NGS-based approach to determine the presence of HPV and their sites of integration in human cancer genome

Abstract

Background:Human papilloma virus (HPV) accounts for the most common cause of all virus-associated human cancers. Here, we describe the first graphic user interface (GUI)-based automated tool ‘HPVDetector', for non-computational biologists, exclusively for detection and annotation of the HPV genome based on next-generation sequencing data sets.Methods:We developed a custom-made reference genome that comprises of human chromosomes along with annotated genome of 143 HPV types as pseudochromosomes. The tool runs on a dual mode as defined by the user: a ‘quick mode' to identify presence of HPV types and an ‘integration mode' to determine genomic location for the site of integration. The input data can be a paired-end whole-exome, whole-genome or whole-transcriptome data set. The HPVDetector is available in public domain for download: http://www.actrec.gov.in/pi-webpages/AmitDutt/HPVdetector/HPVDetector.html.Results:On the basis of our evaluation of 116 whole-exome, 23 whole-transcriptome and 2 whole-genome data, we were able to identify presence of HPV in 20 exomes and 4 transcriptomes of cervical and head and neck cancer tumour samples. Using the inbuilt annotation module of HPVDetector, we found predominant integration of viral gene E7, a known oncogene, at known 17q21, 3q27, 7q35, Xq28 and novel sites of integration in the human genome. Furthermore, co-infection with high-risk HPVs such as 16 and 31 were found to be mutually exclusive compared with low-risk HPV71.Conclusions:HPVDetector is a simple yet precise and robust tool for detecting HPV from tumour samples using variety of next-generation sequencing platforms including whole genome, whole exome and transcriptome. Two different modes (quick detection and integration mode) along with a GUI widen the usability of HPVDetector for biologists and clinicians with minimal computational knowledge.

APOBEC-mediated genomic alterations link immunity and viral infection during human papillomavirus-driven cervical carcinogenesis

“…Breakpoints are distributed throughout the viral genome and are more likely to occur in E1 than in E2 but are less prone to occur in the LCR, while the viral E6 gene may also be disrupted during certain events (21). Furthermore, significant enrichment of viral gene E7>E4>E5>E6 reads has been noted among cervical tumor samples, which is consistent with the known biological roles of the HPV genes in carcinogenesis (24).…”

Functional variants of human papillomavirus type 16 demonstrate host genome integration and transcriptional alterations corresponding to their unique cancer epidemiology

“…Since the virus can integrate into a variety of positions in the human genome, these fusion transcripts are specific to each integration site. In recent years, following the introduction of high-throughput sequencing techniques, multiple softwares for detecting pathogen sequences in host sequence data have become available [38, 57–63]. Here, to identify the viral-human fusion transcripts expressed in our epithelia, we used the ViralFusionSeq (VFS) software [61, 64].…”

Somatic Variations in Cervical Cancers in Indian Patients

“…In our study, HPV infection in the samples and its integration was determined by Luminex Bead Array [8]. Presence of HPV and its integration status was also confirmed in the exome sequencing data of the samples [12]. Thus, our treatment naïve primary cancers could be HPV driven and hence no driver mutations are seen.…”

“…The HPV genotype and viral genome status in these patients was determined from an earlier study [8, 10]. Majority of the samples were positive for HPV16, although HPV18, 45 and 56 were also present [12]. In some of the samples, the virus was integrated in the genome [8].…”