Exploiting genetics to understand paediatric eye disorders

The primary aim of this series of investigations was to identify causal risk factors for paediatric eye disorders (e.g. myopia, hyperopia, strabismus and amblyopia). A series of hypotheses was tested in this project by exploiting state-of-the-art genetic and epidemiological approaches such as genome-wide association studies (GWAS) and Mendelian randomisation (MR). A GWAS for strabismus was performed in order to identify genetic variant(s) conferring susceptibility to the condition. The genetic variant most strongly associated with the phenotype was rs75078292. This SNP, is situated in an LD block on chromosome 17, containing the genes TSPAN10, NPLOC4 and PDE6G. A non-synonymous variant in TSPAN10 – in very high LD with rs75078292 – was previously reported to be associated with myopia. These findings were replicated in a cohort of children (ALSPAC). A Mendelian randomisation approach (both one- and two-sample MR) was used in order to estimate the effect of birth weight within the normal range (2.5 to 4.5kg) on refractive error. The analyses supported the hypothesis that birth weight within normal range plays a causal role in refractive error development. The influence of education on refractive error development was estimated using a Regression Discontinuity design. In this work in UK Biobank, the Raising Of School Leaving Age (ROSLA) 1972 reform was used as a natural experiment; with use of the genetic data such as Principal Components and Polygenic Risk Scores for educational attainment and for refractive error as covariates. The estimated influence of an additional year of education on refractive error development was statistically significant, supporting existing evidence. The hypothesis that hyperopia is causal risk factor for lower educational attainment was tested using non-linear Mendelian randomisation analysis. The results of the analyses revealed that the relationship between refractive error and educational attainment in UK Biobank is non-linear, but did not support the main hypothesis

Stokes inversion techniques with neural networks: analysis of uncertainty in parameter estimation

Magnetic fields are responsible for a multitude of Solar phenomena, including such destructive events as solar flares and coronal mass ejections, with the number of such events rising as we approach the peak of the 11-year solar cycle, in approximately 2025. High-precision spectropolarimetric observations are necessary to understand the variability of the Sun. The field of quantitative inference of magnetic field vectors and related solar atmospheric parameters from such observations has long been investigated. In recent years, very sophisticated codes for spectropolarimetric observations have been developed. Over the past two decades, neural networks have been shown to be a fast and accurate alternative to classic inversion technique methods. However, most of these codes can be used to obtain point estimates of the parameters, so ambiguities, the degeneracies, and the uncertainties of each parameter remain uncovered. In this paper, we provide end-to-end inversion codes based on the simple Milne-Eddington model of the stellar atmosphere and deep neural networks to both parameter estimation and their uncertainty intervals. The proposed framework is designed in such a way that it can be expanded and adapted to other atmospheric models or combinations of them. Additional information can also be incorporated directly into the model. It is demonstrated that the proposed architecture provides high accuracy of results, including a reliable uncertainty estimation, even in the multidimensional case. The models are tested using simulation and real data samples.Comment: 17 pages with 7 figures and 3 tables, submitted to Solar Physic

Exploiting genetics and genomics to improve the understanding of eye diseases [Editorial]

Editorial on the Research Topic Exploiting genetics and genomics to improve the understanding of eye disease

Association between birth weight and refractive error in adulthood:A Mendelian randomisation study

Background Pathological myopia is one of the leading causes of blindness globally. Lower birth weight (BW) within the normal range has been reported to increase the risk of myopia, although findings conflict. We sought to estimate the causal effect of BW on refractive error using Mendelian randomisation (MR), under the assumption of a linear relationship. Methods Genetic variants associated with BW were identified from meta-analysis of a genome-wide association study (GWAS) for self-reported BW in 162 039 UK Biobank participants and a published Early Growth Genetics (EGG) consortium GWAS (n=26 836). We performed a one-sample MR analysis in 39 658 unrelated, adult UK Biobank participants (independent of the GWAS sample) using an allele score for BW as instrumental variable. A two-sample MR sensitivity analysis and conventional ordinary least squares (OLS) regression analyses were also undertaken. Results In OLS analysis, BW showed a small, positive association with refractive error: +0.04 D per SD increase in BW (95% CI 0.02 to 0.07; p=0.002). The one-sample MR-estimated causal effect of BW on refractive error was higher, at +0.28 D per SD increase in BW (95% CI 0.05 to 0.52, p=0.02). A two-sample MR analysis provided similar causal effect estimates, with minimal evidence of directional pleiotropy. Conclusions Our study suggests lower BW within the normal range is causally associated with a more myopic refractive error. However, the impact of the causal effect was modest (range 1.00 D covering approximately 95% of the population)

Education and myopia: assessing the direction of causality by mendelian randomisation

Objectives To determine whether more years spent in education is a causal risk factor for myopia, or whether myopia is a causal risk factor for more years in education. Design Bidirectional, two sample mendelian randomisation study. Setting Publically available genetic data from two consortiums applied to a large, independent population cohort. Genetic variants used as proxies for myopia and years of education were derived from two large genome wide association studies: 23andMe and Social Science Genetic Association Consortium (SSGAC), respectively. Participants 67 798 men and women from England, Scotland, and Wales in the UK Biobank cohort with available information for years of completed education and refractive error. Main outcome measures Mendelian randomisation analyses were performed in two directions: the first exposure was the genetic predisposition to myopia, measured with 44 genetic variants strongly associated with myopia in 23andMe, and the outcome was years in education; and the second exposure was the genetic predisposition to higher levels of education, measured with 69 genetic variants from SSGAC, and the outcome was refractive error. Results Conventional regression analyses of the observational data suggested that every additional year of education was associated with a more myopic refractive error of −0.18 dioptres/y (95% confidence interval −0.19 to −0.17; P<2e-16). Mendelian randomisation analyses suggested the true causal effect was even stronger: −0.27 dioptres/y (−0.37 to −0.17; P=4e-8). By contrast, there was little evidence to suggest myopia affected education (years in education per dioptre of refractive error −0.008 y/dioptre, 95% confidence interval −0.041 to 0.025, P=0.6). Thus, the cumulative effect of more years in education on refractive error means that a university graduate from the United Kingdom with 17 years of education would, on average, be at least −1 dioptre more myopic than someone who left school at age 16 (with 12 years of education). Myopia of this magnitude would be sufficient to necessitate the use of glasses for driving. Sensitivity analyses showed minimal evidence for genetic confounding that could have biased the causal effect estimates. Conclusions This study shows that exposure to more years in education contributes to the rising prevalence of myopia. Increasing the length of time spent in education may inadvertently increase the prevalence of myopia and potential future visual disability

Hyperopia is not causally associated with a major deficit in educational attainment

Purpose: Hyperopia (farsightedness) has been associated with a deficit in children's educational attainment in some studies. We aimed to investigate the causality of the relationship between refractive error and educational attainment. Methods: Mendelian randomization (MR) analysis in 74,463 UK Biobank participants was used to estimate the causal effect of refractive error on years spent in full-time education, which was taken as a measure of educational attainment. A polygenic score for refractive error derived from 129 genetic variants was used as the instrumental variable. Both linear and nonlinear (allowing for a nonlinear relationship between refractive error and educational attainment) MR analyses were performed. Results: Assuming a linear relationship between refractive error and educational attainment, the causal effect of refractive error on years spent in full-time education was estimated as −0.01 yr/D (95% confidence interval, −0.04 to +0.02; P = 0.52), suggesting minimal evidence for a non-zero causal effect. Nonlinear MR supported the hypothesis of the nonlinearity of the relationship (I2 = 80.3%; Cochran's Q = 28.2; P = 8.8e-05) but did not suggest that hyperopia was associated with a major deficit in years spent in education. Conclusions: This work suggested that the causal relationship between refractive error and educational attainment was nonlinear but found no evidence that moderate hyperopia caused a major deficit in educational attainment. Importantly, however, because statistical power was limited and some participants with moderate hyperopia would have worn spectacles as children, modest adverse effects may have gone undetected. Translational Relevance: These findings suggest that moderate hyperopia does not cause a major deficit in educational attainment

High blood pressure and intraocular pressure: a Mendelian randomization study

Purpose: To test for causality with regard to the association between blood pressure (BP) and intraocular pressure (IOP) and glaucoma. Methods: Single nucleotide polymorphisms (SNPs) associated with BP were identified in a genome-wide association study (GWAS) meta-analysis of 526,001 participants of European ancestry. These SNPs were used to assess the BP versus IOP relationship in a distinct sample (n = 70,832) whose corneal-compensated IOP (IOPcc) was measured. To evaluate the BP versus primary open-angle glaucoma (POAG) relationship, additional Mendelian randomization (MR) analyses were conducted using published GWAS summary statistics. Results: Observational analysis revealed a linear relationship between BP traits and IOPcc, with a +0.28 mm Hg increase in IOPcc per 10-mm Hg increase in systolic BP (95% confidence interval [CI], 0.26–0.29); for diastolic blood pressure (DBP) and pulse pressure (PP), these estimates were +0.41 mm Hg and +0.36 mm Hg, respectively. An inverse-variance weighted MR analysis did not support a causal relationship, as the estimated causal effect was +0.01 mm Hg IOPcc per 10-mm Hg increase in systolic blood pressure (SBP); +0.13 mm Hg IOPcc per 10-mm Hg increase in DBP; and +0.02 mm Hg IOPcc per 10-mm Hg increase in PP (all P > 0.05). With regard to the risk of POAG, MR analyse yielded causal effect estimate of odds ratio = 0.98 (95% CI, 0.92–1.04) per 10-mm Hg increase in SBP. Neither DBP nor PP demonstrated evidence of a causal effect on POAG. Conclusions: A range of different MR analysis methods provided evidence, in general, that the causal effect of BP on IOP (and POAG) was modest, or even zero. However, interpretation was complicated by SNPs associated with BP potentially having pleiotropic effects on IOP

A commonly occurring genetic variant within the NPLOC4-TSPAN10-PDE6G gene cluster is associated with the risk of strabismus.

Strabismus refers to an abnormal alignment of the eyes leading to the loss of central binocular vision. Concomitant strabismus occurs when the angle of deviation is constant in all positions of gaze and often manifests in early childhood when it is considered to be a neurodevelopmental disorder of the visual system. As such, it is inherited as a complex genetic trait, affecting 2-4% of the population. A genome-wide association study (GWAS) for self-reported strabismus (1345 cases and 65,349 controls from UK Biobank) revealed a single genome-wide significant locus on chromosome 17q25. Approximately 20 variants across the NPLOC4-TSPAN10-PDE6G gene cluster and in almost perfect linkage disequilibrium (LD) were most strongly associated (lead variant: rs75078292, OR = 1.26, p = 2.24E-08). A recessive model provided a better fit to the data than an additive model. Association with strabismus was independent of refractive error, and the degree of association with strabismus was minimally attenuated after adjustment for amblyopia. The association with strabismus was replicated in an independent cohort of clinician-diagnosed children aged 7 years old (116 cases and 5084 controls; OR = 1.85, p = 0.009). The associated variants included 2 strong candidate causal variants predicted to have functional effects: rs6420484, which substitutes tyrosine for a conserved cysteine (C177Y) in the TSPAN10 gene, and a 4-bp deletion variant, rs397693108, predicted to cause a frameshift in TSPAN10. The population-attributable risk for the locus was approximately 8.4%, indicating an important role in conferring susceptibility to strabismus

Time spent outdoors partly accounts for the effect of education on myopia

Purpose: The purpose of this study was to investigate if education contributes to the risk of myopia because educational activities typically occur indoors or because of other factors, such as prolonged near viewing. Methods: This was a two-sample Mendelian randomization study. Participants were from the UK Biobank, Avon Longitudinal Study of Parents and Children, and Generation R. Genetic variants associated with years spent in education or time spent outdoors were used as instrumental variables. The main outcome measures were: (1) spherical equivalent refractive error attained by adulthood, and (2) risk of an early age-of-onset of spectacle wear (EAOSW), defined as an age-of-onset of 15 years or below. Results: Time spent outdoors was found to have a small genetic component (heritability 9.8%) that tracked from childhood to adulthood. A polygenic score for time outdoors was associated with children's time outdoors; a polygenic score for years spent in education was inversely associated with children's time outdoors. Accounting for the relationship between time spent outdoors and myopia in a multivariable Mendelian randomization analysis reduced the size of the causal effect of more years in education on myopia to −0.17 diopters (D) per additional year of formal education (95% confidence interval [CI] = −0.32 to −0.01) compared with the estimate from a univariable Mendelian randomization analysis of −0.27 D per year (95% CI = −0.41 to −0.13). Comparable results were obtained for the outcome EAOSW. Conclusions: Accounting for the effects of time outdoors reduced the estimated causal effect of education on myopia by 40%. These results suggest about half of the relationship between education and myopia may be mediated by children not being outdoors during schooling

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field