P. Berman^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

17 Scopus citations

Abstract

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: [Figure not available: see fulltext.]

Original language	American English
Article number	158
Pages (from-to)	1-25
Journal	Genome Biology
Volume	23
Issue number	1
DOIs	https://doi.org/10.1186/s13059-022-02710-1
State	Published - Dec 2022

Bibliographical note

Funding Information:
Ben Berman received startup support from The Hebrew University, the Kamea B program of the Israel Ministry of Aliyah and Immigrant Integration, and the Beethoven Foundation. This work was funded by a project grant to Berman from the Israel Cancer Research Fund Project Grant (Grant #845755). Filippo Martignano was supported by the Italian Ministry of Health (SG-2019-12370279).

Publisher Copyright:
© 2022, The Author(s).

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10.1186/s13059-022-02710-1

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title = "Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing",

abstract = "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: [Figure not available: see fulltext.]",

author = "Efrat Katsman and Shari Orlanski and Filippo Martignano and Ilana Fox-Fisher and Ruth Shemer and Yuval Dor and Aviad Zick and Amir Eden and Iacopo Petrini and Conticello, {Silvestro G.} and Berman, {Benjamin P.}",

note = "Funding Information: Ben Berman received startup support from The Hebrew University, the Kamea B program of the Israel Ministry of Aliyah and Immigrant Integration, and the Beethoven Foundation. This work was funded by a project grant to Berman from the Israel Cancer Research Fund Project Grant (Grant #845755). Filippo Martignano was supported by the Italian Ministry of Health (SG-2019-12370279). Publisher Copyright: {\textcopyright} 2022, The Author(s).",

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doi = "10.1186/s13059-022-02710-1",

language = "American English",

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AU - Orlanski, Shari

AU - Martignano, Filippo

AU - Fox-Fisher, Ilana

AU - Shemer, Ruth

AU - Dor, Yuval

AU - Zick, Aviad

AU - Eden, Amir

AU - Petrini, Iacopo

AU - Conticello, Silvestro G.

AU - Berman, Benjamin P.

N1 - Funding Information: Ben Berman received startup support from The Hebrew University, the Kamea B program of the Israel Ministry of Aliyah and Immigrant Integration, and the Beethoven Foundation. This work was funded by a project grant to Berman from the Israel Cancer Research Fund Project Grant (Grant #845755). Filippo Martignano was supported by the Italian Ministry of Health (SG-2019-12370279). Publisher Copyright: © 2022, The Author(s).

PY - 2022/12

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N2 - 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: [Figure not available: see fulltext.]

AB - 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: [Figure not available: see fulltext.]

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

Abstract

Bibliographical note

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