Search

Your search keyword '"Ylstra, Bauke"' showing total 1,115 results
Start Over Author "Ylstra, Bauke"
1,115 results on '"Ylstra, Bauke"'

5. Baseline radiomics features and MYC rearrangement status predict progression in aggressive B-cell lymphoma

Author

Eertink, Jakoba J., Zwezerijnen, Gerben J. C., Wiegers, Sanne E., Pieplenbosch, Simone, Chamuleau, Martine E. D., Lugtenburg, Pieternella J., de Jong, Daphne, Ylstra, Bauke, Mendeville, Matias, Dührsen, Ulrich, Hanoun, Christine, Hüttmann, Andreas, Richter, Julia, Klapper, Wolfram, Jauw, Yvonne W. S., Hoekstra, Otto S., de Vet, Henrica C. W., Boellaard, Ronald, and Zijlstra, Josée M.

Published
2023
Full Text
View/download PDF

6. Hidden RNA profiles of cells in the tumor microenvironment accurately revealed by malignant cell fraction-informed deconvolution

Author

Kim, Yongsoo, primary, Janssen, Jurriaan, additional, Radonic, Teodora, additional, Steketee, Mischa, additional, Asten, Saskia van, additional, Eijk, Paul, additional, Maldegem, Febe van, additional, Noske, David, additional, Bahce, Idris, additional, Vallejo, Juan Garcia, additional, de Wiel, Mark van, additional, and Ylstra, Bauke, additional

Published
2024
Full Text
View/download PDF

7. Response to neoadjuvant chemotherapy and survival in molecular subtypes of resectable gastric cancer: a post hoc analysis of the D1/D2 and CRITICS trials

Author

Biesma, Hedde D., Soeratram, Tanya T. D., Sikorska, Karolina, Caspers, Irene A., van Essen, Hendrik F., Egthuijsen, Jacqueline M. P., Mookhoek, Aart, van Laarhoven, Hanneke W. M., van Berge Henegouwen, Mark I., Nordsmark, Marianne, van der Peet, Donald L., Warmerdam, Fabienne A. R. M., Geenen, Maud M., Loosveld, Olaf J. L., Portielje, Johanneke E. A., Los, Maartje, Heideman, Daniëlle A. M., Meershoek-Klein Kranenbarg, Elma, Hartgrink, Henk H., van Sandick, Johanna, Verheij, Marcel, van de Velde, Cornelis J. H., Cats, Annemieke, Ylstra, Bauke, and van Grieken, Nicole C. T.

Published
2022
Full Text
View/download PDF

8. Genomic and microenvironmental landscape of stage I follicular lymphoma, compared with stage III/IV

Author

Los-de Vries, G. Tjitske, Stevens, Wendy B.C., van Dijk, Erik, Langois-Jacques, Carole, Clear, Andrew J., Stathi, Phylicia, Roemer, Margaretha G.M., Mendeville, Matias, Hijmering, Nathalie J., Sander, Birgitta, Rosenwald, Andreas, Calaminici, Maria, Hoster, Eva, Hiddemann, Wolfgang, Gaulard, Philippe, Salles, Gilles, Horn, Heike, Klapper, Wolfram, Xerri, Luc, Burton, Catherine, Tooze, Reuben M., Smith, Alexandra G., Buske, Christian, Scott, David W., Natkunam, Yasodha, Advani, Ranjana, Sehn, Laurie H., Raemaekers, John, Gribben, John, Kimby, Eva, Kersten, Marie José, Maucort-Boulch, Delphine, Ylstra, Bauke, and de Jong, Daphne

Published
2022
Full Text
View/download PDF

9. Microsatellite instability and sex differences in resectable gastric cancer – A pooled analysis of three European cohorts

Author

Quaas, Alexander, Biesma, Hedde D., Wagner, Anna D., Verheij, Marcel, van Berge Henegouwen, Mark I., Schoemig-Markiefka, Birgid, Pamuk, Aylin, Zander, Thomas, Siemanowski, Janna, Sikorska, Karolina, Egthuijsen, Jacqueline M.P., Meershoek-Klein Kranenbarg, Elma M., van de Velde, Cornelis J.H., Buettner, Reinhard, Alakus, Hakan, Cats, Annemieke, Ylstra, Bauke, van Laarhoven, Hanneke W.M., and van Grieken, Nicole C.T.

Published
2022
Full Text
View/download PDF

11. A multi-platform reference for somatic structural variation detection

Author

Espejo Valle-Inclan, Jose, Besselink, Nicolle J.M., de Bruijn, Ewart, Cameron, Daniel L., Ebler, Jana, Kutzera, Joachim, van Lieshout, Stef, Marschall, Tobias, Nelen, Marcel, Priestley, Peter, Renkens, Ivo, Roemer, Margaretha G.M., van Roosmalen, Markus J., Wenger, Aaron M., Ylstra, Bauke, Fijneman, Remond J.A., Kloosterman, Wigard P., and Cuppen, Edwin

Published
2022
Full Text
View/download PDF

12. Molecular pathways in post-colonoscopy versus detected colorectal cancers: results from a nested case–control study

Author

Bogie, Roel M. M., le Clercq, Chantal M. C., Voorham, Quirinus J. M., Cordes, Martijn, Sie, Daoud, Rausch, Christian, van den Broek, Evert, de Vries, Sara D. J., van Grieken, Nicole C. T., Riedl, Robert G., Sastrowijoto, Prapto, Speel, Ernst-Jan, Vos, Rein, Winkens, Bjorn, van Engeland, Manon, Ylstra, Bauke, Meijer, Gerrit A., Masclee, Ad A. M., and Carvalho, Beatriz

Published
2022
Full Text
View/download PDF

13. Molecular characterization of colorectal cancer related peritoneal metastatic disease

Author

Lenos, Kristiaan J., Bach, Sander, Ferreira Moreno, Leandro, ten Hoorn, Sanne, Sluiter, Nina R., Bootsma, Sanne, Vieira Braga, Felipe A., Nijman, Lisanne E., van den Bosch, Tom, Miedema, Daniel M., van Dijk, Erik, Ylstra, Bauke, Kulicke, Ruth, Davis, Fred P., Stransky, Nicolas, Smolen, Gromoslaw A., Coebergh van den Braak, Robert R. J., IJzermans, Jan N. M., Martens, John W. M., Hallam, Sally, Beggs, Andrew D., Kops, Geert J. P. L., Lansu, Nico, Bastiaenen, Vivian P., Klaver, Charlotte E. L., Lecca, Maria C., El Makrini, Khalid, Elbers, Clara C., Dings, Mark P. G., van Noesel, Carel J. M., Kranenburg, Onno, Medema, Jan Paul, Koster, Jan, Koens, Lianne, Punt, Cornelis J. A., Tanis, Pieter J., de Hingh, Ignace H., Bijlsma, Maarten F., Tuynman, Jurriaan B., and Vermeulen, Louis

Published
2022
Full Text
View/download PDF

14. Evolutionary trajectories of IDH-mutant astrocytoma identify molecular grading markers related to cell cycling

Author

Vallentgoed, Wies R., primary, Hoogstrate, Youri, additional, van Garderen, Karin A., additional, van Hijfte, Levi, additional, van Dijk, Erik, additional, Kouwenhoven, Mathilde C. M., additional, Niers, Johanna M., additional, Draaisma, Kaspar, additional, Martin, Ivonne, additional, de Leng, Wendy W. J., additional, Tesileanu, C. Mircea S., additional, de Heer, Iris, additional, Diepeveen, Maud, additional, Lavrova, Anna, additional, Eijk, Paul P., additional, Bühler, Marcel, additional, Wick, Wolfgang, additional, Clement, Paul M., additional, Sanson, Marc, additional, Franceschi, Enrico, additional, Gorlia, Thierry, additional, Golfinopoulos, Vassilis, additional, Weller, Michael, additional, Weiss, Tobias, additional, Robe, Pierre A., additional, Kros, Johan M., additional, Smits, Marion, additional, van de Wiel, Mark, additional, Ylstra, Bauke, additional, Verhaak, Roel G. W., additional, van den Bent, Martin J., additional, Westerman, Bart A., additional, Wesseling, Pieter, additional, and French, Pim J., additional

Published
2024
Full Text
View/download PDF

15. Table S1 from The Epigenetic Evolution of Glioma Is Determined by the IDH1 Mutation Status and Treatment Regimen

Author

Malta, Tathiane M., primary, Sabedot, Thais S., primary, Morosini, Natalia S., primary, Datta, Indrani, primary, Garofano, Luciano, primary, Vallentgoed, Wies, primary, Varn, Frederick S., primary, Aldape, Kenneth, primary, D'Angelo, Fulvio, primary, Bakas, Spyridon, primary, Barnholtz-Sloan, Jill S., primary, Gan, Hui K., primary, Hasanain, Mohammad, primary, Hau, Ann-Christin, primary, Johnson, Kevin C., primary, Cazacu, Simona, primary, deCarvalho, Ana C., primary, Khasraw, Mustafa, primary, Kocakavuk, Emre, primary, Kouwenhoven, Mathilde C.M., primary, Migliozzi, Simona, primary, Niclou, Simone P., primary, Niers, Johanna M., primary, Ormond, D. Ryan, primary, Paek, Sun Ha, primary, Reifenberger, Guido, primary, Sillevis Smitt, Peter A., primary, Smits, Marion, primary, Stead, Lucy F., primary, van den Bent, Martin J., primary, Van Meir, Erwin G., primary, Walenkamp, Annemiek, primary, Weiss, Tobias, primary, Weller, Michael, primary, Westerman, Bart A., primary, Ylstra, Bauke, primary, Wesseling, Pieter, primary, Lasorella, Anna, primary, French, Pim J., primary, Poisson, Laila M., primary, Woehrer, Adelheid, primary, Lowman, Allison K, primary, deCarvalho, Ana C, primary, Castro, Ana Valeria, primary, Transou, Andrea, primary, Brodbelt, Andrew R, primary, Golebiewska, Anna, primary, Molinaro, Annette M, primary, Iavarone, Antonio, primary, Ismail, Azzam, primary, Westerman, Bart A, primary, Bock, Christoph, primary, Brat, Daniel J, primary, Van Meir, Erwin G, primary, Barthel, Floris P, primary, Varn, Frederick S, primary, Finocchiaro, Gaetano, primary, Rao, Ganesh, primary, Zadeh, Gelareh, primary, ngNg, Ho Keu, primary, Kim, Hoon, primary, Noushmehr, Houtan, primary, Miletic, Hrvoje, primary, Gan, Hui K, primary, Rock, Jack, primary, Snyder, James M, primary, Huse, Jason T, primary, Connelly, Jennifer M, primary, Barnholtz-Sloan, Jill S, primary, Niers, Johanna M, primary, deGroot, John F, primary, Akdemir, Kadir C, primary, Kannan, Kasthuri S, primary, Ligon, Keith L, primary, Bulsara, Ketan R, primary, Johnson, Kevin C, primary, Alfaro, Kristin D, primary, Poisson, Laila M, primary, Stead, Lucy F, primary, Nasrallah, MacLean P, primary, van den Bent, Martin J, primary, Kouwenhoven, Mathilde CM, primary, Gould, Peter V, primary, Smitt, Peter A Sillevis, primary, LaViolette, Peter S, primary, Tatman, Philip D, primary, French, Pim J, primary, Beroukhim, Rameen, primary, Verhaak, Roel G.W., primary, Niclou, Simone P, primary, Kalkanis, Steven, primary, Short, Susan C, primary, Ghazaleh, Tabatabai, primary, Malta, Tathiane M, primary, Sabedot, Thais S, primary, Walbert, Tobias, primary, Baid, Ujjwal, primary, and Yung, W. K. Alfred, primary

Published
2024
Full Text
View/download PDF

16. Supp Figures from The Epigenetic Evolution of Glioma Is Determined by the IDH1 Mutation Status and Treatment Regimen

Author

Malta, Tathiane M., primary, Sabedot, Thais S., primary, Morosini, Natalia S., primary, Datta, Indrani, primary, Garofano, Luciano, primary, Vallentgoed, Wies, primary, Varn, Frederick S., primary, Aldape, Kenneth, primary, D'Angelo, Fulvio, primary, Bakas, Spyridon, primary, Barnholtz-Sloan, Jill S., primary, Gan, Hui K., primary, Hasanain, Mohammad, primary, Hau, Ann-Christin, primary, Johnson, Kevin C., primary, Cazacu, Simona, primary, deCarvalho, Ana C., primary, Khasraw, Mustafa, primary, Kocakavuk, Emre, primary, Kouwenhoven, Mathilde C.M., primary, Migliozzi, Simona, primary, Niclou, Simone P., primary, Niers, Johanna M., primary, Ormond, D. Ryan, primary, Paek, Sun Ha, primary, Reifenberger, Guido, primary, Sillevis Smitt, Peter A., primary, Smits, Marion, primary, Stead, Lucy F., primary, van den Bent, Martin J., primary, Van Meir, Erwin G., primary, Walenkamp, Annemiek, primary, Weiss, Tobias, primary, Weller, Michael, primary, Westerman, Bart A., primary, Ylstra, Bauke, primary, Wesseling, Pieter, primary, Lasorella, Anna, primary, French, Pim J., primary, Poisson, Laila M., primary, Woehrer, Adelheid, primary, Lowman, Allison K, primary, deCarvalho, Ana C, primary, Castro, Ana Valeria, primary, Transou, Andrea, primary, Brodbelt, Andrew R, primary, Golebiewska, Anna, primary, Molinaro, Annette M, primary, Iavarone, Antonio, primary, Ismail, Azzam, primary, Westerman, Bart A, primary, Bock, Christoph, primary, Brat, Daniel J, primary, Van Meir, Erwin G, primary, Barthel, Floris P, primary, Varn, Frederick S, primary, Finocchiaro, Gaetano, primary, Rao, Ganesh, primary, Zadeh, Gelareh, primary, ngNg, Ho Keu, primary, Kim, Hoon, primary, Noushmehr, Houtan, primary, Miletic, Hrvoje, primary, Gan, Hui K, primary, Rock, Jack, primary, Snyder, James M, primary, Huse, Jason T, primary, Connelly, Jennifer M, primary, Barnholtz-Sloan, Jill S, primary, Niers, Johanna M, primary, deGroot, John F, primary, Akdemir, Kadir C, primary, Kannan, Kasthuri S, primary, Ligon, Keith L, primary, Bulsara, Ketan R, primary, Johnson, Kevin C, primary, Alfaro, Kristin D, primary, Poisson, Laila M, primary, Stead, Lucy F, primary, Nasrallah, MacLean P, primary, van den Bent, Martin J, primary, Kouwenhoven, Mathilde CM, primary, Gould, Peter V, primary, Smitt, Peter A Sillevis, primary, LaViolette, Peter S, primary, Tatman, Philip D, primary, French, Pim J, primary, Beroukhim, Rameen, primary, Verhaak, Roel G.W., primary, Niclou, Simone P, primary, Kalkanis, Steven, primary, Short, Susan C, primary, Ghazaleh, Tabatabai, primary, Malta, Tathiane M, primary, Sabedot, Thais S, primary, Walbert, Tobias, primary, Baid, Ujjwal, primary, and Yung, W. K. Alfred, primary

Published
2024
Full Text
View/download PDF

17. Supplemental Figures Legends from The Epigenetic Evolution of Glioma Is Determined by the IDH1 Mutation Status and Treatment Regimen

Author

Malta, Tathiane M., primary, Sabedot, Thais S., primary, Morosini, Natalia S., primary, Datta, Indrani, primary, Garofano, Luciano, primary, Vallentgoed, Wies, primary, Varn, Frederick S., primary, Aldape, Kenneth, primary, D'Angelo, Fulvio, primary, Bakas, Spyridon, primary, Barnholtz-Sloan, Jill S., primary, Gan, Hui K., primary, Hasanain, Mohammad, primary, Hau, Ann-Christin, primary, Johnson, Kevin C., primary, Cazacu, Simona, primary, deCarvalho, Ana C., primary, Khasraw, Mustafa, primary, Kocakavuk, Emre, primary, Kouwenhoven, Mathilde C.M., primary, Migliozzi, Simona, primary, Niclou, Simone P., primary, Niers, Johanna M., primary, Ormond, D. Ryan, primary, Paek, Sun Ha, primary, Reifenberger, Guido, primary, Sillevis Smitt, Peter A., primary, Smits, Marion, primary, Stead, Lucy F., primary, van den Bent, Martin J., primary, Van Meir, Erwin G., primary, Walenkamp, Annemiek, primary, Weiss, Tobias, primary, Weller, Michael, primary, Westerman, Bart A., primary, Ylstra, Bauke, primary, Wesseling, Pieter, primary, Lasorella, Anna, primary, French, Pim J., primary, Poisson, Laila M., primary, Woehrer, Adelheid, primary, Lowman, Allison K, primary, deCarvalho, Ana C, primary, Castro, Ana Valeria, primary, Transou, Andrea, primary, Brodbelt, Andrew R, primary, Golebiewska, Anna, primary, Molinaro, Annette M, primary, Iavarone, Antonio, primary, Ismail, Azzam, primary, Westerman, Bart A, primary, Bock, Christoph, primary, Brat, Daniel J, primary, Van Meir, Erwin G, primary, Barthel, Floris P, primary, Varn, Frederick S, primary, Finocchiaro, Gaetano, primary, Rao, Ganesh, primary, Zadeh, Gelareh, primary, ngNg, Ho Keu, primary, Kim, Hoon, primary, Noushmehr, Houtan, primary, Miletic, Hrvoje, primary, Gan, Hui K, primary, Rock, Jack, primary, Snyder, James M, primary, Huse, Jason T, primary, Connelly, Jennifer M, primary, Barnholtz-Sloan, Jill S, primary, Niers, Johanna M, primary, deGroot, John F, primary, Akdemir, Kadir C, primary, Kannan, Kasthuri S, primary, Ligon, Keith L, primary, Bulsara, Ketan R, primary, Johnson, Kevin C, primary, Alfaro, Kristin D, primary, Poisson, Laila M, primary, Stead, Lucy F, primary, Nasrallah, MacLean P, primary, van den Bent, Martin J, primary, Kouwenhoven, Mathilde CM, primary, Gould, Peter V, primary, Smitt, Peter A Sillevis, primary, LaViolette, Peter S, primary, Tatman, Philip D, primary, French, Pim J, primary, Beroukhim, Rameen, primary, Verhaak, Roel G.W., primary, Niclou, Simone P, primary, Kalkanis, Steven, primary, Short, Susan C, primary, Ghazaleh, Tabatabai, primary, Malta, Tathiane M, primary, Sabedot, Thais S, primary, Walbert, Tobias, primary, Baid, Ujjwal, primary, and Yung, W. K. Alfred, primary

Published
2024
Full Text
View/download PDF

18. Data from The Epigenetic Evolution of Glioma Is Determined by the IDH1 Mutation Status and Treatment Regimen

Author

Malta, Tathiane M., primary, Sabedot, Thais S., primary, Morosini, Natalia S., primary, Datta, Indrani, primary, Garofano, Luciano, primary, Vallentgoed, Wies, primary, Varn, Frederick S., primary, Aldape, Kenneth, primary, D'Angelo, Fulvio, primary, Bakas, Spyridon, primary, Barnholtz-Sloan, Jill S., primary, Gan, Hui K., primary, Hasanain, Mohammad, primary, Hau, Ann-Christin, primary, Johnson, Kevin C., primary, Cazacu, Simona, primary, deCarvalho, Ana C., primary, Khasraw, Mustafa, primary, Kocakavuk, Emre, primary, Kouwenhoven, Mathilde C.M., primary, Migliozzi, Simona, primary, Niclou, Simone P., primary, Niers, Johanna M., primary, Ormond, D. Ryan, primary, Paek, Sun Ha, primary, Reifenberger, Guido, primary, Sillevis Smitt, Peter A., primary, Smits, Marion, primary, Stead, Lucy F., primary, van den Bent, Martin J., primary, Van Meir, Erwin G., primary, Walenkamp, Annemiek, primary, Weiss, Tobias, primary, Weller, Michael, primary, Westerman, Bart A., primary, Ylstra, Bauke, primary, Wesseling, Pieter, primary, Lasorella, Anna, primary, French, Pim J., primary, Poisson, Laila M., primary, Woehrer, Adelheid, primary, Lowman, Allison K, primary, deCarvalho, Ana C, primary, Castro, Ana Valeria, primary, Transou, Andrea, primary, Brodbelt, Andrew R, primary, Golebiewska, Anna, primary, Molinaro, Annette M, primary, Iavarone, Antonio, primary, Ismail, Azzam, primary, Westerman, Bart A, primary, Bock, Christoph, primary, Brat, Daniel J, primary, Van Meir, Erwin G, primary, Barthel, Floris P, primary, Varn, Frederick S, primary, Finocchiaro, Gaetano, primary, Rao, Ganesh, primary, Zadeh, Gelareh, primary, ngNg, Ho Keu, primary, Kim, Hoon, primary, Noushmehr, Houtan, primary, Miletic, Hrvoje, primary, Gan, Hui K, primary, Rock, Jack, primary, Snyder, James M, primary, Huse, Jason T, primary, Connelly, Jennifer M, primary, Barnholtz-Sloan, Jill S, primary, Niers, Johanna M, primary, deGroot, John F, primary, Akdemir, Kadir C, primary, Kannan, Kasthuri S, primary, Ligon, Keith L, primary, Bulsara, Ketan R, primary, Johnson, Kevin C, primary, Alfaro, Kristin D, primary, Poisson, Laila M, primary, Stead, Lucy F, primary, Nasrallah, MacLean P, primary, van den Bent, Martin J, primary, Kouwenhoven, Mathilde CM, primary, Gould, Peter V, primary, Smitt, Peter A Sillevis, primary, LaViolette, Peter S, primary, Tatman, Philip D, primary, French, Pim J, primary, Beroukhim, Rameen, primary, Verhaak, Roel G.W., primary, Niclou, Simone P, primary, Kalkanis, Steven, primary, Short, Susan C, primary, Ghazaleh, Tabatabai, primary, Malta, Tathiane M, primary, Sabedot, Thais S, primary, Walbert, Tobias, primary, Baid, Ujjwal, primary, and Yung, W. K. Alfred, primary

Published
2024
Full Text
View/download PDF

19. Supplementary Appendix from The Epigenetic Evolution of Glioma Is Determined by the IDH1 Mutation Status and Treatment Regimen

Author

Malta, Tathiane M., primary, Sabedot, Thais S., primary, Morosini, Natalia S., primary, Datta, Indrani, primary, Garofano, Luciano, primary, Vallentgoed, Wies, primary, Varn, Frederick S., primary, Aldape, Kenneth, primary, D'Angelo, Fulvio, primary, Bakas, Spyridon, primary, Barnholtz-Sloan, Jill S., primary, Gan, Hui K., primary, Hasanain, Mohammad, primary, Hau, Ann-Christin, primary, Johnson, Kevin C., primary, Cazacu, Simona, primary, deCarvalho, Ana C., primary, Khasraw, Mustafa, primary, Kocakavuk, Emre, primary, Kouwenhoven, Mathilde C.M., primary, Migliozzi, Simona, primary, Niclou, Simone P., primary, Niers, Johanna M., primary, Ormond, D. Ryan, primary, Paek, Sun Ha, primary, Reifenberger, Guido, primary, Sillevis Smitt, Peter A., primary, Smits, Marion, primary, Stead, Lucy F., primary, van den Bent, Martin J., primary, Van Meir, Erwin G., primary, Walenkamp, Annemiek, primary, Weiss, Tobias, primary, Weller, Michael, primary, Westerman, Bart A., primary, Ylstra, Bauke, primary, Wesseling, Pieter, primary, Lasorella, Anna, primary, French, Pim J., primary, Poisson, Laila M., primary, Woehrer, Adelheid, primary, Lowman, Allison K, primary, deCarvalho, Ana C, primary, Castro, Ana Valeria, primary, Transou, Andrea, primary, Brodbelt, Andrew R, primary, Golebiewska, Anna, primary, Molinaro, Annette M, primary, Iavarone, Antonio, primary, Ismail, Azzam, primary, Westerman, Bart A, primary, Bock, Christoph, primary, Brat, Daniel J, primary, Van Meir, Erwin G, primary, Barthel, Floris P, primary, Varn, Frederick S, primary, Finocchiaro, Gaetano, primary, Rao, Ganesh, primary, Zadeh, Gelareh, primary, ngNg, Ho Keu, primary, Kim, Hoon, primary, Noushmehr, Houtan, primary, Miletic, Hrvoje, primary, Gan, Hui K, primary, Rock, Jack, primary, Snyder, James M, primary, Huse, Jason T, primary, Connelly, Jennifer M, primary, Barnholtz-Sloan, Jill S, primary, Niers, Johanna M, primary, deGroot, John F, primary, Akdemir, Kadir C, primary, Kannan, Kasthuri S, primary, Ligon, Keith L, primary, Bulsara, Ketan R, primary, Johnson, Kevin C, primary, Alfaro, Kristin D, primary, Poisson, Laila M, primary, Stead, Lucy F, primary, Nasrallah, MacLean P, primary, van den Bent, Martin J, primary, Kouwenhoven, Mathilde CM, primary, Gould, Peter V, primary, Smitt, Peter A Sillevis, primary, LaViolette, Peter S, primary, Tatman, Philip D, primary, French, Pim J, primary, Beroukhim, Rameen, primary, Verhaak, Roel G.W., primary, Niclou, Simone P, primary, Kalkanis, Steven, primary, Short, Susan C, primary, Ghazaleh, Tabatabai, primary, Malta, Tathiane M, primary, Sabedot, Thais S, primary, Walbert, Tobias, primary, Baid, Ujjwal, primary, and Yung, W. K. Alfred, primary

Published
2024
Full Text
View/download PDF

20. The Epigenetic Evolution of Glioma Is Determined by the IDH1 Mutation Status and Treatment Regimen

Author

Malta, Tathiane M., Sabedot, Thais S., Morosini, Natalia S., Datta, Indrani, Garofano, Luciano, Vallentgoed, Wies, Varn, Frederick S., Aldape, Kenneth, D'Angelo, Fulvio, Bakas, Spyridon, Barnholtz-Sloan, Jill S., Gan, Hui K., Hasanain, Mohammad, Hau, Ann Christin, Johnson, Kevin C., Cazacu, Simona, deCarvalho, Ana C., Khasraw, Mustafa, Kocakavuk, Emre, Kouwenhoven, Mathilde C.M., Migliozzi, Simona, Niclou, Simone P., Niers, Johanna M., Ormond, D. Ryan, Paek, Sun Ha, Reifenberger, Guido, Smitt, Peter A.Sillevis, Smits, Marion, Stead, Lucy F., van den Bent, Martin J., Van Meir, Erwin G., Walenkamp, Annemiek, Weiss, Tobias, Weller, Michael, Westerman, Bart A., Ylstra, Bauke, Wesseling, Pieter, Lasorella, Anna, French, Pim J., Poisson, Laila M., Verhaak, Roel G.W., Iavarone, Antonio, Noushmehr, Houtan, Malta, Tathiane M., Sabedot, Thais S., Morosini, Natalia S., Datta, Indrani, Garofano, Luciano, Vallentgoed, Wies, Varn, Frederick S., Aldape, Kenneth, D'Angelo, Fulvio, Bakas, Spyridon, Barnholtz-Sloan, Jill S., Gan, Hui K., Hasanain, Mohammad, Hau, Ann Christin, Johnson, Kevin C., Cazacu, Simona, deCarvalho, Ana C., Khasraw, Mustafa, Kocakavuk, Emre, Kouwenhoven, Mathilde C.M., Migliozzi, Simona, Niclou, Simone P., Niers, Johanna M., Ormond, D. Ryan, Paek, Sun Ha, Reifenberger, Guido, Smitt, Peter A.Sillevis, Smits, Marion, Stead, Lucy F., van den Bent, Martin J., Van Meir, Erwin G., Walenkamp, Annemiek, Weiss, Tobias, Weller, Michael, Westerman, Bart A., Ylstra, Bauke, Wesseling, Pieter, Lasorella, Anna, French, Pim J., Poisson, Laila M., Verhaak, Roel G.W., Iavarone, Antonio, and Noushmehr, Houtan

Abstract

Tumor adaptation or selection is thought to underlie therapy resistance in glioma. To investigate longitudinal epigenetic evolution of gliomas in response to therapeutic pressure, we performed an epigenomic analysis of 132 matched initial and recurrent tumors from patients with IDH-wildtype (IDHwt) and IDH-mutant (IDHmut) glioma. IDHwt gliomas showed a stable epigenome over time with relatively low levels of global methylation. The epigenome of IDHmut gliomas showed initial high levels of genome-wide DNA methylation that was progressively reduced to levels similar to those of IDHwt tumors. Integration of epigenomics, gene expression, and functional genomics identified HOXD13 as a master regulator of IDHmut astrocytoma evolution. Furthermore, relapse of IDHmut tumors was accompanied by histologic progression that was associated with survival, as validated in an independent cohort. Finally, the initial cell composition of the tumor microenvironment varied between IDHwt and IDHmut tumors and changed differentially following treatment, suggesting increased neoangiogenesis and T-cell infiltration upon treatment of IDHmut gliomas. This study provides one of the largest cohorts of paired longitudinal glioma samples with epigenomic, transcriptomic, and genomic profiling and suggests that treatment of IDHmut glioma is associated with epigenomic evolution toward an IDHwt-like phenotype.

Published
2024

22. Tumor-Educated Platelet RNA for the Detection and (Pseudo)progression Monitoring of Glioblastoma

Author

Sol, Nik, in ‘t Veld, Sjors G.J.G., Vancura, Adrienne, Tjerkstra, Maud, Leurs, Cyra, Rustenburg, François, Schellen, Pepijn, Verschueren, Heleen, Post, Edward, Zwaan, Kenn, Ramaker, Jip, Wedekind, Laurine E., Tannous, Jihane, Ylstra, Bauke, Killestein, Joep, Mateen, Farrah, Idema, Sander, de Witt Hamer, Philip C., Navis, Anna C., Leenders, William P.J., Hoeben, Ann, Moraal, Bastiaan, Noske, David P., Vandertop, W. Peter, Nilsson, R. Jonas A., Tannous, Bakhos A., Wesseling, Pieter, Reijneveld, Jaap C., Best, Myron G., and Wurdinger, Thomas

Published
2020
Full Text
View/download PDF

25. The epigenetic evolution of glioma is determined by the IDH1 mutation status and treatment regimen

Author

Malta, Tathiane M., primary, Sabedot, Thais S., additional, Morosini, Natalia S., additional, Datta, Indrani, additional, Garofano, Luciano, additional, Vallentgoed, Wies R., additional, Varn, Frederick S., additional, Aldape, Kenneth, additional, D'Angelo, Fulvio, additional, Bakas, Spyridon, additional, Barnholtz-Sloan, Jill S., additional, Gan, Hui K., additional, Hasanain, Mohammad, additional, Hau, Ann-Christin, additional, Johnson, Kevin C., additional, Cazacu, Simona, additional, deCarvalho, Ana C., additional, Khasraw, Mustafa, additional, Kocakavuk, Emre, additional, Kouwenhoven, Mathilde C.M., additional, Migliozzi, Simona, additional, Niclou, Simone P., additional, Niers, Johanna M., additional, Ormond, D. Ryan., additional, Paek, Sun Ha, additional, Reifenberger, Guido, additional, Sillevis Smitt, Peter A., additional, Smits, Marion, additional, Stead, Lucy F., additional, van den Bent, Martin J., additional, Van Meir, Erwin G., additional, Walenkamp, Annemiek, additional, Weiss, Tobias, additional, Weller, Michael, additional, Westerman, Bart A., additional, Ylstra, Bauke, additional, Wesseling, Pieter, additional, Lasorella, Anna, additional, French, Pim J., additional, Poisson, Laila M., additional, Consortium, The GLASS, additional, Verhaak, Roel G.W., additional, Iavarone, Antonio, additional, and Noushmehr, Houtan, additional

Published
2023
Full Text
View/download PDF

26. Longitudinal characteristics of T2-FLAIR mismatch in IDH-mutant astrocytomas: relation to grade, histopathology and overall survival in the GLASS-NL cohort

Author

van Garderen, Karin A, primary, Vallentgoed, Wies R, additional, Lavrova, Anna, additional, Niers, Johanna M, additional, de Leng, Wendy W J, additional, Hoogstrate, Youri, additional, de Heer, Iris, additional, Ylstra, Bauke, additional, van Dijk, Erik, additional, Klein, Stefan, additional, Draaisma, Kaspar, additional, Robe, Pierre A J T, additional, Verhaak, Roel G W, additional, Westerman, Bart A, additional, French, Pim J, additional, van den Bent, Martin J, additional, Kouwenhoven, Mathilde C M, additional, Kros, Johan M, additional, Wesseling, Pieter, additional, and Smits, Marion, additional

Published
2023
Full Text
View/download PDF

27. Spatiotemporal regulation of clonogenicity in colorectal cancer xenografts

Author

van der Heijden, Maartje, Miedema, Daniël M., Waclaw, Bartlomiej, Veenstra, Veronique L., Lecca, Maria C., Nijman, Lisanne E., van Dijk, Erik, van Neerven, Sanne M., Lodestijn, Sophie C., Lenos, Kristiaan J., de Groot, Nina E., Prasetyanti, Pramudita R., Varea, Andrea Arricibita, Winton, Douglas J., Medema, Jan Paul, Morrissey, Edward, Ylstra, Bauke, Nowak, Martin A., Bijlsma, Maarten F., and Vermeulen, Louis

Published
2019

28. Chromosomal copy number heterogeneity predicts survival rates across cancers

Author

van Dijk, Erik, van den Bosch, Tom, Lenos, Kristiaan J., El Makrini, Khalid, Nijman, Lisanne E., van Essen, Hendrik F. B., Lansu, Nico, Boekhout, Michiel, Hageman, Joris H., Fitzgerald, Rebecca C., Punt, Cornelis J. A., Tuynman, Jurriaan B., Snippert, Hugo J. G., Kops, Geert J. P. L., Medema, Jan Paul, Ylstra, Bauke, Vermeulen, Louis, and Miedema, Daniël M.

Published
2021
Full Text
View/download PDF

30. Robust detection of translocations in lymphoma FFPE samples using targeted locus capture-based sequencing

Author

Allahyar, Amin, Pieterse, Mark, Swennenhuis, Joost, Los-de Vries, G. Tjitske, Yilmaz, Mehmet, Leguit, Roos, Meijers, Ruud W. J., van der Geize, Robert, Vermaat, Joost, Cleven, Arjen, van Wezel, Tom, Diepstra, Arjan, van Kempen, Léon C., Hijmering, Nathalie J., Stathi, Phylicia, Sharma, Milan, Melquiond, Adrien S. J., de Vree, Paula J. P., Verstegen, Marjon J. A. M., Krijger, Peter H. L., Hajo, Karima, Simonis, Marieke, Rakszewska, Agata, van Min, Max, de Jong, Daphne, Ylstra, Bauke, Feitsma, Harma, Splinter, Erik, and de Laat, Wouter

Published
2021
Full Text
View/download PDF

31. Evolution of DNA repair defects during malignant progression of low-grade gliomas after temozolomide treatment

Author

van Thuijl, Hinke F, Mazor, Tali, Johnson, Brett E, Fouse, Shaun D, Aihara, Koki, Hong, Chibo, Malmström, Annika, Hallbeck, Martin, Heimans, Jan J, Kloezeman, Jenneke J, Stenmark-Askmalm, Marie, Lamfers, Martine LM, Saito, Nobuhito, Aburatani, Hiroyuki, Mukasa, Akitake, Berger, Mitchell S, Söderkvist, Peter, Taylor, Barry S, Molinaro, Annette M, Wesseling, Pieter, Reijneveld, Jaap C, Chang, Susan M, Ylstra, Bauke, and Costello, Joseph F

Subjects
Rare Diseases, Brain Cancer, Brain Disorders, Cancer, Neurosciences, Genetics, Antineoplastic Agents, Alkylating, Brain Neoplasms, Cohort Studies, DNA Methylation, DNA Modification Methylases, DNA Repair Enzymes, DNA Repair-Deficiency Disorders, Dacarbazine, Disease Progression, Female, Glioma, Humans, Male, Mutation, Receptors, Immunologic, Statistics, Nonparametric, Temozolomide, Tumor Suppressor Proteins, Low-grade glioma, Hypermutator, Mismatch repair, MGMT, Clinical Sciences, Neurology & Neurosurgery
Abstract

Temozolomide (TMZ) increases the overall survival of patients with glioblastoma (GBM), but its role in the clinical management of diffuse low-grade gliomas (LGG) is still being defined. DNA hypermethylation of the O (6) -methylguanine-DNA methyltransferase (MGMT) promoter is associated with an improved response to TMZ treatment, while inactivation of the DNA mismatch repair (MMR) pathway is associated with therapeutic resistance and TMZ-induced mutagenesis. We previously demonstrated that TMZ treatment of LGG induces driver mutations in the RB and AKT-mTOR pathways, which may drive malignant progression to secondary GBM. To better understand the mechanisms underlying TMZ-induced mutagenesis and malignant progression, we explored the evolution of MGMT methylation and genetic alterations affecting MMR genes in a cohort of 34 treatment-naïve LGGs and their recurrences. Recurrences with TMZ-associated hypermutation had increased MGMT methylation compared to their untreated initial tumors and higher overall MGMT methylation compared to TMZ-treated non-hypermutated recurrences. A TMZ-associated mutation in one or more MMR genes was observed in five out of six TMZ-treated hypermutated recurrences. In two cases, pre-existing heterozygous deletions encompassing MGMT, or an MMR gene, were followed by TMZ-associated mutations in one of the genes of interest. These results suggest that tumor cells with methylated MGMT may undergo positive selection during TMZ treatment in the context of MMR deficiency.

Published
2015

32. DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly.

Author

Scheinin, Ilari, Sie, Daoud, Bengtsson, Henrik, van de Wiel, Mark A, Olshen, Adam B, van Thuijl, Hinke F, van Essen, Hendrik F, Eijk, Paul P, Rustenburg, François, Meijer, Gerrit A, Reijneveld, Jaap C, Wesseling, Pieter, Pinkel, Daniel, Albertson, Donna G, and Ylstra, Bauke

Subjects
Cell Line, Tumor, Humans, Neoplasms, Computational Biology, Genomics, Base Composition, Genome, Human, Algorithms, Software, Comparative Genomic Hybridization, DNA Copy Number Variations, High-Throughput Nucleotide Sequencing, Cell Line, Tumor, Genome, Human, Genetics, Biotechnology, Human Genome, Bioinformatics, Biological Sciences, Medical and Health Sciences
Abstract

Detection of DNA copy number aberrations by shallow whole-genome sequencing (WGS) faces many challenges, including lack of completion and errors in the human reference genome, repetitive sequences, polymorphisms, variable sample quality, and biases in the sequencing procedures. Formalin-fixed paraffin-embedded (FFPE) archival material, the analysis of which is important for studies of cancer, presents particular analytical difficulties due to degradation of the DNA and frequent lack of matched reference samples. We present a robust, cost-effective WGS method for DNA copy number analysis that addresses these challenges more successfully than currently available procedures. In practice, very useful profiles can be obtained with ∼0.1× genome coverage. We improve on previous methods by first implementing a combined correction for sequence mappability and GC content, and second, by applying this procedure to sequence data from the 1000 Genomes Project in order to develop a blacklist of problematic genome regions. A small subset of these blacklisted regions was previously identified by ENCODE, but the vast majority are novel unappreciated problematic regions. Our procedures are implemented in a pipeline called QDNAseq. We have analyzed over 1000 samples, most of which were obtained from the fixed tissue archives of more than 25 institutions. We demonstrate that for most samples our sequencing and analysis procedures yield genome profiles with noise levels near the statistical limit imposed by read counting. The described procedures also provide better correction of artifacts introduced by low DNA quality than prior approaches and better copy number data than high-resolution microarrays at a substantially lower cost.

Published
2014

33. The Impact of Genetic Subtypes of Diffuse Large B-Cell Lymphoma for Outcome Prediction and Interpretation of FDG-PET treatment Response Monitoring

Author

Ylstra, Bauke, primary, Mendeville, Matias, additional, Janssen, Jurriaan, additional, Vries, G. Tjitske Los-de, additional, Dijk, Erik van, additional, Richter, Julia, additional, Nijland, Marcel, additional, Roemer, Margaretha, additional, Stathi, Phylicia, additional, Hijmering, Nathalie, additional, Bladergroen, Reno, additional, Pelaz, Diego, additional, Diepstra, Arjan, additional, Eertink, Corinne, additional, Burggraaff, Coreline, additional, Kim, Yongsoo, additional, Lugtenburg, Pieternella, additional, Berg, Anke van den, additional, Tzankov, Alexandar, additional, Dirnhofer, Stephan, additional, Duhrsen, Ulrich, additional, Hüttmann, Andreas, additional, Klapper, Wolfram, additional, Zijlstra-Baalbergen, Josée, additional, and de Jong, Daphne, additional

Published
2023
Full Text
View/download PDF

39. Combination of variations in inflammation- and endoplasmic reticulum-associated genes as putative biomarker for bevacizumab response in KRAS wild-type colorectal cancer

Author

Barat, Ana, Smeets, Dominiek, Moran, Bruce, Zhang, Wu, Cao, Shu, Das, Sudipto, Klinger, Rut, Betge, Johannes, Murphy, Verena, Bacon, Orna, Kay, Elaine W., Van Grieken, Nicole C. T., Verheul, Henk M. W., Gaiser, Timo, Schulte, Nadine, Ebert, Matthias P., Fender, Bozena, Hennessy, Bryan T., McNamara, Deborah A., O’Connor, Darran, Gallagher, William M., Cremolini, Chiara, Loupakis, Fotios, Parikh, Aparna, Mancao, Christoph, Ylstra, Bauke, Lambrechts, Diether, Lenz, Heinz-Josef, Byrne, Annette T., and Prehn, Jochen H. M.

