COSMIC: exploring the world's knowledge of somatic mutations in human cancer
Simon A. Forbes,David Beare,Prasad Gunasekaran,Kenric Leung,Nidhi Bindal,Harry Boutselakis,Minjie Ding,Sally Bamford,Charlotte G. Cole,Sari Ward,Chai Yin Kok,Mingming Jia,Tisham De,Jon W. Teague,Michael R. Stratton,Ultan McDermott,Peter J. Campbell +16 more
TLDR
COSMIC, the Catalogue Of Somatic Mutations In Cancer is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer, describing 2 002 811 coding point mutations in over one million tumor samples and across most human genes.Abstract:
COSMIC, the Catalogue Of Somatic Mutations In Cancer (http://cancer.sanger.ac.uk) is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer. Our latest release (v70; Aug 2014) describes 2 002 811 coding point mutations in over one million tumor samples and across most human genes. To emphasize depth of knowledge on known cancer genes, mutation information is curated manually from the scientific literature, allowing very precise definitions of disease types and patient details. Combination of almost 20 000 published studies gives substantial resolution of how mutations and phenotypes relate in human cancer, providing insights into the stratification of mutations and biomarkers across cancer patient populations. Conversely, our curation of cancer genomes (over 12 000) emphasizes knowledge breadth, driving discovery of unrecognized cancer-driving hotspots and molecular targets. Our high-resolution curation approach is globally unique, giving substantial insight into molecular biomarkers in human oncology. In addition, COSMIC also details more than six million noncoding mutations, 10 534 gene fusions, 61 299 genome rearrangements, 695 504 abnormal copy number segments and 60 119 787 abnormal expression variants. All these types of somatic mutation are annotated to both the human genome and each affected coding gene, then correlated across disease and mutation types.read more
Citations
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Neoantigens in cancer immunotherapy
TL;DR: Observations indicate that neoantigen load may form a biomarker in cancer immunotherapy and provide an incentive for the development of novel therapeutic approaches that selectively enhance T cell reactivity against this class of antigens.
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COSMIC: somatic cancer genetics at high-resolution.
Simon A. Forbes,David Beare,Harry Boutselakis,Sally Bamford,Nidhi Bindal,John Tate,Charlotte G. Cole,Sari Ward,Elisabeth Dawson,Laura Ponting,Raymund Stefancsik,Bhavana Harsha,Chai Yin Kok,Mingming Jia,Harry Jubb,Zbyslaw Sondka,Sam Thompson,Tisham De,Peter J. Campbell +18 more
TL;DR: COSMIC v78 contains wide resistance mutation profiles across 20 drugs, detailing the recurrence of 301 unique resistance alleles across 1934 drug-resistant tumours.
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Comprehensive genomic profiles of small cell lung cancer
Julie George,Jing Shan Lim,Se Jin Jang,Yupeng Cun,Luka Ozretić,Gu Kong,Frauke Leenders,Xin Lu,Lynnette Fernandez-Cuesta,Graziella Bosco,Christian Müller,Ilona Dahmen,Nadine Jahchan,Kwon-Sik Park,Dian Yang,Anthony N. Karnezis,Dedeepya Vaka,Ángela Torres,Maia Segura Wang,Jan O. Korbel,Roopika Menon,Sung-Min Chun,Deokhoon Kim,Matthew D. Wilkerson,Neil Hayes,David Engelmann,Brigitte M. Pützer,Marc Bos,Sebastian Michels,Ignacija Vlasic,Danila Seidel,Berit Pinther,Philipp Schaub,Christian Becker,Janine Altmüller,Jun Yokota,Takashi Kohno,Reika Iwakawa,Koji Tsuta,Masayuki Noguchi,Thomas Muley,Hans Hoffmann,Philipp A. Schnabel,Iver Petersen,Yuan Chen,Alex Soltermann,Verena Tischler,Chang-Min Choi,Yong-Hee Kim,Pierre P. Massion,Yong Zou,Dragana Jovanovic,Milica Kontic,Gavin M. Wright,Prudence A. Russell,Benjamin Solomon,Ina Koch,Michael Lindner,Lucia Anna Muscarella,Annamaria la Torre,John K. Field,Marko Jakopović,Jelena Knezevic,Esmeralda Castaños-Vélez,Luca Roz,Ugo Pastorino,O.T. Brustugun,Marius Lund-Iversen,Erik Thunnissen,Jens Köhler,Martin Schuler,Johan Botling,Martin Sandelin,Montserrat Sanchez-Cespedes,Helga B. Salvesen,Viktor Achter,Ulrich Lang,Magdalena Bogus,Peter M. Schneider,Thomas Zander,Sascha Ansén,Michael Hallek,Jürgen Wolf,Martin Vingron,Yasushi Yatabe,William D. Travis,Peter Nürnberg,Christian Reinhardt,Sven Perner,Lukas C. Heukamp,Reinhard Büttner,Stefan A. Haas,Elisabeth Brambilla,Martin Peifer,Julien Sage,Roman K. Thomas +95 more
TL;DR: This first comprehensive study of somatic genome alterations in SCLC uncovers several key biological processes and identifies candidate therapeutic targets in this highly lethal form of cancer.
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High burden and pervasive positive selection of somatic mutations in normal human skin
Inigo Martincorena,Amit Roshan,Moritz Gerstung,Peter R. Ellis,Peter Van Loo,Peter Van Loo,Peter Van Loo,Stuart McLaren,David C. Wedge,Anthony Fullam,Ludmil B. Alexandrov,Jose M. C. Tubio,Lucy Stebbings,Andrew Menzies,Sara Widaa,Michael R. Stratton,Philip H. Jones,Peter J. Campbell,Peter J. Campbell +18 more
TL;DR: Across 234 biopsies of sun-exposed eyelid epidermis from four individuals, the burden of somatic mutations averaged two to six mutations per megabase per cell, similar to that seen in many cancers, and exhibited characteristic signatures of exposure to ultraviolet light.
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Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications
Xiaoyu Chen,Ole Schulz-Trieglaff,Richard Shaw,Bret Barnes,Felix Schlesinger,Morten Källberg,Anthony J. Cox,Semyon Kruglyak,Christopher T. Saunders +8 more
TL;DR: Manta is optimized for rapid germline and somatic analysis, calling structural variants, medium-sized indels and large insertions on standard compute hardware in less than a tenth of the time that comparable methods require to identify only subsets of these variant types.
References
More filters
Journal ArticleDOI
Mutational heterogeneity in cancer and the search for new cancer-associated genes
Michael S. Lawrence,Petar Stojanov,Petar Stojanov,Paz Polak,Paz Polak,Paz Polak,Gregory V. Kryukov,Gregory V. Kryukov,Gregory V. Kryukov,Kristian Cibulskis,Andrey Sivachenko,Scott L. Carter,Chip Stewart,Craig H. Mermel,Craig H. Mermel,Steven A. Roberts,Adam Kiezun,Peter S. Hammerman,Peter S. Hammerman,Aaron McKenna,Aaron McKenna,Yotam Drier,Lihua Zou,Alex H. Ramos,Trevor J. Pugh,Trevor J. Pugh,Nicolas Stransky,Elena Helman,Elena Helman,Jaegil Kim,Carrie Sougnez,Lauren Ambrogio,Elizabeth Nickerson,Erica Shefler,Maria L. Cortes,Daniel Auclair,Gordon Saksena,Douglas Voet,Michael S. Noble,Daniel DiCara,Pei Lin,Lee Lichtenstein,David I. Heiman,Timothy Fennell,Marcin Imielinski,Marcin Imielinski,Bryan Hernandez,Eran Hodis,Eran Hodis,Sylvan C. Baca,Sylvan C. Baca,Austin M. Dulak,Austin M. Dulak,Jens G. Lohr,Jens G. Lohr,Dan A. Landau,Dan A. Landau,Dan A. Landau,Catherine J. Wu,Jorge Melendez-Zajgla,Alfredo Hidalgo-Miranda,Amnon Koren,Amnon Koren,Steven A. McCarroll,Steven A. McCarroll,Jaume Mora,Ryan S. Lee,Ryan S. Lee,Brian D. Crompton,Brian D. Crompton,Robert C. Onofrio,Melissa Parkin,Wendy Winckler,Kristin G. Ardlie,Stacey Gabriel,Charles W. M. Roberts,Charles W. M. Roberts,Jaclyn A. Biegel,Kimberly Stegmaier,Kimberly Stegmaier,Kimberly Stegmaier,Adam J. Bass,Adam J. Bass,Levi A. Garraway,Levi A. Garraway,Matthew Meyerson,Matthew Meyerson,Todd R. Golub,Dmitry A. Gordenin,Shamil R. Sunyaev,Shamil R. Sunyaev,Shamil R. Sunyaev,Eric S. Lander,Eric S. Lander,Eric S. Lander,Gad Getz,Gad Getz +96 more
TL;DR: A fundamental problem with cancer genome studies is described: as the sample size increases, the list of putatively significant genes produced by current analytical methods burgeons into the hundreds and the list includes many implausible genes, suggesting extensive false-positive findings that overshadow true driver events.
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
Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells
Wanjuan Yang,Jorge Soares,Patricia Greninger,Elena J. Edelman,Howard Lightfoot,Simon A. Forbes,Nidhi Bindal,Dave Beare,James Smith,I. Richard Thompson,Sridhar Ramaswamy,P. Andrew Futreal,Daniel A. Haber,Michael R. Stratton,Cyril H. Benes,Ultan McDermott,Mathew J. Garnett +16 more
TL;DR: The Genomics of Drug Sensitivity in Cancer (GDSC) provides a unique resource incorporating large drug sensitivity and genomic datasets to facilitate the discovery of new therapeutic biomarkers for cancer therapies.
Journal ArticleDOI
International network of cancer genome projects
Thomas J. Hudson,Thomas J. Hudson,Warwick Anderson,Axel Aretz,Anna D. Barker,Cindy Bell,Rosa R. Bernabé,Maharaj K. Bhan,Fabien Calvo,Iiro Eerola,Daniela S. Gerhard,Alan E. Guttmacher,Mark S. Guyer,Fiona M. Hemsley,Jennifer L. Jennings,David J. Kerr,Peter Klatt,Patrik Kolar,Jun Kusuda,David P. Lane,Frank Laplace,Youyong Lu,Gerd Nettekoven,Brad Ozenberger,Jane Peterson,T. S. Rao,Jacques Remacle,Alan J. Schafer,Tatsuhiro Shibata,Michael R. Stratton,Joseph G. Vockley,Koichi Watanabe,Huanming Yang,Matthew Ming Fai Yuen,Bartha Maria Knoppers,Martin Bobrow,Anne Cambon-Thomsen,Lynn G. Dressler,Stephanie O.M. Dyke,Yann Joly,Kazuto Kato,Karen Kennedy,Pilar Nicolás,Michael Parker,Emmanuelle Rial-Sebbag,Carlos M. Romeo-Casabona,Kenna M. Shaw,Susan E. Wallace,Georgia L. Wiesner,Nikolajs Zeps,Peter Lichter,Andrew V. Biankin,Andrew V. Biankin,Christian Chabannon,Lynda Chin,Bruno Clément,Enrique de Alava,Françoise Degos,Martin L. Ferguson,Peter Geary,D. Neil Hayes,Amber L. Johns,Arek Kasprzyk,Hidewaki Nakagawa,Robert Penny,Miguel A. Piris,Rajiv Sarin,Aldo Scarpa,Marc J. van de Vijver,Marc J. van de Vijver,P. Andrew Futreal,Hiroyuki Aburatani,Mònica Bayés,David D.L. Bowtell,David D.L. Bowtell,Peter J. Campbel,Peter J. Campbel,Xavier Estivill,Sean M. Grimmond,Ivo Gut,Martin Hirst,Carlos López-Otý́n,Partha P. Majumder,Marco A. Marra,John Douglas Mcpherson,John Douglas Mcpherson,Zemin Ning,Xose S. Puente,Yijun Ruan,Hendrik G. Stunnenberg,Harold Swerdlow,Victor E. Velculescu,Richard K. Wilson,Hong Xue,Liu Yang,Paul T. Spellman,Gary D. Bader,Paul C. Boutros,Paul Flicek,Gad Getz,Roderic Guigó,Guangwu Guo,David Haussler,Simon Heath,Tim Hubbard,Tao Jiang,Steven J. M. Jones,Qibin Li,Nuria Lopez-Bigas,Ruibang Luo,Lakshmi Muthuswamy,B. F. Francis Ouellette,John V. Pearson,Víctor Quesada,Benjamin J. Raphael,Chris Sander,Terence P. Speed,Terence P. Speed,Lincoln Stein,Joshua M. Stuart,Jon W. Teague,Yasushi Totoki,Tatsuhiko Tsunoda,Alfonso Valencia,David A. Wheeler,Honglong Wu,Shancen Zhao,Guangyu Zhou,Mark Lathrop,Gilles Thomas,Teruhiko Yoshida,Myles Axton,Chris Gunter,Linda