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Zhao H, Du C, Yang G, Wang Y. Diagnosis, treatment, and research status of rare diseases related to birth defects. Intractable Rare Dis Res 2023; 12:148-160. [PMID: 37662624 PMCID: PMC10468410 DOI: 10.5582/irdr.2023.01052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 09/05/2023] Open
Abstract
Rare diseases are diseases that occur at low prevalence, and most of them are chronic and serious diseases that are often life-threatening. Currently, there is no unified definition for rare diseases. The diagnosis, treatment, and research of rare diseases have become the focus of medicine and biopharmacology, as well as the breakthrough point of clinical and basic research. Birth defects are the hard-hit area of rare diseases and the frontiers of its research. Since most of these defects have a genetic basis, early screening and diagnosis have important scientific value and social significance for the prevention and control of such diseases. At present, there is no effective treatment for most rare diseases, but progress in prenatal diagnosis and screening can prevent the occurrence of diseases and help prevent and treat rare diseases. This article discusses the progress in genetic-related birth defects and rare diseases.
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Affiliation(s)
- Hongjuan Zhao
- Department of Gynecology and Obstetrics, Shandong Provincial Third Hospital, Shandong University, Ji'nan, China
| | - Chen Du
- Department of Gynecology and Obstetrics, Inner Mongolia Medical University Affiliated Hospital, Hohhot, China
| | - Guang Yang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Wang
- Department of Gynecology and Obstetrics, Inner Mongolia Medical University Affiliated Hospital, Hohhot, China
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Ordoñez-Labastida V, Chacon-Camacho OF, Lopez-Rodriguez VR, Zenteno JC. USH2A mutational spectrum causing syndromic and non-syndromic retinal dystrophies in a large cohort of Mexican patients. Mol Vis 2023; 29:31-38. [PMID: 37287646 PMCID: PMC10243674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 04/28/2023] [Indexed: 06/09/2023] Open
Abstract
Background Mutations in the USH2A gene are the leading cause of both non-syndromic autosomal recessive retinitis pigmentosa (RP) and Usher syndrome, a syndromic form of RP characterized by retinal dystrophy and sensorineural hearing loss. To contribute to the expansion of the USH2A-related molecular spectrum, the results of genetic screening in a large cohort of Mexican patients are presented. Methods The study population comprised 61 patients with a clinical diagnosis of either non-syndromic RP (n = 30) or Usher syndrome type 2 (USH2; n = 31) who were demonstrated to carry biallelic pathogenic variants in USH2A in a three-year period. Genetic screening was performed either by gene panel sequencing or by exome sequencing. A total of 72 available first- or second-degree relatives were also genotyped for familial segregation of the identified variants. Results The USH2A mutational spectrum in RP patients included 39 distinct pathogenic variants, most of them of the missense type. The most common RP-causing variants were p.Cys759Phe (c.2276G>T), p.Glu767Serfs*21 (c.2299delG), and p.Cys319Tyr (c.956G>A), which together accounted for 25% of all RP variants. Novel USH2A mutations included three nonsense, two missense, two frameshift, and one intragenic deletion. The USH2A mutational spectrum in USH2 patients included 26 distinct pathogenic variants, most of them of the nonsense and frameshift types. The most common Usher syndrome-causing variants were p.Glu767Serfs*21 (c.2299delG), p.Arg334Trp (c.1000C>T), and c.12067-2A>G), which together accounted for 42% of all USH2-related variants. Novel Usher syndrome USH2A mutations included six nonsense, four frameshift, and two missense mutations. The c.2299delG mutation was associated with a common haplotype for SNPs located in exons 2-21 of USH2A, indicating a founder mutation effect. Conclusions Our work expands the USH2A mutational profile by identifying 20 novel pathogenic variants causing syndromic and non-syndromic retinal dystrophy. The prevalent c.2299delG allele is shown to arise from a founder effect. Our results emphasize the usefulness of molecular screening in underrepresented populations for a better characterization of the molecular spectrum of common monogenic diseases.
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Affiliation(s)
- Vianey Ordoñez-Labastida
- Rare Disease Diagnostic Unit, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
- Department of Genetics, Institute of Ophthalmology “Conde de Valenciana,” Mexico City, Mexico
- Faculty of Medicine, Autonomous University of the State of Morelos (UAEM), Morelos, Mexico
| | - Oscar F. Chacon-Camacho
- Department of Genetics, Institute of Ophthalmology “Conde de Valenciana,” Mexico City, Mexico
- Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, UNAM, Mexico City, Mexico
| | | | - Juan C. Zenteno
- Rare Disease Diagnostic Unit, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
- Department of Genetics, Institute of Ophthalmology “Conde de Valenciana,” Mexico City, Mexico
- Department of Biochemistry, Faculty of Medicine, UNAM, Mexico City, Mexico
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Adhesion G protein-coupled receptors-Structure and functions. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 195:1-25. [PMID: 36707149 DOI: 10.1016/bs.pmbts.2022.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Adhesion G protein-coupled receptors (aGPCRs) are an ancient class of receptors that represent some of the largest transmembrane-integrated proteins in humans. First recognized as surface markers on immune cells, it took more than a decade to appreciate their 7-transmembrane structure, which is reminiscent of GPCRs. Roughly 30 years went by before the first functional proof of an interaction with a G protein was published. Besides classic features of GPCRs (extracellular N terminus, 7-transmembrane region, intracellular C terminus), aGPCRs display a distinct N-terminal structure, which harbors the highly conserved GPCR autoproteolysis-inducing (GAIN) domain with the GPCR proteolysis site (GPS) in addition to several functional domains. Several human diseases have been associated with variants of aGPCRs and subsequent animal models have been established to investigate these phenotypes. Much progress has been made in recent years to decipher the structure and functions of these receptors. This chapter gives an overview of our current understanding with respect to the molecular structural patterns governing aGPCR activation and the contribution of these giant molecules to the development of pathologies.
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Towards a Cure for HARS Disease. Genes (Basel) 2023; 14:genes14020254. [PMID: 36833180 PMCID: PMC9956352 DOI: 10.3390/genes14020254] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/20/2023] Open
Abstract
Histidyl-tRNA synthetase (HARS) ligates histidine to its cognate transfer RNA (tRNAHis). Mutations in HARS cause the human genetic disorders Usher syndrome type 3B (USH3B) and Charcot-Marie-Tooth syndrome type 2W (CMT2W). Treatment for these diseases remains symptomatic, and no disease specific treatments are currently available. Mutations in HARS can lead to destabilization of the enzyme, reduced aminoacylation, and decreased histidine incorporation into the proteome. Other mutations lead to a toxic gain-of-function and mistranslation of non-cognate amino acids in response to histidine codons, which can be rescued by histidine supplementation in vitro. We discuss recent advances in characterizing HARS mutations and potential applications of amino acid and tRNA therapy for future gene and allele specific therapy.
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The Diagnostic Yield of Next Generation Sequencing in Inherited Retinal Diseases: A Systematic Review and Meta-analysis. Am J Ophthalmol 2022; 249:57-73. [PMID: 36592879 DOI: 10.1016/j.ajo.2022.12.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/16/2022] [Accepted: 12/23/2022] [Indexed: 01/01/2023]
Abstract
PURPOSE Accurate genotyping of individuals with inherited retinal diseases (IRD) is essential for patient management and identifying suitable candidates for gene therapies. This study evaluated the diagnostic yield of next generation sequencing (NGS) in IRDs. DESIGN Systematic review and meta-analysis. METHODS This systematic review was prospectively registered (CRD42021293619). Ovid MEDLINE and Ovid Embase were searched on 6 June 2022. Clinical studies evaluating the diagnostic yield of NGS in individuals with IRDs were eligible for inclusion. Risk of bias assessment was performed. Studies were pooled using a random...effects inverse variance model. Sources of heterogeneity were explored using stratified analysis, meta-regression, and sensitivity analysis. RESULTS This study included 105 publications from 28 countries. Most studies (90 studies) used targeted gene panels. The diagnostic yield of NGS was 61.3% (95% confidence interval: 57.8-64.7%; 51 studies) in mixed IRD phenotypes, 58.2% (51.6-64.6%; 41 studies) in rod-cone dystrophies, 57.7% (46.8-68.3%; eight studies) in macular and cone/cone-rod dystrophies, and 47.6% (95% CI: 41.0-54.3%; four studies) in familial exudative vitreoretinopathy. For mixed IRD phenotypes, a higher diagnostic yield was achieved pooling studies published between 2018-2022 (64.2% [59.5-68.7%]), studies using exome sequencing (73.5% [58.9-86.1%]), and studies using the American College of Medical Genetics variant interpretation standards (65.6% [60.8-70.4%]). CONCLUSION The current diagnostic yield of NGS in IRDs is between 52-74%. The certainty of the evidence was judged as low or very low. A key limitation of the current evidence is the significant heterogeneity between studies. Adoption of standardized reporting guidelines could improve confidence in future meta-analyses.
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Ye H, Sun A, Xiao W, Zhang T, Xu Z, Shi L, Sha X, Yang H. Differential Circular RNA Expression Profiling of Orbital Connective Tissue From Patients With Type I and Type II Thyroid-Associated Ophthalmopathy. Invest Ophthalmol Vis Sci 2022; 63:27. [DOI: 10.1167/iovs.63.12.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Huijing Ye
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Anqi Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Wei Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Te Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Zhihui Xu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Lu Shi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xiaotong Sha
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Huasheng Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
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Wang J, Xiao X, Li S, Jiang H, Sun W, Wang P, Zhang Q. Landscape of pathogenic variants in six pre-mRNA processing factor genes for retinitis pigmentosa based on large in-house data sets and database comparisons. Acta Ophthalmol 2022; 100:e1412-e1425. [PMID: 35138024 DOI: 10.1111/aos.15104] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 12/31/2021] [Accepted: 01/20/2022] [Indexed: 12/29/2022]
Abstract
PURPOSE Variants in six genes encoding pre-mRNA processing factors (PRPFs) are a common cause of autosomal dominant retinitis pigmentosa (ADRP). This study aims to determine the characteristics of potential pathogenic variants (PPVs) in the six genes. METHODS Variants in six PRPF genes were identified from in-house exome sequencing data. PPVs were identified based on comparative bioinformatics analysis, clinical phenotypes and the ACMG/AMP guidelines. The features of PPVs were revealed by comparative analysis of in-house data set, gnomAD and previously published literature. RESULTS Totally, 36 heterozygous PPVs, including 19 novels, were detected from 45 families, which contributed to 4.4% (45/1019) of RP cases. These PPVs were distributed in PRPF31 (17/45, 37.8%), SNRNP200 (12/45, 26.7%), PRPF8 (10/45, 22.2%) and PRPF3 (6/45, 13.3%) but not in PRPF6 or PRPF4. Different types of PPVs were predominant in different PRPF genes, such as loss-of-function variants in PRPF31 and missense variants in the five remaining genes. The clustering of PPVs in specific regions was observed in SNRNP200, PRPF8 and PRPF3. The pathogenicity for certain classes of variants in these genes, such as loss-of-function variants in PRPF6 and missense variants in PRPF31 and PRPF4, requires careful consideration and further validation. The predominant fundus changes were early macular involvement, widespread RPE atrophy and pigmentation in the mid- and far-peripheral retina. CONCLUSION Systemic comparative analysis may shed light on the characterization of PPVs in these genes. Our findings provide a brief landscape of PPVs in PRPF genes and the associated phenotypes and emphasize the careful classification of pathogenicity for certain types of variants that warrant further characterization.
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Affiliation(s)
- Junwen Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Hongmei Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Panfeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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Santos DF, Molina Thurin LJ, Gustavo Vargas J, Izquierdo NJ, Oliver A. A Genotype-Phenotype Analysis of Usher Syndrome in Puerto Rico: A Case Series. Cureus 2022; 14:e28213. [PMID: 36003347 PMCID: PMC9392863 DOI: 10.7759/cureus.28213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2022] [Indexed: 11/15/2022] Open
Abstract
Introduction Patients with Usher syndrome (USH) have retinitis pigmentosa (RP) and hearing loss inherited as an autosomal recessive (ar) trait. Mutations in the USH2A gene are the most common cause of Usher syndrome. We report the genotype-phenotype correlation in 10 patients with Usher syndrome from Puerto Rico (PR). This is the first genotype-phenotype analysis of patients with the syndrome in PR. Methods We conducted a chart review of patients who carried an Usher syndrome diagnosis. They underwent a comprehensive ophthalmic evaluation by at least one of the authors. This included best corrected visual acuity (BCVA), visual field mean deviation (VF MD), pattern standard deviation (PSD), and macular optical coherence tomography (mOCT) average volume and thickness. Genotyping was done using the Invitae Inherited Retinal Disease (IRD) Panel. Results Three patients had a logMAR BCVA of 1.0 or worse. The median VF MD was -29.7 dB and -29.2 dB in the OD and OS, respectively. The median PSD was 5.5 dB and 5.7 dB in the OD and OS, respectively. Upon macular OCT, patients had a median volume of 8.4 μm3 and 8 μm3 in the OD and OS, respectively. The median thickness was 235 μm and 223 μm in the OD and OS, respectively. All patients had pathogenic USH2A variants, and eight of these were compound heterozygotes. The most common variants were p.Cys575Tyr and p.Glu767Serfs*21, each present in four patients. Patients with the p.Cys759Phe variant had the worst phenotype with the worst BCVA, largest VF MD, and slimmer macular thickness. Conclusion Our findings are compatible with previously reported pathogenic mutations in the USH2A gene. However, the p.Cys759Phe variant has previously been correlated with a mild phenotype. In our study, the p.Cys759Phe variant correlated with the most severe phenotype. This variant has a high prevalence in the Spanish population, and PR was a Spanish colony for 400 years. The presence of this variant could be traced back to Spain. Genotyping patients with Usher syndrome is of utmost importance. Further studies to evaluate the common founder effect of patients with the syndrome in PR are warranted.
