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Epigenetics Volume 16, 2021 - Issue 2
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Research Paper

Minimally invasive classification of paediatric solid tumours using reduced representation bisulphite sequencing of cell-free DNA: a proof-of-principle study

Ruben Van Paemela Department of Biomolecular Medicine, Ghent University, Ghent, Belgium;b Department of Pediatric Hematology, Oncology & Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium;c Cancer Research Institute Ghent (CRIG), Ghent, BelgiumORCID Iconhttps://orcid.org/0000-0001-7324-3570View further author information
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Andries De Kokerc Cancer Research Institute Ghent (CRIG), Ghent, Belgium;d Center for Medical Biotechnology, Flemish Institute Biotechnology (VIB), Ghent, BelgiumORCID Iconhttps://orcid.org/0000-0003-3939-7650View further author information
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Charlotte Vandeputtea Department of Biomolecular Medicine, Ghent University, Ghent, Belgium;c Cancer Research Institute Ghent (CRIG), Ghent, BelgiumView further author information
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Lieke van Zogchele Princess Máxima Center for Pediatric Oncology, Utrecht, The NetherlandsORCID Iconhttps://orcid.org/0000-0003-3557-7195View further author information
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Tim Lammensa Department of Biomolecular Medicine, Ghent University, Ghent, Belgium;b Department of Pediatric Hematology, Oncology & Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium;c Cancer Research Institute Ghent (CRIG), Ghent, BelgiumView further author information
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Geneviève Laureysa Department of Biomolecular Medicine, Ghent University, Ghent, Belgium;b Department of Pediatric Hematology, Oncology & Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium;c Cancer Research Institute Ghent (CRIG), Ghent, BelgiumView further author information
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Jo Vandesompelea Department of Biomolecular Medicine, Ghent University, Ghent, Belgium;c Cancer Research Institute Ghent (CRIG), Ghent, BelgiumORCID Iconhttps://orcid.org/0000-0001-6274-0184View further author information
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Gudrun Schleiermacherf INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Research Center, Institut Curie, Paris, France;g SiRIC RTOP « Recherche Translationelle En Oncologie Pédiatrique », Institut Curie, Paris, FranceView further author information
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Mathieu Chicardf INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Research Center, Institut Curie, Paris, France;g SiRIC RTOP « Recherche Translationelle En Oncologie Pédiatrique », Institut Curie, Paris, FranceView further author information
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Nadine Van Roya Department of Biomolecular Medicine, Ghent University, Ghent, Belgium;c Cancer Research Institute Ghent (CRIG), Ghent, BelgiumView further author information
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Ales Vichah Department of Pediatric Hematology and Oncology, Charles University in Prague, Second Faculty of Medicine and University Hospital Motol, Prague, Czech RepublicORCID Iconhttps://orcid.org/0000-0003-3075-5554View further author information
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G.A.M. Tytgate Princess Máxima Center for Pediatric Oncology, Utrecht, The NetherlandsORCID Iconhttps://orcid.org/0000-0003-4452-0748View further author information
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Nico Callewaertc Cancer Research Institute Ghent (CRIG), Ghent, Belgium;d Center for Medical Biotechnology, Flemish Institute Biotechnology (VIB), Ghent, BelgiumORCID Iconhttps://orcid.org/0000-0003-2069-6917View further author information
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Katleen De Pretera Department of Biomolecular Medicine, Ghent University, Ghent, Belgium;c Cancer Research Institute Ghent (CRIG), Ghent, BelgiumORCID Iconhttps://orcid.org/0000-0002-7726-5096View further author information
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Bram De Wildea Department of Biomolecular Medicine, Ghent University, Ghent, Belgium;b Department of Pediatric Hematology, Oncology & Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium;c Cancer Research Institute Ghent (CRIG), Ghent, BelgiumCorrespondence[email protected]
ORCID Iconhttps://orcid.org/0000-0003-0213-1322View further author information
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Pages 196-208 | Received 10 Nov 2019, Accepted 12 May 2020, Published online: 14 Jul 2020

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Ruben Van Paemel, Andries De Koker, Christa Caggiano, Annelien Morlion, Pieter Mestdagh, Bram De Wilde, Jo Vandesompele & Katleen De Preter. (2021) Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome. Epigenetics 16:7, pages 797-807.
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Euan J. Rodger, Peter A. Stockwell, Suzan Almomani, Michael R. Eccles & Aniruddha Chatterjee. (2023) Protocol for generating high-quality genome-scale DNA methylation sequencing data from human cancer biospecimens. STAR Protocols 4:4, pages 102714.
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Srivandana Akshintala, R. Taylor Sundby, Donna Bernstein, John W. Glod, Rosandra N. Kaplan, Marielle E. Yohe, Andrea M. Gross, Joanne Derdak, Haiyan Lei, Alexander Pan, Eva Dombi, Isabel Palacio-Yance, Kailey R. Herrera, Markku M. Miettinen, Helen X. Chen, Seth M. Steinberg, Lee J. Helman, Leo Mascarenhas, Brigitte C. Widemann, Fariba Navid, Jack F. Shern & Christine M. Heske. (2023) Phase I trial of Ganitumab plus Dasatinib to Cotarget the Insulin-Like Growth Factor 1 Receptor and Src Family Kinase YES in Rhabdomyosarcoma. Clinical Cancer Research 29:17, pages 3329-3339.
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Siyu Fu, José D. Debes & André Boonstra. (2023) DNA methylation markers in the detection of hepatocellular carcinoma. European Journal of Cancer 191, pages 112960.
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Monika Grubliauskaite, M. E. Madeleine van der Perk, Annelies M. E. Bos, Annelot J. M. Meijer, Zivile Gudleviciene, Marry M. van den Heuvel-Eibrink & Jelena Rascon. (2023) Minimal Infiltrative Disease Identification in Cryopreserved Ovarian Tissue of Girls with Cancer for Future Use: A Systematic Review. Cancers 15:17, pages 4199.
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Nina U. Gelineau, Astrid van Barneveld, Atia Samim, Lieke Van Zogchel, Nathalie Lak, Michelle L. Tas, Yvette Matser, Annelies M. C. Mavinkurve-Groothuis, Martine van Grotel, Jószef Zsiros, Natasha K. A. van Eijkelenburg, Rutger R. G. Knops, Roelof van Ewijk, Karin P. S. Langenberg, Ronald De Krijger, Laura S. Hiemcke-Jiwa, Ruben Van Paemel, Lotte Cornelli, Katleen De Preter, Bram De Wilde, Ellen Van Der Schoot & Godelieve Tytgat. (2023) Case series on clinical applications of liquid biopsy in pediatric solid tumors: towards improved diagnostics and disease monitoring. Frontiers in Oncology 13.
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Benjamin L. Spector, Lauren Harrell, Drinnan Sante, Gerald J. Wyckoff & Laurel Willig. (2023) The methylome and cell-free DNA: current applications in medicine and pediatric disease. Pediatric Research 94:1, pages 89-95.
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Lieke M. J. van Zogchel, Nathalie S. M. Lak, Nina U. Gelineau, Irina Sergeeva, Ellen Stelloo, Joost Swennenhuis, Harma Feitsma, Max van Min, Erik Splinter, Margit Bleijs, Marian Groot Koerkamp, Willemijn Breunis, Michael Torsten Meister, Waleed Hassan Kholossy, Frank C. P. Holstege, Jan J. Molenaar, Wendy W. J. de Leng, Janine Stutterheim, C. Ellen van der Schoot & Godelieve A. M. Tytgat. (2023) Targeted locus amplification to develop robust patient-specific assays for liquid biopsies in pediatric solid tumors. Frontiers in Oncology 13.
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Gianna Di Sario, Valeria Rossella, Elvira Smeralda Famulari, Aurora Maurizio, Dejan Lazarevic, Francesca Giannese & Claudia Felici. (2023) Enhancing clinical potential of liquid biopsy through a multi-omic approach: A systematic review. Frontiers in Genetics 14.
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Nathalie S.M. Lak, Lieke M.J. van Zogchel, Lily Zappeij-Kannegieter, Ahmad Javadi, Ruben van Paemel, Charlotte Vandeputte, Katleen De Preter, Bram De Wilde, Mathieu Chicard, Yasmine Iddir, Gudrun Schleiermacher, Olivia Ruhen, Janet Shipley, Marta Fiocco, Johannes H.M. Merks, Max M. van Noesel, C. Ellen van der Schoot, Godelieve A.M. Tytgat & Janine Stutterheim. (2023) Cell-Free DNA as a Diagnostic and Prognostic Biomarker in Pediatric Rhabdomyosarcoma. JCO Precision Oncology:7.
