Publications

Authors:

Zapatka, Marc; Borozan, Ivan; Brewer, Daniel S.; Iskar, Murat; Grundhoff, Adam; Alawi, Malik; Desai, Nikita; Sültmann, Holger; Moch, Holger; Alawi, Malik; Borozan, Ivan; Brewer, Daniel S.; Cooper, Colin S.; Desai, Nikita; Eils, Roland; Ferretti, Vincent; Grundhoff, Adam; Iskar, Murat; Kleinheinz, Kortine; Lichter, Peter; Nakagawa, Hidewaki; Ojesina, Akinyemi I.; Pedamallu, Chandra Sekhar; Schlesner, Matthias; Su, Xiaoping; Zapatka, Marc; Cooper, Colin S.; Eils, Roland; Ferretti, Vincent; Lichter, Peter; Aaltonen, Lauri A.; Abascal, Federico; Abeshouse, Adam; Aburatani, Hiroyuki; Adams, David J.; Agrawal, Nishant; Ahn, Keun Soo; Ahn, Sung-Min; Aikata, Hiroshi; Akbani, Rehan; Akdemir, Kadir C.; Al-Ahmadie, Hikmat; Al-Sedairy, Sultan T.; Al-Shahrour, Fatima; Alawi, Malik; Albert, Monique; Aldape, Kenneth; Alexandrov, Ludmil B.; Ally, Adrian; Alsop, Kathryn; Alvarez, Eva G.; Amary, Fernanda; Amin, Samirkumar B.; Aminou, Brice; Ammerpohl, Ole; Anderson, Matthew J.; Ang, Yeng; Antonello, Davide; Anur, Pavana; Aparicio, Samuel; Appelbaum, Elizabeth L.; Arai, Yasuhito; Aretz, Axel; Arihiro, Koji; Ariizumi, Shun-ichi; Armenia, Joshua; Arnould, Laurent; Asa, Sylvia; Assenov, Yassen; Atwal, Gurnit; Aukema, Sietse; Auman, J. Todd; Aure, Miriam R. R.; Awadalla, Philip; Aymerich, Marta; Bader, Gary D.; Baez-Ortega, Adrian; Bailey, Matthew H.; Bailey, Peter J.; Balasundaram, Miruna; Balu, Saianand; Bandopadhayay, Pratiti; Banks, Rosamonde E.; Barbi, Stefano; Barbour, Andrew P.; Barenboim, Jonathan; Barnholtz-Sloan, Jill; Barr, Hugh; Barrera, Elisabet; Bartlett, John; Bartolome, Javier; Bassi, Claudio; Bathe, Oliver F.; Baumhoer, Daniel; Bavi, Prashant; Baylin, Stephen B.; Bazant, Wojciech; Beardsmore, Duncan; Beck, Timothy A.; Behjati, Sam; Behren, Andreas; Niu, Beifang; Bell, Cindy; Beltran, Sergi; Benz, Christopher; Berchuck, Andrew; Bergmann, Anke K.; Bergstrom, Erik N.; Berman, Benjamin P.; Berney, Daniel M.; Bernhart, Stephan H.; Beroukhim, Rameen; Berrios, Mario; Bersani, Samantha; Bertl, Johanna; Betancourt, Miguel; Bhandari, Vinayak; Bhosle, Shriram G.; Biankin, Andrew V.; Bieg, Matthias; Bigner, Darell; Binder, Hans; Birney, Ewan; Birrer, Michael; Biswas, Nidhan K.; Bjerkehagen, Bodil; Bodenheimer, Tom; Boice, Lori; Bonizzato, Giada; De Bono, Johann S.; Boot, Arnoud; Bootwalla, Moiz S.; Borg, Ake; Borkhardt, Arndt; Boroevich, Keith A.; Borozan, Ivan; Borst, Christoph; Bosenberg, Marcus; Bosio, Mattia; Boultwood, Jacqueline; Bourque, Guillaume; Boutros, Paul C.; Bova, G. Steven; Bowen, David T.; Bowlby, Reanne; Bowtell, David D. L.; Boyault, Sandrine; Boyce, Rich; Boyd, Jeffrey; Brazma, Alvis; Brennan, Paul; Brewer, Daniel S.; Brinkman, Arie B.; Bristow, Robert G.; Broaddus, Russell R.; Brock, Jane E.; Brock, Malcolm; Broeks, Annegien; Brooks, Angela N.; Brooks, Denise; Brors, Benedikt; Brunak, Søren; Bruxner, Timothy J. C.; Bruzos, Alicia L.; Buchanan, Alex; Buchhalter, Ivo; Buchholz, Christiane; Bullman, Susan; Burke, Hazel; Burkhardt, Birgit; Burns, Kathleen H.; Busanovich, John; Bustamante, Carlos D.; Butler, Adam P.; Butte, Atul J.; Byrne, Niall J.; Børresen-Dale, Anne-Lise; Caesar-Johnson, Samantha J.; Cafferkey, Andy; Cahill, Declan; Calabrese, Claudia; Caldas, Carlos; Calvo, Fabien; Camacho, Niedzica; Campbell, Peter J.; Campo, Elias; Cantù, Cinzia; Cao, Shaolong; Carey, Thomas E.; Carlevaro-Fita, Joana; Carlsen, Rebecca; Cataldo, Ivana; Cazzola, Mario; Cebon, Jonathan; Cerfolio, Robert; Chadwick, Dianne E.; Chakravarty, Dimple; Chalmers, Don; Chan, Calvin Wing Yiu; Chan, Kin; Chan-Seng-Yue, Michelle; Chandan, Vishal S.; Chang, David K.; Chanock, Stephen J.; Chantrill, Lorraine A.; Chateigner, Aurélien; Chatterjee, Nilanjan; Chayama, Kazuaki; Chen, Hsiao-Wei; Chen, Jieming; Chen, Ken; Chen, Yiwen; Chen, Zhaohong; Cherniack, Andrew D.; Chien, Jeremy; Chiew, Yoke-Eng; Chin, Suet-Feung; Cho, Juok; Cho, Sunghoon; Choi, Jung Kyoon; Choi, Wan; Chomienne, Christine; Chong, Zechen; Ch

Title:

The landscape of viral associations in human cancers

Year:

2020

Type of item:

Articolo in Rivista

Tipologia ANVUR:

Articolo su rivista

Language:

Inglese

Referee:

No

Name of journal:

Nature Genetics

ISSN of journal:

1061-4036

N° Volume:

52

Number or Folder:

3

Page numbers:

320-330

Keyword:

PCAWG, APOBEC, human papilloma virus, Epstein-Barr virus

Short description of contents:

Viral pathogen load in cancer genomes is estimated through analysis of sequencing data from 2,656 tumors across 35 cancer types using multiple pathogen-detection pipelines, identifying viruses in 382 genomic and 68 transcriptome datasets.Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, for which whole-genome and-for a subset-whole-transcriptome sequencing data from 2,658 cancers across 38 tumor types was aggregated, we systematically investigated potential viral pathogens using a consensus approach that integrated three independent pipelines. Viruses were detected in 382 genome and 68 transcriptome datasets. We found a high prevalence of known tumor-associated viruses such as Epstein-Barr virus (EBV), hepatitis B virus (HBV) and human papilloma virus (HPV; for example, HPV16 or HPV18). The study revealed significant exclusivity of HPV and driver mutations in head-and-neck cancer and the association of HPV with APOBEC mutational signatures, which suggests that impaired antiviral defense is a driving force in cervical, bladder and head-and-neck carcinoma. For HBV, HPV16, HPV18 and adeno-associated virus-2 (AAV2), viral integration was associated with local variations in genomic copy numbers. Integrations at the TERT promoter were associated with high telomerase expression evidently activating this tumor-driving process. High levels of endogenous retrovirus (ERV1) expression were linked to a worse survival outcome in patients with kidney cancer.

Note:

Online content: Any methods, additional references, Nature Research report-ing summaries, source data, extended data, supplementary information, acknowledgements, peer review information; details of author contributions and competing interests; and statements of data and code availability are available at https://doi.org/10.1038/s41588-019-0558-9

Product ID:

138016

Handle IRIS:

11562/1120006

Last Modified:

February 2, 2025

Bibliographic citation:

Zapatka, Marc; Borozan, Ivan; Brewer, Daniel S.; Iskar, Murat; Grundhoff, Adam; Alawi, Malik; Desai, Nikita; Sültmann, Holger; Moch, Holger; Alawi, Malik; Borozan, Ivan; Brewer, Daniel S.; Cooper, Colin S.; Desai, Nikita; Eils, Roland; Ferretti, Vincent; Grundhoff, Adam; Iskar, Murat; Kleinheinz, Kortine; Lichter, Peter; Nakagawa, Hidewaki; Ojesina, Akinyemi I.; Pedamallu, Chandra Sekhar; Schlesner, Matthias; Su, Xiaoping; Zapatka, Marc; Cooper, Colin S.; Eils, Roland; Ferretti, Vincent; Lichter, Peter; Aaltonen, Lauri A.; Abascal, Federico; Abeshouse, Adam; Aburatani, Hiroyuki; Adams, David J.; Agrawal, Nishant; Ahn, Keun Soo; Ahn, Sung-Min; Aikata, Hiroshi; Akbani, Rehan; Akdemir, Kadir C.; Al-Ahmadie, Hikmat; Al-Sedairy, Sultan T.; Al-Shahrour, Fatima; Alawi, Malik; Albert, Monique; Aldape, Kenneth; Alexandrov, Ludmil B.; Ally, Adrian; Alsop, Kathryn; Alvarez, Eva G.; Amary, Fernanda; Amin, Samirkumar B.; Aminou, Brice; Ammerpohl, Ole; Anderson, Matthew J.; Ang, Yeng; Antonello, Davide; Anur, Pavana; Aparicio, Samuel; Appelbaum, Elizabeth L.; Arai, Yasuhito; Aretz, Axel; Arihiro, Koji; Ariizumi, Shun-ichi; Armenia, Joshua; Arnould, Laurent; Asa, Sylvia; Assenov, Yassen; Atwal, Gurnit; Aukema, Sietse; Auman, J. Todd; Aure, Miriam R. R.; Awadalla, Philip; Aymerich, Marta; Bader, Gary D.; Baez-Ortega, Adrian; Bailey, Matthew H.; Bailey, Peter J.; Balasundaram, Miruna; Balu, Saianand; Bandopadhayay, Pratiti; Banks, Rosamonde E.; Barbi, Stefano; Barbour, Andrew P.; Barenboim, Jonathan; Barnholtz-Sloan, Jill; Barr, Hugh; Barrera, Elisabet; Bartlett, John; Bartolome, Javier; Bassi, Claudio; Bathe, Oliver F.; Baumhoer, Daniel; Bavi, Prashant; Baylin, Stephen B.; Bazant, Wojciech; Beardsmore, Duncan; Beck, Timothy A.; Behjati, Sam; Behren, Andreas; Niu, Beifang; Bell, Cindy; Beltran, Sergi; Benz, Christopher; Berchuck, Andrew; Bergmann, Anke K.; Bergstrom, Erik N.; Berman, Benjamin P.; Berney, Daniel M.; Bernhart, Stephan H.; Beroukhim, Rameen; Berrios, Mario; Bersani, Samantha; Bertl, Johanna; Betancourt, Miguel; Bhandari, Vinayak; Bhosle, Shriram G.; Biankin, Andrew V.; Bieg, Matthias; Bigner, Darell; Binder, Hans; Birney, Ewan; Birrer, Michael; Biswas, Nidhan K.; Bjerkehagen, Bodil; Bodenheimer, Tom; Boice, Lori; Bonizzato, Giada; De Bono, Johann S.; Boot, Arnoud; Bootwalla, Moiz S.; Borg, Ake; Borkhardt, Arndt; Boroevich, Keith A.; Borozan, Ivan; Borst, Christoph; Bosenberg, Marcus; Bosio, Mattia; Boultwood, Jacqueline; Bourque, Guillaume; Boutros, Paul C.; Bova, G. Steven; Bowen, David T.; Bowlby, Reanne; Bowtell, David D. L.; Boyault, Sandrine; Boyce, Rich; Boyd, Jeffrey; Brazma, Alvis; Brennan, Paul; Brewer, Daniel S.; Brinkman, Arie B.; Bristow, Robert G.; Broaddus, Russell R.; Brock, Jane E.; Brock, Malcolm; Broeks, Annegien; Brooks, Angela N.; Brooks, Denise; Brors, Benedikt; Brunak, Søren; Bruxner, Timothy J. C.; Bruzos, Alicia L.; Buchanan, Alex; Buchhalter, Ivo; Buchholz, Christiane; Bullman, Susan; Burke, Hazel; Burkhardt, Birgit; Burns, Kathleen H.; Busanovich, John; Bustamante, Carlos D.; Butler, Adam P.; Butte, Atul J.; Byrne, Niall J.; Børresen-Dale, Anne-Lise; Caesar-Johnson, Samantha J.; Cafferkey, Andy; Cahill, Declan; Calabrese, Claudia; Caldas, Carlos; Calvo, Fabien; Camacho, Niedzica; Campbell, Peter J.; Campo, Elias; Cantù, Cinzia; Cao, Shaolong; Carey, Thomas E.; Carlevaro-Fita, Joana; Carlsen, Rebecca; Cataldo, Ivana; Cazzola, Mario; Cebon, Jonathan; Cerfolio, Robert; Chadwick, Dianne E.; Chakravarty, Dimple; Chalmers, Don; Chan, Calvin Wing Yiu; Chan, Kin; Chan-Seng-Yue, Michelle; Chandan, Vishal S.; Chang, David K.; Chanock, Stephen J.; Chantrill, Lorraine A.; Chateigner, Aurélien; Chatterjee, Nilanjan; Chayama, Kazuaki; Chen, Hsiao-Wei; Chen, Jieming; Chen, Ken; Chen, Yiwen; Chen, Zhaohong; Cherniack, Andrew D.; Chien, Jeremy; Chiew, Yoke-Eng; Chin, Suet-Feung; Cho, Juok; Cho, Sunghoon; Choi, Jung Kyoon; Choi, Wan; Chomienne, Christine; Chong, Zechen; Ch, The landscape of viral associations in human cancers «Nature Genetics» , vol. 52 , n. 3 , 2020 , pp. 320-330

Consulta la scheda completa presente nel repository istituzionale della Ricerca di Ateneo