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The genetic and phenotypic landscapes of Usher syndrome: from disease mechanisms to a new classification. Hum Genet 2022; 141:709-735. [PMID: 35353227 PMCID: PMC9034986 DOI: 10.1007/s00439-022-02448-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/04/2022] [Indexed: 12/16/2022]
Abstract
Usher syndrome (USH) is the most common cause of deaf–blindness in humans, with a prevalence of about 1/10,000 (~ 400,000 people worldwide). Cochlear implants are currently used to reduce the burden of hearing loss in severe-to-profoundly deaf patients, but many promising treatments including gene, cell, and drug therapies to restore the native function of the inner ear and retinal sensory cells are under investigation. The traditional clinical classification of Usher syndrome defines three major subtypes—USH1, 2 and 3—according to hearing loss severity and onset, the presence or absence of vestibular dysfunction, and age at onset of retinitis pigmentosa. Pathogenic variants of nine USH genes have been initially reported: MYO7A, USH1C, PCDH15, CDH23, and USH1G for USH1, USH2A, ADGRV1, and WHRN for USH2, and CLRN1 for USH3. Based on the co-occurrence of hearing and vision deficits, the list of USH genes has been extended to few other genes, but with limited supporting information. A consensus on combined criteria for Usher syndrome is crucial for the development of accurate diagnosis and to improve patient management. In recent years, a wealth of information has been obtained concerning the properties of the Usher proteins, related molecular networks, potential genotype–phenotype correlations, and the pathogenic mechanisms underlying the impairment or loss of hearing, balance and vision. The advent of precision medicine calls for a clear and more precise diagnosis of Usher syndrome, exploiting all the existing data to develop a combined clinical/genetic/network/functional classification for Usher syndrome.
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Dal Cortivo G, Dell’Orco D. Calcium- and Integrin-Binding Protein 2 (CIB2) in Physiology and Disease: Bright and Dark Sides. Int J Mol Sci 2022; 23:ijms23073552. [PMID: 35408910 PMCID: PMC8999013 DOI: 10.3390/ijms23073552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/19/2022] [Accepted: 03/22/2022] [Indexed: 12/04/2022] Open
Abstract
Calcium- and integrin-binding protein 2 (CIB2) is a small EF-hand protein capable of binding Mg2+ and Ca2+ ions. While its biological function remains largely unclear, an increasing number of studies have shown that CIB2 is an essential component of the mechano-transduction machinery that operates in cochlear hair cells. Mutations in the gene encoding CIB2 have been associated with non-syndromic deafness. In addition to playing an important role in the physiology of hearing, CIB2 has been implicated in a multitude of very different processes, ranging from integrin signaling in platelets and skeletal muscle to autophagy, suggesting extensive functional plasticity. In this review, we summarize the current understanding of biochemical and biophysical properties of CIB2 and the biological roles that have been proposed for the protein in a variety of processes. We also highlight the many molecular aspects that remain unclarified and deserve further investigation.
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Molina Romero M, Yoldi Chaure A, Gañán Parra M, Navas Bastida P, del Pico Sánchez JL, Vaquero Argüelles Á, de la Fuente Vaquero P, Ramírez López JP, Castilla Alcalá JA. Probability of high-risk genetic matching with oocyte and semen donors: complete gene analysis or genotyping test? J Assist Reprod Genet 2022; 39:341-355. [PMID: 35091964 PMCID: PMC8956772 DOI: 10.1007/s10815-021-02381-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 12/17/2021] [Indexed: 02/03/2023] Open
Abstract
PURPOSE To estimate the probability of high-risk genetic matching when assisted reproductive techniques (ART) are applied with double gamete donation, following an NGS carrier test based on a complete study of the genes concerned. We then determine the results that would have been obtained if the genotyping tests most widely used in Spanish gamete banks had been applied. METHODS In this descriptive observational study, 1818 gamete donors were characterised by NGS. The pathogenic variants detected were analysed to estimate the probability of high-risk genetic matching and to determine the results that would have been obtained if the three most commonly used genotyping tests in ART had been applied. RESULTS The probability of high-risk genetic matching with gamete donation, screened by NGS and complete gene analysis, was 5.5%, versus the 0.6-2.7% that would have been obtained with the genotyping test. A total of 1741 variants were detected, including 607 different variants, of which only 22.6% would have been detected by all three genotyping tests considered and 44.7% of which would not have been detected by any of these tests. CONCLUSION Our study highlights the considerable heterogeneity of the genotyping tests, which present significant differences in their ability to detect pathogenic variants. The complete study of the genes by NGS considerably reduces reproductive risks when genetic matching is performed with gamete donors. Accordingly, we recommend that carrier screening in gamete donors be carried out using NGS and a complete study with nontargeted analysis of the variants of the screened genes.
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Affiliation(s)
- Marta Molina Romero
- CEIFER Biobanco - NextClinics, Calle Maestro Bretón, 1, 18004 Granada, Spain
| | | | | | | | | | | | | | | | - José Antonio Castilla Alcalá
- CEIFER Biobanco - NextClinics, Calle Maestro Bretón, 1, 18004 Granada, Spain ,U. Reproducción, UGC Obstetricia y Ginecología, HU Virgen de Las Nieves, Granada, Spain ,Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain
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Abstract
Usher syndrome (USH) is the most common genetic condition responsible for combined loss of hearing and vision. Balance disorders and bilateral vestibular areflexia are also observed in some cases. The syndrome was first described by Albrecht von Graefe in 1858, but later named by Charles Usher, who presented a large number of cases with hearing loss and retinopathy in 1914. USH has been grouped into three main clinical types: 1, 2, and 3, which are caused by mutations in different genes and are further divided into different subtypes. To date, nine causative genes have been identified and confirmed as responsible for the syndrome when mutated: MYO7A, USH1C, CDH23, PCDH15, and USH1G (SANS) for Usher type 1; USH2A, ADGRV1, and WHRN for Usher type 2; CLRN1 for Usher type 3. USH is inherited in an autosomal recessive pattern. Digenic, bi-allelic, and polygenic forms have also been reported, in addition to dominant or nonsyndromic forms of genetic mutations. This narrative review reports the causative forms, diagnosis, prognosis, epidemiology, rehabilitation, research, and new treatments of USH.
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Genetics, pathogenesis and therapeutic developments for Usher syndrome type 2. Hum Genet 2021; 141:737-758. [PMID: 34331125 DOI: 10.1007/s00439-021-02324-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/24/2021] [Indexed: 12/28/2022]
Abstract
Usher syndrome (USH) is a rare, autosomal recessively inherited disorder resulting in a combination of sensorineural hearing loss and a progressive loss of vision resulting from retinitis pigmentosa (RP), occasionally accompanied by an altered vestibular function. More and more evidence is building up indicating that also sleep deprivation, olfactory dysfunction, deficits in tactile perception and reduced sperm motility are part of the disease etiology. USH can be clinically classified into three different types, of which Usher syndrome type 2 (USH2) is the most prevalent. In this review, we, therefore, assess the genetic and clinical aspects, available models and therapeutic developments for USH2. Mutations in USH2A, ADGRV1 and WHRN have been described to be responsible for USH2, with USH2A being the most frequently mutated USH-associated gene, explaining 50% of all cases. The proteins encoded by the USH2 genes together function in a dynamic protein complex that, among others, is found at the photoreceptor periciliary membrane and at the base of the hair bundles of inner ear hair cells. To unravel the pathogenic mechanisms underlying USH2, patient-derived cellular models and animal models including mouse, zebrafish and drosophila, have been generated that all in part mimic the USH phenotype. Multiple cellular and genetic therapeutic approaches are currently under development for USH2, mainly focused on preserving or partially restoring the visual function of which one is already in the clinical phase. These developments are opening a new gate towards a possible treatment for USH2 patients.
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Progressive and Degenerative Peripheral Vestibular Disorders. Otolaryngol Clin North Am 2021; 54:959-971. [PMID: 34301401 DOI: 10.1016/j.otc.2021.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Initial diagnosis of peripheral vestibulopathy requires a detailed history, physical examination, and, in some cases, audiovestibular testing, radiographic imaging, or serology. Differentiation of a peripheral vestibulopathy as progressive or degenerative is often nuanced and influenced by a characterization of a patient's symptoms or natural history over time. A diverse group of vestibular pathology may fit into this category, including Ménière's disease, autoimmune conditions, congenital pathologies, ototoxic medications, radiation therapy, and perilymphatic fistula. Differentiation among these entities may be guided by initial or subsequent symptomatology, with various combinations of audiovestibular testing, serology, and imaging. Treatment options are disparate and disease-specific, ranging from observation to medical management or surgical intervention, underscoring the need for astute investigation and diagnosis.
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Fuster-García C, García-Bohórquez B, Rodríguez-Muñoz A, Aller E, Jaijo T, Millán JM, García-García G. Usher Syndrome: Genetics of a Human Ciliopathy. Int J Mol Sci 2021; 22:ijms22136723. [PMID: 34201633 PMCID: PMC8268283 DOI: 10.3390/ijms22136723] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 12/21/2022] Open
Abstract
Usher syndrome (USH) is an autosomal recessive syndromic ciliopathy characterized by sensorineural hearing loss, retinitis pigmentosa and, sometimes, vestibular dysfunction. There are three clinical types depending on the severity and age of onset of the symptoms; in addition, ten genes are reported to be causative of USH, and six more related to the disease. These genes encode proteins of a diverse nature, which interact and form a dynamic protein network called the “Usher interactome”. In the organ of Corti, the USH proteins are essential for the correct development and maintenance of the structure and cohesion of the stereocilia. In the retina, the USH protein network is principally located in the periciliary region of the photoreceptors, and plays an important role in the maintenance of the periciliary structure and the trafficking of molecules between the inner and the outer segments of photoreceptors. Even though some genes are clearly involved in the syndrome, others are controversial. Moreover, expression of some USH genes has been detected in other tissues, which could explain their involvement in additional mild comorbidities. In this paper, we review the genetics of Usher syndrome and the spectrum of mutations in USH genes. The aim is to identify possible mutation associations with the disease and provide an updated genotype–phenotype correlation.
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Affiliation(s)
- Carla Fuster-García
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (C.F.-G.); (B.G.-B.); (A.R.-M.); (E.A.); (T.J.); (G.G.-G.)
- Unidad Mixta de Enfermedades Raras IIS La Fe-Centro de Investigación Príncipe Felipe, 46026 Valencia, Spain
- Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
| | - Belén García-Bohórquez
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (C.F.-G.); (B.G.-B.); (A.R.-M.); (E.A.); (T.J.); (G.G.-G.)
- Unidad Mixta de Enfermedades Raras IIS La Fe-Centro de Investigación Príncipe Felipe, 46026 Valencia, Spain
| | - Ana Rodríguez-Muñoz
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (C.F.-G.); (B.G.-B.); (A.R.-M.); (E.A.); (T.J.); (G.G.-G.)
- Unidad Mixta de Enfermedades Raras IIS La Fe-Centro de Investigación Príncipe Felipe, 46026 Valencia, Spain
| | - Elena Aller
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (C.F.-G.); (B.G.-B.); (A.R.-M.); (E.A.); (T.J.); (G.G.-G.)
- Unidad Mixta de Enfermedades Raras IIS La Fe-Centro de Investigación Príncipe Felipe, 46026 Valencia, Spain
- Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
- Genetics Unit, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
| | - Teresa Jaijo
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (C.F.-G.); (B.G.-B.); (A.R.-M.); (E.A.); (T.J.); (G.G.-G.)
- Unidad Mixta de Enfermedades Raras IIS La Fe-Centro de Investigación Príncipe Felipe, 46026 Valencia, Spain
- Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
- Genetics Unit, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
| | - José M. Millán
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (C.F.-G.); (B.G.-B.); (A.R.-M.); (E.A.); (T.J.); (G.G.-G.)
- Unidad Mixta de Enfermedades Raras IIS La Fe-Centro de Investigación Príncipe Felipe, 46026 Valencia, Spain
- Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
- Correspondence:
| | - Gema García-García
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (C.F.-G.); (B.G.-B.); (A.R.-M.); (E.A.); (T.J.); (G.G.-G.)
- Unidad Mixta de Enfermedades Raras IIS La Fe-Centro de Investigación Príncipe Felipe, 46026 Valencia, Spain
- Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
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Xiao C, Liu S, Wang H, Ding Y, Chen Y, Liu H. Genetic etiology study of four Chinese families with two nonsyndromic deaf children in succession by targeted next-generation sequencing. Mol Genet Genomic Med 2021; 9:e1634. [PMID: 33638616 PMCID: PMC8123758 DOI: 10.1002/mgg3.1634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 12/09/2020] [Accepted: 02/10/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Genetic components contribute significantly to the cause of hearing loss. Nonsyndromic hearing loss has been shown to have high genetic heterogeneity. For families who had given birth to two nonsyndromic deaf children in succession, it seems that their deafness was highly related to genetics. OBJECTIVES This study aimed to disclose the genetic causes of the subjects from the four Chinese families with two nonsyndromic deaf children in succession who failed to find the genetic etiology of the hearing loss by common deafness genetic screening (GJB2, GJB3, SLC26A4, and MT-RNR1, including 20 hot variants in 4 genes). METHODS Targeted next-generation sequencing (NGS) of 127 known deafness genes was performed in probands of four families, followed by a series of comprehensive analyses of all family members combined with a literature review of related genes. RESULTS We identified pathogenic variants in three families including c.919-2A>G/c.1985G>A in SLC26A4; c.109G>A (p.V37I) in GJB2; and m.7505T>C in MT-TS1. Sanger sequencing confirmed that these variants segregated with the hearing impairment of each family. We also identified c.331C>T/c.625-5C>T/c.5717G>A in CDH23; c.138T>C in POU3F4 in two families, in which the pathogenicity in clinical was likely pathogenic or unknown. CONCLUSIONS Using the NGS detection technology, we found the genetic etiology of the HL in part of deaf families. Our study provided a useful piece of information for the variant spectrum of hearing loss in Chinese families with two deaf children in succession.
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Affiliation(s)
- Caixia Xiao
- Tianjin Women and Children Healthcare CenterTianjinChina
| | - Shuang Liu
- Tianjin Women and Children Healthcare CenterTianjinChina
| | - Hongyue Wang
- Tianjin Women and Children Healthcare CenterTianjinChina
| | - Yibing Ding
- Tianjin Women and Children Healthcare CenterTianjinChina
| | - Yaqiu Chen
- Tianjin Women and Children Healthcare CenterTianjinChina
| | - Haiyan Liu
- Tianjin Women and Children Healthcare CenterTianjinChina
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Bai Z, Xie Y, Liu L, Shao J, Liu Y, Kong X. Genetic investigation of 211 Chinese families expands the mutational and phenotypical spectra of hereditary retinopathy genes through targeted sequencing technology. BMC Med Genomics 2021; 14:92. [PMID: 33781268 PMCID: PMC8008643 DOI: 10.1186/s12920-021-00935-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 03/08/2021] [Indexed: 11/15/2022] Open
Abstract
Background Hereditary retinopathy is a significant cause of blindness worldwide. Despite the discovery of many mutations in various retinopathies, a large number of patients remain genetically undiagnosed. Targeted next-generation sequencing of the human genome is a suitable approach for the molecular diagnosis of retinopathy. Methods We describe a cohort of 211 families from central China with various forms of retinopathy; 95 patients were investigated using multigene panel sequencing, and the other 116 with suspected Leber hereditary optic neuropathy (LHON) were tested by Sanger sequencing. The detected variation of targeted sequencing was verified by PCR-based Sanger sequencing. We performed a comprehensive analysis of the cases using sequencing data and ophthalmologic examination information. Results Potential causal mutations were identified in the majority of families with retinopathy (57.9% of 95 families) and suspected LHON (21.6% of 116 families). There were 68 variants of a certain significance distributed in 31 known disease-causing genes in the 95 families; 37 of the variants are novel and have not been reported to be related to hereditary retinopathy. The NGS panel solution provided a 45.3% potential diagnostic rate for retinopathy families, with candidate gene mutations of undefined pathogenicity revealed in another 12.6%of the families. Conclusion Our study uncovered novel mutations and phenotypic aspects of retinopathy and demonstrated the genetic and clinical heterogeneity of related conditions. The findings show the detection rate of pathogenic variants in patients with hereditary retinopathy in central China as well as the diversity and gene distribution of these variants. The significance of molecular genetic testing for patients with hereditary retinopathy is also highlighted. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-00935-w.
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Affiliation(s)
- Zhouxian Bai
- The Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Yanchuan Xie
- The Department of Central Laboratory, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, 471003, Henan, China
| | - Lina Liu
- The Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Jingzhi Shao
- The Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Yuying Liu
- The Physical Examination Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Xiangdong Kong
- The Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
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Xiao T, Xie Y, Zhang X, Xu K, Zhang X, Jin ZB, Li Y. Variant Profiling of a Large Cohort of 138 Chinese Families With Autosomal Dominant Retinitis Pigmentosa. Front Cell Dev Biol 2021; 8:629994. [PMID: 33598457 PMCID: PMC7882618 DOI: 10.3389/fcell.2020.629994] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
Retinitis pigmentosa (RP) is the most common form of inherited retinal dystrophy, and 15–25% of RP is transmitted as an autosomal dominant (ad) trait. The objectives of this study were to establish the variant profile in a large cohort of adRP families and to elucidate the variant spectrum of each adRP gene in Chinese patients. A total of 138 probands clinically diagnosed with RP as a presumed autosomal dominant trait were recruited. All probands underwent ophthalmic examinations by specialists. A combination of molecular screening methods, including targeted next-generation sequencing, Sanger DNA sequencing, and multiplex ligation probe amplification assay, was used to detect variants. We identified heterozygous variants of 11 adRP genes in 73 probands, hemizygous, or heterozygous variants of X-linked RP genes in six patients, compound heterozygous variants of autosomal recessive RP genes in three pseudodominant families, and one heterozygous variant of one ad cone and rod dystrophy gene in one proband. One proband was found carrying both variants in RPGR and FAM161A. The overall detection rate was 59.4% (82/138). We detected 72 distinct disease-causing variants involving 16 RP genes and one cone-rod dystrophy gene; 33 of these variants have not been reported previously. Disease-causing variants were identified in the adRP genes in 52.9% of the families, followed by 4.3% in the X-linked RP genes, and 2.2% in the autosomal recessive genes. The most frequent mutant genes were RHO, PRPF31, RP1, SNRNP200, and PRPF8, which explained up to 78.0% of the genetically diagnosed families. Most of the variants identified in adRP genes were missense, and copy number variations were common (7/20) in the PRPF31 gene. We established the profile of the mutated genes and the variant spectrum of adRP genes in a large cohort of Chinese patients, providing essential information for genetic counseling and future development of therapeutics for retinal dystrophy inherited as a dominant trait.
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Affiliation(s)
- Ting Xiao
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Yue Xie
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Xin Zhang
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Ke Xu
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Xiaohui Zhang
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Zi-Bing Jin
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Yang Li
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
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Souissi A, Ben Said M, Ben Ayed I, Elloumi I, Bouzid A, Mosrati MA, Hasnaoui M, Belcadhi M, Idriss N, Kamoun H, Gharbi N, Gibriel AA, Tlili A, Masmoudi S. Novel pathogenic mutations and further evidence for clinical relevance of genes and variants causing hearing impairment in Tunisian population. J Adv Res 2021; 31:13-24. [PMID: 34194829 PMCID: PMC8240103 DOI: 10.1016/j.jare.2021.01.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/14/2020] [Accepted: 01/07/2021] [Indexed: 12/22/2022] Open
Abstract
Introduction Hearing impairment (HI) is characterized by complex genetic heterogeneity. The evolution of next generation sequencing, including targeted enrichment panels, has revolutionized HI diagnosis. Objectives In this study, we investigated genetic causes in 22 individuals with non-GJB2 HI. Methods We customized a HaloplexHS kit to include 30 genes known to be associated with autosomal recessive nonsyndromic HI (ARNSHI) and Usher syndrome in North Africa. Results In accordance with the ACMG/AMP guidelines, we report 11 pathogenic variants; as follows; five novel variants including three missense (ESRRB-Tyr295Cys, MYO15A-Phe2089Leu and MYO7A-Tyr560Cys) and two nonsense (USH1C-Gln122Ter and CIB2-Arg104Ter) mutations; two previously reported mutations (OTOF-Glu57Ter and PNPT1-Glu475Gly), but first time identified among Tunisian families; and four other identified mutations namely WHRN-Gly808AspfsX11, SLC22A4-Cys113Tyr and two MYO7A compound heterozygous splice site variants that were previously described in Tunisia. Pathogenic variants in WHRN and CIB2 genes, in patients with convincing phenotype ruling out retinitis pigmentosa, provide strong evidence supporting their association with ARNSHI. Moreover, we shed lights on the pathogenic implication of mutations in PNPT1 gene in auditory function providing new evidence for its association with ARNSHI. Lack of segregation of a previously identified causal mutation OTOA-Val603Phe further supports its classification as variant of unknown significance. Our study reports absence of otoacoustic emission in subjects using bilateral hearing aids for several years indicating the importance of screening genetic alteration in OTOF gene for proper management of those patients. Conclusion In conclusion, our findings do not only expand the spectrum of HI mutations in Tunisian patients, but also improve our knowledge about clinical relevance of HI causing genes and variants.
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Affiliation(s)
- Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Mariem Ben Said
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Ikhlas Ben Ayed
- Medical Genetic Department, University Hedi Chaker Hospital of Sfax, Tunisia
- Faculty of Medicine of Sfax, University of Sfax, Tunisia
| | - Ines Elloumi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Amal Bouzid
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Mohamed Ali Mosrati
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Mehdi Hasnaoui
- Department of Otorhinolaryngology, Taher Sfar University Hospital of Mahdia, Tunisia
| | - Malek Belcadhi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Nabil Idriss
- Department of Otorhinolaryngology, Taher Sfar University Hospital of Mahdia, Tunisia
| | - Hassen Kamoun
- Medical Genetic Department, University Hedi Chaker Hospital of Sfax, Tunisia
- Faculty of Medicine of Sfax, University of Sfax, Tunisia
| | - Nourhene Gharbi
- Medical Genetic Department, University Hedi Chaker Hospital of Sfax, Tunisia
- Faculty of Medicine of Sfax, University of Sfax, Tunisia
| | - Abdullah A. Gibriel
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy. The British University in Egypt (BUE) Cairo, Egypt
| | - Abdelaziz Tlili
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Human Genetics and Stem Cell Laboratory, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah, United Arab Emirates
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
- Corresponding author at: Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, Sidi Mansour road Km 6, BP “1177”, 3018 Sfax, Tunisia.
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Inaba A, Maeda A, Yoshida A, Kawai K, Hirami Y, Kurimoto Y, Kosugi S, Takahashi M. Truncating Variants Contribute to Hearing Loss and Severe Retinopathy in USH2A-Associated Retinitis Pigmentosa in Japanese Patients. Int J Mol Sci 2020; 21:ijms21217817. [PMID: 33105608 PMCID: PMC7659936 DOI: 10.3390/ijms21217817] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/19/2020] [Accepted: 10/19/2020] [Indexed: 01/19/2023] Open
Abstract
USH2A is a common causal gene of retinitis pigmentosa (RP), a progressive blinding disease due to retinal degeneration. Genetic alterations in USH2A can lead to two types of RP, non-syndromic and syndromic RP, which is called Usher syndrome, with impairments of vision and hearing. The complexity of the genotype–phenotype correlation in USH2A-associated RP (USH2A-RP) has been reported. Genetic and clinical characterization of USH2A-RP has not been performed in Japanese patients. In this study, genetic analyses were performed using targeted panel sequencing in 525 Japanese RP patients. Pathogenic variants of USH2A were identified in 36 of 525 (6.9%) patients and genetic features of USH2A-RP were characterized. Among 36 patients with USH2A-RP, 11 patients had syndromic RP with congenital hearing problems. Amino acid changes due to USH2A alterations were similarly located throughout entire regions of the USH2A protein structure in non-syndromic and syndromic RP cases. Notably, truncating variants were detected in all syndromic patients with a more severe retinal phenotype as compared to non-syndromic RP cases. Taken together, truncating variants could contribute to more serious functional and tissue damages in Japanese patients, suggesting important roles for truncating mutations in the pathogenesis of syndromic USH2A-RP.
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Affiliation(s)
- Akira Inaba
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe, Hyogo 650-0047, Japan; (A.I.); (A.Y.); (K.K.); (Y.H.); (Y.K.); (M.T.)
- Laboratory for Retinal Regeneration, RIKEN, Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
- Department of Medical Ethics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan;
| | - Akiko Maeda
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe, Hyogo 650-0047, Japan; (A.I.); (A.Y.); (K.K.); (Y.H.); (Y.K.); (M.T.)
- Laboratory for Retinal Regeneration, RIKEN, Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
- Correspondence: ; Tel.: +81-(0)78-306-3305
| | - Akiko Yoshida
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe, Hyogo 650-0047, Japan; (A.I.); (A.Y.); (K.K.); (Y.H.); (Y.K.); (M.T.)
- Laboratory for Retinal Regeneration, RIKEN, Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Kanako Kawai
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe, Hyogo 650-0047, Japan; (A.I.); (A.Y.); (K.K.); (Y.H.); (Y.K.); (M.T.)
- Laboratory for Retinal Regeneration, RIKEN, Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Yasuhiko Hirami
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe, Hyogo 650-0047, Japan; (A.I.); (A.Y.); (K.K.); (Y.H.); (Y.K.); (M.T.)
- Laboratory for Retinal Regeneration, RIKEN, Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Yasuo Kurimoto
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe, Hyogo 650-0047, Japan; (A.I.); (A.Y.); (K.K.); (Y.H.); (Y.K.); (M.T.)
- Laboratory for Retinal Regeneration, RIKEN, Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Shinji Kosugi
- Department of Medical Ethics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan;
| | - Masayo Takahashi
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe, Hyogo 650-0047, Japan; (A.I.); (A.Y.); (K.K.); (Y.H.); (Y.K.); (M.T.)
- Laboratory for Retinal Regeneration, RIKEN, Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
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Toms M, Pagarkar W, Moosajee M. Usher syndrome: clinical features, molecular genetics and advancing therapeutics. Ther Adv Ophthalmol 2020; 12:2515841420952194. [PMID: 32995707 PMCID: PMC7502997 DOI: 10.1177/2515841420952194] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/27/2020] [Indexed: 01/12/2023] Open
Abstract
Usher syndrome has three subtypes, each being clinically and genetically heterogeneous characterised by sensorineural hearing loss and retinitis pigmentosa (RP), with or without vestibular dysfunction. It is the most common cause of deaf–blindness worldwide with a prevalence of between 4 and 17 in 100 000. To date, 10 causative genes have been identified for Usher syndrome, with MYO7A accounting for >50% of type 1 and USH2A contributing to approximately 80% of type 2 Usher syndrome. Variants in these genes can also cause non-syndromic RP and deafness. Genotype–phenotype correlations have been described for several of the Usher genes. Hearing loss is managed with hearing aids and cochlear implants, which has made a significant improvement in quality of life for patients. While there is currently no available approved treatment for the RP, various therapeutic strategies are in development or in clinical trials for Usher syndrome, including gene replacement, gene editing, antisense oligonucleotides and small molecule drugs.
