Localizing putative markers in genetic association studies by incorporating linkage disequilibrium into bayesian hierarchical models.

ABSTRACT:

Objective

Numerous methods have been proposed to model the association between multiple single nucleotide polymorphisms (SNPs) and a phenotype. Often these methods do not explicitly model the information regarding the linkage disequilibrium (LD) between SNPs. Furthermore, many methods shrink the SNP effects towards zero, rather than to an unknown latent gene-level effect.

Methods

We outline the use of bayesian hierarchical models for gene-level analysis that incorporates LD information. Four different bayesian models, with either the inclusion or exclusion of LD information and 'shrinkage' of SNP effects to a latent gene-level effect or zero, were applied to a pharmacogenomic study and simulation STUDY.

Results

We observed that the inclusion of LD information resulted

SUBMITTER: Fridley BL 

PROVIDER: S-EPMC2918651 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature