Efficient Multivariate Analysis Algorithms for Longitudinal Genome-wide Association Studies

MotivationCurrent dynamic phenotyping system introduces time as an extra dimension to genome-wide association studies (GWAS), which helps to explore the mechanism of dynamical genetic control for complex longitudinal traits. However, existing methods for longitudinal GWAS either ignore the covariance among observations of different time points or encounter computational efficiency issues.\n\nResultsWe herein developed efficient genome-wide multivariate association algorithms (GMA) for longitudinal data. In contrast to existing univariate linear mixed model analyses, the proposed new method has improved statistic power for association detection and computational speed. In addition, the new method can analyze unbalanced longitudinal data with thousands of individuals and more than ten thousand records within a few hours. The corresponding time for balanced longitudinal data is just a few minutes.\n\nAvailability and ImplementationWe wrote a software package to implement the efficient algorithm named GMA (https://github.com/chaoning/GMA), which is available freely for interested users in relevant fields.