Characterization of multilocus linkage disequilibrium
Version of Record online: 6 JAN 2005
© 2005 Wiley-Liss, Inc.
Volume 28, Issue 3, pages 193–206, April 2005
How to Cite
Rinaldo, A., Bacanu, S.-A., Devlin, B., Sonpar, V., Wasserman, L. and Roeder, K. (2005), Characterization of multilocus linkage disequilibrium. Genet. Epidemiol., 28: 193–206. doi: 10.1002/gepi.20056
- Issue online: 9 MAR 2005
- Version of Record online: 6 JAN 2005
- Manuscript Accepted: 3 OCT 2004
- Manuscript Received: 25 JUN 2004
- NIH. Grant Number: MH057881
- haplotype block;
- information theory;
- model selection;
- tag SNP
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. Genet. Epidemiol. © 2005 Wiley-Liss, Inc.