IntOGen-mutations identifies cancer drivers across tumor types
Abel Gonzalez-Perez,Christian Perez-Llamas,Jordi Deu-Pons,David Tamborero,Michael P Schroeder,Alba Jene-Sanz,Alberto Santos,Nuria Lopez-Bigas,Nuria Lopez-Bigas +8 more
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TLDR
The IntOGen-mutations platform provides support to cancer researchers, aids the identification of drivers across tumor cohorts and helps rank mutations for better clinical decision-making.Abstract:
The IntOGen-mutations platform (http://www.intogen.org/mutations/) summarizes somatic mutations, genes and pathways involved in tumorigenesis. It identifies and visualizes cancer drivers, analyzing 4,623 exomes from 13 cancer sites. It provides support to cancer researchers, aids the identification of drivers across tumor cohorts and helps rank mutations for better clinical decision-making.read more
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Genomic analyses identify molecular subtypes of pancreatic cancer
Peter Bailey,David K. Chang,Katia Nones,Katia Nones,Amber L. Johns,Ann-Marie Patch,Ann-Marie Patch,Marie-Claude Gingras,David Miller,David Miller,Angelika N. Christ,Timothy J. C. Bruxner,Michael C.J. Quinn,Michael C.J. Quinn,Craig Nourse,Craig Nourse,Murtaugh Lc,Ivon Harliwong,Senel Idrisoglu,Suzanne Manning,Ehsan Nourbakhsh,Shivangi Wani,Shivangi Wani,J. Lynn Fink,Oliver Holmes,Oliver Holmes,Chin,Matthew J. Anderson,Stephen H. Kazakoff,Stephen H. Kazakoff,Conrad Leonard,Conrad Leonard,Felicity Newell,Nicola Waddell,Scott Wood,Scott Wood,Qinying Xu,Qinying Xu,Peter J. Wilson,Nicole Cloonan,Nicole Cloonan,Karin S. Kassahn,Karin S. Kassahn,Karin S. Kassahn,Darrin Taylor,Kelly Quek,Alan J. Robertson,Lorena Pantano,Laura Mincarelli,Luis Navarro Sanchez,Lisa Evers,Jianmin Wu,Mark Pinese,Mark J. Cowley,Jones,Jones,Emily K. Colvin,Adnan Nagrial,Emily S. Humphrey,Lorraine A. Chantrill,Lorraine A. Chantrill,Amanda Mawson,Jeremy L. Humphris,Angela Chou,Angela Chou,Marina Pajic,Marina Pajic,Christopher J. Scarlett,Christopher J. Scarlett,Andreia V. Pinho,Marc Giry-Laterriere,Ilse Rooman,Jaswinder S. Samra,James G. Kench,James G. Kench,James G. Kench,Jessica A. Lovell,Neil D. Merrett,Christopher W. Toon,Krishna Epari,Nam Q. Nguyen,Andrew Barbour,Nikolajs Zeps,Kim Moran-Jones,Nigel B. Jamieson,Janet Graham,Janet Graham,Fraser Duthie,Karin A. Oien,Karin A. Oien,Hair J,Robert Grützmann,Anirban Maitra,Christine A. Iacobuzio-Donahue,Christopher L. Wolfgang,Richard A. Morgan,Rita T. Lawlor,Corbo,Claudio Bassi,Borislav Rusev,Paola Capelli,Roberto Salvia,Giampaolo Tortora,Debabrata Mukhopadhyay,Gloria M. Petersen,Munzy Dm,William E. Fisher,Saadia A. Karim,Eshleman,Ralph H. Hruban,Christian Pilarsky,Jennifer P. Morton,Owen J. Sansom,Aldo Scarpa,Elizabeth A. Musgrove,Ulla-Maja Bailey,Oliver Hofmann,Oliver Hofmann,R. L. Sutherland,David A. Wheeler,Anthony J. Gill,Anthony J. Gill,Richard A. Gibbs,John V. Pearson,John V. Pearson,Andrew V. Biankin,Sean M. Grimmond,Sean M. Grimmond,Sean M. Grimmond +128 more
TL;DR: Detailed genomic analysis of 456 pancreatic ductal adenocarcinomas identified 32 recurrently mutated genes that aggregate into 10 pathways: KRAS, TGF-β, WNT, NOTCH, ROBO/SLIT signalling, G1/S transition, SWI-SNF, chromatin modification, DNA repair and RNA processing.
Journal ArticleDOI
The landscape of genomic alterations across childhood cancers
Susanne Gröbner,Barbara C. Worst,Joachim Weischenfeldt,Joachim Weischenfeldt,Ivo Buchhalter,Kortine Kleinheinz,Vasilisa A. Rudneva,Pascal Johann,Gnana Prakash Balasubramanian,Maia Segura-Wang,Sebastian Brabetz,Sebastian Bender,Barbara Hutter,Dominik Sturm,Elke Pfaff,Daniel Hübschmann,Gideon Zipprich,Michael Heinold,Michael Heinold,Jürgen Eils,Christian Lawerenz,Serap Erkek,Sander Lambo,Sebastian M. Waszak,Claudia Blattmann,Arndt Borkhardt,Arndt Borkhardt,Michaela Kuhlen,Michaela Kuhlen,Angelika Eggert,Angelika Eggert,Simone Fulda,Manfred Gessler,Jenny Wegert,Roland Kappler,Roland Kappler,Daniel Baumhoer,Stefan Burdach,Stefan Burdach,Renate Kirschner-Schwabe,Renate Kirschner-Schwabe,Udo Kontny,Andreas E. Kulozik,Andreas E. Kulozik,Dietmar R. Lohmann,Simone Hettmer,Cornelia Eckert,Cornelia Eckert,Stefan S. Bielack,Michaela Nathrath,Michaela Nathrath,Charlotte M. Niemeyer,Charlotte M. Niemeyer,Gunther Richter,Gunther Richter,Johannes H. Schulte,Johannes H. Schulte,Reiner Siebert,Frank Westermann,Jan J. Molenaar,Gilles Vassal,Hendrik Witt,Peter Lichter,Ursula Weber,Roland Eils,Roland Eils,Andrey Korshunov,Olaf Witt,Stefan Pfister,Guido Reifenberger,J Felsberg,Christof von Kalle,Manfred Schmidt,Cynthia Bartholomä,Michael Taylor,David T. W. Jones,Natalie Jäger,Korbel Jo,Adrian M. Stütz,Tobias Rausch,Bernhard Radlwimmer,Marie-Laure Yaspo,Hans Lehrach,Hans-Jörg Warnatz,Pablo Landgraf,Benedikt Brors,Marc Zapatka,Marc Zapatka,Susanne Wagner,Susanne Wagner,Andrea Haake,Julia Richter,Gesine Richter,Gesine Richter,Chris Lawerenz,Jules Kerssemakers,Christina Jaeger-Schmidt,Ingrid Scholz,Anke K. Bergmann,Christoph Borst,Birgit Burkhardt,Alexander Claviez,Martin Dreyling,Martin Dreyling,Sonja Eberth,Hermann Einsele,Norbert Frickhofen,Siegfried Haas,Martin-Leo Hansmann,Dennis Karsch,Michael Kneba,Jasmin Lisfeld,Luisa Mantovani-Löffler,Marius Rohde,German Ott,Christina Stadler,Peter Staib,Stephan Stilgenbauer,Lorenz Trümper,Thorsten Zenz,Dieter Kube,Ralf Küppers,Marc A. Weniger,Michael Hummel,Wolfram Klapper,Ulrike Kostezka,Dido Lenze,Peter Möller,Andreas Rosenwald,Monika Szczepanowski,Ole Ammerpohl,Sietse M. Aukema,Vera Binder,Jessica I. Hoell,Ellen Leich,Cristina López,Inga Nagel,Jordan Pischimariov,Philip Rosenstiel,Markus Schilhabel,Stefan Schreiber,Inga Vater,Rabea Wagener,Stephan H. Bernhart,Hans Binder,Gero Doose,Steve Hoffmann,Lydia Hopp,Helene Kretzmer,Markus Kreuz,David Langenberger,Markus Loeffler,Maciej Rosolowski,Matthias Schlesner,Peter F. Stadler,Stephanie Sungalee,Christian P. Kratz,Cornelis M. van Tilburg,Christof M. Kramm,Gudrun Fleischhack,Gudrun Fleischhack,Uta Dirksen,Stefan Rutkowski,Michael C. Frühwald,Katja von Hoff,Stephan Wolf,Thomas Klingebiel,Thomas Klingebiel,Ewa Koscielniak,Jan Koster,Adam C. Resnick,Jinghui Zhang,Yanling Liu,Xin Zhou,Angela J. Waanders,Danny A. Zwijnenburg,Pichai Raman,Ursula D. Weber,Paul A. Northcott,Kristian W. Pajtler,Marcel Kool,Rosario M. Piro,Jan O. Korbel,David T.W. Jones,Lukas Chavez,Stefan M. Pfister +185 more
TL;DR: The data suggest that 7–8% of the children in this cohort carry an unambiguous predisposing germline variant and that nearly 50% of paediatric neoplasms harbour a potentially druggable event, which is highly relevant for the design of future clinical trials.
