Reda Stankunaite1, Sally L George2, Lewis Gallagher3, Sabri Jamal4, Ridwan Shaikh5, Lina Yuan6, Debbie Hughes7, Paula Z Proszek8, Paul Carter9, Grzegorz Pietka10, Timon Heide11, Chela James12, Haider Tari13, Claire Lynn14, Neha Jain15, Laura Rey Portela16, Tony Rogers17, Sucheta J Vaidya18, Julia C Chisholm19, Fernando Carceller20, Elwira Szychot21, Henry Mandeville22, Paola Angelini23, Angela B Jesudason24, Michael Jackson24, Lynley V Marshall25, Susanne A Gatz26, John Anderson27, Andrea Sottoriva28, Louis Chesler29, Michael Hubank30. 1. Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK; Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK. Electronic address: Reda.stankunaite@icr.ac.uk. 2. Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK. Electronic address: sally.george@icr.ac.uk. 3. Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK. Electronic address: lewis.gallagher@icr.ac.uk. 4. Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK. Electronic address: sabri.jamal@icr.ac.uk. 5. Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK. Electronic address: Ridwan.Shaikh@icr.ac.uk. 6. Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK. Electronic address: Lina.Yuan@icr.ac.uk. 7. Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK. Electronic address: debbie.hughes@icr.ac.uk. 8. Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK. Electronic address: Paula.Proszek@icr.ac.uk. 9. Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK. Electronic address: Paul.Carter@icr.ac.uk. 10. Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK. Electronic address: Grzegorz.Pietka@icr.ac.uk. 11. Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK. Electronic address: Timon.Heide@icr.ac.uk. 12. Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK. Electronic address: chela.james@icr.ac.uk. 13. Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK; Glioma Lab, The Institute of Cancer Research, London, UK. Electronic address: Haider.Tari@icr.ac.uk. 14. Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK. Electronic address: Claire.Lynn@icr.ac.uk. 15. Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK. Electronic address: Neha.Jain@gosh.nhs.uk. 16. Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK. Electronic address: Laura.ReyPortela@gosh.nhs.uk. 17. Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK. Electronic address: tony.rogers@icr.ac.uk. 18. Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK. Electronic address: Sucheta.Vaidya@icr.ac.uk. 19. Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK. Electronic address: Julia.Chisholm@icr.ac.uk. 20. Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK. Electronic address: Fernando.Carceller@rmh.nhs.uk. 21. Oak Centre for Children and Young People, Royal Marsden NHS Foundation Trust Hospital, Sutton, UK; Department of Paediatrics, Paediatric Oncology and Immunology, Pomeranian Medical University, Szczecin, Poland. Electronic address: e.szychot@nhs.net. 22. Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK. Electronic address: Henry.Mandeville@rmh.nhs.uk. 23. Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK. Electronic address: paola.angelini@nhs.net. 24. Department of Paediatric Haematology and Oncology, Royal Hospital for Sick Children, Edinburgh, UK. 25. Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK. Electronic address: LynleyVanessa.Marshall@icr.ac.uk. 26. Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK; Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK. Electronic address: S.Gatz@bham.ac.uk. 27. Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK; Developmental Biology and Cancer Programme, UCL GOS Institute of Child Health, London, UK. Electronic address: j.anderson@ucl.ac.uk. 28. Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK. Electronic address: andrea.sottoriva@icr.ac.uk. 29. Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK. Electronic address: Louis.Chesler@icr.ac.uk. 30. Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK. Electronic address: Michael.Hubank@icr.ac.uk.
Abstract
OBJECTIVE: Clinical diagnostic sequencing of circulating tumour DNA (ctDNA) is well advanced for adult patients, but application to paediatric cancer patients lags behind. METHODS: To address this, we have developed a clinically relevant (67 gene) NGS capture panel and accompanying workflow that enables sensitive and reliable detection of low-frequency genetic variants in cell-free DNA (cfDNA) from children with solid tumours. We combined gene panel sequencing with low pass whole-genome sequencing of the same library to inform on genome-wide copy number changes in the blood. RESULTS: Analytical validity was evaluated using control materials, and the method was found to be highly sensitive (0.96 for SNVs and 0.97 for INDEL), specific (0.82 for SNVs and 0.978 for INDEL), repeatable (>0.93 [95% CI: 0.89-0.95]) and reproducible (>0.87 [95% CI: 0.87-0.95]). Potential for clinical application was demonstrated in 39 childhood cancer patients with a spectrum of solid tumours in which the single nucleotide variants expected from tumour sequencing were detected in cfDNA in 94.4% (17/18) of cases with active extracranial disease. In 13 patients, where serial samples were available, we show a close correlation between events detected in cfDNA and treatment response, demonstrate that cfDNA analysis could be a useful tool to monitor disease progression, and show cfDNA sequencing has the potential to identify targetable variants that were not detected in tumour samples. CONCLUSIONS: This is the first pan-cancer DNA sequencing panel that we know to be optimised for cfDNA in children for blood-based molecular diagnostics in paediatric solid tumours.
OBJECTIVE: Clinical diagnostic sequencing of circulating tumour DNA (ctDNA) is well advanced for adult patients, but application to paediatric cancer patients lags behind. METHODS: To address this, we have developed a clinically relevant (67 gene) NGS capture panel and accompanying workflow that enables sensitive and reliable detection of low-frequency genetic variants in cell-free DNA (cfDNA) from children with solid tumours. We combined gene panel sequencing with low pass whole-genome sequencing of the same library to inform on genome-wide copy number changes in the blood. RESULTS: Analytical validity was evaluated using control materials, and the method was found to be highly sensitive (0.96 for SNVs and 0.97 for INDEL), specific (0.82 for SNVs and 0.978 for INDEL), repeatable (>0.93 [95% CI: 0.89-0.95]) and reproducible (>0.87 [95% CI: 0.87-0.95]). Potential for clinical application was demonstrated in 39 childhood cancer patients with a spectrum of solid tumours in which the single nucleotide variants expected from tumour sequencing were detected in cfDNA in 94.4% (17/18) of cases with active extracranial disease. In 13 patients, where serial samples were available, we show a close correlation between events detected in cfDNA and treatment response, demonstrate that cfDNA analysis could be a useful tool to monitor disease progression, and show cfDNA sequencing has the potential to identify targetable variants that were not detected in tumour samples. CONCLUSIONS: This is the first pan-cancer DNA sequencing panel that we know to be optimised for cfDNA in children for blood-based molecular diagnostics in paediatric solid tumours.
Authors: Laura M Madanat-Harjuoja; Lindsay A Renfro; Kelly Klega; Brett Tornwall; Aaron R Thorner; Anwesha Nag; David Dix; Jeffrey S Dome; Lisa R Diller; Conrad V Fernandez; Elizabeth A Mullen; Brian D Crompton Journal: J Clin Oncol Date: 2022-05-17 Impact factor: 50.717
Authors: Markus G Seidel; Karl Kashofer; Tina Moser; Andrea Thueringer; Bernadette Liegl-Atzwanger; Andreas Leithner; Joanna Szkandera; Martin Benesch; Amin El-Heliebi; Ellen Heitzer Journal: Front Pediatr Date: 2022-08-15 Impact factor: 3.569