A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants

Abstract

Advanced age-related macular degeneration (AMD) is the leading cause of blindness in the elderly, with limited therapeutic options. Here we report on a study of >12 million variants, including 163,714 directly genotyped, mostly rare, protein-altering variants. Analyzing 16,144 patients and 17,832 controls, we identify 52 independently associated common and rare variants (P < 5 × 10(-8)) distributed across 34 loci. Although wet and dry AMD subtypes exhibit predominantly shared genetics, we identify the first genetic association signal specific to wet AMD, near MMP9 (difference P value = 4.1 × 10(-10)). Very rare coding variants (frequency <0.1%) in CFH, CFI and TIMP3 suggest causal roles for these genes, as does a splice variant in SLC16A8. Our results support the hypothesis that rare coding variants can pinpoint causal genes within known genetic loci and illustrate that applying the approach systematically to detect new loci requires extremely large sample sizes.

Figure 1. Genome-wide search reveals 34 loci and genes with rare variant burden for AMD

(a) We conducted a genome-wide single variant association analysis for >12 million variants in 16,144 advanced AMD patients versus 17,832 controls. Shown is the Manhattan Plot exhibiting P-values for association highlighting novel (P < 5×10^–8 for the first time, green) and known (blue) AMD loci (see Table 1). (b) We computed independent effect size (Odds Ratios) of each of the 52 identified variants (Supplementary Table 4). Shown are these effect sizes versus the frequency of the AMD risk increasing allele and a 80% power curve. (c) We conducted a genome-wide gene-based test for disease burden based on the protein-altering variants testing 17,044 RefSeq genes by the variable threshold test. Shown is the Manhattan Plot with P-values, the red horizontal line indicating genome-wide significance (P ≤ 0.05/17,044 = 2.9×10^–6) and the yellow line indicating AMD-locus-wide significance (given 703 genes in the 34 AMD loci, P ≤ 0.05/703 = 7.1×10^–5). No gene outside the 34 loci is genome-wide significant; 14 genes are AMD-locus-wide significant (blue), four remain significant after locus-wide conditioning (bold letters, Supplementary Table 11).

Figure 2. Genes with top priority based on biological and statistical evidence combined

We queried 368 genes in the 34 narrow AMD regions (index and proxies, r ≥0.5, ±100kb) for biological (red; expression in retina/RPE/choroid, Supplementary File 6; ocular mouse phenotype, Supplementary File 7), statistical, (blue; ≥1 credible set variant in gene ±50 kb, Supplementary File 3; rare variant burden, Table 2), putative functional (green; ≥ 1 credible set variant in gene ±50 kb being protein-altering, 5′/3′ UTR, other exonic, or putative promoter, Supplementary File 3), and molecular (magenta; enriched molecular pathway, drug target) evidence. We here focus on the gene(s) with the highest gene priority score (GPS) per locus (full list of genes in Supplementary File 9). Shown are (a) the 16 genes with highest GPS in the 15 novel AMD loci (one novel locus without any gene), and (b) the 25 genes with highest GPS in the 18 known AMD loci. Colored fields indicate yes and GPS counts number of colored fields per row.

Figure 3. Comparison of advanced AMD subtypes and intermediate versus advanced AMD

We compared associations of the 34 lead variants across different AMD phenotypes. Shown are effect sizes (log Odds Ratio) per minor allele in controls as well as 95% confidence intervals (widths and heights of diamonds). (a) Comparison of neovascular disease (10,749 CNV cases vs. 17,832 controls) and GA (3,235 GA cases vs. 17,832 controls) identified four variants (in loci MMP9, ARMS2/HTRA1, CETP, and SYN3/TIMP3) with significantly different association comparing CNV with GA (P_diff < 0.05/34, marked in red, see also Supplementary Table 16). (b) Comparison of intermediate AMD (6,657 cases vs. 17,832 controls) with advanced AMD (16,144 cases vs. 17,832 controls) identifies 24 variants with nominally significant (P < 0.05, marked in red) association with intermediate AMD (P_binomial = 4.8 × 10^–24), all of which have the same effect direction and less extreme effect sizes compared to advanced AMD (Supplementary Table 17).

Figure 4. Variance explained and absolute risk of disease based on the 52 identified variants

(a) Absolute disease risk (=proportion of affected) by genetic risk score intervals (deciles and top 10 percentiles in embedded bar plot) based on our cases-control-data weighted to model a general population with 5% disease prevalence (see also Supplementary Table 20). (b) Shown is disease liability explained by the 52 identified variants (bars) compared to the genomic heritability based on all genotyped variants (red lines) assuming disease prevalence of 1%, 5%, or 10%, respectively.