Genome-wide Association Study On Primary Open-angle Glaucoma With A 1000K Gene Chip

Abstract

Purpose: : In order to discover genetic markers for the major type of glaucoma, primary open-angle glaucoma (POAG), we examined a total of 1519 Japanese subjects with a 1000K gene chip (Affymetrix, Santa Clara, CA).

Methods: : This study involved 833 POAG patients (female/male=1.1; mean age 61.5±13.7 years) and 686 normal subjects (female/male=2.0; mean age 58.8±13.5 years) without glaucoma or a family history of glaucoma who are recruited between March 2005 and December 2010 at the University Hospital of Kyoto Prefectural University of Medicine (Kyoto, Japan). This study was approved by the Institutional Review Board of Kyoto Prefectural University of Medicine, and all subjects provided written informed consent. Genomic DNA was extracted from all subjects and genotyped with the 1000K gene chip. The frequency of alleles in the case and control samples was compared using the basic allele test. The odds ratio (OR) and the upper and lower limit of the 95% confidence interval (CI) of each single nucleotide polymorphism (SNP) were calculated for the allele possessing a higher frequency in the case than control samples. We performed SNP quality control (QC) for the population on the autosomal SNPs based on the following QC filters; (i) call rate per SNPs in case and control samples ≥ 95%, (ii) minor allele frequency (MAF) in case and control samples ≥ 1%, and (iii) Hardey-Weinberg equilibrium (HWE) in control samples P ≥ 0.001; HWE evaluated using the chi-square test.

Results: : After genotyping, 653,519 SNPs passed the quality controls and were used for a genome-wide association study (GWAS) that was performed by analyzing the 653,519 autosomal common SNPs. As a result, 5 variants (rs523096, rs518394, rs564398, rs7865618, and rs8181047) that passed the Bonferroni’s correction (0.05/653,519 = 7.65 x 10^-8) were located in CDKN2B-AS1 on chromosome 9p21.3 (OR: 1.85-1.86). However, the association results were not reproducible for the previously reported POAG genes except CDKN2B-AS1.

Conclusions: : In this study, we succeeded in identifying some significant variants in CDKN2B-AS1 that passed the Bonferroni's correction associated with POAG. These findings indicate that those variants could be promising genetic markers for future studies to elucidate the molecular mechanisms of POAG pathogenesis.

Keywords: genetics • gene screening • clinical (human) or epidemiologic studies: biostatistics/epidemiology methodology