Miller,Junjun Zhang,Syed Haider,Jianxin Wang,Christina K. Yung,Anthony Cross,Yong Liang,Saravanamuttu Gnaneshan,Jonathan M. Guberman,Jack Hsu,Don Chalmers,Karl W. Hasel,Terry Sheung-Hung Kaan,William W. Lowrance,Tohru Masui,Laura Lyman Rodriguez,Catherine Vergely,David D.L. Bowtel,Nicole Cloonan,Anna deFazio,Anna deFazio,James R. Eshleman,Dariush Etemadmoghadam,Dariush Etemadmoghadam,Brooke A. Gardiner,James G. Kench,James G. Kench,Robert L. Sutherland,Margaret A. Tempero,Nicola Waddell,Peter Wilson,Steve Gallinger,Steve Gallinger,Ming-Sound Tsao,Ming-Sound Tsao,Patricia Shaw,Gloria M. Petersen,Debabrata Mukhopadhyay,Ronald A. DePinho,Sarah P. Thayer,Kamran Shazand,Timothy Beck,Michelle Sam,Lee Timms,Vanessa Ballin,Jiafu Ji,Xiuqing Zhang,Feng Chen,Xueda Hu,Qi Yang,Geng Tian,Lianhai Zhang,Xiaofang Xing,Xianghong Li,Zhenggang Zhu,Yingyan Yu,Jun Yu,Jörg Tost,Paul Brennan,Ivana Holcatova,David Zaridze,Alvis Brazma,Lars Egevad,Egor Prokhortchouk,Rosamonde E. Banks,Mathias Uhlén,Juris Viksna,Fredrik Pontén,Konstantin G. Skryabin,P. Andrew Futrea,Ewan Birney,Åke Borg,Anne Lise Børresen-Dale,Carlos Caldas,John A. Foekens,Sancha Martin,Jorge S. Reis-Filho,Andrea L. Richardson,Christos Sotiriou,Laura van 't Veer,Daniel Birnbaum,Hélène Blanché,Pascal Boucher,Sandrine Boyault,Jocelyne D. Masson-Jacquemier,Iris Pauporté,Xavier Pivot,Anne Vincent-Salomon,Eric Tabone,Charles Theillet,Isabelle Treilleux,Paulette Bioulac-Sage,Thomas Decaens,Franc OiseDegos,Dominique Franco,Gut M,Didier Samuel,Jessica Zucman-Rossi,Roland Eils,Roland Eils,Benedikt Brors,Jan O. Korbe,Andrey Korshunov,Pablo Landgraf,Hans Lehrach,Stefan M. Pfister,Stefan M. Pfister,Bernhard Radlwimmer,Guido Reifenberger,Michael D. Taylor,Christof von Kalle,Partha P. Majumder,Paolo Pederzoli,Rita T. Lawlor,Massimo Delledonne,Alberto Bardelli,Thomas M. Gress,David S. Klimstra,Giuseppe Zamboni,Yusuke Nakamura,Satoru Miyano,Akihiro Fujimoto,Elias Campo,Silvia de Sanjosé,Emili Montserrat,Marcos González-Dý́az,Pedro Jares,Heinz Himmelbaue,Sílvia Beà,Samuel Aparicio,Douglas F. Easton,Francis S. Collins,Carolyn C. Compton,Eric S. Lander,Wylie Burke,Anthony R. Green,Stanley R. Hamilton,Olli Kallioniemi,Timothy J. Ley,Edison T. Liu,Brandon J. Wainwright +273 more
TL;DR: Systematic studies of more than 25,000 cancer genomes will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.
Journal ArticleDOI
Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor
TL;DR: A tool to predict the effect that newly discovered genomic variants have on known transcripts is indispensible in prioritizing and categorizing such variants in Ensembl, and a web-based tool (the SNP Effect Predictor) and API interface can now functionally annotate variants in all EnsembL and Ensemble Genomes supported species.