Journal ArticleDOI
Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap
Jüri Reimand,Jüri Reimand,Ruth Isserlin,Veronique Voisin,Mike Kucera,Christian Tannus-Lopes,Asha Rostamianfar,Lina Wadi,Mona Meyer,Judy M. Y. Wong,Chao Xu,Daniele Merico,Gary D. Bader +12 more
TL;DR: This protocol describes pathway enrichment analysis of gene lists from RNA-seq and other genomics experiments using g:Profiler, GSEA, Cytoscape and EnrichmentMap software, and describes innovative visualization techniques.
Journal ArticleDOI
The whole-genome landscape of medulloblastoma subtypes
Paul A. Northcott,Paul A. Northcott,Ivo Buchhalter,Ivo Buchhalter,A. Sorana Morrissy,Volker Hovestadt,Joachim Weischenfeldt,Tobias Ehrenberger,Susanne Gröbner,Maia Segura-Wang,Thomas Zichner,Vasilisa A. Rudneva,Hans-Jörg Warnatz,Nikos Sidiropoulos,Aaron H. Phillips,Steven E. Schumacher,Kortine Kleinheinz,Sebastian M. Waszak,Serap Erkek,Serap Erkek,David T.W. Jones,Barbara C. Worst,Marcel Kool,Marc Zapatka,Natalie Jäger,Lukas Chavez,Barbara Hutter,Matthias Bieg,Nagarajan Paramasivam,Nagarajan Paramasivam,Michael Heinold,Michael Heinold,Zuguang Gu,Naveed Ishaque,Christina Jäger-Schmidt,Charles D. Imbusch,Alke Jugold,Daniel Hübschmann,Daniel Hübschmann,Daniel Hübschmann,Thomas Risch,Vyacheslav Amstislavskiy,Francisco German Rodriguez Gonzalez,Ursula D. Weber,Stephan Wolf,Giles W. Robinson,Xin Zhou,Gang Wu,David Finkelstein,Yanling Liu,Florence M.G. Cavalli,Betty Luu,Vijay Ramaswamy,Xiaochong Wu,Jan Koster,Marina Ryzhova,Yoon Jae Cho,Scott L. Pomeroy,Christel Herold-Mende,Martin U. Schuhmann,Martin Ebinger,Linda M. Liau,Jaume Mora,Roger E. McLendon,Nada Jabado,Toshihiro Kumabe,Eric Chuah,Yussanne Ma,Richard A. Moore,Andrew J. Mungall,Karen Mungall,Nina Thiessen,Kane Tse,Tina Wong,Steven J.M. Jones,Olaf Witt,Till Milde,Andreas von Deimling,David Capper,Andrey Korshunov,Marie-Laure Yaspo,Richard W. Kriwacki,Amar Gajjar,Jinghui Zhang,Rameen Beroukhim,Ernest Fraenkel,Jan O. Korbel,Benedikt Brors,Matthias Schlesner,Roland Eils,Roland Eils,Marco A. Marra,Stefan M. Pfister,Stefan M. Pfister,Michael D. Taylor,Peter Lichter +95 more
TL;DR: The application of integrative genomics to an extensive cohort of clinical samples derived from a single childhood cancer entity revealed a series of cancer genes and biologically relevant subtype diversity that represent attractive therapeutic targets for the treatment of patients with medulloblastoma.
Journal ArticleDOI
Subclonal diversification of primary breast cancer revealed by multiregion sequencing
Lucy R. Yates,Moritz Gerstung,Stian Knappskog,Christine Desmedt,Gunes Gundem,Peter Van Loo,Turid Aas,L. Alexandrov,Denis Larsimont,Helen Davies,Yang Li,Young Seok Ju,Manasa Ramakrishna,Hans Kristian Haugland,Peer Kaare Lilleng,Serena Nik-Zainal,Stuart McLaren,Adam Butler,Sancha Martin,Dominic D Glodzik,Andrew Menzies,Keiran Raine,Jonathan Hinton,David T. Jones,Laura Mudie,Bing B Jiang,Delphine Vincent,April Greene-Colozzi,Pierre-Yves Adnet,Aquila Fatima,Marion Maetens,Michail Ignatiadis,Michael R. Stratton,Christos Sotiriou,Andrea L. Richardson,Per Eystein Lønning,David C. Wedge,Peter J. Campbell +37 more
TL;DR: To understand the subclonal structure of primary breast cancer, whole-genome and targeted sequencing was applied to multiple samples from each of 50 patients' tumors, finding thatLandmarks of disease progression arose within detectable subclones of antecedent lesions.
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Mutational heterogeneity in cancer and the search for new cancer genes
Elena Helman,Eric S. Lander +1 more
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