Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity
Austin M. Dulak,Petar Stojanov,Petar Stojanov,Petar Stojanov,Shouyong Peng,Shouyong Peng,Michael S. Lawrence,Cameron Fox,Chip Stewart,Santhoshi Bandla,Yu Imamura,Steven E. Schumacher,Steven E. Schumacher,Erica Shefler,Aaron McKenna,Scott L. Carter,Kristian Cibulskis,Andrey Sivachenko,Gordon Saksena,Douglas Voet,Alex H. Ramos,Daniel Auclair,Kristin Thompson,Carrie Sougnez,Robert C. Onofrio,Candace Guiducci,Rameen Beroukhim,Zhongren Zhou,Lin Lin,Jules Lin,Rishindra M. Reddy,Andrew C. Chang,Rodney Landrenau,Arjun Pennathur,Shuji Ogino,James D. Luketich,Todd R. Golub,Stacey Gabriel,Eric S. Lander,Eric S. Lander,Eric S. Lander,David G. Beer,Tony E. Godfrey,Gad Getz,Gad Getz,Adam J. Bass +45 more
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Abstract:
The incidence of esophageal adenocarcinoma (EAC) has risen 600% over the last 30 years. With a 5-year survival rate of ~15%, the identification of new therapeutic targets for EAC is greatly important. We analyze the mutation spectra from whole-exome sequencing of 149 EAC tumor-normal pairs, 15 of which have also been subjected to whole-genome sequencing. We identify a mutational signature defined by a high prevalence of A>C transversions at AA dinucleotides. Statistical analysis of exome data identified 26 significantly mutated genes. Of these genes, five (TP53, CDKN2A, SMAD4, ARID1A and PIK3CA) have previously been implicated in EAC. The new significantly mutated genes include chromatin-modifying factors and candidate contributors SPG20, TLR4, ELMO1 and DOCK2. Functional analyses of EAC-derived mutations in ELMO1 identifies increased cellular invasion. Therefore, we suggest the potential activation of the RAC1 pathway as a contributor to EAC tumorigenesis.read more
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Journal ArticleDOI
Signatures of mutational processes in human cancer
Ludmil B. Alexandrov,Serena Nik-Zainal,Serena Nik-Zainal,David C. Wedge,Samuel Aparicio,Sam Behjati,Sam Behjati,Andrew V. Biankin,Graham R. Bignell,Niccolo Bolli,Niccolo Bolli,Åke Borg,Anne Lise Børresen-Dale,Anne Lise Børresen-Dale,Sandrine Boyault,Birgit Burkhardt,Adam Butler,Carlos Caldas,Helen Davies,Christine Desmedt,Roland Eils,Jorunn E. Eyfjord,John A. Foekens,Mel Greaves,Fumie Hosoda,Barbara Hutter,Tomislav Ilicic,Sandrine Imbeaud,Sandrine Imbeaud,Marcin Imielinsk,Natalie Jäger,David T. W. Jones,David T. Jones,Stian Knappskog,Stian Knappskog,Marcel Kool,Sunil R. Lakhani,Carlos López-Otín,Sancha Martin,Nikhil C. Munshi,Nikhil C. Munshi,Hiromi Nakamura,Paul A. Northcott,Marina Pajic,Elli Papaemmanuil,Angelo Paradiso,John V. Pearson,Xose S. Puente,Keiran Raine,Manasa Ramakrishna,Andrea L. Richardson,Andrea L. Richardson,Julia Richter,Philip Rosenstiel,Matthias Schlesner,Ton N. Schumacher,Paul N. Span,Jon W. Teague,Yasushi Totoki,Andrew Tutt,Rafael Valdés-Mas,Marit M. van Buuren,Laura van ’t Veer,Anne Vincent-Salomon,Nicola Waddell,Lucy R. Yates,Icgc PedBrain,Jessica Zucman-Rossi,Jessica Zucman-Rossi,P. Andrew Futreal,Ultan McDermott,Peter Lichter,Matthew Meyerson,Matthew Meyerson,Sean M. Grimmond,Reiner Siebert,Elias Campo,Tatsuhiro Shibata,Stefan M. Pfister,Stefan M. Pfister,Peter J. Campbell,Peter J. Campbell,Peter J. Campbell,Michael R. Stratton,Michael R. Stratton +84 more
TL;DR: It is shown that hypermutation localized to small genomic regions, ‘kataegis’, is found in many cancer types, and this results reveal the diversity of mutational processes underlying the development of cancer.
