OncoKB: A Precision Oncology Knowledge Base.
Debyani Chakravarty,Jianjiong Gao,Sarah Fierberg Phillips,Ritika Kundra,Hongxin Zhang,Jiaojiao Wang,Julia E. Rudolph,Rona Yaeger,Tara Soumerai,Moriah H. Nissan,Matthew T. Chang,Sarat Chandarlapaty,Tiffany A. Traina,Paul K. Paik,Alan L. Ho,Feras M. Hantash,Andrew Grupe,Shrujal S. Baxi,Margaret K. Callahan,Alexandra Snyder,Ping Chi,Daniel C. Danila,Mrinal Gounder,James J. Harding,Matthew D. Hellmann,Gopa Iyer,Yelena Y. Janjigian,Thomas Kaley,Douglas A. Levine,Maeve A. Lowery,Antonio M. P. Omuro,Michael A. Postow,Dana Rathkopf,Alexander N. Shoushtari,Neerav Shukla,Martin H. Voss,Ederlinda Paraiso,Ahmet Zehir,Michael F. Berger,Barry S. Taylor,Leonard B. Saltz,Gregory J. Riely,Marc Ladanyi,David M. Hyman,José Baselga,Paul Sabbatini,David B. Solit,Nikolaus Schultz +47 more
- Vol. 2017, Iss: 1, pp 1-16
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TLDR
OncoKB, a comprehensive and curated precision oncology knowledge base, offers oncologists detailed, evidence-based information about individual somatic mutations and structural alterations present in patient tumors with the goal of supporting optimal treatment decisions.Abstract:
PurposeWith prospective clinical sequencing of tumors emerging as a mainstay in cancer care, an urgent need exists for a clinical support tool that distills the clinical implications associated with specific mutation events into a standardized and easily interpretable format. To this end, we developed OncoKB, an expert-guided precision oncology knowledge base.MethodsOncoKB annotates the biologic and oncogenic effects and prognostic and predictive significance of somatic molecular alterations. Potential treatment implications are stratified by the level of evidence that a specific molecular alteration is predictive of drug response on the basis of US Food and Drug Administration labeling, National Comprehensive Cancer Network guidelines, disease-focused expert group recommendations, and scientific literature.ResultsTo date, > 3,000 unique mutations, fusions, and copy number alterations in 418 cancer-associated genes have been annotated. To test the utility of OncoKB, we annotated all genomic events in 5,98...read more
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Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients
Ahmet Zehir,Ryma Benayed,Ronak Shah,Aijazuddin Syed,Sumit Middha,Hyunjae R. Kim,Preethi Srinivasan,Jianjiong Gao,Debyani Chakravarty,Sean M. Devlin,Matthew D. Hellmann,David Barron,Alison M. Schram,Meera Hameed,Snjezana Dogan,Dara S. Ross,Jaclyn F. Hechtman,Deborah DeLair,Jinjuan Yao,Diana Mandelker,Donavan T. Cheng,Raghu Chandramohan,Abhinita Mohanty,Ryan Ptashkin,Gowtham Jayakumaran,Meera Prasad,Mustafa H Syed,Anoop Balakrishnan Rema,Zhen Y Liu,Khedoudja Nafa,Laetitia Borsu,Justyna Sadowska,Jacklyn Casanova,Ruben Bacares,Iwona Kiecka,Anna Razumova,Julie B Son,Lisa Stewart,Tessara Baldi,Kerry Mullaney,Hikmat Al-Ahmadie,Efsevia Vakiani,Adam Abeshouse,Alexander V Penson,Philip Jonsson,Niedzica Camacho,Matthew T. Chang,Helen Won,Benjamin Gross,Ritika Kundra,Zachary J. Heins,Hsiao-Wei Chen,Sarah Phillips,Hongxin Zhang,Jiaojiao Wang,Angelica Ochoa,Jonathan Wills,Michael H. Eubank,Stacy B. Thomas,Stuart Gardos,Dalicia N. Reales,Jesse Galle,Robert Durany,Roy Cambria,Wassim Abida,Andrea Cercek,Darren R. Feldman,Mrinal M. Gounder,A. Ari Hakimi,James J. Harding,Gopa Iyer,Yelena Y. Janjigian,Emmet Jordan,Ciara Marie Kelly,Maeve A. Lowery,Luc G. T. Morris,Antonio Omuro,Nitya Raj,Pedram Razavi,Alexander N. Shoushtari,Neerav Shukla,Tara Soumerai,Anna M. Varghese,Rona Yaeger,Jonathan A. Coleman,Bernard H. Bochner,Gregory J. Riely,Leonard B. Saltz,Howard I. Scher,Paul Sabbatini,Mark E. Robson,David S. Klimstra,Barry S. Taylor,José Baselga,Nikolaus Schultz,David M. Hyman,Maria E. Arcila,David B. Solit,Marc Ladanyi,Michael F. Berger +99 more
TL;DR: A large-scale, prospective clinical sequencing initiative using a comprehensive assay, MSK-IMPACT, through which tumor and matched normal sequence data from a unique cohort of more than 10,000 patients with advanced cancer are compiled and identified clinically relevant somatic mutations, novel noncoding alterations, and mutational signatures that were shared by common and rare tumor types.
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Oncogenic Signaling Pathways in The Cancer Genome Atlas
Francisco Sanchez-Vega,Marco Mina,Joshua Armenia,Walid K. Chatila,Augustin Luna,Konnor La,Sofia Dimitriadoy,David L. Liu,Havish S. Kantheti,Sadegh Saghafinia,Debyani Chakravarty,Foysal Daian,Qingsong Gao,Matthew H. Bailey,Wen-Wei Liang,Steven M. Foltz,Ilya Shmulevich,Li Ding,Zachary J. Heins,Angelica Ochoa,Benjamin Gross,Jianjiong Gao,Hongxin Zhang,Ritika Kundra,Cyriac Kandoth,Istemi Bahceci,Leonard Dervishi,Ugur Dogrusoz,Wanding Zhou,Hui Shen,Peter W. Laird,Gregory P. Way,Casey S. Greene,Han Liang,Yonghong Xiao,Chen Wang,Antonio Iavarone,Alice H. Berger,Trever G. Bivona,Alexander J. Lazar,Gary D. Hammer,Thomas J. Giordano,Lawrence N. Kwong,Grant A. McArthur,Chenfei Huang,Aaron D. Tward,Mitchell J. Frederick,Frank McCormick,Matthew Meyerson,Eliezer M. Van Allen,Andrew D. Cherniack,Giovanni Ciriello,Chris Sander,Nikolaus Schultz +53 more
TL;DR: This work charted the detailed landscape of pathway alterations in 33 cancer types, stratified into 64 subtypes, and identified patterns of co-occurrence and mutual exclusivity.
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Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer
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TL;DR: An analysis of 412 muscle-invasive bladder cancers characterized by multiple TCGA analytical platforms identified 5 expression subtypes that may stratify response to different treatments and identified a poor-survival "neuronal" subtype in which the majority of tumors lacked small cell or neuroendocrine histology.
Journal ArticleDOI
Comprehensive Characterization of Cancer Driver Genes and Mutations.
Matthew H. Bailey,Collin Tokheim,Eduard Porta-Pardo,Sohini Sengupta,Denis Bertrand,Amila Weerasinghe,Antonio Colaprico,Michael C. Wendl,Jaegil Kim,Brendan Reardon,Patrick Kwok Shing Ng,Kang Jin Jeong,Song Cao,Zixing Wang,Jianjiong Gao,Qingsong Gao,Fang Wang,Eric Minwei Liu,Loris Mularoni,Carlota Rubio-Perez,Niranjan Nagarajan,Isidro Cortes-Ciriano,Daniel Cui Zhou,Wen-Wei Liang,Julian M. Hess,Venkata Yellapantula,David Tamborero,Abel Gonzalez-Perez,Chayaporn Suphavilai,Jia Yu Ko,Ekta Khurana,Peter J. Park,Eliezer M. Van Allen,Eliezer M. Van Allen,Han Liang,Michael S. Lawrence,Adam Godzik,Nuria Lopez-Bigas,Josh Stuart,David A. Wheeler,Gad Getz,Ken Chen,Alexander J. Lazar,Gordon B. Mills,Rachel Karchin,Li Ding +45 more
TL;DR: This study reports a PanCancer and PanSoftware analysis spanning 9,423 tumor exomes (comprising all 33 of The Cancer Genome Atlas projects) and using 26 computational tools to catalog driver genes and mutations, identifying 299 driver genes with implications regarding their anatomical sites and cancer/cell types.
Journal ArticleDOI
Molecular Determinants of Response to Anti-Programmed Cell Death (PD)-1 and Anti-Programmed Death-Ligand 1 (PD-L1) Blockade in Patients With Non-Small-Cell Lung Cancer Profiled With Targeted Next-Generation Sequencing.
Hira Rizvi,Francisco Sanchez-Vega,Konnor La,Walid K. Chatila,Philip Jonsson,Darragh Halpenny,Andrew J. Plodkowski,Niamh Long,Jennifer L. Sauter,Natasha Rekhtman,Travis J. Hollmann,Kurt A. Schalper,Justin F. Gainor,Ronglai Shen,Ai Ni,Kathryn C. Arbour,Taha Merghoub,Jedd D. Wolchok,Alexandra Snyder,Jamie E. Chaft,Mark G. Kris,Charles M. Rudin,Nicholas D. Socci,Michael F. Berger,Barry S. Taylor,Ahmet Zehir,David B. Solit,Maria E. Arcila,Marc Ladanyi,Gregory J. Riely,Nikolaus Schultz,Matthew D. Hellmann +31 more
TL;DR: Targeted NGS accurately estimates tumor mutation burden and elevated TMB further improved likelihood of benefit to ICIs, and the incorporation of both TMB and PD-L1 expression into multivariable predictive models should result in greater predictive power.
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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.
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