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  1. Article: Proteogenomic characterization of pancreatic ductal adenocarcinoma

    Cao, Liwei / Huang, Chen / Cui Zhou, Daniel / Hu, Yingwei / Lih, T. Mamie / Savage, Sara R. / Krug, Karsten / Clark, David J. / Schnaubelt, Michael / Chen, Lijun / da Veiga Leprevost, Felipe / Eguez, Rodrigo Vargas / Yang, Weiming / Pan, Jianbo / Wen, Bo / Dou, Yongchao / Jiang, Wen / Liao, Yuxing / Shi, Zhiao /
    Terekhanova, Nadezhda V. / Cao, Song / Lu, Rita Jui-Hsien / Li, Yize / Liu, Ruiyang / Zhu, Houxiang / Ronning, Peter / Wu, Yige / Wyczalkowski, Matthew A. / Easwaran, Hariharan / Danilova, Ludmila / Mer, Arvind Singh / Yoo, Seungyeul / Wang, Joshua M. / Liu, Wenke / Haibe-Kains, Benjamin / Thiagarajan, Mathangi / Jewell, Scott D. / Hostetter, Galen / Newton, Chelsea J. / Li, Qing Kay / Roehrl, Michael H. / Fenyö, David / Wang, Pei / Nesvizhskii, Alexey I. / Mani, D.R. / Omenn, Gilbert S. / Boja, Emily S. / Mesri, Mehdi / Robles, Ana I. / Rodriguez, Henry / Bathe, Oliver F. / Chan, Daniel W. / Hruban, Ralph H. / Ding, Li / Zhang, Bing / Zhang, Hui / Amin, Mitual / An, Eunkyung / Ayad, Christina / Bauer, Thomas / Birger, Chet / Birrer, Michael J. / Boca, Simina M. / Bocik, William / Borucki, Melissa / Cai, Shuang / Carr, Steven A. / Cerda, Sandra / Chen, Huan / Chen, Steven / Chesla, David / Chinnaiyan, Arul M. / Colaprico, Antonio / Cottingham, Sandra / Derejska, Magdalena / Dhanasekaran, Saravana M. / Domagalski, Marcin J. / Druker, Brian J. / Duffy, Elizabeth / Dyer, Maureen A. / Edwards, Nathan J. / Ellis, Matthew J. / Eschbacher, Jennifer / Francis, Alicia / Francis, Jesse / Gabriel, Stacey / Gabrovski, Nikolay / Gardner, Johanna / Getz, Gad / Gillette, Michael A. / Goldthwaite, Charles A. / Grady, Pamela / Guo, Shuai / Hariharan, Pushpa / Hiltke, Tara / Hindenach, Barbara / Hoadley, Katherine A. / Huang, Jasmine / Jones, Corbin D. / Ketchum, Karen A. / Kinsinger, Christopher R. / Koziak, Jennifer M. / Kusnierz, Katarzyna / Liu, Tao / Long, Jiang / Mallery, David / Mareedu, Sailaja / Matteotti, Ronald / Maunganidze, Nicollette / McGarvey, Peter B. / Minoo, Parham / Paklina, Oxana V. / Paulovich, Amanda G. / Payne, Samuel H. / Potapova, Olga / Pruetz, Barbara / Qi, Liqun / Roche, Nancy / Rodland, Karin D. / Rohrer, Daniel C. / Schadt, Eric E. / Shabunin, Alexey V. / Shelton, Troy / Shutack, Yvonne / Singh, Shilpi / Smith, Michael / Smith, Richard D. / Sokoll, Lori J. / Suh, James / Thangudu, Ratna R. / Tsang, Shirley X. / Um, Ki Sung / Valley, Dana R. / Vatanian, Negin / Wang, Wenyi / Wilson, George D. / Wiznerowicz, Maciej / Zhang, Zhen / Zhao, Grace

    Elsevier Inc. Cell. 2021 Sept. 16, v. 184, no. 19

    2021  

    Abstract: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient survival. Toward understanding the underlying molecular alterations that drive PDAC oncogenesis, we conducted comprehensive proteogenomic analysis of 140 pancreatic ... ...

    Institution Clinical Proteomic Tumor Analysis Consortium
    Abstract Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient survival. Toward understanding the underlying molecular alterations that drive PDAC oncogenesis, we conducted comprehensive proteogenomic analysis of 140 pancreatic cancers, 67 normal adjacent tissues, and 9 normal pancreatic ductal tissues. Proteomic, phosphoproteomic, and glycoproteomic analyses were used to characterize proteins and their modifications. In addition, whole-genome sequencing, whole-exome sequencing, methylation, RNA sequencing (RNA-seq), and microRNA sequencing (miRNA-seq) were performed on the same tissues to facilitate an integrated proteogenomic analysis and determine the impact of genomic alterations on protein expression, signaling pathways, and post-translational modifications. To ensure robust downstream analyses, tumor neoplastic cellularity was assessed via multiple orthogonal strategies using molecular features and verified via pathological estimation of tumor cellularity based on histological review. This integrated proteogenomic characterization of PDAC will serve as a valuable resource for the community, paving the way for early detection and identification of novel therapeutic targets.
    Keywords adenocarcinoma ; carcinogenesis ; genomics ; histology ; methylation ; microRNA ; patients ; proteomics ; sequence analysis ; therapeutics
    Language English
    Dates of publication 2021-0916
    Size p. 5031-5052.e26.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2021.08.023
    Database NAL-Catalogue (AGRICOLA)

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  2. Article: Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas

    Abeshouse, Adam / Adebamowo, Clement / Adebamowo, Sally N / Akbani, Rehan / Akeredolu, Teniola / Ally, Adrian / Anderson, Matthew L / Anur, Pavana / Appelbaum, Elizabeth L / Armenia, Joshua / Auman, J. Todd / Bailey, Matthew H / Baker, Laurence / Balasundaram, Miruna / Balu, Saianand / Barthel, Floris P / Bartlett, John / Baylin, Stephen B / Behera, Madhusmita /
    Belyaev, Dmitry / Bennett, Joesph / Benz, Christopher / Beroukhim, Rameen / Birrer, Michael / Bocklage, Thèrése / Bodenheimer, Tom / Boice, Lori / Bootwalla, Moiz S / Bowen, Jay / Bowlby, Reanne / Boyd, Jeff / Brohl, Andrew S / Brooks, Denise / Byers, Lauren / Carlsen, Rebecca / Castro, Patricia / Chen, Hsiao-Wei / Cherniack, Andrew D / Chibon, Fréderic / Chin, Lynda / Cho, Juok / Chuah, Eric / Chudamani, Sudha / Cibulskis, Carrie / Cooper, Lee A.D / Cope, Leslie / Cordes, Matthew G / Crain, Daniel / Curley, Erin / Danilova, Ludmila / Dao, Fanny / Davis, Ian J / Davis, Lara E / Defreitas, Timothy / Delman, Keith / Demchok, John A / Demetri, George D / Demicco, Elizabeth G / Dhalla, Noreen / Diao, Lixia / Ding, Li / DiSaia, Phil / Dottino, Peter / Doyle, Leona A / Drill, Esther / Dubina, Michael / Eschbacher, Jennifer / Fedosenko, Konstantin / Felau, Ina / Ferguson, Martin L / Frazer, Scott / Fronick, Catrina C / Fulidou, Victoria / Fulton, Lucinda A / Fulton, Robert S / Gabriel, Stacey B / Gao, Jianjiong / Gao, Qingsong / Gardner, Johanna / Gastier-Foster, Julie M / Gay, Carl M / Gehlenborg, Nils / Gerken, Mark / Getz, Gad / Godwin, Andrew K / Godwin, Eryn M / Gordienko, Elena / Grilley-Olson, Juneko E / Gutman, David A / Gutmann, David H / Hayes, D. Neil / Hegde, Apurva M / Heiman, David I / Heins, Zachary / Helsel, Carmen / Hepperla, Austin J / Higgins, Kelly / Hoadley, Katherine A / Hobensack, Shital / Holt, Robert A / Hoon, Dave B / Hornick, Jason L / Hoyle, Alan P / Hu, Xin / Huang, Mei / Hutter, Carolyn M / Iacocca, Mary / Ingram, Davis R / Ittmann, Michael / Iype, Lisa / Jefferys, Stuart R / Jones, Kevin B / Jones, Corbin D / Jones, Steven J.M / Kalir, Tamara / Karlan, Beth Y / Karseladze, Apollon / Kasaian, Katayoon / Kim, Jaegil / Kundra, Ritika / Kuo, Hanluen / Ladanyi, Marc / Lai, Phillip H / Laird, Peter W / Larsson, Erik / Lawrence, Michael S / Lazar, Alexander J / Lee, Sanghoon / Lee, Darlene / Lehmann, Kjong-Van / Leraas, Kristen M / Lester, Jenny / Levine, Douglas A / Li, Irene / Lichtenberg, Tara M / Lin, Pei / Liu, Jia / Liu, Wenbin / Liu, Eric Minwei / Lolla, Laxmi / Lu, Yiling / Ma, Yussanne / Madan, Rashna / Maglinte, Dennis T / Magliocco, Anthony / Maki, Robert G / Mallery, David / Manikhas, Georgy / Mardis, Elaine R / Mariamidze, Armaz / Marra, Marco A / Martignetti, John A / Martinez, Cathleen / Mayo, Michael / McLellan, Michael D / Meier, Sam / Meng, Shaowu / Meyerson, Matthew / Mieczkowski, Piotr A / Miller, Christopher A / Mills, Gordon B / Moore, Richard A / Morris, Scott / Mose, Lisle E / Mozgovoy, Evgeny / Mungall, Andrew J / Mungall, Karen / Nalisnik, Michael / Naresh, Rashi / Newton, Yulia / Noble, Michael S / Novak, Janet E / Ochoa, Angelica / Olvera, Narciso / Owonikoko, Taofeek K / Paklina, Oxana / Parfitt, Jeremy / Parker, Joel S / Pastore, Alessandro / Paulauskis, Joseph / Penny, Robert / Pereira, Elena / Perou, Charles M / Perou, Amy H / Pihl, Todd / Pollock, Raphael E / Potapova, Olga / Radenbaugh, Amie J / Ramalingam, Suresh S / Ramirez, Nilsa C / Rathmell, W. Kimryn / Raut, Chandrajit P / Riedel, Richard F / Reilly, Colleen / Reynolds, Sheila M / Roach, Jeffrey / Robertson, A. Gordon / Roszik, Jason / Rubin, Brian P / Sadeghi, Sara / Saksena, Gordon / Salner, Andrew / Sanchez-Vega, Francisco / Sander, Chris / Schein, Jacqueline E / Schmidt, Heather K / Schultz, Nikolaus / Schumacher, Steven E / Sekhon, Harman / Senbabaoglu, Yasin / Setdikova, Galiya / Shelton, Candace / Shelton, Troy / Shen, Ronglai / Shi, Yan / Shih, Juliann / Shmulevich, Ilya / Sica, Gabriel L / Simons, Janae V / Singer, Samuel / Sipahimalani, Payal / Skelly, Tara / Socci, Nicholas / Sofia, Heidi J / Soloway, Matthew G / Spellman, Paul / Sun, Qiang / Swanson, Patricia / Tam, Angela / Tan, Donghui / Tarnuzzer, Roy / Thiessen, Nina / Thompson, Eric / Thorne, Leigh B / Tong, Pan / Torres, Keila E / van de Rijn, Matt / Van Den Berg, David J / Van Tine, Brian A / Veluvolu, Umadevi / Verhaak, Roel / Voet, Doug / Voronina, Olga / Wan, Yunhu / Wang, Zhining / Wang, Jing / Weinstein, John N / Weisenberger, Daniel J / Wilkerson, Matthew D / Wilson, Richard K / Wise, Lisa / Wong, Tina / Wong, Winghing / Wrangle, John / Wu, Ye / Wyczalkowski, Matthew / Yang, Liming / Yau, Christina / Yellapantula, Venkata / Zenklusen, Jean C / Zhang, Jiashan (Julia) / Zhang, Hailei / Zhang, Hongxin / Zmuda, Erik