Journal ArticleDOI
Comprehensive molecular characterization of gastric adenocarcinoma
Adam J. Bass,Vesteinn Thorsson,Ilya Shmulevich,Sheila 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 Pedamallu,Carrie Sougnez,Amaro Taylor-Weiner,Rehan Akbani,Ju Seog Lee,Wenbin Liu,GB Mills,Da Yang,Wei Zhang,Angeliki Pantazi,Michael Parfenov,Margaret L. Gulley,M. Blanca Piazuelo,Barbara G. 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 Kyun Kim,Jay Bowen,Kristen M. 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,Li Ding,Beifang Niu,Adrian Ally,Miruna Balasundaram,Inanc Birol,Denise Brooks,Yaron S.N. Butterfield,Rebecca Carlsen,Justin Chu,Eric Chuah,Hye Jung E. Chun,Amanda Clarke,Noreen Dhalla,Ranabir Guin,Robert A. Holt,Steven J.M. Jones,Darlene Lee,Haiyan A. Li,Emilia L. Lim,Yussanne Ma,Marco A. Marra,Michael Mayo,Richard A. Moore,Karen Mungall,Ka Ming Nip,Jacqueline E. Schein,Angela Tam,Nina Thiessen,Rameen Beroukhim,Scott L. Carter,Andrew D. Cherniack,Juok Cho,Daniel DiCara,Scott Frazer,Nils Gehlenborg,David I. Heiman,Joonil Jung,Jaegil Kim,Pei Lin,Matthew Meyerson,Akinyemi I. Ojesina,Chandra Sekhar Pedamallu,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,Jiabin Tang,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,Sang Bae Kim,Yiling Lu,Gordon B. Mills,Moiz S. Bootwalla,Phillip H. Lai,Timothy J. Triche,David 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 Ramirez,Chris Sander,Yasin Senbabaoglu,Rileen Sinha,S. Onur Sumer,Yichao Sun,Lisa Iype,Roger Kramer,Richard Kreisberg,Hector Rovira,Natalie Tasman,Santa Cruz Sam Ng,David Haussler,Josh Stuart,Roeland Verhaak,Mark D.M. Leiserson,Barry S. Taylor,Aaron D. 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 V. Fedosenko,Georgy Manikhas,Olga Potapova,Olga Voronina,Smitry Belyaev,Oleg Dolzhansky,W. Kimryn Rathmell,Jakub Brzezinski,Matthew Ibbs,Konstanty Korski,Witold Kycler,Radoslaw ŁaŸniak,Ewa Leporowska,Andrzej Mackiewicz,Dawid Murawa,Pawel Murawa,Arkadiusz Spychała,Wiktoria Maria Suchorska,Honorata Tatka,M. Teresiak,Raafat Abdel-Misih,Joseph J. Bennett,Jennifer Brown,Mary Iacocca,Brenda Rabeno,Sun Young 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,Eunjung Cho,Marc Ladanyi,Laura H. Tang,Shannon J. McCall,Young Soo 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 R. Mills Shaw,Roy Tarnuzzer,Zhining Wang,Liming Yang,Jean C. Zenklusen,Tanja M. Davidsen,Carolyn M. Hutter,Heidi J. Sofia,Robert Burton,Sudha Chudamani,Jia Liu +257 more
TL;DR: A comprehensive molecular evaluation of 295 primary gastric adenocarcinomas as part of The Cancer Genome Atlas (TCGA) project is described and a molecular classification dividing gastric cancer into four subtypes is proposed.
Journal ArticleDOI
Integrated Genomic Characterization of Papillary Thyroid Carcinoma
Nishant Agrawal,Rehan Akbani,B. Arman Aksoy,Adrian Ally,Harindra Arachchi,Sylvia L. Asa,J. Todd Auman,Miruna Balasundaram,Saianand Balu,Stephen B. Baylin,Madhusmita Behera,Brady Bernard,Rameen Beroukhim,Justin A. Bishop,Aaron D. Black,Tom Bodenheimer,Lori Boice,Moiz S. Bootwalla,Jay Bowen,Reanne Bowlby,Christopher A. Bristow,Robin Brookens,Denise Brooks,Robert Bryant,Elizabeth Buda,Yaron S.N. Butterfield,Tobias Carling,Rebecca Carlsen,Scott L. Carter,Sally E. Carty,Timothy A. Chan,Amy 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 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 R. 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 J.M. 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 M. Leraas,Tara M. Lichtenberg,Lee Lichtenstein,Pei Lin,Shiyun Ling,Jinze Liu,Wen-Bin 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 L. 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 O. Paull,Chandra Sekhar Pedamallu,Charles M. Perou,Jan F. Prins,Alexei Protopopov,Suresh Ramalingam,Nilsa C. Ramirez,Ricardo Ramirez,Benjamin J. Raphael,W. Kimryn Rathmell,Xiaojia Ren,Sheila 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 Senbabaoglu,Sahil Seth,Samantha Sharpe,Kenna R. Mills Shaw,John Paul Shen,Ronglai Shen,Steven I. Sherman,Margi Sheth,Yan Shi,Ilya Shmulevich,Gabriel 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,Jiabin Tang,Roy Tarnuzzer,Barry S. Taylor,Nina Thiessen,Leigh B. Thorne,Vesteinn Thorsson,R. Michael Tuttle,Christopher B. Umbricht,David 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,Liu Xi,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 +242 more
TL;DR: The genomic landscape of 496 PTCs is described and a reclassification of thyroid cancers into molecular subtypes that better reflect their underlying signaling and differentiation properties is proposed, which has the potential to improve their pathological classification and better inform the management of the disease.
Journal ArticleDOI
Maftools: efficient and comprehensive analysis of somatic variants in cancer.
Anand Mayakonda,Anand Mayakonda,De-Chen Lin,Yassen Assenov,Yassen Assenov,Christoph Plass,Christoph Plass,H. Phillip Koeffler,H. Phillip Koeffler +8 more
TL;DR: An R Bioconductor package, Maftools, is described, which offers a multitude of analysis and visualization modules that are commonly used in cancer genomic studies, including driver gene identification, pathway, signature, enrichment, and association analyses, and is independent of larger alignment files.
Journal ArticleDOI
Integrated genomic characterization of oesophageal carcinoma.
BC Cancer Agency,Brigham,KU Leuven,Tissue Source Sites: Analytic Biologic Services,Asterand Bioscience,BioreclamationIVT,Botkin Municipal Clinic,Cureline,Invidumed,Israelitisches Krankenhaus Hamburg,Ontario Tumour Bank +10 more
TL;DR: The authors' analyses identified three molecular subclasses of oesophageal squamous cell carcinomas, but none showed evidence for an aetiological role of human papillomavirus and these data provide a framework to facilitate more rational categorization of these tumours and a foundation for new therapies.
References
More filters
Journal ArticleDOI
A method and server for predicting damaging missense mutations.
Ivan Adzhubei,Steffen Schmidt,Leonid Peshkin,Vasily Ramensky,Anna Gerasimova,Peer Bork,Alexey S. Kondrashov,Shamil R. Sunyaev +7 more
TL;DR: A new method and the corresponding software tool, PolyPhen-2, which is different from the early tool polyPhen1 in the set of predictive features, alignment pipeline, and the method of classification is presented and performance, as presented by its receiver operating characteristic curves, was consistently superior.
Journal ArticleDOI
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
TL;DR: Three methods of performing normalization at the probe intensity level are presented: a one number scaling based algorithm and a method that uses a non-linear normalizing relation by comparing the variability and bias of an expression measure and the simplest and quickest complete data method is found to perform favorably.
Journal ArticleDOI
Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Erez Lieberman Aiden,Nynke L. van Berkum,Louise Williams,Maxim Imakaev,Tobias Ragoczy,Tobias Ragoczy,Agnes Telling,Agnes Telling,Ido Amit,Bryan R. Lajoie,Peter J. Sabo,Michael O. Dorschner,Richard Sandstrom,Bradley E. Bernstein,Bradley E. Bernstein,Michaël Bender,Mark Groudine,Mark Groudine,Andreas Gnirke,John A. Stamatoyannopoulos,Leonid A. Mirny,Eric S. Lander,Eric S. Lander,Job Dekker +23 more
TL;DR: Hi-C is described, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing and demonstrates the power of Hi-C to map the dynamic conformations of entire genomes.
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
dbSNP: the NCBI database of genetic variation
Stephen T. Sherry,Minghong Ward,Michael Kholodov,Jonathan Baker,Lon Phan,Elizabeth M. Smigielski,Karl Sirotkin +6 more
TL;DR: The dbSNP database is a general catalog of genome variation to address the large-scale sampling designs required by association studies, gene mapping and evolutionary biology, and is integrated with other sources of information at NCBI such as GenBank, PubMed, LocusLink and the Human Genome Project data.
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