Shieh Fwu-Shan, Jongeneel Patrick, Steffen Jamin D, Lin Selena, Jain Surbhi, Song Wei, Su Ying-Hsiu
JBS Science, Inc., Doylestown, Pennsylvania, United States of America.
U-Screen Dx Inc., Doylestown, Pennsylvania, United States of America.
PLoS One. 2017 Aug 22;12(8):e0182843. doi: 10.1371/journal.pone.0182843. eCollection 2017.
Identification of viral integration sites has been important in understanding the pathogenesis and progression of diseases associated with particular viral infections. The advent of next-generation sequencing (NGS) has enabled researchers to understand the impact that viral integration has on the host, such as tumorigenesis. Current computational methods to analyze NGS data of virus-host junction sites have been limited in terms of their accessibility to a broad user base. In this study, we developed a software application (named ChimericSeq), that is the first program of its kind to offer a graphical user interface, compatibility with both Windows and Mac operating systems, and optimized for effectively identifying and annotating virus-host chimeric reads within NGS data. In addition, ChimericSeq's pipeline implements custom filtering to remove artifacts and detect reads with quantitative analytical reporting to provide functional significance to discovered integration sites. The improved accessibility of ChimericSeq through a GUI interface in both Windows and Mac has potential to expand NGS analytical support to a broader spectrum of the scientific community.
病毒整合位点的鉴定对于理解与特定病毒感染相关疾病的发病机制和进展非常重要。新一代测序（NGS）技术的出现使研究人员能够了解病毒整合对宿主的影响，如肿瘤发生。目前用于分析病毒-宿主连接位点NGS数据的计算方法，在广大用户群体的可及性方面存在局限。在本研究中，我们开发了一款软件应用程序（名为ChimericSeq），它是同类程序中首个提供图形用户界面、与Windows和Mac操作系统均兼容，并经过优化以有效识别和注释NGS数据中病毒-宿主嵌合 reads 的程序。此外，ChimericSeq的流程实施定制过滤以去除伪影，并通过定量分析报告检测 reads，为发现的整合位点提供功能意义。ChimericSeq通过Windows和Mac的GUI界面提高了可及性，有可能将NGS分析支持扩展到更广泛的科学界。
