VSeq-Toolkit: Comprehensive Computational Analysis of Viral Vectors in Gene Therapy
VSeq-Toolkit: Comprehensive Computational Analysis of Viral Vectors in Gene Therapy
复制标题
DOI：
10.1016/j.omtm.2020.03.024
复制
发表时间：
2020-06-12
影响因子：
4.7
通讯作者：
Schmidt, Manfred
中科院分区：
文献类型：
--
作者：
Afzal, Saira;Fronza, Raffaele;Schmidt, Manfred
病毒载体的表征和分析是开发安全的基因治疗产品的重要组成部分，阐明了载体的潜在遗传毒性和免疫原性效应，并建立了它们的安全性。在这里，我们提出了VSeq-Toolkit，它为病毒基因治疗数据提供了不同的分析模式。第一种模式确定不需要的已知污染物及其在病毒制剂或其他测序数据中的频率。第二种模式用于分析向量内融合断点，第三种模式用于揭示病毒-宿主融合事件分布。我们工具包的分析模式可以独立执行或一起执行，并允许同时分析多个病毒载体。它已被设计和评估用于分析短读高通量测序数据，包括全基因组或靶向测序。
Viral vector characterization and analysis are important components for the development of safe gene therapeutic products, elucidating the potential genotoxic and immunogenic effects of vectors and establishing their safety profiles. Here, we present VSeq-Toolkit, which offers varying analysis modes for viral gene therapy data. The first mode determines the undesirable known contaminants and their frequency in viral preparations or other sequencing data. The second mode is designed for the analysis of intra-vector fusion breakpoints and the third mode for unraveling the viral-host fusion events distribution. Analysis modes of our toolkit can be executed independently or together and allow the analysis of multiple viral vectors concurrently. It has been designed and evaluated for the analysis of short read high-throughput sequencing data, including whole-genome or targeted sequencing.