51
|
Grunin M, Tiosano L, Jaouni T, Averbukh E, Sharon D, Chowers I. Evaluation of the association of single nucleotide polymorphisms in the PRPH2 gene with adult-onset foveomacular vitelliform dystrophy. Ophthalmic Genet 2016; 37:285-9. [PMID: 26849151 DOI: 10.3109/13816810.2015.1059456] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE A minority of patients with adult-onset foveomacular vitelliform dystrophy (AFVD) carry mutations in the PRPH2 gene. This gene is highly polymorphic and it was suggested that single-nucleotide polymorphisms (SNPs) in PRPH2 may also be associated with AFVD. We aimed to evaluate for such an association. METHODS A single center cohort from a tertiary referral center including 52 consecutive patients with a clinical diagnosis of AFVD and 91 unaffected individuals was assessed. Sanger sequencing was performed for the PRPH2, BEST1, and IMPG1/2 genes. Investigation as to the frequency of minor alleles for SNPs in PRPH2 was performed and compared to HapMap and Exome Variant Server (EVS) data. RESULTS None of the patients carry a mutation in PRPH2, BEST1, or IMPG1/2. Five of 14 known SNPs (rs835, rs361524, rs434102, rs425876, rs390659) in exon 3 of PRPH2 were identified in AFVD patients. A high frequency and percentage of minor alleles of these five SNPs was found in the Israeli AFVD patients and controls compared with European, Chinese, Japanese and African populations identified via HapMap and EVS (p < 0.05). Power calculation suggested that the sample size was sufficient (80%) to rule out an association with an odds ratio above 2.5. CONCLUSIONS These results suggest that genetic variants in PRPH2 do not compose a major genetic risk factor for AFVD. The Israeli population shows a higher percentage of minor allele frequencies in SNPs in the PRPH2 gene, as compared with other populations. This emphasizes the need for appropriate genetic background when performing SNP association testing.
Collapse
Affiliation(s)
- Michelle Grunin
- a Department of Ophthalmology , Hadassah-Hebrew University Medical Center , Jerusalem , Israel
| | - Liran Tiosano
- a Department of Ophthalmology , Hadassah-Hebrew University Medical Center , Jerusalem , Israel
| | - Tareq Jaouni
- a Department of Ophthalmology , Hadassah-Hebrew University Medical Center , Jerusalem , Israel
| | - Edward Averbukh
- a Department of Ophthalmology , Hadassah-Hebrew University Medical Center , Jerusalem , Israel
| | - Dror Sharon
- a Department of Ophthalmology , Hadassah-Hebrew University Medical Center , Jerusalem , Israel
| | - Itay Chowers
- a Department of Ophthalmology , Hadassah-Hebrew University Medical Center , Jerusalem , Israel
| |
Collapse
|
52
|
Adult-onset foveomacular vitelliform dystrophy: A fresh perspective. Prog Retin Eye Res 2015; 47:64-85. [DOI: 10.1016/j.preteyeres.2015.02.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 02/01/2015] [Accepted: 02/04/2015] [Indexed: 01/06/2023]
|
53
|
Nash BM, Wright DC, Grigg JR, Bennetts B, Jamieson RV. Retinal dystrophies, genomic applications in diagnosis and prospects for therapy. Transl Pediatr 2015; 4:139-63. [PMID: 26835369 PMCID: PMC4729094 DOI: 10.3978/j.issn.2224-4336.2015.04.03] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Retinal dystrophies (RDs) are degenerative diseases of the retina which have marked clinical and genetic heterogeneity. Common presentations among these disorders include night or colour blindness, tunnel vision and subsequent progression to complete blindness. The known causative disease genes have a variety of developmental and functional roles with mutations in more than 120 genes shown to be responsible for the phenotypes. In addition, mutations within the same gene have been shown to cause different disease phenotypes, even amongst affected individuals within the same family highlighting further levels of complexity. The known disease genes encode proteins involved in retinal cellular structures, phototransduction, the visual cycle, and photoreceptor structure or gene regulation. This review aims to demonstrate the high degree of genetic complexity in both the causative disease genes and their associated phenotypes, highlighting the more common clinical manifestation of retinitis pigmentosa (RP). The review also provides insight to recent advances in genomic molecular diagnosis and gene and cell-based therapies for the RDs.
Collapse
Affiliation(s)
- Benjamin M Nash
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - Dale C Wright
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - John R Grigg
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - Bruce Bennetts
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - Robyn V Jamieson
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| |
Collapse
|
54
|
Ishikawa M, Sawada Y, Yoshitomi T. Structure and function of the interphotoreceptor matrix surrounding retinal photoreceptor cells. Exp Eye Res 2015; 133:3-18. [DOI: 10.1016/j.exer.2015.02.017] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 02/20/2015] [Accepted: 02/20/2015] [Indexed: 12/21/2022]
|
55
|
Maria M, Ajmal M, Azam M, Waheed NK, Siddiqui SN, Mustafa B, Ayub H, Ali L, Ahmad S, Micheal S, Hussain A, Shah STA, Ali SHB, Ahmed W, Khan YM, den Hollander AI, Haer-Wigman L, Collin RWJ, Khan MI, Qamar R, Cremers FPM. Homozygosity mapping and targeted sanger sequencing reveal genetic defects underlying inherited retinal disease in families from pakistan. PLoS One 2015; 10:e0119806. [PMID: 25775262 PMCID: PMC4361598 DOI: 10.1371/journal.pone.0119806] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 01/13/2015] [Indexed: 11/18/2022] Open
Abstract
Background Homozygosity mapping has facilitated the identification of the genetic causes underlying inherited diseases, particularly in consanguineous families with multiple affected individuals. This knowledge has also resulted in a mutation dataset that can be used in a cost and time effective manner to screen frequent population-specific genetic variations associated with diseases such as inherited retinal disease (IRD). Methods We genetically screened 13 families from a cohort of 81 Pakistani IRD families diagnosed with Leber congenital amaurosis (LCA), retinitis pigmentosa (RP), congenital stationary night blindness (CSNB), or cone dystrophy (CD). We employed genome-wide single nucleotide polymorphism (SNP) array analysis to identify homozygous regions shared by affected individuals and performed Sanger sequencing of IRD-associated genes located in the sizeable homozygous regions. In addition, based on population specific mutation data we performed targeted Sanger sequencing (TSS) of frequent variants in AIPL1, CEP290, CRB1, GUCY2D, LCA5, RPGRIP1 and TULP1, in probands from 28 LCA families. Results Homozygosity mapping and Sanger sequencing of IRD-associated genes revealed the underlying mutations in 10 families. TSS revealed causative variants in three families. In these 13 families four novel mutations were identified in CNGA1, CNGB1, GUCY2D, and RPGRIP1. Conclusions Homozygosity mapping and TSS revealed the underlying genetic cause in 13 IRD families, which is useful for genetic counseling as well as therapeutic interventions that are likely to become available in the near future.
Collapse
Affiliation(s)
- Maleeha Maria
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Muhammad Ajmal
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Maleeha Azam
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nadia Khalida Waheed
- Tufts University Medical School, Boston, Massachusetts, United States of America
| | | | - Bilal Mustafa
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
| | - Humaira Ayub
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
| | - Liaqat Ali
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
| | - Shakeel Ahmad
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
| | - Shazia Micheal
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Alamdar Hussain
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
| | - Syed Tahir Abbas Shah
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
| | - Syeda Hafiza Benish Ali
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
| | - Waqas Ahmed
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
- University of Haripur, Haripur, Pakistan
| | - Yar Muhammad Khan
- Department of Chemistry, University of Science and Technology, Bannu, Pakistan
| | - Anneke I. den Hollander
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Rob W. J. Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Muhammad Imran Khan
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Raheel Qamar
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
- Al-Nafees Medical College & Hospital, Isra University, Islamabad, Pakistan
| | - Frans P. M. Cremers
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
- * E-mail:
| |
Collapse
|
56
|
Meunier I, Manes G, Bocquet B, Marquette V, Baudoin C, Puech B, Defoort-Dhellemmes S, Audo I, Verdet R, Arndt C, Zanlonghi X, Le Meur G, Dhaenens CM, Hamel CP. Frequency and Clinical Pattern of Vitelliform Macular Dystrophy Caused by Mutations of Interphotoreceptor Matrix IMPG1 and IMPG2 Genes. Ophthalmology 2014; 121:2406-14. [DOI: 10.1016/j.ophtha.2014.06.028] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 04/28/2014] [Accepted: 06/18/2014] [Indexed: 11/30/2022] Open
|
57
|
Siemiatkowska AM, Collin RWJ, den Hollander AI, Cremers FPM. Genomic approaches for the discovery of genes mutated in inherited retinal degeneration. Cold Spring Harb Perspect Med 2014; 4:a017137. [PMID: 24939053 PMCID: PMC4109577 DOI: 10.1101/cshperspect.a017137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In view of their high degree of genetic heterogeneity, inherited retinal diseases (IRDs) pose a significant challenge for identifying novel genetic causes. Thus far, more than 200 genes have been found to be mutated in IRDs, which together contain causal variants in >80% of the cases. Accurate genetic diagnostics is particularly important for isolated cases, in which X-linked and de novo autosomal dominant variants are not uncommon. In addition, new gene- or mutation-specific therapies are emerging, underlining the importance of identifying causative mutations in each individual. Sanger sequencing of selected genes followed by cost-effective targeted next-generation sequencing (NGS) can identify defects in known IRD-associated genes in the majority of the cases. Exome NGS in combination with genetic linkage or homozygosity mapping studies can aid the identification of the remaining causal genes. As these are thought to be mutated in <1% of the cases, validation through functional modeling in, for example, zebrafish and/or replication through the genotyping of large patient cohorts is required. In the near future, whole genome NGS in combination with transcriptome NGS may reveal mutations that are currently hidden in the noncoding regions of the human genome.
Collapse
Affiliation(s)
- Anna M Siemiatkowska
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anneke I den Hollander
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| |
Collapse
|
58
|
Emerling CA, Springer MS. Eyes underground: regression of visual protein networks in subterranean mammals. Mol Phylogenet Evol 2014; 78:260-70. [PMID: 24859681 DOI: 10.1016/j.ympev.2014.05.016] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Revised: 04/26/2014] [Accepted: 05/05/2014] [Indexed: 11/26/2022]
Abstract
Regressive evolution involves the degeneration of formerly useful structures in a lineage over time, and may be accompanied by the molecular decay of phenotype-specific genes. The mammalian eye has repeatedly undergone degeneration in taxa that occupy dim-light environments including subterranean habitats. Here we assess whether a decrease in the amount of light that reaches the retina is associated with increased regression of retinal genes, whether the phototransduction and visual cycle pathways degrade in a predictable pattern, and if the timing of retinal gene loss is associated with the entrance of mammalian lineages into subterranean environments. Sequence data were obtained from the publically available genomes of the Cape golden mole (Chrysochloris asiatica), naked mole-rat (Heterocephalus glaber) and star-nosed mole (Condylura cristata) for 65 genes associated with phototransduction, the visual cycle, and other retinal functions. Gene sequences were inspected for inactivating mutations and, when present, pseudogene sequences were compared to sequences from subaerial outgroup species. To test whether retinal degeneration is correlated with historical entrances into subterranean environments, estimated dates of retinal gene inactivation were compared to the fossil record and phylogenetic inferences of ancestral fossoriality. Our results show that (1) lower levels of light available to the retina correspond with an increase in the number of retinal pseudogenes, (2) retinal protein networks generally degrade in a predictable manner, although the extensive loss of cone phototransduction genes in Heterocephalus raises further questions regarding SWS1-cone monochromacy versus functional rod monochromacy in this species, and (3) inactivation dates of retinal genes usually post-date inferred entrances into subterranean habitats.
Collapse
Affiliation(s)
- Christopher A Emerling
- Department of Biology, University of California Riverside, 900 University Ave, Riverside, CA 92521, United States.
| | - Mark S Springer
- Department of Biology, University of California Riverside, 900 University Ave, Riverside, CA 92521, United States.
| |
Collapse
|
59
|
Wain LV, Sayers I, Soler Artigas M, Portelli MA, Zeggini E, Obeidat M, Sin DD, Bossé Y, Nickle D, Brandsma CA, Malarstig A, Vangjeli C, Jelinsky SA, John S, Kilty I, McKeever T, Shrine NRG, Cook JP, Patel S, Spector TD, Hollox EJ, Hall IP, Tobin MD. Whole exome re-sequencing implicates CCDC38 and cilia structure and function in resistance to smoking related airflow obstruction. PLoS Genet 2014; 10:e1004314. [PMID: 24786987 PMCID: PMC4006731 DOI: 10.1371/journal.pgen.1004314] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 03/06/2014] [Indexed: 11/19/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a leading cause of global morbidity and mortality and, whilst smoking remains the single most important risk factor, COPD risk is heritable. Of 26 independent genomic regions showing association with lung function in genome-wide association studies, eleven have been reported to show association with airflow obstruction. Although the main risk factor for COPD is smoking, some individuals are observed to have a high forced expired volume in 1 second (FEV1) despite many years of heavy smoking. We hypothesised that these "resistant smokers" may harbour variants which protect against lung function decline caused by smoking and provide insight into the genetic determinants of lung health. We undertook whole exome re-sequencing of 100 heavy smokers who had healthy lung function given their age, sex, height and smoking history and applied three complementary approaches to explore the genetic architecture of smoking resistance. Firstly, we identified novel functional variants in the "resistant smokers" and looked for enrichment of these novel variants within biological pathways. Secondly, we undertook association testing of all exonic variants individually with two independent control sets. Thirdly, we undertook gene-based association testing of all exonic variants. Our strongest signal of association with smoking resistance for a non-synonymous SNP was for rs10859974 (P = 2.34 × 10(-4)) in CCDC38, a gene which has previously been reported to show association with FEV1/FVC, and we demonstrate moderate expression of CCDC38 in bronchial epithelial cells. We identified an enrichment of novel putatively functional variants in genes related to cilia structure and function in resistant smokers. Ciliary function abnormalities are known to be associated with both smoking and reduced mucociliary clearance in patients with COPD. We suggest that genetic influences on the development or function of cilia in the bronchial epithelium may affect growth of cilia or the extent of damage caused by tobacco smoke.
Collapse
Affiliation(s)
- Louise V. Wain
- University of Leicester, Department of Health Sciences, Leicester, United Kingdom
- * E-mail:
| | - Ian Sayers
- Division of Respiratory Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - María Soler Artigas
- University of Leicester, Department of Health Sciences, Leicester, United Kingdom
| | - Michael A. Portelli
- Division of Respiratory Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | | | - Ma'en Obeidat
- University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, Canada
| | - Don D. Sin
- University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, Canada
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Laval University, Québec, Canada
| | - David Nickle
- Merck Research Laboratories, Boston, Massachusetts, United States of America
- Merck, Rahway, New Jersey, United States of America
| | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, GRIAC Research Institute, Groningen, The Netherlands
| | | | | | - Scott A. Jelinsky
- Pfizer Worldwide R&D, Cambridge, Massachusetts, United States of America
| | - Sally John
- Pfizer Worldwide R&D, Cambridge, Massachusetts, United States of America
| | - Iain Kilty
- Pfizer Worldwide R&D, Cambridge, Massachusetts, United States of America
| | - Tricia McKeever
- School of Community Health Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Nick R. G. Shrine
- University of Leicester, Department of Health Sciences, Leicester, United Kingdom
| | - James P. Cook
- University of Leicester, Department of Health Sciences, Leicester, United Kingdom
| | - Shrina Patel
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Tim D. Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Edward J. Hollox
- University of Leicester, Department of Genetics, Leicester, United Kingdom
| | - Ian P. Hall
- Division of Respiratory Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Martin D. Tobin
- University of Leicester, Department of Health Sciences, Leicester, United Kingdom
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| |
Collapse
|
60
|
Khan MI, Azam M, Ajmal M, Collin RWJ, den Hollander AI, Cremers FPM, Qamar R. The molecular basis of retinal dystrophies in pakistan. Genes (Basel) 2014; 5:176-95. [PMID: 24705292 PMCID: PMC3978518 DOI: 10.3390/genes5010176] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 02/14/2014] [Accepted: 02/14/2014] [Indexed: 12/23/2022] Open
Abstract
The customary consanguineous nuptials in Pakistan underlie the frequent occurrence of autosomal recessive inherited disorders, including retinal dystrophy (RD). In many studies, homozygosity mapping has been shown to be successful in mapping susceptibility loci for autosomal recessive inherited disease. RDs are the most frequent cause of inherited blindness worldwide. To date there is no comprehensive genetic overview of different RDs in Pakistan. In this review, genetic data of syndromic and non-syndromic RD families from Pakistan has been collected. Out of the 132 genes known to be involved in non-syndromic RD, 35 different genes have been reported to be mutated in families of Pakistani origin. In the Pakistani RD families 90% of the mutations causing non-syndromic RD and all mutations causing syndromic forms of the disease have not been reported in other populations. Based on the current inventory of all Pakistani RD-associated gene defects, a cost-efficient allele-specific analysis of 11 RD-associated variants is proposed, which may capture up to 35% of the genetic causes of retinal dystrophy in Pakistan.
Collapse
Affiliation(s)
- Muhammad Imran Khan
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad 45600, Pakistan.
| | - Maleeha Azam
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad 45600, Pakistan.
| | - Muhammad Ajmal
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad 45600, Pakistan.
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands.
| | - Anneke I den Hollander
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands.
| | - Frans P M Cremers
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad 45600, Pakistan.
| | - Raheel Qamar
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad 45600, Pakistan.
| |
Collapse
|
61
|
Zobor D, Balousha G, Baumann B, Wissinger B. Homozygosity mapping reveals new nonsense mutation in the FAM161A gene causing autosomal recessive retinitis pigmentosa in a Palestinian family. Mol Vis 2014; 20:178-82. [PMID: 24520187 PMCID: PMC3919667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 02/04/2014] [Indexed: 11/29/2022] Open
Abstract
PURPOSE Retinitis pigmentosa (RP) is a heterogenous group of inherited retinal degenerations caused by mutations in at least 45 genes. Recently, the FAM161A gene was identified as the causative gene for RP28, an autosomal recessive form of RP. METHODS We performed a clinical and molecular genetic study of a consanguineous Palestinian family with two three siblings affected with retinitis pigmentosa. DNA samples were collected from the index patient, his father, his affected sister, and two non-affected brothers. DNA sample from the index was subjected to high resolution genome-wide SNP array. Assuming identity-by-descent in this consanguineous family we applied homozygosity mapping to identify disease causing genes. RESULTS The index patient reported night blindness since the age of 20 years, followed by moderate disease progression with decrease of peripheral vision, the development of photophobia and later on reduced central vision. At the age of 40 his visual acuity was counting fingers (CF) for both eyes, color discrimination was not possible and his visual fields were severely constricted. Funduscopic examination revealed a typical appearance of advanced RP with optic disc pallor, narrowed retinal vessels, bone-spicule like pigmentary changes in the mid-periphery and atrophic changes in the macula. His younger affected brother (37 years) was reported with overall milder symptoms, while the youngest sister (21 years) reported problems only with night vision. Applying high-density SNP arrays we identified several homozygous genomic regions one of which included the recently identified FAM161A gene mutated in RP28-linked autosomal recessive RP. Sequencing analysis revealed the presence of a novel homozygous nonsense mutation, c.1003C>T/p.R335X in the index patient and the affected sister. CONCLUSION We identified an RP28-linked RP family in the Palestinian population caused by a novel nonsense mutation in FAM161A. RP in this family shows a typical disease onset with moderate to rapid progression into severe visual impairment including central vision in the index and overall milder symptoms in the younger brother and sister.
