A Novel Pipeline for Virus Integration Sites Detection in Tumor Genomes Using Deep Learning

Cancer is one of the leading causes of death worldwide. Pathogenic viruses are estimated to be responsible for 15% of all human cancers globally and pose significant threats to public health. Viruses integrate their genetic material into the host genome, increasing the risk of cancer promoting changes in it. To understand the molecular mechanisms of virus-mediated cancers, it is crucial to identify viral insertion sites in cancer genomes. However, this effort is hindered by the rapidly increasing volume of tumor sequencing data, along with the challenges of accurate data analysis caused by high viral mutation rates and the difficulty of aligning short reads to the reference genome. Thus it is crucial to develop an efficient method for virus integration site detection in tumor genomes. This paper proposes a novel pipeline to identify viral integration sites leveraging deep Convolutional Neural Networks (CNN). Our contributions are twofold: (i) We propose and integrate three novel matrix generation methods into the pipeline, developed after aligning the host and viral genomes with their respective reference genomes.; (ii) We employ one-hot encoded images with reduced computational complexity to represent viral integration sites and harness the capabilities of Deep CNN networks for detection. The paper illustrates our proposed approach and presents experiments conducted using both synthetic and real sequencing data. Our preliminary experimental results are promising, showcasing the effectiveness of the proposed methods in detecting viral integration sites.