期刊
EUROPEAN JOURNAL OF CANCER
卷 162, 期 -, 页码 209-220出版社
ELSEVIER SCI LTD
DOI: 10.1016/j.ejca.2021.09.042
关键词
Liquid biopsy; Cell-free DNA; Clinical targeted sequencing; Paediatric oncology; Personalised medicine; ctDNA; Cancer heterogeneity
类别
资金
- National Institute for Health Research (NIHR) Biomedical Research Centre at The Royal Marsden NHS Foundation Trust
- Institute of Cancer Research, London
- CRUK
- Christopher's Smile
- Royal Marsden Cancer Charity (RMCC)
- Royal Marsden CYP Unit and Children's Unit Fund
- Experimental Cancer Medicines Centre (ECMC)
- CRUK/CRICK Fellowship/Institute of Cancer Research
- CwCUK/CRUK SMPaeds [17e235/A24566]
- CRUK SMPaeds [A24566]
- Great Ormond Street Hospital Charity Infrastructure award [VSO118]
- Great Ormond Street Hospital NIHR Biomedical Research Centre
- ICR HEFCE
- Wellcome Trust [202778/B/16/Z, NCI U54CA217376]
- Cancer Research UK [105104/Z/14/Z]
- National Institute of Health [A22909]
- Oak Foundation/RMCC
- Rosetrees project grant
- Sohn Conference Foundation
- Hopkins family
- Giant Pledge via the RMCC
- Wellcome Trust [202778/B/16/Z] Funding Source: Wellcome Trust
This study developed a clinically relevant NGS capture panel and workflow for detecting low frequency genetic variants in cell-free DNA from children with solid tumors. The method showed high sensitivity, specificity, repeatability, and reproducibility. The potential for clinical application was demonstrated in childhood cancer patients, with a close correlation between cfDNA events and treatment response observed.
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. 2021 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
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