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Cha S, Ahn J, Jeong Y, Lee YH, Kim HK, Lee D, Yoo Y, Goo YS. Stage-Dependent Changes of Visual Function and Electrical Response of the Retina in the rd10 Mouse Model. Front Cell Neurosci 2022; 16:926096. [PMID: 35936494 PMCID: PMC9345760 DOI: 10.3389/fncel.2022.926096] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/23/2022] [Indexed: 12/28/2022] Open
Abstract
One of the critical prerequisites for the successful development of retinal prostheses is understanding the physiological features of retinal ganglion cells (RGCs) in the different stages of retinal degeneration (RD). This study used our custom-made rd10 mice, C57BL/6-Pde6bem1(R560C)Dkl/Korl mutated on the Pde6b gene in C57BL/6J mouse with the CRISPR/Cas9-based gene-editing method. We selected the postnatal day (P) 45, P70, P140, and P238 as representative ages for RD stages. The optomotor response measured the visual acuity across degeneration stages. At P45, the rd10 mice exhibited lower visual acuity than wild-type (WT) mice. At P140 and older, no optomotor response was observed. We classified RGC responses to the flashed light into ON, OFF, and ON/OFF RGCs via in vitro multichannel recording. With degeneration, the number of RGCs responding to the light stimulation decreased in all three types of RGCs. The OFF response disappeared faster than the ON response with older postnatal ages. We elicited RGC spikes with electrical stimulation and analyzed the network-mediated RGC response in the rd10 mice. Across all postnatal ages, the spikes of rd10 RGCs were less elicited by pulse amplitude modulation than in WT RGCs. The ratio of RGCs showing multiple peaks of spike burst increased in older ages. The electrically evoked RGC spikes by the pulse amplitude modulation differ across postnatal ages. Therefore, degeneration stage-dependent stimulation strategies should be considered for developing retinal prosthesis and successful vision restoration.
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Affiliation(s)
- Seongkwang Cha
- Department of Physiology, Chungbuk National University School of Medicine, Cheongju, South Korea
| | - Jungryul Ahn
- Department of Physiology, Chungbuk National University School of Medicine, Cheongju, South Korea
| | - Yurim Jeong
- Department of Physiology, Chungbuk National University School of Medicine, Cheongju, South Korea
| | - Yong Hee Lee
- Department of Biochemistry, Chungbuk National University School of Medicine, Cheongju, South Korea
| | - Hyong Kyu Kim
- Department of Microbiology, Chungbuk National University School of Medicine, Cheongju, South Korea
| | - Daekee Lee
- Department of Life Science, Ewha Womans University, Seoul, South Korea
| | - Yongseok Yoo
- Department of Electronics Engineering, Incheon National University, Incheon, South Korea
- *Correspondence: Yongseok Yoo,
| | - Yong Sook Goo
- Department of Physiology, Chungbuk National University School of Medicine, Cheongju, South Korea
- Yong Sook Goo,
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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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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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Mutation spectrum of PRPF31, genotype-phenotype correlation in retinitis pigmentosa, and opportunities for therapy. Exp Eye Res 2020; 192:107950. [PMID: 32014492 PMCID: PMC7065041 DOI: 10.1016/j.exer.2020.107950] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/13/2020] [Accepted: 01/27/2020] [Indexed: 12/11/2022]
Abstract
Pathogenic variants in pre-messenger RNA (pre-mRNA) splicing factor 31, PRPF31, are the second most common genetic cause of autosomal dominant retinitis pigmentosa (adRP) in most populations. This remains a completely untreatable and incurable form of blindness, and it can be difficult to predict the clinical course of disease. In order to design appropriate targeted therapies, a thorough understanding of the genetics and molecular mechanism of this disease is required. Here, we present the structure of the PRPF31 gene and PRPF31 protein, current understanding of PRPF31 protein function and the full spectrum of all reported clinically relevant variants in PRPF31. We delineate the correlation between specific PRPF31 genotype and RP phenotype, suggesting that, except in cases of complete gene deletion or large-scale deletions, dominant negative effects contribute to phenotype as well as haploinsufficiency. This has important impacts on design of targeted therapies, particularly the feasibility of gene augmentation as a broad approach for treatment of PRPF31-associated RP. We discuss other opportunities for therapy, including antisense oligonucleotide therapy and gene-independent approaches and offer future perspectives on treatment of this form of RP. PRPF31 is the second most common cause of autosomal dominant retinitis pigmentosa and a potential target for gene therapy. We present all reported pathogenic variants in PRPF31 as a resource for clinicians, diagnostic genetics labs, and researchers. Genotype-phenotype correlations suggest that, dominant negative effects contribute to disease in addition to haploinsufficiency. This finding has important impacts on the suitability of gene augmentation approaches across all mutation types. This finding may aid prognosis of disease in PRPF31-associated RP patients.
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Detection of Large Structural Variants Causing Inherited Retinal Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1185:197-202. [PMID: 31884611 DOI: 10.1007/978-3-030-27378-1_32] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Current application of next-generation sequencing (NGS) leads to detection of the underlying disease-causing gene and mutation or mutations in from 60% to 85% of patients with inherited retinal diseases (IRDs), depending on the methods used, disease type, and population tested. In a cohort of 320 families with autosomal dominant retinitis pigmentosa (adRP), we have detected the mutation in 82% of cases using a variety of methods, leaving more than 50 families with "elusive" disease genotypes. All of the remaining families have been screened for mutations in known IRD genes using retinal-targeted-capture NGS, and most have been tested by whole-exome NGS. Linkage mapping has been conducted in several large families. In one of these families, with DNA samples from ten affected family members and six unaffected, linking members, we observed substantial maximum two-point LOD scores for linkage to both chromosomes 2 and 4. Subsequent 10X Genomics Chromium™ sequencing, which facilitates linked-read, phase-known chromosomal analysis, revealed a balanced translocation of the q terminus arms of chromosomes 2 and 4 involving 35 Mb and 73 Mb of 2 and 4, respectively. The balanced translocation is present in all affected family members and absent from all unaffected individuals. Family histories suggest multiple miscarriages are associated with the translocation. The breakpoint on chromosome 4 is within or 5' to the LRAT gene, whereas the chromosome 2 break is in a gene-poor region. We conclude that the balanced translocation is the cause of adRP in this family, which may lead to dysregulation of the LRAT gene. Since multiple miscarriages are a hallmark of balanced translocations, this possibility should be considered in evaluating family histories. Further, large structural variants, which are not easily detected by conventional sequencing methods, may account for a significant fraction of the remaining unsolved families.
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Birtel J, Gliem M, Mangold E, Müller PL, Holz FG, Neuhaus C, Lenzner S, Zahnleiter D, Betz C, Eisenberger T, Bolz HJ, Charbel Issa P. Next-generation sequencing identifies unexpected genotype-phenotype correlations in patients with retinitis pigmentosa. PLoS One 2018; 13:e0207958. [PMID: 30543658 PMCID: PMC6292620 DOI: 10.1371/journal.pone.0207958] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/08/2018] [Indexed: 12/13/2022] Open
Abstract
Retinitis pigmentosa (RP) is an inherited degenerative disease causing severe retinal dystrophy and visual impairment mainly with onset in infancy or adolescence. Targeted next-generation sequencing (NGS) has become an efficient tool to encounter the enormous genetic heterogeneity of diverse retinal dystrophies, including RP. To identify disease-causing mutations in unselected, consecutive RP patients, we conducted Sanger sequencing of genes commonly involved in the suspected genetic RP subtype, followed by targeted large-panel NGS if no mutation was identified, or NGS as primary analysis. A high (70%) detection rate of disease-causing mutations was achieved in a large cohort of 116 unrelated patients. About half (48%) of the solved RP cases were explained by mutations in four genes: RPGR, EYS, PRPF31 and USH2A. Overall, 110 different mutations distributed across 30 different genes were detected, and 46 of these mutations were novel. A molecular diagnosis was achieved in the majority (82–100%) of patients if the family history was suggestive for a particular mode of inheritance, but only in 60% in cases of sporadic RP. The diagnostic potential of extensive molecular analysis in a routine setting is also illustrated by the identification of unexpected genotype-phenotype correlations for RP patients with mutations in CRX, CEP290, RPGRIP1, MFSD8. Furthermore, we identified numerous mutations in autosomal dominant (PRPF31, PRPH2, CRX) and X-linked (RPGR) RP genes in patients with sporadic RP. Variants in RP2 and RPGR were also found in female RP patients with apparently sporadic or dominant disease. In summary, this study demonstrates that massively parallel sequencing of all known retinal dystrophy genes is a valuable diagnostic approach for RP patients.
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Affiliation(s)
- Johannes Birtel
- Department of Ophthalmology, University of Bonn, Bonn, Germany
- Center for Rare Diseases Bonn (ZSEB), University of Bonn, Bonn, Germany
| | - Martin Gliem
- Department of Ophthalmology, University of Bonn, Bonn, Germany
- Center for Rare Diseases Bonn (ZSEB), University of Bonn, Bonn, Germany
| | | | - Philipp L. Müller
- Department of Ophthalmology, University of Bonn, Bonn, Germany
- Center for Rare Diseases Bonn (ZSEB), University of Bonn, Bonn, Germany
| | - Frank G. Holz
- Department of Ophthalmology, University of Bonn, Bonn, Germany
- Center for Rare Diseases Bonn (ZSEB), University of Bonn, Bonn, Germany
| | | | | | | | - Christian Betz
- Bioscientia Center for Human Genetics, Ingelheim, Germany
| | | | - Hanno J. Bolz
- Bioscientia Center for Human Genetics, Ingelheim, Germany
- Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany
| | - Peter Charbel Issa
- Department of Ophthalmology, University of Bonn, Bonn, Germany
- Center for Rare Diseases Bonn (ZSEB), University of Bonn, Bonn, Germany
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, and Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- * E-mail:
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Zhu Y, Tan H, Zeng J, Tao D, Ma Y, Liu Y. A novel CRX variant (p.R98X) is identified in a Chinese family of Retinitis pigmentosa with atypical and mild manifestations. Genes Genomics 2018; 41:359-366. [PMID: 30460480 DOI: 10.1007/s13258-018-0763-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/04/2018] [Indexed: 02/05/2023]
Abstract
BACKGROUND Retinitis pigmentosa (RP) is the most common form of hereditary retinal degeneration that can cause inherited blindness. RP has extreme genetic and clinical heterogeneity, which brings a major obstacle to obtaining an accurate molecular diagnosis. OBJECTIVE To analyze the genetic defect in a Chinese family of RP with a few atypical manifestations. METHODS Whole-exome sequencing (WES) was applied to identify the disease-associated genes. Sanger sequencing was performed to validate the variants of candidate genes in the patient and his parents. In vitro expression analysis was further conducted to examine the potential biological function of the gene variant. RESULTS A heterozygous nonsense variant c.292C > T (p.R98X) of CRX gene was identified to be present in the affected male. The c.292C > T variant of CRX was absent in all of the searched databases, including the 10,000 Chinese exome database. The nonsense variant was supposed to result in a truncated CRX protein with a destroyed homedomain (HD), which is essential for CRX translation. Interestingly, the following assay showed that the potential truncated protein was not detected, indicating that the variant may cause a loss-of-function mutation of CRX gene. CONCLUSION We identified a novel heterozygous null mutation in the CRX gene which was the first evidence of a nonsense mutation in the HD domain of CRX. Our finding suggested that the haploinsufficiency mutation of CRX gene contributed to the atypical and mild manifestations of the autosomal dominant RP in the Chinese family.
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Affiliation(s)
- Yingchuan Zhu
- Department of Medical Genetics, West China Medical School, West China Hospital, Sichuan University, 1st Keyuan 4 Lu, GaoPeng Da Dao, Chengdu, 610041, Sichuan, China
| | - Hao Tan
- Department of Medical Genetics, West China Medical School, West China Hospital, Sichuan University, 1st Keyuan 4 Lu, GaoPeng Da Dao, Chengdu, 610041, Sichuan, China
| | - Jiarong Zeng
- Department of Medical Genetics, West China Medical School, West China Hospital, Sichuan University, 1st Keyuan 4 Lu, GaoPeng Da Dao, Chengdu, 610041, Sichuan, China
| | - Dachang Tao
- Department of Medical Genetics, West China Medical School, West China Hospital, Sichuan University, 1st Keyuan 4 Lu, GaoPeng Da Dao, Chengdu, 610041, Sichuan, China
| | - Yongxin Ma
- Department of Medical Genetics, West China Medical School, West China Hospital, Sichuan University, 1st Keyuan 4 Lu, GaoPeng Da Dao, Chengdu, 610041, Sichuan, China
| | - Yunqiang Liu
- Department of Medical Genetics, West China Medical School, West China Hospital, Sichuan University, 1st Keyuan 4 Lu, GaoPeng Da Dao, Chengdu, 610041, Sichuan, China.
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Systematic evaluation of a targeted gene capture sequencing panel for molecular diagnosis of retinitis pigmentosa. PLoS One 2018; 13:e0185237. [PMID: 29641573 PMCID: PMC5894961 DOI: 10.1371/journal.pone.0185237] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/08/2017] [Indexed: 01/09/2023] Open
Abstract
Background Inherited eye diseases are major causes of vision loss in both children and adults. Inherited eye diseases are characterized by clinical variability and pronounced genetic heterogeneity. Genetic testing may provide an accurate diagnosis for ophthalmic genetic disorders and allow gene therapy for specific diseases. Methods A targeted gene capture panel was designed to capture exons of 283 inherited eye disease genes including 58 known causative retinitis pigmentosa (RP) genes. 180 samples were tested with this panel, 68 were previously tested by Sanger sequencing. Systematic evaluation of our method and comprehensive molecular diagnosis were carried on 99 RP patients. Results 96.85% targeted regions were covered by at least 20 folds, the accuracy of variants detection was 99.994%. In 4 of the 68 samples previously tested by Sanger sequencing, mutations of other diseases not consisting with the clinical diagnosis were detected by next-generation sequencing (NGS) not Sanger. Among the 99 RP patients, 64 (64.6%) were detected with pathogenic mutations, while in 3 patients, it was inconsistent between molecular diagnosis and their initial clinical diagnosis. After revisiting, one patient’s clinical diagnosis was reclassified. In addition, 3 patients were found carrying large deletions. Conclusions We have systematically evaluated our method and compared it with Sanger sequencing, and have identified a large number of novel mutations in a cohort of 99 RP patients. The results showed a sufficient accuracy of our method and suggested the importance of molecular diagnosis in clinical diagnosis.
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Kim BJ, Zack DJ. The Role of c-Jun N-Terminal Kinase (JNK) in Retinal Degeneration and Vision Loss. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1074:351-357. [PMID: 29721963 DOI: 10.1007/978-3-319-75402-4_43] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
c-Jun N-terminal kinase (JNK), a member of stress-induced mitogen-activated protein (MAP) kinase family, has been shown to modulate a variety of biological processes associated with neurodegenerative pathology of the retina. In particular, various retinal cell culture and animal models related to glaucoma, age-related macular degeneration (AMD), and retinitis pigmentosa indicate that JNK signaling may contribute to disease pathogenesis. This mini-review discusses the impact of JNK signaling in retinal disease, with a focus on retinal ganglion cells (RGCs), photoreceptor cells, retinal pigment epithelial (RPE) cells, and animal studies, with particular attention to modulation of JNK signaling as a potential therapeutic target for the treatment of retinal disease.
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Affiliation(s)
- Byung-Jin Kim
- The Wilmer Eye Institute, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Donald J Zack
- The Wilmer Eye Institute, Johns Hopkins University, School of Medicine, Baltimore, MD, USA.
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Daiger SP, Bowne SJ, Sullivan LS, Branham K, Wheaton DK, Jones KD, Avery CE, Cadena ED, Heckenlively JR, Birch DG. Molecular Findings in Families with an Initial Diagnose of Autosomal Dominant Retinitis Pigmentosa (adRP). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1074:237-245. [PMID: 29721949 DOI: 10.1007/978-3-319-75402-4_29] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Genetic testing of probands in families with an initial diagnosis of autosomal dominant retinitis pigmentosa (adRP) usually confirms the diagnosis, but there are exceptions. We report results of genetic testing in a large cohort of adRP families with an emphasis on exceptional cases including X-linked RP with affected females; homozygous affected individuals in families with heterozygous, dominant disease; and independently segregating mutations in the same family. Genetic testing was conducted in more than 700 families with a provisional or probable diagnosis of adRP. Exceptions to the proposed mode of inheritance were extracted from our comprehensive patient and family database. In a subset of 300 well-characterized families with a probable diagnosis of adRP, 195 (70%) have dominant mutations in known adRP genes but 25 (8%) have X-linked mutations, 3 (1%) have multiple segregating mutations, and 3 (1%) have dominant-acting mutations in genes previously associated with recessive disease. It is currently possible to determine the underlying disease-causing gene and mutation in approximately 80% of families with an initial diagnosis of adRP, but 10% of "adRP" families have a variant mode of inheritance. Informed genetic diagnosis requires close collaboration between clinicians, genetic counselors, and laboratory scientists.
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Affiliation(s)
- Stephen P Daiger
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center (UTHealth), Houston, TX, USA. .,Ruiz Department of Ophthalmology and Visual Science, UTHealth, Houston, TX, USA.
| | - Sara J Bowne
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center (UTHealth), Houston, TX, USA
| | - Lori S Sullivan
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center (UTHealth), Houston, TX, USA
| | - Kari Branham
- Kellogg Eye Center, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Cheryl E Avery
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center (UTHealth), Houston, TX, USA
| | - Elizabeth D Cadena
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center (UTHealth), Houston, TX, USA
| | | | - David G Birch
- The Retina Foundation of the Southwest, Dallas, TX, USA
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Costa KA, Salles MV, Whitebirch C, Chiang J, Sallum JMF. Gene panel sequencing in Brazilian patients with retinitis pigmentosa. Int J Retina Vitreous 2017; 3:33. [PMID: 28912962 PMCID: PMC5592712 DOI: 10.1186/s40942-017-0087-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 07/31/2017] [Indexed: 12/17/2022] Open
Abstract
Background Retinal dystrophies constitute a group of diseases characterized by clinical variability and pronounced genetic heterogeneity. Retinitis pigmentosa is the most common subtype of hereditary retinal dystrophy and is characterized by a progressive loss of peripheral field vision (Tunnel Vision), eventual loss of central vision, and progressive night blindness. The characteristics of the fundus changes include bone-spicule formations, attenuated blood vessels, reduced and/or abnormal electroretinograms, changes in structure imaged by optical coherence tomography, and subjective changes in visual function. The different syndromic and nonsyndromic forms of retinal dystrophies can be attributed to mutations in more than 250 genes. Molecular diagnosis for patients with retinitis pigmentosa has been hampered by extreme genetic and clinical heterogeneity between retinitis pigmentosa and other forms of retinal dystrophies. Next generation sequencing (NGS) technologies are among the most promising techniques to identify pathogenic variations in retinal dystrophies. Purpose The purpose of this study was to discover the molecular diagnosis for Brazilian patients clinically diagnosed with a retinitis pigmentosa pattern of inheritance by using NGS technologies. Materials and methods Sixteen patients with the clinical diagnosis of retinitis pigmentosa were included in the study. Their DNA was sequenced in a panel with 132 genes related to retinal dystrophies using the Illumina® platform. Sequence analysis and variation calling was performed using Soft Genetics®, NextGene, and Geneticist Assistant software. The criteria for pathogenicity analysis were established according to the results of prediction programs (Polyphen 2, Mutation taster and MetaCore™) and comparison of pathogenic variations found with databases. Results The identified potentially pathogenic variations were all confirmed by Sanger sequencing. There were 89 variations predicted as pathogenic, but only 10 of them supported the conclusion of the molecular diagnosis. Five of the nine patients were autosomal dominant RP (56%), two (22%) were autosomal recessive RP, and two (22%) were X-linked RP. Nine of the 16 patients (56%) had probably positive or positive results. Conclusion The Next Generation Sequencing used in this study allowed the molecular diagnosis to be confirmed in 56% of the patients and clarified the inheritance pattern of the patient’s retinal dystrophies. Electronic supplementary material The online version of this article (doi:10.1186/s40942-017-0087-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kárita Antunes Costa
- Department of Ophthalmology and Visual Sciences, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Mariana Vallim Salles
- Department of Ophthalmology and Visual Sciences, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Chris Whitebirch
- Casey Eye Institute Molecular Diagnostic Laboratory, Oregon Health and Science University (OHSU), Portland, OR USA
| | - John Chiang
- Casey Eye Institute Molecular Diagnostic Laboratory, Oregon Health and Science University (OHSU), Portland, OR USA
| | - Juliana Maria Ferraz Sallum
- Department of Ophthalmology and Visual Sciences, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
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12
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Genetic characterization and disease mechanism of retinitis pigmentosa; current scenario. 3 Biotech 2017; 7:251. [PMID: 28721681 DOI: 10.1007/s13205-017-0878-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 07/10/2017] [Indexed: 12/21/2022] Open
Abstract
Retinitis pigmentosa is a group of genetically transmitted disorders affecting 1 in 3000-8000 individual people worldwide ultimately affecting the quality of life. Retinitis pigmentosa is characterized as a heterogeneous genetic disorder which leads by progressive devolution of the retina leading to a progressive visual loss. It can occur in syndromic (with Usher syndrome and Bardet-Biedl syndrome) as well as non-syndromic nature. The mode of inheritance can be X-linked, autosomal dominant or autosomal recessive manner. To date 58 genes have been reported to associate with retinitis pigmentosa most of them are either expressed in photoreceptors or the retinal pigment epithelium. This review focuses on the disease mechanisms and genetics of retinitis pigmentosa. As retinitis pigmentosa is tremendously heterogeneous disorder expressing a multiplicity of mutations; different variations in the same gene might induce different disorders. In recent years, latest technologies including whole-exome sequencing contributing effectively to uncover the hidden genesis of retinitis pigmentosa by reporting new genetic mutations. In future, these advancements will help in better understanding the genotype-phenotype correlations of disease and likely to develop new therapies.
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Sullivan LS, Bowne SJ, Koboldt DC, Cadena EL, Heckenlively JR, Branham KE, Wheaton DH, Jones KD, Ruiz RS, Pennesi ME, Yang P, Davis-Boozer D, Northrup H, Gurevich VV, Chen R, Xu M, Li Y, Birch DG, Daiger SP. A Novel Dominant Mutation in SAG, the Arrestin-1 Gene, Is a Common Cause of Retinitis Pigmentosa in Hispanic Families in the Southwestern United States. Invest Ophthalmol Vis Sci 2017; 58:2774-2784. [PMID: 28549094 PMCID: PMC5455168 DOI: 10.1167/iovs.16-21341] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/23/2017] [Indexed: 01/22/2023] Open
Abstract
Purpose To identify the causes of autosomal dominant retinitis pigmentosa (adRP) in a cohort of families without mutations in known adRP genes and consequently to characterize a novel dominant-acting missense mutation in SAG. Methods Patients underwent ophthalmologic testing and were screened for mutations using targeted-capture and whole-exome next-generation sequencing. Confirmation and additional screening were done by Sanger sequencing. Haplotypes segregating with the mutation were determined using short tandem repeat and single nucleotide variant polymorphisms. Genealogies were established by interviews of family members. Results Eight families in a cohort of 300 adRP families, and four additional families, were found to have a novel heterozygous mutation in the SAG gene, c.440G>T; p.Cys147Phe. Patients exhibited symptoms of retinitis pigmentosa and none showed symptoms characteristic of Oguchi disease. All families are of Hispanic descent and most were ascertained in Texas or California. A single haplotype including the SAG mutation was identified in all families. The mutation dramatically alters a conserved amino acid, is extremely rare in global databases, and was not found in 4000+ exomes from Hispanic controls. Molecular modeling based on the crystal structure of bovine arrestin-1 predicts protein misfolding/instability. Conclusions This is the first dominant-acting mutation identified in SAG, a founder mutation possibly originating in Mexico several centuries ago. The phenotype is clearly adRP and is distinct from the previously reported phenotypes of recessive null mutations, that is, Oguchi disease and recessive RP. The mutation accounts for 3% of the 300 families in the adRP Cohort and 36% of Hispanic families in this cohort.
