HPV Integration Site Mapping: A Rapid Method of Viral Integration Site (VIS) Analysis and Visualization Using Automated Workflows in CLC Microbial Genomics

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dc.contributor.authorShen-Gunther, Jane
dc.contributor.authorCai, Hong
dc.contributor.authorWang, Yufeng
dc.date.accessioned2022-08-11T11:50:27Z
dc.date.available2022-08-11T11:50:27Z
dc.date.issued2022-07-23
dc.date.updated2022-08-11T11:50:28Z
dc.description.abstractHuman 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.
dc.description.departmentMolecular Microbiology and Immunology
dc.identifierdoi: 10.3390/ijms23158132
dc.identifier.citationInternational Journal of Molecular Sciences 23 (15): 8132 (2022)
dc.identifier.urihttps://hdl.handle.net/20.500.12588/1085
dc.rightsAttribution 4.0 United States
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectbioinformatics workflow
dc.subjectcervical cancer
dc.subjectHPV taxonomy
dc.subjecthuman papillomavirus
dc.subjecthybrid capture NGS
dc.subjectinsertional mutagenesis
dc.subjectnext generation sequencing
dc.subjectviral mapping
dc.subjectvirus integration
dc.titleHPV Integration Site Mapping: A Rapid Method of Viral Integration Site (VIS) Analysis and Visualization Using Automated Workflows in CLC Microbial Genomics
dc.typeArticle

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