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Ferreira CR, Lima Gomes PCFD, Robison KM, Cooper BR, Shannahan JH. Implementation of multiomic mass spectrometry approaches for the evaluation of human health following environmental exposure. Mol Omics 2024. [PMID: 38623720 DOI: 10.1039/d3mo00214d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Omics analyses collectively refer to the possibility of profiling genetic variants, RNA, epigenetic markers, proteins, lipids, and metabolites. The most common analytical approaches used for detecting molecules present within biofluids related to metabolism are vibrational spectroscopy techniques, represented by infrared, Raman, and nuclear magnetic resonance (NMR) spectroscopies and mass spectrometry (MS). Omics-based assessments utilizing MS are rapidly expanding and being applied to various scientific disciplines and clinical settings. Most of the omics instruments are operated by specialists in dedicated laboratories; however, the development of miniature portable omics has made the technology more available to users for field applications. Variations in molecular information gained from omics approaches are useful for evaluating human health following environmental exposure and the development and progression of numerous diseases. As MS technology develops so do statistical and machine learning methods for the detection of molecular deviations from personalized metabolism, which are correlated to altered health conditions, and they are intended to provide a multi-disciplinary overview for researchers interested in adding multiomic analysis to their current efforts. This includes an introduction to mass spectrometry-based omics technologies, current state-of-the-art capabilities and their respective strengths and limitations for surveying molecular information. Furthermore, we describe how knowledge gained from these assessments can be applied to personalized medicine and diagnostic strategies.
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Affiliation(s)
- Christina R Ferreira
- Purdue Metabolite Profiling Facility, Purdue University, West Lafayette, IN 47907, USA.
| | | | - Kiley Marie Robison
- School of Health Sciences, College of Health and Human Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Bruce R Cooper
- Purdue Metabolite Profiling Facility, Purdue University, West Lafayette, IN 47907, USA.
| | - Jonathan H Shannahan
- School of Health Sciences, College of Health and Human Sciences, Purdue University, West Lafayette, IN 47907, USA
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2
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Sangermano R, Gupta P, Price C, Han J, Navarro J, Condroyer C, Place EM, Antonio A, Mukai S, Zanlonghi X, Sahel JA, Duncan JL, Pierce EA, Zeitz C, Audo I, Huckfeldt RM, Bujakowska KM. Coding and non-coding variants in the ciliopathy gene CFAP410 cause early-onset non-syndromic retinal degeneration. RESEARCH SQUARE 2024:rs.3.rs-3871956. [PMID: 38405922 PMCID: PMC10889070 DOI: 10.21203/rs.3.rs-3871956/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Inherited retinal degenerations are blinding genetic disorders characterized by high genetic and phenotypic heterogeneity. The implementation of next-generation sequencing in routine diagnostics, together with advanced clinical phenotyping including multimodal retinal imaging, have contributed to the increase of reports describing novel genotype-phenotype associations and phenotypic expansions. In this study, we describe sixteen families with early-onset non-syndromic retinal degenerations in which affected probands carried rare bi-allelic variants in CFAP410, a ciliary gene previously associated with syndromic recessive Jeune syndrome. The most common retinal phenotypes were cone-rod and rod-cone dystrophies, but the clinical presentations were unified by their early onset as well as the severe impact on central visual function. Twelve variants were detected (three pathogenic, seven likely pathogenic, two of uncertain significance), eight of which were novel. One deep intronic change, c.373+91A>G, led to the creation of a cryptic splice acceptor site in intron four, followed by the inclusion of a 200- base pair pseudoexon and subsequent premature stop codon formation. To our knowledge this is the first likely pathogenic deep-intronic variant identified in this gene. Meta-analysis of all published and novel CFAP410 variants revealed no clear correlation between the severity of the CFAP410-associated phenotypes and the identified causal variants. This is supported by the fact that the frequently encountered missense variant p.(Arg73Pro), often found in syndromic cases, was also associated with non-syndromic retinal degeneration. This study expands the current knowledge of CFAP410-associated ciliopathy by enriching its mutational landscape and supports its association with non-syndromic retinal degeneration.
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Affiliation(s)
- Riccardo Sangermano
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Priya Gupta
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Cherrell Price
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Jinu Han
- Institute of Vision Research, Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Julien Navarro
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Emily M. Place
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Aline Antonio
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Shizuo Mukai
- Retina Service, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Xavier Zanlonghi
- Centre de compétence maladies rares, Service d’Ophtalmologie, CHU Rennes, Rennes, France
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, Centre de Référence Maladies Rares REFERET and INSERM-DGOS CIC 1423, Paris, France
- Vision Institute, University of Pittsburgh Medical Center and School of Medicine, Pennsylvania, USA
| | - Jacque L. Duncan
- Department of Ophthalmology, University of California, San Francisco, California, USA
| | - Eric A. Pierce
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, Centre de Référence Maladies Rares REFERET and INSERM-DGOS CIC 1423, Paris, France
| | - Rachel M. Huckfeldt
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Kinga M. Bujakowska
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
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3
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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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4
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Peynshaert K, Devoldere J, De Smedt S, Remaut K. Every nano-step counts: a critical reflection on do's and don'ts in researching nanomedicines for retinal gene therapy. Expert Opin Drug Deliv 2023; 20:259-271. [PMID: 36630275 DOI: 10.1080/17425247.2023.2167979] [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: 01/12/2023]
Abstract
INTRODUCTION Retinal disease affects millions of people worldwide, generating a massive social and economic burden. Current clinical trials for retinal diseases are dominated by gene augmentation therapies delivered with recombinant viruses as key players. As an alternative, nanoparticles hold great promise for the delivery of nucleic acid therapeutics as well. Nevertheless, despite numerous attempts, 'nano' is in practice not as successful as aspired and major breakthroughs in retinal gene therapy applying nanomaterials are yet to be seen. AREAS COVERED In this review, we summarize the advantages of nanomaterials and give an overview of nanoparticles designed for retinal nucleic acid delivery up to now. We furthermore critically reflect on the predominant issues that currently limit nano to progress to the clinic, where faulty study design and the absence of representative models play key roles. EXPERT OPINION Since the current approach of in vitro - in vivo experimentation is highly inefficient and creates misinformation, we advocate for a more prominent role for ex vivo testing early on in nanoparticle research. In addition, we elaborate on several concepts, including systematic studies and open science, which could aid in pushing the field of nanomedicine beyond the preclinical stage.
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Affiliation(s)
- Karen Peynshaert
- Lab of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Belgium Belgium.,Ghent Research Group on Nanomedicines, Ghent University, Belgium Belgium
| | - Joke Devoldere
- Lab of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Belgium Belgium.,Ghent Research Group on Nanomedicines, Ghent University, Belgium Belgium
| | - Stefaan De Smedt
- Lab of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Belgium Belgium.,Ghent Research Group on Nanomedicines, Ghent University, Belgium Belgium
| | - Katrien Remaut
- Lab of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Belgium Belgium.,Ghent Research Group on Nanomedicines, Ghent University, Belgium Belgium
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5
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Mc Clinton B, Corradi Z, McKibbin M, Panneman DM, Roosing S, Boonen EGM, Ali M, Watson CM, Steel DH, Cremers FPM, Inglehearn CF, Hitti-Malin RJ, Toomes C. Effective smMIPs-Based Sequencing of Maculopathy-Associated Genes in Stargardt Disease Cases and Allied Maculopathies from the UK. Genes (Basel) 2023; 14:191. [PMID: 36672932 PMCID: PMC9859292 DOI: 10.3390/genes14010191] [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: 12/09/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/13/2023] Open
Abstract
Macular dystrophies are a group of individually rare but collectively common inherited retinal dystrophies characterised by central vision loss and loss of visual acuity. Single molecule Molecular Inversion Probes (smMIPs) have proved effective in identifying genetic variants causing macular dystrophy. Here, a previously established smMIPs panel tailored for genes associated with macular diseases has been used to examine 57 UK macular dystrophy cases, achieving a high solve rate of 63.2% (36/57). Among 27 bi-allelic STGD1 cases, only three novel ABCA4 variants were identified, illustrating that the majority of ABCA4 variants in Caucasian STGD1 cases are currently known. We examined cases with ABCA4-associated disease in detail, comparing our results with a previously reported variant grading system, and found this model to be accurate and clinically useful. In this study, we showed that ABCA4-associated disease could be distinguished from other forms of macular dystrophy based on clinical evaluation in the majority of cases (34/36).
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Affiliation(s)
- Benjamin Mc Clinton
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
| | - Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Martin McKibbin
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
- Department of Ophthalmology, St. James’s University Hospital, Leeds LS9 7TF, UK
| | - Daan M. Panneman
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Erica G. M. Boonen
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Manir Ali
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
| | - Christopher M. Watson
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
- North East and Yorkshire Genomic Laboratory Hub, Central Lab, St. James’s University Hospital, Leeds LS9 7TF, UK
| | - David H. Steel
- Sunderland Eye Infirmary, Sunderland SR2 9HP, UK
- The Bioscience Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Chris F. Inglehearn
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
| | - Rebekkah J. Hitti-Malin
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Carmel Toomes
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
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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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7
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Smirnov VM, Robert MP, Condroyer C, Navarro J, Antonio A, Rozet JM, Sahel JA, Perrault I, Audo I, Zeitz C. Association of Missense Variants in VSX2 With a Peculiar Form of Congenital Stationary Night Blindness Affecting All Bipolar Cells. JAMA Ophthalmol 2022; 140:1163-1173. [PMID: 36264558 PMCID: PMC9585472 DOI: 10.1001/jamaophthalmol.2022.4146] [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: 04/12/2022] [Accepted: 08/23/2022] [Indexed: 01/12/2023]
Abstract
Importance Congenital stationary night blindness (CSNB) is an inherited stationary retinal disorder that is clinically and genetically heterogeneous. To date, the genetic association between some cases with CSNB and an unusual complex clinical picture is unclear. Objective To describe an unreported CSNB phenotype and the associated gene defect in 3 patients from 2 unrelated families. Design, Setting, and Participants This retrospective case series was conducted in 2021 and 2022 at a national referral center for rare ocular diseases. Data for 3 patients from a cohort of 140 genetically unsolved CSNB cases were analyzed clinically and genetically. Exposures Complete ocular examination including full-field electroretinography and multimodal fundus imaging (spectral-domain optical coherence tomography, color, infrared reflectance, and short-wavelength autofluorescence photographs) were performed. The gene defect was identified by exome sequencing and confirmed by Sanger sequencing and co-segregation analysis in 1 family. Screening was performed for genetically unsolved CSNB cases for VSX2 variants by direct Sanger sequencing. Main Outcomes and Measures Ocular and molecular biology findings. Results The series included 3 patients whose clinical investigations occurred at ages in the early 30s, younger than 12 years, and in the mid 40s. They had nystagmus, low stable visual acuity, and myopia from birth and experienced night blindness. Two older patients had bilateral lens luxation and underwent lens extraction. Full-field electroretinography revealed an electronegative Schubert-Bornschein appearance, combining characteristics of incomplete and complete CSNB, affecting the function of rod and cone ON- and OFF-bipolar cells. Exome sequencing and co-segregation analysis in a consanguineous family with 2 affected members identified a homozygous variant in VSX2. Subsequently, screening of the CSNB cohort identified another unrelated patient harboring a distinct VSX2 variant. Conclusions and Relevance This case series revealed a peculiar pan-bipolar cell retinopathy with lens luxation associated with variants in VSX2. Clinicians should be aware of this association and VSX2 added to CSNB diagnostic gene panels.
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Affiliation(s)
- Vasily M. Smirnov
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- Université de Lille, Faculté de Médecine, Lille, France
- Exploration de la Vision et Neuro-Ophtalmologie, CHU de Lille, Lille, France
| | - Matthieu P. Robert
- Ophthalmology Department, Hôpital Universitaire Necker-Enfants Malades, Paris, France
- Borelli Centre, UMR 9010, CNRS-SSA-ENS Paris Saclay-Paris University, Gif-sur-Yvette, France
| | | | - Julien Navarro
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Aline Antonio
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Jean-Michel Rozet
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR 1163, Institute of Genetic Diseases, Imagine Institute, and Paris University, Paris, France
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, Centre de Référence Maladies Rares REFERET and INSERM-DGOS CIC 1423, Paris, France
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Isabelle Perrault
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR 1163, Institute of Genetic Diseases, Imagine Institute, and Paris University, Paris, France
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, Centre de Référence Maladies Rares REFERET and INSERM-DGOS CIC 1423, Paris, France
| | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
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8
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Large Benefit from Simple Things: High-Dose Vitamin A Improves RBP4-Related Retinal Dystrophy. Int J Mol Sci 2022; 23:ijms23126590. [PMID: 35743034 PMCID: PMC9223508 DOI: 10.3390/ijms23126590] [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] [Received: 04/22/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 02/04/2023] Open
Abstract
Inherited retinal diseases (IRD) are a group of heterogeneous disorders, most of which lead to blindness with limited therapeutic options. Pathogenic variants in RBP4, coding for a major blood carrier of retinol, retinol-binding protein 4, are responsible for a peculiar form of IRD. The aim of this study was to investigate if retinal function of an RBP4-related IRD patient can be improved by retinol administration. Our patient presented a peculiar white-dot retinopathy, reminiscent of vitamin A deficient retinopathy. Using a customized next generation sequencing (NGS) IRD panel we discovered a novel loss-of-function homozygous pathogenic variant in RBP4: c.255G >A, p.(Trp85*). Western blotting revealed the absence of RBP4 protein in the patient’s serum. Blood retinol levels were undetectable. The patient was put on a high-dose oral retinol regimen (50,000 UI twice a week). Subjective symptoms and retinal function markedly and sustainably improved at 5-months and 1-year follow-up. Here we show that this novel IRD case can be treated by oral retinol administration.
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9
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Jaffal L, Akhdar H, Joumaa H, Ibrahim M, Chhouri Z, Assi A, Helou C, Lee H, Seo GH, Joumaa WH, El Shamieh S. Novel Missense and Splice Site Mutations in USH2A, CDH23, PCDH15, and ADGRV1 Are Associated With Usher Syndrome in Lebanon. Front Genet 2022; 13:864228. [PMID: 35651951 PMCID: PMC9149366 DOI: 10.3389/fgene.2022.864228] [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] [Received: 01/28/2022] [Accepted: 03/28/2022] [Indexed: 01/02/2023] Open
Abstract
The purpose of this study was to expand the mutation spectrum by searching the causative mutations in nine Lebanese families with Usher syndrome (USH) using whole-exome sequencing. The pathogenicity of candidate mutations was first evaluated according to their frequency, conservation, and in silico prediction tools. Then, it was confirmed via Sanger sequencing, followed by segregation analysis. Finally, a meta-analysis was conducted to calculate the prevalence of USH genes in the Lebanese population. Three missense mutations, two splice site mutations, and one insertion/deletion were detected in eight of the families. Four of these variants were novel: c.5535C > A; p.(Asn1845Lys) in exon 41 of CDH23, c.7130G > A; p.(Arg2377Gln) in exon 32 of ADGRV1, c.11390-1G > A in USH2A, and c.3999–6A > G in PCDH15. All the identified mutations were shown to be likely disease-causing through our bioinformatics analysis and co-segregated with the USH phenotype. The mutations were classified according to the ACMG standards. Finally, our meta-analysis showed that the mutations in ADGRV1, USH2A, and CLRN1 are the most prevalent and responsible for approximately 75% of USH cases in Lebanon. Of note, the frequency USH type 3 showed a relatively high incidence (23%) compared to the worldwide prevalence, which is around 2–4%. In conclusion, our study has broadened the mutational spectrum of USH and showed a high heterogeneity of this disease in the Lebanese population.
