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Original Investigation | Ophthalmic Molecular Genetics

Challenges in Elucidating the Genetics of Diabetic Retinopathy FREE

Jane Z. Kuo, MD, PhD1,2,3; Tien Y. Wong, MD, PhD4,5; Jerome I. Rotter, MD1,6
[+] Author Affiliations
1Medical Genetics Institute and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
2Department of Ophthalmology, University of California San Diego, La Jolla
3Department of Ophthalmology, Chang Gung Memorial Hospital and College of Medicine, Chang Gung University, Chang Gung, Taiwan
4Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
5Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
6Institute for Translational Genomics and Population Sciences, Los Angeles Bio Medical Research Institute, Harbor–UCLA Medical Center, Torrance, California
JAMA Ophthalmol. 2014;132(1):96-107. doi:10.1001/jamaophthalmol.2013.5024.
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Published online

Importance  In the past decade, significant progress in genomic medicine and technologic developments has revolutionized our approach to common complex disorders in many areas of medicine, including ophthalmology. A disorder that still needs major genetic progress is diabetic retinopathy (DR), one of the leading causes of blindness in adults.

Objective  To perform a literature review, present the current findings, and highlight some key challenges in DR genetics.

Design, Setting, and Participants  We performed a thorough literature review of the genetic factors for DR, including heritability scores, twin studies, family studies, candidate gene studies, linkage studies, and genome-wide association studies (GWASs).

Main Outcome Measures  Environmental and genetic factors for DR.

Results  Although there is clear demonstration of a genetic contribution in the development and progression of DR, the identification of susceptibility loci through candidate gene approaches, linkage studies, and GWASs is still in its infancy. The greatest obstacles remain a lack of power because of small sample size of available studies and a lack of phenotype standardization.

Conclusions and Relevance  The field of DR genetics is still in its infancy and is a challenge because of the complexity of the disease. This review outlines some strategies and lessons for future investigation to improve our understanding of this complex genetic disorder.

Figures in this Article

Diabetic retinopathy (DR), an important microvascular complication of diabetes mellitus (DM), is a leading cause of visual impairment in adults 20 to 74 years of age.1 More than 93 million people worldwide have DR, 17 million of whom have proliferative diabetic retinopathy (PDR) and 28 million of whom have vision-threatening DR.2 This number will continue to escalate with an aging population, increasing obesity, and a rapidly progressing DM epidemic. More individuals, especially Hispanics, people of African descent, and Asians, will be vulnerable to blinding DR in coming years.3,4 There is clearly a need to develop strategies to identify at-risk individuals for early interventions.

Compared with other major causes of visual loss, such as age-related macular degeneration,5 myopia6,7 and glaucoma,8,9 the search for genetic clues to DR has not progressed as rapidly. To date, the few studies that have reported on possible susceptibility genes for DR have yielded inconsistent results. There is clearly a familial relationship in DR because twin and family studies1017 indicate a genetic basis. Several candidate gene studies have reported promising genes,1821 but few of them have been replicated, and the few positive findings reveal only weak genetic associations.1820,22 In genome-wide approaches, 3 linkage studies performed in Pima Indians and Mexican Americans have identified regions on chromosomes 1, 3, and 12 to be suggestive of DR.13,23,24

In contrast to age-related macular degeneration, myopia, and glaucoma, few genome-wide association studies (GWASs) have been conducted thus far on DR. The few GWASs are of modest sample sizes in Hispanics, Chinese, and white populations and have reported borderline associations with DR in either type 1 or type 2 DM.2528

In this review, we highlight these key genetic studies of DR with an emphasis on the most recent developments. We also discuss issues and challenges with elucidating the genetics of DR and indicate approaches that will provide the opportunity to advance our knowledge of this complex genetic disorder.

The diagnosis of DR is clinically defined by the presence of retinal microvascular lesions in patients with DM; however, these retinal lesions are not specific and may also be present in individuals without DM.29,30 The classification of DR is graded by severity and divided into nonproliferative diabetic retinopathy (NPDR) and PDR. Key retinal changes in NPDR include microaneurysms, hard exudates, cotton wool spots, intraretinal microvascular abnormalities, and venous beading; these further subdivide NPDR into mild, moderate, and severe forms. Key retinal changes in PDR include neovascularization of the optic disc or elsewhere, preretinal hemorrhage, or vitreous hemorrhage. On the other hand, clinically significant macular edema, which is graded as its own entity, can develop at any stage of the DR spectrum. Thus, the various classifications in DR grading, resulting in heterogeneity of DR phenotype, pose a significant challenge in genetic studies of DR. The assessment of DR via a standardized stereoscopic photograph has been proposed to overcome this issue, and more researchers have used this approach by adopting and grading DR using the Early Treatment Diabetic Retinopathy Study severity scale or a similar modification. Recently, the assessment of DR and diabetic macular edema via optical coherence tomography has been proposed as an imaging modality to better visualize the intraretinal morphologic changes in patients with DM31; however, the classification of DR and diabetic macular edema via optical coherence tomography has not been clearly defined or adopted for use.

Diabetic retinopathy occurs on the background of DM. That genetic factors play a major role in the etiology of DM has long been appreciated because of ethnic differences in frequency, increased familial aggregation, and a markedly higher concordance in monozygotic vs dizygotic twins. This is true for each of the major subforms of DM (type 1 and type 2).

To date, approximately 60 loci have been successfully identified for type 2 DM, of which only 3 were discovered before the GWAS era.32,33 Although most of these studies were performed in individuals of European descent, more recent studies of Asians,34 Hispanics,35 and African Americans3537 have also demonstrated some level of associations for these signals, supporting the hypothesis that these signals (or the causal variants that are in high linkage disequilibrium with these signals) are likely common alleles that are widely distributed in the human population and each contributing a small effect on disease risk.32

These important discoveries through large collaborative efforts by GWAS approaches have led to substantial progress in the understanding of genetics in type 2 DM, leading to the identification of novel pathways, demonstrating mechanistic associations, and supporting prior epidemiologic studies.38 These findings have illustrated some important key lessons that are useful in genetic studies of DR. First, joining forces by international collaborative efforts is necessary to increase statistical power by increasing sample size.38 Second, both analysis by treating the phenotype as a dichotomous trait and analysis of a related, quantitative trait are useful.38 Third, connection of genetic findings with more defined physiologic parameters increases understanding.38 Elucidating the genetic basis of type 2 DM offers an ideal model to approach the genetic study of DR. However, it should be apparent that the phenotype of type 2 DM has several advantages, such as the ease of classification and readily available large samples of patients even without detailed assessment.

The origin of DR remains complex and poorly understood. Large epidemiologic studies2,39,40 have consistently demonstrated that the duration of DM and adequacy of glycemic control are 2 of the major contributors to the development and progression of DR. This was robustly documented in the Wisconsin Epidemiological Study of Diabetic Retinopathy (WESDR), which found that duration of DM was the strongest predictor for progression of DR, with prevalence of DR ranging from 17% in type 1 DM to 29% in type 2 DM for patients with DM for less than 5 years and increasing markedly to almost 100% for type 1 DM and 78% for type 2 DM in patients with DM for more than 15 years.41,42 In other landmark studies,2,39,40,43 such as the Diabetes Control and Complications Trial, UK Prospective Diabetes Study, the Action to Control Cardiovascular Risk in Diabetes (ACCORD) Eye Study, and Meta-Analysis for Eye Disease Study, intensive glycemic control was effective in reducing the rate of DR progression in both type 1 and type 2 DM. Other studies2,44,45 have demonstrated that blood pressure control is another risk modifier, although some studies43 did not support this finding. Recently, increasing evidence has supported an association between dyslipidemia and DR46; the Fenofibrate Intervention and Event Lowering in Diabetes Study47 and the ACCORD Eye Study43 demonstrated that reduction in lipids could also limit DR progression.