    Cell. 2017 Nov. 02, v. 171, no. 4

    2017  

    Abstract: Sarcomas are a broad family of mesenchymal malignancies exhibiting remarkable histologic diversity. We describe the multi-platform molecular landscape of 206 adult soft tissue sarcomas representing 6 major types. Along with novel insights into the ... ...

    Institution The Cancer Genome Atlas Research Network
    Abstract Sarcomas are a broad family of mesenchymal malignancies exhibiting remarkable histologic diversity. We describe the multi-platform molecular landscape of 206 adult soft tissue sarcomas representing 6 major types. Along with novel insights into the biology of individual sarcoma types, we report three overarching findings: (1) unlike most epithelial malignancies, these sarcomas (excepting synovial sarcoma) are characterized predominantly by copy-number changes, with low mutational loads and only a few genes (TP53, ATRX, RB1) highly recurrently mutated across sarcoma types; (2) within sarcoma types, genomic and regulomic diversity of driver pathways defines molecular subtypes associated with patient outcome; and (3) the immune microenvironment, inferred from DNA methylation and mRNA profiles, associates with outcome and may inform clinical trials of immune checkpoint inhibitors. Overall, this large-scale analysis reveals previously unappreciated sarcoma-type-specific changes in copy number, methylation, RNA, and protein, providing insights into refining sarcoma therapy and relationships to other cancer types.
    Keywords DNA methylation ; adults ; clinical trials ; epithelium ; genes ; genomics ; histology ; messenger RNA ; patients ; sarcoma ; therapeutics
    Language English
    Dates of publication 2017-1102
    Size p. 950-965.e28.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2017.10.014
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.

    Linehan, W Marston / Spellman, Paul T / Ricketts, Christopher J / Creighton, Chad J / Fei, Suzanne S / Davis, Caleb / Wheeler, David A / Murray, Bradley A / Schmidt, Laura / Vocke, Cathy D / Peto, Myron / Al Mamun, Abu Amar M / Shinbrot, Eve / Sethi, Anurag / Brooks, Samira / Rathmell, W Kimryn / Brooks, Angela N / Hoadley, Katherine A / Robertson, A Gordon /
    Brooks, Denise / Bowlby, Reanne / Sadeghi, Sara / Shen, Hui / Weisenberger, Daniel J / Bootwalla, Moiz / Baylin, Stephen B / Laird, Peter W / Cherniack, Andrew D / Saksena, Gordon / Haake, Scott / Li, Jun / Liang, Han / Lu, Yiling / Mills, Gordon B / Akbani, Rehan / Leiserson, Mark D M / Raphael, Benjamin J / Anur, Pavana / Bottaro, Donald / Albiges, Laurence / Barnabas, Nandita / Choueiri, Toni K / Czerniak, Bogdan / Godwin, Andrew K / Hakimi, A Ari / Ho, Thai H / Hsieh, James / Ittmann, Michael / Kim, William Y / Krishnan, Bhavani / Merino, Maria J / Mills Shaw, Kenna R / Reuter, Victor E / Reznik, Ed / Shelley, Carl S / Shuch, Brian / Signoretti, Sabina / Srinivasan, Ramaprasad / Tamboli, Pheroze / Thomas, George / Tickoo, Satish / Burnett, Kenneth / Crain, Daniel / Gardner, Johanna / Lau, Kevin / Mallery, David / Morris, Scott / Paulauskis, Joseph D / Penny, Robert J / Shelton, Candace / Shelton, W Troy / Sherman, Mark / Thompson, Eric / Yena, Peggy / Avedon, Melissa T / Bowen, Jay / Gastier-Foster, Julie M / Gerken, Mark / Leraas, Kristen M / Lichtenberg, Tara M / Ramirez, Nilsa C / Santos, Tracie / Wise, Lisa / Zmuda, Erik / Demchok, John A / Felau, Ina / Hutter, Carolyn M / Sheth, Margi / Sofia, Heidi J / Tarnuzzer, Roy / Wang, Zhining / Yang, Liming / Zenklusen, Jean C / Zhang, Jiashan / Ayala, Brenda / Baboud, Julien / Chudamani, Sudha / Liu, Jia / Lolla, Laxmi / Naresh, Rashi / Pihl, Todd / Sun, Qiang / Wan, Yunhu / Wu, Ye / Ally, Adrian / Balasundaram, Miruna / Balu, Saianand / Beroukhim, Rameen / Bodenheimer, Tom / Buhay, Christian / Butterfield, Yaron S N / Carlsen, Rebecca / Carter, Scott L / Chao, Hsu / Chuah, Eric / Clarke, Amanda / Covington, Kyle R / Dahdouli, Mahmoud / Dewal, Ninad / Dhalla, Noreen / Doddapaneni, Harsha V / Drummond, Jennifer A / Gabriel, Stacey B / Gibbs, Richard A / Guin, Ranabir / Hale, Walker / Hawes, Alicia / Hayes, D Neil / Holt, Robert A / Hoyle, Alan P / Jefferys, Stuart R / Jones, Steven J M / Jones, Corbin D / Kalra, Divya / Kovar, Christie / Lewis, Lora / Li, Jie / Ma, Yussanne / Marra, Marco A / Mayo, Michael / Meng, Shaowu / Meyerson, Matthew / Mieczkowski, Piotr A / Moore, Richard A / Morton, Donna / Mose, Lisle E / Mungall, Andrew J / Muzny, Donna / Parker, Joel S / Perou, Charles M / Roach, Jeffrey / Schein, Jacqueline E / Schumacher, Steven E / Shi, Yan / Simons, Janae V / Sipahimalani, Payal / Skelly, Tara / Soloway, Matthew G / Sougnez, Carrie / Tam, Angela / Tan, Donghui / Thiessen, Nina / Veluvolu, Umadevi / Wang, Min / Wilkerson, Matthew D / Wong, Tina / Wu, Junyuan / Xi, Liu / Zhou, Jane / Bedford, Jason / Chen, Fengju / Fu, Yao / Gerstein, Mark / Haussler, David / Kasaian, Katayoon / Lai, Phillip / Ling, Shiyun / Radenbaugh, Amie / Van Den Berg, David / Weinstein, John N / Zhu, Jingchun / Albert, Monique / Alexopoulou, Iakovina / Andersen, Jeremiah J / Auman, J Todd / Bartlett, John / Bastacky, Sheldon / Bergsten, Julie / Blute, Michael L / Boice, Lori / Bollag, Roni J / Boyd, Jeff / Castle, Erik / Chen, Ying-Bei / Cheville, John C / Curley, Erin / Davies, Benjamin / DeVolk, April / Dhir, Rajiv / Dike, Laura / Eckman, John / Engel, Jay / Harr, Jodi / Hrebinko, Ronald / Huang, Mei / Huelsenbeck-Dill, Lori / Iacocca, Mary / Jacobs, Bruce / Lobis, Michael / Maranchie, Jodi K / McMeekin, Scott / Myers, Jerome / Nelson, Joel / Parfitt, Jeremy / Parwani, Anil / Petrelli, Nicholas / Rabeno, Brenda / Roy, Somak / Salner, Andrew L / Slaton, Joel / Stanton, Melissa / Thompson, R Houston / Thorne, Leigh / Tucker, Kelinda / Weinberger, Paul M / Winemiller, Cynthia / Zach, Leigh Anne / Zuna, Rosemary

