Identification and Replication of Three Novel Myopia Common Susceptibility Gene Loci on Chromosome 3q26 using Linkage and Linkage Disequilibrium Mapping

Abstract

Refractive error is a highly heritable quantitative trait responsible for considerable morbidity. Following an initial genome-wide linkage study using microsatellite markers, we confirmed evidence for linkage to chromosome 3q26 and then conducted fine-scale association mapping using high-resolution linkage disequilibrium unit (LDU) maps. We used a preliminary discovery marker set across the 30-Mb region with an average SNP density of 1 SNP/15 kb (Map 1). Map 1 was divided into 51 LDU windows and additional SNPs were genotyped for six regions (Map 2) that showed preliminary evidence of multi-marker association using composite likelihood. A total of 575 cases and controls selected from the tails of the trait distribution were genotyped for the discovery sample. Malecot model estimates indicate three loci with putative common functional variants centred on MFN1 (180,566 kb; 95% confidence interval 180,505–180, 655 kb), approximately 156 kb upstream from alternate-splicing SOX2OT (182,595 kb; 95% CI 182,533–182,688 kb) and PSARL (184,386 kb; 95% CI 184,356–184,411 kb), with the loci showing modest to strong evidence of association for the Map 2 discovery samples ( p<10 ⁻⁷, p<10 ⁻¹⁰, and p = 0.01, respectively). Using an unselected independent sample of 1,430 individuals, results replicated for the MFN1 ( p = 0.006), SOX2OT ( p = 0.0002), and PSARL ( p = 0.0005) gene regions. MFN1 and PSARL both interact with OPA1 to regulate mitochondrial fusion and the inhibition of mitochondrial-led apoptosis, respectively. That two mitochondrial regulatory processes in the retina are implicated in the aetiology of myopia is surprising and is likely to provide novel insight into the molecular genetic basis of common myopia.

Author Summary

Successful gene mapping strategies for common disease continue to require careful consideration of basic study design with the advent of genome-wide association studies. Here, we take advantage of prior information that the heritability of the quantitative trait myopia in the general population is high and shows evidence of replicated linkage to chromosome 3q26. Based on this, we conducted a fine map linkage disequilibrium association study for the region, using a high-resolution genetic map derived from population-based HapMap Phase II data. For analysis, we used efficient multi-locus tests of association using single nucleotide polymorphism markers genotyped for our sample data and placed on the genetic map measured in linkage disequilibrium units. We followed up preliminary evidence of association for the discovery samples with further genotyping in the same samples to improve the model location estimates for the common functional variants we identified. Three locations were replicated using an independent sample. Two of the identified genes are likely to play an unexpected role in myopia with both pivotal in the healthy housekeeping metabolism of retinal mitochondria. Both proteins interact with OPA1, with nonsynonymous OPA1 mutations causing the unrelated Mendelian disease Autosomal Dominant Optic Atrophy (ADOA) by triggering mitochondrial-led retinal ganglia cell apoptosis.