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Abstract
OBJECTIVE To describe the genetic and phenotypic spectrum of Usher syndrome after 6 years of studies by next-generation sequencing, and propose an up-to-date classification of Usher genes in patients with both visual and hearing impairments suggesting Usher syndrome, and in patients with seemingly isolated deafness. STUDY DESIGN The systematic review and meta-analysis protocol was based on Cochrane and Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We performed 1) a meta-analysis of data from 11 next-generation sequencing studies in 684 patients with Usher syndrome; 2) a meta-analysis of data from 21 next-generation studies in 2,476 patients with seemingly isolated deafness, to assess the involvement of Usher genes in seemingly nonsyndromic hearing loss, and thus the proportion of patients at high risk of subsequent retinitis pigmentosa (RP); 3) a statistical analysis of differences between parts 1) and 2). RESULTS In patients with both visual and hearing impairments, the biallelic disease-causing mutation rate was assessed for each Usher gene to propose a classification by frequency: USH2A: 50% (341/684) of patients, MYO7A: 21% (144/684), CDH23: 6% (39/684), ADGRV1: 5% (35/684), PCDH15: 3% (21/684), USH1C: 2% (17/684), CLRN1: 2% (14/684), USH1G: 1% (9/684), WHRN: 0.4% (3/684), PDZD7 0.1% (1/684), CIB2 (0/684). In patients with seemingly isolated sensorineural deafness, 7.5% had disease-causing mutations in Usher genes, and are therefore at high risk of developing RP. These new findings provide evidence that usherome dysfunction is the second cause of genetic sensorineural hearing loss after connexin dysfunction. CONCLUSION These results promote generalization of early molecular screening for Usher syndrome in deaf children.
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Yohe S, Sivasankar M, Ghosh A, Ghosh A, Holle J, Murugan S, Gupta R, Schimmenti LA, Vedam R, Thyagarajan B. Prevalence of mutations in inherited retinal diseases: A comparison between the United States and India. Mol Genet Genomic Med 2019; 8:e1081. [PMID: 31816670 PMCID: PMC7005662 DOI: 10.1002/mgg3.1081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 10/14/2019] [Accepted: 10/30/2019] [Indexed: 11/26/2022] Open
Abstract
Background Studies evaluating next‐generation sequencing (NGS) for retinal disorders may not reflect clinical practice. We report results of retrospective analysis of patients referred for clinical testing at two institutions (US and India). Methods This retrospective study of 131 patients who underwent clinically validated targeted NGS or exome sequencing for a wide variety of clinical phenotypes categorized results into a definitive, indeterminate, or negative molecular diagnosis. Results A definitive molecular diagnosis (52%) was more common in the India cohort (62% vs. 39%, p = .009), while an indeterminate molecular diagnosis occurred only in the US cohort (12%). In the US cohort, a lower diagnostic rate in Hispanic, non‐Caucasians (23%) was seen compared to Caucasians (57%). The India cohort had a high rate of homozygous variants (61%) and different frequency of genes involved compared to the US cohort. Conclusion Despite inherent limitations in clinical testing, the diagnostic rate across the two cohorts (52%) was similar to the 50%–65% diagnostic rate in the literature. However, the diagnostic rate was lower in the US cohort and appears partly explained by racial background. The high rate of consanguinity in the Indian population is reflected in the high rate of homozygosity for pathogenic mutations and may have implications for population level screening and genetic counseling. Clinical laboratories may note diagnostic rates that differ from the literature, due to factors such as heterogeneity in racial background or consanguinity rates in the populations being tested. This information may be useful for post‐test counseling.
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Affiliation(s)
- Sophia Yohe
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | | | | | | | - Jennifer Holle
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | | | | | - Lisa A Schimmenti
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | | | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
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Aberrant Splicing Events Associated to CDH23 Noncanonical Splice Site Mutations in a Proband with Atypical Usher Syndrome 1. Genes (Basel) 2019; 10:genes10100732. [PMID: 31546658 PMCID: PMC6826400 DOI: 10.3390/genes10100732] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/17/2019] [Accepted: 09/19/2019] [Indexed: 12/16/2022] Open
Abstract
Aims: The aim of this study was the genetic diagnosis by next generation sequencing (NGS) of a patient diagnosed with Usher syndrome type 2 and the functional evaluation of the identified genetic variants to establish a phenotype–genotype correlation. Methods: Whole exome sequencing (WES) analysis identified two heterozygous intronic variants in CDH23, a gene responsible of Usher syndrome type 1. Evaluation of the putative splicing effects was performed in vivo, in whole blood samples, and in vitro, by transfection of midigene constructs in HEK293T cells. Results: Two intronic variants were identified in intron 45 of CDH23—one novel, c.6050-15G>A, and the other, c.6050-9G>A, already reported as a noncanonical splice site (NCSS) mutation—with partial functional characterization. In vivo and in vitro analyses showed aberrant transcripts by the addition of 13 and 7 nucleotides to exon 46, respectively. Transcript degradation by nonsense mediated decay (NMD) in blood cells could only be prevented by cycloheximide treatment. Midigene constructs showed that the two variants contributed to exon skipping and generated aberrantly spliced transcripts. Conclusions: A combination of in vivo and in vitro assays provided a comprehensive view of the physiological effects of NCSS variants, which in this case led to a clinical reassignment of the proband as affected with atypical USH1 syndrome.
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Santana EE, Fuster-García C, Aller E, Jaijo T, García-Bohórquez B, García-García G, Millán JM, Lantigua A. Genetic Screening of the Usher Syndrome in Cuba. Front Genet 2019; 10:501. [PMID: 31231422 PMCID: PMC6558366 DOI: 10.3389/fgene.2019.00501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/07/2019] [Indexed: 11/17/2022] Open
Abstract
Background Usher syndrome (USH) is a recessive inherited disease characterized by sensorineural hearing loss, retinitis pigmentosa, and sometimes, vestibular dysfunction. Although the molecular epidemiology of Usher syndrome has been well studied in Europe and United States, there is a lack of studies in other regions like Africa or Central and South America. Methods We designed a NGS panel that included the 10 USH causative genes (MYO7A, USH1C, CDH23, PCDH15, USH1G, CIB2, USH2A, ADGRV1, WHRN, and CLRN1), four USH associated genes (HARS, PDZD7, CEP250, and C2orf71), and the region comprising the deep-intronic c.7595-2144A>G mutation in USH2A. Results NGS sequencing was performed in 11 USH patients from Cuba. All the cases were solved. We found the responsible mutations in the USH2A, ADGRV1, CDH23, PCDH15, and CLRN1 genes. Four mutations have not been previously reported. Two mutations are recurrent in this study: c.619C>T (p.Arg207∗) in CLRN1, previously reported in two unrelated Spanish families of Basque origin, and c.4488G>C (p.Gln1496His) in CDH23, first described in a large Cuban family. Additionally, c.4488G>C has been reported two more times in the literature in two unrelated families of Spanish origin. Conclusion Although the sample size is very small, it is tempting to speculate that the gene frequencies in Cuba are distinct from other populations mainly due to an “island effect” and genetic drift. The two recurrent mutations appear to be of Spanish origin. Further studies with a larger cohort are needed to elucidate the real genetic landscape of Usher syndrome in the Cuban population.
