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Chaurasia AK, Greatbatch CJ, Han X, Gharahkhani P, Mackey DA, MacGregor S, Craig JE, Hewitt AW. Highly Accurate and Precise Automated Cup-to-Disc Ratio Quantification for Glaucoma Screening. OPHTHALMOLOGY SCIENCE 2024; 4:100540. [PMID: 39051045 PMCID: PMC11268341 DOI: 10.1016/j.xops.2024.100540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 03/26/2024] [Accepted: 04/22/2024] [Indexed: 07/27/2024]
Abstract
Objective An enlarged cup-to-disc ratio (CDR) is a hallmark of glaucomatous optic neuropathy. Manual assessment of the CDR may be less accurate and more time-consuming than automated methods. Here, we sought to develop and validate a deep learning-based algorithm to automatically determine the CDR from fundus images. Design Algorithm development for estimating CDR using fundus data from a population-based observational study. Participants A total of 181 768 fundus images from the United Kingdom Biobank (UKBB), Drishti_GS, and EyePACS. Methods FastAI and PyTorch libraries were used to train a convolutional neural network-based model on fundus images from the UKBB. Models were constructed to determine image gradability (classification analysis) as well as to estimate CDR (regression analysis). The best-performing model was then validated for use in glaucoma screening using a multiethnic dataset from EyePACS and Drishti_GS. Main Outcome Measures The area under the receiver operating characteristic curve and coefficient of determination. Results Our gradability model vgg19_batch normalization (bn) achieved an accuracy of 97.13% on a validation set of 16 045 images, with 99.26% precision and area under the receiver operating characteristic curve of 96.56%. Using regression analysis, our best-performing model (trained on the vgg19_bn architecture) attained a coefficient of determination of 0.8514 (95% confidence interval [CI]: 0.8459-0.8568), while the mean squared error was 0.0050 (95% CI: 0.0048-0.0051) and mean absolute error was 0.0551 (95% CI: 0.0543-0.0559) on a validation set of 12 183 images for determining CDR. The regression point was converted into classification metrics using a tolerance of 0.2 for 20 classes; the classification metrics achieved an accuracy of 99.20%. The EyePACS dataset (98 172 healthy, 3270 glaucoma) was then used to externally validate the model for glaucoma classification, with an accuracy, sensitivity, and specificity of 82.49%, 72.02%, and 82.83%, respectively. Conclusions Our models were precise in determining image gradability and estimating CDR. Although our artificial intelligence-derived CDR estimates achieve high accuracy, the CDR threshold for glaucoma screening will vary depending on other clinical parameters. Financial Disclosures Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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Affiliation(s)
- Abadh K. Chaurasia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Connor J. Greatbatch
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Xikun Han
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- School of Medicine, University of Queensland, Brisbane, Australia
| | - Puya Gharahkhani
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- School of Medicine, University of Queensland, Brisbane, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - David A. Mackey
- Lions Eye Institute, Centre for Vision Sciences, University of Western Australia, Nedlands, Australia
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- School of Medicine, University of Queensland, Brisbane, Australia
| | - Jamie E. Craig
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, Australia
| | - Alex W. Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
- Centre for Eye Research Australia, University of Melbourne, Melbourne, Australia
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Yun JS, Jung SH, Lee SN, Jung SM, Won HH, Kim D, Choi JA. Polygenic risk score-based phenome-wide association for glaucoma and its impact on disease susceptibility in two large biobanks. J Transl Med 2024; 22:355. [PMID: 38622600 PMCID: PMC11020996 DOI: 10.1186/s12967-024-05152-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Glaucoma is a leading cause of worldwide irreversible blindness. Considerable uncertainty remains regarding the association between a variety of phenotypes and the genetic risk of glaucoma, as well as the impact they exert on the glaucoma development. METHODS We investigated the associations of genetic liability for primary open angle glaucoma (POAG) with a wide range of potential risk factors and to assess its impact on the risk of incident glaucoma. The phenome-wide association study (PheWAS) approach was applied to determine the association of POAG polygenic risk score (PRS) with a wide range of phenotypes in 377, 852 participants from the UK Biobank study and 43,623 participants from the Penn Medicine Biobank study, all of European ancestry. Participants were stratified into four risk tiers: low, intermediate, high, and very high-risk. Cox proportional hazard models assessed the relationship of POAG PRS and ocular factors with new glaucoma events. RESULTS In both discovery and replication set in the PheWAS, a higher genetic predisposition to POAG was specifically correlated with ocular disease phenotypes. The POAG PRS exhibited correlations with low corneal hysteresis, refractive error, and ocular hypertension, demonstrating a strong association with the onset of glaucoma. Individuals carrying a high genetic burden exhibited a 9.20-fold, 11.88-fold, and 28.85-fold increase in glaucoma incidence when associated with low corneal hysteresis, high myopia, and elevated intraocular pressure, respectively. CONCLUSION Genetic susceptibility to POAG primarily influences ocular conditions, with limited systemic associations. Notably, the baseline polygenic risk for POAG robustly associates with new glaucoma events, revealing a large combined effect of genetic and ocular risk factors on glaucoma incidents.
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Affiliation(s)
- Jae-Seung Yun
- Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sang-Hyuk Jung
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Su-Nam Lee
- Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seung Min Jung
- Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hong-Hee Won
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Samsung Medical Center, Sungkyunkwan University, Seoul, Republic of Korea.
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea.
| | - Dokyoon Kim
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA.
| | - Jin A Choi
- Department of Ophthalmology, College of Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
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Zhang X, Liang Y, Huang Y, Liu S, Li Q, Wang S, Wu G, Du Z, Wang Y, Wang J, Hu Y, Zang S, Hu Y, Shang X, Zhang X, Zhang L, Brown A, Zhu Z, He M, Yu H. Evaluation of the Observational Associations and Shared Genetics Between Glaucoma With Depression and Anxiety. Invest Ophthalmol Vis Sci 2024; 65:12. [PMID: 38466289 PMCID: PMC10929750 DOI: 10.1167/iovs.65.3.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/29/2024] [Indexed: 03/12/2024] Open
Abstract
Purpose Glaucoma, a leading cause of blindness worldwide, is suspected to exhibit a notable association with psychological disturbances. This study aimed to investigate epidemiological associations and explore shared genetic architecture between glaucoma and mental traits, including depression and anxiety. Methods Multivariable logistic regression and Cox proportional hazards regression models were employed to investigate longitudinal associations based on UK Biobank. A stepwise approach was used to explore the shared genetic architecture. First, linkage disequilibrium score regression inferred global genetic correlations. Second, MiXeR analysis quantified the number of shared causal variants. Third, specific shared loci were detected through conditional/conjunctional false discovery rate (condFDR/conjFDR) analysis and characterized for biological insights. Finally, two-sample Mendelian randomization (MR) was conducted to investigate bidirectional causal associations. Results Glaucoma was significantly associated with elevated risks of hospitalized depression (hazard ratio [HR] = 1.54; 95% confidence interval [CI], 1.01-2.34) and anxiety (HR = 2.61; 95% CI, 1.70-4.01) compared to healthy controls. Despite the absence of global genetic correlations, MiXeR analysis revealed 300 variants shared between glaucoma and depression, and 500 variants shared between glaucoma and anxiety. Subsequent condFDR/conjFDR analysis discovered 906 single-nucleotide polymorphisms (SNPs) jointly associated with glaucoma and depression and two associated with glaucoma and anxiety. The MR analysis did not support robust causal associations but indicated the existence of pleiotropic genetic variants influencing both glaucoma and depression. Conclusions Our study enhances the existing epidemiological evidence and underscores the polygenic overlap between glaucoma and mental traits. This observation suggests a correlation shaped by pleiotropic genetic variants rather than being indicative of direct causal relationships.
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Affiliation(s)
- Xiayin Zhang
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yingying Liang
- Department of Ophthalmology, Guangzhou First People's Hospital, Guangzhou, China
| | - Yu Huang
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
- Division of Population Health and Genomics, University of Dundee, Ninewells Hospital and Medical School, Dundee, Scotland, United Kingdom
| | - Shunming Liu
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Qinyi Li
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Shan Wang
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Guanrong Wu
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zijing Du
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yaxin Wang
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jinghui Wang
- Hainan Eye Hospital and Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Haikou, China
| | - Yunyan Hu
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Siwen Zang
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yijun Hu
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xianwen Shang
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Australia
| | - Xueli Zhang
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Lei Zhang
- Clinical Medical Research Center, Children's Hospital of Nanjing Medical University, Nanjing, China
- Artificial Intelligence and Modelling in Epidemiology Program, Melbourne Sexual Health Centre, Alfred Health, Melbourne, Australia
- Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Australia
| | - Andrew Brown
- Division of Population Health and Genomics, University of Dundee, Ninewells Hospital and Medical School, Dundee, Scotland, United Kingdom
| | - Zhuoting Zhu
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Australia
| | - Mingguang He
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
- School of Optometry, The Hong Kong Polytechnic University, Hong Kong, China
| | - Honghua Yu
- Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangzhou, China
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Hollitt GL, Qassim A, Thomson D, Schmidt JM, Nguyen TT, Landers J, MacGregor S, Siggs OM, Souzeau E, Craig JE. Genetic Risk Assessment of Degenerative Eye Disease (GRADE): study protocol of a prospective assessment of polygenic risk scores to predict diagnosis of glaucoma and age-related macular degeneration. BMC Ophthalmol 2023; 23:431. [PMID: 37875865 PMCID: PMC10594830 DOI: 10.1186/s12886-023-03143-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/14/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Glaucoma and age-related macular degeneration (AMD) account for a substantial portion of global blindness. Both conditions are highly heritable, with recognised monogenic and polygenic inheritance patterns. Current screening guidelines lack decisive recommendations. Polygenic risk scores (PRS) allow for cost-effective broad population risk stratification for these conditions. The predictive potential of PRS could facilitate earlier diagnosis and treatment, and prevent unnecessary vision loss. METHODS The Genetic Risk Assessment of Degenerative Eye disease (GRADE) study is a prospective study designed to generate high-quality evidence about the feasibility of PRS to stratify individuals from the general population, enabling identification of those at highest risk of developing glaucoma or AMD. The targeted recruitment is 1000 individuals aged over 50 years, from which blood or saliva samples will be used for genotyping and an individual PRS for glaucoma and AMD will be derived. Individuals with PRS values in the bottom decile (n = 100), top decile (n = 100) and middle 80% (n = 100) for both glaucoma and AMD will undergo a detailed eye examination for glaucoma and/or AMD. DISCUSSION The primary objective will be to compare the prevalence of glaucoma and AMD cases between low, intermediate, and high PRS risk groups. We expect to find a higher prevalence of both diseases in the high PRS risk group, as compared to the middle and low risk groups. This prospective study will assess the clinical validity of a PRS for glaucoma and AMD in the general Australian population. Positive findings will support the implementation of PRS into clinical practice.
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Affiliation(s)
- Georgina L Hollitt
- Department of Ophthalmology, Flinders University, 1 Flinders Drive, 5042, Bedford Park, SA, Australia.
| | - Ayub Qassim
- Department of Ophthalmology, Flinders University, 1 Flinders Drive, 5042, Bedford Park, SA, Australia
| | - Daniel Thomson
- Department of Ophthalmology, Flinders University, 1 Flinders Drive, 5042, Bedford Park, SA, Australia
| | - Joshua M Schmidt
- Department of Ophthalmology, Flinders University, 1 Flinders Drive, 5042, Bedford Park, SA, Australia
| | - Thi Thi Nguyen
- Department of Ophthalmology, Flinders University, 1 Flinders Drive, 5042, Bedford Park, SA, Australia
| | - John Landers
- Department of Ophthalmology, Flinders University, 1 Flinders Drive, 5042, Bedford Park, SA, Australia
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, 4006, Herston, QLD, Australia
| | - Owen M Siggs
- Department of Ophthalmology, Flinders University, 1 Flinders Drive, 5042, Bedford Park, SA, Australia
- Garvan Institute of Medical Research, 2010, Darlinghurst, NSW, Australia
| | - Emmanuelle Souzeau
- Department of Ophthalmology, Flinders University, 1 Flinders Drive, 5042, Bedford Park, SA, Australia
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, 1 Flinders Drive, 5042, Bedford Park, SA, Australia
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Mamidipaka A, Di Rosa I, Lee R, Zhu Y, Chen Y, Salowe R, Addis V, Sankar P, Daniel E, Ying GS, O’Brien JM. Factors Associated with Large Cup-to-Disc Ratio and Blindness in the Primary Open-Angle African American Glaucoma Genetics (POAAGG) Study. Genes (Basel) 2023; 14:1809. [PMID: 37761949 PMCID: PMC10530848 DOI: 10.3390/genes14091809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND/AIMS Primary open-angle glaucoma (POAG) disproportionately affects individuals of African ancestry. In these patients' eyes, a large cup-to-disc ratio (LCDR > 0.90) suggests greater retinal ganglion cell loss, though these patients often display varied visual ability. This study investigated the prevalence and risk factors associated with LCDR in African ancestry individuals with POAG and explored the differences between blind (>20/200) and not blind (≤20/200) LCDR eyes. METHODS A case-control methodology was used to investigate the demographic, optic disc, and genetic risk factors of subjects in the Primary Open-Angle African American Glaucoma Genetics Study. Risk factors were analyzed using univariable and multivariable logistic regression models with inter-eye correlation adjusted using generalized estimating equations. RESULTS Out of 5605 eyes with POAG, 1440 eyes (25.7%) had LCDR. In the multivariable analysis, LCDR was associated with previous glaucoma surgery (OR = 1.72), increased intraocular pressure (OR = 1.04), decreased mean deviation (OR = 1.08), increased pattern standard deviation (OR = 1.06), thinner retinal nerve fiber layer (OR = 1.05), nasalization of vessels (OR = 2.67), bayonetting of vessels (OR = 1.98), visible pores in the lamina cribrosa (OR = 1.68), and a bean-shaped cup (OR = 2.11). Of LCDR eyes, 30.1% were classified as blind (≤20/200). In the multivariable analysis, the statistically significant risk factors of blindness in LCDR eyes were previous glaucoma surgery (OR = 1.72), increased intraocular pressure (OR = 1.05), decreased mean deviation (OR = 1.04), and decreased pattern standard deviation (OR = 0.90). CONCLUSIONS These findings underscore the importance of close monitoring of intraocular pressure and visual function in African ancestry POAG patients, particularly those with LCDR, to preserve visual function.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Joan M. O’Brien
- Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.M.); (I.D.R.); (R.L.); (Y.Z.); (Y.C.); (R.S.); (V.A.); (P.S.); (E.D.); (G.-S.Y.)
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Han X, Gharahkhani P, Hamel AR, Ong JS, Rentería ME, Mehta P, Dong X, Pasutto F, Hammond C, Young TL, Hysi P, Lotery AJ, Jorgenson E, Choquet H, Hauser M, Cooke Bailey JN, Nakazawa T, Akiyama M, Shiga Y, Fuller ZL, Wang X, Hewitt AW, Craig JE, Pasquale LR, Mackey DA, Wiggs JL, Khawaja AP, Segrè AV, MacGregor S. Large-scale multitrait genome-wide association analyses identify hundreds of glaucoma risk loci. Nat Genet 2023; 55:1116-1125. [PMID: 37386247 PMCID: PMC10335935 DOI: 10.1038/s41588-023-01428-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/19/2023] [Indexed: 07/01/2023]
Abstract
Glaucoma, a leading cause of irreversible blindness, is a highly heritable human disease. Previous genome-wide association studies have identified over 100 loci for the most common form, primary open-angle glaucoma. Two key glaucoma-associated traits also show high heritability: intraocular pressure and optic nerve head excavation damage quantified as the vertical cup-to-disc ratio. Here, since much of glaucoma heritability remains unexplained, we conducted a large-scale multitrait genome-wide association study in participants of European ancestry combining primary open-angle glaucoma and its two associated traits (total sample size over 600,000) to substantially improve genetic discovery power (263 loci). We further increased our power by then employing a multiancestry approach, which increased the number of independent risk loci to 312, with the vast majority replicating in a large independent cohort from 23andMe, Inc. (total sample size over 2.8 million; 296 loci replicated at P < 0.05, 240 after Bonferroni correction). Leveraging multiomics datasets, we identified many potential druggable genes, including neuro-protection targets likely to act via the optic nerve, a key advance for glaucoma because all existing drugs only target intraocular pressure. We further used Mendelian randomization and genetic correlation-based approaches to identify novel links to other complex traits, including immune-related diseases such as multiple sclerosis and systemic lupus erythematosus.
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Affiliation(s)
- Xikun Han
- Statistical Genetics Lab, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia.
| | - Puya Gharahkhani
- Statistical Genetics Lab, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Andrew R Hamel
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jue Sheng Ong
- Statistical Genetics Lab, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Miguel E Rentería
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Mental Health and Neuroscience Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Puja Mehta
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Xianjun Dong
- Genomics and Bioinformatics Hub, Brigham and Women's Hospital, Boston, MA, USA
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Francesca Pasutto
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität, Erlangen-Nürnberg, Erlangen, Germany
| | | | - Terri L Young
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Pirro Hysi
- Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Andrew J Lotery
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California (KPNC), Oakland, CA, USA
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Michael Hauser
- Department of Medicine, Duke University, Durham, NC, USA
- Department of Ophthalmology, Duke University, Durham, NC, USA
- Singapore Eye Research Institute, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Jessica N Cooke Bailey
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Toru Nakazawa
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Retinal Disease Control, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Ophthalmic Imaging and Information Analytics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masato Akiyama
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yukihiro Shiga
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Neuroscience, Université de Montréal, Montréal, Quebec, Canada
- Neuroscience Division, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, Quebec, Canada
| | | | - Xin Wang
- 23andMe, Inc., Sunnyvale, CA, USA
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
- Centre for Eye Research Australia, University of Melbourne, Melbourne, Victoria, Australia
| | - Jamie E Craig
- Department of Ophthalmology, Flinders Medical Centre, Flinders University, Bedford Park, South Australia, Australia
| | - Louis R Pasquale
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David A Mackey
- Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Perth, Western Australia, Australia
| | - Janey L Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Anthony P Khawaja
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Ayellet V Segrè
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Stuart MacGregor
- Statistical Genetics Lab, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
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Kravets S, Rupnow RA, Sethi A, Espeland MA, Pasquale LR, Rapp SR, Klein BE, Meuer SM, Haan MN, Maki PM, Hallak JA, Vajaranant TS. Association between cognitive function and large optic nerve cupping, accounting for cup-disc-ratio genetic risk score. PLoS One 2022; 17:e0258564. [PMID: 36315511 PMCID: PMC9621414 DOI: 10.1371/journal.pone.0258564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 09/23/2022] [Indexed: 11/05/2022] Open
Abstract
PURPOSE To investigate if accounting for a cup-to-disc ratio (CDR) genetic risk score (GRS) modified the association between large CDR and cognitive function among women. DESIGN This was a retrospective study using data from the Women's Health Initiative. METHODS Patients with glaucoma or ocular hypertension were excluded. Large CDR was defined as ≥ 0.6 in either eye. Cognitive function was measured by the Modified Mini-Mental State Examination (3MSE). We used the combined effects from 13 single nucleotide polymorphisms (SNPs) to formulate the GRS for CDR. We used logistic regression to investigate associations between weighted GRS and large CDR, then a linear regression to assess the association between weighted GRS and 3MSE scores, and between weighted GRS, CDR, and 3MSE scores, adjusted for demographic and clinical characteristics. RESULTS Final analyses included 1,196 White women with mean age of 69.60 ± 3.62 years and 7.27% with large CDR. Mean GRS in women with and without large CDR was 1.51 ± 0.31 vs. 1.41 ± 0.36, respectively (p = 0.004). The odds of large CDR for a one unit increase in GRS was 2.30 (95% CI: (1.22, 4.36), p = 0.011). Adding the CDR GRS in the model with CDR and 3MSE, women with large CDR still had statistically significantly lower 3MSE scores than those without large CDR, yielding a predicted mean difference in 3MSE scores of 0.84 (p = 0.007). CONCLUSIONS Independent of the CDR GRS, women with large CDR had a lower cognitive function.
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Affiliation(s)
- Sasha Kravets
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Division of Epidemiology and Biostatistics, School of Public Health, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Rawan Allozi Rupnow
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Division of Epidemiology and Biostatistics, School of Public Health, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Abhishek Sethi
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Mark A. Espeland
- Departments of Internal Medicine and Biostatistics and Data Science, Wake Forest University Health Sciences, Winston Salem, North Carolina, United States of America
| | - Louis R. Pasquale
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Stephen R. Rapp
- Psychiatry and Behavioral Medicine, Wake Forest University Health Sciences, Winston Salem, North Carolina, United States of America
| | - Barbara E. Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Stacy M. Meuer
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Mary N. Haan
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, California, United States of America
| | - Pauline M. Maki
- Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Joelle A. Hallak
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Thasarat Sutabutr Vajaranant
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, University of Illinois at Chicago, Chicago, Illinois, United States of America
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8
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Hollitt GL, Siggs OM, Ridge B, Keane MC, Mackey DA, MacGregor S, Hewitt AW, Craig JE, Souzeau E. Attitudes Toward Glaucoma Genetic Risk Assessment in Unaffected Individuals. Transl Vis Sci Technol 2022; 11:38. [DOI: 10.1167/tvst.11.10.38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Georgina L. Hollitt
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, Australia
| | - Owen M. Siggs
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, Australia
- Garvan Institute of Medical Research Institute, Darlinghurst, Sydney, Australia
| | - Bronwyn Ridge
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, Australia
| | - Miriam C. Keane
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, Australia
| | - David A. Mackey
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
- Lions Eye Institute, Centre for Ophthalmology and Vision Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Alex W. Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Jamie E. Craig
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, Australia
| | - Emmanuelle Souzeau
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, Australia
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9
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Wang Z, Wiggs JL, Aung T, Khawaja AP, Khor CC. The genetic basis for adult onset glaucoma: Recent advances and future directions. Prog Retin Eye Res 2022; 90:101066. [PMID: 35589495 DOI: 10.1016/j.preteyeres.2022.101066] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/19/2022] [Accepted: 04/23/2022] [Indexed: 11/26/2022]
Abstract
Glaucoma, a diverse group of eye disorders that results in the degeneration of retinal ganglion cells, is the world's leading cause of irreversible blindness. Apart from age and ancestry, the major risk factor for glaucoma is increased intraocular pressure (IOP). In primary open-angle glaucoma (POAG), the anterior chamber angle is open but there is resistance to aqueous outflow. In primary angle-closure glaucoma (PACG), crowding of the anterior chamber angle due to anatomical alterations impede aqueous drainage through the angle. In exfoliation syndrome and exfoliation glaucoma, deposition of white flaky material throughout the anterior chamber directly interfere with aqueous outflow. Observational studies have established that there is a strong hereditable component for glaucoma onset and progression. Indeed, a succession of genome wide association studies (GWAS) that were centered upon single nucleotide polymorphisms (SNP) have yielded more than a hundred genetic markers associated with glaucoma risk. However, a shortcoming of GWAS studies is the difficulty in identifying the actual effector genes responsible for disease pathogenesis. Building on the foundation laid by GWAS studies, research groups have recently begun to perform whole exome-sequencing to evaluate the contribution of protein-changing, coding sequence genetic variants to glaucoma risk. The adoption of this technology in both large population-based studies as well as family studies are revealing the presence of novel, protein-changing genetic variants that could enrich our understanding of the pathogenesis of glaucoma. This review will cover recent advances in the genetics of primary open-angle glaucoma, primary angle-closure glaucoma and exfoliation glaucoma, which collectively make up the vast majority of all glaucoma cases in the world today. We will discuss how recent advances in research methodology have uncovered new risk genes, and how follow up biological investigations could be undertaken in order to define how the risk encoded by a genetic sequence variant comes into play in patients. We will also hypothesise how data arising from characterising these genetic variants could be utilized to predict glaucoma risk and the manner in which new therapeutic strategies might be informed.
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Affiliation(s)
- Zhenxun Wang
- Duke-NUS Medical School, Singapore; Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore; Singapore Eye Research Institute, Singapore National Eye Centre, Singapore.
| | - Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Tin Aung
- Duke-NUS Medical School, Singapore; Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Anthony P Khawaja
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, United Kingdom
| | - Chiea Chuen Khor
- Duke-NUS Medical School, Singapore; Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore; Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
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10
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Araki MVR, Silva YCO, Rodrigues TAR, Bajano FF, de Souza BB, Costa FF, Costa VP, de Melo MB, de Vasconcellos JPC. Association of ABCA1 (rs2472493) and GAS7 (rs9913911) gene variants with primary open-angle glaucoma in a Brazilian population. Mol Vis 2022; 28:1-10. [PMID: 35400990 PMCID: PMC8942454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 02/20/2022] [Indexed: 11/11/2022] Open
Abstract
Purpose Glaucoma is the world's leading cause of irreversible blindness, with primary open-angle glaucoma (POAG) being the most prevalent subtype. In recent years, there have been advances in knowledge about the genetics involved in POAG, but genetic studies in admixed populations, such as Brazilians, are still rare. This study aimed to evaluate the association of single nucleotide variants (SNV) of the ABCA1 (rs2472493) and GAS7 (rs9913911) genes with POAG in a sample of the Brazilian population. Furthermore, the study aimed to evaluate the relationship between these SNVs and the need for surgical intervention in glaucoma control. Methods A cross-sectional association study with 1,009 subjects (505 patients with POAG and 504 controls) was performed. Participants underwent a comprehensive ocular examination, including the need for surgical procedures for intraocular pressure control. Genotyping of SNVs was performed using the TaqMan genotyping assay. Results SNV rs9913911 of GAS7 was found to be associated with POAG in the presence of the risk allele A (p = 0.0004) and the AA genotype (p = 0.002). There was no association between SNV rs2472493 of ABCA1 for either the allele risk or genotypes. However, the combination of these variants showed an additive effect on the risk for POAG: ABCA1(GG) + GAS7(AA; p = 0.02), ABCA1(GG) + GAS7(AG; p = 0.003), and ABCA1(AG) + GAS7(AG; p = 0.004). Also, POAG patients carrying the AA genotype of the GAS7 gene required antiglaucomatous surgery more frequently than those without the AA genotype (p = 0.01). Conclusions In a Brazilian population sample, there was an association identified between SNV rs9913911 (GAS7) and the risk of POAG, and an additive effect was found when GAS7 was combined with SNV rs2472493 (ABCA1). There was an association between SNV rs9913911 (GAS7) and the risk for antiglaucomatous surgery.
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Affiliation(s)
- Manoel Vinicius Rocha Araki
- Department of Ophthalmology, Faculty of Medical Sciences, University of Campinas – UNICAMP, Campinas – SP, Brazil
| | - Yuri Carvalho Oiamore Silva
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering, University of Campinas – UNICAMP, Campinas – SP, Brazil
| | - Thiago Adalton Rosa Rodrigues
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering, University of Campinas – UNICAMP, Campinas – SP, Brazil
| | - Flavia Fialho Bajano
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering, University of Campinas – UNICAMP, Campinas – SP, Brazil
| | - Bruno Batista de Souza
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering, University of Campinas – UNICAMP, Campinas – SP, Brazil
| | | | - Vital Paulino Costa
- Department of Ophthalmology, Faculty of Medical Sciences, University of Campinas – UNICAMP, Campinas – SP, Brazil
| | - Mônica Barbosa de Melo
- Laboratory of Human Genetics, Center for Molecular Biology and Genetic Engineering, University of Campinas – UNICAMP, Campinas – SP, Brazil
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11
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Attitudes towards polygenic risk testing in individuals with glaucoma. Ophthalmol Glaucoma 2021; 5:436-446. [PMID: 34774858 DOI: 10.1016/j.ogla.2021.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/18/2021] [Accepted: 11/04/2021] [Indexed: 12/22/2022]
Abstract
PURPOSE Glaucoma is the leading cause of irreversible blindness worldwide however, vision loss from glaucoma can generally be prevented through early identification and timely implementation of treatment. Recently, polygenic risk scores (PRS) have shown promise in stratifying individual risk and prognostication for primary open-angle glaucoma to reduce disease burden. Integrating PRS testing into clinical practice is becoming an increasingly realistic prospect, however, little is known about the attitudes of patients towards such testing. DESIGN Cross-sectional, questionnaire-based study. PARTICIPANTS 2369 participants were invited to participate from the Australian and New Zealand Registry of Advanced Glaucoma (ANZRAG), who fit the inclusion criteria of adults with a diagnosis of POAG, had not received genetic results that explain their condition, were not known to be deceased, resided in Australia and had agreed to receive correspondence. METHODS 1169 individuals (response rate 49%) with primary open-angle glaucoma completed the survey evaluating their attitudes towards polygenic risk testing for glaucoma. MAIN OUTCOME MEASURES Sociodemographic, health, perception, and emotional factors were examined to assess associations with interest in PRS testing. Interest in PRS testing was evaluated through assessing likelihood to take the test to predict personal risk of disease and disease severity, and whether the individual would recommend the test to family or non-family members. RESULTS Our results show strong interest in the test, with 69.4% of individuals (798 of 1150) indicating a keenness in testing prior to diagnosis, had it been available. In particular, interest was seen in those from an urban area (OR 1.70, 95%CI (1.15-2.49), p=0.007), those who perceived their risk of developing glaucoma as higher (OR 2.05, 95%CI (1.28-3.29), p=0.003), and those who were worried about developing glaucoma (OR 2.07, 95%CI (1.27-3.37), p=0.004). People who were interested in testing were more likely to change their eye health-seeking intentions and recommend testing to family and non-family members, as well as undergo testing for prognostication. CONCLUSIONS These findings will help to facilitate the clinical implementation of PRS testing for glaucoma to reduce irreversible vision loss.
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12
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Zukerman R, Harris A, Oddone F, Siesky B, Verticchio Vercellin A, Ciulla TA. Glaucoma Heritability: Molecular Mechanisms of Disease. Genes (Basel) 2021; 12:genes12081135. [PMID: 34440309 PMCID: PMC8391305 DOI: 10.3390/genes12081135] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 02/06/2023] Open
Abstract
Glaucoma is one of the world’s leading causes of irreversible blindness. A complex, multifactorial disease, the underlying pathogenesis and reasons for disease progression are not fully understood. The most common form of glaucoma, primary open-angle glaucoma (POAG), was traditionally understood to be the result of elevated intraocular pressure (IOP), leading to optic nerve damage and functional vision loss. Recently, researchers have suggested that POAG may have an underlying genetic component. In fact, studies of genetic association and heritability have yielded encouraging results showing that glaucoma may be influenced by genetic factors, and estimates for the heritability of POAG and disease-related endophenotypes show encouraging results. However, the vast majority of the underlying genetic variants and their molecular mechanisms have not been elucidated. Several genes have been suggested to have molecular mechanisms contributing to alterations in key endophenotypes such as IOP (LMX1B, MADD, NR1H3, and SEPT9), and VCDR (ABCA1, ELN, ASAP1, and ATOH7). Still, genetic studies about glaucoma and its molecular mechanisms are limited by the multifactorial nature of the disease and the large number of genes that have been identified to have an association with glaucoma. Therefore, further study into the molecular mechanisms of the disease itself are required for the future development of therapies targeted at genes leading to POAG endophenotypes and, therefore, increased risk of disease.
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Affiliation(s)
- Ryan Zukerman
- Department of Ophthalmology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA; (R.Z.); (A.H.); (B.S.); (A.V.V.)
- Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Alon Harris
- Department of Ophthalmology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA; (R.Z.); (A.H.); (B.S.); (A.V.V.)
| | | | - Brent Siesky
- Department of Ophthalmology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA; (R.Z.); (A.H.); (B.S.); (A.V.V.)
| | - Alice Verticchio Vercellin
- Department of Ophthalmology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA; (R.Z.); (A.H.); (B.S.); (A.V.V.)
| | - Thomas A. Ciulla
- Midwest Eye Institute, Indianapolis, IN 46290, USA
- Correspondence: ; Tel.: +1-(317)-506-0334 or +1-(317)-817-1822; Fax: +1-(317)-817-1898
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13
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Abstract
Intraocular pressure (IOP) is the cardinal and only modifiable risk factor for glaucoma, the leading cause of irreparable blindness worldwide. Twin and family studies estimate the heritability of IOP to be 40-70%, and linkage studies for IOP have identified numerous loci. Mutations in MYOC can cause markedly elevated IOP and aggressive glaucoma often requiring surgical intervention. However, the majority of the genetic basis for raised IOP and glaucoma in populations is complex, and recent large genome-wide association studies (GWASs) have identified over 100 common variants that contribute to IOP variation. In combination, these loci are predictive for primary open-angle glaucoma in independent populations, achieving an area under the receiver operating characteristic curve of 76% for high-pressure primary open-angle glaucoma; this suggests the possibility of targeted screening in the future. Additionally, GWAS findings have identified important biological pathways underlying IOP regulation, including lymphangiogenesis and lipid metabolism, providing novel targets for new therapies. Expected final online publication date for the Annual Review of Vision Science, Volume 7 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Zihe Xu
- Department of Ophthalmology, King's College London, London SE5 9RS, United Kingdom.,Department of Twin Research & Genetic Epidemiology, King's College London, London SE5 9RS, United Kingdom
| | - Pirro Hysi
- Department of Ophthalmology, King's College London, London SE5 9RS, United Kingdom.,Department of Twin Research & Genetic Epidemiology, King's College London, London SE5 9RS, United Kingdom
| | - Anthony P Khawaja
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London EC1V 2PD, UK;
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14
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The GGLEAM Study: Understanding Glaucoma in the Ohio Amish. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18041551. [PMID: 33561996 PMCID: PMC7915874 DOI: 10.3390/ijerph18041551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 11/17/2022]
Abstract
Glaucoma leads to millions of cases of visual impairment and blindness around the world. Its susceptibility is shaped by both environmental and genetic risk factors. Although over 120 risk loci have been identified for glaucoma, a large portion of its heritability is still unexplained. Here we describe the foundation of the Genetics of GLaucoma Evaluation in the AMish (GGLEAM) study to investigate the genetic architecture of glaucoma in the Ohio Amish, which exhibits lower genetic and environmental heterogeneity compared to the general population. To date, we have enrolled 81 Amish individuals in our study from Holmes County, Ohio. As a part of our enrollment process, 62 GGLEAM study participants (42 glaucoma-affected and 20 unaffected individuals) received comprehensive eye examinations and glaucoma evaluations. Using the data from the Anabaptist Genealogy Database, we found that 80 of the GGLEAM study participants were related to one another through a large, multigenerational pedigree containing 1586 people. We plan to integrate the health and kinship data obtained for the GGLEAM study to interrogate glaucoma genetics and pathophysiology in this unique population.
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15
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Kim YW, Lee YH, Kim JS, Lee J, Kim YJ, Cheong HS, Kim SH, Park KH, Kim DM, Choi HJ, Jeoung JW. Genetic analysis of primary open-angle glaucoma-related risk alleles in a Korean population: the GLAU-GENDISK study. Br J Ophthalmol 2020; 105:1307-1312. [PMID: 32933932 DOI: 10.1136/bjophthalmol-2020-316089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/21/2020] [Accepted: 08/22/2020] [Indexed: 11/04/2022]
Abstract
AIM To validate six previously known primary open-angle glaucoma (POAG)-related loci in a Korean population. METHODS Representative POAG-related single-nucleotide polymorphisms (SNPs) from six loci (cyclin-dependent kinase 4 inhibitor B antisense RNA 1 (CDKN2B)-AS1, sineoculis homeobox homolog 1/sineoculis homeobox homolog 6(SIX1/SIX6), atonal BHLH transcription factor 7 (ATOH7), cell division cycle 7-transforming growth factor beta receptor 3, CAV1, transmembrane and coiled-coil domain family 1 (TMCO1) were selected and genotyped from discovery (POAG=309, heathy=5400) and replication cohorts (POAG=310, healthy=5612 and POAG=221, healthy=6244, respectively). Data were analysed using logistic regression to calculate the OR for POAG risk associated with SNP. RESULTS From the discovery cohort, rs1900004 in ATOH7 (OR=1.29, p=0.0024); rs1063192 (OR=0.69, p=0.0006), rs2157719 (OR=0.63, p=0.0007) and rs7865618 (OR=0.63, p=0.0006) in CDKN2B-AS1, and rs10483727 in SIX1/SIX6 (OR=0.68, p=7.9E-05) were nominally associated with the risk of POAG. The replication cohorts revealed nominal associations with rs2157719 (OR=0.72, p=0.0135), rs1063192 (OR=0.63, p=0.0007) and rs7865618 (OR=0.52, p=0.0004) in CDKN2B-AS1. A mega-analysis from the entire Korean population revealed significance with rs1063192 (OR=0.77, p=6.0E-05), rs2157719 (OR=0.63, p=0.0007) and rs7865618 (OR=0.58, p=1.9E-06) in CDKN2B-AS1 and with rs10483727 in SIX1/SIX6 (OR=0.79, p=9.4E-05), with the same direction of effect between the discovery association and the replication sample. CONCLUSIONS Variants near CDKN2B-AS1 and SIX1/SIX6 may require further investigation to obtain more genetic information on POAG development in a Korean population.
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Affiliation(s)
- Yong Woo Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Department of Ophthalmology, Seoul National University Hospital, Seoul, Korea
| | - Yun Hwan Lee
- Department of Public Health Sciences, Seoul National University, Seoul, Korea
| | - Jin-Soo Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Department of Ophthalmology, Chungnam National University Sejong Hospital, Sejong, Korea
| | - Jinho Lee
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Department of Ophthalmology, Hallym University Chuncheon Sacred Heart Hospital, Chuncheon, Korea
| | - Yu Jeong Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Korea
| | - Seok Hwan Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Department of Ophthalmology, Seoul National University Boramae Medical Center, Seoul, Korea
| | - Ki Ho Park
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Department of Ophthalmology, Seoul National University Hospital, Seoul, Korea
| | - Dong Myung Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea
| | - Hyuk Jin Choi
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea.,Seoul National University Hospital Healthcare System Gangnam Center, Seoul, Korea
| | - Jin Wook Jeoung
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea .,Department of Ophthalmology, Seoul National University Hospital, Seoul, Korea
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16
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Choquet H, Melles RB, Yin J, Hoffmann TJ, Thai KK, Kvale MN, Banda Y, Hardcastle AJ, Tuft SJ, Glymour MM, Schaefer C, Risch N, Nair KS, Hysi PG, Jorgenson E. A multiethnic genome-wide analysis of 44,039 individuals identifies 41 new loci associated with central corneal thickness. Commun Biol 2020; 3:301. [PMID: 32528159 PMCID: PMC7289804 DOI: 10.1038/s42003-020-1037-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/22/2020] [Indexed: 02/08/2023] Open
Abstract
Central corneal thickness (CCT) is one of the most heritable human traits, with broad-sense heritability estimates ranging between 0.68 to 0.95. Despite the high heritability and numerous previous association studies, only 8.5% of CCT variance is currently explained. Here, we report the results of a multiethnic meta-analysis of available genome-wide association studies in which we find association between CCT and 98 genomic loci, of which 41 are novel. Among these loci, 20 were significantly associated with keratoconus, and one (RAPSN rs3740685) was significantly associated with glaucoma after Bonferroni correction. Two-sample Mendelian randomization analysis suggests that thinner CCT does not causally increase the risk of primary open-angle glaucoma. This large CCT study explains up to 14.2% of CCT variance and increases substantially our understanding of the etiology of CCT variation. This may open new avenues of investigation into human ocular traits and their relationship to the risk of vision disorders.
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Affiliation(s)
- Hélène Choquet
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, 94612, USA.
| | - Ronald B Melles
- KPNC, Department of Ophthalmology, Redwood City, CA, 94063, USA
| | - Jie Yin
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, 94612, USA
| | - Thomas J Hoffmann
- Institute for Human Genetics, University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA, 94158, USA
| | - Khanh K Thai
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, 94612, USA
| | - Mark N Kvale
- Institute for Human Genetics, University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Yambazi Banda
- Institute for Human Genetics, University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Alison J Hardcastle
- UCL Institute of Ophthalmology, University College London, London, UK
- National Institute of Health Research Biomedical Research Centre for Ophthalmology, and UCL Institute of Ophthalmology, London, UK
| | | | - M Maria Glymour
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA, 94158, USA
| | - Catherine Schaefer
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, 94612, USA
| | - Neil Risch
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, 94612, USA
- Institute for Human Genetics, University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA, 94158, USA
| | - K Saidas Nair
- Departments of Ophthalmology and Anatomy, School of Medicine, UCSF, San Francisco, CA, 94143, USA
| | - Pirro G Hysi
- King's College London, Section of Ophthalmology, School of Life Course Sciences, London, UK
- King's College London, Department of Twin Research and Genetic Epidemiology, London, UK
- University College London, Great Ormond Street Hospital Institute of Child Health, London, UK
| | - Eric Jorgenson
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, 94612, USA.
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17
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Trivli A, Zervou MI, Goulielmos GN, Spandidos DA, Detorakis ET. Primary open angle glaucoma genetics: The common variants and their clinical associations (Review). Mol Med Rep 2020; 22:1103-1110. [PMID: 32626970 PMCID: PMC7339808 DOI: 10.3892/mmr.2020.11215] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 06/03/2020] [Indexed: 12/11/2022] Open
Abstract
Glaucoma is a group of progressive optic neuropathies that have in common characteristic optic nerve head changes, loss of retinal ganglion cells and visual field defects. Among the large family of glaucomas, primary open‑angle glaucoma (POAG) is the most common type, a complex and heterogeneous disorder with environmental and genetic factors contributing to its pathogenesis. Approximately 5% of POAG is currently attributed to single‑gene or Mendelian forms of glaucoma. Genetic linkage analysis and genome‑wide association studies have identified various genomic loci, paving the path to understanding the pathogenesis of this enigmatic, blinding disease. In this review we summarize the most common variants reported thus far and their possible clinical correlations.
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Affiliation(s)
- Alexandra Trivli
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, 71003 Heraklion, Greece
| | - Maria I Zervou
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, 71003 Heraklion, Greece
| | - George N Goulielmos
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, 71003 Heraklion, Greece
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, 71003 Heraklion, Greece
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18
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Abstract
Keratoconus, a progressive corneal ectasia, is a complex disease with both genetic and environmental risk factors. The exact etiology is not known and is likely variable between individuals. Conditions such as hay fever and allergy are associated with increased risk, while diabetes may be protective. Behaviors such as eye rubbing are also implicated, but direct causality has not been proven. Genetics plays a major role in risk for some individuals, with many large pedigrees showing autosomal inheritance patterns. Several genes have been implicated using linkage and follow-up sequencing in these families. Genome-wide association studies for keratoconus and for quantitative traits such as central corneal thickness have identified several genetic loci that contribute to a cumulative risk for keratoconus, even in people without a family history of the disease. Identification of risk genes for keratoconus is improving our understanding of the biology of this complex disease.
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Affiliation(s)
- Sionne E M Lucas
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania 7001, Australia;
| | - Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania 7001, Australia;
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Kondkar AA, Azad TA, Sultan T, Osman EA, Almobarak FA, Al-Obeidan SA. Association of endothelial nitric oxide synthase (NOS3) gene polymorphisms with primary open-angle glaucoma in a Saudi cohort. PLoS One 2020; 15:e0227417. [PMID: 31914149 PMCID: PMC6948740 DOI: 10.1371/journal.pone.0227417] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/18/2019] [Indexed: 01/25/2023] Open
Abstract
Aim To investigate the association of endothelial nitric oxide synthase (NOS3) gene polymorphisms in patients with primary open-angle glaucoma (POAG) of Saudi origin. Methods This case-control study included 173 patients with POAG (94 men and 79 women) and 171 controls (98 men and 73 women). Genotyping of rs2070744 (T-786C) and rs1799983 (G894T) variants of the NOS3 gene was performed using TaqMan® assay. Results Rs1799983 genotypes showed a significant association with POAG but did not survive Bonferroni correction (pcorrection = 0.01). The minor ‘T’ allele was significantly associated with the risk of POAG among men (p = 0.025, odds ratio (OR) = 1.77, 95% confidence interval (CI) = 1.07–2.94). Likewise, the genotypes were significantly associated with POAG among men in dominant (p = 0.030, OR = 1.92, 95% CI = 1.06–3.48) and log-additive models (p = 0.022, OR = 1.82, 95% CI = 1.08–3.07), and after adjustment for age and smoking. Genotype and allele frequencies of rs2070744 were not significantly different between POAG cases and controls, and after sex stratification. CG haplotype was significantly protective (p = 0.011, OR = 0.52, 95% CI = 0.32–0.87) and CT haplotype conferred significantly increased risk of POAG (p = 0.016, OR = 2.60, 95% CI = 1.16–5.82) among men. Rs1799983 showed trend (p = 0.054) towards risk of POAG independent of age, gender, smoking, and rs2070744 polymorphism in logistic regression analysis. Both the polymorphisms showed no association with POAG phenotypes such as intraocular pressure and cup/disc ratio. Conclusion Our results suggest that the polymorphism rs1799983 and the haplotypes of rs20707440 and rs1799983 in the NOS3 gene may significantly modulate the risk of POAG in Saudi’s, particularly among men. Further larger studies are needed to confirm these findings.
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Affiliation(s)
- Altaf A. Kondkar
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Glaucoma Research Chair in Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
- * E-mail:
| | - Taif A. Azad
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Tahira Sultan
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Essam A. Osman
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Faisal A. Almobarak
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Glaucoma Research Chair in Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Saleh A. Al-Obeidan
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Glaucoma Research Chair in Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
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20
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Asefa NG, Neustaeter A, Jansonius NM, Snieder H. Heritability of glaucoma and glaucoma-related endophenotypes: Systematic review and meta-analysis. Surv Ophthalmol 2019; 64:835-851. [DOI: 10.1016/j.survophthal.2019.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 05/28/2019] [Accepted: 06/07/2019] [Indexed: 02/09/2023]
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Youngblood H, Hauser MA, Liu Y. Update on the genetics of primary open-angle glaucoma. Exp Eye Res 2019; 188:107795. [PMID: 31525344 PMCID: PMC6901111 DOI: 10.1016/j.exer.2019.107795] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/03/2019] [Accepted: 09/10/2019] [Indexed: 12/15/2022]
Abstract
Affecting nearly 80 million individuals, glaucoma is the number one cause of irreversible blindness in the world. This ocular disease describes a set of optic neuropathies of which primary open angle glaucoma (POAG) is the most common. POAG is associated with progressive visual field deterioration resulting from damage to the optic nerve and loss of retinal ganglion cells. Risk factors for POAG include elevated intraocular pressure, aging, African and Hispanic ancestry, and a positive family history of POAG. Multiple genes have been found to contribute to POAG. Much of POAG genetics and pathology has yet to be explained. Recent genome-wide association studies have identified a large number of novel loci associated with POAG and its endophenotypes. Genomic and proteomic profiling of biofluids has contributed to our knowledge of differential gene expression in POAG. Functional studies both in cell culture and animal models have confirmed the effects of variants and differential gene expression on ocular physiology while in silico analyses have increased our understanding of disease risk and progression so that we might better diagnose and treat this complex genetic illness.
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Affiliation(s)
- Hannah Youngblood
- Department of Cellular Biology and Anatomy, Augusta University, 1460 Laney Walker Blvd CB1101, Augusta, GA, 30912, United States.
| | - Michael A Hauser
- Departments of Medicine and Ophthalmology, Duke University Medical Center, Durham, NC, USA; Duke Molecular Physiology Institute, 300 N Duke Street, Durham, NC, 27701, United States.
| | - Yutao Liu
- Department of Cellular Biology and Anatomy, Augusta University, 1460 Laney Walker Blvd CB1101, Augusta, GA, 30912, United States; Center for Biotechnology and Genomic Medicine, Augusta University, 1120 15th Street, Augusta, GA, 30912, United States; James and Jean Culver Vision Discovery Institute, Augusta University, 1460 Laney Walker Blvd CB1101, Augusta, GA, 30912, United States.
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22
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Burdon KP. Use of Corneal Biomechanical Measures as Endophenotypes for Understanding the Genetics of Keratoconus. JAMA Ophthalmol 2019; 137:1013-1014. [PMID: 31246242 DOI: 10.1001/jamaophthalmol.2019.2068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
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23
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Kondkar AA, Azad TA, Sultan T, Al-Mobarak FA, Kalantan H, Al-Obeidan SA. Polymorphisms rs693421 and rs2499601 at locus 1q43 and their haplotypes are not associated with primary open-angle glaucoma: a case-control study. BMC Res Notes 2019; 12:453. [PMID: 31337432 PMCID: PMC6651941 DOI: 10.1186/s13104-019-4491-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 07/17/2019] [Indexed: 11/30/2022] Open
Abstract
Objective The genetic spectrum of primary open-angle glaucoma (POAG) in middle-eastern Saudi’s is still elusive. To this end, we investigated an association between rs693421, rs2499601 and their haplotypes at chromosome 1q43 locus with POAG and its related clinical phenotypes. Genotyping was performed with TaqMan® assays. Haplotypes and their interaction analysis were carried out by SHEsis and SNPStats online tools. Results The minor “T” allele frequency of rs693421 was 0.48 in controls and 0.52 in cases (odds ratio (OR) = 1.15, 95% confidence interval (CI) 0.85–1.54, p = 0.368). Similarly, for rs2499601, the minor “C” allele frequency was 0.49 in controls as compared to 0.53 in cases (OR = 1.19, 95% CI 0.89–1.60, p = 0.236). Besides, genotype distribution for both these polymorphisms was also not significant in additive, dominant and recessive models. rs693421 and rs2499601, showed significant linkage disequilibrium (D’ statistics = 0.69, p < 0.001) but haplotype association was non-significant (p = 0.698). The significance did not vary after adjustment to age and sex. No significant genotype association was observed with intraocular pressure, cup/disc ratio and number of anti-glaucoma medication in POAG group. Furthermore, age, sex and genotypes did not contribute any significant risk of POAG in regression analysis. We report no association between rs693421, rs2499601 and their haplotypes with POAG and related phenotypes. Electronic supplementary material The online version of this article (10.1186/s13104-019-4491-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Altaf A Kondkar
- Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia. .,Glaucoma Research Chair in Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.
| | - Taif A Azad
- Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia
| | - Tahira Sultan
- Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia
| | - Faisal A Al-Mobarak
- Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia.,Glaucoma Research Chair in Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Hatem Kalantan
- Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia
| | - Saleh A Al-Obeidan
- Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia.,Glaucoma Research Chair in Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
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24
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Fan BJ, Chen X, Sondhi N, Sharmila PF, Soumittra N, Sripriya S, Sacikala S, Asokan R, Friedman DS, Pasquale LR, Gao XR, Vijaya L, Cooke Bailey J, Vitart V, MacGregor S, Hammond CJ, Khor CC, Haines JL, George R, Wiggs JL. Family-Based Genome-Wide Association Study of South Indian Pedigrees Supports WNT7B as a Central Corneal Thickness Locus. Invest Ophthalmol Vis Sci 2019; 59:2495-2502. [PMID: 29847655 PMCID: PMC5961220 DOI: 10.1167/iovs.17-23536] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Purpose To identify genetic risk factors contributing to central corneal thickness (CCT) in individuals from South India, a population with a high prevalence of ocular disorders. Methods One hundred ninety-five individuals from 15 large South Indian pedigrees were genotyped using the Omni2.5 bead array. Family-based association for CCT was conducted using the score test in MERLIN. Results Genome-wide association study (GWAS) identified strongest association for single nucleotide polymorphisms (SNPs) in the first intron of WNT7B and CCT (top SNP rs9330813; β = −0.57, 95% confidence interval [CI]: −0.78 to −0.36; P = 1.7 × 10−7). We further investigated rs9330813 in a Latino cohort and four independent European cohorts. A meta-analysis of these data sets demonstrated statistically significant association between rs9330813 and CCT (β = −3.94, 95% CI: −5.23 to −2.66; P = 1.7 × 10−9). WNT7B SNPs located in the same genomic region that includes rs9330813 have previously been associated with CCT in Latinos but with other ocular quantitative traits related to myopia (corneal curvature and axial length) in a Japanese population (rs10453441 and rs200329677). To evaluate the specificity of the observed WNT7B association with CCT in the South Indian families, we completed an ocular phenome-wide association study (PheWAS) for the top WNT7B SNPs using 45 ocular traits measured in these same families including corneal curvature and axial length. The ocular PheWAS results indicate that in the South Indian families WNT7B SNPs are primarily associated with CCT. Conclusions The results indicate robust evidence for association between WNT7B SNPs and CCT in South Indian pedigrees, and suggest that WNT7B SNPs can have population-specific effects on ocular quantitative traits.
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Affiliation(s)
- Bao Jian Fan
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States
| | - Xueli Chen
- Department of Ophthalmology & Visual Science, Eye & Ear Nose Throat Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Nisha Sondhi
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States
| | - P Ferdinamarie Sharmila
- SNONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Sankara Nethralaya, Chennai, India
| | - Nagasamy Soumittra
- SNONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Sankara Nethralaya, Chennai, India
| | - Sarangapani Sripriya
- SNONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Sankara Nethralaya, Chennai, India
| | - Srinivasan Sacikala
- SNONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Sankara Nethralaya, Chennai, India
| | - Rashima Asokan
- Medical Research Foundation, Sankara Nethralaya, Chennai, India
| | - David S Friedman
- The Dana Center for Preventive Ophthalmology, Johns Hopkins Medical School, Wilmer Eye Institute, Baltimore, Maryland, United States
| | - Louis R Pasquale
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States.,Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States
| | - X Raymond Gao
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, Illinois, United States
| | - Lingam Vijaya
- Medical Research Foundation, Sankara Nethralaya, Chennai, India
| | - Jessica Cooke Bailey
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Christopher J Hammond
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Chiea Chuen Khor
- Division of Human Genetics, Genome Institute of Singapore, Singapore
| | - Jonathan L Haines
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States
| | - Ronnie George
- Medical Research Foundation, Sankara Nethralaya, Chennai, India
| | - Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States
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25
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Lack of Association between Variant rs7916697 in ATOH7 and Primary Open Angle Glaucoma in a Saudi Cohort. GENETICS RESEARCH INTERNATIONAL 2018; 2018:2148056. [PMID: 30519491 PMCID: PMC6241241 DOI: 10.1155/2018/2148056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/02/2018] [Accepted: 10/22/2018] [Indexed: 02/06/2023]
Abstract
A case-control genetic association study was performed to investigate whether variant rs7916697 in atonal bHLH transcription factor 7 (ATOH7), which has been previously reported to be associated with optic disc parameters and primary open angle glaucoma (POAG) in different ethnic groups, is a risk factor for POAG or any of its clinical phenotypes in a Saudi cohort. Genotyping of rs7916697 (G>A) variant was performed in 186 unrelated POAG cases and 171 unrelated nonglaucomatous controls of Saudi origin using real-time Taq-Man® assay. Genotypic and allelic association with POAG and its related clinical indices were evaluated. Demographic and systemic disease status did not differ significantly between POAG cases and controls. Association analysis between POAG cases and controls showed no significant genotype effect under additive (p=0.707), dominant (p=0.458), and recessive (p=0.554) models. Besides, the minor ‘A' allele frequency was 0.39 in POAG cases and 0.36 in controls with no significant distribution (p=0.406). In addition, there was no significant difference between genotypes and clinical phenotypes such as intraocular pressure and cup/disc ratio within the POAG group, or any age and sex adjusted genotype effect on the disease outcome in regression analysis. Variant rs7916697 in ATOH7 is not associated with POAG or its clinical indices such as IOP and cup/disc ratio in a Saudi cohort.
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26
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Kondkar AA, Sultan T, Almobarak FA, Kalantan H, Abu-Amero KK, Al-Obeidan SA. Plexin domain containing 2 (PLXDC2) gene polymorphism rs7081455 may not influence POAG risk in a Saudi cohort. BMC Res Notes 2018; 11:733. [PMID: 30326957 PMCID: PMC6192173 DOI: 10.1186/s13104-018-3848-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 10/11/2018] [Indexed: 11/18/2022] Open
Abstract
Objective Plexin domain containing 2 (PLXDC2), a cell surface transmembrane protein receptor for pigment epithelium derived factor, is expressed in many tissues including the eye. Polymorphism rs7081455 flanking PLXDC2 has been associated with primary open angle glaucoma (POAG) and its clinical phenotypes and may have a role in POAG. Rs7081455 was genotyped in POAG cases (n = 188) and non-glaucomatous controls (n = 164) of Saudi origin using Taq-Man® to determine any association of this variant with POAG and its endophenotypes. Results The risk variant, ‘G’ allele, frequency was 0.56 and 0.52 in controls and POAG cases, respectively (p = 0.197) with was no significant deviation from Hardy–Weinberg equilibrium. Genotype analysis between cases and controls revealed no significant distribution under additive (p = 0.482), dominant (p = 0.590) and recessive models (p = 0.228). In addition, glaucoma specific phenotypic traits such as intraocular pressure (IOP) and cup/disc ratio; and number of anti-glaucoma medications, used to assess severity of the disease, were also statistically non-significant. Furthermore, regression analysis showed no significant effect of age, sex and genotype on disease outcome. Rs7081455 was not associated with POAG or its clinical phenotypes such as IOP and cup/disc ratio and hence may not be a significant risk factor for POAG patients of Saudi origin. Electronic supplementary material The online version of this article (10.1186/s13104-018-3848-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Altaf A Kondkar
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia.
| | - Tahira Sultan
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia
| | - Faisal A Almobarak
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia
| | - Hatem Kalantan
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia
| | - Saleh A Al-Obeidan
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, P.O. Box 245, Riyadh, 11411, Saudi Arabia
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27
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Restrepo NA, Laper SM, Farber-Eger E, Crawford DC. Local genetic ancestry in CDKN2B-AS1 is associated with primary open-angle glaucoma in an African American cohort extracted from de-identified electronic health records. BMC Med Genomics 2018; 11:70. [PMID: 30255811 PMCID: PMC6157155 DOI: 10.1186/s12920-018-0392-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Glaucoma is a leading cause of blindness in developed countries. Primary open-angle glaucoma (POAG), the most prevalent clinical subtype of glaucoma in the United States, affects African Americans at a higher rate compared with European Americans. Risk factors identified for POAG include increased age and family history, which coupled with heritability estimates, suggest this complex condition is associated with genetic and environmental factors. To date, several genome-wide studies have identified loci significantly associated with POAG risk, but most of these studies were performed in populations of European-descent. METHODS To identify population-specific and trans-population genetic associations for POAG, we genotyped 11,521 African Americans using the Illumina Metabochip as part of the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) study accessing BioVU, the Vanderbilt University Medical Center's biorepository linked to de-identified electronic health records. Among this study population, we identified 138 cases of POAG and 1376 controls and performed Metabochip-wide tests of association. We also estimated local genetic ancestry at CDKN2B-AS1, a POAG-associated locus established in European-descent populations. RESULTS Overall, we did not identify significant single SNP-POAG associations after adjusting for multiple testing. We did, however, detect a significant association between POAG risk and local African genetic ancestry at CDKN2B-AS1, where on average cases were of 90% African descent compared with controls at 58% (p = 2 × 10- 6). CONCLUSIONS These data suggest that CDKN2B-AS1 is an important locus for POAG risk among African Americans, warranting further investigation to identify the variants underlying this association.
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Affiliation(s)
- Nicole A Restrepo
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University, 2103 Cornell Road, Wolstein Research Building, Suite 2-527, Cleveland, OH, 44106, USA
| | | | - Eric Farber-Eger
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dana C Crawford
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University, 2103 Cornell Road, Wolstein Research Building, Suite 2-527, Cleveland, OH, 44106, USA.
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Asefa NG, Neustaeter A, Jansonius NM, Snieder H. Heritability of glaucoma and glaucoma-related endophenotypes: systematic review and meta-analysis protocol. BMJ Open 2018; 8:e019049. [PMID: 29490960 PMCID: PMC5855254 DOI: 10.1136/bmjopen-2017-019049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
INTRODUCTION Glaucoma is the second leading cause of age-related vision loss worldwide; it is an umbrella term that is used to describe a set of complex ocular disorders with a multifactorial aetiology. Both genetic and lifestyle risk factors for glaucoma are well established. Thus far, however, systematic reviews on the heritability of glaucoma have focused on the heritability of primary open-angle glaucoma only. No systematic review has comprehensively reviewed or meta-analysed the heritability of other types of glaucoma, including glaucoma-related endophenotypes. The aim of this study will be to identify relevant scientific literature regarding the heritability of both glaucoma and related endophenotypes and summarise the evidence by performing a systematic review and meta-analysis. METHODS AND ANALYSIS This systematic review will follow the Preferred Reporting Items for Systematic review and Meta-Analysis Protocols 2015 checklist, which provides a standardised approach for carrying out systematic reviews. To capture as much literature as possible, a comprehensive step-by-step systematic search will be undertaken in MEDLINE (PubMed), EMBASE, Web of Science and ScienceDirect, and studies published until 31 December 2017 will be included. Two reviewers will independently search the articles for eligibility according to predefined selection criteria. A database will be used for screening of eligible articles. The quality of the included studies will be rated independently by two reviewers, using the National Health Institute Quality Assessment tool for Observational Cohort and Cross-Sectional Studies. A random-effects model will be used for the meta-analysis. This systematic review is registered with the International Prospective Register of Systematic Reviews with a registration number: CRD42017064504. ETHICS AND DISSEMINATION We will use secondary data from peer-reviewed published articles, and hence there is no requirement for ethics approval. The results of this systematic review will be disseminated through publication in a peer-reviewed scientific journal.
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Affiliation(s)
- Nigus Gebrmedhin Asefa
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Anna Neustaeter
- Department of Ophthalmology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Nomdo M Jansonius
- Department of Ophthalmology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Harold Snieder
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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29
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Gharahkhani P, Burdon KP, Cooke Bailey JN, Hewitt AW, Law MH, Pasquale LR, Kang JH, Haines JL, Souzeau E, Zhou T, Siggs OM, Landers J, Awadalla M, Sharma S, Mills RA, Ridge B, Lynn D, Casson R, Graham SL, Goldberg I, White A, Healey PR, Grigg J, Lawlor M, Mitchell P, Ruddle J, Coote M, Walland M, Best S, Vincent A, Gale J, RadfordSmith G, Whiteman DC, Montgomery GW, Martin NG, Mackey DA, Wiggs JL, MacGregor S, Craig JE. Analysis combining correlated glaucoma traits identifies five new risk loci for open-angle glaucoma. Sci Rep 2018; 8:3124. [PMID: 29449654 PMCID: PMC5814451 DOI: 10.1038/s41598-018-20435-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 01/18/2018] [Indexed: 01/08/2023] Open
Abstract
Open-angle glaucoma (OAG) is a major cause of blindness worldwide. To identify new risk loci for OAG, we performed a genome-wide association study in 3,071 OAG cases and 6,750 unscreened controls, and meta-analysed the results with GWAS data for intraocular pressure (IOP) and optic disc parameters (the overall meta-analysis sample size varying between 32,000 to 48,000 participants), which are glaucoma-related traits. We identified and independently validated four novel genome-wide significant associations within or near MYOF and CYP26A1, LINC02052 and CRYGS, LMX1B, and LMO7 using single variant tests, one additional locus (C9) using gene-based tests, and two genetic pathways - "response to fluid shear stress" and "abnormal retina morphology" - in pathway-based tests. Interestingly, some of the new risk loci contribute to risk of other genetically-correlated eye diseases including myopia and age-related macular degeneration. To our knowledge, this study is the first integrative study to combine genetic data from OAG and its correlated traits to identify new risk variants and genetic pathways, highlighting the future potential of combining genetic data from genetically-correlated eye traits for the purpose of gene discovery and mapping.
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Affiliation(s)
- Puya Gharahkhani
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
| | | | - Jessica N Cooke Bailey
- Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | | | - Matthew H Law
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Louis R Pasquale
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jae H Kang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan L Haines
- Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Emmanuelle Souzeau
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Tiger Zhou
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Owen M Siggs
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - John Landers
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Mona Awadalla
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Shiwani Sharma
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Richard A Mills
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Bronwyn Ridge
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - David Lynn
- South Australian Health & Medical Research Institute, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - Robert Casson
- South Australian Institute of Ophthalmology, University of Adelaide, Adelaide, South Australia, Australia
| | - Stuart L Graham
- Ophthalmology and Vision Science, Macquarie University, Sydney, New South Wales, Australia
| | - Ivan Goldberg
- Department of Ophthalmology, University of Sydney, Sydney, Australia
| | - Andrew White
- Department of Ophthalmology, University of Sydney, Sydney, Australia.,Centre for Vision Research, The Westmead Institute for Medical Research, University of Sydney, Westmead, NSW, Australia
| | - Paul R Healey
- Department of Ophthalmology, University of Sydney, Sydney, Australia.,Centre for Vision Research, The Westmead Institute for Medical Research, University of Sydney, Westmead, NSW, Australia
| | - John Grigg
- Department of Ophthalmology, University of Sydney, Sydney, Australia
| | - Mitchell Lawlor
- Department of Ophthalmology, University of Sydney, Sydney, Australia
| | - Paul Mitchell
- Centre for Vision Research, The Westmead Institute for Medical Research, University of Sydney, Westmead, NSW, Australia
| | - Jonathan Ruddle
- Centre for Eye Research Australia (CERA), University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
| | - Michael Coote
- Centre for Eye Research Australia (CERA), University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
| | - Mark Walland
- Centre for Eye Research Australia (CERA), University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
| | - Stephen Best
- Department of Ophthalmology, University of Auckland, Auckland, New Zealand
| | - Andrea Vincent
- Department of Ophthalmology, University of Auckland, Auckland, New Zealand
| | - Jesse Gale
- Department of Ophthalmology, University of Otago, Dunedin, Otago, New Zealand
| | - Graham RadfordSmith
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,School of Medicine, University of Queensland, Herston Campus, Brisbane, QLD, Australia
| | - David C Whiteman
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Grant W Montgomery
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - David A Mackey
- University of Tasmania, Hobart, Tasmania, Australia.,Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | - Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia.
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30
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Genetic Risk Score Is Associated with Vertical Cup-to-Disc Ratio and Improves Prediction of Primary Open-Angle Glaucoma in Latinos. Ophthalmology 2018; 125:815-821. [PMID: 29361357 DOI: 10.1016/j.ophtha.2017.12.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 12/04/2017] [Accepted: 12/08/2017] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Genome-wide association studies have identified multiple genetic variants associated with vertical cup-to-disc ratio (VCDR). Genetic risk scores (GRS) examine the aggregate genetic effect of individual variants on a trait by combining these separate genetic variants into a single measure. The purpose of this study was to construct GRS for VCDR and to determine whether the GRS are associated with VCDR and whether the GRS increase the discriminatory ability for primary open-angle glaucoma (POAG) in a Latino population. DESIGN Population-based genetic association study. PARTICIPANTS A total of 4018 Latino participants recruited from Los Angeles. METHODS Weighted and unweighted GRS were constructed using 68 previously reported VCDR single nucleotide polymorphisms (SNPs), as well as SNPs from our own genome-wide association data. Linear and logistic regression analyses examined the associations of GRS with VCDR and POAG, respectively. To evaluate the discriminatory ability of the GRS for POAG, we conducted receiver operating characteristic (ROC) analyses. MAIN OUTCOME MEASURES The relationship between GRS and VCDR in Latinos. RESULTS The GRS were associated significantly with VCDR (P < 0.0001), after adjusting for age, gender, central corneal thickness, intraocular pressure, and education. The weighted GRS explained an additional 2.74% of the variation in VCDR. Adding the weighted GRS derived from previously reported SNPs resulted in a moderate improvement in the discriminatory ability for POAG during ROC analyses, yielding an area under the ROC curve (AUC) of 0.735 (95% CI, 0.701-0.768). When our own SNPs were used, the AUC increased significantly to 0.809 (95% CI, 0.781-0.837; P < 0.0001). We obtained similar results for the unweighted GRS. CONCLUSIONS To our knowledge, we identified a novel association between GRS and VCDR and its improvement in the discriminatory ability of POAG in a Latino population.
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31
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Expression QTL analysis of glaucoma endophenotypes in the Norfolk Island isolate provides evidence that immune-related genes are associated with optic disc size. J Hum Genet 2017; 63:83-87. [PMID: 29215094 DOI: 10.1038/s10038-017-0374-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 09/25/2017] [Accepted: 09/25/2017] [Indexed: 11/08/2022]
Abstract
Primary open-angle glaucoma (POAG) is influenced by both genetic and environmental factors. Despite significant progress in identifying genetic variants associated with POAG, there remains a substantial amount of unexplained heritability. Study design features that may enhance knowledge of the genetic architecture include focusing on multiple quantitative traits related to ocular disorders (i.e. endophenotypes), targeting genetic variants that directly influence gene expression (i.e. cis-eQTLs) and utilising genetically isolated populations to reduce genetic and environmental noise and thus enhance association signals. In this study we performed heritability and blood-based eQTL association analysis of five key POAG endophenotypes in 330 individuals from the Norfolk Island (NI) isolate. Results showed evidence of heritability for all five traits, with H2 estimates ranging from 0.35 for intraocular pressure (IOP) to 0.82 for central corneal thickness (CCT) (P < 0.05). The primary finding was for BTN3A2, whereby both cis-SNP and transcript were significantly associated with disc size within a conditional regression model. Specifically, this model included rs853676 (β = 0.23,P = 0.008) and transcript (β = 0.23, P = 0.03). We also observed a cis-SNP association between optic disc size and LPCAT2 independent of transcript (P = 0.0004). These genes have specific functions in immune system pathways and suggest a role for an inherited immune component of POAG risk. This study also demonstrates an alternate approach to understanding the functional genetic basis of POAG and ocular health more generally.
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32
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Ghanbari M, Iglesias AI, Springelkamp H, van Duijn CM, Ikram MA, Dehghan A, Erkeland SJ, Klaver CCW, Meester-Smoor MA. A Genome-Wide Scan for MicroRNA-Related Genetic Variants Associated With Primary Open-Angle Glaucoma. Invest Ophthalmol Vis Sci 2017; 58:5368-5377. [PMID: 29049738 PMCID: PMC6110129 DOI: 10.1167/iovs.17-22410] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To identify microRNAs (miRNAs) involved in primary open-angle glaucoma (POAG), using genetic data. MiRNAs are small noncoding RNAs that posttranscriptionally regulate gene expression. Genetic variants in miRNAs or miRNA-binding sites within gene 3'-untranslated regions (3'UTRs) are expected to affect miRNA function and contribute to disease risk. Methods Data from the recent genome-wide association studies on intraocular pressure, vertical cup-to-disc ratio (VCDR), cupa area and disc area were used to investigate the association of miRNAs with POAG endophenotypes. Putative targets of the associated miRNAs were studied according to their association with POAG and tested in cell line by transfection experiments for regulation by the miRNAs. Results Of 411 miRNA variants, rs12803915:A/G in the terminal loop of pre-miR-612 and rs2273626:A/C in the seed sequence of miR-4707 were significantly associated with VCDR and cup area (P values < 1.2 × 10-4). The first variant is demonstrated to increase the miR-612 expression. We showed that the second variant does not affect the miR-4707 biogenesis, but reduces the binding of miR-4707-3p to CARD10, a gene known to be involved in glaucoma. Moreover, of 72,052 miRNA-binding-site variants, 47 were significantly associated with four POAG endophenotypes (P value < 6.9 × 10-6). Of these, we highlighted 10 variants that are more likely to affect miRNA-mediated gene regulation in POAG. These include rs3217992 and rs1063192, which have been shown experimentally to affect miR-138-3p- and miR-323b-5p-mediated regulation of CDKN2B. Conclusions We identified a number of miRNAs that are associated with POAG endophenotypes. The identified miRNAs and their target genes are candidates for future studies on miRNA-related therapies for POAG.
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Affiliation(s)
- Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Genetics, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Adriana I Iglesias
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Henriët Springelkamp
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Abbas Dehghan
- Department of Epidemiology & Biostatistics, Imperial College London, London, United Kingdom
| | - Stefan J Erkeland
- Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Caroline C W Klaver
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Ophthalmology, Radbound University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Magda A Meester-Smoor
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
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33
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Mabuchi F, Mabuchi N, Sakurada Y, Yoneyama S, Kashiwagi K, Iijima H, Yamagata Z, Takamoto M, Aihara M, Iwata T, Kawase K, Shiga Y, Nishiguchi KM, Nakazawa T, Ozaki M, Araie M. Additive effects of genetic variants associated with intraocular pressure in primary open-angle glaucoma. PLoS One 2017; 12:e0183709. [PMID: 28832686 PMCID: PMC5568337 DOI: 10.1371/journal.pone.0183709] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/09/2017] [Indexed: 11/18/2022] Open
Abstract
To investigate the association between the additive effects of genetic variants associated with intraocular pressure (IOP) and IOP, vertical cup-to-disc ratio (VCDR), and high tension glaucoma (HTG) or normal tension glaucoma (NTG) as phenotypic features of primary open-angle glaucoma (POAG), and to evaluate the clinical usefulness of the additive effects of IOP-related genetic variants for predicting IOP elevation, Japanese patients with HTG (n = 255) and NTG (n = 261) and 246 control subjects were genotyped for nine IOP-related genetic variants near CAV2, GAS7, GLCCI1/ICA1, ABCA1, ARHGEF12, FAM125B, FNDC3B, ABO, and PTPRJ/AGBL2. The total number of risk alleles of these genetic variants was calculated for each participant as a genetic risk score (GRS), and the association between the GRS and the maximum IOP, mean VCDR, and phenotype (HTG or NTG) of POAG was evaluated. As the GRS increased, the maximum IOP (P = 0.012) and VCDR (P = 0.010) significantly increased. The GRS (9.1±1.9) in patients with HTG was significantly higher (P = 0.011) than that (8.7±1.8) in control subjects. The patients with GRS≥12 as a cut-off value had a 2.54 times higher (P = 0.0085) risk on HTG (maximum IOP≥22mmHg) compared with all patients. The IOP-related GRS approach substantiated that the IOP and VCDR were increased by the additive effects of IOP-related genetic variants in POAG. The high IOP-related GRS in patients with HTG but not NTG shows that there are differences in the genetic background between HTG and NTG and supports the notion that the phenotype (HTG or NTG) in patients with POAG depends on the additive effects of IOP-related genetic variants. The above-mentioned cut-off value of IOP-related GRS may be clinically useful for predicting the risk of IOP elevation.
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Affiliation(s)
- Fumihiko Mabuchi
- Department of Ophthalmology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
- * E-mail:
| | - Nakako Mabuchi
- Department of Ophthalmology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Yoichi Sakurada
- Department of Ophthalmology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Seigo Yoneyama
- Department of Ophthalmology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Kenji Kashiwagi
- Department of Ophthalmology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Hiroyuki Iijima
- Department of Ophthalmology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Zentaro Yamagata
- Department of Health Sciences, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Mitsuko Takamoto
- Department of Ophthalmology, Tokyo Metropolitan Police Hospital, Tokyo, Japan
| | - Makoto Aihara
- Department of Ophthalmology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Takeshi Iwata
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | | | - Yukihiro Shiga
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Koji M. Nishiguchi
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Toru Nakazawa
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Miyagi, Japan
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Miyagi, Japan
- Department of Retinal Disease Control, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | | | - Makoto Araie
- Kanto Central Hospital of the Mutual Aid Association of Public School Teachers, Tokyo, Japan
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34
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Teotia P, Van Hook MJ, Wichman CS, Allingham RR, Hauser MA, Ahmad I. Modeling Glaucoma: Retinal Ganglion Cells Generated from Induced Pluripotent Stem Cells of Patients with SIX6 Risk Allele Show Developmental Abnormalities. Stem Cells 2017; 35:2239-2252. [PMID: 28792678 DOI: 10.1002/stem.2675] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/14/2017] [Accepted: 07/18/2017] [Indexed: 01/01/2023]
Abstract
Glaucoma represents a group of multifactorial diseases with a unifying pathology of progressive retinal ganglion cell (RGC) degeneration, causing irreversible vision loss. To test the hypothesis that RGCs are intrinsically vulnerable in glaucoma, we have developed an in vitro model using the SIX6 risk allele carrying glaucoma patient-specific induced pluripotent stem cells (iPSCs) for generating functional RGCs. Here, we demonstrate that the efficiency of RGC generation by SIX6 risk allele iPSCs is significantly lower than iPSCs-derived from healthy, age- and sex-matched controls. The decrease in the number of RGC generation is accompanied by repressed developmental expression of RGC regulatory genes. The SIX6 risk allele RGCs display short and simple neurites, reduced expression of guidance molecules, and immature electrophysiological signature. In addition, these cells have higher expression of glaucoma-associated genes, CDKN2A and CDKN2B, suggesting an early onset of the disease phenotype. Consistent with the developmental abnormalities, the SIX6 risk allele RGCs display global dysregulation of genes which map on developmentally relevant biological processes for RGC differentiation and signaling pathways such as mammalian target of rapamycin that integrate diverse functions for differentiation, metabolism, and survival. The results suggest that SIX6 influences different stages of RGC differentiation and their survival; therefore, alteration in SIX6 function due to the risk allele may lead to cellular and molecular abnormalities. These abnormalities, if carried into adulthood, may make RGCs vulnerable in glaucoma. Stem Cells 2017;35:2239-2252.
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Affiliation(s)
- Pooja Teotia
- Department of Ophthalmology and Visual Sciences, College of Public Health, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Matthew J Van Hook
- Department of Ophthalmology and Visual Sciences, College of Public Health, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Christopher S Wichman
- Department of Biostatistics, College of Public Health, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - R Rand Allingham
- Department of Ophthalmology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Michael A Hauser
- Department of Ophthalmology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Iqbal Ahmad
- Department of Ophthalmology and Visual Sciences, College of Public Health, University of Nebraska Medical Center, Omaha, Nebraska, USA
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35
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Nannini DR, Torres M, Chen YDI, Taylor KD, Rotter JI, Varma R, Gao X. A Genome-Wide Association Study of Vertical Cup-Disc Ratio in a Latino Population. Invest Ophthalmol Vis Sci 2017; 58:87-95. [PMID: 28061514 PMCID: PMC5231910 DOI: 10.1167/iovs.16-19891] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Vertical cup-disc ratio (VCDR) is used as a clinical assessment measure to identify and monitor glaucomatous damage to the optic nerve. Previous genetic studies conducted in European and Asian populations have identified many loci associated with VCDR. The genetic factors in other ethnic populations, such as Latino, influencing VCDR remain to be determined. Here, we describe the first genome-wide association study (GWAS) on VCDR in Latino individuals. Methods We conducted this GWAS on VCDR using 4537 Latino individuals who were genotyped by using either the Illumina OmniExpress BeadChip (∼730K markers) or the Illumina Hispanic/SOL BeadChip (∼2.5 million markers). Study subjects were 40 years of age and older. Linear regression, adjusting for age, sex, and principal components of genetic ancestry, was conducted to assess the associations between single nucleotide polymorphisms (SNPs) and VCDR. We imputed SNPs from the 1000 Genomes Project to integrate additional SNPs not directly genotyped. Results We replicated two previously reported SNPs that reached GWAS significance, rs1900005 and rs7916697, in the ATOH7-PBLD region, as well as identified two suggestive associations in the CDC7-TGFBR3 region on chromosome 1p22.1 and in the ZNF770-DPH6 region on chromosome 15q14. We discovered a novel SNP, rs56238729 (P = 1.22 × 10−13), in the ATOH7-PBLD region that is significantly associated with VCDR in Latino individuals. We replicated eight previously reported regions, including COL8A1, CDKN2B-CDKN2BAS, BMP2, and CHEK2 (P < 2.17 × 10−3). Conclusions Our results discovered a novel SNP that is significantly associated with VCDR in Latino individuals and confirmed previously reported loci, providing further insight into the genetic architecture of VCDR.
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Affiliation(s)
- Drew R Nannini
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, Illinois, United States
| | - Mina Torres
- USC Roski Eye Institute, Department of Ophthalmology, University of Southern California, Los Angeles, California, United States
| | - Yii-Der I Chen
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics and Medicine at Harbor-UCLA, Torrance, California, United States
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics and Medicine at Harbor-UCLA, Torrance, California, United States
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics and Medicine at Harbor-UCLA, Torrance, California, United States
| | - Rohit Varma
- USC Roski Eye Institute, Department of Ophthalmology, University of Southern California, Los Angeles, California, United States
| | - Xiaoyi Gao
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, Illinois, United States
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36
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Iglesias AI, der Lee SJ, Bonnemaijer PW, Höhn R, Nag A, Gharahkhani P, Khawaja AP, Broer L, Foster PJ, Hammond CJ, Hysi PG, Leeuwen EM, MacGregor S, Mackey DA, Mazur J, Nickels S, Uitterlinden AG, Klaver CC, Amin N, Duijn CM. Haplotype reference consortium panel: Practical implications of imputations with large reference panels. Hum Mutat 2017; 38:1025-1032. [DOI: 10.1002/humu.23247] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 04/18/2017] [Accepted: 05/01/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Adriana I. Iglesias
- Department of Epidemiology Erasmus Medical Center Rotterdam the Netherlands
- Department of Ophthalmology Erasmus Medical Center Rotterdam the Netherlands
| | - Sven J. der Lee
- Department of Epidemiology Erasmus Medical Center Rotterdam the Netherlands
| | - Pieter W.M. Bonnemaijer
- Department of Epidemiology Erasmus Medical Center Rotterdam the Netherlands
- Department of Ophthalmology Erasmus Medical Center Rotterdam the Netherlands
| | - René Höhn
- Department of Ophthalmology Inselspital University Hospital Bern University of Bern Bern Switzerland
- Department of Ophthalmology University Medical Center Mainz Mainz Germany
| | - Abhishek Nag
- Department of Twin Research and Genetic Epidemiology King's College London London UK
| | - Puya Gharahkhani
- Statistical Genetics QIMR Berghofer Medical Research Institute Royal Brisbane Hospital Brisbane Australia
| | - Anthony P. Khawaja
- Department of Public Health and Primary Care University of Cambridge Cambridge UK
- NIHR Biomedical Research Centre Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology London UK
| | - Linda Broer
- Department of Internal Medicine Erasmus Medical Center Rotterdam the Netherlands
| | - Paul J. Foster
- NIHR Biomedical Research Centre Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology London UK
| | | | - Pirro G. Hysi
- Department of Twin Research and Genetic Epidemiology King's College London London UK
| | | | - Stuart MacGregor
- Statistical Genetics QIMR Berghofer Medical Research Institute Royal Brisbane Hospital Brisbane Australia
| | - David A. Mackey
- Centre for Ophthalmology and Visual Science Lions Eye Institute University of Western Australia Perth Australia
- School of Medicine Menzies Research Institute Tasmania University of Tasmania Hobart Australia
| | - Johanna Mazur
- Institute of Medical Biostatistics Epidemiology and Informatics (IMBEI) University Medical Center Mainz Germany
| | - Stefan Nickels
- Department of Ophthalmology University Medical Center Mainz Mainz Germany
| | - André G. Uitterlinden
- Department of Epidemiology Erasmus Medical Center Rotterdam the Netherlands
- Department of Internal Medicine Erasmus Medical Center Rotterdam the Netherlands
- Netherlands Consortium for Healthy Ageing Netherlands Genomics Initiative the Hague the Netherlands
| | - Caroline C.W. Klaver
- Department of Epidemiology Erasmus Medical Center Rotterdam the Netherlands
- Department of Ophthalmology Erasmus Medical Center Rotterdam the Netherlands
- Department of Ophthalmology Radboud University Medical Center Nijmegen the Netherlands
| | - Najaf Amin
- Department of Epidemiology Erasmus Medical Center Rotterdam the Netherlands
| | - Cornelia M. Duijn
- Department of Epidemiology Erasmus Medical Center Rotterdam the Netherlands
- Leiden Academic Centre for Drug Research (LACDR) Leiden University the Netherlands
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37
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Liu Y, Allingham RR. Major review: Molecular genetics of primary open-angle glaucoma. Exp Eye Res 2017; 160:62-84. [PMID: 28499933 DOI: 10.1016/j.exer.2017.05.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/29/2017] [Accepted: 05/07/2017] [Indexed: 12/13/2022]
Abstract
Glaucoma is a leading cause of irreversible blindness worldwide. Primary open-angle glaucoma (POAG), the most common type, is a complex inherited disorder that is characterized by progressive retinal ganglion cell death, optic nerve head excavation, and visual field loss. The discovery of a large, and growing, number of genetic and chromosomal loci has been shown to contribute to POAG risk, which carry implications for disease pathogenesis. Differential gene expression analyses in glaucoma-affected tissues as well as animal models of POAG are enhancing our mechanistic understanding in this common, blinding disorder. In this review we summarize recent developments in POAG genetics and molecular genetics research.
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Affiliation(s)
- Yutao Liu
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, United States; James & Jean Culver Vision Discovery Institute, Augusta University, Augusta, GA, United States; Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA, United States
| | - R Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, United States; Duke - National University of Singapore (Duke-NUS), Singapore.
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38
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Swierkowska J, Gajecka M. Genetic factors influencing the reduction of central corneal thickness in disorders affecting the eye. Ophthalmic Genet 2017; 38:501-510. [DOI: 10.1080/13816810.2017.1313993] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Marzena Gajecka
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
- Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
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39
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Abstract
PURPOSE OF REVIEW The purpose of this review is to summarize the role of central corneal thickness (CCT) in the clinical management of a glaucoma patient. RECENT FINDINGS The prognostic value of CCT is well recognized in patients with ocular hypertension. However, its predictive value in other glaucoma suspects and patients with established glaucoma is less certain. Tonometry artefacts can result from variations in CCT. However, an adequately validated correction algorithm for Goldmann applanation tonometry measurements does not exist. Newer methods of tonometry are potentially less influenced by CCT but are limited in their clinical use. There may also be biological and genetic associations between corneal thickness and glaucoma. Demographics, environmental factors, glaucoma treatment and the measurement device used have a significant influence on CCT, and should be considered when interpreting the effect of cornea thickness in patients with glaucoma. New measurements of the biomechanical properties of the cornea are likely to be better approximations of the globe biomechanics than CCT, but these require further evaluation. SUMMARY The clinical significance of CCT is well recognized in the context of glaucoma diagnosis and management, though the extent of its importance remains debatable. Corneal biomechanical properties may be more significantly associated with glaucoma than CCT.
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40
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Zhou T, Souzeau E, Sharma S, Landers J, Mills R, Goldberg I, Healey PR, Graham S, Hewitt AW, Mackey DA, Galanopoulos A, Casson RJ, Ruddle JB, Ellis J, Leo P, Brown MA, MacGregor S, Lynn DJ, Burdon KP, Craig JE. Whole exome sequencing implicates eye development, the unfolded protein response and plasma membrane homeostasis in primary open-angle glaucoma. PLoS One 2017; 12:e0172427. [PMID: 28264060 PMCID: PMC5338784 DOI: 10.1371/journal.pone.0172427] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 02/03/2017] [Indexed: 11/18/2022] Open
Abstract
PURPOSE To identify biological processes associated with POAG and its subtypes, high-tension (HTG) and normal-tension glaucoma (NTG), by analyzing rare potentially damaging genetic variants. METHODS A total of 122 and 65 unrelated HTG and NTG participants, respectively, with early onset advanced POAG, 103 non-glaucoma controls and 993 unscreened ethnicity-matched controls were included in this study. Study participants without myocilin disease-causing variants and non-glaucoma controls were subjected to whole exome sequencing on an Illumina HiSeq2000. Exomes of participants were sequenced on an Illumina HiSeq2000. Qualifying variants were rare in the general population (MAF < 0.001) and potentially functionally damaging (nonsense, frameshift, splice or predicted pathogenic using SIFT or Polyphen2 software). Genes showing enrichment of qualifying variants in cases were selected for pathway and network analysis using InnateDB. RESULTS POAG cases showed enrichment of rare variants in camera-type eye development genes (p = 1.40×10-7, corrected p = 3.28×10-4). Implicated eye development genes were related to neuronal or retinal development. HTG cases were significantly enriched for key regulators in the unfolded protein response (UPR) (p = 7.72×10-5, corrected p = 0.013). The UPR is known to be involved in myocilin-related glaucoma; our results suggest the UPR has a role in non-myocilin causes of HTG. NTG cases showed enrichment in ion channel transport processes (p = 1.05×10-4, corrected p = 0.027) including calcium, chloride and phospholipid transporters involved in plasma membrane homeostasis. Network analysis also revealed enrichment of the MHC Class I antigen presentation pathway in HTG, and the EGFR1 and cell-cycle pathways in both HTG and NTG. CONCLUSION This study suggests that mutations in eye development genes are enriched in POAG. HTG can result from aberrant responses to protein misfolding which may be amenable to molecular chaperone therapy. NTG is associated with impaired plasma membrane homeostasis increasing susceptibility to apoptosis.
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Affiliation(s)
- Tiger Zhou
- Flinders University, Department of Ophthalmology, Bedford Park, South Australia, Australia
- * E-mail:
| | - Emmanuelle Souzeau
- Flinders University, Department of Ophthalmology, Bedford Park, South Australia, Australia
| | - Shiwani Sharma
- Flinders University, Department of Ophthalmology, Bedford Park, South Australia, Australia
| | - John Landers
- Flinders University, Department of Ophthalmology, Bedford Park, South Australia, Australia
| | - Richard Mills
- Flinders University, Department of Ophthalmology, Bedford Park, South Australia, Australia
| | - Ivan Goldberg
- University of Sydney Discipline of Ophthalmology, Sydney, Australia
- Glaucoma Unit, Sydney Eye Hospital, Sydney, Australia
| | - Paul R. Healey
- University of Sydney Discipline of Ophthalmology, Sydney, Australia
- Centre for Vision Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Stuart Graham
- University of Sydney Discipline of Ophthalmology, Sydney, Australia
| | - Alex W. Hewitt
- University of Tasmania Menzies Institute for Medical Research, Hobart, Australia
| | - David A. Mackey
- University of Western Australia Centre for Ophthalmology and Visual Science, Lions Eye Institute, Perth, Australia
| | - Anna Galanopoulos
- University of Adelaide, Discipline of Ophthalmology & Visual Sciences, Adelaide, Australia
| | - Robert J. Casson
- University of Adelaide, Discipline of Ophthalmology & Visual Sciences, Adelaide, Australia
| | - Jonathan B. Ruddle
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
| | - Jonathan Ellis
- University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Australia
| | - Paul Leo
- University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Australia
| | - Matthew A. Brown
- University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Woolloongabba, Australia
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, Australia
| | - David J. Lynn
- EMBL Australia Group, Infection & Immunity Theme, South Australian Medical and Health Research Institute, Adelaide, Australia
- Flinders University, School of Medicine, Adelaide, Australia
| | - Kathryn P. Burdon
- Flinders University, Department of Ophthalmology, Bedford Park, South Australia, Australia
- University of Tasmania Menzies Institute for Medical Research, Hobart, Australia
| | - Jamie E. Craig
- Flinders University, Department of Ophthalmology, Bedford Park, South Australia, Australia
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Springelkamp H, Iglesias AI, Mishra A, Höhn R, Wojciechowski R, Khawaja AP, Nag A, Wang YX, Wang JJ, Cuellar-Partida G, Gibson J, Bailey JNC, Vithana EN, Gharahkhani P, Boutin T, Ramdas WD, Zeller T, Luben RN, Yonova-Doing E, Viswanathan AC, Yazar S, Cree AJ, Haines JL, Koh JY, Souzeau E, Wilson JF, Amin N, Müller C, Venturini C, Kearns LS, Kang JH, Tham YC, Zhou T, van Leeuwen EM, Nickels S, Sanfilippo P, Liao J, van der Linde H, Zhao W, van Koolwijk LM, Zheng L, Rivadeneira F, Baskaran M, van der Lee SJ, Perera S, de Jong PT, Oostra BA, Uitterlinden AG, Fan Q, Hofman A, Tai ES, Vingerling JR, Sim X, Wolfs RC, Teo YY, Lemij HG, Khor CC, Willemsen R, Lackner KJ, Aung T, Jansonius NM, Montgomery G, Wild PS, Young TL, Burdon KP, Hysi PG, Pasquale LR, Wong TY, Klaver CC, Hewitt AW, Jonas JB, Mitchell P, Lotery AJ, Foster PJ, Vitart V, Pfeiffer N, Craig JE, Mackey DA, Hammond CJ, Wiggs JL, Cheng CY, van Duijn CM, MacGregor S. New insights into the genetics of primary open-angle glaucoma based on meta-analyses of intraocular pressure and optic disc characteristics. Hum Mol Genet 2017; 26:438-453. [PMID: 28073927 PMCID: PMC5968632 DOI: 10.1093/hmg/ddw399] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 08/19/2016] [Accepted: 09/28/2016] [Indexed: 01/04/2023] Open
Abstract
Primary open-angle glaucoma (POAG), the most common optic neuropathy, is a heritable disease. Siblings of POAG cases have a ten-fold increased risk of developing the disease. Intraocular pressure (IOP) and optic nerve head characteristics are used clinically to predict POAG risk. We conducted a genome-wide association meta-analysis of IOP and optic disc parameters and validated our findings in multiple sets of POAG cases and controls. Using imputation to the 1000 genomes (1000G) reference set, we identified 9 new genomic regions associated with vertical cup-disc ratio (VCDR) and 1 new region associated with IOP. Additionally, we found 5 novel loci for optic nerve cup area and 6 for disc area. Previously it was assumed that genetic variation influenced POAG either through IOP or via changes to the optic nerve head; here we present evidence that some genomic regions affect both IOP and the disc parameters. We characterized the effect of the novel loci through pathway analysis and found that pathways involved are not entirely distinct as assumed so far. Further, we identified a novel association between CDKN1A and POAG. Using a zebrafish model we show that six6b (associated with POAG and optic nerve head variation) alters the expression of cdkn1a. In summary, we have identified several novel genes influencing the major clinical risk predictors of POAG and showed that genetic variation in CDKN1A is important in POAG risk.
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Affiliation(s)
- Henriët Springelkamp
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Adriana I. Iglesias
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Aniket Mishra
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, Australia
- Department of Complex Trait Genetics, VU University, Center for Neurogenomics and Cognitive Research, Amsterdam, the Netherlands
| | - René Höhn
- Department of Ophthalmology, Inselspital, University Hospital Bern, University of Bern, Bern, Switzerland
- Department of Ophthalmology, University Medical Center Mainz, Mainz, Germany
| | - Robert Wojciechowski
- Computational and Statistical Genomics Branch, National Human Genome Research Institute (NIH), Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Anthony P. Khawaja
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Abhishek Nag
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Ya Xing Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
- Beijing Ophthalmology and Visual Science Key Lab, Beijing, China
| | - Jie Jin Wang
- Centre for Vision Research, Department of Ophthalmology and Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - Gabriel Cuellar-Partida
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, Australia
| | - Jane Gibson
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, UK
| | - Jessica N. Cooke Bailey
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, USA
| | - Eranga N. Vithana
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Puya Gharahkhani
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, Australia
| | - Thibaud Boutin
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Wishal D. Ramdas
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Tanja Zeller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Hamburg, Luebeck, Kiel, Hamburg/Germany
| | - Robert N. Luben
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | | | - Ananth C. Viswanathan
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Seyhan Yazar
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | - Angela J. Cree
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Jonathan L. Haines
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jia Yu Koh
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | | | - James F. Wilson
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Centre for Global Health Research, The Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Scotland, UK
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Christian Müller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Hamburg, Luebeck, Kiel, Hamburg/Germany
| | - Cristina Venturini
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Lisa S. Kearns
- Centre for Eye Research Australia (CERA), University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
| | - Jae Hee Kang
- Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | | | - Yih Chung Tham
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Tiger Zhou
- Department of Ophthalmology, Flinders University, Adelaide, Australia
| | | | - Stefan Nickels
- Department of Ophthalmology, University Medical Center Mainz, Mainz, Germany
| | - Paul Sanfilippo
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
- Centre for Eye Research Australia (CERA), University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
| | - Jiemin Liao
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Herma van der Linde
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Wanting Zhao
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
| | | | - Li Zheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Division of Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, the Hague, the Netherlands
| | | | - Sven J. van der Lee
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Shamira Perera
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
| | - Paulus T.V.M. de Jong
- Department of Ophthalmology, Academic Medical Center, Amsterdam, the Netherlands
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands
- The Netherlands Institute of Neuroscience KNAW, Amsterdam, the Netherlands
| | - Ben A. Oostra
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, the Hague, the Netherlands
| | - Qiao Fan
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, the Hague, the Netherlands
| | - E-Shyong Tai
- Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
- Department of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | | | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Roger C.W. Wolfs
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - Hans G. Lemij
- Glaucoma Service, The Rotterdam Eye Hospital, Rotterdam, the Netherlands
| | - Chiea Chuen Khor
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Division of Human Genetics, Genome Institute of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore
| | - Rob Willemsen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Karl J. Lackner
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Mainz, Germany
| | - Tin Aung
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Nomdo M. Jansonius
- Department of Ophthalmology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Grant Montgomery
- Department of Molecular Epidemiology, Queensland Institute of Medical Research, Herston, Brisbane, Queensland, Australia
| | - Philipp S. Wild
- Preventive Cardiology and Preventive Medicine/Center for Cardiology, University Medical Center Mainz, Mainz, Germany
- Center for Thrombosis and Hemostasis, University Medical Center Mainz, Mainz, Germany
- German Center for Cardiovascular Research (DZHK), partner site RhineMain, Mainz, Germany
| | - Terri L. Young
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Kathryn P. Burdon
- School of Medicine, Menzies Research Institute Tasmania, University of Tasmania, Hobart, Australia
| | - Pirro G. Hysi
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Louis R. Pasquale
- Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA and
| | - Tien Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Caroline C.W. Klaver
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Alex W. Hewitt
- Centre for Eye Research Australia (CERA), University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- School of Medicine, Menzies Research Institute Tasmania, University of Tasmania, Hobart, Australia
| | - Jost B. Jonas
- Department of Ophthalmology, Medical Faculty Mannheim of the Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany
| | - Paul Mitchell
- Centre for Vision Research, Department of Ophthalmology and Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - Andrew J. Lotery
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Paul J. Foster
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Norbert Pfeiffer
- Department of Ophthalmology, University Medical Center Mainz, Mainz, Germany
| | - Jamie E. Craig
- Department of Ophthalmology, Flinders University, Adelaide, Australia
| | - David A. Mackey
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
- School of Medicine, Menzies Research Institute Tasmania, University of Tasmania, Hobart, Australia
| | | | - Janey L. Wiggs
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA and
| | | | | | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, Australia
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Sardell RJ, Nittala MG, Adams LD, Laux RA, Cooke Bailey JN, Fuzzell D, Fuzzell S, Reinhart-Mercer L, Caywood LJ, Horst V, Mackay T, Dana D, Sadda SR, Scott WK, Stambolian D, Haines JL, Pericak-Vance MA. Heritability of Choroidal Thickness in the Amish. Ophthalmology 2016; 123:2537-2544. [PMID: 27771146 DOI: 10.1016/j.ophtha.2016.09.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 08/22/2016] [Accepted: 09/01/2016] [Indexed: 01/31/2023] Open
Abstract
PURPOSE To evaluate the heritability of choroidal thickness and its relationship to age-related macular degeneration (AMD). DESIGN Cohort study. PARTICIPANTS Six hundred eighty-nine individuals from Amish families with early or intermediate AMD. METHODS Ocular coherence tomography was used to quantify choroidal thickness, and fundus photography was used to classify eyes into categories using a modified Clinical Age-Related Maculopathy Staging (CARMS) system. Repeatability and heritability of choroidal thickness and its phenotypic and genetic correlations with the AMD phenotype (CARMS category) were estimated using a generalized linear mixed model (GLMM) approach that accounted for relatedness, repeated measures (left and right eyes), and the effects of age, gender, and refraction. MAIN OUTCOME MEASURES Heritability of choroidal thickness and its phenotypic and genetic correlation with the AMD phenotype (CARMS category). RESULTS Phenotypic correlation between choroidal thickness and CARMS category was moderate (Spearman's rank correlation, rs = -0.24; n = 1313 eyes) and significant (GLMM posterior mean, -4.27; 95% credible interval [CI], -7.88 to -0.79; P = 0.02) after controlling for relatedness, age, gender, and refraction. Eyes with advanced AMD had thinner choroids than eyes without AMD (posterior mean, -73.8; 95% CI, -94.7 to -54.6; P < 0.001; n = 1178 eyes). Choroidal thickness was highly repeatable within individuals (repeatability, 0.78; 95% CI, 0.68 to 0.89) and moderately heritable (heritability, 0.40; 95% CI, 0.14 to 0.51), but did not show significant genetic correlation with CARMS category, although the effect size was moderate (genetic correlation, -0.18; 95% CI, -0.49 to 0.16). Choroidal thickness also varied with age, gender, and refraction. The CARMS category showed moderate heritability (heritability, 0.49; 95% CI, 0.26 to 0.72). CONCLUSIONS We quantify the heritability of choroidal thickness for the first time, highlighting a heritable, quantitative trait that is measurable in all individuals regardless of AMD affection status, and moderately phenotypically correlated with AMD severity. Choroidal thickness therefore may capture variation not captured by the CARMS system. However, because the genetic correlation between choroidal thickness and AMD severity was not significant in our data set, genes associated with the 2 traits may not overlap substantially. Future studies should therefore test for genetic variation associated with choroidal thickness to determine the overlap in genetic basis with AMD.
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Affiliation(s)
- Rebecca J Sardell
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Muneeswar G Nittala
- Department of Ophthalmology, Doheny Eye Institute, University of California, Los Angeles, Los Angeles, California
| | - Larry D Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Reneé A Laux
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio
| | - Jessica N Cooke Bailey
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio
| | - Denise Fuzzell
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio
| | - Sarada Fuzzell
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio
| | - Lori Reinhart-Mercer
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Laura J Caywood
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Violet Horst
- Departments of Ophthalmology and Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Tine Mackay
- Departments of Ophthalmology and Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Debbie Dana
- Departments of Ophthalmology and Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - SriniVas R Sadda
- Department of Ophthalmology, Doheny Eye Institute, University of California, Los Angeles, Los Angeles, California
| | - William K Scott
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Dwight Stambolian
- Departments of Ophthalmology and Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jonathan L Haines
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida.
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Christopher M, Abràmoff MD, Tang L, Gordon MO, Kass MA, Budenz DL, Fingert JH, Scheetz TE. Stereo Photo Measured ONH Shape Predicts Development of POAG in Subjects With Ocular Hypertension. Invest Ophthalmol Vis Sci 2015; 56:4470-9. [PMID: 26193923 DOI: 10.1167/iovs.14-16142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To identify objective, quantitative optic nerve head (ONH) structural features and model the contributions of glaucoma. METHODS Baseline stereoscopic optic disc images of 1635 glaucoma-free participants at risk for developing primary open-angle glaucoma (POAG) were collected as part of the Ocular Hypertension Treatment Study. A stereo correspondence algorithm designed for fundus images was applied to extract the three-dimensional (3D) information about the ONH. Principal component analysis was used to identify ONH 3D structural features and the contributions of demographic features, clinical variables, and disease were modeled using linear regression and linear component analysis. The computationally identified features were evaluated based on associations with glaucoma and ability to predict which participants would develop POAG. RESULTS The computationally identified features were significantly associated with future POAG, POAG-related demographics (age, ethnicity), and clinical measurements (horizontal and vertical cup-to-disc ratio, central corneal thickness, and refraction). Models predicting future POAG development using the OHTS baseline data and STEP features achieved an AUC of 0.722 in cross-validation testing. This was a significant improvement over using only demographics (age, sex, and ethnicity), which had an AUC of 0.599. CONCLUSIONS Methods for identifying objective, quantitative measurements of 3D ONH structure were developed using a large dataset. The identified features were significantly associated with POAG and POAG-related variables. Further, these features increased predictive model accuracy in predicting future POAG. The results indicate that the computationally identified features might be useful in POAG early screening programs or as endophenotypes to investigate POAG genetics.
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Affiliation(s)
- Mark Christopher
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa, United States 2Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa, United States
| | - Michael D Abràmoff
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa, United States 2Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa, United States 3Department of Electrical and Computer Engineering, University of I
| | - Li Tang
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, United States
| | - Mae O Gordon
- Division of Biostatistics, Washington University, St. Louis, Missouri, United States 7Department of Ophthalmology and Visual Sciences, Washington University, St. Louis, Missouri, United States
| | - Michael A Kass
- Department of Ophthalmology and Visual Sciences, Washington University, St. Louis, Missouri, United States
| | - Donald L Budenz
- Department of Ophthalmology, University of North Carolina, Chapel Hill, North Carolina, United States
| | - John H Fingert
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa, United States 4Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, United States
| | - Todd E Scheetz
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa, United States 2Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa, United States 4Department of Ophthalmology and Visual Sciences, University of Iow
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44
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Gharahkhani P, Burdon KP, Hewitt AW, Law MH, Souzeau E, Montgomery GW, Radford-Smith G, Mackey DA, Craig JE, MacGregor S. Accurate Imputation-Based Screening of Gln368Ter Myocilin Variant in Primary Open-Angle Glaucoma. Invest Ophthalmol Vis Sci 2015; 56:5087-93. [PMID: 26237198 DOI: 10.1167/iovs.15-17305] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Myocilin (MYOC) is a well-established primary open-angle glaucoma (POAG) risk gene, with rare variants known to have high penetrance. The most common clinically relevant risk variant, Gln368Ter, has an allele frequency of 0.1% to 0.3% in populations of European ancestry. Detection of rare MYOC variants has traditionally been conducted using Sanger sequencing. Here we report the use of genotyping arrays and imputation to assess whether rare variants including Gln368Ter can be reliably detected. METHODS A total of 1155 cases with advanced POAG and 1992 unscreened controls genotyped on common variant arrays participated in this study. Accuracy of imputation of Gln368Ter variants was compared with direct sequencing. A genome-wide association study was performed using additive model adjusted for sex and the first six principal components. RESULTS We found that although the arrays we used were designed to tag common variants, we could reliably impute the Gln368Ter variant (rs74315329). When tested in 1155 POAG cases and 1992 controls, rs74315329 was strongly associated with risk (odds ratio = 15.53, P = 1.07 × 10-9). All POAG samples underwent full sequencing of the MYOC gene, and we found a sensitivity of 100%, specificity of 99.91%, positive predictive value of 95.65%, and negative predictive value of 100% between imputation and sequencing. Gln368Ter was also accurately imputed in a further set of 1801 individuals without POAG. Among the total set of 3793 (1992 + 1801) individuals without POAG, six were predicted (probability > 95%) to carry the risk variant. CONCLUSIONS We demonstrate that some clinically important rare variants can be reliably detected using arrays and imputation. These results have important implications for the detection of clinically relevant incidental findings in ongoing and future studies using arrays.
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Affiliation(s)
- Puya Gharahkhani
- Queensland Institute of Medical Research Berghofer Medical Research Institute Brisbane, Queensland, Australia
| | - Kathryn P Burdon
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia 3Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia 4Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
| | - Matthew H Law
- Queensland Institute of Medical Research Berghofer Medical Research Institute Brisbane, Queensland, Australia
| | - Emmanuelle Souzeau
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Grant W Montgomery
- Queensland Institute of Medical Research Berghofer Medical Research Institute Brisbane, Queensland, Australia
| | - Graham Radford-Smith
- Queensland Institute of Medical Research Berghofer Medical Research Institute Brisbane, Queensland, Australia 5School of Medicine, University of Queensland, Herston Campus, Brisbane, Queensland, Australia
| | - David A Mackey
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia 6Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia 7South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Stuart MacGregor
- Queensland Institute of Medical Research Berghofer Medical Research Institute Brisbane, Queensland, Australia
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Philomenadin FS, Asokan R, N V, George R, Lingam V, Sarangapani S. Genetic association of SNPs near ATOH7, CARD10, CDKN2B, CDC7 and SIX1/SIX6 with the endophenotypes of primary open angle glaucoma in Indian population. PLoS One 2015; 10:e0119703. [PMID: 25798827 PMCID: PMC4370747 DOI: 10.1371/journal.pone.0119703] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 01/15/2015] [Indexed: 11/18/2022] Open
Abstract
Primary open angle glaucoma (POAG) belonging to a group of optic neuropathies, result from interaction between genetic and environmental factors. Study of associations with quantitative traits (QTs) is one of the successful strategies to understand the complex genetics of POAG. The current study attempts to explore the association of variations near/in genes like ATOH7, SIX1/SIX6 complex, CDKN2B, CARD10, and CDC7 with POAG and its QTs including vertical cup to disc ratio (VCDR), central corneal thickness (CCT), intra ocular pressure (IOP), and axial length (AL). Case-control study design was carried out in a sample size of 97 POAG cases and 371 controls from South India. Model-based (additive, recessive, dominant) association of the genotypes and their interaction was carried out between cases and controls using chi-square, linear and logistic regression methods. Nominal significance (P<0.05) was observed for QTs like i) VCDR with SNPs rs1900004 (ATOH7); rs1192415 (CDC7); rs10483727 (SIX1/SIX6), rs9607469 (CARD10); ii) CCT with rs1192415; iii) IOP with rs1900004 and iv) AL with rs1900004 and rs1063192 (CDKN2B). We were able to replicate previously known interactions between ATOH7-SIX6 and SIX6-CDKN2B along with few novel interactions between ATOH7—CDC7 and SIX6 with genes including CARD10 and CDC7. In summary, our results suggest that a probable interaction among the candidate genes for QTs, play a major role in determining the individual’s susceptibility to POAG.
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Affiliation(s)
- Ferdinamarie Sharmila Philomenadin
- SNONGC Department of Genetics and Molecular biology, Vision Research foundation, Sankara Nethralaya, Chennai, India
- PhD Scholar, Birla Institute of Technology & Science (BITS), Pilani, 333 031, Rajasthan, India
| | - Rashima Asokan
- Chennai Glaucoma Study, Medical and Vision Research Foundation, Sankara Nethralaya, Chennai, India
| | - Viswanathan N
- Biostatistician, Department of Preventive Ophthalmology, Medical research foundation, Sankara Nethralaya, Chennai, India
| | - Ronnie George
- Chennai Glaucoma Study, Medical and Vision Research Foundation, Sankara Nethralaya, Chennai, India
| | - Vijaya Lingam
- Chennai Glaucoma Study, Medical and Vision Research Foundation, Sankara Nethralaya, Chennai, India
| | - Sripriya Sarangapani
- SNONGC Department of Genetics and Molecular biology, Vision Research foundation, Sankara Nethralaya, Chennai, India
- * E-mail:
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46
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Kim MW, Lee JR, Lee KS, Sung KR. Clinical Characteristics of First-Degree Relatives with Primary Open-Angle Glaucoma. JOURNAL OF THE KOREAN OPHTHALMOLOGICAL SOCIETY 2015. [DOI: 10.3341/jkos.2015.56.3.396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Min Woo Kim
- Department of Ophthalmology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jong Rak Lee
- Department of Ophthalmology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyoung Sub Lee
- Department of Ophthalmology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyung Rim Sung
- Department of Ophthalmology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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Chen F, Klein AP, Klein BEK, Lee KE, Truitt B, Klein R, Iyengar SK, Duggal P. Exome array analysis identifies CAV1/CAV2 as a susceptibility locus for intraocular pressure. Invest Ophthalmol Vis Sci 2014; 56:544-51. [PMID: 25525164 DOI: 10.1167/iovs.14-15204] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
PURPOSE Intraocular pressure (IOP) is an important clinical parameter in the evaluation of ocular health. Elevated IOP is a major risk factor for primary open-angle glaucoma (POAG). The goal of this study was to identify rare and less common variants that influence IOP. METHODS We performed an exome array analysis in a subset of 1660 individuals from a population-based cohort, the Beaver Dam Eye Study. Associations with IOP were tested on 45,849 single nucleotide variants and 12,390 autosomal genes across the genome. RESULTS Intraocular pressure was suggestively associated with novel variants located in FAR2 at 12p11.22 (rs4931170, P = 1.2 × 10(-5)), in GGA3 at 17q25.1 (rs52809447, P = 6.7 × 10(-5)), and in PKDREJ at 22q13.31 (rs7291444, P = 7.4 × 10(-5)). Gene-based analysis found suggestive associations between IOP and the genes HAP1, MTBP, FREM3, and PHF12. We successfully replicated the associations with GAS7 (P = 7.4 × 10(-3)) for IOP, and also identified a previously reported POAG locus in the CAV1/CAV2 region to be associated with IOP (P = 3.3 × 10(-3)). This association was confirmed in a meta-analysis with three published genome-wide association studies (Pcombined = 4.0 × 10(-11)). CONCLUSIONS Our results suggest that novel genetic variants and genes with multiple, less common variants may play a role in the control of IOP. The implication of the caveolin genes, CAV1/CAV2, as a common genetic factor influencing both IOP variations and POAG may provide new insights of the underlying mechanism leading to glaucoma and glaucomatous visual field loss.
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Affiliation(s)
- Fei Chen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
| | - Alison P Klein
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
| | - Barbara E K Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States
| | - Kristine E Lee
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States
| | - Barbara Truitt
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States
| | - Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States
| | - Sudha K Iyengar
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
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48
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Springelkamp H, Höhn R, Mishra A, Hysi PG, Khor CC, Loomis SJ, Bailey JNC, Gibson J, Thorleifsson G, Janssen SF, Luo X, Ramdas WD, Vithana E, Nongpiur ME, Montgomery GW, Xu L, Mountain JE, Gharahkhani P, Lu Y, Amin N, Karssen LC, Sim KS, van Leeuwen EM, Iglesias AI, Verhoeven VJM, Hauser MA, Loon SC, Despriet DDG, Nag A, Venturini C, Sanfilippo PG, Schillert A, Kang JH, Landers J, Jonasson F, Cree AJ, van Koolwijk LME, Rivadeneira F, Souzeau E, Jonsson V, Menon G, Weinreb RN, de Jong PTVM, Oostra BA, Uitterlinden AG, Hofman A, Ennis S, Thorsteinsdottir U, Burdon KP, Spector TD, Mirshahi A, Saw SM, Vingerling JR, Teo YY, Haines JL, Wolfs RCW, Lemij HG, Tai ES, Jansonius NM, Jonas JB, Cheng CY, Aung T, Viswanathan AC, Klaver CCW, Craig JE, Macgregor S, Mackey DA, Lotery AJ, Stefansson K, Bergen AAB, Young TL, Wiggs JL, Pfeiffer N, Wong TY, Pasquale LR, Hewitt AW, van Duijn CM, Hammond CJ. Meta-analysis of genome-wide association studies identifies novel loci that influence cupping and the glaucomatous process. Nat Commun 2014; 5:4883. [PMID: 25241763 PMCID: PMC4199103 DOI: 10.1038/ncomms5883] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 08/04/2014] [Indexed: 11/25/2022] Open
Abstract
Glaucoma is characterized by irreversible optic nerve degeneration and is the most frequent cause of irreversible blindness worldwide. Here, the International Glaucoma Genetics Consortium conducts a meta-analysis of genome-wide association studies of vertical cup-disc ratio (VCDR), an important disease-related optic nerve parameter. In 21,094 individuals of European ancestry and 6,784 individuals of Asian ancestry, we identify 10 new loci associated with variation in VCDR. In a separate risk-score analysis of five case-control studies, Caucasians in the highest quintile have a 2.5-fold increased risk of primary open-angle glaucoma as compared with those in the lowest quintile. This study has more than doubled the known loci associated with optic disc cupping and will allow greater understanding of mechanisms involved in this common blinding condition.
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Affiliation(s)
- Henriët. Springelkamp
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - René Höhn
- Department of Ophthalmology, University Medical Center Mainz, Mainz 55131, Germany
| | - Aniket Mishra
- Department of Genetics and Computational Biology, Statistical Genetics, QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, Queensland 4006, Australia
| | - Pirro G. Hysi
- Department of Twin Research and Genetic Epidemiology, King’s College London, London WC2R 2LS, UK
| | - Chiea-Chuen Khor
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore 119077, Singapore
- Division of Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Stephanie J. Loomis
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear Infirmary, Boston, Massachusetts 02114, USA
| | - Jessica N. Cooke Bailey
- Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Jane Gibson
- Centre for Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | | | - Sarah F. Janssen
- Department of Clinical and Molecular Ophthalmogenetics, The Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam 1105 BA, the Netherlands
| | - Xiaoyan Luo
- Department of Ophthalmology, Duke University Eye Center, Durham, North Carolina 27710, USA
| | - Wishal D. Ramdas
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Eranga Vithana
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore 119077, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore
- Duke-National University of Singapore, Graduate Medical School, Singapore 169857, Singapore
| | - Monisha E. Nongpiur
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore 119077, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore
| | - Grant W. Montgomery
- Department of Genetics and Computational Biology, Molecular Epidemiology Laboratory, QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, Queensland 4006, Australia
| | - Liang Xu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
- Beijing Ophthalmology and Visual Science Key Lab, Beijing 100730, China
| | - Jenny E. Mountain
- Telethon Institute for Child Health Research, Subiaco, Western Australia 6008, Australia
| | - Puya Gharahkhani
- Department of Genetics and Computational Biology, Statistical Genetics, QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, Queensland 4006, Australia
| | - Yi Lu
- Department of Genetics and Computational Biology, Statistical Genetics, QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, Queensland 4006, Australia
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Lennart C. Karssen
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Kar-Seng Sim
- Division of Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore
| | | | - Adriana I. Iglesias
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Virginie J. M. Verhoeven
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Michael A. Hauser
- Departments of Medicine and Ophthalmology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Seng-Chee Loon
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore 119077, Singapore
| | | | - Abhishek Nag
- Department of Twin Research and Genetic Epidemiology, King’s College London, London WC2R 2LS, UK
| | - Cristina Venturini
- Department of Twin Research and Genetic Epidemiology, King’s College London, London WC2R 2LS, UK
- UCL Institute of Ophthalmology, London EC1V 9EL, UK
| | - Paul G. Sanfilippo
- Centre for Eye Research Australia (CERA), University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria 3002, Australia
| | - Arne Schillert
- Institute of Medical Biometry and Statistics, University of Lübeck, Lübeck 23562, Germany
| | - Jae H. Kang
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - John Landers
- Department of Ophthalmology, Flinders University, Adelaide, South Australia 5042, Australia
| | - Fridbert Jonasson
- Faculty of Medicine, University of Iceland, Reykjavik 101, Iceland
- Department of Ophthalmology, Landspitali National University Hospital, Reykjavik 101, Iceland
| | - Angela J. Cree
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | | | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, The Hague 2593 CE, The Netherlands
| | - Emmanuelle Souzeau
- Department of Ophthalmology, Flinders University, Adelaide, South Australia 5042, Australia
| | - Vesteinn Jonsson
- Department of Ophthalmology, Landspitali National University Hospital, Reykjavik 101, Iceland
| | - Geeta Menon
- Department of Ophthalmology, Frimley Park Hospital NHS Foundation Trust, Frimley GU16 7UJ, UK
| | - Robert N. Weinreb
- Department of Ophthalmology and Hamilton Glaucoma Center, University of California, San Diego, California 92093, USA
| | - Paulus T. V. M. de Jong
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
- Department of Retinal Signal Processing, Netherlands Institute for Neuroscience, Amsterdam 1105 BA, The Netherlands
- Department of Ophthalmology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands
- Department of Ophthalmology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Ben A. Oostra
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, The Hague 2593 CE, The Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, The Hague 2593 CE, The Netherlands
| | - Sarah Ennis
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | - Unnur Thorsteinsdottir
- deCODE/Amgen, Reykjavik 101, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik 101, Iceland
| | - Kathryn P. Burdon
- Department of Ophthalmology, Flinders University, Adelaide, South Australia 5042, Australia
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London WC2R 2LS, UK
| | - Alireza Mirshahi
- Department of Ophthalmology, University Medical Center Mainz, Mainz 55131, Germany
| | - Seang-Mei Saw
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore 119077, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore
- Duke-National University of Singapore, Graduate Medical School, Singapore 169857, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117597, Singapore
| | - Johannes R. Vingerling
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117597, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore 119077, Singapore
| | - Jonathan L. Haines
- Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Roger C. W. Wolfs
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Hans G. Lemij
- Glaucoma Service, The Rotterdam Eye Hospital, Rotterdam 3011 BH, The Netherlands
| | - E-Shyong Tai
- Duke-National University of Singapore, Graduate Medical School, Singapore 169857, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117597, Singapore
- Department of Medicine, National University of Singapore and National University Health System, Singapore 119077, Singapore
| | - Nomdo M. Jansonius
- Department of Ophthalmology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, The Netherlands
| | - Jost B. Jonas
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
- Department of Ophthalmology, Medical Faculty Mannheim of the Ruprecht-Karls-University of Heidelberg, Seegartenklinik Heidelberg, Heidelberg 69117, Germany
| | - Ching-Yu Cheng
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore 119077, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore
- Duke-National University of Singapore, Graduate Medical School, Singapore 169857, Singapore
| | - Tin Aung
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore 119077, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore
| | - Ananth C. Viswanathan
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London EC1V 2PD, UK
| | - Caroline C. W. Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Jamie E. Craig
- Department of Ophthalmology, Flinders University, Adelaide, South Australia 5042, Australia
| | - Stuart Macgregor
- Department of Genetics and Computational Biology, Statistical Genetics, QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, Queensland 4006, Australia
| | - David A. Mackey
- Centre for Eye Research Australia (CERA), University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria 3002, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Andrew J. Lotery
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | - Kari Stefansson
- deCODE/Amgen, Reykjavik 101, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik 101, Iceland
| | - Arthur A. B. Bergen
- Department of Clinical and Molecular Ophthalmogenetics, The Netherlands Institute for Neuroscience (NIN), Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam 1105 BA, the Netherlands
- Department of Ophthalmology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands
- Department of Clinical Genetics, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands
| | - Terri L. Young
- Department of Ophthalmology, Duke University Eye Center, Durham, North Carolina 27710, USA
| | - Janey L. Wiggs
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear Infirmary, Boston, Massachusetts 02114, USA
| | - Norbert Pfeiffer
- Department of Ophthalmology, University Medical Center Mainz, Mainz 55131, Germany
| | - Tien-Yin Wong
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore 119077, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore
- Duke-National University of Singapore, Graduate Medical School, Singapore 169857, Singapore
| | - Louis R. Pasquale
- Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear Infirmary, Boston, Massachusetts 02114, USA
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Alex W. Hewitt
- Centre for Eye Research Australia (CERA), University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria 3002, Australia
| | - Cornelia M. van Duijn
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Christopher J. Hammond
- Department of Twin Research and Genetic Epidemiology, King’s College London, London WC2R 2LS, UK
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Abstract
The characterization of genes responsible for glaucoma is the critical first step toward the development of gene-based diagnostic and screening tests, which could identify individuals at risk for disease before irreversible optic nerve damage occurs. Early-onset forms of glaucoma affecting children and young adults are typically inherited as Mendelian autosomal dominant or recessive traits whereas glaucoma affecting older adults has complex inheritance. In this report, we present a comprehensive overview of the genes and genomic regions contributing to inherited glaucoma.
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Affiliation(s)
- Ryan Wang
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts 02114
| | - Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts 02114
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50
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Zhang Z, Srivastava R, Liu H, Chen X, Duan L, Kee Wong DW, Kwoh CK, Wong TY, Liu J. A survey on computer aided diagnosis for ocular diseases. BMC Med Inform Decis Mak 2014; 14:80. [PMID: 25175552 PMCID: PMC4163681 DOI: 10.1186/1472-6947-14-80] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 08/12/2014] [Indexed: 12/12/2022] Open
Abstract
Background Computer Aided Diagnosis (CAD), which can automate the detection process for ocular diseases, has attracted extensive attention from clinicians and researchers alike. It not only alleviates the burden on the clinicians by providing objective opinion with valuable insights, but also offers early detection and easy access for patients. Method We review ocular CAD methodologies for various data types. For each data type, we investigate the databases and the algorithms to detect different ocular diseases. Their advantages and shortcomings are analyzed and discussed. Result We have studied three types of data (i.e., clinical, genetic and imaging) that have been commonly used in existing methods for CAD. The recent developments in methods used in CAD of ocular diseases (such as Diabetic Retinopathy, Glaucoma, Age-related Macular Degeneration and Pathological Myopia) are investigated and summarized comprehensively. Conclusion While CAD for ocular diseases has shown considerable progress over the past years, the clinical importance of fully automatic CAD systems which are able to embed clinical knowledge and integrate heterogeneous data sources still show great potential for future breakthrough.
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Affiliation(s)
- Zhuo Zhang
- Institute for Infocomm Research, 1 Fusionopolis Way, Singapore, Singapore.
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