Identification of Human Papillomavirus Integration Sites in the Human Genome Using NGS-Based Bioinformatics Analysis

Abstract

The majority of cases of cervical cancer worldwide are caused by high-risk genotypes such as HPV-16 and HPV-18, making the human papillomavirus (HPV) one of the most clinically significant viral pathogens. The physical integration of viral DNA into the host genome, which sets off a series of genomic disruptions, is one of the most important stages in the development of HPV-related cancer. Using publicly available next-generation sequencing (NGS) data, we developed and implemented a bioinformatics pipeline in this work to locate these integration sites. We began with raw sequencing reads from the NCBI Sequence Read Archive, performed quality filtering, aligned the cleaned reads to a merged human-HPV reference genome (GRCh38 plus HPV-16), and used variant calling to identify areas exhibiting viral insertion. Our findings provide unambiguous proof of genomic breakpoints associated with HPV and possible integration hotspots present in the human genome. Beyond the particular results, this work demonstrates that open-source computational tools by themselves can reconstruct significant biological signals from publicly available data, providing a useful and repeatable way to investigate how HPV modifies the genomes of the cells it infects.