Chen Li-Ting, Jager Myrthe, Rebergen Dàmi, Brink Geertruid J, van den Ende Tom, Vanderlinden Willem, Kolbeck Pauline, Pagès-Gallego Marc, van der Pol Ymke, Besselink Nicolle, Moldovan Norbert, Hami Nizar, Kloosterman Wigard P, van Laarhoven Hanneke, Mouliere Florent, Zweemer Ronald, Lipfert Jan, Derks Sarah, Marcozzi Alessio, de Ridder Jeroen
Center for Molecular Medicine University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands.
Oncode Institute, 3521 AL Utrecht, The Netherlands.
Genome Res. 2025 Apr 14;35(4):886-899. doi: 10.1101/gr.279144.124.
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.
浅层全基因组游离DNA测序通过提供可靠的拷贝数改变（CNA）和片段组学图谱，在非侵入性癌症监测方面具有巨大潜力。然而，由于测序错误，在低测序深度下很难识别单核苷酸变异（SNV）。在这里，我们提出了纳米孔滚环扩增（RCA）增强的一致性测序（NanoRCS），它利用RCA和基于全基因组长读长纳米孔测序的一致性调用，通过SNV、CNA和片段组学实现同时多模态肿瘤分数（TF）估计。NanoRCS的功效在18例癌症患者样本和7例健康对照上进行了测试，证明其能够可靠地检测低至0.24%的TF。体外实验证实，SNV测量对于检测低于3%的TF至关重要。NanoRCS为经济高效且快速的样本处理提供了机会，这与临床需求高度契合，特别是在快速准确的癌症监测对个性化治疗策略至关重要的情况下。
