Citation: Liao
X, Tan QQ, Lan CJ. Myopia genetics in genome-wide association and
post-genome-wide association study era. Int J Ophthalmol
2019;12(9):1487-1492
DOI:10.18240/ijo.2019.09.18
·Review Article·
Myopia
genetics in genome-wide association and post-genome-wide association study era
Xuan Liao, Qing-Qing Tan, Chang-Jun Lan
Department
of Ophthalmology, Affiliated Hospital of North Sichuan Medical College; Department
of Ophthalmology and Optometry, North Sichuan Medical College, Nanchong 637000,
Sichuan Province, China
Correspondence
to: Xuan Liao
and Chang-Jun Lan. Department of Ophthalmology, Affiliated Hospital of North
Sichuan Medical College, Nanchong 637000, Sichuan Province, China.
aleexand@163.com; eyelanchangjun@163.com
Received:
Abstract
Genome-wide association studies
(GWAS) of myopia and refractive error have generated exciting results and
identified novel risk-associated loci. However, the interpretation of the
findings of GWAS of complex diseases is not straightforward and has remained
challenging. This review provides a brief summary of the main focus on the
advantages and limitations of GWAS of myopia, with potential strategies that
may contribute to further insight into the genetics of myopia in the post-GWAS
or omics era.
KEYWORDS: myopia; genetic variation;
genome-wide association studies; omics
DOI:10.18240/ijo.2019.09.18
Citation: Liao
X, Tan QQ, Lan CJ. Myopia genetics in genome-wide association and
post-genome-wide association study era. Int J Ophthalmol
2019;12(9):1487-1492
INTRODUCTION
Myopia, also known as
near-sightedness or short-sightedness, is characterized by which the images of
distant objects fail to be properly focused on the retina plane but rather in
the front of the retina. Myopia is accepted as a multifactor disorder that
involves in genetic (nature) and non-genetic environmental or behavioral
(nurture) risk factors plus their complex interaction, likely together with the
effects of stochastic factors. Meanwhile, it is considered as a polygenic
disease that involves a critical number of candidate genes joint action or more
complex genetic mechanisms, rather than any of the simple Mendelian patterns of
inheritance. There was a dramatic rise in myopia prevalence over the last 30y
in many countries, especially among younger people in urban East Asia[1-3]. This phenomenon may be caused by
increasing educational pressures or lifestyle changes and potentially
gene-environment interactions, suggesting the role of environmental exposures
in myopia susceptibility. Despite epidemiological heterogeneity, however, the
genetic basis of myopia has been established based on the molecular genetics
studies and genetic epidemiological evidences of myopia in the early stage.
Heritability estimates from family and twin studies for myopia ranging between
50% and 90%, continue to play a significant role in enhancing the
interpretability of genetic evidences.
The advent of the genome-wide
association study (GWAS) era is accompanied with the revolution of molecular
technology and information. The unbiased nature of genome-wide measurements
coupled with the statistical power of association studies have yield new
insights into myopic pathogenesis without any prior knowledge of function.
There are several popular instances such as the Meta-analyses that could
promote power to reveal more loci by pooling information from multiple GWAS:
the imputation that could extend appraisal of associations across the genome by
inferring frequency based on neighboring variant frequencies, the permutation
that could build an empirical estimation of the null distribution by
conservatively multiple corrections. On the basis of the advantages, GWAS has
rapidly become one of powerful and affordable tool to discover common risk
variants of the complex diseases, and also has been successfully applied in
ophthalmic field. Rather than giving an exhaustive review of all reported
findings for myopia, this brief review will focus on recent work on GWAS and
farther strategies in the post-GWAS era of myopia.
IMPLICATIONS OF GWAS WITH REFERENCE TO MYOPIA
Initial
Results and Further Findings In the first place, Nakanishi et
al[4] conducted a two-stage GWAS survey in
Japanese by typing 411 777 single nucleotide polymorphism (SNP) markers,
recruiting 830 pathological myopia cases and 1911 general population controls.
This earliest GWAS of myopia reported the strongest but not genome-wide
significant association at SNP rs577948 on chromosome 11q24.1 (P=2.22×10-7).
It was speculated that this associated locus located upstream of BLID
gene was involved in mitochondrial-led apoptosis and then prompted
mitochondrial regulatory mechanism of myopia. This initial finding, however,
has failed to be replicated in follow-up studies. There are two possible
reasons for this: on the one hand, replicated studies could demonstrate a false
negative (type II error, reject qualified applicants) due to insufficient
statistical power to detect small genetic effects; on the other hand, in most
cases where confounder of population stratification and overestimation of
effect size are involved, the initial finding likely represents a false
positive (type I error, admit unqualified applicants) rather than true
associations. In addition, GWAS requires very stringent significance levels,
that is, P-values less than 5×108 to remain significant after
Bonferroni correction for the very large number of genetic markers tested. In
the circumstance, a great sample size was needed in order to detect robustly
modest genetic effects that are typical for complex disease.
The paucity
of causal variants identified has motivated action to expand sample size
through empowering organizationally a number of international multicenter
collaborative efforts. Two subsequent large-scale GWAS for common refractive
error were performed concurrently each in a total of more than 15 000 European
populations. These GWAS identified successfully and replicated mutually a
number of genome-wide significant association loci located on 15q14 (combined P=2.21×10-14)[5] and on 15q25 (combined P=2.07×10-9)[6], respectively. Since then both loci have been widely
replicated with almost consistent results of the association with myopia at the
15q14 locus but not the 15q25 locus. One of the most comprehensive study came
from a large Consortium of Refractive Error and Myopia (CREAM), which conducted
a Meta-analysis of some polymorphisms observed at 15q14 and 15q
In this
period, with it the application of GWAS for myopia has enabled substantial
progress in the identification of robust and replicable genetic associations
and unveiled several important insights. Over a dozen GWAS for myopia or
related phenotypes have been published and cataloged online by the National
Human Genome Research Institute[9], providing
valuable data for further analysis. These GWAS have identified over 150 SNPs
associated with myopia. Note that GWAS significant variants seem generally to
be of low frequency and/or small effect with the allelic odds ratio range from
1.10-1.20[10]. However, it should be borne in
mind that estimated of odds ratio is only a surrogate for the relative risk
rather than the true genetic effect. Meanwhile, small effects can still uncover
novel relevant insights into pathogenic mechanisms in a complex disease, due to
natural selection, pleiotropic mutation, genetic drift and population history
in evolution.
Significant Progresses Two of the heretofore largest GWAS
of myopic refractive error were conducted independently and published
successively by CREAM[11] and 23andMe company[12]. In addition to confirming previously reported loci[5-6], both two studies provided
compelling results of additional associated loci linked to myopia and
refractive error. The CREAM conducted a genome-wide Meta-analysis comprised of
32 across ancestry cohorts, and discovered 16 novel quantitative trait loci
(QTL) associated with refractive error in 37 382 individuals of European
origin, of which 8 were shared with 8376 individuals of East Asians[11]. The 23andME group reported results from the largest
genome-wide survival analysis in a European derived population. The Cox model
survival analysis of 45 711 discover samples identified 20 new loci, of which
10 were replicated in a separate cohort of 8323 samples with early onset myopia
before 10 years old[12]. The comparison of two
investigations indicated that CREAM and 23andMe overlapped with each other to a
startling extent, as well as associated loci had consistent direction of
estimated effects. Not surprisingly, such robust results could be replicated
again in a Japanese population[13]. These
discoveries strengthened the existing viewpoint of signaling cascade from the
retina triggered to the sclera remodeled and then ultimately leading to eye
growth. More recently, Tedja et al[14]
also further revealed that a light-dependent retina-to-sclera signaling cascade
acted on refractive error by a GWAS in 160 420 participants and replication in
95 505 participants.
These
salient studies have provided additional information to explore the etiology
and pathogenesis of myopia. As compared to CREAM conventional acquirement of
phenotype information, 23andME utilized questionnaire data which may generate
substantial misclassification errors because of lack of validation.
Nevertheless, the Cox proportional hazard survival analysis produced an
increasing statistical power, benefiting from distributional flexibility to
study a wide variety of censored traits such as age of onset. Despite
methodological biases, replication has a crucial role in showing associations
that are identified reflect interesting biological processes. In addition, a
linear relationship between hazard ratio of 23andME and effect size of CREAM
was established, where locus specific hazard ratio for myopia onset age would
predict the degree of refractive error throughout life[15-16]. Such initial attempt to predict risk has a limited
role primarily due to the relatively small effect size of the significantly
associated variants. Hence, risk prediction may not be a good recommendation
before a larger proportion of the risk variants underlying the myopia have been
identified. It is envisioned that the development of risk prediction
algorithms, incorporating massive genetic markers and biomarkers with risk
factors, will facilitate a promising clinical application to determine the
exact individual risk of developing myopia.
The Related GWAS of Myopia These GWAS also have demonstrated
additional insights to shed light on the association of the two major
determinants of refractive error, ocular axial length and corneal curvature,
with myopia. A Meta-analysis in 12 531 Europeans and 8 216 Asians identified
nine genome-wide significant loci for axial length[17];
of which five associated with refraction (LAMA2, GJD2, CD55,
ALPPL2, and ZC3H11B)[11-12]
were replicated, and differential gene expression was further observed in
myopic animal experiments. Another confirmation that linked the attractive
phenotypes trait with myopia was showed in genome-wide significant associated
variants (PDGFRA, MTOR, CMPK1 and RBP3) for corneal
curvature; particularly, a missense rs11204213 of RBP3 indicated larger
effects on both corneal curvature and axial length compared with others[18]. Although these locus were not reported previously in
myopia GWAS, homozygous nonsense mutations of the RBP3 gene was found to
be associated with high myopia[19]. A large-scale
GWAS (n=86 335) for corneal astigmatism identified four novel loci and
one of which (NPLOC4) has previously demonstrated association with
myopia, suggesting further support for the shared genetic susceptibility of
myopia and astigmatism[20]. What’s more, Simpson et
al[21] observed two genome-wide significant
regions on 15q14 and 8q12 for hyperopia, which overlapped with previously
reported loci of myopia age at onset, indicating GWAS also have provided
evidences for myopia and hyperopia as dichotomous refractive error traits
underlying the emmetropization mechanisms.
GWAS in
human complex trait have already proven a resounding success, which have
underpinned effectively the outcomes of genetic variants associated with myopia.
This represents a key milestone in myopia genetics. A number of new loci have
been implicated in myopia phenotype and, in sharp contrast with linkage and
candidate studies, showing predominantly consensus among fellow-up studies.
Albeit many variant loci proved robust, almost all of them did not capture
causal associations but rather only tagged a causative event in a specific
region of the human genome. Thus, those crucial events would still have to be
elaborated. For the time being, GWAS discoveries have significantly broadened
our knowledge of the genetic basis of common forms of myopia development but
they have yet to demonstrate clinical implications. Given this, a great deal
more work will be needed to further explore unexplained information and understand
the underlying biologic mechanisms of these genetic variants.
ROUTE TO FOLLOW IN POST-GWAS ERA
Seeking
Heritability Although GWAS have successfully
proven in identifying multiple genetic variants that contribute to myopia
phenotype, these variants together account for only a minority of the observed
heritability[16]. The missing heritability may
arise potentially from undiscovered common variants that are concealed by
stringent significance thresholds of GWAS, rare variants that are ignored for
GWAS approach on basic of common disease/common variant hypothesis, structural
variations in the genome such as copy number variation (CNV) that escapes from
current genotyping platforms. With the sequencing technologies advanced and
cost decreased rapidly, it will be feasible to utilize whole genome sequencing
in numerous populations to identify both common and rare variants with a modest
effect underlying the myopia traits[22]. As an
important source of human genome variability, CNV is being explored in the
context of myopia. Yip et al[23] adopted a
systematic strategy to investigate the role of CNVs in high myopia, and
identified 22 significant CNVs which still are needed to further explored. One
animal study showed that the CNV of muscarinic acetylcholine receptor genes (CHRM),
especially CHRM3, were significantly different between control and
myopia, even among various degrees of myopia[24].
Metlapally et al[25] reported that TEX28
gene CNV appeared to be associated with the MYP1 locus in X-linked high myopia
phenotypes. Beleggia et al[26] performed
an CNV analysis in two affected individuals from MACOM syndrome with severe
myopia, and identified CRIM1 CNV as an important factor in eye
development. Although CNV has been speculatively involved in susceptibility to
various complex diseases in human, the effect of CNV in missing heritability
for myopia remains largely undefined.
While many
variants surely remain to be found, phantom heritability may be another
hypothesis caused by huge overestimation with no consideration for genetic
interactions[27-28]. Such the
absence of heritability could be partly attributed to gene-environment,
gene-gene or more specifically variant-variant interactions. A series of
epidemiological studies investigated the interactions between the myopia
genetic variants and the main environmental factors, and demonstrated that
educational attainment and genetic effects had strong interactions. Fan et
al[29-30] provides
evidence of the interactions among education stratum and GWAS-associated loci
such as ZMAT4 presented in both Asians and Europeans. Such
education-environment interactions have also been implied for susceptibility
variants in MMPs[31]. A joint
Meta-analysis based on gene-environment-wide interaction study (GEWIS)
demonstrated that several genome-wide significant loci (AREG, GABRR1
and PDE
Epigenetic Studies Epigenetic modifications in the
human genome serve as a genetic mechanism by which environmental exposures
modulate disease risk, as well as play diverse roles in gene expression and
function at different molecular levels[36]. The
most well-known epigenetic modifications are the DNA methylations, histone
modifications, and non-coding RNA activity so far. Methylation at
cytosine-phosphate-guanine (CpG) sites was one of major repressive epigenetic
modification. It was recently revealed that hyper-methylation of CpG in the COL
Integrative Pathway or Network Analysis GWAS approach typically focused on
single SNP-based association test suffering from low power if each tested
marker is incomplete linkage disequilibrium with undefined quantitative trait
loci. Nevertheless, the polygenic basis of complex traits implicated that
epistasis and pleiotropy appeared to be inherent properties of biomolecular
networks rather than isolated occurrences. This has motivated the interest in
multi-locus-based systemic approach to integrate GWAS data and other data
modalities to yield additional insight within a biological context[42]. Actually, pathway analysis has previously been
performed within GWAS. The CREAM identified several novel pathways involved in
myopia by considering all the genes identified in the text and using the
Ingenuity Pathways Analysis (IPA) database and Disease Association
Protein-Protein Link Evaluator (DAPPLE)[11]. The
Wnt receptor signaling pathway was identified in a recent GWAS result for axial
length from CREAM effort, further reinforced that the signaling pathway plays a
prominent role in vertebrate eye development[18].
Some studies have integrated visually significant genotype-phenotype
associations with gene annotations databases to build pathways. The miRNA-mRNA
interaction networks or functionally collaborative networks also have been
conducted to identify the potential signaling pathways involved in
form-deprivation myopia models. For example, Tkatchenko et al[38] found that nine signaling pathways were involved in
regulation of neurogenesis; Mei et al[43]
discovered that the regulation of transcription, axon guidance and TGF-β
signaling pathways were significantly enriched. Meanwhile, it was suggested
that miRNAs may serve as key regulators of the signaling cascades related to
the development of myopia. Reconstruction models of regulatory network,
constituted by binding events of transcription factors, might help understand
and interpret the roles of genetics and epigenetics in myopic mechanism on the
other hand. Despite of so much inaccurate and incomplete, the dynamic
context-specific nature (distinct combinations of factors bind at specific
genomic locations) of regulatory network is beginning to take its role in
dissecting the genetics pathogenesis. Pathway analysis will next be extended to
examining rare variants, other omics and interaction data.
Through
long-term exploration and unremitting efforts, a framework for unraveling the
genetic basis of complex traits has just been initially established. For myopia
genetics research, the present achievements are only the first step in this
process and, ever larger studies would undoubtedly result in more genetic
discoveries but smaller effects. One challenge is how to tackle the fine
mapping and functional dissection of already-identified GWAS loci. Furthermore,
increasing emphasis will be placed on biological understanding and personalized
discovery of diagnostics and therapeutics in clinical settings. Even so, its
phenotypic predictability remains very low. New methodologies and perspectives
will be needed to fully tackle related problems. The promising route for
identification of missing low-frequency and small-effect variants lies through
combining biological functional evidence with statistical genetic evidence.
Identification of remaining trait variance will acquire additional discoveries,
specially underlying rare variants and causal common variants and refined
estimates of heritability. Functional validation, integrating the growing
genetic and omics data, will produce omnibearing analysis of biological
pathways, gene regulation networks and protein interaction maps. The
improvement of molecular genetics combined with other methods is expected to
become widespread medical application in humans in the end.
ACKNOWLEDGEMENTS
Foundation: Supported by Projects of Science
& Technology Department of Sichuan Province (No.2019YJ0381).
Conflicts of
Interest: Liao X, None; Tan QQ, None; Lan CJ, None.
REFERENCES