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Heath Jeffery RC, Thompson JA, Lo J, Chelva ES, Armstrong S, Pulido JS, Procopio R, Vincent AL, Bianco L, Battaglia Parodi M, Ziccardi L, Antonelli G, Barbano L, Marques JP, Geada S, Carvalho AL, Tang WC, Chan CM, Boon CJF, Hensman J, Chen TC, Lin CY, Chen PL, Vincent A, Tumber A, Heon E, Grigg JR, Jamieson RV, Cornish EE, Nash BM, Borooah S, Ayton LN, Britten-Jones AC, Edwards TL, Ruddle JB, Sharma A, Porter RG, Lamey TM, McLaren TL, McLenachan S, Roshandel D, Chen FK. Retinal Dystrophies Associated With Peripherin-2: Genetic Spectrum and Novel Clinical Observations in 241 Patients. Invest Ophthalmol Vis Sci 2024; 65:22. [PMID: 38743414 PMCID: PMC11098050 DOI: 10.1167/iovs.65.5.22] [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: 02/10/2024] [Accepted: 04/12/2024] [Indexed: 05/16/2024] Open
Abstract
Purpose To describe the clinical, electrophysiological and genetic spectrum of inherited retinal diseases associated with variants in the PRPH2 gene. Methods A total of 241 patients from 168 families across 15 sites in 9 countries with pathogenic or likely pathogenic variants in PRPH2 were included. Records were reviewed for age at symptom onset, visual acuity, full-field ERG, fundus colour photography, fundus autofluorescence (FAF), and SD-OCT. Images were graded into six phenotypes. Statistical analyses were performed to determine genotype-phenotype correlations. Results The median age at symptom onset was 40 years (range, 4-78 years). FAF phenotypes included normal (5%), butterfly pattern dystrophy, or vitelliform macular dystrophy (11%), central areolar choroidal dystrophy (28%), pseudo-Stargardt pattern dystrophy (41%), and retinitis pigmentosa (25%). Symptom onset was earlier in retinitis pigmentosa as compared with pseudo-Stargardt pattern dystrophy (34 vs 44 years; P = 0.004). The median visual acuity was 0.18 logMAR (interquartile range, 0-0.54 logMAR) and 0.18 logMAR (interquartile range 0-0.42 logMAR) in the right and left eyes, respectively. ERG showed a significantly reduced amplitude across all components (P < 0.001) and a peak time delay in the light-adapted 30-Hz flicker and single-flash b-wave (P < 0.001). Twenty-two variants were novel. The central areolar choroidal dystrophy phenotype was associated with 13 missense variants. The remaining variants showed marked phenotypic variability. Conclusions We described six distinct FAF phenotypes associated with variants in the PRPH2 gene. One FAF phenotype may have multiple ERG phenotypes, demonstrating a discordance between structure and function. Given the vast spectrum of PRPH2 disease our findings are useful for future clinical trials.
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Affiliation(s)
- Rachael C. Heath Jeffery
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, Western Australia, Australia
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, Western Australia, Australia
- Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Jennifer A. Thompson
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Johnny Lo
- School of Science, Edith Cowan University, Perth, Western Australia, Australia
| | - Enid S. Chelva
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Sean Armstrong
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, Western Australia, Australia
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Jose S. Pulido
- Wills Eye Hospital, Mid Atlantic Retina, Thomas Jefferson University, Philadelphia, PA, United States
| | - Rebecca Procopio
- Wills Eye Hospital, Mid Atlantic Retina, Thomas Jefferson University, Philadelphia, PA, United States
| | - Andrea L. Vincent
- Department of Ophthalmology, FMHS, New Zealand National Eye Centre, University of Auckland, Auckland, New Zealand
- Eye Department, Greenlane Clinical Centre, Auckland District Health Board, Auckland, New Zealand
| | - Lorenzo Bianco
- Department of Ophthalmology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | | | | | | | - João P. Marques
- Ophthalmology Unit, Centro Hospitalar e Universitário de Coimbra (CHUC), Clinical and Academic Centre of Coimbra (CACC), Coimbra, Portugal
| | - Sara Geada
- Ophthalmology Unit, Centro Hospitalar e Universitário de Coimbra (CHUC), Clinical and Academic Centre of Coimbra (CACC), Coimbra, Portugal
| | - Ana L. Carvalho
- Medical Genetics Unit, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
| | - Wei C. Tang
- Singapore National Eye Centre, Singapore, Singapore
- Singapore Eye Research Institute, Singapore, Singapore
| | - Choi M. Chan
- Singapore National Eye Centre, Singapore, Singapore
- Singapore Eye Research Institute, Singapore, Singapore
| | - Camiel J. F. Boon
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Ophthalmology, Amsterdam University Medical Center, University of Amsterdam, the Netherlands
| | - Jonathan Hensman
- Department of Ophthalmology, Amsterdam University Medical Center, University of Amsterdam, the Netherlands
| | - Ta-Ching Chen
- Department of Ophthalmology, National Taiwan University Hospital, Taipei, Taiwan
- Center of Frontier Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Yu Lin
- Department of Ophthalmology, National Taiwan University Hospital, Taipei, Taiwan
| | - Pei-Lung Chen
- Department of Ophthalmology, National Taiwan University Hospital, Taipei, Taiwan
| | - Ajoy Vincent
- Department of Ophthalmology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anupreet Tumber
- Department of Ophthalmology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elise Heon
- Department of Ophthalmology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - John R. Grigg
- Save Sight Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Robyn V. Jamieson
- Save Sight Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Elisa E. Cornish
- Save Sight Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Benjamin M. Nash
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Sydney Children's Hospitals Network, Sydney, New South Wales, Australia
| | - Shyamanga Borooah
- University of California San Diego, La Jolla, California
- The Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California San Diego, La Jolla, CA, United States
| | - Lauren N. Ayton
- Department of Optometry and Vision Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Alexis Ceecee Britten-Jones
- Department of Optometry and Vision Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas L. Edwards
- Department of Optometry and Vision Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Jonathan B. Ruddle
- Department of Optometry and Vision Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
| | - Abhishek Sharma
- Ophthalmology Department, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | | | - Tina M. Lamey
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Terri L. McLaren
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, Western Australia, Australia
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Samuel McLenachan
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, Western Australia, Australia
| | - Danial Roshandel
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, Western Australia, Australia
| | - Fred K. Chen
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, Western Australia, Australia
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, Western Australia, Australia
- Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
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2
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Yang J, Zhou L, Ouyang J, Xiao X, Sun W, Li S, Zhang Q. Genotype-Phenotype Analysis of RPGR Variations: Reporting of 62 Chinese Families and a Literature Review. Front Genet 2021; 12:600210. [PMID: 34745198 PMCID: PMC8565807 DOI: 10.3389/fgene.2021.600210] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 04/27/2021] [Indexed: 02/05/2023] Open
Abstract
Purpose RPGR is the most common cause of X-linked retinitis pigmentosa (RP), of which female carriers are also frequently affected. The aim of the current study was to explore the RPGR variation spectrum and associated phenotype based on the data from our lab and previous studies. Methods Variants in RPGR were selected from exome sequencing data of 7,092 probands with different eye conditions. The probands and their available family members underwent comprehensive ocular examinations. Similar data were collected from previous reports through searches in PubMed, Web of Science, and Google Scholar. Systematic analyses of genotypes, phenotypes and their correlations were performed. Results A total of 46 likely pathogenic variants, including nine missense and one in-frame variants in RCC1-like domain and 36 truncation variants, in RPGR were detected in 62 unrelated families in our in-house cohort. In addition, a total of 585 variants, including 491 (83.9%) truncation variants, were identified from the literature. Systematic analysis of variants from our in-house dataset, literature, and gnomAD suggested that most of the pathogenic variants of RPGR were truncation variants while pathogenic missense and in-frame variants were enriched in the RCC1-like domain. Phenotypic variations were present between males and female carriers, including more severe refractive error but better best corrected visual acuity (BCVA) in female carriers than those in males. The male patients showed a significant reduction of BCVA with increase of age and males with exon1-14 variants presented a better BCVA than those with ORF15 variants. For female carriers, the BCVA also showed significant reduction with increase of age, but BCVA in females with exon1-14 variants was not significant difference compared with those with ORF15 variants. Conclusion Most pathogenic variants of RPGR are truncations. Missense and in-frame variants located outside of the RCC1-like domain might be benign and the pathogenicity criteria for these variants should be considered with greater caution. The BCVA and refractive error are different between males and female carriers. Increase of age and location of variants in ORF15 contribute to the reduction of BCVA in males. These results are valuable for understanding genotypes and phenotypes of RPGR.
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Affiliation(s)
- Junxing Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Lin Zhou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiamin Ouyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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3
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Song F, Owczarek-Lipska M, Ahmels T, Book M, Aisenbrey S, Menghini M, Barthelmes D, Schrader S, Spital G, Neidhardt J. High-Throughput Sequencing to Identify Mutations Associated with Retinal Dystrophies. Genes (Basel) 2021; 12:genes12081269. [PMID: 34440443 PMCID: PMC8391535 DOI: 10.3390/genes12081269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 11/16/2022] Open
Abstract
Retinal dystrophies (RD) are clinically and genetically heterogenous disorders showing mutations in over 270 disease-associated genes. Several millions of people worldwide are affected with different types of RD. Studying the relevance of disease-associated sequence alterations will assist in understanding disorders and may lead to the development of therapeutic approaches. Here, we established a whole exome sequencing (WES) pipeline to rapidly identify disease-associated mutations in patients. Sanger sequencing was applied to identify deep-intronic variants and to verify the co-segregation of WES results within families. We analyzed 26 unrelated patients with different syndromic and non-syndromic clinical manifestations of RD. All patients underwent ophthalmic examinations. We identified nine novel disease-associated sequence variants among 37 variants identified in total. The sequence variants located to 17 different genes. Interestingly, two cases presenting with Stargardt disease carried deep-intronic variants in ABCA4. We have classified 21 variants as pathogenic variants, 4 as benign/likely benign variants, and 12 as variants of uncertain significance. This study highlights the importance of WES-based mutation analyses in RD patients supporting clinical decisions, broadly based genetic diagnosis and support genetic counselling. It is essential for any genetic therapy to expand the mutation spectrum, understand the genes' function, and correlate phenotypes with genotypes.
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Affiliation(s)
- Fei Song
- Human Genetics Faculty VI-School of Medicine and Health Sciences, University of Oldenburg, Ammerländer Heerstrasse 114-118, 26129 Oldenburg, Germany; (F.S.); (M.O.-L.)
| | - Marta Owczarek-Lipska
- Human Genetics Faculty VI-School of Medicine and Health Sciences, University of Oldenburg, Ammerländer Heerstrasse 114-118, 26129 Oldenburg, Germany; (F.S.); (M.O.-L.)
- Research Center Neurosensory Science, University of Oldenburg, 26129 Oldenburg, Germany
| | - Tim Ahmels
- Department of Ophthalmology, Pius-Hospital, University of Oldenburg, 26121 Oldenburg, Germany; (T.A.); (S.S.)
| | - Marius Book
- Eye Centre at the St. Franziskus Hospital, 48145 Münster, Germany; (M.B.); (G.S.)
| | - Sabine Aisenbrey
- Department of Ophthalmology, Vivantes Health Network Ltd., Neukölln Hospital, 12351 Berlin, Germany;
| | - Moreno Menghini
- Department of Ophthalmology, Ospedale Regionale di Lugano, 6900 Lugano, Switzerland;
- Department of Ophthalmology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland;
| | - Daniel Barthelmes
- Department of Ophthalmology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland;
| | - Stefan Schrader
- Department of Ophthalmology, Pius-Hospital, University of Oldenburg, 26121 Oldenburg, Germany; (T.A.); (S.S.)
| | - Georg Spital
- Eye Centre at the St. Franziskus Hospital, 48145 Münster, Germany; (M.B.); (G.S.)
| | - John Neidhardt
- Human Genetics Faculty VI-School of Medicine and Health Sciences, University of Oldenburg, Ammerländer Heerstrasse 114-118, 26129 Oldenburg, Germany; (F.S.); (M.O.-L.)
- Research Center Neurosensory Science, University of Oldenburg, 26129 Oldenburg, Germany
- Correspondence: ; Tel.: +49-(0)441-7983810
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Autosomal Dominant Gyrate Atrophy-Like Choroidal Dystrophy Revisited: 45 Years Follow-Up and Association with a Novel C1QTNF5 Missense Variant. Int J Mol Sci 2021; 22:ijms22042089. [PMID: 33669876 PMCID: PMC7923301 DOI: 10.3390/ijms22042089] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/17/2021] [Accepted: 02/17/2021] [Indexed: 12/13/2022] Open
Abstract
We present a long-term follow-up in autosomal dominant gyrate atrophy-like choroidal dystrophy (adGALCD) and propose a possible genotype/phenotype correlation. Ophthalmic examination of six patients from two families revealed confluent areas of choroidal atrophy resembling gyrate atrophy, starting in the second decade of life. Progression continued centrally, reaching the fovea at about 60 years of age. Subretinal deposits, retinal pigmentation or choroidal neovascularization as seen in late-onset retinal degeneration (LORD) were not observed. Whole genome sequencing revealed a novel missense variant in the C1QTNF5 gene (p.(Q180E)) which was found in heterozygous state in all affected subjects. Haplotype analysis showed that this variant found in both families is identical by descent. Three-dimensional modeling of the possible supramolecular assemblies of C1QTNF5 revealed that the p.(Q180E) variant led to the destabilization of protein tertiary and quaternary structures, affecting both the stability of the single protomer and the entire globular head, thus exerting detrimental effects on the formation of C1QTNF5 trimeric globular domains and their interaction. In conclusion, we propose that the p.(Q180E) variant causes a specific phenotype, adGALCD, that differs in multiple clinical aspects from LORD. Disruption of optimal cell-adhesion mechanisms is expected when analyzing the effects of the point mutation at the protein level.
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Gan L, Yang C, Shu Y, Liu F, Sun R, Deng B, Xu J, Huang G, Qu C, Gong B, Li J. Identification of a novel homozygous nonsense mutation in the CDHR1 gene in a Chinese family with autosomal recessive retinitis pigmentosa. Clin Chim Acta 2020; 507:17-22. [PMID: 32277948 DOI: 10.1016/j.cca.2020.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/07/2020] [Accepted: 04/07/2020] [Indexed: 11/20/2022]
Abstract
BACKGROUND Retinitis pigmentosa (RP) is a group of hereditary retinal diseases that often lead to blindness. Although 80 genes associated with RP have been observed, the genetic mechanism of approximately 40% RP cases remains unknown. This study was to investigate the disease-causing gene in a Han Chinese family with autosomal recessive RP (arRP). METHODS A Chinese arRP family (RP-2373), consisting of three affected siblings and eight unaffected family members, was recruited in this study. All participants underwent complete ophthalmic examinations, including visual field testing, best-corrected visual acuity, fundus photography and electroretinography. Whole exome sequencing was performed on the three patients and Sanger sequencing was utilized to confirm the mutations identified in all family members and 2010 unrelated controls. RESULTS A novel homozygous nonsense mutation, c.1231C > T (p.Q411X) in the Cadherin-Related Family Member 1 (CDHR1) gene was identified in the RP-2373 family. The proband and her two affected sisters were found to carry a homozygous mutation that led to a substitution of Glutamine to a stop codon. Other unaffected members and 2010 ethnic-matched controls lacked this mutation. These data showed a complete co-segregation of the CDHR1 mutation with arRP in this family. The p.Q411X mutation was observed to affect highly conserved amino acid residue of CHDR1. CONCLUSION Our study expanded the CDHR1 mutation spectrum of RP in the Chinese population, which might help to better understand RP molecular pathogenesis.
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Affiliation(s)
- Li Gan
- Department of Laboratory Medicine and Key Laboratory for Human Disease Gene Study of Sichuan Province, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Chen Yang
- Department of Laboratory Medicine and Key Laboratory for Human Disease Gene Study of Sichuan Province, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Yi Shu
- School of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Fang Liu
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Ruiting Sun
- Department of Laboratory Medicine and Key Laboratory for Human Disease Gene Study of Sichuan Province, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Bolin Deng
- Department of Ophthalmology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Jiaxin Xu
- Department of Laboratory Medicine and Key Laboratory for Human Disease Gene Study of Sichuan Province, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Guo Huang
- Department of Laboratory Medicine and Key Laboratory for Human Disease Gene Study of Sichuan Province, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Chao Qu
- Department of Ophthalmology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
| | - Bo Gong
- Department of Laboratory Medicine and Key Laboratory for Human Disease Gene Study of Sichuan Province, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China; Institute of Chengdu Biology, Sichuan Translational Medicine Hospital, Chinese Academy of Sciences, Chengdu 610072, China.
| | - Jing Li
- Department of Ophthalmology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China.
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Shah M, Shanks M, Packham E, Williams J, Haysmoore J, MacLaren RE, Németh AH, Clouston P, Downes SM. Next generation sequencing using phenotype-based panels for genetic testing in inherited retinal diseases. Ophthalmic Genet 2020; 41:331-337. [PMID: 32543920 DOI: 10.1080/13816810.2020.1778736] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
INTRODUCTION Diagnostic next generation sequencing (NGS) services for patients with inherited retinal diseases (IRD) traditionally use gene panel based approaches, which have cost and resource implications. Phenotype-based gene panels use a targeted strategy with further testing protocols, if initial results are negative. We present the molecular findings of the Oxford phenotype-based NGS panels for genetic testing in IRD. METHODS Results of 655 consecutive patients referred for phenotype-based panel testing over 54 months were analysed to assess diagnostic yield. RESULTS Variants were identified in 450 patients (68.7%). The overall diagnostic yield from phenotype-based panels was 42.8%. The diagnostic yield was highest from panels representing distinct clinical phenotypes: Usher panel 90.9% and congenital stationary night blindness panel 75.0%. Retinitis pigmentosa/rod-cone dystrophy was the commonest presenting phenotype (n = 243) and Usher syndrome was the commonest presenting syndromic disease (n = 39). Patients presenting with late-onset (≥50 years) macular disease had a lower diagnostic yield (18.0%) compared with patients <50 years (24.2%). Additionally, a diagnostic yield of 1.8% was attributable to copy number variants. CONCLUSIONS Phenotype-based genetic testing panels provide a targeted testing approach and reduce bioinformatics demand. The overall diagnostic yield achieved in this study reflects the wide range of phenotypes that were referred. This pragmatic approach provides a high yield for early-onset and clearly defined genetically determined disorders but clinical utility is not as clear for late-onset macular disorders. This phenotype-based panel approach is clinician-referrer orientated, and can be used as a front-end virtual panel, when whole genome sequencing is introduced into diagnostic services for IRD.
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Affiliation(s)
- Mital Shah
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust , Oxford, UK.,Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford , Oxford, UK
| | - Morag Shanks
- Oxford Medical Genetics Laboratories, Churchill Hospital , Oxford, UK
| | - Emily Packham
- Oxford Medical Genetics Laboratories, Churchill Hospital , Oxford, UK
| | - Jonathan Williams
- Oxford Medical Genetics Laboratories, Churchill Hospital , Oxford, UK
| | - Jesse Haysmoore
- Oxford Medical Genetics Laboratories, Churchill Hospital , Oxford, UK
| | - Robert E MacLaren
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust , Oxford, UK.,Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford , Oxford, UK
| | - Andrea H Németh
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.,Nuffield Department of Clinical Neurosciences, University of Oxford , Oxford, UK
| | - Penny Clouston
- Oxford Medical Genetics Laboratories, Churchill Hospital , Oxford, UK
| | - Susan M Downes
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust , Oxford, UK.,Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford , Oxford, UK
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7
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Salmaninejad A, Motaee J, Farjami M, Alimardani M, Esmaeilie A, Pasdar A. Next-generation sequencing and its application in diagnosis of retinitis pigmentosa. Ophthalmic Genet 2020; 40:393-402. [PMID: 31755340 DOI: 10.1080/13816810.2019.1675178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Retinitis Pigmentosa (RP) is a major cause of heritable human blindness with a high genetic heterogeneity. It is characterized by the initial degeneration of rod photoreceptors followed by cone photoreceptors. RP is also a prominent reason of visual impairment, by a global prevalence of 1:4000. RP is usually specified with nyctalopia in puberty, followed by concentric visual field loss, that reflects the main impairment of rod photoreceptors; later in the life, as disease progresses, because of cone dysfunction, central vision loss also occurs. A precise molecular diagnosis is crucial for disease characterization and clinical prognosis. DNA sequencing is a powerful tool for deciphering various causes of different human diseases. The arrival of next-generation sequencing (NGS) technologies has diminished sequencing cost and considerably augmented the throughput, making whole-genome sequencing (WGS) a conceivable way for obtaining comprehensive genomic data and a more precise clinical decision. Nevertheless, the advantages gained from NGS technologies are among a number of challenges that must be sufficiently addressed before this technique can be altered from an investigation tools to a helpful method in routine clinical practices. This article aims to provide an overview about NGS technology and its related platforms. The challenges in the analysis and choosing an appropriate NGS method likewise their potential applications in clinical diagnosis are also discussed. The merit of such technique has been reflected in some recent studies where it is shown that using NGS and molecular information could help with clinical diagnosis, providing potential treatment options or changes, up-to-date family counseling and management.
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Affiliation(s)
- Arash Salmaninejad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jamshid Motaee
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahsa Farjami
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maliheh Alimardani
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Alireza Pasdar
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Bioinformatics Research Group, Mashhad University of Medical Sciences, Mashhad, Iran.,Division of Applied Medicine,Medical School, University of Aberdeen, Foresterhill, Aberdeen, UK
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8
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Mutation spectrum of PRPF31, genotype-phenotype correlation in retinitis pigmentosa, and opportunities for therapy. Exp Eye Res 2020; 192:107950. [PMID: 32014492 PMCID: PMC7065041 DOI: 10.1016/j.exer.2020.107950] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/13/2020] [Accepted: 01/27/2020] [Indexed: 12/11/2022]
Abstract
Pathogenic variants in pre-messenger RNA (pre-mRNA) splicing factor 31, PRPF31, are the second most common genetic cause of autosomal dominant retinitis pigmentosa (adRP) in most populations. This remains a completely untreatable and incurable form of blindness, and it can be difficult to predict the clinical course of disease. In order to design appropriate targeted therapies, a thorough understanding of the genetics and molecular mechanism of this disease is required. Here, we present the structure of the PRPF31 gene and PRPF31 protein, current understanding of PRPF31 protein function and the full spectrum of all reported clinically relevant variants in PRPF31. We delineate the correlation between specific PRPF31 genotype and RP phenotype, suggesting that, except in cases of complete gene deletion or large-scale deletions, dominant negative effects contribute to phenotype as well as haploinsufficiency. This has important impacts on design of targeted therapies, particularly the feasibility of gene augmentation as a broad approach for treatment of PRPF31-associated RP. We discuss other opportunities for therapy, including antisense oligonucleotide therapy and gene-independent approaches and offer future perspectives on treatment of this form of RP. PRPF31 is the second most common cause of autosomal dominant retinitis pigmentosa and a potential target for gene therapy. We present all reported pathogenic variants in PRPF31 as a resource for clinicians, diagnostic genetics labs, and researchers. Genotype-phenotype correlations suggest that, dominant negative effects contribute to disease in addition to haploinsufficiency. This finding has important impacts on the suitability of gene augmentation approaches across all mutation types. This finding may aid prognosis of disease in PRPF31-associated RP patients.
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9
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Genetic variations in olfactory receptor gene OR2AG2 in a large multigenerational family with asthma. Sci Rep 2019; 9:19029. [PMID: 31836740 PMCID: PMC6911056 DOI: 10.1038/s41598-019-54718-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 11/13/2019] [Indexed: 01/23/2023] Open
Abstract
It is estimated from twin studies that heritable factors account for at-least half of asthma-risk, of which genetic variants identified through population studies explain only a small fraction. Multi-generation large families with high asthma prevalence can serve as a model to identify highly penetrant genetic variants in closely related individuals that are missed by population studies. To achieve this, a four-generation Indian family with asthma was identified and recruited for examination and genetic testing. Twenty subjects representing all generations were selected for whole genome genotyping, of which eight were subjected to exome sequencing. Non-synonymous and deleterious variants, segregating with the affected individuals, were identified by exome sequencing. A prioritized deleterious missense common variant in the olfactory receptor gene OR2AG2 that segregated with a risk haplotype in asthma, was validated in an asthma cohort of different ethnicity. Phenotypic tests were conducted to verify expected deficits in terms of reduced ability to sense odors. Pathway-level relevance to asthma biology was tested in model systems and unrelated human lung samples. Our study suggests that OR2AG2 and other olfactory receptors may contribute to asthma pathophysiology. Genetic studies on large families of interest can lead to efficient discovery.
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10
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Talib M, van Schooneveld MJ, Van Cauwenbergh C, Wijnholds J, Ten Brink JB, Florijn RJ, Schalij-Delfos NE, Dagnelie G, van Genderen MM, De Baere E, Meester-Smoor MA, De Zaeytijd J, Cremers FPM, van den Born LI, Thiadens AA, Hoyng CB, Klaver CC, Leroy BP, Bergen AA, Boon CJF. The Spectrum of Structural and Functional Abnormalities in Female Carriers of Pathogenic Variants in the RPGR Gene. Invest Ophthalmol Vis Sci 2019; 59:4123-4133. [PMID: 30105367 DOI: 10.1167/iovs.17-23453] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose The purpose of this study was to investigate the phenotype and long-term clinical course of female carriers of RPGR mutations. Methods This was a retrospective cohort study of 125 heterozygous RPGR mutation carriers from 49 families. Results Eighty-three heterozygotes were from retinitis pigmentosa (RP) pedigrees, 37 were from cone-/cone-rod dystrophy (COD/CORD) pedigrees, and 5 heterozygotes were from pedigrees with mixed RP/CORD or unknown diagnosis. Mutations were located in exon 1-14 and in ORF15 in 42 of 125 (34%) and 83 of 125 (66%) subjects, respectively. The mean age at the first examination was 34.4 years (range, 2.1 to 86.0 years). The median follow-up time in heterozygotes with longitudinal data (n = 62) was 12.2 years (range, 1.1 to 52.2 years). Retinal pigmentary changes were present in 73 (58%) individuals. Visual symptoms were reported in 51 (40%) cases. Subjects with both symptoms and pigmentary fundus changes were older than the other heterozygotes (P = 0.01) and had thinner foveal outer retinas (P = 0.006). Complete expression of the RP or CORD phenotype was observed in 29 (23%) heterozygotes, although usually in milder forms than in affected male relatives. Best-corrected visual acuity (BCVA) was <20/40 and <20/400 in at least one eye in 45 of 116 (39%) and 11 of 116 (9%) heterozygotes, respectively. Myopia was observed in 74 of 101 (73%) subjects and was associated with lower BCVA (P = 0.006). Increasing age was associated with lower BCVA (P = 0.002) and decreasing visual field size (P = 0.012; I4e isopter). Conclusions RPGR mutations lead to a phenotypic spectrum in female carriers, with myopia as a significantly aggravating factor. Complete disease expression is observed in some individuals, who may benefit from future (gene) therapeutic options.
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Affiliation(s)
- Mays Talib
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Caroline Van Cauwenbergh
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium.,Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Jan Wijnholds
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jacoline B Ten Brink
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, The Netherlands
| | - Ralph J Florijn
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, The Netherlands
| | | | - Gislin Dagnelie
- Wilmer Eye Institute, Johns Hopkins University, Baltimore, Maryland, United States
| | - Maria M van Genderen
- Bartiméus, Diagnostic Centre for Complex Visual Disorders, Zeist, The Netherlands
| | - Elfride De Baere
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | | | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Frans P M Cremers
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Alberta A Thiadens
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Caroline C Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bart P Leroy
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium.,Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium.,Ophthalmic Genetics & Visual Electrophysiology, Division of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Arthur A Bergen
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, The Netherlands.,The Netherlands Institute for Neuroscience (NIN-KNAW), Amsterdam, The Netherlands
| | - Camiel J F Boon
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands.,Department of Ophthalmology, Amsterdam UMC, University of Amsterdam, The Netherlands
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11
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Martin-Merida I, Aguilera-Garcia D, Fernandez-San JP, Blanco-Kelly F, Zurita O, Almoguera B, Garcia-Sandoval B, Avila-Fernandez A, Arteche A, Minguez P, Carballo M, Corton M, Ayuso C. Toward the Mutational Landscape of Autosomal Dominant Retinitis Pigmentosa: A Comprehensive Analysis of 258 Spanish Families. Invest Ophthalmol Vis Sci 2019; 59:2345-2354. [PMID: 29847639 DOI: 10.1167/iovs.18-23854] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To provide a comprehensive overview of the molecular basis of autosomal dominant retinitis pigmentosa (adRP) in Spanish families. Thus, we established the molecular characterization rate, gene prevalence, and mutational spectrum in the largest European cohort reported to date. Methods A total of 258 unrelated Spanish families with a clinical diagnosis of RP and suspected autosomal dominant inheritance were included. Clinical diagnosis was based on complete ophthalmologic examination and family history. Retrospective and prospective analysis of Spanish adRP families was carried out using a combined strategy consisting of classic genetic techniques and next-generation sequencing (NGS) for single-nucleotide variants and copy number variation (CNV) screening. Results Overall, 60% of our families were genetically solved. Interestingly, 3.1% of the cohort carried pathogenic CNVs. Disease-causing variants were found in an autosomal dominant gene in 55% of the families; however, X-linked and autosomal recessive forms were also identified in 3% and 2%, respectively. Four genes (RHO, PRPF31, RP1, and PRPH2) explained up to 62% of the solved families. Missense changes were most frequently found in adRP-associated genes; however, CNVs represented a relevant disease cause in PRPF31- and CRX-associated forms. Conclusions Implementation of NGS technologies in the adRP study clearly increased the diagnostic yield compared with classic approaches. Our study outcome expands the spectrum of disease-causing variants, provides accurate data on mutation gene prevalence, and highlights the implication of CNVs as important contributors to adRP etiology.
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Affiliation(s)
- Inmaculada Martin-Merida
- 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), ISCIII, Madrid, Spain
| | - Domingo Aguilera-Garcia
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Jose P Fernandez-San
- 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), ISCIII, Madrid, Spain
| | - Fiona Blanco-Kelly
- 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), ISCIII, Madrid, Spain
| | - Olga Zurita
- 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), ISCIII, Madrid, Spain
| | - Berta Almoguera
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Blanca Garcia-Sandoval
- Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Almudena Avila-Fernandez
- 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), ISCIII, Madrid, Spain
| | - Ana Arteche
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Pablo Minguez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Miguel Carballo
- Molecular Genetics Unit, Hospital de Terrassa, Terrassa, Barcelona, Spain
| | - Marta Corton
- 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), ISCIII, Madrid, Spain
| | - 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), ISCIII, Madrid, Spain
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12
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Birtel J, Gliem M, Mangold E, Müller PL, Holz FG, Neuhaus C, Lenzner S, Zahnleiter D, Betz C, Eisenberger T, Bolz HJ, Charbel Issa P. Next-generation sequencing identifies unexpected genotype-phenotype correlations in patients with retinitis pigmentosa. PLoS One 2018; 13:e0207958. [PMID: 30543658 PMCID: PMC6292620 DOI: 10.1371/journal.pone.0207958] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/08/2018] [Indexed: 12/13/2022] Open
Abstract
Retinitis pigmentosa (RP) is an inherited degenerative disease causing severe retinal dystrophy and visual impairment mainly with onset in infancy or adolescence. Targeted next-generation sequencing (NGS) has become an efficient tool to encounter the enormous genetic heterogeneity of diverse retinal dystrophies, including RP. To identify disease-causing mutations in unselected, consecutive RP patients, we conducted Sanger sequencing of genes commonly involved in the suspected genetic RP subtype, followed by targeted large-panel NGS if no mutation was identified, or NGS as primary analysis. A high (70%) detection rate of disease-causing mutations was achieved in a large cohort of 116 unrelated patients. About half (48%) of the solved RP cases were explained by mutations in four genes: RPGR, EYS, PRPF31 and USH2A. Overall, 110 different mutations distributed across 30 different genes were detected, and 46 of these mutations were novel. A molecular diagnosis was achieved in the majority (82–100%) of patients if the family history was suggestive for a particular mode of inheritance, but only in 60% in cases of sporadic RP. The diagnostic potential of extensive molecular analysis in a routine setting is also illustrated by the identification of unexpected genotype-phenotype correlations for RP patients with mutations in CRX, CEP290, RPGRIP1, MFSD8. Furthermore, we identified numerous mutations in autosomal dominant (PRPF31, PRPH2, CRX) and X-linked (RPGR) RP genes in patients with sporadic RP. Variants in RP2 and RPGR were also found in female RP patients with apparently sporadic or dominant disease. In summary, this study demonstrates that massively parallel sequencing of all known retinal dystrophy genes is a valuable diagnostic approach for RP patients.
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Affiliation(s)
- Johannes Birtel
- Department of Ophthalmology, University of Bonn, Bonn, Germany
- Center for Rare Diseases Bonn (ZSEB), University of Bonn, Bonn, Germany
| | - Martin Gliem
- Department of Ophthalmology, University of Bonn, Bonn, Germany
- Center for Rare Diseases Bonn (ZSEB), University of Bonn, Bonn, Germany
| | | | - Philipp L. Müller
- Department of Ophthalmology, University of Bonn, Bonn, Germany
- Center for Rare Diseases Bonn (ZSEB), University of Bonn, Bonn, Germany
| | - Frank G. Holz
- Department of Ophthalmology, University of Bonn, Bonn, Germany
- Center for Rare Diseases Bonn (ZSEB), University of Bonn, Bonn, Germany
| | | | | | | | - Christian Betz
- Bioscientia Center for Human Genetics, Ingelheim, Germany
| | | | - Hanno J. Bolz
- Bioscientia Center for Human Genetics, Ingelheim, Germany
- Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany
| | - Peter Charbel Issa
- Department of Ophthalmology, University of Bonn, Bonn, Germany
- Center for Rare Diseases Bonn (ZSEB), University of Bonn, Bonn, Germany
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, and Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- * E-mail:
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13
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Biallelic sequence and structural variants in RAX2 are a novel cause for autosomal recessive inherited retinal disease. Genet Med 2018; 21:1319-1329. [PMID: 30377383 PMCID: PMC6752271 DOI: 10.1038/s41436-018-0345-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 07/12/2018] [Accepted: 10/09/2018] [Indexed: 12/18/2022] Open
Abstract
Purpose RAX2 encodes a homeobox-containing transcription factor, in which four monoallelic pathogenic variants have been described in autosomal dominant cone-dominated retinal disease. Methods Exome sequencing in a European cohort with inherited retinal disease (IRD) (n = 2086) was combined with protein structure modeling of RAX2 missense variants, bioinformatics analysis of deletion breakpoints, haplotyping of RAX2 variant c.335dup, and clinical assessment of biallelic RAX2-positive cases and carrier family members. Results Biallelic RAX2 sequence and structural variants were found in five unrelated European index cases, displaying nonsyndromic autosomal recessive retinitis pigmentosa (ARRP) with an age of onset ranging from childhood to the mid-40s (average mid-30s). Protein structure modeling points to loss of function of the novel recessive missense variants and to a dominant-negative effect of the reported dominant RAX2 alleles. Structural variants were fine-mapped to disentangle their underlying mechanisms. Haplotyping of c.335dup in two cases suggests a common ancestry. Conclusion This study supports a role for RAX2 as a novel disease gene for recessive IRD, broadening the mutation spectrum from sequence to structural variants and revealing a founder effect. The identification of biallelic RAX2 pathogenic variants in five unrelated families shows that RAX2 loss of function may be a nonnegligible cause of IRD in unsolved ARRP cases.
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14
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Van Schil K, Naessens S, Van de Sompele S, Carron M, Aslanidis A, Van Cauwenbergh C, Kathrin Mayer A, Van Heetvelde M, Bauwens M, Verdin H, Coppieters F, Greenberg ME, Yang MG, Karlstetter M, Langmann T, De Preter K, Kohl S, Cherry TJ, Leroy BP, De Baere E. Mapping the genomic landscape of inherited retinal disease genes prioritizes genes prone to coding and noncoding copy-number variations. Genet Med 2017; 20:202-213. [PMID: 28749477 PMCID: PMC5787040 DOI: 10.1038/gim.2017.97] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/19/2017] [Indexed: 01/08/2023] Open
Abstract
PurposePart of the hidden genetic variation in heterogeneous genetic conditions such as inherited retinal diseases (IRDs) can be explained by copy-number variations (CNVs). Here, we explored the genomic landscape of IRD genes listed in RetNet to identify and prioritize those genes susceptible to CNV formation.MethodsRetNet genes underwent an assessment of genomic features and of CNV occurrence in the Database of Genomic Variants and literature. CNVs identified in an IRD cohort were characterized using targeted locus amplification (TLA) on extracted genomic DNA.ResultsExhaustive literature mining revealed 1,345 reported CNVs in 81 different IRD genes. Correlation analysis between rankings of genomic features and CNV occurrence demonstrated the strongest correlation between gene size and CNV occurrence of IRD genes. Moreover, we identified and delineated 30 new CNVs in IRD cases, 13 of which are novel and three of which affect noncoding, putative cis-regulatory regions. Finally, the breakpoints of six complex CNVs were determined using TLA in a hypothesis-neutral manner.ConclusionWe propose a ranking of CNV-prone IRD genes and demonstrate the efficacy of TLA for the characterization of CNVs on extracted DNA. Finally, this IRD-oriented CNV study can serve as a paradigm for other genetically heterogeneous Mendelian diseases with hidden genetic variation.
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Affiliation(s)
- Kristof Van Schil
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Sarah Naessens
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Stijn Van de Sompele
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Marjolein Carron
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Alexander Aslanidis
- Laboratory for Experimental Immunology of the Eye, Department of Ophthalmology, University of Cologne, Cologne, Germany
| | | | - Anja Kathrin Mayer
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
| | - Mattias Van Heetvelde
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Miriam Bauwens
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Hannah Verdin
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Frauke Coppieters
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Michael E Greenberg
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Marty G Yang
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Marcus Karlstetter
- Laboratory for Experimental Immunology of the Eye, Department of Ophthalmology, University of Cologne, Cologne, Germany
| | - Thomas Langmann
- Laboratory for Experimental Immunology of the Eye, Department of Ophthalmology, University of Cologne, Cologne, Germany
| | - Katleen De Preter
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Susanne Kohl
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
| | - Timothy J Cherry
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA.,Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington, USA
| | - 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, USA
| | | | - Elfride De Baere
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
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15
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Whole exome sequencing using Ion Proton system enables reliable genetic diagnosis of inherited retinal dystrophies. Sci Rep 2017; 7:42078. [PMID: 28181551 PMCID: PMC5299602 DOI: 10.1038/srep42078] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 01/05/2017] [Indexed: 01/17/2023] Open
Abstract
Inherited retinal dystrophies (IRD) comprise a wide group of clinically and genetically complex diseases that progressively affect the retina. Over recent years, the development of next-generation sequencing (NGS) methods has transformed our ability to diagnose heterogeneous diseases. In this work, we have evaluated the implementation of whole exome sequencing (WES) for the molecular diagnosis of IRD. Using Ion ProtonTM system, we simultaneously analyzed 212 genes that are responsible for more than 25 syndromic and non-syndromic IRD. This approach was used to evaluate 59 unrelated families, with the pathogenic variant(s) successfully identified in 71.18% of cases. Interestingly, the mutation detection rate varied substantially depending on the IRD subtype. Overall, we found 63 different mutations (21 novel) in 29 distinct genes, and performed in vivo functional studies to determine the deleterious impact of variants identified in MERTK, CDH23, and RPGRIP1. In addition, we provide evidences that support CDHR1 as a gene responsible for autosomal recessive retinitis pigmentosa with early macular affectation, and present data regarding the disease mechanism of this gene. Altogether, these results demonstrate that targeted WES of all IRD genes is a reliable, hypothesis-free approach, and a cost- and time-effective strategy for the routine genetic diagnosis of retinal dystrophies.
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16
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Lim H, Park YM, Lee JK, Taek Lim H. Single-Exome sequencing identified a novel RP2 mutation in a child with X-linked retinitis pigmentosa. CANADIAN JOURNAL OF OPHTHALMOLOGY 2016; 51:326-330. [DOI: 10.1016/j.jcjo.2016.03.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 12/08/2015] [Accepted: 03/25/2016] [Indexed: 10/21/2022]
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17
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Pàmpols T, Ramos FJ, Lapunzina P, Gozalo‐Salellas I, Pérez‐Jurado LA, Pujol A. A view on clinical genetics and genomics in Spain: of challenges and opportunities. Mol Genet Genomic Med 2016; 4:376-91. [PMID: 27468414 PMCID: PMC4947857 DOI: 10.1002/mgg3.232] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
A view on clinical genetics and genomics in Spain: of challenges and opportunities.
