4.7 Article

VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue

Journal

BIOINFORMATICS
Volume 29, Issue 2, Pages 266-267

Publisher

OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/bts665

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Funding

  1. National Cancer Institute, U.S. National Institutes of Health [U24CA143883, P30 CA016672]
  2. Cancer Center Support Grant
  3. National Center for Research Resources [UL1TR000371]
  4. H. A. and Mary K. Chapman Foundation
  5. Michael and Susan Dell Foundation

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We developed a new algorithmic method, VirusSeq, for detecting known viruses and their integration sites in the human genome using next-generation sequencing data. We evaluated VirusSeq on whole-transcriptome sequencing (RNA-Seq) data of 256 human cancer samples from The Cancer Genome Atlas. Using these data, we showed that VirusSeq accurately detects the known viruses and their integration sites with high sensitivity and specificity. VirusSeq can also perform this function using whole-genome sequencing data of human tissue.

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