Paper
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A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers
Authors
Zhenlin Ju,Han Liang
Shiyun Ling,Yiling Lu,Kwok-Shing Ng,Michael Ryan,Jing Wang,Jiexin Zhang,Adam Abeshouse,Joshua Armenia,Debyani Chakravarty,Walid Chatila,Ino Bruijn,Jianjiong Gao,Benjamin Groß,Zachary Heins,Ritika Kundra,Konnor La,Marc Ladanyi,Augustin Luna,Moriah Nissan,Angelica Ochoa,Sarah Phillips,Ed Reznik,Francisco Sanchez‐Vega,Chris Sander,Nikolaus Schultz,Robert Sheridan,S. Sumer,Yichao Sun,Barry Taylor,Jioajiao Wang,Hongxin Zhang,Pavana Anur,Myron Peto,Paul Spellman,Christopher Benz,Joshua Stuart,Christopher Wong,D. Hayes,Joel Parker,Matthew Wilkerson,Adrian Ally,Miruna Balasundaram,Denise Brooks,Rebecca Carlsen,Eric Chuah,Noreen Dhalla,Robert Holt,Steven Jones,Katayoon Kasaian,Darlene Lee,Yussanne Ma,Marco Marra,M. Mayo,Richard Moore,Sara Sadeghi,Jacqueline Schein,Payal Sipahimalani,Angela Tam,Nina Thiessen,Kane Tse,Tina Wong,Rameen Beroukhim,Carrie Cibulskis,Stacey Gabriel,Galen Gao,Gavin Ha,Matthew Meyerson,Steven Schumacher,Juliann Shih,Melanie Kucherlapati,Raju Kucherlapati,Stephen Baylin,Leslie Cope,Ludmila Danilova,Moiz Bootwalla,Phillip Lai,Dennis Maglinte,David Berg,Daniel Weisenberger,J. Auman,Saianand Balu,Tom Bodenheimer,Cheng Fan,Katherine Hoadley,Alan Hoyle,Stuart Jefferys,Corbin Jones,Shaowu Meng,Piotr Mieczkowski,Lisle Mose,Amy Perou,Charles Perou,Jeffrey Roach,Yan Shi,Janae Simons,Tara Skelly,Matthew Soloway,Donghui Tan,Umadevi Veluvolu,Toshinori Hinoue,Peter Laird,Wanding Zhou,Michelle Bellair,Kyle Chang,Kyle Covington,Chad Creighton,Huyen Dinh,Harsha Doddapaneni,Lawrence Donehower,Jennifer Drummond,Richard Scolyer,Robert Glenn,Walker Hale,Yi Han,Jianhong Hu,Viktoriya Korchina,Sandra Lee,Lora Lewis,Wei Li,Xiuping Liu,Margaret Morgan,Donna Morton,Donna Muzny,Jireh Santibanez,Margi Sheth,Eve Shinbrot,Linghua Wang,Min Wang,David Wheeler,Xi Liu,Fengmei Zhao,Julian Hess,Elizabeth Appelbaum,Matthew Bailey,Matthew Cordes,Ding Li,Catrina Fronick,Lucinda Fulton,Robert Fulton,Cyriac Kandoth,Elaine Mardis,Michael McLellan,Christopher Miller,Heather Schmidt,Richard Wilson,Daniel Crain,Erin Curley,Johanna Gardner,Kevin Lau,David Mallery,Scott Morris,Joseph Paulauskis,Robert Penny,Candace Shelton,Troy Shelton,Mark Sherman,Eric Thompson,Peggy Yena,Jay Bowen,Julie Gastier-Foster,Mark Gerken,Kristen Leraas,Tara Lichtenberg,Nilsa Ramirez,Lisa Wise,Erik Zmuda,Niall Corcoran,Tony Costello,Christopher Hovens,André Carvalho,Ana deCarvalho,José Fregnani,Adhemar Longatto‐Filho,Rui Reis,Cristovam Scapulatempo‐Neto,Henrique Silveira,Daniel Vidal,Andrew Burnette,Fu‐Dong Shi,Beth Hermes,Ardene Noss,Rosy Singh,Matthew Anderson,Patricia Castro,Michael Ittmann,David Huntsman,Bernard Kohl,Xuan Le,Richard Thorp,Chris Andry,Elizabeth Duffy,Vladimir Lyadov,Oxana Paklina,Galiya Setdikova,Alexey Shabunin,М. Тавобилов,Christopher McPherson,Ronald Warnick,Ross Berkowitz,Daniel Cramer,Colleen Feltmate,Neil Horowitz,Adam Kibel,Michael Muto,Chandrajit Raut,Andrei Malykh,Jill Barnholtz‐Sloan,Wendi Barrett,Karen Devine,Jordonna Fulop,Quinn Ostrom,Kristen Shimmel,Yingli Wolinsky,Andrew Sloan,Agostino Rose,Felice Giuliante,Marc Goodman,Beth Karlan,Curt Hagedorn,John Eckman,Jodi Harr,Jerome Myers,Kelinda Tucker,Leigh Zach,Brenda Deyarmin,Hai Hu,Leonid Kvecher,Caroline Larson,Richard Mural,Stella Somiari,Aleš Vícha,Tomáš Zelinka,Joseph Bennett,Mary Iacocca,Brenda Rabeno,Patricia Swanson,Mathieu Latour,Louis Lacombe,Bernard Têtu,Alain Bergeron,Mary McGraw,Susan Staugaitis,John Chabot,Hanina Hibshoosh,Antonia Sepulveda,Tao Su,Timothy Wang,Olga Potapova,Olga Voronina,Laurence Desjardins,Odette Mariani,Sergio Roman‐Roman,Xavier Sastre,Marc‐Henri Stern,Feixiong Cheng,Sabina Signoretti,Andrew Berchuck,Darell Bigner,Eric Lipp,Jeffrey Marks,Shannon McCall,Roger McLendon,Angeles Secord,Alexis Sharp,Madhusmita Behera,Daniel Brat,Amy Chen,Keith Delman,Seth Force,Fadlo Khuri,Kelly Magliocca,Shishir Maithel,Jeffrey Olson,Taofeek Owonikoko,Alan Pickens,Suresh Ramalingam,Dong Shin,Gabriel Sica,Erwin Meir,Hongzheng Zhang,Wil Eijckenboom,Ad Gillis,Esther Korpershoek,Leendert Looijenga,Wolter Oosterhuis,Hans Stoop,Kim Kessel,Ellen Zwarthoff,Chiara Calatozzolo,Lucia Cuppini,Stefania Cuzzubbo,Francesco DiMeco,Gaetano Finocchiaro,Luca Mattei,Alessandro Perin,Bianca Pollo,Chu Chen,J. Houck,Pawadee Lohavanichbutr,Arndt Hartmann,Robert Stoehr,Helge Täubert,Sven Wach,Bernd Wullich,Witold Kycler,Dawid Murawa,Maciej Wiznerowicz,Ki Chung,William Edenfield,Julie Martin,Éric Baudin,Glenn Bubley,Raphael Bueno,Assunta Rienzo,William Richards,Steven Kalkanis,Tom Mikkelsen,Houtan Noushmehr,Lisa Scarpace,Nicolas Girard,Marta Aymerich,Elı́as Campo,Eva Giné,Armando Guillermo,Nguyễn Bang,Phan Hanh,Bui Phu,Yufang Tang,Howard Colman,Kimberley Evason,Peter Dottino,John Martignetti,Hani Gabra,Hartmut Juhl,Teniola Akeredolu,Serghei Stepa,Dave Hoon,Keunsoo Ahn,Koo Kang,Felix Beuschlein,Anne Breggia,Michael Birrer,Abel González-Pérez,Mitesh Borad,Alan Bryce,Erik Castle,Vishal Chandan,John Cheville,John Copland,Michael Farnell,Thomas Flotte,Nasra Giama,Thai Ho,Michael Kendrick,Jean‐Pierre Kocher,Karla Kopp,Catherine Moser,David Nagorney,Daniel O’Brien,Brian O’Neill,Tushar Patel,Gloria Petersen,Florencia Que,Michael Rivera,Lewis Roberts,Robert Smallridge,Thomas Smyrk,Melissa Stanton,R. Thompson,Michael Torbenson,Ju Yang,Lizhi Zhang,Fadi Brimo,Jaffer Ajani,Ana Gonzalez,Carmen Behrens,Jolanta Bondaruk,Russell Broaddus,Bogdan Czerniak,Bita Esmaeli,Junya Fujimoto,Jeffrey Gershenwald,Charles Guo,Christopher Logothetis,Funda Meric‐Bernstam,César Moran,Lois Ramondetta,David Rice,Pheroze Tamboli,Timothy Thompson,Patricia Troncoso,Anne Tsao,Ignacio Wistuba,Candace Carter,Lauren Haydu,Peter Hersey,Valerie Jakrot,Hojabr Kakavand,Richard Kefford,Kenneth Lee,Georgina Long,Graham Mann,Michael Quinn,Robyn Saw,Kerwin Shannon,Andrew Spillane,Jonathan Stretch,Maria Synott,John Thompson,James Wilmott,Hikmat Al‐Ahmadie,Timothy Chan,Ronald Ghossein,Anuradha Gopalan,Vincent Reuter,Samuel Singer,Bhuvanesh Singh,Nguyen Tien,Thomas Broudy,Cyrus Mirsaidi,Praveen Nair,Paul Drwiega,Judy Miller,Jennifer Smith,Howard Zaren,Joong‐Won Park,Nguyễn Hùng,Electron Kebebew,W. Linehan,Adam Metwalli,Karel Pacák,Peter Pinto,Mark Schiffman,Laura Schmidt,Cathy Vocke,Robert Worrell,Hannah Yang,Marc Moncrieff,Chandra Goparaju,Jonathan Melamed,Harvey Pass,Natalia Botnariuc,Irina Caraman,Mircea Cernat,Inga Chemencedji,Adrian Clipca,Serghei Doruc,Ghenadie Gorincioi,Sergiu Mura,Maria Pirtac,Irina Stancul,Diana Tcaciuc,Monique Albert,Iakovina Alexopoulou,Angel Arnaout,John Bartlett,Jay Engel,Sébastien Gilbert,Jeremy Parfitt,Harman Sekhon,George Thomas,Doris Rassl,Robert Rintoul,Carlo Bifulco,Raina Tamakawa,Walter Urba,Nicholas Hayward,Henri Timmers,Anna Antenucci,Francesco Facciolo,Gian Grazi,Mirella Marino,Roberta Merola,Ronald Krijger,Anne‐Paule Gimenez‐Roqueplo,Alain Piché,Simone Chevalier,Ginette McKercher,Kıvanç Birsoy,Gene Barnett,Cathy Brewer,Carol Farver,Theresa Naska,Nathan Pennell,Daniel Raymond,Cathy Schilero,Kathy Smolenski,Carl Morrison,Jeffrey Borgia,Michael Liptay,Mark Pool,Christopher Seder,Kerstin Junker,Larsson Omberg,Mikhail Dinkin,George Manikhas,Domenico Alvaro,Maria Bragazzi,Vincenzo Cardinale,Guido Carpino,Eugenio Gaudio,David Chesla,Sandra Cottingham,Michael Dubina,Fedor Moiseenko,Renumathy Dhanasekaran,Karl‐Friedrich Becker,Klaus‐Peter Janssen,Julia Slotta‐Huspenina,Mohamed Abdel‐Rahman,Dina Aziz,Sue Bell,Colleen Cebulla,Amy Davis,Rebecca Duell,J. Elder,Joe Hilty,Bahavna Kumar,James Lang,Norman Lehman,Randy Mandt,Phuong Nguyen,Robert Pilarski,Karan Rai,Lynn Schoenfield,Kelly Senecal,Paul Wakely,Paul Hansen,Ronald Lechan,James Powers,Arthur Tischler,William Grizzle,Katherine Sexton,Alison Kastl,Joel Henderson,Sima Porten,Jens Waldmann,Martin Fassnacht,L. Sylvia,Dirk Schadendorf,Marta Couce,Markus Graefen,Hartwig Huland,Guido Sauter,Thorsten Schlomm,Ronald Simon,Pierre Tennstedt,Oluwole Olabode,Mark Nelson,Oliver Bathe,Peter Carroll,June Chan,Philip DiSaia,Pat Glenn,Robin Kelley,Charles Landen,Joanna Phillips,Michael Prados,Jeffry Simko,Karen Smith‐McCune,Scott VandenBerg,Kevin Roggin,Ashley Fehrenbach,Ady Kendler,Suzanne Sifri,Ruth Steele,Antonio Jimeno,Francis Carey,Ian Forgie,Massimo Mannelli,Michael Carney,Brenda Hernandez,Benito Campos,Christel Herold‐Mende,Christin Jungk,Andreas Unterberg,Andreas Deimling,Aaron Bossler,Joseph Galbraith,Laura Jacobus,Michael Knudson,Tina Knutson,Deqin Ma,Mohammed Milhem,Rita Sigmund,Rashna Madan,Howard Rosenthal,Alex Boussioutas,David Beer,Thomas Giordano,Anne‐Marie Mes‐Masson,Fred Saad,Thèrése Bocklage,Lisa Landrum,Robert Mannel,Kathleen Moore,Katherine Moxley,Russel Postier,Joan Walker,Michael Feldman,Federico Valdivieso,Rajiv Dhir,James Luketich,Edna Pinero,Mario Quintero-Aguilo,Carlos Carlotti,José Santos,Rafael