28 results on '"Ma, Yussanne"'
Search Results
2. Whole genome and transcriptome integrated analyses guide clinical care of pediatric poor prognosis cancers.
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Deyell, Rebecca J., Shen, Yaoqing, Titmuss, Emma, Dixon, Katherine, Williamson, Laura M., Pleasance, Erin, Nelson, Jessica M. T., Abbasi, Sanna, Krzywinski, Martin, Armstrong, Linlea, Bonakdar, Melika, Ch'ng, Carolyn, Chuah, Eric, Dunham, Chris, Fok, Alexandra, Jones, Martin, Lee, Anna F., Ma, Yussanne, Moore, Richard A., and Mungall, Andrew J.
- Subjects
NUCLEOTIDE sequencing ,CLINICAL medicine ,CANCER prognosis ,PEDIATRIC therapy ,DNA copy number variations ,SOMATIC mutation - Abstract
The role for routine whole genome and transcriptome analysis (WGTA) for poor prognosis pediatric cancers remains undetermined. Here, we characterize somatic mutations, structural rearrangements, copy number variants, gene expression, immuno-profiles and germline cancer predisposition variants in children and adolescents with relapsed, refractory or poor prognosis malignancies who underwent somatic WGTA and matched germline sequencing. Seventy-nine participants with a median age at enrollment of 8.8 y (range 6 months to 21.2 y) are included. Germline pathogenic/likely pathogenic variants are identified in 12% of participants, of which 60% were not known prior. Therapeutically actionable variants are identified by targeted gene report and whole genome in 32% and 62% of participants, respectively, and increase to 96% after integrating transcriptome analyses. Thirty-two molecularly informed therapies are pursued in 28 participants with 54% achieving a clinical benefit rate; objective response or stable disease ≥6 months. Integrated WGTA identifies therapeutically actionable variants in almost all tumors and are directly translatable to clinical care of children with poor prognosis cancers. Efforts to allow routine whole genome and transcriptome analysis (WGTA) for pediatric cancers in the clinic remain critical. Here, the authors present results of a unified genomics and bioinformatics pipeline for WGTA in paediatric cancers, the Personalized OncoGenomics (POG) program, with a focus on potential therapeutic targets. [ABSTRACT FROM AUTHOR]
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- 2024
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3. Retraction Note: Tumor necrosis factor overcomes immune evasion in p53-mutant medulloblastoma
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Garancher, Alexandra, Suzuki, Hiromichi, Haricharan, Svasti, Chau, Lianne Q., Masihi, Meher Beigi, Rusert, Jessica M., Norris, Paula S., Carrette, Florent, Romero, Megan M., Morrissy, Sorana A., Skowron, Patryk, Cavalli, Florence M. G., Farooq, Hamza, Ramaswamy, Vijay, Jones, Steven J. M., Moore, Richard A., Mungall, Andrew J., Ma, Yussanne, Thiessen, Nina, Li, Yisu, Morcavallo, Alaide, Qi, Lin, Kogiso, Mari, Du, Yuchen, Baxter, Patricia, Henderson, Jacob J., Crawford, John R., Levy, Michael L., Olson, James M., Cho, Yoon-Jae, Deshpande, Aniruddha J., Li, Xiao-Nan, Chesler, Louis, Marra, Marco A., Wajant, Harald, Becher, Oren J., Bradley, Linda M., Ware, Carl F., Taylor, Michael D., and Wechsler-Reya, Robert J.
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- 2022
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4. Table S6 from Integrative Molecular Characterization of Malignant Pleural Mesothelioma
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Hmeljak, Julija, primary, Sanchez-Vega, Francisco, primary, Hoadley, Katherine A., primary, Shih, Juliann, primary, Stewart, Chip, primary, Heiman, David, primary, Tarpey, Patrick, primary, Danilova, Ludmila, primary, Drill, Esther, primary, Gibb, Ewan A., primary, Bowlby, Reanne, primary, Kanchi, Rupa, primary, Osmanbeyoglu, Hatice U., primary, Sekido, Yoshitaka, primary, Takeshita, Jumpei, primary, Newton, Yulia, primary, Graim, Kiley, primary, Gupta, Manaswi, primary, Gay, Carl M., primary, Diao, Lixia, primary, Gibbs, David L., primary, Thorsson, Vesteinn, primary, Iype, Lisa, primary, Kantheti, Havish, primary, Severson, David T., primary, Ravegnini, Gloria, primary, Desmeules, Patrice, primary, Jungbluth, Achim A., primary, Travis, William D., primary, Dacic, Sanja, primary, Chirieac, Lucian R., primary, Galateau-Sallé, Françoise, primary, Fujimoto, Junya, primary, Husain, Aliya N., primary, Silveira, Henrique C., primary, Rusch, Valerie W., primary, Rintoul, Robert C., primary, Pass, Harvey, primary, Kindler, Hedy, primary, Zauderer, Marjorie G., primary, Kwiatkowski, David J., primary, Bueno, Raphael, primary, Tsao, Anne S., primary, Creaney, Jenette, primary, Lichtenberg, Tara, primary, Leraas, Kristen, primary, Bowen, Jay, primary, Felau, Ina, primary, Zenklusen, Jean Claude, primary, Akbani, Rehan, primary, Cherniack, Andrew D., primary, Byers, Lauren A., primary, Noble, Michael S., primary, Fletcher, Jonathan A., primary, Robertson, A. Gordon, primary, Shen, Ronglai, primary, Aburatani, Hiroyuki, primary, Robinson, Bruce W., primary, Campbell, Peter, primary, Ladanyi, Marc, primary, Ally, Adrian, primary, Anur, Pavana, primary, Armenia, Joshua, primary, Auman, J. Todd, primary, Balasundaram, Miruna, primary, Balu, Saianand, primary, Baylin, Stephen B., primary, Becich, Michael, primary, Behrens, Carmen, primary, Beroukhim, Rameen, primary, Bielski, Craig, primary, Bodenheimer, Tom, primary, Bootwalla, Moiz S., primary, Brooks, Denise, primary, Byers, Lauren Averett, primary, Cárcano, Flávio M., primary, Carlsen, Rebecca, primary, Carvalho, Andre L., primary, Cheung, Dorothy, primary, Chirieac, Lucian, primary, Cho, Juok, primary, Chuah, Eric, primary, Chudamani, Sudha, primary, Cibulskis, Carrie, primary, Cope, Leslie, primary, Crain, Daniel, primary, Curley, Erin, primary, Rienzo, Assunta De, primary, DeFreitas, Timothy, primary, Demchok, John A., primary, Dhalla, Noreen, primary, Dhir, Rajiv, primary, Feldman, Michael, primary, Ferguson, Martin L., primary, Fukuda, Shiro, primary, Gabriel, Stacey B., primary, Sallé, Françoise Galateau, primary, Gao, Jianjiong, primary, Gardner, Johanna, primary, Gastier-Foster, Julie M., primary, Gehlenborg, Nils, primary, Gerken, Mark, primary, Getz, Gad, primary, Goparaju, Chandra, primary, Gross, Benjamin, primary, Guo, Guangwu, primary, Hasegawa, Seiki, primary, Haussler, David, primary, Hayes, D. Neil, primary, Heiman, David I., primary, Heins, Zachary, primary, Holt, Robert A., primary, Hoyle, Alan P., primary, Husain, Aliya, primary, Hutter, Carolyn M., primary, Jefferys, Stuart R., primary, Jones, Steven J.M., primary, Jones, Corbin D., primary, Kanchi, Rupa S., primary, Kasaian, Katayoon, primary, Kim, Jaegil, primary, Kondo, Nobuyuki, primary, Krausz, Thomas, primary, Kundra, Ritika, primary, Kuribayashi, Kozo, primary, Lai, Phillip H., primary, Laird, Peter W., primary, Lawrence, Michael S., primary, Lee, Darlene, primary, Leraas, Kristen M., primary, Lichtenberg, Tara M., primary, Lin, Pei, primary, Liu, Jia, primary, Liu, Wenbin, primary, Liu, Eric Minwei, primary, Lolla, Laxmi, primary, Longatto-Filho, Adhemar, primary, Lu, Yiling, primary, Luketich, James, primary, Ma, Yussanne, primary, Maglinte, Dennis T., primary, Mallory, David, primary, Marra, Marco A., primary, Mayo, Michael, primary, Meier, Sam, primary, Melamed, Jonathan, primary, Meng, Shaowu, primary, Meyerson, Matthew, primary, Mieczkowski, Piotr A., primary, Mills, Gordon B., primary, Moore, Richard A., primary, Moran, Cesar, primary, Morris, Scott, primary, Mose, Lisle E., primary, Mungall, Andrew J., primary, Mungall, Karen, primary, Nakano, Takashi, primary, Naresh, Rashi, primary, Ochoa, Angelica, primary, Osmanbeyoglu, Hatice, primary, Parker, Joel S., primary, Pass, Harvey I., primary, Paulauskis, Joseph, primary, Pennathur, Arjun, primary, Pennell, Nathan A., primary, Penny, Robert, primary, Perou, Charles M., primary, Pihl, Todd, primary, Ramirez, Nilsa C., primary, Rassl, Doris M., primary, Reid, Glen, primary, Reis, Rui M., primary, Reynolds, Sheila M., primary, Rice, David, primary, Richards, William G, primary, Roach, Jeffrey, primary, Rusch, Valerie, primary, Sadeghi, Sara, primary, Saksena, Gordon, primary, Sander, Chris, primary, Sato, Ayuko, primary, Scapulatempo-Neto, Cristovam, primary, Schein, Jacqueline E., primary, Schultz, Nikolaus, primary, Schumacher, Steven E., primary, Seiwert, Tanguy, primary, Severson, David T, primary, Shelton, Candace, primary, Shelton, Troy, primary, Sheridan, Robert, primary, Shi, Yan, primary, Shiraishi, Yuichi, primary, Shmulevich, Ilya, primary, Silveira, Henrique C. S., primary, Simons, Janae V., primary, Sipahimalani, Payal, primary, Skelly, Tara, primary, Sofia, Heidi J., primary, Soloway, Matthew G., primary, Spellman, Paul, primary, Stuart, Josh, primary, Sun, Qiang, primary, Tam, Angela, primary, Tan, Donghui, primary, Tarnuzzer, Roy, primary, Tatsuno, Kenji, primary, Taylor, Barry S, primary, Thiessen, Nina, primary, Thompson, Eric, primary, Tsao, Anne, primary, Tse, Kane, primary, Tsujimura, Tohru, primary, Valdivieso, Federico, primary, Van Den Berg, David J., primary, van Zandwijk, Nico, primary, Veluvolu, Umadevi, primary, Viana, Luciano S., primary, Voet, Douglas, primary, Wan, Yunhu, primary, Wang, Zhining, primary, Wang, Jing, primary, Weaver, Joellen, primary, Weinstein, John N., primary, Weisenberger, Daniel J., primary, Wilkerson, Matthew D., primary, Wise, Lisa, primary, Wistuba, Ignacio, primary, Wong, Tina, primary, Wu, Ye, primary, Yamamoto, Shogo, primary, Yang, Liming, primary, Zenklusen, Jean C., primary, Zhang, Jiashan, primary, Zhang, Hailei, primary, Zhang, Hongxin, primary, and Zmuda, Erik, primary
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- 2023
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5. Data from Integrative Molecular Characterization of Malignant Pleural Mesothelioma
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Hmeljak, Julija, primary, Sanchez-Vega, Francisco, primary, Hoadley, Katherine A., primary, Shih, Juliann, primary, Stewart, Chip, primary, Heiman, David, primary, Tarpey, Patrick, primary, Danilova, Ludmila, primary, Drill, Esther, primary, Gibb, Ewan A., primary, Bowlby, Reanne, primary, Kanchi, Rupa, primary, Osmanbeyoglu, Hatice U., primary, Sekido, Yoshitaka, primary, Takeshita, Jumpei, primary, Newton, Yulia, primary, Graim, Kiley, primary, Gupta, Manaswi, primary, Gay, Carl M., primary, Diao, Lixia, primary, Gibbs, David L., primary, Thorsson, Vesteinn, primary, Iype, Lisa, primary, Kantheti, Havish, primary, Severson, David T., primary, Ravegnini, Gloria, primary, Desmeules, Patrice, primary, Jungbluth, Achim A., primary, Travis, William D., primary, Dacic, Sanja, primary, Chirieac, Lucian R., primary, Galateau-Sallé, Françoise, primary, Fujimoto, Junya, primary, Husain, Aliya N., primary, Silveira, Henrique C., primary, Rusch, Valerie W., primary, Rintoul, Robert C., primary, Pass, Harvey, primary, Kindler, Hedy, primary, Zauderer, Marjorie G., primary, Kwiatkowski, David J., primary, Bueno, Raphael, primary, Tsao, Anne S., primary, Creaney, Jenette, primary, Lichtenberg, Tara, primary, Leraas, Kristen, primary, Bowen, Jay, primary, Felau, Ina, primary, Zenklusen, Jean Claude, primary, Akbani, Rehan, primary, Cherniack, Andrew D., primary, Byers, Lauren A., primary, Noble, Michael S., primary, Fletcher, Jonathan A., primary, Robertson, A. Gordon, primary, Shen, Ronglai, primary, Aburatani, Hiroyuki, primary, Robinson, Bruce W., primary, Campbell, Peter, primary, Ladanyi, Marc, primary, Ally, Adrian, primary, Anur, Pavana, primary, Armenia, Joshua, primary, Auman, J. Todd, primary, Balasundaram, Miruna, primary, Balu, Saianand, primary, Baylin, Stephen B., primary, Becich, Michael, primary, Behrens, Carmen, primary, Beroukhim, Rameen, primary, Bielski, Craig, primary, Bodenheimer, Tom, primary, Bootwalla, Moiz S., primary, Brooks, Denise, primary, Byers, Lauren Averett, primary, Cárcano, Flávio M., primary, Carlsen, Rebecca, primary, Carvalho, Andre L., primary, Cheung, Dorothy, primary, Chirieac, Lucian, primary, Cho, Juok, primary, Chuah, Eric, primary, Chudamani, Sudha, primary, Cibulskis, Carrie, primary, Cope, Leslie, primary, Crain, Daniel, primary, Curley, Erin, primary, Rienzo, Assunta De, primary, DeFreitas, Timothy, primary, Demchok, John A., primary, Dhalla, Noreen, primary, Dhir, Rajiv, primary, Feldman, Michael, primary, Ferguson, Martin L., primary, Fukuda, Shiro, primary, Gabriel, Stacey B., primary, Sallé, Françoise Galateau, primary, Gao, Jianjiong, primary, Gardner, Johanna, primary, Gastier-Foster, Julie M., primary, Gehlenborg, Nils, primary, Gerken, Mark, primary, Getz, Gad, primary, Goparaju, Chandra, primary, Gross, Benjamin, primary, Guo, Guangwu, primary, Hasegawa, Seiki, primary, Haussler, David, primary, Hayes, D. Neil, primary, Heiman, David I., primary, Heins, Zachary, primary, Holt, Robert A., primary, Hoyle, Alan P., primary, Husain, Aliya, primary, Hutter, Carolyn M., primary, Jefferys, Stuart R., primary, Jones, Steven J.M., primary, Jones, Corbin D., primary, Kanchi, Rupa S., primary, Kasaian, Katayoon, primary, Kim, Jaegil, primary, Kondo, Nobuyuki, primary, Krausz, Thomas, primary, Kundra, Ritika, primary, Kuribayashi, Kozo, primary, Lai, Phillip H., primary, Laird, Peter W., primary, Lawrence, Michael S., primary, Lee, Darlene, primary, Leraas, Kristen M., primary, Lichtenberg, Tara M., primary, Lin, Pei, primary, Liu, Jia, primary, Liu, Wenbin, primary, Liu, Eric Minwei, primary, Lolla, Laxmi, primary, Longatto-Filho, Adhemar, primary, Lu, Yiling, primary, Luketich, James, primary, Ma, Yussanne, primary, Maglinte, Dennis T., primary, Mallory, David, primary, Marra, Marco A., primary, Mayo, Michael, primary, Meier, Sam, primary, Melamed, Jonathan, primary, Meng, Shaowu, primary, Meyerson, Matthew, primary, Mieczkowski, Piotr A., primary, Mills, Gordon B., primary, Moore, Richard A., primary, Moran, Cesar, primary, Morris, Scott, primary, Mose, Lisle E., primary, Mungall, Andrew J., primary, Mungall, Karen, primary, Nakano, Takashi, primary, Naresh, Rashi, primary, Ochoa, Angelica, primary, Osmanbeyoglu, Hatice, primary, Parker, Joel S., primary, Pass, Harvey I., primary, Paulauskis, Joseph, primary, Pennathur, Arjun, primary, Pennell, Nathan A., primary, Penny, Robert, primary, Perou, Charles M., primary, Pihl, Todd, primary, Ramirez, Nilsa C., primary, Rassl, Doris M., primary, Reid, Glen, primary, Reis, Rui M., primary, Reynolds, Sheila M., primary, Rice, David, primary, Richards, William G, primary, Roach, Jeffrey, primary, Rusch, Valerie, primary, Sadeghi, Sara, primary, Saksena, Gordon, primary, Sander, Chris, primary, Sato, Ayuko, primary, Scapulatempo-Neto, Cristovam, primary, Schein, Jacqueline E., primary, Schultz, Nikolaus, primary, Schumacher, Steven E., primary, Seiwert, Tanguy, primary, Severson, David T, primary, Shelton, Candace, primary, Shelton, Troy, primary, Sheridan, Robert, primary, Shi, Yan, primary, Shiraishi, Yuichi, primary, Shmulevich, Ilya, primary, Silveira, Henrique C. S., primary, Simons, Janae V., primary, Sipahimalani, Payal, primary, Skelly, Tara, primary, Sofia, Heidi J., primary, Soloway, Matthew G., primary, Spellman, Paul, primary, Stuart, Josh, primary, Sun, Qiang, primary, Tam, Angela, primary, Tan, Donghui, primary, Tarnuzzer, Roy, primary, Tatsuno, Kenji, primary, Taylor, Barry S, primary, Thiessen, Nina, primary, Thompson, Eric, primary, Tsao, Anne, primary, Tse, Kane, primary, Tsujimura, Tohru, primary, Valdivieso, Federico, primary, Van Den Berg, David J., primary, van Zandwijk, Nico, primary, Veluvolu, Umadevi, primary, Viana, Luciano S., primary, Voet, Douglas, primary, Wan, Yunhu, primary, Wang, Zhining, primary, Wang, Jing, primary, Weaver, Joellen, primary, Weinstein, John N., primary, Weisenberger, Daniel J., primary, Wilkerson, Matthew D., primary, Wise, Lisa, primary, Wistuba, Ignacio, primary, Wong, Tina, primary, Wu, Ye, primary, Yamamoto, Shogo, primary, Yang, Liming, primary, Zenklusen, Jean C., primary, Zhang, Jiashan, primary, Zhang, Hailei, primary, Zhang, Hongxin, primary, and Zmuda, Erik, primary
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- 2023
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6. Supplementary Data from Integrative Molecular Characterization of Malignant Pleural Mesothelioma
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Hmeljak, Julija, primary, Sanchez-Vega, Francisco, primary, Hoadley, Katherine A., primary, Shih, Juliann, primary, Stewart, Chip, primary, Heiman, David, primary, Tarpey, Patrick, primary, Danilova, Ludmila, primary, Drill, Esther, primary, Gibb, Ewan A., primary, Bowlby, Reanne, primary, Kanchi, Rupa, primary, Osmanbeyoglu, Hatice U., primary, Sekido, Yoshitaka, primary, Takeshita, Jumpei, primary, Newton, Yulia, primary, Graim, Kiley, primary, Gupta, Manaswi, primary, Gay, Carl M., primary, Diao, Lixia, primary, Gibbs, David L., primary, Thorsson, Vesteinn, primary, Iype, Lisa, primary, Kantheti, Havish, primary, Severson, David T., primary, Ravegnini, Gloria, primary, Desmeules, Patrice, primary, Jungbluth, Achim A., primary, Travis, William D., primary, Dacic, Sanja, primary, Chirieac, Lucian R., primary, Galateau-Sallé, Françoise, primary, Fujimoto, Junya, primary, Husain, Aliya N., primary, Silveira, Henrique C., primary, Rusch, Valerie W., primary, Rintoul, Robert C., primary, Pass, Harvey, primary, Kindler, Hedy, primary, Zauderer, Marjorie G., primary, Kwiatkowski, David J., primary, Bueno, Raphael, primary, Tsao, Anne S., primary, Creaney, Jenette, primary, Lichtenberg, Tara, primary, Leraas, Kristen, primary, Bowen, Jay, primary, Felau, Ina, primary, Zenklusen, Jean Claude, primary, Akbani, Rehan, primary, Cherniack, Andrew D., primary, Byers, Lauren A., primary, Noble, Michael S., primary, Fletcher, Jonathan A., primary, Robertson, A. Gordon, primary, Shen, Ronglai, primary, Aburatani, Hiroyuki, primary, Robinson, Bruce W., primary, Campbell, Peter, primary, Ladanyi, Marc, primary, Ally, Adrian, primary, Anur, Pavana, primary, Armenia, Joshua, primary, Auman, J. Todd, primary, Balasundaram, Miruna, primary, Balu, Saianand, primary, Baylin, Stephen B., primary, Becich, Michael, primary, Behrens, Carmen, primary, Beroukhim, Rameen, primary, Bielski, Craig, primary, Bodenheimer, Tom, primary, Bootwalla, Moiz S., primary, Brooks, Denise, primary, Byers, Lauren Averett, primary, Cárcano, Flávio M., primary, Carlsen, Rebecca, primary, Carvalho, Andre L., primary, Cheung, Dorothy, primary, Chirieac, Lucian, primary, Cho, Juok, primary, Chuah, Eric, primary, Chudamani, Sudha, primary, Cibulskis, Carrie, primary, Cope, Leslie, primary, Crain, Daniel, primary, Curley, Erin, primary, Rienzo, Assunta De, primary, DeFreitas, Timothy, primary, Demchok, John A., primary, Dhalla, Noreen, primary, Dhir, Rajiv, primary, Feldman, Michael, primary, Ferguson, Martin L., primary, Fukuda, Shiro, primary, Gabriel, Stacey B., primary, Sallé, Françoise Galateau, primary, Gao, Jianjiong, primary, Gardner, Johanna, primary, Gastier-Foster, Julie M., primary, Gehlenborg, Nils, primary, Gerken, Mark, primary, Getz, Gad, primary, Goparaju, Chandra, primary, Gross, Benjamin, primary, Guo, Guangwu, primary, Hasegawa, Seiki, primary, Haussler, David, primary, Hayes, D. Neil, primary, Heiman, David I., primary, Heins, Zachary, primary, Holt, Robert A., primary, Hoyle, Alan P., primary, Husain, Aliya, primary, Hutter, Carolyn M., primary, Jefferys, Stuart R., primary, Jones, Steven J.M., primary, Jones, Corbin D., primary, Kanchi, Rupa S., primary, Kasaian, Katayoon, primary, Kim, Jaegil, primary, Kondo, Nobuyuki, primary, Krausz, Thomas, primary, Kundra, Ritika, primary, Kuribayashi, Kozo, primary, Lai, Phillip H., primary, Laird, Peter W., primary, Lawrence, Michael S., primary, Lee, Darlene, primary, Leraas, Kristen M., primary, Lichtenberg, Tara M., primary, Lin, Pei, primary, Liu, Jia, primary, Liu, Wenbin, primary, Liu, Eric Minwei, primary, Lolla, Laxmi, primary, Longatto-Filho, Adhemar, primary, Lu, Yiling, primary, Luketich, James, primary, Ma, Yussanne, primary, Maglinte, Dennis T., primary, Mallory, David, primary, Marra, Marco A., primary, Mayo, Michael, primary, Meier, Sam, primary, Melamed, Jonathan, primary, Meng, Shaowu, primary, Meyerson, Matthew, primary, Mieczkowski, Piotr A., primary, Mills, Gordon B., primary, Moore, Richard A., primary, Moran, Cesar, primary, Morris, Scott, primary, Mose, Lisle E., primary, Mungall, Andrew J., primary, Mungall, Karen, primary, Nakano, Takashi, primary, Naresh, Rashi, primary, Ochoa, Angelica, primary, Osmanbeyoglu, Hatice, primary, Parker, Joel S., primary, Pass, Harvey I., primary, Paulauskis, Joseph, primary, Pennathur, Arjun, primary, Pennell, Nathan A., primary, Penny, Robert, primary, Perou, Charles M., primary, Pihl, Todd, primary, Ramirez, Nilsa C., primary, Rassl, Doris M., primary, Reid, Glen, primary, Reis, Rui M., primary, Reynolds, Sheila M., primary, Rice, David, primary, Richards, William G, primary, Roach, Jeffrey, primary, Rusch, Valerie, primary, Sadeghi, Sara, primary, Saksena, Gordon, primary, Sander, Chris, primary, Sato, Ayuko, primary, Scapulatempo-Neto, Cristovam, primary, Schein, Jacqueline E., primary, Schultz, Nikolaus, primary, Schumacher, Steven E., primary, Seiwert, Tanguy, primary, Severson, David T, primary, Shelton, Candace, primary, Shelton, Troy, primary, Sheridan, Robert, primary, Shi, Yan, primary, Shiraishi, Yuichi, primary, Shmulevich, Ilya, primary, Silveira, Henrique C. S., primary, Simons, Janae V., primary, Sipahimalani, Payal, primary, Skelly, Tara, primary, Sofia, Heidi J., primary, Soloway, Matthew G., primary, Spellman, Paul, primary, Stuart, Josh, primary, Sun, Qiang, primary, Tam, Angela, primary, Tan, Donghui, primary, Tarnuzzer, Roy, primary, Tatsuno, Kenji, primary, Taylor, Barry S, primary, Thiessen, Nina, primary, Thompson, Eric, primary, Tsao, Anne, primary, Tse, Kane, primary, Tsujimura, Tohru, primary, Valdivieso, Federico, primary, Van Den Berg, David J., primary, van Zandwijk, Nico, primary, Veluvolu, Umadevi, primary, Viana, Luciano S., primary, Voet, Douglas, primary, Wan, Yunhu, primary, Wang, Zhining, primary, Wang, Jing, primary, Weaver, Joellen, primary, Weinstein, John N., primary, Weisenberger, Daniel J., primary, Wilkerson, Matthew D., primary, Wise, Lisa, primary, Wistuba, Ignacio, primary, Wong, Tina, primary, Wu, Ye, primary, Yamamoto, Shogo, primary, Yang, Liming, primary, Zenklusen, Jean C., primary, Zhang, Jiashan, primary, Zhang, Hailei, primary, Zhang, Hongxin, primary, and Zmuda, Erik, primary
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- 2023
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7. Supplementary File 1 from Intratumoral Genetic and Functional Heterogeneity in Pediatric Glioblastoma
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Hoffman, Mary, primary, Gillmor, Aaron H., primary, Kunz, Daniel J., primary, Johnston, Michael J., primary, Nikolic, Ana, primary, Narta, Kiran, primary, Zarrei, Mehdi, primary, King, Jennifer, primary, Ellestad, Katrina, primary, Dang, Ngoc Ha, primary, Cavalli, Florence M.G., primary, Kushida, Michelle M., primary, Coutinho, Fiona J., primary, Zhu, Yuankun, primary, Luu, Betty, primary, Ma, Yussanne, primary, Mungall, Andrew J., primary, Moore, Richard, primary, Marra, Marco A., primary, Taylor, Michael D., primary, Pugh, Trevor J., primary, Dirks, Peter B., primary, Strother, Douglas, primary, Lafay-Cousin, Lucie, primary, Resnick, Adam C., primary, Scherer, Stephen, primary, Senger, Donna L., primary, Simons, Benjamin D., primary, Chan, Jennifer A., primary, Morrissy, A. Sorana, primary, and Gallo, Marco, primary
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- 2023
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8. Supplementary Figure S3 from Pyruvate Kinase Inhibits Proliferation during Postnatal Cerebellar Neurogenesis and Suppresses Medulloblastoma Formation
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Tech, Katherine, primary, Tikunov, Andrey P., primary, Farooq, Hamza, primary, Morrissy, A. Sorana, primary, Meidinger, Jessica, primary, Fish, Taylor, primary, Green, Sarah C., primary, Liu, Hedi, primary, Li, Yisu, primary, Mungall, Andrew J., primary, Moore, Richard A., primary, Ma, Yussanne, primary, Jones, Steven J.M., primary, Marra, Marco A., primary, Vander Heiden, Matthew G., primary, Taylor, Michael D., primary, Macdonald, Jeffrey M., primary, and Gershon, Timothy R., primary
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- 2023
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9. Supplementary Table S1 from Pyruvate Kinase Inhibits Proliferation during Postnatal Cerebellar Neurogenesis and Suppresses Medulloblastoma Formation
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Tech, Katherine, primary, Tikunov, Andrey P., primary, Farooq, Hamza, primary, Morrissy, A. Sorana, primary, Meidinger, Jessica, primary, Fish, Taylor, primary, Green, Sarah C., primary, Liu, Hedi, primary, Li, Yisu, primary, Mungall, Andrew J., primary, Moore, Richard A., primary, Ma, Yussanne, primary, Jones, Steven J.M., primary, Marra, Marco A., primary, Vander Heiden, Matthew G., primary, Taylor, Michael D., primary, Macdonald, Jeffrey M., primary, and Gershon, Timothy R., primary
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- 2023
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10. Supplementary Materials and Methods from Pyruvate Kinase Inhibits Proliferation during Postnatal Cerebellar Neurogenesis and Suppresses Medulloblastoma Formation
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Tech, Katherine, primary, Tikunov, Andrey P., primary, Farooq, Hamza, primary, Morrissy, A. Sorana, primary, Meidinger, Jessica, primary, Fish, Taylor, primary, Green, Sarah C., primary, Liu, Hedi, primary, Li, Yisu, primary, Mungall, Andrew J., primary, Moore, Richard A., primary, Ma, Yussanne, primary, Jones, Steven J.M., primary, Marra, Marco A., primary, Vander Heiden, Matthew G., primary, Taylor, Michael D., primary, Macdonald, Jeffrey M., primary, and Gershon, Timothy R., primary
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- 2023
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11. Supplementary Table 5 from Homologous Recombination Deficiency and Platinum-Based Therapy Outcomes in Advanced Breast Cancer
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Zhao, Eric Y., primary, Shen, Yaoqing, primary, Pleasance, Erin, primary, Kasaian, Katayoon, primary, Leelakumari, Sreeja, primary, Jones, Martin, primary, Bose, Pinaki, primary, Ch'ng, Carolyn, primary, Reisle, Caralyn, primary, Eirew, Peter, primary, Corbett, Richard, primary, Mungall, Karen L., primary, Thiessen, Nina, primary, Ma, Yussanne, primary, Schein, Jacqueline E., primary, Mungall, Andrew J., primary, Zhao, Yongjun, primary, Moore, Richard A., primary, Den Brok, Wendie, primary, Wilson, Sheridan, primary, Villa, Diego, primary, Shenkier, Tamara, primary, Lohrisch, Caroline, primary, Chia, Stephen, primary, Yip, Stephen, primary, Gelmon, Karen, primary, Lim, Howard, primary, Renouf, Daniel, primary, Sun, Sophie, primary, Schrader, Kasmintan A., primary, Young, Sean, primary, Bosdet, Ian, primary, Karsan, Aly, primary, Laskin, Janessa, primary, Marra, Marco A., primary, and Jones, Steven J.M., primary
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- 2023
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12. Data from Pyruvate Kinase Inhibits Proliferation during Postnatal Cerebellar Neurogenesis and Suppresses Medulloblastoma Formation
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Tech, Katherine, primary, Tikunov, Andrey P., primary, Farooq, Hamza, primary, Morrissy, A. Sorana, primary, Meidinger, Jessica, primary, Fish, Taylor, primary, Green, Sarah C., primary, Liu, Hedi, primary, Li, Yisu, primary, Mungall, Andrew J., primary, Moore, Richard A., primary, Ma, Yussanne, primary, Jones, Steven J.M., primary, Marra, Marco A., primary, Vander Heiden, Matthew G., primary, Taylor, Michael D., primary, Macdonald, Jeffrey M., primary, and Gershon, Timothy R., primary
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- 2023
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13. Supplementary File 2 from Intratumoral Genetic and Functional Heterogeneity in Pediatric Glioblastoma
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Hoffman, Mary, primary, Gillmor, Aaron H., primary, Kunz, Daniel J., primary, Johnston, Michael J., primary, Nikolic, Ana, primary, Narta, Kiran, primary, Zarrei, Mehdi, primary, King, Jennifer, primary, Ellestad, Katrina, primary, Dang, Ngoc Ha, primary, Cavalli, Florence M.G., primary, Kushida, Michelle M., primary, Coutinho, Fiona J., primary, Zhu, Yuankun, primary, Luu, Betty, primary, Ma, Yussanne, primary, Mungall, Andrew J., primary, Moore, Richard, primary, Marra, Marco A., primary, Taylor, Michael D., primary, Pugh, Trevor J., primary, Dirks, Peter B., primary, Strother, Douglas, primary, Lafay-Cousin, Lucie, primary, Resnick, Adam C., primary, Scherer, Stephen, primary, Senger, Donna L., primary, Simons, Benjamin D., primary, Chan, Jennifer A., primary, Morrissy, A. Sorana, primary, and Gallo, Marco, primary
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- 2023
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- View/download PDF
14. Supplemental Table S2: Clinicopathological features of 118 DAWTs from Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the Children's Oncology Group
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Ooms, Ariadne H.A.G., primary, Gadd, Samantha, primary, Gerhard, Daniela S., primary, Smith, Malcolm A., primary, Guidry Auvil, Jaime M., primary, Meerzaman, Daoud, primary, Chen, Qing-Rong, primary, Hsu, Chih Hao, primary, Yan, Chunhua, primary, Nguyen, Cu, primary, Hu, Ying, primary, Ma, Yussanne, primary, Zong, Zusheng, primary, Mungall, Andrew J., primary, Moore, Richard A., primary, Marra, Marco A., primary, Huff, Vicki, primary, Dome, Jeffrey S., primary, Chi, Yueh-Yun, primary, Tian, Jing, primary, Geller, James I., primary, Mullighan, Charles G., primary, Ma, Jing, primary, Wheeler, David A., primary, Hampton, Oliver A., primary, Walz, Amy L., primary, van den Heuvel-Eibrink, Marry M., primary, de Krijger, Ronald R., primary, Ross, Nicole, primary, Gastier-Foster, Julie M., primary, and Perlman, Elizabeth J., primary
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- 2023
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15. Supplemental Table S1: TP53 variants identified in 118 DAWTs by WGS or WES from Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the Children's Oncology Group
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Ooms, Ariadne H.A.G., primary, Gadd, Samantha, primary, Gerhard, Daniela S., primary, Smith, Malcolm A., primary, Guidry Auvil, Jaime M., primary, Meerzaman, Daoud, primary, Chen, Qing-Rong, primary, Hsu, Chih Hao, primary, Yan, Chunhua, primary, Nguyen, Cu, primary, Hu, Ying, primary, Ma, Yussanne, primary, Zong, Zusheng, primary, Mungall, Andrew J., primary, Moore, Richard A., primary, Marra, Marco A., primary, Huff, Vicki, primary, Dome, Jeffrey S., primary, Chi, Yueh-Yun, primary, Tian, Jing, primary, Geller, James I., primary, Mullighan, Charles G., primary, Ma, Jing, primary, Wheeler, David A., primary, Hampton, Oliver A., primary, Walz, Amy L., primary, van den Heuvel-Eibrink, Marry M., primary, de Krijger, Ronald R., primary, Ross, Nicole, primary, Gastier-Foster, Julie M., primary, and Perlman, Elizabeth J., primary
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- 2023
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- View/download PDF
16. Supplementary Methods and Data from Intratumoral Genetic and Functional Heterogeneity in Pediatric Glioblastoma
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Hoffman, Mary, primary, Gillmor, Aaron H., primary, Kunz, Daniel J., primary, Johnston, Michael J., primary, Nikolic, Ana, primary, Narta, Kiran, primary, Zarrei, Mehdi, primary, King, Jennifer, primary, Ellestad, Katrina, primary, Dang, Ngoc Ha, primary, Cavalli, Florence M.G., primary, Kushida, Michelle M., primary, Coutinho, Fiona J., primary, Zhu, Yuankun, primary, Luu, Betty, primary, Ma, Yussanne, primary, Mungall, Andrew J., primary, Moore, Richard, primary, Marra, Marco A., primary, Taylor, Michael D., primary, Pugh, Trevor J., primary, Dirks, Peter B., primary, Strother, Douglas, primary, Lafay-Cousin, Lucie, primary, Resnick, Adam C., primary, Scherer, Stephen, primary, Senger, Donna L., primary, Simons, Benjamin D., primary, Chan, Jennifer A., primary, Morrissy, A. Sorana, primary, and Gallo, Marco, primary
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- 2023
- Full Text
- View/download PDF
17. Supplementary Information from Homologous Recombination Deficiency and Platinum-Based Therapy Outcomes in Advanced Breast Cancer
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Zhao, Eric Y., primary, Shen, Yaoqing, primary, Pleasance, Erin, primary, Kasaian, Katayoon, primary, Leelakumari, Sreeja, primary, Jones, Martin, primary, Bose, Pinaki, primary, Ch'ng, Carolyn, primary, Reisle, Caralyn, primary, Eirew, Peter, primary, Corbett, Richard, primary, Mungall, Karen L., primary, Thiessen, Nina, primary, Ma, Yussanne, primary, Schein, Jacqueline E., primary, Mungall, Andrew J., primary, Zhao, Yongjun, primary, Moore, Richard A., primary, Den Brok, Wendie, primary, Wilson, Sheridan, primary, Villa, Diego, primary, Shenkier, Tamara, primary, Lohrisch, Caroline, primary, Chia, Stephen, primary, Yip, Stephen, primary, Gelmon, Karen, primary, Lim, Howard, primary, Renouf, Daniel, primary, Sun, Sophie, primary, Schrader, Kasmintan A., primary, Young, Sean, primary, Bosdet, Ian, primary, Karsan, Aly, primary, Laskin, Janessa, primary, Marra, Marco A., primary, and Jones, Steven J.M., primary
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- 2023
- Full Text
- View/download PDF
18. Supplemental Table S4: Probe sequences used for MLPA from Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the Children's Oncology Group
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Ooms, Ariadne H.A.G., primary, Gadd, Samantha, primary, Gerhard, Daniela S., primary, Smith, Malcolm A., primary, Guidry Auvil, Jaime M., primary, Meerzaman, Daoud, primary, Chen, Qing-Rong, primary, Hsu, Chih Hao, primary, Yan, Chunhua, primary, Nguyen, Cu, primary, Hu, Ying, primary, Ma, Yussanne, primary, Zong, Zusheng, primary, Mungall, Andrew J., primary, Moore, Richard A., primary, Marra, Marco A., primary, Huff, Vicki, primary, Dome, Jeffrey S., primary, Chi, Yueh-Yun, primary, Tian, Jing, primary, Geller, James I., primary, Mullighan, Charles G., primary, Ma, Jing, primary, Wheeler, David A., primary, Hampton, Oliver A., primary, Walz, Amy L., primary, van den Heuvel-Eibrink, Marry M., primary, de Krijger, Ronald R., primary, Ross, Nicole, primary, Gastier-Foster, Julie M., primary, and Perlman, Elizabeth J., primary
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- 2023
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19. Supplemental Table S3: Recurrent mutations and segmental copy losses or gains identified in 39 DAWTs from Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the Children's Oncology Group
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Ooms, Ariadne H.A.G., primary, Gadd, Samantha, primary, Gerhard, Daniela S., primary, Smith, Malcolm A., primary, Guidry Auvil, Jaime M., primary, Meerzaman, Daoud, primary, Chen, Qing-Rong, primary, Hsu, Chih Hao, primary, Yan, Chunhua, primary, Nguyen, Cu, primary, Hu, Ying, primary, Ma, Yussanne, primary, Zong, Zusheng, primary, Mungall, Andrew J., primary, Moore, Richard A., primary, Marra, Marco A., primary, Huff, Vicki, primary, Dome, Jeffrey S., primary, Chi, Yueh-Yun, primary, Tian, Jing, primary, Geller, James I., primary, Mullighan, Charles G., primary, Ma, Jing, primary, Wheeler, David A., primary, Hampton, Oliver A., primary, Walz, Amy L., primary, van den Heuvel-Eibrink, Marry M., primary, de Krijger, Ronald R., primary, Ross, Nicole, primary, Gastier-Foster, Julie M., primary, and Perlman, Elizabeth J., primary
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- 2023
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- View/download PDF
20. Data from Intratumoral Genetic and Functional Heterogeneity in Pediatric Glioblastoma
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Hoffman, Mary, primary, Gillmor, Aaron H., primary, Kunz, Daniel J., primary, Johnston, Michael J., primary, Nikolic, Ana, primary, Narta, Kiran, primary, Zarrei, Mehdi, primary, King, Jennifer, primary, Ellestad, Katrina, primary, Dang, Ngoc Ha, primary, Cavalli, Florence M.G., primary, Kushida, Michelle M., primary, Coutinho, Fiona J., primary, Zhu, Yuankun, primary, Luu, Betty, primary, Ma, Yussanne, primary, Mungall, Andrew J., primary, Moore, Richard, primary, Marra, Marco A., primary, Taylor, Michael D., primary, Pugh, Trevor J., primary, Dirks, Peter B., primary, Strother, Douglas, primary, Lafay-Cousin, Lucie, primary, Resnick, Adam C., primary, Scherer, Stephen, primary, Senger, Donna L., primary, Simons, Benjamin D., primary, Chan, Jennifer A., primary, Morrissy, A. Sorana, primary, and Gallo, Marco, primary
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- 2023
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21. Supplementary File 3 from Intratumoral Genetic and Functional Heterogeneity in Pediatric Glioblastoma
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Hoffman, Mary, primary, Gillmor, Aaron H., primary, Kunz, Daniel J., primary, Johnston, Michael J., primary, Nikolic, Ana, primary, Narta, Kiran, primary, Zarrei, Mehdi, primary, King, Jennifer, primary, Ellestad, Katrina, primary, Dang, Ngoc Ha, primary, Cavalli, Florence M.G., primary, Kushida, Michelle M., primary, Coutinho, Fiona J., primary, Zhu, Yuankun, primary, Luu, Betty, primary, Ma, Yussanne, primary, Mungall, Andrew J., primary, Moore, Richard, primary, Marra, Marco A., primary, Taylor, Michael D., primary, Pugh, Trevor J., primary, Dirks, Peter B., primary, Strother, Douglas, primary, Lafay-Cousin, Lucie, primary, Resnick, Adam C., primary, Scherer, Stephen, primary, Senger, Donna L., primary, Simons, Benjamin D., primary, Chan, Jennifer A., primary, Morrissy, A. Sorana, primary, and Gallo, Marco, primary
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- 2023
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22. 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, 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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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23. Combined burden and functional impact tests for cancer driver discovery using DriverPower
- Author
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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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24. Integrative pathway enrichment analysis of multivariate omics data
- Author
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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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25. 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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26. 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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27. Genomic footprints of activated telomere maintenance mechanisms in cancer
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Haiyan Irene, Li, Jun, Li, Lin, Li, Shantao, Li, Siliang, Li, Xiaobo, Li, Xiaotong, Li, Xinyue, Liang, Han, Liang, Sheng-Ben, Lichter, Peter, Lin, Pei, Lin, Ziao, Linehan, WM, Lingjærde, Ole Christian, Liu, Dongbing, Liu, Eric Minwei, Liu, Fei-Fei Fei, Liu, Fenglin, Liu, Jia, Liu, Xingmin, Livingstone, Julie, Livitz, Dimitri, Livni, Naomi, Lochovsky, Lucas, Loeffler, Markus, Long, Georgina V, Lopez-Guillermo, Armando, Lou, Shaoke, Louis, David N, Lovat, Laurence B, Lu, Yiling, Lu, Yong-Jie, Lu, Youyong, Luchini, Claudio, Lungu, Ilinca, Luo, Xuemei, Luxton, Hayley J, Lype, Lisa, López, Cristina, López-Otín, Carlos, Z, Eric, Ma, Yussanne, MacGrogan, Gaetan, MacRae, Shona, Madsen, Tobias, Maejima, Kazuhiro, Mafficini, Andrea, Maglinte, Dennis T, Maitra, Arindam, Majumder, Partha P, Malcovati, Luca, Malikic, Salem, Malleo, Giuseppe, Mann, Graham J, Mantovani-Löffler, Luisa, Marchal, Kathleen, Marchegiani, Giovanni, Mardis, Elaine R, Margolin, Adam A, Marin, Maximillian G, Markowski, Julia, 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Okusaka, Takuji, Omberg, Larsson, Ong, Choon Kiat, Ott, German, Ouellette, BF Francis, P’ng, Christine, Paczkowska, Marta, Paiella, Salvatore, Pairojkul, Chawalit, Pajic, Marina, Pan-Hammarström, Qiang, Papaemmanuil, Elli, Papatheodorou, Irene, Paramasivam, Nagarajan, Park, Ji Wan, Park, Joong-Won, Park, Keunchil, Park, Kiejung, Parker, Joel S, Parsons, Simon L, Pass, Harvey, Pasternack, Danielle, Pastore, Alessandro, Patch, Ann-Marie, Pauporté, Iris, Pea, Antonio, Pedamallu, Chandra Sekhar, Pedersen, Jakob Skou, 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, Pons, Tirso, Popescu, Irinel, Potapova, Olga, Prasad, Aparna, Preston, Shaun R, 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Elisabetta, Serra, Stefano, Sgroi, Dennis C, Shah, Nimish C, Shahabi, Sagedeh, Shang, Catherine A, Shang, Ping, Shapira, Ofer, Shelton, Troy, Shen, Ciyue, 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, Shrestha, Raunak, Shringarpure, Suyash S, Shriver, Craig, Shuai, Shimin, 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, Sinnott-Armstrong, Nasa, 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, 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Christian
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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.
- Published
- 2023
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28. Retraction Note: Tumor necrosis factor overcomes immune evasion in p53-mutant medulloblastoma
- Author
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Garancher, Alexandra, primary, Suzuki, Hiromichi, additional, Haricharan, Svasti, additional, Chau, Lianne Q., additional, Masihi, Meher Beigi, additional, Rusert, Jessica M., additional, Norris, Paula S., additional, Carrette, Florent, additional, Romero, Megan M., additional, Morrissy, Sorana A., additional, Skowron, Patryk, additional, Cavalli, Florence M. G., additional, Farooq, Hamza, additional, Ramaswamy, Vijay, additional, Jones, Steven J. M., additional, Moore, Richard A., additional, Mungall, Andrew J., additional, Ma, Yussanne, additional, Thiessen, Nina, additional, Li, Yisu, additional, Morcavallo, Alaide, additional, Qi, Lin, additional, Kogiso, Mari, additional, Du, Yuchen, additional, Baxter, Patricia, additional, Henderson, Jacob J., additional, Crawford, John R., additional, Levy, Michael L., additional, Olson, James M., additional, Cho, Yoon-Jae, additional, Deshpande, Aniruddha J., additional, Li, Xiao-Nan, additional, Chesler, Louis, additional, Marra, Marco A., additional, Wajant, Harald, additional, Becher, Oren J., additional, Bradley, Linda M., additional, Ware, Carl F., additional, Taylor, Michael D., additional, and Wechsler-Reya, Robert J., additional
- Published
- 2021
- Full Text
- View/download PDF
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