Identification of Glaucoma Associated SNPs Using SNP Microarray

Abstract

Purpose:: To test the efficacy of SNP microarrays to identify SNPs associated with primary open angle glaucoma in Japanese population.

Methods:: Pooled DNA from 50 POAG patients and 50 age-matched controls were independently analyzed by Affymetrix 25K SNP microarray. Detected SNPs with confidence <0.05 were included in the follow-up analyses. These SNPs were further analyzed individually by direct sequencing. Statistical analysis was performed using single nucleotide polymorphism (SNP) and disease association software, SNPAlyze.

Results:: The 2085 SNPs were detected as heterozygous in glaucoma sample and homozygous in control sample. The 14 SNPs (confidence < 0.05), which were included in the 2085 SNPs, were genotyped individually for the 32 individuals patients genomic DNA and 64 control genomic DNA. Association of 5 SNPs and glaucoma were identified in case-control study using recessive model. In case control haplotype analysis, frequency of haplotype 1 for case and control were 18.7% and 51.7% respectively, indicating protective allele. On the other hand, haplotype 2 gave 7.7-fold increased likelihood of glaucoma.

Conclusions:: The two haplotypes were found associated with Japanese glaucoma population. The results suggest that one of the haplotypes was identified as risk factors and other as protective. More subjects are under investigation for both haplotypes.

Keywords: gene microarray • genetics