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Open Access Research article

G-spots cause incorrect expression measurement in Affymetrix microarrays

Graham JG Upton1, William B Langdon2 and Andrew P Harrison2*

Author Affiliations

1 Department of Mathematical Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK

2 Departments of Mathematical and Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK

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BMC Genomics 2008, 9:613  doi:10.1186/1471-2164-9-613

Published: 18 December 2008

Abstract

Background

High Density Oligonucleotide arrays (HDONAs), such as the Affymetrix HG-U133A GeneChip, use sets of probes chosen to match specified genes, with the expectation that if a particular gene is highly expressed then all the probes in that gene's probe set will provide a consistent message signifying the gene's presence. However, probes that contain a G-spot (a sequence of four or more guanines) behave abnormally and it has been suggested that these probes are responding to some biochemical effect such as the formation of G-quadruplexes.

Results

We have tested this expectation by examining the correlation coefficients between pairs of probes using the data on thousands of arrays that are available in the NCBI Gene Expression Omnibus (GEO) repository. We confirm the finding that G-spot probes are poorly correlated with others in their probesets and reveal that, by contrast, they are highly correlated with one another. We demonstrate that the correlation is most marked when the G-spot is at the 5' end of the probe.

Conclusion

Since these G-spot probes generally show little correlation with the other members of their probesets they are not fit for purpose and their values should be excluded when calculating gene expression values. This has serious implications, since more than 40% of the probesets in the HG-U133A GeneChip contain at least one such probe. Future array designs should avoid these untrustworthy probes.