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Affiliation(s)
- Maria Toms
- UCL Institute of Ophthalmology, London, UK; The Francis Crick Institute, London, UK
| | - Waheeda Pagarkar
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK; University College London Hospitals NHS Foundation Trust, London, UK
| | - Mariya Moosajee
- Development, Ageing and Disease, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
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Nolen RM, Hufnagel RB, Friedman TB, Turriff AE, Brewer CC, Zalewski CK, King KA, Wafa TT, Griffith AJ, Brooks BP, Zein WM. Atypical and ultra-rare Usher syndrome: a review. Ophthalmic Genet 2020; 41:401-412. [PMID: 32372680 DOI: 10.1080/13816810.2020.1747090] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Usher syndrome has classically been described as a combination of hearing loss and rod-cone dystrophy; vestibular dysfunction is present in many patients. Three distinct clinical subtypes were documented in the late 1970s. Genotyping efforts have led to the identification of several genes associated with the disease. Recent literature has seen multiple publications referring to "atypical" Usher syndrome presentations. This manuscript reviews the molecular etiology of Usher syndrome, highlighting rare presentations and molecular causes. Reports of "atypical" disease are summarized noting the wide discrepancy in the spectrum of phenotypic deviations from the classical presentation. Guidelines for establishing a clear nomenclature system are suggested.
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Affiliation(s)
- Rosalie M Nolen
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health , Bethesda, MD, USA
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health , Bethesda, MD, USA
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health , Bethesda, MD, USA
| | - Amy E Turriff
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health , Bethesda, MD, USA
| | - Carmen C Brewer
- Otolaryngology Branch, National Institute of Deafness and Other Communication Disorders, National Institutes of Health , Bethesda, MD, USA
| | - Christopher K Zalewski
- Otolaryngology Branch, National Institute of Deafness and Other Communication Disorders, National Institutes of Health , Bethesda, MD, USA
| | - Kelly A King
- Otolaryngology Branch, National Institute of Deafness and Other Communication Disorders, National Institutes of Health , Bethesda, MD, USA
| | - Talah T Wafa
- Otolaryngology Branch, National Institute of Deafness and Other Communication Disorders, National Institutes of Health , Bethesda, MD, USA
| | - Andrew J Griffith
- Otolaryngology Branch, National Institute of Deafness and Other Communication Disorders, National Institutes of Health , Bethesda, MD, USA
| | - Brian P Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health , Bethesda, MD, USA
| | - Wadih M Zein
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health , Bethesda, MD, USA
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Jiman OA, Taylor RL, Lenassi E, Smith JC, Douzgou S, Ellingford JM, Barton S, Hardcastle C, Fletcher T, Campbell C, Ashworth J, Biswas S, Ramsden SC, Manson FD, Black GC. Diagnostic yield of panel-based genetic testing in syndromic inherited retinal disease. Eur J Hum Genet 2020; 28:576-586. [PMID: 31836858 PMCID: PMC7171123 DOI: 10.1038/s41431-019-0548-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 10/22/2019] [Accepted: 10/29/2019] [Indexed: 01/22/2023] Open
Abstract
Thirty percent of all inherited retinal disease (IRD) is accounted for by conditions with extra-ocular features. This study aimed to establish the genetic diagnostic pick-up rate for IRD patients with one or more extra-ocular features undergoing panel-based screening in a clinical setting. One hundred and six participants, tested on a gene panel which contained both isolated and syndromic IRD genes, were retrospectively ascertained from the Manchester Genomic Diagnostics Laboratory database spanning 6 years (2012-2017). Phenotypic features were extracted from the clinical notes and classified according to Human Phenotype Ontology; all identified genetic variants were interpreted in accordance to the American College of Medical Genetics and Genomics guidelines. Overall, 49% (n = 52) of patients received a probable genetic diagnosis. A further 6% (n = 6) had a single disease-associated variant in an autosomal recessive disease-relevant gene. Fifty-two percent (n = 55) of patients had a clinical diagnosis at the time of testing. Of these, 71% (n = 39) received a probable genetic diagnosis. By contrast, for those without a provisional clinical diagnosis (n = 51), only 25% (n = 13) received a probable genetic diagnosis. The clinical diagnosis of Usher (n = 33) and Bardet-Biedl syndrome (n = 10) was confirmed in 67% (n = 22) and 80% (n = 8), respectively. The testing diagnostic rate in patients with clinically diagnosed multisystemic IRD conditions was significantly higher than those without one (71% versus 25%; p value < 0.001). The lower pick-up rate in patients without a clinical diagnosis suggests that panel-based approaches are unlikely to be the most effective means of achieving a molecular diagnosis for this group. Here, we suggest that genome-wide approaches (whole exome or genome) are more appropriate.
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Affiliation(s)
- Omamah A Jiman
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre (MAHSC), University of Manchester, Manchester, UK
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rachel L Taylor
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre (MAHSC), University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Manchester, UK
| | - Eva Lenassi
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Manchester, UK
| | - Jill Clayton Smith
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre (MAHSC), University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Manchester, UK
| | - Sofia Douzgou
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre (MAHSC), University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Manchester, UK
| | - Jamie M Ellingford
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre (MAHSC), University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Manchester, UK
| | - Stephanie Barton
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Manchester, UK
| | - Claire Hardcastle
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Manchester, UK
| | - Tracy Fletcher
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Manchester, UK
| | - Christopher Campbell
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Manchester, UK
| | - Jane Ashworth
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre (MAHSC), University of Manchester, Manchester, UK
- Manchester Royal Eye Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Susmito Biswas
- Manchester Royal Eye Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Simon C Ramsden
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre (MAHSC), University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Manchester, UK
| | - Forbes D Manson
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre (MAHSC), University of Manchester, Manchester, UK
| | - Graeme C Black
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre (MAHSC), University of Manchester, Manchester, UK.
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Manchester, UK.
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Stiff HA, Sloan-Heggen CM, Ko A, Pfeifer WL, Kolbe DL, Nishimura CJ, Frees KL, Booth KT, Wang D, Weaver AE, Azaiez H, Kamholz J, Smith RJH, Drack AV. Is it Usher syndrome? Collaborative diagnosis and molecular genetics of patients with visual impairment and hearing loss. Ophthalmic Genet 2020; 41:151-158. [PMID: 32281467 PMCID: PMC7489297 DOI: 10.1080/13816810.2020.1747088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 03/04/2020] [Accepted: 03/22/2020] [Indexed: 12/20/2022]
Abstract
Background: Usher syndrome is the most common hereditary syndrome combining deafness and blindness. In the 2017 National Child Count of Children and Youth who are Deaf-Blind, Usher syndrome represented 329 of 10,000 children, but there were also at least 70 other etiologies of deaf-blindness documented. The purpose of this study was to analyze the work-up and ultimate diagnoses of 21 consecutive families who presented to the Genetic Eye-Ear Clinic (GEEC) at the University of Iowa. Our hypothesis was that most families referred to the GEEC would have initial and final diagnoses of Usher syndrome.Materials and Methods: Patients were identified through an IRB approved retrospective chart review of referrals to the GEEC between 2012 and 2019. Details about each patient's history, exam, and clinical and genetic work-up were recorded.Results: From 2012 to 2019, 21 families (25 patients) were referred to the collaborative GEEC. Overall molecular diagnostic rate in this cohort was 14/21 (67%). Evaluation resulted in a change of diagnosis in 11/21 (52%) families. Ultimately, there were eleven unique diagnoses including hereditary, non-hereditary, and independent causes of combined visual impairment and hearing loss. The most common diagnosis was Usher syndrome, which represented 6/21 (29%) families.Conclusions: Providing a correct diagnosis for patients with visual impairment and hearing loss can be challenging for clinicians and their patients, but it can greatly improve clinical care and outcomes. We recommend an algorithm that includes multidisciplinary collaboration, careful clinical evaluation, strategic molecular testing, and consideration of a broad differential diagnosis.
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Affiliation(s)
- Heather A Stiff
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, USA
| | - Christina M Sloan-Heggen
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
- Department of Molecular Physiology & Biophysics, University of Iowa College of Medicine, Iowa City, Iowa, USA
| | - Ashley Ko
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wanda L Pfeifer
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, USA
| | - Diana L Kolbe
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| | - Carla J Nishimura
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| | - Kathy L Frees
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| | - Kevin T Booth
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| | - Donghong Wang
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| | - Amy E Weaver
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| | - Hela Azaiez
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| | - John Kamholz
- Department of Neurology, University of Iowa, Iowa City, Iowa, USA
| | - Richard J H Smith
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, Head and Neck Surgery, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
- Department of Molecular Physiology & Biophysics, University of Iowa College of Medicine, Iowa City, Iowa, USA
| | - Arlene V Drack
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, USA
- The University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
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25
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García-García G, Sanchez-Navarro I, Aller E, Jaijo T, Fuster-Garcia C, Rodríguez-Munoz A, Vallejo E, Tellería JJ, Vázquez S, Beltrán S, Derdak S, Zurita O, Villaverde-Montero C, Avila-Fernández A, Corton M, Blanco-Kelly F, Hakonarson H, Millán JM, Ayuso C. Exome sequencing identifies PEX6 mutations in three cases diagnosed with Retinitis Pigmentosa and hearing impairment. Mol Vis 2020; 26:216-225. [PMID: 32214787 PMCID: PMC7090270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/16/2020] [Indexed: 11/07/2022] Open
Abstract
Purpose The aim of the present work is the molecular diagnosis of three patients with deafness and retinal degeneration. Methods Three patients from two unrelated families were initially analyzed with custom gene panels for Usher genes, non-syndromic hearing loss, or inherited syndromic retinopathies and further investigated by means of clinical or whole exome sequencing. Results The study allowed us to detect likely pathogenic variants in PEX6, a gene typically involved in peroxisomal biogenesis disorders (PBDs). Beside deaf-blindness, both families showed additional features: Siblings from Family 1 showed enamel alteration and abnormal peroxisome. In addition, the brother had mild neurodevelopmental delay and nephrolithiasis. The case II:1 from Family 2 showed intellectual disability, enamel alteration, and dysmorphism. Conclusions We have reported three new cases with pathogenic variants in PEX6 presenting with milder forms of the Zellweger spectrum disorders (ZSD). The three cases showed distinct clinical features. Thus, expanding the phenotypic spectrum of PBDs and ascertaining exome sequencing is an effective strategy for an accurate diagnosis of clinically overlapping and genetically heterogeneous disorders such as deafness-blindness association.
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Affiliation(s)
- Gema García-García
- Research group on Molecular, Cellular and Genomic Biomedicine, Health Research, Institute La Fe (IIS La Fe) and Mixed Unit for Rare diseases IIS La Fe - CIPF, Valencia, Spain,Centre for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Iker Sanchez-Navarro
- Centre for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain,Department of Genetics, IIS-Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain
| | - Elena Aller
- Research group on Molecular, Cellular and Genomic Biomedicine, Health Research, Institute La Fe (IIS La Fe) and Mixed Unit for Rare diseases IIS La Fe - CIPF, Valencia, Spain,Centre for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain,Genetics Unit, La Fe University Hospital, Valencia, Spain
| | - Teresa Jaijo
- Research group on Molecular, Cellular and Genomic Biomedicine, Health Research, Institute La Fe (IIS La Fe) and Mixed Unit for Rare diseases IIS La Fe - CIPF, Valencia, Spain,Centre for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain,Genetics Unit, La Fe University Hospital, Valencia, Spain
| | - Carla Fuster-Garcia
- Research group on Molecular, Cellular and Genomic Biomedicine, Health Research, Institute La Fe (IIS La Fe) and Mixed Unit for Rare diseases IIS La Fe - CIPF, Valencia, Spain
| | - Ana Rodríguez-Munoz
- Research group on Molecular, Cellular and Genomic Biomedicine, Health Research, Institute La Fe (IIS La Fe) and Mixed Unit for Rare diseases IIS La Fe - CIPF, Valencia, Spain
| | - Elena Vallejo
- Department of Ophthalmology, Medina del Campo Hospital, Valladolid, Spain
| | | | - Selma Vázquez
- University Hospital of Valladolid, Valladolid, Spain
| | - Sergi Beltrán
- National Center of Genomic Analysis (CNAG-CRG) Centre for Genomic Regulation, Barcelona, Spain
| | - Sophia Derdak
- National Center of Genomic Analysis (CNAG-CRG) Centre for Genomic Regulation, Barcelona, Spain
| | - Olga Zurita
- Centre for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain,Department of Genetics, IIS-Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain
| | - Cristina Villaverde-Montero
- Centre for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain,Department of Genetics, IIS-Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain
| | - Almudena Avila-Fernández
- Centre for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain,Department of Genetics, IIS-Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain
| | - Marta Corton
- Centre for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain,Department of Genetics, IIS-Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain
| | - Fiona Blanco-Kelly
- Centre for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain,Department of Genetics, IIS-Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain
| | - Hakon Hakonarson
- The Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - José M. Millán
- Research group on Molecular, Cellular and Genomic Biomedicine, Health Research, Institute La Fe (IIS La Fe) and Mixed Unit for Rare diseases IIS La Fe - CIPF, Valencia, Spain,Centre for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Carmen Ayuso
- Centre for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain,Department of Genetics, IIS-Fundación Jiménez Díaz University Hospital (IIS-FJD, UAM), Madrid, Spain
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26
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Liu XZ, Tao TC, Qi H, Feng SN, Chen NN, Zhao L, Ma ZZ, Li GL, Yang LP. Simultaneous expression of two pathogenic genes in four Chinese patients affected with inherited retinal dystrophy. Int J Ophthalmol 2020; 13:220-230. [PMID: 32090030 DOI: 10.18240/ijo.2020.02.04] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/07/2019] [Indexed: 01/14/2023] Open
Abstract
AIM To describe the complex, overlapping phenotype of four Chinese patients with inherited retinal dystrophies (IRDs) who harbored two pathogenic genes simultaneously. METHODS This retrospective study included 4 patients affected with IRDs. Medical and ophthalmic histories were obtained, and clinical examinations were performed. A specific Hereditary Eye Disease Enrichment Panel (HEDEP) based on exome capture technology was used for genetic screening. RESULTS Four patients were identified to harbor disease-causing variants in two different genes. Patient retinitis pigmentosa (RP) 01-II:1 exhibited both classical ABCA4-induced Stargardt disease (STGD) 1 and USH2A-associated RP, patient RP02-III:2 exhibited both classical ABCA4-induced STGD1 and CDH23-associated RP, patient RP03-II:1 exhibited both USH2A-induced autosomal recessive retinitis pigmentosa (arRP) syndrome and SNRNP200-induced autosomal dominant retinitis pigmentosa (adRP), and patient RP04-II:2 exhibited USH2A-induced arRP syndrome and EYS-induced arRP at the same time. CONCLUSION Our study demonstrates that genotype-phenotype correlations and comprehensive genetic screening is crucial for diagnosing IRDs and helping family planning for patients suffering from the disease.
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Affiliation(s)
- Xiao-Zhen Liu
- Department of Ophthalmology, Peking University Third Hospital, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Beijing 100191, China
| | - Tian-Chang Tao
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing 100730, China
| | - Hong Qi
- Department of Ophthalmology, Peking University Third Hospital, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Beijing 100191, China
| | - Shan-Na Feng
- Department of Ophthalmology, Peking University Third Hospital, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Beijing 100191, China
| | - Ning-Ning Chen
- Department of Ophthalmology, Peking University Third Hospital, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Beijing 100191, China
| | - Lin Zhao
- Department of Ophthalmology, Peking University Third Hospital, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Beijing 100191, China
| | - Zhi-Zhong Ma
- Department of Ophthalmology, Peking University Third Hospital, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Beijing 100191, China
| | - Gen-Lin Li
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing 100730, China
| | - Li-Ping Yang
- Department of Ophthalmology, Peking University Third Hospital, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Beijing 100191, China
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27
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González-Del Pozo M, Fernández-Suárez E, Martín-Sánchez M, Bravo-Gil N, Méndez-Vidal C, Rodríguez-de la Rúa E, Borrego S, Antiñolo G. Unmasking Retinitis Pigmentosa complex cases by a whole genome sequencing algorithm based on open-access tools: hidden recessive inheritance and potential oligogenic variants. J Transl Med 2020; 18:73. [PMID: 32050993 PMCID: PMC7014749 DOI: 10.1186/s12967-020-02258-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 02/05/2020] [Indexed: 12/13/2022] Open
Abstract
Background Retinitis Pigmentosa (RP) is a clinically and genetically heterogeneous disorder that results in inherited blindness. Despite the large number of genes identified, only ~ 60% of cases receive a genetic diagnosis using targeted-sequencing. The aim of this study was to design a whole genome sequencing (WGS) based approach to increase the diagnostic yield of complex Retinitis Pigmentosa cases. Methods WGS was conducted in three family members, belonging to one large apparent autosomal dominant RP family that remained unsolved by previous studies, using Illumina TruSeq library preparation kit and Illumina HiSeq X platform. Variant annotation, filtering and prioritization were performed using a number of open-access tools and public databases. Sanger sequencing of candidate variants was conducted in the extended family members. Results We have developed and optimized an algorithm, based on the combination of different open-access tools, for variant prioritization of WGS data which allowed us to reduce significantly the number of likely causative variants pending to be manually assessed and segregated. Following this algorithm, four heterozygous variants in one autosomal recessive gene (USH2A) were identified, segregating in pairs in the affected members. Additionally, two pathogenic alleles in ADGRV1 and PDZD7 could be contributing to the phenotype in one patient. Conclusions The optimization of a diagnostic algorithm for WGS data analysis, accompanied by a hypothesis-free approach, have allowed us to unmask the genetic cause of the disease in one large RP family, as well as to reassign its inheritance pattern which implies differences in the clinical management of these cases. These results contribute to increasing the number of cases with apparently dominant inheritance that carry causal mutations in recessive genes, as well as the possible involvement of various genes in the pathogenesis of RP in one patient. Moreover, our WGS-analysis approach, based on open-access tools, can easily be implemented by other researchers and clinicians to improve the diagnostic yield of additional patients with inherited retinal dystrophies.
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Affiliation(s)
- María González-Del Pozo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Avenida Manuel Siurot s/n, 41013, Seville, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
| | - Elena Fernández-Suárez
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Avenida Manuel Siurot s/n, 41013, Seville, Spain
| | - Marta Martín-Sánchez
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Avenida Manuel Siurot s/n, 41013, Seville, Spain
| | - Nereida Bravo-Gil
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Avenida Manuel Siurot s/n, 41013, Seville, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
| | - Cristina Méndez-Vidal
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Avenida Manuel Siurot s/n, 41013, Seville, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
| | - Enrique Rodríguez-de la Rúa
- Department of Ophthalmology, University Hospital Virgen Macarena, Seville, Spain.,ReticsPatologia Ocular, OFTARED, Instituto de Salud Carlos III, Madrid, Spain
| | - Salud Borrego
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Avenida Manuel Siurot s/n, 41013, Seville, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
| | - Guillermo Antiñolo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Avenida Manuel Siurot s/n, 41013, Seville, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain.
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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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29
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Kalaskar VK, Alur RP, Li LK, Thomas JW, Sergeev YV, Blain D, Hufnagel RB, Cogliati T, Brooks BP. High-throughput custom capture sequencing identifies novel mutations in coloboma-associated genes: Mutation in DNA-binding domain of retinoic acid receptor beta affects nuclear localization causing ocular coloboma. Hum Mutat 2019; 41:678-695. [PMID: 31816153 PMCID: PMC7027867 DOI: 10.1002/humu.23954] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 10/04/2019] [Accepted: 11/09/2019] [Indexed: 12/11/2022]
Abstract
Uveal coloboma is a potentially blinding congenital ocular malformation caused by the failure of optic fissure closure during the fifth week of human gestation. We performed custom capture high‐throughput screening of 38 known coloboma‐associated genes in 66 families. Suspected causative novel variants were identified in TFAP2A and CHD7, as well as two previously reported variants of uncertain significance in RARB and BMP7. The variant in RARB, unlike previously reported disease mutations in the ligand‐binding domain, was a missense change in the highly conserved DNA‐binding domain predicted to affect the protein's DNA‐binding ability. In vitro studies revealed lower steady‐state protein levels, reduced transcriptional activity, and incomplete nuclear localization of the mutant RARB protein compared with wild‐type. Zebrafish studies showed that human RARB messenger RNA partially reduced the ocular phenotype caused by morpholino knockdown of rarga gene, a zebrafish homolog of human RARB. Our study indicates that sequence alterations in known coloboma genes account for a small percentage of coloboma cases and that mutations in the RARB DNA‐binding domain could result in human disease.
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Affiliation(s)
- Vijay K Kalaskar
- Pediatric, Developmental & Genetic Ophthalmology Section, Ophthalmic Genetics and Visual Function Branch (OGVFB), National Eye Institute (NEI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Ramakrishna P Alur
- Pediatric, Developmental & Genetic Ophthalmology Section, Ophthalmic Genetics and Visual Function Branch (OGVFB), National Eye Institute (NEI), National Institutes of Health (NIH), Bethesda, Maryland
| | - LeeAnn K Li
- Pediatric, Developmental & Genetic Ophthalmology Section, Ophthalmic Genetics and Visual Function Branch (OGVFB), National Eye Institute (NEI), National Institutes of Health (NIH), Bethesda, Maryland
| | - James W Thomas
- National Institutes of Health Intramural Sequencing Center, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - Yuri V Sergeev
- Protein Biochemistry and Molecular Modeling Group, OGVFB, NEI, NIH, Bethesda, Maryland
| | - Delphine Blain
- Ophthalmic Clinical Genetics Section, OGVFB, NEI, NIH, Bethesda, Maryland
| | - Robert B Hufnagel
- Medical Genetics and Ophthalmic Genomics Unit, OGVFB, NEI, NIH, Bethesda, Maryland
| | - Tiziana Cogliati
- Pediatric, Developmental & Genetic Ophthalmology Section, Ophthalmic Genetics and Visual Function Branch (OGVFB), National Eye Institute (NEI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Brian P Brooks
- Pediatric, Developmental & Genetic Ophthalmology Section, Ophthalmic Genetics and Visual Function Branch (OGVFB), National Eye Institute (NEI), National Institutes of Health (NIH), Bethesda, Maryland.,Ophthalmic Clinical Genetics Section, OGVFB, NEI, NIH, Bethesda, Maryland
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Identification of a novel CDH23 gene variant associated with non-syndromic progressive hearing loss in a Chinese family: Individualized hearing rehabilitation guided by genetic diagnosis. Int J Pediatr Otorhinolaryngol 2019; 127:109649. [PMID: 31445392 DOI: 10.1016/j.ijporl.2019.109649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 08/16/2019] [Accepted: 08/17/2019] [Indexed: 01/20/2023]
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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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Fuster-García C, García-García G, Jaijo T, Fornés N, Ayuso C, Fernández-Burriel M, Sánchez-De la Morena A, Aller E, Millán JM. High-throughput sequencing for the molecular diagnosis of Usher syndrome reveals 42 novel mutations and consolidates CEP250 as Usher-like disease causative. Sci Rep 2018; 8:17113. [PMID: 30459346 PMCID: PMC6244211 DOI: 10.1038/s41598-018-35085-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/17/2018] [Indexed: 01/09/2023] Open
Abstract
Usher syndrome is a rare disorder causing retinitis pigmentosa, together with sensorineural hearing loss. Due to the phenotypic and genetic heterogeneity of this disease, the best method to screen the causative mutations is by high-throughput sequencing. In this study, we tested a semiconductor chip based sequencing approach with 77 unrelated patients, as a molecular diagnosis routine. In addition, Multiplex Ligation-dependent Probe Amplification and microarray-based Comparative Genomic Hybridization techniques were applied to detect large rearrangements, and minigene assays were performed to confirm the mRNA processing aberrations caused by splice-site mutations. The designed panel included all the USH causative genes (MYO7A, USH1C, CDH23, PCDH15, USH1G, CIB2, USH2A, ADGRV1, WHRN and CLRN1) as well as four uncertainly associated genes (HARS, PDZD7, CEP250 and C2orf71). The outcome showed an overall mutation detection ratio of 82.8% and allowed the identification of 42 novel putatively pathogenic mutations. Furthermore, we detected two novel nonsense mutations in CEP250 in a patient with a disease mimicking Usher syndrome that associates visual impairment due to cone-rod dystrophy and progressive hearing loss. Therefore, this approach proved reliable results for the molecular diagnosis of the disease and also allowed the consolidation of the CEP250 gene as disease causative for an Usher-like phenotype.
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Affiliation(s)
- Carla Fuster-García
- Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Gema García-García
- Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain.
- CIBER de Enfermedades Raras (CIBERER), Madrid, Spain.
| | - Teresa Jaijo
- Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, 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
| | - Neus Fornés
- Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Carmen Ayuso
- CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
- Servicio de Genética, Fundación Jiménez Díaz, University Hospital, Instituto de Investigación Sanitaria Fundación Jiménez Díaz IIS-FJD, UAM, Madrid, Spain
| | | | | | - Elena Aller
- Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, 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
| | - José M Millán
- Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
- CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
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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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Soares de Lima Y, Chiabai M, Shen J, Córdoba MS, Versiani BR, Benício ROA, Pogue R, Mingroni-Netto RC, Lezirovitz K, Pic-Taylor A, Mazzeu JF, Oliveira SF. Syndromic hearing loss molecular diagnosis: Application of massive parallel sequencing. Hear Res 2018; 370:181-188. [PMID: 30390570 DOI: 10.1016/j.heares.2018.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/19/2018] [Accepted: 10/14/2018] [Indexed: 12/17/2022]
Abstract
Syndromic hearing loss accounts for approximately 30% of all cases of hearing loss due to genetic causes. Mutation screening in known genes is important because it potentially sheds light on the genetic etiology of hearing loss and helps in genetic counseling of families. In this study, we describe a customized Ion AmpliSeq Panel, specifically designed for the investigation of syndromic hearing loss. The Ion AmpliSeq Panel was customized to cover the coding sequences of 52 genes. Twenty-four patients were recruited: 17 patients with a clinical diagnosis of a known syndrome, and seven whose clinical signs did not allow identification of a syndrome. Of 24 patients sequenced, potentially causative mutations were found in nine, all of which belonged to the group with a previous clinical diagnostic and none in the group not clinically diagnosed. We were able to provide conclusive molecular diagnosis to six patients, constituting a diagnostic rate of 25% (6/24). In the group of patients with a suspected clinical diagnosis, the diagnostic rate was 35% (6/17). Of the nine different mutations identified, three are novel, and were found in patients with Waardenburg, Treacher Collins and CHARGE syndromes. Since all patients with a conclusive molecular diagnosis through this panel had a previous suspected clinical diagnosis, our results suggest that this panel was more effective in diagnosing this group of patients. Therefore, the panel demonstrated effectiveness in molecular diagnosis when compared to others in the literature, especially for patients with a defined clinical diagnosis.
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Affiliation(s)
- Yasmin Soares de Lima
- Departamento de Genética e Morfologia, Universidade de Brasília, Brasília, Brazil; Programa de Pós-graduação em Biologia Animal, Universidade de Brasília, Brasília, Brazil.
| | - Marcela Chiabai
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, Brasília, Brazil.
| | - Jun Shen
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Mara S Córdoba
- Hospital Universitário de Brasília, Universidade de Brasília, Brasília, Brazil.
| | - Beatriz R Versiani
- Hospital Universitário de Brasília, Universidade de Brasília, Brasília, Brazil.
| | | | - Robert Pogue
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, Brasília, Brazil.
| | - Regina Célia Mingroni-Netto
- Centro de Estudos do Genoma Humano, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
| | - Karina Lezirovitz
- Laboratório de Otorrinolaringologia - LIM32, Hospital das Clínicas, Universidade de São Paulo, São Paulo, Brazil.
| | - Aline Pic-Taylor
- Departamento de Genética e Morfologia, Universidade de Brasília, Brasília, Brazil; Programa de Pós-graduação em Biologia Animal, Universidade de Brasília, Brasília, Brazil.
| | - Juliana F Mazzeu
- Hospital Universitário de Brasília, Universidade de Brasília, Brasília, Brazil; Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil.
| | - Silviene F Oliveira
- Departamento de Genética e Morfologia, Universidade de Brasília, Brasília, Brazil; Programa de Pós-graduação em Biologia Animal, Universidade de Brasília, Brasília, Brazil.
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35
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Analysis of intragenic USH2A copy number variation unveils broad spectrum of unique and recurrent variants. Eur J Med Genet 2018; 61:621-626. [DOI: 10.1016/j.ejmg.2018.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 04/09/2018] [Accepted: 04/11/2018] [Indexed: 11/21/2022]
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Targeted Next-Generation Sequencing Facilitates Genetic Diagnosis and Provides Novel Pathogenetic Insights into Deafness with Enlarged Vestibular Aqueduct. J Mol Diagn 2018; 21:138-148. [PMID: 30268946 DOI: 10.1016/j.jmoldx.2018.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 08/13/2018] [Accepted: 08/30/2018] [Indexed: 12/24/2022] Open
Abstract
Enlarged vestibular aqueduct (EVA) is an inner-ear malformation associated with sensorineural hearing impairment. Most EVAs are associated with Pendred syndrome and nonsyndromic autosomal recessive deafness-4 (DFNB4), two autosomal-recessive disorders caused by mutations in SLC26A4. However, many EVA patients cannot have a confirmed diagnosis by screening common SLC26A4 mutations, constituting an enigma in genetic diagnosis. To enable comprehensive genetic examination and explore the etiologies of EVA, we designed a next-generation sequencing panel targeting the entire length of 3 Pendred syndrome/DFNB4 genes (SLC26A4, FOXI1, and KCNJ10) and exons of 10 other genes related to EVA and performed genetic testing in 50 EVA families without confirmative results on screening for SLC26A4 hotspots (c.919-2A>G and p.H723R). Bi-allelic SLC26A4 mutations were identified in 34 families and EYA1 mutations in two families, yielding a diagnostic rate of 72% (36 of 50). In addition, two variants were identified in KCNJ10 and FOXI1, but findings did not support the previous hypothesis that mutations in these two genes are probable contributors to EVA through recessive inheritance or digenic inheritance with SLC26A4. Of note, a large SLC26A4 deletion was confirmed in one step using our panel. These results show the utility of a next-generation sequencing-based panel to address EVA families by identifying various types of gene mutations with satisfactory diagnostic yields and provide novel insights into the pathogenesis of EVA.
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Kumaran N, Michaelides M, Smith AJ, Ali RR, Bainbridge JWB. Retinal gene therapy. Br Med Bull 2018; 126:13-25. [PMID: 29506236 DOI: 10.1093/bmb/ldy005] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 02/12/2018] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Inherited retinal diseases are the leading cause of sight impairment in people of working age in England and Wales, and the second commonest in childhood. Gene therapy offers the potential for benefit. SOURCES OF DATA Pubmed and clinicaltrials.gov. AREAS OF AGREEMENT Gene therapy can improve vision in RPE65-associated Leber Congenital Amaurosis (RPE65-LCA). Potential benefit depends on efficient gene transfer and is limited by the extent of retinal degeneration. AREAS OF CONTROVERSY The magnitude of vision improvement from RPE65-LCA gene therapy is suboptimal, and its durability may be limited by progressive retinal degeneration. GROWING POINTS The safety and potential benefit of gene therapy for inherited and acquired retinal diseases is being explored in a rapidly expanding number of trials. AREAS TIMELY FOR DEVELOPING RESEARCH Developments in vector design and delivery will enable greater efficiency and safety of gene transfer. Optimization of trial design will accelerate reliable assessment of outcomes.
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Affiliation(s)
- Neruban Kumaran
- NIHR Biomedical Research Centre for Ophthalmology at Moofields Eye Hospital and UCL, 162 City Road, London, UK
| | - Michel Michaelides
- NIHR Biomedical Research Centre for Ophthalmology at Moofields Eye Hospital and UCL, 162 City Road, London, UK
| | - Alexander J Smith
- NIHR Biomedical Research Centre for Ophthalmology at Moofields Eye Hospital and UCL, 162 City Road, London, UK
| | - Robin R Ali
- NIHR Biomedical Research Centre for Ophthalmology at Moofields Eye Hospital and UCL, 162 City Road, London, UK
| | - James W B Bainbridge
- NIHR Biomedical Research Centre for Ophthalmology at Moofields Eye Hospital and UCL, 162 City Road, London, UK
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Alekseyev YO, Fazeli R, Yang S, Basran R, Maher T, Miller NS, Remick D. A Next-Generation Sequencing Primer-How Does It Work and What Can It Do? Acad Pathol 2018; 5:2374289518766521. [PMID: 29761157 PMCID: PMC5944141 DOI: 10.1177/2374289518766521] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 02/14/2018] [Accepted: 02/16/2018] [Indexed: 12/28/2022] Open
Abstract
Next-generation sequencing refers to a high-throughput technology that determines the nucleic acid sequences and identifies variants in a sample. The technology has been introduced into clinical laboratory testing and produces test results for precision medicine. Since next-generation sequencing is relatively new, graduate students, medical students, pathology residents, and other physicians may benefit from a primer to provide a foundation about basic next-generation sequencing methods and applications, as well as specific examples where it has had diagnostic and prognostic utility. Next-generation sequencing technology grew out of advances in multiple fields to produce a sophisticated laboratory test with tremendous potential. Next-generation sequencing may be used in the clinical setting to look for specific genetic alterations in patients with cancer, diagnose inherited conditions such as cystic fibrosis, and detect and profile microbial organisms. This primer will review DNA sequencing technology, the commercialization of next-generation sequencing, and clinical uses of next-generation sequencing. Specific applications where next-generation sequencing has demonstrated utility in oncology are provided.
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Affiliation(s)
- Yuriy O Alekseyev
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Roghayeh Fazeli
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Shi Yang
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Raveen Basran
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Thomas Maher
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Nancy S Miller
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Daniel Remick
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
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Sanchez-Navarro I, R J da Silva L, Blanco-Kelly F, Zurita O, Sanchez-Bolivar N, Villaverde C, Lopez-Molina MI, Garcia-Sandoval B, Tahsin-Swafiri S, Minguez P, Riveiro-Alvarez R, Lorda I, Sanchez-Alcudia R, Perez-Carro R, Valverde D, Liu Y, Tian L, Hakonarson H, Avila-Fernandez A, Corton M, Ayuso C. Combining targeted panel-based resequencing and copy-number variation analysis for the diagnosis of inherited syndromic retinopathies and associated ciliopathies. Sci Rep 2018; 8:5285. [PMID: 29588463 PMCID: PMC5869593 DOI: 10.1038/s41598-018-23520-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 03/13/2018] [Indexed: 01/29/2023] Open
Abstract
Inherited syndromic retinopathies are a highly heterogeneous group of diseases that involve retinal anomalies and systemic manifestations. They include retinal ciliopathies, other well-defined clinical syndromes presenting with retinal alterations and cases of non-specific multisystemic diseases. The heterogeneity of these conditions makes molecular and clinical characterization of patients challenging in daily clinical practice. We explored the capacity of targeted resequencing and copy-number variation analysis to improve diagnosis of a heterogeneous cohort of 47 patients mainly comprising atypical cases that did not clearly fit a specific clinical diagnosis. Thirty-three likely pathogenic variants were identified in 18 genes (ABCC6, ALMS1, BBS1, BBS2, BBS12, CEP41, CEP290, IFT172, IFT27, MKKS, MYO7A, OTX2, PDZD7, PEX1, RPGRIP1, USH2A, VPS13B, and WDPCP). Molecular findings and additional clinical reassessments made it possible to accurately characterize 14 probands (30% of the total). Notably, clinical refinement of complex phenotypes was achieved in 4 cases, including 2 de novo OTX2-related syndromes, a novel phenotypic association for the ciliary CEP41 gene, and the co-existence of biallelic USH2A variants and a Koolen-de-Vries syndrome-related 17q21.31 microdeletion. We demonstrate that combining next-generation sequencing and CNV analysis is a comprehensive and useful approach to unravel the extensive phenotypic and genotypic complexity of inherited syndromic retinopathies.
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Affiliation(s)
- Iker Sanchez-Navarro
- Department of Genetics, Instituto de Investigaciones Sanitarias - Fundacion Jiménez Díaz University Hospital (IIS-FJD-UAM), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Luciana R J da Silva
- Department of Genetics, Instituto de Investigaciones Sanitarias - Fundacion Jiménez Díaz University Hospital (IIS-FJD-UAM), Madrid, Spain.,Universidade de Mogi das Cruzes, São Paulo, Brazil
| | - Fiona Blanco-Kelly
- Department of Genetics, Instituto de Investigaciones Sanitarias - Fundacion Jiménez Díaz University Hospital (IIS-FJD-UAM), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Olga Zurita
- Department of Genetics, Instituto de Investigaciones Sanitarias - Fundacion Jiménez Díaz University Hospital (IIS-FJD-UAM), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Noelia Sanchez-Bolivar
- Department of Genetics, Instituto de Investigaciones Sanitarias - Fundacion Jiménez Díaz University Hospital (IIS-FJD-UAM), Madrid, Spain
| | - Cristina Villaverde
- Department of Genetics, Instituto de Investigaciones Sanitarias - Fundacion Jiménez Díaz University Hospital (IIS-FJD-UAM), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | | | | | - Saoud Tahsin-Swafiri
- Department of Genetics, Instituto de Investigaciones Sanitarias - Fundacion Jiménez Díaz University Hospital (IIS-FJD-UAM), Madrid, Spain
| | - Pablo Minguez
- Department of Genetics, Instituto de Investigaciones Sanitarias - Fundacion Jiménez Díaz University Hospital (IIS-FJD-UAM), Madrid, Spain
| | - Rosa Riveiro-Alvarez
- Department of Genetics, Instituto de Investigaciones Sanitarias - Fundacion Jiménez Díaz University Hospital (IIS-FJD-UAM), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Isabel Lorda
- Department of Genetics, Instituto de Investigaciones Sanitarias - Fundacion Jiménez Díaz University Hospital (IIS-FJD-UAM), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Rocío Sanchez-Alcudia
- Department of Genetics, Instituto de Investigaciones Sanitarias - Fundacion Jiménez Díaz University Hospital (IIS-FJD-UAM), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Raquel Perez-Carro
- Department of Genetics, Instituto de Investigaciones Sanitarias - Fundacion Jiménez Díaz University Hospital (IIS-FJD-UAM), Madrid, Spain
| | - Diana Valverde
- Department of Biochemistry, Genetics and Immunology, Faculty of Biology, Universidad de Vigo, Vigo, Spain
| | - Yichuan Liu
- Center for Applied Genomics, Abramson Pediatric Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lifeng Tian
- Center for Applied Genomics, Abramson Pediatric Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Pediatric Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Almudena Avila-Fernandez
- Department of Genetics, Instituto de Investigaciones Sanitarias - Fundacion Jiménez Díaz University Hospital (IIS-FJD-UAM), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Marta Corton
- Department of Genetics, Instituto de Investigaciones Sanitarias - Fundacion Jiménez Díaz University Hospital (IIS-FJD-UAM), Madrid, Spain. .,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain.
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigaciones Sanitarias - Fundacion Jiménez Díaz University Hospital (IIS-FJD-UAM), Madrid, Spain. .,Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain.
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Abstract
OBJECTIVE PDZD7 was identified in 2009 in a family with apparent nonsyndromic sensorineural hearing loss. However, subsequent clinical reports have associated PDZD7 with digenic Usher syndrome, the most common cause of deaf-blindness, or as a modifier of retinal disease. No further reports have validated this gene for nonsyndromic hearing loss, intuitively calling correct genotype-phenotype association into question. This report describes a validating second case for biallelic mutations in PDZD7 causing nonsyndromic mild to severe sensorineural hearing loss. It also provides detailed audiometric and ophthalmologic data excluding Usher syndrome in both the present proband (proband 1) and the first proband described in 2009 (proband 2). DESIGN Proband 1 was sequenced using a custom-designed next generation sequencing panel consisting of 151 deafness genes. Bioinformatics analysis and filtering disclosed two PDZD7 sequence variants (c.1648C>T, p.Q550* and c.2107del, p.S703Vfs*20). Segregation testing followed in the family. For both probands, audiograms were collected and analyzed for progressive hearing loss and detailed ophthalmic evaluations were performed including electroretinography. RESULTS Proband 1 demonstrated a prelingual, nonsyndromic, sensorineural hearing loss that progressed in the higher frequencies between 4 and 9 years old. PDZD7 segregation analysis confirmed biallelic inheritance (compound heterozygosity). Mutation analysis determined the c.1648C>T mutation as novel and reported the c.2107del deletion as rs397516633 with a calculated minor allele frequency of 0.000018. Clinical evaluation spanning well over a decade in proband 2 disclosed bilateral, nonprogressive hearing loss. Both probands showed healthy retinas, excluding Usher syndrome-like changes in the eye. CONCLUSIONS PDZD7 is confirmed as a bona fide autosomal recessive nonsyndromic hearing loss gene. In both probands, there was no evidence of impaired vision or ophthalmic pathology. As the current understanding of PDZD7 mutations bridge Mendelian and complex phenotypes, the authors recommend careful variant interpretation, since PDZD7 is one of many genes associated with both Usher syndrome and autosomal recessive nonsyndromic hearing loss. Additional reports are required for understanding the complete phenotypic spectrum of this gene, including the possibility of high-frequency progression, as well as noise-induced hearing loss susceptibility in adult carriers. This report rules out all forms of Usher syndrome with an onset before 12 and 15 years old in probands 1 and 2, respectively. However, due to the young ages of the probands, this report is uninformative regarding older patients.
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Wang X, Lin XJ, Tang X, Chai YC, Yu DH, Chen DY, Wu H. Genetic analysis of a Chinese family with members affected with Usher syndrome type II and Waardenburg syndrome type IV. Int J Pediatr Otorhinolaryngol 2017; 102:114-118. [PMID: 29106856 DOI: 10.1016/j.ijporl.2017.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 11/24/2022]
Abstract
AIMS The purpose of this study was to identify the genetic causes of a family presenting with multiple symptoms overlapping Usher syndrome type II (USH2) and Waardenburg syndrome type IV (WS4). METHODS Targeted next-generation sequencing including the exon and flanking intron sequences of 79 deafness genes was performed on the proband. Co-segregation of the disease phenotype and the detected variants were confirmed in all family members by PCR amplification and Sanger sequencing. RESULTS The affected members of this family had two different recessive disorders, USH2 and WS4. By targeted next-generation sequencing, we identified that USH2 was caused by a novel missense mutation, p.V4907D in GPR98; whereas WS4 due to p.V185M in EDNRB. This is the first report of homozygous p.V185M mutation in EDNRB in patient with WS4. CONCLUSION This study reported a Chinese family with multiple independent and overlapping phenotypes. In condition, molecular level analysis was efficient to identify the causative variant p.V4907D in GPR98 and p.V185M in EDNRB, also was helpful to confirm the clinical diagnosis of USH2 and WS4.
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Affiliation(s)
- Xueling Wang
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200011, China; Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases (14DZ2260300), Shanghai, 200011, China
| | - Xiao-Jiang Lin
- Department of Otolaryngology, People's Hospital of Kaihua, Kaihua, 324300, China
| | - Xiangrong Tang
- Department of Otolaryngology, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, 545001, China
| | - Yong-Chuan Chai
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200011, China; Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases (14DZ2260300), Shanghai, 200011, China
| | - De-Hong Yu
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200011, China; Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases (14DZ2260300), Shanghai, 200011, China
| | - Dong-Ye Chen
- Shanghai Jiahui International Hospital, Shanghai, 200000, China.
| | - Hao Wu
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200011, China; Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases (14DZ2260300), Shanghai, 200011, China.
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42
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Guan J, Wang H, Lan L, Wang L, Yang J, Xie L, Yin Z, Xiong W, Zhao L, Wang D, Wang Q. Novel recessive PDZD7 biallelic mutations in two Chinese families with non-syndromic hearing loss. Am J Med Genet A 2017; 176:99-106. [PMID: 29048736 PMCID: PMC5765442 DOI: 10.1002/ajmg.a.38477] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 08/16/2017] [Accepted: 08/21/2017] [Indexed: 11/17/2022]
Abstract
Autosomal recessive non‐syndromic hearing loss (ARNSHL) is a highly heterogeneous genetic condition. PDZD7 has emerged as a new genetic etiology of ARNSHL. Biallelic mutations in the PDZD7 gene have been reported in two German families, four Iranian families, and a Pakistani family with ARNSHL. The effect of PDZD7 on ARNSHL in other population has yet to be elucidated. Two Chinese ARNSHL families, each of which had two affected siblings, were included in this study. The families underwent target region capture and high‐throughput sequencing to analyze the exonic, splice‐site, and intronic sequences of 128 genes. Furthermore, 1751 normal Chinese individuals served as controls, and 122 Chinese families segregating with apparent ARNSHL, who had been previously excluded for variants in the common deafness genes GJB2 and SLC26A4, were subjected to screening for candidate mutations. We identified a novel homozygous missense mutation (p.Arg66Leu) and novel compound heterozygous frameshift mutations (p.Arg56fsTer24 and p.His403fsTer36) in Chinese families with ARNSHL. This is the first report to identify PDZD7 as an ARNSHL‐associated gene in the Chinese population. Our finding could expand the pathogenic spectrum and strengthens the clinical diagnostic role of the PDZD7 gene in ARNSHL patients.
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Affiliation(s)
- Jing Guan
- Chinese PLA Institute of Otolaryngology, Department of Otolaryngology-Head and Neck Surgery, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Hongyang Wang
- Chinese PLA Institute of Otolaryngology, Department of Otolaryngology-Head and Neck Surgery, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Lan Lan
- Chinese PLA Institute of Otolaryngology, Department of Otolaryngology-Head and Neck Surgery, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Li Wang
- Chinese PLA Institute of Otolaryngology, Department of Otolaryngology-Head and Neck Surgery, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Ju Yang
- Chinese PLA Institute of Otolaryngology, Department of Otolaryngology-Head and Neck Surgery, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Linyi Xie
- Chinese PLA Institute of Otolaryngology, Department of Otolaryngology-Head and Neck Surgery, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Zifang Yin
- Chinese PLA Institute of Otolaryngology, Department of Otolaryngology-Head and Neck Surgery, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Wenping Xiong
- Chinese PLA Institute of Otolaryngology, Department of Otolaryngology-Head and Neck Surgery, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Lidong Zhao
- Chinese PLA Institute of Otolaryngology, Department of Otolaryngology-Head and Neck Surgery, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Dayong Wang
- Chinese PLA Institute of Otolaryngology, Department of Otolaryngology-Head and Neck Surgery, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Qiuju Wang
- Chinese PLA Institute of Otolaryngology, Department of Otolaryngology-Head and Neck Surgery, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
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Neuhaus C, Eisenberger T, Decker C, Nagl S, Blank C, Pfister M, Kennerknecht I, Müller-Hofstede C, Charbel Issa P, Heller R, Beck B, Rüther K, Mitter D, Rohrschneider K, Steinhauer U, Korbmacher HM, Huhle D, Elsayed SM, Taha HM, Baig SM, Stöhr H, Preising M, Markus S, Moeller F, Lorenz B, Nagel-Wolfrum K, Khan AO, Bolz HJ. Next-generation sequencing reveals the mutational landscape of clinically diagnosed Usher syndrome: copy number variations, phenocopies, a predominant target for translational read-through, and PEX26 mutated in Heimler syndrome. Mol Genet Genomic Med 2017; 5:531-552. [PMID: 28944237 PMCID: PMC5606877 DOI: 10.1002/mgg3.312] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 06/06/2017] [Accepted: 06/09/2017] [Indexed: 12/23/2022] Open
Abstract
Background Combined retinal degeneration and sensorineural hearing impairment is mostly due to autosomal recessive Usher syndrome (USH1: congenital deafness, early retinitis pigmentosa (RP); USH2: progressive hearing impairment, RP). Methods Sanger sequencing and NGS of 112 genes (Usher syndrome, nonsyndromic deafness, overlapping conditions), MLPA, and array‐CGH were conducted in 138 patients clinically diagnosed with Usher syndrome. Results A molecular diagnosis was achieved in 97% of both USH1 and USH2 patients, with biallelic mutations in 97% (USH1) and 90% (USH2), respectively. Quantitative readout reliably detected CNVs (confirmed by MLPA or array‐CGH), qualifying targeted NGS as one tool for detecting point mutations and CNVs. CNVs accounted for 10% of identified USH2A alleles, often in trans to seemingly monoallelic point mutations. We demonstrate PTC124‐induced read‐through of the common p.Trp3955* nonsense mutation (13% of detected USH2A alleles), a potential therapy target. Usher gene mutations were found in most patients with atypical Usher syndrome, but the diagnosis was adjusted in case of double homozygosity for mutations in OTOA and NR2E3, genes implicated in isolated deafness and RP. Two patients with additional enamel dysplasia had biallelic PEX26 mutations, for the first time linking this gene to Heimler syndrome. Conclusion Targeted NGS not restricted to Usher genes proved beneficial in uncovering conditions mimicking Usher syndrome.
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Affiliation(s)
| | | | | | - Sandra Nagl
- Bioscientia Center for Human GeneticsIngelheimGermany
| | | | - Markus Pfister
- HNO-Praxis SarnenSarnenSwitzerland.,Molecular Genetics, THRCDepartment of OtolaryngologyUniversity of TübingenTübingenGermany
| | - Ingo Kennerknecht
- Institute of Human GeneticsWestfälische Wilhelms-UniversitätMünsterGermany
| | | | - Peter Charbel Issa
- Department of OphthalmologyUniversity of BonnBonnGermany.,Center for Rare Diseases Bonn (ZSEB)University of BonnBonnGermany.,Oxford Eye HospitalUniversity of OxfordOxfordUK
| | - Raoul Heller
- Institute of Human GeneticsUniversity Hospital of CologneCologneGermany
| | - Bodo Beck
- Institute of Human GeneticsUniversity Hospital of CologneCologneGermany
| | | | - Diana Mitter
- Institute of Human GeneticsUniversity of Leipzig Hospitals and ClinicsLeipzigGermany
| | | | | | - Heike M Korbmacher
- Department of OrthodonticsGiessen and Marburg University Hospital, Marburg CampusMarburgGermany
| | | | - Solaf M Elsayed
- Medical Genetics CenterCairoEgypt.,Children's HospitalAin Shams UniversityCairoEgypt
| | | | - Shahid M Baig
- Human Molecular Genetics LaboratoryHealth Biotechnology DivisionNational Institute for Biotechnology and Genetic Engineering (NIBGE)FaisalabadPakistan
| | - Heidi Stöhr
- Department of Human GeneticsUniversity Medical Center RegensburgRegensburgGermany
| | - Markus Preising
- Department of OphthalmologyJustus-Liebig-University GiessenGiessenGermany
| | | | - Fabian Moeller
- Department of Cell and Matrix BiologyInstitute of Zoology, Johannes GutenbergUniversity of MainzMainzGermany
| | - Birgit Lorenz
- Department of OphthalmologyJustus-Liebig-University GiessenGiessenGermany
| | - Kerstin Nagel-Wolfrum
- Department of Cell and Matrix BiologyInstitute of Zoology, Johannes GutenbergUniversity of MainzMainzGermany
| | - Arif O Khan
- Division of Pediatric OphthalmologyKing Khaled Eye Specialist HospitalRiyadhSaudi Arabia.,Eye InstituteCleveland ClinicAbu DhabiUAE
| | - Hanno J Bolz
- Bioscientia Center for Human GeneticsIngelheimGermany.,Institute of Human GeneticsUniversity Hospital of CologneCologneGermany
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May-Simera H, Nagel-Wolfrum K, Wolfrum U. Cilia - The sensory antennae in the eye. Prog Retin Eye Res 2017; 60:144-180. [PMID: 28504201 DOI: 10.1016/j.preteyeres.2017.05.001] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 05/04/2017] [Accepted: 05/08/2017] [Indexed: 12/21/2022]
Abstract
Cilia are hair-like projections found on almost all cells in the human body. Originally believed to function merely in motility, the function of solitary non-motile (primary) cilia was long overlooked. Recent research has demonstrated that primary cilia function as signalling hubs that sense environmental cues and are pivotal for organ development and function, tissue hoemoestasis, and maintenance of human health. Cilia share a common anatomy and their diverse functional features are achieved by evolutionarily conserved functional modules, organized into sub-compartments. Defects in these functional modules are responsible for a rapidly growing list of human diseases collectively termed ciliopathies. Ocular pathogenesis is common in virtually all classes of syndromic ciliopathies, and disruptions in cilia genes have been found to be causative in a growing number of non-syndromic retinal dystrophies. This review will address what is currently known about cilia contribution to visual function. We will focus on the molecular and cellular functions of ciliary proteins and their role in the photoreceptor sensory cilia and their visual phenotypes. We also highlight other ciliated cell types in tissues of the eye (e.g. lens, RPE and Müller glia cells) discussing their possible contribution to disease progression. Progress in basic research on the cilia function in the eye is paving the way for therapeutic options for retinal ciliopathies. In the final section we describe the latest advancements in gene therapy, read-through of non-sense mutations and stem cell therapy, all being adopted to treat cilia dysfunction in the retina.
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Affiliation(s)
- Helen May-Simera
- Institute of Molecular Physiology, Cilia Biology, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany
| | - Kerstin Nagel-Wolfrum
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany
| | - Uwe Wolfrum
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany.
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45
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Whole exome sequencing using Ion Proton system enables reliable genetic diagnosis of inherited retinal dystrophies. Sci Rep 2017; 7:42078. [PMID: 28181551 PMCID: PMC5299602 DOI: 10.1038/srep42078] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 01/05/2017] [Indexed: 01/17/2023] Open
Abstract
Inherited retinal dystrophies (IRD) comprise a wide group of clinically and genetically complex diseases that progressively affect the retina. Over recent years, the development of next-generation sequencing (NGS) methods has transformed our ability to diagnose heterogeneous diseases. In this work, we have evaluated the implementation of whole exome sequencing (WES) for the molecular diagnosis of IRD. Using Ion ProtonTM system, we simultaneously analyzed 212 genes that are responsible for more than 25 syndromic and non-syndromic IRD. This approach was used to evaluate 59 unrelated families, with the pathogenic variant(s) successfully identified in 71.18% of cases. Interestingly, the mutation detection rate varied substantially depending on the IRD subtype. Overall, we found 63 different mutations (21 novel) in 29 distinct genes, and performed in vivo functional studies to determine the deleterious impact of variants identified in MERTK, CDH23, and RPGRIP1. In addition, we provide evidences that support CDHR1 as a gene responsible for autosomal recessive retinitis pigmentosa with early macular affectation, and present data regarding the disease mechanism of this gene. Altogether, these results demonstrate that targeted WES of all IRD genes is a reliable, hypothesis-free approach, and a cost- and time-effective strategy for the routine genetic diagnosis of retinal dystrophies.
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Antisense Oligonucleotide-based Splice Correction for USH2A-associated Retinal Degeneration Caused by a Frequent Deep-intronic Mutation. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 5:e381. [PMID: 27802265 DOI: 10.1038/mtna.2016.89] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 09/07/2016] [Indexed: 12/21/2022]
Abstract
Usher syndrome (USH) is the most common cause of combined deaf-blindness in man. The hearing loss can be partly compensated by providing patients with hearing aids or cochlear implants, but the loss of vision is currently untreatable. In general, mutations in the USH2A gene are the most frequent cause of USH explaining up to 50% of all patients worldwide. The first deep-intronic mutation in the USH2A gene (c.7595-2144A>G) was reported in 2012, leading to the insertion of a pseudoexon (PE40) into the mature USH2A transcript. When translated, this PE40-containing transcript is predicted to result in a truncated non-functional USH2A protein. In this study, we explored the potential of antisense oligonucleotides (AONs) to prevent aberrant splicing of USH2A pre-mRNA as a consequence of the c.7595-2144A>G mutation. Engineered 2'-O-methylphosphorothioate AONs targeting the PE40 splice acceptor site and/or exonic splice enhancer regions displayed significant splice correction potential in both patient derived fibroblasts and a minigene splice assay for USH2A c.7595-2144A>G, whereas a non-binding sense oligonucleotide had no effect on splicing. Altogether, AON-based splice correction could be a promising approach for the development of a future treatment for USH2A-associated retinitis pigmentosa caused by the deep-intronic c.7595-2144A>G mutation.
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Abdi S, Bahloul A, Behlouli A, Hardelin JP, Makrelouf M, Boudjelida K, Louha M, Cheknene A, Belouni R, Rous Y, Merad Z, Selmane D, Hasbelaoui M, Bonnet C, Zenati A, Petit C. Diversity of the Genes Implicated in Algerian Patients Affected by Usher Syndrome. PLoS One 2016; 11:e0161893. [PMID: 27583663 PMCID: PMC5008642 DOI: 10.1371/journal.pone.0161893] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/12/2016] [Indexed: 11/18/2022] Open
Abstract
Usher syndrome (USH) is an autosomal recessive disorder characterized by a dual sensory impairment affecting hearing and vision. USH is clinically and genetically heterogeneous. Ten different causal genes have been reported. We studied the molecular bases of the disease in 18 unrelated Algerian patients by targeted-exome sequencing, and identified the causal biallelic mutations in all of them: 16 patients carried the mutations at the homozygous state and 2 at the compound heterozygous state. Nine of the 17 different mutations detected in MYO7A (1 of 5 mutations), CDH23 (4 of 7 mutations), PCDH15 (1 mutation), USH1C (1 mutation), USH1G (1 mutation), and USH2A (1 of 2 mutations), had not been previously reported. The deleterious consequences of a missense mutation of CDH23 (p.Asp1501Asn) and the in-frame single codon deletion in USH1G (p.Ala397del) on the corresponding proteins were predicted from the solved 3D-structures of extracellular cadherin (EC) domains of cadherin-23 and the sterile alpha motif (SAM) domain of USH1G/sans, respectively. In addition, we were able to show that the USH1G mutation is likely to affect the binding interface between the SAM domain and USH1C/harmonin. This should spur the use of 3D-structures, not only of isolated protein domains, but also of protein-protein interaction interfaces, to predict the functional impact of mutations detected in the USH genes.
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Affiliation(s)
- Samia Abdi
- Laboratoire de biochimie génétique, Service de biologie - CHU de Bab El Oued, Université d'Alger 1, 16 Alger, Algérie
- Laboratoire central de biologie, CHU Frantz Fanon, 09 Blida, Algérie
- Faculté de médecine, Université Saad Dahleb, 09 Blida, Algérie
| | - Amel Bahloul
- Unité de génétique et physiologie de l’audition, INSERM UMRS1120, Institut Pasteur, 75015, Paris, France
| | - Asma Behlouli
- Laboratoire de biochimie génétique, Service de biologie - CHU de Bab El Oued, Université d'Alger 1, 16 Alger, Algérie
- Faculté des sciences biologiques, Université des sciences et de la technologie Houari Boumédiène, 16 Alger, Algérie
| | - Jean-Pierre Hardelin
- Unité de génétique et physiologie de l’audition, INSERM UMRS1120, Institut Pasteur, 75015, Paris, France
| | - Mohamed Makrelouf
- Laboratoire de biochimie génétique, Service de biologie - CHU de Bab El Oued, Université d'Alger 1, 16 Alger, Algérie
| | - Kamel Boudjelida
- Faculté de médecine, Université Saad Dahleb, 09 Blida, Algérie
- Service d’ophtalmologie, CHU Frantz Fanon, 09 Blida, Algérie
| | - Malek Louha
- Service de biochimie et de biologie moléculaire, Hôpital Armand Trousseau, APHP, 75012, Paris, France
| | - Ahmed Cheknene
- Faculté de médecine, Université Saad Dahleb, 09 Blida, Algérie
- Service d’ORL, CHU Frantz Fanon, 09 Blida, Algérie
| | - Rachid Belouni
- Laboratoire central de biologie, CHU Frantz Fanon, 09 Blida, Algérie
- Faculté de médecine, Université Saad Dahleb, 09 Blida, Algérie
| | - Yahia Rous
- Faculté de médecine, Université Saad Dahleb, 09 Blida, Algérie
- Service d’ORL, CHU Frantz Fanon, 09 Blida, Algérie
| | - Zahida Merad
- Faculté de médecine, Université Saad Dahleb, 09 Blida, Algérie
- Service d’ophtalmologie, CHU Frantz Fanon, 09 Blida, Algérie
| | | | | | - Crystel Bonnet
- INSERM UMRS 1120, Institut de la vision, Université Pierre et Marie Curie, 75005, Paris, France
| | - Akila Zenati
- Laboratoire de biochimie génétique, Service de biologie - CHU de Bab El Oued, Université d'Alger 1, 16 Alger, Algérie
| | - Christine Petit
- Unité de génétique et physiologie de l’audition, INSERM UMRS1120, Institut Pasteur, 75015, Paris, France
- INSERM UMRS 1120, Institut de la vision, Université Pierre et Marie Curie, 75005, Paris, France
- Collège de France, 75005, Paris, France
- * E-mail:
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An innovative strategy for the molecular diagnosis of Usher syndrome identifies causal biallelic mutations in 93% of European patients. Eur J Hum Genet 2016; 24:1730-1738. [PMID: 27460420 PMCID: PMC5117943 DOI: 10.1038/ejhg.2016.99] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/23/2016] [Accepted: 06/04/2016] [Indexed: 11/08/2022] Open
Abstract
Usher syndrome (USH), the most prevalent cause of hereditary deafness–blindness, is an autosomal recessive and genetically heterogeneous disorder. Three clinical subtypes (USH1–3) are distinguishable based on the severity of the sensorineural hearing impairment, the presence or absence of vestibular dysfunction, and the age of onset of the retinitis pigmentosa. A total of 10 causal genes, 6 for USH1, 3 for USH2, and 1 for USH3, and an USH2 modifier gene, have been identified. A robust molecular diagnosis is required not only to improve genetic counseling, but also to advance gene therapy in USH patients. Here, we present an improved diagnostic strategy that is both cost- and time-effective. It relies on the sequential use of three different techniques to analyze selected genomic regions: targeted exome sequencing, comparative genome hybridization, and quantitative exon amplification. We screened a large cohort of 427 patients (139 USH1, 282 USH2, and six of undefined clinical subtype) from various European medical centers for mutations in all USH genes and the modifier gene. We identified a total of 421 different sequence variants predicted to be pathogenic, about half of which had not been previously reported. Remarkably, we detected large genomic rearrangements, most of which were novel and unique, in 9% of the patients. Thus, our strategy led to the identification of biallelic and monoallelic mutations in 92.7% and 5.8% of the USH patients, respectively. With an overall 98.5% mutation characterization rate, the diagnosis efficiency was substantially improved compared with previously reported methods.
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Tiwari A, Bahr A, Bähr L, Fleischhauer J, Zinkernagel MS, Winkler N, Barthelmes D, Berger L, Gerth-Kahlert C, Neidhardt J, Berger W. Next generation sequencing based identification of disease-associated mutations in Swiss patients with retinal dystrophies. Sci Rep 2016; 6:28755. [PMID: 27353947 PMCID: PMC4926080 DOI: 10.1038/srep28755] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 06/08/2016] [Indexed: 11/24/2022] Open
Abstract
Inherited monogenic diseases of the retina and vitreous affect approximately 1 in 2000 individuals. They are characterized by tremendous genetic heterogeneity and clinical variability involving mutations in approximately 250 genes and more than 20 different clinical phenotypes. Clinical manifestations of retinal dystrophies (RDs) range from mild retinal dysfunctions to severe congenital forms of blindness. A detailed clinical diagnosis and the identification of causative mutations are crucial for genetic counseling of affected patients and their families, for understanding genotype-phenotype correlations and developing therapeutic approaches. Using whole exome sequencing (WES) we have established a reliable and efficient high-throughput analysis pipeline to identify disease-causing mutations. Our data indicate that this approach enables us to genetically diagnose approximately 64% of the patients (n = 58) with variant(s) in known disease-associated genes. We report 20 novel and 26 recurrent variants in genes associated with RDs. We also identified a novel phenotype for mutations in C2orf71 and provide functional evidence for exon skipping due to a splice-site variant identified in FLVCR1. In conclusion, WES can rapidly identify variants in various families affected with different forms of RDs. Our study also expands the clinical and allelic spectrum of genes associated with RDs in the Swiss population.
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Affiliation(s)
- Amit Tiwari
- Institute of Medical Molecular Genetics, University of Zürich, Wagistrasse 12, CH-8952, Schlieren, Switzerland
| | - Angela Bahr
- Institute of Medical Molecular Genetics, University of Zürich, Wagistrasse 12, CH-8952, Schlieren, Switzerland
| | - Luzy Bähr
- Institute of Medical Molecular Genetics, University of Zürich, Wagistrasse 12, CH-8952, Schlieren, Switzerland
| | - Johannes Fleischhauer
- Department of Ophthalmology, University Hospital Zürich and University of Zürich, Zürich, Switzerland
| | - Martin S Zinkernagel
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Niklas Winkler
- Department of Ophthalmology, University Hospital Zürich and University of Zürich, Zürich, Switzerland
| | - Daniel Barthelmes
- Department of Ophthalmology, University Hospital Zürich and University of Zürich, Zürich, Switzerland
| | - Lieselotte Berger
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Christina Gerth-Kahlert
- Department of Ophthalmology, University Hospital Zürich and University of Zürich, Zürich, Switzerland
| | - John Neidhardt
- Institute of Medical Molecular Genetics, University of Zürich, Wagistrasse 12, CH-8952, Schlieren, Switzerland
| | - Wolfgang Berger
- Institute of Medical Molecular Genetics, University of Zürich, Wagistrasse 12, CH-8952, Schlieren, Switzerland.,Zurich Center for Integrative Human Physiology (ZIHP), University of Zürich, Zürich, Switzerland.,Neuroscience Center Zurich (ZNZ), University and ETH Zürich, Zürich, Switzerland
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50
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Genetic systems for a new approach to risk of progression of diabetic retinopathy. ACTA ACUST UNITED AC 2016; 91:209-16. [PMID: 26948458 DOI: 10.1016/j.oftal.2016.01.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/12/2016] [Accepted: 01/13/2016] [Indexed: 01/08/2023]
Abstract
OBJECTIVE To evaluate the risk of progression of diabetic retinopathy (DR) using new strategies to obtain genetic information in type 2 diabetes (T2D) based on interfering ribonucleic acid (RNA). MATERIAL AND METHODS A prospective multicentre case-control study of 132 participants was distributed into: T2D with (+DR) or without (-DR) (T2DG; n=77), and a control group (CG; n=55). After an eye examination and personal interview, tears were collected for molecular analysis (expression of microRNAs [miRNAs] (miRCURY ™ ARN Isolation Kit, Qiagen)]. Libraries, 137 vs. 140bp (GeneMapper, Applied Biosystems), were obtained in 18 samples (T2DG+DR=6; T2DG-DR=6; CG=6) by performing next-generation sequencing (NGS). SPSS 15.0 statistical program was used to perform data analysis. RESULTS The mean age was 67±12 years in the T2DG vs. 55±21 years in the CG. Distribution men/women: 25/30 in T2DG vs. 51/28 in CG. A family history of DM, diet compliance, smoking, drinking and exercise, showed significant differences between groups (P<.001). A 20-25 microlitre sample of tears contained a mean of 9.42±3.30 ng/mL of purified ARN, with significant differences between T2DG/CG (P=.002) and T2DG+RD/CG (P=.004). Tear expression of miARNs in T2DG directly correlated with age/obesity/T2D duration (P<.05), and indirectly with visual acuity (P<.05). A total of 14 miRNAs related to the presence, pathogenic mechanisms and risk factors for the progression of diabetic retinopathy, were identified. CONCLUSIONS We propose to use tears as a source of genetic information for DM. Specific miRNAs involved in DR development and/or progression can be used as molecular biomarkers, and based on these, for developing future biotherapies.
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