    The New England journal of medicine

    2016  Volume 374, Issue 2, Page(s) 135–145

    Abstract: Background: Papillary renal-cell carcinoma, which accounts for 15 to 20% of renal-cell carcinomas, is a heterogeneous disease that consists of various types of renal cancer, including tumors with indolent, multifocal presentation and solitary tumors ... ...

    Abstract Background: Papillary renal-cell carcinoma, which accounts for 15 to 20% of renal-cell carcinomas, is a heterogeneous disease that consists of various types of renal cancer, including tumors with indolent, multifocal presentation and solitary tumors with an aggressive, highly lethal phenotype. Little is known about the genetic basis of sporadic papillary renal-cell carcinoma, and no effective forms of therapy for advanced disease exist.
    Methods: We performed comprehensive molecular characterization of 161 primary papillary renal-cell carcinomas, using whole-exome sequencing, copy-number analysis, messenger RNA and microRNA sequencing, DNA-methylation analysis, and proteomic analysis.
    Results: Type 1 and type 2 papillary renal-cell carcinomas were shown to be different types of renal cancer characterized by specific genetic alterations, with type 2 further classified into three individual subgroups on the basis of molecular differences associated with patient survival. Type 1 tumors were associated with MET alterations, whereas type 2 tumors were characterized by CDKN2A silencing, SETD2 mutations, TFE3 fusions, and increased expression of the NRF2-antioxidant response element (ARE) pathway. A CpG island methylator phenotype (CIMP) was observed in a distinct subgroup of type 2 papillary renal-cell carcinomas that was characterized by poor survival and mutation of the gene encoding fumarate hydratase (FH).
    Conclusions: Type 1 and type 2 papillary renal-cell carcinomas were shown to be clinically and biologically distinct. Alterations in the MET pathway were associated with type 1, and activation of the NRF2-ARE pathway was associated with type 2; CDKN2A loss and CIMP in type 2 conveyed a poor prognosis. Furthermore, type 2 papillary renal-cell carcinoma consisted of at least three subtypes based on molecular and phenotypic features. (Funded by the National Institutes of Health.).
    MeSH term(s) Carcinoma, Papillary/genetics ; Carcinoma, Papillary/metabolism ; CpG Islands/physiology ; DNA Methylation ; Humans ; Kidney Neoplasms/genetics ; Kidney Neoplasms/metabolism ; MicroRNAs/chemistry ; Mutation ; NF-E2-Related Factor 2/genetics ; NF-E2-Related Factor 2/metabolism ; Phenotype ; Proto-Oncogene Proteins c-met/chemistry ; Proto-Oncogene Proteins c-met/genetics ; Proto-Oncogene Proteins c-met/metabolism ; RNA, Messenger/chemistry ; RNA, Neoplasm/chemistry ; Sequence Analysis, RNA ; Signal Transduction/physiology
    Chemical Substances MicroRNAs ; NF-E2-Related Factor 2 ; NFE2L2 protein, human ; RNA, Messenger ; RNA, Neoplasm ; MET protein, human (EC 2.7.10.1) ; Proto-Oncogene Proteins c-met (EC 2.7.10.1)
    Language English
    Publishing date 2016-01-14
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 207154-x
    ISSN 1533-4406 ; 0028-4793
    ISSN (online) 1533-4406
    ISSN 0028-4793
    DOI 10.1056/NEJMoa1505917
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

