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Molday RS, Garces FA, Scortecci JF, Molday LL. Structure and function of ABCA4 and its role in the visual cycle and Stargardt macular degeneration. Prog Retin Eye Res 2021; 89:101036. [PMID: 34954332 DOI: 10.1016/j.preteyeres.2021.101036] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/07/2021] [Accepted: 12/13/2021] [Indexed: 12/17/2022]
Abstract
ABCA4 is a member of the superfamily of ATP-binding cassette (ABC) transporters that is preferentially localized along the rim region of rod and cone photoreceptor outer segment disc membranes. It uses the energy from ATP binding and hydrolysis to transport N-retinylidene-phosphatidylethanolamine (N-Ret-PE), the Schiff base adduct of retinal and phosphatidylethanolamine, from the lumen to the cytoplasmic leaflet of disc membranes. This ensures that all-trans-retinal and excess 11-cis-retinal are efficiently cleared from photoreceptor cells thereby preventing the accumulation of toxic retinoid compounds. Loss-of-function mutations in the gene encoding ABCA4 cause autosomal recessive Stargardt macular degeneration, also known as Stargardt disease (STGD1), and related autosomal recessive retinopathies characterized by impaired central vision and an accumulation of lipofuscin and bis-retinoid compounds. High resolution structures of ABCA4 in its substrate and nucleotide free state and containing bound N-Ret-PE or ATP have been determined by cryo-electron microscopy providing insight into the molecular architecture of ABCA4 and mechanisms underlying substrate recognition and conformational changes induced by ATP binding. The expression and functional characterization of a large number of disease-causing missense ABCA4 variants have been determined. These studies have shed light into the molecular mechanisms underlying Stargardt disease and a classification that reliably predicts the effect of a specific missense mutation on the severity of the disease. They also provide a framework for developing rational therapeutic treatments for ABCA4-associated diseases.
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Affiliation(s)
- Robert S Molday
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, B.C., Canada; Department of Ophthalmology & Visual Sciences, University of British Columbia, Vancouver, B.C., Canada.
| | - Fabian A Garces
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, B.C., Canada
| | | | - Laurie L Molday
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, B.C., Canada
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2
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Duzkale N, Arslan U. Investigation of genotype-phenotype relationship in Turkish patients with inherited retinal disease by next generation sequencing. Ophthalmic Genet 2021; 42:674-684. [PMID: 34315337 DOI: 10.1080/13816810.2021.1952616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Inherited retinal dystrophies (IRDs) are a group of retinal diseases genetically and clinically highly heterogeneous and associated with more than 300 genes. This study aims to investigate the genetic basis of Turkish patients with IRDs. MATERIALS AND METHODS In the study, genes related to retinal diseases in 86 IRDs patients were analyzed using the Next Generations Sequencing method (NGS). RESULTS The mean age of 86 patients was 35 and the mean age at diagnosis was 18. There was consanguinity between the parents of 62% of these patients. Fifty-six retinal disease-associated genes of 46 patients and 230 retinal disease-associated genes of 40 patients were examined. Genetic analysis provides a molecular diagnosis in a total of 53 (61.6%) patients. The genes responsible for the IRDs phenotype were frequently identified as ABCA4 (25%), EYS (11%), and RDH12 (9%). There was no significant difference between those with and without a molecular diagnosis in terms of demographic characteristics and family history. CONCLUSIONS Determination of genetic cause by NGS method in IRDs subgroups that are difficult to define by ophthalmic examination ensures that patients receive accurate diagnosis, treatment and counseling. This study contributed to the understanding of the genotype-phenotype relationship of Turkish patients with IRDs.
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Affiliation(s)
- Neslihan Duzkale
- Department of Medical Genetic, Diskapi Yildirim Beyazit Training and Research Hospital, Ankara, Turkey
| | - Umut Arslan
- Department of Bioretina, Ankara University Technopolis, Ankara, Turkey
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3
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Maggi J, Koller S, Bähr L, Feil S, Kivrak Pfiffner F, Hanson JVM, Maspoli A, Gerth-Kahlert C, Berger W. Long-Range PCR-Based NGS Applications to Diagnose Mendelian Retinal Diseases. Int J Mol Sci 2021; 22:ijms22041508. [PMID: 33546218 PMCID: PMC7913364 DOI: 10.3390/ijms22041508] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 12/27/2022] Open
Abstract
The purpose of this study was to develop a flexible, cost-efficient, next-generation sequencing (NGS) protocol for genetic testing. Long-range polymerase chain reaction (PCR) amplicons of up to 20 kb in size were designed to amplify entire genomic regions for a panel (n = 35) of inherited retinal disease (IRD)-associated loci. Amplicons were pooled and sequenced by NGS. The analysis was applied to 227 probands diagnosed with IRD: (A) 108 previously molecularly diagnosed, (B) 94 without previous genetic testing, and (C) 25 undiagnosed after whole-exome sequencing (WES). The method was validated with 100% sensitivity on cohort A. Long-range PCR-based sequencing revealed likely causative variant(s) in 51% and 24% of proband from cohorts B and C, respectively. Breakpoints of 3 copy number variants (CNVs) could be characterized. Long-range PCR libraries spike-in extended coverage of WES. Read phasing confirmed compound heterozygosity in 5 probands. The proposed sequencing protocol provided deep coverage of the entire gene, including intronic and promoter regions. Our method can be used (i) as a first-tier assay to reduce genetic testing costs, (ii) to elucidate missing heritability cases, (iii) to characterize breakpoints of CNVs at nucleotide resolution, (iv) to extend WES data to non-coding regions by spiking-in long-range PCR libraries, and (v) to help with phasing of candidate variants.
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Affiliation(s)
- Jordi Maggi
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (L.B.); (S.F.); (F.K.P.); (A.M.)
| | - Samuel Koller
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (L.B.); (S.F.); (F.K.P.); (A.M.)
| | - Luzy Bähr
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (L.B.); (S.F.); (F.K.P.); (A.M.)
| | - Silke Feil
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (L.B.); (S.F.); (F.K.P.); (A.M.)
| | - Fatma Kivrak Pfiffner
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (L.B.); (S.F.); (F.K.P.); (A.M.)
| | - James V. M. Hanson
- Department of Ophthalmology, University Hospital Zurich and University of Zurich, 8091 Zurich, Switzerland; (J.V.M.H.); (C.G.-K.)
| | - Alessandro Maspoli
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (L.B.); (S.F.); (F.K.P.); (A.M.)
| | - Christina Gerth-Kahlert
- Department of Ophthalmology, University Hospital Zurich and University of Zurich, 8091 Zurich, Switzerland; (J.V.M.H.); (C.G.-K.)
| | - Wolfgang Berger
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (L.B.); (S.F.); (F.K.P.); (A.M.)
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, 8057 Zurich, Switzerland
- Neuroscience Center Zurich (ZNZ), University and ETH Zurich, 8057 Zurich, Switzerland
- Correspondence: ; Tel.: +41-44-556-33-50
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4
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Liu XZ, Tao TC, Qi H, Feng SN, Chen NN, Zhao L, Ma ZZ, Li GL, Yang LP. Simultaneous expression of two pathogenic genes in four Chinese patients affected with inherited retinal dystrophy. Int J Ophthalmol 2020; 13:220-230. [PMID: 32090030 DOI: 10.18240/ijo.2020.02.04] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/07/2019] [Indexed: 01/14/2023] Open
Abstract
AIM To describe the complex, overlapping phenotype of four Chinese patients with inherited retinal dystrophies (IRDs) who harbored two pathogenic genes simultaneously. METHODS This retrospective study included 4 patients affected with IRDs. Medical and ophthalmic histories were obtained, and clinical examinations were performed. A specific Hereditary Eye Disease Enrichment Panel (HEDEP) based on exome capture technology was used for genetic screening. RESULTS Four patients were identified to harbor disease-causing variants in two different genes. Patient retinitis pigmentosa (RP) 01-II:1 exhibited both classical ABCA4-induced Stargardt disease (STGD) 1 and USH2A-associated RP, patient RP02-III:2 exhibited both classical ABCA4-induced STGD1 and CDH23-associated RP, patient RP03-II:1 exhibited both USH2A-induced autosomal recessive retinitis pigmentosa (arRP) syndrome and SNRNP200-induced autosomal dominant retinitis pigmentosa (adRP), and patient RP04-II:2 exhibited USH2A-induced arRP syndrome and EYS-induced arRP at the same time. CONCLUSION Our study demonstrates that genotype-phenotype correlations and comprehensive genetic screening is crucial for diagnosing IRDs and helping family planning for patients suffering from the disease.
