First, we compared our results to a previously published GWAS for AMD.
7 Of the 52 AMD variants that were previously associated with AMD,
7 four variants were not present in our WGS dataset because of exclusion of the HLA region, four variants did not pass the GATK filter, and four variants were removed in the quality control steps (
Supplementary Table S2). For two variants that were excluded from the final dataset (i.e., rs3750846 and rs61985136), variants in high LD (rs2284665,
r2 = 0.96; and rs138361575,
r2 = 0.97, respectively) were present in the WGS dataset. In our GWAS, genetic variants at the
CFH,
ARMS2/HTRA1,
APOE, and
C3 loci were genome-wide significantly associated with AMD (
Table 2), and these loci also showed the strongest associations in the GWAS by Fritsche et al.
7 The strongest association was detected for rs6677089 at the
CFH locus with an odds ratio (OR) of 0.37 for allele A vs C (95% CI = 0.36–0.38,
P value 1.08 × 10
−102), which is in perfect LD (r
2 = 1.0) with the top-associated variant at the
CFH locus (rs10922109) reported by Fritsche et al.
7 Similarly, the top-associated variant at the
ARMS2/HTRA1 locus in our GWAS (rs2284665) was in perfect LD (
r2 = 1.0) with the top-associated variant at this locus in the GWAS by Fritsche et al.
7 (rs3750846). At the
APOE and
C3 loci, the same top-associated variants were detected in both GWASs (rs429358 and rs2230199, respectively). The remaining 38 variants previously reported by Fritsche et al.
7 did not reach genome-wide significance in our GWAS. However, 33 of the variants showed similar odds ratios as in the study of Fritsche et al.,
7 whereas five variants (rs62247658, rs114092250, rs67538026, rs73036519, rs191281603) showed a different direction of effect, although confidence intervals of these variants spanned both effect directions in our study (i.e., the odds ratios ranged between <1 to >1) (
Supplementary Table S3). A summary of the AMD-associated variants, in comparison to the results of Fritsche et al.,
7 is presented in
Supplementary Table S3. AMD patients that were included in our study were not part of any previously published AMD-related GWAS studies.