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Please use this identifier to cite or link to this item: http://hdl.handle.net/10481/31189

Title: Bayesian estimates of linkage disequilibrium
Authors: Sebastiani, Paola
Abad-Grau, María M.
Issue Date: 2007
Abstract: [Background] The maximum likelihood estimator of D' – a standard measure of linkage disequilibrium – is biased toward disequilibrium, and the bias is particularly evident in small samples and rare haplotypes. [Results] This paper proposes a Bayesian estimation of D' to address this problem. The reduction of the bias is achieved by using a prior distribution on the pair-wise associations between single nucleotide polymorphisms (SNP)s that increases the likelihood of equilibrium with increasing physical distances between pairs of SNPs. We show how to compute the Bayesian estimate using a stochastic estimation based on MCMC methods, and also propose a numerical approximation to the Bayesian estimates that can be used to estimate patterns of LD in large datasets of SNPs. [Conclusion] Our Bayesian estimator of D' corrects the bias toward disequilibrium that affects the maximum likelihood estimator. A consequence of this feature is a more objective view about the extent of linkage disequilibrium in the human genome, and a more realistic number of tagging SNPs to fully exploit the power of genome wide association studies.
Sponsorship: Research supported by NIH/NHLBI grant R21 HL080463-01, NIH/NIDDK 1R01DK069646-01A1 and the Spanish research program [projects TIN2004-06204-C03-02 and TIN2005-02516].
Publisher: Biomed Central
Keywords: Bayes theorem
Human genome project
Likelihood functions
Linkage disequilibrium
Single nucleotide
URI: http://hdl.handle.net/10481/31189
ISSN: 1471-2156
Rights : Creative Commons Attribution-NonCommercial-NoDerivs 3.0 License
Citation: Sebastiani, P.; Abad-Grau, M.M. Bayesian estimates of linkage disequilibrium. BMC Genetics, 8: 36 (2008). [http://hdl.handle.net/10481/31189]
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