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Affiliation(s)
- Xiao-Zhen Liu
- Department of Ophthalmology, Peking University Third Hospital, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Beijing 100191, China
| | - Tian-Chang Tao
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing 100730, China
| | - Hong Qi
- Department of Ophthalmology, Peking University Third Hospital, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Beijing 100191, China
| | - Shan-Na Feng
- Department of Ophthalmology, Peking University Third Hospital, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Beijing 100191, China
| | - Ning-Ning Chen
- Department of Ophthalmology, Peking University Third Hospital, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Beijing 100191, China
| | - Lin Zhao
- Department of Ophthalmology, Peking University Third Hospital, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Beijing 100191, China
| | - Zhi-Zhong Ma
- Department of Ophthalmology, Peking University Third Hospital, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Beijing 100191, China
| | - Gen-Lin Li
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing 100730, China
| | - Li-Ping Yang
- Department of Ophthalmology, Peking University Third Hospital, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Beijing 100191, China
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5
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Mutation screening in genes known to be responsible for Retinitis Pigmentosa in 98 Small Han Chinese Families. Sci Rep 2017; 7:1948. [PMID: 28512305 PMCID: PMC5434011 DOI: 10.1038/s41598-017-00963-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 03/03/2017] [Indexed: 01/10/2023] Open
Abstract
Retinitis pigmentosa (RP) is highly heterogeneous in both clinical and genetic fields. Accurate mutation screening is very beneficial in improving clinical diagnosis and gene-specific treatment of RP patients. The reason for the difficulties in genetic diagnosis of RP is that the ethnic-specific mutation databases that contain both clinical and genetic information are largely insufficient. In this study, we recruited 98 small Han Chinese families clinically diagnosed as RP, including of 22 dominant, 19 recessive, 52 sporadic, and five X-linked. We then used whole exome sequencing (WES) analysis to detect mutations in the genes known for RP in 101 samples from these 98 families. In total, we identified 57 potential pathogenic mutations in 40 of the 98 (41%) families in 22 known RP genes, including 45 novel mutations. We detected mutations in 13 of the 22 (59%) typical autosomal dominant families, 8 of the 19 (42%) typical autosomal recessive families, 16 of the 52 (31%) sporadic small families, and four of the five (80%) X-linked families. Our results extended the mutation spectrum of known RP genes in Han Chinese, thus making a contribution to RP gene diagnosis and the pathogenetic study of RP genes.