Kemp,Ajith Sankarankuty,Daniela Tirapelli,James Catto,Kathy Agnew,Elizabeth Swisher,Jenette Creaney,B. Robinson,Eryn Godwin,Sara Kendall,Cassaundra Shipman,Carol Bradford,Thomas Carey,Andrea Haddad,Jeffey Moyer,Lisa Peterson,Mark Prince,Laura Rozek,Gregory Wolf,Rayleen Bowman,Kwun Fong,Ian Yang,Robert Korst,W. Rathmell,J. Fantacone-Campbell,Jeffrey Hooke,Albert Kovatich,Craig Shriver,John DiPersio,Bettina Drake,Ramaswamy Govindan,Sharon Heath,Timothy Ley,Brian Tine,Peter Westervelt,Mark Rubin,Jung Lee,Natália Aredes,Jun Li,Ashton Berger,Anil Korkut,Rupa Kanchi,Apurva Hegde,Walter Lenoir,Wenbin Liu,Yuexin Liu,Huihui Fan,Hui Shen,Visweswaran Ravikumar,Arvind Rao,André Schultz,Xubin Li,Pavel Sumazin,Cecilia Williams,Pieter Mestdagh,Preethi Gunaratne,Christina Yau,Reanne Bowlby,A. Robertson,Daniel Tiezzi,Chen Wang,Andrew Cherniack,Andrew Mungall,Nicole Kuderer,Janet Rader,Rosemary Zuna,Anil Sood,Alexander Lazar,Akinyemi Ojesina,Clement Adebamowo,Sally Adebamowo,Keith Baggerly,Ting-Wen Chen,Hua‐Sheng Chiu,Steve Lefever,Liang Liu,Karen MacKenzie,Sandra Oršulić,Jason Roszik,Carl Shelley,Qianqian Song,Christopher Vellano,Nicolas Wentzensen,John Weinstein,Gordon Mills,Douglas Levine,Rehan Akbani,Samantha Caesar-Johnson,John Demchok,Ina Felau,Melpomeni Kasapi,Martin Ferguson,Carolyn Hutter,Heidi Sofia,Roy Tarnuzzer,Zhining Wang,Liming Yang,Jean Zenklusen,Jiashan Zhang,Sudha Chudamani,Jia Liu,Laxmi Lolla,Rashi Naresh,Todd Pihl,Qiang Sun,Yunhu Wan,Ye Wu,Juok Cho,Timothy Defreitas,Scott Frazer,Nils Gehlenborg,Gad Getz,David Heiman,Jaegil Kim,Michael Lawrence,Pei Lin,Sam Meier,Michael Noble,Gordon Saksena,Doug Voet,Hailei Zhang,Brady Bernard,Nyasha Chambwe,Varsha Dhankani,Theo Knijnenburg,Roger Kramer,Kalle Leinonen,Michael Miller,Sheila Reynolds,Ilya Shmulevich,Vésteinn Thórsson,Wei Zhang,Bradley Broom
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,Armaz MariamidzeJournal
Published
Apr 1, 2018
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Abstract
We analyzed molecular data on 2,579 tumors from The Cancer Genome Atlas (TCGA) of four gynecological types plus breast. Our aims were to identify shared and unique molecular features, clinically significant subtypes, and potential therapeutic targets. We found 61 somatic copy-number alterations (SCNAs) and 46 significantly mutated genes (SMGs). Eleven SCNAs and 11 SMGs had not been identified in previous TCGA studies of the individual tumor types. We found functionally significant estrogen receptor-regulated long non-coding RNAs (lncRNAs) and gene/lncRNA interaction networks. Pathway analysis identified subtypes with high leukocyte infiltration, raising potential implications for immunotherapy. Using 16 key molecular features, we identified five prognostic subtypes and developed a decision tree that classified patients into the subtypes based on just six features that are assessable in clinical laboratories.
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