High-throughput sequencing-based investigation of viruses in human cancers by multi-enrichment approach

Sarah Mollerup*, Maria Asplund, Jens Friis-Nielsen, Kristín Rós Kjartansdóttir, Helena Fridholm, Thomas Arn Hansen, José Alejandro Romero Herrera, Christopher James Barnes, Randi Holm Jensen, Stine Raith Richter, Ida Broman Nielsen, Carlotta Pietroni, David E. Alquezar-Planas, Alba Rey-Iglesia, Pernille V. S. Olsen, Ewa Rajpert-De Meyts, Line Groth-Pedersen, Christian von Buchwald, David H. Jensen, Robert Gniadecki & 20 others Estrid Høgdall, Jill Levin Langhoff, Imre Pete, Ildikó Vereczkey, Zsolt Baranyai, Karen Dybkaer, Hans Erik Johnsen, Torben Steiniche, Peter Hokland, Jacob Rosenberg, Ulrik Baandrup, Thomas Sicheritz-Pontén, Eske Willerslev, Søren Brunak, Ole Lund, Tobias Mourier, Lasse Vinner, Jose M. G. Izarzugaza, Lars Peter Nielsen, Anders Johannes Hansen

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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Abstract

Viruses and other infectious agents cause more than 15% of human cancer cases. High-throughput sequencing-based studies of virus-cancer associations have mainly focused on cancer transcriptome data. Here we applied a diverse selection of pre-sequencing enrichment methods targeting all major viral groups, to characterise the viruses present in 197 samples from 18 sample types of cancerous origin. Using high-throughput sequencing we generated 710 datasets constituting 57 billion sequencing reads. Detailed in silico investigation of the viral content, including exclusion of viral artefacts, from de novo assembled contigs and individual sequencing reads yielded a map of the viruses detected. Our data reveals a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained one or more viruses, however, no link between specific viruses and cancer types were found. Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.
Original languageEnglish
JournalJournal of Infectious Diseases
Volume220
Issue number8
Pages (from-to)1312-1324
ISSN0022-1899
DOIs
Publication statusPublished - 2019

Keywords

  • Cancer
  • Virus
  • Virome
  • High-throughput sequencing
  • Next generation sequencing
  • Human
  • Enrichment
  • In-depth analysis
  • Artefacts

