Myopia is the most common eye disorder in the world,
1 affecting over a quarter of all adults in Europe and United States
2 and three-quarters of urban populations in Southeast Asia.
3,4 Myopia is an environmentally driven condition in genetically susceptible individuals. A remarkable rise in the prevalence of myopia worldwide over the last three decades
5,6 and associations of refractive error with a host of environmental factors and behavioral characteristics
7,8 point to a strong environmental influence on refractive errors. Nevertheless, a strong association of myopia with parental history
9 as well as heritability studies
10 has consistently indicated that more than half of the variability of refractive error within populations is determined by genetic factors.
Given the prevalence of refractive error and myopia, the economic costs (estimated at an annual US$268 billion worldwide for myopia alone
11 ), and rising numbers of individuals affected (as many as 2.5 billion by 2020),
2 there is considerable interest in genetic epidemiological studies as a means of uncovering the mechanisms underlying refractive development in humans. The ultimate goal of these studies is to reduce the burden of refractive errors by identifying potential biological targets for treatment and/or prevention strategies. In addition to these direct benefits, general scientific interest is justifiably high regarding a trait that affects the only visible part of the central nervous system and that is associated at a population level with variations of intelligence quotient
12 and academic achievement.
13
The full range of genomic tools has been exploited to study refractive error in human populations and families. At least 23 genome-wide linkage studies in related individuals have identified 17 loci across the human genome (a detailed review of linkage studies can be found elsewhere
14,15 ). In addition, a variety of refractive phenotypes have been studied in numerous candidate gene association studies. Candidate regions were chosen based on prior knowledge of gene functionality (often gleaned from animal models of visually induced myopia) or in combination with genetic linkage evidence (see reviews elsewhere
15,16 ). However, these results were generally poorly reproducible, likely because of factors ranging from genetic and phenotypic heterogeneity to methodological issues that are known to reduce the power of genetic association studies.
17
Contrary to inherently hypothesis-driven candidate-region genetic studies, genome-wide association studies (GWAS) offer an alternative, hypothesis-free approach that is often more appropriate for the genetic dissection of complex traits, which are affected by numerous genetic variants. They were first reported in the field of myopia research in 2009. This review will provide a brief description of the GWAS of refractive phenotypes published to date, along with the early lessons learned and some conclusions regarding the future of genomics research in the field. For ease of presentation we will divide these GWAS into two groups defined by the traits under consideration and their respective study designs: GWAS associated with high myopia in case–control analyses; and population-based GWAS of ocular refraction treated as a quantitative trait, with myopes in the negative part of the distribution, as quantified by the spherical equivalent refraction in diopters (D).
The first published GWAS for refractive error was designed as a two-stage analysis, using a cohort of 297 cases of pathological myopia (axial length > 26 mm) and 977 controls drawn from the general population
18 ; all participants were of declared Japanese ethnicity. Follow-up association of the 22 most suggestive loci from the discovery stage in 533 cases and 977 controls revealed the strongest association at rs577948 (
P = 2.22 × 10
−07), located on 11q24.1 approximately 44 kb upstream of the
BLID gene. The risk allele conferred a relative increase in the odds of high myopia of 1.37 (95% confidence interval: 1.21–1.54).
Li et al.
19 performed another two-stage association analysis of high myopia (≤ −6 D) in Chinese and Japanese subjects. The first stage was a meta-analysis of two cohorts of ethnic Chinese cases: one preadolescent group (65 cases and 238 controls) and the other group comprising young adults (222 cases and 435 controls). After replication in a Japanese cohort (959 cases and 2128 controls, who overlapped the ones used in the previously described association study
18 ), the strongest association was obtained for rs6885224 (Fisher's combined
P = 7.84 × 10
−06). This variant is an intronic single nucleotide polymorphism (SNP) within the
CTNND2 gene on 5p15.2. It should be noted that neither of these initial association signals met the conventional threshold for statistical significance in GWAS (
P < 5 × 10
−08).
Another study of ethnic Han Chinese participants was conducted by Li et al.
20 The genome-wide discovery stage focused on 102 high-grade myopia cases (≤ −8 D) with retinal degeneration and 335 “myopia-free” controls. Replication was attempted in two further stages using 2628 cases and 9485 controls in one stage and 263 cases and 586 controls in the other. The strongest evidence for association was observed for rs10034228 (meta-analysis
P = 7.70 × 10
−13), a high-frequency variant (minor allele frequency [MAF] = 0.5), located in a gene desert within the MYP11
21 myopia linkage locus on 4q25.
Shi et al.
22 identified another locus associated with high myopia (≤ −6 D) using a discovery cohort of 419 cases and 669 controls, all of Han Chinese ancestry, and replicating their findings in a combined 2803 cases and 5642 controls. They found the strongest evidence of association at rs9318086 (
P = 1.91 × 10
−16), an intronic SNP within the
MIPEP gene on chromosome 13q12. This variant is common across populations including Asians (MAF = 42% and 46% in Han Chinese and Japanese HapMap samples, respectively).
The defining characteristic of the above studies is that they were aimed at identifying susceptibility variants for high myopia. These studies were all conducted in East Asia, where the prevalence of this condition is highest and has been increasing the most within the last few decades. Their results, however, have not been replicated in other GWAS of similar design, ethnic background, and phenotypic definition (high myopia).
Among Europeans, the prevalence of high-grade myopia is lower than in East Asians, and the main approach has been to study quantitative association with the whole spectrum of refractive error. This approach has the advantage of utilizing all data from population-based samples. The first two GWAS of refractive error in European subjects included 4270 British
23 and 5328 Dutch
24 individuals from the general population in their respective GWAS discovery cohorts. For replication, both studies used more than 10,000 subjects drawn from each other's main discovery cohorts and a smaller shared pool of replication samples. Associations survived customary GWAS significance thresholds for two separate loci, one near the
RASGRF1 gene and the other near
GJD2 (
P = 2.70 × 10
−09 for rs8027411 on 15q25.1 and 2.21 × 10
−14 for rs634990 on 15q14).
Over a year later, the only case–control GWAS for high-grade myopia in a population of European origin was published from France.
25 Using 192 cases (≤ −6 D) and 1064 controls but no independent replication sample, this study identified suggestive evidence of association for a marker located within the MYP10 linkage locus 3 kb downstream of
PPP1R3B 26 (
P = 6.32 × 10
−7 for rs189798). This study did not replicate any of the previously reported loci for refractive phenotypes.
Major developments in myopia genetics occurred in early 2013. Two studies, one from the international Consortium for Refractive Error and Myopia (CREAM)
27 and one by the direct-to-consumer genotyping company 23andMe
28 (Mountain View, CA, USA), amassed 37,382 and 55,177 subjects of European ancestry, respectively. In addition, the CREAM study reported on 12,332 subjects of various Southeast Asian ancestries. For the first time deploying high statistical power in the field, the two studies followed different study designs and analytical strategies. The CREAM study was a classic meta-analysis of GWAS data from linear regressions on spherical equivalent obtained from 35 participating centers. The 23andMe study involved a GWAS survival analysis on age of onset of myopia (<30 years), obtained from questionnaire data. Both studies replicated associations to the
RASGRF1 and
GJD2 loci previously discovered in British and Dutch populations.
23,24 In addition, the CREAM study identified a total of 24 novel loci in its multiethnic panel while the 23andMe study independently identified 20 novel loci. Very surprisingly for two studies of such different designs, both GWAS independently identified or replicated at near GWAS significance the same 25 genetic loci across the genome
29 (
Fig. 1). Moreover, despite being measured on different scales (diopters for CREAM and hazard ratios for 23andMe), the direction of the estimated effects was consistent across all significant loci. Even though the effects were generally small, the genetic basis underlying both age of onset of myopia and degree of refractive error was shown to be very similar.