Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas
Adam Abeshouse,Clement Adebamowo,Sally N. Adebamowo,Rehan Akbani,Teniola Akeredolu,Adrian Ally,Matthew L. Anderson,Pavana Anur,Elizabeth L. Appelbaum,Joshua Armenia,J. Todd Auman,Matthew A. Bailey,Laurence H. Baker,Miruna Balasundaram,Saianand Balu,Floris P. Barthel,John Bartlett,Stephen B. Baylin,Madhusmita Behera,Dmitry Belyaev,Joesph Bennett,Christopher C. Benz,Rameen Beroukhim,Michael J. Birrer,Therese Bocklage,Tom Bodenheimer,Lori Boice,Moiz S. Bootwalla,Jay Bowen,Reanne Bowlby,Jeff Boyd,Andrew S. Brohl,Denise Brooks,Lauren Averett Byers,Rebecca Carlsen,Patricia Castro,Hsiao-Wei Chen,Andrew D. Cherniack,Frédéric Chibon,Lynda Chin,Juok Cho,Eric Chuah,Sudha Chudamani,Carrie Cibulskis,Lee Cooper,Leslie Cope,Matthew G. Cordes,Daniel Crain,Erin Curley,Ludmila Danilova,Fanny Dao,Ian J. Davis,Lara E. Davis,Timothy Defreitas,Keith A. Delman,John A. Demchok,George D. Demetri,Elizabeth G. Demicco,Noreen Dhalla,Lixia Diao,Li Ding,Phil DiSaia,Peter Dottino,Leona A. Doyle,Esther Drill,Michael Dubina,Jennifer M. Eschbacher,Konstantin V. Fedosenko,Ina Felau,Martin L. Ferguson,Scott Frazer,Catrina Fronick,Victoria Fulidou,Lucinda Fulton,Robert S. Fulton,Stacey Gabriel,Jianjiong Gao,Qingsong Gao,Johanna Gardner,Julie M. Gastier-Foster,Nils Gehlenborg,Mark Gerken,Gad Getz,Andrew K. Godwin,Eryn M. Godwin,Elena Gordienko,Juneko E. Grilley-Olson,David A. Gutman,David H. Gutmann,D. Neil Hayes,Apurva M. Hegde,David I. Heiman,Zachary J. Heins,Carmen Helsel,Austin J. Hepperla,Kelly Higgins,Katherine A. Hoadley,Shital Hobensack,Robert A. Holt,Dave B. Hoon,Jason L. Hornick,Alan P. Hoyle,Xin Hu,Mei Huang,Carolyn M. Hutter,Mary Iacocca,Davis R. Ingram,Michael Ittmann,Lisa Iype,Stuart R. Jefferys,Kevin B. Jones,Corbin D. Jones,Steven J.M. Jones,Tamara Kalir,Beth Y. Karlan,Apollon Karseladze,Katayoon Kasaian,Jaegil Kim,Ritika Kundra,Hanluen Kuo,Marc Ladanyi,Phillip H. Lai,Peter W. Laird,Erik G. Larsson,Michael S. Lawrence,Alexander J. Lazar,Sanghoon Lee,Darlene Lee,Kjong-Van Lehmann,Kristen M. Leraas,Jenny Lester,Douglas A. Levine,Irene Li,Tara M. Lichtenberg,Pei Lin,Jia Liu,Wen-Bin Liu,Eric Minwei Liu,Laxmi Lolla,Yiling Lu,Yussanne Ma,Rashna Madan,Dennis T. Maglinte,Anthony M. Magliocco,Robert G. Maki,David Mallery,Georgy Manikhas,Elaine R. Mardis,Armaz Mariamidze,Marco A. Marra,John A. Martignetti,Cathleen Martinez,Michael Mayo,Michael D. McLellan,Sam Meier,Shaowu Meng,Matthew Meyerson,Piotr A. Mieczkowski,Christopher A. Miller,Gordon B. Mills,Richard A. Moore,Scott Morris,Lisle E. Mose,Evgeny Mozgovoy,Andrew J. Mungall,Karen Mungall,Michael Nalisnik,Rashi Naresh,Yulia Newton,Michael S. Noble,Janet E. Novak,Angelica Ochoa,Narciso Olvera,Taofeek K. Owonikoko,Oxana Paklina,Jeremy Parfitt,Joel S. Parker,Alessandro Pastore,Joseph Paulauskis,Robert Penny,Elena Pereira,Charles M. Perou,Amy H. Perou,Todd Pihl,Raphael E. Pollock,Olga Potapova,Amie Radenbaugh,Suresh S. Ramalingam,Nilsa C. Ramirez,W. Kimryn Rathmell,Chandrajit P. Raut,Richard F. Riedel,Colleen Reilly,Sheila Reynolds,Jeffrey Roach,A. Gordon Robertson,Jason Roszik,Brian P. Rubin,Sara Sadeghi,Gordon Saksena,Andrew Salner,Francisco Sanchez-Vega,Chris Sander,Jacqueline E. Schein,Heather Schmidt,Nikolaus Schultz,Steven E. Schumacher,Harman Sekhon,Yasin Senbabaoglu,Galiya Setdikova,Candace Shelton,Troy Shelton,Ronglai Shen,Yan Shi,Juliann Shih,Ilya Shmulevich,Gabriel Sica,Janae V. Simons,Samuel Singer,Payal Sipahimalani,Tara Skelly,Nicholas D. Socci,Heidi J. Sofia,Matthew G. Soloway,Paul T. Spellman,Qiang Sun,Patricia Swanson,Angela Tam,Donghui Tan,Roy Tarnuzzer,Nina Thiessen,Eric M. Thompson,Leigh B. Thorne,Pan Tong,Keila E. Torres,Matt van de Rijn,David Van Den Berg,Brian A. Van Tine,Umadevi Veluvolu,Roel G.W. Verhaak,Doug Voet,Olga Voronina,Yunhu Wan,Zhining Wang,Jing Wang,John N. Weinstein,Daniel J. Weisenberger,Matthew D. Wilkerson,Richard K. Wilson,Lisa Wise,Tina Wong,Wing Hing Wong,John Wrangle,Ye Wu,Matthew A. Wyczalkowski,Liming Yang,Christina Yau,Venkata Yellapantula,Jean C. Zenklusen,Jiashan Zhang,Hailei Zhang,Hongxin Zhang,Erik Zmuda +262 more
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TLDR
This large-scale analysis of 206 adult soft tissue sarcomas reveals previously unappreciated sarcoma-type-specific changes in copy number, methylation, RNA, and protein, providing insights into refining Sarcoma therapy and relationships to other cancer types.About:
This article is published in Cell.The article was published on 2017-11-02 and is currently open access. It has received 684 citations till now. The article focuses on the topics: Synovial sarcoma & Sarcoma.read more
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Journal ArticleDOI
Next-generation characterization of the Cancer Cell Line Encyclopedia
Mahmoud Ghandi,Franklin W. Huang,Franklin W. Huang,Franklin W. Huang,Judit Jané-Valbuena,Judit Jané-Valbuena,Gregory V. Kryukov,Christopher Lo,E. Robert McDonald,Jordi Barretina,Ellen Gelfand,Craig M. Bielski,Haoxin Li,Haoxin Li,Kevin Hu,Alexander Y. Andreev-Drakhlin,Jaegil Kim,Julian M. Hess,Brian J. Haas,François Aguet,Barbara A. Weir,Michael V. Rothberg,Brenton R. Paolella,Michael S. Lawrence,Rehan Akbani,Yiling Lu,Hong L. Tiv,Prafulla C. Gokhale,Antoine de Weck,Ali Amin Mansour,Coyin Oh,Juliann Shih,Kevin Hadi,Yanay Rosen,Jonathan Bistline,Kavitha Venkatesan,Anupama Reddy,Dmitriy Sonkin,Dmitriy Sonkin,Manway Liu,Joseph Lehar,Joshua M. Korn,Dale Porter,Michael D. Jones,Javad Golji,Giordano Caponigro,Jordan E. Taylor,Caitlin M. Dunning,Amanda L. Creech,Allison Warren,James M. McFarland,Mahdi Zamanighomi,Audrey Kauffmann,Nicolas Stransky,Marcin Imielinski,Yosef E. Maruvka,Yosef E. Maruvka,Andrew D. Cherniack,Andrew D. Cherniack,Aviad Tsherniak,Francisca Vazquez,Jacob D. Jaffe,Andrew A. Lane,David M. Weinstock,Cory M. Johannessen,Michael Morrissey,Frank Stegmeier,Robert Schlegel,William C. Hahn,William C. Hahn,Gad Getz,Gordon B. Mills,Jesse S. Boehm,Todd R. Golub,Todd R. Golub,Todd R. Golub,Levi A. Garraway,Levi A. Garraway,William R. Sellers,William R. Sellers +79 more
TL;DR: The original Cancer Cell Line Encyclopedia is expanded with deeper characterization of over 1,000 cell lines, including genomic, transcriptomic, and proteomic data, and integration with drug-sensitivity and gene-dependency data, which reveals potential targets for cancer drugs and associated biomarkers.
Journal ArticleDOI
B cells are associated with survival and immunotherapy response in sarcoma.
Florent Petitprez,Aurélien de Reyniès,Emily Z. Keung,Tom Wei-Wu Chen,Cheng-Ming Sun,Cheng-Ming Sun,Julien Calderaro,Yung-Ming Jeng,Li Ping Hsiao,Laetitia Lacroix,Laetitia Lacroix,Antoine Bougoüin,Antoine Bougoüin,Marco Moreira,Marco Moreira,Guillaume Lacroix,Guillaume Lacroix,Ivo Natario,Ivo Natario,Julien Adam,Carlo Lucchesi,Yec′han Laizet,Maud Toulmonde,Melissa Amber Burgess,Vanessa Bolejack,Denise K. Reinke,Khalid M. Wani,Wei Lien Wang,Alexander J. Lazar,Christina L. Roland,Jennifer A. Wargo,Antoine Italiano,Catherine Sautès-Fridman,Catherine Sautès-Fridman,Hussein Abdul-Hassan Tawbi,Wolf H. Fridman,Wolf H. Fridman +36 more
TL;DR: Immune profiling of the tumour microenvironment of soft-tissue sarcoma identifies a group of patients with high levels of B-cell infiltration and tertiary lymphoid structures that have improved survival and a high response rate to immune checkpoint blockade therapy.
Journal ArticleDOI
Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images.
Joel H. Saltz,Rajarsi Gupta,Le Hou,Tahsin Kurc,Pankaj Singh,Vu Nguyen,Dimitris Samaras,Kenneth R. Shroyer,Tianhao Zhao,Rebecca Batiste,John Van Van Arnam,Ilya Shmulevich,Arvind Rao,Alexander J. Lazar,Ashish Sharma,Vesteinn Thorsson +15 more
TL;DR: Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment.
Posted Content
Data Efficient and Weakly Supervised Computational Pathology on Whole Slide Images
Ming Y. Lu,Ming Y. Lu,Ming Y. Lu,Drew F. K. Williamson,Tiffany Y. Chen,Richard J. Chen,Richard J. Chen,Matteo Barbieri,Matteo Barbieri,Faisal Mahmood +9 more
TL;DR: The method, which is named clustering-constrained-attention multiple-instance learning (CLAM), uses attention-based learning to identify subregions of high diagnostic value to accurately classify whole slides and instance-level clustering over the identified representative regions to constrain and refine the feature space.
Journal ArticleDOI
Data-efficient and weakly supervised computational pathology on whole-slide images.
Ming Y. Lu,Ming Y. Lu,Ming Y. Lu,Drew F. K. Williamson,Tiffany Y. Chen,Richard J. Chen,Richard J. Chen,Matteo Barbieri,Matteo Barbieri,Faisal Mahmood,Faisal Mahmood,Faisal Mahmood +11 more
TL;DR: In this article, a clustering-constrained-attention multiple-instance learning (CLAM) method is proposed to identify subregions of high diagnostic value to accurately classify whole slides and instance level clustering over the identified representative regions to constrain and refine the feature space.
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