A comprehensive system for detecting rare single nucleotide variants based on competitive DNA probe and duplex-specific nuclease.
A comprehensive system for detecting rare single nucleotide variants based on competitive DNA probe and duplex-specific nuclease.
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DOI：
10.1016/j.aca.2021.338545
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发表时间：
2021-06
影响因子：
6.2
通讯作者：
Li Zhang;Yufeng Wang;Yongcan Guo;Huajian Chen;Wen Yu;Zhang Zhang-Zhang;G. Xie
中科院分区：
文献类型：
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作者：
Li Zhang;Yufeng Wang;Yongcan Guo;Huajian Chen;Wen Yu;Zhang Zhang-Zhang;G. Xie
单核苷酸变异（SNV）已成为越来越重要的生物标志物，特别是在癌症的诊断和预后中。然而，大多数SNV很少在癌症患者的血液样品中检测到，因为它们被大量伴随的野生型核酸包围。在此，我们设计了一个系统，其特征在于竞争性DNA探针系统（CDPS）和DNA特异性核酸酶（DSN）的组合，我们称之为CAD。建立了基于反应网络的CAD系统的理论模型。在理论模型的指导下，我们发现灵敏度的微小损失显着提高了系统的特异性，从而在大多数情况下产生了> 100的理论区分因子（DF）。这种灵敏度和特异性之间的非等效权衡为罕见DNA序列变异的分析提供了新的概念。作为实用性的证明，我们应用所提出的CAD系统来识别合成模板（0.1%VAF）和人类基因组DNA（1%VAF）中的低变异等位基因频率（VAF）。这项工作承诺完全指导酶为基础的核酸分析的设计。
Single nucleotide variants (SNVs) have emerged as increasingly important biomarkers, particularly in the diagnosis and prognosis of cancers. However, most SNVs are rarely detected in blood samples from cancer patients as they are surrounded by abundant concomitant wild-type nucleic acids. Herein, we design a system that features a combination of competitive DNA probe system (CDPS) and duplex-specific nuclease (DSN) that we referred to as CAD. A theoretical model was established for the CAD system based on reaction networks. Guided by the theoretical model, we found that a minor loss in sensitivity significantly improved the specificity of the system, thus creating a theoretical discrimination factor (DF) > 100 for most conditions. This non-equivalent tradeoff between sensitivity and specificity provides a new concept for the analysis of rare DNA-sequence variants. As a demonstration of practicality, we applied as-proposed CAD system to identify low variant allele frequency (VAF) in a synthetic template (0.1% VAF) and human genomic DNA (1% VAF). This work promises complete guidance for the design of enzyme-based nucleic acid analysis.