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Chan J, Holdstock J, Shovelton J, Reid J, Speight G, Molha D, Pullabhatla V, Carpenter S, Uddin E, Washio T, Sato H, Izumi Y, Watanabe R, Niiro H, Fukushima Y, Ashida N, Hirose T, Maeda A. Clinical and analytical validation of an 82-gene comprehensive genome-profiling panel for identifying and interpreting variants responsible for inherited retinal dystrophies. PLoS One 2024; 19:e0305422. [PMID: 38870140 PMCID: PMC11175448 DOI: 10.1371/journal.pone.0305422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/30/2024] [Indexed: 06/15/2024] Open
Abstract
Inherited retinal dystrophies comprise a clinically complex and heterogenous group of diseases characterized by visual impairment due to pathogenic variants of over 300 different genes. Accurately identifying the causative gene and associated variant is crucial for the definitive diagnosis and subsequent selection of precise treatments. Consequently, well-validated genetic tests are required in the clinical practice. Here, we report the analytical and clinical validation of a next-generation sequencing targeted gene panel, the PrismGuide IRD Panel System. This system enables comprehensive genome profiling of 82 genes related to inherited retinal dystrophies. The PrismGuide IRD Panel System demonstrated 100% (n = 43) concordance with Sanger sequencing in detecting single-nucleotide variants, small insertions, and small deletions in the target genes and also in assessing their zygosity. It also identified copy-number loss in four out of five cases. When assessing precision, we evaluated the reproducibility of variant detection with 2,160 variants in 144 replicates and found 100% agreement in terms of single-nucleotide variants (n = 1,584) and small insertions and deletions (n = 576). Furthermore, the PrismGuide IRD Panel System generated sufficient read depth for variant calls across the purine-rich and highly repetitive open-reading frame 15 region of RPGR and detected all five variants tested. These results show that the PrismGuide IRD Panel System can accurately and consistently detect single-nucleotide variants and small insertions and deletions. Thus, the PrismGuide IRD Panel System could serve as useful tool that is applicable in clinical practice for identifying the causative genes based on the detection and interpretation of variants in patients with inherited retinal dystrophies and can contribute to a precise molecular diagnosis and targeted treatments.
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Affiliation(s)
- Jacqueline Chan
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - Jolyon Holdstock
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - John Shovelton
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - James Reid
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - Graham Speight
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - Duarte Molha
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - Venu Pullabhatla
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - Stephanie Carpenter
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - Ezam Uddin
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - Takanori Washio
- Life Innovation Center, Riken Genesis Co. LTD, Kawasaki, Kanagawa, Japan
- Division of Clinical Cancer Genomics, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
| | - Hiroko Sato
- Life Innovation Center, Riken Genesis Co. LTD, Kawasaki, Kanagawa, Japan
| | - Yuuki Izumi
- Technology Innovation, Sysmex Corporation, Kobe, Hyogo, Japan
| | - Reiko Watanabe
- Medical & Scientific Affairs, Sysmex Corporation, Kobe, Hyogo, Japan
| | - Hayato Niiro
- Medical & Scientific Affairs, Sysmex Corporation, Kobe, Hyogo, Japan
| | | | - Naoko Ashida
- Medical & Scientific Affairs, Sysmex Corporation, Kobe, Hyogo, Japan
| | - Takashi Hirose
- Medical & Scientific Affairs, Sysmex Corporation, Kobe, Hyogo, Japan
| | - Akiko Maeda
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe, Hyogo, Japan
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Oh R, Woo SJ, Joo K. Whole genome sequencing for inherited retinal diseases in the Korean National Project of Bio Big Data. Graefes Arch Clin Exp Ophthalmol 2024; 262:1351-1359. [PMID: 37947821 DOI: 10.1007/s00417-023-06309-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/22/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
PURPOSE This study aimed to analyze the genetic results of inherited retinal diseases (IRDs) and evaluate the diagnostic usefulness of whole genome sequencing (WGS) in the Korean National Project of Bio Big Data. METHODS As part of the Korean National Project of Bio Big Data, WGS was performed on 32 individuals with IRDs with no identified pathogenic variants through whole or targeted exome sequencing. RESULTS Individuals with retinitis pigmentosa (n = 23), cone dystrophy (n = 2), cone-rod dystrophy (n = 2), familial exudative vitreoretinopathy (n = 2), pigmented paravenous chorioretinal atrophy (n = 1), North Carolina macular dystrophy (n = 1), and bull's-eye macular dystrophy (n = 1) were included. WGS revealed genetic mutations in the IQCB1, PRPF31, USH2A, and GUCY2D genes in five cases (15.6%). Two large structural variations and an intronic variant were newly detected in three cases. Two individuals had biallelic missense mutations that were not identified in previous exome sequencing. CONCLUSION With WGS, the causative variants in 15.6% of unsolved IRDs from the Korean National Project of Bio Big Data were identified. Further research with a larger cohort might unveil the diagnostic usefulness of WGS in IRDs and other diseases.
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Affiliation(s)
- Richul Oh
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 82, Gumi-ro 173beon-gil, Bundang-gu, Seongnam, Gyeonggido, Republic of Korea, 13620
| | - Se Joon Woo
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 82, Gumi-ro 173beon-gil, Bundang-gu, Seongnam, Gyeonggido, Republic of Korea, 13620
| | - Kwangsic Joo
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 82, Gumi-ro 173beon-gil, Bundang-gu, Seongnam, Gyeonggido, Republic of Korea, 13620.
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Sinim Kahraman N, Özgüç Çalışkan B, Kandemir N, Öner A, Dündar M, Özkul Y. ABCA4 variant screening in a Turkish cohort with Stargardt disease. Ophthalmic Genet 2024; 45:133-139. [PMID: 38369462 DOI: 10.1080/13816810.2024.2313490] [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] [Accepted: 01/29/2024] [Indexed: 02/20/2024]
Abstract
PURPOSE This study aims to evaluate the ABCA4 variants in patients diagnosed with Stargardt disease. METHODS This is a retrospective study designed to investigate variants in the ABCA4 in Stargardt disease and the clinical findings of the cases. Sex, age, age of onset of symptoms, best-corrected visual acuity, color fundus photography, optical coherence tomography, and visual field test of the patients were recorded. Genetic analyses were screened, and patients with at least two variants in the ABCA4 were included in this study. RESULTS Twenty-seven patients diagnosed with Stargardt disease with the ABCA4 variants were included in this study. Twelve of them (44.4%) were female and fifteen (55.5%) were male. The mean age of the cases was 27.44 years (ranging from 8 to 56 years). Thirty different variants were detected in 54 ABCA4 alleles of 27 patients. The two most common pathogenic variants were c.5882 G>A p.(Gly1961Glu) and c.52C>T p.(Arg18Trp) in this cohort. Two novel variants were identified (c.3855_3856dup, c.1554 + 3_1554 + 4del) and the patient with the c.1554 + 3_1554 + 4del variant additionally had a different ABCA4 variant in trans. The other novel variant was homozygous. CONCLUSIONS In this study, two novel variants were described in a Turkish cohort with Stargardt disease. The variant c.52C>T p.(Arg18Trp) was the most common disease-causing variant besides the c.5882 G>A p.(Gly1961Glu) which was identified frequently in the previous studies. A larger sample size is necessary for describing different pathogenic variants and understanding the phenotype-genotype correlations.
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Affiliation(s)
| | - Büşra Özgüç Çalışkan
- Department of Medical Genetics, Erciyes University Medicine Faculty, Kayseri, Türkiye
| | - Nefise Kandemir
- Department of Medical Genetics, Kayseri Education and Research Hospital, Kayseri, Türkiye
| | - Ayşe Öner
- Department of Ophthalmology, Acibadem Hospital, İstanbul, Türkiye
| | - Munis Dündar
- Department of Medical Genetics, Erciyes University Medicine Faculty, Kayseri, Türkiye
| | - Yusuf Özkul
- Department of Medical Genetics, Erciyes University Medicine Faculty, Kayseri, Türkiye
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López-Rodríguez VR, Arce-González R, Martínez-Aguilar A, Rodríguez-López CE, Groman-Lupa S, Neria-González MI, Rodríguez-Uribe G, Zenteno JC. Mutational Profile and Retinal Phenotypes of PCARE-Related Cone-Rod Dystrophies in a Mexican Cohort. J Ophthalmol 2024; 2024:4003914. [PMID: 38468717 PMCID: PMC10927338 DOI: 10.1155/2024/4003914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/31/2024] [Accepted: 02/24/2024] [Indexed: 03/13/2024] Open
Abstract
Purpose The aim of the study is to describe the genotype and phenotype of a Mexican cohort with PCARE-related retinal disease. Methods The study included 14 patients from 11 unrelated pedigrees with retinal dystrophies who were demonstrated to carry biallelic pathogenic variants in PCARE. Visual assessment methods included best corrected visual acuity, color fundus photography, Goldmann visual field test, kinetic perimetry, dark/light adapted chromatic perimetry, full-field electroretinography, autofluorescence imaging, and spectral domain-optical coherence tomography imaging. Genetic screening was performed either by gene panel sequencing or by exome sequencing. Results According to the results of multimodal imaging and functional tests, all 14 patients were diagnosed with cone-rod dystrophy. Six different PCARE pathogenic alleles were identified in our cohort, including three novel mutations: c.3048_3049del (p.Tyr1016∗), c.3314_3315del (p.Ser1105∗), and c.551A > G (p.His184Arg). Notably, alleles p.His184Arg, p.Arg613∗, and p.Arg984∗ were present in 18 of the 22 (82%) PCARE alleles from probands in our cohort. Conclusion Our work expands the PCARE mutational profile by identifying three novel pathogenic variants causing retinal dystrophy. While phenotypic variations occurred among patients, a cone-rod dystrophy pattern was observed in all affected individuals.
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Affiliation(s)
| | - Rocío Arce-González
- Department of Genetics, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | - Alan Martínez-Aguilar
- Retinal Dystrophies Clinic, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | | | | | - M. Isabel Neria-González
- Laboratory of Integrative Microbiology and Molecular Biology, Division of Chemical and Biochemical Engineering, TecNm: Tecnológico de Estudios Superiores de Ecatepec, Ecatepec de Morelos, Estado de México, Mexico
| | - Genaro Rodríguez-Uribe
- CODET Vision Institute, Tijuana, Mexico
- Facultad de Medicina y Psicología, Universidad Autónoma de Baja California, Tijuana, Mexico
| | - Juan C. Zenteno
- Department of Genetics, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
- Department of Biochemistry, Faculty of Medicine, UNAM, Mexico City, Mexico
- Rare Disease Diagnostic Unit, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
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Dueñas Rey A, Del Pozo Valero M, Bouckaert M, Wood KA, Van den Broeck F, Daich Varela M, Thomas HB, Van Heetvelde M, De Bruyne M, Van de Sompele S, Bauwens M, Lenaerts H, Mahieu Q, Josifova D, Rivolta C, O'Keefe RT, Ellingford J, Webster AR, Arno G, Ayuso C, De Zaeytijd J, Leroy BP, De Baere E, Coppieters F. Combining a prioritization strategy and functional studies nominates 5'UTR variants underlying inherited retinal disease. Genome Med 2024; 16:7. [PMID: 38184646 PMCID: PMC10771650 DOI: 10.1186/s13073-023-01277-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/15/2023] [Indexed: 01/08/2024] Open
Abstract
BACKGROUND 5' untranslated regions (5'UTRs) are essential modulators of protein translation. Predicting the impact of 5'UTR variants is challenging and rarely performed in routine diagnostics. Here, we present a combined approach of a comprehensive prioritization strategy and functional assays to evaluate 5'UTR variation in two large cohorts of patients with inherited retinal diseases (IRDs). METHODS We performed an isoform-level re-analysis of retinal RNA-seq data to identify the protein-coding transcripts of 378 IRD genes with highest expression in retina. We evaluated the coverage of their 5'UTRs by different whole exome sequencing (WES) kits. The selected 5'UTRs were analyzed in whole genome sequencing (WGS) and WES data from IRD sub-cohorts from the 100,000 Genomes Project (n = 2397 WGS) and an in-house database (n = 1682 WES), respectively. Identified variants were annotated for 5'UTR-relevant features and classified into seven categories based on their predicted functional consequence. We developed a variant prioritization strategy by integrating population frequency, specific criteria for each category, and family and phenotypic data. A selection of candidate variants underwent functional validation using diverse approaches. RESULTS Isoform-level re-quantification of retinal gene expression revealed 76 IRD genes with a non-canonical retina-enriched isoform, of which 20 display a fully distinct 5'UTR compared to that of their canonical isoform. Depending on the probe design, 3-20% of IRD genes have 5'UTRs fully captured by WES. After analyzing these regions in both cohorts, we prioritized 11 (likely) pathogenic variants in 10 genes (ARL3, MERTK, NDP, NMNAT1, NPHP4, PAX6, PRPF31, PRPF4, RDH12, RD3), of which 7 were novel. Functional analyses further supported the pathogenicity of three variants. Mis-splicing was demonstrated for the PRPF31:c.-9+1G>T variant. The MERTK:c.-125G>A variant, overlapping a transcriptional start site, was shown to significantly reduce both luciferase mRNA levels and activity. The RDH12:c.-123C>T variant was found in cis with the hypomorphic RDH12:c.701G>A (p.Arg234His) variant in 11 patients. This 5'UTR variant, predicted to introduce an upstream open reading frame, was shown to result in reduced RDH12 protein but unaltered mRNA levels. CONCLUSIONS This study demonstrates the importance of 5'UTR variants implicated in IRDs and provides a systematic approach for 5'UTR annotation and validation that is applicable to other inherited diseases.
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Affiliation(s)
- Alfredo Dueñas Rey
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Marta Del Pozo Valero
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Manon Bouckaert
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Katherine A Wood
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Filip Van den Broeck
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Malena Daich Varela
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Huw B Thomas
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Mattias Van Heetvelde
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Marieke De Bruyne
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Stijn Van de Sompele
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Miriam Bauwens
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Hanne Lenaerts
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Quinten Mahieu
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | | | - Carlo Rivolta
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Raymond T O'Keefe
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Jamie Ellingford
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
- Genomics England, London, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Andrew R Webster
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Gavin Arno
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Bart P Leroy
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
- Division of Ophthalmology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elfride De Baere
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Frauke Coppieters
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium.
- Department of Pharmaceutics, Ghent University, Ghent, Belgium.
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Yang TH, Kang EYC, Lin PH, Wu PL, Sachs JA, Wang NK. The Value of Electroretinography in Identifying Candidate Genes for Inherited Retinal Dystrophies: A Diagnostic Guide. Diagnostics (Basel) 2023; 13:3041. [PMID: 37835784 PMCID: PMC10572658 DOI: 10.3390/diagnostics13193041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/08/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023] Open
Abstract
Inherited retinal dystrophies (IRDs) are a group of heterogeneous diseases caused by genetic mutations that specifically affect the function of the rod, cone, or bipolar cells in the retina. Electroretinography (ERG) is a diagnostic tool that measures the electrical activity of the retina in response to light stimuli, and it can help to determine the function of these cells. A normal ERG response consists of two waves, the a-wave and the b-wave, which reflect the activity of the photoreceptor cells and the bipolar and Muller cells, respectively. Despite the growing availability of next-generation sequencing (NGS) technology, identifying the precise genetic mutation causing an IRD can be challenging and costly. However, certain types of IRDs present with unique ERG features that can help guide genetic testing. By combining these ERG findings with other clinical information, such as on family history and retinal imaging, physicians can effectively narrow down the list of candidate genes to be sequenced, thereby reducing the cost of genetic testing. This review article focuses on certain types of IRDs with unique ERG features. We will discuss the pathophysiology and clinical presentation of, and ERG findings on, these disorders, emphasizing the unique role ERG plays in their diagnosis and genetic testing.
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Affiliation(s)
- Tsai-Hsuan Yang
- Department of Education, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan 33305, Taiwan;
- College of Medicine, National Yang Ming Chiao Tung University, Taipei 11217, Taiwan
| | - Eugene Yu-Chuan Kang
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan 33305, Taiwan;
- College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Pei-Hsuan Lin
- National Taiwan University Hospital, Yunlin 640203, Taiwan;
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, Columbia University, New York, NY 10032, USA; (P.-L.W.); (J.A.S.)
| | - Pei-Liang Wu
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, Columbia University, New York, NY 10032, USA; (P.-L.W.); (J.A.S.)
- Department of Medicine, National Taiwan University, Taipei 10617, Taiwan
| | - Jacob Aaron Sachs
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, Columbia University, New York, NY 10032, USA; (P.-L.W.); (J.A.S.)
- College of Arts and Sciences, University of Miami, Coral Gables, FL 33146, USA
| | - Nan-Kai Wang
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan 33305, Taiwan;
- College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, Columbia University, New York, NY 10032, USA; (P.-L.W.); (J.A.S.)
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
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Moran AL, Fehilly JD, Blacque O, Kennedy BN. Gene therapy for RAB28: What can we learn from zebrafish? Vision Res 2023; 210:108270. [PMID: 37321111 DOI: 10.1016/j.visres.2023.108270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/12/2023] [Accepted: 05/12/2023] [Indexed: 06/17/2023]
Abstract
The eye is particularly suited to gene therapy due to its accessibility, immunoprivileged state and compartmentalised structure. Indeed, many clinical trials are underway for therapeutic gene strategies for inherited retinal degenerations (IRDs). However, as there are currently 281 genes associated with IRD, there is still a large unmet need for effective therapies for the majority of IRD-causing genes. In humans, RAB28 null and hypomorphic alleles cause autosomal recessive cone-rod dystrophy (arCORD). Previous work demonstrated that restoring wild type zebrafish Rab28 via germline transgenesis, specifically in cone photoreceptors, is sufficient to rescue the defects in outer segment phagocytosis (OSP) observed in zebrafish rab28-/- knockouts (KO). This rescue suggests that gene therapy for RAB28-associated CORD may be successful by RAB28 gene restoration to cones. It also inspired us to critically consider the scenarios in which zebrafish can provide informative preclinical data for development of gene therapies. Thus, this review focuses on RAB28 biology and disease, and delves into both the opportunities and limitations of using zebrafish as a model for both gene therapy development and as a diagnostic tool for patient variants of unknown significance (VUS).
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Affiliation(s)
- Ailis L Moran
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland; UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - John D Fehilly
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland; UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Oliver Blacque
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland; UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Breandán N Kennedy
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland; UCD Conway Institute, University College Dublin, Dublin, Ireland
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Murro V, Banfi S, Testa F, Iarossi G, Falsini B, Sodi A, Signorini S, Iolascon A, Russo R, Mucciolo DP, Caputo R, Bacci GM, Bargiacchi S, Turco S, Fortini S, Simonelli F. A multidisciplinary approach to inherited retinal dystrophies from diagnosis to initial care: a narrative review with inputs from clinical practice. Orphanet J Rare Dis 2023; 18:223. [PMID: 37525225 PMCID: PMC10388566 DOI: 10.1186/s13023-023-02798-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 07/05/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND Non-syndromic inherited retinal dystrophies (IRDs) such as retinitis pigmentosa or Leber congenital amaurosis generally manifest between early childhood and late adolescence, imposing profound long-term impacts as a result of vision impairment or blindness. IRDs are highly heterogeneous, with often overlapping symptoms among different IRDs, and achieving a definite diagnosis is challenging. This narrative review provides a clinical overview of the non-syndromic generalized photoreceptor dystrophies, particularly retinitis pigmentosa and Leber congenital amaurosis. The clinical investigations and genetic testing needed to establish a diagnosis are outlined, and current management approaches are discussed, focusing on the importance of the involvement of an interdisciplinary team from diagnosis and initial care to long-term follow-up and support. RESULTS The effective management of IRDs requires a multidisciplinary, and ideally interdisciplinary, team of experts knowledgeable about IRDs, with experienced professionals from fields as diverse as ophthalmology, neuropsychiatry, psychology, neurology, genetics, orthoptics, developmental therapy, typhlology, occupational therapy, otolaryngology, and orientation and mobility specialties. Accurate clinical diagnosis encompasses a range of objective and subjective assessments as a prerequisite for the genetic testing essential in establishing an accurate diagnosis necessary for the effective management of IRDs, particularly in the era of gene therapies. Improvements in genome sequencing techniques, such as next-generation sequencing, have greatly facilitated the complex process of determining IRD-causing gene variants and establishing a molecular diagnosis. Genetic counseling is essential to help the individual and their family understand the condition, the potential risk for offspring, and the implications of a diagnosis on visual prognosis and treatment options. Psychological support for patients and caregivers is important at all stages of diagnosis, care, and rehabilitation and is an essential part of the multidisciplinary approach to managing IRDs. Effective communication throughout is essential, and the patient and caregivers' needs and expectations must be acknowledged and discussed. CONCLUSION As IRDs can present at an early age, clinicians need to be aware of the clinical signs suggesting visual impairment and follow up with multidisciplinary support for timely diagnoses to facilitate appropriate therapeutic or rehabilitation intervention to minimize vision loss.
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Affiliation(s)
- Vittoria Murro
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy
- Eye Clinic, Careggi Teaching Hospital, Florence, Italy
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, NA, Italy
- Medical Genetics, Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy.
| | - Giancarlo Iarossi
- Department of Ophthalmology, Bambino Gesù Children's Hospital, Rome, Italy
| | - Benedetto Falsini
- Ophthalmology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Andrea Sodi
- Eye Clinic, Careggi Teaching Hospital, Florence, Italy
| | - Sabrina Signorini
- Center of Child Neuro-Ophthalmology, IRCCS, Mondino Foundation, Pavia, Italy
| | - Achille Iolascon
- Medical Genetics Unit, Azienda Ospedaliera Universitaria Federico II, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
- CEINGE-Biotecnologie Avanzate, Naples, Italy
| | - Roberta Russo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
- CEINGE-Biotecnologie Avanzate, Naples, Italy
| | - Dario Pasquale Mucciolo
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy
- Ophthalmology Unit, San Jacopo Hospital, Pistoia, Italy
| | - Roberto Caputo
- Pediatric Ophthalmology Unit, A. Meyer Children's Hospital IRCCS, Florence, Italy
| | - Giacomo Maria Bacci
- Pediatric Ophthalmology Unit, A. Meyer Children's Hospital IRCCS, Florence, Italy
| | - Sara Bargiacchi
- Medical Genetics Unit, Ospedale Pediatrico Meyer, Florence, Italy
| | - Simona Turco
- National Centre of Services and Research for the Prevention of Blindness and Rehabilitation of the Visually Impaired, International Agency for the Prevention of Blindness-IAPB Italy Onlus, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Stefania Fortini
- National Centre of Services and Research for the Prevention of Blindness and Rehabilitation of the Visually Impaired, International Agency for the Prevention of Blindness-IAPB Italy Onlus, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
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9
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Areblom M, Kjellström S, Andréasson S, Öhberg A, Gränse L, Kjellström U. A Description of the Yield of Genetic Reinvestigation in Patients with Inherited Retinal Dystrophies and Previous Inconclusive Genetic Testing. Genes (Basel) 2023; 14:1413. [PMID: 37510321 PMCID: PMC10379620 DOI: 10.3390/genes14071413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
In the present era of evolving gene-based therapies for inherited retinal dystrophies (IRDs), it has become increasingly important to verify the genotype in every case, to identify all subjects eligible for treatment. Moreover, combined insight concerning phenotypes and genotypes is crucial for improved understanding of thevisual impairment, prognosis, and inheritance. The objective of this study was to investigate to what extent renewed comprehensive genetic testing of patients diagnosed with IRD but with previously inconclusive DNA test results can verify the genotype, if confirmation of the genotype has an impact on the understanding of the clinical picture, and, to describe the genetic spectrum encountered in a Swedish IRD cohort. The study included 279 patients from the retinitis pigmentosa research registry (comprising diagnosis within the whole IRD spectrum), hosted at the Department of Ophthalmology, Skåne University hospital, Sweden. The phenotypes had already been evaluated with electrophysiology and other clinical tests, e.g., visual acuity, Goldmann perimetry, and fundus imaging at the first visit, sometime between 1988-2015 and the previous-in many cases, multiple-genetic testing, performed between 1995 and 2020 had been inconclusive. All patients were aged 0-25 years at the time of their first visit. Renewed genetic testing was performed using a next generation sequencing (NGS) IRD panel including 322 genes (Blueprint Genetics). Class 5 and 4 variants, according to ACMG guidelines, were considered pathogenic. Of the 279 samples tested, a confirmed genotype was determined in 182 (65%). The cohort was genetically heterogenous, including 65 different genes. The most prevailing were ABCA4 (16.5%), RPGR (6%), CEP290 (6%), and RS1 (5.5%). Other prevalent genes were CACNA1F (3%), PROM1 (3%), CHM (3%), and NYX (3%). In 7% of the patients there was a discrepancy between the diagnosis made based on phenotypical or genotypical findings alone. To conclude, repeated DNA-analysis was beneficial also in previously tested patients and improved our ability to verify the genotype-phenotype association increasing the understanding of how visual impairment manifests, prognosis, and the inheritance pattern. Moreover, repeated testing using a widely available method could identify additional patients eligible for future gene-based therapies.
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Affiliation(s)
- Maria Areblom
- Ophthalmology, Department of Clinical Sciences Lund, Lund University, Skane University Hospital, 221 85 Lund, Sweden
| | | | - Sten Andréasson
- Ophthalmology, Department of Clinical Sciences Lund, Lund University, Skane University Hospital, 221 85 Lund, Sweden
| | | | - Lotta Gränse
- Ophthalmology, Department of Clinical Sciences Lund, Lund University, Skane University Hospital, 221 85 Lund, Sweden
| | - Ulrika Kjellström
- Ophthalmology, Department of Clinical Sciences Lund, Lund University, Skane University Hospital, 221 85 Lund, Sweden
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10
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Stephenson KAJ, Whelan L, Zhu J, Dockery A, Wynne NC, Cairns RM, Kirk C, Turner J, Duignan ES, O'Byrne JJ, Silvestri G, Kenna PF, Farrar GJ, Keegan DJ. Usher Syndrome on the Island of Ireland: A Genotype-Phenotype Review. Invest Ophthalmol Vis Sci 2023; 64:23. [PMID: 37466950 PMCID: PMC10362925 DOI: 10.1167/iovs.64.10.23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023] Open
Abstract
Purpose Usher syndrome (USH) is a genetically heterogeneous group of autosomal recessive (AR) syndromic inherited retinal degenerations (IRDs) representing 50% of deaf-blindness. All subtypes include retinitis pigmentosa, sensorineural hearing loss, and vestibular abnormalities. Thorough phenotyping may facilitate genetic diagnosis and intervention. Here we report the clinical/genetic features of an Irish USH cohort. Methods USH patients were selected from the Irish IRD registry (Target 5000). Patients were examined clinically (deep-phenotyping) and genetically using a 254 IRD-associated gene target capture sequencing panel, USH2A exon, and whole genome sequencing. Results The study identified 145 patients (24.1% USH1 [n = 35], 73.8% USH2 [n = 107], 1.4% USH3 [n = 2], and 0.7% USH4 [n = 1]). A genetic diagnosis was reached in 82.1%, the majority (80.7%) being MYO7A or USH2A genotypes. Mean visual acuity and visual field (VF) were 0.47 ± 0.58 LogMAR and 31.3° ± 32.8°, respectively, at a mean age of 43 years. Legal blindness criteria were met in 40.7%. Cataract was present in 77.4%. ADGRV1 genotypes had the most VF loss, whereas USH2A patients had greater myopia and CDH23 had the most astigmatism. Variants absent from gnomAD non-Finnish Europeans and ClinVar represented more than 20% of the variants identified and were detected in ADGRV1, ARSG, CDH23, MYO7A, and USH2A. Conclusions USH is a genetically diverse group of AR IRDs that have a profound impact on affected individuals and their families. The prevalence and phenotype/genotype characteristics of USH in Ireland have, as yet, gone unreported. Understanding the genotype of Irish USH patients may guide clinical and genetic characterization facilitating access to existing/novel therapeutics.
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Affiliation(s)
- Kirk A J Stephenson
- Clinical Ophthalmic Genetics Unit, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Laura Whelan
- The School of Genetics & Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Julia Zhu
- Clinical Ophthalmic Genetics Unit, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Adrian Dockery
- Next Generation Sequencing Laboratory, Pathology Department, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Niamh C Wynne
- The Research Foundation, Royal Victoria Eye & Ear Hospital, Dublin, Ireland
| | - Rebecca M Cairns
- Ophthalmology Department, Belfast Health and Social Care Trust Hospitals, Belfast, Northern Ireland
| | - Claire Kirk
- Ophthalmology Department, Belfast Health and Social Care Trust Hospitals, Belfast, Northern Ireland
| | - Jacqueline Turner
- Clinical Ophthalmic Genetics Unit, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Emma S Duignan
- The Research Foundation, Royal Victoria Eye & Ear Hospital, Dublin, Ireland
| | - James J O'Byrne
- Clinical Ophthalmic Genetics Unit, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Giuliana Silvestri
- Ophthalmology Department, Belfast Health and Social Care Trust Hospitals, Belfast, Northern Ireland
| | - Paul F Kenna
- The School of Genetics & Microbiology, Trinity College Dublin, Dublin, Ireland
- The Research Foundation, Royal Victoria Eye & Ear Hospital, Dublin, Ireland
| | - G Jane Farrar
- The School of Genetics & Microbiology, Trinity College Dublin, Dublin, Ireland
| | - David J Keegan
- Clinical Ophthalmic Genetics Unit, Mater Misericordiae University Hospital, Dublin, Ireland
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11
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Nguyen XTA, Moekotte L, Plomp AS, Bergen AA, van Genderen MM, Boon CJF. Retinitis Pigmentosa: Current Clinical Management and Emerging Therapies. Int J Mol Sci 2023; 24:ijms24087481. [PMID: 37108642 PMCID: PMC10139437 DOI: 10.3390/ijms24087481] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/01/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
Retinitis pigmentosa (RP) comprises a group of inherited retinal dystrophies characterized by the degeneration of rod photoreceptors, followed by the degeneration of cone photoreceptors. As a result of photoreceptor degeneration, affected individuals experience gradual loss of visual function, with primary symptoms of progressive nyctalopia, constricted visual fields and, ultimately, central vision loss. The onset, severity and clinical course of RP shows great variability and unpredictability, with most patients already experiencing some degree of visual disability in childhood. While RP is currently untreatable for the majority of patients, significant efforts have been made in the development of genetic therapies, which offer new hope for treatment for patients affected by inherited retinal dystrophies. In this exciting era of emerging gene therapies, it remains imperative to continue supporting patients with RP using all available options to manage their condition. Patients with RP experience a wide variety of physical, mental and social-emotional difficulties during their lifetime, of which some require timely intervention. This review aims to familiarize readers with clinical management options that are currently available for patients with RP.
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Affiliation(s)
- Xuan-Thanh-An Nguyen
- Department of Ophthalmology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Lude Moekotte
- Department of Ophthalmology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Astrid S Plomp
- Department of Clinical Genetics, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Arthur A Bergen
- Department of Clinical Genetics, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Maria M van Genderen
- Department of Ophthalmology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
- Bartiméus, Diagnostic Center for Complex Visual Disorders, 3703 AJ Zeist, The Netherlands
| | - Camiel J F Boon
- Department of Ophthalmology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- Department of Ophthalmology, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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12
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Ruiz-Ceja KA, Capasso D, Pinelli M, Del Prete E, Carrella D, di Bernardo D, Banfi S. Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data. BMC Genomics 2023; 24:206. [PMID: 37072692 PMCID: PMC10111803 DOI: 10.1186/s12864-023-09300-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 04/07/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND Inherited retinal diseases (IRD) are genetically heterogeneous disorders that cause the dysfunction or loss of photoreceptor cells and ultimately lead to blindness. To date, next-generation sequencing procedures fail to detect pathogenic sequence variants in coding regions of known IRD disease genes in about 30-40% of patients. One of the possible explanations for this missing heritability is the presence of yet unidentified transcripts of known IRD genes. Here, we aimed to define the transcript composition of IRD genes in the human retina by a meta-analysis of publicly available RNA-seq datasets using an ad-hoc designed pipeline. RESULTS We analysed 218 IRD genes and identified 5,054 transcripts, 3,367 of which were not previously reported. We assessed their putative expression levels and focused our attention on 435 transcripts predicted to account for at least 5% of the expression of the corresponding gene. We looked at the possible impact of the newly identified transcripts at the protein level and experimentally validated a subset of them. CONCLUSIONS This study provides an unprecedented, detailed overview of the complexity of the human retinal transcriptome that can be instrumental in contributing to the resolution of some cases of missing heritability in IRD patients.
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Affiliation(s)
- Karla Alejandra Ruiz-Ceja
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80078, Pozzuoli, Italy
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Program in Molecular Life Science, University of Campania "Luigi Vanvitelli", Via Vivaldi, 43, 81100, Caserta, Italy
| | - Dalila Capasso
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80078, Pozzuoli, Italy
- Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomic and Experimental Medicine Program, University of Naples "Federico II", Largo S. Marcellino, 10, 80138, Napoli, Italy
| | - Michele Pinelli
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80078, Pozzuoli, Italy
| | - Eugenio Del Prete
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80078, Pozzuoli, Italy
| | - Diego Carrella
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80078, Pozzuoli, Italy
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80078, Pozzuoli, Italy
- Chemical Engineering, University of Naples "Federico II", Piazzale Tecchio, 80, 80125, Napoli, Italy
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80078, Pozzuoli, Italy.
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via de Crecchio, 7, 80138, Napoli, Italy.
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13
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McClinton B, Crinnion LA, McKibbin M, Mukherjee R, Poulter JA, Smith CEL, Ali M, Watson CM, Inglehearn CF, Toomes C. Targeted nanopore sequencing enables complete characterisation of structural deletions initially identified using exon-based short-read sequencing strategies. Mol Genet Genomic Med 2023:e2164. [PMID: 36934458 DOI: 10.1002/mgg3.2164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/23/2023] [Indexed: 03/20/2023] Open
Abstract
BACKGROUND The widespread adoption of exome sequencing has greatly increased the rate of genetic diagnosis for inherited conditions. However, the detection and validation of large deletions remains challenging. While numerous bioinformatics approaches have been developed to detect deletions from whole - exome sequencing and targeted panels, further work is typically required to define the physical breakpoints or integration sites. Accurate characterisation requires either expensive follow - up whole - genome sequencing or the time - consuming, laborious process of PCR walking, both of which are challenging when dealing with the repeat sequences which frequently intersect deletion breakpoints. The aim of this study was to develop a cost-effective, long-range sequencing method to characterise deletions. METHODS Genomic DNA was amplified with primers spanning the deletion using long-range PCR and the products purified. Sequencing was performed on MinION flongle flowcells. The resulting fast5 files were basecalled using Guppy, trimmed using Porechop and aligned using Minimap2. Filtering was performed using NanoFilt. Nanopore sequencing results were verified by Sanger sequencing. RESULTS Four cases with deletions detected following comparative read-depth analysis of targeted short-read sequencing were analysed. Nanopore sequencing defined breakpoints at the molecular level in all cases including homozygous breakpoints in EYS, CNGA1 and CNGB1 and a heterozygous deletion in PRPF31. All breakpoints were verified by Sanger sequencing. CONCLUSIONS In this study, a quick, accurate and cost - effective method is described to characterise deletions identified from exome, and similar data, using nanopore sequencing.
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Affiliation(s)
- Benjamin McClinton
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Laura A Crinnion
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK.,North East and Yorkshire Genomic Laboratory Hub, Central Lab, St James's University Hospital, Leeds, UK
| | - Martin McKibbin
- Department of Ophthalmology, St James's University Hospital, Leeds, UK
| | | | - James A Poulter
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Claire E L Smith
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Manir Ali
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Christopher M Watson
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK.,North East and Yorkshire Genomic Laboratory Hub, Central Lab, St James's University Hospital, Leeds, UK
| | - Chris F Inglehearn
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Carmel Toomes
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
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14
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Lee NC. The incorporation of next-generation sequencing into pediatric care. Pediatr Neonatol 2023; 64 Suppl 1:S30-S34. [PMID: 36456424 DOI: 10.1016/j.pedneo.2022.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
Abstract
Genetic condition is one of the major etiologies causing morbidity and mortality in infants and children. More and more etiologies can be solved using next-generation sequencing (NGS) as it develops. Currently, whole-exome sequencing (WES) and whole-genome sequencing (WGS) have been highly integrated into clinical practice. The average diagnostic yield of WES/WGS in pediatric patients with genetic condition was around 40% (range: 21%-80%), with acceptable turnaround time and cost. The higher diagnostic yield categories are deafness, ophthalmic, neurological, skeletal conditions, and inborn error of metabolism. Positive results provide benefit with those for actionable diseases, next pregnancy planning, and family members. For those in critical condition, with the emergence of sequencing technology and bioinformatics analysis tools, provisional diagnosis can be made as short as 13.5 h using ultrarapid WGS. We believe this powerful tool has changed pediatric daily practice.
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Affiliation(s)
- Ni-Chung Lee
- Department of Pediatrics and Medical Genetics, National Taiwan University Hospital, 8 Chung-Shan South Road, Taipei 10041, Taiwan.
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15
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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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16
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Mondal AK, Swaroop A. Network Biology and Medicine to Rescue: Applications for Retinal Disease Mechanisms and Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1415:165-171. [PMID: 37440030 DOI: 10.1007/978-3-031-27681-1_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Inherited retinal degenerations (IRDs) are clinically and genetically heterogenous blinding diseases that manifest through dysfunction of target cells, photoreceptors, and retinal pigment epithelium (RPE) in the retina. Despite knowledge of numerous underlying genetic defects, current therapeutic approaches, including gene centric applications, have had limited success, thereby asserting the need of new directions for basic and translational research. Human diseases have commonalities that can be represented in a network form, called diseasome, which captures relationships among disease genes, proteins, metabolites, and patient meta-data. Clinical and genetic information of IRDs suggest shared relationships among pathobiological factors, making these a model case for network medicine. Characterization of the diseasome would considerably improve our understanding of retinal pathologies and permit better design of targeted therapies for disrupted regions within the integrated disease network. Network medicine in synergy with the ongoing artificial intelligence revolution can boost therapeutic developments, especially gene agnostic treatment opportunities.
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Affiliation(s)
- Anupam K Mondal
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Anand Swaroop
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
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17
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Panikker P, Roy S, Ghosh A, Poornachandra B, Ghosh A. Advancing precision medicines for ocular disorders: Diagnostic genomics to tailored therapies. Front Med (Lausanne) 2022; 9:906482. [PMID: 35911417 PMCID: PMC9334564 DOI: 10.3389/fmed.2022.906482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/29/2022] [Indexed: 11/20/2022] Open
Abstract
Successful sequencing of the human genome and evolving functional knowledge of gene products has taken genomic medicine to the forefront, soon combining broadly with traditional diagnostics, therapeutics, and prognostics in patients. Recent years have witnessed an extraordinary leap in our understanding of ocular diseases and their respective genetic underpinnings. As we are entering the age of genomic medicine, rapid advances in genome sequencing, gene delivery, genome surgery, and computational genomics enable an ever-increasing capacity to provide a precise and robust diagnosis of diseases and the development of targeted treatment strategies. Inherited retinal diseases are a major source of blindness around the world where a large number of causative genes have been identified, paving the way for personalized diagnostics in the clinic. Developments in functional genetics and gene transfer techniques has also led to the first FDA approval of gene therapy for LCA, a childhood blindness. Many such retinal diseases are the focus of various clinical trials, making clinical diagnoses of retinal diseases, their underlying genetics and the studies of natural history important. Here, we review methodologies for identifying new genes and variants associated with various ocular disorders and the complexities associated with them. Thereafter we discuss briefly, various retinal diseases and the application of genomic technologies in their diagnosis. We also discuss the strategies, challenges, and potential of gene therapy for the treatment of inherited and acquired retinal diseases. Additionally, we discuss the translational aspects of gene therapy, the important vector types and considerations for human trials that may help advance personalized therapeutics in ophthalmology. Retinal disease research has led the application of precision diagnostics and precision therapies; therefore, this review provides a general understanding of the current status of precision medicine in ophthalmology.
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Affiliation(s)
| | - Shomereeta Roy
- Grow Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
| | - Anuprita Ghosh
- Grow Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
| | | | - Arkasubhra Ghosh
- Grow Research Laboratory, Narayana Nethralaya Foundation, Bengaluru, India
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18
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Palfi A, Chadderton N, Millington-Ward S, Post I, Humphries P, Kenna PF, Farrar GJ. AAV-PHP.eB transduces both the inner and outer retina with high efficacy in mice. Mol Ther Methods Clin Dev 2022; 25:236-249. [PMID: 35474956 PMCID: PMC9018541 DOI: 10.1016/j.omtm.2022.03.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/27/2022] [Indexed: 12/18/2022]
Abstract
Recombinant adeno-associated virus (AAV) vectors are one of the main gene delivery vehicles used in retinal gene therapy approaches; however, there is a need to further improve the efficacy, tropism, and safety of these vectors. In this study, using a CMV-EGFP expression cassette, we characterize the retinal utility of AAV-PHP.eB, a serotype recently developed by in vivo directed evolution, which can cross the blood-brain barrier and target neurons with high efficacy in mice. Systemic and intravitreal delivery of AAV-PHP.eB resulted in the high transduction efficacy of retinal ganglion and horizontal cells, with systemic delivery providing pan-retinal coverage of the mouse retina. Subretinal delivery transduced photoreceptors and retinal pigment epithelium cells robustly. EGFP expression (number of transduced cells and mRNA levels) were similar when the retinas were transduced systemically or intravitreally with AAV-PHP.eB or intravitreally with AAV2/2. Notably, in photoreceptors, EGFP fluorescence intensities and mRNA levels were 50–70 times higher, when subretinal injections with AAV-PHP.eB were compared to AAV2/8. Our results demonstrate the pan-retinal transduction of ganglion cells and extremely efficient transduction of photoreceptor and retinal pigment epithelium cells as the most valuable features of AAV-PHP.eB in the mouse retina.
