Prostate Reference Set Application: William Isaacs-John Hopkins (2010)

Prostate Ref Set App: Isaacs (2010)
Isaacs, WilliamJohns Hopkins University
Feng, ZidingFred Hutchinson Cancer Research Center
14 SNPs
No design specified.
Prostate and Urologic Cancers Research Group

Can SNP genotyping assist in the prediction of biopsy results for prostate cancer.

As an initial quality control for the genotyping data, tests for Hardy-Weinberg equilibrium are performed for each SNP among control subjects using Fisher's exact test. The number of risk alleles of the 14 SNPs, is counted for each subject. Men are classified into eight approximately equal sized groups based on number of risk alleles 8;.7, 8, 9,10,11,12,13, and ~14). Number of risk alleles is modeled as a categorical variable with men who had 11 risk alleles (mode) serving as the 398/2590 (Rev. 06/09) Pags_ Continuation Format Page Program Director/Principallnvestigator (Last, First, Middle): baseline group. ORs for positive biopsy of PCa for men with various combinations of number of risk alleles will be estimated from regression coefficients of these variables in the logistic regression model. Absolute risk will be estimated based on the OR, calibrated incidence rate of PCa for men with the most common number of risk alleles, and mortality rate for all causes excluding PCa in the U.S. The calibrated incidence rates will be calculated based on jOint attributable risk of number of risk alleles estimated from the data and population incidence rates in the U.S. (2006 data). The initial set of 100 samples will allow us to assess the feasibility of this analysis in terms of having sufficient DNA, DNA quality and genotyping call rates and reproducibility. Following completion of this analysis for the first 100 samples additional samples will be requested to increase the power of the study to provide stable positive biopsy risk rates.

No datasets are currently associated with this protocol.

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