Array-Based Binary Analysis for Bacterial Typing
Identifieur interne : 004A13 ( Main/Exploration ); précédent : 004A12; suivant : 004A14Array-Based Binary Analysis for Bacterial Typing
Auteurs : Jason R. E. Shepard [Israël] ; Yael Danin-Poleg [Israël] ; Yechezkel Kashi [Israël] ; David R. Walt [Israël]Source :
- Analytical Chemistry [ 0003-2700 ] ; 2004.
Abstract
An allele-specific oligonucleotide microarray was developed for rapid typing of pathogens based on analysis of genomic variations. Using a panel of Escherichia coli strains as a model system, selected loci were sequenced to uncover differences, such as single- or multiple-nucleotide polymorphisms as well as insertion/deletions (indels). While typical genomic profiling experiments employ specific sequences targeted to genomic DNA unique to a single strain or virulent gene, the present array is designed to type bacteria based on a patterned signature response across multiple loci. In the signature concept, all strains are interrogated by hybridizing their amplified DNA to an array containing multiple probe sequences. Allele-specific oligonucleotide probe sequences targeting each of these variable regions were synthesized and included in a custom fiber-optic array. For each locus, a set of specific probe sequences is selected, such that hybridization gives a binary signal/no signal response to each of the probes. Using this strategy for multiple loci, many pathogens or microorganisms could be classified using a limited number of probes. Because of the advantages of the fiber-optic array platform over other array formats, including sensitivity and speed, the platform described in this paper is capable of supporting a high-throughput diagnostic strategy.
Url:
DOI: 10.1021/ac0488006
Affiliations:
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Walt</name></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:F8EAC66E289EE42248116C1846C0161B39C41104</idno><date when="2005" year="2005">2005</date><idno type="doi">10.1021/ac0488006</idno><idno type="url">https://api.istex.fr/ark:/67375/TPS-WNDMW850-Q/fulltext.pdf</idno><idno type="wicri:Area/Istex/Corpus">001C59</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">001C59</idno><idno type="wicri:Area/Istex/Curation">001C59</idno><idno type="wicri:Area/Istex/Checkpoint">001874</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Checkpoint">001874</idno><idno type="wicri:doubleKey">0003-2700:2005:Shepard J:array:based:binary</idno><idno type="wicri:Area/Main/Merge">004D41</idno><idno type="wicri:Area/Main/Curation">004A13</idno><idno type="wicri:Area/Main/Exploration">004A13</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main">Array-Based Binary Analysis for Bacterial Typing</title><author><name sortKey="Shepard, Jason R E" sort="Shepard, Jason R E" uniqKey="Shepard J" first="Jason R. E." last="Shepard">Jason R. E. Shepard</name><affiliation wicri:level="1"><country xml:lang="fr">Israël</country><wicri:regionArea>Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, and Department ofBiotechnology & Food Engineering, Technion−Israel Institute of Technology, Haifa 32000</wicri:regionArea><wicri:noRegion>Haifa 32000</wicri:noRegion></affiliation></author><author><name sortKey="Danin Poleg, Yael" sort="Danin Poleg, Yael" uniqKey="Danin Poleg Y" first="Yael" last="Danin-Poleg">Yael Danin-Poleg</name><affiliation wicri:level="1"><country xml:lang="fr">Israël</country><wicri:regionArea>Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, and Department ofBiotechnology & Food Engineering, Technion−Israel Institute of Technology, Haifa 32000</wicri:regionArea><wicri:noRegion>Haifa 32000</wicri:noRegion></affiliation><affiliation></affiliation></author><author><name sortKey="Kashi, Yechezkel" sort="Kashi, Yechezkel" uniqKey="Kashi Y" first="Yechezkel" last="Kashi">Yechezkel Kashi</name><affiliation wicri:level="1"><country xml:lang="fr">Israël</country><wicri:regionArea>Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, and Department ofBiotechnology & Food Engineering, Technion−Israel Institute of Technology, Haifa 32000</wicri:regionArea><wicri:noRegion>Haifa 32000</wicri:noRegion></affiliation><affiliation></affiliation><affiliation></affiliation></author><author><name sortKey="Walt, David R" sort="Walt, David R" uniqKey="Walt D" first="David R." last="Walt">David R. Walt</name><affiliation wicri:level="1"><country xml:lang="fr">Israël</country><wicri:regionArea>Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, and Department ofBiotechnology & Food Engineering, Technion−Israel Institute of Technology, Haifa 32000</wicri:regionArea><wicri:noRegion>Haifa 32000</wicri:noRegion></affiliation><affiliation></affiliation><affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Analytical Chemistry</title><title level="j" type="abbrev">Anal. Chem.</title><idno type="ISSN">0003-2700</idno><idno type="eISSN">1520-6882</idno><imprint><publisher>American Chemical Society</publisher><date type="e-published">2004</date><date type="published">2005</date><biblScope unit="vol">77</biblScope><biblScope unit="issue">1</biblScope><biblScope unit="page" from="319">319</biblScope><biblScope unit="page" to="326">326</biblScope></imprint><idno type="ISSN">0003-2700</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0003-2700</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract">An allele-specific oligonucleotide microarray was developed for rapid typing of pathogens based on analysis of genomic variations. Using a panel of Escherichia coli strains as a model system, selected loci were sequenced to uncover differences, such as single- or multiple-nucleotide polymorphisms as well as insertion/deletions (indels). While typical genomic profiling experiments employ specific sequences targeted to genomic DNA unique to a single strain or virulent gene, the present array is designed to type bacteria based on a patterned signature response across multiple loci. In the signature concept, all strains are interrogated by hybridizing their amplified DNA to an array containing multiple probe sequences. Allele-specific oligonucleotide probe sequences targeting each of these variable regions were synthesized and included in a custom fiber-optic array. For each locus, a set of specific probe sequences is selected, such that hybridization gives a binary signal/no signal response to each of the probes. Using this strategy for multiple loci, many pathogens or microorganisms could be classified using a limited number of probes. Because of the advantages of the fiber-optic array platform over other array formats, including sensitivity and speed, the platform described in this paper is capable of supporting a high-throughput diagnostic strategy.</div></front></TEI><affiliations><list><country><li>Israël</li></country></list><tree><country name="Israël"><noRegion><name sortKey="Shepard, Jason R E" sort="Shepard, Jason R E" uniqKey="Shepard J" first="Jason R. E." last="Shepard">Jason R. E. Shepard</name></noRegion><name sortKey="Danin Poleg, Yael" sort="Danin Poleg, Yael" uniqKey="Danin Poleg Y" first="Yael" last="Danin-Poleg">Yael Danin-Poleg</name><name sortKey="Kashi, Yechezkel" sort="Kashi, Yechezkel" uniqKey="Kashi Y" first="Yechezkel" last="Kashi">Yechezkel Kashi</name><name sortKey="Walt, David R" sort="Walt, David R" uniqKey="Walt D" first="David R." last="Walt">David R. Walt</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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