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Chi K, Li B, Huang H, Sun J, Zheng Y, Zhao L. Exploring the Research Landscape of High Myopia: Trends, Contributors, and Key Areas of Focus. Med Sci Monit 2023; 29:e941670. [PMID: 38111192 PMCID: PMC10748438 DOI: 10.12659/msm.941670] [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: 07/04/2023] [Accepted: 09/29/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Myopia results when light rays focus before reaching the retina, causing blurred vision. High myopia (HM), defined by a refractive error of ≤-6 diopters (D) or an axial length of ≥26 mm, is an extreme form of this condition. The progression from HM to pathological myopia (PM) is marked by extensive ocular axis elongation. The rise in myopia has escalated concerns for HM due to its potential progression to pathological myopia. The covert progression of HM calls for thorough analysis of its current research landscape. MATERIAL AND METHODS HM-related publications from 2003-2022 were retrieved from the Web of Science database. Using VOSviewer and Citespace software, we conducted a bibliometric and visualized analysis to create document co-citation network maps. These maps detailed authors, institutions, countries, key terms, and significant literature. RESULTS From 9,079 articles, 8,241 were reviewed. An increasing trend in publications was observed, with Kyoko Ohno-Matsui identified as a top contributor. The Journal of Cataract and Refractive Surgery was the primary publication outlet. Chinese researchers and institutions were notably active. The document citation network identified five focal areas: refractive surgery, clinical manifestations/treatment, prevention/control, genetics, and open angle glaucoma. CONCLUSIONS Research emphasis in HM has shifted from refractive surgery for visual acuity enhancement to the diagnosis, classification, prevention, and control of HM complications. Proposals for early myopia intervention to prevent HM are gaining attention. Genetics and HM's link with open angle glaucoma, though smaller in focus, significantly enhance our understanding of HM.
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Affiliation(s)
- Kaiyao Chi
- Department of Ophthalmology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, PR China
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, PR China
| | - Biao Li
- Department of Ophthalmology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, PR China
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, PR China
| | - Hui Huang
- Department of Ophthalmology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, PR China
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, PR China
| | - Jianhao Sun
- Department of Ophthalmology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, PR China
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, PR China
| | - Yanlin Zheng
- Department of Ophthalmology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, PR China
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, PR China
| | - Lei Zhao
- Department of Ophthalmology, The Second Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, Shenyang, Liaoning, PR China
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Schmitz J, Abbondanza F, Marianski K, Luciano M, Paracchini S. Identification of loci involved in childhood visual acuity and associations with cognitive skills and educational attainment. NPJ SCIENCE OF LEARNING 2023; 8:25. [PMID: 37491545 PMCID: PMC10368730 DOI: 10.1038/s41539-023-00175-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 07/17/2023] [Indexed: 07/27/2023]
Abstract
Visual acuity significantly contributes to quality of life. Deficits in childhood are associated with reading difficulties, which can have detrimental effects on education outcomes. In adults, it has been observed that vision defects such as myopia are associated with higher educational attainment (EA). Understanding genetic factors contributing to visual acuity could help to dissect its links with cognitive skills, neurodevelopmental conditions, and education. We examined associations between distance visual acuity, cognitive measures including school grades, and neurodevelopmental conditions in a longitudinal cohort of British children (ALSPAC, n = 6807, M age = 11.8). We performed a genome-wide association study (GWAS, n = 5571) on visual acuity and tested for genetic associations with relevant phenotypes using polygenic scores (PGS) and genetic correlation analyses. Visual acuity was associated with better cognitive performance and school grades, and reduced in individuals with reading difficulties compared to controls. GWAS revealed genetic associations at the NPLOC4 locus and highlighted other genes involved in sensory function. In line with positive genetic correlations between visual acuity and cognitive measures, EA PGS were positively associated with visual acuity, while there was a less robust negative association with myopia PGS. In conclusion, increased visual acuity is associated with a range of positive outcomes, including better school grades. Our results suggest an association between a higher EA PGS and slightly increased visual acuity in childhood. This could indicate gene-environment correlation, in which environmental exposures linked to higher EA might have detrimental effects on vision offsetting the initial positive effect.
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Affiliation(s)
- Judith Schmitz
- School of Medicine, University of St Andrews, St Andrews, Scotland, UK
- Biological Personality Psychology, Georg-August-University Goettingen, Goettingen, Germany
| | | | | | - Michelle Luciano
- Department of Psychology, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Silvia Paracchini
- School of Medicine, University of St Andrews, St Andrews, Scotland, UK.
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Jiang C, Melles RB, Yin J, Fan Q, Guo X, Cheng CY, He M, Mackey DA, Guggenheim JA, Klaver C, Nair KS, Jorgenson E, Choquet H. A multiethnic genome-wide analysis of 19,420 individuals identifies novel loci associated with axial length and shared genetic influences with refractive error and myopia. Front Genet 2023; 14:1113058. [PMID: 37351342 PMCID: PMC10282939 DOI: 10.3389/fgene.2023.1113058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/25/2023] [Indexed: 06/24/2023] Open
Abstract
Introduction: Long axial length (AL) is a risk factor for myopia. Although family studies indicate that AL has an important genetic component with heritability estimates up to 0.94, there have been few reports of AL-associated loci. Methods: Here, we conducted a multiethnic genome-wide association study (GWAS) of AL in 19,420 adults of European, Latino, Asian, and African ancestry from the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort, with replication in a subset of the Consortium for Refractive Error and Myopia (CREAM) cohorts of European or Asian ancestry. We further examined the effect of the identified loci on the mean spherical equivalent (MSE) within the GERA cohort. We also performed genome-wide genetic correlation analyses to quantify the genetic overlap between AL and MSE or myopia risk in the GERA European ancestry sample. Results: Our multiethnic GWA analysis of AL identified a total of 16 genomic loci, of which 5 are novel. We found that all AL-associated loci were significantly associated with MSE after Bonferroni correction. We also found that AL was genetically correlated with MSE (rg = -0.83; SE, 0.04; p = 1.95 × 10-89) and myopia (rg = 0.80; SE, 0.05; p = 2.84 × 10-55). Finally, we estimated the array heritability for AL in the GERA European ancestry sample using LD score regression, and found an overall heritability estimate of 0.37 (s.e. = 0.04). Discussion: In this large and multiethnic study, we identified novel loci, associated with AL at a genome-wide significance level, increasing substantially our understanding of the etiology of AL variation. Our results also demonstrate an association between AL-associated loci and MSE and a shared genetic basis between AL and myopia risk.
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Affiliation(s)
- Chen Jiang
- Division of Research, Kaiser Permanente Northern California (KPNC), Oakland, CA, United States
| | - Ronald B. Melles
- KPNC, Department of Ophthalmology, Redwood City, CA, United States
| | - Jie Yin
- Division of Research, Kaiser Permanente Northern California (KPNC), Oakland, CA, United States
| | - Qiao Fan
- Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Xiaobo Guo
- Department of Statistical Science, School of Mathematics, Sun Yat-Sen University, Guangzhou, China
- Southern China Center for Statistical Science, Sun Yat-Sen University, Guangzhou, China
| | - Ching-Yu Cheng
- Ocular Epidemiology Research Group, Singapore Eye Research Institute, Singapore, Singapore
| | - Mingguang He
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
- Centre for Eye Research Australia; Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, WA, Australia
| | - David A. Mackey
- Lions Eye Institute, Centre for Ophthalmology and Visual Science, University of Western Australia, Perth, WA, Australia
| | - Jeremy A. Guggenheim
- School of Optometry and Vision Sciences, Cardiff University, Cardiff, United Kingdom
| | - Caroline Klaver
- Department Ophthalmology, Department Epidemiology, Erasmus Medical Center, Rotterdam, Netherlands
| | | | - K. Saidas Nair
- Department of Ophthalmology and Department of Anatomy, School of Medicine, University of California, San Francisco, CA, United States
| | | | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California (KPNC), Oakland, CA, United States
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Iulmetova LN, Kulemin NA, Sharova EI. The approach to patient clustering based on the microchip data confined to distinct loci using the combinations of variants. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2023. [DOI: 10.24075/brsmu.2023.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Fuchs' endothelial corneal dystrophy is a socially significant hereditary disease. More than a half of cases in the European population are caused by the increased number of trinucleotude repeats in the TCF4 gene. The study was aimed to develop and test the approach of dividing patients into groups based on the chip-based genotyping and genome-wide association study (GWAS) results. The analysis was conducted using FECD Genetics Multi-center Study and AREDs project datasets containing the data of 1721 clinical cases and 2408 control patients. When analyzing the GWAS results, the patients and the control group were divided into two groups by means of hierarchical clustering suggesting that patients with the increased number of repeats in the TCF4 gene are carriers of specific combinations of genomic variants (haplotypes). It was shown that individual variants cannot be used for the molecular genetic stratification of patients with the increased number of repeats in TCF4 due to inconsistent results obtained for the variants. Furthermore, the haplotype-based approach outperformed the SNPs in terms of odds ratio. The paper proposes a method that enables further search for the biologically relevant combinations of genomic variants.
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Affiliation(s)
- LN Iulmetova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical Biological Agency, Moscow, Russia
| | - NA Kulemin
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical Biological Agency, Moscow, Russia
| | - EI Sharova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical Biological Agency, Moscow, Russia
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Musolf AM, Haarman AEG, Luben RN, Ong JS, Patasova K, Trapero RH, Marsh J, Jain I, Jain R, Wang PZ, Lewis DD, Tedja MS, Iglesias AI, Li H, Cowan CS, Biino G, Klein AP, Duggal P, Mackey DA, Hayward C, Haller T, Metspalu A, Wedenoja J, Pärssinen O, Cheng CY, Saw SM, Stambolian D, Hysi PG, Khawaja AP, Vitart V, Hammond CJ, van Duijn CM, Verhoeven VJM, Klaver CCW, Bailey-Wilson JE. Rare variant analyses across multiethnic cohorts identify novel genes for refractive error. Commun Biol 2023; 6:6. [PMID: 36596879 PMCID: PMC9810640 DOI: 10.1038/s42003-022-04323-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/30/2022] [Indexed: 01/05/2023] Open
Abstract
Refractive error, measured here as mean spherical equivalent (SER), is a complex eye condition caused by both genetic and environmental factors. Individuals with strong positive or negative values of SER require spectacles or other approaches for vision correction. Common genetic risk factors have been identified by genome-wide association studies (GWAS), but a great part of the refractive error heritability is still missing. Some of this heritability may be explained by rare variants (minor allele frequency [MAF] ≤ 0.01.). We performed multiple gene-based association tests of mean Spherical Equivalent with rare variants in exome array data from the Consortium for Refractive Error and Myopia (CREAM). The dataset consisted of over 27,000 total subjects from five cohorts of Indo-European and Eastern Asian ethnicity. We identified 129 unique genes associated with refractive error, many of which were replicated in multiple cohorts. Our best novel candidates included the retina expressed PDCD6IP, the circadian rhythm gene PER3, and P4HTM, which affects eye morphology. Future work will include functional studies and validation. Identification of genes contributing to refractive error and future understanding of their function may lead to better treatment and prevention of refractive errors, which themselves are important risk factors for various blinding conditions.
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Affiliation(s)
- Anthony M Musolf
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA
| | - Annechien E G Haarman
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Robert N Luben
- MRC Epidemiology, University of Cambridge School of Clinical Medicine, Cambridge, UK
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Jue-Sheng Ong
- Statistical Genetics Laboratory, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Karina Patasova
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Rolando Hernandez Trapero
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Joseph Marsh
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Ishika Jain
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA
| | - Riya Jain
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA
| | - Paul Zhiping Wang
- Institute for Biomedical Sciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Deyana D Lewis
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA
| | - Milly S Tedja
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Adriana I Iglesias
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Hengtong Li
- Data Science Unit, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Cameron S Cowan
- Institute for Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Ginevra Biino
- Institute of Molecular Genetics, National Research Council of Italy, Pavia, Italy
| | - Alison P Klein
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Priya Duggal
- The Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - David A Mackey
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, WA, Australia
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Toomas Haller
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Juho Wedenoja
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Olavi Pärssinen
- Department of Ophthalmology, Central Hospital of Central Finland, Jyväskylä, Finland
- Gerontology Research Center, Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Ching-Yu Cheng
- Centre for Quantitative Medicine, DUKE-National University of Singapore, Singapore, Singapore
- Ocular Epidemiology Research Group, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Seang-Mei Saw
- Saw Swee Hock School of Public Health, National University Health Systems, National University of Singapore, Singapore, Singapore
- Myopia Research Group, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA, USA
| | - Pirro G Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Anthony P Khawaja
- MRC Epidemiology, University of Cambridge School of Clinical Medicine, Cambridge, UK
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Christopher J Hammond
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Virginie J M Verhoeven
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands.
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands.
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.
- Institute for Molecular and Clinical Ophthalmology Basel, Basel, Switzerland.
- Department of Ophthalmology, Radboud University Medical Centre, Nijmegen, The Netherlands.
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA.
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Clark R, Pozarickij A, Hysi PG, Ohno-Matsui K, Williams C, Guggenheim JA. Education interacts with genetic variants near GJD2, RBFOX1, LAMA2, KCNQ5 and LRRC4C to confer susceptibility to myopia. PLoS Genet 2022; 18:e1010478. [PMID: 36395078 PMCID: PMC9671369 DOI: 10.1371/journal.pgen.1010478] [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: 03/02/2022] [Accepted: 10/14/2022] [Indexed: 11/19/2022] Open
Abstract
Myopia most often develops during school age, with the highest incidence in countries with intensive education systems. Interactions between genetic variants and educational exposure are hypothesized to confer susceptibility to myopia, but few such interactions have been identified. Here, we aimed to identify genetic variants that interact with education level to confer susceptibility to myopia. Two groups of unrelated participants of European ancestry from UK Biobank were studied. A 'Stage-I' sample of 88,334 participants whose refractive error (avMSE) was measured by autorefraction and a 'Stage-II' sample of 252,838 participants who self-reported their age-of-onset of spectacle wear (AOSW) but who did not undergo autorefraction. Genetic variants were prioritized via a 2-step screening process in the Stage-I sample: Step 1 was a genome-wide association study for avMSE; Step 2 was a variance heterogeneity analysis for avMSE. Genotype-by-education interaction tests were performed in the Stage-II sample, with University education coded as a binary exposure. On average, participants were 58 years-old and left full-time education when they were 18 years-old; 35% reported University level education. The 2-step screening strategy in the Stage-I sample prioritized 25 genetic variants (GWAS P < 1e-04; variance heterogeneity P < 5e-05). In the Stage-II sample, 19 of the 25 (76%) genetic variants demonstrated evidence of variance heterogeneity, suggesting the majority were true positives. Five genetic variants located near GJD2, RBFOX1, LAMA2, KCNQ5 and LRRC4C had evidence of a genotype-by-education interaction in the Stage-II sample (P < 0.002) and consistent evidence of a genotype-by-education interaction in the Stage-I sample. For all 5 variants, University-level education was associated with an increased effect of the risk allele. In this cohort, additional years of education were associated with an enhanced effect of genetic variants that have roles including axon guidance and the development of neuronal synapses and neural circuits.
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Affiliation(s)
- Rosie Clark
- School of Optometry & Vision Sciences, Cardiff University, Cardiff, United Kingdom
| | - Alfred Pozarickij
- School of Optometry & Vision Sciences, Cardiff University, Cardiff, United Kingdom
| | - Pirro G. Hysi
- Section of Ophthalmology, School of Life Course Sciences, King’s College London, London, United Kingdom
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King’s College London, London, United Kingdom
| | - Kyoko Ohno-Matsui
- Department of Ophthalmology and Visual Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Cathy Williams
- Centre for Academic Child Health, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Jeremy A. Guggenheim
- School of Optometry & Vision Sciences, Cardiff University, Cardiff, United Kingdom
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Association of Physical Activity and Sedentary Behaviors with the Risk of Refractive Error in Chinese Urban/Rural Boys and Girls. SUSTAINABILITY 2022. [DOI: 10.3390/su14095539] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Background: Research shows physical activity (PA) is negatively associated with refractive error, especially outdoor activity. Our study aimed to examine the association of PA levels and sedentary time (SED) with refractive error in boys and girls living in urban and rural areas. Methods: A total of 8506 urban/rural boys and girls (13.5 ± 2.8 years old) in Shaanxi Province, China participated in this study. Questions about PA, SED, outdoor exercises, and digital screen time were asked in the study survey. Non-cycloplegic refractive error was measured by an autorefractor. The differences between sex/area groups have been analyzed by one-way ANOVA. The association of PA/SED with spherical equivalent (SE) and cylinder power was analyzed by general linear regression. The association between PA/SED and the risk of refractive error was determined using the binary logistic regression model. Results: Of the 8506 participants, the prevalence of refractive error was significantly higher in girls and urban students (p < 0.05). Less SED and digital screen time, and more outdoor activity were significantly associated with SE (p < 0.05), respectively. More PA and less SED were significantly associated with lower cylinder power (p < 0.05), respectively. More PA and less SED were significantly associated with lower risks of myopia and astigmatism, respectively (p < 0.05). Conclusions: PA and SED were associated with the risk of refractive error. Maintaining a healthy lifestyle can help to reduce the risk of refractive error in boys and girls.
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Myopia Genetics and Heredity. CHILDREN 2022; 9:children9030382. [PMID: 35327754 PMCID: PMC8947159 DOI: 10.3390/children9030382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/19/2022] [Accepted: 03/03/2022] [Indexed: 11/18/2022]
Abstract
Myopia is the most common eye condition leading to visual impairment and is greatly influenced by genetics. Over the last two decades, more than 400 associated gene loci have been mapped for myopia and refractive errors via family linkage analyses, candidate gene studies, genome-wide association studies (GWAS), and next-generation sequencing (NGS). Lifestyle factors, such as excessive near work and short outdoor time, are the primary external factors affecting myopia onset and progression. Notably, besides becoming a global health issue, myopia is more prevalent and severe among East Asians than among Caucasians, especially individuals of Chinese, Japanese, and Korean ancestry. Myopia, especially high myopia, can be serious in consequences. The etiology of high myopia is complex. Prediction for progression of myopia to high myopia can help with prevention and early interventions. Prediction models are thus warranted for risk stratification. There have been vigorous investigations on molecular genetics and lifestyle factors to establish polygenic risk estimations for myopia. However, genes causing myopia have to be identified in order to shed light on pathogenesis and pathway mechanisms. This report aims to examine current evidence regarding (1) the genetic architecture of myopia; (2) currently associated myopia loci identified from the OMIM database, genetic association studies, and NGS studies; (3) gene-environment interactions; and (4) the prediction of myopia via polygenic risk scores (PRSs). The report also discusses various perspectives on myopia genetics and heredity.
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9
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van der Sande E, Haarman AEG, Quint WH, Tadema KCD, Meester-Smoor MA, Kamermans M, De Zeeuw CI, Klaver CCW, Winkelman BHJ, Iglesias AI. The Role of GJD2(Cx36) in Refractive Error Development. Invest Ophthalmol Vis Sci 2022; 63:5. [PMID: 35262731 PMCID: PMC8934558 DOI: 10.1167/iovs.63.3.5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/16/2022] [Indexed: 02/06/2023] Open
Abstract
Refractive errors are common eye disorders characterized by a mismatch between the focal power of the eye and its axial length. An increased axial length is a common cause of the refractive error myopia (nearsightedness). The substantial increase in myopia prevalence over the last decades has raised public health concerns because myopia can lead to severe ocular complications later in life. Genomewide association studies (GWAS) have made considerable contributions to the understanding of the genetic architecture of refractive errors. Among the hundreds of genetic variants identified, common variants near the gap junction delta-2 (GJD2) gene have consistently been reported as one of the top hits. GJD2 encodes the connexin 36 (Cx36) protein, which forms gap junction channels and is highly expressed in the neural retina. In this review, we provide current evidence that links GJD2(Cx36) to the development of myopia. We summarize the gap junctional communication in the eye and the specific role of GJD2(Cx36) in retinal processing of visual signals. Finally, we discuss the pathways involving dopamine and gap junction phosphorylation and coupling as potential mechanisms that may explain the role of GJD2(Cx36) in refractive error development.
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Affiliation(s)
- Emilie van der Sande
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Institute for Neuroscience (NIN), Royal Dutch Academy of Art & Science (KNAW), Amsterdam, The Netherlands
| | - Annechien E. G. Haarman
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Wim H. Quint
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Kirke C. D. Tadema
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Magda A. Meester-Smoor
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Maarten Kamermans
- Netherlands Institute for Neuroscience (NIN), Royal Dutch Academy of Art & Science (KNAW), Amsterdam, The Netherlands
- Department of Biomedical Physics and Biomedical Photonics, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Chris I. De Zeeuw
- Netherlands Institute for Neuroscience (NIN), Royal Dutch Academy of Art & Science (KNAW), Amsterdam, The Netherlands
- Department of Neuroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Caroline C. W. Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
- Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland
| | - Beerend H. J. Winkelman
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Institute for Neuroscience (NIN), Royal Dutch Academy of Art & Science (KNAW), Amsterdam, The Netherlands
- Department of Neuroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Adriana I. Iglesias
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
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Simpson CL, Musolf AM, Cordero RY, Cordero JB, Portas L, Murgia F, Lewis DD, Middlebrooks CD, Ciner EB, Bailey-Wilson JE, Stambolian D. Myopia in African Americans Is Significantly Linked to Chromosome 7p15.2-14.2. Invest Ophthalmol Vis Sci 2021; 62:16. [PMID: 34241624 PMCID: PMC8287048 DOI: 10.1167/iovs.62.9.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 01/20/2021] [Indexed: 11/24/2022] Open
Abstract
Purpose The purpose of this study was to perform genetic linkage analysis and association analysis on exome genotyping from highly aggregated African American families with nonpathogenic myopia. African Americans are a particularly understudied population with respect to myopia. Methods One hundred six African American families from the Philadelphia area with a family history of myopia were genotyped using an Illumina ExomePlus array and merged with previous microsatellite data. Myopia was initially measured in mean spherical equivalent (MSE) and converted to a binary phenotype where individuals were identified as affected, unaffected, or unknown. Parametric linkage analysis was performed on both individual variants (single-nucleotide polymorphisms [SNPs] and microsatellites) as well as gene-based markers. Family-based association analysis and transmission disequilibrium test (TDT) analysis modified for rare variants was also performed. Results Genetic linkage analysis identified 2 genomewide significant variants at 7p15.2 and 7p14.2 (in the intergenic region between MIR148A and NFE2L3 and in the noncoding RNA LOC401324) and 2 genomewide significant genes (CRHR2 and AVL9) both at 7p14.3. No genomewide results were found in the association analyses. Conclusions This study identified a significant linkage peak in African American families for myopia at 7p15.2 to 7p14.2, the first potential risk locus for myopia in African Americans. Interesting candidate genes are located in the region, including PDE1C, which is highly expressed in the eyes, and known to be involved in retinal development. Further identification of the causal variants at this linkage peak will help elucidate the genetics of myopia in this understudied population.
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Affiliation(s)
- Claire L. Simpson
- Department of Genetics, Genomics and Informatics and Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee, United States
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States
| | - Anthony M. Musolf
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States
| | - Roberto Y. Cordero
- Department of Genetics, Genomics and Informatics and Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee, United States
| | - Jennifer B. Cordero
- Department of Genetics, Genomics and Informatics and Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee, United States
| | - Laura Portas
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States
| | - Federico Murgia
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States
| | - Deyana D. Lewis
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States
| | - Candace D. Middlebrooks
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States
| | - Elise B. Ciner
- The Pennsylvania College of Optometry at Salus University, Elkins Park, Pennsylvania, United States
| | - Joan E. Bailey-Wilson
- Department of Genetics, Genomics and Informatics and Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee, United States
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, United States
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11
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Chen LJ, Li FF, Lu SY, Zhang XJ, Kam KW, Tang SM, Tam PO, Yip WW, Young AL, Tham CC, Pang CP, Yam JC. Association of polymorphisms in ZFHX1B, KCNQ5 and GJD2 with myopia progression and polygenic risk prediction in children. Br J Ophthalmol 2021; 105:1751-1757. [PMID: 33811038 DOI: 10.1136/bjophthalmol-2020-318708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/10/2021] [Accepted: 03/19/2021] [Indexed: 11/03/2022]
Abstract
AIMS To assess the association of single-nucleotide polymorphisms (SNPs) with myopia progression for polygenic risk prediction in children. METHODS Six SNPs (ZC3H11B rs4373767, ZFHX1B rs13382811, KCNQ5 rs7744813, MET rs2073560, SNTB1 rs7839488 and GJD2 rs524952) were analysed in 1043 school children, who completed 3-year follow-up, using TaqMan genotyping assays. SNP associations with progression in spherical equivalent (SE) were analysed by logistic regression. Polygenic risk scores (PRS) were applied for computing the sum of the risk alleles of multiple SNPs corresponding to myopia progression, weighted by the effect sizes of corresponding SNPs. RESULTS GJD2 rs524952 showed significant association with fast progression (OR=1.32, 95% CI 1.10 to 1.59; p=0.003) and KCNQ5 rs7744813 had nominal association (OR=1.32, 95% CI 1.04 to 1.67; p=0.02). In quantitative traits locus analysis, GJD2 rs524952 and KCNQ5 rs7744813 were associated with progression in SE (β=-0.038 D/year, p=0.008 and β=-0.042 D/year, p=0.02) and axial elongation (β=0.016 mm/year, p=0.01 and β=0.017 mm/year, p=0.027). ZFHX1B rs13382811 also showed nominal association with faster progression in SE (β=-0.041 D/year, p=0.02). PRS analysis showed that children with the highest PRS defined by rs13382811, rs7744813 and rs524952 had a 2.26-fold of increased risk of fast myopia progression (p=4.61×10-5). PRS was also significantly associated with SE progression (R2=1.6%, p=3.15×10-5) and axial elongation (R2=1.2%, p=2.6×10-4). CONCLUSIONS In this study, multi-tiered evidence suggested SNPs in ZFHX1B, KCNQ5 and GJD2 as risk factors for myopia progression in children. Additional attention and appropriate interventions should be given for myopic children with high-risk PRS as defined by GJD2 rs524952, KCNQ5 rs7744813 and ZFHX1B rs13382811.
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Affiliation(s)
- Li Jia Chen
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China .,Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, Hong Kong, China.,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
| | - Fen Fen Li
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Ophthalmology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shi Yao Lu
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiu Juan Zhang
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ka Wai Kam
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, Hong Kong, China
| | - Shu Min Tang
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Ophthalmology, First Affiliated Hospital of Fujian Medical University, Xiamen, China
| | - Pancy Os Tam
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Wilson Wk Yip
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, Hong Kong, China
| | - Alvin L Young
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, Hong Kong, China
| | - Clement C Tham
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, Hong Kong, China.,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China.,Hong Kong Eye Hospital, Hong Kong, China
| | - Chi Pui Pang
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, Hong Kong, China.,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
| | - Jason C Yam
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China .,Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, Hong Kong, China.,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China.,Hong Kong Eye Hospital, Hong Kong, China
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12
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A Bibliometric and Citation Network Analysis of Myopia Genetics. Genes (Basel) 2021; 12:genes12030447. [PMID: 33801043 PMCID: PMC8003911 DOI: 10.3390/genes12030447] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/08/2021] [Accepted: 03/17/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND To aim of the study was describe the growth of publications on genetic myopia and understand the current research landscape through the analysis of citation networks, as well as determining the different research areas and the most cited publications. METHODS The Web of Science database was used to perform the publication search, looking for the terms "genetic*" AND "myopia" within the period between 2009 and October 2020. The CitNetExplorer and CiteSpace software were then used to conduct the publication analysis. To obtain the graphics, the VOSviewer software was used. RESULTS A total of 721 publications were found with 2999 citations generated within the network. The year 2019 was singled out as a "key year", taking into account the number of publications that emerged in that year and given that in 2019, 200 loci associated with refractive errors and myopia were found, which is considered to be great progress. The most widely cited publication was "Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia", an article by Verhoeven et al., which was published in 2013. By using the clustering function, we were able to establish three groups that encompassed the different research areas within this field: heritability rate of myopia and its possible association with environmental factors, retinal syndromes associated with myopia and the genetic factors that control and influence axial growth of the eye. CONCLUSIONS The citation network offers a comprehensive and objective analysis of the main papers that address genetic myopia.
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13
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RNA-seq and GSEA identifies suppression of ligand-gated chloride efflux channels as the major gene pathway contributing to form deprivation myopia. Sci Rep 2021; 11:5280. [PMID: 33674625 PMCID: PMC7935918 DOI: 10.1038/s41598-021-84338-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/15/2021] [Indexed: 12/13/2022] Open
Abstract
Currently there is no consensus regarding the aetiology of the excessive ocular volume that characterizes high myopia. Thus, we aimed to test whether the gene pathways identified by gene set enrichment analysis of RNA-seq transcriptomics refutes the predictions of the Retinal Ion Driven Efflux (RIDE) hypothesis when applied to the induction of form-deprivation myopia (FDM) and subsequent recovery (post-occluder removal). We found that the induction of profound FDM led to significant suppression in the ligand-gated chloride ion channel transport pathway via suppression of glycine, GABAA and GABAC ionotropic receptors. Post-occluder removal for short term recovery from FDM of 6 h and 24 h, induced significant upregulation of the gene families linked to cone receptor phototransduction, mitochondrial energy, and complement pathways. These findings support a model of form deprivation myopia as a Cl− ion driven adaptive fluid response to the modulation of the visual signal cascade by form deprivation that in turn affects the resultant ionic environment of the outer and inner retinal tissues, axial and vitreal elongation as predicted by the RIDE model. Occluder removal and return to normal light conditions led to return to more normal upregulation of phototransduction, slowed growth rate, refractive recovery and apparent return towards physiological homeostasis.
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14
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Genome-wide association study for circulating fibroblast growth factor 21 and 23. Sci Rep 2020; 10:14578. [PMID: 32884031 PMCID: PMC7471933 DOI: 10.1038/s41598-020-71569-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 08/06/2020] [Indexed: 11/09/2022] Open
Abstract
Fibroblast growth factors (FGFs) 21 and 23 are recently identified hormones regulating metabolism of glucose, lipid, phosphate and vitamin D. Here we conducted a genome-wide association study (GWAS) for circulating FGF21 and FGF23 concentrations to identify their genetic determinants. We enrolled 5,000 participants from Taiwan Biobank for this GWAS. After excluding participants with diabetes mellitus and quality control, association of single nucleotide polymorphisms (SNPs) with log-transformed FGF21 and FGF23 serum concentrations adjusted for age, sex and principal components of ancestry were analyzed. A second model additionally adjusted for body mass index (BMI) and a third model additionally adjusted for BMI and estimated glomerular filtration rate (eGFR) were used. A total of 4,201 participants underwent GWAS analysis. rs67327215, located within RGS6 (a gene involved in fatty acid synthesis), and two other SNPs (rs12565114 and rs9520257, located between PHC2-ZSCAN20 and ARGLU1-FAM155A respectively) showed suggestive associations with serum FGF21 level (P = 6.66 × 10–7, 6.00 × 10–7 and 6.11 × 10–7 respectively). The SNPs rs17111495 and rs17843626 were significantly associated with FGF23 level, with the former near PCSK9 gene and the latter near HLA-DQA1 gene (P = 1.04 × 10–10 and 1.80 × 10–8 respectively). SNP rs2798631, located within the TGFB2 gene, was suggestively associated with serum FGF23 level (P = 4.97 × 10–7). Additional adjustment for BMI yielded similar results. For FGF23, further adjustment for eGFR had similar results. We conducted the first GWAS of circulating FGF21 levels to date. Novel candidate genetic loci associated with circulating FGF21 or FGF23 levels were found. Further replication and functional studies are needed to support our findings.
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15
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Li FF, Lu SY, Tang SM, Kam KW, Pancy O S T, Yip WWK, Young AL, Tham CC, Pang CP, Yam JC, Chen LJ. Genetic associations of myopia severities and endophenotypes in children. Br J Ophthalmol 2020; 105:1178-1183. [PMID: 32816751 DOI: 10.1136/bjophthalmol-2020-316728] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/20/2020] [Accepted: 07/07/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To investigate the associations of multiple single-nucleotide polymorphisms (SNPs) with the severities and endophenotypes of myopia in children. METHODS A total of 3300 children aged 5-10 years were recruited: 137 moderate and high myopia (SE≤-3.0D), 670 mild myopia (-3.0D<SE≤-0.5D) and 2493 controls (SE>-0.5D). 13 SNPs in 13 genes/loci were selected for genotyping in all subjects using TaqMan assays. Associations between each SNP with myopia severities and ocular traits (spherical equivalent (SE), axial length (AL) and corneal radius (CR)) were analysed. RESULTS When compared with controls, SNPs ZC3H11B rs4373767 (OR=1.15, p=0.038), BICC1 rs7084402 (OR=1.18, p=0.005) and GJD2 rs524952 (OR=1.14, p=0.025) showed nominal associations with overall myopia. ZC3H11B rs4373767 and BICC1 rs7084402 showed stronger associations with moderate and high myopia (rs4373767: OR=1.42, p=0.018; rs7084402: OR=1.33, p=0.025), while GJD2 rs524952 had a stronger association with mild myopia (OR=1.14, p=0.025). GJD2 rs524952 also showed a difference between emmetropia and hyperopia (p=0.018). In quantitative trait locus analysis, ZC3H11B rs4373767, KCNQ5 rs7744813 and GJD2 rs524952 were correlated with both myopic SE (β=-0.09, p=0.03; β=-0.12, p=0.007; β=-0.13, p=0.0006, respectively) and AL (β=0.07, p=0.002; β=0.09, p=0.0008; β=0.07, p=0.0003, respectively). SNTB1 rs7839488 was correlated with both AL (β=0.07, p=0.005) and CR (β=0.02, p=0.006). Moreover, ZC3H11B rs4373767-T (β=0.006; p=0.018), KCNQ5 rs7744813-A (β=0.007; p=0.015) and GJD2 rs524952-T (β=0.009; p=0.0006) were correlated with AL-CR ratio. CONCLUSIONS AND RELEVANCE ZC3H11B and BICC1 are genetic risk factors for moderate and high myopia, while ZC3H11B, KCNQ5, SNTB1 and GJD2 confer risk to excessive AL in children.
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Affiliation(s)
- Fen Fen Li
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Shi Yao Lu
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Shu Min Tang
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Ophthalmology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Ka Wai Kam
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, Hong Kong, China
| | - Tam Pancy O S
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Wilson W K Yip
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, Hong Kong, China
| | - Alvin L Young
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, Hong Kong, China
| | - Clement C Tham
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Hong Kong Eye Hospital, Hong Kong, China
| | - Chi Pui Pang
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jason C Yam
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Li Jia Chen
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China .,Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, Hong Kong, China
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16
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Cai XB, Shen SR, Chen DF, Zhang Q, Jin ZB. An overview of myopia genetics. Exp Eye Res 2019; 188:107778. [DOI: 10.1016/j.exer.2019.107778] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/27/2019] [Accepted: 08/23/2019] [Indexed: 11/15/2022]
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17
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Wong YL, Hysi P, Cheung G, Tedja M, Hoang QV, Tompson SWJ, Whisenhunt KN, Verhoeven V, Zhao W, Hess M, Wong CW, Kifley A, Hosoda Y, Haarman AEG, Hopf S, Laspas P, Sensaki S, Sim X, Miyake M, Tsujikawa A, Lamoureux E, Ohno-Matsui K, Nickels S, Mitchell P, Wong TY, Wang JJ, Hammond CJ, Barathi VA, Cheng CY, Yamashiro K, Young TL, Klaver CCW, Saw SM. Genetic variants linked to myopic macular degeneration in persons with high myopia: CREAM Consortium. PLoS One 2019; 14:e0220143. [PMID: 31415580 PMCID: PMC6695159 DOI: 10.1371/journal.pone.0220143] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/20/2019] [Indexed: 11/19/2022] Open
Abstract
Purpose To evaluate the roles of known myopia-associated genetic variants for development of myopic macular degeneration (MMD) in individuals with high myopia (HM), using case-control studies from the Consortium of Refractive Error and Myopia (CREAM). Methods A candidate gene approach tested 50 myopia-associated loci for association with HM and MMD, using meta-analyses of case-control studies comprising subjects of European and Asian ancestry aged 30 to 80 years from 10 studies. Fifty loci with the strongest associations with myopia were chosen from a previous published GWAS study. Highly myopic (spherical equivalent [SE] ≤ -5.0 diopters [D]) cases with MMD (N = 348), and two sets of controls were enrolled: (1) the first set included 16,275 emmetropes (SE ≤ -0.5 D); and (2) second set included 898 highly myopic subjects (SE ≤ -5.0 D) without MMD. MMD was classified based on the International photographic classification for pathologic myopia (META-PM). Results In the first analysis, comprising highly myopic cases with MMD (N = 348) versus emmetropic controls without MMD (N = 16,275), two SNPs were significantly associated with high myopia in adults with HM and MMD: (1) rs10824518 (P = 6.20E-07) in KCNMA1, which is highly expressed in human retinal and scleral tissues; and (2) rs524952 (P = 2.32E-16) near GJD2. In the second analysis, comprising highly myopic cases with MMD (N = 348) versus highly myopic controls without MMD (N = 898), none of the SNPs studied reached Bonferroni-corrected significance. Conclusions Of the 50 myopia-associated loci, we did not find any variant specifically associated with MMD, but the KCNMA1 and GJD2 loci were significantly associated with HM in highly myopic subjects with MMD, compared to emmetropes.
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Affiliation(s)
- Yee-Ling Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- R&D Vision Sciences AMERA, Essilor International, Singapore, Singapore
| | - Pirro Hysi
- Section of Academic Ophthalmology, School of Life Course Sciences, King’s College London, London, United Kingdom
| | - Gemmy Cheung
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Milly Tedja
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Quan V. Hoang
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Columbia University Medical Center, New York, NY, United States of America
| | - Stuart W. J. Tompson
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison WI, United States of America
| | - Kristina N. Whisenhunt
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison WI, United States of America
| | - Virginie Verhoeven
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Wanting Zhao
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Moritz Hess
- Institute for Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg—University Mainz, Mainz, Germany
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center—University of Freiburg, Freiburg, Germany
| | - Chee-Wai Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Annette Kifley
- Department of Ophthalmology, Centre for Vision Research, Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - Yoshikatsu Hosoda
- Department of Ophthalmology and Visual Sciences, University Graduate School of Medicine, Kyoto, Japan
| | - Annechien E. G. Haarman
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Susanne Hopf
- Department of Ophthalmology, University Medical Center of the Johannes Gutenberg—University Mainz, Mainz, Germany
| | - Panagiotis Laspas
- Department of Ophthalmology, University Medical Center of the Johannes Gutenberg—University Mainz, Mainz, Germany
| | - Sonoko Sensaki
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Masahiro Miyake
- Department of Ophthalmology and Visual Sciences, University Graduate School of Medicine, Kyoto, Japan
| | - Akitaka Tsujikawa
- Department of Ophthalmology and Visual Sciences, University Graduate School of Medicine, Kyoto, Japan
| | - Ecosse Lamoureux
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Kyoko Ohno-Matsui
- Department of Ophthalmology and Visual Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Stefan Nickels
- Department of Ophthalmology, University Medical Center of the Johannes Gutenberg—University Mainz, Mainz, Germany
| | - Paul Mitchell
- Department of Ophthalmology, Centre for Vision Research, Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - Tien-Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | | | - Christopher J. Hammond
- Section of Academic Ophthalmology, School of Life Course Sciences, King’s College London, London, United Kingdom
| | - Veluchamy A. Barathi
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Kenji Yamashiro
- Department of Ophthalmology and Visual Sciences, University Graduate School of Medicine, Kyoto, Japan
- Department of Ophthalmology, Otsu Red-Cross Hospital, Otsu, Japan
| | - Terri L. Young
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison WI, United States of America
| | - Caroline C. W. Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Seang-Mei Saw
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- * E-mail:
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18
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Tang SM, Li FF, Lu SY, Kam KW, Tam POS, Tham CC, Pang CP, Yam JCS, Chen LJ. Association of the ZC3H11B, ZFHX1B and SNTB1 genes with myopia of different severities. Br J Ophthalmol 2019; 104:1472-1476. [PMID: 31300455 DOI: 10.1136/bjophthalmol-2019-314203] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/30/2019] [Accepted: 06/27/2019] [Indexed: 11/03/2022]
Abstract
OBJECTIVE To investigate the associations of single-nucleotide polymorphisms (SNPs) in the ZC3H11B, ZFHX1B, VIPR2, SNTB1 and MIPEP genes with severities of myopia in Chinese populations. METHODS Based on previous myopia genome-wide association studies, five SNPs (ZC3H11B rs4373767, ZFHX1B rs13382811, VIPR2 rs2730260, SNTB1 rs7839488 and MIPEP rs9318086) were selected for genotyping in a Chinese cohort of 2079 subjects: 252 extreme myopia, 277 high myopia, 393 moderate myopia, 366 mild myopia and 791 non-myopic controls. Genotyping was performed by TaqMan assays. Allelic frequencies of the SNPs were compared with myopia severities and ophthalmic biometric measurements. RESULTS The risk allele T of ZC3H11B SNP rs4373767 was significantly associated with high myopia (OR=1.39, p=0.007) and extreme myopia (OR=1.34, p=0.013) when compared with controls, whereas ZFHX1B rs13382811 (allele T, OR=1.33, p=0.018) and SNTB1 rs7839488 (allele G, OR=1.71, p=8.44E-05) were significantly associated with extreme myopia only. In contrast, there was no significant association of these SNPs with moderate or mild myopia. When compared with mild myopia, subjects carrying T allele of rs4373767 had a risk of progressing to high myopia (spherical equivalent ≤-6 dioptres) (OR=1.29, p=0.017). Similarly, the T allele of rs13382811 also imposed a significant risk to high myopia (OR=1.36, p=0.007). In quantitative traits analysis, SNPs rs4373767, rs13382811 and rs7839488 were correlated with axial length and refractive errors. CONCLUSIONS We confirmed ZC3H11B as a susceptibility gene for high and extreme myopia, and ZFHX1B and SNTB for extreme myopia in Chinese populations. Instead of myopia onset, these three genes were more likely to impose risks of progressing to high and extreme myopia.
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Affiliation(s)
- Shu Min Tang
- Department of Ophthalmology and Visual Sciences, Chinese University of Hong Kong, New Territories, Hong Kong.,Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, New Territories, Hong Kong.,Department of Ophthalmology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Fen Fen Li
- Department of Ophthalmology and Visual Sciences, Chinese University of Hong Kong, New Territories, Hong Kong
| | - Shi Yao Lu
- Department of Ophthalmology and Visual Sciences, Chinese University of Hong Kong, New Territories, Hong Kong
| | - Ka Wai Kam
- Department of Ophthalmology and Visual Sciences, Chinese University of Hong Kong, New Territories, Hong Kong.,Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, New Territories, Hong Kong
| | - Pancy O S Tam
- Department of Ophthalmology and Visual Sciences, Chinese University of Hong Kong, New Territories, Hong Kong
| | - Clement C Tham
- Department of Ophthalmology and Visual Sciences, Chinese University of Hong Kong, New Territories, Hong Kong
| | - Chi Pui Pang
- Department of Ophthalmology and Visual Sciences, Chinese University of Hong Kong, New Territories, Hong Kong
| | - Jason C S Yam
- Department of Ophthalmology and Visual Sciences, Chinese University of Hong Kong, New Territories, Hong Kong
| | - Li Jia Chen
- Department of Ophthalmology and Visual Sciences, Chinese University of Hong Kong, New Territories, Hong Kong .,Department of Ophthalmology and Visual Sciences, Prince of Wales Hospital, New Territories, Hong Kong
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19
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Musolf AM, Simpson CL, Alexander TA, Portas L, Murgia F, Ciner EB, Stambolian D, Bailey-Wilson JE. Genome-wide scans of myopia in Pennsylvania Amish families reveal significant linkage to 12q15, 8q21.3 and 5p15.33. Hum Genet 2019; 138:339-354. [PMID: 30826882 DOI: 10.1007/s00439-019-01991-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/20/2019] [Indexed: 12/14/2022]
Abstract
Myopia is one of the most common ocular disorders in the world, yet the genetic etiology of the disease remains poorly understood. Specialized founder populations, such as the Pennsylvania Amish, provide the opportunity to utilize exclusive genomic architecture, like unique haplotypes, to better understand the genetic causes of myopia. We perform genetic linkage analysis on Pennsylvania Amish families that have a strong familial history of myopia to map any potential causal variants and genes for the disease. 293 individuals from 25 extended families were genotyped on the Illumina ExomePlus array and merged with previous microsatellite data. We coded myopia affection as a binary phenotype; myopia was defined as having a mean spherical equivalent (MSE) of less than or equal to - 1 D (diopters). Two-point and multipoint parametric linkage analyses were performed under an autosomal dominant model. When allowing for locus heterogeneity, we identified two novel genome-wide significantly linked variants at 12q15 (heterogeneity LOD, HLOD = 3.77) in PTPRB and at 8q21.3 (HLOD = 3.35) in CNGB3. We identified further three genome-wide significant variants within a single family. These three variants were located in exons of SLC6A18 at 5p15.33 (LODs ranged from 3.51 to 3.37). Multipoint analysis confirmed the significant signal at 5p15.33 with six genome-wide significant variants (LODs ranged from 3.6 to 3.3). Further suggestive evidence of linkage was observed in several other regions of the genome. All three novel linked regions contain strong candidate genes, especially CNGB3 on 8q21.3, which has been shown to affect photoreceptors and cause complete color blindness. Whole genome sequencing on these regions is planned to conclusively elucidate the causal variants.
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Affiliation(s)
- Anthony M Musolf
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr, Suite 1200, Baltimore, MD, 21224, USA
| | - Claire L Simpson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr, Suite 1200, Baltimore, MD, 21224, USA.,Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.,Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Theresa A Alexander
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr, Suite 1200, Baltimore, MD, 21224, USA
| | - Laura Portas
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr, Suite 1200, Baltimore, MD, 21224, USA
| | - Federico Murgia
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr, Suite 1200, Baltimore, MD, 21224, USA
| | - Elise B Ciner
- The Pennsylvania College of Optometry at Salus University, Elkins Park, PA, USA
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA, USA
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr, Suite 1200, Baltimore, MD, 21224, USA.
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20
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Tedja MS, Haarman AEG, Meester-Smoor MA, Kaprio J, Mackey DA, Guggenheim JA, Hammond CJ, Verhoeven VJM, Klaver CCW. IMI - Myopia Genetics Report. Invest Ophthalmol Vis Sci 2019; 60:M89-M105. [PMID: 30817828 PMCID: PMC6892384 DOI: 10.1167/iovs.18-25965] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/09/2019] [Indexed: 02/07/2023] Open
Abstract
The knowledge on the genetic background of refractive error and myopia has expanded dramatically in the past few years. This white paper aims to provide a concise summary of current genetic findings and defines the direction where development is needed. We performed an extensive literature search and conducted informal discussions with key stakeholders. Specific topics reviewed included common refractive error, any and high myopia, and myopia related to syndromes. To date, almost 200 genetic loci have been identified for refractive error and myopia, and risk variants mostly carry low risk but are highly prevalent in the general population. Several genes for secondary syndromic myopia overlap with those for common myopia. Polygenic risk scores show overrepresentation of high myopia in the higher deciles of risk. Annotated genes have a wide variety of functions, and all retinal layers appear to be sites of expression. The current genetic findings offer a world of new molecules involved in myopiagenesis. As the missing heritability is still large, further genetic advances are needed. This Committee recommends expanding large-scale, in-depth genetic studies using complementary big data analytics, consideration of gene-environment effects by thorough measurement of environmental exposures, and focus on subgroups with extreme phenotypes and high familial occurrence. Functional characterization of associated variants is simultaneously needed to bridge the knowledge gap between sequence variance and consequence for eye growth.
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Affiliation(s)
- Milly S. Tedja
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Annechien E. G. Haarman
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Magda A. Meester-Smoor
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jaakko Kaprio
- Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - David A. Mackey
- Centre for Eye Research Australia, Ophthalmology, Department of Surgery, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Department of Ophthalmology, Menzies Institute of Medical Research, University of Tasmania, Hobart, Tasmania, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Jeremy A. Guggenheim
- School of Optometry and Vision Sciences, Cardiff University, Cardiff, United Kingdom
| | - Christopher J. Hammond
- Section of Academic Ophthalmology, School of Life Course Sciences, King's College London, London, United Kingdom
| | - Virginie J. M. Verhoeven
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Caroline C. W. Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - for the CREAM Consortium
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Centre for Eye Research Australia, Ophthalmology, Department of Surgery, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Department of Ophthalmology, Menzies Institute of Medical Research, University of Tasmania, Hobart, Tasmania, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Western Australia, Australia
- School of Optometry and Vision Sciences, Cardiff University, Cardiff, United Kingdom
- Section of Academic Ophthalmology, School of Life Course Sciences, King's College London, London, United Kingdom
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
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21
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Simpson CL, Musolf AM, Li Q, Portas L, Murgia F, Cordero RY, Cordero JB, Moiz BA, Holzinger ER, Middlebrooks CD, Lewis DD, Bailey-Wilson JE, Stambolian D. Exome genotyping and linkage analysis identifies two novel linked regions and replicates two others for myopia in Ashkenazi Jewish families. BMC MEDICAL GENETICS 2019; 20:27. [PMID: 30704416 PMCID: PMC6357511 DOI: 10.1186/s12881-019-0752-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/11/2019] [Indexed: 01/10/2023]
Abstract
BACKGROUND Myopia is one of most common eye diseases in the world and affects 1 in 4 Americans. It is a complex disease caused by both environmental and genetics effects; the genetics effects are still not well understood. In this study, we performed genetic linkage analyses on Ashkenazi Jewish families with a strong familial history of myopia to elucidate any potential causal genes. METHODS Sixty-four extended Ashkenazi Jewish families were previously collected from New Jersey. Genotypes from the Illumina ExomePlus array were merged with prior microsatellite linkage data from these families. Additional custom markers were added for candidate regions reported in literature for myopia or refractive error. Myopia was defined as mean spherical equivalent (MSE) of -1D or worse and parametric two-point linkage analyses (using TwoPointLods) and multi-point linkage analyses (using SimWalk2) were performed as well as collapsed haplotype pattern (CHP) analysis in SEQLinkage and association analyses performed with FBAT and rv-TDT. RESULTS Strongest evidence of linkage was on 1p36(two-point LOD = 4.47) a region previously linked to refractive error (MYP14) but not myopia. Another genome-wide significant locus was found on 8q24.22 with a maximum two-point LOD score of 3.75. CHP analysis also detected the signal on 1p36, localized to the LINC00339 gene with a maximum HLOD of 3.47, as well as genome-wide significant signals on 7q36.1 and 11p15, which overlaps with the MYP7 locus. CONCLUSIONS We identified 2 novel linkage peaks for myopia on chromosomes 7 and 8 in these Ashkenazi Jewish families and replicated 2 more loci on chromosomes 1 and 11, one previously reported in refractive error but not myopia in these families and the other locus previously reported in the literature. Strong candidate genes have been identified within these linkage peaks in our families. Targeted sequencing in these regions will be necessary to definitively identify causal variants under these linkage peaks.