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Affiliation(s)
- Teresa Pàmpols
- Division of Inborn Errors of MetabolismDepartment of Biochemistry and Molecular GeneticsHospital ClinicBarcelonaSpain
- Center for Biomedical Research on Rare Diseases CIBERER U737BarcelonaSpain
| | - Feliciano J. Ramos
- Unit of Clinical GeneticsService of PediatricsUniversity Hospital “Lozano Blesa”ZaragozaSpain
- Functional GenomicsDepartment PediatricsUniversity of Zaragoza Medical SchoolZaragozaSpain
- Center for Biomedical Research on Rare Diseases CIBERER‐GCV02ZaragozaSpain
| | - Pablo Lapunzina
- Clinical Genetics UnitInstitute of Medical and Molecular Genetics (INGEMM)IdiPAZHospital Universitario La PazMadridSpain
- Center for Biomedical Research on Rare Diseases CIBERER U753MadridSpain
| | - Ignasi Gozalo‐Salellas
- Department of Romance LanguagesUniversity of Pennsylvania521 Williams Hall 255 S. 36th StreetPhiladelphiaPennsylvania19104
| | - Luis A. Pérez‐Jurado
- Genetics UnitDepartment of Experimental and Health SciencesPompeu Fabra University (UPF)BarcelonaSpain
- Hospital del Mar Research Institute (IMIM)BarcelonaSpain
- Center for Biomedical Research on Rare Diseases CIBERER U735BarcelonaSpain
| | - Aurora Pujol
- Neurometabolic Diseases LaboratoryInstitute of NeuropathologyIDIBELLBarcelonaSpain
- Center for Biomedical Research on Rare Diseases CIBERER U759BarcelonaSpain
- Catalan Institution of Research and Advanced Studies (ICREA)BarcelonaSpain
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18
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Jo H, Park M, Woo H, Han M, Kim B, Choi B, Chung K, Koo S. Application of whole‐exome sequencing for detecting copy number variants in CMT1A/HNPP. Clin Genet 2016; 90:177-81. [DOI: 10.1111/cge.12714] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 11/30/2015] [Accepted: 12/08/2015] [Indexed: 11/26/2022]
Affiliation(s)
- H.‐Y. Jo
- Division of Intractable Diseases, Center for Biomedical Sciences Korea National Institute of Health Cheongju South Korea
| | - M.‐H. Park
- Division of Intractable Diseases, Center for Biomedical Sciences Korea National Institute of Health Cheongju South Korea
| | - H.‐M. Woo
- Division of Intractable Diseases, Center for Biomedical Sciences Korea National Institute of Health Cheongju South Korea
| | - M.H. Han
- Division of Intractable Diseases, Center for Biomedical Sciences Korea National Institute of Health Cheongju South Korea
| | - B.‐Y. Kim
- Division of Intractable Diseases, Center for Biomedical Sciences Korea National Institute of Health Cheongju South Korea
| | - B.‐O. Choi
- Department of Neurology, Samsung Medical Center Sungkyunkwan University School of Medicine Seoul South Korea
| | - K.W. Chung
- Department of Biological Sciences Kongju National University Gongju South Korea
| | - S.K. Koo
- Division of Intractable Diseases, Center for Biomedical Sciences Korea National Institute of Health Cheongju South Korea
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19
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Weisschuh N, Mayer AK, Strom TM, Kohl S, Glöckle N, Schubach M, Andreasson S, Bernd A, Birch DG, Hamel CP, Heckenlively JR, Jacobson SG, Kamme C, Kellner U, Kunstmann E, Maffei P, Reiff CM, Rohrschneider K, Rosenberg T, Rudolph G, Vámos R, Varsányi B, Weleber RG, Wissinger B. Mutation Detection in Patients with Retinal Dystrophies Using Targeted Next Generation Sequencing. PLoS One 2016; 11:e0145951. [PMID: 26766544 PMCID: PMC4713063 DOI: 10.1371/journal.pone.0145951] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 12/10/2015] [Indexed: 11/24/2022] Open
Abstract
Retinal dystrophies (RD) constitute a group of blinding diseases that are characterized by clinical variability and pronounced genetic heterogeneity. The different nonsyndromic and syndromic forms of RD can be attributed to mutations in more than 200 genes. Consequently, next generation sequencing (NGS) technologies are among the most promising approaches to identify mutations in RD. We screened a large cohort of patients comprising 89 independent cases and families with various subforms of RD applying different NGS platforms. While mutation screening in 50 cases was performed using a RD gene capture panel, 47 cases were analyzed using whole exome sequencing. One family was analyzed using whole genome sequencing. A detection rate of 61% was achieved including mutations in 34 known and two novel RD genes. A total of 69 distinct mutations were identified, including 39 novel mutations. Notably, genetic findings in several families were not consistent with the initial clinical diagnosis. Clinical reassessment resulted in refinement of the clinical diagnosis in some of these families and confirmed the broad clinical spectrum associated with mutations in RD genes.
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Affiliation(s)
- Nicole Weisschuh
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
- * E-mail:
| | - Anja K. Mayer
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
| | - Tim M. Strom
- Institute of Human Genetics, Helmholtz Zentrum Muenchen, Neuherberg, Germany
| | - Susanne Kohl
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
| | | | - Max Schubach
- Institute of Medical Genetics and Human Genetics, Charité – Universitaetsmedizin Berlin, Berlin, Germany
| | | | - Antje Bernd
- University Eye Hospital, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
| | - David G. Birch
- The Retina Foundation of the Southwest, Dallas, Texas, United States of America
| | | | - John R. Heckenlively
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Samuel G. Jacobson
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | - Ulrich Kellner
- Rare Retinal Disease Center, AugenZentrum Siegburg, MVZ ADTC Siegburg GmbH, Siegburg, Germany
| | - Erdmute Kunstmann
- Institute of Human Genetics, Julius-Maximilian-University, Wuerzburg, Germany
| | - Pietro Maffei
- Department of Medicine, University Hospital of Padua, Padua, Italy
| | | | | | - Thomas Rosenberg
- National Eye Clinic, Department of Ophthalmology, Glostrup Hospital, Glostrup, Denmark
| | - Günther Rudolph
- University Eye Hospital, Ludwig Maximilians University, Munich, Germany
| | - Rita Vámos
- Department of Ophthalmology, Semmelweis University, Budapest, Hungary
| | - Balázs Varsányi
- Department of Ophthalmology, Semmelweis University, Budapest, Hungary
- Department of Ophthalmology, University of Pécs Medical School, Pécs, Hungary
| | - Richard G. Weleber
- Casey Eye Institute, Oregon Retinal Degeneration Center, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Bernd Wissinger
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tuebingen, Tuebingen, Germany
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