Set-based joint test of interaction between SNPs in the VEGF pathway and exogenous estrogen finds association with age-related macular degeneration

Monique D. Courtenay, William H. Cade, Stephen G. Schwartz, Jaclyn L. Kovach, Anita Agarwal, Gaofeng Wang, Jonathan L. Haines, Margaret A. Pericak-Vance, William K. Scott

Research output: Contribution to journalArticlepeer-review

4 Scopus citations

Abstract

PURPOSE. Age-related macular degeneration (AMD) is the leading cause of irreversible visual loss in developed countries. Its etiology includes genetic and environmental factors. Although VEGFA variants are associated with AMD, the joint action of variants within the VEGF pathway and their interaction with nongenetic factors have not been investigated. METHODS. Affymetrix 6.0 chipsets were used to genotype 668,238 single nucleotide polymorphisms (SNPs) in 1207 AMD cases and 686 controls. Environmental exposures were collected by questionnaire. A set-based test was conducted using the χ2 statistic at each SNP derived from Kraft's two degree of freedom (2df) joint test. Pathway- and gene-based test statistics were calculated as the mean of all independent SNP statistics. Phenotype labels were permuted 10,000 times to generate an empirical P value. RESULTS. While a main effect of the VEGF pathway was not identified, the pathway was associated with neovascular AMD in women when accounting for birth control pill (BCP) use (P = 0.017). Analysis of VEGF's subpathways showed that SNPs in the proliferation subpathway were associated with neovascular AMD (P = 0.029) when accounting for BCP use. Nominally significant genes within this subpathway were also observed. Stratification by BCP use revealed novel significant genetic effects in women who had taken BCPs. CONCLUSIONS. These results illustrate that some AMD genetic risk factors may be revealed only when complex relationships among risk factors are considered. This shows the utility of exploring pathways of previously associated genes to find novel effects. It also demonstrates the importance of incorporating environmental exposures in tests of genetic association at the SNP, gene, or pathway level.

Original languageEnglish (US)
Pages (from-to)4873-4879
Number of pages7
JournalInvestigative Ophthalmology and Visual Science
Volume55
Issue number8
DOIs
StatePublished - Aug 8 2014

Keywords

  • Age-related macular degeneration
  • Candidate genes
  • Case-control study
  • Epidemiology
  • Statistics

ASJC Scopus subject areas

  • Ophthalmology
  • Sensory Systems
  • Cellular and Molecular Neuroscience

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