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2. Data from AACR Project GENIE: Powering Precision Medicine through an International Consortium

Author

André, Fabrice, primary, Arnedos, Monica, primary, Baras, Alexander S., primary, Baselga, José, primary, Bedard, Philippe L., primary, Berger, Michael F., primary, Bierkens, Mariska, primary, Calvo, Fabien, primary, Cerami, Ethan, primary, Chakravarty, Debyani, primary, Dang, Kristen K., primary, Davidson, Nancy E., primary, Del Vecchio Fitz, Catherine, primary, Dogan, Semih, primary, DuBois, Raymond N., primary, Ducar, Matthew D., primary, Futreal, P. Andrew, primary, Gao, Jianjiong, primary, Garcia, Francisco, primary, Gardos, Stu, primary, Gocke, Christopher D., primary, Gross, Benjamin E., primary, Guinney, Justin, primary, Heins, Zachary J., primary, Hintzen, Stephanie, primary, Horlings, Hugo, primary, Hudeček, Jan, primary, Hyman, David M., primary, Kamel-Reid, Suzanne, primary, Kandoth, Cyriac, primary, Kinyua, Walter, primary, Kumari, Priti, primary, Kundra, Ritika, primary, Ladanyi, Marc, primary, Lefebvre, Céline, primary, LeNoue-Newton, Michele L., primary, Lepisto, Eva M., primary, Levy, Mia A., primary, Lindeman, Neal I., primary, Lindsay, James, primary, Liu, David, primary, Lu, Zhibin, primary, MacConaill, Laura E., primary, Maurer, Ian, primary, Maxwell, David S., primary, Meijer, Gerrit A., primary, Meric-Bernstam, Funda, primary, Micheel, Christine M., primary, Miller, Clinton, primary, Mills, Gordon, primary, Moore, Nathanael D., primary, Nederlof, Petra M., primary, Omberg, Larsson, primary, Orechia, John A., primary, Park, Ben Ho, primary, Pugh, Trevor J., primary, Reardon, Brendan, primary, Rollins, Barrett J., primary, Routbort, Mark J., primary, Sawyers, Charles L., primary, Schrag, Deborah, primary, Schultz, Nikolaus, primary, Shaw, Kenna R Mills, primary, Shivdasani, Priyanka, primary, Siu, Lillian L., primary, Solit, David B., primary, Sonke, Gabe S., primary, Soria, Jean Charles, primary, Sripakdeevong, Parin, primary, Stickle, Natalie H., primary, Stricker, Thomas P., primary, Sweeney, Shawn M., primary, Taylor, Barry S., primary, ten Hoeve, Jelle J., primary, Thomas, Stacy B., primary, Van Allen, Eliezer M., primary, Van 'T Veer, Laura J., primary, van de Velde, Tony, primary, van Tinteren, Harm, primary, Velculescu, Victor E., primary, Virtanen, Carl, primary, Voest, Emile E., primary, Wang, Lucy L., primary, Wathoo, Chetna, primary, Watt, Stuart, primary, Yu, Celeste, primary, Yu, Thomas V., primary, Yu, Emily, primary, Zehir, Ahmet, primary, and Zhang, Hongxin, primary

Published
2023
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3. Table S3 from AACR Project GENIE: Powering Precision Medicine through an International Consortium

