Pubblicazioni

Autori:

Jiao, Wei; Atwal, Gurnit; Polak, Paz; Karlic, Rosa; Cuppen, Edwin; Al-Shahrour, Fatima; Atwal, Gurnit; Bailey, Peter J.; Biankin, Andrew V.; Boutros, Paul C.; Campbell, Peter J.; Chang, David K.; Cooke, Susanna L.; Deshpande, Vikram; Faltas, Bishoy M.; Faquin, William C.; Garraway, Levi; Getz, Gad; Grimmond, Sean M.; Haider, Syed; Hoadley, Katherine A.; Jiao, Wei; Kaiser, Vera B.; Karlic, Rosa; Kato, Mamoru; Kübler, Kirsten; Lazar, Alexander J.; Li, Constance H.; Louis, David N.; Margolin, Adam; Martin, Sancha; Nahal-Bose, Hardeep K.; Nielsen, G. Petur; Nik-Zainal, Serena; Omberg, Larsson; P’Ng, Christine; Perry, Marc D.; Polak, Paz; Rheinbay, Esther; Rubin, Mark A.; Semple, Colin A.; Sgroi, Dennis C.; Shibata, Tatsuhiro; Siebert, Reiner; Smith, Jaclyn; Stein, Lincoln D.; Stobbe, Miranda D.; Sun, Ren X.; Thai, Kevin; Wright, Derek W.; Wu, Chin-Lee; Yuan, Ke; Zhang, Junjun; Danyi, Alexandra; de Ridder, Jeroen; van Herpen, Carla; Lolkema, Martijn P.; Steeghs, Neeltje; Getz, Gad; Morris, Quaid D.; Stein, Lincoln D.; 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, Jonath

Titolo:

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

Anno:

2020

Tipologia prodotto:

Articolo in Rivista

Tipologia ANVUR:

Articolo su rivista

Lingua:

Inglese

Referee:

No

Nome rivista:

NATURE COMMUNICATIONS

ISSN Rivista:

2041-1723

N° Volume:

11

Numero o Fascicolo:

1

Intervallo pagine:

728-739

Parole chiave:

deep learning, passenger mutations, ICGC, TCGA, PCAWG

Breve descrizione dei contenuti:

In cancer, the primary tumour's organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here,as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types produced by the PCAWG Consortium. Our classifier achieves an accuracy of 91% on held-out tumor samples and 88% and 83% respectively on independent primary and metastatic samples, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced accuracy. Our results have clinical applicability, underscore how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of circulating tumour DNA.

Id prodotto:

138174

Handle IRIS:

11562/1120667

ultima modifica:

7 marzo 2024

Citazione bibliografica:

Jiao, Wei; Atwal, Gurnit; Polak, Paz; Karlic, Rosa; Cuppen, Edwin; Al-Shahrour, Fatima; Atwal, Gurnit; Bailey, Peter J.; Biankin, Andrew V.; Boutros, Paul C.; Campbell, Peter J.; Chang, David K.; Cooke, Susanna L.; Deshpande, Vikram; Faltas, Bishoy M.; Faquin, William C.; Garraway, Levi; Getz, Gad; Grimmond, Sean M.; Haider, Syed; Hoadley, Katherine A.; Jiao, Wei; Kaiser, Vera B.; Karlic, Rosa; Kato, Mamoru; Kübler, Kirsten; Lazar, Alexander J.; Li, Constance H.; Louis, David N.; Margolin, Adam; Martin, Sancha; Nahal-Bose, Hardeep K.; Nielsen, G. Petur; Nik-Zainal, Serena; Omberg, Larsson; P’Ng, Christine; Perry, Marc D.; Polak, Paz; Rheinbay, Esther; Rubin, Mark A.; Semple, Colin A.; Sgroi, Dennis C.; Shibata, Tatsuhiro; Siebert, Reiner; Smith, Jaclyn; Stein, Lincoln D.; Stobbe, Miranda D.; Sun, Ren X.; Thai, Kevin; Wright, Derek W.; Wu, Chin-Lee; Yuan, Ke; Zhang, Junjun; Danyi, Alexandra; de Ridder, Jeroen; van Herpen, Carla; Lolkema, Martijn P.; Steeghs, Neeltje; Getz, Gad; Morris, Quaid D.; Stein, Lincoln D.; 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, Jonath, A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns «NATURE COMMUNICATIONS» , vol. 11 , n. 1 , 2020 , pp. 728-739

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