Accurate detection of circulating tumor DNA using nanopore consensus sequencing
Accurate detection of circulating tumor DNA using nanopore consensus sequencing
ABSTRACT Levels of circulating tumor DNA (ctDNA) in liquid biopsies may serve as a sensitive biomarker for real-time, minimally-invasive tumor diagnostics and monitoring. However, detecting ctDNA is challenging, as much fewer than 5% of the cell-free DNA in the blood typically originates from the tumor. To detect lowly abundant ctDNA molecules based on somatic variants, extremely sensitive sequencing methods are required. Here, we describe a new technique, CyclomicsSeq, which is based on Oxford Nanopore sequencing of concatenated copies of a single DNA molecule. Consensus calling of the DNA copies increased the base-calling accuracy ～60x, enabling accurate detection of TP53 mutations at frequencies down to 0.02%. We demonstrate that a TP53-specific CyclomicsSeq assay can be successfully used to monitor tumor burden during treatment for head-and-neck cancer patients. CyclomicsSeq can be applied to any genomic locus and offers an accurate diagnostic liquid biopsy approach that can be implemented in point-of-care clinical workflows.
de Bree Remco、Devriese Lot A.、Willems Stefan M.、Chen Li-Ting、van Kuik Joyce、Elferink Martin、Kloosterman Wigard P.、Terhaard Chris、de Ridder Jeroen、Jager Myrthe、Marcozzi Alessio、Straver Roy、Renkens Ivo、Peltenburg Boris、van Ginkel Joost H.
Department of Head and Neck Surgical Oncology, UMC Utrecht Cancer Center, University Medical Center UtrechtDepartment of Medical Oncology, UMC Utrecht Cancer Center, University Medical Center UtrechtDepartment of pathology, University Medical Center Utrecht, Utrecht University||Department of Pathology and Medical Biology, University Medical Center GroningenCenter for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht UniversityDepartment of pathology, University Medical Center Utrecht, Utrecht UniversityDepartment of Genetics, University Medical Center Utrecht, Utrecht UniversityCyclomics||Center for Molecular Medicine, University Medical Center Utrecht, Utrecht UniversityDepartment of Radiotherapy, UMC Utrecht Cancer Center, University Medical Center UtrechtCenter for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University||CyclomicsCenter for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht UniversityCenter for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University||CyclomicsCenter for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht UniversityCenter for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht UniversityDepartment of Radiotherapy, UMC Utrecht Cancer Center, University Medical Center Utrecht||Department of Head and Neck Surgical Oncology, UMC Utrecht Cancer Center, University Medical Center UtrechtDepartment of pathology, University Medical Center Utrecht, Utrecht University||Department of Oral and Maxillofacial Surgery, University Medical Center Utrecht, Utrecht University
医学研究方法肿瘤学分子生物学
de Bree Remco,Devriese Lot A.,Willems Stefan M.,Chen Li-Ting,van Kuik Joyce,Elferink Martin,Kloosterman Wigard P.,Terhaard Chris,de Ridder Jeroen,Jager Myrthe,Marcozzi Alessio,Straver Roy,Renkens Ivo,Peltenburg Boris,van Ginkel Joost H..Accurate detection of circulating tumor DNA using nanopore consensus sequencing[EB/OL].(2025-03-28)[2025-05-05].https://www.biorxiv.org/content/10.1101/2020.07.14.202010.点此复制
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