小的染色体外环状DNA（eccDNA）潜在地可以作为癌症生物标志物。然而，在癌症发生中选择的小eccDNA的形成机制和功能尚不清楚，并且癌症患者血浆中的小eccDNA剖析是否代表了癌症组织中的小eccDNA剖析也有待阐明。基于纳米孔测序平台的新型测序工作流程被用来测序来自25名癌症患者（包括前列腺癌、肝细胞癌和结肠直肠癌）的组织和血浆中自然存在的全长小eccDNA，以及独立的验证队列（包括7份癌症血浆和14份健康血浆）。与非癌症组织相比，癌症组织中检测到的小eccDNA数量和大小显著增加（P = 0.040和2.2e-16，分别），并具有更均匀的分布和不同的形成机制。尽管癌症组织和相配血浆中的小eccDNA在一般特征和基因组注释方面有所不同，但它们具有相似的形成机制和与癌症相关的功能。一些特定基因来源的小eccDNA在组织（AUC ≥ 0.8）和血浆（AUC > 0.9）中具有良好的多癌症诊断价值，特别是提高了CEA/CA19-9水平的多癌症预测准确性。来自ALK＆ETV6的小eccDNA的高多癌症诊断价值可以从组织（AUC = 0.804）推广到血浆，并在验证队列中显示出很高的阳性预测值（100%）和阴性预测值（82.35%）。作为独立稳定的环状DNA分子，组织和血浆中的小eccDNA均可用作成本效益高的多癌症诊断和监测的理想生物标志物。© 2023年作者们。由约翰·威利·爱儿出版社代表上海临床生物信息学研究所出版的《临床与转化医学》。

Small extrachromosomal circular DNAs (eccDNAs) have the potential to be cancer biomarkers. However, the formation mechanisms and functions of small eccDNAs selected in carcinogenesis are not clear, and whether the small eccDNA profile in the plasma of cancer patients represents that in cancer tissues remains to be elucidated.A novel sequencing workflow based on the nanopore sequencing platform was used to sequence naturally existing full-length small eccDNAs in tissues and plasma collected from 25 cancer patients (including prostate cancer, hepatocellular carcinoma and colorectal cancer), and from an independent validation cohort (including 7 cancer plasma and 14 healthy plasma).Compared with those in non-cancer tissues, small eccDNAs detected in cancer tissues had a significantly larger number and size (P = 0.040 and 2.2e-16, respectively), along with more even distribution and different formation mechanisms. Although small eccDNAs had different general characteristics and genomic annotation between cancer tissues and the paired plasma, they had similar formation mechanisms and cancer-related functions. Small eccDNAs originated from some specific genes had great multi-cancer diagnostic value in tissues (AUC ≥ 0.8) and plasma (AUC > 0.9), especially increasing the accuracy of multi-cancer prediction of CEA/CA19-9 levels. The high multi-cancer diagnostic value of small eccDNAs originated from ALK&ETV6 could be extrapolated from tissues (AUC = 0.804) to plasma and showed high positive predictive value (100%) and negative predictive value (82.35%) in a validation cohort.As independent and stable circular DNA molecules, small eccDNAs in both tissues and plasma can be used as ideal biomarkers for cost-effective multi-cancer diagnosis and monitoring.© 2023 The Authors. Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.