Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington.
Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.
J Mol Diagn. 2022 May;24(5):476-484. doi: 10.1016/j.jmoldx.2022.01.007. Epub 2022 Feb 22.
Sequencing of plasma cell-free DNA (cfDNA) is a promising milieu for broad-based cancer and infectious disease diagnostics. The performance of cfDNA sequencing for infectious disease diagnostics is chiefly limited by inadequate analytical sensitivity. The current study investigated whether the analytical sensitivity of cfDNA sequencing for viral diagnostics could be improved by selective sequencing of short cfDNA fragments, given prior observations of shorter fragment size distribution in microbial and cytomegalovirus-derived cfDNA compared with human-derived cfDNA. It shows that the shorter plasma cfDNA fragment size distribution is a general feature of multiple DNA viruses, including adenovirus [interquartile range (IQR), 87 to 165 bp], herpes simplex virus 2 (IQR, 114 to 195 bp), human herpesvirus 6 (IQR, 145 to 176 bp), and varicella zoster virus (IQR, 98 to 182 bp), compared with human (IQR, 148 to 178 bp). It was used to further optimize a size selection-based cfDNA sequencing method, demonstrating an enrichment of viral sequences up to 16.6-fold, with a median fold enrichment of 6.7×, 4.6×, 2.2×, and 10.3× for adenovirus, herpes simplex virus 2, human herpesvirus 6, and varicella zoster virus, respectively. These findings demonstrate a simple yet scalable method for enhanced detection of DNA viremia that maintains the unbiased nature of cfDNA sequencing.
血浆游离 DNA（cfDNA）测序是一种很有前途的广泛用于癌症和传染病诊断的方法。cfDNA 测序在传染病诊断中的性能主要受到分析灵敏度不足的限制。本研究旨在探讨选择性测序短 cfDNA 片段是否可以提高 cfDNA 测序用于病毒诊断的分析灵敏度，因为先前的研究观察到微生物和巨细胞病毒衍生的 cfDNA 片段比人源 cfDNA 具有更短的片段大小分布。结果表明，较短的血浆 cfDNA 片段大小分布是多种 DNA 病毒的普遍特征，包括腺病毒[四分位间距（IQR），87 至 165bp]、单纯疱疹病毒 2（IQR，114 至 195bp）、人类疱疹病毒 6（IQR，145 至 176bp）和水痘带状疱疹病毒（IQR，98 至 182bp），而人源 cfDNA 的 IQR 为 148 至 178bp。该方法进一步优化了基于大小选择的 cfDNA 测序方法，证明病毒序列的富集高达 16.6 倍，腺病毒、单纯疱疹病毒 2、人类疱疹病毒 6 和水痘带状疱疹病毒的中位数富集倍数分别为 6.7×、4.6×、2.2×和 10.3×。这些发现证明了一种简单但可扩展的方法，用于增强 DNA 血症的检测，同时保持 cfDNA 测序的无偏倚性质。
