Circulating tumour DNA sequencing to determine therapeutic response and identify tumour heterogeneity in patients with paediatric solid tumours

Reda Stankunaite; Sally L George; Lewis Gallagher; Sabri Jamal; Ridwan Shaikh; Lina Yuan; Debbie Hughes; Paula Z Proszek; Paul Carter; Grzegorz Pietka; Timon Heide; Chela James; Haider Tari; Claire Lynn; Neha Jain; Laura Rey Portela; Tony Rogers; Sucheta J Vaidya; Julia C Chisholm; Fernando Carceller; Elwira Szychot; Henry Mandeville; Paola Angelini; Angela B Jesudason; Michael Jackson; Lynley V Marshall; Susanne A Gatz; John Anderson; Andrea Sottoriva; Louis Chesler; Michael Hubank

doi:10.1016/j.ejca.2021.09.042

Circulating tumour DNA sequencing to determine therapeutic response and identify tumour heterogeneity in patients with paediatric solid tumours

Eur J Cancer. 2022 Feb:162:209-220. doi: 10.1016/j.ejca.2021.09.042. Epub 2021 Dec 18.

Authors

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

Affiliations

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: [email protected].
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: [email protected].
³ Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK. Electronic address: [email protected].
⁴ Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK. Electronic address: [email protected].
⁵ Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK. Electronic address: [email protected].
⁶ Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK. Electronic address: [email protected].
⁷ Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK. Electronic address: [email protected].
⁸ Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK. Electronic address: [email protected].
⁹ Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK. Electronic address: [email protected].
¹⁰ Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK. Electronic address: [email protected].
¹¹ Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK. Electronic address: [email protected].
¹² Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK. Electronic address: [email protected].
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: [email protected].
¹⁴ Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK. Electronic address: [email protected].
¹⁵ Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK. Electronic address: [email protected].
¹⁶ Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK. Electronic address: [email protected].
¹⁷ Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK. Electronic address: [email protected].
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: [email protected].
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: [email protected].
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: [email protected].
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: [email protected].
²² Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK. Electronic address: [email protected].
²³ Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK. Electronic address: [email protected].
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: [email protected].
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: [email protected].
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: [email protected].
²⁸ Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK. Electronic address: [email protected].
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: [email protected].
³⁰ Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK. Electronic address: [email protected].

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.

Keywords: Cancer heterogeneity; Cell-free DNA; Clinical targeted sequencing; Liquid biopsy; Paediatric oncology; Personalised medicine; ctDNA.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Adult
Biomarkers, Tumor / genetics
Cell-Free Nucleic Acids* / genetics
Child
Circulating Tumor DNA*
High-Throughput Nucleotide Sequencing / methods
Humans
Mutation
Neoplasms* / diagnosis
Neoplasms* / genetics
Neoplasms* / pathology
Whole Genome Sequencing / methods

Substances

Biomarkers, Tumor
Cell-Free Nucleic Acids
Circulating Tumor DNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding