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1.  Progression Rate From Intermediate to Advanced Age-Related Macular Degeneration Is Correlated With the Number of Risk Alleles at the CFH Locus 
Purpose
Progression rate of age-related macular degeneration (AMD) varies substantially, yet its association with genetic variation has not been widely examined.
Methods
We tested whether progression rate from intermediate AMD to geographic atrophy (GA) or choroidal neovascularization (CNV) was correlated with genotype at seven single nucleotide polymorphisms (SNPs) in the four genes most strongly associated with risk of advanced AMD. Cox proportional hazards survival models examined the association between progression time and SNP genotype while adjusting for age and sex and accounting for variable follow-up time, right censored data, and repeated measures (left and right eyes).
Results
Progression rate varied with the number of risk alleles at the CFH:rs10737680 but not the CFH:rs1061170 (Y402H) SNP; individuals with two risk alleles progressed faster than those with one allele (hazard ratio [HR] = 1.61, 95% confidence interval [CI] = 1.08–2.40, P < 0.02, n = 547 eyes), although this was not significant after Bonferroni correction. This signal was likely driven by an association at the correlated protective variant, CFH:rs6677604, which tags the CFHR1-3 deletion; individuals with at least one protective allele progressed more slowly. Considering GA and CNV separately showed that the effect of CFH:rs10737680 was stronger for progression to CNV.
Conclusions
Results support previous findings that AMD progression rate is influenced by CFH, and suggest that variants within CFH may have different effects on risk versus progression. However, since CFH:rs10737680 was not significant after Bonferroni correction and explained only a relatively small portion of variation in progression rate beyond that explained by age, we suggest that additional factors contribute to progression.
doi:10.1167/iovs.16-19519
PMCID: PMC5104418  PMID: 27832277
age-related macular degeneration (AMD); genetics; progression
2.  Genetic Association Analysis of Drusen Progression 
Purpose
Age-related macular degeneration is a common form of vision loss affecting older adults. The etiology of AMD is multifactorial and is influenced by environmental and genetic risk factors. In this study, we examine how 19 common risk variants contribute to drusen progression, a hallmark of AMD pathogenesis.
Methods
Exome chip data was made available through the International AMD Genomics Consortium (IAMDGC). Drusen quantification was carried out with color fundus photographs using an automated drusen detection and quantification algorithm. A genetic risk score (GRS) was calculated per subject by summing risk allele counts at 19 common genetic risk variants weighted by their respective effect sizes. Pathway analysis of drusen progression was carried out with the software package Pathway Analysis by Randomization Incorporating Structure.
Results
We observed significant correlation with drusen baseline area and the GRS in the age-related eye disease study (AREDS) dataset (ρ = 0.175, P = 0.006). Measures of association were not statistically significant between drusen progression and the GRS (P = 0.54). Pathway analysis revealed the cell adhesion molecules pathway as the most highly significant pathway associated with drusen progression (corrected P = 0.02).
Conclusions
In this study, we explored the potential influence of known common AMD genetic risk factors on drusen progression. Our results from the GRS analysis showed association of increasing genetic burden (from 19 AMD associated loci) to baseline drusen load but not drusen progression in the AREDS dataset while pathway analysis suggests additional genetic contributors to AMD risk.
doi:10.1167/iovs.15-18571
PMCID: PMC4849854  PMID: 27116550
age-related macular degeneration; drusen; genetic risk score analysis; image analysis
3.  Genetics and age-related macular degeneration: a practical review for the clinician 
Age-related macular degeneration is a complex disease, with both genetic and environmental risk factors interacting in unknown ways. Currently, 52 gene variants within 34 loci have been significantly associated with age-related macular degeneration. Two well-studied major genes are complement factor H (CFH) and age-related maculopathy susceptibility 2 (ARMS2). There exist several commercially available tests that are proposed to stratify patients into high-risk and low-risk groups, as well as predict response to nutritional supplementation. However, at present, the bulk of the available peer-reviewed evidence suggests that genetic testing is more useful as a research tool than for clinical management of patients.
doi:10.2147/OPTH.S109723
PMCID: PMC4938141  PMID: 27445455
age-related macular degeneration; age-related maculopathy susceptibility 2; ARMS2; complement factor H; CFH; pharmacogenetics; vascular endothelial growth factor
4.  A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants 
Fritsche, Lars G. | Igl, Wilmar | Cooke Bailey, Jessica N. | Grassmann, Felix | Sengupta, Sebanti | Bragg-Gresham, Jennifer L. | Burdon, Kathryn P. | Hebbring, Scott J. | Wen, Cindy | Gorski, Mathias | Kim, Ivana K. | Cho, David | Zack, Donald | Souied, Eric | Scholl, Hendrik P. N. | Bala, Elisa | Lee, Kristine E. | Hunter, David J. | Sardell, Rebecca J. | Mitchell, Paul | Merriam, Joanna E. | Cipriani, Valentina | Hoffman, Joshua D. | Schick, Tina | Lechanteur, Yara T. E. | Guymer, Robyn H. | Johnson, Matthew P. | Jiang, Yingda | Stanton, Chloe M. | Buitendijk, Gabriëlle H. S. | Zhan, Xiaowei | Kwong, Alan M. | Boleda, Alexis | Brooks, Matthew | Gieser, Linn | Ratnapriya, Rinki | Branham, Kari E. | Foerster, Johanna R. | Heckenlively, John R. | Othman, Mohammad I. | Vote, Brendan J. | Liang, Helena Hai | Souzeau, Emmanuelle | McAllister, Ian L. | Isaacs, Timothy | Hall, Janette | Lake, Stewart | Mackey, David A. | Constable, Ian J. | Craig, Jamie E. | Kitchner, Terrie E. | Yang, Zhenglin | Su, Zhiguang | Luo, Hongrong | Chen, Daniel | Ouyang, Hong | Flagg, Ken | Lin, Danni | Mao, Guanping | Ferreyra, Henry | Stark, Klaus | von Strachwitz, Claudia N. | Wolf, Armin | Brandl, Caroline | Rudolph, Guenther | Olden, Matthias | Morrison, Margaux A. | Morgan, Denise J. | Schu, Matthew | Ahn, Jeeyun | Silvestri, Giuliana | Tsironi, Evangelia E. | Park, Kyu Hyung | Farrer, Lindsay A. | Orlin, Anton | Brucker, Alexander | Li, Mingyao | Curcio, Christine | Mohand-Saïd, Saddek | Sahel, José-Alain | Audo, Isabelle | Benchaboune, Mustapha | Cree, Angela J. | Rennie, Christina A. | Goverdhan, Srinivas V. | Grunin, Michelle | Hagbi-Levi, Shira | Campochiaro, Peter | Katsanis, Nicholas | Holz, Frank G. | Blond, Frédéric | Blanché, Hélène | Deleuze, Jean-François | Igo, Robert P. | Truitt, Barbara | Peachey, Neal S. | Meuer, Stacy M. | Myers, Chelsea E. | Moore, Emily L. | Klein, Ronald | Hauser, Michael A. | Postel, Eric A. | Courtenay, Monique D. | Schwartz, Stephen G. | Kovach, Jaclyn L. | Scott, William K. | Liew, Gerald | Tƒan, Ava G. | Gopinath, Bamini | Merriam, John C. | Smith, R. Theodore | Khan, Jane C. | Shahid, Humma | Moore, Anthony T. | McGrath, J. Allie | Laux, Reneé | Brantley, Milam A. | Agarwal, Anita | Ersoy, Lebriz | Caramoy, Albert | Langmann, Thomas | Saksens, Nicole T. M. | de Jong, Eiko K. | Hoyng, Carel B. | Cain, Melinda S. | Richardson, Andrea J. | Martin, Tammy M. | Blangero, John | Weeks, Daniel E. | Dhillon, Bal | van Duijn, Cornelia M. | Doheny, Kimberly F. | Romm, Jane | Klaver, Caroline C. W. | Hayward, Caroline | Gorin, Michael B. | Klein, Michael L. | Baird, Paul N. | den Hollander, Anneke I. | Fauser, Sascha | Yates, John R. W. | Allikmets, Rando | Wang, Jie Jin | Schaumberg, Debra A. | Klein, Barbara E. K. | Hagstrom, Stephanie A. | Chowers, Itay | Lotery, Andrew J. | Léveillard, Thierry | Zhang, Kang | Brilliant, Murray H. | Hewitt, Alex W. | Swaroop, Anand | Chew, Emily Y. | Pericak-Vance, Margaret A. | DeAngelis, Margaret | Stambolian, Dwight | Haines, Jonathan L. | Iyengar, Sudha K. | Weber, Bernhard H. F. | Abecasis, Gonçalo R. | Heid, Iris M.
Nature genetics  2015;48(2):134-143.
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, most rare, protein-altering variant. 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. While wet and dry AMD subtypes exhibit predominantly shared genetics, we identify the first signal specific to wet AMD, near MMP9 (difference-P = 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.
doi:10.1038/ng.3448
PMCID: PMC4745342  PMID: 26691988
5.  Metabolome-Wide Association Study of Primary Open Angle Glaucoma 
Purpose
To determine if primary open-angle glaucoma (POAG) patients can be differentiated from controls based on metabolic characteristics.
Methods
We used ultra-high resolution mass spectrometry with C18 liquid chromatography for metabolomic analysis on frozen plasma samples from 72 POAG patients and 72 controls. Metabolome-wide Spearman correlation was performed to select differentially expressed metabolites (DEM) correlated with POAG. We corrected P values for multiple testing using Benjamini and Hochberg false discovery rate (FDR). Hierarchical cluster analysis (HCA) was used to depict the relationship between participants and DEM. Differentially expressed metabolites were matched to the METLIN metabolomics database; both DEM and metabolites significantly correlating with DEM were analyzed using MetaboAnalyst to identify metabolic pathways altered in POAG.
Results
Of the 2440 m/z (mass/charge) features recovered after filtering, 41 differed between POAG cases and controls at FDR = 0.05. Hierarchical cluster analysis revealed these DEM to associate into eight clusters; three of these clusters contained the majority of the DEM and included palmitoylcarnitine, hydroxyergocalciferol, and high-resolution METLIN matches to sphingolipids, other vitamin D-related metabolites, and terpenes. MetaboAnalyst also indicated likely alteration in steroid biosynthesis pathways.
Conclusions
Global ultrahigh resolution metabolomics emphasized the importance of altered lipid metabolism in POAG. The results suggest specific metabolic processes, such as those involving palmitoylcarnitine, sphingolipids, vitamin D-related compounds, and steroid precursors, may contribute to POAG status and merit more detailed study with targeted methods.
Plasma metabolomic analysis demonstrates that metabolic signatures can distinguish patients with primary open angle glaucoma (POAG) from controls. The resulting metabolic profiles indicate that palmitoylcarnitine, sphingolipids, and vitamin D-related compounds all likely influence POAG.
doi:10.1167/iovs.15-16702
PMCID: PMC4525636  PMID: 26230767
glaucoma; metabolomics; plasma; sphingosine; vitamin D; palmitoylcarnitine
6.  Whole exome sequencing of extreme age-related macular degeneration phenotypes 
Molecular Vision  2016;22:1062-1076.
Purpose
Demographic, environmental, and genetic risk factors for age-related macular degeneration (AMD) have been identified; however, a substantial portion of the variance in AMD disease risk and heritability remains unexplained. To identify AMD risk variants and generate hypotheses for future studies, we performed whole exome sequencing for 75 individuals whose phenotype was not well predicted by their genotype at known risk loci. We hypothesized that these phenotypically extreme individuals were more likely to carry rare risk or protective variants with large effect sizes.
Methods
A genetic risk score was calculated in a case–control set of 864 individuals (467 AMD cases, 397 controls) based on 19 common (≥1% minor allele frequency, MAF) single nucleotide variants previously associated with the risk of advanced AMD in a large meta-analysis of advanced cases and controls. We then selected for sequencing 39 cases with bilateral choroidal neovascularization with the lowest genetic risk scores to detect risk variants and 36 unaffected controls with the highest genetic risk score to detect protective variants. After minimizing the influence of 19 common genetic risk loci on case-control status, we targeted single variants of large effect and the aggregate effect of weaker variants within genes and pathways. Single variant tests were conducted on all variants, while gene-based and pathway analyses were conducted on three subsets of data: 1) rare (≤1% MAF in the European population) stop, splice, or damaging missense variants, 2) all rare variants, and 3) all variants. All analyses controlled for the effects of age and sex.
Results
No variant, gene, or pathway outside regions known to be associated with risk for advanced AMD reached genome-wide significance. However, we identified several variants with substantial differences in allele frequency between cases and controls with strong additive effects on affection status after controlling for age and sex. Protective effects trending toward significance were detected at two loci identified in single-variant analyses: an intronic variant in FBLN7 (the gene encoding fibulin 7) and at three variants near pyridoxal (pyridoxine, vitamin B6) kinase (PDXK). Aggregate rare-variant analyses suggested evidence for association at ASRGL1, a gene previously linked to photoreceptor cell death, and at BSDC1. In known AMD loci we also identified 29 novel or rare damaging missense or stop/splice variants in our sample of cases and controls.
Conclusions
Identified variants and genes may highlight regions important in the pathogenesis of AMD and are key targets for replication.
PMCID: PMC5007100  PMID: 27625572
7.  Update on genetics and diabetic retinopathy 
Clinical risk factors for diabetic retinopathy (DR), such as duration of disease and degree of glucose control, do not adequately predict disease progression in individual patients, suggesting the presence of a genetic component. Multiple smaller studies have investigated genotype–phenotype correlations in genes encoding vascular endothelial growth factor, aldose reductase, the receptor for advanced glycation end products, and many others. In general, reported results have been conflicting, due to factors including small sample sizes, variations in study design, differences in clinical end points, and underlying genetic differences between study groups. At this time, there is no confirmed association with any risk allele reported. As we continue to collect data from additional studies, the role of genetics in DR may become more apparent.
doi:10.2147/OPTH.S94508
PMCID: PMC4664538  PMID: 26648684
diabetic retinopathy; genetics; single nucleotide polymorphism; genome-wide association study
8.  Estimating cumulative pathway effects on risk for age-related macular degeneration using mixed linear models 
BMC Bioinformatics  2015;16:329.
Background
Age-related macular degeneration (AMD) is the leading cause of irreversible visual loss in the elderly in developed countries and typically affects more than 10 % of individuals over age 80. AMD has a large genetic component, with heritability estimated to be between 45 % and 70 %. Numerous variants have been identified and implicate various molecular mechanisms and pathways for AMD pathogenesis but those variants only explain a portion of AMD’s heritability. The goal of our study was to estimate the cumulative genetic contribution of common variants on AMD risk for multiple pathways related to the etiology of AMD, including angiogenesis, antioxidant activity, apoptotic signaling, complement activation, inflammatory response, response to nicotine, oxidative phosphorylation, and the tricarboxylic acid cycle. While these mechanisms have been associated with AMD in literature, the overall extent of the contribution to AMD risk for each is unknown.
Methods
In a case–control dataset with 1,813 individuals genotyped for over 600,000 SNPs we used Genome-wide Complex Trait Analysis (GCTA) to estimate the proportion of AMD risk explained by SNPs in genes associated with each pathway. SNPs within a 50 kb region flanking each gene were also assessed, as well as more distant, putatively regulatory SNPs, based on DNaseI hypersensitivity data from ocular tissue in the ENCODE project.
Results
We found that 19 previously associated AMD risk SNPs contributed to 13.3 % of the risk for AMD in our dataset, while the remaining genotyped SNPs contributed to 36.7 % of AMD risk. Adjusting for the 19 risk SNPs, the complement activation and inflammatory response pathways still explained a statistically significant proportion of additional risk for AMD (9.8 % and 17.9 %, respectively), with other pathways showing no significant effects (0.3 % – 4.4 %).
Discussion
Our results show that SNPs associated with complement activation and inflammation significantly contribute to AMD risk, separately from the risk explained by the 19 known risk SNPs. We found that SNPs within 50 kb regions flanking genes explained additional risk beyond genic SNPs, suggesting a potential regulatory role, but that more distant SNPs explained less than 0.5 % additional risk for each pathway.
Conclusions
From these analyses we find that the impact of complement SNPs on risk for AMD extends beyond the established genome-wide significant SNPs.
Electronic supplementary material
The online version of this article (doi:10.1186/s12859-015-0760-4) contains supplementary material, which is available to authorized users.
doi:10.1186/s12859-015-0760-4
PMCID: PMC4606903  PMID: 26467978
Age-related macular degeneration (AMD); Heritability; Pathway analysis; Mixed linear model (MLM); Proportion of variance explained (PVE)
9.  Mitochondrial Haplogroups Are Associated With Severity of Diabetic Retinopathy 
Purpose.
To determine if specific mitochondrial haplogroups associate with nonproliferative diabetic retinopathy (NPDR) and proliferative diabetic retinopathy (PDR).
Methods.
Deidentified medical records for Caucasian patients with diabetic retinopathy (DR; 153 NPDR and 138 PDR) were obtained from BioVU, Vanderbilt University's electronic, deidentified DNA databank. An independent cohort of Caucasian patients with DR (44 NPDR and 57 PDR) from the Vanderbilt Eye Institute (VEI) was used for validation. We tested for an association between mitochondrial haplogroups and PDR among patients with DR.
Results.
In the BioVU cohort, PDR frequency among Caucasian DR patients differed significantly by mitochondrial haplogroup (P = 0.027). Replication in the VEI cohort confirmed this association (P = 0.0064). In the combined cohort, patients from the common haplogroup H were more likely to have PDR (odds ratio [OR] = 2.0 [95% confidence interval (CI) = 1.3–3.0], P = 0.0012), while patients from haplogroup Uk were less likely to have PDR (OR = 0.5 [95% CI = 0.3–0.8], P = 0.0049). In logistic regression analyses, the addition of diabetes duration, hemoglobin A1c (HgbA1c) levels, and hypertension had no effect on the associations of haplogroups H and Uk with PDR.
Conclusions.
In this study, DR patients from mitochondrial haplogroup H were more likely to have PDR, while DR patients from haplogroup Uk were less likely to have PDR. The association was independent of the major clinical variables affecting PDR. The mitochondrial haplogroups were as strong a risk factor for PDR as were elevated HgbA1c levels.
Using BioVU, Vanderbilt's deidentified DNA databank, and an independent clinical cohort, the authors demonstrate that among patients with diabetic retinopathy, proliferative retinopathy is positively associated with European mitochondrial haplogroup H and negatively associated with haplogroup Uk.
doi:10.1167/iovs.14-15149
PMCID: PMC4160073  PMID: 25118268
diabetes; diabetic retinopathy; proliferative diabetic retinopathy; genetics; mitochondrial haplogroup; mitochondrial genetics; mitochondrial DNA
10.  Elevated Transforming Growth Factor β1 in Plasma of Primary Open-Angle Glaucoma Patients 
Purpose.
To test the hypothesis that primary open-angle glaucoma (POAG) patients have a systemic elevation of transforming growth factor β1 (TGFβ1).
Methods.
Plasma was prepared from blood samples drawn from patients of the Vanderbilt Eye Institute during clinic visits. Concentrations of total TGFβ1 and thrombospondin-1 (TSP1) in plasma were determined by ELISA. Statistical significance of differences between POAG and control samples was evaluated by Mann-Whitney test. Regression analysis was used to evaluate correlations between plasma TGFβ1 and patient age and between plasma TGFβ1 and TSP1.
Results.
Plasma samples were obtained from 148 POAG patients and 150 controls. Concentration of total TGFβ1 in the plasma of POAG patients (median = 3.25 ng/mL) was significantly higher (P < 0.0001) than in controls (median = 2.46 ng/mL). Plasma TGFβ1 was not correlated with age of patient (P = 0.17). Thrombospondin-1 concentration was also significantly higher (P < 0.0001) in POAG patients (median = 0.774 μg/mL) as compared to controls (median = 0.567 μg/mL). Plasma total TGFβ1 and TSP1 concentrations were linearly correlated (P < 0.0001).
Conclusions.
Plasma samples from POAG patients display elevated total TGFβ1 compared to controls, consistent with elevated systemic TGFβ1 in POAG patients.
Transforming growth factor β1 concentration was determined in plasma samples from 148 control subjects and 150 POAG patients and found to be significantly elevated in plasma from POAG patients.
doi:10.1167/iovs.14-14578
PMCID: PMC4142830  PMID: 25061114
glaucoma; transforming growth factor beta; plasma; platelet; aqueous humor
11.  Heritability and Genome-wide Association Study To Assess Genetic Differences Between Advanced Age-Related Macular Degeneration Subtypes  
Ophthalmology  2012;119(9):1874-1885.
Purpose
To investigate whether the two subtypes of advanced age-related macular degeneration (AMD), choroidal neovascularization (CNV) and geographic atrophy (GA), segregate separately in families and to identify which genetic variants are associated with these two subtypes.
Design
Sibling correlation study and genome-wide association study (GWAS)
Participants
For the sibling correlation study, we included 209 sibling pairs with advanced AMD. For the GWAS, we included 2594 participants with advanced AMD subtypes and 4134 controls. Replication cohorts included 5383 advanced AMD participants and 15,240 controls.
Methods
Participants had AMD grade assigned based on fundus photography and/or examination. To determine heritability of advanced AMD subtypes, we performed a sibling correlation study. For the GWAS, we conducted genome-wide genotyping and imputed 6,036,699 single nucleotide polymorphism (SNPs). We then analyzed SNPs with a generalized linear model controlling for genotyping platform and genetic ancestry. The most significant associations were evaluated in independent cohorts.
Main Outcome Measures
Concordance of advanced AMD subtypes in sibling pairs and associations between SNPs with GA and CNV advanced AMD subtypes.
Results
The difference between the observed and expected proportion of siblings concordant for the same subtype of advanced AMD was different to a statistically significant degree (P=4.2 x 10−5) meaning that siblings of probands with CNV or GA are more likely to develop CNV or GA, respectively. In the analysis comparing participants with CNV to those with GA, we observed a statistically significant association at the ARMS2/HTRA1 locus [rs10490924, odds ratio (OR)=1.47, P=4.3 ×10−9] which was confirmed in the replication samples (OR=1.38, P=7.4 x 10−14 for combined discovery and replication analysis).
Conclusions
Whether a patient with AMD develops CNV vs. GA is determined in part by genetic variation. In this large GWAS meta-analysis and replication analysis, the ARMS2/HTRA1 locus confers increased risk for both advanced AMD subtypes but imparts greater risk for CNV than for GA. This locus explains a small proportion of the excess sibling correlation for advanced AMD subtype. Other loci were detected with suggestive associations which differ for advanced AMD subtypes and deserve follow-up in additional studies.
doi:10.1016/j.ophtha.2012.03.014
PMCID: PMC3899891  PMID: 22705344
12.  Metabolome-Wide Association Study of Neovascular Age-Related Macular Degeneration 
PLoS ONE  2013;8(8):e72737.
Purpose
To determine if plasma metabolic profiles can detect differences between patients with neovascular age-related macular degeneration (NVAMD) and similarly-aged controls.
Methods
Metabolomic analysis using liquid chromatography with Fourier-transform mass spectrometry (LC-FTMS) was performed on plasma samples from 26 NVAMD patients and 19 controls. Data were collected from mass/charge ratio (m/z) 85 to 850 on a Thermo LTQ-FT mass spectrometer, and metabolic features were extracted using an adaptive processing software package. Both non-transformed and log2 transformed data were corrected using Benjamini and Hochberg False Discovery Rate (FDR) to account for multiple testing. Orthogonal Partial Least Squares-Discriminant Analysis was performed to determine metabolic features that distinguished NVAMD patients from controls. Individual m/z features were matched to the Kyoto Encyclopedia of Genes and Genomes database and the Metlin metabolomics database, and metabolic pathways associated with NVAMD were identified using MetScape.
Results
Of the 1680 total m/z features detected by LC-FTMS, 94 unique m/z features were significantly different between NVAMD patients and controls using FDR (q = 0.05). A comparison of these features to those found with log2 transformed data (n = 132, q = 0.2) revealed 40 features in common, reaffirming the involvement of certain metabolites. Such metabolites included di- and tripeptides, covalently modified amino acids, bile acids, and vitamin D-related metabolites. Correlation analysis revealed associations among certain significant features, and pathway analysis demonstrated broader changes in tyrosine metabolism, sulfur amino acid metabolism, and amino acids related to urea metabolism.
Conclusions
These data suggest that metabolomic analysis can identify a panel of individual metabolites that differ between NVAMD cases and controls. Pathway analysis can assess the involvement of certain metabolic pathways, such as tyrosine and urea metabolism, and can provide further insight into the pathophysiology of AMD.
doi:10.1371/journal.pone.0072737
PMCID: PMC3754980  PMID: 24015273
13.  The short-term effects of antioxidant and zinc supplements on oxidative stress biomarker levels in plasma: a pilot investigation 
American Journal of Ophthalmology  2012;153(6):1104-1109.e2.
Purpose
To determine if short-term Age-Related Eye Disease Study (AREDS) antioxidant and zinc supplementation affects biomarkers of oxidative stress, possibly serving as a predictor of their efficacy.
Design
Prospective interventional case series
Methods
Nineteen subjects, 12 with intermediate or advanced age-related macular degeneration (AMD) (AREDS categories 3 or 4) and 7 non-AMD controls, were admitted to the Vanderbilt General Clinical Research Center and placed on a controlled diet for 7 days. Antioxidant and zinc supplements were stopped two weeks prior to study enrollment. Dietary supplementation with 500 mg vitamin C, 400 IU vitamin E, 15 mg β-carotene, 80 mg zinc oxide, and 2 mg cupric oxide per day was instituted on Study Day 2. Blood was drawn on Study Days 2 and 7, and plasma concentrations of cysteine (Cys), cystine (CySS), glutathione (GSH), isoprostane (IsoP), and isofuran (IsoF) were determined.
Results
Short-term AREDS supplementation significantly lowered mean plasma levels of CySS in participants on a regulated diet (p = 0.034). No significant differences were observed for Cys, GSH, IsoP, or IsoF. There were no significant differences between AMD patients and controls.
Conclusions
This pilot interventional study shows that a 5-day course of antioxidant and zinc supplements can modify plasma levels of CySS, suggesting that this oxidative stress biomarker could help predict how likely an individual is to benefit from AREDS supplementation. Further, CySS may be useful for the evaluation of new AMD therapies, particularly those hypothesized to affect redox status.
doi:10.1016/j.ajo.2011.12.010
PMCID: PMC3358482  PMID: 22381365
14.  The effect of genetic variants in SERPING1 on the risk of neovascular age-related macular degeneration 
Purpose
Genetic factors influence an individual’s risk for developing age-related macular degeneration (AMD), a leading cause of irreversible vision loss. Previous studies investigating the potential association between all AMD subtypes and the SERPING1 gene, which encodes a key regulator of the classical complement pathway, have yielded conflicting results. The purpose of this study was to determine whether variations in SERPING1 are associated with the neovascular form of AMD.
Methods
A total of 556 patients with neovascular AMD and 256 ethnically-matched controls were genotyped for polymorphisms in SERPING1. A tagging single nucleotide polymorphism (tSNP) approach was used to cover the SERPING1 gene plus 2 kilobases (kb) on each side, spanning the promoter and the 3′ untranslated regions. Ten SNPs with a minimum allele frequency of 0.10 were covered by three tSNPs (rs1005510, rs11603020, rs2511989).
Results
SERPING1 SNPs rs1005510 and rs2511989 were significantly associated with neovascular AMD in our cohort, with rs1005510 conferring an adverse risk effect (OR 1.49, 95% CI 1.18–1.88) and rs2511989 conferring a protective effect (OR 0.73, 95% CI 0.59–0.90). For both tSNPs, logistic regression of individual genotypes demonstrated statistically-significant stepwise changes in the risk of developing AMD. Combined analysis of rs1005510 with variants in CFH and HTRA1 confirmed an independent risk effect. The rs11603020 variant had no effect on AMD susceptibility in this study (OR 0.98, 95% CI 0.78–1.24).
Conclusions
This study comprehensively investigates the SERPING1 gene (using three tSNPs) and evaluates these genetic variants in the largest neovascular AMD cohort to date. Our results support the hypothesis that SERPING1 has a modest effect on the risk of neovascular AMD.
doi:10.1136/bjo.2009.172007
PMCID: PMC3655725  PMID: 20606025
SERPING1; Complement cascade; Age-Related Macular Degeneration; Choroidal Neovascularization
15.  Plasma biomarkers of oxidative stress and genetic variants in age-related macular degeneration 
American journal of ophthalmology  2011;153(3):460-467.e1.
Purpose
To compare plasma levels of oxidative stress biomarkers in patients with age-related macular degeneration (AMD) and controls and to evaluate a potential relationship between biochemical markers of oxidative stress and AMD susceptibility genotypes.
Design
Prospective case-control study
Methods
Plasma levels of oxidative stress biomarkers were determined in 77 AMD patients and 75 controls recruited from a clinical practice. Cysteine (Cys), cystine (CySS), glutathione (GSH), isoprostane (IsoP), and isofuran (IsoF) were measured, and participants were genotyped for polymorphisms in the complement factor H (CFH) and age-related maculopathy susceptibility 2 (ARMS2) genes.
Results
CySS was elevated in cases compared to controls (p = 0.013). After adjustment for age, gender, and smoking, this association was not significant. In all participants, CySS levels were associated with the CFH polymorphism rs3753394 (p = 0.028) as well as an eight-allele CFH haplotype (p = 0.029) after correction for age, gender, and smoking. None of the other plasma markers was related to AMD status in our cohort.
Conclusions
Our investigation of the gene/environment interaction involved in AMD revealed a relationship between a plasma biomarker of oxidative stress (CySS) and CFH genotype. These data suggest a potential association between inflammatory regulators and redox status in AMD pathogenesis.
doi:10.1016/j.ajo.2011.08.033
PMCID: PMC3288635  PMID: 22035603
16.  Pharmacogenetics of Complement Factor H (Y402H) and treatment of exudative age-related macular degeneration with ranibizumab 
Aims
To determine whether complement factor H (CFH) genotypes have a pharmacogenetic effect on the treatment of exudative age-related macular degeneration (AMD) with ranibizumab.
Methods
A retrospective study of 156 patients with exudative AMD treated with intravitreal ranibizumab monotherapy was conducted. AMD phenotypes were characterized by clinical examination, visual acuity, fundus photography, fluorescein angiography, and injection timing. Patients received intravitreal ranibizumab injections as part of routine ophthalmologic care and were followed for a minimum of nine months. Each patient was genotyped for the single nucleotide polymorphism rs1061170 (Y402H) in the CFH gene.
Results
Baseline lesion size and angiographic type, as well as mean visual acuities at baseline, 6 months, and 9 months were similar among the three CFH genotypes. Over 9 months, patients with both risk alleles received approximately one more injection (p = 0.09). In a recurrent event analysis, patients homozygous for the CFH Y402H risk allele had a 37% significantly higher risk of requiring additional ranibizumab injections (p = 0.04)
Conclusions
In our cohort, response to treatment of AMD with ranibizumab differed according to CFH genotype, suggesting that determining patients' CFH genotype may be helpful in the future in tailoring treatment for exudative AMD with intravitreal ranibizumab.
doi:10.1136/bjo.2008.150995
PMCID: PMC3490485  PMID: 19091853
Complement Factor H; Ranibizumab; Age-Related Macular Degeneration; Pharmacogenetics
17.  Pharmacogenetics and Age-Related Macular Degeneration 
Journal of Ophthalmology  2011;2011:252549.
Pharmacogenetics seeks to explain interpatient variability in response to medications by investigating genotype-phenotype correlations. There is a small but growing body of data regarding the pharmacogenetics of both nonexudative and exudative age-related macular degeneration. Most reported data concern polymorphisms in the complement factor H and age-related maculopathy susceptibility 2 genes. At this time, the data are not consistent and no definite conclusions may be drawn. As clinical trials data continue to accumulate, these relationships may become more apparent.
doi:10.1155/2011/252549
PMCID: PMC3199209  PMID: 22046503
18.  Common variants near FRK/COL10A1 and VEGFA are associated with advanced age-related macular degeneration 
Human Molecular Genetics  2011;20(18):3699-3709.
Despite significant progress in the identification of genetic loci for age-related macular degeneration (AMD), not all of the heritability has been explained. To identify variants which contribute to the remaining genetic susceptibility, we performed the largest meta-analysis of genome-wide association studies to date for advanced AMD. We imputed 6 036 699 single-nucleotide polymorphisms with the 1000 Genomes Project reference genotypes on 2594 cases and 4134 controls with follow-up replication of top signals in 5640 cases and 52 174 controls. We identified two new common susceptibility alleles, rs1999930 on 6q21-q22.3 near FRK/COL10A1 [odds ratio (OR) 0.87; P = 1.1 × 10−8] and rs4711751 on 6p12 near VEGFA (OR 1.15; P = 8.7 × 10−9). In addition to the two novel loci, 10 previously reported loci in ARMS2/HTRA1 (rs10490924), CFH (rs1061170, and rs1410996), CFB (rs641153), C3 (rs2230199), C2 (rs9332739), CFI (rs10033900), LIPC (rs10468017), TIMP3 (rs9621532) and CETP (rs3764261) were confirmed with genome-wide significant signals in this large study. Loci in the recently reported genes ABCA1 and COL8A1 were also detected with suggestive evidence of association with advanced AMD. The novel variants identified in this study suggest that angiogenesis (VEGFA) and extracellular collagen matrix (FRK/COL10A1) pathways contribute to the development of advanced AMD.
doi:10.1093/hmg/ddr270
PMCID: PMC3159552  PMID: 21665990
19.  Optic Nerve Dysfunction in a Mouse Model of Neurofibromatosis-1 Optic Glioma 
Individuals with neurofibromatosis type 1 (NF1) are prone to develop optic pathway gliomas that can result in significant visual impairment. To explore the cellular basis for the reduced visual function resulting from optic glioma formation, we employed a genetically engineered mouse model of Nf1 optic glioma (Nf1+/−GFAPCKO mice). We performed multi-modal functional and structural analyses both before and after the appearance of macroscopic tumors. At 6 weeks of age, prior to obvious glioma formation, Nf1+/−GFAPCKO mice had decreased visual evoked potential amplitudes and increased optic nerve axon calibers. By 3 months of age, Nf1+/−GFAPCKO mice exhibited pronounced optic nerve axonopathy and apoptosis of neurons in the retinal ganglion cell layer. Magnetic resonance diffusion tensor imaging showed a progressive increase in radial diffusivity between 6 weeks and 6 months of age in the optic nerve proximal to the tumor indicating ongoing deterioration of axons. These data suggest that optic glioma formation results in early axonal disorganization and damage that culminates in retinal ganglion cell death. The Nf1+/−GFAPCKO mice provide a useful model for defining mechanisms of visual abnormalities in children with NF1 and lay the foundations for future interventional studies aimed at reducing visual loss.
doi:10.1097/NEN.0b013e3181a3240b
PMCID: PMC2746323  PMID: 19525901
Apoptosis; Magnetic resonance imaging; Neurofibromatosis-1; Optic pathway glioma; Retinal ganglion cell; Visual evoked potential
20.  Neurturin-mediated Ret activation is required for retinal function 
The GDNF family ligands (GFLs: GDNF, NRTN, ARTN, and PSPN), interact with GDNF family receptors (GFRαs) and activate intracellular signaling through the Ret receptor tyrosine kinase. To characterize the role of Ret signaling in retinal activity, we examined Ret hypomorphic and Ret conditional mice using electroretinography. We found that aberrant Ret function resulted in markedly diminished scotopic and photopic responses. Using mice deficient in individual GFLs, we found that only NRTN deficiency led to reduced retinal activity. To determine the potential target cell-type for NRTN, we examined the retinal expression of its coreceptors (GFRα1 and GFRα2) and Ret using mice expressing fluorescence reporter EGFP from their respective loci. We found robust GFRα1 and Ret expression in horizontal, amacrine, and ganglion cells, whereas GFRα2 expression was only detected in a subset of amacrine and ganglion cells. In contrast to previous studies, no expression of GFRα1, GFRα2, or Ret was detected in photoreceptors or Müller cells, suggesting these cells are not directly affected by Ret. Finally, detailed morphologic analyses of retinas from NRTN- and Ret-deficient mice demonstrated a reduction in normal horizontal cell dendrites and axons, abnormal extensions of horizontal cell and bipolar cell processes into the outer nuclear layer, and mislocalized synaptic complexes. These anatomic abnormalities indicate a possible basis for the abnormal retinal activity in the Ret and NRTN mutant mice.
doi:10.1523/JNEUROSCI.0249-08.2008
PMCID: PMC2704905  PMID: 18417692
RET; Neurturin; retina; ERG; horizontal; outer plexiform layer
21.  Clinical phenotypes associated with the Complement Factor H Y402H variant in age-related macular degeneration 
American journal of ophthalmology  2007;144(3):404-408.
Purpose
To determine whether the complement factor H (CFH) Y402H variant is associated with specific age-related macular degeneration (AMD) clinical phenotypes.
Design
Retrospective, case-control study.
Methods
188 Caucasian subjects with AMD and 189 control subjects were genotyped for the T-to-C polymorphism in exon-9 of the CFH gene by restriction-fragment length analysis and DNA sequencing using genomic DNA from mouthwash samples. AMD phenotypes were characterized by clinical examination, fundus photography, and fluorescein angiography.
Results
Heterozygosity for the at-risk genotype (TC) increased the likelihood for AMD 2.1-fold (95% CI 1.3–3.3) while homozygosity for the genotype (CC) increased the likelihood for AMD 6.5-fold (95% CI 3.4–12.5) in our population. The C allele was significantly associated with predominantly classic choroidal neovascularization (OR 2.01, 95% CI 1.34–3.30). Neovascular lesion size was similar among the three genotypes (p=0.67).
Conclusions
The Y402H CFH variant carried a significantly increased risk for developing AMD in our population. Genotype/phenotype correlations regarding choroidal neovascular lesion type were observed
doi:10.1016/j.ajo.2007.05.018
PMCID: PMC2140051  PMID: 17631852

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