Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

Mclellan, Michael D.; Zhang, Jiashan; Zhang, Jianhua; Zhang, Nianxiang; Zhang, Qunyuan; Zhang, Wei; Zhao, Wei; Zheng, Siyuan; Zhu, Jing; Zmuda, Erik; Zou, Lihua; Ye, Kai; Hoadley, Katherine A.; Yoshihara, Kosuke; Yuan, Yuan; Yung, Alfred K.; Zack, Travis; Zeng, Dong; Zenklusen, Jean Claude; Van 't Veer, Laura J.; Zhang, Hailei; Gordon Robertson, A.; Waes, Van; Yau, Christina; Van't Veer, L. J.; Arman Aksoy, B.; Todd Auman, J.; Abbott, Rachel; Abbott, Scott; Aldape, Kenneth; Ally, Adrian; Amin, Samirkumar; Aksoy, B. Arman; Anastassiou, Dimitris; Baggerly, Keith A.; Wolf, Denise M.; Balasundaram, Miruna; Balu, Saianand; Baylin, Stephen B.; Auman, J. Todd; Benz, Stephen C.; Berman, Benjamin P.; Carter, Scott L.; Bernard, Brady; Bhatt, Ami S.; Birol, Inanc; Black, Aaron D.; Cherniack, Andrew D.; Bodenheimer, Tom; Bootwalla, Moiz S.; Bowen, Jay; Bressler, Ryan; Bristow, Christopher A.; Brooks, Angela N.; Broom, Bradley; Buda, Elizabeth; Burton, Robert; Butterfield, Yaron S. N.; Tamborero, David; Carlin, Daniel; Casasent, Tod D.; Chang, Kyle; Chanock, Stephen; Chin, Lynda; Cho, Dong-Yeon; Cho, Juok; Chuah, Eric; Chun, Hye-Jung E.; Cibulskis, Kristian; Ng, Sam; Ciriello, Giovanni; Cleland, James; Cline, Melisssa; Craft, Brian; Creighton, Chad J.; Danilova, Ludmila; Doddapaneni, Harsha Vardhan; Davidsen, Tanja; Davis, Caleb; Dees, Nathan D.; Delehaunty, Kim; Demchok, John A.; Leiserson, Max Dm M.; Dhalla, Noreen; DiCara, Daniel; Dinh, Huyen; Dobson, Jason R.; Dodda, Deepti; Donehower, Lawrence; Dooling, David J.; Dresdner, Gideon; Drummond, Jennifer; Eakin, Andrea; Niu, Beifang; Edgerton, Mary; Eldred, Jim M.; López-Bigas, Nuria; Eley, Greg; Ellrott, Kyle; Fan, Cheng; Fei, Suzanne; Felau, Ina; Frazer, Scott; Freeman, Samuel S.; Frick, Jessica; Fronick, Catrina C.; Fulton, Lucinda L.; Miller, Martin Lee; Fulton, Robert; Gabriel, Stacey B.; Gao, Jianjiong; Gastier Foster, Julie M.; Gehlenborg, Nils; George, Myra; Getz, Gad; Uzunangelov, Vladislav; Gibbs, Richard; Goldman, Mary; Neil Hayes, D.; Gonzalez-Perez, Abel; Gross, Benjamin; David,; Guin, Ranabir; Gunaratne, Preethi; Hadjipanayis, Angela; Hamilton, Mark P.; Hamilton, Stanley R.; Han, Leng; Han, Yi; Harper, Hollie A.; Haseley, Psalm; Kandoth, Cyriac; Haussler, David; Heiman, David I.; Helman, Elena; Hayes, D. Neil; Helsel, Carmen; Corbin, D.; Herbrich, Shelley M.; Herman, James G.; Hinoue, Toshinori; Jones, Steven J. M.; Akbani, Rehan; Hirst, Carrie; Hirst, Martin; Holt, Robert A.; Hoyle, Alan P.; Iype, Lisa; Jacobsen, Anders; Jeffreys, Stuart R.; Jensen, Mark A.; Jones, Corbin D.; Ju, Zhenlin; Shen, Hui; Jung, Joonil; Kahles, Andre; Kahn, Ari; Kalicki-Veizer, Joelle; Kalra, Divya; Kanchi, Krishna-Latha; Kane, David W.; Kim, Hoon; Kim, Jaegil; Knijnenburg, Theo; Omberg, Larsson; Koboldt, Daniel C.; Kovar, Christie; Kramer, Roger; Kreisberg, Richard; Kucherlapati, Raju; Ladanyi, Marc; Lander, Eric S.; Van Lehmann, Kjong; Larson, David E.; Lawrence, Michael S.; Chu, Andy; Lee, Darlene; Lee, Eunjung; Lee, Semin; Lee, William; Leinonen, Kalle; Lehmann, Kjong-Van; Leraas, Kristen M.; Lerner, Seth; Margolin, Adam A.; Levine, Douglas A.; Lewis, Lora; Ley, Timothy J.; Li, Haiyan I.; Li, Jun; Li, Wei; Liang, Han; Lichtenberg, Tara M.; Lin, Jake; Wenbin,; van’t Veer, Laura J.; Lin, Ling; Lin, Pei; Liu, Wenbin; Liu, Yingchun; Liu, Yuexin; Lorenzi, Philip L.; Lu, Charles; Lovelace,; Lu, Yiling; Luquette, Lovelace J.; Singer,; Ma, Singer; Lopez-Bigas, Nuria; Magrini, Vincent J.; Mahadeshwar, Harshad S.; Mardis, Elaine R.; Marra, Marco A.; Mayo, Michael; McAllister, Cynthia; McGuire, Sean E.; McMichael, Joshua F.; Melott, James; Meng, Shaowu; Meyerson, Matthew; Laird, Peter W.; Mieczkowski, Piotr A.; Miller, Christopher A.; Miller, Martin L.; Miller, Michael; Moore, Richard A.; Morgan, Margaret; Morton, Donna; Mose, Lisle E.; Mungall, Andrew J.; Muzny, Donna; Raphael, Benjamin J.; Nguyen, Lam; Noble, Michael S.; Noushmehr, Houtan; O'Laughlin, Michelle; O’Laughlin, Michelle; Yang, TaiHsien Ou; Ojesina, Akinyemi I.; Ozenberger, Brad; Hsien, Tai; Pantazi, Angeliki; Ding, Li; Yang, T.-H. Ou; Parfenov, Michael; Park, Peter J.; Parker, Joel S.; Paull, Evan; Pedamallu, Chandra Sekhar; Pihl, Todd; Pohl, Craig; Pot, David; Protopopov, Alexei; Robertson, A. Gordon; Przytycka, Teresa; Radenbaugh, Amie; Ratsch, Gunnar; Ramirez, Nilsa C.; Ramirez, Ricardo; Rätsch, G.; Reid, Jeffrey; Ren, Xiaojia; Reva, Boris; Reynolds, Sheila M.; Byers, Lauren A.; Ra¨tsch, Gunnar; Rhie, Suhn K.; Roach, Jeffrey; Rovira, Hector; Ryan, Michael; Saksena, Gordon; Salama, Sofie; Sander, Chris; Santoso, Netty; Schein, Jacqueline E.; Mills, Gordon B.; Schmidt, Heather; Schultz, Nikolaus; Schumacher, Steven E.; Seidman, Jonathan; Senbabaoglu, Yasin; Seth, Sahil; Sharpe, Samantha; Shen, Ronglai; Sheth, Margi; Shi, Yan; Shmulevich, Ilya; Weinstein, John N.; Silva, Grace O.; Simons, Janae V.; Sinha, Rileen; Sipahimalani, Payal; Smith, Scott M.; Sofia, Heidi J.; Sokolov, Artem; Soloway, Mathew G.; Song, Xingzhi; Sougnez, Carrie; Van Waes, Carter; Spellman, Paul; Staudt, Louis; Stewart, Chip; Stojanov, Petar; Sumer, S. Onur; Su, Xiaoping; Sun, Yichao; Swatloski, Teresa; Tabak, Barbara; Tam, Angela; Chen, Zhong; Tan, Donghui; Tang, Jiabin; Onur Sumer, S.; Tarnuzzer, Roy; Taylor, Barry S.; Thiessen, Nina; Thorsson, Vesteinn; Triche, Timothy; Van Den Berg, David J.; Vandin, Fabio; Varhol, Richard J.; Collisson, Eric A.; Vaske, Charles J.; Veluvolu, Umadevi; Verhaak, Roeland; Voet, Doug; Walker, Jason; Wallis, John W.; Waltman, Peter; Wan, Yunhu; Wang, Min; Wang, Wenyi; Benz, Christopher C.; Wang, Zhining; Waring, Scot; Weinhold, Nils; Weisenberger, Daniel J.; Wendl, Michael C.; Wheeler, David; Wu, Chang-Jiun; Wilkerson, Matthew D.; Wu, Chia-Chin; Wilson, Richard K.; Perou, Charles M.; Wu, Hsin-Ta; Wu, Junyuan; Wise, Lisa; Wong, Andrew; Wu, C.-J.; Wu, C.-C.; Wylie, Todd; Xi, Liu; Xi, Ruibin; Xia, Zheng; Stuart, Joshua M.; Xu, Andrew W.; Yang, Da; Yang, Liming; Yang, Lixing; Yang, Yang; Yao, Jun; Yao, Rong

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Katherine Hoadley
Mclellan et al., 2014

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Elsevier, Cell, 4(158), p. 929-944, 2014

DOI: 10.1016/j.cell.2014.06.049

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@article{Mclellan2014,
  abstract = {Recent genomic analyses of pathologically defined tumor types identify ''within-a-tissue'' disease sub-types. However, the extent to which genomic sig-natures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform on 3,527 specimens from 12 cancer types, revealing a unified classification into 11 major subtypes. Five subtypes were nearly identical to their tissue-of-origin counterparts, but several distinct cancer types were found to converge into common subtypes. Lung squamous, head and neck, and a subset of bladder cancers coalesced into one subtype typified by TP53 alterations, TP63 amplifications, and high expression of immune and proliferation pathway genes. Of note, bladder cancers split into three pan-cancer subtypes. The multiplatform classification, while correlated with tissue-of-origin, provides inde-pendent information for predicting clinical outcomes. All data sets are available for data-mining from a uni-fied resource to support further biological discov-eries and insights into novel therapeutic strategies. INTRODUCTION},
  author = {Mclellan, Michael D. and Zhang, Jiashan and Zhang, Jianhua and Zhang, Nianxiang and Zhang, Qunyuan and Zhang, Wei and Zhao, Wei and Zheng, Siyuan and Zhu, Jing and Zmuda, Erik and Zou, Lihua and Ye, Kai and Hoadley, Katherine A. and Yoshihara, Kosuke and Yuan, Yuan and Yung, Alfred K. and Zack, Travis and Zeng, Dong and Zenklusen, Jean Claude and Van 't Veer, Laura J. and Zhang, Hailei and Gordon Robertson, A. and Waes, Van and Yau, Christina and Van't Veer, L. J. and Arman Aksoy, B. and Todd Auman, J. and Abbott, Rachel and Abbott, Scott and Aldape, Kenneth and Ally, Adrian and Amin, Samirkumar and Aksoy, B. Arman and Anastassiou, Dimitris and Baggerly, Keith A. and Wolf, Denise M. and Balasundaram, Miruna and Balu, Saianand and Baylin, Stephen B. and Auman, J. Todd and Benz, Stephen C. and Berman, Benjamin P. and Carter, Scott L. and Bernard, Brady and Bhatt, Ami S. and Birol, Inanc and Black, Aaron D. and Cherniack, Andrew D. and Bodenheimer, Tom and Bootwalla, Moiz S. and Bowen, Jay and Bressler, Ryan and Bristow, Christopher A. and Brooks, Angela N. and Broom, Bradley and Buda, Elizabeth and Burton, Robert and Butterfield, Yaron S. N. and Tamborero, David and Carlin, Daniel and Casasent, Tod D. and Chang, Kyle and Chanock, Stephen and Chin, Lynda and Cho, Dong-Yeon and Cho, Juok and Chuah, Eric and Chun, Hye-Jung E. and Cibulskis, Kristian and Ng, Sam and Ciriello, Giovanni and Cleland, James and Cline, Melisssa and Craft, Brian and Creighton, Chad J. and Danilova, Ludmila and Doddapaneni, Harsha Vardhan and Davidsen, Tanja and Davis, Caleb and Dees, Nathan D. and Delehaunty, Kim and Demchok, John A. and Leiserson, Max Dm M. and Dhalla, Noreen and DiCara, Daniel and Dinh, Huyen and Dobson, Jason R. and Dodda, Deepti and Donehower, Lawrence and Dooling, David J. and Dresdner, Gideon and Drummond, Jennifer and Eakin, Andrea and Niu, Beifang and Edgerton, Mary and Eldred, Jim M. and López-Bigas, Nuria and Eley, Greg and Ellrott, Kyle and Fan, Cheng and Fei, Suzanne and Felau, Ina and Frazer, Scott and Freeman, Samuel S. and Frick, Jessica and Fronick, Catrina C. and Fulton, Lucinda L. and Miller, Martin Lee and Fulton, Robert and Gabriel, Stacey B. and Gao, Jianjiong and Gastier Foster, Julie M. and Gehlenborg, Nils and George, Myra and Getz, Gad and Uzunangelov, Vladislav and Gibbs, Richard and Goldman, Mary and Neil Hayes, D. and Gonzalez-Perez, Abel and Gross, Benjamin and David,  and Guin, Ranabir and Gunaratne, Preethi and Hadjipanayis, Angela and Hamilton, Mark P. and Hamilton, Stanley R. and Han, Leng and Han, Yi and Harper, Hollie A. and Haseley, Psalm and Kandoth, Cyriac and Haussler, David and Heiman, David I. and Helman, Elena and Hayes, D. Neil and Helsel, Carmen and Corbin, D. and Herbrich, Shelley M. and Herman, James G. and Hinoue, Toshinori and Jones, Steven J. M. and Akbani, Rehan and Hirst, Carrie and Hirst, Martin and Holt, Robert A. and Hoyle, Alan P. and Iype, Lisa and Jacobsen, Anders and Jeffreys, Stuart R. and Jensen, Mark A. and Jones, Corbin D. and Ju, Zhenlin and Shen, Hui and Jung, Joonil and Kahles, Andre and Kahn, Ari and Kalicki-Veizer, Joelle and Kalra, Divya and Kanchi, Krishna-Latha and Kane, David W. and Kim, Hoon and Kim, Jaegil and Knijnenburg, Theo and Omberg, Larsson and Koboldt, Daniel C. and Kovar, Christie and Kramer, Roger and Kreisberg, Richard and Kucherlapati, Raju and Ladanyi, Marc and Lander, Eric S. and Van Lehmann, Kjong and Larson, David E. and Lawrence, Michael S. and Chu, Andy and Lee, Darlene and Lee, Eunjung and Lee, Semin and Lee, William and Leinonen, Kalle and Lehmann, Kjong-Van and Leraas, Kristen M. and Lerner, Seth and Margolin, Adam A. and Levine, Douglas A. and Lewis, Lora and Ley, Timothy J. and Li, Haiyan I. and Li, Jun and Li, Wei and Liang, Han and Lichtenberg, Tara M. and Lin, Jake and Wenbin,  and van’t Veer, Laura J. and Lin, Ling and Lin, Pei and Liu, Wenbin and Liu, Yingchun and Liu, Yuexin and Lorenzi, Philip L. and Lu, Charles and Lovelace,  and Lu, Yiling and Luquette, Lovelace J. and Singer,  and Ma, Singer and Lopez-Bigas, Nuria and Magrini, Vincent J. and Mahadeshwar, Harshad S. and Mardis, Elaine R. and Marra, Marco A. and Mayo, Michael and McAllister, Cynthia and McGuire, Sean E. and McMichael, Joshua F. and Melott, James and Meng, Shaowu and Meyerson, Matthew and Laird, Peter W. and Mieczkowski, Piotr A. and Miller, Christopher A. and Miller, Martin L. and Miller, Michael and Moore, Richard A. and Morgan, Margaret and Morton, Donna and Mose, Lisle E. and Mungall, Andrew J. and Muzny, Donna and Raphael, Benjamin J. and Nguyen, Lam and Noble, Michael S. and Noushmehr, Houtan and O'Laughlin, Michelle and O’Laughlin, Michelle and Yang, TaiHsien Ou and Ojesina, Akinyemi I. and Ozenberger, Brad and Hsien, Tai and Pantazi, Angeliki and Ding, Li and Yang, T.-H. Ou and Parfenov, Michael and Park, Peter J. and Parker, Joel S. and Paull, Evan and Pedamallu, Chandra Sekhar and Pihl, Todd and Pohl, Craig and Pot, David and Protopopov, Alexei and Robertson, A. Gordon and Przytycka, Teresa and Radenbaugh, Amie and Ratsch, Gunnar and Ramirez, Nilsa C. and Ramirez, Ricardo and Rätsch, G. and Reid, Jeffrey and Ren, Xiaojia and Reva, Boris and Reynolds, Sheila M. and Byers, Lauren A. and Ra¨tsch, Gunnar and Rhie, Suhn K. and Roach, Jeffrey and Rovira, Hector and Ryan, Michael and Saksena, Gordon and Salama, Sofie and Sander, Chris and Santoso, Netty and Schein, Jacqueline E. and Mills, Gordon B. and Schmidt, Heather and Schultz, Nikolaus and Schumacher, Steven E. and Seidman, Jonathan and Senbabaoglu, Yasin and Seth, Sahil and Sharpe, Samantha and Shen, Ronglai and Sheth, Margi and Shi, Yan and Shmulevich, Ilya and Weinstein, John N. and Silva, Grace O. and Simons, Janae V. and Sinha, Rileen and Sipahimalani, Payal and Smith, Scott M. and Sofia, Heidi J. and Sokolov, Artem and Soloway, Mathew G. and Song, Xingzhi and Sougnez, Carrie and Van Waes, Carter and Spellman, Paul and Staudt, Louis and Stewart, Chip and Stojanov, Petar and Sumer, S. Onur and Su, Xiaoping and Sun, Yichao and Swatloski, Teresa and Tabak, Barbara and Tam, Angela and Chen, Zhong and Tan, Donghui and Tang, Jiabin and Onur Sumer, S. and Tarnuzzer, Roy and Taylor, Barry S. and Thiessen, Nina and Thorsson, Vesteinn and Triche, Timothy and Van Den Berg, David J. and Vandin, Fabio and Varhol, Richard J. and Collisson, Eric A. and Vaske, Charles J. and Veluvolu, Umadevi and Verhaak, Roeland and Voet, Doug and Walker, Jason and Wallis, John W. and Waltman, Peter and Wan, Yunhu and Wang, Min and Wang, Wenyi and Benz, Christopher C. and Wang, Zhining and Waring, Scot and Weinhold, Nils and Weisenberger, Daniel J. and Wendl, Michael C. and Wheeler, David and Wu, Chang-Jiun and Wilkerson, Matthew D. and Wu, Chia-Chin and Wilson, Richard K. and Perou, Charles M. and Wu, Hsin-Ta and Wu, Junyuan and Wise, Lisa and Wong, Andrew and Wu, C.-J. and Wu, C.-C. and Wylie, Todd and Xi, Liu and Xi, Ruibin and Xia, Zheng and Stuart, Joshua M. and Xu, Andrew W. and Yang, Da and Yang, Liming and Yang, Lixing and Yang, Yang and Yao, Jun and Yao, Rong},
  doi = {10.1016/j.cell.2014.06.049},
  journal = {Cell},
  month = {aug},
  pages = {929-944},
  title = {Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin},
  url = {http://www.ncbi.nlm.nih.gov/pubmed/25109877},
  volume = {158},
  year = {2014}
}

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Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

Journal article published in 2014 by Michael D. Mclellan, Jiashan Zhang, Jianhua Zhang, Nianxiang Zhang, Qunyuan Zhang, Wei Zhang, Wei Zhao, Siyuan Zheng, Jing Zhu, Erik Zmuda, Lihua Zou, Kai Ye, Katherine A. Hoadley

, Kosuke Yoshihara, Yuan Yuan and other authors. Michael D. Mclellan, Jiashan Zhang, Jianhua Zhang, Nianxiang Zhang, Qunyuan Zhang, Wei Zhang, Wei Zhao, Siyuan Zheng, Jing Zhu, Erik Zmuda, Lihua Zou, Kai Ye, Katherine A. Hoadley

, Kosuke Yoshihara, Yuan Yuan, Alfred K. Yung, Travis Zack, Dong Zeng, Jean Claude Zenklusen, Laura J. Van 't Veer, Hailei Zhang, A. Gordon Robertson, Van Waes, Christina Yau, L. J. Van't Veer, B. Arman Aksoy, J. Todd Auman, Rachel Abbott, Scott Abbott, Kenneth Aldape, Adrian Ally, Samirkumar Amin, B. Arman Aksoy, Dimitris Anastassiou, Keith A. Baggerly, Denise M. Wolf, Miruna Balasundaram, Saianand Balu, Stephen B. Baylin, J. Todd Auman, Stephen C. Benz, Benjamin P. Berman, Scott L. Carter, Brady Bernard, Ami S. Bhatt, Inanc Birol, Aaron D. Black, Andrew D. Cherniack, Tom Bodenheimer, Moiz S. Bootwalla, Jay Bowen