Despite strong evidence of DR susceptibility, these environmental risk modifiers by themselves do not account for the complete risk susceptibility. First, this is exemplified by clinical observations that some individuals develop DR despite good glycemic control and short duration of disease, whereas others do not develop DR, even with poor glycemic control and longer duration of DM.48 Second, the strongest environmental factors (duration of DM and glycosylated hemoglobin) only explained approximately 11% of the variation in retinopathy risk in the Diabetes Control and Complications Trial.49,50 Similarly, a combination of glycosylated hemoglobin, blood pressure, and total cholesterol only explained approximately 10% of the variation in retinopathy risk in the WESDR,51 suggesting that the remaining approximately 90% of the variation in retinopathy risk is presumably explained by other risk factors. Finally, population studies indicate that retinopathy signs, such as microaneurysms, were detectable in 7% to 13% of patients without DM and patients in whom the glycosylated hemoglobin level was well below 5%.29 In addition, single-nucleotide polymorphisms (SNPs) associated with DM or hypertension were not associated with retinopathy in individuals without DM,52 suggesting that other risk factors, independent of hyperglycemia and DM, contribute to the development and progression of retinopathy signs similar to DR.

Attempts to identify gene(s) in the development of DR have been conducted during the past few decades. To date, these studies have been limited to twin studies,10 family studies,1117 candidate gene studies,1822 linkage studies,13,23,24 and small-scale GWASs with modest sample sizes.2528

In support of a genetic hypothesis of DR, several studies3,4 have found a discrepant rate of the prevalence of DR among US populations, with a significantly higher prevalence observed in Hispanics, African Americans, and Chinese Americans. Compared with whites, in African Americans other risk modifiers, such as duration of DM, glycemic control, and blood pressure, appear to account for the higher prevalence of DR, but these factors do not explain the higher prevalence seen in Hispanics,5356 suggesting that other factors, including genetic factors, may influence susceptibility to DR.

Twin and Family Studies

In twin studies, Leslie and Pyke10 found the same degree of severity in 35 of 37 concordant twins with type 2 DM (95%) compared with only 21 of 31 concordant twins with type 1 DM (68%). This early observation was extended by familial aggregation studies, with siblings and relatives of diabetic patients with DR having as high as a 3-fold increased risk of DR compared with siblings and relatives of diabetic patients without DR1117 (Table 1). This trend was seen in either type 1 or type 2 DM and across different ethnicities. Furthermore, evidence of a familial aggregation is more consistently seen in the presence of more severe retinopathy and less in the presence of any retinopathy, with heritability scores ranging from 18% to 27% for any DR13,17 and 25% to 52% for PDR12,17 in either type 1 or type 2 DM (Figure). Thus, as previously mentioned, it is important to not only provide a standardized assessment of DR but also compare those without DR with those with more severe stages of DR. The Family Investigation of Nephropathy and Diabetes–Eye study, in which nearly half of the 2368 diabetic patients are Mexican Americans, demonstrated that the heritability of any DR in this population of type 2 DM is as high as 24%.17

Table Graphic Jump LocationTable 1.  Summary of Familial Aggregation Studies in Diabetic Retinopathy
Place holder to copy figure label and caption
Figure.
Heritability Estimates for Diabetic Retinopathy

DCCT indicates Diabetes Control and Complications Trial; DR, diabetic retinopathy; FIND-Eye Study, Family Investigation of Nephropathy and Diabetes–Eye Study; PDR, proliferative diabetic retinopathy.

Graphic Jump Location
Candidate Gene Studies

Most genetic research in DR has used the candidate gene approach. Several pathways and processes have been proposed to play an important role in the pathogenesis of DR, which led to the testing of a number of hypothesized candidate genes. Although a number of candidate genes and genetic variants have been proposed in the literature, few of them have been replicated, and the few positive findings only revealed weak genetic associations with DR.18,19

In this approach, the analysis compares the frequency of a particular genetic variant in individuals with (cases) or without (controls) DR. Several pathways and processes have been proposed, including the renin-angiotensin system, glucose-induced pathways, vascular endothelial dysfunction, tissue matrix remodeling, and angiogenesis.18,19 Potential candidate genes involved in these pathways and processes include ACE, AGTR1, AGT, VEGF, AKR1B1, RAGE, GLUT1, APOE, MTHFR, PAI-1, ITGA2, PPAR-γ, and NOS3. Their associations or lack thereof with DR have been extensively documented in prior reviews.1821 We summarize the most important findings with a focus on AKR1B1 and VEGF because of their biological implications.

Encoded by the AKR1B1 gene, aldose reductase is an enzyme that catalyzes the reduction of glucose to sorbitol during glucose metabolism. Increased activation of aldose reductase has been reported to induce metabolic and biochemical changes, leading to the development of early DR and PDR.57,58 For these reasons, AKR1B1 was proposed as a highly suspect candidate for genetic association studies in DR. Although a great deal of prior work has found inconsistent results, a recent meta-analysis by Abhary et al20 examining 20 candidate genes in DR found that variants in AKR1B1 had the most significant association with DR. In particular, the meta-analysis identified that the Z − 2 microsatellite confers risk of DR (odds ratio [OR],  2.33; 95% CI, 1.49-3.64; P = 2E-04) in either type 1 or type 2 DM. This trend was similar and significant in the subgroup analysis of NPDR (P = .008) and PDR (P = .002). On the other hand, the Z + 2 microsatellites conferred protection against overall DR (OR, 0.58; 95% CI, 0.36-0.93; P = .02), but this association was only seen in patients with type 1 DM and was independent of the studied ethnicity. In addition, a few studies20 examining the association of another AKR1B1 polymorphism at the promoter (rs759853) found that the T allele confers protection for DR (OR, 0.49; 95% CI, 0.36-0.68; P < 1E-04) in type 1 DM but was not significant in type 2 DM.

VEGF, a key player involved in angiogenesis and a potent mediator of vascular permeability, is activated by microvascular changes associated with DM due to hypoxia. This activation of VEGF leads to breakdown of the blood-retinal barrier and retinal neovascularization.59,60 Conversely, anti-VEGF therapies, such as bevacizumab (Avastin; Genentech), ranibizumab (Lucentis; Genentech), and aflibercept (Eyelea; Bayer and Regeneron), have been reported to ameliorate these changes.59,61,62 A number of polymorphisms (rs2010963,20,21,6371 rs25648,20,63,68 rs1570360,20,63,72 rs3095039,20,63,70 rs35569394,20,73 rs699947,20,66,7477 rs13207351,63,72,75 rs735286,72 rs2146323,72,77 rs833061,63,68,69,75 rs3025021,75,76 rs10434,76 rs833068,76 and rs83307077) in VEGF have been analyzed with DR or severe DR. The only conclusive finding from these efforts is that the C allele of rs2010963 (-634C/G), although insignificantly associated with DR or PDR, confers risk for NPDR (OR, 1.61; 95% CI, 1.23-2.10; P = 5E-04) in the meta-analyses.20,21

A number of other individual candidate genes have been examined with DR,20,65,7894 and their findings are summarized in Table 2. However, it is difficult to draw any conclusions from these studies because the sample sizes of individual studies were often small. The P values obtained from these efforts are sometimes nominally significant but cannot withstand corrections for multiple testing. In most cases, no replication has been attempted. Furthermore, there are also conflicting findings from multiple studies. Although meta-analysis techniques have been undertaken, findings remain largely inconclusive because of problems with analysis in multiple and different ethnicities (direction of effect and allele frequencies may be different), publication bias, and lack of standardization for DR phenotype.

