An increasingly common way to find answers to gene expression is by microarray. Oligonucleotide microarrays allow researchers to examine the relative expression level of thousands of genes simultaneously. If this technology is reliable, it can provide a huge insight to the regulation of genes for a given situation. Specifically, I examined the reliability of Affymetrix short oligonucleotide arrays in measuring relative difference of gene expression between two different inbred mouse strains.

Microarrays measure the amount of gene expressed by the amount of complimentary DNA (cDNA) that anneals to a complimentary sequence on the chip. But different inbred strains are not genetically identical. In addition to other possible genetic differences, they may have one nucleotide mismatches. These are called single nucleotide polymorphisms or SNPs. If a SNP were to occur in the target sequence (the part of the gene that anneals to the microarray) would that affect the annealing of the cDNA to the array enough to alter the perceived relative expression of the gene?

In order to answer this question I found genes that were differentially expressed in a manner that suggested that the difference could be a false positive caused by SNPs: genes for which a difference in expression was reported regardless of cellular environment. I selected three candidate genes from genes that were differentially expressed in a consistent manner in saline-treated animals of the two strains across all brain regions examined (the prefrontal cortex, the nucleus accumbens and the ventral tegmental area.)

For each selected gene, real time reverse transcriptase polymerase chain reaction showed a different fold change in gene expression than that predicted by the microarray data, suggesting that polymorphisms did have a significant effect on the validity of Affymetrix microarrays.

Examination of the individual probes used for each gene supports the evidence gathered from the PCR experiments.

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