G
Gordon Saksena
Researcher at Massachusetts Institute of Technology
Publications - 38
Citations - 54495
Gordon Saksena is an academic researcher from Massachusetts Institute of Technology. The author has contributed to research in topics: Biology & Gene. The author has an hindex of 25, co-authored 27 publications receiving 44753 citations. Previous affiliations of Gordon Saksena include Harvard University & Broad Institute.
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Journal ArticleDOI
Comprehensive molecular portraits of human breast tumours
Daniel C. Koboldt,Robert S. Fulton,Michael D. McLellan,Heather Schmidt,Joelle Kalicki-Veizer,Joshua F. McMichael,Lucinda Fulton,David J. Dooling,Li Ding,Elaine R. Mardis,Richard K. Wilson,Adrian Ally,Miruna Balasundaram,Yaron S.N. Butterfield,Rebecca Carlsen,Candace Carter,Andy Chu,Eric Chuah,Hye Jung E. Chun,Robin J.N. Coope,Noreen Dhalla,Ranabir Guin,Carrie Hirst,Martin Hirst,Robert A. Holt,Darlene Lee,Haiyan I. Li,Michael Mayo,Richard A. Moore,Andrew J. Mungall,Erin Pleasance,A. Gordon Robertson,Jacqueline E. Schein,Arash Shafiei,Payal Sipahimalani,Jared R. Slobodan,Dominik Stoll,Angela Tam,Nina Thiessen,Richard Varhol,Natasja Wye,Thomas Zeng,Yongjun Zhao,Inanc Birol,Steven J.M. Jones,Marco A. Marra,Andrew D. Cherniack,Gordon Saksena,Gordon Saksena,Robert C. Onofrio,Nam H. Pho,Scott L. Carter,Steven E. Schumacher,Steven E. Schumacher,Barbara Tabak,Barbara Tabak,Bryan Hernandez,Jeff Gentry,Huy Nguyen,Andrew Crenshaw,Kristin G. Ardlie,Rameen Beroukhim,Rameen Beroukhim,Wendy Winckler,Gad Getz,Gad Getz,Stacey Gabriel,Matthew Meyerson,Matthew Meyerson,Lynda Chin,Lynda Chin,Raju Kucherlapati,Katherine A. Hoadley,J. Todd Auman,Cheng Fan,Yidi J. Turman,Yan Shi,Ling Li,Michael D. Topal,Xiaping He,Hann Hsiang Chao,Aleix Prat,Grace O. Silva,Michael D. Iglesia,Wei Zhao,Jerry Usary,Jonathan S. Berg,Michael C. Adams,Jessica K. Booker,Junyuan Wu,Anisha Gulabani,Tom Bodenheimer,Alan P. Hoyle,Janae V. Simons,Matthew G. Soloway,Lisle E. Mose,Stuart R. Jefferys,Saianand Balu,Joel S. Parker,D. Neil Hayes,Charles M. Perou,Simeen Malik,Swapna Mahurkar,Hui Shen,Daniel J. Weisenberger,Timothy J. Triche,Phillip H. Lai,Moiz S. Bootwalla,Dennis T. Maglinte,Benjamin P. Berman,David Van Den Berg,Stephen B. Baylin,Peter W. Laird,Chad J. Creighton,Lawrence A. Donehower,Michael S. Noble,Doug Voet,Nils Gehlenborg,Daniel Di Cara,Juinhua Zhang,Hailei Zhang,Chang-Jiun Wu,Spring Yingchun Liu,Michael S. Lawrence,Lihua Zou,Andrey Sivachenko,Pei Lin,Petar Stojanov,Rui Jing,Juok Cho,Raktim Sinha,Richard W. Park,Marc Danie Nazaire,James A. Robinson,Helga Thorvaldsdottir,Jill P. Mesirov,Peter J. Park,Sheila Reynolds,Richard Kreisberg,Brady Bernard,Ryan Bressler,Timo Erkkilä,Jake Lin,Vesteinn Thorsson,Wei Zhang,Ilya Shmulevich,Giovanni Ciriello,Nils Weinhold,Nikolaus Schultz,Jianjiong Gao,Ethan Cerami,Benjamin Gross,Anders Jacobsen,Rileen Sinha,B. Arman Aksoy,Yevgeniy Antipin,Boris Reva,Ronglai Shen,Barry S. Taylor,Marc Ladanyi,Chris Sander,Pavana Anur,Paul T. Spellman,Yiling Lu,Wenbin Liu,Roel R.G. Verhaak,Gordon B. Mills,Gordon B. Mills,Rehan Akbani,Nianxiang Zhang,Bradley M. Broom,Tod D. Casasent,Chris Wakefield,Anna K. Unruh,Keith A. Baggerly,Kevin R. Coombes,John N. Weinstein,David Haussler,Christopher C. Benz,Joshua M. Stuart,Stephen C. Benz,Jingchun Zhu,Christopher Szeto,Gary K. Scott,Christina Yau,Evan O. Paull,Daniel E. Carlin,Christopher K. Wong,Artem Sokolov,Janita Thusberg,Sean D. Mooney,Sam Ng,Theodore C. Goldstein,Kyle Ellrott,Mia Grifford,Christopher Wilks,Singer Ma,Brian Craft,Chunhua Yan,Ying Hu,Daoud Meerzaman,Julie M. Gastier-Foster,Julie M. Gastier-Foster,Jay Bowen,Nilsa C. Ramirez,Nilsa C. Ramirez,Aaron D. Black,Robert E. Pyatt,Robert E. Pyatt,Peter White,Peter White,Erik Zmuda,Jessica Frick,Tara M. Lichtenberg,Robin Brookens,Myra M. George,Mark Gerken,Hollie A. Harper,Kristen M. Leraas,Lisa Wise,Teresa R. Tabler,Cynthia McAllister,Thomas Barr,Melissa Hart-Kothari,Katie Tarvin,Charles Saller,George E. Sandusky,Colleen Mitchell,Mary Iacocca,Jennifer Brown,Brenda Rabeno,Christine Czerwinski,Nicholas J. Petrelli,Oleg Dolzhansky,Mikhail Abramov,Olga Voronina,Olga Potapova,Jeffrey R. Marks,Wiktoria Maria Suchorska,Dawid Murawa,Witold Kycler,Matthew Ibbs,Konstanty Korski,Arkadiusz Spychała,Pawel Murawa,Jacek J. Brzeziński,Hanna Perz,Radoslaw Łaźniak,M. Teresiak,Honorata Tatka,Ewa Leporowska,Marta Bogusz-Czerniewicz,Julian Malicki,Andrzej Mackiewicz,Maciej Wiznerowicz,Xuan Van Le,Bernard Kohl,Nguyen Viet Tien,Richard Thorp,Nguyen Van Bang,Howard H. Sussman,Bui Duc Phu,Richard A. Hajek,Nguyen Phi Hung,Huynh Quyet Thang,Khurram Z. Khan,Robert Penny,David Mallery,Erin Curley,Candace Shelton,Peggy Yena,James N. Ingle,Fergus J. Couch,Wilma L. Lingle,Tari A. King,Ana M. Gonzalez-Angulo,Ana M. Gonzalez-Angulo,Mary D. Dyer,Shuying Liu,Xiaolong Meng,Modesto Patangan,Frederic Waldman,Frederic Waldman,Hubert Stoppler,W. Kimryn Rathmell,Leigh B. Thorne,Mei Huang,Lori Boice,Ashley Hill,Carl Morrison,Carmelo Gaudioso,Wiam Bshara,Kelly Daily,Sophie C. Egea,Mark D. Pegram,Carmen Gomez-Fernandez,Rajiv Dhir,Rohit Bhargava,Adam Brufsky,Craig D. Shriver,Jeffrey A. Hooke,Jamie Leigh Campbell,Richard J. Mural,Hai Hu,Stella Somiari,Caroline Larson,Brenda Deyarmin,Leonid Kvecher,Albert J. Kovatich,Matthew J. Ellis,Thomas Stricker,Kevin P. White,Olufunmilayo I. Olopade,Chunqing Luo,Yaqin Chen,Ron Bose,Li-Wei Chang,Andrew H. Beck,Todd Pihl,Mark A. Jensen,Robert Sfeir,Ari B. Kahn,Anna Chu,Prachi Kothiyal,Zhining Wang,Eric E. Snyder,Joan Pontius,Brenda Ayala,Mark Backus,Jessica Walton,Julien Baboud,Dominique L. Berton,Matthew C. Nicholls,Deepak Srinivasan,Rohini Raman,Stanley Girshik,Peter A. Kigonya,Shelley Alonso,Rashmi N. Sanbhadti,Sean P. Barletta,David Pot,Margi Sheth,John A. Demchok,Kenna R. Mills Shaw,Liming Yang,Greg Eley,Martin L. Ferguson,Roy Tarnuzzer,Jiashan Zhang,Laura A.L. Dillon,Kenneth H. Buetow,Peter Fielding,Bradley A. Ozenberger,Mark S. Guyer,Heidi J. Sofia,Jacqueline D. Palchik +355 more
TL;DR: The ability to integrate information across platforms provided key insights into previously defined gene expression subtypes and demonstrated the existence of four main breast cancer classes when combining data from five platforms, each of which shows significant molecular heterogeneity.
Journal ArticleDOI
Comprehensive molecular characterization of human colon and rectal cancer
Donna M. Muzny,Matthew N. Bainbridge,Kyle Chang,Huyen Dinh,Jennifer Drummond,Gerald R. Fowler,Christie Kovar,Lora Lewis,Margaret Morgan,Irene Newsham,Jeffrey G. Reid,Jireh Santibanez,Eve Shinbrot,Lisa R. Trevino,Yuan Qing Wu,Min Wang,Preethi H. Gunaratne,Preethi H. Gunaratne,Lawrence A. Donehower,Chad J. Creighton,David A. Wheeler,Richard A. Gibbs,Michael S. Lawrence,Douglas Voet,Rui Jing,Kristian Cibulskis,Andrey Sivachenko,Andrey Sivachenko,Petar Stojanov,Aaron McKenna,Eric S. Lander,Eric S. Lander,Stacey Gabriel,Li Ding,Robert S. Fulton,Daniel C. Koboldt,Todd Wylie,Jason Walker,David J. Dooling,Lucinda Fulton,Kim D. Delehaunty,Catrina Fronick,Ryan Demeter,Elaine R. Mardis,Richard K. Wilson,Andy Chu,Hye Jung E. Chun,Andrew J. Mungall,Erin Pleasance,A. Gordon Robertson,Dominik Stoll,Miruna Balasundaram,Inanc Birol,Yaron S.N. Butterfield,Eric Chuah,Robin J.N. Coope,Noreen Dhalla,Ranabir Guin,Carrie Hirst,Martin Hirst,Robert A. Holt,Darlene Lee,Haiyan I. Li,Michael Mayo,Richard A. Moore,Jacqueline E. Schein,Jared R. Slobodan,Angela Tam,Nina Thiessen,Richard Varhol,Thomas Zeng,Yongjun Zhao,Steven J.M. Jones,Marco A. Marra,Adam J. Bass,Alex H. Ramos,Gordon Saksena,Andrew D. Cherniack,Stephen E. Schumacher,Barbara Tabak,Scott L. Carter,Nam Pho,Huy V. Nguyen,Robert C. Onofrio,Andrew Crenshaw,Kristin G. Ardlie,Rameen Beroukhim,Wendy Winckler,Matthew Meyerson,Alexei Protopopov,Angela Hadjipanayis,Eunjung Lee,Ruibin Xi,Lixing Yang,Xiaojia Ren,Narayanan Sathiamoorthy,Peng Chieh Chen,Psalm Haseley,Yonghong Xiao,Semin Lee,Jonathan G. Seidman,Lynda Chin,Peter J. Park,Raju Kucherlapati,J. Todd Auman,Katherine A. Hoadley,Ying Du,Matthew D. Wilkerson,Yan Shi,Christina Liquori,Shaowu Meng,Ling Li,Yidi J. Turman,Michael D. Topal,Donghui Tan,Scot Waring,Elizabeth Buda,Jesse Walsh,Corbin D. Jones,Piotr A. Mieczkowski,Darshan Singh,Junyuan Wu,Anisha Gulabani,Peter Dolina,Tom Bodenheimer,Alan P. Hoyle,Janae V. Simons,Matthew G. Soloway,Lisle E. Mose,Stuart R. Jefferys,Saianand Balu,Brian O'Connor,Jan F. Prins,Derek Y. Chiang,D. Neil Hayes,Charles M. Perou,Toshinori Hinoue,Daniel J. Weisenberger,Dennis T. Maglinte,Fei Pan,Benjamin P. Berman,David Van Den Berg,Hui Shen,Timothy J. Triche,Stephen B. Baylin,Peter W. Laird,Gad Getz,Michael S. Noble,Doug Voat,Nils Gehlenborg,Daniel DiCara,Juinhua Zhang,Hailei Zhang,Chang-Jiun Wu,Spring Yingchun Liu,Sachet A. Shukla,Lihua Zhou,Pei Lin,Richard W. Park,Marc Danie Nazaire,James A. Robinson,Helga Thorvaldsdottir,Jill P. Mesirov,Vesteinn Thorsson,Sheila Reynolds,Brady Bernard,Richard Kreisberg,Jake Lin,Lisa Iype,Ryan Bressler,Timo Erkkilä,Madhumati Gundapuneni,Yuexin Liu,Adam Norberg,Thomas Robinson,Da Yang,Wei Zhang,Ilya Shmulevich,Jorma J. de Ronde,Jorma J. de Ronde,Nikolaus Schultz,Ethan Cerami,Giovanni Ciriello,Arthur P. Goldberg,Benjamin Gross,Anders Jacobsen,Jianjiong Gao,Bogumil Kaczkowski,Rileen Sinha,B. Arman Aksoy,Yevgeniy Antipin,Boris Reva,Ronglai Shen,Barry S. Taylor,Marc Ladanyi,Chris Sander,Rehan Akbani,Nianxiang Zhang,Bradley M. Broom,Tod D. Casasent,Anna K. Unruh,Chris Wakefield,Stanley R. Hamilton,R. Craig Cason,Keith A. Baggerly,John N. Weinstein,David Haussler,Christopher C. Benz,Joshua M. Stuart,Stephen C. Benz,J. Zachary Sanborn,Charles J. Vaske,Jingchun Zhu,Christopher Szeto,Gary K. Scott,Christina Yau,Sam Ng,Theodore C. Goldstein,Kyle Ellrott,Eric A. Collisson,Aaron E. Cozen,Daniel R. Zerbino,Christopher Wilks,Brian Craft,Paul T. Spellman,Robert Penny,Troy Shelton,Martha Hatfield,Scott Morris,Peggy Yena,Candace Shelton,Mark Sherman,Joseph Paulauskis,Julie M. Gastier-Foster,Julie M. Gastier-Foster,Jay Bowen,Nilsa C. Ramirez,Nilsa C. Ramirez,Aaron D. Black,Robert E. Pyatt,Robert E. Pyatt,Lisa Wise,Peter White,Peter White,Monica M. Bertagnolli,Jen Brown,Timothy A. Chan,Gerald C. Chu,Christine Czerwinski,Fred Denstman,Rajiv Dhir,Arnulf Dörner,Charles S. Fuchs,Jose G. Guillem,Mary Iacocca,Hartmut Juhl,Andrew Kaufman,Bernard Kohl,Xuan Van Le,Maria C. Mariano,Elizabeth N. Medina,Michael Meyers,Garrett M. Nash,P. Paty,Nicholas J. Petrelli,Brenda Rabeno,William G. Richards,David B. Solit,Pat Swanson,Larissa K. Temple,Joel E. Tepper,Richard Thorp,Efsevia Vakiani,Martin R. Weiser,Joseph Willis,Gary Witkin,Zhaoshi Zeng,Michael J. Zinner,Carsten Zornig,Mark A. Jensen,Robert Sfeir,Ari B. Kahn,Anna L. Chu,Prachi Kothiyal,Zhining Wang,Eric E. Snyder,Joan Pontius,Todd Pihl,Brenda Ayala,Mark Backus,Jessica Walton,Jon Whitmore,Julien Baboud,Dominique L. Berton,Matthew C. Nicholls,Deepak Srinivasan,Rohini Raman,Stanley Girshik,Peter A. Kigonya,Shelley Alonso,Rashmi N. Sanbhadti,Sean P. Barletta,John M. Greene,David Pot,Kenna R. Mills Shaw,Laura A.L. Dillon,Kenneth H. Buetow,Tanja Davidsen,John A. Demchok,Greg Eley,Martin L. Ferguson,Peter Fielding,Carl F. Schaefer,Margi Sheth,Liming Yang,Mark S. Guyer,Bradley A. Ozenberger,Jacqueline D. Palchik,Jane Peterson,Heidi J. Sofia,Elizabeth J. Thomson +320 more
TL;DR: Integrative analyses suggest new markers for aggressive colorectal carcinoma and an important role for MYC-directed transcriptional activation and repression.
Journal ArticleDOI
The cancer genome atlas pan-cancer analysis project
John N. Weinstein,John N. Weinstein,Eric A. Collisson,Gordon B. Mills,Kenna R. Mills Shaw,Kenna R. Mills Shaw,Brad Ozenberger,Kyle Ellrott,Kyle Ellrott,Chris Sander,Joshua M. Stuart,Joshua M. Stuart,Kyle Chang,Chad J. Creighton,Caleb F. Davis,Lawrence A. Donehower,Jennifer Drummond,David A. Wheeler,Adrian Ally,Miruna Balasundaram,Inanc Birol,Inanc Birol,Inanc Birol,Yaron S.N. Butterfield,Andy Chu,Eric Chuah,Hye Jung E. Chun,Noreen Dhalla,Ranabir Guin,Martin Hirst,Carrie Hirst,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,Richard Varhol,Rameen Beroukhim,Ami S. Bhatt,Angela N. Brooks,Andrew D. Cherniack,Samuel S. Freeman,Stacey Gabriel,Elena Helman,Joonil Jung,Matthew Meyerson,Akinyemi I. Ojesina,Chandra Sekhar Pedamallu,Gordon Saksena,Steven E. Schumacher,Barbara Tabak,Travis I. Zack,Travis I. Zack,Eric S. Lander,Christopher A. Bristow,Angela Hadjipanayis,Psalm Haseley,Raju Kucherlapati,Semin Lee,Eunjung Lee,Lovelace J. Luquette,Harshad S. Mahadeshwar,Angeliki Pantazi,Michael Parfenov,Michael Parfenov,Peter J. Park,Alexei Protopopov,Xiaojia Ren,Netty Santoso,Jonathan G. Seidman,Sahil Seth,Xingzhi Song,Jiabin Tang,Ruibin Xi,Ruibin Xi,Ruibin Xi,Andrew Wei Xu,Lixing Yang,Dong Zeng,J. Todd Auman,Saianand Balu,Elizabeth Buda,Cheng Fan,Katherine A. Hoadley,Corbin D. Jones,Shaowu Meng,Piotr A. Mieczkowski,Joel S. Parker,Charles M. Perou,Jeffrey Roach,Yan Shi,Grace O. Silva,Donghui Tan,Umadevi Veluvolu,Scot Waring,Matthew D. Wilkerson,Junyuan Wu,Wei Zhao,Tom Bodenheimer,D. Neil Hayes,D. Neil Hayes,Alan P. Hoyle,Stuart R. Jeffreys,Lisle E. Mose,Janae V. Simons,Mathew G. Soloway,Stephen B. Baylin,Benjamin P. Berman,Moiz S. Bootwalla,Ludmila Danilova,James G. Herman,Toshinori Hinoue,Peter W. Laird,Suhn K. Rhie,Hui Shen,Timothy J. Triche,Daniel J. Weisenberger,Scott L. Carter,Kristian Cibulskis,Lynda Chin,Jianhua Zhang,Carrie Sougnez,Min Wang,Gad Getz,Gad Getz,Huyen Dinh,Harshavardhan Doddapaneni,Richard A. Gibbs,Preethi Gunaratne,Preethi Gunaratne,Yi Han,Divya Kalra,Christie Kovar,Lora