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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
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2. Formalin-Fixed, Paraffin-Embedded–Targeted Locus Capture: A Next-Generation Sequencing Technology for Accurate DNA-Based Gene Fusion Detection in Bone and Soft Tissue Tumors

Author

Stelloo, Ellen, Meijers, Ruud W.J., Swennenhuis, Joost F., Allahyar, Amin, Hajo, Karima, Cangiano, Mario, de Leng, Wendy W.J., van Helvert, Sjoerd, Van der Meulen, Joni, Creytens, David, van Kempen, Léon C., Cleton-Jansen, Anne-Marie, Bovee, Judith V.M.G., de Laat, Wouter, Splinter, Erik, and Feitsma, Harma

Published
2023
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4. 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
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5. Long-Range Chromatin Contacts in Embryonic Stem Cells Reveal a Role for Pluripotency Factors and Polycomb Proteins in Genome Organization

Author

Denholtz, Matthew, Bonora, Giancarlo, Chronis, Constantinos, Splinter, Erik, de Laat, Wouter, Ernst, Jason, Pellegrini, Matteo, and Plath, Kathrin

Subjects
Biochemistry and Cell Biology, Bioinformatics and Computational Biology, Biological Sciences, Stem Cell Research, Regenerative Medicine, Genetics, Stem Cell Research - Embryonic - Non-Human, Human Genome, 1.1 Normal biological development and functioning, Generic health relevance, Animals, Chromatin, Embryonic Stem Cells, Histones, In Situ Hybridization, Fluorescence, Mice, Polycomb-Group Proteins, Protein Binding, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

The relationship between 3D organization of the genome and gene-regulatory networks is poorly understood. Here, we examined long-range chromatin interactions genome-wide in mouse embryonic stem cells (ESCs), iPSCs, and fibroblasts and uncovered a pluripotency-specific genome organization that is gradually reestablished during reprogramming. Our data confirm that long-range chromatin interactions are primarily associated with the spatial segregation of open and closed chromatin, defining overall chromosome conformation. Additionally, we identified two further levels of genome organization in ESCs characterized by colocalization of regions with high pluripotency factor occupancy and strong enrichment for Polycomb proteins/H3K27me3, respectively. Underlining the independence of these networks and their functional relevance for genome organization, loss of the Polycomb protein Eed diminishes interactions between Polycomb-regulated regions without altering overarching chromosome conformation. Together, our data highlight a pluripotency-specific genome organization in which pluripotency factors such as Nanog and H3K27me3 occupy distinct nuclear spaces and reveal a role for cell-type-specific gene-regulatory networks in genome organization.

Published
2013

7. Targeted locus amplification to develop robust patient-specific assays for liquid biopsies in pediatric solid tumors

Author

van Zogchel, Lieke M. J., primary, Lak, Nathalie S. M., additional, Gelineau, Nina U., additional, Sergeeva, Irina, additional, Stelloo, Ellen, additional, Swennenhuis, Joost, additional, Feitsma, Harma, additional, van Min, Max, additional, Splinter, Erik, additional, Bleijs, Margit, additional, Groot Koerkamp, Marian, additional, Breunis, Willemijn, additional, Meister, Michael Torsten, additional, Kholossy, Waleed Hassan, additional, Holstege, Frank C. P., additional, Molenaar, Jan J., additional, de Leng, Wendy W. J., additional, Stutterheim, Janine, additional, van der Schoot, C. Ellen, additional, and Tytgat, Godelieve A. M., additional

Published
2023
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8. Targeted locus amplification to develop robust patient-specific assays for liquid biopsies in pediatric solid tumors

Author

van Zogchel, Lieke M.J., Lak, Nathalie S.M., Gelineau, Nina U., Sergeeva, Irina, Stelloo, Ellen, Swennenhuis, Joost, Feitsma, Harma, van Min, Max, Splinter, Erik, Bleijs, Margit, Groot Koerkamp, Marian, Breunis, Willemijn, Meister, Michael Torsten, Kholossy, Waleed Hassan, Holstege, Frank C.P., Molenaar, Jan J., de Leng, Wendy W.J., Stutterheim, Janine, van der Schoot, C. Ellen, Tytgat, Godelieve A.M., van Zogchel, Lieke M.J., Lak, Nathalie S.M., Gelineau, Nina U., Sergeeva, Irina, Stelloo, Ellen, Swennenhuis, Joost, Feitsma, Harma, van Min, Max, Splinter, Erik, Bleijs, Margit, Groot Koerkamp, Marian, Breunis, Willemijn, Meister, Michael Torsten, Kholossy, Waleed Hassan, Holstege, Frank C.P., Molenaar, Jan J., de Leng, Wendy W.J., Stutterheim, Janine, van der Schoot, C. Ellen, and Tytgat, Godelieve A.M.