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Affiliation(s)
- Arpad Palfi
- Department of Genetics, School of Genetics and Microbiology, Trinity College Dublin, D02 VF25, Dublin, Ireland
| | - Naomi Chadderton
- Department of Genetics, School of Genetics and Microbiology, Trinity College Dublin, D02 VF25, Dublin, Ireland
| | - Sophia Millington-Ward
- Department of Genetics, School of Genetics and Microbiology, Trinity College Dublin, D02 VF25, Dublin, Ireland
| | - Iris Post
- Department of Genetics, School of Genetics and Microbiology, Trinity College Dublin, D02 VF25, Dublin, Ireland
| | - Pete Humphries
- Department of Genetics, School of Genetics and Microbiology, Trinity College Dublin, D02 VF25, Dublin, Ireland
| | - Paul F Kenna
- Department of Genetics, School of Genetics and Microbiology, Trinity College Dublin, D02 VF25, Dublin, Ireland.,The Research Foundation, Royal Victoria Eye and Ear Hospital, D02 XK51, Dublin, Ireland
| | - G Jane Farrar
- Department of Genetics, School of Genetics and Microbiology, Trinity College Dublin, D02 VF25, Dublin, Ireland
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19
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Ganapathi M, Thomas-Wilson A, Buchovecky C, Dharmadhikari A, Barua S, Lee W, Ruan MZC, Soucy M, Ragi S, Tanaka J, Clark LN, Naini AB, Liao J, Mansukhani M, Tsang S, Jobanputra V. Clinical exome sequencing for inherited retinal degenerations at a tertiary care center. Sci Rep 2022; 12:9358. [PMID: 35672425 PMCID: PMC9174483 DOI: 10.1038/s41598-022-13026-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/19/2022] [Indexed: 11/18/2022] Open
Abstract
Inherited retinal degenerations are clinically and genetically heterogeneous diseases characterized by progressive deterioration of vision. This study aimed at assessing the diagnostic yield of exome sequencing (ES) for an unselected cohort of individuals with hereditary retinal disorders. It is a retrospective study of 357 unrelated affected individuals, diagnosed with retinal disorders who underwent clinical ES. Variants from ES were filtered, prioritized, and classified using the ACMG recommendations. Clinical diagnosis of the individuals included rod-cone dystrophy (60%), macular dystrophy (20%), cone-rod dystrophy (9%), cone dystrophy (4%) and other phenotypes (7%). Majority of the cases (74%) were singletons and 6% were trios. A confirmed molecular diagnosis was obtained in 24% of cases. In 6% of cases, two pathogenic variants were identified with phase unknown, bringing the potential molecular diagnostic rate to ~ 30%. Including the variants of uncertain significance (VUS), potentially significant findings were reported in 57% of cases. Among cases with a confirmed molecular diagnosis, variants in EYS, ABCA4, USH2A, KIZ, CERKL, DHDDS, PROM1, NR2E3, CNGB1, ABCC6, PRPH2, RHO, PRPF31, PRPF8, SNRNP200, RP1, CHM, RPGR were identified in more than one affected individual. Our results support the utility of clinical ES in the diagnosis of genetically heterogeneous retinal disorders.
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Affiliation(s)
- Mythily Ganapathi
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Amanda Thomas-Wilson
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Christie Buchovecky
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Avinash Dharmadhikari
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Subit Barua
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Winston Lee
- Department of Ophthalmology, Columbia University, Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Merry Z C Ruan
- College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Megan Soucy
- Department of Ophthalmology, Columbia University, Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Sara Ragi
- Department of Ophthalmology, Columbia University, Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Joy Tanaka
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Lorraine N Clark
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Ali B Naini
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Jun Liao
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Mahesh Mansukhani
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Stephen Tsang
- Department of Ophthalmology, Columbia University, Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
- Jonas Children's Vision Care, Bernard & Shirlee Brown Glaucoma Laboratory, Columbia Stem Cell Initiative-Departments of Ophthalmology, Biomedical Engineering, Pathology & Cell Biology, Institute of Human Nutrition, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Vaidehi Jobanputra
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA.
- Precision Genomics Laboratory, Columbia University Irving Medical Center, 701 West 168th St., HHSC 1412, New York, NY, 10032, USA.
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20
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Zhu J, Stephenson KAJ, Dockery A, Turner J, O’Byrne JJ, Fitzsimon S, Farrar GJ, Flitcroft DI, Keegan DJ. Electrophysiology-Guided Genetic Characterisation Maximises Molecular Diagnosis in an Irish Paediatric Inherited Retinal Degeneration Population. Genes (Basel) 2022; 13:genes13040615. [PMID: 35456422 PMCID: PMC9033125 DOI: 10.3390/genes13040615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 11/16/2022] Open
Abstract
Inherited retinal degenerations (IRDs) account for over one third of the underlying causes of blindness in the paediatric population. Patients with IRDs often experience long delays prior to reaching a definitive diagnosis. Children attending a tertiary care paediatric ophthalmology department with phenotypic (i.e., clinical and/or electrophysiologic) evidence suggestive of IRD were contacted for genetic testing during the SARS-CoV-2-19 pandemic using a “telegenetics” approach. Genetic testing approach was panel-based next generation sequencing (351 genes) via a commercial laboratory (Blueprint Genetics, Helsinki, Finland). Of 70 patient samples from 57 pedigrees undergoing genetic testing, a causative genetic variant(s) was detected for 60 patients (85.7%) from 47 (82.5%) pedigrees. Of the 60 genetically resolved IRD patients, 5% (n = 3) are eligible for approved therapies (RPE65) and 38.3% (n = 23) are eligible for clinical trial-based gene therapies including CEP290 (n = 2), CNGA3 (n = 3), CNGB3 (n = 6), RPGR (n = 5) and RS1 (n = 7). The early introduction of genetic testing in the diagnostic/care pathway for children with IRDs is critical for genetic counselling of these families prior to upcoming gene therapy trials. Herein, we describe the pathway used, the clinical and genetic findings, and the therapeutic implications of the first systematic coordinated round of genetic testing of a paediatric IRD cohort in Ireland.
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Affiliation(s)
- Julia Zhu
- Mater Clinical Ophthalmic Genetics Unit, The Mater Misericordiae University Hospital, D07 R2WY Dublin, Ireland; (K.A.J.S.); (J.T.); (J.J.O.); (D.J.K.)
- Correspondence: or
| | - Kirk A. J. Stephenson
- Mater Clinical Ophthalmic Genetics Unit, The Mater Misericordiae University Hospital, D07 R2WY Dublin, Ireland; (K.A.J.S.); (J.T.); (J.J.O.); (D.J.K.)
- Ophthalmology Department, Children’s University Hospital, Temple Street, D01 XD99 Dublin, Ireland; (S.F.); (D.I.F.)
| | - Adrian Dockery
- Next Generation Sequencing Laboratory, Pathology Department, The Mater Misericordiae University Hospital, D07 R2WY Dublin, Ireland;
| | - Jacqueline Turner
- Mater Clinical Ophthalmic Genetics Unit, The Mater Misericordiae University Hospital, D07 R2WY Dublin, Ireland; (K.A.J.S.); (J.T.); (J.J.O.); (D.J.K.)
| | - James J. O’Byrne
- Mater Clinical Ophthalmic Genetics Unit, The Mater Misericordiae University Hospital, D07 R2WY Dublin, Ireland; (K.A.J.S.); (J.T.); (J.J.O.); (D.J.K.)
| | - Susan Fitzsimon
- Ophthalmology Department, Children’s University Hospital, Temple Street, D01 XD99 Dublin, Ireland; (S.F.); (D.I.F.)
| | - G. Jane Farrar
- The School of Genetics & Microbiology, Trinity College Dublin, D02 PN40 Dublin, Ireland;
| | - D. Ian Flitcroft
- Ophthalmology Department, Children’s University Hospital, Temple Street, D01 XD99 Dublin, Ireland; (S.F.); (D.I.F.)
| | - David J. Keegan
- Mater Clinical Ophthalmic Genetics Unit, The Mater Misericordiae University Hospital, D07 R2WY Dublin, Ireland; (K.A.J.S.); (J.T.); (J.J.O.); (D.J.K.)
- Ophthalmology Department, Children’s University Hospital, Temple Street, D01 XD99 Dublin, Ireland; (S.F.); (D.I.F.)
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21
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[Diagnosis of inherited retinal dystrophies. Relevance of molecular genetic testing from the patient's perspective]. Ophthalmologe 2022; 119:820-826. [PMID: 35312834 DOI: 10.1007/s00347-022-01602-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/10/2022] [Accepted: 02/16/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND The diagnostic process of inherited retinal dystrophies (IRD) is impeded by their low prevalence and the variability of the clinical presentations; however, for patients a valid diagnosis is vital for future planning and evaluating the potential of an appropriate early treatment to delay disease progression. OBJECTIVE Aim of the current study was to outline the patients' journeys until they receive the final diagnosis. This should help uncover diagnostic shortcomings and highlight potential for improvement with respect to the use of genetic diagnostic testing. MATERIAL AND METHODS Data were collected by questionnaires and an online survey conducted by the self-help association PRO RETINA Deutschland e. V. among patients with IRD. Data were analyzed by descriptive statistics. RESULTS From 15 March to 22 April 2021, 183 questionnaires were completed and 42 online interviews conducted. The surveyed population consisted of 48% female patients, mean age was 55 years and first symptoms occurred at a mean age of 22 years. On average about 14 years passed from first symptoms until final diagnosis. Only 66% of the patients reported that they had received at least 1 diagnostic genetic testing; less than half of the patients (47%) received genetic counseling. The huge majority of patients (85%) would be interested in gene therapy. CONCLUSION From the perspective of affected patients, a shortening of the time to diagnosis, the use of molecular genetic testing and the offer of genetic counseling are important to improve patient care for patients with IRD.
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22
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A comprehensive WGS-based pipeline for the identification of new candidate genes in inherited retinal dystrophies. NPJ Genom Med 2022; 7:17. [PMID: 35246562 PMCID: PMC8897414 DOI: 10.1038/s41525-022-00286-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 02/04/2022] [Indexed: 12/11/2022] Open
Abstract
To enhance the use of Whole Genome Sequencing (WGS) in clinical practice, it is still necessary to standardize data analysis pipelines. Herein, we aimed to define a WGS-based algorithm for the accurate interpretation of variants in inherited retinal dystrophies (IRD). This study comprised 429 phenotyped individuals divided into three cohorts. A comparison of 14 pathogenicity predictors, and the re-definition of its cutoffs, were performed using panel-sequencing curated data from 209 genetically diagnosed individuals with IRD (training cohort). The optimal tool combinations, previously validated in 50 additional IRD individuals, were also tested in patients with hereditary cancer (n = 109), and with neurological diseases (n = 47) to evaluate the translational value of this approach (validation cohort). Then, our workflow was applied for the WGS-data analysis of 14 individuals from genetically undiagnosed IRD families (discovery cohort). The statistical analysis showed that the optimal filtering combination included CADDv1.6, MAPP, Grantham, and SIFT tools. Our pipeline allowed the identification of one homozygous variant in the candidate gene CFAP20 (c.337 C > T; p.Arg113Trp), a conserved ciliary gene, which was abundantly expressed in human retina and was located in the photoreceptors layer. Although further studies are needed, we propose CFAP20 as a candidate gene for autosomal recessive retinitis pigmentosa. Moreover, we offer a translational strategy for accurate WGS-data prioritization, which is essential for the advancement of personalized medicine.
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23
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Clinical and Genetic Re-Evaluation of Inherited Retinal Degeneration Pedigrees following Initial Negative Findings on Panel-Based Next Generation Sequencing. Int J Mol Sci 2022; 23:ijms23020995. [PMID: 35055178 PMCID: PMC8780304 DOI: 10.3390/ijms23020995] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/03/2022] [Accepted: 01/12/2022] [Indexed: 02/06/2023] Open
Abstract
Although rare, inherited retinal degenerations (IRDs) are the most common reason for blind registration in the working age population. They are highly genetically heterogeneous (>300 known genetic loci), and confirmation of a molecular diagnosis is a prerequisite for many therapeutic clinical trials and approved treatments. First-tier genetic testing of IRDs with panel-based next-generation sequencing (pNGS) has a diagnostic yield of ≈70-80%, leaving the remaining more challenging cases to be resolved by second-tier testing methods. This study describes the phenotypic reassessment of patients with a negative result from first-tier pNGS and the rationale, outcomes, and cost of second-tier genetic testing approaches. Removing non-IRD cases from consideration and utilizing case-appropriate second-tier genetic testing techniques, we genetically resolved 56% of previously unresolved pedigrees, bringing the overall resolve rate to 92% (388/423). At present, pNGS remains the most cost-effective first-tier approach for the molecular assessment of diverse IRD populations Second-tier genetic testing should be guided by clinical (i.e., reassessment, multimodal imaging, electrophysiology), and genetic (i.e., single alleles in autosomal recessive disease) indications to achieve a genetic diagnosis in the most cost-effective manner.
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