TRAB: Testing Whether Mutation Frequencies Are Above an Unknown Background

Parmigiani Giovanni, Chen Sining and Velculescu Victor E.
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Parmigiani Giovanni: Johns Hopkins University
Chen Sining: Johns Hopkins University
Velculescu Victor E.: Johns Hopkins University

Statistical Applications in Genetics and Molecular Biology, 2008, vol. 7, issue 1, 11

Abstract: To rigorously determine whether a gene or a set of genes have alterations that are involved in carcinogenesis requires a comparison of the prevalence of identified changes to a control mutation frequency present in tumor DNA. To facilitate this task, we develop a testing approach and the associated R library, called TRAB, that evaluates whether the frequency of somatic mutation in a given gene is higher than that observed in a control group of genes. Specifically, we test the null hypothesis that the frequency belongs to a control population of frequencies, against the alternative hypothesis that the frequency is higher. Mutation frequencies in the control group are themselves allowed to be variable. TRAB computes the a posteriori probability and the Bayes factor for the hypothesis using a hierarchical Bayesian approach.

Keywords: hierarchical Bayesian models; mutation analysis (search for similar items in EconPapers)
Date: 2008
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DOI: 10.2202/1544-6115.1277

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