, Ryan Bressler, Christopher A. Bristow, Angela N. Brooks, Bradley Broom, Elizabeth Buda, Robert Burton, Yaron S. N. Butterfield, David Tamborero, Daniel Carlin, Tod D. Casasent, Kyle Chang, Stephen Chanock, Lynda Chin, Dong-Yeon Cho, Juok Cho, Eric Chuah, Hye-Jung E. Chun, Kristian Cibulskis, Sam Ng, Giovanni Ciriello, James Cleland, Melisssa Cline, Brian Craft, Chad J. Creighton, Ludmila Danilova, Harsha Vardhan Doddapaneni, Tanja Davidsen, Caleb Davis, Nathan D. Dees, Kim Delehaunty, John A. Demchok, Max Dm M. Leiserson, Noreen Dhalla, Daniel DiCara, Huyen Dinh, Jason R. Dobson, Deepti Dodda, Lawrence Donehower, David J. Dooling, Gideon Dresdner, Jennifer Drummond, Andrea Eakin, Beifang Niu, Mary Edgerton, Jim M. Eldred, Nuria López-Bigas, Greg Eley, Kyle Ellrott, Cheng Fan, Suzanne Fei, Ina Felau, Scott Frazer, Samuel S. Freeman

, Jessica Frick, Catrina C. Fronick, Lucinda L. Fulton, Martin Lee Miller, Robert Fulton, Stacey B. Gabriel, Jianjiong Gao, Julie M. Gastier Foster, Nils Gehlenborg, Myra George, Gad Getz, Vladislav Uzunangelov, Richard Gibbs, Mary Goldman, D. Neil Hayes, Abel Gonzalez-Perez, Benjamin Gross, David, Ranabir Guin, Preethi Gunaratne, Angela Hadjipanayis, Mark P. Hamilton, Stanley R. Hamilton, Leng Han, Yi Han, Hollie A. Harper, Psalm Haseley, Cyriac Kandoth, David Haussler, David I. Heiman

, Elena Helman, D. Neil Hayes, Carmen Helsel, D. Corbin, Shelley M. Herbrich, James G. Herman, Toshinori Hinoue, Steven J. M. Jones, Rehan Akbani, Carrie Hirst, Martin Hirst, Robert A. Holt, Alan P. Hoyle, Lisa Iype, Anders Jacobsen, Stuart R. Jeffreys, Mark A. Jensen, Corbin D. Jones, Zhenlin Ju, Hui Shen, Joonil Jung, Andre Kahles, Ari Kahn, Joelle Kalicki-Veizer, Divya Kalra, Krishna-Latha Kanchi, David W. Kane, Hoon Kim

, Jaegil Kim, Theo Knijnenburg, Larsson Omberg, Daniel C. Koboldt, Christie Kovar, Roger Kramer, Richard Kreisberg, Raju Kucherlapati, Marc Ladanyi, Eric S. Lander, Kjong Van Lehmann, David E. Larson, Michael S. Lawrence, Andy Chu, Darlene Lee, Eunjung Lee, Semin Lee, William Lee, Kalle Leinonen, Kjong-Van Lehmann

, Kristen M. Leraas, Seth Lerner, Adam A. Margolin, Douglas A. Levine, Lora Lewis, Timothy J. Ley, Haiyan I. Li, Jun Li, Wei Li, Han Liang, Tara M. Lichtenberg, Jake Lin, Wenbin, Laura J. van’t Veer, Ling Lin, Pei Lin, Wenbin Liu, Yingchun Liu, Yuexin Liu, Philip L. Lorenzi, Charles Lu, Lovelace, Yiling Lu, Lovelace J. Luquette, Singer, Singer Ma, Nuria Lopez-Bigas, Vincent J. Magrini, Harshad S. Mahadeshwar, Elaine R. Mardis, Marco A. Marra, Michael Mayo, Cynthia McAllister, Sean E. McGuire, Joshua F. McMichael, James Melott, Shaowu Meng, Matthew Meyerson, Peter W. Laird, Piotr A. Mieczkowski, Christopher A. Miller, Martin L. Miller, Michael Miller, Richard A. Moore, Margaret Morgan, Donna Morton, Lisle E. Mose, Andrew J. Mungall, Donna Muzny, Benjamin J. Raphael, Lam Nguyen, Michael S. Noble, Houtan Noushmehr, Michelle O'Laughlin, Michelle O’Laughlin, TaiHsien Ou Yang, Akinyemi I. Ojesina, Brad Ozenberger, Tai Hsien, Angeliki Pantazi, Li Ding, T.-H. Ou Yang, Michael Parfenov, Peter J. Park, Joel S. Parker, Evan Paull, Chandra Sekhar Pedamallu, Todd Pihl, Craig Pohl, David Pot, Alexei Protopopov, A. Gordon Robertson, Teresa Przytycka, Amie Radenbaugh, Gunnar Ratsch, Nilsa C. Ramirez, Ricardo Ramirez, G. Rätsch, Jeffrey Reid, Xiaojia Ren, Boris Reva, Sheila M. Reynolds, Lauren A. Byers, Gunnar Ra¨tsch, Suhn K. Rhie, Jeffrey Roach, Hector Rovira, Michael Ryan, Gordon Saksena, Sofie Salama

, Chris Sander, Netty Santoso, Jacqueline E. Schein, Gordon B. Mills, Heather Schmidt, Nikolaus Schultz, Steven E. Schumacher, Jonathan Seidman, Yasin Senbabaoglu, Sahil Seth, Samantha Sharpe, Ronglai Shen, Margi Sheth, Yan Shi, Ilya Shmulevich, John N. Weinstein, Grace O. Silva, Janae V. Simons, Rileen Sinha, Payal Sipahimalani, Scott M. Smith, Heidi J. Sofia, Artem Sokolov, Mathew G. Soloway, Xingzhi Song, Carrie Sougnez, Carter Van Waes, Paul Spellman, Louis Staudt, Chip Stewart, Petar Stojanov, S. Onur Sumer, Xiaoping Su, Yichao Sun, Teresa Swatloski, Barbara Tabak, Angela Tam, Zhong Chen, Donghui Tan, Jiabin Tang, S. Onur Sumer, Roy Tarnuzzer, Barry S. Taylor, Nina Thiessen, Vesteinn Thorsson, Timothy Triche, David J. Van Den Berg, Fabio Vandin, Richard J. Varhol, Eric A. Collisson, Charles J. Vaske, Umadevi Veluvolu, Roeland Verhaak, Doug Voet, Jason Walker, John W. Wallis, Peter Waltman, Yunhu Wan, Min Wang, Wenyi Wang, Christopher C. Benz, Zhining Wang, Scot Waring

, Nils Weinhold, Daniel J. Weisenberger, Michael C. Wendl, David Wheeler, Chang-Jiun Wu, Matthew D. Wilkerson, Chia-Chin Wu, Richard K. Wilson, Charles M. Perou, Hsin-Ta Wu, Junyuan Wu, Lisa Wise, Andrew Wong, C.-J. Wu, C.-C. Wu, Todd Wylie, Liu Xi, Ruibin Xi, Zheng Xia, Joshua M. Stuart

, Andrew W. Xu, Da Yang, Liming Yang, Lixing Yang, Yang Yang, Jun Yao, Rong Yao

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Abstract

Recent genomic analyses of pathologically defined tumor types identify ''within-a-tissue'' disease sub-types. However, the extent to which genomic sig-natures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform on 3,527 specimens from 12 cancer types, revealing a unified classification into 11 major subtypes. Five subtypes were nearly identical to their tissue-of-origin counterparts, but several distinct cancer types were found to converge into common subtypes. Lung squamous, head and neck, and a subset of bladder cancers coalesced into one subtype typified by TP53 alterations, TP63 amplifications, and high expression of immune and proliferation pathway genes. Of note, bladder cancers split into three pan-cancer subtypes. The multiplatform classification, while correlated with tissue-of-origin, provides inde-pendent information for predicting clinical outcomes. All data sets are available for data-mining from a uni-fied resource to support further biological discov-eries and insights into novel therapeutic strategies. INTRODUCTION

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Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

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