Abstract

As more genetic loci are genotyped simultaneously and as the interest in effects of combinations of loci increases, the need for more powerful analysis methods is increased. In the present paper we present a method aimed at increasing the power of likelihood ratio tests for case-control studies investigating possible two-locus effects. The method is based on the notion that the expected effect pattern of one locus, as well as the expected pattern of a penetrance matrix representing the effect of two loci, is a monotone one. By using an algorithm for making the estimated penetrance matrix monotone, the alternative hypothesis is restricted to monotone penetrance matrices only. The evaluation of the likelihood ratio tests for several underlying monotone models shows that the power is substantially increased by using a monotone alternative as compared to when an unrestricted alternative is used.

Submitted: January 7, 2008 · Accepted: May 20, 2008 · Published: June 10, 2008

Recommended Citation

Henningsson, Susanne and Nilsson, Staffan I. (2008) "Detecting Two-Locus Gene-Gene Effects Using Monotonisation of the Penetrance Matrix," Statistical Applications in Genetics and Molecular Biology: Vol. 7 : Iss. 1, Article 17.
DOI: 10.2202/1544-6115.1343
Available at: http://www.bepress.com/sagmb/vol7/iss1/art17