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Discovering a
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biomarker
A scientist is trying to identify a new genetic biomarker for HER2/neu negative stage I breast cancer patients. Using a caGrid-aware client, the scientist queries for HER2/neu negative tissue specimens of Stage I breast cancer patients at LCCC that also have corresponding microarray experiments. Analysis of the microarray experiments identify genes that are significantly over-expressed and under-expressed in a number of cases. The scientist decides that these results are significant, and related literature suggest a hypothesis that gene A may serve as a biomarker in HER2/neu negative Stage I breast cancer. To validate this hypothesis in a significant number of cases the scientist needs a larger data set, so the scientist queries for all the HER2/neu negative specimens of Stage I breast cancer patients with corresponding microarray data and also for appropriate control data from other cancer centers. After retrieving the microarray experiments the scientist analyzes the data for over-expression of genes A.
Finding
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biomaterial to
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validate a
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biomarker
In scenario 1, the scientist has validated a biomarker based on available microarray experiments provided by various cancer centers. Now, the scientist would like to request biomaterial in the form of formalin-fixed, paraffin embedded tissue specimens from patients with the appropriate clinical outcomes. The scientist would like to validate the genetic biomarker in a different series of cases, this time using a different technique such as immunohistochemistry. The scientist queries for the presence of appropriate tissue using a caGrid-aware client and for the appropriate contact information of the person(s) responsible for the tissue repository. The scientist contacts the person(s) to begin the protocol for retrieving biomaterials.
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