Identifying progressive imaging genetic patterns via multi-task sparse canonical correlation analysis: A longitudinal study of the ADNI cohort

Lei Du, Kefei Liu, Lei Zhu, Xiaohui Yao, Shannon L. Risacher, Lei Guo, Andrew J. Saykin, Li Shen

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Motivation: Identifying the genetic basis of the brain structure, function and disorder by using the imaging quantitative traits (QTs) as endophenotypes is an important task in brain science. Brain QTs often change over time while the disorder progresses and thus understanding how the genetic factors play roles on the progressive brain QT changes is of great importance and meaning. Most existing imaging genetics methods only analyze the baseline neuroimaging data, and thus those longitudinal imaging data across multiple time points containing important disease progression information are omitted. Results: We propose a novel temporal imaging genetic model which performs the multi-task sparse canonical correlation analysis (T-MTSCCA). Our model uses longitudinal neuroimaging data to uncover that how single nucleotide polymorphisms (SNPs) play roles on affecting brain QTs over the time. Incorporating the relationship of the longitudinal imaging data and that within SNPs, T-MTSCCA could identify a trajectory of progressive imaging genetic patterns over the time. We propose an efficient algorithm to solve the problem and show its convergence. We evaluate T-MTSCCA on 408 subjects from the Alzheimer's Disease Neuroimaging Initiative database with longitudinal magnetic resonance imaging data and genetic data available. The experimental results show that T-MTSCCA performs either better than or equally to the state-of-the-art methods. In particular, T-MTSCCA could identify higher canonical correlation coefficients and capture clearer canonical weight patterns. This suggests that T-MTSCCA identifies time-consistent and time-dependent SNPs and imaging QTs, which further help understand the genetic basis of the brain QT changes over the time during the disease progression.

Original languageEnglish (US)
Article numberbtz320
Pages (from-to)i474-i483
JournalBioinformatics
Volume35
Issue number14
DOIs
StatePublished - Jul 15 2019

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Canonical Correlation Analysis
Longitudinal Study
Longitudinal Studies
Imaging
Imaging techniques
Brain
Neuroimaging
Single nucleotide Polymorphism
Nucleotides
Polymorphism
Single Nucleotide Polymorphism
Progression
Disorder
Disease Progression
Canonical Correlation
Alzheimer's Disease
Endophenotypes
Magnetic Resonance Imaging
Structure-function
Genetic Models

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Identifying progressive imaging genetic patterns via multi-task sparse canonical correlation analysis : A longitudinal study of the ADNI cohort. / Du, Lei; Liu, Kefei; Zhu, Lei; Yao, Xiaohui; Risacher, Shannon L.; Guo, Lei; Saykin, Andrew J.; Shen, Li.

In: Bioinformatics, Vol. 35, No. 14, btz320, 15.07.2019, p. i474-i483.

Research output: Contribution to journalArticle

Du, Lei ; Liu, Kefei ; Zhu, Lei ; Yao, Xiaohui ; Risacher, Shannon L. ; Guo, Lei ; Saykin, Andrew J. ; Shen, Li. / Identifying progressive imaging genetic patterns via multi-task sparse canonical correlation analysis : A longitudinal study of the ADNI cohort. In: Bioinformatics. 2019 ; Vol. 35, No. 14. pp. i474-i483.
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