Longitudinal genotype-phenotype association study through temporal structure auto-learning predictive model

Xiaoqian Wang, Jingwen Yan, Xiaohui Yao, Sungeun Kim, Kwangsik Nho, Shannon L. Risacher, Andrew J. Saykin, Li Shen, Heng Huang

Research output: Contribution to journalArticle

2 Scopus citations


With the rapid development of high-throughput genotyping and neuroimaging techniques, imaging genetics has drawn significant attention in the study of complex brain diseases such as Alzheimer's disease (AD). Research on the associations between genotype and phenotype improves the understanding of the genetic basis and biological mechanisms of brain structure and function. AD is a progressive neurodegenerative disease; therefore, the study on the relationship between single nucleotide polymorphism (SNP) and longitudinal variations of neuroimaging phenotype is crucial. Although some machine learning models have recently been proposed to capture longitudinal patterns in genotype-phenotype association studies, most machine-learning models base the learning on fixed structure among longitudinal prediction tasks rather than automatically learning the interrelationships. In response to this challenge, we propose a new automated time structure learning model to automatically reveal the longitudinal genotype-phenotype interactions and exploits such learned structure to enhance the phenotypic predictions. We proposed an efficient optimization algorithm for our model and provided rigorous theoretical convergence proof. We performed experiments on the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort for longitudinal phenotype prediction, including 3123 SNPs and 2 biomarkers (Voxel-Based Morphometry and FreeSurfer). The empirical results validate that our proposed model is superior to the counterparts. In addition, the best SNPs identified by our model have been replicated in the literature, which justifies our prediction.

Original languageEnglish (US)
Pages (from-to)809-824
Number of pages16
JournalJournal of Computational Biology
Issue number7
StatePublished - Jul 2018


  • Alzheimer's disease
  • genotype-phenotype association prediction
  • longitudinal study
  • low-rank model
  • temporal structure auto-learning

ASJC Scopus subject areas

  • Modeling and Simulation
  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics

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