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Affiliation(s)
- Claire L Simpson
- Department of Genetics, Genomics and Informatics and Department of Ophthalmology, University of Tennessee Health Science Center, 71 S. Manassas Room 417, Memphis, TN, 38163, USA.,Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr., Suite 1200, Baltimore, MD, 21224, USA
| | - Anthony M Musolf
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr., Suite 1200, Baltimore, MD, 21224, USA
| | - Qing Li
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr., Suite 1200, Baltimore, MD, 21224, USA
| | - Laura Portas
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr., Suite 1200, Baltimore, MD, 21224, USA
| | - Federico Murgia
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr., Suite 1200, Baltimore, MD, 21224, USA
| | - Roberto Y Cordero
- Department of Genetics, Genomics and Informatics and Department of Ophthalmology, University of Tennessee Health Science Center, 71 S. Manassas Room 417, Memphis, TN, 38163, USA
| | - Jennifer B Cordero
- Department of Genetics, Genomics and Informatics and Department of Ophthalmology, University of Tennessee Health Science Center, 71 S. Manassas Room 417, Memphis, TN, 38163, USA
| | - Bilal A Moiz
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr., Suite 1200, Baltimore, MD, 21224, USA
| | - Emily R Holzinger
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr., Suite 1200, Baltimore, MD, 21224, USA
| | - Candace D Middlebrooks
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr., Suite 1200, Baltimore, MD, 21224, USA
| | - Deyana D Lewis
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr., Suite 1200, Baltimore, MD, 21224, USA
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr., Suite 1200, Baltimore, MD, 21224, USA.
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Rm. 313, Stellar Chance Labs, 422 Curie Blvd, Philadelphia, PA, 19104, USA
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22
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Flitcroft DI, Loughman J, Wildsoet CF, Williams C, Guggenheim JA. Novel Myopia Genes and Pathways Identified From Syndromic Forms of Myopia. Invest Ophthalmol Vis Sci 2018; 59:338-348. [PMID: 29346494 PMCID: PMC5773233 DOI: 10.1167/iovs.17-22173] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Purpose To test the hypothesis that genes known to cause clinical syndromes featuring myopia also harbor polymorphisms contributing to nonsyndromic refractive errors. Methods Clinical phenotypes and syndromes that have refractive errors as a recognized feature were identified using the Online Mendelian Inheritance in Man (OMIM) database. One hundred fifty-four unique causative genes were identified, of which 119 were specifically linked with myopia and 114 represented syndromic myopia (i.e., myopia and at least one other clinical feature). Myopia was the only refractive error listed for 98 genes and hyperopia and the only refractive error noted for 28 genes, with the remaining 28 genes linked to phenotypes with multiple forms of refractive error. Pathway analysis was carried out to find biological processes overrepresented within these sets of genes. Genetic variants located within 50 kb of the 119 myopia-related genes were evaluated for involvement in refractive error by analysis of summary statistics from genome-wide association studies (GWAS) conducted by the CREAM Consortium and 23andMe, using both single-marker and gene-based tests. Results Pathway analysis identified several biological processes already implicated in refractive error development through prior GWAS analyses and animal studies, including extracellular matrix remodeling, focal adhesion, and axon guidance, supporting the research hypothesis. Novel pathways also implicated in myopia development included mannosylation, glycosylation, lens development, gliogenesis, and Schwann cell differentiation. Hyperopia was found to be linked to a different pattern of biological processes, mostly related to organogenesis. Comparison with GWAS findings further confirmed that syndromic myopia genes were enriched for genetic variants that influence refractive errors in the general population. Gene-based analyses implicated 21 novel candidate myopia genes (ADAMTS18, ADAMTS2, ADAMTSL4, AGK, ALDH18A1, ASXL1, COL4A1, COL9A2, ERBB3, FBN1, GJA1, GNPTG, IFIH1, KIF11, LTBP2, OCA2, POLR3B, POMT1, PTPN11, TFAP2A, ZNF469). Conclusions Common genetic variants within or nearby genes that cause syndromic myopia are enriched for variants that cause nonsyndromic, common myopia. Analysis of syndromic forms of refractive errors can provide new insights into the etiology of myopia and additional potential targets for therapeutic interventions.
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Affiliation(s)
- D Ian Flitcroft
- Children's University Hospital and University College Dublin, Dublin, Ireland.,College of Sciences and Health, Dublin Institute of Technology, Dublin, Ireland
| | - James Loughman
- College of Sciences and Health, Dublin Institute of Technology, Dublin, Ireland
| | - Christine F Wildsoet
- Center for Eye Disease and Development, School of Optometry, University of California-Berkeley, Berkeley, California, United States
| | - Cathy Williams
- Bristol Eye Hospital and Bristol University, Bristol, United Kingdom
| | - Jeremy A Guggenheim
- School of Optometry & Vision Sciences, Cardiff University, Cardiff, United Kingdom
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23
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Tedja MS, Wojciechowski R, Hysi PG, Eriksson N, Furlotte NA, Verhoeven VJ, Iglesias AI, Meester-Smoor MA, Tompson SW, Fan Q, Khawaja AP, Cheng CY, Höhn R, Yamashiro K, Wenocur A, Grazal C, Haller T, Metspalu A, Wedenoja J, Jonas JB, Wang YX, Xie J, Mitchell P, Foster PJ, Klein BE, Klein R, Paterson AD, Hosseini SM, Shah RL, Williams C, Teo YY, Tham YC, Gupta P, Zhao W, Shi Y, Saw WY, Tai ES, Sim XL, Huffman JE, Polašek O, Hayward C, Bencic G, Rudan I, Wilson JF, Joshi PK, Tsujikawa A, Matsuda F, Whisenhunt KN, Zeller T, van der Spek PJ, Haak R, Meijers-Heijboer H, van Leeuwen EM, Iyengar SK, Lass JH, Hofman A, Rivadeneira F, Uitterlinden AG, Vingerling JR, Lehtimäki T, Raitakari OT, Biino G, Concas MP, Schwantes-An TH, Igo RP, Cuellar-Partida G, Martin NG, Craig JE, Gharahkhani P, Williams KM, Nag A, Rahi JS, Cumberland PM, Delcourt C, Bellenguez C, Ried JS, Bergen AA, Meitinger T, Gieger C, Wong TY, Hewitt AW, Mackey DA, Simpson CL, Pfeiffer N, Pärssinen O, Baird PN, Vitart V, Amin N, van Duijn CM, Bailey-Wilson JE, Young TL, Saw SM, Stambolian D, MacGregor S, Guggenheim JA, Tung JY, Hammond CJ, Klaver CC. Genome-wide association meta-analysis highlights light-induced signaling as a driver for refractive error. Nat Genet 2018; 50:834-848. [PMID: 29808027 PMCID: PMC5980758 DOI: 10.1038/s41588-018-0127-7] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 03/26/2018] [Indexed: 12/18/2022]
Abstract
Refractive errors, including myopia, are the most frequent eye disorders worldwide and an increasingly common cause of blindness. This genome-wide association meta-analysis in 160,420 participants and replication in 95,505 participants increased the number of established independent signals from 37 to 161 and showed high genetic correlation between Europeans and Asians (>0.78). Expression experiments and comprehensive in silico analyses identified retinal cell physiology and light processing as prominent mechanisms, and also identified functional contributions to refractive-error development in all cell types of the neurosensory retina, retinal pigment epithelium, vascular endothelium and extracellular matrix. Newly identified genes implicate novel mechanisms such as rod-and-cone bipolar synaptic neurotransmission, anterior-segment morphology and angiogenesis. Thirty-one loci resided in or near regions transcribing small RNAs, thus suggesting a role for post-transcriptional regulation. Our results support the notion that refractive errors are caused by a light-dependent retina-to-sclera signaling cascade and delineate potential pathobiological molecular drivers.
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Affiliation(s)
- Milly S. Tedja
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Robert Wojciechowski
- Department of Epidemiology and Medicine, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
- Wilmer Eye Institute, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Pirro G. Hysi
- Section of Academic Ophthalmology, School of Life Course Sciences, King’s College London, London, UK
| | | | | | - Virginie J.M. Verhoeven
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Adriana I. Iglesias
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Magda A. Meester-Smoor
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Stuart W. Tompson
- Department of Ophthalmology and Visual Sciences, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Qiao Fan
- Centre for Quantitative Medicine, DUKE-National University of Singapore, Singapore
| | - 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
| | - Ching-Yu Cheng
- Centre for Quantitative Medicine, DUKE-National University of Singapore, Singapore
- Ocular Epidemiology Research Group, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - René Höhn
- Department of Ophthalmology, University Hospital Bern, Inselspital, University of Bern, Bern, Switzerland
- Department of Ophthalmology, University Medical Center Mainz, Mainz, Germany
| | - Kenji Yamashiro
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Adam Wenocur
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Clare Grazal
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Toomas Haller
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | | | - Juho Wedenoja
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Jost B. Jonas
- Department of Ophthalmology, Medical Faculty Mannheim of the Ruprecht-Karls-University of Heidelberg, Mannheim, Germany
- Beijing Institute of Ophthalmology, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Ya Xing Wang
- Beijing Institute of Ophthalmology, Beijing Key Laboratory of Ophthalmology and Visual Sciences, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Jing Xie
- Centre for Eye Research Australia, Ophthalmology, Department of Surgery, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
| | - Paul Mitchell
- Department of Ophthalmology, Centre for Vision Research, Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Paul J. Foster
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Barbara E.K. Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Andrew D. Paterson
- Program in Genetics and Genome Biology, Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - S. Mohsen Hosseini
- Program in Genetics and Genome Biology, Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - Rupal L. Shah
- School of Optometry & Vision Sciences, Cardiff University, Cardiff, UK
| | - Cathy Williams
- Department of Population Health Sciences, Bristol Medical School, Bristol, UK
| | - Yik Ying Teo
- Department of Statistics and Applied Probability, National University of Singapore, Singapore
- Saw Swee Hock School of Public Health, National University Health Systems, National University of Singapore, Singapore
| | - Yih Chung Tham
- Ocular Epidemiology Research Group, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Preeti Gupta
- Department of Health Service Research, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Wanting Zhao
- Centre for Quantitative Medicine, DUKE-National University of Singapore, Singapore
- Statistics Support Platform, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Yuan Shi
- Statistics Support Platform, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Woei-Yuh Saw
- Life Sciences Institute, National University of Singapore, Singapore
| | - E-Shyong Tai
- Saw Swee Hock School of Public Health, National University Health Systems, National University of Singapore, Singapore
| | - Xue Ling Sim
- Saw Swee Hock School of Public Health, National University Health Systems, National University of Singapore, Singapore
| | - Jennifer E. Huffman
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ozren Polašek
- Faculty of Medicine, University of Split, Split, Croatia
| | - Caroline Hayward
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Goran Bencic
- Department of Ophthalmology, Sisters of Mercy University Hospital, Zagreb, Croatia
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - James F. Wilson
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | | | | | | | - Peter K. Joshi
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Akitaka Tsujikawa
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kristina N. Whisenhunt
- Department of Ophthalmology and Visual Sciences, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Tanja Zeller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, Germany
| | | | - Roxanna Haak
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Hanne Meijers-Heijboer
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Elisabeth M. van Leeuwen
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Sudha K. Iyengar
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University and University Hospitals Eye Institute, Cleveland, Ohio, USA
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jonathan H. Lass
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University and University Hospitals Eye Institute, Cleveland, Ohio, USA
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Harvard T.HChan School of Public Health, Boston, Massachusetts, USA
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, the Hague, the Netherlands
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, the Hague, the Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, the Hague, the Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Terho Lehtimäki
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, University of Tampere
- Department of Clinical Chemistry, Fimlab Laboratories, University of Tampere, Tampere, Finland
| | - Olli T. Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Ginevra Biino
- Institute of Molecular Genetics, National Research Council of Italy, Sassari, Italy
| | - Maria Pina Concas
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”, Trieste, Italy
| | - Tae-Hwi Schwantes-An
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
- Department of Medical and Molecular Genetics, Indiana University, School of Medicine, Indianapolis, Indiana, USA
| | - Robert P. Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | | | - Nicholas G. Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jamie E. Craig
- Department of Ophthalmology, Flinders University, Adelaide, Australia
| | - Puya Gharahkhani
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Katie M. Williams
- Section of Academic Ophthalmology, School of Life Course Sciences, King’s College London, London, UK
| | - Abhishek Nag
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Jugnoo S. Rahi
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
- Great Ormond Street Institute of Child Health, University College London, London, UK
- Ulverscroft Vision Research Group, University College London, London, UK
| | | | - Cécile Delcourt
- Université de Bordeaux, Inserm, Bordeaux Population Health Research Center, team LEHA, UMR 1219, F-33000 Bordeaux, France
| | - Céline Bellenguez
- Institut Pasteur de Lille, Lille, France
- Inserm, U1167, RID-AGE - Risk factors and molecular determinants of aging-related diseases, Lille, France
- Université de Lille, U1167 - Excellence Laboratory LabEx DISTALZ, Lille, France
| | - Janina S. Ried
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
| | - Arthur A. Bergen
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
- Department of Ophthalmology, Academic Medical Center, Amsterdam, The Netherlands
- The Netherlands Institute for Neurosciences (NIN-KNAW), Amsterdam, The Netherlands
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
| | - Tien Yin Wong
- Academic Medicine Research Institute, Singapore
- Retino Center, Singapore National Eye Centre, Singapore, Singapore
| | - Alex W. Hewitt
- Centre for Eye Research Australia, Ophthalmology, Department of Surgery, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Department of Ophthalmology, Menzies Institute of Medical Research, University of Tasmania, Hobart, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | - David A. Mackey
- Centre for Eye Research Australia, Ophthalmology, Department of Surgery, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Department of Ophthalmology, Menzies Institute of Medical Research, University of Tasmania, Hobart, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | - Claire L. Simpson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Sciences Center, Memphis, Tenessee
| | - Norbert Pfeiffer
- Department of Ophthalmology, University Medical Center Mainz, Mainz, Germany
| | - Olavi Pärssinen
- Department of Ophthalmology, Central Hospital of Central Finland, Jyväskylä, Finland
- Gerontology Research Center, Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Paul N. Baird
- Centre for Eye Research Australia, Ophthalmology, Department of Surgery, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
| | - Veronique Vitart
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Joan E. Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Terri L. Young
- Department of Ophthalmology and Visual Sciences, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Seang-Mei Saw
- Saw Swee Hock School of Public Health, National University Health Systems, National University of Singapore, Singapore
- Myopia Research Group, Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | | | - Christopher J. Hammond
- Section of Academic Ophthalmology, School of Life Course Sciences, King’s College London, London, UK
| | - Caroline C.W. Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
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Zagajewska K, Piątkowska M, Goryca K, Bałabas A, Kluska A, Paziewska A, Pośpiech E, Grabska-Liberek I, Hennig EE. GWAS links variants in neuronal development and actin remodeling related loci with pseudoexfoliation syndrome without glaucoma. Exp Eye Res 2018; 168:138-148. [DOI: 10.1016/j.exer.2017.12.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 12/05/2017] [Accepted: 12/20/2017] [Indexed: 01/13/2023]
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Abstract
PURPOSE The prevalence of myopia has increased dramatically worldwide within the last three decades. Recent studies have shown that refractive development is influenced by environmental, behavioral, and inherited factors. This review aims to analyze recent progress in the genetics of refractive error and myopia. METHODS A comprehensive literature search of PubMed and OMIM was conducted to identify relevant articles in the genetics of refractive error. RESULTS Genome-wide association and sequencing studies have increased our understanding of the genetics involved in refractive error. These studies have identified interesting candidate genes. All genetic loci discovered to date indicate that refractive development is a heterogeneous process mediated by a number of overlapping biological processes. The exact mechanisms by which these biological networks regulate eye growth are poorly understood. Although several individual genes and/or molecular pathways have been investigated in animal models, a systematic network-based approach in modeling human refractive development is necessary to understand the complex interplay between genes and environment in refractive error. CONCLUSION New biomedical technologies and better-designed studies will continue to refine our understanding of the genetics and molecular pathways of refractive error, and may lead to preventative and therapeutic measures to combat the myopia epidemic.
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Tang SM, Ma L, Lu SY, Wang YM, Kam KW, Tam POS, Young AL, Pang CP, Yam JCS, Chen LJ. Association of the PAX6 gene with extreme myopia rather than lower grade myopias. Br J Ophthalmol 2018; 102:570-574. [DOI: 10.1136/bjophthalmol-2017-311327] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 01/12/2018] [Accepted: 01/20/2018] [Indexed: 11/03/2022]
Abstract
AimsTo investigate the association of the paired box gene 6 (PAX6) with different severities of myopia.MethodsA total of four haplotype-tagging single-nucleotide polymorphisms (SNPs; rs2071754, rs3026354, rs3026390 and rs628224) and two previously reported SNPs (rs644242 and rs662702) in the PAX6 gene were analysed in a Hong Kong Chinese cohort of 1288 myopia subjects (including 252 extreme myopia, 277 high myopia, 393 moderate myopia and 366 mild myopia) and 791 no myopia controls. Allelic association analyses were performed for individual SNPs in different subgroups of myopia and in combined myopia, followed by a meta-analysis of our current data with reported data on PAX6 in myopia.ResultsThe association of tagging SNPs rs2071754 and rs644242 with extreme myopia could not withstand multiple correction (rs2071754: OR=1.25, P value=0.031; rs644242: OR=1.33, P value=0.032). In the meta-analysis, rs644242 showed an enhanced, significant association with extreme myopia (OR=1.27, 95% CI 1.10 to 1.46, P value=0.001; I2=0%). In contrast, there was no significant association between the PAX6SNPs and high, moderate or mild myopia. No linear correlation was found between the PAX6SNPs and axial length.ConclusionThis study provides additional evidence suggesting that the PAX6 SNP rs644242 is associated with extreme myopia but not lower grade myopia. Thus, PAX6 may be implicated in the development or progression into severe myopia. Further longitudinal studies are warranted.
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Musolf AM, Simpson CL, Long KA, Moiz BA, Lewis DD, Middlebrooks CD, Portas L, Murgia F, Ciner EB, Bailey-Wilson JE, Stambolian D. Myopia in Chinese families shows linkage to 10q26.13. Mol Vis 2018; 24:29-42. [PMID: 29383007 PMCID: PMC5767476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/12/2018] [Indexed: 11/09/2022] Open
Abstract
Purpose To determine genetic linkage between myopia and Han Chinese patients with a family history of the disease. Methods One hundred seventy-six Han Chinese patients from 34 extended families were given eye examinations, and mean spherical equivalent (MSE) in diopters (D) was calculated by adding the spherical component of the refraction to one-half the cylindrical component and taking the average of both eyes. The MSE was converted to a binary phenotype, where all patients with an MSE of -1.00 D or less were coded as affected. Unaffected individuals had an MSE greater than 0.00 D (ages 21 years and up), +1.50 (ages 11-20), or +2.00 D (ages 6-10 years). Individuals between the given upper threshold and -1.00 were coded as unknown. Patients were genotyped on an exome chip. Three types of linkage analyses were performed: single-variant two-point, multipoint, and collapsed haplotype pattern (CHP) variant two-point. Results The CHP variant two-point results identified a significant peak (heterogeneity logarithm of the odds [HLOD] = 3.73) at 10q26.13 in TACC2. The single-variant two-point and multipoint analyses showed highly suggestive linkage to the same region. The single-variant two-point results identified 25 suggestive variants at HTRA1, also at 10q26.13. Conclusions We report a significant genetic linkage between myopia and Han Chinese patients at 10q26.13. 10q26.13 contains several good candidate genes, such as TACC2 and the known age-related macular degeneration gene HTRA1. Targeted sequencing of the region is planned to identify the causal variant(s).
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Affiliation(s)
- Anthony M. Musolf
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD
| | - Claire L. Simpson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN
| | - Kyle A. Long
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD
| | - Bilal A. Moiz
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD
| | - Deyana D. Lewis
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD
| | - Candace D. Middlebrooks
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD
| | - Laura Portas
- Institute of Population Genetics, CNR, Li Punti, Sassari, Italy
| | - Federico Murgia
- Institute of Population Genetics, CNR, Li Punti, Sassari, Italy
| | - Elise B. Ciner
- The Pennsylvania College of Optometry at Salus University, Elkins Park, PA
| | - Joan E. Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA
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Lebel M, Monnat RJ. Werner syndrome (WRN) gene variants and their association with altered function and age-associated diseases. Ageing Res Rev 2018; 41:82-97. [PMID: 29146545 DOI: 10.1016/j.arr.2017.11.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 11/07/2017] [Accepted: 11/09/2017] [Indexed: 01/14/2023]
Abstract
Werner syndrome (WS) is a heritable autosomal recessive human disorder characterized by the premature onset of several age-associated pathologies including cancer. The protein defective in WS patients, WRN, is encoded by a member of the human RECQ gene family that contains both a DNA exonuclease and a helicase domain. WRN has been shown to participate in several DNA metabolic pathways including DNA replication, recombination and repair, as well as telomere maintenance and transcription modulation. Here we review base pair-level genetic variation that has been documented in WRN, with an emphasis on non-synonymous coding single nucleotide polymorphisms (SNPs) and their associations with anthropomorphic features, longevity and disease risk. These associations have been challenging to identify, as many reported WRN SNP associations appear to be further conditioned upon ethnic, age, gender or other environmental co-variables. The WRN variant phenotypic associations identified to date are intriguing, and several are of clear clinical import. Consequently, it will be important to extend these initial associations and to identify the mechanisms and conditions under which specific WRN variants may compromise WRN function to drive cellular and organismal phenotypes as well as disease risk.
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Affiliation(s)
- Michel Lebel
- Centre de recherche du CHU de Québec, Pavillon CHUL Université Laval, Faculté de Médecine, Québec City, Québec, G1V 4G2, Canada.
| | - Raymond J Monnat
- Departments of Pathology and Genome Sciences, University of Washington, Seattle, WA 98195, USA
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Musolf AM, Simpson CL, Moiz BA, Long KA, Portas L, Murgia F, Ciner EB, Stambolian D, Bailey-Wilson JE. Caucasian Families Exhibit Significant Linkage of Myopia to Chromosome 11p. Invest Ophthalmol Vis Sci 2017; 58:3547-3554. [PMID: 28715588 PMCID: PMC5510992 DOI: 10.1167/iovs.16-21271] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 05/29/2017] [Indexed: 11/24/2022] Open
Abstract
Purpose Myopia is a common visual disorder caused by eye overgrowth, resulting in blurry vision. It affects one in four Americans, and its prevalence is increasing. The genetic mechanisms that underpin myopia are not completely understood. Here, we use genotype data and linkage analyses to identify high-risk genetic loci that are significantly linked to myopia. Methods Individuals from 56 Caucasian families with a history of myopia were genotyped on an exome-based array, and the single nucleotide polymorphism (SNP) data were merged with microsatellite genotype data. Refractive error measures on the samples were converted into binary phenotypes consisting of affected, unaffected, or unknown myopia status. Parametric linkage analyses assuming an autosomal dominant model with 90% penetrance and 10% phenocopy rate were performed. Results Single variant two-point analyses yielded three significantly linked SNPs at 11p14.1 and 11p11.2; a further 45 SNPs at 11p were found to be suggestive. No other chromosome had any significant SNPs or more than seven suggestive linkages. Two of the significant SNPs were located in BBOX1-AS1 and one in the intergenic region between ORA47 and TRIM49B. Collapsed haplotype pattern two-point analysis and multipoint analyses also yielded multiple suggestively linked genes at 11p. Multipoint analysis also identified suggestive evidence of linkage on 20q13. Conclusions We identified three genome-wide significant linked variants on 11p for myopia in Caucasians. Although the novel specific signals still need to be replicated, 11p is a promising region that has been identified by other linkage studies with a number of potentially interesting candidate genes. We hope that the identification of these regions on 11p as potential causal regions for myopia will lead to more focus on these regions and maybe possible replication of our specific linkage peaks in other studies. We further plan targeted sequencing on 11p for our most highly linked families to more clearly understand the source of the linkage in this region.
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Affiliation(s)
- Anthony M. Musolf
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States
| | - Claire L. Simpson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States
| | - Bilal A. Moiz
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States
| | - Kyle A. Long
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States
| | - Laura Portas
- Institute of Population Genetics, CNR, Li Punti, Sassari, Italy
| | - Federico Murgia
- Institute of Population Genetics, CNR, Li Punti, Sassari, Italy
| | - Elise B. Ciner
- The Pennsylvania College of Optometry at Salus University, Elkins Park, Pennsylvania, United States
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Joan E. Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States
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Afshari NA, Igo RP, Morris NJ, Stambolian D, Sharma S, Pulagam VL, Dunn S, Stamler JF, Truitt BJ, Rimmler J, Kuot A, Croasdale CR, Qin X, Burdon KP, Riazuddin SA, Mills R, Klebe S, Minear MA, Zhao J, Balajonda E, Rosenwasser GO, Baratz KH, Mootha VV, Patel SV, Gregory SG, Bailey-Wilson JE, Price MO, Price FW, Craig JE, Fingert JH, Gottsch JD, Aldave AJ, Klintworth GK, Lass JH, Li YJ, Iyengar SK. Genome-wide association study identifies three novel loci in Fuchs endothelial corneal dystrophy. Nat Commun 2017; 8:14898. [PMID: 28358029 PMCID: PMC5379100 DOI: 10.1038/ncomms14898] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 02/06/2017] [Indexed: 12/13/2022] Open
Abstract
The structure of the cornea is vital to its transparency, and dystrophies that disrupt corneal organization are highly heritable. To understand the genetic aetiology of Fuchs endothelial corneal dystrophy (FECD), the most prevalent corneal disorder requiring transplantation, we conducted a genome-wide association study (GWAS) on 1,404 FECD cases and 2,564 controls of European ancestry, followed by replication and meta-analysis, for a total of 2,075 cases and 3,342 controls. We identify three novel loci meeting genome-wide significance (P<5 × 10-8): KANK4 rs79742895, LAMC1 rs3768617 and LINC00970/ATP1B1 rs1200114. We also observe an overwhelming effect of the established TCF4 locus. Interestingly, we detect differential sex-specific association at LAMC1, with greater risk in women, and TCF4, with greater risk in men. Combining GWAS results with biological evidence we expand the knowledge of common FECD loci from one to four, and provide a deeper understanding of the underlying pathogenic basis of FECD.
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Affiliation(s)
- Natalie A. Afshari
- Shiley Eye Institute, University of California, La Jolla, California 92093, USA
| | - Robert P. Igo
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Nathan J. Morris
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Shiwani Sharma
- Department of Ophthalmology, Flinders Medical Centre, Flinders University, Adelaide, South Australia 5042, Australia
| | - V. Lakshmi Pulagam
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Steven Dunn
- Michigan Cornea Consultants, PC, Southfield, Michigan 48034, USA
| | - John F. Stamler
- Department of Ophthalmology, University of Iowa, College of Medicine, Iowa City, Iowa 52242, USA
| | - Barbara J. Truitt
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Jacqueline Rimmler
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina 27701, USA
| | - Abraham Kuot
- Department of Ophthalmology, Flinders Medical Centre, Flinders University, Adelaide, South Australia 5042, Australia
| | | | - Xuejun Qin
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina 27701, USA
| | - Kathryn P. Burdon
- Department of Ophthalmology, Flinders Medical Centre, Flinders University, Adelaide, South Australia 5042, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - S. Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Richard Mills
- Department of Ophthalmology, Flinders Medical Centre, Flinders University, Adelaide, South Australia 5042, Australia
| | - Sonja Klebe
- Department of Ophthalmology, Flinders Medical Centre, Flinders University, Adelaide, South Australia 5042, Australia
- Department of Pathology, Flinders Medical Centre, Flinders University, Adelaide, South Australia 5042, Australia
| | - Mollie A. Minear
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina 27701, USA
| | - Jiagang Zhao
- Shiley Eye Institute, University of California, La Jolla, California 92093, USA
| | - Elmer Balajonda
- Duke University Eye Center, Duke University Medical Center, Durham, North Carolina 27710, USA
| | | | - Keith H Baratz
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - V. Vinod Mootha
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas 75235, USA
| | - Sanjay V. Patel
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Simon G. Gregory
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina 27701, USA
| | - Joan E. Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health and Johns Hopkins University, Baltimore, Maryland 21224, USA
| | | | | | - Jamie E. Craig
- Department of Ophthalmology, Flinders Medical Centre, Flinders University, Adelaide, South Australia 5042, Australia
| | - John H. Fingert
- Department of Ophthalmology, University of Iowa, College of Medicine, Iowa City, Iowa 52242, USA
| | - John D. Gottsch
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Anthony J. Aldave
- Stein Eye Institute, University of California, Los Angeles, California 90095, USA
| | - Gordon K. Klintworth
- Duke University Eye Center, Duke University Medical Center, Durham, North Carolina 27710, USA
- Department of Pathology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Jonathan H. Lass
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University and University Hospitals Eye Institute, Cleveland, Ohio 44106, USA
| | - Yi-Ju Li
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, North Carolina 27701, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Sudha K. Iyengar
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University and University Hospitals Eye Institute, Cleveland, Ohio 44106, USA
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Conboy JG. Developmental regulation of RNA processing by Rbfox proteins. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27748060 DOI: 10.1002/wrna.1398] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/17/2016] [Accepted: 08/27/2016] [Indexed: 12/15/2022]
Abstract
The Rbfox genes encode an ancient family of sequence-specific RNA binding proteins (RBPs) that are critical developmental regulators in multiple tissues including skeletal muscle, cardiac muscle, and brain. The hallmark of Rbfox proteins is a single high-affinity RRM domain, highly conserved from insects to humans, that binds preferentially to UGCAUG motifs at diverse regulatory sites in pre-mRNA introns, mRNA 3'UTRs, and pre-miRNAs hairpin structures. Versatile regulatory circuits operate on Rbfox pre-mRNA and mRNA to ensure proper expression of Rbfox1 protein isoforms, which then act on the broader transcriptome to regulate alternative splicing networks, mRNA stability and translation, and microRNA processing. Complex Rbfox expression is encoded in large genes encompassing multiple promoters and alternative splicing options that govern spatiotemporal expression of structurally distinct and tissue-specific protein isoforms with different classes of RNA targets. Nuclear Rbfox1 is a candidate master regulator that binds intronic UGCAUG elements to impact splicing efficiency of target alternative exons, many in transcripts for other splicing regulators. Tissue-specificity of Rbfox-mediated alternative splicing is executed by combinatorial regulation through the integrated activity of Rbfox proteins and synergistic or antagonistic splicing factors. Studies in animal models show that Rbfox1-related genes are critical for diverse developmental processes including germ cell differentiation and memory in Drosophila, neuronal migration and function in mouse brain, myoblast fusion and skeletal muscle function, and normal heart function. Finally, genetic and biochemical evidence suggest that aberrations in Rbfox-regulated circuitry are risk factors for multiple human disorders, especially neurodevelopmental disorders including epilepsy and autism, and cardiac hypertrophy. WIREs RNA 2017, 8:e1398. doi: 10.1002/wrna.1398 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- John G Conboy
- Biological Systems and Engineering Division Lawrence Berkeley National Laboratory Berkeley, CA 94720, USA
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Chen F, Duggal P, Klein BEK, Lee KE, Truitt B, Klein R, Iyengar SK, Klein AP. Variation in PTCHD2, CRISP3, NAP1L4, FSCB, and AP3B2 associated with spherical equivalent. Mol Vis 2016; 22:783-96. [PMID: 27440996 DOI: pmid/27440996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 07/12/2016] [Indexed: 11/10/2022] Open
Abstract
PURPOSE Ocular refraction is measured in spherical equivalent as the power of the external lens required to focus images on the retina. Myopia (nearsightedness) and hyperopia (farsightedness) are the most common refractive errors, and the leading causes of visual impairment and blindness in the world. The goal of this study is to identify rare and low-frequency variants that influence spherical equivalent. METHODS We conducted variant-level and gene-level quantitative trait association analyses for mean spherical equivalent, using data from 1,560 individuals in the Beaver Dam Eye Study. Genotyping was conducted using the Illumina exome array. We analyzed 34,976 single nucleotide variants and 11,571 autosomal genes across the genome, using single-variant tests as well as gene-based tests. RESULTS Spherical equivalent was significantly associated with five genes in gene-based analysis: PTCHD2 at 1p36.22 (p = 3.6 × 10(-7)), CRISP3 at 6p12.3 (p = 4.3 × 10(-6)), NAP1L4 at 11p15.5 (p = 3.6 × 10(-6)), FSCB at 14q21.2 (p = 1.5 × 10(-7)), and AP3B2 at 15q25.2 (p = 1.6 × 10(-7)). The variant-based tests identified evidence suggestive of association with two novel variants in linkage disequilibrium (pairwise r(2) = 0.80) in the TCTE1 gene region at 6p21.1 (rs2297336, minor allele frequency (MAF) = 14.1%, β = -0.62 p = 3.7 × 10(-6); rs324146, MAF = 16.9%, β = -0.55, p = 1.4 × 10(-5)). In addition to these novel findings, we successfully replicated a previously reported association with rs634990 near GJD2 at 15q14 (MAF = 47%, β = -0.29, p=1.8 × 10(-3)). We also found evidence of association with spherical equivalent on 2q37.1 in PRSS56 at rs1550094 (MAF = 31%, β = -0.33, p = 1.7 × 10(-3)), a region previously associated with myopia. CONCLUSIONS We identified several novel candidate genes that may play a role in the control of spherical equivalent. However, further studies are needed to replicate these findings. In addition, our results contribute to the increasing evidence that variation in the GJD2 and PRSS56 genes influence the development of refractive errors. Identifying that variation in these genes is associated with spherical equivalent may provide further insight into the etiology of myopia and consequent vision loss.
