Cerebrospinal fluid liquid biopsy for detecting somatic mosaicism in brain
Open accessAbstract
Brain somatic mutations are an increasingly recognized cause of epilepsy, brain malformations and autism spectrum disorders and may be a hidden cause of other neurodevelopmental and neurodegenerative disorders. At present, brain mosaicism can be detected only in the rare situations of autopsy or brain biopsy. Liquid biopsy using cell-free DNA derived from cerebrospinal fluid has detected somatic mutations in malignant brain tumours. Here, we asked if cerebrospinal fluid liquid biopsy can be used to detect somatic mosaicism in non-malignant brain diseases. First, we reliably quantified cerebrospinal fluid cell-free DNA in 28 patients with focal epilepsy and 28 controls using droplet digital PCR. Then, in three patients we identified somatic mutations in cerebrospinal fluid: in one patient with subcortical band heterotopia the LIS1 p. Lys64* variant at 9.4% frequency; in a second patient with focal cortical dysplasia the TSC1 p. Phe581His*6 variant at 7.8% frequency; and in a third patient with ganglioglioma the BRAF p. Val600Glu variant at 3.2% frequency. To determine if cerebrospinal fluid cell-free DNA was brain-derived, whole-genome bisulphite sequencing was performed and brain-specific DNA methylation patterns were found to be significantly enriched (P = 0.03). Our proof of principle study shows that cerebrospinal fluid liquid biopsy is valuable in investigating mosaic neurological disorders where brain tissue is unavailable.
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Somatic mosaicism can be found in brain-derived DNA at low levels on surgical specimens, cerebrospinal fluid or implanted EEG electrodes.
“Somatic mosaicism can be found in brain-derived DNA at low levels on surgical specimens, cerebrospinal fluid or implanted EEG electrodes 122, 177, 178 .”
From Developmental and epileptic encephalopathies (2024) · cites this paper as [178]
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- Authors
- Ye, Z., Chatterton, Z., Pflueger, J., Damiano, J. A., McQuillan, L., Simon Harvey, A., Malone, S., Do, H., Maixner, W., Schneider, A., Nolan, B., Wood, M., Lee, W. S., Gillies, G., Pope, K., Wilson, M., Lockhart, P. J., Dobrovic, A., Scheffer, I. E., Bahlo, M., Leventer, R. J., Lister, R., Berkovic, S. F., & Hildebrand, M. S.
- Affiliations
- The University of Melbourne (AU)
- The University of Sydney (AU)
- The University of Western Australia (AU)
- Murdoch Children’s Research Institute, Melbourne, Victoria 3052, Australia
- Children's Health Queensland Hospital and Health Service (AU)
- Royal Children's Hospital (AU)
- Murdoch Children's Research Institute (AU)
- Corresponding author
- Dobrovic, Alexander
- Berkovic, Samuel F
- Hildebrand, Michael S
- ORCID
- Venue
- Brain Communications
- Publisher
- Oxford University Press (OUP)
- Published
- 2021
- Volume
- 3
- Issue
- 1
- Pages
- fcaa235-fcaa235
- ISSN
- 2632-1297 (ISSN-L)
- PMC
- PMC7954394
- OpenAlex
- W3121975692
- Cited by
- 77
- References
- 29
- Citations by year
- 2026: 7 · 2025: 10 · 2024: 17 · 2023: 12 · 2022: 20 · 2021: 11
- FWCI
- 5.95
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Brain Communications (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Minerva Access (University of Melbourne) (submittedVersion, cc-by)
- UWA Profiles and Research Repository (UWA) (submittedVersion, cc-by)
- Figshare (submittedVersion, cc-by)
- La Trobe University (cc-by)
- Funders
- National Health and Medical Research Council Program
- Grant (1091593)
- Project Grant (1129054, 1079058)
- a Practitioner Fellowship (1006110)
- a Senior Research Fellowship (1102971)
- R.D Wright Career Development Fellowship (1063799)
- Melbourne Children’s Clinician Scientist Fellowship
- Vincent Ciodo Foundation
- University of Melbourne Australian Postgraduate Award International Graduate Research Training Scholarship
- Tang Lixin Education Development Fund
- Australian Epilepsy Research Fund Scheme Grant from the Epilepsy Foundation
- University of Sydney Postdoctoral Fellowship
- Sylvia and Charles Viertel Senior Medical Research Fellowship, Howard Hughes Medical Institute International Research Scholarship
- the Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology (CE140100008)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Health Sciences › Medicine › Psychiatry and Mental health › Epilepsy research and treatment
- Keywords
- somatic mosaicism, focal epilepsy, subcortical band heterotopia, focal cortical dysplasia, ganglioglioma, LIS1, TSC1
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