- THIS ARTICLE
- Full Text (Rapid PDF)
-
All Versions of this Article:
genetics.105.042978v1
172/4/2583 most recent - Alert me when this article is cited
- Alert me if a correction is posted
- SERVICES
- Similar articles in this journal
- Similar articles in PubMed
- Alert me to new issues of the journal
- Download to citation manager
- Reprints & Permissions
- CITING ARTICLES
- Citing Articles via Google Scholar
- GOOGLE SCHOLAR
- Articles by Greenspan, G. D.
- Articles by Geiger, D.
- Search for Related Content
- PUBMED
- PubMed Citation
- Articles by Greenspan, G. D.
- Articles by Geiger, D.
doi:10.1534/genetics.105.042978
A more recent version of this article appeared on April 1, 2006.
REGULAR RESEARCH PAPERS |
Modeling Haplotype Block Variation using Markov Chains
Gideon D. Greenspan 1* and Dan Geiger 1
1 Technion--Israel Institute of Technology
* To whom correspondence should be addressed. E-mail: gdg{at}cs.technion.ac.il.
Submitted on March 7, 2005
Revised on April 12, 2005
Accepted on 23 November 2005
Models of background variation in genomic regions form the basis of linkage disequilibrium mapping methods. In this work we analyze a background model which 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 which assumes 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.
Key Words: LD mapping, Markov models, haplotype blocks, linkage disequilibrium, recombination hotspots