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Affiliation(s)
- Lori S. Sullivan
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, Texas, United States
| | - Sara J. Bowne
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, Texas, United States
| | | | - Elizabeth L. Cadena
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, Texas, United States
| | | | - Kari E. Branham
- Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States
| | | | - Kaylie D. Jones
- Retina Foundation of the Southwest, Dallas, Texas, United States
| | - Richard S. Ruiz
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School, The University of Texas Health Science Center, Houston, Texas, United States
| | - Mark E. Pennesi
- Casey Eye Institute, Oregon Health and Science University, Portland, Oregon, United States
| | - Paul Yang
- Casey Eye Institute, Oregon Health and Science University, Portland, Oregon, United States
| | - David Davis-Boozer
- Casey Eye Institute, Oregon Health and Science University, Portland, Oregon, United States
| | - Hope Northrup
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center, Houston, Texas, United States
| | | | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Mingchu Xu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - David G. Birch
- Retina Foundation of the Southwest, Dallas, Texas, United States
| | - Stephen P. Daiger
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, Texas, United States
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School, The University of Texas Health Science Center, Houston, Texas, United States
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Ezquerra-Inchausti M, Barandika O, Anasagasti A, Irigoyen C, López de Munain A, Ruiz-Ederra J. High prevalence of mutations affecting the splicing process in a Spanish cohort with autosomal dominant retinitis pigmentosa. Sci Rep 2017; 7:39652. [PMID: 28045043 PMCID: PMC5206707 DOI: 10.1038/srep39652] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 11/24/2016] [Indexed: 01/24/2023] Open
Abstract
Retinitis pigmentosa is the most frequent group of inherited retinal dystrophies. It is highly heterogeneous, with more than 80 disease-causing genes 27 of which are known to cause autosomal dominant RP (adRP), having been identified. In this study a total of 29 index cases were ascertained based on a family tree compatible with adRP. A custom panel of 31 adRP genes was analysed by targeted next-generation sequencing using the Ion PGM platform in combination with Sanger sequencing. This allowed us to detect putative disease-causing mutations in 14 out of the 29 (48.28%) families analysed. Remarkably, around 38% of all adRP cases analysed showed mutations affecting the splicing process, mainly due to mutations in genes coding for spliceosome factors (SNRNP200 and PRPF8) but also due to splice-site mutations in RHO. Twelve of the 14 mutations found had been reported previously and two were novel mutations found in PRPF8 in two unrelated patients. In conclusion, our results will lead to more accurate genetic counselling and will contribute to a better characterisation of the disease. In addition, they may have a therapeutic impact in the future given the large number of studies currently underway based on targeted RNA splicing for therapeutic purposes.
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Affiliation(s)
| | - Olatz Barandika
- Division of Neurosciences, Biodonostia Health Research Institute, San Sebastián, Spain
| | - Ander Anasagasti
- Division of Neurosciences, Biodonostia Health Research Institute, San Sebastián, Spain
| | - Cristina Irigoyen
- Division of Neurosciences, Biodonostia Health Research Institute, San Sebastián, Spain.,Department of Ophthalmology, Donostia University Hospital, San Sebastián, Spain
| | - Adolfo López de Munain
- Division of Neurosciences, Biodonostia Health Research Institute, San Sebastián, Spain.,Department of Neurology, Donostia University Hospital, San Sebastián, Spain.,CIBERNED, Center for Networked Biomedical Research on Neurodegenerative Diseases, Institute of Health Carlos III, Ministry of Economy and Competitiveness, Spain.,Department of Neurosciences, University of the Basque Country UPV-EHU, Spain
| | - Javier Ruiz-Ederra
- Division of Neurosciences, Biodonostia Health Research Institute, San Sebastián, Spain
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Zhang Q, Xu M, Verriotto JD, Li Y, Wang H, Gan L, Lam BL, Chen R. Next-generation sequencing-based molecular diagnosis of 35 Hispanic retinitis pigmentosa probands. Sci Rep 2016; 6:32792. [PMID: 27596865 PMCID: PMC5011706 DOI: 10.1038/srep32792] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/29/2016] [Indexed: 12/13/2022] Open
Abstract
Retinitis pigmentosa (RP) is a heterogeneous group of inherited retinal diseases. The prevalence of RP and the mutation spectrum vary across populations. Hispanic people account for approximately 17% of the United States population, and the genetic etiologies of RP of this ethnic group still remain not well defined. Utilizing next-generation sequencing (NGS), we screened mutations in known retinal disease-causing genes in an RP cohort of 35 unrelated Hispanic probands from the Miami area. We achieved a solving rate of 66% and identified 15 novel putative pathogenic mutations, including a frequent founder mutation disrupting PRPF31 splicing. Our data show that the mutation spectrum of Hispanic RP receives a significant impact from disease-causing alleles of Spanish origin and may also contain population-specific alleles.
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Affiliation(s)
- Qi Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Mingchu Xu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Jennifer D. Verriotto
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Hui Wang
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Lin Gan
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Byron L. Lam
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, Texas, USA
- The Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA
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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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Comparative sequence analyses of rhodopsin and RPE65 reveal patterns of selective constraint across hereditary retinal disease mutations. Vis Neurosci 2016; 33:e002. [DOI: 10.1017/s0952523815000322] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
AbstractRetinitis pigmentosa (RP) comprises several heritable diseases that involve photoreceptor, and ultimately retinal, degeneration. Currently, mutations in over 50 genes have known links to RP. Despite advances in clinical characterization, molecular characterization of RP remains challenging due to the heterogeneous nature of causal genes, mutations, and clinical phenotypes. In this study, we compiled large datasets of two important visual genes associated with RP: rhodopsin, which initiates the phototransduction cascade, and the retinoid isomerase RPE65, which regenerates the visual cycle. We used a comparative evolutionary approach to investigate the relationship between interspecific sequence variation and pathogenic mutations that lead to degenerative retinal disease. Using codon-based likelihood methods, we estimated evolutionary rates (dN/dS) across both genes in a phylogenetic context to investigate differences between pathogenic and nonpathogenic amino acid sites. In both genes, disease-associated sites showed significantly lower evolutionary rates compared to nondisease sites, and were more likely to occur in functionally critical areas of the proteins. The nature of the dataset (e.g., vertebrate or mammalian sequences), as well as selection of pathogenic sites, affected the differences observed between pathogenic and nonpathogenic sites. Our results illustrate that these methods can serve as an intermediate step in understanding protein structure and function in a clinical context, particularly in predicting the relative pathogenicity (i.e., functional impact) of point mutations and their downstream phenotypic effects. Extensions of this approach may also contribute to current methods for predicting the deleterious effects of candidate mutations and to the identification of protein regions under strong constraint where we expect pathogenic mutations to occur.
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18
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de Sousa Dias M, Hernan I, Delás B, Pascual B, Borràs E, Gamundi MJ, Mañé B, Fernández-San José P, Ayuso C, Carballo M. New COL6A6 variant detected by whole-exome sequencing is linked to break points in intron 4 and 3'-UTR, deleting exon 5 of RHO, and causing adRP. Mol Vis 2015; 21:857-70. [PMID: 26321861 PMCID: PMC4539015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 08/15/2015] [Indexed: 11/30/2022] Open
Abstract
PURPOSE This study aimed to test a newly devised cost-effective multiplex PCR assay for the molecular diagnosis of autosomal dominant retinitis pigmentosa (adRP), as well as the use of whole-exome sequencing (WES) to detect disease-causing mutations in adRP. METHODS Genomic DNA was extracted from peripheral blood lymphocytes of index patients with adRP and their affected and unaffected family members. We used a newly devised multiplex PCR assay capable of amplifying the genetic loci of RHO, PRPH2, RP1, PRPF3, PRPF8, PRPF31, IMPDH1, NRL, CRX, KLHL7, and NR2E3 to molecularly diagnose 18 index patients with adRP. We also performed WES in affected and unaffected members of four families with adRP in whom a disease-causing mutation was previously not found. RESULTS We identified five previously reported mutations (p.Arg677X in the RP1 gene, p.Asp133Val and p.Arg195Leu in the PRPH2 gene, and p.Pro171Leu and p.Pro215Leu in the RHO gene) and one novel mutation (p.Val345Gly in the RHO gene) representing 33% detection of causative mutations in our adRP cohort. Comparative WES analysis showed a new variant (p.Gly103Arg in the COL6A6 gene) that segregated with the disease in one family with adRP. As this variant was linked with the RHO locus, we sequenced the complete RHO gene, which revealed a deletion in intron 4 that encompassed all of exon 5 and 28 bp of the 3'-untranslated region (UTR). CONCLUSIONS The novel multiplex PCR assay with next-generation sequencing (NGS) proved effective for detecting most of the adRP-causing mutations. A WES approach led to identification of a deletion in RHO through detection of a new linked variant in COL6A6. No pathogenic variants were identified in the remaining three families. Moreover, NGS and WES were inefficient for detecting the complete deletion of exon 5 in the RHO gene in one family with adRP. Carriers of this deletion showed variable clinical status, and two of these carriers had not previously been diagnosed with RP.
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Affiliation(s)
| | - Imma Hernan
- Molecular Genetics Unit, Hospital of Terrassa, Barcelona, Spain
| | - Barbara Delás
- Ophthalmology Service, Hospital of Terrassa Barcelona, Spain
| | - Beatriz Pascual
- Molecular Genetics Unit, Hospital of Terrassa, Barcelona, Spain
| | - Emma Borràs
- Molecular Genetics Unit, Hospital of Terrassa, Barcelona, Spain
| | | | - Begoña Mañé
- Molecular Genetics Unit, Hospital of Terrassa, Barcelona, Spain
| | - Patricia Fernández-San José
- Department of Genetics, IIS-Jimenez Diaz Foundation (IIS-FJD), Madrid, Spain,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics, IIS-Jimenez Diaz Foundation (IIS-FJD), Madrid, Spain,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Miguel Carballo
- Molecular Genetics Unit, Hospital of Terrassa, Barcelona, Spain
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Application of Whole Exome Sequencing in Six Families with an Initial Diagnosis of Autosomal Dominant Retinitis Pigmentosa: Lessons Learned. PLoS One 2015. [PMID: 26197217 PMCID: PMC4509755 DOI: 10.1371/journal.pone.0133624] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
This study aimed to identify the genetics underlying dominant forms of inherited retinal dystrophies using whole exome sequencing (WES) in six families extensively screened for known mutations or genes. Thirty-eight individuals were subjected to WES. Causative variants were searched among single nucleotide variants (SNVs) and insertion/deletion variants (indels) and whenever no potential candidate emerged, copy number variant (CNV) analysis was performed. Variants or regions harboring a candidate variant were prioritized and segregation of the variant with the disease was further assessed using Sanger sequencing in case of SNVs and indels, and quantitative PCR (qPCR) for CNVs. SNV and indel analysis led to the identification of a previously reported mutation in PRPH2. Two additional mutations linked to different forms of retinal dystrophies were identified in two families: a known frameshift deletion in RPGR, a gene responsible for X-linked retinitis pigmentosa and p.Ser163Arg in C1QTNF5 associated with Late-Onset Retinal Degeneration. A novel heterozygous deletion spanning the entire region of PRPF31 was also identified in the affected members of a fourth family, which was confirmed with qPCR. This study allowed the identification of the genetic cause of the retinal dystrophy and the establishment of a correct diagnosis in four families, including a large heterozygous deletion in PRPF31, typically considered one of the pitfalls of this method. Since all findings in this study are restricted to known genes, we propose that targeted sequencing using gene-panel is an optimal first approach for the genetic screening and that once known genetic causes are ruled out, WES might be used to uncover new genes involved in inherited retinal dystrophies.
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Yang HJ, Ratnapriya R, Cogliati T, Kim JW, Swaroop A. Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease. Prog Retin Eye Res 2015; 46:1-30. [PMID: 25668385 PMCID: PMC4402139 DOI: 10.1016/j.preteyeres.2015.01.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 01/18/2015] [Accepted: 01/21/2015] [Indexed: 01/10/2023]
Abstract
Genomics and genetics have invaded all aspects of biology and medicine, opening uncharted territory for scientific exploration. The definition of "gene" itself has become ambiguous, and the central dogma is continuously being revised and expanded. Computational biology and computational medicine are no longer intellectual domains of the chosen few. Next generation sequencing (NGS) technology, together with novel methods of pattern recognition and network analyses, has revolutionized the way we think about fundamental biological mechanisms and cellular pathways. In this review, we discuss NGS-based genome-wide approaches that can provide deeper insights into retinal development, aging and disease pathogenesis. We first focus on gene regulatory networks (GRNs) that govern the differentiation of retinal photoreceptors and modulate adaptive response during aging. Then, we discuss NGS technology in the context of retinal disease and develop a vision for therapies based on network biology. We should emphasize that basic strategies for network construction and analyses can be transported to any tissue or cell type. We believe that specific and uniform guidelines are required for generation of genome, transcriptome and epigenome data to facilitate comparative analysis and integration of multi-dimensional data sets, and for constructing networks underlying complex biological processes. As cellular homeostasis and organismal survival are dependent on gene-gene and gene-environment interactions, we believe that network-based biology will provide the foundation for deciphering disease mechanisms and discovering novel drug targets for retinal neurodegenerative diseases.
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Affiliation(s)
- Hyun-Jin Yang
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Rinki Ratnapriya
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Tiziana Cogliati
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Jung-Woong Kim
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA.
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21
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Wu Z, Hiriyanna S, Qian H, Mookherjee S, Campos MM, Gao C, Fariss R, Sieving PA, Li T, Colosi P, Swaroop A. A long-term efficacy study of gene replacement therapy for RPGR-associated retinal degeneration. Hum Mol Genet 2015; 24:3956-70. [PMID: 25877300 DOI: 10.1093/hmg/ddv134] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 04/13/2015] [Indexed: 11/14/2022] Open
Abstract
Mutations in the retinitis pigmentosa GTPase regulator (RPGR) gene account for >70% of X-linked retinitis pigmentosa (XLRP) and 15-20% of all inherited retinal degeneration. Gene replacement therapy for RPGR-XLRP was hampered by the relatively slow disease progression in mouse models and by difficulties in cloning the full-length RPGR-ORF15 cDNA that includes a purine-rich 3'-coding region; however, its effectiveness has recently been demonstrated in four dogs with RPGR mutations. To advance the therapy to clinical stage, we generated new stable vectors in AAV8 or AAV9 carrying mouse and human full-length RPGR-ORF15-coding sequence and conducted a comprehensive long-term dose-efficacy study in Rpgr-knockout mice. After validating their ability to produce full-length proteins that localize to photoreceptor connecting cilia, we evaluated various vector doses in mice during a 2-year study. We demonstrate that eyes treated with a single injection of mouse or human RPGR-ORF15 vector at an optimal dose maintained the expression of RPGR-ORF15 throughout the study duration and exhibited higher electroretinogram amplitude, thicker photoreceptor layer and better targeting of opsins to outer segments compared with sham-treated eyes. Furthermore, mice that received treatment at an advanced age also showed remarkable preservation of retinal structure and function. Retinal toxicity was observed at high vector doses, highlighting the importance of careful dose optimization in future clinical experiments. Our long-term dose-efficacy study should facilitate the design of human trials with human RPGR-ORF15 vector as a clinical candidate.
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Affiliation(s)
- Zhijian Wu
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Suja Hiriyanna
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Haohua Qian
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Maria M Campos
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chun Gao
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert Fariss
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul A Sieving
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tiansen Li
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Colosi
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anand Swaroop
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
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22
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Fernandez-San Jose P, Blanco-Kelly F, Corton M, Trujillo-Tiebas MJ, Gimenez A, Avila-Fernandez A, Garcia-Sandoval B, Lopez-Molina MI, Hernan I, Carballo M, Riveiro-Alvarez R, Ayuso C. Prevalence of Rhodopsin mutations in autosomal dominant Retinitis Pigmentosa in Spain: clinical and analytical review in 200 families. Acta Ophthalmol 2015; 93:e38-44. [PMID: 25408095 DOI: 10.1111/aos.12486] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 05/24/2014] [Indexed: 01/31/2023]
Abstract
PURPOSE We aimed to determine the prevalence of mutations in the RHO gene in Spanish families with autosomal dominant Retinitis Pigmentosa (adRP), to assess genotype-phenotype correlations and to establish an accurate diagnostic algorithm after 23 years of data collection. PATIENTS AND METHODS Two hundred patients were analysed through a combination of denaturing gradient gel electrophoresis, single-strand conformation polymorphism, genotyping microarray and Sanger sequencing of the RHO gene. RESULTS Overall, 42 of 200 Spanish adRP families were mutated for RHO (21.0%). Twenty-seven different RHO mutations were detected; seven of them were novel. A genotype-phenotype correlation was established with clinical data from 107 patients. The most prevalent p.Pro347Leu mutation, responsible for 4.5% (9/200) of all mutated adRP families, was associated with a phenotype of early onset and severe course diffuse RP. CONCLUSIONS This retrospective study provides a wide spectrum of mutations in the RHO gene in Spanish patients with adRP. Also, the prevalence of mutations is similar to that reported in European population. Genotyping microarray followed by RHO sequencing is proposed as a first step in molecular diagnosis of adRP Spanish families. An increasing understanding of causal RHO alleles in adRP facilitates disease diagnosis and prognosis, especially for the prevalent p.Pro347Leu mutation.
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Affiliation(s)
- Patricia Fernandez-San Jose
- Department of Genetics; Health Research Institute Fundacion Jimenez Diaz; University Hospital (IIS-FJD, UAM); Madrid Spain
- Centre for Biomedical Network Research on Rare Diseases CIBERER; ISCIII; Madrid Spain
| | - Fiona Blanco-Kelly
- Department of Genetics; Health Research Institute Fundacion Jimenez Diaz; University Hospital (IIS-FJD, UAM); Madrid Spain
- Centre for Biomedical Network Research on Rare Diseases CIBERER; ISCIII; Madrid Spain
| | - Marta Corton
- Department of Genetics; Health Research Institute Fundacion Jimenez Diaz; University Hospital (IIS-FJD, UAM); Madrid Spain
- Centre for Biomedical Network Research on Rare Diseases CIBERER; ISCIII; Madrid Spain
| | - Maria-Jose Trujillo-Tiebas
- Department of Genetics; Health Research Institute Fundacion Jimenez Diaz; University Hospital (IIS-FJD, UAM); Madrid Spain
- Centre for Biomedical Network Research on Rare Diseases CIBERER; ISCIII; Madrid Spain
| | - Ascension Gimenez
- Department of Genetics; Health Research Institute Fundacion Jimenez Diaz; University Hospital (IIS-FJD, UAM); Madrid Spain
- Centre for Biomedical Network Research on Rare Diseases CIBERER; ISCIII; Madrid Spain
| | - Almudena Avila-Fernandez
- Department of Genetics; Health Research Institute Fundacion Jimenez Diaz; University Hospital (IIS-FJD, UAM); Madrid Spain
- Centre for Biomedical Network Research on Rare Diseases CIBERER; ISCIII; Madrid Spain
| | - Blanca Garcia-Sandoval
- Centre for Biomedical Network Research on Rare Diseases CIBERER; ISCIII; Madrid Spain
- Department of Ophthalmology; Health Research Institute Fundacion Jimenez Diaz; University Hospital (IIS-FJD, UAM); Madrid Spain
| | - Maria-Isabel Lopez-Molina
- Centre for Biomedical Network Research on Rare Diseases CIBERER; ISCIII; Madrid Spain
- Department of Ophthalmology; Health Research Institute Fundacion Jimenez Diaz; University Hospital (IIS-FJD, UAM); Madrid Spain
| | - Inma Hernan
- Molecular Genetics Unit; Hospital de Terrassa; Terrassa Barcelona Spain
| | - Miguel Carballo
- Molecular Genetics Unit; Hospital de Terrassa; Terrassa Barcelona Spain
| | - Rosa Riveiro-Alvarez
- Department of Genetics; Health Research Institute Fundacion Jimenez Diaz; University Hospital (IIS-FJD, UAM); Madrid Spain
- Centre for Biomedical Network Research on Rare Diseases CIBERER; ISCIII; Madrid Spain
| | - Carmen Ayuso
- Department of Genetics; Health Research Institute Fundacion Jimenez Diaz; University Hospital (IIS-FJD, UAM); Madrid Spain
- Centre for Biomedical Network Research on Rare Diseases CIBERER; ISCIII; Madrid Spain
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23
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Lenarduzzi S, Vozzi D, Morgan A, Rubinato E, D'Eustacchio A, Osland TM, Rossi C, Graziano C, Castorina P, Ambrosetti U, Morgutti M, Girotto G. Usher syndrome: an effective sequencing approach to establish a genetic and clinical diagnosis. Hear Res 2015; 320:18-23. [PMID: 25575603 DOI: 10.1016/j.heares.2014.12.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 12/18/2014] [Accepted: 12/22/2014] [Indexed: 02/06/2023]
Abstract
Usher syndrome is an autosomal recessive disorder characterized by retinitis pigmentosa, sensorineural hearing loss and, in some cases, vestibular dysfunction. The disorder is clinically and genetically heterogeneous and, to date, mutations in 11 genes have been described. This finding makes difficult to get a precise molecular diagnosis and offer patients accurate genetic counselling. To overcome this problem and to increase our knowledge of the molecular basis of Usher syndrome, we designed a targeted resequencing custom panel. In a first validation step a series of 16 Italian patients with known molecular diagnosis were analysed and 31 out of 32 alleles were detected (97% of accuracy). After this step, 31 patients without a molecular diagnosis were enrolled in the study. Three out of them with an uncertain Usher diagnosis were excluded. One causative allele was detected in 24 out 28 patients (86%) while the presence of both causative alleles characterized 19 patients out 28 (68%). Sixteen novel and 27 known alleles were found in the following genes: USH2A (50%), MYO7A (7%), CDH23 (11%), PCDH15 (7%) and USH1G (2%). Overall, on the 44 patients the protocol was able to characterize 74 alleles out of 88 (84%). These results suggest that our panel is an effective approach for the genetic diagnosis of Usher syndrome leading to: 1) an accurate molecular diagnosis, 2) better genetic counselling, 3) more precise molecular epidemiology data fundamental for future interventional plans.
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Affiliation(s)
- S Lenarduzzi
- Department of Medical Sciences, University of Trieste, Italy
| | - D Vozzi
- Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", Trieste, Italy
| | - A Morgan
- Department of Medical Sciences, University of Trieste, Italy
| | - E Rubinato
- Department of Medical Sciences, University of Trieste, Italy
| | - A D'Eustacchio
- Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", Trieste, Italy
| | - T M Osland
- Department of Medical Sciences, University of Trieste, Italy
| | - C Rossi
- Department of Genetics, University of Bologna, Policlinico S. Orsola-Malpighi, Bologna, Italy
| | - C Graziano
- Department of Genetics, University of Bologna, Policlinico S. Orsola-Malpighi, Bologna, Italy
| | - P Castorina
- UO Audiology, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Mangiagalli e Regina Elena, Milan, Italy
| | - U Ambrosetti
- UO Audiology, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Mangiagalli e Regina Elena, Milan, Italy; Audiology Unit, Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - M Morgutti
- Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", Trieste, Italy
| | - G Girotto
- Department of Medical Sciences, University of Trieste, Italy.
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24
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Rossmiller BP, Ryals RC, Lewin AS. Gene therapy to rescue retinal degeneration caused by mutations in rhodopsin. Methods Mol Biol 2015; 1271:391-410. [PMID: 25697537 PMCID: PMC4696870 DOI: 10.1007/978-1-4939-2330-4_25] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Retinal gene therapy has proven safe and at least partially successful in clinical trials and in numerous animal models. Gene therapy requires characterization of the progression of the disease and understanding of its genetic cause. Testing gene therapies usually requires an animal model that recapitulates the key features of the human disease, though photoreceptors and cells of the retinal pigment epithelium produced from patient-derived stem cells may provide an alternative test system for retinal gene therapy. Gene therapy also requires a delivery system that introduces the therapeutic gene to the correct cell type and does not cause unintended damage to the tissue. Current systems being tested in the eye are nanoparticles, pseudotyped lentiviruses, and adeno-associated virus (AAV) of various serotypes. Here, we describe the techniques of AAV vector design as well as the in vivo and ex vivo tests necessary for assessing the efficacy of retinal gene therapy to treat retinal degeneration caused by mutations in the rhodopsin gene.
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Affiliation(s)
- Brian P Rossmiller
- Department of Opthalmology, University of Florida, Box 100284, Gainesville, FL, 32610-0284, USA
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25
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Daiger SP, Bowne SJ, Sullivan LS. Genes and Mutations Causing Autosomal Dominant Retinitis Pigmentosa. Cold Spring Harb Perspect Med 2014; 5:a017129. [PMID: 25304133 PMCID: PMC4588133 DOI: 10.1101/cshperspect.a017129] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Retinitis pigmentosa (RP) has a prevalence of approximately one in 4000; 25%-30% of these cases are autosomal dominant retinitis pigmentosa (adRP). Like other forms of inherited retinal disease, adRP is exceptionally heterogeneous. Mutations in more than 25 genes are known to cause adRP, more than 1000 mutations have been reported in these genes, clinical findings are highly variable, and there is considerable overlap with other types of inherited disease. Currently, it is possible to detect disease-causing mutations in 50%-75% of adRP families in select populations. Genetic diagnosis of adRP has advantages over other forms of RP because segregation of disease in families is a useful tool for identifying and confirming potentially pathogenic variants, but there are disadvantages too. In addition to identifying the cause of disease in the remaining 25% of adRP families, a central challenge is reconciling clinical diagnosis, family history, and molecular findings in patients and families.
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Affiliation(s)
- Stephen P Daiger
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, Texas 77030
| | - Sara J Bowne
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, Texas 77030
| | - Lori S Sullivan
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, Texas 77030
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26
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Sullivan LS, Koboldt DC, Bowne SJ, Lang S, Blanton SH, Cadena E, Avery CE, Lewis RA, Webb-Jones K, Wheaton DH, Birch DG, Coussa R, Ren H, Lopez I, Chakarova C, Koenekoop RK, Garcia CA, Fulton RS, Wilson RK, Weinstock GM, Daiger SP. A dominant mutation in hexokinase 1 (HK1) causes retinitis pigmentosa. Invest Ophthalmol Vis Sci 2014; 55:7147-58. [PMID: 25190649 DOI: 10.1167/iovs.14-15419] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To identify the cause of retinitis pigmentosa (RP) in UTAD003, a large, six-generation Louisiana family with autosomal dominant retinitis pigmentosa (adRP). METHODS A series of strategies, including candidate gene screening, linkage exclusion, genome-wide linkage mapping, and whole-exome next-generation sequencing, was used to identify a mutation in a novel disease gene on chromosome 10q22.1. Probands from an additional 404 retinal degeneration families were subsequently screened for mutations in this gene. RESULTS Exome sequencing in UTAD003 led to identification of a single, novel coding variant (c.2539G>A, p.Glu847Lys) in hexokinase 1 (HK1) present in all affected individuals and absent from normal controls. One affected family member carries two copies of the mutation and has an unusually severe form of disease, consistent with homozygosity for this mutation. Screening of additional adRP probands identified four other families (American, Canadian, and Sicilian) with the same mutation and a similar range of phenotypes. The families share a rare 450-kilobase haplotype containing the mutation, suggesting a founder mutation among otherwise unrelated families. CONCLUSIONS We identified an HK1 mutation in five adRP families. Hexokinase 1 catalyzes phosphorylation of glucose to glucose-6-phosphate. HK1 is expressed in retina, with two abundant isoforms expressed at similar levels. The Glu847Lys mutation is located at a highly conserved position in the protein, outside the catalytic domains. We hypothesize that the effect of this mutation is limited to the retina, as no systemic abnormalities in glycolysis were detected. Prevalence of the HK1 mutation in our cohort of RP families is 1%.
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Affiliation(s)
- Lori S Sullivan
- Human Genetics Center, University of Texas Health Science Center, Houston, Texas, United States
| | - Daniel C Koboldt
- The Genome Institute at Washington University, St. Louis, Missouri, United States
| | - Sara J Bowne
- Human Genetics Center, University of Texas Health Science Center, Houston, Texas, United States
| | - Steven Lang
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, United States
| | - Susan H Blanton
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, United States
| | - Elizabeth Cadena
- Human Genetics Center, University of Texas Health Science Center, Houston, Texas, United States
| | - Cheryl E Avery
- Human Genetics Center, University of Texas Health Science Center, Houston, Texas, United States
| | - Richard A Lewis
- Departments of Ophthalmology, Medicine, Pediatrics, and Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Kaylie Webb-Jones
- The Retina Foundation of the Southwest, Dallas, Texas, United States
| | - Dianna H Wheaton
- The Retina Foundation of the Southwest, Dallas, Texas, United States
| | - David G Birch
- The Retina Foundation of the Southwest, Dallas, Texas, United States
| | - Razck Coussa
- McGill Ocular Genetics Laboratory, Departments of Paediatric Surgery, Human Genetics, and Ophthalmology, McGill University Health Center, Montreal, Quebec, Canada
| | - Huanan Ren
- McGill Ocular Genetics Laboratory, Departments of Paediatric Surgery, Human Genetics, and Ophthalmology, McGill University Health Center, Montreal, Quebec, Canada
| | - Irma Lopez
- McGill Ocular Genetics Laboratory, Departments of Paediatric Surgery, Human Genetics, and Ophthalmology, McGill University Health Center, Montreal, Quebec, Canada
| | - Christina Chakarova
- Institute of Ophthalmology, University College London, London, United Kingdom
| | - Robert K Koenekoop
- McGill Ocular Genetics Laboratory, Departments of Paediatric Surgery, Human Genetics, and Ophthalmology, McGill University Health Center, Montreal, Quebec, Canada
| | - Charles A Garcia
- Department of Ophthalmology and Visual Sciences, University of Texas Health Science Center, Houston, Texas, United States
| | - Robert S Fulton
- The Genome Institute at Washington University, St. Louis, Missouri, United States
| | - Richard K Wilson
- The Genome Institute at Washington University, St. Louis, Missouri, United States
| | - George M Weinstock
- The Genome Institute at Washington University, St. Louis, Missouri, United States
| | - Stephen P Daiger
- Human Genetics Center, University of Texas Health Science Center, Houston, Texas, United States Department of Ophthalmology and Visual Sciences, University of Texas Health Science Center, Houston, Texas, United States
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27
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Watson CM, El-Asrag M, Parry DA, Morgan JE, Logan CV, Carr IM, Sheridan E, Charlton R, Johnson CA, Taylor G, Toomes C, McKibbin M, Inglehearn CF, Ali M. Mutation screening of retinal dystrophy patients by targeted capture from tagged pooled DNAs and next generation sequencing. PLoS One 2014; 9:e104281. [PMID: 25133751 PMCID: PMC4136783 DOI: 10.1371/journal.pone.0104281] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 07/07/2014] [Indexed: 12/30/2022] Open
Abstract
Purpose Retinal dystrophies are genetically heterogeneous, resulting from mutations in over 200 genes. Prior to the development of massively parallel sequencing, comprehensive genetic screening was unobtainable for most patients. Identifying the causative genetic mutation facilitates genetic counselling, carrier testing and prenatal/pre-implantation diagnosis, and often leads to a clearer prognosis. In addition, in a proportion of cases, when the mutation is known treatment can be optimised and patients are eligible for enrolment into clinical trials for gene-specific therapies. Methods Patient genomic DNA was sheared, tagged and pooled in batches of four samples, prior to targeted capture and next generation sequencing. The enrichment reagent was designed against genes listed on the RetNet database (July 2010). Sequence data were aligned to the human genome and variants were filtered to identify potential pathogenic mutations. These were confirmed by Sanger sequencing. Results Molecular analysis of 20 DNAs from retinal dystrophy patients identified likely pathogenic mutations in 12 cases, many of them known and/or confirmed by segregation. These included previously described mutations in ABCA4 (c.6088C>T,p.R2030*; c.5882G>A,p.G1961E), BBS2 (c.1895G>C,p.R632P), GUCY2D (c.2512C>T,p.R838C), PROM1 (c.1117C>T,p.R373C), RDH12 (c.601T>C,p.C201R; c.506G>A,p.R169Q), RPGRIP1 (c.3565C>T,p.R1189*) and SPATA7 (c.253C>T,p.R85*) and new mutations in ABCA4 (c.3328+1G>C), CRB1 (c.2832_2842+23del), RP2 (c.884-1G>T) and USH2A (c.12874A>G,p.N4292D). Conclusions Tagging and pooling DNA prior to targeted capture of known retinal dystrophy genes identified mutations in 60% of cases. This relatively high success rate may reflect enrichment for consanguineous cases in the local Yorkshire population, and the use of multiplex families. Nevertheless this is a promising high throughput approach to retinal dystrophy diagnostics.
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Affiliation(s)
- Christopher M. Watson
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, United Kingdom
| | - Mohammed El-Asrag
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - David A. Parry
- Section of Genetics, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Joanne E. Morgan
- Section of Genetics, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Clare V. Logan
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Ian M. Carr
- Section of Genetics, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Eamonn Sheridan
- Section of Genetics, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Ruth Charlton
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, United Kingdom
| | - Colin A. Johnson
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Graham Taylor
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, United Kingdom
| | - Carmel Toomes
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Martin McKibbin
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom
- Department of Ophthalmology, St. James's University Hospital, Leeds, United Kingdom
| | - Chris F. Inglehearn
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Manir Ali
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, Leeds, United Kingdom
- * E-mail:
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28
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Shen S, Sujirakul T, Tsang SH. Next-generation sequencing revealed a novel mutation in the gene encoding the beta subunit of rod phosphodiesterase. Ophthalmic Genet 2014; 35:142-50. [PMID: 24828262 DOI: 10.3109/13816810.2014.915328] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE To report the phenotypes caused by a novel mutation in the PDE6B gene in a family with two affected siblings and one affected cousin with a 2-year follow-up. DESIGN Three patients from a family with a history of retinitis pigmentosa underwent clinical evaluations. The affected patients' DNA was analyzed using next-generation sequencing and segregation analyses were performed for the family. SETTING Edward S. Harkness Eye Institute, New York Presbyterian Hospital. PARTICIPANTS Two siblings, one cousin, and five unaffected family members. MAIN OUTCOME MEASURES Macular appearance assessed by funduscopy, autofluorescence imaging, spectral-domain optical coherence tomography and visual function assessed by electroretinography. RESULTS The proband, brother, and cousin had rod-cone degeneration with cystoid macular edema. Fundus autofluorescence showed hyperautofluorescent ring constriction over time. Spectral-domain optical coherence tomography revealed retinal pigment epithelium atrophy, loss of external limiting membrane, retinal layer thinning, and reduction in ellipsoid zone length over time. Next-generation whole exome sequencing revealed a homozygous c.1923_1969ins6del47 nonsense PDE6B mutation, which has not been previously described, that segregated with the disease in the family. CONCLUSIONS The homozygous PDE6B mutation causes retinitis pigmentosa. Acetazolamide treatment improved visual acuity but rod degeneration continued. Despite having the same mutation and living in the same environment, the proband's brother progressed at a faster rate starting at a younger age, suggesting that gene modifiers may influence the expressivity of the phenotype. Next-generation sequencing, used to discover this mutation, is a practical new technology that can detect novel disease-causing alleles, where previous arrayed primer extension (APEX) technology could not.
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Affiliation(s)
- Sherry Shen
- College of Physicians & Surgeons, Columbia University , New York, NY , USA
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Abstract
Genetics has been revolutionised by recent technologies. The latest addition to these advances is next-generation sequencing, which is set to transform clinical diagnostics in every branch of medicine. In the research arena this has already been instrumental in identifying hundreds of novel genetic syndromes, making a molecular diagnosis possible for the first time in numerous refractory cases. However, the pace of change has left many clinicians bewildered by new terminology and the implications of next-generation sequencing for their clinical practice. The rapid developments have also left many diagnostic laboratories struggling to implement these new technologies with limited resources. This review explains the basic concepts of next-generation sequencing, gives examples of its role in clinically applied research and examines the challenges of its introduction into clinical practice.
