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Vaché C, Faugère V, Baux D, Mansard L, Van Goethem C, Dhaenens CM, Grunewald O, Audo I, Zeitz C, Meunier I, Bocquet B, Cossée M, Bergougnoux A, Kalatzis V, Roux AF. Validation of Nanopore long-read sequencing to resolve RPGR ORF15 genotypes in individuals with X-linked retinitis pigmentosa. Eur J Hum Genet 2024:10.1038/s41431-024-01649-0. [PMID: 38969740 DOI: 10.1038/s41431-024-01649-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/15/2024] [Accepted: 06/11/2024] [Indexed: 07/07/2024] Open
Abstract
X-linked retinitis pigmentosa (XLRP) is characterized by progressive vision loss leading to legal blindness in males and a broad severity spectrum in carrier females. Pathogenic alterations of the retinitis pigmentosa GTPase regulator gene (RPGR) are responsible for over 70% of XLRP cases. In the retina, the RPGRORF15 transcript includes a terminal exon, called ORF15, that is altered in the large majority of RPGR-XLRP cases. Unfortunately, due to its highly repetitive sequence, ORF15 represents a considerable challenge in terms of sequencing for molecular diagnostic laboratories. However, in a recent preliminary work Yahya et al. reported a long-read sequencing approach seeming promising. Here, the aim of the study was to validate and integrate this new sequencing strategy in a routine screening workflow. For that purpose, we performed a masked test on 52 genomic DNA samples from male and female individuals carrying 32 different pathogenic ORF15 variations including 20 located in the highly repetitive region of the exon. For the latter, we have obtained a detection rate of 80-85% in males and 60-80% in females after bioinformatic analyses. These numbers raised to 100% for both status after adding a complementary visual inspection of ORF15 long-reads. In accordance with these results, and considering the frequency of ORF15 pathogenic variations in XLRP, we suggest that a long-read screening of ORF15 should be systematically considered before any other sequencing approach in subjects with a diagnosis compatible with XLRP.
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Affiliation(s)
- Christel Vaché
- Molecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France.
- Institute for Neurosciences of Montpellier (INM), Univ Montpellier, Inserm, Montpellier, France.
| | - Valérie Faugère
- Molecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
| | - David Baux
- Molecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
- Institute for Neurosciences of Montpellier (INM), Univ Montpellier, Inserm, Montpellier, France
- Montpellier BioInformatique pour le Diagnostic Clinique (MOBIDIC), CHU Montpellier, Montpellier, France
| | - Luke Mansard
- Molecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
- Institute for Neurosciences of Montpellier (INM), Univ Montpellier, Inserm, Montpellier, France
| | - Charles Van Goethem
- Molecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
- Montpellier BioInformatique pour le Diagnostic Clinique (MOBIDIC), CHU Montpellier, Montpellier, France
| | - Claire-Marie Dhaenens
- Univ. Lille, Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience and Cognition, Lille, France
| | - Olivier Grunewald
- Univ. Lille, Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience and Cognition, Lille, France
| | - Isabelle Audo
- Sorbonne Université, Inserm, CNRS, Institut de la Vision, Paris, France
- CHNO des Quinze-Vingts, Centre de Référence Maladies Rares REFERET, Inserm-DGOS CIC1423, Paris, France
| | - Christina Zeitz
- Sorbonne Université, Inserm, CNRS, Institut de la Vision, Paris, France
| | - Isabelle Meunier
- Institute for Neurosciences of Montpellier (INM), Univ Montpellier, Inserm, Montpellier, France
- National Reference Center for Inherited Sensory Diseases, Univ Montpellier, CHU, Montpellier, France
| | - Béatrice Bocquet
- Institute for Neurosciences of Montpellier (INM), Univ Montpellier, Inserm, Montpellier, France
- National Reference Center for Inherited Sensory Diseases, Univ Montpellier, CHU, Montpellier, France
| | - Mireille Cossée
- Molecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
- PhyMedExp, Univ Montpellier, Inserm, CNRS, Montpellier, France
| | - Anne Bergougnoux
- Molecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
- PhyMedExp, Univ Montpellier, Inserm, CNRS, Montpellier, France
| | - Vasiliki Kalatzis
- Institute for Neurosciences of Montpellier (INM), Univ Montpellier, Inserm, Montpellier, France
- National Reference Center for Inherited Sensory Diseases, Univ Montpellier, CHU, Montpellier, France
| | - Anne-Françoise Roux
- Molecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
- Institute for Neurosciences of Montpellier (INM), Univ Montpellier, Inserm, Montpellier, France
- GCS AURAGEN, Lyon, France
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Li X, Jiang Z, Su Y, Wang K, Jiang X, Sun K, Yang Y, Zhou Y, Zhu X, Zhang L. Deletion of Emc1 in photoreceptor cells causes retinal degeneration in mice. FEBS J 2023; 290:4356-4370. [PMID: 37098815 DOI: 10.1111/febs.16807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/30/2023] [Accepted: 04/25/2023] [Indexed: 04/27/2023]
Abstract
The endoplasmic reticulum membrane protein complex (EMC) plays a critical role in the synthesis of multipass membrane proteins. Genetic studies indicated that mutations in EMC1 gene were associated with retinal degeneration diseases; however, the role of EMC1 in photoreceptor has not been confirmed. Here, we show that Emc1 ablation in the photoreceptor cells of mice recapitulated the retinitis pigmentosa phenotypes, including an attenuated scotopic electroretinogram response and the progressive degeneration of rod cells and cone cells. Histopathological examination of tissues from rod-specific Emc1 knockout mice revealed mislocalized rhodopsin and irregularly arranged cone cells at the age of 2 months. Further immunoblotting analysis revealed decreased levels of membrane proteins and endoplasmic reticulum chaperones in 1-month-old rod-specific Emc1 knockout mice retinae, and this led us to speculate that the loss of membrane proteins is the main cause of the degeneration of photoreceptors. EMC1 most likely regulated the membrane protein levels at an earlier step in the biosynthetic process before the proteins translocated into the endoplasmic reticulum. The present study demonstrates the essential roles of Emc1 in photoreceptor cells, and reveals the mechanism through which EMC1 mutations are linked to retinitis pigmentosa.
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Affiliation(s)
- Xiao Li
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Center for Medical Genetics, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhilin Jiang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Center for Medical Genetics, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yujing Su
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Center for Medical Genetics, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Kaifang Wang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Center for Medical Genetics, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaoyan Jiang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Center for Medical Genetics, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Kuanxiang Sun
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Center for Medical Genetics, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yeming Yang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Center for Medical Genetics, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yu Zhou
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Center for Medical Genetics, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xianjun Zhu
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Center for Medical Genetics, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Key Laboratory of Tibetan Medicine Research, Chinese Academy of Sciences and Qinghai Provincial Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China
| | - Lin Zhang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Center for Medical Genetics, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Key Laboratory of Tibetan Medicine Research, Chinese Academy of Sciences and Qinghai Provincial Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China
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3
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Yahya S, Watson CM, Carr I, McKibbin M, Crinnion LA, Taylor M, Bonin H, Fletcher T, El-Asrag ME, Ali M, Toomes C, Inglehearn CF. Long-Read Nanopore Sequencing of RPGR ORF15 is Enhanced Following DNase I Treatment of MinION Flow Cells. Mol Diagn Ther 2023; 27:525-535. [PMID: 37284979 PMCID: PMC10299921 DOI: 10.1007/s40291-023-00656-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2023] [Indexed: 06/08/2023]
Abstract
INTRODUCTION RPGR ORF15 is an exon present almost exclusively in the retinal transcript of RPGR. It is purine-rich, repetitive and notoriously hard to sequence, but is a hotspot for mutations causing X-linked retinitis pigmentosa. METHODS Long-read nanopore sequencing on MinION and Flongle flow cells was used to sequence RPGR ORF15 in genomic DNA from patients with inherited retinal dystrophy. A flow cell wash kit was used on a MinION flow cell to increase yield. Findings were confirmed by PacBio SMRT long-read sequencing. RESULTS We showed that long-read nanopore sequencing successfully reads through a 2 kb PCR-amplified fragment containing ORF15. We generated reads of sufficient quality and cumulative read-depth to detect pathogenic RP-causing variants. However, we observed that this G-rich, repetitive DNA segment rapidly blocks the available pores, resulting in sequence yields less than 5% of the expected output. This limited the extent to which samples could be pooled, increasing cost. We tested the utility of a MinION wash kit containing DNase I to digest DNA fragments remaining on the flow cell, regenerating the pores. Use of the DNase I treatment allowed repeated re-loading, increasing the sequence reads obtained. Our customised workflow was used to screen pooled amplification products from previously unsolved inherited retinal disease (IRD) in patients, identifying two new cases with pathogenic ORF15 variants. DISCUSSION We report the novel finding that long-read nanopore sequencing can read through RPGR-ORF15, a DNA sequence not captured by short-read next-generation sequencing (NGS), but with a more reduced yield. Use of a flow cell wash kit containing DNase I unblocks the pores, allowing reloading of further library aliquots over a 72-h period, increasing yield. The workflow we describe provides a novel solution to the need for a rapid, robust, scalable, cost-effective ORF15 screening protocol.
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Affiliation(s)
- Samar Yahya
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
- Department of Medical Genetics, School of Medicine, King Abdulaziz University, Rabigh, Kingdom of Saudi Arabia
| | - Christopher M Watson
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
- North East and Yorkshire Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, UK
| | - Ian Carr
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
| | - Martin McKibbin
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
- Department of Ophthalmology, St. James's University Hospital, Leeds, UK
| | - Laura A Crinnion
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
| | - Morag Taylor
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
| | - Hope Bonin
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester, UK
| | - Tracy Fletcher
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester, UK
| | - Mohammed E El-Asrag
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
- Department of Zoology, Faculty of Science, Benha University, Banha, Egypt
- Institute of Cancer and Genomic Science, University of Birmingham, Birmingham, UK
| | - Manir Ali
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
| | - Carmel Toomes
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
| | - Chris F Inglehearn
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK.
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Genetic characteristics of suspected retinitis pigmentosa in a cohort of Chinese patients. Gene 2023; 853:147087. [PMID: 36464167 DOI: 10.1016/j.gene.2022.147087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
The study aimed to screen for the causative variants in Chinese patients with suspected retinitis pigmentosa (RP). A cohort of 75 unrelated Chinese patients with a clinical diagnosis of RP and their available family members were enrolled in this study. Genomic DNA of all subjects was extracted and whole-exome sequencing (WES) was applied. Candidate variants were identified, and minigene assays were conducted to evaluate the pathogenicity of novel splicing variants. Totally, the diagnostic yield was 44 % (33/75) and 16 novel variants that had not been reported previously were found. Among the genetically solved 33 cases, 31 patients were identified as carrying causative variants of RP and 2 patients carried pathogenic variants implicated in other retinal diseases. USH2A, CYP4V2, and RPGR were the most common causative genes, accounting for about half of the genetically solved cases. Moreover, minigene assays validated that the novel splicing variants were detrimental. Additionally, 9 patients carried a single deleterious heterozygous variant in 6 genes with autosomal recessive hereditary patterns, and no corresponding copy number variants (CNVs) was detected. The findings of this study revealed the genetic landscape of RP in China and provided guidance for clinicians.
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Appelbaum T, Aguirre GD, Beltran WA. Identification of circular RNAs hosted by the RPGR ORF15 genomic locus. RNA Biol 2023; 20:31-47. [PMID: 36593651 PMCID: PMC9817113 DOI: 10.1080/15476286.2022.2159165] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/23/2022] [Accepted: 12/07/2022] [Indexed: 01/04/2023] Open
Abstract
Mutations in the retina-specific isoform of the gene encoding retinitis pigmentosa GTPase regulator (RPGRorf15) cause X-linked retinitis pigmentosa, a severe and early onset inherited retinal degeneration. The underlying pathogenic mechanisms and variability in disease severity remain to be fully elucidated. The present study examines structural features of the ORF15 exonic region to provide new insights into the disease pathogenesis. Using canine and human RNA samples, we identified several novel RPGR ORF15-like linear RNA transcripts containing cryptic introns (exitrons) within the annotated exon ORF15. Furthermore, using outward-facing primers designed inside exitrons in the ORF15 exonic region, we found many of previously unidentified circular RNAs (circRNAs) that formed via back fusion of linear parts of the RPGRorf15 pre-mRNAs. These circRNAs (resistant to RNAse R treatment) were found in all studied cells and tissues. Notably, some circRNAs were present in cytoplasmic and polysomal RNA fractions. Although certain RPGR circRNAs may be cell type specific, we found some of the same circRNAs expressed in different cell types, suggesting similarities in their biogenesis and functions. Sequence analysis of RPGR circRNAs revealed several remarkable features, including identification of N6-methyladenosine (m6A) consensus sequence motifs and high prevalence of predictive microRNA binding sites pointing to the functional roles of these circRNAs. Our findings also illustrate the presence of non-canonical RPGR circRNA biogenesis pathways independent of the known back splicing mechanism. The obtained data on novel RPGR circRNAs further underline structural complexity of the RPGR ORF15 region and provide a potential molecular basis for the disease phenotypic heterogeneity.
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Affiliation(s)
- Tatyana Appelbaum
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gustavo D. Aguirre
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - William A. Beltran
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Zamani M, Sedighzadeh S, Seifi T, Negahdari S, Zeighami J, Sedaghat A, Shariati G, Galehdari H. Whole-exome sequencing deciphers the genetic profile of visual impairments in patients from Southwest Iran. Mol Genet Genomics 2022; 297:1289-1300. [PMID: 35754085 DOI: 10.1007/s00438-022-01917-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 05/27/2022] [Indexed: 10/17/2022]
Abstract
Genetic ocular diseases are heterogeneous disorders. Recent advances have led to a paradigm shift in the discovery of eye disease-associated genetic variants from linkage and genome-wide association studies to next-generation sequencing-based genome studies. The aim of the current study was to investigate the spectrum of possible vision impairment-related variants in 66 Iranian patients. Whole-exome sequencing (WES) technology followed by bioinformatics analysis, Sanger validation, and co-segregation study were done to find eye disease-causing variants in the patients with vision impairments from Southwest Iran. WES revealed disease-causing variants in 82% of the enrolled cases. WES of understudied cohorts presented an effective strategy for determining pathogenic variants in heterogeneous eye diseases and demonstrated the distribution of causative genetic mutations in Iranian patients. The present data could provide the potential to accelerate genetic screening and a reference for treatment modalities for patients with different types of eye disorders from Southwest Iran.
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Affiliation(s)
- Mina Zamani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.,Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran
| | - Sahar Sedighzadeh
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.,Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran
| | - Tahereh Seifi
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.,Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran
| | - Samira Negahdari
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran.,Legal Medicine Research Center, Legal Medicine Organization, Ahvaz, Iran
| | - Jawaher Zeighami
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran
| | - Alireza Sedaghat
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran.,Diabetes Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Gholamreza Shariati
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran. .,Department of Medical Genetics, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
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Pulido JS, Procopio R, Davila HJ, Bello N, Ku C, Pennesi ME, Yang P, Nagiel A, Mahroo OA, Aleman TS, Salido EM, Reynolds M. Inherited Retinal Disease Panels-Caveat Emptor-Truly Know Your Inherited Retinal Disease Panel. Retina 2022; 42:1-3. [PMID: 34690342 PMCID: PMC8702468 DOI: 10.1097/iae.0000000000003319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Jose S Pulido
- Department of Ophthalmology, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Rebecca Procopio
- Department of Ophthalmology, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Hiram J Davila
- Department of Ophthalmology, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Nicholas Bello
- Department of Ophthalmology, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Cristy Ku
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, Oregon
| | - Mark E Pennesi
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, Oregon
| | - Paul Yang
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, Oregon
| | - Aaron Nagiel
- The Vision Center, Children's Hospital Los Angeles, USC Roski Eye Institute, Keck School of Medicine University of Southern California, Los Angeles, California
| | - Omar A Mahroo
- UCL Institute of Ophthalmology, University College London, London, United Kingdom
- Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
- Department of Ophthalmology, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
- Section of Ophthalmology, King's College London, London, United Kingdom
- Physiology, Development, and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Tomas S Aleman
- Department of Ophthalmology, Scheie Eye Institute at the Perelman Center for Advance Medicine and the Center for Advanced Retinal and Ocular Therapeutics (CAROT), University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- The Children's Hospital of Philadelphia (CHOP), Philadelphia, Pennsylvania
| | - Ezequiel M Salido
- Department of Biochemistry, Ophthalmology, and Visual Sciences, West Virginia University, Morgantown, West Virginia; and
| | - Margaret Reynolds
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, Missouri
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An adaptive method of defining negative mutation status for multi-sample comparison using next-generation sequencing. BMC Med Genomics 2021; 14:32. [PMID: 34856988 PMCID: PMC8638096 DOI: 10.1186/s12920-021-00880-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Multi-sample comparison is commonly used in cancer genomics studies. By using next-generation sequencing (NGS), a mutation's status in a specific sample can be measured by the number of reads supporting mutant or wildtype alleles. When no mutant reads are detected, it could represent either a true negative mutation status or a false negative due to an insufficient number of reads, so-called "coverage". To minimize the chance of false-negative, we should consider the mutation status as "unknown" instead of "negative" when the coverage is inadequately low. There is no established method for determining the coverage threshold between negative and unknown statuses. A common solution is to apply a universal minimum coverage (UMC). However, this method relies on an arbitrarily chosen threshold, and it does not take into account the mutations' relative abundances, which can vary dramatically by the type of mutations. The result could be misclassification between negative and unknown statuses. METHODS We propose an adaptive mutation-specific negative (MSN) method to improve the discrimination between negative and unknown mutation statuses. For a specific mutation, a non-positive sample is compared with every known positive sample to test the null hypothesis that they may contain the same frequency of mutant reads. The non-positive sample can only be claimed as "negative" when this null hypothesis is rejected with all known positive samples; otherwise, the status would be "unknown". RESULTS We first compared the performance of MSN and UMC methods in a simulated dataset containing varying tumor cell fractions. Only the MSN methods appropriately assigned negative statuses for samples with both high- and low-tumor cell fractions. When evaluated on a real dual-platform single-cell sequencing dataset, the MSN method not only provided more accurate assessments of negative statuses but also yielded three times more available data after excluding the "unknown" statuses, compared with the UMC method. CONCLUSIONS We developed a new adaptive method for distinguishing unknown from negative statuses in multi-sample comparison NGS data. The method can provide more accurate negative statuses than the conventional UMC method and generate a remarkably higher amount of available data by reducing unnecessary "unknown" calls.
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9
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Yang J, Zhou L, Ouyang J, Xiao X, Sun W, Li S, Zhang Q. Genotype-Phenotype Analysis of RPGR Variations: Reporting of 62 Chinese Families and a Literature Review. Front Genet 2021; 12:600210. [PMID: 34745198 PMCID: PMC8565807 DOI: 10.3389/fgene.2021.600210] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 04/27/2021] [Indexed: 02/05/2023] Open
Abstract
Purpose RPGR is the most common cause of X-linked retinitis pigmentosa (RP), of which female carriers are also frequently affected. The aim of the current study was to explore the RPGR variation spectrum and associated phenotype based on the data from our lab and previous studies. Methods Variants in RPGR were selected from exome sequencing data of 7,092 probands with different eye conditions. The probands and their available family members underwent comprehensive ocular examinations. Similar data were collected from previous reports through searches in PubMed, Web of Science, and Google Scholar. Systematic analyses of genotypes, phenotypes and their correlations were performed. Results A total of 46 likely pathogenic variants, including nine missense and one in-frame variants in RCC1-like domain and 36 truncation variants, in RPGR were detected in 62 unrelated families in our in-house cohort. In addition, a total of 585 variants, including 491 (83.9%) truncation variants, were identified from the literature. Systematic analysis of variants from our in-house dataset, literature, and gnomAD suggested that most of the pathogenic variants of RPGR were truncation variants while pathogenic missense and in-frame variants were enriched in the RCC1-like domain. Phenotypic variations were present between males and female carriers, including more severe refractive error but better best corrected visual acuity (BCVA) in female carriers than those in males. The male patients showed a significant reduction of BCVA with increase of age and males with exon1-14 variants presented a better BCVA than those with ORF15 variants. For female carriers, the BCVA also showed significant reduction with increase of age, but BCVA in females with exon1-14 variants was not significant difference compared with those with ORF15 variants. Conclusion Most pathogenic variants of RPGR are truncations. Missense and in-frame variants located outside of the RCC1-like domain might be benign and the pathogenicity criteria for these variants should be considered with greater caution. The BCVA and refractive error are different between males and female carriers. Increase of age and location of variants in ORF15 contribute to the reduction of BCVA in males. These results are valuable for understanding genotypes and phenotypes of RPGR.
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Affiliation(s)
- Junxing Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Lin Zhou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiamin Ouyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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10
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Marques JP, Marta A, Geada S, Carvalho AL, Menéres P, Murta J, Saraiva J, Silva R. Clinical/Demographic Functional Testing and Multimodal Imaging Differences between Genetically Solved and Unsolved Retinitis Pigmentosa. Ophthalmologica 2021; 245:134-143. [PMID: 34695833 DOI: 10.1159/000520305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/19/2021] [Indexed: 11/19/2022]
Abstract
INTRODUCTION The purpose of this study was to compare clinical/demographic functional testing and multimodal imaging features between genetically solved and genetically unsolved nonsyndromic retinitis pigmentosa (nsRP) patients. METHODS A cross-sectional study was conducted at an inherited retinal dystrophies reference center. Consecutive patients with nsRP and available genetic testing results performed between 2018 and 2020 were included. Genetic testing was clinically oriented, and variants were classified according to the American College of Medical Genetics and Genomics. Only class IV or V variants were considered disease-causing. Clinical/demographic, functional, and imaging features were compared between genetically unsolved (G1) and genetically solved (G2) patients. RESULTS A total of 175 patients (146 families) were included: 68 patients (59 families) in G1 and 107 patients (87 families) in G2. First symptoms <25 years, consanguinity, evidence for a particular inheritance pattern, and the absence of indicators for phenocopies were significantly more prevalent in G2. No significant differences were observed on best-corrected visual acuity. The visual field index and mean central retinal layer thickness were significantly higher in G1. The frequency of atypical features on multimodal imaging did not differ between groups. CONCLUSION Individual clinical/demographic functional testing and multimodal imaging features should be considered when counseling patients about the probability of identifying disease-causing variants.
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Affiliation(s)
- João Pedro Marques
- Department of Ophthalmology, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal.,Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal.,University Clinic of Ophthalmology, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal
| | - Ana Marta
- Department of Ophthalmology, Centro Hospitalar e Universitário do Porto (CHUP), Porto, Portugal.,Instituto Ciências Biomédicas Abel Salazar (ICBAS), Porto, Portugal
| | - Sara Geada
- Department of Ophthalmology, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
| | - Ana Luísa Carvalho
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal.,Department of Medical Genetics, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal.,University Clinic of Medical Genetics, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal
| | - Pedro Menéres
- Department of Ophthalmology, Centro Hospitalar e Universitário do Porto (CHUP), Porto, Portugal.,Instituto Ciências Biomédicas Abel Salazar (ICBAS), Porto, Portugal
| | - Joaquim Murta
- Department of Ophthalmology, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal.,Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal.,University Clinic of Ophthalmology, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal
| | - Jorge Saraiva
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal.,Department of Medical Genetics, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal.,University Clinic of Pediatrics, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal
| | - Rufino Silva
- Department of Ophthalmology, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal.,Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal.,University Clinic of Ophthalmology, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal
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11
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Beigi F, Del Pozo-Valero M, Martin-Merida I, Manaviat MR, Ayuso C, Ghasemi N. Homozygous females for a X-linked RPGR-ORF15 mutation in an Iranian family with retinitis pigmentosa. Exp Eye Res 2021; 211:108714. [PMID: 34390733 DOI: 10.1016/j.exer.2021.108714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/10/2021] [Accepted: 07/30/2021] [Indexed: 11/17/2022]
Abstract
Mutations in Retinitis pigmentosa GTPase regulator gene (RPGR) are the most common cause of X-linked retinitis pigmentosa (RP). Almost 60% of disease-causing RPGR mutations are located in ORF-15 region which cannot be detected by Next Generation Sequencing (NGS) due to the existence of highly repetitive regions. An Iranian family with a priori diagnosis of autosomal dominant RP was studied by Sanger sequencing of ORF15 of RPGR gene after an inconclusive NGS result. A frameshift two-base-pair deletion (c.2323_2324del, p.Arg775Glufs*59) in this region was segregating in both affected hemizygous males and affected homozygous females. To our knowledge, this is the first example of homozygous females for RPGR-ORF15 mutations.
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Affiliation(s)
- Fahimeh Beigi
- Department of Medical Genetics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Marta Del Pozo-Valero
- Department of Clinical Genetics and Genomics, University Hospital Fundacion Jimenez Diaz, Health Research Institute Fundacion Jimenez Diaz (IIS-FJD, UAM), Madrid, Spain; CIBERER (Biomedical Research Network Centre for Rare Diseases), ISCIII, Madrid, Spain
| | - Inmaculada Martin-Merida
- Department of Clinical Genetics and Genomics, University Hospital Fundacion Jimenez Diaz, Health Research Institute Fundacion Jimenez Diaz (IIS-FJD, UAM), Madrid, Spain; CIBERER (Biomedical Research Network Centre for Rare Diseases), ISCIII, Madrid, Spain
| | - Masoud Reza Manaviat
- Department of Ophthalmology, Shahid Sadoughi University of Medical Science, Yazd Diabetes Research Center, Yazd, Iran
| | - Carmen Ayuso
- Department of Clinical Genetics and Genomics, University Hospital Fundacion Jimenez Diaz, Health Research Institute Fundacion Jimenez Diaz (IIS-FJD, UAM), Madrid, Spain; CIBERER (Biomedical Research Network Centre for Rare Diseases), ISCIII, Madrid, Spain.
| | - Nasrin Ghasemi
- Abortion Research Centre, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
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12
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Shen RJ, Wang JG, Li Y, Jin ZB. Consanguinity-based analysis of exome sequencing yields likely genetic causes in patients with inherited retinal dystrophy. Orphanet J Rare Dis 2021; 16:278. [PMID: 34130719 PMCID: PMC8204521 DOI: 10.1186/s13023-021-01902-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 06/07/2021] [Indexed: 12/11/2022] Open
Abstract
Background Consanguineous families have a relatively high prevalence of genetic disorders caused by bi-allelic mutations in recessive genes. This study aims to evaluate the effectiveness and efficiency of a consanguinity-based exome sequencing approach to capturing genetic mutations in inherited retinal dystrophy families with consanguineous marriages. Methods Ten unrelated consanguineous families with a proband affected by inherited retinal dystrophy were recruited in this study. All participants underwent comprehensive ophthalmic examinations. Whole exome sequencing was performed, followed by a homozygote-prior strategy to rapidly filter disease-causing mutations. Bioinformatic prediction of pathogenicity, Sanger sequencing and co-segregation analysis were carried out for further validation. Results In ten consanguineous families, a total of 10 homozygous mutations in 8 IRD genes were identified, including 2 novel mutations, c.1654_1655delAG (p. R552Afs*5) in gene FAM161A in a patient diagnosed with retinitis pigmentosa, and c.830T > C (p.L277P) in gene CEP78 in a patient diagnosed with cone and rod dystrophy. Conclusion The genetic etiology in consanguineous families with IRD were successfully identified using consanguinity-based analysis of exome sequencing data, suggesting that this approach could provide complementary insights into genetic diagnoses in consanguineous families with variant genetic disorders. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-021-01902-5.
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Affiliation(s)
- Ren-Juan Shen
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China
| | - Jun-Gang Wang
- Department of Ophthalmology, Eye Hospital of Shandong First Medical University, State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Yang Li
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China.
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13
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Zhang H, Su B, Jiao L, Xu ZH, Zhang CJ, Nie J, Gao ML, Zhang YV, Jin ZB. Transplantation of GMP-grade human iPSC-derived retinal pigment epithelial cells in rodent model: the first pre-clinical study for safety and efficacy in China. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:245. [PMID: 33708872 PMCID: PMC7940887 DOI: 10.21037/atm-20-4707] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Background Age-related macular degeneration (AMD) is the leading cause of blindness in the elderly due in large part to age-dependent atrophy of retinal pigment epithelium (RPE) cells. RPE cells form a monolayer located between the choroid and the outer segments of photoreceptors, playing multifarious roles in maintenance of visual function. Allogeneically induced pluripotent stem cell-derived RPE (iPSC-RPE or iRPE) has become a potential approach for providing an abundant source of donors for clinical cell products. Transplantation of iRPE has been proven effective in rescuing impaired retinas in Royal College of Surgeons (RCS) rats after approximately 5 to 6 weeks. Here, we explore the long-term (19 weeks) safety and efficacy of human iRPE cell transplantation in pre-clinical animal models. Methods The expression of human RPE-specific markers in iRPE cells was determined using immunofluorescence staining. For the proliferative test, Ki-67 expression was also verified by immunofluorescence and flow cytometric analysis. Then, iRPE cells were transplanted into the subretinal space of immune-deficient NOD/SCID/IL-2Rgcnull (NSG) mice to assess their safety. To evaluate whether the transplanted cells could survive and rescue visual function, we performed color fundus photography, focal electroretinogram and immunostaining after delivering iRPE cells into the subretinal space of RCS rats. Results Human iRPE cells expressed native RPE-specific markers, such as microphthalmia-associated transcription factor (MiTF), retinal pigment epithelium-specific 65-kDa protein (RPE65) and tight-junction associated structural protein (ZO-1), and their proliferative capacity (Ki-67 expression) was poor after 25 days of induction. A tumorigenicity test revealed no tumor formation or abnormal proliferation in the immunodeficient mice after subretinal injection of 5×105 iRPE cells. The transplanted iRPE cells survived for at least 19 weeks and maintained visual function for 15 weeks. Conclusions In the present study, we provided further evidence for the use of human iRPE transplantation to treat retinal degenerative disease in pre-clinical animal models. Therefore, we consider human iRPE cells a promising source of cell replacement therapy for AMD.
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Affiliation(s)
- Hang Zhang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China.,Laboratory of Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Bingnan Su
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China
| | - Luyan Jiao
- Nuwacell Biotechnologies Co., Ltd, Hefei, China
| | - Ze-Hua Xu
- Laboratory of Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Chang-Jun Zhang
- Laboratory of Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jinfu Nie
- Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Mei-Ling Gao
- Laboratory of Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | | | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Laboratory, Beijing, China.,National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
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14
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Xiao T, Xie Y, Zhang X, Xu K, Zhang X, Jin ZB, Li Y. Variant Profiling of a Large Cohort of 138 Chinese Families With Autosomal Dominant Retinitis Pigmentosa. Front Cell Dev Biol 2021; 8:629994. [PMID: 33598457 PMCID: PMC7882618 DOI: 10.3389/fcell.2020.629994] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
Retinitis pigmentosa (RP) is the most common form of inherited retinal dystrophy, and 15–25% of RP is transmitted as an autosomal dominant (ad) trait. The objectives of this study were to establish the variant profile in a large cohort of adRP families and to elucidate the variant spectrum of each adRP gene in Chinese patients. A total of 138 probands clinically diagnosed with RP as a presumed autosomal dominant trait were recruited. All probands underwent ophthalmic examinations by specialists. A combination of molecular screening methods, including targeted next-generation sequencing, Sanger DNA sequencing, and multiplex ligation probe amplification assay, was used to detect variants. We identified heterozygous variants of 11 adRP genes in 73 probands, hemizygous, or heterozygous variants of X-linked RP genes in six patients, compound heterozygous variants of autosomal recessive RP genes in three pseudodominant families, and one heterozygous variant of one ad cone and rod dystrophy gene in one proband. One proband was found carrying both variants in RPGR and FAM161A. The overall detection rate was 59.4% (82/138). We detected 72 distinct disease-causing variants involving 16 RP genes and one cone-rod dystrophy gene; 33 of these variants have not been reported previously. Disease-causing variants were identified in the adRP genes in 52.9% of the families, followed by 4.3% in the X-linked RP genes, and 2.2% in the autosomal recessive genes. The most frequent mutant genes were RHO, PRPF31, RP1, SNRNP200, and PRPF8, which explained up to 78.0% of the genetically diagnosed families. Most of the variants identified in adRP genes were missense, and copy number variations were common (7/20) in the PRPF31 gene. We established the profile of the mutated genes and the variant spectrum of adRP genes in a large cohort of Chinese patients, providing essential information for genetic counseling and future development of therapeutics for retinal dystrophy inherited as a dominant trait.
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Affiliation(s)
- Ting Xiao
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Yue Xie
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Xin Zhang
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Ke Xu
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Xiaohui Zhang
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Zi-Bing Jin
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Yang Li
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
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15
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Xing D, Zhou H, Yu R, Wang L, Hu L, Li Z, Li X. Targeted exome sequencing identified a novel USH2A mutation in a Chinese usher syndrome family: a case report. BMC Ophthalmol 2020; 20:485. [PMID: 33302902 PMCID: PMC7727220 DOI: 10.1186/s12886-020-01711-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 10/29/2020] [Indexed: 12/14/2022] Open
Abstract
Background Usher syndrome is a disease with a heterogeneous phenotype and genotype. Our purpose was to identify the gene mutation in a Chinese family with Usher syndrome type 2 and describe the clinical features. Case presentation A 23-year-old man complained of a 10-year duration of nyctalopia and a 3-year decline in visual acuity of both eyes accompanied by congenital dysaudia. To clarify the diagnosis, the clinical symptoms were observed and analysed in combination with comprehensive ophthalmologic examinations as well as genetic analysis (targeted exome sequencing, TES). A typical clinical presentation of Usher syndrome of the fundus was found, including a waxy yellow-like disc, bone-spicule formations and retinal vessel stenosis. Optical coherence tomography (OCT) and optical coherence tomography angiography (OCTA) showed loss of the ellipsoid zone and a reduction in paracaval vessel density in both eyes. Genetic analysis identified a novel homozygous c.8483_8486del (p.Ser2828*) mutation in USH2A. The mutation resulted in premature termination of translation and caused the deletion of 19 fibronectin type 3 domains (FN3), transmembrane (TM) region and PDZ-binding motif domain, which play an important role in protein binding. After combining the clinical manifestations and genetic results, the patient was diagnosed with Usher syndrome type 2. Conclusion We found a novel c.8483_8486del mutation in the USH2A gene through TES techniques. The results broaden the spectrum of mutations in Usher syndrome type 2 and suggest that a combination of clinical information and molecular diagnosis via TES could help Usher syndrome patients obtain a better diagnosis. Supplementary Information The online version contains supplementary material available at 10.1186/s12886-020-01711-7.
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Affiliation(s)
- Dongjun Xing
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin International Joint Research and Development Centre of Ophthalmology and Vision Science, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, 251 Fukang Road, Tianjin, 300384, China
| | - Huaiyu Zhou
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin International Joint Research and Development Centre of Ophthalmology and Vision Science, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, 251 Fukang Road, Tianjin, 300384, China
| | - Rongguo Yu
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin International Joint Research and Development Centre of Ophthalmology and Vision Science, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, 251 Fukang Road, Tianjin, 300384, China
| | - Linni Wang
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin International Joint Research and Development Centre of Ophthalmology and Vision Science, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, 251 Fukang Road, Tianjin, 300384, China
| | - Liying Hu
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin International Joint Research and Development Centre of Ophthalmology and Vision Science, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, 251 Fukang Road, Tianjin, 300384, China
| | - Zhiqing Li
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin International Joint Research and Development Centre of Ophthalmology and Vision Science, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, 251 Fukang Road, Tianjin, 300384, China.
| | - Xiaorong Li
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin International Joint Research and Development Centre of Ophthalmology and Vision Science, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, 251 Fukang Road, Tianjin, 300384, China.
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16
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Zou X, Fang S, Wu S, Li H, Sun Z, Zhu T, Wei X, Sui R. Detailed comparison of phenotype between male patients carrying variants in exons 1-14 and ORF15 of RPGR. Exp Eye Res 2020; 198:108147. [PMID: 32702353 DOI: 10.1016/j.exer.2020.108147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/05/2020] [Accepted: 07/08/2020] [Indexed: 12/19/2022]
Abstract
PURPOSE To compare disease severity in detail between patients carrying variants in exons 1-14 and ORF15 of retinitis pigmentosa GTPase regulator (RPGR). METHODS Systematic next-generation sequencing data analysis, Sanger sequencing validation and segregation analysis were utilised to identify the pathogenic variants. Detailed ophthalmic examinations, including electroretinograms, fundus photography, fundus autofluorescence and optical coherence tomography were performed. Statistical analysis, including age adjustment and comparison, were performed based on cross-sectional level to compare disease severity between variants in the two RPGR variant groups. RESULTS Sixty-two variants were identified in RPGR in 86 patients from 77 unrelated families. Twenty-nine (37.7%) had variants in RPGR-exons 1-14 (group 1) and 48 (62.3%) in RPGR-ORF15 (group 2). Eighty-four patients were diagnosed with X-linked retinitis pigmentosa and only two patients with cone-rod dystrophy. LogMAR visual acuity increased 0.035 and 0.022 each year on average in group 1 and group 2, respectively. Group 2 patients had better visual acuity with a mean logMAR difference of 0.4378, which is significant after age adjustment (P < 0.01). Neither the value of log (ellipsoid zone width) nor central retinal thickness was significantly correlated with variant grouping after considering the effect of the age variable (P = 0.56 and 0.40, respectively). Spherical refractive error did not differ significantly between the two variant groups (P = 0.17). Patterns of autofluorescence included a hyperfluorescent ring at the posterior pole, diffuse hyperfluorescence in the macular area, and dark macular autofluorescence with or without fovea hyperfluorescence. The age and proportion of fundus autofluorescence patterns between the two variant groups were significantly different (P < 0.01). CONCLUSIONS Patients with variants in exons 1-14 retained less visual acuity than patients with ORF15 variants and deteriorated faster. However, the ellipsoid zone widths, central retinal thickness and refractions were comparable between the two groups. Autofluorescence pattern relates to the age and the variant grouping.
