A genome-wide association study in the Japanese population confirms 9p21 and 14q23 as susceptibility loci for primary open angle glaucoma

Human Molecular Genetics

Volumn 21, Issue 12, 2012, Pages 2836-2842

  Osman, Wael ^a   Low, Siew Kee ^a   Takahashi, Atsushi ^b   Kubo, Michiaki ^b   Nakamura, Yusuke ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b RIKEN   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN DEPENDENT KINASE INHIBITOR 2A; CYCLIN DEPENDENT KINASE INHIBITOR 2B;

ALLELE; ARTICLE; CHROMOSOME; CHROMOSOME 14Q23; CHROMOSOME 9P21; CONTROLLED STUDY; DISEASE ASSOCIATION; GENE; GENE EXPRESSION; GENE LOCUS; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; HUMAN; HUMAN TISSUE; JAPANESE; MAJOR CLINICAL STUDY; OPEN ANGLE GLAUCOMA; PRIORITY JOURNAL; RETINA; RISK; SINGLE NUCLEOTIDE POLYMORPHISM; SIX6 GENE;

ADULT; AGED; AGED, 80 AND OVER; ALLELES; ASIAN CONTINENTAL ANCESTRY GROUP; CASE-CONTROL STUDIES; CHROMOSOMES, HUMAN, PAIR 14; CHROMOSOMES, HUMAN, PAIR 9; CYCLIN-DEPENDENT KINASE INHIBITOR P15; CYCLIN-DEPENDENT KINASE INHIBITOR P16; FEMALE; GENE FREQUENCY; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; GLAUCOMA, OPEN-ANGLE; HOMEODOMAIN PROTEINS; HUMANS; JAPAN; MALE; MIDDLE AGED; POLYMORPHISM, SINGLE NUCLEOTIDE; PRINCIPAL COMPONENT ANALYSIS; RISK FACTORS; TRANS-ACTIVATORS;

EID: 84861724751     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/dds103     Document Type: Article

References (40)

1. Resnikoff, S., Pascolini, D., Etya'ale, D., Kocur, I., Pararajasegaram, R., Pokharel, G.P. and Mariotti, S.P. (2004) Global data on visual impairment in the year 2002. Bull World Health Organ, 82, 844-851.
2. Iwase, A., Suzuki, Y., Araie, M., Yamamoto, T., Abe, H., Shirato, S., Kuwayama, Y., Mishima, H.K., Shimizu, H., Tomita, G. et al. (2004) The prevalence of primary open-angle glaucoma in Japanese: the Tajimi Study. Ophthalmology, 111, 1641-1648.
3. Allingham, R., Liu, Y. and Rhee, D. (2009) The genetics of primary open-angle glaucoma: a review. Exp. Eye Res., 88, 837-844.
4. Tielsch, J.M., Katz, J., Sommer, A., Quigley, H.A. and Javitt, J.C. (1994) Family history and risk of primary open angle glaucoma. The Baltimore Eye Survey. Arch. Ophthalmol., 112, 69-73.
5. Fan, B.J., Wang, D.Y., Lam, D.S. and Pang, C.P. (2006) Gene mapping for primary open angle glaucoma. Clin. Biochem., 39, 249-258.
6. Stone, E.M., Fingert, J.H., Alward, W.L., Nguyen, T.D., Polansky, J.R., Sunden, S.L., Nishimura, D., Clark, A.F., Nystuen, A., Nichols, B.E. et al. (1997) Identification of a gene that causes primary open angle glaucoma. Science, 275, 668-670.
7. Rezaie, T., Child, A., Hitchings, R., Brice, G., Miller, L., Coca-Prados, M., Héon, E., Krupin, T., Ritch, R., Kreutzer, D. et al. (2002) Adult-onset primary open-angle glaucoma caused by mutations in optineurin. Science, 295, 1077-1079.
8. Monemi, S., Spaeth, G., DaSilva, A., Popinchalk, S., Ilitchev, E., Liebmann, J., Ritch, R., Héon, E., Crick, R.P., Child, A. et al. (2005) Identification of a novel adult-onset primary open-angle glaucoma (POAG) gene on 5q22.1. Hum. Mol. Genet., 14, 725-733.
9. Hewitt, A.W., Craig, J.E. and Mackey, D.A. (2006) Complex genetics of complex traits: the case of primary open-angle glaucoma. Clin. Exp. Ophthalmol., 34, 472-484.
10. Nakano, M., Ikeda, Y., Taniguchi, T., Yagi, T., Fuwa, M., Omi, N., Tokuda, Y., Tanaka, M., Yoshii, K., Kageyama, M. et al. (2009) Three susceptible loci associated with primary open-angle glaucoma identified by genome-wide association study in a Japanese population. Proc. Natl Acad. Sci. USA, 106, 12838-12842.
11. Meguro, A., Inoko, H., Ota, M., Mizuki, N. and Bahram, S. Writing Committee for the Normal Tension Glaucoma Genetic Study Group of Japan Glaucoma Society. (2010) Genome-wide association study of normal tension glaucoma: common variants in SRBD1 and ELOVL5 contribute to disease susceptibility. Ophthalmology, 117, 1331-1338.e1335.
12. Thorleifsson, G., Walters, G.B., Hewitt, A.W., Masson, G., Helgason, A., DeWan, A., Sigurdsson, A., Jonasdottir, A., Gudjonsson, S.A., Magnusson, K.P. et al. (2010) Common variants near CAV1 and CAV2 are associated with primary open-angle glaucoma. Nat. Genet., 42, 906-909.
13. Burdon, K.P., Macgregor, S., Hewitt, A.W., Sharma, S., Chidlow, G., Mills, R.A., Danoy, P., Casson, R., Viswanathan, A.C., Liu, J.Z. et al. (2011) Genome-wide association study identifies susceptibility loci for open angle glaucoma at TMCO1 and CDKN2B-AS1. Nat. Genet., 43, 574-578.
14. Yamaguchi-Kabata, Y., Nakazono, K., Takahashi, A., Saito, S., Hosono, N., Kubo, M., Nakamura, Y. and Kamatani, N. (2008) Japanese population structure, based on SNP genotypes from 7003 individuals compared to other ethnic groups: effects on population-based association studies. Am. J. Hum. Genet., 83, 445-456.
15. Devlin, B. and Roeder, K. (1999) Genomic control for association studies. Biometrics, 55, 997-1004.
16. Bilguvar, K., Yasuno, K., Niemelä, M., Ruigrok, Y.M., von Und Zu Fraunberg, M., van Duijn, C.M., van den Berg, L.H., Mane, S., Mason, C.E., Choi, M. et al. (2008) Susceptibility loci for intracranial aneurysm in European and Japanese populations. Nat. Genet., 40, 1472-1477.
17. Shea, J., Agarwala, V., Philippakis, A.A., Maguire, J., Banks, E., Depristo, M., Thomson, B., Guiducci, C., Onofrio, R.C., Kathiresan, S. et al. (2011) Comparing strategies to fine-map the association of common SNPs at chromosome 9p21 with type 2 diabetes and myocardial infarction. Nat. Genet., 43, 801-805.
18. Helgadottir, A., Thorleifsson, G., Magnusson, K.P., Grétarsdottir, S., Steinthorsdottir, V., Manolescu, A., Jones, G.T., Rinkel, G.J., Blankensteijn, J.D., Ronkainen, A. et al. (2008) The same sequence variant on 9p21 associates with myocardial infarction, abdominal aortic aneurysm and intracranial aneurysm. Nat. Genet., 40, 217-224.
19. Helgadottir, A., Thorleifsson, G., Manolescu, A., Gretarsdottir, S., Blondal, T., Jonasdottir, A., Sigurdsson, A., Baker, A., Palsson, A., Masson, G. et al. (2007) A common variant on chromosome 9p21 affects the risk of myocardial infarction. Science, 316, 1491-1493.
20. McPherson, R., Pertsemlidis, A., Kavaslar, N., Stewart, A., Roberts, R., Cox, D.R., Hinds, D.A., Pennacchio, L.A., Tybjaerg-Hansen, A., Folsom, A.R. et al. (2007) A common allele on chromosome 9 associated with coronary heart disease. Science, 316, 1488-1491.
21. Zeggini, E., Weedon, M.N., Lindgren, C.M., Frayling, T.M., Elliott, K.S., Lango, H., Timpson, N.J., Perry, J.R., Rayner, N.W., Freathy, R.M. et al. (2007) Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes. Science, 316, 1336-1341.
22. Saxena, R., Voight, B.F., Lyssenko, V., Burtt, N.P., de Bakker, P.I., Chen, H., Roix, J.J., Kathiresan, S., Hirschhorn, J.N., Daly, M.J. et al. (2007) Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science, 316, 1331-1336.
23. Scott, L.J., Mohlke, K.L., Bonnycastle, L.L., Willer, C.J., Li, Y., Duren, W.L., Erdos, M.R., Stringham, H.M., Chines, P.S., Jackson, A.U. et al. (2007) A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science, 316, 1341-1345.
24. Shete, S., Hosking, F.J., Robertson, L.B., Dobbins, S.E., Sanson, M., Malmer, B., Simon, M., Marie, Y., Boisselier, B., Delattre, J.Y. et al. (2009) Genome-wide association study identifies five susceptibility loci for glioma. Nat. Genet., 41, 899-904.
25. Uno, S., Zembutsu, H., Hirasawa, A., Takahashi, A., Kubo, M., Akahane, T., Aoki, D., Kamatani, N., Hirata, K. and Nakamura, Y. (2010) A genome-wide association study identifies genetic variants in the CDKN2BAS locus associated with endometriosis in Japanese. Nat. Genet., 42, 707-710.
26. Ramdas, W.D., van Koolwijk, L.M., Ikram, M.K., Jansonius, N.M., de Jong, P.T., Bergen, A.A., Isaacs, A., Amin, N., Aulchenko, Y.S., Wolfs, R.C. et al. (2010) A genome-wide association study of optic disc parameters. PLoS Genet., 6, e1000978.
27. Ramdas, W.D., van Koolwijk, L.M., Lemij, H.G., Pasutto, F., Cree, A.J., Thorleifsson, G., Janssen, S.F., Jacoline, T.B., Amin, N., Rivadeneira, F. et al. (2011) Common genetic variants associated with open-angle glaucoma. Hum. Mol. Genet., 20, 2464-2471.
28. Fan, B.J., Wang, D.Y., Pasquale, L.R., Haines, J.L. and Wiggs, J.L. (2011) Genetic variants associated with optic nerve vertical cup-to-disc ratio are risk factors for primary open angle glaucoma in a US Caucasian population. Invest. Ophthalmol. Vis. Sci., 52, 1788-1792.
29. Xu, Z. and Taylor, J.A. (2009) SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies. Nucleic Acids Res., 37, W600-W605.
30. Jean, D., Bernier, G. and Gruss, P. (1999) Six6 (Optx2) is a novel murine Six3-related homeobox gene that demarcates the presumptive pituitary/hypothalamic axis and the ventral optic stalk. Mech. Dev., 84, 31-40.
31. Toy, J., Yang, J.M., Leppert, G.S. and Sundin, O.H. (1998) The optx2 homeobox gene is expressed in early precursors of the eye and activates retina-specific genes. Proc. Natl Acad. Sci. USA, 95, 10643-10648.
32. Gallardo, M.E., Lopez-Rios, J., Fernaud-Espinosa, I., Granadino, B., Sanz, R., Ramos, C., Ayuso, C., Seller, M.J., Brunner, H.G., Bovolenta, P. et al. (1999) Genomic cloning and characterization of the human homeobox gene SIX6 reveals a cluster of SIX genes in chromosome 14 and associates SIX6 hemizygosity with bilateral anophthalmia and pituitary anomalies. Genomics, 61, 82-91.
33. Lin, X., Duan, X., Liang, Y.Y., Su, Y., Wrighton, K.H., Long, J., Hu, M., Davis, C.M., Wang, J., Brunicardi, F.C. et al. (2006) PPM1A functions as a Smad phosphatase to terminate TGFbeta signaling. Cell, 125, 915-928.
34. Axenovich, T., Zorkoltseva, I., Belonogova, N., van Koolwijk, L., Borodin, P., Kirichenko, A., Babenko, V., Ramdas, W., Amin, N., Despriet, D. et al. (2011) Linkage and association analyses of glaucoma related traits in a large pedigree from a Dutch genetically isolated population. J. Med. Genet., 48, 802-809.
35. Matuoka, K., Miki, H., Takahashi, K. and Takenawa, T. (1997) A novel ligand for an SH3 domain of the adaptor protein Nck bears an SH2 domain and nuclear signaling motifs. Biochem. Biophys. Res. Commun., 239, 488-492.
36. Macgregor, S., Hewitt, A.W., Hysi, P.G., Ruddle, J.B., Medland, S.E., Henders, A.K., Gordon, S.D., Andrew, T., McEvoy, B., Sanfilippo, P.G. et al. (2010) Genome-wide association identifies ATOH7 as a major gene determining human optic disc size. Hum. Mol. Genet., 19, 2716-2724.
37. Wiggs, J.L., Kang, J.H., Yaspan, B.L., Mirel, D.B., Laurie, C., Crenshaw, A., Brodeur, W., Gogarten, S., Olson, L.M., Abdrabou, W. et al. (2011) Common variants near CAV1 and CAV2 are associated with primary open-angle glaucoma in Caucasians from the USA. Hum. Mol. Genet., 20, 4707-4713.
38. Nakamura, Y. (2007) The BioBank Japan Project. Clin. Adv. Hematol. Oncol, 5, 696-697.
39. Ohnishi, Y., Tanaka, T., Ozaki, K., Yamada, R., Suzuki, H. and Nakamura, Y. (2001) A high-throughput SNP typing system for genome-wide association studies. J. Hum. Genet., 46, 471-477.
40. Li, Y., Willer, C., Sanna, S. and Abecasis, G. (2009) Genotype imputation. Annu. Rev. Genomics Hum. Genet., 10, 387-406.