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Anasagasti A, Barandika O, Irigoyen C, Benitez BA, Cooper B, Cruchaga C, López de Munain A, Ruiz-Ederra J. Genetic high throughput screening in Retinitis Pigmentosa based on high resolution melting (HRM) analysis. Exp Eye Res 2014; 116:386-394. [PMID: 24416769 DOI: 10.1016/j.exer.2013.10.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Retinitis Pigmentosa (RP) involves a group of genetically determined retinal diseases caused by a large number of mutations that result in rod photoreceptor cell death followed by gradual death of cone cells. Most cases of RP are monogenic, with more than 80 associated genes identified so far. The high number of genes and variants involved in RP, among other factors, is making the molecular characterization of RP a real challenge for many patients. Although HRM has been used for the analysis of isolated variants or single RP genes, as far as we are concerned, this is the first study that uses HRM analysis for a high-throughput screening of several RP genes. Our main goal was to test the suitability of HRM analysis as a genetic screening technique in RP, and to compare its performance with two of the most widely used NGS platforms, Illumina and PGM-Ion Torrent technologies. RP patients (n = 96) were clinically diagnosed at the Ophthalmology Department of Donostia University Hospital, Spain. We analyzed a total of 16 RP genes that meet the following inclusion criteria: 1) size: genes with transcripts of less than 4 kb; 2) number of exons: genes with up to 22 exons; and 3) prevalence: genes reported to account for, at least, 0.4% of total RP cases worldwide. For comparison purposes, RHO gene was also sequenced with Illumina (GAII; Illumina), Ion semiconductor technologies (PGM; Life Technologies) and Sanger sequencing (ABI 3130xl platform; Applied Biosystems). Detected variants were confirmed in all cases by Sanger sequencing and tested for co-segregation in the family of affected probands. We identified a total of 65 genetic variants, 15 of which (23%) were novel, in 49 out of 96 patients. Among them, 14 (4 novel) are probable disease-causing genetic variants in 7 RP genes, affecting 15 patients. Our HRM analysis-based study, proved to be a cost-effective and rapid method that provides an accurate identification of genetic RP variants. This approach is effective for medium sized (<4 kb transcript) RP genes, which constitute over 80% of the total of known RP genes.
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Affiliation(s)
- Ander Anasagasti
- Department of Neuroscience, Instituto Biodonostia, Paseo Dr. Begiristain s/n, E-20014 San Sebastián, Spain
| | - Olatz Barandika
- Department of Neuroscience, Instituto Biodonostia, Paseo Dr. Begiristain s/n, E-20014 San Sebastián, Spain
| | - Cristina Irigoyen
- Department of Ophthalmology, Hospital Universitario Donostia, San Sebastián, Spain
| | - Bruno A Benitez
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Breanna Cooper
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University, St. Louis, MO, USA; Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University, St. Louis, MO, USA
| | - Adolfo López de Munain
- Department of Neuroscience, Instituto Biodonostia, Paseo Dr. Begiristain s/n, E-20014 San Sebastián, Spain; Department of Neurology, Hospital Universitario Donostia, San Sebastián, Spain; CIBERNED, Centro de Investigaciones Biomédicas en Red sobre Enfermedades Neurodegenerativas, Instituto Carlos III, Ministerio de Economía y Competitividad, Spain; Department of Neurosciences, University of the Basque Country UPV-EHU, Spain; Euskampus, University of the Basque Country UPV-EHU, Spain
| | - Javier Ruiz-Ederra
- Department of Neuroscience, Instituto Biodonostia, Paseo Dr. Begiristain s/n, E-20014 San Sebastián, Spain.
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31
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Daiger SP, Bowne SJ, Sullivan LS, Blanton SH, Weinstock GM, Koboldt DC, Fulton RS, Larsen D, Humphries P, Humphries MM, Pierce EA, Chen R, Li Y. Application of next-generation sequencing to identify genes and mutations causing autosomal dominant retinitis pigmentosa (adRP). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 801:123-9. [PMID: 24664689 DOI: 10.1007/978-1-4614-3209-8_16] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The goal of our research is to identify genes and mutations causing autosomal dominant retinitis pigmentosa (adRP). For this purpose we established a cohort of more than 250 independently ascertained families with adRP in the Houston Laboratory for Molecular Diagnosis of Inherited Eye Diseases. Affected members of each family were screened for disease-causing mutations in genes and gene regions that are commonly associated with adRP. By this approach, we detected mutations in 65 % of the families, leaving 85 families that are likely to harbor mutations outside of the "common" regions or in novel genes. Of these, 32 families were tested by several types of next-generation sequencing (NGS), including (a) targeted polymerase chain reaction (PCR) NGS, (b) whole exome NGS, and (c) targeted retinal-capture NGS. We detected mutations in 11 of these families (31 %) bringing the total detected in the adRP cohort to 70 %. Several large families have also been tested for linkage using Afymetrix single nucleotide polymorphism (SNP) arrays.
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Affiliation(s)
- Stephen P Daiger
- Human Genetics Center, School of Public Health, Univ. of Texas HSC, 1200 Herman Pressler Dr., 77030, Houston, TX, USA,
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32
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Schorderet DF, Bernasconi M, Tiab L, Favez T, Escher P. IROme, a new high-throughput molecular tool for the diagnosis of inherited retinal dystrophies-a price comparison with Sanger sequencing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 801:171-6. [PMID: 24664695 DOI: 10.1007/978-1-4614-3209-8_22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The molecular diagnosis of retinal dystrophies (RD) is difficult because of genetic and clinical heterogeneity. Previously, the molecular screening of genes was done one by one, sometimes in a scheme based on the frequency of sequence variants and the number of exons/length of the candidate genes. Payment for these procedures was complicated and the sequential billing of several genes created endless paperwork. We therefore evaluated the costs of generating and sequencing a hybridization-based DNA library enriched for the 64 most frequently mutated genes in RD, called IROme, and compared them to the costs of amplifying and sequencing these genes by the Sanger method. The production cost generated by the high-throughput (HT) sequencing of IROme was established at CHF 2,875.75 per case. Sanger sequencing of the same exons cost CHF 69,399.02. Turnaround time of the analysis was 3 days for IROme. For Sanger sequencing, it could only be estimated, as we never sequenced all 64 genes in one single patient. Sale cost for IROme calculated on the basis of the sale cost of one exon by Sanger sequencing is CHF 8,445.88, which corresponds to the sale price of 40 exons. In conclusion, IROme is cheaper and faster than Sanger sequencing and therefore represents a sound approach for the diagnosis of RD, both scientifically and economically. As a drop in the costs of HT sequencing is anticipated, target resequencing might become the new gold standard in the molecular diagnosis of RD.
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Affiliation(s)
- Daniel F Schorderet
- IRO, Institute for Research in Ophthalmology, 64 Avenue du Grand-Champsec, 1950, Sion, Switzerland,
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33
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Bowne SJ, Sullivan LS, Avery CE, Sasser EM, Roorda A, Duncan JL, Wheaton DH, Birch DG, Branham KE, Heckenlively JR, Sieving PA, Daiger SP. Mutations in the small nuclear riboprotein 200 kDa gene (SNRNP200) cause 1.6% of autosomal dominant retinitis pigmentosa. Mol Vis 2013; 19:2407-17. [PMID: 24319334 PMCID: PMC3850977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 11/22/2013] [Indexed: 12/02/2022] Open
Abstract
PURPOSE The purpose of this project was to determine the spectrum and frequency of mutations in the small nuclear riboprotein 200 kDa gene (SNRNP200) that cause autosomal dominant retinitis pigmentosa (adRP). METHODS A well-characterized adRP cohort of 251 families was tested for mutations in the exons and intron/exon junctions of SNRNP200 using fluorescent dideoxy sequencing. An additional 21 adRP families from the eyeGENE® Network were tested for possible mutations. Bioinformatic and segregation analysis was performed on novel variants. RESULTS SNRNP200 mutations were identified in seven of the families tested. Two previously reported mutations, p.Arg681Cys and p.Ser1087Leu, were found in two families each. One family had the previously reported p.Arg681His mutation. Two novel SNRNP200 variants, p.Pro682Ser and p.Ala542Val, were also identified in one family each. Bioinformatic and segregation analyses suggested that these novel variants are likely to be pathogenic. Clinical examination of patients with SNRNP200 mutations showed a wide range of clinical symptoms and severity, including one instance of non-penetrance. CONCLUSIONS Mutations in SNRNP200 caused 1.6% of disease in our adRP cohort. Pathogenic mutations were found primarily in exons 16 and 25, but the novel p.Ala542Val mutation in exon 13 suggests that variation in other genetic regions is also responsible for causing dominant disease. SNRNP200 mutations were associated with a wide range of clinical symptoms similar to those of individuals with other splice-factor gene mutations.
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Affiliation(s)
- Sara J. Bowne
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center Houston, TX
| | - Lori S. Sullivan
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center Houston, TX
| | - Cheryl E. Avery
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center Houston, TX
| | - Elizabeth M. Sasser
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center Houston, TX
| | - Austin Roorda
- School of Optometry and Vision Sciences Graduate Group, University of California, Berkeley, CA
| | - Jacque L. Duncan
- Department of Ophthalmology, University of California, San Francisco, CA
| | | | | | | | | | - Paul A. Sieving
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - Stephen P. Daiger
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center Houston, TX
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Eisenberger T, Neuhaus C, Khan AO, Decker C, Preising MN, Friedburg C, Bieg A, Gliem M, Issa PC, Holz FG, Baig SM, Hellenbroich Y, Galvez A, Platzer K, Wollnik B, Laddach N, Ghaffari SR, Rafati M, Botzenhart E, Tinschert S, Börger D, Bohring A, Schreml J, Körtge-Jung S, Schell-Apacik C, Bakur K, Al-Aama JY, Neuhann T, Herkenrath P, Nürnberg G, Nürnberg P, Davis JS, Gal A, Bergmann C, Lorenz B, Bolz HJ. Increasing the yield in targeted next-generation sequencing by implicating CNV analysis, non-coding exons and the overall variant load: the example of retinal dystrophies. PLoS One 2013; 8:e78496. [PMID: 24265693 PMCID: PMC3827063 DOI: 10.1371/journal.pone.0078496] [Citation(s) in RCA: 170] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 09/12/2013] [Indexed: 01/30/2023] Open
Abstract
Retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA) are major causes of blindness. They result from mutations in many genes which has long hampered comprehensive genetic analysis. Recently, targeted next-generation sequencing (NGS) has proven useful to overcome this limitation. To uncover “hidden mutations” such as copy number variations (CNVs) and mutations in non-coding regions, we extended the use of NGS data by quantitative readout for the exons of 55 RP and LCA genes in 126 patients, and by including non-coding 5′ exons. We detected several causative CNVs which were key to the diagnosis in hitherto unsolved constellations, e.g. hemizygous point mutations in consanguineous families, and CNVs complemented apparently monoallelic recessive alleles. Mutations of non-coding exon 1 of EYS revealed its contribution to disease. In view of the high carrier frequency for retinal disease gene mutations in the general population, we considered the overall variant load in each patient to assess if a mutation was causative or reflected accidental carriership in patients with mutations in several genes or with single recessive alleles. For example, truncating mutations in RP1, a gene implicated in both recessive and dominant RP, were causative in biallelic constellations, unrelated to disease when heterozygous on a biallelic mutation background of another gene, or even non-pathogenic if close to the C-terminus. Patients with mutations in several loci were common, but without evidence for di- or oligogenic inheritance. Although the number of targeted genes was low compared to previous studies, the mutation detection rate was highest (70%) which likely results from completeness and depth of coverage, and quantitative data analysis. CNV analysis should routinely be applied in targeted NGS, and mutations in non-coding exons give reason to systematically include 5′-UTRs in disease gene or exome panels. Consideration of all variants is indispensable because even truncating mutations may be misleading.
