Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

TitlePhysico-chemical foundations underpinning microarray and next-generation sequencing experiments
Publication TypeJournal Article
Year of Publication2013
AuthorsHarrison A., Binder H., Buhot A., Burden C.J, Carlon E., Gibas C., Gamble L.J, Halperin A., Hooyberghs J., Kreil D.P, Levicky R., Noble P.A, Ott A., Pettitt B.M, Tautz D., Pozhitkov A.E
JournalNucleic Acids Research
Volume41
Pagination2779-2796
Date PublishedMar
ISBN Number0305-1048
Keywordsaffymetrix-genechips, density oligonucleotide arrays, DNA microarrays, expression arrays, genechip-microarrays, hook-calibration, hybridization isotherms, point mutations, probe design criteria, thermodynamic approach
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 physicochemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized.

DOI10.1093/Nar/Gks1358