Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
- Li-Ting Chen1,2,
- Myrthe Jager1,2,
- Dàmi Rebergen3,
- Geertruid J. Brink4,
- Tom van den Ende5,6,
- Willem Vanderlinden7,8,
- Pauline Kolbeck7,9,
- Marc Pagès-Gallego1,2,
- Ymke van der Pol10,
- Nicolle Besselink1,2,
- Norbert Moldovan6,10,
- Nizar Hami4,
- Wigard P. Kloosterman3,
- Hanneke van Laarhoven5,6,
- Florent Mouliere6,10,11,
- Ronald Zweemer4,
- Jan Lipfert7,
- Sarah Derks2,10,
- Alessio Marcozzi3 and
- Jeroen de Ridder1,2,3
- 1Center for Molecular Medicine University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands;
- 2Oncode Institute, 3521 AL Utrecht, The Netherlands;
- 3Cyclomics, 3584 CG Utrecht, The Netherlands;
- 4Department of Gynecologic Oncology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands;
- 5Department of Medical Oncology, Amsterdam UMC, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands;
- 6Cancer Center Amsterdam, Imaging and Biomarkers, 1105 AZ, Amsterdam, The Netherlands;
- 7Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, 3584 CC Utrecht, The Netherlands;
- 8School of Physics and Astronomy, University of Edinburgh, EH9 3FD Edinburgh, United Kingdom;
- 9Department of Physics and Center for NanoScience, LMU Munich, 80799 Munich, Germany;
- 10Department of Pathology, Cancer Centre Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1105 AZ, Amsterdam, The Netherlands;
- 11Cancer Research UK National Biomarker Centre, University of Manchester, Manchester M20 4BX, United Kingdom
Abstract
Shallow genome-wide cell-free DNA sequencing holds great promise for noninvasive cancer monitoring by providing reliable copy number alteration (CNA) and fragmentomic profiles. Single-nucleotide variations (SNVs) are, however, much harder to identify with low sequencing depth due to sequencing errors. Here, we present Nanopore Rolling Circle Amplification (RCA)-enhanced Consensus Sequencing (NanoRCS), which leverages RCA and consensus calling based on genome-wide long-read nanopore sequencing to enable simultaneous multimodal tumor fraction (TF) estimation through SNVs, CNAs, and fragmentomics. The efficacy of NanoRCS is tested on 18 cancer patient samples and seven healthy controls, demonstrating its ability to reliably detect TFs as low as 0.24%. In vitro experiments confirm that SNV measurements are essential for detecting TFs below 3%. NanoRCS provides an opportunity for cost-effective and rapid sample processing, which aligns well with clinical needs, particularly in settings where quick and accurate cancer monitoring is essential for personalized treatment strategies.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.279144.124.
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Freely available online through the Genome Research Open Access option.
- Received February 22, 2024.
- Accepted January 6, 2025.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
