如果癌症能够早期发现，就可以降低患癌症的发病率和死亡率。细胞外游离DNA（cfDNA）片段组学已被确定为早期癌症检测的一种新型表观遗传标志物，然而，该技术目前处于初级阶段，还需要技术改进。我们试图应用一种单链DNA测序技术，测量cfDNA的遗传和片段组学特征，并评估其在检测多种癌症中的性能。本研究纳入了来自六种癌症类型（结直肠癌、食管癌、胃癌、肝癌、肺癌和卵巢癌）的364名患者和675名健康个体的血样。检测了循环肿瘤DNA突变、cfDNA片段组学特征和一组蛋白质标志物。根据癌症类型和分期报告了敏感性和特异性。循环连接扩增测序（CLAmp-seq）作为一种单链DNA测序技术，产生了一个比双链DNA制备方案更短的超短片段（<100 bp），并且在癌症和健康cfDNA片段之间显示了更显著的大小差异（25.84 bp vs. 16.05 bp）。对超短cfDNA片段中的亚核体峰进行分析表明，这些峰是调控元素的“足迹”，并与基因表达和癌症分期相关。在98％的特异性下，单独使用ctDNA突变的预测模型显示了总体敏感性为46％；当加入蛋白质时，敏感性达到60％；当还整合片段组学时，敏感性进一步提高到66％。对于代表早期癌症阶段的样本，观察到了更多的改进。这些结果表明蛋白质、遗传和片段组学特征在早期癌症鉴定中具有协同作用。© 2023作者，由De Gruyter出版，柏林/波士顿。

Cancer morbidity and mortality can be reduced if the cancer is detected early. Cell-free DNA (cfDNA) fragmentomics emerged as a novel epigenetic biomarker for early cancer detection, however, it is still at its infancy and requires technical improvement. We sought to apply a single-strand DNA sequencing technology, for measuring genetic and fragmentomic features of cfDNA and evaluate the performance in detecting multiple cancers.Blood samples of 364 patients from six cancer types (colorectal, esophageal, gastric, liver, lung, and ovarian cancers) and 675 healthy individuals were included in this study. Circulating tumor DNA mutations, cfDNA fragmentomic features and a set of protein biomarkers were assayed. Sensitivity and specificity were reported by cancer types and stages.Circular Ligation Amplification and sequencing (CLAmp-seq), a single-strand DNA sequencing technology, yielded a population of ultra-short fragments (<100 bp) than double-strand DNA preparation protocols and reveals a more significant size difference between cancer and healthy cfDNA fragments (25.84 bp vs. 16.05 bp). Analysis of the subnucleosomal peaks in ultra-short cfDNA fragments indicates that these peaks are regulatory element "footprints" and correlates with gene expression and cancer stages. At 98 % specificity, a prediction model using ctDNA mutations alone showed an overall sensitivity of 46 %; sensitivity reaches 60 % when protein is added, sensitivity further increases to 66 % when fragmentomics is also integrated. More improvements observed for samples representing earlier cancer stages than later ones.These results suggest synergistic properties of protein, genetic and fragmentomics features in the identification of early-stage cancers.© 2023 the author(s), published by De Gruyter, Berlin/Boston.