Table Graphic Jump LocationTable 2.  Summary of Individual Candidate Gene Studies of Diabetic Retinopathya

Thus, alternatively, 2 studies with a larger scale have examined candidate genes and DR using a method that mimics a genome-wide approach. This method is useful when the effect sizes of individual variants, such as DR, are small and the study population is limited. The first study, the Candidate Gene Association Resource, did not find genes previously associated with type 2 DM, diabetic nephropathy, and DR to be associated with DR.22 The most interesting finding of this study is that variants in SELP, after adjusting for known DR risk factors, remained significantly associated with DR in the European Americans but were not seen in the African Americans, Hispanic Americans, or Asian Americans.22 The second study, which examined 193 candidate genes with DR of African Americans with type 1 DM, found nominal associations in 13 genes with progression of DR.95 A number of these genes are involved in pathways related to glucose metabolism, inflammatory processes, angiogenesis and vascular permeability, insulin signaling, retinal development, or blood pressure regulation, not only highlighting the implications of these genes but also suggesting that a number of biological pathways are simultaneously involved in DR. Even with these large-scale attempts of examining candidate genes in DR, no definite conclusion can be drawn at this time without replication efforts in larger cohorts.

Linkage Studies

A potential problem with the candidate gene approach is that it depends on an a priori hypothesis that implies that a particular gene has a functional importance in the pathophysiology of DR. If the hypothesis is wrong, then the genetic association will be negative or inconsistent. This method has led to hypothesis-free approaches (also known as agnostic approaches), first by linkage and recently by GWASs. In these 2 approaches, no initial biochemical or pathophysiologic induction is proposed; the results are instead driven by chromosomal location.

Linkage analysis is based on the principles of genetic recombination to map genomic regions by the observations seen in family members. It is based on the assumption of cosegregation of genetic marker with DR susceptibility loci within the family. If linkage is present, the marker is inherited together with the causal variant. If it is not present, the marker is inherited independently. As a result, the closer the physical distance of the marker to DR susceptibility loci, the stronger the evidence is for linkage.

Linkage analysis has been the mainstay approach for studying mendelian disorders and has succeeded for a handful of common complex disorders, such as Crohn disease; the success with Crohn disease occurred with the identification of NOD2/CARD15 on chromosome 16.96 However, certain presentations of DR pose significant challenges in family studies. For example, the late onset of DR, especially for those with type 2 DM, suggests that the parents of the proband are often deceased, leaving only one generation of family members available to study. Thus, other study designs, such as sib-pair analysis, have been the dominant model used for linkage studies in DR.

Three linkage studies13,23,24 performed in Pima Indians and Mexican Americans have implicated regions on chromosomes 1, 3, and 12 for DR (Table 3). However, with the possible exception of 1p36, none of these regions reached genome-wide statistical linkage significance of a logarithm of odds (LOD) score greater than 3.3. One study13 demonstrated a LOD score of 3.01 for single-point and 2.58 for multiple-point analysis at 1p36 in the Pima Indians, indicating suggestive evidence of linkage for DR in this population. This approach has several limitations. First, linkage studies only offer rough estimates of the genomic region because the mapping resolution is generally low, literally a test of millions of basepairs. Much more extensive efforts are required to pinpoint specific causal variants responsible for DR. Second, linkage studies often benefit from large families. Linkage studies on DR have thus far been conducted in Pima Indians and Mexican Americans, where large families are available for study. It has not been reported in other ethnicities. Third, the effect size (penetrance) of individual variants may be of sufficiently small magnitude that most study would be underpowered to detect genomic locations via cosegregation expected for complex multifactorial disorders such as DR.

Table Graphic Jump LocationTable 3.  Summary of Linkage Studies of DR
Genome-Wide Association Studies

More recent technologic advances have revolutionized the field toward the second hypothesis-free generating approach, GWASs, in which up to millions of SNPs can be tested against traits such as DR. These developments include microarray-based technology with tag SNPs, using the concept of linkage disequilibrium where adjacent or correlated SNPs cosegregate together in populations. Data from publicly available databases, such as the HapMap and the 1000 Genome Project, have been instrumental in developing such arrays.

