An intergenic region between the tagSNP rs3793917 and rs11200638 in the HTRA1 gene indicates association with age-related macular degeneration

Richardson, Andrea J. and Islam, F. M. Amirul and Aung, Khin Zaw and Guymer, Robyn H. and Baird, Paul N. (2010) An intergenic region between the tagSNP rs3793917 and rs11200638 in the HTRA1 gene indicates association with age-related macular degeneration. Investigative Ophthalmology and Visual Science , 51 (10). pp. 4932-4936. ISSN 0146-0404

Abstract

Purpose. There is still a debate as to whether the LOC387715 or HTRA1 genes represent the key significant association identified with age-related macular degeneration (AMD) on the long arm of chromosome 10, region 26.
Methods. An Australian patient cohort was genotyped by using tagged single nucleotide polymorphisms (tSNPs) to identify a causal SNP within this region.
Results. Multiple tSNPs across the region showed association with AMD with the tSNP rs3793917 (odds ratio [OR], 3.45; 95% confidence interval [CI], 2.36–5.05, P = 2.8 × 10−13) having the highest association with AMD. This tSNP occurred in the intergenic region between the LOC387715 and HTRA1 genes. A second tSNP rs2672587 (OR, 2.92; 95% CI, 2.04–4.17; P = 7.7 × 10−11) located in intron 1 of the HTRA1 gene had the second highest association with AMD. After logistic regression analysis, the only tSNP to survive covariate testing was rs3793917, which occurred in the same LD block as the HTRA1 promoter SNP rs11200638 (r2 = 0.88, D′ = 0.97).
Conclusions. The findings indicate that the intergenic region between the tSNP rs3793917 and the SNP rs11200638 in the HTRA1 gene is the most likely site explaining the significant association with AMD.


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Item Type: Article (Commonwealth Reporting Category C)
Refereed: Yes
Item Status: Live Archive
Additional Information: © Association for Research in Vision and Ophthalmology. Permanent restricted access to published version in accordance with the copyright policy of the publisher.
Faculty / Department / School: Historic - Faculty of Sciences - Department of Maths and Computing
Date Deposited: 25 Jul 2014 05:56
Last Modified: 27 Aug 2014 04:01
Uncontrolled Keywords: aged; choroidal neovascularization; intergenic DNA; genotype; geographic atrophy; linkage (genetics); macular degeneration; serine endopeptidases
Fields of Research : 06 Biological Sciences > 0604 Genetics > 060412 Quantitative Genetics (incl. Disease and Trait Mapping Genetics)
11 Medical and Health Sciences > 1117 Public Health and Health Services > 111702 Aged Health Care
11 Medical and Health Sciences > 1113 Ophthalmology and Optometry > 111303 Vision Science
Socio-Economic Objective: C Society > 92 Health > 9205 Specific Population Health (excl. Indigenous Health) > 920502 Health Related to Ageing
C Society > 92 Health > 9201 Clinical Health (Organs, Diseases and Abnormal Conditions) > 920107 Hearing, Vision, Speech and Their Disorders
Identification Number or DOI: 10.1167/iovs.09-5114
URI: http://eprints.usq.edu.au/id/eprint/20746

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