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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. Treviño,Yuan Wu,Min Wang,Preethi H. Gunaratne,Lawrence A. Donehower,Chad J. Creighton,David A. Wheeler,Richard A. Gibbs,Michael S. Lawrence,Douglas Voet,Rui Jiang,Kristian Cibulskis,Andrey Sivachenko,Petar Stojanov,Aaron McKenna,Eric S. Lander,Stacey Gabriel,Ding Li,Robert S. Fulton,Daniel C. Koboldt,Todd Wylie,Jason Walker,David J. Dooling,Lucinda L. Fulton,Kim D. Delehaunty,Catrina C. Fronick,Ryan Demeter,Elaine R. Mardis,Richard K. Wilson,Andy Chu,Hye Jung Chun,Andrew J. Mungall,Erin Pleasance,A. Gordon Robertson,Dominik Stoll,Miruna Balasundaram,İnanç Birol,Yaron S.N. Butterfield,Eric Chuah,Robin 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 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 Nguyen,Robert C. Onofrio,Andrew Crenshaw,Kristin Ardlie,Rameen Beroukhim,Wendy Winckler,Matthew Meyerson,Alexei Protopopov,Angela Hadjipanayis,Eunjung Lee,Ruibin Xi,Lixing Yang,Xiaojia Ren,N. 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 D. 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 J. Van Den Berg,Hui Shen,Tim 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,Jim Robinson,Helga Thorvaldsdóttir,Jill P. Mesirov,Vésteinn Thórsson,Sheila M. Reynolds,Brady Bernard,Richard Kreisberg,Jake Lin,Lisa Iype,Ryan Bressler,Timo Erkkilä,Madhumati Gundapuneni,Yuexin Liu,Adam Norberg,Thompson G. Robinson,Da Yang,Wei Zhang,Ilya Shmulevich,Jorma J. de Ronde,Nikolaus Schultz,Ethan Cerami,Giovanni Ciriello,Arthur P. Goldberg,Benjamin Groß,Anders Jacobsen,Jianjiong Gao,Bogumił Kaczkowski,Rileen Sinha,Bülent Arman Aksoy,Yevgeniy Antipin,Boris Reva,Ronglai Shen,Barry S. Taylor,Marc Ladanyi,Chris Sander,Rehan Akbani,Nianxiang Zhang,Bradley M. Broom,Anna Casasent,Anna K. Unruh,Chris Wakefield,Stanley R. Hamilton,Ronald C. Cason,Keith Baggerly,John N. Weinstein,David Haussler,Christopher C. Benz,Joshua M. Stuart,Stephen C. Benz,J. Zachary Sanborn,Charles Vaske,Jingchun Zhu,Christopher Szeto,Gary K. Scott,Christina Yau,Sam Ng,Ted 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 E. Sherman,Joseph Paulauskis,Julie M. Gastier‐Foster,Jay Bowen,Nilsa C. Ramirez,Aaron Black,Robert E. Pyatt,Lisa Wise,Peter White,Monica M. Bertagnolli,J. R. Brown,Timothy A. Chan,Gerald C. Chu,Christine Czerwinski,Fred Denstman,Rajiv Dhir,Arnulf Dörner,Charles S. Fuchs,José G. Guillem,Mary Iacocca,Hartmut Juhl,Andrew Kaufman,Bernard Kohl,Xuan Le,Maria Mariano,Elizabeth N. Medina,Michael L. Meyers,Garrett M. Nash,Phillip 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 B. Witkin,Zhaoshi Zeng,Michael J. Zinner,C. Zornig,Mark A. Jensen,Robert Sfeir,A 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 Berton,Matthew Nicholls,Deepak Srinivasan,Rohini Raman,Stanley Girshik,Peter A. Kigonya,Shelley Alonso,Rashmi N. Sanbhadti,Sean P. Barletta,J. M. Greene,David Pot,Kenna Shaw,Laura A. L. Dillon,Ken H. Buetow,Tanja M. 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