Author

André, Fabrice, primary, Arnedos, Monica, primary, Baras, Alexander S., primary, Baselga, José, primary, Bedard, Philippe L., primary, Berger, Michael F., primary, Bierkens, Mariska, primary, Calvo, Fabien, primary, Cerami, Ethan, primary, Chakravarty, Debyani, primary, Dang, Kristen K., primary, Davidson, Nancy E., primary, Del Vecchio Fitz, Catherine, primary, Dogan, Semih, primary, DuBois, Raymond N., primary, Ducar, Matthew D., primary, Futreal, P. Andrew, primary, Gao, Jianjiong, primary, Garcia, Francisco, primary, Gardos, Stu, primary, Gocke, Christopher D., primary, Gross, Benjamin E., primary, Guinney, Justin, primary, Heins, Zachary J., primary, Hintzen, Stephanie, primary, Horlings, Hugo, primary, Hudeček, Jan, primary, Hyman, David M., primary, Kamel-Reid, Suzanne, primary, Kandoth, Cyriac, primary, Kinyua, Walter, primary, Kumari, Priti, primary, Kundra, Ritika, primary, Ladanyi, Marc, primary, Lefebvre, Céline, primary, LeNoue-Newton, Michele L., primary, Lepisto, Eva M., primary, Levy, Mia A., primary, Lindeman, Neal I., primary, Lindsay, James, primary, Liu, David, primary, Lu, Zhibin, primary, MacConaill, Laura E., primary, Maurer, Ian, primary, Maxwell, David S., primary, Meijer, Gerrit A., primary, Meric-Bernstam, Funda, primary, Micheel, Christine M., primary, Miller, Clinton, primary, Mills, Gordon, primary, Moore, Nathanael D., primary, Nederlof, Petra M., primary, Omberg, Larsson, primary, Orechia, John A., primary, Park, Ben Ho, primary, Pugh, Trevor J., primary, Reardon, Brendan, primary, Rollins, Barrett J., primary, Routbort, Mark J., primary, Sawyers, Charles L., primary, Schrag, Deborah, primary, Schultz, Nikolaus, primary, Shaw, Kenna R Mills, primary, Shivdasani, Priyanka, primary, Siu, Lillian L., primary, Solit, David B., primary, Sonke, Gabe S., primary, Soria, Jean Charles, primary, Sripakdeevong, Parin, primary, Stickle, Natalie H., primary, Stricker, Thomas P., primary, Sweeney, Shawn M., primary, Taylor, Barry S., primary, ten Hoeve, Jelle J., primary, Thomas, Stacy B., primary, Van Allen, Eliezer M., primary, Van 'T Veer, Laura J., primary, van de Velde, Tony, primary, van Tinteren, Harm, primary, Velculescu, Victor E., primary, Virtanen, Carl, primary, Voest, Emile E., primary, Wang, Lucy L., primary, Wathoo, Chetna, primary, Watt, Stuart, primary, Yu, Celeste, primary, Yu, Thomas V., primary, Yu, Emily, primary, Zehir, Ahmet, primary, and Zhang, Hongxin, primary

Published
2023
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4. Supplemental Methods, Supplemental Tables 1-2, Supplemental Figures 1-4 from AACR Project GENIE: Powering Precision Medicine through an International Consortium

Author

André, Fabrice, primary, Arnedos, Monica, primary, Baras, Alexander S., primary, Baselga, José, primary, Bedard, Philippe L., primary, Berger, Michael F., primary, Bierkens, Mariska, primary, Calvo, Fabien, primary, Cerami, Ethan, primary, Chakravarty, Debyani, primary, Dang, Kristen K., primary, Davidson, Nancy E., primary, Del Vecchio Fitz, Catherine, primary, Dogan, Semih, primary, DuBois, Raymond N., primary, Ducar, Matthew D., primary, Futreal, P. Andrew, primary, Gao, Jianjiong, primary, Garcia, Francisco, primary, Gardos, Stu, primary, Gocke, Christopher D., primary, Gross, Benjamin E., primary, Guinney, Justin, primary, Heins, Zachary J., primary, Hintzen, Stephanie, primary, Horlings, Hugo, primary, Hudeček, Jan, primary, Hyman, David M., primary, Kamel-Reid, Suzanne, primary, Kandoth, Cyriac, primary, Kinyua, Walter, primary, Kumari, Priti, primary, Kundra, Ritika, primary, Ladanyi, Marc, primary, Lefebvre, Céline, primary, LeNoue-Newton, Michele L., primary, Lepisto, Eva M., primary, Levy, Mia A., primary, Lindeman, Neal I., primary, Lindsay, James, primary, Liu, David, primary, Lu, Zhibin, primary, MacConaill, Laura E., primary, Maurer, Ian, primary, Maxwell, David S., primary, Meijer, Gerrit A., primary, Meric-Bernstam, Funda, primary, Micheel, Christine M., primary, Miller, Clinton, primary, Mills, Gordon, primary, Moore, Nathanael D., primary, Nederlof, Petra M., primary, Omberg, Larsson, primary, Orechia, John A., primary, Park, Ben Ho, primary, Pugh, Trevor J., primary, Reardon, Brendan, primary, Rollins, Barrett J., primary, Routbort, Mark J., primary, Sawyers, Charles L., primary, Schrag, Deborah, primary, Schultz, Nikolaus, primary, Shaw, Kenna R Mills, primary, Shivdasani, Priyanka, primary, Siu, Lillian L., primary, Solit, David B., primary, Sonke, Gabe S., primary, Soria, Jean Charles, primary, Sripakdeevong, Parin, primary, Stickle, Natalie H., primary, Stricker, Thomas P., primary, Sweeney, Shawn M., primary, Taylor, Barry S., primary, ten Hoeve, Jelle J., primary, Thomas, Stacy B., primary, Van Allen, Eliezer M., primary, Van 'T Veer, Laura J., primary, van de Velde, Tony, primary, van Tinteren, Harm, primary, Velculescu, Victor E., primary, Virtanen, Carl, primary, Voest, Emile E., primary, Wang, Lucy L., primary, Wathoo, Chetna, primary, Watt, Stuart, primary, Yu, Celeste, primary, Yu, Thomas V., primary, Yu, Emily, primary, Zehir, Ahmet, primary, and Zhang, Hongxin, primary

