Combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes (COMPARE-MS) for the rapid, sensitive and quantitative detection of DNA methylation
Identifieur interne : 000A07 ( Istex/Corpus ); précédent : 000A06; suivant : 000A08Combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes (COMPARE-MS) for the rapid, sensitive and quantitative detection of DNA methylation
Auteurs : Srinivasan Yegnasubramanian ; Xiaohui Lin ; Michael C. Haffner ; Angelo M. Demarzo ; William G. NelsonSource :
- Nucleic Acids Research [ 0305-1048 ] ; 2006.
Abstract
Hypermethylation of CpG island (CGI) sequences is a nearly universal somatic genome alteration in cancer. Rapid and sensitive detection of DNA hypermethylation would aid in cancer diagnosis and risk stratification. We present a novel technique, called COMPARE-MS, that can rapidly and quantitatively detect CGI hypermethylation with high sensitivity and specificity in hundreds of samples simultaneously. To quantitate CGI hypermethylation, COMPARE-MS uses real-time PCR of DNA that was first digested by methylation-sensitive restriction enzymes and then precipitated by methyl-binding domain polypeptides immobilized on a magnetic solid matrix. We show that COMPARE-MS could detect five genome equivalents of methylated CGIs in a 1000- to 10 000-fold excess of unmethylated DNA. COMPARE-MS was used to rapidly quantitate hypermethylation at multiple CGIs in >155 prostate tissues, including benign and malignant prostate specimens, and prostate cell lines. This analysis showed that GSTP1, MDR1 and PTGS2 CGI hypermethylation as determined by COMPARE-MS could differentiate between malignant and benign prostate with sensitivities >95% and specificities approaching 100%. This novel technology could significantly improve our ability to detect CGI hypermethylation.
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DOI: 10.1093/nar/gnj022
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This analysis showed that GSTP1, MDR1 and PTGS2 CGI hypermethylation as determined by COMPARE-MS could differentiate between malignant and benign prostate with sensitivities >95% and specificities approaching 100%. This novel technology could significantly improve our ability to detect CGI hypermethylation.</div></front></TEI><istex><corpusName>oup</corpusName><author><json:item><name>Srinivasan Yegnasubramanian</name><affiliations><json:string>Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine 1650 Orleans Street, CRB 116, Baltimore, MD 21231, USA</json:string></affiliations></json:item><json:item><name>Xiaohui Lin</name><affiliations><json:string>Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine 1650 Orleans Street, CRB 116, Baltimore, MD 21231, USA</json:string></affiliations></json:item><json:item><name>Michael C. 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Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org</p></availability><date>2006</date></publicationStmt><notesStmt><note>*To whom correspondence should be addressed. Tel: +1 410 614 1661; Fax: +1 410 502 9817; Email: bnelson@jhmi.edu</note></notesStmt><sourceDesc><biblStruct type="inbook"><analytic><title level="a" type="main" xml:lang="en">Combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes (COMPARE-MS) for the rapid, sensitive and quantitative detection of DNA methylation</title><author xml:id="author-1"><persName><forename type="first">Srinivasan</forename><surname>Yegnasubramanian</surname></persName><affiliation>Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine 1650 Orleans Street, CRB 116, Baltimore, MD 21231, USA</affiliation></author><author xml:id="author-2"><persName><forename type="first">Xiaohui</forename><surname>Lin</surname></persName><affiliation>Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine 1650 Orleans Street, CRB 116, Baltimore, MD 21231, USA</affiliation></author><author xml:id="author-3"><persName><forename type="first">Michael C.</forename><surname>Haffner</surname></persName><affiliation>Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine 1650 Orleans Street, CRB 116, Baltimore, MD 21231, USA</affiliation><affiliation>Innsbruck Medical University, Christoph-Probst-Platz 1 Innrain 52, A-6020 Innsbruck, Austria</affiliation></author><author xml:id="author-4"><persName><forename type="first">Angelo M.</forename><surname>DeMarzo</surname></persName><affiliation>Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine 1650 Orleans Street, CRB 116, Baltimore, MD 21231, USA</affiliation></author><author xml:id="author-5"><persName><forename type="first">William G.</forename><surname>Nelson</surname></persName><affiliation>Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine 1650 Orleans Street, CRB 116, Baltimore, MD 21231, USA</affiliation><affiliation>To whom correspondence should be addressed. Tel: +1 410 614 1661; Fax: +1 410 502 9817; Email: bnelson@jhmi.edu</affiliation></author></analytic><monogr><title level="j">Nucleic Acids Research</title><title level="j" type="abbrev">Nucl. Acids Res.</title><idno type="pISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><publisher>Oxford University Press</publisher><date type="published" when="2006"></date><biblScope unit="volume">34</biblScope><biblScope unit="issue">3</biblScope><biblScope unit="page" from="19">e19</biblScope><biblScope unit="page" to="19">e19</biblScope></imprint></monogr><idno type="istex">4A23170DC133F7E07C7AB7B397DA383106790CFA</idno><idno type="DOI">10.1093/nar/gnj022</idno><idno type="local">gnj022</idno></biblStruct></sourceDesc></fileDesc><profileDesc><creation><date>2006</date></creation><langUsage><language ident="en">en</language></langUsage><abstract xml:lang="en"><p>Hypermethylation of CpG island (CGI) sequences is a nearly universal somatic genome alteration in cancer. Rapid and sensitive detection of DNA hypermethylation would aid in cancer diagnosis and risk stratification. We present a novel technique, called COMPARE-MS, that can rapidly and quantitatively detect CGI hypermethylation with high sensitivity and specificity in hundreds of samples simultaneously. To quantitate CGI hypermethylation, COMPARE-MS uses real-time PCR of DNA that was first digested by methylation-sensitive restriction enzymes and then precipitated by methyl-binding domain polypeptides immobilized on a magnetic solid matrix. We show that COMPARE-MS could detect five genome equivalents of methylated CGIs in a 1000- to 10 000-fold excess of unmethylated DNA. COMPARE-MS was used to rapidly quantitate hypermethylation at multiple CGIs in >155 prostate tissues, including benign and malignant prostate specimens, and prostate cell lines. This analysis showed that GSTP1, MDR1 and PTGS2 CGI hypermethylation as determined by COMPARE-MS could differentiate between malignant and benign prostate with sensitivities >95% and specificities approaching 100%. This novel technology could significantly improve our ability to detect CGI hypermethylation.</p></abstract><textClass><keywords scheme="keyword"><list><head>hwp-journal-coll</head><item><term>4</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="2006">Published</change><change xml:id="refBibs-istex" who="#ISTEX-API" when="2016-10-14">References added</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><original>false</original><mimetype>text/plain</mimetype><extension>txt</extension><uri>https://api.istex.fr/document/4A23170DC133F7E07C7AB7B397DA383106790CFA/fulltext/txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="corpus oup" wicri:toSee="no header"><istex:xmlDeclaration>version="1.0" encoding="US-ASCII"</istex:xmlDeclaration><istex:docType PUBLIC="-//NLM//DTD Journal Publishing DTD v2.3 20070202//EN" URI="journalpublishing.dtd" name="istex:docType"></istex:docType><istex:document><article xml:lang="en" article-type="other"><front><journal-meta><journal-id journal-id-type="hwp">nar</journal-id><journal-id journal-id-type="nlm-ta">Nucleic Acids Res</journal-id><journal-id journal-id-type="publisher-id">nar</journal-id><journal-title>Nucleic Acids Research</journal-title><abbrev-journal-title abbrev-type="publisher">Nucl. Acids Res.</abbrev-journal-title><issn pub-type="ppub">0305-1048</issn><issn pub-type="epub">1362-4962</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="other">gnj022</article-id><article-id pub-id-type="doi">10.1093/nar/gnj022</article-id><article-categories><subj-group subj-group-type="heading"><subject>Methods Online</subject></subj-group><subj-group subj-group-type="hwp-journal-coll"><subject>4</subject></subj-group></article-categories><title-group><article-title>Combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes (COMPARE-MS) for the rapid, sensitive and quantitative detection of DNA methylation</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Yegnasubramanian</surname><given-names>Srinivasan</given-names></name><xref rid="AU1">1</xref></contrib><contrib contrib-type="author"><name><surname>Lin</surname><given-names>Xiaohui</given-names></name><xref rid="AU1">1</xref></contrib><contrib contrib-type="author"><name><surname>Haffner</surname><given-names>Michael C.</given-names></name><xref rid="AU1">1</xref><xref rid="AU2">2</xref></contrib><contrib contrib-type="author"><name><surname>DeMarzo</surname><given-names>Angelo M.</given-names></name><xref rid="AU1">1</xref></contrib><contrib contrib-type="author"><name><surname>Nelson</surname><given-names>William G.</given-names></name><xref rid="AU1">1</xref><xref rid="COR1">*</xref></contrib><aff id="AU1"><sup>1</sup>Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine 1650 Orleans Street, CRB 116, Baltimore, MD 21231, USA</aff><aff id="AU2"><sup>2</sup>Innsbruck Medical University, Christoph-Probst-Platz 1 Innrain 52, A-6020 Innsbruck, Austria</aff></contrib-group><author-notes><corresp id="COR1"><sup>*</sup>To whom correspondence should be addressed. Tel: +1 410 614 1661; Fax: +1 410 502 9817; Email: <ext-link xlink:href="bnelson@jhmi.edu" ext-link-type="email">bnelson@jhmi.edu</ext-link></corresp></author-notes><pub-date pub-type="ppub"><year>2006</year></pub-date><volume>34</volume><issue>3</issue><fpage>e19</fpage><lpage>e19</lpage><history><date date-type="accepted"><day>23</day><month>1</month><year>2006</year></date><date date-type="received"><day>7</day><month>11</month><year>2005</year></date><date date-type="rev-recd"><day>8</day><month>1</month><year>2006</year></date></history><permissions><copyright-statement>© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact <ext-link xlink:href="journals.permissions@oxfordjournals.org" ext-link-type="email">journals.permissions@oxfordjournals.org</ext-link></copyright-statement><copyright-year>2006</copyright-year><license license-type="open-access"><p></p></license></permissions><abstract xml:lang="en"><p>Hypermethylation of CpG island (CGI) sequences is a nearly universal somatic genome alteration in cancer. Rapid and sensitive detection of DNA hypermethylation would aid in cancer diagnosis and risk stratification. We present a novel technique, called COMPARE-MS, that can rapidly and quantitatively detect CGI hypermethylation with high sensitivity and specificity in hundreds of samples simultaneously. To quantitate CGI hypermethylation, COMPARE-MS uses real-time PCR of DNA that was first digested by methylation-sensitive restriction enzymes and then precipitated by methyl-binding domain polypeptides immobilized on a magnetic solid matrix. We show that COMPARE-MS could detect five genome equivalents of methylated CGIs in a 1000- to 10 000-fold excess of unmethylated DNA. COMPARE-MS was used to rapidly quantitate hypermethylation at multiple CGIs in >155 prostate tissues, including benign and malignant prostate specimens, and prostate cell lines. This analysis showed that <italic>GSTP1</italic>, <italic>MDR1</italic> and <italic>PTGS2</italic> CGI hypermethylation as determined by COMPARE-MS could differentiate between malignant and benign prostate with sensitivities >95% and specificities approaching 100%. This novel technology could significantly improve our ability to detect CGI hypermethylation.</p></abstract><custom-meta-wrap><custom-meta><meta-name>hwp-legacy-fpage</meta-name><meta-value>e19</meta-value></custom-meta><custom-meta><meta-name>cover-date</meta-name><meta-value></meta-value></custom-meta><custom-meta><meta-name>hwp-legacy-dochead</meta-name><meta-value>research-article</meta-value></custom-meta></custom-meta-wrap></article-meta></front></article></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes (COMPARE-MS) for the rapid, sensitive and quantitative detection of DNA methylation</title></titleInfo><titleInfo type="alternative" lang="en" contentType="CDATA"><title>Combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes (COMPARE-MS) for the rapid, sensitive and quantitative detection of DNA methylation</title></titleInfo><name type="personal"><namePart type="given">Srinivasan</namePart><namePart type="family">Yegnasubramanian</namePart><affiliation>Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine 1650 Orleans Street, CRB 116, Baltimore, MD 21231, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Xiaohui</namePart><namePart type="family">Lin</namePart><affiliation>Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine 1650 Orleans Street, CRB 116, Baltimore, MD 21231, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Michael C.</namePart><namePart type="family">Haffner</namePart><affiliation>Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine 1650 Orleans Street, CRB 116, Baltimore, MD 21231, USA</affiliation><affiliation>Innsbruck Medical University, Christoph-Probst-Platz 1 Innrain 52, A-6020 Innsbruck, Austria</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Angelo M.</namePart><namePart type="family">DeMarzo</namePart><affiliation>Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine 1650 Orleans Street, CRB 116, Baltimore, MD 21231, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">William G.</namePart><namePart type="family">Nelson</namePart><affiliation>Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine 1650 Orleans Street, CRB 116, Baltimore, MD 21231, USA</affiliation><affiliation>To whom correspondence should be addressed. Tel: +1 410 614 1661; Fax: +1 410 502 9817; Email: bnelson@jhmi.edu</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="other" displayLabel="other"></genre><subject><genre>hwp-journal-coll</genre><topic>4</topic></subject><originInfo><publisher>Oxford University Press</publisher><dateIssued encoding="w3cdtf">2006</dateIssued><copyrightDate encoding="w3cdtf">2006</copyrightDate></originInfo><language><languageTerm type="code" authority="iso639-2b">eng</languageTerm><languageTerm type="code" authority="rfc3066">en</languageTerm></language><physicalDescription><internetMediaType>text/html</internetMediaType></physicalDescription><abstract lang="en">Hypermethylation of CpG island (CGI) sequences is a nearly universal somatic genome alteration in cancer. Rapid and sensitive detection of DNA hypermethylation would aid in cancer diagnosis and risk stratification. We present a novel technique, called COMPARE-MS, that can rapidly and quantitatively detect CGI hypermethylation with high sensitivity and specificity in hundreds of samples simultaneously. To quantitate CGI hypermethylation, COMPARE-MS uses real-time PCR of DNA that was first digested by methylation-sensitive restriction enzymes and then precipitated by methyl-binding domain polypeptides immobilized on a magnetic solid matrix. We show that COMPARE-MS could detect five genome equivalents of methylated CGIs in a 1000- to 10 000-fold excess of unmethylated DNA. COMPARE-MS was used to rapidly quantitate hypermethylation at multiple CGIs in >155 prostate tissues, including benign and malignant prostate specimens, and prostate cell lines. This analysis showed that GSTP1, MDR1 and PTGS2 CGI hypermethylation as determined by COMPARE-MS could differentiate between malignant and benign prostate with sensitivities >95% and specificities approaching 100%. This novel technology could significantly improve our ability to detect CGI hypermethylation.</abstract><note type="author-notes">*To whom correspondence should be addressed. Tel: +1 410 614 1661; Fax: +1 410 502 9817; Email: bnelson@jhmi.edu</note><relatedItem type="host"><titleInfo><title>Nucleic Acids Research</title></titleInfo><titleInfo type="abbreviated"><title>Nucl. Acids Res.</title></titleInfo><genre type="journal">journal</genre><identifier type="ISSN">0305-1048</identifier><identifier type="eISSN">1362-4962</identifier><identifier type="PublisherID">nar</identifier><identifier type="PublisherID-hwp">nar</identifier><identifier type="PublisherID-nlm-ta">Nucleic Acids Res</identifier><part><date>2006</date><detail type="volume"><caption>vol.</caption><number>34</number></detail><detail type="issue"><caption>no.</caption><number>3</number></detail><extent unit="pages"><start>e19</start><end>e19</end></extent></part></relatedItem><identifier type="istex">4A23170DC133F7E07C7AB7B397DA383106790CFA</identifier><identifier type="DOI">10.1093/nar/gnj022</identifier><identifier type="local">gnj022</identifier><accessCondition type="use and reproduction" contentType="copyright">© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org</accessCondition><recordInfo><recordContentSource>OUP</recordContentSource></recordInfo></mods></metadata><annexes><json:item><original>true</original><mimetype>image/jpeg</mimetype><extension>jpeg</extension><uri>https://api.istex.fr/document/4A23170DC133F7E07C7AB7B397DA383106790CFA/annexes/jpeg</uri></json:item><json:item><original>true</original><mimetype>image/gif</mimetype><extension>gif</extension><uri>https://api.istex.fr/document/4A23170DC133F7E07C7AB7B397DA383106790CFA/annexes/gif</uri></json:item></annexes><enrichments><istex:catWosTEI uri="https://api.istex.fr/document/4A23170DC133F7E07C7AB7B397DA383106790CFA/enrichments/catWos"><teiHeader><profileDesc><textClass><classCode scheme="WOS">BIOCHEMISTRY & MOLECULAR BIOLOGY</classCode></textClass></profileDesc></teiHeader></istex:catWosTEI><json:item><type>refBibs</type><uri>https://api.istex.fr/document/4A23170DC133F7E07C7AB7B397DA383106790CFA/enrichments/refBibs</uri></json:item></enrichments><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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