( B) HPV genotype composition of samples grouped by cytological grade i.e., LSIL and HSIL. Deep sequencing of HPV E6/E7 amplicons derived from each LSIL ( n = 95) or HSIL ( n = 60) sample identified 32 unique HPV genotypes with the top 20 shown (legend) and quantitated their composition (%) based on abundance ( n) of mapped reads to total mapped reads.

HPV type-specific carcinogenicity (carcinogenic, possibly carcinogenic, and not carcinogenic) are colorized in shades of red, blue, and green, respectively (legend). ( A) Abundance of HPV genotypes found in individual LSIL and HSIL samples are shown as stacked bars. Taxonomic profiling results based on the HPV Reference Index. HPV genotyping bioinformatics cervical cancer deep sequencing human papillomavirus metagenome next generation sequencing taxonomic classification virome. 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. Integrating clinically relevant, taxonomized HPV reference genomes within automated workflows proved to be an ultra-fast method of virome profiling. 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. Tabular output conversion to visualizations entailed 1-2 keystrokes. 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). 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. 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. However, viral computational analysis remains a bottleneck due to semantic discrepancies between computational tools and curated reference genomes.

Next-generation sequencing (NGS) has actualized the human papillomavirus (HPV) virome profiling for in-depth investigation of viral evolution and pathogenesis.

Clc genomics workbench volcano plot