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Reda Stankunaite, Lynley V. Marshall, Fernando Carceller, Louis Chesler, Michael Hubank & Sally L. George. (2022) Liquid biopsy for children with central nervous system tumours: Clinical integration and technical considerations. Frontiers in Pediatrics 10.
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Mary L. Stackpole, Weihua Zeng, Shuo Li, Chun-Chi Liu, Yonggang Zhou, Shanshan He, Angela Yeh, Ziye Wang, Fengzhu Sun, Qingjiao Li, Zuyang Yuan, Asli Yildirim, Pin-Jung Chen, Paul Winograd, Benjamin Tran, Yi-Te Lee, Paul Shize Li, Zorawar Noor, Megumi Yokomizo, Preeti Ahuja, Yazhen Zhu, Hsian-Rong Tseng, James S. Tomlinson, Edward Garon, Samuel French, Clara E. Magyar, Sarah Dry, Clara Lajonchere, Daniel Geschwind, Gina Choi, Sammy Saab, Frank Alber, Wing Hung Wong, Steven M. Dubinett, Denise R. Aberle, Vatche Agopian, Steven-Huy B. Han, Xiaohui Ni, Wenyuan Li & Xianghong Jasmine Zhou. (2022) Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer. Nature Communications 13:1.
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Nathalie S. M. Lak, Elvera J. van der Kooi, Agustin Enciso-Martinez, Estefanía Lozano-Andrés, Cees Otto, Marca H. M. Wauben & Godelieve A. M. Tytgat. (2022) Extracellular Vesicles: A New Source of Biomarkers in Pediatric Solid Tumors? A Systematic Review. Frontiers in Oncology 12.
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Araceli Diez-Fraile, Joke De Ceulaer, Charlotte Derpoorter, Christophe Spaas, Tom De Backer, Philippe Lamoral, Johan Abeloos & Tim Lammens. (2022) Tracking the Molecular Fingerprint of Head and Neck Cancer for Recurrence Detection in Liquid Biopsies. International Journal of Molecular Sciences 23:5, pages 2403.
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Anthony Pak-Yin Liu, Paul A. Northcott, Giles W. Robinson & Amar Gajjar. (2022) Circulating tumor DNA profiling for childhood brain tumors: Technical challenges and evidence for utility. Laboratory Investigation 102:2, pages 134-142.
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Joyce Varkey & Theodore Nicolaides. (2021) Tumor-Educated Platelets: A Review of Current and Potential Applications in Solid Tumors. Cureus.
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Lieke M. J. van Zogchel, Nathalie S. M. Lak, Onno J. H. M. Verhagen, Ahmed Tissoudali, Mohammed Gussmalla Nuru, Nina U. Gelineau, Lily Zappeij-Kannengieter, Ahmad Javadi, Eline A. M. Zijtregtop, Johannes H. M. Merks, Marry van den Heuvel-Eibrink, Antoinette Y. N. Schouten-van Meeteren, Janine Stutterheim, C. Ellen van der Schoot & Godelieve A. M. Tytgat. (2021) Novel Circulating Hypermethylated RASSF1A ddPCR for Liquid Biopsies in Patients With Pediatric Solid Tumors. JCO Precision Oncology:5, pages 1738-1748.
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Filippo Spreafico, Conrad V. Fernandez, Jesper Brok, Kayo Nakata, Gordan Vujanic, James I. Geller, Manfred Gessler, Mariana Maschietto, Sam Behjati, Angela Polanco, Vivian Paintsil, Sandra Luna-Fineman & Kathy Pritchard-Jones. (2021) Wilms tumour. Nature Reviews Disease Primers 7:1.
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Aitor Rodriguez-Casanova, Nicolás Costa-Fraga, Aida Bao-Caamano, Rafael López-López, Laura Muinelo-Romay & Angel Diaz-Lagares. (2021) Epigenetic Landscape of Liquid Biopsy in Colorectal Cancer. Frontiers in Cell and Developmental Biology 9.
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