Published
2020
Full Text
View/download PDF

40. Breast tumor copy number aberration phenotypes and genomic instability

Author

Fridlyand, Jane, Snijders, Antoine M, Ylstra, Bauke, Li, Hua, Olshen, Adam, Segraves, Richard, Dairkee, Shanaz, Tokuyasu, Taku, Ljung, Britt Marie, Jain, Ajay N, McLennan, Jane, Ziegler, John, Chin, Koei, Devries, Sandy, Feiler, Heidi, Gray, Joe W, Waldman, Frederic, Pinkel, Daniel, and Albertson, Donna G

Abstract

Background: Genomic DNA copy number aberrations are frequent in solid tumors, although the underlying causes of chromosomal instability in tumors remain obscure. Genes likely to have genomic instability phenotypes when mutated ( e. g. those involved in mitosis, replication, repair, and telomeres) are rarely mutated in chromosomally unstable sporadic tumors, even though such mutations are associated with some heritable cancer prone syndromes. Methods: We applied array comparative genomic hybridization (CGH) to the analysis of breast tumors. The variation in the levels of genomic instability amongst tumors prompted us to investigate whether alterations in processes/genes involved in maintenance and/or manipulation of the genome were associated with particular types of genomic instability. Results: We discriminated three breast tumor subtypes based on genomic DNA copy number alterations. The subtypes varied with respect to level of genomic instability. We find that shorter telomeres and altered telomere related gene expression are associated with amplification, implicating telomere attrition as a promoter of this type of aberration in breast cancer. On the other hand, the numbers of chromosomal alterations, particularly low level changes, are associated with altered expression of genes in other functional classes (mitosis, cell cycle, DNA replication and repair). Further, although loss of function instability phenotypes have been demonstrated for many of the genes in model systems, we observed enhanced expression of most genes in tumors, indicating that over expression, rather than deficiency underlies instability. Conclusion: Many of the genes associated with higher frequency of copy number aberrations are direct targets of E2F, supporting the hypothesis that deregulation of the Rb pathway is a major contributor to chromosomal instability in breast tumors. These observations are consistent with failure to find mutations in sporadic tumors in genes that have roles in maintenance or manipulation of the genome.

Published
2006

42. Copy number signatures and mutational processes in ovarian carcinoma

Author

Macintyre, Geoff, Goranova, Teodora E., De Silva, Dilrini, Ennis, Darren, Piskorz, Anna M., Eldridge, Matthew, Sie, Daoud, Lewsley, Liz-Anne, Hanif, Aishah, Wilson, Cheryl, Dowson, Suzanne, Glasspool, Rosalind M., Lockley, Michelle, Brockbank, Elly, Montes, Ana, Walther, Axel, Sundar, Sudha, Edmondson, Richard, Hall, Geoff D., Clamp, Andrew, Gourley, Charlie, Hall, Marcia, Fotopoulou, Christina, Gabra, Hani, Paul, James, Supernat, Anna, Millan, David, Hoyle, Aoisha, Bryson, Gareth, Nourse, Craig, Mincarelli, Laura, Sanchez, Luis Navarro, Ylstra, Bauke, Jimenez-Linan, Mercedes, Moore, Luiza, Hofmann, Oliver, Markowetz, Florian, McNeish, Iain A., and Brenton, James D.

Published
2018
Full Text
View/download PDF

47. Genetic and Microenvironment Features Do Not Distinguish Follicular Lymphoma Patients Requiring Immediate or Deferred Treatment

Author

Stevens, Wendy B. C., primary, Los-de Vries, G. Tjitske, additional, Langois-Jacques, Carole, additional, Clear, Andrew J., additional, Stathi, Phylicia, additional, Sander, Birgitta, additional, Rosenwald, Andreas, additional, Calaminici, Maria, additional, Hoster, Eva, additional, Hiddemann, Wolfgang, additional, Gaulard, Philippe, additional, Salles, Gilles, additional, Klapper, Wolfram, additional, Xerri, Luc, additional, Burton, Catherine, additional, Tooze, Reuben M., additional, Smith, Alexandra G., additional, Buske, Christian, additional, Scott, David W., additional, Natkunam, Yasodha, additional, Advani, Ranjana, additional, Sehn, Laurie H., additional, Raemaekers, John, additional, Gribben, John, additional, Lockmer, Sandra, additional, Kimby, Eva, additional, Kersten, Marie José, additional, Maucort-Boulch, Delphine, additional, Ylstra, Bauke, additional, van Dijk, Erik, additional, and de Jong, Daphne, additional

Published
2023
Full Text
View/download PDF

48. Supplementary Table 1 from Mismatch Repair Status and BRAF Mutation Status in Metastatic Colorectal Cancer Patients: A Pooled Analysis of the CAIRO, CAIRO2, COIN, and FOCUS Studies

Author

Venderbosch, Sabine, primary, Nagtegaal, Iris D., primary, Maughan, Tim S., primary, Smith, Christopher G., primary, Cheadle, Jeremy P., primary, Fisher, David, primary, Kaplan, Richard, primary, Quirke, Philip, primary, Seymour, Matthew T., primary, Richman, Susan D., primary, Meijer, Gerrit A., primary, Ylstra, Bauke, primary, Heideman, Danielle A.M., primary, de Haan, Anton F.J., primary, Punt, Cornelis J.A., primary, and Koopman, Miriam, primary

Published
2023
Full Text
View/download PDF

50. Supplementary Figure 2 from Chromosome 5q Loss in Colorectal Flat Adenomas

Author

Voorham, Quirinus J.M., primary, Carvalho, Beatriz, primary, Spiertz, Angela J., primary, van Grieken, Nicole C.T., primary, Mongera, Sandra, primary, Rondagh, Eveline J.A., primary, van de Wiel, Mark A., primary, Jordanova, Ekaterina S., primary, Ylstra, Bauke, primary, Kliment, Martin, primary, Grabsch, Heike, primary, Rembacken, Bjorn J., primary, Arai, Tomio, primary, de Bruïne, Adriaan P., primary, Sanduleanu, Silvia, primary, Quirke, Philip, primary, Mulder, Chris J.J., primary, van Engeland, Manon, primary, and Meijer, Gerrit A., primary

Published
2023
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results