18 results on '"Zenklusen, Jean Claude"'
Search Results
2. Resource requirements to accelerate clinical applications of next-generation sequencing and radiomics: workshop commentary and review.
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Harris, Lyndsay, Shankar, Lalitha K, Hildebrandt, Claire, Rubinstein, Wendy S, Langlais, Kristofor, Rodriguez, Henry, Berger, Adam, Freymann, John, Huang, Erich P, Williams, P Mickey, Zenklusen, Jean Claude, Ochs, Robert, Tezak, Zivana, and Sahiner, Berkman
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NUCLEOTIDE sequencing ,ARTIFICIAL intelligence ,MACHINE learning ,RADIOMICS ,SCIENTIFIC community - Abstract
The National Institutes of Health–US Food and Drug Administration Joint Leadership Council Next-Generation Sequencing and Radiomics Working Group was formed by the National Institutes of Health–Food and Drug Administration Joint Leadership Council to promote the development and validation of innovative next-generation sequencing tests, radiomic tools, and associated data analysis and interpretation enhanced by artificial intelligence and machine learning technologies. A 2-day workshop was held on September 29-30, 2021, to convene members of the scientific community to discuss how to overcome the "ground truth" gap that has frequently been acknowledged as 1 of the limiting factors impeding high-quality research, development, validation, and regulatory science in these fields. This report provides a summary of the resource gaps identified by the working group and attendees, highlights existing resources and the ways they can potentially be employed to accelerate growth in these fields, and presents opportunities to support next-generation sequencing and radiomic tool development and validation using technologies such as artificial intelligence and machine learning. [ABSTRACT FROM AUTHOR]
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- 2024
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3. Integrated genomic characterization of oesophageal carcinoma
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Kim, Jihun, Bowlby, Reanne, Mungall, Andrew J., Robertson, Gordon A., Odze, Robert D., Cherniack, Andrew D., Shih, Juliann, Pedamallu, Chandra Sekhar, Cibulskis, Carrie, Dunford, Andrew, Meier, Samuel R., Kim, Jaegil, Raphael, Benjamin J., Wu, Hsin-Ta, Wong, Alexandra M., Willis, Joseph E., Bass, Adam J., Derks, Sarah, Garman, Katherine, McCall, Shannon J., Wiznerowicz, Maciej, Pantazi, Angeliki, Parfenov, Michael, Thorsson, Vésteinn, Shmulevich, Ilya, Dhankani, Varsha, Miller, Michael, Sakai, Ryo, Wang, Kenneth, Schultz, Nikolaus, Shen, Ronglai, Arora, Arshi, Weinhold, Nils, Sánchez-Vega, Francisco, Kelsen, David P., Zhang, Julia, Felau, Ina, Demchok, John, Rabkin, Charles S., Camargo, Constanza M., Zenklusen, Jean Claude, Bowen, Jay, Leraas, Kristen, Lichtenberg, Tara M., Curtis, Christina, Seoane, Jose A., Ojesina, Akinyemi I., Beer, David G., Gulley, Margaret L., Pennathur, Arjun, Luketich, James D., Zhou, Zhongren, Weisenberger, Daniel J., Akbani, Rehan, Lee, Ju-Seog, Liu, Wenbin, Mills, Gordon B., Zhang, Wei, Reid, Brian J, Hinoue, Toshinori, Laird, Peter W., Shen, Hui, Piazuelo, Blanca M., Schneider, Barbara G., McLellan, Michael, Taylor-Weiner, Amaro, Cibulskis, Carrie, Lawrence, Michael, Cibulskis, Kristian, Stewart, Chip, Getz, Gad, Lander, Eric, Gabriel, Stacey B., Ding, Li, McLellan, Michael D., Miller, Christopher A., Appelbaum, Elizabeth L., Cordes, Matthew G., Fronick, Catrina C., Fulton, Lucinda A., Mardis, Elaine R., Wilson, Richard K., Schmidt, Heather K., Fulton, Robert S., Ally, Adrian, Balasundaram, Miruna, Bowlby, Reanne, Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Holt, Robert A., Jones, Steven J. M., Kasaian, Katayoon, Brooks, Denise, Li, Haiyan I., Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Mungall, Karen L., Robertson, Gordon A., Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Wong, Tina, Cherniack, Andrew D., Shih, Juliann, Pedamallu, Chandra Sekhar, Beroukhim, Rameen, Bullman, Susan, Cibulskis, Carrie, Murray, Bradley A., Saksena, Gordon, Schumacher, Steven E., Gabriel, Stacey, Meyerson, Matthew, Hadjipanayis, Angela, Kucherlapati, Raju, Pantazi, Angeliki, Parfenov, Michael, Ren, Xiaojia, Park, Peter J., Lee, Semin, Kucherlapati, Melanie, Yang, Lixing, Baylin, Stephen B., Hoadley, Katherine A., Weisenberger, Daniel J., Bootwalla, Moiz S., Lai, Phillip H., Van Den Berg, David J., Berrios, Mario, Holbrook, Andrea, Akbani, Rehan, Hwang, Jun-Eul, Jang, Hee-Jin, Liu, Wenbin, Weinstein, John N., Lee, Ju-Seog, Lu, Yiling, Sohn, Bo Hwa, Mills, Gordon, Seth, Sahil, Protopopov, Alexei, Bristow, Christopher A., Mahadeshwar, Harshad S., Tang, Jiabin, Song, Xingzhi, Zhang, Jianhua, Laird, Peter W., Hinoue, Toshinori, Shen, Hui, Cho, Juok, Defrietas, Timothy, Frazer, Scott, Gehlenborg, Nils, Heiman, David I., Lawrence, Michael S., Lin, Pei, Meier, Samuel R., Noble, Michael S., Voet, Doug, Zhang, Hailei, Kim, Jaegil, Polak, Paz, Saksena, Gordon, Chin, Lynda, Getz, Gad, Wong, Alexandra M., Raphael, Benjamin J., Wu, Hsin-Ta, Lee, Semin, Park, Peter J., Yang, Lixing, Thorsson, Vésteinn, Bernard, Brady, Iype, Lisa, Miller, Michael, Reynolds, Sheila M., Shmulevich, Ilya, Dhankani, Varsha, Abeshouse, Adam, Arora, Arshi, Armenia, Joshua, Kundra, Ritika, Ladanyi, Marc, Lehmann, Kjong-Van, Gao, Jianjiong, Sander, Chris, Schultz, Nikolaus, Sánchez-Vega, Francisco, Shen, Ronglai, Weinhold, Nils, Chakravarty, Debyani, Zhang, Hongxin, Radenbaugh, Amie, Hegde, Apruva, Akbani, Rehan, Liu, Wenbin, Weinstein, John N., Chin, Lynda, Bristow, Christopher A., Lu, Yiling, Penny, Robert, Crain, Daniel, Gardner, Johanna, Curley, Erin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Shelton, Troy, Shelton, Candace, Bowen, Jay, Frick, Jessica, Gastier-Foster, Julie M., Gerken, Mark, Leraas, Kristen M., Lichtenberg, Tara M., Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Tarvin, Katherine, Saller, Charles, Park, Young Soo, Button, Michael, Carvalho, Andre L., Reis, Rui Manuel, Matsushita, Marcus Medeiros, Lucchesi, Fabiano, de Oliveira, Antonio Talvane, Le, Xuan, Paklina, Oxana, Setdikova, Galiya, Lee, Jae-Hyuck, Bennett, Joseph, Iacocca, Mary, Huelsenbeck-Dill, Lori, Potapova, Olga, Voronina, Olga, Liu, Ouida, Fulidou, Victoria, Cates, Crystal, Sharp, Alexis, Behera, Madhusmitara, Force, Seth, Khuri, Fadio, Owonikoko, Taofeek, Pickens, Allan, Ramalingam, Suresh, Sica, Gabriel, Dinjens, Winand, van Nistelrooij, Anna, Wijnhoven, Bas, Sandusky, George, Stepa, Serghei, Crain, Daniel, Paulauskis, Joseph, Penny, Robert, Gardner, Johanna, Mallery, David, Morris, Scott, Shelton, Troy, Shelton, Candace, Curley, Erin, Juhl, Hartmut, Zornig, Carsten, Kwon, Sun Young, Kelsen, David, Kim, Hark Kyun, Bartlett, John, Parfitt, Jeremy, Chetty, Runjan, Darling, Gail, Knox, Jennifer, Wong, Rebecca, El-Zimaity, Haila, Liu, Geoffrey, Boussioutas, Alex, Park, Do Young, Kemp, Rafael, Carlotti, Carlos Gilberto, da Cunha Tirapelli, Daniela Pretti, Saggioro, Fabiano Pinto, Sankarankutty, Ajith Kumar, Noushmehr, Houtan, dos Santos, Jose Sebastião, Trevisan, Felipe Amstalden, Eschbacher, Jennifer, Dubina, Michael, Mozgovoy, Eugene, Carey, Frank, Chalmers, Sally, Forgie, Ian, Godwin, Andrew, Reilly, Colleen, Madan, Rashna, Naima, Zaid, Ferrer-Torres, Daysha, Vinco, Michele, Rathmell, Kimryn W., Dhir, Rajiv, Luketich, James, Pennathur, Arjun, Ajani, Jaffer A., McCall, Shannon J., Janjigian, Yelena, Kelsen, David, Ladanyi, Marc, Tang, Laura, Camargo, Constanza M., Ajani, Jaffer A., Cheong, Jae-Ho, Chudamani, Sudha, Liu, Jai, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Demchok, John A., Felau, Ina, Ferguson, Martin L., Shaw, Kenna R. Mills, Sheth, Margi, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean Claude, Hutter, Carolyn M., Sofia, Heidi J., and Zhang, Jiashan
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- 2017
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4. Facilitating a culture of responsible and effective sharing of cancer genome data
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Siu, Lillian L., Lawler, Mark, Haussler, David, Knoppers, Bartha Maria, Lewin, Jeremy, Vis, Daniel J., Liao, Rachel G., Andre, Fabrice, Banks, Ian, Barrett, J.Carl, Caldas, Carlos, Camargo, Anamaria Aranha, Fitzgerald, Rebecca C., Mao, Mao, Mattison, John E., Pao, William, Sellers, William R., Sullivan, Patrick, Teh, Bin Tean, Ward, Robyn L., ZenKlusen, Jean Claude, Sawyers, Charles L., and Voest, Emile E.
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Medical records -- Management ,Cancer -- Care and treatment ,Clinical trials -- Ethical aspects ,Electronic records -- Management ,Company business management ,Biological sciences ,Health - Abstract
Rapid and affordable tumor molecular profiling has led to an explosion of clinical and genomic data poised to enhance the diagnosis, prognostication and treatment of cancer. A critical point has now been reached at which the analysis and storage of annotated clinical and genomic information in unconnected silos will stall the advancement of precision cancer care. Information systems must be harmonized to overcome the multiple technical and logistical barriers to data sharing. Against this backdrop, the Global Alliance for Genomic Health (GA4GH) was established in 2013 to create a common framework that enables responsible, voluntary and secure sharing of clinical and genomic data. This Perspective from the GA4GH Clinical Working Group Cancer Task Team highlights the data-aggregation challenges faced by the field, suggests potential collaborative solutions and describes how GA4GH can catalyze a harmonized data-sharing culture., There is broad consensus that the identification of aberrations in tumor DNA is key not only to achieving a better understanding of cancer but also to developing an improved process [...]
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- 2016
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5. Gene pathways and subnetworks distinguish between major glioma subtypes and elucidate potential underlying biology
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Wuchty, Stefan, Zhang, Alice, Walling, Jennifer, Ahn, Susie, Li, Aiguo, Quezado, Martha, Oberholtzer, Carl, Zenklusen, Jean-Claude, and Fine, Howard A.
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- 2010
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6. Comprehensive genomic characterization of head and neck squamous cell carcinomas
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Lawrence, Michael S., Sougnez, Carrie, Lichtenstein, Lee, Cibulskis, Kristian, Lander, Eric, Gabriel, Stacey B., Getz, Gad, Ally, Adrian, Balasundaram, Miruna, Birol, Inanc, Bowlby, Reanne, Brooks, Denise, Butterfield, Yaron S. N., Carlsen, Rebecca, Cheng, Dean, Chu, Andy, Dhalla, Noreen, Guin, Ranabir, Holt, Robert A., Jones, Steven J. M., Lee, Darlene, Li, Haiyan I., Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Robertson, Gordon A., Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Wong, Tina, Protopopov, Alexei, Santoso, Netty, Lee, Semin, Parfenov, Michael, Zhang, Jianhua, Mahadeshwar, Harshad S., Tang, Jiabin, Ren, Xiaojia, Seth, Sahil, Haseley, Psalm, Zeng, Dong, Yang, Lixing, Xu, Andrew W., Song, Xingzhi, Pantazi, Angeliki, Bristow, Christopher A., Hadjipanayis, Angela, Seidman, Jonathan, Chin, Lynda, Park, Peter J., Kucherlapati, Raju, Akbani, Rehan, Casasent, Tod, Liu, Wenbin, Lu, Yiling, Mills, Gordon, Motter, Thomas, Weinstein, John, Diao, Lixia, Wang, Jing, Fan, You Hong, Liu, Jinze, Wang, Kai, Auman, Todd J., Balu, Saianand, Bodenheimer, Thomas, Buda, Elizabeth, Hayes, Neil D., Hoadley, Katherine A., Hoyle, Alan P., Jefferys, Stuart R., Jones, Corbin D., Kimes, Patrick K., Liu, Yufeng, Meng, Shaowu, Mieczkowski, Piotr A., Mose, Lisle E., Parker, Joel S., Perou, Charles M., Prins, Jan F., Roach, Jeffrey, Shi, Yan, Simons, Janae V., Singh, Darshan, Soloway, Matthew G., Tan, Donghui, Veluvolu, Umadevi, Walter, Vonn, Waring, Scot, Wilkerson, Matthew D., Wu, Junyuan, Zhao, Ni, Cherniack, Andrew D., Hammerman, Peter S., Tward, Aaron D., Pedamallu, Chandra Sekhar, Saksena, Gordon, Jung, Joonil, Ojesina, Akinyemi I., Carter, Scott L., Zack, Travis I., Schumacher, Steven E., Beroukhim, Rameen, Freeman, Samuel S., Meyerson, Matthew, Cho, Juok, Noble, Michael S., DiCara, Daniel, Zhang, Hailei, Heiman, David I., Gehlenborg, Nils, Voet, Doug, Lin, Pei, Frazer, Scott, Stojanov, Petar, Liu, Yingchun, Zou, Lihua, Kim, Jaegil, Muzny, Donna, Doddapaneni, HarshaVardhan, Kovar, Christie, Reid, Jeff, Morton, Donna, Han, Yi, Hale, Walker, Chao, Hsu, Chang, Kyle, Drummond, Jennifer A., Gibbs, Richard A., Kakkar, Nipun, Wheeler, David, Xi, Liu, Ciriello, Giovanni, Ladanyi, Marc, Lee, William, Ramirez, Ricardo, Sander, Chris, Shen, Ronglai, Sinha, Rileen, Weinhold, Nils, Taylor, Barry S., Aksoy, Arman B., Dresdner, Gideon, Gao, Jianjiong, Gross, Benjamin, Jacobsen, Anders, Reva, Boris, Schultz, Nikolaus, Sumer, Onur S., Sun, Yichao, Chan, Timothy A., Morris, Luc G., Stuart, Joshua, Benz, Stephen, Ng, Sam, Benz, Christopher, Yau, Christina, Baylin, Stephen B., Cope, Leslie, Danilova, Ludmila, Herman, James G., Bootwalla, Moiz, Maglinte, Dennis T., Laird, Peter W., Triche, Timothy, Jr, Weisenberger, Daniel J., Van Den Berg, David J., Agrawal, Nishant, Bishop, Justin, Boutros, Paul C., Bruce, Jeff P., Byers, Lauren Averett, Califano, Joseph, Carey, Thomas E., Chen, Zhong, Cheng, Hui, Chiosea, Simion I., Cohen, Ezra, Diergaarde, Brenda, Egloff, Ann Marie, El-Naggar, Adel K., Ferris, Robert L., Frederick, Mitchell J., Grandis, Jennifer R., Guo, Yan, Haddad, Robert I., Harris, Thomas, Hui, Angela B. Y., Lee, Jack J., Lippman, Scott M., Liu, Fei-Fei, McHugh, Jonathan B., Myers, Jeff, Ng, Patrick Kwok Shing, Perez-Ordonez, Bayardo, Pickering, Curtis R., Prystowsky, Michael, Romkes, Marjorie, Saleh, Anthony D., Sartor, Maureen A., Seethala, Raja, Seiwert, Tanguy Y., Si, Han, Van Waes, Carter, Waggott, Daryl M., Wiznerowicz, Maciej, Yarbrough, Wendell G., Zhang, Jiexin, Zuo, Zhixiang, Burnett, Ken, Crain, Daniel, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Candace, Shelton, Troy, Sherman, Mark, Yena, Peggy, Black, Aaron D., Bowen, Jay, Frick, Jessica, Gastier-Foster, Julie M., Harper, Hollie A., Leraas, Kristen, Lichtenberg, Tara M., Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Baboud, Julien, Jensen, Mark A., Kahn, Ari B., Pihl, Todd D., Pot, David A., Srinivasan, Deepak, Walton, Jessica S., Wan, Yunhu, Burton, Robert A., Davidsen, Tanja, Demchok, John A., Eley, Greg, Ferguson, Martin L., Shaw, Kenna Mills R., Ozenberger, Bradley A., Sheth, Margi, Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean Claude, Saller, Charles, Tarvin, Katherine, Chen, Chu, Bollag, Roni, Weinberger, Paul, Golusiński, Wojciech, Golusiński, Paweł, Ibbs, Matthew, Korski, Konstanty, Mackiewicz, Andrzej, Suchorska, Wiktoria, Szybiak, Bartosz, Curley, Erin, Beard, Christina, Mitchell, Colleen, Sandusky, George, Ahn, Julie, Khan, Zubair, Irish, Jonathan, Waldron, John, William, William N., Jr, Egea, Sophie, Gomez-Fernandez, Carmen, Herbert, Lynn, Bradford, Carol R., Chepeha, Douglas B., Haddad, Andrea S., Jones, Tamara R., Komarck, Christine M., Malakh, Mayya, Moyer, Jeffrey S., Nguyen, Ariane, Peterson, Lisa A., Prince, Mark E., Rozek, Laura S., Taylor, Evan G., Walline, Heather M., Wolf, Gregory T., Boice, Lori, Chera, Bhishamjit S., Funkhouser, William K., Gulley, Margaret L., Hackman, Trevor G., Hayward, Michele C., Huang, Mei, Rathmell, Kimryn W., Salazar, Ashley H., Shockley, William W., Shores, Carol G., Thorne, Leigh, Weissler, Mark C., Wrenn, Sylvia, Zanation, Adam M., Brown, Brandee T., and Pham, Michelle
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- 2015
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7. Localization and characterization of ST7 in cancer
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Charong, Nurdina, Patmasiriwat, Pimpicha, and Zenklusen, Jean Claude
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- 2011
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8. Epigenetic-Mediated Dysfunction of the Bone Morphogenetic Protein Pathway Inhibits Differentiation of Glioblastoma-Initiating Cells
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Lee, Jeongwu, Son, Myung Jin, Woolard, Kevin, Donin, Nicholas M., Li, Aiguo, Cheng, Chui H., Kotliarova, Svetlana, Kotliarov, Yuri, Walling, Jennifer, Ahn, Susie, Kim, Misuk, Totonchy, Mariam, Cusack, Thomas, Ene, Chibawanye, Ma, Hilary, Su, Qin, Zenklusen, Jean Claude, Zhang, Wei, Maric, Dragan, and Fine, Howard A.
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- 2008
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9. Comprehensive molecular characterization of gastric adenocarcinoma
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Bass, Adam J., Thorsson, Vesteinn, Shmulevich, Ilya, Reynolds, Sheila M., Miller, Michael, Bernard, Brady, Hinoue, Toshinori, Laird, Peter W., Curtis, Christina, Shen, Hui, Weisenberger, Daniel J., Schultz, Nikolaus, Shen, Ronglai, Weinhold, Nils, Kelsen, David P., Bowlby, Reanne, Chu, Andy, Kasaian, Katayoon, Mungall, Andrew J., Robertson, Gordon A., Sipahimalani, Payal, Cherniack, Andrew, Getz, Gad, Liu, Yingchun, Noble, Michael S., Pedamallu, Chandra, Sougnez, Carrie, Akbani, Rehan, Lee, Ju-Seog, Liu, Wenbin, Mills, Gordon B., Yang, Da, Zhang, Wei, Pantazi, Angeliki, Gulley, Margaret, Piazuelo, Blanca M., Schneider, Barbara G., Kim, Jihun, Boussioutas, Alex, Sheth, Margi, Demchok, John A., Rabkin, Charles S., Willis, Joseph E., Ng, Sam, Garman, Katherine, Beer, David G., Pennathur, Arjun, Raphael, Benjamin J., Wu, Hsin-Ta, Odze, Robert, Kim, Hark K., Bowen, Jay, Leraas, Kristen M., Lichtenberg, Tara M., Weaver, Stephanie, McLellan, Michael, Wiznerowicz, Maciej, Sakai, Ryo, Lawrence, Michael S., Cibulskis, Kristian, Lichtenstein, Lee, Fisher, Sheila, Gabriel, Stacey B., Lander, Eric S., Ding, Li, Niu, Beifang, Ally, Adrian, Balasundaram, Miruna, Birol, Inanc, Brooks, Denise, Butterfield, Yaron S. N., Carlsen, Rebecca, Chu, Justin, Chuah, Eric, Chun, Hye-Jung E., Clarke, Amanda, Dhalla, Noreen, Guin, Ranabir, Holt, Robert A., Jones, Steven J. M., Lee, Darlene, Li, Haiyan A., Lim, Emilia, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Karen L., Nip, Ka Ming, Schein, Jacqueline E., Tam, Angela, Thiessen, Nina, Beroukhim, Rameen, Carter, Scott L., Cherniack, Andrew D., Cho, Juok, DiCara, Daniel, Frazer, Scott, Gehlenborg, Nils, Heiman, David I., Jung, Joonil, Kim, Jaegil, Lin, Pei, Meyerson, Matthew, Ojesina, Akinyemi I., Pedamallu, Chandra Sekhar, Saksena, Gordon, Schumacher, Steven E., Stojanov, Petar, Tabak, Barbara, Voet, Doug, Rosenberg, Mara, Zack, Travis I., Zhang, Hailei, Zou, Lihua, Protopopov, Alexei, Santoso, Netty, Parfenov, Michael, Lee, Semin, Zhang, Jianhua, Mahadeshwar, Harshad S., Tang, Jiabin, Ren, Xiaojia, Seth, Sahil, Yang, Lixing, Xu, Andrew W., Song, Xingzhi, Xi, Ruibin, Bristow, Christopher A., Hadjipanayis, Angela, Seidman, Jonathan, Chin, Lynda, Park, Peter J., Kucherlapati, Raju, Ling, Shiyun, Rao, Arvind, Weinstein, John