Table1_Application of PCR-based approaches for evaluation of cell-free DNA fragmentation in colorectal cancer.XLSX

Cell-free DNA (cfDNA) testing is the core of most liquid biopsy assays. In particular, cfDNA fragmentation features could facilitate non-invasive cancer detection due to their interconnection with tumor-specific epigenetic alterations. However, the final cfDNA fragmentation profile in a purified sample is the result of a complex interplay between informative biological and artificial technical factors. In this work, we use ddPCR to study cfDNA lengths in colorectal cancer patients and observe shorter and more variable cfDNA fragments in accessible chromatin loci compared to the densely packed pericentromeric region. We also report a convenient qPCR system suitable for screening cfDNA samples for artificial high molecular weight DNA contamination.无细胞脱氧核糖核酸（cell-free DNA, cfDNA）检测是绝大多数液体活检检测实验的核心技术。具体而言，cfDNA的片段化特征与肿瘤特异性表观遗传改变存在紧密关联，因此可助力无创癌症检测。然而，纯化样本中最终的cfDNA片段化图谱，是信息性生物学因素与人工技术因素复杂相互作用的产物。本研究采用微滴式数字聚合酶链式反应（droplet digital PCR, ddPCR）分析结直肠癌患者的cfDNA长度，发现相较于紧密聚集的着丝粒周边区域，开放染色质位点中的cfDNA片段更短且片段长度变异度更高。本研究同时报道了一套便捷的实时荧光定量聚合酶链式反应（quantitative PCR, qPCR）体系，可用于筛查cfDNA样本中是否存在人工高分子量DNA污染。