Adjusting for founder relatedness in a linkage analysis using prior information.

In genetic linkage studies, while the pedigrees are generally known, background relatedness between the founding individuals, assumed by definition to be unrelated, can seriously affect the results of the analysis. Likelihood approaches to relationship estimation from genetic marker data can all be expressed in terms of finding the most likely pedigree connecting the individuals of interest. When the true relationship is the main focus, the set of all possible alternative pedigrees can be too large to consider. However, prior information is often available which, when incorporated in a formal and structured way, can restrict this set to a manageable size thus enabling the calculation of a posterior distribution from which inferences can be drawn. Here, the unknown relationships are more of a nuisance factor than of interest in their own right, so the focus is on adjusting the results of the analysis rather than on direct estimation. In this paper, we show how prior information on founder relationships can be exploited in some applications to generate a set of candidate extended pedigrees. We then weight the relevant pedigree-specific likelihoods by their posterior probabilities to adjust the lod score statistics.