Accurate detection of circulating tumor DNA using nanopore consensus sequencing

• Published in: Npj genomic medicine Vol. 6; no. 1; p. 106
• Main Authors: Marcozzi, Alessio, Jager, Myrthe, Elferink, Martin, Straver, Roy, van Ginkel, Joost H, Peltenburg, Boris, Chen, Li-Ting, Renkens, Ivo, van Kuik, Joyce, Terhaard, Chris, de Bree, Remco, Devriese, Lot A, Willems, Stefan M, Kloosterman, Wigard P, de Ridder, Jeroen
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 09.12.2021; Nature Publishing Group UK; Nature Portfolio
• Subjects: Biomarkers; Biopsy; Cancer therapies; Data processing; Deoxyribonucleic acid; DNA; DNA sequencing; Head & neck cancer; Human papillomavirus; Medical prognosis; Mutation; Patients; Tumors
• DOI: 10.1038/s41525-021-00272-y
• ISSN: 2056-7944

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 ~60×, 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 clinical workflows.