Journal Article

DZNE-2022-01595

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png 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, P. ; Devonshire, A. S. ; Redshaw, N. ; von Baumgarten, L. ; Whale, A. S. ; Jones, G. M. ; Fernandez-Gonzalez, A. ; Martin, J. ; Foy, C. A. ; Alexopoulos, P. ; Huggett, J. F. ; Perneczky, R. (Last author)DZNE*

2022
Elsevier New York, NY [u.a.]

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Please use a persistent id in citations: doi:10.1016/j.nbt.2022.10.001

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 standardized 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 normalization of extraction yield can help control pre-analytical variability influencing biomarker measurements.

Keyword(s): Humans (MeSH) ; Cell-Free Nucleic Acids (MeSH) ; Alzheimer Disease: diagnosis (MeSH) ; Biomarkers (MeSH) ; Brain Neoplasms (MeSH) ; Dementia ; biomarker ; brain tumour ; diagnosis ; genetics ; metastasis

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Contributing Institute(s):

1. Vascular cognitive impairment & Post-stroke dementia (AG Dichgans)

Research Program(s):

1. 353 - Clinical and Health Care Research (POF4-353) (POF4-353)

Appears in the scientific report 2022

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