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Del Pozo-Valero M, Almoallem B, Dueñas Rey A, Mahieu Q, Van Heetvelde M, Jeddawi L, Bauwens M, De Baere E. Autozygome-guided exome-first study in a consanguineous cohort with early-onset retinal disease uncovers an isolated RIMS2 phenotype and a retina-enriched RIMS2 isoform. Clin Genet 2024; 106:127-139. [PMID: 38468396 DOI: 10.1111/cge.14517] [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: 12/20/2023] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 03/13/2024]
Abstract
Leber congenital amaurosis (LCA) and early-onset retinal degeneration (EORD) are inherited retinal diseases (IRD) characterized by early-onset vision impairment. Herein, we studied 15 Saudi families by whole exome sequencing (WES) and run-of-homozygosity (ROH) detection via AutoMap in 12/15 consanguineous families. This revealed (likely) pathogenic variants in 11/15 families (73%). A potential founder variant was found in RPGRIP1. Homozygous pathogenic variants were identified in known IRD genes (ATF6, CRB1, CABP4, RDH12, RIMS2, RPGRIP1, SPATA7). We established genotype-driven clinical reclassifications for ATF6, CABP4, and RIMS2. Specifically, we observed isolated IRD in the individual with the novel RIMS2 variant, and we found a retina-enriched RIMS2 isoform conserved but not annotated in mouse. The latter illustrates potential different phenotypic consequences of pathogenic variants depending on the particular tissue/cell-type specific isoforms they affect. Lastly, a compound heterozygous genotype in GUCY2D in one non-consanguineous family was demonstrated, and homozygous variants in novel candidate genes ATG2B and RUFY3 were found in the two remaining consanguineous families. Reporting these genes will allow to validate them in other IRD cohorts. Finally, the missing heritability of the two unsolved IRD cases may be attributed to variants in non-coding regions or structural variants that remained undetected, warranting future WGS studies.
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Affiliation(s)
- Marta Del Pozo-Valero
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Basamat Almoallem
- Department of Ophthalmology, College of Medicine, King Saud University (KSU), Riyadh, Saudi Arabia
- Department of Ophthalmology, King Saud University Medical City (KSUMC), Riyadh, Saudi Arabia
| | - Alfredo Dueñas Rey
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Quinten Mahieu
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Mattias Van Heetvelde
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Laila Jeddawi
- Pediatric Ophthalmology Division, Dr. Sulaiman AL Habib Medical Group, AL Khobar, Saudi Arabia
| | - Miriam Bauwens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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2
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Zeuli R, Karali M, de Bruijn SE, Rodenburg K, Scarpato M, Capasso D, Astuti GDN, Gilissen C, Rodríguez-Hidalgo M, Ruiz-Ederra J, Testa F, Simonelli F, Cremers FPM, Banfi S, Roosing S. Whole genome sequencing identifies elusive variants in genetically unsolved Italian inherited retinal disease patients. HGG ADVANCES 2024; 5:100314. [PMID: 38816995 PMCID: PMC11225895 DOI: 10.1016/j.xhgg.2024.100314] [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: 03/15/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/01/2024] Open
Abstract
Inherited retinal diseases (IRDs) are a group of rare monogenic diseases with high genetic heterogeneity (pathogenic variants identified in over 280 causative genes). The genetic diagnostic rate for IRDs is around 60%, mainly thanks to the routine application of next-generation sequencing (NGS) approaches such as extensive gene panels or whole exome analyses. Whole-genome sequencing (WGS) has been reported to improve this diagnostic rate by revealing elusive variants, such as structural variants (SVs) and deep intronic variants (DIVs). We performed WGS on 33 unsolved cases with suspected autosomal recessive IRD, aiming to identify causative genetic variants in non-coding regions or to detect SVs that were unexplored in the initial screening. Most of the selected cases (30 of 33, 90.9%) carried monoallelic pathogenic variants in genes associated with their clinical presentation, hence we first analyzed the non-coding regions of these candidate genes. Whenever additional pathogenic variants were not identified with this approach, we extended the search for SVs and DIVs to all IRD-associated genes. Overall, we identified the missing causative variants in 11 patients (11 of 33, 33.3%). These included three DIVs in ABCA4, CEP290 and RPGRIP1; one non-canonical splice site (NCSS) variant in PROM1 and three SVs (large deletions) in EYS, PCDH15 and USH2A. For the previously unreported DIV in CEP290 and for the NCCS variant in PROM1, we confirmed the effect on splicing by reverse transcription (RT)-PCR on patient-derived RNA. This study demonstrates the power and clinical utility of WGS as an all-in-one test to identify disease-causing variants missed by standard NGS diagnostic methodologies.
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Affiliation(s)
- Roberta Zeuli
- Medical Genetics, Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Marianthi Karali
- Medical Genetics, Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy; Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Suzanne E de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Kim Rodenburg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Margherita Scarpato
- Medical Genetics, Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Dalila Capasso
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomic and Experimental Medicine Program, Naples, Italy
| | - Galuh D N Astuti
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - María Rodríguez-Hidalgo
- Department of Neuroscience, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Department of Dermatology, Ophthalmology, and Otorhinolaryngology, University of the Basque Country (UPV/EHU), Donostia-San Sebastián, Spain
| | - Javier Ruiz-Ederra
- Department of Neuroscience, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Department of Dermatology, Ophthalmology, and Otorhinolaryngology, University of the Basque Country (UPV/EHU), Donostia-San Sebastián, Spain
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sandro Banfi
- Medical Genetics, Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
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Puertas-Neyra K, Coco-Martin RM, Hernandez-Rodriguez LA, Gobelli D, Garcia-Ferrer Y, Palma-Vecino R, Tellería JJ, Simarro M, de la Fuente MA, Fernandez-Bueno I. Clinical exome analysis and targeted gene repair of the c.1354dupT variant in iPSC lines from patients with PROM1-related retinopathies exhibiting diverse phenotypes. Stem Cell Res Ther 2024; 15:192. [PMID: 38956727 PMCID: PMC11218195 DOI: 10.1186/s13287-024-03804-2] [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: 02/02/2024] [Accepted: 06/16/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Inherited retinal dystrophies (IRD) are one of the main causes of incurable blindness worldwide. IRD are caused by mutations in genes that encode essential proteins for the retina, leading to photoreceptor degeneration and loss of visual function. IRD generates an enormous global financial burden due to the lack of understanding of a significant part of its pathophysiology, molecular diagnosis, and the near absence of non-palliative treatment options. Patient-derived induced pluripotent stem cells (iPSC) for IRD seem to be an excellent option for addressing these questions, serving as exceptional tools for in-depth studies of IRD pathophysiology and testing new therapeutic approaches. METHODS From a cohort of 8 patients with PROM1-related IRD, we identified 3 patients carrying the same variant (c.1354dupT) but expressing three different IRD phenotypes: Cone and rod dystrophy (CORD), Retinitis pigmentosa (RP), and Stargardt disease type 4 (STGD4). These three target patients, along with one healthy relative from each, underwent comprehensive ophthalmic examinations and their genetic panel study was expanded through clinical exome sequencing (CES). Subsequently, non-integrative patient-derived iPSC were generated and fully characterized. Correction of the c.1354dupT mutation was performed using CRISPR/Cas9, and the genetic restoration of the PROM1 gene was confirmed through flow cytometry and western blotting in the patient-derived iPSC lines. RESULTS CES revealed that 2 target patients with the c.1354dupT mutation presented monoallelic variants in genes associated with the complement system or photoreceptor differentiation and peroxisome biogenesis disorders, respectively. The pluripotency and functionality of the patient-derived iPSC lines were confirmed, and the correction of the target mutation fully restored the capability of encoding Prominin-1 (CD133) in the genetically repaired patient-derived iPSC lines. CONCLUSIONS The c.1354dupT mutation in the PROM1 gene is associated to three distinct AR phenotypes of IRD. This pleotropic effect might be related to the influence of monoallelic variants in other genes associated with retinal dystrophies. However, further evidence needs to be provided. Future experiments should include gene-edited patient-derived iPSC due to its potential as disease modelling tools to elucidate this matter in question.
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Affiliation(s)
- Kevin Puertas-Neyra
- Instituto Universitario de Oftalmobiología Aplicada (IOBA), Universidad de Valladolid, Valladolid, Spain
| | - Rosa M Coco-Martin
- Instituto Universitario de Oftalmobiología Aplicada (IOBA), Universidad de Valladolid, Valladolid, Spain.
- Redes de Investigación Cooperativa Orientadas a Resultados en Salud (RICORS-REI), Inflamación E Inmunopatologia de Organos y Sistemas, Instituto de Salud Carlos III, Valladolid, Spain.
- Centro en Red de Medicina Regenerativa, y Terapia Celular de Castilla y León, Valladolid, Spain.
| | | | - Dino Gobelli
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular (IBGM), Universidad de Valladolid y Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
- Departamento de Biología Celular, Genética, Histología y Farmacología, Facultad de Medicina, Universidad de Valladolid, Valladolid, Spain
| | - Yenisey Garcia-Ferrer
- Instituto Universitario de Oftalmobiología Aplicada (IOBA), Universidad de Valladolid, Valladolid, Spain
| | - Raicel Palma-Vecino
- Instituto Universitario de Oftalmobiología Aplicada (IOBA), Universidad de Valladolid, Valladolid, Spain
| | - Juan José Tellería
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular (IBGM), Universidad de Valladolid y Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
| | - Maria Simarro
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular (IBGM), Universidad de Valladolid y Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
- Departamento de Biología Celular, Genética, Histología y Farmacología, Facultad de Medicina, Universidad de Valladolid, Valladolid, Spain
| | - Miguel A de la Fuente
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular (IBGM), Universidad de Valladolid y Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
- Departamento de Biología Celular, Genética, Histología y Farmacología, Facultad de Medicina, Universidad de Valladolid, Valladolid, Spain
| | - Ivan Fernandez-Bueno
- Instituto Universitario de Oftalmobiología Aplicada (IOBA), Universidad de Valladolid, Valladolid, Spain
- Redes de Investigación Cooperativa Orientadas a Resultados en Salud (RICORS-REI), Inflamación E Inmunopatologia de Organos y Sistemas, Instituto de Salud Carlos III, Valladolid, Spain
- Centro en Red de Medicina Regenerativa, y Terapia Celular de Castilla y León, Valladolid, Spain
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Basharat R, de Bruijn SE, Zahid M, Rodenburg K, Hitti-Malin RJ, Rodríguez-Hidalgo M, Boonen EGM, Jarral A, Mahmood A, Corominas J, Khalil S, Zai JA, Ali G, Ruiz-Ederra J, Gilissen C, Cremers FPM, Ansar M, Panneman DM, Roosing S. Next-generation sequencing to genetically diagnose a diverse range of inherited eye disorders in 15 consanguineous families from Pakistan. Exp Eye Res 2024; 244:109945. [PMID: 38815792 DOI: 10.1016/j.exer.2024.109945] [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: 02/28/2024] [Revised: 04/19/2024] [Accepted: 05/27/2024] [Indexed: 06/01/2024]
Abstract
Inherited retinal dystrophies (IRDs) are characterized by photoreceptor dysfunction or degeneration. Clinical and phenotypic overlap between IRDs makes the genetic diagnosis very challenging and comprehensive genomic approaches for accurate diagnosis are frequently required. While there are previous studies on IRDs in Pakistan, causative genes and variants are still unknown for a significant portion of patients. Therefore, there is a need to expand the knowledge of the genetic spectrum of IRDs in Pakistan. Here, we recruited 52 affected and 53 normal individuals from 15 consanguineous Pakistani families presenting non-syndromic and syndromic forms of IRDs. We employed single molecule Molecular Inversion Probes (smMIPs) based panel sequencing and whole genome sequencing to identify the probable disease-causing variants in these families. Using this approach, we obtained a 93% genetic solve rate and identified 16 (likely) causative variants in 14 families, of which seven novel variants were identified in ATOH7, COL18A1, MERTK, NDP, PROM1, PRPF8 and USH2A while nine recurrent variants were identified in CNGA3, CNGB1, HGSNAT, NMNAT1, SIX6 and TULP1. The novel MERTK variant and one recurrent TULP1 variant explained the intra-familial locus heterogeneity in one of the screened families while two recurrent CNGA3 variants explained compound heterozygosity in another family. The identification of variants in known disease-associated genes emphasizes the utilization of time and cost-effective screening approaches for rapid diagnosis. The timely genetic diagnosis will not only identify any associated systemic issues in case of syndromic IRDs, but will also aid in the acceleration of personalized medicine for patients affected with IRDs.
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Affiliation(s)
- Rabia Basharat
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Suzanne E de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Muhammad Zahid
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Kim Rodenburg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rebekkah J Hitti-Malin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - María Rodríguez-Hidalgo
- Department of Neuroscience, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Department of Dermatology, Ophthalmology, and Otorhinolaryngology, University of the Basque Country (UPV/EHU), Donostia-San Sebastián, Spain
| | - Erica G M Boonen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Afeefa Jarral
- Department of Biotechnology, Mirpur University of Science and Technology, Mirpur, (AJK), Pakistan
| | - Arif Mahmood
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Jordi Corominas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sharqa Khalil
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Jawaid Ahmed Zai
- Department of Physiology and MLT, University of Sindh, Jamshoro, Pakistan
| | - Ghazanfar Ali
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Javier Ruiz-Ederra
- Department of Neuroscience, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Department of Dermatology, Ophthalmology, and Otorhinolaryngology, University of the Basque Country (UPV/EHU), Donostia-San Sebastián, Spain
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Muhammad Ansar
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Daan M Panneman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
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Matczyńska E, Beć-Gajowniczek M, Sivitskaya L, Gregorczyk E, Łyszkiewicz P, Szymańczak R, Jędrzejowska M, Wylęgała E, Krawczyński MR, Teper S, Boguszewska-Chachulska A. Optimised, Broad NGS Panel for Inherited Eye Diseases to Diagnose 1000 Patients in Poland. Biomedicines 2024; 12:1355. [PMID: 38927562 PMCID: PMC11202224 DOI: 10.3390/biomedicines12061355] [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: 04/30/2024] [Revised: 06/10/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Advances in gene therapy and genome editing give hope that new treatments will soon be available for inherited eye diseases that together affect a significant proportion of the adult population. New solutions are needed to make genetic diagnosis fast and affordable. This is the first study of such a large group of patients with inherited retinal dystrophies (IRD) and inherited optic neuropathies (ION) in the Polish population. It is based on four years of diagnostic analysis using a broad, targeted NGS approach. The results include the most common pathogenic variants, as well as 91 novel causative variants, including frameshifts in the cumbersome RPGR ORF15 region. The high frequency of the ABCA4 complex haplotype p.(Leu541Pro;Ala1038Val) was confirmed. Additionally, a deletion of exons 22-24 in USH2A, probably specific to the Polish population, was uncovered as the most frequent copy number variation. The diagnostic yield of the broad NGS panel reached 64.3% and is comparable to the results reported for genetic studies of IRD and ION performed for other populations with more extensive WES or WGS methods. A combined approach to identify genetic causes of all known diseases manifesting in the posterior eye segment appears to be the optimal choice given the currently available treatment options and advanced clinical trials.
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Affiliation(s)
- Ewa Matczyńska
- Genomed S.A., 02-971 Warsaw, Poland
- Chair and Clinical Department of Ophthalmology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland
| | | | | | | | | | | | | | - Edward Wylęgała
- Chair and Clinical Department of Ophthalmology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland
| | - Maciej R. Krawczyński
- Chair and Department of Medical Genetics, Poznań University of Medical Sciences, 61-701 Poznań, Poland
- Centers for Medical Genetics Genesis, 60-529 Poznań, Poland
| | - Sławomir Teper
- Chair and Clinical Department of Ophthalmology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland
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Lopez-de la Rosa A, Telleria JJ, Posada de la Paz M, Hermosilla-Gimeno IM, Rivas MA, Gilabert R, Coco-Martín RM. Clinical and genetic characterization of patients with eye diseases included in the Spanish Rare Diseases Patient Registry. Orphanet J Rare Dis 2024; 19:234. [PMID: 38872169 PMCID: PMC11170770 DOI: 10.1186/s13023-024-03242-6] [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: 07/13/2023] [Accepted: 06/05/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND The low prevalence of rare diseases poses a significant challenge in advancing their understanding. This study aims to delineate the clinical and genetic characteristics of patients with rare eye diseases (RED) enrolled in the Spanish Rare Diseases Patient Registry. METHODS A total of 864 patients from the registry database were included. Diseases were categorized into inherited retinal dystrophies (n=688); anterior segment diseases (n=48); congenital malformations (n=27); and syndromic diseases with ocular involvement including muscular (n=46), neurological (n=34), or metabolic (n=13); inflammatory diseases (n=4); and tumors (n=4). Data on visual acuity (VA) and/or visual field (VF), symptoms and signs, concurrent diseases in syndromic cases, age of onset and at diagnosis, affected genes, disability rating, inability to work and dependency grade recognition were collected. RESULTS A mean diagnostic delay of 7 years from symptom onset was observed. Commonly reported symptoms included photophobia, night blindness, and progressive vision loss (≥57% of patients). Cataract was the most prevalent secondary disease (46%), with pseudophakia being the most common ocular surgery (26%). Hearing loss and cardiovascular diseases were the most prevalent concurrent systemic diseases (≥13%). Certificates of disability, incapacity for work, and dependency were held by 87%, 42%, and 19% of patients, respectively. Among the 719 patients with available VA data, 193 (27%) were blind, and 188 (26%) had moderate to severe visual impairment. Over half of the patients (54%) exhibited VF defects, and 216 (25%) had concentric contraction ≤5° or abolished VF. Most had genetic diseases with autosomal recessive (55%), autosomal dominant (30%), X-linked (9%), and mitochondrial (6%) patterns. One patient had mutations in both recessive USH2A and dominant RHO genes simultaneously. Of the 656 patients (75.7%) who underwent genetic testing, only 461 (70.3%) received a positive result (pathogenic or likely pathogenic mutations explaining the phenotype). We found 62 new gene variants related to RED not previously reported in databases of genetic variants related to specific phenotypes. CONCLUSIONS This study delineates the clinical and genotypic profiles of RED in Spain. Genetic diseases, particularly retinal disorders, predominate, but a significant proportion of affected patients remain genetically undiagnosed, hindering potential gene therapy endeavors. Despite notable improvements in reducing diagnosis delays, it is still remarkable. RED frequently lead to disability and blindness among young populations.
