Association studies with imputed variants using expectation-maximization likelihood-ratio tests.

ABSTRACT: Genotype imputation has become standard practice in modern genetic studies. As sequencing-based reference panels continue to grow, increasingly more markers are being well or better imputed but at the same time, even more markers with relatively low minor allele frequency are being imputed with low imputation quality. Here, we propose new methods that incorporate imputation uncertainty for downstream association analysis, with improved power and/or computational efficiency. We consider two scenarios: I) when posterior probabilities of all potential genotypes are estimated; and II) when only the one-dimensional summary statistic, imputed dosage, is available. For scenario I, we have developed an expectation-maximization likelihood-ratio test for association based on posterior probabilities.

SUBMITTER: Huang KC 

PROVIDER: S-EPMC4226494 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature