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Strong position-dependent effects of sequence mismatches on signal ratios measured using long oligonucleotide microarrays

Rennie, Catriona; Noyes, Harry A.; Kemp, Stephen J.; Hulme, Helen; Brass, Andy and Hoyle, David C (2008) Strong position-dependent effects of sequence mismatches on signal ratios measured using long oligonucleotide microarrays. BMC Genomics, 9 . Article Number: 317. ISSN 1471-2164

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Abstract

Background: Microarrays are an important and widely used tool. Applications include capturing genomic DNA for high-throughput sequencing in addition to the traditional monitoring of gene expression and identifying DNA copy number variations. Sequence mismatches between probe andtarget strands are known to affect the stability of the probe-target duplex, and hence the strength of the observed signals from microarrays. Results: We describe a large-scale investigation of microarray hybridisations to murine probes with known sequence mismatches, demonstrating that the effect of mismatches is strongly position-dependent and for small numbers of sequence mismatches is correlated with themaximum length of perfectly matched probe-target duplex. Length of perfect match explained 43% of the variance in log2 signal ratios between probes with one and two mismatches. The correlation with maximum length of perfect match does not conform to expectations based on considering the effect of mismatches purely in terms of reducing the binding energy. However, it can be explained qualitatively by considering the entropic contribution to duplex stability from configurations of differing perfect match length. Conclusion: The results of this study have implications in terms of array design and analysis. They highlight the significant effect that short sequence mismatches can have upon microarray hybridisation intensities even for long oligonucleotide probes.All microarray data presented in this study are available from the GEO database [1], under accession number [GEO: GSE9669]

Item Type:Article
Additional Information:Published: 3 July 2008. 11 pages (page numbers not for citation purposes).
Uncontrolled Keywords:genomic DNA; DNA; gene; gene expression; murine; microarray hybridisation; mismatches; probe-target duplex; oligonucleotide probes; array design and analysis; perfect match; entropic contribution
Subjects:Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Q Science > QH Natural history > QH426 Genetics
Q Science > QH Natural history > QH301 Biology
Departments, Research Centres and Related Units:Academic Faculties, Institutes and Research Centres > Faculty of Science > Department of Biological Sciences
DOI:10.1186/1471-2164-9-317
Publisher's Statement:© 2008 Rennie et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Please see link in Related URL field for more information.
Related URLs:
Refereed:Yes
Status:Published
ID Code:891
Deposited On:08 Apr 2009 12:08
Last Modified:19 May 2011 19:49

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