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TRAB: Testing Whether Mutation Frequencies Are Above an Unknown Background

Author

Listed:
  • Parmigiani Giovanni

    (Johns Hopkins University)

  • Chen Sining

    (Johns Hopkins University)

  • Velculescu Victor E.

    (Johns Hopkins University)

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.

Suggested Citation

  • Parmigiani Giovanni & Chen Sining & Velculescu Victor E., 2008. "TRAB: Testing Whether Mutation Frequencies Are Above an Unknown Background," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 7(1), pages 1-11, March.
    • Handle: RePEc:bpj:sagmbi:v:7:y:2008:i:1:n:11
    DOI: 10.2202/1544-6115.1277
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