Association between nsSNPs in
C3 (rs1047286 and rs2230199) and AMD has been established in multiple studies.
14 15 16 17 Most of the effect on AMD risk appears to localize to a maximum 12 kb region spanning these two nsSNPs. However, because of high LD and the low frequency of recombinant haplotypes, conditional SNP and haplotype analyses with rs1047286 and rs2230199 could not determine which nsSNP explains the effect on AMD risk
(Tables 2 4) . Thus, our observations in the Mayo and AREDS subjects differed from studies of other subject groups that concluded that rs2230199 (R102G) explained the association with AMD.
14 15 16 Yates et al.
15 performed stepwise logistic regression analysis and showed significant association with AMD adding R102G in the P314L model (
P = 0.02). However, this association was not observed adding P314L in the R102G model (
P = 0.90). Spencer et al.
16 evaluated the effect of C3 R102G in C3 P314L carriers and vice versa. They also proposed that P314L (
P = 0.2) was not, whereas R102G (
P = 0.01) was significantly associated with AMD. Maller et al.
14 did not genotype rs1047286, but examined publically available resequencing data from (http://pga.gs.washington.edu) across this region of
C3 in 23 CEPH samples, and reported no other nsSNPs in high LD. Thus, although genetic studies do not allow for clear separation between the effects of these two nsSNPs on AMD risk, no other nearby variation is known that could explain the effect on AMD.
Unlike previous studies, we observed that haplotypes from the three SNPs (rs11569536, rs344542, and rs3745565) in the 3′ end of
C3 showed significant association with AMD in the Mayo and AREDS subjects
(Table 5) . The effect persisted after conditioning on the nsSNPs in the Mayo subjects, but not the AREDS subjects
(Table 5) . Thus, at this time additional study is needed to determine whether the 3′ end of
C3 has an independent impact on AMD risk. We found no coding DNA sequence variation in publically available SNP databases (dbSNP, HapMap) or 46 Caucasian chromosomes sequenced by Seattle SNPs (http://pga.gs.washington.edu) that would explain the independent AMD risk in the 3′ region of
C3. There are at least 292 DNA sequence variants across the
C3 locus that could impact splicing or other regulatory functions (http://pga.gs.washington.edu). It is possible that some of these uncommon variants affect
C3 expression, but functional studies would be necessary to evaluate the effects. At this time most, if not all, of the effect of
C3 on AMD can be explained by the two nsSNPs.
Although it has been established that the extent of the maculopathy (drusen, pigment) characterizing AMD is the major predictor of the development of geographic atrophy and exudation, there is great interest in identifying genetic risks that might promote these two complications of AMD.
27 We used statistical modeling to examine the relative impact of rs2230199 on the common AMD subtypes: early AMD characterized by large drusen, primary geographic atrophy, and exudation. Unlike a previous report,
15 we observed a similar risk for rs2230199 on early and exudative AMD in Mayo subjects. However, we observed an increased risk (1.5-fold) of geographic atrophy compared with early AMD in the Mayo subjects that was not observed in previous studies.
14 15 16 Others have reported that the
C3 nsSNPs along with
C2/CFB,
CFH, and
LOC387715/HTRA1 variants promoted progression to advanced AMD in the AREDS subjects.
28 29
The replication study with AREDS subjects showed a significantly increased risk of both types of advanced AMD (
P = 0.039 for geographic atrophy,
P = 0.004 for exudative AMD) compared with early AMD. We obtained similar results with rs1047286, as would be expected given the tight LD (data not shown). Yates et al.
15 reported that their 189 exudative AMD subjects (but not the 261 early AMD subjects) were associated with this SNP in their Scottish group. Maller et al.
14 reported no difference in association between exudative AMD and GA compared to controls, but did not include subjects with early AMD. Spencer et al.
16 observed no difference between the frequency of the risk allele for rs2230199 (R102G) between all AMD (701 subjects) and neovascular AMD subjects comprising 61% of these subjects. Our analysis of the pooled Mayo and AREDS subjects suggests that
C3 nsSNPs preferentially associate with advanced AMD subtypes
(Fig. 2) . Thus, variation in
C3 may contribute preferentially to the development of advanced AMD, but additional study in prospective cohorts is warranted.
As noted, genetic studies in the Mayo subjects did not enable us to distinguish the effect of R102G and P314L on AMD risk. POLYPHEN analysis
30 predicted R102G to be a benign alteration, and P314L to be probably damaging. The nsSNP R102G corresponds to the electrophoretically slow (C3S, arginine) and fast (C3F, glycine) forms of
C3.
31 The other nsSNP P314L has not been reported to affect electrophoretic migration as would be expected based on proline and leucine having the same charge. The P314L substitution is in the third macroglobulin domain and is not near a functional domain in C3 based on the structure reported by Janssen et al.,
32 33 whereas the arginine at amino acid 102 in the first macroglobulin domain is thought to be important in maintaining the structure of the thioester domain.
The C3 allotypes have been associated with other diseases. C3F (102G) was reported to be protective for improved survival of transplanted kidneys, and a risk for Indian childhood cirrhosis, partial lipodystrophy, IgA nephropathy, Chagas disease cardiomyopathy, nephritic factor, type II mesangiocapillary glomerulonephritis, and systemic vasculitis.
34 35 36 37 38 39 40 Most of the studies did not look directly at the differences between C3S and C3F and cannot distinguish between the effects of these two nsSNPs on disease risk. Further study to evaluate the functional effects of rs2230199 and rs1047286 variants is needed to understand how the
C3 nsSNPs alter the risk of AMD.
This study has several limitations. Case–control studies are well known to be influenced by non-representative sampling of the underlying population. Although we have not observed such effects in our ongoing work, the possibility cannot be completely excluded. We have performed a large number of exploratory investigations, creating the possibility for random events to reach nominal significance. Nominal P-values are reported without correction for multiple testing, but can be readily converted to corrected ones by the reader. Rather than relying on the P-values, we have chosen a two-stage analysis method in which findings in one group of subjects were studied in a second independent group of subjects to determine whether the observation could be replicated. This strategy is more rigorous than relying on the magnitude of individual P-values. The ultimate value of this study is to generate hypotheses based on the genetic data that can be tested in functional studies.
In summary, we observed that the effect of the nsSNPs rs2230199 and rs1047286 on AMD risk could not be separated. The minor alleles for these two nsSNPs define haplotypes that increase the risk of developing any AMD. The two nsSNPs were significantly associated with advanced AMD compared with early AMD, suggesting that they may promote the development of these complications of early AMD. The possibility that haplotypes in the 3′ end of C3 locus may be associated with AMD requires further study.
The authors thank the local research participants, the AREDS participants, and the AREDS Research Group for their contributions to the research.