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Wiggs JL, Pasquale LR. Genetics of glaucoma. Hum Mol Genet 2017; 26:R21-R27. [PMID: 28505344 DOI: 10.1093/hmg/ddx184] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 05/08/2017] [Indexed: 12/15/2022] Open
Abstract
Genetic and genomic studies, including genome-wide association studies (GWAS) have accelerated the discovery of genes contributing to glaucoma, the leading cause of irreversible blindness world-wide. Glaucoma can occur at all ages, with Mendelian inheritance typical for the rare early onset disease (before age 40) and complex inheritance evident in common adult-onset forms of disease. Recent studies have suggested possible therapeutic targets for some patients with early-onset glaucoma based on the molecular and cellular events caused by MYOC, OPTN and TBK1 mutations. Diagnostic genetic tests using early-onset glaucoma genes are also proving useful for pre-symptomatic disease detection and genetic counseling. Recent GWAS completed for three types of common adult-onset glaucoma have identified novel loci for POAG (primary-open-angle glaucoma) (ABCA1, AFAP1, GMDS, PMM2, TGFBR3, FNDC3B, ARHGEF12, GAS7, FOXC1, ATXN2, TXNRD2); PACG (primary angle-closure glaucoma (EPDR1, CHAT, GLIS3, FERMT2, DPM2-FAM102); and exfoliation syndrome (XFS) glaucoma (CACNA1A). In total sixteen genomic regions have been associated with POAG (including the normal tension glaucoma (NTG) subgroup), 8 with PACG and 2 with XFS. These studies are defining important biological pathways and processes that contribute to disease pathogenesis.
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Affiliation(s)
- Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear, Boston, MA 02114, USA
| | - Louis R Pasquale
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear, Boston, MA 02114, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02114, USA
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A Multi-Locus Genetic Risk Score for Primary Open-Angle Glaucoma (POAG) Variants Is Associated with POAG Risk in a Mediterranean Population: Inverse Correlations with Plasma Vitamin C and E Concentrations. Int J Mol Sci 2017; 18:ijms18112302. [PMID: 29104244 PMCID: PMC5713272 DOI: 10.3390/ijms18112302] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 10/25/2017] [Accepted: 10/29/2017] [Indexed: 12/28/2022] Open
Abstract
Primary open-angle glaucoma (POAG) is a leading cause of blindness worldwide. The genetics of POAG are complex, and population-specific effects have been reported. Although many polymorphisms associated with POAG risk have been reported, few studies have analyzed their additive effects. We investigated, in a southern European Mediterranean population, the association between relevant POAG polymorphisms, identified by initial genome-wide association studies (GWASs) and POAG risk, both separately and as an aggregated multi-locus genetic risk score (GRS). Also, bearing in mind that oxidative stress is a factor increasingly recognized in the pathogenesis of POAG, we analyzed the potential association of the GRS with plasma concentrations of antioxidant vitamins (C and E). We carried out a case–control study including 391 POAG cases and 383 healthy controls, and analyzed four genetic polymorphisms (rs4656461-TMCO1, rs4236601-CAV1/CAV2, rs2157719-CDKN2B-AS1 and rs3088440-CDKN2A). An unweighted GRS including the four non-linked polymorphisms was constructed. A strong association between the GRS and POAG risk was found. When three categories of the GRS were considered, subjects in the top category of the GRS were 2.92 (95% confidence interval (CI): 1.79–4.77) times more likely to have POAG compared with participants in the bottom category (p < 0.001). Moreover, the GRS was inversely correlated with plasma vitamin C (p = 0.002) and vitamin E (p = 0.001) concentrations, even after additional adjustment for POAG status. In conclusion, we have found a strong association between the GRS and POAG risk in this Mediterranean population. While the additional correlation found between GRS and low levels of vitamins C and E does not indicated a causal relationship, it does suggest the need for new and deeper research into the effects of oxidative stress as a potential mechanism for those associations.
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Gong B, Shi Y, Qu C, Ye Z, Yin Y, Tan C, Shuai P, Li J, Guo X, Cheng Y, Yang Z, Lin Y, Liu X. Association of catalase polymorphisms with primary open-angle glaucoma in a Chinese population. Ophthalmic Genet 2017; 39:35-40. [PMID: 28829657 DOI: 10.1080/13816810.2017.1342132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
PURPOSE Many genes have been associated with primary open-angle glaucoma (POAG). This study was conducted to investigate whether catalase (CAT) polymorphisms play a significant role in POAG in a Chinese population. METHODS A cohort of 416 unrelated POAG patients and 997 unrelated control subjects was included in this case-control association study. CAT functional single-nucleotide polymorphisms (SNPs), including rs1001179, rs7943316, and rs769217, were genotyped by SNaPshot method. The genotype and allele frequencies were evaluated using the χ2 tests. The linkage disequilibrium (LD) and haplotype block structure association were examined using the program Haploview (Broad Institute, Cambridge, MA). RESULTS There was a statistically significant difference for CAT functional SNP rs769217 between POAG cases and controls in the allelic model (p = 0.004, OR = 1.27, 95% CI 1.08-1.49). At this SNP, the allele frequency of the C allele in POAG cases was 0.587, which was higher than that in controls (0.528). However, no association was found for rs1001179 and rs7943316 with POAG. Pairwise LD analysis showed high LD between rs769217 and rs7943316 (D' = 0.857, r2 = 0.252, confidence bounds 0.71-0.93). After the association analysis for haplotype block structure generated from rs769217 with rs7943316, the data showed no significant association between the cases and controls. CONCLUSIONS This study showed that CAT functional SNP rs769217 was significantly associated with POAG, implying that the CAT gene variants may play a role in the pathogenesis of POAG in the Chinese population.
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Affiliation(s)
- Bo Gong
- a Sichuan Key Laboratory for Disease Gene Study, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital , University of Electronic Science and Technology of China , Chengdu , China.,b Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital , University of Electronic Science and Technology of China , Chengdu , China
| | - Yi Shi
- a Sichuan Key Laboratory for Disease Gene Study, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital , University of Electronic Science and Technology of China , Chengdu , China.,b Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital , University of Electronic Science and Technology of China , Chengdu , China
| | - Chao Qu
- c Department of Ophthalmology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital , University of Electronic Science and Technology of China , Chengdu , China
| | - Zimeng Ye
- a Sichuan Key Laboratory for Disease Gene Study, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital , University of Electronic Science and Technology of China , Chengdu , China
| | - Yilin Yin
- d Department of Biology, Northeastern University , Boston , MA , USA
| | - Chang Tan
- a Sichuan Key Laboratory for Disease Gene Study, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital , University of Electronic Science and Technology of China , Chengdu , China
| | - Ping Shuai
- a Sichuan Key Laboratory for Disease Gene Study, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital , University of Electronic Science and Technology of China , Chengdu , China
| | - Jing Li
- c Department of Ophthalmology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital , University of Electronic Science and Technology of China , Chengdu , China
| | - Xiaoxin Guo
- a Sichuan Key Laboratory for Disease Gene Study, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital , University of Electronic Science and Technology of China , Chengdu , China
| | - Yilian Cheng
- c Department of Ophthalmology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital , University of Electronic Science and Technology of China , Chengdu , China
| | - Zhenglin Yang
- a Sichuan Key Laboratory for Disease Gene Study, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital , University of Electronic Science and Technology of China , Chengdu , China.,b Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital , University of Electronic Science and Technology of China , Chengdu , China
| | - Ying Lin
- a Sichuan Key Laboratory for Disease Gene Study, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital , University of Electronic Science and Technology of China , Chengdu , China.,b Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital , University of Electronic Science and Technology of China , Chengdu , China.,e Clinical Laboratory of Tianfu New Area People's Hospital , Chengdu , China
| | - Xiaoqi Liu
- a Sichuan Key Laboratory for Disease Gene Study, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital , University of Electronic Science and Technology of China , Chengdu , China.,b Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital , University of Electronic Science and Technology of China , Chengdu , China.,f School of Materials Science and Engineering, Southwest Jiaotong University , Chengdu , Sichuan , China
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He S, Stankowska DL, Ellis DZ, Krishnamoorthy RR, Yorio T. Targets of Neuroprotection in Glaucoma. J Ocul Pharmacol Ther 2017; 34:85-106. [PMID: 28820649 DOI: 10.1089/jop.2017.0041] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Progressive neurodegeneration of the optic nerve and the loss of retinal ganglion cells is a hallmark of glaucoma, the leading cause of irreversible blindness worldwide, with primary open-angle glaucoma (POAG) being the most frequent form of glaucoma in the Western world. While some genetic mutations have been identified for some glaucomas, those associated with POAG are limited and for most POAG patients, the etiology is still unclear. Unfortunately, treatment of this neurodegenerative disease and other retinal degenerative diseases is lacking. For POAG, most of the treatments focus on reducing aqueous humor formation, enhancing uveoscleral or conventional outflow, or lowering intraocular pressure through surgical means. These efforts, in some cases, do not always lead to a prevention of vision loss and therefore other strategies are needed to reduce or reverse the progressive neurodegeneration. In this review, we will highlight some of the ocular pharmacological approaches that are being tested to reduce neurodegeneration and provide some form of neuroprotection.
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Affiliation(s)
- Shaoqing He
- North Texas Eye Research Institute, University of North Texas Health Science Center , Fort Worth, Texas
| | - Dorota L Stankowska
- North Texas Eye Research Institute, University of North Texas Health Science Center , Fort Worth, Texas
| | - Dorette Z Ellis
- North Texas Eye Research Institute, University of North Texas Health Science Center , Fort Worth, Texas
| | - Raghu R Krishnamoorthy
- North Texas Eye Research Institute, University of North Texas Health Science Center , Fort Worth, Texas
| | - Thomas Yorio
- North Texas Eye Research Institute, University of North Texas Health Science Center , Fort Worth, Texas
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Yoshikawa M, Yamashiro K, Nakanishi H, Miyata M, Miyake M, Hosoda Y, Tabara Y, Matsuda F, Yoshimura N. Association of SIX1/SIX6 locus polymorphisms with regional circumpapillary retinal nerve fibre layer thickness: The Nagahama study. Sci Rep 2017; 7:4393. [PMID: 28663559 PMCID: PMC5491508 DOI: 10.1038/s41598-017-02299-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 04/07/2017] [Indexed: 12/23/2022] Open
Abstract
SIX1 and SIX6 are glaucoma susceptibility genes. Previous reports indicate that the single nucleotide polymorphism (SNP) rs33912345 in SIX6 is associated with inferior circumpapillary retinal nerve fibre layer (cpRNFL) thickness (cpRNFLT). Although the region of visual field defect in glaucoma patients is directly related to cpRNFL thinning, a detailed sector analysis has not been performed in genetic association studies. In the present study, we evaluated 26 tagging SNPs in the SIX1/SIX6 locus ±50 kb region in a population of 2,306 Japanese subjects with 4- and 32-sector cpRNFLT analysis. While no SNPs showed a significant association with cpRNFLT in the 4-sectored analysis, the finer 32-sector assessment clearly showed a significant association between rs33912345 in the SIX1/SIX6 locus with inferior cpRNFL thinning at 292.5-303.8° (β = -4.55, P = 3.0 × 10-5). Furthermore, the fine-sectored cpRNFLT analysis indicated that SIX1/SIX6 polymorphisms would affect cpRNFL thinning at 281.3-303.8°, which corresponds to parafoveal scotoma in a visual field test of glaucoma patients.
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Affiliation(s)
- Munemitsu Yoshikawa
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, 54 Kawahara, Shogoin, Sakyo, Kyoto, 606-8507, Japan
| | - Kenji Yamashiro
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, 54 Kawahara, Shogoin, Sakyo, Kyoto, 606-8507, Japan. .,Department of Ophthalmology, Otsu Red Cross Hospital, 1-1-35 Nagara, Otsu, 520-8511, Japan.
| | - Hideo Nakanishi
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, 54 Kawahara, Shogoin, Sakyo, Kyoto, 606-8507, Japan
| | - Manabu Miyata
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, 54 Kawahara, Shogoin, Sakyo, Kyoto, 606-8507, Japan
| | - Masahiro Miyake
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, 54 Kawahara, Shogoin, Sakyo, Kyoto, 606-8507, Japan.,Center for Genomic Medicine, Kyoto University Graduate School of Medicine, 54 Kawahara, Shogoin, Sakyo, Kyoto, 606-8507, Japan
| | - Yoshikatsu Hosoda
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, 54 Kawahara, Shogoin, Sakyo, Kyoto, 606-8507, Japan
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, 54 Kawahara, Shogoin, Sakyo, Kyoto, 606-8507, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, 54 Kawahara, Shogoin, Sakyo, Kyoto, 606-8507, Japan
| | - Nagahisa Yoshimura
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, 54 Kawahara, Shogoin, Sakyo, Kyoto, 606-8507, Japan
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Liu K, He W, Zhao J, Zeng Y, Cheng H. Association of WDR36 polymorphisms with primary open angle glaucoma: A systematic review and meta-analysis. Medicine (Baltimore) 2017; 96:e7291. [PMID: 28658128 PMCID: PMC5500050 DOI: 10.1097/md.0000000000007291] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The association of the WDR36 gene with glaucoma has been controversial in the literature. We therefore conducted a systematic review and meta-analysis to assess the association of all reported common polymorphisms in WDR36 with primary open angle glaucoma (POAG) and its subtypes: high tension glaucoma (HTG) and normal tension glaucoma (NTG). METHODS Publications in PUBMED and EMBASE databases up to March 9, 2016 were searched for case-control association studies of WDR36 with POAG, HTG, and/or NTG. Reported studies giving adequate genotype and/or allele information were included. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) of individual polymorphisms were estimated using the allelic model. RESULTS Our literature search yielded 122 records, among which 5 studies were eligible for meta-analysis, involving a total of 1352 POAG patients and 894 controls. Five WDR36 polymorphisms were meta-analyzed, rs11241095, rs10038177, rs17553936, rs13186912, and rs13153937. However, none of them was significantly associated with POAG, HTG, or NTG. The most-investigated polymorphisms, rs11241095 and rs10038177, had a pooled-OR of 1.09 (95% CI: 0.94-1.28, P = .25, I = 0) and 0.99 (95% CI: 0.71-1.39, P = .97, I = 77%), respectively, for POAG. CONCLUSION The existing data in the literature do not support a significant role of WDR36 in the genetic susceptibility of POAG or its subtypes. Further replication studies in specific populations are warranted.
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Affiliation(s)
- Ke Liu
- Shenzhen Key Laboratory of Ophthalmology, Shenzhen Eye Hospital Affiliated to Jinan University School of Ophthalmology & Optometry Affiliated to Shenzhen University, Shenzhen, Guangdong, China
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Hu Z, He C. CDKN2B gene rs1063192 polymorphism decreases the risk of glaucoma. Oncotarget 2017; 8:21167-21176. [PMID: 28416752 PMCID: PMC5400574 DOI: 10.18632/oncotarget.15504] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/08/2017] [Indexed: 01/07/2023] Open
Abstract
The aim of this meta-analysis was to evaluate the association between cyclin-dependent kinase Inhibitor-2B (CDKN2B) gene rs1063192 polymorphism and glaucoma risk. We searched the databases of PubMed, and Embase. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by using fixed-effect or random-effect models. A total of 14 case-control studies involving 11,316 cases and 24,055 controls were included. Meta-analysis showed that CDKN2B gene rs1063192 polymorphism was associated with a decreased risk of glaucoma. Stratification analysis of ethnicity indicated that rs1063192 polymorphism decreased the risk of glaucoma among Caucasians and Asians. Stratification analysis by type of glaucoma revealed that rs1063192 polymorphism conferred a protective factor of primary open-angle glaucoma (POAG) and non-POAG. Stratification by source of controls uncovered an association between rs1063192 polymorphism and glaucoma in groups of population-based controls. In conclusion, this meta-analysis indicates that CDKN2B gene rs1063192 polymorphism is significantly associated with a decreased risk of glaucoma.
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Affiliation(s)
- Zhenxian Hu
- Department of Ophthalmology, Tongde Hospital of Zhejiang Province, Hangzhou 310012, Zhejiang, China
| | - Chenliang He
- Department of Ophthalmology, Tongde Hospital of Zhejiang Province, Hangzhou 310012, Zhejiang, China
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58
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Liu Y, Allingham RR. Major review: Molecular genetics of primary open-angle glaucoma. Exp Eye Res 2017; 160:62-84. [PMID: 28499933 DOI: 10.1016/j.exer.2017.05.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/29/2017] [Accepted: 05/07/2017] [Indexed: 12/13/2022]
Abstract
Glaucoma is a leading cause of irreversible blindness worldwide. Primary open-angle glaucoma (POAG), the most common type, is a complex inherited disorder that is characterized by progressive retinal ganglion cell death, optic nerve head excavation, and visual field loss. The discovery of a large, and growing, number of genetic and chromosomal loci has been shown to contribute to POAG risk, which carry implications for disease pathogenesis. Differential gene expression analyses in glaucoma-affected tissues as well as animal models of POAG are enhancing our mechanistic understanding in this common, blinding disorder. In this review we summarize recent developments in POAG genetics and molecular genetics research.
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Affiliation(s)
- Yutao Liu
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, United States; James & Jean Culver Vision Discovery Institute, Augusta University, Augusta, GA, United States; Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA, United States
| | - R Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, United States; Duke - National University of Singapore (Duke-NUS), Singapore.
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Shah MH, Tabanera N, Krishnadas SR, Pillai MR, Bovolenta P, Sundaresan P. Identification and characterization of variants and a novel 4 bp deletion in the regulatory region of SIX6, a risk factor for primary open-angle glaucoma. Mol Genet Genomic Med 2017; 5:323-335. [PMID: 28717659 PMCID: PMC5511802 DOI: 10.1002/mgg3.290] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 03/20/2017] [Accepted: 03/21/2017] [Indexed: 12/23/2022] Open
Abstract
Background Primary open‐angle glaucoma (POAG) is a complex disease of multigenic inheritance and the most common subtype of glaucoma. SIX6 encodes a transcription factor involved in retina, optic nerve, and pituitary development. Previous studies showed a genetic association between the SIX6 locus and POAG, identifying risk alleles. Whether these alleles are present also in the south Indian population is unclear. Methods To address this question, the SIX6 gene and an already characterized and highly conserved SIX6 enhancer (Ch14:60974427‐60974430) were sequenced in two south Indian cohorts, respectively, composed of 65/65 and 200/200 POAG cases/age‐matched controls. We next used Taqman‐based allelic discrimination assay to genotype a common variant (rs33912345: c.421A>C) and the rs1048372 SNP in two cohorts, respectively, composed of 557/387 and 590/448 POAG cases/age‐matched controls. An additional cohort of 153 POAG cases was subsequently recruited to assess the association of the rs33912345:c.421A>C and rs10483727 variants with more prominent changes in two POAG diagnostic parameters: retinal nerve fiber layer thickness and vertical cup/disc ratio, using spectral domain optical coherence tomography. The activity of the newly identified enhancer variants was assessed by transgenesis in zebrafish and luciferase assays. Results We identified two known rare and two common variants in the SIX6 locus and a novel 4 bp deletion in the analyzed enhancer. Contrary to previous studies, we could not establish a significant association between the rs10483727 and rs33912345:c.421A>C variants and PAOG in the south Indian ethnicity but patients carrying the corresponding C or T risk alleles exhibited a dose‐dependent reduction of the thickness of the retinal nerve fiber layer and a significant increase in the vertical cup/disc ratio. Transgenesis in zebrafish and luciferase assays demonstrated that the newly identified 4 bp deletion significantly reduced reporter expression in cells of the retinal ganglion and amacrine layers, where human SIX6 is expressed. Conclusion Altogether, our data further support the implication of SIX6 variants as POAG risk factors and implicates SIX6 haploinsufficiency in POAG pathogenesis.
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Affiliation(s)
- Mohd Hussain Shah
- Department of Molecular GeneticsAravind Medical Research FoundationMaduraiIndia
| | - Noemi Tabanera
- Centro de Biología Molecular Severo OchoaCSIC-UAMMadridSpain.,CIBERER, ISCIIIMadridSpain
| | | | | | - Paola Bovolenta
- Centro de Biología Molecular Severo OchoaCSIC-UAMMadridSpain.,CIBERER, ISCIIIMadridSpain
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Li LU, Zhao Y, Zhang H. P16INK4a upregulation mediated by TBK1 induces retinal ganglion cell senescence in ischemic injury. Cell Death Dis 2017; 8:e2752. [PMID: 28425986 PMCID: PMC5477587 DOI: 10.1038/cddis.2017.169] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 03/13/2017] [Accepted: 03/20/2017] [Indexed: 12/13/2022]
Abstract
Glaucoma is a leading cause of irreversible blindness worldwide that is characterized by progressive retinal ganglion cell (RGC) death. However, RGC senescence as a phase before RGC death, and the mechanism of RGC senescence remains unclear. Here, we demonstrate that TANK-binding protein 1 (TBK1) is upregulated in acute IOP elevation-induced ischemic retinas mouse model. Moreover, pre-treatment with the TBK1 inhibitor BX-795 reduced p16INK4a (p16) expression and RGC senescence. Upregulation of TBK1 via plasmid transfection increased Akt phosphorylation at Ser473 and Bmi1 phosphorylation. The Akt inhibitor MK-2206 decreased the expression of p16 and Bmi1 serine phosphorylation. A Bmi1 Ser316 mutation also attenuated TBK1-induced p16 upregulation. Finally, silencing of TBK1 via shRNA knockdown reduced the expression of p16 as well as Akt and Bmi1 phosphorylation, reducing RGC senescence in vivo. These data suggest that acute IOP elevation-induced ischemia increases TBK1 expression, which then increases p16 expression through the Akt- Bmi1 phosphorylation pathway. This study therefore elucidates a novel mechanism whereby TBK1 regulates p16 expression and RGC senescence, suggesting a potential novel treatment strategy for minimizing RGC senescence in retinal ischemia and glaucoma.
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Affiliation(s)
- L U Li
- Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Ophthalmology, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, Xinjiang, People's Republic of China
| | - Yin Zhao
- Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hong Zhang
- Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Yu L, Wang J, Wang S, Zhang D, Zhao Y, Wang R, Zhao J. DNA Methylation Regulates Gene Expression in Intracranial Aneurysms. World Neurosurg 2017; 105:28-36. [PMID: 28433851 DOI: 10.1016/j.wneu.2017.04.064] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/06/2017] [Accepted: 04/07/2017] [Indexed: 11/28/2022]
Abstract
BACKGROUND Different gene expression profiles are observed in intracranial aneurysm tissues. Understanding these genes and what regulates their expression will provide insight into the pathogenesis of intracranial aneurysms. We investigated whether differences in DNA methylation regulate gene expression in intracranial aneurysms. METHODS We compared 20 intracranial aneurysm tissue specimens with 20 matched specimens from the superficial temporal artery as controls. We identified the gene expression profiles in these samples using the GeneChip Human U133 Plus 2.0 array and evaluated DNA methylation modifications using the Infinium HumanMethylation450 BeadChip Kit. RESULTS A total of 11,022 differentially methylated sites between aneurysm tissues and matched control tissues were identified, and 2142 differentially expressed gene transcripts were detected based on the 2 gene expression profiles. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses and verification analysis showed that the MYH11, LIFR, and TLR4 genes were associated with the occurrence and development of intracranial aneurysms. These genes mainly encode cell adhesion molecules or are involved in the NF-κB, JAK-STAT, and ERK/JNK signaling pathways. CONCLUSIONS In the development of intracranial aneurysms, DNA methylation plays an important role in the regulation of genetic expression involved in immune and inflammatory reactions, cell function, cell maintenance, and cell signal transduction.
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Affiliation(s)
- Lanbing Yu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jia Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China; National Clinical Research Center for Neurological Diseases (NCRC-ND), Beijing, China
| | - Shuo Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Dong Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yuanli Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Rong Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jizong Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China; National Clinical Research Center for Neurological Diseases (NCRC-ND), Beijing, China; Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China; Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China.
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Carnes MU, Allingham RR, Ashley-Koch A, Hauser MA. Transcriptome analysis of adult and fetal trabecular meshwork, cornea, and ciliary body tissues by RNA sequencing. Exp Eye Res 2016; 167:91-99. [PMID: 27914989 DOI: 10.1016/j.exer.2016.11.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 11/28/2016] [Accepted: 11/30/2016] [Indexed: 11/26/2022]
Abstract
PURPOSE To characterize the transcriptional landscape of human adult and fetal trabecular meshwork (TM), cornea, and ciliary body (CB) tissues, and to evaluate the expression level of candidate genes selected from genetic association studies of primary-open angle glaucoma, central corneal thickness, intraocular pressure, vertical cup to disc ratio, and optic nerve parameters. METHODS Deep RNA sequencing was performed on the selected human tissues. Transcriptome analyses were performed to 1) characterize the total number of expressed genes, 2) identify the most highly expressed genes, 3) estimate the number of novel transcripts, and 4) evaluate the expression of candidate genes in each tissue. Finally, a differential gene expression analysis was conducted to compare the adult and fetal ocular tissues. RESULTS There was an average of 12,362 protein coding genes and 3725 novel transcripts expressed in each tissue. The top most expressed genes in each tissue included SPARC (fetal cornea and TM), APOD (adult TM), CLU (adult cornea), and PTGDS (adult and fetal CB). Twenty-nine candidate genes selected from genetic association studies primarily showed high expression levels in the trabecular meshwork and cornea. Comparison of adult and fetal samples identified 2012 and 1261 differentially expressed protein-coding genes within the cornea and trabecular meshwork, respectively. CONCLUSIONS This study has provided an unbiased glimpse into the transcriptome of three essential anterior ocular tissues, resulting in the development of several novel hypotheses. These data can be used in the future to better guide ocular research questions.
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Affiliation(s)
- Megan Ulmer Carnes
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA.
| | - R Rand Allingham
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, USA
| | - Allison Ashley-Koch
- Department of Medicine, Duke University Medical Center, Durham, NC, USA; Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA
| | - Michael A Hauser
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, USA; Department of Medicine, Duke University Medical Center, Durham, NC, USA; Duke Molecular Physiology Institute, Durham, NC, USA
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Cui XJ, Zhao AG, Wang XL. Correlations of AFAP1
,GMDS
and PTGFR
gene polymorphisms with intra-ocular pressure response to latanoprost in patients with primary open-angle glaucoma. J Clin Pharm Ther 2016; 42:87-92. [PMID: 27862086 DOI: 10.1111/jcpt.12468] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 09/20/2016] [Indexed: 01/20/2023]
Affiliation(s)
- X.-J. Cui
- Department of Ophthalmology; Linyi People's Hospital; Linyi Shandong China
| | - A.-G. Zhao
- Department of Ophthalmology; Feixian County People's Hospital; Linyi Shandong China
| | - X.-L. Wang
- Department of Ophthalmology; Linyi People's Hospital; Linyi Shandong China
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Zhou T, Souzeau E, Sharma S, Siggs OM, Goldberg I, Healey PR, Graham S, Hewitt AW, Mackey DA, Casson RJ, Landers J, Mills R, Ellis J, Leo P, Brown MA, MacGregor S, Burdon KP, Craig JE. Rare variants in optic disc area gene CARD10 enriched in primary open-angle glaucoma. Mol Genet Genomic Med 2016; 4:624-633. [PMID: 27896285 PMCID: PMC5118207 DOI: 10.1002/mgg3.248] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/08/2016] [Accepted: 08/26/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified association of common alleles with primary open-angle glaucoma (POAG) and its quantitative endophenotypes near numerous genes. This study aims to determine whether rare pathogenic variants in these disease-associated genes contribute to POAG. METHODS Participants fulfilled strict inclusion criteria of advanced POAG at a young age of diagnosis. Myocilin mutation carriers were excluded using direct sequencing. Whole exome sequencing was performed on 187 glaucoma cases and 103 local screened nonglaucoma controls then joint-called with exomes of 993 previously sequenced Australian controls. GWAS-associated genes were assessed for enrichment of rare predicted pathogenic variants in POAG. Significantly enriched genes were compared against Exome Aggregation Consortium (ExAC) public control. RESULTS Eighty-six GWAS disease or trait-associated glaucoma genes were captured and sequenced. CARD10 showed enrichment after Bonferroni correction for rare variants in glaucoma cases (OR = 13.2, P = 6.94 × 10-5) with mutations identified in 4.28% of our POAG cohort compared to 0.27% in controls. CARD10 was significantly associated with optic disc parameters in previous GWAS. The whole GWAS gene set showed no enrichment in POAG overall (OR = 1.12, P = 0.51). CONCLUSION We report here an enrichment of rare predicted pathogenic coding variants within a GWAS-associated locus in POAG (CARD10). These findings indicate that both common and rare pathogenic coding variants in CARD10 may contribute to POAG pathogenesis.
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Affiliation(s)
- Tiger Zhou
- Department of Ophthalmology Flinders University Adelaide SA Australia
| | | | - Shiwani Sharma
- Department of Ophthalmology Flinders University Adelaide SA Australia
| | - Owen M Siggs
- Department of Ophthalmology Flinders University Adelaide SA Australia
| | - Ivan Goldberg
- Discipline of OphthalmologyUniversity of SydneySydneyNSWAustralia; Glaucoma UnitSydney Eye HospitalSydneyNSWAustralia
| | - Paul R Healey
- Discipline of Ophthalmology University of Sydney Sydney NSW Australia
| | - Stuart Graham
- Discipline of Ophthalmology University of Sydney Sydney NSW Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research University of Tasmania Hobart TAS Australia
| | - David A Mackey
- Centre for Ophthalmology and Visual Science Lions Eye Institute University of Western Australia Perth WA Australia
| | - Robert J Casson
- Discipline of Ophthalmology & Visual Sciences University of Adelaide Adelaide SA Australia
| | - John Landers
- Department of Ophthalmology Flinders University Adelaide SA Australia
| | - Richard Mills
- Department of Ophthalmology Flinders University Adelaide SA Australia
| | - Jonathan Ellis
- Diamantina Institute Translational Research Institute Princess Alexandra Hospital University of Queensland Woolloongabba QLD Australia
| | - Paul Leo
- Diamantina Institute Translational Research Institute Princess Alexandra Hospital University of Queensland Woolloongabba QLD Australia
| | - Matthew A Brown
- Diamantina Institute Translational Research Institute Princess Alexandra Hospital University of Queensland Woolloongabba QLD Australia
| | - Stuart MacGregor
- Statistical Genetics QIMR Berghofer Medical Research Institute Royal Brisbane Hospital Brisbane QLD Australia
| | - Kathryn P Burdon
- Department of OphthalmologyFlinders UniversityAdelaideSAAustralia; Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTASAustralia
| | - Jamie E Craig
- Department of Ophthalmology Flinders University Adelaide SA Australia
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Scheetz TE, Faga B, Ortega L, Roos BR, Gordon MO, Kass MA, Wang K, Fingert JH. Glaucoma Risk Alleles in the Ocular Hypertension Treatment Study. Ophthalmology 2016; 123:2527-2536. [PMID: 27707548 DOI: 10.1016/j.ophtha.2016.08.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 08/19/2016] [Accepted: 08/23/2016] [Indexed: 10/20/2022] Open
Abstract
PURPOSE Primary open-angle glaucoma (POAG) is a major cause of blindness and visual disability. Several genetic risk factors for POAG and optic nerve features have been identified. We measured the relative risk for glaucoma that these factors contribute to participants in the Ocular Hypertension Treatment Study (OHTS). DESIGN Comparative series. PARTICIPANTS One thousand fifty-seven of 1636 participants (65%) of the OHTS were enrolled in this genetics ancillary study. METHODS Samples of DNA were available from 1057 OHTS participants. Of these, 209 developed POAG (cases) and 848 did not develop glaucoma (controls) between 1994 and 2009. The frequencies of 13 risk alleles previously associated with POAG or with optic disc features in other cohorts were compared between POAG cases and controls in the OHTS cohort using analyses of variance. The 2 largest subgroups, non-Hispanic whites (n = 752; 70.7%) and blacks (n = 249, 23.7%), also were analyzed separately. The probability of glaucoma developing over the course of the OHTS was compared between participants stratified for transmembrane and coiled-coil domains 1 (TMCO1) risk alleles using Kaplan-Meier and Cox proportional hazards analyses. MAIN OUTCOME MEASURES Association of POAG with known genetic factors. RESULTS No association was detected between the known POAG risk alleles when the OHTS cohort was examined as a whole. However, in the subgroup of non-Hispanic whites, allele frequencies at the TMCO1 locus were statistically different between cases and controls (P = 0.00028). By 13 years, non-Hispanic white participants with TMCO1 risk alleles had a 12% higher cumulative frequency of glaucoma developing than participants with no TMCO1 risk alleles. Moreover, the Cox proportional hazard analysis demonstrated that TMCO1 alleles increased relative risk comparable with that of some previously analyzed clinical measures (i.e., intraocular pressure). CONCLUSIONS The size of the OHTS cohort and its composition of 2 large racial subgroups may limit its power to detect some glaucoma risk factors. However, TMCO1 genotype was found to increase the risk of glaucoma developing among non-Hispanic whites, the largest racial subgroup in the OHTS cohort, at a magnitude similar to clinical predictors of disease that long have been associated with glaucoma.
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Affiliation(s)
- Todd E Scheetz
- Department Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa; Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa
| | - Ben Faga
- Department Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa; Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa
| | - Lizette Ortega
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, Iowa
| | - Ben R Roos
- Department Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa; Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa
| | - Mae O Gordon
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
| | - Michael A Kass
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri
| | - Kai Wang
- Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa; Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, Iowa
| | - John H Fingert
- Department Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa; Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, Iowa.
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Abu-Amero KK, Kondkar AA, Mousa A, Almobarak FA, Alawad A, Altuwaijri S, Sultan T, Azad TA, Al-Obeidan SA. Analysis of Cyclin-Dependent Kinase Inhibitor-2B rs1063192 Polymorphism in Saudi Patients with Primary Open-Angle Glaucoma. Genet Test Mol Biomarkers 2016; 20:637-641. [PMID: 27541204 DOI: 10.1089/gtmb.2016.0140] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
AIMS To investigate whether the polymorphism rs1063192 (A>G) in the cyclin-dependent kinase Inhibitor-2B (CDKN2B) gene is a risk factor for primary open-angle glaucoma (POAG). METHOD A case-control study was conducted wherein we genotyped 87 unrelated POAG cases and 94 control subjects from Saudi Arabia using the Taq-Man® assay. RESULTS The minor allele frequency was 0.20 in POAG cases and 0.21 in controls. Both the genotype and allele frequencies were not significantly different between cases and controls. No significant association was found between genotypes and glaucoma clinical indices, except that the mutant homozygous genotype (G/G) was associated with the family history of glaucoma (p = 0.024). CONCLUSION Polymorphism rs1063192 in CDKN2B is not a risk factor for POAG in Saudi cohort.
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Affiliation(s)
- Khaled K Abu-Amero
- 1 Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University , Riyadh, Saudi Arabia .,2 Department of Ophthalmology, College of Medicine, University of Florida , Jacksonville, Florida
| | - Altaf A Kondkar
- 1 Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University , Riyadh, Saudi Arabia
| | - Ahmed Mousa
- 1 Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University , Riyadh, Saudi Arabia
| | - Faisal A Almobarak
- 1 Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University , Riyadh, Saudi Arabia
| | - Abdullah Alawad
- 3 National Center for Stem Cell Technology (NCSCT), Life Sciences and Environmental Research Institute , King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Saleh Altuwaijri
- 4 Clinical Research Laboratory, SAAD Research and Development Center, SAAD Specialist Hospital , Al Khobar, Saudi Arabia .,5 Veterinary College, Qassim University , Qassim, Saudi Arabia
| | - Tahira Sultan
- 1 Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University , Riyadh, Saudi Arabia
| | - Taif A Azad
- 1 Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University , Riyadh, Saudi Arabia
| | - Saleh A Al-Obeidan
- 1 Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University , Riyadh, Saudi Arabia
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Kader MA, Namburi P, Ramugade S, Ramakrishnan R, Krishnadas SR, Roos BR, Periasamy S, Robin AL, Fingert JH. Clinical and genetic characterization of a large primary open angle glaucoma pedigree. Ophthalmic Genet 2016; 38:222-225. [PMID: 27355837 DOI: 10.1080/13816810.2016.1193883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
PURPOSE To both characterize the clinical features of large primary open angle glaucoma (POAG) pedigree from a village in southern India and to investigate the genetic basis of their disease. MATERIALS AND METHODS Eighty-four members of a large pedigree received complete eye examinations including slit lamp examination, tonometry, gonioscopy, and ophthalmoscopy. Some were further studied with perimetry. Those diagnosed with POAG were tested for disease-causing mutations in the myocilin and optineurin genes with Sanger sequencing. RESULTS Fourteen of 84 family members were diagnosed with POAG, while eight were clinically judged to be POAG-suspects. The family structure and the pattern of glaucoma in the pedigree are complex. Features of glaucoma in this pedigree include relatively early age at diagnosis (mean 50 ± 14 years) and maximum intraocular pressures ranging from 14 to 36 mm Hg with a mean of 23 mm Hg ± 6.5 mm Hg. Patients had an average central corneal thickness (mean 529 ± 37.8 microns) and moderate cup-to-disc ratios (0.74 ± 0.14). No mutations were detected in myocilin, optineurin, or TANK binding kinase 1 (TBK1). CONCLUSIONS We report a five-generation pedigree with a complex pattern of POAG inheritance that includes 22 POAG patients and glaucoma suspects. Although the familial clustering of POAG in this pedigree is consistent with dominant inheritance of a glaucoma-causing gene, mutations were not detected in genes previously associated with autosomal dominant glaucoma, suggesting the involvement of a novel disease-causing gene in this pedigree.
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Affiliation(s)
- Mohideen Abdul Kader
- a Department of Genetics, Aravind Medical Research Foundation , Aravind Eye Hospital , Madurai , India.,b Glaucoma Clinic , Aravind Eye Hospital , Tirunelveli , India
| | - Prasanthi Namburi
- c Department of Ophthalmology , Hadassah-Hebrew University Medical Center , Jerusalem , Israel
| | - Sarika Ramugade
- a Department of Genetics, Aravind Medical Research Foundation , Aravind Eye Hospital , Madurai , India
| | - R Ramakrishnan
- a Department of Genetics, Aravind Medical Research Foundation , Aravind Eye Hospital , Madurai , India.,b Glaucoma Clinic , Aravind Eye Hospital , Tirunelveli , India
| | - Subbiah R Krishnadas
- a Department of Genetics, Aravind Medical Research Foundation , Aravind Eye Hospital , Madurai , India.,d Glaucoma Clinic , Aravind Eye Hospital , Madurai , India
| | - Ben R Roos
- e Department of Ophthalmology and Visual Sciences, Carver College of Medicine , University of Iowa , Iowa City , Iowa , USA.,f Stephen A. Wynn Institute for Vision Research, University of Iowa , Iowa City , Iowa , USA
| | - Sundaresan Periasamy
- a Department of Genetics, Aravind Medical Research Foundation , Aravind Eye Hospital , Madurai , India
| | - Alan L Robin
- g Departments of Ophthalmology and International Health, School of Medicine and the Bloomberg School of Public Health , Johns Hopkins University , Baltimore , Maryland , USA.,h Department of Ophthalmology , University of Maryland , Baltimore , Maryland , USA
| | - John H Fingert
- e Department of Ophthalmology and Visual Sciences, Carver College of Medicine , University of Iowa , Iowa City , Iowa , USA.,f Stephen A. Wynn Institute for Vision Research, University of Iowa , Iowa City , Iowa , USA
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Valente TS, Baldi F, Sant’Anna AC, Albuquerque LG, Paranhos da Costa MJR. Genome-Wide Association Study between Single Nucleotide Polymorphisms and Flight Speed in Nellore Cattle. PLoS One 2016; 11:e0156956. [PMID: 27300296 PMCID: PMC4907449 DOI: 10.1371/journal.pone.0156956] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 05/23/2016] [Indexed: 12/17/2022] Open
Abstract
Introduction Cattle temperament is an important factor that affects the profitability of beef cattle enterprises, due to its relationship with productivity traits, animal welfare and labor safety. Temperament is a complex phenotype often assessed by measuring a series of behavioral traits, which result from the effects of multiple environmental and genetic factors, and their interactions. The aims of this study were to perform a genome-wide association study and detect genomic regions, potential candidate genes and their biological mechanisms underlying temperament, measured by flight speed (FS) test in Nellore cattle. Materials and Methods The genome-wide association study (GWAS) was performed using a single-step procedure (ssGBLUP) which combined simultaneously all 16,600 phenotypes from genotyped and non-genotyped animals, full pedigree information of 162,645 animals and 1,384 genotyped animals in one step. The animals were genotyped with High Density Bovine SNP BeadChip which contains 777,962 SNP markers. After quality control (QC) a total of 455,374 SNPs remained. Results Heritability estimated for FS was 0.21 ± 0.02. Consecutive SNPs explaining 1% or more of the total additive genetic variance were considered as windows associated with FS. Nine candidate regions located on eight different Bos taurus chromosomes (BTA) (1 at 73 Mb, 2 at 65 Mb, 5 at 22 Mb and 119 Mb, 9 at 98 Mb, 11 at 67 Mb, 15 at 16 Mb, 17 at 63 Kb, and 26 at 47 Mb) were identified. The candidate genes identified in these regions were NCKAP5 (BTA2), PARK2 (BTA9), ANTXR1 (BTA11), GUCY1A2 (BTA15), CPE (BTA17) and DOCK1 (BTA26). Among these genes PARK2, GUCY1A2, CPE and DOCK1 are related to dopaminergic system, memory formation, biosynthesis of peptide hormone and neurotransmitter and brain development, respectively. Conclusions Our findings allowed us to identify nine genomic regions (SNP windows) associated with beef cattle temperament, measured by FS test. Within these windows, six promising candidate genes and their biological functions were identified. These results may contribute to a better comprehension into the genetic control of temperament expression in Nellore cattle.
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Affiliation(s)
- Tiago Silva Valente
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de Acesso Professor Paulo Donato Castellane, Jaboticabal, SP 14.884-900, Brazil
| | - Fernando Baldi
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de Acesso Professor Paulo Donato Castellane, Jaboticabal, SP 14.884-900, Brazil
| | - Aline Cristina Sant’Anna
- Universidade Federal de Juiz de Fora (UFJF), Instituto de Ciências Biológicas, Departamento de Zoologia, Rua José Lourenço Kelmer, Juiz de Fora, MG 36.036-900, Brazil
| | - Lucia Galvão Albuquerque
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de Acesso Professor Paulo Donato Castellane, Jaboticabal, SP 14.884-900, Brazil
| | - Mateus José Rodrigues Paranhos da Costa
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de Acesso Professor Paulo Donato Castellane, Jaboticabal, SP 14.884-900, Brazil
- * E-mail:
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Sang J, Jia L, Zhao B, Wang H, Zhang N, Wang N. Association of three single nucleotide polymorphisms at the SIX1-SIX6 locus with primary open angle glaucoma in the Chinese population. SCIENCE CHINA-LIFE SCIENCES 2016; 59:694-9. [PMID: 27260188 DOI: 10.1007/s11427-016-5073-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 03/16/2016] [Indexed: 01/29/2023]
Abstract
This study investigated the genetic association of three single nucleotide polymorphisms (SNPs; rs10483727, rs33912345, and rs146737847) at the SIX1-SIX6 locus with primary open angle glaucoma (POAG) in the Chinese population. A total of 866 subjects with POAG (685 high-tension glaucoma (HTG) and 181 normal-tension glaucoma (NTG)) and 266 control individuals were included. Significant genetic association was identified for rs10483727 in HTG (P=0.02; odds ratio (OR)=1.31), NTG (P=7.41×10(-6); OR=2.71), and POAG (i.e., HTG and NTG combined; P=0.001; OR=1.44). rs33912345 was also significantly associated with HTG (P=0.008; OR=1.36), NTG(P=2.72×10(-6); OR=2.27), and POAG (P=3.84×10(-4); OR=1.49). The rare SIX6 mutation, rs146737847, was not found in the subjects enrolled in this study. Stratification by patient age identified that both rs10483727 and rs33912345 were significantly associated with NTG in patients aged above 40 years (P=2.08×10(-5); OR=2.28), whereas in patients aged between 20-40 years, rs33912345 was significantly associated with NTG (P=0.017; OR=2.06). In HTG, the genetic associations for both rs10483727 and rs33912345 were significant in patients aged between 20-40 years (P=0.006; OR=1.56) but not in those aged above 40 years (P=0.118, OR=1.21 and P=0.042, OR=1.29, respectively). This study replicated the association of POAG with two SNPs at the SIX1-SIX6 locus and demonstrated that SNPs, rs10483727 and rs33912345, are significantly associated with POAG, especially with NTG in patients aged above 40 years.
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Affiliation(s)
- Jinghong Sang
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
- Beijing Ophthalmology & Visual Science Key Laboratory, Capital Medical University, Beijing, 100730, China
| | - Liyun Jia
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
- Beijing Ophthalmology & Visual Science Key Laboratory, Capital Medical University, Beijing, 100730, China
| | - Bowen Zhao
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
- Beijing Ophthalmology & Visual Science Key Laboratory, Capital Medical University, Beijing, 100730, China
| | - Huaizhou Wang
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
- Beijing Ophthalmology & Visual Science Key Laboratory, Capital Medical University, Beijing, 100730, China
| | - Nihong Zhang
- The First Affiliated Hospital of Nanyang Medical College, Nanyang, 473000, China
| | - Ningli Wang
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China.
- Beijing Ophthalmology & Visual Science Key Laboratory, Capital Medical University, Beijing, 100730, China.
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China.
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Gao S, Jakobs TC. Mice Homozygous for a Deletion in the Glaucoma Susceptibility Locus INK4 Show Increased Vulnerability of Retinal Ganglion Cells to Elevated Intraocular Pressure. THE AMERICAN JOURNAL OF PATHOLOGY 2016; 186:985-1005. [PMID: 26883755 DOI: 10.1016/j.ajpath.2015.11.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/30/2015] [Accepted: 11/17/2015] [Indexed: 12/13/2022]
Abstract
A genomic region located on chromosome 9p21 is associated with primary open-angle glaucoma and normal tension glaucoma in genome-wide association studies. The genomic region contains the gene for a long noncoding RNA called CDKN2B-AS, two genes that code for cyclin-dependent kinase inhibitors 2A and 2B (CDKN2A/p16(INK4A) and CDKN2B/p15(INK4B)) and an additional protein (p14(ARF)). We used a transgenic mouse model in which 70 kb of murine chromosome 4, syntenic to human chromosome 9p21, are deleted to study whether this deletion leads to a discernible phenotype in ocular structures implicated in glaucoma. Homozygous mice of this strain were previously reported to show persistent hyperplastic primary vitreous. Fundus photography and optical coherence tomography confirmed that finding but showed no abnormalities for heterozygous mice. Optokinetic response, eletroretinogram, and histology indicated that the heterozygous and mutant retinas were normal functionally and morphologically, whereas glial cells were activated in the retina and optic nerve head of mutant eyes. In quantitative PCR, CDKN2B expression was reduced by approximately 50% in the heterozygous mice and by 90% in the homozygous mice, which suggested that the CDKN2B knock down had no deleterious consequences for the retina under normal conditions. However, compared with wild-type and heterozygous animals, the homozygous mice are more vulnerable to retinal ganglion cell loss in response to elevated intraocular pressure.
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Affiliation(s)
- Shan Gao
- Department of Ophthalmology, The First Affiliated Hospital, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China; Department of Ophthalmology, Massachusetts Eye and Ear Infirmary/Schepens Eye Research Institute, Harvard Medical School, Boston, Massachusetts
| | - Tatjana C Jakobs
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary/Schepens Eye Research Institute, Harvard Medical School, Boston, Massachusetts.
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Kumar S, Malik MA, Goswami S, Sihota R, Kaur J. Candidate genes involved in the susceptibility of primary open angle glaucoma. Gene 2016; 577:119-31. [PMID: 26621382 DOI: 10.1016/j.gene.2015.11.032] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 11/05/2015] [Accepted: 11/23/2015] [Indexed: 12/30/2022]
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Abu-Amero K, Kondkar AA, Chalam KV. An Updated Review on the Genetics of Primary Open Angle Glaucoma. Int J Mol Sci 2015; 16:28886-911. [PMID: 26690118 PMCID: PMC4691082 DOI: 10.3390/ijms161226135] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 11/19/2015] [Accepted: 11/27/2015] [Indexed: 01/07/2023] Open
Abstract
Epidemiological studies suggest that by 2020 the prevalence of primary open angle glaucoma (POAG) is estimated to increase to 76.0 million, and to 111.8 million by 2040 globally due to the population aging. The prevalence of POAG is the highest among those of African descent, followed by Asians, and the lowest in Europeans. POAG is a genetically complex trait with a substantial fraction exhibiting a significant heritability. Less than 10% of POAG cases in the general population are caused by specific gene mutations and the remaining cases are polygenic. Quantitative traits related to POAG pathogenesis such as intra-ocular pressure (IOP), vertical cup/disc ratio (VCDR), optic disc area, and central corneal thickness (CCT) are highly heritable, and likely to be influenced at least in part by genes and show substantial variation in human populations. Recent genome-wide association studies (GWAS) have identified several single nucleotide polymorphisms (SNPs) at different loci including CAV1/CAV2, TMCO1, CDKN2B-AS1, CDC7-TGFBR3, SIX1/SIX6, GAS7 and ATOH7 to be associated with POAG and its related quantitative traits (endophenotypes). The chapter provides a brief overview on the different GWAS and SNP association studies and their correlation with various clinical parameters important for POAG in the population worldwide, including the Middle East.
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Affiliation(s)
- Khaled Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh 11424, Saudi Arabia.
- Department of Ophthalmology, University of Florida College of Medicine, 580, W, 8th Street, Tower-2, Jacksonville, FL 32209, USA.
| | - Altaf A Kondkar
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh 11424, Saudi Arabia.
| | - Kakarla V Chalam
- Department of Ophthalmology, University of Florida College of Medicine, 580, W, 8th Street, Tower-2, Jacksonville, FL 32209, USA.
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Skowronska-Krawczyk D, Zhao L, Zhu J, Weinreb RN, Cao G, Luo J, Flagg K, Patel S, Wen C, Krupa M, Luo H, Ouyang H, Lin D, Wang W, Li G, Xu Y, Li O, Chung C, Yeh E, Jafari M, Ai M, Zhong Z, Shi W, Zheng L, Krawczyk M, Chen D, Shi C, Zin C, Zhu J, Mellon PL, Gao W, Abagyan R, Zhang L, Sun X, Zhong S, Zhuo Y, Rosenfeld MG, Liu Y, Zhang K. P16INK4a Upregulation Mediated by SIX6 Defines Retinal Ganglion Cell Pathogenesis in Glaucoma. Mol Cell 2015; 59:931-40. [PMID: 26365380 DOI: 10.1016/j.molcel.2015.07.027] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 06/08/2015] [Accepted: 07/24/2015] [Indexed: 02/06/2023]
Abstract
Glaucoma, a blinding neurodegenerative disease, whose risk factors include elevated intraocular pressure (IOP), age, and genetics, is characterized by accelerated and progressive retinal ganglion cell (RGC) death. Despite decades of research, the mechanism of RGC death in glaucoma is still unknown. Here, we demonstrate that the genetic effect of the SIX6 risk variant (rs33912345, His141Asn) is enhanced by another major POAG risk gene, p16INK4a (cyclin-dependent kinase inhibitor 2A, isoform INK4a). We further show that the upregulation of homozygous SIX6 risk alleles (CC) leads to an increase in p16INK4a expression, with subsequent cellular senescence, as evidenced in a mouse model of elevated IOP and in human POAG eyes. Our data indicate that SIX6 and/or IOP promotes POAG by directly increasing p16INK4a expression, leading to RGC senescence in adult human retinas. Our study provides important insights linking genetic susceptibility to the underlying mechanism of RGC death and provides a unified theory of glaucoma pathogenesis.
