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465 results on '"Kloosterman, Wigard P."'

1. 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
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2. Figure S10 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy

Author

Martin, Michael V., primary, Aguilar-Rosas, Salvador, primary, Franke, Katka, primary, Pieterse, Mark, primary, Langelaar, Jamie van, primary, Schreurs, Renée, primary, Bijlsma, Maarten F., primary, Besselink, Marc G., primary, Koster, Jan, primary, Timens, Wim, primary, Khasraw, Mustafa, primary, Ashley, David M., primary, Keir, Stephen T., primary, Ottensmeier, Christian H., primary, King, Emma V., primary, Verheij, Joanne, primary, Waasdorp, Cynthia, primary, Valk, Peter J.M., primary, Engels, Sem A.G., primary, Oostenbach, Ellen, primary, van Dinter, Jip T., primary, Hofman, Damon A., primary, Mok, Juk Yee, primary, van Esch, Wim J.E., primary, Wilmink, Hanneke, primary, Monkhorst, Kim, primary, Verheul, Henk M.W., primary, Poel, Dennis, primary, Hiltermann, T. Jeroen N., primary, Kempen, Léon C.L.T. van, primary, Groen, Harry J.M., primary, Aerts, Joachim G.J.V., primary, Heesch, Sebastiaan van, primary, Löwenberg, Bob, primary, Plasterk, Ronald, primary, and Kloosterman, Wigard P., primary

Published
2024
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3. Data from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy

Author

Martin, Michael V., primary, Aguilar-Rosas, Salvador, primary, Franke, Katka, primary, Pieterse, Mark, primary, Langelaar, Jamie van, primary, Schreurs, Renée, primary, Bijlsma, Maarten F., primary, Besselink, Marc G., primary, Koster, Jan, primary, Timens, Wim, primary, Khasraw, Mustafa, primary, Ashley, David M., primary, Keir, Stephen T., primary, Ottensmeier, Christian H., primary, King, Emma V., primary, Verheij, Joanne, primary, Waasdorp, Cynthia, primary, Valk, Peter J.M., primary, Engels, Sem A.G., primary, Oostenbach, Ellen, primary, van Dinter, Jip T., primary, Hofman, Damon A., primary, Mok, Juk Yee, primary, van Esch, Wim J.E., primary, Wilmink, Hanneke, primary, Monkhorst, Kim, primary, Verheul, Henk M.W., primary, Poel, Dennis, primary, Hiltermann, T. Jeroen N., primary, Kempen, Léon C.L.T. van, primary, Groen, Harry J.M., primary, Aerts, Joachim G.J.V., primary, Heesch, Sebastiaan van, primary, Löwenberg, Bob, primary, Plasterk, Ronald, primary, and Kloosterman, Wigard P., primary

Published
2024
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4. Supplementary Tables S1-S12 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy

Author

Martin, Michael V., primary, Aguilar-Rosas, Salvador, primary, Franke, Katka, primary, Pieterse, Mark, primary, Langelaar, Jamie van, primary, Schreurs, Renée, primary, Bijlsma, Maarten F., primary, Besselink, Marc G., primary, Koster, Jan, primary, Timens, Wim, primary, Khasraw, Mustafa, primary, Ashley, David M., primary, Keir, Stephen T., primary, Ottensmeier, Christian H., primary, King, Emma V., primary, Verheij, Joanne, primary, Waasdorp, Cynthia, primary, Valk, Peter J.M., primary, Engels, Sem A.G., primary, Oostenbach, Ellen, primary, van Dinter, Jip T., primary, Hofman, Damon A., primary, Mok, Juk Yee, primary, van Esch, Wim J.E., primary, Wilmink, Hanneke, primary, Monkhorst, Kim, primary, Verheul, Henk M.W., primary, Poel, Dennis, primary, Hiltermann, T. Jeroen N., primary, Kempen, Léon C.L.T. van, primary, Groen, Harry J.M., primary, Aerts, Joachim G.J.V., primary, Heesch, Sebastiaan van, primary, Löwenberg, Bob, primary, Plasterk, Ronald, primary, and Kloosterman, Wigard P., primary

Published
2024
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5. Reconstructing single-cell karyotype alterations in colorectal cancer identifies punctuated and gradual diversification patterns

Author

Bollen, Yannik, Stelloo, Ellen, van Leenen, Petra, van den Bos, Myrna, Ponsioen, Bas, Lu, Bingxin, van Roosmalen, Markus J., Bolhaqueiro, Ana C. F., Kimberley, Christopher, Mossner, Maximilian, Cross, William C. H., Besselink, Nicolle J. M., van der Roest, Bastiaan, Boymans, Sander, Oost, Koen C., de Vries, Sippe G., Rehmann, Holger, Cuppen, Edwin, Lens, Susanne M. A., Kops, Geert J. P. L., Kloosterman, Wigard P., Terstappen, Leon W. M. M., Barnes, Chris P., Sottoriva, Andrea, Graham, Trevor A., and Snippert, Hugo J. G.

Published
2021
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6. A high-quality human reference panel reveals the complexity and distribution of genomic structural variants.

Author

Hehir-Kwa, Jayne Y, Marschall, Tobias, Kloosterman, Wigard P, Francioli, Laurent C, Baaijens, Jasmijn A, Dijkstra, Louis J, Abdellaoui, Abdel, Koval, Vyacheslav, Thung, Djie Tjwan, Wardenaar, René, Renkens, Ivo, Coe, Bradley P, Deelen, Patrick, de Ligt, Joep, Lameijer, Eric-Wubbo, van Dijk, Freerk, Hormozdiari, Fereydoun, Genome of the Netherlands Consortium, Uitterlinden, André G, van Duijn, Cornelia M, Eichler, Evan E, de Bakker, Paul IW, Swertz, Morris A, Wijmenga, Cisca, van Ommen, Gert-Jan B, Slagboom, P Eline, Boomsma, Dorret I, Schönhuth, Alexander, Ye, Kai, and Guryev, Victor

Subjects
Genome of the Netherlands Consortium, Chromosomes, Humans, RNA, Polymerase Chain Reaction, Sequence Analysis, DNA, Sequence Analysis, RNA, Computational Biology, Genomics, Gene Deletion, Genotype, Haplotypes, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Genome, Human, Algorithms, Software, Netherlands, INDEL Mutation, Genomic Structural Variation, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, Genome, Human
Abstract

Structural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority of studies provide neither a global view of the full spectrum of these variants nor integrate them into reference panels of genetic variation. Here, we analyse whole genome sequencing data of 769 individuals from 250 Dutch families, and provide a haplotype-resolved map of 1.9 million genome variants across 9 different variant classes, including novel forms of complex indels, and retrotransposition-mediated insertions of mobile elements and processed RNAs. A large proportion are previously under reported variants sized between 21 and 100 bp. We detect 4 megabases of novel sequence, encoding 11 new transcripts. Finally, we show 191 known, trait-associated SNPs to be in strong linkage disequilibrium with SVs and demonstrate that our panel facilitates accurate imputation of SVs in unrelated individuals.

Published
2016

7. The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy

Author

Martin, Michael V., Aguilar-Rosas, Salvador, Franke, Katka, Pieterse, Mark, Langelaar, Jamie van, Schreurs, Renee, Poel, D., Plasterk, Ronald, Kloosterman, Wigard P., Martin, Michael V., Aguilar-Rosas, Salvador, Franke, Katka, Pieterse, Mark, Langelaar, Jamie van, Schreurs, Renee, Poel, D., Plasterk, Ronald, and Kloosterman, Wigard P.

Abstract

Item does not contain fulltext

Published
2024

8. Characteristics of de novo structural changes in the human genome

Author

Kloosterman, Wigard P, Francioli, Laurent C, Hormozdiari, Fereydoun, Marschall, Tobias, Hehir-Kwa, Jayne Y, Abdellaoui, Abdel, Lameijer, Eric-Wubbo, Moed, Matthijs H, Koval, Vyacheslav, Renkens, Ivo, van Roosmalen, Markus J, Arp, Pascal, Karssen, Lennart C, Coe, Bradley P, Handsaker, Robert E, Suchiman, Eka D, Cuppen, Edwin, Thung, Djie Tjwan, McVey, Mitch, Wendl, Michael C, Consortium, Genome of the Netherlands, Uitterlinden, André, van Duijn, Cornelia M, Swertz, Morris A, Wijmenga, Cisca, van Ommen, GertJan B, Slagboom, P Eline, Boomsma, Dorret I, Schönhuth, Alexander, Eichler, Evan E, de Bakker, Paul IW, Ye, Kai, and Guryev, Victor

Subjects
Genetics, Human Genome, Alleles, Amino Acid Sequence, Female, Genetic Variation, Genome, Human, Genomics, Haplotypes, Humans, INDEL Mutation, Male, Molecular Sequence Data, Mutation Rate, Polymorphism, Single Nucleotide, Retroelements, Sequence Alignment, Sequence Analysis, DNA, Genome of Netherlands Consortium, Biological Sciences, Medical and Health Sciences, Bioinformatics
Abstract

Small insertions and deletions (indels) and large structural variations (SVs) are major contributors to human genetic diversity and disease. However, mutation rates and characteristics of de novo indels and SVs in the general population have remained largely unexplored. We report 332 validated de novo structural changes identified in whole genomes of 250 families, including complex indels, retrotransposon insertions, and interchromosomal events. These data indicate a mutation rate of 2.94 indels (1-20 bp) and 0.16 SVs (>20 bp) per generation. De novo structural changes affect on average 4.1 kbp of genomic sequence and 29 coding bases per generation, which is 91 and 52 times more nucleotides than de novo substitutions, respectively. This contrasts with the equal genomic footprint of inherited SVs and substitutions. An excess of structural changes originated on paternal haplotypes. Additionally, we observed a nonuniform distribution of de novo SVs across offspring. These results reveal the importance of different mutational mechanisms to changes in human genome structure across generations.

Published
2015

10. Optimizing Nanopore sequencing-based detection of structural variants enables individualized circulating tumor DNA-based disease monitoring in cancer patients

Author

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., and Kloosterman, Wigard P.

Published
2021
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13. An organoid platform for ovarian cancer captures intra- and interpatient heterogeneity

Author

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., and Clevers, Hans

Published
2019
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14. Ankyrin repeat and zinc-finger domain-containing 1 mutations are associated with infantile-onset inflammatory bowel disease

Author

van Haaften-Visser, Désirée Y., Harakalova, Magdalena, Mocholi, Enric, van Montfrans, Joris M., Elkadri, Abdul, Rieter, Ester, Fiedler, Karoline, van Hasselt, Peter M., Triffaux, Emily M.M., van Haelst, Mieke M., Nijman, Isaac J., Kloosterman, Wigard P., Nieuwenhuis, Edward E.S., Muise, Aleixo M., Cuppen, Edwin, Houwen, Roderick H.J., and Coffer, Paul J.

Published
2017
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16. Enhancer hubs and loop collisions identified from single-allele topologies

Author

Allahyar, Amin, Vermeulen, Carlo, Bouwman, Britta A. M., Krijger, Peter H. L., Verstegen, Marjon J. A. M., Geeven, Geert, van Kranenburg, Melissa, Pieterse, Mark, Straver, Roy, Haarhuis, Judith H. I., Jalink, Kees, Teunissen, Hans, Renkens, Ivo J., Kloosterman, Wigard P., Rowland, Benjamin D., de Wit, Elzo, de Ridder, Jeroen, and de Laat, Wouter

Published
2018
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17. Author Correction: Accurate detection of circulating tumor DNA using nanopore consensus sequencing

Author

Marcozzi, Alessio, primary, Jager, Myrthe, additional, Elferink, Martin, additional, Straver, Roy, additional, van Ginkel, Joost H., additional, Peltenburg, Boris, additional, Chen, Li-Ting, additional, Renkens, Ivo, additional, van Kuik, Joyce, additional, Terhaard, Chris, additional, de Bree, Remco, additional, Devriese, Lot A., additional, Willems, Stefan M., additional, Kloosterman, Wigard P., additional, and de Ridder, Jeroen, additional

Published
2023
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21. Author Correction: Accurate detection of circulating tumor DNA using nanopore consensus sequencing (npj Genomic Medicine, (2021), 6, 1, (106), 10.1038/s41525-021-00272-y)

