A standardised methodology for the extraction and quantification of cell-free DNA in cerebrospinal fluid and application to evaluation of Alzheimer's disease and brain cancers.

Takousis, Petros; Devonshire, Alison S; Redshaw, Nicholas; von Baumgarten, Louisa; Whale, Alexandra S; Jones, Gerwyn M; Fernandez-Gonzalez, Ana; Martin, Jan; Foy, Carole A; Alexopoulos, Panagiotis; Huggett, Jim F; Perneczky, Robert

doi:10.1016/j.nbt.2022.10.001

2022

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Title:: A standardised methodology for the extraction and quantification of cell-free DNA in cerebrospinal fluid and application to evaluation of Alzheimer's disease and brain cancers.
Document type:: Journal Article
Author(s):: Takousis, Petros; Devonshire, Alison S; Redshaw, Nicholas; von Baumgarten, Louisa; Whale, Alexandra S; Jones, Gerwyn M; Fernandez-Gonzalez, Ana; Martin, Jan; Foy, Carole A; Alexopoulos, Panagiotis; Huggett, Jim F; Perneczky, Robert
Abstract:: Cerebrospinal fluid (CSF) is a source of diagnostic biomarkers for a range of neurological conditions. Cell-free DNA (cfDNA) is detected in CSF and differences in the concentration of cell-free mitochondrial DNA have been reported in studies of neurodegenerative disorders including Alzheimer's disease (AD). However, the influence of pre-analytical steps has not been investigated for cfDNA in CSF and there is no standardised approach for quantification of total cfDNA (copies of nuclear genome or mitochondria-derived gene targets). In this study, the suitability of four extraction methods was evaluated: QIAamp Circulating Nucleic Acid (Qiagen), Quick-cfDNA Serum & Plasma (Zymo), NucleoSnap® DNA Plasma (Macherey-Nagel) and Plasma/Serum Circulating DNA Purification Mini (Norgen) kits, for cfDNA extraction from CSF of controls and AD dementia patients, utilising a spike-in control for extraction efficiency and fragment size. One of the optimal extraction methods was applied to a comparison of cfDNA concentrations in CSF from control subjects, AD dementia and primary and secondary brain tumour patients. Extraction efficiency based on spike-in recovery was similar in all three groups whilst both endogenous mitochondrial and nucleus-derived cfDNA was significantly higher in CSF from cancer patients compared to control and AD groups, which typically contained < 100 genome copies/mL. This study shows that it is feasible to measure low concentration nuclear and mitochondrial gene targets in CSF and that normalisation of extraction yield can help control pre-analytical variability influencing biomarker measurements.
Journal title abbreviation:: N Biotechnol
Year:: 2022
Journal volume:: 72
Pages contribution:: 97-106
Fulltext / DOI:: doi:10.1016/j.nbt.2022.10.001
Pubmed ID:: http://view.ncbi.nlm.nih.gov/pubmed/36202346
Print-ISSN:: 1871-6784
TUM Institution:: Klinik und Poliklinik für Psychiatrie und Psychotherapie
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mediaTUM Gesamtbestand Einrichtungen Schools TUM School of Medicine and Health Departments Clinical Medicine Klinik und Poliklinik für Psychiatrie und Psychotherapie (Prof. Priller)2022