Abstract

Background: Liquid biopsies combine minimally invasive sample collection with sensitive detection of residual disease. Pediatric malignancies harbor tumor-driving copy number alterations or fusion genes, rather than recurrent point mutations. These regions contain tumor-specific DNA breakpoint sequences. We investigated the feasibility to use these breakpoints to design patient-specific markers to detect tumor-derived cell-free DNA (cfDNA) in plasma from patients with pediatric solid tumors. Materials and methods: Regions of interest (ROI) were identified through standard clinical diagnostic pipelines, using SNP array for CNAs, and FISH or RT-qPCR for fusion genes. Using targeted locus amplification (TLA) on tumor organoids grown from tumor material or targeted locus capture (TLC) on FFPE material, ROI-specific primers and probes were designed, which were used to design droplet digital PCR (ddPCR) assays. cfDNA from patient plasma at diagnosis and during therapy was analyzed. Results: TLA was performed on material from 2 rhabdomyosarcoma, 1 Ewing sarcoma and 3 neuroblastoma. FFPE-TLC was performed on 8 neuroblastoma tumors. For all patients, at least one patient-specific ddPCR was successfully designed and in all diagnostic plasma samples the patient-specific markers were detected. In the rhabdomyosarcoma and Ewing sarcoma patients, all samples after start of therapy were negative. In neuroblastoma patients, presence of patient-specific markers in cfDNA tracked tumor burden, decreasing during induction therapy, disappearing at complete remission and re-appearing at relapse. Conclusion: We demonstrate the feasibility to determine tumor-specific breakpoints using TLA/TLC in different pediatric solid tumors and use these for analysis of cfDNA from plasma. Considering the high prevalence of CNAs and fusion genes in pediatric solid tumors, this approach holds great promise and deserves further study in a larger cohort with standardized plasma sampling protocols.

Published
2023

9. Targeted locus amplification to develop robust patient-specific assays for liquid biopsies in pediatric solid tumors

Author

Afd Pharmaceutics, Pharmaceutics, van Zogchel, Lieke M.J., Lak, Nathalie S.M., Gelineau, Nina U., Sergeeva, Irina, Stelloo, Ellen, Swennenhuis, Joost, Feitsma, Harma, van Min, Max, Splinter, Erik, Bleijs, Margit, Groot Koerkamp, Marian, Breunis, Willemijn, Meister, Michael Torsten, Kholossy, Waleed Hassan, Holstege, Frank C.P., Molenaar, Jan J., de Leng, Wendy W.J., Stutterheim, Janine, van der Schoot, C. Ellen, Tytgat, Godelieve A.M., Afd Pharmaceutics, Pharmaceutics, van Zogchel, Lieke M.J., Lak, Nathalie S.M., Gelineau, Nina U., Sergeeva, Irina, Stelloo, Ellen, Swennenhuis, Joost, Feitsma, Harma, van Min, Max, Splinter, Erik, Bleijs, Margit, Groot Koerkamp, Marian, Breunis, Willemijn, Meister, Michael Torsten, Kholossy, Waleed Hassan, Holstege, Frank C.P., Molenaar, Jan J., de Leng, Wendy W.J., Stutterheim, Janine, van der Schoot, C. Ellen, and Tytgat, Godelieve A.M.

Published
2023

10. 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

11. Targeted Locus Amplification and Haplotyping

Author

Lefferts, Juliet W., Boersma, Vera, Hagemeijer, Marne C., Hajo, Karima, Beekman, Jeffrey M., Splinter, Erik, Lefferts, Juliet W., Boersma, Vera, Hagemeijer, Marne C., Hajo, Karima, Beekman, Jeffrey M., and Splinter, Erik

Abstract

Targeted locus amplification (TLA) allows for the detection of all genetic variation (including structural variation) in a genomic region of interest. As TLA is based on proximity ligation, variants can be linked to each other, thereby enabling allelic phasing and the generation of haplotypes. This allows for the study of genetic variants in an allele-specific manner. Here, we provide a step-by-step protocol for TLA sample preparation and a complete bioinformatics pipeline for the allelic phasing of TLA data. Additionally, to illustrate the protocol, we show the ability of TLA to re-sequence and haplotype the complete cystic fibrosis transmembrane (CFTR) gene (> 200 kb in size) from patient-derived intestinal organoids.

Published
2023

12. Formalin-Fixed, Paraffin-Embedded-Targeted Locus Capture: A Next-Generation Sequencing Technology for Accurate DNA-Based Gene Fusion Detection in Bone and Soft Tissue Tumors

