Comprehensive genomic characterization of head and neck squamous cell carcinomas

Lawrence, Michael S.; Wong, Tina; Zhang, Jianhua; Zeng, Dong; Xu, Andrew W.; Sougnez, Carrie; Weinstein, John; Yang, Liming; Tam, Angela; Thiessen, Nina; Robertson, A. Gordon; Schein, Jacqueline E.; Protopopov, Alexei; Tang, Jiabin; Todd Auman, J.; Santoso, Netty; Sipahimalani, Payal; Wang, Jing; Ren, Xiaojia; Sipahimalan, Payal; Wang, Kai; Seth, Sahil; Wilkerson, Matthew D.; Parfenov, Michael; Wu, Junyuan; Song, Xingzhi; Zhao, Ni; Seidman, Jonathan; Liu, W.; Zack, Travis I.; Pantazi, Angeliki; Veluvolu, Umadevi; Park, Peter J.; Zhang, Hailei; Walter, Vonn; Waring, Scot; Sekhar Pedamallu, Chandra; Zou, Lihua; Tward, Aaron D.; Lichtenstein, Lee; Lander, Eric; Tan, Donghui; Prins, Jan F.; Roach, Jeffrey; Wheeler, David; Shi, Yan; Xi, Liu; Simons, Janae V.; Ramirez, Ricardo; Voet, Doug; Singh, Darshan; Holt, Robert A.; Liu, Y.; Getz, Gad; Jones, Steven J. M.; Soloway, Matthew G.; Lee, Darlene; Parker, Joel S.; Gabriel, Stacey B.; Li, Haiyan I.; Perou, Charles M.; Marra, Marco A.; Mayo, Michael; Sinhal, Rileen; Moore, Richard A.; Mungall, Andrew J.; Saksena, Gordon; Bowlby, Reanne; Yau, Christina; Brooks, Denise; Guin, Ranabir; Lee, Semin; Schumacher, Steven E.; Pedamallu, Chandra Sekhar; Butterfield, Yaron S. N.; Mahadeshwar, Harshad S.; Ojesina, Akinyemi I.; Carlsen, Rebecca; Cheng, Dean; Weisenberger, Daniel J.; Chu, Andy; Stojanov, Petar; Noble, Michael S.; Dhalla, Noreen; Lee, W.; Chin, Lynda; Kucherlapati, Raju; Ally, Adrian; Reid, Jeff; Onur Sumer, S.; Van Den Berg, David J.; Balasundaram, Miruna; Haseley, Psalm; Motter, Thomas; Birol, Inanc; Ramirez, R.; Weinhold, Nils; Hadjipanayis, Angela; Sander, Chris; Hoyle, Alan P.; Jefferys, Stuart R.; Jones, Corbin D.; Kimes, Patrick K.; Shen, Ronglai; Wiznerowicz, Maciej; Lu, Yiling; Marron, J. S.; Yarbrough, Wendell G.; Zhang, Jiexin; Sinha, Rileen; Meng, Shaowu; Mills, Gordon; Zuo, Zhixiang; Mieczkowski, Piotr A.; Bristow, Christopher A.; Mose, Lisle E.; Stuart, Joshua; Shaw, Kenna R. Mills; Hong Fan, You; Tarvi, Katherine; Casasent, Tod; Van Waes, Carter; Yena, Peggy; Liu, J.; Taylor, Barry S.; Waggott, Daryl M.; Ladanyi, Marc; Cibulskisl, Kristian; Liu, Wenbin; Hayes, D. Neil; Le, Yiling; Wise, Lisa; Ng, Sam; Mille, Gordon; Diao, Lixia; Zmuda, Erik; Fan, You Hong; Jung, Joonil; Hoadley, Katherine A.; Yang, Lixing; Lie, Jinze; Akbani, Rehan; Ciriello, Giovanni; Buda, Elizabeth; Meyerson, Matthew; Liu, Yufeng; Zenklusen, Jean Claude; Walton, Jessica S.; Cibulskis, Kristian; Wan, Yunhu; Prystowsky, Michael; Auman, J. Todd; Balu, Saianand; Romkes, Marjorie; Saleh, Anthony D.; Hammerman, Peter S.; Bodenheimer, Thomas; Sartor, Maureen A.; Lin, Pei; Wang, Zhining; Seethala, Raja; Seiwert, Tanguy Y.; Si, Han; Kim, Jaegil; William, William N.; Weinberger, Paul; Cherniack, Andrew D.; Ng, P. K. Sam; Muzny, Donna; Reva, Boris; Kovar, Christie; Perez-Ordonez, Bayardo; Askoy, B. A.; Heiman, David I.; Morton, Donna; Tarvin, Katherine; Gehlenborg, Nils; Pickering, Curtis R.; Liu, Yingchun; Schultz, Nikolaus; Carter, Scott L.; Shelton, Candace; Shelton, Troy; Waldron, John; Sumer, S. Onur; Kakkar, Nipun; Sherman, Mark; Wolf, Gregory T.; Cho, Juok; Sun, Yichao; DiCara, Daniel; Network, Cancer Genome Atlas; Han, Yi; Paulauskis, Joseph; Ramirez, Nilsa C.; Hale, Walker; Penny, Robert; Weissler, Mark C.; Freeman, Samuel S.; Wrenn, Sylvia; Walline, Heather M.; Pihl, Todd D.; Zanation, Adam M.; Pot, David A.; Beroukhim, Rameen; Frazer, Scott; Gibbs, Richard A.; Tarnuzzer, Roy; Lee, William; Srinivasan, Deepak; Gao, Jianjiong; Doddapaneni, HarshaVardhan; Dresdner, Gideon; Jacobsen, Anders; Sheth, Margi; Liu, Jinze; Triche, Timothy J.; Sofia, Heidi J.; Chao, Hsu; Suchorska, Wiktoria; Gross, Benjamin; Chang, Kyle; Neil Hayes, D.; Szybiak, Bartosz; Drummond, Jennifer A.; Saller, Charles; Maglinte, Dennis T.; Laird, Peter W.; Ozenberger, Bradley A.; Sandusky, George; Herman, James G.; Larid, Peter W.; Taylor, Evan G.; Morris, Luc G.; Aksoy, B. Arman; Prince, Mark E.; Hui, Angela B. Y.; Cope, Leslie; Rozek, Laura S.; Marie Egloff, Ann; Danilova, Ludmila; Lippman, Scott M.; Liu, Fei-F.; Nguyen, Ariane; Peterson, Lisa A.; Lee, J. Jack; Thorne, Leigh; Jack Lee, J.; McHugh, Jonathan B.; Chan, Timothy A.; Kwok Shing Ng, Patrick; Myers, Jeff; Salazar, Ashley H.; Rathmell, W. Kimryn; Shockley, William W.; Bruce, Jeff P.; Grandis, Jennifer R.; Shores, Carol G.; Benz, Stephen; Guo, Yan; Califano, Joseph; Haddad, Robert I.; Carey, Thomas E.; Benz, Christopher; Byers, Lauren Averett; Chen, Zhong; Harris, Thomas; Cheng, Hui; Baylin, Stephen B.; Chiosea, Simion I.; Pham, Michelle; Bootwalla, Moiz; Cohen, Ezra; Diergaarde, Brenda; Agrawal, Nishant; Bishop, Justin; Lau, Kevin; El-Naggar, Adel K.; Boutros, Paul C.; Egloff, Ann Marie; Ferris, Robert L.; Mallery, David; Morris, Scott; Frederick, Mitchell J.; Kahn, Ari B.; Gardner, Johanna; Leraas, Kristen; Lichtenberg, Tara M.; Mills Shaw, Kenna R.; Jensen, Mark A.; Kimryn Rathmell, W.; Lauskis, Joseph Pau; Frick, Jessica; Gastier-Foster, Julie M.; Harper, Hollie A.; Gordon Robertson, A.; Burnett, Ken; Crain, Daniel; Ibbs, Matthew; Black, Aaron D.; Korski, Konstanty; Bowen, Jay; Mackiewicz, Andrzej; Burton, Robert A.; Baboud, Julien; Davidsen, Tanja; Demchok, John A.; Eley, Greg; Golusiński, Wojciech; Mitchell, Colleen; Ferguson, Martin L.; Golusiński, Paweł; Khan, Zubair; Irish, Jonathan; Chen, Chu; Bollag, Roni; Jones, Tamara R.; Gomez-Fernandez, Carmen; Komarck, Christine M.; Herbert, Lynn; Malakh, Mayya; Curley, Erin; Moyer, Jeffrey S.; Haddad, Andrea S.; Beard, Christina; Ahn, Julie; Egea, Sophie; Bradford, Carol R.; Huang, Mei; Chepeha, Douglas B.; Funkhouser, William K.; Gulley, Margaret L.; Hackman, Trevor G.; Hayward, Michele C.; Chera, Bhishamjit S.; Claude Zenklusen, Jean; Boice, Lori; Arman Aksoy, B.; Brown, Brandee T.; Averett Byers, Lauren; Et, A. L.

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Stephen Waring
Lawrence et al., 2015

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Nature Research, Nature, 7536(517), p. 576-582, 2015

DOI: 10.1038/nature14129

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@article{Lawrence2015,
  abstract = {The Cancer Genome Atlas profiled 279 head and neck squamous cell carcinomas (HNSCCs) to provide a comprehensive landscape of somatic genomic alterations. Here we show that human-papillomavirus-associated tumours are dominated by helical domain mutations of the oncogene PIK3CA, novel alterations involving loss of TRAF3, and amplification of the cell cycle gene E2F1. Smoking-related HNSCCs demonstrate near universal loss-of-function TP53 mutations and CDKN2A inactivation with frequent copy number alterations including amplification of 3q26/28 and 11q13/22. A subgroup of oral cavity tumours with favourable clinical outcomes displayed infrequent copy number alterations in conjunction with activating mutations of HRAS or PIK3CA, coupled with inactivating mutations of CASP8, NOTCH1 and TP53. Other distinct subgroups contained loss-of-function alterations of the chromatin modifier NSD1, WNT pathway genes AJUBA and FAT1, and activation of oxidative stress factor NFE2L2, mainly in laryngeal tumours. Therapeutic candidate alterations were identified in most HNSCCs.},
  author = {Lawrence, Michael S. and Wong, Tina and Zhang, Jianhua and Zeng, Dong and Xu, Andrew W. and Sougnez, Carrie and Weinstein, John and Yang, Liming and Tam, Angela and Thiessen, Nina and Robertson, A. Gordon and Schein, Jacqueline E. and Protopopov, Alexei and Tang, Jiabin and Todd Auman, J. and Santoso, Netty and Sipahimalani, Payal and Wang, Jing and Ren, Xiaojia and Sipahimalan, Payal and Wang, Kai and Seth, Sahil and Wilkerson, Matthew D. and Parfenov, Michael and Wu, Junyuan and Song, Xingzhi and Zhao, Ni and Seidman, Jonathan and Liu, W. and Zack, Travis I. and Pantazi, Angeliki and Veluvolu, Umadevi and Park, Peter J. and Zhang, Hailei and Walter, Vonn and Waring, Scot and Sekhar Pedamallu, Chandra and Zou, Lihua and Tward, Aaron D. and Lichtenstein, Lee and Lander, Eric and Tan, Donghui and Prins, Jan F. and Roach, Jeffrey and Wheeler, David and Shi, Yan and Xi, Liu and Simons, Janae V. and Ramirez, Ricardo and Voet, Doug and Singh, Darshan and Holt, Robert A. and Liu, Y. and Getz, Gad and Jones, Steven J. M. and Soloway, Matthew G. and Lee, Darlene and Parker, Joel S. and Gabriel, Stacey B. and Li, Haiyan I. and Perou, Charles M. and Marra, Marco A. and Mayo, Michael and Sinhal, Rileen and Moore, Richard A. and Mungall, Andrew J. and Saksena, Gordon and Bowlby, Reanne and Yau, Christina and Brooks, Denise and Guin, Ranabir and Lee, Semin and Schumacher, Steven E. and Pedamallu, Chandra Sekhar and Butterfield, Yaron