Cite this

Mollerup, S., Asplund, M., Friis-Nielsen, J., Kjartansdóttir, K. R., Fridholm, H., Hansen, T. A., ... Hansen, A. J. (2019). High-throughput sequencing-based investigation of viruses in human cancers by multi-enrichment approach. Journal of Infectious Diseases, 220(8), 1312-1324. https://doi.org/10.1093/infdis/jiz318
Mollerup, Sarah ; Asplund, Maria ; Friis-Nielsen, Jens ; Kjartansdóttir, Kristín Rós ; Fridholm, Helena ; Hansen, Thomas Arn ; Herrera, José Alejandro Romero ; Barnes, Christopher James ; Jensen, Randi Holm ; Richter, Stine Raith ; Nielsen, Ida Broman ; Pietroni, Carlotta ; Alquezar-Planas, David E. ; Rey-Iglesia, Alba ; Olsen, Pernille V. S. ; Rajpert-De Meyts, Ewa ; Groth-Pedersen, Line ; von Buchwald, Christian ; Jensen, David H. ; Gniadecki, Robert ; Høgdall, Estrid ; Langhoff, Jill Levin ; Pete, Imre ; Vereczkey, Ildikó ; Baranyai, Zsolt ; Dybkaer, Karen ; Johnsen, Hans Erik ; Steiniche, Torben ; Hokland, Peter ; Rosenberg, Jacob ; Baandrup, Ulrik ; Sicheritz-Pontén, Thomas ; Willerslev, Eske ; Brunak, Søren ; Lund, Ole ; Mourier, Tobias ; Vinner, Lasse ; Izarzugaza, Jose M. G. ; Nielsen, Lars Peter ; Hansen, Anders Johannes. / High-throughput sequencing-based investigation of viruses in human cancers by multi-enrichment approach. In: Journal of Infectious Diseases. 2019 ; Vol. 220, No. 8. pp. 1312-1324.
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title = "High-throughput sequencing-based investigation of viruses in human cancers by multi-enrichment approach",
abstract = "Viruses and other infectious agents cause more than 15{\%} of human cancer cases. High-throughput sequencing-based studies of virus-cancer associations have mainly focused on cancer transcriptome data. Here we applied a diverse selection of pre-sequencing enrichment methods targeting all major viral groups, to characterise the viruses present in 197 samples from 18 sample types of cancerous origin. Using high-throughput sequencing we generated 710 datasets constituting 57 billion sequencing reads. Detailed in silico investigation of the viral content, including exclusion of viral artefacts, from de novo assembled contigs and individual sequencing reads yielded a map of the viruses detected. Our data reveals a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained one or more viruses, however, no link between specific viruses and cancer types were found. Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.",
keywords = "Cancer, Virus, Virome, High-throughput sequencing, Next generation sequencing, Human, Enrichment, In-depth analysis, Artefacts",
author = "Sarah Mollerup and Maria Asplund and Jens Friis-Nielsen and Kjartansd{\'o}ttir, {Krist{\'i}n R{\'o}s} and Helena Fridholm and Hansen, {Thomas Arn} and Herrera, {Jos{\'e} Alejandro Romero} and Barnes, {Christopher James} and Jensen, {Randi Holm} and Richter, {Stine Raith} and Nielsen, {Ida Broman} and Carlotta Pietroni and Alquezar-Planas, {David E.} and Alba Rey-Iglesia and Olsen, {Pernille V. S.} and {Rajpert-De Meyts}, Ewa and Line Groth-Pedersen and {von Buchwald}, Christian and Jensen, {David H.} and Robert Gniadecki and Estrid H{\o}gdall and Langhoff, {Jill Levin} and Imre Pete and Ildik{\'o} Vereczkey and Zsolt Baranyai and Karen Dybkaer and Johnsen, {Hans Erik} and Torben Steiniche and Peter Hokland and Jacob Rosenberg and Ulrik Baandrup and Thomas Sicheritz-Pont{\'e}n and Eske Willerslev and S{\o}ren Brunak and Ole Lund and Tobias Mourier and Lasse Vinner and Izarzugaza, {Jose M. G.} and Nielsen, {Lars Peter} and Hansen, {Anders Johannes}",
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Mollerup, S, Asplund, M, Friis-Nielsen, J, Kjartansdóttir, KR, Fridholm, H, Hansen, TA, Herrera, JAR, Barnes, CJ, Jensen, RH, Richter, SR, Nielsen, IB, Pietroni, C, Alquezar-Planas, DE, Rey-Iglesia, A, Olsen, PVS, Rajpert-De Meyts, E, Groth-Pedersen, L, von Buchwald, C, Jensen, DH, Gniadecki, R, Høgdall, E, Langhoff, JL, Pete, I, Vereczkey, I, Baranyai, Z, Dybkaer, K, Johnsen, HE, Steiniche, T, Hokland, P, Rosenberg, J, Baandrup, U, Sicheritz-Pontén, T, Willerslev, E, Brunak, S, Lund, O, Mourier, T, Vinner, L, Izarzugaza, JMG, Nielsen, LP & Hansen, AJ 2019, 'High-throughput sequencing-based investigation of viruses in human cancers by multi-enrichment approach', Journal of Infectious Diseases, vol. 220, no. 8, pp. 1312-1324. https://doi.org/10.1093/infdis/jiz318

High-throughput sequencing-based investigation of viruses in human cancers by multi-enrichment approach. / Mollerup, Sarah; Asplund, Maria; Friis-Nielsen, Jens; Kjartansdóttir, Kristín Rós; Fridholm, Helena; Hansen, Thomas Arn; Herrera, José Alejandro Romero; Barnes, Christopher James; Jensen, Randi Holm; Richter, Stine Raith; Nielsen, Ida Broman; Pietroni, Carlotta; Alquezar-Planas, David E.; Rey-Iglesia, Alba; Olsen, Pernille V. S.; Rajpert-De Meyts, Ewa ; Groth-Pedersen, Line; von Buchwald, Christian; Jensen, David H.; Gniadecki, Robert; Høgdall, Estrid; Langhoff, Jill Levin; Pete, Imre; Vereczkey, Ildikó; Baranyai, Zsolt; Dybkaer, Karen; Johnsen, Hans Erik; Steiniche, Torben; Hokland, Peter; Rosenberg, Jacob; Baandrup, Ulrik; Sicheritz-Pontén, Thomas; Willerslev, Eske; Brunak, Søren; Lund, Ole; Mourier, Tobias; Vinner, Lasse; Izarzugaza, Jose M. G.; Nielsen, Lars Peter; Hansen, Anders Johannes.

