Bayesian estimates of linkage disequilibrium
Metadatos
Afficher la notice complèteEditorial
Biomed Central
Materia
Bayes theorem Haplotypes Human genome project Humans Likelihood functions Linkage disequilibrium Models Genetic Polymorphism Single nucleotide
Date
2007Referencia bibliográfica
Sebastiani, P.; Abad-Grau, M.M. Bayesian estimates of linkage disequilibrium. BMC Genetics, 8: 36 (2008). [http://hdl.handle.net/10481/31189]
Patrocinador
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].Résumé
[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.