Collapse
Affiliation(s)
- Ditta Zobor
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Germany
| | - Ghassan Balousha
- Department of Pathology and Histology, Al-Quds University, Eastern Jerusalem, Palestinian Authority
| | - Britta Baumann
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Germany
| | - Bernd Wissinger
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Germany
| |
Collapse
|
62
|
Bocquet B, Marzouka NAD, Hebrard M, Manes G, Sénéchal A, Meunier I, Hamel CP. Homozygosity mapping in autosomal recessive retinitis pigmentosa families detects novel mutations. Mol Vis 2013; 19:2487-500. [PMID: 24339724 PMCID: PMC3857159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 12/06/2013] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Autosomal recessive retinitis pigmentosa (arRP) is a genetically heterogeneous disease resulting in progressive loss of photoreceptors that leads to blindness. To date, 36 genes are known to cause arRP, rendering the molecular diagnosis a challenge. The aim of this study was to use homozygosity mapping to identify the causative mutation in a series of inbred families with arRP. METHODS arRP patients underwent standard ophthalmic examination, Goldman perimetry, fundus examination, retinal OCT, autofluorescence measurement, and full-field electroretinogram. Fifteen consanguineous families with arRP excluded for USH2A and EYS were genotyped on 250 K SNP arrays. Homozygous regions were listed, and known genes within these regions were PCR sequenced. Familial segregation and mutation analyzes were performed. RESULTS We found ten mutations, seven of which were novel mutations in eight known genes, including RP1, IMPG2, NR2E3, PDE6A, PDE6B, RLBP1, CNGB1, and C2ORF71, in ten out of 15 families. The patients carrying RP1, C2ORF71, and IMPG2 mutations presented with severe RP, while those with PDE6A, PDE6B, and CNGB1 mutations were less severely affected. The five families without mutations in known genes could be a source of identification of novel genes. CONCLUSIONS Homozygosity mapping combined with systematic screening of known genes results in a positive molecular diagnosis in 66.7% of families.
Collapse
Affiliation(s)
- Béatrice Bocquet
- INSERM U. 1051, Institute for Neurosciences of Montpellier, Montpellier, France,Université Montpellier 1, Montpellier, France,Université Montpellier 2, Montpellier, France
| | - Nour al Dain Marzouka
- INSERM U. 1051, Institute for Neurosciences of Montpellier, Montpellier, France,Université Montpellier 1, Montpellier, France,Université Montpellier 2, Montpellier, France
| | - Maxime Hebrard
- INSERM U. 1051, Institute for Neurosciences of Montpellier, Montpellier, France,Université Montpellier 1, Montpellier, France,Université Montpellier 2, Montpellier, France
| | - Gaël Manes
- INSERM U. 1051, Institute for Neurosciences of Montpellier, Montpellier, France,Université Montpellier 1, Montpellier, France,Université Montpellier 2, Montpellier, France
| | - Audrey Sénéchal
- INSERM U. 1051, Institute for Neurosciences of Montpellier, Montpellier, France,Université Montpellier 1, Montpellier, France,Université Montpellier 2, Montpellier, France
| | - Isabelle Meunier
- INSERM U. 1051, Institute for Neurosciences of Montpellier, Montpellier, France,Université Montpellier 1, Montpellier, France,Université Montpellier 2, Montpellier, France,Genetics of Sensory Diseases, CHRU, Montpellier, France
| | - Christian P. Hamel
- INSERM U. 1051, Institute for Neurosciences of Montpellier, Montpellier, France,Université Montpellier 1, Montpellier, France,Université Montpellier 2, Montpellier, France,Genetics of Sensory Diseases, CHRU, Montpellier, France
| |
Collapse
|
63
|
Cottet S, Jüttner R, Voirol N, Chambon P, Rathjen FG, Schorderet DF, Escher P. Retinal pigment epithelium protein of 65 kDA gene-linked retinal degeneration is not modulated by chicken acidic leucine-rich epidermal growth factor-like domain containing brain protein/Neuroglycan C/ chondroitin sulfate proteoglycan 5. Mol Vis 2013; 19:2312-20. [PMID: 24265546 PMCID: PMC3834887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/14/2013] [Indexed: 10/26/2022] Open
Abstract
PURPOSE To analyze in vivo the function of chicken acidic leucine-rich epidermal growth factor-like domain containing brain protein/Neuroglycan C (gene symbol: Cspg5) during retinal degeneration in the Rpe65⁻/⁻ mouse model of Leber congenital amaurosis. METHODS We resorted to mice with targeted deletions in the Cspg5 and retinal pigment epithelium protein of 65 kDa (Rpe65) genes (Cspg5⁻/⁻/Rpe65⁻/⁻). Cone degeneration was assessed with cone-specific peanut agglutinin staining. Transcriptional expression of rhodopsin (Rho), S-opsin (Opn1sw), M-opsin (Opn1mw), rod transducin α subunit (Gnat1), and cone transducin α subunit (Gnat2) genes was assessed with quantitative PCR from 2 weeks to 12 months. The retinal pigment epithelium (RPE) was analyzed at P14 with immunodetection of the retinol-binding protein membrane receptor Stra6. RESULTS No differences in the progression of retinal degeneration were observed between the Rpe65⁻/⁻ and Cspg5⁻/⁻/Rpe65⁻/⁻ mice. No retinal phenotype was detected in the late postnatal and adult Cspg5⁻/⁻ mice, when compared to the wild-type mice. CONCLUSIONS Despite the previously reported upregulation of Cspg5 during retinal degeneration in Rpe65⁻/⁻ mice, no protective effect or any involvement of Cspg5 in disease progression was identified.
Collapse
Affiliation(s)
- Sandra Cottet
- Institute for Research in Ophthalmology, Sion, Switzerland,Department of Ophthalmology, University of Lausanne, Lausanne, Switzerland
| | | | | | - Pierre Chambon
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Collège de France, Strasbourg, France
| | | | - Daniel F. Schorderet
- Institute for Research in Ophthalmology, Sion, Switzerland,Department of Ophthalmology, University of Lausanne, Lausanne, Switzerland,EPFL-Ecole Polytechnique Fédérale, Lausanne, Switzerland
| | - Pascal Escher
- Institute for Research in Ophthalmology, Sion, Switzerland,Department of Ophthalmology, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
64
|
Thompson DA, Lyons RJ, Russell-Eggitt I, Liasis A, Jägle H, Grünewald S. Retinal characteristics of the congenital disorder of glycosylation PMM2-CDG. J Inherit Metab Dis 2013; 36:1039-47. [PMID: 23430200 DOI: 10.1007/s10545-013-9594-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 12/30/2012] [Accepted: 01/24/2013] [Indexed: 10/27/2022]
Abstract
The congenital disorder of glycosylation, PMM2-CDG, is associated with progressive photoreceptor degeneration, which causes a pigmentary retinopathy. We identified a sibling pair, mildly affected with PMM2-CDG, who showed preserved photoreceptor function, but profound deficits of the 'on-pathway' in the retina. This localises the site of early, or initial, retinal dysfunction in PMM2-CDG to the synapse in the outer plexiform layer between bipolar cells, photoreceptors and horizontal cells. We sought wider evidence to support this novel finding by reviewing retrospectively the case notes of eight patients, diagnosed with PMM2-CDG between the ages of 7 months to 16 years. We compared the clinical presentation and electroretinograms, (ERGs), of these patients with the sibling pair. We found that five of eight patients showed characteristic ERG features of on-pathway dysfunction in the form of reduced ERG b-wave amplitude. The remaining three patients had significant photoreceptor dysfunction by the time of ERG recording, and both a- and b-wave amplitudes were markedly attenuated. We conclude that ERG signs of on-pathway dysfunction can be detected in the early stages of PMM2-CDG. Referral for electroretinography evidence of this specific on-pathway deficit, with preservation of oscillatory potentials, can help establish the diagnosis of infants with developmental delay or failure to thrive in whom a glycosylation defect is suspected. Also by increasing our understanding of the interaction of N-glycoproteins at this synapse we may be able to design future therapeutic intervention to prevent or ameliorate the progressive visual loss associated with PMM2-CDG.
Collapse
Affiliation(s)
- Dorothy A Thompson
- Clinical and Academic Department of Ophthalmology, Great Ormond Street Hospital for Children, UCL ICH, Great Ormond Street, London, WC1N 3JH, UK,
| | | | | | | | | | | |
Collapse
|
65
|
Audo I, Bujakowska K, Orhan E, El Shamieh S, Sennlaub F, Guillonneau X, Antonio A, Michiels C, Lancelot ME, Letexier M, Saraiva JP, Nguyen H, Luu TD, Léveillard T, Poch O, Dollfus H, Paques M, Goureau O, Mohand-Saïd S, Bhattacharya SS, Sahel JA, Zeitz C. The familial dementia gene revisited: a missense mutation revealed by whole-exome sequencing identifies ITM2B as a candidate gene underlying a novel autosomal dominant retinal dystrophy in a large family. Hum Mol Genet 2013; 23:491-501. [PMID: 24026677 DOI: 10.1093/hmg/ddt439] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Inherited retinal diseases are a group of clinically and genetically heterogeneous disorders for which a significant number of cases remain genetically unresolved. Increasing knowledge on underlying pathogenic mechanisms with precise phenotype-genotype correlation is, however, critical for establishing novel therapeutic interventions for these yet incurable neurodegenerative conditions. We report phenotypic and genetic characterization of a large family presenting an unusual autosomal dominant retinal dystrophy. Phenotypic characterization revealed a retinopathy dominated by inner retinal dysfunction and ganglion cell abnormalities. Whole-exome sequencing identified a missense variant (c.782A>C, p.Glu261Ala) in ITM2B coding for Integral Membrane Protein 2B, which co-segregates with the disease in this large family and lies within the 24.6 Mb interval identified by microsatellite haplotyping. The physiological role of ITM2B remains unclear and has never been investigated in the retina. RNA in situ hybridization reveals Itm2b mRNA in inner nuclear and ganglion cell layers within the retina, with immunostaining demonstrating the presence of the corresponding protein in the same layers. Furthermore, ITM2B in the retina co-localizes with its known interacting partner in cerebral tissue, the amyloid β precursor protein, critical in Alzheimer disease physiopathology. Interestingly, two distinct ITM2B mutations, both resulting in a longer protein product, had already been reported in two large autosomal dominant families with Alzheimer-like dementia but never in subjects with isolated retinal diseases. These findings should better define pathogenic mechanism(s) associated with ITM2B mutations underlying dementia or retinal disease and add a new candidate to the list of genes involved in inherited retinal dystrophies.
Collapse
|
66
|
Mutations in IMPG1 cause vitelliform macular dystrophies. Am J Hum Genet 2013; 93:571-8. [PMID: 23993198 DOI: 10.1016/j.ajhg.2013.07.018] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Revised: 05/27/2013] [Accepted: 07/19/2013] [Indexed: 11/21/2022] Open
Abstract
Vitelliform macular dystrophies (VMD) are inherited retinal dystrophies characterized by yellow, round deposits visible upon fundus examination and encountered in individuals with juvenile Best macular dystrophy (BMD) or adult-onset vitelliform macular dystrophy (AVMD). Although many BMD and some AVMD cases harbor mutations in BEST1 or PRPH2, the underlying genetic cause remains unknown for many affected individuals. In a large family with autosomal-dominant VMD, gene mapping and whole-exome sequencing led to the identification of a c.713T>G (p.Leu238Arg) IMPG1 mutation, which was subsequently found in two other families with autosomal-dominant VMD and the same phenotype. IMPG1 encodes the SPACR protein, a component of the rod and cone photoreceptor extracellular matrix domains. Structural modeling indicates that the p.Leu238Arg substitution destabilizes the conserved SEA1 domain of SPACR. Screening of 144 probands who had various forms of macular dystrophy revealed three other IMPG1 mutations. Two individuals from one family affected by autosomal-recessive VMD were homozygous for the splice-site mutation c.807+1G>T, and two from another family were compound heterozygous for the mutations c.461T>C (p.Leu154Pro) and c.1519C>T (p.Arg507(∗)). Most cases had a normal or moderately decreased electrooculogram Arden ratio. We conclude that IMPG1 mutations cause both autosomal-dominant and -recessive forms of VMD, thus indicating that impairment of the interphotoreceptor matrix might be a general cause of VMD.
Collapse
|
67
|
Garlipp MA, Gonzalez-Fernandez F. Cone outer segment and Müller microvilli pericellular matrices provide binding domains for interphotoreceptor retinoid-binding protein (IRBP). Exp Eye Res 2013; 113:192-202. [DOI: 10.1016/j.exer.2013.02.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 01/24/2013] [Accepted: 02/04/2013] [Indexed: 10/27/2022]
|
68
|
Daiger SP, Sullivan LS, Bowne SJ. Genes and mutations causing retinitis pigmentosa. Clin Genet 2013; 84:132-41. [PMID: 23701314 PMCID: PMC3856531 DOI: 10.1111/cge.12203] [Citation(s) in RCA: 409] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 05/20/2013] [Accepted: 05/20/2013] [Indexed: 12/19/2022]
Abstract
Retinitis pigmentosa (RP) is a heterogeneous set of inherited retinopathies with many disease-causing genes, many known mutations, and highly varied clinical consequences. Progress in finding treatments is dependent on determining the genes and mutations causing these diseases, which includes both gene discovery and mutation screening in affected individuals and families. Despite the complexity, substantial progress has been made in finding RP genes and mutations. Depending on the type of RP, and the technology used, it is possible to detect mutations in 30-80% of cases. One of the most powerful approaches to genetic testing is high-throughput 'deep sequencing', that is, next-generation sequencing (NGS). NGS has identified several novel RP genes but a substantial fraction of previously unsolved cases have mutations in genes that are known causes of retinal disease but not necessarily RP. Apparent discrepancy between the molecular defect and clinical findings may warrant reevaluation of patients and families. In this review, we summarize the current approaches to gene discovery and mutation detection for RP, and indicate pitfalls and unsolved problems. Similar considerations apply to other forms of inherited retinal disease.
Collapse
Affiliation(s)
- S P Daiger
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, TX 77030, USA.
| | | | | |
Collapse
|
69
|
|
70
|
Chang S, Vaccarella L, Olatunji S, Cebulla C, Christoforidis J. Diagnostic challenges in retinitis pigmentosa: genotypic multiplicity and phenotypic variability. Curr Genomics 2012; 12:267-75. [PMID: 22131872 PMCID: PMC3131734 DOI: 10.2174/138920211795860116] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 04/06/2011] [Accepted: 04/15/2011] [Indexed: 12/03/2022] Open
Abstract
Retinitis pigmentosa (RP) is a heterogeneous group of inherited retinal disorders. Diagnosis can be challenging as more than 40 genes are known to cause non-syndromic RP and phenotypic expression can differ significantly resulting in variations in disease severity, age of onset, rate of progression, and clinical findings. We describe the clinical manifestations of RP, the more commonly known causative gene mutations, and the genotypic-phenotypic correlation of RP.
Collapse
Affiliation(s)
- Susie Chang
- Retina Division, Havener Eye Institute, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | | | | | | | | |
Collapse
|
71
|
Neveling K, Collin RWJ, Gilissen C, van Huet RAC, Visser L, Kwint MP, Gijsen SJ, Zonneveld MN, Wieskamp N, de Ligt J, Siemiatkowska AM, Hoefsloot LH, Buckley MF, Kellner U, Branham KE, den Hollander AI, Hoischen A, Hoyng C, Klevering BJ, van den Born LI, Veltman JA, Cremers FPM, Scheffer H. Next-generation genetic testing for retinitis pigmentosa. Hum Mutat 2012; 33:963-72. [PMID: 22334370 PMCID: PMC3490376 DOI: 10.1002/humu.22045] [Citation(s) in RCA: 213] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 01/18/2012] [Indexed: 01/07/2023]
Abstract
Molecular diagnostics for patients with retinitis pigmentosa (RP) has been hampered by extreme genetic and clinical heterogeneity, with 52 causative genes known to date. Here, we developed a comprehensive next-generation sequencing (NGS) approach for the clinical molecular diagnostics of RP. All known inherited retinal disease genes (n = 111) were captured and simultaneously analyzed using NGS in 100 RP patients without a molecular diagnosis. A systematic data analysis pipeline was developed and validated to prioritize and predict the pathogenicity of all genetic variants identified in each patient, which enabled us to reduce the number of potential pathogenic variants from approximately 1,200 to zero to nine per patient. Subsequent segregation analysis and in silico predictions of pathogenicity resulted in a molecular diagnosis in 36 RP patients, comprising 27 recessive, six dominant, and three X-linked cases. Intriguingly, De novo mutations were present in at least three out of 28 isolated cases with causative mutations. This study demonstrates the enormous potential and clinical utility of NGS in molecular diagnosis of genetically heterogeneous diseases such as RP. De novo dominant mutations appear to play a significant role in patients with isolated RP, having major implications for genetic counselling.
Collapse
Affiliation(s)
- Kornelia Neveling
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
72
|
Audo I, Bujakowska KM, Léveillard T, Mohand-Saïd S, Lancelot ME, Germain A, Antonio A, Michiels C, Saraiva JP, Letexier M, Sahel JA, Bhattacharya SS, Zeitz C. Development and application of a next-generation-sequencing (NGS) approach to detect known and novel gene defects underlying retinal diseases. Orphanet J Rare Dis 2012; 7:8. [PMID: 22277662 PMCID: PMC3352121 DOI: 10.1186/1750-1172-7-8] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 01/25/2012] [Indexed: 12/25/2022] Open
Abstract
Background Inherited retinal disorders are clinically and genetically heterogeneous with more than 150 gene defects accounting for the diversity of disease phenotypes. So far, mutation detection was mainly performed by APEX technology and direct Sanger sequencing of known genes. However, these methods are time consuming, expensive and unable to provide a result if the patient carries a new gene mutation. In addition, multiplicity of phenotypes associated with the same gene defect may be overlooked. Methods To overcome these challenges, we designed an exon sequencing array to target 254 known and candidate genes using Agilent capture. Subsequently, 20 DNA samples from 17 different families, including four patients with known mutations were sequenced using Illumina Genome Analyzer IIx next-generation-sequencing (NGS) platform. Different filtering approaches were applied to identify the genetic defect. The most likely disease causing variants were analyzed by Sanger sequencing. Co-segregation and sequencing analysis of control samples validated the pathogenicity of the observed variants. Results The phenotype of the patients included retinitis pigmentosa, congenital stationary night blindness, Best disease, early-onset cone dystrophy and Stargardt disease. In three of four control samples with known genotypes NGS detected the expected mutations. Three known and five novel mutations were identified in NR2E3, PRPF3, EYS, PRPF8, CRB1, TRPM1 and CACNA1F. One of the control samples with a known genotype belongs to a family with two clinical phenotypes (Best and CSNB), where a novel mutation was identified for CSNB. In six families the disease associated mutations were not found, indicating that novel gene defects remain to be identified. Conclusions In summary, this unbiased and time-efficient NGS approach allowed mutation detection in 75% of control cases and in 57% of test cases. Furthermore, it has the possibility of associating known gene defects with novel phenotypes and mode of inheritance.
Collapse
|
73
|
Estrada-Cuzcano A, Neveling K, Kohl S, Banin E, Rotenstreich Y, Sharon D, Falik-Zaccai T, Hipp S, Roepman R, Wissinger B, Letteboer S, Mans D, Blokland E, Kwint M, Gijsen S, van Huet R, Collin R, Scheffer H, Veltman J, Zrenner E, den Hollander A, Klevering B, Cremers F, Cremers FPM. Mutations in C8orf37, encoding a ciliary protein, are associated with autosomal-recessive retinal dystrophies with early macular involvement. Am J Hum Genet 2012; 90:102-9. [PMID: 22177090 DOI: 10.1016/j.ajhg.2011.11.015] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 10/28/2011] [Accepted: 11/18/2011] [Indexed: 01/06/2023] Open
Abstract
Cone-rod dystrophy (CRD) and retinitis pigmentosa (RP) are clinically and genetically overlapping heterogeneous retinal dystrophies. By using homozygosity mapping in an individual with autosomal-recessive (ar) RP from a consanguineous family, we identified three sizeable homozygous regions, together encompassing 46 Mb. Next-generation sequencing of all exons, flanking intron sequences, microRNAs, and other highly conserved genomic elements in these three regions revealed a homozygous nonsense mutation (c.497T>A [p.Leu166(∗)]) in C8orf37, located on chromosome 8q22.1. This mutation was not present in 150 ethnically matched control individuals, single-nucleotide polymorphism databases, or the 1000 Genomes database. Immunohistochemical studies revealed C8orf37 localization at the base of the primary cilium of human retinal pigment epithelium cells and at the base of connecting cilia of mouse photoreceptors. C8orf37 sequence analysis of individuals who had retinal dystrophy and carried conspicuously large homozygous regions encompassing C8orf37 revealed a homozygous splice-site mutation (c.156-2A>G) in two siblings of a consanguineous family and homozygous missense mutations (c.529C>T [p.Arg177Trp]; c.545A>G [p.Gln182Arg]) in siblings of two other consanguineous families. The missense mutations affect highly conserved amino acids, and in silico analyses predicted that both variants are probably pathogenic. Clinical assessment revealed CRD in four individuals and RP with early macular involvement in two individuals. The two CRD siblings with the c.156-2A>G mutation also showed unilateral postaxial polydactyly. These results underline the importance of disrupted ciliary processes in the pathogenesis of retinal dystrophies.
Collapse
|
74
|
Littink KW, den Hollander AI, Cremers FPM, Collin RWJ. The power of homozygosity mapping: discovery of new genetic defects in patients with retinal dystrophy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 723:345-51. [PMID: 22183352 DOI: 10.1007/978-1-4614-0631-0_45] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Karin W Littink
- The Rotterdam Eye Hospital, 70030, 3000 LM, Rotterdam, The Netherlands
| | | | | | | |
Collapse
|
75
|
Hollingsworth TJ, Gross AK. Defective trafficking of rhodopsin and its role in retinal degenerations. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2012; 293:1-44. [PMID: 22251557 DOI: 10.1016/b978-0-12-394304-0.00006-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Retinitis pigmentosa is a retinal degeneration transmitted by varied modes of inheritance and affects approximately 1 in 4000 individuals. The photoreceptors of the outer retina, as well as the retinal pigmented epithelium which supports the outer retina metabolically and structurally, are the retinal regions most affected by the disorder. In several forms of retinitis pigmentosa, the mislocalization of the rod photoreceptor protein rhodopsin is thought to be a contributing factor underlying the pathophysiology seen in patients. The mutations causing this mislocalization often occur in genes coding proteins involved in ciliary formation, vesicular transport, rod outer segment disc formation, and stability, as well as the rhodopsin protein itself. Often, these mutations result in the most early-onset cases of both recessive and dominant retinitis pigmentosa, and the following presents a discussion of the proteins, their degenerative phenotypes, and possible treatments of the disease.
Collapse
Affiliation(s)
- T J Hollingsworth
- Department of Vision Sciences, University of Alabama, Birmingham, Alabama, USA
| | | |
Collapse
|
76
|
Neveling K, den Hollander AI, Cremers FPM, Collin RWJ. Identification and analysis of inherited retinal disease genes. Methods Mol Biol 2012; 935:3-23. [PMID: 23150357 DOI: 10.1007/978-1-62703-080-9_1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Inherited retinal diseases display a very high degree of clinical and genetic heterogeneity, which poses challenges in identifying the underlying defects in known genes and in identifying novel retinal disease genes. Here, we outline the state-of-the-art techniques to find the causative DNA variants, with special attention for next-generation sequencing which can combine molecular diagnostics and retinal disease gene identification.
Collapse
Affiliation(s)
- Kornelia Neveling
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | | | | | | |
Collapse
|
77
|
Siemiatkowska AM, Arimadyo K, Moruz LM, Astuti GD, de Castro-Miro M, Zonneveld MN, Strom TM, de Wijs IJ, Hoefsloot LH, Faradz SM, Cremers FP, den Hollander AI, Collin RW. Molecular genetic analysis of retinitis pigmentosa in Indonesia using genome-wide homozygosity mapping. Mol Vis 2011; 17:3013-24. [PMID: 22128245 PMCID: PMC3224842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 11/14/2011] [Indexed: 11/17/2022] Open
Abstract
PURPOSE Retinitis pigmentosa (RP) is a clinically and genetically heterogeneous retinal disorder. Despite tremendous knowledge about the genes involved in RP, little is known about the genetic causes of RP in Indonesia. Here, we aim to identify the molecular genetic causes underlying RP in a small cohort of Indonesian patients, using genome-wide homozygosity mapping. METHODS DNA samples from affected and healthy individuals from 14 Indonesian families segregating autosomal recessive, X-linked, or isolated RP were collected. Homozygosity mapping was conducted using Illumina 6k or Affymetrix 5.0 single nucleotide polymorphism (SNP) arrays. Known autosomal recessive RP (arRP) genes residing in homozygous regions and X-linked RP genes were sequenced for mutations. RESULTS In ten out of the 14 families, homozygous regions were identified that contained genes known to be involved in the pathogenesis of RP. Sequence analysis of these genes revealed seven novel homozygous mutations in ATP-binding cassette, sub-family A, member 4 (ABCA4), crumbs homolog 1 (CRB1), eyes shut homolog (Drosophila) (EYS), c-mer proto-oncogene tyrosine kinase (MERTK), nuclear receptor subfamily 2, group E, member 3 (NR2E3) and phosphodiesterase 6A, cGMP-specific, rod, alpha (PDE6A), all segregating in the respective families. No mutations were identified in the X-linked genes retinitis pigmentosa GTPase regulator (RPGR) and retinitis pigmentosa 2 (X-linked recessive; RP2). CONCLUSIONS Homozygosity mapping is a powerful tool to identify the genetic defects underlying RP in the Indonesian population. Compared to studies involving patients from other populations, the same genes appear to be implicated in the etiology of recessive RP in Indonesia, although all mutations that were discovered are novel and as such may be unique for this population.
Collapse
Affiliation(s)
- Anna M. Siemiatkowska
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Kentar Arimadyo
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands,Department of Ophthalmology, Diponegoro University, Semarang, Java, Indonesia
| | - Luminita M. Moruz
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Galuh D.N. Astuti
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands,Division of Human Genetics, Center for Biomedical Research, Faculty of Medicine, Diponegoro University, Java, Indonesia
| | - Marta de Castro-Miro
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Marijke N. Zonneveld
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Tim M. Strom
- Institute of Human Genetics, Helmholtz Zentrum Munchen, Neuherberg, Germany
| | - Ilse J. de Wijs
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Lies H. Hoefsloot
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Sultana M.H. Faradz
- Division of Human Genetics, Center for Biomedical Research, Faculty of Medicine, Diponegoro University, Java, Indonesia
| | - Frans P.M. Cremers
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands,Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Anneke I. den Hollander
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands,Department of Ophthalmology, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands,Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Rob W.J. Collin
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands,Department of Ophthalmology, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands,Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, the Netherlands
| |
Collapse
|
78
|
Audo I, Bujakowska K, Mohand-Saïd S, Tronche S, Lancelot ME, Antonio A, Germain A, Lonjou C, Carpentier W, Sahel JA, Bhattacharya S, Zeitz C. A novel DFNB31 mutation associated with Usher type 2 syndrome showing variable degrees of auditory loss in a consanguineous Portuguese family. Mol Vis 2011; 17:1598-606. [PMID: 21738389 PMCID: PMC3123164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 06/10/2011] [Indexed: 11/07/2022] Open
Abstract
PURPOSE To identify the genetic defect of a consanguineous Portuguese family with rod-cone dystrophy and varying degrees of decreased audition. METHODS A detailed ophthalmic and auditory examination was performed on a Portuguese patient with severe autosomal recessive rod-cone dystrophy. Known genetic defects were excluded by performing autosomal recessive retinitis pigmentosa (arRP) genotyping microarray analysis and by Sanger sequencing of the coding exons and flanking intronic regions of eyes shut homolog-drosophila (EYS) and chromosome 2 open reading frame 71 (C2orf71). Subsequently, genome-wide homozygosity mapping was performed in DNA samples from available family members using a 700K single nucleotide polymorphism (SNP) microarray. Candidate genes present in the significantly large homozygous regions were screened for mutations using Sanger sequencing. RESULTS The largest homozygous region (~11 Mb) in the affected family members was mapped to chromosome 9, which harbors deafness, autosomal recessive 31 (DFNB31; a gene previously associated with Usher syndrome). Mutation analysis of DFNB31 in the index patient identified a novel one-base-pair deletion (c.737delC), which is predicted to lead to a truncated protein (p.Pro246HisfsX13) and co-segregated with the disease in the family. Ophthalmic examination of the index patient and the affected siblings showed severe rod-cone dystrophy. Pure tone audiometry revealed a moderate hearing loss in the index patient, whereas the affected siblings were reported with more profound and early onset hearing impairment. CONCLUSIONS We report a novel truncating mutation in DFNB31 associated with severe rod-cone dystrophy and varying degrees of hearing impairment in a consanguineous family of Portuguese origin. This is the second report of DFNB31 implication in Usher type 2.
Collapse
Affiliation(s)
- Isabelle Audo
- INSERM, U968, Paris, France,CNRS, UMR_7210, Paris, France,UPMC Univ Paris 06, UMR_S 968, Department of Genetics, Institut de la Vision, Paris, France,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM-DHOS CIC 503,Paris, France,Department of Molecular Genetics, Institute of Ophthalmology, London, UK
| | - Kinga Bujakowska
- INSERM, U968, Paris, France,CNRS, UMR_7210, Paris, France,UPMC Univ Paris 06, UMR_S 968, Department of Genetics, Institut de la Vision, Paris, France
| | - Saddek Mohand-Saïd
- INSERM, U968, Paris, France,CNRS, UMR_7210, Paris, France,UPMC Univ Paris 06, UMR_S 968, Department of Genetics, Institut de la Vision, Paris, France,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM-DHOS CIC 503,Paris, France
| | - Sophie Tronche
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM-DHOS CIC 503,Paris, France,Commission Expertise et Evaluation de la SFORL, Paris, France
| | - Marie-Elise Lancelot
- INSERM, U968, Paris, France,CNRS, UMR_7210, Paris, France,UPMC Univ Paris 06, UMR_S 968, Department of Genetics, Institut de la Vision, Paris, France
| | - Aline Antonio
- INSERM, U968, Paris, France,CNRS, UMR_7210, Paris, France,UPMC Univ Paris 06, UMR_S 968, Department of Genetics, Institut de la Vision, Paris, France,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM-DHOS CIC 503,Paris, France
| | - Aurore Germain
- INSERM, U968, Paris, France,CNRS, UMR_7210, Paris, France,UPMC Univ Paris 06, UMR_S 968, Department of Genetics, Institut de la Vision, Paris, France
| | - Christine Lonjou
- Plate-forme Post-Génomique P3S, Hôpital Pitié Salpêtrière UPMC, Faculté de Médecine, Paris, France
| | - Wassila Carpentier
- Plate-forme Post-Génomique P3S, Hôpital Pitié Salpêtrière UPMC, Faculté de Médecine, Paris, France
| | - José-Alain Sahel
- INSERM, U968, Paris, France,CNRS, UMR_7210, Paris, France,UPMC Univ Paris 06, UMR_S 968, Department of Genetics, Institut de la Vision, Paris, France,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM-DHOS CIC 503,Paris, France,Department of Molecular Genetics, Institute of Ophthalmology, London, UK,Fondation Ophtalmologique Adolphe de Rothschild, Paris, France
| | - Shomi Bhattacharya
- INSERM, U968, Paris, France,CNRS, UMR_7210, Paris, France,UPMC Univ Paris 06, UMR_S 968, Department of Genetics, Institut de la Vision, Paris, France,Department of Molecular Genetics, Institute of Ophthalmology, London, UK,Department of Cellular Therapy and Regenerative Medicine, Andalusian Molecular Biology and Regenerative Medicine Centre (CABIMER), Seville, Spain
| | - Christina Zeitz
- INSERM, U968, Paris, France,CNRS, UMR_7210, Paris, France,UPMC Univ Paris 06, UMR_S 968, Department of Genetics, Institut de la Vision, Paris, France
| |
Collapse
|