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Targeted next-generation sequencing identifies ABCA4 mutations in Chinese families with childhood-onset and adult-onset Stargardt disease. Biosci Rep 2021; 41:228645. [PMID: 33988224 PMCID: PMC8173525 DOI: 10.1042/bsr20203497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 11/17/2022] Open
Abstract
Background: Stargardt disease (STGD) is the most common form of juvenile macular dystrophy associated with progressive central vision loss, and is agenetically and clinically heterogeneous disease. Molecular diagnosis is of great significance in aiding the clinical diagnosis, helping to determine the phenotypic severity and visual prognosis. In the present study, we determined the clinical and genetic features of seven childhood-onset and three adult-onset Chinese STGD families. We performed capture next-generation sequencing (NGS) of the probands and searched for potentially disease-causing genetic variants in previously identified retinal or macular dystrophy genes. Methods: In all, ten unrelated Chinese families were enrolled. Panel-based NGS was performed to identify potentially disease-causing genetic variants in previously identified retinal or macular dystrophy genes, including the five known STGD genes (ABCA4, PROM1, PRPH2, VMD2, and ELOVL4). Variant analysis, Sanger validation, and segregation tests were utilized to validate the disease-causing mutations in these families. Results: Using systematic data analysis with an established bioinformatics pipeline and segregation analysis, 17 pathogenic mutations in ABCA4 were identified in the 10 STGD families. Four of these mutations were novel: c.371delG, c.681T > G, c.5509C > T, and EX37del. Childhood-onset STGD was associated with severe visual loss, generalized retinal dysfunction and was due to more severe variants in ABCA4 than those found in adult-onset disease. Conclusions: We expand the existing spectrum of STGD and reveal the genotype–phenotype relationships of the ABCA4 mutations in Chinese patients. Childhood-onset STGD lies at the severe end of the spectrum of ABCA4-associated retinal phenotypes.
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Whole exome sequencing and homozygosity mapping reveals genetic defects in consanguineous Iranian families with inherited retinal dystrophies. Sci Rep 2020; 10:19413. [PMID: 33173045 PMCID: PMC7655865 DOI: 10.1038/s41598-020-75841-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/08/2020] [Indexed: 12/17/2022] Open
Abstract
Inherited retinal dystrophies (IRDs), displaying pronounced genetic and clinical heterogeneity, comprise of a broad range of diseases characterized by progressive retinal cell death and gradual loss of vision. By the combined use of whole exome sequencing (WES), SNP-array and WES-based homozygosity mapping, as well as directed DNA sequencing (Sanger), we have identified nine pathogenic variants in six genes (ABCA4, RPE65, MERTK, USH2A, SPATA7, TULP1) in 10 consanguineous Iranian families. Six of the nine identified variants were novel, including a putative founder mutation in ABCA4 (c.3260A>G, p.Glu1087Gly), detected in two families from Northeastern Iran. Our findings provide additional information to the molecular pathology of IRDs in Iran, hopefully contributing to better genetic counselling and patient management in the respective families from this country.
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Tao T, Wang L, Chong W, Yang L, Li G. Characteristics of genotype and phenotype in Chinese patients with Bardet-Biedl syndrome. Int Ophthalmol 2020; 40:2325-2343. [PMID: 32448990 DOI: 10.1007/s10792-020-01415-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 05/02/2020] [Indexed: 12/31/2022]
Abstract
PURPOSE To investigate complex and different phenotypes in seven Chinese patients diagnosed with Bardet-Biedl syndrome (BBS) and carrying pathogenic mutations. METHODS Seven unrelated BBS patients were enrolled. Their medical and ophthalmic histories were reviewed, and comprehensive clinical examinations, such as fundus photography, optical coherence tomography, and medical imaging, were performed. A specific hereditary eye disease enrichment panel based on exome-capture technology was used to collect and amplify the protein-coding regions of 441 targeted hereditary eye disease genes, followed by high-throughput sequencing using the Illumina HiSeq platform. RESULTS All patients exhibited the primary clinical phenotype of BBS. Seven BBS mutations were found in five patients (BBS7 in two patients, BBS10 in two patients, BBS12 in one patient), for a detection rate of 71% (5/7). The ratio of novel to known BBS mutations was 5:2. CONCLUSIONS This study showed the phenotypic and genotypic spectrum of BBS patients from China, and the findings underscore the importance of obtaining comprehensive clinical observations and molecular analyses for ciliopathies.
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Affiliation(s)
- Tianchang Tao
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University; Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, People's Republic of China
| | - Lei Wang
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University; Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, People's Republic of China
| | - Weihua Chong
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University; Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, People's Republic of China
| | - Liping Yang
- Department of Ophthalmology, Peking University Third Hospital, Key Laboratory of Restoration of Damaged Ocular Nerve Beijing, Beijing, People's Republic of China
| | - Genlin Li
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University; Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, People's Republic of China.
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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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Zhuo L, Huang L, Yang Z, Li G, Wang L. A comprehensive analysis of NPHS1 gene mutations in patients with sporadic focal segmental glomerulosclerosis. BMC MEDICAL GENETICS 2019; 20:111. [PMID: 31216994 PMCID: PMC6585123 DOI: 10.1186/s12881-019-0845-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 06/06/2019] [Indexed: 01/01/2023]
Abstract
BACKGROUND Focal segmental glomerulosclerosis (FSGS) is still one of the common causes of refractory nephrotic syndrome. Nephrin, encoded by podocyte-specific NPHS1 gene, participated in the pathogenesis of FSGS. The sites of NPHS1 mutations in FSGS is not clarified very well. In this study, we investigated the specific mutations of NPHS1 gene in Chinese patients with sporadic FSGS. METHODS A total of 309 patients with sporadic FSGS were collected and screened for NPHS1 mutations by second-generation sequencing. The variants were compared with those extracted from 2504 healthy controls in the 1000 Genomes Project. The possible pathogenic roles of missense variants were predicted by three different software. We also compared these candidate causal mutations with those summarized from the previous studies. RESULTS Thirty-two genetic mutations of NPHS1 gene were identified in FSGS patients, including 12 synonymous mutations, 17 missense mutations, 1 splicing mutation, and 2 intron mutations, of which c.G3315A (p.S1105S) was the most common variant (261/309). A novel missense mutation c.G2638 T (p.V880F) and a novel splicing mutation 35830957 C > T were identified in FSGS patients. The frequencies of the four synonymous mutations (c.C294T [p.I98I], c.C2223T [p.T741 T], c.C2289T [p.V763 V], c.G3315A [p.S1105S]) were much higher in FSGS patients than in controls. The frequencies of the four missense mutations (c.G349A [p.E117K], c.G1339A [p.E447K], c.G1802C [p.G601A], c.C2398T [p.R800C]) were much higher and one (c.A3230G [p.N1077S]) was lower in FSGS patients than in controls. Five missense mutations, c.C616A (p.P206T), c.G1802C (p.G601A), c.C2309T (p.P770L), c.G2869C (p.V957 L), and c.C3274T (p.R1092C), were predicted to be pathogenic mutations by software analysis. CONCLUSIONS NPHS1 gene mutations were quite common in sporadic FSGS patients. We strongly recommend mutation analysis of the NPHS1 gene in the clinical management of FSGS patients.
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Affiliation(s)
- Ling Zhuo
- Renal Department and Institute of Nephrology, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, No. 32, West 2nd Duan, 1st Circle Road, Qingyang District, Chengdu, Sichuan, 610072, People's Republic of China
| | - Lulin Huang
- Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, 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, 610072, China
| | - Guisen Li
- Renal Department and Institute of Nephrology, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, No. 32, West 2nd Duan, 1st Circle Road, Qingyang District, Chengdu, Sichuan, 610072, People's Republic of China.
| | - Li Wang
- Renal Department and Institute of Nephrology, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, No. 32, West 2nd Duan, 1st Circle Road, Qingyang District, Chengdu, Sichuan, 610072, People's Republic of China
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Singh M, Tyagi SC. Genes and genetics in eye diseases: a genomic medicine approach for investigating hereditary and inflammatory ocular disorders. Int J Ophthalmol 2018; 11:117-134. [PMID: 29376001 DOI: 10.18240/ijo.2018.01.20] [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: 01/17/2017] [Accepted: 10/31/2017] [Indexed: 12/27/2022] Open
Abstract
Past 25y have witnessed an exponential increase in knowledge and understanding of ocular diseases and their respective genetic underpinnings. As a result, scientists have mapped many genes and their variants that can influence vision and health of our eyes. Based on these findings, it is becoming clear that an early diagnosis employing genetic testing can help evaluate patients' conditions for instituting treatment plan(s) and follow-up care to avoid vision complications later. For example, knowing family history becomes crucial for inherited eye diseases as it can benefit members in family who may have similar eye diseases or predispositions. Therefore, gathering information from an elaborate examination along with complete assessment of past medical illness by ophthalmologists followed by consultation with geneticists can help create a roadmap for making diagnosis and treatment precise and beneficial. In this review, we present an update on ocular genomic medicine that we believe has tremendous potential towards unraveling genetic implications in ocular diseases and patients' susceptibilities. We also discuss translational aspects of genetic ophthalmology and genome engineering that may help advance molecular diagnostics and therapeutics.
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Affiliation(s)
- Mahavir Singh
- Eye and Vision Science Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky 40202, USA
| | - Suresh C Tyagi
- Eye and Vision Science Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, Kentucky 40202, USA
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7
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Zhang J, Qi A, Wang X, Pan H, Mo H, Huang J, Li H, Chen Z, Wei M, Wang B. Novel compound heterozygous mutations in ABCA4 in a Chinese pedigree with Stargardt disease. Mol Vis 2016; 22:1514-1521. [PMID: 28050124 PMCID: PMC5204459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 12/28/2016] [Indexed: 11/12/2022] Open
Abstract
PURPOSE Stargardt disease (STGD) is a common macular dystrophy in juveniles that is commonly inherited as an autosomal recessive trait. Mutations in five genes (ABCA4, PROM1, ELOVL4, BEST1, and PRPH2) have been reported to be associated with STGD. In the present study, we aimed to identify the pathogenic mutations in affected members in a Chinese STGD pedigree. METHODS One patient was selected for whole-exome sequencing. Variants in five candidate genes were identified initially, followed by several filtering steps against public and private variation databases (1000Genomes, ESP6500si, ExAC, and in-house database), as well as bioinformatic analysis of the putative pathogenic roles. Sanger sequencing was used for cosegregation analysis among all members with available DNA. RESULTS Two mutations in ABCA4 (NM_000350.2; c.5646G>A; p.Met1882Ile and NM_000350.2; c.3523-2A>G) were found using whole-exome sequencing. Cosegregation analysis confirmed all the affected members carried the compound heterozygous mutations while the other healthy members had at most one. The missense mutation was extremely rare in public databases and predicted to be deleterious. The splice-site mutation was absent from all public and private databases and was predicted to alter the splice pattern, resulting in an exon skip and a frameshift. CONCLUSIONS Using whole-exome sequencing, we found novel compound heterozygous mutations in ABCA4 in a Chinese STGD pedigree. These mutations are reported for the first time, therefore widening the mutation spectrum of Stargardt disease. The present study also illustrates the potential of whole-exome sequencing in determining the genetic cause of STGD.
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Affiliation(s)
- Jianping Zhang
- Department of Ophthalmology, Liuzhou Maternal and Child Healthcare Hospital, Liuzhou, Guangxi, China
| | - Anhui Qi
- Graduate School of Peking Union Medical College, Beijing, China,National Research Institute of Family Planning, Beijing, China
| | - Xi Wang
- National Research Institute of Family Planning, Beijing, China
| | - Hong Pan
- Graduate School of Peking Union Medical College, Beijing, China,National Research Institute of Family Planning, Beijing, China
| | - Haiming Mo
- Department of Ophthalmology, Liuzhou Maternal and Child Healthcare Hospital, Liuzhou, Guangxi, China
| | - Jiwei Huang
- Department of Ophthalmology, Liuzhou Maternal and Child Healthcare Hospital, Liuzhou, Guangxi, China
| | - Honghui Li
- Department of Ophthalmology, Liuzhou Maternal and Child Healthcare Hospital, Liuzhou, Guangxi, China
| | - Zhenwen Chen
- Department of Ophthalmology, Liuzhou Maternal and Child Healthcare Hospital, Liuzhou, Guangxi, China
| | - Meirong Wei
- Department of Ophthalmology, Liuzhou Maternal and Child Healthcare Hospital, Liuzhou, Guangxi, China
| | - Binbin Wang
- National Research Institute of Family Planning, Beijing, China
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Zolnikova IV, Strelnikov VV, Skvortsova NA, Tanas AS, Barh D, Rogatina EV, Egorova IV, Levina DV, Demenkova ON, Prikaziuk EG, Ivanova ME. Stargardt disease-associated mutation spectrum of a Russian Federation cohort. Eur J Med Genet 2016; 60:140-147. [PMID: 27939946 DOI: 10.1016/j.ejmg.2016.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 11/26/2016] [Accepted: 12/01/2016] [Indexed: 12/24/2022]
Abstract
ABCA4-associated mutation screening is extensively performed in European, African, American and several other populations for various retinopathies. However, it has not been well studied in a Russian cohort. Using next-generation (325 genes inherited disease panel) and Sanger sequencing technologies for the first time we documented the spectrum of genetic variations in a Russian retinopathy cohort of 51 patients from 10 ethnic groups. We found ABCA4 variations in 70.5% cases and one case with BEST1 variation. Multiple ABCA4 variations, ABCA4 + RDH12, and ABCA4 + BEST1 variations are also observed and the disease severity is found proportionate to the variation burden. Ten novel ABCA4 variations are detected of which 8 belongs to non-Slavonian population. Most of the detected known variations are found in European and American Stargardt disease populations. No retinopathy causing variation is detected in 14 (27%) cases suggesting that in this Russian retinopathies cohort the causal variants could be in genes that are not covered by our 325 gene panel. Therefore, whole genome/exome analysis is required to identify novel retinopathy associated genes and provide better disease management for this heterogeneous cohort.
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Affiliation(s)
- Inna V Zolnikova
- Moscow Helmholtz Research Institute of Eye Diseases, Sadovaya Chernogryazskaya Str. 14/19, Moscow 105062, Russia
| | | | - Natalia A Skvortsova
- Posterior Eye Segment Diagnostics and Surgery Centre, 2nd Vladimirskaya Str. b.2, 4th Floor, Moscow 111123, Russia
| | - Alexander S Tanas
- Research Centre for Medical Genetics, Moskvorechie Str. 1, Moscow 15478, Russia
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB 721172, India; Xcode Life Sciences, 3D Eldorado, 112 Nungambakkam High Road, Nungambakkam, Chennai, Tamil Nadu 600034, India.
| | - Elena V Rogatina
- Moscow Helmholtz Research Institute of Eye Diseases, Sadovaya Chernogryazskaya Str. 14/19, Moscow 105062, Russia
| | - Irina V Egorova
- Moscow Helmholtz Research Institute of Eye Diseases, Sadovaya Chernogryazskaya Str. 14/19, Moscow 105062, Russia
| | - Darja V Levina
- Moscow Helmholtz Research Institute of Eye Diseases, Sadovaya Chernogryazskaya Str. 14/19, Moscow 105062, Russia
| | - Olga N Demenkova
- Moscow Helmholtz Research Institute of Eye Diseases, Sadovaya Chernogryazskaya Str. 14/19, Moscow 105062, Russia
| | - Egor G Prikaziuk
- Bioinformatics Institute, Kantemirovskaya Str. b.2a, Saint Petersburg 197342, Russia
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9
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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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10
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Liu S, Xie L, Yue J, Ma T, Peng C, Qiu B, Yang Z, Yang J. Whole-exome sequencing identifies a novel homozygous frameshift mutation in the PROM1 gene as a causative mutation in two patients with sporadic retinitis pigmentosa. Int J Mol Med 2016; 37:1528-34. [PMID: 27082927 PMCID: PMC4866957 DOI: 10.3892/ijmm.2016.2551] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 03/30/2016] [Indexed: 01/02/2023] Open
Abstract
Retinitis pigmentosa (RP) refers to a heterogeneous group of inherited retinal diseases caused by the loss of photoreceptors. The present study aimed to identify the gene mutations responsible for RP in two patients diagnosed with sporadic RP using next-generation sequencing technology. For this purpose, two patients with sporadic RP and family members (namely parents and siblings) were recruited into this study and underwent a complete ophthalmological assessment. Whole-exome sequencing (WES) was performed on genomic DNA samples isolated from peripheral leukocytes which had been obtained from the two patients diagnosed with sporadic RP. WES data were annotated and filtered against four public databases and one in-house database. Subsequently, Sanger sequencing was performed in order to determine whether any of the candidate variants co-segregated with the disease phenotype in the families. A homozygous frameshift mutation, c.1445dupT (p.F482fs) in exon 12 of the PROM1 gene (MIM: 604365), satisfied a recessive inheritance model and showed complete co-segregation of the mutation with the disease phenotype in the families. The same mutation was not detected in the 200 ethnically-matched control samples by Sanger sequencing. The novel homozygous mutation c.1445dupT (p.F482fs) in the PROM1 gene was identified as a causative mutation for RP. Thus, the identification of this mutation has further expanded the existing spectrum of PROM1 mutations in patients with RP, thereby assisting in the molecular diagnosis of RP and enhancing our understanding of genotype-phenotype correlations in order to provide effective genetic counseling.
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Affiliation(s)
- Sanmei Liu
- Department of Ophthalmology, Hospital of The University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu, Sichuan, P.R. China
| | - Lan Xie
- Department of Gynecology and Obstetrics, Hospital of The University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu, Sichuan, P.R. China
| | - Jun Yue
- Department of Gynecology and Obstetrics, Hospital of The University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu, Sichuan, P.R. China
| | - Tao Ma
- Department of Gynecology and Obstetrics, Hospital of The University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu, Sichuan, P.R. China
| | - Chunyan Peng
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Hospital of the University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu, Sichuan, P.R. China
| | - Biyuan Qiu
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Hospital of the University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu, Sichuan, P.R. China
| | - Zhenglin Yang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Hospital of the University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu, Sichuan, P.R. China
| | - Jiyun Yang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Hospital of the University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu, Sichuan, P.R. China
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11
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Whole-exome sequencing reveals a novel frameshift mutation in the FAM161A gene causing autosomal recessive retinitis pigmentosa in the Indian population. J Hum Genet 2015; 60:625-30. [PMID: 26246154 DOI: 10.1038/jhg.2015.92] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/18/2015] [Accepted: 06/30/2015] [Indexed: 11/08/2022]
Abstract
Retinitis pigmentosa (RP) is a heterogenous group of inherited retinal degenerations caused by mutations in at least 50 genes. To identify genetic mutations underlying autosomal recessive RP (arRP), we performed whole-exome sequencing study on two consanguineous marriage Indian families (RP-252 and RP-182) and 100 sporadic RP patients. Here we reported novel mutation in FAM161A in RP-252 and RP-182 with two patients affected with RP in each family. The FAM161A gene was identified as the causative gene for RP28, an autosomal recessive form of RP. By whole-exome sequencing we identified several homozygous genomic regions, one of which included the recently identified FAM161A gene mutated in RP28-linked arRP. Sequencing analysis revealed the presence of a novel homozygous frameshift mutation p.R592FsX2 in both patients of family RP-252 and family RP-182. In 100 sporadic Indian RP patients, this novel homozygous frameshift mutation p.R592FsX2 was identified in one sporadic patient ARRP-S-I-46 by whole-exome sequencing and validated by Sanger sequencing. Meanwhile, this homozygous frameshift mutation was absent in 1000 ethnicity-matched control samples screened by direct Sanger sequencing. In conclusion, we identified a novel homozygous frameshift mutations of RP28-linked RP gene FAM161A in Indian population.
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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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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.
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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
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