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Affiliation(s)
- Fei Chen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Barbara E K Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Kristine E Lee
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Barbara Truitt
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH
| | - Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Sudha K Iyengar
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH
| | - Alison P Klein
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD; Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
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Fan Q, Guo X, Tideman JWL, Williams KM, Yazar S, Hosseini SM, Howe LD, Pourcain BS, Evans DM, Timpson NJ, McMahon G, Hysi PG, Krapohl E, Wang YX, Jonas JB, Baird PN, Wang JJ, Cheng CY, Teo YY, Wong TY, Ding X, Wojciechowski R, Young TL, Pärssinen O, Oexle K, Pfeiffer N, Bailey-Wilson JE, Paterson AD, Klaver CCW, Plomin R, Hammond CJ, Mackey DA, He M, Saw SM, Williams C, Guggenheim JA. Childhood gene-environment interactions and age-dependent effects of genetic variants associated with refractive error and myopia: The CREAM Consortium. Sci Rep 2016; 6:25853. [PMID: 27174397 PMCID: PMC4865831 DOI: 10.1038/srep25853] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 04/25/2016] [Indexed: 12/19/2022] Open
Abstract
Myopia, currently at epidemic levels in East Asia, is a leading cause of untreatable visual impairment. Genome-wide association studies (GWAS) in adults have identified 39 loci associated with refractive error and myopia. Here, the age-of-onset of association between genetic variants at these 39 loci and refractive error was investigated in 5200 children assessed longitudinally across ages 7-15 years, along with gene-environment interactions involving the major environmental risk-factors, nearwork and time outdoors. Specific variants could be categorized as showing evidence of: (a) early-onset effects remaining stable through childhood, (b) early-onset effects that progressed further with increasing age, or (c) onset later in childhood (N = 10, 5 and 11 variants, respectively). A genetic risk score (GRS) for all 39 variants explained 0.6% (P = 6.6E-08) and 2.3% (P = 6.9E-21) of the variance in refractive error at ages 7 and 15, respectively, supporting increased effects from these genetic variants at older ages. Replication in multi-ancestry samples (combined N = 5599) yielded evidence of childhood onset for 6 of 12 variants present in both Asians and Europeans. There was no indication that variant or GRS effects altered depending on time outdoors, however 5 variants showed nominal evidence of interactions with nearwork (top variant, rs7829127 in ZMAT4; P = 6.3E-04).
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Affiliation(s)
- Qiao Fan
- Centre for Quantitative Medicine, Duke-NUS Medial School,
Singapore
| | - Xiaobo Guo
- Department of Statistical Science, School of Mathematics
& Computational Science, Sun Yat-Sen University, Guangzhou,
China
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic
Center, Sun Yat-sen University, Guangzhou, China
| | - J. Willem L. Tideman
- Department of Epidemiology, Erasmus Medical Center,
Rotterdam, The Netherlands
- Department of Ophthalmology, Erasmus Medical Center,
Rotterdam, The Netherlands
| | - Katie M. Williams
- Department of Ophthalmology, King’s College London,
St Thomas’ Hospital campus, London, UK
- Department of Twin Research and Genetic Epidemiology,
King’s College London School of Medicine, London,
UK
| | - Seyhan Yazar
- Centre for Ophthalmology and Visual Science, Lions Eye
Institute, University of Western Australia, Perth,
Australia
| | - S. Mohsen Hosseini
- Genetics and Genome Biology Program, Hospital for Sick Children
and University of Toronto, Toronto, Ontario, Canada
| | - Laura D. Howe
- MRC Integrative Epidemiology Unit (IEU) at the University of
Bristol, Bristol, UK
- School of Social and Community Medicine, University of
Bristol, Bristol, UK
| | - Beaté St Pourcain
- MRC Integrative Epidemiology Unit (IEU) at the University of
Bristol, Bristol, UK
- Max Planck Institute for Psycholinguistics, Wundtlaan 1,
6525 XD Nijmegen, The Netherlands
| | - David M. Evans
- MRC Integrative Epidemiology Unit (IEU) at the University of
Bristol, Bristol, UK
- University of Queensland Diamantina Institute, Translational
Research Institute, Brisbane, Queensland, Australia
| | - Nicholas J. Timpson
- MRC Integrative Epidemiology Unit (IEU) at the University of
Bristol, Bristol, UK
| | - George McMahon
- MRC Integrative Epidemiology Unit (IEU) at the University of
Bristol, Bristol, UK
| | - Pirro G. Hysi
- Department of Twin Research and Genetic Epidemiology,
King’s College London School of Medicine, London,
UK
| | - Eva Krapohl
- MRC Social, Genetic and Developmental Psychiatry Centre,
Institute of Psychiatry, Psychology & Neuroscience, King’s
College London, London, UK
| | - Ya Xing Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital,
Capital Medical University, Beijing, China
- Beijing Ophthalmology and Visual Science Key Lab,
Beijing, China
| | - Jost B. Jonas
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital,
Capital Medical University, Beijing, China
- Beijing Ophthalmology and Visual Science Key Lab,
Beijing, China
- Department of Ophthalmology, Medical Faculty Mannheim,
Ruprecht-Karls-University Heidelberg, Mannheim, Germany
| | - Paul Nigel Baird
- Centre for Eye Research Australia (CERA), University of
Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria,
Australia
| | - Jie Jin Wang
- Centre for Eye Research Australia (CERA), University of
Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria,
Australia
- Centre for Vision Research, Department of Ophthalmology and
Westmead Institute for Medical Research, University of Sydney, Sydney,
Australia
| | - Ching-Yu Cheng
- Department of Ophthalmology, National University Health
Systems, National University of Singapore, Singapore
- Singapore Eye Research Institute, Singapore National Eye
Centre, Singapore, Singapore
| | - Yik-Ying Teo
- Department of Statistics and Applied Probability, National
University of Singapore, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University
Health Systems, National University of Singapore, Singapore,
Singapore
| | - Tien-Yin Wong
- Department of Ophthalmology, National University Health
Systems, National University of Singapore, Singapore
- Singapore Eye Research Institute, Singapore National Eye
Centre, Singapore, Singapore
| | - Xiaohu Ding
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic
Center, Sun Yat-sen University, Guangzhou, China
| | - Robert Wojciechowski
- Computational and Statistical Genomics Branch, National Human
Genome Research Institute, National Institutes of Health, Baltimore, MD,
USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of
Public Health, Baltimore, Maryland, USA
- Wilmer Eye Institute, Johns Hopkins School of Medicine,
Baltimore, MD
| | - Terri L. Young
- Ophthalmology and Visual Sciences, University of
Wisconsin-Madison, Madison, WI, USA
- Duke-National University of Singapore Graduate Medical
School, Singapore, Singapore
| | - Olavi Pärssinen
- Department of Health Sciences and Gerontology Research Center,
University of Jyväskylä,
Jyväskylä, Finland
- Department of Ophthalmology, Central Hospital of Central
Finland, Jyväskylä, Finland
| | - Konrad Oexle
- Institute of Human Genetics, Technical University Munich,
Munich, Germany
| | - Norbert Pfeiffer
- Department of Ophthalmology, University Medical Center
Mainz, Mainz, Germany
| | - Joan E. Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human
Genome Research Institute, National Institutes of Health, Baltimore, MD,
USA
| | - Andrew D. Paterson
- Genetics and Genome Biology Program, Hospital for Sick Children
and University of Toronto, Toronto, Ontario, Canada
| | - Caroline C. W. Klaver
- Department of Epidemiology, Erasmus Medical Center,
Rotterdam, The Netherlands
- Department of Ophthalmology, Erasmus Medical Center,
Rotterdam, The Netherlands
| | - Robert Plomin
- MRC Social, Genetic and Developmental Psychiatry Centre,
Institute of Psychiatry, Psychology & Neuroscience, King’s
College London, London, UK
| | - Christopher J. Hammond
- Department of Ophthalmology, King’s College London,
St Thomas’ Hospital campus, London, UK
- Department of Twin Research and Genetic Epidemiology,
King’s College London School of Medicine, London,
UK
| | - David A. Mackey
- 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
| | - Mingguang He
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic
Center, Sun Yat-sen University, Guangzhou, China
- Centre for Eye Research Australia (CERA), University of
Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria,
Australia
| | - Seang-Mei Saw
- Singapore Eye Research Institute, Singapore National Eye
Centre, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University
Health Systems, National University of Singapore, Singapore,
Singapore
| | - Cathy Williams
- School of Social and Community Medicine, University of
Bristol, Bristol, UK
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Williams KM, Hammond CJ. GWAS in myopia: insights into disease and implications for the clinic. EXPERT REVIEW OF OPHTHALMOLOGY 2016. [DOI: 10.1586/17469899.2016.1164597] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Szymczak S, Holzinger E, Dasgupta A, Malley JD, Molloy AM, Mills JL, Brody LC, Stambolian D, Bailey-Wilson JE. r2VIM: A new variable selection method for random forests in genome-wide association studies. BioData Min 2016; 9:7. [PMID: 26839594 PMCID: PMC4736152 DOI: 10.1186/s13040-016-0087-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 01/19/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Machine learning methods and in particular random forests (RFs) are a promising alternative to standard single SNP analyses in genome-wide association studies (GWAS). RFs provide variable importance measures (VIMs) to rank SNPs according to their predictive power. However, in contrast to the established genome-wide significance threshold, no clear criteria exist to determine how many SNPs should be selected for downstream analyses. RESULTS We propose a new variable selection approach, recurrent relative variable importance measure (r2VIM). Importance values are calculated relative to an observed minimal importance score for several runs of RF and only SNPs with large relative VIMs in all of the runs are selected as important. Evaluations on simulated GWAS data show that the new method controls the number of false-positives under the null hypothesis. Under a simple alternative hypothesis with several independent main effects it is only slightly less powerful than logistic regression. In an experimental GWAS data set, the same strong signal is identified while the approach selects none of the SNPs in an underpowered GWAS. CONCLUSIONS The novel variable selection method r2VIM is a promising extension to standard RF for objectively selecting relevant SNPs in GWAS while controlling the number of false-positive results.
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Affiliation(s)
- Silke Szymczak
- Statistical Genetics Section, Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr, 21224 Baltimore, USA ; Current address: Institute of Medical Informatics and Statistics, University of Kiel, Brunswiker Str. 10, 24105 Kiel, Germany
| | - Emily Holzinger
- Statistical Genetics Section, Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr, 21224 Baltimore, USA
| | - Abhijit Dasgupta
- Clinical Trials and Outcomes Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, 1 AMS Circle, 20892 Bethesda, USA
| | - James D Malley
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, 12 South Dr, 20892 Bethesda, USA
| | - Anne M Molloy
- Department of Clinical Medicine, School of Medicine, Trinity College Dublin, 152-160 Pearse Street, 2 Dublin, Ireland
| | - James L Mills
- Division of Intramural Population Health Research, Eunice Shriver National Institute of Child Health and Human Development, National Institutes of Health, 6100 Executive Blvd, 20892 Bethesda, USA
| | - Lawrence C Brody
- Molecular Pathogenesis Section, Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, 50 South Dr, 20892 Bethesda, USA
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, 422 Curie Blvd, 19104 Philadelphia, USA
| | - Joan E Bailey-Wilson
- Statistical Genetics Section, Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, 333 Cassell Dr, 21224 Baltimore, USA
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Lin YT, Lee WC. Importance of presenting the variability of the false discovery rate control. BMC Genet 2015; 16:97. [PMID: 26239642 PMCID: PMC4523994 DOI: 10.1186/s12863-015-0259-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 07/28/2015] [Indexed: 11/10/2022] Open
Abstract
Background Multiple hypothesis testing is a pervasive problem in genomic data analysis. The conventional Bonferroni method which controls the family-wise error rate is conservative and with low power. The current paradigm is to control the false discovery rate. Results We characterize the variability of the false discovery rate indices (local false discovery rates, q-value and false discovery proportion) using the bootstrapped method. A colon cancer gene-expression data and a visual refractive errors genome-wide association study data are analyzed as demonstration. We found a high variability in false discovery rate controls for typical genomic studies. Conclusions We advise researchers to present the bootstrapped standard errors alongside with the false discovery rate indices. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0259-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yi-Ting Lin
- Research Center for Genes, Environment and Human Health and Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Rm. 536, No. 17, Xuzhou Rd., Taipei, 100, Taiwan.
| | - Wen-Chung Lee
- Research Center for Genes, Environment and Human Health and Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Rm. 536, No. 17, Xuzhou Rd., Taipei, 100, Taiwan.
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Abstract
Background With one million new cases of colorectal cancer (CRC) diagnosed annually in the world, CRC is the third most commonly diagnosed cancer in the Western world. Patients with stage I-III CRC can be cured with surgery but are at risk for recurrence. Colorectal cancer is characterized by the presence of chromosomal deletions and gains. Large genomic profiling studies have however not been conducted in this disease. The number of a specific genetic aberration in a tumour sample could correlate with recurrence-free survival or overall survival, possibly leading to its use as biomarker for therapeutic decisions. At this point there are not sufficient markers for prediction of disease recurrence in colorectal cancer, which can be used in the clinic to discriminate between stage II patients who will benefit from adjuvant chemotherapy. For instance, the benefit of adjuvant chemotherapy has been most clearly demonstrated in stage III disease with an approximately 30 percent relative reduction in the risk of disease recurrence. The benefits of adjuvant chemotherapy in stage II disease are less certain, the risk for relapse is much smaller in the overall group and the specific patients at risk are hard to identify. Materials and Methods In this study, array-comparative genomic hybridization analysis (array-CGH) was applied to study high-resolution DNA copy number alterations in 93 colon carcinoma samples. These genomic data were combined with parameters like KRAS mutation status, microsatellite status and clinicopathological characteristics. Results Both large and small chromosomal losses and gains were identified in our sample cohort. Recurrent gains were found for chromosome 1q, 7, 8q, 13 and 20 and losses were mostly found for 1p, 4, 8p, 14, 15, 17p, 18, 21 and 22. Data analysis demonstrated that loss of chromosome 4 is linked to a worse prognosis in our patients series. Besides these alterations, two interesting small regions of overlap were identified, which could be associated with disease recurrence. Gain of the 16p13.3 locus (including the RNA binding protein, fox-1 homolog gene, RBFOX1) was linked with a worse recurrence-free survival in our patient cohort. On the other hand, loss of RBFOX1 was only found in patients without disease recurrence. Most interestingly, above mentioned characteristics were also found in stage II patients, for whom there is a high medical need for the identification of new prognostic biomarkers. Conclusions In conclusion, copy number variation of the 16p13.3 locus seems to be an important parameter for prediction of disease recurrence in colon cancer.
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Li Q, Wojciechowski R, Simpson CL, Hysi PG, Verhoeven VJM, Ikram MK, Höhn R, Vitart V, Hewitt AW, Oexle K, Mäkelä KM, MacGregor S, Pirastu M, Fan Q, Cheng CY, St Pourcain B, McMahon G, Kemp JP, Northstone K, Rahi JS, Cumberland PM, Martin NG, Sanfilippo PG, Lu Y, Wang YX, Hayward C, Polašek O, Campbell H, Bencic G, Wright AF, Wedenoja J, Zeller T, Schillert A, Mirshahi A, Lackner K, Yip SP, Yap MKH, Ried JS, Gieger C, Murgia F, Wilson JF, Fleck B, Yazar S, Vingerling JR, Hofman A, Uitterlinden A, Rivadeneira F, Amin N, Karssen L, Oostra BA, Zhou X, Teo YY, Tai ES, Vithana E, Barathi V, Zheng Y, Siantar RG, Neelam K, Shin Y, Lam J, Yonova-Doing E, Venturini C, Hosseini SM, Wong HS, Lehtimäki T, Kähönen M, Raitakari O, Timpson NJ, Evans DM, Khor CC, Aung T, Young TL, Mitchell P, Klein B, van Duijn CM, Meitinger T, Jonas JB, Baird PN, Mackey DA, Wong TY, Saw SM, Pärssinen O, Stambolian D, Hammond CJ, Klaver CCW, Williams C, Paterson AD, Bailey-Wilson JE, Guggenheim JA. Genome-wide association study for refractive astigmatism reveals genetic co-determination with spherical equivalent refractive error: the CREAM consortium. Hum Genet 2015; 134:131-46. [PMID: 25367360 PMCID: PMC4291519 DOI: 10.1007/s00439-014-1500-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 09/30/2014] [Indexed: 11/24/2022]
Abstract
To identify genetic variants associated with refractive astigmatism in the general population, meta-analyses of genome-wide association studies were performed for: White Europeans aged at least 25 years (20 cohorts, N = 31,968); Asian subjects aged at least 25 years (7 cohorts, N = 9,295); White Europeans aged <25 years (4 cohorts, N = 5,640); and all independent individuals from the above three samples combined with a sample of Chinese subjects aged <25 years (N = 45,931). Participants were classified as cases with refractive astigmatism if the average cylinder power in their two eyes was at least 1.00 diopter and as controls otherwise. Genome-wide association analysis was carried out for each cohort separately using logistic regression. Meta-analysis was conducted using a fixed effects model. In the older European group the most strongly associated marker was downstream of the neurexin-1 (NRXN1) gene (rs1401327, P = 3.92E-8). No other region reached genome-wide significance, and association signals were lower for the younger European group and Asian group. In the meta-analysis of all cohorts, no marker reached genome-wide significance: The most strongly associated regions were, NRXN1 (rs1401327, P = 2.93E-07), TOX (rs7823467, P = 3.47E-07) and LINC00340 (rs12212674, P = 1.49E-06). For 34 markers identified in prior GWAS for spherical equivalent refractive error, the beta coefficients for genotype versus spherical equivalent, and genotype versus refractive astigmatism, were highly correlated (r = -0.59, P = 2.10E-04). This work revealed no consistent or strong genetic signals for refractive astigmatism; however, the TOX gene region previously identified in GWAS for spherical equivalent refractive error was the second most strongly associated region. Analysis of additional markers provided evidence supporting widespread genetic co-susceptibility for spherical and astigmatic refractive errors.
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Affiliation(s)
- Qing Li
- National Human Genome Research Institute, National Institutes of Health, 333 Cassell Drive Suite 1200, Baltimore, MD 21224 USA
| | - Robert Wojciechowski
- National Human Genome Research Institute, National Institutes of Health, 333 Cassell Drive Suite 1200, Baltimore, MD 21224 USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
- Wilmer Eye Institute, Johns Hopkins Medical Institutions, Baltimore, MD USA
| | - Claire L. Simpson
- National Human Genome Research Institute, National Institutes of Health, 333 Cassell Drive Suite 1200, Baltimore, MD 21224 USA
| | - Pirro G. Hysi
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Hospital Campus, London, UK
| | - Virginie J. M. Verhoeven
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Mohammad Kamran Ikram
- Singapore Eye Research Institute, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Office of Clinical Sciences, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - René Höhn
- Department of Ophthalmology, University Medical Center Mainz, Mainz, Germany
- Klinik Pallas, Olten, Switzerland
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Alex W. Hewitt
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | - Konrad Oexle
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Kari-Matti Mäkelä
- Department of Clinical Chemistry, Filmlab laboratories, Tampere University Hospital and School of Medicine, University of Tampere, 33520 Tampere, Finland
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute Royal Brisbane Hospital, Brisbane, Australia
| | - Mario Pirastu
- Institute of Population Genetics CNR, Traversa La Crucca, 3-07040 Reg. Baldinca, Li Punti, Sassari, Italy
| | - Qiao Fan
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Office of Clinical Sciences, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Beaté St Pourcain
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, BS8 2BN UK
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
| | - George McMahon
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, BS8 2BN UK
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
| | - John P. Kemp
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, BS8 2BN UK
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
| | - Kate Northstone
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
| | - Jugnoo S. Rahi
- Centre of Epidemiology and Biostatistics, UCL Institute of Child Health, London, UK
- Institute of Ophthalmology, University College London, London, UK
- Ulverscroft Vision Research Group, UCL Institute of Child Health, London, UK
| | - Phillippa M. Cumberland
- Centre of Epidemiology and Biostatistics, UCL Institute of Child Health, London, UK
- Ulverscroft Vision Research Group, UCL Institute of Child Health, London, UK
| | - Nicholas G. Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute Royal Brisbane Hospital, Brisbane, Australia
| | - Paul G. Sanfilippo
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | - Yi Lu
- Statistical Genetics, QIMR Berghofer Medical Research Institute Royal Brisbane Hospital, Brisbane, Australia
| | - Ya Xing Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital University of Medical Science, Beijing, China
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Ozren Polašek
- Faculty of Medicine, University of Split, Split, Croatia
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, EH8 9AG UK
| | - Goran Bencic
- Department of Ophthalmology, Sisters of Mercy University Hospital, Zagreb, Croatia
| | - Alan F. Wright
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Juho Wedenoja
- Department of Public Health, Hjelt Institute, University of Helsinki, Helsinki, Finland
- Department of Ophthalmology, Helsinki University Central Hospital, Helsinki, Finland
| | - Tanja Zeller
- University Heart Center Hamburg, Clinic for general and interventional Cardiology, Hamburg, Germany
| | - Arne Schillert
- Institute for Medical Biometry and Statistics, Universität zu Lübeck, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Lübeck, Germany
| | - Alireza Mirshahi
- Department of Ophthalmology, University Medical Center Mainz, Mainz, Germany
- Dardenne Eye Hospital, Bonn, Germany
| | - Karl Lackner
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Mainz, Germany
| | - Shea Ping Yip
- Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hong Kong SAR, China
- Centre for Myopia Research, School of Optometry, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Maurice K. H. Yap
- Centre for Myopia Research, School of Optometry, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Janina S. Ried
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Federico Murgia
- Institute of Population Genetics CNR, Traversa La Crucca, 3-07040 Reg. Baldinca, Li Punti, Sassari, Italy
| | - James F. Wilson
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, EH8 9AG UK
| | - Brian Fleck
- Princess Alexandra Eye Pavilion, Edinburgh, EH3 9HA UK
| | - Seyhan Yazar
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | | | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, The Hague, The Netherlands
| | - André Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, The Hague, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, The Hague, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lennart Karssen
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ben A. Oostra
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Xin Zhou
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - E. Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Department of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
| | - Eranga Vithana
- Singapore Eye Research Institute, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Neuroscience and Behavioural Disorders (NBD) Program, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Veluchamy Barathi
- Singapore Eye Research Institute, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
| | | | | | - Kumari Neelam
- Singapore Eye Research Institute, Singapore, Singapore
| | - Youchan Shin
- Singapore Eye Research Institute, Singapore, Singapore
| | - Janice Lam
- Singapore Eye Research Institute, Singapore, Singapore
| | - Ekaterina Yonova-Doing
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Hospital Campus, London, UK
| | - Cristina Venturini
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Hospital Campus, London, UK
- Institute of Ophthalmology, University College London, London, UK
| | - S. Mohsen Hosseini
- Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, PGCRL Rm 12.9835, 686 Bay Street, Toronto, ON M5G 0A4 Canada
| | - Hoi-Suen Wong
- Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, PGCRL Rm 12.9835, 686 Bay Street, Toronto, ON M5G 0A4 Canada
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Filmlab laboratories, Tampere University Hospital and School of Medicine, University of Tampere, 33520 Tampere, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital and School of Medicine, University of Tampere, 33521 Tampere, Finland
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, 20041 Turku, Finland
| | - Nicholas J. Timpson
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, BS8 2BN UK
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
| | - David M. Evans
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, BS8 2BN UK
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
- Translational Research Institute, University of Queensland Diamantina Institute, Brisbane, QLD Australia
| | - Chiea-Chuen Khor
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Division of Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Tin Aung
- Singapore Eye Research Institute, Singapore, Singapore
| | - Terri L. Young
- Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
- Duke Eye Center, Duke University School of Medicine, Durham, NC USA
| | - Paul Mitchell
- University of Sydney, Sydney, Australia
- Western Sydney Local Health Network, Sydney, Australia
- Westmead Millennium Institute, Westmead, Australia
| | - Barbara Klein
- Ophthalmology and Visual Sciences, Ocular Epidemiology, University of Wisconsin-Madison, 610 North Walnut Street, Room 409, Madison, WI 53726 USA
| | | | - Thomas Meitinger
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Jost B. Jonas
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Lab, Beijing, China
- Department of Ophthalmology, Medical Faculty Mannheim of the Ruprecht-Karls-University of Heidelberg, Mannheim, Germany
| | - Paul N. Baird
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
| | - David A. Mackey
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | - Tien Yin Wong
- Singapore Eye Research Institute, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Office of Clinical Sciences, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Seang-Mei Saw
- Singapore Eye Research Institute, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
| | - Olavi Pärssinen
- Department of Health Sciences and Gerontology Research Center, University of Jyväskylä, Jyväskylä, Finland
- Department of Ophthalmology, Central Hospital of Central Finland, Jyväskylä, Finland
| | - Dwight Stambolian
- University of Pennsylvania School of Medicine, Rm. 314 Stellar Chance Labs, 422 Curie Blvd, Philadelphia, PA 19104 USA
| | - Christopher J. Hammond
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Hospital Campus, London, UK
- Department of Ophthalmology, King’s College London, St Thomas’ Hospital Campus, London, UK
| | - Caroline C. W. Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Cathy Williams
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
| | - Andrew D. Paterson
- Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, PGCRL Rm 12.9835, 686 Bay Street, Toronto, ON M5G 0A4 Canada
- Dala Lanna School of Public Health, University of Toronto, Toronto, ON Canada
| | - Joan E. Bailey-Wilson
- National Human Genome Research Institute, National Institutes of Health, 333 Cassell Drive Suite 1200, Baltimore, MD 21224 USA
| | - Jeremy A. Guggenheim
- Centre for Myopia Research, School of Optometry, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - The CREAM Consortium
- National Human Genome Research Institute, National Institutes of Health, 333 Cassell Drive Suite 1200, Baltimore, MD 21224 USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
- Wilmer Eye Institute, Johns Hopkins Medical Institutions, Baltimore, MD USA
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Hospital Campus, London, UK
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Singapore Eye Research Institute, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Office of Clinical Sciences, Duke-NUS Graduate Medical School, Singapore, Singapore
- Department of Ophthalmology, University Medical Center Mainz, Mainz, Germany
- Klinik Pallas, Olten, Switzerland
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
- Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Department of Clinical Chemistry, Filmlab laboratories, Tampere University Hospital and School of Medicine, University of Tampere, 33520 Tampere, Finland
- Statistical Genetics, QIMR Berghofer Medical Research Institute Royal Brisbane Hospital, Brisbane, Australia
- Institute of Population Genetics CNR, Traversa La Crucca, 3-07040 Reg. Baldinca, Li Punti, Sassari, Italy
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, BS8 2BN UK
- School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN UK
- Centre of Epidemiology and Biostatistics, UCL Institute of Child Health, London, UK
- Institute of Ophthalmology, University College London, London, UK
- Ulverscroft Vision Research Group, UCL Institute of Child Health, London, UK
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute Royal Brisbane Hospital, Brisbane, Australia
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital University of Medical Science, Beijing, China
- Faculty of Medicine, University of Split, Split, Croatia
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, EH8 9AG UK
- Department of Ophthalmology, Sisters of Mercy University Hospital, Zagreb, Croatia
- Department of Public Health, Hjelt Institute, University of Helsinki, Helsinki, Finland
- Department of Ophthalmology, Helsinki University Central Hospital, Helsinki, Finland
- University Heart Center Hamburg, Clinic for general and interventional Cardiology, Hamburg, Germany
- Institute for Medical Biometry and Statistics, Universität zu Lübeck, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Kiel/Lübeck, Lübeck, Germany
- Dardenne Eye Hospital, Bonn, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Mainz, Germany
- Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hong Kong SAR, China
- Centre for Myopia Research, School of Optometry, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
- Princess Alexandra Eye Pavilion, Edinburgh, EH3 9HA UK
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, The Hague, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
- Department of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
- Neuroscience and Behavioural Disorders (NBD) Program, Duke-NUS Graduate Medical School, Singapore, Singapore
- Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, PGCRL Rm 12.9835, 686 Bay Street, Toronto, ON M5G 0A4 Canada
- Department of Clinical Physiology, Tampere University Hospital and School of Medicine, University of Tampere, 33521 Tampere, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, 20041 Turku, Finland
- Translational Research Institute, University of Queensland Diamantina Institute, Brisbane, QLD Australia
- Division of Human Genetics, Genome Institute of Singapore, Singapore, Singapore
- Duke Eye Center, Duke University School of Medicine, Durham, NC USA
- University of Sydney, Sydney, Australia
- Western Sydney Local Health Network, Sydney, Australia
- Westmead Millennium Institute, Westmead, Australia
- Ophthalmology and Visual Sciences, Ocular Epidemiology, University of Wisconsin-Madison, 610 North Walnut Street, Room 409, Madison, WI 53726 USA
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Lab, Beijing, China
- Department of Ophthalmology, Medical Faculty Mannheim of the Ruprecht-Karls-University of Heidelberg, Mannheim, Germany
- Department of Health Sciences and Gerontology Research Center, University of Jyväskylä, Jyväskylä, Finland
- Department of Ophthalmology, Central Hospital of Central Finland, Jyväskylä, Finland
- University of Pennsylvania School of Medicine, Rm. 314 Stellar Chance Labs, 422 Curie Blvd, Philadelphia, PA 19104 USA
- Department of Ophthalmology, King’s College London, St Thomas’ Hospital Campus, London, UK
- Dala Lanna School of Public Health, University of Toronto, Toronto, ON Canada
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Hassan MA, Saeij JP. Incorporating alternative splicing and mRNA editing into the genetic analysis of complex traits. Bioessays 2014; 36:1032-40. [PMID: 25171292 PMCID: PMC4280019 DOI: 10.1002/bies.201400079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The nomination of candidate genes underlying complex traits is often focused on genetic variations that alter mRNA abundance or result in non-conservative changes in amino acids. Although inconspicuous in complex trait analysis, genetic variants that affect splicing or RNA editing can also generate proteomic diversity and impact genetic traits. Indeed, it is known that splicing and RNA editing modulate several traits in humans and model organisms. Using high-throughput RNA sequencing (RNA-seq) analysis, it is now possible to integrate the genetics of transcript abundance, alternative splicing (AS) and editing with the analysis of complex traits. We recently demonstrated that both AS and mRNA editing are modulated by genetic and environmental factors, and potentially engender phenotypic diversity in a genetically segregating mouse population. Therefore, the analysis of splicing and RNA editing can expand not only the regulatory landscape of transcriptome and proteome complexity, but also the repertoire of candidate genes for complex traits.
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Affiliation(s)
- Musa A. Hassan
- Massachusetts Institute of Technology, Department of Biology, Cambridge, MA, USA
| | - Jeroen P.J. Saeij
- Massachusetts Institute of Technology, Department of Biology, Cambridge, MA, USA
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40
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Leslie R, O'Donnell CJ, Johnson AD. GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database. Bioinformatics 2014; 30:i185-94. [PMID: 24931982 DOI: 10.1093/bioinformatics/btu273] [Citation(s) in RCA: 179] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
SUMMARY We created a deeply extracted and annotated database of genome-wide association studies (GWAS) results. GRASP v1.0 contains >6.2 million SNP-phenotype association from among 1390 GWAS studies. We re-annotated GWAS results with 16 annotation sources including some rarely compared to GWAS results (e.g. RNAediting sites, lincRNAs, PTMs). MOTIVATION To create a high-quality resource to facilitate further use and interpretation of human GWAS results in order to address important scientific questions. RESULTS GWAS have grown exponentially, with increases in sample sizes and markers tested, and continuing bias toward European ancestry samples. GRASP contains >100 000 phenotypes, roughly: eQTLs (71.5%), metabolite QTLs (21.2%), methylation QTLs (4.4%) and diseases, biomarkers and other traits (2.8%). cis-eQTLs, meQTLs, mQTLs and MHC region SNPs are highly enriched among significant results. After removing these categories, GRASP still contains a greater proportion of studies and results than comparable GWAS catalogs. Cardiovascular disease and related risk factors pre-dominate remaining GWAS results, followed by immunological, neurological and cancer traits. Significant results in GWAS display a highly gene-centric tendency. Sex chromosome X (OR = 0.18[0.16-0.20]) and Y (OR = 0.003[0.001-0.01]) genes are depleted for GWAS results. Gene length is correlated with GWAS results at nominal significance (P ≤ 0.05) levels. We show this gene-length correlation decays at increasingly more stringent P-value thresholds. Potential pleotropic genes and SNPs enriched for multi-phenotype association in GWAS are identified. However, we note possible population stratification at some of these loci. Finally, via re-annotation we identify compelling functional hypotheses at GWAS loci, in some cases unrealized in studies to date. CONCLUSION Pooling summary-level GWAS results and re-annotating with bioinformatics predictions and molecular features provides a good platform for new insights. AVAILABILITY The GRASP database is available at http://apps.nhlbi.nih.gov/grasp.
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Affiliation(s)
- Richard Leslie
- Cardiovascular Epidemiology and Human Genomics Branch, National Heart, Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, University of Massachusetts Medical School, Worcester, MA 01655 and Division of Cardiology, Massachusetts General Hospital, Boston, MA 02114, USACardiovascular Epidemiology and Human Genomics Branch, National Heart, Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, University of Massachusetts Medical School, Worcester, MA 01655 and Division of Cardiology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Christopher J O'Donnell
- Cardiovascular Epidemiology and Human Genomics Branch, National Heart, Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, University of Massachusetts Medical School, Worcester, MA 01655 and Division of Cardiology, Massachusetts General Hospital, Boston, MA 02114, USACardiovascular Epidemiology and Human Genomics Branch, National Heart, Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, University of Massachusetts Medical School, Worcester, MA 01655 and Division of Cardiology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Andrew D Johnson
- Cardiovascular Epidemiology and Human Genomics Branch, National Heart, Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, University of Massachusetts Medical School, Worcester, MA 01655 and Division of Cardiology, Massachusetts General Hospital, Boston, MA 02114, USA
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41
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Simpson CL, Wojciechowski R, Oexle K, Murgia F, Portas L, Li X, Verhoeven VJM, Vitart V, Schache M, Hosseini SM, Hysi PG, Raffel LJ, Cotch MF, Chew E, Klein BEK, Klein R, Wong TY, van Duijn CM, Mitchell P, Saw SM, Fossarello M, Wang JJ, Polašek O, Campbell H, Rudan I, Oostra BA, Uitterlinden AG, Hofman A, Rivadeneira F, Amin N, Karssen LC, Vingerling JR, Döring A, Bettecken T, Bencic G, Gieger C, Wichmann HE, Wilson JF, Venturini C, Fleck B, Cumberland PM, Rahi JS, Hammond CJ, Hayward C, Wright AF, Paterson AD, Baird PN, Klaver CCW, Rotter JI, Pirastu M, Meitinger T, Bailey-Wilson JE, Stambolian D. Genome-wide meta-analysis of myopia and hyperopia provides evidence for replication of 11 loci. PLoS One 2014; 9:e107110. [PMID: 25233373 PMCID: PMC4169415 DOI: 10.1371/journal.pone.0107110] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 08/12/2014] [Indexed: 01/01/2023] Open
Abstract
Refractive error (RE) is a complex, multifactorial disorder characterized by a mismatch between the optical power of the eye and its axial length that causes object images to be focused off the retina. The two major subtypes of RE are myopia (nearsightedness) and hyperopia (farsightedness), which represent opposite ends of the distribution of the quantitative measure of spherical refraction. We performed a fixed effects meta-analysis of genome-wide association results of myopia and hyperopia from 9 studies of European-derived populations: AREDS, KORA, FES, OGP-Talana, MESA, RSI, RSII, RSIII and ERF. One genome-wide significant region was observed for myopia, corresponding to a previously identified myopia locus on 8q12 (p = 1.25×10(-8)), which has been reported by Kiefer et al. as significantly associated with myopia age at onset and Verhoeven et al. as significantly associated to mean spherical-equivalent (MSE) refractive error. We observed two genome-wide significant associations with hyperopia. These regions overlapped with loci on 15q14 (minimum p value = 9.11×10(-11)) and 8q12 (minimum p value 1.82×10(-11)) previously reported for MSE and myopia age at onset. We also used an intermarker linkage- disequilibrium-based method for calculating the effective number of tests in targeted regional replication analyses. We analyzed myopia (which represents the closest phenotype in our data to the one used by Kiefer et al.) and showed replication of 10 additional loci associated with myopia previously reported by Kiefer et al. This is the first replication of these loci using myopia as the trait under analysis. "Replication-level" association was also seen between hyperopia and 12 of Kiefer et al.'s published loci. For the loci that show evidence of association to both myopia and hyperopia, the estimated effect of the risk alleles were in opposite directions for the two traits. This suggests that these loci are important contributors to variation of refractive error across the distribution.
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Affiliation(s)
- Claire L. Simpson
- National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Robert Wojciechowski
- National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States of America
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Konrad Oexle
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Federico Murgia
- Institute of Population Genetics, National Research Council of Italy, Sassari, Italy
| | - Laura Portas
- Institute of Population Genetics, National Research Council of Italy, Sassari, Italy
| | - Xiaohui Li
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Virginie J. M. Verhoeven
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Veronique Vitart
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, United Kingdom
| | - Maria Schache
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
| | - S. Mohsen Hosseini
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, and DCCT/EDIC Research Group, The Diabetes Control and Complications Trial and Follow-up Study, The Biostatistics Center, The George Washington University, Rockville, Maryland, United States of America
| | - Pirro G. Hysi
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, London, United Kingdom
| | - Leslie J. Raffel
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Mary Frances Cotch
- Division of Epidemiology and Clinical Applications, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Emily Chew
- Division of Epidemiology and Clinical Applications, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Barbara E. K. Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Tien Yin Wong
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Singapore Eye Research Institute, National University of Singapore, Singapore, Singapore
| | | | - Paul Mitchell
- Centre for Vision Research, Department of Ophthalmology and Westmead Millennium Institute, University of Sydney, Sydney, Australia
| | - Seang Mei Saw
- Department of Epidemiology and Public Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Maurizio Fossarello
- Dipartimento di Scienze Chirurgiche, Clinica Oculistica Universita' degli studi di Cagliari, Cagliari, Italy
| | - Jie Jin Wang
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- Centre for Vision Research, Department of Ophthalmology and Westmead Millennium Institute, University of Sydney, Sydney, Australia
| | - DCCT/EDIC Research Group
- The Diabetes Control and Complications Trial and Follow-up Study, The Biostatistics Center, The George Washington University, Rockville, Maryland, United States of America
| | - Ozren Polašek
- Croatian Centre for Global Health, University of Split Medical School, Split, Croatia
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Igor Rudan
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - 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
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Netherlands Consortium for Healthy Ageing, Netherlands Genomics Initiative, The Hague, the Netherlands
| | - 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
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Lennart C. Karssen
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Johannes R. Vingerling
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Angela Döring
- Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Thomas Bettecken
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Goran Bencic
- Department of Ophthalmology, Hospital “Sestre Milosrdnice”, Zagreb, Croatia
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - H.-Erich Wichmann
- Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - James F. Wilson
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Cristina Venturini
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, London, United Kingdom
| | - Brian Fleck
- Princess Alexandra Eye Pavilion, Edinburgh, United Kingdom
| | - Phillippa M. Cumberland
- MRC Centre of Epidemiology for Child Health, Institute of Child Health, University College London, London, United Kingdom
| | - Jugnoo S. Rahi
- MRC Centre of Epidemiology for Child Health, Institute of Child Health, University College London, London, United Kingdom
- Institute of Ophthalmology, University College London, London, United Kingdom
- Ulverscroft Vision Research Group, Institute of Child Health, University College London, London, United Kingdom
| | - Chris J. Hammond
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital, London, United Kingdom
| | - Caroline Hayward
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, United Kingdom
| | - Alan F. Wright
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew D. Paterson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, and DCCT/EDIC Research Group, The Diabetes Control and Complications Trial and Follow-up Study, The Biostatistics Center, The George Washington University, Rockville, Maryland, United States of America
| | - Paul N. Baird
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
| | - Caroline C. W. Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Mario Pirastu
- Institute of Population Genetics, National Research Council of Italy, Sassari, Italy
| | - Thomas Meitinger
- Institute of Human Genetics, Technische Universität München, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Joan E. Bailey-Wilson
- National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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Orchestration of neurodevelopmental programs by RBFOX1: implications for autism spectrum disorder. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2014; 113:251-67. [PMID: 24290388 DOI: 10.1016/b978-0-12-418700-9.00008-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Neurodevelopmental and neuropsychiatric disorders result from complex interactions between critical genetic factors and as-yet-unknown environmental components. To gain clinical insight, it is critical to develop a comprehensive understanding of these genetic components. RBFOX1, an RNA splicing factor, regulates expression of large genetic networks during early neuronal development, and haploinsufficiency causes severe neurodevelopmental phenotypes including autism spectrum disorder (ASD), intellectual disability, and epilepsy. Genomic testing in individuals and large patient cohorts has identified phenotypically similar cases possessing copy number variations in RBFOX1, implicating the gene as an important cause of neurodevelopmental disease. However, a significant proportion of the observed structural variation is inherited from phenotypically normal individuals, raising questions regarding overall pathogenicity of variation at the RBFOX1 locus. In this chapter, we discuss the molecular, cellular, and clinical evidence supporting the role of RBFOX1 in neurodevelopment and present a comprehensive model for the contribution of structural variation in RBFOX1 to ASD.
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Abstract
PURPOSE The PAX6 gene is among the most studied genes in high myopia, but reported findings of association studies on PAX6 and high myopia are inconsistent. We conducted a systematic review and meta-analysis to evaluate the association of PAX6 polymorphisms and high myopia. METHODS All case-control association studies on PAX6 and high myopia reported in EMBASE and MEDLINE were retrieved. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated for single-nucleotide polymorphisms (SNPs) that have been involved in at least two studies. Heterogeneity and publication bias analyses were also conducted. RESULTS There were totally 63 publications on PAX6 and myopia. Among them, six articles met all the inclusion criteria, involving 3626 patients and 3262 controls of Asian ancestry. Five PAX6 SNPs, rs3026354, rs667773, rs2071754, rs644242, and rs3026393, were meta-analyzed in high myopia and two, rs667773 and rs644242, in extreme myopia. Single-nucleotide polymorphism rs644242 was associated with high myopia in the dominant model (OR = 0.87; 95% CI, 0.76 to 0.99; p = 0.035) and heterozygous model (OR = 0.85; 95% CI, 0.74 to 0.97; p = 0.019) and with extreme myopia in the dominant model (OR = 0.79; 95% CI, 0.65 to 0.95; p = 0.015), allelic model (OR = 0.81; 95% CI, 0.68 to 0.96; p = 0.014), and heterozygous model (OR = 0.80; 95% CI, 0.65 to 0.97; p = 0.024). However, the associations cannot withstand Bonferroni correction (p > 0.005). The other four SNPs did not show significant association with high myopia. CONCLUSIONS Meta-analysis of existing data revealed a suggestive association of PAX6 rs644242 with extreme and high myopia, which awaits validation in further studies. Nevertheless, PAX6 may only confer a small effect to myopia development.
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Aboobakar IF, Allingham RR. Developments in Ocular Genetics: 2013 Annual Review. Asia Pac J Ophthalmol (Phila) 2014; 3:181-93. [PMID: 25097799 PMCID: PMC4119463 DOI: 10.1097/apo.0000000000000063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
PURPOSE To highlight major advancements in ocular genetics from the year 2013. DESIGN Literature review. METHODS A literature search was conducted on PubMed to identify articles pertaining to genetic influences on human eye diseases. This review focuses on manuscripts published in print or online in the English language between January 1, 2013 and December 31, 2013. A total of 120 papers from 2013 were included in this review. RESULTS Significant progress has been made in our understanding of the genetic basis of a broad group of ocular disorders, including glaucoma, age-related macular degeneration, cataract, diabetic retinopathy, keratoconus, Fuchs' endothelial dystrophy, and refractive error. CONCLUSIONS The latest next-generation sequencing technologies have become extremely effective tools for identifying gene mutations associated with ocular disease. These technological advancements have also paved the way for utilization of genetic information in clinical practice, including disease diagnosis, prediction of treatment response and molecular interventions guided by gene-based knowledge.
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Affiliation(s)
- Inas F Aboobakar
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, USA
| | - R Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, USA
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Cooke Bailey JN, Sobrin L, Pericak-Vance MA, Haines JL, Hammond CJ, Wiggs JL. Advances in the genomics of common eye diseases. Hum Mol Genet 2013; 22:R59-65. [PMID: 23962718 DOI: 10.1093/hmg/ddt396] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Genome-wide association studies (GWAS) and other genomic technologies have accelerated the discovery of genes and genomic regions contributing to common human ocular disorders with complex inheritance. Age-related macular degeneration (AMD), diabetic retinopathy (DR), glaucoma and myopia account for the majority of visual impairment worldwide. Over 19 genes and/or genomic regions have been associated with AMD. Current investigations are assessing the clinical utility of risk score panels and therapies targeting disease-specific pathways. DR is the leading cause of blindness in the United States and globally is a major cause of vision loss. Genomic investigations have identified molecular pathways associated with DR in animal models which could suggest novel therapeutic targets. Three types of glaucoma, primary-open-angle glaucoma (POAG), angle-closure glaucoma and exfoliation syndrome (XFS) glaucoma, are common age-related conditions. Five genomic regions have been associated with POAG, three with angle-closure glaucoma and one with XFS. Myopia causes substantial ocular morbidity throughout the world. Recent large GWAS have identified >20 associated loci for this condition. In this report, we present a comprehensive overview of the genes and genomic regions contributing to disease susceptibility for these common blinding ocular disorders and discuss the next steps toward translation to effective gene-based screening tests and novel therapies targeting the molecular events contributing to disease.
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Khor CC, Miyake M, Chen LJ, Shi Y, Barathi VA, Qiao F, Nakata I, Yamashiro K, Zhou X, Tam POS, Cheng CY, Tai ES, Vithana EN, Aung T, Teo YY, Wong TY, Moriyama M, Ohno-Matsui K, Mochizuki M, Matsuda F, Yong RYY, Yap EPH, Yang Z, Pang CP, Saw SM, Yoshimura N. Genome-wide association study identifies ZFHX1B as a susceptibility locus for severe myopia. Hum Mol Genet 2013; 22:5288-94. [PMID: 23933737 DOI: 10.1093/hmg/ddt385] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Severe myopia (defined as spherical equivalent < -6.0 D) is a predominant problem in Asian countries, resulting in substantial morbidity. We performed a meta-analysis of four genome-wide association studies (GWAS), all of East Asian descent totaling 1603 cases and 3427 controls. Two single nucleotide polymorphisms (SNPs) (rs13382811 from ZFHX1B [encoding for ZEB2] and rs6469937 from SNTB1) showed highly suggestive evidence of association with disease (P < 1 × 10(-7)) and were brought forward for replication analysis in a further 1241 severe myopia cases and 3559 controls from a further three independent sample collections. Significant evidence of replication was observed, and both SNP markers surpassed the formal threshold for genome-wide significance upon meta-analysis of both discovery and replication stages (P = 5.79 × 10(-10), per-allele odds ratio (OR) = 1.26 for rs13382811 and P = 2.01 × 10(-9), per-allele OR = 0.79 for rs6469937). The observation at SNTB1 is confirmatory of a very recent GWAS on severe myopia. Both genes were expressed in the human retina, sclera, as well as the retinal pigmented epithelium. In an experimental mouse model for myopia, we observed significant alterations to gene and protein expression in the retina and sclera of the unilateral induced myopic eyes for Zfhx1b and Sntb1. These new data advance our understanding of the molecular pathogenesis of severe myopia.
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Affiliation(s)
- Chiea Chuen Khor
- Division of Human Genetics, Genome Institute of Singapore, Singapore, Singapore
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Stambolian D. Genetic susceptibility and mechanisms for refractive error. Clin Genet 2013; 84:102-8. [PMID: 23647423 DOI: 10.1111/cge.12180] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 04/29/2013] [Accepted: 04/29/2013] [Indexed: 12/19/2022]
Abstract
Refractive errors, myopia and hyperopia, are the most common causes of visual impairment worldwide. Recent advances in genetics have been utilized to identify a wealth of genetic loci believed to contain susceptibility genes for refractive error (RE). The current genetic evidence confirms that RE is influenced by both common and rare variants with a significant environmental component. These studies argue that only by combining genetic and environmental knowledge with in vivo measurements of biological states will it be possible to understand the underlying biology of RE that will lead to novel therapeutic targets and accurate genetic predictions.
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Affiliation(s)
- D Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Zhao F, Wu J, Xue A, Su Y, Wang X, Lu X, Zhou Z, Qu J, Zhou X. Exome sequencing reveals CCDC111 mutation associated with high myopia. Hum Genet 2013; 132:913-21. [DOI: 10.1007/s00439-013-1303-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 04/02/2013] [Indexed: 11/28/2022]
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