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Experimental Selection and Performance of 60-mer Oligonucleotide Probes for Profiling Global Gene Expression

Abstract: Synopsis: Agilent has developed a novel experimental method for the selection and validation of highly specific oligonucleotide microarray probes. This probe optimization strategy is based on the assumption that, if multiple probes for a particular gene are specific for that gene, then they will show similar differential expression behavior. Optimized 60-mer probes to represent genes are selected from clusters of computationally determined candidate probes that perform similarly across a number of differential gene expression experiments. This method also enables verification of computationally predicted gene assemblies. Agilent’s Human 1A Oligo microarray consists of 88% experimentally validated optimized probes that hybridize to all known splice-variants of the genes to which they were designed. Data are presented which demonstrate the power of this experimental method for selection of microarray probes which provide extremely accurate and reliable gene expression data.

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