Mixed logistic regression in genome-wide association studies.

ABSTRACT:

Background

Mixed linear models (MLM) have been widely used to account for population structure in case-control genome-wide association studies, the status being analyzed as a quantitative phenotype. Chen et al. proved in 2016 that this method is inappropriate in some situations and proposed GMMAT, a score test for the mixed logistic regression (MLR). However, this test does not produces an estimation of the variants' effects. We propose two computationally efficient methods to estimate the variants' effects. Their properties and those of other methods (MLM, logistic regression) are evaluated using both simulated and real genomic data from a recent GWAS in two geographically close population in West Africa.

Results

We show that, when the disease prevalence differs between pop

SUBMITTER: Milet J 

PROVIDER: S-EPMC7684894 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature