Pathway analysis of complex diseases for GWAS, extending to consider rare variants, multi-omics and interactions.

BACKGROUND: Genome-wide association studies (GWAS) is a major method for studying the genetics of complex diseases. Finding all sequence variants to explain fully the aetiology of a disease is difficult because of their small effect sizes. To better explain disease mechanisms, pathway analysis is used to consolidate the effects of multiple variants, and hence increase the power of the study. While pathway analysis has previously been performed within GWAS only, it can now be extended to examining rare variants, other "-omics" and interaction data. SCOPE OF REVIEW: 1. Factors to consider in the choice of software for GWAS pathway analysis. 2. Examples of how pathway analysis is used to analyse rare variants, other "-omics" and interaction data. MAJOR CONCLUSIONS: To choose appropriate software tools, factors for consideration include covariate compatibility, null hypothesis, one- or two-step analysis required, curation method of gene sets, size of pathways, and size of flanking regions to define gene boundaries. For rare variants, analysis performance depends on consistency between assumed and actual effect distribution of variants. Integration of other "-omics" data and interaction can better explain gene functions. GENERAL SIGNIFICANCE: Pathway analysis methods will be more readily used for integration of multiple sources of data, and enable more accurate prediction of phenotypes.

Genome-wide association study for refractive astigmatism reveals genetic co-determination with spherical equivalent refractive error: the CREAM consortium.

To identify genetic variants associated with refractive astigmatism in the general population, meta-analyses of genome-wide association studies were performed for: White Europeans aged at least 25 years (20 cohorts, N = 31,968); Asian subjects aged at least 25 years (7 cohorts, N = 9,295); White Europeans aged <25 years (4 cohorts, N = 5,640); and all independent individuals from the above three samples combined with a sample of Chinese subjects aged <25 years (N = 45,931). Participants were classified as cases with refractive astigmatism if the average cylinder power in their two eyes was at least 1.00 diopter and as controls otherwise. Genome-wide association analysis was carried out for each cohort separately using logistic regression. Meta-analysis was conducted using a fixed effects model. In the older European group the most strongly associated marker was downstream of the neurexin-1 (NRXN1) gene (rs1401327, P = 3.92E-8). No other region reached genome-wide significance, and association signals were lower for the younger European group and Asian group. In the meta-analysis of all cohorts, no marker reached genome-wide significance: The most strongly associated regions were, NRXN1 (rs1401327, P = 2.93E-07), TOX (rs7823467, P = 3.47E-07) and LINC00340 (rs12212674, P = 1.49E-06). For 34 markers identified in prior GWAS for spherical equivalent refractive error, the beta coefficients for genotype versus spherical equivalent, and genotype versus refractive astigmatism, were highly correlated (r = -0.59, P = 2.10E-04). This work revealed no consistent or strong genetic signals for refractive astigmatism; however, the TOX gene region previously identified in GWAS for spherical equivalent refractive error was the second most strongly associated region. Analysis of additional markers provided evidence supporting widespread genetic co-susceptibility for spherical and astigmatic refractive errors.

Prevalence of myopia-related retinal changes among 12-18 year old Hong Kong Chinese high myopes.

PURPOSE: To determine the prevalence and risk factors of myopia-related retinal changes in Hong Kong Chinese adolescents with high myopia. METHODS: A cross-sectional study on Hong Kong Chinese teenage subjects with high myopia was conducted between January 2005 and June 2009. Subjects were recruited via newspaper advertisements, invitation letters to schools, leaflets and posters. Data collected included history related to myopia progression and retinal characteristics. RESULTS: In total, 120 subjects (61 boys and 59 girls) were recruited. The mean age was 14.8 ± 1.6 years (range: 12-18 years). The mean SER of the eyes was -8.41 ± 1.60 D. Ninety four of the 120 adolescents were found to have a retinal change of which 0.8% were sight-threatening, 2.5% were posterior pole changes, and 61.7% were peripheral retinal changes. The five most frequent retinal changes found were optic nerve crescents (52.5%), white-without-pressure (51.7%), lattice degeneration (5.8%), microcystoid degeneration (5%) and pigmentary degeneration (4.2%). After adjusting for myopia over -8 D, age, gender, duration of myopia, family retinal history and intraocular pressure (IOP), binary logistic regressions showed that an axial length longer than 26.5 mm was a significant risk factor for peripheral retinal changes, optic nerve crescents and white-without-pressure. CONCLUSIONS: Peripheral retinal degenerative changes and optic nerve crescent were found in a significant proportion of high myopic teenage subjects. There is increased risk of retinal changes in eyes with an axial length >26.5 mm in 12-18 year-olds.

Corneal changes following near work in myopic anisometropia.

PURPOSE: To examine the symmetry of corneal changes following near work in the fellow eyes of non-amblyopic myopic anisometropes. METHODS: Thirty-four non-amblyopic, myopic anisometropes (minimum 1 D spherical equivalent anisometropia) had corneal topography measured before and after a controlled near work task. Subjects were positioned in a headrest to minimise head movements and read continuous text on a computer monitor for 10 min at an angle of 25 degrees downward gaze and an accommodation demand of 2.5 D. Measures of the morphology of the palpebral aperture during primary and downward gaze were also obtained. RESULTS: The more and less myopic eyes exhibited a high degree of interocular symmetry for measures of palpebral aperture morphology during both primary and downward gaze. Following the near work task, fellow eyes also displayed a symmetrical change in superior corneal topography (hyperopic defocus) which correlated with the position of the upper eyelid during downward gaze. Greater changes in the spherical corneal power vector (M) following reading were associated with a narrower palpebral aperture during downward gaze (p = 0.07 for more myopic and p = 0.03 for less myopic eyes). A significantly greater change in J0 (an increase in against the rule astigmatism) was observed in the more myopic eyes (-0.04 ± 0.04 D) compared to the less myopic eyes (-0.02 ± 0.06 D) over a 6 mm corneal diameter (p = 0.01). CONCLUSIONS: Changes in corneal topography following near work are highly symmetrical between the fellow eyes of myopic anisometropes due to the interocular symmetry of the palpebral aperture. However, the more myopic eye exhibits changes in corneal astigmatism of greater magnitude compared to the less myopic eye.

A novel missense mutation in the NYX gene associated with high myopia.

PURPOSE: Myopia is a complex eye disorder. The X-linked form of complete congenital stationary night blindness (CSNB1A) is usually associated with moderate to high myopia, and is caused by mutations in the NYX gene. We explored if NYX mutations could be associated with high myopia, but not CSNB1A. METHODS: The coding regions of the NYX gene were sequenced for 204 Chinese males with high myopia (-8.00 dioptres or worse for both eyes). The frequencies of any sequence variations identified were determined in 200 Chinese males without myopia. Electro-oculography, electroretinography and standard cone function tests were performed on a male high myope carrying a mutation. RESULTS: A missense mutation (c.529_530GC>AT or p.Ala177Met) was identified in one male subject with high myopia, but not in 200 male emmetropes. Neither was this variant found in any of the 529 male and 567 female subjects of various ethnic backgrounds whose genome sequences are documented in the 1000 Genomes Project database. The mutation was predicted to affect the protein function. From ocular electrophysiological tests, the proband was found to have normal rod function, but mildly abnormal cone function and inner retina function. He did not seem to suffer from CSNB1A. CONCLUSIONS: One novel missense NYX mutation was identified in an adult male presented with high myopia, but without the major electrophysiological features normally associated with CSNB1A. NYX gene mutations may be considered as one of the rare genetic risk factors for high myopia without key features of CSNB1A.

Investigating the relationship between UMODL1 gene polymorphisms and high myopia: a case-control study in Chinese.

BACKGROUND: The UMODL1 gene was found to be associated with high myopia in Japanese. This study aimed to investigate this gene for association with high myopia in Chinese. METHODS: Two groups of unrelated Han Chinese from Hong Kong were recruited using the same criteria: Sample Set 1 comprising 356 controls (spherical equivalent, SE, within ±1 diopter or D) and 356 cases (SE ≤ -8D), and Sample Set 2 comprising 394 controls and 526 cases. Fifty-nine tag single nucleotide polymorphisms (SNPs) were selected and genotyped for Sample Set 1. Four SNPs were followed up with Sample Set 2. Both single-marker and haplotype analyses were performed with cases defined by different SE thresholds. Secondary phenotypes were also analyzed for association with genotypes. RESULTS: Data filtering left 57 SNPs for analysis. Single-marker analysis did not reveal any significant differences between cases and controls in the initial study. However, haplotype GCT for markers rs220168-rs220170-rs11911271 showed marginal significance (empirical P = 0.076; SE ≤ -12D for cases), but could not be replicated in the follow-up study. In contrast, non-synonymous SNP rs3819142 was associated with high myopia (SE ≤ -10D) in the follow-up study, but could not be confirmed using Sample Set 1. The SNP rs2839471, positive in the original Japanese study, gave negative results in all our analyses. Exploratory analysis of secondary phenotypes indicated that allele C of rs220120 was associated with anterior chamber depth (adjusted P = 0.0460). CONCLUSIONS: Common UMODL1 polymorphisms were unlikely to be important in the genetic susceptibility to high myopia in Han Chinese.

UPDG: utilities package for data analysis of pooled DNA GWAS.

BACKGROUND: Despite being a well-established strategy for cost reduction in disease gene mapping, pooled DNA association study is much less popular than the individual DNA approach. This situation is especially true for pooled DNA genomewide association study (GWAS), for which very few computer resources have been developed for its data analysis. This motivates the development of UPDG (Utilities package for data analysis of Pooled DNA GWAS). RESULTS: UPDG represents a generalized framework for data analysis of pooled DNA GWAS with the integration of Unix/Linux shell operations, Perl programs and R scripts. With the input of raw intensity data from GWAS, UPDG performs the following tasks in a stepwise manner: raw data manipulation, correction for allelic preferential amplification, normalization, nested analysis of variance for genetic association testing, and summarization of analysis results. Detailed instructions, procedures and commands are provided in the comprehensive user manual describing the whole process from preliminary preparation of software installation to final outcome acquisition. An example dataset (input files and sample output files) is also included in the package so that users can easily familiarize themselves with the data file formats, working procedures and expected output. Therefore, UPDG is especially useful for users with some computer knowledge, but without a sophisticated programming background. CONCLUSIONS: UPDG provides a free, simple and platform-independent one-stop service to scientists working on pooled DNA GWAS data analysis, but with less advanced programming knowledge. It is our vision and mission to reduce the hindrance for performing data analysis of pooled DNA GWAS through our contribution of UPDG. More importantly, we hope to promote the popularity of pooled DNA GWAS, which is a very useful research strategy.

A DNA pooling-based case-control study of myopia candidate genes COL11A1, COL18A1, FBN1, and PLOD1 in a Chinese population.

PURPOSE: We examined the relationship between high myopia and common polymorphisms in four candidate genes: collagen, type XI, alpha 1 (COL11A1); collagen, type XVIII, alpha 1 (COL18A1); fibrillin 1 (FBN1); and procollagen-lysine 1,2-oxoglutarate 5-dioxygenase 1 (PLOD1). These genes were selected because rare pathogenic mutations in these genes cause disease syndromes that have myopia, usually high myopia, as one of the common presenting features. METHODS: This study recruited 600 unrelated Han Chinese subjects including 300 cases with high myopia (spherical equivalent or SE≤-8.00 diopters) and 300 controls (SE within ±1.00 diopter). A total of 66 tag single nucleotide polymorphisms (SNPs) were selected for study from these four candidate genes. The study adopted a DNA pooling strategy with an initial screen of DNA pools to identify putatively positive SNPs and then confirmed the "positive" SNPs by genotyping individual samples forming the original DNA pools. DNA pools were each constructed by mixing equal amounts of DNA from 50 individuals with the same phenotype status. Six case pools were prepared from 300 cases and six control pools from 300 controls. Allele frequencies of DNA pools were estimated by analyzing the primer-extended products with denaturing high performance liquid chromatography and compared between case pools and control pools with nested ANOVA. RESULTS: In the first stage, 60 SNPs from the 4 candidate genes were successfully screened using the DNA pooling approach. Of these, 6 SNPs showed a statistical significant difference in estimated allele frequencies between case pools and controls at p<0.10. In the second stage, these "positive" SNPs were followed up by individual genotyping, but failed to be confirmed via standard single-marker and haplotype analyses. CONCLUSIONS: Common polymorphisms in these four candidate genes (COL11A1, COL18A1, FBN1 and PLOD1) were unlikely to play important roles in the genetic susceptibility to high myopia.

Interocular symmetry in myopic anisometropia.

PURPOSE: To investigate the interocular symmetry of optical, biometric, and biomechanical characteristics between the fellow eyes of myopic anisometropes. METHODS: Thirty-four young, healthy myopic anisometropic adults (≥ 1 D spherical equivalent difference between eyes) without amblyopia or strabismus were recruited. A range of biometric and optical parameters were measured in both eyes of each subject including axial length, ocular aberrations, intraocular pressure, corneal topography, and biomechanics. Ocular sighting dominance was also measured. RESULTS: Mean absolute spherical equivalent anisometropia was 1.70 ± 0.74 D, and there was a strong correlation between the degree of anisometropia and the interocular difference in axial length (r = 0.81, p < 0.001). The more and less myopic eyes displayed a high degree of interocular symmetry for the majority of biometric, biomechanical, and optical parameters measured. When the level of anisometropia exceeded 1.75 D, the more myopic eye was more likely to be the dominant sighting eye than for lower levels of anisometropia (p = 0.002). Subjects with greater levels of anisometropia (>1.75 D) also showed high levels of correlation between the dominant and non-dominant eyes in their biometric, biomechanical, and optical characteristics. CONCLUSIONS: Although significantly different in axial length, anisometropic eyes display a high degree of interocular symmetry for a range of anterior eye biometrics and optical parameters. For higher levels of anisometropia, the more myopic eye tends to be the dominant sighting eye.

Retinal thickness in myopic and non-myopic eyes.

PURPOSE: To investigate the retinal thickness profile in myopic and non-myopic eyes. METHODS: The retinal thickness profile of 30 myopic eyes [spherical equivalent error (SER) between -6.00 and -13.63 D] and 31 non-myopic eyes (SER between +2.75 and -0.50 D) were measured using the Stratus OCT (Carl Zeiss Meditec, Dublin, CA, USA). Two scan types were used: the Macular Thickness Map and the Customized Line Scan for a central 80° horizontal retinal thickness profile. RESULTS: At foveal center and fovea, myopic eyes had a thicker retina than the non-myopic group (p = 0.002 and 0.044, respectively). At other zones of the macula, the retina was significantly thinner in myopic eyes compared to non-myopic eyes (p < 0.01, unpaired t-test). From 40° nasal to 40° temporal retina, a general reduction of retinal thickness was observed across the myopic retina compared to the non-myopic retina except at 20° nasal to fixation. CONCLUSIONS: There was general reduction in retinal thickness within the horizontal central 80° in myopic eyes compared with non-myopic eyes.

The myopia susceptibility locus vasoactive intestinal peptide receptor 2 (VIPR2) contains variants with opposite effects.

Myopia is the commonest eye disorder in the world. High myopes are predisposed to ocular pathologies. The vasoactive intestinal peptide receptor 2 (VIPR2) gene was identified as a myopia susceptibility locus by our group and another group. We continued to fine-map this locus. A case-control study was performed in 4 sequential stages with a total of 941 highly myopic subjects and 846 control subjects, all unrelated Chinese. Stage 1 experimentally genotyped 64.4% of the entire cohort for 152 single-nucleotide polymorphisms (SNPs) and Stage 2 the remaining subjects for 21 SNPs. Stage 3 combined the genotypes for 21 SNPs for the entire cohort, and identified one group of high-risk haplotypes and one group of protective haplotypes significantly associated with high myopia. Stage 4 imputed genotypes for variants in the VIPR2 region and identified two independent groups of variants: one group with high-risk minor alleles and another with protective minor alleles. Variants within each group were generally in strong linkage disequilibrium among themselves while high-risk variants were in linkage equilibrium with protective variants. Therefore, the VIPR2 locus seems to contain variants with opposite effects. This is the first study that has examined the genetic architecture of a myopia susceptibility locus in detail.

A review of current approaches to identifying human genes involved in myopia.

The prevalence of myopia is high in many parts of the world, particularly among the Orientals such as Chinese and Japanese. Like other complex diseases such as diabetes and hypertension, myopia is likely to be caused by both genetic and environmental factors, and possibly their interactions. Owing to multiple genes with small effects, genetic heterogeneity and phenotypic complexity, the study of the genetics of myopia poses a complex challenge. This paper reviews the current approaches to the genetic analysis of complex diseases and how these can be applied to the identification of genes that predispose humans to myopia. These approaches include parametric linkage analysis, non-parametric linkage analysis like allele-sharing methods and genetic association studies. Basic concepts, advantages and disadvantages of these approaches are discussed and explained using examples from the literature on myopia. Microsatellites and single nucleotide polymorphisms are common genetic markers in the human genome and are indispensable tools for gene mapping. High throughput genotyping of millions of such markers has become feasible and efficient with recent technological advances. In turn, this makes the identification of myopia susceptibility genes a reality.

Use of the Optomap with lid retraction and its sensitivity and specificity.

BACKGROUND: Optomap uses the ultra-wide field scanning laser ophthalmoscopy to provide retinal examination. It permits fundus examination without the use of a mydriatic, which is more comfortable for the patients. This paper determines the sensitivity and specificity of the Optomap for detecting retinal signs under non-mydriatic conditions. METHODS: Fifty-four eyes identified with retinal/choroidal signs and eight normal eyes were recruited from 31 Hong Kong Chinese subjects. Photo-documentation of fundal changes was obtained with the Optomap under non-mydriatic conditions before a dilated fundus examination by a clinician using standard procedures. The eyelid was retracted using a cotton bud when necessary. Dilated fundus examinations were performed by another clinician using binocular indirect ophthalmoscopy and slitlamp biomicroscopy with a fundus lens. The Optomap images were evaluated by four other investigators under masked condition. The International Classification of Disease, Ninth Revision (ICD-9-CM) was adopted for recording retinal features. Screening results were compared with those obtained using the dilated fundus examination as the gold standard. RESULTS: The cotton bud method for eyelid retraction showed an improvement in the area of retina that could be visualised. The sensitivity and specificity of the Optomap averaged 76.4 and 71.9 per cent, respectively. Some fundal signs were missed by all observers in the Optomap but not with the biomicroscope. These included white-without-pressure, lattice degeneration, paramacular drusen and pigmentary changes at central fundus. CONCLUSION: Optomap serves as a reliable screening tool for fundus examination especially because it covers a much wider area of the peripheral retina than other digital instruments for fundus photography.

Awareness of diabetic retinopathy and its association with attendance for systematic screening at the public primary care setting: a cross-sectional study in Hong Kong.

OBJECTIVE: To assess the association between awareness of diabetic retinopathy (DR) and actual attendance for DR screening. DESIGN: Cross-sectional study. SETTING: Two public general outpatient clinics. PARTICIPANTS: The subjects were people with diabetes mellitus (DM) who participated in a randomised controlled trial, set up in 2008, to test the impact of a copayment on attendance for DR screening. PRIMARY AND SECONDARY OUTCOME MEASURES: The subjects' awareness of DR was evaluated using a structured questionnaire conducted via a telephone interview. The attendance for screening was from the actual attendance data. Association between awareness and attendance for screening was determined using multivariate logistic regression model and was reported as ORs. RESULTS: A total of 2593 participants completed the questionnaire. A total of 42.9% (1113/2593) said they would worry if they had any vision loss and 79.6% (2063/2593) knew that DM could cause blindness. Only 17.5% (453/2593) knew that treatment was available for DR and 11.5% (297/2593) knew that early DR could be asymptomatic. The importance of having a regular eye examination was acknowledged by 75.7% (1964/2593), but 34% (881/2593) did not know how frequently their eyes should be examined. Worry about vision loss (OR=1.72, P<0.001), awareness of the importance of regular eye examination (OR=1.83, P=0.002) and awareness of the frequency of eye examinations ('every year' (OR=2.64, P<0.001) or 'every 6 months' (OR=3.27, P<0.001)) were the most significant factors associated with attendance. CONCLUSIONS: Deficits in knowledge of DR and screening were found among subjects with DM, and three awareness factors were associated with attendance for screening. These factors could be targeted for future interventions.

Linkage and association of myocilin (MYOC) polymorphisms with high myopia in a Chinese population.

PURPOSE: To test the association between myocilin gene (MYOC) polymorphisms and high myopia in Hong Kong Chinese by using family-based association study. METHODS: A total of 162 Chinese nuclear families, consisting of 557 members, were recruited from an optometry clinic. Each family had two parents and at least one offspring with high myopia (defined as -6.00D or less for both eyes). All offspring were healthy with no clinical evidence of syndromic disease and other ocular abnormality. Genotyping was performed for two MYOC microsatellites (NGA17 and NGA19) and five tag single nucleotide polymorphisms (SNPs) spreading across the gene. The genotype data were analyzed with Family-Based Association Test (FBAT) software to check linkage and association between the genetic markers and myopia, and with GenAssoc to generate case and pseudocontrol subjects for investigating main effects of genetic markers and calculating the genotype relative risks (GRR). RESULTS: FBAT analysis showed linkage and association with high myopia for two microsatellites and two SNPs under one to three genetic models after correction for multiple comparisons by false discovery rate. NGA17 at the promoter was significant under an additive model (p=0.0084), while NGA19 at the 3' flanking region showed significant results under both additive (p=0.0172) and dominant (p=0.0053) models. SNP rs2421853 (C>T) exhibited both linkage and association under additive (p=0.0009) and dominant/recessive (p=0.0041) models. SNP rs235858 (T>C) was also significant under additive (p=4.0E-6) and dominant/recessive (p=2.5E-5) models. Both SNPs were downstream of NGA19 at the 3' flanking region. Positive results for these SNPs were novel findings. A stepwise conditional logistic regression analysis of the case-pseudocontrol dataset generated by GenAssoc from the families showed that both SNPs could separately account for the association of NGA17 or NGA19, and that both SNPs contributed separate main effects to high myopia. For rs2421853 and with C/C as the reference genotype, the GRR increased from 1.678 for G/A to 2.738 for A/A (p=9.0E-4, global Wald test). For rs235858 and with G/G as the reference, the GRR increased 2.083 for G/A to 3.931 for A/A (p=2.0E-2, global Wald test). GRR estimates thus suggested an additive model for both SNPs, which was consistent with the finding that, of the three models tested, the additive model gave the lowest p values in FBAT analysis. CONCLUSIONS: Linkage and association was shown between the MYOC polymorphisms and high myopia in our family-based association study. The SNP rs235858 at the 3' flanking region showed the highest degree of confidence for association.

Genetic Association Study of KCNQ5 Polymorphisms with High Myopia.

Identification of genetic variations related to high myopia may advance our knowledge of the etiopathogenesis of refractive error. This study investigated the role of potassium channel gene (KCNQ5) polymorphisms in high myopia. We performed a case-control study of 1563 unrelated Han Chinese subjects (809 cases of high myopia and 754 emmetropic controls). Five tag single-nucleotide polymorphisms (SNPs) of KCNQ5 were genotyped, and association testing with high myopia was conducted using logistic regression analysis adjusted for sex and age to give Pasym values, and multiple comparisons were corrected by permutation test to give Pemp values. All five noncoding SNPs were associated with high myopia. The SNP rs7744813, previously shown to be associated with refractive error and myopia in two GWAS, showed an odds ratio of 0.75 (95% CI 0.63-0.90; Pemp = 0.0058) for the minor allele. The top SNP rs9342979 showed an odds ratio of 0.75 (95% CI 0.64-0.89; Pemp = 0.0045) for the minor allele. Both SNPs are located within enhancer histone marks and DNase-hypersensitive sites. Our data support the involvement of KCNQ5 gene polymorphisms in the genetic susceptibility to high myopia and further exploration of KCNQ5 as a risk factor for high myopia.

Family-based association analysis of hepatocyte growth factor (HGF) gene polymorphisms in high myopia.

PURPOSE: To investigate the association of high myopia with polymorphisms in the hepatocyte growth factor (HGF) gene, a potential candidate for myopia development. METHODS: Single nucleotide polymorphisms (SNPs) were screened and identified in the HGF gene region with denaturing high-performance liquid chromatography, and their linkage disequilibrium pattern was established in a Han Chinese population (n=150). Tag SNPs were selected and genotyped using restriction digestion and fluorescence polarization assays for 128 nuclear families with 133 severely myopic (mean spherical equivalent [MSE]

[Establishing the linkage disequilibrium pattern for the all-trans-retinol dehydrogenase (RDH8) gene].

OBJECTIVE: As part of an on-going effort to map genes involved in complex eye diseases, myopia in particular, single nucleotide polymorphisms (SNPs) and linkage disequilibrium (LD) pattern were used to identified the gene within and around the All-trans-retinol dehydrogenase (RDH8). METHODS: Denaturing high-performance liquid chromatography (DHPLC) was used to screen SNPs in 4 DNA pools each consisting of DNA from five individuals, and genotypes identified SNPs coupled with DNA pooling strategy were performed in 150 Chinese subjects from Hong Kong. The identified common SNPs were included in LD and haplotype analysis using the Haploview2.05 and EH programs. RESULTS: Fifteen SNPs were identified: 7 were common with the minor allele frequency > 0.05, and 10 were novel. Four SNPs in the 3' region exhibited significant LD (/|D'/ > 0.75 and its confidence interval suggesting strong LD, r2 > 0.33, P < 0.031) and formed a haplotype block while 3 common SNPs in the 5' region did not exhibit obvious LD. CONCLUSION: The block-like LD pattern existed around the RDH8 gene region suggest that one SNP (RDH8E5a probably) in the 3' region and at least 2 SNPs in the 5' region (RDH851 particularly) were needed in association studies involving RDH8.

Retinal stretching limits peripheral visual acuity in myopia.

Axial elongation of the myopic eye has the potential to stretch the retina, thereby reducing the sampling density of retinal neurons. Resolution acuity in the peripheral field of normal eyes is known to be sampling-limited, which suggests that retinal stretching in the myopic eye should have a direct effect on resolution acuity everywhere in the visual field except perhaps the fovea, which is usually optically limited. We tested this prediction that neural sampling density is reduced in myopic eyes by measuring resolution acuity for sinusoidal gratings in the fovea plus five peripheral locations in 60 myopic subjects exhibiting a wide range of refractive errors. Control experiments using a detection paradigm to provoke spatial aliasing verified that peripheral resolution was sampling limited. Retinal spatial frequencies of the grating stimulus were computed assuming Knapps' Law of visual optics, which ensures that retinal image size (in mm) is independent of refractive error when axial myopia is corrected by a spectacle lens located in the anterior focal plane of the eye. Results obtained at every retinal locus showed that resolution acuity declined linearly with magnitude of refractive error. Regression of the population data indicated that approximately 15 D of refractive error doubles the spacing between retinal neurons, thereby halving peripheral resolution acuity relative to the emmetropic eye. Several subjects also demonstrated sampling-limited performance in the fovea, which indicated that optical filtering by the eye's optical system failed to protect the fovea from aliasing artifacts of neural undersampling in these eyes. We conclude that stretching of the retina is a primary cause of reduced spatial resolution of the peripheral field, and occasionally of the fovea, in myopic eyes. Stretching appears to be locally uniform over the central +/-15 degrees of visual field but is globally non-uniform since the foveal region appears to stretch more than the globe itself.

Identification of myopia-associated WNT7B polymorphisms provides insights into the mechanism underlying the development of myopia.

Myopia can cause severe visual impairment. Here, we report a two-stage genome-wide association study for three myopia-related traits in 9,804 Japanese individuals, which was extended with trans-ethnic replication in 2,674 Chinese and 2,690 Caucasian individuals. We identify WNT7B as a novel susceptibility gene for axial length (rs10453441, Pmeta=3.9 × 10(-13)) and corneal curvature (Pmeta=2.9 × 10(-40)) and confirm the previously reported association between GJD2 and myopia. WNT7B significantly associates with extreme myopia in a case-control study with 1,478 Asian patients and 4,689 controls (odds ratio (OR)meta=1.13, Pmeta=0.011). We also find in a mouse model of myopia downregulation of WNT7B expression in the cornea and upregulation in the retina, suggesting its possible role in the development of myopia.