SNP imputation bias reduces effect size determination.

ABSTRACT: Imputation is a commonly used technique that exploits linkage disequilibrium to infer missing genotypes in genetic datasets, using a well-characterized reference population. While there is agreement that the reference population has to match the ethnicity of the query dataset, it is common practice to use the same reference to impute genotypes for a wide variety of phenotypes. We hypothesized that using a reference composed of samples with a different phenotype than the query dataset would introduce imputation bias. To test this hypothesis we used GWAS datasets from Amyotrophic Lateral Sclerosis (ALS), Parkinson Disease (PD), and Crohn's Disease (CD). First, we masked and then performed imputation of 100 disease-associated markers and 100 non-associated markers from each study. Two referen

SUBMITTER: Khankhanian P 

PROVIDER: S-EPMC4321633 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature