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 journalArticlepeer-review

17 Scopus citations


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 languageAmerican English
Article number158
Pages (from-to)1-25
JournalGenome Biology
Issue number1
StatePublished - 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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