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Gao FJ, Wang DD, Chen F, Sun HX, Hu FY, Xu P, Li J, Liu W, Qi YH, Li W, Wang M, Zhang S, Xu GZ, Chang Q, Wu JH. Prevalence and genetic-phenotypic characteristics of patients with USH2A mutations in a large cohort of Chinese patients with inherited retinal disease. Br J Ophthalmol 2020; 105:87-92. [PMID: 32188678 PMCID: PMC7788223 DOI: 10.1136/bjophthalmol-2020-315878] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/27/2020] [Accepted: 02/29/2020] [Indexed: 11/10/2022]
Abstract
Aims To investigate the frequency of USH2A mutation and the clinical and genetic differences between Usher syndrome type II (USH2) and retinitis pigmentosa (RP) in a large cohort of Chinese patients. Methods A total of 1381 patients with inherited retinal disease (IRD) were recruited. The phenotypic and genotypic information of patients with USH2A mutations was evaluated. Results The prevalence of patients with USH2A mutations was 15.75%, which was the most frequently detected gene in this cohort of patients. Hotspot of USH2A mutations was c.8559-2A >G and c.2802T >G. Patients with USH2 had an earlier and more serious decline of visual function and damage to retina structure than did patients with RP in the first 10 years (p<0.05), but there was no difference in the visual prognosis between the two groups when the course of disease exceeded 10 years (p>0.05). Missense variants had less severe consequences and were found more commonly in RP, whereas more deleterious genotypes were associated with an earlier onset of disease and were found more commonly in USH2. Conclusions This study provides detailed clinical–genetic assessment of patients with USH2A mutations of Chinese origin, enabling precise genetic diagnoses, better management of these patients and putative therapeutic approaches.
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Affiliation(s)
- Feng-Juan Gao
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shang Hai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shang Hai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shang Hai, China
| | - Dan-Dan Wang
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shang Hai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shang Hai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shang Hai, China
| | - Fang Chen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Shenzhen Engineering Laboratory for Birth Defects Screening, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | | | - Fang-Yuan Hu
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shang Hai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shang Hai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shang Hai, China
| | - Ping Xu
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shang Hai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shang Hai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shang Hai, China
| | - Jiankang Li
- BGI-Shenzhen, Shenzhen, China.,Dept of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Wei Liu
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shang Hai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shang Hai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shang Hai, China
| | - Yu-He Qi
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shang Hai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shang Hai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shang Hai, China
| | - Wei Li
- BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Ming Wang
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shang Hai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shang Hai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shang Hai, China
| | - Shenghai Zhang
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shang Hai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shang Hai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shang Hai, China
| | - Ge-Zhi Xu
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shang Hai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shang Hai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shang Hai, China
| | - Qing Chang
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shang Hai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shang Hai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shang Hai, China
| | - Ji-Hong Wu
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shang Hai, China .,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shang Hai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shang Hai, China
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Sun Y, Li W, Li J, Wang Z, Bai J, Xu L, Xing B, Yang W, Wang Z, Wang L, He W, Chen F. Genetic and clinical findings of panel-based targeted exome sequencing in a northeast Chinese cohort with retinitis pigmentosa. Mol Genet Genomic Med 2020; 8:e1184. [PMID: 32100970 PMCID: PMC7196472 DOI: 10.1002/mgg3.1184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/15/2020] [Accepted: 01/31/2020] [Indexed: 12/18/2022] Open
Abstract
Background Panel‐based targeted exome sequencing was used to analyze the genetic and clinical findings of targeted genes in a cohort of northeast Chinese with retinitis pigmentosa. Methods A total of 87 subjects, comprising 23 probands and their family members (total patients: 32) with confirmed retinitis pigmentosa were recruited in the study. Panel‐based targeted exome sequencing was used to sequence the patients and family members, all subjects with retinitis pigmentosa underwent a complete ophthalmologic examination. Results Of the 23 probands, the clinical manifestations include night blindness, narrowing of vision, secondary cataracts, choroidal atrophy, color blindness, and high myopia, the average age of onset of night blindness is 12.9 ± 14 (range, 0–65; median, 8). Posterior subcapsular opacities is the most common forms of secondary cataracts (nine cases, 39.1%), and peripheral choroidal atrophy is the most common form of secondary choroidal atrophy (12 cases, 52.2%). Of these probands with complication peripheral choroidal atrophy, there were eight probands (66.7%, 8/12) caused by the pathogenic variation in USH2A gene. A total of 17 genes and 45 variants were detected in 23 probands. Among these genes, the commonest genes were USH2A (40%; 18/45), RP1 (15.6%; 7/45), and EYS (8.9%; 4/45), and the top three genes account for 56.5% (13/23) of diagnostic probands. Among these variants, comprising 22 (48.9%) pathogenic variants, 14 (31%) likely pathogenic variants, and nine (20%) uncertain clinical significance variants, and 22 variants was discovered first time. Most of the mutations associated with RP were missense (53.3%, 24/45), and the remaining mutation types include frameshift (35.6%, 16/45), nonsense (6.7%, 3/45), and spliceSite (4.4%, 2/45). Among the probands with mutations detected, compound heterozygous forms was detected in 13 (56.5%, 13/23) probands, and digenic inheritance (DI) forms was detected in five (21.7%, 5/23) probands. Conclusion Panel‐based targeted exome sequencing revealed 23 novel mutations, recognized different combinations forms of variants, and extended the mutational spectrum of retinitis pigmentosa and depicted common variants in northeast China.
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Affiliation(s)
- Yan Sun
- Shenyang He Eye Specialist HospitalShenyangChina
- He UniversityShenyangChina
| | - Wei Li
- He UniversityShenyangChina
- BGI Education CenterUniversity of Chinese Academy of SciencesShenzhenChina
- BGI‐ShenzhenShenzhenChina
| | - Jian‐kang Li
- BGI‐ShenzhenShenzhenChina
- Department of Computer ScienceCity University of Hong KongKowloonHong Kong
- Guangdong Provincial Key Laboratory of Human Disease Genomics Shenzhen Key Laboratory of GenomicsBGI-ShenzhenShenzhenChina
| | - Zhuo‐shi Wang
- Shenyang He Eye Specialist HospitalShenyangChina
- He UniversityShenyangChina
| | - Jin‐yue Bai
- School of Basic MedicineQingdao UniversityQingdaoChina
| | - Ling Xu
- Shenyang He Eye Specialist HospitalShenyangChina
- He UniversityShenyangChina
| | - Bo Xing
- School of Basic MedicineQingdao UniversityQingdaoChina
| | - Wen Yang
- BGI‐ShenzhenShenzhenChina
- Department of Computer ScienceCity University of Hong KongKowloonHong Kong
| | - Zi‐wei Wang
- BGI Education CenterUniversity of Chinese Academy of SciencesShenzhenChina
- BGI‐ShenzhenShenzhenChina
| | - Lu‐sheng Wang
- BGI‐ShenzhenShenzhenChina
- Department of Computer ScienceCity University of Hong KongKowloonHong Kong
| | - Wei He
- Shenyang He Eye Specialist HospitalShenyangChina
- He UniversityShenyangChina
| | - Fang Chen
- BGI‐ShenzhenShenzhenChina
- Guangdong Provincial Key Laboratory of Human Disease Genomics Shenzhen Key Laboratory of GenomicsBGI-ShenzhenShenzhenChina
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González-Del Pozo M, Fernández-Suárez E, Martín-Sánchez M, Bravo-Gil N, Méndez-Vidal C, Rodríguez-de la Rúa E, Borrego S, Antiñolo G. Unmasking Retinitis Pigmentosa complex cases by a whole genome sequencing algorithm based on open-access tools: hidden recessive inheritance and potential oligogenic variants. J Transl Med 2020; 18:73. [PMID: 32050993 PMCID: PMC7014749 DOI: 10.1186/s12967-020-02258-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 02/05/2020] [Indexed: 12/13/2022] Open
Abstract
Background Retinitis Pigmentosa (RP) is a clinically and genetically heterogeneous disorder that results in inherited blindness. Despite the large number of genes identified, only ~ 60% of cases receive a genetic diagnosis using targeted-sequencing. The aim of this study was to design a whole genome sequencing (WGS) based approach to increase the diagnostic yield of complex Retinitis Pigmentosa cases. Methods WGS was conducted in three family members, belonging to one large apparent autosomal dominant RP family that remained unsolved by previous studies, using Illumina TruSeq library preparation kit and Illumina HiSeq X platform. Variant annotation, filtering and prioritization were performed using a number of open-access tools and public databases. Sanger sequencing of candidate variants was conducted in the extended family members. Results We have developed and optimized an algorithm, based on the combination of different open-access tools, for variant prioritization of WGS data which allowed us to reduce significantly the number of likely causative variants pending to be manually assessed and segregated. Following this algorithm, four heterozygous variants in one autosomal recessive gene (USH2A) were identified, segregating in pairs in the affected members. Additionally, two pathogenic alleles in ADGRV1 and PDZD7 could be contributing to the phenotype in one patient. Conclusions The optimization of a diagnostic algorithm for WGS data analysis, accompanied by a hypothesis-free approach, have allowed us to unmask the genetic cause of the disease in one large RP family, as well as to reassign its inheritance pattern which implies differences in the clinical management of these cases. These results contribute to increasing the number of cases with apparently dominant inheritance that carry causal mutations in recessive genes, as well as the possible involvement of various genes in the pathogenesis of RP in one patient. Moreover, our WGS-analysis approach, based on open-access tools, can easily be implemented by other researchers and clinicians to improve the diagnostic yield of additional patients with inherited retinal dystrophies.
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Affiliation(s)
- María González-Del Pozo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Avenida Manuel Siurot s/n, 41013, Seville, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
| | - Elena Fernández-Suárez
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Avenida Manuel Siurot s/n, 41013, Seville, Spain
| | - Marta Martín-Sánchez
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Avenida Manuel Siurot s/n, 41013, Seville, Spain
| | - Nereida Bravo-Gil
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Avenida Manuel Siurot s/n, 41013, Seville, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
| | - Cristina Méndez-Vidal
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Avenida Manuel Siurot s/n, 41013, Seville, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
| | - Enrique Rodríguez-de la Rúa
- Department of Ophthalmology, University Hospital Virgen Macarena, Seville, Spain.,ReticsPatologia Ocular, OFTARED, Instituto de Salud Carlos III, Madrid, Spain
| | - Salud Borrego
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Avenida Manuel Siurot s/n, 41013, Seville, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
| | - Guillermo Antiñolo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Avenida Manuel Siurot s/n, 41013, Seville, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain.
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Chen ZJ, Lin KH, Lee SH, Shen RJ, Feng ZK, Wang XF, Huang XF, Huang ZQ, Jin ZB. Mutation spectrum and genotype-phenotype correlation of inherited retinal dystrophy in Taiwan. Clin Exp Ophthalmol 2020; 48:486-499. [PMID: 31872526 DOI: 10.1111/ceo.13708] [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] [Received: 07/11/2019] [Revised: 12/15/2019] [Accepted: 12/15/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND Inherited retinal dystrophy (IRD) is a group of irreversible retinal degenerative disorders with significant genotypic and phenotypic heterogeneity, which cause difficulty in making a precise clinical diagnosis. Furthermore, the mutation spectrum of IRD in Taiwan remains unknown. Therefore, our study focused on investigating the spectrum of mutations among Taiwanese families with IRD using targeted exome sequencing (TES) technology. METHODS We recruited a total of 60 unrelated Taiwanese families with IRD; most of them were retinitis pigmentosa. We employed TES to investigate 284 candidate genes. Bioinformatics analysis, Sanger sequencing-based co-segregation testing, and computational assessment were performed to validate each mutation and its pathogenicity. The genotype-phenotype correlation was analysed in all patients with mutations defined in the guidelines provided by the American College of Medical Genetics. RESULTS We successfully identified genetic causes in 32 families (detection rate of 53.3%). Among them, 16 had a sporadic inheritance (16/36, 44.4%); eight had an autosomal recessive inheritance (8/14, 57.1%); four had an autosomal dominant inheritance (4/5, 80%); four had an X-linked inheritance (4/5, 80%). Among 38 pathological mutations in 19 known genes, 20 mutations are reported here for the first time. Novel mutation spectrum and genotype-phenotype correlations were revealed as well. CONCLUSION Here we achieved a detection rate of 53.3% and elucidated the mutation spectrum in Taiwanese families with IRD for the first time. The results indicated that CYP4V2 and USH2A might be the most common pathogenic genes in IRD patients in Taiwan.
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Affiliation(s)
- Zhen-Ji Chen
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Wenzhou Medical University, Wenzhou, China.,National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ocular Diseases, Wenzhou Medical University, Wenzhou, China
| | - Keng-Hung Lin
- Department of Ophthalmology, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Shi-Huang Lee
- Department of Ophthalmology, Taichung Tzu Chi Hospital, Taichung, Taiwan
| | - Ren-Juan Shen
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Wenzhou Medical University, Wenzhou, China.,National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ocular Diseases, Wenzhou Medical University, Wenzhou, China
| | - Zhuo-Kun Feng
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Wenzhou Medical University, Wenzhou, China.,National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ocular Diseases, Wenzhou Medical University, Wenzhou, China
| | - Xiao-Fang Wang
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Wenzhou Medical University, Wenzhou, China.,National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ocular Diseases, Wenzhou Medical University, Wenzhou, China
| | - Xiu-Feng Huang
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Wenzhou Medical University, Wenzhou, China.,National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ocular Diseases, Wenzhou Medical University, Wenzhou, China
| | - Zhi-Qin Huang
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Wenzhou Medical University, Wenzhou, China.,National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ocular Diseases, Wenzhou Medical University, Wenzhou, China
| | - Zi-Bing Jin
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Wenzhou Medical University, Wenzhou, China.,National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ocular Diseases, Wenzhou Medical University, Wenzhou, China
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Whelan L, Dockery A, Wynne N, Zhu J, Stephenson K, Silvestri G, Turner J, O’Byrne JJ, Carrigan M, Humphries P, Keegan D, Kenna PF, Farrar GJ. Findings from a Genotyping Study of Over 1000 People with Inherited Retinal Disorders in Ireland. Genes (Basel) 2020; 11:E105. [PMID: 31963381 PMCID: PMC7016747 DOI: 10.3390/genes11010105] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/13/2019] [Accepted: 01/13/2020] [Indexed: 12/15/2022] Open
Abstract
The Irish national registry for inherited retinal degenerations (Target 5000) is a clinical and scientific program to identify individuals in Ireland with inherited retinal disorders and to attempt to ascertain the genetic cause underlying the disease pathology. Potential participants first undergo a clinical assessment, which includes clinical history and analysis with multimodal retinal imaging, electrophysiology, and visual field testing. If suitable for recruitment, a sample is taken and used for genetic analysis. Genetic analysis is conducted by use of a retinal gene panel target capture sequencing approach. With over 1000 participants from 710 pedigrees now screened, there is a positive candidate variant detection rate of approximately 70% (495/710). Where an autosomal recessive inheritance pattern is observed, an additional 9% (64/710) of probands have tested positive for a single candidate variant. Many novel variants have also been detected as part of this endeavor. The target capture approach is an economic and effective means of screening patients with inherited retinal disorders. Despite the advances in sequencing technology and the ever-decreasing associated processing costs, target capture remains an attractive option as the data produced is easily processed, analyzed, and stored compared to more comprehensive methods. However, with decreasing costs of whole genome and whole exome sequencing, the focus will likely move towards these methods for more comprehensive data generation.
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Affiliation(s)
- Laura Whelan
- The School of Genetics & Microbiology, Trinity College Dublin, D02 VF25 Dublin, Ireland; (A.D.); (M.C.); (P.H.); (P.F.K.); (G.J.F.)
| | - Adrian Dockery
- The School of Genetics & Microbiology, Trinity College Dublin, D02 VF25 Dublin, Ireland; (A.D.); (M.C.); (P.H.); (P.F.K.); (G.J.F.)
| | - Niamh Wynne
- The Research Foundation, Royal Victoria Eye and Ear Hospital, D02 XK51 Dublin, Ireland;
| | - Julia Zhu
- Clinical Genetics Centre for Ophthalmology, The Mater Misericordiae University Hospital, D07 R2WY Dublin, Ireland; (J.Z.); (K.S.); (J.T.); (J.J.O.); (D.K.)
| | - Kirk Stephenson
- Clinical Genetics Centre for Ophthalmology, The Mater Misericordiae University Hospital, D07 R2WY Dublin, Ireland; (J.Z.); (K.S.); (J.T.); (J.J.O.); (D.K.)
| | - Giuliana Silvestri
- Department of Ophthalmology, The Royal Victoria Hospital, Belfast BT12 6BA, Northern Ireland, UK;
- Centre for Experimental Medicine, Queen’s University Belfast, Belfast BT7 1NN, Northern Ireland, UK
| | - Jacqueline Turner
- Clinical Genetics Centre for Ophthalmology, The Mater Misericordiae University Hospital, D07 R2WY Dublin, Ireland; (J.Z.); (K.S.); (J.T.); (J.J.O.); (D.K.)
| | - James J. O’Byrne
- Clinical Genetics Centre for Ophthalmology, The Mater Misericordiae University Hospital, D07 R2WY Dublin, Ireland; (J.Z.); (K.S.); (J.T.); (J.J.O.); (D.K.)
| | - Matthew Carrigan
- The School of Genetics & Microbiology, Trinity College Dublin, D02 VF25 Dublin, Ireland; (A.D.); (M.C.); (P.H.); (P.F.K.); (G.J.F.)
| | - Peter Humphries
- The School of Genetics & Microbiology, Trinity College Dublin, D02 VF25 Dublin, Ireland; (A.D.); (M.C.); (P.H.); (P.F.K.); (G.J.F.)
| | - David Keegan
- Clinical Genetics Centre for Ophthalmology, The Mater Misericordiae University Hospital, D07 R2WY Dublin, Ireland; (J.Z.); (K.S.); (J.T.); (J.J.O.); (D.K.)
| | - Paul F. Kenna
- The School of Genetics & Microbiology, Trinity College Dublin, D02 VF25 Dublin, Ireland; (A.D.); (M.C.); (P.H.); (P.F.K.); (G.J.F.)
- The Research Foundation, Royal Victoria Eye and Ear Hospital, D02 XK51 Dublin, Ireland;
| | - G. Jane Farrar
- The School of Genetics & Microbiology, Trinity College Dublin, D02 VF25 Dublin, Ireland; (A.D.); (M.C.); (P.H.); (P.F.K.); (G.J.F.)
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Méjécase C, Malka S, Guan Z, Slater A, Arno G, Moosajee M. Practical guide to genetic screening for inherited eye diseases. Ther Adv Ophthalmol 2020; 12:2515841420954592. [PMID: 33015543 PMCID: PMC7513416 DOI: 10.1177/2515841420954592] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/29/2020] [Indexed: 12/16/2022] Open
Abstract
Genetic eye diseases affect around one in 1000 people worldwide for which the molecular aetiology remains unknown in the majority. The identification of disease-causing gene variant(s) allows a better understanding of the disorder and its inheritance. There is now an approved retinal gene therapy for autosomal recessive RPE65-retinopathy, and numerous ocular gene/mutation-targeted clinical trials underway, highlighting the importance of establishing a genetic diagnosis so patients can fully access the latest research developments and treatment options. In this review, we will provide a practical guide to managing patients with these conditions including an overview of inheritance patterns, required pre- and post-test genetic counselling, different types of cytogenetic and genetic testing available, with a focus on next generation sequencing using targeted gene panels, whole exome and genome sequencing. We will expand on the pros and cons of each modality, variant interpretation and options for family planning for the patient and their family. With the advent of genomic medicine, genetic screening will soon become mainstream within all ophthalmology subspecialties for prevention of disease and provision of precision therapeutics.
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Affiliation(s)
- Cécile Méjécase
- Institute of Ophthalmology, University College
London, London, UK
| | - Samantha Malka
- Institute of Ophthalmology, University College
London, London, UK
- Moorfields Eye Hospital NHS Foundation Trust,
London, UK
| | - Zeyu Guan
- Moorfields Eye Hospital NHS Foundation Trust,
London, UK
| | - Amy Slater
- Royal Brompton and Harefield NHS Foundation
Trust, London, UK
| | - Gavin Arno
- Institute of Ophthalmology, University College
London, London, UK
- Moorfields Eye Hospital NHS Foundation Trust,
London, UK
- Great Ormond Street Hospital for Children NHS
Trust, London, UK
| | - Mariya Moosajee
- Professor, Institute of Ophthalmology,
University College London, 11-43 Bath Street, London EC1V 9EL, UK
- Moorfields Eye Hospital NHS Foundation Trust,
London, UK
- Great Ormond Street Hospital for Children NHS
Trust, London, UK
- The Francis Crick Institute, London, UK
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Ataluren for the Treatment of Usher Syndrome 2A Caused by Nonsense Mutations. Int J Mol Sci 2019; 20:ijms20246274. [PMID: 31842393 PMCID: PMC6940777 DOI: 10.3390/ijms20246274] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/05/2019] [Accepted: 12/10/2019] [Indexed: 12/18/2022] Open
Abstract
The identification of genetic defects that underlie inherited retinal diseases (IRDs) paves the way for the development of therapeutic strategies. Nonsense mutations caused approximately 12% of all IRD cases, resulting in a premature termination codon (PTC). Therefore, an approach that targets nonsense mutations could be a promising pharmacogenetic strategy for the treatment of IRDs. Small molecules (translational read-through inducing drugs; TRIDs) have the potential to mediate the read-through of nonsense mutations by inducing expression of the full-length protein. We provide novel data on the read-through efficacy of Ataluren on a nonsense mutation in the Usher syndrome gene USH2A that causes deaf-blindness in humans. We demonstrate Ataluren´s efficacy in both transiently USH2AG3142*-transfected HEK293T cells and patient-derived fibroblasts by restoring USH2A protein expression. Furthermore, we observed enhanced ciliogenesis in patient-derived fibroblasts after treatment with TRIDs, thereby restoring a phenotype that is similar to that found in healthy donors. In light of recent findings, we validated Ataluren´s efficacy to induce read-through on a nonsense mutation in USH2A-related IRD. In line with published data, our findings support the use of patient-derived fibroblasts as a platform for the validation of preclinical therapies. The excellent biocompatibility combined with sustained read-through efficacy makes Ataluren an ideal TRID for treating nonsense mutations based IRDs.
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Sanjurjo-Soriano C, Erkilic N, Baux D, Mamaeva D, Hamel CP, Meunier I, Roux AF, Kalatzis V. Genome Editing in Patient iPSCs Corrects the Most Prevalent USH2A Mutations and Reveals Intriguing Mutant mRNA Expression Profiles. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2019; 17:156-173. [PMID: 31909088 PMCID: PMC6938853 DOI: 10.1016/j.omtm.2019.11.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 11/15/2019] [Indexed: 12/13/2022]
Abstract
Inherited retinal dystrophies (IRDs) are characterized by progressive photoreceptor degeneration and vision loss. Usher syndrome (USH) is a syndromic IRD characterized by retinitis pigmentosa (RP) and hearing loss. USH is clinically and genetically heterogeneous, and the most prevalent causative gene is USH2A. USH2A mutations also account for a large number of isolated autosomal recessive RP (arRP) cases. This high prevalence is due to two recurrent USH2A mutations, c.2276G>T and c.2299delG. Due to the large size of the USH2A cDNA, gene augmentation therapy is inaccessible. However, CRISPR/Cas9-mediated genome editing is a viable alternative. We used enhanced specificity Cas9 of Streptococcus pyogenes (eSpCas9) to successfully achieve seamless correction of the two most prevalent USH2A mutations in induced pluripotent stem cells (iPSCs) of patients with USH or arRP. Our results highlight features that promote high target efficacy and specificity of eSpCas9. Consistently, we did not identify any off-target mutagenesis in the corrected iPSCs, which also retained pluripotency and genetic stability. Furthermore, analysis of USH2A expression unexpectedly identified aberrant mRNA levels associated with the c.2276G>T and c.2299delG mutations that were reverted following correction. Taken together, our efficient CRISPR/Cas9-mediated strategy for USH2A mutation correction brings hope for a potential treatment for USH and arRP patients.
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Affiliation(s)
- Carla Sanjurjo-Soriano
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier, France.,University of Montpellier, 34095 Montpellier, France
| | - Nejla Erkilic
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier, France.,University of Montpellier, 34095 Montpellier, France
| | - David Baux
- University of Montpellier, 34095 Montpellier, France.,Medical Genetics Laboratory, CHU, 34093 Montpellier, France
| | - Daria Mamaeva
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier, France.,University of Montpellier, 34095 Montpellier, France
| | - Christian P Hamel
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier, France.,University of Montpellier, 34095 Montpellier, France.,National Reference Centre for Inherited Sensory Disorders, CHU, 34295 Montpellier, France
| | - Isabelle Meunier
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier, France.,University of Montpellier, 34095 Montpellier, France.,National Reference Centre for Inherited Sensory Disorders, CHU, 34295 Montpellier, France
| | - Anne-Françoise Roux
- University of Montpellier, 34095 Montpellier, France.,Medical Genetics Laboratory, CHU, 34093 Montpellier, France
| | - Vasiliki Kalatzis
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier, France.,University of Montpellier, 34095 Montpellier, France
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Fakin A, Šuštar M, Brecelj J, Bonnet C, Petit C, Zupan A, Glavač D, Jarc-Vidmar M, Battelino S, Hawlina M. Double Hyperautofluorescent Rings in Patients with USH2A-Retinopathy. Genes (Basel) 2019; 10:genes10120956. [PMID: 31766479 PMCID: PMC6947471 DOI: 10.3390/genes10120956] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/17/2019] [Accepted: 11/18/2019] [Indexed: 11/16/2022] Open
Abstract
USH2A mutation is the most common cause of retinitis pigmentosa, with or without hearing impairment. Patients most commonly exhibit hyperautofluorescent ring on fundus autofluorescence imaging (FAF) and rod-cone dystrophy on electrophysiology. A detailed study of three USH2A patients with a rare pattern of double hyperautofluorescent rings was performed. Twenty-four patients with typical single hyperautofluorescent rings were used for comparison of the ages of onset, visual fields, optical coherence tomography, electrophysiology, and audiograms. Double rings delineated the area of pericentral retinal degeneration in all cases. Two patients exhibited rod-cone dystrophy, whereas the third had a cone-rod dystrophy type of dysfunction on electrophysiology. There was minimal progression on follow-up in all three. Patients with double rings had significantly better visual acuity, cone function, and auditory performance than the single ring group. Double rings were associated with combinations of null and missense mutations, none of the latter found in the single ring patients. According to these findings, the double hyperautofluorescent rings indicate a mild subtype of USH2A disease, characterized by pericentral retinal degeneration, mild to moderate hearing loss, and either a rod-cone or cone-rod pattern on electrophysiology, the latter expanding the known clinical spectrum of USH2A-retinopathy.
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Affiliation(s)
- Ana Fakin
- Eye Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (M.Š.); (J.B.); (M.J.-V.); (M.H.)
- Correspondence: ; Tel.: +386-1522-1900
| | - Maja Šuštar
- Eye Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (M.Š.); (J.B.); (M.J.-V.); (M.H.)
| | - Jelka Brecelj
- Eye Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (M.Š.); (J.B.); (M.J.-V.); (M.H.)
| | - Crystel Bonnet
- Unité de Génétique et Physiologie de l’Audition, Institut Pasteur, 75015 Paris, France; (C.B.); (C.P.)
- Unité Mixte de Recherche en Santé (UMRS) 1120, Institut National de la Santé et de la Recherche Médicale (INSERM), 75015 Paris, France
- Complexité du Vivant, Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, 75005 Paris, France
- Institut de l’Audition, 75012 Paris, France
- Syndrome de Usher et Autres Atteintes Rétino-Cochléaires, Institut de la Vision, 75012 Paris, France
| | - Christine Petit
- Unité de Génétique et Physiologie de l’Audition, Institut Pasteur, 75015 Paris, France; (C.B.); (C.P.)
- Unité Mixte de Recherche en Santé (UMRS) 1120, Institut National de la Santé et de la Recherche Médicale (INSERM), 75015 Paris, France
- Complexité du Vivant, Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, 75005 Paris, France
- Institut de l’Audition, 75012 Paris, France
- Syndrome de Usher et Autres Atteintes Rétino-Cochléaires, Institut de la Vision, 75012 Paris, France
- Collège de France, 75005 Paris, France
| | - Andrej Zupan
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (D.G.)
| | - Damjan Glavač
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (D.G.)
| | - Martina Jarc-Vidmar
- Eye Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (M.Š.); (J.B.); (M.J.-V.); (M.H.)
| | - Saba Battelino
- Department of Otorhinolaryngology and Cervicofacial Surgery, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia;
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Marko Hawlina
- Eye Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (M.Š.); (J.B.); (M.J.-V.); (M.H.)
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Lee SY, Joo K, Oh J, Han JH, Park HR, Lee S, Oh DY, Woo SJ, Choi BY. Severe or Profound Sensorineural Hearing Loss Caused by Novel USH2A Variants in Korea: Potential Genotype-Phenotype Correlation. Clin Exp Otorhinolaryngol 2019; 13:113-122. [PMID: 31674169 PMCID: PMC7248602 DOI: 10.21053/ceo.2019.00990] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/16/2019] [Indexed: 11/22/2022] Open
Abstract
Objectives We, herein, report two novel USH2A variants from two unrelated Korean families and their clinical phenotypes, with attention to severe or more than severe sensorineural hearing loss (SNHL). Methods Two postlingually deafened subjects (SB237-461, M/46 and SB354-692, F/34) with more than severe SNHL and also with suspicion of Usher syndrome type II (USH2) were enrolled. A comprehensive audiological and ophthalmological assessments were evaluated. We conducted the whole exome sequencing and subsequent pathogenicity prediction analysis. Results We identified the following variants of USH2A from the two probands manifesting more than severe SNHL and retinitis pigmentosa (RP): compound heterozygosity for a nonsense (c.8176C>T: p.R2723X) and a missense variant (c.1823G>A: p.C608Y) in SB237, and compound heterozygosity for two frameshift variants (c.14835delT: p.S4945fs & c.13112_13115delAAAT: p.G4371fs) in SB354. Based on the American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines, two novel variants, c.1823G>A: p.C608Y and c.14835delT: p.Ser4945fs, can be classified as “uncertain significance” and “pathogenic,” respectively. The audiogram exhibited more than severe SNHL and a down-sloping configuration, necessitating cochlear implantation. The ophthalmic examinations revealed typical features of RP. Interestingly, one proband (SB 354-692) carrying two truncating compound heterozygous variants exhibited more severe hearing loss than the other proband (SB 237-461), carrying one truncation with one missense variant. Conclusion Our results provide insight on the expansion of audiological spectrum encompassing more than severe SNHL in Korean subjects harboring USH2A variants, suggesting that USH2A should also be included in the candidate gene of cochlear implantation. A specific combination of USH2A variants causing truncating proteins in both alleles could demonstrate more severe audiological phenotype than that of USH2A variants carrying one truncating mutation and one missense mutation, suggesting a possible genotype-phenotype correlation. The understanding of audiological complexity associated with USH2A will be helpful for genetic counseling and treatment starategy.
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Affiliation(s)
- Sang-Yeon Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Kwangsic Joo
- Department of Ophthalmology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Jayoung Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Jin Hee Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Hye-Rim Park
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Seungmin Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Doo-Yi Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Se Joon Woo
- Department of Ophthalmology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
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Kim MS, Joo K, Seong MW, Kim MJ, Park KH, Park SS, Woo SJ. Genetic Mutation Profiles in Korean Patients with Inherited Retinal Diseases. J Korean Med Sci 2019; 34:e161. [PMID: 31144483 PMCID: PMC6543061 DOI: 10.3346/jkms.2019.34.e161] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/13/2019] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Because of genetically and phenotypically heterogenous features, identification of causative genes for inherited retinal diseases (IRD) is essential for diagnosis and treatment in coming gene therapy era. To date, there are no large-scale data of the genes responsible for IRD in Korea. The aim of this study was to identify the distribution of genetic defects in IRD patients in Korea. METHODS Medical records and DNA samples from 86 clinically diagnosed IRD patients were consecutively collected between July 2011 and May 2015. We applied the next-generation sequencing strategy (gene panel) for screening 204 known pathogenic genes associated with IRD. RESULTS Molecular diagnoses were made in 38/86 (44.2%) IRD patients: 18/44 (40.9%) retinitis pigmentosa (RP), 8/22 (36.4%) cone dystrophy, 6/7 (85.7%) Stargardt disease, 1/1 (100%) Best disease, 1/1 (100%) Bardet-Biedl syndrome, 1/1 (100%) congenital stationary night blindness, 1/1 (100%) choroideremia, and 2/8 (25%) other macular dystrophies. ABCA4 was the most common causative gene associated with IRD and was responsible for causing Stargardt disease (n = 6), RP (n = 1), and cone dystrophy (n = 1). In particular, mutations in EYS were found in 4 of 14 autosomal recessive RP (29%). All cases of Stargardt disease had a mutation in the ABCA4 gene with an autosomal recessive trait. CONCLUSION This study provided the distribution of genetic mutations responsible for causing IRD in the Korean patients. This data will serve as a reference for future genetic screening and treatment for Korean IRD patients.
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Affiliation(s)
- Min Seok Kim
- Department of Ophthalmology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Kwangsic Joo
- Department of Ophthalmology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Moon Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Kyu Hyung Park
- Department of Ophthalmology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.
| | - Se Joon Woo
- Department of Ophthalmology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea.
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Pater JA, Green J, O'Rielly DD, Griffin A, Squires J, Burt T, Fernandez S, Fernandez B, Houston J, Zhou J, Roslin NM, Young TL. Novel Usher syndrome pathogenic variants identified in cases with hearing and vision loss. BMC MEDICAL GENETICS 2019; 20:68. [PMID: 31046701 PMCID: PMC6498547 DOI: 10.1186/s12881-019-0777-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 03/01/2019] [Indexed: 12/14/2022]
Abstract
Background Usher syndrome, the most common form of inherited deaf-blindness, is unlike many other forms of syndromic hereditary hearing loss in that the extra aural clinical manifestations are also detrimental to communication. Usher syndrome patients with early onset deafness also experience vision loss due to progressive retinitis pigmentosa that can lead to legal blindness in their third or fourth decade. Methods Using a multi-omic approach, we identified three novel pathogenic variants in two Usher syndrome genes (USH2A and ADGRV1) in cases initially referred for isolated vision or hearing loss. Results In a multiplex hearing loss family, two affected sisters, the product of a second cousin union, are homozygous for a novel nonsense pathogenic variant in ADGRV1 (c.17062C > T, p.Arg5688*), predicted to create a premature stop codon near the N-terminus of ADGRV1. Ophthalmological examination of the sisters confirmed typical retinitis pigmentosa and prompted a corrected Usher syndrome diagnosis. In an unrelated clinical case, a child with hearing loss tested positive for two novel USH2A splicing variants (c.5777-1G > A, p. Glu1926_Ala1952del and c.10388-2A > G, p.Asp3463Alafs*6) and RNA studies confirmed that both pathogenic variants cause splicing errors. Interestingly, these same USH2A variants are also identified in another family with vision loss where subsequent clinical follow-up confirmed pre-existing hearing loss since early childhood, eventually resulting in a reassigned diagnosis of Usher syndrome. Conclusion These findings provide empirical evidence to increase Usher syndrome surveillance of at-risk children. Given that novel antisense oligonucleotide therapies have been shown to rescue retinal degeneration caused by USH2A splicing pathogenic variants, these solved USH2A patients may now be eligible to be enrolled in therapeutic trials.
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Affiliation(s)
- Justin A Pater
- Craig L. Dobbin Research Centre, Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland & Labrador, AIB 3V6, Canada
| | - Jane Green
- Craig L. Dobbin Research Centre, Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland & Labrador, AIB 3V6, Canada
| | - Darren D O'Rielly
- Molecular Diagnostic Laboratory, Eastern Health, Craig L. Dobbin Genetics Research Centre, Faculty of Medicine, Memorial University, 300 Prince Phillip Drive, St. John's, Newfoundland and Labrador, A1B 3V6, Canada
| | - Anne Griffin
- Craig L. Dobbin Research Centre, Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland & Labrador, AIB 3V6, Canada
| | - Jessica Squires
- Craig L. Dobbin Research Centre, Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland & Labrador, AIB 3V6, Canada
| | - Taylor Burt
- Craig L. Dobbin Research Centre, Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland & Labrador, AIB 3V6, Canada
| | - Sara Fernandez
- Provincial Medical Genetics, Craig L. Dobbin Research Centre, Eastern Health, 300 Prince Phillip Drive, St. John's, Newfoundland and Labrador, A1B 3V6, Canada
| | - Bridget Fernandez
- Craig L. Dobbin Research Centre, Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland & Labrador, AIB 3V6, Canada.,Provincial Medical Genetics, Craig L. Dobbin Research Centre, Eastern Health, 300 Prince Phillip Drive, St. John's, Newfoundland and Labrador, A1B 3V6, Canada
| | - Jim Houston
- Craig L. Dobbin Research Centre, Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland & Labrador, AIB 3V6, Canada
| | - Jiayi Zhou
- Craig L. Dobbin Research Centre, Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland & Labrador, AIB 3V6, Canada
| | - Nicole M Roslin
- The Centre for Applied Genomics, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario, M5G 0A4, Canada
| | - Terry-Lynn Young
- Craig L. Dobbin Research Centre, Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland & Labrador, AIB 3V6, Canada. .,Molecular Diagnostic Laboratory, Eastern Health, Craig L. Dobbin Genetics Research Centre, Faculty of Medicine, Memorial University, 300 Prince Phillip Drive, St. John's, Newfoundland and Labrador, A1B 3V6, Canada.
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Ng TK, Tang W, Cao Y, Chen S, Zheng Y, Xiao X, Chen H. Whole exome sequencing identifies novel USH2A mutations and confirms Usher syndrome 2 diagnosis in Chinese retinitis pigmentosa patients. Sci Rep 2019; 9:5628. [PMID: 30948794 PMCID: PMC6449333 DOI: 10.1038/s41598-019-42105-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 03/11/2019] [Indexed: 02/05/2023] Open
Abstract
Retinitis pigmentosa (RP) is a common phenotype in multiple inherited retinal dystrophies (IRD). Disease gene identification can assist the clinical diagnosis of IRD patients for better clinical management, treatment and counseling. In this study, we aimed to delineate and characterize the disease-causing mutations in Chinese familial and sporadic patients with initial diagnosis of RP. Four unrelated Chinese families and 118 sporadic RP patients were recruited for whole exome sequencing analysis. A total of 5 reported and 3 novel USH2A mutations were identified in four Chinese probands. The probands and their family members showed typical RP features and mild to severe hearing impairment, confirming the diagnosis of Usher syndrome 2 (USH). Moreover, 11 sporadic RP patients were identified to carry the compound heterozygous mutations in the USH2A gene, confirming the diagnosis of USH2. The patients carried the truncating mutations had a younger age of first visit than the patients carried only the missense mutations (p = 0.017). In summary, this study revealed 8 novel USH2A variants in Chinese familial and sporadic RP patients, assuring that whole exome sequencing analysis is an adequate strategy to facilitate the clinical diagnosis of USH from the sporadic RP patients.
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Affiliation(s)
- Tsz Kin Ng
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, Guangdong, China
- Shantou University Medical College, Shantou, Guangdong, China
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Kowloon, Hong Kong
| | - Wenyu Tang
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Yingjie Cao
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Shaowan Chen
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Yuqian Zheng
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Xiaoqiang Xiao
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Haoyu Chen
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, Guangdong, China.
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Sanjurjo-Soriano C, Erkilic N, Manes G, Dubois G, Hamel CP, Meunier I, Kalatzis V. Generation of a human iPSC line, INMi002-A, carrying the most prevalent USH2A variant associated with Usher syndrome type 2. Stem Cell Res 2018; 33:247-250. [PMID: 30468996 DOI: 10.1016/j.scr.2018.11.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 10/27/2022] Open
Abstract
We generated an induced pluripotent stem cell (iPSC) line using dermal fibroblasts from a patient with Usher syndrome type 2 (USH2). This individual was homozygous for the most prevalent variant reported in the USH2A gene, c.2299delG localized in exon 13. Reprogramming was performed using the non-integrative Sendai virus reprogramming method and the human OSKM transcription factor cocktail under feeder-free culture conditions. This iPSC line will be an invaluable tool for studying the pathophysiology of USH2 and for testing the efficacy of novel treatments.
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Affiliation(s)
- Carla Sanjurjo-Soriano
- Inserm U1051, Institute for Neurosciences of Montpellier, Montpellier, France; University of Montpellier, Montpellier, France
| | - Nejla Erkilic
- Inserm U1051, Institute for Neurosciences of Montpellier, Montpellier, France; University of Montpellier, Montpellier, France
| | - Gaël Manes
- Inserm U1051, Institute for Neurosciences of Montpellier, Montpellier, France; University of Montpellier, Montpellier, France
| | - Gregor Dubois
- Inserm U1051, Institute for Neurosciences of Montpellier, Montpellier, France; University of Montpellier, Montpellier, France
| | - Christian P Hamel
- Inserm U1051, Institute for Neurosciences of Montpellier, Montpellier, France; University of Montpellier, Montpellier, France; Centre of Reference for Genetic Sensory Diseases, CHU, Montpellier, France
| | - Isabelle Meunier
- Inserm U1051, Institute for Neurosciences of Montpellier, Montpellier, France; University of Montpellier, Montpellier, France; Centre of Reference for Genetic Sensory Diseases, CHU, Montpellier, France
| | - Vasiliki Kalatzis
- Inserm U1051, Institute for Neurosciences of Montpellier, Montpellier, France; University of Montpellier, Montpellier, France.
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65
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Sanjurjo-Soriano C, Erkilic N, Manes G, Dubois G, Hamel CP, Meunier I, Kalatzis V. Generation of an iPSC line, INMi001-A, carrying the two most common USH2A mutations from a compound heterozygote with non-syndromic retinitis pigmentosa. Stem Cell Res 2018; 33:228-232. [PMID: 30453153 DOI: 10.1016/j.scr.2018.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/06/2018] [Accepted: 11/09/2018] [Indexed: 10/27/2022] Open
Abstract
We generated an induced pluripotent stem cell (iPSC) line from a patient with non-syndromic retinitis pigmentosa who is a compound heterozygote for the two most frequent USH2A variants, c.2276G > T and c.2299delG localized in exon 13. Patient fibroblasts were reprogrammed using the non-integrative Sendai virus reprogramming method and the human OSKM transcription factor cocktail. The generated cells were pluripotent and genetically stable. This iPSC line will be an important tool for studying the pathogenesis of these USH2A mutations and for developing treatments that, due their high prevalence, will target a large patient population.
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Affiliation(s)
- Carla Sanjurjo-Soriano
- Inserm U1051, Institute for Neurosciences of Montpellier, Montpellier, France; University of Montpellier, Montpellier, France
| | - Nejla Erkilic
- Inserm U1051, Institute for Neurosciences of Montpellier, Montpellier, France; University of Montpellier, Montpellier, France
| | - Gaël Manes
- Inserm U1051, Institute for Neurosciences of Montpellier, Montpellier, France; University of Montpellier, Montpellier, France
| | - Gregor Dubois
- Inserm U1051, Institute for Neurosciences of Montpellier, Montpellier, France; University of Montpellier, Montpellier, France
| | - Christian P Hamel
- Inserm U1051, Institute for Neurosciences of Montpellier, Montpellier, France; University of Montpellier, Montpellier, France; Centre of Reference for Genetic Sensory Diseases, CHU, Montpellier, France
| | - Isabelle Meunier
- Inserm U1051, Institute for Neurosciences of Montpellier, Montpellier, France; University of Montpellier, Montpellier, France; Centre of Reference for Genetic Sensory Diseases, CHU, Montpellier, France
| | - Vasiliki Kalatzis
- Inserm U1051, Institute for Neurosciences of Montpellier, Montpellier, France; University of Montpellier, Montpellier, France.
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Analysis of intragenic USH2A copy number variation unveils broad spectrum of unique and recurrent variants. Eur J Med Genet 2018; 61:621-626. [DOI: 10.1016/j.ejmg.2018.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 04/09/2018] [Accepted: 04/11/2018] [Indexed: 11/21/2022]
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Pérez-Carro R, Blanco-Kelly F, Galbis-Martínez L, García-García G, Aller E, García-Sandoval B, Mínguez P, Corton M, Mahíllo-Fernández I, Martín-Mérida I, Avila-Fernández A, Millán JM, Ayuso C. Unravelling the pathogenic role and genotype-phenotype correlation of the USH2A p.(Cys759Phe) variant among Spanish families. PLoS One 2018; 13:e0199048. [PMID: 29912909 PMCID: PMC6005481 DOI: 10.1371/journal.pone.0199048] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/30/2018] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Mutations in USH2A cause both isolated Retinitis Pigmentosa (RP) and Usher syndrome (that implies RP and hearing impairment). One of the most frequent variants identified in this gene and among these patients is the p.(Cys759Phe) change. However, the pathogenic role of this allele has been questioned since it was found in homozygosity in two healthy siblings of a Spanish family. To assess the causative role of USH2A p.(Cys759Phe) in autosomal recessive RP (ARRP) and Usher syndrome type II (USH2) and to establish possible genotype-phenotype correlations associated with p.(Cys759Phe), we performed a comprehensive genetic and clinical study in patients suffering from any of the two above-mentioned diseases and carrying at least one p.(Cys759Phe) allele. MATERIALS AND METHODS Diagnosis was set according to previously reported protocols. Genetic analyses were performed by using classical molecular and Next-Generation Sequencing approaches. Probands of 57 unrelated families were molecularly studied and 63 patients belonging to these families were phenotypically evaluated. RESULTS Molecular analysis characterized 100% of the cases, identifying: 11 homozygous patients for USH2A p.(Cys759Phe), 42 compound heterozygous patients (12 of them with another missense USH2A pathogenic variant and 30 with a truncating USH2A variant), and 4 patients carrying the p.(Cys759Phe) allele and a pathogenic variant in another RP gene (PROM1, CNGB1 or RP1). No additional causative variants were identified in symptomatic homozygous patients. Statistical analysis of clinical differences between zygosity states yielded differences (p≤0.05) in age at diagnosis of RP and hypoacusis, and progression of visual field loss. Homozygosity of p.(Cys759Phe) and compound heterozygosity with another USH2A missense variant is associated with ARRP or ARRP plus late onset hypoacusis (OR = 20.62, CI = 95%, p = 0.041). CONCLUSIONS The present study supports the role of USH2A p.(Cys759Phe) in ARRP and USH2 pathogenesis, and demonstrates the clinical differences between different zygosity states. Phenotype-genotype correlations may guide the genetic characterization based upon specific clinical signs and may advise on the clinical management and prognosis based upon a specific genotype.
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Affiliation(s)
- Raquel Pérez-Carro
- Department of Genetics, Instituto de Investigación Sanitaria–Fundación Jimenez Diaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics, Instituto de Investigación Sanitaria–Fundación Jimenez Diaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Lilián Galbis-Martínez
- Department of Genetics, Instituto de Investigación Sanitaria–Fundación Jimenez Diaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Gema García-García
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
- Research group on Molecular, Cellular and Genomic Biomedicine, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
| | - Elena Aller
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
- Research group on Molecular, Cellular and Genomic Biomedicine, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
| | - Blanca García-Sandoval
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
- Department of Ophthalmology, Instituto de Investigación Sanitaria–Fundación Jimenez Diaz University Hospital–Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Pablo Mínguez
- Department of Genetics, Instituto de Investigación Sanitaria–Fundación Jimenez Diaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Marta Corton
- Department of Genetics, Instituto de Investigación Sanitaria–Fundación Jimenez Diaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Ignacio Mahíllo-Fernández
- Department of Epidemiology and Biostatistics, Instituto de Investigación Sanitaria-Fundación Jimenez Diaz-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Inmaculada Martín-Mérida
- Department of Genetics, Instituto de Investigación Sanitaria–Fundación Jimenez Diaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Almudena Avila-Fernández
- Department of Genetics, Instituto de Investigación Sanitaria–Fundación Jimenez Diaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - José M. Millán
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
- Research group on Molecular, Cellular and Genomic Biomedicine, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria–Fundación Jimenez Diaz 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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Dona M, Slijkerman R, Lerner K, Broekman S, Wegner J, Howat T, Peters T, Hetterschijt L, Boon N, de Vrieze E, Sorusch N, Wolfrum U, Kremer H, Neuhauss S, Zang J, Kamermans M, Westerfield M, Phillips J, van Wijk E. Usherin defects lead to early-onset retinal dysfunction in zebrafish. Exp Eye Res 2018; 173:148-159. [PMID: 29777677 DOI: 10.1016/j.exer.2018.05.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/15/2018] [Accepted: 05/15/2018] [Indexed: 01/24/2023]
Abstract
Mutations in USH2A are the most frequent cause of Usher syndrome and autosomal recessive nonsyndromic retinitis pigmentosa. To unravel the pathogenic mechanisms underlying USH2A-associated retinal degeneration and to evaluate future therapeutic strategies that could potentially halt the progression of this devastating disorder, an animal model is needed. The available Ush2a knock-out mouse model does not mimic the human phenotype, because it presents with only a mild and late-onset retinal degeneration. Using CRISPR/Cas9-technology, we introduced protein-truncating germline lesions into the zebrafish ush2a gene (ush2armc1: c.2337_2342delinsAC; p.Cys780GlnfsTer32 and ush2ab1245: c.15520_15523delinsTG; p.Ala5174fsTer). Homozygous mutants were viable and displayed no obvious morphological or developmental defects. Immunohistochemical analyses with antibodies recognizing the N- or C-terminal region of the ush2a-encoded protein, usherin, demonstrated complete absence of usherin in photoreceptors of ush2armc1, but presence of the ectodomain of usherin at the periciliary membrane of ush2ab1245-derived photoreceptors. Furthermore, defects of usherin led to a reduction in localization of USH2 complex members, whirlin and Adgrv1, at the photoreceptor periciliary membrane of both mutants. Significantly elevated levels of apoptotic photoreceptors could be observed in both mutants when kept under constant bright illumination for three days. Electroretinogram (ERG) recordings revealed a significant and similar decrease in both a- and b-wave amplitudes in ush2armc1 as well as ush2ab1245 larvae as compared to strain- and age-matched wild-type larvae. In conclusion, this study shows that mutant ush2a zebrafish models present with early-onset retinal dysfunction that is exacerbated by light exposure. These models provide a better understanding of the pathophysiology underlying USH2A-associated RP and a unique opportunity to evaluate future therapeutic strategies.
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Affiliation(s)
- Margo Dona
- Department of Otorhinolaryngology, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Geert Grooteplein Zuid 28, 6525 GA Nijmegen, The Netherlands
| | - Ralph Slijkerman
- Department of Otorhinolaryngology, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Geert Grooteplein Zuid 28, 6525 GA Nijmegen, The Netherlands
| | - Kimberly Lerner
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403-1254, USA
| | - Sanne Broekman
- Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands; Donders Institute for Brain, Cognition, and Behavior, Montessorilaan 3, 6525 HR Nijmegen, The Netherlands
| | - Jeremy Wegner
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403-1254, USA
| | - Taylor Howat
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403-1254, USA
| | - Theo Peters
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403-1254, USA; Donders Institute for Brain, Cognition, and Behavior, Montessorilaan 3, 6525 HR Nijmegen, The Netherlands
| | - Lisette Hetterschijt
- Department of Otorhinolaryngology, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands; Donders Institute for Brain, Cognition, and Behavior, Montessorilaan 3, 6525 HR Nijmegen, The Netherlands
| | - Nanda Boon
- Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands
| | - Erik de Vrieze
- Department of Otorhinolaryngology, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands; Donders Institute for Brain, Cognition, and Behavior, Montessorilaan 3, 6525 HR Nijmegen, The Netherlands
| | - Nasrin Sorusch
- Institute of Molecular Physiology, Johannes Gutenberg University, Johannes-von-Muellerweg 6, D-55099 Mainz, Germany
| | - Uwe Wolfrum
- Institute of Molecular Physiology, Johannes Gutenberg University, Johannes-von-Muellerweg 6, D-55099 Mainz, Germany
| | - Hannie Kremer
- Department of Otorhinolaryngology, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands; Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands; Donders Institute for Brain, Cognition, and Behavior, Montessorilaan 3, 6525 HR Nijmegen, The Netherlands
| | - Stephan Neuhauss
- University of Zürich, Institute of Molecular Life Sciences, Winterthurerstrasse 190, Zürich, CH - 8057, Switzerland
| | - Jingjing Zang
- University of Zürich, Institute of Molecular Life Sciences, Winterthurerstrasse 190, Zürich, CH - 8057, Switzerland
| | - Maarten Kamermans
- Retinal Signal Processing Lab, Netherlands Institute for Neuroscience, Meibergdreef 47, 1105 BA Amsterdam, The Netherlands; Department of Biomedical Physics, Academisch Medisch Centrum, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Monte Westerfield
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403-1254, USA
| | - Jennifer Phillips
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403-1254, USA
| | - Erwin van Wijk
- Department of Otorhinolaryngology, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands; Donders Institute for Brain, Cognition, and Behavior, Montessorilaan 3, 6525 HR Nijmegen, The Netherlands.
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Target 5000: Target Capture Sequencing for Inherited Retinal Degenerations. Genes (Basel) 2017; 8:genes8110304. [PMID: 29099798 PMCID: PMC5704217 DOI: 10.3390/genes8110304] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 10/23/2017] [Accepted: 10/27/2017] [Indexed: 01/02/2023] Open
Abstract
There are an estimated 5000 people in Ireland who currently have an inherited retinal degeneration (IRD). It is the goal of this study, through genetic diagnosis, to better enable these 5000 individuals to obtain a clearer understanding of their condition and improved access to potentially applicable therapies. Here we show the current findings of a target capture next-generation sequencing study of over 750 patients from over 520 pedigrees currently situated in Ireland. We also demonstrate how processes can be implemented to retrospectively analyse patient datasets for the detection of structural variants in previously obtained sequencing reads. Pathogenic or likely pathogenic mutations were detected in 68% of pedigrees tested. We report nearly 30 novel mutations including three large structural variants. The population statistics related to our findings are presented by condition and credited to their respective candidate gene mutations. Rediagnosis rates of clinical phenotypes after genotyping are discussed. Possible causes of failure to detect a candidate mutation are evaluated. Future elements of this project, with a specific emphasis on structural variants and non-coding pathogenic variants, are expected to increase detection rates further and thereby produce an even more comprehensive representation of the genetic landscape of IRDs in Ireland.
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Villanueva A, Biswas P, Kishaba K, Suk J, Tadimeti K, Raghavendra PB, Nadeau K, Lamontagne B, Busque L, Geoffroy S, Mongrain I, Asselin G, Provost S, Dubé MP, Nudleman E, Ayyagari R. Identification of the genetic determinants responsible for retinal degeneration in families of Mexican descent. Ophthalmic Genet 2017; 39:73-79. [PMID: 28945494 DOI: 10.1080/13816810.2017.1373830] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
PURPOSE To investigate the clinical characteristics and genetic basis of inherited retinal degeneration (IRD) in six unrelated pedigrees from Mexico. METHODS A complete ophthalmic evaluation including measurement of visual acuities, Goldman kinetic or Humphrey dynamic perimetry, Amsler test, fundus photography, and color vision testing was performed. Family history and blood samples were collected from available family members. DNA from members of two pedigrees was examined for known mutations using the APEX ARRP genotyping microarray and one pedigree using the APEX LCA genotyping microarray. The remaining three pedigrees were analyzed using a custom-designed targeted capture array covering the exons of 233 known retinal degeneration genes. Sequencing was performed on Illumina HiSeq. Reads were mapped against hg19, and variants were annotated using GATK and filtered by exomeSuite. Segregation and ethnicity-matched control sample analyses were performed by dideoxy sequencing. RESULTS Six pedigrees with IRD were analyzed. Nine rare or novel, potentially pathogenic variants segregating with the phenotype were detected in IMPDH1, USH2A, RPE65, ABCA4, and FAM161A genes. Among these, six were known mutations while the remaining three changes in USH2A, RPE65, and FAM161A genes have not been previously reported to be associated with IRD. Analysis of 100 ethnicity-matched controls did not detect the presence of these three novel variants indicating, these are rare variants in the Mexican population. CONCLUSIONS Screening patients diagnosed with IRD from Mexico identified six known mutations and three rare or novel potentially damaging variants in IMPDH1, USH2A, RPE65, ABCA4, and FAM161A genes that segregated with disease.
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Affiliation(s)
- Adda Villanueva
- a Retina Department Genomics Institute, Mejora Vision MD/Virtual Eye Care MD , Mérida , Yucatán , México.,b Laboratoire de Diagnostic Moleculaire , Hôpital Maisonneuve Rosemont , Montreal , Quebec , Canada
| | - Pooja Biswas
- c School of Biotechnology , REVA University , Bengaluru , India.,d Shiley Eye Institute, University of California San Diego , La Jolla , CA , USA
| | - Kameron Kishaba
- d Shiley Eye Institute, University of California San Diego , La Jolla , CA , USA
| | - John Suk
- d Shiley Eye Institute, University of California San Diego , La Jolla , CA , USA
| | - Keerti Tadimeti
- d Shiley Eye Institute, University of California San Diego , La Jolla , CA , USA
| | | | - Karine Nadeau
- a Retina Department Genomics Institute, Mejora Vision MD/Virtual Eye Care MD , Mérida , Yucatán , México.,b Laboratoire de Diagnostic Moleculaire , Hôpital Maisonneuve Rosemont , Montreal , Quebec , Canada
| | - Bruno Lamontagne
- a Retina Department Genomics Institute, Mejora Vision MD/Virtual Eye Care MD , Mérida , Yucatán , México.,b Laboratoire de Diagnostic Moleculaire , Hôpital Maisonneuve Rosemont , Montreal , Quebec , Canada
| | - Lambert Busque
- a Retina Department Genomics Institute, Mejora Vision MD/Virtual Eye Care MD , Mérida , Yucatán , México.,b Laboratoire de Diagnostic Moleculaire , Hôpital Maisonneuve Rosemont , Montreal , Quebec , Canada
| | - Steve Geoffroy
- e Montreal Heart Institute, Université de Montréal , Montreal , Canada.,f Université de Montréal Beaulieu-Saucier Pharmacogenomics Center, Montreal Heart Institute, Université de Montréal , Montreal , Canada
| | - Ian Mongrain
- e Montreal Heart Institute, Université de Montréal , Montreal , Canada.,f Université de Montréal Beaulieu-Saucier Pharmacogenomics Center, Montreal Heart Institute, Université de Montréal , Montreal , Canada
| | - Géraldine Asselin
- e Montreal Heart Institute, Université de Montréal , Montreal , Canada.,f Université de Montréal Beaulieu-Saucier Pharmacogenomics Center, Montreal Heart Institute, Université de Montréal , Montreal , Canada
| | - Sylvie Provost
- e Montreal Heart Institute, Université de Montréal , Montreal , Canada.,f Université de Montréal Beaulieu-Saucier Pharmacogenomics Center, Montreal Heart Institute, Université de Montréal , Montreal , Canada
| | - Marie-Pierre Dubé
- e Montreal Heart Institute, Université de Montréal , Montreal , Canada.,f Université de Montréal Beaulieu-Saucier Pharmacogenomics Center, Montreal Heart Institute, Université de Montréal , Montreal , Canada.,g Department of Medicine, Université de Montréal , Montreal , Canada
| | - Eric Nudleman
- d Shiley Eye Institute, University of California San Diego , La Jolla , CA , USA
| | - Radha Ayyagari
- d Shiley Eye Institute, University of California San Diego , La Jolla , CA , USA
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Sengillo JD, Cabral T, Schuerch K, Duong J, Lee W, Boudreault K, Xu Y, Justus S, Sparrow JR, Mahajan VB, Tsang SH. Electroretinography Reveals Difference in Cone Function between Syndromic and Nonsyndromic USH2A Patients. Sci Rep 2017; 7:11170. [PMID: 28894305 PMCID: PMC5593892 DOI: 10.1038/s41598-017-11679-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 08/15/2017] [Indexed: 11/23/2022] Open
Abstract
Usher syndrome is an inherited and irreversible disease that manifests as retinitis pigmentosa (RP) and bilateral neurosensory hearing loss. Mutations in Usherin 2A (USH2A) are not only a frequent cause of Usher syndrome, but also nonsyndromic RP. Although gene- and cell-based therapies are on the horizon for RP and Usher syndrome, studies characterizing natural disease are lacking. In this retrospective analysis, retinal function of USH2A patients was quantified with electroretinography. Both groups had markedly reduced rod and cone responses, but nonsyndromic USH2A patients had 30 Hz-flicker electroretinogram amplitudes that were significantly higher than syndromic patients, suggesting superior residual cone function. There was a tendency for Usher syndrome patients to have a higher distribution of severe mutations, and alleles in this group had a higher odds of containing nonsense or frame-shift mutations. These data suggest that the previously reported severe visual phenotype seen in syndromic USH2A patients could relate to a greater extent of cone dysfunction. Additionally, a genetic threshold may exist where mutation burden relates to visual phenotype and the presence of hearing deficits. The auditory phenotype and allelic hierarchy observed among patients should be considered in prospective studies of disease progression and during enrollment for future clinical trials.
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Affiliation(s)
- Jesse D Sengillo
- Jonas Children's Vision Care, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University Medical Center, New York, NY, USA.,Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA.,State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | - Thiago Cabral
- Jonas Children's Vision Care, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University Medical Center, New York, NY, USA.,Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA.,Department of Ophthalmology, Federal University of Espírito Santo, Vitoria, Brazil.,Department of Ophthalmology, Federal University of São Paulo, Sao Paulo, Brazil
| | - Kaspar Schuerch
- Jonas Children's Vision Care, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University Medical Center, New York, NY, USA.,Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Jimmy Duong
- Department of Biostatistics, Columbia University, New York, NY, USA
| | - Winston Lee
- Jonas Children's Vision Care, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University Medical Center, New York, NY, USA.,Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Katherine Boudreault
- Jonas Children's Vision Care, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University Medical Center, New York, NY, USA.,Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA.,Department of Ophthalmology, University of Montreal, Montreal, Canada
| | - Yu Xu
- Department of Ophthalmology, Xin Hua Hospital affiliate of Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sally Justus
- Jonas Children's Vision Care, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University Medical Center, New York, NY, USA.,Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Janet R Sparrow
- Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA.,Department of Pathology & Cell Biology, Stem Cell Initiative (CSCI), Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Vinit B Mahajan
- Omics Laboratory, Byers Eye Institute, Department of Ophthalmology, Stanford University, Palo Alto, CA, USA
| | - Stephen H Tsang
- Jonas Children's Vision Care, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University Medical Center, New York, NY, USA. .,Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA. .,Department of Pathology & Cell Biology, Stem Cell Initiative (CSCI), Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY, USA.
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Wang X, Zein WM, D'Souza L, Roberson C, Wetherby K, He H, Villarta A, Turriff A, Johnson KR, Fann YC. Applying next generation sequencing with microdroplet PCR to determine the disease-causing mutations in retinal dystrophies. BMC Ophthalmol 2017; 17:157. [PMID: 28838317 PMCID: PMC5571584 DOI: 10.1186/s12886-017-0549-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 08/14/2017] [Indexed: 01/07/2023] Open
Abstract
Background Inherited Retinal dystrophy (IRD) is a broad group of inherited retinal disorders with heterogeneous genotypes and phenotypes. Next generation sequencing (NGS) methods have been broadly applied for analyzing patients with IRD. Here we report a novel approach to enrich the target gene panel by microdroplet PCR. Methods This assay involved a primer library which targeted 3071 amplicons from 2078 exons comprised of 184 genes involved in retinal function and/or retinal development. We amplified the target regions using the RainDance target enrichment PCR method and sequenced the products using the MiSeq NGS platform. Results In this study, we analyzed 82 samples from 67 families with IRD. Bioinformatics analysis indicated that this procedure was able to reach 99% coverage of target sequences with an average sequence depth of reads at 119×. The variants detected by this study were filtered, validated, and prioritized by pathogenicity analysis. Genotypes and phenotypes were correlated by determining a consistent relationship in 38 propands (56.7%). Pathogenic variants in genes related to retinal function were found in another 11 probands (16.4%), but the clinical correlations showed inconsistencies and insufficiencies in these patients. Conclusions The application of NGS in IRD clinical molecular diagnosis provides a powerful approach to exploring the etiology and pathology in patients. It is important for the clinical laboratory to interpret the molecular findings in the context of patient clinical presentations because accurate interpretation of pathogenic variants is critical for delivering solid clinical molecular diagnosis to clinicians and patients and improving the standard care of patients. Electronic supplementary material The online version of this article (doi:10.1186/s12886-017-0549-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xinjing Wang
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, 10D43, 10 Center Drive, Bethesda, MD, 20892, USA.
| | - Wadih M Zein
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, 10D43, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Leera D'Souza
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, 10D43, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Chimere Roberson
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, 10D43, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Keith Wetherby
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, 10D43, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Hong He
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, 10D43, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Angela Villarta
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, 10D43, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Amy Turriff
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, 10D43, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Kory R Johnson
- Intramural IT and Bioinformatics Program, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Yang C Fann
- Intramural IT and Bioinformatics Program, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
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Neuhaus C, Eisenberger T, Decker C, Nagl S, Blank C, Pfister M, Kennerknecht I, Müller-Hofstede C, Charbel Issa P, Heller R, Beck B, Rüther K, Mitter D, Rohrschneider K, Steinhauer U, Korbmacher HM, Huhle D, Elsayed SM, Taha HM, Baig SM, Stöhr H, Preising M, Markus S, Moeller F, Lorenz B, Nagel-Wolfrum K, Khan AO, Bolz HJ. Next-generation sequencing reveals the mutational landscape of clinically diagnosed Usher syndrome: copy number variations, phenocopies, a predominant target for translational read-through, and PEX26 mutated in Heimler syndrome. Mol Genet Genomic Med 2017; 5:531-552. [PMID: 28944237 PMCID: PMC5606877 DOI: 10.1002/mgg3.312] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 06/06/2017] [Accepted: 06/09/2017] [Indexed: 12/23/2022] Open
Abstract
Background Combined retinal degeneration and sensorineural hearing impairment is mostly due to autosomal recessive Usher syndrome (USH1: congenital deafness, early retinitis pigmentosa (RP); USH2: progressive hearing impairment, RP). Methods Sanger sequencing and NGS of 112 genes (Usher syndrome, nonsyndromic deafness, overlapping conditions), MLPA, and array‐CGH were conducted in 138 patients clinically diagnosed with Usher syndrome. Results A molecular diagnosis was achieved in 97% of both USH1 and USH2 patients, with biallelic mutations in 97% (USH1) and 90% (USH2), respectively. Quantitative readout reliably detected CNVs (confirmed by MLPA or array‐CGH), qualifying targeted NGS as one tool for detecting point mutations and CNVs. CNVs accounted for 10% of identified USH2A alleles, often in trans to seemingly monoallelic point mutations. We demonstrate PTC124‐induced read‐through of the common p.Trp3955* nonsense mutation (13% of detected USH2A alleles), a potential therapy target. Usher gene mutations were found in most patients with atypical Usher syndrome, but the diagnosis was adjusted in case of double homozygosity for mutations in OTOA and NR2E3, genes implicated in isolated deafness and RP. Two patients with additional enamel dysplasia had biallelic PEX26 mutations, for the first time linking this gene to Heimler syndrome. Conclusion Targeted NGS not restricted to Usher genes proved beneficial in uncovering conditions mimicking Usher syndrome.
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Affiliation(s)
| | | | | | - Sandra Nagl
- Bioscientia Center for Human GeneticsIngelheimGermany
| | | | - Markus Pfister
- HNO-Praxis SarnenSarnenSwitzerland.,Molecular Genetics, THRCDepartment of OtolaryngologyUniversity of TübingenTübingenGermany
| | - Ingo Kennerknecht
- Institute of Human GeneticsWestfälische Wilhelms-UniversitätMünsterGermany
| | | | - Peter Charbel Issa
- Department of OphthalmologyUniversity of BonnBonnGermany.,Center for Rare Diseases Bonn (ZSEB)University of BonnBonnGermany.,Oxford Eye HospitalUniversity of OxfordOxfordUK
| | - Raoul Heller
- Institute of Human GeneticsUniversity Hospital of CologneCologneGermany
| | - Bodo Beck
- Institute of Human GeneticsUniversity Hospital of CologneCologneGermany
| | | | - Diana Mitter
- Institute of Human GeneticsUniversity of Leipzig Hospitals and ClinicsLeipzigGermany
| | | | | | - Heike M Korbmacher
- Department of OrthodonticsGiessen and Marburg University Hospital, Marburg CampusMarburgGermany
| | | | - Solaf M Elsayed
- Medical Genetics CenterCairoEgypt.,Children's HospitalAin Shams UniversityCairoEgypt
| | | | - Shahid M Baig
- Human Molecular Genetics LaboratoryHealth Biotechnology DivisionNational Institute for Biotechnology and Genetic Engineering (NIBGE)FaisalabadPakistan
| | - Heidi Stöhr
- Department of Human GeneticsUniversity Medical Center RegensburgRegensburgGermany
| | - Markus Preising
- Department of OphthalmologyJustus-Liebig-University GiessenGiessenGermany
| | | | - Fabian Moeller
- Department of Cell and Matrix BiologyInstitute of Zoology, Johannes GutenbergUniversity of MainzMainzGermany
| | - Birgit Lorenz
- Department of OphthalmologyJustus-Liebig-University GiessenGiessenGermany
| | - Kerstin Nagel-Wolfrum
- Department of Cell and Matrix BiologyInstitute of Zoology, Johannes GutenbergUniversity of MainzMainzGermany
| | - Arif O Khan
- Division of Pediatric OphthalmologyKing Khaled Eye Specialist HospitalRiyadhSaudi Arabia.,Eye InstituteCleveland ClinicAbu DhabiUAE
| | - Hanno J Bolz
- Bioscientia Center for Human GeneticsIngelheimGermany.,Institute of Human GeneticsUniversity Hospital of CologneCologneGermany
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74
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May-Simera H, Nagel-Wolfrum K, Wolfrum U. Cilia - The sensory antennae in the eye. Prog Retin Eye Res 2017; 60:144-180. [PMID: 28504201 DOI: 10.1016/j.preteyeres.2017.05.001] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 05/04/2017] [Accepted: 05/08/2017] [Indexed: 12/21/2022]
Abstract
Cilia are hair-like projections found on almost all cells in the human body. Originally believed to function merely in motility, the function of solitary non-motile (primary) cilia was long overlooked. Recent research has demonstrated that primary cilia function as signalling hubs that sense environmental cues and are pivotal for organ development and function, tissue hoemoestasis, and maintenance of human health. Cilia share a common anatomy and their diverse functional features are achieved by evolutionarily conserved functional modules, organized into sub-compartments. Defects in these functional modules are responsible for a rapidly growing list of human diseases collectively termed ciliopathies. Ocular pathogenesis is common in virtually all classes of syndromic ciliopathies, and disruptions in cilia genes have been found to be causative in a growing number of non-syndromic retinal dystrophies. This review will address what is currently known about cilia contribution to visual function. We will focus on the molecular and cellular functions of ciliary proteins and their role in the photoreceptor sensory cilia and their visual phenotypes. We also highlight other ciliated cell types in tissues of the eye (e.g. lens, RPE and Müller glia cells) discussing their possible contribution to disease progression. Progress in basic research on the cilia function in the eye is paving the way for therapeutic options for retinal ciliopathies. In the final section we describe the latest advancements in gene therapy, read-through of non-sense mutations and stem cell therapy, all being adopted to treat cilia dysfunction in the retina.
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Affiliation(s)
- Helen May-Simera
- Institute of Molecular Physiology, Cilia Biology, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany
| | - Kerstin Nagel-Wolfrum
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany
| | - Uwe Wolfrum
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany.
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75
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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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76
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Kletke S, Batmanabane V, Dai T, Vincent A, Li S, Gordon KA, Papsin BC, Cushing SL, Héon E. The combination of vestibular impairment and congenital sensorineural hearing loss predisposes patients to ocular anomalies, including Usher syndrome. Clin Genet 2017; 92:26-33. [PMID: 27743452 DOI: 10.1111/cge.12895] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/05/2016] [Accepted: 10/12/2016] [Indexed: 11/29/2022]
Abstract
The co-occurrence of hearing impairment and visual dysfunction is devastating. Most deaf-blind etiologies are genetically determined, the commonest being Usher syndrome (USH). While studies of the congenitally deaf population reveal a variable degree of visual problems, there are no effective ophthalmic screening guidelines. We hypothesized that children with congenital sensorineural hearing loss (SNHL) and vestibular impairment were at an increased risk of having USH. A retrospective chart review of 33 cochlear implants recipients for severe to profound SNHL and measured vestibular dysfunction was performed to determine the ocular phenotype. All the cases had undergone ocular examination and electroretinogram (ERG). Patients with an abnormal ERG underwent genetic testing for USH. We found an underlying ocular abnormality in 81.81% (27/33) of cases; of which 75% had refractive errors, and 50% of those patients showed visual improvement with refractive correction. A total of 14 cases (42.42%; 14/33) had generalized rod-cone dysfunction on ERG suggestive of Usher syndrome type 1, confirmed by mutational analysis. This work shows that adding vestibular impairment as a criterion for requesting an eye exam and adding the ERG to detect USH increases the chances of detecting ocular anomalies, when compared with previous literature focusing only on congenital SNHL.
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Affiliation(s)
- S Kletke
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Ontario, Canada
| | - V Batmanabane
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - T Dai
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Ontario, Canada
| | - A Vincent
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Ontario, Canada.,Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - S Li
- Program of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - K A Gordon
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Ontario, Canada.,Department of Otolaryngology - Head & Neck Surgery, The Hospital for Sick Children, Toronto, Ontario, Canada.,Archie's Cochlear Implant Laboratory, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - B C Papsin
- Department of Otolaryngology - Head & Neck Surgery, The Hospital for Sick Children, Toronto, Ontario, Canada.,Archie's Cochlear Implant Laboratory, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - S L Cushing
- Department of Otolaryngology - Head & Neck Surgery, The Hospital for Sick Children, Toronto, Ontario, Canada.,Archie's Cochlear Implant Laboratory, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - E Héon
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Ontario, Canada.,Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
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77
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Unravelling the Complexity of Inherited Retinal Dystrophies Molecular Testing: Added Value of Targeted Next-Generation Sequencing. BIOMED RESEARCH INTERNATIONAL 2016; 2016:6341870. [PMID: 28127548 PMCID: PMC5227126 DOI: 10.1155/2016/6341870] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/30/2016] [Accepted: 10/20/2016] [Indexed: 11/18/2022]
Abstract
To assess the clinical utility of targeted Next-Generation Sequencing (NGS) for the diagnosis of Inherited Retinal Dystrophies (IRDs), a total of 109 subjects were enrolled in the study, including 88 IRD affected probands and 21 healthy relatives. Clinical diagnoses included Retinitis Pigmentosa (RP), Leber Congenital Amaurosis (LCA), Stargardt Disease (STGD), Best Macular Dystrophy (BMD), Usher Syndrome (USH), and other IRDs with undefined clinical diagnosis. Participants underwent a complete ophthalmologic examination followed by genetic counseling. A custom AmpliSeq™ panel of 72 IRD-related genes was designed for the analysis and tested using Ion semiconductor Next-Generation Sequencing (NGS). Potential disease-causing mutations were identified in 59.1% of probands, comprising mutations in 16 genes. The highest diagnostic yields were achieved for BMD, LCA, USH, and STGD patients, whereas RP confirmed its high genetic heterogeneity. Causative mutations were identified in 17.6% of probands with undefined diagnosis. Revision of the initial diagnosis was performed for 9.6% of genetically diagnosed patients. This study demonstrates that NGS represents a comprehensive cost-effective approach for IRDs molecular diagnosis. The identification of the genetic alterations underlying the phenotype enabled the clinicians to achieve a more accurate diagnosis. The results emphasize the importance of molecular diagnosis coupled with clinic information to unravel the extensive phenotypic heterogeneity of these diseases.
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78
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Nikopoulos K, Farinelli P, Giangreco B, Tsika C, Royer-Bertrand B, Mbefo M, Bedoni N, Kjellström U, El Zaoui I, Di Gioia S, Balzano S, Cisarova K, Messina A, Decembrini S, Plainis S, Blazaki S, Khan M, Micheal S, Boldt K, Ueffing M, Moulin A, Cremers F, Roepman R, Arsenijevic Y, Tsilimbaris M, Andréasson S, Rivolta C. Mutations in CEP78 Cause Cone-Rod Dystrophy and Hearing Loss Associated with Primary-Cilia Defects. Am J Hum Genet 2016; 99:770-776. [PMID: 27588451 DOI: 10.1016/j.ajhg.2016.07.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 07/07/2016] [Indexed: 02/08/2023] Open
Abstract
Cone-rod degeneration (CRD) belongs to the disease spectrum of retinal degenerations, a group of hereditary disorders characterized by an extreme clinical and genetic heterogeneity. It mainly differentiates from other retinal dystrophies, and in particular from the more frequent disease retinitis pigmentosa, because cone photoreceptors degenerate at a higher rate than rod photoreceptors, causing severe deficiency of central vision. After exome analysis of a cohort of individuals with CRD, we identified biallelic mutations in the orphan gene CEP78 in three subjects from two families: one from Greece and another from Sweden. The Greek subject, from the island of Crete, was homozygous for the c.499+1G>T (IVS3+1G>T) mutation in intron 3. The Swedish subjects, two siblings, were compound heterozygotes for the nearby mutation c.499+5G>A (IVS3+5G>A) and for the frameshift-causing variant c.633delC (p.Trp212Glyfs(∗)18). In addition to CRD, these three individuals had hearing loss or hearing deficit. Immunostaining highlighted the presence of CEP78 in the inner segments of retinal photoreceptors, predominantly of cones, and at the base of the primary cilium of fibroblasts. Interaction studies also showed that CEP78 binds to FAM161A, another ciliary protein associated with retinal degeneration. Finally, analysis of skin fibroblasts derived from affected individuals revealed abnormal ciliary morphology, as compared to that of control cells. Altogether, our data strongly suggest that mutations in CEP78 cause a previously undescribed clinical entity of a ciliary nature characterized by blindness and deafness but clearly distinct from Usher syndrome, a condition for which visual impairment is due to retinitis pigmentosa.
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79
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Coppieters F, Ascari G, Dannhausen K, Nikopoulos K, Peelman F, Karlstetter M, Xu M, Brachet C, Meunier I, Tsilimbaris M, Tsika C, Blazaki S, Vergult S, Farinelli P, Van Laethem T, Bauwens M, De Bruyne M, Chen R, Langmann T, Sui R, Meire F, Rivolta C, Hamel C, Leroy B, De Baere E. Isolated and Syndromic Retinal Dystrophy Caused by Biallelic Mutations in RCBTB1, a Gene Implicated in Ubiquitination. Am J Hum Genet 2016; 99:470-80. [PMID: 27486781 PMCID: PMC4974088 DOI: 10.1016/j.ajhg.2016.06.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 06/20/2016] [Indexed: 11/24/2022] Open
Abstract
Inherited retinal dystrophies (iRDs) are a group of genetically and clinically heterogeneous conditions resulting from mutations in over 250 genes. Here, homozygosity mapping and whole-exome sequencing (WES) in a consanguineous family revealed a homozygous missense mutation, c.973C>T (p.His325Tyr), in RCBTB1. In affected individuals, it was found to segregate with retinitis pigmentosa (RP), goiter, primary ovarian insufficiency, and mild intellectual disability. Subsequent analysis of WES data in different cohorts uncovered four additional homozygous missense mutations in five unrelated families in whom iRD segregates with or without syndromic features. Ocular phenotypes ranged from typical RP starting in the second decade to chorioretinal dystrophy with a later age of onset. The five missense mutations affect highly conserved residues either in the sixth repeat of the RCC1 domain or in the BTB1 domain. A founder haplotype was identified for mutation c.919G>A (p.Val307Met), occurring in two families of Mediterranean origin. We showed ubiquitous mRNA expression of RCBTB1 and demonstrated predominant RCBTB1 localization in human inner retina. RCBTB1 was very recently shown to be involved in ubiquitination, more specifically as a CUL3 substrate adaptor. Therefore, the effect on different components of the CUL3 and NFE2L2 (NRF2) pathway was assessed in affected individuals’ lymphocytes, revealing decreased mRNA expression of NFE2L2 and several NFE2L2 target genes. In conclusion, our study puts forward mutations in RCBTB1 as a cause of autosomal-recessive non-syndromic and syndromic iRD. Finally, our data support a role for impaired ubiquitination in the pathogenetic mechanism of RCBTB1 mutations.
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80
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Khan KN, Chana R, Ali N, Wright G, Webster AR, Moore AT, Michaelides M. Advanced diagnostic genetic testing in inherited retinal disease: experience from a single tertiary referral centre in the UK National Health Service. Clin Genet 2016; 91:38-45. [PMID: 27160483 DOI: 10.1111/cge.12798] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/15/2016] [Accepted: 05/05/2016] [Indexed: 11/29/2022]
Abstract
In 2013, as part of our genetic investigation of patients with inherited retinal disease, we utilized multigene panel testing of 105 genes known to cause retinal disease in our patient cohorts. This test was performed in a UK National Health Service (NHS) accredited laboratory. The results of all multigene panel tests requested between 1.4.13 and 31.8.14 were retrospectively reviewed. All patients had been previously seen at Moorfields Eye Hospital, London, UK and diagnosed with an inherited retinal dystrophy after clinical examination and detailed retinal imaging. The results were categorized into three groups: (i) Testing helped establish a certain molecular diagnosis in 45 out of 115 (39%). Variants in USH2A (n = 6) and RP1 (n = 4) were most common. (ii) Definitive conclusions could not be drawn from molecular testing alone in 13 out of 115 (11%) as either insufficient pathogenic variants were discovered or those identified were not consistent with the phenotype. (iii) Testing did not identify any pathogenic variants responsible for the phenotype in 57 out of 115 (50%). Multigene panel testing performed in an NHS setting has enabled a molecular diagnosis to be confidently made in 40% of cases. Novel variants accounted for 38% of all identified variants. Detailed retinal phenotyping helped the interpretation of specific variants. Additional care needs to be taken when assessing polymorphisms in genes that have been infrequently associated with disease, as historical techniques were not as rigorous as contemporary ones. Future iterations of sequencing are likely to offer higher sensitivity, testing a broader range of genes, more rapidly and at a reduced cost.
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Affiliation(s)
- K N Khan
- Moorfields Eye Hospital, London, UK.,UCL Institute of Ophthalmology, London, UK.,St. James's University Hospital, Leeds, UK
| | - R Chana
- Moorfields Eye Hospital, London, UK.,UCL Institute of Ophthalmology, London, UK
| | - N Ali
- Moorfields Eye Hospital, London, UK
| | - G Wright
- Moorfields Eye Hospital, London, UK.,UCL Institute of Ophthalmology, London, UK
| | - A R Webster
- Moorfields Eye Hospital, London, UK.,UCL Institute of Ophthalmology, London, UK
| | - A T Moore
- Moorfields Eye Hospital, London, UK.,UCL Institute of Ophthalmology, London, UK
| | - M Michaelides
- Moorfields Eye Hospital, London, UK.,UCL Institute of Ophthalmology, London, UK
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81
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Pierrache LH, Hartel BP, van Wijk E, Meester-Smoor MA, Cremers FP, de Baere E, de Zaeytijd J, van Schooneveld MJ, Cremers CW, Dagnelie G, Hoyng CB, Bergen AA, Leroy BP, Pennings RJ, van den Born LI, Klaver CC. Visual Prognosis in USH2A-Associated Retinitis Pigmentosa Is Worse for Patients with Usher Syndrome Type IIa Than for Those with Nonsyndromic Retinitis Pigmentosa. Ophthalmology 2016; 123:1151-60. [DOI: 10.1016/j.ophtha.2016.01.021] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 01/09/2016] [Accepted: 01/13/2016] [Indexed: 12/25/2022] Open
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82
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Genomic screening of ABCA4 and array CGH analysis underline the genetic variability of Greek patients with inherited retinal diseases. Meta Gene 2016; 8:37-43. [PMID: 27014590 PMCID: PMC4792891 DOI: 10.1016/j.mgene.2016.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 01/12/2016] [Accepted: 02/10/2016] [Indexed: 11/22/2022] Open
Abstract
Background Retinal dystrophies are a clinically and genetically heterogeneous group of disorders which affect more than two million people worldwide. The present study focused on the role of the ABCA4 gene in the pathogenesis of hereditary retinal dystrophies (autosomal recessive Stargardt disease, autosomal recessive cone-rod dystrophy, and autosomal recessive retinitis pigmentosa) in patients of Greek origin. Materials and methods Our cohort included 26 unrelated patients and their first degree healthy relatives. The ABCA4 mutation screening involved Sanger sequencing of all exons and flanking regions. Evaluation of novel variants included sequencing of control samples, family segregation analysis and characterization by in silico prediction tools. Twenty five patients were also screened for copy number variations by array-comparative genomic hybridization. Results Excluding known disease-causing mutations and polymorphisms, two novel variants were identified in coding and non-coding regions of ABCA4. Array-CGH analysis revealed two partial deletions of USH2A and MYO3A in two patients with nonsyndromic autosomal recessive retinitis pigmentosa. Conclusions The ABCA4 mutation spectrum in Greek patients differs from other populations. Bioinformatic tools, segregation analysis along with clinical data from the patients seemed to be crucial for the evaluation of genetic variants and particularly for the discrimination between causative and non-causative variants. Sixteen known pathological genetic variants were identified in ABCA4 gene in Greek patients with retinal dystrophies. Two novel variants were found in patients with Stargardt’s disease and cone-rod dystrophy respectively. Two reported mutations in Stargardt's patients were identified in retinitis pigmentosa and cone-rod dystrophy patients. The mutations p.Gly1961Glu and p.Ala1038Val, which are common in other populations, where also found in our cohort consisted of 26 Greek patients. Array-comparative genome hybridization revealed large deletions in two out of the 25 cases studied.
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83
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Panel-based NGS Reveals Novel Pathogenic Mutations in Autosomal Recessive Retinitis Pigmentosa. Sci Rep 2016; 6:19531. [PMID: 26806561 PMCID: PMC4726392 DOI: 10.1038/srep19531] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/14/2015] [Indexed: 12/22/2022] Open
Abstract
Retinitis pigmentosa (RP) is a group of inherited progressive retinal dystrophies (RD) characterized by photoreceptor degeneration. RP is highly heterogeneous both clinically and genetically, which complicates the identification of causative genes and mutations. Targeted next-generation sequencing (NGS) has been demonstrated to be an effective strategy for the detection of mutations in RP. In our study, an in-house gene panel comprising 75 known RP genes was used to analyze a cohort of 47 unrelated Spanish families pre-classified as autosomal recessive or isolated RP. Disease-causing mutations were found in 27 out of 47 cases achieving a mutation detection rate of 57.4%. In total, 33 pathogenic mutations were identified, 20 of which were novel mutations (60.6%). Furthermore, not only single nucleotide variations but also copy-number variations, including three large deletions in the USH2A and EYS genes, were identified. Finally seven out of 27 families, displaying mutations in the ABCA4, RP1, RP2 and USH2A genes, could be genetically or clinically reclassified. These results demonstrate the potential of our panel-based NGS strategy in RP diagnosis.
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84
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Liquori A, Vaché C, Baux D, Blanchet C, Hamel C, Malcolm S, Koenig M, Claustres M, Roux AF. Whole USH2A Gene Sequencing Identifies Several New Deep Intronic Mutations. Hum Mutat 2015; 37:184-93. [PMID: 26629787 DOI: 10.1002/humu.22926] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/19/2015] [Indexed: 01/01/2023]
Abstract
Deep intronic mutations leading to pseudoexon (PE) insertions are underestimated and most of these splicing alterations have been identified by transcript analysis, for instance, the first deep intronic mutation in USH2A, the gene most frequently involved in Usher syndrome type II (USH2). Unfortunately, analyzing USH2A transcripts is challenging and for 1.8%-19% of USH2 individuals carrying a single USH2A recessive mutation, a second mutation is yet to be identified. We have developed and validated a DNA next-generation sequencing approach to identify deep intronic variants in USH2A and evaluated their consequences on splicing. Three distinct novel deep intronic mutations have been identified. All were predicted to affect splicing and resulted in the insertion of PEs, as shown by minigene assays. We present a new and attractive strategy to identify deep intronic mutations, when RNA analyses are not possible. Moreover, the bioinformatics pipeline developed is independent of the gene size, implying the possible application of this approach to any disease-linked gene. Finally, an antisense morpholino oligonucleotide tested in vitro for its ability to restore splicing caused by the c.9959-4159A>G mutation provided high inhibition rates, which are indicative of its potential for molecular therapy.
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Affiliation(s)
- Alessandro Liquori
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France
| | - Christel Vaché
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHRU Montpellier, Montpellier, France
| | - David Baux
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHRU Montpellier, Montpellier, France
| | - Catherine Blanchet
- Service ORL, CHRU Montpellier, Montpellier, France.,CHU Montpellier, Centre National de Référence Maladies Rares, "Affections Sensorielles Génétiques, France
| | - Christian Hamel
- CHU Montpellier, Centre National de Référence Maladies Rares, "Affections Sensorielles Génétiques, France
| | - Sue Malcolm
- Genetics and Genomic Medicine Programme, Institute of Child Health, UCL, London, UK
| | - Michel Koenig
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHRU Montpellier, Montpellier, France
| | - Mireille Claustres
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHRU Montpellier, Montpellier, France
| | - Anne-Françoise Roux
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHRU Montpellier, Montpellier, France
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