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Genomic Classification of Cutaneous Melanoma

Rehan Akbani,Kadir C. Akdemir,Bülent Arman Aksoy,Monique Albert,Adrian Ally,Samirkumar B. Amin,Harindra Arachchi,Arshi Arora,J. Todd Auman,Brenda Ayala,Julien Baboud,Miruna Balasundaram,Saianand Balu,Nandita Barnabas,John M.S. Bartlett,Pam Bartlett,Boris C. Bastian,Stephen B. Baylin,Madhusmita Behera,D. K. Belyaev,Christopher C. Benz,Brady Bernard,Rameen Beroukhim,Natalie Bir,Aaron Black,Tom Bodenheimer,Lori Boice,Genevieve M. Boland,R. Bono,Moiz S. Bootwalla,Marcus W. Bosenberg,Jay Bowen,Reanne Bowlby,Christopher A. Bristow,Laura Brockway-Lunardi,Denise Brooks,Jakub Brzezinski,Wiam Bshara,Elizabeth Buda,William R. Burns,Yaron S.N. Butterfield,M. Button,Tiffany L. Calderone,Giancarlo Antonini Cappellini,Candace Carter,Scott L. Carter,Lynn Cherney,Andrew D. Cherniack,Aaron Chevalier,Lynda Chin,Juok Cho,Raymond J. Cho,Yoon La Choi,Andy Chu,Sudha Chudamani,Kristian Cibulskis,Giovanni Ciriello,Amanda Clarke,Stephen W. Coons,Leslie Cope,Daniel Crain,Erin Curley,Ludmila Danilova,Stefania D’Atri,Tanja M. Davidsen,Michael A. Davies,Keith A. Delman,John A. Demchok,Qixia A. Deng,Yonathan Lissanu Deribe,Noreen Dhalla,Rajiv Dhir,Daniel DiCara,М С Диникин,Michael Dubina,J. Stephen Ebrom,Sophie C. Egea,Greg Eley,Jay Engel,Jennifer Eschbacher,Konstantin Fedosenko,Ina Felau,Timothy Fennell,Martin L. Ferguson,Sheila Fisher,Keith T. Flaherty,Scott Frazer,Jessica Frick,Victoria Fulidou,Stacey Gabriel,Jianjiong Gao,Johanna Gardner,Levi A. Garraway,Julie M. Gastier‐Foster,Carmelo Gaudioso,Nils Gehlenborg,Giannicola Genovese,Mark Gerken,Jeffrey E. Gershenwald,Gad Getz,Carmen Gomez-Fernández,Thomas Gribbin,Jonna Grimsby,Benjamin Groß,Ranabir Guin,Tony Gutschner,Angela Hadjipanayis,Ruth Halaban,Benjamin Hanf,David Haussler,Lauren E. Haydu,D. Neil Hayes,Nicholas K. Hayward,David I. Heiman,Lynn M. Herbert,James G. Herman,Peter Hersey,Katherine A. Hoadley,Eran Hodis,Robert A. Holt,Dave S.B. Hoon,Susan Hoppough,Alan P. Hoyle,Franklin W. Huang,Mei Huang,Sharon K. Huang,Carolyn M. Hutter,Matthew Ibbs,Lisa Iype,Anders Jacobsen,Valerie Jakrot,Alyssa Janning,William R. Jeck,Stuart R. Jefferys,Mark A. Jensen,Corbin D. Jones,Steven Jones,Ju Zhang,Hojabr Kakavand,Hyojin Kang,Richard Kefford,Fadlo R. Khuri,Jaegil Kim,John M. Kirkwood,Joachim Klode,Anil Korkut,Konstanty Korski,Michael Krauthammer,Raju Kucherlapati,Lawrence N. Kwong,Witold Kycler,Marc Ladanyi,Phillip H. Lai,Peter W. Laird,Eric S. Lander,Michael S. Lawrence,Alexander J. Lazar,Radosław Łaźniak,Darlene Lee,Jeffrey E. Lee,Junehawk Lee,Kenneth Lee,Semin Lee,William Lee,Ewa Leporowska,Kristen Leraas,Haiyan I. Li,Tara M. Lichtenberg,Lee Lichtenstein,Pei Lin,Shiyun Ling,Jia Liu,Ouida Liu,Wenbin Liu,Georgina V. Long,Yiling Lu,Xiaotu Ma,Yussanne Ma,Andrzej Maćkiewicz,Harshad S. Mahadeshwar,Jared Malke,David Mallery,Georgy M. Manikhas,Graham J. Mann,Marco A. Marra,Brenna Matejka,Michael Mayo,Sousan Mehrabi,Shaowu Meng,Matthew Meyerson,Piotr A. Mieczkowski,John P. Miller,Martin L. Miller,Gordon B. Mills,Fedor Moiseenko,Richard A. Moore,Scott Morris,Carl Morrison,Donald L. Morton,Stergios J. Moschos,Lisle E. Mose,Florian L. Muller,Andrew J. Mungall,Dawid Murawa,P. Murawa,Bradley A. Murray,Luigi Nezi,Sam Ng,Dana Nicholson,Michael S. Noble,Adeboye O. Osunkoya,Taofeek K. Owonikoko,Bradley A. Ozenberger,Elena Pagani,O V Paklina,Angeliki Pantazi,Michael Parfenov,Jeremy Parfitt,Peter J. Park,Woong-Yang Park,Joel S. Parker,Francesca Passarelli,Robert Penny,Charles M. Perou,Todd Pihl,Olga Potapova,Víctor G. Prieto,Alexei Protopopov,Michael J. Quinn,Amie Radenbaugh,Kunal Rai,Suresh S. Ramalingam,Ayush T. Raman,Nilsa C. Ramirez,Ricardo J. Ramirez,Uma Rao,W. Kimryn Rathmell,Xiaojia Ren,Sheila M. Reynolds,Jeffrey Roach,A. Gordon Robertson,Merrick I. Ross,Jason Roszik,Giandomenico Russo,Gordon Saksena,Charles Saller,Yardena Samuels,Chris Sander,Cindy Sander,George E. Sandusky,Netty Santoso,Melissa Saul,Robyn P.M. Saw,Dirk Schadendorf,Jacqueline E. Schein,Nikolaus Schultz,Steven E. Schumacher,Charles Schwallier,Jonathan G. Seidman,Pedamallu Chandra Sekhar,Harmanjatinder S. Sekhon,Yasin Şenbabaoğlu,Sahil Seth,Kerwin F. Shannon,Samantha Sharpe,Norman E. Sharpless,Kenna Shaw,Candace Shelton,Troy Shelton,Ronglai Shen,Margi Sheth,Yan Shi,Carolyn J. Shiau,Ilya Shmulevich,Gabriel L. Sica,Janae V. Simons,Rileen Sinha,Payal Sipahimalani,Heidi J. Sofia,Matthew G. Soloway,Xingzhi Song,Carrie Sougnez,Andrew J. Spillane,Arkadiusz Spychała,Jonathan R. Stretch,Joshua M. Stuart,Wiktoria Maria Suchorska,Antje Sucker,S. Onur Sumer,Yichao Sun,Maria Synott,Barbara Tabak,Teresa R. Tabler,Angela Tam,Donghui Tan,Jie Hu,Roy Tarnuzzer,Katherine Tarvin,Honorata Tatka,Barry S. Taylor,M. Teresiak,Nina Thiessen,John F. Thompson,Leigh B. Thorne,Vésteinn Thórsson,Jeffrey M. Trent,Timothy J. Triche,Kenneth Y. Tsai,Peiling Tsou,David J. Van Den Berg,Eliezer M. Van Allen,Umadevi Veluvolu,Roeland Verhaak,Douglas Voet,Olga Voronina,Vonn Walter,Jessica Walton,Yunhu Wan,Yuling Wang,Zhining Wang,Scot Waring,Ian R. Watson,Nils Weinhold,John N. Weinstein,Daniel J. Weisenberger,Peter White,Matthew D. Wilkerson,James S. Wilmott,Lisa Wise,Maciej Wiznerowicz,Scott E. Woodman,Chang Jiun Wu,Chia Chin Wu,Junyuan Wu,Ye Wu,Ruibin Xi,Andrew Wei Xu,Da Yang,Liming Yang,Lixing Yang,Travis I. Zack,Jean C. Zenklusen,Hailei Zhang,Jianhua Zhang,Wei Zhang,Xiaobei Zhao,Jingchun Zhu,Kelsey Zhu,Lisa Zimmer,Erik Zmuda,Lihua Zou

