Cell-free DNA (cfDNA) can be isolated and sequenced from blood and/or urine of cancer patients. Conventional short-read sequencing lacks deployability and speed and can be biased for short cfDNA fragments. Here, we demonstrate that with Oxford Nanopore Technologies (ONT) sequencing we can achieve delivery of genomic and fragmentomic data from liquid biopsies. Copy number aberrations and cfDNA fragmentation patterns can be determined in less than 24 h from sample collection. The tumor-derived cfDNA fraction calculated from plasma of lung cancer patients and urine of bladder cancer patients was highly correlated (R = 0.98) with the tumor fraction calculated from short-read sequencing of the same samples. cfDNA size profile, fragmentation patterns, fragment-end composition, and nucleosome profiling near transcription start sites in plasma and urine exhibited the typical cfDNA features. Additionally, a high proportion of long tumor-derived cfDNA fragments (> 300 bp) are recovered in plasma and urine using ONT sequencing. ONT sequencing is a cost-effective, fast, and deployable approach for obtaining genomic and fragmentomic results from liquid biopsies, allowing the analysis of previously understudied cfDNA populations.

中文翻译：

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使用纳米孔测序实时分析血浆和尿液游离 DNA 中的癌症基因组和片段组

可以从癌症患者的血液和/或尿液中分离游离 DNA (cfDNA) 并进行测序。传统的短读长测序缺乏可部署性和速度，并且可能对短 cfDNA 片段产生偏差。在这里，我们证明，通过牛津纳米孔技术 (ONT) 测序，我们可以实现从液体活检中获取基因组和片段组数据。可以在样品采集后 24 小时内确定拷贝数畸变和 cfDNA 片段模式。根据肺癌患者血浆和膀胱癌患者尿液计算出的肿瘤来源 cfDNA 分数 与根据相同样本的短读长测序计算出的肿瘤分数高度相关（ R = 0.98）。血浆和尿液中转录起始位点附近的 cfDNA 大小谱、片段化模式、片段末端组成和核小体谱显示出典型的 cfDNA 特征。此外，使用 ONT 测序在血浆和尿液中回收了高比例的长肿瘤衍生 cfDNA 片段（> 300 bp）。ONT 测序是一种经济高效、快速且可部署的方法，用于从液体活检中获取基因组和片段组结果，从而可以对先前研究不足的 cfDNA 群体进行分析。