Bayesian estimates of linkage disequilibrium Sebastiani, Paola Abad Grau, María Del Mar Bayes theorem Haplotypes Human genome project Humans Likelihood functions Linkage disequilibrium Models Genetic Polymorphism Single nucleotide [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. 2014-04-02T09:39:33Z 2014-04-02T09:39:33Z 2007 info:eu-repo/semantics/article Sebastiani, P.; Abad-Grau, M.M. Bayesian estimates of linkage disequilibrium. BMC Genetics, 8: 36 (2008). [http://hdl.handle.net/10481/31189] 1471-2156 doi: 10.1186/1471-2156-8-36 http://hdl.handle.net/10481/31189 eng http://creativecommons.org/licenses/by-nc-nd/3.0/ info:eu-repo/semantics/openAccess Creative Commons Attribution-NonCommercial-NoDerivs 3.0 License Biomed Central