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Viral sequences in human cancer.

Authors
  • Cantalupo, Paul G1
  • Katz, Joshua P1
  • Pipas, James M2
  • 1 Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
  • 2 Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA. Electronic address: [email protected]
Type
Published Article
Journal
Virology
Publisher
Elsevier
Publication Date
Jan 01, 2018
Volume
513
Pages
208–216
Identifiers
DOI: 10.1016/j.virol.2017.10.017
PMID: 29107929
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

We have developed a virus detection and discovery computational pipeline, Pickaxe, and applied it to NGS databases provided by The Cancer Genome Atlas (TCGA). We analyzed a collection of whole genome (WGS), exome (WXS), and RNA (RNA-Seq) sequencing libraries from 3052 participants across 22 different cancers. NGS data from nearly all tumor and normal tissues examined contained contaminating viral sequences. Intensive computational and manual efforts are required to remove these artifacts. We found that several different types of cancers harbored Herpesviruses including EBV, CMV, HHV1, HHV2, HHV6 and HHV7. In addition to the reported associations of Hepatitis B and C virus (HBV & HCV) with liver cancer, and Human papillomaviruses (HPV) with cervical cancer and a subset of head and neck cancers, we found additional cases of HPV integrated in a small number of bladder cancers. Gene expression and mutational profiles suggest that HPV drives tumorigenesis in these cases. Copyright © 2017 Elsevier Inc. All rights reserved.

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