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Zhao K, Xiang X, Zheng Z, Zhang Q, Gu B, Zhang Y, Tang Z, Wei Y, Yuan L, Yang S, Lang L. COVID-19 and retinal layer thickness: A bidirectional Mendelian randomization study. Mult Scler Relat Disord 2024; 88:105700. [PMID: 38880027 DOI: 10.1016/j.msard.2024.105700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/16/2024] [Accepted: 06/02/2024] [Indexed: 06/18/2024]
Abstract
BACKGROUND Observational studies have reported that COVID-19 is associated with alterations in retinal layer thickness, including changes in the ganglion cell inner plexiform layer (GCIPL) and retinal nerve fiber layer (RNFL). However, the causal relationships remain unknown. Therefore, we assessed the direction and strength of the causal relationship between COVID-19 and GCIPL and RNFL thicknesses using a bidirectional two-sample Mendelian randomization (MR) design. METHODS Data were obtained from a large-scale COVID-19 Host Genetics Initiative (Nsample = 6,512,887), GCIPL dataset (Ncase = 31,434), and RNFL dataset (Ncase = 31,434). The inverse-variance weighted (IVW) method is the primary approach used to estimate causal effects. MR Egger, weighted median, weighted mode, MR Egger (bootstrap), and penalized weighted median methods were applied. Sensitivity analyses were implemented with RadialMR, MRPRESSO, MR-Egger regression, Cochran's Q statistic, leave-one-out analysis, and the funnel plot. RESULTS Forward MR analysis revealed that genetically identified COVID-19 susceptibility significantly increased the risk of GCIPL thickness (OR = 2.428, 95 % confidence interval [CI]:1.493-3.947, PIVW = 3.579 × 10-4) and RNFL thickness (OR = 1.735, 95 % CI:1.198-2.513, PIVW = 3.580 × 10-3) after Bonferroni correction. Reverse MR analysis did not indicate a significant causal association between GCIPL and RNFL thicknesses and COVID-19 phenotypes. No significant horizontal pleiotropy was found in the sensitivity analysis. CONCLUSIONS The host genetic liability to COVID-19 susceptibility was causally associated with increased GCIPL and RNFL thicknesses. Documenting this association increases our understanding of the pathophysiological mechanisms underlying COVID -19 susceptibility in retinopathy.
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Affiliation(s)
- Kun Zhao
- Department of PET-CT Molecular Imaging Center, Shanghai Jiaotong University Affiliated Sixth People's Hospital South Campus, Shanghai, PR China
| | - Xiqiao Xiang
- Department of PET-CT Molecular Imaging Center, Shanghai Jiaotong University Affiliated Sixth People's Hospital South Campus, Shanghai, PR China
| | - Ziwei Zheng
- Department of Ultrasonography, Shanghai Eighth People's Hospital, Shanghai, PR China
| | - Qingwei Zhang
- Department of Gastroenterology and Hepatology, NHC Key Laboratory of Digestive Diseases (Renji Hospital, Shanghai Jiaotong University School of Medicine), Shanghai, PR China
| | - Bingxin Gu
- Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, Shanghai, PR China
| | - Yanyan Zhang
- Pudong Institute of Preventive Medicine, Fudan University, Shanghai, PR China
| | - Zhen Tang
- Department of PET-CT Molecular Imaging Center, Shanghai Jiaotong University Affiliated Sixth People's Hospital South Campus, Shanghai, PR China
| | - Yuanhao Wei
- School of Public Health, Harbin Medical University, Harbin, PR China
| | - Lin Yuan
- Department of PET-CT Molecular Imaging Center, Shanghai Jiaotong University Affiliated Sixth People's Hospital South Campus, Shanghai, PR China
| | - Shaoling Yang
- Department of Ultrasonography, Shanghai Eighth People's Hospital, Shanghai, PR China.
| | - Lili Lang
- Department of Ophthalmology, Shanghai JiaoTong University Affiliated Sixth People's Hospital South Campus, Shanghai, PR China.
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Untaroiu A, Reis LM, Higgins BP, Walesa A, Zacharias S, Nikezic D, Costakos DM, Carroll J, Semina EV. In Vivo Assessment of Retinal Phenotypes in Axenfeld-Rieger Syndrome. Invest Ophthalmol Vis Sci 2024; 65:20. [PMID: 38587439 PMCID: PMC11005067 DOI: 10.1167/iovs.65.4.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/22/2024] [Indexed: 04/09/2024] Open
Abstract
Purpose Axenfeld-Rieger syndrome (ARS) is characterized by ocular anomalies including posterior embryotoxon, iridocorneal adhesions, corectopia/iris hypoplasia, and developmental glaucoma. Although anterior segment defects and glaucoma contribute to decreased visual acuity, the role of potential posterior segment abnormalities has not been explored. We used high-resolution retinal imaging to test the hypothesis that individuals with ARS have posterior segment pathology. Methods Three individuals with FOXC1-ARS and 10 with PITX2-ARS completed slit-lamp and fundus photography, optical coherence tomography (OCT), OCT angiography, and adaptive optics scanning light ophthalmoscopy (AOSLO). Quantitative metrics were compared to previously published values for individuals with normal vision. Results All individuals demonstrated typical anterior segment phenotypes. Average ganglion cell and inner plexiform layer thickness was lower in PITX2-ARS, consistent with the glaucoma history in this group. A novel phenotype of foveal hypoplasia was noted in 40% of individuals with PITX2-ARS (but none with FOXC1-ARS). Moreover, the depth and volume of the foveal pit were significantly lower in PITX2-ARS compared to normal controls, even excluding individuals with foveal hypoplasia. Analysis of known foveal hypoplasia genes failed to identify an alternative explanation. Foveal cone density was decreased in one individual with foveal hypoplasia and normal in six without foveal hypoplasia. Two individuals (one from each group) demonstrated non-foveal retinal irregularities with regions of photoreceptor anomalies on OCT and AOSLO. Conclusions These findings implicate PITX2 in the development of the posterior segment, particularly the fovea, in humans. The identified posterior segment phenotypes may contribute to visual acuity deficits in individuals with PITX2-ARS.
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Affiliation(s)
- Ana Untaroiu
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Linda M. Reis
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Brian P. Higgins
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Ashleigh Walesa
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Serena Zacharias
- School of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Danica Nikezic
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Deborah M. Costakos
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Joseph Carroll
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Elena V. Semina
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Childrens Wisconsin, Milwaukee, Wisconsin, United States
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Sekimitsu S, Shweikh Y, Shareef S, Zhao Y, Elze T, Segrè A, Wiggs J, Zebardast N. Association of retinal optical coherence tomography metrics and polygenic risk scores with cognitive function and future cognitive decline. Br J Ophthalmol 2024; 108:599-606. [PMID: 36990674 DOI: 10.1136/bjo-2022-322762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 03/15/2023] [Indexed: 03/31/2023]
Abstract
PURPOSE To evaluate the potential of retinal optical coherence tomography (OCT) measurements and polygenic risk scores (PRS) to identify people at risk of cognitive impairment. METHODS Using OCT images from 50 342 UK Biobank participants, we examined associations between retinal layer thickness and genetic risk for neurodegenerative disease and combined these metrics with PRS to predict baseline cognitive function and future cognitive deterioration. Multivariate Cox proportional hazard models were used to predict cognitive performance. P values for retinal thickness analyses are false-discovery-rate-adjusted. RESULTS Higher Alzheimer's disease PRS was associated with a thicker inner nuclear layer (INL), chorio-scleral interface (CSI) and inner plexiform layer (IPL) (all p<0.05). Higher Parkinson's disease PRS was associated with thinner outer plexiform layer (p<0.001). Worse baseline cognitive performance was associated with thinner retinal nerve fibre layer (RNFL) (aOR=1.038, 95% CI (1.029 to 1.047), p<0.001) and photoreceptor (PR) segment (aOR=1.035, 95% CI (1.019 to 1.051), p<0.001), ganglion cell complex (aOR=1.007, 95% CI (1.002 to 1.013), p=0.004) and thicker ganglion cell layer (aOR=0.981, 95% CI (0.967 to 0.995), p=0.009), IPL (aOR=0.976, 95% CI (0.961 to 0.992), p=0.003), INL (aOR=0.923, 95% CI (0.905 to 0.941), p<0.001) and CSI (aOR=0.998, 95% CI (0.997 to 0.999), p<0.001). Worse future cognitive performance was associated with thicker IPL (aOR=0.945, 95% CI (0.915 to 0.999), p=0.045) and CSI (aOR=0.996, 95% CI (0.993 to 0.999) 95% CI, p=0.014). Prediction of cognitive decline was significantly improved with the addition of PRS and retinal measurements. CONCLUSIONS AND RELEVANCE Retinal OCT measurements are significantly associated with genetic risk of neurodegenerative disease and may serve as biomarkers predictive of future cognitive impairment.
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Affiliation(s)
| | - Yusrah Shweikh
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
- Sussex Eye Hospital, University Hospitals Sussex NHS Foundation Trust, Sussex, UK
| | - Sarah Shareef
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
| | - Yan Zhao
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Tobias Elze
- Schepens Eye Research Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Ayellet Segrè
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Janey Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Nazlee Zebardast
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
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Zhou X, Xu J, Zhang X, Zhao Y, Duan X. Causal relationships between Gut microbiota and primary open-angle Glaucoma: A Mendelian randomization and mediation analysis of Glaucoma endophenotypes. Exp Eye Res 2024; 240:109788. [PMID: 38218362 DOI: 10.1016/j.exer.2024.109788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 01/15/2024]
Abstract
Primary open-angle glaucoma (POAG) is a widespread condition responsible for irreversible blindness, and its prevalence is expected to increase substantially in the coming decades. Despite its significance, the exact cause of POAG remains elusive, necessitating a comprehensive exploration of its pathogenesis. Emerging research suggests a potential link between alterations in gut microbiota composition and POAG. However, establishing causality in these associations remains a challenge. In this study, we employed Mendelian randomization (MR) analysis to investigate the potential causal relationships between gut microbiota (GM) and POAG. Significant bacteria taxa were further analyzed with POAG endophenotypes. We utilized data from genome-wide association studies (GWAS) for GM and POAG, as well as for glaucoma endophenotypes, including intraocular pressure (IOP), retinal nerve fiber layer (RNFL) thickness, vertical cup-to-disc ratio (VCDR), and central corneal thickness (CCT). Univariable, multivariable MR and mediation effect analysis were conducted. Our analysis revealed that certain taxa, including phylum Euryarchaeota, genus Odoribacter, Rumnicoccaceae UCG009, Ruminiclostridium9, unknown genus id.2071, and Eubacterium rectale group, were associated with an increased risk of POAG. On the other hand, family Victivallaceae, Lacchnospiraceae, genus Lachnoclostridium, Oscillospira, Ruminococcaceae UCG011, Alloprevotella, and Faecalibacterium were found to be associated with a decreased risk of POAG. Furthermore, some of these taxa were found to be connected to glaucoma endophenotypes. Through further multivariable MR analysis, it was determined that IOP, VCDR, and CCT might played mediating roles between GM and POAG. In conclusion, this study utilizes MR analysis to elucidate potential causal associations between GM and POAG, providing insights into specific GM taxa that influence POAG risk and related endophenotypes. These findings emphasize the potential role of the gut microbiota in the pathogenesis of POAG and pave the way for future research and therapeutic interventions.
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Affiliation(s)
- Xiaoyu Zhou
- Aier Glaucoma Institute, Hunan Engineering Research Center for Glaucoma with Artificial Intelligence in Diagnosis and Application of New Materials, Changsha Aier Eye Hospital, Changsha, Hunan, China; The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Jiahao Xu
- Aier Glaucoma Institute, Hunan Engineering Research Center for Glaucoma with Artificial Intelligence in Diagnosis and Application of New Materials, Changsha Aier Eye Hospital, Changsha, Hunan, China; The Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Xinyue Zhang
- Aier Glaucoma Institute, Hunan Engineering Research Center for Glaucoma with Artificial Intelligence in Diagnosis and Application of New Materials, Changsha Aier Eye Hospital, Changsha, Hunan, China; The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Yang Zhao
- Aier Glaucoma Institute, Hunan Engineering Research Center for Glaucoma with Artificial Intelligence in Diagnosis and Application of New Materials, Changsha Aier Eye Hospital, Changsha, Hunan, China; The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Xuanchu Duan
- Aier Glaucoma Institute, Hunan Engineering Research Center for Glaucoma with Artificial Intelligence in Diagnosis and Application of New Materials, Changsha Aier Eye Hospital, Changsha, Hunan, China.
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Saks DG, Schulz A, Qassim A, Marshall H, Hewitt AW, MacGregor S, Craig JE, Graham SL. Genetic risk of glaucoma is associated with vascular and retinal nerve fibre wedge defects. Acta Ophthalmol 2024; 102:e185-e194. [PMID: 37800621 DOI: 10.1111/aos.15775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 08/31/2023] [Accepted: 09/18/2023] [Indexed: 10/07/2023]
Abstract
PURPOSE To evaluate the association between localised vascular and retinal nerve fibre layer (RNFL) loss and genetic risk for glaucoma and cardiovascular disease using polygenic risk scores (PRS). METHODS 858 eyes were included from 455 individuals with suspect and early manifest primary open angle glaucoma. Eyes were characterised as having localised vascular and/or RNFL wedge-shaped defects by scrutiny of optical coherence tomography angiography (OCTA) and OCT images, respectively. Investigations included associations with pre-established scores for genetic risk of glaucoma and cardiovascular disease in the context of glaucoma risk factors and systemic vascular disease outcomes. RESULTS Higher genetic risk for glaucoma was associated with both vascular wedge defects and RNFL defects (p < 0.001 and p = 0.020, respectively). A greater genetic risk of glaucoma was associated with the presence of multiple vascular wedges per eye (p = 0.005). Glaucoma progression based on global RNFL loss was associated with vascular and RNFL wedge defects (p ≤ 0.001 and p = 0.008, respectively). The glaucoma PRS was significantly associated with vascular, but not RNFL, wedge defects after controlling for disc haemorrhage (p = 0.007 and p = 0.070, respectively). Vascular wedge defects were not related to the cardiovascular PRS. CONCLUSION Individuals with a higher genetic risk of glaucoma based on the PRS were more likely to have retinal vascular defects, as well as structural glaucomatous loss, but this did not relate to systemic cardiovascular risk. This possibly implies a local pathophysiology for the vascular defects in some cases, which may have clinical relevance in the early stages of glaucoma and in individuals at high genetic risk.
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Affiliation(s)
- Danit G Saks
- Macquarie Medical School, Macquarie University, Sydney, New South Wale, Australia
| | - Angela Schulz
- Macquarie Medical School, Macquarie University, Sydney, New South Wale, Australia
| | - Ayub Qassim
- Flinders Medical Centre, Flinders University, Adelaide, South Australia, Australia
| | - Henry Marshall
- Flinders Medical Centre, Flinders University, Adelaide, South Australia, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jamie E Craig
- Flinders Medical Centre, Flinders University, Adelaide, South Australia, Australia
| | - Stuart L Graham
- Macquarie Medical School, Macquarie University, Sydney, New South Wale, Australia
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Sáez ME, García-Sánchez A, de Rojas I, Alarcón-Martín E, Martínez J, Cano A, García-González P, Puerta R, Olivé C, Capdevila M, García-Gutiérrez F, Castilla-Martí M, Castilla-Martí L, Espinosa A, Alegret M, Ricciardi M, Pytel V, Valero S, Tárraga L, Boada M, Ruiz A, Marquié M. Genome-wide association study and polygenic risk scores of retinal thickness across the cognitive continuum: data from the NORFACE cohort. Alzheimers Res Ther 2024; 16:38. [PMID: 38365752 PMCID: PMC10870444 DOI: 10.1186/s13195-024-01398-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 01/26/2024] [Indexed: 02/18/2024]
Abstract
BACKGROUND Several studies have reported a relationship between retinal thickness and dementia. Therefore, optical coherence tomography (OCT) has been proposed as an early diagnosis method for Alzheimer's disease (AD). In this study, we performed a genome-wide association study (GWAS) aimed at identifying genes associated with retinal nerve fiber layer (RNFL) and ganglion cell inner plexiform layer (GCIPL) thickness assessed by OCT and exploring the relationships between the spectrum of cognitive decline (including AD and non-AD cases) and retinal thickness. METHODS RNFL and GCIPL thickness at the macula were determined using two different OCT devices (Triton and Maestro). These determinations were tested for association with common single nucleotide polymorphism (SNPs) using adjusted linear regression models and combined using meta-analysis methods. Polygenic risk scores (PRSs) for retinal thickness and AD were generated. RESULTS Several genetic loci affecting retinal thickness were identified across the genome in accordance with previous reports. The genetic overlap between retinal thickness and dementia, however, was weak and limited to the GCIPL layer; only those observable with all-type dementia cases were considered. CONCLUSIONS Our study does not support the existence of a genetic link between dementia and retinal thickness.
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Grants
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- Intramural Funding ACE alzheimer Center Barcelona
- PI19/00335, PI17/01474, AC17/00100, PI19/01301, PI22/01403, PMP22/00022 Instituto de Salud Carlos III (ISCIII)
- PI19/00335, PI17/01474, AC17/00100, PI19/01301, PI22/01403, PMP22/00022 Instituto de Salud Carlos III (ISCIII)
- PI19/00335, PI17/01474, AC17/00100, PI19/01301, PI22/01403, PMP22/00022 Instituto de Salud Carlos III (ISCIII)
- PI19/00335, PI17/01474, AC17/00100, PI19/01301, PI22/01403, PMP22/00022 Instituto de Salud Carlos III (ISCIII)
- PI19/00335, PI17/01474, AC17/00100, PI19/01301, PI22/01403, PMP22/00022 Instituto de Salud Carlos III (ISCIII)
- PI19/00335, PI17/01474, AC17/00100, PI19/01301, PI22/01403, PMP22/00022 Instituto de Salud Carlos III (ISCIII)
- PI19/00335, PI17/01474, AC17/00100, PI19/01301, PI22/01403, PMP22/00022 Instituto de Salud Carlos III (ISCIII)
- PI19/00335, PI17/01474, AC17/00100, PI19/01301, PI22/01403, PMP22/00022 Instituto de Salud Carlos III (ISCIII)
- PI19/00335, PI17/01474, AC17/00100, PI19/01301, PI22/01403, PMP22/00022 Instituto de Salud Carlos III (ISCIII)
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Affiliation(s)
- María Eugenia Sáez
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
- Centro Andaluz de Estudios Bioinformáticos (CAEBI), Seville, Spain
| | - Ainhoa García-Sánchez
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
| | - Itziar de Rojas
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Emilio Alarcón-Martín
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
| | - Joan Martínez
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
| | - Amanda Cano
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Pablo García-González
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
| | - Raquel Puerta
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
| | - Clàudia Olivé
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
| | - Maria Capdevila
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
| | | | - Miguel Castilla-Martí
- Clínica Oftalmológica Dr. Castilla, Barcelona, Spain
- Vista Alpina Eye Clinic, Visp, Switzerland
| | - Luis Castilla-Martí
- PhD Programme in Surgery and Morphological Sciences, Universitat Autònoma de Barcelona, Barcelona, Spain
- Hôpital ophtalmique Jules-Gonin, Fondation asiles des aveugles, University of Lausanne, Lausanne, Switzerland
| | - Ana Espinosa
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Montserrat Alegret
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Mario Ricciardi
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
| | - Vanesa Pytel
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
| | - Sergi Valero
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Lluís Tárraga
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Mercè Boada
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Agustín Ruiz
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain.
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain.
- Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, Texas, USA.
| | - Marta Marquié
- Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya (UIC), Barcelona, Spain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
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Xiong K, Zhang Q, Mao H, Congdon N, Liang Y. Assessment of Causality Between Diet-Derived Antioxidants and Primary Open-Angle Glaucoma: A Mendelian Randomization Study. Transl Vis Sci Technol 2024; 13:20. [PMID: 38411971 PMCID: PMC10910435 DOI: 10.1167/tvst.13.2.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/19/2024] [Indexed: 02/28/2024] Open
Abstract
Purpose This study aimed to investigate the genetic causal relationships among diet-derived circulating antioxidants, primary open-angle glaucoma (POAG), and glaucoma-related traits using two-sample Mendelian randomization (MR). Methods Genetic variants associated with diet-derived circulating antioxidants (retinol, ascorbate, β-carotene, lycopene, α-tocopherol, and γ-tocopherol) were assessed as absolute and metabolic instrumental variables. POAG and glaucoma-related traits data were derived from a large, recently published genome-wide association study database; these traits included intraocular pressure (IOP), macular retinal nerve fiber layer (mRNFL) thickness, macular ganglion cell-inner plexiform layer (mGCIPL) thickness, and vertical cup-to-disc ratio (vCDR). MR analyses were performed per outcome for each exposure. Results We found no causal association between six diet-derived antioxidants and POAG using the International Glaucoma Genetics Consortium data. For absolute antioxidants, the odds ratios (ORs) ranged from 1.011 (95% confidence interval [CI], 0.854-1.199; P = 0.895) per natural log-transformed β-carotene to 1.052 (95% CI, 0.911-1.215; P = 0.490) for 1 µmol/L of ascorbate. For antioxidant metabolites, the OR ranged from 0.998 (95% CI, 0.801-1.244; P = 0.989) for ascorbate to 1.210 (95% CI, 0.870-1.682; P = 0.257) for γ-tocopherol, using log-transformed levels. A similar result was obtained with the FinnGen Biobank. Furthermore, our results showed no significant genetic association between six diet-derived antioxidants and glaucoma-related traits. Conclusions Our study did not support a causal association among six diet-derived circulating antioxidants, POAG, and glaucoma-related traits. This suggests that the intake of antioxidants may not have a preventive effect on POAG and offers no protection to retinal nerve cells. Translational Relevance This study provides valid evidence regarding the use of diet-derived antioxidants for glaucoma patients.
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Affiliation(s)
- Kun Xiong
- Department of Glaucoma, National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qi'ao Zhang
- Department of Glaucoma, National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Huiyan Mao
- Department of Glaucoma, National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Nathan Congdon
- Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
- Centre for Public Health, Queen's University Belfast, Belfast, UK
- Orbis International, New York, NY, USA
| | - Yuanbo Liang
- Department of Glaucoma, National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
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Zekavat SM, Jorshery SD, Rauscher FG, Horn K, Sekimitsu S, Koyama S, Nguyen TT, Costanzo MC, Jang D, Burtt NP, Kühnapfel A, Shweikh Y, Ye Y, Raghu V, Zhao H, Ghassemi M, Elze T, Segrè AV, Wiggs JL, Del Priore L, Scholz M, Wang JC, Natarajan P, Zebardast N. Phenome- and genome-wide analyses of retinal optical coherence tomography images identify links between ocular and systemic health. Sci Transl Med 2024; 16:eadg4517. [PMID: 38266105 DOI: 10.1126/scitranslmed.adg4517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/03/2024] [Indexed: 01/26/2024]
Abstract
The human retina is a multilayered tissue that offers a unique window into systemic health. Optical coherence tomography (OCT) is widely used in eye care and allows the noninvasive, rapid capture of retinal anatomy in exquisite detail. We conducted genotypic and phenotypic analyses of retinal layer thicknesses using macular OCT images from 44,823 UK Biobank participants. We performed OCT layer cross-phenotype association analyses (OCT-XWAS), associating retinal thicknesses with 1866 incident conditions (median 10-year follow-up) and 88 quantitative traits and blood biomarkers. We performed genome-wide association studies (GWASs), identifying inherited genetic markers that influence retinal layer thicknesses and replicated our associations among the LIFE-Adult Study (N = 6313). Last, we performed a comparative analysis of phenome- and genome-wide associations to identify putative causal links between retinal layer thicknesses and both ocular and systemic conditions. Independent associations with incident mortality were detected for thinner photoreceptor segments (PSs) and, separately, ganglion cell complex layers. Phenotypic associations were detected between thinner retinal layers and ocular, neuropsychiatric, cardiometabolic, and pulmonary conditions. A GWAS of retinal layer thicknesses yielded 259 unique loci. Consistency between epidemiologic and genetic associations suggested links between a thinner retinal nerve fiber layer with glaucoma, thinner PS with age-related macular degeneration, and poor cardiometabolic and pulmonary function with a thinner PS. In conclusion, we identified multiple inherited genetic loci and acquired systemic cardio-metabolic-pulmonary conditions associated with thinner retinal layers and identify retinal layers wherein thinning is predictive of future ocular and systemic conditions.
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Affiliation(s)
- Seyedeh Maryam Zekavat
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Saman Doroodgar Jorshery
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Computer Science/Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
- Vector Institute for Artificial Intelligence, Toronto, ON M5G 1M1, Canada
- Department of Computer Science and Electrical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Cardiovascular Imaging Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Franziska G Rauscher
- Institute for Medical Informatics, Statistics, and Epidemiology (IMISE), Leipzig University, Leipzig 04107, Germany
- Leipzig Research Centre for Civilization Diseases (LIFE), Leipzig University, Leipzig 04103, Germany
| | - Katrin Horn
- Institute for Medical Informatics, Statistics, and Epidemiology (IMISE), Leipzig University, Leipzig 04107, Germany
| | | | - Satoshi Koyama
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Trang T Nguyen
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Maria C Costanzo
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dongkeun Jang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Noël P Burtt
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andreas Kühnapfel
- Institute for Medical Informatics, Statistics, and Epidemiology (IMISE), Leipzig University, Leipzig 04107, Germany
| | - Yusrah Shweikh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
| | - Yixuan Ye
- Computational Biology and Bioinformatics Program, Yale School of Medicine, New Haven, CT 06511, USA
| | - Vineet Raghu
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Cardiovascular Imaging Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Hongyu Zhao
- Computational Biology and Bioinformatics Program, Yale School of Medicine, New Haven, CT 06511, USA
- School of Public Health, Yale University, New Haven, CT 06510, USA
| | - Marzyeh Ghassemi
- Departments of Computer Science/Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
- Vector Institute for Artificial Intelligence, Toronto, ON M5G 1M1, Canada
- Department of Computer Science and Electrical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tobias Elze
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
| | - Ayellet V Segrè
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Janey L Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lucian Del Priore
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT 06510, USA
| | - Markus Scholz
- Institute for Medical Informatics, Statistics, and Epidemiology (IMISE), Leipzig University, Leipzig 04107, Germany
- Leipzig Research Centre for Civilization Diseases (LIFE), Leipzig University, Leipzig 04103, Germany
| | - Jay C Wang
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT 06510, USA
- Northern California Retina Vitreous Associates, Mountain View, CA 94040, USA
| | - Pradeep Natarajan
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nazlee Zebardast
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Pan Y, Zhang J, He T. SARS-CoV-2 neurovascular invasion supported by Mendelian randomization. J Transl Med 2024; 22:101. [PMID: 38268029 PMCID: PMC10809787 DOI: 10.1186/s12967-024-04907-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/18/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is known to affect vessels and nerves and can be easily visualized in the retina. However, the effect of SARS-CoV-2 on retinal morphology remains controversial. In the present research, we applied Mendelian randomization (MR) analysis to estimate the association between SARS-CoV-2 and changes in the thickness of the inner retina. METHODS Two-sample MR analysis was conducted using summary-level data from 3 open genome-wide association study databases concerning COVID-19 infection (2,942,817 participants) and COVID-19 hospitalization (2,401,372 participants); moreover, the dataset of inner retina thickness, including the macular retinal nerve fiber layer (mRNFL) and macular ganglion cell-inner plexiform layer (mGCIPL), included 31,434 optical coherence tomography (OCT) images derived from healthy UK Biobank participants. All the participants were of European ancestry. The inverse variance weighted (IVW) meta-analysis was used as our primary method. Various complementary MR approaches were established to provide robust causal estimates under different assumptions. RESULTS According to our MR analysis, genetically predicted COVID-19 infection was associated with an increased risk of mRNFL and mGCIPL thickness (OR = 1.74, 95% CI 1.20-2.52, P = 3.58 × 10-3; OR = 2.43, 95% CI 1.49-3.96, P = 3.6 × 10-4). The other MR methods produced consistent results. However, genetically predicted COVID-19 hospitalization did not affect the thickness of the inner retina (OR = 1.11, 95% CI 0.90-1.37, P = 0.32; OR = 1.28, 95% CI 0.88-1.85, P = 0.19). CONCLUSION This work provides the first genetically predictive causal evidence between COVID-19 infection and inner retinal thickness in a European population. These findings will contribute to further understanding of the pathogenesis of COVID-19 and stimulate improvements in treatment modalities.
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Affiliation(s)
- Yiji Pan
- Department of Ophthalmology, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, 430060, Hubei, China
- Eye Research Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jun Zhang
- Department of Ophthalmology, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, 430060, Hubei, China
- Eye Research Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Tao He
- Department of Ophthalmology, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, 430060, Hubei, China.
- Eye Research Center, Renmin Hospital of Wuhan University, Wuhan, China.
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10
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Zhou H, Shen B, Huang Z, Zhu S, Yang W, Xie F, Luo Y, Yuan F, Zhu Z, Deng C, Zheng W, Yang C, Lin CH, Xiao B, Tan EK, Wang Q. Mendelian randomization reveals association between retinal thickness and non-motor symptoms of Parkinson's disease. NPJ Parkinsons Dis 2023; 9:163. [PMID: 38092812 PMCID: PMC10719335 DOI: 10.1038/s41531-023-00611-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 11/24/2023] [Indexed: 12/17/2023] Open
Abstract
Retinal thickness is related to Parkinson's disease (PD), but its association with the severity of PD is still unclear. We conducted a Mendelian randomized (MR) study to explore the association between retinal thickness and PD. For the two-sample MR analysis, the summary statistics obtained from genome-wide association studies on the thickness of Retinal nerve fiber layer (RNFL) and ganglion cell inner plexiform layer (GCIPL) were employed as exposure, while the summary statistics associated with PD were used as the outcome. The primary approach utilized was inverse variance weighted. To correct for multiple testing, the false discovery rate (FDR) was employed. For sensitivity analysis, an array of robust MR methods was utilized. We found genetically predicted significant association between reduced RNFL thickness and a reduced risk of constipation in PD (odds ratio [OR] = 0.854, 95% confidence interval [CI] (0.782, 0.933), P < 0.001, FDR-corrected P = 0.018). Genetically predicted reduced RNFL thickness was associated with a reduced Unified Parkinson's Disease Rating Scale total score (β = -0.042, 95% CI (-0.079, 0.005), P = 0.025), and reduced GCIPL thickness was associated with a lower risk of constipation (OR = 0.901, 95% CI (0.821, 0.988), P = 0.027) but a higher risk of depression (OR = 1.103, 95% CI (1.016, 1.198), P = 0.020), insomnia (OR = 1.090, 95% CI (1.013, 1.172), P = 0.021), and rapid eye movement sleep behaviour disorder (RBD) (OR = 1.198, 95% CI (1.061, 1.352), P = 0.003). In conclusion, we identify an association between retinal thickness and non-motor symptoms (constipation, depression, insomnia and RBD) in PD, highlighting the potential of retinal thickness as a biomarker for PD nonmotor symptoms.
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Affiliation(s)
- Hang Zhou
- Department of Neurology, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, 510282, P.R. China
| | - Bibiao Shen
- Department of Neurology, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, 510282, P.R. China
| | - Zifeng Huang
- Department of Neurology, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, 510282, P.R. China
| | - Shuzhen Zhu
- Department of Neurology, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, 510282, P.R. China
| | - Wanlin Yang
- Department of Neurology, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, 510282, P.R. China
| | - Fen Xie
- Department of Neurology, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, 510282, P.R. China
| | - Yuqi Luo
- Department of Neurology, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, 510282, P.R. China
| | - Feilan Yuan
- Department of Neurology, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, 510282, P.R. China
| | - Zhaohua Zhu
- Clinical Research Centre, Orthopedic Centre, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, 510282, P.R. China
| | - Chao Deng
- School of Medical, Indigenous and Health Sciences, and Molecular Horizons, University of Wollongong, Wollongong, Australia
| | - Wenhua Zheng
- Centre of Reproduction, Development & Aging and Institute of Translation Medicine, Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau, China
| | - Chengwu Yang
- Division of Biostatistics and Health Services Research, Department of Population and Quantitative Health Sciences, T.H. Chan School of Medicine, UMass Chan Medical School, Massachusetts, 01605, USA
| | - Chin-Hsien Lin
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Bin Xiao
- Department of Neurology, National Neuroscience Institute, Singapore General Hospital, Singapore; Duke-NUS Medical School, Singapore, Singapore
| | - Eng-King Tan
- Department of Neurology, National Neuroscience Institute, Singapore General Hospital, Singapore; Duke-NUS Medical School, Singapore, Singapore.
| | - Qing Wang
- Department of Neurology, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, 510282, P.R. China.
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11
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Madjedi KM, Stuart KV, Chua SYL, Ramulu PY, Warwick A, Luben RN, Sun Z, Chia MA, Aschard H, Wiggs JL, Kang JH, Pasquale LR, Foster PJ, Khawaja AP. The Association of Physical Activity with Glaucoma and Related Traits in the UK Biobank. Ophthalmology 2023; 130:1024-1036. [PMID: 37331483 PMCID: PMC10913205 DOI: 10.1016/j.ophtha.2023.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/18/2023] [Accepted: 06/02/2023] [Indexed: 06/20/2023] Open
Abstract
PURPOSE To examine the association of physical activity (PA) with glaucoma and related traits, to assess whether genetic predisposition to glaucoma modified these associations, and to probe causal relationships using Mendelian randomization (MR). DESIGN Cross-sectional observational and gene-environment interaction analyses in the UK Biobank. Two-sample MR experiments using summary statistics from large genetic consortia. PARTICIPANTS UK Biobank participants with data on self-reported or accelerometer-derived PA and intraocular pressure (IOP; n = 94 206 and n = 27 777, respectively), macular inner retinal OCT measurements (n = 36 274 and n = 9991, respectively), and glaucoma status (n = 86 803 and n = 23 556, respectively). METHODS We evaluated multivariable-adjusted associations of self-reported (International Physical Activity Questionnaire) and accelerometer-derived PA with IOP and macular inner retinal OCT parameters using linear regression and with glaucoma status using logistic regression. For all outcomes, we examined gene-PA interactions using a polygenic risk score (PRS) that combined the effects of 2673 genetic variants associated with glaucoma. MAIN OUTCOME MEASURES Intraocular pressure, macular retinal nerve fiber layer (mRNFL) thickness, macular ganglion cell-inner plexiform layer (mGCIPL) thickness, and glaucoma status. RESULTS In multivariable-adjusted regression models, we found no association of PA level or time spent in PA with glaucoma status. Higher overall levels and greater time spent in higher levels of both self-reported and accelerometer-derived PA were associated positively with thicker mGCIPL (P < 0.001 for trend for each). Compared with the lowest quartile of PA, participants in the highest quartiles of accelerometer-derived moderate- and vigorous-intensity PA showed a thicker mGCIPL by +0.57 μm (P < 0.001) and +0.42 μm (P = 0.005). No association was found with mRNFL thickness. High overall level of self-reported PA was associated with a modestly higher IOP of +0.08 mmHg (P = 0.01), but this was not replicated in the accelerometry data. No associations were modified by a glaucoma PRS, and MR analyses did not support a causal relationship between PA and any glaucoma-related outcome. CONCLUSIONS Higher overall PA level and greater time spent in moderate and vigorous PA were not associated with glaucoma status but were associated with thicker mGCIPL. Associations with IOP were modest and inconsistent. Despite the well-documented acute reduction in IOP after PA, we found no evidence that high levels of habitual PA are associated with glaucoma status or IOP in the general population. FINANCIAL DISCLOSURE(S) Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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Affiliation(s)
- Kian M Madjedi
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust & UCL Institute of Ophthalmology, London, United Kingdom; Department of Ophthalmology, University of Calgary, Calgary, Alberta, Canada
| | - Kelsey V Stuart
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust & UCL Institute of Ophthalmology, London, United Kingdom
| | - Sharon Y L Chua
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust & UCL Institute of Ophthalmology, London, United Kingdom
| | - Pradeep Y Ramulu
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Robert N Luben
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust & UCL Institute of Ophthalmology, London, United Kingdom; MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Zihan Sun
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust & UCL Institute of Ophthalmology, London, United Kingdom
| | - Mark A Chia
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust & UCL Institute of Ophthalmology, London, United Kingdom
| | - Hugues Aschard
- Department of Computational Biology, Institute Pasteur, Paris, France
| | - Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts
| | - Jae H Kang
- Brigham and Women's Hospital / Harvard Medical School, Boston, Massachusetts
| | - Louis R Pasquale
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Paul J Foster
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust & UCL Institute of Ophthalmology, London, United Kingdom
| | - Anthony P Khawaja
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust & UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Cardiovascular Science, London, United Kingdom.
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12
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Boothman I, Clayton LM, McCormack M, Driscoll AM, Stevelink R, Moloney P, Krause R, Kunz WS, Diehl S, O’Brien TJ, Sills GJ, de Haan GJ, Zara F, Koeleman BP, Depondt C, Marson AG, Stefansson H, Stefansson K, Craig J, Johnson MR, Striano P, Lerche H, Furney SJ, Delanty N, Sisodiya SM, Cavalleri GL. Testing for pharmacogenomic predictors of ppRNFL thinning in individuals exposed to vigabatrin. Front Neurosci 2023; 17:1156362. [PMID: 37790589 PMCID: PMC10542409 DOI: 10.3389/fnins.2023.1156362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/25/2023] [Indexed: 10/05/2023] Open
Abstract
Background The anti-seizure medication vigabatrin (VGB) is effective for controlling seizures, especially infantile spasms. However, use is limited by VGB-associated visual field loss (VAVFL). The mechanisms by which VGB causes VAVFL remains unknown. Average peripapillary retinal nerve fibre layer (ppRNFL) thickness correlates with the degree of visual field loss (measured by mean radial degrees). Duration of VGB exposure, maximum daily VGB dose, and male sex are associated with ppRNFL thinning. Here we test the hypothesis that common genetic variation is a predictor of ppRNFL thinning in VGB exposed individuals. Identifying pharmacogenomic predictors of ppRNFL thinning in VGB exposed individuals could potentially enable safe prescribing of VGB and broader use of a highly effective drug. Methods Optical coherence topography (OCT) and GWAS data were processed from VGB-exposed individuals (n = 71) recruited through the EpiPGX Consortium. We conducted quantitative GWAS analyses for the following OCT measurements: (1) average ppRNFL, (2) inferior quadrant, (3) nasal quadrant, (4) superior quadrant, (5) temporal quadrant, (6) inferior nasal sector, (7) nasal inferior sector, (8) superior nasal sector, and (9) nasal superior sector. Using the summary statistics from the GWAS analyses we conducted gene-based testing using VEGAS2. We conducted nine different PRS analyses using the OCT measurements. To determine if VGB-exposed individuals were predisposed to having a thinner RNFL, we calculated their polygenic burden for retinal thickness. PRS alleles for retinal thickness were calculated using published summary statistics from a large-scale GWAS of inner retinal morphology using the OCT images of UK Biobank participants. Results The GWAS analyses did not identify a significant association after correction for multiple testing. Similarly, the gene-based and PRS analyses did not reveal a significant association that survived multiple testing. Conclusion We set out to identify common genetic predictors for VGB induced ppRNFL thinning. Results suggest that large-effect common genetic predictors are unlikely to exist for ppRNFL thinning (as a marker of VAVFL). Sample size was a limitation of this study. However, further recruitment is a challenge as VGB is rarely used today because of this adverse reaction. Rare variants may be predictors of this adverse drug reaction and were not studied here.
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Affiliation(s)
- Isabelle Boothman
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
- The SFI Futureneuro Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- The SFI Centre for Research Training in Genomics Data Science, Galway, Ireland
| | - Lisa M. Clayton
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, United Kingdom
- Chalfont Centre for Epilepsy, Bucks, United Kingdom
| | - Mark McCormack
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | - Remi Stevelink
- Department of Genetics, University Medical Center Utrecht, Utrecht, Netherlands
| | - Patrick Moloney
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Roland Krause
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Wolfram S. Kunz
- Division of Neurochemistry, Department of Epileptology, University Bonn Medical Center, Bonn, Germany
| | - Sarah Diehl
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Terence J. O’Brien
- Departments of Neuroscience and Neurology, Central Clinical School, The Alfred Hospital, Monash University, Melbourne, VIC, Australia
| | - Graeme J. Sills
- School of Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Gerrit-Jan de Haan
- Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, Netherlands
| | - Federico Zara
- "IRCCS”G. Gaslini" Institute, Genova, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genova, Italy
| | - Bobby P. Koeleman
- Department of Genetics, University Medical Center Utrecht, Utrecht, Netherlands
| | - Chantal Depondt
- Department of Neurology, Hôpital Erasme, Hôpital Universitaire de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium
| | - Anthony G. Marson
- Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool, United Kingdom
| | | | | | - John Craig
- Department of Neurology, Royal Victoria Hospital, Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Michael R. Johnson
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, United Kingdom
| | - Pasquale Striano
- "IRCCS”G. Gaslini" Institute, Genova, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genova, Italy
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Simon J. Furney
- Genomic Oncology Research Group, Deptartment of Physiology and Medical Physics, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland
| | - Norman Delanty
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Sanjay M. Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, United Kingdom
- Chalfont Centre for Epilepsy, Bucks, United Kingdom
| | - Gianpiero L. Cavalleri
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
- The SFI Futureneuro Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- The SFI Centre for Research Training in Genomics Data Science, Galway, Ireland
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13
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Sekimitsu S, Xiang D, Smith SL, Curran K, Elze T, Friedman DS, Foster PJ, Luo Y, Pasquale LR, Peto T, Segrè AV, Shweikh Y, Warwick A, Zhao Y, Wiggs JL, Zebardast N. Deep Ocular Phenotyping Across Primary Open-Angle Glaucoma Genetic Burden. JAMA Ophthalmol 2023; 141:891-899. [PMID: 37589995 PMCID: PMC10436188 DOI: 10.1001/jamaophthalmol.2023.3645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/25/2023] [Indexed: 08/18/2023]
Abstract
Importance Better understanding of primary open-angle glaucoma (POAG) genetics could enable timely screening and promote individualized disease risk prognostication. Objective To evaluate phenotypic features across genetic burden for POAG. Design, Setting, and Participants This was a cross-sectional, population-based study conducted from 2006 to 2010. Included participants were individuals from the UK Biobank aged 40 to 69 years. Individuals with non-POAG forms of glaucoma were excluded from the analysis. Data were statistically analyzed from October 2022 to January 2023. Main Outcomes and Measures POAG prevalence based on structural coding, self-reports, and glaucoma-related traits. Results Among 407 667 participants (mean [SD] age, 56.3 [8.1] years; 219 183 majority sex [53.8%]) were 14 171 POAG cases. Area under receiver operating characteristic curve for POAG detection was 0.748 in a model including polygenic risk score (PRS), age, sex, and ancestry. POAG prevalence in the highest decile of PRS was 7.4% (3005 of 40 644) vs 1.3% (544 of 40 795) in lowest decile (P < .001). A 1-SD increase in PRS was associated with 1.74 times higher odds of POAG (95% CI, 1.71-1.77), a 0.61-mm Hg increase in corneal-compensated intraocular pressure (IOP; 95% CI, 0.59-0.64), a -0.09-mm Hg decrease in corneal hysteresis (95% CI, -0.10 to -0.08), a 0.08-mm Hg increase in corneal resistance factor (95% CI, 0.06-0.09), and a -0.08-diopter decrease in spherical equivalent (95% CI, -0.11 to -0.07; P < .001 for all). A 1-SD increase in PRS was associated with a thinning of the macula-region retinal nerve fiber layer (mRNFL) of 0.14 μm and macular ganglion cell complex (GCC) of 0.26 μm (P < .001 for both). In the subset of individuals with fundus photographs, a 1-SD increase in PRS was associated with 1.42 times higher odds of suspicious optic disc features (95% CI, 1.19-1.69) and a 0.013 increase in cup-disc ratio (CDR; 95% CI, 0.012-0.014; P < .001 for both). A total of 22 of 5193 fundus photographs (0.4%) in decile 10 had disc hemorrhages, and 27 of 5257 (0.5%) had suspicious optic disc features compared with 9 of 5158 (0.2%) and 10 of 5219 (0.2%), respectively, in decile 1 (P < .001 for both). CDR in decile 10 was 0.46 compared with 0.41 in decile 1 (P < .001). Conclusion and Relevance Results suggest that PRS identified a group of individuals at substantially higher risk for POAG. Higher genetic risk was associated with more advanced disease, namely higher CDR and corneal-compensated IOP, thinner mRNFL, and thinner GCC. Associations with POAG PRS and corneal hysteresis and greater prevalence of disc hemorrhages were identified. These results suggest that genetic risk is an increasingly important parameter for risk stratification to consider in clinical practice.
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Affiliation(s)
| | - David Xiang
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston
- Harvard Medical School, Boston, Massachusetts
| | | | - Katie Curran
- Centre for Public Health, Queen’s University Belfast, Belfast, United Kingdom
| | - Tobias Elze
- Schepens Eye Research Institute, Harvard Medical School, Boston, Massachusetts
| | - David S. Friedman
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston
| | - Paul J. Foster
- NIHR Biomedical Research Centre, Moorfields Eye Hospital & UCL Institute of Ophthalmology, London, United Kingdom
| | - Yuyang Luo
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston
- Ocular Genomics Institute, Harvard Medical School, Boston, Massachusetts
| | - Louis R. Pasquale
- Icahn School of Medicine at Mount Sinai, Department of Ophthalmology, New York, New York
| | - Tunde Peto
- Centre for Public Health, Queen’s University Belfast, Belfast, United Kingdom
| | - Ayellet V. Segrè
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston
- Ocular Genomics Institute, Harvard Medical School, Boston, Massachusetts
| | - Yusrah Shweikh
- Sussex Eye Hospital, University Hospitals Sussex NHS Foundation Trust, Sussex, United Kingdom
| | - Alasdair Warwick
- University College London, Institute of Cardiovascular Science, London, United Kingdom
- Medical Retina Service, Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
| | - Yan Zhao
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston
- Ocular Genomics Institute, Harvard Medical School, Boston, Massachusetts
| | - Janey L. Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston
- Ocular Genomics Institute, Harvard Medical School, Boston, Massachusetts
| | - Nazlee Zebardast
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston
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14
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Flynn BI, Javan EM, Lin E, Trutner Z, Koenig K, Anighoro KO, Kun E, Gupta A, Singh T, Jayakumar P, Narasimhan VM. Deep learning based phenotyping of medical images improves power for gene discovery of complex disease. NPJ Digit Med 2023; 6:155. [PMID: 37604895 PMCID: PMC10442423 DOI: 10.1038/s41746-023-00903-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/10/2023] [Indexed: 08/23/2023] Open
Abstract
Electronic health records are often incomplete, reducing the power of genetic association studies. For some diseases, such as knee osteoarthritis where the routine course of diagnosis involves an X-ray, image-based phenotyping offers an alternate and unbiased way to ascertain disease cases. We investigated this by training a deep-learning model to ascertain knee osteoarthritis cases from knee DXA scans that achieved clinician-level performance. Using our model, we identified 1931 (178%) more cases than currently diagnosed in the health record. Individuals diagnosed as cases by our model had higher rates of self-reported knee pain, for longer durations and with increased severity compared to control individuals. We trained another deep-learning model to measure the knee joint space width, a quantitative phenotype linked to knee osteoarthritis severity. In performing genetic association analysis, we found that use of a quantitative measure improved the number of genome-wide significant loci we discovered by an order of magnitude compared with our binary model of cases and controls despite the two phenotypes being highly genetically correlated. In addition we discovered associations between our quantitative measure of knee osteoarthritis and increased risk of adult fractures- a leading cause of injury-related death in older individuals-, illustrating the capability of image-based phenotyping to reveal epidemiological associations not captured in the electronic health record. For diseases with radiographic diagnosis, our results demonstrate the potential for using deep learning to phenotype at biobank scale, improving power for both genetic and epidemiological association analysis.
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Affiliation(s)
- Brianna I Flynn
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA.
| | - Emily M Javan
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Eugenia Lin
- Department of Surgery and Perioperative Care, Dell Medical School, Austin, TX, USA
| | - Zoe Trutner
- Department of Surgery and Perioperative Care, Dell Medical School, Austin, TX, USA
| | - Karl Koenig
- Department of Surgery and Perioperative Care, Dell Medical School, Austin, TX, USA
| | - Kenoma O Anighoro
- Department of Surgery and Perioperative Care, Dell Medical School, Austin, TX, USA
| | - Eucharist Kun
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Alaukik Gupta
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Tarjinder Singh
- The Department of Psychiatry at Columbia University Irving Medical Center, New York, NY, USA
- The New York Genome Center, New York, NY, USA
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, New York, NY, USA
| | - Prakash Jayakumar
- Department of Surgery and Perioperative Care, Dell Medical School, Austin, TX, USA.
| | - Vagheesh M Narasimhan
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA.
- Department of Statistics and Data Science, The University of Texas at Austin, Austin, TX, USA.
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15
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Kun E, Javan EM, Smith O, Gulamali F, de la Fuente J, Flynn BI, Vajrala K, Trutner Z, Jayakumar P, Tucker-Drob EM, Sohail M, Singh T, Narasimhan VM. The genetic architecture and evolution of the human skeletal form. Science 2023; 381:eadf8009. [PMID: 37471560 PMCID: PMC11075689 DOI: 10.1126/science.adf8009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 06/20/2023] [Indexed: 07/22/2023]
Abstract
The human skeletal form underlies bipedalism, but the genetic basis of skeletal proportions (SPs) is not well characterized. We applied deep-learning models to 31,221 x-rays from the UK Biobank to extract a comprehensive set of SPs, which were associated with 145 independent loci genome-wide. Structural equation modeling suggested that limb proportions exhibited strong genetic sharing but were independent of width and torso proportions. Polygenic score analysis identified specific associations between osteoarthritis and hip and knee SPs. In contrast to other traits, SP loci were enriched in human accelerated regions and in regulatory elements of genes that are differentially expressed between humans and great apes. Combined, our work identifies specific genetic variants that affect the skeletal form and ties a major evolutionary facet of human anatomical change to pathogenesis.
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Affiliation(s)
- Eucharist Kun
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Emily M. Javan
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Olivia Smith
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Faris Gulamali
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Javier de la Fuente
- Department of Psychology, The University of Texas at Austin, Austin, TX, USA
| | - Brianna I. Flynn
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Kushal Vajrala
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Zoe Trutner
- Department of Surgery and Perioperative Care, The University of Texas at Austin, Austin, TX, USA
| | - Prakash Jayakumar
- Department of Surgery and Perioperative Care, The University of Texas at Austin, Austin, TX, USA
| | | | - Mashaal Sohail
- Centro de Ciencias Genómicas (CCG), Universidad Nacional Autónoma de México (UNAM), 62209 Cuernavaca, Mexico
| | - Tarjinder Singh
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
- The New York Genome Center, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute at Columbia University, New York, NY, USA
| | - Vagheesh M. Narasimhan
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
- Department of Statistics and Data Science, The University of Texas at Austin, Austin, TX, USA
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16
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Loftus SK, Gillis MF, Lundh L, Baxter LL, Wedel JC, Watkins-Chow DE, Donovan FX, Sergeev YV, Oetting WS, Pavan WJ, Adams DR. Haplotype-based analysis resolves missing heritability in oculocutaneous albinism type 1B. Am J Hum Genet 2023; 110:1123-1137. [PMID: 37327787 PMCID: PMC10357474 DOI: 10.1016/j.ajhg.2023.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/18/2023] Open
Abstract
Oculocutaneous albinism (OCA) is a rare disorder of pigment production. Affected individuals have variably decreased global pigmentation and visual-developmental changes that lead to low vision. OCA is notable for significant missing heritability, particularly among individuals with residual pigmentation. Tyrosinase (TYR) is the rate-limiting enzyme in melanin pigment biosynthesis and mutations that decrease enzyme function are one of the most common causes of OCA. We present the analysis of high-depth short-read TYR sequencing data for a cohort of 352 OCA probands, ∼50% of whom were previously sequenced without yielding a definitive diagnostic result. Our analysis identified 66 TYR single-nucleotide variants (SNVs) and small insertion/deletions (indels), 3 structural variants, and a rare haplotype comprised of two common frequency variants (p.Ser192Tyr and p.Arg402Gln) in cis-orientation, present in 149/352 OCA probands. We further describe a detailed analysis of the disease-causing haplotype, p.[Ser192Tyr; Arg402Gln] ("cis-YQ"). Haplotype analysis suggests that the cis-YQ allele arose by recombination and that multiple cis-YQ haplotypes are segregating in OCA-affected individuals and control populations. The cis-YQ allele is the most common disease-causing allele in our cohort, representing 19.1% (57/298) of TYR pathogenic alleles in individuals with type 1 (TYR-associated) OCA. Finally, among the 66 TYR variants, we found several additional alleles defined by a cis-oriented combination of minor, potentially hypomorph-producing alleles at common variant sites plus a second, rare pathogenic variant. Together, these results suggest that identification of phased variants for the full TYR locus are required for an exhaustive assessment for potentially disease-causing alleles.
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Affiliation(s)
- Stacie K Loftus
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Meredith F Gillis
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Linnea Lundh
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laura L Baxter
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Julia C Wedel
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dawn E Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frank X Donovan
- Cancer Genomics Unit, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yuri V Sergeev
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - William S Oetting
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David R Adams
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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17
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Pan XB, He YS, Lu Z, Pan HR, Wei ZY, Jin YY, Wang J, Chen JH. Epitranscriptomic investigation of myopia-associated RNA editing in the retina. Front Neurosci 2023; 17:1220114. [PMID: 37449273 PMCID: PMC10336353 DOI: 10.3389/fnins.2023.1220114] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 05/31/2023] [Indexed: 07/18/2023] Open
Abstract
Myopia is one of the most common causes of vision loss globally and is significantly affected by epigenetics. Adenosine-to-inosine (A-to-I RNA) editing is an epigenetic process involved in neurological disorders, yet its role in myopia remains undetermined. We performed a transcriptome-wide analysis of A-to-I RNA editing in the retina of form-deprivation myopia mice. Our study identified 91 A-to-I RNA editing sites in 84 genes associated with myopia. Notably, at least 27 (32.1%) of these genes with myopia-associated RNA editing showed existing evidence to be associated with myopia or related ocular phenotypes in humans or animal models, such as very low-density lipoprotein receptor (Vldlr) in retinal neovascularization and hypoxia-induced factor 1 alpha (Hif1a). Moreover, functional enrichment showed that RNA editing enriched in FDM was primarily involved in response to fungicides, a potentially druggable process for myopia prevention, and epigenetic regulation. In contrast, RNA editing enriched in controls was mostly involved in post-embryonic eye morphogenesis. Our results demonstrate altered A-to-I RNA editing associated with myopia in an experimental mouse model and warrant further study on its role in myopia development.
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Affiliation(s)
- Xu-Bin Pan
- Department of Ophthalmology, Affiliated Hospital of Jiangnan University, Wuxi, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Yu-Shan He
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Zijing Lu
- Department of Ophthalmology, Affiliated Hospital of Jiangnan University, Wuxi, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Hao-Ran Pan
- Department of Ophthalmology, Affiliated Hospital of Jiangnan University, Wuxi, China
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Zhi-Yuan Wei
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Yun-Yun Jin
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
| | - Jihong Wang
- Department of Ophthalmology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Joint Primate Research Center for Chronic Diseases, Institute of Zoology of Guangdong Academy of Science, Jiangnan University, Wuxi, Jiangsu, China
- Jiangnan University Brain Institute, Wuxi, Jiangsu, China
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18
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Diaz-Torres S, He W, Thorp J, Seddighi S, Mullany S, Hammond CJ, Hysi PG, Pasquale LR, Khawaja AP, Hewitt AW, Craig JE, Mackey DA, Wiggs JL, van Duijn C, Lupton MK, Ong JS, MacGregor S, Gharahkhani P. Disentangling the genetic overlap and causal relationships between primary open-angle glaucoma, brain morphology and four major neurodegenerative disorders. EBioMedicine 2023; 92:104615. [PMID: 37201334 PMCID: PMC10206164 DOI: 10.1016/j.ebiom.2023.104615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/21/2023] [Accepted: 04/28/2023] [Indexed: 05/20/2023] Open
Abstract
BACKGROUND Primary open-angle glaucoma (POAG) is an optic neuropathy characterized by progressive degeneration of the optic nerve that leads to irreversible visual impairment. Multiple epidemiological studies suggest an association between POAG and major neurodegenerative disorders (Alzheimer's disease, amyotrophic lateral sclerosis, frontotemporal dementia, and Parkinson's disease). However, the nature of the overlap between neurodegenerative disorders, brain morphology and glaucoma remains inconclusive. METHOD In this study, we performed a comprehensive assessment of the genetic and causal relationship between POAG and neurodegenerative disorders, leveraging genome-wide association data from studies of magnetic resonance imaging of the brain, POAG, and four major neurodegenerative disorders. FINDINGS This study found a genetic overlap and causal relationship between POAG and its related phenotypes (i.e., intraocular pressure and optic nerve morphology traits) and brain morphology in 19 regions. We also identified 11 loci with a significant local genetic correlation and a high probability of sharing the same causal variant between neurodegenerative disorders and POAG or its related phenotypes. Of interest, a region on chromosome 17 corresponding to MAPT, a well-known risk locus for Alzheimer's and Parkinson's disease, was shared between POAG, optic nerve degeneration traits, and Alzheimer's and Parkinson's diseases. Despite these local genetic overlaps, we did not identify strong evidence of a causal association between these neurodegenerative disorders and glaucoma. INTERPRETATION Our findings indicate a distinctive and likely independent neurodegenerative process for POAG involving several brain regions although several POAG or optic nerve degeneration risk loci are shared with neurodegenerative disorders, consistent with a pleiotropic effect rather than a causal relationship between these traits. FUNDING PG was supported by an NHMRC Investigator Grant (#1173390), SM by an NHMRC Senior Research Fellowship and an NHMRC Program Grant (APP1150144), DM by an NHMRC Fellowship, LP is funded by the NEIEY015473 and EY032559 grants, SS is supported by an NIH-Oxford Cambridge Fellowship and NIH T32 grant (GM136577), APK is supported by a UK Research and Innovation Future Leaders Fellowship, an Alcon Research Institute Young Investigator Award and a Lister Institute for Preventive Medicine Award.
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Affiliation(s)
- Santiago Diaz-Torres
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; Faculty of Medicine, University of Queensland (UQ), Brisbane, QLD, Australia.
| | - Weixiong He
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Jackson Thorp
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Sahba Seddighi
- Nuffield Department of Population Health, Oxford University, Oxford, UK; Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sean Mullany
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, Australia
| | - Christopher J Hammond
- Departments of Ophthalmology & Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Pirro G Hysi
- Departments of Ophthalmology & Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Louis R Pasquale
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Anthony P Khawaja
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, Australia
| | - David A Mackey
- Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Australia
| | - Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School, Boston, 02114, MA, USA
| | | | - Michelle K Lupton
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Jue-Sheng Ong
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Stuart MacGregor
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; Faculty of Medicine, University of Queensland (UQ), Brisbane, QLD, Australia
| | - Puya Gharahkhani
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; Faculty of Medicine, University of Queensland (UQ), Brisbane, QLD, Australia; School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, Australia.
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19
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Zekavat SM, Jorshery SD, Shweikh Y, Horn K, Rauscher FG, Sekimitsu S, Kayoma S, Ye Y, Raghu V, Zhao H, Ghassemi M, Elze T, Segrè AV, Wiggs JL, Scholz M, Priore LD, Wang JC, Natarajan P, Zebardast N. Insights into human health from phenome- and genome-wide analyses of UK Biobank retinal optical coherence tomography phenotypes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.16.23290063. [PMID: 37292770 PMCID: PMC10246137 DOI: 10.1101/2023.05.16.23290063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The human retina is a complex multi-layered tissue which offers a unique window into systemic health and disease. Optical coherence tomography (OCT) is widely used in eye care and allows the non-invasive, rapid capture of retinal measurements in exquisite detail. We conducted genome- and phenome-wide analyses of retinal layer thicknesses using macular OCT images from 44,823 UK Biobank participants. We performed phenome-wide association analyses, associating retinal thicknesses with 1,866 incident ICD-based conditions (median 10-year follow-up) and 88 quantitative traits and blood biomarkers. We performed genome-wide association analyses, identifying inherited genetic markers which influence the retina, and replicated our associations among 6,313 individuals from the LIFE-Adult Study. And lastly, we performed comparative association of phenome- and genome- wide associations to identify putative causal links between systemic conditions, retinal layer thicknesses, and ocular disease. Independent associations with incident mortality were detected for photoreceptor thinning and ganglion cell complex thinning. Significant phenotypic associations were detected between retinal layer thinning and ocular, neuropsychiatric, cardiometabolic and pulmonary conditions. Genome-wide association of retinal layer thicknesses yielded 259 loci. Consistency between epidemiologic and genetic associations suggested putative causal links between thinning of the retinal nerve fiber layer with glaucoma, photoreceptor segment with AMD, as well as poor cardiometabolic and pulmonary function with PS thinning, among other findings. In conclusion, retinal layer thinning predicts risk of future ocular and systemic disease. Furthermore, systemic cardio-metabolic-pulmonary conditions promote retinal thinning. Retinal imaging biomarkers, integrated into electronic health records, may inform risk prediction and potential therapeutic strategies.
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Affiliation(s)
- Seyedeh Maryam Zekavat
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Saman Doroodgar Jorshery
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Departments of Computer Science/Medicine, University of Toronto, Toronto, Canada
- Vector Institute for Artificial Intelligence, Toronto, ON, Canada
- Department of Computer Science and Electrical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Cardiovascular Imaging Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Yusrah Shweikh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Katrin Horn
- Institute for Medical Informatics, Statistics and Epidemiology University of Leipzig, Germany and Leipzig Research Centre for Civilization Diseases (LIFE), Leipzig University, Leipzig, Germany
| | - Franziska G. Rauscher
- Institute for Medical Informatics, Statistics and Epidemiology University of Leipzig, Germany and Leipzig Research Centre for Civilization Diseases (LIFE), Leipzig University, Leipzig, Germany
| | | | - Satoshi Kayoma
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yixuan Ye
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
| | - Vineet Raghu
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Imaging Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hongyu Zhao
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
- School of Public Health, Yale University, New Haven, CT, USA
| | - Marzyeh Ghassemi
- Departments of Computer Science/Medicine, University of Toronto, Toronto, Canada
- Vector Institute for Artificial Intelligence, Toronto, ON, Canada
- Department of Computer Science and Electrical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tobias Elze
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Ayellet V. Segrè
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Janey L. Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology University of Leipzig, Germany and Leipzig Research Centre for Civilization Diseases (LIFE), Leipzig University, Leipzig, Germany
| | - Lucian Del Priore
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT, USA
| | - Jay C. Wang
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT, USA
- Northern California Retina Vitreous Associates, Mountain View, CA
| | - Pradeep Natarajan
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nazlee Zebardast
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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20
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Villaplana-Velasco A, Pigeyre M, Engelmann J, Rawlik K, Canela-Xandri O, Tochel C, Lona-Durazo F, Mookiah MRK, Doney A, Parra EJ, Trucco E, MacGillivray T, Rannikmae K, Tenesa A, Pairo-Castineira E, Bernabeu MO. Fine-mapping of retinal vascular complexity loci identifies Notch regulation as a shared mechanism with myocardial infarction outcomes. Commun Biol 2023; 6:523. [PMID: 37188768 PMCID: PMC10185685 DOI: 10.1038/s42003-023-04836-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
There is increasing evidence that the complexity of the retinal vasculature measured as fractal dimension, Df, might offer earlier insights into the progression of coronary artery disease (CAD) before traditional biomarkers can be detected. This association could be partly explained by a common genetic basis; however, the genetic component of Df is poorly understood. We present a genome-wide association study (GWAS) of 38,000 individuals with white British ancestry from the UK Biobank aimed to comprehensively study the genetic component of Df and analyse its relationship with CAD. We replicated 5 Df loci and found 4 additional loci with suggestive significance (P < 1e-05) to contribute to Df variation, which previously were reported in retinal tortuosity and complexity, hypertension, and CAD studies. Significant negative genetic correlation estimates support the inverse relationship between Df and CAD, and between Df and myocardial infarction (MI), one of CAD's fatal outcomes. Fine-mapping of Df loci revealed Notch signalling regulatory variants supporting a shared mechanism with MI outcomes. We developed a predictive model for MI incident cases, recorded over a 10-year period following clinical and ophthalmic evaluation, combining clinical information, Df, and a CAD polygenic risk score. Internal cross-validation demonstrated a considerable improvement in the area under the curve (AUC) of our predictive model (AUC = 0.770 ± 0.001) when comparing with an established risk model, SCORE, (AUC = 0.741 ± 0.002) and extensions thereof leveraging the PRS (AUC = 0.728 ± 0.001). This evidences that Df provides risk information beyond demographic, lifestyle, and genetic risk factors. Our findings shed new light on the genetic basis of Df, unveiling a common control with MI, and highlighting the benefits of its application in individualised MI risk prediction.
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Affiliation(s)
- Ana Villaplana-Velasco
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, Scotland, UK
- Centre for Medical Informatics, Usher Institute, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Marie Pigeyre
- Population Health Research Institute (PHRI), Department of Medicine, Faculty of Health Sciences, McMaster University, McMaster University, Hamilton, Ontario, Canada
| | - Justin Engelmann
- Centre for Medical Informatics, Usher Institute, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Konrad Rawlik
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Oriol Canela-Xandri
- MRC Human Genetics Unit, IGC, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Claire Tochel
- Centre for Medical Informatics, Usher Institute, The University of Edinburgh, Edinburgh, Scotland, UK
| | | | | | - Alex Doney
- VAMPIRE project, Computing, School of Science and Engineering, University of Dundee, Dundee, Scotland, UK
| | - Esteban J Parra
- University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Emanuele Trucco
- VAMPIRE project, Computing, School of Science and Engineering, University of Dundee, Dundee, Scotland, UK
| | - Tom MacGillivray
- VAMPIRE project, Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Kristiina Rannikmae
- Centre for Medical Informatics, Usher Institute, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Albert Tenesa
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, Scotland, UK
- Centre for Medical Informatics, Usher Institute, The University of Edinburgh, Edinburgh, Scotland, UK
- MRC Human Genetics Unit, IGC, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Erola Pairo-Castineira
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Miguel O Bernabeu
- Centre for Medical Informatics, Usher Institute, The University of Edinburgh, Edinburgh, Scotland, UK.
- The Bayes Centre, The University of Edinburgh, Edinburgh, Scotland, UK.
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21
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Chong RS, Li H, Cheong AJY, Fan Q, Koh V, Raghavan L, Nongpiur ME, Cheng CY. Mendelian Randomization Implicates Bidirectional Association between Myopia and Primary Open-Angle Glaucoma or Intraocular Pressure. Ophthalmology 2023; 130:394-403. [PMID: 36493903 DOI: 10.1016/j.ophtha.2022.11.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 11/08/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Observational studies suggest that myopic eyes carry a greater risk of primary open-angle glaucoma (POAG); however, the evidence for this association is inconsistent. This may be the result of confounding factors that arise from myopia that complicate clinical tests for glaucoma. This study used Mendelian randomization (MR) analysis to determine genetic causal associations among myopia, glaucoma, and glaucoma-related traits that overcome the effects of external confounders. DESIGN Bidirectional genetic associations between myopia and refractive spherical equivalent (RSE), POAG, and POAG endophenotypes were investigated. PARTICIPANTS Data from the largest publicly available genetic banks (n = 216,257-542,934) were analyzed. METHODS Multiple MR models and multivariate genomic structural modeling to identify significant mediators for the relationship between myopia and POAG. MAIN OUTCOME MEASURES Genetic causal associations between myopia and POAG and POAG endophenotypes. RESULTS We found consistent bidirectional genetic associations between myopia and POAG and between myopia and intraocular pressure (IOP) using multiple MR models at Bonferroni-corrected levels of significance. Intraocular pressure showed the most significant mediation effect on RSE and POAG (Sobel test, 0.13; 95% confidence interval, 0.09-0.17; P = 1.37 × 10-8). CONCLUSIONS A strong bidirectional genetic causal link exists between myopia and POAG that is mediated mainly by IOP. Our findings suggest that IOP-lowering treatment for glaucoma may be beneficial in myopic eyes, despite the challenges of establishing a clear clinical diagnosis. FINANCIAL DISCLOSURE(S) Proprietary or commercial disclosure may be found after the references.
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Affiliation(s)
- Rachel S Chong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Republic of Singapore; Ophthalmology & Visual Sciences Academic Clinical Program, Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Hengtong Li
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Republic of Singapore
| | - Alex J Y Cheong
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Qiao Fan
- Centre for Innovation and Precision Eye Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Victor Koh
- Centre for Innovation and Precision Eye Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore; Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Lavanya Raghavan
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Republic of Singapore
| | - Monisha E Nongpiur
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Republic of Singapore; Ophthalmology & Visual Sciences Academic Clinical Program, Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Republic of Singapore; Ophthalmology & Visual Sciences Academic Clinical Program, Duke-NUS Medical School, Singapore, Republic of Singapore; Centre for Innovation and Precision Eye Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore; Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore.
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22
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Zhao B, Li Y, Fan Z, Wu Z, Shu J, Yang X, Yang Y, Wang X, Li B, Wang X, Copana C, Yang Y, Lin J, Li Y, Stein JL, O'Brien JM, Li T, Zhu H. Eye-brain connections revealed by multimodal retinal and brain imaging genetics in the UK Biobank. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.16.23286035. [PMID: 36824893 PMCID: PMC9949187 DOI: 10.1101/2023.02.16.23286035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
As an anatomical extension of the brain, the retina of the eye is synaptically connected to the visual cortex, establishing physiological connections between the eye and the brain. Despite the unique opportunity retinal structures offer for assessing brain disorders, less is known about their relationship to brain structure and function. Here we present a systematic cross-organ genetic architecture analysis of eye-brain connections using retina and brain imaging endophenotypes. Novel phenotypic and genetic links were identified between retinal imaging biomarkers and brain structure and function measures derived from multimodal magnetic resonance imaging (MRI), many of which were involved in the visual pathways, including the primary visual cortex. In 65 genomic regions, retinal imaging biomarkers shared genetic influences with brain diseases and complex traits, 18 showing more genetic overlaps with brain MRI traits. Mendelian randomization suggests that retinal structures have bidirectional genetic causal links with neurological and neuropsychiatric disorders, such as Alzheimer's disease. Overall, cross-organ imaging genetics reveals a genetic basis for eye-brain connections, suggesting that the retinal images can elucidate genetic risk factors for brain disorders and disease-related changes in intracranial structure and function.
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Affiliation(s)
- Bingxin Zhao
- Department of Statistics and Data Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Statistics, Purdue University, West Lafayette, IN 47907, USA
| | - Yujue Li
- Department of Statistics, Purdue University, West Lafayette, IN 47907, USA
| | - Zirui Fan
- Department of Statistics and Data Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhenyi Wu
- Department of Statistics, Purdue University, West Lafayette, IN 47907, USA
| | - Juan Shu
- Department of Statistics, Purdue University, West Lafayette, IN 47907, USA
| | - Xiaochen Yang
- Department of Statistics, Purdue University, West Lafayette, IN 47907, USA
| | - Yilin Yang
- Department of Computer and Information Science and Electrical and Systems Engineering, School of Engineering & Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xifeng Wang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bingxuan Li
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
| | - Xiyao Wang
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
| | - Carlos Copana
- Department of Statistics, Purdue University, West Lafayette, IN 47907, USA
| | - Yue Yang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jinjie Lin
- Yale School of Management, Yale University, New Haven, CT 06511, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jason L. Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joan M. O'Brien
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn Medicine Center for Ophthalmic Genetics in Complex Diseases, PA, 19104, USA
| | - Tengfei Li
- Department of Radiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Biomedical Research Imaging Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hongtu Zhu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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23
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Tran JH, Stuart KV, de Vries V, Vergroesen JE, Cousins CC, Hysi PG, Do R, Rocheleau G, Kang JH, Wiggs JL, MacGregor S, Khawaja AP, Mackey DA, Klaver CCW, Ramdas WD, Pasquale LR. Genetic Associations Between Smoking- and Glaucoma-Related Traits. Transl Vis Sci Technol 2023; 12:20. [PMID: 36786746 PMCID: PMC9932549 DOI: 10.1167/tvst.12.2.20] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
Purpose The purpose of this study was to describe the genetic relationship between smoking and glaucoma. Methods We used summary-level genetic data for smoking initiation, smoking intensity (cigarettes per day [CPD]), intraocular pressure (IOP), vertical cup-disc ratio, and open-angle glaucoma (OAG) to estimate global genetic correlations (rg) and perform two-sample Mendelian randomization (MR) experiments that explored relations between traits. Finally, we examined associations between smoking genetic risk scores (GRS) and smoking traits with measured IOP and OAG in Rotterdam Study participants. Results We identified weak inverse rg between smoking- and glaucoma-related traits that were insignificant after Bonferroni correction. However, MR analysis revealed that genetically predicted smoking initiation was associated with lower IOP (-0.18 mm Hg per SD, 95% confidence interval [CI] = -0.30 to -0.06, P = 0.003). Furthermore, genetically predicted smoking intensity was associated with decreased OAG risk (odds ratio [OR] = 0.74 per SD, 95% CI = 0.61 to 0.90, P = 0.002). In the Rotterdam Study, the smoking initiation GRS was associated with lower IOP (-0.09 mm Hg per SD, 95% CI = -0.17 to -0.01, P = 0.04) and lower odds of OAG (OR = 0.84 per SD, 95% CI = 0.73 to 0.98, P = 0.02) in multivariable-adjusted analyses. In contrast, neither smoking history nor CPD was associated with IOP (P ≥ 0.38) or OAG (P ≥ 0.54). Associations between the smoking intensity GRS and glaucoma traits were null (P ≥ 0.13). Conclusions MR experiments and GRS generated from Rotterdam Study participants support an inverse relationship between smoking and glaucoma. Translational Relevance Understanding the genetic drivers of the inverse relationship between smoking and glaucoma could yield new insights into glaucoma pathophysiology.
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Affiliation(s)
- Jessica H. Tran
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kelsey V. Stuart
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust & UCL Institute of Ophthalmology, London, UK
| | - Victor de Vries
- Departments of Ophthalmology and Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joëlle E. Vergroesen
- Departments of Ophthalmology and Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Clara C. Cousins
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Pirro G. Hysi
- Department of Ophthalmology, King's College London, St. Thomas’ Hospital, London, UK
- Department of Twin Research & Genetic Epidemiology, King's College London, St. Thomas’ Hospital, London, UK
| | - Ron Do
- Charles Bronfman Institute for Personalized Medicine, Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ghislain Rocheleau
- Charles Bronfman Institute for Personalized Medicine, Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jae H. Kang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Janey L. Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Stuart MacGregor
- Department of Statistical Genetics, QIMR Bergohofer Medical Research Institute, Brisbane, Australia
| | - Anthony P. Khawaja
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust & UCL Institute of Ophthalmology, London, UK
| | - David A. Mackey
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Western Australia, Australia
| | - Caroline C. W. Klaver
- Departments of Ophthalmology and Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Ophthalmology, Radboudumc, Radboud University Medical Center, Nijmegen, The Netherlands
- Institute of Molecular and Clinical Ophthalmology, University of Basel, Basel, Switzerland
| | - Wishal D. Ramdas
- Departments of Ophthalmology and Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Louis R. Pasquale
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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24
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Currant H, Fitzgerald TW, Patel PJ, Khawaja AP, Webster AR, Mahroo OA, Birney E. Sub-cellular level resolution of common genetic variation in the photoreceptor layer identifies continuum between rare disease and common variation. PLoS Genet 2023; 19:e1010587. [PMID: 36848389 PMCID: PMC9997913 DOI: 10.1371/journal.pgen.1010587] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 03/09/2023] [Accepted: 12/20/2022] [Indexed: 03/01/2023] Open
Abstract
Photoreceptor cells (PRCs) are the light-detecting cells of the retina. Such cells can be non-invasively imaged using optical coherence tomography (OCT) which is used in clinical settings to diagnose and monitor ocular diseases. Here we present the largest genome-wide association study of PRC morphology to date utilising quantitative phenotypes extracted from OCT images within the UK Biobank. We discovered 111 loci associated with the thickness of one or more of the PRC layers, many of which had prior associations to ocular phenotypes and pathologies, and 27 with no prior associations. We further identified 10 genes associated with PRC thickness through gene burden testing using exome data. In both cases there was a significant enrichment for genes involved in rare eye pathologies, in particular retinitis pigmentosa. There was evidence for an interaction effect between common genetic variants, VSX2 involved in eye development and PRPH2 known to be involved in retinal dystrophies. We further identified a number of genetic variants with a differential effect across the macular spatial field. Our results suggest a continuum between common and rare variation which impacts retinal structure, sometimes leading to disease.