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Affiliation(s)
- Lama Jaffal
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon.,Department of Biological and Chemical Sciences, School of Arts and Sciences, Lebanese International University, Beirut, Lebanon
| | - Hanane Akhdar
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon.,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
| | - Mariam Ibrahim
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Zahraa Chhouri
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Alexandre Assi
- Retinal Service, Beirut Eye & ENT Specialist Hospital, Beirut, Lebanon
| | - Charles Helou
- Retinal Service, Beirut Eye & ENT Specialist Hospital, Beirut, Lebanon
| | - Hane Lee
- Rare Genetic Disease Research Center, 3billion Inc, Seoul, South Korea
| | - Go Hun Seo
- Rare Genetic Disease Research Center, 3billion Inc, Seoul, South Korea
| | - Wissam H Joumaa
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Said El Shamieh
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon.,Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
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Assessing Photoreceptor Status in Retinal Dystrophies: From High-Resolution Imaging to Functional Vision. Am J Ophthalmol 2021; 230:12-47. [PMID: 34000280 PMCID: PMC8682761 DOI: 10.1016/j.ajo.2021.04.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/15/2021] [Accepted: 04/15/2021] [Indexed: 01/05/2023]
Abstract
Purpose To describe the value of integrating phenotype/genotype data, disease staging, and evaluation of functional vision in patient-centered management of retinal dystrophies. Methods (1) Cross-sectional structure-function and retrospective longitudinal studies to assess the correlations between standard fundus autofluorescence (FAF), optical coherence tomography, visual acuity (VA), and perimetry (visual field [VF]) examinations to evaluate photoreceptor functional loss in a cohort of patients with rod-cone dystrophy (RCD); (2) flood-illumination adaptive optics (FIAO) imaging focusing on photoreceptor misalignment and orientation of outer segments; and (3) evaluation of the impact of visual impairment in daily life activities, based on functional (visual and mobility) vision assessment in a naturalistic environment in visually impaired subjects with RCD and subjects treated with LuxturnaⓇ for RPE65-related Leber congenital amaurosis before and after therapy. Results The results of the cross-sectional transversal study showed that (1) VA and macular sensitivity were weakly correlated with the structural variables; and (2) functional impairment (VF) was correlated with reduction of anatomical markers of photoreceptor structure and increased width of autofluorescent ring. The dimensions of the ring of increased FAF evolved faster. Other criteria that differed among groups were the lengths of the ellipsoid zone, the external limiting membrane, and the foveal thickness. FIAO revealed a variety of phenotypes: paradoxical visibility of foveal cones; heterogeneous brightness of cones; dim, inner segment–like, and RPE-like mosaic. Directional illumination by varying orientation of incident light (Stiles-Crawford effect) and the amount of side illumination (gaze-dependent imaging) affected photoreceptor visibility. Mobility assessment under different lighting conditions showed correlation with VF, VA, contrast sensitivity (CS), and dark adaptation, with different predictive values depending on mobility study paradigms and illumination level. At high illumination level (235 lux), VF was a predictor for all mobility performance models. Under low illumination (1 and 2 lux), VF was the most significant predictor of mobility performance variables, while CS best explained the number of collisions and segments. In subjects treated with LuxturnaⓇ, a very favorable impact on travel speed and reduction in the number of collisions, especially at low luminance, was observable 6 months following injection, in both children and adults. Conclusions Our results suggest the benefit of development and implementation of quantitative and reproducible tools to evaluate the status of photoreceptors and the impact of both visual impairment and novel therapies in real-life conditions. NOTE: Publication of this article is sponsored by the American Ophthalmological Society.
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11
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Koschak A, Fernandez-Quintero ML, Heigl T, Ruzza M, Seitter H, Zanetti L. Cav1.4 dysfunction and congenital stationary night blindness type 2. Pflugers Arch 2021; 473:1437-1454. [PMID: 34212239 PMCID: PMC8370969 DOI: 10.1007/s00424-021-02570-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/14/2021] [Accepted: 04/18/2021] [Indexed: 12/04/2022]
Abstract
Cav1.4 L-type Ca2+ channels are predominantly expressed in retinal neurons, particularly at the photoreceptor terminals where they mediate sustained Ca2+ entry needed for continuous neurotransmitter release at their ribbon synapses. Cav1.4 channel gating properties are controlled by accessory subunits, associated regulatory proteins, and also alternative splicing. In humans, mutations in the CACNA1F gene encoding for Cav1.4 channels are associated with X-linked retinal disorders such as congenital stationary night blindness type 2. Mutations in the Cav1.4 protein result in a spectrum of altered functional channel activity. Several mouse models broadened our understanding of the role of Cav1.4 channels not only as Ca2+ source at retinal synapses but also as synaptic organizers. In this review, we highlight different structural and functional phenotypes of Cav1.4 mutations that might also occur in patients with congenital stationary night blindness type 2. A further important yet mostly neglected aspect that we discuss is the influence of alternative splicing on channel dysfunction. We conclude that currently available functional phenotyping strategies should be refined and summarize potential specific therapeutic options for patients carrying Cav1.4 mutations. Importantly, the development of new therapeutic approaches will permit a deeper understanding of not only the disease pathophysiology but also the physiological function of Cav1.4 channels in the retina.
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MESH Headings
- 3-Pyridinecarboxylic acid, 1,4-dihydro-2,6-dimethyl-5-nitro-4-(2-(trifluoromethyl)phenyl)-, Methyl ester/pharmacology
- Animals
- Calcium Channel Agonists/pharmacology
- Calcium Channels, L-Type/genetics
- Calcium Channels, L-Type/metabolism
- Eye Diseases, Hereditary/genetics
- Eye Diseases, Hereditary/metabolism
- Genetic Diseases, X-Linked/genetics
- Genetic Diseases, X-Linked/metabolism
- Humans
- Mutation/physiology
- Myopia/genetics
- Myopia/metabolism
- Night Blindness/genetics
- Night Blindness/metabolism
- Retina/drug effects
- Retina/metabolism
- Synapses/drug effects
- Synapses/genetics
- Synapses/metabolism
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Affiliation(s)
- Alexandra Koschak
- Institute of Pharmacy, Pharmacology and Toxicology, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82/III, 6020, Innsbruck, Austria.
| | - Monica L Fernandez-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82/III, 6020, Innsbruck, Austria
| | - Thomas Heigl
- Institute of Pharmacy, Pharmacology and Toxicology, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82/III, 6020, Innsbruck, Austria
| | - Marco Ruzza
- Institute of Pharmacy, Pharmacology and Toxicology, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82/III, 6020, Innsbruck, Austria
| | - Hartwig Seitter
- Institute of Pharmacy, Pharmacology and Toxicology, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82/III, 6020, Innsbruck, Austria
| | - Lucia Zanetti
- Institute of Pharmacy, Pharmacology and Toxicology, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82/III, 6020, Innsbruck, Austria
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12
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Mutated CCDC51 Coding for a Mitochondrial Protein, MITOK Is a Candidate Gene Defect for Autosomal Recessive Rod-Cone Dystrophy. Int J Mol Sci 2021; 22:ijms22157875. [PMID: 34360642 PMCID: PMC8346125 DOI: 10.3390/ijms22157875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/05/2021] [Accepted: 07/15/2021] [Indexed: 11/17/2022] Open
Abstract
The purpose of this work was to identify the gene defect underlying a relatively mild rod-cone dystrophy (RCD), lacking disease-causing variants in known genes implicated in inherited retinal disorders (IRD), and provide transcriptomic and immunolocalization data to highlight the best candidate. The DNA of the female patient originating from a consanguineous family revealed no large duplication or deletion, but several large homozygous regions. In one of these, a homozygous frameshift variant, c.244_246delins17 p.(Trp82Valfs*4); predicted to lead to a nonfunctional protein, was identified in CCDC51. CCDC51 encodes the mitochondrial coiled-coil domain containing 51 protein, also called MITOK. MITOK ablation causes mitochondrial dysfunction. Here we show for the first time that CCDC51/MITOK localizes in the retina and more specifically in the inner segments of the photoreceptors, well known to contain mitochondria. Mitochondrial proteins have previously been implicated in IRD, although usually in association with syndromic disease, unlike our present case. Together, our findings add another ultra-rare mutation implicated in non-syndromic IRD, whose pathogenic mechanism in the retina needs to be further elucidated.
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13
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Colombo L, Maltese PE, Castori M, El Shamieh S, Zeitz C, Audo I, Zulian A, Marinelli C, Benedetti S, Costantini A, Bressan S, Percio M, Ferri P, Abeshi A, Bertelli M, Rossetti L. Molecular Epidemiology in 591 Italian Probands With Nonsyndromic Retinitis Pigmentosa and Usher Syndrome. Invest Ophthalmol Vis Sci 2021; 62:13. [PMID: 33576794 PMCID: PMC7884295 DOI: 10.1167/iovs.62.2.13] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Purpose To describe the molecular epidemiology of nonsyndromic retinitis pigmentosa (RP) and Usher syndrome (US) in Italian patients. Methods A total of 591 probands (315 with family history and 276 sporadics) were analyzed. For 155 of them, we performed a family segregation study, considering a total of 382 relatives. Probands were analyzed by a customized multigene panel approach. Sanger sequencing was used to validate all genetic variants and to perform family segregation studies. Copy number variants of selected genes were analyzed by multiplex ligation-dependent probe amplification. Four patients who tested negative to targeted next-generation sequencing analysis underwent clinical exome sequencing. Results The mean diagnostic yield of molecular testing among patients with a family history of retinal disorders was 55.2% while the diagnostic yield including sporadic cases was 37.4%. We found 468 potentially pathogenic variants, 147 of which were unpublished, in 308 probands and 66 relatives. Mean ages of onset of the different classes of RP were autosomal dominant RP, 19.3 ± 12.6 years; autosomal recessive RP, 23.2 ± 16.6 years; X-linked RP, 13.9 ± 9.9 years; and Usher syndrome, 18.9 ± 9.5 years. We reported potential new genotype-phenotype correlations in three probands, two revealed by TruSight One testing. All three probands showed isolated RP caused by biallelic variants in genes usually associated with syndromes such as PERCHING and Senior-Loken or with retinal dystrophy, iris coloboma, and comedogenic acne syndrome. Conclusions This is the largest molecular study of Italian patients with RP in the literature, thus reflecting the epidemiology of the disease in Italy with reasonable accuracy.
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Affiliation(s)
- Leonardo Colombo
- Department of Ophthalmology, ASST Santi Paolo e Carlo Hospital, University of Milan, Milan, Italy
| | | | - Marco Castori
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Said El Shamieh
- Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon.,Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHUSight Restore, INSERM-DGOS CIC1423, Paris, France
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHUSight Restore, INSERM-DGOS CIC1423, Paris, France
| | | | | | | | | | | | | | - Paolo Ferri
- Department of Ophthalmology, ASST Santi Paolo e Carlo Hospital, University of Milan, Milan, Italy
| | - Andi Abeshi
- MAGI's Lab s.r.l., Rovereto, Italy.,Department of Otolaryngology, Sant'Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | | | - Luca Rossetti
- Department of Ophthalmology, ASST Santi Paolo e Carlo Hospital, University of Milan, Milan, Italy
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14
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Partial recovery of visual function in a blind patient after optogenetic therapy. Nat Med 2021; 27:1223-1229. [PMID: 34031601 DOI: 10.1038/s41591-021-01351-4] [Citation(s) in RCA: 266] [Impact Index Per Article: 88.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 04/13/2021] [Indexed: 02/04/2023]
Abstract
Optogenetics may enable mutation-independent, circuit-specific restoration of neuronal function in neurological diseases. Retinitis pigmentosa is a neurodegenerative eye disease where loss of photoreceptors can lead to complete blindness. In a blind patient, we combined intraocular injection of an adeno-associated viral vector encoding ChrimsonR with light stimulation via engineered goggles. The goggles detect local changes in light intensity and project corresponding light pulses onto the retina in real time to activate optogenetically transduced retinal ganglion cells. The patient perceived, located, counted and touched different objects using the vector-treated eye alone while wearing the goggles. During visual perception, multichannel electroencephalographic recordings revealed object-related activity above the visual cortex. The patient could not visually detect any objects before injection with or without the goggles or after injection without the goggles. This is the first reported case of partial functional recovery in a neurodegenerative disease after optogenetic therapy.
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15
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Smirnov V, Grunewald O, Muller J, Zeitz C, Obermaier CD, Devos A, Pelletier V, Bocquet B, Andrieu C, Bacquet JL, Lebredonchel E, Mohand-Saïd S, Defoort-Dhellemmes S, Sahel JA, Dollfus H, Zanlonghi X, Audo I, Meunier I, Boulanger-Scemama E, Dhaenens CM. Novel TTLL5 Variants Associated with Cone-Rod Dystrophy and Early-Onset Severe Retinal Dystrophy. Int J Mol Sci 2021; 22:ijms22126410. [PMID: 34203883 PMCID: PMC8232641 DOI: 10.3390/ijms22126410] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 01/05/2023] Open
Abstract
Variants of the TTLL5 gene, which encodes tubulin tyrosine ligase-like family member five, are a rare cause of cone dystrophy (COD) or cone-rod dystrophy (CORD). To date, only a few TTLL5 patients have been clinically and genetically described. In this study, we report five patients harbouring biallelic variants of TTLL5. Four adult patients presented either COD or CORD with onset in the late teenage years. The youngest patient had a phenotype of early onset severe retinal dystrophy (EOSRD). Genetic analysis was performed by targeted next generation sequencing of gene panels and assessment of copy number variants (CNV). We identified eight variants, of which six were novel, including two large multiexon deletions in patients with COD or CORD, while the EOSRD patient harboured the novel homozygous p.(Trp640*) variant and three distinct USH2A variants, which might explain the observed rod involvement. Our study highlights the role of TTLL5 in COD/CORD and the importance of large deletions. These findings suggest that COD or CORD patients lacking variants in known genes may harbour CNVs to be discovered in TTLL5, previously undetected by classical sequencing methods. In addition, variable phenotypes in TTLL5-associated patients might be due to the presence of additional gene defects.
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Affiliation(s)
- Vasily Smirnov
- Université de Lille, Faculté de Médecine, 59037 Lille, France;
- CHU Lille, Service d’Exploration Fonctionnelle de la Vision et de Neuro-Ophtalmologie, Hôpital Salengro, 59037 Lille, France;
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (C.Z.); (S.M.-S.); (J.-A.S.); (I.A.)
| | - Olivier Grunewald
- Univ. Lille, Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience & Cognition, 59045 Lille, France;
| | - Jean Muller
- Laboratoire de Génétique Médicale, Institut de Génétique Médicale d’Alsace (IGMA), INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg UMRS_1112, 67000 Strasbourg, France;
- Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d’Alsace (IGMA), 67000 Strasbourg, France
| | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (C.Z.); (S.M.-S.); (J.-A.S.); (I.A.)
| | - Carolin D. Obermaier
- Praxis für Humangenetik Tuebingen & Center for Genomics and Transcriptomics, CeGaT GmbH, 72076 Tuebingen, Germany;
| | - Aurore Devos
- Univ. Lille, CHU Lille, Service de Toxicologie et Génopathies, 59037 Lille, France; (A.D.); (E.L.)
| | - Valérie Pelletier
- Centre de Référence pour les Affections Rares en Génétique Ophtalmologiques, Hopitaux Universitaires de Strasbourg, 67000 Strasbourg, France; (V.P.); (J.-L.B.); (H.D.)
| | - Béatrice Bocquet
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, Montpellier University Hospital, Sensgene Care Network, ERN-EYE Network, 34295 Montpellier, France; (B.B.); (I.M.)
- Institute for Neurosciences of Montpellier (INM), INSERM, University of Montpellier, INSERM, 34295 Montpellier, France
| | - Camille Andrieu
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, INSERM-DHOS CIC 1423, 75012 Paris, France;
| | - Jean-Louis Bacquet
- Centre de Référence pour les Affections Rares en Génétique Ophtalmologiques, Hopitaux Universitaires de Strasbourg, 67000 Strasbourg, France; (V.P.); (J.-L.B.); (H.D.)
| | - Elodie Lebredonchel
- Univ. Lille, CHU Lille, Service de Toxicologie et Génopathies, 59037 Lille, France; (A.D.); (E.L.)
| | - Saddek Mohand-Saïd
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (C.Z.); (S.M.-S.); (J.-A.S.); (I.A.)
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, INSERM-DHOS CIC 1423, 75012 Paris, France;
| | - Sabine Defoort-Dhellemmes
- CHU Lille, Service d’Exploration Fonctionnelle de la Vision et de Neuro-Ophtalmologie, Hôpital Salengro, 59037 Lille, France;
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (C.Z.); (S.M.-S.); (J.-A.S.); (I.A.)
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, INSERM-DHOS CIC 1423, 75012 Paris, France;
- Fondation Ophtalmologique Adolphe de Rothschild, 75019 Paris, France;
- Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Hélène Dollfus
- Centre de Référence pour les Affections Rares en Génétique Ophtalmologiques, Hopitaux Universitaires de Strasbourg, 67000 Strasbourg, France; (V.P.); (J.-L.B.); (H.D.)
| | | | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (C.Z.); (S.M.-S.); (J.-A.S.); (I.A.)
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, INSERM-DHOS CIC 1423, 75012 Paris, France;
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Isabelle Meunier
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, Montpellier University Hospital, Sensgene Care Network, ERN-EYE Network, 34295 Montpellier, France; (B.B.); (I.M.)
- Institute for Neurosciences of Montpellier (INM), INSERM, University of Montpellier, INSERM, 34295 Montpellier, France
| | | | - Claire-Marie Dhaenens
- Univ. Lille, Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience & Cognition, 59045 Lille, France;
- Correspondence: ; Tel.: +33-320-444-953
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16
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Nassisi M, Smirnov VM, Solis Hernandez C, Mohand‐Saïd S, Condroyer C, Antonio A, Kühlewein L, Kempf M, Kohl S, Wissinger B, Nasser F, Ragi SD, Wang N, Sparrow JR, Greenstein VC, Michalakis S, Mahroo OA, Ba‐Abbad R, Michaelides M, Webster AR, Degli Esposti S, Saffren B, Capasso J, Levin A, Hauswirth WW, Dhaenens C, Defoort‐Dhellemmes S, Tsang SH, Zrenner E, Sahel J, Petersen‐Jones SM, Zeitz C, Audo I. CNGB1-related rod-cone dystrophy: A mutation review and update. Hum Mutat 2021; 42:641-666. [PMID: 33847019 PMCID: PMC8218941 DOI: 10.1002/humu.24205] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/26/2021] [Accepted: 04/08/2021] [Indexed: 12/29/2022]
Abstract
Cyclic nucleotide-gated channel β1 (CNGB1) encodes the 240-kDa β subunit of the rod photoreceptor cyclic nucleotide-gated ion channel. Disease-causing sequence variants in CNGB1 lead to autosomal recessive rod-cone dystrophy/retinitis pigmentosa (RP). We herein present a comprehensive review and analysis of all previously reported CNGB1 sequence variants, and add 22 novel variants, thereby enlarging the spectrum to 84 variants in total, including 24 missense variants (two of which may also affect splicing), 21 nonsense, 19 splicing defects (7 at noncanonical positions), 10 small deletions, 1 small insertion, 1 small insertion-deletion, 7 small duplications, and 1 gross deletion. According to the American College of Medical Genetics and Genomics classification criteria, 59 variants were considered pathogenic or likely pathogenic and 25 were variants of uncertain significance. In addition, we provide further phenotypic data from 34 CNGB1-related RP cases, which, overall, are in line with previous findings suggesting that this form of RP has long-term retention of useful central vision despite the early onset of night blindness, which is valuable for patient counseling, but also has implications for it being considered a priority target for gene therapy trials.
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Affiliation(s)
- Marco Nassisi
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
- Centre Hospitalier National d'Ophtalmologie des Quinze‐Vingts, INSERM‐DGOS CIC1423ParisFrance
- Department of Clinical Sciences and Community HealthUniversity of MilanMilanItaly
- Ophthalmological Unit, Fondazione IRCCS Ca' GrandaOspedale Maggiore PoliclinicoMilanItaly
| | - Vasily M. Smirnov
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
- Exploration de la vision et Neuro‐Ophthalmologie, CHU de LilleLilleFrance
- Faculté de MédecineUniversité de LilleLilleFrance
| | - Cyntia Solis Hernandez
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
| | - Saddek Mohand‐Saïd
- Centre Hospitalier National d'Ophtalmologie des Quinze‐Vingts, INSERM‐DGOS CIC1423ParisFrance
| | - Christel Condroyer
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
| | - Aline Antonio
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
| | - Laura Kühlewein
- University Eye Hospital, Centre for OphthalmologyUniversity of TübingenTübingenGermany
- Institute for Ophthalmic Research, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Melanie Kempf
- University Eye Hospital, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Susanne Kohl
- Institute for Ophthalmic Research, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Bernd Wissinger
- Institute for Ophthalmic Research, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Fadi Nasser
- University Eye Hospital, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Sara D. Ragi
- Department of OphthalmologyColumbia University, New YorkNew YorkUSA
| | - Nan‐Kai Wang
- Department of OphthalmologyColumbia University, New YorkNew YorkUSA
- College of MedicineChang Gung UniversityTaoyuanTaiwan
- Department of Ophthalmology, Chang Gung Memorial HospitalLinkou Medical CenterTaoyuanTaiwan
| | - Janet R. Sparrow
- Department of OphthalmologyColumbia University, New YorkNew YorkUSA
| | | | | | - Omar A. Mahroo
- Moorfields Eye HospitalLondonUK
- UCL Institute of Ophthalmology, University College LondonLondonUK
| | - Rola Ba‐Abbad
- Moorfields Eye HospitalLondonUK
- UCL Institute of Ophthalmology, University College LondonLondonUK
| | - Michel Michaelides
- Moorfields Eye HospitalLondonUK
- UCL Institute of Ophthalmology, University College LondonLondonUK
| | - Andrew R. Webster
- Moorfields Eye HospitalLondonUK
- UCL Institute of Ophthalmology, University College LondonLondonUK
| | - Simona Degli Esposti
- Moorfields Eye HospitalLondonUK
- UCL Institute of Ophthalmology, University College LondonLondonUK
| | - Brooke Saffren
- Philadelphia College of Osteopathic MedicinePhiladelphiaPennsylvaniaUSA
| | | | - Alex Levin
- Pediatric Ophthalmology and Ocular Genetics, Flaum Eye Institute, Pediatric Genetics, Golisano Children's HospitalUniversity of RochesterRochesterNew YorkUSA
| | | | - Claire‐Marie Dhaenens
- Univ. Lille, Inserm, CHU Lille, U1172‐LilNCog‐Lille Neuroscience & CognitionLilleFrance
| | | | - Stephen H. Tsang
- Department of OphthalmologyColumbia University, New YorkNew YorkUSA
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma LaboratoryNew YorkNew YorkUSA
- Department of Pathology and Cell BiologyColumbia UniversityNew YorkNew YorkUSA
- Stem Cell Initiative (CSCI), Institute of Human Nutrition, Vagelos College of Physicians and SurgeonsNew YorkNew YorkUSA
| | - Eberhart Zrenner
- University Eye Hospital, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Jose‐Alain Sahel
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
- Department of OphthalmologyThe University of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Fondation Ophtalmologique Adolphe de RothschildParisFrance
| | - Simon M. Petersen‐Jones
- Department of Small Animal Clinical SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Christina Zeitz
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
| | - Isabelle Audo
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
- Centre Hospitalier National d'Ophtalmologie des Quinze‐Vingts, INSERM‐DGOS CIC1423ParisFrance
- University College London Institute of OphthalmologyLondonUK
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17
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Next-Generation Sequencing Applications for Inherited Retinal Diseases. Int J Mol Sci 2021; 22:ijms22115684. [PMID: 34073611 PMCID: PMC8198572 DOI: 10.3390/ijms22115684] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 12/12/2022] Open
Abstract
Inherited retinal diseases (IRDs) represent a collection of phenotypically and genetically diverse conditions. IRDs phenotype(s) can be isolated to the eye or can involve multiple tissues. These conditions are associated with diverse forms of inheritance, and variants within the same gene often can be associated with multiple distinct phenotypes. Such aspects of the IRDs highlight the difficulty met when establishing a genetic diagnosis in patients. Here we provide an overview of cutting-edge next-generation sequencing techniques and strategies currently in use to maximise the effectivity of IRD gene screening. These techniques have helped researchers globally to find elusive causes of IRDs, including copy number variants, structural variants, new IRD genes and deep intronic variants, among others. Resolving a genetic diagnosis with thorough testing enables a more accurate diagnosis and more informed prognosis and should also provide information on inheritance patterns which may be of particular interest to patients of a child-bearing age. Given that IRDs are heritable conditions, genetic counselling may be offered to help inform family planning, carrier testing and prenatal screening. Additionally, a verified genetic diagnosis may enable access to appropriate clinical trials or approved medications that may be available for the condition.
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Nassisi M, Lavia C, Mohand-Said S, Smirnov V, Antonio A, Condroyer C, Sancho S, Varin J, Gaudric A, Zeitz C, Sahel JA, Audo I. Near-infrared fundus autofluorescence alterations correlate with swept-source optical coherence tomography angiography findings in patients with retinitis pigmentosa. Sci Rep 2021; 11:3180. [PMID: 33542393 PMCID: PMC7862375 DOI: 10.1038/s41598-021-82757-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 12/21/2020] [Indexed: 11/09/2022] Open
Abstract
Thirty-eight patients from 37 families with retinitis pigmentosa (RP) underwent macular 6 × 6-mm swept-source optical coherence tomography angiography (SS-OCTA) and 30° near-infrared fundus autofluorescence (NIR-FAF) acquisitions in one eye. Superficial vascular complex (SVC), deep capillary complex (DCC) and choriocapillaris (CC) angiograms were registered with NIR-FAF acquisitions to comparatively assess subjects with and without central area of preserved NIR-FAF (APA). On the subset of patients showing an APA, the vessel densities for SVC and DCC and flow deficits for CC were assessed in three directions (superior, inferior and temporal) from the fovea and compared to healthy 1:1 age-matched controls. Nine patients with no APA had evidence of severe central OCTA alterations at all levels, especially in the DCC. In the other 29 subjects presenting APA, all OCTA parameters were similar to healthy eyes within the APA, where the retina preserves its structural integrity. Outside the APA, both the DCC and CC were significantly reduced in all directions. These alterations are probably related to the outer retinal atrophy outside the APA. Comparing OCTA to other imaging modalities is helpful to determine the potential interest of OCTA findings as an outcome measure for disease status and progression.
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Affiliation(s)
- Marco Nassisi
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012, Paris, France. .,CHNO des Quinze-Vingts, INSERM-DGOS CIC1423, 28 rue de Charenton, 75012, Paris, France. .,Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy. .,Ophthalmological Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy.
| | - Carlo Lavia
- Université de Paris, Ophthalmology Department, AP-HP, Hôpital Lariboisière, 75010, Paris, France.,Surgical Department, Ophthalmology Service, Azienda Sanitaria Locale TO 5, 10023, Chieri, Italy
| | - Saddek Mohand-Said
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012, Paris, France.,CHNO des Quinze-Vingts, INSERM-DGOS CIC1423, 28 rue de Charenton, 75012, Paris, France
| | - Vasily Smirnov
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012, Paris, France
| | - Aline Antonio
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012, Paris, France
| | - Christel Condroyer
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012, Paris, France
| | - Serge Sancho
- CHNO des Quinze-Vingts, INSERM-DGOS CIC1423, 28 rue de Charenton, 75012, Paris, France
| | - Juliette Varin
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012, Paris, France
| | - Alain Gaudric
- Université de Paris, Ophthalmology Department, AP-HP, Hôpital Lariboisière, 75010, Paris, France
| | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012, Paris, France
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012, Paris, France.,CHNO des Quinze-Vingts, INSERM-DGOS CIC1423, 28 rue de Charenton, 75012, Paris, France.,Fondation Ophtalmologique Adolphe de Rothschild, 75019, Paris, France.,Department of Ophthalmology, University of Pittsburgh Medical School, Pittsburgh, PA, 15213, USA.,Académie des Sciences-Institut de France, 75006, Paris, France
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012, Paris, France. .,CHNO des Quinze-Vingts, INSERM-DGOS CIC1423, 28 rue de Charenton, 75012, Paris, France. .,Institute of Ophthalmology, University College of London, London, EC1V 9EL, UK.
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Diñeiro M, Capín R, Cifuentes GÁ, Fernández‐Vega B, Villota E, Otero A, Santiago A, Pruneda PC, Castillo D, Viejo‐Díaz M, Hernando I, Durán NS, Álvarez R, Lago CG, Ordóñez GR, Fernández‐Vega Á, Cabanillas R, Cadiñanos J. Comprehensive genomic diagnosis of inherited retinal and optical nerve disorders reveals hidden syndromes and personalized therapeutic options. Acta Ophthalmol 2020; 98:e1034-e1048. [PMID: 32483926 PMCID: PMC7754416 DOI: 10.1111/aos.14479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/29/2020] [Indexed: 01/14/2023]
Abstract
PURPOSE In the era of precision medicine, genomic characterization of blind patients is critical. Here, we evaluate the effects of comprehensive genetic analysis on the etiologic diagnosis of potentially hereditary vision loss and its impact on clinical management. METHODS We studied 100 non-syndromic and syndromic Spanish patients with a clinical diagnosis of blindness caused by alterations on the retina, choroid, vitreous and/or optic nerve. We used a next-generation sequencing (NGS) panel (OFTALMOgenics™), developed and validated within this study, including up to 362 genes previously associated with these conditions. RESULTS We identified the genetic cause of blindness in 45% of patients (45/100). A total of 28.9% of genetically diagnosed cases (13/45) were syndromic and, of those, in 30.8% (4/13) extraophthalmic features had been overlooked and/or not related to visual impairment before genetic testing, including cases with Mainzer-Saldino, Bardet-Biedl, mucolipidosis and MLCRD syndromes. In two additional cases-syndromic blindness had been proposed before, but not specifically diagnosed, and one patient with Heimler syndrome had been misdiagnosed as an Usher case before testing. 33.3% of the genetically diagnosed patients (15/45) had causative variants in genes targeted by clinical trials exploring the curative potential of gene therapy approaches. CONCLUSION Comprehensive genomic testing provided clinically relevant insights in a large proportion of blind patients, identifying potential therapeutic opportunities or previously undiagnosed syndromes in 42.2% of the genetically diagnosed cases (19/45).
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Affiliation(s)
- Marta Diñeiro
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Raquel Capín
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | | | | | - Eva Villota
- Instituto Oftalmológico Fernández‐Vega (IOFV)OviedoSpain
| | - Andrea Otero
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Adrián Santiago
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | | | - David Castillo
- Disease Research And Medicine (DREAMgenics) S. L.OviedoSpain
| | | | - Inés Hernando
- Hospital Universitario Central de AsturiasOviedoSpain
| | - Noelia S. Durán
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Rebeca Álvarez
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Claudia G. Lago
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | | | | | - Rubén Cabanillas
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Juan Cadiñanos
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
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20
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Al-khuzaei S, Broadgate S, Halford S, Jolly JK, Shanks M, Clouston P, Downes SM. Novel Pathogenic Sequence Variants in NR2E3 and Clinical Findings in Three Patients. Genes (Basel) 2020; 11:genes11111288. [PMID: 33138239 PMCID: PMC7716234 DOI: 10.3390/genes11111288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/21/2020] [Accepted: 10/28/2020] [Indexed: 01/08/2023] Open
Abstract
A retrospective review of the clinical records of patients seen at the Oxford Eye Hospital identified as having NR2E3 mutations was performed. The data included symptoms, best-corrected visual acuity, multimodal retinal imaging, visual fields and electrophysiology testing. Three participants were identified with biallelic NR2E3 pathogenic sequence variants detected using a targeted NGS gene panel, two of which were novel. Participant I was a Nepalese male aged 68 years, and participants II and III were white Caucasian females aged 69 and 10 years old, respectively. All three had childhood onset nyctalopia, a progressive decrease in central vision, and visual field loss. Patients I and III had photopsia, patient II had photosensitivity and patient III also had photophobia. Visual acuities in patients I and II were preserved even into the seventh decade, with the worst visual acuity measured at 6/36. Visual field constriction was severe in participant I, less so in II, and fields were full to bright targets targets in participant III. Electrophysiology testing in all three demonstrated loss of rod function. The three patients share some of the typical distinctive features of NR2E3 retinopathies, as well as a novel clinical observation of foveal ellipsoid thickening.
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Affiliation(s)
- Saoud Al-khuzaei
- Oxford Eye Hospital, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK; (S.A.-k.); (J.K.J.)
| | - Suzanne Broadgate
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Level 6 John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (S.B.); (S.H.)
| | - Stephanie Halford
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Level 6 John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (S.B.); (S.H.)
| | - Jasleen K. Jolly
- Oxford Eye Hospital, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK; (S.A.-k.); (J.K.J.)
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Level 6 John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (S.B.); (S.H.)
| | - Morag Shanks
- Oxford Medical Genetics Laboratory, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK; (M.S.); (P.C.)
| | - Penny Clouston
- Oxford Medical Genetics Laboratory, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK; (M.S.); (P.C.)
| | - Susan M. Downes
- Oxford Eye Hospital, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK; (S.A.-k.); (J.K.J.)
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Level 6 John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (S.B.); (S.H.)
- Correspondence:
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21
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Hull S, Kiray G, Chiang JPW, Vincent AL. Molecular and phenotypic investigation of a New Zealand cohort of childhood-onset retinal dystrophy. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:708-717. [PMID: 32856788 DOI: 10.1002/ajmg.c.31836] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/31/2020] [Accepted: 08/05/2020] [Indexed: 12/20/2022]
Abstract
Inherited retinal diseases are clinically heterogeneous and are associated with nearly 300 different genes. In this retrospective, observational study of a consecutive cohort of 159 patients (134 families) with childhood-onset (<16 years of age) retinal dystrophy, molecular investigations, and in-depth phenotyping were performed to determine key clinical and molecular characteristics. The most common ocular phenotype was rod-cone dystrophy in 40 patients. Leber Congenital Amaurosis, the most severe form of retinal dystrophy, was present in 10 patients, and early onset severe retinal dystrophy in 22 patients. Analysis has so far identified 131 pathogenic or likely pathogenic variants including 22 novel variants. Molecular diagnosis was achieved in 112 of 134 families (83.6%) by NGS gene panel investigation in 60 families, Sanger sequencing in 27 families, and Asper microarray in 25 families. An additional nine variants of uncertain significance were also found including three novel variants. Variants in 36 genes have been identified with the most common being ABCA4 retinopathy in 36 families. Five sporadic retinal dystrophy patients were found to have variants in dominant and X-linked genes (CRX, RHO, RP2, and RPGR) resulting in more accurate genetic counseling of inheritance for these families. Variants in syndromic associated genes including ALMS1, SDCCAG8, and PPT1 were identified in eight families enabling directed systemic care.
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Affiliation(s)
- Sarah Hull
- Department of Ophthalmology, University of Auckland, Auckland, New Zealand.,Department of Ophthalmology, Greenlane Clinical Centre, Auckland District Health Board, Auckland, New Zealand.,Institute of Ophthalmology, University College London, London, UK
| | - Gulunay Kiray
- Department of Ophthalmology, University of Auckland, Auckland, New Zealand.,Department of Ophthalmology, Greenlane Clinical Centre, Auckland District Health Board, Auckland, New Zealand
| | | | - Andrea L Vincent
- Department of Ophthalmology, University of Auckland, Auckland, New Zealand.,Department of Ophthalmology, Greenlane Clinical Centre, Auckland District Health Board, Auckland, New Zealand
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22
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Jackson D, Malka S, Harding P, Palma J, Dunbar H, Moosajee M. Molecular diagnostic challenges for non-retinal developmental eye disorders in the United Kingdom. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:578-589. [PMID: 32830442 PMCID: PMC8432170 DOI: 10.1002/ajmg.c.31837] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/30/2020] [Accepted: 08/05/2020] [Indexed: 12/14/2022]
Abstract
Overall, approximately one‐quarter of patients with genetic eye diseases will receive a molecular diagnosis. Patients with developmental eye disorders face a number of diagnostic challenges including phenotypic heterogeneity with significant asymmetry, coexisting ocular and systemic disease, limited understanding of human eye development and the associated genetic repertoire, and lack of access to next generation sequencing as regarded not to impact on patient outcomes/management with cost implications. Herein, we report our real world experience from a pediatric ocular genetics service over a 12 month period with 72 consecutive patients from 62 families, and that from a cohort of 322 patients undergoing whole genome sequencing (WGS) through the Genomics England 100,000 Genomes Project; encompassing microphthalmia, anophthalmia, ocular coloboma (MAC), anterior segment dysgenesis anomalies (ASDA), primary congenital glaucoma, congenital cataract, infantile nystagmus, and albinism. Overall molecular diagnostic rates reached 24.9% for those recruited to the 100,000 Genomes Project (73/293 families were solved), but up to 33.9% in the clinic setting (20/59 families). WGS was able to improve genetic diagnosis for MAC patients (15.7%), but not for ASDA (15.0%) and congenital cataracts (44.7%). Increased sample sizes and accurate human phenotype ontology (HPO) terms are required to improve diagnostic accuracy. The significant mixed complex ocular phenotypes distort these rates and lead to missed variants if the correct gene panel is not applied. Increased molecular diagnoses will help to explain the genotype–phenotype relationships of these developmental eye disorders. In turn, this will lead to improved integrated care pathways, understanding of disease, and future therapeutic development.
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Affiliation(s)
- Daniel Jackson
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Samantha Malka
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | | | - Juliana Palma
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Hannah Dunbar
- Moorfields Eye Hospital NHS Foundation Trust, London, UK.,UCL Institute of Ophthalmology, London, UK
| | - Mariya Moosajee
- Moorfields Eye Hospital NHS Foundation Trust, London, UK.,UCL Institute of Ophthalmology, London, UK.,Great Ormond Street Hospital for Children NHS Trust, London, UK.,The Francis Crick Institute, London, UK
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Garafalo AV, Cideciyan AV, Héon E, Sheplock R, Pearson A, WeiYang Yu C, Sumaroka A, Aguirre GD, Jacobson SG. Progress in treating inherited retinal diseases: Early subretinal gene therapy clinical trials and candidates for future initiatives. Prog Retin Eye Res 2020; 77:100827. [PMID: 31899291 PMCID: PMC8714059 DOI: 10.1016/j.preteyeres.2019.100827] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 12/21/2019] [Accepted: 12/26/2019] [Indexed: 12/15/2022]
Abstract
Due to improved phenotyping and genetic characterization, the field of 'incurable' and 'blinding' inherited retinal diseases (IRDs) has moved substantially forward. Decades of ascertainment of IRD patient data from Philadelphia and Toronto centers illustrate the progress from Mendelian genetic types to molecular diagnoses. Molecular genetics have been used not only to clarify diagnoses and to direct counseling but also to enable the first clinical trials of gene-based treatment in these diseases. An overview of the recent reports of gene augmentation clinical trials by subretinal injections is used to reflect on the reasons why there has been limited success in this early venture into therapy. These first-in human experiences have taught that there is a need for advancing the techniques of delivery of the gene products - not only for refining further subretinal trials, but also for evaluating intravitreal delivery. Candidate IRDs for intravitreal gene delivery are then suggested to illustrate some of the disorders that may be amenable to improvement of remaining central vision with the least photoreceptor trauma. A more detailed understanding of the human IRDs to be considered for therapy and the calculated potential for efficacy should be among the routine prerequisites for initiating a clinical trial.
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Affiliation(s)
- Alexandra V Garafalo
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Artur V Cideciyan
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Elise Héon
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Rebecca Sheplock
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alexander Pearson
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Caberry WeiYang Yu
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Alexander Sumaroka
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gustavo D Aguirre
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Samuel G Jacobson
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Wilgucki J, Williams PJ, Westfall E, Jain N, Yan J. Feasibility and Efficacy of Same-Day, In-Office Genetic Testing for Inherited Retinal Diseases. JOURNAL OF VITREORETINAL DISEASES 2020; 4:181-185. [PMID: 37007438 PMCID: PMC9982248 DOI: 10.1177/2474126419878145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
PURPOSE This article analyzes 2 practice patterns our institution uses for genetic testing of patients with inherited retinal diseases (IRDs) and compares testing completion and diagnostic yield rates. METHODS A retrospective, consecutive chart review series was conducted of patients with a clinically diagnosed rod-mediated IRD. All IRDs were diagnosed between 2 intervals: November 1, 2015, through November 30, 2016 (referral to a medical genetics clinic for testing) or December 1, 2016, through December 30, 2017 (same-day, in-office genetic testing). RESULTS A total of 189 patients were included in the study. Of patients who received an out-of-office referral for genetic testing, 10 of 84 (12%) patients proceeded with testing, whereas 74 of 84 (88%) patients did not complete testing. For patients who received in-office genetic testing, 104 of 105 (99%) completed testing. The difference in test completion was statistically significant (P < .001). In addition, genetic testing for out-of-office referrals identified a causative mutation in 5 of 10 (50%) patients, whereas in-office genetic testing identified a causative mutation in 42 of 104 (40.4%) patients. The difference in causative mutation discovery was not statistically significant (P = .18) between the 2 groups. CONCLUSIONS In-office genetic testing is a novel practice pattern that provides a more consistent and accessible method for IRD genetic diagnosis. Compared with an out-of-office referral for genetic testing, in-office genetic testing offers a similar rate of causative gene mutation identification but a greatly higher rate of test completion, therefore potentially offering a much higher yield for genetic diagnosis of IRDs.
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McGowan H, Madreperla OR, Snyder AL, Fine HF. Utility of a Genetic Screening Panel in Patients With Suspected Inherited Retinal Dystrophies. Ophthalmic Surg Lasers Imaging Retina 2020; 51:338-345. [PMID: 32579692 DOI: 10.3928/23258160-20200603-04] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/08/2020] [Indexed: 11/20/2022]
Abstract
BACKGROUND AND OBJECTIVE To evaluate disease characteristics and frequencies of genetic mutations in a cohort of patients with known or suspected retinal dystrophies. PATIENTS AND METHODS A cohort of 37 patients with known or suspected retinal dystrophies received genetic testing with a panel of 31 genes known to result in the development of retinal dystrophies. Disease characteristics identified during chart review were analyzed and related back to their associated genetic mutations in an attempt to link clinical features with genotypes. RESULTS Eighteen of 37 patients (48.6%) tested positive for a variant(s) in one or more of the 31 genes tested. Mutations were discovered in 14 of the 31 genes, with USH2A being the most frequently mutated gene. Both gene-positive and gene-negative patient groups had similar disease characteristics including reduced visual acuity, legal blindness, dyschromatopsia, nyctalopia, and reduced peripheral vision. CONCLUSIONS This investigation demonstrates the utility of genetic testing in a cohort of patients who carry a clinical diagnosis of retinal dystrophy. In this cohort, a significant number of patients had a genetic mutation or variant identified. [Ophthalmic Surg Lasers Imaging Retina. 2020;51:338-345.].
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26
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Roca I, González-Castro L, Maynou J, Palacios L, Fernández H, Couce ML, Fernández-Marmiesse A. PattRec: An easy-to-use CNV detection tool optimized for targeted NGS assays with diagnostic purposes. Genomics 2020; 112:1245-1256. [DOI: 10.1016/j.ygeno.2019.07.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/25/2019] [Accepted: 07/21/2019] [Indexed: 12/17/2022]
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27
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Sun Y, Li W, Li J, Wang Z, Bai J, Xu L, Xing B, Yang W, Wang Z, Wang L, He W, Chen F. Genetic and clinical findings of panel-based targeted exome sequencing in a northeast Chinese cohort with retinitis pigmentosa. Mol Genet Genomic Med 2020; 8:e1184. [PMID: 32100970 PMCID: PMC7196472 DOI: 10.1002/mgg3.1184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/15/2020] [Accepted: 01/31/2020] [Indexed: 12/18/2022] Open
Abstract
Background Panel‐based targeted exome sequencing was used to analyze the genetic and clinical findings of targeted genes in a cohort of northeast Chinese with retinitis pigmentosa. Methods A total of 87 subjects, comprising 23 probands and their family members (total patients: 32) with confirmed retinitis pigmentosa were recruited in the study. Panel‐based targeted exome sequencing was used to sequence the patients and family members, all subjects with retinitis pigmentosa underwent a complete ophthalmologic examination. Results Of the 23 probands, the clinical manifestations include night blindness, narrowing of vision, secondary cataracts, choroidal atrophy, color blindness, and high myopia, the average age of onset of night blindness is 12.9 ± 14 (range, 0–65; median, 8). Posterior subcapsular opacities is the most common forms of secondary cataracts (nine cases, 39.1%), and peripheral choroidal atrophy is the most common form of secondary choroidal atrophy (12 cases, 52.2%). Of these probands with complication peripheral choroidal atrophy, there were eight probands (66.7%, 8/12) caused by the pathogenic variation in USH2A gene. A total of 17 genes and 45 variants were detected in 23 probands. Among these genes, the commonest genes were USH2A (40%; 18/45), RP1 (15.6%; 7/45), and EYS (8.9%; 4/45), and the top three genes account for 56.5% (13/23) of diagnostic probands. Among these variants, comprising 22 (48.9%) pathogenic variants, 14 (31%) likely pathogenic variants, and nine (20%) uncertain clinical significance variants, and 22 variants was discovered first time. Most of the mutations associated with RP were missense (53.3%, 24/45), and the remaining mutation types include frameshift (35.6%, 16/45), nonsense (6.7%, 3/45), and spliceSite (4.4%, 2/45). Among the probands with mutations detected, compound heterozygous forms was detected in 13 (56.5%, 13/23) probands, and digenic inheritance (DI) forms was detected in five (21.7%, 5/23) probands. Conclusion Panel‐based targeted exome sequencing revealed 23 novel mutations, recognized different combinations forms of variants, and extended the mutational spectrum of retinitis pigmentosa and depicted common variants in northeast China.
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Affiliation(s)
- Yan Sun
- Shenyang He Eye Specialist HospitalShenyangChina
- He UniversityShenyangChina
| | - Wei Li
- He UniversityShenyangChina
- BGI Education CenterUniversity of Chinese Academy of SciencesShenzhenChina
- BGI‐ShenzhenShenzhenChina
| | - Jian‐kang Li
- BGI‐ShenzhenShenzhenChina
- Department of Computer ScienceCity University of Hong KongKowloonHong Kong
- Guangdong Provincial Key Laboratory of Human Disease Genomics Shenzhen Key Laboratory of GenomicsBGI-ShenzhenShenzhenChina
| | - Zhuo‐shi Wang
- Shenyang He Eye Specialist HospitalShenyangChina
- He UniversityShenyangChina
| | - Jin‐yue Bai
- School of Basic MedicineQingdao UniversityQingdaoChina
| | - Ling Xu
- Shenyang He Eye Specialist HospitalShenyangChina
- He UniversityShenyangChina
| | - Bo Xing
- School of Basic MedicineQingdao UniversityQingdaoChina
| | - Wen Yang
- BGI‐ShenzhenShenzhenChina
- Department of Computer ScienceCity University of Hong KongKowloonHong Kong
| | - Zi‐wei Wang
- BGI Education CenterUniversity of Chinese Academy of SciencesShenzhenChina
- BGI‐ShenzhenShenzhenChina
| | - Lu‐sheng Wang
- BGI‐ShenzhenShenzhenChina
- Department of Computer ScienceCity University of Hong KongKowloonHong Kong
| | - Wei He
- Shenyang He Eye Specialist HospitalShenyangChina
- He UniversityShenyangChina
| | - Fang Chen
- BGI‐ShenzhenShenzhenChina
- Guangdong Provincial Key Laboratory of Human Disease Genomics Shenzhen Key Laboratory of GenomicsBGI-ShenzhenShenzhenChina
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Khateb S, Nassisi M, Bujakowska KM, Méjécase C, Condroyer C, Antonio A, Foussard M, Démontant V, Mohand-Saïd S, Sahel JA, Zeitz C, Audo I. Longitudinal Clinical Follow-up and Genetic Spectrum of Patients With Rod-Cone Dystrophy Associated With Mutations in PDE6A and PDE6B. JAMA Ophthalmol 2020; 137:669-679. [PMID: 30998820 DOI: 10.1001/jamaophthalmol.2018.6367] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Importance A precise phenotypic characterization of retinal dystrophies is needed for disease modeling as a basis for future therapeutic interventions. Objective To compare genotype, phenotype, and structural changes in patients with rod-cone dystrophy (RCD) associated with mutations in PDE6A or PDE6B. Design, Setting, and Participants In a retrospective cohort study conducted in Paris, France, from January 2007 to September 2017, 54 patients from a cohort of 1095 index patients with RCD underwent clinical examination, including personal and familial history, best-corrected visual acuity (BCVA), color vision, slitlamp examination, full-field electroretinography, kinetic visual fields (VFs), retinophotography, optical coherence tomography, near-infrared fundus autofluorescence, and short-wavelength fundus autofluorescence imaging. Genotyping was performed using microarray analysis, targeted next-generation sequencing, and Sanger sequencing validation with familial segregation when possible. Data were analyzed from September 1, 2017, to February 1, 2018. Clinical variables were subsequently analyzed in 2018. Main Outcomes and Measures Phenotype and genotype comparison of patients carrying mutations in PDE6A or PDE6B. Results Of the 54 patients included in the study, 19 patients of 17 families (11 women [58%]; mean [SD] age at diagnosis, 14.83 [10.63] years) carried pathogenic mutations in PDE6A, and 35 patients of 26 families (17 women [49%]; mean [SD] age at diagnosis, 21.10 [11.56] years) had mutations in PDE6B, accounting for prevalences of 1.6% and 2.4%, respectively. Among 49 identified genetic variants, 14 in PDE6A and 15 in PDE6B were novel. Overall, phenotypic analysis revealed no substantial differences between the 2 groups except for night blindness as a presenting symptom that was noted to be more prevalent in the PDE6A than PDE6B group (80% vs 37%, respectively; P = .005). The mean binocular BCVA and VF decrease over time (measured as mean individual slopes coefficients) was comparable between patients with PDE6A and PDE6B mutations: 0.04 (0.12) vs 0.02 (0.05) for BCVA (P = .89) and 14.33 (7.12) vs 13.27 (6.77) for VF (P = .48). Conclusions and Relevance Mutations in PDE6A and PDE6B accounted for 1.6% and 2.4%, respectively, in a cohort of French patients with RCD. The functional and structural findings reported may constitute the basis of disease modeling that might be used for better prognostic estimation and candidate selection for photoreceptor therapeutic rescue.
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Affiliation(s)
- Samer Khateb
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre national de la recherche scientifique, Institut de la Vision, Paris, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU Sight Restore, Inserm-Direction Générale de l'Offre de Soins, CIC1423, Paris, France.,Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Marco Nassisi
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre national de la recherche scientifique, Institut de la Vision, Paris, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU Sight Restore, Inserm-Direction Générale de l'Offre de Soins, CIC1423, Paris, France
| | - Kinga M Bujakowska
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre national de la recherche scientifique, Institut de la Vision, Paris, France.,Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts
| | - Cécile Méjécase
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre national de la recherche scientifique, Institut de la Vision, Paris, France
| | - Christel Condroyer
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre national de la recherche scientifique, Institut de la Vision, Paris, France
| | - Aline Antonio
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre national de la recherche scientifique, Institut de la Vision, Paris, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU Sight Restore, Inserm-Direction Générale de l'Offre de Soins, CIC1423, Paris, France
| | - Marine Foussard
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre national de la recherche scientifique, Institut de la Vision, Paris, France
| | - Vanessa Démontant
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre national de la recherche scientifique, Institut de la Vision, Paris, France
| | - Saddek Mohand-Saïd
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre national de la recherche scientifique, Institut de la Vision, Paris, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU Sight Restore, Inserm-Direction Générale de l'Offre de Soins, CIC1423, Paris, France
| | - José-Alain Sahel
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre national de la recherche scientifique, Institut de la Vision, Paris, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU Sight Restore, Inserm-Direction Générale de l'Offre de Soins, CIC1423, Paris, France.,Fondation Ophtalmologique Adolphe de Rothschild, Paris, France.,Department of Ophthalmology, The University of Pittsburgh Medical School, Pittsburgh, Pennsylvania.,Académie des Sciences-Institut de France, Paris, France
| | - Christina Zeitz
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre national de la recherche scientifique, Institut de la Vision, Paris, France
| | - Isabelle Audo
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre national de la recherche scientifique, Institut de la Vision, Paris, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU Sight Restore, Inserm-Direction Générale de l'Offre de Soins, CIC1423, Paris, France.,Institute of Ophthalmology, University College London, London, United Kingdom
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29
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MacDonald IM, Moen C, Duncan JL, Tsang SH, Cehajic-Kapetanovic J, Aleman TS. Perspectives on Gene Therapy: Choroideremia Represents a Challenging Model for the Treatment of Other Inherited Retinal Degenerations. Transl Vis Sci Technol 2020; 9:17. [PMID: 32714643 PMCID: PMC7351877 DOI: 10.1167/tvst.9.3.17] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Purpose To report combined viewpoints on ocular gene therapy from a select group of clinician scientists and a patient advocacy group. Methods With the support of Randy Wheelock and Dr. Chris Moen from the Choroideremia Research Foundation (CRF), a special interest group at the 2019 Annual meeting of the Association for Research in Vision and Ophthalmology in Vancouver, Canada, shared their knowledge, experience, concepts, and ideas and provided a forum to discuss therapeutic strategies for the treatment of inherited retinal disorders, using experience in choroideremia (CHM) as a model. Results A member of the CRF presented the patient perspective and role in clinical trials. Five clinician scientists presented reasons for limited long-term visual improvement in many gene therapy trials, including challenges with dose, incomplete understanding of photoreceptor metabolism, vector delivery, inflammation, and identification of patients likely to benefit from treatment. Conclusions The shared experience of the five clinician scientists indicates that the results of ocular gene therapy for choroideremia have been less successful than for RPE65-related Leber congenital amaurosis. Improvement in vector delivery and developing a better understanding of gene expression in target tissues, treatment dose and side effects, and inflammation, as well as identifying patients who are most likely to benefit without suffering excessive risk, are necessary to advance the development of effective therapies for inherited retinal degenerations. Translational Relevance Additional long-term data are required to determine if ocular gene therapy will be sufficient to alter natural progression in choroideremia. Combination therapies may have to be considered, as well as alternative vectors that minimize risk.
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Affiliation(s)
- Ian M. MacDonald
- Department of Ophthalmology and Visual Sciences, University of Alberta, Edmonton, Canada
| | | | - Jacque L. Duncan
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
| | - Stephen H. Tsang
- Jonas Children's Vision Care, Columbia Stem Cell Initiative, Departments of Ophthalmology, Pathology, and Cell Biology, Institute of Human Nutrition, Vagelos College of Physicians and Surgeons, Columbia University,New York, NY, USA
- Edward S. Harkness Eye Institute, New York–Presbyterian Hospital, New York, NY, USA
| | | | - Tomas S. Aleman
- Center for Advanced Research and Ocular Therapeutics, Scheie Eye Institute at the Perelman Center for Advanced Medicine, Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA, USA
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30
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Albrecht NE, Alevy J, Jiang D, Burger CA, Liu BI, Li F, Wang J, Kim SY, Hsu CW, Kalaga S, Udensi U, Asomugha C, Bohat R, Gaspero A, Justice MJ, Westenskow PD, Yamamoto S, Seavitt JR, Beaudet AL, Dickinson ME, Samuel MA. Rapid and Integrative Discovery of Retina Regulatory Molecules. Cell Rep 2020; 24:2506-2519. [PMID: 30157441 DOI: 10.1016/j.celrep.2018.07.090] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/15/2018] [Accepted: 07/27/2018] [Indexed: 12/26/2022] Open
Abstract
Retinal function relies on precisely organized neurons and synapses and a properly patterned vasculature to support them. Alterations in these features can result in vision loss. However, our understanding of retinal organization pathways remains incomplete because of a lack of methods to rapidly identify neuron and vasculature regulators in mammals. Here we developed a pipeline for the identification of neural and synaptic integrity genes by high-throughput retinal screening (INSiGHT) that analyzes candidate expression, vascular patterning, cellular organization, and synaptic arrangement. Using this system, we examined 102 mutant mouse lines and identified 16 unique retinal regulatory genes. Fifteen of these candidates are identified as novel retina regulators, and many (9 of 16) are associated with human neural diseases. These results expand the genetic landscape involved in retinal circuit organization and provide a road map for continued discovery of mammalian retinal regulators and disease-causing alleles.
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Affiliation(s)
- Nicholas E Albrecht
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jonathan Alevy
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Danye Jiang
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Courtney A Burger
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brian I Liu
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fenge Li
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Julia Wang
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Seon-Young Kim
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sowmya Kalaga
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Uchechukwu Udensi
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chinwe Asomugha
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ritu Bohat
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Angelina Gaspero
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Monica J Justice
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Peter D Westenskow
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Department of Ophthalmology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - John R Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mary E Dickinson
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Melanie A Samuel
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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31
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Motta FL, Martin RP, Porto FBO, Wohler ES, Resende RG, Gomes CP, Pesquero JB, Sallum JMF. Pathogenicity Reclasssification of RPE65 Missense Variants Related to Leber Congenital Amaurosis and Early-Onset Retinal Dystrophy. Genes (Basel) 2019; 11:E24. [PMID: 31878136 PMCID: PMC7016655 DOI: 10.3390/genes11010024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 12/14/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022] Open
Abstract
A challenge in molecular diagnosis and genetic counseling is the interpretation of variants of uncertain significance. Proper pathogenicity classification of new variants is important for the conclusion of molecular diagnosis and the medical management of patient treatments. The purpose of this study was to reclassify two RPE65 missense variants, c.247T>C (p.Phe83Leu) and c.560G>A (p.Gly187Glu), found in Brazilian families. To achieve this aim, we reviewed the sequencing data of a 224-gene retinopathy panel from 556 patients (513 families) with inherited retinal dystrophies. Five patients with p.Phe83Leu and seven with p.Gly187Glu were selected and their families investigated. To comprehend the pathogenicity of these variants, we evaluated them based on the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) classification guidelines. Initially, these RPE65 variants met only three pathogenic criteria: (i) absence or low frequency in the population, (ii) several missense pathogenic RPE65 variants, and (iii) 15 out of 16 lines of computational evidence supporting them as damaging, which together allowed the variants to be classified as uncertain significance. Two other pieces of evidence were accepted after further analysis of these Brazilian families: (i) p.Phe83Leu and p.Gly187Glu segregate with childhood retinal dystrophy within families, and (ii) their prevalence in Leber congenital amaurosis (LCA)/early-onset retinal dystrophy (EORD) patients can be considered higher than in other inherited retinal dystrophy patients. Therefore, these variants can now be classified as likely pathogenic according to ACMG/AMP classification guidelines.
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Affiliation(s)
- Fabiana L. Motta
- Department of Ophthalmology, Universidade Federal de São Paulo, Sao Paulo SP 04039-032, Brazil;
- Instituto de Genética Ocular, Sao Paulo SP 04552-050, Brazil
| | - Renan P. Martin
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins Medicine, Baltimore, MD 21205, USA; (R.P.M.); (E.S.W.)
| | - Fernanda B. O. Porto
- INRET Clínica e Centro de Pesquisa, Belo Horizonte MG 30150-270, Brazil;
- Centro Oftalmológico de Minas Gerais, Belo Horizonte MG 30180-070, Brazil
| | - Elizabeth S. Wohler
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins Medicine, Baltimore, MD 21205, USA; (R.P.M.); (E.S.W.)
| | | | - Caio P. Gomes
- Department of Biophysics, Universidade Federal de São Paulo, São Paulo SP 04039-032, Brazil; (C.P.G.); (J.B.P.)
| | - João B. Pesquero
- Department of Biophysics, Universidade Federal de São Paulo, São Paulo SP 04039-032, Brazil; (C.P.G.); (J.B.P.)
| | - Juliana M. F. Sallum
- Department of Ophthalmology, Universidade Federal de São Paulo, Sao Paulo SP 04039-032, Brazil;
- Instituto de Genética Ocular, Sao Paulo SP 04552-050, Brazil
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32
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Jaffal L, Joumaa WH, Assi A, Helou C, Cherfan G, Zibara K, Audo I, Zeitz C, El Shamieh S. Next Generation Sequencing Identifies Five Novel Mutations in Lebanese Patients with Bardet-Biedl and Usher Syndromes. Genes (Basel) 2019; 10:genes10121047. [PMID: 31888296 PMCID: PMC6947157 DOI: 10.3390/genes10121047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/10/2019] [Accepted: 12/10/2019] [Indexed: 01/15/2023] Open
Abstract
AIM To identify disease-causing mutations in four Lebanese families: three families with Bardet-Biedl and one family with Usher syndrome (BBS and USH respectively), using next generation sequencing (NGS). METHODS We applied targeted NGS in two families and whole exome sequencing (WES) in two other families. Pathogenicity of candidate mutations was evaluated according to frequency, conservation, in silico prediction tools, segregation with disease, and compatibility with inheritance pattern. The presence of pathogenic variants was confirmed via Sanger sequencing followed by segregation analysis. RESULTS Most likely disease-causing mutations were identified in all included patients. In BBS patients, we found (M1): c.2258A > T, p. (Glu753Val) in BBS9, (M2): c.68T > C; p. (Leu23Pro) in ARL6, (M3): c.265_266delTT; p. (Leu89Valfs*11) and (M4): c.880T > G; p. (Tyr294Asp) in BBS12. A previously known variant (M5): c.551A > G; p. (Asp184Ser) was also detected in BBS5. In the USH patient, we found (M6): c.188A > C, p. (Tyr63Ser) in CLRN1. M2, M3, M4, and M6 were novel. All of the candidate mutations were shown to be likely disease-causing through our bioinformatic analysis. They also segregated with the corresponding phenotype in available family members. CONCLUSION This study expanded the mutational spectrum and showed the genetic diversity of BBS and USH. It also spotlighted the efficiency of NGS techniques in revealing mutations underlying clinically and genetically heterogeneous disorders.
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Affiliation(s)
- Lama Jaffal
- Department of Biological and Environmental Sciences, Faculty of Science, Beirut Arab University, Debbieh 1107 2809, Lebanon;
| | - Wissam H Joumaa
- Rammal Hassan Rammal Research Laboratory, Physiotoxicity (PhyTox), Faculty of Sciences, Lebanese University, Nabatieh 1700, Lebanon;
| | - Alexandre Assi
- Retinal Service, Beirut Eye & ENT Specialist Hospital, Beirut 1106, Lebanon; (A.A.); (C.H.); (G.C.)
| | - Charles Helou
- Retinal Service, Beirut Eye & ENT Specialist Hospital, Beirut 1106, Lebanon; (A.A.); (C.H.); (G.C.)
| | - George Cherfan
- Retinal Service, Beirut Eye & ENT Specialist Hospital, Beirut 1106, Lebanon; (A.A.); (C.H.); (G.C.)
| | - Kazem Zibara
- ER045, PRASE, DSST, Lebanese University, Beirut 1700, Lebanon;
- Biology Department, Faculty of Sciences-I, Lebanese University, Beirut 1700, Lebanon
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (I.A.); (C.Z.)
- CHNO des Quinze-Vingts, INSERM-DGOS CIC1423, 75012 Paris, France
- University College London Institute of Ophthalmology, London EC1V 9EL, UK
| | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (I.A.); (C.Z.)
| | - Said El Shamieh
- Rammal Hassan Rammal Research Laboratory, Physiotoxicity (PhyTox), Faculty of Sciences, Lebanese University, Nabatieh 1700, Lebanon;
- Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut 1107 2809, Lebanon
- Correspondence:
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33
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Yohe S, Sivasankar M, Ghosh A, Ghosh A, Holle J, Murugan S, Gupta R, Schimmenti LA, Vedam R, Thyagarajan B. Prevalence of mutations in inherited retinal diseases: A comparison between the United States and India. Mol Genet Genomic Med 2019; 8:e1081. [PMID: 31816670 PMCID: PMC7005662 DOI: 10.1002/mgg3.1081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 10/14/2019] [Accepted: 10/30/2019] [Indexed: 11/26/2022] Open
Abstract
Background Studies evaluating next‐generation sequencing (NGS) for retinal disorders may not reflect clinical practice. We report results of retrospective analysis of patients referred for clinical testing at two institutions (US and India). Methods This retrospective study of 131 patients who underwent clinically validated targeted NGS or exome sequencing for a wide variety of clinical phenotypes categorized results into a definitive, indeterminate, or negative molecular diagnosis. Results A definitive molecular diagnosis (52%) was more common in the India cohort (62% vs. 39%, p = .009), while an indeterminate molecular diagnosis occurred only in the US cohort (12%). In the US cohort, a lower diagnostic rate in Hispanic, non‐Caucasians (23%) was seen compared to Caucasians (57%). The India cohort had a high rate of homozygous variants (61%) and different frequency of genes involved compared to the US cohort. Conclusion Despite inherent limitations in clinical testing, the diagnostic rate across the two cohorts (52%) was similar to the 50%–65% diagnostic rate in the literature. However, the diagnostic rate was lower in the US cohort and appears partly explained by racial background. The high rate of consanguinity in the Indian population is reflected in the high rate of homozygosity for pathogenic mutations and may have implications for population level screening and genetic counseling. Clinical laboratories may note diagnostic rates that differ from the literature, due to factors such as heterogeneity in racial background or consanguinity rates in the populations being tested. This information may be useful for post‐test counseling.
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Affiliation(s)
- Sophia Yohe
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | | | | | | | - Jennifer Holle
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | | | | | - Lisa A Schimmenti
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | | | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
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34
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Méjécase C, Mohand-Saïd S, El Shamieh S, Antonio A, Condroyer C, Blanchard S, Letexier M, Saraiva JP, Sahel JA, Audo I, Zeitz C. A novel nonsense variant in REEP6 is involved in a sporadic rod-cone dystrophy case. Clin Genet 2019; 93:707-711. [PMID: 29120066 DOI: 10.1111/cge.13171] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/03/2017] [Accepted: 11/05/2017] [Indexed: 12/22/2022]
Abstract
Rod-cone dystrophy (RCD), also called retinitis pigmentosa, is the most common form of progressive inherited retinal disorders secondary to photoreceptor degeneration. It is a genetically heterogeneous disease characterized by night blindness, followed by visual field constriction and, in most severe cases, total blindness. The aim of our study was to identify the underlying gene defect leading to severe RCD in a 60-year-old woman. The patient's DNA was investigated by targeted next generation sequencing followed by whole exome sequencing. A novel nonsense variant, c.267G>A p.(Trp89*), was identified at a homozygous state in the proband in REEP6 gene, recently reported mutated in 7 unrelated families with RCD. Further functional studies will help to understand the physiopathology associated with REEP6 mutations that may be linked to a protein trafficking defect.
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Affiliation(s)
- C Méjécase
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - S Mohand-Saïd
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC 1423, Paris, France
| | - S El Shamieh
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
| | - A Antonio
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC 1423, Paris, France
| | - C Condroyer
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - S Blanchard
- IntegraGen SA, Genopole Campus, Evry, France
| | - M Letexier
- IntegraGen SA, Genopole Campus, Evry, France
| | - J-P Saraiva
- IntegraGen SA, Genopole Campus, Evry, France
| | - J-A Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC 1423, Paris, France.,Institute of Ophthalmology, University College of London, London, UK.,Fondation Ophtalmologique Adolphe de Rothschild, Paris, France.,Academie des Sciences, Institut de France, Paris, France.,Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburg, Pennsylvania, USA
| | - I Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC 1423, Paris, France.,Institute of Ophthalmology, University College of London, London, UK
| | - C Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
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TRPM1 Mutations are the Most Common Cause of Autosomal Recessive Congenital Stationary Night Blindness (CSNB) in the Palestinian and Israeli Populations. Sci Rep 2019; 9:12047. [PMID: 31427709 PMCID: PMC6700182 DOI: 10.1038/s41598-019-46811-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 06/14/2019] [Indexed: 11/08/2022] Open
Abstract
Precise genetic and phenotypic characterization of congenital stationary night blindness (CSNB) patients is needed for future therapeutic interventions. The aim of this study was to estimate the prevalence of CSNB in our populations and to study clinical and genetic aspects of the autosomal recessive (AR) form of CSNB. This is a retrospective cohort study of Palestinian and Israeli CSNB patients harboring mutations in TRPM1 underwent comprehensive ocular examination. Genetic analysis was performed using homozygosity mapping and sequencing. 161 patients (from 76 families) were recruited for this study, leading to a prevalence of 1:6210 in the vicinity of Jerusalem, much higher than the worldwide prevalence. 61% of the families were consanguineous with AR inheritance pattern. Biallelic pathogenic TRPM1 mutations were identified in 36 families (72 patients). Two founder mutations explain the vast majority of cases: a nonsense mutation c.880A>T (p.Lys294*) identified in 22 Palestinian families and a large genomic deletion (36,445 bp) encompassing exons 2-7 of TRPM1 present in 13 Ashkenazi Jewish families. Most patients were myopic (with mean BCVA of 0.40 LogMAR) and all had absent rod responses in full field electroretinography. To the best of our knowledge, this is the largest report of a clinical and genetic analysis of patients affected with CSNB due to TRPM1 mutations.
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36
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Zeitz C, Michiels C, Neuillé M, Friedburg C, Condroyer C, Boyard F, Antonio A, Bouzidi N, Milicevic D, Veaux R, Tourville A, Zoumba A, Seneina I, Foussard M, Andrieu C, N Preising M, Blanchard S, Saraiva JP, Mesrob L, Le Floch E, Jubin C, Meyer V, Blanché H, Boland A, Deleuze JF, Sharon D, Drumare I, Defoort-Dhellemmes S, De Baere E, Leroy BP, Zanlonghi X, Casteels I, de Ravel TJ, Balikova I, Koenekoop RK, Laffargue F, McLean R, Gottlob I, Bonneau D, Schorderet DF, L Munier F, McKibbin M, Prescott K, Pelletier V, Dollfus H, Perdomo-Trujillo Y, Faure C, Reiff C, Wissinger B, Meunier I, Kohl S, Banin E, Zrenner E, Jurklies B, Lorenz B, Sahel JA, Audo I. Where are the missing gene defects in inherited retinal disorders? Intronic and synonymous variants contribute at least to 4% of CACNA1F-mediated inherited retinal disorders. Hum Mutat 2019; 40:765-787. [PMID: 30825406 DOI: 10.1002/humu.23735] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/15/2019] [Accepted: 02/26/2019] [Indexed: 12/27/2022]
Abstract
Inherited retinal disorders (IRD) represent clinically and genetically heterogeneous diseases. To date, pathogenic variants have been identified in ~260 genes. Albeit that many genes are implicated in IRD, for 30-50% of the cases, the gene defect is unknown. These cases may be explained by novel gene defects, by overlooked structural variants, by variants in intronic, promoter or more distant regulatory regions, and represent synonymous variants of known genes contributing to the dysfunction of the respective proteins. Patients with one subgroup of IRD, namely incomplete congenital stationary night blindness (icCSNB), show a very specific phenotype. The major cause of this condition is the presence of a hemizygous pathogenic variant in CACNA1F. A comprehensive study applying direct Sanger sequencing of the gene-coding regions, exome and genome sequencing applied to a large cohort of patients with a clinical diagnosis of icCSNB revealed indeed that seven of the 189 CACNA1F-related cases have intronic and synonymous disease-causing variants leading to missplicing as validated by minigene approaches. These findings highlight that gene-locus sequencing may be a very efficient method in detecting disease-causing variants in clinically well-characterized patients with a diagnosis of IRD, like icCSNB.
