Epidemiology of Biomarkers of AMD Progression
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PROVIDER: PRJNA1019457 | ENA |
REPOSITORIES: ENA
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Project description:Epidemiology of Biomarkers of AMD Progression
| PRJNA1019456 | ENA
Project description:Age related macular degeneration (AMD) is one of the leading causes of irreversible central vision loss in the elderly population. According to the WHO estimates, AMD globally ranks third in causing vision impairment with a blindness prevalence of 8.7%.There is no cure for AMD; however,if it is diagnosed at an early stage, its progression can be slowed down by maintaining a healthy life style. Studies have been carried out to identify biomarkers in the plasma or serum of AMD patients. However, a consensus has not been reached with respect to an ideal biomarker which can predict and prognosticate the disease at an earlier stage. This can be attributed to the differences in the ethnicity and other geographical differences, which makes it important to conduct the study in specific regions.The current study aims to findnon-invasive prognostic biomarkers in the urine specimens of the AMD patients. Comparative proteomic analysis of urine samples from Early AMD, Choroidalneovascular membrane(CNVM) , Geographic atrophy(GA) and healthy controls was performed using Tandem mass tags (TMT) followed by mass spectrometry. Out of 751 proteins identified 383 proteins were found to be differentially expressed in various groups of AMD patients. Gene ontology classification of differentially expressed proteins revealed majority of them were involved in catalytic functions and binding activities. Pathway analysis showed, cell adhesion molecule pathways (CAMs), Complement and coagulation cascades, to be significantly deregulated in AMD. Upon validation by ELISA, SERPINA-1, TIMP-1, APOA-1 were significantly over expressed in AMD patients compared to the controls. A logistic model of APOA-1 in combination with CFH and C3 polymorphisms predicted the risk of developing AMD with 82% accuracy. This study gives us a preliminary data on non invasive biomarkers for AMD, which can be further validated in a large cohort and translated for diagnostic use.
2022-03-02 | PXD007531 | Pride
Project description:Age-related macular degeneration (AMD) is a major cause of blindness in the western world. While genetic studies have linked both common and rare variants in genes involved in regulation of the complement system to increased risk of development of AMD, environmental factors, such as smoking and nutrition, can also significantly affect the risk of developing the disease and the rate of disease progression. Since epigenetics has been implicated in mediating, in part, the disease risk associated with some environmental factors, we investigated a possible epigenetic contribution to AMD. We performed genome-wide DNA methylation profiling of blood from AMD patients and controls. No differential methylation site reached genome-wide significance; however, when epigenetic changes in and around known GWASdefined AMD risk loci were explored, we found small but significant DNA methylation differences in the blood of neovascular AMD patients near age-related maculopathy susceptibility 2 (ARMS2), a top-ranked GWAS locus preferentially associated with neovascular AMD. The methylation level of one of the CpG sites significantly correlated with the genotype of the risk SNP rs10490924, suggesting a possible epigenetic mechanism of risk. Integrating genome-wide DNA methylation analysis of retina samples with and without AMD together with blood samples, we further identified a consistent, replicable change in DNA methylation in the promoter region of protease serine 50 (PRSS50). These methylation changes may identify sites in novel genes that are susceptible to non-genetic factors known to contribute to AMD development and progression.
2017-08-23 | GSE102952 | GEO
Project description:Hydrotalea sp. AMD isolate:AMD Genome sequencing and assembly
| PRJNA513256 | ENA
Project description:<p>Numerous studies have identified common and rare genetic variation associated with risk of advanced age-related macular degeneration (AMD). However, risk is just one facet of AMD disease architecture. Both disease progression and response to treatment are two critical elements that may also be influenced by genetic variation.</p> <p>The primary aim of this study was to identify genetic variation influencing progression and response to treatment for AMD, with a secondary aim of further elucidating the genetic etiology of AMD risk. We ascertained AMD cases and controls of European ancestry from Vanderbilt Eye Institute (VEI) and the Bascom Palmer Eye Institute (BPEI) and obtained blood samples from all participants. Eyes were examined using standard ophthalmological methods, and graded according the modified Age-Related Eye Disease Study scale (AREDS grades 1-5) using fundus photography. Individuals were re-examined in follow-up exams at regular intervals to assess any change in AMD grade. Eyes with advanced neovascular AMD that were examined using ocular coherence tomography imaging (OCT), treated with anti-angiogenesis therapy and monitored for response to treatment.</p> <p>All individuals ascertained for the study were exome-chipped for genome-wide single nucleotide variation coverage. To target rare genetic variation, whole exome sequencing was performed on individuals at the phenotypic extremes based on 1) AMD grade, 2) rate of progression from intermediate to advanced AMD and 3) response to anti-VEGF treatment for eyes with advanced neovascular AMD. </p>
| phs001046 | dbGaP
Project description:DNA methylation biomarkers predict Wilms tumor disease progression
| PRJNA1120797 | ENA
Project description:Comparing fibroblasts and derived -iPSC and - RPE cells from human AMD and non-AMD donors Retinal pigment epithelium (RPE) generated from skin biopsies of donors with age-related macular degeneration (AMD) exhibit a disease phenotype and a distinct transcriptome compared to age-matched controls. We investigated whether similar differences existed in the skin fibroblasts and induced pluripotent stem cells (iPSCs) derived from them. Hierarchical cluster and principal component analyses revealed significant overlap in the transcriptome of fibroblasts of AMD and non-AMD donors. After reprogramming, iPSCs exhibited slight differences. In contrast, the transcriptome of RPE derived from AMD and normal donors segregated into two distinct clusters. Differences in the expression of specific genes that were evident between normal and AMD-derived RPE were not observed in fibroblasts or iPSCs. Mitochondrial respiration was reduced in RPE from AMD patients but not in fibroblast or iPSCs. RPE derived from AMD patients have a distinct transcriptome and phenotype compared to controls that is not observed in their corresponding skin fibroblasts or iPSCs.
2024-04-23 | GSE149202 | GEO
Project description:To identify urinary RNA as non-invasive biomarkers for progression of chronic kidney disease
2018-10-31 | GSE121978 | GEO