Journal ArticleDOI
Comprehensive molecular portraits of human breast tumours
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This article is published in Yearbook of Pathology and Laboratory Medicine.The article was published on 2013-01-01. It has received 5867 citations till now.read more
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TP53 Mutation Spectrum in Breast Cancer Is Subtype Specific and Has Distinct Prognostic Relevance
Laxmi Silwal-Pandit,Hans Kristian Moen Vollan,Suet-Feung Chin,Oscar M. Rueda,Steven McKinney,Tomo Osako,David A. Quigley,Vessela N. Kristensen,Samuel Aparicio,Anne Lise Børresen-Dale,Carlos Caldas,Anita Langerød +11 more
TL;DR: This study reveals that TP53 mutations have different clinical relevance in molecular subtypes of breast cancer, and suggests diverse roles for TP53 in the biology underlying breast cancer development.
Journal ArticleDOI
Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C
Nicola H. Dryden,Laura Broome,Frank Dudbridge,Nichola Johnson,Nick Orr,Stefan Schoenfelder,Takashi Nagano,Simon Andrews,Steven W. Wingett,Iwanka Kozarewa,Ioannis Assiotis,Kerry Fenwick,Sarah Maguire,James Campbell,Rachael Natrajan,Maryou B K Lambros,Eleni Perrakis,Alan Ashworth,Peter Fraser,Olivia Fletcher +19 more
TL;DR: Capture Hi-C (CHi-C), which, by incorporating a sequence capture step into aHi-C protocol, allows high-resolution analysis of targeted regions of the genome, and defines two SNPs that were highly correlated with the published risk variant and that mapped within the bait end of an interaction peak.
Journal ArticleDOI
Aberrant FGFR signaling mediates resistance to CDK4/6 inhibitors in ER+ breast cancer
Luigi Formisano,Yao Lu,Alberto Servetto,Ariella B. Hanker,Ariella B. Hanker,Valerie M. Jansen,Joshua A. Bauer,Dhivya R. Sudhan,Dhivya R. Sudhan,Angel Guerrero-Zotano,Sarah Croessmann,Yan Guo,Paula Gonzalez Ericsson,Kyungmin Lee,Mellissa J. Nixon,Luis J. Schwarz,Melinda E. Sanders,Teresa C. Dugger,Marcelo Rocha Cruz,Amir Behdad,Massimo Cristofanilli,Aditya Bardia,Joyce O'Shaughnessy,Rebecca J. Nagy,Richard B. Lanman,Nadia Solovieff,Wei He,Michelle Miller,Fei Su,Yu Shyr,Ingrid A. Mayer,Justin M. Balko,Carlos L. Arteaga,Carlos L. Arteaga +33 more
TL;DR: It is shown that FGFR1 amplification is a resistance mechanism to CDK4/6 inhibitor and endocrine therapy and that combined treatment with FGFR, CDK 4/6, and anti-estrogens is a potential therapeutic strategy in Era+ breast cancer tumors.
Journal Article
Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors
Gavin Ha,Samuel S. Freeman,Atish D. Choudhury,Daniel G. Stover,Heather A. Parsons,Gregory Gydush,Sarah C. Reed,Denisse Rotem,Justin Rhoades,Dimitri Livitz,Daniel Rosebrock,Ignaty Leshchiner,Jaegil Kim,Chip Stewart,Mara Rosenberg,Joshua M. Francis,Cheng-Zhong Zhang,Ofir Cohen,Coyin Oh,Paz Polak,Max Lloyd,Sairah Mahmud,Karla Helvie,Margaret S. Merrill,Rebecca A. Santiago,Edward P. O’Connor,Seong Ho Jeong,Joseph F. Kramkowski,Zhenwei Zhang,Laura Polacek,Jens G. Lohr,Molly Schleicher,Emily Lipscomb,Andrea Saltzman,Nelly Oliver,Lori Marini,Adrienne G. Waks,Lauren C. Harshman,Sara M. Tolaney,Eliezer M. Van Allen,Eric P. Winer,Nan Lin,Mari Nakabayashi,Mary-Ellen Taplin,Cory M. Johannessen,Levi A. Garraway,Todd R. Golub,Jesse S. Boehm,Nikhil Wagle,Gad Getz,Matthew Meyerson,Viktor A. Adalsteinsson,Denis Loginov,Huiming Ding,Rachel Leeson,Rachel M. Barry,John C Love +56 more
TL;DR: The authors provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-exome sequencing.
Journal ArticleDOI
A multivariate approach to the integration of multi-omics datasets
TL;DR: Multiple co-inertia analysis (MCIA), an exploratory data analysis method that identifies co-relationships between multiple high dimensional datasets, is described, an attractive method for data integration and visualization of several datasets of multi-omics features observed on the same set of individuals.
References
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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.