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.

Erratum

The original citation for this article published on March 14th 2008 was as follows:

Parmigiani, Giovanni and Chen, Sining (2008) "TRAB: Testing Whether Mutation Frequencies Are Above an Unknown Background," Statistical Applications in Genetics and Molecular Biology: Vol. 7 : Iss. 1, Article 11.
Available at: http://www.bepress.com/sagmb/vol7/iss1/art11

The citation was corrected on April 10th 2008 as follows:

Parmigiani, Giovanni; Chen, Sining; and Velculescu, Victor E. (2008) "TRAB: Testing Whether Mutation Frequencies Are Above an Unknown Background," Statistical Applications in Genetics and Molecular Biology: Vol. 7 : Iss. 1, Article 11.
Available at: http://www.bepress.com/cgi/cview.cgi/sagmb/vol7/iss1/art11

Submitted: January 19, 2007 · Accepted: March 1, 2007 · Published: March 14, 2008

Recommended Citation

Parmigiani, Giovanni; Chen, Sining; and Velculescu, Victor E. (2008) "TRAB: Testing Whether Mutation Frequencies Are Above an Unknown Background," Statistical Applications in Genetics and Molecular Biology: Vol. 7 : Iss. 1, Article 11.
Available at: http://www.bepress.com/sagmb/vol7/iss1/art11