Gupta receives American Cancer Society grant to improve virus detection in cancer genomes through deep learning

Pathogenic viruses pose significant threats to public health worldwide and can lead to cancer. Thanks to a grant from the American Cancer Society, Vibhuti Gupta, assistant professor, computer science and data science, will build tools that empower cancer researchers to investigate the etiologic association of viruses with cancer, the understanding of which is still in preliminary stages.

Gupta recently received a $30,000 Diversity in Cancer Research Institutional Development one-year pilot grant from the American Cancer Society (ACS). The ACS pilot awards are established to support early career investigators to collect preliminary data for a larger cancer research study and encouraging research independence early in faculty member’s career.

Gupta received the award for his proposal titled “Improving Detection of Virus Integration in Tumor Genomes using Deep Learning.” The project seeks to develop next generation of tools utilizing deep learning algorithms to effectively detect viruses and their insertion sites in cancer genomes.

Gupta says that viruses are estimated to be responsible for 15 percent of all human cancers globally.

“Some viruses can integrate their genetic material into a human cell genome to promote tumorigenesis,” says Gupta. “The process of viral integration causes damages to the host cell DNA and increases the risk of cancer-promoting changes occurring in the host genome.”

In order to understand these viral mediated cancers, researchers need to detect viruses and their insertion sites in cancer genomes. That process requires both identifying pathogens and tumors and effectively managing the exponentially increasing volume of genomics data.

Gupta plans to address those challenges using deep learning.

“We will use other open-source tools, such as VirusFinder, as a platform and apply deep learning to develop new algorithms to improve the detection of virus integration,” says Gupta. “The result will be a new state-of-the-art tool that the scientific community can use to improve the understanding of viruses and cancer.”