Author

CMM Groep Cuppen, Pathologie Moleculair, CMM Groep De Ridder, Cancer, Pathologie Pathologen staf, CMM Groep Burgering, Genetica, Hubrecht Institute with UMC, Stelloo, Ellen, Meijers, Ruud W J, Swennenhuis, Joost F, Allahyar, Amin, Hajo, Karima, Cangiano, Mario, de Leng, Wendy W J, van Helvert, Sjoerd, Van der Meulen, Joni, Creytens, David, van Kempen, Léon C, Cleton-Jansen, Anne-Marie, Bovee, Judith V M G, de Laat, Wouter, Splinter, Erik, Feitsma, Harma, CMM Groep Cuppen, Pathologie Moleculair, CMM Groep De Ridder, Cancer, Pathologie Pathologen staf, CMM Groep Burgering, Genetica, Hubrecht Institute with UMC, Stelloo, Ellen, Meijers, Ruud W J, Swennenhuis, Joost F, Allahyar, Amin, Hajo, Karima, Cangiano, Mario, de Leng, Wendy W J, van Helvert, Sjoerd, Van der Meulen, Joni, Creytens, David, van Kempen, Léon C, Cleton-Jansen, Anne-Marie, Bovee, Judith V M G, de Laat, Wouter, Splinter, Erik, and Feitsma, Harma

Published
2023

13. Targeted locus amplification to develop robust patient-specific assays for liquid biopsies in pediatric solid tumors

Author

CMM Groep Cuppen, Groep Holstege, Pathologie Pathologen staf, Cancer, van Zogchel, Lieke M J, Lak, Nathalie S M, Gelineau, Nina U, Sergeeva, Irina, Stelloo, Ellen, Swennenhuis, Joost, Feitsma, Harma, van Min, Max, Splinter, Erik, Bleijs, Margit, Groot Koerkamp, Marian, Breunis, Willemijn, Meister, Michael Torsten, Kholossy, Waleed Hassan, Holstege, Frank C P, Molenaar, Jan J, de Leng, Wendy W J, Stutterheim, Janine, van der Schoot, C Ellen, Tytgat, Godelieve A M, CMM Groep Cuppen, Groep Holstege, Pathologie Pathologen staf, Cancer, van Zogchel, Lieke M J, Lak, Nathalie S M, Gelineau, Nina U, Sergeeva, Irina, Stelloo, Ellen, Swennenhuis, Joost, Feitsma, Harma, van Min, Max, Splinter, Erik, Bleijs, Margit, Groot Koerkamp, Marian, Breunis, Willemijn, Meister, Michael Torsten, Kholossy, Waleed Hassan, Holstege, Frank C P, Molenaar, Jan J, de Leng, Wendy W J, Stutterheim, Janine, van der Schoot, C Ellen, and Tytgat, Godelieve A M

Published
2023

14. 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

15. Targeted Locus Amplification and Haplotyping

Author

Longziekten onderzoek 2, Cancer, Longziekten onderzoek 1, Onderzoek, Child Health, Regenerative Medicine and Stem Cells, Lefferts, Juliet W., Boersma, Vera, Hagemeijer, Marne C., Hajo, Karima, Beekman, Jeffrey M., Splinter, Erik, Longziekten onderzoek 2, Cancer, Longziekten onderzoek 1, Onderzoek, Child Health, Regenerative Medicine and Stem Cells, Lefferts, Juliet W., Boersma, Vera, Hagemeijer, Marne C., Hajo, Karima, Beekman, Jeffrey M., and Splinter, Erik

Published
2023

16. Targeted locus amplification to develop robust patient-specific assays for liquid biopsies in pediatric solid tumors

Author

van Zogchel, Lieke M J, Lak, Nathalie S M; https://orcid.org/0000-0003-3743-8826, Gelineau, Nina U, Sergeeva, Irina, Stelloo, Ellen, Swennenhuis, Joost, Feitsma, Harma, van Min, Max, Splinter, Erik, Bleijs, Margit, Groot Koerkamp, Marian, Breunis, Willemijn, Meister, Michael Torsten, Kholossy, Waleed Hassan, Holstege, Frank C P; https://orcid.org/0000-0002-8090-5146, Molenaar, Jan J, de Leng, Wendy W J, Stutterheim, Janine; https://orcid.org/0000-0002-9828-0834, van der Schoot, C Ellen, Tytgat, Godelieve A M, van Zogchel, Lieke M J, Lak, Nathalie S M; https://orcid.org/0000-0003-3743-8826, Gelineau, Nina U, Sergeeva, Irina, Stelloo, Ellen, Swennenhuis, Joost, Feitsma, Harma, van Min, Max, Splinter, Erik, Bleijs, Margit, Groot Koerkamp, Marian, Breunis, Willemijn, Meister, Michael Torsten, Kholossy, Waleed Hassan, Holstege, Frank C P; https://orcid.org/0000-0002-8090-5146, Molenaar, Jan J, de Leng, Wendy W J, Stutterheim, Janine; https://orcid.org/0000-0002-9828-0834, van der Schoot, C Ellen, and Tytgat, Godelieve A M

Abstract

BACKGROUND Liquid biopsies combine minimally invasive sample collection with sensitive detection of residual disease. Pediatric malignancies harbor tumor-driving copy number alterations or fusion genes, rather than recurrent point mutations. These regions contain tumor-specific DNA breakpoint sequences. We investigated the feasibility to use these breakpoints to design patient-specific markers to detect tumor-derived cell-free DNA (cfDNA) in plasma from patients with pediatric solid tumors. MATERIALS AND METHODS Regions of interest (ROI) were identified through standard clinical diagnostic pipelines, using SNP array for CNAs, and FISH or RT-qPCR for fusion genes. Using targeted locus amplification (TLA) on tumor organoids grown from tumor material or targeted locus capture (TLC) on FFPE material, ROI-specific primers and probes were designed, which were used to design droplet digital PCR (ddPCR) assays. cfDNA from patient plasma at diagnosis and during therapy was analyzed. RESULTS TLA was performed on material from 2 rhabdomyosarcoma, 1 Ewing sarcoma and 3 neuroblastoma. FFPE-TLC was performed on 8 neuroblastoma tumors. For all patients, at least one patient-specific ddPCR was successfully designed and in all diagnostic plasma samples the patient-specific markers were detected. In the rhabdomyosarcoma and Ewing sarcoma patients, all samples after start of therapy were negative. In neuroblastoma patients, presence of patient-specific markers in cfDNA tracked tumor burden, decreasing during induction therapy, disappearing at complete remission and re-appearing at relapse. CONCLUSION We demonstrate the feasibility to determine tumor-specific breakpoints using TLA/TLC in different pediatric solid tumors and use these for analysis of cfDNA from plasma. Considering the high prevalence of CNAs and fusion genes in pediatric solid tumors, this approach holds great promise and deserves further study in a larger cohort with standardized plasma sampling protocols.

Published
2023

18. 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
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19. The pluripotent genome in three dimensions is shaped around pluripotency factors

Author

de Wit, Elzo, Bouwman, Britta A.M., Zhu, Yun, Klous, Petra, Splinter, Erik, Verstegen, Marjon J.A.M., Krijger, Peter H.L., Festuccia, Nicola, Nora, Elphege P., Welling, Maaike, Heard, Edith, Geijsen, Niels, Poot, Raymond A., Chambers, Ian, and de Laat, Wouter

Subjects
Nucleotide sequencing -- Research, Stem cells -- Properties, DNA sequencing -- Research, Genetic regulation -- Research, Chromosomes -- Properties, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

It is becoming increasingly clear that the shape of the genome importantly influences transcription regulation. Pluripotent stem cells such as embryonic stem cells were recently shown to organize their chromosomes into topological domains that are largely invariant between cell types (1,2). Here we combine chromatin conformation capture technologies with chromatin factor binding data to demonstrate that inactive chromatin is unusually disorganized in pluripotent stem-cell nuclei. We show that gene promoters engage in contacts between topological domains in a largely tissue-independent manner, whereas enhancers have a more tissue-restricted interaction profile. Notably, genomic clusters of pluripotency factor binding sites find each other very efficiently, in a manner that is strictly pluripotent-stem-cell-specific, dependent on the presence of Oct4 and Nanog protein and inducible after artificial recruitment of Nanog to a selected chromosomal site. We conclude that pluripotent stem cells have a unique higher-order genome structure shaped by pluripotency factors. We speculate that this interactome enhances the robustness of the pluripotent state., In recent years, several technological advances have made it possible to delineate the three-dimensional shape of the genome (3). Spatial organization of DNA has been recognized as an additional regulatory [...]

Published
2013

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

Author

CMM Groep De Ridder, Cancer, CMM Groep Kloosterman, Pathologie Pathologen staf, Pathologie Moleculair, CMM Onderwijs, Pathologie Moleculair Path., CMM Groep Burgering, Genetica, Hubrecht Institute with UMC, 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, de Laat, Wouter, CMM Groep De Ridder, Cancer, CMM Groep Kloosterman, Pathologie Pathologen staf, Pathologie Moleculair, CMM Onderwijs, Pathologie Moleculair Path., CMM Groep Burgering, Genetica, Hubrecht Institute with UMC, 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

22. Targeted locus amplification to detect molecular markers in mantle cell and follicular lymphoma

Author

Genuardi, Elisa, primary, Klous, Petra, additional, Mantoan, Barbara, additional, Drandi, Daniela, additional, Ferrante, Martina, additional, Cavallo, Federica, additional, Alessandria, Beatrice, additional, Dogliotti, Irene, additional, Grimaldi, Daniele, additional, Ragaini, Simone, additional, Clerico, Michele, additional, Lo Schirico, Mariella, additional, Saraci, Elona, additional, Yilmaz, Mehmet, additional, Zaccaria, Gian Maria, additional, Cortelazzo, Sergio, additional, Vitolo, Umberto, additional, Luminari, Stefano, additional, Federico, Massimo, additional, Boccadoro, Mario, additional, Min, Max, additional, Splinter, Erik, additional, Ladetto, Marco, additional, and Ferrero, Simone, additional

Published
2021
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23. Elevated Enhancer-Oncogene Contacts and Higher Oncogene Expression Levels by Recurrent CTCF Inactivating Mutations in Acute T Cell Leukemia

Author

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

Published
2021
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24. 4C Technology: Protocols and Data Analysis

Author

van de Werken, Harmen J.G., primary, de Vree, Paula J.P., additional, Splinter, Erik, additional, Holwerda, Sjoerd J.B., additional, Klous, Petra, additional, de Wit, Elzo, additional, and de Laat, Wouter, additional

Published
2012
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25. The active spatial organization of the beta-globin locus requires the transcription factor EKLF

Author

Drissen, Roy, Philipsen, Sjaak, Palstra, Robert-Jan, Laat, Wouter de, Gillemans, Nynke, Splinter, Erik, and Grosveld, Frank

Subjects
Chromatin -- Research, Genetic transcription -- Research, Globin genes -- Research, Biological sciences
Abstract

Three-dimensional organization of a gene locus is important for its regulation, as recently demonstrated for the beta-globin locus. It is reported that erythroid Kruppel-like transcription factor (EKLF), an erythroid transcription factor required for adult beta-globin gene transcription is also required for active chromatin Hub (ACH).

Published
2004

28. Abstract PO-45: Robust detection of translocations in lymphoma FFPE samples using Targeted Locus Capture-based sequencing

Author

Allahyar, Amin, primary, Pieterse, Mark, additional, Swennenhuis, Joost, additional, Los-de Vries, Tjitske, additional, Yilmaz, Mehmet, additional, Leguit, Roos, additional, Meijers, Ruud, additional, Hijmering, Nathalie, additional, de Jong, Daphne, additional, Ylstra, Bauke, additional, van der Geize, Robert, additional, Vermaat, Joost, additional, Cleven, Arjen, additional, van Wezel, Tom, additional, Diepstra, Arjan, additional, van Kempen, Leon, additional, Hajo, Karima, additional, Feitsma, Harma, additional, Simonis, Marieke, additional, van Min, Max, additional, Splinter, Erik, additional, and de Laat, Wouter, additional

Published
2020
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30. Enhanced CHO Clone Screening: Application of Targeted Locus Amplification and Next‐Generation Sequencing Technologies for Cell Line Development

Author

Aeschlimann, Samuel H., primary, Graf, Christian, additional, Mayilo, Dmytro, additional, Lindecker, Hélène, additional, Urda, Lorena, additional, Kappes, Nora, additional, Burr, Alicia Leone, additional, Simonis, Marieke, additional, Splinter, Erik, additional, Min, Max, additional, and Laux, Holger, additional

Published
2019
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31. Large-scale discovery of mouse transgenic integration sites reveals frequent structural variation and insertional mutagenesis

Author

Goodwin, Leslie O., primary, Splinter, Erik, additional, Davis, Tiffany L., additional, Urban, Rachel, additional, He, Hao, additional, Braun, Robert E., additional, Chesler, Elissa J., additional, Kumar, Vivek, additional, van Min, Max, additional, Ndukum, Juliet, additional, Philip, Vivek M., additional, Reinholdt, Laura G., additional, Svenson, Karen, additional, White, Jacqueline K., additional, Sasner, Michael, additional, Lutz, Cathleen, additional, and Murray, Stephen A., additional

Published
2019
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32. Supplementary Table 1. Genes Included in the XIC deletion from X chromosome inactivation in a female carrier of a 1.28 Mb deletion encompassing the human X inactivation centre

Author

B. De Hoon, Splinter, Erik, B. Eussen, J. C. W. Douben, E. Rentmeester, M. Van De Heijning, J. S. E. Laven, J. E. M. M. De Klein, J. Liebelt, and J. Gribnau

Abstract

Table showing genes that are affected by the XIC deletion, with their location, protein coding ability and their associated GO terms.

Published
2017
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33. Supplementary Methods: Primersets used in qPCR from X chromosome inactivation in a female carrier of a 1.28 Mb deletion encompassing the human X inactivation centre

Author

B. De Hoon, Splinter, Erik, B. Eussen, J. C. W. Douben, E. Rentmeester, M. Van De Heijning, J. S. E. Laven, J. E. M. M. De Klein, J. Liebelt, and J. Gribnau

Abstract

List of primers used in copy number determination by qPCR along the breakpoint regions. Top part shows primers for the centromeric breakpoint region, bottom part shows primers for the telomeric breakpoint region.

Published
2017
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34. Supplementary Figure 1. Overview of genome integrity from X chromosome inactivation in a female carrier of a 1.28 Mb deletion encompassing the human X inactivation centre

Author

B. De Hoon, Splinter, Erik, B. Eussen, J. C. W. Douben, E. Rentmeester, M. Van De Heijning, J. S. E. Laven, J. E. M. M. De Klein, J. Liebelt, and J. Gribnau

Abstract

A. Whole genome CGH analysis reveals no major aberrations. The X axis shows the chromosomes. Signal intensity of each probe is plotted against its chromsomal position. B. Graph displaying overview of zygosity along all chromosomes (B allele frequency (BAF) of 100% or 0%).

Published
2017
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35. Genetic Screening Test to Detect Translocations in Acute Leukemias by Use of Targeted Locus Amplification

Author

Alimohamed, Mohamed Z, primary, Johansson, Lennart F, primary, de Boer, Eddy N, primary, Splinter, Erik, primary, Klous, Petra, primary, Yilmaz, Mehmet, primary, Bosga, Anneke, primary, van Min, Max, primary, Mulder, André B, primary, Vellenga, Edo, primary, Sinke, Richard J, primary, Sijmons, Rolf H, primary, van den Berg, Eva, primary, and Sikkema-Raddatz, Birgit, primary

Published
2018
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36. Large-scale discovery of mouse transgenic integration sites reveals frequent structural variation and insertional mutagenesis

Author

Goodwin, Leslie O., primary, Splinter, Erik, additional, Davis, Tiffany L., additional, Urban, Rachel, additional, He, Hao, additional, Braun, Robert E., additional, Chesler, Elissa J., additional, Kumar, Vivek, additional, van Min, Max, additional, Ndukum, Juliet, additional, Philip, Vivek M., additional, Reinholdt, Laura G., additional, Svenson, Karen, additional, White, Jacqueline K., additional, Sasner, Michael, additional, Lutz, Cathleen, additional, and Murray, Stephen A., additional

Published
2017
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37. Sensitive Monogenic Noninvasive Prenatal Diagnosis by Targeted Haplotyping

Author

Vermeulen, Carlo, Geeven, Geert, de Wit, Elzo, Verstegen, Marjon J A M, Jansen, Rumo P.M., van Kranenburg, Melissa, de Bruijn, Ewart, Pulit, Sara L., Kruisselbrink, Evelien, Shahsavari, Zahra, Omrani, Davood, Zeinali, Fatemeh, Najmabadi, Hossein, Katsila, Theodora, Vrettou, Christina, Patrinos, George P., Traeger-Synodinos, Joanne, Splinter, Erik, Beekman, Jeffrey M., Kheradmand Kia, Sima, Te Meerman, Gerard J, Ploos van Amstel, Hans Kristian, de Laat, Wouter, Vermeulen, Carlo, Geeven, Geert, de Wit, Elzo, Verstegen, Marjon J A M, Jansen, Rumo P.M., van Kranenburg, Melissa, de Bruijn, Ewart, Pulit, Sara L., Kruisselbrink, Evelien, Shahsavari, Zahra, Omrani, Davood, Zeinali, Fatemeh, Najmabadi, Hossein, Katsila, Theodora, Vrettou, Christina, Patrinos, George P., Traeger-Synodinos, Joanne, Splinter, Erik, Beekman, Jeffrey M., Kheradmand Kia, Sima, Te Meerman, Gerard J, Ploos van Amstel, Hans Kristian, and de Laat, Wouter

Published
2017

38. Sensitive Monogenic Noninvasive Prenatal Diagnosis by Targeted Haplotyping

Author

Cancer, CMM Groep De Ridder, Genetica, CMM Groep Cuppen, Neurogenetica, Circulatory Health, CTI, Longziekten onderzoek 2, Beekman, Child Health, Regenerative Medicine and Stem Cells, Genetica Sectie Genoomdiagnostiek, Divisie Biomedische Genetica, Hubrecht Institute with UMC, Vermeulen, Carlo, Geeven, Geert, de Wit, Elzo, Verstegen, Marjon J A M, Jansen, Rumo P.M., van Kranenburg, Melissa, de Bruijn, Ewart, Pulit, Sara L., Kruisselbrink, Evelien, Shahsavari, Zahra, Omrani, Davood, Zeinali, Fatemeh, Najmabadi, Hossein, Katsila, Theodora, Vrettou, Christina, Patrinos, George P., Traeger-Synodinos, Joanne, Splinter, Erik, Beekman, Jeffrey M., Kheradmand Kia, Sima, Te Meerman, Gerard J, Ploos van Amstel, Hans Kristian, de Laat, Wouter, Cancer, CMM Groep De Ridder, Genetica, CMM Groep Cuppen, Neurogenetica, Circulatory Health, CTI, Longziekten onderzoek 2, Beekman, Child Health, Regenerative Medicine and Stem Cells, Genetica Sectie Genoomdiagnostiek, Divisie Biomedische Genetica, Hubrecht Institute with UMC, Vermeulen, Carlo, Geeven, Geert, de Wit, Elzo, Verstegen, Marjon J A M, Jansen, Rumo P.M., van Kranenburg, Melissa, de Bruijn, Ewart, Pulit, Sara L., Kruisselbrink, Evelien, Shahsavari, Zahra, Omrani, Davood, Zeinali, Fatemeh, Najmabadi, Hossein, Katsila, Theodora, Vrettou, Christina, Patrinos, George P., Traeger-Synodinos, Joanne, Splinter, Erik, Beekman, Jeffrey M., Kheradmand Kia, Sima, Te Meerman, Gerard J, Ploos van Amstel, Hans Kristian, and de Laat, Wouter

Published
2017

39. Erratum to: Dynamics of gene silencing during X inactivation using allele-specific RNA-seq [Genome Biol. 2015;16:149]

Author

Marks, Hendrik, Kerstens, Hindrik H D, Barakat, Tahsin Stefan, Splinter, Erik, Dirks, René A M, van Mierlo, Guido, Joshi, Onkar, Wang, Shuang Yin, Babak, Tomas, Albers, Cornelis A., Kalkan, Tüzer, Smith, Austin, Jouneau, Alice, de Laat, Wouter, Gribnau, Joost, and Stunnenberg, Hendrik G.

Subjects
Published Erratum, Genetics, Cell Biology, Ecology, Evolution, Behavior and Systematics
Published
2016

40. CTCF mediates long-range chromatin looping and local histone modification in the Beta-globin locus

Author

Splinter, Erik, Heath, Helen, Kooren, Jurgen, Palstra, Robert-Jan, Klous, Petra, Grosveld, Frank, Galjart, Niels, and de Laat, Wouter

Subjects
Biological sciences
Abstract

CTCf (CCCTC-binding factor) binds sites around the mouse Beta-globin locus that spatially cluster in the erythroid cell nucleus. A demonstration that both conditional deletion of CTCF and targeted disruption of a DNA-binding site destabilize these long-range interactions and cause local loss of histone acetylation and gain of histone methylation, apparently without affecting transcription at the locus is presented.

Published
2006

41. Genetic and epigenetic features direct differential efficiency of Xist-mediated silencing at X-chromosomal and autosomal locations

Author

Loda, Agnese, primary, Brandsma, Johannes H., additional, Vassilev, Ivaylo, additional, Servant, Nicolas, additional, Loos, Friedemann, additional, Amirnasr, Azadeh, additional, Splinter, Erik, additional, Barillot, Emmanuel, additional, Poot, Raymond A., additional, Heard, Edith, additional, and Gribnau, Joost, additional

Published
2017
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42. Sensitive Monogenic Noninvasive Prenatal Diagnosis by Targeted Haplotyping

Author

Vermeulen, Carlo, primary, Geeven, Geert, additional, de Wit, Elzo, additional, Verstegen, Marjon J.A.M., additional, Jansen, Rumo P.M., additional, van Kranenburg, Melissa, additional, de Bruijn, Ewart, additional, Pulit, Sara L., additional, Kruisselbrink, Evelien, additional, Shahsavari, Zahra, additional, Omrani, Davood, additional, Zeinali, Fatemeh, additional, Najmabadi, Hossein, additional, Katsila, Theodora, additional, Vrettou, Christina, additional, Patrinos, George P., additional, Traeger-Synodinos, Joanne, additional, Splinter, Erik, additional, Beekman, Jeffrey M., additional, Kheradmand Kia, Sima, additional, te Meerman, Gerard J., additional, Ploos van Amstel, Hans Kristian, additional, and de Laat, Wouter, additional

Published
2017
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44. Additional file 1: Figure S1. of Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

Author

Zepeda-Mendoza, Cinthya, Swagatam Mukhopadhyay, Wong, Emily, Harder, Nathalie, Splinter, Erik, Wit, Elzo De, Eckersley-Maslin, Melanie, Ried, Thomas, Eils, Roland, Rohr, Karl, Alea Mills, Laat, Wouter De, Flicek, Paul, Anirvan Sengupta, and Spector, David

Abstract

Result of bias-correction for a simulation of biases in multi-viewpoint 4C experiment (with 100 viewpoints). Figure S2. Overview of PE-4Cseq methodology. Figure S3. Positions of DIRs for all viewpoints 1, 2, 11 and 12 are compared against structural protein binding sites. First track is for Df and + 129 comparisons and second track is for + D Bl6 and + Bl6 comparison. Figure S4. Calculated ν per viewpoint for + D Bl6 vs + Bl6 . + D Bl6 (red squares). Figure S5. Distance distributions between query probes for (A) BACset1, (B) BACset2, (C) BACset3, (D) BACset4, FISH experiments. (DOCX 1390 kb)

Published
2015
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45. Erratum to: Dynamics of gene silencing during X inactivation using allele-specific RNA-seq

Author

Marks, Hendrik, Kerstens, Hindrik H D, Barakat, Tahsin Stefan, Splinter, Erik, Dirks, René A M, van Mierlo, Guido, Joshi, Onkar, Wang, Shuang-Yin, Babak, Tomas, Albers, Cornelis A, Kalkan, Tüzer, Smith, Austin, Jouneau, Alice, de Laat, Wouter, Gribnau, Joost, Stunnenberg, Hendrik G, Marks, Hendrik, Kerstens, Hindrik H D, Barakat, Tahsin Stefan, Splinter, Erik, Dirks, René A M, van Mierlo, Guido, Joshi, Onkar, Wang, Shuang-Yin, Babak, Tomas, Albers, Cornelis A, Kalkan, Tüzer, Smith, Austin, Jouneau, Alice, de Laat, Wouter, Gribnau, Joost, and Stunnenberg, Hendrik G

Published
2016

46. Erratum to: Dynamics of gene silencing during X inactivation using allele-specific RNA-seq [Genome Biol. 2015;16:149]

Author

Hubrecht Institute with UMC, Divisie Biomedische Genetica, Cancer, Marks, Hendrik, Kerstens, Hindrik H D, Barakat, Tahsin Stefan, Splinter, Erik, Dirks, René A M, van Mierlo, Guido, Joshi, Onkar, Wang, Shuang Yin, Babak, Tomas, Albers, Cornelis A., Kalkan, Tüzer, Smith, Austin, Jouneau, Alice, de Laat, Wouter, Gribnau, Joost, Stunnenberg, Hendrik G., Hubrecht Institute with UMC, Divisie Biomedische Genetica, Cancer, Marks, Hendrik, Kerstens, Hindrik H D, Barakat, Tahsin Stefan, Splinter, Erik, Dirks, René A M, van Mierlo, Guido, Joshi, Onkar, Wang, Shuang Yin, Babak, Tomas, Albers, Cornelis A., Kalkan, Tüzer, Smith, Austin, Jouneau, Alice, de Laat, Wouter, Gribnau, Joost, and Stunnenberg, Hendrik G.

Published
2016

47. Dynamics of gene silencing during X inactivation using allele-specific RNA-seq

Author

Marks, Hendrik, Kerstens, Hindrik H D, Barakat, Tahsin Stefan, Splinter, Erik, Dirks, René A M, van Mierlo, Guido, Joshi, Onkar, Wang, Shuang-Yin, Babak, Tomas, Albers, Cornelis A, Kalkan, Tüzer, Smith, Austin, Jouneau, Alice, de Laat, Wouter, Gribnau, Joost, Stunnenberg, Hendrik G, Marks, Hendrik, Kerstens, Hindrik H D, Barakat, Tahsin Stefan, Splinter, Erik, Dirks, René A M, van Mierlo, Guido, Joshi, Onkar, Wang, Shuang-Yin, Babak, Tomas, Albers, Cornelis A, Kalkan, Tüzer, Smith, Austin, Jouneau, Alice, de Laat, Wouter, Gribnau, Joost, and Stunnenberg, Hendrik G

Published
2015

48. Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

Author

Zepeda-Mendoza, Cinthya J, Mukhopadhyay, Swagatam, Wong, Emily S, Harder, Nathalie, Splinter, Erik, de Wit, Elzo, Eckersley-Maslin, Melanie A, Ried, Thomas, Eils, Roland, Rohr, Karl, Mills, Alea, de Laat, Wouter, Flicek, Paul, Sengupta, Anirvan M, Spector, David L, Zepeda-Mendoza, Cinthya J, Mukhopadhyay, Swagatam, Wong, Emily S, Harder, Nathalie, Splinter, Erik, de Wit, Elzo, Eckersley-Maslin, Melanie A, Ried, Thomas, Eils, Roland, Rohr, Karl, Mills, Alea, de Laat, Wouter, Flicek, Paul, Sengupta, Anirvan M, and Spector, David L

Published
2015

49. CTCF Binding Polarity Determines Chromatin Looping

Author

de Wit, Elzo, Vos, Erica S M, Holwerda, Sjoerd J B, Valdes-Quezada, Christian, Verstegen, Marjon J A M, Teunissen, Hans, Splinter, Erik, Wijchers, Patrick J, Krijger, Peter H L, de Laat, Wouter, de Wit, Elzo, Vos, Erica S M, Holwerda, Sjoerd J B, Valdes-Quezada, Christian, Verstegen, Marjon J A M, Teunissen, Hans, Splinter, Erik, Wijchers, Patrick J, Krijger, Peter H L, and de Laat, Wouter

Published
2015

50. Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

Author

Divisie Biomedische Genetica, Hubrecht Institute with UMC, Cancer, Zepeda-Mendoza, Cinthya J, Mukhopadhyay, Swagatam, Wong, Emily S, Harder, Nathalie, Splinter, Erik, de Wit, Elzo, Eckersley-Maslin, Melanie A, Ried, Thomas, Eils, Roland, Rohr, Karl, Mills, Alea, de Laat, Wouter, Flicek, Paul, Sengupta, Anirvan M, Spector, David L, Divisie Biomedische Genetica, Hubrecht Institute with UMC, Cancer, Zepeda-Mendoza, Cinthya J, Mukhopadhyay, Swagatam, Wong, Emily S, Harder, Nathalie, Splinter, Erik, de Wit, Elzo, Eckersley-Maslin, Melanie A, Ried, Thomas, Eils, Roland, Rohr, Karl, Mills, Alea, de Laat, Wouter, Flicek, Paul, Sengupta, Anirvan M, and Spector, David L

Published
2015

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