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

Jane Shen-Gunther,Qingqing Xia,Hong Cai,Yufeng Wang

doi:10.3390/pathogens10081026

Abstract

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.

Highlights

Hippocrates was the first to describe cervical cancer and its destructive nature around400 BCE [1]
Two thousand years elapsed before zur Hausen and his “papillomavirus crew” made the breakthrough discovery of identifying human papillomavirus (HPV)-16 in cervical, vulvar, and penile cancers in 1983 [1,2,3]
We aimed to develop and test automated workflows for HPV taxonomic profiling and visualization within the CLC Microbial Genomics Module (MGM) plugged into the main Workbench (WB)

Summary

Introduction

Hippocrates was the first to describe cervical cancer and its destructive nature around400 BCE [1]. Hippocrates was the first to describe cervical cancer and its destructive nature around. Two thousand years elapsed before zur Hausen and his “papillomavirus crew” made the breakthrough discovery of identifying human papillomavirus (HPV)-16 in cervical, vulvar, and penile cancers in 1983 [1,2,3]. The etiological role of HPV in breast and esophageal cancers has been postulated for several decades but remains controversial due to conflicting findings [6,7]. HPV is the second most prevalent primary infectious cause of cancer worldwide. The annual global burden of 570,000 new cervical and 120,000 other anogenital and oropharyngeal cancer cases have been attributed to HPV [8,9]

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Conclusion