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Affiliation(s)
- Christina Zeitz
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | | | - Marion Neuillé
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | | | | | - Fiona Boyard
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Aline Antonio
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, Paris, France
| | - Nassima Bouzidi
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Diana Milicevic
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Robin Veaux
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Aurore Tourville
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Axelle Zoumba
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Imene Seneina
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Marine Foussard
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Camille Andrieu
- CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, Paris, France
| | - Markus N Preising
- Department of Ophthalmology, Justus-Liebig-University Giessen, Germany
| | | | | | - Lilia Mesrob
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France.,INSERM, Sorbonne Université, Paris, France
| | - Edith Le Floch
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Claire Jubin
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Vincent Meyer
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Hélène Blanché
- Fondation Jean Dausset-CEPH (Centre d'Etude du Polymorphisme Humain), Paris, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France.,Fondation Jean Dausset-CEPH (Centre d'Etude du Polymorphisme Humain), Paris, France
| | - Dror Sharon
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Isabelle Drumare
- Service d'Exploration de la Vision et Neuro-ophtalmologie, CHRU de Lille, Lille, France
| | | | - Elfride De Baere
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Bart P Leroy
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium.,Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium.,Division of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Xavier Zanlonghi
- Clinique Jules Verne, Centre de Compétence Maladies Rares, Nantes, France
| | - Ingele Casteels
- Department of Ophthalmology, University Hospitals Leuven, Leuven, Belgium
| | | | - Irina Balikova
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium.,Department of Ophthalmology, Queen Fabiola Children's University Hospital, Brussels, Belgium
| | - Rob K Koenekoop
- Departments of Ophthalmology, Human Genetics, and Pediatric Surgery, Montreal Children's Hospital, McGill University Health Centre, McGill University, Montreal, Quebec, Canada
| | | | - Rebecca McLean
- Department of Neuroscience, Psychology and Behaviour, Ulverscroft Eye Unit, University of Leicester, Leicester, United Kingdom
| | - Irene Gottlob
- Department of Neuroscience, Psychology and Behaviour, Ulverscroft Eye Unit, University of Leicester, Leicester, United Kingdom
| | - Dominique Bonneau
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire, Angers, France.,Mitovasc, UMR CNRS 6015-INSERM 1083, Université d'Angers, France
| | - Daniel F Schorderet
- Department of Ophthalmology, Jules-Gonin Eye Hospital, University of Lausanne, Lausanne, Switzerland.,IRO-Institute for Research in Ophthalmology, Sion, Switzerland.,Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Francis L Munier
- Department of Ophthalmology, Jules-Gonin Eye Hospital, University of Lausanne, Lausanne, Switzerland
| | - Martin McKibbin
- Department of Ophthalmology, St. James's University Hospital, Leeds, United Kingdom
| | | | - Valerie Pelletier
- Centre de référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), Hôpital Civil, Strasbourg, France.,Service de Génétique Médicale, Hôpital de Hautepierre, Strasbourg, France
| | - Hélène Dollfus
- Centre de référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), Hôpital Civil, Strasbourg, France.,Service de Génétique Médicale, Hôpital de Hautepierre, Strasbourg, France.,Laboratoire de Génétique Médicale, INSERM U1112, Strasbourg, France
| | - Yaumara Perdomo-Trujillo
- Centre de référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), Hôpital Civil, Strasbourg, France
| | - Céline Faure
- CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, Paris, France.,Hôpital Privé Saint Martin, Ramsay Générale de Santé, Caen, France
| | | | - Bernd Wissinger
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Isabelle Meunier
- Centre de Référence Maladies Sensorielles Génétiques, Hôpital Gui de Chauliac, Montpellier, France.,Institute for Neurosciences of Montpellier, Montpellier University and INSERM U1051, Montpellier, France
| | - Susanne Kohl
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Eyal Banin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Eberhart Zrenner
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany.,Werner Reichardt Center for Integrative Neuroscience, University of Tübingen, Tübingen, Germany
| | | | - Birgit Lorenz
- Department of Ophthalmology, Justus-Liebig-University Giessen, Germany
| | - José-Alain Sahel
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, Paris, France.,Fondation Ophtalmologique Adolphe de Rothschild, Paris, France.,Academie des Sciences, Institut de France, Paris, France.,Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Isabelle Audo
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, Paris, France.,Institute of Ophthalmology, University College of London, London, United Kingdom
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Vossen DM, Verhagen CVM, Grénman R, Kluin RJC, Verheij M, van den Brekel MWM, Wessels LFA, Vens C. Role of variant allele fraction and rare SNP filtering to improve cellular DNA repair endpoint association. PLoS One 2018; 13:e0206632. [PMID: 30408064 PMCID: PMC6224072 DOI: 10.1371/journal.pone.0206632] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/16/2018] [Indexed: 12/23/2022] Open
Abstract
Background Large cancer genome studies continue to reveal new players in treatment response and tumorigenesis. The discrimination of functional alterations from the abundance of passenger genetic alterations still poses challenges and determines DNA sequence variant selection procedures. Here we evaluate variant selection strategies that select homozygous variants and rare SNPs and assess its value in detecting tumor cells with DNA repair defects. Methods To this end we employed a panel of 29 patient-derived head and neck squamous cell carcinoma (HNSCC) cell lines, of which a subset harbors DNA repair defects. Mitomycin C (MMC) sensitivity was used as functional endpoint of DNA crosslink repair deficiency. 556 genes including the Fanconi anemia (FA) and homologous recombination (HR) genes, whose products strongly determine MMC response, were capture-sequenced. Results We show a strong association between MMC sensitivity, thus loss of DNA repair function, and the presence of homozygous and rare SNPs in the relevant FA/HR genes. Excluding such selection criteria impedes the discrimination of crosslink repair status by mutation analysis. Applied to all KEGG pathways, we find that the association with MMC sensitivity is strongest in the KEGG FA pathway, therefore also demonstrating the value of such selection strategies for exploratory analyses. Variant analyses in 56 clinical samples demonstrate that homozygous variants occur more frequently in tumor suppressor genes than oncogenes further supporting the role of a homozygosity criterion to improve gene function association or tumor suppressor gene identification studies. Conclusion Together our data show that the detection of relevant genes or of repair pathway defected tumor cells can be improved by the consideration of allele zygosity and SNP allele frequencies.
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Affiliation(s)
- David M. Vossen
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Head and Neck Oncology and Surgery, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Caroline V. M. Verhagen
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Head and Neck Oncology and Surgery, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Reidar Grénman
- Department of Otorhinolaryngology—Head and Neck Surgery, Hospital and University of Turku, Turku, Finland
- Department of Medical Biochemistry and Genetics, Turku University, Turku, Finland
| | - Roelof J. C. Kluin
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marcel Verheij
- Department of Radiation Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Michiel W. M. van den Brekel
- Institute of Phonetic Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Department of Oral and Maxillofacial Surgery, Academic Medical Center, Amsterdam, The Netherlands
| | - Lodewyk F. A. Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of EEMCS, Delft University of Technology, Delft, The Netherlands
| | - Conchita Vens
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Radiation Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- * E-mail:
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Pasutto F, Ekici A, Reis A, Kremers J, Huchzermeyer C. Novel truncating mutation in CACNA1F in a young male patient diagnosed with optic atrophy. Ophthalmic Genet 2018; 39:741-748. [PMID: 30260717 DOI: 10.1080/13816810.2018.1520263] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Low vision in children can be accompanied by pallor of the optic disc with little or no characteristic morphologic changes of the retina. A variety of diseases can be the underlying cause, including hereditary optic atrophy, Leber's congenital amaurosis (LCA), achromatopsia, and calcium channel, voltage-dependent, L-type, alpha-1F subunit gene (CACNA1F)-associated retinopathy (most widely known as incomplete congenital stationary night blindness: iCSNB). Differentiation at early age is desirable due to large differences in prognosis, but may be difficult because phenotypes overlap and electrophysiological testing is challenging in young patients. We present the case of a 6-year-old boy with unexplained low vision and pallor of the optic disc who originally had been diagnosed with hereditary optic atrophy in the absence of recordable full-field electroretinography (ERG) due to poor patient cooperation. MATERIALS AND METHODS Standard Sanger sequencing excluded mutations in the OPA1 gene (autosomal-dominant optic atrophy). To identify the underlying genetic cause, whole-exome sequencing was performed on patient's DNA. Recording of the full-field ERG was successfully performed 6 months later. RESULTS We identified a novel truncating mutation in CACNA1F gene (NM_001256789: c.3895C > T in exon 33) which led to the correct diagnosis of CACNA1F-associated retinopathy in the young boy. ERG recordings showed a negative scotopic mixed response with preserved oscillatory potentials and a flicker ERG with reduced amplitude and biphasic waveform, compatible with a CACNA1F-asssociated phenotype. CONCLUSIONS We show that genetic testing may help to differentiate between optic atrophy, LCA, and CACNA1F-associated retinopathy at a much earlier age, in absence of electrophysiological examination and by widely overlapping phenotypes.
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Affiliation(s)
- Francesca Pasutto
- a Institute of Human Genetics , Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) , Erlangen , Germany
| | - Arif Ekici
- a Institute of Human Genetics , Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) , Erlangen , Germany
| | - André Reis
- a Institute of Human Genetics , Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) , Erlangen , Germany
| | - Jan Kremers
- b Department of Ophthalmology , Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) , Erlangen , Germany
| | - Cord Huchzermeyer
- b Department of Ophthalmology , Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) , Erlangen , Germany
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Audo I, Mohand-Said S, Boulanger-Scemama E, Zanlonghi X, Condroyer C, Démontant V, Boyard F, Antonio A, Méjécase C, El Shamieh S, Sahel JA, Zeitz C. MERTK
mutation update in inherited retinal diseases. Hum Mutat 2018; 39:887-913. [DOI: 10.1002/humu.23431] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 03/22/2018] [Accepted: 03/29/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Isabelle Audo
- Sorbonne Université; INSERM; CNRS; Institut de la Vision; Paris France
- CHNO des Quinze-Vingts; DHU Sight Restore; INSERM-DGOS CIC1423 Paris France
- University College London Institute of Ophthalmology; London UK
| | - Saddek Mohand-Said
- Sorbonne Université; INSERM; CNRS; Institut de la Vision; Paris France
- CHNO des Quinze-Vingts; DHU Sight Restore; INSERM-DGOS CIC1423 Paris France
| | - Elise Boulanger-Scemama
- Sorbonne Université; INSERM; CNRS; Institut de la Vision; Paris France
- Fondation Ophtalmologique Adolphe de Rothschild; Paris France
| | | | | | - Vanessa Démontant
- Sorbonne Université; INSERM; CNRS; Institut de la Vision; Paris France
| | - Fiona Boyard
- Sorbonne Université; INSERM; CNRS; Institut de la Vision; Paris France
| | - Aline Antonio
- Sorbonne Université; INSERM; CNRS; Institut de la Vision; Paris France
| | - Cécile Méjécase
- Sorbonne Université; INSERM; CNRS; Institut de la Vision; Paris France
| | - Said El Shamieh
- Sorbonne Université; INSERM; CNRS; Institut de la Vision; Paris France
- Department of Medical Laboratory Technology; Faculty of Health Sciences; Beirut Arab University; Beirut Lebanon
| | - José-Alain Sahel
- Sorbonne Université; INSERM; CNRS; Institut de la Vision; Paris France
- CHNO des Quinze-Vingts; DHU Sight Restore; INSERM-DGOS CIC1423 Paris France
- University College London Institute of Ophthalmology; London UK
- Fondation Ophtalmologique Adolphe de Rothschild; Paris France
- Académie des Sciences-Institut de France; Paris France. Department of Ophthalmology; University of Pittsburgh Medical School; Pittsburgh Pennsylvania
| | - Christina Zeitz
- Sorbonne Université; INSERM; CNRS; Institut de la Vision; Paris France
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Wood EH, Drenser KA, Hariprasad SM. Genetic Testing for Retina Specialists. Ophthalmic Surg Lasers Imaging Retina 2018; 49:292-295. [DOI: 10.3928/23258160-20180501-01] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Di Resta C, Spiga I, Presi S, Merella S, Pipitone GB, Manitto MP, Querques G, Parodi MB, Ferrari M, Carrera P. Integration of multigene panels for the diagnosis of hereditary retinal disorders using Next Generation Sequencing and bioinformatics approaches. EJIFCC 2018; 29:15-25. [PMID: 29765283 PMCID: PMC5949615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
In recent years, Next-Generation Sequencing (NGS) opened a new way for the study of pathogenic mechanisms and for molecular diagnosis of inherited disorders. In the present work, we focused our attention on the inherited retinal dystrophies (IRDs), a group of specific disorders of the retina, displaying a very high clinical and genetic heterogeneity, whose genetic diagnosis is not easily feasible. It represents a paradigmatic example for the integration of clinical and molecular examination toward precision medicine. In this paper, we discuss the use of targeted NGS resequencing of selected gene panels in a cohort of patients affected by IRDs. We tested the hypothesis to apply a selective approach based on a careful clinical examination. By this approach we reached a 66% overall detection rate for pathogenic variants, with a 52% diagnostic yield. Reduction of the efforts for validation and classification of variants is a clear advantage for the management of genetic testing in a clinical setting.
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Affiliation(s)
- Chiara Di Resta
- Vita-Salute San Raffaele University, Milan, Italy, Unit of Genomics for Human Disease Diagnosis, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ivana Spiga
- Clinical Molecular Biology Laboratory, IRCCS San Raffaele Hospital, Milan, Italy
| | - Silvia Presi
- Clinical Molecular Biology Laboratory, IRCCS San Raffaele Hospital, Milan, Italy
| | - Stefania Merella
- Clinical Molecular Biology Laboratory, IRCCS San Raffaele Hospital, Milan, Italy
| | | | - Maria Pia Manitto
- Department of Ophthalmology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giuseppe Querques
- Medical Retina & Imaging Unit, Department of Ophthalmology IRCCS San Raffaele Hospital, Vita-Salute San Raffaele University, Milan, Italy
| | | | - Maurizio Ferrari
- Vita-Salute San Raffaele University, Milan, Italy, Unit of Genomics for Human Disease Diagnosis, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy, Clinical Molecular Biology Laboratory, IRCCS San Raffaele Hospital, Milan, Italy,Corresponding author: Maurizio Ferrari; Genomic Unit for the Diagnosis of Human Pathologies; Division of Genetics and Cellular Biology; IRCCS San Raffaele Hospital; Via Olgettina 60; 20132 Milan, Italy; Phone: 02-26432303; Fax: 02-26434351; E-mail:
| | - Paola Carrera
- Unit of Genomics for Human Disease Diagnosis, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy, Clinical Molecular Biology Laboratory, IRCCS San Raffaele Hospital, Milan, Italy
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Special Issue Introduction: Inherited Retinal Disease: Novel Candidate Genes, Genotype-Phenotype Correlations, and Inheritance Models. Genes (Basel) 2018; 9:genes9040215. [PMID: 29659558 PMCID: PMC5924557 DOI: 10.3390/genes9040215] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 04/13/2018] [Indexed: 02/06/2023] Open
Abstract
Inherited retinal diseases (IRDs) are genetically and clinically heterogeneous disorders.[...].
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Systematic evaluation of a targeted gene capture sequencing panel for molecular diagnosis of retinitis pigmentosa. PLoS One 2018; 13:e0185237. [PMID: 29641573 PMCID: PMC5894961 DOI: 10.1371/journal.pone.0185237] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/08/2017] [Indexed: 01/09/2023] Open
Abstract
Background Inherited eye diseases are major causes of vision loss in both children and adults. Inherited eye diseases are characterized by clinical variability and pronounced genetic heterogeneity. Genetic testing may provide an accurate diagnosis for ophthalmic genetic disorders and allow gene therapy for specific diseases. Methods A targeted gene capture panel was designed to capture exons of 283 inherited eye disease genes including 58 known causative retinitis pigmentosa (RP) genes. 180 samples were tested with this panel, 68 were previously tested by Sanger sequencing. Systematic evaluation of our method and comprehensive molecular diagnosis were carried on 99 RP patients. Results 96.85% targeted regions were covered by at least 20 folds, the accuracy of variants detection was 99.994%. In 4 of the 68 samples previously tested by Sanger sequencing, mutations of other diseases not consisting with the clinical diagnosis were detected by next-generation sequencing (NGS) not Sanger. Among the 99 RP patients, 64 (64.6%) were detected with pathogenic mutations, while in 3 patients, it was inconsistent between molecular diagnosis and their initial clinical diagnosis. After revisiting, one patient’s clinical diagnosis was reclassified. In addition, 3 patients were found carrying large deletions. Conclusions We have systematically evaluated our method and compared it with Sanger sequencing, and have identified a large number of novel mutations in a cohort of 99 RP patients. The results showed a sufficient accuracy of our method and suggested the importance of molecular diagnosis in clinical diagnosis.
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Miraldi Utz V, Pfeifer W, Longmuir SQ, Olson RJ, Wang K, Drack AV. Presentation of TRPM1-Associated Congenital Stationary Night Blindness in Children. JAMA Ophthalmol 2018; 136. [PMID: 29522070 PMCID: PMC5876850 DOI: 10.1001/jamaophthalmol.2018.0185] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
IMPORTANCE Congenital stationary night blindness (CSNB) implies a stable condition, with the major symptom being nyctalopia present at birth. Pediatric clinical presentation and the course of different genetic subtypes of CSNB have not, to our knowledge, been well described in the era of molecular genetic diagnosis. OBJECTIVE To describe the presentation and longitudinal clinical characteristics of pediatric patients with molecularly confirmed TRPM1-associated complete CSNB (cCSNB). DESIGN, SETTING, PARTICIPANTS This study was conducted at the University of Iowa from January 1, 1990, to July 1, 2015, and was a retrospective, longitudinal case series of 7 children (5 [71.4%] female) with TRPM1-associated cCSNB followed up for a mean (SD) of 11.1 (2.8) years. MAIN OUTCOMES AND MEASURES History, ophthalmologic examination findings, full-field electroretinogram (ffERG) results, full-field stimulus threshold testing results, Goldmann visual field results, optical coherence tomography results, and molecular genetic results were evaluated. Presenting symptoms and signs, the correlation of refractive error with electroretinography, and clinical evolution were analyzed. RESULTS Seven patients (5 [71.4%] female) presented early in childhood with strabismus (n = 6 [86%]), myopia (n = 5 [71%]), and/or nystagmus (n = 3 [43%]). The mean (SD) age at presentation was 8 (4) months and for receiving a diagnosis by ffERG was 7.3 years, with molecular diagnosis at 9.7 years. The mean (SD) length of follow-up was 11 (2.8) years. The best-corrected visual acuity at the most recent visit averaged 20/30 in the better-seeing eye (range, 20/20-20/60). The mean (SD) initial refraction was -2.80 (4.42) diopters (D) and the mean refraction at the most recent visit was -8.75 (3.53) D (range, -4.00 to -13.75 D), with the greatest rate of myopic shift before age 5 years. Full-field electroretinogram results were electronegative, consistent with cCSNB, without a significant change in amplitude over time. No patient or parent noted night blindness at presentation; however, subjective nyctalopia was eventually reported in 5 of 7 patients (71%). The full-field stimulus threshold testing results were moderately subnormal (-29.7 [3.8] dB; normal -59.8 [4.0] dB). Goldmann visual field results were significant for full I-4e, but constricted I-2e isopter. Eight different mutations or rare variants in TRPM1 predicted to be pathogenic were detected, with 3 novel variants. CONCLUSIONS AND RELEVANCE Children with TRPM1-associated cCSNB presented before school age with progressive myopia as well as strabismus and nystagmus (but not nyctalopia), with stable, electronegative ffERG results, mildly subnormal full-field stimulus threshold testing results, and a constricted I2e isopter on perimetry. These findings suggest that ffERG and cCSNB genetic testing should be considered for children who present with early-onset myopia, especially in the presence of strabismus and/or nystagmus, and that TRPM1-associated cCSNB is a channelopathy that may present without complaints of night blindness in childhood.
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Affiliation(s)
- Virginia Miraldi Utz
- Abrahamson Pediatric Eye Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Department of Ophthalmology, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Wanda Pfeifer
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City
- University of Iowa Institute for Vision Research, Iowa City
| | - Susannah Q. Longmuir
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City
- Private practice, Nashville, Tennessee
| | - Richard John Olson
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City
| | - Kai Wang
- University of Iowa Institute for Vision Research, Iowa City
- Department of Biostatistics, University of Iowa, Iowa City
| | - Arlene V. Drack
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City
- University of Iowa Institute for Vision Research, Iowa City
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Fernández-Marmiesse A, Gouveia S, Couce ML. NGS Technologies as a Turning Point in Rare Disease Research , Diagnosis and Treatment. Curr Med Chem 2018; 25:404-432. [PMID: 28721829 PMCID: PMC5815091 DOI: 10.2174/0929867324666170718101946] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/19/2017] [Accepted: 07/14/2017] [Indexed: 01/17/2023]
Abstract
Approximately 25-50 million Americans, 30 million Europeans, and 8% of the Australian population have a rare disease. Rare diseases are thus a common problem for clinicians and account for enormous healthcare costs worldwide due to the difficulty of establishing a specific diagnosis. In this article, we review the milestones achieved in our understanding of rare diseases since the emergence of next-generation sequencing (NGS) technologies and analyze how these advances have influenced research and diagnosis. The first half of this review describes how NGS has changed diagnostic workflows and provided an unprecedented, simple way of discovering novel disease-associated genes. We focus particularly on metabolic and neurodevelopmental disorders. NGS has enabled cheap and rapid genetic diagnosis, highlighted the relevance of mosaic and de novo mutations, brought to light the wide phenotypic spectrum of most genes, detected digenic inheritance or the presence of more than one rare disease in the same patient, and paved the way for promising new therapies. In the second part of the review, we look at the limitations and challenges of NGS, including determination of variant causality, the loss of variants in coding and non-coding regions, and the detection of somatic mosaicism variants and epigenetic mutations, and discuss how these can be overcome in the near future.
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Affiliation(s)
- Ana Fernández-Marmiesse
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Sofía Gouveia
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - María L. Couce
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
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Imani S, Ijaz I, Shasaltaneh MD, Fu S, Cheng J, Fu J. Molecular genetics characterization and homology modeling of the CHM gene mutation: A study on its association with choroideremia. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 775:39-50. [DOI: 10.1016/j.mrrev.2018.02.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 01/21/2018] [Accepted: 02/13/2018] [Indexed: 12/19/2022]
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47
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Messchaert M, Haer-Wigman L, Khan MI, Cremers FPM, Collin RWJ. EYS mutation update: In silico assessment of 271 reported and 26 novel variants in patients with retinitis pigmentosa. Hum Mutat 2017; 39:177-186. [PMID: 29159838 DOI: 10.1002/humu.23371] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/07/2017] [Accepted: 11/12/2017] [Indexed: 01/22/2023]
Abstract
Mutations in Eyes shut homolog (EYS) are one of the most common causes of autosomal recessive (ar) retinitis pigmentosa (RP), a progressive blinding disorder. The exact function of the EYS protein and the pathogenic mechanisms underlying EYS-associated RP are still poorly understood, which hampers the interpretation of the causality of many EYS variants discovered to date. We collected all reported EYS variants present in 377 arRP index cases published before June 2017, and uploaded them in the Leiden Open Variation Database (www.LOVD.nl/EYS). We also describe 36 additional index cases, carrying 26 novel variants. Of the 297 unique EYS variants identified, almost half (n = 130) are predicted to result in premature truncation of the EYS protein. Classification of all variants using the American College of Medical Genetics and Genomics guidelines revealed that the predicted pathogenicity of these variants cover the complete spectrum ranging from likely benign to pathogenic, although especially missense variants largely fall in the category of uncertain significance. Besides the identification of likely benign alleles previously reported as being probably pathogenic, our comprehensive analysis underscores the need of functional assays to assess the causality of EYS variants, in order to improve molecular diagnostics and counseling of patients with EYS-associated RP.
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Affiliation(s)
- Muriël Messchaert
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Muhammad I Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
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Farrar GJ, Carrigan M, Dockery A, Millington-Ward S, Palfi A, Chadderton N, Humphries M, Kiang AS, Kenna PF, Humphries P. Toward an elucidation of the molecular genetics of inherited retinal degenerations. Hum Mol Genet 2017; 26:R2-R11. [PMID: 28510639 PMCID: PMC5886474 DOI: 10.1093/hmg/ddx185] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 05/08/2017] [Indexed: 02/06/2023] Open
Abstract
While individually classed as rare diseases, hereditary retinal degenerations (IRDs) are the major cause of registered visual handicap in the developed world. Given their hereditary nature, some degree of intergenic heterogeneity was expected, with genes segregating in autosomal dominant, recessive, X-linked recessive, and more rarely in digenic or mitochondrial modes. Today, it is recognized that IRDs, as a group, represent one of the most genetically diverse of hereditary conditions - at least 260 genes having been implicated, with 70 genes identified in the most common IRD, retinitis pigmentosa (RP). However, targeted sequencing studies of exons from known IRD genes have resulted in the identification of candidate mutations in only approximately 60% of IRD cases. Given recent advances in the development of gene-based medicines, characterization of IRD patient cohorts for known IRD genes and elucidation of the molecular pathologies of disease in those remaining unresolved cases has become an endeavor of the highest priority. Here, we provide an outline of progress in this area.
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Affiliation(s)
- G Jane Farrar
- Institute of Genetics, School of Genetics and Microbiology, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Matthew Carrigan
- Institute of Genetics, School of Genetics and Microbiology, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Adrian Dockery
- Institute of Genetics, School of Genetics and Microbiology, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Sophia Millington-Ward
- Institute of Genetics, School of Genetics and Microbiology, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Arpad Palfi
- Institute of Genetics, School of Genetics and Microbiology, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Naomi Chadderton
- Institute of Genetics, School of Genetics and Microbiology, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Marian Humphries
- Institute of Genetics, School of Genetics and Microbiology, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Anna Sophia Kiang
- Institute of Genetics, School of Genetics and Microbiology, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Paul F Kenna
- Research Foundation, Royal Victoria Eye and Ear Hospital, Dublin 2, Ireland
| | - Pete Humphries
- Institute of Genetics, School of Genetics and Microbiology, University of Dublin, Trinity College, Dublin 2, Ireland
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49
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Target 5000: Target Capture Sequencing for Inherited Retinal Degenerations. Genes (Basel) 2017; 8:genes8110304. [PMID: 29099798 PMCID: PMC5704217 DOI: 10.3390/genes8110304] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 10/23/2017] [Accepted: 10/27/2017] [Indexed: 01/02/2023] Open
Abstract
There are an estimated 5000 people in Ireland who currently have an inherited retinal degeneration (IRD). It is the goal of this study, through genetic diagnosis, to better enable these 5000 individuals to obtain a clearer understanding of their condition and improved access to potentially applicable therapies. Here we show the current findings of a target capture next-generation sequencing study of over 750 patients from over 520 pedigrees currently situated in Ireland. We also demonstrate how processes can be implemented to retrospectively analyse patient datasets for the detection of structural variants in previously obtained sequencing reads. Pathogenic or likely pathogenic mutations were detected in 68% of pedigrees tested. We report nearly 30 novel mutations including three large structural variants. The population statistics related to our findings are presented by condition and credited to their respective candidate gene mutations. Rediagnosis rates of clinical phenotypes after genotyping are discussed. Possible causes of failure to detect a candidate mutation are evaluated. Future elements of this project, with a specific emphasis on structural variants and non-coding pathogenic variants, are expected to increase detection rates further and thereby produce an even more comprehensive representation of the genetic landscape of IRDs in Ireland.
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50
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Di Iorio V, Karali M, Brunetti-Pierri R, Filippelli M, Di Fruscio G, Pizzo M, Mutarelli M, Nigro V, Testa F, Banfi S, Simonelli F. Clinical and Genetic Evaluation of a Cohort of Pediatric Patients with Severe Inherited Retinal Dystrophies. Genes (Basel) 2017; 8:genes8100280. [PMID: 29053603 PMCID: PMC5664130 DOI: 10.3390/genes8100280] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/02/2017] [Accepted: 10/13/2017] [Indexed: 12/30/2022] Open
Abstract
We performed a clinical and genetic characterization of a pediatric cohort of patients with inherited retinal dystrophy (IRD) to identify the most suitable cases for gene therapy. The cohort comprised 43 patients, aged between 2 and 18 years, with severe isolated IRD at the time of presentation. The ophthalmological characterization also included assessment of the photoreceptor layer integrity in the macular region (ellipsoid zone (EZ) band). In parallel, we carried out a targeted, next-generation sequencing (NGS)-based analysis using a panel that covers over 150 genes with either an established or a candidate role in IRD pathogenesis. Based on the ophthalmological assessment, the cohort was composed of 24 Leber congenital amaurosis, 14 early onset retinitis pigmentosa, and 5 achromatopsia patients. We identified causative mutations in 58.1% of the cases. We also found novel genotype-phenotype correlations in patients harboring mutations in the CEP290 and CNGB3 genes. The EZ band was detectable in 40% of the analyzed cases, also in patients with genotypes usually associated with severe clinical manifestations. This study provides the first detailed clinical-genetic assessment of severe IRDs with infantile onset and lays the foundation of a standardized protocol for the selection of patients that are more likely to benefit from gene replacement therapeutic approaches.
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Affiliation(s)
- Valentina Di Iorio
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Università degli Studi della Campania Luigi Vanvitelli, via Pansini 5, Naples 80131, Italy.
| | - Marianthi Karali
- Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Università degli Studi della Campania Luigi Vanvitelli, via Luigi De Crecchio 7, Naples 80138, Italy.
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, Pozzuoli 80078, Italy.
| | - Raffaella Brunetti-Pierri
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Università degli Studi della Campania Luigi Vanvitelli, via Pansini 5, Naples 80131, Italy.
| | - Mariaelena Filippelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Università degli Studi della Campania Luigi Vanvitelli, via Pansini 5, Naples 80131, Italy.
| | - Giuseppina Di Fruscio
- Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Università degli Studi della Campania Luigi Vanvitelli, via Luigi De Crecchio 7, Naples 80138, Italy.
| | - Mariateresa Pizzo
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, Pozzuoli 80078, Italy.
| | - Margherita Mutarelli
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, Pozzuoli 80078, Italy.
| | - Vincenzo Nigro
- Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Università degli Studi della Campania Luigi Vanvitelli, via Luigi De Crecchio 7, Naples 80138, Italy.
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, Pozzuoli 80078, Italy.
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Università degli Studi della Campania Luigi Vanvitelli, via Pansini 5, Naples 80131, Italy.
| | - Sandro Banfi
- Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Università degli Studi della Campania Luigi Vanvitelli, via Luigi De Crecchio 7, Naples 80138, Italy.
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, Pozzuoli 80078, Italy.
| | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Università degli Studi della Campania Luigi Vanvitelli, via Pansini 5, Naples 80131, Italy.
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