Comprehensive genomic characterization of head and neck squamous cell carcinomas View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2015-01-28

AUTHORS

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

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. More... »

PAGES

576-582

Journal

TITLE

Nature

ISSUE

7536

VOLUME

517

Author Affiliations

  • The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, 02142, Cambridge, Massachusetts, USA
  • Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, USA.
  • Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada.
  • The University of Texas MD Anderson Cancer Center, 77030, Houston, Texas, USA
  • Harvard Medical School, 02115, Boston, Massachusetts, USA
  • Brigham and Women’s Hospital, 02115, Boston, Massachusetts, USA
  • Boston Children’s Hospital, 02115, Boston, Massachusetts, USA
  • University of Kentucky, 40506, Lexington, Kentucky, USA
  • University of North Carolina at Chapel Hill, 27599, Chapel Hill, North Carolina, USA
  • Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA.
  • Harvard University, 02115, Boston, Massachusetts, USA
  • Baylor College of Medicine, 77030, Houston, Texas, USA
  • Memorial Sloan-Kettering Cancer Center, 1275 York Ave, New York, New York 10065, USA.
  • University of California Santa Cruz, 95064, Santa Cruz, California, USA
  • The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, 21287, Baltimore, Maryland, USA
  • University of Southern California,1450 Biggy Street, NRT G511, Los Angeles, California 90033, USA.
  • Johns Hopkins Medical Institutions, 21205, Baltimore, Maryland, USA
  • Ontario Institute for Cancer Research 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada.
  • Ontario Cancer Institute, Toronto, Ontario M5G 2M9, Canada.
  • University of Michigan Comprehensive Cancer Center, 48109, Ann Arbor, Michigan, USA
  • National Institute on Deafness and Other Communication Disorders, National Institutes of Health, 20892, Bethesda, Maryland, USA
  • University of Pittsburgh, 15213, Pittsburgh, Pennsylvania, USA
  • The University of Chicago, 60637, Chicago, Illinois, USA
  • Vanderbilt University Medical Center 7209 Medical Center East, 37232, South Tower Nashville, Tennessee, USA
  • Albert Einstein College of Medicine, 10461, Bronx, New York, USA
  • University of California San Diego, 92093, San Diego, California, USA
  • University of Toronto, Toronto, Ontario M5G 2M9, Canada.
  • University Health Network, Toronto, Ontario M5G 2C4, Canada.
  • Greater Poland Cancer Centre, Garbary 15, 61-866, Poznań, Poland.
  • Yale School of Medicine, 800 Howard Avenue, 4th Floor Yale Physicians Building, 06520-8041, New Haven, Connecticut, USA
  • International Genomics Consortium, 445 North 5th Street, Phoenix, Arizona 85004, USA.
  • The Research Institute at Nationwide Children’s Hospital, 43205, Columbus, Ohio, USA
  • SRA International, 22033, Fairfax, Virginia, USA
  • Frederick National Laboratory for Cancer Research, 1050 Boyles Street, Frederick, Maryland 21702, USA.
  • National Cancer Institute, 31 Center Drive 3A20, Bethesda, Maryland 20892, USA.
  • Scimentis, LLC, Atlanta, Georgia 30666, USA.
  • National Human Genome Research Institute, National Institutes of Health, 20892, Bethesda, Maryland, USA
  • Analytical Biological Services, Inc., 701 Cornell Drive, Wilmington, Delaware 19801, USA.
  • Fred Hutchinson Cancer Research Center, Mailstop M5-C800, 1100 Fairview Avenue North, Seattle, Washington 98109, USA.
  • Georgia Regents University, 30912, Augusta, Georgia, USA
  • Indiana University Simon Cancer Center, 46202, Indianapolis, Indiana, USA
  • University of Miami, Sylvester Comprehensive Cancer Center, 1550 NW 10th Avenue, Miami, Florida 33136, USA.
  • Clinical Trials linked to this publication

    Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nature14129

    DOI

    http://dx.doi.org/10.1038/nature14129

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1045934545

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/25631445


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