View in EDS

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.

Saved in:
Bibliographic Details
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.
Authors: Takousis, Petros1 (AUTHOR), Devonshire, Alison S.1,2 (AUTHOR) alison.devonshire@lgcgroup.com, Redshaw, Nicholas2 (AUTHOR), von Baumgarten, Louisa3,4 (AUTHOR), Whale, Alexandra S.2 (AUTHOR), Jones, Gerwyn M.2 (AUTHOR), Fernandez-Gonzalez, Ana2 (AUTHOR), Martin, Jan5 (AUTHOR), Foy, Carole A.2 (AUTHOR), Alexopoulos, Panagiotis6,7 (AUTHOR), Huggett, Jim F.2,8 (AUTHOR), Perneczky, Robert1,9,10,11,12 (AUTHOR)
Source: New Biotechnology. Dec2022, Vol. 72, p97-106. 10p.
Subjects: Cell-free DNA, Alzheimer's disease, Brain diseases, Mitochondrial DNA, Brain cancer, Plant mitochondria, DNA, Cerebrospinal fluid, Brain tumors
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. [Display omitted] • Approaches to cell-free DNA biomarkers in cerebrospinal fluid vary between studies. • Kits for cell-free DNA (cfDNA) extraction from cerebrospinal fluid were compared. • Spike-in recovery correlated with mitochondrial and nuclear genomic cfDNA yield. • Sensitive assays to repetitive elements are required for nuclear cfDNA detection. • Ratio of mitochondrial to nuclear cfDNA is a potential normalisation strategy. [ABSTRACT FROM AUTHOR]
Copyright of New Biotechnology is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Database: Engineering Source
FullText Text:
  Availability: 0
Header DbId: egs
DbLabel: Engineering Source
An: 160631449
AccessLevel: 6
PubType: Academic Journal
PubTypeId: academicJournal
PreciseRelevancyScore: 0
IllustrationInfo
Items – Name: Title
  Label: Title
  Group: Ti
  Data: A standardised methodology for the extraction and quantification of cell-free DNA in cerebrospinal fluid and application to evaluation of Alzheimer&#39;s disease and brain cancers.
– Name: Author
  Label: Authors
  Group: Au
  Data: &lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Takousis%2C+Petros%22&quot;&gt;Takousis, Petros&lt;/searchLink&gt;&lt;relatesTo&gt;1&lt;/relatesTo&gt; (AUTHOR)&lt;br /&gt;&lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Devonshire%2C+Alison+S%2E%22&quot;&gt;Devonshire, Alison S.&lt;/searchLink&gt;&lt;relatesTo&gt;1,2&lt;/relatesTo&gt; (AUTHOR)&lt;i&gt; alison.devonshire@lgcgroup.com&lt;/i&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Redshaw%2C+Nicholas%22&quot;&gt;Redshaw, Nicholas&lt;/searchLink&gt;&lt;relatesTo&gt;2&lt;/relatesTo&gt; (AUTHOR)&lt;br /&gt;&lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22von+Baumgarten%2C+Louisa%22&quot;&gt;von Baumgarten, Louisa&lt;/searchLink&gt;&lt;relatesTo&gt;3,4&lt;/relatesTo&gt; (AUTHOR)&lt;br /&gt;&lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Whale%2C+Alexandra+S%2E%22&quot;&gt;Whale, Alexandra S.&lt;/searchLink&gt;&lt;relatesTo&gt;2&lt;/relatesTo&gt; (AUTHOR)&lt;br /&gt;&lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Jones%2C+Gerwyn+M%2E%22&quot;&gt;Jones, Gerwyn M.&lt;/searchLink&gt;&lt;relatesTo&gt;2&lt;/relatesTo&gt; (AUTHOR)&lt;br /&gt;&lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Fernandez-Gonzalez%2C+Ana%22&quot;&gt;Fernandez-Gonzalez, Ana&lt;/searchLink&gt;&lt;relatesTo&gt;2&lt;/relatesTo&gt; (AUTHOR)&lt;br /&gt;&lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Martin%2C+Jan%22&quot;&gt;Martin, Jan&lt;/searchLink&gt;&lt;relatesTo&gt;5&lt;/relatesTo&gt; (AUTHOR)&lt;br /&gt;&lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Foy%2C+Carole+A%2E%22&quot;&gt;Foy, Carole A.&lt;/searchLink&gt;&lt;relatesTo&gt;2&lt;/relatesTo&gt; (AUTHOR)&lt;br /&gt;&lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Alexopoulos%2C+Panagiotis%22&quot;&gt;Alexopoulos, Panagiotis&lt;/searchLink&gt;&lt;relatesTo&gt;6,7&lt;/relatesTo&gt; (AUTHOR)&lt;br /&gt;&lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Huggett%2C+Jim+F%2E%22&quot;&gt;Huggett, Jim F.&lt;/searchLink&gt;&lt;relatesTo&gt;2,8&lt;/relatesTo&gt; (AUTHOR)&lt;br /&gt;&lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Perneczky%2C+Robert%22&quot;&gt;Perneczky, Robert&lt;/searchLink&gt;&lt;relatesTo&gt;1,9,10,11,12&lt;/relatesTo&gt; (AUTHOR)
– Name: TitleSource
  Label: Source
  Group: Src
  Data: &lt;searchLink fieldCode=&quot;JN&quot; term=&quot;%22New+Biotechnology%22&quot;&gt;New Biotechnology&lt;/searchLink&gt;. Dec2022, Vol. 72, p97-106. 10p.
– Name: Subject
  Label: Subjects
  Group: Su
  Data: &lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Cell-free+DNA%22&quot;&gt;Cell-free DNA&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Alzheimer&#39;s+disease%22&quot;&gt;Alzheimer&#39;s disease&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Brain+diseases%22&quot;&gt;Brain diseases&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Mitochondrial+DNA%22&quot;&gt;Mitochondrial DNA&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Brain+cancer%22&quot;&gt;Brain cancer&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Plant+mitochondria%22&quot;&gt;Plant mitochondria&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22DNA%22&quot;&gt;DNA&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Cerebrospinal+fluid%22&quot;&gt;Cerebrospinal fluid&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Brain+tumors%22&quot;&gt;Brain tumors&lt;/searchLink&gt;
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: 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&#39;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 &amp; Plasma (Zymo), NucleoSnap&#174; 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 &lt; 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. [Display omitted] • Approaches to cell-free DNA biomarkers in cerebrospinal fluid vary between studies. • Kits for cell-free DNA (cfDNA) extraction from cerebrospinal fluid were compared. • Spike-in recovery correlated with mitochondrial and nuclear genomic cfDNA yield. • Sensitive assays to repetitive elements are required for nuclear cfDNA detection. • Ratio of mitochondrial to nuclear cfDNA is a potential normalisation strategy. [ABSTRACT FROM AUTHOR]
– Name: AbstractSuppliedCopyright
  Label:
  Group: Ab
  Data: &lt;i&gt;Copyright of New Biotechnology is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites without the copyright holder&#39;s express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.&lt;/i&gt; (Copyright applies to all Abstracts.)
PLink https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=egs&AN=160631449
RecordInfo BibRecord:
  BibEntity:
    Identifiers:
      – Type: doi
        Value: 10.1016/j.nbt.2022.10.001
    Languages:
      – Code: eng
        Text: English
    PhysicalDescription:
      Pagination:
        PageCount: 10
        StartPage: 97
    Subjects:
      – SubjectFull: Cell-free DNA
        Type: general
      – SubjectFull: Alzheimer's disease
        Type: general
      – SubjectFull: Brain diseases
        Type: general
      – SubjectFull: Mitochondrial DNA
        Type: general
      – SubjectFull: Brain cancer
        Type: general
      – SubjectFull: Plant mitochondria
        Type: general
      – SubjectFull: DNA
        Type: general
      – SubjectFull: Cerebrospinal fluid
        Type: general
      – SubjectFull: Brain tumors
        Type: general
    Titles:
      – TitleFull: 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.
        Type: main
  BibRelationships:
    HasContributorRelationships:
      – PersonEntity:
          Name:
            NameFull: Takousis, Petros
      – PersonEntity:
          Name:
            NameFull: Devonshire, Alison S.
      – PersonEntity:
          Name:
            NameFull: Redshaw, Nicholas
      – PersonEntity:
          Name:
            NameFull: von Baumgarten, Louisa
      – PersonEntity:
          Name:
            NameFull: Whale, Alexandra S.
      – PersonEntity:
          Name:
            NameFull: Jones, Gerwyn M.
      – PersonEntity:
          Name:
            NameFull: Fernandez-Gonzalez, Ana
      – PersonEntity:
          Name:
            NameFull: Martin, Jan
      – PersonEntity:
          Name:
            NameFull: Foy, Carole A.
      – PersonEntity:
          Name:
            NameFull: Alexopoulos, Panagiotis
      – PersonEntity:
          Name:
            NameFull: Huggett, Jim F.
      – PersonEntity:
          Name:
            NameFull: Perneczky, Robert
    IsPartOfRelationships:
      – BibEntity:
          Dates:
            – D: 01
              M: 12
              Text: Dec2022
              Type: published
              Y: 2022
          Identifiers:
            – Type: issn-print
              Value: 18716784
          Numbering:
            – Type: volume
              Value: 72
          Titles:
            – TitleFull: New Biotechnology
              Type: main
ResultId 1