Primary open-angle glaucoma (POAG) is the major type of glaucoma. the allele frequency comparison. In the stage 2 analysis, we tested these 255 SNPs for association in DNA samples from a separate group of 409 POAG and 448 control subjects. High-quality genotype data were selected and used to calculate the combined values of stages 1 and 2 by the MantelCHaenszel test. These analyses yielded 6 SNPs with < 0.0001. 72835-26-8 manufacture All 6 SNPs showed a significant association (< 0.05) in stage 2, demonstrating a confirmed association with POAG. Although we could not link the SNPs to the annotated gene(s), it turned out that we have identified 3 genetic loci probably associated with POAG. These findings would provide the foundation for future studies 72835-26-8 manufacture to build on, such as for the metaanalysis, to reveal the molecular mechanism of the POAG pathogenesis. and a hypothetical gene, SNPs were combined with SNPs on the other susceptibility genes in predicting 72835-26-8 manufacture the risk for developing AMD (14, 15). In this study, to identify genetic markers of POAG, we conducted a GWAS in 2 stages at the Kyoto Prefectural University of Medicine using data from a total of 1 1,575 Japanese POAG patients and control subjects without glaucoma. We obtained a few modestly associated SNPs with POAG belonging to 3 different loci of the genome. The results suggested that the SNPs and the loci identified in this study would be promising genetic markers for the further studies to reveal Rabbit polyclonal to ZAP70.Tyrosine kinase that plays an essential role in regulation of the adaptive immune response.Regulates motility, adhesion and cytokine expression of mature T-cells, as well as thymocyte development.Contributes also to the development and activation of pri the molecular mechanism of POAG pathogenesis. Results GWAS Stage 1 Analysis. We performed the GWAS for stage 1 by screening 500,568 SNPs to discover genetic markers associated with POAG. We then attempted to reduce the false-positive associations from the results of stage 1 using an independent population in stage 2. Finally, we combined the results of stages 1 and 2 by the MantelCHaenszel 72835-26-8 manufacture test to evaluate the SNPs identified in this study (Fig. 1). In both stages, we performed allele frequency comparison to analyze combined values of stages 1 and 2 by the MantelCHaenszel test. Fig. 1. Project overview for the discovery of genetic markers of POAG. Several hundred SNPs of < 0.001 selected in the GWAS (stage 1) were screened with another study population (stage 2). We identified 6 SNPs of < 0.0001, evaluated by the ... Based on our power calculation (see and Fig. S1), we analyzed 718 samples, from 418 POAG patients (case subjects) and 300 control subjects without glaucoma (controls), in stage 1. The clinical characteristics of the study subjects are shown in Table 1. Between the case subjects and controls, no significant difference was observed in gender ratio (female/male: 1.0 vs. 1.3), but a significant difference was observed in their age at the time of blood sampling [64.6 13.5 (= 418) vs. 51.1 13.9 (= 300)], which was also seen at the age at diagnosis [58.3 13.4 (= 324) vs. 51.1 13.9 (= 300)]. Table 1. Clinical characteristics of case and control samples After genotyping the 718 samples, we selected 331,838 SNPs for further analysis, using the stringent criteria chosen for our quality-control (QC) filter (see and Fig. 1). To identify SNPs associated with POAG, we compared the allele frequency of each SNP between case and control samples. In a quantile-quantile plot, the observed value deviated from the expected value between = 10?3 and = 10?4. Therefore, we set the threshold at = 10?3 for further analysis (Fig. S2). In total, 431 SNPs showed < 0.001 in the allele frequency comparison (Fig. S2). We then visually checked the 2D cluster plots of these 431 SNPs and selected 255 SNPs as candidates (Fig. 1 and Fig. S3< 10?3 group showed a significant deviation (< 10?10) from the HardyCWeinberg equilibrium (HWE) in the control population, no significant HWE deviation (> 10?2) was observed among the 21 SNPs in the < 10?4 group. We evaluated the SNPs neighboring these 21 SNPs on the 500K array set and found a similar value (= 10?3-10?4) throughout the linkage disequilibrium (LD) block. These results supported a high confidence in the genotyping results for these SNPs. Stage 2.