Journal ArticleDOI
Recurrent Fusion of TMPRSS2 and ETS Transcription Factor Genes in Prostate Cancer
Scott A. Tomlins,Daniel R. Rhodes,Sven Perner,Saravana M. Dhanasekaran,Rohit Mehra,Xiao-Wei Sun,Sooryanarayana Varambally,Xuhong Cao,Joelle Tchinda,Rainer Kuefer,Charles Lee,James E. Montie,Rajal B. Shah,Kenneth J. Pienta,Mark A. Rubin,Arul M. Chinnaiyan +15 more
TLDR
In this article, the authors used a bioinformatics approach to discover candidate oncogenic chromosomal aberrations on the basis of outlier gene expression and identified recurrent gene fusions of the 5' untranslated region of TMPRSS2 to ERG or ETV1.Abstract:
Recurrent chromosomal rearrangements have not been well characterized in common carcinomas. We used a bioinformatics approach to discover candidate oncogenic chromosomal aberrations on the basis of outlier gene expression. Two ETS transcription factors, ERG and ETV1, were identified as outliers in prostate cancer. We identified recurrent gene fusions of the 5' untranslated region of TMPRSS2 to ERG or ETV1 in prostate cancer tissues with outlier expression. By using fluorescence in situ hybridization, we demonstrated that 23 of 29 prostate cancer samples harbor rearrangements in ERG or ETV1. Cell line experiments suggest that the androgen-responsive promoter elements of TMPRSS2 mediate the overexpression of ETS family members in prostate cancer. These results have implications in the development of carcinomas and the molecular diagnosis and treatment of prostate cancer.read more
Citations
More filters
Journal ArticleDOI
Anomaly detection: A survey
TL;DR: This survey tries to provide a structured and comprehensive overview of the research on anomaly detection by grouping existing techniques into different categories based on the underlying approach adopted by each technique.
Journal ArticleDOI
Cancer Genome Landscapes
Bert Vogelstein,Nickolas Papadopoulos,Victor E. Velculescu,Shibin Zhou,Luis A. Diaz,Kenneth W. Kinzler +5 more
TL;DR: This work has revealed the genomic landscapes of common forms of human cancer, which consists of a small number of “mountains” (genes altered in a high percentage of tumors) and a much larger number of "hills" (Genes altered infrequently).
Journal ArticleDOI
GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses.
TL;DR: GEPIA (Gene Expression Profiling Interactive Analysis) fills in the gap between cancer genomics big data and the delivery of integrated information to end users, thus helping unleash the value of the current data resources.
Journal ArticleDOI
The cancer genome atlas pan-cancer analysis project
John N. Weinstein,John N. Weinstein,Eric A. Collisson,Gordon B. Mills,Kenna R. Mills Shaw,Kenna R. Mills Shaw,Brad Ozenberger,Kyle Ellrott,Kyle Ellrott,Chris Sander,Joshua M. Stuart,Joshua M. Stuart,Kyle Chang,Chad J. Creighton,Caleb F. Davis,Lawrence A. Donehower,Jennifer Drummond,David A. Wheeler,Adrian Ally,Miruna Balasundaram,Inanc Birol,Inanc Birol,Inanc Birol,Yaron S.N. Butterfield,Andy Chu,Eric Chuah,Hye Jung E. Chun,Noreen Dhalla,Ranabir Guin,Martin Hirst,Carrie Hirst,Robert A. Holt,Steven J.M. Jones,Darlene Lee,Haiyan I. Li,Marco A. Marra,Michael Mayo,Richard A. Moore,Andrew J. Mungall,A. Gordon Robertson,Jacqueline E. Schein,Payal Sipahimalani,Angela Tam,Nina Thiessen,Richard Varhol,Rameen Beroukhim,Ami S. Bhatt,Angela N. Brooks,Andrew D. Cherniack,Samuel S. Freeman,Stacey Gabriel,Elena Helman,Joonil Jung,Matthew Meyerson,Akinyemi I. Ojesina,Chandra Sekhar Pedamallu,Gordon Saksena,Steven E. Schumacher,Barbara Tabak,Travis I. Zack,Travis I. Zack,Eric S. Lander,Christopher A. Bristow,Angela Hadjipanayis,Psalm Haseley,Raju Kucherlapati,Semin Lee,Eunjung Lee,Lovelace J. Luquette,Harshad S. Mahadeshwar,Angeliki Pantazi,Michael Parfenov,Michael Parfenov,Peter J. Park,Alexei Protopopov,Xiaojia Ren,Netty Santoso,Jonathan G. Seidman,Sahil Seth,Xingzhi Song,Jiabin Tang,Ruibin Xi,Ruibin Xi,Ruibin Xi,Andrew Wei Xu,Lixing Yang,Dong Zeng,J. Todd Auman,Saianand Balu,Elizabeth Buda,Cheng Fan,Katherine A. Hoadley,Corbin D. Jones,Shaowu Meng,Piotr A. Mieczkowski,Joel S. Parker,Charles M. Perou,Jeffrey Roach,Yan Shi,Grace O. Silva,Donghui Tan,Umadevi Veluvolu,Scot Waring,Matthew D. Wilkerson,Junyuan Wu,Wei Zhao,Tom Bodenheimer,D. Neil Hayes,D. Neil Hayes,Alan P. Hoyle,Stuart R. Jeffreys,Lisle E. Mose,Janae V. Simons,Mathew G. Soloway,Stephen B. Baylin,Benjamin P. Berman,Moiz S. Bootwalla,Ludmila Danilova,James G. Herman,Toshinori Hinoue,Peter W. Laird,Suhn K. Rhie,Hui Shen,Timothy J. Triche,Daniel J. Weisenberger,Scott L. Carter,Kristian Cibulskis,Lynda Chin,Jianhua Zhang,Carrie Sougnez,Min Wang,Gad Getz,Gad Getz,Huyen Dinh,Harshavardhan Doddapaneni,Richard A. Gibbs,Preethi Gunaratne,Preethi Gunaratne,Yi Han,Divya Kalra,Christie Kovar,Lora Lewis,Margaret B. Morgan,Donna Morton,Donna Muzny,Jeffrey G. Reid,Liu Xi,Juok Cho,Daniel DiCara,Scott Frazer,Nils Gehlenborg,David I. Heiman,Jaegil Kim,Michael S. Lawrence,Pei Lin,Yingchun Liu,Michael S. Noble,Petar Stojanov,Doug Voet,Hailei Zhang,Lihua Zou,Chip Stewart,Brady Bernard,Ryan Bressler,Andrea Eakin,Lisa Iype,Theo A. Knijnenburg,Roger Kramer,Richard Kreisberg,Kalle Leinonen,Jake Lin,Yuexin Liu,Michael Miller,Sheila M. Reynolds,Hector Rovira,Ilya Shmulevich,Vesteinn Thorsson,Da Yang,Wei Zhang,Samirkumar B. Amin,Chang-Jiun Wu,Chia Chin Wu,Rehan Akbani,Kenneth Aldape,Keith A. Baggerly,Bradley McIntosh Broom,Tod D. Casasent,James Cleland,Deepti Dodda,Mary Elizabeth Edgerton,Leng Han,Shelley M. Herbrich,Zhenlin Ju,Hoon Kim,Hoon Kim,Seth Lerner,Jun Li,Han Liang,Wenbin Liu,Philip L. Lorenzi,Yiling Lu,James M. Melott,Lam Nguyen,Lam Nguyen,Xiaoping Su,Roeland Verhaak,Wenyi Wang,Andrew J. Wong,Andrew J. Wong,Yang Yang,Jun Yao,Rong Yao,Kosuke Yoshihara,Yuan Yuan,Yuan Yuan,W. K. Alfred Yung,Nianxiang Zhang,Siyuan Zheng,Michael B. Ryan,Michael B. Ryan,David W. Kane,David W. Kane,B. Arman Aksoy,Giovanni Ciriello,Gideon Dresdner,Jianjiong Gao,Benjamin Gross,Anders Jacobsen,André Kahles,Marc Ladanyi,William Lee,Kjong-Van Lehmann,Martin L. Miller,Ricardo Ramirez,Gunnar Rätsch,Boris Reva,Nikolaus Schultz,Yasin Senbabaoglu,Ronglai Shen,Rileen Sinha,S. Onur Sumer,Yichao Sun,Barry S. Taylor,Barry S. Taylor,Barry S. Taylor,Nils Weinhold,Suzanne S. Fei,Paul T. Spellman,Christopher C. Benz,Christopher C. Benz,Daniel E. Carlin,Daniel E. Carlin,Melisssa Cline,Melisssa Cline,Brian Craft,Brian Craft,Mary Goldman,David Haussler,David Haussler,David Haussler,Singer Ma,Singer Ma,Sam Ng,Sam Ng,Evan O. Paull,Evan O. Paull,Amie Radenbaugh,Amie Radenbaugh,Sofie R. Salama,Sofie R. Salama,Sofie R. Salama,Artem Sokolov,Artem Sokolov,Teresa Swatloski,Teresa Swatloski,Vladislav Uzunangelov,Vladislav Uzunangelov,Peter Waltman,Peter Waltman,Christina Yau,Jing Zhu,Jing Zhu,Stanley R. Hamilton,Scott Abbott,Rachel Abbott,Nathan D. Dees,Kim D. Delehaunty,Li Ding,David J. Dooling,James M. Eldred,Catrina Fronick,Robert S. Fulton,Lucinda Fulton,Joelle Kalicki-Veizer,Krishna L. Kanchi,Cyriac Kandoth,Daniel C. Koboldt,David E. Larson,Timothy J. Ley,Ling Lin,Charles Lu,Vincent Magrini,Elaine R. Mardis,Michael D. McLellan,Joshua F. McMichael,Christopher A. Miller,Michelle O'Laughlin,Craig Pohl,Heather Schmidt,Scott M. Smith,Jason Walker,John W. Wallis,Michael C. Wendl,Michael C. Wendl,Richard K. Wilson,Todd Wylie,Qunyuan Zhang,Robert A. Burton,Mark A. Jensen,Ari B. Kahn,Todd Pihl,David A. Pot,Yunhu Wan,Douglas A. Levine,Aaron D. Black,Jay Bowen,Jessica Frick,Julie M. Gastier-Foster,Julie M. Gastier-Foster,Hollie A. Harper,Carmen Helsel,Kristen M. Leraas,Tara M. Lichtenberg,Cynthia McAllister,Nilsa C. Ramirez,Nilsa C. Ramirez,Samantha Sharpe,Lisa Wise,Erik Zmuda,Stephen J. Chanock,Tanja Davidsen,John A. Demchok,Greg Eley,Ina Felau,Margi Sheth,Heidi J. Sofia,Louis M. Staudt,Roy Tarnuzzer,Zhining Wang,Liming Yang,Jiashan Zhang,Larsson Omberg,Adam Margolin,Benjamin J. Raphael,Fabio Vandin,Hsin-Ta Wu,Mark D.M. Leiserson,Stephen C. Benz,Charles J. Vaske,Houtan Noushmehr,Houtan Noushmehr,Denise M. Wolf,Laura van 't Veer,Dimitris Anastassiou,Tai Hsien Ou Yang,Nuria Lopez-Bigas,Abel Gonzalez-Perez,David Tamborero,Zheng Xia,Wei Li,Dong Yeon Cho,Teresa M. Przytycka,Mark P. Hamilton,Sean E. McGuire,Sven Nelander,Sven Nelander,Patrik Johansson,Rebecka Jörnsten,Rebecka Jörnsten,Teresia Kling +379 more
TL;DR: The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA with a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages.
Journal ArticleDOI
Inferring tumour purity and stromal and immune cell admixture from expression data
Kosuke Yoshihara,Maria Shahmoradgoli,Emmanuel Martinez,Rahulsimham Vegesna,Hoon Kim,Wandaliz Torres-Garcia,Victor Trevino,Hui Shen,Peter W. Laird,Douglas A. Levine,Scott L. Carter,Gad Getz,Katherine Stemke-Hale,Gordon B. Mills,Roel G.W. Verhaak +14 more
TL;DR: A method that uses gene expression signatures to infer the fraction of stromal and immune cells in tumour samples and prediction accuracy is corroborated using 3,809 transcriptional profiles available elsewhere in the public domain.
References
More filters
Journal ArticleDOI
Cancer statistics, 2005.
Ahmedin Jemal,Taylor Murray,Elizabeth Ward,Alicia Samuels,Ram C. Tiwari,Asma Ghafoor,Eric J. Feuer,Michael J. Thun +7 more
TL;DR: Cancer incidence and death rates are lower in other racial and ethnic groups than in Whites and African Americans for all sites combined and for the four major cancer sites, however, these groups generally have higher rates for stomach, liver, and cervical cancers than Whites.
Journal ArticleDOI
Letter: A new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining.
TL;DR: An unsuspected abnormality in all cells from the nine patients with chronic myelogenous leukaemia has been detected with quinacrine fluorescence and various Giemsa staining techniques, suggesting that there may be a hitherto undetected translocation between the long arm of 22 and thelong arm of 9, producing the 9q+ chromosome.
Journal ArticleDOI
ONCOMINE: A Cancer Microarray Database and Integrated Data-Mining Platform
Daniel R. Rhodes,Jianjun Yu,K. Shanker,Nandan P. Deshpande,Radhika Varambally,Debashis Ghosh,Terrence R. Barrette,Akhilesh Pandey,Arul M. Chinnaiyan +8 more
TL;DR: ONCOMINE is presented, a cancer microarray database and web-based data-mining platform aimed at facilitating discovery from genome-wide expression analyses and novel biomarkers and therapeutic targets are discovered.
Journal ArticleDOI
A census of human cancer genes
P. Andrew Futreal,Lachlan J. M. Coin,Mhairi Marshall,Thomas A. Down,Tim Hubbard,Richard Wooster,Nazneen Rahman,Michael R. Stratton +7 more
TL;DR: A 'census' of cancer genes is conducted that indicates that mutations in more than 1% of genes contribute to human cancer.
Journal ArticleDOI
Breast cancer classification and prognosis based on gene expression profiles from a population-based study
Christos Sotiriou,Soek-Ying Neo,Lisa M. McShane,Edward L. Korn,Philip M. Long,Amir A. Jazaeri,Philippe Martiat,Simon Fox,Adrian L. Harris,Edison T. Liu,Edison T. Liu +10 more
TL;DR: Gene expression patterns were found to be strongly associated with estrogen receptor (ER) status and moderately associated with grade, but not associated with menopausal status, nodal status, or tumor size, in an unselected group of 99 node-negative and node-positive breast cancer patients.
Related Papers (5)
Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer
Scott A. Tomlins,Bharathi Laxman,Saravana M. Dhanasekaran,Beth E. Helgeson,Xuhong Cao,David S. Morris,Anjana Menon,Xiaojun Jing,Qi Cao,Bo Han,Jindan Yu,Lei Wang,James E. Montie,Mark A. Rubin,Kenneth J. Pienta,Diane Roulston,Rajal B. Shah,Sooryanarayana Varambally,Rohit Mehra,Arul M. Chinnaiyan +19 more
Integrative genomic profiling of human prostate cancer
Barry S. Taylor,Nikolaus Schultz,Haley Hieronymus,Anuradha Gopalan,Yonghong Xiao,Brett S. Carver,Vivek K. Arora,Poorvi Kaushik,Ethan Cerami,Boris Reva,Yevgeniy Antipin,Nicholas Mitsiades,Thomas Landers,Igor Dolgalev,John E. Major,Manda Wilson,Nicholas D. Socci,Alex E. Lash,Adriana Heguy,James A. Eastham,Howard I. Scher,Victor E. Reuter,Peter T. Scardino,Chris Sander,Charles L. Sawyers,Charles L. Sawyers,William L. Gerald +26 more
The mutational landscape of lethal castration-resistant prostate cancer
Catherine S. Grasso,Yi-Mi Wu,Dan R. Robinson,Xuhong Cao,Saravana M. Dhanasekaran,Amjad Khan,Michael J. Quist,Xiaojun Jing,Robert J. Lonigro,J. Chad Brenner,Irfan A. Asangani,Bushra Ateeq,Sang Y. Chun,Javed Siddiqui,Lee Sam,Matt Anstett,Rohit Mehra,John R. Prensner,Nallasivam Palanisamy,Gregory A. Ryslik,Fabio Vandin,Benjamin J. Raphael,Lakshmi P. Kunju,Daniel R. Rhodes,Kenneth J. Pienta,Arul M. Chinnaiyan,Scott A. Tomlins +26 more