ArticleBMC genomics2008
Strong position-dependent effects of sequence mismatches on signal ratios measured using long oligonucleotide microarrays.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
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- Cycling of Rational Hybridization Chain Reaction To Enable Enzyme-Free DNA-Based Clinical Diagnosis.ACS nano · 2018Article
- Comparison between Proteome and Transcriptome Response in Potato (Solanum tuberosum L.) Leaves Following Potato Virus Y (PVY) Infection.Proteomes · 2017Article
- Species and gene divergence in Littorina snails detected by array comparative genomic hybridization.BMC genomics · 2014Article
- Resolving the polymorphism-in-probe problem is critical for correct interpretation of expression QTL studies.Nucleic acids research · 2013Article
- The illusion of specific capture: surface and solution studies of suboptimal oligonucleotide hybridization.BMC research notes · 2013Article
- Fourteen-genome comparison identifies DNA markers for severe-disease-associated strains of Clostridium difficile.Journal of clinical microbiology · 2011Article
- A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus.BMC genomics · 2011Article
- A comprehensive genetic analysis of candidate genes regulating response to Trypanosoma congolense infection in mice.PLoS neglected tropical diseases · 2010Article
- Hybridization properties of long nucleic acid probes for detection of variable target sequences, and development of a hybridization prediction algorithm.Nucleic acids research · 2010Article
- Array comparative genomic hybridization analysis of Trichoderma reesei strains with enhanced cellulase production properties.BMC genomics · 2010Article
- Gene expression profiling in C57BL/6J and A/J mouse inbred strains reveals gene networks specific for brain regions independent of genetic background.BMC genomics · 2010Article
- Identification of brain transcriptional variation reproduced in peripheral blood: an approach for mapping brain expression traits.Human molecular genetics · 2009Article
- Position dependent mismatch discrimination on DNA microarrays - experiments and model.BMC bioinformatics · 2008Article
- A snapshot of CNVs in the pig genome.PloS one · 2008Article
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6 authors.
Funding
Abstract
backgroundMicroarrays 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 and target strands are known to affect the stability of the probe-target duplex, and hence the strength of the observed signals from microarrays.
resultsWe 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 the maximum 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.
conclusionThe 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]
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