Author

CMM Groep De Ridder, Cancer, Genetica Medische Informatica, Child Health, MS Mondziekten/Kaakchirurgie, MS Hoofd-Hals Chirurgische Oncologie, CMM USEQ Facility, MS Radiotherapie, MS Medische Oncologie, Pathologie Pathologen staf, Marcozzi, Alessio, Jager, Myrthe, Elferink, Martin, Straver, Roy, van Ginkel, Joost H, Peltenburg, Boris, Chen, Li-Ting, Renkens, Ivo, van Kuik, Joyce, Terhaard, Chris, de Bree, Remco, Devriese, Lot A, Willems, Stefan M, Kloosterman, Wigard P, de Ridder, Jeroen, CMM Groep De Ridder, Cancer, Genetica Medische Informatica, Child Health, MS Mondziekten/Kaakchirurgie, MS Hoofd-Hals Chirurgische Oncologie, CMM USEQ Facility, MS Radiotherapie, MS Medische Oncologie, Pathologie Pathologen staf, Marcozzi, Alessio, Jager, Myrthe, Elferink, Martin, Straver, Roy, van Ginkel, Joost H, Peltenburg, Boris, Chen, Li-Ting, Renkens, Ivo, van Kuik, Joyce, Terhaard, Chris, de Bree, Remco, Devriese, Lot A, Willems, Stefan M, Kloosterman, Wigard P, and de Ridder, Jeroen

Published
2023

22. Supplementary Table S3 from A Systematic Analysis of Oncogenic Gene Fusions in Primary Colon Cancer

Author

Kloosterman, Wigard P., primary, Coebergh van den Braak, Robert R.J., primary, Pieterse, Mark, primary, van Roosmalen, Markus J., primary, Sieuwerts, Anieta M., primary, Stangl, Christina, primary, Brunekreef, Ronne, primary, Lalmahomed, Zarina S., primary, Ooft, Salo, primary, van Galen, Anne, primary, Smid, Marcel, primary, Lefebvre, Armel, primary, Zwartkruis, Fried, primary, Martens, John W.M., primary, Foekens, John A., primary, Biermann, Katharina, primary, Koudijs, Marco J., primary, Ijzermans, Jan N.M., primary, and Voest, Emile E., primary

Published
2023
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23. Supplementary Data file from A Systematic Analysis of Oncogenic Gene Fusions in Primary Colon Cancer

Author

Kloosterman, Wigard P., primary, Coebergh van den Braak, Robert R.J., primary, Pieterse, Mark, primary, van Roosmalen, Markus J., primary, Sieuwerts, Anieta M., primary, Stangl, Christina, primary, Brunekreef, Ronne, primary, Lalmahomed, Zarina S., primary, Ooft, Salo, primary, van Galen, Anne, primary, Smid, Marcel, primary, Lefebvre, Armel, primary, Zwartkruis, Fried, primary, Martens, John W.M., primary, Foekens, John A., primary, Biermann, Katharina, primary, Koudijs, Marco J., primary, Ijzermans, Jan N.M., primary, and Voest, Emile E., primary

Published
2023
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24. Data from A Systematic Analysis of Oncogenic Gene Fusions in Primary Colon Cancer

Author

Kloosterman, Wigard P., primary, Coebergh van den Braak, Robert R.J., primary, Pieterse, Mark, primary, van Roosmalen, Markus J., primary, Sieuwerts, Anieta M., primary, Stangl, Christina, primary, Brunekreef, Ronne, primary, Lalmahomed, Zarina S., primary, Ooft, Salo, primary, van Galen, Anne, primary, Smid, Marcel, primary, Lefebvre, Armel, primary, Zwartkruis, Fried, primary, Martens, John W.M., primary, Foekens, John A., primary, Biermann, Katharina, primary, Koudijs, Marco J., primary, Ijzermans, Jan N.M., primary, and Voest, Emile E., primary

Published
2023
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28. Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

Author

Smid, Marcel, Coebergh van den Braak, Robert R. J., van de Werken, Harmen J. G., van Riet, Job, van Galen, Anne, de Weerd, Vanja, van der Vlugt-Daane, Michelle, Bril, Sandra I., Lalmahomed, Zarina S., Kloosterman, Wigard P., Wilting, Saskia M., Foekens, John A., IJzermans, Jan N. M., on behalf of the MATCH study group, Martens, John W. M., and Sieuwerts, Anieta M.

Published
2018
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29. Destabilized SMC5/6 complex leads to chromosome breakage syndrome with severe lung disease

Author

van der Crabben, Saskia N., Hennus, Marije P., McGregor, Grant A., Ritter, Deborah I., Nagamani, Sandesh C.S., Wells, Owen S., Harakalova, Magdalena, Chinn, Ivan K., Alt, Aaron, Vondrova, Lucie, Hochstenbach, Ron, van Montfrans, Joris M., Terheggen-Lagro, Suzanne W., van Lieshout, Stef, van Roosmalen, Markus J., Renkens, Ivo, Duran, Karen, Nijman, Isaac J., Kloosterman, Wigard P., Hennekam, Eric, Orange, Jordan S., van Hasselt, Peter M., Wheeler, David A., Palecek, Jan J., Lehmann, Alan R., Oliver, Antony W., Pearl, Laurence H., Plon, Sharon E., Murray, Johanne M., and van Haaften, Gijs

Subjects
Complications and side effects, Development and progression, Genetic aspects, Health aspects, Chromosome abnormalities -- Complications and side effects, Pediatric diseases -- Genetic aspects -- Development and progression, Gene mutation -- Health aspects, Adult respiratory distress syndrome -- Genetic aspects -- Development and progression, Gene mutations -- Health aspects, Children -- Diseases, Acute respiratory distress syndrome -- Genetic aspects -- Development and progression
Abstract

Introduction Chromosome dynamics in eukaryotes are controlled by the structural maintenance of the chromosome complex (SMC) family of proteins, which form 3 highly conserved and functional complexes: cohesin (SMC1/SMC3), condensin [...], The structural maintenance of chromosomes (SMC) family of proteins supports mitotic proliferation, meiosis, and DNA repair to control genomic stability. Impairments in chromosome maintenance are linked to rare chromosome breakage disorders. Here, we have identified a chromosome breakage syndrome associated with severe lung disease in early childhood. Four children from two unrelated kindreds died of severe pulmonary disease during infancy following viral pneumonia with evidence of combined T and B cell immunodeficiency. Whole exome sequencing revealed biallelic missense mutations in the NSMCE3 (also known as NDNL2) gene, which encodes a subunit of the SMC5/6 complex that is essential for DNA damage response and chromosome segregation. The NSMCE3 mutations disrupted interactions within the SMC5/6 complex, leading to destabilization of the complex. Patient cells showed chromosome rearrangements, micronuclei, sensitivity to replication stress and DNA damage, and defective homologous recombination. This work associates missense mutations in NSMCE3 with an autosomal recessive chromosome breakage syndrome that leads to defective T and B cell function and acute respiratory distress syndrome in early childhood.

Published
2016
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31. Computational pan-genomics: status, promises and challenges

Author

Marschall, Tobias, Marz, Manja, Abeel, Thomas, Dijkstra, Louis, Dutilh, Bas E, Ghaffaari, Ali, Kersey, Paul, Kloosterman, Wigard P, Mäkinen, Veli, Novak, Adam M, Paten, Benedict, Porubsky, David, Rivals, Eric, Alkan, Can, Baaijens, Jasmijn A, De Bakker, Paul I W, Boeva, Valentina, Bonnal, Raoul J P, Chiaromonte, Francesca, Chikhi, Rayan, Ciccarelli, Francesca D, Cijvat, Robin, Datema, Erwin, Van Duijn, Cornelia M, Eichler, Evan E, Ernst, Corinna, Eskin, Eleazar, Garrison, Erik, El-Kebir, Mohammed, Klau, Gunnar W, Korbel, Jan O, Lameijer, Eric-Wubbo, Langmead, Benjamin, Martin, Marcel, Medvedev, Paul, Mu, John C, Neerincx, Pieter, Ouwens, Klaasjan, Peterlongo, Pierre, Pisanti, Nadia, Rahmann, Sven, Raphael, Ben, Reinert, Knut, de Ridder, Dick, de Ridder, Jeroen, Schlesner, Matthias, Schulz-Trieglaff, Ole, Sanders, Ashley D, Sheikhizadeh, Siavash, Shneider, Carl, Smit, Sandra, Valenzuela, Daniel, Wang, Jiayin, Wessels, Lodewyk, Zhang, Ying, Guryev, Victor, Vandin, Fabio, Ye, Kai, and Schönhuth, Alexander

Published
2018
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33. Development of a Personalized Tumor Neoantigen Based Vaccine Formulation (FRAME-001) for Use in a Phase II Trial for the Treatment of Advanced Non-Small Cell Lung Cancer

Author

Oosting, Linette T., primary, Franke, Katka, additional, Martin, Michael V., additional, Kloosterman, Wigard P., additional, Jamieson, Jennifer A., additional, Glenn, Laura A., additional, de Jager, Miranda W., additional, van Zanten, Jacoba, additional, Allersma, Derk P., additional, and Gareb, Bahez, additional

Published
2022
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34. A multi-platform reference for somatic structural variation detection

Author

CMM Groep Cuppen, CMM Groep De Ridder, Cancer, CMM Groep Kloosterman, Child Health, 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, CMM Groep Cuppen, CMM Groep De Ridder, Cancer, CMM Groep Kloosterman, Child Health, 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

35. Distinct Genomic Profiles Are Associated with Treatment Response and Survival in Ovarian Cancer

Author

de Witte, Chris J., Kutzera, Joachim, van Hoeck, Arne, Nguyen, Luan, Boere, Ingrid A., Jalving, Mathilde, Ottevanger, Petronella B., van Schaik-Van de Mheen, Christa, Stevense, Marion, Kloosterman, Wigard P., Zweemer, Ronald P., Cuppen, Edwin, Witteveen, Petronella O., de Witte, Chris J., Kutzera, Joachim, van Hoeck, Arne, Nguyen, Luan, Boere, Ingrid A., Jalving, Mathilde, Ottevanger, Petronella B., van Schaik-Van de Mheen, Christa, Stevense, Marion, Kloosterman, Wigard P., Zweemer, Ronald P., Cuppen, Edwin, and Witteveen, Petronella O.

Abstract

The majority of patients with ovarian cancer ultimately develop recurrent chemotherapy-resistant disease. Treatment stratification is mainly based on histological subtype and stage, prior response to platinum-based chemotherapy, and time to recurrent disease. Here, we integrated clinical treatment, treatment response, and survival data with whole-genome sequencing profiles of 132 solid tumor biopsies of metastatic epithelial ovarian cancer to explore genome-informed stratification opportunities. Samples from primary and recurrent disease harbored comparable numbers of single nucleotide variants and structural variants. Mutational signatures represented platinum exposure, homologous recombination deficiency, and aging. Unsupervised hierarchical clustering based on genomic input data identified specific ovarian cancer subgroups, characterized by homologous recombination deficiency, genome stability, and duplications. The clusters exhibited distinct response rates and survival probabilities which could thus potentially be used for genome-informed therapy stratification for more personalized ovarian cancer treatment.

Published
2022

36. Distinct Genomic Profiles Are Associated with Treatment Response and Survival in Ovarian Cancer

Author

CMM Groep Cuppen, CMM Groep De Ridder, Cancer, Child Health, MS Gynaecologische Oncologie, MS Medische Oncologie, de Witte, Chris J, Kutzera, Joachim, van Hoeck, Arne, Nguyen, Luan, Boere, Ingrid A, Jalving, Mathilde, Ottevanger, Petronella B, van Schaik-van de Mheen, Christa, Stevense, Marion, Kloosterman, Wigard P, Zweemer, Ronald P, Cuppen, Edwin, Witteveen, Petronella O, CMM Groep Cuppen, CMM Groep De Ridder, Cancer, Child Health, MS Gynaecologische Oncologie, MS Medische Oncologie, de Witte, Chris J, Kutzera, Joachim, van Hoeck, Arne, Nguyen, Luan, Boere, Ingrid A, Jalving, Mathilde, Ottevanger, Petronella B, van Schaik-van de Mheen, Christa, Stevense, Marion, Kloosterman, Wigard P, Zweemer, Ronald P, Cuppen, Edwin, and Witteveen, Petronella O

Published
2022

37. Distinct Genomic Profiles Are Associated with Treatment Response and Survival in Ovarian Cancer

Author

de Witte, Chris J., primary, Kutzera, Joachim, additional, van Hoeck, Arne, additional, Nguyen, Luan, additional, Boere, Ingrid A., additional, Jalving, Mathilde, additional, Ottevanger, Petronella B., additional, van Schaik-van de Mheen, Christa, additional, Stevense, Marion, additional, Kloosterman, Wigard P., additional, Zweemer, Ronald P., additional, Cuppen, Edwin, additional, and Witteveen, Petronella O., additional

Published
2022
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43. Additional file 2 of Optimizing Nanopore sequencing-based detection of structural variants enables individualized circulating tumor DNA-based disease monitoring in cancer patients

Author

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., and Kloosterman, Wigard P.

Abstract

Additional file 2: Supplementary Figures.

Published
2021
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44. Accurate detection of circulating tumor DNA using nanopore consensus sequencing

Author

CMM Groep De Ridder, Cancer, Genetica Medische Informatica, Child Health, MS Mondziekten/Kaakchirurgie, MS Hoofd-Hals Chirurgische Oncologie, MS Radiotherapie, MS Medische Oncologie, Pathologie Pathologen staf, Marcozzi, Alessio, Jager, Myrthe, Elferink, Martin, Straver, Roy, van Ginkel, Joost H, Peltenburg, Boris, Chen, Li-Ting, Renkens, Ivo, van Kuik, Joyce, Terhaard, Chris, de Bree, Remco, Devriese, Lot A, Willems, Stefan M, Kloosterman, Wigard P, de Ridder, Jeroen, CMM Groep De Ridder, Cancer, Genetica Medische Informatica, Child Health, MS Mondziekten/Kaakchirurgie, MS Hoofd-Hals Chirurgische Oncologie, MS Radiotherapie, MS Medische Oncologie, Pathologie Pathologen staf, Marcozzi, Alessio, Jager, Myrthe, Elferink, Martin, Straver, Roy, van Ginkel, Joost H, Peltenburg, Boris, Chen, Li-Ting, Renkens, Ivo, van Kuik, Joyce, Terhaard, Chris, de Bree, Remco, Devriese, Lot A, Willems, Stefan M, Kloosterman, Wigard P, and de Ridder, Jeroen

Published
2021

45. Reconstructing single-cell karyotype alterations in colorectal cancer identifies punctuated and gradual diversification patterns

Author

CMM Sectie Molecular Cancer Research, CMM Groep Snippert, Regenerative Medicine and Stem Cells, Cancer, Genetica, MS Medische Oncologie, CMM Groep Kloosterman, Lab Reumatologie/Klinische Immunologie, Epi Infectieziekten Team 2, Infection & Immunity, CMM USEQ Facility, CMM Groep Bos, CMM Groep Lens, CMM, CMM Groep Cuppen, Hubrecht Institute with UMC, CMM Groep De Ridder, Child Health, Bollen, Yannik, Stelloo, Ellen, van Leenen, Petra, van den Bos, Myrna, Ponsioen, Bas, Lu, Bingxin, van Roosmalen, Markus J., Bolhaqueiro, Ana C.F., Kimberley, Christopher, Mossner, Maximilian, Cross, William C.H., Besselink, Nicolle J.M., van der Roest, Bastiaan, Boymans, Sander, Oost, Koen C., de Vries, Sippe G., Rehmann, Holger, Cuppen, Edwin, Lens, Susanne M.A., Kops, Geert J.P.L., Kloosterman, Wigard P., Terstappen, Leon W.M.M., Barnes, Chris P., Sottoriva, Andrea, Graham, Trevor A., Snippert, Hugo J.G., CMM Sectie Molecular Cancer Research, CMM Groep Snippert, Regenerative Medicine and Stem Cells, Cancer, Genetica, MS Medische Oncologie, CMM Groep Kloosterman, Lab Reumatologie/Klinische Immunologie, Epi Infectieziekten Team 2, Infection & Immunity, CMM USEQ Facility, CMM Groep Bos, CMM Groep Lens, CMM, CMM Groep Cuppen, Hubrecht Institute with UMC, CMM Groep De Ridder, Child Health, Bollen, Yannik, Stelloo, Ellen, van Leenen, Petra, van den Bos, Myrna, Ponsioen, Bas, Lu, Bingxin, van Roosmalen, Markus J., Bolhaqueiro, Ana C.F., Kimberley, Christopher, Mossner, Maximilian, Cross, William C.H., Besselink, Nicolle J.M., van der Roest, Bastiaan, Boymans, Sander, Oost, Koen C., de Vries, Sippe G., Rehmann, Holger, Cuppen, Edwin, Lens, Susanne M.A., Kops, Geert J.P.L., Kloosterman, Wigard P., Terstappen, Leon W.M.M., Barnes, Chris P., Sottoriva, Andrea, Graham, Trevor A., and Snippert, Hugo J.G.

Published
2021

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

Author

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

Published
2020
Full Text
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50. Accurate detection of circulating tumor DNA using nanopore consensus sequencing

Author

Marcozzi, Alessio, primary, Jager, Myrthe, additional, Elferink, Martin, additional, Straver, Roy, additional, van Ginkel, Joost H., additional, Peltenburg, Boris, additional, Chen, Li-Ting, additional, Renkens, Ivo, additional, van Kuik, Joyce, additional, Terhaard, Chris, additional, de Bree, Remco, additional, Devriese, Lot A., additional, Willems, Stefan M., additional, Kloosterman, Wigard P., additional, and de Ridder, Jeroen, additional

Published
2020
Full Text
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