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Affiliation(s)
- Hannah Currant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tomas W. Fitzgerald
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - Praveen J. Patel
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, United Kingdom
| | - Anthony P. Khawaja
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, United Kingdom
| | | | - Andrew R. Webster
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, United Kingdom
| | - Omar A. Mahroo
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, United Kingdom
- Section of Ophthalmology, King’s College London, St Thomas’ Hospital Campus, London, United Kingdom
- Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (OAM); (EB)
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
- * E-mail: (OAM); (EB)
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25
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Kun E, Javan EM, Smith O, Gulamali F, de la Fuente J, Flynn BI, Vajrala K, Trutner Z, Jayakumar P, Tucker-Drob EM, Sohail M, Singh T, Narasimhan VM. The genetic architecture of the human skeletal form. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.521284. [PMID: 36712136 PMCID: PMC9881884 DOI: 10.1101/2023.01.03.521284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The human skeletal form underlies our ability to walk on two legs, but unlike standing height, the genetic basis of limb lengths and skeletal proportions is less well understood. Here we applied a deep learning model to 31,221 whole body dual-energy X-ray absorptiometry (DXA) images from the UK Biobank (UKB) to extract 23 different image-derived phenotypes (IDPs) that include all long bone lengths as well as hip and shoulder width, which we analyzed while controlling for height. All skeletal proportions are highly heritable (∼40-50%), and genome-wide association studies (GWAS) of these traits identified 179 independent loci, of which 102 loci were not associated with height. These loci are enriched in genes regulating skeletal development as well as associated with rare human skeletal diseases and abnormal mouse skeletal phenotypes. Genetic correlation and genomic structural equation modeling indicated that limb proportions exhibited strong genetic sharing but were genetically independent of width and torso proportions. Phenotypic and polygenic risk score analyses identified specific associations between osteoarthritis (OA) of the hip and knee, the leading causes of adult disability in the United States, and skeletal proportions of the corresponding regions. We also found genomic evidence of evolutionary change in arm-to-leg and hip-width proportions in humans consistent with striking anatomical changes in these skeletal proportions in the hominin fossil record. In contrast to cardiovascular, auto-immune, metabolic, and other categories of traits, loci associated with these skeletal proportions are significantly enriched in human accelerated regions (HARs), and regulatory elements of genes differentially expressed through development between humans and the great apes. Taken together, our work validates the use of deep learning models on DXA images to identify novel and specific genetic variants affecting the human skeletal form and ties a major evolutionary facet of human anatomical change to pathogenesis.
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Affiliation(s)
- Eucharist Kun
- Department of Integrative Biology, The University of Texas at Austin
| | - Emily M Javan
- Department of Integrative Biology, The University of Texas at Austin
| | - Olivia Smith
- Department of Integrative Biology, The University of Texas at Austin
| | | | | | - Brianna I Flynn
- Department of Integrative Biology, The University of Texas at Austin
| | - Kushal Vajrala
- Department of Integrative Biology, The University of Texas at Austin
| | - Zoe Trutner
- Department of Surgery and Perioperative Care, The University of Texas at Austin
| | - Prakash Jayakumar
- Department of Surgery and Perioperative Care, The University of Texas at Austin
| | | | - Mashaal Sohail
- Centro de Ciencias Genómicas (CCG), Universidad Nacional Autónoma de México (UNAM)
| | - Tarjinder Singh
- The Department of Psychiatry at Columbia University Irving Medical Center
- The New York Genome Center
- Mortimer B. Zuckerman Mind Brain Behavior Institute at Columbia University
| | - Vagheesh M Narasimhan
- Department of Integrative Biology, The University of Texas at Austin
- Department of Statistics and Data Science, The University of Texas at Austin
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26
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Li J, Li C, Huang Y, Guan P, Huang D, Yu H, Yang X, Liu L. Mendelian randomization analyses in ocular disease: a powerful approach to causal inference with human genetic data. J Transl Med 2022; 20:621. [PMID: 36572895 PMCID: PMC9793675 DOI: 10.1186/s12967-022-03822-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 12/11/2022] [Indexed: 12/27/2022] Open
Abstract
Ophthalmic epidemiology is concerned with the prevalence, distribution and other factors relating to human eye disease. While observational studies cannot avoid confounding factors from interventions, human eye composition and structure are unique, thus, eye disease pathogenesis, which greatly impairs quality of life and visual health, remains to be fully explored. Notwithstanding, inheritance has had a vital role in ophthalmic disease. Mendelian randomization (MR) is an emerging method that uses genetic variations as instrumental variables (IVs) to avoid confounders and reverse causality issues; it reveals causal relationships between exposure and a range of eyes disorders. Thus far, many MR studies have identified potentially causal associations between lifestyles or biological exposures and eye diseases, thus providing opportunities for further mechanistic research, and interventional development. However, MR results/data must be interpreted based on comprehensive evidence, whereas MR applications in ophthalmic epidemiology have some limitations worth exploring. Here, we review key principles, assumptions and MR methods, summarise contemporary evidence from MR studies on eye disease and provide new ideas uncovering aetiology in ophthalmology.
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Affiliation(s)
- Jiaxin Li
- grid.412449.e0000 0000 9678 1884Department of Epidemiology, School of Public Health, China Medical University, Shenyang, Liaoning China
| | - Cong Li
- grid.413405.70000 0004 1808 0686Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080 China
| | - Yu Huang
- grid.413405.70000 0004 1808 0686Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080 China ,grid.413405.70000 0004 1808 0686Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Peng Guan
- grid.412449.e0000 0000 9678 1884Department of Epidemiology, School of Public Health, China Medical University, Shenyang, Liaoning China
| | - Desheng Huang
- grid.412449.e0000 0000 9678 1884Department of Mathematics, School of Fundamental Sciences, China Medical University, Shenyang, Liaoning China
| | - Honghua Yu
- grid.413405.70000 0004 1808 0686Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080 China
| | - Xiaohong Yang
- grid.413405.70000 0004 1808 0686Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080 China
| | - Lei Liu
- grid.413405.70000 0004 1808 0686Guangdong Eye Institute, Department of Ophthalmology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080 China
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27
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Olvera-Barrios A, Kihara Y, Wu Y, N. Warwick A, Müller PL, Williams KM, Rudnicka AR, Owen CG, Lee AY, Egan C, Tufail A. Foveal Curvature and Its Associations in UK Biobank Participants. Invest Ophthalmol Vis Sci 2022; 63:26. [PMID: 35900728 PMCID: PMC9344217 DOI: 10.1167/iovs.63.8.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 07/08/2022] [Indexed: 11/24/2022] Open
Abstract
Purpose To examine whether sociodemographic, and ocular factors relate to optical coherence tomography (OCT)-derived foveal curvature (FC) in healthy individuals. Methods We developed a deep learning model to quantify OCT-derived FC from 63,939 participants (age range, 39-70 years). Associations of FC with sociodemographic, and ocular factors were obtained using multilevel regression analysis (to allow for right and left eyes) adjusting for age, sex, ethnicity, height (model 1), visual acuity, spherical equivalent, corneal astigmatism, center point retinal thickness (CPRT), intraocular pressure (model 2), deprivation (Townsend index), higher education, annual income, and birth order (model 3). Fovea curvature was modeled as a z-score. Results Males had on average steeper FC (0.077; 95% confidence interval [CI] 0.077-0.078) than females (0.068; 95% CI 0.068-0.069). Compared with whites, non-white individuals showed flatter FC, particularly those of black ethnicity. In black males, -0.80 standard deviation (SD) change when compared with whites (95% CI -0.89, -0.71; P 5.2e10-68). In black females, -0.70 SD change when compared with whites (95% CI -0.77, -0.63; p 2.3e10-93). Ocular factors (visual acuity, refractive status, and CPRT) showed a graded inverse association with FC that persisted after adjustment. Macular curvature showed a positive association with FC. Income showed a linear trend increase in males (P for linear trend = 0.005). Conclusions We demonstrate marked differences in FC with ethnicity on the largest cohort studied for this purpose to date. Ocular factors showed a graded association with FC. Implementation of FC quantification in research and on the clinical setting can enhance the understanding of clinical macular phenotypes in health and disease.
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Affiliation(s)
- Abraham Olvera-Barrios
- Medical retina, Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
- Institute of Ophthalmology, University College London, London, United Kingdom
| | - Yuka Kihara
- Roger and Angie Karalis Johnson Retina Center, University of Washington, Seattle, WA, United States
- Department of Ophthalmology, School of Medicine, University of Washington, Seattle, WA, United States
| | - Yue Wu
- Roger and Angie Karalis Johnson Retina Center, University of Washington, Seattle, WA, United States
- Department of Ophthalmology, School of Medicine, University of Washington, Seattle, WA, United States
| | - Alasdair N. Warwick
- Medical retina, Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
- Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Philipp L. Müller
- Medical retina, Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
- Macula Center, Südblick Eye Centers, Augsburg, Germany
- Department of Ophthalmology, University of Bonn, Bonn, Germany
| | - Katie M. Williams
- Medical retina, Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
- Section of Ophthalmology, School of Life Course Sciences, FoLSM, King's College London, United Kingdom
| | - Alicja R. Rudnicka
- Population Health Research Institute, St. Georges, University of London, London, United Kingdom
| | - Christopher G. Owen
- Population Health Research Institute, St. Georges, University of London, London, United Kingdom
| | - Aaron Y. Lee
- Roger and Angie Karalis Johnson Retina Center, University of Washington, Seattle, WA, United States
- Department of Ophthalmology, School of Medicine, University of Washington, Seattle, WA, United States
| | - Catherine Egan
- Medical retina, Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
- Institute of Ophthalmology, University College London, London, United Kingdom
| | - Adnan Tufail
- Medical retina, Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
- Institute of Ophthalmology, University College London, London, United Kingdom
| | - on behalf of the UK Biobank Eyes and Vision Consortium
- Medical retina, Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
- Institute of Ophthalmology, University College London, London, United Kingdom
- Roger and Angie Karalis Johnson Retina Center, University of Washington, Seattle, WA, United States
- Department of Ophthalmology, School of Medicine, University of Washington, Seattle, WA, United States
- Institute of Cardiovascular Science, University College London, London, United Kingdom
- Macula Center, Südblick Eye Centers, Augsburg, Germany
- Department of Ophthalmology, University of Bonn, Bonn, Germany
- Section of Ophthalmology, School of Life Course Sciences, FoLSM, King's College London, United Kingdom
- Population Health Research Institute, St. Georges, University of London, London, United Kingdom
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28
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Zekavat SM, Sekimitsu S, Ye Y, Raghu V, Zhao H, Elze T, Segrè AV, Wiggs JL, Natarajan P, Del Priore L, Zebardast N, Wang JC. Photoreceptor Layer Thinning Is an Early Biomarker for Age-Related Macular Degeneration: Epidemiologic and Genetic Evidence from UK Biobank OCT Data. Ophthalmology 2022; 129:694-707. [PMID: 35149155 PMCID: PMC9134644 DOI: 10.1016/j.ophtha.2022.02.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Despite widespread use of OCT, an early-stage imaging biomarker for age-related macular degeneration (AMD) has not been identified. Pathophysiologically, the timing of drusen accumulation in relationship to photoreceptor degeneration in AMD remains unclear, as are the inherited genetic variants contributing to these processes. Herein, we jointly analyzed OCT, electronic health record data, and genomic data to characterize the time sequence of changes in retinal layer thicknesses in AMD, as well as epidemiologic and genetic associations between retinal layer thicknesses and AMD. DESIGN Cohort study. PARTICIPANTS Forty-four thousand eight hundred twenty-three individuals from the UK Biobank (enrollment age range, 40-70 years; 54% women; median follow-up, 10 years). METHODS The Topcon Advanced Boundary Segmentation algorithm was used for retinal layer segmentation. We associated 9 retinal layer thicknesses with prevalent AMD (present at enrollment) in a logistic regression model and with incident AMD (diagnosed after enrollment) in a Cox proportional hazards model. Next, we associated AMD-associated genetic alleles, individually and as a polygenic risk score (PRS), with retinal layer thicknesses. All analyses were adjusted for age, age-squared (age2), sex, smoking status, and principal components of ancestry. MAIN OUTCOME MEASURES Prevalent and incident AMD. RESULTS Photoreceptor segment (PS) thinning was observed throughout the lifespan of individuals analyzed, whereas retinal pigment epithelium (RPE) and Bruch's membrane (BM) complex thickening started after 57 years of age. Each standard deviation (SD) of PS thinning and RPE-BM complex thickening was associated with incident AMD (PS: hazard ratio [HR], 1.35; 95% confidence interval [CI], 1.23-1.47; P = 3.7 × 10-11; RPE-BM complex: HR, 1.14; 95% CI, 1.06-1.22; P = 0.00024). The AMD PRS was associated with PS thinning (β, -0.21 SD per twofold genetically increased risk of AMD; 95% CI, -0.23 to -0.19; P = 2.8 × 10-74), and its association with RPE-BM complex was U-shaped (thinning with AMD PRS less than the 92nd percentile and thickening with AMD PRS more than the 92nd percentile). The loci with strongest support for genetic correlation were AMD risk-raising variants Complement Factor H (CFH):rs570618-T, CFH:rs10922109-C, and Age-Related Maculopathy Susceptibility 2 (ARMS2)/High-Temperature Requirement Serine Protease 1 (HTRA1):rs3750846-C on PS thinning and SYN3/Tissue Inhibitor of Metalloprotease 3 (TIMP3):rs5754227-T on RPE-BM complex thickening. CONCLUSIONS Epidemiologically, PS thinning precedes RPE-BM complex thickening by decades and is the retinal layer most strongly predictive of future AMD risk. Genetically, AMD risk variants are associated with decreased PS thickness. Overall, these findings support PS thinning as an early-stage biomarker for future AMD development.
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Affiliation(s)
- Seyedeh Maryam Zekavat
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, Connecticut; Computational Biology & Bioinformatics Program, Yale University, New Haven, Connecticut; Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Yixuan Ye
- Computational Biology & Bioinformatics Program, Yale University, New Haven, Connecticut
| | - Vineet Raghu
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Cardiovascular Imaging Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Hongyu Zhao
- Computational Biology & Bioinformatics Program, Yale University, New Haven, Connecticut; School of Public Health, Yale University, New Haven, Connecticut
| | - Tobias Elze
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts
| | - Ayellet V Segrè
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts
| | - Janey L Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts
| | - Pradeep Natarajan
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lucian Del Priore
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, Connecticut
| | - Nazlee Zebardast
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts
| | - Jay C Wang
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, Connecticut; Northern California Retina Vitreous Associates, Mountain View, California.
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29
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Baraas RC, Pedersen HR, Knoblauch K, Gilson SJ. Human Foveal Cone and RPE Cell Topographies and Their Correspondence With Foveal Shape. Invest Ophthalmol Vis Sci 2022; 63:8. [PMID: 35113142 PMCID: PMC8819292 DOI: 10.1167/iovs.63.2.8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Purpose To characterize the association between foveal shape and cone and retinal pigment epithelium (RPE) cell topographies in healthy humans. Methods Multimodal adaptive scanning light ophthalmoscopy and optical coherence tomography (OCT) were used to acquire images of foveal cones, RPE cells, and retinal layers in eyes of 23 healthy participants with normal foveas. Distributions of cone and RPE cell densities were fitted with nonlinear mixed-effects models. A linear mixed-effects model was used to examine the relationship between cone and RPE inter-cell distances and foveal shape as obtained from the OCT scans of retinal thickness. Results The best-fit model to the cone densities was a power function with a nasal–temporal asymmetry. There was a significant linear relationship among cone and RPE cell spacing, foveal shape, and foveal cell topography. The model predictions of the central 10° show that the contributions of both the cones and RPE cells are necessary to account for foveal shape. Conclusions The results indicate that there is a strong relationship between cone and RPE cell spacing and the shape of the human adolescent and adult fovea. This finding adds to the existing evidence of the critical role that the RPE serves in fetal foveal development and through adolescence, possibly via the imposition of constraints on the number and distribution of foveal cones.
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Affiliation(s)
- Rigmor C Baraas
- National Centre for Optics, Vision and Eye Care, Faculty of Health and Social Sciences, University of South-Eastern Norway, Kongsberg, Norway
| | - Hilde R Pedersen
- National Centre for Optics, Vision and Eye Care, Faculty of Health and Social Sciences, University of South-Eastern Norway, Kongsberg, Norway
| | - Kenneth Knoblauch
- National Centre for Optics, Vision and Eye Care, Faculty of Health and Social Sciences, University of South-Eastern Norway, Kongsberg, Norway.,Stem Cell and Brain Research Institute, INSERM U1208, Bron, France.,Université de Lyon, Lyon, France
| | - Stuart J Gilson
- National Centre for Optics, Vision and Eye Care, Faculty of Health and Social Sciences, University of South-Eastern Norway, Kongsberg, Norway
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30
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Zekavat SM, Raghu VK, Trinder M, Ye Y, Koyama S, Honigberg MC, Yu Z, Pampana A, Urbut S, Haidermota S, O’Regan DP, Zhao H, Ellinor PT, Segrè AV, Elze T, Wiggs JL, Martone J, Adelman RA, Zebardast N, Del Priore L, Wang JC, Natarajan P. Deep Learning of the Retina Enables Phenome- and Genome-Wide Analyses of the Microvasculature. Circulation 2022; 145:134-150. [PMID: 34743558 PMCID: PMC8746912 DOI: 10.1161/circulationaha.121.057709] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/03/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND The microvasculature, the smallest blood vessels in the body, has key roles in maintenance of organ health and tumorigenesis. The retinal fundus is a window for human in vivo noninvasive assessment of the microvasculature. Large-scale complementary machine learning-based assessment of the retinal vasculature with phenome-wide and genome-wide analyses may yield new insights into human health and disease. METHODS We used 97 895 retinal fundus images from 54 813 UK Biobank participants. Using convolutional neural networks to segment the retinal microvasculature, we calculated vascular density and fractal dimension as a measure of vascular branching complexity. We associated these indices with 1866 incident International Classification of Diseases-based conditions (median 10-year follow-up) and 88 quantitative traits, adjusting for age, sex, smoking status, and ethnicity. RESULTS Low retinal vascular fractal dimension and density were significantly associated with higher risks for incident mortality, hypertension, congestive heart failure, renal failure, type 2 diabetes, sleep apnea, anemia, and multiple ocular conditions, as well as corresponding quantitative traits. Genome-wide association of vascular fractal dimension and density identified 7 and 13 novel loci, respectively, that were enriched for pathways linked to angiogenesis (eg, vascular endothelial growth factor, platelet-derived growth factor receptor, angiopoietin, and WNT signaling pathways) and inflammation (eg, interleukin, cytokine signaling). CONCLUSIONS Our results indicate that the retinal vasculature may serve as a biomarker for future cardiometabolic and ocular disease and provide insights into genes and biological pathways influencing microvascular indices. Moreover, such a framework highlights how deep learning of images can quantify an interpretable phenotype for integration with electronic health record, biomarker, and genetic data to inform risk prediction and risk modification.
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Affiliation(s)
- Seyedeh Maryam Zekavat
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT (S.M.Z., J.M., R.A.A., L.D.P., J.C.W.)
- Computational Biology & Bioinformatics Program (S.M.Z., Y.Y., H.Z.), Yale University, New Haven, CT
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA (S.M.Z., V.K.R., M.T., S.K., M.C.H., Z.Y., A.P., S.U., P.T.E., P.N.)
| | - Vineet K. Raghu
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA (S.M.Z., V.K.R., M.T., S.K., M.C.H., Z.Y., A.P., S.U., P.T.E., P.N.)
- Cardiovascular Research Center (S.M.Z., V.K.R., M.C.H., S.U., S.H., P.T.E., P.N.), Massachusetts General Hospital, Harvard Medical School, Boston
- Cardiovascular Imaging Research Center (V.K.R.), Massachusetts General Hospital, Harvard Medical School, Boston
| | - Mark Trinder
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada (M.T.)
| | - Yixuan Ye
- Computational Biology & Bioinformatics Program (S.M.Z., Y.Y., H.Z.), Yale University, New Haven, CT
| | - Satoshi Koyama
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA (S.M.Z., V.K.R., M.T., S.K., M.C.H., Z.Y., A.P., S.U., P.T.E., P.N.)
| | - Michael C. Honigberg
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA (S.M.Z., V.K.R., M.T., S.K., M.C.H., Z.Y., A.P., S.U., P.T.E., P.N.)
- Cardiovascular Research Center (S.M.Z., V.K.R., M.C.H., S.U., S.H., P.T.E., P.N.), Massachusetts General Hospital, Harvard Medical School, Boston
| | - Zhi Yu
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA (S.M.Z., V.K.R., M.T., S.K., M.C.H., Z.Y., A.P., S.U., P.T.E., P.N.)
| | - Akhil Pampana
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA (S.M.Z., V.K.R., M.T., S.K., M.C.H., Z.Y., A.P., S.U., P.T.E., P.N.)
| | - Sarah Urbut
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA (S.M.Z., V.K.R., M.T., S.K., M.C.H., Z.Y., A.P., S.U., P.T.E., P.N.)
- Cardiovascular Research Center (S.M.Z., V.K.R., M.C.H., S.U., S.H., P.T.E., P.N.), Massachusetts General Hospital, Harvard Medical School, Boston
| | - Sara Haidermota
- Cardiovascular Research Center (S.M.Z., V.K.R., M.C.H., S.U., S.H., P.T.E., P.N.), Massachusetts General Hospital, Harvard Medical School, Boston
| | - Declan P. O’Regan
- MRC London Institute of Medical Sciences, Imperial College London, UK (D.P.O.)
| | - Hongyu Zhao
- Computational Biology & Bioinformatics Program (S.M.Z., Y.Y., H.Z.), Yale University, New Haven, CT
- School of Public Health (H.Z.), Yale University, New Haven, CT
| | - Patrick T. Ellinor
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA (S.M.Z., V.K.R., M.T., S.K., M.C.H., Z.Y., A.P., S.U., P.T.E., P.N.)
- Cardiovascular Research Center (S.M.Z., V.K.R., M.C.H., S.U., S.H., P.T.E., P.N.), Massachusetts General Hospital, Harvard Medical School, Boston
| | - Ayellet V. Segrè
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston (A.V.S., T.E., J.L.W., N.Z.)
| | - Tobias Elze
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston (A.V.S., T.E., J.L.W., N.Z.)
| | - Janey L. Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston (A.V.S., T.E., J.L.W., N.Z.)
| | - James Martone
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT (S.M.Z., J.M., R.A.A., L.D.P., J.C.W.)
| | - Ron A. Adelman
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT (S.M.Z., J.M., R.A.A., L.D.P., J.C.W.)
| | - Nazlee Zebardast
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston (A.V.S., T.E., J.L.W., N.Z.)
| | - Lucian Del Priore
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT (S.M.Z., J.M., R.A.A., L.D.P., J.C.W.)
| | - Jay C. Wang
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT (S.M.Z., J.M., R.A.A., L.D.P., J.C.W.)
| | - Pradeep Natarajan
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA (S.M.Z., V.K.R., M.T., S.K., M.C.H., Z.Y., A.P., S.U., P.T.E., P.N.)
- Cardiovascular Research Center (S.M.Z., V.K.R., M.C.H., S.U., S.H., P.T.E., P.N.), Massachusetts General Hospital, Harvard Medical School, Boston
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31
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Currant H, Hysi P, Fitzgerald TW, Gharahkhani P, Bonnemaijer PWM, Senabouth A, Hewitt AW, Atan D, Aung T, Charng J, Choquet H, Craig J, Khaw PT, Klaver CCW, Kubo M, Ong JS, Pasquale LR, Reisman CA, Daniszewski M, Powell JE, Pébay A, Simcoe MJ, Thiadens AAHJ, van Duijn CM, Yazar S, Jorgenson E, MacGregor S, Hammond CJ, Mackey DA, Wiggs JL, Foster PJ, Patel PJ, Birney E, Khawaja AP. Correction: Genetic variation affects morphological retinal phenotypes extracted from UK Biobank optical coherence tomography images. PLoS Genet 2021; 17:e1009858. [PMID: 34662343 PMCID: PMC8523050 DOI: 10.1371/journal.pgen.1009858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pgen.1009497.].
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32
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Alipanahi B, Hormozdiari F, Behsaz B, Cosentino J, McCaw ZR, Schorsch E, Sculley D, Dorfman EH, Foster PJ, Peng LH, Phene S, Hammel N, Carroll A, Khawaja AP, McLean CY. Large-scale machine-learning-based phenotyping significantly improves genomic discovery for optic nerve head morphology. Am J Hum Genet 2021; 108:1217-1230. [PMID: 34077760 PMCID: PMC8322934 DOI: 10.1016/j.ajhg.2021.05.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/10/2021] [Indexed: 02/06/2023] Open
Abstract
Genome-wide association studies (GWASs) require accurate cohort phenotyping, but expert labeling can be costly, time intensive, and variable. Here, we develop a machine learning (ML) model to predict glaucomatous optic nerve head features from color fundus photographs. We used the model to predict vertical cup-to-disc ratio (VCDR), a diagnostic parameter and cardinal endophenotype for glaucoma, in 65,680 Europeans in the UK Biobank (UKB). A GWAS of ML-based VCDR identified 299 independent genome-wide significant (GWS; p ≤ 5 × 10-8) hits in 156 loci. The ML-based GWAS replicated 62 of 65 GWS loci from a recent VCDR GWAS in the UKB for which two ophthalmologists manually labeled images for 67,040 Europeans. The ML-based GWAS also identified 93 novel loci, significantly expanding our understanding of the genetic etiologies of glaucoma and VCDR. Pathway analyses support the biological significance of the novel hits to VCDR: select loci near genes involved in neuronal and synaptic biology or harboring variants are known to cause severe Mendelian ophthalmic disease. Finally, the ML-based GWAS results significantly improve polygenic prediction of VCDR and primary open-angle glaucoma in the independent EPIC-Norfolk cohort.
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Affiliation(s)
| | | | | | | | | | | | - D Sculley
- Google Health, Cambridge, MA 02142, USA
| | | | - Paul J Foster
- NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of Ophthalmology, London EC1V 9EL, UK
| | | | | | | | | | - Anthony P Khawaja
- NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of Ophthalmology, London EC1V 9EL, UK; MRC Epidemiology Unit, University of Cambridge, Cambridge CB2 0SL, UK
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