Team Project

MSA Bladder Reference Set Application: Charles Rosser-Hawaii (2014)

MSA Bladder Ref Set App: Rosser (2014)
Feng, ZidingFred Hutchinson Cancer Research Center
IL8, MMP9, A1AT, VEGFA, CA9, APOE, MMP10, SDC1, PAI-1 and ANG.
No design specified.
Prostate and Urologic Cancers Research Group

The goal of this proposal is straightforward. We wish to assay in a discovery set, reference set from EDRN, both PAI-1 and ANG promoters and genes for mutations. Then the results will be confirmed in a test cohort comprised of DNA extracted from fresh frozen tissue (n = 80 BCa patients). DNA from matching buffy coat from these 80 patients will serve as control. Extracted RNA can be assessed for difference in transcription. Furthermore, matched voided urine samples from these 80 patients are available to assess protein levels of PAI-1 and ANG by ELISA in addition to assessing activity of PAI-1 and ANG. At the end, we will link any genetic alteration with changes in RNA, protein and protein activity level as well as clinical features (e.g., age, race, tobacco history, grade, stage and outcomes). This comprehensive study will allow us with certainty to state if there are mutations in the promoters and genes of PAI-1 and ANG that are functional and thus may lead to the growth advantage that we previously demonstrated in our experiments.

Discovery cohort - 200 DNA samples from exfoliated cells (100 BCa and 100 controls) from a reference set at EDRN will be screened via direct PCR and sequencing for mutations with PAI-1 (promoter and exons 1-9) and ANG (promoter and exons 1-3).
Mutational analysis will be assessed using Ion Reporter™ Software located in our Genomic Shared Resource. Fisher’s exact test will be used to assess the association of PAI-1 and ANG genetic alterations with clinicopathologic factors or mutations with each other. A P-value of < 0.05 will be considered to be statistically significant.

No datasets are currently associated with this protocol.

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