High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment 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; 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

doi:10.1093/infdis/jiz318

High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment 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 GniadeckiEstrid 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

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Abstract

BACKGROUND: 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.

METHODS: In this study, we applied a diverse selection of presequencing enrichment methods targeting all major viral groups, to characterize 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.

RESULTS: 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 reveal a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained 1 or more viruses; however, no link between specific viruses and cancer types were found.

CONCLUSIONS: Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.

Originalsprog	Engelsk
Tidsskrift	The Journal of Infectious Diseases
Vol/bind	220
Udgave nummer	8
Sider (fra-til)	1312-1324
ISSN	0022-1899
DOI	https://doi.org/10.1093/infdis/jiz318
Status	Udgivet - 13 sep. 2019

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10.1093/infdis/jiz318Licens: CC BY

High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment ApproachForlagets udgivne version, 879 KBLicens: CC BY

Citationsformater

Mollerup, S., Asplund, M., Friis-Nielsen, J., Kjartansdóttir, K. R., Fridholm, H., Hansen, T. A., Herrera, J. A. R., Barnes, C. J., Jensen, R. H., Richter, S. R., Nielsen, I. B., Pietroni, C., Alquezar-Planas, D. E., Rey-Iglesia, A., Olsen, P. V. S., Rajpert-De Meyts, E., Groth-Pedersen, L., von Buchwald, C., Jensen, D. H., ... Hansen, A. J. (2019). High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach. The Journal of Infectious Diseases, 220(8), 1312-1324. https://doi.org/10.1093/infdis/jiz318

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 Multienrichment Approach', The Journal of Infectious Diseases, bind 220, nr. 8, s. 1312-1324. https://doi.org/10.1093/infdis/jiz318

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title = "High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach",

abstract = "BACKGROUND: 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.METHODS: In this study, we applied a diverse selection of presequencing enrichment methods targeting all major viral groups, to characterize 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.RESULTS: 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 reveal a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained 1 or more viruses; however, no link between specific viruses and cancer types were found.CONCLUSIONS: Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.",

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}",

note = "{\textcopyright} The Author(s) 2019. Published by Oxford University Press for the Infectious Diseases Society of America.",

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doi = "10.1093/infdis/jiz318",

language = "English",

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T1 - High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment 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 - 2019/9/13

Y1 - 2019/9/13

N2 - BACKGROUND: 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.METHODS: In this study, we applied a diverse selection of presequencing enrichment methods targeting all major viral groups, to characterize 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.RESULTS: 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 reveal a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained 1 or more viruses; however, no link between specific viruses and cancer types were found.CONCLUSIONS: Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.

AB - BACKGROUND: 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.METHODS: In this study, we applied a diverse selection of presequencing enrichment methods targeting all major viral groups, to characterize 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.RESULTS: 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 reveal a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained 1 or more viruses; however, no link between specific viruses and cancer types were found.CONCLUSIONS: Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.

U2 - 10.1093/infdis/jiz318

DO - 10.1093/infdis/jiz318

M3 - Journal article

C2 - 31253993

SN - 0022-1899

VL - 220

SP - 1312

EP - 1324

JO - The Journal of Infectious Diseases

JF - The Journal of Infectious Diseases

IS - 8

ER -

High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach

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