    Ding, Li / Bailey, Matthew H. / Porta-Pardo, Eduard / Thorsson, Vesteinn / Colaprico, Antonio / Bertrand, Denis / Gibbs, David L. / Weerasinghe, Amila / Huang, Kuan-lin / Tokheim, Collin / Cortés-Ciriano, Isidro / Jayasinghe, Reyka / Chen, Feng / Yu, Lihua / Sun, Sam / Olsen, Catharina / Kim, Jaegil / Taylor, Alison M. / Cherniack, Andrew D. /
    Akbani, Rehan / Suphavilai, Chayaporn / Nagarajan, Niranjan / Stuart, Joshua M. / Mills, Gordon B. / Wyczalkowski, Matthew A. / Vincent, Benjamin G. / Hutter, Carolyn M. / Zenklusen, Jean Claude / Hoadley, Katherine A. / Wendl, Michael C. / Shmulevich, llya / Lazar, Alexander / Wheeler, David A. / Getz, Gad / Caesar-Johnson, Samantha J. / Demchok, John A. / Felau, Ina / Kasapi, Melpomeni / Ferguson, Martin L. / Sofia, Heidi J. / Tarnuzzer, Roy / Wang, Zhining / Yang, Liming / Zenklusen, Jean C. / Zhang, Jiashan (Julia) / Chudamani, Sudha / Liu, Jia / Lolla, Laxmi / Naresh, Rashi / Pihl, Todd / Sun, Qiang / Wan, Yunhu / Wu, Ye / Cho, Juok / DeFreitas, Timothy / Frazer, Scott / Gehlenborg, Nils / Heiman, David I. / Lawrence, Michael S. / Lin, Pei / Meier, Samuel A. / Noble, Michael S. / Saksena, Gordon / Voet, Doug / Zhang, Hailei / Bernard, Brady / Chambwe, Nyasha / Dhankani, Varsha / Knijnenburg, Theo / Kramer, Roger / Leinonen, Kalle / Liu, Yuexin / Miller, Michael / Reynolds, Sheila / Shmulevich, Ilya / Zhang, Wei / Broom, Bradley M. / Hegde, Apurva M. / Ju, Zhenlin / Kanchi, Rupa S. / Korkut, Anil / Li, Jun / Liang, Han / Ling, Shiyun / Liu, Wenbin / Lu, Yiling / Ng, Kwok-Shing / Rao, Arvind / Ryan, Michael / Wang, Jing / Weinstein, John N. / Zhang, Jiexin / Abeshouse, Adam / Armenia, Joshua / Chakravarty, Debyani / Chatila, Walid K. / de Bruijn, Ino / Gao, Jianjiong / Gross, Benjamin E. / Heins, Zachary J. / Kundra, Ritika / La, Konnor / Ladanyi, Marc / Luna, Augustin / Nissan, Moriah G. / Ochoa, Angelica / Phillips, Sarah M. / Reznik, Ed / Sanchez-Vega, Francisco / Sander, Chris / Schultz, Nikolaus / Sheridan, Robert / Sumer, S. Onur / Sun, Yichao / Taylor, Barry S. / Wang, Jioajiao / Zhang, Hongxin / Anur, Pavana / Peto, Myron / Spellman, Paul / Benz, Christopher / Wong, Christopher K. / Yau, Christina / Hayes, D. Neil / Parker, Joel S. / Wilkerson, Matthew D. / Ally, Adrian / Balasundaram, Miruna / Bowlby, Reanne / Brooks, Denise / Carlsen, Rebecca / Chuah, Eric / Dhalla, Noreen / Holt, Robert / Jones, Steven J.M. / Kasaian, Katayoon / Lee, Darlene / Ma, Yussanne / Marra, Marco A. / Mayo, Michael / Moore, Richard A. / Mungall, Andrew J. / Mungall, Karen / Robertson, A. Gordon / Sadeghi, Sara / Schein, Jacqueline E. / Sipahimalani, Payal / Tam, Angela / Thiessen, Nina / Tse, Kane / Wong, Tina / Berger, Ashton C. / Beroukhim, Rameen / Cibulskis, Carrie / Gabriel, Stacey B. / Gao, Galen F. / Ha, Gavin / Meyerson, Matthew / Schumacher, Steven E. / Shih, Juliann / Kucherlapati, Melanie H. / Kucherlapati, Raju S. / Baylin, Stephen / Cope, Leslie / Danilova, Ludmila / Bootwalla, Moiz S. / Lai, Phillip H. / Maglinte, Dennis T. / Van Den Berg, David J. / Weisenberger, Daniel J. / Auman, J. Todd / Balu, Saianand / Bodenheimer, Thomas / Fan, Cheng / Hoyle, Alan P. / Jefferys, Stuart R. / Jones, Corbin D. / Meng, Shaowu / Mieczkowski, Piotr A. / Mose, Lisle E. / Perou, Amy H. / Perou, Charles M. / Roach, Jeffrey / Shi, Yan / Simons, Janae V. / Skelly, Tara / Soloway, Matthew G. / Tan, Donghui / Veluvolu, Umadevi / Fan, Huihui / Hinoue, Toshinori / Laird, Peter W. / Shen, Hui / Zhou, Wanding / Bellair, Michelle / Chang, Kyle / Covington, Kyle / Creighton, Chad J. / Dinh, Huyen / Doddapaneni, HarshaVardhan / Donehower, Lawrence A. / Drummond, Jennifer / Gibbs, Richard / Glenn, Robert / Hale, Walker / Han, Yi / Hu, Jianhong / Korchina, Viktoriya / Lee, Sandra / Lewis, Lora / Li, Wei / Liu, Xiuping / Morgan, Margaret / Morton, Donna / Muzny, Donna / Santibanez, Jireh / Sheth, Margi / Shinbrot, Eve / Wang, Linghua / Wang, Min / Xi, Liu / Zhao, Fengmei / Hess, Julian / Appelbaum, Elizabeth L. / Bailey, Matthew / Cordes, Matthew G. / Fronick, Catrina C. / Fulton, Lucinda A. / Fulton, Robert S. / Kandoth, Cyriac / Mardis, Elaine R. / McLellan, Michael D. / Miller, Christopher A. / Schmidt, Heather K. / Wilson, Richard K. / Crain, Daniel / Curley, Erin / Gardner, Johanna / Lau, Kevin / Mallery, David / Morris, Scott / Paulauskis, Joseph / Penny, Robert / Shelton, Candace / Shelton, Troy / Sherman, Mark / Thompson, Eric / Yena, Peggy / Bowen, Jay / Gastier-Foster, Julie M. / Gerken, Mark / Leraas, Kristen M. / Lichtenberg, Tara M. / Ramirez, Nilsa C. / Wise, Lisa / Zmuda, Erik / Corcoran, Niall / Costello, Tony / Hovens, Christopher / Carvalho, Andre L. / de Carvalho, Ana C. / Fregnani, José H. / Filho, Adhemar Longatto / Reis, Rui M. / Scapulatempo-Neto, Cristovam / Silveira, Henrique C.S. / Vidal, Daniel O. / Burnette, Andrew / Eschbacher, Jennifer / Hermes, Beth / Noss, Ardene / Singh, Rosy / Anderson, Matthew L. / Castro, Patricia D. / Ittmann, Michael / Huntsman, David / Kohl, Bernard / Lệ Xuân / Thorp, Richard / Andry, Chris / Duffy, Elizabeth R. / Lyadov, Vladimir / Paklina, Oxana / Setdikova, Galiya / Shabunin, Alexey / Tavobilov, Mikhail / McPherson, Christopher / Warnick, Ronald / Berkowitz, Ross / Cramer, Daniel / Feltmate, Colleen / Horowitz, Neil / Kibel, Adam / Muto, Michael / Raut, Chandrajit P. / Malykh, Andrei / Barnholtz-Sloan, Jill S. / Barrett, Wendi / Devine, Karen / Fulop, Jordonna / Ostrom, Quinn T. / Shimmel, Kristen / Wolinsky, Yingli / Sloan, Andrew E. / De Rose, Agostino / Giuliante, Felice / Goodman, Marc / Karlan, Beth Y. / Hagedorn, C. H. / Eckman, John / Harr, Jodi / Myers, Jerome / Tucker, Kelinda / Zach, Leigh Anne / Deyarmin, Brenda / Hu, Hai / Kvecher, Leonid / Larson, Caroline / Mural, Richard J. / Somiari, Stella / Vicha, Ales / Zelinka, Tomas / Bennett, Joseph / Iacocca, Mary / Rabeno, Brenda / Swanson, Patricia / Latour, Mathieu / Lacombe, Louis / Têtu, Bernard / Bergeron, Alain / McGraw, Mary / Staugaitis, Susan M. / Chabot, John / Hibshoosh, Hanina / Sepulveda, Antonia / Su, Tao / Wang, Timothy / Potapova, Olga / Voronina, Olga / Desjardins, Laurence / Mariani, Odette / Roman-Roman, Sergio / Sastre, Xavier / Stern, Marc-Henri / Cheng, Feixiong / Signoretti, Sabina / Berchuck, Andrew / Bigner, Darell / Lipp, Eric / Marks, Jeffrey / McCall, Shannon / McLendon, Roger / Secord, Angeles / Sharp, Alexis / Behera, Madhusmita / Brat, Daniel J. / Chen, Amy / Delman, Keith / Force, Seth / Khuri, Fadlo / Magliocca, Kelly / Maithel, Shishir / Olson, Jeffrey J. / Owonikoko, Taofeek / Pickens, Alan / Ramalingam, Suresh / Shin, Dong M. / Sica, Gabriel / Van Meir, Erwin G. / Zhang, Hongzheng / Eijckenboom, Wil / Gillis, Ad / Korpershoek, Esther / Looijenga, Leendert / Oosterhuis, Wolter / Stoop, Hans / van Kessel, Kim E. / Zwarthoff, Ellen C. / Calatozzolo, Chiara / Cuppini, Lucia / Cuzzubbo, Stefania / DiMeco, Francesco / Finocchiaro, Gaetano / Mattei, Luca / Perin, Alessandro / Pollo, Bianca / Chen, Chu / Houck, John / Lohavanichbutr, Pawadee / Hartmann, Arndt / Stoehr, Christine / Stoehr, Robert / Taubert, Helge / Wach, Sven / Wullich, Bernd / Kycler, Witold / Murawa, Dawid / Wiznerowicz, Maciej / Chung, Ki / Edenfield, W. Jeffrey / Martin, Julie / Baudin, Eric / Bubley, Glenn / Bueno, Raphael / De Rienzo, Assunta / Richards, William G. / Kalkanis, Steven / Mikkelsen, Tom / Noushmehr, Houtan / Scarpace, Lisa / Girard, Nicolas / Aymerich, Marta / Campo, Elias / Giné, Eva / Guillermo, Armando López / Van Bang, Nguyen / Hanh, Phan Thi / Phu, Bui Duc / Tang, Yufang / Colman, Howard / Evason, Kimberley / Dottino, Peter R. / Martignetti, John A. / Gabra, Hani / Juhl, Hartmut / Akeredolu, Teniola / Stepa, Serghei / Hoon, Dave / Ahn, Keunsoo / Kang, Koo Jeong / Beuschlein, Felix / Breggia, Anne / Birrer, Michael / Bell, Debra / Borad, Mitesh / Bryce, Alan H. / Castle, Erik / Chandan, Vishal / Cheville, John / Copland, John A. / Farnell, Michael / Flotte, Thomas / Giama, Nasra / Ho, Thai / Kendrick, Michael / Kocher, Jean-Pierre / Kopp, Karla / Moser, Catherine / Nagorney, David / O’Brien, Daniel / O’Neill, Brian Patrick / Patel, Tushar / Petersen, Gloria / Que, Florencia / Rivera, Michael / Roberts, Lewis / Smallridge, Robert / Smyrk, Thomas / Stanton, Melissa / Thompson, R. 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Bradley / Hilty, Joe / Kumar, Bahavna / Lang, James / Lehman, Norman L. / Mandt, Randy / Nguyen, Phuong / Pilarski, Robert / Rai, Karan / Schoenfield, Lynn / Senecal, Kelly / Wakely, Paul / Hansen, Paul / Lechan, Ronald / Powers, James / Tischler, Arthur / Grizzle, William E. / Sexton, Katherine C. / Kastl, Alison / Henderson, Joel / Porten, Sima / Waldmann, Jens / Fassnacht, Martin / Asa, Sylvia L. / Schadendorf, Dirk / Couce, Marta / Graefen, Markus / Huland, Hartwig / Sauter, Guido / Schlomm, Thorsten / Simon, Ronald / Tennstedt, Pierre / Olabode, Oluwole / Nelson, Mark / Bathe, Oliver / Carroll, Peter R. / Chan, June M. / Disaia, Philip / Glenn, Pat / Kelley, Robin K. / Landen, Charles N. / Phillips, Joanna / Prados, Michael / Simko, Jeffry / Smith-McCune, Karen / VandenBerg, Scott / Roggin, Kevin / Fehrenbach, Ashley / Kendler, Ady / Sifri, Suzanne / Steele, Ruth / Jimeno, Antonio / Carey, Francis / Forgie, Ian / Mannelli, Massimo / Carney, Michael / Hernandez, Brenda / Campos, Benito / Herold-Mende, Christel / Jungk, Christin / Unterberg, A. / Deimling, Andreas von / Bossler, Aaron / Galbraith, Joseph / Jacobus, Laura / Knudson, Michael / Knutson, Tina / Ma, Deqin / Milhem, Mohammed / Sigmund, Rita / Godwin, Andrew K. / Madan, Rashna / Rosenthal, Howard G. / Adebamowo, Clement / Adebamowo, Sally N. / Boussioutas, Alex / Beer, David / Giordano, Thomas / Mes-Masson, Anne-Marie / Saad, Fred / Bocklage, Therese / Landrum, Lisa / Mannel, Robert / Moore, Kathleen / Moxley, Katherine / Postier, Russel / Walker, Joan / Zuna, Rosemary / Feldman, Michael / Valdivieso, Federico / Dhir, Rajiv / Luketich, James / Pinero, Edna M. 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    Cell. 2018 Apr. 05, v. 173, no. 2 p.305-320.e10

