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Integrated Genomic Characterization of Papillary Thyroid Carcinoma

Nishant Agrawal,Rehan Akbani,Bülent Arman Aksoy,Adrian Ally,Harindra Arachchi,L. Sylvia,J. Todd Auman,Miruna Balasundaram,Saianand Balu,Stephen B. Baylin,Madhusmita Behera,Brady Bernard,Rameen Beroukhim,Justin A. Bishop,Aaron Black,Tom Bodenheimer,Lori Boice,Moiz S. Bootwalla,Jay Bowen,Reanne Bowlby,Christopher A. Bristow,Robin Brookens,Denise Brooks,R M T Bonita Bryant,Elizabeth Buda,Yaron S.N. Butterfield,Tobias Carling,Rebecca Carlsen,Scott L. Carter,Sally E. Carty,Timothy A. Chan,Amy Y. Chen,Andrew D. Cherniack,Dorothy Cheung,Lynda Chin,Juok Cho,Andy Chu,Eric Chuah,Kristian Cibulskis,Giovanni Ciriello,Amanda Clarke,Gary L. Clayman,Leslie Cope,John A. Copland,Kyle R. Covington,Ludmila Danilova,Tanja M. Davidsen,John A. Demchok,Daniel DiCara,Noreen Dhalla,Rajiv Dhir,Sheliann S. Dookran,Gideon Dresdner,Jonathan V. Eldridge,Greg Eley,Adel K. El‐Naggar,Stephanie Eng,James A. Fagin,Timothy Fennell,Robert L. Ferris,Sheila Fisher,Scott Frazer,Jessica Frick,Stacey Gabriel,Ian Ganly,Jianjiong Gao,Levi A. Garraway,Julie M. Gastier‐Foster,Gad Getz,Nils Gehlenborg,Ronald Ghossein,Richard A. Gibbs,Thomas J. Giordano,Karen Gomez-Hernandez,Jonna Grimsby,Benjamin Groß,Ranabir Guin,Angela Hadjipanayis,Hollie A. Harper,D. Neil Hayes,David I. Heiman,James G. Herman,Katherine A. Hoadley,Matan Hofree,Robert A. Holt,Alan P. Hoyle,Franklin W. Huang,Mei Huang,Carolyn M. Hutter,Trey Ideker,Lisa Iype,Anders Jacobsen,Stuart R. Jefferys,Corbin D. Jones,Steven Jones,Katayoon Kasaian,Electron Kebebew,Fadlo R. Khuri,Jaegil Kim,Roger Kramer,Richard Kreisberg,Raju Kucherlapati,David J. Kwiatkowski,Marc Ladanyi,Phillip H. Lai,Peter W. Laird,Eric S. Lander,Michael S. Lawrence,Darlene Lee,Eunjung Lee,Semin Lee,William Lee,Kristen Leraas,Tara M. Lichtenberg,Lee Lichtenstein,Pei Lin,Shiyun Ling,Jinze Liu,Wenbin Liu,Yingchun Liu,Virginia A. LiVolsi,Yiling Lu,Yussanne Ma,Harshad S. Mahadeshwar,Marco A. Marra,Michael Mayo,David G. McFadden,Shaowu Meng,Matthew Meyerson,Piotr A. Mieczkowski,Michael Miller,Gordon B. Mills,Richard A. Moore,Lisle E. Mose,Andrew J. Mungall,Bradley A. Murray,Yuri E. Nikiforov,Michael S. Noble,Akinyemi I. Ojesina,Taofeek K. Owonikoko,Bradley A. Ozenberger,Angeliki Pantazi,Michael Parfenov,Peter J. Park,Joel S. Parker,Evan Paull,Chandra Sekhar Pedamallu,Charles M. Perou,Jan F. Prins,Alexei Protopopov,Suresh S. Ramalingam,Nilsa C. Ramirez,Ricardo J. Ramirez,Benjamin J. Raphael,W. Kimryn Rathmell,Xiaojia Ren,Sheila M. Reynolds,Esther Rheinbay,Matthew D. Ringel,Michael Rivera,Jeffrey Roach,A. Gordon Robertson,Mara Rosenberg,Matthew Rosenthal,Sara Sadeghi,Gordon Saksena,Chris Sander,Netty Santoso,Jacqueline E. Schein,Nikolaus Schultz,Steven E. Schumacher,Raja R. Seethala,Jonathan G. Seidman,Yasin Şenbabaoğlu,Sahil Seth,Samantha Sharpe,Kenna Shaw,John Paul Shen,Ronglai Shen,Steven I. Sherman,Margi Sheth,Yan Shi,Ilya Shmulevich,Gabriel L. Sica,Janae V. Simons,Rileen Sinha,Payal Sipahimalani,Robert C. Smallridge,Heidi J. Sofia,Matthew G. Soloway,Xingzhi Song,Carrie Sougnez,Chip Stewart,Petar Stojanov,Joshua M. Stuart,S. Onur Sumer,Yichao Sun,Barbara Tabak,Angela Tam,Donghui Tan,Jie Hu,Roy Tarnuzzer,Barry S. Taylor,Nina Thiessen,Leigh B. Thorne,Vésteinn Thórsson,R. Michael Tuttle,Christopher B. Umbricht,David J. Van Den Berg,Fabio Vandin,Umadevi Veluvolu,Roeland Verhaak,Michelle Vinco,Doug Voet,Vonn Walter,Zhining Wang,Scot Waring,Paul M. Weinberger,Nils Weinhold,John N. Weinstein,Daniel J. Weisenberger,David A. Wheeler,Matthew D. Wilkerson,Jocelyn Wilson,Michelle D. Williams,Daniel A. Winer,Lisa Wise,Junyuan Wu,Xi Liu,Andrew Wei Xu,Liming Yang,Lixing Yang,Travis I. Zack,Martha A. Zeiger,Dong Zeng,Jean C. Zenklusen,Ni Zhao,Hailei Zhang,Jianhua Zhang,Jiashan Zhang,Wei Zhang,Erik Zmuda,Lihua Zou

