Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing

Lasse Vinner*, Tobias Mourier, Jens Friis-Nielsen, Robert Gniadecki, Karen Dybkaer, Jacob Rosenberg, Jill Levin Langhoff, David Flores Santa Cruz, Jannik Fonager, Jose M.G. Izarzugaza, Ramneek Gupta, Thomas Sicheritz-Ponten, Søren Brunak, Eske Willerslev, Lars Peter Nielsen, Anders Johannes Hansen

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

29 Scopus citations


Although nearly one fifth of all human cancers have an infectious aetiology, the causes for the majority of cancers remain unexplained. Despite the enormous data output from high-throughput shotgun sequencing, viral DNA in a clinical sample typically constitutes a proportion of host DNA that is too small to be detected. Sequence variation among virus genomes complicates application of sequence-specific, and highly sensitive, PCR methods. Therefore, we aimed to develop and characterize a method that permits sensitive detection of sequences despite considerable variation. We demonstrate that our low-stringency in-solution hybridization method enables detection of <100 viral copies. Furthermore, distantly related proviral sequences may be enriched by orders of magnitude, enabling discovery of hitherto unknown viral sequences by high-throughput sequencing. The sensitivity was sufficient to detect retroviral sequences in clinical samples. We used this method to conduct an investigation for novel retrovirus in samples from three cancer types. In accordance with recent studies our investigation revealed no retroviral infections in human B-cell lymphoma cells, cutaneous T-cell lymphoma or colorectal cancer biopsies. Nonetheless, our generally applicable method makes sensitive detection possible and permits sequencing of distantly related sequences from complex material.

Original languageEnglish (US)
Article number13201
JournalScientific Reports
StatePublished - Aug 19 2015
Externally publishedYes

Bibliographical note

Funding Information:
The authors would like to acknowledge Yasuhiro Takeuchi for HEK293/PERV cells; Danish National High throughput Sequencing Centre for sequencing; BGI Europe for sequencing; Sarah Natalie Vitcetz for technical assistance; Ellinor Lindberg for qPCR and Lea Brandt and Sanne Skov Jensen for PBMCs; Kristoffer Rapacki, John D. Sørensen, Kirstine Belling, Simon Rasmussen and the other members of the NGS analysis pipeline at CBS for the scientific discussion and the technical support provided. The work was supported by the Innovation Fund Denmark (The GenomeDenmark platform, grant no. 019-2011-2).

ASJC Scopus subject areas

  • General


Dive into the research topics of 'Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing'. Together they form a unique fingerprint.

Cite this