    2018  

    Abstract: The Cancer Genome Atlas (TCGA) has catalyzed systematic characterization of diverse genomic alterations underlying human cancers. At this historic junction marking the completion of genomic characterization of over 11,000 tumors from 33 cancer types, we ... ...

    Institution The Cancer Genome Atlas Research Network
    Abstract The Cancer Genome Atlas (TCGA) has catalyzed systematic characterization of diverse genomic alterations underlying human cancers. At this historic junction marking the completion of genomic characterization of over 11,000 tumors from 33 cancer types, we present our current understanding of the molecular processes governing oncogenesis. We illustrate our insights into cancer through synthesis of the findings of the TCGA PanCancer Atlas project on three facets of oncogenesis: (1) somatic driver mutations, germline pathogenic variants, and their interactions in the tumor; (2) the influence of the tumor genome and epigenome on transcriptome and proteome; and (3) the relationship between tumor and the microenvironment, including implications for drugs targeting driver events and immunotherapies. These results will anchor future characterization of rare and common tumor types, primary and relapsed tumors, and cancers across ancestry groups and will guide the deployment of clinical genomic sequencing.
    Keywords ancestry ; carcinogenesis ; epigenome ; genomics ; germ cells ; humans ; neoplasms ; proteome ; transcriptome ; oncogenic process ; TCGA ; omics ; cancer ; cancer genomics
    Language English
    Dates of publication 2018-0405
    Size p. 305-320.e10.
    Publishing place Elsevier Inc.
    Document type Article ; Online
    Note NAL-AP-2-clean ; Resource is Open Access
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2018.03.033
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

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

    Elsevier Inc. Cell. 2018 Apr. 05, v. 173, no. 2 p.400-416.e11

    2018  

    Abstract: For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features ... ...

    Institution The Cancer Genome Atlas Research Network
    Abstract For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale.
    Keywords data collection ; genome ; genomics ; humans ; The Cancer Genome Atlas ; TCGA ; clinical data resource ; translational research ; follow-up time ; overall survival ; disease-specific survival ; disease-free interval ; progression-free interval ; Cox proportional hazards regression model
    Language English
    Dates of publication 2018-0405
    Size p. 400-416.e11.
    Publishing place Elsevier Inc.
    Document type Article ; Online
    Note NAL-AP-2-clean ; Resource is Open Access
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2018.02.052
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

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

    Elsevier Inc. Cell. 2018 Apr. 05, v. 173, no. 2 p.291-304.e6

    2018  

    Abstract: We conducted comprehensive integrative molecular analyses of the complete set of tumors in The Cancer Genome Atlas (TCGA), consisting of approximately 10,000 specimens and representing 33 types of cancer. We performed molecular clustering using data on ... ...

    Institution The Cancer Genome Atlas Network
    Abstract We conducted comprehensive integrative molecular analyses of the complete set of tumors in The Cancer Genome Atlas (TCGA), consisting of approximately 10,000 specimens and representing 33 types of cancer. We performed molecular clustering using data on chromosome-arm-level aneuploidy, DNA hypermethylation, mRNA, and miRNA expression levels and reverse-phase protein arrays, of which all, except for aneuploidy, revealed clustering primarily organized by histology, tissue type, or anatomic origin. The influence of cell type was evident in DNA-methylation-based clustering, even after excluding sites with known preexisting tissue-type-specific methylation. Integrative clustering further emphasized the dominant role of cell-of-origin patterns. Molecular similarities among histologically or anatomically related cancer types provide a basis for focused pan-cancer analyses, such as pan-gastrointestinal, pan-gynecological, pan-kidney, and pan-squamous cancers, and those related by stemness features, which in turn may inform strategies for future therapeutic development.
    Keywords DNA hypermethylation ; aneuploidy ; genome ; histology ; microRNA ; therapeutics ; cancer ; TCGA ; transcriptome ; proteome ; methylome ; subtypes ; tissues ; organs ; cell-of-origin
    Language English
    Dates of publication 2018-0405
    Size p. 291-304.e6.
    Publishing place Elsevier Inc.
    Document type Article ; Online
    Note NAL-AP-2-clean ; Resource is Open Access
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2018.03.022
    Database NAL-Catalogue (AGRICOLA)

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  7. Article: A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples

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

    Cell. 2018 Apr. 05, v. 173, no. 2

    2018  

    Abstract: The role of enhancers, a key class of non-coding regulatory DNA elements, in cancer development has increasingly been appreciated. Here, we present the detection and characterization of a large number of expressed enhancers in a genome-wide analysis of ... ...

    Institution The Cancer Genome Atlas Research Network
    Abstract The role of enhancers, a key class of non-coding regulatory DNA elements, in cancer development has increasingly been appreciated. Here, we present the detection and characterization of a large number of expressed enhancers in a genome-wide analysis of 8928 tumor samples across 33 cancer types using TCGA RNA-seq data. Compared with matched normal tissues, global enhancer activation was observed in most cancers. Across cancer types, global enhancer activity was positively associated with aneuploidy, but not mutation load, suggesting a hypothesis centered on “chromatin-state” to explain their interplay. Integrating eQTL, mRNA co-expression, and Hi-C data analysis, we developed a computational method to infer causal enhancer-gene interactions, revealing enhancers of clinically actionable genes. Having identified an enhancer ∼140 kb downstream of PD-L1, a major immunotherapy target, we validated it experimentally. This study provides a systematic view of enhancer activity in diverse tumor contexts and suggests the clinical implications of enhancers.
    Keywords DNA ; aneuploidy ; carcinogenesis ; genome-wide association study ; immunotherapy ; mutation ; neoplasms ; patients ; sequence analysis
    Language English
    Dates of publication 2018-0405
    Size p. 386-399.e12.
    Publishing place Elsevier Inc.
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2018.03.027
    Database NAL-Catalogue (AGRICOLA)

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  8. Article ; Online: Pathogenic Germline Variants in 10,389 Adult Cancers

    Huang, Kuan-lin / Mashl, R. Jay / Wu, Yige / Ritter, Deborah I. / Wang, Jiayin / Oh, Clara / Paczkowska, Marta / Reynolds, Sheila / Wyczalkowski, Matthew A. / Oak, Ninad / Scott, Adam D. / Krassowski, Michal / Cherniack, Andrew D. / Houlahan, Kathleen E. / Jayasinghe, Reyka / Wang, Liang-Bo / Zhou, Daniel Cui / Liu, Di / Cao, Song /
    Kim, Young-Won / Koire, Amanda / McMichael, Joshua F. / Hucthagowder, Vishwanathan / Kim, Tae-Beom / Hahn, Abigail / Wang, Chen / McLellan, Michael D. / Al-Mulla, Fahd / Johnson, Kimberly J. / Lichtarge, Olivier / Boutros, Paul C. / Raphael, Benjamin / Lazar, Alexander / Zhang, Wei / Wendl, Michael C. / Govindan, Ramaswamy / Jaina, Sañjaya / Wheeler, David / Kulkarni, Shashikant / DiPersio, John F. / Reimand, Jüri / Meric-Bernstam, Funda / Chen, Ken / Shmulevich, Ilya / Plon, Sharon E. / Chen, Feng / Ding, Li / Caesar-Johnson, Samantha J. / Demchok, John A. / Felau, Ina / Kasapi, Melpomeni / Ferguson, Martin L. / Hutter, Carolyn M. / Sofia, Heidi J. / Tarnuzzer, Roy / Wang, Zhining / Yang, Liming / Zenklusen, Jean C. / Zhang, Jiashan (Julia) / Chudamani, Sudha / Liu, Jia / Lolla, Laxmi / Naresh, Rashi / Pihl, Todd / Sun, Qiang / Wan, Yunhu / Wu, Ye / Cho, Juok / DeFreitas, Timothy / Frazer, Scott / Gehlenborg, Nils / Getz, Gad / Heiman, David I. / Kim, Jaegil / Lawrence, Michael S. / Lin, Pei / Meier, Samuel A. / Noble, Michael S. / Saksena, Gordon / Voet, Doug / Zhang, Hailei / Bernard, Brady / Chambwe, Nyasha / Dhankani, Varsha / Knijnenburg, Theo / Kramer, Roger / Leinonen, Kalle / Liu, Yuexin / Miller, Michael / Thorsson, Vesteinn / Akbani, Rehan / Broom, Bradley M. / Hegde, Apurva M. / Ju, Zhenlin / Kanchi, Rupa S. / Korkut, Anil / Li, Jun / Liang, Han / Ling, Shiyun / Liu, Wenbin / Lu, Yiling / Mills, Gordon B. / Ng, Kwok-Shing / Rao, Arvind / Ryan, Michael / Wang, Jing / Weinstein, John N. / Zhang, Jiexin / Abeshouse, Adam / Armenia, Joshua / Chakravarty, Debyani / Chatila, Walid K. / de Bruijn, Ino / Gao, Jianjiong / Gross, Benjamin E. / Heins, Zachary J. / Kundra, Ritika / La, Konnor / Ladanyi, Marc / Luna, Augustin / Nissan, Moriah G. / Ochoa, Angelica / Phillips, Sarah M. / Reznik, Ed / Sanchez-Vega, Francisco / Sander, Chris / Schultz, Nikolaus / Sheridan, Robert / Sumer, S. Onur / Sun, Yichao / Taylor, Barry S. / Wang, Jioajiao / Zhang, Hongxin / Anur, Pavana / Peto, Myron / Spellman, Paul / Benz, Christopher / Stuart, Joshua M. / Wong, Christopher K. / Yau, Christina / Hayes, D. Neil / Parker, Joel S. / Wilkerson, Matthew D. / Ally, Adrian / Balasundaram, Miruna / Bowlby, Reanne / Brooks, Denise / Carlsen, Rebecca / Chuah, Eric / Dhalla, Noreen / Holt, Robert / Jones, Steven J.M. / Kasaian, Katayoon / Lee, Darlene / Ma, Yussanne / Marra, Marco A. / Mayo, Michael / Moore, Richard A. / Mungall, Andrew J. / Mungall, Karen / Robertson, A. Gordon / Sadeghi, Sara / Schein, Jacqueline E. / Sipahimalani, Payal / Tam, Angela / Thiessen, Nina / Tse, Kane / Wong, Tina / Berger, Ashton C. / Beroukhim, Rameen / Cibulskis, Carrie / Gabriel, Stacey B. / Gao, Galen F. / Ha, Gavin / Meyerson, Matthew / Schumacher, Steven E. / Shih, Juliann / Kucherlapati, Melanie H. / Kucherlapati, Raju S. / Baylin, Stephen / Cope, Leslie / Danilova, Ludmila / Bootwalla, Moiz S. / Lai, Phillip H. / Maglinte, Dennis T. / Van Den Berg, David J. / Weisenberger, Daniel J. / Auman, J. Todd / Balu, Saianand / Bodenheimer, Thomas / Fan, Cheng / Hoadley, Katherine A. / Hoyle, Alan P. / Jefferys, Stuart R. / Jones, Corbin D. / Meng, Shaowu / Mieczkowski, Piotr A. / Mose, Lisle E. / Perou, Amy H. / Perou, Charles M. / Roach, Jeffrey / Shi, Yan / Simons, Janae V. / Skelly, Tara / Soloway, Matthew G. / Tan, Donghui / Veluvolu, Umadevi / Fan, Huihui / Hinoue, Toshinori / Laird, Peter W. / Shen, Hui / Zhou, Wanding / Bellair, Michelle / Chang, Kyle / Covington, Kyle / Creighton, Chad J. / Dinh, Huyen / Doddapaneni, HarshaVardhan / Donehower, Lawrence A. / Drummond, Jennifer / Gibbs, Richard / Glenn, Robert / Hale, Walker / Han, Yi / Hu, Jianhong / Korchina, Viktoriya / Lee, Sandra / Lewis, Lora / Li, Wei / Liu, Xiuping / Morgan, Margaret / Morton, Donna / Muzny, Donna / Santibanez, Jireh / Sheth, Margi / Shinbrot, Eve / Wang, Linghua / Wang, Min / Wheeler, David A. / Xi, Liu / Zhao, Fengmei / Hess, Julian / Appelbaum, Elizabeth L. / Bailey, Matthew / Cordes, Matthew G. / Fronick, Catrina C. / Fulton, Lucinda A. / Fulton, Robert S. / Kandoth, Cyriac / Mardis, Elaine R. / Miller, Christopher A. / Schmidt, Heather K. / Wilson, Richard K. / Crain, Daniel / Curley, Erin / Gardner, Johanna / Lau, Kevin / Mallery, David / Morris, Scott / Paulauskis, Joseph / Penny, Robert / Shelton, Candace / Shelton, Troy / Sherman, Mark / Thompson, Eric / Yena, Peggy / Bowen, Jay / Gastier-Foster, Julie M. / Gerken, Mark / Leraas, Kristen M. / Lichtenberg, Tara M. / Ramirez, Nilsa C. / Wise, Lisa / Zmuda, Erik / Corcoran, Niall / Costello, Tony / Hovens, Christopher / Carvalho, Andre L. / de Carvalho, Ana C. / Fregnani, José H. / Filho, Adhemar Longatto / Reis, Rui M. / Scapulatempo-Neto, Cristovam / Silveira, Henrique C.S. / Vidal, Daniel O. / Burnette, Andrew / Eschbacher, Jennifer / Hermes, Beth / Noss, Ardene / Singh, Rosy / Anderson, Matthew L. / Castro, Patricia D. / Ittmann, Michael / Huntsman, David / Kohl, Bernard / Lệ Xuân / Thorp, Richard / Andry, Chris / Duffy, Elizabeth R. / Lyadov, Vladimir / Paklina, Oxana / Setdikova, Galiya / Shabunin, Alexey / Tavobilov, Mikhail / McPherson, Christopher / Warnick, Ronald / Berkowitz, Ross / Cramer, Daniel / Feltmate, Colleen / Horowitz, Neil / Kibel, Adam / Muto, Michael / Raut, Chandrajit P. / Malykh, Andrei / Barnholtz-Sloan, Jill S. / Barrett, Wendi / Devine, Karen / Fulop, Jordonna / Ostrom, Quinn T. / Shimmel, Kristen / Wolinsky, Yingli / Sloan, Andrew E. / De Rose, Agostino / Giuliante, Felice / Goodman, Marc / Karlan, Beth Y. / Hagedorn, C. 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    Cell. 2018 Apr. 05, v. 173, no. 2 p.355-370.e14

    2018  

    Abstract: We conducted the largest investigation of predisposition variants in cancer to date, discovering 853 pathogenic or likely pathogenic variants in 8% of 10,389 cases from 33 cancer types. Twenty-one genes showed single or cross-cancer associations, ... ...

    Institution The Cancer Genome Atlas Research Network
    Abstract We conducted the largest investigation of predisposition variants in cancer to date, discovering 853 pathogenic or likely pathogenic variants in 8% of 10,389 cases from 33 cancer types. Twenty-one genes showed single or cross-cancer associations, including novel associations of SDHA in melanoma and PALB2 in stomach adenocarcinoma. The 659 predisposition variants and 18 additional large deletions in tumor suppressors, including ATM, BRCA1, and NF1, showed low gene expression and frequent (43%) loss of heterozygosity or biallelic two-hit events. We also discovered 33 such variants in oncogenes, including missenses in MET, RET, and PTPN11 associated with high gene expression. We nominated 47 additional predisposition variants from prioritized VUSs supported by multiple evidences involving case-control frequency, loss of heterozygosity, expression effect, and co-localization with mutations and modified residues. Our integrative approach links rare predisposition variants to functional consequences, informing future guidelines of variant classification and germline genetic testing in cancer.
    Keywords adenocarcinoma ; adults ; gene expression ; germ cells ; loss of heterozygosity ; melanoma ; oncogenes ; stomach ; tumor suppressor proteins ; cancer predisposition ; germline and somatic genomes ; LOH ; variant pathogenicity
    Language English
    Dates of publication 2018-0405
    Size p. 355-370.e14.
    Publishing place Elsevier Inc.
    Document type Article ; Online
    Note NAL-AP-2-clean ; Resource is Open Access
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2018.03.039
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: Oncogenic Signaling Pathways in The Cancer Genome Atlas

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H. / Eckman, John / Harr, Jodi / Myers, Jerome / Tucker, Kelinda / Zach, Leigh Anne / Deyarmin, Brenda / Hu, Hai / Kvecher, Leonid / Larson, Caroline / Mural, Richard J. / Somiari, Stella / Vicha, Ales / Zelinka, Tomas / Bennett, Joseph / Iacocca, Mary / Rabeno, Brenda / Swanson, Patricia / Latour, Mathieu / Lacombe, Louis / Têtu, Bernard / Bergeron, Alain / McGraw, Mary / Staugaitis, Susan M. / Chabot, John / Hibshoosh, Hanina / Sepulveda, Antonia / Su, Tao / Wang, Timothy / Potapova, Olga / Voronina, Olga / Desjardins, Laurence / Mariani, Odette / Roman-Roman, Sergio / Sastre, Xavier / Stern, Marc-Henri / Cheng, Feixiong / Signoretti, Sabina / Berchuck, Andrew / Bigner, Darell / Lipp, Eric / Marks, Jeffrey / McCall, Shannon / McLendon, Roger / Secord, Angeles / Sharp, Alexis / Behera, Madhusmita / Brat, Daniel J. / Chen, Amy / Delman, Keith / Force, Seth / Khuri, Fadlo / Magliocca, Kelly / Maithel, Shishir / Olson, Jeffrey J. / Owonikoko, Taofeek / Pickens, Alan / Ramalingam, Suresh / Shin, Dong M. / Sica, Gabriel / Van Meir, Erwin G. / Zhang, Hongzheng / Eijckenboom, Wil / Gillis, Ad / Korpershoek, Esther / Looijenga, Leendert / Oosterhuis, Wolter / Stoop, Hans / van Kessel, Kim E. / Zwarthoff, Ellen C. / Calatozzolo, Chiara / Cuppini, Lucia / Cuzzubbo, Stefania / DiMeco, Francesco / Finocchiaro, Gaetano / Mattei, Luca / Perin, Alessandro / Pollo, Bianca / Chen, Chu / Houck, John / Lohavanichbutr, Pawadee / Hartmann, Arndt / Stoehr, Christine / Stoehr, Robert / Taubert, Helge / Wach, Sven / Wullich, Bernd / Kycler, Witold / Murawa, Dawid / Wiznerowicz, Maciej / Chung, Ki / Edenfield, W. Jeffrey / Martin, Julie / Baudin, Eric / Bubley, Glenn / Bueno, Raphael / De Rienzo, Assunta / Richards, William G. / Kalkanis, Steven / Mikkelsen, Tom / Noushmehr, Houtan / Scarpace, Lisa / Girard, Nicolas / Aymerich, Marta / Campo, Elias / Giné, Eva / Guillermo, Armando López / Van Bang, Nguyen / Hanh, Phan Thi / Phu, Bui Duc / Tang, Yufang / Colman, Howard / Evason, Kimberley / Dottino, Peter R. / Martignetti, John A. / Gabra, Hani / Juhl, Hartmut / Akeredolu, Teniola / Stepa, Serghei / Hoon, Dave / Ahn, Keunsoo / Kang, Koo Jeong / Beuschlein, Felix / Breggia, Anne / Birrer, Michael / Bell, Debra / Borad, Mitesh / Bryce, Alan H. / Castle, Erik / Chandan, Vishal / Cheville, John / Copland, John A. / Farnell, Michael / Flotte, Thomas / Giama, Nasra / Ho, Thai / Kendrick, Michael / Kocher, Jean-Pierre / Kopp, Karla / Moser, Catherine / Nagorney, David / O’Brien, Daniel / O’Neill, Brian Patrick / Patel, Tushar / Petersen, Gloria / Que, Florencia / Rivera, Michael / Roberts, Lewis / Smallridge, Robert / Smyrk, Thomas / Stanton, Melissa / Thompson, R. Houston / Torbenson, Michael / Yang, Ju Dong / Zhang, Lizhi / Brimo, Fadi / Ajani, Jaffer A. / Gonzalez, Ana Maria Angulo / Behrens, Carmen / Bondaruk, Jolanta / Broaddus, Russell / Czerniak, Bogdan / Esmaeli, Bita / Fujimoto, Junya / Gershenwald, Jeffrey / Guo, Charles / Logothetis, Christopher / Meric-Bernstam, Funda / Moran, Cesar / Ramondetta, Lois / Rice, David / Sood, Anil / Tamboli, Pheroze / Thompson, Timothy / Troncoso, Patricia / Tsao, Anne / Wistuba, Ignacio / Carter, Candace / Haydu, Lauren / Hersey, Peter / Jakrot, Valerie / Kakavand, Hojabr / Kefford, Richard / Lee, Kenneth / Long, Georgina / Mann, Graham / Quinn, Michael / Saw, Robyn / Scolyer, Richard / Shannon, Kerwin / Spillane, Andrew / Stretch, Jonathan / Synott, Maria / Thompson, John / Wilmott, James / Al-Ahmadie, Hikmat / Chan, Timothy A. / Ghossein, Ronald / Gopalan, Anuradha / Levine, Douglas A. / Reuter, Victor / Singer, Samuel / Singh, Bhuvanesh / Tien, Nguyen Viet / Broudy, Thomas / Mirsaidi, Cyrus / Nair, Praveen / Drwiega, Paul / Miller, Judy / Smith, Jennifer / Zaren, Howard / Park, Joong-Won / Hung, Nguyen Phi / Kebebew, Electron / Linehan, Marston / Metwalli, Adam R. / Pacak, Karel / Pinto, Peter A. / Schiffman, Mark / Schmidt, Laura S. / Vocke, Cathy D. / Wentzensen, Nicolas / Worrell, Robert / Yang, Hannah / Moncrieff, Marc / Goparaju, Chandra / Melamed, Jonathan / Pass, Harvey / Botnariuc, Natalia / Caraman, Irina / Cernat, Mircea / Chemencedji, Inga / Clipca, Adrian / Doruc, Serghei / Gorincioi, Ghenadie / Mura, Sergiu / Pirtac, Maria / Stancul, Irina / Tcaciuc, Diana / Albert, Monique / Alexopoulou, Iakovina / Arnaout, Angel / Bartlett, John / Engel, Jay / Gilbert, Sebastien / Parfitt, Jeremy / Sekhon, Harman / Thomas, George / Rassl, Doris M. / Rintoul, Robert C. / Bifulco, Carlo / Tamakawa, Raina / Urba, Walter / Hayward, Nicholas / Timmers, Henri / Antenucci, Anna / Facciolo, Francesco / Grazi, Gianluca / Marino, Mirella / Merola, Roberta / de Krijger, Ronald / Gimenez-Roqueplo, Anne-Paule / Piché, Alain / Chevalier, Simone / McKercher, Ginette / Birsoy, Kivanc / Barnett, Gene / Brewer, Cathy / Farver, Carol / Naska, Theresa / Pennell, Nathan A. / Raymond, Daniel / Schilero, Cathy / Smolenski, Kathy / Williams, F. / Morrison, Carl / Borgia, Jeffrey A. / Liptay, Michael J. / Pool, Mark / Seder, Christopher W. / Junker, Kerstin / Omberg, Larsson / Dinkin, Mikhail / Manikhas, George / Alvaro, Domenico / Bragazzi, Maria Consiglia / Cardinale, Vincenzo / Carpino, Guido / Gaudio, Eugenio / Chesla, David / Cottingham, Sandra / Dubina, Michael / Moiseenko, Fedor / Dhanasekaran, Renumathy / Becker, Karl Friedrich / Janssen, Klaus-Peter / Slotta-Huspenina, Julia / Abdel-Rahman, Mohamed H. / Aziz, Dina / Bell, Sue / Cebulla, Colleen M. / Davis, Amy / Duell, Rebecca / Elder, J. Bradley / Hilty, Joe / Kumar, Bahavna / Lang, James / Lehman, Norman L. / Mandt, Randy / Nguyen, Phuong / Pilarski, Robert / Rai, Karan / Schoenfield, Lynn / Senecal, Kelly / Wakely, Paul / Hansen, Paul / Lechan, Ronald / Powers, James / Tischler, Arthur / Grizzle, William E. / Sexton, Katherine C. / Kastl, Alison / Henderson, Joel / Porten, Sima / Waldmann, Jens / Fassnacht, Martin / Asa, Sylvia L. / Schadendorf, Dirk / Couce, Marta / Graefen, Markus / Huland, Hartwig / Sauter, Guido / Schlomm, Thorsten / Simon, Ronald / Tennstedt, Pierre / Olabode, Oluwole / Nelson, Mark / Bathe, Oliver / Carroll, Peter R. / Chan, June M. / Disaia, Philip / Glenn, Pat / Kelley, Robin K. / Landen, Charles N. / Phillips, Joanna / Prados, Michael / Simko, Jeffry / Smith-McCune, Karen / VandenBerg, Scott / Roggin, Kevin / Fehrenbach, Ashley / Kendler, Ady / Sifri, Suzanne / Steele, Ruth / Jimeno, Antonio / Carey, Francis / Forgie, Ian / Mannelli, Massimo / Carney, Michael / Hernandez, Brenda / Campos, Benito / Herold-Mende, Christel / Jungk, Christin / Unterberg, A. / Deimling, Andreas von / Bossler, Aaron / Galbraith, Joseph / Jacobus, Laura / Knudson, Michael / Knutson, Tina / Ma, Deqin / Milhem, Mohammed / Sigmund, Rita / Godwin, Andrew K. / Madan, Rashna / Rosenthal, Howard G. / Adebamowo, Clement / Adebamowo, Sally N. / Boussioutas, Alex / Beer, David / Mes-Masson, Anne-Marie / Saad, Fred / Bocklage, Therese / Landrum, Lisa / Mannel, Robert / Moore, Kathleen / Moxley, Katherine / Postier, Russel / Walker, Joan / Zuna, Rosemary / Feldman, Michael / Valdivieso, Federico / Dhir, Rajiv / Luketich, James / Pinero, Edna M. Mora / Quintero-Aguilo, Mario / Carlotti, Carlos Gilberto / Santos, José Sebastião dos / Kemp, Rafael / Sankarankuty, Ajith / Tirapelli, Daniela / Catto, James / Agnew, Kathy / Swisher, Elizabeth / Creaney, Jenette / Robinson, Bruce / Shelley, Carl Simon / Godwin, Eryn M. / Kendall, Sara / Shipman, Cassaundra / Bradford, Carol / Carey, Thomas / Haddad, Andrea / Moyer, Jeffey / Peterson, Lisa / Prince, Mark / Rozek, Laura / Wolf, Gregory / Bowman, Rayleen / Fong, Kwun M. / Yang, Ian / Korst, Robert / Rathmell, W. Kimryn / Fantacone-Campbell, J. Leigh / Hooke, Jeffrey A. / Kovatich, Albert J. / Shriver, Craig D. / DiPersio, John / Drake, Bettina / Govindan, Ramaswamy / Heath, Sharon / Ley, Timothy / Van Tine, Brian / Westervelt, Peter / Rubin, Mark A. / Lee, Jung Il / Aredes, Natália D. / Mariamidze, Armaz

    Cell. 2018 Apr. 05, v. 173, no. 2 p.321-337.e10

    2018  

    Abstract: Genetic alterations in signaling pathways that control cell-cycle progression, apoptosis, and cell growth are common hallmarks of cancer, but the extent, mechanisms, and co-occurrence of alterations in these pathways differ between individual tumors and ... ...

    Institution The Cancer Genome Atlas Research Network
    Abstract Genetic alterations in signaling pathways that control cell-cycle progression, apoptosis, and cell growth are common hallmarks of cancer, but the extent, mechanisms, and co-occurrence of alterations in these pathways differ between individual tumors and tumor types. Using mutations, copy-number changes, mRNA expression, gene fusions and DNA methylation in 9,125 tumors profiled by The Cancer Genome Atlas (TCGA), we analyzed the mechanisms and patterns of somatic alterations in ten canonical pathways: cell cycle, Hippo, Myc, Notch, Nrf2, PI-3-Kinase/Akt, RTK-RAS, TGFβ signaling, p53 and β-catenin/Wnt. We charted the detailed landscape of pathway alterations in 33 cancer types, stratified into 64 subtypes, and identified patterns of co-occurrence and mutual exclusivity. Eighty-nine percent of tumors had at least one driver alteration in these pathways, and 57% percent of tumors had at least one alteration potentially targetable by currently available drugs. Thirty percent of tumors had multiple targetable alterations, indicating opportunities for combination therapy.
    Keywords DNA methylation ; apoptosis ; cell cycle ; cell growth ; gene expression ; genes ; landscapes ; neoplasms ; therapeutics ; pan-cancer ; signaling pathways ; whole exome sequencing ; combination therapy ; TCGA ; PanCanAtlas ; cancer genome atlas ; cancer genomics ; precision oncology
    Language English
    Dates of publication 2018-0405
    Size p. 321-337.e10.
    Publishing place Elsevier Inc.
    Document type Article ; Online
    Note NAL-AP-2-clean ; Resource is Open Access
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2018.03.035
    Database NAL-Catalogue (AGRICOLA)

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  10. Article ; Online: Comprehensive Characterization of Cancer Driver Genes and Mutations

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Bradley / Hilty, Joe / Kumar, Bahavna / Lang, James / Lehman, Norman L. / Mandt, Randy / Nguyen, Phuong / Pilarski, Robert / Rai, Karan / Schoenfield, Lynn / Senecal, Kelly / Wakely, Paul / Hansen, Paul / Lechan, Ronald / Powers, James / Tischler, Arthur / Grizzle, William E. / Sexton, Katherine C. / Kastl, Alison / Henderson, Joel / Porten, Sima / Waldmann, Jens / Fassnacht, Martin / Asa, Sylvia L. / Schadendorf, Dirk / Couce, Marta / Graefen, Markus / Huland, Hartwig / Sauter, Guido / Schlomm, Thorsten / Simon, Ronald / Tennstedt, Pierre / Olabode, Oluwole / Nelson, Mark / Bathe, Oliver / Carroll, Peter R. / Chan, June M. / Disaia, Philip / Glenn, Pat / Kelley, Robin K. / Landen, Charles N. / Phillips, Joanna / Prados, Michael / Simko, Jeffry / Smith-McCune, Karen / VandenBerg, Scott / Roggin, Kevin / Fehrenbach, Ashley / Kendler, Ady / Sifri, Suzanne / Steele, Ruth / Jimeno, Antonio / Carey, Francis / Forgie, Ian / Mannelli, Massimo / Carney, Michael / Hernandez, Brenda / Campos, Benito / Herold-Mende, Christel / Jungk, Christin / Unterberg, A. / Deimling, Andreas von / Bossler, Aaron / Galbraith, Joseph / Jacobus, Laura / Knudson, Michael / Knutson, Tina / Ma, Deqin / Milhem, Mohammed / Sigmund, Rita / Godwin, Andrew K. / Madan, Rashna / Rosenthal, Howard G. / Adebamowo, Clement / Adebamowo, Sally N. / Boussioutas, Alex / Beer, David / Giordano, Thomas / Mes-Masson, Anne-Marie / Saad, Fred / Bocklage, Therese / Landrum, Lisa / Mannel, Robert / Moore, Kathleen / Moxley, Katherine / Postier, Russel / Walker, Joan / Zuna, Rosemary / Feldman, Michael / Valdivieso, Federico / Dhir, Rajiv / Luketich, James / Pinero, Edna M. 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    Cell. 2018 Apr. 05, v. 173, no. 2 p.371-385.e18

    2018  

    Abstract: Identifying molecular cancer drivers is critical for precision oncology. Multiple advanced algorithms to identify drivers now exist, but systematic attempts to combine and optimize them on large datasets are few. We report a PanCancer and PanSoftware ... ...

    Institution The MC3 Working Group
    The Cancer Genome Atlas Research Network
    Abstract Identifying molecular cancer drivers is critical for precision oncology. Multiple advanced algorithms to identify drivers now exist, but systematic attempts to combine and optimize them on large datasets are few. We report 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. We identify 299 driver genes with implications regarding their anatomical sites and cancer/cell types. Sequence- and structure-based analyses identified >3,400 putative missense driver mutations supported by multiple lines of evidence. Experimental validation confirmed 60%–85% of predicted mutations as likely drivers. We found that >300 MSI tumors are associated with high PD-1/PD-L1, and 57% of tumors analyzed harbor putative clinically actionable events. Our study represents the most comprehensive discovery of cancer genes and mutations to date and will serve as a blueprint for future biological and clinical endeavors.
    Keywords algorithms ; cataloging ; cells ; data collection ; genes ; missense mutation ; neoplasms ; topographic maps ; wills ; oncology ; driver gene discovery ; structure analysis ; mutations of clinical relevance
    Language English
    Dates of publication 2018-0405
    Size p. 371-385.e18.
    Publishing place Elsevier Inc.
    Document type Article ; Online
    Note NALT-AP-4-rerunAP2-fuzzy ; Resource is Open Access
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2018.02.060
    Database NAL-Catalogue (AGRICOLA)

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