Fragmentomic features of circulating cell free mitochondrial DNA (ccf-mtDNA) including fragmentation profile, 5' end base preference and motif diversity are poorly understood. Here, we generated ccf-mtDNA sequencing data of 1607 plasma samples using capture-based next generation sequencing. We firstly found that fragmentomic features of ccf-mtDNA were remarkably different from those of circulating cell free nuclear DNA. Furthermore, region-specific fragmentomic features of ccf-mtDNA were observed, which was associated with protein binding, base composition and special structure of mitochondrial DNA. When comparing to non-cancer controls, six types of cancer patients exhibited aberrant fragmentomic features. Then, cancer detection models were built based on the fragmentomic features. Both internal and external validation cohorts demonstrated the excellent capacity of our model in distinguishing cancer patients from non-cancer control, with all area under curve higher than 0.9322. The overall accuracy of tissue-of-origin was 89.24% and 87.92% for six cancer types in two validation cohort, respectively. Altogether, our study comprehensively describes cancer-specific fragmentomic features of ccf-mtDNA and provides a proof-of-principle for the ccf-mtDNA fragmentomics-based multi-cancer detection and tissue-of-origin classification.

中文翻译：

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循环游离线粒体 DNA 的异常片段组学特征作为多癌症检测的新型生物标志物。


循环游离线粒体 DNA （ccf-mtDNA） 的片段组学特征（包括片段化谱、5' 末端碱基偏好和基序多样性）知之甚少。在这里，我们使用基于捕获的下一代测序生成了 1607 个血浆样本的 ccf-mtDNA 测序数据。我们首先发现 ccf-mtDNA 的片段组学特征与循环游离细胞核 DNA 的片段组学特征显着不同。此外，观察到 ccf-mtDNA 的区域特异性片段组学特征，这与蛋白质结合、碱基组成和线粒体 DNA 的特殊结构有关。与非癌症对照相比，六种类型的癌症患者表现出异常的片段组学特征。然后，基于片段组学特征构建癌症检测模型。内部和外部验证队列都证明了我们的模型在区分癌症患者和非癌症对照方面的出色能力，所有曲线下面积均高于 0.9322。两个验证队列中 6 种癌症类型的组织来源总体准确率分别为 89.24% 和 87.92%。总之，我们的研究全面描述了 ccf-mtDNA 的癌症特异性片段组学特征，并为基于 ccf-mtDNA 片段组学的多癌种检测和组织来源分类提供了原理验证。