Binary Trait Analysis

Quantitative trait locus (QTL) mapping methodology for continuous normally distributed traits is the subject of much attention in the literature. Binary trait locus (BTL) mapping in experimental populations has received much less attention. BTL are thought of as one or two loci of major effect that are primarily responsible for the binary trait of interest. In the case of incomplete penetrance, a binary trait by definition has only two possible values, and the penetrance parameter is restricted to values between zero and one.

We use a general probability model based on classical transmission genetics to develop a likelihood for the binary phenotype and to estimate recombination and penetrance for multiple BTL under complex genetic models.

A new SAS procedure, PROC BTL, has been developed and is freely available by filling out the form at the bottom of this page. PROC BTL includes model selection for a wide range of model selection criteria and implements all of the standard model selection techniques.

Full BTL documentation

Publications supported by this project:

• McIntyre, L.M., Martin, E.R., Simonsen, K.L., Kaplan, N.L. 2000.Circumventing multiple testing: a multilocus Monte Carlo approach to testing for association. Genet Epidemiol. 19: 18-29.
• McIntyre, L., Coffman, C., Doerge, R. 2001. Detection and Location of Single Binary Trait Loci in Experimental Populations. Genetical Research. 78:79-92.
  >Single gene analyses documentation and software for QTL cartographer
• Coffman, C., Doerge, R., Wayne, M., McIntyre, L.M. 2003.Intersection tests for single marker QTL analysis can be more powerful than two marker QTL analysis. BMC Genetics 4:10.
• Simonsen,K. 2003. A General Probability Model for Binary Trait Loci. Technical Report Department of Statistics, Purdue University.
• Coffman, C., Doerge, R.W., Simonsen, K., Nichols, K., Duarte, C., Wolfinger, R., McIntyre, L.M. 2005. An effective model selection strategy for detecting multiple BTL. Genetics 170:1281-1297.
  

To receive your free copy of PROC BTL please fill out the below request form: