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  1. Article ; Online: Chromosome conformation capture.

    Cope, Nathan F / Fraser, Peter

    Cold Spring Harbor protocols

    2010  Volume 2009, Issue 2, Page(s) pdb.prot5137

    MeSH term(s) Animals ; Chromosomes, Mammalian/genetics ; DNA/chemistry ; DNA/genetics ; DNA/metabolism ; Deoxyribonuclease HindIII/metabolism ; Formaldehyde ; Mice ; Models, Molecular ; Nucleic Acid Conformation ; Polymerase Chain Reaction/methods
    Chemical Substances Formaldehyde (1HG84L3525) ; DNA (9007-49-2) ; Deoxyribonuclease HindIII (EC 3.1.21.-)
    Language English
    Publishing date 2010-02-10
    Publishing country United States
    Document type Journal Article
    ISSN 1559-6095
    ISSN (online) 1559-6095
    DOI 10.1101/pdb.prot5137
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Environmental and Structural Factors Associated with Bacterial Diversity in Household Dust Across the Arizona-Sonora Border.

    Benton, Lauren / Lopez-Galvez, Nicolas / Herman, Chloe / Caporaso, Greg / Cope, Emily / Rosales, Cecilia / Gameros, Mercedes / Lothrop, Nathan / Martínez, Fernando / Wright, Anne / Carr, Tara / Beamer, Paloma

    Research square

    2023  

    Abstract: We previously reported that asthma prevalence was higher in the United States (US) compared to Mexico (MX) (25.8% vs 8.4%). This investigation assessed differences in microbial dust composition in relation to demographic and housing characteristics on ... ...

    Abstract We previously reported that asthma prevalence was higher in the United States (US) compared to Mexico (MX) (25.8% vs 8.4%). This investigation assessed differences in microbial dust composition in relation to demographic and housing characteristics on both sides of the US-MX Border. Forty homes were recruited in the US and MX. Home visits collected floor dust and documented occupants' demographics, asthma prevalence, and housing structure and use characteristics. US households were more likely to have inhabitants who reported asthma when compared with MX households (30% vs 5%) and had significantly different flooring types. The percentage of households on paved roads, with flushing toilets, with piped water and with air conditioning was higher in the US, while dust load was higher in MX. Significant differences exist between countries in the microbial composition of the floor dust. Dust from US homes was enriched with
    Language English
    Publishing date 2023-09-29
    Publishing country United States
    Document type Preprint
    DOI 10.21203/rs.3.rs-3325336/v1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: The yin and yang of chromatin spatial organization.

    Cope, Nathan F / Fraser, Peter / Eskiw, Christopher H

    Genome biology

    2010  Volume 11, Issue 3, Page(s) 204

    Abstract: Spatial organization of the genome is non-random. Preferential chromatin interactions, both in cis and in trans and between transcriptionally active and silent regions, influence organization. ...

    Abstract Spatial organization of the genome is non-random. Preferential chromatin interactions, both in cis and in trans and between transcriptionally active and silent regions, influence organization.
    MeSH term(s) Chromatin/genetics ; Chromatin/metabolism ; Chromatin Assembly and Disassembly ; Gene Expression Regulation/genetics ; Genome/genetics ; Nucleic Acid Conformation ; Transcription Factors/metabolism ; Transcription, Genetic
    Chemical Substances Chromatin ; Transcription Factors
    Language English
    Publishing date 2010-03-29
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1474-760X
    ISSN (online) 1474-760X
    ISSN 1474-760X
    DOI 10.1186/gb-2010-11-3-204
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: The yin and yang of chromatin spatial organization

    Cope, Nathan F / Christopher H Eskiw / Peter Fraser

    Genome biology. 2010 Mar., v. 11, no. 3

    2010  

    Abstract: Spatial organization of the genome is non-random. Preferential chromatin interactions, both in cis and in trans and between transcriptionally active and silent regions, influence organization. ...

    Abstract Spatial organization of the genome is non-random. Preferential chromatin interactions, both in cis and in trans and between transcriptionally active and silent regions, influence organization.
    Keywords chromatin ; genome ; transcription (genetics)
    Language English
    Dates of publication 2010-03
    Size p. 2407.
    Publishing place Springer-Verlag
    Document type Article
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1465-6914 ; 1465-6906
    ISSN (online) 1474-760X ; 1465-6914
    ISSN 1465-6906
    DOI 10.1186/gb-2010-11-3-204
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells.

