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Lisbjerg K, Bertelsen M, Grønskov K, Kessel L. Clinical characterization of patients with PRPF31-related retinitis pigmentosa and asymptomatic carriers: a cross-sectional study. Ophthalmic Genet 2023; 44:456-464. [PMID: 37293790 DOI: 10.1080/13816810.2023.2219732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/27/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023]
Abstract
BACKGROUND/AIM To describe the clinical phenotype of retinitis pigmentosa (RP) caused by PRPF31-variants and clinical characterization of asymptomatic PRPF31 carriers. MATERIALS AND METHODS We conducted a descriptive cross-sectional deep phenotyping study. We included subjects with PRPF31 variants predicted to be disease-causing, both individuals with RP and asymptomatic carriers. Participants underwent a comprehensive clinical examination of standard visual function parameters (visual acuity, contrast sensitivity, Goldmann visual field), full-field stimulus threshold (FST), full-field electroretinogram (ff-ERG), and a structural investigation with slit lamp and multimodal imaging. We used Spearman correlation analyses to evaluate associations between quantitative outcomes. RESULTS We included 21 individuals with disease-causing PRPF31-variants: 16 symptomatic and 5 asymptomatic subjects. The symptomatic subjects demonstrated a typical RP phenotype with constricted visual fields, extinguished ff-ERG, and disrupted outer retinal anatomy. FST was impaired and correlated significantly with other outcome measures in RP subjects. Structure-function correlations with Spearman correlation analysis showed moderate correlation coefficients due to a few outliers in each analysis. The asymptomatic individuals had normal best-corrected visual acuity and visual fields, but showed reduced ff-ERG amplitudes, borderline FST sensitivity, and structural abnormalities on OCT and fundoscopy. CONCLUSIONS RP11 has a typical RP phenotype but varies in terms of severity. FST measurements correlated well with other functional and structural metrics and may be a reliable outcome measure in future trials as it is sensitive to a broad range of disease severities. Asymptomatic carriers showed sub-clinical disease manifestations, and our findings underline that reported non-penetrance in PRPF31-related RP is not an all-or-none phenomenon.
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Affiliation(s)
- Kristian Lisbjerg
- Department of Ophthalmology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Mette Bertelsen
- Department of Clinical Genetics, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Karen Grønskov
- Department of Clinical Genetics, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Line Kessel
- Department of Ophthalmology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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2
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Wen S, Wang M, Qian X, Li Y, Wang K, Choi J, Pennesi ME, Yang P, Marra M, Koenekoop RK, Lopez I, Matynia A, Gorin M, Sui R, Yao F, Goetz K, Porto FBO, Chen R. Systematic assessment of the contribution of structural variants to inherited retinal diseases. Hum Mol Genet 2023; 32:2005-2015. [PMID: 36811936 PMCID: PMC10244226 DOI: 10.1093/hmg/ddad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/03/2023] [Accepted: 02/11/2023] [Indexed: 02/24/2023] Open
Abstract
Despite increasing success in determining genetic diagnosis for patients with inherited retinal diseases (IRDs), mutations in about 30% of the IRD cases remain unclear or unsettled after targeted gene panel or whole exome sequencing. In this study, we aimed to investigate the contributions of structural variants (SVs) to settling the molecular diagnosis of IRD with whole-genome sequencing (WGS). A cohort of 755 IRD patients whose pathogenic mutations remain undefined were subjected to WGS. Four SV calling algorithms including include MANTA, DELLY, LUMPY and CNVnator were used to detect SVs throughout the genome. All SVs identified by any one of these four algorithms were included for further analysis. AnnotSV was used to annotate these SVs. SVs that overlap with known IRD-associated genes were examined with sequencing coverage, junction reads and discordant read pairs. Polymerase Chain Reaction (PCR) followed by Sanger sequencing was used to further confirm the SVs and identify the breakpoints. Segregation of the candidate pathogenic alleles with the disease was performed when possible. A total of 16 candidate pathogenic SVs were identified in 16 families, including deletions and inversions, representing 2.1% of patients with previously unsolved IRDs. Autosomal dominant, autosomal recessive and X-linked inheritance of disease-causing SVs were observed in 12 different genes. Among these, SVs in CLN3, EYS and PRPF31 were found in multiple families. Our study suggests that the contribution of SVs detected by short-read WGS is about 0.25% of our IRD patient cohort and is significantly lower than that of single nucleotide changes and small insertions and deletions.
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Affiliation(s)
- Shu Wen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Meng Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xinye Qian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Keqing Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jongsu Choi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mark E Pennesi
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Paul Yang
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Molly Marra
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Robert K Koenekoop
- McGill Ocular Genetics Laboratory and Centre, Department of Paediatric Surgery, Human Genetics, and Ophthalmology, McGill University Health Centre, Montreal, Quebec, H4A 3S5, Canada
| | - Irma Lopez
- McGill Ocular Genetics Laboratory and Centre, Department of Paediatric Surgery, Human Genetics, and Ophthalmology, McGill University Health Centre, Montreal, Quebec, H4A 3S5, Canada
| | - Anna Matynia
- Jules Stein Eye Institute, Los Angeles, CA 90095, USA
- Ophthalmology, University of California Los Angeles David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Michael Gorin
- Jules Stein Eye Institute, Los Angeles, CA 90095, USA
- Ophthalmology, University of California Los Angeles David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Ruifang Sui
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Fengxia Yao
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Kerry Goetz
- Office of the Director, National Eye Institute/National Institutes of Health, Bethesda, MD 20892, USA
| | - Fernanda Belga Ottoni Porto
- INRET Clínica e Centro de Pesquisa, Belo Horizonte, Minas Gerais, 30150270, Brazil
- Department of Ophthalmology, Santa Casa de Misericórdia de Belo Horizonte, Belo Horizonte, Minas Gerais, 30150221, Brazil
- Centro Oftalmológico de Minas Gerais, Belo Horizonte, Minas Gerais, 30180070, Brazil
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
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3
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Lisbjerg K, Grønskov K, Bertelsen M, Møller LB, Kessel L. Genetic Modifiers of Non-Penetrance and RNA Expression Levels in PRPF31-Associated Retinitis Pigmentosa in a Danish Cohort. Genes (Basel) 2023; 14:435. [PMID: 36833363 PMCID: PMC9956082 DOI: 10.3390/genes14020435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
(1) Background/aims: To examine potential genetic modifiers of disease penetrance in PRPF31-associated retinitis pigmentosa 11 (RP11). (2) Methods: Blood samples from individuals (n = 37) with PRPF31 variants believed to be disease-causing were used for molecular genetic testing and, in some cases (n = 23), also for mRNA expression analyses. Medical charts were used to establish if individuals were symptomatic (RP) or asymptomatic non-penetrant carriers (NPC). RNA expression levels of PRPF31 and CNOT3 were measured on peripheral whole blood using quantitative real-time PCR normalized to GAPDH. Copy number variation of minisatellite repeat element 1 (MSR1) was performed with DNA fragment analysis. (3) Results: mRNA expression analyses on 22 individuals (17 with RP and 5 non-penetrant carriers) revealed no statistically significant differences in PRPF31 or CNOT3 mRNA expression levels between individuals with RP and non-penetrant carriers. Among 37 individuals, we found that all three carriers of a 4-copy MSR1 sequence on their wild-type (WT) allele were non-penetrant carriers. However, copy number variation of MSR1 is not the sole determinant factor of non-penetrance, as not all non-penetrant carriers carried a 4-copy WT allele. A 4-copy MSR1 mutant allele was not associated with non-penetrance. (4) Conclusions: In this Danish cohort, a 4-copy MSR1 WT allele was associated with non-penetrance of retinitis pigmentosa caused by PRPF31 variants. The level of PRPF31 mRNA expression in peripheral whole blood was not a useful indicator of disease status.
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Affiliation(s)
- Kristian Lisbjerg
- Department of Ophthalmology, Copenhagen University Hospital-Rigshospitalet, 2600 Glostrup, Denmark
| | - Karen Grønskov
- Department of Clinical Genetics, Copenhagen University Hospital-Rigshospitalet, 2100 Copenhagen, Denmark
| | - Mette Bertelsen
- Department of Clinical Genetics, Copenhagen University Hospital-Rigshospitalet, 2100 Copenhagen, Denmark
| | - Lisbeth Birk Møller
- Department of Clinical Genetics, Copenhagen University Hospital-Rigshospitalet, 2100 Copenhagen, Denmark
| | - Line Kessel
- Department of Ophthalmology, Copenhagen University Hospital-Rigshospitalet, 2600 Glostrup, Denmark
- Department of Clinical Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
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4
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Wen S, Wang M, Qian X, Li Y, Wang K, Choi J, Pennesi ME, Yang P, Marra M, Koenekoop RK, Lopez I, Matynia A, Gorin M, Sui R, Yao F, Goetz K, Porto FBO, Chen R. Systematic assessment of the contribution of structural variants to inherited retinal diseases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.02.522522. [PMID: 36789417 PMCID: PMC9928032 DOI: 10.1101/2023.01.02.522522] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Despite increasing success in determining genetic diagnosis for patients with inherited retinal diseases (IRDs), mutations in about 30% of the IRD cases remain unclear or unsettled after targeted gene panel or whole exome sequencing. In this study, we aimed to investigate the contributions of structural variants (SVs) to settling the molecular diagnosis of IRD with whole-genome sequencing (WGS). A cohort of 755 IRD patients whose pathogenic mutations remain undefined was subjected to WGS. Four SV calling algorithms including include MANTA, DELLY, LUMPY, and CNVnator were used to detect SVs throughout the genome. All SVs identified by any one of these four algorithms were included for further analysis. AnnotSV was used to annotate these SVs. SVs that overlap with known IRD-associated genes were examined with sequencing coverage, junction reads, and discordant read pairs. PCR followed by Sanger sequencing was used to further confirm the SVs and identify the breakpoints. Segregation of the candidate pathogenic alleles with the disease was performed when possible. In total, sixteen candidate pathogenic SVs were identified in sixteen families, including deletions and inversions, representing 2.1% of patients with previously unsolved IRDs. Autosomal dominant, autosomal recessive, and X-linked inheritance of disease-causing SVs were observed in 12 different genes. Among these, SVs in CLN3, EYS, PRPF31 were found in multiple families. Our study suggests that the contribution of SVs detected by short-read WGS is about 0.25% of our IRD patient cohort and is significantly lower than that of single nucleotide changes and small insertions and deletions.
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5
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Roshandel D, Thompson JA, Heath Jeffery RC, Zhang D, Lamey TM, McLaren TL, De Roach JN, McLenachan S, Mackey DA, Chen FK. Clinical Evidence for the Importance of the Wild-Type PRPF31 Allele in the Phenotypic Expression of RP11. Genes (Basel) 2021; 12:genes12060915. [PMID: 34198599 PMCID: PMC8232116 DOI: 10.3390/genes12060915] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/09/2021] [Accepted: 06/12/2021] [Indexed: 11/16/2022] Open
Abstract
PRPF31-associated retinopathy (RP11) is a common form of autosomal dominant retinitis pigmentosa (adRP) that exhibits wide variation in phenotype ranging from non-penetrance to early-onset RP. Herein, we report inter-familial and intra-familial variation in the natural history of RP11 using multimodal imaging and microperimetry. Patients were recruited prospectively. The age of symptom onset, best-corrected visual acuity, microperimetry mean sensitivity (MS), residual ellipsoid zone span and hyperautofluorescent ring area were recorded. Genotyping was performed using targeted next-generation and Sanger sequencing and copy number variant analysis. PRPF31 mutations were found in 14 individuals from seven unrelated families. Four disease patterns were observed: (A) childhood onset with rapid progression (N = 4), (B) adult-onset with rapid progression (N = 4), (C) adult-onset with slow progression (N = 4) and (D) non-penetrance (N = 2). Four different patterns were observed in a family harbouring c.267del; patterns B, C and D were observed in a family with c.772_773delins16 and patterns A, B and C were observed in 3 unrelated individuals with large deletions. Our findings suggest that the RP11 phenotype may be related to the wild-type PRPF31 allele rather than the type of mutation. Further studies that correlate in vitro wild-type PRPF31 allele expression level with the disease patterns are required to investigate this association.
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Affiliation(s)
- Danial Roshandel
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, WA 6009, Australia;
| | - Jennifer A. Thompson
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia;
| | - Rachael C. Heath Jeffery
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, WA 6009, Australia;
- Department of Ophthalmology, Royal Perth Hospital, Perth, WA 6000, Australia
| | - Dan Zhang
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, WA 6009, Australia;
| | - Tina M. Lamey
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia;
| | - Terri L. McLaren
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia;
| | - John N. De Roach
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia;
| | - Samuel McLenachan
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, WA 6009, Australia;
| | - David A. Mackey
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, WA 6009, Australia;
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia;
| | - Fred K. Chen
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, WA 6009, Australia;
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia;
- Department of Ophthalmology, Royal Perth Hospital, Perth, WA 6000, Australia
- Department of Ophthalmology, Perth Children’s Hospital, Nedlands, WA 6009, Australia
- Correspondence: ; Tel.: +61-08-9381-0777
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6
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Roshandel D, Thompson JA, Charng J, Zhang D, Chelva E, Arunachalam S, Attia MS, Lamey TM, McLaren TL, De Roach JN, Mackey DA, Wilton SD, Fletcher S, McLenachan S, Chen FK. Exploring microperimetry and autofluorescence endpoints for monitoring disease progression in PRPF31-associated retinopathy. Ophthalmic Genet 2020; 42:1-14. [PMID: 32985313 DOI: 10.1080/13816810.2020.1827442] [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] [Indexed: 01/24/2023]
Abstract
BACKGROUND Mutations in the splicing factor pre-messenger RNA processing factor 31 (PRPF31) gene cause autosomal dominant retinitis pigmentosa 11 (RP11) through a haplo-insufficiency mechanism. We describe the phenotype and progression of microperimetry and autofluorescence endpoints in an Indigenous Australian RP11 family. PATIENTS AND METHODS Ophthalmic examination, optical coherence tomography, fundus autofluorescence and microperimetry were performed at baseline and every 6-12 months. Baseline and annual change in best-corrected visual acuity (BCVA), microperimetry mean sensitivity (MS) and number of scotoma loci, residual ellipsoid zone (EZ) span and hyperautofluorescent ring (HAR) area were reported. Next-generation and Sanger sequencing were performed in available members. RESULTS 12 affected members from three generations were examined. Mean (SD, range) age at onset of symptoms was 11 (4.5, 4-19) years. MS declined steadily from the third decade and EZ span and HAR area declined rapidly during the second decade. Serial microperimetry showed negligible change in MS over 2-3 years. However, mean EZ span, near-infrared and short-wavelength HAR area reduction was 203 (6.4%) µm/year, 1.8 (8.7%) mm2/year and 1.1 (8.6%) mm2/year, respectively. Genetic testing was performed on 11 affected and 10 asymptomatic members and PRPF31 c.1205 C > A (p.Ser402Ter) mutation was detected in all affected and two asymptomatic members (non-penetrant carriers). CONCLUSIONS Our findings suggest that in the studied cohort, the optimal window for therapeutic intervention is the second decade of life and residual EZ span and HAR area can be considered as efficacy outcome measures. Further studies on larger samples with different PRPF31 mutations and longer follow-up duration are recommended.
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Affiliation(s)
- Danial Roshandel
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Jennifer A Thompson
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - Jason Charng
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Dan Zhang
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Enid Chelva
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - Sukanya Arunachalam
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Mary S Attia
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Tina M Lamey
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - Terri L McLaren
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - John N De Roach
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - David A Mackey
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - Steve D Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University , Murdoch, Australia.,The Perron Institute, The University of Western Australia , Nedlands, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University , Murdoch, Australia.,The Perron Institute, The University of Western Australia , Nedlands, Australia
| | - Samuel McLenachan
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Fred K Chen
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia.,Department of Ophthalmology, Royal Perth Hospital , Perth, Australia.,Department of Ophthalmology, Perth Children's Hospital , Nedlands, Australia
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Yang D, Yao Q, Li Y, Xu Y, Wang J, Zhao H, Liu F, Zhang Z, Liu Y, Bie X, Wang Y, Xu L, Luan Y, Yang S, Yang G, He Y. A c.544_618del75bp mutation in the splicing factor gene PRPF31 is involved in non-syndromic retinitis pigmentosa by reducing the level of mRNA expression. Ophthalmic Physiol Opt 2020; 40:289-299. [PMID: 32031697 DOI: 10.1111/opo.12672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 01/02/2020] [Indexed: 01/08/2023]
Abstract
PURPOSE A previous study reported a novel c.544_618del75bp mutation in exon 7 of the PRPF31 gene in a Chinese family with autosomal dominant retinal pigmentosa (ADRP). However, the selected pedigree was a small part of the whole family and the function of the c.544_618del75bp mutation was not explored deeply. The aim of the present study was to validate the previous results and explore the functional significance of the c.544_618del75bp mutation. METHODS We extended the size of the ADRP pedigree and sequenced DNA and cDNA of the PRPF31 gene for all members of the family and 100 healthy controls. Real-time quantitative polymerase chain reaction (PCR) analysis was performed on the cDNA of patients in the family and cell culture, plasmids transfection and western blot analysis were done to evaluate the functional effect of the mutation in vitro. RESULTS Sanger sequencing showed that the mutation was present in all patients and absent in all normal individuals, except for participant III-9. Bioinformatics analysis revealed that the c.544_618del75bp mutation caused a 25 amino acid deletion in the PRPF31 protein. In addition, the mRNA expression assay revealed that the mRNA expression level of the PRPF31 and RP9 genes were significantly lower in RP patients than controls (p < 0.05). Finally, the in vitro transfection assay demonstrated that the mRNA expression level of the mutant transfection group was significantly lower than the wild-type transfection group (p < 0.05). CONCLUSIONS Our study suggested that the c.544_618del75bp mutation in the PRPF31 gene was a causative mutation in this ADRP family and affected the expression of RP9 gene by influencing the formation of U4/U6-U5 tri-snRNP, eventually leading to the occurrence of RP.
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Affiliation(s)
- Dongzhi Yang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Qihui Yao
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Ya Li
- Henan Eye Institute, Henan Provincial People's Hospital, Zhengzhou, China
| | - Yan Xu
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jun Wang
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Huiling Zhao
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Fuyong Liu
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhaojing Zhang
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yang Liu
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Xiaoshuai Bie
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yuanli Wang
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Liyan Xu
- Henan Eye Institute, Henan Provincial People's Hospital, Zhengzhou, China
| | - Yingying Luan
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Shangdong Yang
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Ge Yang
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying He
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
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8
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Mutation spectrum of PRPF31, genotype-phenotype correlation in retinitis pigmentosa, and opportunities for therapy. Exp Eye Res 2020; 192:107950. [PMID: 32014492 PMCID: PMC7065041 DOI: 10.1016/j.exer.2020.107950] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/13/2020] [Accepted: 01/27/2020] [Indexed: 12/11/2022]
Abstract
Pathogenic variants in pre-messenger RNA (pre-mRNA) splicing factor 31, PRPF31, are the second most common genetic cause of autosomal dominant retinitis pigmentosa (adRP) in most populations. This remains a completely untreatable and incurable form of blindness, and it can be difficult to predict the clinical course of disease. In order to design appropriate targeted therapies, a thorough understanding of the genetics and molecular mechanism of this disease is required. Here, we present the structure of the PRPF31 gene and PRPF31 protein, current understanding of PRPF31 protein function and the full spectrum of all reported clinically relevant variants in PRPF31. We delineate the correlation between specific PRPF31 genotype and RP phenotype, suggesting that, except in cases of complete gene deletion or large-scale deletions, dominant negative effects contribute to phenotype as well as haploinsufficiency. This has important impacts on design of targeted therapies, particularly the feasibility of gene augmentation as a broad approach for treatment of PRPF31-associated RP. We discuss other opportunities for therapy, including antisense oligonucleotide therapy and gene-independent approaches and offer future perspectives on treatment of this form of RP. PRPF31 is the second most common cause of autosomal dominant retinitis pigmentosa and a potential target for gene therapy. We present all reported pathogenic variants in PRPF31 as a resource for clinicians, diagnostic genetics labs, and researchers. Genotype-phenotype correlations suggest that, dominant negative effects contribute to disease in addition to haploinsufficiency. This finding has important impacts on the suitability of gene augmentation approaches across all mutation types. This finding may aid prognosis of disease in PRPF31-associated RP patients.
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9
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Zenteno JC, García-Montaño LA, Cruz-Aguilar M, Ronquillo J, Rodas-Serrano A, Aguilar-Castul L, Matsui R, Vencedor-Meraz CI, Arce-González R, Graue-Wiechers F, Gutiérrez-Paz M, Urrea-Victoria T, de Dios Cuadras U, Chacón-Camacho OF. Extensive genic and allelic heterogeneity underlying inherited retinal dystrophies in Mexican patients molecularly analyzed by next-generation sequencing. Mol Genet Genomic Med 2019; 8. [PMID: 31736247 PMCID: PMC6978239 DOI: 10.1002/mgg3.1044] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 10/23/2019] [Indexed: 12/27/2022] Open
Abstract
Background Retinal dystrophies (RDs) are one of the most genetically heterogeneous monogenic disorders with ~270 associated loci identified by early 2019. The recent application of next‐generation sequencing (NGS) has greatly improved the molecular diagnosis of RD patients. Genetic characterization of RD cohorts from different ethnic groups is justified, as it would improve the knowledge of molecular basis of the disease. Here, we present the results of genetic analysis in a large cohort of 143 unrelated Mexican subjects with a variety of RDs. Methods A targeted NGS approach covering 199 RD genes was employed for molecular screening of 143 unrelated patients. In addition to probands, 258 relatives were genotyped by Sanger sequencing for familial segregation of pathogenic variants. Results A solving rate of 66% (95/143) was achieved, with evidence of extensive loci (44 genes) and allelic (110 pathogenic variants) heterogeneity. Forty‐eight percent of the identified pathogenic variants were novel while ABCA4, CRB1, USH2A, and RPE65 carried the greatest number of alterations. Novel deleterious variants in IDH3B and ARL6 were identified, supporting their involvement in RD. Familial segregation of causal variants allowed the recognition of 124 autosomal or X‐linked carriers. Conclusion Our results illustrate the utility of NGS for genetic diagnosis of RDs of different populations for a better knowledge of the mutational landscape associated with the disease.
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Affiliation(s)
- Juan C Zenteno
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico.,Department of Biochemistry, Faculty of Medicine, UNAM, Mexico City, Mexico
| | | | - Marisa Cruz-Aguilar
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | - Josué Ronquillo
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | - Agustín Rodas-Serrano
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | | | - Rodrigo Matsui
- Department of Retina, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | | | - Rocío Arce-González
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | | | - Mario Gutiérrez-Paz
- Department of Retina, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | - Tatiana Urrea-Victoria
- Department of Retina, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | - Ulises de Dios Cuadras
- Department of Retina, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | - Oscar F Chacón-Camacho
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
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10
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Identification of CRB1 mutations in two Chinese consanguineous families exhibiting autosomal recessive retinitis pigmentosa. Mol Med Rep 2019; 20:2922-2928. [PMID: 31322236 DOI: 10.3892/mmr.2019.10495] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/12/2019] [Indexed: 11/05/2022] Open
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11
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Chapman NH, Bernier RA, Webb SJ, Munson J, Blue EM, Chen DH, Heigham E, Raskind WH, Wijsman EM. Replication of a rare risk haplotype on 1p36.33 for autism spectrum disorder. Hum Genet 2018; 137:807-815. [PMID: 30276537 PMCID: PMC6309233 DOI: 10.1007/s00439-018-1939-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/22/2018] [Indexed: 01/15/2023]
Abstract
Hundreds of genes have been implicated in autism spectrum disorders (ASDs). In genetically heterogeneous conditions, large families with multiple affected individuals provide strong evidence implicating a rare variant, and replication of the same variant in multiple families is unusual. We previously published linkage analyses and follow-up exome sequencing in seven large families with ASDs, implicating 14 rare exome variants. These included rs200195897, which was transmitted to four affected individuals in one family. We attempted replication of those variants in the MSSNG database. MSSNG is a unique resource for replication of ASD risk loci, containing whole genome sequence (WGS) on thousands of individuals diagnosed with ASDs and family members. For each exome variant, we obtained all carriers and their relatives in MSSNG, using a TDT test to quantify evidence for transmission and association. We replicated the transmission of rs200195897 to four affected individuals in three additional families. rs200195897 was also present in three singleton affected individuals, and no unaffected individuals other than transmitting parents. We identified two additional rare variants (rs566472488 and rs185038034) transmitted with rs200195897 on 1p36.33. Sanger sequencing confirmed the presence of these variants in the original family segregating rs200195897. To our knowledge, this is the first example of a rare haplotype being transmitted with ASD in multiple families. The candidate risk variants include a missense mutation in SAMD11, an intronic variant in NOC2L, and a regulatory region variant close to both genes. NOC2L is a transcription repressor, and several genes involved in transcription regulation have been previously associated with ASDs.
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Affiliation(s)
- N H Chapman
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 359460, Seattle, WA, 98195, USA
| | - R A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA
- Center on Human Development and Disability, University of Washington, Seattle, WA, 98195, USA
| | - S J Webb
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA
- Center on Human Development and Disability, University of Washington, Seattle, WA, 98195, USA
| | - J Munson
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA
- Center on Human Development and Disability, University of Washington, Seattle, WA, 98195, USA
| | - E M Blue
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 359460, Seattle, WA, 98195, USA
| | - D-H Chen
- Department of Neurology, University of Washington, Seattle, WA, 98195, USA
| | - E Heigham
- Department of Neurology, University of Washington, Seattle, WA, 98195, USA
| | - W H Raskind
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 359460, Seattle, WA, 98195, USA
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Ellen M Wijsman
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 359460, Seattle, WA, 98195, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA.
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12
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A novel mutation in the PRPF31 in a North Indian adRP family with incomplete penetrance. Doc Ophthalmol 2018; 137:103-119. [PMID: 30099644 DOI: 10.1007/s10633-018-9654-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 08/03/2018] [Indexed: 12/27/2022]
Abstract
PURPOSE To identify the underlying genetic defect for non-syndromic autosomal dominant retinitis pigmentosa (adRP) with incomplete penetrance in a North Indian family. METHODS Family history and clinical data were collected. Linkage analysis using 72 fluorescently labeled microsatellite markers flanking all the 26 candidate genes known for adRP was performed. Mutation screening in candidate gene at the mapped region was performed by bi-directional DNA sequencing. RESULTS Positive two-point lod scores > 1.0 (θ = 0.000) suggestive of linkage were obtained with markers D19S572, D19S927 and D19S926 at 19q13.42, in the vicinity of PRPF31 gene. Mutation screening in all the 14 exonic regions and intron-exon boundaries of PRPF31 revealed a novel change, i.e. c.896G>A (p.Cys299Tyr) in exon eight. The observed change segregated in heterozygous form in all the six affected members and in three carriers, consistent with incomplete penetrance. This substitution was not observed in tested 15 unaffected members and in 200 ethnically matched controls. CONCLUSION Present study describes mapping of a locus for non-syndromic adRP with incomplete penetrance at 19q13.42 in a North Indian family and identifies a novel missense mutation (p.Cys299Tyr) in PRPF31 localized at the mapped interval. The observed substitution lies in the NOP domain of PRPF31 that exhibit RNA and protein binding surfaces and thus may interfere in the formation of spliceosome complex. Due to p.Cys299Tyr substitution hydrogen bonds are generated, which may result in conformational changes and PRPF31 protein deformity. Present findings further substantiate the role of PRPF31 in adRP with incomplete penetrance and expand the mutation spectrum of PRPF31.
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13
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Zhang S, Li J, Li S, Yang Y, Yang M, Yang Z, Zhu X, Zhang L. Targeted next-generation sequencing reveals that a compound heterozygous mutation in phosphodiesterase 6a gene leads to retinitis pigmentosa in a Chinese family. Ophthalmic Genet 2018; 39:487-491. [PMID: 29693493 DOI: 10.1080/13816810.2018.1461912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Shanshan Zhang
- Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Jie Li
- Department of Ophthalmology, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Shujin Li
- Institute of Chengdu Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yeming Yang
- Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Mu Yang
- Institute of Chengdu Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zhenglin Yang
- Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Department of Ophthalmology, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Institute of Chengdu Biology, Chinese Academy of Sciences, Chengdu, China
- Center of Information in Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Xianjun Zhu
- Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Department of Ophthalmology, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Institute of Chengdu Biology, Chinese Academy of Sciences, Chengdu, China
- Center of Information in Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Lin Zhang
- Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Department of Ophthalmology, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Center of Information in Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
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14
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Meyer KJ, Anderson MG. Genetic modifiers as relevant biological variables of eye disorders. Hum Mol Genet 2017; 26:R58-R67. [PMID: 28482014 DOI: 10.1093/hmg/ddx180] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 05/05/2017] [Indexed: 12/19/2022] Open
Abstract
From early in the study of mammalian genetics, it was clear that modifiers can have a striking influence on phenotypes. Today, several modifiers have now been studied in enough detail to allow a glimpse of how they function and influence our perspective of disease. With respect to diseases of the eye, some modifiers are an important source of phenotypic variation that can elucidate how genes function in networks to collectively shape ocular anatomy and physiology, thus influencing our understanding of basic biology. Other modifiers represent an opportunity for new therapeutic targets, whose manipulation could be used to mitigate ophthalmic disease. Here, we review progress in the study of genetic modifiers of eye disorders, with examples from mice and humans that together illustrate the ubiquitous nature of genetic modifiers and why they are relevant biological variables in experimental design. Special emphasis is given to ophthalmic modifiers in mice, especially those relevant to selection of genetic background and those that might inadvertently be a source of experimental variability. These modifiers are capable of influencing interpretations of many experiments using targeted genome manipulations such as knockouts or transgenics. Whereas there are fewer examples of modifiers of eye disorders in humans with a molecular identification, there is ample evidence that they exist and should be considered as a relevant biological variable in human genetic studies as well.
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Affiliation(s)
- Kacie J Meyer
- Department of Molecular Physiology and Biophysics.,Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA
| | - Michael G Anderson
- Department of Molecular Physiology and Biophysics.,Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.,Stephen A. Wynn Institute for Vision Research, University of Iowa, Iowa City, IA 52242, USA.,Center for Prevention and Treatment of Visual Loss, Iowa City Veterans Administration Medical Center, Iowa City, IA 52242, USA
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15
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Villanueva A, Biswas P, Kishaba K, Suk J, Tadimeti K, Raghavendra PB, Nadeau K, Lamontagne B, Busque L, Geoffroy S, Mongrain I, Asselin G, Provost S, Dubé MP, Nudleman E, Ayyagari R. Identification of the genetic determinants responsible for retinal degeneration in families of Mexican descent. Ophthalmic Genet 2017; 39:73-79. [PMID: 28945494 DOI: 10.1080/13816810.2017.1373830] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
PURPOSE To investigate the clinical characteristics and genetic basis of inherited retinal degeneration (IRD) in six unrelated pedigrees from Mexico. METHODS A complete ophthalmic evaluation including measurement of visual acuities, Goldman kinetic or Humphrey dynamic perimetry, Amsler test, fundus photography, and color vision testing was performed. Family history and blood samples were collected from available family members. DNA from members of two pedigrees was examined for known mutations using the APEX ARRP genotyping microarray and one pedigree using the APEX LCA genotyping microarray. The remaining three pedigrees were analyzed using a custom-designed targeted capture array covering the exons of 233 known retinal degeneration genes. Sequencing was performed on Illumina HiSeq. Reads were mapped against hg19, and variants were annotated using GATK and filtered by exomeSuite. Segregation and ethnicity-matched control sample analyses were performed by dideoxy sequencing. RESULTS Six pedigrees with IRD were analyzed. Nine rare or novel, potentially pathogenic variants segregating with the phenotype were detected in IMPDH1, USH2A, RPE65, ABCA4, and FAM161A genes. Among these, six were known mutations while the remaining three changes in USH2A, RPE65, and FAM161A genes have not been previously reported to be associated with IRD. Analysis of 100 ethnicity-matched controls did not detect the presence of these three novel variants indicating, these are rare variants in the Mexican population. CONCLUSIONS Screening patients diagnosed with IRD from Mexico identified six known mutations and three rare or novel potentially damaging variants in IMPDH1, USH2A, RPE65, ABCA4, and FAM161A genes that segregated with disease.
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Affiliation(s)
- Adda Villanueva
- a Retina Department Genomics Institute, Mejora Vision MD/Virtual Eye Care MD , Mérida , Yucatán , México.,b Laboratoire de Diagnostic Moleculaire , Hôpital Maisonneuve Rosemont , Montreal , Quebec , Canada
| | - Pooja Biswas
- c School of Biotechnology , REVA University , Bengaluru , India.,d Shiley Eye Institute, University of California San Diego , La Jolla , CA , USA
| | - Kameron Kishaba
- d Shiley Eye Institute, University of California San Diego , La Jolla , CA , USA
| | - John Suk
- d Shiley Eye Institute, University of California San Diego , La Jolla , CA , USA
| | - Keerti Tadimeti
- d Shiley Eye Institute, University of California San Diego , La Jolla , CA , USA
| | | | - Karine Nadeau
- a Retina Department Genomics Institute, Mejora Vision MD/Virtual Eye Care MD , Mérida , Yucatán , México.,b Laboratoire de Diagnostic Moleculaire , Hôpital Maisonneuve Rosemont , Montreal , Quebec , Canada
| | - Bruno Lamontagne
- a Retina Department Genomics Institute, Mejora Vision MD/Virtual Eye Care MD , Mérida , Yucatán , México.,b Laboratoire de Diagnostic Moleculaire , Hôpital Maisonneuve Rosemont , Montreal , Quebec , Canada
| | - Lambert Busque
- a Retina Department Genomics Institute, Mejora Vision MD/Virtual Eye Care MD , Mérida , Yucatán , México.,b Laboratoire de Diagnostic Moleculaire , Hôpital Maisonneuve Rosemont , Montreal , Quebec , Canada
| | - Steve Geoffroy
- e Montreal Heart Institute, Université de Montréal , Montreal , Canada.,f Université de Montréal Beaulieu-Saucier Pharmacogenomics Center, Montreal Heart Institute, Université de Montréal , Montreal , Canada
| | - Ian Mongrain
- e Montreal Heart Institute, Université de Montréal , Montreal , Canada.,f Université de Montréal Beaulieu-Saucier Pharmacogenomics Center, Montreal Heart Institute, Université de Montréal , Montreal , Canada
| | - Géraldine Asselin
- e Montreal Heart Institute, Université de Montréal , Montreal , Canada.,f Université de Montréal Beaulieu-Saucier Pharmacogenomics Center, Montreal Heart Institute, Université de Montréal , Montreal , Canada
| | - Sylvie Provost
- e Montreal Heart Institute, Université de Montréal , Montreal , Canada.,f Université de Montréal Beaulieu-Saucier Pharmacogenomics Center, Montreal Heart Institute, Université de Montréal , Montreal , Canada
| | - Marie-Pierre Dubé
- e Montreal Heart Institute, Université de Montréal , Montreal , Canada.,f Université de Montréal Beaulieu-Saucier Pharmacogenomics Center, Montreal Heart Institute, Université de Montréal , Montreal , Canada.,g Department of Medicine, Université de Montréal , Montreal , Canada
| | - Eric Nudleman
- d Shiley Eye Institute, University of California San Diego , La Jolla , CA , USA
| | - Radha Ayyagari
- d Shiley Eye Institute, University of California San Diego , La Jolla , CA , USA
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16
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Rose AM, Luo R, Radia UK, Bhattacharya SS. Gene of the month: PRPF31. J Clin Pathol 2017; 70:729-732. [PMID: 28663330 DOI: 10.1136/jclinpath-2016-203971] [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] [Received: 05/26/2017] [Accepted: 06/01/2017] [Indexed: 11/04/2022]
Abstract
Pre-mRNA splicing is an essential process in eukaryotic cells where the transcribed intronic sequences are removed, prior to translation into protein. PRPF31 is a ubiquitously expressed splicing factor, which aids in the assembly of the macromolecular spliceosome. Mutations in PRPF31 cause autosomal dominant retinitis pigmentosa (adRP), a form of retinal degeneration that causes progressive visual impairment. Interestingly, mutations in PRPF31 are non-penetrant, with some mutation carriers being phenotypically unaffected. In this review, the gene organisation, protein structure and biological function of PRPF31 are discussed, and the mechanisms of non-penetrance in PRPF31-associated adRP are discussed.
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Affiliation(s)
- Anna M Rose
- Department of Genetics, UCL Institute of Ophthalmology, London, UK.,Department of Medicine, Imperial College, London, UK
| | - Rong Luo
- Department of Medicine, Imperial College, London, UK
| | - Utsav K Radia
- Department of Medicine, Imperial College, London, UK
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17
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Karolak JA, Gajecka M. Genomic strategies to understand causes of keratoconus. Mol Genet Genomics 2016; 292:251-269. [PMID: 28032277 PMCID: PMC5357269 DOI: 10.1007/s00438-016-1283-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 12/19/2016] [Indexed: 12/12/2022]
Abstract
Keratoconus (KTCN) is a degenerative disorder of the eye characterized by the conical shape and thinning of the cornea. The abnormal structure of KTCN-affected cornea results in loss of visual acuity. While many studies examine how environmental factors influence disease development, finding the genetic triggers has been a major emphasis of KTCN research. This paper focuses on genomic strategies that were implemented for finding candidate genes, including linkage and association studies, and presents different approaches of mutation screening. The advantages and limitations of particular tools are discussed based on literature and personal experience. Since etiology underlying KTCN is complex, numerous findings indicating heterogeneity of genetic factors involved KTCN etiology are presented.
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Affiliation(s)
- Justyna A Karolak
- Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Swiecickiego 4, Poznan, 60-781, Poland.,Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, Poznan, 60-479, Poland
| | - Marzena Gajecka
- Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Swiecickiego 4, Poznan, 60-781, Poland. .,Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, Poznan, 60-479, Poland.
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18
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Yang Y, Yang Y, Huang L, Zhai Y, Li J, Jiang Z, Gong B, Fang H, Kim R, Yang Z, Sundaresan P, Zhu X, Zhou Y. Whole exome sequencing identified novel CRB1 mutations in Chinese and Indian populations with autosomal recessive retinitis pigmentosa. Sci Rep 2016; 6:33681. [PMID: 27670293 PMCID: PMC5037368 DOI: 10.1038/srep33681] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 08/31/2016] [Indexed: 01/02/2023] Open
Abstract
Retinitis pigmentosa (RP) is a leading cause of inherited blindness characterized by progressive degeneration of the retinal photoreceptor cells. This study aims to identify genetic mutations in a Chinese family RP-2236, an Indian family RP-IC-90 and 100 sporadic Indian individuals with autosomal recessive RP (arRP). Whole exome sequencing was performed on the index patients of RP-2236, RP-IC-90 and all of the 100 sporadic Indian patients. Direct Sanger sequencing was used to validate the mutations identified. Four novel mutations and one reported mutation in the crumbs homolog 1 (CRB1) gene, which has been known to cause severe retinal dystrophies, were identified. A novel homozygous splicing mutation c.2129-1G>C was found in the three patients In family RP-2236. A homozygous point mutation p.R664C was found in RP-IC-90. A novel homozygous mutation p.G1310C was identified in patient I-44, while novel compound heterozygous mutations p.N629D and p.A593T were found in patient I-7. All mutations described above were not present in the 1000 normal controls. In conclusion, we identified four novel mutations in CRB1 in a cohort of RP patients from the Chinese and Indian populations. Our data enlarges the CRB1 mutation spectrums and may provide new target loci for RP diagnose and treatment.
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Affiliation(s)
- Yin Yang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, School of Medicine, Sichuan Academy of Medical Sciences &Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.,Department of Ophthalmology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Yeming Yang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, School of Medicine, Sichuan Academy of Medical Sciences &Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.,Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, China.,Institute of Laboratory Animal Sciences, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China.,Key Laboratory for NeuroInformation of Ministry of Education and Medicine Information Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Lulin Huang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, School of Medicine, Sichuan Academy of Medical Sciences &Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.,Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, China
| | - Yaru Zhai
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, School of Medicine, Sichuan Academy of Medical Sciences &Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Jie Li
- Department of Ophthalmology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Zhilin Jiang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, School of Medicine, Sichuan Academy of Medical Sciences &Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.,Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, China
| | - Bo Gong
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, School of Medicine, Sichuan Academy of Medical Sciences &Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.,Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, China
| | - Hao Fang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, School of Medicine, Sichuan Academy of Medical Sciences &Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.,Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, China
| | - Ramasamy Kim
- Retina-vitreous services, Aravind Eye Hospital, Madurai, Tamilnadu, India
| | - Zhenglin Yang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, School of Medicine, Sichuan Academy of Medical Sciences &Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.,Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, China.,Key Laboratory for NeuroInformation of Ministry of Education and Medicine Information Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Periasamy Sundaresan
- Department of Genetics, Aravind Medical Research Foundation, Aravind Eye Hospital, Madurai, Tamilnadu, India
| | - Xianjun Zhu
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, School of Medicine, Sichuan Academy of Medical Sciences &Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.,Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, China.,Institute of Laboratory Animal Sciences, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China.,Key Laboratory for NeuroInformation of Ministry of Education and Medicine Information Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.,Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, Sichuan, China
| | - Yu Zhou
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, School of Medicine, Sichuan Academy of Medical Sciences &Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.,Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan 610072, China.,Key Laboratory for NeuroInformation of Ministry of Education and Medicine Information Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.,Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, Sichuan, China
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19
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Zhang Q, Xu M, Verriotto JD, Li Y, Wang H, Gan L, Lam BL, Chen R. Next-generation sequencing-based molecular diagnosis of 35 Hispanic retinitis pigmentosa probands. Sci Rep 2016; 6:32792. [PMID: 27596865 PMCID: PMC5011706 DOI: 10.1038/srep32792] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/29/2016] [Indexed: 12/13/2022] Open
Abstract
Retinitis pigmentosa (RP) is a heterogeneous group of inherited retinal diseases. The prevalence of RP and the mutation spectrum vary across populations. Hispanic people account for approximately 17% of the United States population, and the genetic etiologies of RP of this ethnic group still remain not well defined. Utilizing next-generation sequencing (NGS), we screened mutations in known retinal disease-causing genes in an RP cohort of 35 unrelated Hispanic probands from the Miami area. We achieved a solving rate of 66% and identified 15 novel putative pathogenic mutations, including a frequent founder mutation disrupting PRPF31 splicing. Our data show that the mutation spectrum of Hispanic RP receives a significant impact from disease-causing alleles of Spanish origin and may also contain population-specific alleles.
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Affiliation(s)
- Qi Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Mingchu Xu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Jennifer D. Verriotto
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Hui Wang
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Lin Gan
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Byron L. Lam
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, Texas, USA
- The Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA
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A challenge to the striking genotypic heterogeneity of retinitis pigmentosa: a better understanding of the pathophysiology using the newest genetic strategies. Eye (Lond) 2016; 30:1542-1548. [PMID: 27564722 DOI: 10.1038/eye.2016.197] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 07/13/2016] [Indexed: 11/08/2022] Open
Abstract
Retinitis pigmentosa (RP) is a group of inherited retinal disorders characterized by a complex association between tremendous genotypic multiplicity and great phenotypic heterogeneity. The severity of the clinical manifestation depends on penetrance and expressivity of the disease-gene. Also, various interactions between gene expression and environmental factors have been hypothesized. More than 250 genes with ~4500 causative mutations have been reported to be involved in different RP-related mechanisms. Nowadays, not more than the 50% of RPs are attributable to identified genes, whereas the rest of molecular defects are still undetectable, especially in populations where few genetic screenings have been performed. Therefore, new genetic strategies can be a remarkably useful tool to aid clinical diagnosis, potentially modifying treatment options, and family counseling. Genome-wide analytical techniques (array comparative genomic hybridization and single-nucleotide polymorphism genotyping) and DNA sequencing strategies (arrayed primer extension, Sanger sequencing, and ultra high-throughput sequencing) are successfully used to early make molecular diagnosis detecting single or multiple mutations in the huge heterogeneity of RPs. To date, further research needs to be carried out to better investigate the genotype/phenotype correlation, putting together genetic and clinical findings to provide detailed information concerning the risk of RP development and novel effective treatments.
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21
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Abdulridha-Aboud W, Kjellström U, Andréasson S, Ponjavic V. Characterization of macular structure and function in two Swedish families with genetically identified autosomal dominant retinitis pigmentosa. Mol Vis 2016; 22:362-73. [PMID: 27212874 PMCID: PMC4860447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/20/2016] [Indexed: 10/31/2022] Open
Abstract
PURPOSE To study the phenotype in two families with genetically identified autosomal dominant retinitis pigmentosa (adRP) focusing on macular structure and function. METHODS Clinical data were collected at the Department of Ophthalmology, Lund University, Sweden, for affected and unaffected family members from two pedigrees with adRP. Examinations included optical coherence tomography (OCT), full-field electroretinography (ffERG), and multifocal electroretinography (mfERG). Molecular genetic screening was performed for known mutations associated with adRP. RESULTS The mode of inheritance was autosomal dominant in both families. The members of the family with a mutation in the PRPF31 (p.IVS6+1G>T) gene had clinical features characteristic of RP, with severely reduced retinal rod and cone function. The degree of deterioration correlated well with increasing age. The mfERG showed only centrally preserved macular function that correlated well with retinal thinning on OCT. The family with a mutation in the RHO (p.R135W) gene had an extreme intrafamilial variability of the phenotype, with more severe disease in the younger generations. OCT showed pathology, but the degree of morphological changes was not correlated with age or with the mfERG results. The mother, with a de novo mutation in the RHO (p.R135W) gene, had a normal ffERG, and her retinal degeneration was detected merely with the reduced mfERG. CONCLUSIONS These two families demonstrate the extreme inter- and intrafamilial variability in the clinical phenotype of adRP. This is the first Swedish report of the clinical phenotype associated with a mutation in the PRPF31 (p.IVS6+1G>T) gene. Our results indicate that methods for assessment of the central retinal structure and function may improve the detection and characterization of the RP phenotype.
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Barandika O, Irigoyen C, Anasagasti A, Egiguren G, Ezquerra-Inchausti M, López de Munain A, Ruiz-Ederra J. A Cost-Effective Mutation Screening Strategy for Inherited Retinal Dystrophies. Ophthalmic Res 2016; 56:123-31. [PMID: 27160245 DOI: 10.1159/000445690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/21/2016] [Indexed: 11/19/2022]
Abstract
OBJECTIVE We developed a simple, time- and cost-effective Excel-based genetic screening strategy for the diagnosis of inherited retinal dystrophies (IRD). DESIGN 76 patients diagnosed with IRD and 112 nonaffected family members, from 55 unrelated families, were included. DNA samples were analyzed using Axiom Exome Genotyping Array Plates (Affymetrix) that contain over 300,000 genetic variants, including more than 5,000 variants present in 181 genes involved in IRD. We used a simple Excel-based data mining strategy in order to screen IRD variants likely involved in the development of IRD. RESULTS A total of 5 relevant genetic variants were found in 5 IRD genes. Four variants were reported either as pathogenic or with a prediction of probably damaging, and 1 variant was reported to affect a regulatory region. These variants were present in 14 patients and in 11 carriers, in 10 unrelated families. CONCLUSION Using our Excel-based data screening strategy, we were able to assign likely genetic diagnoses in a fast and cost-effective manner to over 18% of patients analyzed, with a comparable ratio of genetic findings to that reported with retina-specific arrays for about 1/5 of the cost. Our approach proved efficient in reducing costs and time for IRD diagnosis as a first tier genetic screening method.
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Affiliation(s)
- Olatz Barandika
- Division of Neurosciences, Instituto Biodonostia, Donostia-San Sebastián, Spain
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Rose AM, Bhattacharya SS. Variant haploinsufficiency and phenotypic non-penetrance in PRPF31-associated retinitis pigmentosa. Clin Genet 2016; 90:118-26. [PMID: 26853529 DOI: 10.1111/cge.12758] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 02/02/2016] [Accepted: 02/03/2016] [Indexed: 11/30/2022]
Abstract
Retinitis pigmentosa (RP) is a genetically heterogenous group of inherited disorders, characterized by death of the retinal photoreceptor cells, leading to progressive visual impairment. One form of RP is caused by mutations in the ubiquitously expressed splicing factor, PRPF31, this form being known as RP11. An intriguing feature of RP11 is the presence of non-penetrance, which has been observed in the majority of PRPF31 mutation-carrying families. In contrast to variable expressivity, which is highly pervasive, true non-penetrance is a very rare phenomenon in Mendelian disorders. In this article, the molecular mechanisms underlying phenotypic non-penetrance in RP11 are explored. It is an elegant example of how our understanding of monogenic disorders has evolved from studying only the disease gene, to considering a mutation on the genetic background of the individual - the logical evolution in this genomic era.
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Affiliation(s)
- A M Rose
- Department of Genetics, UCL Institute of Ophthalmology, London, UK
| | - S S Bhattacharya
- Department of Genetics, UCL Institute of Ophthalmology, London, UK
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Exome Sequencing Identified a Recessive RDH12 Mutation in a Family with Severe Early-Onset Retinitis Pigmentosa. J Ophthalmol 2015; 2015:942740. [PMID: 26124963 PMCID: PMC4466393 DOI: 10.1155/2015/942740] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 04/08/2015] [Accepted: 04/10/2015] [Indexed: 01/11/2023] Open
Abstract
Retinitis pigmentosa (RP) is the most important hereditary retinal disease caused by progressive degeneration of the photoreceptor cells. This study is to identify gene mutations responsible for autosomal recessive retinitis pigmentosa (arRP) in a Chinese family using next-generation sequencing technology. A Chinese family with 7 members including two individuals affected with severe early-onset RP was studied. All patients underwent a complete ophthalmic examination. Exome sequencing was performed on a single RP patient (the proband of this family) and direct Sanger sequencing on other family members and normal controls was followed to confirm the causal mutations. A homozygous mutation c.437T<A (p.V146D) in the retinol dehydrogenase 12 (RDH12) gene, which encodes an NADPH-dependent retinal reductase, was identified as being related to the phenotype of this arRP family. This homozygous mutation was detected in the two affected patients, but not present in other family members and 600 normal controls. Another three normal members in the family were found to carry this heterozygous missense mutation. Our results emphasize the importance of c.437T<A (p.V146D) substitution in RDH12 and provide further support for the causative role of this mutation in the pathogenesis and clinical diagnosis of RP.
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