On a family-based haplotype pattern mining method for linkage disequilibrium mapping

Linkage disequilibrium mapping is an important tool in disease gene mapping. Recently, Toivonen et al. [1] introduced a haplotype mining (HPM) method that is applicable to data consisting of unrelated high-risk and normal haplotypes. The HPM method orders haplotypes by their strength of association with trait values, and uses all haplotypes exceeding a given threshold of strength of association to predict the gene location. In this study, we extend the HPM method to pedigree data by measuring the strength of association between a haplotype and quantitative traits of interest using the Quantitative Pedigree Disequilibrium Test proposed by Zhang et al. [2]. This family-based HPM (F-HPM) method can incorporate haplotype information across a set of markers and allow both missing marker data and ambiguous haplotype information. We use a simulation procedure to evaluate the statistical significance of the patterns identified from the F-HPM method. When the F-HPM method is applied to analyze the sequence data from the seven candidate genes in the simulated data sets in the 12th Genetic Analysis Workshop, the association between genes and traits can be detected with high power, and the estimated locations of the trait loci are close to the true sites.