The use of Mx for association and linkage analysis

Abstract

Evidence for genetic linkage, obtained from a correlation between phenotypic similarity and genetic similarity at a specific chromosomal location typically yields a broad genomic region in which a candidate locus might be found. Evidence for association is usually gathered from case control studies and is subject to false positives from phenomena such as population stratification. Data from relatives may be used to distinguish population stratification from genuine allelic effects in an association context. Of special interest is joint linkage and association which may be used for fine mapping because evidence for linkage will be reduced in the presence of evidence for association. This article describes the implementation of these methods using Mx, in both path diagram and script formats, and discusses a number of possible extensions to the model.