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6
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Biswas P, Duncan JL, Maranhao B, Kozak I, Branham K, Gabriel L, Lin JH, Barteselli G, Navani M, Suk J, Parke M, Schlechter C, Weleber RG, Heckenlively JR, Dagnelie G, Lee P, Riazuddin SA, Ayyagari R. Genetic analysis of 10 pedigrees with inherited retinal degeneration by exome sequencing and phenotype-genotype association. Physiol Genomics 2017; 49:216-229. [PMID: 28130426 PMCID: PMC5407181 DOI: 10.1152/physiolgenomics.00096.2016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 12/31/2022] Open
Abstract
Our purpose was to identify causative mutations and characterize the phenotype associated with the genotype in 10 unrelated families with autosomal recessive retinal degeneration. Ophthalmic evaluation and DNA isolation were carried out in 10 pedigrees with inherited retinal degenerations (IRD). Exomes of probands from eight pedigrees were captured using Nimblegen V2/V3 or Agilent V5+UTR kits, and sequencing was performed on Illumina HiSeq. The DHDDS gene was screened for mutations in the remaining two pedigrees with Ashkenazi Jewish ancestry. Exome variants were filtered to detect candidate causal variants using exomeSuite software. Segregation and ethnicity-matched control sample analysis were performed by dideoxy sequencing. Retinal histology of a patient with DHDDS mutation was studied by microscopy. Genetic analysis identified six known mutations in ABCA4 (p.Gly1961Glu, p.Ala1773Val, c.5461-10T>C), RPE65 (p.Tyr249Cys, p.Gly484Asp), PDE6B (p.Lys706Ter) and DHDDS (p.Lys42Glu) and ten novel potentially pathogenic variants in CERKL (p.Met323Val fsX20), RPE65 (p.Phe252Ser, Thr454Leu fsX31), ARL6 (p.Arg121His), USH2A (p.Gly3142Ter, p.Cys3294Trp), PDE6B (p.Gln652Ter), and DHDDS (p.Thr206Ala) genes. Among these, variants/mutations in two separate genes were observed to segregate with IRD in two pedigrees. Retinal histopathology of a patient with a DHDDS mutation showed severe degeneration of retinal layers with relative preservation of the retinal pigment epithelium. Analysis of exome variants in ten pedigrees revealed nine novel potential disease-causing variants and nine previously reported homozygous or compound heterozygous mutations in the CERKL, ABCA4, RPE65, ARL6, USH2A, PDE6B, and DHDDS genes. Mutations that could be sufficient to cause pathology were observed in more than one gene in one pedigree.
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Affiliation(s)
- Pooja Biswas
- Shiley Eye Institute, University of California San Diego, La Jolla, California
| | - Jacque L Duncan
- Ophthalmology, University of California San Francisco, San Francisco, California
| | - Bruno Maranhao
- Shiley Eye Institute, University of California San Diego, La Jolla, California
| | - Igor Kozak
- King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - Kari Branham
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan
| | - Luis Gabriel
- Genetics and Ophthalmology, Genelabor, Goiânia, Brazil
| | - Jonathan H Lin
- Shiley Eye Institute, University of California San Diego, La Jolla, California
| | - Giulio Barteselli
- Shiley Eye Institute, University of California San Diego, La Jolla, California
| | - Mili Navani
- Shiley Eye Institute, University of California San Diego, La Jolla, California
| | - John Suk
- Shiley Eye Institute, University of California San Diego, La Jolla, California
| | - Michelle Parke
- Shiley Eye Institute, University of California San Diego, La Jolla, California
| | | | - Richard G Weleber
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon; and
| | - John R Heckenlively
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan
| | - Gislin Dagnelie
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Pauline Lee
- Shiley Eye Institute, University of California San Diego, La Jolla, California
| | - S Amer Riazuddin
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Radha Ayyagari
- Shiley Eye Institute, University of California San Diego, La Jolla, California;
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7
