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Accurate detection of circulating tumor DNA using nanopore consensus sequencing

By Alessio Marcozzi, Myrthe Jager, Martin Elferink, Roy Straver, Joost H van Ginkel, Boris Peltenburg, Li-Ting Chen, Ivo Renkens, Joyce van Kuik, Chris Terhaard, Remco de Bree, Lot A Devriese, Stefan M Willems, Wigard P. Kloosterman, Jeroen de Ridder

Posted 15 Jul 2020
bioRxiv DOI: 10.1101/2020.07.14.202010

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 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. ### Competing Interest Statement The authors declare the following financial competing interest: A.M., R.S., W.P.K., and J.d.R filed patents and A.M., W.P.K., and J.d.R founded a company (Cyclomics) based on CyclomicsSeq.

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