Screening ancient tuberculosis with qPCR: challenges and opportunities
Identifieur interne : 000293 ( Pmc/Corpus ); précédent : 000292; suivant : 000294Screening ancient tuberculosis with qPCR: challenges and opportunities
Auteurs : Kelly M. Harkins ; Jane E. Buikstra ; Tessa Campbell ; Kirsten I. Bos ; Eric D. Johnson ; Johannes Krause ; Anne C. StoneSource :
- Philosophical Transactions of the Royal Society B: Biological Sciences [ 0962-8436 ] ; 2015.
Abstract
The field of ancient DNA (aDNA) has rapidly accelerated in recent years as a result of new methods in next-generation sequencing, library preparation and targeted enrichment. Such research is restricted, however, by the highly variable DNA preservation within different tissues, especially when isolating ancient pathogens from human remains. Identifying positive candidate samples via quantitative PCR (qPCR) for downstream procedures can reduce reagent costs, increase capture efficiency and maximize the number of sequencing reads of the target. This study uses four qPCR assays designed to target regions within the
Url:
DOI: 10.1098/rstb.2013.0622
PubMed: 25487341
PubMed Central: 4275897
Links to Exploration step
PMC:4275897Le document en format XML
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<front><div type="abstract" xml:lang="en"><p>The field of ancient DNA (aDNA) has rapidly accelerated in recent years as a result of new methods in next-generation sequencing, library preparation and targeted enrichment. Such research is restricted, however, by the highly variable DNA preservation within different tissues, especially when isolating ancient pathogens from human remains. Identifying positive candidate samples via quantitative PCR (qPCR) for downstream procedures can reduce reagent costs, increase capture efficiency and maximize the number of sequencing reads of the target. This study uses four qPCR assays designed to target regions within the <italic>Mycobacterium tuberculosis</italic>
complex (MTBC) to examine 133 human skeletal samples from a wide geographical and temporal range, identified by the presence of skeletal lesions typical of chronic disseminated tuberculosis. Given the inherent challenges working with ancient mycobacteria, strict criteria must be used and primer/probe design continually re-evaluated as new data from bacteria become available. Seven samples tested positive for multiple MTBC loci, supporting them as strong candidates for downstream analyses. Using strict and conservative criteria, qPCR remains a fast and effective screening tool when compared with screening by more expensive sequencing and enrichment technologies.</p>
</div>
</front>
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<pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Philos Trans R Soc Lond B Biol Sci</journal-id>
<journal-id journal-id-type="iso-abbrev">Philos. Trans. R. Soc. Lond., B, Biol. Sci</journal-id>
<journal-id journal-id-type="publisher-id">RSTB</journal-id>
<journal-id journal-id-type="hwp">royptb</journal-id>
<journal-title-group><journal-title>Philosophical Transactions of the Royal Society B: Biological Sciences</journal-title>
</journal-title-group>
<issn pub-type="ppub">0962-8436</issn>
<issn pub-type="epub">1471-2970</issn>
<publisher><publisher-name>The Royal Society</publisher-name>
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<article-meta><article-id pub-id-type="pmid">25487341</article-id>
<article-id pub-id-type="pmc">4275897</article-id>
<article-id pub-id-type="doi">10.1098/rstb.2013.0622</article-id>
<article-id pub-id-type="publisher-id">rstb20130622</article-id>
<article-categories><subj-group subj-group-type="hwp-journal-coll"><subject>1001</subject>
<subject>197</subject>
</subj-group>
<subj-group subj-group-type="heading"><subject>Part II: Human Evolution and Ancient Diseases</subject>
</subj-group>
<subj-group subj-group-type="leader"><subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Screening ancient tuberculosis with qPCR: challenges and opportunities</article-title>
<alt-title alt-title-type="short">Screening Ancient Tuberculosis with qPCR</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Harkins</surname>
<given-names>Kelly M.</given-names>
</name>
<xref ref-type="aff" rid="af1">1</xref>
<xref ref-type="author-notes" rid="AN2">†</xref>
<contrib-id contrib-id-type="orcid">http://orcid.org/0000-0002-0756-4250</contrib-id>
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<contrib contrib-type="author"><name><surname>Buikstra</surname>
<given-names>Jane E.</given-names>
</name>
<xref ref-type="aff" rid="af1">1</xref>
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<contrib contrib-type="author"><name><surname>Campbell</surname>
<given-names>Tessa</given-names>
</name>
<xref ref-type="aff" rid="af3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Bos</surname>
<given-names>Kirsten I.</given-names>
</name>
<xref ref-type="aff" rid="af4">4</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Johnson</surname>
<given-names>Eric D.</given-names>
</name>
<xref ref-type="aff" rid="af2">2</xref>
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<contrib contrib-type="author"><name><surname>Krause</surname>
<given-names>Johannes</given-names>
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<xref ref-type="aff" rid="af4">4</xref>
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<contrib contrib-type="author"><name><surname>Stone</surname>
<given-names>Anne C.</given-names>
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<xref ref-type="aff" rid="af1">1</xref>
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<aff id="af1"><label>1</label>
<addr-line>School of Human Evolution and Social Change</addr-line>
,<institution>Arizona State University</institution>
,<addr-line>Tempe, AZ</addr-line>
,<country>USA</country>
</aff>
<aff id="af2"><label>2</label>
<addr-line>School of Life Sciences</addr-line>
,<institution>Arizona State University</institution>
,<addr-line>Tempe, AZ</addr-line>
,<country>USA</country>
</aff>
<aff id="af3"><label>3</label>
<addr-line>Department of Archaeology</addr-line>
,<institution>University of Cape Town</institution>
,<addr-line>Cape Town</addr-line>
,<country>South Africa</country>
</aff>
<aff id="af4"><label>4</label>
<addr-line>Institute for Archaeological Sciences</addr-line>
,<institution>University of Tübingen</institution>
,<addr-line>Tübingen</addr-line>
,<country>Germany</country>
</aff>
<author-notes><corresp id="cor1">e-mail: <email>acstone@asu.edu</email>
</corresp>
<fn fn-type="present-address" id="AN2"><label>†</label>
<p>Present address: Department of Anthropology, University of California, Santa Cruz, CA, USA.</p>
</fn>
<fn fn-type="other"><p>One contribution of 19 to a discussion meeting issue ‘<ext-link ext-link-type="uri" xlink:href="http://rstb.royalsocietypublishing.org/content/370/1660.toc">Ancient DNA: the first three decades</ext-link>
’.</p>
</fn>
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<pub-date pub-type="ppub"><day>19</day>
<month>1</month>
<year>2015</year>
</pub-date>
<volume>370</volume>
<issue>1660</issue>
<issue-title>Discussion meeting issue ‘Ancient DNA: the first three decades’ organized and edited by Erika Hagelberg, Michael Hofreiter and Christine Keyser</issue-title>
<elocation-id>20130622</elocation-id>
<permissions><copyright-statement>© 2014 The Author(s) Published by the Royal Society. All rights reserved.</copyright-statement>
<copyright-year>2014</copyright-year>
</permissions>
<self-uri content-type="pdf" xlink:type="simple" xlink:href="rstb20130622.pdf"></self-uri>
<abstract><p>The field of ancient DNA (aDNA) has rapidly accelerated in recent years as a result of new methods in next-generation sequencing, library preparation and targeted enrichment. Such research is restricted, however, by the highly variable DNA preservation within different tissues, especially when isolating ancient pathogens from human remains. Identifying positive candidate samples via quantitative PCR (qPCR) for downstream procedures can reduce reagent costs, increase capture efficiency and maximize the number of sequencing reads of the target. This study uses four qPCR assays designed to target regions within the <italic>Mycobacterium tuberculosis</italic>
complex (MTBC) to examine 133 human skeletal samples from a wide geographical and temporal range, identified by the presence of skeletal lesions typical of chronic disseminated tuberculosis. Given the inherent challenges working with ancient mycobacteria, strict criteria must be used and primer/probe design continually re-evaluated as new data from bacteria become available. Seven samples tested positive for multiple MTBC loci, supporting them as strong candidates for downstream analyses. Using strict and conservative criteria, qPCR remains a fast and effective screening tool when compared with screening by more expensive sequencing and enrichment technologies.</p>
</abstract>
<kwd-group><kwd>ancient DNA</kwd>
<kwd>tuberculosis</kwd>
<kwd>bioarchaeology</kwd>
<kwd>qPCR</kwd>
</kwd-group>
<custom-meta-group><custom-meta><meta-name>cover-date</meta-name>
<meta-value>January 19, 2015</meta-value>
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</front>
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