@misc{10481/31189,
year = {2007},
url = {http://hdl.handle.net/10481/31189},
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.},
organization = {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},
keywords = {Haplotypes},
keywords = {Human genome project},
keywords = {Humans},
keywords = {Likelihood functions},
keywords = {Linkage disequilibrium},
keywords = {Models},
keywords = {Genetic},
keywords = {Polymorphism},
keywords = {Single nucleotide},
title = {Bayesian estimates of linkage disequilibrium},
author = {Sebastiani, Paola and Abad Grau, María Del Mar},
}