    Schoenfelder, Stefan / Sexton, Tom / Chakalova, Lyubomira / Cope, Nathan F / Horton, Alice / Andrews, Simon / Kurukuti, Sreenivasulu / Mitchell, Jennifer A / Umlauf, David / Dimitrova, Daniela S / Eskiw, Christopher H / Luo, Yanquan / Wei, Chia-Lin / Ruan, Yijun / Bieker, James J / Fraser, Peter

    Nature genetics

    2009  Volume 42, Issue 1, Page(s) 53–61

    Abstract: The discovery of interchromosomal interactions in higher eukaryotes points to a functional interplay between genome architecture and gene expression, challenging the view of transcription as a one-dimensional process. However, the extent of ... ...

    Abstract The discovery of interchromosomal interactions in higher eukaryotes points to a functional interplay between genome architecture and gene expression, challenging the view of transcription as a one-dimensional process. However, the extent of interchromosomal interactions and the underlying mechanisms are unknown. Here we present the first genome-wide analysis of transcriptional interactions using the mouse globin genes in erythroid tissues. Our results show that the active globin genes associate with hundreds of other transcribed genes, revealing extensive and preferential intra- and interchromosomal transcription interactomes. We show that the transcription factor Klf1 mediates preferential co-associations of Klf1-regulated genes at a limited number of specialized transcription factories. Our results establish a new gene expression paradigm, implying that active co-regulated genes and their regulatory factors cooperate to create specialized nuclear hot spots optimized for efficient and coordinated transcriptional control.
    MeSH term(s) Animals ; Chromatin Immunoprecipitation ; Erythroid Cells/cytology ; Erythroid Cells/metabolism ; Fluorescent Antibody Technique ; Gene Expression Profiling ; Gene Regulatory Networks/genetics ; Genome-Wide Association Study/methods ; Globins/genetics ; Globins/metabolism ; Humans ; In Situ Hybridization, Fluorescence/methods ; Kruppel-Like Transcription Factors/genetics ; Kruppel-Like Transcription Factors/metabolism ; Mice ; Mice, Knockout ; Mice, Transgenic ; Models, Biological ; Oligonucleotide Array Sequence Analysis/methods ; Protein Binding
    Chemical Substances Kruppel-Like Transcription Factors ; erythroid Kruppel-like factor ; Globins (9004-22-2)
    Language English
    Publishing date 2009-12-13
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1108734-1
    ISSN 1546-1718 ; 1061-4036
    ISSN (online) 1546-1718
    ISSN 1061-4036
    DOI 10.1038/ng.496
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Long-range DNA looping and gene expression analyses identify DEXI as an autoimmune disease candidate gene.

    Davison, Lucy J / Wallace, Chris / Cooper, Jason D / Cope, Nathan F / Wilson, Nicola K / Smyth, Deborah J / Howson, Joanna M M / Saleh, Nada / Al-Jeffery, Abdullah / Angus, Karen L / Stevens, Helen E / Nutland, Sarah / Duley, Simon / Coulson, Richard M R / Walker, Neil M / Burren, Oliver S / Rice, Catherine M / Cambien, Francois / Zeller, Tanja /
    Munzel, Thomas / Lackner, Karl / Blakenberg, Stefan / Fraser, Peter / Gottgens, Berthold / Todd, John A / Attwood, Tony / Belz, Stephanie / Braund, Peter / Cambien, François / Cooper, Jason / Crisp-Hihn, Abi / Diemert, Patrick / Deloukas, Panos / Foad, Nicola / Erdmann, Jeanette / Goodall, Alison H / Gracey, Jay / Gray, Emma / Williams, Rhian G / Heimerl, Susanne / Hengstenberg, Christian / Jolley, Jennifer / Krishnan, Unni / Lloyd-Jones, Heather / Lugauer, Ingrid / Lundmark, Per / Maouche, Seraya / Moore, Jasbir S / Muir, David / Murray, Elizabeth / Nelson, Chris P / Neudert, Jessica / Niblett, David / O'Leary, Karen / Ouwehand, Willem H / Pollard, Helen / Rankin, Angela / Sager, Hendrik / Samani, Nilesh J / Sambrook, Jennifer / Schmitz, Gerd / Scholz, Michael / Schroeder, Laura / Schunkert, Heribert / Syvannen, Ann-Christine / Tennstedt, Stefanie

    Human molecular genetics

    2011  Volume 21, Issue 2, Page(s) 322–333

    Abstract: The chromosome 16p13 region has been associated with several autoimmune diseases, including type 1 diabetes (T1D) and multiple sclerosis (MS). CLEC16A has been reported as the most likely candidate gene in the region, since it contains the most disease- ... ...

