142 results on '"Liang, Sheng-Ben"'
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2. A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns
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Notta, Faiyaz, Chan-Seng-Yue, Michelle, Lemire, Mathieu, Li, Yilong, Wilson, Gavin W, Connor, Ashton A, Denroche, Robert E, Liang, Sheng-Ben, Brown, Andrew MK, Kim, Jaeseung C, Wang, Tao, Simpson, Jared T, Beck, Timothy, Borgida, Ayelet, Buchner, Nicholas, Chadwick, Dianne, Hafezi-Bakhtiari, Sara, Dick, John E, Heisler, Lawrence, Hollingsworth, Michael A, Ibrahimov, Emin, Jang, Gun Ho, Johns, Jeremy, Jorgensen, Lars GT, Law, Calvin, Ludkovski, Olga, Lungu, Ilinca, Ng, Karen, Pasternack, Danielle, Petersen, Gloria M, Shlush, Liran I, Timms, Lee, Tsao, Ming-Sound, Wilson, Julie M, Yung, Christina K, Zogopoulos, George, Bartlett, John MS, Alexandrov, Ludmil B, Real, Francisco X, Cleary, Sean P, Roehrl, Michael H, McPherson, John D, Stein, Lincoln D, Hudson, Thomas J, Campbell, Peter J, and Gallinger, Steven
- Subjects
Biological Sciences ,Biomedical and Clinical Sciences ,Genetics ,Oncology and Carcinogenesis ,Pancreatic Cancer ,Human Genome ,Cancer ,Biotechnology ,Digestive Diseases ,Orphan Drug ,Rare Diseases ,Development of treatments and therapeutic interventions ,2.1 Biological and endogenous factors ,5.1 Pharmaceuticals ,Aetiology ,Carcinogenesis ,Carcinoma in Situ ,Chromothripsis ,DNA Copy Number Variations ,Disease Progression ,Evolution ,Molecular ,Female ,Gene Rearrangement ,Genes ,Neoplasm ,Genome ,Human ,Humans ,Male ,Mitosis ,Models ,Biological ,Mutagenesis ,Mutation ,Neoplasm Invasiveness ,Neoplasm Metastasis ,Pancreatic Neoplasms ,Polyploidy ,Precancerous Conditions ,General Science & Technology - Abstract
Pancreatic cancer, a highly aggressive tumour type with uniformly poor prognosis, exemplifies the classically held view of stepwise cancer development. The current model of tumorigenesis, based on analyses of precursor lesions, termed pancreatic intraepithelial neoplasm (PanINs) lesions, makes two predictions: first, that pancreatic cancer develops through a particular sequence of genetic alterations (KRAS, followed by CDKN2A, then TP53 and SMAD4); and second, that the evolutionary trajectory of pancreatic cancer progression is gradual because each alteration is acquired independently. A shortcoming of this model is that clonally expanded precursor lesions do not always belong to the tumour lineage, indicating that the evolutionary trajectory of the tumour lineage and precursor lesions can be divergent. This prevailing model of tumorigenesis has contributed to the clinical notion that pancreatic cancer evolves slowly and presents at a late stage. However, the propensity for this disease to rapidly metastasize and the inability to improve patient outcomes, despite efforts aimed at early detection, suggest that pancreatic cancer progression is not gradual. Here, using newly developed informatics tools, we tracked changes in DNA copy number and their associated rearrangements in tumour-enriched genomes and found that pancreatic cancer tumorigenesis is neither gradual nor follows the accepted mutation order. Two-thirds of tumours harbour complex rearrangement patterns associated with mitotic errors, consistent with punctuated equilibrium as the principal evolutionary trajectory. In a subset of cases, the consequence of such errors is the simultaneous, rather than sequential, knockout of canonical preneoplastic genetic drivers that are likely to set-off invasive cancer growth. These findings challenge the current progression model of pancreatic cancer and provide insights into the mutational processes that give rise to these aggressive tumours.
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- 2016
3. Data from Genomics-Driven Precision Medicine for Advanced Pancreatic Cancer: Early Results from the COMPASS Trial
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Aung, Kyaw L., primary, Fischer, Sandra E., primary, Denroche, Robert E., primary, Jang, Gun-Ho, primary, Dodd, Anna, primary, Creighton, Sean, primary, Southwood, Bernadette, primary, Liang, Sheng-Ben, primary, Chadwick, Dianne, primary, Zhang, Amy, primary, O'Kane, Grainne M., primary, Albaba, Hamzeh, primary, Moura, Shari, primary, Grant, Robert C., primary, Miller, Jessica K., primary, Mbabaali, Faridah, primary, Pasternack, Danielle, primary, Lungu, Ilinca M., primary, Bartlett, John M.S., primary, Ghai, Sangeet, primary, Lemire, Mathieu, primary, Holter, Spring, primary, Connor, Ashton A., primary, Moffitt, Richard A., primary, Yeh, Jen Jen, primary, Timms, Lee, primary, Krzyzanowski, Paul M., primary, Dhani, Neesha, primary, Hedley, David, primary, Notta, Faiyaz, primary, Wilson, Julie M., primary, Moore, Malcolm J., primary, Gallinger, Steven, primary, and Knox, Jennifer J., primary
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- 2023
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4. Figure S6 from A Four-Chemokine Signature Is Associated with a T-cell–Inflamed Phenotype in Primary and Metastatic Pancreatic Cancer
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Romero, Joan M., primary, Grünwald, Barbara, primary, Jang, Gun-Ho, primary, Bavi, Prashant P., primary, Jhaveri, Aaditeya, primary, Masoomian, Mehdi, primary, Fischer, Sandra E., primary, Zhang, Amy, primary, Denroche, Robert E., primary, Lungu, Ilinca M., primary, De Luca, Angela, primary, Bartlett, John M.S., primary, Xu, Jing, primary, Li, Niandong, primary, Dhaliwal, Sharon, primary, Liang, Sheng-Ben, primary, Chadwick, Dianne, primary, Vyas, Foram, primary, Bronsert, Peter, primary, Khokha, Rama, primary, McGaha, Tracy L., primary, Notta, Faiyaz, primary, Ohashi, Pamela S., primary, Done, Susan J., primary, O'Kane, Grainne M., primary, Wilson, Julie M., primary, Knox, Jennifer J., primary, Connor, Ashton, primary, Wang, Yifan, primary, Zogopoulos, George, primary, and Gallinger, Steven, primary
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- 2023
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5. Table S3 from A Four-Chemokine Signature Is Associated with a T-cell–Inflamed Phenotype in Primary and Metastatic Pancreatic Cancer
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Romero, Joan M., primary, Grünwald, Barbara, primary, Jang, Gun-Ho, primary, Bavi, Prashant P., primary, Jhaveri, Aaditeya, primary, Masoomian, Mehdi, primary, Fischer, Sandra E., primary, Zhang, Amy, primary, Denroche, Robert E., primary, Lungu, Ilinca M., primary, De Luca, Angela, primary, Bartlett, John M.S., primary, Xu, Jing, primary, Li, Niandong, primary, Dhaliwal, Sharon, primary, Liang, Sheng-Ben, primary, Chadwick, Dianne, primary, Vyas, Foram, primary, Bronsert, Peter, primary, Khokha, Rama, primary, McGaha, Tracy L., primary, Notta, Faiyaz, primary, Ohashi, Pamela S., primary, Done, Susan J., primary, O'Kane, Grainne M., primary, Wilson, Julie M., primary, Knox, Jennifer J., primary, Connor, Ashton, primary, Wang, Yifan, primary, Zogopoulos, George, primary, and Gallinger, Steven, primary
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- 2023
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6. Online Supplementary Materials from Genomics-Driven Precision Medicine for Advanced Pancreatic Cancer: Early Results from the COMPASS Trial
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Aung, Kyaw L., primary, Fischer, Sandra E., primary, Denroche, Robert E., primary, Jang, Gun-Ho, primary, Dodd, Anna, primary, Creighton, Sean, primary, Southwood, Bernadette, primary, Liang, Sheng-Ben, primary, Chadwick, Dianne, primary, Zhang, Amy, primary, O'Kane, Grainne M., primary, Albaba, Hamzeh, primary, Moura, Shari, primary, Grant, Robert C., primary, Miller, Jessica K., primary, Mbabaali, Faridah, primary, Pasternack, Danielle, primary, Lungu, Ilinca M., primary, Bartlett, John M.S., primary, Ghai, Sangeet, primary, Lemire, Mathieu, primary, Holter, Spring, primary, Connor, Ashton A., primary, Moffitt, Richard A., primary, Yeh, Jen Jen, primary, Timms, Lee, primary, Krzyzanowski, Paul M., primary, Dhani, Neesha, primary, Hedley, David, primary, Notta, Faiyaz, primary, Wilson, Julie M., primary, Moore, Malcolm J., primary, Gallinger, Steven, primary, and Knox, Jennifer J., primary
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- 2023
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7. Supplementary Tables 1-3, Figures 1-3 from Molecular Target Characterization and Antimyeloma Activity of the Novel, Insulin-like Growth Factor 1 Receptor Inhibitor, GTx-134
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Liang, Sheng-Ben, primary, Yang, Xiu-Zhi, primary, Trieu, Young, primary, Li, Zhihua, primary, Zive, Jessica, primary, Leung-Hagesteijn, Chungyee, primary, Wei, Ellen, primary, Zozulya, Sergey, primary, Coss, Christopher C., primary, Dalton, James T., primary, Fantus, Ivan George, primary, and Trudel, Suzanne, primary
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- 2023
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8. Supplementary Methods, Figure Legends 1-3 from Molecular Target Characterization and Antimyeloma Activity of the Novel, Insulin-like Growth Factor 1 Receptor Inhibitor, GTx-134
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Liang, Sheng-Ben, primary, Yang, Xiu-Zhi, primary, Trieu, Young, primary, Li, Zhihua, primary, Zive, Jessica, primary, Leung-Hagesteijn, Chungyee, primary, Wei, Ellen, primary, Zozulya, Sergey, primary, Coss, Christopher C., primary, Dalton, James T., primary, Fantus, Ivan George, primary, and Trudel, Suzanne, primary
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- 2023
- Full Text
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9. 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, Demeulemeester, Jonas, Demidov, German M, Demircioğlu, Deniz, Dennis, Nening M, Denroche, Robert E, Dentro, Stefan C, Desai, Nikita, Deshwar, Amit G, Desmedt, Christine, Deu-Pons, Jordi, Dhalla, Noreen, Dhani, Neesha C, Dhingra, Priyanka, Dhir, Rajiv, DiBiase, Anthony, Diamanti, Klev, 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, Fan, Daiming, Fan, Yu, Farcas, Claudiu, Fassan, Matteo, Fatima, Aquila, Favero, Francesco, Fayzullaev, Nodirjon, Felau, Ina, Fereday, Sian, Ferguson, Martin L, Ferretti, Vincent, Feuerbach, Lars, Field, Matthew A, Fink, J Lynn, 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, Fonseca, Nuno A, Foster, Christopher S, Fox, Natalie S, Fraser, Michael, Frazer, Scott, Frenkel-Morgenstern, Milana, Friedman, William, Frigola, Joan, 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, Gallinger, Steven, Gambacorti-Passerini, Carlo, Gao, Jianjiong, Gao, Shengjie, Garred, Øystein, Garrison, Erik, Garsed, Dale W, Gehlenborg, Nils, Gelpi, Josep LL, George, Joshy, Gerhard, Daniela S, Gerhauser, Clarissa, Gershenwald, Jeffrey E, Gerstein, Mark, 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, Grossman, Robert L, Grundhoff, Adam, Gundem, Gunes, Guo, Qianyun, Gupta, Manaswi, Gupta, Shailja, Gut, Ivo G, Gut, Marta, Göke, Jonathan, Ha, Gavin, Haake, Andrea, Haan, David, Haas, Siegfried, Haase, Kerstin, Haber, James E, Habermann, Nina, Hach, Faraz, Hama, Natsuko, Hamdy, Freddie C, Hamilton, Anne, Hamilton, Mark P, Han, Leng, Hanna, George B, Hansmann, Martin, Haradhvala, Nicholas J, Harismendy, Olivier, Harliwong, Ivon, Harmanci, Arif O, 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, Helmy, Mohamed, Heo, Seong Gu, Hepperla, Austin J, Heredia-Genestar, José María, Herrmann, Carl, Hersey, Peter, Hess, Julian M, Hilmarsdottir, Holmfridur, Hinton, Jonathan, Hirano, Satoshi, Hiraoka, Nobuyoshi, Hobolth, Asger, Hodzic, Ermin, Hoell, Jessica I, Hoffmann, Steve, Hofmann, Oliver, Holbrook, Andrea, Holik, Aliaksei Z, Hollingsworth, Michael A, Holmes, Oliver, Holt, Robert A, Hong, Chen, Hong, Eun Pyo, Hong, Jongwhi H, Hooijer, Gerrit K, Hornshøj, Henrik, 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, Isaev, Keren, Ishikawa, Shumpei, Iskar, Murat, Islam, SM Ashiqul, Ittmann, Michael, Ivkovic, Sinisa, Izarzugaza, Jose MG, 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, Johansson, Peter A, Johns, Amber L, Johns, Jeremy, Johnson, Rory, Johnson, Todd A, 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, Malene, Juul, Randi Istrup, Juul, Sissel, Jäger, Natalie, Kabbe, Rolf, Kahles, Andre, Kahraman, Abdullah, 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, Katoh, Hiroto, Kawakami, Yoshiiku, Kay, Jonathan D, Kazakoff, Stephen H, Kazanov, Marat D, Keays, Maria, Kebebew, Electron, Kefford, Richard F, Kellis, Manolis, Kench, James G, Kennedy, Catherine J, Kerssemakers, Jules NA, Khoo, David, Khoo, Vincent, Khuntikeo, Narong, Khurana, Ekta, Kilpinen, Helena, Kim, Hark Kyun, Kim, Hyung-Lae, Kim, Hyung-Yong, Kim, Hyunghwan, Kim, Jaegil, Kim, Jihoon, Kim, Jong K, Kim, Youngwook, King, Tari A, Klapper, Wolfram, Kleinheinz, Kortine, Klimczak, Leszek J, Knappskog, Stian, Kneba, Michael, Knoppers, Bartha M, Koh, Youngil, Komorowski, Jan, Komura, Daisuke, Komura, Mitsuhiro, Kong, Gu, Kool, Marcel, Korbel, Jan O, 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, Sushant, Kumar, Yogesh, Kundra, Ritika, 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, Lanzós, Andrés, Larsimont, Denis, Larsson, Erik, Lathrop, Mark, Lau, Loretta MS, Lawerenz, Chris, Lawlor, Rita T, Lawrence, Michael S, Lazic, Ana Mijalkovic, Le, Xuan, Lee, Darlene, Lee, Donghoon, Lee, Eunjung Alice, Lee, Hee Jin, Lee, Jake June-Koo, Lee, Jeong-Yeon, Lee, Juhee, Lee, Ming Ta Michael, Lee-Six, Henry, Lehmann, Kjong-Van, 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, Haiyan Irene, Li, Jun, Li, Lin, Li, Shantao, Li, Siliang, Li, Xiaobo, Li, Xiaotong, Li, Xinyue, Li, Yilong, 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, 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, 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, Markowetz, Florian, Markowski, Julia, Marks, Jeffrey, Marques-Bonet, Tomas, Marra, Marco A, Marsden, Luke, Martens, John WM, Martin-Subero, Jose I, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Maruvka, Yosef E, Mashl, R Jay, Massie, Charlie E, Matthew, Thomas J, Matthews, Lucy, Mayer, Erik, Mayes, Simon, Mayo, Michael, Mbabaali, Faridah, McCune, Karen, McDermott, Ultan, McGillivray, Patrick D, 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, Meyerson, William, 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, Morrison, Carl, Mose, Lisle E, Moser, Catherine D, Muiños, Ferran, Mularoni, Loris, Mungall, Andrew J, Mungall, 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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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10. Combined burden and functional impact tests for cancer driver discovery using DriverPower
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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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11. Integrative pathway enrichment analysis of multivariate omics data
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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, Lixing, Yang, Shanlin, Yang, Tsun-Po, Yang, Yang, Yao, Xiaotong, Yaspo, Marie-Laure, Yates, Lucy, Yau, Christina, Ye, Chen, Ye, Kai, Yellapantula, Venkata D, Yoon, Christopher J, Yoon, Sung-Soo, Yousif, Fouad, Yu, Kaixian, Yu, Willie, Yu, Yingyan, Yuan, Ke, Yuan, Yuan, Yuen, Denis, Yung, Christina K, Zaikova, Olga, Zamora, Jorge, Zapatka, Marc, Zenklusen, Jean C, Zenz, Thorsten, Zeps, Nikolajs, Zhang, Cheng-Zhong, Zhang, Fan, Zhang, Hailei, Zhang, Hongwei, Zhang, Hongxin, Zhang, Jiashan, Zhang, Junjun, Zhang, Xiuqing, Zhang, Zemin, Zheng, Liangtao, Zheng, Xiuqing, Zhou, Wanding, Zhou, Yong, Zhu, Bin, Zhu, Hongtu, Zhu, Jingchun, Zhu, Shida, Zou, Xueqing, deFazio, Anna, van As, Nicholas, van Deurzen, Carolien HM, van de Vijver, Marc J, and Veer, L van’t
- Subjects
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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12. Pathway and network analysis of more than 2500 whole cancer genomes
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Reyna, Matthew A, Haan, David, Paczkowska, Marta, Verbeke, Lieven PC, Vazquez, Miguel, Kahraman, Abdullah, Pulido-Tamayo, Sergio, Barenboim, Jonathan, Wadi, Lina, Dhingra, Priyanka, Shrestha, Raunak, Getz, Gad, Lawrence, Michael S, Pedersen, Jakob Skou, Rubin, Mark A, Wheeler, David A, Brunak, Søren, Izarzugaza, Jose MG, Khurana, Ekta, Marchal, Kathleen, von Mering, Christian, Sahinalp, S Cenk, Valencia, Alfonso, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Bandopadhayay, Pratiti, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Busanovich, John, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Guo, Qianyun, Gut, Ivo G, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, 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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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13. Divergent mutational processes distinguish hypoxic and normoxic tumours
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Bhandari, Vinayak, Li, Constance H, Bristow, Robert G, Boutros, Paul C, 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, Al-Shahrour, Fatima, 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, Atwal, Gurnit, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Bader, Gary D, Baez-Ortega, Adrian, Bailey, Matthew H, Bailey, Peter J, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, 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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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14. Genomic footprints of activated telomere maintenance mechanisms in cancer
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Steven JM, Jonkers, Jos, Juhl, Hartmut, Jung, Jongsun, Juul, Malene, Juul, Randi Istrup, Juul, Sissel, Jäger, Natalie, Kahles, Andre, Kahraman, Abdullah, 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, Keays, Maria, Kebebew, Electron, Kefford, Richard F, Kellis, Manolis, Kench, James G, Kennedy, Catherine J, Kerssemakers, Jules NA, Khoo, David, Khoo, Vincent, Khuntikeo, Narong, Khurana, Ekta, Kilpinen, Helena, Kim, Hark Kyun, Kim, Hyung-Lae, Kim, Hyung-Yong, Kim, Hyunghwan, Kim, Jaegil, Kim, Jihoon, Kim, Jong K, Kim, Youngwook, King, Tari A, Klapper, Wolfram, Knappskog, Stian, Kneba, Michael, Knoppers, Bartha M, Komorowski, Jan, 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, Pardeep, Kumar, Sushant, 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, Lanzós, Andrés, Larsimont, Denis, Larsson, Erik, Lathrop, Mark, Lau, Loretta MS, Lawerenz, Chris, Lawlor, Rita T, Lawrence, Michael S, Lazar, Alexander J, Lazic, Ana Mijalkovic, Le, Xuan, Lee, Darlene, Lee, Donghoon, Lee, Hee Jin, Lee, Jeong-Yeon, Lee, Juhee, Lee, Ming Ta Michael, Lee-Six, Henry, Lehmann, Kjong-Van, 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, 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, Marks, Jeffrey, Marques-Bonet, Tomas, Marra, Marco A, Marsden, Luke, Martens, John WM, Martin, Sancha, Martin-Subero, Jose I, Maruvka, Yosef E, Mashl, R Jay, Massie, Charlie E, Matthew, Thomas J, Matthews, Lucy, Mayer, Erik, Mayes, Simon, Mayo, Michael, Mbabaali, Faridah, McCune, Karen, McDermott, Ultan, McGillivray, Patrick D, 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, William, 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, 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, Muiños, Ferran, Mularoni, Loris, 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, 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, Nielsen, Morten Muhlig, 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, 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, Prinz, Manuel, Pritchard, Antonia L, Prokopec, Stephenie D, Provenzano, Elena, Puente, Xose S, Puig, Sonia, Pulido-Tamayo, Sergio, 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, Raphael, Benjamin J, Rathmell, W Kimryn, Rausch, Tobias, Reifenberger, Guido, Reimand, Jüri, Reis-Filho, Jorge, Reuter, Victor, Reyes-Salazar, Iker, Reyna, Matthew A, Reynolds, Sheila M, Rheinbay, Esther, Riazalhosseini, Yasser, Richardson, Andrea L, Richter, Julia, Ringel, Matthew, Ringnér, Markus, Rino, Yasushi, Roach, Jeffrey, Roberts, Lewis R, Robertson, A Gordon, Robertson, Alan J, Rodriguez, Javier Bartolomé, 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, 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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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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
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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.
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- 2023
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15. Author Correction: Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution
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Chan-Seng-Yue, Michelle, Kim, Jaeseung C., Wilson, Gavin W., Ng, Karen, Figueroa, Eugenia Flores, O’Kane, Grainne M., Connor, Ashton A., Denroche, Robert E., Grant, Robert C., McLeod, Jessica, Wilson, Julie M., Jang, Gun Ho, Zhang, Amy, Liang, Sheng-Ben, Borgida, Ayelet, Chadwick, Dianne, Kalimuthu, Sangeetha, Lungu, Ilinca, Bartlett, John M. S., Krzyzanowski, Paul M., Sandhu, Vandana, Tiriac, Hervé, Froeling, Fieke E. M., Karasinska, Joanna M., Topham, James T., Renouf, Daniel J., Schaeffer, David F., Jones, Steven J. M., Marra, Marco A., Laskin, Janessa, Chetty, Runjan, Stein, Lincoln D., Zogopoulos, George, Haibe-Kains, Benjamin, Campbell, Peter J., Tuveson, David A., Knox, Jennifer J., Fischer, Sandra E., Gallinger, Steven, and Notta, Faiyaz
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- 2020
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16. Erratum: A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns
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Notta, Faiyaz, Chan-Seng-Yue, Michelle, Lemire, Mathieu, Li, Yilong, Wilson, Gavin W., Connor, Ashton A., Denroche, Robert E., Liang, Sheng-Ben, Brown, Andrew M. K., Kim, Jaeseung C., Wang, Tao, Simpson, Jared T., Beck, Timothy, Borgida, Ayelet, Buchner, Nicholas, Chadwick, Dianne, Hafezi-Bakhtiari, Sara, Dick, John E., Heisler, Lawrence, Hollingsworth, Michael A., Ibrahimov, Emin, Jang, Gun Ho, Johns, Jeremy, Jorgensen, Lars G. T., Law, Calvin, Ludkovski, Olga, Lungu, Ilinca, Ng, Karen, Pasternack, Danielle, Petersen, Gloria M., Shlush, Liran I., Timms, Lee, Tsao, Ming-Sound, Wilson, Julie M., Yung, Christina K., Zogopoulos, George, Bartlett, John M. S., Alexandrov, Ludmil B., Real, Francisco X., Cleary, Sean P., Roehrl, Michael H., McPherson, John D., Stein, Lincoln D., Hudson, Thomas J., Campbell, Peter J., and Gallinger, Steven
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- 2017
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17. Cyproheptadine displays preclinical activity in myeloma and leukemia
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Mao, Xinliang, Liang, Sheng-ben, Hurren, Rose, Gronda, Marcela, Chow, Sue, Xu, G. Wei, Wang, Xiaoming, Zavareh, Reza Beheshti, Jamal, Nazir, Messner, Hans, Hedley, David W., Datti, Alessandro, Wrana, Jeff L., Zhu, Yuanxiao, Shi, Chang-xin, Lee, Kyle, Tiedemann, Rodger, Trudel, Suzanne, Stewart, A. Keith, and Schimmer, Aaron D.
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- 2008
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18. Efficient transfer of PSA and PSMA cDNAs into DCs generates antibody and T cell antitumor responses in vivo
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Medin, Jeffrey A, Liang, Sheng-Ben, Hou, Jeannie Whit-Shan, Kelley, Leslie S, Peace, David J, and Fowler, Daniel H
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- 2005
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19. Reduced human mismatch repair protein expression in the development of precancerous skin lesions to squamous cell carcinoma
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Liang, Sheng-Ben, Furihata, Mutsuo, Takeuchi, Tamotsu, Sonobe, Hiroshi, and Ohtsuki, Yuji
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- 2001
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20. Sun-exposure- and aging-dependent p53 protein accumulation results in growth advantage for tumour cells in carcinogenesis of nonmelanocytic skin cancer
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Liang, Sheng-Ben, Ohtsuki, Y., Furihata, Mutsuo, Takeuchi, Tamotsu, Iwata, J., Chen, Bing-Kun, and Sonobe, Hiroshi
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- 1999
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21. A Four-Chemokine Signature Is Associated with a T-cell–Inflamed Phenotype in Primary and Metastatic Pancreatic Cancer
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Romero, Joan M., primary, Grünwald, Barbara, additional, Jang, Gun-Ho, additional, Bavi, Prashant P., additional, Jhaveri, Aaditeya, additional, Masoomian, Mehdi, additional, Fischer, Sandra E., additional, Zhang, Amy, additional, Denroche, Robert E., additional, Lungu, Ilinca M., additional, De Luca, Angela, additional, Bartlett, John M.S., additional, Xu, Jing, additional, Li, Niandong, additional, Dhaliwal, Sharon, additional, Liang, Sheng-Ben, additional, Chadwick, Dianne, additional, Vyas, Foram, additional, Bronsert, Peter, additional, Khokha, Rama, additional, McGaha, Tracy L., additional, Notta, Faiyaz, additional, Ohashi, Pamela S., additional, Done, Susan J., additional, O'Kane, Grainne M., additional, Wilson, Julie M., additional, Knox, Jennifer J., additional, Connor, Ashton, additional, Wang, Yifan, additional, Zogopoulos, George, additional, and Gallinger, Steven, additional
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- 2020
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22. Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution
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Chan-Seng-Yue, Michelle, primary, Kim, Jaeseung C., additional, Wilson, Gavin W., additional, Ng, Karen, additional, Figueroa, Eugenia Flores, additional, O’Kane, Grainne M., additional, Connor, Ashton A., additional, Denroche, Robert E., additional, Grant, Robert C., additional, McLeod, Jessica, additional, Wilson, Julie M., additional, Jang, Gun Ho, additional, Zhang, Amy, additional, Dodd, Anna, additional, Liang, Sheng-Ben, additional, Borgida, Ayelet, additional, Chadwick, Dianne, additional, Kalimuthu, Sangeetha, additional, Lungu, Ilinca, additional, Bartlett, John M. S., additional, Krzyzanowski, Paul M., additional, Sandhu, Vandana, additional, Tiriac, Hervé, additional, Froeling, Fieke E. M., additional, Karasinska, Joanna M., additional, Topham, James T., additional, Renouf, Daniel J., additional, Schaeffer, David F., additional, Jones, Steven J. M., additional, Marra, Marco A., additional, Laskin, Janessa, additional, Chetty, Runjan, additional, Stein, Lincoln D., additional, Zogopoulos, George, additional, Haibe-Kains, Benjamin, additional, Campbell, Peter J., additional, Tuveson, David A., additional, Knox, Jennifer J., additional, Fischer, Sandra E., additional, Gallinger, Steven, additional, and Notta, Faiyaz, additional
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- 2020
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23. Melanosis of the prostate: an immunohistochemical study
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Ohtsuki, Yuji, Furihata, Mutsuo, Sonobe, Hiroshi, Iwata, Jun, Ido, Eiji, Chen, Bing-kun, Liang, Sheng-ben, and Ochi, Kenji
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- 1998
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24. Expression of T-Cadherin in Basal Keratinocytes of Skin
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Zhou, Shuxia, Matsuyoshi, Norihisa, Liang, Sheng-Ben, Takeuchi, Tamotsu, Ohtsuki, Yuji, and Miyachi, Yoshiki
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- 2002
25. Tetrasomy 12 in ovarian tumors of thecoma-fibroma group: A fluorescence in situ hybridization analysis using paraffin sections
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Liang, Sheng-Ben, Sonobe, Hiroshi, Taguchi, Takahiro, Takeuchi, Tamotsu, Furihata, Mutsuo, Yuri, Kazunari, and Ohtsuki, Yuji
- Published
- 2001
26. Expression of T-Cadherin (CDH13, H-Cadherin) in Human Brain and Its Characteristics as a Negative Growth Regulator of Epidermal Growth Factor in Neuroblastoma Cells
- Author
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Takeuchi, Tamotsu, Misaki, Akiko, Liang, Sheng-Ben, Tachibana, Akiko, Hayashi, Nakanobu, Sonobe, Hiroshi, and Ohtsuki, Yuji
- Published
- 2000
27. Integration of Genomic and Transcriptional Features in Pancreatic Cancer Reveals Increased Cell Cycle Progression in Metastases
- Author
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Connor, Ashton A., primary, Denroche, Robert E., additional, Jang, Gun Ho, additional, Lemire, Mathieu, additional, Zhang, Amy, additional, Chan-Seng-Yue, Michelle, additional, Wilson, Gavin, additional, Grant, Robert C., additional, Merico, Daniele, additional, Lungu, Ilinca, additional, Bartlett, John M.S., additional, Chadwick, Dianne, additional, Liang, Sheng-Ben, additional, Eagles, Jenna, additional, Mbabaali, Faridah, additional, Miller, Jessica K., additional, Krzyzanowski, Paul, additional, Armstrong, Heather, additional, Luo, Xuemei, additional, Jorgensen, Lars G.T., additional, Romero, Joan M., additional, Bavi, Prashant, additional, Fischer, Sandra E., additional, Serra, Stefano, additional, Hafezi-Bakhtiari, Sara, additional, Caglar, Derin, additional, Roehrl, Michael H.A., additional, Cleary, Sean, additional, Hollingsworth, Michael A., additional, Petersen, Gloria M., additional, Thayer, Sarah, additional, Law, Calvin H.L., additional, Nanji, Sulaiman, additional, Golan, Talia, additional, Smith, Alyssa L., additional, Borgida, Ayelet, additional, Dodd, Anna, additional, Hedley, David, additional, Wouters, Bradly G., additional, O'Kane, Grainne M., additional, Wilson, Julie M., additional, Zogopoulos, George, additional, Notta, Faiyaz, additional, Knox, Jennifer J., additional, and Gallinger, Steven, additional
- Published
- 2019
- Full Text
- View/download PDF
28. Human mismatch repair gene (hMSH2) product expression in relation to recurrence of transitional cell carcinoma of the urinary bladder
- Author
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Jin, Tie-Xiong, Furihata, Mutsuo, Yamasaki, Ichiro, Kamada, Masayuki, Liang, Sheng-Ben, Ohtsuki, Yuji, and Shuin, Taro
- Subjects
Bladder cancer -- Physiological aspects ,Cancer -- Relapse ,Health - Published
- 1999
29. Loss of T-Cadherin (CDH13, H-Cadherin) Expression in Cutaneous Squamous Cell Carcinoma
- Author
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Takeuchi, Tamotsu, Liang, Sheng-Ben, Matsuyoshi, Norihisa, Zhou, Shuxia, Miyachi, Yoshiki, Sonobe, Hiroshi, and Ohtsuki, Yuji
- Published
- 2002
- Full Text
- View/download PDF
30. Genomics-Driven Precision Medicine for Advanced Pancreatic Cancer: Early Results from the COMPASS Trial
- Author
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Aung, Kyaw L., primary, Fischer, Sandra E., additional, Denroche, Robert E., additional, Jang, Gun-Ho, additional, Dodd, Anna, additional, Creighton, Sean, additional, Southwood, Bernadette, additional, Liang, Sheng-Ben, additional, Chadwick, Dianne, additional, Zhang, Amy, additional, O'Kane, Grainne M., additional, Albaba, Hamzeh, additional, Moura, Shari, additional, Grant, Robert C., additional, Miller, Jessica K., additional, Mbabaali, Faridah, additional, Pasternack, Danielle, additional, Lungu, Ilinca M., additional, Bartlett, John M.S., additional, Ghai, Sangeet, additional, Lemire, Mathieu, additional, Holter, Spring, additional, Connor, Ashton A., additional, Moffitt, Richard A., additional, Yeh, Jen Jen, additional, Timms, Lee, additional, Krzyzanowski, Paul M., additional, Dhani, Neesha, additional, Hedley, David, additional, Notta, Faiyaz, additional, Wilson, Julie M., additional, Moore, Malcolm J., additional, Gallinger, Steven, additional, and Knox, Jennifer J., additional
- Published
- 2018
- Full Text
- View/download PDF
31. Integration of Genomic and Transcriptomic Features in Pancreatic Cancer Reveals Increased Cell Cycle Progression in Metastases
- Author
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Connor, Ashton A., primary, Denroche, Robert E., additional, Jang, Gun Ho, additional, Lemire, Mathieu, additional, Zhang, Amy, additional, Chan-Seng-Yue, Michelle, additional, Wilson, Gavin, additional, Merico, Daniele, additional, Lungu, Ilinca, additional, Bartlett, John M. S., additional, Chadwick, Dianne, additional, Liang, Sheng-Ben, additional, Eagles, Jenna, additional, Mbabaali, Faridah, additional, Miller, Jessica K., additional, Krzyzanowski, Paul, additional, Armstrong, Heather, additional, Luo, Xuemei, additional, Jorgensen, Lars G. T., additional, Romero, Joan M., additional, Bavi, Prashant, additional, Fischer, Sandra E., additional, Serra, Stefano, additional, Bakhtiari, Sara Hafezi, additional, Caglar, Derin, additional, Roehrl, Michael H. A., additional, Cleary, Sean, additional, Hollingsworth, Michael A., additional, Petersen, Gloria, additional, Thayer, Sarah, additional, Law, Calvin H. L., additional, Nanji, Sulaiman, additional, Golan, Talia, additional, Smith, Alyssa L., additional, Borgida, Ayelet, additional, Dodd, Anna, additional, Hedley, David, additional, Wouters, Bradly G., additional, OOKane, Grainne M., additional, Wilson, Julie M., additional, Zogopoulos, George, additional, Notta, Faiyaz, additional, Knox, Jennifer J., additional, and Gallinger, Steven, additional
