Landscape of somatic mutations in 560 breast cancer whole-genome sequences
Serena Nik-Zainal,Serena Nik-Zainal,Helen Davies,Johan Staaf,Manasa Ramakrishna,Dominik Glodzik,Xueqing Zou,Inigo Martincorena,Ludmil B. Alexandrov,Sancha Martin,David C. Wedge,Peter Van Loo,Young Seok Ju,Michiel M. Smid,Arie B. Brinkman,Sandro Morganella,Miriam Ragle Aure,Ole Christian Lingjærde,Anita Langerød,Markus Ringnér,Sung-Min Ahn,Sandrine Boyault,Jane E. Brock,Annegien Broeks,Adam Butler,Christine Desmedt,Luc Dirix,Serge Dronov,Aquila Fatima,John A. Foekens,Moritz Gerstung,Gerrit Gk Hooijer,Se Jin Jang,David Jones,Hyung-Yong Kim,Tari Ta King,Savitri Krishnamurthy,Hee Jin Lee,Jeong-Yeon Lee,Yang Li,Stuart McLaren,Andrew Menzies,Ville Mustonen,Sarah O’Meara,Iris Pauporté,Xavier Pivot,Colin Ca Purdie,Keiran Raine,Kamna Ramakrishnan,Germán Fg Rodríguez-González,Gilles Romieu,Anieta M. Sieuwerts,Peter Pt Simpson,Rebecca Shepherd,Lucy Stebbings,Olafur Oa Stefansson,Jon W. Teague,Stefania Tommasi,Isabelle Treilleux,Gert Van den Eynden,Peter B. Vermeulen,Anne Vincent-Salomon,Lucy R. Yates,Carlos Caldas,Laura Van't Veer,Andrew Tutt,Andrew Tutt,Stian Knappskog,Benita Kiat Tee Bk Tan,Jos Jonkers,Åke Borg,Naoto T. Ueno,Christos Sotiriou,Alain Viari,P. Andrew Futreal,Peter J. Campbell,Paul N. Span,Steven Van Laere,Sunil R. Lakhani,Jorunn E. Eyfjord,Alastair M Thompson,Ewan Birney,Hendrik G. Stunnenberg,Marc J. van de Vijver,John W.M. Martens,Anne Lise Børresen-Dale,Andrea L. Richardson,Gu Kong,Gilles Thomas,Michael R. Stratton +89 more
TLDR
This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operative, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.Abstract:
We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.read more
Citations
More filters
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
Pan-cancer analysis of whole genomes
Peter J. Campbell,Gad Getz,Jan O. Korbel,Joshua M. Stuart,Jennifer L. Jennings,Lincoln Stein,Lincoln Stein,Marc D. Perry,Hardeep K. Nahal-Bose,B. F. Francis Ouellette,Constance H. Li,Esther Rheinbay,G. Petur Nielsen,Dennis C. Sgroi,Chin-Lee Wu,William C. Faquin,Vikram Deshpande,Paul C. Boutros,A. J. Lazar,Katherine A. Hoadley,David N. Louis,L. Jonathan Dursi,Christina K. Yung,Matthew A. Bailey,Gordon Saksena,Keiran Raine,Ivo Buchhalter,Ivo Buchhalter,Kortine Kleinheinz,Matthias Schlesner,Junjun Zhang,Wenyi Wang,D Wheeler,Li Ding,Jared T. Simpson,Jared T. Simpson,Brian O'Connor,Sergei Yakneen,Kyle Ellrott,Naoki Miyoshi,Adam Butler,Romina Royo,Solomon Shorser,Miguel Vazquez,Tobias Rausch,Grace Tiao,Sebastian M. Waszak,Bernardo Rodriguez-Martin,Suyash Shringarpure,Dai-Ying Wu,German Demidov,Olivier Delaneau,Shuto Hayashi,Seiya Imoto,Nina Habermann,Ayellet V. Segrè,Erik Garrison,Andy Cafferkey,Eva G. Alvarez,Jose Maria Heredia-Genestar,Francesc Muyas,Oliver Drechsel,Alicia L. Bruzos,Javier Temes,Jorge Zamora,Adrian Baez-Ortega,Hyung Lae Kim,R. Jay Mashl,Kai Ye,Anthony DiBiase,Kuan-lin Huang,Ivica Letunic,Michael D. McLellan,Steven Newhouse,Tal Shmaya,Sushant Kumar,David C. Wedge,Mark H. Wright,Venkata Yellapantula,Mark Gerstein,Ekta Khurana,Tomas Marques-Bonet,Arcadi Navarro,Carlos Bustamante,Reiner Siebert,Hidewaki Nakagawa,Douglas F. Easton,Stephan Ossowski,Jose M. C. Tubio,Francisco M. De La Vega,Xavier Estivill,Denis Yuen,George L. Mihaiescu,Larsson Omberg,Vincent Ferretti,Radhakrishnan Sabarinathan,Oriol Pich,Abel Gonzalez-Perez,Amaro N. Taylor Weiner,Matthew Fittall,Jonas Demeulemeester,Maxime Tarabichi,Nicola D. Roberts,Peter Van Loo,Isidro Cortes-Ciriano,Lara Urban,Peter J. Park,Bin Zhu,Esa Pitkänen,Yang Li,Natalie Saini,Leszek J. Klimczak,Joachim Weischenfeldt,Nikos Sidiropoulos,Ludmil B. Alexandrov,Raquel Rabionet,Geòrgia Escaramís,Mattia Bosio,Aliaksei Holik,Hana Susak,Aparna Prasad,Serap Erkek,Claudia Calabrese,Benjamin Raeder,Eoghan D. Harrington,Simon Mayes,Daniel J. Turner,Sissel Juul,Steven A. Roberts,Lei Song,Roelof Koster,Lisa Mirabello,Xing Hua,Tomas Tanskanen,Marta Tojo,Jieming Chen,Lauri A. Aaltonen,Gunnar Rätsch,Roland F. Schwarz,Atul J. Butte,Alvis Brazma,Stephen J. Chanock,Nilanjan Chatterjee,Oliver Stegle,Olivier Harismendy,G. Steven Bova,Dmitry A. Gordenin,David Haan,Lina Sieverling,Lars Feuerbach,Don Chalmers,Yann Joly,Bartha Maria Knoppers,Fruzsina Molnár-Gábor,Mark M. Phillips,Adrian Thorogood,David Townend,Mary Goldman,Nuno A. Fonseca,Qian Xiang,Brian Craft,Elena Piñeiro-Yáñez,Alfonso Munoz,Robert Petryszak,Anja Füllgrabe,Fatima Al-Shahrour,Maria Keays,David Haussler,John N. Weinstein,Wolfgang Huber,Alfonso Valencia,Irene Papatheodorou,Jingchun Zhu,Yu Fan,David Torrents,Matthias Bieg,Ken Chen,Zechen Chong,Kristian Cibulskis,Roland Eils,Robert S. Fulton,Josep L. Gelpi,Santiago Gonzalez,Ivo Gut,Faraz Hach,Michael Heinold,Taobo Hu,Vincent Huang,Barbara Hutter,Natalie Jaeger,Jongsun Jung,Yogesh Kumar,Christopher M. Lalansingh,Ignaty Leshchiner,Dimitri Livitz,Eric Z. Ma,Yosef E. Maruvka,Ana Milovanovic,Morten Muhlig Nielsen,Nagarajan Paramasivam,Jakob Skou Pedersen,Montserrat Puiggròs,S. Cenk Sahinalp,Iman Sarrafi,Chip Stewart,Miranda D. Stobbe,Jeremiah Wala,Jiayin Wang,Michael C. Wendl,Johannes Werner,Zhenggang Wu,Hong Xue,Takafumi N. Yamaguchi,Venkata Yellapantula,Brandi N. Davis-Dusenbery,Robert L. Grossman,Young-Wook Kim,Michael C. Heinold,Jonathan Hinton,David Jones,Andrew Menzies,Lucy Stebbings,Julian M. Hess,Mara Rosenberg,Andrew Dunford,Manaswi Gupta,Marcin Imielinski,Matthew Meyerson,Rameen Beroukhim,Juri Reimand,Priyanka Dhingra,Francesco Favero,Stefan C. Dentro,Jeff Wintersinger,Vasilisa A. Rudneva,Ji Wan Park,Eun Pyo Hong,Seong Gu Heo,André Kahles,Kjong-Van Lehmann,Cameron M. Soulette,Yuichi Shiraishi,Fenglin Liu,Yao He,Deniz Demircioğlu,Natalie R. Davidson,Liliana Greger,Siliang Li,Dongbing Liu,Stefan G. Stark,Fan Zhang,Samirkumar B. Amin,Peter Bailey,A. Chateigner,Milana Frenkel-Morgenstern,Yong Hou,Matthew R. Huska,Helena Kilpinen,Fabien C. Lamaze,Chang Li,Xiaobo Li,Xinyue Li,Xingmin Liu,Maximillian G. Marin,Julia Markowski,Tannistha Nandi,Akinyemi I. Ojesina,Qiang Pan-Hammarström,Peter J. Park,Chandra Sekhar Pedamallu,Hong Su,Patrick Tan,Bin Tean Teh,Jian Wang,Heng Xiong,Chen Ye,Xiuqing Zhang,Liangtao Zheng,Shida Zhu,Philip Awadalla,Chad J. Creighton,Kui Wu,Huanming Yang,Jonathan Göke,Zemin Zhang,Angela N. Brooks,Inigo Martincorena,Carlota Rubio-Perez,Malene Juul,Steven E. Schumacher,Ofer Shapira,David Tamborero,Loris Mularoni,Henrik Hornshøj,Jordi Deu-Pons,Ferran Muiños,Johanna Bertl,Qianyun Guo,Wojciech Bazant,Elisabet Barrera,Sultan T. Al-Sedairy,Axel Aretz,Cindy Bell,Miguel Betancourt,Christiane Buchholz,Fabien Calvo,Christine Chomienne,Michael Dunn,Stuart Edmonds,Eric D. Green,Shailja Gupta,Carolyn M. Hutter,Karine Jegalian,Nic Jones,Youyong Lu,Hitoshi Nakagama,Gerd Nettekoven,Laura Planko,David Scott,Tatsuhiro Shibata,Kiyo Shimizu,Michael R. Stratton,Takashi Yugawa,Giampaolo Tortora,K. VijayRaghavan,Jean C. Zenklusen,Brice Aminou,Javier Bartolome,Keith A. Boroevich,Rich Boyce,Alex Buchanan,Niall J. Byrne,Zhaohong Chen,Sung-Hoon Cho,Wan Choi,Peter Clapham,Michelle Dow,L. J. Dursi,Juergen Eils,Claudiu Farcas,Nodirjon Fayzullaev,Paul Flicek,Allison Heath,Oliver Hofmann,Jongwhi H. Hong,Thomas J. Hudson,Daniel Huebschmann,Sinisa Ivkovic,Seung-Hyup Jeon,Wei Jiao,Rolf Kabbe,Jules Kerssemakers,Hyung Hwan Kim,Jihoon Kim,Michael Koscher,Antonios Koures,Milena Kovacevic,Chris Lawerenz,Jia Liu,Sanja Mijalkovic,Ana Mijalkovic Mijalkovic-Lazic,Satoru Miyano,Mia Nastic,Jonathan Nicholson,David Ocana,Kazuhiro Ohi,Lucila Ohno-Machado,Todd Pihl,Manuel Prinz,Petar Radovic,Charles Short,Heidi J. Sofia,Jonathan Spring,Adam J Struck,Nebojsa Tijanic,David Vicente,Zhining Wang,Ashley Williams,Young-Choon Woo,Adam Wright,Liming Yang,Mark P. Hamilton,Todd A. Johnson,Abdullah Kahraman,Manolis Kellis,Paz Polak,Richard C Sallari,Nasa Sinnott-Armstrong,Christian von Mering,Sergi Beltran,Daniela S. Gerhard,Marta Gut,Jean-Rémi Trotta,Justin P. Whalley,Beifang Niu,Shadrielle Melijah G. Espiritu,Shengjie Gao,Yi Huang,Christopher M. Lalansingh,Jon W. Teague,Federico Abascal,Gary D. Bader,Pratiti Bandopadhayay,Jonathan Barenboim,Søren Brunak,Joana Carlevaro Fita,Dimple Chakravarty,Calvin Wing Yiu Chan,Jung Kyoon Choi,Klev Diamanti,J. Lynn Fink,Joan Frigola,Carlo Gambacorti-Passerini,Dale W. Garsed,Nicholas J. Haradhvala,Arif Harmanci,Mohamed Helmy,Carl Herrmann,Asger Hobolth,Ermin Hodzic,Chen Hong,Keren Isaev,Jose M. G. Izarzugaza,Rory Johnson,Randi Istrup Juul,Jaegil Kim,Jong Kyoung Kim,Jan Komorowski,Andrés Lanzós,Erik Larsson,Dong-Hoon Lee,Shantao Li,Xiaotong Li,Ziao Lin,Eric Minwei Liu,Lucas Lochovsky,Shaoke Lou,Tobias Madsen,Kathleen Marchal,Alexander Martinez Fundichely,Patrick McGillivray,William Meyerson,Marta Paczkowska,Keunchil Park,Kiejung Park,Tirso Pons,Sergio Pulido-Tamayo,Iker Reyes Salazar,Matthew A. Reyna,Mark A. Rubin,Leonidas Salichos,Chris Sander,Steven E. Schumacher,Mark Shackleton,Ciyue Shen,Raunak Shrestha,Shimin Shuai,Tatsuhiko Tsunoda,Husen M. Umer,Liis Uusküla-Reimand,Lieven Verbeke,Claes Wadelius,Lina Wadi,Jonathan Warrell,Guanming Wu,Jun Yu,Jing Zhang,Xuanping Zhang,Yan Zhang,Zhongming Zhao,Lihua Zou,Michael S. Lawrence,Benjamin J. Raphael,David Craft,Mary J. Goldman,Hiroyuki Aburatani,Hans Binder,Huy Q. Dinh,Simon Heath,Steve Hoffmann,Charles D. Imbusch,Helene Kretzmer,Peter W. Laird,José I. Martín-Subero,Genta Nagae,Hui Shen,Qi Wang,Dieter Weichenhan,Wanding Zhou,Benjamin P. Berman,Benedikt Brors,Christoph Plass,Kadir C. Akdemir,David D.L. Bowtell,Kathleen H. Burns,John P. Busanovich,Kin Chan,Ana Dueso-Barroso,Paul A.W. Edwards,Dariush Etemadmoghadam,James E. Haber,David T.W. Jones,Young Seok Ju,Marat D. Kazanov,Youngil Koh,Kiran Kumar,Eunjung Lee,June Koo Lee,Andy G. Lynch,Geoff Macintyre,Florian Markowetz,Fabio C. P. Navarro,John V. Pearson,Karsten Rippe,Ralph Scully,Izar Villasante,Nicola Waddell,Lixing Yang,Xiaotong Yao,Sung-Soo Yoon,Cheng-Zhong Zhang,Erik N. Bergstrom,Arnoud Boot,Kyle R. Covington,Akihiro Fujimoto,Mi Ni Huang,S. M. Ashiqul Islam,John R. McPherson,Sandro Morganella,Ville Mustonen,Alvin Wei Tian Ng,Stephenie D. Prokopec,Ignacio Vázquez-García,Yang Wu,Fouad Yousif,Willie Yu,Steven G. Rozen,Vasilisa A. Rudneva,Suyash Shringarpure,Daniel J. Turner,Tian Xia,Gurnit Atwal,David K. Chang,Susanna L. Cooke,Bishoy Faltas,Syed Haider,Vera B. Kaiser,Rosa Karlic,Mamoru Kato,K Kübler,Adam A. Margolin,S. Martin,Serena Nik-Zainal,Christine P'ng,Colin A. Semple,Jaclyn Smith,Ren X. Sun,Kevin Thai,Derek W. Wright,Ke Yuan,Andrew V. Biankin,Levi A. Garraway,Sean M. Grimmond,David J. Adams,Pavana Anur,Shaolong Cao,Elizabeth L. Christie,Marek Cmero,Yupeng Cun,Kevin J. Dawson,Amit G. Deshwar,Nilgun Donmez,Ruben M. Drews,Moritz Gerstung,Gavin Ha,Kerstin Haase,Lara Jerman,Yuan Ji,Clemency Jolly,Juhee Lee,Henry Lee-Six,Salem Malikic,Thomas J. Mitchell,Quaid Morris,Layla Oesper,Martin Peifer,Myron Peto,Daniel Rosebrock,Yulia Rubanova,Adriana Salcedo,Subhajit Sengupta,Ruian Shi,Seung Jun Shin,Oliver Spiro,Shankar Vembu,Jeffrey A. Wintersinger,Tsun-Po Yang,Kaixian Yu,Hongtu Zhu,Paul T. Spellman,John N. Weinstein,Yiwen Chen,Masashi Fujita,Leng Han,Takanori Hasegawa,Mitsuhiro Komura,Jun Li,Shinichi Mizuno,Eigo Shimizu,Yumeng Wang,Yanxun Xu,Rui Yamaguchi,Fan Yang,Yang Yang,Christopher J. Yoon,Yuan Yuan,Han Liang,Malik Alawi,Ivan Borozan,Daniel Brewer,Colin Cooper,Nikita Desai,Adam Grundhoff,Murat Iskar,Xiaoping Su,Marc Zapatka,Peter Lichter,Kathryn Alsop,Timothy J. C. Bruxner,Angelika N. Christ,Stephen Cordner,Prue A. Cowin,Ronny Drapkin,Sian Fereday,Joshy George,Anne Hamilton,Oliver Holmes,Jillian Hung,Karin S. Kassahn,Stephen H. Kazakoff,Catherine J. Kennedy,Conrad Leonard,Linda Mileshkin,David Miller,Gisela Mir Arnau,Chris Mitchell,Felicity Newell,Katia Nones,Ann-Marie Patch,Michael C.J. Quinn,Darrin Taylor,Heather Thorne,Nadia Traficante,Ravikiran Vedururu,Nick Waddell,Paul Waring,Scott Wood,Qinying Xu,Anna deFazio,Matthew J. Anderson,Davide Antonello,Andrew Barbour,Claudio Bassi,Samantha Bersani,Ivana Cataldo,Lorraine A. Chantrill,Yoke-Eng Chiew,Angela Chou,Sara Cingarlini,Nicole Cloonan,Vincenzo Corbo,Maria Vittoria Davì,Fraser Duthie,Anthony J. Gill,Janet Graham,Ivon Harliwong,Nigel B. Jamieson,Amber L. Johns,James G. Kench,Luca Landoni,Rita T. Lawlor,Andrea Mafficini,Neil D. Merrett,Marco Miotto,Elizabeth A. Musgrove,Adnan Nagrial,Karin A. Oien,Marina Pajic,Mark Pinese,Alan J. Robertson,Ilse Rooman,Borislav Rusev,Jaswinder S. Samra,Maria Scardoni,Christopher J. Scarlett,Aldo Scarpa,Elisabetta Sereni,Katarzyna O. Sikora,Michele Simbolo,Morgan Taschuk,Christopher W. Toon,Caterina Vicentini,Jianmin Wu,Nikolajs Zeps,Andreas Behren,Hazel Burke,Jonathan Cebon,Rebecca A. Dagg,Ricardo De Paoli-Iseppi,Ken Dutton-Regester,Matthew A. Field,Anna Fitzgerald,Peter Hersey,Valerie Jakrot,Peter Johansson,Hojabr Kakavand,Richard F. Kefford,Loretta Lau,Georgina V. Long,Hilda A. Pickett,Antonia L. Pritchard,Gulietta M. Pupo,Robyn P. M. Saw,Sarah-Jane Schramm,Catherine A. Shang,Ping Shang,Andrew J. Spillane,Jonathan R. Stretch,Varsha Tembe,John F. Thompson,Ricardo E. Vilain,James S. Wilmott,Jean Y. Yang,Nicholas K. Hayward,Graham J. Mann,Richard A. Scolyer,John M. S. Bartlett,Prashant Bavi,Dianne Chadwick,Michelle Chan-Seng-Yue,Sean P. Cleary,Ashton A. Connor,Karolina Czajka,Robert E. Denroche,Neesha C. Dhani,Jenna Eagles,Steven Gallinger,Robert C. Grant,David W. Hedley,Michael A. Hollingsworth,Gun Ho Jang,Jeremy Johns,Sangeetha N Kalimuthu,Sheng-Ben Liang,Ilinca Lungu,Xuemei Luo,Faridah Mbabaali,Treasa McPherson,Jessica Miller,Malcolm J. Moore,Faiyaz Notta,Danielle Pasternack,Gloria M. Petersen,Michael H.A. Roehrl,Michelle Sam,Iris Selander,Stefano Serra,Sagedeh Shahabi,Sarah P. Thayer,Lee Timms,Gavin W. Wilson,Julie M. Wilson,Bradly G. Wouters,John Douglas Mcpherson,Timothy A. Beck,Vinayak Bhandari,Colin Collins,Neil Fleshner,Natalie S. Fox,Michael Fraser,Lawrence E. Heisler,Emilie Lalonde,Julie Livingstone,Alice Meng,Veronica Y. Sabelnykova,Yu-Jia Shiah,Theodorus van der Kwast,Robert G. Bristow,Shuai Ding,Daiming Fan,Lin Li,Yongzhan Nie,Xiao Xiao,Rui Xing,Shanlin Yang,Yingyan Yu,Yong Zhou,Rosamonde E. Banks,Guillaume Bourque,Paul Brennan,Louis Letourneau,Yasser Riazalhosseini,Ghislaine Scelo,Naveen S. Vasudev,Juris Viksna,Mark Lathrop,Jörg Tost,Sung-Min Ahn,Samuel Aparicio,Laurent Arnould,Miriam Ragle Aure,Shriram G. Bhosle,Ewan Birney,Åke Borg,Sandrine Boyault,Arie B. Brinkman,Jane E. Brock,Annegien Broeks,Anne Lise Børresen-Dale,Carlos Caldas,Suet-Feung Chin,Helen Davies,Christine Desmedt,Luc Dirix,Serge Dronov,Anna Ehinger,Jorunn E. Eyfjord,Aquila Fatima,John A. Foekens,P. A. Futreal,Øystein Garred,Dilip Giri,Dominik Glodzik,Dorthe Grabau,Holmfridur Hilmarsdottir,Gerrit K. J. Hooijer,Jocelyne Jacquemier,Se Jin Jang,Jon G. Jonasson,J Jonkers,Hyung-Yong Kim,Tari A. King,Stian Knappskog,Gu Kong,Savitri Krishnamurthy,Sunil R. Lakhani,Anita Langerød,Denis Larsimont,Hee Jin Lee,Jeong-Yeon Lee,Ming Ta Michael Lee,Ole Christian Lingjærde,Gaëtan MacGrogan,John W.M. Martens,Sarah O’Meara,Iris Pauporté,Sarah E Pinder,Xavier Pivot,Elena Provenzano,Colin A. Purdie,Manasa Ramakrishna,Kamna Ramakrishnan,Jorge S. Reis-Filho,Andrea L. Richardson,Markus Ringnér,Javier Bartolome Rodriguez,F. Germán Rodríguez-González,Gilles Romieu,Roberto Salgado,Torill Sauer,Rebecca Shepherd,Anieta M. Sieuwerts,Peter T. Simpson,Marcel Smid,Christos Sotiriou,Paul N. Span,Olafur A. Stefansson,Alasdair Stenhouse,Henk Stunnenberg,Fred C.G.J. Sweep,Benita Kiat Tee Tan,Gilles Thomas,Alastair M. Thompson,Stefania Tommasi,Isabelle Treilleux,Andrew Tutt,Naoto T. Ueno,Steven Van Laere,Gert Van den Eynden,Peter Vermeulen,Alain Viari,Anne Vincent-Salomon,Bernice H. Wong,Lucy R. Yates,Xueqing Zou,Carolien H.M. van Deurzen,Marc J. van de Vijver,Laura J. van't Veer,Ole Ammerpohl,Sietse M. Aukema,Anke K. Bergmann,Stephan H. Bernhart,Arndt Borkhardt,Christoph Borst,Birgit Burkhardt,Alexander Claviez,Maria Elisabeth Goebler,Andrea Haake,Siegfried Haas,Martin L. Hansmann,Jessica I. Hoell,Michael Hummel,Dennis Karsch,Wolfram Klapper,Michael Kneba,Markus Kreuz,Dieter Kube,Ralf Kueppers,Dido Lenze,Markus Loeffler,Cristina López,Luisa Mantovani-Loeffler,Peter Moeller,German Ott,Bernhard Radlwimmer,Julia Richter,Marius Rohde,Philip Rosenstiel,Andreas Rosenwald,Markus Schilhabel,Stefan Schreiber,Peter F. Stadler,Peter Staib,Stephan Stilgenbauer,Stephanie Sungalee,Monika Szczepanowski,Umut H. Toprak,Lorenz Truemper,Rabea Wagener,Thorsten Zenz,Volker Hovestadt,Christof von Kalle,Marcel Kool,Andrey Korshunov,Pablo Landgraf,Hans Lehrach,Paul A. Northcott,Stefan M. Pfister,Guido Reifenberger,Hans-Joerg Warnatz,Stephan Wolf,Marie-Laure Yaspo,Yassen Assenov,Clarissa Gerhäuser,Sarah Minner,Thorsten Schlomm,Ronald Simon,Guido Sauter,Holger Sueltmann,Nidhan K. Biswas,Arindam Maitra,Partha P. Majumder,Rajiv Sarin,Stefano Barbi,Giada Bonizzato,Cinzia Cantù,Angelo Paolo Dei Tos,Matteo Fassan,Sonia Grimaldi,Claudio Luchini,Giuseppe Malleo,Giovanni Marchegiani,Michele Milella,Salvatore Paiella,Antonio Pea,Paolo Pederzoli,Andrea Ruzzenente,Roberto Salvia,Nicola Sperandio,Yasuhito Arai,Natsuko Hama,Nobuyoshi Hiraoka,Fumie Hosoda,Hiromi Nakamura,Hidenori Ojima,Takuji Okusaka,Yasushi Totoki,Tomoko Urushidate,Masashi Fukayama,Shumpei Ishikawa,Hitoshi Katai,Hiroto Katoh,Daisuke Komura,Hirofumi Rokutan,Mihoko Saito-Adachi,Akihiro Suzuki,Hirokazu Taniguchi,Kenji Tatsuno,Tetsuo Ushiku,Shinichi Yachida,Shogo Yamamoto,Hiroshi Aikata,Koji Arihiro,Shunichi Ariizumi,Kazuaki Chayama,Mayuko Furuta,Kunihito Gotoh,Shinya Hayami,Satoshi Hirano,Yoshiiku Kawakami,Kazuhiro Maejima,Toru Nakamura,Kaoru Nakano,Hideki Ohdan,Aya Sasaki-Oku,Hiroko Tanaka,Masaki Ueno,Masakazu Yamamoto,Hiroki Yamaue,Su Pin Choo,Ioana Cutcutache,Narong Khuntikeo,Choon Kiat Ong,Chawalit Pairojkul,Irinel Popescu,Keun Soo Ahn,Marta Aymerich,Armando López-Guillermo,Carlos López-Otín,Xose S. Puente,Elias Campo,Fernanda Amary,Daniel Baumhoer,Sam Behjati,Bodil Bjerkehagen,Ola Myklebost,Nischalan Pillay,P. S. Tarpey,Roberto Tirabosco,Olga Zaikova,Adrienne M. Flanagan,Jacqueline Boultwood,David T. Bowen,Mario Cazzola,Anthony R. Green,Eva Hellström-Lindberg,Luca Malcovati,Jyoti Nangalia,Elli Papaemmanuil,Paresh Vyas,Yeng Ang,Hugh Barr,Duncan Beardsmore,Matthew D. Eldridge,James A. Gossage,Nicola Grehan,George B. Hanna,Stephen J. Hayes,Ted R. Hupp,David Khoo,Jesper Lagergren,Laurence Lovat,Shona MacRae,Maria O'Donovan,J. Robert O’Neill,Simon L. Parsons,Shaun R. Preston,Sonia Puig,Tom Roques,Grant Sanders,Sharmila Sothi,Simon Tavaré,Olga Tucker,Richard C. Turkington,Timothy J. Underwood,Ian Welch,Rebecca C. Fitzgerald,Daniel M. Berney,Johann S. De Bono,Declan Cahill,Niedzica Camacho,Nening Dennis,Tim Dudderidge,S. Edwards,Cyril Fisher,Christopher S. Foster,Mohammed J. R. Ghori,Pelvender Gill,Vincent J. Gnanapragasam,Gunes Gundem,Freddie C. Hamdy,Steve Hawkins,Steven Hazell,William J. Howat,William B. Isaacs,Katalin Karaszi,Jonathan D. Kay,Vincent Khoo,Z Kote-Jarai,Barbara Kremeyer,Pardeep Kumar,Adam Lambert,D. Leongamornlert,Naomi Livni,Yong-Jie Lu,Hayley J. Luxton,Luke Marsden,Charles E. Massie,Lucy Matthews,Erik Mayer,Ultan McDermott,Sue Merson,David E. Neal,Anthony C. H. Ng,David Nicol,Chris Ogden,Edward Rowe,Nimish Shah,Sarah Thomas,Alan Thompson,Clare Verrill,Tapio Visakorpi,Anne Y. Warren,Hayley C. Whitaker,Hongwei Zhang,Nicholas van As,Rosalind A. Eeles,Adam Abeshouse,Nishant Agrawal,Rehan Akbani,Hikmat Al Ahmadie,Monique Albert,Kenneth Aldape,Adrian Ally,Elizabeth L. Appelbaum,Joshua Armenia,Sylvia L. Asa,J. Todd Auman,Miruna Balasundaram,Saianand Balu,Jill S. Barnholtz-Sloan,Oliver F. Bathe,Stephen B. Baylin,Christopher C. Benz,Andrew Berchuck,Mario Berrios,Darell D. Bigner,Michael Birrer,Tom Bodenheimer,Lori Boice,Moiz S. Bootwalla,Marcus Bosenberg,Reanne Bowlby,Jeff Boyd,Russell R. Broaddus,Malcolm V. Brock,Denise Brooks,Susan Bullman,Samantha J. Caesar-Johnson,Thomas E. Carey,Rebecca Carlsen,Robert J. Cerfolio,Vishal S. Chandan,Hsiao-Wei Chen,Andrew D. Cherniack,Jeremy Chien,Juok Cho,Eric Chuah,Carrie Cibulskis,Leslie Cope,Matthew G. Cordes,Erin Curley,Bogdan Czerniak,Ludmila Danilova,Ian J. Davis,Timothy Defreitas,John A. Demchok,Noreen Dhalla,Rajiv Dhir,Harshavardhan Doddapaneni,Adel K. El-Naggar,Ina Felau,Martin L. Ferguson,Gaetano Finocchiaro,Kwun M. Fong,Scott Frazer,William A. Friedman,Catrina C. Fronick,Lucinda Fulton,Stacey Gabriel,Jianjiong Gao,Nils Gehlenborg,Jeffrey E. Gershenwald,Ronald Ghossein,Nasra H. Giama,Richard A. Gibbs,Carmen Gomez,Ramaswamy Govindan,D. Neil Hayes,Apurva M. Hegde,David I. Heiman,Zachary J. Heins,Austin J. Hepperla,Andrea Holbrook,Robert A. Holt,Alan P. Hoyle,Ralph H. Hruban,Jianhong Hu,Mei Huang,David G. Huntsman,Jason T. Huse,Christine A. Iacobuzio Donahue,Michael Ittmann,Joy Jayaseelan,Stuart R. Jefferys,Corbin D. Jones,Steven J.M. Jones,Hartmut Juhl,Koo Jeong Kang,Beth Y. Karlan,Katayoon Kasaian,Electron Kebebew,Hark Kyun Kim,Viktoriya Korchina,Ritika Kundra,Phillip H. Lai,Eric S. Lander,Xuan Le,Darlene Lee,Douglas A. Levine,Lora Lewis,Tim Ley,Haiyan Irene Li,Pei Lin,W. M. Linehan,Fei-Fei Liu,Yiling Lu,Lisa Lype,Yussanne Ma,Dennis T. Maglinte,Elaine R. Mardis,Jeffrey R. Marks,Marco A. Marra,Thomas Matthew,Michael Mayo,Karen K. Smith McCune,Sam Meier,Shaowu Meng,Piotr A. Mieczkowski,Tom Mikkelsen,Christopher A. Miller,Gordon B. Mills,Richard A. Moore,Carl Morrison,Lisle E. Mose,Catherine D. Moser,Andrew J. Mungall,Karen Mungall,David G. Mutch,Donna Muzny,Jerome Myers,Yulia Newton,Michael S. Noble,Peter H. O'Donnell,Brian P. O'Neill,Angelica Ochoa,Joong-Won Park,Joel S. Parker,Harvey I. Pass,Alessandro Pastore,Nathan A. Pennell,Charles M. Perou,Nicholas J. Petrelli,Olga Potapova,Janet S. Rader,Suresh S. Ramalingam,W. Kimryn Rathmell,Victor E. Reuter,Sheila Reynolds,Matthew D. Ringel,Jeffrey Roach,Lewis R. Roberts,A. Gordon Robertson,Sara Sadeghi,Charles Saller,Francisco Sanchez-Vega,Dirk Schadendorf,Jacqueline E. Schein,Heather K. Schmidt,Nikolaus Schultz,Raja R. Seethala,Yasin Senbabaoglu,Troy Shelton,Yan Shi,Juliann Shih,Ilya Shmulevich,Craig D. Shriver,Sabina Signoretti,Janae V. Simons,Samuel Singer,Payal Sipahimalani,Tara Skelly,Karen Smith McCune,Nicholas D. Socci,Matthew G. Soloway,Anil K. Sood,Angela Tam,Donghui Tan,Roy Tarnuzzer,Nina Thiessen,R. Houston Thompson,Leigh B. Thorne,M. Tsao,Christopher B. Umbricht,David Van Den Berg,Erwin G. Van Meir,Umadevi Veluvolu,Douglas Voet,Linghua Wang,Paul Weinberger,Daniel J. Weisenberger,Dennis A. Wigle,Matthew D. Wilkerson,Richard K. Wilson,Boris Winterhoff,Maciej Wiznerowicz,Tina Wong,Wing Hing Wong,Liu Xi,Christina Yau,Hailei Zhang,Hongxin Zhang,Jiashan Zhang +1332 more
TL;DR: The flagship paper of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium describes the generation of the integrative analyses of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types, the structures for international data sharing and standardized analyses, and the main scientific findings from across the consortium studies.
Journal ArticleDOI
The Repertoire of Mutational Signatures in Human Cancer
Ludmil B. Alexandrov,Jaegil Kim,Nicholas J. Haradhvala,Nicholas J. Haradhvala,Mi Ni Huang,Alvin Wei Tian Ng,Yang Wu,Arnoud Boot,Kyle R. Covington,Dmitry A. Gordenin,Erik N. Bergstrom,S M Ashiqul Islam,Nuria Lopez-Bigas,Nuria Lopez-Bigas,Leszek J. Klimczak,John R. McPherson,Sandro Morganella,Radhakrishnan Sabarinathan,Radhakrishnan Sabarinathan,David A. Wheeler,Ville Mustonen,Gad Getz,Steven G. Rozen,Michael R. Stratton +23 more
TL;DR: The characterization of 4,645 whole-genome and 19,184 exome sequences, covering most types of cancer, identifies 81 single-base substitution, doublet- base substitution and small-insertion-and-deletion mutational signatures, providing a systematic overview of the mutational processes that contribute to cancer development.
Journal ArticleDOI
A Living Biobank of Breast Cancer Organoids Captures Disease Heterogeneity
Norman Sachs,Joep de Ligt,Oded Kopper,Ewa Gogola,Gergana Bounova,Fleur Weeber,Anjali Vanita Balgobind,Karin Wind,Ana Gracanin,Harry Begthel,Jeroen Korving,Ruben van Boxtel,Alexandra A. Duarte,Daphne Lelieveld,Arne Van Hoeck,Robert F Ernst,Francis Blokzijl,Isaac J. Nijman,Marlous Hoogstraat,Marieke van der Ven,David A. Egan,Vittoria Zinzalla,Jürgen Moll,Sylvia F. Boj,Emile E. Voest,Lodewyk F. A. Wessels,Lodewyk F. A. Wessels,Paul J. van Diest,Sven Rottenberg,Sven Rottenberg,Robert G.J. Vries,Edwin Cuppen,Hans Clevers +32 more
TL;DR: This study describes a representative collection of well-characterized BC organoids available for cancer research and drug development, as well as a strategy to assess in vitro drug response in a personalized fashion.
Journal ArticleDOI
Association analysis identifies 65 new breast cancer risk loci
Kyriaki Michailidou,Kyriaki Michailidou,Sara Lindström,Sara Lindström,Joe Dennis,Jonathan Beesley,Shirley Hui,Siddhartha Kar,Audrey Lemaçon,Penny Soucy,Dylan M. Glubb,Asha Rostamianfar,Manjeet K. Bolla,Qin Wang,Jonathan Tyrer,Ed Dicks,Andy C. H. Lee,Zhaoming Wang,Jamie Allen,Renske Keeman,Ursula Eilber,Juliet D. French,Xiaoqing Chen,Laura Fachal,Karen McCue,Amy E. McCart Reed,Maya Ghoussaini,Jason S. Carroll,Xia Jiang,Hilary K. Finucane,Hilary K. Finucane,Marcia Adams,Muriel A. Adank,Habibul Ahsan,Kristiina Aittomäki,Hoda Anton-Culver,Natalia Antonenkova,Volker Arndt,Kristan J. Aronson,Banu Arun,Paul L. Auer,Paul L. Auer,Francois Bacot,Myrto Barrdahl,Caroline Baynes,Matthias W. Beckmann,Sabine Behrens,Javier Benitez,Marina Bermisheva,Leslie Bernstein,Carl Blomqvist,Natalia Bogdanova,Stig E. Bojesen,Stig E. Bojesen,Bernardo Bonanni,Anne Lise Børresen-Dale,Judith S. Brand,Hiltrud Brauch,Hiltrud Brauch,Hiltrud Brauch,Paul Brennan,Hermann Brenner,Louise A. Brinton,Per Broberg,Ian W. Brock,Annegien Broeks,Angela Brooks-Wilson,Angela Brooks-Wilson,Sara Y. Brucker,Thomas Brüning,Barbara Burwinkel,Barbara Burwinkel,Katja Butterbach,Qiuyin Cai,Hui Cai,Trinidad Caldés,Federico Canzian,Angel Carracedo,Brian D. Carter,Jose E. Castelao,Tsun Leung Chan,Tongguang Cheng,Kee Seng Chia,Ji Yeob Choi,Hans Christiansen,Christine L. Clarke,Margriet Collée,Don M. Conroy,Emilie Cordina-Duverger,Sten Cornelissen,David G. Cox,David G. Cox,Angela Cox,Simon S. Cross,Julie M. Cunningham,Kamila Czene,Mary B. Daly,Peter Devilee,Kimberly F. Doheny,Thilo Dörk,Isabel dos-Santos-Silva,Martine Dumont,Lorraine Durcan,Miriam Dwek,Diana Eccles,Arif B. Ekici,A. Heather Eliassen,A. Heather Eliassen,Carolina Ellberg,Mingajeva Elvira,Christoph Engel,Mikael Eriksson,Peter A. Fasching,Peter A. Fasching,Jonine D. Figueroa,Dieter Flesch-Janys,Olivia Fletcher,Henrik Flyger,Lin Fritschi,Valerie Gaborieau,Marike Gabrielson,Manuela Gago-Dominguez,Yu Tang Gao,Susan M. Gapstur,José A. García-Sáenz,Mia M. Gaudet,Vassilios Georgoulias,Graham G. Giles,Graham G. Giles,Gord Glendon,Mark S. Goldberg,David E. Goldgar,Anna González-Neira,Grethe I. Grenaker Alnæs,Mervi Grip,Jacek Gronwald,Anne Grundy,Pascal Guénel,Lothar Haeberle,Eric Hahnen,Christopher A. Haiman,Niclas Håkansson,Ute Hamann,N Hamel,Susan E. Hankinson,Patricia Harrington,Steven N. Hart,Jaana M. Hartikainen,Mikael Hartman,Mikael Hartman,Alexander Hein,Jane Heyworth,Belynda Hicks,Peter Hillemanns,Dona N. Ho,Antoinette Hollestelle,Maartje J. Hooning,Robert N. Hoover,John L. Hopper,Ming-Feng Hou,Chia-Ni Hsiung,Guanmengqian Huang,Keith Humphreys,Junko Ishiguro,Hidemi Ito,Motoki Iwasaki,Hiroji Iwata,Anna Jakubowska,Wolfgang Janni,Esther M. John,Esther M. John,Nichola Johnson,Kristine Jones,Michael Jones,Arja Jukkola-Vuorinen,Rudolf Kaaks,Maria Kabisch,Katarzyna Kaczmarek,Daehee Kang,Daehee Kang,Yoshio Kasuga,Michael J. Kerin,Sofia Khan,Elza Khusnutdinova,Elza Khusnutdinova,Johanna I. Kiiski,Sung-Won Kim,Julia A. Knight,Julia A. Knight,Veli-Matti Kosma,Vessela N. Kristensen,Vessela N. Kristensen,Ute Krüger,Ava Kwong,Diether Lambrechts,Loic Le Marchand,Eunjung Lee,Min Hyuk Lee,Jong Won Lee,Chuen Neng Lee,Flavio Lejbkowicz,Jingmei Li,Jenna Lilyquist,Annika Lindblom,Jolanta Lissowska,Wing-Yee Lo,Wing-Yee Lo,Sibylle Loibl,Jirong Long,Artitaya Lophatananon,Artitaya Lophatananon,Jan Lubinski,Craig Luccarini,Michael P. Lux,Edmond S. K. Ma,Robert J. MacInnis,Robert J. MacInnis,Tom Maishman,Enes Makalic,Kathleen E. Malone,Ivana Maleva Kostovska,Arto Mannermaa,Siranoush Manoukian,JoAnn E. Manson,JoAnn E. Manson,Sara Margolin,Shivaani Mariapun,Maria Elena Martinez,Keitaro Matsuo,Dimitrios Mavroudis,James McKay,Catriona McLean,Hanne Meijers-Heijboer,Alfons Meindl,Primitiva Menéndez,Usha Menon,J.-P. Meyer,Hui Miao,Nicola Miller,Nur Aishah Taib,Kenneth Muir,Kenneth Muir,Anna Marie Mulligan,Anna Marie Mulligan,Claire Mulot,Susan L. Neuhausen,Heli Nevanlinna,Patrick Neven,Sune F. Nielsen,Dong-Young Noh,Børge G. Nordestgaard,Børge G. Nordestgaard,Aaron D. Norman,Olufunmilayo I. Olopade,Janet E. Olson,Håkan Olsson,Curtis Olswold,Nick Orr,V. Shane Pankratz,Sue K. Park,Sue K. Park,Tjoung-Won Park-Simon,Rachel Lloyd,Jose Ignacio Arias Perez,Paolo Peterlongo,Julian Peto,Kelly-Anne Phillips,Mila Pinchev,Dijana Plaseska-Karanfilska,Ross L. Prentice,Nadege Presneau,Darya Prokofyeva,Elizabeth W. Pugh,Katri Pylkäs,Brigitte Rack,Paolo Radice,Nazneen Rahman,Gadi Rennert,Hedy S. Rennert,Valerie Rhenius,Atocha Romero,Jane Romm,Kathryn J. Ruddy,Thomas Rüdiger,Anja Rudolph,Matthias Ruebner,Emiel J. Th. Rutgers,Emmanouil Saloustros,Dale P. Sandler,Suleeporn Sangrajrang,Elinor J. Sawyer,Daniel F. Schmidt,Rita K. Schmutzler,Andreas Schneeweiss,Minouk J. Schoemaker,Fredrick R. Schumacher,Peter Schürmann,Rodney J. Scott,Rodney J. Scott,Christopher G. Scott,Sheila Seal,Caroline Seynaeve,Mitul Shah,Priyanka Sharma,Chen-Yang Shen,Chen-Yang Shen,Grace Sheng,Mark E. Sherman,Martha J. Shrubsole,Xiao-Ou Shu,Ann Smeets,Christof Sohn,Melissa C. Southey,John J. Spinelli,John J. Spinelli,Christa Stegmaier,Sarah Stewart-Brown,Jennifer Stone,Jennifer Stone,Daniel O. Stram,Harald Surowy,Harald Surowy,Anthony J. Swerdlow,Rulla M. Tamimi,Rulla M. Tamimi,Jack A. Taylor,Maria Tengström,Soo Hwang Teo,Mary Beth Terry,Daniel C. Tessier,Somchai Thanasitthichai,Kathrin Thöne,Rob A. E. M. Tollenaar,Ian Tomlinson,Ling Tong,Diana Torres,Diana Torres,Thérèse Truong,Chiu-Chen Tseng,Shoichiro Tsugane,Hans-Ulrich Ulmer,Giske Ursin,Michael Untch,Celine M. Vachon,Christi J. van Asperen,David Van Den Berg,Ans M.W. van den Ouweland,Lizet E. van der Kolk,Rob B. van der Luijt,Daniel Vincent,Jason Vollenweider,Quinten Waisfisz,Shan Wang-Gohrke,Clarice R. Weinberg,Camilla Wendt,Alice S. Whittemore,Hans Wildiers,Walter C. Willett,Robert Winqvist,Alicja Wolk,Anna H. Wu,Lucy Xia,Taiki Yamaji,Xiaohong R. Yang,Cheng Har Yip,Keun-Young Yoo,Jyh-Cherng Yu,Wei Zheng,Ying Zheng,Bin Zhu,Argyrios Ziogas,Elad Ziv,Sunil R. Lakhani,Sunil R. Lakhani,Antonis C. Antoniou,Arnaud Droit,Irene L. Andrulis,Irene L. Andrulis,Christopher I. Amos,Fergus J. Couch,Paul D.P. Pharoah,Jenny Chang-Claude,Jenny Chang-Claude,Per Hall,David J. Hunter,Roger L. Milne,Roger L. Milne,Montserrat Garcia-Closas,Marjanka K. Schmidt,Stephen J. Chanock,Alison M. Dunning,Stacey L. Edwards,Gary D. Bader,Georgia Chenevix-Trench,Jacques Simard,Peter Kraft,Douglas F. Easton +396 more
TL;DR: A genome-wide association study of breast cancer in 122,977 cases and 105,974 controls of European ancestry and 14,068 cases and 13,104 controls of East Asian ancestry finds that heritability of Breast cancer due to all single-nucleotide polymorphisms in regulatory features was 2–5-fold enriched relative to the genome- wide average.
References
More filters
Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Journal ArticleDOI
An integrated encyclopedia of DNA elements in the human genome
TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
Journal ArticleDOI
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
Daniel R. Zerbino,Ewan Birney +1 more
TL;DR: Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies and is in close agreement with simulated results without read-pair information.
Journal ArticleDOI
Comprehensive molecular portraits of human breast tumours
Daniel C. Koboldt,Robert S. Fulton,Michael D. McLellan,Heather Schmidt,Joelle Kalicki-Veizer,Joshua F. McMichael,Lucinda Fulton,David J. Dooling,Li Ding,Elaine R. Mardis,Richard K. Wilson,Adrian Ally,Miruna Balasundaram,Yaron S.N. Butterfield,Rebecca Carlsen,Candace Carter,Andy Chu,Eric Chuah,Hye Jung E. Chun,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,Andrew J. Mungall,Erin Pleasance,A. Gordon Robertson,Jacqueline E. Schein,Arash Shafiei,Payal Sipahimalani,Jared R. Slobodan,Dominik Stoll,Angela Tam,Nina Thiessen,Richard Varhol,Natasja Wye,Thomas Zeng,Yongjun Zhao,Inanc Birol,Steven J.M. Jones,Marco A. Marra,Andrew D. Cherniack,Gordon Saksena,Gordon Saksena,Robert C. Onofrio,Nam H. Pho,Scott L. Carter,Steven E. Schumacher,Steven E. Schumacher,Barbara Tabak,Barbara Tabak,Bryan Hernandez,Jeff Gentry,Huy Nguyen,Andrew Crenshaw,Kristin G. Ardlie,Rameen Beroukhim,Rameen Beroukhim,Wendy Winckler,Gad Getz,Gad Getz,Stacey Gabriel,Matthew Meyerson,Matthew Meyerson,Lynda Chin,Lynda Chin,Raju Kucherlapati,Katherine A. Hoadley,J. Todd Auman,Cheng Fan,Yidi J. Turman,Yan Shi,Ling Li,Michael D. Topal,Xiaping He,Hann Hsiang Chao,Aleix Prat,Grace O. Silva,Michael D. Iglesia,Wei Zhao,Jerry Usary,Jonathan S. Berg,Michael C. Adams,Jessica K. Booker,Junyuan Wu,Anisha Gulabani,Tom Bodenheimer,Alan P. Hoyle,Janae V. Simons,Matthew G. Soloway,Lisle E. Mose,Stuart R. Jefferys,Saianand Balu,Joel S. Parker,D. Neil Hayes,Charles M. Perou,Simeen Malik,Swapna Mahurkar,Hui Shen,Daniel J. Weisenberger,Timothy J. Triche,Phillip H. Lai,Moiz S. Bootwalla,Dennis T. Maglinte,Benjamin P. Berman,David Van Den Berg,Stephen B. Baylin,Peter W. Laird,Chad J. Creighton,Lawrence A. Donehower,Michael S. Noble,Doug Voet,Nils Gehlenborg,Daniel Di Cara,Juinhua Zhang,Hailei Zhang,Chang-Jiun Wu,Spring Yingchun Liu,Michael S. Lawrence,Lihua Zou,Andrey Sivachenko,Pei Lin,Petar Stojanov,Rui Jing,Juok Cho,Raktim Sinha,Richard W. Park,Marc Danie Nazaire,James A. Robinson,Helga Thorvaldsdottir,Jill P. Mesirov,Peter J. Park,Sheila Reynolds,Richard Kreisberg,Brady Bernard,Ryan Bressler,Timo Erkkilä,Jake Lin,Vesteinn Thorsson,Wei Zhang,Ilya Shmulevich,Giovanni Ciriello,Nils Weinhold,Nikolaus Schultz,Jianjiong Gao,Ethan Cerami,Benjamin Gross,Anders Jacobsen,Rileen Sinha,B. Arman Aksoy,Yevgeniy Antipin,Boris Reva,Ronglai Shen,Barry S. Taylor,Marc Ladanyi,Chris Sander,Pavana Anur,Paul T. Spellman,Yiling Lu,Wenbin Liu,Roel R.G. Verhaak,Gordon B. Mills,Gordon B. Mills,Rehan Akbani,Nianxiang Zhang,Bradley M. Broom,Tod D. Casasent,Chris Wakefield,Anna K. Unruh,Keith A. Baggerly,Kevin R. Coombes,John N. Weinstein,David Haussler,Christopher C. Benz,Joshua M. Stuart,Stephen C. Benz,Jingchun Zhu,Christopher Szeto,Gary K. Scott,Christina Yau,Evan O. Paull,Daniel E. Carlin,Christopher K. Wong,Artem Sokolov,Janita Thusberg,Sean D. Mooney,Sam Ng,Theodore C. Goldstein,Kyle Ellrott,Mia Grifford,Christopher Wilks,Singer Ma,Brian Craft,Chunhua Yan,Ying Hu,Daoud Meerzaman,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,Peter White,Peter White,Erik Zmuda,Jessica Frick,Tara M. Lichtenberg,Robin Brookens,Myra M. George,Mark Gerken,Hollie A. Harper,Kristen M. Leraas,Lisa Wise,Teresa R. Tabler,Cynthia McAllister,Thomas Barr,Melissa Hart-Kothari,Katie Tarvin,Charles Saller,George E. Sandusky,Colleen Mitchell,Mary Iacocca,Jennifer Brown,Brenda Rabeno,Christine Czerwinski,Nicholas J. Petrelli,Oleg Dolzhansky,Mikhail Abramov,Olga Voronina,Olga Potapova,Jeffrey R. Marks,Wiktoria Maria Suchorska,Dawid Murawa,Witold Kycler,Matthew Ibbs,Konstanty Korski,Arkadiusz Spychała,Pawel Murawa,Jacek J. Brzeziński,Hanna Perz,Radoslaw Łaźniak,M. Teresiak,Honorata Tatka,Ewa Leporowska,Marta Bogusz-Czerniewicz,Julian Malicki,Andrzej Mackiewicz,Maciej Wiznerowicz,Xuan Van Le,Bernard Kohl,Nguyen Viet Tien,Richard Thorp,Nguyen Van Bang,Howard H. Sussman,Bui Duc Phu,Richard A. Hajek,Nguyen Phi Hung,Huynh Quyet Thang,Khurram Z. Khan,Robert Penny,David Mallery,Erin Curley,Candace Shelton,Peggy Yena,James N. Ingle,Fergus J. Couch,Wilma L. Lingle,Tari A. King,Ana M. Gonzalez-Angulo,Ana M. Gonzalez-Angulo,Mary D. Dyer,Shuying Liu,Xiaolong Meng,Modesto Patangan,Frederic Waldman,Frederic Waldman,Hubert Stoppler,W. Kimryn Rathmell,Leigh B. Thorne,Mei Huang,Lori Boice,Ashley Hill,Carl Morrison,Carmelo Gaudioso,Wiam Bshara,Kelly Daily,Sophie C. Egea,Mark D. Pegram,Carmen Gomez-Fernandez,Rajiv Dhir,Rohit Bhargava,Adam Brufsky,Craig D. Shriver,Jeffrey A. Hooke,Jamie Leigh Campbell,Richard J. Mural,Hai Hu,Stella Somiari,Caroline Larson,Brenda Deyarmin,Leonid Kvecher,Albert J. Kovatich,Matthew J. Ellis,Thomas Stricker,Kevin P. White,Olufunmilayo I. Olopade,Chunqing Luo,Yaqin Chen,Ron Bose,Li-Wei Chang,Andrew H. Beck,Todd Pihl,Mark A. Jensen,Robert Sfeir,Ari B. Kahn,Anna Chu,Prachi Kothiyal,Zhining Wang,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,Kenna R. Mills Shaw,Liming Yang,Greg Eley,Martin L. Ferguson,Roy Tarnuzzer,Jiashan Zhang,Laura A.L. Dillon,Kenneth H. Buetow,Peter Fielding,Bradley A. Ozenberger,Mark S. Guyer,Heidi J. Sofia,Jacqueline D. Palchik +355 more
TL;DR: The ability to integrate information across platforms provided key insights into previously defined gene expression subtypes and demonstrated the existence of four main breast cancer classes when combining data from five platforms, each of which shows significant molecular heterogeneity.
Journal Article
An integrated encyclopedia of DNA elements in the human genome.
TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
Related Papers (5)
Signatures of mutational processes in human cancer
Ludmil B. Alexandrov,Serena Nik-Zainal,Serena Nik-Zainal,David C. Wedge,Samuel Aparicio,Sam Behjati,Sam Behjati,Andrew V. Biankin,Graham R. Bignell,Niccolo Bolli,Niccolo Bolli,Åke Borg,Anne Lise Børresen-Dale,Anne Lise Børresen-Dale,Sandrine Boyault,Birgit Burkhardt,Adam Butler,Carlos Caldas,Helen Davies,Christine Desmedt,Roland Eils,Jorunn E. Eyfjord,John A. Foekens,Mel Greaves,Fumie Hosoda,Barbara Hutter,Tomislav Ilicic,Sandrine Imbeaud,Sandrine Imbeaud,Marcin Imielinsk,Natalie Jäger,David T. W. Jones,David T. Jones,Stian Knappskog,Stian Knappskog,Marcel Kool,Sunil R. Lakhani,Carlos López-Otín,Sancha Martin,Nikhil C. Munshi,Nikhil C. Munshi,Hiromi Nakamura,Paul A. Northcott,Marina Pajic,Elli Papaemmanuil,Angelo Paradiso,John V. Pearson,Xose S. Puente,Keiran Raine,Manasa Ramakrishna,Andrea L. Richardson,Andrea L. Richardson,Julia Richter,Philip Rosenstiel,Matthias Schlesner,Ton N. Schumacher,Paul N. Span,Jon W. Teague,Yasushi Totoki,Andrew Tutt,Rafael Valdés-Mas,Marit M. van Buuren,Laura van ’t Veer,Anne Vincent-Salomon,Nicola Waddell,Lucy R. Yates,Icgc PedBrain,Jessica Zucman-Rossi,Jessica Zucman-Rossi,P. Andrew Futreal,Ultan McDermott,Peter Lichter,Matthew Meyerson,Matthew Meyerson,Sean M. Grimmond,Reiner Siebert,Elias Campo,Tatsuhiro Shibata,Stefan M. Pfister,Stefan M. Pfister,Peter J. Campbell,Peter J. Campbell,Peter J. Campbell,Michael R. Stratton,Michael R. Stratton +84 more
Comprehensive molecular portraits of human breast tumours
Daniel C. Koboldt,Robert S. Fulton,Michael D. McLellan,Heather Schmidt,Joelle Kalicki-Veizer,Joshua F. McMichael,Lucinda Fulton,David J. Dooling,Li Ding,Elaine R. Mardis,Richard K. Wilson,Adrian Ally,Miruna Balasundaram,Yaron S.N. Butterfield,Rebecca Carlsen,Candace Carter,Andy Chu,Eric Chuah,Hye Jung E. Chun,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,Andrew J. Mungall,Erin Pleasance,A. Gordon Robertson,Jacqueline E. Schein,Arash Shafiei,Payal Sipahimalani,Jared R. Slobodan,Dominik Stoll,Angela Tam,Nina Thiessen,Richard Varhol,Natasja Wye,Thomas Zeng,Yongjun Zhao,Inanc Birol,Steven J.M. Jones,Marco A. Marra,Andrew D. Cherniack,Gordon Saksena,Gordon Saksena,Robert C. Onofrio,Nam H. Pho,Scott L. Carter,Steven E. Schumacher,Steven E. Schumacher,Barbara Tabak,Barbara Tabak,Bryan Hernandez,Jeff Gentry,Huy Nguyen,Andrew Crenshaw,Kristin G. Ardlie,Rameen Beroukhim,Rameen Beroukhim,Wendy Winckler,Gad Getz,Gad Getz,Stacey Gabriel,Matthew Meyerson,Matthew Meyerson,Lynda Chin,Lynda Chin,Raju Kucherlapati,Katherine