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Affiliation(s)
- Xuan Zou
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Sha Fang
- School of Statistics, Capital University of Economics and Business, Beijing, 100070, China
| | - Shijing Wu
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Hui Li
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zixi Sun
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Tian Zhu
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xing Wei
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Ruifang Sui
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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17
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Maggi J, Roberts L, Koller S, Rebello G, Berger W, Ramesar R. De Novo Assembly-Based Analysis of RPGR Exon ORF15 in an Indigenous African Cohort Overcomes Limitations of a Standard Next-Generation Sequencing (NGS) Data Analysis Pipeline. Genes (Basel) 2020; 11:genes11070800. [PMID: 32679846 PMCID: PMC7396994 DOI: 10.3390/genes11070800] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 06/24/2020] [Accepted: 07/13/2020] [Indexed: 01/10/2023] Open
Abstract
RPGR exon ORF15 variants are one of the most frequent causes for inherited retinal disorders (IRDs), in particular retinitis pigmentosa. The low sequence complexity of this mutation hotspot makes it prone to indels and challenging for sequence data analysis. Whole-exome sequencing generally fails to provide adequate coverage in this region. Therefore, complementary methods are needed to avoid false positives as well as negative results. In this study, next-generation sequencing (NGS) was used to sequence long-range PCR amplicons for an IRD cohort of African ancestry. By developing a novel secondary analysis pipeline based on de novo assembly, we were able to avoid the miscalling of variants generated by standard NGS analysis tools. We identified pathogenic variants in 11 patients (13% of the cohort), two of which have not been reported previously. We provide a novel and alternative end-to-end secondary analysis pipeline for targeted NGS of ORF15 that is less prone to false positive and negative variant calls.
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Affiliation(s)
- Jordi Maggi
- Institute of Medical Molecular Genetic, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.)
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, 8006 Zurich, Switzerland
| | - Lisa Roberts
- University of Cape Town/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (L.R.); (G.R.); (R.R.)
| | - Samuel Koller
- Institute of Medical Molecular Genetic, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.)
| | - George Rebello
- University of Cape Town/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (L.R.); (G.R.); (R.R.)
| | - Wolfgang Berger
- Institute of Medical Molecular Genetic, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.)
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, 8006 Zurich, Switzerland
- Neuroscience Center Zurich (ZNZ), University and ETH Zurich, 8006 Zurich, Switzerland
- Correspondence:
| | - Rajkumar Ramesar
- University of Cape Town/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa; (L.R.); (G.R.); (R.R.)
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18
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Zhang CJ, Xiang L, Chen XJ, Wang XY, Wu KC, Zhang BW, Chen DF, Jin GH, Zhang H, Chen YC, Liu WQ, Li ML, Ma Y, Jin ZB. Ablation of Mature miR-183 Leads to Retinal Dysfunction in Mice. Invest Ophthalmol Vis Sci 2020; 61:12. [PMID: 32176259 PMCID: PMC7401733 DOI: 10.1167/iovs.61.3.12] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Purpose The microRNA cluster miR-183C, which includes miR-183 and two other genes, is critical for multiple sensory systems. In mouse retina, removal of this cluster results in photoreceptor defects in polarization, phototransduction, and outer segment elongation. However, the individual roles of the three components of this cluster are not clearly known. We studied the separate role of mouse miR-183 in in vivo. Methods miR-183 knockout mice were generated using the CRISPR/Cas9 genome-editing system. Electroretinography were carried out to investigate the changes of retinal structures and function. miR-183 was overexpressed by subretinal adeno-associated virus (AAV) injection in vivo. Rnf217, a target of miR-183 was overexpressed by cell transfection of the photoreceptor-derived cell line 661W in vitro. RNA sequencing and quantitative real-time polymerase chain reaction (qRT-PCR) were performed to compare the gene expression changes in AAV-injected mice and transfected cells. Results The miR-183 knockout mice showed progressively attenuated electroretinogram responses. Over- or under-expression of Rnf217, a direct target of miR-183, misregulated expression of cilia-related BBSome genes. Rnf217 overexpression also led to compromised electroretinography responses in WT mice, indicating that it may contribute to functional abnormalities in miR-183 knockout mice. Conclusions miR-183 is essential for mouse retinal function mediated directly and indirectly through Rnf217 and cilia-related genes. Our findings provide valuable insights into the explanation and analysis of the regulatory role of the individual miR-183 in miR-183C.
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Salmaninejad A, Motaee J, Farjami M, Alimardani M, Esmaeilie A, Pasdar A. Next-generation sequencing and its application in diagnosis of retinitis pigmentosa. Ophthalmic Genet 2020; 40:393-402. [PMID: 31755340 DOI: 10.1080/13816810.2019.1675178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Retinitis Pigmentosa (RP) is a major cause of heritable human blindness with a high genetic heterogeneity. It is characterized by the initial degeneration of rod photoreceptors followed by cone photoreceptors. RP is also a prominent reason of visual impairment, by a global prevalence of 1:4000. RP is usually specified with nyctalopia in puberty, followed by concentric visual field loss, that reflects the main impairment of rod photoreceptors; later in the life, as disease progresses, because of cone dysfunction, central vision loss also occurs. A precise molecular diagnosis is crucial for disease characterization and clinical prognosis. DNA sequencing is a powerful tool for deciphering various causes of different human diseases. The arrival of next-generation sequencing (NGS) technologies has diminished sequencing cost and considerably augmented the throughput, making whole-genome sequencing (WGS) a conceivable way for obtaining comprehensive genomic data and a more precise clinical decision. Nevertheless, the advantages gained from NGS technologies are among a number of challenges that must be sufficiently addressed before this technique can be altered from an investigation tools to a helpful method in routine clinical practices. This article aims to provide an overview about NGS technology and its related platforms. The challenges in the analysis and choosing an appropriate NGS method likewise their potential applications in clinical diagnosis are also discussed. The merit of such technique has been reflected in some recent studies where it is shown that using NGS and molecular information could help with clinical diagnosis, providing potential treatment options or changes, up-to-date family counseling and management.
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Affiliation(s)
- Arash Salmaninejad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jamshid Motaee
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahsa Farjami
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maliheh Alimardani
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Alireza Pasdar
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Bioinformatics Research Group, Mashhad University of Medical Sciences, Mashhad, Iran.,Division of Applied Medicine,Medical School, University of Aberdeen, Foresterhill, Aberdeen, UK
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20
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Xu X, Yang X, Su Z, Wang H, Li X, Sun C, Wang W, Chen Y, Zhang C, Zhang H, Jin F, Zheng J. Identification of Novel Compound Heterozygous Mutations in the GAN Gene of a Chinese Patient Diagnosed With Giant Axonal Neuropathy. Front Neurosci 2020; 14:85. [PMID: 32158379 PMCID: PMC7052293 DOI: 10.3389/fnins.2020.00085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 01/21/2020] [Indexed: 12/24/2022] Open
Abstract
Giant axonal neuropathy (GAN) is a very rare autosomal recessive disorder characterized by abnormally large and dysfunctional neuronal axons. Mutations in the GAN gene have been identified as the cause of this disorder. In this report, we performed a detailed phenotypic assessment of a Chinese patient with GAN. An array-based exon capture test and targeted next-generation sequencing were used to detect the suspected mutation sites. Compound heterozygous mutations of p.S79L (c.236C > T) in the BTB domain and p.T489S (c.1466C > G) in the kelch domain were identified in the proband’s genome. S79L was a known mutation, and T489S was reported for the first time. The p.S79L and p.T489S were confirmed in the proband’s mother and father, respectively. Both mutations were located in highly conserved regions and affected the predicted protein crystal structures. The proband’s sural biopsy revealed the classical GAN phenotype of swollen axons filled with closely packed neurofilaments. The combined application of the next-generation sequencing platform and bioinformatics analyses was an effective method for diagnosing GAN. The novel compound mutations of S79L and T489S in the GAN gene were likely the cause of the patient’s GAN symptoms. Our findings enrich the spectrum of mutations associated with this rare type of axonopathy.
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Affiliation(s)
- Xiaomin Xu
- Wenzhou People's Hospital, Wenzhou Maternal and Child Health Care Hospital, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou, China.,Wenzhou City Key Laboratory of Gynecology and Obstetrics, Wenzhou, China
| | - Xiaokai Yang
- Wenzhou People's Hospital, Wenzhou Maternal and Child Health Care Hospital, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou, China
| | - Zhongliang Su
- Wenzhou People's Hospital, Wenzhou Maternal and Child Health Care Hospital, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou, China
| | - Hai Wang
- Wenzhou People's Hospital, Wenzhou Maternal and Child Health Care Hospital, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou, China.,Wenzhou City Key Laboratory of Gynecology and Obstetrics, Wenzhou, China
| | - Xiaoqing Li
- Wenzhou People's Hospital, Wenzhou Maternal and Child Health Care Hospital, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou, China.,Wenzhou City Key Laboratory of Gynecology and Obstetrics, Wenzhou, China
| | - Congcong Sun
- Wenzhou People's Hospital, Wenzhou Maternal and Child Health Care Hospital, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou, China.,Wenzhou City Key Laboratory of Gynecology and Obstetrics, Wenzhou, China
| | - Wenhuan Wang
- Wenzhou People's Hospital, Wenzhou Maternal and Child Health Care Hospital, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou, China.,Wenzhou City Key Laboratory of Gynecology and Obstetrics, Wenzhou, China
| | - Yao Chen
- Hangzhou Fuyang Women and Children Hospital, Fuyang, China
| | - Chenhui Zhang
- Wenzhou People's Hospital, Wenzhou Maternal and Child Health Care Hospital, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou, China.,Wenzhou City Key Laboratory of Gynecology and Obstetrics, Wenzhou, China
| | - Hongping Zhang
- Wenzhou People's Hospital, Wenzhou Maternal and Child Health Care Hospital, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou, China
| | - Fan Jin
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jiayong Zheng
- Wenzhou People's Hospital, Wenzhou Maternal and Child Health Care Hospital, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou, China.,Wenzhou City Key Laboratory of Gynecology and Obstetrics, Wenzhou, China
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21
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Xia X, Jin J, Chen ZJ, Zhou Z, Chen H, Zhang C, Zhang L, Sun L. Unraveling the genetic causes in large pedigrees with gout by whole‑exome sequencing. Int J Mol Med 2020; 45:1047-1058. [PMID: 32124961 PMCID: PMC7053847 DOI: 10.3892/ijmm.2020.4501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/08/2020] [Indexed: 11/06/2022] Open
Abstract
Gout is a common type of inflammatory arthritis that is clinically and genetically heterogeneous. The genetic aetiology remains unclear, and mainly relies on previous genome-wide association studies focused on sporadic cases. The present study aimed to identify the genetic basis of gout in three families using whole-exome sequencing (WES). WES was performed in the probands, and family members were involved in the co-segregation analysis. In total, three deleterious rare or novel missense mutations were identified in ATP-binding cassette super-family G member 2 (ABCG2), protein kinase CGMP-dependent 2 (PRKG2) and adrenoceptor β3 (ADRB3) genes in three different families. In addition, certain gout-associated candidate genes were revealed to be shared among the co-expression and protein-protein interaction (PPI) networks of ABCG2, PRKG2 and ADRB3. Furthermore, the disease ontology analysis of the genes present in the co-expression network exhibited significant (P<0.05) enrichment in hyperuricemia, gout, cardiovascular system disease and metabolic disease. In addition, genes involved in the PPI network were significantly enriched in the purine nucleoside monophosphate biosynthetic process, urate transport and biological processes associated with glycose metabolism. Collectively, to the best of our knowledge, the present study was the first to use WES to identify three candidate rare or novel deleterious mutations in three families with gout. The present results provided novel insights that may improve the current understanding of the molecular genetic basis underlying gout. Importantly, the present results may facilitate the improvement of clinical diagnosis and the development of novel personalized therapies.
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Affiliation(s)
- Xiaoru Xia
- Department of Rheumatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325003, P.R. China
| | - Jing Jin
- Zhejiang Center for Clinical Laboratory, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P.R. China
| | - Zhen-Ji Chen
- Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Zhenni Zhou
- Department of Internal Medicine, Yueqing People's Hospital, Yueqing, Wenzhou, Zhejiang 325600, P.R. China
| | - Hui Chen
- Department of Nephrology, Wenzhou Central Hospital, Wenzhou, Zhejiang 325000, P.R. China
| | - Chunwu Zhang
- Department of Injury Orthopaedics, The First Affiliated Hospital of Wenzhou University, Wenzhou, Zhejiang 325023, P.R. China
| | - Linhua Zhang
- Department of Clinical Laboratory, Yuhuan People's Hospital, Taizhou, Zhejiang 317600, P.R. China
| | - Li Sun
- Department of Rheumatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325003, P.R. China
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22
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Whole-Exome Sequencing Reveals a Rare Missense Variant in SLC16A9 in a Pedigree with Early-Onset Gout. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4321419. [PMID: 32090094 PMCID: PMC7013288 DOI: 10.1155/2020/4321419] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 12/28/2019] [Accepted: 01/10/2020] [Indexed: 02/06/2023]
Abstract
Gout is a common inflammatory arthritis triggered by monosodium urate deposition after longstanding hyperuricemia. In the general community, the disease is largely polygenic in genetic architecture, with many polymorphisms having been identified in gout or urate-associated traits. In a small proportion of cases, rare high penetrant mutations associated with monogenic segregation of the disease in families have been demonstrated to be disease causative. In this study, we recruited a two-generation pedigree with early-onset gout. To elucidate the genetic predisposition, whole-exome sequencing (WES) was performed. After comprehensive variant analyses and cosegregation testing, we identified a missense variant (c.277C>A, p.L93M) in SLC16A9, an extremely rare variant in genetic databases. Moreover, in silico assessments showed strong pathogenicity. This variant cosegregated with the disease phenotype perfectly in the family and is located in a highly conserved functional domain. A few studies supported our results of the association between SLC16A9 and gout and serum urate levels. In conclusion, we provide the first evidence for the association of rare missense in SLC16A9 with early-onset gout. These findings not only expand our current understanding of gout but also may have further implications for the treatment and prevention of gout.
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23
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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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24
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Dan H, Huang X, Xing Y, Shen Y. Application of targeted panel sequencing and whole exome sequencing for 76 Chinese families with retinitis pigmentosa. Mol Genet Genomic Med 2020; 8:e1131. [PMID: 31960602 PMCID: PMC7057118 DOI: 10.1002/mgg3.1131] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 11/28/2019] [Accepted: 01/06/2020] [Indexed: 12/21/2022] Open
Abstract
Background This study aimed to identify the gene variants and molecular etiologies in 76 unrelated Chinese families with retinitis pigmentosa (RP). Methods In total, 76 families with syndromic or nonsyndromic RP, diagnosed on the basis of clinical manifestations, were recruited for this study. Genomic DNA samples from probands were analyzed by targeted panels or whole exome sequencing. Bioinformatics analysis, Sanger sequencing, and available family member segregation were used to validate sequencing data and confirm the identities of disease‐causing genes. Results The participants enrolled in the study included 62 families that exhibited nonsyndromic RP, 13 that exhibited Usher syndrome, and one that exhibited Bardet–Biedl syndrome. We found that 43 families (56.6%) had disease‐causing variants in 15 genes, including RHO, PRPF31, USH2A, CLRN1, BBS2, CYP4V2, EYS, RPE65, CNGA1, CNGB1, PDE6B, MERTK, RP1, RP2, and RPGR; moreover, 12 families (15.8%) had only one heterozygous variant in seven autosomal recessive RP genes, including USH2A, EYS, CLRN1, CERKL, RP1, CRB1, and SLC7A14. We did not detect any variants in the remaining 21 families (27.6%). We also identified 67 potential pathogenic gene variants, of which 24 were novel. Conclusion The gene variants identified in this study expand the variant frequency and spectrum of RP genes; moreover, the identification of these variants supplies foundational clues for future RP diagnosis and therapy.
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Affiliation(s)
- Handong Dan
- Eye Center, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xin Huang
- Eye Center, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yiqiao Xing
- Eye Center, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yin Shen
- Eye Center, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
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25
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Zenteno JC, García-Montaño LA, Cruz-Aguilar M, Ronquillo J, Rodas-Serrano A, Aguilar-Castul L, Matsui R, Vencedor-Meraz CI, Arce-González R, Graue-Wiechers F, Gutiérrez-Paz M, Urrea-Victoria T, de Dios Cuadras U, Chacón-Camacho OF. Extensive genic and allelic heterogeneity underlying inherited retinal dystrophies in Mexican patients molecularly analyzed by next-generation sequencing. Mol Genet Genomic Med 2019; 8. [PMID: 31736247 PMCID: PMC6978239 DOI: 10.1002/mgg3.1044] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 10/23/2019] [Indexed: 12/27/2022] Open
Abstract
Background Retinal dystrophies (RDs) are one of the most genetically heterogeneous monogenic disorders with ~270 associated loci identified by early 2019. The recent application of next‐generation sequencing (NGS) has greatly improved the molecular diagnosis of RD patients. Genetic characterization of RD cohorts from different ethnic groups is justified, as it would improve the knowledge of molecular basis of the disease. Here, we present the results of genetic analysis in a large cohort of 143 unrelated Mexican subjects with a variety of RDs. Methods A targeted NGS approach covering 199 RD genes was employed for molecular screening of 143 unrelated patients. In addition to probands, 258 relatives were genotyped by Sanger sequencing for familial segregation of pathogenic variants. Results A solving rate of 66% (95/143) was achieved, with evidence of extensive loci (44 genes) and allelic (110 pathogenic variants) heterogeneity. Forty‐eight percent of the identified pathogenic variants were novel while ABCA4, CRB1, USH2A, and RPE65 carried the greatest number of alterations. Novel deleterious variants in IDH3B and ARL6 were identified, supporting their involvement in RD. Familial segregation of causal variants allowed the recognition of 124 autosomal or X‐linked carriers. Conclusion Our results illustrate the utility of NGS for genetic diagnosis of RDs of different populations for a better knowledge of the mutational landscape associated with the disease.
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Affiliation(s)
- Juan C Zenteno
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico.,Department of Biochemistry, Faculty of Medicine, UNAM, Mexico City, Mexico
| | | | - Marisa Cruz-Aguilar
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | - Josué Ronquillo
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | - Agustín Rodas-Serrano
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | | | - Rodrigo Matsui
- Department of Retina, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | | | - Rocío Arce-González
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | | | - Mario Gutiérrez-Paz
- Department of Retina, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | - Tatiana Urrea-Victoria
- Department of Retina, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | - Ulises de Dios Cuadras
- Department of Retina, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | - Oscar F Chacón-Camacho
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
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26
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Huang XF, Xiang L, Fang XL, Liu WQ, Zhuang YY, Chen ZJ, Shen RJ, Cheng W, Han RY, Zheng SS, Chen XJ, Liu X, Jin ZB. Functional characterization of CEP250 variant identified in nonsyndromic retinitis pigmentosa. Hum Mutat 2019; 40:1039-1045. [PMID: 30998843 DOI: 10.1002/humu.23759] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 03/16/2019] [Accepted: 04/02/2019] [Indexed: 12/29/2022]
Abstract
Retinitis pigmentosa (RP) is the most common manifestation of inherited retinal diseases with high degree of genetic, allelic, and phenotypic heterogeneity. CEP250 encodes the C-Nap1 protein and has been associated with various retinal phenotypes. Here, we report the identification of a mutation (c.562C>T, p.R188*) in the CEP250 in a consanguineous family with nonsyndromic RP. To gain insights into the molecular pathomechanism underlying CEP250 defects and the functional relevance of CEP250 variants in humans, we conducted a functional characterization of CEP250 variant using a novel Cep250 knockin mouse line. Remarkably, the disruption of Cep250 resulted in severe impairment of retinal function and significant retinal morphological alterations. The homozygous knockin mice showed significantly reduced retinal thickness and ERG responses. This study not only broadens the spectrum of phenotypes associated with CEP250 mutations, but also, for the first time, elucidates the function of CEP250 in photoreceptors using a newly established animal model.
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Affiliation(s)
- Xiu-Feng Huang
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Lue Xiang
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Xiao-Long Fang
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Wei-Qin Liu
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - You-Yuan Zhuang
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Zhen-Ji Chen
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Ren-Juan Shen
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Wan Cheng
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Ru-Yi Han
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Si-Si Zheng
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Xue-Jiao Chen
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Xiaoling Liu
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
- Department of Medical Retina, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Zi-Bing Jin
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
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Wan A, Place E, Pierce EA, Comander J. Characterizing variants of unknown significance in rhodopsin: A functional genomics approach. Hum Mutat 2019; 40:1127-1144. [PMID: 30977563 PMCID: PMC7027811 DOI: 10.1002/humu.23762] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 03/31/2019] [Accepted: 04/08/2019] [Indexed: 01/19/2023]
Abstract
Characterizing the pathogenicity of DNA sequence variants of unknown significance (VUS) is a major bottleneck in human genetics, and is increasingly important in determining which patients with inherited retinal diseases could benefit from gene therapy. A library of 210 rhodopsin (RHO) variants from literature and in‐house genetic diagnostic testing were created to efficiently detect pathogenic RHO variants that fail to express on the cell surface. This study, while focused on RHO, demonstrates a streamlined, generalizable method for detecting pathogenic VUS. A relatively simple next‐generation sequencing‐based readout was developed so that a flow cytometry‐based assay could be performed simultaneously on all variants in a pooled format, without the need for barcodes or viral transduction. The resulting dataset characterized the surface expression of every RHO library variant with a high degree of reproducibility (r2 = 0.92–0.95), recategorizing 37 variants. For example, three retinitis pigmentosa pedigrees were solved by identifying VUS which showed low expression levels (p.G18D, p.G101V, and p.P180T). Results were validated across multiple assays and correlated with clinical disease severity. This study presents a parallelized, higher‐throughput cell‐based assay for the functional characterization of VUS in RHO, and can be applied more broadly to other inherited retinal disease genes and other disorders.
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Affiliation(s)
- Aliete Wan
- Department of Ophthalmology, Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts
| | - Emily Place
- Department of Ophthalmology, Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts
| | - Eric A Pierce
- Department of Ophthalmology, Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts
| | - Jason Comander
- Department of Ophthalmology, Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts
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Guo LY, Zheng SL, Li J, Zhu Q, Duan WH, Zhang Y, Zhu YT, Hu M. Phenotypic variability of SLC7A14 mutations in patients with inherited retinal dystrophy. Ophthalmic Genet 2019; 40:118-123. [PMID: 30924391 DOI: 10.1080/13816810.2019.1586964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
BACKGROUND Inherited retinal dystrophy (IRD) is a group of retinal disorders that are both clinically and genetically diverse, typically with loss of photoreceptor function. Herein, we aimed to identify the underlying genetic defect in IRD patients with mutations in the SLC7A14 gene. METHODS A targeted exome capture panel was applied for mutational screening of SLC7A14. Targeted exome sequencing (TES) was performed on 200 non-syndromic and unrelated autosomal recessive or sporadic IRD families. Candidate variants were validated by direct sequencing and further examined using bioinformatics analyses for determination of their potential effect. RESULTS We identified compound heterozygous missense mutations (c.988G>A, p.G330R; c.1970G>A, p.R657Q) in an autosomal recessive retinitis pigmentosa (RP) case and a homozygous mutation (c.988G>A, p.G330R) in a simplex case with Leber congenital amaurosis (LCA) in the SLC7A14 gene. Both G330R and R657Q were deleterious based on in silico predictive tools. Our proposed topological model of the SLC7A14 polypeptide suggested that both G330R and R657Q affected evolutionarily highly conserved amino acid residues in SLC7A14 that occurred in transmembrane helixes. Structural modeling revealed a broken arginine and aspartic acid connection between residues 657 and 406. CONCLUSIONS We applied TES to the molecular diagnosis of patients with IRD and for the first time identified SLC7A14 mutations in two unrelated families with RP and LCA separately. Our findings uniquely add the knowledge of the phenotypic variability of SLC7A14 mutations.
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Affiliation(s)
- Li-Yun Guo
- a Department of Ophthalmology, the Second People's Hospital of Yunnan Province , Kunming , China.,b Key Laboratory of Yunnan Province for the Prevention and Treatment of ophthalmology , Kunming , China.,c Department of Ophthalmology , Fourth Affiliated Hospital of Kunming Medical University , Kunming , China
| | - Sui-Lian Zheng
- d Department of Ophthalmology, the Second Affiliated Hospital , Wenzhou Medical University , Wenzhou , China
| | - Jun Li
- a Department of Ophthalmology, the Second People's Hospital of Yunnan Province , Kunming , China.,b Key Laboratory of Yunnan Province for the Prevention and Treatment of ophthalmology , Kunming , China.,c Department of Ophthalmology , Fourth Affiliated Hospital of Kunming Medical University , Kunming , China
| | - Qin Zhu
- a Department of Ophthalmology, the Second People's Hospital of Yunnan Province , Kunming , China.,b Key Laboratory of Yunnan Province for the Prevention and Treatment of ophthalmology , Kunming , China.,c Department of Ophthalmology , Fourth Affiliated Hospital of Kunming Medical University , Kunming , China
| | - Wen-Hua Duan
- a Department of Ophthalmology, the Second People's Hospital of Yunnan Province , Kunming , China.,b Key Laboratory of Yunnan Province for the Prevention and Treatment of ophthalmology , Kunming , China.,c Department of Ophthalmology , Fourth Affiliated Hospital of Kunming Medical University , Kunming , China
| | - Yuan Zhang
- e Research and Development Department , Tissue Tech, Inc , Miami , FL , USA
| | - Ying-Ting Zhu
- e Research and Development Department , Tissue Tech, Inc , Miami , FL , USA
| | - Min Hu
- a Department of Ophthalmology, the Second People's Hospital of Yunnan Province , Kunming , China.,b Key Laboratory of Yunnan Province for the Prevention and Treatment of ophthalmology , Kunming , China.,c Department of Ophthalmology , Fourth Affiliated Hospital of Kunming Medical University , Kunming , China
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Identification of a Disease-Causing Mutation in a Chinese Patient with Retinitis Pigmentosa by Targeted Next-Generation Sequencing. Eur J Ophthalmol 2018; 27:791-796. [PMID: 28430325 DOI: 10.5301/ejo.5000971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
PURPOSE To identify disease-causing mutations in a Chinese patient with retinitis pigmentosa (RP). METHODS A detailed clinical examination was performed on the proband. Targeted next-generation sequencing (NGS) combined with bioinformatics analysis was performed on the proband to detect candidate disease-causing mutations. Sanger sequencing was performed on all subjects to confirm the candidate mutations and assess cosegregation within the family. RESULTS Clinical examinations of the proband showed typical characteristics of RP. Three candidate heterozygous mutations in 3 genes associated with RP were detected in the proband by targeted NGS. The 3 mutations were confirmed by Sanger sequencing and the deletion (c.357_358delAA) in PRPF31 was shown to cosegregate with RP phenotype in 7 affected family members, but not in 3 unaffected family members. CONCLUSIONS The deletion (c.357_358delAA) in PRPF31 was the disease-causing mutation for the proband and his affected family members with RP. To our knowledge, this is the second report of the deletion and the first report of the other 2 mutations in the Chinese population. Targeted NGS combined with bioinformatics analysis proved to be an effective molecular diagnostic tool for RP.
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30
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Lessons learned from the DFNA37 gene discovery odyssey. Genet Med 2018; 21:1481-1482. [DOI: 10.1038/s41436-018-0395-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/20/2018] [Indexed: 01/23/2023] Open
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31
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Jin ZB, Gao ML, Deng WL, Wu KC, Sugita S, Mandai M, Takahashi M. Stemming retinal regeneration with pluripotent stem cells. Prog Retin Eye Res 2018; 69:38-56. [PMID: 30419340 DOI: 10.1016/j.preteyeres.2018.11.003] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 08/09/2018] [Accepted: 11/07/2018] [Indexed: 12/18/2022]
Abstract
Cell replacement therapy is a promising treatment for irreversible retinal cell death in diverse diseases, such as age-related macular degeneration (AMD), Stargardt's disease, retinitis pigmentosa (RP) and glaucoma. These diseases are all characterized by the degeneration of one or two retinal cell types that cannot regenerate spontaneously in humans. Aberrant retinal pigment epithelial (RPE) cells can be observed through optical coherence tomography (OCT) in AMD patients. In RP patients, the morphological and functional abnormalities of RPE and photoreceptor layers are caused by a genetic abnormality. Stargardt's disease or juvenile macular degeneration, which is characterized by the loss of the RPE and photoreceptors in the macular area, causes central vision loss at an early age. Loss of retinal ganglion cells (RGCs) can be observed in patients with glaucoma. Once the retinal cell degeneration is triggered, no treatments can reverse it. Transplantation-based approaches have been proposed as a universal therapy to target patients with various concomitant diseases. Both the replacement of dead cells and neuroprotection are strategies used to rescue visual function in animal models of retinal degeneration. Diverse retinal cell types derived from pluripotent stem cells, including RPE cells, photoreceptors, RGCs and even retinal organoids with a layered structure, provide unlimited cell sources for transplantation. In addition, mesenchymal stem cells (MSCs) are multifunctional and protect degenerating retinal cells. The aim of this review is to summarize current findings from preclinical and clinical studies. We begin with a brief introduction to retinal degenerative diseases and cell death in diverse diseases, followed by methods for retinal cell generation. Preclinical and clinical studies are discussed, and future concerns about efficacy, safety and immunorejection are also addressed.
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Affiliation(s)
- Zi-Bing Jin
- Laboratory for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, State Key Laboratory for Ophthalmology, Optometry & Visual Science, National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou, 325027, China.
| | - Mei-Ling Gao
- Laboratory for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, State Key Laboratory for Ophthalmology, Optometry & Visual Science, National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou, 325027, China
| | - Wen-Li Deng
- Laboratory for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, State Key Laboratory for Ophthalmology, Optometry & Visual Science, National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou, 325027, China
| | - Kun-Chao Wu
- Laboratory for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, State Key Laboratory for Ophthalmology, Optometry & Visual Science, National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou, 325027, China
| | - Sunao Sugita
- Laboratory for Retinal Regeneration, RIKEN Center for Developmental Biology, Kobe, Hyogo, 650-0047, Japan
| | - Michiko Mandai
- Laboratory for Retinal Regeneration, RIKEN Center for Developmental Biology, Kobe, Hyogo, 650-0047, Japan
| | - Masayo Takahashi
- Laboratory for Retinal Regeneration, RIKEN Center for Developmental Biology, Kobe, Hyogo, 650-0047, Japan
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32
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Motta FL, Martin RP, Filippelli-Silva R, Salles MV, Sallum JMF. Relative frequency of inherited retinal dystrophies in Brazil. Sci Rep 2018; 8:15939. [PMID: 30374144 PMCID: PMC6206004 DOI: 10.1038/s41598-018-34380-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/15/2018] [Indexed: 11/09/2022] Open
Abstract
Among the Brazilian population, the frequency rates of inherited retinal dystrophies and their causative genes are underreported. To increase the knowledge about these dystrophies in our population, we retrospectively studied the medical records of 1,246 Brazilian patients with hereditary retinopathies during 20 years of specialized outpatient clinic care. Of these patients, 559 had undergone at least one genetic test. In this cohort, the most prevalent dystrophies were non-syndromic retinitis pigmentosa (35%), Stargardt disease (21%), Leber congenital amaurosis (9%), and syndromic inherited retinal dystrophies (12%). Most patients had never undergone genetic testing (55%), and among the individuals with molecular test results, 28.4% had negative or inconclusive results compared to 71.6% with a conclusive molecular diagnosis. ABCA4 was the most frequent disease-causing gene, accounting for 20% of the positive cases. Pathogenic variants also occurred frequently in the CEP290, USH2A, CRB1, RPGR, and CHM genes. The relative frequency rates of different inherited retinal dystrophies in Brazil are similar to those found globally. Although mutations in more than 250 genes lead to hereditary retinopathies, only 66 genes were responsible for 70% of the cases, which indicated that smaller and cheaper gene panels can be just as effective and provide more affordable solutions for implementation by the Brazilian public health system.
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Affiliation(s)
- Fabiana Louise Motta
- Department of Ophthalmology, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Renan Paulo Martin
- Department of Biophysics, Universidade Federal de São Paulo, São Paulo, Brazil.,Institute of Genetic Medicine, Johns Hopkins Medicine, Baltimore, USA
| | | | | | - Juliana Maria Ferraz Sallum
- Department of Ophthalmology, Universidade Federal de São Paulo, São Paulo, Brazil. .,Instituto de Genética Ocular, Sao Paulo, Brazil.
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Nandakumar P, Morrison AC, Grove ML, Boerwinkle E, Chakravarti A. Contributions of rare coding variants in hypotension syndrome genes to population blood pressure variation. Medicine (Baltimore) 2018; 97:e11865. [PMID: 30113482 PMCID: PMC6113003 DOI: 10.1097/md.0000000000011865] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Rare variants, in particular renal salt handling genes, contribute to monogenic forms of hypertension and hypotension syndromes with electrolyte abnormalities. A study by Ji et al (2008) demonstrated this effect for rare loss-of-function coding variants in SLC12A3 (NCCT), SLC12A1 (NKCC2), and KCNJ1 (ROMK) that led to reduction of ∼6 mm Hg for SBP and ∼3 mm Hg for DBP among carriers in 2492 European ancestry Framingham Heart Study (FHS) subjects. These findings support a potentially large role for these variants in interindividual variation in systolic and diastolic blood pressure (SBP, DBP) in the population. The present study focuses on replicating the analyses completed by Ji et al to identify effects of rare variants in the population-based Atherosclerosis Risk in Communities (ARIC) study.We attempted to replicate the findings by Ji et al by applying their criteria to identify putative loss-of-function variants with allele frequency <0.001 and complete conservation across a set of orthologs, to exome sequencing data from 7444 European ancestry participants of the ARIC study.Although we failed to replicate the previous findings when applying their methods to the ARIC study data, we observed a similar effect when we restricted analyses to the subset of variants they observed.These results simultaneously support the utility of exome sequencing data for studying extremely rare coding variants in hypertension and underscore the need for improved filtering methods for identifying functional variants in human sequences.
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Affiliation(s)
- Priyanka Nandakumar
- Center for Complex Disease Genomics Predoctoral Training Program in Human Genetics and Molecular Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD Human Genome Sequencing Center, Baylor College of Medicine Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX. Center for Human Genetics and Genomics, NYU School of Medicine, New York, NY
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Mutation of IPO13 causes recessive ocular coloboma, microphthalmia, and cataract. Exp Mol Med 2018; 50:1-11. [PMID: 29700284 PMCID: PMC5938035 DOI: 10.1038/s12276-018-0079-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/22/2018] [Accepted: 02/14/2018] [Indexed: 11/12/2022] Open
Abstract
Ocular coloboma is a developmental structural defect of the eye that often occurs as complex ocular anomalies. However, its genetic etiology remains largely unexplored. Here we report the identification of mutation (c.331C>T, p.R111C) in the IPO13 gene in a consanguineous family with ocular coloboma, microphthalmia, and cataract by a combination of whole-exome sequencing and homozygosity mapping. IPO13 encodes an importin-B family protein and has been proven to be associated with the pathogenesis of coloboma and microphthalmia. We found that Ipo13 was expressed in the cornea, sclera, lens, and retina in mice. Additionally, the mRNA expression level of Ipo13 decreased significantly in the patient compared with its expression in a healthy individual. Morpholino-oligonucleotide-induced knockdown of ipo13 in zebrafish caused dose-dependent microphthalmia and coloboma, which is highly similar to the ocular phenotypes in the patient. Moreover, both visual motor response and optokinetic response were impaired severely. Notably, these ocular phenotypes in ipo13-deficient zebrafish could be rescued remarkably by full-length ipo13 mRNA, suggesting that the phenotypes observed in zebrafish were due to insufficient ipo13 function. Altogether, our findings demonstrate, for the first time, a new role of IPO13 in eye morphogenesis and that loss of function of IPO13 could lead to ocular coloboma, microphthalmia, and cataract in humans and zebrafish. In-depth genomic analysis of the family of a young man with severe visual impairment reveals a new gene involved in eye development. Ocular coloboma encompasses various hereditary disorders in which the eyes form improperly. Many of the underlying genetic factors remain unidentified. Researchers led by Zi-Bing Jin at Wenzhou Medical University in China sequenced the genes of 28-year-old man with a recessive form of ocular coloboma. By comparing these genetic data against equivalent genome sequences from his healthy parents, Jin’s team identified a gene called IPO13 as the culprit. IPO13 has not been linked to human disease before, but the researchers demonstrated that switching off IPO13 expression in zebrafish embryos gave rise to underdeveloped eyes with defects in the iris and cornea. These findings give clinicians another potential indicator for early diagnosis of ocular coloboma.
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Mahamdallie S, Ruark E, Yost S, Münz M, Renwick A, Poyastro-Pearson E, Strydom A, Seal S, Rahman N. The Quality Sequencing Minimum (QSM): providing comprehensive, consistent, transparent next generation sequencing data quality assurance. Wellcome Open Res 2018; 3:37. [PMID: 29992192 PMCID: PMC6020721 DOI: 10.12688/wellcomeopenres.14307.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2018] [Indexed: 11/20/2022] Open
Abstract
Next generation sequencing (NGS) is routinely used in clinical genetic testing. Quality management of NGS testing is essential to ensure performance is consistently and rigorously evaluated. Three primary metrics are used in NGS quality evaluation: depth of coverage, base quality and mapping quality. To provide consistency and transparency in the utilisation of these metrics we present the Quality Sequencing Minimum (QSM). The QSM defines the minimum quality requirement a laboratory has selected for depth of coverage (C), base quality (B) and mapping quality (M) and can be applied per base, exon, gene or other genomic region, as appropriate. The QSM format is CX_BY(P
Y)_MZ(P
Z). X is the parameter threshold for C, Y the parameter threshold for B, P
Y the percentage of reads that must reach Y, Z the parameter threshold for M, P
Z the percentage of reads that must reach Z. The data underlying the QSM is in the BAM file, so a QSM can be easily and automatically calculated in any NGS pipeline. We used the QSM to optimise cancer predisposition gene testing using the TruSight Cancer Panel (TSCP). We set the QSM as C50_B10(85)_M20(95). Test regions falling below the QSM were automatically flagged for review, with 100/1471 test regions QSM-flagged in multiple individuals. Supplementing these regions with 132 additional probes improved performance in 85/100. We also used the QSM to optimise testing of genes with pseudogenes such as
PTEN and
PMS2. In TSCP data from 960 individuals the median number of regions that passed QSM per sample was 1429 (97%). Importantly, the QSM can be used at an individual report level to provide succinct, comprehensive quality assurance information about individual test performance. We believe many laboratories would find the QSM useful. Furthermore, widespread adoption of the QSM would facilitate consistent, transparent reporting of genetic test performance by different laboratories.
