Rxivist logo

Efficient Multivariate Analysis Algorithms for Longitudinal Genome-wide Association Studies

By Chao Ning, Dan Wang, Lei Zhou, Julong Wei, Yuanxin Liu, Huimin Kang, Shengli Zhang, Xiang Zhou, Shizhong Xu, Jian-Feng Liu

Posted 17 Aug 2018
bioRxiv DOI: 10.1101/394197 (published DOI: 10.1093/bioinformatics/btz304)

Motivation Current 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. Results We 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. Availability and Implementation We 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.

Download data

  • Downloaded 968 times
  • Download rankings, all-time:
    • Site-wide: 27,860
    • In bioinformatics: 3,109
  • Year to date:
    • Site-wide: 64,220
  • Since beginning of last month:
    • Site-wide: 56,180

Altmetric data

Downloads over time

Distribution of downloads per paper, site-wide