Physico-chemical foundations underpinning microarray and next-generation sequencing experiments
Identifieur interne : 004548 ( Main/Curation ); précédent : 004547; suivant : 004549Physico-chemical foundations underpinning microarray and next-generation sequencing experiments
Auteurs : Andrew Harrison [Royaume-Uni] ; Hans Binder [Allemagne] ; Arnaud Buhot [France] ; Conrad J. Burden [Australie] ; Enrico Carlon [Belgique] ; Cynthia Gibas [États-Unis] ; Lara J. Gamble [États-Unis] ; Avraham Halperin [France] ; Jef Hooyberghs [Belgique] ; David P. Kreil [Autriche, Royaume-Uni] ; Rastislav Levicky [États-Unis] ; Peter A. Noble [États-Unis] ; Albrecht Ott [Allemagne] ; B. Montgomery Pettitt [États-Unis] ; Diethard Tautz [Allemagne] ; Alexander E. Pozhitkov [États-Unis, Allemagne]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2013.
Abstract
Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized.
Url:
DOI: 10.1093/nar/gks1358
PubMed: 23307556
PubMed Central: 3597649
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Montgomery" last="Pettitt">B. Montgomery Pettitt</name><affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="gks1358-AFF1">The University of Texas Medical Branch - Sealy Center for Structural Biology and Molecular Biophysics, Galveston, TX 77204, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>The University of Texas Medical Branch - Sealy Center for Structural Biology and Molecular Biophysics, Galveston, TX 77204</wicri:regionArea><placeName><region type="state">Texas</region></placeName></affiliation></author><author><name sortKey="Tautz, Diethard" sort="Tautz, Diethard" uniqKey="Tautz D" first="Diethard" last="Tautz">Diethard Tautz</name><affiliation wicri:level="1"><nlm:aff id="gks1358-AFF1">Max-Planck-Institut - Evolutionsbiologie, Ploen, 24306 Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max-Planck-Institut - Evolutionsbiologie, Ploen</wicri:regionArea><wicri:noRegion>Ploen</wicri:noRegion><wicri:noRegion>Ploen</wicri:noRegion><wicri:noRegion>Ploen</wicri:noRegion></affiliation></author><author><name sortKey="Pozhitkov, Alexander E" sort="Pozhitkov, Alexander E" uniqKey="Pozhitkov A" first="Alexander E." last="Pozhitkov">Alexander E. 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Burden</name><affiliation wicri:level="1"><nlm:aff id="gks1358-AFF1">Centre for Bioinformation Science, Mathematical Sciences Institute Building 27 Australian National University, Canberra, Australian Capital Territory 0200, Australia,</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Centre for Bioinformation Science, Mathematical Sciences Institute Building 27 Australian National University, Canberra, Australian Capital Territory 0200</wicri:regionArea><wicri:noRegion>Australian Capital Territory 0200</wicri:noRegion></affiliation></author><author><name sortKey="Carlon, Enrico" sort="Carlon, Enrico" uniqKey="Carlon E" first="Enrico" last="Carlon">Enrico Carlon</name><affiliation wicri:level="1"><nlm:aff id="gks1358-AFF1">K.U. Leuven - Physics, Celestijnenlaan 200D B-3000 Leuven, Belgium,</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>K.U. Leuven - Physics, Celestijnenlaan 200D B-3000 Leuven</wicri:regionArea><wicri:noRegion>Celestijnenlaan 200D B-3000 Leuven</wicri:noRegion></affiliation></author><author><name sortKey="Gibas, Cynthia" sort="Gibas, Cynthia" uniqKey="Gibas C" first="Cynthia" last="Gibas">Cynthia Gibas</name><affiliation wicri:level="2"><nlm:aff id="gks1358-AFF1">University of North Carolina at Charlotte-Bioinformatics Research Center, Charlotte, NC 28223-0001, USA,</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>University of North Carolina at Charlotte-Bioinformatics Research Center, Charlotte, NC 28223-0001</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></affiliation></author><author><name sortKey="Gamble, Lara J" sort="Gamble, Lara J" uniqKey="Gamble L" first="Lara J." last="Gamble">Lara J. Gamble</name><affiliation wicri:level="2"><nlm:aff id="gks1358-AFF1">University of Washington-Bioengineering, Seattle, WA 98195, USA,</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>University of Washington-Bioengineering, Seattle, WA 98195</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Halperin, Avraham" sort="Halperin, Avraham" uniqKey="Halperin A" first="Avraham" last="Halperin">Avraham Halperin</name><affiliation wicri:level="3"><nlm:aff id="gks1358-AFF1">University of Grenoble - National Center for Scientific Research, 38041, Grenoble, France,</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>University of Grenoble - National Center for Scientific Research, 38041, Grenoble</wicri:regionArea><placeName><region type="region" nuts="2">Auvergne-Rhône-Alpes</region><region type="old region" nuts="2">Rhône-Alpes</region><settlement type="city">Grenoble</settlement></placeName></affiliation></author><author><name sortKey="Hooyberghs, Jef" sort="Hooyberghs, Jef" uniqKey="Hooyberghs J" first="Jef" last="Hooyberghs">Jef Hooyberghs</name><affiliation wicri:level="1"><nlm:aff id="gks1358-AFF1">Flemish Institute for Technological Research (VITO) - Toxicology, Boeretang 200, Mol 2400, Belgium,</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Flemish Institute for Technological Research (VITO) - Toxicology, Boeretang 200, Mol 2400</wicri:regionArea><wicri:noRegion>Mol 2400</wicri:noRegion></affiliation></author><author><name sortKey="Kreil, David P" sort="Kreil, David P" uniqKey="Kreil D" first="David P." last="Kreil">David P. Kreil</name><affiliation wicri:level="3"><nlm:aff id="gks1358-AFF1">Universität für Bodenkultur Wien - Biotechnologie, Wien, Austria,</nlm:aff><country xml:lang="fr">Autriche</country><wicri:regionArea>Universität für Bodenkultur Wien - Biotechnologie, Wien</wicri:regionArea><placeName><settlement type="city">Vienne (Autriche)</settlement><region nuts="2" type="province">Vienne (Autriche)</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="gks1358-AFF1">Life Sciences, University of Warwick, Coventry CV4 7AL, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Life Sciences, University of Warwick, Coventry CV4 7AL</wicri:regionArea><wicri:noRegion>Coventry CV4 7AL</wicri:noRegion></affiliation></author><author><name sortKey="Levicky, Rastislav" sort="Levicky, Rastislav" uniqKey="Levicky R" first="Rastislav" last="Levicky">Rastislav Levicky</name><affiliation wicri:level="2"><nlm:aff id="gks1358-AFF1">Polytechnic Institute of New York University - Chemical and Biological Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA,</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Polytechnic Institute of New York University - Chemical and Biological Engineering, 6 MetroTech Center, Brooklyn, NY 11201</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Noble, Peter A" sort="Noble, Peter A" uniqKey="Noble P" first="Peter A." last="Noble">Peter A. Noble</name><affiliation wicri:level="2"><nlm:aff id="gks1358-AFF1">Alabama State University - PhD Program in Microbiology, 325, Montgomery, AL 36101-0271, USA,</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Alabama State University - PhD Program in Microbiology, 325, Montgomery, AL 36101-0271</wicri:regionArea><placeName><region type="state">Alabama</region></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="gks1358-AFF1">University of Washington, Department of Periodontology, Seattle, WA 98105, USA,</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>University of Washington, Department of Periodontology, Seattle, WA 98105</wicri:regionArea><placeName><region