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Affiliation(s)
- Elayne E Santana
- Centro Provincial de Genética, Universidad de Ciencias Médicas de Holguín, Holguín, Cuba
| | - Carla Fuster-García
- Health Research Institute La Fe, University Hospital La Fe, Valencia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), Madrid, Spain
| | - Elena Aller
- Health Research Institute La Fe, University Hospital La Fe, Valencia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), Madrid, Spain
| | - Teresa Jaijo
- Health Research Institute La Fe, University Hospital La Fe, Valencia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), Madrid, Spain
| | | | - Gema García-García
- Health Research Institute La Fe, University Hospital La Fe, Valencia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), Madrid, Spain
| | - José M Millán
- Health Research Institute La Fe, University Hospital La Fe, Valencia, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), Madrid, Spain
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Li T, Feng Y, Liu Y, He C, Liu J, Chen H, Deng Y, Li M, Li W, Song J, Niu Z, Sang S, Wen J, Men M, Chen X, Li J, Liu X, Ling J. A novel ABHD12 nonsense variant in Usher syndrome type 3 family with genotype-phenotype spectrum review. Gene 2019; 704:113-120. [PMID: 30974196 DOI: 10.1016/j.gene.2019.04.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 03/08/2019] [Accepted: 04/02/2019] [Indexed: 12/15/2022]
Abstract
Usher syndrome (USH) is a clinically common autosomal recessive disorder characterized by retinitis pigmentosa (RP) and sensorineural hearing loss with or without vestibular dysfunction. In this study, we identified a Hunan family of Chinese descent with two affected members clinically diagnosed with Usher syndrome type 3 (USH3) displaying hearing, visual acuity, and olfactory decline. Whole-exome sequencing (WES) identified a nonsense variant in ABHD12 gene that was confirmed to be segregated in this family by Sanger sequencing and exhibited a recessive inheritance pattern. In this family, two patients carried homozygous variant in the ABHD12 (NM_015600: c.249C>G). Mutation of ABHD12, an enzyme that hydrolyzes an endocannabinoid lipid transmitter, caused incomplete PHARC syndrome, as demonstrated in previous reports. Therefore, we also conducted a summary based on variants in ABHD12 in PHARC patients, and in PHARC patients showing that there was no obvious correlation between the genotype and phenotype. We believe that this should be considered during the differential diagnosis of USH. Our findings predicted the potential function of this gene in the development of hearing and vision loss, particularly with regard to impaired signal transmission, and identified a novel nonsense variant to expand the variant spectrum in ABHD12.
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Affiliation(s)
- Taoxi Li
- Department of Otolaryngology-Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Key Laboratory of Otolaryngology Major Disease Research of Hunan Province, Changsha, Hunan 410008, China; Center for Medical Genetics, Central South University, Changsha, Hunan 410008, China
| | - Yong Feng
- Department of Otolaryngology-Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Key Laboratory of Otolaryngology Major Disease Research of Hunan Province, Changsha, Hunan 410008, China; Center for Medical Genetics, Central South University, Changsha, Hunan 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yalan Liu
- Department of Otolaryngology-Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Key Laboratory of Otolaryngology Major Disease Research of Hunan Province, Changsha, Hunan 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Chufeng He
- Department of Otolaryngology-Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Key Laboratory of Otolaryngology Major Disease Research of Hunan Province, Changsha, Hunan 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jing Liu
- Department of Otolaryngology-Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Key Laboratory of Otolaryngology Major Disease Research of Hunan Province, Changsha, Hunan 410008, China
| | - Hongsheng Chen
- Department of Otolaryngology-Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Key Laboratory of Otolaryngology Major Disease Research of Hunan Province, Changsha, Hunan 410008, China
| | - Yuyuan Deng
- Department of Otolaryngology-Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Key Laboratory of Otolaryngology Major Disease Research of Hunan Province, Changsha, Hunan 410008, China
| | - Meng Li
- Department of Otolaryngology-Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Key Laboratory of Otolaryngology Major Disease Research of Hunan Province, Changsha, Hunan 410008, China
| | - Wu Li
- Department of Otolaryngology-Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Key Laboratory of Otolaryngology Major Disease Research of Hunan Province, Changsha, Hunan 410008, China
| | - Jian Song
- Department of Otolaryngology-Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Key Laboratory of Otolaryngology Major Disease Research of Hunan Province, Changsha, Hunan 410008, China
| | - Zhijie Niu
- Department of Otolaryngology-Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Key Laboratory of Otolaryngology Major Disease Research of Hunan Province, Changsha, Hunan 410008, China
| | - Shushan Sang
- Department of Otolaryngology-Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Key Laboratory of Otolaryngology Major Disease Research of Hunan Province, Changsha, Hunan 410008, China
| | - Jie Wen
- Department of Otolaryngology-Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Key Laboratory of Otolaryngology Major Disease Research of Hunan Province, Changsha, Hunan 410008, China
| | - Meichao Men
- Department of Otolaryngology-Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Key Laboratory of Otolaryngology Major Disease Research of Hunan Province, Changsha, Hunan 410008, China
| | - Xiaoya Chen
- Department of Otolaryngology-Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Key Laboratory of Otolaryngology Major Disease Research of Hunan Province, Changsha, Hunan 410008, China
| | - Jiada Li
- Center for Medical Genetics, Central South University, Changsha, Hunan 410008, China
| | - Xuezhong Liu
- Department of Otolaryngology-Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Department of Otolaryngology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Jie Ling
- Department of Otolaryngology-Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
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Ivanova ME, Trubilin VN, Atarshchikov DS, Demchinsky AM, Strelnikov VV, Tanas AS, Orlova OM, Machalov AS, Overchenko KV, Markova TV, Golenkova DM, Anoshkin KI, Volodin IV, Zaletaev DV, Pulin AA, Nadelyaeva II, Kalinkin AI, Barh D. Genetic screening of Russian Usher syndrome patients toward selection for gene therapy. Ophthalmic Genet 2018; 39:706-713. [PMID: 30358468 DOI: 10.1080/13816810.2018.1532527] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
BACKGROUND Usher syndrome (USH) is heterogeneous in nature and requires genetic test for diagnosis and management. Mutations in USH associated genes are reported in some populations except Russians. Here, we first time represented the mutation spectrum of a Russian USH cohort. METHODS Twenty-eight patients with USH were selected from 3214 patients from Deaf-Blind Support Foundation "Con-nection" during 2014-2016 following the observational study NCT03319524. Complete ophthalmologic, ENT, and vestibular medical tests were done for clinical characterization. NGS, MLPA, and Sanger sequencing were considered for genetic analysis. RESULTS Around 53.57% and 39.28% patients had USH1 and USH2, respectively; 17.85% cases (n = 5/28) had no known mutation. Eleven (73.33%) subjects showed variations in USH1 associated genes MYO7A (72.72%), CDH23 (9.09%), PCDH15 (9.09%), and USH1C (9.09%). Eleven mutations are detected in MYO7A where 54.54% are novel. MYO7A: p.Q18* was most frequent (27.27%) mutation and is associated with early manifestation and most severe clinical picture. Two novel mutations (p.E1301* and c.158-?_318+?del) are detected in PCDH15 gene. Around 90.90% patients suspected to be USH2 are confirmed by genetic testing. Eleven mutations detected in the USH2A gene, where 27.27% were novel. Most common USH2A mutation is p.W3955* (50%) followed by p.E767fs, p.R1653*, and c.8682-9A> G (20% each). CONCLUSION The Russian USH cohort shows both novel and known USH mutations. Clinically the prevalence of USH2 is low (39.28%) and the frequency of MYO7A mutations responsible for USH1B is very high (63.63%, N = 7/11) compared to other cohorts. These seven patients carrying MYO7A mutations are preliminarily eligible for the UshStat® gene therapy.
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Affiliation(s)
| | - Vladimir N Trubilin
- b Center of Ophthalmology , Federal Medical-Biological Agency State Research Center , Burnasyan, Moscow , Russia
| | | | | | - Vladimir V Strelnikov
- e Federal State Budgetary Institution , Research Centre for Medical Genetics , Moscow , Russia
| | - Alexander S Tanas
- e Federal State Budgetary Institution , Research Centre for Medical Genetics , Moscow , Russia
| | - Olga M Orlova
- b Center of Ophthalmology , Federal Medical-Biological Agency State Research Center , Burnasyan, Moscow , Russia
| | - Anton S Machalov
- f Surdology and Otoneurology Departments , Scientific and Clinical Center for Otorhinolaryngology of FMBA of Russia , Moscow , Russia
| | - Kira V Overchenko
- f Surdology and Otoneurology Departments , Scientific and Clinical Center for Otorhinolaryngology of FMBA of Russia , Moscow , Russia
| | - Tatiana V Markova
- e Federal State Budgetary Institution , Research Centre for Medical Genetics , Moscow , Russia
| | - Daria M Golenkova
- b Center of Ophthalmology , Federal Medical-Biological Agency State Research Center , Burnasyan, Moscow , Russia
| | - Kirill I Anoshkin
- e Federal State Budgetary Institution , Research Centre for Medical Genetics , Moscow , Russia
| | - Ilya V Volodin
- e Federal State Budgetary Institution , Research Centre for Medical Genetics , Moscow , Russia
| | - Dmitry V Zaletaev
- g Laboratory of Medical Genetics, Institute of Molecular Medicine , I. M. Sechenov First Moscow State Medical University , Moscow , Russia
| | - Andrey A Pulin
- h Laboratory of Cell Biology and Developmental Pathology , Federal State Budgetary Scientific Institution "Institute of General Pathology and Pathophysiology" , Moscow , Russia
| | - Irina I Nadelyaeva
- i Federal State Budget Institution of Higher Education , A.I. Yevdokimov Moscow State University of Medicine and Dentistry, The Ministry of Health Care of the Russia
| | - Alexey I Kalinkin
- e Federal State Budgetary Institution , Research Centre for Medical Genetics , Moscow , Russia.,g Laboratory of Medical Genetics, Institute of Molecular Medicine , I. M. Sechenov First Moscow State Medical University , Moscow , Russia
| | - Debmalya Barh
- j Center for Genomics and Applied Gene Technology , Institute of Integrative Omics and Applied Biotechnology (IIOAB) , Nonakuri, Purba Medinipur , West Bengal , India.,k Division of Bioinformatics and Computational Genomics , NITTE University Center for Science Education and Research (NUCSER), NITTE (Deemed to be University) , Mangaluru , Karnataka , India
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Gupta S, Chatterjee S, Mukherjee A, Mutsuddi M. Whole exome sequencing: Uncovering causal genetic variants for ocular diseases. Exp Eye Res 2017; 164:139-150. [PMID: 28844620 DOI: 10.1016/j.exer.2017.08.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/22/2017] [Accepted: 08/22/2017] [Indexed: 01/23/2023]
Abstract
Identification of causal genetic defects for human diseases took a significant leap when the first generation DNA sequencing technologies enabled biologists extract sequence-based genetic information from living beings. However, these sequencing methods had unavoidable constraints of throughput, scalability, rapidity, and resolution. In this direction, next-generation sequencing (NGS) since the time of its advent has revolutionized the process of gene discovery for both monogenic and multifactorial genetic diseases. Among several variations of NGS, whole exome sequencing (WES) has emerged as a smart strategy that enables identification of disease causing variants present within the coding region of the human genome. The current review focuses primarily on the application of WES in identification of causal variants for ocular diseases. WES has successfully revealed pathogenic variants in a variety of ocular diseases such as retinal degenerations, refractive errors, lens diseases, corneal dystrophies, and developmental ocular defects. It has demonstrated immense potential for molecular diagnosis of genetic ocular diseases. WES has been extensively used in Mendelian and complex cases, familial and sporadic cases, simplex and multiplex cases, and syndromic and non-syndromic cases of ocular diseases. Although many such ocular diseases have been investigated using WES, reports indicate that it has been employed overwhelmingly for heterogeneous retinal degenerations. WES, within a short period of time, has proved to be a cost-effective and promising approach for understanding the genetic basis of ocular diseases.
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Affiliation(s)
- Shashank Gupta
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Souradip Chatterjee
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Ashim Mukherjee
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Mousumi Mutsuddi
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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Ben-Rebeh I, Grati M, Bonnet C, Bouassida W, Hadjamor I, Ayadi H, Ghorbel A, Petit C, Masmoudi S. Genetic analysis of Tunisian families with Usher syndrome type 1: toward improving early molecular diagnosis. Mol Vis 2016; 22:827-35. [PMID: 27440999 PMCID: PMC4950652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 07/16/2016] [Indexed: 10/26/2022] Open
Abstract
PURPOSE Usher syndrome accounts for about 50% of all hereditary deaf-blindness cases. The most severe form of this syndrome, Usher syndrome type I (USH1), is characterized by profound congenital sensorineural deafness, vestibular dysfunction, and retinitis pigmentosa. Six USH1 genes have been identified, MYO7A, CDH23, PCDH15, USH1C, SANS, and CIB2, encoding myosin VIIA, cadherin-23, protocadherin-15, harmonin, scaffold protein containing ankyrin repeats and a sterile alpha motif (SAM) domain, and calcium- and integrin-binding member 2, respectively. METHODS In the present study, we recruited four Tunisian families with a diagnosis of USH1, together with healthy unrelated controls. Affected members underwent detailed audiologic and ocular examinations. We used the North African Deafness (NADf) chip to search for known North African mutations associated with USH. Then, we selected microsatellite markers covering USH1 known loci to genotype the DNA samples. Finally, we performed DNA sequencing of three known USH1 genes: MYO7A, PCDH15, and USH1C. RESULTS Four biallelic mutations, all single base changes, were found in the MYO7A, USH1C, and PCDH15 genes. These mutations consist of a previously reported splicing defect c.470+1G>A in MYO7A, three novel variants, including two nonsense (p.Arg3X and p.Arg134X) in USH1C and PCDH15, respectively, and one frameshift (p.Lys615Asnfs*6) in MYO7A. CONCLUSIONS We found a remarkable genetic heterogeneity in the studied families with USH1 with a variety of mutations, among which three were novel. These novel mutations will be included in the NADf mutation screening chip that will allow a higher diagnosis efficiency of this extremely genetically heterogeneous disease. Ultimately, efficient molecular diagnosis of USH in a patient's early childhood is of utmost importance, allowing better educational and therapeutic management.
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Affiliation(s)
- Imen Ben-Rebeh
- Laboratoire de Procédés de criblage moléculaire et cellulaire, Centre de Biotechnologie de Sfax, Université de Sfax, Tunisie
| | - Mhamed Grati
- Unité de Génétique et Physiologie de l'Audition, INSERM UMRS 1120, Institut Pasteur, Paris, France
| | | | - Walid Bouassida
- Service d'Ophtalmologie, C.H.U. H. Bourguiba de Sfax, Tunisie
| | - Imen Hadjamor
- Laboratoire de Procédés de criblage moléculaire et cellulaire, Centre de Biotechnologie de Sfax, Université de Sfax, Tunisie
| | - Hammadi Ayadi
- Laboratoire de Procédés de criblage moléculaire et cellulaire, Centre de Biotechnologie de Sfax, Université de Sfax, Tunisie
| | | | - Christine Petit
- Unité de Génétique et Physiologie de l'Audition, INSERM UMRS 1120, Institut Pasteur, Paris, France; INSERM UMRS 1120, Institut de la Vision, Paris, France; Collège de France, Paris, France
| | - Saber Masmoudi
- Laboratoire de Procédés de criblage moléculaire et cellulaire, Centre de Biotechnologie de Sfax, Université de Sfax, Tunisie
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Whole-exome sequencing identifies USH2A mutations in a pseudo-dominant Usher syndrome family. Int J Mol Med 2015; 36:1035-41. [PMID: 26310143 PMCID: PMC4564089 DOI: 10.3892/ijmm.2015.2322] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 08/17/2015] [Indexed: 11/05/2022] Open
Abstract
Usher syndrome (USH) is an autosomal recessive (AR) multi-sensory degenerative disorder leading to deaf-blindness. USH is clinically subdivided into three subclasses, and 10 genes have been identified thus far. Clinical and genetic heterogeneities in USH make a precise diagnosis difficult. A dominant-like USH family in successive generations was identified, and the present study aimed to determine the genetic predisposition of this family. Whole-exome sequencing was performed in two affected patients and an unaffected relative. Systematic data were analyzed by bioinformatic analysis to remove the candidate mutations via step-wise filtering. Direct Sanger sequencing and co-segregation analysis were performed in the pedigree. One novel and two known mutations in the USH2A gene were identified, and were further confirmed by direct sequencing and co-segregation analysis. The affected mother carried compound mutations in the USH2A gene, while the unaffected father carried a heterozygous mutation. The present study demonstrates that whole-exome sequencing is a robust approach for the molecular diagnosis of disorders with high levels of genetic heterogeneity.
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Marfany G, Gonzàlez-Duarte R. Clinical applications of high-throughput genetic diagnosis in inherited retinal dystrophies: Present challenges and future directions. World J Med Genet 2015; 5:14-22. [DOI: 10.5496/wjmg.v5.i2.14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 12/30/2014] [Accepted: 02/09/2015] [Indexed: 02/06/2023] Open
Abstract
The advent of next generation sequencing (NGS) techniques has greatly simplified the molecular diagnosis and gene identification in very rare and highly heterogeneous Mendelian disorders. Over the last two years, these approaches, especially whole exome sequencing (WES), alone or combined with homozygosity mapping and linkage analysis, have proved to be successful in the identification of more than 25 new causative retinal dystrophy genes. NGS-approaches have also identified a wealth of new mutations in previously reported genes and have provided more comprehensive information concerning the landscape of genotype-phenotype correlations and the genetic complexity/diversity of human control populations. Although whole genome sequencing is far more informative than WES, the functional meaning of the genetic variants identified by the latter can be more easily interpreted, and final diagnosis of inherited retinal dystrophies is extremely successful, reaching 80%, particularly for recessive cases. Even considering the present limitations of WES, the reductions in costs and time, the continual technical improvements, the implementation of refined bioinformatic tools and the unbiased comprehensive genetic information it provides, make WES a very promising diagnostic tool for routine clinical and genetic diagnosis in the future.
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Sodi A, Mariottini A, Passerini I, Murro V, Tachyla I, Bianchi B, Menchini U, Torricelli F. MYO7A and USH2A gene sequence variants in Italian patients with Usher syndrome. Mol Vis 2014; 20:1717-31. [PMID: 25558175 PMCID: PMC4279600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 12/20/2014] [Indexed: 10/28/2022] Open
Abstract
PURPOSE To analyze the spectrum of sequence variants in the MYO7A and USH2A genes in a group of Italian patients affected by Usher syndrome (USH). METHODS Thirty-six Italian patients with a diagnosis of USH were recruited. They received a standard ophthalmologic examination, visual field testing, optical coherence tomography (OCT) scan, and electrophysiological tests. Fluorescein angiography and fundus autofluorescence imaging were performed in selected cases. All the patients underwent an audiologic examination for the 0.25-8,000 Hz frequencies. Vestibular function was evaluated with specific tests. DNA samples were analyzed for sequence variants of the MYO7A gene (for USH1) and the USH2A gene (for USH2) with direct sequencing techniques. A few patients were analyzed for both genes. RESULTS In the MYO7A gene, ten missense variants were found; three patients were compound heterozygous, and two were homozygous. Thirty-four USH2A gene variants were detected, including eight missense variants, nine nonsense variants, six splicing variants, and 11 duplications/deletions; 19 patients were compound heterozygous, and three were homozygous. Four MYO7A and 17 USH2A variants have already been described in the literature. Among the novel mutations there are four USH2A large deletions, detected with multiplex ligation dependent probe amplification (MLPA) technology. Two potentially pathogenic variants were found in 27 patients (75%). Affected patients showed variable clinical pictures without a clear genotype-phenotype correlation. CONCLUSIONS Ten variants in the MYO7A gene and 34 variants in the USH2A gene were detected in Italian patients with USH at a high detection rate. A selective analysis of these genes may be valuable for molecular analysis, combining diagnostic efficiency with little time wastage and less resource consumption.
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Affiliation(s)
- Andrea Sodi
- Department of Ophthalmology, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Alessandro Mariottini
- Department of Genetic Diagnosis, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Ilaria Passerini
- Department of Genetic Diagnosis, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Vittoria Murro
- Department of Ophthalmology, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Iryna Tachyla
- Department of Ophthalmology, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Benedetta Bianchi
- Department of Otolaryngology, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Ugo Menchini
- Department of Ophthalmology, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Francesca Torricelli
- Department of Genetic Diagnosis, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
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Aparisi MJ, Aller E, Fuster-García C, García-García G, Rodrigo R, Vázquez-Manrique RP, Blanco-Kelly F, Ayuso C, Roux AF, Jaijo T, Millán JM. Targeted next generation sequencing for molecular diagnosis of Usher syndrome. Orphanet J Rare Dis 2014; 9:168. [PMID: 25404053 PMCID: PMC4245769 DOI: 10.1186/s13023-014-0168-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 10/27/2014] [Indexed: 11/17/2022] Open
Abstract
Background Usher syndrome is an autosomal recessive disease that associates sensorineural hearing loss, retinitis pigmentosa and, in some cases, vestibular dysfunction. It is clinically and genetically heterogeneous. To date, 10 genes have been associated with the disease, making its molecular diagnosis based on Sanger sequencing, expensive and time-consuming. Consequently, the aim of the present study was to develop a molecular diagnostics method for Usher syndrome, based on targeted next generation sequencing. Methods A custom HaloPlex panel for Illumina platforms was designed to capture all exons of the 10 known causative Usher syndrome genes (MYO7A, USH1C, CDH23, PCDH15, USH1G, CIB2, USH2A, GPR98, DFNB31 and CLRN1), the two Usher syndrome-related genes (HARS and PDZD7) and the two candidate genes VEZT and MYO15A. A cohort of 44 patients suffering from Usher syndrome was selected for this study. This cohort was divided into two groups: a test group of 11 patients with known mutations and another group of 33 patients with unknown mutations. Results Forty USH patients were successfully sequenced, 8 USH patients from the test group and 32 patients from the group composed of USH patients without genetic diagnosis. We were able to detect biallelic mutations in one USH gene in 22 out of 32 USH patients (68.75%) and to identify 79.7% of the expected mutated alleles. Fifty-three different mutations were detected. These mutations included 21 missense, 8 nonsense, 9 frameshifts, 9 intronic mutations and 6 large rearrangements. Conclusions Targeted next generation sequencing allowed us to detect both point mutations and large rearrangements in a single experiment, minimizing the economic cost of the study, increasing the detection ratio of the genetic cause of the disease and improving the genetic diagnosis of Usher syndrome patients.
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Affiliation(s)
- María J Aparisi
- Grupo de Investigación en Enfermedades Neurosensoriales. Instituto de Investigación Sanitaria IIS-La Fe, Semisótano Escuela de Enfermería, Hospital Universitario La Fe, Avda. Campanar, 21, 46009, Valencia, Spain. .,CIBER de Enfermedades Raras (CIBERER), Valencia, Spain.
| | - Elena Aller
- Grupo de Investigación en Enfermedades Neurosensoriales. Instituto de Investigación Sanitaria IIS-La Fe, Semisótano Escuela de Enfermería, Hospital Universitario La Fe, Avda. Campanar, 21, 46009, Valencia, Spain. .,CIBER de Enfermedades Raras (CIBERER), Valencia, Spain.
| | - Carla Fuster-García
- Grupo de Investigación en Enfermedades Neurosensoriales. Instituto de Investigación Sanitaria IIS-La Fe, Semisótano Escuela de Enfermería, Hospital Universitario La Fe, Avda. Campanar, 21, 46009, Valencia, Spain.
| | - Gema García-García
- Grupo de Investigación en Enfermedades Neurosensoriales. Instituto de Investigación Sanitaria IIS-La Fe, Semisótano Escuela de Enfermería, Hospital Universitario La Fe, Avda. Campanar, 21, 46009, Valencia, Spain. .,CHU Montpellier, Laboratoire de Génétique Moléculaire and Inserm, U827, Montpellier, F-34000, France.
| | - Regina Rodrigo
- Grupo de Investigación en Enfermedades Neurosensoriales. Instituto de Investigación Sanitaria IIS-La Fe, Semisótano Escuela de Enfermería, Hospital Universitario La Fe, Avda. Campanar, 21, 46009, Valencia, Spain. .,CIBER de Enfermedades Raras (CIBERER), Valencia, Spain.
| | - Rafael P Vázquez-Manrique
- Grupo de Investigación en Enfermedades Neurosensoriales. Instituto de Investigación Sanitaria IIS-La Fe, Semisótano Escuela de Enfermería, Hospital Universitario La Fe, Avda. Campanar, 21, 46009, Valencia, Spain. .,CIBER de Enfermedades Raras (CIBERER), Valencia, Spain.
| | - Fiona Blanco-Kelly
- CIBER de Enfermedades Raras (CIBERER), Valencia, Spain. .,Servicio de Genética, IIS - Fundación Jiménez Díaz, University Hospital, UAM, Madrid, Spain.
| | - Carmen Ayuso
- CIBER de Enfermedades Raras (CIBERER), Valencia, Spain. .,Servicio de Genética, IIS - Fundación Jiménez Díaz, University Hospital, UAM, Madrid, Spain.
| | - Anne-Françoise Roux
- CHU Montpellier, Laboratoire de Génétique Moléculaire and Inserm, U827, Montpellier, F-34000, France.
| | - Teresa Jaijo
- Grupo de Investigación en Enfermedades Neurosensoriales. Instituto de Investigación Sanitaria IIS-La Fe, Semisótano Escuela de Enfermería, Hospital Universitario La Fe, Avda. Campanar, 21, 46009, Valencia, Spain. .,CIBER de Enfermedades Raras (CIBERER), Valencia, Spain.
| | - José M Millán
- Grupo de Investigación en Enfermedades Neurosensoriales. Instituto de Investigación Sanitaria IIS-La Fe, Semisótano Escuela de Enfermería, Hospital Universitario La Fe, Avda. Campanar, 21, 46009, Valencia, Spain. .,CIBER de Enfermedades Raras (CIBERER), Valencia, Spain. .,Unidad de Genética y Diagnóstico Prenatal, Hospital Universitario y Politécnico La Fe, Valencia, Spain.
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García-García G, Aller E, Jaijo T, Aparisi MJ, Larrieu L, Faugère V, Blanco-Kelly F, Ayuso C, Roux AF, Millán JM. Novel deletions involving the USH2A gene in patients with Usher syndrome and retinitis pigmentosa. Mol Vis 2014; 20:1398-410. [PMID: 25352746 PMCID: PMC4173666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 09/23/2014] [Indexed: 10/29/2022] Open
Abstract
PURPOSE The aim of the present work was to identify and characterize large rearrangements involving the USH2A gene in patients with Usher syndrome and nonsyndromic retinitis pigmentosa. METHODS The multiplex ligation-dependent probe amplification (MLPA) technique combined with a customized array-based comparative genomic hybridization (aCGH) analysis was applied to 40 unrelated patients previously screened for point mutations in the USH2A gene in which none or only one pathologic mutation was identified. RESULTS We detected six large deletions involving USH2A in six out of the 40 cases studied. Three of the patients were homozygous for the deletion, and the remaining three were compound heterozygous with a previously identified USH2A point mutation. In five of these cases, the patients displayed Usher type 2, and the remaining case displayed nonsyndromic retinitis pigmentosa. The exact breakpoint junctions of the deletions found in USH2A in four of these cases were characterized. CONCLUSIONS Our study highlights the need to develop improved efficient strategies of mutation screening based upon next generation sequencing (NGS) that reduce cost, time, and complexity and allow simultaneous identification of all types of disease-causing mutations in diagnostic procedures.
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Affiliation(s)
- Gema García-García
- Grupo de Investigación en Enfermedades Neurosensoriales, Instituto de Investigación Sanitaria La Fe (IIS-La Fe), Valencia, Spain,Inserm, U827, Montpellier, F-34000, France
| | - Elena Aller
- Grupo de Investigación en Enfermedades Neurosensoriales, Instituto de Investigación Sanitaria La Fe (IIS-La Fe), Valencia, Spain,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Teresa Jaijo
- Grupo de Investigación en Enfermedades Neurosensoriales, Instituto de Investigación Sanitaria La Fe (IIS-La Fe), Valencia, Spain,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Maria J. Aparisi
- Grupo de Investigación en Enfermedades Neurosensoriales, Instituto de Investigación Sanitaria La Fe (IIS-La Fe), Valencia, Spain,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Lise Larrieu
- CHU Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, F-34000, France
| | - Valérie Faugère
- CHU Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, F-34000, France
| | | | - Carmen Ayuso
- CIBER de Enfermedades Raras (CIBERER), Madrid, Spain,Servicio de Genetica, IIS - Fundación Jiménez Diaz, UAM, Madrid, Spain
| | - Anne-Francoise Roux
- Inserm, U827, Montpellier, F-34000, France,CHU Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, F-34000, France
| | - José M. Millán
- Grupo de Investigación en Enfermedades Neurosensoriales, Instituto de Investigación Sanitaria La Fe (IIS-La Fe), Valencia, Spain,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain,Unidad de Genética y Diagnóstico Prenatal, Hospital Universitario y Politécnico La Fe, Valencia, Spain
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14
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Krawitz PM, Schiska D, Krüger U, Appelt S, Heinrich V, Parkhomchuk D, Timmermann B, Millan JM, Robinson PN, Mundlos S, Hecht J, Gross M. Screening for single nucleotide variants, small indels and exon deletions with a next-generation sequencing based gene panel approach for Usher syndrome. Mol Genet Genomic Med 2014; 2:393-401. [PMID: 25333064 PMCID: PMC4190874 DOI: 10.1002/mgg3.92] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 05/13/2014] [Accepted: 05/13/2014] [Indexed: 12/11/2022] Open
Abstract
Usher syndrome is an autosomal recessive disorder characterized both by deafness and blindness. For the three clinical subtypes of Usher syndrome causal mutations in altogether 12 genes and a modifier gene have been identified. Due to the genetic heterogeneity of Usher syndrome, the molecular analysis is predestined for a comprehensive and parallelized analysis of all known genes by next-generation sequencing (NGS) approaches. We describe here the targeted enrichment and deep sequencing for exons of Usher genes and compare the costs and workload of this approach compared to Sanger sequencing. We also present a bioinformatics analysis pipeline that allows us to detect single-nucleotide variants, short insertions and deletions, as well as copy number variations of one or more exons on the same sequence data. Additionally, we present a flexible in silico gene panel for the analysis of sequence variants, in which newly identified genes can easily be included. We applied this approach to a cohort of 44 Usher patients and detected biallelic pathogenic mutations in 35 individuals and monoallelic mutations in eight individuals of our cohort. Thirty-nine of the sequence variants, including two heterozygous deletions comprising several exons of USH2A, have not been reported so far. Our NGS-based approach allowed us to assess single-nucleotide variants, small indels, and whole exon deletions in a single test. The described diagnostic approach is fast and cost-effective with a high molecular diagnostic yield.
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Affiliation(s)
- Peter M Krawitz
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin Berlin, Germany
| | - Daniela Schiska
- Department of Audiology and Phoniatrics, Charité Universitätsmedizin Berlin Berlin, Germany
| | - Ulrike Krüger
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin Berlin, Germany
| | - Sandra Appelt
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin Berlin, Germany
| | - Verena Heinrich
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin Berlin, Germany
| | - Dmitri Parkhomchuk
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin Berlin, Germany
| | | | - Jose M Millan
- Unidad de Genetica, Hospital Universitario La Fe and CIBERER Valencia, Spain
| | - Peter N Robinson
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin Berlin, Germany
| | - Stefan Mundlos
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin Berlin, Germany
| | - Jochen Hecht
- Berlin Brandenburg Center for Regenerative Therapies BCRT Berlin, Germany
| | - Manfred Gross
- Department of Audiology and Phoniatrics, Charité Universitätsmedizin Berlin Berlin, Germany
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15
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The retinal phenotype of Usher syndrome: pathophysiological insights from animal models. C R Biol 2014; 337:167-77. [PMID: 24702843 DOI: 10.1016/j.crvi.2013.12.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 12/03/2013] [Indexed: 01/26/2023]
Abstract
The Usher syndrome (USH) is the most prevalent cause of inherited deaf-blindness. Three clinical subtypes, USH1-3, have been defined, and ten USH genes identified. The hearing impairment due to USH gene defects has been shown to result from improper organisation of the hair bundle, the sound receptive structure of sensory hair cells. In contrast, the cellular basis of the visual defect is less well understood as this phenotype is absent in almost all the USH mouse models that faithfully mimic the human hearing impairment. Structural and molecular interspecies discrepancies regarding photoreceptor calyceal processes and the association with the distribution of USH1 proteins have recently been unravelled, and have led to the conclusion that a defect in the USH1 protein complex-mediated connection between the photoreceptor outer segment and the surrounding calyceal processes (in both rods and cones), and the inner segment (in rods only), probably causes the USH1 retinal dystrophy in humans.
