A multi-ethnic genome-wide association study implicates collagen matrix integrity and cell differentiation pathways in keratoconus

Abstract

Keratoconus is characterised by reduced rigidity of the cornea with distortion and focal thinning that causes blurred vision, however, the pathogenetic mechanisms are unknown. It can lead to severe visual morbidity in children and young adults and is a common indication for corneal transplantation worldwide. Here we report the first large scale genome-wide association study of keratoconus including 4,669 cases and 116,547 controls. We have identified significant association with 36 genomic loci that, for the first time, implicate both dysregulation of corneal collagen matrix integrity and cell differentiation pathways as primary disease-causing mechanisms. The results also suggest pleiotropy, with some disease mechanisms shared with other corneal diseases, such as Fuchs endothelial corneal dystrophy. The common variants associated with keratoconus explain 12.5% of the genetic variance, which shows potential for the future development of a diagnostic test to detect susceptibility to disease.

Fig. 1. Work flowchart showing the flow of the genetic association analyses described in the manuscript.

There were three main phases: a discovery in a European cohort of 2116 cases and 24,626 controls, a replication in a combined meta-analysis of three other European cohorts as well as in two smaller non-European cohorts, and a final meta-analysis involving all the multi-ethnic cases and controls from the previous stages.

Fig. 2. Comparison of effect sizes of associations for the same SNPs in individuals of African (405 cases and 4185 controls) and South Asian (759 cases and 8009 controls) ancestries.

Each dot represents SNPs shown in Supplementary Data 3 and their labels are the respective chromosomal band on which they are located. The shapes of each data point refer to a previous GWAS association with keratoconus (empty circles), with CCT only (empty triangles) or novel associations (solidly filled circular shapes). The colors of both the points and their labels represent the significance (−log10(p-value) of association observed in the European discovery cohort. Polymorphisms identified in the discovery cohort but not shown here were not available for analysis in the replication cohorts.

Fig. 3. An annotated Manhattan plot of the final trans-ethnic meta-analysis data for all keratoconus cohorts in this study.

Analyses were conducted in 4669 cases and 116,547 controls. The log10(p-value) from the final meta-analysis is shown on the y-axis for all the SNPs along the different autosomes (x-axis). Novel associations for keratoconus are in pink. The names of the coding genes nearest to the most significantly associated SNPs are shown, or “no gene” when the association was >250 kb from a coding gene. Different colors are used for genetic loci and genes that to our knowledge, were previously associated with CCT (dark green) keratoconus (dark gray).

Fig. 4. Comparison of the same SNP allele effect sizes over central corneal thickness (CCT; in microns, the x-axis).

Data reported by Choquet et al. (also in Supplementary Data 14), with those over keratoconus (4669 cases and 116,547 controls, natural logarithm of the ORs, the y-axis). The alleles increasing susceptibility to keratoconus were selected as reference alleles. The genes located nearest to the most significant SNPs are shown in the labels and their color-codes denote the significance (−log10(p-value) of the association with CCT. For the sake of clarity, only some of the genes are labeled. Unlabeled points denote SNPs in intragenic regions (distance from the nearest known protein-coding transcript greater than 250kbp). The variants are annotated to the nearest known protein-coding transcript. Because of their proximity with other SNPs, some loci in this figure are not labeled. Polymorphisms identified in the discovery cohort, but not shown in this figure were not available for analysis in the replication cohorts.

Fig. 5. The predictive value of a genetic testing model based on common polymorphisms in an independent European case-control cohort.

The area under the receiver operating characteristic curve for the performance of a keratoconus predictive model that used the SNPs identified through the multi-ethnic analysis. The model was trained in the discovery populations of European ancestry and was replicated in a completely independent European panel of 222 keratoconus patients and 2208 controls.