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Affiliation(s)
| | | | - Arif O. Khan
- Division of Pediatric Ophthalmology, King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | | | - Markus N. Preising
- Department of Ophthalmology, Justus-Liebig-University Giessen, University Hospital Giessen and Marburg GmbH, Giessen Campus, Giessen, Germany
| | - Christoph Friedburg
- Department of Ophthalmology, Justus-Liebig-University Giessen, University Hospital Giessen and Marburg GmbH, Giessen Campus, Giessen, Germany
| | - Anika Bieg
- Bioscientia Center for Human Genetics, Ingelheim, Germany
| | - Martin Gliem
- Department of Ophthalmology, University of Bonn, Bonn, Germany
| | | | - Frank G. Holz
- Department of Ophthalmology, University of Bonn, Bonn, Germany
| | - Shahid M. Baig
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | | | - Alberto Galvez
- Division of Pediatric Ophthalmology, King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - Konrad Platzer
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | | | - Saeed Reza Ghaffari
- Comprehensive Genetic Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Rafati
- Avicenna Biotechnology Research Institute, Tehran, Iran
| | | | - Sigrid Tinschert
- Institute of Clinical Genetics, Technical University Dresden, Dresden, Germany
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | | | - Axel Bohring
- Institute of Human Genetics, Westfälische Wilhelms-University, Münster, Germany
| | - Julia Schreml
- Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | | | | | - Khadijah Bakur
- Princess Al Jawhara Albrahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jumana Y. Al-Aama
- Princess Al Jawhara Albrahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Peter Herkenrath
- Department of Pediatrics, University Hospital of Cologne, Cologne, Germany
| | - Gudrun Nürnberg
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cologne Center for Genomics and Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cologne Center for Genomics and Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - John S. Davis
- Department of Ophthalmology, Zayed Military Hospital, Abu Dhabi, United Arab Emirates
| | - Andreas Gal
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Carsten Bergmann
- Bioscientia Center for Human Genetics, Ingelheim, Germany
- Center for Clinical Research, University Hospital of Freiburg, Freiburg, Germany
| | - Birgit Lorenz
- Department of Ophthalmology, Justus-Liebig-University Giessen, University Hospital Giessen and Marburg GmbH, Giessen Campus, Giessen, Germany
| | - Hanno J. Bolz
- Bioscientia Center for Human Genetics, Ingelheim, Germany
- Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany
- * E-mail:
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D'Argenio V, Frisso G, Precone V, Boccia A, Fienga A, Pacileo G, Limongelli G, Paolella G, Calabrò R, Salvatore F. DNA sequence capture and next-generation sequencing for the molecular diagnosis of genetic cardiomyopathies. J Mol Diagn 2013; 16:32-44. [PMID: 24183960 DOI: 10.1016/j.jmoldx.2013.07.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 07/03/2013] [Accepted: 07/30/2013] [Indexed: 12/15/2022] Open
Abstract
Hypertrophic cardiomyopathy is a relatively frequent disease with a prevalence of 0.2% worldwide and a remarkable genetic heterogeneity, with more than 30 causative genes reported to date. Current PCR-based strategies are inadequate for genomic investigations involving many candidate genes. Here, we report a next-generation sequencing procedure associated with DNA sequence capture that is able to sequence 202 cardiomyopathy-related genes simultaneously. We developed a complementary data analysis pipeline to select and prioritize genetic variants. The overall procedure can screen a large number of target genes simultaneously, thereby potentially revealing new disease-causing and modifier genes. By using this procedure, we analyzed hypertrophic cardiomyopathy patients in a shorter time and at a lower cost than with current procedures. The specificity of the next-generation sequencing-based procedure is at least as good as other techniques routinely used for mutation searching, and the sensitivity is much better. Analysis of the results showed some novel variants potentially involved in the pathogenesis of hypertrophic cardiomyopathy: a missense mutation in MYH7 and a nonsense variant in INS-IGF2 (patient 1), a splicing variant in MYBPC3 and an indel/frameshift variant in KCNQ1 (patient 2), and two concomitant variations in CACNA1C (patient 3). Sequencing of DNA from the three patients within a pool allowed detection of most variants identified in each individual patient, indicating that this approach is a feasible and cost-effective procedure.
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Affiliation(s)
- Valeria D'Argenio
- CEINGE-Biotecnologie Avanzate, Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Giulia Frisso
- CEINGE-Biotecnologie Avanzate, Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Vincenza Precone
- CEINGE-Biotecnologie Avanzate, Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | | | - Antonella Fienga
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Giuseppe Pacileo
- Cardiomyopathy and Inherited Heart Disease Clinic, UOC Cardiology, Second University of Naples, Naples, Italy
| | - Giuseppe Limongelli
- Cardiomyopathy and Inherited Heart Disease Clinic, UOC Cardiology, Second University of Naples, Naples, Italy
| | - Giovanni Paolella
- CEINGE-Biotecnologie Avanzate, Naples, Italy; Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Raffaele Calabrò
- Cardiomyopathy and Inherited Heart Disease Clinic, UOC Cardiology, Second University of Naples, Naples, Italy
| | - Francesco Salvatore
- CEINGE-Biotecnologie Avanzate, Naples, Italy; IRCCS-Fondazione SDN, Naples, Italy.
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36
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Ratnapriya R, Swaroop A. Genetic architecture of retinal and macular degenerative diseases: the promise and challenges of next-generation sequencing. Genome Med 2013; 5:84. [PMID: 24112618 PMCID: PMC4066589 DOI: 10.1186/gm488] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Inherited retinal degenerative diseases (RDDs) display wide variation in their mode of inheritance, underlying genetic defects, age of onset, and phenotypic severity. Molecular mechanisms have not been delineated for many retinal diseases, and treatment options are limited. In most instances, genotype-phenotype correlations have not been elucidated because of extensive clinical and genetic heterogeneity. Next-generation sequencing (NGS) methods, including exome, genome, transcriptome and epigenome sequencing, provide novel avenues towards achieving comprehensive understanding of the genetic architecture of RDDs. Whole-exome sequencing (WES) has already revealed several new RDD genes, whereas RNA-Seq and ChIP-Seq analyses are expected to uncover novel aspects of gene regulation and biological networks that are involved in retinal development, aging and disease. In this review, we focus on the genetic characterization of retinal and macular degeneration using NGS technology and discuss the basic framework for further investigations. We also examine the challenges of NGS application in clinical diagnosis and management.
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Affiliation(s)
- Rinki Ratnapriya
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Sullivan LS, Bowne SJ, Reeves MJ, Blain D, Goetz K, Ndifor V, Vitez S, Wang X, Tumminia SJ, Daiger SP. Prevalence of mutations in eyeGENE probands with a diagnosis of autosomal dominant retinitis pigmentosa. Invest Ophthalmol Vis Sci 2013; 54:6255-61. [PMID: 23950152 DOI: 10.1167/iovs.13-12605] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
PURPOSE To screen samples from patients with presumed autosomal dominant retinitis pigmentosa (adRP) for mutations in 12 disease genes as a contribution to the research and treatment goals of the National Ophthalmic Disease Genotyping and Phenotyping Network (eyeGENE). METHODS DNA samples were obtained from eyeGENE. A total of 170 probands with an intake diagnosis of adRP were tested through enrollment in eyeGENE. The 10 most common genes causing adRP (IMPDH1, KLHL7, NR2E3, PRPF3/RP18, PRPF31/RP11, PRPF8/RP13, PRPH2/RDS, RHO, RP1, and TOPORS) were chosen for PCR-based dideoxy sequencing, along with the two X-linked RP genes, RPGR and RP2. RHO, PRPH2, PRPF31, RPGR, and RP2 were completely sequenced, while only mutation hotspots in the other genes were analyzed. RESULTS Disease-causing mutations were identified in 52% of the probands. The frequencies of disease-causing mutations in the 12 genes were consistent with previous studies. CONCLUSIONS The Laboratory for Molecular Diagnosis of Inherited Eye Disease at the University of Texas in Houston has thus far received DNA samples from 170 families with a diagnosis of adRP from the eyeGENE Network. Disease-causing mutations in autosomal genes were identified in 48% (81/170) of these families while mutations in X-linked genes accounted for an additional 4% (7/170). Of the 55 distinct mutations detected, 19 (33%) have not been previously reported. All diagnostic results were returned by eyeGENE to participating patients via their referring clinician. These genotyped samples along with their corresponding phenotypic information are also available to researchers who may request access to them for further study of these ophthalmic disorders. (ClinicalTrials.gov number, NCT00378742.).
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Affiliation(s)
- Lori S Sullivan
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas
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38
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Corton M, Nishiguchi KM, Avila-Fernández A, Nikopoulos K, Riveiro-Alvarez R, Tatu SD, Ayuso C, Rivolta C. Exome sequencing of index patients with retinal dystrophies as a tool for molecular diagnosis. PLoS One 2013; 8:e65574. [PMID: 23940504 PMCID: PMC3683009 DOI: 10.1371/journal.pone.0065574] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/28/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Retinal dystrophies (RD) are a group of hereditary diseases that lead to debilitating visual impairment and are usually transmitted as a Mendelian trait. Pathogenic mutations can occur in any of the 100 or more disease genes identified so far, making molecular diagnosis a rather laborious process. In this work we explored the use of whole exome sequencing (WES) as a tool for identification of RD mutations, with the aim of assessing its applicability in a diagnostic context. METHODOLOGY/PRINCIPAL FINDINGS We ascertained 12 Spanish families with seemingly recessive RD. All of the index patients underwent mutational pre-screening by chip-based sequence hybridization and resulted to be negative for known RD mutations. With the exception of one pedigree, to simulate a standard diagnostic scenario we processed by WES only the DNA from the index patient of each family, followed by in silico data analysis. We successfully identified causative mutations in patients from 10 different families, which were later verified by Sanger sequencing and co-segregation analyses. Specifically, we detected pathogenic DNA variants (∼50% novel mutations) in the genes RP1, USH2A, CNGB3, NMNAT1, CHM, and ABCA4, responsible for retinitis pigmentosa, Usher syndrome, achromatopsia, Leber congenital amaurosis, choroideremia, or recessive Stargardt/cone-rod dystrophy cases. CONCLUSIONS/SIGNIFICANCE Despite the absence of genetic information from other family members that could help excluding nonpathogenic DNA variants, we could detect causative mutations in a variety of genes known to represent a wide spectrum of clinical phenotypes in 83% of the patients analyzed. Considering the constant drop in costs for human exome sequencing and the relative simplicity of the analyses made, this technique could represent a valuable tool for molecular diagnostics or genetic research, even in cases for which no genotypes from family members are available.
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Affiliation(s)
- Marta Corton
- Department of Genetics, IIS- Fundacion Jimenez Diaz, CIBERER, Madrid, Spain
| | - Koji M. Nishiguchi
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | | | | | | | - Sorina D. Tatu
- Department of Genetics, IIS- Fundacion Jimenez Diaz, CIBERER, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics, IIS- Fundacion Jimenez Diaz, CIBERER, Madrid, Spain
| | - Carlo Rivolta
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- * E-mail:
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Blain D, Goetz KE, Ayyagari R, Tumminia SJ. eyeGENE®: a vision community resource facilitating patient care and paving the path for research through molecular diagnostic testing. Clin Genet 2013; 84:190-7. [PMID: 23662816 DOI: 10.1111/cge.12193] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 05/08/2013] [Accepted: 05/08/2013] [Indexed: 11/28/2022]
Abstract
Molecular genetics and genomics are revolutionizing the study and treatment of inherited eye diseases. In recognition of the impact of molecular genetics on vision and ophthalmology, the National Eye Institute established the National Ophthalmic Disease Genotyping and Phenotyping Network (eyeGENE®) as a multidirectional research initiative whereby a clinical component for patients diagnosed with inherited eye disease fosters research into the causes and mechanisms of these ophthalmic diseases. This is accomplished by broadening access to genetic diagnostic testing and maintaining a repository of DNA samples from clinically characterized individuals and their families to allow investigations of the causes, interventions, and management of genetic eye disorders. The eyeGENE® Network currently includes Clinical Laboratory Improvement Amendments (CLIA)-certified diagnostic laboratory partners, over 270 registered clinical organizations with 500 registered users from around the United States and Canada, and is now testing approximately 100 genes representing 35 inherited eye diseases. To date, the Network has received 4400 samples from individuals with rare inherited eye diseases, which are available for access by the vision research community. eyeGENE® is a model partnership between the U.S. federal government, eye health care providers, CLIA-approved molecular diagnostic laboratories, private industry, and scientists who represent a broad research constituency.
