H2N2V1, Main, Exploration, bibRecord, 000D84

Use of consensus sequences for the design of high density resequencing microarrays: the influenza virus paradigm

Identifieur interne : 000D84 ( Main/Exploration ); précédent : 000D83; suivant : 000D85

Use of consensus sequences for the design of high density resequencing microarrays: the influenza virus paradigm

Auteurs : India Leclercq [France] ; Nicolas Berthet [France] ; Christophe Batéjat [France] ; Claudine Rousseaux [France] ; Philip Dickinson [États-Unis] ; Iain Old [France] ; Katherine Kong [États-Unis] ; Giulia Kennedy [États-Unis] ; Stewart Cole [Suisse] ; Jean-Claude Manuguerra [France]

Source :

BMC Genomics [ 1471-2164 ] ; 2010.

RBID : Hal:pasteur-00670619

Abstract

Background
A resequencing microarray called PathogenID v2.0 has been developed and used to explore various strategies of sequence selection for its design. The part dedicated to influenza viruses was based on consensus sequences specific for one gene generated from global alignments of a large number of influenza virus sequences available in databanks.
Results
For each HA (H1, H2, H3, H5, H7 and H9) and NA (N1, N2 and N7) molecular type chosen to be tested, 1 to 3 consensus sequences were computed and tiled on the microarray. A total of 12 influenza virus samples from different host origins (humans, pigs, horses and birds) and isolated over a period of about 50 years were used in this study. Influenza viruses were correctly identified, and in most cases with the accurate information of the time of their emergence.
Conclusions
PathogenID v2.0 microarray demonstrated its ability to type and subtype influenza viruses, often to the level of viral variants, with a minimum number of tiled sequences. This validated the strategy of using consensus sequences, which do not exist in nature, for our microarray design. The versatility, rapidity and high discriminatory power of the PathogenID v2.0 microarray could prove critical to detect and identify viral genome reassortment events resulting in a novel virus with epidemic or pandemic potential and therefore assist health authorities to make efficient decisions about patient treatment and outbreak management.

Url:

https://hal-pasteur.archives-ouvertes.fr/pasteur-00670619

DOI: 10.1186/1471-2164-11-586

Affiliations:

Links toward previous steps (curation, corpus...)

to stream Hal, to step Corpus: 000309
to stream Hal, to step Curation: 000309
to stream Hal, to step Checkpoint: 000269
to stream Main, to step Merge: 000D90
to stream Main, to step Curation: 000D84

Le document en format XML

<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Use of consensus sequences for the design of high density resequencing microarrays: the influenza virus paradigm</title>
<author><name sortKey="Leclercq, India" sort="Leclercq, India" uniqKey="Leclercq I" first="India" last="Leclercq">India Leclercq</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-31437" status="VALID">          <orgName>Cellule d'Intervention Biologique d'Urgence</orgName>
          <orgName type="acronym">CIBU</orgName>
          <desc>            <address>              <addrLine>Département Infection et Epidémiologie, 25-28 rue du Docteur Roux F-75724 Paris Cedex 15</addrLine>
              <country key="FR"></country>
            </address>
            <ref type="url">https://research.pasteur.fr/en/nrc/laboratory-for-urgence-response-to-biological-threats/</ref>
          </desc>
          <listRelation>            <relation active="#struct-300027" type="direct"></relation>
          </listRelation>
        <tutelles><tutelle active="#struct-300027" type="direct"><org type="institution" xml:id="struct-300027" status="VALID">          <idno type="IdRef">027936643</idno>
          <idno type="ISNI">0000 0001 2353 6535</idno>
          <orgName>Institut Pasteur [Paris]</orgName>
          <date type="start">1887-06-04</date>
          <desc>            <address>              <addrLine>25-28, rue du docteur Roux, 75724 Paris cedex 15</addrLine>
              <country key="FR"></country>
            </address>
            <ref type="url">https://www.pasteur.fr</ref>
          </desc>
        </org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>France</country>
</affiliation>
</author>
<author><name sortKey="Berthet, Nicolas" sort="Berthet, Nicolas" uniqKey="Berthet N" first="Nicolas" last="Berthet">Nicolas Berthet</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-35814" status="OLD">          <orgName>Epidémiologie et Physiopathologie des Virus Oncogènes</orgName>
          <desc>            <address>              <addrLine>25-28 rue du Docteur Roux F-75724 Paris Cedex 15</addrLine>
              <country key="FR"></country>
            </address>
          </desc>
          <listRelation>            <relation active="#struct-300027" type="direct"></relation>
            <relation name="URA3015" active="#struct-441569" type="direct"></relation>
          </listRelation>
        <tutelles><tutelle active="#struct-300027" type="direct"><org type="institution" xml:id="struct-300027" status="VALID">          <idno type="IdRef">027936643</idno>
          <idno type="ISNI">0000 0001 2353 6535</idno>
          <orgName>Institut Pasteur [Paris]</orgName>
          <date type="start">1887-06-04</date>
          <desc>            <address>              <addrLine>25-28, rue du docteur Roux, 75724 Paris cedex 15</addrLine>
              <country key="FR"></country>
            </address>
            <ref type="url">https://www.pasteur.fr</ref>
          </desc>
        </org>
</tutelle>
<tutelle name="URA3015" active="#struct-441569" type="direct"><org type="institution" xml:id="struct-441569" status="VALID">          <idno type="IdRef">02636817X</idno>
          <idno type="ISNI">0000000122597504</idno>
          <orgName>Centre National de la Recherche Scientifique</orgName>
          <orgName type="acronym">CNRS</orgName>
          <date type="start">1939-10-19</date>
          <desc>            <address>              <country key="FR"></country>
            </address>
            <ref type="url">http://www.cnrs.fr/</ref>
          </desc>
        </org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>France</country>
</affiliation>
</author>
<author><name sortKey="Batejat, Christophe" sort="Batejat, Christophe" uniqKey="Batejat C" first="Christophe" last="Batéjat">Christophe Batéjat</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-31437" status="VALID">          <orgName>Cellule d'Intervention Biologique d'Urgence</orgName>
          <orgName type="acronym">CIBU</orgName>
          <desc>            <address>              <addrLine>Département Infection et Epidémiologie, 25-28 rue du Docteur Roux F-75724 Paris Cedex 15</addrLine>
              <country key="FR"></country>
            </address>
            <ref type="url">https://research.pasteur.fr/en/nrc/laboratory-for-urgence-response-to-biological-threats/</ref>
          </desc>
          <listRelation>            <relation active="#struct-300027" type="direct"></relation>
          </listRelation>
        <tutelles><tutelle active="#struct-300027" type="direct"><org type="institution" xml:id="struct-300027" status="VALID">          <idno type="IdRef">027936643</idno>
          <idno type="ISNI">0000 0001 2353 6535</idno>
          <orgName>Institut Pasteur [Paris]</orgName>
          <date type="start">1887-06-04</date>
          <desc>            <address>              <addrLine>25-28, rue du docteur Roux, 75724 Paris cedex 15</addrLine>
              <country key="FR"></country>
            </address>
            <ref type="url">https://www.pasteur.fr</ref>
          </desc>
        </org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>France</country>
</affiliation>
</author>
<author><name sortKey="Rousseaux, Claudine" sort="Rousseaux, Claudine" uniqKey="Rousseaux C" first="Claudine" last="Rousseaux">Claudine Rousseaux</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-31437" status="VALID">          <orgName>Cellule d'Intervention Biologique d'Urgence</orgName>
          <orgName type="acronym">CIBU</orgName>
          <desc>            <address>              <addrLine>Département Infection et Epidémiologie, 25-28 rue du Docteur Roux F-75724 Paris Cedex 15</addrLine>
              <country key="FR"></country>
            </address>
            <ref type="url">https://research.pasteur.fr/en/nrc/laboratory-for-urgence-response-to-biological-threats/</ref>
          </desc>
          <listRelation>            <relation active="#struct-300027" type="direct"></relation>
          </listRelation>
        <tutelles><tutelle active="#struct-300027" type="direct"><org type="institution" xml:id="struct-300027" status="VALID">          <idno type="IdRef">027936643</idno>
          <idno type="ISNI">0000 0001 2353 6535</idno>
          <orgName>Institut Pasteur [Paris]</orgName>
          <date type="start">1887-06-04</date>
          <desc>            <address>              <addrLine>25-28, rue du docteur Roux, 75724 Paris cedex 15</addrLine>
              <country key="FR"></country>
            </address>
            <ref type="url">https://www.pasteur.fr</ref>
          </desc>
        </org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>France</country>
</affiliation>
</author>
<author><name sortKey="Dickinson, Philip" sort="Dickinson, Philip" uniqKey="Dickinson P" first="Philip" last="Dickinson">Philip Dickinson</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-202384" status="VALID">          <orgName>Affymetrix</orgName>
          <desc>            <address>              <addrLine>3420 Central Expressway Santa Clara, CA 95051 Phone (toll-free in US): +1-888-362-2447 Phone: +1-408-731-5000 Fax: +1-408-731-5380</addrLine>
              <country key="US"></country>
            </address>
            <ref type="url">http://www.affymetrix.com/estore/</ref>
          </desc>
          <listRelation>            <relation active="#struct-329776" type="direct"></relation>
          </listRelation>
        <tutelles><tutelle active="#struct-329776" type="direct"><org type="institution" xml:id="struct-329776" status="INCOMING">          <orgName>Affymetrix</orgName>
          <desc>            <address>              <country key="FR"></country>
            </address>
          </desc>
        </org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>États-Unis</country>
</affiliation>
</author>
<author><name sortKey="Old, Iain" sort="Old, Iain" uniqKey="Old I" first="Iain" last="Old">Iain Old</name>
<affiliation wicri:level="1"><hal:affiliation type="institution" xml:id="struct-300027" status="VALID">          <idno type="IdRef">027936643</idno>
          <idno type="ISNI">0000 0001 2353 6535</idno>
          <orgName>Institut Pasteur [Paris]</orgName>
          <date type="start">1887-06-04</date>
          <desc>            <address>              <addrLine>25-28, rue du docteur Roux, 75724 Paris cedex 15</addrLine>
              <country key="FR"></country>
            </address>
            <ref type="url">https://www.pasteur.fr</ref>
          </desc>
        </hal:affiliation>
<country>France</country>
</affiliation>
</author>
<author><name sortKey="Kong, Katherine" sort="Kong, Katherine" uniqKey="Kong K" first="Katherine" last="Kong">Katherine Kong</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-202384" status="VALID">          <orgName>Affymetrix</orgName>
          <desc>            <address>              <addrLine>3420 Central Expressway Santa Clara, CA 95051 Phone (toll-free in US): +1-888-362-2447 Phone: +1-408-731-5000 Fax: +1-408-731-5380</addrLine>
              <country key="US"></country>
            </address>
            <ref type="url">http://www.affymetrix.com/estore/</ref>
          </desc>
          <listRelation>            <relation active="#struct-329776" type="direct"></relation>
          </listRelation>
        <tutelles><tutelle active="#struct-329776" type="direct"><org type="institution" xml:id="struct-329776" status="INCOMING">          <orgName>Affymetrix</orgName>