In: Journal of Infectious Diseases, Vol. 220, No. 8, 2019, p. 1312-1324.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - High-throughput sequencing-based investigation of viruses in human cancers by multi-enrichment approach

AU - Mollerup, Sarah

AU - Asplund, Maria

AU - Friis-Nielsen, Jens

AU - Kjartansdóttir, Kristín Rós

AU - Fridholm, Helena

AU - Hansen, Thomas Arn

AU - Herrera, José Alejandro Romero

AU - Barnes, Christopher James

AU - Jensen, Randi Holm

AU - Richter, Stine Raith

AU - Nielsen, Ida Broman

AU - Pietroni, Carlotta

AU - Alquezar-Planas, David E.

AU - Rey-Iglesia, Alba

AU - Olsen, Pernille V. S.

AU - Rajpert-De Meyts, Ewa

AU - Groth-Pedersen, Line

AU - von Buchwald, Christian

AU - Jensen, David H.

AU - Gniadecki, Robert

AU - Høgdall, Estrid

AU - Langhoff, Jill Levin

AU - Pete, Imre

AU - Vereczkey, Ildikó

AU - Baranyai, Zsolt

AU - Dybkaer, Karen

AU - Johnsen, Hans Erik

AU - Steiniche, Torben

AU - Hokland, Peter

AU - Rosenberg, Jacob

AU - Baandrup, Ulrik

AU - Sicheritz-Pontén, Thomas

AU - Willerslev, Eske

AU - Brunak, Søren

AU - Lund, Ole

AU - Mourier, Tobias

AU - Vinner, Lasse

AU - Izarzugaza, Jose M. G.

AU - Nielsen, Lars Peter

AU - Hansen, Anders Johannes

PY - 2019

Y1 - 2019

N2 - Viruses and other infectious agents cause more than 15% of human cancer cases. High-throughput sequencing-based studies of virus-cancer associations have mainly focused on cancer transcriptome data. Here we applied a diverse selection of pre-sequencing enrichment methods targeting all major viral groups, to characterise the viruses present in 197 samples from 18 sample types of cancerous origin. Using high-throughput sequencing we generated 710 datasets constituting 57 billion sequencing reads. Detailed in silico investigation of the viral content, including exclusion of viral artefacts, from de novo assembled contigs and individual sequencing reads yielded a map of the viruses detected. Our data reveals a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained one or more viruses, however, no link between specific viruses and cancer types were found. Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.

AB - Viruses and other infectious agents cause more than 15% of human cancer cases. High-throughput sequencing-based studies of virus-cancer associations have mainly focused on cancer transcriptome data. Here we applied a diverse selection of pre-sequencing enrichment methods targeting all major viral groups, to characterise the viruses present in 197 samples from 18 sample types of cancerous origin. Using high-throughput sequencing we generated 710 datasets constituting 57 billion sequencing reads. Detailed in silico investigation of the viral content, including exclusion of viral artefacts, from de novo assembled contigs and individual sequencing reads yielded a map of the viruses detected. Our data reveals a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained one or more viruses, however, no link between specific viruses and cancer types were found. Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.

KW - Cancer

KW - Virus

KW - Virome

KW - High-throughput sequencing

KW - Next generation sequencing

KW - Human

KW - Enrichment

KW - In-depth analysis

KW - Artefacts

U2 - 10.1093/infdis/jiz318

DO - 10.1093/infdis/jiz318

M3 - Journal article

VL - 220

SP - 1312

EP - 1324

JO - Journal of Infectious Diseases

JF - Journal of Infectious Diseases

SN - 0022-1899

IS - 8

ER -

Mollerup S, Asplund M, Friis-Nielsen J, Kjartansdóttir KR, Fridholm H, Hansen TA et al. High-throughput sequencing-based investigation of viruses in human cancers by multi-enrichment approach. Journal of Infectious Diseases. 2019;220(8):1312-1324. https://doi.org/10.1093/infdis/jiz318