N., Kim, Sang-Bae, Lu, Yiling, Mills, Gordon, Bootwalla, Moiz S., Lai, Phillip H., Triche, Timothy, Jr, Van Den Berg, David J., Baylin, Stephen B., Herman, James G., Murray, Bradley A., Askoy, Arman B., Ciriello, Giovanni, Dresdner, Gideon, Gao, Jianjiong, Gross, Benjamin, Jacobsen, Anders, Lee, William, Ramirez, Ricardo, Sander, Chris, Senbabaoglu, Yasin, Sinha, Rileen, Sumer, Onur S., Sun, Yichao, Thorsson, Vésteinn, Iype, Lisa, Kramer, Roger W., Kreisberg, Richard, Rovira, Hector, Tasman, Natalie, Haussler, David, Stuart, Josh M., Verhaak, Roeland G. W., Leiserson, Mark D. M., Taylor, Barry S., Black, Aaron D., Carney, Julie Ann, Gastier-Foster, Julie M., Helsel, Carmen, McAllister, Cynthia, Ramirez, Nilsa C., Tabler, Teresa R., Wise, Lisa, Zmuda, Erik, Penny, Robert, Crain, Daniel, Gardner, Johanna, Lau, Kevin, Curely, Erin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Shelton, Troy, Shelton, Candace, Sherman, Mark, Benz, Christopher, Lee, Jae-Hyuk, Fedosenko, Konstantin, Manikhas, Georgy, Potapova, Olga, Voronina, Olga, Belyaev, Dmitry, Dolzhansky, Oleg, Rathmell, Kimryn W., Brzezinski, Jakub, Ibbs, Matthew, Korski, Konstanty, Kycler, Witold, Łaźniak, Radoslaw, Leporowska, Ewa, Mackiewicz, Andrzej, Murawa, Dawid, Murawa, Pawel, Spychała, Arkadiusz, Suchorska, Wiktoria M., Tatka, Honorata, Teresiak, Marek, Abdel-Misih, Raafat, Bennett, Joseph, Brown, Jennifer, Iacocca, Mary, Rabeno, Brenda, Kwon, Sun-Young, Kemkes, Ariane, Curley, Erin, Alexopoulou, Iakovina, Engel, Jay, Bartlett, John, Albert, Monique, Park, Do-Youn, Dhir, Rajiv, Luketich, James, Landreneau, Rodney, Janjigian, Yelena Y., Cho, Eunjung, Ladanyi, Marc, Tang, Laura, McCall, Shannon J., Park, Young S., Cheong, Jae-Ho, Ajani, Jaffer, Camargo, Constanza M., Alonso, Shelley, Ayala, Brenda, Jensen, Mark A., Pihl, Todd, Raman, Rohini, Walton, Jessica, Wan, Yunhu, Eley, Greg, Mills Shaw, Kenna R., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean Claude, Davidsen, Tanja, Hutter, Carolyn M., Sofia, Heidi J., Burton, Robert, Chudamani, Sudha, and Liu, Jia
- Published
- 2014
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10. Comprehensive molecular characterization of urothelial bladder carcinoma
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Weinstein, John N., Akbani, Rehan, Broom, Bradley M., Wang, Wenyi, Verhaak, Roeland G. W., McConkey, David, Lerner, Seth, Morgan, Margaret, Creighton, Chad J., Smith, Carolyn, Kwiatkowski, David J., Cherniack, Andrew D., Kim, Jaegil, Pedamallu, Chandra Sekhar, Noble, Michael S., Al-Ahmadie, Hikmat A., Reuter, Victor E., Rosenberg, Jonathan E., Bajorin, Dean F., Bochner, Bernard H., Solit, David B., Koppie, Theresa, Robinson, Brian, Gordenin, Dmitry A., Fargo, David, Klimczak, Leszek J., Roberts, Steven A., Au, Jessie, Laird, Peter W., Hinoue, Toshinori, Schultz, Nikolaus, Ramirez, Ricardo, Hansel, Donna, Hoadley, Katherine A., Kim, William Y., Damrauer, Jeffrey S., Baylin, Stephen B., Mungall, Andrew J., Robertson, Gordon A., Chu., Andy, Sougnez, Carrie, Cibulskis, Kristian, Lichtenstein, Lee, Sivachenko, Andrey, Stewart, Chip, Lawrence, Michael S., Getz, Gad, Lander, Eric, Gabriel., Stacey B., Donehower, Lawrence, Carter, Scott L., Saksena, Gordon, Schumacher, Steven E., Freeman, Samuel S., Jung, Joonil, Bhatt, Ami S., Pugh, Trevor, Beroukhim, Rameen, Gabriel, Stacey B., Meyerson, Matthew, Chu, Andy, Ally, Adrian, Balasundaram, Miruna, Butterfield, Yaron S. N., Dhalla, Noreen, Hirst, Carrie, Holt, Robert A., Jones, Steven J. M., Lee, Darlene, Li, Haiyan I., Marra, Marco A., Mayo, Michael, Moore, Richard A., Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Wong, Tina, Wye, Natasja, Bowlby, Reanne, Chuah, Eric, Guin, Ranabir, Shen, Hui, Bootwalla, Moiz S., Jr, Timothy Triche, Lai, Phillip H., Van Den Berg, David J., Weisenberger, Daniel J., Balu, Saianand, Bodenheimer, Tom, Damrauer Alan P. Hoyle, Jeffrey S., Jefferys, Stuart R., Meng, Shaowu, Mose, Lisle E., Simons, Janae V., Soloway, Mathew G., Wu, Junyuan, Parker, Joel S., Hayes, Neil D., Roach, Jeffrey, Buda, Elizabeth, Jones, Corbin D., Mieczkowski, Piotr A., Tan, Donghui, Veluvolu, Umadevi, Waring, Scot, Auman, Todd J., Perou, Charles M., Wilkerson, Matthew D., Santoso, Netty, Parfenov, Michael, Ren, Xiaojia, Pantazi, Angeliki, Hadjipanayis, Angela, Seidman, Jonathan, Kucherlapati, Raju, Lee, Semin, Yang, Lixing, Park, Peter J., Xu, Andrew