Physico-chemical foundations underpinning microarray and next-generation sequencing experiments
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 o...
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| Published in | Nucleic acids research Vol. 41; no. 5; pp. 2779 - 2796 |
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| Main Authors | , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford University Press
01.03.2013
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| Subjects | |
| Online Access | Get full text |
| ISSN | 0305-1048 1362-4962 1362-4954 1362-4962 |
| DOI | 10.1093/nar/gks1358 |
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| 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. |
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| AbstractList | 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. 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.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. |
| Author | Binder, H. Pettitt, B. M. Harrison, A. Burden, C. J. Ott, A. Halperin, A. Noble, P. A. Buhot, A. Pozhitkov, A. E. Gamble, L. J. Carlon, E. Kreil, D. P. Tautz, D. Levicky, R. Gibas, C. Hooyberghs, J. |
| AuthorAffiliation | 1 University of Essex-Mathematical Sciences, Colchester CO4 3SQ, Essex, United Kingdom, 2 University Leipzig, Interdisciplinary Center for Bioinformatics, Leipzig, D-4107, Germany, 3 SPrAM (UMR 5819: CEA, CNRS, UJF), INAC, CEA Grenoble, 17 rue des Martyrs, 38054 Grenoble cedex 9, France, 4 Centre for Bioinformation Science, Mathematical Sciences Institute Building 27 Australian National University, Canberra, Australian Capital Territory 0200, Australia, 5 K.U. Leuven - Physics, Celestijnenlaan 200D B-3000 Leuven, Belgium, 6 University of North Carolina at Charlotte-Bioinformatics Research Center, Charlotte, NC 28223-0001, USA, 7 University of Washington-Bioengineering, Seattle, WA 98195, USA, 8 University of Grenoble - National Center for Scientific Research, 38041, Grenoble, France, 9 Flemish Institute for Technological Research (VITO) - Toxicology, Boeretang 200, Mol 2400, Belgium, 10 Universität für Bodenkultur Wien - Biotechnologie, Wien, Austria, 11 Life Sciences, University of Wa |
| AuthorAffiliation_xml | – name: 1 University of Essex-Mathematical Sciences, Colchester CO4 3SQ, Essex, United Kingdom, 2 University Leipzig, Interdisciplinary Center for Bioinformatics, Leipzig, D-4107, Germany, 3 SPrAM (UMR 5819: CEA, CNRS, UJF), INAC, CEA Grenoble, 17 rue des Martyrs, 38054 Grenoble cedex 9, France, 4 Centre for Bioinformation Science, Mathematical Sciences Institute Building 27 Australian National University, Canberra, Australian Capital Territory 0200, Australia, 5 K.U. Leuven - Physics, Celestijnenlaan 200D B-3000 Leuven, Belgium, 6 University of North Carolina at Charlotte-Bioinformatics Research Center, Charlotte, NC 28223-0001, USA, 7 University of Washington-Bioengineering, Seattle, WA 98195, USA, 8 University of Grenoble - National Center for Scientific Research, 38041, Grenoble, France, 9 Flemish Institute for Technological Research (VITO) - Toxicology, Boeretang 200, Mol 2400, Belgium, 10 Universität für Bodenkultur Wien - Biotechnologie, Wien, Austria, 11 Life Sciences, University of Warwick, Coventry CV4 7AL, UK 12 Polytechnic Institute of New York University - Chemical and Biological Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA, 13 Alabama State University - PhD Program in Microbiology, 325, Montgomery, AL 36101-0271, USA, 14 University of Washington, Department of Periodontology, Seattle, WA 98105, USA, 15 Universitaet des Saarlandes - Biologische Experimentalphysic, Saarbruecken, D-66041 Germany, 16 The University of Texas Medical Branch - Sealy Center for Structural Biology and Molecular Biophysics, Galveston, TX 77204, USA and 17 Max-Planck-Institut - Evolutionsbiologie, Ploen, 24306 Germany |
| Author_xml | – sequence: 1 givenname: A. surname: Harrison fullname: Harrison, A. – sequence: 2 givenname: H. surname: Binder fullname: Binder, H. – sequence: 3 givenname: A. surname: Buhot fullname: Buhot, A. – sequence: 4 givenname: C. J. surname: Burden fullname: Burden, C. J. – sequence: 5 givenname: E. surname: Carlon fullname: Carlon, E. – sequence: 6 givenname: C. surname: Gibas fullname: Gibas, C. – sequence: 7 givenname: L. J. surname: Gamble fullname: Gamble, L. J. – sequence: 8 givenname: A. surname: Halperin fullname: Halperin, A. – sequence: 9 givenname: J. surname: Hooyberghs fullname: Hooyberghs, J. – sequence: 10 givenname: D. P. surname: Kreil fullname: Kreil, D. P. – sequence: 11 givenname: R. surname: Levicky fullname: Levicky, R. – sequence: 12 givenname: P. A. surname: Noble fullname: Noble, P. A. – sequence: 13 givenname: A. surname: Ott fullname: Ott, A. – sequence: 14 givenname: B. M. surname: Pettitt fullname: Pettitt, B. M. – sequence: 15 givenname: D. surname: Tautz fullname: Tautz, D. – sequence: 16 givenname: A. E. surname: Pozhitkov fullname: Pozhitkov, A. E. |
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| Snippet | Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases,... |
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| SubjectTerms | Algorithms Base Pairing Bioengineering Biomaterials Calibration DNA DNA - chemistry DNA - genetics DNA Probes DNA Probes - chemistry DNA Probes - genetics High-Throughput Nucleotide Sequencing Humans Image Processing, Computer-Assisted Life Sciences Models, Biological Nucleic Acid Hybridization Nucleic Acid Hybridization - methods Oligonucleotide Array Sequence Analysis Surface Properties Survey and Summaries Thermodynamics |
| Title | Physico-chemical foundations underpinning microarray and next-generation sequencing experiments |
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