- Published
- 2018
- Full Text
- View/download PDF
32. Erratum: A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns
- Author
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Notta, Faiyaz, primary, Chan-Seng-Yue, Michelle, additional, Lemire, Mathieu, additional, Li, Yilong, additional, Wilson, Gavin W., additional, Connor, Ashton A., additional, Denroche, Robert E., additional, Liang, Sheng-Ben, additional, Brown, Andrew M. K., additional, Kim, Jaeseung C., additional, Wang, Tao, additional, Simpson, Jared T., additional, Beck, Timothy, additional, Borgida, Ayelet, additional, Buchner, Nicholas, additional, Chadwick, Dianne, additional, Hafezi-Bakhtiari, Sara, additional, Dick, John E., additional, Heisler, Lawrence, additional, Hollingsworth, Michael A., additional, Ibrahimov, Emin, additional, Jang, Gun Ho, additional, Johns, Jeremy, additional, Jorgensen, Lars G. T., additional, Law, Calvin, additional, Ludkovski, Olga, additional, Lungu, Ilinca, additional, Ng, Karen, additional, Pasternack, Danielle, additional, Petersen, Gloria M., additional, Shlush, Liran I., additional, Timms, Lee, additional, Tsao, Ming-Sound, additional, Wilson, Julie M., additional, Yung, Christina K., additional, Zogopoulos, George, additional, Bartlett, John M. S., additional, Alexandrov, Ludmil B., additional, Real, Francisco X., additional, Cleary, Sean P., additional, Roehrl, Michael H., additional, McPherson, John D., additional, Stein, Lincoln D., additional, Hudson, Thomas J., additional, Campbell, Peter J., additional, and Gallinger, Steven, additional
- Published
- 2016
- Full Text
- View/download PDF
33. Abstract 3124: Prognostic biomarkers for pancreatic cancer
- Author
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Baciu, Cristina, primary, Grant, Robert, additional, He, Hansen, additional, Ahmed, Musaddeque, additional, Denroche, Robert E., additional, Timms, Lee, additional, Jang, Gun Ho, additional, Borgida, Ayelet, additional, Lin, Xihui, additional, Boutros, Paul C., additional, Chadwich, Dianne, additional, Liang, Sheng-Ben, additional, Shahabi, Sagedeh, additional, Roehrl, Michael H.A., additional, Cleary, Sean, additional, Wilson, Julie M., additional, McPherson, John D., additional, Stein, Lincoln, additional, and Gallinger, Steven, additional
- Published
- 2016
- Full Text
- View/download PDF
34. Abstract A1-17: Genomic analysis of metachronous pancreatic ductal adenocarcinoma
- Author
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Connor, Ashton A., primary, Chan-Seng-Yue, Michelle, additional, Denroche, Robert E., additional, Borgida, Ayelet, additional, Liang, Sheng-Ben, additional, Notta, Faiyaz, additional, Stein, Lincoln, additional, Roehrl, Michael H., additional, McPherson, John, additional, and Gallinger, Steven, additional
- Published
- 2015
- Full Text
- View/download PDF
35. Abstract B2-57: Genomic analysis of metachronous pancreatic ductal adenocarcinoma
- Author
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Connor, Ashton A., primary, Chan-Seng-Yue, Michelle, additional, Denroche, Robert E., additional, Borgida, Ayelet, additional, Liang, Sheng-Ben, additional, Notta, Faiyaz, additional, Stein, Lincoln, additional, Roehrl, Michael H., additional, McPherson, John, additional, and Gallinger, Steven, additional
- Published
- 2015
- Full Text
- View/download PDF
36. Abstract 3381: Standardizing the analysis of Ki-67 immunohistochemical assays
- Author
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Liu, Tian Yu, primary, Chang, Trillium, additional, Adeoye, Adewunmi, additional, Shi, Willa, additional, Liang, Sheng-Ben, additional, Chadwick, Dianne, additional, Roehrl, Michael H.A., additional, Miller, Naomi, additional, Liu, Fei-Fei, additional, and Done, Susan J., additional
- Published
- 2015
- Full Text
- View/download PDF
37. Molecular Target Characterization and Antimyeloma Activity of the Novel, Insulin-like Growth Factor 1 Receptor Inhibitor, GTx-134
- Author
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Liang, Sheng-Ben, primary, Yang, Xiu-Zhi, additional, Trieu, Young, additional, Li, Zhihua, additional, Zive, Jessica, additional, Leung-Hagesteijn, Chungyee, additional, Wei, Ellen, additional, Zozulya, Sergey, additional, Coss, Christopher C., additional, Dalton, James T., additional, Fantus, Ivan George, additional, and Trudel, Suzanne, additional
- Published
- 2011
- Full Text
- View/download PDF
38. Pre-Clinical Evaluation of a Small Molecule Inhibitor of CDK1 as Potential Therapy for MYC Expressing Mutiple Myeloma Tumors
- Author
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Zeng, Seda, primary, Li, Zhi Hua, additional, Chesi, Marta, additional, Leung-Hagesteijn, Chungyee, additional, Liang, Sheng-ben, additional, Bergsagel, P. Leif, additional, and Trudel, Suzanne, additional
- Published
- 2008
- Full Text
- View/download PDF
39. Evaluation of XL999, a Potent Inhibitor of FGFR3, for the Potential Treatment of t(4;14) Positive Multiple Myeloma.
- Author
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Trudel, Suzanne, primary, Yang, Xiu Zhi, primary, Li, Zhi Hua, primary, Liang, Sheng-ben, primary, and Aftab, Dana T., primary
- Published
- 2007
- Full Text
- View/download PDF
40. Multiple Reduced-intensity Conditioning Regimens Facilitate Correction of Fabry Mice After Transplantation of Transduced Cells
- Author
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Liang, Sheng-Ben, primary, Yoshimitsu, Makoto, additional, Poeppl, Armando, additional, Rasaiah, Vanessa I, additional, Cai, Jianhui, additional, Fowler, Daniel H, additional, and Medin, Jeffrey A, additional
- Published
- 2007
- Full Text
- View/download PDF
41. The Bcl-2 Family Protein Inhibitor, ABT-737, Has Substantial Antimyeloma Activity and Shows Synergistic Effect with Dexamethasone and Melphalan
- Author
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Trudel, Suzanne, primary, Stewart, A. Keith, additional, Li, Zhihua, additional, Shu, Yanjun, additional, Liang, Sheng-Ben, additional, Trieu, Young, additional, Reece, Donna, additional, Paterson, Josh, additional, Wang, Dingyan, additional, and Wen, Xiao-Yan, additional
- Published
- 2007
- Full Text
- View/download PDF
42. The inhibitory anti-FGFR3 antibody, PRO-001, is cytotoxic to t(4;14) multiple myeloma cells
- Author
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Trudel, Suzanne, primary, Stewart, A. Keith, additional, Rom, Eran, additional, Wei, Ellen, additional, Li, Zhi Hua, additional, Kotzer, Sarit, additional, Chumakov, Irina, additional, Singer, Yossi, additional, Chang, Hong, additional, Liang, Sheng-Ben, additional, and Yayon, Avner, additional
- Published
- 2006
- Full Text
- View/download PDF
43. Long-Term and Sustained Correction of the α-Galactosidase A Deficiency in Fabry Mice and Patient Cells Receiving Lentivirally Transduced Hematopoietic Stem/Progenitor Cells.
- Author
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Yoshimitsu, Makoto, primary, Siatskas, Christopher, primary, Liang, Sheng-Ben, primary, Rasaiah, Vanessa I., primary, Higuchi, Koji, primary, Murray, Gary J., primary, Takenaka, Toshihiro, primary, Tei, Chuwa, primary, Brady, Roscoe O., primary, and Medin, Jeffrey A., primary
- Published
- 2005
- Full Text
- View/download PDF
44. Functional Engraftment of Retrovirally Transduced and Pre-Selected Hematopoietic Cells into Partially Ablated Recipient Fabry Mice.
- Author
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Medin, Jeffrey A., primary, Liang, Sheng-Ben, primary, Poeppl, Armando, primary, Yoshimitsu, Makoto, primary, Walia, Jagdeep S., primary, Cai, Jianhui, primary, Rasaiah, Vanessa I., primary, and Fowler, Daniel H., primary
- Published
- 2005
- Full Text
- View/download PDF
45. Down-Regulation of a Novel Actin-Binding Molecule, Skeletrophin, in Malignant Melanoma
- Author
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Takeuchi, Tamotsu, primary, Heng, Henry H.Q., additional, Ye, Christine J., additional, Liang, Sheng-Ben, additional, Iwata, Jun, additional, Sonobe, Hiroshi, additional, and Ohtsuki, Yuji, additional
- Published
- 2003
- Full Text
- View/download PDF
46. Downregulation of expression of a novel cadherin molecule, T‐cadherin, in basal cell carcinoma of the skin
- Author
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Takeuchi, Tamotsu, primary, Liang, Sheng‐Ben, additional, and Ohtsuki, Yuji, additional
- Published
- 2002
- Full Text
- View/download PDF
47. Expression of T-Cadherin (CDH13, H-Cadherin) in Human Brain and Its Characteristics as a Negative Growth Regulator of Epidermal Growth Factor in Neuroblastoma Cells
- Author
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Takeuchi, Tamotsu, primary, Misaki, Akiko, additional, Liang, Sheng-Ben, additional, Tachibana, Akiko, additional, Hayashi, Nakanobu, additional, Sonobe, Hiroshi, additional, and Ohtsuki, Yuji, additional
- Published
- 2002
- Full Text
- View/download PDF
48. Multinucleated giant cells in submucosal layer of human urinary bladder: An Immunohistochemical and Electron Microscopic Study
- Author
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Ohtsuki, Yuji, primary, Furihata, Mutsuo, additional, Iwata, Jun, additional, Takeuchi, Tamotsu, additional, Sonobe, Hiroshi, additional, Chen, Bing-Kun, additional, Liang, Sheng-Ben, additional, Kuwahara, Morimasa, additional, Ochi, Kenji, additional, and Terao, Naotami, additional
- Published
- 2000
- Full Text
- View/download PDF
49. Overexpression of c-Met Protein in Human Thyroid Tumors Correlated with Lymph Node Metastasis and Clinicopathologic Stage
- Author
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Chen, Bing-Kun, primary, Ohtsuki, Yuji, additional, Furihata, Mutsuo, additional, Takeuchi, Tamotsu, additional, Iwata, Jun, additional, Liang, Sheng-Ben, additional, and Sonobe, Hiroshi, additional
- Published
- 1999
- Full Text
- View/download PDF
50. Osteoclast-like Giant Cell Tumor of the Pancreas with Metastases to Gallbladder and Lymph Nodes. A Case Report
- Author
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Sun, A-Ping, primary, Ohtsuki, Yuji, additional, Liang, Sheng-Ben, additional, Sonobe, Hiroshi, additional, Iwata, Jun, additional, Furihata, Mutsuo, additional, Takeuchi, Tamotsu, additional, Qiu, Yue, additional, Chen, Bing-Kun, additional, Watanabe, Ryohei, additional, and Ohmori, Katsusuke, additional
- Published
- 1998
- Full Text
- View/download PDF
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