Published
2023
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5. Supplemental File 1 from AACR Project GENIE: Powering Precision Medicine through an International Consortium

Author

André, Fabrice, primary, Arnedos, Monica, primary, Baras, Alexander S., primary, Baselga, José, primary, Bedard, Philippe L., primary, Berger, Michael F., primary, Bierkens, Mariska, primary, Calvo, Fabien, primary, Cerami, Ethan, primary, Chakravarty, Debyani, primary, Dang, Kristen K., primary, Davidson, Nancy E., primary, Del Vecchio Fitz, Catherine, primary, Dogan, Semih, primary, DuBois, Raymond N., primary, Ducar, Matthew D., primary, Futreal, P. Andrew, primary, Gao, Jianjiong, primary, Garcia, Francisco, primary, Gardos, Stu, primary, Gocke, Christopher D., primary, Gross, Benjamin E., primary, Guinney, Justin, primary, Heins, Zachary J., primary, Hintzen, Stephanie, primary, Horlings, Hugo, primary, Hudeček, Jan, primary, Hyman, David M., primary, Kamel-Reid, Suzanne, primary, Kandoth, Cyriac, primary, Kinyua, Walter, primary, Kumari, Priti, primary, Kundra, Ritika, primary, Ladanyi, Marc, primary, Lefebvre, Céline, primary, LeNoue-Newton, Michele L., primary, Lepisto, Eva M., primary, Levy, Mia A., primary, Lindeman, Neal I., primary, Lindsay, James, primary, Liu, David, primary, Lu, Zhibin, primary, MacConaill, Laura E., primary, Maurer, Ian, primary, Maxwell, David S., primary, Meijer, Gerrit A., primary, Meric-Bernstam, Funda, primary, Micheel, Christine M., primary, Miller, Clinton, primary, Mills, Gordon, primary, Moore, Nathanael D., primary, Nederlof, Petra M., primary, Omberg, Larsson, primary, Orechia, John A., primary, Park, Ben Ho, primary, Pugh, Trevor J., primary, Reardon, Brendan, primary, Rollins, Barrett J., primary, Routbort, Mark J., primary, Sawyers, Charles L., primary, Schrag, Deborah, primary, Schultz, Nikolaus, primary, Shaw, Kenna R Mills, primary, Shivdasani, Priyanka, primary, Siu, Lillian L., primary, Solit, David B., primary, Sonke, Gabe S., primary, Soria, Jean Charles, primary, Sripakdeevong, Parin, primary, Stickle, Natalie H., primary, Stricker, Thomas P., primary, Sweeney, Shawn M., primary, Taylor, Barry S., primary, ten Hoeve, Jelle J., primary, Thomas, Stacy B., primary, Van Allen, Eliezer M., primary, Van 'T Veer, Laura J., primary, van de Velde, Tony, primary, van Tinteren, Harm, primary, Velculescu, Victor E., primary, Virtanen, Carl, primary, Voest, Emile E., primary, Wang, Lucy L., primary, Wathoo, Chetna, primary, Watt, Stuart, primary, Yu, Celeste, primary, Yu, Thomas V., primary, Yu, Emily, primary, Zehir, Ahmet, primary, and Zhang, Hongxin, primary

Published
2023
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6. Supplementary Information from Pretreatment microRNA Expression Impacting on Epithelial-to-Mesenchymal Transition Predicts Intrinsic Radiosensitivity in Head and Neck Cancer Cell Lines and Patients

Author

de Jong, Monique C., primary, ten Hoeve, Jelle J., primary, Grénman, Reidar, primary, Wessels, Lodewyk F., primary, Kerkhoven, Ron, primary, te Riele, Hein, primary, van den Brekel, Michiel W.M., primary, Verheij, Marcel, primary, and Begg, Adrian C., primary

Published
2023
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8. Supplementary Figure 1 and Tables 1-8 from Pretreatment microRNA Expression Impacting on Epithelial-to-Mesenchymal Transition Predicts Intrinsic Radiosensitivity in Head and Neck Cancer Cell Lines and Patients

Author

de Jong, Monique C., primary, ten Hoeve, Jelle J., primary, Grénman, Reidar, primary, Wessels, Lodewyk F., primary, Kerkhoven, Ron, primary, te Riele, Hein, primary, van den Brekel, Michiel W.M., primary, Verheij, Marcel, primary, and Begg, Adrian C., primary

Published
2023
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9. Data from MicroRNA Sequence and Expression Analysis in Breast Tumors by Deep Sequencing

Author

Farazi, Thalia A., primary, Horlings, Hugo M., primary, ten Hoeve, Jelle J., primary, Mihailovic, Aleksandra, primary, Halfwerk, Hans, primary, Morozov, Pavel, primary, Brown, Miguel, primary, Hafner, Markus, primary, Reyal, Fabien, primary, van Kouwenhove, Marieke, primary, Kreike, Bas, primary, Sie, Daoud, primary, Hovestadt, Volker, primary, Wessels, Lodewyk F.A., primary, van de Vijver, Marc J., primary, and Tuschl, Thomas, primary

Published
2023
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10. Supplementary Figure 3 from MicroRNA Sequence and Expression Analysis in Breast Tumors by Deep Sequencing

Author

Farazi, Thalia A., primary, Horlings, Hugo M., primary, ten Hoeve, Jelle J., primary, Mihailovic, Aleksandra, primary, Halfwerk, Hans, primary, Morozov, Pavel, primary, Brown, Miguel, primary, Hafner, Markus, primary, Reyal, Fabien, primary, van Kouwenhove, Marieke, primary, Kreike, Bas, primary, Sie, Daoud, primary, Hovestadt, Volker, primary, Wessels, Lodewyk F.A., primary, van de Vijver, Marc J., primary, and Tuschl, Thomas, primary

Published
2023
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11. Supplementary Figure 5 from MicroRNA Sequence and Expression Analysis in Breast Tumors by Deep Sequencing

Author

Farazi, Thalia A., primary, Horlings, Hugo M., primary, ten Hoeve, Jelle J., primary, Mihailovic, Aleksandra, primary, Halfwerk, Hans, primary, Morozov, Pavel, primary, Brown, Miguel, primary, Hafner, Markus, primary, Reyal, Fabien, primary, van Kouwenhove, Marieke, primary, Kreike, Bas, primary, Sie, Daoud, primary, Hovestadt, Volker, primary, Wessels, Lodewyk F.A., primary, van de Vijver, Marc J., primary, and Tuschl, Thomas, primary

Published
2023
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12. Supplementary Figure 4 from MicroRNA Sequence and Expression Analysis in Breast Tumors by Deep Sequencing

Author

Farazi, Thalia A., primary, Horlings, Hugo M., primary, ten Hoeve, Jelle J., primary, Mihailovic, Aleksandra, primary, Halfwerk, Hans, primary, Morozov, Pavel, primary, Brown, Miguel, primary, Hafner, Markus, primary, Reyal, Fabien, primary, van Kouwenhove, Marieke, primary, Kreike, Bas, primary, Sie, Daoud, primary, Hovestadt, Volker, primary, Wessels, Lodewyk F.A., primary, van de Vijver, Marc J., primary, and Tuschl, Thomas, primary

Published
2023
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13. Supplementary Figure 2B from MicroRNA Sequence and Expression Analysis in Breast Tumors by Deep Sequencing

Author

Farazi, Thalia A., primary, Horlings, Hugo M., primary, ten Hoeve, Jelle J., primary, Mihailovic, Aleksandra, primary, Halfwerk, Hans, primary, Morozov, Pavel, primary, Brown, Miguel, primary, Hafner, Markus, primary, Reyal, Fabien, primary, van Kouwenhove, Marieke, primary, Kreike, Bas, primary, Sie, Daoud, primary, Hovestadt, Volker, primary, Wessels, Lodewyk F.A., primary, van de Vijver, Marc J., primary, and Tuschl, Thomas, primary

Published
2023
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14. Supplementary Figure 1 from MicroRNA Sequence and Expression Analysis in Breast Tumors by Deep Sequencing

Author

Farazi, Thalia A., primary, Horlings, Hugo M., primary, ten Hoeve, Jelle J., primary, Mihailovic, Aleksandra, primary, Halfwerk, Hans, primary, Morozov, Pavel, primary, Brown, Miguel, primary, Hafner, Markus, primary, Reyal, Fabien, primary, van Kouwenhove, Marieke, primary, Kreike, Bas, primary, Sie, Daoud, primary, Hovestadt, Volker, primary, Wessels, Lodewyk F.A., primary, van de Vijver, Marc J., primary, and Tuschl, Thomas, primary

Published
2023
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15. Supplementary Methods, Figure and Table Legends from MicroRNA Sequence and Expression Analysis in Breast Tumors by Deep Sequencing

Author

Farazi, Thalia A., primary, Horlings, Hugo M., primary, ten Hoeve, Jelle J., primary, Mihailovic, Aleksandra, primary, Halfwerk, Hans, primary, Morozov, Pavel, primary, Brown, Miguel, primary, Hafner, Markus, primary, Reyal, Fabien, primary, van Kouwenhove, Marieke, primary, Kreike, Bas, primary, Sie, Daoud, primary, Hovestadt, Volker, primary, Wessels, Lodewyk F.A., primary, van de Vijver, Marc J., primary, and Tuschl, Thomas, primary

Published
2023
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16. Supplementary Figure 6 from MicroRNA Sequence and Expression Analysis in Breast Tumors by Deep Sequencing

Author

Farazi, Thalia A., primary, Horlings, Hugo M., primary, ten Hoeve, Jelle J., primary, Mihailovic, Aleksandra, primary, Halfwerk, Hans, primary, Morozov, Pavel, primary, Brown, Miguel, primary, Hafner, Markus, primary, Reyal, Fabien, primary, van Kouwenhove, Marieke, primary, Kreike, Bas, primary, Sie, Daoud, primary, Hovestadt, Volker, primary, Wessels, Lodewyk F.A., primary, van de Vijver, Marc J., primary, and Tuschl, Thomas, primary

Published
2023
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17. Supplementary Tables 1-8C from MicroRNA Sequence and Expression Analysis in Breast Tumors by Deep Sequencing

Author

Farazi, Thalia A., primary, Horlings, Hugo M., primary, ten Hoeve, Jelle J., primary, Mihailovic, Aleksandra, primary, Halfwerk, Hans, primary, Morozov, Pavel, primary, Brown, Miguel, primary, Hafner, Markus, primary, Reyal, Fabien, primary, van Kouwenhove, Marieke, primary, Kreike, Bas, primary, Sie, Daoud, primary, Hovestadt, Volker, primary, Wessels, Lodewyk F.A., primary, van de Vijver, Marc J., primary, and Tuschl, Thomas, primary

Published
2023
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18. A conditional piggyBac transposition system for genetic screening in mice identifies oncogenic networks in pancreatic cancer

Author

Rad, Roland, Rad, Lena, Wang, Wei, Strong, Alexander, Ponstingl, Hannes, Bronner, Iraad F, Mayho, Matthew, Steiger, Katja, Weber, Julia, Hieber, Maren, Veltkamp, Christian, Eser, Stefan, Geumann, Ulf, Öllinger, Rupert, Zukowska, Magdalena, Barenboim, Maxim, Maresch, Roman, Cadiñanos, Juan, Friedrich, Mathias, Varela, Ignacio, Constantino-Casas, Fernando, Sarver, Aaron, ten Hoeve, Jelle, Prosser, Haydn, Seidler, Barbara, Bauer, Judith, Heikenwälder, Mathias, Metzakopian, Emmanouil, Krug, Anne, Ehmer, Ursula, Schneider, Günter, Knösel, Thomas, Rümmele, Petra, Aust, Daniela, Grützmann, Robert, Pilarsky, Christian, Ning, Zemin, Wessels, Lodewyk, Schmid, Roland M, Quail, Michael A, Vassiliou, George, Esposito, Irene, Liu, Pentao, Saur, Dieter, and Bradley, Allan

Published
2015
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20. Erratum to: Validation of a clinical blood-based decision aid to guide immunotherapy treatment in patients with non-small cell lung cancer

Author

Muller, Mirte, primary, Hoogendoorn, Roland, additional, Moritz, Ruben J.G., additional, van der Noort, Vincent, additional, Lanfermeijer, Mirthe, additional, Korse, Catharina M., additional, van den Broek, Daan, additional, ten Hoeve, Jelle J., additional, Baas, Paul, additional, van Rossum, Huub H., additional, and van den Heuvel, Michel M., additional

Published
2021
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21. Validation of a clinical blood-based decision aid to guide immunotherapy treatment in patients with non-small cell lung cancer

Author

Muller, Mirte, primary, Hoogendoorn, Roland, additional, Moritz, Ruben J.G., additional, van der Noort, Vincent, additional, Lanfermeijer, Mirthe, additional, Korse, Catharina M., additional, van den Broek, Daan, additional, ten Hoeve, Jelle J., additional, Baas, Paul, additional, van Rossum, Huub H., additional, and van den Heuvel, Michel M., additional

Published
2021
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22. The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma

Author

Perez-Mancera, Pedro A., Rust, Alistair G., van der Weyden, Louise, Kristiansen, Glen, Li, Allen, Sarver, Aaron L., Silverstein, Kevin A.T., Grutzmann, Robert, Aust, Daniela, Rummele, Petra, Knosel, Thomas, Herd, Colin, Stemple, Derek L., Kettleborough, Ross, Brosnan, Jacqueline A., Li, Ang, Morgan, Richard, Knight, Spencer, Yu, Jun, Stegeman, Shane, Collier, Lara S., ten Hoeve, Jelle J., de Ridder, Jeroen, Klein, Alison P., Goggins, Michael, Hruban, Ralph H., Chang, David K., Biankin, Andrew V., Grimmond, Sean M., Wessels, Lodewyk F.A., Wood, Stephen A., Iacobuzio-Donahue, Christine A., Pilarsky, Christian, Largaespada, David A., Adams, David J., and Tuveson, David A.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Pancreatic ductal adenocarcinoma (PDA) remains a lethal malignancy despite much progress concerning its molecular characterization. PDA tumours harbour four signature somatic mutations (1-4) in addition to numerous lower frequency genetic events of uncertain significance (5). Here we use Sleeping Beauty (SB) transposon-mediated insertional mutagenesis (6,7) in a mouse model of pancreatic ductal preneoplasia (8) to identify genes that cooperate with oncogenic [Kras.sup.G12D] to accelerate tumorigenesis and promote progression. Our screen revealed new candidate genes for PDA and confirmed the importance of many genes and pathways previously implicated in human PDA. The most commonly mutated gene was the X-linked deubiquitinase Usp9x, which was inactivated in over 50% of the tumours. Although previous work had attributed a pro-survival role to USP9X in human neoplasia (9), we found instead that loss of Usp9x enhances transformation and protects pancreatic cancer cells from anoikis. Clinically, low USP9X protein and messenger RNA expression in PDA correlates with poor survival after surgery, and USP9X levels are inversely associated with metastatic burden in advanced disease. Furthermore, chromatin modulation with trichostatin A or 5-aza-2'-deoxycytidine elevates USP9X expression in human PDA cell lines, indicating a clinical approach for certain patients. The conditional deletion of Usp9x cooperated with [Kras.sup.G12D] to accelerate pancreatic tumorigenesis in mice, validating their genetic interaction. We propose that USP9X is a major tumour suppressor gene with prognostic and therapeutic relevance in PDA., The biological sequelae of PDA has been partially attributed to frequent and well characterized mutations in KRAS (>90%), CDKN2A (>90%), TP53 (70%) and SMAD4 (55%) (1-4). Recent genomewide analyses have [...]

Published
2012
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23. Insertional mutagenesis identifies drivers of a novel oncogenic pathway in invasive lobular breast carcinoma

Author

Kas, Sjors M, primary, de Ruiter, Julian R, additional, Schipper, Koen, additional, Annunziato, Stefano, additional, Schut, Eva, additional, Klarenbeek, Sjoerd, additional, Drenth, Anne Paulien, additional, van der Burg, Eline, additional, Klijn, Christiaan, additional, ten Hoeve, Jelle J, additional, Adams, David J, additional, Koudijs, Marco J, additional, Wesseling, Jelle, additional, Nethe, Micha, additional, Wessels, Lodewyk F A, additional, and Jonkers, Jos, additional

Published
2017
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25. Pretreatment microRNA Expression Impacting on Epithelial-to-Mesenchymal Transition Predicts Intrinsic Radiosensitivity in Head and Neck Cancer Cell Lines and Patients

Author

de Jong, Monique C., primary, ten Hoeve, Jelle J., additional, Grénman, Reidar, additional, Wessels, Lodewyk F., additional, Kerkhoven, Ron, additional, te Riele, Hein, additional, van den Brekel, Michiel W.M., additional, Verheij, Marcel, additional, and Begg, Adrian C., additional

Published
2015
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26. Double somatic mutations in mismatch repair genes are frequent in colorectal cancer after Hodgkin's lymphoma treatment.

Author

Rigter, Lisanne S., Snaebjornsson, Petur, Rosenberg, Efraim H., Atmodimedjo, Peggy N., Aleman, Berthe M., ten Hoeve, Jelle, Geurts-Giele, Willemina R., van Ravesteyn, Thomas W., Hoeksel, Johan, Meijer, Gerrit A., te Riele, Hein, van Leeuwen, Flora E., Dinjens, Winand N., and van Leerdam, Monique E.

Subjects
HODGKIN'S disease, COLON cancer treatment, RADIOGRAPHY, CANCER chemotherapy, IMMUNOHISTOCHEMISTRY
Published
2018
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27. Optimizing sharing of hospital biobank samples

Author

Riegman, Peter H. J., primary, de Jong, Bas, additional, Daidone, Maria Grazia, additional, Söderström, Tommy, additional, Thompson, James, additional, Hall, Jacqueline A., additional, Mendy, Maimuna, additional, ten Hoeve, Jelle, additional, Broeks, Annegien, additional, Reed, Wenche, additional, Morente, Manuel M., additional, López-Guerrero, José Antonio, additional, Collins, V. Peter, additional, Rogan, Jane, additional, and Ringborg, Ulrik, additional

Published
2015
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29. A conditional piggyBac transposition system for genetic screening in mice identifies oncogenic networks in pancreatic cancer

Author

Rad, Roland, primary, Rad, Lena, additional, Wang, Wei, additional, Strong, Alexander, additional, Ponstingl, Hannes, additional, Bronner, Iraad F, additional, Mayho, Matthew, additional, Steiger, Katja, additional, Weber, Julia, additional, Hieber, Maren, additional, Veltkamp, Christian, additional, Eser, Stefan, additional, Geumann, Ulf, additional, Öllinger, Rupert, additional, Zukowska, Magdalena, additional, Barenboim, Maxim, additional, Maresch, Roman, additional, Cadiñanos, Juan, additional, Friedrich, Mathias, additional, Varela, Ignacio, additional, Constantino-Casas, Fernando, additional, Sarver, Aaron, additional, ten Hoeve, Jelle, additional, Prosser, Haydn, additional, Seidler, Barbara, additional, Bauer, Judith, additional, Heikenwälder, Mathias, additional, Metzakopian, Emmanouil, additional, Krug, Anne, additional, Ehmer, Ursula, additional, Schneider, Günter, additional, Knösel, Thomas, additional, Rümmele, Petra, additional, Aust, Daniela, additional, Grützmann, Robert, additional, Pilarsky, Christian, additional, Ning, Zemin, additional, Wessels, Lodewyk, additional, Schmid, Roland M, additional, Quail, Michael A, additional, Vassiliou, George, additional, Esposito, Irene, additional, Liu, Pentao, additional, Saur, Dieter, additional, and Bradley, Allan, additional

Published
2014
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31. Analysis of Tumor Heterogeneity and Cancer Gene Networks Using Deep Sequencing of MMTV-Induced Mouse Mammary Tumors

Author

Klijn, Christiaan, primary, Koudijs, Marco J., additional, Kool, Jaap, additional, ten Hoeve, Jelle, additional, Boer, Mandy, additional, de Moes, Joost, additional, Akhtar, Waseem, additional, van Miltenburg, Martine, additional, Vendel-Zwaagstra, Annabel, additional, Reinders, Marcel J. T., additional, Adams, David J., additional, van Lohuizen, Maarten, additional, Hilkens, John, additional, Wessels, Lodewyk F. A., additional, and Jonkers, Jos, additional

Published
2013
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32. Erratum: Corrigendum: The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma

Author

Pérez-Mancera, Pedro A., primary, Rust, Alistair G., additional, van der Weyden, Louise, additional, Kristiansen, Glen, additional, Li, Allen, additional, Sarver, Aaron L., additional, Silverstein, Kevin A. T., additional, Grützmann, Robert, additional, Aust, Daniela, additional, Rümmele, Petra, additional, Knösel, Thomas, additional, Herd, Colin, additional, Stemple, Derek L., additional, Kettleborough, Ross, additional, Brosnan, Jacqueline A., additional, Li, Ang, additional, Morgan, Richard, additional, Knight, Spencer, additional, Yu, Jun, additional, Stegeman, Shane, additional, Collier, Lara S., additional, ten Hoeve, Jelle J., additional, de Ridder, Jeroen, additional, Klein, Alison P., additional, Goggins, Michael, additional, Hruban, Ralph H., additional, Chang, David K., additional, Biankin, Andrew V., additional, Grimmond, Sean M., additional, Initiative, Australian Pancreatic Cancer Genome, additional, Wessels, Lodewyk F. A., additional, Wood, Stephen A., additional, Iacobuzio-Donahue, Christine A., additional, Pilarsky, Christian, additional, Largaespada, David A., additional, Adams, David J., additional, and Tuveson, David A., additional

Published
2013
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33. Insertional mutagenesis identifies multiple networks of cooperating genes driving intestinal tumorigenesis

