title: The power of two-locus affected sib-pair linkage analysis to detect interacting disease loci.
abstract: It has been shown that two-locus linkage analysis can, for some two-locus disease models, be used to detect effects at disease loci that do not reach significance in a genome scan. However, few examples exist where two-locus linkage has been successfully used to map genes. We study the possible gain in power of affected sib-pair nonparametric two-locus linkage analysis for two-locus models which fulfil the two-locus triangle constraints. Using a new parameterization of the two-locus joint identity-by-descent sharing probabilities we can, for fixed marginal sharing at both of two unlinked disease loci, derive a two-locus distribution such that the power of a two-locus analysis is maximized. In a simulation study we look at two test statistics, the two-locus maximum likelihood score and the correlation between nonparametric linkage scores, and study power as a function of marginal sharing. We show that in a best-case scenario two-locus linkage can have considerable power to detect pairs of interacting loci if there is a moderate increase in allele sharing at one of the two loci, even if there is a very small increase in allele sharing at the other locus. But we also show that the power to detect interacting loci in a two-locus analysis decreases as the marginal sharing at the two loci decreases and for any distribution with a small increase in allele sharing at both loci the power of a two-locus analysis is always low.
authors.affiliation: Department of Statistics, University of California, Berkeley, California, USA. ingileif@stats.ox.ac.uk
authors.forename: Ingileif B
authors.initials: IB
authors.lastname: Hallgrímsdóttir
authors.forename: Terence P
authors.initials: TP
authors.lastname: Speed
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D003198:Computer Simulation; D008040:Genetic Linkage; D006801:Humans; D008957:Models, Genetic; D009679:Nuclear Family; D035781:Siblings