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Your search keyword '"Derks, Lucca L.M."' showing total 10 results
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10 results on '"Derks, Lucca L.M."'

2. Comprehensive single-cell genome analysis at nucleotide resolution using the PTA Analysis Toolbox

Author

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., and van Boxtel, Ruben

Published
2023
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4. Selective pressures of platinum compounds shape the evolution of therapy-related myeloid neoplasms

Author

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, 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., and van Boxtel, Ruben

Abstract

Therapy-related myeloid neoplasms (t-MN) arise as a complication of chemo- and/or radiotherapy. Although t-MN can occur both in adult and childhood cancer survivors, the mechanisms driving therapy-related leukemogenesis likely vary across different ages. Chemotherapy is thought to induce driver mutations in children, whereas in adults pre-existing mutant clones are selected by the exposure. However, selective pressures induced by chemotherapy early in life are less well studied. Here, we use single-cell whole genome sequencing and phylogenetic inference to show that the founding cell of t-MN in children starts expanding after cessation of platinum exposure. In patients with Li-Fraumeni syndrome, characterized by a germline TP53 mutation, we find that the t-MN already expands during treatment, suggesting that platinum-induced growth inhibition is TP53-dependent. Our results demonstrate that germline aberrations can interact with treatment exposures in inducing t-MN, which is important for the development of more targeted, patient-specific treatment regimens and follow-up.

Published
2024

5. Comprehensive single-cell genome analysis at nucleotide resolution using the PTA Analysis Toolbox

Author

CMM Groep Snippert, CMM Groep Kloosterman, CTI Leusen, SCT patientenzorg, Child Health, Infection & Immunity, Regenerative Medicine and Stem Cells, Arts-assistenten Kinderen, CMM Groep Cuppen, 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, CMM Groep Snippert, CMM Groep Kloosterman, CTI Leusen, SCT patientenzorg, Child Health, Infection & Immunity, Regenerative Medicine and Stem Cells, Arts-assistenten Kinderen, CMM Groep Cuppen, 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., and van Boxtel, Ruben

Published
2023

6. One-step generation of tumor models by base editor multiplexing in adult stem cell-derived organoids

Author

Hubrecht Institute with UMC, CMM, Cancer, Geurts, Maarten H., Gandhi, Shashank, Boretto, Matteo G., Akkerman, Ninouk, Derks, Lucca L.M., van Son, Gijs, Celotti, Martina, Harshuk-Shabso, Sarina, Peci, Flavia, Begthel, Harry, Hendriks, Delilah, Schürmann, Paul, Andersson-Rolf, Amanda, Chuva de Sousa Lopes, Susana M., van Es, Johan H., van Boxtel, Ruben, Clevers, Hans, Hubrecht Institute with UMC, CMM, Cancer, Geurts, Maarten H., Gandhi, Shashank, Boretto, Matteo G., Akkerman, Ninouk, Derks, Lucca L.M., van Son, Gijs, Celotti, Martina, Harshuk-Shabso, Sarina, Peci, Flavia, Begthel, Harry, Hendriks, Delilah, Schürmann, Paul, Andersson-Rolf, Amanda, Chuva de Sousa Lopes, Susana M., van Es, Johan H., van Boxtel, Ruben, and Clevers, Hans

Published
2023

7. Comprehensive single-cell genome analysis at nucleotide resolution using the PTA Analysis Toolbox

Author

Middelkamp, Sjors, primary, Manders, Freek, additional, Peci, Flavia, additional, van Roosmalen, Markus J., additional, González, Diego Montiel, additional, Bertrums, Eline J.M., additional, van der Werf, Inge, additional, Derks, Lucca L.M., additional, Groenen, Niels M., additional, Verheul, Mark, additional, Trabut, Laurianne, additional, Brandsma, Arianne M., additional, Antoniou, Evangelia, additional, Reinhardt, Dirk, additional, Bierings, Marc, additional, Belderbos, Mirjam E., additional, and van Boxtel, Ruben, additional

Published
2023
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10. Protocol for genome-wide analysis of somatic variants at single-cell resolution using primary template-directed DNA amplification

Author

Derks, Lucca L.M., van Leeuwen, Anaïs J.C.N., Steemers, Alexander S., Trabut, Laurianne, van Roosmalen, Markus J., Poort, Vera M., Hagelaar, Rico, Verheul, Mark, Middelkamp, Sjors, and van Boxtel, Ruben

Abstract

The study of somatic mutations in single cells provides insights into aging and carcinogenesis, which is complicated by the dependency on whole-genome amplification (WGA). Here, we describe a detailed workflow starting from single-cell isolation to WGA by primary template-directed amplification (PTA), sequencing, quality control, and downstream analyses. A machine learning approach, the PTA Analysis Toolkit (PTATO), is used to filter the hundreds to thousands of artificial variants induced by WGA from true mutations at high sensitivity and accuracy.

Published
2025
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