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Amorim AM, Rebelo D, Ramada AB, Lopes AC, Lemos J, Ribeiro JC. Otolith function in Usher type II syndrome. Acta Otolaryngol 2024:1-6. [PMID: 39151018 DOI: 10.1080/00016489.2024.2390661] [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: 07/02/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 08/18/2024]
Abstract
BACKGROUND Usher's syndrome type II (USH2) is a rare genetic disorder encompassing hearing loss, vision impairment, and apparent intact vestibular function. Recent research suggests a potential involvement of the otolith vestibular receptors in USH2. AIMS/OBJECTIVES Evaluate otolith dynamic function in USH2. MATERIAL AND METHODS Twenty-two USH2 (median age 53.9 ± 2.99) and age-matched controls underwent a complete battery vestibular testing including air conducted cervical and ocular vestibular evoked myogenic potentials (c-VEMPs and o-VEMPs). Vestibular function tests were correlated with Activities Balance Scale (ABC) and Dizziness Handicap Inventory (DHI) scores. RESULTS Fourteen USH2 reported previous vertigo (vs none control). Among 88 ears, c-VEMPs were absent in 15 USH2 cases and 4 controls (p = 0.034), while o-VEMPs were absent in 22 USH2 cases and 12 controls (p = 0.129). There were significant differences between USH2 vs controls in right ear o-VEMP N1 latencies (median 11.60/10.40, p < 0.010), N1-P1 amplitudes (median 5.15/10.10, p < 0.003) and in o-VEMP N1-P1 asymmetry ratio (median 24.78/40.50, p < 0.014). USH2 showed a strong correlation between o-VEMP amplitude and DHI score (p = 0.003, ρ = 0.769). No association was found between vertigo and VEMPs subgroups. CONCLUSIONS AND SIGNIFICANCE Our findings suggest the presence of otolith dysfunction in USH2, which is independent from subjectively reported dizziness. Incorporating vestibular testing into USH2 evaluation and monitoring could enhance characterization of this multisensory disease.
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Affiliation(s)
- Ana Margarida Amorim
- Otorhinolaringology Department, Coimbra Local Health Unit, EPE, Coimbra, Portugal
- Faculty of Medicine, Coimbra University, Coimbra, Portugal
| | - Diliana Rebelo
- Otorhinolaringology Department, Coimbra Local Health Unit, EPE, Coimbra, Portugal
| | - Ana Beatriz Ramada
- Otorhinolaringology Department, Coimbra Local Health Unit, EPE, Coimbra, Portugal
| | - Ana Cristina Lopes
- Otorhinolaringology Department, Coimbra Local Health Unit, EPE, Coimbra, Portugal
| | - João Lemos
- Faculty of Medicine, Coimbra University, Coimbra, Portugal
- Neurology Department, Coimbra Local Health Unit, EPE, Coimbra, Portugal
| | - João Carlos Ribeiro
- Otorhinolaringology Department, Coimbra Local Health Unit, EPE, Coimbra, Portugal
- Faculty of Medicine, Coimbra University, Coimbra, Portugal
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Lin S, Vermeirsch S, Pontikos N, Martin-Gutierrez MP, Daich Varela M, Malka S, Schiff E, Knight H, Wright G, Jurkute N, Simcoe MJ, Yu-Wai-Man P, Moosajee M, Michaelides M, Mahroo OA, Webster AR, Arno G. Spectrum of Genetic Variants in the Most Common Genes Causing Inherited Retinal Disease in a Large Molecularly Characterized United Kingdom Cohort. Ophthalmol Retina 2024; 8:699-709. [PMID: 38219857 DOI: 10.1016/j.oret.2024.01.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/12/2023] [Accepted: 01/08/2024] [Indexed: 01/16/2024]
Abstract
PURPOSE Inherited retinal disease (IRD) is a leading cause of blindness. Recent advances in gene-directed therapies highlight the importance of understanding the genetic basis of these disorders. This study details the molecular spectrum in a large United Kingdom (UK) IRD patient cohort. DESIGN Retrospective study of electronic patient records. PARTICIPANTS Patients with IRD who attended the Genetics Service at Moorfields Eye Hospital between 2003 and July 2020, in whom a molecular diagnosis was identified. METHODS Genetic testing was undertaken via a combination of single-gene testing, gene panel testing, whole exome sequencing, and more recently, whole genome sequencing. Likely disease-causing variants were identified from entries within the genetics module of the hospital electronic patient record (OpenEyes Electronic Medical Record). Analysis was restricted to only genes listed in the Genomics England PanelApp R32 Retinal Disorders panel (version 3.24), which includes 412 genes associated with IRD. Manual curation ensured consistent variant annotation and included only plausible disease-associated variants. MAIN OUTCOME MEASURES Detailed analysis was performed for variants in the 5 most frequent genes (ABCA4, USH2A, RPGR, PRPH2, and BEST1), as well as for the most common variants encountered in the IRD study cohort. RESULTS We identified 4415 individuals from 3953 families with molecularly diagnosed IRD (variants in 166 genes). Of the families, 42.7% had variants in 1 of the 5 most common IRD genes. Complex disease alleles contributed to disease in 16.9% of affected families with ABCA4-associated retinopathy. USH2A exon 13 variants were identified in 43% of affected individuals with USH2A-associated IRD. Of the RPGR variants, 71% were clustered in the ORF15 region. PRPH2 and BEST1 variants were associated with a range of dominant and recessive IRD phenotypes. Of the 20 most prevalent variants identified, 5 were not in the most common genes; these included founder variants in CNGB3, BBS1, TIMP3, EFEMP1, and RP1. CONCLUSIONS We describe the most common pathogenic IRD alleles in a large single-center multiethnic UK cohort and the burden of disease, in terms of families affected, attributable to these variants. Our findings will inform IRD diagnoses in future patients and help delineate the cohort of patients eligible for gene-directed therapies under development. FINANCIAL DISCLOSURE(S) Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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Affiliation(s)
- Siying Lin
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Sandra Vermeirsch
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom
| | - Nikolas Pontikos
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Maria Pilar Martin-Gutierrez
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom
| | - Malena Daich Varela
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Samantha Malka
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Elena Schiff
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Hannah Knight
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Genevieve Wright
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Neringa Jurkute
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom; Department of Neuro-Ophhalmology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Mark J Simcoe
- UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Patrick Yu-Wai-Man
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Mariya Moosajee
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Michel Michaelides
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Omar A Mahroo
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom; Department of Ophthalmology, St Thomas' Hospital, London, United Kingdom
| | - Andrew R Webster
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Gavin Arno
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom.
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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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Markova TG, Lalayants MR, Alekseeva NN, Ryzhkova OP, Shatokhina OL, Galeeva NM, Bliznetz EA, Weener ME, Belov OA, Chibisova SS, Polyakov AV, Tavartkiladze GA. Early audiological phenotype in patients with mutations in the USH2A gene. Int J Pediatr Otorhinolaryngol 2022; 157:111140. [PMID: 35452909 DOI: 10.1016/j.ijporl.2022.111140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 03/16/2022] [Accepted: 04/11/2022] [Indexed: 11/27/2022]
Abstract
INTRODUCTION Nowadays, due to universal newborn hearing screening (UNHS) the number of children with mild-to-moderate hearing loss diagnosed in the first year of life has increased significantly. Aside from that, identification of the genetic cause improves the genetic counselling of the families and allows to reveal possible comorbidities which may need a special approach. OBJECTIVE To present the characteristics of the early audiologic phenotype in hearing impaired patients with biallelic mutations in the USH2A gene based on systematic analysis of the audiological data. PATIENTS AND METHODS 13 patients with mutations in the USH2A gene underwent audiological examination. Most of them were found among a large group of infants with bilateral nonsyndromic sensorineural hearing loss (SNHL) examined under 12 months. RESULTS Eight out of eleven children failed UNHS and were initially diagnosed as having bilateral nonsyndromic SNHL. Seven children underwent an audiological assessment before the age of 9 months. The earliest audiological examination was carried out at 1 and 3 months. The children with pathogenic variants in the USH2A gene in our examined group were identified in the first year of life via UNHS. The hearing threshold levels (HTL) for the USH2A group are compactly distributed between 51.25 dB and 66.25 dB, quartiles are 54 dB and 63.4 dB, with a median of 60 dB. The audiological profile of patients with biallelic USH2A mutations differs from audiograms of patients who had STRC-related hearing loss. We have not found any significant elevation in hearing thresholds in the first decade of life. We also estimated the prevalence of the USH2A and STRC mutations among GJB2-negative infants with bilateral nonsyndromic SNHL examined under 12 months, and it was 7.5% and 16.1%, respectively. CONCLUSION According to our results, the early hearing phenotype in pediatric patients with biallelic mutations in the USH2A- gene is characterized by nonsyndromic mild-to-moderate SNHL in the first decade of life. Our results indicate that the presence of mutations in the USH2A or STRC genes can be expected in a child with congenital mild-to-moderate nonsyndromic SNHL. This information is of practical importance for parents, as they have to know the prognosis of hearing loss for their child from the very beginning. Post-screening follow-up should include adequate clinical, genetic, and social support for children and their parents.
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Affiliation(s)
- T G Markova
- National Research Centre for Audiology and Hearing Rehabilitation, Moscow, 117513, Russia; Russian Medical Academy of Continuing Professional Education, Moscow, 125993, Russia
| | - M R Lalayants
- National Research Centre for Audiology and Hearing Rehabilitation, Moscow, 117513, Russia; Russian Medical Academy of Continuing Professional Education, Moscow, 125993, Russia
| | - N N Alekseeva
- National Research Centre for Audiology and Hearing Rehabilitation, Moscow, 117513, Russia; Russian Medical Academy of Continuing Professional Education, Moscow, 125993, Russia
| | - O P Ryzhkova
- Research Centre for Medical Genetics, Moscow, 115478, Russia
| | - O L Shatokhina
- Research Centre for Medical Genetics, Moscow, 115478, Russia
| | - N M Galeeva
- Research Centre for Medical Genetics, Moscow, 115478, Russia
| | - E A Bliznetz
- Research Centre for Medical Genetics, Moscow, 115478, Russia
| | - M E Weener
- CRO LLC «Oftalmic», Moscow, 125167, Russia
| | - O A Belov
- National Research Centre for Audiology and Hearing Rehabilitation, Moscow, 117513, Russia
| | - S S Chibisova
- National Research Centre for Audiology and Hearing Rehabilitation, Moscow, 117513, Russia; Russian Medical Academy of Continuing Professional Education, Moscow, 125993, Russia
| | - A V Polyakov
- Research Centre for Medical Genetics, Moscow, 115478, Russia
| | - G A Tavartkiladze
- National Research Centre for Audiology and Hearing Rehabilitation, Moscow, 117513, Russia; Russian Medical Academy of Continuing Professional Education, Moscow, 125993, Russia.
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Caracterización fenotípica de la retinitis pigmentaria asociada a sordera. BIOMÉDICA 2022; 42:130-143. [PMID: 35866736 PMCID: PMC9385447 DOI: 10.7705/biomedica.6129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Indexed: 11/21/2022]
Abstract
Introducción. El síndrome de Usher es una alteración genética caracterizada por la asociación de retinitis pigmentaria y sordera. Sin embargo, hay casos con familias en las cuales, a pesar de presentarse dicha asociación, no se puede diagnosticar un síndrome de Usher ni ninguno otro. Objetivo. Reevaluar fenotípicamente a 103 familias con diagnóstico previo de posible síndrome de Usher o retinitis pigmentaria asociada con sordera. Materiales y métodos. Se revisaron las historias clínicas de 103 familias con un posible diagnóstico clínico de síndrome de Usher o retinitis pigmentaria asociada con sordera. Se seleccionaron las familias cuyo diagnóstico clínico no correspondía a un síndrome de Usher típico. Los afectados fueron valorados oftalmológica y audiológicamente. Se analizaron variables demográficas y clínicas. Resultados. Se reevaluaron 14 familias cuyo diagnóstico clínico no correspondía al de síndrome de Usher. De las familias con diagnóstico inicial de síndrome de Usher típico, el 13,6 % recibieron uno posterior de “retinitis pigmentaria asociada con sordera” de “otro síntoma ocular asociado con hipoacusia’,’ o en forma aislada en una misma familia, de “retinitis pigmentaria” o “hipoacusia’.’ Conclusiones. Es fundamental el estudio familiar en los casos en que la clínica no concuerda con el diagnóstico de síndrome de Usher típico. En los pacientes con retinitis pigmentaria asociada con sordera, el diagnóstico clínico acertado permite enfocar los análisis moleculares y, así, establecer un diagnóstico diferencial. Es necesario elaborar guías de nomenclatura en los casos con estos hallazgos atípicos para orientar a médicos e investigadores en cuanto a su correcto manejo.
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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: 42] [Impact Index Per Article: 21.0] [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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Zhou C, Xiao Y, Xie H, Liu S, Wang J. A novel USH2A variant in a patient with hearing loss and prenatal diagnosis of a familial fetus: a case report. BMC Med Genomics 2021; 14:200. [PMID: 34376197 PMCID: PMC8353764 DOI: 10.1186/s12920-021-01052-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 08/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Usher syndrome (USH) is the most common cause of inherited deaf-blindness. The current study aimed to identify pathogenic variants in a Chinese patient with hearing loss and to report the identification of a novel p.(Phe1583Leufs*10) variant in USH2A, which met the needs of prenatal diagnosis of the patient's mother. CASE PRESENTATION Genomic DNA obtained from a five-year-old girl with hearing loss was analyzed via the hearing loss-targeted gene panels. We identified the compound heterozygous variants c.8559-2A>G and c.4749delT in Usher syndrome type 2A (USH2A) gene as the underlying cause of the patient; the former variation has been reported in the literature, but not the latter. The parents of the girl were heterozygous carriers. The two variants were classified as pathogenic. Based on these findings, amniotic fluid samples were used for prenatal diagnosis of the couple's fetus, which was found to carry c.4749delT but not c.8559-2A>G variation. During the follow-up period of more than 9 months after the birth of the fetus, it was confirmed that the infant was healthy. CONCLUSIONS The results of the present study identified two compound heterozygous USH2A variants in a patient with hearing loss and reported a novel USH2A variant which expands the spectrum of USH2A variants in USH.
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Affiliation(s)
- Cong Zhou
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Prenatal Diagnosis Center of Sichuan Province, 20 Section 3 Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, People's Republic of China
| | - Yuanyuan Xiao
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Prenatal Diagnosis Center of Sichuan Province, 20 Section 3 Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, People's Republic of China
| | - Hanbing Xie
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Prenatal Diagnosis Center of Sichuan Province, 20 Section 3 Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, People's Republic of China
| | - Shanling Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Prenatal Diagnosis Center of Sichuan Province, 20 Section 3 Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, People's Republic of China.
| | - Jing Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Prenatal Diagnosis Center of Sichuan Province, 20 Section 3 Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, People's Republic of China.
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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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Torkamandi S, Bayat S, Mirfakhraie R, Rezaei S, Askari M, Piltan S, Gholami M. Targeted sequencing of CDH23 and GJB2 genes in an Iranian pedigree with Usher syndrome and non-syndromic hearing loss. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Ahmed AN, Tahir R, Khan N, Ahmad M, Dawood M, Basit A, Yasin M, Nowshid M, Marwan M, Sultan K, Saleha S. USH2A gene variants cause Keratoconus and Usher syndrome phenotypes in Pakistani families. BMC Ophthalmol 2021; 21:191. [PMID: 33926394 PMCID: PMC8086330 DOI: 10.1186/s12886-021-01957-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/21/2021] [Indexed: 01/07/2023] Open
Abstract
Background Retinitis pigmentosa (RP) is the most common inherited retinal dystrophy, affecting approximately 1 in 4000 individuals worldwide. The most common form of syndromic RP is Usher syndrome (USH) accounting for approximately 20–30 % of RP cases. Mutations in the USH2A gene cause a significant proportion of recessive non-syndromic RP and USH type II (USH2). This study aimed to determine the causative role of the USH2A gene in autosomal recessive inherited ocular diseases and to establish genotype-phenotype correlation associated with USH2A variants. Methods We performed direct Sanger sequencing and co-segregation analysis of the USH2A gene to identify disease causing variants in a non-syndromic RP family, two USH2 families and two Keratoconus (KC) families. Results Disease causing variants in the USH2A gene were identified in two families displayed KC and USH2 phenotypes. A novel variant c.4029T > G, p.Asn1343Lys in the USH2A gene was detected in a Pakistani family with KC phenotype. In addition, a missense variant (c.7334 C > T, p. Ser2445Phe) in the USH2A gene was found segregating in another Pakistani family with USH2 phenotype. Homozygosity of identified missense USH2A variants was found associated with autosomal recessive inherited KC and USH2 phenotypes in investigated families. These variants were not detected in ethnically matched healthy controls. Moreover, the USH2A variants were predicted to be deleterious or potentially disease causing by PolyPhen-2, PROVEAN and SIFT. Conclusions This study provided first evidence for association of a novel USH2A variant with KC phenotype in a Pakistani family as well as established the phenotype-genotype correlation of a USH2A variant (c.7334 C > T, p. Ser2445Phe) with USH2 phenotype in another Pakistani family. The phenotype-genotype correlations established in present study may improve clinical diagnosis of affected individuals for better management and counseling.
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Affiliation(s)
- Asif Naveed Ahmed
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Raheel Tahir
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Niamat Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Mushtaq Ahmad
- Medical Teaching Institution, Hayatabad Medical Complex, Peshawar, 25000, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Dawood
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Abdul Basit
- Medical Teaching Institution, Hayatabad Medical Complex, Peshawar, 25000, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Yasin
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Maha Nowshid
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Marwan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Komal Sultan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Shamim Saleha
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat, 26000, Khyber Pakhtunkhwa, Pakistan.
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11
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Qian X, Wang J, Wang M, Igelman AD, Jones KD, Li Y, Wang K, Goetz KE, Birch DG, Yang P, Pennesi ME, Chen R. Identification of Deep-Intronic Splice Mutations in a Large Cohort of Patients With Inherited Retinal Diseases. Front Genet 2021; 12:647400. [PMID: 33737949 PMCID: PMC7960924 DOI: 10.3389/fgene.2021.647400] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/11/2021] [Indexed: 12/13/2022] Open
Abstract
High throughput sequencing technologies have revolutionized the identification of mutations responsible for a diverse set of Mendelian disorders, including inherited retinal disorders (IRDs). However, the causal mutations remain elusive for a significant proportion of patients. This may be partially due to pathogenic mutations located in non-coding regions, which are largely missed by capture sequencing targeting the coding regions. The advent of whole-genome sequencing (WGS) allows us to systematically detect non-coding variations. However, the interpretation of these variations remains a significant bottleneck. In this study, we investigated the contribution of deep-intronic splice variants to IRDs. WGS was performed for a cohort of 571 IRD patients who lack a confident molecular diagnosis, and potential deep intronic variants that affect proper splicing were identified using SpliceAI. A total of six deleterious deep intronic variants were identified in eight patients. An in vitro minigene system was applied to further validate the effect of these variants on the splicing pattern of the associated genes. The prediction scores assigned to splice-site disruption positively correlated with the impact of mutations on splicing, as those with lower prediction scores demonstrated partial splicing. Through this study, we estimated the contribution of deep-intronic splice mutations to unassigned IRD patients and leveraged in silico and in vitro methods to establish a framework for prioritizing deep intronic variant candidates for mechanistic and functional analyses.
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Affiliation(s)
- Xinye Qian
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States
| | - Jun Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Meng Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Austin D Igelman
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, OR, United States
| | - Kaylie D Jones
- Retina Foundation of the Southwest and Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States
| | - Keqing Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States
| | - Kerry E Goetz
- Office of the Director, National Eye Institute/National Institutes of Health, Bethesda, MD, United States
| | - David G Birch
- Retina Foundation of the Southwest and Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Paul Yang
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, OR, United States
| | - Mark E Pennesi
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, OR, United States
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
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12
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Wafa TT, Faridi R, King KA, Zalewski C, Yousaf R, Schultz JM, Morell RJ, Muskett J, Turriff A, Tsilou E, Griffith AJ, Friedman TB, Zein WM, Brewer CC. Vestibular phenotype-genotype correlation in a cohort of 90 patients with Usher syndrome. Clin Genet 2021; 99:226-235. [PMID: 33089500 PMCID: PMC7821283 DOI: 10.1111/cge.13868] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 10/14/2020] [Accepted: 10/18/2020] [Indexed: 12/11/2022]
Abstract
Usher syndrome has been historically categorized into one of three classical types based on the patient phenotype. However, the vestibular phenotype does not infallibly predict which Usher genes are mutated. Conversely, the Usher syndrome genotype is not sufficient to reliably predict vestibular function. Here we present a characterization of the vestibular phenotype of 90 patients with clinical presentation of Usher syndrome (59 females), aged 10.9 to 75.5 years, with genetic variants in eight Usher syndromic genes and expand the description of atypical Usher syndrome. We identified unexpected horizontal semicircular canal reactivity in response to caloric and rotational stimuli in 12.5% (3 of 24) and 41.7% (10 of 24), respectively, of our USH1 cohort. These findings are not consistent with the classical phenotypic definition of vestibular areflexia in USH1. Similarly, 17% (6 of 35) of our cohort with USH2A mutations had saccular dysfunction as evidenced by absent cervical vestibular evoked myogenic potentials in contradiction to the classical assumption of normal vestibular function. The surprising lack of consistent genotypic to vestibular phenotypic findings as well as no clear vestibular phenotypic patterns among atypical USH cases, indicate that even rigorous vestibular phenotyping data will not reliably differentiate the three USH types.
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Affiliation(s)
- Talah T. Wafa
- Otolaryngology BranchNational Institute on Deafness and Other Communication Disorders, National Institutes of HealthBethesdaMarylandUSA
| | - Rabia Faridi
- Laboratory of Molecular GeneticsNational Institute on Deafness and Other Communication Disorders, National Institutes of HealthBethesdaMarylandUSA
| | - Kelly A. King
- Otolaryngology BranchNational Institute on Deafness and Other Communication Disorders, National Institutes of HealthBethesdaMarylandUSA
| | - Christopher Zalewski
- Otolaryngology BranchNational Institute on Deafness and Other Communication Disorders, National Institutes of HealthBethesdaMarylandUSA
| | - Rizwan Yousaf
- Laboratory of Molecular GeneticsNational Institute on Deafness and Other Communication Disorders, National Institutes of HealthBethesdaMarylandUSA
| | - Julie M. Schultz
- Laboratory of Molecular GeneticsNational Institute on Deafness and Other Communication Disorders, National Institutes of HealthBethesdaMarylandUSA
- Review Analysis DepartmentGeneDxGaithersburgMarylandUSA
| | - Robert J. Morell
- Genomics and Computational Biology CoreNational Institute on Deafness and Other Communication Disorders, National Institutes of HealthBethesdaMarylandUSA
| | - Julie Muskett
- Otolaryngology BranchNational Institute on Deafness and Other Communication Disorders, National Institutes of HealthBethesdaMarylandUSA
| | - Amy Turriff
- Ophthalmic Genetics and Visual Function BranchNational Eye Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Ekaterini Tsilou
- Ophthalmic Genetics and Visual Function BranchNational Eye Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Andrew J. Griffith
- Otolaryngology BranchNational Institute on Deafness and Other Communication Disorders, National Institutes of HealthBethesdaMarylandUSA
| | - Thomas B. Friedman
- Laboratory of Molecular GeneticsNational Institute on Deafness and Other Communication Disorders, National Institutes of HealthBethesdaMarylandUSA
| | - Wadih M. Zein
- Ophthalmic Genetics and Visual Function BranchNational Eye Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Carmen C. Brewer
- Otolaryngology BranchNational Institute on Deafness and Other Communication Disorders, National Institutes of HealthBethesdaMarylandUSA
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13
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Fu J, Cheng J, Zhou Q, Khan MA, Duan C, Peng J, Lv H, Fu J. Novel compound heterozygous nonsense variants, p.L150* and p.Y3565*, of the USH2A gene in a Chinese pedigree are associated with Usher syndrome type IIA. Mol Med Rep 2020; 22:3464-3472. [PMID: 32945453 PMCID: PMC7453661 DOI: 10.3892/mmr.2020.11400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 07/06/2020] [Indexed: 12/14/2022] Open
Abstract
Usher syndrome refers to a group of genetically and clinically heterogeneous autosomal recessive diseases with retinitis pigmentosa (RP) and hearing deficiencies. The association between Usher syndrome-causative genes and resultant Usher syndrome phenotypes in patients are highly variable. In the present study, a Chinese family with Usher syndrome was recruited, and targeted next-generation sequencing, Sanger sequencing and segregation analysis were performed. The expression profiles and functional effects of the pathogenic variants of USH2A identified were analyzed. Novel nonsense compound heterozygous variants, c.T449G (p.L150*) and c.T10695A (p.Y3565*), were identified in the USH2A gene, which showed co-segregation with the disease phenotype causing Usher syndrome type IIA in the recruited Chinese pedigree. The p.L150* variant was predicted to produce a truncated protein which lacked almost all the functional domains of USH2A, whereas the p.Y3565* variant is located in one of the fibronectin type 3 domains, resulting in the loss of several fibronectin type 3 domains at the C-terminus of USH2A by producing the truncated protein. It was shown that Ush2a mRNA expression levels were higher in the retina compared with those in the eye tissues (lens, sclera and cornea), uterus, ovary, breast, testis, spleen, kidney, liver, intestine, brain, skeletal muscle and blood. Additionally, the protein structure was shown to be highly conserved by comparing Homo sapiens USH2A to eight other species. To the best of our knowledge, the present study is the first to identify two novel pathogenic variants, c.T449G (p.L150*) and c.T10695A (p.Y3565*), in the USH2A gene in a patient with Usher syndrome type IIA, thereby expanding the known spectrums of USH2A causative mutations. The present discovery may assist in understanding the molecular pathogenesis underlying the development of RP and Usher syndrome type IIA, and in the development of diagnostic, therapeutic and genetic counseling strategies in patients with Usher syndrome type IIA disease.
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Affiliation(s)
- Jiewen Fu
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Jingliang Cheng
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Qi Zhou
- Department of Ophthalmology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Md Asaduzzaman Khan
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Chengxia Duan
- Department of Ophthalmology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Jiangzhou Peng
- Department of Thoracic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong 510630, P.R. China
| | - Hongbin Lv
- Department of Ophthalmology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000, P.R. ChinaDepartment of Ophthalmology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000
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14
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Wang J, Liu H, Bertrand RE, Sarrion-Perdigones A, Gonzalez Y, Venken KJT, Chen R. A novel statistical method for interpreting the pathogenicity of rare variants. Genet Med 2020; 23:59-68. [PMID: 32884132 PMCID: PMC7796914 DOI: 10.1038/s41436-020-00948-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 01/09/2023] Open
Abstract
Purpose: To achieve the ultimate goal of personalized treatment of patients, accurate molecular diagnosis and precise interpretation of the impact of genetic variants on gene function is essential. With the sequencing cost becoming increasingly affordable, accurate distinguishing benign from pathogenic variants upon sequencing becomes the major bottleneck. Although large normal population sequence databases have become a key resource in filtering benign variants, they are not effective at filtering extremely rare variants. Methods: To address this challenge, we developed a novel statistical test by combining sequencing data from a patient cohort with a normal control population database. By comparing the expected and observed allele frequency in the patient cohort, variants that are likely benign can be identified. Results: The performance of this new method is evaluated on both simulated and real datasets coupled with experimental validation. As a result, we demonstrate this new test is well-powered to identify benign variants, particularly effective for variants with low frequency in the normal population. Conclusion: Overall, as a general test that can be applied to any type of variants in the context of all Mendelian diseases, our work provides a general framework for filtering benign variants with very low population allele frequency.
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Affiliation(s)
- Jun Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Hehe Liu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Renae Elaine Bertrand
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Alejandro Sarrion-Perdigones
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Yezabel Gonzalez
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Koen J T Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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15
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Xue K, MacLaren RE. Antisense oligonucleotide therapeutics in clinical trials for the treatment of inherited retinal diseases. Expert Opin Investig Drugs 2020; 29:1163-1170. [PMID: 32741234 DOI: 10.1080/13543784.2020.1804853] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Antisense oligonucleotides (ASOs) represent a class of drugs which can be rationally designed to complement the coding or non-coding regions of target RNA transcripts. They could modulate pre-messenger RNA splicing, induce mRNA knockdown, or block translation of disease-causing genes, thereby slowing disease progression. The pharmacokinetics of intravitreal delivery may enable ASOs to be effective in the treatment of inherited retinal diseases. AREAS COVERED We review the current status of clinical trials of ASO therapies for inherited retinal diseases, which have demonstrated safety, viable durability, and early efficacy. Future applications are discussed in the context of alternative genetic approaches, including gene augmentation and gene editing. EXPERT OPINION Early efficacy data suggest that the splicing-modulating ASO, sepofarsen, is a promising treatment for Leber congenital amaurosis associated with the common c.2991+1655A>G mutation in CEP290. However, potential variability in clinical response to ASO-mediated correction of splicing defect on one allele in patients who are compound heterozygotes needs to be assessed. ASOs hold great therapeutic potential for numerous other inherited retinal diseases with common deep-intronic and dominant gain-of-function mutations. These would complement viral vector-mediated gene augmentation which is generally limited by the size of the transgene and to the treatment of recessive diseases.
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Affiliation(s)
- Kanmin Xue
- Wellcome Trust Clinical Research Career Development Fellow, Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford & Honorary Consultant Vitreoretinal Surgeon, Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust , Oxford, UK
| | - Robert E MacLaren
- Professor of Ophthalmology, Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford & Honorary Consultant Vitreoretinal Surgeon, Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust , Oxford, UK
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16
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Yu D, Zou J, Chen Q, Zhu T, Sui R, Yang J. Structural modeling, mutation analysis, and in vitro expression of usherin, a major protein in inherited retinal degeneration and hearing loss. Comput Struct Biotechnol J 2020; 18:1363-1382. [PMID: 32637036 PMCID: PMC7317166 DOI: 10.1016/j.csbj.2020.05.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 11/15/2022] Open
Abstract
Usherin is the most common causative protein associated with autosomal recessive retinitis pigmentosa (RP) and Usher syndrome (USH), which are characterized by retinal degeneration alone and in combination with hearing loss, respectively. Usherin is essential for photoreceptor survival and hair cell bundle integrity. However, the molecular mechanism underlying usherin function in normal and disease conditions is unclear. In this study, we investigated structural models of usherin domains and localization of usherin pathogenic small in-frame mutations, mainly homozygous missense mutations. We found that usherin fibronectin III (FN3) domains and most laminin-related domains have a β-sandwich structure. Some FN3 domains are predicted to interact with each other and with laminin-related domains. The usherin protein may bend at some FN3 linker regions. RP- and USH-associated small in-frame mutations are differentially located in usherin domains. Most of them are located at the periphery of β-sandwiches, with some at the interface between interacting domains. The usherin laminin epidermal growth factor repeats adopt a rod-shaped structure, which is maintained by disulfide bonds. Most missense mutations and deletion of exon 13 in this region disrupt the disulfide bonds and may affect local protein folding. Despite low expression of the recombinant entire protein and protein fragments in mammalian cell culture, usherin FN3 fragments are more robustly expressed and secreted than its laminin-related fragments. Our findings provide new insights into the usherin structure and the disease mechanisms caused by pathogenic small in-frame mutations, which will help inform future experimental research on diagnosis, disease mechanisms, and therapeutic approaches.
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Key Words
- Cell adhesion
- DCC, deleted in colorectal cancer
- FN3, fibronectin III
- GMQE, global quality estimation score
- HGMD, Human Gene Mutation Database
- Hair cell
- I-TASSER, Iterative Threading ASSEmbly Refinement
- LE, laminin EGF
- LG, laminin globular
- LGL, laminin globular-like
- LN, laminin N-terminal
- Membrane protein
- NCBI, National Center for Biotechnology Information
- Photoreceptor
- Protein folding
- QMEAN, qualitative model energy analysis score
- QSQE, Quaternary Structure Quality Estimation
- RMSD, root mean square deviation
- RP, retinitis pigmentosa
- Recombinant protein expression
- Retinitis pigmentosa
- SMTL, SWISS-MODEL template library
- Structural model
- TM-score, template modeling score
- USH, Usher syndrome
- Usher syndrome
- hFc, human Fc fragment
- mFc, mouse Fc fragment
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Affiliation(s)
- Dongmei Yu
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT, United States
| | - Junhuang Zou
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT, United States
| | - Qian Chen
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT, United States
| | - Tian Zhu
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ruifang Sui
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jun Yang
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT, United States
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT, United States
- Division of Otolaryngology, Department of Surgery, University of Utah, Salt Lake City, UT, United States
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17
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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: 18] [Impact Index Per Article: 4.5] [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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18
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He C, Liu X, Zhong Z, Chen J. Mutation screening of the USH2A gene reveals two novel pathogenic variants in Chinese patients causing simplex usher syndrome 2. BMC Ophthalmol 2020; 20:70. [PMID: 32093671 PMCID: PMC7038606 DOI: 10.1186/s12886-020-01342-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 02/13/2020] [Indexed: 12/19/2022] Open
Abstract
Background Usher syndrome (USH) is the most prevalent cause of the human genetic deafness and blindness. USH type II (USH2) is the most common form of USH, and USH2A is the major pathogenic gene for USH2. For expanding the spectrum of USH2A mutations and further revealing the role of USH2A in USH2, we performed the USH2A gene variant screening in Chinese patients with USH2. Methods Genomic DNA was extracted from peripheral blood of unrelated Chinese USH2 patients, we designed specific primers for amplifying the coding region (exons 2–72) of the USH2A gene. Sanger sequencing was used to study alleles. Silico prediction tools were used to predict the pathogenicity of the variants identified in these patients. Results Five heterozygous pathogenic variants were detected in four patients. Two patients were found to have two-mutations and two patients only have one. Two novel variants c.4217C > A (p.Ser1406X) and c.11780A > G (p.Asp3927Gly)) were predicted deleterious by computer prediction algorithms. In addition, three reported mutations (c.8559-2A > G, c.8232G > C and c.11389 + 3A > T) were also found in this study. Conclusions We identified five heterozygous pathogenic variants in the USH2A gene in Chinese patients diagnosed with Usher syndrome type 2, two of which were not reported. It expands the spectrum of USH2A variants in USH.
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Affiliation(s)
- Chenhao He
- Birth defect group, Translation Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, 200081, China.,Department of Medical Genetics, Tongji University School of Medicine, Shanghai, 200092, China.,Department of Pediatrics of Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200092, China
| | - Xinyu Liu
- Birth defect group, Translation Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, 200081, China.,Department of Medical Genetics, Tongji University School of Medicine, Shanghai, 200092, China.,Department of Pediatrics of Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200092, China
| | - Zilin Zhong
- Birth defect group, Translation Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, 200081, China.,Department of Medical Genetics, Tongji University School of Medicine, Shanghai, 200092, China.,Department of Pediatrics of Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200092, China.,Department of Ophthalmology of Shanghai Tenth People's Hospital, and Tongji Eye Institute, Tongji University School of Medicine, Shanghai, 200092, China
| | - Jianjun Chen
- Birth defect group, Translation Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, 200081, China. .,Department of Medical Genetics, Tongji University School of Medicine, Shanghai, 200092, China. .,Department of Pediatrics of Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200092, China. .,Department of Ophthalmology of Shanghai Tenth People's Hospital, and Tongji Eye Institute, Tongji University School of Medicine, Shanghai, 200092, China. .,Birth defect group, Medical wing building, Tongji University School of Medicine, 1239 SipingRoad Yangpu District, Shanghai, 200092, China.
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19
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Rodríguez-Muñoz A, Aller E, Jaijo T, González-García E, Cabrera-Peset A, Gallego-Pinazo R, Udaondo P, Salom D, García-García G, Millán JM. Expanding the Clinical and Molecular Heterogeneity of Nonsyndromic Inherited Retinal Dystrophies. J Mol Diagn 2020; 22:532-543. [PMID: 32036094 DOI: 10.1016/j.jmoldx.2020.01.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/01/2019] [Accepted: 01/12/2020] [Indexed: 12/21/2022] Open
Abstract
A cohort of 172 patients diagnosed clinically with nonsyndromic retinal dystrophies, from 110 families underwent full ophthalmologic examination, including retinal imaging, electrophysiology, and optical coherence tomography, when feasible. Molecular analysis was performed using targeted next-generation sequencing (NGS). Variants were filtered and prioritized according to the minimum allele frequency, and finally classified according to the American College of Medical Genetics and Genomics guidelines. Multiplex ligation-dependent probe amplification and array comparative genomic hybridization were performed to validate copy number variations identified by NGS. The diagnostic yield of this study was 62% of studied families. Thirty novel mutations were identified. The study found phenotypic intra- and interfamilial variability in families with mutations in C1QTNF5, CERKL, and PROM1; biallelic mutations in PDE6B in a unilateral retinitis pigmentosa patient; interocular asymmetry RP in 50% of the symptomatic RPGR-mutated females; the first case with possible digenism between CNGA1 and CNGB1; and a ROM1 duplication in two unrelated retinitis pigmentosa families. Ten unrelated cases were reclassified. This study highlights the clinical utility of targeted NGS for nonsyndromic inherited retinal dystrophy cases and the importance of full ophthalmologic examination, which allows new genotype-phenotype associations and expands the knowledge of this group of disorders. Identifying the cause of disease is essential to improve patient management, provide accurate genetic counseling, and take advantage of gene therapy-based treatments.
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Affiliation(s)
- Ana Rodríguez-Muñoz
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Unidad Mixta de Enfermedades raras IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain; Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Elena Aller
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Unidad Mixta de Enfermedades raras IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain; Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, Valencia, Spain; Genetics Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Teresa Jaijo
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Unidad Mixta de Enfermedades raras IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain; Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, Valencia, Spain; Genetics Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Emilio González-García
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Departments of Neurophysiology, Hospital de Manises, Valencia, Spain
| | | | - Roberto Gallego-Pinazo
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Macula Unit, Oftalvist Clinic, Valencia, Spain
| | - Patricia Udaondo
- Ophthalmology, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - David Salom
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, Valencia, Spain; Departments of Ophthalmology, Hospital de Manises, Valencia, Spain
| | - Gema García-García
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Unidad Mixta de Enfermedades raras IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain; Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, Valencia, Spain.
| | - José M Millán
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Unidad Mixta de Enfermedades raras IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain; Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, Valencia, Spain.
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20
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Sanjurjo-Soriano C, Erkilic N, Baux D, Mamaeva D, Hamel CP, Meunier I, Roux AF, Kalatzis V. Genome Editing in Patient iPSCs Corrects the Most Prevalent USH2A Mutations and Reveals Intriguing Mutant mRNA Expression Profiles. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2019; 17:156-173. [PMID: 31909088 PMCID: PMC6938853 DOI: 10.1016/j.omtm.2019.11.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 11/15/2019] [Indexed: 12/13/2022]
Abstract
Inherited retinal dystrophies (IRDs) are characterized by progressive photoreceptor degeneration and vision loss. Usher syndrome (USH) is a syndromic IRD characterized by retinitis pigmentosa (RP) and hearing loss. USH is clinically and genetically heterogeneous, and the most prevalent causative gene is USH2A. USH2A mutations also account for a large number of isolated autosomal recessive RP (arRP) cases. This high prevalence is due to two recurrent USH2A mutations, c.2276G>T and c.2299delG. Due to the large size of the USH2A cDNA, gene augmentation therapy is inaccessible. However, CRISPR/Cas9-mediated genome editing is a viable alternative. We used enhanced specificity Cas9 of Streptococcus pyogenes (eSpCas9) to successfully achieve seamless correction of the two most prevalent USH2A mutations in induced pluripotent stem cells (iPSCs) of patients with USH or arRP. Our results highlight features that promote high target efficacy and specificity of eSpCas9. Consistently, we did not identify any off-target mutagenesis in the corrected iPSCs, which also retained pluripotency and genetic stability. Furthermore, analysis of USH2A expression unexpectedly identified aberrant mRNA levels associated with the c.2276G>T and c.2299delG mutations that were reverted following correction. Taken together, our efficient CRISPR/Cas9-mediated strategy for USH2A mutation correction brings hope for a potential treatment for USH and arRP patients.
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Affiliation(s)
- Carla Sanjurjo-Soriano
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier, France.,University of Montpellier, 34095 Montpellier, France
| | - Nejla Erkilic
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier, France.,University of Montpellier, 34095 Montpellier, France
| | - David Baux
- University of Montpellier, 34095 Montpellier, France.,Medical Genetics Laboratory, CHU, 34093 Montpellier, France
| | - Daria Mamaeva
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier, France.,University of Montpellier, 34095 Montpellier, France
| | - Christian P Hamel
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier, France.,University of Montpellier, 34095 Montpellier, France.,National Reference Centre for Inherited Sensory Disorders, CHU, 34295 Montpellier, France
| | - Isabelle Meunier
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier, France.,University of Montpellier, 34095 Montpellier, France.,National Reference Centre for Inherited Sensory Disorders, CHU, 34295 Montpellier, France
| | - Anne-Françoise Roux
- University of Montpellier, 34095 Montpellier, France.,Medical Genetics Laboratory, CHU, 34093 Montpellier, France
| | - Vasiliki Kalatzis
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier, France.,University of Montpellier, 34095 Montpellier, France
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21
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Fakin A, Šuštar M, Brecelj J, Bonnet C, Petit C, Zupan A, Glavač D, Jarc-Vidmar M, Battelino S, Hawlina M. Double Hyperautofluorescent Rings in Patients with USH2A-Retinopathy. Genes (Basel) 2019; 10:genes10120956. [PMID: 31766479 PMCID: PMC6947471 DOI: 10.3390/genes10120956] [Citation(s) in RCA: 9] [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: 10/30/2019] [Revised: 11/17/2019] [Accepted: 11/18/2019] [Indexed: 11/16/2022] Open
Abstract
USH2A mutation is the most common cause of retinitis pigmentosa, with or without hearing impairment. Patients most commonly exhibit hyperautofluorescent ring on fundus autofluorescence imaging (FAF) and rod-cone dystrophy on electrophysiology. A detailed study of three USH2A patients with a rare pattern of double hyperautofluorescent rings was performed. Twenty-four patients with typical single hyperautofluorescent rings were used for comparison of the ages of onset, visual fields, optical coherence tomography, electrophysiology, and audiograms. Double rings delineated the area of pericentral retinal degeneration in all cases. Two patients exhibited rod-cone dystrophy, whereas the third had a cone-rod dystrophy type of dysfunction on electrophysiology. There was minimal progression on follow-up in all three. Patients with double rings had significantly better visual acuity, cone function, and auditory performance than the single ring group. Double rings were associated with combinations of null and missense mutations, none of the latter found in the single ring patients. According to these findings, the double hyperautofluorescent rings indicate a mild subtype of USH2A disease, characterized by pericentral retinal degeneration, mild to moderate hearing loss, and either a rod-cone or cone-rod pattern on electrophysiology, the latter expanding the known clinical spectrum of USH2A-retinopathy.
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Affiliation(s)
- Ana Fakin
- Eye Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (M.Š.); (J.B.); (M.J.-V.); (M.H.)
- Correspondence: ; Tel.: +386-1522-1900
| | - Maja Šuštar
- Eye Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (M.Š.); (J.B.); (M.J.-V.); (M.H.)
| | - Jelka Brecelj
- Eye Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (M.Š.); (J.B.); (M.J.-V.); (M.H.)
| | - Crystel Bonnet
- Unité de Génétique et Physiologie de l’Audition, Institut Pasteur, 75015 Paris, France; (C.B.); (C.P.)
- Unité Mixte de Recherche en Santé (UMRS) 1120, Institut National de la Santé et de la Recherche Médicale (INSERM), 75015 Paris, France
- Complexité du Vivant, Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, 75005 Paris, France
- Institut de l’Audition, 75012 Paris, France
- Syndrome de Usher et Autres Atteintes Rétino-Cochléaires, Institut de la Vision, 75012 Paris, France
| | - Christine Petit
- Unité de Génétique et Physiologie de l’Audition, Institut Pasteur, 75015 Paris, France; (C.B.); (C.P.)
- Unité Mixte de Recherche en Santé (UMRS) 1120, Institut National de la Santé et de la Recherche Médicale (INSERM), 75015 Paris, France
- Complexité du Vivant, Sorbonne Universités, Université Pierre et Marie Curie, Université Paris 06, 75005 Paris, France
- Institut de l’Audition, 75012 Paris, France
- Syndrome de Usher et Autres Atteintes Rétino-Cochléaires, Institut de la Vision, 75012 Paris, France
- Collège de France, 75005 Paris, France
| | - Andrej Zupan
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (D.G.)
| | - Damjan Glavač
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (D.G.)
| | - Martina Jarc-Vidmar
- Eye Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (M.Š.); (J.B.); (M.J.-V.); (M.H.)
| | - Saba Battelino
- Department of Otorhinolaryngology and Cervicofacial Surgery, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia;
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Marko Hawlina
- Eye Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (M.Š.); (J.B.); (M.J.-V.); (M.H.)
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22
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Hagag AM, Mitsios A, Gill JS, Nunez Do Rio JM, Theofylaktopoulos V, Houston S, Webster AR, Dubis AM, Moosajee M. Characterisation of microvascular abnormalities using OCT angiography in patients with biallelic variants in USH2A and MYO7A. Br J Ophthalmol 2019; 104:480-486. [PMID: 31266775 DOI: 10.1136/bjophthalmol-2019-314243] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/21/2019] [Accepted: 06/10/2019] [Indexed: 01/26/2023]
Abstract
AIMS Using optical coherence tomography angiography (OCTA) to characterise microvascular changes in the retinal plexuses and choriocapillaris (CC) of patients with MYO7A and USH2A mutations and correlate with genotype, retinal structure and function. METHODS Twenty-seven patients with molecularly confirmed USH2A (n=21) and MYO7A (n=6) mutations underwent macular 6×6 mm OCTA using the AngioVue. Heidelberg spectral-domain OCT scans and MAIA microperimetry were also performed, the preserved ellipsoid zone (EZ) band width and mean macular sensitivity (MS) were recorded. OCTA of the inner retina, superficial capillary plexus (SCP), deep capillary plexus (DCP) and CC were analysed. Vessel density (VD) was calculated from the en face OCT angiograms of retinal circulation. RESULTS Forty-eight eyes with either USH2A (n=37, mean age: 34.4±12.2 years) or MYO7A (n=11, mean age: 37.1±12.4 years), and 35 eyes from 18 age-matched healthy participants were included. VD was significantly decreased in the retinal circulation of patients with USH2A and MYO7A mutations compared with controls (p<0.001). Changes were observed in both the SCP and DCP, but no differences in retinal perfusion were detected between USH2A and MYO7A groups. No vascular defects were detected in CC of the USH2A group, but peripheral defects were detected in older MYO7A patients from the fourth decade of life. VD in the DCP showed strong association with MS and EZ width (Spearman's rho =0.64 and 0.59, respectively, p<0.001). CONCLUSION OCTA was able to detect similar retinal microvascular changes in patients with USH2A and MYO7A mutations. The CC was generally affected in MYO7A mutations. OCT angiography may further enhance our understanding of inherited eye diseases and their phenotype-genotype associations.
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Affiliation(s)
- Ahmed M Hagag
- NIHR Clinical Research Facility, Moorfields Eye Hospital NHS Foundation Trust, London, UK.,Institute of Ophthalmology, University College London, London, UK
| | - Andreas Mitsios
- NIHR Clinical Research Facility, Moorfields Eye Hospital NHS Foundation Trust, London, UK.,Institute of Ophthalmology, University College London, London, UK
| | - Jasdeep S Gill
- Institute of Ophthalmology, University College London, London, UK
| | | | | | - Sarah Houston
- Institute of Ophthalmology, University College London, London, UK
| | - Andrew R Webster
- Institute of Ophthalmology, University College London, London, UK.,Genetics Service, Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Adam M Dubis
- NIHR Clinical Research Facility, Moorfields Eye Hospital NHS Foundation Trust, London, UK.,Institute of Ophthalmology, University College London, London, UK
| | - Mariya Moosajee
- Institute of Ophthalmology, University College London, London, UK .,Genetics Service, Moorfields Eye Hospital NHS Foundation Trust, London, UK.,Department of Ophthalmology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
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23
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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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24
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A new approach based on targeted pooled DNA sequencing identifies novel mutations in patients with Inherited Retinal Dystrophies. Sci Rep 2018; 8:15457. [PMID: 30337596 PMCID: PMC6194132 DOI: 10.1038/s41598-018-33810-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 10/04/2018] [Indexed: 01/28/2023] Open
Abstract
Inherited retinal diseases (IRD) are a heterogeneous group of diseases that mainly affect the retina; more than 250 genes have been linked to the disease and more than 20 different clinical phenotypes have been described. This heterogeneity both at the clinical and genetic levels complicates the identification of causative mutations. Therefore, a detailed genetic characterization is important for genetic counselling and decisions regarding treatment. In this study, we developed a method consisting on pooled targeted next generation sequencing (NGS) that we applied to 316 eye disease related genes, followed by High Resolution Melting and copy number variation analysis. DNA from 115 unrelated test samples was pooled and samples with known mutations were used as positive controls to assess the sensitivity of our approach. Causal mutations for IRDs were found in 36 patients achieving a detection rate of 31.3%. Overall, 49 likely causative mutations were identified in characterized patients, 14 of which were first described in this study (28.6%). Our study shows that this new approach is a cost-effective tool for detection of causative mutations in patients with inherited retinopathies.
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25
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Pérez-Carro R, Blanco-Kelly F, Galbis-Martínez L, García-García G, Aller E, García-Sandoval B, Mínguez P, Corton M, Mahíllo-Fernández I, Martín-Mérida I, Avila-Fernández A, Millán JM, Ayuso C. Unravelling the pathogenic role and genotype-phenotype correlation of the USH2A p.(Cys759Phe) variant among Spanish families. PLoS One 2018; 13:e0199048. [PMID: 29912909 PMCID: PMC6005481 DOI: 10.1371/journal.pone.0199048] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/30/2018] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Mutations in USH2A cause both isolated Retinitis Pigmentosa (RP) and Usher syndrome (that implies RP and hearing impairment). One of the most frequent variants identified in this gene and among these patients is the p.(Cys759Phe) change. However, the pathogenic role of this allele has been questioned since it was found in homozygosity in two healthy siblings of a Spanish family. To assess the causative role of USH2A p.(Cys759Phe) in autosomal recessive RP (ARRP) and Usher syndrome type II (USH2) and to establish possible genotype-phenotype correlations associated with p.(Cys759Phe), we performed a comprehensive genetic and clinical study in patients suffering from any of the two above-mentioned diseases and carrying at least one p.(Cys759Phe) allele. MATERIALS AND METHODS Diagnosis was set according to previously reported protocols. Genetic analyses were performed by using classical molecular and Next-Generation Sequencing approaches. Probands of 57 unrelated families were molecularly studied and 63 patients belonging to these families were phenotypically evaluated. RESULTS Molecular analysis characterized 100% of the cases, identifying: 11 homozygous patients for USH2A p.(Cys759Phe), 42 compound heterozygous patients (12 of them with another missense USH2A pathogenic variant and 30 with a truncating USH2A variant), and 4 patients carrying the p.(Cys759Phe) allele and a pathogenic variant in another RP gene (PROM1, CNGB1 or RP1). No additional causative variants were identified in symptomatic homozygous patients. Statistical analysis of clinical differences between zygosity states yielded differences (p≤0.05) in age at diagnosis of RP and hypoacusis, and progression of visual field loss. Homozygosity of p.(Cys759Phe) and compound heterozygosity with another USH2A missense variant is associated with ARRP or ARRP plus late onset hypoacusis (OR = 20.62, CI = 95%, p = 0.041). CONCLUSIONS The present study supports the role of USH2A p.(Cys759Phe) in ARRP and USH2 pathogenesis, and demonstrates the clinical differences between different zygosity states. Phenotype-genotype correlations may guide the genetic characterization based upon specific clinical signs and may advise on the clinical management and prognosis based upon a specific genotype.
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Affiliation(s)
- Raquel Pérez-Carro
- Department of Genetics, Instituto de Investigación Sanitaria–Fundación Jimenez Diaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics, Instituto de Investigación Sanitaria–Fundación Jimenez Diaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Lilián Galbis-Martínez
- Department of Genetics, Instituto de Investigación Sanitaria–Fundación Jimenez Diaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Gema García-García
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
- Research group on Molecular, Cellular and Genomic Biomedicine, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
| | - Elena Aller
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
- Research group on Molecular, Cellular and Genomic Biomedicine, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
| | - Blanca García-Sandoval
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
- Department of Ophthalmology, Instituto de Investigación Sanitaria–Fundación Jimenez Diaz University Hospital–Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Pablo Mínguez
- Department of Genetics, Instituto de Investigación Sanitaria–Fundación Jimenez Diaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Marta Corton
- Department of Genetics, Instituto de Investigación Sanitaria–Fundación Jimenez Diaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Ignacio Mahíllo-Fernández
- Department of Epidemiology and Biostatistics, Instituto de Investigación Sanitaria-Fundación Jimenez Diaz-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Inmaculada Martín-Mérida
- Department of Genetics, Instituto de Investigación Sanitaria–Fundación Jimenez Diaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Almudena Avila-Fernández
- Department of Genetics, Instituto de Investigación Sanitaria–Fundación Jimenez Diaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - José M. Millán
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
- Research group on Molecular, Cellular and Genomic Biomedicine, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria–Fundación Jimenez Diaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
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26
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Wang X, Zein WM, D'Souza L, Roberson C, Wetherby K, He H, Villarta A, Turriff A, Johnson KR, Fann YC. Applying next generation sequencing with microdroplet PCR to determine the disease-causing mutations in retinal dystrophies. BMC Ophthalmol 2017; 17:157. [PMID: 28838317 PMCID: PMC5571584 DOI: 10.1186/s12886-017-0549-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 08/14/2017] [Indexed: 01/07/2023] Open
Abstract
Background Inherited Retinal dystrophy (IRD) is a broad group of inherited retinal disorders with heterogeneous genotypes and phenotypes. Next generation sequencing (NGS) methods have been broadly applied for analyzing patients with IRD. Here we report a novel approach to enrich the target gene panel by microdroplet PCR. Methods This assay involved a primer library which targeted 3071 amplicons from 2078 exons comprised of 184 genes involved in retinal function and/or retinal development. We amplified the target regions using the RainDance target enrichment PCR method and sequenced the products using the MiSeq NGS platform. Results In this study, we analyzed 82 samples from 67 families with IRD. Bioinformatics analysis indicated that this procedure was able to reach 99% coverage of target sequences with an average sequence depth of reads at 119×. The variants detected by this study were filtered, validated, and prioritized by pathogenicity analysis. Genotypes and phenotypes were correlated by determining a consistent relationship in 38 propands (56.7%). Pathogenic variants in genes related to retinal function were found in another 11 probands (16.4%), but the clinical correlations showed inconsistencies and insufficiencies in these patients. Conclusions The application of NGS in IRD clinical molecular diagnosis provides a powerful approach to exploring the etiology and pathology in patients. It is important for the clinical laboratory to interpret the molecular findings in the context of patient clinical presentations because accurate interpretation of pathogenic variants is critical for delivering solid clinical molecular diagnosis to clinicians and patients and improving the standard care of patients. Electronic supplementary material The online version of this article (doi:10.1186/s12886-017-0549-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xinjing Wang
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, 10D43, 10 Center Drive, Bethesda, MD, 20892, USA.
| | - Wadih M Zein
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, 10D43, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Leera D'Souza
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, 10D43, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Chimere Roberson
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, 10D43, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Keith Wetherby
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, 10D43, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Hong He
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, 10D43, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Angela Villarta
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, 10D43, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Amy Turriff
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, 10D43, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Kory R Johnson
- Intramural IT and Bioinformatics Program, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Yang C Fann
- Intramural IT and Bioinformatics Program, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
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27
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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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28
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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: 46] [Impact Index Per Article: 6.6] [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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29
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Dad S, Rendtorff ND, Tranebjærg L, Grønskov K, Karstensen HG, Brox V, Nilssen Ø, Roux AF, Rosenberg T, Jensen H, Møller LB. Usher syndrome in Denmark: mutation spectrum and some clinical observations. Mol Genet Genomic Med 2016; 4:527-539. [PMID: 27957503 PMCID: PMC5023938 DOI: 10.1002/mgg3.228] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 12/22/2022] Open
Abstract
Background Usher syndrome (USH) is a genetically heterogeneous deafness‐blindness syndrome, divided into three clinical subtypes: USH1, USH2 and USH3. Methods Mutations in 21 out of 26 investigated Danish unrelated individuals with USH were identified, using a combination of molecular diagnostic methods. Results Before Next Generation Sequencing (NGS) became available mutations in nine individuals (1 USH1, 7 USH2, 1 USH3) were identified by Sanger sequencing of USH1C,USH2A or CLRN1 or by Arrayed Primer EXtension (APEX) method. Mutations in 12 individuals (7 USH1, 5 USH2) were found by targeted NGS of ten known USH genes. Five novel pathogenic variants were identified. We combined our data with previously published, and obtained an overview of the USH mutation spectrum in Denmark, including 100 unrelated individuals; 32 with USH1, 67 with USH2, and 1 with USH3. Macular edema was observed in 44 of 117 individuals. Olfactory function was tested in 12 individuals and found to be within normal range in all. Conclusion Mutations that lead to USH1 were predominantly identified in MYO7A (75%), whereas all mutations in USH2 cases were identified in USH2A. The MYO7A mutation c.93C>A, p.(Cys31*) accounted for 33% of all USH1 mutations and the USH2A c.2299delG, p.(Glu767Serfs*21) variant accounted for 45% of all USH2 mutations in the Danish cohort.
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Affiliation(s)
- Shzeena Dad
- Applied Human Genetics Kennedy Center Department of Clinical Genetics Copenhagen University Rigshospitalet Glostrup Denmark
| | - Nanna Dahl Rendtorff
- Applied Human GeneticsKennedy CenterDepartment of Clinical GeneticsCopenhagen UniversityRigshospitaletGlostrupDenmark; Department of Cellular and Molecular MedicineThe Faculty of Health SciencesUniversity of Copenhagen2200CopenhagenDenmark; Department of Otorhinolaryngology, Head & Neck Surgery and AudiologyBispebjerg Hospital/RigshospitaletCopenhagenDenmark
| | - Lisbeth Tranebjærg
- Applied Human GeneticsKennedy CenterDepartment of Clinical GeneticsCopenhagen UniversityRigshospitaletGlostrupDenmark; Department of Cellular and Molecular MedicineThe Faculty of Health SciencesUniversity of Copenhagen2200CopenhagenDenmark; Department of Otorhinolaryngology, Head & Neck Surgery and AudiologyBispebjerg Hospital/RigshospitaletCopenhagenDenmark
| | - Karen Grønskov
- Applied Human GeneticsKennedy CenterDepartment of Clinical GeneticsCopenhagen UniversityRigshospitaletGlostrupDenmark; Department of Cellular and Molecular MedicineThe Faculty of Health SciencesUniversity of Copenhagen2200CopenhagenDenmark
| | - Helena Gásdal Karstensen
- Department of Cellular and Molecular Medicine The Faculty of Health Sciences University of Copenhagen 2200 Copenhagen Denmark
| | - Vigdis Brox
- Department of Medical Genetics University Hospital of North-Norway N-9038 Tromsø Norway
| | - Øivind Nilssen
- Department of Medical GeneticsUniversity Hospital of North-NorwayN-9038TromsøNorway; Department of Clinical Medicine, Medical GeneticsUniversity of TromsøNO-9037TromsøNorway
| | - Anne-Françoise Roux
- Laboratoire de Génétique MoléculaireCHU MontpellierMontpellierF-34000France; U827InsermMontpellierF-34000France
| | - Thomas Rosenberg
- The National Eye ClinicThe Kennedy CenterDepartment of OphthalmologyCopenhagen University Hospital2600RigshospitaletGlostrupDenmark; Institute of Clinical MedicineThe Faculty of Health SciencesUniversity of Copenhagen2200Copenhagen NDenmark
| | - Hanne Jensen
- The National Eye Clinic The Kennedy Center Department of Ophthalmology Copenhagen University Hospital 2600 Rigshospitalet Glostrup Denmark
| | - Lisbeth Birk Møller
- Applied Human GeneticsKennedy CenterDepartment of Clinical GeneticsCopenhagen UniversityRigshospitaletGlostrupDenmark; Department of Cellular and Molecular MedicineThe Faculty of Health SciencesUniversity of Copenhagen2200CopenhagenDenmark; Department of Science Systems and Models (NSM)Roskilde UniversityDK 4000RoskildeDenmark
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30
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Pierrache LH, Hartel BP, van Wijk E, Meester-Smoor MA, Cremers FP, de Baere E, de Zaeytijd J, van Schooneveld MJ, Cremers CW, Dagnelie G, Hoyng CB, Bergen AA, Leroy BP, Pennings RJ, van den Born LI, Klaver CC. Visual Prognosis in USH2A-Associated Retinitis Pigmentosa Is Worse for Patients with Usher Syndrome Type IIa Than for Those with Nonsyndromic Retinitis Pigmentosa. Ophthalmology 2016; 123:1151-60. [DOI: 10.1016/j.ophtha.2016.01.021] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 01/09/2016] [Accepted: 01/13/2016] [Indexed: 12/25/2022] Open
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31
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Pham H, Lingao MD, Ganesh A, Capasso JE, Keep R, Sadagopan KA, Levin AV. Organophosphate retinopathy. Oman J Ophthalmol 2016; 9:49-51. [PMID: 27013829 PMCID: PMC4785709 DOI: 10.4103/0974-620x.176101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Organophosphates have rarely been reported to cause various ocular sequelae including retinal degeneration. Retinal manifestations have been rarely reported and poorly characterized. We describe a case of a 76-year-old man with vision loss beginning in his 20s due to acute on chronic exposure to dimethoate, an organophosphate. He presented with bilateral geographic macular atrophy and midperipheral pigmentary clumping which we characterized by dilated fundoscopic examination, optical coherence tomography, and fundus autofluorescence.
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Affiliation(s)
- Hang Pham
- Sidney Kimmel Medical College, Thomas Jefferson University, Philippines
| | - Michelle D Lingao
- Department of Pediatric Ophthalmology and Asian Eye Institute, Makati, Philippines
| | - Anuradha Ganesh
- Department of Ophthalmology, Sultan Qaboos University Hospital, Muscat, Oman
| | - Jenina E Capasso
- Department of Pediatric Ophthalmology and Ocular Genetics, Wills Eye Hospital, Philippines
| | | | - Karthikeyan A Sadagopan
- Department of Pediatric Ophthalmology and Ocular Genetics, CMER (Shenzhen) Dennis Lam Eye Hospital, Shenzhen, China
| | - Alex V Levin
- Sidney Kimmel Medical College, Thomas Jefferson University, Philippines; Department of Pediatric Ophthalmology and Ocular Genetics, Wills Eye Hospital, Philippines
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32
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Yang J, Chen X, Bai J, Fang D, Qiu Y, Jiang W, Yuan H, Bian C, Lu J, He S, Pan X, Zhang Y, Wang X, You X, Wang Y, Sun Y, Mao D, Liu Y, Fan G, Zhang H, Chen X, Zhang X, Zheng L, Wang J, Cheng L, Chen J, Ruan Z, Li J, Yu H, Peng C, Ma X, Xu J, He Y, Xu Z, Xu P, Wang J, Yang H, Wang J, Whitten T, Xu X, Shi Q. The Sinocyclocheilus cavefish genome provides insights into cave adaptation. BMC Biol 2016; 14:1. [PMID: 26728391 PMCID: PMC4698820 DOI: 10.1186/s12915-015-0223-4] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/17/2015] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND An emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively. RESULTS The assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes. CONCLUSION As the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology.
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Affiliation(s)
- Junxing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | | | - Jie Bai
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. .,Fauna & Flora International, Cambridge, CB1 2JD, UK.
| | - Dongming Fang
- BGI-Shenzhen, Shenzhen, 518083, China. .,Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| | - Ying Qiu
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. .,China National Genebank, Shenzhen, 518083, China.
| | - Wansheng Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Hui Yuan
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Chao Bian
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | - Jiang Lu
- BGI-Shenzhen, Shenzhen, 518083, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Shiyang He
- BGI-Shenzhen, Shenzhen, 518083, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiaofu Pan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Yaolei Zhang
- BGI-Shenzhen, Shenzhen, 518083, China. .,School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.
| | - Xiaoai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Xinxin You
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | | | - Ying Sun
- BGI-Shenzhen, Shenzhen, 518083, China. .,China National Genebank, Shenzhen, 518083, China.
| | | | - Yong Liu
- BGI-Shenzhen, Shenzhen, 518083, China.
| | | | - He Zhang
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Xiaoyong Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Xinhui Zhang
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | - Lanping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | | | - Le Cheng
- China National Genebank, Shenzhen, 518083, China. .,BGI-Yunnan, Kunming, 650106, China.
| | - Jieming Chen
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | - Zhiqiang Ruan
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | - Jia Li
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Hui Yu
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Chao Peng
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China.
| | - Xingyu Ma
- Shenzhen BGI Fisheries Sci & Tech Co. Ltd., Shenzhen, 518083, China. .,Zhenjiang BGI Fisheries Science & Technology Industrial Co. Ltd., Zhenjiang, 212000, China.
| | - Junmin Xu
- Shenzhen BGI Fisheries Sci & Tech Co. Ltd., Shenzhen, 518083, China. .,Zhenjiang BGI Fisheries Science & Technology Industrial Co. Ltd., Zhenjiang, 212000, China.
| | - You He
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201204, China.
| | - Zhengfeng Xu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, 210029, China.
| | - Pao Xu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China. .,James D. Watson Institute of Genome Science, Hangzhou, 310008, China.
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China. .,James D. Watson Institute of Genome Science, Hangzhou, 310008, China.
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, 518083, China. .,Department of Biology, Ole Maaløes Vej 5, University of Copenhagen, DK-2200, Copenhagen, Denmark.
| | - Tony Whitten
- Fauna & Flora International, Cambridge, CB1 2JD, UK.
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Qiong Shi
- BGI-Shenzhen, Shenzhen, 518083, China. .,Shenzhen Key Lab of Marine Genomics, State Key Laboratory of Agricultural Genomics, Shenzhen, 518083, China. .,Shenzhen BGI Fisheries Sci & Tech Co. Ltd., Shenzhen, 518083, China. .,Zhenjiang BGI Fisheries Science & Technology Industrial Co. Ltd., Zhenjiang, 212000, China.
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Liquori A, Vaché C, Baux D, Blanchet C, Hamel C, Malcolm S, Koenig M, Claustres M, Roux AF. Whole USH2A Gene Sequencing Identifies Several New Deep Intronic Mutations. Hum Mutat 2015; 37:184-93. [PMID: 26629787 DOI: 10.1002/humu.22926] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/19/2015] [Indexed: 01/01/2023]
Abstract
Deep intronic mutations leading to pseudoexon (PE) insertions are underestimated and most of these splicing alterations have been identified by transcript analysis, for instance, the first deep intronic mutation in USH2A, the gene most frequently involved in Usher syndrome type II (USH2). Unfortunately, analyzing USH2A transcripts is challenging and for 1.8%-19% of USH2 individuals carrying a single USH2A recessive mutation, a second mutation is yet to be identified. We have developed and validated a DNA next-generation sequencing approach to identify deep intronic variants in USH2A and evaluated their consequences on splicing. Three distinct novel deep intronic mutations have been identified. All were predicted to affect splicing and resulted in the insertion of PEs, as shown by minigene assays. We present a new and attractive strategy to identify deep intronic mutations, when RNA analyses are not possible. Moreover, the bioinformatics pipeline developed is independent of the gene size, implying the possible application of this approach to any disease-linked gene. Finally, an antisense morpholino oligonucleotide tested in vitro for its ability to restore splicing caused by the c.9959-4159A>G mutation provided high inhibition rates, which are indicative of its potential for molecular therapy.
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Affiliation(s)
- Alessandro Liquori
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France
| | - Christel Vaché
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHRU Montpellier, Montpellier, France
| | - David Baux
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHRU Montpellier, Montpellier, France
| | - Catherine Blanchet
- Service ORL, CHRU Montpellier, Montpellier, France.,CHU Montpellier, Centre National de Référence Maladies Rares, "Affections Sensorielles Génétiques, France
| | - Christian Hamel
- CHU Montpellier, Centre National de Référence Maladies Rares, "Affections Sensorielles Génétiques, France
| | - Sue Malcolm
- Genetics and Genomic Medicine Programme, Institute of Child Health, UCL, London, UK
| | - Michel Koenig
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHRU Montpellier, Montpellier, France
| | - Mireille Claustres
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHRU Montpellier, Montpellier, France
| | - Anne-Françoise Roux
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHRU Montpellier, Montpellier, France
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Lee K, Berg JS, Milko L, Crooks K, Lu M, Bizon C, Owen P, Wilhelmsen KC, Weck KE, Evans JP, Garg S. High Diagnostic Yield of Whole Exome Sequencing in Participants With Retinal Dystrophies in a Clinical Ophthalmology Setting. Am J Ophthalmol 2015; 160:354-363.e9. [PMID: 25910913 DOI: 10.1016/j.ajo.2015.04.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/14/2015] [Accepted: 04/15/2015] [Indexed: 11/17/2022]
Abstract
PURPOSE To assess the diagnostic yield and the practicality of implementing whole exome sequencing within a clinical ophthalmology setting. DESIGN Evaluation of a diagnostic protocol. METHODS setting: Patient participants were enrolled during clinical appointments in a university-based ophthalmic genetics clinic. PATIENT POPULATION Twenty-six patients with a variety of presumed hereditary retinal dystrophies. INTERVENTION Participants were offered whole exome sequencing in addition to clinically available sequencing gene panels between July 2012 and January 2013 to determine the molecular etiology of their retinal dystrophy. MAIN OUTCOME MEASURES Diagnostic yield and acceptability of whole exome sequencing in patients with retinal disorders. RESULTS Twenty-six of 29 eligible patients (∼90%) who were approached opted to undergo molecular testing. Each participant chose whole exome sequencing in addition to, or in lieu of, clinically available sequencing gene panels. Time to obtain informed consent was manageable in the clinical context. Whole exome sequencing successfully identified known pathogenic mutations or suspected deleterious variants in 57.7% of participants. Additionally, 1 participant had 2 autosomal dominant medically actionable incidental findings (unrelated to retinopathy) that were reported to enable the participant to take preventive action and reduce risk for future disease. CONCLUSIONS In this study, we identified the molecular etiology for more than half of all participants. Additionally, we found that participants were widely accepting of whole exome sequencing and the possibility of being informed about medically actionable incidental findings.
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Affiliation(s)
- Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Laura Milko
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kristy Crooks
- Department of Pathology & Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Mei Lu
- Department of Pathology & Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Chris Bizon
- The Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Phillips Owen
- The Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kirk C Wilhelmsen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; The Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Karen E Weck
- Department of Pathology & Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - James P Evans
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Seema Garg
- Department of Ophthalmology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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Lenassi E, Vincent A, Li Z, Saihan Z, Coffey AJ, Steele-Stallard HB, Moore AT, Steel KP, Luxon LM, Héon E, Bitner-Glindzicz M, Webster AR. A detailed clinical and molecular survey of subjects with nonsyndromic USH2A retinopathy reveals an allelic hierarchy of disease-causing variants. Eur J Hum Genet 2015; 23:1318-27. [PMID: 25649381 PMCID: PMC4592079 DOI: 10.1038/ejhg.2014.283] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 11/20/2014] [Accepted: 12/02/2014] [Indexed: 12/19/2022] Open
Abstract
Defects in USH2A cause both isolated retinal disease and Usher syndrome (ie, retinal disease and deafness). To gain insights into isolated/nonsyndromic USH2A retinopathy, we screened USH2A in 186 probands with recessive retinal disease and no hearing complaint in childhood (discovery cohort) and in 84 probands with recessive retinal disease (replication cohort). Detailed phenotyping, including retinal imaging and audiological assessment, was performed in individuals with two likely disease-causing USH2A variants. Further genetic testing, including screening for a deep-intronic disease-causing variant and large deletions/duplications, was performed in those with one likely disease-causing change. Overall, 23 of 186 probands (discovery cohort) were found to harbour two likely disease-causing variants in USH2A. Some of these variants were predominantly associated with nonsyndromic retinal degeneration (‘retinal disease-specific'); these included the common c.2276 G>T, p.(Cys759Phe) mutation and five additional variants: c.2802 T>G, p.(Cys934Trp); c.10073 G>A, p.(Cys3358Tyr); c.11156 G>A, p.(Arg3719His); c.12295-3 T>A; and c.12575 G>A, p.(Arg4192His). An allelic hierarchy was observed in the discovery cohort and confirmed in the replication cohort. In nonsyndromic USH2A disease, retinopathy was consistent with retinitis pigmentosa and the audiological phenotype was variable. USH2A retinopathy is a common cause of nonsyndromic recessive retinal degeneration and has a different mutational spectrum to that observed in Usher syndrome. The following model is proposed: the presence of at least one ‘retinal disease-specific' USH2A allele in a patient with USH2A-related disease results in the preservation of normal hearing. Careful genotype–phenotype studies such as this will become increasingly important, especially now that high-throughput sequencing is widely used in the clinical setting.
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Affiliation(s)
- Eva Lenassi
- UCL Institute of Ophthalmology and Moorfields Eye Hospital, University College of London, London, UK.,Eye Hospital, University Medical Centre, Ljubljana, Slovenia
| | - Ajoy Vincent
- The Hospital for Sick Children, Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada
| | - Zheng Li
- UCL Institute of Ophthalmology and Moorfields Eye Hospital, University College of London, London, UK.,Ocular Genetics, Singapore Eye Research Institute, Singapore, Singapore
| | - Zubin Saihan
- UCL Institute of Ophthalmology and Moorfields Eye Hospital, University College of London, London, UK
| | | | | | - Anthony T Moore
- UCL Institute of Ophthalmology and Moorfields Eye Hospital, University College of London, London, UK
| | | | - Linda M Luxon
- UCL Ear Institute, London, UK.,National Hospital for Neurology and Neurosurgery, London, UK
| | - Elise Héon
- The Hospital for Sick Children, Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada
| | | | - Andrew R Webster
- UCL Institute of Ophthalmology and Moorfields Eye Hospital, University College of London, London, UK
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Sodi A, Mariottini A, Passerini I, Murro V, Tachyla I, Bianchi B, Menchini U, Torricelli F. MYO7A and USH2A gene sequence variants in Italian patients with Usher syndrome. Mol Vis 2014; 20:1717-31. [PMID: 25558175 PMCID: PMC4279600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 12/20/2014] [Indexed: 10/28/2022] Open
Abstract
PURPOSE To analyze the spectrum of sequence variants in the MYO7A and USH2A genes in a group of Italian patients affected by Usher syndrome (USH). METHODS Thirty-six Italian patients with a diagnosis of USH were recruited. They received a standard ophthalmologic examination, visual field testing, optical coherence tomography (OCT) scan, and electrophysiological tests. Fluorescein angiography and fundus autofluorescence imaging were performed in selected cases. All the patients underwent an audiologic examination for the 0.25-8,000 Hz frequencies. Vestibular function was evaluated with specific tests. DNA samples were analyzed for sequence variants of the MYO7A gene (for USH1) and the USH2A gene (for USH2) with direct sequencing techniques. A few patients were analyzed for both genes. RESULTS In the MYO7A gene, ten missense variants were found; three patients were compound heterozygous, and two were homozygous. Thirty-four USH2A gene variants were detected, including eight missense variants, nine nonsense variants, six splicing variants, and 11 duplications/deletions; 19 patients were compound heterozygous, and three were homozygous. Four MYO7A and 17 USH2A variants have already been described in the literature. Among the novel mutations there are four USH2A large deletions, detected with multiplex ligation dependent probe amplification (MLPA) technology. Two potentially pathogenic variants were found in 27 patients (75%). Affected patients showed variable clinical pictures without a clear genotype-phenotype correlation. CONCLUSIONS Ten variants in the MYO7A gene and 34 variants in the USH2A gene were detected in Italian patients with USH at a high detection rate. A selective analysis of these genes may be valuable for molecular analysis, combining diagnostic efficiency with little time wastage and less resource consumption.