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Affiliation(s)
- Alberto Lopez-de la Rosa
- Instituto de Oftalmobiología Aplicada (IOBA), Universidad de Valladolid, Campus Miguel Delibes, Paseo de Belén 17, E-47011, Valladolid, Spain
- Observatorio Nacional de Enfermedades Raras Oculares (ONERO), 47011, Valladolid, Spain
| | - Juan J Telleria
- Instituto de Biomedicina y Genética Molecular (IBGM), Universidad de Valladolid, 47001, Valladolid, Spain
- Facultad de Medicina, Universidad de Valladolid, 47001, Valladolid, Spain
| | - Manuel Posada de la Paz
- Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Isabel M Hermosilla-Gimeno
- Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Miren Agurtzane Rivas
- Observatorio Nacional de Enfermedades Raras Oculares (ONERO), 47011, Valladolid, Spain
| | - Raúl Gilabert
- Observatorio Nacional de Enfermedades Raras Oculares (ONERO), 47011, Valladolid, Spain
| | - Rosa M Coco-Martín
- Instituto de Oftalmobiología Aplicada (IOBA), Universidad de Valladolid, Campus Miguel Delibes, Paseo de Belén 17, E-47011, Valladolid, Spain.
- Facultad de Medicina, Universidad de Valladolid, 47001, Valladolid, Spain.
- RICORS de Enfermedades Inflamatorias, Carlos III Health Institute, 28220, Madrid, Spain.
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7
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Chan J, Holdstock J, Shovelton J, Reid J, Speight G, Molha D, Pullabhatla V, Carpenter S, Uddin E, Washio T, Sato H, Izumi Y, Watanabe R, Niiro H, Fukushima Y, Ashida N, Hirose T, Maeda A. Clinical and analytical validation of an 82-gene comprehensive genome-profiling panel for identifying and interpreting variants responsible for inherited retinal dystrophies. PLoS One 2024; 19:e0305422. [PMID: 38870140 PMCID: PMC11175448 DOI: 10.1371/journal.pone.0305422] [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: 02/20/2024] [Accepted: 05/30/2024] [Indexed: 06/15/2024] Open
Abstract
Inherited retinal dystrophies comprise a clinically complex and heterogenous group of diseases characterized by visual impairment due to pathogenic variants of over 300 different genes. Accurately identifying the causative gene and associated variant is crucial for the definitive diagnosis and subsequent selection of precise treatments. Consequently, well-validated genetic tests are required in the clinical practice. Here, we report the analytical and clinical validation of a next-generation sequencing targeted gene panel, the PrismGuide IRD Panel System. This system enables comprehensive genome profiling of 82 genes related to inherited retinal dystrophies. The PrismGuide IRD Panel System demonstrated 100% (n = 43) concordance with Sanger sequencing in detecting single-nucleotide variants, small insertions, and small deletions in the target genes and also in assessing their zygosity. It also identified copy-number loss in four out of five cases. When assessing precision, we evaluated the reproducibility of variant detection with 2,160 variants in 144 replicates and found 100% agreement in terms of single-nucleotide variants (n = 1,584) and small insertions and deletions (n = 576). Furthermore, the PrismGuide IRD Panel System generated sufficient read depth for variant calls across the purine-rich and highly repetitive open-reading frame 15 region of RPGR and detected all five variants tested. These results show that the PrismGuide IRD Panel System can accurately and consistently detect single-nucleotide variants and small insertions and deletions. Thus, the PrismGuide IRD Panel System could serve as useful tool that is applicable in clinical practice for identifying the causative genes based on the detection and interpretation of variants in patients with inherited retinal dystrophies and can contribute to a precise molecular diagnosis and targeted treatments.
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Affiliation(s)
- Jacqueline Chan
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - Jolyon Holdstock
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - John Shovelton
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - James Reid
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - Graham Speight
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - Duarte Molha
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - Venu Pullabhatla
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - Stephanie Carpenter
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - Ezam Uddin
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - Takanori Washio
- Life Innovation Center, Riken Genesis Co. LTD, Kawasaki, Kanagawa, Japan
- Division of Clinical Cancer Genomics, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
| | - Hiroko Sato
- Life Innovation Center, Riken Genesis Co. LTD, Kawasaki, Kanagawa, Japan
| | - Yuuki Izumi
- Technology Innovation, Sysmex Corporation, Kobe, Hyogo, Japan
| | - Reiko Watanabe
- Medical & Scientific Affairs, Sysmex Corporation, Kobe, Hyogo, Japan
| | - Hayato Niiro
- Medical & Scientific Affairs, Sysmex Corporation, Kobe, Hyogo, Japan
| | | | - Naoko Ashida
- Medical & Scientific Affairs, Sysmex Corporation, Kobe, Hyogo, Japan
| | - Takashi Hirose
- Medical & Scientific Affairs, Sysmex Corporation, Kobe, Hyogo, Japan
| | - Akiko Maeda
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe, Hyogo, Japan
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8
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Cortinhal T, Santos C, Vaz-Pereira S, Marta A, Duarte L, Miranda V, Costa J, Sousa AB, Peter VG, Kaminska K, Rivolta C, Carvalho AL, Saraiva J, Soares CA, Silva R, Murta J, Santos LC, Marques JP. Genetic profile of syndromic retinitis pigmentosa in Portugal. Graefes Arch Clin Exp Ophthalmol 2024; 262:1883-1897. [PMID: 38189974 PMCID: PMC11106148 DOI: 10.1007/s00417-023-06360-2] [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: 05/04/2023] [Revised: 12/11/2023] [Accepted: 12/28/2023] [Indexed: 01/09/2024] Open
Abstract
PURPOSE Retinitis pigmentosa (RP) comprises a genetically and clinically heterogeneous group of inherited retinal degenerations, where 20-30% of patients exhibit extra-ocular manifestations (syndromic RP). Understanding the genetic profile of RP has important implications for disease prognosis and genetic counseling. This study aimed to characterize the genetic profile of syndromic RP in Portugal. METHODS Multicenter, retrospective cohort study. Six Portuguese healthcare providers identified patients with a clinical diagnosis of syndromic RP and available genetic testing results. All patients had been previously subjected to a detailed ophthalmologic examination and clinically oriented genetic testing. Genetic variants were classified according to the American College of Medical Genetics and Genomics; only likely pathogenic or pathogenic variants were considered relevant for disease etiology. RESULTS One hundred and twenty-two patients (53.3% males) from 100 families were included. Usher syndrome was the most frequent diagnosis (62.0%), followed by Bardet-Biedl (19.0%) and Senior-Løken syndromes (7.0%). Deleterious variants were identified in 86/100 families for a diagnostic yield of 86.0% (87.1% for Usher and 94.7% for Bardet-Biedl). A total of 81 genetic variants were identified in 25 different genes, 22 of which are novel. USH2A and MYO7A were responsible for most type II and type I Usher syndrome cases, respectively. BBS1 variants were the cause of Bardet-Biedl syndrome in 52.6% of families. Best-corrected visual acuity (BCVA) records were available at baseline and last visit for 99 patients (198 eyes), with a median follow-up of 62.0 months. The mean BCVA was 56.5 ETDRS letters at baseline (Snellen equivalent ~ 20/80), declining to 44.9 ETDRS letters (Snellen equivalent ~ 20/125) at the last available follow-up (p < 0.001). CONCLUSION This is the first multicenter study depicting the genetic profile of syndromic RP in Portugal, thus contributing toward a better understanding of this heterogeneous disease group. Usher and Bardet-Biedl syndromes were found to be the most common types of syndromic RP in this large Portuguese cohort. A high diagnostic yield was obtained, highlighting current genetic testing capabilities in providing a molecular diagnosis to most affected individuals. This has major implications in determining disease-related prognosis and providing targeted genetic counseling for syndromic RP patients in Portugal.
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Affiliation(s)
- Telmo Cortinhal
- Department of Ophthalmology, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
| | - Cristina Santos
- Instituto de Oftalmologia Dr. Gama Pinto (IOGP), Lisboa, Portugal
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Sara Vaz-Pereira
- Department of Ophthalmology, Centro Hospitalar Universitário de Lisboa Norte (CHULN), Lisboa, Portugal
- Department of Ophthalmology, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Ana Marta
- Department of Ophthalmology, Centro Hospitalar e Universitário de Santo António (CHUdSA), Porto, Portugal
- Instituto Ciências Biomédicas Abel Salazar (ICBAS), Porto, Portugal
| | - Lilianne Duarte
- Department of Ophthalmology, Centro Hospitalar de Entre Douro e Vouga (CHEDV), Santa Maria da Feira, Portugal
| | - Vitor Miranda
- Department of Ophthalmology, Centro Hospitalar de Entre Douro e Vouga (CHEDV), Santa Maria da Feira, Portugal
| | - José Costa
- Department of Ophthalmology, Hospital de Braga (HB), Braga, Portugal
| | - Ana Berta Sousa
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Lisboa Norte (CHULN), Lisboa, Portugal
| | - Virginie G Peter
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031, Basel, Switzerland
- Department of Ophthalmology, University of Basel, 4031, Basel, Switzerland
- Department of Ophthalmology, Inselspital, Bern University Hospital, 3010, Bern, Switzerland
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031, Basel, Switzerland
- Department of Ophthalmology, University of Basel, 4031, Basel, Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031, Basel, Switzerland
- Department of Ophthalmology, University of Basel, 4031, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Ana Luísa Carvalho
- Medical Genetics Unit, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
- University Clinic of Medical Genetics, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal
| | - Jorge Saraiva
- Medical Genetics Unit, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
- University Clinic of Pediatrics, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal
| | - Célia Azevedo Soares
- Medical Genetics Department, Centro de Genética Médica Jacinto Magalhães, Centro Hospitalar e Universitário do Porto (CHUP), Porto, Portugal
- Unit for Multidisciplinary Research in Biomedicine, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
- Medical Science Department, Universidade de Aveiro, Aveiro, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Rufino Silva
- Department of Ophthalmology, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
- University Clinic of Ophthalmology, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal
| | - Joaquim Murta
- Department of Ophthalmology, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
- University Clinic of Ophthalmology, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal
| | | | - João Pedro Marques
- Department of Ophthalmology, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal.
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal.
- University Clinic of Ophthalmology, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal.
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9
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Ibrahim M, Jaffal L, Assi A, Helou C, El Shamieh S. ABCA4-related retinopathies in Lebanon. Heliyon 2024; 10:e30304. [PMID: 38694055 PMCID: PMC11061736 DOI: 10.1016/j.heliyon.2024.e30304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 04/20/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024] Open
Abstract
Variants in ATP-binding cassette transporter type A4 (ABCA4) have been linked to several forms of inherited retinal diseases (IRDs) besides the classically defined Stargardt disease (STGD), known collectively as ABCA4 retinopathies. ABCA4 is a sizable locus harboring 50 exons; thus, its analysis has revealed over 2,400 variants described, of which more than 2,000 are causal. Due to the clinical and genetic heterogeneity, diagnosing ABCA4 retinopathies is challenging. To date, no ABCA4-related retinopathy has been detected in Lebanon. Using next-generation sequencing, we analyzed our IRDs' cohort retrospectively (61 families) and identified five with ABCA4-related retinopathies, making it a relatively abundant cause of IRDs (about 8 %). Three families were diagnosed with rod-cone dystrophy (RCD), two with STGD, and one with cone-rod dystrophy (CRD). In conclusion, our study showed the presence of ABCA4 variants with a high degree of heterogeneity in Lebanon.
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Affiliation(s)
- Mariam Ibrahim
- Molecular Testing Laboratory, Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Lama Jaffal
- Department of Biological and Chemical Sciences, School of Arts and Sciences, Lebanese International University, Beirut, Lebanon
| | | | - Charles Helou
- Retinal Service, Beirut Eye & ENT Specialist Hospital, Beirut, Lebanon
| | - Said El Shamieh
- Molecular Testing Laboratory, Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
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10
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Fernández-Suárez E, González-Del Pozo M, Méndez-Vidal C, Martín-Sánchez M, Mena M, de la Morena-Barrio B, Corral J, Borrego S, Antiñolo G. Long-read sequencing improves the genetic diagnosis of retinitis pigmentosa by identifying an Alu retrotransposon insertion in the EYS gene. Mob DNA 2024; 15:9. [PMID: 38704576 PMCID: PMC11069205 DOI: 10.1186/s13100-024-00320-1] [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: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Biallelic variants in EYS are the major cause of autosomal recessive retinitis pigmentosa (arRP) in certain populations, a clinically and genetically heterogeneous disease that may lead to legal blindness. EYS is one of the largest genes (~ 2 Mb) expressed in the retina, in which structural variants (SVs) represent a common cause of disease. However, their identification using short-read sequencing (SRS) is not always feasible. Here, we conducted targeted long-read sequencing (T-LRS) using adaptive sampling of EYS on the MinION sequencing platform (Oxford Nanopore Technologies) to definitively diagnose an arRP family, whose affected individuals (n = 3) carried the heterozygous pathogenic deletion of exons 32-33 in the EYS gene. As this was a recurrent variant identified in three additional families in our cohort, we also aimed to characterize the known deletion at the nucleotide level to assess a possible founder effect. RESULTS T-LRS in family A unveiled a heterozygous AluYa5 insertion in the coding exon 43 of EYS (chr6(GRCh37):g.64430524_64430525ins352), which segregated with the disease in compound heterozygosity with the previously identified deletion. Visual inspection of previous SRS alignments using IGV revealed several reads containing soft-clipped bases, accompanied by a slight drop in coverage at the Alu insertion site. This prompted us to develop a simplified program using grep command to investigate the recurrence of this variant in our cohort from SRS data. Moreover, LRS also allowed the characterization of the CNV as a ~ 56.4kb deletion spanning exons 32-33 of EYS (chr6(GRCh37):g.64764235_64820592del). The results of further characterization by Sanger sequencing and linkage analysis in the four families were consistent with a founder variant. CONCLUSIONS To our knowledge, this is the first report of a mobile element insertion into the coding sequence of EYS, as a likely cause of arRP in a family. Our study highlights the value of LRS technology in characterizing and identifying hidden pathogenic SVs, such as retrotransposon insertions, whose contribution to the etiopathogenesis of rare diseases may be underestimated.
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Affiliation(s)
- Elena Fernández-Suárez
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC, University of Seville, Seville, Spain
- Center for Biomedical Network Research On Rare Diseases (CIBERER), Seville, Spain
| | - María González-Del Pozo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC, University of Seville, Seville, Spain
- Center for Biomedical Network Research On Rare Diseases (CIBERER), Seville, Spain
| | - Cristina Méndez-Vidal
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC, University of Seville, Seville, Spain
- Center for Biomedical Network Research On Rare Diseases (CIBERER), Seville, Spain
| | - Marta Martín-Sánchez
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC, University of Seville, Seville, Spain
- Center for Biomedical Network Research On Rare Diseases (CIBERER), Seville, Spain
| | - Marcela Mena
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC, University of Seville, Seville, Spain
- Center for Biomedical Network Research On Rare Diseases (CIBERER), Seville, Spain
| | - Belén de la Morena-Barrio
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - Javier Corral
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - Salud Borrego
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC, University of Seville, Seville, Spain.
- Center for Biomedical Network Research On Rare Diseases (CIBERER), Seville, Spain.
| | - Guillermo Antiñolo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC, University of Seville, Seville, Spain.
- Center for Biomedical Network Research On Rare Diseases (CIBERER), Seville, Spain.
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11
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Donato L, Scimone C, Alibrandi S, Mordà D, Anchesi I, Scalinci SZ, Rinaldi C, D'Angelo R, Sidoti A. Investigating G-quadruplex structures in RPGR gene: Implications for understanding X-linked retinal degeneration. Heliyon 2024; 10:e29828. [PMID: 38699732 PMCID: PMC11063440 DOI: 10.1016/j.heliyon.2024.e29828] [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: 02/19/2024] [Revised: 03/31/2024] [Accepted: 04/16/2024] [Indexed: 05/05/2024] Open
Abstract
Aims This pilot study investigates the potential pathogenic role of G-quadruplex (G4) structures in RPGR-associated retinal degeneration, starting from a case of suspected X-linked form affected family. We hypothesize that the stabilization of these structures might alter DNA replication and transcription, inducing genetic instability and influencing gene expression. Main methods We conducted whole genome amplification experiments and next-generation sequencing to detect the blockade of polymerase activity by G4 structures. Our specific focus was the RPGR gene, which hosts a high concentration of predicted G4-forming motifs and is implicated in most X-linked retinal degeneration cases. To understand the potential interference of G4 structures, we applied computational and 3D molecular modeling to visualize interferences in DNA replication and transcription regulation. Key findings Our data confirmed the obstruction of DNA polymerase enzymes by G4 structures, particularly when stabilized by the compound pyridostatin. This obstruction was evident in the reduced amplification of RPGR gene regions and a shift in the start/end sites of putative G4 motifs. Moreover, the modeling indicated a potential disruption of critical promoter elements and RNA polymerase binding, which could drastically alter gene expression. Significance Our findings suggest that G4 formation in the RPGR gene could lead to genetic instability and affect the expression of RPGR, contributing to retinal dystrophy. Moreover, this study underscores the broader implications of G4 structures in other genetic disorders. Improved understanding of G4 structures could reveal novel therapeutic targets to combat genetic disorders, promoting the advancement of personalized medicine and precision health.
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Affiliation(s)
- Luigi Donato
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Messina, 98125, Italy
- Department of Biomolecular Strategies, Genetics and Cutting-Edge Therapies, I.E.ME.S.T., Palermo, 90139, Italy
| | - Concetta Scimone
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Messina, 98125, Italy
- Department of Biomolecular Strategies, Genetics and Cutting-Edge Therapies, I.E.ME.S.T., Palermo, 90139, Italy
| | - Simona Alibrandi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Messina, 98125, Italy
- Department of Biomolecular Strategies, Genetics and Cutting-Edge Therapies, I.E.ME.S.T., Palermo, 90139, Italy
| | - Domenico Mordà
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Messina, 98125, Italy
- Department of Biomolecular Strategies, Genetics and Cutting-Edge Therapies, I.E.ME.S.T., Palermo, 90139, Italy
- Department of Veterinary Sciences, University of Messina, 98122, Messina, Italy
| | - Ivan Anchesi
- IRCCS Centro Neurolesi "Bonino-Pulejo", Via Provinciale Palermo, Contrada Casazza, 98124, Messina, Italy
| | | | - Carmela Rinaldi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Messina, 98125, Italy
| | - Rosalia D'Angelo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Messina, 98125, Italy
| | - Antonina Sidoti
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Messina, 98125, Italy
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12
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Marta A, Marques JP, Santos C, Coutinho-Santos L, Vaz-Pereira S, Costa J, Arede P, Félix R, Geada S, Gouveia N, Silva R, Baptista M, Lume M, Parreira R, Azevedo Soares C, Menéres MJ, Lemos C, Melo Beirão J. The socioeconomic epidemiology of inherited retinal diseases in Portugal. Orphanet J Rare Dis 2024; 19:151. [PMID: 38594754 PMCID: PMC11003026 DOI: 10.1186/s13023-024-03161-6] [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: 05/16/2023] [Accepted: 03/30/2024] [Indexed: 04/11/2024] Open
Abstract
BACKGROUND Inherited retinal diseases (IRDs) are a group of rare degenerative disorders of the retina that can lead to blindness from birth to late middle age. Knowing the target population and its resources is essential to better plan support measures. The aim of this study was to evaluate the socioeconomic characteristics of regions in Portugal where IRD patients reside to inform the planning of vision aid and rehabilitation intervention measures. RESULTS This study included 1082 patients from 973 families, aged 3 to 92 years, with a mean age of 44.8 ± 18.1 years. Patients living with an IRD were identified in 190 of the 308 municipalities. According to this study, the estimated IRD prevalence in Portugal was 10.4 per 100,000 inhabitants, and by municipalities, it ranged from 0 to 131.2 per 100,000 inhabitants. Overall, regions with a higher prevalence of IRD have a lower population density (r=-0.371, p < 0.001), a higher illiteracy rate (r = 0.404, p < 0.001) and an overall older population (r = 0.475, p < 0.001). Additionally, there is a lower proportion of doctor per capita (r = 0.350, p < 0.001), higher social security pensions beneficiaries (r = 0.439, p < 0.001), worse water quality for human consumption (r=-0.194, p = 0.008), fewer audiences at the cinema (r=-0.315, p < 0.001) and lower proportion of foreign guests in tourist accommodations (r=-0.287, p < 0.001). CONCLUSION The number of identified patients with IRD varied between regions. Using data from national statistics (PORDATA), we observed differences in socioeconomic characteristics between regions. Multiple targeted aid strategies can be developed to ensure that all IRD patients are granted full clinical and socioeconomic support.
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Affiliation(s)
- Ana Marta
- Department of Ophthalmology, Centro Hospitalar Universitário de Santo António, EPE (CHUdSA), Porto, Portugal.
- Instituto Ciências Biomédicas Abel Salazar (ICBAS), Porto, Portugal.
| | - João Pedro Marques
- Centro de Responsabilidade Integrado de Oftalmologia do Centro Hospitalar e Universitário de Coimbra, EPE (CRIO-CHUC), Coimbra, Portugal
- Clinical Academic Center of Coimbra, Coimbra, Portugal
- Faculty of Medicine, University Clinic of Ophthalmology, University of Coimbra (FMUC), Coimbra, Portugal
| | - Cristina Santos
- Instituto de Oftalmologia Dr. Gama Pinto (IOGP), Lisboa, Portugal
- Faculdade de Ciências Médicas, NMS, FCM, NOVA Medical School, Universidade NOVA de Lisboa, 7 iNOVA4Health, Lisboa, Portugal
| | | | - Sara Vaz-Pereira
- Department of Ophthalmology, Centro Hospitalar Universitário de Lisboa Norte (CHULN), Lisboa, Portugal
- Department of Ophthalmology, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - José Costa
- Department of Ophthalmology, Hospital de Braga (HB), Braga, Portugal
| | - Pedro Arede
- Department of Ophthalmology, Centro Hospitalar Lisboa Ocidental, EPE (CHLO), Lisboa, Portugal
| | - Raquel Félix
- Centro de Responsabilidade Integrado de Oftalmologia do Centro Hospitalar e Universitário de Coimbra, EPE (CRIO-CHUC), Coimbra, Portugal
| | - Sara Geada
- Centro de Responsabilidade Integrado de Oftalmologia do Centro Hospitalar e Universitário de Coimbra, EPE (CRIO-CHUC), Coimbra, Portugal
| | - Nuno Gouveia
- Centro de Responsabilidade Integrado de Oftalmologia do Centro Hospitalar e Universitário de Coimbra, EPE (CRIO-CHUC), Coimbra, Portugal
| | - Rui Silva
- Department of Ophthalmology, Hospital de Braga (HB), Braga, Portugal
| | - Margarida Baptista
- Department of Ophthalmology, Centro Hospitalar Lisboa Ocidental, EPE (CHLO), Lisboa, Portugal
| | - Miguel Lume
- Department of Ophthalmology, Centro Hospitalar Universitário de Santo António, EPE (CHUdSA), Porto, Portugal
| | - Ricardo Parreira
- Department of Ophthalmology, Centro Hospitalar Universitário de Santo António, EPE (CHUdSA), Porto, Portugal
| | - Célia Azevedo Soares
- Medical Genetics Department, Centro de Genética Médica Jacinto Magalhães, Centro Hospitalar Universitário de Santo António, EPE (CHUdSA), Porto, Portugal
- Unit for Multidisciplinary Research in Biomedicine, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
- Medical Science Department, Universidade de Aveiro, Aveiro, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Maria João Menéres
- Department of Ophthalmology, Centro Hospitalar Universitário de Santo António, EPE (CHUdSA), Porto, Portugal
- Instituto Ciências Biomédicas Abel Salazar (ICBAS), Porto, Portugal
| | - Carolina Lemos
- Instituto Ciências Biomédicas Abel Salazar (ICBAS), Porto, Portugal
- Centro Hospitalar Universitário de Santo António, EPE (CHUdSA), Largo do Prof. Abel Salazar, 4099-001, Porto, Portugal
| | - João Melo Beirão
- Department of Ophthalmology, Centro Hospitalar Universitário de Santo António, EPE (CHUdSA), Porto, Portugal
- Instituto Ciências Biomédicas Abel Salazar (ICBAS), Porto, Portugal
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13
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Quinodoz M, Kaminska K, Cancellieri F, Han JH, Peter VG, Celik E, Janeschitz-Kriegl L, Schärer N, Hauenstein D, György B, Calzetti G, Hahaut V, Custódio S, Sousa AC, Wada Y, Murakami Y, Fernández AA, Hernández CR, Minguez P, Ayuso C, Nishiguchi KM, Santos C, Santos LC, Tran VH, Vaclavik V, Scholl HPN, Rivolta C. Detection of elusive DNA copy-number variations in hereditary disease and cancer through the use of noncoding and off-target sequencing reads. Am J Hum Genet 2024; 111:701-713. [PMID: 38531366 PMCID: PMC11023916 DOI: 10.1016/j.ajhg.2024.03.001] [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: 10/23/2023] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 03/28/2024] Open
Abstract
Copy-number variants (CNVs) play a substantial role in the molecular pathogenesis of hereditary disease and cancer, as well as in normal human interindividual variation. However, they are still rather difficult to identify in mainstream sequencing projects, especially involving exome sequencing, because they often occur in DNA regions that are not targeted for analysis. To overcome this problem, we developed OFF-PEAK, a user-friendly CNV detection tool that builds on a denoising approach and the use of "off-target" DNA reads, which are usually discarded by sequencing pipelines. We benchmarked OFF-PEAK on data from targeted sequencing of 96 cancer samples, as well as 130 exomes of individuals with inherited retinal disease from three different populations. For both sets of data, OFF-PEAK demonstrated excellent performance (>95% sensitivity and >80% specificity vs. experimental validation) in detecting CNVs from in silico data alone, indicating its immediate applicability to molecular diagnosis and genetic research.
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Affiliation(s)
- Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Ji Hoon Han
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Virginie G Peter
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Department of Ophthalmology, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Elifnaz Celik
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Lucas Janeschitz-Kriegl
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Nils Schärer
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Daniela Hauenstein
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Bence György
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Giacomo Calzetti
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Vincent Hahaut
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Sónia Custódio
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon, Portugal
| | - Ana Cristina Sousa
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon, Portugal
| | | | - Yusuke Murakami
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Almudena Avila Fernández
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain; Centre for Biomedical Network Research On Rare Diseases (CIBERER), Madrid, Spain
| | - Cristina Rodilla Hernández
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain; Centre for Biomedical Network Research On Rare Diseases (CIBERER), Madrid, Spain
| | - Pablo Minguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain; Centre for Biomedical Network Research On Rare Diseases (CIBERER), Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain; Centre for Biomedical Network Research On Rare Diseases (CIBERER), Madrid, Spain
| | - Koji M Nishiguchi
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Cristina Santos
- NOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisbon, Portugal; Instituto de Oftalmologia Dr Gama Pinto (IOGP), Lisbon, Portugal
| | | | - Viet H Tran
- Unité d'oculogénétique, Jules Gonin Eye Hospital, University of Lausanne, Lausanne, Switzerland; Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
| | - Veronika Vaclavik
- Unité d'oculogénétique, Jules Gonin Eye Hospital, University of Lausanne, Lausanne, Switzerland
| | - Hendrik P N Scholl
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
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14
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Moseley J, Leest T, Larsson K, Magrelli A, Stoyanova-Beninska V. Inherited retinal dystrophies and orphan designations in the European Union. Eur J Ophthalmol 2024:11206721241236214. [PMID: 38500388 DOI: 10.1177/11206721241236214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Inherited Retinal Dystrophies (IRD) are diverse rare diseases that affect the retina and lead to visual impairment or blindness. Research in this field is ongoing, with over 60 EU orphan medicinal products designated in this therapeutic area by the Committee for Orphan Medicinal Products (COMP) at the European Medicines Agency (EMA). Up to now, COMP has used traditional disease terms, like retinitis pigmentosa, for orphan designation regardless of the product's mechanism of action. The COMP reviewed the designation approach for IRDs taking into account all previous Orphan Designations (OD) experience in IRDs, the most relevant up to date scientific literature and input from patients and clinical experts. Following the review, the COMP decided that there should be three options available for orphan designation concerning the condition: i) an amended set of OD groups for therapies that might be used in a broad spectrum of conditions, ii) a gene-specific designation for targeted therapies, and iii) an occasional term for products that do not fit in the above two categories. The change in the approach to orphan designation in IRDs caters for different scenarios to allow an optimum approach for future OD applications including the option of a gene-specific designation. By applying this new approach, the COMP increases the regulatory clarity, efficiency, and predictability for sponsors, aligns EU regulatory tools with the latest scientific and medical developments in the field of IRDs, and ensures that all potentially treatable patients will be included in the scope of an OD.
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Affiliation(s)
- Jane Moseley
- European Medicines Agency, Amsterdam, The Netherlands
| | - Tim Leest
- Committee for Orphan Medicinal Products at the European Medicines Agency, Amsterdam, The Netherlands
- Federal Agency for Medicines and Health Products, Brussels, Belgium
| | | | - Armando Magrelli
- Committee for Orphan Medicinal Products at the European Medicines Agency, Amsterdam, The Netherlands
- National Center for Drug Research and Evaluation- Istituto Superiore di Sanità, Rome, Italy
| | - Violeta Stoyanova-Beninska
- Committee for Orphan Medicinal Products at the European Medicines Agency, Amsterdam, The Netherlands
- Medicines Evaluation Board (MEB), Utrecht, The Netherlands
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15
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Fernández-Caballero L, Martín-Merida I, Blanco-Kelly F, Avila-Fernandez A, Carreño E, Fernandez-San Jose P, Irigoyen C, Jimenez-Rolando B, Lopez-Grondona F, Mahillo I, Martin-Gutierrez MP, Minguez P, Perea-Romero I, Del Pozo-Valero M, Riveiro-Alvarez R, Rodilla C, Rodriguez-Peña L, Sánchez-Barbero AI, Swafiri ST, Trujillo-Tiebas MJ, Zurita O, García-Sandoval B, Corton M, Ayuso C. PRPH2-Related Retinal Dystrophies: Mutational Spectrum in 103 Families from a Spanish Cohort. Int J Mol Sci 2024; 25:2913. [PMID: 38474159 PMCID: PMC10931554 DOI: 10.3390/ijms25052913] [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: 02/01/2024] [Revised: 02/26/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
PRPH2, one of the most frequently inherited retinal dystrophy (IRD)-causing genes, implies a high phenotypic variability. This study aims to analyze the PRPH2 mutational spectrum in one of the largest cohorts worldwide, and to describe novel pathogenic variants and genotype-phenotype correlations. A study of 220 patients from 103 families recruited from a database of 5000 families. A molecular diagnosis was performed using classical molecular approaches and next-generation sequencing. Common haplotypes were ascertained by analyzing single-nucleotide polymorphisms. We identified 56 variants, including 11 novel variants. Most of them were missense variants (64%) and were located in the D2-loop protein domain (77%). The most frequently occurring variants were p.Gly167Ser, p.Gly208Asp and p.Pro221_Cys222del. Haplotype analysis revealed a shared region in families carrying p.Leu41Pro or p.Pro221_Cys222del. Patients with retinitis pigmentosa presented an earlier disease onset. We describe the largest cohort of IRD families associated with PRPH2 from a single center. Most variants were located in the D2-loop domain, highlighting its importance in interacting with other proteins. Our work suggests a likely founder effect for the variants p.Leu41Pro and p.Pro221_Cys222del in our Spanish cohort. Phenotypes with a primary rod alteration presented more severe affectation. Finally, the high phenotypic variability in PRPH2 hinders the possibility of drawing genotype-phenotype correlations.
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Affiliation(s)
- Lidia Fernández-Caballero
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Inmaculada Martín-Merida
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Almudena Avila-Fernandez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ester Carreño
- Department of Ophthalmology, Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (E.C.); (B.J.-R.); (M.P.M.-G.); (B.G.-S.)
| | - Patricia Fernandez-San Jose
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Genetics, Ramón y Cajal University Hospital, 28034 Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Cristina Irigoyen
- Ophthalmology Service, Donostia University Hospital, 20014 Donostia-San Sebastián, Spain
| | - Belen Jimenez-Rolando
- Department of Ophthalmology, Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (E.C.); (B.J.-R.); (M.P.M.-G.); (B.G.-S.)
| | - Fermina Lopez-Grondona
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ignacio Mahillo
- Department of Statistics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain;
| | - María Pilar Martin-Gutierrez
- Department of Ophthalmology, Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (E.C.); (B.J.-R.); (M.P.M.-G.); (B.G.-S.)
| | - Pablo Minguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Irene Perea-Romero
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Marta Del Pozo-Valero
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Rosa Riveiro-Alvarez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Cristina Rodilla
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Lidya Rodriguez-Peña
- Sección de Genética Medica, Servicio de Pediatría, HCU Virgen de la Arrixaca, 30120 Murcia, Spain
| | - Ana Isabel Sánchez-Barbero
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Saoud T. Swafiri
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - María José Trujillo-Tiebas
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Olga Zurita
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Blanca García-Sandoval
- Department of Ophthalmology, Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (E.C.); (B.J.-R.); (M.P.M.-G.); (B.G.-S.)
| | - Marta Corton
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
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Esteve-Garcia A, Cobos E, Sau C, Padró-Miquel A, Català-Mora J, Barberán-Martínez P, Millán JM, García-García G, Aguilera C. Deciphering complexity: TULP1 variants linked to an atypical retinal dystrophy phenotype. Front Genet 2024; 15:1352063. [PMID: 38450199 PMCID: PMC10915255 DOI: 10.3389/fgene.2024.1352063] [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: 12/07/2023] [Accepted: 01/29/2024] [Indexed: 03/08/2024] Open
Abstract
Introduction: TULP1 exemplifies the remarkable clinical and genetic heterogeneity observed in inherited retinal dystrophies. Our research describes the clinical and molecular characteristics of a patient manifesting an atypical retinal dystrophy pattern, marked by the identification of both a previously unreported and a rarely encountered TULP1 variant. Methods: Whole-exome sequencing was performed to identify potential causative variants. The pathogenicity of the identified TULP1 variants was evaluated through in silico predictors and a minigene splice assay, specifically designed to assess the effect of the unreported TULP1 variant. Results: We identified two TULP1 gene variants in a patient exhibiting unusual and symmetrical alterations in both retinas, characterized by an increase in autofluorescence along the distribution of retinal vessels. These variants included a known rare missense variant, c.1376T>C, and a novel splice site variant, c.822G>T. For the latter variant (c.822G>T), we conducted a minigene splice assay that demonstrated the incorporation of a premature stop codon. This finding suggests a likely activation of the nonsense-mediated mRNA decay mechanism, ultimately resulting in the absence of protein production from this allele. Segregation analysis confirmed that these variants were in trans. Discussion: Our data support that individuals with biallelic TULP1 variants may present with a unique pattern of macular degeneration and periarteriolar vascular pigmentation. This study highlights the importance of further clinical and molecular characterization of TULP1 variants to elucidate genotype-phenotype correlations in the context of inherited retinal dystrophies.
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Affiliation(s)
- Anna Esteve-Garcia
- Department of Clinical Genetics, Bellvitge University Hospital, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Estefania Cobos
- Department of Ophthalmology, Bellvitge University Hospital, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Cristina Sau
- Department of Clinical Genetics, Bellvitge University Hospital, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ariadna Padró-Miquel
- Genetics Laboratory, Bellvitge University Hospital, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Jaume Català-Mora
- Department of Ophthalmology, SJD Barcelona Children’s Hospital, Barcelona, Spain
| | - Pilar Barberán-Martínez
- Molecular, Cellular, and Genomic Biomedicine Group, Valencia, Spain
- Joint Unit CIPF-IIS La Fe Molecular, Cellular and Genomic Biomedicine, Valencia, Spain
| | - José M. Millán
- Molecular, Cellular, and Genomic Biomedicine Group, Valencia, Spain
- Joint Unit CIPF-IIS La Fe Molecular, Cellular and Genomic Biomedicine, Valencia, Spain
- Center for Rare Diseases (CIBERER), Madrid, Spain
- University and Polytechnic La Fe Hospital of Valencia, Valencia, Spain
| | - Gema García-García
- Molecular, Cellular, and Genomic Biomedicine Group, Valencia, Spain
- Joint Unit CIPF-IIS La Fe Molecular, Cellular and Genomic Biomedicine, Valencia, Spain
- Center for Rare Diseases (CIBERER), Madrid, Spain
| | - Cinthia Aguilera
- Genetics Laboratory, Bellvitge University Hospital, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
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Pantrangi M, Rath J, Kaetterhenry N, Branham K, Talsness D, Weber JL. Clinical sequencing of the retinitis pigmentosa gene RPGR in over 1,000 cases of vision loss. Mol Vis 2024; 30:49-57. [PMID: 38586605 PMCID: PMC10994678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 02/17/2024] [Indexed: 04/09/2024] Open
Abstract
RPGR pathogenic variants are the major cause of X-linked retinitis pigmentosa. Here, we report the results from 1,033 clinical DNA tests that included sequencing of RPGR. A total of 184 RPGR variants were identified: 78 pathogenic or likely pathogenic, 14 uncertain, and 92 likely benign or benign. Among the pathogenic and likely pathogenic variants, 23 were novel, and most were frameshift or nonsense mutations (87%) and enriched (67%) in RPGR exon 15 (ORF15). Identical pathogenic variants found in different families were largely on different haplotype backgrounds, indicating relatively frequent, recurrent RPGR mutations. None of the 16 mother/affected son pairs showed de novo mutations; all 16 mothers were heterozygous for the pathogenic variant. These last two observations support the occurrence of most RPGR mutations in the male germline.
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Affiliation(s)
- Madhulatha Pantrangi
- PreventionGenetics, part of Exact Sciences, Marshfield, WI
- Weill Cornell Medicine, Department of Pathology and Laboratory Medicine, New York, NY
| | - Julie Rath
- PreventionGenetics, part of Exact Sciences, Marshfield, WI
| | | | - Kari Branham
- University of Michigan, Kellogg Eye Center, Department of Ophthalmology and Visual Sciences, Ann Arbor, MI
| | - Dana Talsness
- PreventionGenetics, part of Exact Sciences, Marshfield, WI
| | - James L Weber
- PreventionGenetics, part of Exact Sciences, Marshfield, WI
- University of Wisconsin, School of Medicine and Public Health, Department of Pediatrics, Madison, WI
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Munir A, Afsar S, Rehman AU. A systematic review of inherited retinal dystrophies in Pakistan: updates from 1999 to April 2023. BMC Ophthalmol 2024; 24:55. [PMID: 38317096 PMCID: PMC10840256 DOI: 10.1186/s12886-024-03319-7] [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: 06/01/2023] [Accepted: 01/19/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Inherited retinal degenerations (IRDs) are a group of rare genetic conditions affecting retina of the eye that range in prevalence from 1 in 2000 to 1 in 4000 people globally. This review is based on a retrospective analysis of research articles reporting IRDs associated genetic findings in Pakistani families between 1999 and April 2023. METHODS Articles were retrieved through survey of online sources, notably, PubMed, Google Scholar, and Web of Science. Following a stringent selection criterion, a total of 126 research articles and conference abstracts were considered. All reported variants were cross-checked and validated for their correct genomic nomenclature using different online resources/databases, and their pathogenicity scores were explained as per ACMG guidelines. RESULTS A total of 277 unique sequence variants in 87 distinct genes, previously known to cause IRDs, were uncovered. In around 70% cases, parents of the index patient were consanguineously married, and approximately 88.81% of the detected variants were found in a homozygous state. Overall, more than 95% of the IRDs cases were recessively inherited. Missense variants were predominant (41.88%), followed by Indels/frameshift (26.35%), nonsense (19.13%), splice site (12.27%) and synonymous change (0.36%). Non-syndromic IRDs were significantly higher than syndromic IRDs (77.32% vs. 22.68%). Retinitis pigmentosa (RP) was the most frequently observed IRD followed by Leber's congenital amaurosis (LCA). Altogether, mutations in PDE6A gene was the leading cause of IRDs in Pakistani families followed by mutations in TULP1 gene. CONCLUSION In summary, Pakistani families are notable in expressing recessively inherited monogenic disorders including IRDs likely due to the highest prevalence of consanguinity in the country that leads to expression of rare pathogenic variants in homozygous state.
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Affiliation(s)
- Asad Munir
- Department of Zoology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, 21300, Khyber Pakhtunkhwa, Pakistan
| | - Salma Afsar
- Department of Zoology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, 21300, Khyber Pakhtunkhwa, Pakistan
| | - Atta Ur Rehman
- Department of Zoology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, 21300, Khyber Pakhtunkhwa, Pakistan.
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Hanany M, Shalom S, Ben-Yosef T, Sharon D. Comparison of Worldwide Disease Prevalence and Genetic Prevalence of Inherited Retinal Diseases and Variant Interpretation Considerations. Cold Spring Harb Perspect Med 2024; 14:a041277. [PMID: 37460155 PMCID: PMC10835612 DOI: 10.1101/cshperspect.a041277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
One of the considerations in planning the development of novel therapeutic modalities is disease prevalence that is usually defined by studying large national/regional populations. Such studies are rare and might suffer from inaccuracies and challenging clinical characterization in heterogeneous diseases, such as inherited retinal diseases (IRDs). Here we collected reported disease prevalence information on various IRDs in different populations. The most common IRD, retinitis pigmentosa, has an average disease prevalence of ∼1:4500 individuals, Stargardt disease ∼1:17,000, Usher syndrome ∼1:25,000, Leber congenital amaurosis ∼1:42,000, and all IRDs ∼1:3450. We compared these values to genetic prevalence (GP) calculated based on allele frequency of autosomal-recessive IRD mutations. Although most values did correlate, some differences were observed that can be explained by discordant, presumably null mutations that are likely to be either nonpathogenic or hypomorphic. Our analysis highlights the importance of performing additional disease prevalence studies and to couple them with population-dependent allele frequency data.
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Affiliation(s)
- Mor Hanany
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120001, Israel
| | - Sapir Shalom
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120001, Israel
- Department of Military Medicine and "Tzameret," Faculty of Medicine, Hebrew University of Jerusalem and Medical Corps, Israel Defense Forces, Jerusalem 9112102, Israel
| | - Tamar Ben-Yosef
- Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120001, Israel
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20
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Dueñas Rey A, Del Pozo Valero M, Bouckaert M, Wood KA, Van den Broeck F, Daich Varela M, Thomas HB, Van Heetvelde M, De Bruyne M, Van de Sompele S, Bauwens M, Lenaerts H, Mahieu Q, Josifova D, Rivolta C, O'Keefe RT, Ellingford J, Webster AR, Arno G, Ayuso C, De Zaeytijd J, Leroy BP, De Baere E, Coppieters F. Combining a prioritization strategy and functional studies nominates 5'UTR variants underlying inherited retinal disease. Genome Med 2024; 16:7. [PMID: 38184646 PMCID: PMC10771650 DOI: 10.1186/s13073-023-01277-1] [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: 06/16/2023] [Accepted: 12/15/2023] [Indexed: 01/08/2024] Open
Abstract
BACKGROUND 5' untranslated regions (5'UTRs) are essential modulators of protein translation. Predicting the impact of 5'UTR variants is challenging and rarely performed in routine diagnostics. Here, we present a combined approach of a comprehensive prioritization strategy and functional assays to evaluate 5'UTR variation in two large cohorts of patients with inherited retinal diseases (IRDs). METHODS We performed an isoform-level re-analysis of retinal RNA-seq data to identify the protein-coding transcripts of 378 IRD genes with highest expression in retina. We evaluated the coverage of their 5'UTRs by different whole exome sequencing (WES) kits. The selected 5'UTRs were analyzed in whole genome sequencing (WGS) and WES data from IRD sub-cohorts from the 100,000 Genomes Project (n = 2397 WGS) and an in-house database (n = 1682 WES), respectively. Identified variants were annotated for 5'UTR-relevant features and classified into seven categories based on their predicted functional consequence. We developed a variant prioritization strategy by integrating population frequency, specific criteria for each category, and family and phenotypic data. A selection of candidate variants underwent functional validation using diverse approaches. RESULTS Isoform-level re-quantification of retinal gene expression revealed 76 IRD genes with a non-canonical retina-enriched isoform, of which 20 display a fully distinct 5'UTR compared to that of their canonical isoform. Depending on the probe design, 3-20% of IRD genes have 5'UTRs fully captured by WES. After analyzing these regions in both cohorts, we prioritized 11 (likely) pathogenic variants in 10 genes (ARL3, MERTK, NDP, NMNAT1, NPHP4, PAX6, PRPF31, PRPF4, RDH12, RD3), of which 7 were novel. Functional analyses further supported the pathogenicity of three variants. Mis-splicing was demonstrated for the PRPF31:c.-9+1G>T variant. The MERTK:c.-125G>A variant, overlapping a transcriptional start site, was shown to significantly reduce both luciferase mRNA levels and activity. The RDH12:c.-123C>T variant was found in cis with the hypomorphic RDH12:c.701G>A (p.Arg234His) variant in 11 patients. This 5'UTR variant, predicted to introduce an upstream open reading frame, was shown to result in reduced RDH12 protein but unaltered mRNA levels. CONCLUSIONS This study demonstrates the importance of 5'UTR variants implicated in IRDs and provides a systematic approach for 5'UTR annotation and validation that is applicable to other inherited diseases.
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Affiliation(s)
- Alfredo Dueñas Rey
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Marta Del Pozo Valero
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Manon Bouckaert
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Katherine A Wood
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Filip Van den Broeck
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Malena Daich Varela
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Huw B Thomas
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Mattias Van Heetvelde
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Marieke De Bruyne
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Stijn Van de Sompele
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Miriam Bauwens
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Hanne Lenaerts
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Quinten Mahieu
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | | | - Carlo Rivolta
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Raymond T O'Keefe
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Jamie Ellingford
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
- Genomics England, London, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Andrew R Webster
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Gavin Arno
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Bart P Leroy
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
- Division of Ophthalmology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elfride De Baere
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Frauke Coppieters
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium.
- Department of Pharmaceutics, Ghent University, Ghent, Belgium.
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21
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Wong WM, Tham YC, Simunovic MP, Chen FK, Luu CD, Chen H, Jin ZB, Shen RJ, Li S, Sui R, Zhao C, Yang L, Bhende M, Raman R, Sen P, Ghosh A, Poornachandra B, Sasongko MB, Arianti A, Chia V, Mangunsong CO, Manurung F, Fujinami K, Ikeda H, Woo SJ, Kim SJ, Mohd Khialdin S, Othman O, Bastion MLC, Kamalden AT, Lott PWP, Fong K, Shunmugam M, Lim A, Thapa R, Pradhan E, Rajkarnikar SP, Adhikari S, Ibañez BMBI, Koh A, Chan CMM, Fenner BJ, Tan TE, Laude A, Ngo WK, Holder GE, Su X, Chen TC, Wang NK, Kang EYC, Huang CH, Surawatsatien N, Pisuchpen P, Sujirakul T, Kumaramanickavel G, Singh M, Leroy B, Michaelides M, Cheng CY, Chen LJ, Chan HW. Rationale and protocol paper for the Asia Pacific Network for inherited eye diseases. Asia Pac J Ophthalmol (Phila) 2024; 13:100030. [PMID: 38233300 DOI: 10.1016/j.apjo.2023.100030] [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: 09/29/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 01/19/2024] Open
Abstract
PURPOSE There are major gaps in our knowledge of hereditary ocular conditions in the Asia-Pacific population, which comprises approximately 60% of the world's population. Therefore, a concerted regional effort is urgently needed to close this critical knowledge gap and apply precision medicine technology to improve the quality of lives of these patients in the Asia-Pacific region. DESIGN Multi-national, multi-center collaborative network. METHODS The Research Standing Committee of the Asia-Pacific Academy of Ophthalmology and the Asia-Pacific Society of Eye Genetics fostered this research collaboration, which brings together renowned institutions and experts for inherited eye diseases in the Asia-Pacific region. The immediate priority of the network will be inherited retinal diseases (IRDs), where there is a lack of detailed characterization of these conditions and in the number of established registries. RESULTS The network comprises 55 members from 35 centers, spanning 12 countries and regions, including Australia, China, India, Indonesia, Japan, South Korea, Malaysia, Nepal, Philippines, Singapore, Taiwan, and Thailand. The steering committee comprises ophthalmologists with experience in consortia for eye diseases in the Asia-Pacific region, leading ophthalmologists and vision scientists in the field of IRDs internationally, and ophthalmic geneticists. CONCLUSIONS The Asia Pacific Inherited Eye Disease (APIED) network aims to (1) improve genotyping capabilities and expertise to increase early and accurate genetic diagnosis of IRDs, (2) harmonise deep phenotyping practices and utilization of ontological terms, and (3) establish high-quality, multi-user, federated disease registries that will facilitate patient care, genetic counseling, and research of IRDs regionally and internationally.
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Affiliation(s)
- Wendy M Wong
- Centre for Innovation & Precision Eye Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Ophthalmology, National University Hospital, National University Health System, Singapore
| | - Yih Chung Tham
- Centre for Innovation & Precision Eye Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Matthew P Simunovic
- Save Sight Institute, The University of Sydney, Sydney, Australia; Retinal Unit, Sydney Eye Hospital, Sydney, Australia
| | - Fred Kuanfu Chen
- Centre for Ophthalmology and Visual Science (Lions Eye Institute), The University of Western Australia, Nedlands, Western Australia, Australia; Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Chi D Luu
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, Victoria, Australia
| | - Haoyu Chen
- Joint Shantou International Eye Center, Shantou University & The Chinese University of Hong Kong, Shantou, China
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China
| | - Ren-Juan Shen
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China
| | - Shiying Li
- Department of Ophthalmology in Xiang'an Hospital of Xiamen University and Medical Center of Xiamen University, School of Medicine in Xiamen University, Eye Institute of Xiamen University, Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Fujian Engineering and Research Center of Eye Regenerative Medicine, Xiamen, Fujian, China
| | - Ruifang Sui
- Department of Ophthalmology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 1, Shuai Fu Yuan, Beijing, China
| | - Chen Zhao
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China
| | - Liping Yang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China; Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Muna Bhende
- Shri Bhagwan Mahavir Vitreoretinal services, Medical Research Foundation, Sankara Nethralaya, Chennai, India
| | - Rajiv Raman
- Shri Bhagwan Mahavir Vitreoretinal services, Medical Research Foundation, Sankara Nethralaya, Chennai, India
| | - Parveen Sen
- Shri Bhagwan Mahavir Vitreoretinal services, Medical Research Foundation, Sankara Nethralaya, Chennai, India; Dr Agarwal Eye Hospital, Chandigarh, India
| | - Arkasubhra Ghosh
- GROW Lab, Narayana Nethralaya Foundation, Bangalore, Karnataka, India
| | - B Poornachandra
- Vitreo-Retina Services, Narayana Nethralaya, Bangalore, India
| | - Muhammad Bayu Sasongko
- Department of Ophthalmology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada - Sardjito Eye Center, Dr. Sardjito General Hospital, Yogyakarta, Indonesia
| | - Alia Arianti
- JEC Eye Hospitals and Clinics, Jakarta, Indonesia
| | - Valen Chia
- JEC Eye Hospitals and Clinics, Jakarta, Indonesia
| | | | | | - Kaoru Fujinami
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, NHO Tokyo Medical Center, Tokyo, Japan
| | - Hanako Ikeda
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto, Japan
| | - Se Joon Woo
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Sang Jin Kim
- Department of Ophthalmology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Safinaz Mohd Khialdin
- Department of Ophthalmology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Center, Kuala Lumpur, Malaysia; UKM Specialist Children's Hospital, Kuala Lumpur, Malaysia
| | - Othmaliza Othman
- Department of Ophthalmology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Center, Kuala Lumpur, Malaysia
| | - Mae-Lynn Catherine Bastion
- Department of Ophthalmology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Center, Kuala Lumpur, Malaysia; Hospital Canselor Tuanku Muhriz, Jalan Yaacob Latif, Bandar Tun Razak, Kuala Lumpur, Malaysia
| | - Ain Tengku Kamalden
- UM Eye Research Centre, Department of Ophthalmology, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Pooi Wah Penny Lott
- UM Eye Research Centre, Department of Ophthalmology, Universiti Malaya, Kuala Lumpur, Malaysia
| | | | | | - Amelia Lim
- Ophthalmology, Penang Gleneagles, Malaysia
| | - Raba Thapa
- Tilganga Institute of Ophthalmology, Kathmandu, Nepal
| | - Eli Pradhan
- Tilganga Institute of Ophthalmology, Kathmandu, Nepal
| | | | | | - B Manuel Benjamin Iv Ibañez
- Makati Medical Center, Makati City, Philippines; DOH Eye Center, East Avenue Medical Center, Quezon City, Philippines
| | - Adrian Koh
- Eye & Retina Surgeons, Camden Medical Centre, Singapore, Singapore
| | - Choi Mun M Chan
- Singapore National Eye Centre, Singapore Eye Research Institute, Singapore; Ophthalmology & Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Medical School, Singapore
| | - Beau J Fenner
- Singapore National Eye Centre, Singapore Eye Research Institute, Singapore; Ophthalmology & Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Medical School, Singapore
| | - Tien-En Tan
- Singapore National Eye Centre, Singapore Eye Research Institute, Singapore; Ophthalmology & Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Medical School, Singapore
| | - Augustinus Laude
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Wei Kiong Ngo
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore
| | - Graham E Holder
- Centre for Innovation & Precision Eye Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Ophthalmology, National University Hospital, National University Health System, Singapore
| | - Xinyi Su
- Centre for Innovation & Precision Eye Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Ophthalmology, National University Hospital, National University Health System, Singapore
| | - Ta-Ching Chen
- Department of Ophthalmology, National Taiwan University Hospital, Taipei, Taiwan; Center of Frontier Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Nan-Kai Wang
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University, New York, NY, USA; Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Eugene Yu-Chuan Kang
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan; Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chu-Hsuan Huang
- Department of Ophthalmology, Cathay General Hospital, Taipei, Taiwan
| | - Nuntachai Surawatsatien
- Center of Excellence in Retina, Department of Ophthalmology, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Phattrawan Pisuchpen
- Department of Ophthalmology and Division of Academic Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Tharikarn Sujirakul
- Department of Ophthalmology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | | | - Mandeep Singh
- Wilmer Eye Institute, Johns Hopkins Hospital, Baltimore, MD 21287, USA
| | - Bart Leroy
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
| | - Michel Michaelides
- Moorfields Eye Hospital, London, United Kingdom and UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Ching-Yu Cheng
- Centre for Innovation & Precision Eye Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Singapore National Eye Centre, Singapore Eye Research Institute, Singapore
| | - Li Jia Chen
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Hwei Wuen Chan
- Centre for Innovation & Precision Eye Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Ophthalmology, National University Hospital, National University Health System, Singapore; Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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22
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Kherani IZ, Andrews C, Pereira JA, Moniz LS, Qian CX. Impact of inherited retinal diseases on Canadian patients and families: a mixed-methods study. CANADIAN JOURNAL OF OPHTHALMOLOGY 2023; 58:532-538. [PMID: 35905942 DOI: 10.1016/j.jcjo.2022.06.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 04/05/2022] [Accepted: 06/28/2022] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To understand the physical, psychosocial, and practical challenges faced by Canadian patients with inherited retinal diseases (IRDs) and their families. DESIGN Mixed methods. PARTICIPANTS A total of 408 Canadians living with or caring for someone with an IRD (mean age = 51.4 ± 16.7 years) completed an online survey. Twenty cohort respondents participated in additional telephone interviews. METHODS The online survey was comprised of questions concerning demographics, self-reported vision, genetic testing, information preferences, health care experiences, treatment goals, and disease impact on daily life. Recruitment occurred through Fighting Blindness Canada's community database. Survey dissemination also occurred via social media and not-for-profit stakeholder outreach. Subsequent to survey completion, a subset of respondents participated in semistructured telephone interviews to further elucidate illness experience. RESULTS Respondents identified having 1 of more than 14 IRDs, with 72% specifying retinitis pigmentosa. Sixty-eight percent reported being legally blind, and more than 85% self-reported moderate to low vision or worse. IRDs impacted daily functioning, with 53% of respondents indicating that they affected employment or education. Psychological challenges were evident, with more than 70% worried about coping with daily life and more than 60% indicating fear and stress. Qualitative data described hopelessness around suitable work, loss of independence, and challenges with social interaction. Sixty-five percent reported a negative impact on family life. Many had not accessed social support services because of a lack of perceived need, awareness, or availability. CONCLUSION Canadian patients with IRDs report moderate to severe visual impairment, and both patients and their families describe an impact on psychosocial well-being and functioning during daily activities. Vision rehabilitation with a psychosocial approach is necessary, alongside facilitating access to emerging treatments.
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Affiliation(s)
- Imaan Z Kherani
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON
| | - Chad Andrews
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON
| | | | | | - Cynthia X Qian
- Department of Ophthalmology, Centre Universitaire d'Ophtalmologie (CUO), Hôpital Maisonneuve-Rosemont, University of Montreal, Montréal, QC..
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23
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Jedlickova J, Vajter M, Barta T, Black GCM, Perveen R, Mares J, Fichtl M, Kousal B, Dudakova L, Liskova P. MIR204 n.37C>T variant as a cause of chorioretinal dystrophy variably associated with iris coloboma, early-onset cataracts and congenital glaucoma. Clin Genet 2023; 104:418-426. [PMID: 37321975 DOI: 10.1111/cge.14391] [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: 03/29/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023]
Abstract
Four members of a three-generation Czech family with early-onset chorioretinal dystrophy were shown to be heterozygous carriers of the n.37C>T in MIR204. The identification of this previously reported pathogenic variant confirms the existence of a distinct clinical entity caused by a sequence change in MIR204. Chorioretinal dystrophy was variably associated with iris coloboma, congenital glaucoma, and premature cataracts extending the phenotypic range of the condition. In silico analysis of the n.37C>T variant revealed 713 novel targets. Additionally, four family members were shown to be affected by albinism resulting from biallelic pathogenic OCA2 variants. Haplotype analysis excluded relatedness with the original family reported to harbour the n.37C>T variant in MIR204. Identification of a second independent family confirms the existence of a distinct MIR204-associated clinical entity and suggests that the phenotype may also involve congenital glaucoma.
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Affiliation(s)
- Jana Jedlickova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Marie Vajter
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Tomas Barta
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Graeme C M Black
- Division of Evolution, and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Rahat Perveen
- Division of Evolution, and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Jan Mares
- Department of Ophthalmology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Marek Fichtl
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Bohdan Kousal
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Lubica Dudakova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Petra Liskova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
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24
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Rodilla C, Martín-Merida I, Blanco-Kelly F, Trujillo-Tiebas MJ, Avila-Fernandez A, Riveiro-Alvarez R, Del Pozo-Valero M, Perea-Romero I, Swafiri ST, Zurita O, Villaverde C, López MÁ, Romero R, Iancu IF, Núñez-Moreno G, Jiménez-Rolando B, Martin-Gutierrez MP, Carreño E, Minguez P, García-Sandoval B, Ayuso C, Corton M. Comprehensive Genotyping and Phenotyping Analysis of GUCY2D-Associated Rod- and Cone-Dominated Dystrophies. Am J Ophthalmol 2023; 254:87-103. [PMID: 37327959 DOI: 10.1016/j.ajo.2023.05.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/03/2023] [Accepted: 05/15/2023] [Indexed: 06/18/2023]
Abstract
PURPOSE To describe the genetic and clinical spectrum of GUCY2D-associated retinopathies and to accurately establish their prevalence in a large cohort of patients. DESIGN Retrospective case series. METHODS Institutional study of 47 patients from 27 unrelated families with retinal dystrophies carrying disease-causing GUCY2D variants from the Fundación Jiménez Díaz hospital dataset of 8000 patients. Patients underwent ophthalmological examination and molecular testing by Sanger or exome sequencing approaches. Statistical and principal component analyses were performed to determine genotype-phenotype correlations. RESULTS Four clinically different associated phenotypes were identified: 66.7% of families with cone/cone-rod dystrophy, 22.2% with Leber congenital amaurosis, 7.4% with early-onset retinitis pigmentosa, and 3.7% with congenital night blindness. Twenty-three disease-causing GUCY2D variants were identified, including 6 novel variants. Biallelic variants accounted for 28% of patients, whereas most carried dominant alleles associated with cone/cone-rod dystrophy. The disease onset had statistically significant differences according to the functional variant effect. Patients carrying GUCY2D variants were projected into 3 subgroups by allelic combination, disease onset, and presence of nystagmus or night blindness. In contrast to patients with the most severe phenotype of Leber congenital amaurosis, 7 patients with biallelic GUCY2D had a later and milder rod form with night blindness in infancy as the first symptom. CONCLUSIONS This study represents the largest GUCY2D cohort in which 4 distinctly different phenotypes were identified, including rare intermediate presentations of rod-dominated retinopathies. We established that GUCY2D is linked to about 1% of approximately 3000 molecularly characterized families of our cohort. All of these findings are critical for defining cohorts for inclusion in future clinical trials.
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Affiliation(s)
- Cristina Rodilla
- From the Department of Genetics and Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I., G.N.-M., P.M., C.A., M.C.; Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I, G.N.-M., P.M., C.A., M.C.)
| | - Inmaculada Martín-Merida
- From the Department of Genetics and Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I., G.N.-M., P.M., C.A., M.C.; Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I, G.N.-M., P.M., C.A., M.C.)
| | - Fiona Blanco-Kelly
- From the Department of Genetics and Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I., G.N.-M., P.M., C.A., M.C.; Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I, G.N.-M., P.M., C.A., M.C.)
| | - María José Trujillo-Tiebas
- From the Department of Genetics and Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I., G.N.-M., P.M., C.A., M.C.; Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I, G.N.-M., P.M., C.A., M.C.)
| | - Almudena Avila-Fernandez
- From the Department of Genetics and Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I., G.N.-M., P.M., C.A., M.C.; Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I, G.N.-M., P.M., C.A., M.C.)
| | - Rosa Riveiro-Alvarez
- From the Department of Genetics and Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I., G.N.-M., P.M., C.A., M.C.; Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I, G.N.-M., P.M., C.A., M.C.)
| | - Marta Del Pozo-Valero
- From the Department of Genetics and Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I., G.N.-M., P.M., C.A., M.C.; Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I, G.N.-M., P.M., C.A., M.C.)
| | - Irene Perea-Romero
- From the Department of Genetics and Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I., G.N.-M., P.M., C.A., M.C.; Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I, G.N.-M., P.M., C.A., M.C.)
| | - Saoud Tahsin Swafiri
- From the Department of Genetics and Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I., G.N.-M., P.M., C.A., M.C.; Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I, G.N.-M., P.M., C.A., M.C.)
| | - Olga Zurita
- From the Department of Genetics and Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I., G.N.-M., P.M., C.A., M.C.; Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I, G.N.-M., P.M., C.A., M.C.)
| | - Cristina Villaverde
- From the Department of Genetics and Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I., G.N.-M., P.M., C.A., M.C.; Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I, G.N.-M., P.M., C.A., M.C.)
| | - Miguel Ángel López
- From the Department of Genetics and Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I., G.N.-M., P.M., C.A., M.C.; Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I, G.N.-M., P.M., C.A., M.C.)
| | - Raquel Romero
- From the Department of Genetics and Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I., G.N.-M., P.M., C.A., M.C.; Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I, G.N.-M., P.M., C.A., M.C.); Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain (R.R., I.F.I., G.N.-M., P.M.)
| | - Ionut Florin Iancu
- From the Department of Genetics and Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I., G.N.-M., P.M., C.A., M.C.; Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I, G.N.-M., P.M., C.A., M.C.); Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain (R.R., I.F.I., G.N.-M., P.M.)
| | - Gonzalo Núñez-Moreno
- From the Department of Genetics and Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I., G.N.-M., P.M., C.A., M.C.; Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I, G.N.-M., P.M., C.A., M.C.); Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain (R.R., I.F.I., G.N.-M., P.M.)
| | - Belén Jiménez-Rolando
- Department of Ophthalmology, Fundación Jiménez Díaz University Hospital, Madrid, Spain (B.J.-R., M.P.M.-G., E.C., B.G.-S.)
| | - María Pilar Martin-Gutierrez
- Department of Ophthalmology, Fundación Jiménez Díaz University Hospital, Madrid, Spain (B.J.-R., M.P.M.-G., E.C., B.G.-S.)
| | - Ester Carreño
- Department of Ophthalmology, Fundación Jiménez Díaz University Hospital, Madrid, Spain (B.J.-R., M.P.M.-G., E.C., B.G.-S.)
| | - Pablo Minguez
- From the Department of Genetics and Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I., G.N.-M., P.M., C.A., M.C.; Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I, G.N.-M., P.M., C.A., M.C.); Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain (R.R., I.F.I., G.N.-M., P.M.)
| | - Blanca García-Sandoval
- Department of Ophthalmology, Fundación Jiménez Díaz University Hospital, Madrid, Spain (B.J.-R., M.P.M.-G., E.C., B.G.-S.)
| | - Carmen Ayuso
- From the Department of Genetics and Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I., G.N.-M., P.M., C.A., M.C.; Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I, G.N.-M., P.M., C.A., M.C.).
| | - Marta Corton
- From the Department of Genetics and Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I., G.N.-M., P.M., C.A., M.C.; Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain (C.R., I.M.-M., F.B.-K., M.J.T.-T., A.A.-F., R.R.-A., M.d.P.V., I.P.-R., S.T.S., O.Z., C.V., M.A.L., R.R., I.F.I, G.N.-M., P.M., C.A., M.C.).
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Rodríguez-Hidalgo M, de Bruijn SE, Corradi Z, Rodenburg K, Lara-López A, Valverde-Megías A, Ávila-Fernández A, Fernandez-Caballero L, Del Pozo-Valero M, Corominas J, Gilissen C, Irigoyen C, Cremers FPM, Ayuso C, Ruiz-Ederra J, Roosing S. ABCA4 c.6480-35A>G, a novel branchpoint variant associated with Stargardt disease. Front Genet 2023; 14:1234032. [PMID: 37779911 PMCID: PMC10539688 DOI: 10.3389/fgene.2023.1234032] [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: 06/03/2023] [Accepted: 08/15/2023] [Indexed: 10/03/2023] Open
Abstract
Introduction: Inherited retinal dystrophies (IRDs) can be caused by variants in more than 280 genes. The ATP-binding cassette transporter type A4 (ABCA4) gene is one of these genes and has been linked to Stargardt disease type 1 (STGD1), fundus flavimaculatus, cone-rod dystrophy (CRD), and pan-retinal CRD. Approximately 25% of the reported ABCA4 variants affect RNA splicing. In most cases, it is necessary to perform a functional assay to determine the effect of these variants. Methods: Whole genome sequencing (WGS) was performed in one Spanish proband with Stargardt disease. The putative pathogenicity of c.6480-35A>G on splicing was investigated both in silico and in vitro. The in silico approach was based on the deep-learning tool SpliceAI. For the in vitro approach we used a midigene splice assay in HEK293T cells, based on a previously established wild-type midigene (BA29) containing ABCA4 exons 46 to 48. Results: Through the analysis of WGS data, we identified two candidate variants in ABCA4 in one proband: a previously described deletion, c.699_768+342del (p.(Gln234Phefs*5)), and a novel branchpoint variant, c.6480-35A>G. Segregation analysis confirmed that the variants were in trans. For the branchpoint variant, SpliceAI predicted an acceptor gain with a high score (0.47) at position c.6480-47. A midigene splice assay in HEK293T cells revealed the inclusion of the last 47 nucleotides of intron 47 creating a premature stop codon and allowed to categorize the variant as moderately severe. Subsequent analysis revealed the presence of this variant as a second allele besides c.1958G>A p.(Arg653His) in an additional Spanish proband in a large cohort of IRD cases. Conclusion: A splice-altering effect of the branchpoint variant, confirmed by the midigene splice assay, along with the identification of this variant in a second unrelated individual affected with STGD, provides sufficient evidence to classify the variant as likely pathogenic. In addition, this research highlights the importance of studying non-coding regions and performing functional assays to provide a conclusive molecular diagnosis.
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Affiliation(s)
- María Rodríguez-Hidalgo
- Department of Neuroscience, Biodonostia Health Research Institute, Donostia-San Sebastián, Spain
- Department of Genetic, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Suzanne E. de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Kim Rodenburg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | | | | | - Almudena Ávila-Fernández
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Lidia Fernandez-Caballero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Del Pozo-Valero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Jordi Corominas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Cristina Irigoyen
- Department of Neuroscience, Biodonostia Health Research Institute, Donostia-San Sebastián, Spain
- Ophthalmology Service, Donostia Universy Hospital, Donostia-San Sebastián, Spain
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Carmen Ayuso
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Ruiz-Ederra
- Department of Neuroscience, Biodonostia Health Research Institute, Donostia-San Sebastián, Spain
- Department of Ophthalmology, University of the Basque Country (UPV/EHU), San Sebastián, Spain
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
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Gocuk SA, Jolly JK, Edwards TL, Ayton LN. Female carriers of X-linked inherited retinal diseases - Genetics, diagnosis, and potential therapies. Prog Retin Eye Res 2023; 96:101190. [PMID: 37406879 DOI: 10.1016/j.preteyeres.2023.101190] [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: 03/09/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/07/2023]
Abstract
Inherited retinal diseases (IRDs) are a group of heterogeneous conditions that cause progressive vision loss, typically due to monogenic mutations. Female carriers of X-linked IRDs have a single copy of the disease-causing gene, and therefore, may exhibit variable clinical signs that vary from near normal retina to severe disease and vision loss. The relationships between individual genetic mutations and disease severity in X-linked carriers requires further study. This review summarises the current literature surrounding the spectrum of disease seen in female carriers of choroideremia and X-linked retinitis pigmentosa. Various classification systems are contrasted to accurately grade retinal disease. Furthermore, genetic mechanisms at the early embryonic stage are explored to potentially explain the variability of disease seen in female carriers. Future research in this area will provide insight into the association between genotype and retinal phenotypes of female carriers, which will guide in the management of these patients. This review acknowledges the importance of identifying which patients may be at high risk of developing severe symptoms, and therefore should be considered for emerging treatments, such as retinal gene therapy.
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Affiliation(s)
- Sena A Gocuk
- Department of Optometry and Vision Sciences, The University of Melbourne, Melbourne, Victoria, Australia; Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jasleen K Jolly
- Vision and Eye Research Institute, Anglia Ruskin University, Cambridge, UK
| | - Thomas L Edwards
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, The University of Melbourne, Melbourne, Victoria, Australia
| | - Lauren N Ayton
- Department of Optometry and Vision Sciences, The University of Melbourne, Melbourne, Victoria, Australia; Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia; Ophthalmology, Department of Surgery, The University of Melbourne, Melbourne, Victoria, Australia.
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Priglinger CS, Gerhardt MJ, Rudolph G, Priglinger SG, Michalakis S. [Gene therapy in ophthalmology]. DIE OPHTHALMOLOGIE 2023; 120:867-882. [PMID: 37418021 DOI: 10.1007/s00347-023-01883-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/25/2023] [Indexed: 07/08/2023]
Abstract
In 2017 the gene therapy medication voretigene neparvovec-rzyl was approved by the U.S. Food and Drug Administration (FDA) for retinal gene therapy of hereditary retinal dystrophies caused by mutations in the RPE65 gene. Voretigene neparvovec-rzyl is a gene augmentation therapy using an adeno-associated virus-based vector to express a healthy copy of the human RPE65 gene in the patient's retinal pigment epithelial (RPE) cells. The success of gene augmentation therapy in RPE65-linked retinal dystrophy encouraged research activities on the concept of gene supplementation to be extended to nongenetic diseases, such as age-related macular degeneration; however, it also showed that the principle of success cannot be easily extended to other retinal dystrophies. This review article presents the most commonly used principles and technologies of gene therapy and provides an overview of the current challenges and limitations. Furthermore, practice-relevant aspects of the indications and the treatment procedure are discussed. Particular attention is paid to the consideration of disease stages, especially with respect to patient's expectations and the evaluation of treatment success.
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Affiliation(s)
- Claudia S Priglinger
- Augenklinik, Ludwig-Maximilians-Universität München, Mathildenstr. 8, 80336, München, Deutschland.
| | - Maximilian J Gerhardt
- Augenklinik, Ludwig-Maximilians-Universität München, Mathildenstr. 8, 80336, München, Deutschland
| | - Günther Rudolph
- Augenklinik, Ludwig-Maximilians-Universität München, Mathildenstr. 8, 80336, München, Deutschland
| | - Siegfried G Priglinger
- Augenklinik, Ludwig-Maximilians-Universität München, Mathildenstr. 8, 80336, München, Deutschland
| | - Stylianos Michalakis
- Augenklinik, Ludwig-Maximilians-Universität München, Mathildenstr. 8, 80336, München, Deutschland
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Murro V, Banfi S, Testa F, Iarossi G, Falsini B, Sodi A, Signorini S, Iolascon A, Russo R, Mucciolo DP, Caputo R, Bacci GM, Bargiacchi S, Turco S, Fortini S, Simonelli F. A multidisciplinary approach to inherited retinal dystrophies from diagnosis to initial care: a narrative review with inputs from clinical practice. Orphanet J Rare Dis 2023; 18:223. [PMID: 37525225 PMCID: PMC10388566 DOI: 10.1186/s13023-023-02798-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 07/05/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND Non-syndromic inherited retinal dystrophies (IRDs) such as retinitis pigmentosa or Leber congenital amaurosis generally manifest between early childhood and late adolescence, imposing profound long-term impacts as a result of vision impairment or blindness. IRDs are highly heterogeneous, with often overlapping symptoms among different IRDs, and achieving a definite diagnosis is challenging. This narrative review provides a clinical overview of the non-syndromic generalized photoreceptor dystrophies, particularly retinitis pigmentosa and Leber congenital amaurosis. The clinical investigations and genetic testing needed to establish a diagnosis are outlined, and current management approaches are discussed, focusing on the importance of the involvement of an interdisciplinary team from diagnosis and initial care to long-term follow-up and support. RESULTS The effective management of IRDs requires a multidisciplinary, and ideally interdisciplinary, team of experts knowledgeable about IRDs, with experienced professionals from fields as diverse as ophthalmology, neuropsychiatry, psychology, neurology, genetics, orthoptics, developmental therapy, typhlology, occupational therapy, otolaryngology, and orientation and mobility specialties. Accurate clinical diagnosis encompasses a range of objective and subjective assessments as a prerequisite for the genetic testing essential in establishing an accurate diagnosis necessary for the effective management of IRDs, particularly in the era of gene therapies. Improvements in genome sequencing techniques, such as next-generation sequencing, have greatly facilitated the complex process of determining IRD-causing gene variants and establishing a molecular diagnosis. Genetic counseling is essential to help the individual and their family understand the condition, the potential risk for offspring, and the implications of a diagnosis on visual prognosis and treatment options. Psychological support for patients and caregivers is important at all stages of diagnosis, care, and rehabilitation and is an essential part of the multidisciplinary approach to managing IRDs. Effective communication throughout is essential, and the patient and caregivers' needs and expectations must be acknowledged and discussed. CONCLUSION As IRDs can present at an early age, clinicians need to be aware of the clinical signs suggesting visual impairment and follow up with multidisciplinary support for timely diagnoses to facilitate appropriate therapeutic or rehabilitation intervention to minimize vision loss.
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Affiliation(s)
- Vittoria Murro
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy
- Eye Clinic, Careggi Teaching Hospital, Florence, Italy
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, NA, Italy
- Medical Genetics, Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy.
| | - Giancarlo Iarossi
- Department of Ophthalmology, Bambino Gesù Children's Hospital, Rome, Italy
| | - Benedetto Falsini
- Ophthalmology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Andrea Sodi
- Eye Clinic, Careggi Teaching Hospital, Florence, Italy
| | - Sabrina Signorini
- Center of Child Neuro-Ophthalmology, IRCCS, Mondino Foundation, Pavia, Italy
| | - Achille Iolascon
- Medical Genetics Unit, Azienda Ospedaliera Universitaria Federico II, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
- CEINGE-Biotecnologie Avanzate, Naples, Italy
| | - Roberta Russo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
- CEINGE-Biotecnologie Avanzate, Naples, Italy
| | - Dario Pasquale Mucciolo
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy
- Ophthalmology Unit, San Jacopo Hospital, Pistoia, Italy
| | - Roberto Caputo
- Pediatric Ophthalmology Unit, A. Meyer Children's Hospital IRCCS, Florence, Italy
| | - Giacomo Maria Bacci
- Pediatric Ophthalmology Unit, A. Meyer Children's Hospital IRCCS, Florence, Italy
| | - Sara Bargiacchi
- Medical Genetics Unit, Ospedale Pediatrico Meyer, Florence, Italy
| | - Simona Turco
- National Centre of Services and Research for the Prevention of Blindness and Rehabilitation of the Visually Impaired, International Agency for the Prevention of Blindness-IAPB Italy Onlus, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Stefania Fortini
- National Centre of Services and Research for the Prevention of Blindness and Rehabilitation of the Visually Impaired, International Agency for the Prevention of Blindness-IAPB Italy Onlus, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
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Sather R, Ihinger J, Simmons M, Khundkar T, Lobo GP, Montezuma SR. Clinical Characteristics and Genetic Variants of a Large Cohort of Patients with Retinitis Pigmentosa Using Multimodal Imaging and Next Generation Sequencing. Int J Mol Sci 2023; 24:10895. [PMID: 37446072 DOI: 10.3390/ijms241310895] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
This retrospective study identifies patients with RP at the Inherited Retinal Disease Clinic at the University of Minnesota (UMN)/M Health System who had genetic testing via next generation sequencing. A database was curated to record history and examination, genetic findings, and ocular imaging. Causative pathogenic and likely pathogenic variants were recorded. Disease status was further characterized by ocular coherence tomography (OCT) and fundus autofluorescence (AF). Our study cohort included a total of 199 patients evaluated between 1 May 2015-5 August 2022. The cohort included 151 patients with non-syndromic RP and 48 with syndromic RP. Presenting symptoms included nyctalopia (85.4%) photosensitivity/hemeralopia (60.5%), and decreased color vision (55.8%). On average, 38.9% had visual acuity of worse than 20/80. Ellipsoid zone band width on OCT scan of less than 1500 μm was noted in 73.6%. Ninety-nine percent had fundus autofluorescence (AF) findings of a hypo- or hyper-fluorescent ring within the macula and/or peripheral hypo-AF. Of the 127 subjects who underwent genetic testing, a diagnostic pathogenic and/or likely pathogenic variant was identified in 67 (52.8%) patients-33.3% of syndromic RP and 66.6% of non-syndromic RP patients had a diagnostic gene variant identified. It was found that 23.6% of the cohort had negative genetic testing results or only variants of uncertain significance identified, which were deemed as non-diagnostic. We concluded that patients with RP often present with advanced disease. In our population, next generation sequencing panels identified a genotype consistent with the exam in just over half the patients. Additional work will be needed to identify the underlying genetic etiology for the remainder.
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Affiliation(s)
- Richard Sather
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jacie Ihinger
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael Simmons
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tahsin Khundkar
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Glenn P Lobo
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sandra R Montezuma
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN 55455, USA
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Schlottmann PG, Luna JD, Labat N, Yadarola MB, Bainttein S, Esposito E, Ibañez A, Barbaro EI, Álvarez Mendiara A, Picotti CP, Chirino Misisian A, Andreussi L, Gras J, Capalbo L, Visotto M, Dipierri JE, Alcoba E, Fernández Gabrielli L, Ávila S, Aucar ME, Martin DM, Ormaechea GJ, Inga ME, Francone AA, Charles M, Zompa T, Pérez PJ, Lotersztein V, Nuova PJ, Canonero IB, Mahroo OA, Michaelides M, Arno G, Daich Varela M. Nationwide genetic analysis of more than 600 families with inherited eye diseases in Argentina. NPJ Genom Med 2023; 8:8. [PMID: 37217489 DOI: 10.1038/s41525-023-00352-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/05/2023] [Indexed: 05/24/2023] Open
Abstract
This study corresponds to the first large-scale genetic analysis of inherited eye diseases (IED) in Argentina and describes the comprehensive genetic profile of a large cohort of patients. Medical records of 22 ophthalmology and genetics services throughout 13 Argentinian provinces were analyzed retrospectively. Patients with a clinical diagnosis of an ophthalmic genetic disease and a history of genetic testing were included. Medical, ophthalmological and family history was collected. A total of 773 patients from 637 families were included, with 98% having inherited retinal disease. The most common phenotype was retinitis pigmentosa (RP, 62%). Causative variants were detected in 379 (59%) patients. USH2A, RPGR, and ABCA4 were the most common disease-associated genes. USH2A was the most frequent gene associated with RP, RDH12 early-onset severe retinal dystrophy, ABCA4 Stargardt disease, PROM1 cone-rod dystrophy, and BEST1 macular dystrophy. The most frequent variants were RPGR c.1345 C > T, p.(Arg449*) and USH2A c.15089 C > A, p.(Ser5030*). The study revealed 156/448 (35%) previously unreported pathogenic/likely pathogenic variants and 8 possible founder mutations. We present the genetic landscape of IED in Argentina and the largest cohort in South America. This data will serve as a reference for future genetic studies, aid diagnosis, inform counseling, and assist in addressing the largely unmet need for clinical trials to be conducted in the region.
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Affiliation(s)
| | - José D Luna
- Centro Privado de Ojos Romagosa SA, Córdoba, Argentina
| | - Natalia Labat
- Centro Privado de Ojos Romagosa SA, Córdoba, Argentina
| | | | | | - Evangelina Esposito
- University Clinic Reina Fabiola, Córdoba, Córdoba, Argentina
- Catholic University of Cordoba, Cordoba, Argentina
| | - Agustina Ibañez
- University Clinic Reina Fabiola, Córdoba, Córdoba, Argentina
- Catholic University of Cordoba, Cordoba, Argentina
| | | | | | | | | | | | | | | | - Mauro Visotto
- Instituto Oftalmológico Trelew, Trelew, Chubut, Argentina
| | | | - Emilio Alcoba
- Hospital Materno Infantil Dr Héctor Quintana, Jujuy, Argentina
| | | | - Silvia Ávila
- Facultad de Ciencias Médicas, Universidad Nacional del Comahue, Río Negro, Argentina
| | | | | | | | - M Eugenia Inga
- Organización Medica de Investigación, Buenos Aires, Argentina
| | | | | | - Tamara Zompa
- Charles Centro Oftalmológico, Buenos Aires, Argentina
| | | | | | - Pedro J Nuova
- Ocularyb Oftalmoclinica, Yerba Buena, Tucumán, Argentina
| | | | - Omar A Mahroo
- Moorfields Eye Hospital, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Michel Michaelides
- Moorfields Eye Hospital, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Gavin Arno
- Moorfields Eye Hospital, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Malena Daich Varela
- Moorfields Eye Hospital, London, UK.
- UCL Institute of Ophthalmology, University College London, London, UK.
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31
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Jaffal L, Joumaa H, Noureldine J, Banjak M, Ibrahim M, Mrad Z, Salami A, Shamieh SE. The genetic landscape of inherited retinal dystrophies in Arabs. BMC Med Genomics 2023; 16:89. [PMID: 37127645 PMCID: PMC10150479 DOI: 10.1186/s12920-023-01518-7] [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: 11/20/2022] [Accepted: 04/13/2023] [Indexed: 05/03/2023] Open
Abstract
Inherited retinal dystrophies (IRDs) are a major cause of vision loss. Altogether are highly heterogeneous genotypically and phenotypically, exhibiting substantial differences worldwide. To shed more light on these conditions, we investigated the genetic and phenotypic landscape of IRDs in the Arabs globally and per country.We analyzed 1,621 affected individuals from 16 Arabic countries reported in 198 articles. At the phenotypic level, rod-cone dystrophy (RCD) and Usher syndrome were the most prevalent conditions among non-syndromic and syndromic IRDs. At the gene level, TULP1, ABCA4, RP1, CRB1, MYO7A, RPE65, KCNV2, and IMPG2 were the most mutated genes. Interestingly, all except CRB1 were highly prevalent because they harbored founder mutations, implying that consanguinity is a major determinant in Arab countries. Of note, ~ 93% of the investigated individuals carried homozygous mutations. The country analysis for the IRDs conditions and their associated genotypes revealed that whereas Leber Congenital Amaurosis, RCD, and USHER syndrome were widely distributed, bestrophinopathies and non-syndromic hearing loss were restricted to specific countries (till now).This study could be a starting point for initiating suitable health policies towards IRDs in the Arab world. The high degree of homozygosity urges the need for genetic counsellors to provide personalized information and support the affected individuals.
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Affiliation(s)
- Lama Jaffal
- Department of Biological and Chemical Sciences, School of Arts and Sciences, Lebanese International University, Beirut, Lebanon
| | - Hawraa Joumaa
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Jinane Noureldine
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Malak Banjak
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Mariam Ibrahim
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Zamzam Mrad
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Ali Salami
- Department of Mathematics, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Said El Shamieh
- Molecular Testing Laboratory, Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon.
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Zhen F, Zou T, Wang T, Zhou Y, Dong S, Zhang H. Rhodopsin-associated retinal dystrophy: Disease mechanisms and therapeutic strategies. Front Neurosci 2023; 17:1132179. [PMID: 37077319 PMCID: PMC10106759 DOI: 10.3389/fnins.2023.1132179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/13/2023] [Indexed: 04/05/2023] Open
Abstract
Rhodopsin is a light-sensitive G protein-coupled receptor that initiates the phototransduction cascade in rod photoreceptors. Mutations in the rhodopsin-encoding gene RHO are the leading cause of autosomal dominant retinitis pigmentosa (ADRP). To date, more than 200 mutations have been identified in RHO. The high allelic heterogeneity of RHO mutations suggests complicated pathogenic mechanisms. Here, we discuss representative RHO mutations as examples to briefly summarize the mechanisms underlying rhodopsin-related retinal dystrophy, which include but are not limited to endoplasmic reticulum stress and calcium ion dysregulation resulting from protein misfolding, mistrafficking, and malfunction. Based on recent advances in our understanding of disease mechanisms, various treatment methods, including adaptation, whole-eye electrical stimulation, and small molecular compounds, have been developed. Additionally, innovative therapeutic treatment strategies, such as antisense oligonucleotide therapy, gene therapy, optogenetic therapy, and stem cell therapy, have achieved promising outcomes in preclinical disease models of rhodopsin mutations. Successful translation of these treatment strategies may effectively ameliorate, prevent or rescue vision loss related to rhodopsin mutations.
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Affiliation(s)
- Fangyuan Zhen
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Henan Provincial Ophthalmic Hospital, Zhengzhou, China
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Institute of Laboratory Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Tongdan Zou
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Institute of Laboratory Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Ting Wang
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Institute of Laboratory Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Yongwei Zhou
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Henan Provincial Ophthalmic Hospital, Zhengzhou, China
| | - Shuqian Dong
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Henan Provincial Ophthalmic Hospital, Zhengzhou, China
- *Correspondence: Shuqian Dong, ; Houbin Zhang,
| | - Houbin Zhang
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Institute of Laboratory Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Research Unit for Blindness Prevention, Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, Sichuan, China
- *Correspondence: Shuqian Dong, ; Houbin Zhang,
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Lee BJH, Tham YC, Tan TE, Bylstra Y, Lim WK, Jain K, Chan CM, Mathur R, Cheung CMG, Fenner BJ. Characterizing the genotypic spectrum of retinitis pigmentosa in East Asian populations: a systematic review. Ophthalmic Genet 2023; 44:109-118. [PMID: 36856324 DOI: 10.1080/13816810.2023.2182329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
BACKGROUND Ongoing trials for retinitis pigmentosa (RP) are genotype-specific, with most trials conducted on European cohorts. Due to genetic differences across diverse ancestries and populations, these therapies may not be efficacious in East Asians. MATERIALS AND METHODS A literature search was conducted from 1966 to September 2022 for cohort studies on East Asian populations reporting on non-syndromic RP genotypes and variants. Population-weighted prevalence was used to determine the genotypes and individual variants across the entire cohort. The carrier prevalence of common variants was compared against those in Europe. RESULTS A total of 12 articles describing 2,932 clinically diagnosed East Asian RP probands were included. We identified 876 variants across 54 genes. The most common genotypes included USH2A, EYS, RPGR, ABCA4, PRPF31, RHO, RP1, RP2, PDE6B and SNRNP200, with USH2A as the most common (17.1%). Overall, 60.5% of probands with clinically relevant variants were found to have one of the genotypes above, with 543/876 (62.0%) of the variants occurring in these genes. The most frequently reported variant was USH2A missense variant c.2802T>G/p.C934W (4.9%). Carrier prevalence of these variants was significantly different (p < 0.0001) than in Europe. CONCLUSIONS USH2A was the most commonly affected RP gene in this East Asian cohort, although sub-population analysis revealed distinct genotype prevalence patterns. While the genotypes are similar between East Asia and European cohorts, variants are specific to East Asia. The identification of several prevalent variants in USH2A and EYS provides an opportunity for the development of therapeutics that are relevant for East Asia patients.
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Affiliation(s)
- Brian Juin Hsien Lee
- Department of Medical Retina, Singapore National Eye Centre, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Yih-Chung Tham
- Retina Research Group Singapore Eye Research Institute, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Medical School, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Centre for Innovation & Precision Eye Health, Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore
| | - Tien-En Tan
- Department of Medical Retina, Singapore National Eye Centre, Singapore
- Retina Research Group Singapore Eye Research Institute, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Medical School, Singapore
| | - Yasmin Bylstra
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore
| | - Kanika Jain
- POLARIS, Genome Institute of Singapore, Singapore
| | - Choi Mun Chan
- Department of Medical Retina, Singapore National Eye Centre, Singapore
- Retina Research Group Singapore Eye Research Institute, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Medical School, Singapore
| | - Ranjana Mathur
- Department of Medical Retina, Singapore National Eye Centre, Singapore
- Retina Research Group Singapore Eye Research Institute, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Medical School, Singapore
| | - Chui Ming Gemmy Cheung
- Department of Medical Retina, Singapore National Eye Centre, Singapore
- Retina Research Group Singapore Eye Research Institute, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Medical School, Singapore
| | - Beau J Fenner
- Department of Medical Retina, Singapore National Eye Centre, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Retina Research Group Singapore Eye Research Institute, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Medical School, Singapore
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Peter VG, Kaminska K, Santos C, Quinodoz M, Cancellieri F, Cisarova K, Pescini Gobert R, Rodrigues R, Custódio S, Paris LP, Sousa AB, Coutinho Santos L, Rivolta C. The first genetic landscape of inherited retinal dystrophies in Portuguese patients identifies recurrent homozygous mutations as a frequent cause of pathogenesis. PNAS NEXUS 2023; 2:pgad043. [PMID: 36909829 PMCID: PMC10003751 DOI: 10.1093/pnasnexus/pgad043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/15/2023]
Abstract
Inherited retinal diseases (IRDs) are a group of ocular conditions characterized by an elevated genetic and clinical heterogeneity. They are transmitted almost invariantly as monogenic traits. However, with more than 280 disease genes identified so far, association of clinical phenotypes with genotypes can be very challenging, and molecular diagnosis is essential for genetic counseling and correct management of the disease. In addition, the prevalence and the assortment of IRD mutations are often population-specific. In this work, we examined 230 families from Portugal, with individuals suffering from a variety of IRD diagnostic classes (270 subjects in total). Overall, we identified 157 unique mutations (34 previously unreported) in 57 distinct genes, with a diagnostic rate of 76%. The IRD mutational landscape was, to some extent, different from those reported in other European populations, including Spanish cohorts. For instance, the EYS gene appeared to be the most frequently mutated, with a prevalence of 10% among all IRD cases. This was, in part, due to the presence of a recurrent and seemingly founder mutation involving the deletion of exons 13 and 14 of this gene. Moreover, our analysis highlighted that as many as 51% of our cases had mutations in a homozygous state. To our knowledge, this is the first study assessing a cross-sectional genotype-phenotype landscape of IRDs in Portugal. Our data reveal a rather unique distribution of mutations, possibly shaped by a small number of rare ancestral events that have now become prevalent alleles in patients.
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Affiliation(s)
- Virginie G Peter
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland.,Department of Ophthalmology, Inselspital, Bern University Hospital, Bern 3010, Switzerland
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Cristina Santos
- Department of Ophthalmology, Instituto de Oftalmologia Dr Gama Pinto (IOGP), Lisbon 1169-019, Portugal.,iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisbon 1169-056, Portugal
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Katarina Cisarova
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | | | - Raquel Rodrigues
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon 1649-035, Portugal
| | - Sónia Custódio
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon 1649-035, Portugal
| | - Liliana P Paris
- Department of Ophthalmology, Instituto de Oftalmologia Dr Gama Pinto (IOGP), Lisbon 1169-019, Portugal
| | - Ana Berta Sousa
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon 1649-035, Portugal.,Laboratory of Basic Immunology, Faculty of Medicine, University of Lisbon, Lisbon 1649-028, Portugal
| | - Luisa Coutinho Santos
- Department of Ophthalmology, Instituto de Oftalmologia Dr Gama Pinto (IOGP), Lisbon 1169-019, Portugal
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
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35
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Wu KY, Kulbay M, Toameh D, Xu AQ, Kalevar A, Tran SD. Retinitis Pigmentosa: Novel Therapeutic Targets and Drug Development. Pharmaceutics 2023; 15:685. [PMID: 36840007 PMCID: PMC9963330 DOI: 10.3390/pharmaceutics15020685] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/12/2023] [Accepted: 02/16/2023] [Indexed: 02/19/2023] Open
Abstract
Retinitis pigmentosa (RP) is a heterogeneous group of hereditary diseases characterized by progressive degeneration of retinal photoreceptors leading to progressive visual decline. It is the most common type of inherited retinal dystrophy and has a high burden on both patients and society. This condition causes gradual loss of vision, with its typical manifestations including nyctalopia, concentric visual field loss, and ultimately bilateral central vision loss. It is one of the leading causes of visual disability and blindness in people under 60 years old and affects over 1.5 million people worldwide. There is currently no curative treatment for people with RP, and only a small group of patients with confirmed RPE65 mutations are eligible to receive the only gene therapy on the market: voretigene neparvovec. The current therapeutic armamentarium is limited to retinoids, vitamin A supplements, protection from sunlight, visual aids, and medical and surgical interventions to treat ophthalmic comorbidities, which only aim to slow down the progression of the disease. Considering such a limited therapeutic landscape, there is an urgent need for developing new and individualized therapeutic modalities targeting retinal degeneration. Although the heterogeneity of gene mutations involved in RP makes its target treatment development difficult, recent fundamental studies showed promising progress in elucidation of the photoreceptor degeneration mechanism. The discovery of novel molecule therapeutics that can selectively target specific receptors or specific pathways will serve as a solid foundation for advanced drug development. This article is a review of recent progress in novel treatment of RP focusing on preclinical stage fundamental research on molecular targets, which will serve as a starting point for advanced drug development. We will review the alterations in the molecular pathways involved in the development of RP, mainly those regarding endoplasmic reticulum (ER) stress and apoptotic pathways, maintenance of the redox balance, and genomic stability. We will then discuss the therapeutic approaches under development, such as gene and cell therapy, as well as the recent literature identifying novel potential drug targets for RP.
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Affiliation(s)
- Kevin Y. Wu
- Division of Ophthalmology, Department of Surgery, University of Sherbrooke, Sherbrooke, QC J1G 2E8, Canada
| | - Merve Kulbay
- Faculty of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Dana Toameh
- Faculty of Medicine, McGill University, Montreal, QC H3G 2M1, Canada
| | - An Qi Xu
- Faculty of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Ananda Kalevar
- Division of Ophthalmology, Department of Surgery, University of Sherbrooke, Sherbrooke, QC J1G 2E8, Canada
| | - Simon D. Tran
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC H3A 1G1, Canada
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36
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Li W, He XD, Yang ZT, Han DM, Sun Y, Chen YX, Han XT, Guo SC, Ma YT, Jin X, Yang HM, Gao Y, Wang ZS, Li JK, He W. De Novo Mutations Contributes Approximately 7% of Pathogenicity in Inherited Eye Diseases. Invest Ophthalmol Vis Sci 2023; 64:5. [PMID: 36729443 PMCID: PMC9907368 DOI: 10.1167/iovs.64.2.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Purpose The purpose of this study was to describe genotype-phenotype associations and novel insights into genetic characteristics in a trio-based cohort of inherited eye diseases (IEDs). Methods To determine the etiological role of de novo mutations (DNMs) and genetic profile in IEDs, we retrospectively reviewed a large cohort of proband-parent trios of Chinese origin. The patients underwent a detailed examination and was clinically diagnosed by an ophthalmologist. Panel-based targeted exome sequencing was performed on DNA extracted from blood samples, containing coding regions of 792 IED-causative genes and their flanking exons. All participants underwent genetic testing. Results All proband-parent trios were divided into 22 subgroups, the overall diagnostic yield was 48.67% (605/1243), ranging from 4% to 94.44% for each of the subgroups. A total of 108 IED-causative genes were identified, with the top 24 genes explaining 67% of the 605 genetically solved trios. The genetic etiology of 6.76% (84/1243) of the trio was attributed to disease-causative DNMs, and the top 3 subgroups with the highest incidence of DNM were aniridia (n = 40%), Marfan syndrome/ectopia lentis (n = 38.78%), and retinoblastoma (n = 37.04%). The top 10 genes have a diagnostic yield of DNM greater than 3.5% in their subgroups, including PAX6 (40.00%), FBN1 (38.78%), RB1 (37.04%), CRX (10.34%), CHM (9.09%), WFS1 (8.00%), RP1L1 (5.88%), RS1 (5.26%), PCDH15 (4.00%), and ABCA4 (3.51%). Additionally, the incidence of DNM in offspring showed a trend of correlation with paternal age at reproduction, but not statistically significant with paternal (P = 0.154) and maternal (P = 0.959) age at reproduction. Conclusions Trios-based genetic analysis has high accuracy and validity. Our study helps to quantify the burden of the full spectrum IED caused by each gene, offers novel potential for elucidating etiology, and plays a crucial role in genetic counseling and patient management.
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Affiliation(s)
- Wei Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China,BGI-Shenzhen, Shenzhen, China
| | | | - Zheng-Tao Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China,BGI-Shenzhen, Shenzhen, China
| | - Dong-Ming Han
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China,BGI-Shenzhen, Shenzhen, China
| | - Yan Sun
- He University, Shenyang, China
| | - Yan-Xian Chen
- Department of Ophthalmology, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Xiao-Tong Han
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, China
| | - Si-Cheng Guo
- BGI-Shenzhen, Shenzhen, China,College of Plant Protection, Hunan Agricultural University, Changsha, Hunan, China
| | - Yu-Ting Ma
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China,BGI-Shenzhen, Shenzhen, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, China
| | - Huan-Ming Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China,BGI-Shenzhen, Shenzhen, China
| | - Ya Gao
- BGI-Shenzhen, Shenzhen, China
| | | | | | - Wei He
- He University, Shenyang, China
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37
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de la Fuente L, Del Pozo-Valero M, Perea-Romero I, Blanco-Kelly F, Fernández-Caballero L, Cortón M, Ayuso C, Mínguez P. Prioritization of New Candidate Genes for Rare Genetic Diseases by a Disease-Aware Evaluation of Heterogeneous Molecular Networks. Int J Mol Sci 2023; 24:ijms24021661. [PMID: 36675175 PMCID: PMC9864172 DOI: 10.3390/ijms24021661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Screening for pathogenic variants in the diagnosis of rare genetic diseases can now be performed on all genes thanks to the application of whole exome and genome sequencing (WES, WGS). Yet the repertoire of gene-disease associations is not complete. Several computer-based algorithms and databases integrate distinct gene-gene functional networks to accelerate the discovery of gene-disease associations. We hypothesize that the ability of every type of information to extract relevant insights is disease-dependent. We compiled 33 functional networks classified into 13 knowledge categories (KCs) and observed large variability in their ability to recover genes associated with 91 genetic diseases, as measured using efficiency and exclusivity. We developed GLOWgenes, a network-based algorithm that applies random walk with restart to evaluate KCs' ability to recover genes from a given list associated with a phenotype and modulates the prediction of new candidates accordingly. Comparison with other integration strategies and tools shows that our disease-aware approach can boost the discovery of new gene-disease associations, especially for the less obvious ones. KC contribution also varies if obtained using recently discovered genes. Applied to 15 unsolved WES, GLOWgenes proposed three new genes to be involved in the phenotypes of patients with syndromic inherited retinal dystrophies.
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Affiliation(s)
- Lorena de la Fuente
- Department of Genetics, Health Research Institute–Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28049 Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), 28040 Madrid, Spain
- Bioinformatics Unit, Health Research Institute–Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28049 Madrid, Spain
| | - Marta Del Pozo-Valero
- Department of Genetics, Health Research Institute–Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28049 Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), 28040 Madrid, Spain
| | - Irene Perea-Romero
- Department of Genetics, Health Research Institute–Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28049 Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), 28040 Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics, Health Research Institute–Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28049 Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), 28040 Madrid, Spain
| | - Lidia Fernández-Caballero
- Department of Genetics, Health Research Institute–Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28049 Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), 28040 Madrid, Spain
| | - Marta Cortón
- Department of Genetics, Health Research Institute–Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28049 Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), 28040 Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics, Health Research Institute–Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28049 Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), 28040 Madrid, Spain
| | - Pablo Mínguez
- Department of Genetics, Health Research Institute–Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28049 Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), 28040 Madrid, Spain
- Bioinformatics Unit, Health Research Institute–Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28049 Madrid, Spain
- Correspondence:
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38
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Lynn J, Raney A, Britton N, Ramoin J, Yang RW, Radojevic B, McClard CK, Kingsley R, Coussa RG, Bennett LD. Genetic Diagnosis for 64 Patients with Inherited Retinal Disease. Genes (Basel) 2022; 14:74. [PMID: 36672815 PMCID: PMC9859429 DOI: 10.3390/genes14010074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/07/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
The overlapping genetic and clinical spectrum in inherited retinal degeneration (IRD) creates challenges for accurate diagnoses. The goal of this work was to determine the genetic diagnosis and clinical features for patients diagnosed with an IRD. After signing informed consent, peripheral blood or saliva was collected from 64 patients diagnosed with an IRD. Genetic testing was performed on each patient in a Clinical Laboratory Improvement Amendments of 1988 (CLIA) certified laboratory. Mutations were verified with Sanger sequencing and segregation analysis when possible. Visual acuity was measured with a traditional Snellen chart and converted to a logarithm of minimal angle of resolution (logMAR). Fundus images of dilated eyes were acquired with the Optos® camera (Dunfermline, UK). Horizontal line scans were obtained with spectral-domain optical coherence tomography (SDOCT; Spectralis, Heidelberg, Germany). Genetic testing combined with segregation analysis resolved molecular and clinical diagnoses for 75% of patients. Ten novel mutations were found and unique genotype phenotype associations were made for the genes RP2 and CEP83. Collective knowledge is thereby expanded of the genetic basis and phenotypic correlation in IRD.
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Affiliation(s)
- Jacob Lynn
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Austin Raney
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Nathaniel Britton
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Josh Ramoin
- College of Osteopathic Medicine, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ryan W. Yang
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Bojana Radojevic
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Dean McGee Eye Institute, Oklahoma City, OK 73104, USA
| | - Cynthia K. McClard
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Dean McGee Eye Institute, Oklahoma City, OK 73104, USA
| | - Ronald Kingsley
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Dean McGee Eye Institute, Oklahoma City, OK 73104, USA
| | - Razek Georges Coussa
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Dean McGee Eye Institute, Oklahoma City, OK 73104, USA
| | - Lea D. Bennett
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Dean McGee Eye Institute, Oklahoma City, OK 73104, USA
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39
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Karali M, Testa F, Di Iorio V, Torella A, Zeuli R, Scarpato M, Romano F, Onore ME, Pizzo M, Melillo P, Brunetti-Pierri R, Passerini I, Pelo E, Cremers FPM, Esposito G, Nigro V, Simonelli F, Banfi S. Genetic epidemiology of inherited retinal diseases in a large patient cohort followed at a single center in Italy. Sci Rep 2022; 12:20815. [PMID: 36460718 PMCID: PMC9718770 DOI: 10.1038/s41598-022-24636-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 11/17/2022] [Indexed: 12/04/2022] Open
Abstract
Inherited retinal diseases (IRDs) are the leading cause of vision loss in the working-age population. We performed a retrospective epidemiological study to determine the genetic basis of IRDs in a large Italian cohort (n = 2790) followed at a single referral center. We provided, mainly by next generation sequencing, potentially conclusive molecular diagnosis for 2036 patients (from 1683 unrelated families). We identified a total of 1319 causative sequence variations in 132 genes, including 353 novel variants, and 866 possibly actionable genotypes for therapeutic approaches. ABCA4 was the most frequently mutated gene (n = 535; 26.3% of solved cases), followed by USH2A (n = 228; 11.2%) and RPGR (n = 102; 5.01%). The other 129 genes had a lower contribution to IRD pathogenesis (e.g. CHM 3.5%, RHO 3.5%; MYO7A 3.4%; CRB1 2.7%; RPE65 2%, RP1 1.8%; GUCY2D 1.7%). Seventy-eight genes were mutated in five patients or less. Mitochondrial DNA variants were responsible for 2.1% of cases. Our analysis confirms the complex genetic etiology of IRDs and reveals the high prevalence of ABCA4 and USH2A mutations. This study also uncovers genetic associations with a spectrum of clinical subgroups and highlights a valuable number of cases potentially eligible for clinical trials and, ultimately, for molecular therapies.
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Affiliation(s)
- Marianthi Karali
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy ,grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Francesco Testa
- grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Valentina Di Iorio
- grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Annalaura Torella
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy ,grid.410439.b0000 0004 1758 1171Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Roberta Zeuli
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy
| | - Margherita Scarpato
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy
| | - Francesca Romano
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy
| | - Maria Elena Onore
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy
| | - Mariateresa Pizzo
- grid.410439.b0000 0004 1758 1171Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Paolo Melillo
- grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Raffaella Brunetti-Pierri
- grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Ilaria Passerini
- grid.24704.350000 0004 1759 9494Department of Genetic Diagnosis, Careggi Teaching Hospital, Florence, Italy
| | - Elisabetta Pelo
- grid.24704.350000 0004 1759 9494Department of Genetic Diagnosis, Careggi Teaching Hospital, Florence, Italy
| | - Frans P. M. Cremers
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gabriella Esposito
- grid.4691.a0000 0001 0790 385XDepartment of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy ,CEINGE-Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Vincenzo Nigro
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy ,grid.410439.b0000 0004 1758 1171Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Francesca Simonelli
- grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Sandro Banfi
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy ,grid.410439.b0000 0004 1758 1171Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
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40
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Sather III R, Ihinger J, Khundkar T, Montezuma SR. Pathogenic gene variants identified in patients with retinitis pigmentosa at the referral center clinic of the University of Minnesota (UMN). Ophthalmic Genet 2022:1-3. [DOI: 10.1080/13816810.2022.2135110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Richard Sather III
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jacie Ihinger
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, Minnesota, USA
| | - Tahsin Khundkar
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, Minnesota, USA
| | - Sandra R. Montezuma
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, Minnesota, USA
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41
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Daich Varela M, Bellingham J, Motta F, Jurkute N, Ellingford JM, Quinodoz M, Oprych K, Niblock M, Janeschitz-Kriegl L, Kaminska K, Cancellieri F, Scholl HPN, Lenassi E, Schiff E, Knight H, Black G, Rivolta C, Cheetham ME, Michaelides M, Mahroo OA, Moore AT, Webster AR, Arno G. Multidisciplinary team directed analysis of whole genome sequencing reveals pathogenic non-coding variants in molecularly undiagnosed inherited retinal dystrophies. Hum Mol Genet 2022; 32:595-607. [PMID: 36084042 PMCID: PMC9896476 DOI: 10.1093/hmg/ddac227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/23/2022] [Accepted: 09/04/2022] [Indexed: 02/07/2023] Open
Abstract
The purpose of this paper is to identify likely pathogenic non-coding variants in inherited retinal dystrophy (IRD) genes, using genome sequencing (GS). Patients with IRD were recruited to the study and underwent comprehensive ophthalmological evaluation and GS. The results of GS were investigated through virtual gene panel analysis, and plausible pathogenic variants and clinical phenotype evaluated by the multidisciplinary team (MDT) discussion. For unsolved patients in whom a specific gene was suspected to harbor a missed pathogenic variant, targeted re-analysis of non-coding regions was performed on GS data. Candidate variants were functionally tested by messenger RNA analysis, minigene or luciferase reporter assays. Previously unreported, likely pathogenic, non-coding variants in 7 genes (PRPF31, NDP, IFT140, CRB1, USH2A, BBS10 and GUCY2D), were identified in 11 patients. These were shown to lead to mis-splicing (PRPF31, IFT140, CRB1 and USH2A) or altered transcription levels (BBS10 and GUCY2D). MDT-led, phenotype-driven, non-coding variant re-analysis of GS is effective in identifying the missing causative alleles.
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Affiliation(s)
- Malena Daich Varela
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | | | - Fabiana Motta
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Department of Ophthalmology, Universidade Federal de Sao Paulo, Sao Paulo 04021001, Brazil
| | - Neringa Jurkute
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Jamie M Ellingford
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WL, UK,Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | | | | | - Lucas Janeschitz-Kriegl
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Hendrik P N Scholl
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Eva Lenassi
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WL, UK,Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | | | | | - Graeme Black
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WL, UK,Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | | | - Michel Michaelides
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Omar A Mahroo
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Anthony T Moore
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK,University of California, San Francisco, CA 94607, USA
| | - Andrew R Webster
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Gavin Arno
- To whom correspondence should be addressed at: UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1 9EL, UK. Tel: +44 2076086971;
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Effects and Prognosis of Cataract Surgery in Patients with Retinitis Pigmentosa. Ophthalmol Ther 2022; 11:1975-1989. [PMID: 36057888 DOI: 10.1007/s40123-022-00563-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/22/2022] [Indexed: 10/14/2022] Open
Abstract
INTRODUCTION Cataract extraction could improve visual acuity (VA) for patients with retinitis pigmentosa (RP), while the surgery may increase photoreceptor degeneration through light damage. In this study, we conducted a systematic review and meta-analysis to investigate the effectiveness and prediction of VA after cataract surgery in patients with RP. METHODS We comprehensively extracted data from literature of available studies with quality control processing. Improvement of VA before and after cataract surgery of different durations of follow-up and different structural integrity of the preoperative macular ellipsoid zone (EZ) in patients with RP were compared. VA was measured by the logarithm of the minimum angle of resolution (logMAR). RESULTS Sixteen studies were subjected to analysis. Postoperative VA was significantly improved versus preoperative, with a mean difference (MD) of 0.57 [95% confidence interval (CI) 0.45, 0.69], and a fixed-effect model was applied during follow-up durations of 1 day to 1 month (I2 = 0%). Similarly, for follow-up durations of 1-3 months, 3-6 months, and 6-12 months, postoperative VAs were all better than preoperative values, with MDs of 0.36 (95% CI 0.31, 0.41), 0.35 (95% CI 0.23, 0.46), and 0.22 (95% CI 0.14, 0.30) (I2 < 50%). For follow-up duration of 1-5 years, the random-effect model was applied for higher heterogeneity (I2 = 81%), with an MD of 0.26 (95% CI 0.09, 0.43). There was no significant difference in the improvement of the EZ-invisible group, with an MD of 0.27 (95% CI - 0.17, 0.70) (I2 = 82%). There were significant differences between EZ-abnormal and EZ-normal groups in preoperative and postoperative VA, with MDs of 0.56 (95% CI 0.27, 0.85) and 0.46 (95% CI 0.27, 0.65) (I2 > 50%). CONCLUSIONS Cataract surgery could improve VA for patients with RP during long-term follow-up, and the surgery is not recommended for patients with invisible preoperative macular EZ. However, further studies are required to address the problem of excessive light exposure to the degenerated retina in patients with RP with the cataract removed. The study protocol was registered on the International Prospective Register of Systematic Reviews (PROSPERO) (CRD42022340165).
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43
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Santos DF, Molina Thurin LJ, Vargas JG, Izquierdo NJ, Oliver A. Retinitis Pigmentosa in the Puerto Rican Population: A Geographic Distribution. Clin Ophthalmol 2022; 16:3175-3179. [PMID: 36196406 PMCID: PMC9527035 DOI: 10.2147/opth.s375365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/12/2022] [Indexed: 11/23/2022] Open
Abstract
Background Previous studies have reported on retinitis pigmentosa (RP) in Puerto Rico. Information on the geographic distribution of RP mutations in Puerto Rico may lead to higher rates of diagnosis and co-management. We aimed to evaluate whether there are areas with increased incidence of genes leading to RP in the Island. Materials and Methods We conducted a non-concurrent prospective study on the genotype of 241 patients with RP in Puerto Rico. We evaluated their townships to determine whether there are clusters of genes leading to RP. Genetic studies were done using the Invitae inherited retinal diseases panel analyzing 330 genes. Results A total of 100 patients were evaluated. Clusters of patients with mutations were found in certain townships. As depicted in the map, a cluster of patients with a mutation in the PDE6B gene was found in San Juan (9), those with the BBS1 gene occurred in San Juan (6) and Bayamón (4), mutations on the USH2A gene were found in Toa Baja (5), mutations in the CRB1 gene appeared in Ciales (4), and mutations in the BBS7 were found in Aibonito (2). Other mutations are scattered throughout the Island. Conclusion Clusters of mutations were identified in several townships including San Juan, Bayamón, Toa Baja, Ciales, and Aibonito. Some of these are isolated geographically. Additional mutations were identified but only the most pertinent were reported. Genetic studies are warranted in all patients with RP in Puerto Rico.
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Affiliation(s)
- David F Santos
- School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, PR, USA
| | | | | | - Natalio J Izquierdo
- Department of Surgery, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, PR, USA
- Correspondence: Natalio J Izquierdo, Email
| | - Armando Oliver
- Department of Ophthalmology, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, PR, USA
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44
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Vinikoor-Imler LC, Simpson C, Narayanan D, Abbasi S, Lally C. Prevalence of RPGR-mutated X-linked retinitis pigmentosa among males. Ophthalmic Genet 2022; 43:581-588. [PMID: 36004681 DOI: 10.1080/13816810.2022.2109686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
BACKGROUND X-linked retinitis pigmentosa (XLRP) is a rare inherited retinal disease predominantly affecting males. MATERIALS AND METHODS A comprehensive literature review was conducted to determine the prevalence of retinitis pigmentosa GTPase regulator (RPGR)-mutated XLRP. Identified studies were used to estimate four components among males: the prevalence of retinitis pigmentosa (RP), the proportion of RP that was X-linked, the proportion of misclassified inheritance type among RP cases, and the proportion of XLRP that was RPGR-mutated. Studies providing a direct estimate of XLRP prevalence were also included. The components' sample size-weighted averages were combined to determine an overall prevalence estimate. RESULTS The prevalence of XLRP was estimated to be between 2.7-3.5 per 100,000 males in the US, Europe, and Australia. After correction for misclassification, the prevalence increased to 4.0-5.2 per 100,000 males. Finally, the proportion of XLRP cases due to RPGR mutations was applied, resulting in an RPGR-mutated XLRP estimate of 3.4-4.4 per 100,000 males. Studies from other countries were consistent with the results for the overall XLRP prevalence but were not included in the final calculation because of regional variations and lack of detailed information. CONCLUSIONS These findings address an important gap in the understanding of RPGR-mutated XLRP by summarizing the global burden of this condition.
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Affiliation(s)
| | | | - Divya Narayanan
- Global Medical Affairs, Biogen, Cambridge, Massachusetts, USA
| | - Saad Abbasi
- Global Medical Affairs, Biogen, Cambridge, Massachusetts, USA
| | - Cathy Lally
- Epidemiologic Research & Methods, LLC, Atlanta, Georgia, USA
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45
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El Shamieh S, Maltese PE. Editorial: The genetics of inherited retinal diseases in understudied ethnic groups: Novel associations, challenges, and perspectives. Front Genet 2022; 13:990782. [PMID: 36081992 PMCID: PMC9445133 DOI: 10.3389/fgene.2022.990782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Said El Shamieh
- Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
- *Correspondence: Said El Shamieh, ; Paolo Enrico Maltese,
| | - Paolo Enrico Maltese
- Magi’s Lab SRL, Rovereto, Italy
- *Correspondence: Said El Shamieh, ; Paolo Enrico Maltese,
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46
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Aggregated Genomic Data as Cohort-Specific Allelic Frequencies can Boost Variants and Genes Prioritization in Non-Solved Cases of Inherited Retinal Dystrophies. Int J Mol Sci 2022; 23:ijms23158431. [PMID: 35955564 PMCID: PMC9368980 DOI: 10.3390/ijms23158431] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 02/04/2023] Open
Abstract
The introduction of NGS in genetic diagnosis has increased the repertoire of variants and genes involved and the amount of genomic information produced. We built an allelic-frequency (AF) database for a heterogeneous cohort of genetic diseases to explore the aggregated genomic information and boost diagnosis in inherited retinal dystrophies (IRD). We retrospectively selected 5683 index-cases with clinical exome sequencing tests available, 1766 with IRD and the rest with diverse genetic diseases. We calculated a subcohort’s IRD-specific AF and compared it with suitable pseudocontrols. For non-solved IRD cases, we prioritized variants with a significant increment of frequencies, with eight variants that may help to explain the phenotype, and 10/11 of uncertain significance that were reclassified as probably pathogenic according to ACMG. Moreover, we developed a method to highlight genes with more frequent pathogenic variants in IRD cases than in pseudocontrols weighted by the increment of benign variants in the same comparison. We identified 18 genes for further studies that provided new insights in five cases. This resource can also help one to calculate the carrier frequency in IRD genes. A cohort-specific AF database assists with variants and genes prioritization and operates as an engine that provides a new hypothesis in non-solved cases, augmenting the diagnosis rate.
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47
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Panikker P, Roy S, Ghosh A, Poornachandra B, Ghosh A. Advancing precision medicines for ocular disorders: Diagnostic genomics to tailored therapies. Front Med (Lausanne) 2022; 9:906482. [PMID: 35911417 PMCID: PMC9334564 DOI: 10.3389/fmed.2022.906482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/29/2022] [Indexed: 11/20/2022] Open
Abstract
Successful sequencing of the human genome and evolving functional knowledge of gene products has taken genomic medicine to the forefront, soon combining broadly with traditional diagnostics, therapeutics, and prognostics in patients. Recent years have witnessed an extraordinary leap in our understanding of ocular diseases and their respective genetic underpinnings. As we are entering the age of genomic medicine, rapid advances in genome sequencing, gene delivery, genome surgery, and computational genomics enable an ever-increasing capacity to provide a precise and robust diagnosis of diseases and the development of targeted treatment strategies. Inherited retinal diseases are a major source of blindness around the world where a large number of causative genes have been identified, paving the way for personalized diagnostics in the clinic. Developments in functional genetics and gene transfer techniques has also led to the first FDA approval of gene therapy for LCA, a childhood blindness. Many such retinal diseases are the focus of various clinical trials, making clinical diagnoses of retinal diseases, their underlying genetics and the studies of natural history important. Here, we review methodologies for identifying new genes and variants associated with various ocular disorders and the complexities associated with them. Thereafter we discuss briefly, various retinal diseases and the application of genomic technologies in their diagnosis. We also discuss the strategies, challenges, and potential of gene therapy for the treatment of inherited and acquired retinal diseases. Additionally, we discuss the translational aspects of gene therapy, the important vector types and considerations for human trials that may help advance personalized therapeutics in ophthalmology. Retinal disease research has led the application of precision diagnostics and precision therapies; therefore, this review provides a general understanding of the current status of precision medicine in ophthalmology.
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Affiliation(s)
| | - Shomereeta Roy
- Grow Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
| | - Anuprita Ghosh
- Grow Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
| | | | - Arkasubhra Ghosh
- Grow Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
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Perea-Romero I, Solarat C, Blanco-Kelly F, Sanchez-Navarro I, Bea-Mascato B, Martin-Salazar E, Lorda-Sanchez I, Swafiri ST, Avila-Fernandez A, Martin-Merida I, Trujillo-Tiebas MJ, Carreño E, Jimenez-Rolando B, Garcia-Sandoval B, Minguez P, Corton M, Valverde D, Ayuso C. Allelic overload and its clinical modifier effect in Bardet-Biedl syndrome. NPJ Genom Med 2022; 7:41. [PMID: 35835773 PMCID: PMC9283419 DOI: 10.1038/s41525-022-00311-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/29/2022] [Indexed: 11/17/2022] Open
Abstract
Bardet–Biedl syndrome (BBS) is an autosomal recessive ciliopathy characterized by extensive inter- and intra-familial variability, in which oligogenic interactions have been also reported. Our main goal is to elucidate the role of mutational load in the clinical variability of BBS. A cohort of 99 patients from 77 different families with biallelic pathogenic variants in a BBS-associated gene was retrospectively recruited. Human Phenotype Ontology terms were used in the annotation of clinical symptoms. The mutational load in 39 BBS-related genes was studied in index cases using different molecular and next-generation sequencing (NGS) approaches. Candidate allele combinations were analysed using the in silico tools ORVAL and DiGePred. After clinical annotation, 76 out of the 99 cases a priori fulfilled established criteria for diagnosis of BBS or BBS-like. BBS1 alleles, found in 42% of families, were the most represented in our cohort. An increased mutational load was excluded in 41% of the index cases (22/54). Oligogenic inheritance was suspected in 52% of the screened families (23/45), being 40 tested by means of NGS data and 5 only by traditional methods. Together, ORVAL and DiGePred platforms predicted an oligogenic effect in 44% of the triallelic families (10/23). Intrafamilial variable severity could be clinically confirmed in six of the families. Our findings show that the presence of more than two alleles in BBS-associated genes correlated in six families with a more severe phenotype and associated with specific findings, highlighting the role of the mutational load in the management of BBS cases.
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Affiliation(s)
- Irene Perea-Romero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Solarat
- CINBIO, Universidade de Vigo, Vigo, Spain.,Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), Álvaro Cunqueiro Hospital, Vigo, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Iker Sanchez-Navarro
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Brais Bea-Mascato
- CINBIO, Universidade de Vigo, Vigo, Spain.,Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), Álvaro Cunqueiro Hospital, Vigo, Spain
| | - Eduardo Martin-Salazar
- CINBIO, Universidade de Vigo, Vigo, Spain.,Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), Álvaro Cunqueiro Hospital, Vigo, Spain
| | - Isabel Lorda-Sanchez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Saoud Tahsin Swafiri
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Almudena Avila-Fernandez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Inmaculada Martin-Merida
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Maria Jose Trujillo-Tiebas
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Ester Carreño
- Department of Ophthalmology, Fundación Jiménez Díaz University Hospital (FJD), Madrid, Spain
| | - Belen Jimenez-Rolando
- Department of Ophthalmology, Fundación Jiménez Díaz University Hospital (FJD), Madrid, Spain
| | - Blanca Garcia-Sandoval
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Department of Ophthalmology, Fundación Jiménez Díaz University Hospital (FJD), Madrid, Spain
| | - Pablo Minguez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Corton
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Diana Valverde
- CINBIO, Universidade de Vigo, Vigo, Spain. .,Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), Álvaro Cunqueiro Hospital, Vigo, Spain.
| | - Carmen Ayuso
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain. .,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
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49
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Burgess FR, Hall HN, Megaw R. Emerging Gene Manipulation Strategies for the Treatment of Monogenic Eye Disease. Asia Pac J Ophthalmol (Phila) 2022; 11:380-391. [PMID: 36041151 DOI: 10.1097/apo.0000000000000545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/27/2022] [Indexed: 12/15/2022] Open
Abstract
Genetic eye diseases, representing a wide spectrum of simple and complex conditions, are one of the leading causes of visual loss in children and working adults, and progress in the field has led to changes in disease investigation, diagnosis, and management. The past 15 years have seen the emergence of novel therapies for these previously untreatable conditions to the extent that we now have a licensed therapy for one form of genetic eye disease and many more in clinical trial. This is a systematic review of published and ongoing clinical trials of gene therapies for monogenic eye diseases. Databases of clinical trials and the published literature were searched for interventional studies of gene therapies for eye diseases. Standard methodological procedures were used to assess the relevance of search results. A total of 59 registered clinical trials are referenced, showing the significant level of interest in the potential for translation of these therapies from bench to bedside. The breadth of therapy design is encouraging, providing multiple possible therapeutic mechanisms. Some fundamental questions regarding gene therapy for genetic eye diseases remain, such as optimal dosing, the relative benefits of adeno-associated virus (AAV)-packaging and the potential for a significant inflammatory response to the therapy itself. As a result, despite the promise of the eye as a target, it has proven difficult to deliver clinically effective gene therapies to the eye. Despite setbacks, the licensing of Luxturna (voretigene neparvovec, Novartis) for the treatment of RPE65-mediated Leber congenital amaurosis (LCA) is a major advance in efforts to treat these rare, but devastating, causes of visual loss.
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Affiliation(s)
- Frederick R Burgess
- Princess Alexandra Eye Pavilion, NHS Lothian, UK
- Ophthalmology Department, School of Medicine, University of St Andrews, UK
| | - Hildegard Nikki Hall
- Princess Alexandra Eye Pavilion, NHS Lothian, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, UK
| | - Roly Megaw
- Princess Alexandra Eye Pavilion, NHS Lothian, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, UK
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50
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Ratra D, Ozdek S, Raviselvan M, Elchuri S, Sharma T. Approach to inherited retinal diseases. Indian J Ophthalmol 2022; 70:2305-2315. [PMID: 35791111 PMCID: PMC9426075 DOI: 10.4103/ijo.ijo_314_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Inherited retinal diseases (IRDs) are a group of phenotypically diverse disorders with varied genetic mutations, which result in retinal degeneration leading to visual impairment. When a patient presents to a clinician who is not an IRD expert, establishing a correct diagnosis can be challenging. The patient and the family members are often anxious about further vision loss. They are eager to know the prognosis and chance of further worsening of the vision. It is important for every eye specialist to educate himself/herself about the basics of IRD. It would help to familiarize oneself about how to approach a patient with an IRD. An early and accurate diagnosis can help predict the vision loss and also help the patient plan his/her education and choose appropriate career choices. An updated knowledge about the genetic mutations, mode of inheritance, and possible therapies would empower the eye specialist to help his/her patients. This article gives a broad plan of how to approach a patient with IRD with regards to characterization and diagnosis of the disorder, visual rehabilitation, and possible therapy.
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Affiliation(s)
- Dhanashree Ratra
- Department of Vitreoretinal Diseases, Medical Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, India
| | - Sengul Ozdek
- School of Medicine, Gazi University, Besevler, Ankara, Turkey
| | - Munispriyan Raviselvan
- Department of Vitreoretinal Diseases, Medical Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, India
| | - Sailaja Elchuri
- Department of Nanotechnology, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, India
| | - Tarun Sharma
- Department of Ophthalmology, Columbia University, New York, USA
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