Biology

Thyroid carcinoma

Thyroid cancer

2014

<h2>Summary</h2> Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. Here, we describe the genomic landscape of 496 PTCs. We observed a low frequency of somatic alterations (relative to other carcinomas) and extended the set of known PTC driver alterations to include <i>EIF1AX</i>, <i>PPM1D</i>, and <i>CHEK2</i> and diverse gene fusions. These discoveries reduced the fraction of PTC cases with unknown oncogenic driver from 25% to 3.5%. Combined analyses of genomic variants, gene expression, and methylation demonstrated that different driver groups lead to different pathologies with distinct signaling and differentiation characteristics. Similarly, we identified distinct molecular subgroups of <i>BRAF</i>-mutant tumors, and multidimensional analyses highlighted a potential involvement of oncomiRs in less-differentiated subgroups. Our results propose a reclassification of thyroid cancers into molecular subtypes that better reflect their underlying signaling and differentiation properties, which has the potential to improve their pathological classification and better inform the management of the disease.

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“Integrated Genomic Characterization of Papillary Thyroid Carcinoma” is a paper by Nishant Agrawal Rehan Akbani Bülent Arman Aksoy Adrian Ally Harindra Arachchi L. Sylvia J. Todd Auman Miruna Balasundaram Saianand Balu Stephen B. Baylin Madhusmita Behera Brady Bernard Rameen Beroukhim Justin A. Bishop Aaron Black Tom Bodenheimer Lori Boice Moiz S. Bootwalla Jay Bowen Reanne Bowlby Christopher A. Bristow Robin Brookens Denise Brooks R M T Bonita Bryant Elizabeth Buda Yaron S.N. Butterfield Tobias Carling Rebecca Carlsen Scott L. Carter Sally E. Carty Timothy A. Chan Amy Y. Chen Andrew D. Cherniack Dorothy Cheung Lynda Chin Juok Cho Andy Chu Eric Chuah Kristian Cibulskis Giovanni Ciriello Amanda Clarke Gary L. Clayman Leslie Cope John A. Copland Kyle R. Covington Ludmila Danilova Tanja M. Davidsen John A. Demchok Daniel DiCara Noreen Dhalla Rajiv Dhir Sheliann S. Dookran Gideon Dresdner Jonathan V. Eldridge Greg Eley Adel K. El‐Naggar Stephanie Eng James A. Fagin Timothy Fennell Robert L. Ferris Sheila Fisher Scott Frazer Jessica Frick Stacey Gabriel Ian Ganly Jianjiong Gao Levi A. Garraway Julie M. Gastier‐Foster Gad Getz Nils Gehlenborg Ronald Ghossein Richard A. Gibbs Thomas J. Giordano Karen Gomez-Hernandez Jonna Grimsby Benjamin Groß Ranabir Guin Angela Hadjipanayis Hollie A. Harper D. Neil Hayes David I. Heiman James G. Herman Katherine A. Hoadley Matan Hofree Robert A. Holt Alan P. Hoyle Franklin W. Huang Mei Huang Carolyn M. Hutter Trey Ideker Lisa Iype Anders Jacobsen Stuart R. Jefferys Corbin D. Jones Steven Jones Katayoon Kasaian Electron Kebebew Fadlo R. Khuri Jaegil Kim Roger Kramer Richard Kreisberg Raju Kucherlapati David J. Kwiatkowski Marc Ladanyi Phillip H. Lai Peter W. Laird Eric S. Lander Michael S. Lawrence Darlene Lee Eunjung Lee Semin Lee William Lee Kristen Leraas Tara M. Lichtenberg Lee Lichtenstein Pei Lin Shiyun Ling Jinze Liu Wenbin Liu Yingchun Liu Virginia A. LiVolsi Yiling Lu Yussanne Ma Harshad S. Mahadeshwar Marco A. Marra Michael Mayo David G. McFadden Shaowu Meng Matthew Meyerson Piotr A. Mieczkowski Michael Miller Gordon B. Mills Richard A. Moore Lisle E. Mose Andrew J. Mungall Bradley A. Murray Yuri E. Nikiforov Michael S. Noble Akinyemi I. Ojesina Taofeek K. Owonikoko Bradley A. Ozenberger Angeliki Pantazi Michael Parfenov Peter J. Park Joel S. Parker Evan Paull Chandra Sekhar Pedamallu Charles M. Perou Jan F. Prins Alexei Protopopov Suresh S. Ramalingam Nilsa C. Ramirez Ricardo J. Ramirez Benjamin J. Raphael W. Kimryn Rathmell Xiaojia Ren Sheila M. Reynolds Esther Rheinbay Matthew D. Ringel Michael Rivera Jeffrey Roach A. Gordon Robertson Mara Rosenberg Matthew Rosenthal Sara Sadeghi Gordon Saksena Chris Sander Netty Santoso Jacqueline E. Schein Nikolaus Schultz Steven E. Schumacher Raja R. Seethala Jonathan G. Seidman Yasin Şenbabaoğlu Sahil Seth Samantha Sharpe Kenna Shaw John Paul Shen Ronglai Shen Steven I. Sherman Margi Sheth Yan Shi Ilya Shmulevich Gabriel L. Sica Janae V. Simons Rileen Sinha Payal Sipahimalani Robert C. Smallridge Heidi J. Sofia Matthew G. Soloway Xingzhi Song Carrie Sougnez Chip Stewart Petar Stojanov Joshua M. Stuart S. Onur Sumer Yichao Sun Barbara Tabak Angela Tam Donghui Tan Jie Hu Roy Tarnuzzer Barry S. Taylor Nina Thiessen Leigh B. Thorne Vésteinn Thórsson R. Michael Tuttle Christopher B. Umbricht David J. Van Den Berg Fabio Vandin Umadevi Veluvolu Roeland Verhaak Michelle Vinco Doug Voet Vonn Walter Zhining Wang Scot Waring Paul M. Weinberger Nils Weinhold John N. Weinstein Daniel J. Weisenberger David A. Wheeler Matthew D. Wilkerson Jocelyn Wilson Michelle D. Williams Daniel A. Winer Lisa Wise Junyuan Wu Xi Liu Andrew Wei Xu Liming Yang Lixing Yang Travis I. Zack Martha A. Zeiger Dong Zeng Jean C. Zenklusen Ni Zhao Hailei Zhang Jianhua Zhang Jiashan Zhang Wei Zhang Erik Zmuda Lihua Zou published in 2014. It has an Open Access status of “hybrid”. You can read and download a PDF Full Text of this paper here.