Afzal Saira, Fronza Raffaele, Schmidt Manfred
Department of Translational Oncology, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), Heidelberg, Germany.
GeneWerk GmbH, Heidelberg, Germany.
Mol Ther Methods Clin Dev. 2020 Mar 30;17:752-757. doi: 10.1016/j.omtm.2020.03.024. eCollection 2020 Jun 12.
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. VSeq-Toolkit is developed in Perl and Bash programming languages and is available at https://github.com/CompMeth/VSeq-Toolkit.
病毒载体的表征和分析是安全基因治疗产品开发的重要组成部分，可阐明载体潜在的基因毒性和免疫原性作用，并确定其安全性概况。在此，我们介绍VSeq-Toolkit，它为病毒基因治疗数据提供了多种分析模式。第一种模式可确定病毒制剂或其他测序数据中不良的已知污染物及其频率。第二种模式用于分析载体内部的融合断点，第三种模式用于揭示病毒-宿主融合事件的分布。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。它专为分析短读高通量测序数据而设计和评估，包括全基因组测序或靶向测序。VSeq-Toolkit是用Perl和Bash编程语言开发的，可在https://github.com/CompMeth/VSeq-Toolkit上获取。
