A new and free computational tool for HPV detection

08 Jul 2015

A new and free computational tool for HPV detection

A new and free computational tool for HPV detection

Dr Amit Dutt, Intermediate Fellow, ACTREC, Tata Memorial Centre, Mumbai

Human papilloma virus (HPV) accounts for the most common cause of all virus-associated human cancers. However, despite large-scale genome wide DNA sequencing efforts of the cancer genome there is no dedicated informatics tool to rapidly detect the presence of HPV in these genomes, in an exclusive manner. In this study, we present a novel freely distributable computational tool “HPVDetector” (through a weblink download-- https://www.actrec.gov.in/pi-webpages/AmitDutt/HPVdetector/HPVDetector.html.) to detect all known HPV types along with their sites of integration in the host genome using next generation sequencing data set, along with a widely compatible annotated reference of 143 HPV genome as a resource. This user friendly tool has been designed for researchers who has limited computational expertise using graphical user interface (GUI) that requires minimal third party tools. Using HPVDetector, one can analyze paired end whole exome, whole genome or whole transcriptome dataset to detect all known HPV types along with their sites of integration in the host genome. The tool can run in two modes: a quick detect mode can identify co-infection of HPVs and their quantitative abundance while integration mode can identify HPV integration loci in human genome and provide comprehensive HPV specific annotations (see figure).

Based on our evaluation with 116 exome, 23 transcriptome and 1 whole genomes, HPVDetector was able to identify presence of HPV in 20 exome and 4 transcriptome data.Using the annotation module, we could show that viral gene E7 was most widely rerpresented among all the reads detected that is a known viral oncogene. Additionally, the integration module allowed us to validate known HPV integration sites, identify known fragile sites of the human genome as HPV integration site and novel integration sites (Fig 2). In summary, HPVDetector is a simple yet precise and robust tool for detecting HPV from tumour samples using variety of NGS platforms including whole genome, whole exome and transcriptome-- first tool of its kind solely dedicated to detect the presence of HPV types from a diverse variety of NGS data set.


Conceptual workflow of the HPVDetector. The flowchart represents workflow for HPVDetector. Paired-end reads obtained from next-generation sequencing data are aligned to a combined Human–HPV reference database. All discordant read pairs with one read aligning to human and other to the HPV genome are identified and annotated utilising human and HPV database using an inbuilt annotator module.

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

P Chandrani, V Kulkarni, P Iyer, P Upadhyay, R Chaubal, P Das, R Mulherkar, R Singh and A Dutt