Biology

KRAS

MLH1

2012

To characterize somatic alterations in colorectal carcinoma, we conducted a genome-scale analysis of 276 samples, analysing exome sequence, DNA copy number, promoter methylation and messenger RNA and microRNA expression. A subset of these samples (97) underwent low-depth-of-coverage whole-genome sequencing. In total, 16% of colorectal carcinomas were found to be hypermutated: three-quarters of these had the expected high microsatellite instability, usually with hypermethylation and MLH1 silencing, and one-quarter had somatic mismatch-repair gene and polymerase ε (POLE) mutations. Excluding the hypermutated cancers, colon and rectum cancers were found to have considerably similar patterns of genomic alteration. Twenty-four genes were significantly mutated, and in addition to the expected APC, TP53, SMAD4, PIK3CA and KRAS mutations, we found frequent mutations in ARID1A, SOX9 and FAM123B. Recurrent copy-number alterations include potentially drug-targetable amplifications of ERBB2 and newly discovered amplification of IGF2. Recurrent chromosomal translocations include the fusion of NAV2 and WNT pathway member TCF7L1. Integrative analyses suggest new markers for aggressive colorectal carcinoma and an important role for MYC-directed transcriptional activation and repression.

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“Comprehensive molecular characterization of human colon and rectal cancer” is a paper by 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. Treviño Yuan Wu Min Wang Preethi H. Gunaratne Lawrence A. Donehower Chad J. Creighton David A. Wheeler Richard A. Gibbs Michael S. Lawrence Douglas Voet Rui Jiang Kristian Cibulskis Andrey Sivachenko Petar Stojanov Aaron McKenna Eric S. Lander Stacey Gabriel Ding Li Robert S. Fulton Daniel C. Koboldt Todd Wylie Jason Walker David J. Dooling Lucinda L. Fulton Kim D. Delehaunty Catrina C. Fronick Ryan Demeter Elaine R. Mardis Richard K. Wilson Andy Chu Hye Jung Chun Andrew J. Mungall Erin Pleasance A. Gordon Robertson Dominik Stoll Miruna Balasundaram İnanç Birol Yaron S.N. Butterfield Eric Chuah Robin 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 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 Nguyen Robert C. Onofrio Andrew Crenshaw Kristin Ardlie Rameen Beroukhim Wendy Winckler Matthew Meyerson Alexei Protopopov Angela Hadjipanayis Eunjung Lee Ruibin Xi Lixing Yang Xiaojia Ren N. 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 D. 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 J. Van Den Berg Hui Shen Tim 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 Jim Robinson Helga Thorvaldsdóttir Jill P. Mesirov Vésteinn Thórsson Sheila M. Reynolds Brady Bernard Richard Kreisberg Jake Lin Lisa Iype Ryan Bressler Timo Erkkilä Madhumati Gundapuneni Yuexin Liu Adam Norberg Thompson G. Robinson Da Yang Wei Zhang Ilya Shmulevich Jorma J. de Ronde Nikolaus Schultz Ethan Cerami Giovanni Ciriello Arthur P. Goldberg Benjamin Groß Anders Jacobsen Jianjiong Gao Bogumił Kaczkowski Rileen Sinha Bülent Arman Aksoy Yevgeniy Antipin Boris Reva Ronglai Shen Barry S. Taylor Marc Ladanyi Chris Sander Rehan Akbani Nianxiang Zhang Bradley M. Broom Anna Casasent Anna K. Unruh Chris Wakefield Stanley R. Hamilton Ronald C. Cason Keith Baggerly John N. Weinstein David Haussler Christopher C. Benz Joshua M. Stuart Stephen C. Benz J. Zachary Sanborn Charles Vaske Jingchun Zhu Christopher Szeto Gary K. Scott Christina Yau Sam Ng Ted 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 E. Sherman Joseph Paulauskis Julie M. Gastier‐Foster Jay Bowen Nilsa C. Ramirez Aaron Black Robert E. Pyatt Lisa Wise Peter White Monica M. Bertagnolli J. R. Brown Timothy A. Chan Gerald C. Chu Christine Czerwinski Fred Denstman Rajiv Dhir Arnulf Dörner Charles S. Fuchs José G. Guillem Mary Iacocca Hartmut Juhl Andrew Kaufman Bernard Kohl Xuan Le Maria Mariano Elizabeth N. Medina Michael L. Meyers Garrett M. Nash Phillip 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 B. Witkin Zhaoshi Zeng Michael J. Zinner C. Zornig Mark A. Jensen Robert Sfeir A 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 Berton Matthew Nicholls Deepak Srinivasan Rohini Raman Stanley Girshik Peter A. Kigonya Shelley Alonso Rashmi N. Sanbhadti Sean P. Barletta J. M. Greene David Pot Kenna Shaw Laura A. L. Dillon Ken H. Buetow Tanja M. 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 published in 2012. It has an Open Access status of “hybrid”. You can read and download a PDF Full Text of this paper here.