Abstract：
Plasma cell-free DNA (cfDNA) fragmentation patterns are emerging directions in cancer liquid biopsy with high translational significance. Conventionally, the cfDNA sequencing reads are aligned to a reference genome to extract their fragmentomic features. In this study, through cfDNA fragmentomics profiling using different reference genomes on the same datasets in parallel, we report systematic biases in such conventional reference-based approaches. The biases in cfDNA fragmentomic features vary among races in a sample-dependent manner and therefore might adversely affect the performances of cancer diagnosis assays across multiple clinical centers. In addition, to circumvent the analytical biases, we develop Freefly, a reference-free approach for cfDNA fragmentomics profiling. Freefly runs ∼60-fold faster than the conventional reference-based approach while generating highly consistent results. Moreover, cfDNA fragmentomic features reported by Freefly can be directly used for cancer diagnosis. Hence, Freefly possesses translational merit toward the rapid and unbiased measurement of cfDNA fragmentomics.
摘要：
无浆细胞DNA（cfDNA）片段化模式是癌症液体活检中具有高度翻译意义的新兴方向。传统上,将cfDNA测序读数与参考基因组进行比对以提取它们的片段组特征。在这项研究中,通过在相同的数据集上并行使用不同的参考基因组的cfDNA片段组学分析，我们报告了这种传统的基于参考的方法存在系统偏差。cfDNA片段组特征的偏差在种族之间以样品依赖性方式变化，因此可能会对多个临床中心的癌症诊断测定的性能产生不利影响。此外,为了规避分析偏见，我们主要发展，cfDNA片段组学分析的无参考方法。Freefly的运行速度比传统的基于参考的方法快60倍，同时产生高度一致的结果。此外，Freefly报道的cfDNA片段组学特征可直接用于癌症诊断。因此，Freefly对cfDNA片段组学的快速无偏测量具有翻译价值。
