Ruben Van Paemel1, Charlotte Vandeputte2, Lennart Raman3, Jolien Van Thorre4, Leen Willems5, Jo Van Dorpe6, Malaïka Van Der Linden3, Jilke De Wilde3, Andries De Koker7, Björn Menten2, Christine Devalck8, Ales Vicha9, Marek Grega10, Gudrun Schleiermacher11, Yasmine Iddir11, Mathieu Chicard11, Lieke van Zogchel12, Janine Stutterheim13, Nathalie S M Lak12, G A M Tytgat13, Geneviève Laureys14, Frank Speleman2, Bram De Wilde15, Tim Lammens14, Katleen De Preter2, Nadine Van Roy16. 1. Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Research Foundation Flanders, Belgium. 2. Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium. 3. Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pathology, Ghent University Hospital, Ghent, Belgium. 4. Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium. 5. Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium. 6. Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pathology, Ghent University Hospital, Ghent, Belgium. 7. Center for Medical Biotechnology, Flemish Institute Biotechnology (VIB), Ghent, Belgium; Research Foundation Flanders, Belgium. 8. Hôpital Universitaire des Enfants Reine Fabiola, Brussels, Belgium. 9. Department of Pediatric Hematology and Oncology, Charles University, Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic. 10. Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic. 11. Translational Pediatric Oncology, Centre de recherche de l'Institut Curie, Paris, France. 12. Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, Amsterdam, the Netherlands. 13. Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands. 14. Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium. 15. Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium. 16. Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium. Electronic address: Nadine.VanRoy@UGent.be.
Abstract
BACKGROUND: Paediatric tumours are often characterised by the presence of recurrent DNA copy number alterations (CNAs). These DNA copy number profiles, obtained from a tissue biopsy, can aid in the correct prognostic classification and therapeutic stratification of several paediatric cancer entities (e.g. MYCN amplification in neuroblastoma) and are part of the routine diagnostic practice. Liquid biopsies (LQBs) offer a potentially safer alternative for such invasive tumour tissue biopsies and can provide deeper insight into tumour heterogeneity. PROCEDURE: The robustness and reliability of LQB CNA analyses was evaluated. We performed retrospective CNA profiling using shallow whole-genome sequencing (sWGS) on paired plasma circulating cell-free DNA (cfDNA) and tissue DNA samples from routinely collected samples from paediatric patients (n = 128) representing different tumour entities, including osteosarcoma, Ewing sarcoma, rhabdomyosarcoma, Wilms tumour, brain tumours and neuroblastoma. RESULTS: Overall, we observed a good concordance between CNAs in tissue DNA and cfDNA. The main cause of CNA discordance was found to be low cfDNA sample quality (i.e. the ratio of cfDNA (<700 bp) and high molecular weight DNA (>700 bp)). Furthermore, CNAs were observed that were present in cfDNA and not in tissue DNA, or vice-versa. In neuroblastoma samples, no false-positives or false-negatives were identified for the detection of the prognostic marker MYCN amplification. CONCLUSION: In future prospective studies, CNA analysis on LQBs that are of sufficient quality can serve as a complementary assay for CNA analysis on tissue biopsies, as either cfDNA or tissue DNA can contain CNAs that cannot be identified in the other biomaterial.
BACKGROUND: Paediatric tumours are often characterised by the presence of recurrent DNA copy number alterations (CNAs). These DNA copy number profiles, obtained from a tissue biopsy, can aid in the correct prognostic classification and therapeutic stratification of several paediatric cancer entities (e.g. MYCN amplification in neuroblastoma) and are part of the routine diagnostic practice. Liquid biopsies (LQBs) offer a potentially safer alternative for such invasive tumour tissue biopsies and can provide deeper insight into tumour heterogeneity. PROCEDURE: The robustness and reliability of LQB CNA analyses was evaluated. We performed retrospective CNA profiling using shallow whole-genome sequencing (sWGS) on paired plasma circulating cell-free DNA (cfDNA) and tissue DNA samples from routinely collected samples from paediatric patients (n = 128) representing different tumour entities, including osteosarcoma, Ewing sarcoma, rhabdomyosarcoma, Wilms tumour, brain tumours and neuroblastoma. RESULTS: Overall, we observed a good concordance between CNAs in tissue DNA and cfDNA. The main cause of CNA discordance was found to be low cfDNA sample quality (i.e. the ratio of cfDNA (<700 bp) and high molecular weight DNA (>700 bp)). Furthermore, CNAs were observed that were present in cfDNA and not in tissue DNA, or vice-versa. In neuroblastoma samples, no false-positives or false-negatives were identified for the detection of the prognostic marker MYCN amplification. CONCLUSION: In future prospective studies, CNA analysis on LQBs that are of sufficient quality can serve as a complementary assay for CNA analysis on tissue biopsies, as either cfDNA or tissue DNA can contain CNAs that cannot be identified in the other biomaterial.
Authors: Marco Lodrini; Jasmin Wünschel; Theresa M Thole-Kliesch; Maddalena Grimaldi; Annika Sprüssel; Rasmus B Linke; Jan F Hollander; Daniela Tiburtius; Annette Künkele; Johannes H Schulte; Erwin Lankes; Thomas Elgeti; Patrick Hundsdörfer; Kathy Astrahantseff; Thorsten Simon; Angelika Eggert; Hedwig E Deubzer Journal: Cancers (Basel) Date: 2022-04-21 Impact factor: 6.575
Authors: 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 Journal: Front Oncol Date: 2022-05-24 Impact factor: 5.738