Since the first reported success of a well-designed GWAS, more than 2000 loci have demonstrated significant and often replicated associations with one or more common complex disorders.32 Although this field has received a number of criticisms, the reality is that the use of GWASs has been the most successful approach in the genetics of common diseases to date. The use of this technology in the study of DR is relatively recent. Four small-scale GWASs with modest sample sizes conducted in Mexican American, Chinese, and white populations have found borderline or weak associations with DR in either type 1 or type 2 DM.2528 The first study,25 conducted in 103 cases (individuals with moderate to severe NPDR and PDR) and 183 controls (individuals with normal to early NPDR) of Mexican American descent, found borderline significance with DR at 6 loci (Table 4). The second study,26 conducted in 174 cases (individuals with NPDR and PDR) vs 675 controls (individuals with DM but no DR and nondiabetic individuals) of Chinese descent, found several SNPs that have appeared to attain genome-wide statistical significance with DR (Table 4). The main problem in this latter study was the use of all 6 genetic models (genotype, allele, trend, additive, dominant, and recessive) simultaneously in their analysis to determine the most significant P value. Had proper corrections for multiple testing been used, the stringent cutoff for the P value should have been multiplied by 6 because of 6 different genetic models run on each SNP. In this way, none of the SNPs or loci reached the typical genome-wide statistical significance of P < 5E-08 after correction for multiple comparisons. The third study,27 conducted in 973 cases (patients with PDR and diabetic macular edema) vs 1856 controls (all others, including those with NPDR) who were white and had type 1 DM, found borderline significance at several SNPs or loci with DR in a combined meta-analysis (Table 4). However, a replication analysis conducted on the top signals in the WESDR of those with type 1 DM did not confirm these associations.97 The most recent DR GWAS, conducted by the authors and colleagues, compared 1007 Chinese patients with type 2 DM with extreme DR phenotype, defined as 570 individuals with DM of 8 years or longer without DR (controls) vs 437 individuals with PDR (cases) (Table 4). Both groups had similar levels of hemoglobin A1c and duration of DM, 2 of the most important epidemiologic confounders in the study of DR. Association analysis resulted in 3 top loci. Although these findings were of borderline significance, the authors hypothesized that if the detected loci are true associations with DR, then patients with the clinically intermediate eye phenotype (NPDR) would have intermediate frequencies of the risk allele. They then extended these top findings to 479 patients with NPDR and observed that the risk allele of the top 3 SNPs had an intermediate frequency in the NPDR group, suggesting potential DR susceptibility genes in the Chinese that are independent of the level of hemoglobin A1c and DM duration.28 To summarize the GWASs of DR to date, none of the regions reached genome-wide statistical significance. Some of the limitations in these studies include modest sample size by GWAS standard, combining heterogeneous phenotypes (patients with PDR, NPDR, and diabetic macular edema) as cases, poor characterization of healthy individuals (those with no DR) because these individuals are often only assessed one point in time, and poor DR standardization.2528

Table Graphic Jump LocationTable 4.  Summary of Genome-Wide Association Studies of Diabetic Retinopathy
Biomarkers, Proteomics, and Metabolomics

An interesting approach to find genetic susceptibility genes in DR is through the intermediate associations with biomarkers (also known as intermediate phenotypes), an approach analogous to that of the investigations seen in lipids with myocardial infarctions98 and glucose-related traits and obesity with type 2 DM.99,100 A number of systemic biomarkers have been a subject of investigation for association with DR. Many of these biomarkers are related to markers of systemic inflammation,101106 angiogenesis,106 endothelial dysfunction,102 insulin resistance,101 hemostatic disturbance,103 and homocysteinemia,102,103 suggesting that one or more of these processes are involved in the pathogenesis of DR. Analyzing the genetic associations of these biomarkers (genes for the quantitative assessments of biomarkers) might shed some important knowledge about the genetic interplays that are responsible for the development and progressions of DR.

Similarly, proteomics and metabolomics and their relationship to the genome (also called functional genomics) will be another area of investigation in the study of DR. Proteomics is a large-scale study of the structure and function of proteins. A prior study107 examining the vitreous proteome in nondiabetic, diabetic without DR, and PDR patients using label-free mass spectrometry–based spectral counting approaches found a number of proteins associated with key biological pathways in the kallikrein-kinin, coagulation, and complement systems to exhibit protein alterations in patients with PDR compared with the other groups. A review of key findings of proteomics in DR of both animal and human studies concluded that multiple proteins, such as apolipoprotein A-I and apolipoprotein H, are more likely to contribute to retinal disease than single proteins alone.108

Metabolomics is a global measurement of the immediate cellular state within a given biological system, taking into account the genetic profiles, altered enzymatic activities, and environmental and lifestyle factors. A recent, small study,109 examining the metabolomics in DR of 89 Chinese patients, found disturbances in fatty acid (stearic acid, linoleic acid, and arachidonic acid), amino acids (aspartic acid), and glucose alterations to vary differently among diabetic patients without DR, NPDR, and PDR. Although the study of metabolomics in ophthalmology is rather new, its applications in other fields, such as oncology, has demonstrated successful clinical utility, ranging from quantitative assessment of metabolomic biomarkers for cancer diagnosis, optimization of therapeutic agents, evaluation of treatment efficacy and response, and prediction of treatment toxicity or resistance.110 In the future, the application of proteomics and metabolomics to the study of DR may facilitate in the discovery, identification, or quantification of biomarkers to aid in early disease detection, diagnosis, and treatment response.

Next-Generation Sequencing and Exome Chip Studies

Massively parallel sequencing technology has been a breakthrough in the transformation of genomic medicine for mendelian disorders. With high-throughput sequencing, scientists have been able to use large amounts of sequenced data with lower-cost reads to address a range of biological diseases,111113 examine the origin of human protein-coding variants,114 and determine population-specific whole-genome sequencing databases.115 Although current exome sequencing studies are well powered to discover functional variants, current exome sequencing studies are not as well powered to establish an association. Thus, the exome chip was design to provide a cost-effective way to examine large number of samples. The exome chip array was designed to test approximately 250 000 SNPs covering putative functional exonic variants (nonsynonymous variants, splice variants, and stop-altering variants) from a range of diseases and populations.116 This approach has been successfully applied to the identification of low-frequency and rare nonsynonymous variants that contribute to processes such as fasting insulin processing and secretion in nondiabetic individuals.117 It is without a doubt that the future directions in the genetics of DR will encompass a number of these novel technologies.

To approach the genetics of DR in a systematic way would require large collaborative efforts and several methodologic improvements. First, the establishment of large-scale consortia has been successful for a number of disorders, such as DM,99,118 lipids,98 blood pressure, and cardiovascular diseases,119 and can be organized based on disease phenotypes or cohort.120 Second, an important aim is the standardization of a DR phenotype, classified with the Early Treatment Diabetic Retinopathy Study severity scale or a similar modification. A third aim is the standardization of associated phenotypes (DM duration, glycemic controls, blood pressure, lipid profiles, and medications) to minimize heterogeneity in the comparison. Fourth, the genetic effect of each variant on DR is likely to be modest, and larger sample cohorts are required to find modest associations. Fifth, large meta-analyses between different cohorts and different ethnicities have proven difficult to conduct to date because of technical challenges. Standardization of study protocols among different studies could be improved on to increase power. Sixth, novel statistical approaches, such as using a combination of GWASs and genome-wide linkage studies to first prioritize the genome, could be a more efficient means to identify candidate genes for DR,121 although this approach would require strong evidence of linkage peaks in families. Furthermore, studies of different ethnicities need to be conducted to find population-specific signals in DR, given the different prevalence rate observed in different populations. Lastly, novel approaches, such as biomarkers as intermediate phenotypes, proteomics, metabolomics, exome array, and next-generation sequencing, may integrate systematic information in the field of functional genomics or systems biology to better our understanding of the complexity of DR.

Diabetic retinopathy remains as one of the most complex, heterogeneous, multifactorial disorders of all genetic studies. The identification of genetic susceptibility loci for DR through candidate gene approaches, linkage studies, and GWASs has not proven markedly successful to date, given the often conflicting and inconclusive results. It is clear that the study of the genetics of DR is still in its infancy and faces many challenges because of the complexity of the disease. A number of challenges and strategies are detailed in this review. Only when we achieve these important milestones will it be possible to understand the genetic contributions in DR, identify true genetic variants, and subsequently develop early screening assays for at-risk individuals and novel therapies to combat this common cause of blindness in adults.

Corresponding Author: Jerome I. Rotter, MD, Institute for Translational Genomics and Population Sciences, Los Angeles Bio Medical Research Institute, Harbor–UCLA Medical Center, 1124 W Carson St, Torrance, CA 90502 (jrotter@labiomed.org).

Submitted for Publication: January 26, 2013; final revision received April 24, 2013; accepted April 30, 2013.

Published Online: November 7, 2013. doi:10.1001/jamaophthalmol.2013.5024.

Author Contributions: Dr Rotter had full access to all of the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis.

Study concept and design: All authors.

Acquisition of data: Kuo.

Analysis and interpretation of data: All authors.

Drafting of the manuscript: Kuo.

Critical revision of the manuscript for important intellectual content: Wong, Rotter.

Obtained funding: Rotter.

Administrative, technical, or material support: All authors.

Study supervision: Rotter.

Conflict of Interest Disclosures: None reported.

Funding/Support: This study was supported by grant EY014684 from the National Institutes of Health (Dr Rotter), grants EY014684-03S1 and EY014684-04S1 from the American Recovery and Reinvestment Act Supplement (Dr Rotter), grant DK063491 to the Southern California Diabetes Endocrinology Research Center from the National Institute of Diabetes and Digestive and Kidney Disease, the Eye Birth Defects Foundation Inc, and the Cedars-Sinai Board of Governor’s Chair in Medical Genetics. The Clinical and Translational Science Institute was supported by grant UL1TR000124 from the National Center for Advancing Translational Sciences.

Role of the Sponsor: The funding agencies had no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; and preparation, review, or approval of the manuscript; and decision to submit the manuscript for publication.

Disclaimer: The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Additional Contributions: Kent D. Taylor, PhD, provided assistance in language and structure of manuscript.

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Yoo  YJ, Bull  SB, Paterson  AD, Waggott  D, Sun  L; Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications Research Group.  Were genome-wide linkage studies a waste of time? exploiting candidate regions within genome-wide association studies. Genet Epidemiol. 2010;34(2):107-118.
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Figures

Place holder to copy figure label and caption
Figure.
Heritability Estimates for Diabetic Retinopathy

DCCT indicates Diabetes Control and Complications Trial; DR, diabetic retinopathy; FIND-Eye Study, Family Investigation of Nephropathy and Diabetes–Eye Study; PDR, proliferative diabetic retinopathy.

Graphic Jump Location

Tables

Table Graphic Jump LocationTable 1.  Summary of Familial Aggregation Studies in Diabetic Retinopathy
Table Graphic Jump LocationTable 2.  Summary of Individual Candidate Gene Studies of Diabetic Retinopathya
Table Graphic Jump LocationTable 3.  Summary of Linkage Studies of DR
Table Graphic Jump LocationTable 4.  Summary of Genome-Wide Association Studies of Diabetic Retinopathy

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