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Boulanger-Scemama E, El Shamieh S, Démontant V, Condroyer C, Antonio A, Michiels C, Boyard F, Saraiva JP, Letexier M, Souied E, Mohand-Saïd S, Sahel JA, Zeitz C, Audo I. Next-generation sequencing applied to a large French cone and cone-rod dystrophy cohort: mutation spectrum and new genotype-phenotype correlation. Orphanet J Rare Dis 2015; 10:85. [PMID: 26103963 PMCID: PMC4566196 DOI: 10.1186/s13023-015-0300-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 06/15/2015] [Indexed: 12/21/2022] Open
Abstract
Background Cone and cone-rod dystrophies are clinically and genetically heterogeneous inherited retinal disorders with predominant cone impairment. They should be distinguished from the more common group of rod-cone dystrophies (retinitis pigmentosa) due to their more severe visual prognosis with early central vision loss. The purpose of our study was to document mutation spectrum of a large French cohort of cone and cone-rod dystrophies. Methods We applied Next-Generation Sequencing targeting a panel of 123 genes implicated in retinal diseases to 96 patients. A systematic filtering approach was used to identify likely disease causing variants, subsequently confirmed by Sanger sequencing and co-segregation analysis when possible. Results Overall, the likely causative mutations were detected in 62.1 % of cases, revealing 33 known and 35 novel mutations. This rate was higher for autosomal dominant (100 %) than autosomal recessive cases (53.8 %). Mutations in ABCA4 and GUCY2D were responsible for 19.2 % and 29.4 % of resolved cases with recessive and dominant inheritance, respectively. Furthermore, unexpected genotype-phenotype correlations were identified, confirming the complexity of inherited retinal disorders with phenotypic overlap between cone-rod dystrophies and other retinal diseases. Conclusions In summary, this time-efficient approach allowed mutation detection in the most important cohort of cone-rod dystrophies investigated so far covering the largest number of genes. Association of known gene defects with novel phenotypes and mode of inheritance were established. Electronic supplementary material The online version of this article (doi:10.1186/s13023-015-0300-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elise Boulanger-Scemama
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France
| | - Said El Shamieh
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France
| | - Vanessa Démontant
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France
| | - Christel Condroyer
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France
| | - Aline Antonio
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU ViewMaintain, INSERM-DHOS CIC 1423, Paris, F-75012, France
| | - Christelle Michiels
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France
| | - Fiona Boyard
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France
| | - Jean-Paul Saraiva
- IntegraGen SA, Genopole CAMPUS 1 bat G8 FR-91030 EVRY, Paris, France
| | - Mélanie Letexier
- IntegraGen SA, Genopole CAMPUS 1 bat G8 FR-91030 EVRY, Paris, France
| | - Eric Souied
- Centre Hospitalier Intercommunal de Créteil, Department of Ophthalmology, Université Paris-Est Créteil, 94000, Créteil, France
| | - Saddek Mohand-Saïd
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU ViewMaintain, INSERM-DHOS CIC 1423, Paris, F-75012, France
| | - José-Alain Sahel
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU ViewMaintain, INSERM-DHOS CIC 1423, Paris, F-75012, France.,Fondation Ophtalmologique Adolphe de Rothschild, 75019, Paris, France.,Académie des Sciences-Institut de France, 75006, Paris, France.,University College London Institute of Ophthalmology, 11-43 Bath Street, London, EC1V 9EL, UK
| | - Christina Zeitz
- INSERM, U968, Paris, F-75012, France. .,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France. .,CNRS, UMR_7210, Paris, F-75012, France.
| | - Isabelle Audo
- INSERM, U968, Paris, F-75012, France. .,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France. .,CNRS, UMR_7210, Paris, F-75012, France. .,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU ViewMaintain, INSERM-DHOS CIC 1423, Paris, F-75012, France. .,University College London Institute of Ophthalmology, 11-43 Bath Street, London, EC1V 9EL, UK.
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8
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Mutations of 60 known causative genes in 157 families with retinitis pigmentosa based on exome sequencing. Hum Genet 2014; 133:1255-71. [DOI: 10.1007/s00439-014-1460-2] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 06/03/2014] [Indexed: 12/01/2022]
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9
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Utz VM, Chappelow AV, Marino MJ, Beight CD, Sturgill-Short GM, Pauer GJT, Crowe S, Hagstrom SA, Traboulsi EI. Identification of three ABCA4 sequence variations exclusive to African American patients in a cohort of patients with Stargardt disease. Am J Ophthalmol 2013; 156:1220-1227.e2. [PMID: 24011517 DOI: 10.1016/j.ajo.2013.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 07/10/2013] [Accepted: 07/11/2013] [Indexed: 11/18/2022]
Abstract
PURPOSE To describe the clinical and molecular findings in ten unrelated African American patients with Stargardt disease. DESIGN Retrospective, observational case series. METHODS We reviewed the clinical histories, examinations, and genotypes of 85 patients with molecular diagnoses of Stargardt disease. Three ABCA4 sequence variations identified exclusively in African Americans were evaluated in 300 African American controls and by in silico analysis. RESULTS ABCA4 sequence changes were identified in 85 patients from 80 families, of which 11 patients identified themselves as African American. Of these 11 patients, 10 unrelated patients shared 1 of 3 ABCA4 sequence variations: c.3602T>G (p.L1201R); c.3899G>A (p.R1300Q); or c.6320G>A (p.R2107H). The minor allele frequencies in the African American control population for each variation were 7.5%, 6.3%, and 2%, respectively. This is comparable to the allele frequency in African Americans in the Exome Variant Server. In contrast, the allele frequency of all three of these variations was less than or equal to 0.05% in European Americans. Although both c.3602T>G and c.3899G>A have been reported as likely disease-causing variations, one of our control patients was homozygous for each variant, suggesting that these are nonpathogenic. In contrast, the absence of c.6320G>A in the control population in the homozygous state, combined with the results of bioinformatics analysis, support its pathogenicity. CONCLUSIONS Three ABCA4 sequence variations were identified exclusively in 10 unrelated African American patients: p.L1201R and p.R1300Q likely represent nonpathogenic sequence variants, whereas the p.R2107H substitution appears to be pathogenic. Characterization of population-specific disease alleles may have important implications for the development of genetic screening algorithms.
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10
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Eminoglu TF, Ezgu FS, Hasanoglu A, Tumer L. Rapid screening of 12 common mutations in Turkish GSD 1a patients using electronic DNA microarray. Gene 2013; 518:346-50. [DOI: 10.1016/j.gene.2012.12.104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 11/27/2012] [Accepted: 12/22/2012] [Indexed: 10/27/2022]
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11
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Chacón-Camacho OF, Granillo-Alvarez M, Ayala-Ramírez R, Zenteno JC. ABCA4 mutational spectrum in Mexican patients with Stargardt disease: Identification of 12 novel mutations and evidence of a founder effect for the common p.A1773V mutation. Exp Eye Res 2013; 109:77-82. [PMID: 23419329 DOI: 10.1016/j.exer.2013.02.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 01/16/2013] [Accepted: 02/04/2013] [Indexed: 01/10/2023]
Abstract
The aim of this study was to assess the mutational spectrum of the ABCA4 gene in a cohort of patients with Stargardt disease from Mexico, a previously uncharacterized population. Clinical diagnosis in each patient was supported by a complete ophthalmological assessment that included visual acuity measurement, a slit lamp examination, a fundus examination and photography, electroretinography, fluorescein angiography, and computerized visual fields testing. Molecular analysis was performed by PCR amplification and direct nucleotide sequence of the 50 exons of the ABCA4 gene in genomic DNA. A total of 31 unrelated subjects with the disease were enrolled in the study. Molecular analysis in the total group of 62 alleles allowed the identification of 46 mutant ABCA4 alleles carrying 29 different pathogenic disease-associated mutations. Two ABCA4 mutant alleles were detected in 20 of the 31 patients (64.5%), a single disease allele was identified in six (19.4%), and no mutant alleles were detected in five of the cases (16.1%). Most patients with two ABCA4 mutations (11/20, 55%) were compound heterozygotes. Twelve variants were novel ABCA4 mutations. Nucleotide substitutions were the most frequent type of variation, occurring in 26 out of 29 (89.7%) different mutations. The two most common mutations in our study were the missense changes p.A1773V and p.G818E, which were identified in eight (17%) and seven (15%) of the total 46 disease-associated alleles, respectively. Haplotype analyses of intragenic SNPs in four subjects carrying the p.A1773V mutation supported a common origin for this mutation. In conclusion, this is the first report of ABCA4 molecular screening in Latin American Stargardt disease patients. Our results expand the mutational spectrum of the disease by adding 12 novel ABCA4 pathogenic variants and support the occurrence of a founder effect for the p.A1773V mutation in the Mexican population. The identification of recurrent mutations in our cohort will direct future ABCA4 molecular screening in patients from this ethnic group.
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Affiliation(s)
- Oscar F Chacón-Camacho
- Department of Genetics-Research Unit, Institute of Ophthalmology Conde de Valenciana, Mexico City, Mexico
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Booij JC, Bakker A, Kulumbetova J, Moutaoukil Y, Smeets B, Verheij J, Kroes HY, Klaver CCW, van Schooneveld M, Bergen AAB, Florijn RJ. Simultaneous mutation detection in 90 retinal disease genes in multiple patients using a custom-designed 300-kb retinal resequencing chip. Ophthalmology 2011; 118:160-167.e1-3. [PMID: 20801516 DOI: 10.1016/j.ophtha.2010.04.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 04/14/2010] [Accepted: 04/14/2010] [Indexed: 11/30/2022] Open
Abstract
PURPOSE To develop a high-throughput, cost-effective diagnostic strategy for the identification of known and new mutations in 90 retinal disease genes. DESIGN Evidence-based study. PARTICIPANTS Sixty patients with a variety of retinal disorders, including Leber's congenital amaurosis, ocular albinism, pseudoxanthoma elasticum, retinitis pigmentosa, and Stargardt's disease. METHODS We designed a custom 300-kb resequencing chip. Polymerase chain reaction (PCR) amplification, DNA fragmentation, and chip hybridization were performed according to Affymetrix recommendations. Hybridization signals were analyzed using Sequence pilot module seq-C mutation detection software (2009). This resequencing approach was validated by Sanger sequence technology. MAIN OUTCOME MEASURES Disease-causing sequence changes. RESULTS We developed a retinal resequencing chip that covers all exons of 90 retinal disease genes. We developed and tested multiplex primer sets for 1445 amplicons representing the genes included on the chip. We validated our approach by screening 87 exons from 25 retinal disease genes containing 87 known sequence changes previously identified in our patient group using Sanger sequencing. Call rates for successfully hybridized amplicons were 98% to 100%. Of the known single nucleotide changes, 99% could be detected on the chip. As expected, deletions could not be detected reliably. CONCLUSIONS We designed a custom resequencing chip that can detect known and new sequence changes in 90 retinal disease genes using a new high-throughput strategy with a high sensitivity and specificity for one tenth of the cost of conventional direct sequencing. The developed amplification strategy allows for the pooling of multiple patients with non-overlapping phenotypes, enabling many patients to be analyzed simultaneously in a fast and cost-effective manner.
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Affiliation(s)
- Judith C Booij
- Department of Clinical and Molecular Ophthalmogenetics, Netherlands Institute for Neuroscience, an institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
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Ayuso C, Millan JM. Retinitis pigmentosa and allied conditions today: a paradigm of translational research. Genome Med 2010; 2:34. [PMID: 20519033 PMCID: PMC2887078 DOI: 10.1186/gm155] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Monogenic human retinal dystrophies are a group of disorders characterized by progressive loss of photoreceptor cells leading to visual handicap. Retinitis pigmentosa is a type of retinal dystrophy where degeneration of rod photoreceptors occurs at the early stages. At present, there are no available effective therapies to maintain or improve vision in patients affected with retinitis pigmentosa, but post-genomic studies are allowing the development of potential therapeutic approaches. This review summarizes current knowledge on genes that have been identified to be responsible for retinitis pigmentosa, the involvement of these genes in the different forms of the disorder, the role of the proteins encoded by these genes in retinal function, the utility of genotyping, and current efforts to develop novel therapies.
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Affiliation(s)
- Carmen Ayuso
- Department of Medical Genetics, IIS-Fundación Jiménez Díaz/CIBERER, Av/Reyes Católicos no, 2; 28040, Madrid, Spain.
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Fingerman M, Fingerman SW. The effects of 5-hydroxytryptamine depletors and monoamine oxidase inhibitors on color changes of the fiddler crab, Uca pugilator: further evidence in support of the hypothesis that 5-hydroxytryptamine controls the release of red pigment-dispersing hormone. ACTA ACUST UNITED AC 1976; 48:1229-34. [PMID: 205 DOI: 10.1515/cclm.2010.244] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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