Open AccessPerspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics
Author(s) -
Li Ding,
Matthew H. Bailey,
Eduard PortaPardo,
Vésteinn Thórsson,
Antonio Colaprico,
Denis Bertrand,
David L. Gibbs,
Amila Weerasinghe,
Kuanlin Huang,
Collin Tokheim,
Isidro CortésCiriano,
Reyka G. Jayasinghe,
Feng Chen,
Lihua Yu,
Sam Q. Sun,
Catharina Olsen,
Jaegil Kim,
Alison M. Taylor,
Andrew D. Cherniack,
Rehan Akbani,
Chayaporn Suphavilai,
Niranjan Nagarajan,
Joshua M. Stuart,
Gordon B. Mills,
Matthew A. Wyczalkowski,
Benjamin G. Vincent,
Carolyn M. Hutter,
Jean C. Zenklusen,
Katherine A. Hoadley,
Michael C. Wendl,
llya Shmulevich,
Alexander J. Lazar,
David A. Wheeler,
Gad Getz,
Rory Johnson,
John A. Demchok,
Ina Felau,
Melpomeni Kasapi,
Martin L. Ferguson,
Heidi J. Sofia,
Roy Tarnuzzer,
Zhining Wang,
Liming Yang,
Jiashan Zhang,
Sudha Chudamani,
Jia Liu,
Laxmi Lolla,
Rashi Naresh,
Todd Pihl,
Qiang Sun,
Yunhu Wan,
Ye Wu,
Juok Cho,
Timothy Defreitas,
Scott Frazer,
Nils Gehlenborg,
David I. Heiman,
Seungchan Kim,
Michael S. Lawrence,
Pei Lin,
Thomas J. Giordano,
Michael S. Noble,
Gordon Saksena,
Doug Voet,
Hailei Zhang,
Brady Bernard,
Nyasha Chambwe,
Varsha Dhankani,
Theo Knijnenburg,
Roger Kramer,
Kalle Lein,
Yuexin Liu,
Michael Miller,
Sheila M. Reynolds,
Ilya Shmulevich,
Wei Zhang,
Bradley M. Broom,
Apurva M. Hegde,
Zhenlin Ju,
Rupa S. Kanchi,
Anil Korkut,
Jun Li,
Han Liang,
Shiyun Ling,
Wenbin Liu,
Yiling Lu,
Kwok-Shing Ng,
Arvind Rao,
Michaël Ryan,
Jing Wang,
John N. Weinstein,
Jiexin Zhang,
Adam Abeshouse,
Joshua Armenia,
Debyani Chakravarty,
Walid K. Chatila,
Ino de Bruijn,
Galen F. Gao,
Benjamin E. Gross,
Zachary Heins,
Ritika Kundra,
Konnor La,
Marc Ladanyi,
Augustin Luna,
Moriah G. Nissan,
Angelica Ochoa,
Sarah Phillips,
Ed Reznik,
Francisco Sánchez-Vega,
Chris Sander,
Nikolaus Schultz,
Robert P. Sheridan,
S. Onur Sumer,
Yichao Sun,
Barry S. Taylor,
Jioajiao Wang,
Hongxin Zhang,
Pavana Anur,
Myron Peto,
Paul T. Spellman,
Christopher C. Benz,
Christopher K. Wong,
Christina Yau,
D. Neil Hayes,
Joel S. Parker,
Matthew D. Wilkerson,
Adrian Ally,
Miruna Balasundaram,
Reanne Bowlby,
Denise Brooks,
Rebecca Carlsen,
Eric Chuah,
Noreen Dhalla,
Robert A. Holt,
Steven J.M. Jones,
L. Sylvia,
Darlene Lee,
Yussanne Ma,
Marco A. Marra,
Michael Mayo,
Richard A. Moore,
Andrew J. Mungall,
Karen Mungall,
A. Gordon Robertson,
Sara Sadeghi,
Jacqueline E. Schein,
Payal Sipahimalani,
Angela Tam,
Nina Thiessen,
Kane Tse,
Tina Wong,
Ashton C. Berger,
Rameen Beroukhim,
Carrie Cibulskis,
Stacey Gabriel,
Gavin Ha,
Matthew Meyerson,
Steven E. Schumacher,
Juliann Shih,
Melanie H. Kucherlapati,
Raju Kucherlapati,
Stephen B. Baylin,
Leslie Cope,
Ludmila Danilova,
Arnoud Boot,
Phillip H. Lai,
Dennis T. Maglinte,
David Van Den Berg,
Daniel J. Weisenberger,
J. Todd Auman,
Saianand Balu,
Tom Bodenheimer,
Huihui Fan,
Alan P. Hoyle,
Corbin D. Jones,
Shaowu Meng,
Piotr A. Mieczkowski,
Lisle E. Mose,
Amy H. Perou,
Charles M. Perou,
Jeffrey Roach,
Yan Shi,
Janae V. Simons,
Tara Skelly,
Matthew G. Soloway,
Donghui Tan,
Umadevi Veluvolu,
Toshinori Hinoue,
Peter W. Laird,
Hui Shen,
Wanding Zhou,
Michelle Bellair,
Kyle Chang,
Kyle R. Covington,
Chad J. Creighton,
Huyen Dinh,
HarshaVardhan Doddapaneni,
Lawrence A. Donehower,
Jennifer Drummond,
Richard A. Gibbs,
Robert Glenn,
Walker Hale,
Yi Han,
Hai Hu,
Viktoriya Korchina,
Charles Lee,
Lora Lewis,
Wei Li,
Xiuping Liu,
Margaret Morgan,
Donna Morton,
Donna M. Muzny,
Jireh Santibanez,
Margi Sheth,
Eve Shinbrot,
Linghua Wang,
Min Wang,
Xi Liu,
Fengmei Zhao,
Julian M. Hess,
Elizabeth L. Appelbaum,
Matthew G. Cordes,
Catrina C. Fronick,
Lucinda A. Fulton,
Robert S. Fulton,
Cyriac Kandoth,
Elaine R. Mardis,
Michael D. McLellan,
Christopher A. Miller,
Heather K. Schmidt,
Richard K. Wilson,
Daniel Crain,
Erin Curley,
Johanna Gardner,
Kevin Lau,
David Mallery,
Scott Morris,
Joseph Paulauskis,
Robert Penny,
Candace Shelton,
Troy Shelton,
Mark E. Sherman,
Eric M. Thompson,
Peggy Yena,
Jay Bowen,
Julie M. GastierFoster,
Mark Gerken,
Kristen M. Leraas,
Tara M. Lichtenberg,
Nilsa C. Ramirez,
Lisa Wise,
Erik Zmuda,
Niall M. Corcoran,
Tony Costello,
Christopher M. Hovens,
André Lopes Carvalho,
Ana Carolina de Carvalho,
José Humberto Tavares Guerreiro Fregnani,
Adhemar LongattoFilho,
Rui Manuel Reis,
Cristovam ScapulatempoNeto,
Henrique C.S. Silveira,
Daniel Onofre Vidal,
Andrew Burnette,
Jennifer Eschbacher,
Beth Hermes,
Ardene Noss,
Rosy Singh,
Matthew L. Anderson,
Patricia D. Castro,
Michael Ittmann,
David G. Huntsman,
Bernard Kohl,
Xuan Le,
Richard Thorp,
Chris Andry,
Elizabeth R. Duffy,
Vladimir Lyadov,
Oxana Paklina,
Galiya Setdikova,
Shabunin Av,
Mikhail Tavobilov,
Christopher McPherson,
Ronald E. Warnick,
Ross S. Berkowitz,
Daniel Cramer,
Colleen M. Feltmate,
Neil S. Horowitz,
Adam S. Kibel,
Michael G. Muto,
Chandrajit P. Raut,
Andrei Malykh,
Jill S. BarnholtzSloan,
Wendi Barrett,
Karen Devine,
Jordonna Fulop,
Quinn T. Ostrom,
Kristen Shimmel,
Yingli Wolinsky,
Andrew E. Sloan,
Agostino Maria De Rose,
Felice Giuliante,
Marc T. Goodman,
Beth Y. Karlan,
Curt H. Hagedorn,
John Eckman,
Jodi Harr,
Jerome K. Myers,
Kelinda Tucker,
Leigh Anne Zach,
Brenda Deyarmin,
Leonid Kvecher,
Caroline Larson,
Richard Mural,
Stella Somiari,
Aleš Vícha,
Tomáš Zelinka,
Joseph Bennett,
Mary Iacocca,
Brenda Rabeno,
Patricia Swanson,
Mathieu Latour,
Louis Lacombe,
Bernard Têtu,
Alain Bergeron,
Mary McGraw,
Susan M. Staugaitis,
John A. Chabot,
Hanina Hibshoosh,
Antonia R. Sepulveda,
Tao Su,
Timothy C. Wang,
Olga Potapova,
О. Л. Воронина,
Laurence Desjardins,