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Affiliation(s)
- D Blain
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
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40
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Targeted exome sequencing identified novel USH2A mutations in Usher syndrome families. PLoS One 2013; 8:e63832. [PMID: 23737954 PMCID: PMC3667821 DOI: 10.1371/journal.pone.0063832] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 04/07/2013] [Indexed: 12/16/2022] Open
Abstract
Usher syndrome (USH) is a leading cause of deaf-blindness in autosomal recessive trait. Phenotypic and genetic heterogeneities in USH make molecular diagnosis much difficult. This is a pilot study aiming to develop an approach based on next-generation sequencing to determine the genetic defects in patients with USH or allied diseases precisely and effectively. Eight affected patients and twelve unaffected relatives from five unrelated Chinese USH families, including 2 pseudo-dominant ones, were recruited. A total of 144 known genes of inherited retinal diseases were selected for deep exome resequencing. Through systematic data analysis using established bioinformatics pipeline and segregation analysis, a number of genetic variants were released. Eleven mutations, eight of them were novel, in the USH2A gene were identified. Biparental mutations in USH2A were revealed in 2 families with pseudo-dominant inheritance. A proband was found to have triple mutations, two of them were supposed to locate in the same chromosome. In conclusion, this study revealed the genetic defects in the USH2A gene and demonstrated the robustness of targeted exome sequencing to precisely and rapidly determine genetic defects. The methodology provides a reliable strategy for routine gene diagnosis of USH.
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Borràs E, de Sousa Dias M, Hernan I, Pascual B, Mañé B, Gamundi MJ, Delás B, Carballo M. Detection of novel genetic variation in autosomal dominant retinitis pigmentosa. Clin Genet 2013; 84:441-52. [PMID: 23534816 DOI: 10.1111/cge.12151] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 03/22/2013] [Accepted: 03/22/2013] [Indexed: 02/03/2023]
Abstract
We explored an approach to detect disease-causing sequence variants in 448 candidate genes from five index cases of autosomal dominant retinitis pigmentosa (adRP) by sequence DNA capture and next-generation DNA sequencing (NGS). Detection of sequence variants was carried out by sequence capture NimbleGen and NGS in a SOLiD platform. After filtering out variants previously reported in genomic databases, novel potential adRP-causing variants were validated by dideoxy capillary electrophoresis (Sanger) sequencing and co-segregation in the families. A total of 55 novel sequence variants in the coding or splicing regions of adRP candidate genes were detected, 49 of which were confirmed by Sanger sequencing. Segregation of these variants in the corresponding adRP families showed three variants present in all the RP-affected members of the family. A novel mutation, p.L270R in IMPDH1, was found to be disease causing in one family. In another family a variant, p.M96T in the NRL gene was detected; this variant was previously reported as probably causing adRP. However, the previously reported p.A76V mutation in NRL as a cause of RP was excluded by co-segregation in the family. We discuss the benefits and limitations of our approach in the context of mutation detection in adRP patients.
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Dias MDS, Hernan I, Pascual B, Borràs E, Mañé B, Gamundi MJ, Carballo M. Detection of novel mutations that cause autosomal dominant retinitis pigmentosa in candidate genes by long-range PCR amplification and next-generation sequencing. Mol Vis 2013; 19:654-64. [PMID: 23559859 PMCID: PMC3611935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 03/19/2013] [Indexed: 10/27/2022] Open
Abstract
PURPOSE To devise an effective method for detecting mutations in 12 genes (CA4, CRX, IMPDH1, NR2E3, RP9, PRPF3, PRPF8, PRPF31, PRPH2, RHO, RP1, and TOPORS) commonly associated with autosomal dominant retinitis pigmentosa (adRP) that account for more than 95% of known mutations. METHODS We used long-range PCR (LR-PCR) amplification and next-generation sequencing (NGS) performed in a GS Junior 454 benchtop sequencing platform. Twenty LR-PCR fragments, between 3,000 and 10,000 bp, containing all coding exons and flanking regions of the 12 genes, were obtained from DNA samples of patients with adRP. Sequencing libraries were prepared with an enzymatic (Fragmentase technology) method. RESULTS Complete coverage of the coding and flanking sequences of the 12 genes assayed was obtained with NGS, with an average sequence depth of 380× (ranging from 128× to 1,077×). Five previous known mutations in the adRP genes were detected with a sequence variation percentage between 35% and 65%. We also performed a parallel sequence analysis of four samples, three of them new patients with index adRP, in which two novel mutations were detected in RHO (p.Asn73del) and PRPF31 (p.Ile109del). CONCLUSIONS The results demonstrate that genomic LR-PCR amplification together with NGS is an effective method for analyzing individual patient samples for mutations in a monogenic heterogeneous disease such as adRP. This approach proved effective for the parallel analysis of adRP and has been introduced as routine. Additionally, this approach could be extended to other heterogeneous genetic diseases.
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Summers KM, West JA, Hattam A, Stark D, McGill JJ, West MJ. Recent developments in the diagnosis of Marfan syndrome and related disorders. Med J Aust 2013; 197:494-7. [PMID: 23121584 DOI: 10.5694/mja12.10560] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Marfan syndrome is a multisystem disorder of connective tissue that is inherited in an autosomal dominant fashion, and results from mutation of the FBN1 gene on human chromosome 15. There are a number of conditions of the connective tissue with a similar phenotype that can be confused with Marfan syndrome. Modifications of the diagnostic criteria have recently been published, facilitating the differentiation of Marfan syndrome from these conditions. It is still difficult to use modern genetic testing for diagnosis because Marfan syndrome can be caused by many different mutations in FBN1, a large gene with 65 coding segments, while mutations in other genes can cause overlapping phenotypes. Several clinical trials of drug therapy, including the antihypertensive drug losartan, are in progress.
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Affiliation(s)
- Kim M Summers
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
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44
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Churchill JD, Bowne SJ, Sullivan LS, Lewis RA, Wheaton DK, Birch DG, Branham KE, Heckenlively JR, Daiger SP. Mutations in the X-linked retinitis pigmentosa genes RPGR and RP2 found in 8.5% of families with a provisional diagnosis of autosomal dominant retinitis pigmentosa. Invest Ophthalmol Vis Sci 2013; 54:1411-6. [PMID: 23372056 DOI: 10.1167/iovs.12-11541] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE We determined the fraction of families in a well-characterized cohort with a provisional diagnosis of autosomal dominant retinitis pigmentosa (adRP) that have disease-causing mutations in the X-linked retinitis pigmentosa GTPase regulator (RPGR) gene or the retinitis pigmentosa 2 (RP2) gene. METHODS Families with a provisional clinical diagnosis of adRP, and a pedigree consistent with adRP but no male-to-male transmission were selected from a cohort of 258 families, and tested for mutations in the RPGR and RP2 genes with di-deoxy sequencing. To facilitate testing of RPGR in "adRP" families that had no male members available for testing, the repetitive and purine-rich ORF15 of RPGR was subcloned and sequenced in heterozygous female subjects from 16 unrelated families. RESULTS Direct sequencing of RPGR and RP2 allowed for identification of a disease-causing mutation in 21 families. Of these "adRP" families 19 had RPGR mutations, and two had RP2 mutations. Subcloning and sequencing of ORF15 of RPGR in female subjects identified one additional RPGR mutation. Of the 22 mutations identified, 15 have been reported previously. CONCLUSIONS These data show that 8.5% (22 in 258) of families thought to have adRP truly have X-linked retinitis pigmentosa (XLRP). These results have substantive implications for calculation of recurrence risk, genetic counseling, and potential treatment options, and illustrate the importance of screening families with a provisional diagnosis of autosomal inheritance and no male-to-male transmission for mutations in X-linked genes. Mutations in RPGR are one of the most common causes of all forms of retinitis pigmentosa.
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Affiliation(s)
- Jennifer D Churchill
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
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Swaroop A. What's in a name? RPGR mutations redefine the genetic and phenotypic landscape in retinal degenerative diseases. Invest Ophthalmol Vis Sci 2013; 54:1417. [PMID: 23423174 DOI: 10.1167/iovs.13-11750] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Anand Swaroop
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA.
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Wan M, Faruq J, Rosenberg JN, Xia J, Oyler GA, Betenbaugh MJ. Achieving high throughput sequencing of a cDNA library utilizing an alternative protocol for the bench top next-generation sequencing system. J Microbiol Methods 2013; 92:122-6. [DOI: 10.1016/j.mimet.2012.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 10/26/2012] [Accepted: 10/26/2012] [Indexed: 10/27/2022]
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IROme, a new high-throughput molecular tool for the diagnosis of inherited retinal dystrophies. BIOMED RESEARCH INTERNATIONAL 2012; 2013:198089. [PMID: 23484092 PMCID: PMC3591198 DOI: 10.1155/2013/198089] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Accepted: 11/27/2012] [Indexed: 02/08/2023]
Abstract
The molecular diagnosis of retinal dystrophies is difficult because of the very important number of genes implicated and is rarely helped by genotype-phenotype correlations. This prompted us to develop IROme, a custom designed in solution-based targeted exon capture assay (SeqCap EZ Choice library, Roche NimbleGen) for 60 retinitis pigmentosa-linked genes and three candidate genes (942 exons). Pyrosequencing was performed on a Roche 454 GS Junior benchtop high-throughput sequencing platform. In total, 23 patients affected by retinitis pigmentosa were analyzed. Per patient, 39.6 Mb were generated, and 1111 sequence variants were detected on average, at a median coverage of 17-fold. After data filtering and sequence variant prioritization, disease-causing mutations were identified in ABCA4, CNGB1, GUCY2D, PROM1, PRPF8, PRPF31, PRPH2, RHO, RP2, and TULP1 for twelve patients (55%), ten mutations having never been reported previously. Potential mutations were identified in 5 additional patients, and in only 6 patients no molecular diagnosis could be established (26%). In conclusion, targeted exon capture and next-generation sequencing are a valuable and efficient approach to identify disease-causing sequence variants in retinal dystrophies.
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Unilateral retinitis pigmentosa: a proposal of genetic pathogenic mechanisms. Eur J Ophthalmol 2012; 22:654-60. [PMID: 22139616 DOI: 10.5301/ejo.5000086] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2011] [Indexed: 11/20/2022]
Abstract
PURPOSE To investigate and integrate anatomic and physiologic findings from a group of patients who present retinitis pigmentosa affecting just one eye and use this information to propose mechanisms of disease pathogenesis. METHODS This prospective cross-sectional study examined 5 patients, all female, from 8 to 60 years old. The study was conducted in 4 university hospitals. The patients were selected according to the characteristics of ocular involvement, notably unilateral presentation of similar anatomic and functional abnormalities. Full-field electroretinogram, fundus photography, fundus autofluorescence, infrared imaging, optical coherence tomography, and genetic testing were performed. RESULTS Full-field electroretinogram showed unilateral decrease in amplitude and increase in implicit time; autofluorescence showed unilateral areas of decreased intensity. The USH2AW4149R mutation was confirmed in one patient. CONCLUSIONS Imaging and functional testing are important in elucidating the unilateral pattern of the disease and in monitoring these individuals. Mosaicism or somatic mutation may cause unilateral genetic disease presentation.
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Anasagasti A, Irigoyen C, Barandika O, López de Munain A, Ruiz-Ederra J. Current mutation discovery approaches in Retinitis Pigmentosa. Vision Res 2012; 75:117-29. [PMID: 23022136 DOI: 10.1016/j.visres.2012.09.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 09/08/2012] [Accepted: 09/13/2012] [Indexed: 12/22/2022]
Abstract
With a worldwide prevalence of about 1 in 3500-5000 individuals, Retinitis Pigmentosa (RP) is the most common form of hereditary retinal degeneration. It is an extremely heterogeneous group of genetically determined retinal diseases leading to progressive loss of vision due to impairment of rod and cone photoreceptors. RP can be inherited as an autosomal-recessive, autosomal-dominant, or X-linked trait. Non-Mendelian inheritance patterns such as digenic, maternal (mitochondrial) or compound heterozygosity have also been reported. To date, more than 65 genes have been implicated in syndromic and non-syndromic forms of RP, which account for only about 60% of all RP cases. Due to this high heterogeneity and diversity of inheritance patterns, the molecular diagnosis of syndromic and non-syndromic RP is very challenging, and the heritability of 40% of total RP cases worldwide remains unknown. However new sequencing methodologies, boosted by the human genome project, have contributed to exponential plummeting in sequencing costs, thereby making it feasible to include molecular testing for RP patients in routine clinical practice within the coming years. Here, we summarize the most widely used state-of-the-art technologies currently applied for the molecular diagnosis of RP, and address their strengths and weaknesses for the molecular diagnosis of such a complex genetic disease.
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Affiliation(s)
- Ander Anasagasti
- Division of Neurosciences, Instituto Biodonostia, San Sebastián, Gipuzkoa, Spain
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