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Mismatches between probe and target sequences have a strong position-dependent effect on signal ratios from aCGH using 60mer oligonucleotide microarrays

Rennie, C.; Noyes, H.A.; Kemp, S.J.; Hulme, H.; Brass, A. and Hoyle, D.C. Mismatches between probe and target sequences have a strong position-dependent effect on signal ratios from aCGH using 60mer oligonucleotide microarrays. In: Genomes to Systems Conference, 17-20 March 2008, Manchester Convention Centre. (Unpublished)

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Abstract

Sequence mismatches between probe and fluorescently-labelled target strands are known to affect the stability of the probe-target duplex formed, and hence the strength of the observed fluorescent signals in microarray experiments. However, the exact effects of sequence mismatches on microarray hybridisations are not well characterised. Array-based Comparative Genomic Hybridisation (aCGH) is a common technique for identifying DNA copy number variations. aCGH data are particularly suitable for analysing the effects of probe-target sequence mismatches because using genomic DNA avoids complications due to the large ranges of intracellular mRNA levels. A previous study provided data for hybridisations comparing three mouse strains to a C57BL/6 reference, using Agilent 60mer oligonucleotide arrays. Sequence mismatches between targets and probes were identified using the Perlegen 8 million mouse SNP dataset, and their effect on log2 signal ratio between test and reference strains was assessed. Observations indicated a strong effect of sequence mismatches on log2 signal ratio, dependent on the number of mismatches and on their position relative to the probe sequence. Ratios for probes with 1 mismatch or 2 mismatches were strongly correlated when probes were matched on the maximum length of perfectly matched sequence between probe and target. An existing model of nucleic acid melting was tested, but predictions did not correspond to these results. Progress has been made in developing a new computational model to reproduce these findings.

Item Type:Conference or Workshop Item (Poster)
Additional Information:Presentation produced by Bovine Trypanosomiasis Consortium
Uncontrolled Keywords:SEQUENCE; microarray; DNA; Number; GENOMIC DNA; Levels; Level; Mouse; Mouse strains; Strains; Strain; Dependent; 1; Model; poster
Subjects:Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Q Science > QH Natural history > QH426 Genetics
Departments, Research Centres and Related Units:Academic Faculties, Institutes and Research Centres > Faculty of Science > Department of Biological Sciences
Related URLs:
Refereed:No
Status:Unpublished
ID Code:661
Deposited On:15 Mar 2011 12:34
Last Modified:21 May 2012 10:20

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