title: Characterization of multilocus linkage disequilibrium.
abstract: Linkage disequilibrium (LD) in the human genome, often measured as pairwise correlation between adjacent markers, shows substantial spatial heterogeneity. Congruent with these results, studies have found that certain regions of the genome have far less haplotype diversity than expected if the alleles at multiple markers were independent, while other sets of adjacent markers behave almost independently. Regions with limited haplotype diversity have been described as "blocked" or "haplotype blocks." In this article, we propose a new method that aims to distinguish between blocked and unblocked regions in the genome. Like some other approaches, the method analyses haplotype diversity. Unlike other methods, it allows for adjacent, distinct blocks and also multiple, independent single nucleotide polymorphisms (SNPs) separating blocks. Based on an approximate likelihood model and a parsimony criterion to penalize for model complexity, the method partitions a genomic region into blocks relatively quickly, and simulations suggest that its partitions are accurate. We also propose a new, efficient method to select SNPs for association analysis, namely tag SNPs. These methods compare favorably to similar blocking and tagging methods using simulations.
authors.affiliation: Department of Statistics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Rinaldo
authors.forename: Silviu-Alin
authors.initials: SA
authors.lastname: Bacanu
authors.forename: B
authors.initials: B
authors.lastname: Devlin
authors.forename: Vibhor
authors.initials: V
authors.lastname: Sonpar
authors.forename: Larry
authors.initials: L
authors.lastname: Wasserman
authors.forename: Kathryn
authors.initials: K
authors.lastname: Roeder
mesh_terms: D000465:Algorithms; D000483:Alleles; D005819:Genetic Markers; D015894:Genome, Human; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide
chemical_list: D005819:Genetic Markers