HPV DeepSeq: An Ultra-Fast Method of NGS Data Analysis and Visualization Using Automated Workflows and a Customized Papillomavirus Database in CLC Genomics Workbench

Pathogens

Hong Cai¹  Yufeng Wang¹  Qingqing Xia²  Jane Shen-Gunther³ 

[1] Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA;Department of Clinical Investigation, Brooke Army Medical Center, Fort Sam Houston, San Antonio, TX 78234, USA;Gynecologic Oncology & Clinical Investigation, Department of Clinical Investigation, Brooke Army Medical Center, Fort Sam Houston, San Antonio, TX 78234, USA;

关键词: bioinformatics;    cervical cancer;    deep sequencing;    human papillomavirus;    HPV genotyping;    metagenome;   

DOI  :  10.3390/pathogens10081026

来源: DOAJ

【 摘 要 】

Next-generation sequencing (NGS) has actualized the human papillomavirus (HPV) virome profiling for in-depth investigation of viral evolution and pathogenesis. However, viral computational analysis remains a bottleneck due to semantic discrepancies between computational tools and curated reference genomes. To address this, we developed and tested automated workflows for HPV taxonomic profiling and visualization using a customized papillomavirus database in the CLC Microbial Genomics Module. HPV genomes from Papilloma Virus Episteme were customized and incorporated into CLC “ready-to-use” workflows for stepwise data processing to include: (1) Taxonomic Analysis, (2) Estimate Alpha/Beta Diversities, and (3) Map Reads to Reference. Low-grade (n = 95) and high-grade (n = 60) Pap smears were tested with ensuing collective runtimes: Taxonomic Analysis (36 min); Alpha/Beta Diversities (5 s); Map Reads (45 min). Tabular output conversion to visualizations entailed 1–2 keystrokes. Biodiversity analysis between low- (LSIL) and high-grade squamous intraepithelial lesions (HSIL) revealed loss of species richness and gain of dominance by HPV-16 in HSIL. Integrating clinically relevant, taxonomized HPV reference genomes within automated workflows proved to be an ultra-fast method of virome profiling. The entire process named “HPV DeepSeq” provides a simple, accurate and practical means of NGS data analysis for a broad range of applications in viral research.

【 授权许可】

Unknown