Genome-wide association study success in ophthalmology

Current Opinion in Ophthalmology

Volumn 25, Issue 5, 2014, Pages 386-393

  MacKey, David A ^a,b,c   Hewitt, Alex W ^a,b,c  

^a UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^b UNIVERSITY OF MELBOURNE   (Australia)

^c UNIVERSITY OF TASMANIA   (Australia)

Author keywords

age related macular degeneration; gene environment interaction; keratoconus; myopia; primary open angle glaucoma

Indexed keywords

BIOMETRY; CATARACT; CENTRAL CORNEAL THICKNESS; CLOSED ANGLE GLAUCOMA; ENDOPHENOTYPE; EXOME; EYE DISEASE; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC RISK; GENETIC VARIABILITY; GENOME; GENOTYPE ENVIRONMENT INTERACTION; GENOTYPE PHENOTYPE CORRELATION; GLAUCOMA; HUMAN; KERATOCONUS; MYOPIA; PRIORITY JOURNAL; RETINA MACULA AGE RELATED DEGENERATION; REVIEW; SENSITIVITY AND SPECIFICITY;

EYE DISEASES; GENE-ENVIRONMENT INTERACTION; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; GLAUCOMA, OPEN-ANGLE; HUMANS; KERATOCONUS; MACULAR DEGENERATION; MYOPIA; OPHTHALMOLOGY;

EID: 84905985257     PISSN: 10408738     EISSN: 15317021     Source Type: Journal    
DOI: 10.1097/ICU.0000000000000090     Document Type: Review

References (67)

1. Venter JC, Adams MD, Myers EW, et al. The sequence of the human genome. Science 2001; 291:1304-1351. (Pubitemid 32173090)
2. Lander ES, Linton LM, Birren B, et al. Initial sequencing and analysis of the human genome. Nature 2001; 409:860-921. (Pubitemid 32165345)
3. CB International HapMap Consortium. The International HapMap Project. Nature 2003; 426:789-796.
4. Manolio TA. Genomewide association studies and assessment of the risk of disease. N Engl J Med 2010; 363:166-176.
5. Edwards AO, Ritter R 3rd, Abel KJ, et al. Complement factor H polymorphism and age-related macular degeneration. Science 2005; 308:421-424. (Pubitemid 40530082)
6. Haines JL, Hauser MA, Schmidt S, et al. Complement factorHvariant increases the risk of age-related macular degeneration. Science 2005; 308:419-421. (Pubitemid 40530081)
7. Klein RJ, Zeiss C, Chew EY, et al. Complement factor H polymorphism in age-related macular degeneration. Science 2005; 308:385-389. (Pubitemid 40530070)
8. Dewan A, Liu M, Hartman S, et al. HTRA1 promoter polymorphism in wet age-related macular degeneration. Science 2006; 314:989-992. (Pubitemid 44749943)
9. Yang Z, Camp NJ, Sun H, et al. A variant of the HTRA1 gene increases susceptibility to age-related macular degeneration. Science 2006; 314:992-993. (Pubitemid 44749944)
10. Blue Mountains Eye Study (BMES), Wellcome Trust Case Control Consor tium 2 (WTCCC2). Genome-wide association study of intraocular pressure identifies the GLCCI1/ICA1 region as a glaucoma susceptibility locus. Hum Mol Genet 2013; 22:4653-4660.
11. Fritsche LG, Chen W, Schu M, et al. Seven new loci associated with age-related macular degeneration. Nat Genet 2013; 45:433-439; . The largest GWAS study for AMD performed to date identified 19 loci significantly associated with disease.
12. Holliday EG, Smith AV, Cornes BK, et al. Insights into the genetic architecture of early stage age-related macular degeneration: a genome-wide association study meta-analysis. PLoS One 2013; 8:e53830.
13. Ardeljan D, Meyerle CB, Agron E, et al. Influence of TIMP3/SYN3 polymorphisms on the phenotypic presentation of age-related macular degeneration. Eur J Hum Genet 2013; 21:1152-1157.
14. Zhang X, Li M, Wen F, et al. Different impact of high-density lipoprotein-related genetic variants on polypoidal choroidal vasculopathy and neovascular age-related macular degeneration in a Chinese Han population. Exp Eye Res 2013; 108:16-22.
15. Ratnapriya R, Chew EY. Age-related macular degeneration-clinical review and genetics update. Clin Genet 2013; 84:160-166.
16. Zhan X, Larson DE, Wang C, et al. Identification of a rare coding variant in complement 3 associated with age-related macular degeneration. Nat Genet 2013; 45:1375-1379.
17. Seddon JM, Yu Y, Miller EC, et al. Rare variants in CFI, C3 and C9 are associated with high risk of advanced age-related macular degeneration. Nat Genet 2013; 45:1366-1370.
18. Naj AC, Scott WK, Courtenay MD, et al. Genetic factors in nonsmokers with age-related macular degeneration revealed through genome-wide gene-environment interaction analysis. Ann Hum Genet 2013; 77:215-231.
19. Cooke Bailey JN, Sobrin L, Pericak-Vance MA, et al. Advances in the genomics of common eye diseases. Hum Mol Genet 2013; 22:R59-R65.
20. Sherwin JC, Mackey DA. Update on the epidemiology and genetics of myopic refractive error. Expert Rev Ophthalmol 2013; 8:63-87.
21. Hysi PG, Young TL, Mackey DA, et al. A genome-wide association study for myopia and refractive error identifies a susceptibility locus at 15q25. Nat Genet 2010; 42:902-905.
22. Verhoeven VJ, Hysi PG, Saw SM, et al. Large scale international replication and meta-analysis study confirms association of the 15q14 locus with myopia. The CREAM consortium. Hum Genet 2012; 131:1467-1480.
23. Verhoeven VJ, Hysi PG, Wojciechowski R, et al. Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia. Nat Genet 2013; 45:314-318.
24. Kiefer AK, Tung JY, Do CB, et al. Genome-wide analysis points to roles for extracellular matrix remodeling, the visual cycle, and neuronal development in myopia. PLoS Genet 2013; 9:e1003299.
25. Wojciechowski R, Hysi PG. Focusing in on the complex genetics of myopia. PLoS Genet 2013; 9:e1003442.
26. Darnovsky M, Cussins J. FDA halts 23andMe personal genetic tests. What might this mean for the future of direct-to-consumer testing? MLO Med Lab Obs 2014; 46:33.
27. Hysi PG, Mahroo OA, Cumberland P, et al. Common mechanisms underlying refractive error identified in functional analysis of gene lists from genome-wide association study results in 2 European British cohorts. JAMA Ophthalmol 2014; 132:50-56.
28. Verhoeven VJ, Buitendijk GH, Rivadeneira F, et al. Education influences the role of genetics in myopia. Eur J Epidemiol 2013; 28:973-980.
29. Fan Q, Wojciechowski R, Kamran Ikram M, et al. Education influences the association between genetic variants and refractive error: a meta-analysis of five Singapore studies. Hum Mol Genet 2014; 23:546-554.
30. Cheng CY, Schache M, Ikram MK, et al. Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error. Am J Hum Genet 2013; 93:264-277.
31. Guggenheim JA, McMahon G, Kemp JP, et al. A genome-wide association study for corneal curvature identifies the platelet-derived growth factor receptor alpha gene as a quantitative trait locus for eye size in white Europeans. Mol Vis 2013; 19:243-253.
32. Lopes MC, Hysi PG, Verhoeven VJ, et al. Identification of a candidate gene for astigmatism. Invest Ophthalmol Vis Sci 2013; 54:1260-1267.
33. Yazar S, Mishra A, Ang W, et al. Interrogation of the platelet-derived growth factor receptor alpha locus and corneal astigmatism in Australians of Northern European ancestry: results of a genome-wide association study. Mol Vis 2013; 19:1238-1246.
34. Khor CC, Miyake M, Chen LJ, et al. Genome-wide association study identifies ZFHX1B as a susceptibility locus for severe myopia. Hum Mol Genet 2013; 22:5288-5294.
35. Meng W, Butterworth J, Bradley DT, et al. A genome-wide association study provides evidence for association of chromosome 8p23 (MYP10) and 10q21.1 (MYP15) with high myopia in the French Population. Invest Ophthal-mol Vis Sci 2012; 53:7983-7988.
36. Oishi M, Yamashiro K, Miyake M, et al. Association between ZIC2, RASGRF1, and SHISA6 genes and high myopia in Japanese subjects. Invest Ophthalmol Vis Sci 2013; 54:7492-7497.
37. Shi Y, Gong B, Chen L, et al. A genome-wide meta-analysis identifies two novel loci associated with high myopia in the Han Chinese population. Hum Mol Genet 2013; 22:2325-2333.
38. Stambolian D, Wojciechowski R, Oexle K, et al. Meta-analysis of genome-wide association studies in five cohorts reveals common variants in RBFOX1, a regulator of tissue-specific splicing, associated with refractive error. Hum Mol Genet 2013; 22:2754-2764.
39. Schache M, Richardson AJ, Mitchell P, et al. Genetic association of refractive error and axial length with 15q14 but not 15q25 in the Blue Mountains Eye Study cohort. Ophthalmology 2013; 120:292-297.
40. Simpson CL, Wojciechowski R, Yee SS, et al. Regional replication of association with refractive error on 15q14 and 15q25 in the Age-Related Eye Disease Study cohort. Mol Vis 2013; 19:2173-2186.
41. Lu Y, Vitart V, Burdon KP, et al. Genome-wide association analyses identify multiple loci associated with central corneal thickness and keratoconus. Nat Genet 2013; 45:155-163.
42. Sahebjada S, Schache M, Richardson AJ, et al. Evaluating the association between keratoconus and the corneal thickness genes in an independent Australian population. Invest Ophthalmol Vis Sci 2013; 54:8224-8228.
43. Bae HA, Mills RA, Lindsay RG, et al. Replication and meta-analysis of candidate loci identified variation at RAB3GAP1 associated with keratoco-nus. Invest Ophthalmol Vis Sci 2013; 54:5132-5135.
44. Li X, Bykhovskaya Y, Canedo AL, et al. Genetic association of COL5A1 variants in keratoconus patients suggests a complex connection between corneal thinning and keratoconus. Invest Ophthalmol Vis Sci 2013; 54:2696-2704.
45. Gao X, Gauderman WJ, Liu Y, et al. A genome-wide association study of central corneal thickness in Latinos. Invest Ophthalmol Vis Sci 2013; 54:2435-2443.
46. Scheetz TE, Fingert JH, Wang K, et al. A genome-wide association study for primary open angle glaucoma and macular degeneration reveals novel Loci. PLoS One 2013; 8:e58657.
47. Nag A, Venturini C, Hysi PG, et al. Copy number variation at chromosome 5q21.2 is associated with intraocular pressure. Invest Ophthalmol Vis Sci 2013; 54:3607-3612.
48. Thorleifsson G, Magnusson KP, Sulem P, et al. Common sequence variants in the LOXL1 gene confer susceptibility to exfoliation glaucoma. Science 2007; 317:1397-1400. (Pubitemid 47417481)
49. Thorleifsson G, Walters GB, Hewitt AW, et al. Common variants near CAV1 and CAV2 are associated with primary open-angle glaucoma. Nat Genet 2010; 42:906-909.
50. Burdon KP, Macgregor S, Hewitt AW, et al. Genome-wide association study identifies susceptibility loci for open angle glaucoma at TMCO1 and CDKN2B-AS1. Nat Genet 2011; 43:574-578.
51. Ng SK, Casson RJ, Burdon KP, Craig JE. Chromosome 9p21 primary open-angle glaucoma susceptibility locus: a review. Clin Experiment Ophthalmol 2014; 42:25-32.
52. Liu Y, Hauser MA, Akafo SK, et al. Investigation of known genetic risk factors for primary open angle glaucoma in two populations of African ancestry. Invest Ophthalmol Vis Sci 2013; 54:6248-6254.
53. Shi D, Funayama T, Mashima Y, et al. AssociationofHK2and NCK2withnormal tension glaucoma in the Japanese population. PLoS One 2013; 8:e54115.
54. Nag A, Venturini C, Small KS, et al. A genome-wide association study of intraocular pressure suggests a novel association in the gene FAM125B in the TwinsUK cohort. Hum Mol Genet 2014; 23:3343-3348.
55. Ozel AB, Moroi SE, Reed DM, et al. Genome-wide association study and meta-analysis of intraocular pressure. Hum Genet 2014; 133:41-57.
56. Venturini C, Nag A, Hysi PG, et al. Clarifying the role of ATOH7 in glaucoma endophenotypes. Br J Ophthalmol 2014; 98:562-566.
57. Shi H, Zhu R, Hu N, et al. An extensive replication study on three new susceptibility loci of primary angle closure glaucoma in Han Chinese: Jiangsu eye study. J Ophthalmol 2013; 2013:641596.
58. Day AC, Luben R, Khawaja AP, et al. Genotype-phenotype analysis of SNPs associated with primary angle closure glaucoma (rs1015213, rs3753841 and rs11024102) and ocular biometry in the EPIC-Norfolk Eye Study. Br J Ophthalmol 2013; 97:704-707.
59. Sheu WH, Kuo JZ, Lee IT, et al. Genome-wide association study in a Chinese population with diabetic retinopathy. Hum Mol Genet 2013; 22:3165-3173.
60. Sim X, Jensen RA, Ikram MK, et al. Genetic loci for retinal arteriolar microcirculation. PLoS One 2013; 8:e65804.
61. Jensen RA, Sim X, Li X, et al. Genome-wide association study of retinopathy in individuals without diabetes. PLoS One 2013; 8:e54232.
62. Kirin M, Chandra A, Charteris DG, et al. Genome-wide association study identifies genetic risk underlying primary rhegmatogenous retinal detachment. Hum Mol Genet 2013; 22:3174-3185.
63. Li Y, Zhang K, Chen H, et al. Agenome-wide association study inHan Chinese identifies a susceptibility locus for primary Sjogren's syndrome at 7q11.23. Nat Genet 2013; 45:1361-1365.
64. Bosten JM, Hogg RE, Bargary G, et al. Suggestive association with ocular phoria at chromosome 6p22. Invest Ophthalmol Vis Sci 2014; 55:345-352.
65. Liu F, Wollstein A, Hysi PG, et al. Digital quantification of human eye color highlights genetic association of three new loci. PLoS Genet 2010; 6:e1000934.
66. Kenealy SJ, Schmidt S, Agarwal A, et al. Linkage analysis for age-related macular degeneration supports a gene on chromosome 10q26. Mol Vis 2004; 10:57-61. (Pubitemid 38628976)
67. Sanfilippo PG, Hewitt AW, Hammond CJ, Mackey DA. The heritability of ocular traits. Surv Ophthalmol 2010; 55:561-583.