          <desc>            <address>              <country key="FR"></country>
            </address>
          </desc>
        </org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>États-Unis</country>
</affiliation>
</author>
<author><name sortKey="Kennedy, Giulia" sort="Kennedy, Giulia" uniqKey="Kennedy G" first="Giulia" last="Kennedy">Giulia Kennedy</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-202384" status="VALID">          <orgName>Affymetrix</orgName>
          <desc>            <address>              <addrLine>3420 Central Expressway Santa Clara, CA 95051 Phone (toll-free in US): +1-888-362-2447 Phone: +1-408-731-5000 Fax: +1-408-731-5380</addrLine>
              <country key="US"></country>
            </address>
            <ref type="url">http://www.affymetrix.com/estore/</ref>
          </desc>
          <listRelation>            <relation active="#struct-329776" type="direct"></relation>
          </listRelation>
        <tutelles><tutelle active="#struct-329776" type="direct"><org type="institution" xml:id="struct-329776" status="INCOMING">          <orgName>Affymetrix</orgName>
          <desc>            <address>              <country key="FR"></country>
            </address>
          </desc>
        </org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>États-Unis</country>
</affiliation>
</author>
<author><name sortKey="Cole, Stewart" sort="Cole, Stewart" uniqKey="Cole S" first="Stewart" last="Cole">Stewart Cole</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-184585" status="INCOMING">          <orgName>Global Health Institute</orgName>
          <desc>            <address>              <addrLine>Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, CH-1015 Lausanne, Switzerland</addrLine>
              <country key="CH"></country>
            </address>
          </desc>
          <listRelation>            <relation active="#struct-302851" type="direct"></relation>
          </listRelation>
        <tutelles><tutelle active="#struct-302851" type="direct"><org type="institution" xml:id="struct-302851" status="VALID">          <orgName>Ecole Polytechnique Fédérale de Lausanne</orgName>
          <orgName type="acronym">EPFL</orgName>
          <desc>            <address>              <addrLine>CH-1015 Lausanne, Switzerland </addrLine>
              <country key="CH"></country>
            </address>
            <ref type="url">https://www.epfl.ch</ref>
          </desc>
        </org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>Suisse</country>
<placeName><settlement type="city">Lausanne</settlement>
<region nuts="3" type="region">Canton de Vaud</region>
</placeName>
<orgName type="university">École polytechnique fédérale de Lausanne</orgName>
</affiliation>
</author>
<author><name sortKey="Manuguerra, Jean Claude" sort="Manuguerra, Jean Claude" uniqKey="Manuguerra J" first="Jean-Claude" last="Manuguerra">Jean-Claude Manuguerra</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-31437" status="VALID">          <orgName>Cellule d'Intervention Biologique d'Urgence</orgName>
          <orgName type="acronym">CIBU</orgName>
          <desc>            <address>              <addrLine>Département Infection et Epidémiologie, 25-28 rue du Docteur Roux F-75724 Paris Cedex 15</addrLine>
              <country key="FR"></country>
            </address>
            <ref type="url">https://research.pasteur.fr/en/nrc/laboratory-for-urgence-response-to-biological-threats/</ref>
          </desc>
          <listRelation>            <relation active="#struct-300027" type="direct"></relation>
          </listRelation>
        <tutelles><tutelle active="#struct-300027" type="direct"><org type="institution" xml:id="struct-300027" status="VALID">          <idno type="IdRef">027936643</idno>
          <idno type="ISNI">0000 0001 2353 6535</idno>
          <orgName>Institut Pasteur [Paris]</orgName>
          <date type="start">1887-06-04</date>
          <desc>            <address>              <addrLine>25-28, rue du docteur Roux, 75724 Paris cedex 15</addrLine>
              <country key="FR"></country>
            </address>
            <ref type="url">https://www.pasteur.fr</ref>
          </desc>
        </org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>France</country>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">HAL</idno>
<idno type="RBID">Hal:pasteur-00670619</idno>
<idno type="halId">pasteur-00670619</idno>
<idno type="halUri">https://hal-pasteur.archives-ouvertes.fr/pasteur-00670619</idno>
<idno type="url">https://hal-pasteur.archives-ouvertes.fr/pasteur-00670619</idno>
<idno type="doi">10.1186/1471-2164-11-586</idno>
<date when="2010">2010</date>
<idno type="wicri:Area/Hal/Corpus">000309</idno>
<idno type="wicri:Area/Hal/Curation">000309</idno>
<idno type="wicri:Area/Hal/Checkpoint">000269</idno>
<idno type="wicri:explorRef" wicri:stream="Hal" wicri:step="Checkpoint">000269</idno>
<idno type="wicri:doubleKey">1471-2164:2010:Leclercq I:use:of:consensus</idno>
<idno type="wicri:Area/Main/Merge">000D90</idno>
<idno type="wicri:Area/Main/Curation">000D84</idno>
<idno type="wicri:Area/Main/Exploration">000D84</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">Use of consensus sequences for the design of high density resequencing microarrays: the influenza virus paradigm</title>
<author><name sortKey="Leclercq, India" sort="Leclercq, India" uniqKey="Leclercq I" first="India" last="Leclercq">India Leclercq</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-31437" status="VALID">          <orgName>Cellule d'Intervention Biologique d'Urgence</orgName>
          <orgName type="acronym">CIBU</orgName>
          <desc>            <address>              <addrLine>Département Infection et Epidémiologie, 25-28 rue du Docteur Roux F-75724 Paris Cedex 15</addrLine>
              <country key="FR"></country>
            </address>
            <ref type="url">https://research.pasteur.fr/en/nrc/laboratory-for-urgence-response-to-biological-threats/</ref>
          </desc>
          <listRelation>            <relation active="#struct-300027" type="direct"></relation>
          </listRelation>
        <tutelles><tutelle active="#struct-300027" type="direct"><org type="institution" xml:id="struct-300027" status="VALID">          <idno type="IdRef">027936643</idno>
          <idno type="ISNI">0000 0001 2353 6535</idno>
          <orgName>Institut Pasteur [Paris]</orgName>
          <date type="start">1887-06-04</date>
          <desc>            <address>              <addrLine>25-28, rue du docteur Roux, 75724 Paris cedex 15</addrLine>
              <country key="FR"></country>
            </address>
            <ref type="url">https://www.pasteur.fr</ref>
          </desc>
        </org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>France</country>
</affiliation>
</author>
<author><name sortKey="Berthet, Nicolas" sort="Berthet, Nicolas" uniqKey="Berthet N" first="Nicolas" last="Berthet">Nicolas Berthet</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-35814" status="OLD">          <orgName>Epidémiologie et Physiopathologie des Virus Oncogènes</orgName>
          <desc>            <address>              <addrLine>25-28 rue du Docteur Roux F-75724 Paris Cedex 15</addrLine>
              <country key="FR"></country>
            </address>
          </desc>
          <listRelation>            <relation active="#struct-300027" type="direct"></relation>
            <relation name="URA3015" active="#struct-441569" type="direct"></relation>
          </listRelation>
        <tutelles><tutelle active="#struct-300027" type="direct"><org type="institution" xml:id="struct-300027" status="VALID">          <idno type="IdRef">027936643</idno>
          <idno type="ISNI">0000 0001 2353 6535</idno>
          <orgName>Institut Pasteur [Paris]</orgName>
          <date type="start">1887-06-04</date>
          <desc>            <address>              <addrLine>25-28, rue du docteur Roux, 75724 Paris cedex 15</addrLine>
              <country key="FR"></country>
            </address>
            <ref type="url">https://www.pasteur.fr</ref>
          </desc>
        </org>
</tutelle>
<tutelle name="URA3015" active="#struct-441569" type="direct"><org type="institution" xml:id="struct-441569" status="VALID">          <idno type="IdRef">02636817X</idno>
          <idno type="ISNI">0000000122597504</idno>
          <orgName>Centre National de la Recherche Scientifique</orgName>
          <orgName type="acronym">CNRS</orgName>
          <date type="start">1939-10-19</date>
          <desc>            <address>              <country key="FR"></country>
            </address>
            <ref type="url">http://www.cnrs.fr/</ref>
          </desc>
        </org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>France</country>
</affiliation>
</author>
<author><name sortKey="Batejat, Christophe" sort="Batejat, Christophe" uniqKey="Batejat C" first="Christophe" last="Batéjat">Christophe Batéjat</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-31437" status="VALID">          <orgName>Cellule d'Intervention Biologique d'Urgence</orgName>
          <orgName type="acronym">CIBU</orgName>
          <desc>            <address>              <addrLine>Département Infection et Epidémiologie, 25-28 rue du Docteur Roux F-75724 Paris Cedex 15</addrLine>
              <country key="FR"></country>
            </address>
            <ref type="url">https://research.pasteur.fr/en/nrc/laboratory-for-urgence-response-to-biological-threats/</ref>
          </desc>
          <listRelation>            <relation active="#struct-300027" type="direct"></relation>
          </listRelation>
        <tutelles><tutelle active="#struct-300027" type="direct"><org type="institution" xml:id="struct-300027" status="VALID">          <idno type="IdRef">027936643</idno>
          <idno type="ISNI">0000 0001 2353 6535</idno>
          <orgName>Institut Pasteur [Paris]</orgName>
          <date type="start">1887-06-04</date>
          <desc>            <address>              <addrLine>25-28, rue du docteur Roux, 75724 Paris cedex 15</addrLine>
              <country key="FR"></country>
            </address>
            <ref type="url">https://www.pasteur.fr</ref>
          </desc>
        </org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>France</country>
</affiliation>
</author>
<author><name sortKey="Rousseaux, Claudine" sort="Rousseaux, Claudine" uniqKey="Rousseaux C" first="Claudine" last="Rousseaux">Claudine Rousseaux</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-31437" status="VALID">          <orgName>Cellule d'Intervention Biologique d'Urgence</orgName>
          <orgName type="acronym">CIBU</orgName>
          <desc>            <address>              <addrLine>Département Infection et Epidémiologie, 25-28 rue du Docteur Roux F-75724 Paris Cedex 15</addrLine>
              <country key="FR"></country>
            </address>
            <ref type="url">https://research.pasteur.fr/en/nrc/laboratory-for-urgence-response-to-biological-threats/</ref>
          </desc>
          <listRelation>            <relation active="#struct-300027" type="direct"></relation>
          </listRelation>
        <tutelles><tutelle active="#struct-300027" type="direct"><org type="institution" xml:id="struct-300027" status="VALID">          <idno type="IdRef">027936643</idno>
          <idno type="ISNI">0000 0001 2353 6535</idno>
          <orgName>Institut Pasteur [Paris]</orgName>
          <date type="start">1887-06-04</date>
          <desc>            <address>              <addrLine>25-28, rue du docteur Roux, 75724 Paris cedex 15</addrLine>
              <country key="FR"></country>
            </address>
            <ref type="url">https://www.pasteur.fr</ref>
          </desc>
        </org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>France</country>
</affiliation>
</author>
<author><name sortKey="Dickinson, Philip" sort="Dickinson, Philip" uniqKey="Dickinson P" first="Philip" last="Dickinson">Philip Dickinson</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-202384" status="VALID">          <orgName>Affymetrix</orgName>
          <desc>            <address>              <addrLine>3420 Central Expressway Santa Clara, CA 95051 Phone (toll-free in US): +1-888-362-2447 Phone: +1-408-731-5000 Fax: +1-408-731-5380</addrLine>
              <country key="US"></country>
            </address>
            <ref type="url">http://www.affymetrix.com/estore/</ref>
          </desc>
          <listRelation>            <relation active="#struct-329776" type="direct"></relation>
          </listRelation>
        <tutelles><tutelle active="#struct-329776" type="direct"><org type="institution" xml:id="struct-329776" status="INCOMING">          <orgName>Affymetrix</orgName>
          <desc>            <address>              <country key="FR"></country>
            </address>
          </desc>
        </org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>États-Unis</country>
</affiliation>
</author>
<author><name sortKey="Old, Iain" sort="Old, Iain" uniqKey="Old I" first="Iain" last="Old">Iain Old</name>
<affiliation wicri:level="1"><hal:affiliation type="institution" xml:id="struct-300027" status="VALID">          <idno type="IdRef">027936643</idno>
          <idno type="ISNI">0000 0001 2353 6535</idno>
          <orgName>Institut Pasteur [Paris]</orgName>
          <date type="start">1887-06-04</date>
          <desc>            <address>              <addrLine>25-28, rue du docteur Roux, 75724 Paris cedex 15</addrLine>
              <country key="FR"></country>
            </address>
            <ref type="url">https://www.pasteur.fr</ref>
          </desc>
        </hal:affiliation>
<country>France</country>
</affiliation>
</author>
<author><name sortKey="Kong, Katherine" sort="Kong, Katherine" uniqKey="Kong K" first="Katherine" last="Kong">Katherine Kong</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-202384" status="VALID">          <orgName>Affymetrix</orgName>
          <desc>            <address>              <addrLine>3420 Central Expressway Santa Clara, CA 95051 Phone (toll-free in US): +1-888-362-2447 Phone: +1-408-731-5000 Fax: +1-408-731-5380</addrLine>
              <country key="US"></country>
            </address>
            <ref type="url">http://www.affymetrix.com/estore/</ref>
          </desc>
          <listRelation>            <relation active="#struct-329776" type="direct"></relation>
          </listRelation>
        <tutelles><tutelle active="#struct-329776" type="direct"><org type="institution" xml:id="struct-329776" status="INCOMING">          <orgName>Affymetrix</orgName>
          <desc>            <address>              <country key="FR"></country>
            </address>
          </desc>
        </org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>États-Unis</country>
</affiliation>
</author>
<author><name sortKey="Kennedy, Giulia" sort="Kennedy, Giulia" uniqKey="Kennedy G" first="Giulia" last="Kennedy">Giulia Kennedy</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-202384" status="VALID">          <orgName>Affymetrix</orgName>
          <desc>            <address>              <addrLine>3420 Central Expressway Santa Clara, CA 95051 Phone (toll-free in US): +1-888-362-2447 Phone: +1-408-731-5000 Fax: +1-408-731-5380</addrLine>
              <country key="US"></country>
            </address>
            <ref type="url">http://www.affymetrix.com/estore/</ref>
          </desc>
          <listRelation>            <relation active="#struct-329776" type="direct"></relation>
          </listRelation>
        <tutelles><tutelle active="#struct-329776" type="direct"><org type="institution" xml:id="struct-329776" status="INCOMING">          <orgName>Affymetrix</orgName>
          <desc>            <address>              <country key="FR"></country>
            </address>
          </desc>
        </org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>États-Unis</country>
</affiliation>
</author>
<author><name sortKey="Cole, Stewart" sort="Cole, Stewart" uniqKey="Cole S" first="Stewart" last="Cole">Stewart Cole</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-184585" status="INCOMING">          <orgName>Global Health Institute</orgName>
          <desc>            <address>              <addrLine>Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, CH-1015 Lausanne, Switzerland</addrLine>
              <country key="CH"></country>
            </address>
          </desc>
          <listRelation>            <relation active="#struct-302851" type="direct"></relation>
          </listRelation>
        <tutelles><tutelle active="#struct-302851" type="direct"><org type="institution" xml:id="struct-302851" status="VALID">          <orgName>Ecole Polytechnique Fédérale de Lausanne</orgName>
          <orgName type="acronym">EPFL</orgName>
          <desc>            <address>              <addrLine>CH-1015 Lausanne, Switzerland </addrLine>
              <country key="CH"></country>
            </address>
            <ref type="url">https://www.epfl.ch</ref>
          </desc>
        </org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>Suisse</country>
<placeName><settlement type="city">Lausanne</settlement>
<region nuts="3" type="region">Canton de Vaud</region>
</placeName>
<orgName type="university">École polytechnique fédérale de Lausanne</orgName>
</affiliation>
</author>
<author><name sortKey="Manuguerra, Jean Claude" sort="Manuguerra, Jean Claude" uniqKey="Manuguerra J" first="Jean-Claude" last="Manuguerra">Jean-Claude Manuguerra</name>
<affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-31437" status="VALID">          <orgName>Cellule d'Intervention Biologique d'Urgence</orgName>
          <orgName type="acronym">CIBU</orgName>
          <desc>            <address>              <addrLine>Département Infection et Epidémiologie, 25-28 rue du Docteur Roux F-75724 Paris Cedex 15</addrLine>
              <country key="FR"></country>
            </address>
            <ref type="url">https://research.pasteur.fr/en/nrc/laboratory-for-urgence-response-to-biological-threats/</ref>
          </desc>
          <listRelation>            <relation active="#struct-300027" type="direct"></relation>
          </listRelation>
        <tutelles><tutelle active="#struct-300027" type="direct"><org type="institution" xml:id="struct-300027" status="VALID">          <idno type="IdRef">027936643</idno>
          <idno type="ISNI">0000 0001 2353 6535</idno>
          <orgName>Institut Pasteur [Paris]</orgName>
          <date type="start">1887-06-04</date>
          <desc>            <address>              <addrLine>25-28, rue du docteur Roux, 75724 Paris cedex 15</addrLine>
              <country key="FR"></country>
            </address>
            <ref type="url">https://www.pasteur.fr</ref>
          </desc>
        </org>
</tutelle>
</tutelles>
</hal:affiliation>
<country>France</country>
</affiliation>
</author>
</analytic>
<idno type="DOI">10.1186/1471-2164-11-586</idno>
<series><title level="j">BMC Genomics</title>
<idno type="ISSN">1471-2164</idno>
<imprint><date type="datePub">2010</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">              <p>Background
A resequencing microarray called PathogenID v2.0 has been developed and used to explore various strategies of sequence selection for its design. The part dedicated to influenza viruses was based on consensus sequences specific for one gene generated from global alignments of a large number of influenza virus sequences available in databanks.
Results
For each HA (H1, H2, H3, H5, H7 and H9) and NA (N1, N2 and N7) molecular type chosen to be tested, 1 to 3 consensus sequences were computed and tiled on the microarray. A total of 12 influenza virus samples from different host origins (humans, pigs, horses and birds) and isolated over a period of about 50 years were used in this study. Influenza viruses were correctly identified, and in most cases with the accurate information of the time of their emergence.
Conclusions
PathogenID v2.0 microarray demonstrated its ability to type and subtype influenza viruses, often to the level of viral variants, with a minimum number of tiled sequences. This validated the strategy of using consensus sequences, which do not exist in nature, for our microarray design. The versatility, rapidity and high discriminatory power of the PathogenID v2.0 microarray could prove critical to detect and identify viral genome reassortment events resulting in a novel virus with epidemic or pandemic potential and therefore assist health authorities to make efficient decisions about patient treatment and outbreak management.</p>
            </div>
</front>
</TEI>
<affiliations><list><country><li>France</li>
<li>Suisse</li>
<li>États-Unis</li>
</country>
<region><li>Canton de Vaud</li>
</region>
<settlement><li>Lausanne</li>
</settlement>
<orgName><li>École polytechnique fédérale de Lausanne</li>
</orgName>
</list>
<tree><country name="France"><noRegion><name sortKey="Leclercq, India" sort="Leclercq, India" uniqKey="Leclercq I" first="India" last="Leclercq">India Leclercq</name>
</noRegion>
<name sortKey="Batejat, Christophe" sort="Batejat, Christophe" uniqKey="Batejat C" first="Christophe" last="Batéjat">Christophe Batéjat</name>
<name sortKey="Berthet, Nicolas" sort="Berthet, Nicolas" uniqKey="Berthet N" first="Nicolas" last="Berthet">Nicolas Berthet</name>
<name sortKey="Manuguerra, Jean Claude" sort="Manuguerra, Jean Claude" uniqKey="Manuguerra J" first="Jean-Claude" last="Manuguerra">Jean-Claude Manuguerra</name>
<name sortKey="Old, Iain" sort="Old, Iain" uniqKey="Old I" first="Iain" last="Old">Iain Old</name>
<name sortKey="Rousseaux, Claudine" sort="Rousseaux, Claudine" uniqKey="Rousseaux C" first="Claudine" last="Rousseaux">Claudine Rousseaux</name>
</country>
<country name="États-Unis"><noRegion><name sortKey="Dickinson, Philip" sort="Dickinson, Philip" uniqKey="Dickinson P" first="Philip" last="Dickinson">Philip Dickinson</name>
</noRegion>
<name sortKey="Kennedy, Giulia" sort="Kennedy, Giulia" uniqKey="Kennedy G" first="Giulia" last="Kennedy">Giulia Kennedy</name>
<name sortKey="Kong, Katherine" sort="Kong, Katherine" uniqKey="Kong K" first="Katherine" last="Kong">Katherine Kong</name>
</country>
<country name="Suisse"><region name="Canton de Vaud"><name sortKey="Cole, Stewart" sort="Cole, Stewart" uniqKey="Cole S" first="Stewart" last="Cole">Stewart Cole</name>
</region>
</country>
</tree>
</affiliations>
</record>

Pour manipuler ce document sous Unix (Dilib)

EXPLOR_STEP=$WICRI_ROOT/Sante/explor/H2N2V1/Data/Main/Exploration

HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000D84 | SxmlIndent | more

HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000D84 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Sante
   |area=    H2N2V1
   |flux=    Main
   |étape=   Exploration
   |type=    RBID
   |clé=     Hal:pasteur-00670619
   |texte=   Use of consensus sequences for the design of high density resequencing microarrays: the influenza virus paradigm
}}

This area was generated with Dilib version V0.6.33.
Data generation: Tue Apr 14 19:59:40 2020. Site generation: Thu Mar 25 15:38:26 2021

	Serveur d'exploration H2N2
	Attention, ce site est en cours de développement ! Attention, site généré par des moyens informatiques à partir de corpus bruts. Les informations ne sont donc pas validées.

Serveur d'exploration H2N2

Use of consensus sequences for the design of high density resequencing microarrays: the influenza virus paradigm

Use of consensus sequences for the design of high density resequencing microarrays: the influenza virus paradigm

Source :

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri