A method and program for estimating graphical models for linkage disequilibrium that scale linearly with the number of loci, and their application to gene drop simulation.

Abstract

Efficient models for genetic linkage disequilibrium (LD) are needed to enable appropriate statistical analysis of the dense, genome-wide single nucleotide polymorphism assays currently available. Estimation of graphical models for LD within a restricted class of decomposable models is shown to be possible using computer time and storage that scale linearly with the number of loci. Programs for estimation and for simulating from these models on a whole-genome basis are described and provided. Java classes and source code for IntervalLD and GeneDrops are freely available over the internet at http://bioinformatics.med.utah.edu/~alun.