ArticlePLoS genetics2020
A mega-analysis of expression quantitative trait loci in retinal tissue.
Article in PLoS genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers, 1 of them a synthesis that pooled it.
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Who cites it
34 citing papers in PubMed, 1 synthesis or guideline pooled it, 81 citations in OpenAlex.
- Genome-wide analysis of genetic pleiotropy and causal genes across three age-related ocular disorders.Human genetics · 2023Pooled it
- Foundation model reveals the shared organization of transcription and topologically associating domains.Cell systems · 2026Article
- Revisiting retinal and macular degeneration in the genomics era.Nature reviews. Genetics · 2026Review
- Retinal Transcriptome-Wide Association Study Identifies Novel Alzheimer's Disease Risk Genes.medRxiv : the preprint server for health sciences · 2026Article
- Mendelian randomisation in ophthalmology: An overview and practical guide for clinicians.European journal of ophthalmology · 2026Review
- Paired DNA and RNA sequencing uncovers common and rare variation regulating human retinal gene expression.Nature communications · 2026Article
- Genetic Architecture of Trans-Laminar Cribrosa Pressure Difference and Primary Open-Angle Glaucoma.Investigative ophthalmology & visual science · 2026Article
- Decoding cell-class specific roles of non-coding variants in human retina.Scientific reports · 2025Article
- HTRA1/lncRNA HTRA1-AS1 dominates in age-related macular degeneration reticular pseudodrusen genetic risk with no complement involvement.Nature communications · 2025Article
- Leveraging Alzheimer's Disease Omics to Identify Pleiotropic Genes Contributing to Neurodegeneration in Primary Open-Angle Glaucoma.Molecular neurobiology · 2025Article
- Integration of multi-omics quantitative trait loci evidence reveals novel susceptibility genes for Alzheimer's disease.Scientific reports · 2025Article
- Association Between Omega-3 Polyunsaturated Fatty Acids and Myopia: Results From the Two-Sample and Multi-Tissue Genomic Mendelian Randomization Study and KNHANES.Food science & nutrition · 2025Article
- Integrating explainable machine learning and transcriptomics data reveals cell-type specific immune signatures underlying macular degeneration.NPJ genomic medicine · 2025Article
- Machine Learning Prediction of Non-Coding Variant Impact in Cell-Class-Specific Human RetinalbioRxiv : the preprint server for biology · 2025Article
- Loss of paired immunoglobin-like type 2 receptor B gene associated with age-related macular degeneration impairs photoreceptor function in mouse retina.Human molecular genetics · 2025Article
- Structural framework to address variant-gene relationship in primary open-angle glaucoma.Vision research · 2025Review
- Epigenome-metabolism nexus in the retina: implications for aging and disease.Trends in genetics : TIG · 2024Review
- Identification of Potential Drug Targets for Myopia Through Mendelian Randomization.Investigative ophthalmology & visual science · 2024Article
- QTL mapping of human retina DNA methylation identifies 87 gene-epigenome interactions in age-related macular degeneration.Nature communications · 2024Article
- Whole genome sequencing of 4,787 individuals identifies gene-based rare variants in age-related macular degeneration.Human molecular genetics · 2024Article
Corrections and comments
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Authors and funding
12 authors at 8 institutions in 4 countries.
Funding
Abstract
Significant association signals from genome-wide association studies (GWAS) point to genomic regions of interest. However, for most loci the causative genetic variant remains undefined. Determining expression quantitative trait loci (eQTL) in a disease relevant tissue is an excellent approach to zoom in on disease- or trait-associated association signals and hitherto on relevant disease mechanisms. To this end, we explored regulation of gene expression in healthy retina (n = 311) and generated the largest cis-eQTL data set available to date. Genotype- and RNA-Seq data underwent rigorous quality control protocols before FastQTL was applied to assess the influence of genetic markers on local (cis) gene expression. Our analysis identified 403,151 significant eQTL variants (eVariants) that regulate 3,007 genes (eGenes) (Q-Value < 0.05). A conditional analysis revealed 744 independent secondary eQTL signals for 598 of the 3,007 eGenes. Interestingly, 99,165 (24.71%) of all unique eVariants regulate the expression of more than one eGene. Filtering the dataset for eVariants regulating three or more eGenes revealed 96 potential regulatory clusters. Of these, 31 harbour 130 genes which are partially regulated by the same genetic signal. To correlate eQTL and association signals, GWAS data from twelve complex eye diseases or traits were included and resulted in identification of 80 eGenes with potential association. Remarkably, expression of 10 genes is regulated by eVariants associated with multiple eye diseases or traits. In conclusion, we generated a unique catalogue of gene expression regulation in healthy retinal tissue and applied this resource to identify potentially pleiotropic effects in highly prevalent human eye diseases. Our study provides an excellent basis to further explore mechanisms of various retinal disease etiologies.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.