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Abstract
Genetics has been revolutionised by recent technologies. The latest addition to these advances is next-generation sequencing, which is set to transform clinical diagnostics in every branch of medicine. In the research arena this has already been instrumental in identifying hundreds of novel genetic syndromes, making a molecular diagnosis possible for the first time in numerous refractory cases. However, the pace of change has left many clinicians bewildered by new terminology and the implications of next-generation sequencing for their clinical practice. The rapid developments have also left many diagnostic laboratories struggling to implement these new technologies with limited resources. This review explains the basic concepts of next-generation sequencing, gives examples of its role in clinically applied research and examines the challenges of its introduction into clinical practice.
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de Castro-Miró M, Pomares E, Lorés-Motta L, Tonda R, Dopazo J, Marfany G, Gonzàlez-Duarte R. Combined genetic and high-throughput strategies for molecular diagnosis of inherited retinal dystrophies. PLoS One 2014; 9:e88410. [PMID: 24516651 PMCID: PMC3917917 DOI: 10.1371/journal.pone.0088410] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 01/06/2014] [Indexed: 12/30/2022] Open
Abstract
Most diagnostic laboratories are confronted with the increasing demand for molecular diagnosis from patients and families and the ever-increasing genetic heterogeneity of visual disorders. Concerning Retinal Dystrophies (RD), almost 200 causative genes have been reported to date, and most families carry private mutations. We aimed to approach RD genetic diagnosis using all the available genetic information to prioritize candidates for mutational screening, and then restrict the number of cases to be analyzed by massive sequencing. We constructed and optimized a comprehensive cosegregation RD-chip based on SNP genotyping and haplotype analysis. The RD-chip allows to genotype 768 selected SNPs (closely linked to 100 RD causative genes) in a single cost-, time-effective step. Full diagnosis was attained in 17/36 Spanish pedigrees, yielding 12 new and 12 previously reported mutations in 9 RD genes. The most frequently mutated genes were USH2A and CRB1. Notably, RD3–up to now only associated to Leber Congenital Amaurosis– was identified as causative of Retinitis Pigmentosa. The main assets of the RD-chip are: i) the robustness of the genetic information that underscores the most probable candidates, ii) the invaluable clues in cases of shared haplotypes, which are indicative of a common founder effect, and iii) the detection of extended haplotypes over closely mapping genes, which substantiates cosegregation, although the assumptions in which the genetic analysis is based could exceptionally lead astray. The combination of the genetic approach with whole exome sequencing (WES) greatly increases the diagnosis efficiency, and revealed novel mutations in USH2A and GUCY2D. Overall, the RD-chip diagnosis efficiency ranges from 16% in dominant, to 80% in consanguineous recessive pedigrees, with an average of 47%, well within the upper range of massive sequencing approaches, highlighting the validity of this time- and cost-effective approach whilst high-throughput methodologies become amenable for routine diagnosis in medium sized labs.
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Affiliation(s)
- Marta de Castro-Miró
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Esther Pomares
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Laura Lorés-Motta
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Raul Tonda
- Centre Nacional d’Anàlisi Genòmica, PCB, Barcelona, Spain
| | - Joaquín Dopazo
- Department of Computational Genomics, Centro de Investigación Príncipe Felipe, Valencia, Spain
- BIER, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Gemma Marfany
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Roser Gonzàlez-Duarte
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
- * E-mail:
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18
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Exome sequencing greatly expedites the progressive research of Mendelian diseases. Front Med 2014; 8:42-57. [PMID: 24384736 DOI: 10.1007/s11684-014-0303-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 09/30/2013] [Indexed: 12/23/2022]
Abstract
The advent of whole-exome sequencing (WES) has facilitated the discovery of rare structure and functional genetic variants. Combining exome sequencing with linkage studies is one of the most efficient strategies in searching disease genes for Mendelian diseases. WES has achieved great success in the past three years for Mendelian disease genetics and has identified over 150 new Mendelian disease genes. We illustrate the workflow of exome capture and sequencing to highlight the advantages of WES. We also indicate the progress and limitations of WES that can potentially result in failure to identify disease-causing mutations in part of patients. With an affordable cost, WES is expected to become the most commonly used tool for Mendelian disease gene identification. The variants detected cumulatively from previous WES studies will be widely used in future clinical services.
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Davies WI. Challenges using diagnostic next-generation sequencing in the clinical environment for inherited retinal disorders. Per Med 2014; 11:99-111. [PMID: 29751394 DOI: 10.2217/pme.13.95] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Visual impairment, and in particular the inherited retinopathies, is a significant problem worldwide. Many disorders are progressive so their early and accurate detection is crucial to the development and application of appropriate disease management and treatment strategies, some of which are currently being tested in clinical trials. Over the past few decades, the identification of genetic causes that mediate many inherited diseases has largely been based on traditional 'Sanger sequencing' and microchip approaches that are expensive and time consuming. However, with the advent of next-generation sequencing it is now possible to apply high-throughput technologies to the clinical arena and sequence the entire exome or genome of an affected individual. Despite the potential for a paradigm shift in the clinical diagnosis of retinal disease, it may prove difficult to interpret and confirm the pathogenicity of any variants discovered by next-generation sequencing pipelines. In this review, I examine the application of next-generation sequencing to inherited retinal disorders and discuss current limitations and future perspectives.
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Affiliation(s)
- Wayne Il Davies
- School of Animal Biology & University of Western Australia Oceans Institute, University of Western Australia, 35 Stirling Highway, Perth, Western Australia, WA 6009, Australia.
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Besnard T, García-García G, Baux D, Vaché C, Faugère V, Larrieu L, Léonard S, Millan JM, Malcolm S, Claustres M, Roux AF. Experience of targeted Usher exome sequencing as a clinical test. Mol Genet Genomic Med 2013; 2:30-43. [PMID: 24498627 PMCID: PMC3907913 DOI: 10.1002/mgg3.25] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 06/06/2013] [Indexed: 12/15/2022] Open
Abstract
We show that massively parallel targeted sequencing of 19 genes provides a new and reliable strategy for molecular diagnosis of Usher syndrome (USH) and nonsyndromic deafness, particularly appropriate for these disorders characterized by a high clinical and genetic heterogeneity and a complex structure of several of the genes involved. A series of 71 patients including Usher patients previously screened by Sanger sequencing plus newly referred patients was studied. Ninety-eight percent of the variants previously identified by Sanger sequencing were found by next-generation sequencing (NGS). NGS proved to be efficient as it offers analysis of all relevant genes which is laborious to reach with Sanger sequencing. Among the 13 newly referred Usher patients, both mutations in the same gene were identified in 77% of cases (10 patients) and one candidate pathogenic variant in two additional patients. This work can be considered as pilot for implementing NGS for genetically heterogeneous diseases in clinical service.
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Affiliation(s)
- Thomas Besnard
- U827, Inserm Montpellier, F-34000, France ; Univ, Montpellier I Montpellier, F-34000, France
| | - Gema García-García
- U827, Inserm Montpellier, F-34000, France ; Grupo de Investigación en Enfermedades Neurosensoriales, Instituto de Investigación Sanitaria IIS-La Fe and CIBERER Valencia, Spain
| | - David Baux
- Laboratoire de Génétique Moléculaire, CHU Montpellier Montpellier, F-34000, France
| | - Christel Vaché
- Laboratoire de Génétique Moléculaire, CHU Montpellier Montpellier, F-34000, France
| | - Valérie Faugère
- Laboratoire de Génétique Moléculaire, CHU Montpellier Montpellier, F-34000, France
| | - Lise Larrieu
- Laboratoire de Génétique Moléculaire, CHU Montpellier Montpellier, F-34000, France
| | - Susana Léonard
- Laboratoire de Génétique Moléculaire, CHU Montpellier Montpellier, F-34000, France
| | - Jose M Millan
- Grupo de Investigación en Enfermedades Neurosensoriales, Instituto de Investigación Sanitaria IIS-La Fe and CIBERER Valencia, Spain
| | - Sue Malcolm
- Clinical and Molecular Genetics, Institute of Child Health, University College London London, United Kingdom
| | - Mireille Claustres
- U827, Inserm Montpellier, F-34000, France ; Univ, Montpellier I Montpellier, F-34000, France ; Laboratoire de Génétique Moléculaire, CHU Montpellier Montpellier, F-34000, France
| | - Anne-Françoise Roux
- U827, Inserm Montpellier, F-34000, France ; Laboratoire de Génétique Moléculaire, CHU Montpellier Montpellier, F-34000, France
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21
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Corton M, Nishiguchi KM, Avila-Fernández A, Nikopoulos K, Riveiro-Alvarez R, Tatu SD, Ayuso C, Rivolta C. Exome sequencing of index patients with retinal dystrophies as a tool for molecular diagnosis. PLoS One 2013; 8:e65574. [PMID: 23940504 PMCID: PMC3683009 DOI: 10.1371/journal.pone.0065574] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/28/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Retinal dystrophies (RD) are a group of hereditary diseases that lead to debilitating visual impairment and are usually transmitted as a Mendelian trait. Pathogenic mutations can occur in any of the 100 or more disease genes identified so far, making molecular diagnosis a rather laborious process. In this work we explored the use of whole exome sequencing (WES) as a tool for identification of RD mutations, with the aim of assessing its applicability in a diagnostic context. METHODOLOGY/PRINCIPAL FINDINGS We ascertained 12 Spanish families with seemingly recessive RD. All of the index patients underwent mutational pre-screening by chip-based sequence hybridization and resulted to be negative for known RD mutations. With the exception of one pedigree, to simulate a standard diagnostic scenario we processed by WES only the DNA from the index patient of each family, followed by in silico data analysis. We successfully identified causative mutations in patients from 10 different families, which were later verified by Sanger sequencing and co-segregation analyses. Specifically, we detected pathogenic DNA variants (∼50% novel mutations) in the genes RP1, USH2A, CNGB3, NMNAT1, CHM, and ABCA4, responsible for retinitis pigmentosa, Usher syndrome, achromatopsia, Leber congenital amaurosis, choroideremia, or recessive Stargardt/cone-rod dystrophy cases. CONCLUSIONS/SIGNIFICANCE Despite the absence of genetic information from other family members that could help excluding nonpathogenic DNA variants, we could detect causative mutations in a variety of genes known to represent a wide spectrum of clinical phenotypes in 83% of the patients analyzed. Considering the constant drop in costs for human exome sequencing and the relative simplicity of the analyses made, this technique could represent a valuable tool for molecular diagnostics or genetic research, even in cases for which no genotypes from family members are available.
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Affiliation(s)
- Marta Corton
- Department of Genetics, IIS- Fundacion Jimenez Diaz, CIBERER, Madrid, Spain
| | - Koji M. Nishiguchi
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | | | | | | | - Sorina D. Tatu
- Department of Genetics, IIS- Fundacion Jimenez Diaz, CIBERER, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics, IIS- Fundacion Jimenez Diaz, CIBERER, Madrid, Spain
| | - Carlo Rivolta
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- * E-mail:
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Dinwiddie DL, Smith LD, Miller NA, Atherton AM, Farrow EG, Strenk ME, Soden SE, Saunders CJ, Kingsmore SF. Diagnosis of mitochondrial disorders by concomitant next-generation sequencing of the exome and mitochondrial genome. Genomics 2013; 102:148-56. [PMID: 23631824 DOI: 10.1016/j.ygeno.2013.04.013] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/18/2013] [Accepted: 04/19/2013] [Indexed: 01/22/2023]
Abstract
Mitochondrial diseases are notoriously difficult to diagnose due to extreme locus and allelic heterogeneity, with both nuclear and mitochondrial genomes potentially liable. Using exome sequencing we demonstrate the ability to rapidly and cost effectively evaluate both the nuclear and mitochondrial genomes to obtain a molecular diagnosis for four patients with three distinct mitochondrial disorders. One patient was found to have Leigh syndrome due to a mutation in MT-ATP6, two affected siblings were discovered to be compound heterozygous for mutations in the NDUFV1 gene, which causes mitochondrial complex I deficiency, and one patient was found to have coenzyme Q10 deficiency due to compound heterozygous mutations in COQ2. In all cases conventional diagnostic testing failed to identify a molecular diagnosis. We suggest that additional studies should be conducted to evaluate exome sequencing as a primary diagnostic test for mitochondrial diseases, including those due to mtDNA mutations.
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Affiliation(s)
- Darrell L Dinwiddie
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA.
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Next generation sequencing (NGS) strategies for the genetic testing of myopathies. ACTA MYOLOGICA : MYOPATHIES AND CARDIOMYOPATHIES : OFFICIAL JOURNAL OF THE MEDITERRANEAN SOCIETY OF MYOLOGY 2012; 31:196-200. [PMID: 23620651 PMCID: PMC3631804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Next generation sequencing (NGS) technologies offer the possibility to map entire genomes at affordable costs. This brings the genetic testing procedure to a higher level of complexity. The positive aspect is the ease to cope with the complex diagnosis of genetically heterogeneous disorders and to identify novel disease genes. Worries arise from the management of too many DNA variations with unpredictable meaning and incidental findings that can cause ethical and clinical dilemmas. The technology of enrichment makes possible to focus the sequencing to the exome or to a more specific DNA target. This is being used to provide insights into the genetics underlying Mendelian traits involved in myopathies and to set up cost-effective diagnostic tests. This huge potential of the NGS applications makes likely that these will soon become the first approach in genetic diagnostic laboratories.
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