Biology

Melanoma

Mutant

2015

We describe the landscape of genomic alterations in cutaneous melanomas through DNA, RNA, and protein-based analysis of 333 primary and/or metastatic melanomas from 331 patients. We establish a framework for genomic classification into one of four subtypes based on the pattern of the most prevalent significantly mutated genes: mutant BRAF, mutant RAS, mutant NF1, and Triple-WT (wild-type). Integrative analysis reveals enrichment of KIT mutations and focal amplifications and complex structural rearrangements as a feature of the Triple-WT subtype. We found no significant outcome correlation with genomic classification, but samples assigned a transcriptomic subclass enriched for immune gene expression associated with lymphocyte infiltrate on pathology review and high LCK protein expression, a T cell marker, were associated with improved patient survival. This clinicopathological and multi-dimensional analysis suggests that the prognosis of melanoma patients with regional metastases is influenced by tumor stroma immunobiology, offering insights to further personalize therapeutic decision-making.

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“Genomic Classification of Cutaneous Melanoma” is a paper by Rehan Akbani Kadir C. Akdemir Bülent Arman Aksoy Monique Albert Adrian Ally Samirkumar B. Amin Harindra Arachchi Arshi Arora J. Todd Auman Brenda Ayala Julien Baboud Miruna Balasundaram Saianand Balu Nandita Barnabas John M.S. Bartlett Pam Bartlett Boris C. Bastian Stephen B. Baylin Madhusmita Behera D. K. Belyaev Christopher C. Benz Brady Bernard Rameen Beroukhim Natalie Bir Aaron Black Tom Bodenheimer Lori Boice Genevieve M. Boland R. Bono Moiz S. Bootwalla Marcus W. Bosenberg Jay Bowen Reanne Bowlby Christopher A. Bristow Laura Brockway-Lunardi Denise Brooks Jakub Brzezinski Wiam Bshara Elizabeth Buda William R. Burns Yaron S.N. Butterfield M. Button Tiffany L. Calderone Giancarlo Antonini Cappellini Candace Carter Scott L. Carter Lynn Cherney Andrew D. Cherniack Aaron Chevalier Lynda Chin Juok Cho Raymond J. Cho Yoon La Choi Andy Chu Sudha Chudamani Kristian Cibulskis Giovanni Ciriello Amanda Clarke Stephen W. Coons Leslie Cope Daniel Crain Erin Curley Ludmila Danilova Stefania D’Atri Tanja M. Davidsen Michael A. Davies Keith A. Delman John A. Demchok Qixia A. Deng Yonathan Lissanu Deribe Noreen Dhalla Rajiv Dhir Daniel DiCara М С Диникин Michael Dubina J. Stephen Ebrom Sophie C. Egea Greg Eley Jay Engel Jennifer Eschbacher Konstantin Fedosenko Ina Felau Timothy Fennell Martin L. Ferguson Sheila Fisher Keith T. Flaherty Scott Frazer Jessica Frick Victoria Fulidou Stacey Gabriel Jianjiong Gao Johanna Gardner Levi A. Garraway Julie M. Gastier‐Foster Carmelo Gaudioso Nils Gehlenborg Giannicola Genovese Mark Gerken Jeffrey E. Gershenwald Gad Getz Carmen Gomez-Fernández Thomas Gribbin Jonna Grimsby Benjamin Groß Ranabir Guin Tony Gutschner Angela Hadjipanayis Ruth Halaban Benjamin Hanf David Haussler Lauren E. Haydu D. Neil Hayes Nicholas K. Hayward David I. Heiman Lynn M. Herbert James G. Herman Peter Hersey Katherine A. Hoadley Eran Hodis Robert A. Holt Dave S.B. Hoon Susan Hoppough Alan P. Hoyle Franklin W. Huang Mei Huang Sharon K. Huang Carolyn M. Hutter Matthew Ibbs Lisa Iype Anders Jacobsen Valerie Jakrot Alyssa Janning William R. Jeck Stuart R. Jefferys Mark A. Jensen Corbin D. Jones Steven Jones Ju Zhang Hojabr Kakavand Hyojin Kang Richard Kefford Fadlo R. Khuri Jaegil Kim John M. Kirkwood Joachim Klode Anil Korkut Konstanty Korski Michael Krauthammer Raju Kucherlapati Lawrence N. Kwong Witold Kycler Marc Ladanyi Phillip H. Lai Peter W. Laird Eric S. Lander Michael S. Lawrence Alexander J. Lazar Radosław Łaźniak Darlene Lee Jeffrey E. Lee Junehawk Lee Kenneth Lee Semin Lee William Lee Ewa Leporowska Kristen Leraas Haiyan I. Li Tara M. Lichtenberg Lee Lichtenstein Pei Lin Shiyun Ling Jia Liu Ouida Liu Wenbin Liu Georgina V. Long Yiling Lu Xiaotu Ma Yussanne Ma Andrzej Maćkiewicz Harshad S. Mahadeshwar Jared Malke David Mallery Georgy M. Manikhas Graham J. Mann Marco A. Marra Brenna Matejka Michael Mayo Sousan Mehrabi Shaowu Meng Matthew Meyerson Piotr A. Mieczkowski John P. Miller Martin L. Miller Gordon B. Mills Fedor Moiseenko Richard A. Moore Scott Morris Carl Morrison Donald L. Morton Stergios J. Moschos Lisle E. Mose Florian L. Muller Andrew J. Mungall Dawid Murawa P. Murawa Bradley A. Murray Luigi Nezi Sam Ng Dana Nicholson Michael S. Noble Adeboye O. Osunkoya Taofeek K. Owonikoko Bradley A. Ozenberger Elena Pagani O V Paklina Angeliki Pantazi Michael Parfenov Jeremy Parfitt Peter J. Park Woong-Yang Park Joel S. Parker Francesca Passarelli Robert Penny Charles M. Perou Todd Pihl Olga Potapova Víctor G. Prieto Alexei Protopopov Michael J. Quinn Amie Radenbaugh Kunal Rai Suresh S. Ramalingam Ayush T. Raman Nilsa C. Ramirez Ricardo J. Ramirez Uma Rao W. Kimryn Rathmell Xiaojia Ren Sheila M. Reynolds Jeffrey Roach A. Gordon Robertson Merrick I. Ross Jason Roszik Giandomenico Russo Gordon Saksena Charles Saller Yardena Samuels Chris Sander Cindy Sander George E. Sandusky Netty Santoso Melissa Saul Robyn P.M. Saw Dirk Schadendorf Jacqueline E. Schein Nikolaus Schultz Steven E. Schumacher Charles Schwallier Jonathan G. Seidman Pedamallu Chandra Sekhar Harmanjatinder S. Sekhon Yasin Şenbabaoğlu Sahil Seth Kerwin F. Shannon Samantha Sharpe Norman E. Sharpless Kenna Shaw Candace Shelton Troy Shelton Ronglai Shen Margi Sheth Yan Shi Carolyn J. Shiau Ilya Shmulevich Gabriel L. Sica Janae V. Simons Rileen Sinha Payal Sipahimalani Heidi J. Sofia Matthew G. Soloway Xingzhi Song Carrie Sougnez Andrew J. Spillane Arkadiusz Spychała Jonathan R. Stretch Joshua M. Stuart Wiktoria Maria Suchorska Antje Sucker S. Onur Sumer Yichao Sun Maria Synott Barbara Tabak Teresa R. Tabler Angela Tam Donghui Tan Jie Hu Roy Tarnuzzer Katherine Tarvin Honorata Tatka Barry S. Taylor M. Teresiak Nina Thiessen John F. Thompson Leigh B. Thorne Vésteinn Thórsson Jeffrey M. Trent Timothy J. Triche Kenneth Y. Tsai Peiling Tsou David J. Van Den Berg Eliezer M. Van Allen Umadevi Veluvolu Roeland Verhaak Douglas Voet Olga Voronina Vonn Walter Jessica Walton Yunhu Wan Yuling Wang Zhining Wang Scot Waring Ian R. Watson Nils Weinhold John N. Weinstein Daniel J. Weisenberger Peter White Matthew D. Wilkerson James S. Wilmott Lisa Wise Maciej Wiznerowicz Scott E. Woodman Chang Jiun Wu Chia Chin Wu Junyuan Wu Ye Wu Ruibin Xi Andrew Wei Xu Da Yang Liming Yang Lixing Yang Travis I. Zack Jean C. Zenklusen Hailei Zhang Jianhua Zhang Wei Zhang Xiaobei Zhao Jingchun Zhu Kelsey Zhu Lisa Zimmer Erik Zmuda Lihua Zou published in 2015. It has an Open Access status of “hybrid”. You can read and download a PDF Full Text of this paper here.