Gynecologic Oncology & Clinical Investigation, Department of Clinical Investigation, Brooke Army Medical Center, Fort Sam Houston, TX 78234, USA.
Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA.
Int J Mol Sci. 2022 Jul 23;23(15):8132. doi: 10.3390/ijms23158132.
Human papillomavirus (HPV) integration within the host genome may contribute to carcinogenesis through various disruptive mechanisms. With next-generation sequencing (NGS), identification of viral and host genomic breakpoints and chimeric sequences are now possible. However, a simple, streamlined bioinformatics workflow has been non-existent until recently. Here, we tested two new, automated workflows in CLC Microbial Genomics, i.e., Viral Hybrid Capture (VHC) Data Analysis and Viral Integration Site (VIS) Identification for software performance and efficiency. The workflows embedded with HPV and human reference genomes were used to analyze a publicly available NGS dataset derived from pre- and cancerous HPV+ cervical cytology of 21 Gabonese women. The VHC and VIS workflow median runtimes were 19 and 7 min per sample, respectively. The VIS dynamic graphical outputs included read mappings, virus-host genomic breakpoints, and virus-host integration circular plots. Key findings, including disrupted and nearby genes, were summarized in an auto-generated report. Overall, the VHC and VIS workflows proved to be a rapid and accurate means of localizing viral-host integration site(s) and identifying disrupted and neighboring human genes. Applying HPV VIS-mapping to pre- or invasive tumors will advance our understanding of viral oncogenesis and facilitate the discovery of prognostic biomarkers and therapeutic targets.
人乳头瘤病毒（HPV）整合到宿主基因组中可能通过各种破坏机制促进癌变。随着下一代测序（NGS）的发展，现在可以识别病毒和宿主基因组断点以及嵌合序列。然而，直到最近，仍然缺乏一种简单、流畅的生物信息学工作流程。在这里，我们在 CLC 微生物基因组学中测试了两种新的自动化工作流程，即病毒杂交捕获（VHC）数据分析和病毒整合位点（VIS）鉴定，以测试软件的性能和效率。使用带有 HPV 和人类参考基因组的工作流程来分析来自 21 名加蓬妇女的 HPV+宫颈癌前和宫颈癌细胞学的公开可用 NGS 数据集。VHC 和 VIS 工作流程的中位数运行时间分别为每个样本 19 分钟和 7 分钟。VIS 动态图形输出包括读取映射、病毒-宿主基因组断点以及病毒-宿主整合圆形图。关键发现，包括中断和附近的基因，总结在自动生成的报告中。总体而言，VHC 和 VIS 工作流程被证明是一种快速、准确的定位病毒-宿主整合位点并识别中断和相邻人类基因的方法。将 HPV VIS 映射应用于前驱或侵袭性肿瘤将有助于我们了解病毒致癌作用，并促进预后生物标志物和治疗靶点的发现。
