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Y. Liu, X. Qin, S. Schmidt, R. R. Allingham, M. A. Hauser; Association Between Chromosome 2p16.3 Variants and Glaucoma in Populations of African Descent. Invest. Ophthalmol. Vis. Sci. 2010;51(13):2162.
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A significant association has been reported between SNPs on chromosome 2p and risk for primary open-angle glaucoma (POAG) in the Barbados population (Jiao et al, PNAS, 2009). We investigated the association of these sequence variants with POAG in our African American and Ghanaian (West African) datasets.
POAG was defined as the presence of glaucomatous optic nerve damage and associated visual field loss. The African American dataset included 382 POAG and 275 control subjects and the Ghanaian population contained 170 POAG and 132 control subjects. Three SNPs (rs12994401, rs10202118, and rs1533428) on chromosome 2p16.3 were genotyped by TaqMan allelic discrimination assays in the African American and Ghanaian populations. Within each population, genotype frequencies of cases and controls from each population were compared by logistic regression with adjustment for gender using SAS software.
Of the 3 SNPs examined only rs12994401 was significantly associated with an increased risk of POAG in the African American population (p= 0.003). T allele frequencies in our African American controls and the Barbados controls were nearly identical. However, risk was conferred by the C allele at rs12994401, rather than the T allele as reported by Jiao et. al. We observed no linkage disequilibrium (LD) between the three SNPs in either population based on r2 (r2<0.35 for all SNP pairs in the respective cases and controls).
We identified a significant association between SNP rs12994401 and POAG in the North Carolina African American population. However the risk allele was the opposite of that reported by Jiao et. al. in the Barbados population. This suggests that the as-yet-unidentified causal variant in this region of chromosome 2 has different levels of LD with the genotyped SNP in these distinct populations of African descent. Further study will be necessary to identify the true causal variant(s) for POAG in this genomic region.
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