Summary statistics-based association test for identifying the pleiotropic effects with set of genetic variants

MOTIVATION: Traditional genome-wide association study focuses on testing one-to-one relationship between genetic variants and complex human diseases or traits. While its success in the past decade, this one-to-one paradigm lacks efficiency because it does not utilize the information of intrinsic genetic structure and pleiotropic effects. Due to privacy reasons, only summary statistics of current genome-wide association study data are publicly available. Existing summary statistics-based association tests do not consider covariates for regression model, while adjusting for covariates including population stratification factors is a routine issue. RESULTS: In this work, we first derive the correlation coefficients between summary Wald statistics obtained from linear regression model with covariates. Then, a new test is proposed by integrating three-level information including the intrinsic genetic structure, pleiotropy, and the potential information combinations. Extensive simulations demonstrate that the proposed test outperforms three other existing methods under most of the considered scenarios. Real data analysis of polyunsaturated fatty acids further shows that the proposed test can identify more genes than the compared existing methods. AVAILABILITY AND IMPLEMENTATION: Code is available at https://github.com/bschilder/ThreeWayTest.