Comparison of robust tests for genetic association analysis incorporating uncertain genotype

Genome-wide association studies are effective in investigating the loci related with complex diseases. Sometimes, the genotype is not exactly decoded and only genotype probability is obtained. In this case, F-test based on imputed genotype is usually used for the association analysis. Simulations show that existing methods such as the dosage test have poor performance when the genetic model is misspecified. In this study, we develop a robust test to detect the association of a disease and genetic loci while the genotype is uncertain and the genetic model is unknown.