Journal ArticleDOI
Germline and sporadic mTOR pathway mutations in low-grade oncocytic tumor of the kidney.
Payal Kapur,Payal Kapur,Joanna Zawiejska-Rataj,Ming Gao,Hua Zhong,Suneetha Chintalapati,Midori Mitui,Spencer D. Barnes,Qinbo Zhou,Jeffrey Miyata,Deyssy Carrillo,Venkat S. Malladi,Dinesh Rakheja,Ivan Pedrosa,Lin Xu,Lisa N. Kinch,James Brugarolas +16 more
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In this article, the authors describe 22 low-grade oncocytic tumor (LOT) cases corresponding to 7 patients presenting with a median age of 75 years (range 63-86 years) and male to female ratio 2:5.About:
This article is published in Modern Pathology.The article was published on 2021-09-20. It has received 23 citations till now. The article focuses on the topics: Eosinophilic & TSC1.read more
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Journal ArticleDOI
Renal Cell Carcinoma in Tuberous Sclerosis Complex.
TL;DR: A detailed understanding of the pathologic features of these distinctive tumors, which include chromophobe-like features and eosinophilia, with some of the tumors unclassified, is provided in this paper.
Journal ArticleDOI
Renal cell carcinoma associated with tuberous sclerosis complex (TSC)/mammalian target of rapamycin (MTOR) genetic alterations
Pedram Argani,Rohit Mehra +1 more
TL;DR:
Journal ArticleDOI
Low‐grade oncocytic tumour of the kidney is characterised by genetic alterations of TSC1, TSC2, MTOR or PIK3CA and consistent GATA3 positivity
Sean R. Williamson,Ondrej Hes,Kiril Trpkov,Aditi Aggarwal,Abhishek Satapathy,Sourav Mishra,Shivani Sharma,Ankur R. Sangoi,Liang Cheng,Mahmut Akgul,Muhammad Idrees,Albert M. Levin,Sudha M. Sadasivan,Pilar San Miguel Fraile,Joanna Rogala,Eva Comperat,Daniel M. Berney,Stela Bulimbasic,Jesse K. McKenney,Shilpy Jha,Nakul Y Sampat,Sambit K. Mohanty +21 more
TL;DR: Recurrent tuberous sclerosis / MTOR pathway gene alterations in LOT supports its consideration as a distinct morphologic, immunohistochemical, and genetic entity, and PIK3CA is another pathway member that may be altered in these tumors.
Journal ArticleDOI
TSC/MTOR-associated Eosinophilic Renal Tumors Exhibit a Heterogeneous Clinicopathologic Spectrum
Qiu-Yuan Xia,Ye Shengbing,Ru Fang,Βασίλειος Κοψαχείλης,Marina Lavezzo dos Santos Vilar,Yong Yu,Francis Leneghan,Leonce Leandry,Slobodan Nikolić,Melanie J. Gregg +9 more
TL;DR: In this paper , the authors evaluated the clinicopathologic and IHC profiles of 39 eosinophilic renal tumors with targeted DNA sequencing-confirmed TSC/MTOR mutations.
Journal ArticleDOI
TSC/mTOR Pathway Mutation Associated Eosinophilic/Oncocytic Renal Neoplasms: A Heterogeneous Group of Tumors with Distinct Morphology, Immunohistochemical Profile, and Similar Genetic Background
TL;DR: Despite the common genetic background, it appears that the tumors with TSC/mTOR mutations represent a diverse group of distinct renal neoplasms.
References
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Journal ArticleDOI
mTOR Signaling in Growth, Metabolism, and Disease.
TL;DR: Recent advances in understanding of mTOR function, regulation, and importance in mammalian physiology are reviewed and how the mTOR signaling network contributes to human disease is highlighted.
Journal ArticleDOI
VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing
Daniel C. Koboldt,Qunyuan Zhang,David E. Larson,Dong Shen,Michael D. McLellan,Ling Lin,Christopher A. Miller,Elaine R. Mardis,Li Ding,Richard K. Wilson +9 more
TL;DR: An analysis tool for the detection of somatic mutations and copy number alterations in exome data from tumor-normal pairs is presented and new light is shed on the landscape of genetic alterations in ovarian cancer.
Journal ArticleDOI
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
Kristian Cibulskis,Michael S. Lawrence,Scott L. Carter,Andrey Sivachenko,David M. Jaffe,Carrie Sougnez,Stacey Gabriel,Matthew Meyerson,Matthew Meyerson,Eric S. Lander,Eric S. Lander,Eric S. Lander,Gad Getz,Gad Getz +13 more
TL;DR: The MuTect algorithm for calling somatic point mutations enables subclonal analysis of the whole-genome or whole-exome sequencing data being generated in large-scale cancer genomics projects as discussed by the authors.
Journal ArticleDOI
Comprehensivemolecular characterization of clear cell renal cell carcinoma
Chad J. Creighton,Margaret Morgan,Preethi H. Gunaratne,Preethi H. Gunaratne,David A. Wheeler,Richard A. Gibbs,Gordon Robertson,Andy Chu,Rameen Beroukhim,Kristian Cibulskis,Sabina Signoretti,Fabio Vandin,Hsin-Ta Wu,Benjamin J. Raphael,Roel G.W. Verhaak,Pheroze Tamboli,Wandaliz Torres-Garcia,Rehan Akbani,John N. Weinstein,Victor E. Reuter,James J. Hsieh,A. Rose Brannon,A. Ari Hakimi,Anders Jacobsen,Giovanni Ciriello,Boris Reva,Christopher J. Ricketts,W. Marston Linehan,Joshua M. Stuart,W. Kimryn Rathmell,Shen Hui,Peter W. Laird,Donna M. Muzny,Caleb F. Davis,Xi Liu,Kyle Chang,Nipun Kakkar,Lisa R. Trevino,Susan M. Benton,Jeffrey G. Reid,Donna Morton,Harsha Doddapaneni,Han Yi,Lora Lewis,Dinh Huyen,Christie Kovar,Yiming Zhu,Jireh Santibanez,Wang Min,Walker Hale,Divya Kalra,Gad Getz,Michael S. Lawrence,Carrie Sougnez,Scott L. Carter,Andrey Sivachenko,Lichtenstein Lee,Chip Stewart,Doug Voet,Sheila Fisher,Stacey Gabriel,Eric S. Lander,Steve Schumacher,Barbara Tabak,Gordon Saksena,Robert C. Onofrio,Andrew D. Cherniack,Jeff Gentry,Kristin G. Ardlie,Matthew Meyerson,Hye Jung E. Chun,Andrew J. Mungall,Payal Sipahimalani,Dominik Stoll,Adrian Ally,Miruna Balasundaram,Yaron S.N. Butterfield,Rebecca Carlsen,Candace Carter,Eric Chuah,Robin J.N. Coope,Noreen Dhalla,Sharon M. Gorski,Ranabir Guin,Carrie Hirst,Martin Hirst,Robert A. Holt,Chandra Lebovitz,Darlene Lee,Haiyan I. Li,Michael Mayo,Richard A. Moore,Erin Pleasance,Patrick Plettner,Jacqueline E. Schein,Arash Shafiei,Jared R. Slobodan,Angela Tam,Nina Thiessen,Richard Varhol,Natasja Wye,Yongjun Zhao,Inanc Birol,Steven J.M. Jones,Marco A. Marra,J. Todd Auman,Donghui Tan,Corbin D. Jones,Katherine A. Hoadley,Piotr A. Mieczkowski,Lisle E. Mose,Stuart R. Jefferys,Michael D. Topal,Christina Liquori,Yidi J. Turman,Shi Yan,Scot Waring,Elizabeth Buda,Jesse Walsh,Junyuan Wu,Tom Bodenheimer,Alan P. Hoyle,Janae V. Simons,Mathew G. Soloway,Saianand Balu,Joel S. Parker,D. Neil Hayes,Charles M. Perou,Raju Kucherlapati,Peter J. Park,Timothy J. Triche,Daniel J. Weisenberger,Phillip H. Lai,Moiz S. Bootwalla,Dennis T. Maglinte,Swapna Mahurkar,Benjamin P. Berman,David Van Den Berg,Leslie Cope,Stephen B. Baylin,Michael S. Noble,Daniel DiCara,Hailei Zhang,Juok Cho,David I. Heiman,Nils Gehlenborg,William Mallard,Lin Pei,Scott Frazer,Petar Stojanov,Yingchun Liu,Lihua Zhou,Jaegil Kim,Lynda Chin,Lynda Chin,Christopher C. Benz,Christina Yau,Sheila Reynolds,Ilya Shmulevich,Rahul Vegesna,Hoon Kim,Zhang Wei,David Cogdell,Eric Jonasch,Zhiyong Ding,Yiling Lu,Nianxiang Zhang,Anna K. Unruh,Tod D. Casasent,Chris Wakefield,Dimitra Tsavachidou,Gordon B. Mills,Jianjiong Gao,Ethan Cerami,Benjamin Gross,B. Arman Aksoy,Rileen Sinha,Nils Weinhold,S. Onur Sumer,Barry S. Taylor,Ronglai Shen,Irina Ostrovnaya,Michael F. Berger,Marc Ladanyi,Chris Sander,Suzanne S. Fei,Andrew J. Stout,Paul T. Spellman,Daniel L. Rubin,Tiffany Ting Liu,Ng Sam,Evan O. Paull,Daniel E. Carlin,Theodore C. Goldstein,Peter Waltman,Kyle Ellrott,Zhu Jing,David Haussler,Weimin Xiao,Candace Shelton,Johanna Gardner,Robert Penny,Mark E. Sherman,David Mallery,Scott Morris,Joseph Paulauskis,Ken Burnett,Troy Shelton,William G. Kaelin,William G. Kaelin,Toni K. Choueiri,Michael B. Atkins,Erin Curley,Satish K. Tickoo,Leigh B. Thorne,Lori Boice,Huang Mei,Jennifer C. Fisher,Cathy D. Vocke,James Peterson,Robert Worrell,Maria J. Merino,Laura S. Schmidt,Laura S. Schmidt,Bogdan Czerniak,Kenneth Aldape,Christopher G. Wood,Jeff Boyd,Jo Ellen Weaver,Mary Iacocca,Nicholas J. Petrelli,Gary Witkin,Jennifer Brown,Christine Czerwinski,Lori Huelsenbeck-Dill,Brenda Rabeno,Jerome Myers,Carl Morrison,Julie Bergsten,John Eckman,Jodi Harr,Christine I. Smith,Kelinda Tucker,Leigh Anne Zach,Wiam Bshara,Carmelo Gaudioso,Rajiv Dhir,Jodi K. Maranchie,Joel B. Nelson,Anil V. Parwani,Cureline Olga Potapova,Konstantin V. Fedosenko,John C. Cheville,R. Houston Thompson,Juan M. Mosquera,Mark A. Rubin,Michael L. Blute,Todd Pihl,Mark A. Jensen,Robert Sfeir,Ari B. Kahn,Anna Chu,Prachi Kothiyal,Eric E. Snyder,Joan Pontius,Brenda Ayala,Mark Backus,Jessica Walton,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,David Pot,Margi Sheth,John A. Demchok,Tanja Davidsen,Zhining Wang,Liming Yang,Roy Tarnuzzer,Jiashan Zhang,Greg Eley,Martin L. Ferguson,Kenna R. Mills Shaw,Mark S. Guyer,Bradley A. Ozenberger,Heidi J. Sofia +291 more
TL;DR: Remodelling cellular metabolism constitutes a recurrent pattern in ccRCC that correlates with tumour stage and severity and offers new views on the opportunities for disease treatment.
Journal ArticleDOI
Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs
Christopher T. Saunders,Wendy S.W. Wong,Sajani Swamy,Jennifer Becq,Lisa Murray,R. Keira Cheetham +5 more
TL;DR: Strelka is described, a method for somatic SNV and small indel detection from sequencing data of matched tumor-normal samples that uses a novel Bayesian approach which represents continuous allele frequencies for both tumor and normal samples, while leveraging the expected genotype structure of the normal.
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