The concentration of circulating cell-free DNA (cfDNA) in plasma is an important determinant of the robustness of liquid biopsies. However, biological mechanisms that lead to inter-individual differences in cfDNA concentrations remain unexplored. The concentration of plasma cfDNA is governed by an interplay between its release and clearance. We hypothesize that cfDNA clearance by nucleases might be one mechanism that contributes towards inter-individual variations in cfDNA concentrations. We performed fragmentomic analysis of the plasma cfDNA from 862 healthy individuals, with a cfDNA concentration range of 1.61 - 41.01 ng/mL. We observed an increase in large DNA fragments (231-600 bp), a decreased frequencies of shorter DNA fragments (20-160 bp), and an increased frequency of G-end motifs with increasing cfDNA concentrations. End motif deconvolution analysis revealed a decreased contribution of DNASE1L3 and DFFB in subjects with higher cfDNA concentration. The five subjects with the highest plasma DNA concentration (top 0.58%) had aberrantly decreased levels of DNASE1L3 protein in plasma. The cfDNA concentration could be inferred from the fragmentomic profile through machine learning, and was well correlated to the measured cfDNA concentration. Such an approach could infer the fractional DNA concentration from particular tissue types, such as the fetal and tumor fraction. This work shows that individuals with different cfDNA concentrations were associated with characteristic fragmentomic patterns of the cfDNA pool; and that nuclease-mediated clearance of DNA is a key parameter that affects cfDNA concentration. Understanding these mechanisms has facilitated the enhanced measurement of cfDNA species of clinical interest, including circulating fetal and tumor DNA.

中文翻译：

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基于游离 DNA 的癌症筛查队列分析将片段组谱、核酸酶水平和血浆 DNA 浓度联系起来


血浆中循环游离 DNA （cfDNA） 的浓度是液体活检稳定性的重要决定因素。然而，导致 cfDNA 浓度个体间差异的生物学机制仍未得到探索。血浆 cfDNA 的浓度受其释放和清除之间的相互作用控制。我们假设核酸酶清除 cfDNA 可能是导致 cfDNA 浓度个体间变化的一种机制。我们对 862 名健康个体的血浆 cfDNA 进行了片段组学分析，cfDNA 浓度范围为 1.61 - 41.01 ng/mL。我们观察到随着 cfDNA 浓度的增加，大 DNA 片段 （231-600 bp） 的增加，较短的 DNA 片段 （20-160 bp） 的频率降低，G 端基序的频率增加。末端基序反卷积分析显示 DNASE1L3 和 DFFB 在 cfDNA 浓度较高的受试者中的贡献降低。血浆 DNA 浓度最高的 5 名受试者 （前 0.58%） 血浆中 DNASE1L3 蛋白水平异常降低。cfDNA 浓度可以通过机器学习从片段组学谱中推断出来，并且与测得的 cfDNA 浓度密切相关。这种方法可以从特定组织类型（例如胎儿和肿瘤部分）推断 DNA 浓度分数。这项工作表明，具有不同 cfDNA 浓度的个体与 cfDNA 库的特征片段组模式相关;核酸酶介导的 DNA 清除是影响 cfDNA 浓度的关键参数。 了解这些机制有助于增强临床关注的 cfDNA 种类的测量，包括循环胎儿和肿瘤 DNA。