Quality of DNA Extracted from Mouthwashes
Identifieur interne : 002A30 ( Pmc/Curation ); précédent : 002A29; suivant : 002A31Quality of DNA Extracted from Mouthwashes
Auteurs : Tetyana Zayats [Royaume-Uni] ; Terri L. Young [États-Unis] ; David A. Mackey [Australie] ; François Malecaze [France] ; Patrick Calvas [France] ; Jeremy A. Guggenheim [Royaume-Uni]Source :
- PLoS ONE [ 1932-6203 ] ; 2009.
Abstract
A cost effective, safe and efficient method of obtaining DNA samples is essential in large scale genetic analyses. Buccal cells are an attractive source of DNA, as their collection is non-invasive and can be carried out by mail. However, little attention has been given to the quality of DNA extracted from mouthwashes.
Mouthwash-derived DNA was extracted from 500 subjects participating in a genetic study of high myopia. DNA quality was investigated using two standard techniques: agarose gel electrophoresis and quantitative polymerase chain reaction (qPCR).
Whereas the majority of mouthwash-derived DNA samples showed a single band of high molecular weight DNA by gel electrophoresis, 8.9% (95% CI: 7.1–10.7%) of samples contained only a smear of low-to-medium molecular weight, degraded DNA. The odds of DNA degradation in a subject's second mouthwash sample, given degradation of the first, was significantly greater than one (OR = 3.13; 95% CI: 1.22–7.39; Fisher's test P = 0.009), suggesting that DNA degradation was at least partially a subject-specific phenomenon. Approximately 12.4% (95% CI: 10.4–14.4%) of mouthwash-derived DNA failed to PCR amplify efficiently (using an ∼200 bp microsatellite marker). However, we found there was no significant difference in amplification success rate between DNA samples judged to be degraded or non-degraded by gel electrophoresis (Fisher's test P = 0.5).
This study demonstrated that DNA degradation affects a significant minority of saline mouthwashes, and that the phenomenon is partially subject-specific. Whilst the level of degradation did not significantly prevent successful amplification of short PCR fragments, previous studies suggest that such DNA degradation would compromise more demanding applications.
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DOI: 10.1371/journal.pone.0006165
PubMed: 19582144
PubMed Central: 2701599
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Young</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Duke University, Center for Human Genetics, Durham, North Carolina, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Duke University, Center for Human Genetics, Durham, North Carolina</wicri:regionArea></affiliation></author><author><name sortKey="Mackey, David A" sort="Mackey, David A" uniqKey="Mackey D" first="David A." last="Mackey">David A. Mackey</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Department of Ophthalmology, University of Tasmania, Royal Hobart Hospital, Hobart, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Department of Ophthalmology, University of Tasmania, Royal Hobart Hospital, Hobart</wicri:regionArea></affiliation></author><author><name sortKey="Malecaze, Francois" sort="Malecaze, Francois" uniqKey="Malecaze F" first="François" last="Malecaze">François Malecaze</name><affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>Inserm U563 Hopital Purpan CHU Toulouse, Toulouse, France</addr-line></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Inserm U563 Hopital Purpan CHU Toulouse, Toulouse</wicri:regionArea></affiliation></author><author><name sortKey="Calvas, Patrick" sort="Calvas, Patrick" uniqKey="Calvas P" first="Patrick" last="Calvas">Patrick Calvas</name><affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>Inserm U563 Hopital Purpan CHU Toulouse, Toulouse, France</addr-line></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Inserm U563 Hopital Purpan CHU Toulouse, Toulouse</wicri:regionArea></affiliation></author><author><name sortKey="Guggenheim, Jeremy A" sort="Guggenheim, Jeremy A" uniqKey="Guggenheim J" first="Jeremy A." last="Guggenheim">Jeremy A. Guggenheim</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>School of Optometry and Vision Sciences, Cardiff University, Wales, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>School of Optometry and Vision Sciences, Cardiff University, Wales</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">19582144</idno><idno type="pmc">2701599</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2701599</idno><idno type="RBID">PMC:2701599</idno><idno type="doi">10.1371/journal.pone.0006165</idno><date when="2009">2009</date><idno type="wicri:Area/Pmc/Corpus">002B80</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">002B80</idno><idno type="wicri:Area/Pmc/Curation">002A30</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">002A30</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Quality of DNA Extracted from Mouthwashes</title><author><name sortKey="Zayats, Tetyana" sort="Zayats, Tetyana" uniqKey="Zayats T" first="Tetyana" last="Zayats">Tetyana Zayats</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>School of Optometry and Vision Sciences, Cardiff University, Wales, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>School of Optometry and Vision Sciences, Cardiff University, Wales</wicri:regionArea></affiliation></author><author><name sortKey="Young, Terri L" sort="Young, Terri L" uniqKey="Young T" first="Terri L." last="Young">Terri L. Young</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Duke University, Center for Human Genetics, Durham, North Carolina, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Duke University, Center for Human Genetics, Durham, North Carolina</wicri:regionArea></affiliation></author><author><name sortKey="Mackey, David A" sort="Mackey, David A" uniqKey="Mackey D" first="David A." last="Mackey">David A. Mackey</name><affiliation wicri:level="1"><nlm:aff id="aff3"><addr-line>Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Department of Ophthalmology, University of Tasmania, Royal Hobart Hospital, Hobart, Australia</addr-line></nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Department of Ophthalmology, University of Tasmania, Royal Hobart Hospital, Hobart</wicri:regionArea></affiliation></author><author><name sortKey="Malecaze, Francois" sort="Malecaze, Francois" uniqKey="Malecaze F" first="François" last="Malecaze">François Malecaze</name><affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>Inserm U563 Hopital Purpan CHU Toulouse, Toulouse, France</addr-line></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Inserm U563 Hopital Purpan CHU Toulouse, Toulouse</wicri:regionArea></affiliation></author><author><name sortKey="Calvas, Patrick" sort="Calvas, Patrick" uniqKey="Calvas P" first="Patrick" last="Calvas">Patrick Calvas</name><affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>Inserm U563 Hopital Purpan CHU Toulouse, Toulouse, France</addr-line></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Inserm U563 Hopital Purpan CHU Toulouse, Toulouse</wicri:regionArea></affiliation></author><author><name sortKey="Guggenheim, Jeremy A" sort="Guggenheim, Jeremy A" uniqKey="Guggenheim J" first="Jeremy A." last="Guggenheim">Jeremy A. Guggenheim</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>School of Optometry and Vision Sciences, Cardiff University, Wales, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>School of Optometry and Vision Sciences, Cardiff University, Wales</wicri:regionArea></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2009">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>A cost effective, safe and efficient method of obtaining DNA samples is essential in large scale genetic analyses. Buccal cells are an attractive source of DNA, as their collection is non-invasive and can be carried out by mail. However, little attention has been given to the quality of DNA extracted from mouthwashes.</p></sec><sec><title>Methodology</title><p>Mouthwash-derived DNA was extracted from 500 subjects participating in a genetic study of high myopia. DNA quality was investigated using two standard techniques: agarose gel electrophoresis and quantitative polymerase chain reaction (qPCR).</p></sec><sec><title>Principal Findings</title><p>Whereas the majority of mouthwash-derived DNA samples showed a single band of high molecular weight DNA by gel electrophoresis, 8.9% (95% CI: 7.1–10.7%) of samples contained only a smear of low-to-medium molecular weight, degraded DNA. The odds of DNA degradation in a subject's second mouthwash sample, given degradation of the first, was significantly greater than one (OR = 3.13; 95% CI: 1.22–7.39; Fisher's test P = 0.009), suggesting that DNA degradation was at least partially a subject-specific phenomenon. Approximately 12.4% (95% CI: 10.4–14.4%) of mouthwash-derived DNA failed to PCR amplify efficiently (using an ∼200 bp microsatellite marker). However, we found there was no significant difference in amplification success rate between DNA samples judged to be degraded or non-degraded by gel electrophoresis (Fisher's test P = 0.5).</p></sec><sec><title>Conclusions</title><p>This study demonstrated that DNA degradation affects a significant minority of saline mouthwashes, and that the phenomenon is partially subject-specific. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">19582144</article-id><article-id pub-id-type="pmc">2701599</article-id><article-id pub-id-type="publisher-id">09-PONE-RA-09500R1</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0006165</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline"><subject>Genetics and Genomics/Complex Traits</subject><subject>Genetics and Genomics/Gene Discovery</subject><subject>Genetics and Genomics/Genetics of Disease</subject></subj-group></article-categories><title-group><article-title>Quality of DNA Extracted from Mouthwashes</article-title><alt-title alt-title-type="running-head">DNA Quality</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Zayats</surname><given-names>Tetyana</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Young</surname><given-names>Terri L.</given-names></name><xref ref-type="aff" rid="aff2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Mackey</surname><given-names>David A.</given-names></name><xref ref-type="aff" rid="aff3"><sup>3</sup></xref><xref ref-type="aff" rid="aff4"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Malecaze</surname><given-names>François</given-names></name><xref ref-type="aff" rid="aff5"><sup>5</sup></xref></contrib><contrib contrib-type="author"><name><surname>Calvas</surname><given-names>Patrick</given-names></name><xref ref-type="aff" rid="aff5"><sup>5</sup></xref></contrib><contrib contrib-type="author"><name><surname>Guggenheim</surname><given-names>Jeremy A.</given-names></name><xref ref-type="aff" rid="aff1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib></contrib-group><contrib-group><contrib contrib-type="editor"><name><surname>Reitsma</surname><given-names>Pieter H.</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="aff1"><label>1</label><addr-line>School of Optometry and Vision Sciences, Cardiff University, Wales, United Kingdom</addr-line></aff><aff id="aff2"><label>2</label><addr-line>Duke University, Center for Human Genetics, Durham, North Carolina, United States of America</addr-line></aff><aff id="aff3"><label>3</label><addr-line>Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia</addr-line></aff><aff id="aff4"><label>4</label><addr-line>Department of Ophthalmology, University of Tasmania, Royal Hobart Hospital, Hobart, Australia</addr-line></aff><aff id="aff5"><label>5</label><addr-line>Inserm U563 Hopital Purpan CHU Toulouse, Toulouse, France</addr-line></aff><aff id="edit1">Leiden University Medical Center, Netherlands</aff><author-notes><corresp id="cor1">* E-mail: <email>guggenheim@cf.ac.uk</email></corresp><fn fn-type="con"><p>Conceived and designed the experiments: TZ JAG. Performed the experiments: TZ JAG. Analyzed the data: TZ JAG. Contributed reagents/materials/analysis tools: TZ TLY DM FM PC JAG. Wrote the paper: TZ TLY DM JAG.</p></fn></author-notes><pub-date pub-type="collection"><year>2009</year></pub-date><pub-date pub-type="epub"><day>7</day><month>7</month><year>2009</year></pub-date><volume>4</volume><issue>7</issue><elocation-id>e6165</elocation-id><history><date date-type="received"><day>31</day><month>3</month><year>2009</year></date><date date-type="accepted"><day>3</day><month>6</month><year>2009</year></date></history><permissions><copyright-statement>Zayats et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</copyright-statement></permissions><abstract><sec><title>Background</title><p>A cost effective, safe and efficient method of obtaining DNA samples is essential in large scale genetic analyses. Buccal cells are an attractive source of DNA, as their collection is non-invasive and can be carried out by mail. However, little attention has been given to the quality of DNA extracted from mouthwashes.</p></sec><sec><title>Methodology</title><p>Mouthwash-derived DNA was extracted from 500 subjects participating in a genetic study of high myopia. DNA quality was investigated using two standard techniques: agarose gel electrophoresis and quantitative polymerase chain reaction (qPCR).</p></sec><sec><title>Principal Findings</title><p>Whereas the majority of mouthwash-derived DNA samples showed a single band of high molecular weight DNA by gel electrophoresis, 8.9% (95% CI: 7.1–10.7%) of samples contained only a smear of low-to-medium molecular weight, degraded DNA. The odds of DNA degradation in a subject's second mouthwash sample, given degradation of the first, was significantly greater than one (OR = 3.13; 95% CI: 1.22–7.39; Fisher's test P = 0.009), suggesting that DNA degradation was at least partially a subject-specific phenomenon. Approximately 12.4% (95% CI: 10.4–14.4%) of mouthwash-derived DNA failed to PCR amplify efficiently (using an ∼200 bp microsatellite marker). However, we found there was no significant difference in amplification success rate between DNA samples judged to be degraded or non-degraded by gel electrophoresis (Fisher's test P = 0.5).</p></sec><sec><title>Conclusions</title><p>This study demonstrated that DNA degradation affects a significant minority of saline mouthwashes, and that the phenomenon is partially subject-specific. Whilst the level of degradation did not significantly prevent successful amplification of short PCR fragments, previous studies suggest that such DNA degradation would compromise more demanding applications.</p></sec></abstract><counts><page-count count="5"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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