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Affiliation(s)
- Shazia Mahamdallie
- Division of Genetics & Epidemiology , The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Elise Ruark
- Division of Genetics & Epidemiology , The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Shawn Yost
- Division of Genetics & Epidemiology , The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Márton Münz
- Division of Genetics & Epidemiology , The Institute of Cancer Research, London, SM2 5NG, UK
| | - Anthony Renwick
- Division of Genetics & Epidemiology , The Institute of Cancer Research, London, SM2 5NG, UK
| | - Emma Poyastro-Pearson
- Division of Genetics & Epidemiology , The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Ann Strydom
- Division of Genetics & Epidemiology , The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Sheila Seal
- Division of Genetics & Epidemiology , The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Nazneen Rahman
- Division of Genetics & Epidemiology , The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK.,Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, SM2 5PT, UK
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Münz M, Mahamdallie S, Yost S, Rimmer A, Poyastro-Pearson E, Strydom A, Seal S, Ruark E, Rahman N. CoverView: a sequence quality evaluation tool for next generation sequencing data. Wellcome Open Res 2018; 3:36. [PMID: 29881786 PMCID: PMC5964631 DOI: 10.12688/wellcomeopenres.14306.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2018] [Indexed: 01/05/2023] Open
Abstract
Quality assurance and quality control are essential for robust next generation sequencing (NGS). Here we present CoverView, a fast, flexible, user-friendly quality evaluation tool for NGS data. CoverView processes mapped sequencing reads and user-specified regions to report depth of coverage, base and mapping quality metrics with increasing levels of detail from a chromosome-level summary to per-base profiles. CoverView can flag regions that do not fulfil user-specified quality requirements, allowing suboptimal data to be systematically and automatically presented for review. It also provides an interactive graphical user interface (GUI) that can be opened in a web browser and allows intuitive exploration of results. We have integrated CoverView into our accredited clinical cancer predisposition gene testing laboratory that uses the TruSight Cancer Panel (TSCP). CoverView has been invaluable for optimisation and quality control of our testing pipeline, providing transparent, consistent quality metric information and automatic flagging of regions that fall below quality thresholds. We demonstrate this utility with TSCP data from the Genome in a Bottle reference sample, which CoverView analysed in 13 seconds. CoverView uses data routinely generated by NGS pipelines, reads standard input formats, and rapidly creates easy-to-parse output text (.txt) files that are customised by a simple configuration file. CoverView can therefore be easily integrated into any NGS pipeline. CoverView and detailed documentation for its use are freely available at
github.com/RahmanTeamDevelopment/CoverView/releases and
www.icr.ac.uk/CoverView
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Affiliation(s)
- Márton Münz
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Shazia Mahamdallie
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Shawn Yost
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Andrew Rimmer
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Emma Poyastro-Pearson
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Ann Strydom
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Sheila Seal
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Elise Ruark
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Nazneen Rahman
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK.,Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, SM2 5PT, UK
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Verbakel SK, van Huet RAC, Boon CJF, den Hollander AI, Collin RWJ, Klaver CCW, Hoyng CB, Roepman R, Klevering BJ. Non-syndromic retinitis pigmentosa. Prog Retin Eye Res 2018; 66:157-186. [PMID: 29597005 DOI: 10.1016/j.preteyeres.2018.03.005] [Citation(s) in RCA: 492] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 03/20/2018] [Accepted: 03/22/2018] [Indexed: 12/23/2022]
Abstract
Retinitis pigmentosa (RP) encompasses a group of inherited retinal dystrophies characterized by the primary degeneration of rod and cone photoreceptors. RP is a leading cause of visual disability, with a worldwide prevalence of 1:4000. Although the majority of RP cases are non-syndromic, 20-30% of patients with RP also have an associated non-ocular condition. RP typically manifests with night blindness in adolescence, followed by concentric visual field loss, reflecting the principal dysfunction of rod photoreceptors; central vision loss occurs later in life due to cone dysfunction. Photoreceptor function measured with an electroretinogram is markedly reduced or even absent. Optical coherence tomography (OCT) and fundus autofluorescence (FAF) imaging show a progressive loss of outer retinal layers and altered lipofuscin distribution in a characteristic pattern. Over the past three decades, a vast number of disease-causing variants in more than 80 genes have been associated with non-syndromic RP. The wide heterogeneity of RP makes it challenging to describe the clinical findings and pathogenesis. In this review, we provide a comprehensive overview of the clinical characteristics of RP specific to genetically defined patient subsets. We supply a unique atlas with color fundus photographs of most RP subtypes, and we discuss the relevant considerations with respect to differential diagnoses. In addition, we discuss the genes involved in the pathogenesis of RP, as well as the retinal processes that are affected by pathogenic mutations in these genes. Finally, we review management strategies for patients with RP, including counseling, visual rehabilitation, and current and emerging therapeutic options.
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Affiliation(s)
- Sanne K Verbakel
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ramon A C van Huet
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Camiel J F Boon
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands; Department of Ophthalmology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Anneke I den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rob W J Collin
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Caroline C W Klaver
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald Roepman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - B Jeroen Klevering
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands.
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Deng WL, Gao ML, Lei XL, Lv JN, Zhao H, He KW, Xia XX, Li LY, Chen YC, Li YP, Pan D, Xue T, Jin ZB. Gene Correction Reverses Ciliopathy and Photoreceptor Loss in iPSC-Derived Retinal Organoids from Retinitis Pigmentosa Patients. Stem Cell Reports 2018. [PMID: 29526738 PMCID: PMC5998840 DOI: 10.1016/j.stemcr.2018.02.003] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Retinitis pigmentosa (RP) is an irreversible, inherited retinopathy in which early-onset nyctalopia is observed. Despite the genetic heterogeneity of RP, RPGR mutations are the most common causes of this disease. Here, we generated induced pluripotent stem cells (iPSCs) from three RP patients with different frameshift mutations in the RPGR gene, which were then differentiated into retinal pigment epithelium (RPE) cells and well-structured retinal organoids possessing electrophysiological properties. We observed significant defects in photoreceptor in terms of morphology, localization, transcriptional profiling, and electrophysiological activity. Furthermore, shorted cilium was found in patient iPSCs, RPE cells, and three-dimensional retinal organoids. CRISPR-Cas9-mediated correction of RPGR mutation rescued photoreceptor structure and electrophysiological property, reversed the observed ciliopathy, and restored gene expression to a level in accordance with that in the control using transcriptome-based analysis. This study recapitulated the pathogenesis of RPGR using patient-specific organoids and achieved targeted gene therapy of RPGR mutations in a dish as proof-of-concept evidence. HiPSC-derived 3D retinae with outer segments and electrophysiological properties RPGR mutation results in diseased photoreceptor in patient iPSC-derived 3D retinae Mutation correction rescues defects in photoreceptor morphology and electrophysiology Ciliogenesis defects appear in RPGR patient-specific iPSCs, iPSC-RPE, and 3D retinae
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Affiliation(s)
- Wen-Li Deng
- Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou 325027, China
| | - Mei-Ling Gao
- Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou 325027, China
| | - Xin-Lan Lei
- Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou 325027, China
| | - Ji-Neng Lv
- Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou 325027, China
| | - Huan Zhao
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Brain Function and Disease, Neurodegenerative Disorder Research Center, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Kai-Wen He
- Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou 325027, China
| | - Xi-Xi Xia
- Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou 325027, China
| | - Ling-Yun Li
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Brain Function and Disease, Neurodegenerative Disorder Research Center, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Yu-Chen Chen
- Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou 325027, China
| | - Yan-Ping Li
- Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou 325027, China
| | - Deng Pan
- Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou 325027, China
| | - Tian Xue
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Brain Function and Disease, Neurodegenerative Disorder Research Center, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Zi-Bing Jin
- Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou 325027, China.
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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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40
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Zahed H, Sparks TN, Li B, Alsadah A, Shieh JTC. Potential Role of Genomic Sequencing in the Early Diagnosis of Treatable Genetic Conditions. J Pediatr 2017; 189:222-226.e1. [PMID: 28947054 PMCID: PMC6037534 DOI: 10.1016/j.jpeds.2017.06.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 04/02/2017] [Accepted: 06/15/2017] [Indexed: 12/18/2022]
Abstract
We present cases of 3 children diagnosed with the same genetic condition, Gitelman syndrome, at different stages using various genetic methods: panel testing, targeted single gene sequencing, and exome sequencing. We discuss the advantages and disadvantages of each method and review the potential of genomic sequencing for early disease detection.
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Affiliation(s)
- Hengameh Zahed
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA
| | - Teresa N. Sparks
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA
,Department of Obstetrics, Gynecology and Reproductive Medicine, University of California San Francisco, San Francisco, CA
| | - Ben Li
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA
,Department of Obstetrics, Gynecology and Reproductive Medicine, University of California San Francisco, San Francisco, CA
| | - Adnan Alsadah
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA
| | - Joseph T. C. Shieh
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA
,Institute for Human Genetics, Benioff Children’s Hospital San Francisco, University of California San Francisco, San Francisco, CA
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41
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Unraveling the genetic cause of a consanguineous family with unilateral coloboma and retinoschisis: expanding the phenotypic variability of RAX mutations. Sci Rep 2017; 7:9064. [PMID: 28831107 PMCID: PMC5567291 DOI: 10.1038/s41598-017-09276-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/25/2017] [Indexed: 01/08/2023] Open
Abstract
Ocular coloboma is a common eye malformation arising from incomplete closure of the human optic fissure during development. Multiple genetic mutations contribute to the disease process, showing extensive genetic heterogeneity and complexity of coloboma spectrum diseases. In this study, we aimed to unravel the genetic cause of a consanguineous family with unilateral coloboma and retinoschisis. The subjects were recruited and underwent specialized ophthalmologic clinical examination. A combination of whole exome sequencing (WES), homozygosity mapping, and comprehensive variant analyses was performed to uncover the causative mutation. Only one homozygous mutation (c.113 T > C, p.I38T) in RAX gene survived our strict variant filtering process, consistent with an autosomal recessive inheritance pattern. This mutation segregated perfectly in the family and is located in a highly conserved functional domain. Crystal structure modeling indicated that I38T affected the protein structure. We describe a patient from a consanguineous Chinese family with unusual coloboma, proven to harbor a novel RAX mutation (c.113 T > C, p.I38T, homozygous), expanding the phenotypic variability of ocular coloboma and RAX mutations.
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42
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Motta FL, Salles MV, Costa KA, Filippelli-Silva R, Martin RP, Sallum JMF. The correlation between CRB1 variants and the clinical severity of Brazilian patients with different inherited retinal dystrophy phenotypes. Sci Rep 2017; 7:8654. [PMID: 28819299 PMCID: PMC5561187 DOI: 10.1038/s41598-017-09035-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 07/20/2017] [Indexed: 12/18/2022] Open
Abstract
Inherited retinal dystrophies are characterized by progressive retina degeneration and mutations in at least 250 genes have been associated as disease-causing. CRB1 is one of many genes analyzed in molecular diagnosis for inherited retinal dystrophy. Crumbs homolog-1 protein encoded by CRB1 is important for cell-to-cell contact, polarization of epithelial cells and the morphogenesis of photoreceptors. Pathogenic variants in CRB1 lead to a huge variety of phenotypes ranging from milder forms of inherited retinal dystrophy, such as retinitis pigmentosa to more severe phenotypes such as Leber congenital amaurosis. In this study, seven novel likely-pathogenic variants were identified: four missense variants (p.Leu479Pro, p.Ala921Pro, p.Cys948Arg and p.Asp1031Asn), two frameshift deletions (c.2536_2542del7 and c.3460_3461delTG) and one frameshift indel variant (c.276_294delinsTGAACACTGTAC). Furthermore, two patients with cone-rod dystrophy due to mutations in CRB1 were reported, supporting previous data, in which mutations in CRB1 can also cause cone-rod dystrophy. Finally, our data suggested there was a direct relation between phenotype severity and the mutation effect on protein functionality in 15 Brazilian CRB1 patients.
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Affiliation(s)
| | | | | | | | - Renan Paulo Martin
- Department of Biophysics, Federal University of Sao Paulo, Sao Paulo, Brazil
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43
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Huang XF, Huang ZQ, Fang XL, Chen ZJ, Cheng W, Jin ZB. Retinal miRNAs variations in a large cohort of inherited retinal disease. Ophthalmic Genet 2017; 39:175-179. [PMID: 28704127 DOI: 10.1080/13816810.2017.1329448] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Although great efforts have been paid on identification of genetic predisposition in the inherited retinal disease (IRD), genetic causes of a large proportion of patients remain a mystery. This dilemma makes us attempt to speculate that genetic components other than coding genes might be an additional pool predisposing IRD. In this study, we aim to perform a mutational screening in a large cohort of IRD patients with a particular focus on retina-specific or abundant microRNAs (miRs). MATERIAL AND METHODS A total of 324 unrelated patients with IRD were recruited. Targeted next-generation sequencing (tNGS) was performed to survey genetic mutations in 32 known miRs highly expressed in the retina, followed by validation with Sanger sequencing, co-segregation analysis in each family, and computational assessments. RESULTS Novel genotype-phenotype associations have been uncovered. In total, six different variants in the miRs were identified, including four rare ones, miR-216a (n.56C>A), miR-216b (n.43_44insG), miR-7-2 (n.107C>T), and miR-7-3 (n.95G>A). The other two variants, miR-182 (n.106G>A) and miR-216a (n.105T>A), were considered as polymorphic. CONCLUSIONS We for the first time screened candidate retinal miRs in patients with IRD. Although there is no convincing evidence that these variants are responsible for the IRD, the results enhance the current knowledge of the associations between IRD and miRNAs variants.
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Affiliation(s)
- Xiu-Feng Huang
- a Division of Ophthalmic Genetics , Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University , Wenzhou , China
| | - Zhi-Qin Huang
- a Division of Ophthalmic Genetics , Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University , Wenzhou , China
| | - Xiao-Long Fang
- a Division of Ophthalmic Genetics , Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University , Wenzhou , China
| | - Zhen-Ji Chen
- a Division of Ophthalmic Genetics , Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University , Wenzhou , China
| | - Wan Cheng
- a Division of Ophthalmic Genetics , Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University , Wenzhou , China
| | - Zi-Bing Jin
- a Division of Ophthalmic Genetics , Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University , Wenzhou , China
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44
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Haer-Wigman L, van Zelst-Stams WA, Pfundt R, van den Born LI, Klaver CC, Verheij JB, Hoyng CB, Breuning MH, Boon CJ, Kievit AJ, Verhoeven VJ, Pott JW, Sallevelt SC, van Hagen JM, Plomp AS, Kroes HY, Lelieveld SH, Hehir-Kwa JY, Castelein S, Nelen M, Scheffer H, Lugtenberg D, Cremers FP, Hoefsloot L, Yntema HG. Diagnostic exome sequencing in 266 Dutch patients with visual impairment. Eur J Hum Genet 2017; 25:591-599. [PMID: 28224992 PMCID: PMC5437915 DOI: 10.1038/ejhg.2017.9] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 12/16/2016] [Accepted: 01/11/2017] [Indexed: 11/13/2022] Open
Abstract
Inherited eye disorders have a large clinical and genetic heterogeneity, which makes genetic diagnosis cumbersome. An exome-sequencing approach was developed in which data analysis was divided into two steps: the vision gene panel and exome analysis. In the vision gene panel analysis, variants in genes known to cause inherited eye disorders were assessed for pathogenicity. If no causative variants were detected and when the patient consented, the entire exome data was analyzed. A total of 266 Dutch patients with different types of inherited eye disorders, including inherited retinal dystrophies, cataract, developmental eye disorders and optic atrophy, were investigated. In the vision gene panel analysis (likely), causative variants were detected in 49% and in the exome analysis in an additional 2% of the patients. The highest detection rate of (likely) causative variants was in patients with inherited retinal dystrophies, for instance a yield of 63% in patients with retinitis pigmentosa. In patients with developmental eye defects, cataract and optic atrophy, the detection rate was 50, 33 and 17%, respectively. An exome-sequencing approach enables a genetic diagnosis in patients with different types of inherited eye disorders using one test. The exome approach has the same detection rate as targeted panel sequencing tests, but offers a number of advantages. For instance, the vision gene panel can be frequently and easily updated with additional (novel) eye disorder genes. Determination of the genetic diagnosis improved the clinical diagnosis, regarding the assessment of the inheritance pattern as well as future disease perspective.
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Affiliation(s)
- Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | | | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | | | - Caroline Cw Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Joke Bgm Verheij
- Department of Medical Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Martijn H Breuning
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Camiel Jf Boon
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Anneke J Kievit
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Virginie Jm Verhoeven
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jan Wr Pott
- Department of Ophthalmology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Suzanne Ceh Sallevelt
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Johanna M van Hagen
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Astrid S Plomp
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Hester Y Kroes
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Stefan H Lelieveld
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Jayne Y Hehir-Kwa
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Steven Castelein
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Marcel Nelen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Hans Scheffer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Dorien Lugtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Frans Pm Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Lies Hoefsloot
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
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45
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Wang X, Feng Y, Li J, Zhang W, Wang J, Lewis RA, Wong LJ. Retinal Diseases Caused by Mutations in Genes Not Specifically Associated with the Clinical Diagnosis. PLoS One 2016; 11:e0165405. [PMID: 27788217 PMCID: PMC5082937 DOI: 10.1371/journal.pone.0165405] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 10/11/2016] [Indexed: 12/15/2022] Open
Abstract
Purpose When seeking a confirmed molecular diagnosis in the research setting, patients with one descriptive diagnosis of retinal disease could carry pathogenic variants in genes not specifically associated with that description. However, this event has not been evaluated systematically in clinical diagnostic laboratories that validate fully all target genes to minimize false negatives/positives. Methods We performed targeted next-generation sequencing analysis on 207 ocular disease-related genes for 42 patients whose DNA had been tested negative for disease-specific panels of genes known to be associated with retinitis pigmentosa, Leber congenital amaurosis, or exudative vitreoretinopathy. Results Pathogenic variants, including single nucleotide variations and copy number variations, were identified in 9 patients, including 6 with variants in syndromic retinal disease genes and 3 whose molecular diagnosis could not be distinguished easily from their submitted clinical diagnosis, accounting for 21% (9/42) of the unsolved cases. Conclusion Our study underscores the clinical and genetic heterogeneity of retinal disorders and provides valuable reference to estimate the fraction of clinical samples whose retinal disorders could be explained by genes not specifically associated with the corresponding clinical diagnosis. Our data suggest that sequencing a larger set of retinal disorder related genes can increase the molecular diagnostic yield, especially for clinically hard-to-distinguish cases.
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Affiliation(s)
- Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Yanming Feng
- Baylor Genetics, Houston, Texas, United States of America
| | - Jianli Li
- Baylor Genetics, Houston, Texas, United States of America
| | - Wei Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jing Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard A. Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lee-Jun Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Baylor Genetics, Houston, Texas, United States of America
- * E-mail:
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46
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Lebaron C, Rosado A, Sauvage C, Gauffier C, German-Retana S, Moury B, Gallois JL. A new eIF4E1 allele characterized by RNAseq data mining is associated with resistance to potato virus Y in tomato albeit with a low durability. J Gen Virol 2016; 97:3063-3072. [PMID: 27655175 DOI: 10.1099/jgv.0.000609] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Allele mining on susceptibility factors offers opportunities to find new sources of resistance among crop wild relatives for breeding purposes. As a proof of concept, we used available RNAseq data to investigate polymorphisms among the four tomato genes encoding translation initiation factors [eIF4E1 and eIF4E2, eIFiso4E and the related gene new cap-binding protein(nCBP)] to look for new potential resistance alleles to potyviruses. By analysing polymorphism among RNAseq data obtained for 20 tomato accessions, 10 belonging to the cultivated type Solanum lycopersicum and 10 belonging to the closest related wild species Solanum pimpinellifolium, we isolated one new eIF4E1 allele, in the S. pimpinellifolium LA0411 accession, which encodes a potential new resistance allele, mainly due to a polymorphism associated with an amino acid change within eIF4E1 region II. We confirmed that this new allele, pot12, is indeed associated with resistance to potato virus Y, although with a restricted resistance spectrum and a very low durability potential. This suggests that mutations occurring in eIF4E region II only may not be sufficient to provide efficient and durable resistance in plants. However, our study emphasizes the opportunity brought by RNAseq data to mine for new resistance alleles. Moreover, this approach could be extended to seek for putative new resistance alleles by screening for variant forms of susceptibility genes encoding plant host proteins known to interact with viral proteins.
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Affiliation(s)
| | | | | | | | | | - Benoît Moury
- Pathologie Végétale, INRA, 84140 Montfavet, France
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47
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Improved Diagnosis of Inherited Retinal Dystrophies by High-Fidelity PCR of ORF15 followed by Next-Generation Sequencing. J Mol Diagn 2016; 18:817-824. [PMID: 27620828 DOI: 10.1016/j.jmoldx.2016.06.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 06/10/2016] [Accepted: 06/16/2016] [Indexed: 11/21/2022] Open
Abstract
Retinitis pigmentosa (RP) is the most common form of retinal dystrophy. The disease is characterized by the progressive degeneration of photoreceptors, ultimately leading to blindness. The exon ORF15 of RP GTPase regulator (RPGR) is a mutation hot spot for X-linked RP and one form of cone dystrophy. However, accurate molecular testing of ORF15 is challenging because of a large segment of highly repetitive purine-rich sequence in this exon. ORF15 performs poorly in next-generation sequencing-based panels or whole exome sequencing analysis, whereas Sanger sequencing of ORF15 requires special reagents and PCR conditions with multiple pairs of overlapping primers that often do not provide a clean sequence. Because of these technical difficulties, molecular analysis of ORF15 is performed mostly in research laboratories without validation for clinical application. Herein, we report the development of a single step of high-fidelity PCR followed by next-generation sequencing for accurate mutation detection, which is easily integrated into routine clinical practice. Our approach has improved coverage depth of ORF15 with the ability to detect single-nucleotide variants and deletions/duplications. Using this method, we were able to identify ORF15 pathogenic variants in approximately 31% of undiagnosed RP patients. Our results underline the clinical importance of complete and accurate sequence analysis of ORF15 for patients with retinal dystrophies.
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Ogino K, Oishi A, Oishi M, Gotoh N, Morooka S, Sugahara M, Hasegawa T, Miyata M, Yoshimura N. Efficacy of Column Scatter Plots for Presenting Retinitis Pigmentosa Phenotypes in a Japanese Cohort. Transl Vis Sci Technol 2016; 5:4. [PMID: 26966640 PMCID: PMC4782824 DOI: 10.1167/tvst.5.2.4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/27/2016] [Indexed: 11/25/2022] Open
Abstract
Purpose We evaluated the efficacy of column scatter plots to describe genotype–phenotype correlations in a Japanese cohort with retinitis pigmentosa (RP). Methods Clinical records of 121 patients with RP with identified causative mutations were reviewed. Visual acuity, central and peripheral visual fields, electroretinography (ERG), lens status, and measurements of optical coherence tomography were evaluated according to causative genes using column scatter plots. Values for three common genes (EYS, USH2A, and RHO) were compared statistically. Results All patients with PDE6B, PRPH2, and RPGR mutations, those 55 years old or younger with RP1L1 and USH2A mutations, and those 45 years old or younger with EYS and RHO mutations retained visual acuity of at least 0.1. All patients with RPGR mutations showed at least −20 dB mean deviation. Goldmann perimeter measures of 4/6 patients with RHO mutations showed remaining peripheral visual fields. Dark-adapted 0.01 and 3.0 ERGs were extinguished for most genes. Half of the patients with RHO RP maintained cone responses in light-adapted 3.0 and 3.0 flicker ERG. All patients with PRPH2, those 55 years old or younger with USH2A and RP1L1, and those 45 years old or younger with PDE6B and EYS mutations maintained subfoveal ellipsoid zones. No differences were identified between EYS and USH2A or RHO and USH2A. Conclusions Column scatter plots enabled comparisons of the associated severities and illustration of the ophthalmological measurements for every RP causative gene. Translational Relevance Analysis of mutations in specific genes may be helpful for determining visual prognoses in the clinical setting.
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Affiliation(s)
- Ken Ogino
- Department of Ophthalmology and Visual Sciences Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Akio Oishi
- Department of Ophthalmology and Visual Sciences Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Maho Oishi
- Department of Ophthalmology and Visual Sciences Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Norimoto Gotoh
- Department of Ophthalmology and Visual Sciences Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Satoshi Morooka
- Department of Ophthalmology and Visual Sciences Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masako Sugahara
- Department of Ophthalmology and Visual Sciences Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tomoko Hasegawa
- Department of Ophthalmology and Visual Sciences Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Manabu Miyata
- Department of Ophthalmology and Visual Sciences Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Nagahisa Yoshimura
- Department of Ophthalmology and Visual Sciences Kyoto University Graduate School of Medicine, Kyoto, Japan
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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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