Research Article

Genome-wide analysis of single nucleotide polymorphisms in patients with atrophic age-related macular degeneration in oldest old Han Chinese

Published: December 21, 2015
Genet. Mol. Res. 14 (4) : 17432-17438 DOI: https://doi.org/10.4238/2015.December.21.13
Cite this Article:
T.Q. Zhou, H.J. Guan, J.Y. Hu (2015). Genome-wide analysis of single nucleotide polymorphisms in patients with atrophic age-related macular degeneration in oldest old Han Chinese. Genet. Mol. Res. 14(4): 17432-17438. https://doi.org/10.4238/2015.December.21.13
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Abstract

The aim of this study was to identify disease-associated loci in oldest old Han Chinese with atrophic age-related macular degeneration (AMD). This genome-wide association study (GWAS) only included oldest old (≥95 years old) subjects in Rugao County, China. Thirty atrophic AMD patients and 47 age-matched non-AMD controls were enrolled. The study subjects underwent a complete ophthalmic examination. Genomic DNA was extracted from peripheral blood samples. Single nucleotide polymorphisms (SNPs) were scanned by Genome-Wide Human Mapping SNP 6.0 Arrays and GeneChip Scanner 3000 7G. The results were read and analyzed by the Affymetrix Genotyping Console software. We filtered out the SNPs with a no-call rate ≥10%, MAF P < 0.05, and HWE P < 0.001. The remaining 561,277 SNPs were included in the association analysis. We found that the following 2 SNPs had the highest association with atrophic AMD: rs7624556 (located on 3q24) and rs13119914 (located on 4q34.3). In conclusion, we identified two atrophic AMD-associated SNPs (rs7624556 and rs13119914) in an oldest old Han Chinese population. This finding may lead to new strategies for screening of atrophic AMD for Han Chinese.

The aim of this study was to identify disease-associated loci in oldest old Han Chinese with atrophic age-related macular degeneration (AMD). This genome-wide association study (GWAS) only included oldest old (≥95 years old) subjects in Rugao County, China. Thirty atrophic AMD patients and 47 age-matched non-AMD controls were enrolled. The study subjects underwent a complete ophthalmic examination. Genomic DNA was extracted from peripheral blood samples. Single nucleotide polymorphisms (SNPs) were scanned by Genome-Wide Human Mapping SNP 6.0 Arrays and GeneChip Scanner 3000 7G. The results were read and analyzed by the Affymetrix Genotyping Console software. We filtered out the SNPs with a no-call rate ≥10%, MAF P < 0.05, and HWE P < 0.001. The remaining 561,277 SNPs were included in the association analysis. We found that the following 2 SNPs had the highest association with atrophic AMD: rs7624556 (located on 3q24) and rs13119914 (located on 4q34.3). In conclusion, we identified two atrophic AMD-associated SNPs (rs7624556 and rs13119914) in an oldest old Han Chinese population. This finding may lead to new strategies for screening of atrophic AMD for Han Chinese.

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