VIRUSBreakend: Viral Integration Recognition Using Single Breakends

Daniel L Cameron, Nina Jacobs, Paul Roepman, Peter Priestley, Edwin Cuppen, Anthony T Papenfuss

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Abstract

Motivation: Integration of viruses into infected host cell DNA can cause DNA damage and disrupt genes. Recent cost reductions and growth of whole genome sequencing has produced a wealth of data in which viral presence and integration detection is possible. While key research and clinically relevant insights can be uncovered, existing software has not achieved widespread adoption, limited in part due to high computational costs, the inability to detect a wide range of viruses, as well as precision and sensitivity. Results: Here, we describe VIRUSBreakend, a high-speed tool that identifies viral DNA presence and genomic integration. It utilizes single breakends, breakpoints in which only one side can be unambiguously placed, in a novel virus-centric variant calling and assembly approach to identify viral integrations with high sensitivity and a nearzero false discovery rate. VIRUSBreakend detects viral integrations anywhere in the host genome including regions such as centromeres and telomeres unable to be called by existing tools. Applying VIRUSBreakend to a large metastatic cancer cohort, we demonstrate that it can reliably detect clinically relevant viral presence and integration including HPV, HBV, MCPyV, EBV and HHV-8.

Original languageEnglish
Pages (from-to)3115-3119
Number of pages5
JournalBioinformatics (Oxford, England)
Volume37
Issue number19
Early online date11 May 2021
DOIs
Publication statusPublished - 1 Oct 2021

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