Genome-wide analysis of disease progression in age-related macular degeneration

Abstract

Family- and population-based genetic studies have successfully identified multiple disease-susceptibility loci for Age-related macular degeneration (AMD), one of the first batch and most successful examples of genome-wide association study. However, most genetic studies to date have focused on case-control studies of late AMD (choroidal neovascularization or geographic atrophy). The genetic influences on disease progression are largely unexplored. We assembled unique resources to perform a genome-wide bivariate time-to-event analysis to test for association of time-to-late-AMD with ∼9 million variants on 2721 Caucasians from a large multi-center randomized clinical trial, the Age-Related Eye Disease Study. To our knowledge, this is the first genome-wide association study of disease progression (bivariate survival outcome) in AMD genetic studies, thus providing novel insights to AMD genetics. We used a robust Cox proportional hazards model to appropriately account for between-eye correlation when analyzing the progression time in the two eyes of each participant. We identified four previously reported susceptibility loci showing genome-wide significant association with AMD progression: ARMS2-HTRA1 (P = 8.1 × 10-43), CFH (P = 3.5 × 10-37), C2-CFB-SKIV2L (P = 8.1 × 10-10) and C3 (P = 1.2 × 10-9). Furthermore, we detected association of rs58978565 near TNR (P = 2.3 × 10-8), rs28368872 near ATF7IP2 (P = 2.9 × 10-8) and rs142450006 near MMP9 (P = 0.0006) with progression to choroidal neovascularization but not geographic atrophy. Secondary analysis limited to 34 reported risk variants revealed that LIPC and CTRB2-CTRB1 were also associated with AMD progression (P < 0.0015). Our genome-wide analysis thus expands the genetics in both development and progression of AMD and should assist in early identification of high risk individuals.

Figure 1.

Manhattan plots of GWAS results of AMD progression. (A) GWAS results with adjustment for baseline severity score, and (B) GWAS results without adjustment for baseline severity score. Summary of genome-wide association results using Cox model with robust variance for paired eyes. The red horizontal line is the conservative significance level (P = 5 × 10⁻⁸) and the blue horizontal line is the suggestive significance level (P = 1 × 10⁻⁵).

Figure 2.

KM curves for SNPs from the four known genes identified by case–control studies. (A)ARMS2-HTRA1 (rs2284665), (B)CFH (rs10922109), (C)C2-CFB-SKIV2L (rs116503776) and (D)C3 (rs2230199). For all the KM plots (Figures 2, 3,5–7), the 1st column shows the KM curves of total samples. The second to fourth columns show the KM curves of samples with baseline severity 1–3, 4–6 and 7–8, respectively. The bottom left legend shows the number of samples for each genotype category and the percentage of how many these samples progressed to late AMD. The genotypes were derived from dosages: common homozygotes when dosage ≤ 0.5, heterozygotes when 0.5 < dosage < 1.5 and rare homozygotes when dosage ≥ 1.5.

Figure 3.

KM curves for SNPs from the three novel genes. (A)POC5/SV2C (rs79069165), (B)HERC1 (rs74320127) and (C)ACKR3 (rs56072732).

Figure 4.

Manhattan plots of GWAS results of CNV and GA progression. (A) progression to CNV and (B) progression to GA. The baseline severity was not included as a covariate. Summary of genome-wide association results using Cox model with robust variance for paired eyes. The red horizontal line is the conservative significance level (P = 5 × 10⁻⁸) and the blue horizontal line is the suggestive significance level (P = 1 × 10⁻⁵).

Figure 5.

KM curves for rs58978565 in TNR. It was associated with progression to CNV at significance level of 5 × 10⁻⁸, but not with progression to GA.

Figure 6.

KM curves for rs28368872 in ATF7IP2. It was associated with progression to CNV at significance level of 5 × 10⁻⁸, but not with progression to GA.

Figure 7.

KM curves for rs142450006 in MMP9. It was identified by the case–control study to be exclusively associated with CNV.