S. N. and Mahadeshwar, Harshad S. and Ojesina, Akinyemi I. and Carlsen, Rebecca and Cheng, Dean and Weisenberger, Daniel J. and Chu, Andy and Stojanov, Petar and Noble, Michael S. and Dhalla, Noreen and Lee, W. and Chin, Lynda and Kucherlapati, Raju and Ally, Adrian and Reid, Jeff and Onur Sumer, S. and Van Den Berg, David J. and Balasundaram, Miruna and Haseley, Psalm and Motter, Thomas and Birol, Inanc and Ramirez, R. and Weinhold, Nils and Hadjipanayis, Angela and Sander, Chris and Hoyle, Alan P. and Jefferys, Stuart R. and Jones, Corbin D. and Kimes, Patrick K. and Shen, Ronglai and Wiznerowicz, Maciej and Lu, Yiling and Marron, J. S. and Yarbrough, Wendell G. and Zhang, Jiexin and Sinha, Rileen and Meng, Shaowu and Mills, Gordon and Zuo, Zhixiang and Mieczkowski, Piotr A. and Bristow, Christopher A. and Mose, Lisle E. and Stuart, Joshua and Shaw, Kenna R. Mills and Hong Fan, You and Tarvi, Katherine and Casasent, Tod and Van Waes, Carter and Yena, Peggy and Liu, J. and Taylor, Barry S. and Waggott, Daryl M. and Ladanyi, Marc and Cibulskisl, Kristian and Liu, Wenbin and Hayes, D. Neil and Le, Yiling and Wise, Lisa and Ng, Sam and Mille, Gordon and Diao, Lixia and Zmuda, Erik and Fan, You Hong and Jung, Joonil and Hoadley, Katherine A. and Yang, Lixing and Lie, Jinze and Akbani, Rehan and Ciriello, Giovanni and Buda, Elizabeth and Meyerson, Matthew and Liu, Yufeng and Zenklusen, Jean Claude and Walton, Jessica S. and Cibulskis, Kristian and Wan, Yunhu and Prystowsky, Michael and Auman, J. Todd and Balu, Saianand and Romkes, Marjorie and Saleh, Anthony D. and Hammerman, Peter S. and Bodenheimer, Thomas and Sartor, Maureen A. and Lin, Pei and Wang, Zhining and Seethala, Raja and Seiwert, Tanguy Y. and Si, Han and Kim, Jaegil and William, William N. and Weinberger, Paul and Cherniack, Andrew D. and Ng, P. K. Sam and Muzny, Donna and Reva, Boris and Kovar, Christie and Perez-Ordonez, Bayardo and Askoy, B. A. and Heiman, David I. and Morton, Donna and Tarvin, Katherine and Gehlenborg, Nils and Pickering, Curtis R. and Liu, Yingchun and Schultz, Nikolaus and Carter, Scott L. and Shelton, Candace and Shelton, Troy and Waldron, John and Sumer, S. Onur and Kakkar, Nipun and Sherman, Mark and Wolf, Gregory T. and Cho, Juok and Sun, Yichao and DiCara, Daniel and Network, Cancer Genome Atlas and Han, Yi and Paulauskis, Joseph and Ramirez, Nilsa C. and Hale, Walker and Penny, Robert and Weissler, Mark C. and Freeman, Samuel S. and Wrenn, Sylvia and Walline, Heather M. and Pihl, Todd D. and Zanation, Adam M. and Pot, David A. and Beroukhim, Rameen and Frazer, Scott and Gibbs, Richard A. and Tarnuzzer, Roy and Lee, William and Srinivasan, Deepak and Gao, Jianjiong and Doddapaneni, HarshaVardhan and Dresdner, Gideon and Jacobsen, Anders and Sheth, Margi and Liu, Jinze and Triche, Timothy J. and Sofia, Heidi J. and Chao, Hsu and Suchorska, Wiktoria and Gross, Benjamin and Chang, Kyle and Neil Hayes, D. and Szybiak, Bartosz and Drummond, Jennifer A. and Saller, Charles and Maglinte, Dennis T. and Laird, Peter W. and Ozenberger, Bradley A. and Sandusky, George and Herman, James G. and Larid, Peter W. and Taylor, Evan G. and Morris, Luc G. and Aksoy, B. Arman and Prince, Mark E. and Hui, Angela B. Y. and Cope, Leslie and Rozek, Laura S. and Marie Egloff, Ann and Danilova, Ludmila and Lippman, Scott M. and Liu, Fei-F. and Nguyen, Ariane and Peterson, Lisa A. and Lee, J. Jack and Thorne, Leigh and Jack Lee, J. and McHugh, Jonathan B. and Chan, Timothy A. and Kwok Shing Ng, Patrick and Myers, Jeff and Salazar, Ashley H. and Rathmell, W. Kimryn and Shockley, William W. and Bruce, Jeff P. and Grandis, Jennifer R. and Shores, Carol G. and Benz, Stephen and Guo, Yan and Califano, Joseph and Haddad, Robert I. and Carey, Thomas E. and Benz, Christopher and Byers, Lauren Averett and Chen, Zhong and Harris, Thomas and Cheng, Hui and Baylin, Stephen B. and Chiosea, Simion I. and Pham, Michelle and Bootwalla, Moiz and Cohen, Ezra and Diergaarde, Brenda and Agrawal, Nishant and Bishop, Justin and Lau, Kevin and El-Naggar, Adel K. and Boutros, Paul C. and Egloff, Ann Marie and Ferris, Robert L. and Mallery, David and Morris, Scott and Frederick, Mitchell J. and Kahn, Ari B. and Gardner, Johanna and Leraas, Kristen and Lichtenberg, Tara M. and Mills Shaw, Kenna R. and Jensen, Mark A. and Kimryn Rathmell, W. and Lauskis, Joseph Pau and Frick, Jessica and Gastier-Foster, Julie M. and Harper, Hollie A. and Gordon Robertson, A. and Burnett, Ken and Crain, Daniel and Ibbs, Matthew and Black, Aaron D. and Korski, Konstanty and Bowen, Jay and Mackiewicz, Andrzej and Burton, Robert A. and Baboud, Julien and Davidsen, Tanja and Demchok, John A. and Eley, Greg and Golusiński, Wojciech and Mitchell, Colleen and Ferguson, Martin L. and Golusiński, Paweł and Khan, Zubair and Irish, Jonathan and Chen, Chu and Bollag, Roni and Jones, Tamara R. and Gomez-Fernandez, Carmen and Komarck, Christine M. and Herbert, Lynn and Malakh, Mayya and Curley, Erin and Moyer, Jeffrey S. and Haddad, Andrea S. and Beard, Christina and Ahn, Julie and Egea, Sophie and Bradford, Carol R. and Huang, Mei and Chepeha, Douglas B. and Funkhouser, William K. and Gulley, Margaret L. and Hackman, Trevor G. and Hayward, Michele C. and Chera, Bhishamjit S. and Claude Zenklusen, Jean and Boice, Lori and Arman Aksoy, B. and Brown, Brandee T. and Averett Byers, Lauren and Et, A. L.},
  doi = {10.1038/nature14129},
  journal = {Nature},
  month = {jan},
  pages = {576-582},
  title = {Comprehensive genomic characterization of head and neck squamous cell carcinomas},
  url = {http://www.nature.com/articles/nature14129.pdf},
  volume = {517},
  year = {2015}
}

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Comprehensive genomic characterization of head and neck squamous cell carcinomas

Journal article published in 2015 by Michael S. Lawrence, Tina Wong, Jianhua Zhang, Dong Zeng, Andrew W. Xu, Carrie Sougnez, John Weinstein, Liming Yang, Angela Tam, Nina Thiessen, A. Gordon Robertson, Jacqueline E. Schein, Alexei Protopopov, Jiabin Tang, J. Todd Auman and other authors. Michael S. Lawrence, Tina Wong, Jianhua Zhang, Dong Zeng, Andrew W. Xu, Carrie Sougnez, John Weinstein, Liming Yang, Angela Tam, Nina Thiessen, A. Gordon Robertson, Jacqueline E. Schein, Alexei Protopopov, Jiabin Tang, J. Todd Auman, Netty Santoso, Payal Sipahimalani, Jing Wang, Xiaojia Ren, Payal Sipahimalan, Kai Wang, Sahil Seth, Matthew D. Wilkerson, Michael Parfenov, Junyuan Wu, Xingzhi Song, Ni Zhao, Jonathan Seidman, W. Liu, Travis I. Zack, Angeliki Pantazi, Umadevi Veluvolu, Peter J. Park, Hailei Zhang, Vonn Walter, Scot Waring

, Chandra Sekhar Pedamallu, Lihua Zou, Aaron D. Tward, Lee Lichtenstein, Eric Lander, Donghui Tan, Jan F. Prins, Jeffrey Roach, David Wheeler, Yan Shi, Liu Xi, Janae V. Simons, Ricardo Ramirez, Doug Voet, Darshan Singh, Robert A. Holt, Y. Liu, Gad Getz, Steven J. M. Jones, Matthew G. Soloway, Darlene Lee, Joel S. Parker, Stacey B. Gabriel, Haiyan I. Li, Charles M. Perou, Marco A. Marra, Michael Mayo, Rileen Sinhal, Richard A. Moore, Andrew J. Mungall

, Gordon Saksena, Reanne Bowlby, Christina Yau, Denise Brooks, Ranabir Guin, Semin Lee, Steven E. Schumacher, Chandra Sekhar Pedamallu, Yaron S. N. Butterfield, Harshad S. Mahadeshwar, Akinyemi I. Ojesina, Rebecca Carlsen, Dean Cheng, Daniel J. Weisenberger, Andy Chu, Petar Stojanov, Michael S. Noble, Noreen Dhalla, W. Lee, Lynda Chin, Raju Kucherlapati, Adrian Ally, Jeff Reid, S. Onur Sumer, David J. Van Den Berg, Miruna Balasundaram, Psalm Haseley, Thomas Motter, Inanc Birol, R. Ramirez, Nils Weinhold, Angela Hadjipanayis, Chris Sander, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Patrick K. Kimes, Ronglai Shen, Maciej Wiznerowicz, Yiling Lu, J. S. Marron, Wendell G. Yarbrough, Jiexin Zhang, Rileen Sinha, Shaowu Meng, Gordon Mills, Zhixiang Zuo, Piotr A. Mieczkowski, Christopher A. Bristow, Lisle E. Mose, Joshua Stuart

, Kenna R. Mills Shaw, You Hong Fan, Katherine Tarvi, Tod Casasent, Carter Van Waes, Peggy Yena, J. Liu, Barry S. Taylor, Daryl M. Waggott, Marc Ladanyi, Kristian Cibulskisl, Wenbin Liu, D. Neil Hayes, Yiling Le, Lisa Wise, Sam Ng, Gordon Mille, Lixia Diao, Erik Zmuda, You Hong Fan, Joonil Jung, Katherine A. Hoadley

, Lixing Yang, Jinze Lie, Rehan Akbani, Giovanni Ciriello, Elizabeth Buda, Matthew Meyerson, Yufeng Liu, Jean Claude Zenklusen, Jessica S. Walton, Kristian Cibulskis, Yunhu Wan, Michael Prystowsky, J. Todd Auman, Saianand Balu, Marjorie Romkes, Anthony D. Saleh, Peter S. Hammerman, Thomas Bodenheimer, Maureen A. Sartor, Pei Lin, Zhining Wang, Raja Seethala, Tanguy Y. Seiwert, Han Si, Jaegil Kim, William N. William, Paul Weinberger, Andrew D. Cherniack, P. K. Sam Ng, Donna Muzny, Boris Reva, Christie Kovar, Bayardo Perez-Ordonez, B. A. Askoy, David I. Heiman

, Donna Morton, Katherine Tarvin, Nils Gehlenborg, Curtis R. Pickering

, Yingchun Liu, Nikolaus Schultz

, Scott L. Carter, Candace Shelton, Troy Shelton, John Waldron, S. Onur Sumer, Nipun Kakkar, Mark Sherman, Gregory T. Wolf, Juok Cho, Yichao Sun, Daniel DiCara, Cancer Genome Atlas Network, Yi Han, Joseph Paulauskis, Nilsa C. Ramirez, Walker Hale, Robert Penny, Mark C. Weissler, Samuel S. Freeman

, Sylvia Wrenn, Heather M. Walline, Todd D. Pihl, Adam M. Zanation, David A. Pot, Rameen Beroukhim, Scott Frazer, Richard A. Gibbs, Roy Tarnuzzer, William Lee, Deepak Srinivasan, Jianjiong Gao, HarshaVardhan Doddapaneni, Gideon Dresdner, Anders Jacobsen, Margi Sheth, Jinze Liu, Timothy J. Triche

, Heidi J. Sofia, Hsu Chao, Wiktoria Suchorska, Benjamin Gross, Kyle Chang, D. Neil Hayes, Bartosz Szybiak, Jennifer A. Drummond, Charles Saller, Dennis T. Maglinte, Peter W. Laird, Bradley A. Ozenberger, George Sandusky, James G. Herman, Peter W. Larid, Evan G. Taylor, Luc G. Morris, B. Arman Aksoy, Mark E. Prince, Angela B. Y. Hui, Leslie Cope, Laura S. Rozek, Ann Marie Egloff, Ludmila Danilova, Scott M. Lippman, Fei-F. Liu, Ariane Nguyen, Lisa A. Peterson, J. Jack Lee, Leigh Thorne, J. Jack Lee, Jonathan B. McHugh, Timothy A. Chan, Patrick Kwok Shing Ng, Jeff Myers, Ashley H. Salazar, W. Kimryn Rathmell, William W. Shockley, Jeff P. Bruce, Jennifer R. Grandis, Carol G. Shores, Stephen Benz, Yan Guo, Joseph Califano, Robert I. Haddad, Thomas E. Carey, Christopher Benz, Lauren Averett Byers, Zhong Chen, Thomas Harris, Hui Cheng, Stephen B. Baylin, Simion I. Chiosea

, Michelle Pham, Moiz Bootwalla, Ezra Cohen, Brenda Diergaarde, Nishant Agrawal, Justin Bishop, Kevin Lau, Adel K. El-Naggar, Paul C. Boutros, Ann Marie Egloff, Robert L. Ferris, David Mallery, Scott Morris, Mitchell J. Frederick, Ari B. Kahn, Johanna Gardner, Kristen Leraas, Tara M. Lichtenberg, Kenna R. Mills Shaw, Mark A. Jensen, W. Kimryn Rathmell, Joseph Pau Lauskis, Jessica Frick, Julie M. Gastier-Foster, Hollie A. Harper, A. Gordon Robertson, Ken Burnett, Daniel Crain, Matthew Ibbs, Aaron D. Black, Konstanty Korski, Jay Bowen

, Andrzej Mackiewicz, Robert A. Burton, Julien Baboud, Tanja Davidsen, John A. Demchok, Greg Eley, Wojciech Golusiński, Colleen Mitchell, Martin L. Ferguson, Paweł Golusiński, Zubair Khan, Jonathan Irish, Chu Chen, Roni Bollag, Tamara R. Jones, Carmen Gomez-Fernandez, Christine M. Komarck, Lynn Herbert, Mayya Malakh, Erin Curley, Jeffrey S. Moyer, Andrea S. Haddad, Christina Beard, Julie Ahn, Sophie Egea, Carol R. Bradford, Mei Huang, Douglas B. Chepeha, William K. Funkhouser, Margaret L. Gulley, Trevor G. Hackman, Michele C. Hayward, Bhishamjit S. Chera, Jean Claude Zenklusen, Lori Boice, B. Arman Aksoy, Brandee T. Brown, Lauren Averett Byers, A. L. Et

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Abstract

The Cancer Genome Atlas profiled 279 head and neck squamous cell carcinomas (HNSCCs) to provide a comprehensive landscape of somatic genomic alterations. Here we show that human-papillomavirus-associated tumours are dominated by helical domain mutations of the oncogene PIK3CA, novel alterations involving loss of TRAF3, and amplification of the cell cycle gene E2F1. Smoking-related HNSCCs demonstrate near universal loss-of-function TP53 mutations and CDKN2A inactivation with frequent copy number alterations including amplification of 3q26/28 and 11q13/22. A subgroup of oral cavity tumours with favourable clinical outcomes displayed infrequent copy number alterations in conjunction with activating mutations of HRAS or PIK3CA, coupled with inactivating mutations of CASP8, NOTCH1 and TP53. Other distinct subgroups contained loss-of-function alterations of the chromatin modifier NSD1, WNT pathway genes AJUBA and FAT1, and activation of oxidative stress factor NFE2L2, mainly in laryngeal tumours. Therapeutic candidate alterations were identified in most HNSCCs.

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Comprehensive genomic characterization of head and neck squamous cell carcinomas

Abstract