Genotype imputation in case-only studies of gene-environment interaction: validity and power.

ABSTRACT: Case-only (CO) studies are a powerful means to uncover gene-environment (G × E) interactions for complex human diseases. Moreover, such studies may in principle also draw upon genotype imputation to increase statistical power even further. However, genotype imputation usually employs healthy controls such as the Haplotype Reference Consortium (HRC) data as an imputation base, which may systematically perturb CO studies in genomic regions with main effects upon disease risk. Using genotype data from 719 German Crohn Disease (CD) patients, we investigated the level of imputation accuracy achievable for single nucleotide polymorphisms (SNPs) with or without a genetic main effect, and with varying minor allele frequency (MAF). Genotypes were imputed from neighbouring SNPs at different levels o

SUBMITTER: Aleknonyte-Resch M 

PROVIDER: S-EPMC8263402 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature