Genotype distribution-based inference of collective effects in genome-wide association studies: insights to age-related macular degeneration disease mechanism

BMC Genomics. 2016 Aug 30;17(1):695. doi: 10.1186/s12864-016-2871-3.


Background: Genome-wide association studies provide important insights to the genetic component of disease risks. However, an existing challenge is how to incorporate collective effects of interactions beyond the level of independent single nucleotide polymorphism (SNP) tests. While methods considering each SNP pair separately have provided insights, a large portion of expected heritability may reside in higher-order interaction effects.

Results: We describe an inference approach (discrete discriminant analysis; DDA) designed to probe collective interactions while treating both genotypes and phenotypes as random variables. The genotype distributions in case and control groups are modeled separately based on empirical allele frequency and covariance data, whose differences yield disease risk parameters. We compared pairwise tests and collective inference methods, the latter based both on DDA and logistic regression. Analyses using simulated data demonstrated that significantly higher sensitivity and specificity can be achieved with collective inference in comparison to pairwise tests, and with DDA in comparison to logistic regression. Using age-related macular degeneration (AMD) data, we demonstrated two possible applications of DDA. In the first application, a genome-wide SNP set is reduced into a small number (∼100) of variants via filtering and SNP pairs with significant interactions are identified. We found that interactions between SNPs with highest AMD association were epigenetically active in the liver, adipocytes, and mesenchymal stem cells. In the other application, multiple groups of SNPs were formed from the genome-wide data and their relative strengths of association were compared using cross-validation. This analysis allowed us to discover novel collections of loci for which interactions between SNPs play significant roles in their disease association. In particular, we considered pathway-based groups of SNPs containing up to ∼10, 000 variants in each group. In addition to pathways related to complement activation, our collective inference pointed to pathway groups involved in phospholipid synthesis, oxidative stress, and apoptosis, consistent with the AMD pathogenesis mechanism where the dysfunction of retinal pigment epithelium cells plays central roles.

Conclusions: The simultaneous inference of collective interaction effects within a set of SNPs has the potential to reveal novel aspects of disease association.

Keywords: Age-related macular degeneration; Epistasis; Genome-wide association; Machine learning; Single-nucleotide polymorphism.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Epistasis, Genetic*
  • Gene Frequency
  • Genetic Predisposition to Disease*
  • Genome-Wide Association Study*
  • Genotype
  • Humans
  • Machine Learning
  • Macular Degeneration / genetics*
  • Macular Degeneration / pathology
  • Phenotype
  • Polymorphism, Single Nucleotide / genetics
  • Risk Factors