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Optimization of a Protocol for Isolating Cell-free DNA From Cerebrospinal Fluidopen access

Authors
Song, Ho HyunPark, HyeranCho, DoohwanBang, Hae InOh, Hyuk-JinKim, Jieun
Issue Date
May-2024
Publisher
KOREAN SOC LABORATORY MEDICINE
Keywords
Cell-free nucleic acids; Cerebrospinal fluid; Circulating tumor DNA; Droplet digi- tal PCR; Vacuum
Citation
ANNALS OF LABORATORY MEDICINE, v.44, no.3, pp 294 - 298
Pages
5
Journal Title
ANNALS OF LABORATORY MEDICINE
Volume
44
Number
3
Start Page
294
End Page
298
URI
https://scholarworks.bwise.kr/sch/handle/2021.sw.sch/26084
DOI
10.3343/alm.2023.0267
ISSN
2234-3806
2234-3814
Abstract
A standardized protocol for the isolation of cell-free DNA (cfDNA) from cerebrospinal fluid (CSF) is lacking. Therefore, we established a cfDNA isolation protocol optimized for clinical CSF specimens, integrating acceptable modifications and using artificial CSF generated from remnant CSF spiked with reference cell-free tumor DNA (ctDNA). We compared the isolation yields of in vitro diagnostic (IVD)-certified column-based (CB) and magnetic beadbased (MB) isolation. Furthermore, we modified both methods, including pre- and postelution steps. To confirm ctDNA integrity and quantify the variant allele frequency after isolation, we performed droplet digital PCR (ddPCR) targeting IDH1 R132C in the reference ctDNA. MB isolation had a higher yield than CB isolation (P < 0.0001), and post-isolation vacuum increased the final concentration in both methods, with little effect on cfDNA integrity. Our study provides a protocol to maximize CSF-ctDNA concentrations in IVD testing and future studies.
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College of Medicine > Department of Anesthesiology > 1. Journal Articles
College of Medicine > Department of Neurosurgery > 1. Journal Articles
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