Standardized Gene Expression Core Facility Development

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DESCRIPTION (provided by applicant): There is a need for sensitive, high throughput, standardized gene expression analysis at the Medical College of Ohio specifically and for the cancer research community in general. Empiric association between gene expression patterns and clinically important phenotypes will provide improved markers to predict cancer behavior and response to treatment with specific agents. In addition, such associations will provide an informed basis for new mechanistic studies aimed at improving cancer prevention, diagnosis and treatment. Microarray (cDNA and/or oligonucleotide) gene expression analysis is a valuable screening tool and for this reason, the Medical College of Ohio currently is in the process of establishing a microarray core facility. However, it is clear that microarray analysis is not sufficiently sensitive, reproducible, or flexible for many clinical applications. Consequently, microarray data generally must be validated in follow-up quantitative gene expression analyses. The group of six NCI sponsored investigators at the Medical College of Ohio join in supporting this application to establish a high throughput, standardized gene expression analysis facility based on standardized RT (StaRT)-PCR. This will be a completely new resource, This group will be joined in Aim 4 by investigators at other institutions who are using microarrays and support the use of StaRT-PCR as a "gold standard" by which they may optimize microarray analysis protocols. This facility will be available to the general research community at low cost. The high reproducibility, sensitivity, and low detection threshold of the StaRT-PCR gene expression method have been validated in multiple independent studies. In a blinded study, expression of ten genes was measured in a common cDNA by four laboratories. The average inter-laboratory correlation of variance (CV) was 0.48, confirming that 2-3 fold differences in gene expression could be detected with confidence. Using microchannel capillary electrophoresis the CV was reduced to 0.26. The Specific Aims of this proposal are as follows. I; establish an automated StaRT-PCR core facility capable of 4,000 gene expression assays/24 hours. AIM 2; Provide this service at low cost to the NCI-funded investigators at MCO as well as interested investigators at other institutions, 3; Develop an annotated gene expression database to service both NCI-funded investigators at MCO as well as other institutions, ,AIM: 4 develop an acceptable method for standardizing microarray data analysis.