A Fast and Accurate Algorithm to Test for Binary Phenotypes and Its Application to PheWAS.

ABSTRACT: The availability of electronic health record (EHR)-based phenotypes allows for genome-wide association analyses in thousands of traits and has great potential to enable identification of genetic variants associated with clinical phenotypes. We can interpret the phenome-wide association study (PheWAS) result for a single genetic variant by observing its association across a landscape of phenotypes. Because a PheWAS can test thousands of binary phenotypes, and most of them have unbalanced or often extremely unbalanced case-control ratios (1:10 or 1:600, respectively), existing methods cannot provide an accurate and scalable way to test for associations. Here, we propose a computationally fast score-test-based method that estimates the distribution of the test statistic by using the saddlepoi

SUBMITTER: Dey R 

PROVIDER: S-EPMC5501775 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature