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Comprehensive molecular characterization of gastric adenocarcinoma

Adam J. Bass,Vésteinn Thórsson,Ilya Shmulevich,Sheila M. Reynolds,Michael Miller,Brady Bernard,Toshinori Hinoue,Peter W. Laird,Christina Curtis,Hui Shen,Daniel J. Weisenberger,Nikolaus Schultz,Ronglai Shen,Nils Weinhold,David P. Kelsen,Reanne Bowlby,Andy Chu,Katayoon Kasaian,Andrew J. Mungall,A. Gordon Robertson,Payal Sipahimalani,Andrew D. Cherniack,Gad Getz,Yingchun Liu,Michael S. Noble,Chandra Sekhar Pedamallu,Carrie Sougnez,Amaro Taylor-Weiner,Rehan Akbani,Ju-Seog Lee,Wenbin Liu,Gordon B. Mills,Da Yang,Wei Zhang,Angeliki Pantazi,Michael Parfenov,Margaret L. Gulley,M. Blanca Piazuelo,Barbara Schneider,Jihun Kim,Alex Boussioutas,Margi Sheth,John A. Demchok,Charles S. Rabkin,Joseph Willis,Sam Ng,Katherine S. Garman,David G. Beer,Arjun Pennathur,Benjamin J. Raphael,Hsin-Ta Wu,Robert D. Odze,Hark K. Kim,Jay Bowen,Kristen Leraas,Tara M. Lichtenberg,Stephanie Weaver,Michael D. McLellan,Maciej Wiznerowicz,Ryo Sakai,Michael S. Lawrence,Kristian Cibulskis,Lee Lichtenstein,Sheila Fisher,Stacey Gabriel,Eric S. Lander,Ding Li,Beifang Niu,Adrian Ally,Miruna Balasundaram,İnanç Birol,Denise Brooks,Yaron S.N. Butterfield,Rebecca Carlsen,Justin Chu,Eric Chuah,Hye-Jung Chun,Amanda Clarke,Noreen Dhalla,Ranabir Guin,Robert A. Holt,Steve Jones,Darlene Lee,Haiyan A. Li,Emilia L. Lim,Yussanne Ma,Marco A. Marra,Michael Mayo,Richard A. Moore,Ka Ming Nip,Jacqueline E. Schein,Angela Tam,Nina Thiessen,Rameen Beroukhim,Scott L. Carter,Juok Cho,Daniel DiCara,Scott Frazer,Nils Gehlenborg,David I. Heiman,Joonil Jung,Jaegil Kim,Pei Lin,Matthew Meyerson,Akinyemi I. Ojesina,Gordon Saksena,Steven E. Schumacher,Petar Stojanov,Barbara Tabak,Doug Voet,Mara Rosenberg,Travis I. Zack,Hailei Zhang,Lihua Zou,Alexei Protopopov,Netty Santoso,Semin Lee,Jianhua Zhang,Harshad S. Mahadeshwar,Jie Hu,Xiaojia Ren,Sahil Seth,Lixing Yang,Andrew Wei Xu,Xingzhi Song,Ruibin Xi,Christopher A. Bristow,Angela Hadjipanayis,Jonathan G. Seidman,Lynda Chin,Peter J. Park,Raju Kucherlapati,Shiyun Ling,Arvind Rao,John N. Weinstein,Sangbae Kim,Yiling Lu,Moiz S. Bootwalla,Phillip H. Lai,Timothy J. Triche,David J. Van Den Berg,Stephen B. Baylin,James G. Herman,Bradley A. Murray,B. Arman Askoy,Giovanni Ciriello,Gideon Dresdner,Jianjiong Gao,Benjamin Groß,Anders Jacobsen,William Lee,Ricardo J. Ramirez,Chris Sander,Yasin Şenbabaoğlu,Rileen Sinha,S. Onur Sumer,Yichao Sun,Lisa Iype,Roger Kramer,Richard Kreisberg,Hector Rovira,Natalie Tasman,Santa Cruz Sam Ng,David Haussler,Joshua M. Stuart,Roeland Verhaak,Mark D.M. Leiserson,Barry S. Taylor,Aaron Black,Julie Ann Carney,Julie M. Gastier‐Foster,Carmen Helsel,Cynthia McAllister,Nilsa C. Ramirez,Teresa R. Tabler,Lisa Wise,Erik Zmuda,Robert Penny,Daniel Crain,Johanna Gardner,Kevin Lau,Erin Curely,David Mallery,Scott Morris,Joseph Paulauskis,Troy Shelton,Candace Shelton,Mark E. Sherman,Christopher C. Benz,Jae-Hyuk Lee,Konstantin Fedosenko,Georgy M. Manikhas,Olga Potapova,Olga Voronina,Smitry Belyaev,O V Dolzhansky,W. Kimryn Rathmell,Jakub Brzezinski,Matthew Ibbs,Konstanty Korski,Witold Kycler,Radoslaw ŁaŸniak,Ewa Leporowska,Andrzej Maćkiewicz,Dawid Murawa,P. Murawa,Arkadiusz Spychała,Wiktoria Maria Suchorska,Honorata Tatka,M. Teresiak,Raafat Abdel‐Misih,Joseph Bennett,Jennifer Brown,Mary Iacocca,Brenda Rabeno,Sunyoung Kwon,Ariane Kemkes,Erin Curley,Iakovina Alexopoulou,Jay Engel,John M.S. Bartlett,Monique Albert,Do–Youn Park,Rajiv Dhir,James D. Luketich,Rodney J. Landreneau,Yelena Y. Janjigian,Eun Jung Cho,Marc Ladanyi,Laura H. Tang,Shannon J. McCall,Young S. Park,Jae‐Ho Cheong,Jaffer A. Ajani,M. Constanza Camargo,Shelley Alonso,Brenda Ayala,Mark A. Jensen,Todd Pihl,Rohini Raman,Jessica Walton,Yunhu Wan,Greg Eley,Kenna Shaw,Roy Tarnuzzer,Zhining Wang,Liming Yang,Jean C. Zenklusen,Tanja M. Davidsen,Carolyn M. Hutter,Heidi J. Sofia,Robert C. Burton,Sudha Chudamani,Jia Liu

Microsatellite instability

Cancer research

Chromosome instability

2014

Gastric cancer is a leading cause of cancer deaths, but analysis of its molecular and clinical characteristics has been complicated by histological and aetiological heterogeneity. Here we describe a comprehensive molecular evaluation of 295 primary gastric adenocarcinomas as part of The Cancer Genome Atlas (TCGA) project. We propose a molecular classification dividing gastric cancer into four subtypes: tumours positive for Epstein-Barr virus, which display recurrent PIK3CA mutations, extreme DNA hypermethylation, and amplification of JAK2, CD274 (also known as PD-L1) and PDCD1LG2 (also known as PD-L2); microsatellite unstable tumours, which show elevated mutation rates, including mutations of genes encoding targetable oncogenic signalling proteins; genomically stable tumours, which are enriched for the diffuse histological variant and mutations of RHOA or fusions involving RHO-family GTPase-activating proteins; and tumours with chromosomal instability, which show marked aneuploidy and focal amplification of receptor tyrosine kinases. Identification of these subtypes provides a roadmap for patient stratification and trials of targeted therapies.

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“Comprehensive molecular characterization of gastric adenocarcinoma” is a paper by Adam J. Bass Vésteinn Thórsson Ilya Shmulevich Sheila M. Reynolds Michael Miller Brady Bernard Toshinori Hinoue Peter W. Laird Christina Curtis Hui Shen Daniel J. Weisenberger Nikolaus Schultz Ronglai Shen Nils Weinhold David P. Kelsen Reanne Bowlby Andy Chu Katayoon Kasaian Andrew J. Mungall A. Gordon Robertson Payal Sipahimalani Andrew D. Cherniack Gad Getz Yingchun Liu Michael S. Noble Chandra Sekhar Pedamallu Carrie Sougnez Amaro Taylor-Weiner Rehan Akbani Ju-Seog Lee Wenbin Liu Gordon B. Mills Da Yang Wei Zhang Angeliki Pantazi Michael Parfenov Margaret L. Gulley M. Blanca Piazuelo Barbara Schneider Jihun Kim Alex Boussioutas Margi Sheth John A. Demchok Charles S. Rabkin Joseph Willis Sam Ng Katherine S. Garman David G. Beer Arjun Pennathur Benjamin J. Raphael Hsin-Ta Wu Robert D. Odze Hark K. Kim Jay Bowen Kristen Leraas Tara M. Lichtenberg Stephanie Weaver Michael D. McLellan Maciej Wiznerowicz Ryo Sakai Michael S. Lawrence Kristian Cibulskis Lee Lichtenstein Sheila Fisher Stacey Gabriel Eric S. Lander Ding Li Beifang Niu Adrian Ally Miruna Balasundaram İnanç Birol Denise Brooks Yaron S.N. Butterfield Rebecca Carlsen Justin Chu Eric Chuah Hye-Jung Chun Amanda Clarke Noreen Dhalla Ranabir Guin Robert A. Holt Steve Jones Darlene Lee Haiyan A. Li Emilia L. Lim Yussanne Ma Marco A. Marra Michael Mayo Richard A. Moore Ka Ming Nip Jacqueline E. Schein Angela Tam Nina Thiessen Rameen Beroukhim Scott L. Carter Juok Cho Daniel DiCara Scott Frazer Nils Gehlenborg David I. Heiman Joonil Jung Jaegil Kim Pei Lin Matthew Meyerson Akinyemi I. Ojesina Gordon Saksena Steven E. Schumacher Petar Stojanov Barbara Tabak Doug Voet Mara Rosenberg Travis I. Zack Hailei Zhang Lihua Zou Alexei Protopopov Netty Santoso Semin Lee Jianhua Zhang Harshad S. Mahadeshwar Jie Hu Xiaojia Ren Sahil Seth Lixing Yang Andrew Wei Xu Xingzhi Song Ruibin Xi Christopher A. Bristow Angela Hadjipanayis Jonathan G. Seidman Lynda Chin Peter J. Park Raju Kucherlapati Shiyun Ling Arvind Rao John N. Weinstein Sangbae Kim Yiling Lu Moiz S. Bootwalla Phillip H. Lai Timothy J. Triche David J. Van Den Berg Stephen B. Baylin James G. Herman Bradley A. Murray B. Arman Askoy Giovanni Ciriello Gideon Dresdner Jianjiong Gao Benjamin Groß Anders Jacobsen William Lee Ricardo J. Ramirez Chris Sander Yasin Şenbabaoğlu Rileen Sinha S. Onur Sumer Yichao Sun Lisa Iype Roger Kramer Richard Kreisberg Hector Rovira Natalie Tasman Santa Cruz Sam Ng David Haussler Joshua M. Stuart Roeland Verhaak Mark D.M. Leiserson Barry S. Taylor Aaron Black Julie Ann Carney Julie M. Gastier‐Foster Carmen Helsel Cynthia McAllister Nilsa C. Ramirez Teresa R. Tabler Lisa Wise Erik Zmuda Robert Penny Daniel Crain Johanna Gardner Kevin Lau Erin Curely David Mallery Scott Morris Joseph Paulauskis Troy Shelton Candace Shelton Mark E. Sherman Christopher C. Benz Jae-Hyuk Lee Konstantin Fedosenko Georgy M. Manikhas Olga Potapova Olga Voronina Smitry Belyaev O V Dolzhansky W. Kimryn Rathmell Jakub Brzezinski Matthew Ibbs Konstanty Korski Witold Kycler Radoslaw ŁaŸniak Ewa Leporowska Andrzej Maćkiewicz Dawid Murawa P. Murawa Arkadiusz Spychała Wiktoria Maria Suchorska Honorata Tatka M. Teresiak Raafat Abdel‐Misih Joseph Bennett Jennifer Brown Mary Iacocca Brenda Rabeno Sunyoung Kwon Ariane Kemkes Erin Curley Iakovina Alexopoulou Jay Engel John M.S. Bartlett Monique Albert Do–Youn Park Rajiv Dhir James D. Luketich Rodney J. Landreneau Yelena Y. Janjigian Eun Jung Cho Marc Ladanyi Laura H. Tang Shannon J. McCall Young S. Park Jae‐Ho Cheong Jaffer A. Ajani M. Constanza Camargo Shelley Alonso Brenda Ayala Mark A. Jensen Todd Pihl Rohini Raman Jessica Walton Yunhu Wan Greg Eley Kenna Shaw Roy Tarnuzzer Zhining Wang Liming Yang Jean C. Zenklusen Tanja M. Davidsen Carolyn M. Hutter Heidi J. Sofia Robert C. Burton Sudha Chudamani Jia Liu published in 2014. It has an Open Access status of “hybrid”. You can read and download a PDF Full Text of this paper here.