Lewis,Margaret B. Morgan,Donna Morton,Donna Muzny,Jeffrey G. Reid,Liu Xi,Juok Cho,Daniel DiCara,Scott Frazer,Nils Gehlenborg,David I. Heiman,Jaegil Kim,Michael S. Lawrence,Pei Lin,Yingchun Liu,Michael S. Noble,Petar Stojanov,Doug Voet,Hailei Zhang,Lihua Zou,Chip Stewart,Brady Bernard,Ryan Bressler,Andrea Eakin,Lisa Iype,Theo A. Knijnenburg,Roger Kramer,Richard Kreisberg,Kalle Leinonen,Jake Lin,Yuexin Liu,Michael Miller,Sheila M. Reynolds,Hector Rovira,Ilya Shmulevich,Vesteinn Thorsson,Da Yang,Wei Zhang,Samirkumar B. Amin,Chang-Jiun Wu,Chia Chin Wu,Rehan Akbani,Kenneth Aldape,Keith A. Baggerly,Bradley McIntosh Broom,Tod D. Casasent,James Cleland,Deepti Dodda,Mary Elizabeth Edgerton,Leng Han,Shelley M. Herbrich,Zhenlin Ju,Hoon Kim,Hoon Kim,Seth Lerner,Jun Li,Han Liang,Wenbin Liu,Philip L. Lorenzi,Yiling Lu,James M. Melott,Lam Nguyen,Lam Nguyen,Xiaoping Su,Roeland Verhaak,Wenyi Wang,Andrew J. Wong,Andrew J. Wong,Yang Yang,Jun Yao,Rong Yao,Kosuke Yoshihara,Yuan Yuan,Yuan Yuan,W. K. Alfred Yung,Nianxiang Zhang,Siyuan Zheng,Michael B. Ryan,Michael B. Ryan,David W. Kane,David W. Kane,B. Arman Aksoy,Giovanni Ciriello,Gideon Dresdner,Jianjiong Gao,Benjamin Gross,Anders Jacobsen,André Kahles,Marc Ladanyi,William Lee,Kjong-Van Lehmann,Martin L. Miller,Ricardo Ramirez,Gunnar Rätsch,Boris Reva,Nikolaus Schultz,Yasin Senbabaoglu,Ronglai Shen,Rileen Sinha,S. Onur Sumer,Yichao Sun,Barry S. Taylor,Barry S. Taylor,Barry S. Taylor,Nils Weinhold,Suzanne S. Fei,Paul T. Spellman,Christopher C. Benz,Christopher C. Benz,Daniel E. Carlin,Daniel E. Carlin,Melisssa Cline,Melisssa Cline,Brian Craft,Brian Craft,Mary Goldman,David Haussler,David Haussler,David Haussler,Singer Ma,Singer Ma,Sam Ng,Sam Ng,Evan O. Paull,Evan O. Paull,Amie Radenbaugh,Amie Radenbaugh,Sofie R. Salama,Sofie R. Salama,Sofie R. Salama,Artem Sokolov,Artem Sokolov,Teresa Swatloski,Teresa Swatloski,Vladislav Uzunangelov,Vladislav Uzunangelov,Peter Waltman,Peter Waltman,Christina Yau,Jing Zhu,Jing Zhu,Stanley R. Hamilton,Scott Abbott,Rachel Abbott,Nathan D. Dees,Kim D. Delehaunty,Li Ding,David J. Dooling,James M. Eldred,Catrina Fronick,Robert S. Fulton,Lucinda Fulton,Joelle Kalicki-Veizer,Krishna L. Kanchi,Cyriac Kandoth,Daniel C. Koboldt,David E. Larson,Timothy J. Ley,Ling Lin,Charles Lu,Vincent Magrini,Elaine R. Mardis,Michael D. McLellan,Joshua F. McMichael,Christopher A. Miller,Michelle O'Laughlin,Craig Pohl,Heather Schmidt,Scott M. Smith,Jason Walker,John W. Wallis,Michael C. Wendl,Michael C. Wendl,Richard K. Wilson,Todd Wylie,Qunyuan Zhang,Robert A. Burton,Mark A. Jensen,Ari B. Kahn,Todd Pihl,David A. Pot,Yunhu Wan,Douglas A. Levine,Aaron D. Black,Jay Bowen,Jessica Frick,Julie M. Gastier-Foster,Julie M. Gastier-Foster,Hollie A. Harper,Carmen Helsel,Kristen M. Leraas,Tara M. Lichtenberg,Cynthia McAllister,Nilsa C. Ramirez,Nilsa C. Ramirez,Samantha Sharpe,Lisa Wise,Erik Zmuda,Stephen J. Chanock,Tanja Davidsen,John A. Demchok,Greg Eley,Ina Felau,Margi Sheth,Heidi J. Sofia,Louis M. Staudt,Roy Tarnuzzer,Zhining Wang,Liming Yang,Jiashan Zhang,Larsson Omberg,Adam Margolin,Benjamin J. Raphael,Fabio Vandin,Hsin-Ta Wu,Mark D.M. Leiserson,Stephen C. Benz,Charles J. Vaske,Houtan Noushmehr,Houtan Noushmehr,Denise M. Wolf,Laura van 't Veer,Dimitris Anastassiou,Tai Hsien Ou Yang,Nuria Lopez-Bigas,Abel Gonzalez-Perez,David Tamborero,Zheng Xia,Wei Li,Dong Yeon Cho,Teresa M. Przytycka,Mark P. Hamilton,Sean E. McGuire,Sven Nelander,Sven Nelander,Patrik Johansson,Rebecka Jörnsten,Rebecka Jörnsten,Teresia Kling +379 more
TL;DR: The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA with a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages.
Journal ArticleDOI
Integrated genomic characterization of endometrial carcinoma
Gad Getz,Stacey Gabriel,Kristian Cibulskis,Eric S. Lander,Andrey Sivachenko,Carrie Sougnez,Michael S. Lawrence,Cyriac Kandoth,David J. Dooling,Robert S. Fulton,Lucinda Fulton,Joelle Kalicki-Veizer,Michael D. McLellan,Michelle O'Laughlin,Heather Schmidt,Richard K. Wilson,Kai Ye,Ding Li,Adrian Ally,Miruna Balasundaram,Inanc Birol,Yaron S.N. Butterfield,Rebecca Carlsen,Candace Carter,Andy Chu,Eric Chuah,Hye Jung E. Chun,Noreen Dhalla,Ranabir Guin,Carrie Hirst,Robert A. Holt,Steven J.M. Jones,Darlene Lee,Haiyan I. Li,Marco A. Marra,Michael Mayo,Richard A. Moore,Andrew J. Mungall,Patrick Plettner,Jacqueline E. Schein,Payal Sipahimalani,Angela Tam,Richard Varhol,A. Gordon Robertson,Andrew D. Cherniack,Itai Pashtan,Gordon Saksena,Robert C. Onofrio,Steven E. Schumacher,Barbara Tabak,Scott L. Carter,Bryan Hernandez,Jeff Gentry,Helga B. Salvesen,Helga B. Salvesen,Kristin G. Ardlie,Wendy Winckler,Rameen Beroukhim,Rameen Beroukhim,Matthew Meyerson,Angela Hadjipanayis,Semin Lee,Harshad S. Mahadeshwar,Peter J. Park,Alexei Protopopov,Xiaojia Ren,Sahil Seth,Xingzhi Song,Jiabin Tang,Ruibin Xi,Lixing Yang,Zeng Dong,Raju Kucherlapati,Lynda Chin,Lynda Chin,Jianhua Zhang,Jianhua Zhang,J. Todd Auman,Saianand Balu,Tom Bodenheimer,Elizabeth Buda,D. Neil Hayes,Alan P. Hoyle,Stuart R. Jefferys,Corbin D. Jones,Shaowu Meng,Piotr A. Mieczkowski,Lisle E. Mose,Joel S. Parker,Charles M. Perou,Jeff Roach,Shi Yan,Janae V. Simons,Mathew G. Soloway,Donghui Tan,Michael D. Topal,Scot Waring,Junyuan Wu,Katherine A. Hoadley,Stephen B. Baylin,Moiz S. Bootwalla,Phillip H. Lai,Timothy J. Triche,David Van Den Berg,Daniel J. Weisenberger,Peter W. Laird,Hui Shen,Hui Shen,Hui Shen,Juok Cho,Daniel DiCara,Scott Frazer,David I. Heiman,Rui Jing,Pei Lin,Will Mallard,Petar Stojanov,Doug Voet,Hailei Zhang,Lihua Zou,Michael S. Noble,Sheila Reynolds,Ilya Shmulevich,B. Arman Aksoy,Yevgeniy Antipin,Giovanni Ciriello,Gideon Dresdner,Jianjiong Gao,Benjamin Gross,Anders Jacobsen,Marc Ladanyi,Boris Reva,Chris Sander,Rileen Sinha,S. Onur Sumer,Barry S. Taylor,Ethan Cerami,Nils Weinhold,Nikolaus Schultz,Ronglai Shen,Stephen C. Benz,Theodore C. Goldstein,David Haussler,Sam Ng,Christopher Szeto,Joshua M. Stuart,Christopher C. Benz,Christina Yau,Wei Zhang,Matti Annala,Matti Annala,Bradley M. Broom,Tod D. Casasent,Zhenlin Ju,Han Liang,Guoyan Liu,Yiling Lu,Anna K. Unruh,Chris Wakefield,John N. Weinstein,Nianxiang Zhang,Yuexin Liu,Russell Broaddus,Rehan Akbani,Gordon B. Mills,Christopher Adams,Thomas Barr,Aaron D. Black,Jay Bowen,John Deardurff,Jessica Frick,Julie M. Gastier-Foster,Julie M. Gastier-Foster,Thomas Grossman,Hollie A. Harper,Melissa Hart-Kothari,Carmen Helsel,Aaron Hobensack,Harkness Kuck,Kelley Kneile,Kristen M. Leraas,Tara M. Lichtenberg,Cynthia McAllister,Robert E. Pyatt,Nilsa C. Ramirez,Nilsa C. Ramirez,Teresa R. Tabler,Nathan Vanhoose,Peter White,Lisa Wise,Erik Zmuda,Nandita Barnabas,Charlenia Berry-Green,Victoria Blanc,Lori Boice,Michael Button,Adam M. Farkas,Alexander A. Green,Jean MacKenzie,Dana Nicholson,Steve E. Kalloger,C. Blake Gilks,Beth Y. Karlan,Jenny Lester,Sandra Orsulic,Mark E. Borowsky,Mark G. Cadungog,Christine Czerwinski,Lori Huelsenbeck-Dill,Mary Iacocca,Nicholas J. Petrelli,Brenda Rabeno,Gary Witkin,Elena Nemirovich-Danchenko,Olga Potapova,D L Rotin,Andrew Berchuck,Michael J. Birrer,P.J. DiSaia,Laura Monovich,Erin Curley,Johanna Gardner,David Mallery,Robert Penny,Sean C. Dowdy,Boris Winterhoff,Linda Dao,Bobbie S. Gostout,Alexandra Meuter,Attila Teoman,Fanny Dao,Narciso Olvera,Faina Bogomolniy,Karuna Garg,Robert A. Soslow,Mikhail Abramov,John M. S. Bartlett,Sugy Kodeeswaran,Jeremy Parfitt,Fedor Moiseenko,Blaise A. Clarke,Marc T. Goodman,Michael E. Carney,Rayna K. Matsuno,Jennifer O. Fisher,Mei Huang,W. Kimryn Rathmell,Leigh B. Thorne,Linda Van Le,Rajiv Dhir,Robert Edwards,Esther Elishaev,Kristin K. Zorn,Paul J. Goodfellow,Paul J. Goodfellow,Paul J. Goodfellow,David G. Mutch,Ari B. Kahn,Daphne W. Bell,Pamela M. Pollock,Chen Wang,David A. Wheeler,Eve Shinbrot,Li Ding,Elaine R. Mardis,Brenda Ayala,Anna L. Chu,Mark A. Jensen,Prachi Kothiyal,Todd Pihl,Joan Pontius,David Pot,Eric E. Snyder,Deepak Srinivasan,Kenna R. Mills Shaw,Margi Sheth,Tanja Davidsen,Greg Eley,Martin L. Ferguson,Liming Yang,Mark S. Guyer,Bradley A. Ozenberger,Heidi J. Sofia,Douglas A. Levine +283 more
TL;DR: In this paper, the authors performed an integrated genomic, transcriptomic and proteomic characterization of 373 endometrial carcinomas using array-and-sequencing-based technologies, and classified them into four categories: POLE ultramutated, microsatellite instability hypermutated, copy-number low, and copy number high.
Journal ArticleDOI
Comprehensive genomic characterization of squamous cell lung cancers
Peter S. Hammerman,Doug Voet,Michael S. Lawrence,Douglas Voet,Rui Jing,Kristian Cibulskis,Andrey Sivachenko,Petar Stojanov,Aaron McKenna,Eric S. Lander,Eric S. Lander,Stacey Gabriel,Gad Getz,Marcin Imielinski,Elena Helman,Bryan Hernandez,Nam Pho,Matthew Meyerson,Andy Chu,Jung E. Hye-Chun,Andrew J. Mungall,Erin Pleasance,A. Gordon Robertson,Payal Sipahimalani,Dominik Stoll,Miruna Balasundaram,Inanc Birol,Yaron S.N. Butterfield,Eric Chuah,Robin J.N. Coope,Richard Corbett,Noreen Dhalla,Ranabir Guin,An He,Carrie Hirst,Martin Hirst,Robert A. Holt,Darlene Lee,Haiyan I. Li,Michael Mayo,Richard A. Moore,Karen Mungall,Ka Ming Nip,Adam B. Olshen,Jacqueline E. Schein,Jared R. Slobodan,Angela Tam,Nina Thiessen,Richard Varhol,Thomas Zeng,Yongjun Zhao,Steven J.M. Jones,Marco A. Marra,Gordon Saksena,Andrew D. Cherniack,Stephen E. Schumacher,Barbara Tabak,Scott L. Carter,Huy V. Nguyen,Robert C. Onofrio,Andrew Crenshaw,Kristin G. Ardlie,Rameen Beroukhim,Wendy Winckler,Alexei Protopopov,Alexei Protopopov,Jianhua Zhang,Jianhua Zhang,Angela Hadjipanayis,Semin Lee,Ruibin Xi,Lixing Yang,Xiaojia Ren,Hailei Zhang,Sachet A. Shukla,Peng Chieh Chen,Psalm Haseley,Eunjung Lee,Lynda Chin,Lynda Chin,Peter J. Park,Raju Kucherlapati,Nicholas D. Socci,Yupu Liang,Nikolaus Schultz,Laetitia Borsu,Alex E. Lash,Agnes Viale,Chris Sander,Marc Ladanyi,J. Todd Auman,Katherine A. Hoadley,Matthew D. Wilkerson,Yan Shi,Christina Liquori,Shaowu Meng,Ling Li,Yidi J. Turman,Michael D. Topal,Donghui Tan,Scot Waring,Elizabeth Buda,Jesse Walsh,Corbin D. Jones,Piotr A. Mieczkowski,Darshan Singh,Junyuan Wu,Anisha Gulabani,Peter Dolina,Tom Bodenheimer,Alan P. Hoyle,Janae V. Simons,Matthew G. Soloway,Joshua M. Stuart,Lisle E. Mose,Stuart R. Jefferys,Saianand Balu,Brian O'Connor,Derek Y. Chiang,Jinze Liu,Derek Y. Chiang,D. Neil Hayes,Charles M. Perou,Leslie Cope,Daniel J. Weisenberger,Ludmila Danilova,Daniel J. Weisenberger,Dennis T. Maglinte,Fei Pan,David Van Den Berg,Timothy J. Triche,James G. Herman,Stephen B. Baylin,Peter W. Laird,Michael S. Noble,Nils Gehlenborg,Daniel DiCara,Jinhua Zhang,Jinhua Zhang,Chang-Jiun Wu,Chang-Jiun Wu,Spring Yingchun Liu,Lihua Zou,Pei Lin,Juok Cho,Marc Danie Nazaire,James A. Robinson,Helga Thorvaldsdottir,Jill P. Mesirov,Rileen Sinha,Giovanni Ciriello,Ethan Cerami,Benjamin Gross,Anders Jacobsen,Jianjiong Gao,B. Arman Aksoy,Nils Weinhold,Ricardo Ramirez,Barry S. Taylor,Yevgeniy Antipin,Boris Reva,Qianxing Mo,Venkatraman E. Seshan,Paul K. Paik,Rehan Akbani,Nianxiang Zhang,Bradley M. Broom,Tod D. Casasent,Anna K. Unruh,Chris Wakefield,R. Craig Cason,Keith A. Baggerly,John N. Weinstein,David Haussler,Christopher C. Benz,Joshua M. Stuart,Jingchun Zhu,Christopher Szeto,Gary K. Scott,Christina Yau,Sam Ng,Theodore C. Goldstein,Peter Waltman,Artem Sokolov,Eric A. Collisson,Kyle Ellrott,Collisson E,Daniel R. Zerbino,Singer Ma,Brian Craft,Ying Du,Christopher R. Cabanski,Vonn Walter,James Stephen Marron,Yufeng Liu,Kai Wang,Jan F. Prins,Chad J. Creighton,Yiqun Zhang,William D. Travis,Natasha Rekhtman,Joanne Yi,Marie Christine Aubry,Richard T. Cheney,Sanja Dacic,Douglas B. Flieder,William K. Funkhouser,Peter B. Illei,Jerome Myers,Ming-Sound Tsao,Robert Penny,David Mallery,Troy Shelton,Martha Hatfield,Scott Morris,Peggy Yena,Candace Shelton,Mark Sherman,Joseph Paulauskis,Ramaswamy Govindan,Ijeoma Azodo,David G. Beer,Ron Bose,Lauren Averett Byers,David P. Carbone,Li-Wei Chang,Elizabeth Chun,Li Ding,John V. Heymach,Cristiane M. Ida,Bruce E. Johnson,Igor Jurisica,Jacob M. Kaufman,Farhad Kosari,David J. Kwiatkowski,Christopher G. Maher,William Pao,Martin Peifer,Martin Peifer,Gordon Robertson,Valerie W. Rusch,Jill M. Siegfried,Carrie Sougnez,Roman K. Thomas,Roman K. Thomas,Sandra C. Tomaszek,Charles J. Vaske,David A. Wheeler,Dennis A. Wigle,Christopher Wilks,Christopher Wilks,Jianjua John Zhang,Jianjua John Zhang,Mark A. Jensen,Robert Sfeir,Ari B. Kahn,Anna L. Chu,Prachi Kothiyal,Zhining Wang,Eric E. Snyder,Joan Pontius,Todd Pihl,Mark Backus,Jessica Walton,Julien Baboud,Dominique L. Berton,Matthew C. Nicholls,Deepak Srinivasan,Rohini Raman,Stanley Girshik,Peter A. Kigonya,Shelley Alonso,Rashmi N. Sanbhadti,Sean P. Barletta,John M. Greene,David Pot,Bizhan Bandarchi-Chamkhaleh,Jeff Boyd,JoEllen Weaver,Ijeoma A. Azodo,Sandra C. Tomaszek,Ping Yang,Malcolm V. Brock,Kristen Rogers,Marian Rutledge,Travis Brown,Beverly Lee,James Shin,Dante Trusty,Rajiv Dhir,Jill M. Siegfried,Olga Potapova,Konstantin V. Fedosenko,Maureen F. Zakowski,Elena Nemirovich-Danchenko,Mary Iacocca,Jennifer Brown,Brenda Rabeno,Christine Czerwinski,Nicholas J. Petrelli,Zhen Fan,Nicole Todaro,John Eckman,W. Kimryn Rathmell,Leigh B. Thorne,Mei Huang,Lori Boice,Ashley Hill,Erin Curley,Carl Morrison,Carmelo Gaudioso,John M. S. Bartlett,Sugy Kodeeswaran,Brent W. Zanke,Harman Sekhon,Kerstin David,Hartmut Juhl,Xuan Van Le,Bernard Kohl,Richard Thorp,Nguyen Viet Tien,Nguyen Van Bang,Howard H. Sussman,Bui Duc Phu,Richard A. Hajek,Nguyen Phi Hung,Khurram Z. Khan,Thomas Muley,Kenna R. Mills Shaw,Margi Sheth,Liming Yang,John A. Demchok,Tanja Davidsen,Kenneth H. Buetow,Greg Eley,Martin L. Ferguson,Laura A.L. Dillon,Carl F. Schaefer,Mark S. Guyer,Bradley A. Ozenberger,Jacqueline D. Palchik,Jane Peterson,Heidi J. Sofia,Elizabeth J. Thomson,Bruce E. Johnson,Ronglai Shen +345 more
TL;DR: It is shown that the tumour type is characterized by complex genomic alterations, with a mean of 360 exonic mutations, 165 genomic rearrangements, and 323 segments of copy number alteration per tumour.