Droplet digital PCR-based detection of circulating tumor DNA from pediatric high grade and diffuse midline glioma patients

Izquierdo, Elisa; Proszek, Paula; Pericoli, Giulia; Temelso, Sara; Clarke, Matthew; Carvalho, Diana M; Mackay, Alan; Marshall, Lynley V; Carceller, Fernando; Hargrave, Darren; Lannering, Birgitta; Pavelka, Zdenek; Bailey, Simon; Entz-Werle, Natacha; Grill, Jacques; Vassal, Gilles; Rodriguez, Daniel; Morgan, Paul S; Jaspan, Tim; Mastronuzzi, Angela; Vinci, Mara; Hubank, Michael; Jones, Chris

Abstract

Background
The use of liquid biopsy is of potential high importance for children with high grade (HGG) and diffuse midline gliomas (DMG), particularly where surgical procedures are limited, and invasive biopsy sampling not without risk. To date, however, the evidence that detection of cell-free DNA (cfDNA) or circulating tumor DNA (ctDNA) could provide useful information for these patients has been limited, or contradictory.

Methods
We optimized droplet digital PCR (ddPCR) assays for the detection of common somatic mutations observed in pediatric HGG/DMG, and applied them to liquid biopsies from plasma, serum, cerebrospinal fluid (CSF), and cystic fluid collected from 32 patients.

Results
Although detectable in all biomaterial types, ctDNA presented at significantly higher levels in CSF compared to plasma and/or serum. When applied to a cohort of 127 plasma specimens from 41 patients collected from 2011 to 2018 as part of a randomized clinical trial in pediatric non-brainstem HGG/DMG, ctDNA profiling by ddPCR was of limited use due to the small volumes (mean = 0.49 mL) available. In anecdotal cases where sufficient material was available, cfDNA concentration correlated with disease progression in two examples each of poor response in H3F3A_K27M-mutant DMG, and longer survival times in hemispheric BRAF_V600E-mutant cases.

Conclusion
Tumor-specific DNA alterations are more readily detected in CSF than plasma. Although we demonstrate the potential of the approach to assessing tumor burden, our results highlight the necessity for adequate sample collection and approach to improve detection if plasma samples are to be used.

Citation

Izquierdo, E., Proszek, P., Pericoli, G., Temelso, S., Clarke, M., Carvalho, D. M., Mackay, A., Marshall, L. V., Carceller, F., Hargrave, D., Lannering, B., Pavelka, Z., Bailey, S., Entz-Werle, N., Grill, J., Vassal, G., Rodriguez, D., Morgan, P. S., Jaspan, T., Mastronuzzi, A., …Jones, C. (2021). Droplet digital PCR-based detection of circulating tumor DNA from pediatric high grade and diffuse midline glioma patients. Neuro-Oncology Advances, 3(1), Article vdab013. https://doi.org/10.1093/noajnl/vdab013

• Journal Article Type: Article
• Acceptance Date: Nov 19, 2020
• Online Publication Date: Jan 27, 2021
• Publication Date: Jan 1, 2021
• Deposit Date: Dec 5, 2023
• Publicly Available Date: Dec 6, 2023
• Journal: Neuro-Oncology Advances
• Electronic ISSN: 2632-2498
• Publisher: Oxford University Press (OUP)
• Peer Reviewed: Peer Reviewed
• Volume: 3
• Issue: 1
• Article Number: vdab013
• DOI: https://doi.org/10.1093/noajnl/vdab013
• Keywords: General Medicine
• Public URL: https://nottingham-repository.worktribe.com/output/28140272
• Publisher URL: https://academic.oup.com/noa/article/3/1/vdab013/6121367