Accurate detection of circulating tumor DNA using nanopore consensus sequencing

Marcozzi, A.; Jager, M.; Elferink, M.; Straver, R.; van Ginkel, J. H.; Peltenburg, B.; Chen, L.-T.; Renkens, I.; van Kuik, J.; Terhaard, C.; de Bree, R.; Devriese, L. A.; Willems, S. M.; Kloosterman, W. P.; de Ridder, J.

doi:10.1101/2020.07.14.202010

bioRxiv · 10.1101/2020.07.14.202010

Accurate detection of circulating tumor DNA using nanopore consensus sequencing

Marcozzi, A.·Jager, M.·Elferink, M.·Straver, R.·van Ginkel, J. H.·Peltenburg, B.·Chen, L.-T.·Renkens, I.·van Kuik, J.·Terhaard, C.·de Bree, R.·Devriese, L. A.·Willems, S. M.·Kloosterman, W. P.·de Ridder, J.

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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.

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Marcozzi, A., Jager, M., Elferink, M., Straver, R., van Ginkel, J. H., Peltenburg, B., Chen, L.-T., Renkens, I., van Kuik, J., Terhaard, C., de Bree, R., Devriese, L. A., Willems, S. M., Kloosterman, W. P., de Ridder, J.. 2020-07-15. Accurate detection of circulating tumor DNA using nanopore consensus sequencing. https://doi.org/10.1101/2020.07.14.202010

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