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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Detalles Bibliográficos
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
Descripción
Sumario: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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