Using imputed genotype data in the joint score tests for genetic association and gene-environment interactions in case-control studies.

ABSTRACT: Genome-wide association studies (GWAS) are now routinely imputed for untyped single nucleotide polymorphisms (SNPs) based on various powerful statistical algorithms for imputation trained on reference datasets. The use of predicted allele counts for imputed SNPs as the dosage variable is known to produce valid score test for genetic association. In this paper, we investigate how to best handle imputed SNPs in various modern complex tests for genetic associations incorporating gene-environment interactions. We focus on case-control association studies where inference for an underlying logistic regression model can be performed using alternative methods that rely on varying degree on an assumption of gene-environment independence in the underlying population. As increasingly large-scale GWAS

SUBMITTER: Song M 

PROVIDER: S-EPMC5811375 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature