ArticleGenetics2006
Modeling haplotype block variation using Markov chains.
Article in Genetics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Haplotype block partitioning as a tool for dimensionality reduction in SNP association studies.BMC genomics · 2008Article
- High density linkage disequilibrium maps of chromosome 14 in Holstein and Angus cattle.BMC genetics · 2008Article
- Inference of the haplotype effect in a matched case-control study using unphased genotype data.The international journal of biostatistics · 2008Article
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Authors and funding
2 authors.
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Abstract
Models of background variation in genomic regions form the basis of linkage disequilibrium mapping methods. In this work we analyze a background model that groups SNPs into haplotype blocks and represents the dependencies between blocks by a Markov chain. We develop an error measure to compare the performance of this model against the common model that assumes that blocks are independent. By examining data from the International Haplotype Mapping project, we show how the Markov model over haplotype blocks is most accurate when representing blocks in strong linkage disequilibrium. This contrasts with the independent model, which is rendered less accurate by linkage disequilibrium. We provide a theoretical explanation for this surprising property of the Markov model and relate its behavior to allele diversity.
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