type="state">Washington (État)</region><settlement type="city">Seattle</settlement></placeName><orgName type="university">Université de Washington</orgName></affiliation></author><author><name sortKey="Ott, Albrecht" sort="Ott, Albrecht" uniqKey="Ott A" first="Albrecht" last="Ott">Albrecht Ott</name><affiliation wicri:level="3"><nlm:aff id="gks1358-AFF1">Universitaet des Saarlandes - Biologische Experimentalphysic, Saarbruecken, D-66041 Germany,</nlm:aff><country wicri:rule="zip">Allemagne</country><wicri:regionArea>Universitaet des Saarlandes - Biologische Experimentalphysic, Saarbruecken, D-66041 Germany</wicri:regionArea><placeName><region type="land" nuts="2">Sarre (Land)</region><settlement type="city">Sarrebruck</settlement></placeName></affiliation></author><author><name sortKey="Pettitt, B Montgomery" sort="Pettitt, B Montgomery" uniqKey="Pettitt B" first="B. Montgomery" last="Pettitt">B. Montgomery Pettitt</name><affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="gks1358-AFF1">The University of Texas Medical Branch - Sealy Center for Structural Biology and Molecular Biophysics, Galveston, TX 77204, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>The University of Texas Medical Branch - Sealy Center for Structural Biology and Molecular Biophysics, Galveston, TX 77204</wicri:regionArea><placeName><region type="state">Texas</region></placeName></affiliation></author><author><name sortKey="Tautz, Diethard" sort="Tautz, Diethard" uniqKey="Tautz D" first="Diethard" last="Tautz">Diethard Tautz</name><affiliation wicri:level="1"><nlm:aff id="gks1358-AFF1">Max-Planck-Institut - Evolutionsbiologie, Ploen, 24306 Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max-Planck-Institut - Evolutionsbiologie, Ploen</wicri:regionArea><wicri:noRegion>Ploen</wicri:noRegion><wicri:noRegion>Ploen</wicri:noRegion><wicri:noRegion>Ploen</wicri:noRegion></affiliation></author><author><name sortKey="Pozhitkov, Alexander E" sort="Pozhitkov, Alexander E" uniqKey="Pozhitkov A" first="Alexander E." last="Pozhitkov">Alexander E. Pozhitkov</name><affiliation wicri:level="4"><nlm:aff id="gks1358-AFF1">University of Washington, Department of Periodontology, Seattle, WA 98105, USA,</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>University of Washington, Department of Periodontology, Seattle, WA 98105</wicri:regionArea><placeName><region type="state">Washington (État)</region><settlement type="city">Seattle</settlement></placeName><orgName type="university">Université de Washington</orgName></affiliation><affiliation wicri:level="1"><nlm:aff id="gks1358-AFF1">Max-Planck-Institut - Evolutionsbiologie, Ploen, 24306 Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max-Planck-Institut - Evolutionsbiologie, Ploen</wicri:regionArea><wicri:noRegion>Ploen</wicri:noRegion><wicri:noRegion>Ploen</wicri:noRegion><wicri:noRegion>Ploen</wicri:noRegion></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Pozhitkov, A" uniqKey="Pozhitkov A">A Pozhitkov</name></author><author><name sortKey="Noble, Pa" uniqKey="Noble P">PA Noble</name></author><author><name sortKey="Domazet Loso, T" uniqKey="Domazet Loso T">T Domazet-Loso</name></author><author><name sortKey="Nolte, Aw" uniqKey="Nolte A">AW Nolte</name></author><author><name sortKey="Sonnenberg, R" uniqKey="Sonnenberg R">R Sonnenberg</name></author><author><name sortKey="Staehler, P" uniqKey="Staehler P">P Staehler</name></author><author><name sortKey="Beier, M" uniqKey="Beier M">M Beier</name></author><author><name sortKey="Tautz, D" uniqKey="Tautz D">D Tautz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mei, R" uniqKey="Mei R">R Mei</name></author><author><name sortKey="Hubbell, E" uniqKey="Hubbell E">E 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