    Abstract The chromosome 16p13 region has been associated with several autoimmune diseases, including type 1 diabetes (T1D) and multiple sclerosis (MS). CLEC16A has been reported as the most likely candidate gene in the region, since it contains the most disease-associated single-nucleotide polymorphisms (SNPs), as well as an imunoreceptor tyrosine-based activation motif. However, here we report that intron 19 of CLEC16A, containing the most autoimmune disease-associated SNPs, appears to behave as a regulatory sequence, affecting the expression of a neighbouring gene, DEXI. The CLEC16A alleles that are protective from T1D and MS are associated with increased expression of DEXI, and no other genes in the region, in two independent monocyte gene expression data sets. Critically, using chromosome conformation capture (3C), we identified physical proximity between the DEXI promoter region and intron 19 of CLEC16A, separated by a loop of >150 kb. In reciprocal experiments, a 20 kb fragment of intron 19 of CLEC16A, containing SNPs associated with T1D and MS, as well as with DEXI expression, interacted with the promotor region of DEXI but not with candidate DNA fragments containing other potential causal genes in the region, including CLEC16A. Intron 19 of CLEC16A is highly enriched for transcription-factor-binding events and markers associated with enhancer activity. Taken together, these data indicate that although the causal variants in the 16p13 region lie within CLEC16A, DEXI is an unappreciated autoimmune disease candidate gene, and illustrate the power of the 3C approach in progressing from genome-wide association studies results to candidate causal genes.
    MeSH term(s) Autoimmune Diseases/genetics ; Chromosomes, Human, Pair 16 ; DNA/genetics ; DNA-Binding Proteins/genetics ; Humans ; Membrane Proteins/genetics ; Monocytes/metabolism ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci
    Chemical Substances DEXI protein, human ; DNA-Binding Proteins ; Membrane Proteins ; DNA (9007-49-2)
    Language English
    Publishing date 2011-10-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1108742-0
    ISSN 1460-2083 ; 0964-6906
    ISSN (online) 1460-2083
    ISSN 0964-6906
    DOI 10.1093/hmg/ddr468
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  7. 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. 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 / 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 / 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.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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  8. 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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  9. Article ; Online: Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

    Malta, Tathiane M. / Sokolov, Artëm / Gentles, Andrew J. / Burzykowski, Tomasz / Poisson, Laila / Weinstein, John N. / Kaminska, B. / Huelsken, Joerg / Omberg, Larsson / Gevaert, Olivier / Colaprico, Antonio / Czerwińska, Patrycja / Mazurek, Sylwia / Mishra, Lopa / Heyn, Holger / Krasnitz, Alex / Godwin, Andrew K. / Lazar, Alexander / Stuart, Joshua M. /
    Hoadley, Katherine A. / Laird, Peter W. / Noushmehr, Houtan / Wiznerowicz, Maciej / 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 / Thorsson, Vesteinn / 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 / 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 / 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, 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 / 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, 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 / 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 / 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

    Cell. 2018 Apr. 05, v. 173, no. 2 p.338-354.e15

    2018  

    Abstract: Cancer progression involves the gradual loss of a differentiated phenotype and acquisition of progenitor and stem-cell-like features. Here, we provide novel stemness indices for assessing the degree of oncogenic dedifferentiation. We used an innovative ... ...

    Institution The Cancer Genome Atlas Research Network
    Abstract Cancer progression involves the gradual loss of a differentiated phenotype and acquisition of progenitor and stem-cell-like features. Here, we provide novel stemness indices for assessing the degree of oncogenic dedifferentiation. We used an innovative one-class logistic regression (OCLR) machine-learning algorithm to extract transcriptomic and epigenetic feature sets derived from non-transformed pluripotent stem cells and their differentiated progeny. Using OCLR, we were able to identify previously undiscovered biological mechanisms associated with the dedifferentiated oncogenic state. Analyses of the tumor microenvironment revealed unanticipated correlation of cancer stemness with immune checkpoint expression and infiltrating immune cells. We found that the dedifferentiated oncogenic phenotype was generally most prominent in metastatic tumors. Application of our stemness indices to single-cell data revealed patterns of intra-tumor molecular heterogeneity. Finally, the indices allowed for the identification of novel targets and possible targeted therapies aimed at tumor differentiation.[Display omitted]
    Keywords algorithms ; artificial intelligence ; epigenetics ; metastasis ; neoplasm progression ; neoplasms ; phenotype ; progeny ; regression analysis ; transcriptomics ; The Cancer Genome Atlas ; stemness ; cancer stem cells ; genomic ; epigenomic ; machine learning ; pan-cancer ; dedifferentiation
    Language English
    Dates of publication 2018-0405
    Size p. 338-354.e15.
    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.2018.03.034
    Database NAL-Catalogue (AGRICOLA)

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  10. 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. 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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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