A. Hoadley,J. Todd Auman,Cheng Fan,Yidi J. Turman,Yan Shi,Ling Li,Michael D. Topal,Xiaping He,Hann Hsiang Chao,Aleix Prat,Grace O. Silva,Michael D. Iglesia,Wei Zhao,Jerry Usary,Jonathan S. Berg,Michael C. Adams,Jessica K. Booker,Junyuan Wu,Anisha Gulabani,Tom Bodenheimer,Alan P. Hoyle,Janae V. Simons,Matthew G. Soloway,Lisle E. Mose,Stuart R. Jefferys,Saianand Balu,Joel S. Parker,D. Neil Hayes,Charles M. Perou,Simeen Malik,Swapna Mahurkar,Hui Shen,Daniel J. Weisenberger,Timothy J. Triche,Phillip H. Lai,Moiz S. Bootwalla,Dennis T. Maglinte,Benjamin P. Berman,David Van Den Berg,Stephen B. Baylin,Peter W. Laird,Chad J. Creighton,Lawrence A. Donehower,Michael S. Noble,Doug Voet,Nils Gehlenborg,Daniel Di Cara,Juinhua Zhang,Hailei Zhang,Chang-Jiun Wu,Spring Yingchun Liu,Michael S. Lawrence,Lihua Zou,Andrey Sivachenko,Pei Lin,Petar Stojanov,Rui Jing,Juok Cho,Raktim Sinha,Richard W. Park,Marc Danie Nazaire,James A. Robinson,Helga Thorvaldsdottir,Jill P. Mesirov,Peter J. Park,Sheila Reynolds,Richard Kreisberg,Brady Bernard,Ryan Bressler,Timo Erkkilä,Jake Lin,Vesteinn Thorsson,Wei Zhang,Ilya Shmulevich,Giovanni Ciriello,Nils Weinhold,Nikolaus Schultz,Jianjiong Gao,Ethan Cerami,Benjamin Gross,Anders Jacobsen,Rileen Sinha,B. Arman Aksoy,Yevgeniy Antipin,Boris Reva,Ronglai Shen,Barry S. Taylor,Marc Ladanyi,Chris Sander,Pavana Anur,Paul T. Spellman,Yiling Lu,Wenbin Liu,Roel R.G. Verhaak,Gordon B. Mills,Gordon B. Mills,Rehan Akbani,Nianxiang Zhang,Bradley M. Broom,Tod D. Casasent,Chris Wakefield,Anna K. Unruh,Keith A. Baggerly,Kevin R. Coombes,John N. Weinstein,David Haussler,Christopher C. Benz,Joshua M. Stuart,Stephen C. Benz,Jingchun Zhu,Christopher Szeto,Gary K. Scott,Christina Yau,Evan O. Paull,Daniel E. Carlin,Christopher K. Wong,Artem Sokolov,Janita Thusberg,Sean D. Mooney,Sam Ng,Theodore C. Goldstein,Kyle Ellrott,Mia Grifford,Christopher Wilks,Singer Ma,Brian Craft,Chunhua Yan,Ying Hu,Daoud Meerzaman,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,Peter White,Peter White,Erik Zmuda,Jessica Frick,Tara M. Lichtenberg,Robin Brookens,Myra M. George,Mark Gerken,Hollie A. Harper,Kristen M. Leraas,Lisa Wise,Teresa R. Tabler,Cynthia McAllister,Thomas Barr,Melissa Hart-Kothari,Katie Tarvin,Charles Saller,George E. Sandusky,Colleen Mitchell,Mary Iacocca,Jennifer Brown,Brenda Rabeno,Christine Czerwinski,Nicholas J. Petrelli,Oleg Dolzhansky,Mikhail Abramov,Olga Voronina,Olga Potapova,Jeffrey R. Marks,Wiktoria Maria Suchorska,Dawid Murawa,Witold Kycler,Matthew Ibbs,Konstanty Korski,Arkadiusz Spychała,Pawel Murawa,Jacek J. Brzeziński,Hanna Perz,Radoslaw Łaźniak,M. Teresiak,Honorata Tatka,Ewa Leporowska,Marta Bogusz-Czerniewicz,Julian Malicki,Andrzej Mackiewicz,Maciej Wiznerowicz,Xuan Van Le,Bernard Kohl,Nguyen Viet Tien,Richard Thorp,Nguyen Van Bang,Howard H. Sussman,Bui Duc Phu,Richard A. Hajek,Nguyen Phi Hung,Huynh Quyet Thang,Khurram Z. Khan,Robert Penny,David Mallery,Erin Curley,Candace Shelton,Peggy Yena,James N. Ingle,Fergus J. Couch,Wilma L. Lingle,Tari A. King,Ana M. Gonzalez-Angulo,Ana M. Gonzalez-Angulo,Mary D. Dyer,Shuying Liu,Xiaolong Meng,Modesto Patangan,Frederic Waldman,Frederic Waldman,Hubert Stoppler,W. Kimryn Rathmell,Leigh B. Thorne,Mei Huang,Lori Boice,Ashley Hill,Carl Morrison,Carmelo Gaudioso,Wiam Bshara,Kelly Daily,Sophie C. Egea,Mark D. Pegram,Carmen Gomez-Fernandez,Rajiv Dhir,Rohit Bhargava,Adam Brufsky,Craig D. Shriver,Jeffrey A. Hooke,Jamie Leigh Campbell,Richard J. Mural,Hai Hu,Stella Somiari,Caroline Larson,Brenda Deyarmin,Leonid Kvecher,Albert J. Kovatich,Matthew J. Ellis,Thomas Stricker,Kevin P. White,Olufunmilayo I. Olopade,Chunqing Luo,Yaqin Chen,Ron Bose,Li-Wei Chang,Andrew H. Beck,Todd Pihl,Mark A. Jensen,Robert Sfeir,Ari B. Kahn,Anna Chu,Prachi Kothiyal,Zhining Wang,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,Kenna R. Mills Shaw,Liming Yang,Greg Eley,Martin L. Ferguson,Roy Tarnuzzer,Jiashan Zhang,Laura A.L. Dillon,Kenneth H. Buetow,Peter Fielding,Bradley A. Ozenberger,Mark S. Guyer,Heidi J. Sofia,Jacqueline D. Palchik +355 more
Mutational Processes Molding the Genomes of 21 Breast Cancers
Serena Nik-Zainal,Ludmil B. Alexandrov,David C. Wedge,Peter Van Loo,Peter Van Loo,Peter Van Loo,Christopher Greenman,Christopher Greenman,Christopher Greenman,Keiran Raine,David T. Jones,Jonathan Hinton,John D Marshall,Lucy Stebbings,Andrew Menzies,Sancha Martin,Kenric Leung,Lina Chen,Catherine Leroy,Manasa Ramakrishna,Richard Rance,King Wai Lau,Laura Mudie,Ignacio Varela,David J. McBride,Graham R. Bignell,Susanna L. Cooke,Adam Shlien,John Gamble,Ian Whitmore,Mark Maddison,Patrick S. Tarpey,Helen Davies,Elli Papaemmanuil,Philip J. Stephens,Stuart McLaren,Adam Butler,Jon W. Teague,Göran Jönsson,Judy Garber,Daniel P. Silver,Penelope Miron,Aquila Fatima,Sandrine Boyault,Anita Langerød,Andrew Tutt,John W.M. Martens,Samuel Aparicio,Åke Borg,Anne Vincent Salomon,Gilles Thomas,Anne Lise Børresen-Dale,Anne Lise Børresen-Dale,Andrea L. Richardson,Michael S. Neuberger,P. Andrew Futreal,Peter J. Campbell,Peter J. Campbell,Peter J. Campbell,Michael R. Stratton +59 more
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
Christina Curtis,Christina Curtis,Sohrab P. Shah,Suet-Feung Chin,Gulisa Turashvili,Oscar M. Rueda,Mark J Dunning,Doug Speed,Doug Speed,Andy G. Lynch,Shamith A. Samarajiwa,Yinyin Yuan,Stefan Gräf,Gavin Ha,Gholamreza Haffari,Ali Bashashati,Roslin Russell,Steven McKinney,Anita Langerød,Andrew R. Green,Elena Provenzano,Gordon C. Wishart,Sarah E Pinder,Peter H. Watson,Peter H. Watson,Florian Markowetz,Leigh C. Murphy,Ian O. Ellis,Arnie Purushotham,Arnie Purushotham,Anne Lise Børresen-Dale,Anne Lise Børresen-Dale,James D. Brenton,Simon Tavaré,Carlos Caldas,Samuel Aparicio +35 more