Evaluation of clustering and genotype distribution for replication in genome wide association studies: the age-related eye disease study

Role of complement factor B rs4151667 (L9H) polymorphisms and its interactional role with CFH Y402H and C3 rs2230199 (R102G) risk variants in age-related macular degeneration: a case control study

Background

Age-related Macular Degeneration (AMD) is a complex eye disease, which is genetically associated with different susceptibility loci. We planned to investigate the possible association of Complement Factor B (CFB) rs4151667 (L9H) variants and their possible interaction with Complement Factor H (CFH) Y402H and Complement factor 3 (C3) rs2230199 (R102G) in AMD.

Methods

This case-control association study included 216 advanced type AMD patients and 191 healthy individuals for evaluation. Extracted-DNA samples were genotyped for the polymorphic regions of CFB rs4151667 (L9H), CFH Y402H and C3 rs2230199 (R102G).

Results

The distribution of CFB rs4151667 (L9H) genotypes was not significantly different in the AMD patients compared to that of controls (P = 0.18). The AT genotype frequencies for CFB was non significantly lower in AMD group (6.5% vs. 13.1%, AOR = 0.49, CI = 0.23–1.04, P = 0.064(. The A allele of CFB rs4151667 (L9H) was found to be non-significantly lower in AMD patients. CFB rs4151667 (L9H) had no protective interactional effect against CFH (Y402H) and C3 (R102G) risk variants.

Conclusions

This study showed that the protective role of CFB rs4151667 (L9H) in AMD is not significant and it has no significant protective interactional effect against CFH (Y402H) and C3 (R102G) risk variants.

The effect of complement factor B gene variation on age-related macular degeneration in Iranian patients

Purpose

To determine the possible association of rs4151667 (L9H) complement factor B (CFB) gene with age-related macular degeneration (AMD). The L9H is one of the functional variations of the CFB. CFB gene encodes the most important protein of the complement system.

Methods

Two hundred sixty-six patients with AMD and 194 unrelated age/sex-matched controls were genotyped for CFB gene (rs4151667) using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. All research subjects were selected from three regions of Iran (Tehran, Tabriz, and Gonabad).

Results

The results showed a significant difference between the frequency of non-TT genotype in total patients and controls [odds ratio (OR) = 0.424, P = 0.038]. The analysis for each studied region showed that in patients originating from the Gonabad population, the frequency of TT and non-TT genotypes between patients and the control group were significantly different (OR = 2.894, P = 0.046 for TT genotype and OR = 0.346, P = 0.026 for non-TT genotype). In patients originating from Tabriz population, TT and non-TT genotypes and A allele revealed considerably different frequencies between the patient and control groups (OR = 3.043, P = 0.017; OR = 0.329, P = 0.013 and OR = 0.347, P = 0.048, respectively). Analysis of patients from Tehran also showed that there was a significant difference in the frequency of TT genotype between patients and controls (OR = 2.168, P = 0.04).

Conclusions

The results of the current study indicated a possible protective role for non-TT genotype in L9H variation CFB gene against AMD in a sample of the Iranian population. The region segregation results showed that TT genotype might be a risk factor for susceptibility to AMD.

Association between genetic variation of complement C3 and the susceptibility to advanced age-related macular degeneration: a meta-analysis

BACKGROUND

The purpose of this study is to discuss whether genetic variants (rs2230199, rs1047286, rs2230205, and rs2250656) in the C3 gene account for a significant risk of advanced AMD.

METHODS

We performed a meta-analysis using electronic databases to search relevant articles. A total of 40 case-control studies from 38 available articles (20,673 cases and 20,025 controls) were included in our study.

RESULTS

In our meta-analysis, the pooled results showed that the carriage of G allele for rs2230199 and the T allele for rs1047286 had a tendency to the risk of advanced AMD (OR = 1.49, 95% CI = 1.39-1.59, P < 0.001; OR = 1.45, 95% CI = 1.37-1.54, P < 0.001). Moreover, in the subgroup analysis based on ethnicity, rs2230199 and rs1047286 polymorphisms were more likely to be a predictor of response for Caucasian region (OR = 1.48, 95% CI = 1.38-1.59, P < 0.001; OR = 1.45, 95% CI = 1.37-1.54, P < 0.001). Besides, pooled results suggested that the G allele of rs2230199 could confer susceptibility to advanced AMD in Middle East (OR = 1.62, 95% CI = 1.33-1.97, P < 0.001).

CONCLUSION

In our meta-analysis, C3 genetic polymorphisms unveiled a positive effect on the risk of advanced AMD, especially in Caucasians. Furthermore, numerous well-designed studies with large sample-size are required to validate this conclusion.

Association Between Complement Factor C2/C3/CFB/CFH Polymorphisms and Age-Related Macular Degeneration: A Meta-Analysis

BACKGROUND

Several previous studies have assessed the contribution of polymorphisms in genes encoding the complement factors C2/C3/CFB/CFH with the risk of age-related macular degeneration (AMD), however the results have been inconsistent. We conducted a meta-analysis to systematically review the potential association between complement factor polymorphisms and AMD.

METHODS

Studies that investigated associations between C2 (rs547154 and rs9332739), C3 (rs1047286), CFB (rs4151667 and rs641153), and CFH (rs551397 and rs2274700) polymorphisms and AMD were identified by searching PubMed, EMBASE, Web of Science, and Cochrane Library databases for articles published prior to January 1, 2018. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated to evaluate the association between these polymorphisms and AMD using Stata 12.0 software. Q and I² statistics were used to evaluate between-study heterogeneity. Publication bias analyses were conducted using Begg's test. We also conducted an ethnic subgroup analysis.

RESULTS

A total of 53 studies that included data for 53,774 patients and 56,973 healthy controls were evaluated. The pooled ORs for rs551397, rs2274700, rs4151667, rs641153, rs1047286, rs9332739, and rs547154 in the heterozygote model were 0.53 (95% CI: 0.45-0.61), 0.53 (95% CI: 0.40-0.70), 0.54 (95% CI: 0.46-0.63), 0.48 (95% CI: 0.4-0.57), 1.42 (95% CI: 1.22-1.66), 0.5 (95% CI: 0.45-0.56), and 0.52 (95% CI: 0.43-0.62), respectively.

CONCLUSION

Our findings from this analysis confirmed the protective role of C2/CFB/CFH polymorphisms in the development of AMD, but showed that the single nucleotide polymorphism in C3 was a high-risk factor for AMD. The racial analysis results suggested that the effect of variant alleles was stronger in Caucasians than Asians.

Protective coding variants in CFH and PELI3 and a variant near CTRB1 are associated with age-related macular degeneration†

Although numerous common age-related macular degeneration (AMD) alleles have been discovered using genome-wide association studies, substantial disease heritability remains unexplained. We sought to identify additional common and rare variants associated with advanced AMD. A total of 4,332 cases and 25,268 controls of European ancestry from three different populations were genotyped using the Illumina Infinium HumanExome BeadChip. We performed meta-analyses to identify associations with common variants, and single variant and gene-based burden tests to identify rare variants. Two protective, low-frequency, non-synonymous variants were significantly associated with a decrease in AMD risk: A307V in PELI3 (odds ratio [OR] = 0.14, P = 4.3 × 10-10) and N1050Y in CFH (OR = 0.76, P = 6.2 × 10-12). The new variants have a large effect size, similar to some rare mutations we reported previously in a targeted sequencing study, which remain significant in this analysis: CFH R1210C (OR = 18.82, P = 3.5 × 10-07), C3 K155Q (OR = 3.27, P = 1.5 × 10-10) and C9 P167S (OR = 2.04, P = 2.8 × 10-07). We also identified a strong protective signal for a common variant (rs8056814) near CTRB1 associated with a decrease in AMD risk (logistic regression: OR = 0.71, P = 1.8 × 10-07). Suggestive protective loci were identified in the COL4A3 and APOH genes. Our results support the involvement of common and low-frequency protective variants in this vision-threatening condition. This study expands the roles of the innate immune pathway as well as the extracellular matrix and high-density lipoprotein pathways in the aetiology of AMD.

Synthesis of docosahexaenoic acid from eicosapentaenoic acid in retina neurons protects photoreceptors from oxidative stress

Oxidative stress is involved in activating photoreceptor death in several retinal degenerations. Docosahexaenoic acid (DHA), the major polyunsaturated fatty acid in the retina, protects cultured retina photoreceptors from apoptosis induced by oxidative stress and promotes photoreceptor differentiation. Here, we investigated whether eicosapentaenoic acid (EPA), a metabolic precursor to DHA, had similar effects and whether retinal neurons could metabolize EPA to DHA. Adding EPA to rat retina neuronal cultures increased opsin expression and protected photoreceptors from apoptosis induced by the oxidants paraquat and hydrogen peroxide (H2 O2 ). Palmitic, oleic, and arachidonic acids had no protective effect, showing the specificity for DHA. We found that EPA supplementation significantly increased DHA percentage in retinal neurons, but not EPA percentage. Photoreceptors and glial cells expressed Δ6 desaturase (FADS2), which introduces the last double bond in DHA biosynthetic pathway. Pre-treatment of neuronal cultures with CP-24879 hydrochloride, a Δ5/Δ6 desaturase inhibitor, prevented EPA-induced increase in DHA percentage and completely blocked EPA protection and its effect on photoreceptor differentiation. These results suggest that EPA promoted photoreceptor differentiation and rescued photoreceptors from oxidative stress-induced apoptosis through its elongation and desaturation to DHA. Our data show, for the first time, that isolated retinal neurons can synthesize DHA in culture. Docosahexaenoic acid (DHA), the major polyunsaturated fatty acid in retina photoreceptors, and its precursor, eicosapentaenoic acid (EPA) have multiple beneficial effects. Here, we show that retina neurons in vitro express the desaturase FADS2 and can synthesize DHA from EPA. Moreover, addition of EPA to these cultures protects photoreceptors from oxidative stress and promotes their differentiation through its metabolization to DHA.

Endophenotypes for Age-Related Macular Degeneration: Extending Our Reach into the Preclinical Stages of Disease

The key to reducing the individual and societal burden of age-related macular degeneration (AMD)-related vision loss, is to be able to initiate therapies that slow or halt the progression at a point that will yield the maximum benefit while minimizing personal risk and cost. There is a critical need to find clinical markers that, when combined with the specificity of genetic testing, will identify individuals at the earliest stages of AMD who would benefit from preventive therapies. These clinical markers are endophenotypes for AMD, present in those who are likely to develop AMD, as well as in those who have clinical evidence of AMD. Clinical characteristics associated with AMD may also be possible endophenotypes if they can be detected before or at the earliest stages of the condition, but we and others have shown that this may not always be valid. Several studies have suggested that dynamic changes in rhodopsin regeneration (dark adaptation kinetics and/or critical flicker fusion frequencies) may be more subtle indicators of AMD-associated early retinal dysfunction. One can test for the relevance of these measures using genetic risk profiles based on known genetic risk variants. These functional measures may improve the sensitivity and specificity of predictive models for AMD and may also serve to delineate clinical subtypes of AMD that may differ with respect to prognosis and treatment.

Netrin-1 - DCC Signaling Systems and Age-Related Macular Degeneration

We conducted a nested candidate gene study and pathway-based enrichment analysis on data from a multi-national 77,000-person project on the molecular genetics of age-related macular degeneration (AMD) to identify AMD-associated DNA-sequence variants in genes encoding constituents of a netrin-1 (NTN1)-based signaling pathway that converges on DNA-binding transcription complexes through a 3'-5'-cyclic adenosine monophosphate-calcineurin (cAMP-CN)-dependent axis. AMD-associated single nucleotide polymorphisms (SNPs) existed in 9 linkage disequilibrium-independent genomic regions; these included loci overlapping NTN1 (rs9899630, P ≤ 9.48 x 10^-5), DCC (Deleted in Colorectal Cancer)—the gene encoding a primary NTN1 receptor (rs8097127, P ≤ 3.03 x 10^-5), and 6 other netrin-related genes. Analysis of the NTN1-DCC pathway with exact methods demonstrated robust enrichment with AMD-associated SNPs (corrected P-value = 0.038), supporting the idea that processes driven by NTN1-DCC signaling systems operate in advanced AMD. The NTN1-DCC pathway contains targets of FDA-approved drugs and may offer promise for guiding applied clinical research on preventive and therapeutic interventions for AMD.

Nonsynonymous single nucleotide polymorphisms in the complement component 3 gene are associated with risk of age-related macular degeneration: a meta-analysis

Nonsynonymous single nucleotide polymorphisms (SNPs) in complement component 3 (CC3) are associated with the risk of age-related macular degeneration (AMD), however, this association is not consistent among studies. To thoroughly address this issue, we performed an updated meta-analysis to evaluate the association between nine SNPs in the CC3 gene and AMD risk. A search was conducted of the PubMed database through 3rd Aug, 2014. Odds ratios (ORs) and 95% confidence intervals (CIs) were used to assess the strength of associations. Based on the search criteria for manuscripts reporting AMD susceptibility related to CC3 in nine SNPs, 57 case-control studies from 22 different articles were retrieved. Significantly positive associations were found for the rs2230199 C/G SNP and AMD in the Caucasian population, as well as for the rs1047286 C/T SNP. Moreover, a relationship between the rs11569536 G/A SNP and AMD was detected. By contrast, a negative association was observed between rs2250656 A/G SNP and AMD risk. The present meta-analysis suggests that these four SNPs in the CC3 gene are potentially associated with the risk of AMD development. Further studies using larger sample sizes and accounting for gene-environment interactions should be conducted to elucidate the role of CC3 gene polymorphisms in AMD risk.

Identification of genome-wide SNP-SNP and SNP-clinical Boolean interactions in age-related macular degeneration

We propose here a methodology to uncover modularities in the network of SNP-SNP interactions most associated with disease. We start by computing all possible Boolean binary SNP interactions across the whole genome. By constructing a weighted graph of the most relevant interactions and via a combinatorial optimization approach, we find the most highly interconnected SNPs. We show that the method can be easily extended to find SNP/environment interactions. Using a modestly sized GWAS dataset of age-related macular degeneration (AMD), we identify a group of only 19 SNPs, which include those in previously reported regions associated to AMD. We also uncover a larger set of loci pointing to a matrix of key processes and functions that are affected. The proposed integrative methodology extends and overlaps traditional statistical analysis in a natural way. Combinatorial optimization techniques allow us to find the kernel of the most central interactions, complementing current methods of GWAS analysis and also enhancing the search for gene-environment interaction.

Genomic aspects of age-related macular degeneration

Age-related macular degeneration (AMD) is a major late-onset posterior eye disease that causes central vision to deteriorate among elderly populations. The predominant lesion of AMD is the macula, at the interface between the outer retina and the inner choroid. Recent advances in genetics have revealed that inflammatory and angiogenic pathways play critical roles in the pathophysiology of AMD. Genome-wide association studies have identified ARMS2/HTRA1 and CFH as major AMD susceptibility genes. Genetic studies for AMD will contribute to the prevention of central vision loss, the development of new treatment, and the maintenance of quality of vision for productive aging.

Complement C3, C2, and factor B gene polymorphisms and age-related macular degeneration in a Greek cohort study

PURPOSE

To elucidate whether polymorphisms of C2, C3, and CFB genes are major genetic determinants of age-related macular degeneration (AMD) in a Greek population.

METHODS

This was a case-control association study comprising 120 Greek patients with early and late-stage AMD and 140 independent controls of Caucasian origin. All participants were genotyped for rs547154, rs2230199, rs641153, and rs12614 polymorphisms by a combination of PCR and direct DNA sequencing assays.

RESULTS

The frequency of the rs2230199 G allele (minor allele) was significantly higher in patients with AMD in comparison with controls (0.34 vs 0.22, p = 0.0031) and similar to the frequency of other reported populations. There was a significant difference in the frequencies of the rs2230199 genotypes among cases and controls (p = 0.0055). rs2230199 was found to be a significant predictor of advanced AMD status (odds ratio 6.41, confidence interval [CI] 2.72-15.09, p<0.0001; area under the curve 0.706, CI 0.61-0.78, p<0.0001]). For the other single nucleotide polymorphism (SNP) loci, the allele and genotype frequencies did not reach statistical significance. The minor allele frequencies in controls and cases were similar and still much lower than the frequencies reported in other populations.

CONCLUSIONS

The rs547154, rs641153, and rs12614 SNPs were not associated with AMD development in Greek patients. However, this finding should be viewed with caution as the particular polymorphisms presented with very low frequencies in the Greek population. Finally, the replication of the reported associations of C3 with AMD suggests that the presence of the C3 G allele could serve as a high-risk genetic marker for the development of AMD and the progression of the disease to the advanced clinical stage.

CFH haplotypes and ARMS2, C2, C3, and CFB alleles show association with susceptibility to age-related macular degeneration in Mexicans

PURPOSE

To evaluate the contribution of genetic variants of complement factor H (CFH), complement component 2 and 3 (C2 and C3), complement factor B (CFB), and age-related maculopathy susceptibility 2 (ARMS2) to age-related macular degeneration (AMD) risk in the Mexican Mestizo population.

METHODS

Analysis included 282 unrelated Mexican patients with advanced AMD, 205 healthy controls, and 280 population controls. Stereoscopic fundus images were graded on the Clinical Age-Related Maculopathy System (CARMS). We designed a resequencing strategy using primers with M13 adaptor for the 23 exons of the CFH gene in a subgroup of 96 individuals clinically evaluated: 48 AMD cases and 48 age- and sex-matched healthy controls. Single nucleotide polymorphisms (SNPs) in C3 (Arg80Gly and Pro292Leu), C2 (rs547154), CFB (Leu9His), and ARMS2 (Ala69Ser) were genotyped in all patients, healthy and population controls using TaqMan assay.

RESULTS

All evaluated individuals were Mexican Mestizos, and their genetic ancestry was validated using 224 ancestry informative markers and calculating F(st) values. The CFH resequencing revealed 19 SNPs and a common variant in the intron 2 splice acceptor site; three CFH haplotypes inferred from individual genotypes, showed significant differences between cases and controls. The risk alleles in C3 (rs1047286, odds ratio [OR]=2.48, 95% confidence interval [CI]=1.64-3.75, p=1.59E-05; rs2230199, OR=2.15, 95% CI=1.48-3.13, p=6.28E-05) and in ARMS2 (rs10490924, OR=3.09, 95% CI=2.48-3.86, p=5.42E-23) were strongly associated with risk of AMD. The protective effect of alleles in C2 (rs547154) and CFB (rs4151667) showed a trend but was not significantly associated after correction for multiple testing.

CONCLUSIONS

Our results show that ARMS2 and C3 are major contributors to advanced AMD in Mexican patients, while the contributions of CFH, C2, and CFB are minor to those of other populations, reveling significant ethnic differences in minor allele frequencies. We provide evidence that two specific common haplotypes in the CFH gene predispose individuals to AMD, while another may confer reduced risk of disease in this admixed population.

Retinal angiomatous proliferation associated with risk alleles of ARMS2/HTRA1 gene polymorphisms in Japanese patients

Background

The purpose of this study was to investigate the association between ARMS2/HTRA1, CFH, and C3 gene polymorphisms and retinal angiomatous proliferation (RAP), an infrequent and severe form of exudative age-related macular degeneration, which is characterized by intraretinal neovascularization.

Methods

Diagnosis of RAP was based on fundus photographs, images of fluorescein and indocyanine green angiographies, and optical coherence tomography findings. Six single nucleotide polymorphisms (SNPs), A69S (rs10490924) in ARMS2, rs11200638 in HTRA1, I62V (rs800292) in CFH, Y402H (rs1061170) in CFH, R80G (rs2230199) in C3, and rs2241394 in C3, were genotyped in eight Japanese patients with RAP.

Results

The two SNPs in the ARMS2/HTRA1 were in complete linkage disequilibrium. The frequency of the risk T allele in ARMS2 (the risk A allele in HTRA1) was 93.8% in the RAP patients. The frequency of homozygosity for the risk genotype TT of ARMS2 (the risk genotype AA of HTRA1) was 87.5%. The frequency of the non-risk allele (A) of I62V was 100%. The frequencies of risk alleles of Y402H, R80G, and rs2241394 were 12.5%, 0%, and 18.8%, respectively.

Conclusion

Our results suggest that the risk alleles of the ARMS2/HTRA1 SNPs may be associated with development of RAP and play a major role in the pathogenesis of intraretinal angiogenesis.

TOMM40 rs2075650 polymorphism shows no association with neovascular age-related macular degeneration or polypoidal choroidal vasculopathy in a Chinese population

PURPOSE

Age-related macular degeneration (AMD) and Alzheimer disease (AD) are age-related neurodegenerative diseases that share similar environmental risk factors, cellular pathologies, and genetic backgrounds. Recently, the rs2075650 single nucleotide polymorphism in the translocase of outer mitochondrial membrane 40 homolog (TOMM40) gene was identified as a risk factor for AMD and Alzheimer disease. We aimed to examine the associations between the TOMM40 rs2075650 polymorphism and neovascular age-related macular degeneration (nAMD) and polypoidal choroidal vasculopathy (PCV) in a Chinese population.

METHODS

The study consisted of 900 subjects, including 300 controls, 300 cases with nAMD, and 300 cases with PCV. Genomic DNA was extracted from venous blood leukocytes. The allelic variant of rs2075650 was determined with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Differences in the observed genotypic distributions between the case and control groups were tested using chi-square tests, with age and gender adjusted using logistic regression analysis.

RESULTS

The TOMM40 rs2075650 polymorphism was not statistically significantly associated with the nAMD or PCV phenotype (p>0.05). The difference remained insignificant after correction for age and gender differences based on the logistic regression models (p>0.05).

CONCLUSIONS

Our data provide no evidence to support an association of rs2075650 in TOMM40 with nAMD or PCV, suggesting that this gene is unlikely to be a major AMD and PCV susceptibility gene locus in the Chinese population.

The association between complement component 2/complement factor B polymorphisms and age-related macular degeneration: a HuGE review and meta-analysis

The authors performed a systematic review of the association of complement component 2(C2)/complement factor B (CFB) gene polymorphisms with age-related macular degeneration (AMD). In total, data from 19 studies published between 2006 and 2011 were pooled for 4 polymorphisms: rs9332739 and rs547154 in the C2 gene and rs4151667 and rs641153 in the CFB gene. Data extraction and assessments for risk of bias were independently performed by 2 reviewers. Allele frequencies and allele and genotypic effects were pooled. Heterogeneity and publication bias were explored. Pooled minor allele frequencies for all 4 SNPs were between 4.7% and 9.6% for all polymorphisms, except for an Indian population in which the C allele at rs9332739 was the major allele. For the C2 polymorphisms, the minor C allele at rs9332739 and the minor T allele at rs547154 carried estimated relative risks (odds ratios) of 0.55 (95% confidence interval (CI): 0.46, 0.65) and 0.47 (95% CI: 0.39, 0.57), respectively. For the CFB polymorphisms, the minor A alleles at rs4151667 and rs614153 carried estimated risks of 0.54 (95% CI: 0.45, 0.64) and 0.41 (95% CI: 0.34, 0.51), respectively. These allele effects contributed to an absolute lowering of the risk of all AMD in Caucasian populations by 2.0%-6.0%. This meta-analysis provides a robust estimate of the protective association of C2/CFB with AMD.

CFB/C2 gene polymorphisms and risk of age-related macular degeneration: a systematic review and meta-analysis

PURPOSE

To investigate whether the polymorphisms of CFB/C2 gene are associated with age-related macular degeneration (AMD), and to evaluate the magnitude of gene effect.

METHODS

We performed a meta-analysis of the association between four SNPs in CFB/C2 gene (rs9332739, rs547154, rs4151667, and rs641153) and risk of AMD using data from 15 case-control studies involving 8905 subjects. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using fixed- and random-effects models. The Q and I(2) statistics were used to evaluate between-study heterogeneity. Harbord's modified test was used to detect small study effects. Sensitivity analysis, cumulative meta-analysis, and meta-regression were also performed.

RESULTS

For rs9332739, rs547154, rs4151667, and rs641153, the pooled ORs in a dominant genetic model were 0.474 (fixed effects, P < 0.001, 95% CI 0.378-0.596), 0.399 (random effects, 95% CI 0.289-0.551, P < 0.001), 0.496 (fixed effects, 95% CI 0.390-0.632, P < 0.001), and 0.557 (random effects, P = 0.008, 95% CI 0.362-0.856), respectively. These results suggested that variant alleles of all the four SNPs has significant protective effect against AMD. Contour-enhanced funnel plots and Harbord's test showed moderate small study effects for rs9332739 and rs4151667. Heterogeneity were found for rs547154 and rs641153, subgroup analysis suggested that ethnicity was the main source for heterogeneity. Stratification by ethnicity indicated stronger protective effects of rare alleles in Caucasians. Genotype distribution analysis also suggested that frequencies of rare homozygous genotype were higher in Caucasian group.

CONCLUSIONS

Our meta-analysis indicated strong protective effects of the variant alleles of four SNPs in CFB/C2 gene (rs9332739, rs547154, rs4151667, and rs641153) against AMD. The disease risk descended to nearly one half for individuals carrying at least one copy of the rare alleles. The protective effects seemed to be stronger in Caucasians, of which the genotype frequencies were also higher.

Association of polymorphisms in C2, CFB and C3 with exudative age-related macular degeneration in a Korean population

This study was to investigate the association of genetic polymorphisms in complement component 2 (C2), complement factor B (CFB) and complement component 3 (C3) with exudative age-related macular degeneration (AMD) in a Korean population and the gene-gene and gene-environment interactions in the development of AMD. A total of six SNPs that are located in the C2 (rs547154, rs9332739), CFB (rs4151667, rs641153) and C3 (rs1047286, rs2230199) genes were genotyped in 350 samples comprised of 153 cases, 197 controls. The risk allele frequencies for rs547154 in C2 were 6.54% and 8.12% in AMD patients and controls. Those for rs641153 in CFB were 6.54% and 8.63% in AMD patients and controls. The risk allele frequency for rs9332739 in C2 (AMD, 0.65%, control, 2.03%) and rs4151667 in CFB (AMD, 0.65%, control, 1.78%) was very low. The protective allele of four SNPs was not significantly associated with decreased risk for AMD (P = 0.427, P = 0.199, P = 0.312, P = 0.303, respectively). The homozygotes for the protective allele of four SNPs were not significantly associated with decreased risk for AMD (P = 0.324, P = 0.474, P = 0.309, P = 0.411, respectively). The genetic effect of two SNPs in C3 could not be investigated because the variants were not observed. There was no evidence to support an interaction of these SNPs with LOC387715/HTRA1 variants or with environmental exposure like smoking. In conclusion, the genetic effect of C2, CFB and C3 polymorphisms, which are known to be important for AMD in Caucasian, were not significant in the Korean population. The low minor allele frequency of these SNPs in Koreans might have affected the results of this study. Ethnic differences in the roles of C2, CFB and C3 in conferring a risk of AMD should be further investigated.

Copy number variation in the complement factor H-related genes and age-related macular degeneration

PURPOSE

To determine the contribution of copy number variation (CNV) in the regulation of complement activation (RCA) locus to the development of age-related macular degeneration (AMD).

METHODS

A multiplex ligation-dependent probe amplification assay was developed to quantify the number of copies of CFH, CFHR3, CFHR1, CFHR4, CFHR2, and CFHR5 in humans. Subjects with (451) and without (362) AMD were genotyped using the assay, and the impact on AMD risk was evaluated.

RESULTS

Eight unique combinations of copy number variation were observed in the 813 subjects. Combined deletion of CFHR3 and CFHR1 was protective (OR=0.47, 95% confidence interval 0.36-0.62) against AMD and was observed in 88 (82 [18.6%] with one deletion, 6 [1.4%] with two deletions) subjects with AMD and 127 (108 [30.7%] with one deletion, 19 [5.4%] with two deletions) subjects without AMD. Other deletions were much less common: CFH intron 1 (n=2), CFH exon 18 (n=2), combined CFH exon 18 and CFHR3 (n=1), CFHR3 (n=2), CFHR1 (n=1), combined CFHR1 and CFHR4 (n=15), and CFHR2 deletion (n=7, 0.9%). The combined CFHR3 and CFHR1 deletion was observed on a common protective haplotype, while the others appeared to have arisen on multiple different haplotypes.

CONCLUSIONS

We found copy number variations of CFHR3, CFHR1, CFHR4, and CFHR2. Combined deletion of CFHR3 and CFHR1 was associated with a decreased risk of developing AMD. Other deletions were not sufficiently common to have a statistically detectable impact on the risk of AMD, and duplications were not observed.

Systematic review and meta-analysis of the association between complement component 3 and age-related macular degeneration: a HuGE review and meta-analysis

The authors performed a meta-analysis to estimate the magnitude of polymorphism effects for the complement component C3 gene (C3) and their possible mode of action on age-related macular degeneration (AMD). The meta-analysis included 16 and 7 studies for rs2230199 and rs1047286, respectively. Data extraction and risk of bias assessments were performed in duplicate, and heterogeneity and publication bias were explored. There was moderate evidence for association between both polymorphisms and AMD in Caucasians. For rs2230199, patients with CG and GG genotypes were 1.44 (95% confidence interval (CI): 1.33, 1.56) and 1.88 (95% CI: 1.59, 2.23) times more likely to have AMD than patients with the CC genotype. For rs1047286, GA and AA genotypes had 1.27 (95% CI: 1.15, 1.41) and 1.70 (95% CI: 1.27, 2.11) times higher risk of AMD than did GG genotypes. These gene effects suggested an additive model. The population attributable risks for the GG/GC and AA/GA genotypes are approximately 5%-10%. Subgroup analysis by ethnicity indicates that these variants are very infrequent in Asians and that the observed gene effects are based largely on the high frequency within Caucasian populations. This meta-analysis supports the association between C3 and AMD and provides a robust estimate of the genetic risk.

The alternative pathway is required, but not alone sufficient, for retinal pathology in mouse laser-induced choroidal neovascularization

Human genetic studies have demonstrated that polymorphisms in different complement proteins can increase the risk for developing AMD. There are three pathways of complement activation, classical (CP), alternative (AP), and lectin (LP), which all activate a final common pathway. Proteins encoded by the AMD risk genes participate in the AP (CFB), CP/LP (C2), or in the AP and final common pathway (C3). Here we tested which pathway is essential in mouse laser-induced CNV. CNV was analyzed using single complement pathway knockouts (i.e., eliminating one complement pathway at a time), followed by a double knockout in which only the AP is present, and the CP and LP are disabled, using molecular, histological and electrophysiological outcomes. First, single-gene knockouts were analyzed and compared to wild type mice; C1q(-/-) (no CP), MBL(-/-) (no LP), and CFB(-/-) (no AP). Six days after the laser-induced lesion, mice without a functional AP had reduced CNV progression (P<0.001) and preserved ERG amplitudes, whereas those without a functional CP or LP were indistinguishable from the wild type controls (P>0.3). Second, AP-only mice (C1q(-/-)MBL(-/-)) were as protected from developing CNV as the CFB(-/-) mice. The degree of pathology in each strain correlated with protein levels of the angiogenic and anti-angiogenic protein VEGF and PEDF, respectively, as well as levels of terminal pathway activation product C5a, and C9. The analysis of complement activation pathways in mouse laser-induced CNV allows for the following conclusions. Comparing the single pathway knockouts with those having only a functional AP showed: (1) that AP activation is necessary, but not alone sufficient for injury; and (2) that initial complement activation proceeds via both the LP and CP. Thus, these data indicate an important role for the AP in the generation of complement-dependent injury in the RPE and choroid via amplification of CP- and LP-initiated complement activation. Improving our understanding of the local regulation of this pathway in the eye is essential for developing improved treatment approaches for AMD.

Genome-wide association analyses of genetic, phenotypic, and environmental risks in the age-related eye disease study

PURPOSE

To present genome-wide association analyses of genotypic and environmental risks on age-related macular degeneration (AMD) using 593 subjects from the age-related eye disease study (AREDS), after adjusting for population stratification and including questionable controls.

METHODS

Single nucleotide polymorphism (SNP) associations with AMD for the non-Hispanic white population were investigated using a log-additive model after adjusting for population stratification. Replication of possible SNP-disease association was performed by genotyping an independent group of 444 AMD case and 300 control subjects. Logistic regression models were used to assess interaction effects between smoking and SNPs associated with AMD. Independent genetic risk effects among the disease-associated SNPs were also investigated using multiple logistic regression models.

RESULTS

Population stratification was observed among the individuals having a self-reported race of non-Hispanic white. Risk allele frequencies at established AMD loci demonstrated that questionable control subjects were similar to control subjects in the AREDS, suggesting that they could be used as true controls in the analyses. Genetic loci (complement factor H [CFH], complement factor B [CFB], the age-related maculopathy susceptibility 2 locus containing the hypothetical gene [LOC387715]/the high-temperature requirement A-1 [HTRA1], and complement component 3 [C3]) that were already known to be associated with AMD were identified. An additional 26 novel SNPs potentially associated with AMD were identified, but none were definitely replicated in a second independent group of subjects. Smoking did not interact with known AMD loci, but was associated with late AMD. Statistically independent genetic signals were observed within the Pleckstrin homology domain-containing family A member 1 (PLEKHA1) region near LOC387715/HTRA1 and within a haplotype spanning exon 19 of the C3 gene.

CONCLUSIONS

Population stratification among Caucasian subjects from the multicentered AREDS was observed, suggesting that it should be adjusted for in future studies. The AREDS questionable control subjects can be used as control subjects in the AREDS genome-wide association study (GWAS). Smoking was an independent risk factor for advanced AMD in the AREDS subjects. There continues to be evidence that the 10q26 (age-related maculopathy susceptibility 2 gene [ARMS2]) locus spanning PLEKHA1-LOC387715-HTRA1 and the C3 gene may contain multiple independent genetic risks contributing to AMD.

Genome-wide association identifies SKIV2L and MYRIP as protective factors for age-related macular degeneration

Age-related macular degeneration (AMD) is the leading cause of blindness in the elderly in the developed world. We conducted a genome-wide association study in a series of families enriched for AMD and completed a meta-analysis of this new data with results from reanalysis of an existing study of a late-stage case-control cohort. We tested the top findings for replication in 1896 cases and 1866 controls and identified two novel genetic protective factors for AMD. In addition to the complement factor H (CFH) (P=2.3 × 10⁻⁶⁴) and age-related maculopathy susceptibility 2 (ARMS2) (P=1.2 × 10⁻⁶⁰) loci, we observed a protective effect at rs429608, an intronic SNP in SKIV2L (P=5.3 × 10⁻¹⁵), a gene near the complement component 2 (C2)/complement factor B (BF) locus, that indicates the protective effect may be mediated by variants other than the C2/BF variants previously studied. Haplotype analysis at this locus identified three protective haplotypes defined by the rs429608 protective allele. We also identified a new potentially protective effect at rs2679798 in MYRIP (P=2.9 × 10⁻⁴), a gene involved in retinal pigment epithelium melanosome trafficking. Interestingly, MYRIP was initially identified in the family-based scan and was confirmed in the case-control set. From these efforts, we report the identification of two novel protective factors for AMD and confirm the previously known associations at CFH, ARMS2 and C3.

Genetic analysis of typical wet-type age-related macular degeneration and polypoidal choroidal vasculopathy in Japanese population

Age-related macular degeneration (AMD) is a common cause of blindness in the elderly. Caucasian patients are predominantly affected by the dry form of AMD, whereas Japanese patients have predominantly the wet form of AMD and/or polypoidal choroidal vasculopathy (PCV). Although genetic association in the 10q26 (ARMS2/HTRA1) region has been established in many ethnic groups for dry-type AMD, typical wet-type AMD, and PCV, the contribution of the 1q32 (CFH) region seem to differ among these groups. Here we show a single nucleotide polymorphism (SNP) in the ARMS2/HTRA1 locus is associated in the whole genome for Japanese typical wet-type AMD (rs10490924: \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ p = 4.1 \times 10 ^{ - 4}$$\end{document}, OR = 4.16) and PCV (rs10490924: \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ p = 3.7 \times 10 ^{ -8}$$\end{document}, OR = 2.72) followed by CFH (rs800292: \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ p = 7.4 \times 10 ^{ -5}$$\end{document}, OR = 2.08; \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ p = 2.6 \times {10^{ - 4}} $$\end{document}, OR = 2.00), which differs from previous studies in Caucasian populations. Moreover, a SNP (rs2241394) in complement component C3 gene showed significant association with PCV (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ p = 2.5 \times {10^{ - 3}} $$\end{document}, OR = 3.47). We conclude that dry-type AMD, typical wet-type AMD, and PCV have both common and distinct genetic risks that become apparent when comparing Japanese versus Caucasian populations.

The complement component 5 gene and age-related macular degeneration

OBJECTIVE

To investigate the association between variants in the complement component 5 (C5) gene and age-related macular degeneration (AMD).

DESIGN

Separate and combined data from 3 large AMD case-control studies and a prospective population-based study (The Rotterdam Study).

PARTICIPANTS

A total of 2599 AMD cases and 3458 ethnically matched controls.

METHODS

Fifteen single nucleotide polymorphisms (SNPs) spanning the C5 gene were initially genotyped in 375 cases and 199 controls from The Netherlands (The Amsterdam/Rotterdam-Netherlands [AMRO-NL] study population). Replication testing of selected SNPs was performed in the Rotterdam Study (NL) and study populations from Southampton, United Kingdom (UK), and New York, United States (US).

MAIN OUTCOME MEASURES

Early and late stages of prevalent and incident AMD, graded according to (a modification of) the international grading and classification system of AMD.

RESULTS

Significant allelic or genotypic associations between 8 C5 SNPs and AMD were found in the AMRO-NL study and this risk seemed to be independent of CFH Y402H, LOC387715 A69S, age, and gender. None of these findings could be confirmed consistently in 3 replication populations.

CONCLUSIONS

Although the complement pathway, including C5, plays a crucial role in AMD, and the C5 protein is present in drusen, no consistent significant associations between C5 SNPs and AMD were found in any of these studies. The implications for genetic screening of AMD are discussed.

Polymorphisms in the VEGFA and VEGFR-2 genes and neovascular age-related macular degeneration

PURPOSE

Genetic factors influence an individual's risk for developing neovascular age-related macular degeneration (AMD), a leading cause of irreversible blindness. Previous studies on the potential genetic link between AMD and vascular endothelial growth factor (VEGF), a key regulator of angiogenesis and vascular permeability, have yielded conflicting results. In the present case-control association study, we aimed to determine whether VEGF or its main receptor tyrosine kinase VEGFR-2 is genetically associated with neovascular AMD.

METHODS

A total of 515 Caucasian patients with neovascular AMD and 253 ethically-matched controls were genotyped for polymorphisms in the VEGFA and VEGFR-2 genes. A tagging single nucleotide polymorphism (tSNP) approach was employed to cover each gene plus two kilobases on each side, spanning the promoter and 3' untranslated regions. SNPs with a minimum allele frequency of 10% were covered by seven tSNPs in VEGFA and 20 tSNPs in VEGFR-2. Two VEGFA SNPs previously linked with AMD, rs1413711 and rs3025039, were also analyzed.

RESULTS

The 29 VEGFA and VEGFR-2 SNPs analyzed in our cohort demonstrated no significant association with neovascular AMD. A single rare haplotype in the VEGFR-2 gene was associated with the presence of neovascular AMD (p=0.034).

CONCLUSIONS

This study is the first to investigate the association of VEGFR-2 polymorphisms with AMD and evaluates VEGFA genetic variants in the largest neovascular AMD cohort to date. Despite the angiogenic and permeability-enhancing effects of VEGF/VEGFR-2 signaling, we found minimal evidence of a significant link between polymorphisms in the VEGFA and VEGFR-2 genes and neovascular AMD.

Genetics of COPD and emphysema

COPD is a highly prevalent disorder that results from the interplay of genetic susceptibility and environmental exposures. Over the past 2 decades, significant technological advances have been made in genetic investigations of complex diseases, yet limited progress has been made in the identification of additional COPD susceptibility genes. Genetic and phenotypic heterogeneity, limited power due to modest study population sizes, and significant modification of genetic effects by environmental factors pose significant challenges in COPD and emphysema genetic studies. More refined characterization of the emphysema and airway components of COPD can now be obtained through the systematic use of CT scans. These improved phenotypes can be applied in genome-wide association studies and will likely lead to the discovery of additional susceptibility loci and therapeutic targets.

Common variation in the SERPING1 gene is not associated with age-related macular degeneration in two independent groups of subjects

PURPOSE

Common genetic variation in the complement component 1 inhibitor gene (SERPING1) was recently reported to increase the risk of developing age-related macular degeneration (AMD). This study was performed to replicate the association between SERPING1 and AMD.

METHODS

Seven single nucleotide polymorphisms (SNPs) tagging common haplotypes across SERPING1 were genotyped on 786 (The Mayo Clinic) subjects and the association with AMD studied using single SNP and haplotype association analyses. The SNP in intron 6 (rs2511989) previously reported to increase the risk of AMD was studied in an additional 1,541 subjects from the Age-Related Eye Disease Study (AREDS). Association with specific subtypes of AMD and interaction with four other loci: complement factor H (CFH), age-related maculopathy susceptibility 2 (ARMS2/LOC387715), High Temperature Requirement Factor A1 (HTRA1), complement factor B/complement component 2 (CFB/C2), and complement component 3 (C3) involved in AMD was explored.

RESULTS

The seven tag-SNPs were not associated with AMD in the Mayo subjects (p=0.13-0.70) and rs2511989 was also not associated with AMD in the Mayo or AREDS subjects (p=0.44-0.45). Evaluation of haplotypes across SERPING1 did not reveal association with AMD (p=0.14-0.97). SNPs were not associated with AMD subtypes (early, geographic atrophy, or exudation). No interaction with other AMD risk variants was observed.

CONCLUSIONS

We were unable to replicate the reported association between SERPING1 and AMD in two independent groups of subjects.