Meta-analysis of functional enrichment results from five GWAS studies reveals biological processes involved in human refractive variation

Abstract

Purpose: Genomewide Association Studies (GWAS) have been successful in identifying a handful of susceptibility loci for myopia and ocular refraction. However, these loci account for a small proportion of the heritability of refraction within populations. We combined two methods to increase power to detect variants and relevant gene sets responsible for refraction: gene set enrichment analysis and GWAS meta-analysis.

Methods: : GWAS for spherical equivalent refraction were performed in five adult cohorts of European ancestry: AREDS, KORA, Framingham Eye Study, Twins UK, and the 1958 British cohort. All SNPs with variance inflation-corrected p-values≤10e-3 were extracted and annotated by their nearest gene. Redundant genes were removed to produce sets of unique genes for each study. Enrichment analysis of gene lists was performed using the DAVID clustering tool with gene ontology (GO) terms as annotation categories. Exact enrichment p-values from all studies were combined in a meta-analysis using Fisher’s combined probability test.

Results: Enrichment analysis with medium clustering stringency was conducted using the three main GO categories: biological process (BP); cellular component (CC); and molecular function (MF). For BP, the most highly enriched GO terms included: cell and biological adhesion; synaptic and nerve impulse transmission; ion transport; and cell-cell signaling (all meta-p<10e-25). For CC, the top 4 GO terms included the plasma membrane (all meta-p<10e-40). Enriched CC terms also included: synapse; cell projection; and extracellular matrix (all meta-p<10e-14). For MF, the most highly significant terms involved ion channel or transmembrane transporter activity (all meta-p<10e-15).

Conclusions: Our meta-enrichment analyses of refraction reveal a robust picture of the biological processes involved in human refractive variation. The enriched ontological categories are biologically plausible and remarkably similar across studies. We show that combined systems-based approaches can more fully characterize the genetic architecture of refractive error in human populations. Specifically, genes involved in synaptic and cell signaling, ion transport and cell adhesion appear to be particularly important in refraction. Consistent with these biological processes, plasma membrane constituents are significantly overrepresented in refraction-mediating systems.

Keywords: 676 refraction • 539 genetics • 605 myopia