Joint sparse canonical correlation analysis for detecting differential imaging genetics modules

Bioinformatics. 2016 Nov 15;32(22):3480-3488. doi: 10.1093/bioinformatics/btw485. Epub 2016 Jul 27.


Motivation: Imaging genetics combines brain imaging and genetic information to identify the relationships between genetic variants and brain activities. When the data samples belong to different classes (e.g. disease status), the relationships may exhibit class-specific patterns that can be used to facilitate the understanding of a disease. Conventional approaches often perform separate analysis on each class and report the differences, but ignore important shared patterns.

Results: In this paper, we develop a multivariate method to analyze the differential dependency across multiple classes. We propose a joint sparse canonical correlation analysis method, which uses a generalized fused lasso penalty to jointly estimate multiple pairs of canonical vectors with both shared and class-specific patterns. Using a data fusion approach, the method is able to detect differentially correlated modules effectively and efficiently. The results from simulation studies demonstrate its higher accuracy in discovering both common and differential canonical correlations compared to conventional sparse CCA. Using a schizophrenia dataset with 92 cases and 116 controls including a single nucleotide polymorphism (SNP) array and functional magnetic resonance imaging data, the proposed method reveals a set of distinct SNP-voxel interaction modules for the schizophrenia patients, which are verified to be both statistically and biologically significant.

Availability and implementation: The Matlab code is available at CONTACT: wyp@tulane.eduSupplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • Brain Mapping*
  • Brain*
  • Genetic Variation
  • Humans
  • Magnetic Resonance Imaging*
  • Polymorphism, Single Nucleotide
  • Schizophrenia