Author

March, H Nikki, primary, Rust, Alistair G, additional, Wright, Nicholas A, additional, ten Hoeve, Jelle, additional, de Ridder, Jeroen, additional, Eldridge, Matthew, additional, van der Weyden, Louise, additional, Berns, Anton, additional, Gadiot, Jules, additional, Uren, Anthony, additional, Kemp, Richard, additional, Arends, Mark J, additional, Wessels, Lodewyk F A, additional, Winton, Douglas J, additional, and Adams, David J, additional

Published
2011
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34. MicroRNA Sequence and Expression Analysis in Breast Tumors by Deep Sequencing

Author

Farazi, Thalia A., primary, Horlings, Hugo M., additional, ten Hoeve, Jelle J., additional, Mihailovic, Aleksandra, additional, Halfwerk, Hans, additional, Morozov, Pavel, additional, Brown, Miguel, additional, Hafner, Markus, additional, Reyal, Fabien, additional, van Kouwenhove, Marieke, additional, Kreike, Bas, additional, Sie, Daoud, additional, Hovestadt, Volker, additional, Wessels, Lodewyk F.A., additional, van de Vijver, Marc J., additional, and Tuschl, Thomas, additional

Published
2011
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36. Bioinformatic analysis of barcoded cDNA libraries for small RNA profiling by next-generation sequencing

Author

Farazi, Thalia A., Brown, Miguel, Morozov, Pavel, ten Hoeve, Jelle J., Ben-Dov, Iddo Z., Hovestadt, Volker, Hafner, Markus, Renwick, Neil, Mihailović, Aleksandra, Wessels, Lodewyk F.A., and Tuschl, Thomas

Subjects
*ANTISENSE DNA, *BIOINFORMATICS, *BAR codes, *NON-coding RNA, *GENETIC regulation, *NUCLEOTIDE sequence
Abstract

Abstract: The characterization of post-transcriptional gene regulation by small regulatory RNAs of 20–30 nt length, particularly miRNAs and piRNAs, has become a major focus of research in recent years. A prerequisite for the characterization of small RNAs is their identification and quantification across different developmental stages, normal and diseased tissues, as well as model cell lines. Here we present a step-by-step protocol for the bioinformatic analysis of barcoded cDNA libraries for small RNA profiling generated by Illumina sequencing, thereby facilitating miRNA and other small RNA profiling of large sample collections. [Copyright &y& Elsevier]

Published
2012
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37. High-throughput semiquantitative analysis of insertional mutations in heterogeneous tumors.

Author

Koudijs MJ, Klijn C, van der Weyden L, Kool J, ten Hoeve J, Sie D, Prasetyanti PR, Schut E, Kas S, Whipp T, Cuppen E, Wessels L, Adams DJ, and Jonkers J

Subjects
Animals, DNA Mutational Analysis methods, Mice, DNA, Neoplasm genetics, Databases, Genetic, Mammary Tumor Virus, Mouse, Mutagenesis, Insertional, Retroviridae Infections genetics, Tumor Virus Infections genetics
Abstract

Retroviral and transposon-based insertional mutagenesis (IM) screens are widely used for cancer gene discovery in mice. Exploiting the full potential of IM screens requires methods for high-throughput sequencing and mapping of transposon and retroviral insertion sites. Current protocols are based on ligation-mediated PCR amplification of junction fragments from restriction endonuclease-digested genomic DNA, resulting in amplification biases due to uneven genomic distribution of restriction enzyme recognition sites. Consequently, sequence coverage cannot be used to assess the clonality of individual insertions. We have developed a novel method, called shear-splink, for the semiquantitative high-throughput analysis of insertional mutations. Shear-splink employs random fragmentation of genomic DNA, which reduces unwanted amplification biases. Additionally, shear-splink enables us to assess clonality of individual insertions by determining the number of unique ligation points (LPs) between the adapter and genomic DNA. This parameter serves as a semiquantitative measure of the relative clonality of individual insertions within heterogeneous tumors. Mixing experiments with clonal cell lines derived from mouse mammary tumor virus (MMTV)-induced tumors showed that shear-splink enables the semiquantitative assessment of the clonality of MMTV insertions. Further, shear-splink analysis of 16 MMTV- and 127 Sleeping Beauty (SB)-induced tumors showed enrichment for cancer-relevant insertions by exclusion of irrelevant background insertions marked by single LPs, thereby facilitating the discovery of candidate cancer genes. To fully exploit the use of the shear-splink method, we set up the Insertional Mutagenesis Database (iMDB), offering a publicly available web-based application to analyze both retroviral- and transposon-based insertional mutagenesis data.

Published
2011
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