SNP genotyping using alkali cleavage of RNA/DNA chimeras and MALDI time-of-flight mass spectrometry
Identifieur interne : 000818 ( Istex/Corpus ); précédent : 000817; suivant : 000819SNP genotyping using alkali cleavage of RNA/DNA chimeras and MALDI time-of-flight mass spectrometry
Auteurs : Florence Mauger ; Olivier Jaunay ; Vale Rie Chamblain ; Fred Reichert ; Keith Bauer ; Ivo G. Gut ; David H. GelfandSource :
- Nucleic Acids Research [ 0305-1048 ] ; 2006.
Abstract
Single nucleotide polymorphisms (SNPs) are now widely used for many DNA analysis applications such as linkage disequilibrium mapping, pharmacogenomics and traceability. Many methods for SNP genotyping exist with diverse strategies for allele-distinction. Mass spectrometers are used most commonly in conjunction with primer extension procedures with allele-specific termination. Here we present a novel concept for allele-preparation for SNP genotyping. Primer extension is carried out with an extension primer positioned immediately upstream of the SNP that is to be genotyped, a complete set of four ribonucleotides and a ribonucleotide incorporating DNA polymerase. The allele-extension products are then treated with alkali, which results in the cleavage immediately after the first added ribonucleotide. In addition, to obtain fragments easily detectable by mass spectrometry, we have included a ribonucleotide in the primer usually at the fourth nucleotide from the 3′ terminus. The method was tested on four SNPs each with a different combination of nucleotides. The advantage over other mass spectrometry-based SNP genotyping assays is that this one only requires a PCR, a primer extension reaction with a universal extension mix and an inexpensive facile cleavage reaction, which makes it overall very cost effective and easy in handling.
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DOI: 10.1093/nar/gnj021
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ISTEX:2DCA1D233DD4A51CEA609A83AB718A84D938516ALe document en format XML
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Many methods for SNP genotyping exist with diverse strategies for allele-distinction. Mass spectrometers are used most commonly in conjunction with primer extension procedures with allele-specific termination. Here we present a novel concept for allele-preparation for SNP genotyping. Primer extension is carried out with an extension primer positioned immediately upstream of the SNP that is to be genotyped, a complete set of four ribonucleotides and a ribonucleotide incorporating DNA polymerase. The allele-extension products are then treated with alkali, which results in the cleavage immediately after the first added ribonucleotide. In addition, to obtain fragments easily detectable by mass spectrometry, we have included a ribonucleotide in the primer usually at the fourth nucleotide from the 3′ terminus. The method was tested on four SNPs each with a different combination of nucleotides. 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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: +33 160 87 84 00; Fax: +33 160 87 83 83; Email: ivo.gut@cng.fr</note></notesStmt><sourceDesc><biblStruct type="inbook"><analytic><title level="a" type="main" xml:lang="en">SNP genotyping using alkali cleavage of RNA/DNA chimeras and MALDI time-of-flight mass spectrometry</title><author xml:id="author-1"><persName><forename type="first">Florence</forename><surname>Mauger</surname></persName></author><author xml:id="author-2"><persName><forename type="first">Olivier</forename><surname>Jaunay</surname></persName></author><author xml:id="author-3"><persName><forename type="first">Valérie</forename><surname>Chamblain</surname></persName></author><author xml:id="author-4"><persName><forename type="first">Fred</forename><surname>Reichert</surname></persName><affiliation>Roche Molecular Systems Inc. 1145 Atlantic Avenue, Alameda, CA 94501, USA</affiliation></author><author xml:id="author-5"><persName><forename type="first">Keith</forename><surname>Bauer</surname></persName><affiliation>Roche Molecular Systems Inc. 1145 Atlantic Avenue, Alameda, CA 94501, USA</affiliation></author><author xml:id="author-6"><persName><forename type="first">Ivo G.</forename><surname>Gut</surname></persName></author><author xml:id="author-7"><persName><forename type="first">David H.</forename><surname>Gelfand</surname></persName><affiliation>Roche Molecular Systems Inc. 1145 Atlantic Avenue, Alameda, CA 94501, USA</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="18">e18</biblScope><biblScope unit="page" to="18">e18</biblScope></imprint></monogr><idno type="istex">2DCA1D233DD4A51CEA609A83AB718A84D938516A</idno><idno type="DOI">10.1093/nar/gnj021</idno><idno type="local">gnj021</idno></biblStruct></sourceDesc></fileDesc><profileDesc><creation><date>2006</date></creation><langUsage><language ident="en">en</language></langUsage><abstract xml:lang="en"><p>Single nucleotide polymorphisms (SNPs) are now widely used for many DNA analysis applications such as linkage disequilibrium mapping, pharmacogenomics and traceability. Many methods for SNP genotyping exist with diverse strategies for allele-distinction. Mass spectrometers are used most commonly in conjunction with primer extension procedures with allele-specific termination. Here we present a novel concept for allele-preparation for SNP genotyping. Primer extension is carried out with an extension primer positioned immediately upstream of the SNP that is to be genotyped, a complete set of four ribonucleotides and a ribonucleotide incorporating DNA polymerase. The allele-extension products are then treated with alkali, which results in the cleavage immediately after the first added ribonucleotide. In addition, to obtain fragments easily detectable by mass spectrometry, we have included a ribonucleotide in the primer usually at the fourth nucleotide from the 3′ terminus. The method was tested on four SNPs each with a different combination of nucleotides. The advantage over other mass spectrometry-based SNP genotyping assays is that this one only requires a PCR, a primer extension reaction with a universal extension mix and an inexpensive facile cleavage reaction, which makes it overall very cost effective and easy in handling.</p></abstract><textClass><keywords scheme="keyword"><list><head>hwp-journal-coll</head><item><term>15</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/2DCA1D233DD4A51CEA609A83AB718A84D938516A/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">gnj021</article-id><article-id pub-id-type="doi">10.1093/nar/gnj021</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>15</subject></subj-group></article-categories><title-group><article-title>SNP genotyping using alkali cleavage of RNA/DNA chimeras and MALDI time-of-flight mass spectrometry</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Mauger</surname><given-names>Florence</given-names></name></contrib><contrib contrib-type="author"><name><surname>Jaunay</surname><given-names>Olivier</given-names></name></contrib><contrib contrib-type="author"><name><surname>Chamblain</surname><given-names>Valérie</given-names></name></contrib><contrib contrib-type="author"><name><surname>Reichert</surname><given-names>Fred</given-names></name><xref rid="AU1">1</xref></contrib><contrib contrib-type="author"><name><surname>Bauer</surname><given-names>Keith</given-names></name><xref rid="AU1">1</xref></contrib><contrib contrib-type="author"><name><surname>Gut</surname><given-names>Ivo G.</given-names></name><xref rid="COR1">*</xref></contrib><contrib contrib-type="author"><name><surname>Gelfand</surname><given-names>David H.</given-names></name><xref rid="AU1">1</xref></contrib><aff>Centre National de Génotypage, Bâtiment G2 2 Rue Gaston Crémieux, 91057 Evry Cedex, France</aff><aff id="AU1"><sup>1</sup>Roche Molecular Systems Inc. 1145 Atlantic Avenue, Alameda, CA 94501, USA</aff></contrib-group><author-notes><corresp id="COR1"><sup>*</sup>To whom correspondence should be addressed. Tel: +33 160 87 84 00; Fax: +33 160 87 83 83; Email: <ext-link xlink:href="ivo.gut@cng.fr" ext-link-type="email">ivo.gut@cng.fr</ext-link></corresp></author-notes><pub-date pub-type="ppub"><year>2006</year></pub-date><volume>34</volume><issue>3</issue><fpage>e18</fpage><lpage>e18</lpage><history><date date-type="accepted"><day>19</day><month>1</month><year>2006</year></date><date date-type="received"><day>21</day><month>11</month><year>2005</year></date><date date-type="rev-recd"><day>19</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>Single nucleotide polymorphisms (SNPs) are now widely used for many DNA analysis applications such as linkage disequilibrium mapping, pharmacogenomics and traceability. Many methods for SNP genotyping exist with diverse strategies for allele-distinction. Mass spectrometers are used most commonly in conjunction with primer extension procedures with allele-specific termination. Here we present a novel concept for allele-preparation for SNP genotyping. Primer extension is carried out with an extension primer positioned immediately upstream of the SNP that is to be genotyped, a complete set of four ribonucleotides and a ribonucleotide incorporating DNA polymerase. The allele-extension products are then treated with alkali, which results in the cleavage immediately after the first added ribonucleotide. In addition, to obtain fragments easily detectable by mass spectrometry, we have included a ribonucleotide in the primer usually at the fourth nucleotide from the 3′ terminus. The method was tested on four SNPs each with a different combination of nucleotides. The advantage over other mass spectrometry-based SNP genotyping assays is that this one only requires a PCR, a primer extension reaction with a universal extension mix and an inexpensive facile cleavage reaction, which makes it overall very cost effective and easy in handling.</p></abstract><custom-meta-wrap><custom-meta><meta-name>hwp-legacy-fpage</meta-name><meta-value>e18</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>SNP genotyping using alkali cleavage of RNA/DNA chimeras and MALDI time-of-flight mass spectrometry</title></titleInfo><titleInfo type="alternative" lang="en" contentType="CDATA"><title>SNP genotyping using alkali cleavage of RNA/DNA chimeras and MALDI time-of-flight mass spectrometry</title></titleInfo><name type="personal"><namePart type="given">Florence</namePart><namePart type="family">Mauger</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Olivier</namePart><namePart type="family">Jaunay</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Valérie</namePart><namePart type="family">Chamblain</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Fred</namePart><namePart type="family">Reichert</namePart><affiliation>Roche Molecular Systems Inc. 1145 Atlantic Avenue, Alameda, CA 94501, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Keith</namePart><namePart type="family">Bauer</namePart><affiliation>Roche Molecular Systems Inc. 1145 Atlantic Avenue, Alameda, CA 94501, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Ivo G.</namePart><namePart type="family">Gut</namePart><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">David H.</namePart><namePart type="family">Gelfand</namePart><affiliation>Roche Molecular Systems Inc. 1145 Atlantic Avenue, Alameda, CA 94501, USA</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>15</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">Single nucleotide polymorphisms (SNPs) are now widely used for many DNA analysis applications such as linkage disequilibrium mapping, pharmacogenomics and traceability. Many methods for SNP genotyping exist with diverse strategies for allele-distinction. Mass spectrometers are used most commonly in conjunction with primer extension procedures with allele-specific termination. Here we present a novel concept for allele-preparation for SNP genotyping. Primer extension is carried out with an extension primer positioned immediately upstream of the SNP that is to be genotyped, a complete set of four ribonucleotides and a ribonucleotide incorporating DNA polymerase. The allele-extension products are then treated with alkali, which results in the cleavage immediately after the first added ribonucleotide. In addition, to obtain fragments easily detectable by mass spectrometry, we have included a ribonucleotide in the primer usually at the fourth nucleotide from the 3′ terminus. The method was tested on four SNPs each with a different combination of nucleotides. The advantage over other mass spectrometry-based SNP genotyping assays is that this one only requires a PCR, a primer extension reaction with a universal extension mix and an inexpensive facile cleavage reaction, which makes it overall very cost effective and easy in handling.</abstract><note type="author-notes">*To whom correspondence should be addressed. Tel: +33 160 87 84 00; Fax: +33 160 87 83 83; Email: ivo.gut@cng.fr</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>e18</start><end>e18</end></extent></part></relatedItem><identifier type="istex">2DCA1D233DD4A51CEA609A83AB718A84D938516A</identifier><identifier type="DOI">10.1093/nar/gnj021</identifier><identifier type="local">gnj021</identifier><accessCondition type="use and reproduction" contentType="copyright">© The Author 2006. Published by Oxford University Press. All rights reserved
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