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Affiliation(s)
- Dorota Skowronska-Krawczyk
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ling Zhao
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Jie Zhu
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Ophthalmology, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Robert N Weinreb
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Guiqun Cao
- Molecular Medicine Research Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Sichuan 610041, China
| | - Jing Luo
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ken Flagg
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sherrina Patel
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Cindy Wen
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Martin Krupa
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hongrong Luo
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hong Ouyang
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Danni Lin
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wenqiu Wang
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Ophthalmology, Shanghai First People's Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai 20080, China
| | - Gen Li
- Molecular Medicine Research Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Sichuan 610041, China
| | - Yanxin Xu
- Molecular Medicine Research Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Sichuan 610041, China
| | - Oulan Li
- Molecular Medicine Research Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Sichuan 610041, China; Guangzhou KangRui Biological Pharmaceutical Technology Company Ltd., Guangzhou 510005, China
| | - Christopher Chung
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emily Yeh
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Maryam Jafari
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael Ai
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zheng Zhong
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - William Shi
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lianghong Zheng
- Guangzhou KangRui Biological Pharmaceutical Technology Company Ltd., Guangzhou 510005, China
| | - Michal Krawczyk
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daniel Chen
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Catherine Shi
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Carolyn Zin
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jin Zhu
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Pamela L Mellon
- Department of Reproductive Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Weiwei Gao
- Department of Nanoengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ruben Abagyan
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Liangfang Zhang
- Department of Nanoengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xiaodong Sun
- Department of Ophthalmology, Shanghai First People's Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai 20080, China
| | - Sheng Zhong
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yehong Zhuo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China.
| | - Kang Zhang
- Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China; Molecular Medicine Research Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Sichuan 610041, China; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Veterans Administration Healthcare System, San Diego, CA 92093, USA.
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74
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Kimura Y, Akagi T, Miyake M, Yamashiro K, Yoshikawa M, Yamada H, Hasegawa T, Suda K, Nakanishi H, Ohashi-Ikeda H, Gotoh N, Hangai M, Moriyama M, Ohno-Matsui K, Yoshimura N. Association between the CDKN2B-AS1 Gene and Primary Open Angle Glaucoma with High Myopia in Japanese Patients. Ophthalmic Genet 2015; 37:242-4. [PMID: 26332839 DOI: 10.3109/13816810.2015.1020559] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Yugo Kimura
- a Department of Ophthalmology and Visual Sciences , Kyoto University Graduate School of Medicine , Kyoto , Japan and
| | - Tadamichi Akagi
- a Department of Ophthalmology and Visual Sciences , Kyoto University Graduate School of Medicine , Kyoto , Japan and
| | - Masahiro Miyake
- a Department of Ophthalmology and Visual Sciences , Kyoto University Graduate School of Medicine , Kyoto , Japan and
| | - Kenji Yamashiro
- a Department of Ophthalmology and Visual Sciences , Kyoto University Graduate School of Medicine , Kyoto , Japan and
| | - Munemitsu Yoshikawa
- a Department of Ophthalmology and Visual Sciences , Kyoto University Graduate School of Medicine , Kyoto , Japan and
| | - Hiroshi Yamada
- a Department of Ophthalmology and Visual Sciences , Kyoto University Graduate School of Medicine , Kyoto , Japan and
| | - Tomoko Hasegawa
- a Department of Ophthalmology and Visual Sciences , Kyoto University Graduate School of Medicine , Kyoto , Japan and
| | - Kenji Suda
- a Department of Ophthalmology and Visual Sciences , Kyoto University Graduate School of Medicine , Kyoto , Japan and
| | - Hideo Nakanishi
- a Department of Ophthalmology and Visual Sciences , Kyoto University Graduate School of Medicine , Kyoto , Japan and
| | - Hanako Ohashi-Ikeda
- a Department of Ophthalmology and Visual Sciences , Kyoto University Graduate School of Medicine , Kyoto , Japan and
| | - Norimoto Gotoh
- a Department of Ophthalmology and Visual Sciences , Kyoto University Graduate School of Medicine , Kyoto , Japan and
| | - Masanori Hangai
- a Department of Ophthalmology and Visual Sciences , Kyoto University Graduate School of Medicine , Kyoto , Japan and
| | - Muka Moriyama
- b Department of Ophthalmology and Visual Science , Tokyo Medical and Dental University , Tokyo , Japan
| | - Kyoko Ohno-Matsui
- b Department of Ophthalmology and Visual Science , Tokyo Medical and Dental University , Tokyo , Japan
| | - Nagahisa Yoshimura
- a Department of Ophthalmology and Visual Sciences , Kyoto University Graduate School of Medicine , Kyoto , Japan and
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75
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Kuo JZ, Zangwill LM, Medeiros FA, Liebmann JM, Girkin CA, Hammel N, Rotter JI, Weinreb RN. Quantitative Trait Locus Analysis of SIX1-SIX6 With Retinal Nerve Fiber Layer Thickness in Individuals of European Descent. Am J Ophthalmol 2015; 160:123-30.e1. [PMID: 25849520 PMCID: PMC4509729 DOI: 10.1016/j.ajo.2015.04.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 01/21/2023]
Abstract
PURPOSE To perform a quantitative trait locus (QTL) analysis and evaluate whether a locus between SIX1 and SIX6 is associated with retinal nerve fiber layer (RNFL) thickness in individuals of European descent. DESIGN Observational, multicenter, cross-sectional study. METHODS A total of 231 participants were recruited from the Diagnostic Innovations in Glaucoma Study and the African Descent and Glaucoma Evaluation Study. Association of rs10483727 in SIX1-SIX6 with global and sectoral RNFL thickness was performed. Quantitative trait analysis with the additive model of inheritance was analyzed using linear regression. Trend analysis was performed to evaluate the mean global and sectoral RNFL thickness with 3 genotypes of interest (T/T, C/T, C/C). All models were adjusted for age and sex. RESULTS Direction of association between T allele and RNFL thickness was consistent in the global and different sectoral RNFL regions. Each copy of the T risk allele in rs10483727 was associated with -0.16 μm thinner global RNFL thickness (β = -0.16, 95% confidence interval: -0.28 to -0.03; P = .01). Similar patterns were found for the sectoral regions, including inferior (P = .03), inferior-nasal (P = .017), superior-nasal (P = .0025), superior (P = .002) and superior-temporal (P = .008). The greatest differences were observed in the superior and inferior quadrants, supporting clinical observations for RNFL thinning in glaucoma. Thinner global RNFL was found in subjects with T/T genotypes compared to subjects with C/T and C/C genotypes (P = .044). CONCLUSIONS Each copy of the T risk allele has an additive effect and was associated with thinner global and sectoral RNFL. Findings from this QTL analysis further support a genetic contribution to glaucoma pathophysiology.
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Affiliation(s)
- Jane Z Kuo
- Hamilton Glaucoma Center and Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, California; Pathway Genomics Corporation, San Diego, California
| | - Linda M Zangwill
- Hamilton Glaucoma Center and Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, California
| | - Felipe A Medeiros
- Hamilton Glaucoma Center and Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, California
| | - Jeffery M Liebmann
- Harkness Eye Institute, Columbia University Medical Center, New York, New York
| | - Christopher A Girkin
- Department of Ophthalmology, University of Alabama, Callahan Eye Hospital, Birmingham, Alabama
| | - Na'ama Hammel
- Hamilton Glaucoma Center and Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, California
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-University of California Los Angeles Medical Center, Torrance, California
| | - Robert N Weinreb
- Hamilton Glaucoma Center and Department of Ophthalmology, Shiley Eye Institute, University of California San Diego, La Jolla, California.
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76
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Restrepo NA, Farber-Eger E, Goodloe R, Haines JL, Crawford DC. Extracting Primary Open-Angle Glaucoma from Electronic Medical Records for Genetic Association Studies. PLoS One 2015; 10:e0127817. [PMID: 26061293 PMCID: PMC4465698 DOI: 10.1371/journal.pone.0127817] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 04/20/2015] [Indexed: 11/08/2022] Open
Abstract
Electronic medical records (EMRs) are being widely implemented for use in genetic and genomic studies. As a phenotypic rich resource, EMRs provide researchers with the opportunity to identify disease cohorts and perform genotype-phenotype association studies. The Epidemiologic Architecture for Genes Linked to Environment (EAGLE) study, as part of the Population Architecture using Genomics and Epidemiology (PAGE) I study, has genotyped more than 15,000 individuals of diverse genetic ancestry in BioVU, the Vanderbilt University Medical Center’s biorepository linked to a de-identified version of the EMR (EAGLE BioVU). Here we develop and deploy an algorithm utilizing data mining techniques to identify primary open-angle glaucoma (POAG) in African Americans from EAGLE BioVU for genetic association studies. The algorithm described here was designed using a combination of diagnostic codes, current procedural terminology billing codes, and free text searches to identify POAG status in situations where gold-standard digital photography cannot be accessed. The case algorithm identified 267 potential POAG subjects but underperformed after manual review with a positive predictive value of 51.6% and an accuracy of 76.3%. The control algorithm identified controls with a negative predictive value of 98.3%. Although the case algorithm requires more downstream manual review for use in large-scale studies, it provides a basis by which to extract a specific clinical subtype of glaucoma from EMRs in the absence of digital photographs.
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Affiliation(s)
- Nicole A. Restrepo
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Eric Farber-Eger
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Robert Goodloe
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jonathan L. Haines
- Department of Epidemiology & Biostatistics, Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Dana C. Crawford
- Department of Epidemiology & Biostatistics, Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail:
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77
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Philomenadin FS, Asokan R, N V, George R, Lingam V, Sarangapani S. Genetic association of SNPs near ATOH7, CARD10, CDKN2B, CDC7 and SIX1/SIX6 with the endophenotypes of primary open angle glaucoma in Indian population. PLoS One 2015; 10:e0119703. [PMID: 25798827 PMCID: PMC4370747 DOI: 10.1371/journal.pone.0119703] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 01/15/2015] [Indexed: 11/18/2022] Open
Abstract
Primary open angle glaucoma (POAG) belonging to a group of optic neuropathies, result from interaction between genetic and environmental factors. Study of associations with quantitative traits (QTs) is one of the successful strategies to understand the complex genetics of POAG. The current study attempts to explore the association of variations near/in genes like ATOH7, SIX1/SIX6 complex, CDKN2B, CARD10, and CDC7 with POAG and its QTs including vertical cup to disc ratio (VCDR), central corneal thickness (CCT), intra ocular pressure (IOP), and axial length (AL). Case-control study design was carried out in a sample size of 97 POAG cases and 371 controls from South India. Model-based (additive, recessive, dominant) association of the genotypes and their interaction was carried out between cases and controls using chi-square, linear and logistic regression methods. Nominal significance (P<0.05) was observed for QTs like i) VCDR with SNPs rs1900004 (ATOH7); rs1192415 (CDC7); rs10483727 (SIX1/SIX6), rs9607469 (CARD10); ii) CCT with rs1192415; iii) IOP with rs1900004 and iv) AL with rs1900004 and rs1063192 (CDKN2B). We were able to replicate previously known interactions between ATOH7-SIX6 and SIX6-CDKN2B along with few novel interactions between ATOH7—CDC7 and SIX6 with genes including CARD10 and CDC7. In summary, our results suggest that a probable interaction among the candidate genes for QTs, play a major role in determining the individual’s susceptibility to POAG.
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Affiliation(s)
- Ferdinamarie Sharmila Philomenadin
- SNONGC Department of Genetics and Molecular biology, Vision Research foundation, Sankara Nethralaya, Chennai, India
- PhD Scholar, Birla Institute of Technology & Science (BITS), Pilani, 333 031, Rajasthan, India
| | - Rashima Asokan
- Chennai Glaucoma Study, Medical and Vision Research Foundation, Sankara Nethralaya, Chennai, India
| | - Viswanathan N
- Biostatistician, Department of Preventive Ophthalmology, Medical research foundation, Sankara Nethralaya, Chennai, India
| | - Ronnie George
- Chennai Glaucoma Study, Medical and Vision Research Foundation, Sankara Nethralaya, Chennai, India
| | - Vijaya Lingam
- Chennai Glaucoma Study, Medical and Vision Research Foundation, Sankara Nethralaya, Chennai, India
| | - Sripriya Sarangapani
- SNONGC Department of Genetics and Molecular biology, Vision Research foundation, Sankara Nethralaya, Chennai, India
- * E-mail:
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78
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Mabuchi F, Sakurada Y, Kashiwagi K, Yamagata Z, Iijima H, Tsukahara S. Involvement of genetic variants associated with primary open-angle glaucoma in pathogenic mechanisms and family history of glaucoma. Am J Ophthalmol 2015; 159:437-44.e2. [PMID: 25461262 DOI: 10.1016/j.ajo.2014.11.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 11/11/2014] [Accepted: 11/12/2014] [Indexed: 11/18/2022]
Abstract
PURPOSE To investigate the associations between the non-intraocular pressure (IOP)-related genetic variants (genetic variants associated with vulnerability of the optic nerve independent of IOP) and primary open-angle glaucoma (POAG), including normal-tension glaucoma (NTG) and high-tension glaucoma (HTG), and between the non-IOP-related genetic variants and a family history of glaucoma. DESIGN Case-control study. METHODS Japanese patients with NTG (n = 213) and HTG (n = 212) and 191 control subjects were genotyped for 5 non-IOP-related genetic variants predisposing to POAG near the SRBD1, ELOVL5, CDKN2B/CDKN2B-AS1, SIX1/SIX6, and ATOH7 genes. The load of these genetic variants was compared between the control subjects and patients with NTG or HTG and between the POAG patients with and without a family history of glaucoma. RESULTS The total number of POAG risk alleles and the product of the odds ratios (POAG risk) of these genetic variants were significantly larger (P < .0025) in patients with both NTG and HTG than in the control subjects, and were significantly larger (P = .0042 and P = .023, respectively) in POAG patients with a family history of glaucoma than in those without. As the number of relatives with glaucoma increased, the total number of risk alleles and the product of the odds ratios increased (P = .012 and P = .047, respectively). CONCLUSIONS Non-IOP-related genetic variants contribute to the pathogenesis of HTG as well as NTG. A positive family history of glaucoma in cases of POAG is thought to reflect the influence of genetic variants predisposing to POAG.
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Affiliation(s)
- Fumihiko Mabuchi
- Department of Ophthalmology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan.
| | - Yoichi Sakurada
- Department of Ophthalmology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Kenji Kashiwagi
- Department of Ophthalmology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Zentaro Yamagata
- Department of Health Sciences, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Hiroyuki Iijima
- Department of Ophthalmology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Shigeo Tsukahara
- Department of Ophthalmology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
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79
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Williams SEI, Carmichael TR, Allingham RR, Hauser M, Ramsay M. The genetics of POAG in black South Africans: a candidate gene association study. Sci Rep 2015; 5:8378. [PMID: 25669751 PMCID: PMC4323640 DOI: 10.1038/srep08378] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 01/19/2015] [Indexed: 12/15/2022] Open
Abstract
Multiple loci have been associated with either primary open angle glaucoma (POAG) or heritable ocular quantitative traits associated with this condition. This study examined the association of these loci with POAG, with central corneal thickness (CCT), vertical cup-to-disc ratio (VCDR) and with diabetes mellitus in a group of black South Africans (215 POAG cases and 214 controls). The population was homogeneous and distinct from other African and European populations. Single SNPs in the MYOC, COL8A2, COL1A1 and ZNF469 gene regions showed marginal associations with POAG. No association with POAG was identified with tagging SNPs in TMCO1, CAV1/CAV2, CYP1B1, COL1A2, COL5A1, CDKN2B/CDKN2BAS-1, SIX1/SIX6 or the chromosome 2p16 regions and there were no associations with CCT or VCDR. However, SNP rs12522383 in WDR36 was associated with diabetes mellitus (p = 0.00008). This first POAG genetic association study in black South Africans has therefore identified associations that require additional investigation in this and other populations to determine their significance. This highlights the need for larger studies in this population if we are to achieve the goal of facilitating early POAG detection and ultimately preventing irreversible blindness from this condition.
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Affiliation(s)
- Susan E I Williams
- Division of Ophthalmology, Department of Neurosciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Trevor R Carmichael
- Division of Ophthalmology, Department of Neurosciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Michael Hauser
- Duke Center for Human Genetics, Duke University, Durham, USA
| | - Michele Ramsay
- 1] Division of Human Genetics, National Health Laboratory Service, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa [2] Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
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80
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Abstract
The 9p21.3 locus was the first to yield to genome-wide association studies (GWAS) seeking common genetic variants predisposing to increased risk of coronary artery atherosclerotic disease (CAD). The 59 single nucleotide polymorphisms that show highest association with CAD are clustered in a region 100,000 to 150,000 base pairs 5' to the cyclin-dependent kinase inhibitors CDKN2B (coding for p15(ink4b)) and CDKN2A (coding for p16(ink4a) and p14(ARF)). This region also covers the 3' end of a long noncoding RNA transcribed antisense to CDKN2B (CDKN2BAS, aka ANRIL for antisense noncoding RNA at the ink4 locus) whose expression has been linked to chromatin remodeling at the locus. Despite intensive investigation over the past 7 years, the functional significance of the 9p21.3 locus remains elusive. Other variants at this locus have been associated with glaucoma, glioma, and type 2 diabetes mellitus, diseases that implicate tissue-resident macrophages. Here, we review the evidence that genetic variants at 9p21.3 disrupt tissue-specific enhancers and propose new insights to guide future studies.
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Sakurada Y, Mabuchi F. Advances in glaucoma genetics. PROGRESS IN BRAIN RESEARCH 2015; 220:107-26. [DOI: 10.1016/bs.pbr.2015.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Cheng CY, Allingham RR, Aung T, Tham YC, Hauser MA, Vithana EN, Khor CC, Wong TY. Association of common SIX6 polymorphisms with peripapillary retinal nerve fiber layer thickness: the Singapore Chinese Eye Study. Invest Ophthalmol Vis Sci 2014; 56:478-83. [PMID: 25537207 DOI: 10.1167/iovs.14-15863] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Recently the common SIX6 missense variant rs33912345 was found to be highly associated with glaucoma. The aim of this study was to investigate the association between this SIX6 variant and peripapillary retinal nerve fiber layer (RNFL) thickness measured by spectral-domain optical coherence tomography (SD-OCT) in a population setting. METHODS Study subjects were enrolled from the Singapore Chinese Eye Study (SCES), a population-based survey of Singaporean Chinese aged 40 years or older. Subjects underwent a comprehensive ocular examination. Spectral-domain OCT was used to measure RNFL thicknesses. Genotyping of SIX6 rs33912345 (Asn141His) was performed using HumanExome BeadChip. RESULTS A total of 2129 eyes from 1243 SCES subjects (mean age: 55.0 ± 7.4 years) with rs33912345 genotype data and SD-OCT images were included for the analysis. Of these, 26 eyes of 21 subjects had glaucoma. The frequency of rs33912345 risk variant C (His141) was 80% in the study subjects. Each rs33912345 C allele was associated with a decrease of 1.44 μm in RNFL thickness after adjusting for age, sex, genetic principal components, and axial length (P = 0.001). These associations remained similar in 2096 nonglaucoma eyes in which each C allele was associated with a decrease of 1.39 μm in RNFL thickness (P = 0.001). The strongest association was observed in the superior RNFL sector (a decrease of 2.83 μm per risk allele, P < 0.001) followed by the inferior RNFL sector (a decrease of 2.24 μm per risk allele, P = 0.003), while the association did not reach significance in the nasal and temporal sectors. CONCLUSIONS Nonglaucomatous individuals with the SIX6 missense variant have reduced RNFL thickness in regions known to be particularly affected in those with glaucoma. This may be the primary mechanism for increased risk of POAG in individuals who carry the SIX6 His141 risk variant.
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Affiliation(s)
- Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - R Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Tin Aung
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
| | - Yih-Chung Tham
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
| | - Michael A Hauser
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Eranga N Vithana
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore Duke-NUS Graduate Medical School, Singapore
| | - Chiea Chuen Khor
- Division of Human Genetics, Genome Institute of Singapore, Singapore
| | - Tien Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
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Chen F, Klein AP, Klein BEK, Lee KE, Truitt B, Klein R, Iyengar SK, Duggal P. Exome array analysis identifies CAV1/CAV2 as a susceptibility locus for intraocular pressure. Invest Ophthalmol Vis Sci 2014; 56:544-51. [PMID: 25525164 DOI: 10.1167/iovs.14-15204] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
PURPOSE Intraocular pressure (IOP) is an important clinical parameter in the evaluation of ocular health. Elevated IOP is a major risk factor for primary open-angle glaucoma (POAG). The goal of this study was to identify rare and less common variants that influence IOP. METHODS We performed an exome array analysis in a subset of 1660 individuals from a population-based cohort, the Beaver Dam Eye Study. Associations with IOP were tested on 45,849 single nucleotide variants and 12,390 autosomal genes across the genome. RESULTS Intraocular pressure was suggestively associated with novel variants located in FAR2 at 12p11.22 (rs4931170, P = 1.2 × 10(-5)), in GGA3 at 17q25.1 (rs52809447, P = 6.7 × 10(-5)), and in PKDREJ at 22q13.31 (rs7291444, P = 7.4 × 10(-5)). Gene-based analysis found suggestive associations between IOP and the genes HAP1, MTBP, FREM3, and PHF12. We successfully replicated the associations with GAS7 (P = 7.4 × 10(-3)) for IOP, and also identified a previously reported POAG locus in the CAV1/CAV2 region to be associated with IOP (P = 3.3 × 10(-3)). This association was confirmed in a meta-analysis with three published genome-wide association studies (Pcombined = 4.0 × 10(-11)). CONCLUSIONS Our results suggest that novel genetic variants and genes with multiple, less common variants may play a role in the control of IOP. The implication of the caveolin genes, CAV1/CAV2, as a common genetic factor influencing both IOP variations and POAG may provide new insights of the underlying mechanism leading to glaucoma and glaucomatous visual field loss.
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Affiliation(s)
- Fei Chen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
| | - Alison P Klein
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
| | - Barbara E K Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States
| | - Kristine E Lee
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States
| | - Barbara Truitt
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States
| | - Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States
| | - Sudha K Iyengar
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
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Li WQ, Pfeiffer RM, Hyland PL, Shi J, Gu F, Wang Z, Bhattacharjee S, Luo J, Xiong X, Yeager M, Deng X, Hu N, Taylor PR, Albanes D, Caporaso NE, Gapstur SM, Amundadottir L, Chanock SJ, Chatterjee N, Landi MT, Tucker MA, Goldstein AM, Yang XR. Genetic polymorphisms in the 9p21 region associated with risk of multiple cancers. Carcinogenesis 2014; 35:2698-705. [PMID: 25239644 DOI: 10.1093/carcin/bgu203] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The chromosome 9p21 region has been implicated in the pathogenesis of multiple cancers. We analyzed 9p21 single nucleotide polymorphisms (SNPs) from eight genome-wide association studies (GWAS) with data deposited in dbGaP, including studies of esophageal squamous cell carcinoma (ESCC), gastric cancer (GC), pancreatic cancer, renal cell carcinoma (RCC), lung cancer (LC), breast cancer (BrC), bladder cancer (BC) and prostate cancer (PrC). The number of subjects ranged from 2252 (PrC) to 7619 (LC). SNP-level analyses for each cancer were conducted by logistic regression or random-effects meta-analysis. A subset-based statistical approach (ASSET) was performed to combine SNP-level P values across multiple cancers. We calculated gene-level P values using the adaptive rank truncated product method. We identified that rs1063192 and rs2157719 in the CDKN2A/2B region were significantly associated with ESCC and rs2764736 (3' of TUSC1) was associated with BC (P ≤ 2.59 × 10(-6)). ASSET analyses identified four SNPs significantly associated with multiple cancers: rs3731239 (CDKN2A intronic) with ESCC, GC and BC (P = 3.96 × 10(-) (4)); rs10811474 (3' of IFNW1) with RCC and BrC (P = 0.001); rs12683422 (LINGO2 intronic) with RCC and BC (P = 5.93 × 10(-) (4)) and rs10511729 (3' of ELAVL2) with LC and BrC (P = 8.63 × 10(-) (4)). At gene level, CDKN2B, CDKN2A and CDKN2B-AS1 were significantly associated with ESCC (P ≤ 4.70 × 10(-) (5)). Rs10511729 and rs10811474 were associated with cis-expression of 9p21 genes in corresponding cancer tissues in the expression quantitative trait loci analysis. In conclusion, we identified several genetic variants in the 9p21 region associated with the risk of multiple cancers, suggesting that this region may contribute to a shared susceptibility across different cancer types.
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Affiliation(s)
- Wen-Qing Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA, Department of Dermatology, Warren Alpert Medical School, Brown University, Providence, RI, USA,
| | - Ruth M Pfeiffer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Paula L Hyland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Fangyi Gu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-Frederick, SAIC-Frederick Inc., Frederick, MD, USA
| | | | - Jun Luo
- Information Management Services, Inc., Calverton, MD, USA and
| | - Xiaoqin Xiong
- Information Management Services, Inc., Calverton, MD, USA and
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-Frederick, SAIC-Frederick Inc., Frederick, MD, USA
| | - Xiang Deng
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-Frederick, SAIC-Frederick Inc., Frederick, MD, USA
| | - Nan Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Philip R Taylor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Laufey Amundadottir
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
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Hoffmann TJ, Tang H, Thornton TA, Caan B, Haan M, Millen AE, Thomas F, Risch N. Genome-wide association and admixture analysis of glaucoma in the Women's Health Initiative. Hum Mol Genet 2014; 23:6634-43. [PMID: 25027321 DOI: 10.1093/hmg/ddu364] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We report a genome-wide association study (GWAS) and admixture analysis of glaucoma in 12 008 African-American and Hispanic women (age 50-79 years) from the Women's Health Initiative (WHI). Although GWAS of glaucoma have been conducted on several populations, this is the first to look at glaucoma in individuals of African-American and Hispanic race/ethnicity. Prevalent and incident glaucoma was determined by self-report from study questionnaires administered at baseline (1993-1998) and annually through 2005. For African Americans, there was a total of 658 prevalent cases, 1062 incident cases and 6067 individuals who never progressed to glaucoma. For our replication cohort, we used the WHI Hispanics, including 153 prevalent cases, 336 incident cases and 2685 non-cases. We found an association of African ancestry with glaucoma incidence in African Americans (hazards ratio 1.62, 95% CI 1.023-2.56, P = 0.038) and in Hispanics (hazards ratio 3.21, 95% CI 1.32-7.80, P = 0.011). Although we found that no previously identified glaucoma SNPs replicated in either the WHI African Americans or Hispanics, a risk score combining all previously reported hits was significant in African-American prevalent cases (P = 0.0046), and was in the expected direction in the incident cases, as well as in the Hispanic incident cases. Additionally, after imputing to 1000 Genomes, two less common independent SNPs were suggestive in African Americans, but had too low of an allele frequency in Hispanics to test for replication. These results suggest the possibility of a distinct genetic architecture underlying glaucoma in individuals of African ancestry.
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Affiliation(s)
- Thomas J Hoffmann
- Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA,
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Bette Caan
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| | - Mary Haan
- Department of Epidemiology and Biostatistics and
| | - Amy E Millen
- Department of Epidemiology and Environmental Health, University at Buffalo, The State University of New York, Buffalo, NY 14214, USA and
| | - Fridtjof Thomas
- Department of Preventative Medicine, University of Tennessee Health Science Center, Memphis, TN 38105, USA
| | - Neil Risch
- Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA, Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
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Chandra A, Mitry D, Wright A, Campbell H, Charteris DG. Genome-wide association studies: applications and insights gained in Ophthalmology. Eye (Lond) 2014; 28:1066-79. [PMID: 24971990 DOI: 10.1038/eye.2014.145] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 05/18/2014] [Indexed: 12/20/2022] Open
Abstract
Genome-wide association studies (GWAS) use high-throughput genotyping technologies to genotype thousands of single-nucleotide polymorphisms (SNPs) and relate them to the development of clinical and quantitative traits. Their use has been highly successful in the field of ophthalmology, and since the advent of GWAS in 2005, many genes not previously suspected of having a role in disease have been identified and the findings replicated. We conducted an extensive literature review and describe the concept, design, advantages, and limitations of GWAS and provide a detailed description of the applications and discoveries of GWAS in the field of eye disease to date. There have been many novel findings revealing previously unknown biological insights in a diverse range of common ocular conditions. GWAS have been a highly successful modality for investigating the pathogenesis of a wide variety of ophthalmic conditions. The insights gained into the pathogenesis of disease provide not only a better understanding of underlying disease mechanism but also offer a rationale for targeted treatment and preventative strategies. Expansive international collaboration and standardised phenotyping will permit the continued success of this investigative technique.
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Affiliation(s)
- A Chandra
- 1] Department of Ophthalmology, Moorfields Eye Hospital, London, UK [2] UCL Institute of Ophthalmology, London, UK
| | - D Mitry
- 1] Department of Ophthalmology, Moorfields Eye Hospital, London, UK [2] Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - A Wright
- Medical Research Council Human Genetics Unit, Western General Hospital, Edinburgh, UK
| | - H Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - D G Charteris
- Department of Ophthalmology, Moorfields Eye Hospital, London, UK
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Discovery and functional annotation of SIX6 variants in primary open-angle glaucoma. PLoS Genet 2014; 10:e1004372. [PMID: 24875647 PMCID: PMC4038608 DOI: 10.1371/journal.pgen.1004372] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 03/26/2014] [Indexed: 12/05/2022] Open
Abstract
Glaucoma is a leading cause of blindness worldwide. Primary open-angle glaucoma (POAG) is the most common subtype and is a complex trait with multigenic inheritance. Genome-wide association studies have previously identified a significant association between POAG and the SIX6 locus (rs10483727, odds ratio (OR) = 1.32, p = 3.87×10−11). SIX6 plays a role in ocular development and has been associated with the morphology of the optic nerve. We sequenced the SIX6 coding and regulatory regions in 262 POAG cases and 256 controls and identified six nonsynonymous coding variants, including five rare and one common variant, Asn141His (rs33912345), which was associated significantly with POAG (OR = 1.27, p = 4.2×10−10) in the NEIGHBOR/GLAUGEN datasets. These variants were tested in an in vivo Danio rerio (zebrafish) complementation assay to evaluate ocular metrics such as eye size and optic nerve structure. Five variants, found primarily in POAG cases, were hypomorphic or null, while the sixth variant, found only in controls, was benign. One variant in the SIX6 enhancer increased expression of SIX6 and disrupted its regulation. Finally, to our knowledge for the first time, we have identified a clinical feature in POAG patients that appears to be dependent upon SIX6 genotype: patients who are homozygous for the SIX6 risk allele (His141) have a statistically thinner retinal nerve fiber layer than patients homozygous for the SIX6 non-risk allele (Asn141). Our results, in combination with previous SIX6 work, lead us to hypothesize that SIX6 risk variants disrupt the development of the neural retina, leading to a reduced number of retinal ganglion cells, thereby increasing the risk of glaucoma-associated vision loss. Primary open angle glaucoma is a blinding disease for which there is currently no cure, only treatments that may slow its progress. To help understand the mechanisms of this disease and to design more effective treatments, we identified previously a locus, SIX6, that increases the risk of glaucoma. This gene is involved in early eye development and helps to form the retina. In this paper, we test specific sequence variants in SIX6 that are found in glaucoma patients. We show that these variants have a reduced function that interferes with their ability to direct proper formation of the retina. One variant in particular is common, and may be the main reason that this gene is important in the glaucoma disease process. Patients who have two copies of this sequence variant show a change in the structure of their eye consistent with fewer neurons that carry the visual signal to the brain. These neurons typically die as people age, and people who begin life with fewer visual neurons may have an increased risk of glaucoma. Additional research in this topic may lead to new treatments that preserve sight.
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Shpak M, Hall AW, Goldberg MM, Derryberry DZ, Ni Y, Iyer VR, Cowperthwaite MC. An eQTL analysis of the human glioblastoma multiforme genome. Genomics 2014; 103:252-63. [DOI: 10.1016/j.ygeno.2014.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/11/2014] [Accepted: 02/24/2014] [Indexed: 12/20/2022]
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89
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Rahmioglu N, Nyholt DR, Morris AP, Missmer SA, Montgomery GW, Zondervan KT. Genetic variants underlying risk of endometriosis: insights from meta-analysis of eight genome-wide association and replication datasets. Hum Reprod Update 2014; 20:702-16. [PMID: 24676469 PMCID: PMC4132588 DOI: 10.1093/humupd/dmu015] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Endometriosis is a heritable common gynaecological condition influenced by multiple genetic and environmental factors. Genome-wide association studies (GWASs) have proved successful in identifying common genetic variants of moderate effects for various complex diseases. To date, eight GWAS and replication studies from multiple populations have been published on endometriosis. In this review, we investigate the consistency and heterogeneity of the results across all the studies and their implications for an improved understanding of the aetiology of the condition. METHODS Meta-analyses were conducted on four GWASs and four replication studies including a total of 11 506 cases and 32 678 controls, and on the subset of studies that investigated associations for revised American Fertility Society (rAFS) Stage III/IV including 2859 cases. The datasets included 9039 cases and 27 343 controls of European (Australia, Belgium, Italy, UK, USA) and 2467 cases and 5335 controls of Japanese ancestry. Fixed and Han and Elkin random-effects models, and heterogeneity statistics (Cochran's Q test), were used to investigate the evidence of the nine reported genome-wide significant loci across datasets and populations. RESULTS Meta-analysis showed that seven out of nine loci had consistent directions of effect across studies and populations, and six out of nine remained genome-wide significant (P < 5 × 10−8), including rs12700667 on 7p15.2 (P = 1.6 × 10−9), rs7521902 near WNT4 (P = 1.8 × 10−15), rs10859871 near VEZT (P = 4.7 × 10−15), rs1537377 near CDKN2B-AS1 (P = 1.5 × 10−8), rs7739264 near ID4 (P = 6.2 × 10−10) and rs13394619 in GREB1 (P = 4.5 × 10−8). In addition to the six loci, two showed borderline genome-wide significant associations with Stage III/IV endometriosis, including rs1250248 in FN1 (P = 8 × 10−8) and rs4141819 on 2p14 (P = 9.2 × 10−8). Two independent inter-genic loci, rs4141819 and rs6734792 on chromosome 2, showed significant evidence of heterogeneity across datasets (P < 0.005). Eight of the nine loci had stronger effect sizes among Stage III/IV cases, implying that they are likely to be implicated in the development of moderate to severe, or ovarian, disease. While three out of nine loci were inter-genic, the remaining were in or near genes with known functions of biological relevance to endometriosis, varying from roles in developmental pathways to cellular growth/carcinogenesis. CONCLUSIONS Our meta-analysis shows remarkable consistency in endometriosis GWAS results across studies, with little evidence of population-based heterogeneity. They also show that the phenotypic classifications used in GWAS to date have been limited. Stronger associations with Stage III/IV disease observed for most loci emphasize the importance for future studies to include detailed sub-phenotype information. Functional studies in relevant tissues are needed to understand the effect of the variants on downstream biological pathways.
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Affiliation(s)
- Nilufer Rahmioglu
- Wellcome Trust Center for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Dale R Nyholt
- Neurogenetics, QIMR Berghofer Medical Research Institute, Brisbane QLD 4029, Australia
| | - Andrew P Morris
- Wellcome Trust Center for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Department of Biostatistics, University of Liverpool, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - Stacey A Missmer
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - Grant W Montgomery
- Molecular Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane QLD 4029, Australia
| | - Krina T Zondervan
- Wellcome Trust Center for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Nuffield Department of Obstetrics and Gynaecology, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
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90
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Takamoto M, Araie M. Genetics of primary open angle glaucoma. Jpn J Ophthalmol 2013; 58:1-15. [DOI: 10.1007/s10384-013-0286-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 09/17/2013] [Indexed: 04/21/2023]
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91
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Janssen SF, Gorgels TG, Ramdas WD, Klaver CC, van Duijn CM, Jansonius NM, Bergen AA. The vast complexity of primary open angle glaucoma: Disease genes, risks, molecular mechanisms and pathobiology. Prog Retin Eye Res 2013; 37:31-67. [DOI: 10.1016/j.preteyeres.2013.09.001] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 07/26/2013] [Accepted: 09/03/2013] [Indexed: 12/21/2022]
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92
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Ng SK, Casson RJ, Burdon KP, Craig JE. Chromosome 9p21 primary open-angle glaucoma susceptibility locus: a review. Clin Exp Ophthalmol 2013; 42:25-32. [DOI: 10.1111/ceo.12234] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 09/09/2013] [Indexed: 01/07/2023]
Affiliation(s)
- Soo Khai Ng
- South Australian Institute of Ophthalmology; Royal Adelaide Hospital; Adelaide South Australia Australia
- University of Adelaide; Adelaide South Australia Australia
| | - Robert J Casson
- South Australian Institute of Ophthalmology; Royal Adelaide Hospital; Adelaide South Australia Australia
- University of Adelaide; Adelaide South Australia Australia
| | - Kathryn P Burdon
- Department of Ophthalmology; Flinders University, Flinders Medical Centre; Adelaide South Australia Australia
| | - Jamie E Craig
- Department of Ophthalmology; Flinders University, Flinders Medical Centre; Adelaide South Australia Australia
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Iglesias AI, Springelkamp H, van der Linde H, Severijnen LA, Amin N, Oostra B, Kockx CEM, van den Hout MCGN, van IJcken WFJ, Hofman A, Uitterlinden AG, Verdijk RM, Klaver CCW, Willemsen R, van Duijn CM. Exome sequencing and functional analyses suggest that SIX6 is a gene involved in an altered proliferation–differentiation balance early in life and optic nerve degeneration at old age. Hum Mol Genet 2013; 23:1320-32. [DOI: 10.1093/hmg/ddt522] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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94
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Chidlow G, Wood JPM, Sharma S, Dimasi DP, Burdon KP, Casson RJ, Craig JE. Ocular expression and distribution of products of the POAG-associated chromosome 9p21 gene region. PLoS One 2013; 8:e75067. [PMID: 24069379 PMCID: PMC3777912 DOI: 10.1371/journal.pone.0075067] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 08/10/2013] [Indexed: 11/18/2022] Open
Abstract
It has recently been shown that there are highly significant associations for common single nucleotide polymorphisms (SNPs) near the CDKN2B-AS1 gene region at the 9p21 locus with primary open angle glaucoma (POAG), a leading cause of irreversible blindness. This gene region houses the CDKN2B/p15INK4B,CDKN2A/p16INK4A and p14ARF (rat equivalent, p19ARF) tumour suppressor genes and is adjacent to the S-methyl-5′-thioadenosine phosphorylase (MTAP) gene. In order to understand the ocular function of these genes and, therefore, how they may be involved in the pathogenesis of POAG, we studied the distribution patterns of each of their products within human and rat ocular tissues. MTAP mRNA was detected in the rat retina and optic nerve and its protein product was localised to the corneal epithelium, trabecular meshwork and retinal glial cells in both human and rat eyes. There was a very low level of p16INK4A mRNA present within the rat retina and slightly more in the optic nerve, although no protein product could be detected in either rat or human eyes with any of the antibodies tested. P19ARF mRNA was likewise only present at very low levels in rat retina and slightly higher levels in the optic nerve. However, no unambiguous evidence was found to indicate expression of specific P19ARF/p14ARF proteins in either rat or human eyes, respectively. In contrast, p15INK4B mRNA was detected in much higher amounts in both retina and optic nerve compared with the other genes under analysis. Moreover, p15INK4B protein was clearly localised to the retinal inner nuclear and ganglion cell layers and the corneal epithelium and trabecular meshwork in rat and human eyes. The presented data provide the basis for future studies that can explore the roles that these gene products may play in the pathogenesis of glaucoma and other models of optic nerve damage.
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Affiliation(s)
- Glyn Chidlow
- Ophthalmic Research Laboratories, South Australian Institute of Ophthalmology, Hanson Institute Centre for Neurological Diseases, Adelaide, South Australia, Australia
- Department of Ophthalmology and Visual Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - John P. M. Wood
- Ophthalmic Research Laboratories, South Australian Institute of Ophthalmology, Hanson Institute Centre for Neurological Diseases, Adelaide, South Australia, Australia
- Department of Ophthalmology and Visual Sciences, University of Adelaide, Adelaide, South Australia, Australia
- * E-mail:
| | - Shiwani Sharma
- Department of Ophthalmology, Flinders University, Bedford Park, South Australia, Australia
| | - David P. Dimasi
- Department of Ophthalmology, Flinders University, Bedford Park, South Australia, Australia
| | - Kathryn P. Burdon
- Department of Ophthalmology, Flinders University, Bedford Park, South Australia, Australia
| | - Robert J. Casson
- Ophthalmic Research Laboratories, South Australian Institute of Ophthalmology, Hanson Institute Centre for Neurological Diseases, Adelaide, South Australia, Australia
- Department of Ophthalmology and Visual Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Jamie E. Craig
- Department of Ophthalmology, Flinders University, Bedford Park, South Australia, Australia
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95
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Liu Y, Hauser MA, Akafo SK, Qin X, Miura S, Gibson JR, Wheeler J, Gaasterland DE, Challa P, Herndon LW, Ritch R, Moroi SE, Pasquale LR, Girkin CA, Budenz DL, Wiggs JL, Richards JE, Ashley-Koch AE, Allingham RR. Investigation of known genetic risk factors for primary open angle glaucoma in two populations of African ancestry. Invest Ophthalmol Vis Sci 2013; 54:6248-54. [PMID: 23963167 PMCID: PMC3776712 DOI: 10.1167/iovs.13-12779] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 08/12/2013] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Multiple genes have been associated with primary open angle glaucoma (POAG) in Caucasian populations. We now examine the association of these loci in populations of African ancestry, populations at particularly high risk for POAG. METHODS We genotyped DNA samples from two populations: African American (1150 cases and 999 controls) and those from Ghana, West Africa (483 cases and 593 controls). Our analysis included 57 single nucleotide polymorphisms (SNPs) in five loci previously associated with POAG at the genome-wide level, including CDKN2B-AS1, TMCO1, CAV1/CAV2, chromosome 8q22 intergenic region, and SIX1/SIX6. We evaluated association in the full datasets, as well as subgroups with normal pressure glaucoma (NPG, maximum IOP ≤21 mm Hg) and high pressure glaucoma (HPG, IOP >21 mm Hg). RESULTS In African Americans, we identified an association of rs10120688 in the CDNK2B-AS1 region with POAG (P = 0.0020). Several other SNPs were nominally associated, but did not survive correction for multiple testing. In the subgroup analyses, significant associations were identified for rs10965245 (P = 0.0005) in the CDKN2B-AS1 region with HPG and rs11849906 in the SIX1/SIX6 region with NPG (P = 0.006). No significant association was identified with any loci in the Ghanaian samples. CONCLUSIONS POAG genetic susceptibility alleles associated in Caucasians appear to play a greatly reduced role in populations of African ancestry. Thus, the major genetic components of POAG of African origin remain to be identified. This finding underscores the critical need to pursue large-scale genome-wide association studies in this understudied, yet disproportionately affected population.
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Affiliation(s)
- Yutao Liu
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina
| | - Michael A. Hauser
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina
| | - Stephen K. Akafo
- Unit of Ophthalmology, Department of Surgery, University of Ghana Medical School, Accra, Ghana
| | - Xuejun Qin
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Shiroh Miura
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Jason R. Gibson
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Joshua Wheeler
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | | | - Pratap Challa
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina
| | - Leon W. Herndon
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina
| | | | - Robert Ritch
- Einhorn Clinical Research Center, Department of Ophthalmology, New York Eye and Ear Infirmary, New York, New York
| | - Sayoko E. Moroi
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan
| | - Louis R. Pasquale
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts
| | - Christopher A. Girkin
- Department of Ophthalmology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Donald L. Budenz
- Department of Ophthalmology, University of North Carolina, Chapel Hill, North Carolina
| | - Janey L. Wiggs
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts
| | - Julia E. Richards
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan
| | | | - R. Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina
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96
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Lack of association of apolipoprotein E (Apo E) ε2/ε3/ε4 polymorphisms with primary open-angle glaucoma: a meta-analysis from 1916 cases and 1756 controls. PLoS One 2013; 8:e72644. [PMID: 24023758 PMCID: PMC3759379 DOI: 10.1371/journal.pone.0072644] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 07/12/2013] [Indexed: 01/11/2023] Open
Abstract
Background A number of case-control studies were conducted to investigate the association of apolipoprotein E (Apo E) polymorphisms with primary open angle glaucoma (POAG). But the results remain controversial. This meta-analysis aims to comprehensively evaluate the relationship between a common ε2/ε3/ε4 polymorphism in Apo E gene on the risk of POAG. Method A comprehensive literature search for studies published up to April 2013 was performed. Summary odds ratios (ORs) and 95% confidence intervals (CI) were calculated employing random-effects models irrespective of between-study heterogeneity. Publication bias of literatures was evaluated using funnel plots and Egger's test. Results A total of 12 studies including 1916 cases and 1756 controls meeting the predefined criteria were involved in this meta-analysis. Overall, the Apo E ε2 allele and ε4 allele were not associated with POAG, compared with those carrying ε3 allele, with ORs of 0.98 (95% CI, 0.79 to 1.23; P = 0.872) and 1.05 (95% CI, 0.78 to 1.41; P = 0.743), respectively. Genotypic analysis also found no significant association between the ε4 carriers (ε3/ε4+ε4/ε4), ε2 carriers (ε2/ε3+ε2/ε2) and POAG, compared with participants with Apo E ε3/3, with ORs of 0.91 (95% CI, 0.66 to 1.25; P = 0.543) and 1.08 (95% CI, 0.74 to 1.57; P = 0.694), respectively. In the subgroup analysis by ethnicity, source of controls, genotyping methods, Hardy-Weinberg equilibrium or not, or type of the POAG, still no obvious associations were found. Conclusions This meta-analysis suggests that Apo E ε2/ε3/ε4 polymorphisms may not be associated with the risk of POAG. However, well-designed studies with larger sample size and more ethnic groups are required to further validate the results.
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97
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Genome-wide association study identifies a novel canine glaucoma locus. PLoS One 2013; 8:e70903. [PMID: 23951034 PMCID: PMC3737263 DOI: 10.1371/journal.pone.0070903] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 06/28/2013] [Indexed: 01/25/2023] Open
Abstract
Glaucoma is an optic neuropathy and one of the leading causes of blindness. Its hereditary forms are classified into primary closed-angle (PCAG), primary open-angle (POAG) and primary congenital glaucoma (PCG). Although many loci have been mapped in human, only a few genes have been identified that are associated with the development of glaucoma and the genetic basis of the disease remains poorly understood. Glaucoma has also been described in many dog breeds, including Dandie Dinmont Terriers (DDT) in which it is a late-onset (>7 years) disease. We designed clinical and genetic studies to better define the clinical features of glaucoma in the DDT and to identify the genetic cause. Clinical diagnosis was based on ophthalmic examinations of the affected dogs and 18 additionally investigated unaffected DDTs. We collected DNA from over 400 DTTs and a genome wide association study was performed in a cohort of 23 affected and 23 controls, followed by a fine mapping, a replication study and candidate gene sequencing. The clinical study suggested that ocular abnormalities including abnormal iridocorneal angles and pectinate ligament dysplasia are common (50% and 72%, respectively) in the breed and the disease resembles human PCAG. The genetic study identified a novel 9.5 Mb locus on canine chromosome 8 including the 1.6 Mb best associated region (p = 1.63 × 10(-10), OR = 32 for homozygosity). Mutation screening in five candidate genes did not reveal any causative variants. This study indicates that although ocular abnormalities are common in DDTs, the genetic risk for glaucoma is conferred by a novel locus on CFA8. The canine locus shares synteny to a region in human chromosome 14q, which harbors several loci associated with POAG and PCG. Our study reveals a new locus for canine glaucoma and ongoing molecular studies will likely help to understand the genetic etiology of the disease.
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98
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Expansive marker analysis replicating the association of glaucoma susceptibility with human chromosome loci 1q43 and 10p12.31. Eur J Hum Genet 2013; 22:409-13. [PMID: 23838595 DOI: 10.1038/ejhg.2013.149] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 05/18/2013] [Accepted: 06/06/2013] [Indexed: 01/30/2023] Open
Abstract
Three human chromosome loci (1q43, 10p12.31, and 12q21.31) were recently associated with the susceptibility to primary open-angle glaucoma (POAG) in a Japanese population; however, this was not replicated in three subsequent studies using South Indian, Afro-Caribbean, and Chinese populations. To identify genetic markers that are robustly associated across ethnic populations, numerous markers in addition to the six in the three reported loci were examined in this study. A total of 31 single-nucleotide polymorphism (SNP) markers were genotyped for 1115 Korean participants, and many neighboring SNPs were imputed using the Korean HapMap Project genotype data. Each SNP was statistically tested for association with POAG susceptibility by comparisons among 211 POAG patients with 904 unaffected controls. A strong and statistically significant association was found with a previously unreported SNP, rs7098387 (odds ratio, OR=2.0 (1.4-3.0), P=0.00038) at the 10p12.31 locus (where 11 SNPs were typed and 38 imputed) in contrast to the reported rs7081455, which was too poorly correlated with newly associated rs7098387 (r2=0.003, D'=0.40) to show association. Additionally, a modest association was observed with the reported rs693421 (OR=1.4 (1.1-1.7), P=0.0082) and several other SNPs located within and around ZP4 at the 1q43 locus (10 SNPs typed and 14 imputed). However, no association was observed with the reported rs7961953 SNP or any other SNPs at the 12q21.31 locus, upstream of TMTC2 (10 SNPs typed and 29 imputed). Accordingly, POAG susceptibility association was replicated using rs7098387 (C) rather than rs7081455 (T) at the 10p12.31 locus and additionally with rs693421 (T) at the 1q43 locus.
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99
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Kato T, Meguro A, Nomura E, Uemoto R, Nomura N, Ota M, Kashiwagi K, Mabuchi F, Iijima H, Kawase K, Yamamoto T, Nakamura M, Negi A, Sagara T, Nishida T, Inatani M, Tanihara H, Aihara M, Araie M, Fukuchi T, Abe H, Higashide T, Sugiyama K, Kanamoto T, Kiuchi Y, Iwase A, Chin S, Ohno S, Inoko H, Mizuki N. Association study of genetic variants on chromosome 7q31 with susceptibility to normal tension glaucoma in a Japanese population. Eye (Lond) 2013; 27:979-83. [PMID: 23743525 DOI: 10.1038/eye.2013.123] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 05/04/2013] [Indexed: 12/14/2022] Open
Abstract
The caveolin 1 to caveolin 2 (CAV1-CAV2) gene region on chromosome 7q31 has been reported to be associated with susceptibility to primary open angle glaucoma (POAG) and normal tension glaucoma (NTG) in previous studies. We investigated whether genetic variants in the CAV1-CAV2 region are associated with NTG in Japanese patients. Two hundred and ninety-two Japanese patients with NTG and 352 Japanese healthy controls were recruited. We genotyped three single-nucleotide polymorphisms; that is, rs1052990, rs4236601, and rs7795356, in the CAV1-CAV2 gene region and assessed the allelic diversity among cases and controls. The frequency of the minor allele (G) of rs1052990 was significantly decreased in NTG cases compared with controls (P=0.014, OR=0.71), whereas NTG or POAG cases had a significantly higher frequency of the allele than controls in previous studies. Conversely, rs7795356 did not show any significant association with NTG cases, and rs4236601 was monomorphic in the Japanese study population. Our findings did not correspond with previous positive results, suggesting that CAV1-CAV2 variants studied in the present study are not important risk factors for NTG susceptibility in all populations. Further studies are needed to elucidate the possible contribution of the CAV1-CAV2 region to the development of glaucoma.
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Affiliation(s)
- T Kato
- Department of Ophthalmology, Yokohama City University School of Medicine, Kanagawa, Japan
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100
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Whigham BT, Allingham RR. Developments in Ocular Genetics: Annual Review. ASIA-PACIFIC JOURNAL OF OPHTHALMOLOGY (PHILADELPHIA, PA.) 2013; 2:177-86. [PMID: 26108111 DOI: 10.1097/apo.0b013e318294b837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE The purpose of this study was to summarize major developments in ocular genetics over the past year. DESIGN A literature review was performed for articles relating to the genetics of eye diseases and morphology. The search focused on articles published between September 15, 2011, and September 15, 2012. METHODS PubMed and Google Scholar search tools were used to search for ocular genetics articles in the desired date range. RESULTS Major advances have been reported in numerous areas including glaucoma, age-related macular degeneration, and keratoconus. Numerous novel associations have been identified through large genome-wide association studies. In addition, numerous disease genes have been identified through next-generation sequencing technologies. CONCLUSIONS Ocular genetics continues to advance at a rapid pace and benefit from new technologies. Numerous discoveries in the past year point toward areas for continued research.
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Affiliation(s)
- Benjamin T Whigham
- From the Department of Ophthalmology, Duke University Eye Center, Durham, NC
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