Wei, Protopopov, Alexei, Zhang, Jianhua, Bristow, Christopher, Mahadeshwar, Harshad S., Seth, Sahil, Song, Xingzhi, Tang, Jiabin, Zeng, Dong, Chin, Lynda, Guo, Charles, Casasent, Tod D., Liu, Wenbin, Ju, Zhenlin, Motter, Thomas, Peng, Bo, Ryan, Michael, Su, Xiaoping, Yang, Ji-Yeon, Lorenzi, Philip L., Yao, Hui, Zhang, Nianxiang, Zhang, Jiexin, Mills, Gordon B., Cho, Juok, DiCara, Daniel, Frazer, Scott, Gehlenborg, Nils, Heiman, David I., Lin, Pei, Liu, Yingchun, Stojanov, Petar, Voet, Doug, Zhang, Hailei, Zou, Lihua, Bernard, Brady, Kreisberg, Dick, Reynolds, Sheila, Rovira, Hector, Shmulevich, Ilya, Gao, Jianjiong, Jacobsen, Anders, Aksoy, Arman B., Antipin, Yevgeniy, Ciriello, Giovanni, Dresdner, Gideon, Gross, Benjamin, Lee, William, Reva, Boris, Shen, Ronglai, Sinha, Rileen, Sumer, Onur S., Weinhold, Nils, Ladanyi, Marc, Sander, Chris, Benz, Christopher, Carlin, Daniel, Haussler, David, Ng, Sam, Paull, Evan O., Stuart, Joshua, Zhu, Jing, Liu, Yuexin, Zhang, Wei, Taylor, Barry S., Lichtenberg, Tara M., Zmuda, Erik, Barr, Thomas, Black, Aaron D., George, Myra, Hanf, Benjamin, Helsel, Carmen, McAllister, Cynthia, Ramirez, Nilsa C., Tabler, Teresa R., Weaver, Stephanie, Wise, Lisa, Bowen, Jay, Gastier-Foster, Julie M., Jian, Weiguo, Tello, Sebrina, Ittman, Michael, Castro, Patricia, McClenden, Whitney D., Gibbs, Richard, Saller, Charles, Tarvin, Katherine, DiPiero, Jennifer M., Owens, Jennifer, Bollag, Roni, Li, Qiang, Weinberger, Paul, Czerwinski, Christine, Huelsenbeck-Dill, Lori, Iacocca, Mary, Petrelli, Nicholas, Rabeno, Brenda, Swanson, Pat, Shelton, Troy, Curley, Erin, Gardner, Johanna, Mallery, David, Penny, Robert, Van Bang, Nguyen, Thi Hanh, Phan, Kohl, Bernard, Van Le, Xuan, Duc Phu, Bui, Thorp, Richard, Tien, Nguyen Viet, Vinh, Le Quang, Sandusky, George, Burks, Eric, Christ, Kimberly, Gee, Jason, Holway, Antonia, Moinzadeh, Alireza, Sorcini, Andrea, Sullivan, Travis, Garcia-Grossman, Ilana R., Regazzi, Ashley M., Boice, Lori, Rathmell, Wendy Kimryn, Thorne, Leigh, Bastacky, Sheldon, Davies, Benjamin, Dhir, Rajiv, Gingrich, Jeffrey, Hrebinko, Ronald, Maranchie, Jodi, Nelson, Joel, Parwani, Anil, Bshara, Wiam, Gaudioso, Carmelo, Morrison, Carl, Alexopoulou, Vina, Bartlett, John, Engel, Jay, Kodeeswaran, Sugy, Antic, Tatjana, O’Donnell, Peter H., Smith, Norm D., Steinberg, Gary D., Egea, Sophie, Gomez-Fernandez, Carmen, Herbert, Lynn, Jorda, Merce, Soloway, Mark, Beaver, Allison, Carter, Suzie, Kapur, Payal, Lewis, Cheryl, Lotan, Yair, Bondaruk, Jolanta, Czerniak, Bogdan, Skinner, Eila, Aldape, Kenneth, Jensen, Mark A., Kahn, Ari B., Pihl, Todd D., Pot, David A., Srinivasan, Deepak, Wan, Yunhu, Ferguson, Martin L., Zenklusen, Jean Claude, Davidsen, Tanja, Demchok, John A., Mills Shaw, Kenna R., Sheth, Margi, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Hutter, Carolyn, Ozenberger, Bradley A., Sofia, Heidi J., and Eley, Greg
- Published
- 2014
- Full Text
- View/download PDF
11. CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations
- Author
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Zenklusen Jean-Claude, Wuchty Stefan, Cheng Hangjiong, Bozdag Serdar, Kotliarov Yuri, and Fine Howard A
- Subjects
Internal medicine ,RC31-1245 ,Genetics ,QH426-470 - Abstract
Abstract Background Genomic copy number alterations are widely associated with a broad range of human tumors and offer the potential to be used as a diagnostic tool. Especially in the emerging era of personalized medicine medical informatics tools that allow the fast visualization and analysis of genomic alterations of a patient's genomic profile for diagnostic and potential treatment purposes increasingly gain importance. Results We developed CNAReporter, a software tool that allows users to visualize SNP-specific data obtained from Affymetrix arrays and generate PDF-reports as output. We combined standard algorithms for the analysis of chromosomal alterations, utilizing the widely applied GenePattern framework. As an example, we show genome analyses of two patients with distinctly different CNA profiles using the tool. Conclusions Glioma subtypes, characterized by different genomic alterations, are often treated differently but can be difficult to differentiate pathologically. CNAReporter offers a user-friendly way to visualize and analyse genomic changes of any given tumor genomic profile, thereby leading to an accurate diagnosis and patient-specific treatment.
- Published
- 2010
- Full Text
- View/download PDF
12. The next horizon in precision oncology: Proteogenomics to inform cancer diagnosis and treatment.
- Author
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Rodriguez, Henry, Zenklusen, Jean Claude, Staudt, Louis M., Doroshow, James H., and Lowy, Douglas R.
- Subjects
- *
CANCER diagnosis , *CANCER treatment , *ONCOLOGY , *PATIENTS' rights , *CLINICAL trials - Abstract
When it comes to precision oncology, proteogenomics may provide better prospects to the clinical characterization of tumors, help make a more accurate diagnosis of cancer, and improve treatment for patients with cancer. This perspective describes the significant contributions of The Cancer Genome Atlas and the Clinical Proteomic Tumor Analysis Consortium to precision oncology and makes the case that proteogenomics needs to be fully integrated into clinical trials and patient care in order for precision oncology to deliver the right cancer treatment to the right patient at the right dose and at the right time. Multiomics approaches that collectively integrate proteomics and genomics provide new layers into our understanding of the mechanisms of tumorigenesis across diverse cancer types and patients and provide the path towards treatment through rationalized precision oncology. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
13. The International Collaboration for Cancer Classification and Research.
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Cree, Ian A., Indave Ruiz, Blanca Iciar, Zavadil, Jiri, McKay, James, Olivier, Magali, Kozlakidis, Zisis, Lazar, Alexander J., Hyde, Chris, Holdenrieder, Stefan, Hastings, Ros, Rajpoot, Nasir, Fouchardiere, Arnaud, Rous, Brian, Zenklusen, Jean Claude, Normanno, Nicola, and Schilsky, Richard L.
- Subjects
TUMOR classification ,CANCER research ,INFORMATION overload ,CLASSIFICATION ,TRANSLATIONAL research - Abstract
Gaps in the translation of research findings to clinical management have been recognized for decades. They exist for the diagnosis as well as the management of cancer. The international standards for cancer diagnosis are contained within the World Health Organization (WHO) Classification of Tumours, published by the International Agency for Research on Cancer (IARC) and known worldwide as the WHO Blue Books. In addition to their relevance to individual patients, these volumes provide a valuable contribution to cancer research and surveillance, fulfilling an important role in scientific evidence synthesis and international standard setting. However, the multidimensional nature of cancer classification, the way in which the WHO Classification of Tumours is constructed, and the scientific information overload in the field pose important challenges for the translation of research findings to tumour classification and hence cancer diagnosis. To help address these challenges, we have established the International Collaboration for Cancer Classification and Research (IC3R) to provide a forum for the coordination of efforts in evidence generation, standard setting and best practice recommendations in the field of tumour classification. The first IC3R meeting, held in Lyon, France, in February 2019, gathered representatives of major institutions involved in tumour classification and related fields to identify and discuss translational challenges in data comparability, standard setting, quality management, evidence evaluation and copyright, as well as to develop a collaborative plan for addressing these challenges. What's new? The World Health Organization Classification of Tumours has been informing cancer research and clinical practice by providing an international consensus on the tumour criteria for cancer diagnosis. In a new initiative coordinated by the International Agency for Research on Cancer, major institutions are now joining forces to address the remaining challenges in translational research and facilitate the application of research results to clinical practice. The newly‐established International Collaboration for Cancer Classification and Research (IC3R) aims to provide a forum for the coordination of efforts in generating evidence, setting standards, and providing best practice recommendations for tumor classification and cancer research. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
14. The Exceptional Responders Initiative: Feasibility of a National Cancer Institute Pilot Study.
- Author
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Conley, Barbara A, Staudt, Lou, Takebe, Naoko, Wheeler, David A, Wang, Linghua, Cardenas, Maria F, Korchina, Viktoriya, Zenklusen, Jean Claude, McShane, Lisa M, Tricoli, James V, Williams, Paul M, Lubensky, Irina, O'Sullivan-Coyne, Geraldine, Kohn, Elise, Little, Richard F, White, Jeffrey, Malik, Shakun, Harris, Lyndsay N, Mann, Bhupinder, and Weil, Carol
- Subjects
INVESTIGATIONAL therapies ,PILOT projects ,NUCLEOTIDE sequence ,TUMOR treatment ,NUCLEIC acids ,SEQUENCE analysis ,GENETIC mutation ,RETROSPECTIVE studies ,GENE expression profiling ,RESEARCH funding ,TUMORS - Abstract
Background: Tumor molecular profiling from patients experiencing exceptional responses to systemic therapy may provide insights into cancer biology and improve treatment tailoring. This pilot study evaluates the feasibility of identifying exceptional responders retrospectively, obtaining pre-exceptional response treatment tumor tissues, and analyzing them with state-of-the-art molecular analysis tools to identify potential molecular explanations for responses.Methods: Exceptional response was defined as partial (PR) or complete (CR) response to a systemic treatment with population PR or CR rate less than 10% or an unusually long response (eg, duration >3 times published median). Cases proposed by patients' clinicians were reviewed by clinical and translational experts. Tumor and normal tissue (if possible) were profiled with whole exome sequencing and, if possible, targeted deep sequencing, RNA sequencing, methylation arrays, and immunohistochemistry. Potential germline mutations were tracked for relevance to disease.Results: Cases reflected a variety of tumors and standard and investigational treatments. Of 520 cases, 476 (91.5%) were accepted for further review, and 222 of 476 (46.6%) proposed cases met requirements as exceptional responders. Clinical data were obtained from 168 of 222 cases (75.7%). Tumor was provided from 130 of 168 cases (77.4%). Of 117 of the 130 (90.0%) cases with sufficient nucleic acids, 109 (93.2%) were successfully analyzed; 6 patients had potentially actionable germline mutations.Conclusion: Exceptional responses occur with standard and investigational treatment. Retrospective identification of exceptional responders, accessioning, and sequencing of pretreatment archived tissue is feasible. Data from molecular analyses of tumors, particularly when combining results from patients who received similar treatments, may elucidate molecular bases for exceptional responses. [ABSTRACT FROM AUTHOR]- Published
- 2021
- Full Text
- View/download PDF
15. Prediction of Associations between microRNAs and Gene Expression in Glioma Biology.
- Author
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Wuchty, Stefan, Arjona, Dolores, Aiguo Li, Kotliarov, Yuri, Walling, Jennifer, Ahn, Susie, Zhang, Alice, Maric, Dragan, Anolik, Rachel, Zenklusen, Jean Claude, and Fine, Howard A.
- Subjects
GENE expression ,BIOCHEMISTRY ,HEREDITY ,MESSENGER RNA ,PROTEIN kinases - Abstract
Despite progress in the determination of miR interactions, their regulatory role in cancer is only beginning to be unraveled. Utilizing gene expression data from 27 glioblastoma samples we found that the mere knowledge of physical interactions between specific mRNAs and miRs can be used to determine associated regulatory interactions, allowing us to identify 626 associated interactions, involving 128 miRs that putatively modulate the expression of 246 mRNAs. Experimentally determining the expression of miRs, we found an over-representation of over(under)-expressed miRs with various predicted mRNA target sequences. Such significantly associated miRs that putatively bind over-expressed genes strongly tend to have binding sites nearby the 39UTR of the corresponding mRNAs, suggesting that the presence of the miRs near the translation stop site may be a factor in their regulatory ability. Our analysis predicted a significant association between miR-128 and the protein kinase WEE1, which we subsequently validated experimentally by showing that the over-expression of the naturally under-expressed miR-128 in glioma cells resulted in the inhibition of WEE1 in glioblastoma cells. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
- View/download PDF
16. CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations.
- Author
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Kotliarov, Yuri, Bozdag, Serdar, Hangjiong Cheng, Wuchty, Stefan, Zenklusen, Jean-Claude, and Fine, Howard A.
- Subjects
GENOMICS ,COMPUTER software ,TUMOR diagnosis ,MEDICAL informatics ,ALGORITHMS ,GENOMES ,MEDICAL information storage & retrieval systems ,COMPUTERS in medicine ,CHROMOSOMES - Abstract
Background: Genomic copy number alterations are widely associated with a broad range of human tumors and offer the potential to be used as a diagnostic tool. Especially in the emerging era of personalized medicine medical informatics tools that allow the fast visualization and analysis of genomic alterations of a patient's genomic profile for diagnostic and potential treatment purposes increasingly gain importance. Results: We developed CNAReporter, a software tool that allows users to visualize SNP-specific data obtained from Affymetrix arrays and generate PDF-reports as output. We combined standard algorithms for the analysis of chromosomal alterations, utilizing the widely applied GenePattern framework. As an example, we show genome analyses of two patients with distinctly different CNA profiles using the tool. Conclusions: Glioma subtypes, characterized by different genomic alterations, are often treated differently but can be difficult to differentiate pathologically. CNAReporter offers a user-friendly way to visualize and analyse genomic changes of any given tumor genomic profile, thereby leading to an accurate diagnosis and patient-specific treatment. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
17. Altered expression of transforming growth factor-β1 mrna and protein in mouse skin carcinogenesis.
- Author
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Patamalai, Benjamas, Burow, David L., Gimenez-Conti, Irma, Zenklusen, Jean Claude, Conti, Claudio J., Klein-Szanto, Andres J. P., and Fischer, Susan M.
- Published
- 1994
- Full Text
- View/download PDF
18. Molecular Features of Cancers Exhibiting Exceptional Responses to Treatment.
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Wheeler, David A., Takebe, Naoko, Hinoue, Toshinori, Hoadley, Katherine A., Cardenas, Maria F., Hamilton, Alina M., Laird, Peter W., Wang, Linghua, Johnson, Adrienne, Dewal, Ninad, Miller, Vincent, Piñeyro, David, Castro de Moura, Manuel, Esteller, Manel, Shen, Hui, Zenklusen, Jean Claude, Tarnuzzer, Roy, McShane, Lisa M., Tricoli, James V., and Williams, Paul M.
- Subjects
- *
GENOMICS , *PHENOTYPES , *DNA repair , *DNA damage , *DNA analysis , *TUMOR microenvironment , *ALKYLATING agents , *ONCOGENES - Abstract
A small fraction of cancer patients with advanced disease survive significantly longer than patients with clinically comparable tumors. Molecular mechanisms for exceptional responses to therapy have been identified by genomic analysis of tumor biopsies from individual patients. Here, we analyzed tumor biopsies from an unbiased cohort of 111 exceptional responder patients using multiple platforms to profile genetic and epigenetic aberrations as well as the tumor microenvironment. Integrative analysis uncovered plausible mechanisms for the therapeutic response in nearly a quarter of the patients. The mechanisms were assigned to four broad categories—DNA damage response, intracellular signaling, immune engagement, and genetic alterations characteristic of favorable prognosis—with many tumors falling into multiple categories. These analyses revealed synthetic lethal relationships that may be exploited therapeutically and rare genetic lesions that favor therapeutic success, while also providing a wealth of testable hypotheses regarding oncogenic mechanisms that may influence the response to cancer therapy. • Genomics of 110 patients with exceptional response to therapy profiled • Plausible molecular mechanisms related to therapy identified in ∼23% of cases • Proposed mechanisms involve DNA damage, signaling, and the immune response • Synthetic lethality with temozolomide in tumors with a defective DNA damage response Profiling multi-platform genomics of 110 cancer patients with an exceptional therapeutic response, Wheeler et al. identify putative molecular mechanisms explaining this survival phenotype in ∼23% of cases. Therapeutic success is related to rare molecular features of responding tumors, exploiting synthetic lethality and oncogene addiction. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
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