Odette Mariani,
Sergio Román-Román,
Xavier Sastre,
MarcHenri Stern,
Feixiong Cheng,
Sabina Signoretti,
Andrew Berchuck,
Darell D. Bigner,
Eric Lipp,
Jeffrey S. Marks,
Shan J. McCall,
Roger E. McLendon,
Angeles Alvarez Secord,
Alexis Sharp,
Madhusmita Behera,
Daniel J. Brat,
Amy Chen,
Keith A. Delman,
Seth Force,
Fadlo R. Khuri,
Kelly R. Magliocca,
Shishir K. Maithel,
Jeffrey J. Olson,
Taofeek K. Owonikoko,
Alan Pickens,
Suresh Ramalingam,
Dong M. Shin,
Gabriel Sica,
Erwin G. Van Meir,
Hongzheng Zhang,
Wil Eijckenboom,
Ad Gillis,
Esther Korpershoek,
Leendert H. J. Looijenga,
Wolter Oosterhuis,
Hans Stoop,
Kim E. van Kessel,
Ellen C. Zwarthoff,
Chiara Calatozzolo,
Lucia Cuppini,
Stefania Cuzzubbo,
Francesco DiMeco,
Gaetano Finocchiaro,
Luca Mattei,
Alessandro Perin,
Bianca Pollo,
Chu Chen,
J. C. Houck,
Pawadee Lohavanichbutr,
Arndt Hartmann,
Robert Stoehr,
Helge Täubert,
Sven Wach,
Bernd Wullich,
Witold Kycler,
Dawid Murawa,
Maciej Wiznerowicz,
Ki Wung Chung,
W. Jeffrey Edenfield,
Julie Martin,
Éric Baudin,
Glenn J. Bubley,
Raphael Bueno,
Assunta De Rienzo,
William G. Richards,
Steven N. Kalkanis,
Tom Mikkelsen,
Houtan Noushmehr,
Lisa Scarpace,
Nicolas Girard,
Marta Aymerich,
Elı́as Campo,
Eva Giné,
Armando López Guillermo,
Nguyen Van Bang,
Phan Thi Hanh,
Bùi Đức Phú,
Yufang Tang,
Howard Colman,
Kimberley Evason,
Peter Dottino,
John A. Martignetti,
Hani Gabra,
Hartmut Juhl,
Teniola Akeredolu,
Serghei Stepa,
Dave S.�B. Hoon,
Keunsoo Ahn,
Koo Jeong Kang,
Felix Beuschlein,
Anne Breggia,
Michael Birrer,
Debra Bell,
Mitesh J. Borad,
Alan H. Bryce,
Erik P. Castle,
Vishal S. Chandan,
John C. Cheville,
John A. Copland,
Michael B. Farnell,
Thomas J. Flotte,
Nasra H. Giama,
Thai H. Ho,
Michael L. Kendrick,
JeanPierre Kocher,
Karla Kopp,
Catherine D. Moser,
David M. Nagorney,
Daniel R. O’Brien,
Brian Patrick O’Neill,
Tushar Patel,
Gloria M. Petersen,
Florencia G. Que,
Michael Rivera,
Lewis R. Roberts,
Robert C. Smallridge,
Thomas C. Smyrk,
Melissa Stanton,
R. Houston Thompson,
Michael Torbenson,
Ju Dong Yang,
Lizhi Zhang,
Fadi Brimo,
Jaffer A. Ajani,
Ana Maria Angulo Gonzalez,
Carmen Behrens,
Jolanta Bondaruk,
Russell Broaddus,
Bogdan Czerniak,
Bita Esmaeli,
Junya Fujimoto,
Charles C. Guo,
Christopher J. Logothetis,
Funda MericBernstam,
César A. Moran,
Lois M. Ramondetta,
David C. Rice,
Anil K. Sood,
Pheroze Tamboli,
Timothy Thompson,
Patricia Troncoso,
Anne S. Tsao,
Ignacio Wistuba,
Candace Carter,
Lauren E. Haydu,
Peter Hersey,
Valerie Jakrot,
Hojabr Kakavand,
Richard Kefford,
Kenneth Lee,
Georgina V. Long,
Graham J. Mann,
Michael Quinn,
Robyn P.M. Saw,
Richard A. Scolyer,
Kerwin F. Shan,
Andrew J. Spillane,
Jonathan R. Stretch,
Maria Synott,
John F. Thompson,
James S. Wilmott,
Hikmat AlAhmadie,
Timothy A. Chan,
Ronald Ghossein,
Anuradha Gopalan,
Douglas A. Levine,
Victor Reuter,
Samuel Singer,
Bhuvanesh Singh,
Nguyen Viet Tien,
Thomas Broudy,
Cyrus Mirsaidi,
Praveen Nair,
Paul Drwiega,
Judith Miller,
Jennifer R. Smith,
Howard Zaren,
Joong-Won Park,
Nguyễn Phi Hùng,
Electron Kebebew,
W. Marston Linehan,
Adam R. Metwalli,
Karel Pacák,
Peter A. Pinto,
Mark Schiffman,
Laura S. Schmidt,
Cathy D. Vocke,
Nicolas Wentzensen,
Robert Worrell,
Hannah Yang,
Marc Moncrieff,
Chandra Goparaju,
Jonathan Melamed,
Harvey I. Pass,
Natalia Botnariuc,
Irina Caraman,
Mircea Cernat,
Inga Chemencedji,
Adrian Clipca,
Serghei Doruc,
Ghenadie Gorincioi,
Sergiu Mura,
Maria Pirtac,
Irina Stancul,
Diana Tcaciuc,
Monique Albert,
Iakovina Alexopoulou,
Angel Arnaout,
John G. Bartlett,
Jay Engel,
Sebastién Gilbert,
Jeremy Parfitt,
Harman Sekhon,
George Thomas,
Doris M. Rassl,
Robert C. Rintoul,
Carlo Bifulco,
Raina Tamakawa,
Walter J. Urba,
Nicholas K. Hayward,
Henri Timmers,
Anna Antenucci,
Francesco Facciolo,
Gian Luca Grazi,
Mirella Marino,
Roberta Merola,
Ronald R. de Krijger,
AnnePaule GimenezRoqueplo,
Alain Piché,
Simone Chevalier,
Ginette McKercher,
Kıvanç Birsoy,
Gene H. Barnett,
Cathy Brewer,
Carol Farver,
Theresa Naska,
Nathan A. Pennell,
Daniel Raymond,
Cathy Schilero,
Kathy Smolenski,
Cecilia Williams,
Quaid Morris,
Jeffrey A. Borgia,
Mark Pool,
Christopher W. Seder,
Kerstin Junker,
Larsson Omberg,
Mikhail Dinkin,
George Manikhas,
Domenico Alvaro,
Maria Consiglia Bragazzi,
Vincenzo Cardinale,
Guido Carpino,
Eugenio Gaudio,
David Chesla,
Sandra Cottingham,
Michael Dubina,
Fedor Moiseenko,
Renumathy Dhanasekaran,
KarlFriedrich Becker,
Klaus–Peter Janssen,
Julia SlottaHuspenina,
Mohamed H. AbdelRahman,
Dina Aziz,
Sue Bell,
Colleen M. Cebulla,
Amy Davis,
Rebecca Duell,
J. Bradley Elder,
Joe Hilty,
Bahavna Kumar,
James C. Lang,
Norman L. Lehman,
Randy Mandt,
Phuong L. Nguyen,
Robert Pilarski,
Karan Rai,
Lynn Schoenfield,
Kelly Senecal,
Paul E. Wakely,
Paul Hansen,
Ronald M. Lechan,
James Powers,
Arthur S. Tischler,
William E. Grizzle,
Katherine C. Sexton,
Alison Kastl,
Joel Henderson,
Sima P. Porten,
Jens Waldmann,
Martin Faßnacht,
Dirk Schadendorf,
Marta Couce,
Markus Graefen,
Hartwig Huland,
Guido Sauter,
Thorsten Schlomm,
Ronald Simon,
Pierre Tennstedt,
Oluwole Olabode,
Mark A. Nelson,
Oliver F. Bathe,
Peter R. Carroll,
June M. Chan,
Philip J. DiSaia,
Pat Glenn,
Robin Kate Kelley,
Charles N. Landen,
Joanna Phillips,
Michael D. Prados,
Jeffry Simko,
Karen SmithMcCune,
Scott Vandenberg,
Kevin K. Roggin,
Ashley Fehrenbach,
Ady Kendler,
Suzanne Sifri,
Ruth Steele,
Antonio Jimeno,
Francis A. Carey,
Ian Forgie,
Massimo Mannelli,
Michael E. Carney,
Brenda Hernandez,
Benito Campos,
Christel HeroldMende,
Christin Jungk,
Andreas Unterberg,
Andreas von Deimling,
Aaron Bossler,
Joseph Galbraith,
Laura Jacobus,
Michael Knudson,
Tina Knutson,
Deqin Ma,
Mohammed Milhem,
Rita Sigmund,
Andrew K. Godwin,
Rashna Madan,
Howard G. Rosenthal,
Clement Adebamowo,
Sally N. Adebamowo,
Alex Boussioutas,
David G. Beer,
AnneMarie MesMasson,
Fred Saad,
Thèrése Bocklage,
Lisa M. Landrum,
Robert S. Mannel,
Kathleen N. Moore,
Katherine Moxley,
Russel Postier,
Joan Walker,
Rosemary E. Zuna,
Michael D. Feldman,
Federico Valdivieso,
Rajiv Dhir,
James D. Luketich,
Edna M. Mora Pinero,
Mario Quintero-Aguilo,
Carlos Gilberto Carlotti,
José Sebastião dos Santos,
Rafael Kemp,
Ajith Sankarankuty,
Daniela Pretti da Cunha Tirapelli,
James W.F. Catto,
Kathy Agnew,
Elizabeth M. Swisher,
Jenette Creaney,
Bruce Robinson,
Carl Simon Shelley,
Eryn M. Godwin,
Sara Kendall,
Cassaundra Shipman,
Carol R. Bradford,
Thomas E. Carey,
Robert I. Haddad,
Jeffey Moyer,
Lisa A. Peterson,
Mark E. Prince,
Laura S. Rozek,
Gregory T. Wolf,
Rayleen Bowman,
Kwun M. Fong,
Ian A. Yang,
Robert J. Korst,
W. Kimryn Rathmell,
J. Leigh Fantacone-Campbell,
Jeffrey A. Hooke,
Albert J. Kovatich,
Craig D. Shriver,
John F. DiPersio,
Bettina F. Drake,
Ramaswamy Govindan,
Sharon E. Heath,
Timothy J. Ley,
Brian A. Van Tine,
Peter Westervelt,
Mark A. Rubin,
Jung Il Lee,
Natália D. Aredes,
Armaz Mariamidze
Publication year - 2018
Publication title -
cell
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 26.304
H-Index - 776
eISSN - 1097-4172
pISSN - 0092-8674
DOI - 10.1016/j.cell.2018.03.033
Subject(s) - biology , genomics , perspective (graphical) , cancer , computational biology , genetics , genome biology , genome , evolutionary biology , gene , artificial intelligence , computer science
The Cancer Genome Atlas (TCGA) has catalyzed systematic characterization of diverse genomic alterations underlying human cancers. At this historic junction marking the completion of genomic characterization of over 11,000 tumors from 33 cancer types, we present our current understanding of the molecular processes governing oncogenesis. We illustrate our insights into cancer through synthesis of the findings of the TCGA PanCancer Atlas project on three facets of oncogenesis: (1) somatic driver mutations, germline pathogenic variants, and their interactions in the tumor; (2) the influence of the tumor genome and epigenome on transcriptome and proteome; and (3) the relationship between tumor and the microenvironment, including implications for drugs targeting driver events and immunotherapies. These results will anchor future characterization of rare and common tumor types, primary and relapsed tumors, and cancers across ancestry groups and will guide the deployment of clinical genomic sequencing.
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