Supplementary Figure 2: Manhattan plot for association of genome-wide SNPs with primary open-angle glaucoma.
From: Common variants near ABCA1, AFAP1 and GMDS confer risk of primary open-angle glaucoma
This plot was created using R software for association of genome-wide SNPs (using logistic regression with sex and the first 6 principal components fitted as covariates) with the development of primary open-angle glaucoma in stage 1 of this study using the discovery cohort (1,155 advanced POAG cases and 1,992 controls). The SNPs have been plotted against their chromosomal positions (the x-axis) and -log10(P-values) calculated through the genome-wide association analysis (the y-axis). All the SNPs on each chromosome have been shown in the same color but a distinct color from that of the adjacent chromosome in the plot. Chromosome 23 is the X chromosome. The texts in the figure indicate the chromosome, position (base pair) and the name of the adjacent genes for the top hits. The horizontal line in the figure indicates the genome-wide significance level (-log10(P-value) = 7.30). The two-sided P-values used to create this figure were corrected for the genomic inflation factor lambda (λ = 1.06 for imputed SNPs). Two regions on chromosome 9, and one region on chromosome 11 reached genome-wide significance (P < 5 × 10-8; -log10P > 7.30). In addition, one region on chromosome 6 also came close to genome-wide significance (P = 7.0 × 10-8; -log10P = 7.15). The previously identified region at TMCO1 did not reach genome-wide significance in the stage 1 analysis (control sample was changed relative to previous work to allow a larger set of SNPs to be used as the basis of imputation in stage 1) but TMCO1 SNPs exceeded P < 1 × 10-5, with P < 5 × 10-8 obtained at TMCO1 when stage 1 and 2 samples were combined.
