428 results on '"Thorne, Leigh"'
Search Results
2. Integrated Molecular Characterization of Testicular Germ Cell Tumors
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Wang, Linghua, Xi, Liu, Wheeler, David, Hughes, Daniel, Covington, Kyle, Jayaseelan, Joy C., Korchina, Viktoriya, Lewis, Lora, Hu, Jianhong, Doddapaneni, HarshaVardhan, Muzny, Donna, Gibbs, Richard, Hoadley, Katherine A., Hollern, Daniel, Vincent, Benjamin G., Chai, Shengjie, Smith, Christof C., Auman, J. Todd, Shi, Yan, Meng, Shaowu, Skelly, Tara, Tan, Donghui, Veluvolu, Umadevi, Mieczkowski, Piotr A., Jones, Corbin D., Wilkerson, Matthew D., Balu, Saianand, Bodenheimer, Tom, Hoyle, Alan P., Jefferys, Stuart R., Mose, Lisle E., Simons, Janae V., Soloway, Matthew G., Roach, Jeffrey, Parker, Joel S., Hayes, D. Neil, Perou, Charles M., Shih, Juliann, Cherniack, Andrew D., Meyerson, Matthew, Saksena, Gordon, Cibulskis, Carrie, Schumacher, Steven E., Beroukhim, Rameen, Gabriel, Stacey B., Bowlby, Reanne, Mungall, Andrew J., Brooks, Denise, Kasaian, Katayoon, Ally, Adrian, Balasundaram, Miruna, Carlsen, Rebecca, Cheung, Dorothy, Chuah, Eric, Dhalla, Noreen, Holt, Robert A., Jones, Steven J.M., Ma, Yussanne, Mayo, Michael, Moore, Richard A., Robertson, A. Gordon, Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Wong, Tina, Marra, Marco A., Shen, Hui, Zhou, Wanding, Laird, Peter W., Weisenberger, Daniel J., Van Den Berg, David J., Lai, Phillip H., Berrios, Mario, Holbrook, Andrea, Bootwalla, Moiz S., Maglinte, Dennis T., Armenia, Joshua, Sánchez-Vega, Francisco, Schultz, Nikolaus, Chakravarty, Debyani, Gao, Jianjiong, Heins, Zachary, Kundra, Ritika, Ochoa, Angelica, Liu, Minwei, Sander, Chris, Ladanyi, Marc, Thorsson, Vesteinn, Radenbaugh, Amie J., Newton, Yulia, Stuart, Joshua M., Cho, Juok, Heiman, David I., Noble, Michael S., Zhang, Hailei, Getz, Gad, Gehlenborg, Nils, Voet, Doug, Lin, Pei, Frazer, Scott, Kim, Jaegil, Lawrence, Michael S., Meier, Sam, Defreitas, Timothy, Chin, Lynda, Hegde, Apurva M., Akbani, Rehan, Weinstein, John N., Liu, Wenbin, Mills, Gordon B., Lu, Yiling, Pyle, Louise C., Pluta, John, Nathanson, Katherine L., Tickoo, Satish K., Reuter, Victor E., Mehra, Rohit, Looijenga, Leendert, Bryce, Alan H., Cárcano, Flavio M., Carvalho, André L., Cortessis, Victoria K., Feldman, Darren, Godoy, Guilherme, Ittmann, Michael, Jones, Jeffrey, Kulis, Tomislav, Lerner, Seth, Lessel, Davor, Shelley, Carl S., Vidal, Daniel O., Leraas, Kristen M., Lichtenberg, Tara M., Bowen, Jay, Gastier-Foster, Julie M., Gerken, Mark, Helsel, Carmen, Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Cottingham, Sandra, Chesla, David, Saller, Charles, Tarvin, Katherine, Lopes, Luiz Fernando, Scapulatempo-Neto, Cristovam, Aredes, Natália D.A., Oosterhuis, Wolter, Gillis, Ad, Stoop, Hans, Eijkenboom, Wil, Sandusky, George, Martin, Sue Ellen, Aron, Manju, Daneshmand, Siamak, Djaladat, Hooman, Quinn, David, Dorff, Tanya, Lennerz, Jochen K., Thorne, Leigh B., Gamulin, Marija, Kastelan, Zeljko, Hudolin, Tvrtko, Kubisch, Christian, Boice, Lori, Huang, Mei, Perou, Amy H., Rathmell, W. Kimryn, Pihl, Todd, Wan, Yunhu, Sun, Qiang, Naresh, Rashi, Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Wu, Ye, Ferguson, Martin L., Zenklusen, Jean C., Felau, Ina, Zhang, Jiashan (Julia), Sheth, Margi, Demchok, John A., Yang, Liming, Wang, Zhining, Tarnuzzer, Roy, Hutter, Carolyn M., Sofia, Heidi J., Davidsen, Tanja M., Hollern, Daniel P., Thorsson, Vésteinn, Feldman, Darren R., ZenKlusen, Jean C., Zhang, Jiashan, and Wheeler, David A.
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- 2018
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3. Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas
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Abeshouse, Adam, Adebamowo, Clement, Adebamowo, Sally N., Akbani, Rehan, Akeredolu, Teniola, Ally, Adrian, Anderson, Matthew L., Anur, Pavana, Appelbaum, Elizabeth L., Armenia, Joshua, Auman, J. Todd, Bailey, Matthew H., Baker, Laurence, Balasundaram, Miruna, Balu, Saianand, Barthel, Floris P., Bartlett, John, Baylin, Stephen B., Behera, Madhusmita, Belyaev, Dmitry, Bennett, Joesph, Benz, Christopher, Beroukhim, Rameen, Birrer, Michael, Bocklage, Thèrése, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Bowen, Jay, Bowlby, Reanne, Boyd, Jeff, Brohl, Andrew S., Brooks, Denise, Byers, Lauren, Carlsen, Rebecca, Castro, Patricia, Chen, Hsiao-Wei, Cherniack, Andrew D., Chibon, Fréderic, Chin, Lynda, Cho, Juok, Chuah, Eric, Chudamani, Sudha, Cibulskis, Carrie, Cooper, Lee A.D., Cope, Leslie, Cordes, Matthew G., Crain, Daniel, Curley, Erin, Danilova, Ludmila, Dao, Fanny, Davis, Ian J., Davis, Lara E., Defreitas, Timothy, Delman, Keith, Demchok, John A., Demetri, George D., Demicco, Elizabeth G., Dhalla, Noreen, Diao, Lixia, Ding, Li, DiSaia, Phil, Dottino, Peter, Doyle, Leona A., Drill, Esther, Dubina, Michael, Eschbacher, Jennifer, Fedosenko, Konstantin, Felau, Ina, Ferguson, Martin L., Frazer, Scott, Fronick, Catrina C., Fulidou, Victoria, Fulton, Lucinda A., Fulton, Robert S., Gabriel, Stacey B., Gao, Jianjiong, Gao, Qingsong, Gardner, Johanna, Gastier-Foster, Julie M., Gay, Carl M., Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Godwin, Andrew K., Godwin, Eryn M., Gordienko, Elena, Grilley-Olson, Juneko E., Gutman, David A., Gutmann, David H., Hayes, D. Neil, Hegde, Apurva M., Heiman, David I., Heins, Zachary, Helsel, Carmen, Hepperla, Austin J., Higgins, Kelly, Hoadley, Katherine A., Hobensack, Shital, Holt, Robert A., Hoon, Dave B., Hornick, Jason L., Hoyle, Alan P., Hu, Xin, Huang, Mei, Hutter, Carolyn M., Iacocca, Mary, Ingram, Davis R., Ittmann, Michael, Iype, Lisa, Jefferys, Stuart R., Jones, Kevin B., Jones, Corbin D., Jones, Steven J.M., Kalir, Tamara, Karlan, Beth Y., Karseladze, Apollon, Kasaian, Katayoon, Kim, Jaegil, Kundra, Ritika, Kuo, Hanluen, Ladanyi, Marc, Lai, Phillip H., Laird, Peter W., Larsson, Erik, Lawrence, Michael S., Lazar, Alexander J., Lee, Sanghoon, Lee, Darlene, Lehmann, Kjong-Van, Leraas, Kristen M., Lester, Jenny, Levine, Douglas A., Li, Irene, Lichtenberg, Tara M., Lin, Pei, Liu, Jia, Liu, Wenbin, Liu, Eric Minwei, Lolla, Laxmi, Lu, Yiling, Ma, Yussanne, Madan, Rashna, Maglinte, Dennis T., Magliocco, Anthony, Maki, Robert G., Mallery, David, Manikhas, Georgy, Mardis, Elaine R., Mariamidze, Armaz, Marra, Marco A., Martignetti, John A., Martinez, Cathleen, Mayo, Michael, McLellan, Michael D., Meier, Sam, Meng, Shaowu, Meyerson, Matthew, Mieczkowski, Piotr A., Miller, Christopher A., Mills, Gordon B., Moore, Richard A., Morris, Scott, Mose, Lisle E., Mozgovoy, Evgeny, Mungall, Andrew J., Mungall, Karen, Nalisnik, Michael, Naresh, Rashi, Newton, Yulia, Noble, Michael S., Novak, Janet E., Ochoa, Angelica, Olvera, Narciso, Owonikoko, Taofeek K., Paklina, Oxana, Parfitt, Jeremy, Parker, Joel S., Pastore, Alessandro, Paulauskis, Joseph, Penny, Robert, Pereira, Elena, Perou, Charles M., Perou, Amy H., Pihl, Todd, Pollock, Raphael E., Potapova, Olga, Radenbaugh, Amie J., Ramalingam, Suresh S., Ramirez, Nilsa C., Rathmell, W. Kimryn, Raut, Chandrajit P., Riedel, Richard F., Reilly, Colleen, Reynolds, Sheila M., Roach, Jeffrey, Robertson, A. Gordon, Roszik, Jason, Rubin, Brian P., Sadeghi, Sara, Saksena, Gordon, Salner, Andrew, Sanchez-Vega, Francisco, Sander, Chris, Schein, Jacqueline E., Schmidt, Heather K., Schultz, Nikolaus, Schumacher, Steven E., Sekhon, Harman, Senbabaoglu, Yasin, Setdikova, Galiya, Shelton, Candace, Shelton, Troy, Shen, Ronglai, Shi, Yan, Shih, Juliann, Shmulevich, Ilya, Sica, Gabriel L., Simons, Janae V., Singer, Samuel, Sipahimalani, Payal, Skelly, Tara, Socci, Nicholas, Sofia, Heidi J., Soloway, Matthew G., Spellman, Paul, Sun, Qiang, Swanson, Patricia, Tam, Angela, Tan, Donghui, Tarnuzzer, Roy, Thiessen, Nina, Thompson, Eric, Thorne, Leigh B., Tong, Pan, Torres, Keila E., van de Rijn, Matt, Van Den Berg, David J., Van Tine, Brian A., Veluvolu, Umadevi, Verhaak, Roel, Voet, Doug, Voronina, Olga, Wan, Yunhu, Wang, Zhining, Wang, Jing, Weinstein, John N., Weisenberger, Daniel J., Wilkerson, Matthew D., Wilson, Richard K., Wise, Lisa, Wong, Tina, Wong, Winghing, Wrangle, John, Wu, Ye, Wyczalkowski, Matthew, Yang, Liming, Yau, Christina, Yellapantula, Venkata, Zenklusen, Jean C., Zhang, Jiashan (Julia), Zhang, Hailei, Zhang, Hongxin, and Zmuda, Erik
- Published
- 2017
- Full Text
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4. Rapid idiosyncratic mechanisms of clinical resistance to KRAS G12C inhibition
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Tsai, Yihsuan S., Woodcock, Mark G., Azam, Salma H., Thorne, Leigh B., Kanchi, Krishna L., Parker, Joel S., Vincent, Benjamin G., and Pecot, Chad V.
- Subjects
Drug therapy ,Complications and side effects ,Case studies ,Genetic aspects ,Health aspects ,Lung cancer -- Case studies -- Drug therapy -- Genetic aspects ,Proto-oncogenes -- Case studies -- Health aspects ,Drug resistance -- Case studies -- Genetic aspects ,Antineoplastic agents -- Complications and side effects -- Case studies ,Antimitotic agents -- Complications and side effects -- Case studies - Abstract
Introduction Constitutively activated, mutant KRAS continuously stimulates downstream effector signaling and promotes nearly all cancer hallmarks (1). Hotspot mutations that predominately occur in codons 12 and 13 result in defective [...], BACKGROUND. The KRAS proto-oncogene is among the most frequently mutated genes in cancer, yet for 40 years it remained an elusive therapeutic target. Recently, allosteric inhibitors that covalently bind to KRAS G12C mutations have been approved for use in lung adenocarcinomas. Although responses are observed, they are often short-lived, thus making in-depth characterization of the mechanisms of resistance of paramount importance. METHODS. Here, we present a rapid-autopsy case of a patient who had a [KRAS.sup.G12C]-mutant lung adenocarcinoma who initially responded to a KRAS G12C inhibitor but then rapidly developed resistance. Using deep-RNA and whole-exome sequencing comparing pretreatment, posttreatment, and matched normal tissues, we uncover numerous mechanisms of resistance to direct KRAS inhibition. RESULTS. In addition to decreased KRAS G12C-mutant allele frequency in refractory tumors, we also found reactivation of the MAPK pathway despite no new mutations in KRAS or its downstream mediators. Tumor cell-intrinsic and non-cell autonomous mechanisms included increased complement activation, coagulation, and tumor angiogenesis, and several lines of evidence of immunologic evasion. CONCLUSION. Together, our findings reveal numerous mechanisms of resistance to current KRAS G12C inhibitors through enrichment of clonal populations, KRAS-independent downstream signaling, and diverse remodeling of the tumor microenvironment. FUNDING. Richard and Fran Duley, Jimmy and Kay Mann, the NIH, and the North Carolina Biotechnology Center.
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- 2022
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5. Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer
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Akbani, Rehan, Al-Ahmadie, Hikmat, Albert, Monique, Alexopoulou, Iakovina, Ally, Adrian, Antic, Tatjana, Aron, Manju, Balasundaram, Miruna, Bartlett, John, Baylin, Stephen B., Beaver, Allison, Bellmunt, Joaquim, Birol, Inanc, Boice, Lori, Bootwalla, Moiz S., Bowen, Jay, Bowlby, Reanne, Brooks, Denise, Broom, Bradley M., Bshara, Wiam, Bullman, Susan, Burks, Eric, Cárcano, Flavio M., Carlsen, Rebecca, Carvalho, Benilton S., Carvalho, Andre L., Castle, Eric P., Castro, Mauro A.A., Castro, Patricia, Catto, James W., Chagas, Vinicius S., Cherniack, Andrew D., Chesla, David W., Choo, Caleb, Chuah, Eric, Chudamani, Sudha, Cortessis, Victoria K., Cottingham, Sandra L., Crain, Daniel, Curley, Erin, Czerniak, Bogdan A., Daneshmand, Siamak, Demchok, John A., Dhalla, Noreen, Djaladat, Hooman, Eckman, John, Egea, Sophie C., Engel, Jay, Felau, Ina, Ferguson, Martin L., Gardner, Johanna, Gastier-Foster, Julie M., Gerken, Mark, Getz, Gad, Gibb, Ewan A., Gomez-Fernandez, Carmen R., Gordenin, Dmitry A., Guo, Guangwu, Hansel, Donna E., Harr, Jodi, Hartmann, Arndt, Herbert, Lynn M., Hinoue, Toshinori, Ho, Thai H., Hoadley, Katherine A., Holt, Robert A., Hutter, Carolyn M., Jones, Steven J.M., Jorda, Merce, Kahnoski, Richard J., Kanchi, Rupa S., Kasaian, Katayoon, Kim, Jaegil, Klimczak, Leszek J., Kwiatkowski, David J., Lai, Phillip H., Laird, Peter W., Lane, Brian R., Leraas, Kristen M., Lerner, Seth P., Lichtenberg, Tara M., Liu, Jia, Lolla, Laxmi, Lotan, Yair, Lu, Yiling, Lucchesi, Fabiano R., Ma, Yussanne, Machado, Roberto D., Maglinte, Dennis T., Mallery, David, Marra, Marco A., Martin, Sue E., Mayo, Michael, McConkey, David J., Meraney, Anoop, Meyerson, Matthew, Mills, Gordon B., Moinzadeh, Alireza, Moore, Richard A., Mora Pinero, Edna M., Morris, Scott, Morrison, Carl, Mungall, Karen L., Mungall, Andrew J., Myers, Jerome B., Naresh, Rashi, O'Donnell, Peter H., Ojesina, Akinyemi I., Parekh, Dipen J., Parfitt, Jeremy, Paulauskis, Joseph D., Sekhar Pedamallu, Chandra, Penny, Robert J., Pihl, Todd, Porten, Sima, Quintero-Aguilo, Mario E., Ramirez, Nilsa C., Rathmell, W. Kimryn, Reuter, Victor E., Rieger-Christ, Kimberly, Robertson, A. Gordon, Sadeghi, Sara, Saller, Charles, Salner, Andrew, Sanchez-Vega, Francisco, Sandusky, George, Scapulatempo-Neto, Cristovam, Schein, Jacqueline E., Schuckman, Anne K., Schultz, Nikolaus, Shelton, Candace, Shelton, Troy, Shukla, Sachet A., Simko, Jeff, Singh, Parminder, Sipahimalani, Payal, Smith, Norm D., Sofia, Heidi J., Sorcini, Andrea, Stanton, Melissa L., Steinberg, Gary D., Stoehr, Robert, Su, Xiaoping, Sullivan, Travis, Sun, Qiang, Tam, Angela, Tarnuzzer, Roy, Tarvin, Katherine, Taubert, Helge, Thiessen, Nina, Thorne, Leigh, Tse, Kane, Tucker, Kelinda, Van Den Berg, David J., van Kessel, Kim E., Wach, Sven, Wan, Yunhu, Wang, Zhining, Weinstein, John N., Weisenberger, Daniel J., Wise, Lisa, Wong, Tina, Wu, Ye, Wu, Catherine J., Yang, Liming, Zach, Leigh Anne, Zenklusen, Jean C., Zhang, Jiashan (Julia), Zhang, Jiexin, Zmuda, Erik, Zwarthoff, Ellen C., de Sa Carvalho, Benilton, Pedamallu, Chandra Sekhar, and Schultz, Nicholaus
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- 2017
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6. Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma
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Raphael, Benjamin J., Hruban, Ralph H., Aguirre, Andrew J., Moffitt, Richard A., Yeh, Jen Jen, Stewart, Chip, Robertson, A. Gordon, Cherniack, Andrew D., Gupta, Manaswi, Getz, Gad, Gabriel, Stacey B., Meyerson, Matthew, Cibulskis, Carrie, Fei, Suzanne S., Hinoue, Toshinori, Shen, Hui, Laird, Peter W., Ling, Shiyun, Lu, Yiling, Mills, Gordon B., Akbani, Rehan, Loher, Phillipe, Londin, Eric R., Rigoutsos, Isidore, Telonis, Aristeidis G., Gibb, Ewan A., Goldenberg, Anna, Mezlini, Aziz M., Hoadley, Katherine A., Collisson, Eric, Lander, Eric, Murray, Bradley A., Hess, Julian, Rosenberg, Mara, Bergelson, Louis, Zhang, Hailei, Cho, Juok, Tiao, Grace, Kim, Jaegil, Livitz, Dimitri, Leshchiner, Ignaty, Reardon, Brendan, Van Allen, Eliezer, Kamburov, Atanas, Beroukhim, Rameen, Saksena, Gordon, Schumacher, Steven E., Noble, Michael S., Heiman, David I., Gehlenborg, Nils, Lawrence, Michael S., Adsay, Volkan, Petersen, Gloria, Klimstra, David, Bardeesy, Nabeel, Leiserson, Mark D.M., Bowlby, Reanne, Kasaian, Katayoon, Birol, Inanc, Mungall, Karen L., Sadeghi, Sara, Weinstein, John N., Spellman, Paul T., Liu, Yuexin, Amundadottir, Laufey T., Tepper, Joel, Singhi, Aatur D., Dhir, Rajiv, Paul, Drwiega, Smyrk, Thomas, Zhang, Lizhi, Kim, Paula, Bowen, Jay, Frick, Jessica, Gastier-Foster, Julie M., Gerken, Mark, Lau, Kevin, Leraas, Kristen M., Lichtenberg, Tara M., Ramirez, Nilsa C., Renkel, Jeremy, Sherman, Mark, Wise, Lisa, Yena, Peggy, Zmuda, Erik, Shih, Juliann, Ally, Adrian, Balasundaram, Miruna, Carlsen, Rebecca, Chu, Andy, Chuah, Eric, Clarke, Amanda, Dhalla, Noreen, Holt, Robert A., Jones, Steven J.M., Lee, Darlene, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Tse, Kane, Wong, Tina, Brooks, Denise, Auman, J. Todd, Balu, Saianand, Bodenheimer, Tom, Hayes, D. Neil, Hoyle, Alan P., Jefferys, Stuart R., Jones, Corbin D., Meng, Shaowu, Mieczkowski, Piotr A., Mose, Lisle E., Perou, Charles M., Perou, Amy H., Roach, Jeffrey, Shi, Yan, Simons, Janae V., Skelly, Tara, Soloway, Matthew G., Tan, Donghui, Veluvolu, Umadevi, Parker, Joel S., Wilkerson, Matthew D., Korkut, Anil, Senbabaoglu, Yasin, Burch, Patrick, McWilliams, Robert, Chaffee, Kari, Oberg, Ann, Zhang, Wei, Gingras, Marie-Claude, Wheeler, David A., Xi, Liu, Albert, Monique, Bartlett, John, Sekhon, Harman, Stephen, Yeager, Howard, Zaren, Judy, Miller, Breggia, Anne, Shroff, Rachna T., Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Jennifer, Smith, Roggin, Kevin, Becker, Karl-Friedrich, Behera, Madhusmita, Bennett, Joseph, Boice, Lori, Burks, Eric, Carlotti Junior, Carlos Gilberto, Chabot, John, Pretti da Cunha Tirapelli, Daniela, Sebastião dos Santos, Jose, Dubina, Michael, Eschbacher, Jennifer, Huang, Mei, Huelsenbeck-Dill, Lori, Jenkins, Roger, Karpov, Alexey, Kemp, Rafael, Lyadov, Vladimir, Maithel, Shishir, Manikhas, Georgy, Montgomery, Eric, Noushmehr, Houtan, Osunkoya, Adeboye, Owonikoko, Taofeek, Paklina, Oxana, Potapova, Olga, Ramalingam, Suresh, Rathmell, W. Kimryn, Rieger-Christ, Kimberly, Saller, Charles, Setdikova, Galiya, Shabunin, Alexey, Sica, Gabriel, Su, Tao, Sullivan, Travis, Swanson, Pat, Tarvin, Katherine, Tavobilov, Michael, Thorne, Leigh B., Urbanski, Stefan, Voronina, Olga, Wang, Timothy, Crain, Daniel, Curley, Erin, Gardner, Johanna, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Candace, Shelton, Troy, Janssen, Klaus-Peter, Bathe, Oliver, Bahary, Nathan, Slotta-Huspenina, Julia, Johns, Amber, Hibshoosh, Hanina, Hwang, Rosa F., Sepulveda, Antonia, Radenbaugh, Amie, Baylin, Stephen B., Berrios, Mario, Bootwalla, Moiz S., Holbrook, Andrea, Lai, Phillip H., Maglinte, Dennis T., Mahurkar, Swapna, Triche, Timothy J., Jr., Van Den Berg, David J., Weisenberger, Daniel J., Chin, Lynda, Kucherlapati, Raju, Kucherlapati, Melanie, Pantazi, Angeliki, Park, Peter, Voet, Doug, Lin, Pei, Frazer, Scott, Defreitas, Timothy, Meier, Sam, Kwon, Sun Young, Kim, Yong Hoon, Park, Sang-Jae, Han, Sung-Sik, Kim, Seong Hoon, Kim, Hark, Furth, Emma, Tempero, Margaret, Sander, Chris, Biankin, Andrew, Chang, David, Bailey, Peter, Gill, Anthony, Kench, James, Grimmond, Sean, Cancer Genome Initiative (APGI, Australian Pancreatic, Postier, Russell, Zuna, Rosemary, Sicotte, Hugues, Demchok, John A., Ferguson, Martin L., Hutter, Carolyn M., Mills Shaw, Kenna R., Sheth, Margi, Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zhang, Jiashan (Julia), Felau, Ina, and Zenklusen, Jean C.
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- 2017
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7. Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma
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Ally, Adrian, Balasundaram, Miruna, Carlsen, Rebecca, Chuah, Eric, Clarke, Amanda, Dhalla, Noreen, Holt, Robert A., Jones, Steven J.M., Lee, Darlene, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Cheung, Dorothy, Wong, Tina, Brooks, Denise, Robertson, A. Gordon, Bowlby, Reanne, Mungall, Karen, Sadeghi, Sara, Xi, Liu, Covington, Kyle, Shinbrot, Eve, Wheeler, David A., Gibbs, Richard A., Donehower, Lawrence A., Wang, Linghua, Bowen, Jay, Gastier-Foster, Julie M., Gerken, Mark, Helsel, Carmen, Leraas, Kristen M., Lichtenberg, Tara M., Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Gabriel, Stacey B., Meyerson, Matthew, Cibulskis, Carrie, Murray, Bradley A., Shih, Juliann, Beroukhim, Rameen, Cherniack, Andrew D., Schumacher, Steven E., Saksena, Gordon, Pedamallu, Chandra Sekhar, Chin, Lynda, Getz, Gad, Noble, Michael, Zhang, Hailei, Heiman, David, Cho, Juok, Gehlenborg, Nils, Voet, Douglas, Lin, Pei, Frazer, Scott, Defreitas, Timothy, Meier, Sam, Lawrence, Michael, Kim, Jaegil, Creighton, Chad J., Muzny, Donna, Doddapaneni, HarshaVardhan, Hu, Jianhong, Wang, Min, Morton, Donna, Korchina, Viktoriya, Han, Yi, Dinh, Huyen, Lewis, Lora, Bellair, Michelle, Liu, Xiuping, Santibanez, Jireh, Glenn, Robert, Lee, Sandra, Hale, Walker, Parker, Joel S., Wilkerson, Matthew D., Hayes, D. Neil, Reynolds, Sheila M., Shmulevich, Ilya, Zhang, Wei, Liu, Yuexin, Iype, Lisa, Makhlouf, Hala, Torbenson, Michael S., Kakar, Sanjay, Yeh, Matthew M., Jain, Dhanpat, Kleiner, David E., Dhanasekaran, Renumathy, El-Serag, Hashem B., Yim, Sun Young, Weinstein, John N., Mishra, Lopa, Zhang, Jianping, Akbani, Rehan, Ling, Shiyun, Ju, Zhenlin, Su, Xiaoping, Hegde, Apurva M., Mills, Gordon B., Lu, Yiling, Chen, Jian, Lee, Ju-Seog, Sohn, Bo Hwa, Shim, Jae Jun, Tong, Pan, Aburatani, Hiroyuki, Yamamoto, Shogo, Tatsuno, Kenji, Li, Wei, Xia, Zheng, Stransky, Nicolas, Seiser, Eric, Innocenti, Federico, Gao, Jianjiong, Kundra, Ritika, Zhang, Hongxin, Heins, Zachary, Ochoa, Angelica, Sander, Chris, Ladanyi, Marc, Shen, Ronglai, Arora, Arshi, Sanchez-Vega, Francisco, Schultz, Nikolaus, Kasaian, Katayoon, Radenbaugh, Amie, Bissig, Karl-Dimiter, Moore, David D., Totoki, Yasushi, Nakamura, Hiromi, Shibata, Tatsuhiro, Yau, Christina, Graim, Kiley, Stuart, Josh, Haussler, David, Slagle, Betty L., Ojesina, Akinyemi I., Katsonis, Panagiotis, Koire, Amanda, Lichtarge, Olivier, Hsu, Teng-Kuei, Ferguson, Martin L., Demchok, John A., Felau, Ina, Sheth, Margi, Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan, Hutter, Carolyn M., Sofia, Heidi J., Verhaak, Roel G.W., Zheng, Siyuan, Lang, Frederick, Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Wu, Ye, Naresh, Rashi, Pihl, Todd, Sun, Charlie, Wan, Yunhu, Benz, Christopher, Perou, Amy H., Thorne, Leigh B., Boice, Lori, Huang, Mei, Rathmell, W. Kimryn, Noushmehr, Houtan, Saggioro, Fabiano Pinto, Tirapelli, Daniela Pretti da Cunha, Junior, Carlos Gilberto Carlotti, Mente, Enio David, Silva, Orlando de Castro, Jr., Trevisan, Felipe Amstalden, Kang, Koo Jeong, Ahn, Keun Soo, Giama, Nasra H., Moser, Catherine D., Giordano, Thomas J., Vinco, Michelle, Welling, Theodore H., Crain, Daniel, Curley, Erin, Gardner, Johanna, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Candace, Shelton, Troy, Kelley, Robin, Park, Joong-Won, Chandan, Vishal S., Roberts, Lewis R., Bathe, Oliver F., Hagedorn, Curt H., Auman, J. Todd, O'Brien, Daniel R., Kocher, Jean-Pierre A., Jones, Corbin D., Mieczkowski, Piotr A., Perou, Charles M., Skelly, Tara, Tan, Donghui, Veluvolu, Umadevi, Balu, Saianand, Bodenheimer, Tom, Hoyle, Alan P., Jefferys, Stuart R., Meng, Shaowu, Mose, Lisle E., Shi, Yan, Simons, Janae V., Soloway, Matthew G., Roach, Jeffrey, Hoadley, Katherine A., Baylin, Stephen B., Shen, Hui, Hinoue, Toshinori, Bootwalla, Moiz S., Van Den Berg, David J., Weisenberger, Daniel J., Lai, Phillip H., Holbrook, Andrea, Berrios, Mario, and Laird, Peter W.
- Published
- 2017
- Full Text
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8. Integrated Molecular Characterization of Uterine Carcinosarcoma
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Akbani, Rehan, Ally, Adrian, Auman, J. Todd, Balasundaram, Miruna, Balu, Saianand, Baylin, Stephen B., Beroukhim, Rameen, Bodenheimer, Tom, Bogomolniy, Faina, Boice, Lori, Bootwalla, Moiz S., Bowen, Jay, Bowlby, Reanne, Broaddus, Russell, Brooks, Denise, Carlsen, Rebecca, Cherniack, Andrew D., Cho, Juok, Chuah, Eric, Chudamani, Sudha, Cibulskis, Kristian, Cline, Melissa, Dao, Fanny, David, Mutch, Demchok, John A., Dhalla, Noreen, Dowdy, Sean, Felau, Ina, Ferguson, Martin L., Frazer, Scott, Frick, Jessica, Gabriel, Stacey, Gastier-Foster, Julie M., Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Gupta, Manaswi, Haussler, David, Hayes, D. Neil, Heiman, David I., Hess, Julian, Hoadley, Katherine A., Hoffmann, Robert, Holt, Robert A., Hoyle, Alan P., Hu, Xin, Huang, Mei, Hutter, Carolyn M., Jefferys, Stuart R., Jones, Steven J.M., Jones, Corbin D., Kanchi, Rupa S., Kandoth, Cyriac, Kasaian, Katayoon, Kerr, Sarah, Kim, Jaegil, Lai, Phillip H., Laird, Peter W., Lander, Eric, Lawrence, Michael S., Lee, Darlene, Leraas, Kristen M., Leshchiner, Ignaty, Levine, Douglas A., Lichtenberg, Tara M., Lin, Pei, Ling, Shiyun, Liu, Jia, Liu, Wenbin, Liu, Yuexin, Lolla, Laxmi, Lu, Yiling, Ma, Yussanne, Maglinte, Dennis T., Marra, Marco A., Mayo, Michael, Meng, Shaowu, Meyerson, Matthew, Mieczkowski, Piotr A., Mills, Gordon B., Moore, Richard A., Mose, Lisle E., Mungall, Andrew J., Mungall, Karen, Murray, Bradley A., Naresh, Rashi, Noble, Michael S., Olvera, Narciso, Parker, Joel S., Perou, Charles M., Perou, Amy H., Pihl, Todd, Radenbaugh, Amie J., Ramirez, Nilsa C., Rathmell, W. Kimryn, Roach, Jeffrey, Robertson, A. Gordon, Sadeghi, Sara, Saksena, Gordon, Salvesen, Helga B., Schein, Jacqueline E., Schumacher, Steven E., Shen, Hui, Sheth, Margi, Shi, Yan, Shih, Juliann, Simons, Janae V., Sipahimalani, Payal, Skelly, Tara, Sofia, Heidi J., Soloway, Matthew G., Soslow, Robert A., Sougnez, Carrie, Stewart, Chip, Sun, Charlie, Tam, Angela, Tan, Donghui, Tarnuzzer, Roy, Thiessen, Nina, Thorne, Leigh B., Tse, Kane, Tseng, Jill, Van Den Berg, David J., Veluvolu, Umadevi, Verhaak, Roel G.W., Voet, Doug, von Bismarck, Amanda, Walter, Vonn, Wan, Yunhu, Wang, Zhining, Wang, Chen, Weinstein, John N., Weisenberger, Daniel J., Wilkerson, Matthew D., Winterhoff, Boris, Wise, Lisa, Wong, Tina, Wu, Ye, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Zhang, Hailei, Zhang, Wei, Zhu, Jing-chun, Zmuda, Erik, Zuna, Rosemary E., Broaddus, Russell R., Robertson, Gordon, Kucherlapati, Raju, and Zhang, Jiashan
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- 2017
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9. Comprehensive Molecular Characterization of Pheochromocytoma and Paraganglioma
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Akbani, Rehan, Ally, Adrian, Amar, Laurence, Amelio, Antonio L., Arachchi, Harindra, Asa, Sylvia L., Auchus, Richard J., Auman, J. Todd, Baertsch, Robert, Balasundaram, Miruna, Balu, Saianand, Bartsch, Detlef K., Baudin, Eric, Bauer, Thomas, Beaver, Allison, Benz, Christopher, Beroukhim, Rameen, Beuschlein, Felix, Bodenheimer, Tom, Boice, Lori, Bowen, Jay, Bowlby, Reanne, Brooks, Denise, Carlsen, Rebecca, Carter, Suzie, Cassol, Clarissa A., Cherniack, Andrew D., Chin, Lynda, Cho, Juok, Chuah, Eric, Chudamani, Sudha, Cope, Leslie, Crain, Daniel, Curley, Erin, Danilova, Ludmila, de Cubas, Aguirre A., de Krijger, Ronald R., Demchok, John A., Deutschbein, Timo, Dhalla, Noreen, Dimmock, David, Dinjens, Winand N.M., Else, Tobias, Eng, Charis, Eschbacher, Jennifer, Fassnacht, Martin, Felau, Ina, Feldman, Michael, Ferguson, Martin L., Fiddes, Ian, Fishbein, Lauren, Frazer, Scott, Gabriel, Stacey B., Gardner, Johanna, Gastier-Foster, Julie M., Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Geurts, Jennifer, Ghayee, Hans K., Gimenez-Roqueplo, Anne-Paule, Giordano, Thomas J., Goldman, Mary, Graim, Kiley, Gupta, Manaswi, Haan, David, Hahner, Stefanie, Hantel, Constanze, Haussler, David, Hayes, D. Neil, Heiman, David I., Hoadley, Katherine A., Holt, Robert A., Hoyle, Alan P., Huang, Mei, Hunt, Bryan, Hutter, Carolyn M., Jefferys, Stuart R., Johnson, Amy R., Jones, Steven J.M., Jones, Corbin D., Kasaian, Katayoon, Kebebew, Electron, Kim, Jaegil, Kimes, Patrick, Knijnenburg, Theo, Korpershoek, Esther, Lander, Eric, Lawrence, Michael S., Lechan, Ronald, Lee, Darlene, Leraas, Kristen M., Lerario, Antonio, Leshchiner, Ignaty, Lichtenberg, Tara M., Lin, Pei, Ling, Shiyun, Liu, Jia, LiVolsi, Virginia A., Lolla, Laxmi, Lotan, Yair, Lu, Yiling, Ma, Yussanne, Maison, Nicole, Makowski, Liza, Mallery, David, Mannelli, Massimo, Marquard, Jessica, Marra, Marco A., Matthew, Thomas, Mayo, Michael, Méatchi, Tchao, Meng, Shaowu, Merino, Maria J., Mete, Ozgur, Meyerson, Matthew, Mieczkowski, Piotr A., Mills, Gordon B., Moore, Richard A., Morozova, Olena, Morris, Scott, Mose, Lisle E., Mungall, Andrew J., Murray, Bradley A., Naresh, Rashi, Nathanson, Katherine L., Newton, Yulia, Ng, Sam, Ni, Ying, Noble, Michael S., Nwariaku, Fiemu, Pacak, Karel, Parker, Joel S., Paul, Evan, Penny, Robert, Perou, Charles M., Perou, Amy H., Pihl, Todd, Powers, James, Rabaglia, Jennifer, Radenbaugh, Amie, Ramirez, Nilsa C., Rao, Arjun, Rathmell, W. Kimryn, Riester, Anna, Roach, Jeffrey, Robertson, A. Gordon, Sadeghi, Sara, Saksena, Gordon, Salama, Sofie, Saller, Charles, Sandusky, George, Sbiera, Silviu, Schein, Jacqueline E., Schumacher, Steven E., Shelton, Candace, Shelton, Troy, Sheth, Margi, Shi, Yan, Shih, Juliann, Shmulevich, Ilya, Simons, Janae V., Sipahimalani, Payal, Skelly, Tara, Sofia, Heidi J., Sokolov, Artem, Soloway, Matthew G., Sougnez, Carrie, Stuart, Josh, Sun, Charlie, Swatloski, Teresa, Tam, Angela, Tan, Donghui, Tarnuzzer, Roy, Tarvin, Katherine, Thiessen, Nina, Thorne, Leigh B., Timmers, Henri J., Tischler, Arthur S., Tse, Kane, Uzunangelov, Vlado, van Berkel, Anouk, Veluvolu, Umadevi, Vicha, Ales, Voet, Doug, Waldmann, Jens, Walter, Vonn, Wan, Yunhu, Wang, Zhining, Wang, Tracy S., Weaver, Joellen, Weinstein, John N., Weismann, Dirk, Wenz, Brandon, Wilkerson, Matthew D., Wise, Lisa, Wong, Tina, Wong, Christopher, Wu, Ye, Yang, Liming, Zelinka, Tomas, Zenklusen, Jean C., Zhang, Jiashan (Julia), Zhang, Wei, Zhu, Jingchun, Zinzindohoué, Franck, and Zmuda, Erik
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- 2017
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10. Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancer
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Siegel, Marni B., He, Xiaping, Hoadley, Katherine A., Hoyle, Alan, Pearce, Julia B., Garrett, Amy L., Kumar, Sunil, Moylan, Vincent J., Brady, Claudia M., Van Swearingen, Amanda E.D., Marron, David, Gupta, Gaorav P., Thorne, Leigh B., Kieran, Niamh, Livasy, Chad, Mardis, Elaine R., Parker, Joel S., Chen, Mengjie, Anders, Carey K., Carey, Lisa A., and Perou, Charles M.
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Usage ,Development and progression ,Genetic aspects ,Research ,Health aspects ,Cancer genetics -- Research ,DNA sequencing -- Usage -- Health aspects ,RNA sequencing -- Usage -- Health aspects ,Breast cancer -- Genetic aspects -- Development and progression ,Cancer metastasis -- Genetic aspects -- Development and progression - Abstract
Introduction Breast cancer remains the second leading cause of cancer-related death in women in the United States and is typically caused by metastasis. Significant genetic heterogeneity exists both within a [...], Breast cancer metastasis remains a clinical challenge, even within a single patient across multiple sites of the disease. Genome-wide comparisons of both the DNA and gene expression of primary tumors and metastases in multiple patients could help elucidate the underlying mechanisms that cause breast cancer metastasis. To address this issue, we performed DNA exome and RNA sequencing of matched primary tumors and multiple metastases from 16 patients, totaling 83 distinct specimens. We identified tumor-specific drivers by integrating known protein-protein network information with RNA expression and somatic DNA alterations and found that genetic drivers were predominantly established in the primary tumor and maintained through metastatic spreading. In addition, our analyses revealed that most genetic drivers were DNA copy number changes, the TP53 mutation was a recurrent founding mutation regardless of subtype, and that multiclonal seeding of metastases was frequent and occurred in multiple subtypes. Genetic drivers unique to metastasis were identified as somatic mutations in the estrogen and androgen receptor genes. These results highlight the complexity of metastatic spreading, be it monoclonal or multiclonal, and suggest that most metastatic drivers are established in the primary tumor, despite the substantial heterogeneity seen in the metastases.
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- 2018
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11. Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma
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Anjum, Samreen, Arachchi, Harindra, Auman, J. Todd, Balasundaram, Miruna, Balu, Saianand, Barnett, Gene, Baylin, Stephen, Bell, Sue, Benz, Christopher, Bir, Natalie, Black, Keith L., Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Bowen, Jay, Bristow, Christopher A., Butterfield, Yaron S.N., Chen, Qing-Rong, Chin, Lynda, Cho, Juok, Chuah, Eric, Chudamani, Sudha, Coetzee, Simon G., Cohen, Mark L., Colman, Howard, Couce, Marta, D’Angelo, Fulvio, Davidsen, Tanja, Davis, Amy, Demchok, John A., Devine, Karen, Ding, Li, Duell, Rebecca, Elder, J. Bradley, Eschbacher, Jennifer M., Fehrenbach, Ashley, Ferguson, Martin, Frazer, Scott, Fuller, Gregory, Fulop, Jordonna, Gabriel, Stacey B., Garofano, Luciano, Gastier-Foster, Julie M., Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Giannini, Caterina, Gibson, William J., Hadjipanayis, Angela, Hayes, D. Neil, Heiman, David I., Hermes, Beth, Hilty, Joe, Hoadley, Katherine A., Hoyle, Alan P., Huang, Mei, Jefferys, Stuart R., Jones, Corbin D., Jones, Steven J.M., Ju, Zhenlin, Kastl, Alison, Kendler, Ady, Kim, Jaegil, Kucherlapati, Raju, Lai, Phillip H., Lawrence, Michael S., Lee, Semin, Leraas, Kristen M., Lichtenberg, Tara M., Lin, Pei, Liu, Yuexin, Liu, Jia, Ljubimova, Julia Y., Lu, Yiling, Ma, Yussanne, Maglinte, Dennis T., Mahadeshwar, Harshad S., Marra, Marco A., McGraw, Mary, McPherson, Christopher, Meng, Shaowu, Mieczkowski, Piotr A., Miller, C. Ryan, Mills, Gordon B., Moore, Richard A., Mose, Lisle E., Mungall, Andrew J., Naresh, Rashi, Naska, Theresa, Neder, Luciano, Noble, Michael S., Noss, Ardene, O’Neill, Brian Patrick, Ostrom, Quinn T., Palmer, Cheryl, Pantazi, Angeliki, Parfenov, Michael, Park, Peter J., Parker, Joel S., Perou, Charles M., Pierson, Christopher R., Pihl, Todd, Protopopov, Alexei, Radenbaugh, Amie, Ramirez, Nilsa C., Rathmell, W. Kimryn, Ren, Xiaojia, Roach, Jeffrey, Robertson, A. Gordon, Saksena, Gordon, Schein, Jacqueline E., Schumacher, Steven E., Seidman, Jonathan, Senecal, Kelly, Seth, Sahil, Shen, Hui, Shi, Yan, Shih, Juliann, Shimmel, Kristen, Sicotte, Hugues, Sifri, Suzanne, Silva, Tiago, Simons, Janae V., Singh, Rosy, Skelly, Tara, Sloan, Andrew E., Sofia, Heidi J., Soloway, Matthew G., Song, Xingzhi, Sougnez, Carrie, Souza, Camila, Staugaitis, Susan M., Sun, Huandong, Sun, Charlie, Tan, Donghui, Tang, Jiabin, Tang, Yufang, Thorne, Leigh, Trevisan, Felipe Amstalden, Triche, Timothy, Van Den Berg, David J., Veluvolu, Umadevi, Voet, Doug, Wan, Yunhu, Wang, Zhining, Warnick, Ronald, Weinstein, John N., Weisenberger, Daniel J., Wilkerson, Matthew D., Williams, Felicia, Wise, Lisa, Wolinsky, Yingli, Wu, Junyuan, Xu, Andrew W., Yang, Lixing, Yang, Liming, Zack, Travis I., Zenklusen, Jean C., Zhang, Jianhua, Zhang, Wei, Zhang, Jiashan, Zmuda, Erik, Ceccarelli, Michele, Barthel, Floris P., Malta, Tathiane M., Sabedot, Thais S., Salama, Sofie R., Murray, Bradley A., Morozova, Olena, Newton, Yulia, Pagnotta, Stefano M., Wang, Jiguang, Manyam, Ganiraju, Zoppoli, Pietro, Ling, Shiyun, Rao, Arjun A., Grifford, Mia, Cherniack, Andrew D., Zhang, Hailei, Poisson, Laila, Carlotti, Carlos Gilberto, Jr., Tirapelli, Daniela Pretti da Cunha, Rao, Arvind, Mikkelsen, Tom, Lau, Ching C., Yung, W.K. Alfred, Rabadan, Raul, Huse, Jason, Brat, Daniel J., Lehman, Norman L., Barnholtz-Sloan, Jill S., Zheng, Siyuan, Hess, Kenneth, Rao, Ganesh, Meyerson, Matthew, Beroukhim, Rameen, Cooper, Lee, Akbani, Rehan, Wrensch, Margaret, Haussler, David, Aldape, Kenneth D., Laird, Peter W., Gutmann, David H., Noushmehr, Houtan, Iavarone, Antonio, and Verhaak, Roel G.W.
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- 2016
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12. Evidence for infection but not transmission of Zika virus by Aedes albopictus (Diptera: Culicidae) from Spain
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Hernández-Triana, Luis M., Barrero, Elsa, Delacour-Estrella, Sarah, Ruiz-Arrondo, Ignacio, Lucientes, Javier, Fernández de Marco, Maria del Mar, Thorne, Leigh, Lumley, Sarah, Johnson, Nicholas, Mansfield, Karen L., and Fooks, Anthony R.
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- 2019
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13. Supplementary Materials and Methods. Immunohistochemical staining and automated analysis methods from Performance of Three-Biomarker Immunohistochemistry for Intrinsic Breast Cancer Subtyping in the AMBER Consortium
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Allott, Emma H., primary, Cohen, Stephanie M., primary, Geradts, Joseph, primary, Sun, Xuezheng, primary, Khoury, Thaer, primary, Bshara, Wiam, primary, Zirpoli, Gary R., primary, Miller, C. Ryan, primary, Hwang, Helena, primary, Thorne, Leigh B., primary, O'Connor, Siobhan, primary, Tse, Chiu-Kit, primary, Bell, Mary B., primary, Hu, Zhiyuan, primary, Li, Yan, primary, Kirk, Erin L., primary, Bethea, Traci N., primary, Perou, Charles M., primary, Palmer, Julie R., primary, Ambrosone, Christine B., primary, Olshan, Andrew F., primary, and Troester, Melissa A., primary
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- 2023
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14. Supplementary Table S2. Agreement between IHC-based and intrinsic subtype, using dichotomous biomarker IHC status from Performance of Three-Biomarker Immunohistochemistry for Intrinsic Breast Cancer Subtyping in the AMBER Consortium
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Allott, Emma H., primary, Cohen, Stephanie M., primary, Geradts, Joseph, primary, Sun, Xuezheng, primary, Khoury, Thaer, primary, Bshara, Wiam, primary, Zirpoli, Gary R., primary, Miller, C. Ryan, primary, Hwang, Helena, primary, Thorne, Leigh B., primary, O'Connor, Siobhan, primary, Tse, Chiu-Kit, primary, Bell, Mary B., primary, Hu, Zhiyuan, primary, Li, Yan, primary, Kirk, Erin L., primary, Bethea, Traci N., primary, Perou, Charles M., primary, Palmer, Julie R., primary, Ambrosone, Christine B., primary, Olshan, Andrew F., primary, and Troester, Melissa A., primary
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- 2023
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15. Supplementary Figure 1 from High XRCC1 Protein Expression Is Associated with Poorer Survival in Patients with Head and Neck Squamous Cell Carcinoma
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Ang, Mei-Kim, primary, Patel, Mihir R., primary, Yin, Xiao-Ying, primary, Sundaram, Sneha, primary, Fritchie, Karen, primary, Zhao, Ni, primary, Liu, Yufeng, primary, Freemerman, Alex J., primary, Wilkerson, Matthew D., primary, Walter, Vonn, primary, Weissler, Mark C., primary, Shockley, William W., primary, Couch, Marion E., primary, Zanation, Adam M., primary, Hackman, Trevor, primary, Chera, Bhishamjit S., primary, Harris, Stephen L., primary, Miller, C. Ryan, primary, Thorne, Leigh B., primary, Hayward, Michele C., primary, Funkhouser, William K., primary, Olshan, Andrew F., primary, Shores, Carol G., primary, Makowski, Liza, primary, and Hayes, D. Neil, primary
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- 2023
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16. Supplementary Data from Lung Squamous Cell Carcinoma mRNA Expression Subtypes Are Reproducible, Clinically Important, and Correspond to Normal Cell Types
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Wilkerson, Matthew D., primary, Yin, Xiaoying, primary, Hoadley, Katherine A., primary, Liu, Yufeng, primary, Hayward, Michele C., primary, Cabanski, Christopher R., primary, Muldrew, Kenneth, primary, Miller, C. Ryan, primary, Randell, Scott H., primary, Socinski, Mark A., primary, Parsons, Alden M., primary, Funkhouser, William K., primary, Lee, Carrie B., primary, Roberts, Patrick J., primary, Thorne, Leigh, primary, Bernard, Philip S., primary, Perou, Charles M., primary, and Hayes, D. Neil, primary
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- 2023
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17. Data from Lung Squamous Cell Carcinoma mRNA Expression Subtypes Are Reproducible, Clinically Important, and Correspond to Normal Cell Types
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Wilkerson, Matthew D., primary, Yin, Xiaoying, primary, Hoadley, Katherine A., primary, Liu, Yufeng, primary, Hayward, Michele C., primary, Cabanski, Christopher R., primary, Muldrew, Kenneth, primary, Miller, C. Ryan, primary, Randell, Scott H., primary, Socinski, Mark A., primary, Parsons, Alden M., primary, Funkhouser, William K., primary, Lee, Carrie B., primary, Roberts, Patrick J., primary, Thorne, Leigh, primary, Bernard, Philip S., primary, Perou, Charles M., primary, and Hayes, D. Neil, primary
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- 2023
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18. Supplementary Table S1. Core level agreement between automated and manual scoring of central tissue microarrays from Performance of Three-Biomarker Immunohistochemistry for Intrinsic Breast Cancer Subtyping in the AMBER Consortium
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Allott, Emma H., primary, Cohen, Stephanie M., primary, Geradts, Joseph, primary, Sun, Xuezheng, primary, Khoury, Thaer, primary, Bshara, Wiam, primary, Zirpoli, Gary R., primary, Miller, C. Ryan, primary, Hwang, Helena, primary, Thorne, Leigh B., primary, O'Connor, Siobhan, primary, Tse, Chiu-Kit, primary, Bell, Mary B., primary, Hu, Zhiyuan, primary, Li, Yan, primary, Kirk, Erin L., primary, Bethea, Traci N., primary, Perou, Charles M., primary, Palmer, Julie R., primary, Ambrosone, Christine B., primary, Olshan, Andrew F., primary, and Troester, Melissa A., primary
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- 2023
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19. Data from High XRCC1 Protein Expression Is Associated with Poorer Survival in Patients with Head and Neck Squamous Cell Carcinoma
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Ang, Mei-Kim, primary, Patel, Mihir R., primary, Yin, Xiao-Ying, primary, Sundaram, Sneha, primary, Fritchie, Karen, primary, Zhao, Ni, primary, Liu, Yufeng, primary, Freemerman, Alex J., primary, Wilkerson, Matthew D., primary, Walter, Vonn, primary, Weissler, Mark C., primary, Shockley, William W., primary, Couch, Marion E., primary, Zanation, Adam M., primary, Hackman, Trevor, primary, Chera, Bhishamjit S., primary, Harris, Stephen L., primary, Miller, C. Ryan, primary, Thorne, Leigh B., primary, Hayward, Michele C., primary, Funkhouser, William K., primary, Olshan, Andrew F., primary, Shores, Carol G., primary, Makowski, Liza, primary, and Hayes, D. Neil, primary
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- 2023
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20. Supplementary Figure Legend from High XRCC1 Protein Expression Is Associated with Poorer Survival in Patients with Head and Neck Squamous Cell Carcinoma
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Ang, Mei-Kim, primary, Patel, Mihir R., primary, Yin, Xiao-Ying, primary, Sundaram, Sneha, primary, Fritchie, Karen, primary, Zhao, Ni, primary, Liu, Yufeng, primary, Freemerman, Alex J., primary, Wilkerson, Matthew D., primary, Walter, Vonn, primary, Weissler, Mark C., primary, Shockley, William W., primary, Couch, Marion E., primary, Zanation, Adam M., primary, Hackman, Trevor, primary, Chera, Bhishamjit S., primary, Harris, Stephen L., primary, Miller, C. Ryan, primary, Thorne, Leigh B., primary, Hayward, Michele C., primary, Funkhouser, William K., primary, Olshan, Andrew F., primary, Shores, Carol G., primary, Makowski, Liza, primary, and Hayes, D. Neil, primary
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- 2023
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21. Supplementary Table S3. Agreement between three biomarker IHC-based and intrinsic subtypes: impact of adding tumor grade to distinguish between luminal A and luminal B cases. from Performance of Three-Biomarker Immunohistochemistry for Intrinsic Breast Cancer Subtyping in the AMBER Consortium
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Allott, Emma H., primary, Cohen, Stephanie M., primary, Geradts, Joseph, primary, Sun, Xuezheng, primary, Khoury, Thaer, primary, Bshara, Wiam, primary, Zirpoli, Gary R., primary, Miller, C. Ryan, primary, Hwang, Helena, primary, Thorne, Leigh B., primary, O'Connor, Siobhan, primary, Tse, Chiu-Kit, primary, Bell, Mary B., primary, Hu, Zhiyuan, primary, Li, Yan, primary, Kirk, Erin L., primary, Bethea, Traci N., primary, Perou, Charles M., primary, Palmer, Julie R., primary, Ambrosone, Christine B., primary, Olshan, Andrew F., primary, and Troester, Melissa A., primary
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- 2023
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22. Supplementary Table 1 from High XRCC1 Protein Expression Is Associated with Poorer Survival in Patients with Head and Neck Squamous Cell Carcinoma
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Ang, Mei-Kim, primary, Patel, Mihir R., primary, Yin, Xiao-Ying, primary, Sundaram, Sneha, primary, Fritchie, Karen, primary, Zhao, Ni, primary, Liu, Yufeng, primary, Freemerman, Alex J., primary, Wilkerson, Matthew D., primary, Walter, Vonn, primary, Weissler, Mark C., primary, Shockley, William W., primary, Couch, Marion E., primary, Zanation, Adam M., primary, Hackman, Trevor, primary, Chera, Bhishamjit S., primary, Harris, Stephen L., primary, Miller, C. Ryan, primary, Thorne, Leigh B., primary, Hayward, Michele C., primary, Funkhouser, William K., primary, Olshan, Andrew F., primary, Shores, Carol G., primary, Makowski, Liza, primary, and Hayes, D. Neil, primary
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- 2023
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23. The Molecular Taxonomy of Primary Prostate Cancer
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Abeshouse, Adam, Ahn, Jaeil, Akbani, Rehan, Ally, Adrian, Amin, Samirkumar, Andry, Christopher D., Annala, Matti, Aprikian, Armen, Armenia, Joshua, Arora, Arshi, Auman, J. Todd, Balasundaram, Miruna, Balu, Saianand, Barbieri, Christopher E., Bauer, Thomas, Benz, Christopher C., Bergeron, Alain, Beroukhim, Rameen, Berrios, Mario, Bivol, Adrian, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Borges dos Reis, Rodolfo, Boutros, Paul C., Bowen, Jay, Bowlby, Reanne, Boyd, Jeffrey, Bradley, Robert K., Breggia, Anne, Brimo, Fadi, Bristow, Christopher A., Brooks, Denise, Broom, Bradley M., Bryce, Alan H., Bubley, Glenn, Burks, Eric, Butterfield, Yaron S.N., Button, Michael, Canes, David, Carlotti, Carlos G., Carlsen, Rebecca, Carmel, Michel, Carroll, Peter R., Carter, Scott L., Cartun, Richard, Carver, Brett S., Chan, June M., Chang, Matthew T., Chen, Yu, Cherniack, Andrew D., Chevalier, Simone, Chin, Lynda, Cho, Juok, Chu, Andy, Chuah, Eric, Chudamani, Sudha, Cibulskis, Kristian, Ciriello, Giovanni, Clarke, Amanda, Cooperberg, Matthew R., Corcoran, Niall M., Costello, Anthony J., Cowan, Janet, Crain, Daniel, Curley, Erin, David, Kerstin, Demchok, John A., Demichelis, Francesca, Dhalla, Noreen, Dhir, Rajiv, Doueik, Alexandre, Drake, Bettina, Dvinge, Heidi, Dyakova, Natalya, Felau, Ina, Ferguson, Martin L., Frazer, Scott, Freedland, Stephen, Fu, Yao, Gabriel, Stacey B., Gao, Jianjiong, Gardner, Johanna, Gastier-Foster, Julie M., Gehlenborg, Nils, Gerken, Mark, Gerstein, Mark B., Getz, Gad, Godwin, Andrew K., Gopalan, Anuradha, Graefen, Markus, Graim, Kiley, Gribbin, Thomas, Guin, Ranabir, Gupta, Manaswi, Hadjipanayis, Angela, Haider, Syed, Hamel, Lucie, Hayes, D. Neil, Heiman, David I., Hess, Julian, Hoadley, Katherine A., Holbrook, Andrea H., Holt, Robert A., Holway, Antonia, Hovens, Christopher M., Hoyle, Alan P., Huang, Mei, Hutter, Carolyn M., Ittmann, Michael, Iype, Lisa, Jefferys, Stuart R., Jones, Corbin D., Jones, Steven J.M., Juhl, Hartmut, Kahles, Andre, Kane, Christopher J., Kasaian, Katayoon, Kerger, Michael, Khurana, Ekta, Kim, Jaegil, Klein, Robert J., Kucherlapati, Raju, Lacombe, Louis, Ladanyi, Marc, Lai, Phillip H., Laird, Peter W., Lander, Eric S., Latour, Mathieu, Lawrence, Michael S., Lau, Kevin, LeBien, Tucker, Lee, Darlene, Lee, Semin, Lehmann, Kjong-Van, Leraas, Kristen M., Leshchiner, Ignaty, Leung, Robert, Libertino, John A., Lichtenberg, Tara M., Lin, Pei, Linehan, W. Marston, Ling, Shiyun, Lippman, Scott M., Liu, Jia, Liu, Wenbin, Lochovsky, Lucas, Loda, Massimo, Logothetis, Christopher, Lolla, Laxmi, Longacre, Teri, Lu, Yiling, Luo, Jianhua, Ma, Yussanne, Mahadeshwar, Harshad S., Mallery, David, Mariamidze, Armaz, Marra, Marco A., Mayo, Michael, McCall, Shannon, McKercher, Ginette, Meng, Shaowu, Mes-Masson, Anne-Marie, Merino, Maria J., Meyerson, Matthew, Mieczkowski, Piotr A., Mills, Gordon B., Shaw, Kenna R. Mills, Minner, Sarah, Moinzadeh, Alireza, Moore, Richard A., Morris, Scott, Morrison, Carl, Mose, Lisle E., Mungall, Andrew J., Murray, Bradley A., Myers, Jerome B., Naresh, Rashi, Nelson, Joel, Nelson, Mark A., Nelson, Peter S., Newton, Yulia, Noble, Michael S., Noushmehr, Houtan, Nykter, Matti, Pantazi, Angeliki, Parfenov, Michael, Park, Peter J., Parker, Joel S., Paulauskis, Joseph, Penny, Robert, Perou, Charles M., Piché, Alain, Pihl, Todd, Pinto, Peter A., Prandi, Davide, Protopopov, Alexei, Ramirez, Nilsa C., Rao, Arvind, Rathmell, W. Kimryn, Rätsch, Gunnar, Ren, Xiaojia, Reuter, Victor E., Reynolds, Sheila M., Rhie, Suhn K., Rieger-Christ, Kimberly, Roach, Jeffrey, Robertson, A. Gordon, Robinson, Brian, Rubin, Mark A., Saad, Fred, Sadeghi, Sara, Saksena, Gordon, Saller, Charles, Salner, Andrew, Sanchez-Vega, Francisco, Sander, Chris, Sandusky, George, Sauter, Guido, Sboner, Andrea, Scardino, Peter T., Scarlata, Eleonora, Schein, Jacqueline E., Schlomm, Thorsten, Schmidt, Laura S., Schultz, Nikolaus, Schumacher, Steven E., Seidman, Jonathan, Neder, Luciano, Seth, Sahil, Sharp, Alexis, Shelton, Candace, Shelton, Troy, Shen, Hui, Shen, Ronglai, Sherman, Mark, Sheth, Margi, Shi, Yan, Shih, Juliann, Shmulevich, Ilya, Simko, Jeffry, Simon, Ronald, Simons, Janae V., Sipahimalani, Payal, Skelly, Tara, Sofia, Heidi J., Soloway, Matthew G., Song, Xingzhi, Sorcini, Andrea, Sougnez, Carrie, Stepa, Serghei, Stewart, Chip, Stewart, John, Stuart, Joshua M., Sullivan, Travis B., Sun, Charlie, Sun, Huandong, Tam, Angela, Tan, Donghui, Tang, Jiabin, Tarnuzzer, Roy, Tarvin, Katherine, Taylor, Barry S., Teebagy, Patrick, Tenggara, Imelda, Têtu, Bernard, Tewari, Ashutosh, Thiessen, Nina, Thompson, Timothy, Thorne, Leigh B., Tirapelli, Daniela P., Tomlins, Scott A., Trevisan, Felipe Amstalden, Troncoso, Patricia, True, Lawrence D., Tsourlakis, Maria Christina, Tyekucheva, Svitlana, Van Allen, Eliezer, Van Den Berg, David J., Veluvolu, Umadevi, Verhaak, Roel, Vocke, Cathy D., Voet, Doug, Wan, Yunhu, Wang, Qingguo, Wang, Wenyi, Wang, Zhining, Weinhold, Nils, Weinstein, John N., Weisenberger, Daniel J., Wilkerson, Matthew D., Wise, Lisa, Witte, John, Wu, Chia-Chin, Wu, Junyuan, Wu, Ye, Xu, Andrew W., Yadav, Shalini S., Yang, Liming, Yang, Lixing, Yau, Christina, Ye, Huihui, Yena, Peggy, Zeng, Thomas, Zenklusen, Jean C., Zhang, Hailei, Zhang, Jianhua, Zhang, Jiashan, Zhang, Wei, Zhong, Yi, Zhu, Kelsey, and Zmuda, Erik
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- 2015
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24. Genomic Classification of Cutaneous Melanoma
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Akbani, Rehan, Akdemir, Kadir C., Aksoy, B. Arman, Albert, Monique, Ally, Adrian, Amin, Samirkumar B., Arachchi, Harindra, Arora, Arshi, Auman, J. Todd, Ayala, Brenda, Baboud, Julien, Balasundaram, Miruna, Balu, Saianand, Barnabas, Nandita, Bartlett, John, Bartlett, Pam, Bastian, Boris C., Baylin, Stephen B., Behera, Madhusmita, Belyaev, Dmitry, Benz, Christopher, Bernard, Brady, Beroukhim, Rameen, Bir, Natalie, Black, Aaron D., Bodenheimer, Tom, Boice, Lori, Boland, Genevieve M., Bono, Riccardo, Bootwalla, Moiz S., Bosenberg, Marcus, Bowen, Jay, Bowlby, Reanne, Bristow, Christopher A., Brockway-Lunardi, Laura, Brooks, Denise, Brzezinski, Jakub, Bshara, Wiam, Buda, Elizabeth, Burns, William R., Butterfield, Yaron S.N., Button, Michael, Calderone, Tiffany, Cappellini, Giancarlo Antonini, Carter, Candace, Carter, Scott L., Cherney, Lynn, Cherniack, Andrew D., Chevalier, Aaron, Chin, Lynda, Cho, Juok, Cho, Raymond J., Choi, Yoon-La, Chu, Andy, Chudamani, Sudha, Cibulskis, Kristian, Ciriello, Giovanni, Clarke, Amanda, Coons, Stephen, Cope, Leslie, Crain, Daniel, Curley, Erin, Danilova, Ludmila, D’Atri, Stefania, Davidsen, Tanja, Davies, Michael A., Delman, Keith A., Demchok, John A., Deng, Qixia A., Deribe, Yonathan Lissanu, Dhalla, Noreen, Dhir, Rajiv, DiCara, Daniel, Dinikin, Michael, Dubina, Michael, Ebrom, J. Stephen, Egea, Sophie, Eley, Greg, Engel, Jay, Eschbacher, Jennifer M., Fedosenko, Konstantin V., Felau, Ina, Fennell, Timothy, Ferguson, Martin L., Fisher, Sheila, Flaherty, Keith T., Frazer, Scott, Frick, Jessica, Fulidou, Victoria, Gabriel, Stacey B., Gao, Jianjiong, Gardner, Johanna, Garraway, Levi A., Gastier-Foster, Julie M., Gaudioso, Carmelo, Gehlenborg, Nils, Genovese, Giannicola, Gerken, Mark, Gershenwald, Jeffrey E., Getz, Gad, Gomez-Fernandez, Carmen, Gribbin, Thomas, Grimsby, Jonna, Gross, Benjamin, Guin, Ranabir, Gutschner, Tony, Hadjipanayis, Angela, Halaban, Ruth, Hanf, Benjamin, Haussler, David, Haydu, Lauren E., Hayes, D. Neil, Hayward, Nicholas K., Heiman, David I., Herbert, Lynn, Herman, James G., Hersey, Peter, Hoadley, Katherine A., Hodis, Eran, Holt, Robert A., Hoon, Dave SB., Hoppough, Susan, Hoyle, Alan P., Huang, Franklin W., Huang, Mei, Huang, Sharon, Hutter, Carolyn M., Ibbs, Matthew, Iype, Lisa, Jacobsen, Anders, Jakrot, Valerie, Janning, Alyssa, Jeck, William R., Jefferys, Stuart R., Jensen, Mark A., Jones, Corbin D., Jones, Steven J.M., Ju, Zhenlin, Kakavand, Hojabr, Kang, Hyojin, Kefford, Richard F., Khuri, Fadlo R., Kim, Jaegil, Kirkwood, John M., Klode, Joachim, Korkut, Anil, Korski, Konstanty, Krauthammer, Michael, Kucherlapati, Raju, Kwong, Lawrence N., Kycler, Witold, Ladanyi, Marc, Lai, Phillip H., Laird, Peter W., Lander, Eric, Lawrence, Michael S., Lazar, Alexander J., Łaźniak, Radoslaw, Lee, Darlene, Lee, Jeffrey E., Lee, Junehawk, Lee, Kenneth, Lee, Semin, Lee, William, Leporowska, Ewa, Leraas, Kristen M., Li, Haiyan I., Lichtenberg, Tara M., Lichtenstein, Lee, Lin, Pei, Ling, Shiyun, Liu, Jia, Liu, Ouida, Liu, Wenbin, Long, Georgina V., Lu, Yiling, Ma, Singer, Ma, Yussanne, Mackiewicz, Andrzej, Mahadeshwar, Harshad S., Malke, Jared, Mallery, David, Manikhas, Georgy M., Mann, Graham J., Marra, Marco A., Matejka, Brenna, Mayo, Michael, Mehrabi, Sousan, Meng, Shaowu, Meyerson, Matthew, Mieczkowski, Piotr A., Miller, John P., Miller, Martin L., Mills, Gordon B., Moiseenko, Fedor, Moore, Richard A., Morris, Scott, Morrison, Carl, Morton, Donald, Moschos, Stergios, Mose, Lisle E., Muller, Florian L., Mungall, Andrew J., Murawa, Dawid, Murawa, Pawel, Murray, Bradley A., Nezi, Luigi, Ng, Sam, Nicholson, Dana, Noble, Michael S., Osunkoya, Adeboye, Owonikoko, Taofeek K., Ozenberger, Bradley A., Pagani, Elena, Paklina, Oxana V., Pantazi, Angeliki, Parfenov, Michael, Parfitt, Jeremy, Park, Peter J., Park, Woong-Yang, Parker, Joel S., Passarelli, Francesca, Penny, Robert, Perou, Charles M., Pihl, Todd D., Potapova, Olga, Prieto, Victor G., Protopopov, Alexei, Quinn, Michael J., Radenbaugh, Amie, Rai, Kunal, Ramalingam, Suresh S., Raman, Ayush T., Ramirez, Nilsa C., Ramirez, Ricardo, Rao, Uma, Rathmell, W. Kimryn, Ren, Xiaojia, Reynolds, Sheila M., Roach, Jeffrey, Robertson, A. Gordon, Ross, Merrick I., Roszik, Jason, Russo, Giandomenico, Saksena, Gordon, Saller, Charles, Samuels, Yardena, Sander, Chris, Sander, Cindy, Sandusky, George, Santoso, Netty, Saul, Melissa, Saw, Robyn PM., Schadendorf, Dirk, Schein, Jacqueline E., Schultz, Nikolaus, Schumacher, Steven E., Schwallier, Charles, Scolyer, Richard A., Seidman, Jonathan, Sekhar, Pedamallu Chandra, Sekhon, Harmanjatinder S., Senbabaoglu, Yasin, Seth, Sahil, Shannon, Kerwin F., Sharpe, Samantha, Sharpless, Norman E., Shaw, Kenna R. Mills, Shelton, Candace, Shelton, Troy, Shen, Ronglai, Sheth, Margi, Shi, Yan, Shiau, Carolyn J., Shmulevich, Ilya, Sica, Gabriel L., Simons, Janae V., Sinha, Rileen, Sipahimalani, Payal, Sofia, Heidi J., Soloway, Matthew G., Song, Xingzhi, Sougnez, Carrie, Spillane, Andrew J., Spychała, Arkadiusz, Stretch, Jonathan R., Stuart, Joshua, Suchorska, Wiktoria M., Sucker, Antje, Sumer, S. Onur, Sun, Yichao, Synott, Maria, Tabak, Barbara, Tabler, Teresa R., Tam, Angela, Tan, Donghui, Tang, Jiabin, Tarnuzzer, Roy, Tarvin, Katherine, Tatka, Honorata, Taylor, Barry S., Teresiak, Marek, Thiessen, Nina, Thompson, John F., Thorne, Leigh, Thorsson, Vesteinn, Trent, Jeffrey M., Triche, Timothy J., Jr., Tsai, Kenneth Y., Tsou, Peiling, Van Den Berg, David J., Van Allen, Eliezer M., Veluvolu, Umadevi, Verhaak, Roeland G., Voet, Douglas, Voronina, Olga, Walter, Vonn, Walton, Jessica S., Wan, Yunhu, Wang, Yuling, Wang, Zhining, Waring, Scot, Watson, Ian R., Weinhold, Nils, Weinstein, John N., Weisenberger, Daniel J., White, Peter, Wilkerson, Matthew D., Wilmott, James S., Wise, Lisa, Wiznerowicz, Maciej, Woodman, Scott E., Wu, Chang-Jiun, Wu, Chia-Chin, Wu, Junyuan, Wu, Ye, Xi, Ruibin, Xu, Andrew Wei, Yang, Da, Yang, Liming, Yang, Lixing, Zack, Travis I., Zenklusen, Jean C., Zhang, Hailei, Zhang, Jianhua, Zhang, Wei, Zhao, Xiaobei, Zhu, Jingchun, Zhu, Kelsey, Zimmer, Lisa, Zmuda, Erik, and Zou, Lihua
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- 2015
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25. Integrated genomic and molecular characterization of cervical cancer
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Burk, Robert D., Chen, Zigui, Saller, Charles, Tarvin, Katherine, Carvalho, Andre L., Scapulatempo-Neto, Cristovam, Silveira, Henrique C., Fregnani, Jos H., Creighton, Chad J., Anderson, Matthew L., Castro, Patricia, Wang, Sophia S., Yau, Christina, Benz, Christopher, Robertson, A. Gordon, Mungall, Karen, Lim, Lynette, Bowlby, Reanne, Sadeghi, Sara, Brooks, Denise, Sipahimalani, Payal, Mar, Richard, Ally, Adrian, Clarke, Amanda, Mungall, Andrew J., Tam, Angela, Lee, Darlene, Chuah, Eric, Schein, Jacqueline E., Tse, Kane, Kasaian, Katayoon, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Balasundaram, Miruna, Thiessen, Nina, Dhalla, Noreen, Carlsen, Rebecca, Moore, Richard A., Holt, Robert A., Jones, Steven J. M., Wong, Tina, Pantazi, Angeliki, Parfenov, Michael, Kucherlapati, Raju, Hadjipanayis, Angela, Seidman, Jonathan, Kucherlapati, Melanie, Ren, Xiaojia, Xu, Andrew W., Yang, Lixing, Park, Peter J., Lee, Semin, Rabeno, Brenda, Huelsenbeck-Dill, Lori, Borowsky, Mark, Cadungog, Mark, Iacocca, Mary, Petrelli, Nicholas, Swanson, Patricia, Ojesina, Akinyemi I., Le, Xuan, Sandusky, George, Adebamowo, Sally N., Akeredolu, Teniola, Adebamowo, Clement, Reynolds, Sheila M., Shmulevich, Ilya, Shelton, Candace, Crain, Daniel, Mallery, David, Curley, Erin, Gardner, Johanna, Penny, Robert, Morris, Scott, Shelton, Troy, Liu, Jia, Lolla, Laxmi, Chudamani, Sudha, Wu, Ye, Birrer, Michael, McLellan, Michael D., Bailey, Matthew H., Miller, Christopher A., Wyczalkowski, Matthew A., Fulton, Robert S., Fronick, Catrina C., Lu, Charles, Mardis, Elaine R., Appelbaum, Elizabeth L., Schmidt, Heather K., Fulton, Lucinda A., Cordes, Matthew G., Li, Tiandao, Ding, Li, Wilson, Richard K., Rader, Janet S., Behmaram, Behnaz, Uyar, Denise, Bradley, William, Wrangle, John, Pastore, Alessandro, Levine, Douglas A., Dao, Fanny, Gao, Jianjiong, Schultz, Nikolaus, Sander, Chris, Ladanyi, Marc, Einstein, Mark, Teeter, Randall, Benz, Stephen, Wentzensen, Nicolas, Felau, Ina, Zenklusen, Jean C., Bodelon, Clara, Demchok, John A., Yang, Liming, Sheth, Margi, Ferguson, Martin L., Tarnuzzer, Roy, Yang, Hannah, Schiffman, Mark, Zhang, Jiashan, Wang, Zhining, Davidsen, Tanja, Olaniyan, Olayinka, Hutter, Carolyn M., Sofia, Heidi J., Gordenin, Dmitry A., Chan, Kin, Roberts, Steven A., Klimczak, Leszek J., Van Waes, Carter, Chen, Zhong, Saleh, Anthony D., Cheng, Hui, Parfitt, Jeremy, Bartlett, John, Albert, Monique, Arnaout, Angel, Sekhon, Harman, Gilbert, Sebastien, Peto, Myron, Myers, Jerome, Harr, Jodi, Eckman, John, Bergsten, Julie, Tucker, Kelinda, Zach, Leigh Anne, Karlan, Beth Y., Lester, Jenny, Orsulic, Sandra, Sun, Qiang, Naresh, Rashi, Pihl, Todd, Wan, Yunhu, Zaren, Howard, Sapp, Jennifer, Miller, Judy, Drwiega, Paul, Murray, Bradley A., Zhang, Hailei, Cherniack, Andrew D., Sougnez, Carrie, Pedamallu, Chandra Sekhar, Lichtenstein, Lee, Meyerson, Matthew, Noble, Michael S., Heiman, David I., Voet, Doug, Getz, Gad, Saksena, Gordon, Kim, Jaegil, Shih, Juliann, Cho, Juok, Lawrence, Michael S., Gehlenborg, Nils, Lin, Pei, Beroukhim, Rameen, Frazer, Scott, Gabriel, Stacey B., Schumacher, Steven E., Leraas, Kristen M., Lichtenberg, Tara M., Zmuda, Erik, Bowen, Jay, Frick, Jessica, Gastier-Foster, Julie M., Wise, Lisa, Gerken, Mark, Ramirez, Nilsa C., Danilova, Ludmila, Cope, Leslie, Baylin, Stephen B., Salvesen, Helga B., Vellano, Christopher P., Ju, Zhenlin, Diao, Lixia, Zhao, Hao, Chong, Zechen, Ryan, Michael C., Martinez-Ledesma, Emmanuel, Verhaak, Roeland G., Averett Byers, Lauren, Yuan, Yuan, Chen, Ken, Ling, Shiyun, Mills, Gordon B., Lu, Yiling, Akbani, Rehan, Seth, Sahil, Liang, Han, Wang, Jing, Han, Leng, Weinstein, John N., Bristow, Christopher A., Zhang, Wei, Mahadeshwar, Harshad S., Sun, Huandong, Tang, Jiabin, Zhang, Jianhua, Song, Xingzhi, Protopopov, Alexei, Shaw, Kenna R. Mills, Chin, Lynda, Olabode, Oluwole, DiSaia, Philip, Radenbaugh, Amie, Haussler, David, Zhu, Jingchun, Stuart, Josh, Chalise, Prabhakar, Koestler, Devin, Fridley, Brooke L., Godwin, Andrew K., Madan, Rashna, Ciriello, Giovanni, Martinez, Cathleen, Higgins, Kelly, Bocklage, Therese, Auman, J. Todd, Perou, Charles M., Tan, Donghui, Parker, Joel S., Hoadley, Katherine A., Wilkerson, Matthew D., Mieczkowski, Piotr A., Skelly, Tara, Veluvolu, Umadevi, Hayes, D. Neil, Rathmell, W. Kimryn, Hoyle, Alan P., Simons, Janae V., Wu, Junyuan, Mose, Lisle E., Soloway, Matthew G., Balu, Saianand, Meng, Shaowu, Jefferys, Stuart R., Bodenheimer, Tom, Shi, Yan, Roach, Jeffrey, Thorne, Leigh B., Boice, Lori, Huang, Mei, Jones, Corbin D., Zuna, Rosemary, Walker, Joan, Gunderson, Camille, Snowbarger, Carie, Brown, David, Moxley, Katherine, Moore, Kathleen, Andrade, Kelsi, Landrum, Lisa, Mannel, Robert, McMeekin, Scott, Johnson, Starla, Nelson, Tina, Elishaev, Esther, Dhir, Rajiv, Edwards, Robert, Bhargava, Rohit, Tiezzi, Daniel G., Andrade, Jurandyr M., Noushmehr, Houtan, Gilberto Carlotti, Carlos, Jr, Tirapelli, Daniela Pretti da Cunha, Weisenberger, Daniel J., Van Den Berg, David J., Maglinte, Dennis T., Bootwalla, Moiz S., Lai, Phillip H., Triche, Timothy, Jr, Swisher, Elizabeth M., Agnew, Kathy J., Shelley, Carl Simon, Laird, Peter W., Schwarz, Julie, Grigsby, Perry, and Mutch, David
- Subjects
Care and treatment ,Genetic aspects ,Causes of ,Health aspects ,Cervical cancer -- Genetic aspects -- Care and treatment -- Causes of ,Gene mutation -- Health aspects - Abstract
Author(s): The Cancer Genome Atlas Research Network; Albert Einstein College of Medicine; Robert D. Burk [1]; Zigui Chen [1]; Analytical Biological Services; Charles Saller [2]; Katherine Tarvin [2]; Barretos Cancer [...], Cervical cancer remains one of the leading causes of cancer-related deaths worldwide. Here we report the extensive molecular characterization of 228 primary cervical cancers, one of the largest comprehensive genomic studies of cervical cancer to date. We observed notable APOBEC mutagenesis patterns and identified SHKBP1, ERBB3, CASP8, HLA-A and TGFBR2 as novel significantly mutated genes in cervical cancer. We also discovered amplifications in immune targets CD274 (also known as PD-L1) and PDCD1LG2 (also known as PD-L2), and the BCAR4 long non-coding RNA, which has been associated with response to lapatinib. Integration of human papilloma virus (HPV) was observed in all HPV18-related samples and 76% of HPV16-related samples, and was associated with structural aberrations and increased target-gene expression. We identified a unique set of endometrial-like cervical cancers, comprised predominantly of HPV-negative tumours with relatively high frequencies of KRAS, ARID1A and PTEN mutations. Integrative clustering of 178 samples identified keratin-low squamous, keratin-high squamous and adenocarcinoma-rich subgroups. These molecular analyses reveal new potential therapeutic targets for cervical cancers.
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- 2017
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26. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns
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Jiao, Wei, Atwal, Gurnit, Polak, Paz, Karlic, Rosa, Cuppen, Edwin, Al-Shahrour, Fatima, Bailey, Peter J, Biankin, Andrew V, Boutros, Paul C, Campbell, Peter J, Chang, David K, Cooke, Susanna L, Deshpande, Vikram, Faltas, Bishoy M, Faquin, William C, Garraway, Levi, Getz, Gad, Grimmond, Sean M, Haider, Syed, Hoadley, Katherine A, Kaiser, Vera B, Kato, Mamoru, Kübler, Kirsten, Lazar, Alexander J, Li, Constance H, Louis, David N, Margolin, Adam, Martin, Sancha, Nahal-Bose, Hardeep K, Nielsen, G Petur, Nik-Zainal, Serena, Omberg, Larsson, P’ng, Christine, Perry, Marc D, Rheinbay, Esther, Rubin, Mark A, Semple, Colin A, Sgroi, Dennis C, Shibata, Tatsuhiro, Siebert, Reiner, Smith, Jaclyn, Stein, Lincoln D, Stobbe, Miranda D, Sun, Ren X, Thai, Kevin, Wright, Derek W, Wu, Chin-Lee, Yuan, Ke, Zhang, Junjun, Danyi, Alexandra, de Ridder, Jeroen, van Herpen, Carla, Lolkema, Martijn P, Steeghs, Neeltje, Morris, Quaid D, Aaltonen, Lauri A, Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Amin, Samirkumar B, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Bader, Gary D, Baez-Ortega, Adrian, Bailey, Matthew H, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barenboim, Jonathan, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Beroukhim, Rameen, Berrios, Mario, Bersani, Samantha, Bertl, Johanna, Betancourt, Miguel, Bhandari, Vinayak, Bhosle, Shriram G, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Boroevich, Keith A, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, Guillaume, Bova, G Steven, Bowen, David T, Bowlby, Reanne, Bowtell, David DL, Boyault, Sandrine, Boyce, Rich, Boyd, Jeffrey, Brazma, Alvis, Brennan, Paul, Brewer, Daniel S, Brinkman, Arie B, Bristow, Robert G, Broaddus, Russell R, Brock, Jane E, Brock, Malcolm, Broeks, Annegien, Brooks, Angela N, Brooks, Denise, Brors, Benedikt, Brunak, Søren, Bruxner, Timothy JC, Bruzos, Alicia L, Buchanan, Alex, Buchhalter, Ivo, Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H, Busanovich, John, Bustamante, Carlos D, Butler, Adam P, Butte, Atul J, Byrne, Niall J, Børresen-Dale, Anne-Lise, Caesar-Johnson, Samantha J, Cafferkey, Andy, Cahill, Declan, Calabrese, Claudia, Caldas, Carlos, Calvo, Fabien, Camacho, Niedzica, Campo, Elias, Cantù, Cinzia, Cao, Shaolong, Carey, Thomas E, Carlevaro-Fita, Joana, Carlsen, Rebecca, Cataldo, Ivana, Cazzola, Mario, Cebon, Jonathan, Cerfolio, Robert, Chadwick, Dianne E, Chakravarty, Dimple, Chalmers, Don, Chan, Calvin Wing Yiu, Chan, Kin, Chan-Seng-Yue, Michelle, Chandan, Vishal S, Chanock, Stephen J, Chantrill, Lorraine A, Chateigner, Aurélien, Chatterjee, Nilanjan, Chayama, Kazuaki, Chen, Hsiao-Wei, Chen, Jieming, Chen, Ken, Chen, Yiwen, Chen, Zhaohong, Cherniack, Andrew D, Chien, Jeremy, Chiew, Yoke-Eng, Chin, Suet-Feung, Cho, Juok, Cho, Sunghoon, Choi, Jung Kyoon, Choi, Wan, Chomienne, Christine, Chong, Zechen, Choo, Su Pin, Chou, Angela, Christ, Angelika N, Christie, Elizabeth L, Chuah, Eric, Cibulskis, Carrie, Cibulskis, Kristian, Cingarlini, Sara, Clapham, Peter, Claviez, Alexander, Cleary, Sean, Cloonan, Nicole, Cmero, Marek, Collins, Colin C, Connor, Ashton A, Cooper, Colin S, Cope, Leslie, Corbo, Vincenzo, Cordes, Matthew G, Cordner, Stephen M, Cortés-Ciriano, Isidro, Covington, Kyle, Cowin, Prue A, Craft, Brian, Craft, David, Creighton, Chad J, Cun, Yupeng, Curley, Erin, Cutcutache, Ioana, Czajka, Karolina, Czerniak, Bogdan, Dagg, Rebecca A, Danilova, Ludmila, Davi, Maria Vittoria, Davidson, Natalie R, Davies, Helen, Davis, Ian J, Davis-Dusenbery, Brandi N, Dawson, Kevin J, De La Vega, Francisco M, De Paoli-Iseppi, Ricardo, Defreitas, Timothy, Dei Tos, Angelo P, Delaneau, Olivier, Demchok, John A, 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Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
In cancer, the primary tumour’s organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types produced by the PCAWG Consortium. Our classifier achieves an accuracy of 91% on held-out tumor samples and 88% and 83% respectively on independent primary and metastatic samples, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced accuracy. Our results have clinical applicability, underscore how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of circulating tumour DNA.
- Published
- 2023
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27. Combined burden and functional impact tests for cancer driver discovery using DriverPower
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Shuai, Shimin, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Bandopadhayay, Pratiti, Barenboim, Jonathan, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Brunak, Søren, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Dhingra, Priyanka, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Getz, Gad, Guo, Qianyun, Gut, Ivo G, Haan, David, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Izarzugaza, Jose MG, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kahraman, Abdullah, Kellis, Manolis, Khurana, Ekta, Kim, Jaegil, Kim, Jong K, Kim, Youngwook, Komorowski, Jan, Korbel, Jan O, Kumar, Sushant, Lanzós, Andrés, Larsson, Erik, Lawrence, Michael S, Lee, Donghoon, Lehmann, Kjong-Van, Li, Shantao, Li, Xiaotong, Lin, Ziao, Liu, Eric Minwei, Lochovsky, Lucas, Lou, Shaoke, Madsen, Tobias, Marchal, Kathleen, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Maruvka, Yosef E, McGillivray, Patrick D, Meyerson, William, Muiños, Ferran, Mularoni, Loris, Nakagawa, Hidewaki, Nielsen, Morten Muhlig, Paczkowska, Marta, Park, Keunchil, Park, Kiejung, Pedersen, Jakob Skou, Pons, Tirso, Pulido-Tamayo, Sergio, Raphael, Benjamin J, Reimand, Jüri, Reyes-Salazar, Iker, Reyna, Matthew A, Rheinbay, Esther, Rubin, Mark A, Rubio-Perez, Carlota, Sahinalp, S Cenk, Saksena, Gordon, Salichos, Leonidas, Sander, Chris, Schumacher, Steven E, Shackleton, Mark, Shapira, Ofer, Shen, Ciyue, Shrestha, Raunak, Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stein, Lincoln D, Stuart, Joshua M, Tamborero, David, Tiao, Grace, Tsunoda, Tatsuhiko, Umer, Husen M, Uusküla-Reimand, Liis, Valencia, Alfonso, Vazquez, Miguel, Verbeke, Lieven PC, Wadelius, Claes, Wadi, Lina, Wang, Jiayin, Warrell, Jonathan, Waszak, Sebastian M, Weischenfeldt, Joachim, Wheeler, David A, Wu, Guanming, Yu, Jun, Zhang, Jing, Zhang, Xuanping, Zhang, Yan, Zhao, Zhongming, Zou, Lihua, von Mering, Christian, Gallinger, Steven, Aaltonen, Lauri A, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Al-Shahrour, Fatima, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Atwal, Gurnit, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Baez-Ortega, Adrian, Bailey, Matthew H, Bailey, Peter J, Balasundaram, Miruna, Balu, Saianand, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Berrios, Mario, Bersani, Samantha, Betancourt, Miguel, Bhandari, Vinayak, Bhosle, Shriram G, Biankin, Andrew V, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, Guillaume, Boutros, Paul C, Bova, G Steven, Bowen, David T, Bowlby, Reanne, Bowtell, David DL, Boyault, Sandrine, Boyce, Rich, Boyd, Jeffrey, Brazma, Alvis, Brennan, Paul, Brewer, Daniel S, Brinkman, Arie B, Bristow, Robert G, Broaddus, Russell R, Brock, Jane E, Brock, Malcolm, Broeks, Annegien, Brooks, Angela N, Brooks, Denise, Brors, Benedikt, Bruxner, Timothy JC, Bruzos, Alicia L, Buchanan, Alex, Buchhalter, Ivo, Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H, Busanovich, John, Bustamante, Carlos D, Butler, Adam P, Butte, Atul J, Byrne, Niall J, Børresen-Dale, Anne-Lise, Caesar-Johnson, Samantha J, Cafferkey, Andy, Cahill, Declan, Calabrese, Claudia, Caldas, Carlos, Calvo, Fabien, Camacho, Niedzica, Campo, Elias, Cantù, Cinzia, Cao, Shaolong, Carey, Thomas E, Carlsen, Rebecca, Cataldo, Ivana, Cazzola, Mario, Cebon, Jonathan, Cerfolio, Robert, Chadwick, Dianne E, Chalmers, Don, Chan, Kin, Chan-Seng-Yue, Michelle, Chandan, Vishal S, Chang, David K, Chanock, Stephen J, Chantrill, Lorraine A, Chateigner, Aurélien, Chatterjee, Nilanjan, Chayama, Kazuaki, Chen, Hsiao-Wei, Chen, Jieming, Chen, Yiwen, Chen, Zhaohong, Cherniack, Andrew D, Chien, Jeremy, Chiew, Yoke-Eng, Chin, Suet-Feung, Cho, Juok, Cho, Sunghoon, Choi, Wan, Chomienne, Christine, Chong, Zechen, Choo, Su Pin, Chou, Angela, Christ, Angelika N, Christie, Elizabeth L, Chuah, Eric, Cibulskis, Carrie, Cibulskis, Kristian, Cingarlini, Sara, Clapham, Peter, Claviez, Alexander, Cleary, Sean, Cloonan, Nicole, Cmero, Marek, Collins, Colin C, Connor, Ashton A, Cooke, Susanna L, Cooper, Colin S, Cope, Leslie, Corbo, Vincenzo, Cordes, Matthew G, Cordner, Stephen M, Cortés-Ciriano, Isidro, Covington, Kyle, Cowin, Prue A, Craft, Brian, Craft, David, Creighton, Chad J, Cun, Yupeng, Curley, Erin, Cutcutache, Ioana, Czajka, Karolina, Czerniak, Bogdan, Dagg, Rebecca A, Danilova, Ludmila, Davi, Maria Vittoria, Davidson, Natalie R, Davies, Helen, Davis, Ian J, Davis-Dusenbery, Brandi N, Dawson, Kevin J, De La Vega, Francisco M, De Paoli-Iseppi, Ricardo, Defreitas, Timothy, Dei Tos, Angelo P, Delaneau, Olivier, Demchok, John A, Demeulemeester, Jonas, Demidov, German M, Demircioğlu, Deniz, Dennis, Nening M, Denroche, Robert E, Dentro, Stefan C, Desai, Nikita, Deshpande, Vikram, Deshwar, Amit G, Desmedt, Christine, Dhalla, Noreen, Dhani, Neesha C, Dhir, Rajiv, DiBiase, Anthony, Ding, Li, Ding, Shuai, Dinh, Huy Q, Dirix, Luc, Doddapaneni, HarshaVardhan, Donmez, Nilgun, Dow, Michelle T, Drapkin, Ronny, Drechsel, Oliver, Drews, Ruben M, Serge, Serge, Dudderidge, Tim, Dueso-Barroso, Ana, Dunford, Andrew J, Dunn, Michael, Dursi, Lewis Jonathan, Duthie, Fraser R, Dutton-Regester, Ken, Eagles, Jenna, Easton, Douglas F, Edmonds, Stuart, Edwards, Paul A, Edwards, Sandra E, Eeles, Rosalind A, Ehinger, Anna, Eils, Juergen, Eils, Roland, El-Naggar, Adel, Eldridge, Matthew, Ellrott, Kyle, Erkek, Serap, Escaramis, Georgia, Espiritu, Shadrielle MG, Estivill, Xavier, Etemadmoghadam, Dariush, Eyfjord, Jorunn E, Faltas, Bishoy M, Fan, Daiming, Fan, Yu, Faquin, William C, Farcas, Claudiu, Fassan, Matteo, Fatima, Aquila, Favero, Francesco, Fayzullaev, Nodirjon, Felau, Ina, Fereday, Sian, Ferguson, Martin L, Ferretti, Vincent, Field, Matthew A, Finocchiaro, Gaetano, Fisher, Cyril, Fittall, Matthew W, Fitzgerald, Anna, Fitzgerald, Rebecca C, Flanagan, Adrienne M, Fleshner, Neil E, Flicek, Paul, Foekens, John A, Fong, Kwun M, Foster, Christopher S, Fox, Natalie S, Fraser, Michael, Frazer, Scott, Frenkel-Morgenstern, Milana, Friedman, William, Fronick, Catrina C, Fujimoto, Akihiro, Fujita, Masashi, Fukayama, Masashi, Fulton, Lucinda A, Fulton, Robert S, Furuta, Mayuko, Futreal, P Andrew, Füllgrabe, Anja, Gabriel, Stacey B, Gao, Jianjiong, Gao, Shengjie, Garraway, Levi, Garred, Øystein, Garrison, Erik, Gehlenborg, Nils, Gelpi, Josep LL, George, Joshy, Gerhard, Daniela S, Gerhauser, Clarissa, Gershenwald, Jeffrey E, Gerstung, Moritz, Ghori, Mohammed, Ghossein, Ronald, Giama, Nasra H, Gibbs, Richard A, Gibson, Bob, Gill, Anthony J, Gill, Pelvender, Giri, Dilip D, Glodzik, Dominik, Gnanapragasam, Vincent J, Goebler, Maria Elisabeth, Goldman, Mary J, Gomez, Carmen, Gonzalez, Santiago, Gonzalez-Perez, Abel, Gordenin, Dmitry A, Gossage, James, Gotoh, Kunihito, Govindan, Ramaswamy, Grabau, Dorthe, Graham, Janet S, Grant, Robert C, Green, Anthony R, Green, Eric, Greger, Liliana, Grehan, Nicola, Grimaldi, Sonia, Grimmond, Sean M, Grossman, Robert L, Grundhoff, Adam, Gundem, Gunes, Gupta, Manaswi, Gupta, Shailja, Gut, Marta, Göke, Jonathan, Ha, Gavin, Haake, Andrea, Haas, Siegfried, Haase, Kerstin, Haber, James E, Habermann, Nina, Hach, Faraz, Haider, Syed, Hama, Natsuko, Hamdy, Freddie C, Hamilton, Anne, Han, Leng, Hanna, George B, Hansmann, Martin, Harismendy, Olivier, Harliwong, Ivon, Harrington, Eoghan, Hasegawa, Takanori, Haussler, David, Hawkins, Steve, Hayami, Shinya, Hayashi, Shuto, Hayes, D Neil, Hayes, Stephen J, Hayward, Nicholas K, Hazell, Steven, He, Yao, Heath, Allison P, Heath, Simon C, Hedley, David, Hegde, Apurva M, Heiman, David I, Heinold, Michael C, Heins, Zachary, Heisler, Lawrence E, Hellstrom-Lindberg, Eva, Heo, Seong Gu, Hepperla, Austin J, Heredia-Genestar, José María, Hersey, Peter, Hilmarsdottir, Holmfridur, Hinton, Jonathan, Hirano, Satoshi, Hiraoka, Nobuyoshi, Hoadley, Katherine A, Hoell, Jessica I, Hoffmann, Steve, Hofmann, Oliver, Holbrook, Andrea, Holik, Aliaksei Z, Hollingsworth, Michael A, Holmes, Oliver, Holt, Robert A, Hong, Eun Pyo, Hong, Jongwhi H, Hooijer, Gerrit K, Hosoda, Fumie, Hou, Yong, Hovestadt, Volker, Howat, William, Hoyle, Alan P, Hruban, Ralph H, Hu, Jianhong, Hu, Taobo, Hua, Xing, Huang, Kuan-lin, Huang, Mei, Huang, Mi Ni, Huang, Vincent, Huang, Yi, Huber, Wolfgang, Hudson, Thomas J, Hummel, Michael, Hung, Jillian A, Huntsman, David, Hupp, Ted R, Huse, Jason, Huska, Matthew R, Hutter, Barbara, Hutter, Carolyn M, Hübschmann, Daniel, Iacobuzio-Donahue, Christine A, Imbusch, Charles David, Imielinski, Marcin, Imoto, Seiya, Isaacs, William B, Ishikawa, Shumpei, Iskar, Murat, Islam, SM Ashiqul, Ittmann, Michael, Ivkovic, Sinisa, Jacquemier, Jocelyne, Jakrot, Valerie, Jamieson, Nigel B, Jang, Gun Ho, Jang, Se Jin, Jayaseelan, Joy C, Jayasinghe, Reyka, Jefferys, Stuart R, Jegalian, Karine, Jennings, Jennifer L, Jeon, Seung-Hyup, Jerman, Lara, Ji, Yuan, Jiao, Wei, Johansson, Peter A, Johns, Amber L, Johns, Jeremy, Jolly, Clemency, Joly, Yann, Jonasson, Jon G, Jones, Corbin D, Jones, David R, Jones, David TW, Jones, Nic, Jones, Steven JM, Jonkers, Jos, Ju, Young Seok, Juhl, Hartmut, Jung, Jongsun, Juul, Sissel, Jäger, Natalie, Kabbe, Rolf, Kaiser, Vera B, Kakavand, Hojabr, Kalimuthu, Sangeetha, von Kalle, Christof, Kang, Koo Jeong, Karaszi, Katalin, Karlan, Beth, Karlić, Rosa, Karsch, Dennis, Kasaian, Katayoon, Kassahn, Karin S, Katai, Hitoshi, Kato, Mamoru, Katoh, Hiroto, Kawakami, Yoshiiku, Kay, Jonathan D, Kazakoff, Stephen H, Kazanov, Marat D, Keays, Maria, Kebebew, Electron, Kefford, Richard F, Kench, James G, Kennedy, Catherine J, Kerssemakers, Jules NA, Khoo, David, Khoo, Vincent, Khuntikeo, Narong, Kilpinen, Helena, Kim, Hark Kyun, Kim, Hyung-Lae, Kim, Hyung-Yong, Kim, Hyunghwan, Kim, Jihoon, King, Tari A, Klapper, Wolfram, Kleinheinz, Kortine, Klimczak, Leszek J, Knappskog, Stian, Kneba, Michael, Knoppers, Bartha M, Koh, Youngil, Komura, Daisuke, Komura, Mitsuhiro, Kong, Gu, Kool, Marcel, Korchina, Viktoriya, Korshunov, Andrey, Koscher, Michael, Koster, Roelof, Kote-Jarai, Zsofia, Koures, Antonios, Kovacevic, Milena, Kremeyer, Barbara, Kretzmer, Helene, Kreuz, Markus, Krishnamurthy, Savitri, Kube, Dieter, Kumar, Kiran, Kumar, Pardeep, Kumar, Yogesh, Kundra, Ritika, Kübler, Kirsten, Küppers, Ralf, Lagergren, Jesper, Lai, Phillip H, Laird, Peter W, Lakhani, Sunil R, Lalansingh, Christopher M, Lalonde, Emilie, Lamaze, Fabien C, Lambert, Adam, Lander, Eric, Landgraf, Pablo, Landoni, Luca, Langerød, Anita, Larsimont, Denis, Lathrop, Mark, Lau, Loretta MS, Lawerenz, Chris, Lawlor, Rita T, Lazar, Alexander J, Lazic, Ana Mijalkovic, Le, Xuan, Lee, Darlene, Lee, Eunjung Alice, Lee, Hee Jin, Lee, Jake June-Koo, Lee, Jeong-Yeon, Lee, Juhee, Lee, Ming Ta Michael, Lee-Six, Henry, Lehrach, Hans, Lenze, Dido, Leonard, Conrad R, Leongamornlert, Daniel A, Leshchiner, Ignaty, Letourneau, Louis, Letunic, Ivica, Levine, Douglas A, Lewis, Lora, Ley, Tim, Li, Chang, Li, Constance H, Li, Haiyan Irene, Li, Jun, Li, Lin, Li, Siliang, Li, Xiaobo, Li, Xinyue, Li, Yilong, Liang, Han, Liang, Sheng-Ben, Lichter, Peter, Lin, Pei, Linehan, WM, Lingjærde, Ole Christian, Liu, Dongbing, Liu, Fei-Fei Fei, Liu, Fenglin, Liu, Jia, Liu, Xingmin, Livingstone, Julie, Livitz, Dimitri, Livni, Naomi, Loeffler, Markus, Long, Georgina V, Lopez-Guillermo, Armando, Louis, David N, Lovat, Laurence B, Lu, Yiling, Lu, Yong-Jie, Lu, Youyong, Luchini, Claudio, Lungu, Ilinca, Luo, Xuemei, Luxton, Hayley J, Lynch, Andy G, Lype, Lisa, López, Cristina, López-Otín, Carlos, Z, Eric, Ma, Yussanne, MacGrogan, Gaetan, MacRae, Shona, Macintyre, Geoff, Maejima, Kazuhiro, Mafficini, Andrea, Maglinte, Dennis T, Maitra, Arindam, Majumder, Partha P, Malcovati, Luca, Malikic, Salem, Malleo, Giuseppe, Mann, Graham J, Mantovani-Löffler, Luisa, Marchegiani, Giovanni, Mardis, Elaine R, Margolin, Adam A, Marin, Maximillian G, Markowetz, Florian, Markowski, Julia, Marks, Jeffrey, Marques-Bonet, Tomas, Marra, Marco A, Marsden, Luke, Martens, John WM, Martin, Sancha, Martin-Subero, Jose I, Mashl, R Jay, Massie, Charlie E, Matthew, Thomas J, Matthews, Lucy, Mayer, Erik, Mayes, Simon, Mayo, Michael, Mbabaali, Faridah, McCune, Karen, McDermott, Ultan, McLellan, Michael D, McPherson, John D, McPherson, John R, McPherson, Treasa A, Meier, Samuel R, Meng, Alice, Meng, Shaowu, Menzies, Andrew, Merrett, Neil D, Merson, Sue, Meyerson, Matthew, Mieczkowski, Piotr A, Mihaiescu, George L, Mijalkovic, Sanja, Mikkelsen, Tom, Milella, Michele, Mileshkin, Linda, Miller, Christopher A, Miller, David K, Miller, Jessica K, Mills, Gordon B, Milovanovic, Ana, Minner, Sarah, Miotto, Marco, Arnau, Gisela Mir, Mirabello, Lisa, Mitchell, Chris, Mitchell, Thomas J, Miyano, Satoru, Miyoshi, Naoki, Mizuno, Shinichi, Molnár-Gábor, Fruzsina, Moore, Malcolm J, Moore, Richard A, Morganella, Sandro, Morris, Quaid D, Morrison, Carl, Mose, Lisle E, Moser, Catherine D, Mungall, Andrew J, Mungall, Karen, Musgrove, Elizabeth A, Mustonen, Ville, Mutch, David, Muyas, Francesc, Muzny, Donna M, Muñoz, Alfonso, Myers, Jerome, Myklebost, Ola, Möller, Peter, Nagae, Genta, Nagrial, Adnan M, Nahal-Bose, Hardeep K, Nakagama, Hitoshi, Nakamura, Hiromi, Nakamura, Toru, Nakano, Kaoru, Nandi, Tannistha, Nangalia, Jyoti, Nastic, Mia, Navarro, Arcadi, Navarro, Fabio CP, Neal, David E, Nettekoven, Gerd, Newell, Felicity, Newhouse, Steven J, Newton, Yulia, Ng, Alvin Wei Tian, Ng, Anthony, Nicholson, Jonathan, Nicol, David, Nie, Yongzhan, Nielsen, G Petur, Nik-Zainal, Serena, Noble, Michael S, Nones, Katia, Northcott, Paul A, Notta, Faiyaz, O’Connor, Brian D, O’Donnell, Peter, O’Donovan, Maria, O’Meara, Sarah, O’Neill, Brian Patrick, O’Neill, J Robert, Ocana, David, Ochoa, Angelica, Oesper, Layla, Ogden, Christopher, Ohdan, Hideki, Ohi, Kazuhiro, Ohno-Machado, Lucila, Oien, Karin A, Ojesina, Akinyemi I, Ojima, Hidenori, Okusaka, Takuji, Omberg, Larsson, Ong, Choon Kiat, Ossowski, Stephan, Ott, German, Ouellette, BF Francis, P’ng, Christine, Paiella, Salvatore, Pairojkul, Chawalit, Pajic, Marina, Pan-Hammarström, Qiang, Papaemmanuil, Elli, Papatheodorou, Irene, Paramasivam, Nagarajan, Park, Ji Wan, Park, Joong-Won, Park, Peter J, Parker, Joel S, Parsons, Simon L, Pass, Harvey, Pasternack, Danielle, Pastore, Alessandro, Patch, Ann-Marie, Pauporté, Iris, Pea, Antonio, Pearson, John V, Pedamallu, Chandra Sekhar, Pederzoli, Paolo, Peifer, Martin, Pennell, Nathan A, Perou, Charles M, Perry, Marc D, Petersen, Gloria M, Peto, Myron, Petrelli, Nicholas, Petryszak, Robert, Pfister, Stefan M, Phillips, Mark, Pich, Oriol, Pickett, Hilda A, Pihl, Todd D, Pillay, Nischalan, Pinder, Sarah, Pinese, Mark, Pinho, Andreia V, Pitkänen, Esa, Pivot, Xavier, Piñeiro-Yáñez, Elena, Planko, Laura, Plass, Christoph, Polak, Paz, Popescu, Irinel, Potapova, Olga, Prasad, Aparna, Preston, Shaun R, Prinz, Manuel, Pritchard, Antonia L, Prokopec, Stephenie D, Provenzano, Elena, Puente, Xose S, Puig, Sonia, Puiggròs, Montserrat, Pupo, Gulietta M, Purdie, Colin A, Quinn, Michael C, Rabionet, Raquel, Rader, Janet S, Radlwimmer, Bernhard, Radovic, Petar, Raeder, Benjamin, Raine, Keiran M, Ramakrishna, Manasa, Ramakrishnan, Kamna, Ramalingam, Suresh, Rathmell, W Kimryn, Rausch, Tobias, Reifenberger, Guido, Reis-Filho, Jorge, Reuter, Victor, Reynolds, Sheila M, Riazalhosseini, Yasser, Richardson, Andrea L, Richter, Julia, Ringel, Matthew, Ringnér, Markus, Rino, Yasushi, Rippe, Karsten, Roach, Jeffrey, Roberts, Lewis R, Roberts, Nicola D, Roberts, Steven A, Robertson, A Gordon, Robertson, Alan J, Rodriguez, Javier Bartolomé, Rodriguez-Martin, Bernardo, Rodríguez-González, F Germán, Roehrl, Michael HA, Rohde, Marius, Rokutan, Hirofumi, Romieu, Gilles, Rooman, Ilse, Roques, Tom, Rosebrock, Daniel, Rosenberg, Mara, Rosenstiel, Philip C, Rosenwald, Andreas, Rowe, Edward W, Royo, Romina, Rozen, Steven G, Rubanova, Yulia, Rudneva, Vasilisa A, Rusev, Borislav C, Ruzzenente, Andrea, Rätsch, Gunnar, Sabarinathan, Radhakrishnan, Sabelnykova, Veronica Y, Sadeghi, Sara, Saini, Natalie, Saito-Adachi, Mihoko, Salcedo, Adriana, Salgado, Roberto, Sallari, Richard, Saller, Charles, Salvia, Roberto, Sam, Michelle, Samra, Jaswinder S, Sanchez-Vega, Francisco, Sanders, Grant, Sarin, Rajiv, Sarrafi, Iman, Sasaki-Oku, Aya, Sauer, Torill, Sauter, Guido, Saw, Robyn PM, Scardoni, Maria, Scarlett, Christopher J, Scarpa, Aldo, Scelo, Ghislaine, Schadendorf, Dirk, Schein, Jacqueline E, Schilhabel, Markus B, Schlesner, Matthias, Schlomm, Thorsten, Schmidt, Heather K, Schramm, Sarah-Jane, Schreiber, Stefan, Schultz, Nikolaus, Schwarz, Roland F, Scolyer, Richard A, Scott, David, Scully, Ralph, Seethala, Raja, Segre, Ayellet V, Selander, Iris, Semple, Colin A, Senbabaoglu, Yasin, Sengupta, Subhajit, Sereni, Elisabetta, Serra, Stefano, Sgroi, Dennis C, Shah, Nimish C, Shahabi, Sagedeh, Shang, Catherine A, Shang, Ping, Shelton, Troy, Shen, Hui, Shepherd, Rebecca, Shi, Ruian, Shi, Yan, Shiah, Yu-Jia, Shibata, Tatsuhiro, Shih, Juliann, Shimizu, Eigo, Shimizu, Kiyo, Shin, Seung Jun, Shiraishi, Yuichi, Shmaya, Tal, Shmulevich, Ilya, Shorser, Solomon I, Short, Charles, Shringarpure, Suyash S, Shriver, Craig, Siebert, Reiner, Sieuwerts, Anieta M, Signoretti, Sabina, Sikora, Katarzyna O, Simbolo, Michele, Simon, Ronald, Simons, Janae V, Simpson, Jared T, Simpson, Peter T, Singer, Samuel, Sipahimalani, Payal, Skelly, Tara J, Smid, Marcel, Smith, Jaclyn, Smith-McCune, Karen, Socci, Nicholas D, Sofia, Heidi J, Soloway, Matthew G, Song, Lei, Sood, Anil K, Sothi, Sharmila, Sotiriou, Christos, Soulette, Cameron M, Span, Paul N, Spellman, Paul T, Sperandio, Nicola, Spillane, Andrew J, Spiro, Oliver, Spring, Jonathan, Staaf, Johan, Stadler, Peter F, Staib, Peter, Stark, Stefan G, Stebbings, Lucy, Stefánsson, Ólafur Andri, Stegle, Oliver, Stenhouse, Alasdair, Stewart, Chip, Stilgenbauer, Stephan, Stobbe, Miranda D, Stratton, Michael R, Stretch, Jonathan R, Struck, Adam J, Stunnenberg, Henk G, Su, Hong, Su, Xiaoping, Sun, Ren X, Sungalee, Stephanie, Susak, Hana, Suzuki, Akihiro, Sweep, Fred, Szczepanowski, Monika, Sültmann, Holger, Yugawa, Takashi, Tam, Angela, Tan, Benita Kiat Tee, Tan, Donghui, Tan, Patrick, Tanaka, Hiroko, Taniguchi, Hirokazu, Tanskanen, Tomas J, Tarabichi, Maxime, Tarnuzzer, Roy, Tarpey, Patrick, Taschuk, Morgan L, Tatsuno, Kenji, Tavaré, Simon, Taylor, Darrin F, Taylor-Weiner, Amaro, Teague, Jon W, Teh, Bin Tean, Tembe, Varsha, Temes, Javier, Thai, Kevin, Thayer, Sarah P, Thiessen, Nina, Thomas, Gilles, Thomas, Sarah, Thompson, Alan, Thompson, Alastair M, Thompson, John FF, Thompson, R Houston, Thorne, Heather, Thorne, Leigh B, Thorogood, Adrian, Tijanic, Nebojsa, Timms, Lee E, Tirabosco, Roberto, Tojo, Marta, Tommasi, Stefania, Toon, Christopher W, Toprak, Umut H, Torrents, David, Tortora, Giampaolo, Tost, Jörg, Totoki, Yasushi, Townend, David, Traficante, Nadia, Treilleux, Isabelle, Trotta, Jean-Rémi, Trümper, Lorenz HP, Tsao, Ming, MC Tubio, Jose, Tucker, Olga, Turkington, Richard, Turner, Daniel J, Tutt, Andrew, Ueno, Masaki, Ueno, Naoto T, Umbricht, Christopher, Underwood, Timothy J, Urban, Lara, Urushidate, Tomoko, Ushiku, Tetsuo, Van Den Berg, David J, Van Laere, Steven, Van Loo, Peter, Van Meir, Erwin G, Van den Eynden, Gert G, Van der Kwast, Theodorus, Vasudev, Naveen, Vedururu, Ravikiran, Veluvolu, Umadevi, Vembu, Shankar, Vermeulen, Peter, Verrill, Clare, Viari, Alain, Vicente, David, Vicentini, Caterina, VijayRaghavan, K, Viksna, Juris, Vilain, Ricardo E, Villasante, Izar, 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- Subjects
Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1373 genomic features derived from public sources, DriverPower’s background mutation model explains up to 93% of the regional variance in the mutation rate across multiple tumour types. By incorporating functional impact scores, we are able to further increase the accuracy of driver discovery. Testing across a collection of 2583 cancer genomes from the PCAWG project, DriverPower identifies 217 coding and 95 non-coding driver candidates. Comparing to six published methods used by the PCAWG Drivers and Functional Interpretation Working Group, DriverPower has the highest F1 score for both coding and non-coding driver discovery. This demonstrates that DriverPower is an effective framework for computational driver discovery.
- Published
- 2023
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28. Integrative pathway enrichment analysis of multivariate omics data
- Author
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Paczkowska, Marta, Barenboim, Jonathan, Sintupisut, Nardnisa, Fox, Natalie S, Zhu, Helen, Abd-Rabbo, Diala, Mee, Miles W, Boutros, Paul C, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Brunak, Søren, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Dhingra, Priyanka, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Getz, Gad, Gonzalez-Perez, Abel, Guo, Qianyun, Gut, Ivo G, Haan, David, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Izarzugaza, Jose MG, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kahraman, Abdullah, Kellis, Manolis, Khurana, Ekta, Kim, Jaegil, Kim, Jong K, Kim, 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Vijver, Marc J, and Veer, L van’t
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated genes with coding and non-coding mutations and revealed frequently mutated pathways and additional cancer genes with infrequent mutations. We also analyzed prognostic molecular pathways by integrating genomic and transcriptomic features of 1780 breast cancers and highlighted associations with immune response and anti-apoptotic signaling. Integration of ChIP-seq and RNA-seq data for master regulators of the Hippo pathway across normal human tissues identified processes of tissue regeneration and stem cell regulation. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations.
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- 2023
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29. Pathway and network analysis of more than 2500 whole cancer genomes
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding mutations across 2583 whole cancer genomes from 27 tumor types compiled by the ICGC/TCGA PCAWG project that was motivated by the success of pathway and network analyses in prioritizing rare mutations in protein-coding genes. While few non-coding genomic elements are recurrently mutated in this cohort, we identify 93 genes harboring non-coding mutations that cluster into several modules of interacting proteins. Among these are promoter mutations associated with reduced mRNA expression in TP53, TLE4, and TCF4. We find that biological processes had variable proportions of coding and non-coding mutations, with chromatin remodeling and proliferation pathways altered primarily by coding mutations, while developmental pathways, including Wnt and Notch, altered by both coding and non-coding mutations. RNA splicing is primarily altered by non-coding mutations in this cohort, and samples containing non-coding mutations in well-known RNA splicing factors exhibit similar gene expression signatures as samples with coding mutations in these genes. These analyses contribute a new repertoire of possible cancer genes and mechanisms that are altered by non-coding mutations and offer insights into additional cancer vulnerabilities that can be investigated for potential therapeutic treatments.
- Published
- 2023
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30. Divergent mutational processes distinguish hypoxic and normoxic tumours
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Many primary tumours have low levels of molecular oxygen (hypoxia), and hypoxic tumours respond poorly to therapy. Pan-cancer molecular hallmarks of tumour hypoxia remain poorly understood, with limited comprehension of its associations with specific mutational processes, non-coding driver genes and evolutionary features. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we quantify hypoxia in 1188 tumours spanning 27 cancer types. Elevated hypoxia associates with increased mutational load across cancer types, irrespective of underlying mutational class. The proportion of mutations attributed to several mutational signatures of unknown aetiology directly associates with the level of hypoxia, suggesting underlying mutational processes for these signatures. At the gene level, driver mutations in TP53, MYC and PTEN are enriched in hypoxic tumours, and mutations in PTEN interact with hypoxia to direct tumour evolutionary trajectories. Overall, hypoxia plays a critical role in shaping the genomic and evolutionary landscapes of cancer.
- Published
- 2023
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31. Genomic footprints of activated telomere maintenance mechanisms in cancer
- Author
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Sieverling, Lina, Hong, Chen, Koser, Sandra D, Ginsbach, Philip, Kleinheinz, Kortine, Hutter, Barbara, Braun, Delia M, Cortés-Ciriano, Isidro, Xi, Ruibin, Kabbe, Rolf, Park, Peter J, Eils, Roland, Schlesner, Matthias, Akdemir, Kadir C, Alvarez, Eva G, Baez-Ortega, Adrian, Beroukhim, Rameen, Boutros, Paul C, Bowtell, David DL, Brors, Benedikt, Burns, Kathleen H, Campbell, Peter J, Chan, Kin, Chen, Ken, Dueso-Barroso, Ana, Dunford, Andrew J, Edwards, Paul A, Estivill, Xavier, Etemadmoghadam, Dariush, Feuerbach, Lars, Fink, J Lynn, Frenkel-Morgenstern, Milana, Garsed, Dale W, Gerstein, Mark, Gordenin, Dmitry A, Haan, David, Haber, James E, Hess, Julian M, Imielinski, Marcin, Jones, David TW, Ju, Young Seok, Kazanov, Marat D, Klimczak, Leszek J, Koh, Youngil, Korbel, Jan O, Kumar, Kiran, Lee, Eunjung Alice, Lee, Jake June-Koo, Li, Yilong, Lynch, Andy G, Macintyre, Geoff, Markowetz, Florian, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Meyerson, Matthew, Miyano, Satoru, Nakagawa, 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Staaf, Johan, Stadler, Peter F, Staib, Peter, Stark, Stefan G, Stebbings, Lucy, Stefánsson, Ólafur Andri, Stegle, Oliver, Stein, Lincoln D, Stenhouse, Alasdair, Stilgenbauer, Stephan, Stobbe, Miranda D, Stratton, Michael R, Stretch, Jonathan R, Struck, Adam J, Stuart, Joshua M, Stunnenberg, Henk G, Su, Hong, Su, Xiaoping, Sun, Ren X, Sungalee, Stephanie, Susak, Hana, Suzuki, Akihiro, Sweep, Fred, Szczepanowski, Monika, Sültmann, Holger, Yugawa, Takashi, Tam, Angela, Tamborero, David, Tan, Benita Kiat Tee, Tan, Donghui, Tan, Patrick, Tanaka, Hiroko, Taniguchi, Hirokazu, Tanskanen, Tomas J, Tarabichi, Maxime, Tarnuzzer, Roy, Tarpey, Patrick, Taschuk, Morgan L, Tatsuno, Kenji, Tavaré, Simon, Taylor, Darrin F, Taylor-Weiner, Amaro, Teague, Jon W, Teh, Bin Tean, Tembe, Varsha, Temes, Javier, Thai, Kevin, Thayer, Sarah P, Thiessen, Nina, Thomas, Gilles, Thomas, Sarah, Thompson, Alan, Thompson, Alastair M, Thompson, John FF, Thompson, R Houston, Thorne, Heather, Thorne, Leigh B, Thorogood, Adrian, Tiao, Grace, Tijanic, Nebojsa, Timms, Lee E, Tirabosco, Roberto, Tojo, Marta, Tommasi, Stefania, Toon, Christopher W, Toprak, Umut H, Tortora, Giampaolo, Tost, Jörg, Totoki, Yasushi, Townend, David, Traficante, Nadia, Treilleux, Isabelle, Trotta, Jean-Rémi, Trümper, Lorenz HP, Tsao, Ming, Tsunoda, Tatsuhiko, Tucker, Olga, Turkington, Richard, Turner, Daniel J, Tutt, Andrew, Ueno, Masaki, Ueno, Naoto T, Umbricht, Christopher, Umer, Husen M, Underwood, Timothy J, Urban, Lara, Urushidate, Tomoko, Ushiku, Tetsuo, Uusküla-Reimand, Liis, Valencia, Alfonso, Van Den Berg, David J, Van Laere, Steven, Van Loo, Peter, Van Meir, Erwin G, Van den Eynden, Gert G, Van der Kwast, Theodorus, Vasudev, Naveen, Vazquez, Miguel, Vedururu, Ravikiran, Veluvolu, Umadevi, Vembu, Shankar, Verbeke, Lieven PC, Vermeulen, Peter, Verrill, Clare, Viari, Alain, Vicente, David, Vicentini, Caterina, VijayRaghavan, K, Viksna, Juris, Vilain, Ricardo E, Vincent-Salomon, Anne, Visakorpi, Tapio, Voet, Douglas, Vyas, Paresh, Vázquez-García, Ignacio, Waddell, Nick M, Wadelius, Claes, Wadi, Lina, Wagener, Rabea, Wang, Jian, Wang, Jiayin, Wang, Linghua, Wang, Qi, Wang, Wenyi, Wang, Yumeng, Wang, Zhining, Waring, Paul M, Warnatz, Hans-Jörg, Warrell, Jonathan, Warren, Anne Y, Waszak, Sebastian M, Wedge, David C, Weichenhan, Dieter, Weinberger, Paul, Weinstein, John N, Weisenberger, Daniel J, Welch, Ian, Wendl, Michael C, Werner, Johannes, Whalley, Justin P, Wheeler, David A, Whitaker, Hayley C, Wigle, Dennis, Wilkerson, Matthew D, Williams, Ashley, Wilmott, James S, Wilson, Gavin W, Wilson, Julie M, Wilson, Richard K, Winterhoff, Boris, Wintersinger, Jeffrey A, Wiznerowicz, Maciej, Wolf, Stephan, Wong, Bernice H, Wong, Tina, Wong, Winghing, Woo, Youngchoon, Wood, Scott, Wouters, Bradly G, Wright, Adam J, Wright, Derek W, Wright, Mark H, Wu, Chin-Lee, Wu, Dai-Ying, Wu, Guanming, Wu, Jianmin, Wu, Kui, Wu, Yang, Wu, Zhenggang, Xi, Liu, Xia, Tian, Xiang, Qian, Xiao, Xiao, Xing, Rui, Xiong, Heng, Xu, Qinying, Xu, Yanxun, Xue, Hong, Yachida, Shinichi, Yakneen, Sergei, Yamaguchi, Rui, Yamaguchi, Takafumi N, Yamamoto, Masakazu, Yamamoto, Shogo, Yamaue, Hiroki, Yang, Fan, Yang, Huanming, Yang, Jean Y, Yang, Liming, Yang, Shanlin, Yang, Tsun-Po, Yang, Yang, Yaspo, Marie-Laure, Yates, Lucy, Yau, Christina, Ye, Chen, Ye, Kai, Yellapantula, Venkata D, Yoon, Christopher J, Yousif, Fouad, Yu, Jun, Yu, Kaixian, Yu, Willie, Yu, Yingyan, Yuan, Ke, Yuan, Yuan, Yuen, Denis, Yung, Christina K, Zaikova, Olga, Zapatka, Marc, Zenklusen, Jean C, Zenz, Thorsten, Zeps, Nikolajs, Zhang, Fan, Zhang, Hailei, Zhang, Hongwei, Zhang, Hongxin, Zhang, Jiashan, Zhang, Jing, Zhang, Junjun, Zhang, Xiuqing, Zhang, Xuanping, Zhang, Yan, Zhang, Zemin, Zhao, Zhongming, Zheng, Liangtao, Zheng, Xiuqing, Zhou, Wanding, Zhou, Yong, Zhu, Bin, Zhu, Hongtu, Zhu, Jingchun, Zhu, Shida, Zou, Lihua, Zou, Xueqing, deFazio, Anna, van As, Nicholas, van Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian
- Subjects
Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the telomere content of tumors with ATRX or DAXX mutations (ATRX/DAXXtrunc) is increased, tumors with TERT modifications show a moderate decrease of telomere content. One quarter of all tumor samples contain somatic integrations of telomeric sequences into non-telomeric DNA. This fraction is increased to 80% prevalence in ATRX/DAXXtrunc tumors, which carry an aberrant telomere variant repeat (TVR) distribution as another genomic marker. The latter feature includes enrichment or depletion of the previously undescribed singleton TVRs TTCGGG and TTTGGG, respectively. Our systematic analysis provides new insight into the recurrent genomic alterations associated with telomere maintenance mechanisms in cancer.
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- 2023
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32. Racial Differences in PAM50 Subtypes in the Carolina Breast Cancer Study
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Troester, Melissa A., Sun, Xuezheng, Allott, Emma H., Geradts, Joseph, Cohen, Stephanie M., Tse, Chiu-Kit, Kirk, Erin L., Thorne, Leigh B., Mathews, Michelle, Li, Yan, Hu, Zhiyuan, Robinson, Whitney R., Hoadley, Katherine A., Olopade, Olufunmilayo I., Reeder-Hayes, Katherine E., Earp, H. Shelton, Olshan, Andrew F., Carey, Lisa A., and Perou, Charles M.
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- 2018
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33. Prevalence and Mechanisms of Mucus Accumulation in COVID-19 Lung Disease
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Kato, Takafumi, primary, Asakura, Takanori, additional, Edwards, Caitlin E., additional, Dang, Hong, additional, Mikami, Yu, additional, Okuda, Kenichi, additional, Chen, Gang, additional, Sun, Ling, additional, Gilmore, Rodney C., additional, Hawkins, Padraig, additional, De la Cruz, Gabriela, additional, Cooley, Michelle R., additional, Bailey, Alexis B., additional, Hewitt, Stephen M., additional, Chertow, Daniel S., additional, Borczuk, Alain C., additional, Salvatore, Steven, additional, Martinez, Fernando J., additional, Thorne, Leigh B., additional, Askin, Frederic B., additional, Ehre, Camille, additional, Randell, Scott H., additional, O’Neal, Wanda K., additional, Baric, Ralph S., additional, and Boucher, Richard C., additional
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- 2022
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34. Alterations of LKB1 and KRAS and risk of brain metastasis: Comprehensive characterization by mutation analysis, copy number, and gene expression in non-small-cell lung carcinoma
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Zhao, Ni, Wilkerson, Matthew D., Shah, Usman, Yin, Xiaoying, Wang, Anyou, Hayward, Michele C., Roberts, Patrick, Lee, Carrie B., Parsons, Alden M., Thorne, Leigh B., Haithcock, Benjamin E., Grilley-Olson, Juneko E., Stinchcombe, Thomas E., Funkhouser, William K., Wong, Kwok-Kin, Sharpless, Norman E., and Hayes, D. Neil
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- 2014
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35. Integrated Genomic Characterization of Papillary Thyroid Carcinoma
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Agrawal, Nishant, Akbani, Rehan, Aksoy, B. Arman, Ally, Adrian, Arachchi, Harindra, Asa, Sylvia L., Auman, J. Todd, Balasundaram, Miruna, Balu, Saianand, Baylin, Stephen B., Behera, Madhusmita, Bernard, Brady, Beroukhim, Rameen, Bishop, Justin A., Black, Aaron D., Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Bowen, Jay, Bowlby, Reanne, Bristow, Christopher A., Brookens, Robin, Brooks, Denise, Bryant, Robert, Buda, Elizabeth, Butterfield, Yaron S.N., Carling, Tobias, Carlsen, Rebecca, Carter, Scott L., Carty, Sally E., Chan, Timothy A., Chen, Amy Y., Cherniack, Andrew D., Cheung, Dorothy, Chin, Lynda, Cho, Juok, Chu, Andy, Chuah, Eric, Cibulskis, Kristian, Ciriello, Giovanni, Clarke, Amanda, Clayman, Gary L., Cope, Leslie, Copland, John A., Covington, Kyle, Danilova, Ludmila, Davidsen, Tanja, Demchok, John A., DiCara, Daniel, Dhalla, Noreen, Dhir, Rajiv, Dookran, Sheliann S., Dresdner, Gideon, Eldridge, Jonathan, Eley, Greg, El-Naggar, Adel K., Eng, Stephanie, Fagin, James A., Fennell, Timothy, Ferris, Robert L., Fisher, Sheila, Frazer, Scott, Frick, Jessica, Gabriel, Stacey B., Ganly, Ian, Gao, Jianjiong, Garraway, Levi A., Gastier-Foster, Julie M., Getz, Gad, Gehlenborg, Nils, Ghossein, Ronald, Gibbs, Richard A., Giordano, Thomas J., Gomez-Hernandez, Karen, Grimsby, Jonna, Gross, Benjamin, Guin, Ranabir, Hadjipanayis, Angela, Harper, Hollie A., Hayes, D. Neil, Heiman, David I., Herman, James G., Hoadley, Katherine A., Hofree, Matan, Holt, Robert A., Hoyle, Alan P., Huang, Franklin W., Huang, Mei, Hutter, Carolyn M., Ideker, Trey, Iype, Lisa, Jacobsen, Anders, Jefferys, Stuart R., Jones, Corbin D., Jones, Steven J.M., Kasaian, Katayoon, Kebebew, Electron, Khuri, Fadlo R., Kim, Jaegil, Kramer, Roger, Kreisberg, Richard, Kucherlapati, Raju, Kwiatkowski, David J., Ladanyi, Marc, Lai, Phillip H., Laird, Peter W., Lander, Eric, Lawrence, Michael S., Lee, Darlene, Lee, Eunjung, Lee, Semin, Lee, William, Leraas, Kristen M., Lichtenberg, Tara M., Lichtenstein, Lee, Lin, Pei, Ling, Shiyun, Liu, Jinze, Liu, Wenbin, Liu, Yingchun, LiVolsi, Virginia A., Lu, Yiling, Ma, Yussanne, Mahadeshwar, Harshad S., Marra, Marco A., Mayo, Michael, McFadden, David G., Meng, Shaowu, Meyerson, Matthew, Mieczkowski, Piotr A., Miller, Michael, Mills, Gordon, Moore, Richard A., Mose, Lisle E., Mungall, Andrew J., Murray, Bradley A., Nikiforov, Yuri E., Noble, Michael S., Ojesina, Akinyemi I., Owonikoko, Taofeek K., Ozenberger, Bradley A., Pantazi, Angeliki, Parfenov, Michael, Park, Peter J., Parker, Joel S., Paull, Evan O., Pedamallu, Chandra Sekhar, Perou, Charles M., Prins, Jan F., Protopopov, Alexei, Ramalingam, Suresh S., Ramirez, Nilsa C., Ramirez, Ricardo, Raphael, Benjamin J., Rathmell, W. Kimryn, Ren, Xiaojia, Reynolds, Sheila M., Rheinbay, Esther, Ringel, Matthew D., Rivera, Michael, Roach, Jeffrey, Robertson, A. Gordon, Rosenberg, Mara W., Rosenthal, Matthew, Sadeghi, Sara, Saksena, Gordon, Sander, Chris, Santoso, Netty, Schein, Jacqueline E., Schultz, Nikolaus, Schumacher, Steven E., Seethala, Raja R., Seidman, Jonathan, Senbabaoglu, Yasin, Seth, Sahil, Sharpe, Samantha, Shaw, Kenna R. Mills, Shen, John P., Shen, Ronglai, Sherman, Steven, Sheth, Margi, Shi, Yan, Shmulevich, Ilya, Sica, Gabriel L., Simons, Janae V., Sinha, Rileen, Sipahimalani, Payal, Smallridge, Robert C., Sofia, Heidi J., Soloway, Matthew G., Song, Xingzhi, Sougnez, Carrie, Stewart, Chip, Stojanov, Petar, Stuart, Joshua M., Sumer, S. Onur, Sun, Yichao, Tabak, Barbara, Tam, Angela, Tan, Donghui, Tang, Jiabin, Tarnuzzer, Roy, Taylor, Barry S., Thiessen, Nina, Thorne, Leigh, Thorsson, Vésteinn, Tuttle, R. Michael, Umbricht, Christopher B., Van Den Berg, David J., Vandin, Fabio, Veluvolu, Umadevi, Verhaak, Roel G.W., Vinco, Michelle, Voet, Doug, Walter, Vonn, Wang, Zhining, Waring, Scot, Weinberger, Paul M., Weinhold, Nils, Weinstein, John N., Weisenberger, Daniel J., Wheeler, David, Wilkerson, Matthew D., Wilson, Jocelyn, Williams, Michelle, Winer, Daniel A., Wise, Lisa, Wu, Junyuan, Xi, Liu, Xu, Andrew W., Yang, Liming, Yang, Lixing, Zack, Travis I., Zeiger, Martha A., Zeng, Dong, Zenklusen, Jean Claude, Zhao, Ni, Zhang, Hailei, Zhang, Jianhua, Zhang, Jiashan (Julia), Zhang, Wei, Zmuda, Erik, and Zou, Lihua
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- 2014
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36. The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma
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Creighton, Chad J., Davis, Caleb F., Morgan, Margaret, Gunaratne, Preethi H., Donehower, Lawrence A., Kaipparettu, Benny A., Wheeler, David A., Gibbs, Richard A., Signoretti, Sabina, Cherniack, Andrew D., Robertson, A. Gordon, Chu, Andy, Choueiri, Toni K., Henske, Elizabeth P., Kwiatkowski, David J., Reuter, Victor, Hsieh, James J., Hakimi, A. Ari, Tickoo, Satish K., Ricketts, Christopher, Linehan, W. Marston, Schmidt, Laura S., Gordenin, Dmitry A., Bhanot, Gyan, Seiler, Michael, Tamboli, Pheroze, Rathmell, W. Kimryn, Fahey, Catherine C., Hacker, Kathryn E., Smith, Angela B., Wallen, Eric M., Shen, Hui, Laird, Peter W., Shuch, Brian, Muzny, Donna, Buhay, Christian, Wang, Min, Chao, Hsu, Dahdouli, Mike, Xi, Liu, Kakkar, Nipun, Reid, Jeffrey G., Downs, Brittany, Drummond, Jennifer, Morton, Donna, Doddapaneni, Harsha, Lewis, Lora, English, Adam, Meng, Qingchang, Kovar, Christie, Wang, Qiaoyan, Hale, Walker, Hawes, Alicia, Kalra, Divya, Walker, Kimberly, Murray, Bradley A., Sougnez, Carrie, Saksena, Gordon, Carter, Scott L., Schumacher, Steven E., Tabak, Barbara, Zack, Travis I., Getz, Gad, Beroukhim, Rameen, Gabriel, Stacey B., Meyerson, Matthew, Ally, Adrian, Balasundaram, Miruna, Birol, Inanc, Brooks, Denise, Butterfield, Yaron S.N., Chuah, Eric, Clarke, Amanda, Dhalla, Noreen, Guin, Ranabir, Holt, Robert A., Kasaian, Katayoon, Lee, Darlene, Li, Haiyan I., Lim, Emilia, Ma, Yussanne, Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Wong, Tina, Jones, Steven J.M., Marra, Marco A., Auman, J. Todd, Tan, Donghui, Meng, Shaowu, Jones, Corbin D., Hoadley, Katherine A., Mieczkowski, Piotr A., Mose, Lisle E., Jefferys, Stuart R., Roach, Jeffrey, Veluvolu, Umadevi, Wilkerson, Matthew D., Waring, Scot, Buda, Elizabeth, Wu, Junyuan, Bodenheimer, Tom, Hoyle, Alan P., Simons, Janae V., Soloway, Mathew G., Balu, Saianand, Parker, Joel S., Hayes, D. Neil, Perou, Charles M., Weisenberger, Daniel J., Bootwalla, Moiz S., Triche, Timothy, Jr., Lai, Phillip H., Van Den Berg, David J., Baylin, Stephen B., Chen, Fengju, Coarfa, Cristian, Noble, Michael S., DiCara, Daniel, Zhang, Hailei, Cho, Juok, Heiman, David I., Gehlenborg, Nils, Voet, Doug, Lin, Pei, Frazer, Scott, Stojanov, Petar, Liu, Yingchun, Zou, Lihua, Kim, Jaegil, Lawrence, Michael S., Chin, Lynda, Yang, Lixing, Seth, Sahil, Bristow, Christopher A., Protopopov, Alexei, Song, Xingzhi, Zhang, Jianhua, Pantazi, Angeliki, Hadjipanayis, Angela, Lee, Eunjung, Luquette, Lovelace J., Lee, Semin, Parfenov, Michael, Santoso, Netty, Seidman, Jonathan, Xu, Andrew W., Kucherlapati, Raju, Park, Peter J., Kang, Hyojin, Lee, Junehawk, Roberts, Steven A., Klimczak, Leszek J., Fargo, David, Lang, Martin, Choi, Yoon-La, Kim, Sang Cheol, Lee, June-Koo, Park, Woong-Yang, Wang, Wenyi, Fan, Yu, Ahn, Jaeil, Akbani, Rehan, Weinstein, John N., Haussler, David, Ma, Singer, Radenbaugh, Amie, Zhul, Jingchun, Biehl, Michael, Lichtenberg, Tara M., Zmuda, Erik, Black, Aaron D., Hanf, Benjamin, Ramirez, Nilsa C., Wise, Lisa, Bowen, Jay, Leraas, Kristen M., Hall, Tracy M., Gastier-Foster, Julie M., Kaelin, William G., Thorne, Leigh, Boice, Lori, Huang, Mei, Vocke, Cathy, Peterson, James, Worrell, Robert, Merino, Maria, Czerniak, Bogdan A., Aldape, Kenneth D., Wood, Christopher G., Spellman, Paul T., Atkins, Michael B., Cheville, John, Thompson, R. Houston, Jensen, Mark A., Pihl, Todd, Wan, Yunhu, Ayala, Brenda, Baboud, Julien, Velaga, Sudhakar, Walton, Jessica, Liu, Jia, Chudamani, Sudha, Wu, Ye, Sheth, Margi, Mills Shaw, Kenna R., Demchok, John A., Davidsen, Tanja, Yang, Liming, Wang, Zhining, Tarnuzzer, Roy W., Zhang, Jiashan, Eley, Greg, Felau, Ina, Zenklusen, Jean Claude, Hutter, Carolyn M., Guyer, Mark S., Ozenberger, Bradley A., Sofia, Heidi J., and Ricketts, Christopher J.
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- 2014
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37. Assessment of vector competence of UK mosquitoes for Usutu virus of African origin
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Hernández-Triana, Luis M., de Marco, Maria Fernández, Mansfield, Karen L., Thorne, Leigh, Lumley, Sarah, Marston, Denise, Fooks, Anthony A., and Johnson, Nick
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- 2018
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38. Generalized Modules for Membrane Antigens (GMMA), an outer membrane vesicle‐based vaccine platform, for efficient viral antigen delivery
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Hu, Kai, primary, Palmieri, Elena, additional, Samnuan, Karnyart, additional, Ricchetti, Beatrice, additional, Oldrini, Davide, additional, McKay, Paul F., additional, Wu, Guanghui, additional, Thorne, Leigh, additional, Fooks, Anthony R., additional, McElhinney, Lorraine M., additional, Goharriz, Hooman, additional, Golding, Megan, additional, Shattock, Robin J., additional, and Micoli, Francesca, additional
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- 2022
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39. SARS-CoV-2 infection produces chronic pulmonary epithelial and immune cell dysfunction with fibrosis in mice
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Dinnon, Kenneth H., primary, Leist, Sarah R., additional, Okuda, Kenichi, additional, Dang, Hong, additional, Fritch, Ethan J., additional, Gully, Kendra L., additional, De la Cruz, Gabriela, additional, Evangelista, Mia D., additional, Asakura, Takanori, additional, Gilmore, Rodney C., additional, Hawkins, Padraig, additional, Nakano, Satoko, additional, West, Ande, additional, Schäfer, Alexandra, additional, Gralinski, Lisa E., additional, Everman, Jamie L., additional, Sajuthi, Satria P., additional, Zweigart, Mark R., additional, Dong, Stephanie, additional, McBride, Jennifer, additional, Cooley, Michelle R., additional, Hines, Jesse B., additional, Love, Miriya K., additional, Groshong, Steve D., additional, VanSchoiack, Alison, additional, Phelan, Stefan J., additional, Liang, Yan, additional, Hether, Tyler, additional, Leon, Michael, additional, Zumwalt, Ross E., additional, Barton, Lisa M., additional, Duval, Eric J., additional, Mukhopadhyay, Sanjay, additional, Stroberg, Edana, additional, Borczuk, Alain, additional, Thorne, Leigh B., additional, Sakthivel, Muthu K., additional, Lee, Yueh Z., additional, Hagood, James S., additional, Mock, Jason R., additional, Seibold, Max A., additional, O’Neal, Wanda K., additional, Montgomery, Stephanie A., additional, Boucher, Richard C., additional, and Baric, Ralph S., additional
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- 2022
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40. Prediction of Lung Cancer Histological Types by RT-qPCR Gene Expression in FFPE Specimens
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Wilkerson, Matthew D., Schallheim, Jason M., Hayes, D. Neil, Roberts, Patrick J., Bastien, Roy R.L., Mullins, Michael, Yin, Xiaoying, Miller, C. Ryan, Thorne, Leigh B., Geiersbach, Katherine B., Muldrew, Kenneth L., Funkhouser, William K., Fan, Cheng, Hayward, Michele C., Bayer, Steven, Perou, Charles M., and Bernard, Philip S.
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- 2013
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41. PPARγ coactivator-1α contributes to exercise-induced regulation of intramuscular lipid droplet programming in mice and humans
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Koves, Timothy R., Sparks, Lauren M., Kovalik, J.P., Mosedale, Merrie, Arumugam, Ramamani, DeBalsi, Karen L., Everingham, Karen, Thorne, Leigh, Phielix, Esther, Meex, Ruth C., Kien, C. Lawrence, Hesselink, Matthijs K.C., Schrauwen, Patrick, and Muoio, Deborah M.
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- 2013
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42. Prions Are Secreted into the Oral Cavity in Sheep with Preclinical Scrapie
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Maddison, Ben C., Rees, Helen C., Baker, Claire A., Taema, Maged, Bellworthy, Susan J., Thorne, Leigh, Terry, Linda A., and Gough, Kevin C.
- Published
- 2010
43. Supplement to: Comprehensive, integrative genomic analysis of diffuse lower-grade gliomas.
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Brat, Daniel J, Verhaak, Roel GW, Salama, Sofie R., Cooper, Lee, Aldape, Kenneth D, Yung, Alfred W.K, Akbani, Rehan, Barnholtz-Sloan, Jill S., Berger, Mitchel S., Brennan, Cameron, Bristow, Christopher A., Cherniack, Andrew D., Ciriello, Giovanni, Colen, Rivka, Colman, Howard, Flanders, Adam E., Giannini, Caterina, Grifford, Mia, Huse, Jason T., Iavarone, Antonio, Jain, Rajan, Joseph, Isaac, Kim, Jaegil, Kasaian, Katayoon, Laird, Peter W., Mikkelsen, Tom, Miller, Ryan C., Morozova, Olena, Murray, Bradley A., Noushmehr, Houtan, OʼNeill, Brian Patrick, Pachter, Lior, Parsons, Donald W., Poisson, Laila M., Rheinbay, Esther, Robertson, Gordon A., Sougnez, Carrie, Sulman, Erik P., Vandenberg, Scott R., Van Meir, Erwin G., Vitucci, Mark, Deimling, Andreas von, Yoshihara, Kosuke, Zhang, Hailei, Zheng, Siyuan, Crain, Daniel, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Troy, Sherman, Mark, Yena, Peggy, Black, Aaron, Bowen, Jay, Dicostanzo, Katie, Gastier-Foster, Julie, Leraas, Kristen M., Lichtenberg, Tara M., Pierson, Christopher R., Ramirez, Nilsa C., Taylor, Cynthia, Weaver, Stephanie, Wise, Lisa, Zmuda, Erik, Davidsen, Tanja, Demchok, John A., Eley, Greg, Ferguson, Martin L., Hutter, Carolyn M., Mills Shaw, Kenna R., Ozenberger, Bradley A., Sheth, Margi, Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean Claude, Ayala, Brenda, Baboud, Julien, Chudamani, Sudha, Jensen, Mark A., Liu, Jia, Pihl, Todd, Raman, Rohini, Wan, Yunhu, Wu, Ye, Ally, Adrian, Auman, Todd J., Balasundaram, Miruna, Balu, Saianand, Baylin, Stephen B., Beroukhim, Rameen, Bootwalla, Moiz S., Bowlby, Reanne, Brooks, Denise, Butterfield, Yaron, Carlsen, Rebecca, Carter, Scott, Chin, Lynda, Chu, Andy, Chuah, Eric, Cibulskis, Kristian, Clarke, Amanda, Coetzee, Simon G., Dhalla, Noreen, Fennell, Tim, Fisher, Sheila, Gabriel, Stacey, Getz, Gad, Gibbs, Richard, Grimsby, Jonna L., Guin, Ranabir, Hadjipanayis, Angela, Hayes, Neil D., Hinoue, Toshinori, Hoadley, Katherine, Holt, Robert A., Hoyle, Alan P., Huang, Franklin, Jefferys, Stuart R., Jones, Steven, Jones, Corbin D., Kucherlapati, Raju, Lai, Phillip H., Lander, Eric, Lee, Semin, Lichtenstein, Lee, Ma, Yussanne, Maglinte, Dennis T., Mahadeshwar, Harshad S., Marra, Marco A., Mayo, Michael, Meng, Shaowu, Meyerson, Matthew L., Mieczkowski, Piotr A., Moore, Richard A., Mose, Lisle E., Mungall, Andrew J., Pantazi, Angeliki, Parfenov, Michael, Park, Peter J., Parker, Joel S., Perou, Charles M., Protopopov, Alexei, Ren, Xiaojia, Roach, Jeffrey, Rosenberg, Mara, Sabedot, Thaís S., Sadeghi, Sara, Schein, Jacqueline, Schumacher, Steven E., Seidman, Jonathan G., Seth, Sahil, Shen, Hui, Simons, Janae V., Sipahimalani, Payal, Soloway, Matthew G., Song, Xingzhi, Stewart, Chip, Sun, Huandong, Tabak, Barbara, Tam, Angela, Tan, Donghui, Tang, Jiabin, Thiessen, Nina, Triche, Timothy, Jr., Van Den Berg, David J., Veluvolu, Umadevi, Waring, Scot, Weisenberger, Daniel J., Wilkerson, Matthew D., Wong, Tina, Wu, Junyuan, Xi, Liu, Xu, Andrew W., Yang, Lixing, Zack, Travis I., Zhang, Jianhua, Aksoy, Arman B., Arachchi, Harindra, Benz, Chris, Bernard, Brady, Carlin, Daniel, Cho, Juok, DiCara, Daniel, Frazer, Scott, Fuller, Gregory N., Gao, JianJiong, Gehlenborg, Nils, Haussler, David, Heiman, David I., Iype, Lisa, Jacobsen, Anders, Ju, Zhenlin, Katzman, Sol, Kim, Hoon, Knijnenburg, Theo, Kreisberg, Richard Bailey, Lawrence, Michael S., Lee, William, Leinonen, Kalle, Lin, Pei, Ling, Shiyun, Liu, Wenbin, Liu, Yingchun, Liu, Yuexin, Lu, Yiling, Mills, Gordon, Ng, Sam, Noble, Michael S., Paull, Evan, Radenbaugh, Amie J., Rao, Arvind, Reynolds, Sheila, Saksena, Gordon, Sanborn, Zack, Sander, Chris, Schultz, Nikolaus, Senbabaoglu, Yasin, Shen, Ronglai, Shmulevich, Ilya, Sinha, Rileen, Stuart, Josh, Sumer, Onur S., Sun, Yichao, Tasman, Natalie, Taylor, Barry S., Voet, Doug, Weinhold, Nils, Weinstein, John N., Yang, Da, Zhang, Wei, Zou, Lihua, Abel, Ty, Brat, Daniel J., Cohen, Mark L., Eschbacher, Jenny, Hattab, Eyas M., Raghunathan, Aditya, Schniederjan, Matthew J., Aziz, Dina, Barnett, Gene, Barrett, Wendi, Bigner, Darell D., Boice, Lori, Brewer, Cathy, Calatozzolo, Chiara, Carlotti, Carlos Gilberto, Jr, Chan, Timothy A., Cuppini, Lucia, Curley, Erin, Cuzzubbo, Stefania, Devine, Karen, DiMeco, Francesco, Duell, Rebecca, Elder, Bradley J, Fehrenbach, Ashley, Finocchiaro, Gaetano, Friedman, William, Fulop, Jordonna, Gardner, Johanna, Hermes, Beth, Kendler, Ady, Lehman, Norman L., Lipp, Eric, Liu, Ouida, Mandt, Randy, McGraw, Mary, McLendon, Roger, McPherson, Christopher, Neder, Luciano, Nguyen, Phuong, Noss, Ardene, Nunziata, Raffaele, Ostrom, Quinn T., Palmer, Cheryl, Perin, Alessandro, Pollo, Bianca, Potapov, Alexander, Potapova, Olga, Rathmell, Kimryn W., Rotin, Daniil, Scarpace, Lisa, Schilero, Cathy, Senecal, Kelly, Shimmel, Kristen, Shurkhay, Vsevolod, Sifri, Suzanne, Singh, Rosy, Sloan, Andrew E., Smolenski, Kathy, Staugaitis, Susan M., Steele, Ruth, Thorne, Leigh, Tirapelli, Daniela P.C., Vallurupalli, Mahitha, Wang, Yun, Warnick, Ronald, Williams, Felicia, Wolinsky, Yingli, Zhang, Jianan, Bell, Sue, Campos, Benito, Herold-Mende, Christel, Jungk, Christine, and Unterberg, Andreas
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- 2015
44. Prevalence and Mechanisms of Mucus Accumulation in COVID-19 Lung Disease
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Martinez, Fernando J., Edwards, Caitlin E, Chertow, Daniel S., Hawkins, Padraig, Chen, Gang, NIH COVID-19 Autopsy Consortium, Boucher, Richard C, Ehre, Camille, Gilmore, Rodney C, Dang, Hong, Okuda, Kenichi, Borczuk, Alain C, Mikami, Yu, Randell, Scott H, De la Cruz, Gabriela, Thorne, Leigh B, Sun, Ling, Cooley, Michelle R, Kato, Takafumi, Salvatore, Steven, Bailey, Alexis B, O'Neal, Wanda K, Baric, Ralph S., Askin, Frederic B, Asakura, Takanori, and Hewitt, Stephen M
- Abstract
Rationale: The incidence and sites of mucus accumulation, and molecular regulation of mucin gene expression, in COVID-19 lung disease have not been reported. Objectives: Characterize incidence of mucus accumulation and the mechanisms mediating mucin hypersecretion in COVID-19 lung disease. Methods: Airway mucus and mucins were evaluated in COVID-19 autopsy lungs by AB-PAS and immunohistochemical staining, RNA in situ hybridization, and spatial transcriptional profiling. SARS-CoV-2-infected human bronchial epithelial (HBE) cultures were utilized to investigate mechanisms of SARS-CoV-2-induced mucin expression and synthesis and test candidate countermeasures. Measurements and Main Results: MUC5B and variably MUC5AC RNA levels were increased throughout all airway regions of COVID-19 autopsy lungs, notably in the sub-acute/chronic disease phase following SARS-CoV-2 clearance. In the distal lung, MUC5B-dominated mucus plugging was observed in 90% of COVID-19 subjects in both morphologically identified bronchioles and microcysts, and MUC5B accumulated in damaged alveolar spaces. SARS-CoV-2-infected HBE cultures exhibited peak titers 3 days post inoculation, whereas induction of MUC5B/MUC5AC peaked 7-14 days post inoculation. SARS-CoV-2 infection of HBE cultures induced expression of EGFR ligands and inflammatory cytokines (e.g., IL-1α/β) associated with mucin gene regulation. Inhibiting EGFR/IL-1R pathways, or dexamethasone administration, reduced SARS-CoV-2-induced mucin expression. Conclusions: SARS-CoV-2 infection is associated with a high prevalence of distal airspace mucus accumulation and increased MUC5B expression in COVID-19 autopsy lungs. HBE culture studies identified roles for EGFR and IL-1R signaling in mucin gene regulation post SARS-CoV-2 infection. These data suggest that time-sensitive mucolytic agents, specific pathway inhibitors, or corticosteroid administration may be therapeutic for COVID-19 lung disease. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0 (http://creativecommons.org.libproxy.lib.unc.edu/licenses/by-nc-nd/4.0/).
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- 2022
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45. Amplification of thymidylate synthetase in metastatic colorectal cancer patients pretreated with 5-fluorouracil-based chemotherapy
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Watson, Roshawn G., Muhale, Filipe, Thorne, Leigh B., Yu, Jinsheng, O’Neil, Bert H., Hoskins, Janelle M., Meyers, Michael O., Deal, Allison M., Ibrahim, Joseph G., Hudson, Michael L., Walko, Christine M., McLeod, Howard L., and Auman, James T.
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- 2010
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46. A model of persistent post SARS-CoV-2 induced lung disease for target identification and testing of therapeutic strategies
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Dinnon, Kenneth H., primary, Leist, Sarah R., additional, Okuda, Kenichi, additional, Dang, Hong, additional, Fritch, Ethan J., additional, Gully, Kendra L., additional, De la Cruz, Gabriela, additional, Evangelista, Mia D., additional, Asakura, Takanori, additional, Gilmore, Rodney C., additional, Hawkins, Padraig, additional, Nakano, Satoko, additional, West, Ande, additional, Schäfer, Alexandra, additional, Gralinski, Lisa E., additional, Everman, Jamie L., additional, Sajuthi, Satria P., additional, Zweigart, Mark R., additional, Dong, Stephanie, additional, McBride, Jennifer, additional, Cooley, Michelle R., additional, Hines, Jesse B., additional, Love, Miriya K., additional, Groshong, Steve D., additional, VanSchoiack, Alison, additional, Phelan, Stefan J., additional, Liang, Yan, additional, Hether, Tyler, additional, Leon, Michael, additional, Zumwalt, Ross E., additional, Barton, Lisa M., additional, Duval, Eric J., additional, Mukhopadhyay, Sanjay, additional, Stroberg, Edana, additional, Borczuk, Alain, additional, Thorne, Leigh B., additional, Sakthivel, Muthu K., additional, Lee, Yueh Z., additional, Hagood, James S., additional, Mock, Jason R., additional, Seibold, Max A., additional, O’Neal, Wanda K., additional, Montgomery, Stephanie A., additional, Boucher, Richard C., additional, and Baric, Ralph S., additional
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- 2022
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47. Plastic bronchitis: Autopsy findings in the sudden death of a healthy pediatric patient with sickle cell disease
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Saunders, Katherine, primary, Garrett, Erin, additional, Crosby, Ashley, additional, Park, Yara, additional, Kasow, Kimberly, additional, Moylan, Vincent, additional, and Thorne, Leigh, additional
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- 2022
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48. Transmissible spongiform encephalopathy in goats: is PrP rapid test sensitivity affected by genotype?
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Simmons, Marion, Thorne, Leigh, Ortiz-Pelaez, Angel, Spiropoulos, John, Georgiadou, Soteria, Papasavva-Stylianou, Penelope, Andreoletti, Olivier, Hawkins, Stephen A.C., Hawkins, Stephen, Meloni, Daniela, Cassar, Claire, Animal and Plant Health Agency [Addlestone, UK] (APHA), European Food Safety Authority (EFSA), Veterinary Services of Cyprus, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, and This work was funded by the EC and Defra through the activities of the EURL for TSE at APHA. The UMR INRA ENVT 1225 was funded for this work by the EU FEDER/INTERREG (EFA148/16 REDPRION)
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goats ,Genotype ,Prions ,040301 veterinary sciences ,[SDV]Life Sciences [q-bio] ,animal diseases ,Population ,Scrapie ,Disease ,Prion Proteins ,Epitope ,PRNP ,0403 veterinary science ,03 medical and health sciences ,medicine ,Animals ,Full Scientific Reports ,education ,transmissible spongiform encephalopathy ,030304 developmental biology ,0303 health sciences ,education.field_of_study ,Goat Diseases ,Polymorphism, Genetic ,Transmissible spongiform encephalopathy ,General Veterinary ,biology ,scrapie ,04 agricultural and veterinary sciences ,medicine.disease ,Virology ,nervous system diseases ,prion protein ,biology.protein ,ELISA ,Antibody - Abstract
Transmissible spongiform encephalopathy (TSE) surveillance in goats relies on tests initially approved for cattle, subsequently assessed for sheep, and approval extrapolated for use in “small ruminants.” The current EU-approved immunodetection tests employ antibodies against various epitopes of the prion protein PrPSc, which is encoded by the host PRNP gene. The caprine PRNP gene is polymorphic, mostly at codons different from the ovine PRNP. The EU goat population is much more heterogeneous than the sheep population, with more PRNP-related polymorphisms, and with marked breed-related differences. The ability of the current tests to detect disease-specific PrPSc generated against these different genetic backgrounds is currently assumed, rather than proven. We examined whether common polymorphisms within the goat PRNP gene might have any adverse effect on the relative performance of EU-approved rapid tests. The sample panel comprised goats from the UK, Cyprus, France, and Italy, with either experimental or naturally acquired scrapie at both the preclinical and/or unknown and clinical stages of disease. Test sensitivity was significantly lower and more variable when compared using samples from animals that were preclinical or of unknown status. However, all of the rapid tests included in our study were able to correctly identify all samples from animals in the clinical stages of disease, apart from samples from animals polymorphic for serine or aspartic acid at codon 146, in which the performance of the Bio-Rad tests was profoundly affected. Our data show that some polymorphisms may adversely affect one test and not another, as well as underline the dangers of extrapolating from other species.
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- 2020
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49. High levels of Epstein–Barr virus DNA in latently infected gastric adenocarcinoma
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Ryan, Julie L, Morgan, Douglas R, Dominguez, Ricardo L, Thorne, Leigh B, Elmore, Sandra H, Mino-Kenudson, Mari, Lauwers, Gregory Y, Booker, Jessica K, and Gulley, Margaret L
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- 2009
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50. Epstein-Barr Virus Infection Is Common in Inflamed Gastrointestinal Mucosa
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Ryan, Julie L., Shen, You-Jun, Morgan, Douglas R., Thorne, Leigh B., Kenney, Shannon C., Dominguez, Ricardo L., and Gulley, Margaret L.
- Published
- 2012
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