A common variant near TGFBR3 is associated with primary open angle glaucoma

Primary open angle glaucoma (POAG), a major cause of blindness worldwide, is a complex disease with a significant genetic contribution. We performed Exome Array (Illumina) analysis on 3504 POAG cases and 9746 controls with replication of the most significant findings in 9173 POAG cases and 26 780 controls across 18 collections of Asian, African and European descent. Apart from confirming strong evidence of association at CDKN2B-AS1 (rs2157719 [G], odds ratio [OR] = 0.71, P = 2.81 × 10−33), we observed one SNP showing significant association to POAG (CDC7–TGFBR3 rs1192415, ORG-allele = 1.13, Pmeta = 1.60 × 10−8). This particular SNP has previously been shown to be strongly associated with optic disc area and vertical cup-to-disc ratio, which are regarded as glaucoma-related quantitative traits. Our study now extends this by directly implicating it in POAG disease pathogenesis

A common variant near TGFBR3 is associated with primary open angle glaucoma

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/ licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.Primary open angle glaucoma (POAG), a major cause of blindness worldwide, is a complex disease with a significant genetic contribution.We performed Exome Array (Illumina) analysis on 3504 POAG cases and 9746 controls with replication of the most significant findings in 9173 POAG cases and 26 780 controls across 18 collections of Asian, African and European descent. Apart from confirming strong evidence of association at CDKN2B-AS1 (rs2157719 [G], odds ratio [OR] = 0.71, P = 2.81 × 10−33), we observed one SNP showing significant association to POAG (CDC7–TGFBR3 rs1192415, ORG-allele = 1.13, Pmeta = 1.60 × 10−8). This particular SNP has previously been shown to be strongly associated with optic disc area and vertical cup-to-disc ratio, which are regarded as glaucoma-related quantitative traits. Our study now extends this by directly implicating it in POAG disease pathogenesis

Integrating genetic regulation and single-cell expression with GWAS prioritizes causal genes and cell types for glaucoma

Primary open-angle glaucoma (POAG), characterized by retinal ganglion cell death, is a leading cause of irreversible blindness worldwide; however, the molecular and cellular causes are not well understood. Elevated intraocular pressure (IOP) is a major risk factor, but many patients have normal IOP. Colocalization and Mendelian randomization analysis of >240 POAG and IOP genome-wide association study (GWAS) loci and of overlapping expression and splicing quantitative trait loci (e/QTLs and sQTLs) in 49 GTEx tissues and retina prioritizesd causal genes for 60% of loci. These genes awere enriched in pathways implicated in extracellular matrix organization, cell adhesion, and vascular development. Analysis of single-nucleus RNA-seq of glaucoma-relevant eye tissues revealesd that the colocalizing genes and genome-wide POAG and IOP associations awere enriched in specific cell types in the aqueous outflow pathways, retina, optic nerve head, peripapillary sclera, and choroid. This study nominatesd IOP-dependent and independent regulatory mechanisms, genes, and cell types that may contribute to POAG pathogenesis

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Abstract Primary open angle glaucoma (POAG), a major cause of blindness worldwide, is a complex disease with a significant genetic contribution. We performed Exome Array ), we observed one SNP showing significant association to POAG (CDC7-TGFBR3 rs1192415, OR G-allele = 1.13, P meta = 1.60 × 10 −8 ). This particular SNP has previously been shown to be strongly associated with optic disc area and vertical cup-to-disc ratio, which are regarded as glaucoma-related quantitative traits. Our study now extends this by directly implicating it in POAG disease pathogenesis

Unravelling Molecular Mechanisms Underlying Inherited Corneal Endothelial Disease

Fuchs endothelial corneal dystrophy (FECD) and posterior polymorphous corneal dystrophy (PPCD) are clinically distinct heritable conditions associated with corneal endothelial barrier dysfunction that ultimately result in loss of corneal clarity and subsequent visual impairment. FECD is a common age-related corneal dystrophy that, in up to 80% of patients, is associated with a trinucleotide repeat expansion (termed CTG18.1) within an intronic region of the transcription factor encoding gene TCF4. PPCD is a rare autosomal dominant corneal dystrophy attributed to mutations in three distinct transcription factor encoding genes, (OVOL2 [PPCD1], ZEB1 [PPCD3] and GRHL2 [PPCD4]) that are all established regulators of epithelial-mesenchymal transition (EMT), suggesting a shared mechanisms of dysregulation may underlie distinct genetic subtypes of this disease. In this thesis I present the use of established patient-derived corneal endothelial cell (CEC) culture techniques in combination with next generation sequencing (NGS) based technologies to probe the genetic aetiologies and transcriptomic signatures of dysregulation underlying these diseases. Specifically, a novel amplification-free approach was developed, utilised, and refined to enable the CTG18.1 repeat expansions to be interrogated at the nucleotide level within a FECD patient cohort. This approach revealed striking levels of repeat length instability and mosaicism are associated with CTG18.1 expansion, advancing our understating of FECD pathophysiology in addition to more broadly illustrating the power of this long-read non-amplification dependant sequencing methodology to study repetitive genomic regions. RNA-seq data was generated from PPCD patient- and control-derived CEC cultures to define mechanism of transcriptomic dysregulation underlying disease and advance our understanding of the pathophysiology of this genetically heterogenous disease. Bioinformatic interrogation of these data highlighted dysregulated expression of the PPCD-associated OVOL2/ZEB1/GRHL2 axis and EMT-associated genes, and ectopic expression of corneal progenitor epithelium cell-type markers within the PPCD1 and PPCD3 corneal endothelium. Furthermore, epithelial cell-type- specific gene isoforms were upregulated in PPCD1 and PPCD3 corneal endothelium including targets of the epithelial splicing regulator protein, ESRP1. Over-expression of ESRP1 was subsequently modelled in immortalised endothelial cell line (HCEC12). Consequently, an upregulation of ESRP1 target gene epithelial-cell-type specific isoforms and corneal progenitor epithelium markers was discovered, suggesting a major role of ESRP1 in PPCD pathogenicity. Finally, a refined cohort of genetically unresolved PPCD patients recruited at Moorfields Eye Hospital (MEH) and General University Hospital (GUH), Prague, was established to identify additional genetic causes of PPCD

Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era.

The horse reference genome from the Thoroughbred mare Twilight has been available for a decade and, together with advances in genomics technologies, has led to unparalleled developments in equine genomics. At the core of this progress is the continuing improvement of the quality, contiguity and completeness of the reference genome, and its functional annotation. Recent achievements include the release of the next version of the reference genome (EquCab3.0) and generation of a reference sequence for the Y chromosome. Horse satellite-free centromeres provide unique models for mammalian centromere research. Despite extremely low genetic diversity of the Y chromosome, it has been possible to trace patrilines of breeds and pedigrees and show that Y variation was lost in the past approximately 2300 years owing to selective breeding. The high-quality reference genome has led to the development of three different SNP arrays and WGSs of almost 2000 modern individual horses. The collection of WGS of hundreds of ancient horses is unique and not available for any other domestic species. These tools and resources have led to global population studies dissecting the natural history of the species and genetic makeup and ancestry of modern breeds. Most importantly, the available tools and resources, together with the discovery of functional elements, are dissecting molecular causes of a growing number of Mendelian and complex traits. The improved understanding of molecular underpinnings of various traits continues to benefit the health and performance of the horse whereas also serving as a model for complex disease across species

Disease networks identify specific conditions and pleiotropy influencing multimorbidity in the general population

Multimorbidity is an emerging topic in public health policy because of its increasing prevalence and socio-economic impact. However, the age- and gender-dependent trends of disease associations at fine resolution, and the underlying genetic factors, remain incompletely understood. Here, by analyzing disease networks from electronic medical records of primary health care, we identify key conditions and shared genetic factors influencing multimorbidity. Three types of diseases are outlined: “central”, which include chronic and non-chronic conditions, have higher cumulative risks of disease associations; “community roots” have lower cumulative risks, but inform on continuing clustered disease associations with age; and “seeds of bursts”, which most are chronic, reveal outbreaks of disease associations leading to multimorbidity. The diseases with a major impact on multimorbidity are caused by genes that occupy central positions in the network of human disease genes. Alteration of lipid metabolism connects breast cancer, diabetic neuropathy and nutritional anemia. Evaluation of key disease associations by a genome-wide association study identifies shared genetic factors and further supports causal commonalities between nervous system diseases and nutritional anemias. This study also reveals many shared genetic signals with other diseases. Collectively, our results depict novel population-based multimorbidity patterns, identify key diseases within them, and highlight pleiotropy influencing multimorbidity.Postprint (author's final draft