Search

Your search keyword '"Van De Geer, Ellen"' showing total 16 results
Start Over Author "Van De Geer, Ellen"
16 results on '"Van De Geer, Ellen"'

1. Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia

Author

Smits, Willem K., Vermeulen, Carlo, Hagelaar, Rico, Kimura, Shunsuke, Vroegindeweij, Eric M., Buijs-Gladdines, Jessica G.C.A.M., van de Geer, Ellen, Verstegen, Marjon J.A.M., Splinter, Erik, van Reijmersdal, Simon V., Buijs, Arjan, Galjart, Niels, van Eyndhoven, Winfried, van Min, Max, Kuiper, Roland, Kemmeren, Patrick, Mullighan, Charles G., de Laat, Wouter, and Meijerink, Jules P.P.

Published
2023
Full Text
View/download PDF

4. Supplementary Methods from DNA Methylation Profiling Identifies Distinct Clusters in Angiosarcomas

Author

Weidema, Marije E., primary, van de Geer, Ellen, primary, Koelsche, Christian, primary, Desar, Ingrid M.E., primary, Kemmeren, Patrick, primary, Hillebrandt-Roeffen, Melissa H.S., primary, Ho, Vincent K.Y., primary, van der Graaf, Winette T.A., primary, Versleijen-Jonkers, Yvonne M.H., primary, von Deimling, Andreas, primary, and Flucke, Uta E., primary

Published
2023
Full Text
View/download PDF

7. Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia

Author

Smits, Willem K, Vermeulen, Carlo, Hagelaar, Rico, Kimura, Shunsuke, Vroegindeweij, Eric M, Buijs-Gladdines, Jessica G C A M, van de Geer, Ellen, Verstegen, Marjon J A M, Splinter, Erik, van Reijmersdal, Simon V, Buijs, Arjan, Galjart, Niels, van Eyndhoven, Winfried, van Min, Max, Kuiper, Roland, Kemmeren, Patrick, Mullighan, Charles G, de Laat, Wouter, Meijerink, Jules P P, Smits, Willem K, Vermeulen, Carlo, Hagelaar, Rico, Kimura, Shunsuke, Vroegindeweij, Eric M, Buijs-Gladdines, Jessica G C A M, van de Geer, Ellen, Verstegen, Marjon J A M, Splinter, Erik, van Reijmersdal, Simon V, Buijs, Arjan, Galjart, Niels, van Eyndhoven, Winfried, van Min, Max, Kuiper, Roland, Kemmeren, Patrick, Mullighan, Charles G, de Laat, Wouter, and Meijerink, Jules P P

Abstract

Monoallelic inactivation of CCCTC-binding factor (CTCF) in human cancer drives altered methylated genomic states, altered CTCF occupancy at promoter and enhancer regions, and deregulated global gene expression. In patients with T cell acute lymphoblastic leukemia (T-ALL), we find that acquired monoallelic CTCF-inactivating events drive subtle and local genomic effects in nearly half of t(5; 14) (q35; q32.2) rearranged patients, especially when CTCF-binding sites are preserved in between the BCL11B enhancer and the TLX3 oncogene. These solitary intervening sites insulate TLX3 from the enhancer by inducing competitive looping to multiple binding sites near the TLX3 promoter. Reduced CTCF levels or deletion of the intervening CTCF site abrogates enhancer insulation by weakening competitive looping while favoring TLX3 promoter to BCL11B enhancer looping, which elevates oncogene expression levels and leukemia burden.

Published
2023

8. Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia

Author

Genetica Sectie Genoomdiagnostiek, Cancer, Genetica, CMM, CMM Groep Burgering, Hubrecht Institute with UMC, Smits, Willem K, Vermeulen, Carlo, Hagelaar, Rico, Kimura, Shunsuke, Vroegindeweij, Eric M, Buijs-Gladdines, Jessica G C A M, van de Geer, Ellen, Verstegen, Marjon J A M, Splinter, Erik, van Reijmersdal, Simon V, Buijs, Arjan, Galjart, Niels, van Eyndhoven, Winfried, van Min, Max, Kuiper, Roland, Kemmeren, Patrick, Mullighan, Charles G, de Laat, Wouter, Meijerink, Jules P P, Genetica Sectie Genoomdiagnostiek, Cancer, Genetica, CMM, CMM Groep Burgering, Hubrecht Institute with UMC, Smits, Willem K, Vermeulen, Carlo, Hagelaar, Rico, Kimura, Shunsuke, Vroegindeweij, Eric M, Buijs-Gladdines, Jessica G C A M, van de Geer, Ellen, Verstegen, Marjon J A M, Splinter, Erik, van Reijmersdal, Simon V, Buijs, Arjan, Galjart, Niels, van Eyndhoven, Winfried, van Min, Max, Kuiper, Roland, Kemmeren, Patrick, Mullighan, Charles G, de Laat, Wouter, and Meijerink, Jules P P

Published
2023

9. Trecode: A FAIR Eco-System for the Analysis and Archiving of Omics Data in a Combined Diagnostic and Research Setting

Author

Kerstens, Hindrik HD, primary, Hehir-Kwa, Jayne Y, additional, van de Geer, Ellen, additional, van Run, Chris, additional, Badloe, Shashi, additional, Janse, Alex, additional, Baker-Hernandez, John, additional, de Vos, Sam, additional, van der Leest, Douwe, additional, Verwiel, Eugène TP, additional, Tops, Bastiaan BJ, additional, and Kemmeren, Patrick, additional

Published
2022
Full Text
View/download PDF

10. Improved Gene Fusion Detection in Childhood Cancer Diagnostics Using RNA Sequencing

Author

Genetica Sectie Genoomdiagnostiek, Pathologie Moleculair, Cancer, Pathologie Groep Van Diest, PMC Medisch specialisten, Pathologie Pathologen staf, CMM, Hehir-Kwa, Jayne Y, Koudijs, Marco J, Verwiel, Eugene T P, Kester, Lennart A, van Tuil, Marc, Strengman, Eric, Buijs, Arjan, Kranendonk, Mariëtte E G, Hiemcke-Jiwa, Laura S, de Haas, Valerie, van de Geer, Ellen, de Leng, Wendy, van der Lugt, Jasper, Lijnzaad, Philip, Holstege, Frank C P, Kemmeren, Patrick, Tops, Bastiaan B J, Genetica Sectie Genoomdiagnostiek, Pathologie Moleculair, Cancer, Pathologie Groep Van Diest, PMC Medisch specialisten, Pathologie Pathologen staf, CMM, Hehir-Kwa, Jayne Y, Koudijs, Marco J, Verwiel, Eugene T P, Kester, Lennart A, van Tuil, Marc, Strengman, Eric, Buijs, Arjan, Kranendonk, Mariëtte E G, Hiemcke-Jiwa, Laura S, de Haas, Valerie, van de Geer, Ellen, de Leng, Wendy, van der Lugt, Jasper, Lijnzaad, Philip, Holstege, Frank C P, Kemmeren, Patrick, and Tops, Bastiaan B J

Published
2022

11. Trecode: A FAIR Eco-System for the Analysis and Archiving of Omics Data in a Combined Diagnostic and Research Setting.

Author

Kerstens, Hindrik HD, Hehir-Kwa, Jayne Y, van de Geer, Ellen, van Run, Chris, Badloe, Shashi, Janse, Alex, Baker-Hernandez, John, de Vos, Sam, van der Leest, Douwe, Verwiel, Eugène TP, Tops, Bastiaan BJ, and Kemmeren, Patrick

Subjects
DNA sequencing, TRANSCRIPTOMES, EXOMES, RNA sequencing, COMPUTATIONAL biology
Abstract

The increase in speed, reliability, and cost-effectiveness of high-throughput sequencing has led to the widespread clinical application of genome (WGS), exome (WXS), and transcriptome analysis. WXS and RNA sequencing is now being implemented as the standard of care for patients and for patients included in clinical studies. To keep track of sample relationships and analyses, a platform is needed that can unify metadata for diverse sequencing strategies with sample metadata whilst supporting automated and reproducible analyses, in essence ensuring that analyses are conducted consistently and data are Findable, Accessible, Interoperable, and Reusable (FAIR).We present "Trecode", a framework that records both clinical and research sample (meta) data and manages computational genome analysis workflows executed for both settings, thereby achieving tight integration between analysis results and sample metadata. With complete, consistent, and FAIR (meta) data management in a single platform, stacked bioinformatic analyses are performed automatically and tracked by the database, ensuring data provenance, reproducibility, and reusability, which is key in worldwide collaborative translational research. The Trecode data model, codebooks, NGS workflows, and client programs are publicly available. In addition, the complete software stack is coded in an Ansible playbook to facilitate automated deployment and adoption of Trecode by other users. [ABSTRACT FROM AUTHOR]

Published
2023
Full Text
View/download PDF

12. Elevated Enhancer-Oncogene Contacts and Higher Oncogene Expression Levels By Recurrent CTCF inactivating Mutations in T Cell Acute Lymphoblastic Leukemia

Author

Smits, Willem K., primary, Vermeulen, Carlo, additional, Hagelaar, Rico, additional, Kimura, Shunsuke, additional, Vroegindeweij, Eric, additional, Buijs-Gladdines, Jessica G.C.A.M., additional, Van De Geer, Ellen, additional, Verstegen, Marjon J.A.M., additional, Splinter, Erik, additional, van Reijmersdal, Simon V., additional, Buijs, Arjan, additional, Galjart, Niels, additional, Van Eyndhoven, Winfried, additional, Van Min, Max Jan, additional, Kuiper, Roland P, additional, Kemmeren, Patrick, additional, Mullighan, Charles G., additional, De Laat, Wouter, additional, and Meijerink, Jules P.P., additional

Published
2021
Full Text
View/download PDF

14. DNA Methylation Profiling Identifies Distinct Clusters in Angiosarcomas

Author

Weidema, Marije E., primary, van de Geer, Ellen, additional, Koelsche, Christian, additional, Desar, Ingrid M.E., additional, Kemmeren, Patrick, additional, Hillebrandt-Roeffen, Melissa H.S., additional, Ho, Vincent K.Y., additional, van der Graaf, Winette T.A., additional, Versleijen-Jonkers, Yvonne M.H., additional, von Deimling, Andreas, additional, and Flucke, Uta E., additional

Published
2020
Full Text
View/download PDF

15. Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCFinactivating mutations in acute T cell leukemia

Author

Smits, Willem K., Vermeulen, Carlo, Hagelaar, Rico, Kimura, Shunsuke, Vroegindeweij, Eric M., Buijs-Gladdines, Jessica G.C.A.M., van de Geer, Ellen, Verstegen, Marjon J.A.M., Splinter, Erik, van Reijmersdal, Simon V., Buijs, Arjan, Galjart, Niels, van Eyndhoven, Winfried, van Min, Max, Kuiper, Roland, Kemmeren, Patrick, Mullighan, Charles G., de Laat, Wouter, and Meijerink, Jules P.P.

Abstract

Monoallelic inactivation of CCCTC-binding factor (CTCF) in human cancer drives altered methylated genomic states, altered CTCF occupancy at promoter and enhancer regions, and deregulated global gene expression. In T-ALL patients, we find that acquired monoallelic CTCF-inactivating events drive subtle and local genomic effects in nearly half of t(5;14)(q35;q32.2) rearranged patients, and especially when CTCF bindings sites are preserved in between the BCL11B-enhancer and the TLX3oncogene. These solitary intervening sites insulate TLX3from the enhancer by inducing competitive looping to multiple binding sites near the TLX3promoter. Reduced CTCF levels, or deletion of the intervening CTCF site abrogates enhancer insulation by weakening competitive looping while favoring TLX3promoter to BCL11B-enhancer looping that elevates oncogene expression levels and leukemia burden.

Published
2023
Full Text
View/download PDF

16. Elevated Enhancer-Oncogene Contacts and Higher Oncogene Expression Levels By Recurrent CTCFinactivating Mutations in T Cell Acute Lymphoblastic Leukemia

Author

Smits, Willem K., Vermeulen, Carlo, Hagelaar, Rico, Kimura, Shunsuke, Vroegindeweij, Eric, Buijs-Gladdines, Jessica G.C.A.M., Van De Geer, Ellen, Verstegen, Marjon J.A.M., Splinter, Erik, van Reijmersdal, Simon V., Buijs, Arjan, Galjart, Niels, Van Eyndhoven, Winfried, Van Min, Max Jan, Kuiper, Roland P, Kemmeren, Patrick, Mullighan, Charles G., De Laat, Wouter, and Meijerink, Jules P.P.

Abstract

Introduction.The CCCTC-binding factor (CTCF) regulates the 3D chromatin architecture by facilitating chromosomal loops and forming the boundaries of structural domains. In addition, CTCF is an important transcription factor and regulator of antigen receptor and T cell receptor recombination events. CTCFinactivating events have been found in various human cancers. Loss-of-heterozygosity (LOH) or inactivating missense mutations in specific zinc- fingers have been identified in many human cancers including sporadic breast cancer, prostate cancer, Wilms-tumors and acute lymphoblastic leukemia (ALL). Heterozygous deletions or point mutations have been identified in over half of the patients with breast cancer or uterine endometrial cancers, deregulating global gene expression by altering methylated genomic states and poor survival. Here, we investigated the functional significance and molecular-cytogenetic associations of CTCFaberrations in T-cell acute lymphoblastic leukemia patients.

Published
2021
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results