Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and long read nanopore sequencing von Stangl, Christina, de Blank, Sam, Renkens, Ivo, Westera, Liset, Verbeek, Tamara, Valle-Inclan, Jose Espejo, González, Rocio Chamorro, Henssen, Anton G., van Roosmalen, Markus J., Stam, Ronald W., Voest, Emile E., Kloosterman, Wigard P., van Haaften, Gijs, Monroe, Glen R.

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A Systematic Analysis of Oncogenic Gene Fusions in Primary Colon Cancer von Kloosterman, Wigard P, Coebergh van den Braak, Robert R J, Pieterse, Mark, van Roosmalen, Markus J, Sieuwerts, Anieta M, Stangl, Christina, Brunekreef, Ronne, Lalmahomed, Zarina S, Ooft, Salo, van Galen, Anne, Smid, Marcel, Lefebvre, Armel, Zwartkruis, Fried, Martens, John W M, Foekens, John A, Biermann, Katharina, Koudijs, Marco J, Ijzermans, Jan N M, Voest, Emile E

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Micronuclei-based model system reveals functional consequences of chromothripsis in human cells von Kneissig, Maja, Keuper, Kristina, de Pagter, Mirjam S, van Roosmalen, Markus J, Martin, Jana, Otto, Hannah, Passerini, Verena, Campos Sparr, Aline, Renkens, Ivo, Kropveld, Fenna, Vasudevan, Anand, Sheltzer, Jason M, Kloosterman, Wigard P, Storchova, Zuzana

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Chromothripsis in Healthy Individuals Affects Multiple Protein-Coding Genes and Can Result in Severe Congenital Abnormalities in Offspring von de Pagter, Mirjam S., van Roosmalen, Markus J., Baas, Annette F., Renkens, Ivo, Duran, Karen J., van Binsbergen, Ellen, Tavakoli-Yaraki, Masoumeh, Hochstenbach, Ron, van der Veken, Lars T., Cuppen, Edwin, Kloosterman, Wigard P.

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Constitutional Chromothripsis Rearrangements Involve Clustered Double-Stranded DNA Breaks and Nonhomologous Repair Mechanisms von Kloosterman, Wigard P., Tavakoli-Yaraki, Masoumeh, van Roosmalen, Markus J., van Binsbergen, Ellen, Renkens, Ivo, Duran, Karen, Ballarati, Lucia, Vergult, Sarah, Giardino, Daniela, Hansson, Kerstin, Ruivenkamp, Claudia A.L., Jager, Myrthe, van Haeringen, Arie, Ippel, Elly F., Haaf, Thomas, Passarge, Eberhard, Hochstenbach, Ron, Menten, Björn, Larizza, Lidia, Guryev, Victor, Poot, Martin, Cuppen, Edwin

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An organoid platform for ovarian cancer captures intra- and interpatient heterogeneity von Kopper, Oded, de Witte, Chris J., Lõhmussaar, Kadi, Valle-Inclan, Jose Espejo, Hami, Nizar, Kester, Lennart, Balgobind, Anjali Vanita, Korving, Jeroen, Proost, Natalie, Begthel, Harry, van Wijk, Lise M., Revilla, Sonia Aristín, Theeuwsen, Rebecca, van de Ven, Marieke, van Roosmalen, Markus J., Ponsioen, Bas, Ho, Victor W. H., Neel, Benjamin G., Bosse, Tjalling, Gaarenstroom, Katja N., Vrieling, Harry, Vreeswijk, Maaike P. G., van Diest, Paul J., Witteveen, Petronella O., Jonges, Trudy, Bos, Johannes L., van Oudenaarden, Alexander, Zweemer, Ronald P., Snippert, Hugo J. G., Kloosterman, Wigard P., Clevers, Hans

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MutationalPatterns: the one stop shop for the analysis of mutational processes von Manders, Freek, Brandsma, Arianne M, de Kanter, Jurrian, Verheul, Mark, Oka, Rurika, van Roosmalen, Markus J, van der Roest, Bastiaan, van Hoeck, Arne, Cuppen, Edwin, van Boxtel, Ruben

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Mapping and phasing of structural variation in patient genomes using nanopore sequencing von Cretu Stancu, Mircea, van Roosmalen, Markus J., Renkens, Ivo, Nieboer, Marleen M., Middelkamp, Sjors, de Ligt, Joep, Pregno, Giulia, Giachino, Daniela, Mandrile, Giorgia, Espejo Valle-Inclan, Jose, Korzelius, Jerome, de Bruijn, Ewart, Cuppen, Edwin, Talkowski, Michael E., Marschall, Tobias, de Ridder, Jeroen, Kloosterman, Wigard P.

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Identification of human D lactate dehydrogenase deficiency von Monroe, Glen R., van Eerde, Albertien M., Tessadori, Federico, Duran, Karen J., Savelberg, Sanne M. C., van Alfen, Johanna C., Terhal, Paulien A., van der Crabben, Saskia N., Lichtenbelt, Klaske D., Fuchs, Sabine A., Gerrits, Johan, van Roosmalen, Markus J., van Gassen, Koen L., van Aalderen, Mirjam, Koot, Bart G., Oostendorp, Marlies, Duran, Marinus, Visser, Gepke, de Koning, Tom J., Calì, Francesco, Bosco, Paolo, Geleijns, Karin, de Sain-van der Velden, Monique G. M., Knoers, Nine V., Bakkers, Jeroen, Verhoeven-Duif, Nanda M., van Haaften, Gijs, Jans, Judith J.

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Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer von Kloosterman, Wigard P, Hoogstraat, Marlous, Paling, Oscar, Tavakoli-Yaraki, Masoumeh, Renkens, Ivo, Vermaat, Joost S, van Roosmalen, Markus J, van Lieshout, Stef, Nijman, Isaac J, Roessingh, Wijnand, van’t Slot, Ruben, van de Belt, José, Guryev, Victor, Koudijs, Marco, Voest, Emile, Cuppen, Edwin

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A multi-platform reference for somatic structural variation detection von 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., Cuppen, Edwin

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Mitochondrial H2O2 release does not directly cause damage to chromosomal DNA von van Soest, Daan M. K., Polderman, Paulien E., den Toom, Wytze T. F., Keijer, Janneke P., van Roosmalen, Markus J., Leyten, Tim M. F., Lehmann, Johannes, Zwakenberg, Susan, De Henau, Sasha, van Boxtel, Ruben, Burgering, Boudewijn M. T., Dansen, Tobias B.

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Selective pressures of platinum compounds shape the evolution of therapy-related myeloid neoplasms von Bertrums, Eline J. M., de Kanter, Jurrian K., Derks, Lucca L. M., Verheul, Mark, Trabut, Laurianne, van Roosmalen, Markus J., Hasle, Henrik, Antoniou, Evangelia, Reinhardt, Dirk, Dworzak, Michael N., Mühlegger, Nora, van den Heuvel-Eibrink, Marry M., Zwaan, C. Michel, Goemans, Bianca F., van Boxtel, Ruben

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Genomic and transcriptomic plasticity in treatment-naive ovarian cancer von Hoogstraat, Marlous, de Pagter, Mirjam S, Cirkel, Geert A, van Roosmalen, Markus J, Harkins, Timothy T, Duran, Karen, Kreeftmeijer, Jennifer, Renkens, Ivo, Witteveen, Petronella O, Lee, Clarence C, Nijman, Isaac J, Guy, Tanisha, van 't Slot, Ruben, Jonges, Trudy N, Lolkema, Martijn P, Koudijs, Marco J, Zweemer, Ronald P, Voest, Emile E, Cuppen, Edwin, Kloosterman, Wigard P

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Optimizing Nanopore sequencing-based detection of structural variants enables individualized circulating tumor DNA-based disease monitoring in cancer patients von Valle-Inclan, Jose Espejo, Stangl, Christina, de Jong, Anouk C., van Dessel, Lisanne F., van Roosmalen, Markus J., Helmijr, Jean C. A., Renkens, Ivo, Janssen, Roel, de Blank, Sam, de Witte, Chris J., Martens, John W. M., Jansen, Maurice P. H. M., Lolkema, Martijn P., Kloosterman, Wigard P.

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Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants von Middelkamp, Sjors, Vlaar, Judith M, Giltay, Jacques, Korzelius, Jerome, Besselink, Nicolle, Boymans, Sander, Janssen, Roel, de la Fonteijne, Lisanne, van Binsbergen, Ellen, van Roosmalen, Markus J, Hochstenbach, Ron, Giachino, Daniela, Talkowski, Michael E, Kloosterman, Wigard P, Cuppen, Edwin

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Comprehensive single-cell genome analysis at nucleotide resolution using the PTA Analysis Toolbox von Middelkamp, Sjors, Manders, Freek, Peci, Flavia, van Roosmalen, Markus J., González, Diego Montiel, Bertrums, Eline J.M., van der Werf, Inge, Derks, Lucca L.M., Groenen, Niels M., Verheul, Mark, Trabut, Laurianne, Pleguezuelos-Manzano, Cayetano, Brandsma, Arianne M., Antoniou, Evangelia, Reinhardt, Dirk, Bierings, Marc, Belderbos, Mirjam E., van Boxtel, Ruben

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Human induced pluripotent stem cells display a similar mutation burden as embryonic pluripotent cells in vivo von Hasaart, Karlijn A.L., Manders, Freek, Ubels, Joske, Verheul, Mark, van Roosmalen, Markus J., Groenen, Niels M., Oka, Rurika, Kuijk, Ewart, Lopes, Susana M. Chuva de Sousa, Boxtel, Ruben van

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Antiviral treatment causes a unique mutational signature in cancers of transplantation recipients von de Kanter, Jurrian K., Peci, Flavia, Bertrums, Eline, Rosendahl Huber, Axel, van Leeuwen, Anaïs, van Roosmalen, Markus J., Manders, Freek, Verheul, Mark, Oka, Rurika, Brandsma, Arianne M., Bierings, Marc, Belderbos, Mirjam, van Boxtel, Ruben

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Genomic and Functional Overlap between Somatic and Germline Chromosomal Rearrangements von van Heesch, Sebastiaan, Simonis, Marieke, van Roosmalen, Markus J., Pillalamarri, Vamsee, Brand, Harrison, Kuijk, Ewart W., de Luca, Kim L., Lansu, Nico, Braat, A. Koen, Menelaou, Androniki, Hao, Wensi, Korving, Jeroen, Snijder, Simone, van der Veken, Lars T., Hochstenbach, Ron, Knegt, Alida C., Duran, Karen, Renkens, Ivo, Alekozai, Najla, Jager, Myrthe, Vergult, Sarah, Menten, Björn, de Bruijn, Ewart, Boymans, Sander, Ippel, Elly, van Binsbergen, Ellen, Talkowski, Michael E., Lichtenbelt, Klaske, Cuppen, Edwin, Kloosterman, Wigard P.

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