title: Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers.
abstract: Virus discovery from high throughput sequencing data often follows a bottom-up approach where taxonomic annotation takes place prior to association to disease. Albeit effective in some cases, the approach fails to detect novel pathogens and remote variants not present in reference databases. We have developed a species independent pipeline that utilises sequence clustering for the identification of nucleotide sequences that co-occur across multiple sequencing data instances. We applied the workflow to 686 sequencing libraries from 252 cancer samples of different cancer and tissue types, 32 non-template controls, and 24 test samples. Recurrent sequences were statistically associated to biological, methodological or technical features with the aim to identify novel pathogens or plausible contaminants that may associate to a particular kit or method. We provide examples of identified inhabitants of the healthy tissue flora as well as experimental contaminants. Unmapped sequences that co-occur with high statistical significance potentially represent the unknown sequence space where novel pathogens can be identified.
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark. jef@cbs.dtu.dk.
authors.forename: Jens
authors.initials: J
authors.lastname: Friis-Nielsen
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark. kristin.kjartansdottir@snm.ku.dk.
authors.forename: Kristín Rós
authors.initials: KR
authors.lastname: Kjartansdóttir
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark. sarah.mollerup@snm.ku.dk.
authors.forename: Sarah
authors.initials: S
authors.lastname: Mollerup
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark. amasplund@snm.ku.dk.
authors.forename: Maria
authors.initials: M
authors.lastname: Asplund
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark. tmourier@snm.ku.dk.
authors.forename: Tobias
authors.initials: T
authors.lastname: Mourier
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark. randi.jensen@snm.ku.dk.
authors.forename: Randi Holm
authors.initials: RH
authors.lastname: Jensen
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark. thomas.hansen@snm.ku.dk.
authors.forename: Thomas Arn
authors.initials: TA
authors.lastname: Hansen
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark. zld305@alumni.ku.dk.
authors.forename: Alba
authors.initials: A
authors.lastname: Rey-Iglesia
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark. srichter@snm.ku.dk.
authors.forename: Stine Raith
authors.initials: SR
authors.lastname: Richter
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark. ida.nielsen@snm.ku.dk.
authors.forename: Ida Broman
authors.initials: IB
authors.lastname: Nielsen
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark. d.e.alquezar@gmail.com.
authors.forename: David E
authors.initials: DE
authors.lastname: Alquezar-Planas
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark. pvsolsen@snm.ku.dk.
authors.forename: Pernille V S
authors.initials: PV
authors.lastname: Olsen
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark. lasse.vinner@snm.ku.dk.
authors.forename: Lasse
authors.initials: L
authors.lastname: Vinner
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark. helena.fridholm@gmail.com.
authors.forename: Helena
authors.initials: H
authors.lastname: Fridholm
authors.affiliation: Department of Autoimmunology and Biomarkers, Statens Serum Institut, DK-2300 Copenhagen S, Denmark. lpn@ssi.dk.
authors.forename: Lars Peter
authors.initials: LP
authors.lastname: Nielsen
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark. ewillerslev@snm.ku.dk.
authors.forename: Eske
authors.initials: E
authors.lastname: Willerslev
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark. thomas@cbs.dtu.dk.
authors.forename: Thomas
authors.initials: T
authors.lastname: Sicheritz-Pontén
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark. lund@cbs.dtu.dk.
authors.forename: Ole
authors.initials: O
authors.lastname: Lund
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark. AJHansen@snm.ku.dk.
authors.forename: Anders Johannes
authors.initials: AJ
authors.lastname: Hansen
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark. txema@cbs.dtu.dk.
authors.forename: Jose M G
authors.initials: JM
authors.lastname: Izarzugaza
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark. soren.brunak@cpr.ku.dk.|NNF Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark. soren.brunak@cpr.ku.dk.
authors.forename: Søren
authors.initials: S
authors.lastname: Brunak
mesh_terms: D019295:Computational Biology; D017124:Conserved Sequence; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009369:Neoplasms / Q000821:virology*; D012367:RNA, Viral / Q000235:genetics; D014780:Viruses / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*
chemical_list: D012367:RNA, Viral
keywords: assay contamination; cancer causing viruses; next generation sequencing; novel sequence identification; oncoviruses; sequence clustering; taxonomic characterisation