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Affiliation(s)
- Andrea Sodi
- Department of Ophthalmology, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Alessandro Mariottini
- Department of Genetic Diagnosis, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Ilaria Passerini
- Department of Genetic Diagnosis, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Vittoria Murro
- Department of Ophthalmology, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Iryna Tachyla
- Department of Ophthalmology, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Benedetta Bianchi
- Department of Otolaryngology, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Ugo Menchini
- Department of Ophthalmology, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Francesca Torricelli
- Department of Genetic Diagnosis, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
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37
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Aparisi MJ, Aller E, Fuster-García C, García-García G, Rodrigo R, Vázquez-Manrique RP, Blanco-Kelly F, Ayuso C, Roux AF, Jaijo T, Millán JM. Targeted next generation sequencing for molecular diagnosis of Usher syndrome. Orphanet J Rare Dis 2014; 9:168. [PMID: 25404053 PMCID: PMC4245769 DOI: 10.1186/s13023-014-0168-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 10/27/2014] [Indexed: 11/17/2022] Open
Abstract
Background Usher syndrome is an autosomal recessive disease that associates sensorineural hearing loss, retinitis pigmentosa and, in some cases, vestibular dysfunction. It is clinically and genetically heterogeneous. To date, 10 genes have been associated with the disease, making its molecular diagnosis based on Sanger sequencing, expensive and time-consuming. Consequently, the aim of the present study was to develop a molecular diagnostics method for Usher syndrome, based on targeted next generation sequencing. Methods A custom HaloPlex panel for Illumina platforms was designed to capture all exons of the 10 known causative Usher syndrome genes (MYO7A, USH1C, CDH23, PCDH15, USH1G, CIB2, USH2A, GPR98, DFNB31 and CLRN1), the two Usher syndrome-related genes (HARS and PDZD7) and the two candidate genes VEZT and MYO15A. A cohort of 44 patients suffering from Usher syndrome was selected for this study. This cohort was divided into two groups: a test group of 11 patients with known mutations and another group of 33 patients with unknown mutations. Results Forty USH patients were successfully sequenced, 8 USH patients from the test group and 32 patients from the group composed of USH patients without genetic diagnosis. We were able to detect biallelic mutations in one USH gene in 22 out of 32 USH patients (68.75%) and to identify 79.7% of the expected mutated alleles. Fifty-three different mutations were detected. These mutations included 21 missense, 8 nonsense, 9 frameshifts, 9 intronic mutations and 6 large rearrangements. Conclusions Targeted next generation sequencing allowed us to detect both point mutations and large rearrangements in a single experiment, minimizing the economic cost of the study, increasing the detection ratio of the genetic cause of the disease and improving the genetic diagnosis of Usher syndrome patients.
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Affiliation(s)
- María J Aparisi
- Grupo de Investigación en Enfermedades Neurosensoriales. Instituto de Investigación Sanitaria IIS-La Fe, Semisótano Escuela de Enfermería, Hospital Universitario La Fe, Avda. Campanar, 21, 46009, Valencia, Spain. .,CIBER de Enfermedades Raras (CIBERER), Valencia, Spain.
| | - Elena Aller
- Grupo de Investigación en Enfermedades Neurosensoriales. Instituto de Investigación Sanitaria IIS-La Fe, Semisótano Escuela de Enfermería, Hospital Universitario La Fe, Avda. Campanar, 21, 46009, Valencia, Spain. .,CIBER de Enfermedades Raras (CIBERER), Valencia, Spain.
| | - Carla Fuster-García
- Grupo de Investigación en Enfermedades Neurosensoriales. Instituto de Investigación Sanitaria IIS-La Fe, Semisótano Escuela de Enfermería, Hospital Universitario La Fe, Avda. Campanar, 21, 46009, Valencia, Spain.
| | - Gema García-García
- Grupo de Investigación en Enfermedades Neurosensoriales. Instituto de Investigación Sanitaria IIS-La Fe, Semisótano Escuela de Enfermería, Hospital Universitario La Fe, Avda. Campanar, 21, 46009, Valencia, Spain. .,CHU Montpellier, Laboratoire de Génétique Moléculaire and Inserm, U827, Montpellier, F-34000, France.
| | - Regina Rodrigo
- Grupo de Investigación en Enfermedades Neurosensoriales. Instituto de Investigación Sanitaria IIS-La Fe, Semisótano Escuela de Enfermería, Hospital Universitario La Fe, Avda. Campanar, 21, 46009, Valencia, Spain. .,CIBER de Enfermedades Raras (CIBERER), Valencia, Spain.
| | - Rafael P Vázquez-Manrique
- Grupo de Investigación en Enfermedades Neurosensoriales. Instituto de Investigación Sanitaria IIS-La Fe, Semisótano Escuela de Enfermería, Hospital Universitario La Fe, Avda. Campanar, 21, 46009, Valencia, Spain. .,CIBER de Enfermedades Raras (CIBERER), Valencia, Spain.
| | - Fiona Blanco-Kelly
- CIBER de Enfermedades Raras (CIBERER), Valencia, Spain. .,Servicio de Genética, IIS - Fundación Jiménez Díaz, University Hospital, UAM, Madrid, Spain.
| | - Carmen Ayuso
- CIBER de Enfermedades Raras (CIBERER), Valencia, Spain. .,Servicio de Genética, IIS - Fundación Jiménez Díaz, University Hospital, UAM, Madrid, Spain.
| | - Anne-Françoise Roux
- CHU Montpellier, Laboratoire de Génétique Moléculaire and Inserm, U827, Montpellier, F-34000, France.
| | - Teresa Jaijo
- Grupo de Investigación en Enfermedades Neurosensoriales. Instituto de Investigación Sanitaria IIS-La Fe, Semisótano Escuela de Enfermería, Hospital Universitario La Fe, Avda. Campanar, 21, 46009, Valencia, Spain. .,CIBER de Enfermedades Raras (CIBERER), Valencia, Spain.
| | - José M Millán
- Grupo de Investigación en Enfermedades Neurosensoriales. Instituto de Investigación Sanitaria IIS-La Fe, Semisótano Escuela de Enfermería, Hospital Universitario La Fe, Avda. Campanar, 21, 46009, Valencia, Spain. .,CIBER de Enfermedades Raras (CIBERER), Valencia, Spain. .,Unidad de Genética y Diagnóstico Prenatal, Hospital Universitario y Politécnico La Fe, Valencia, Spain.
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García-García G, Aller E, Jaijo T, Aparisi MJ, Larrieu L, Faugère V, Blanco-Kelly F, Ayuso C, Roux AF, Millán JM. Novel deletions involving the USH2A gene in patients with Usher syndrome and retinitis pigmentosa. Mol Vis 2014; 20:1398-410. [PMID: 25352746 PMCID: PMC4173666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 09/23/2014] [Indexed: 10/29/2022] Open
Abstract
PURPOSE The aim of the present work was to identify and characterize large rearrangements involving the USH2A gene in patients with Usher syndrome and nonsyndromic retinitis pigmentosa. METHODS The multiplex ligation-dependent probe amplification (MLPA) technique combined with a customized array-based comparative genomic hybridization (aCGH) analysis was applied to 40 unrelated patients previously screened for point mutations in the USH2A gene in which none or only one pathologic mutation was identified. RESULTS We detected six large deletions involving USH2A in six out of the 40 cases studied. Three of the patients were homozygous for the deletion, and the remaining three were compound heterozygous with a previously identified USH2A point mutation. In five of these cases, the patients displayed Usher type 2, and the remaining case displayed nonsyndromic retinitis pigmentosa. The exact breakpoint junctions of the deletions found in USH2A in four of these cases were characterized. CONCLUSIONS Our study highlights the need to develop improved efficient strategies of mutation screening based upon next generation sequencing (NGS) that reduce cost, time, and complexity and allow simultaneous identification of all types of disease-causing mutations in diagnostic procedures.
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Affiliation(s)
- Gema García-García
- Grupo de Investigación en Enfermedades Neurosensoriales, Instituto de Investigación Sanitaria La Fe (IIS-La Fe), Valencia, Spain,Inserm, U827, Montpellier, F-34000, France
| | - Elena Aller
- Grupo de Investigación en Enfermedades Neurosensoriales, Instituto de Investigación Sanitaria La Fe (IIS-La Fe), Valencia, Spain,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Teresa Jaijo
- Grupo de Investigación en Enfermedades Neurosensoriales, Instituto de Investigación Sanitaria La Fe (IIS-La Fe), Valencia, Spain,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Maria J. Aparisi
- Grupo de Investigación en Enfermedades Neurosensoriales, Instituto de Investigación Sanitaria La Fe (IIS-La Fe), Valencia, Spain,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Lise Larrieu
- CHU Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, F-34000, France
| | - Valérie Faugère
- CHU Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, F-34000, France
| | | | - Carmen Ayuso
- CIBER de Enfermedades Raras (CIBERER), Madrid, Spain,Servicio de Genetica, IIS - Fundación Jiménez Diaz, UAM, Madrid, Spain
| | - Anne-Francoise Roux
- Inserm, U827, Montpellier, F-34000, France,CHU Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, F-34000, France
| | - José M. Millán
- Grupo de Investigación en Enfermedades Neurosensoriales, Instituto de Investigación Sanitaria La Fe (IIS-La Fe), Valencia, Spain,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain,Unidad de Genética y Diagnóstico Prenatal, Hospital Universitario y Politécnico La Fe, Valencia, Spain
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Baux D, Blanchet C, Hamel C, Meunier I, Larrieu L, Faugère V, Vaché C, Castorina P, Puech B, Bonneau D, Malcolm S, Claustres M, Roux AF. Enrichment of LOVD-USHbases with 152 USH2A genotypes defines an extensive mutational spectrum and highlights missense hotspots. Hum Mutat 2014; 35:1179-86. [PMID: 24944099 DOI: 10.1002/humu.22608] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 06/09/2014] [Indexed: 12/19/2022]
Abstract
Alterations of USH2A, encoding usherin, are responsible for more than 70% of cases of Usher syndrome type II (USH2), a recessive disorder that combines moderate to severe hearing loss and retinal degeneration. The longest USH2A transcript encodes usherin isoform b, a 5,202-amino-acid transmembrane protein with an exceptionally large extracellular domain consisting notably of a Laminin N-terminal domain and numerous Laminin EGF-like (LE) and Fibronectin type III (FN3) repeats. Mutations of USH2A are scattered throughout the gene and mostly private. Annotating these variants is therefore of major importance to correctly assign pathogenicity. We have extensively genotyped a novel cohort of 152 Usher patients and identified 158 different mutations, of which 93 are newly described. Pooling this new data with the existing pathogenic variants already incorporated in USHbases reveals several previously unappreciated features of the mutational spectrum. We show that parts of the protein are more likely to tolerate single amino acid variations, whereas others constitute pathogenic missense hotspots. We have found, in repeated LE and FN3 domains, a nonequal distribution of the missense mutations that highlights some crucial positions in usherin with possible consequences for the assessment of the pathogenicity of the numerous missense variants identified in USH2A.
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Affiliation(s)
- David Baux
- CHU Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, F-34000, France
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de Castro-Miró M, Pomares E, Lorés-Motta L, Tonda R, Dopazo J, Marfany G, Gonzàlez-Duarte R. Combined genetic and high-throughput strategies for molecular diagnosis of inherited retinal dystrophies. PLoS One 2014; 9:e88410. [PMID: 24516651 PMCID: PMC3917917 DOI: 10.1371/journal.pone.0088410] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 01/06/2014] [Indexed: 12/30/2022] Open
Abstract
Most diagnostic laboratories are confronted with the increasing demand for molecular diagnosis from patients and families and the ever-increasing genetic heterogeneity of visual disorders. Concerning Retinal Dystrophies (RD), almost 200 causative genes have been reported to date, and most families carry private mutations. We aimed to approach RD genetic diagnosis using all the available genetic information to prioritize candidates for mutational screening, and then restrict the number of cases to be analyzed by massive sequencing. We constructed and optimized a comprehensive cosegregation RD-chip based on SNP genotyping and haplotype analysis. The RD-chip allows to genotype 768 selected SNPs (closely linked to 100 RD causative genes) in a single cost-, time-effective step. Full diagnosis was attained in 17/36 Spanish pedigrees, yielding 12 new and 12 previously reported mutations in 9 RD genes. The most frequently mutated genes were USH2A and CRB1. Notably, RD3–up to now only associated to Leber Congenital Amaurosis– was identified as causative of Retinitis Pigmentosa. The main assets of the RD-chip are: i) the robustness of the genetic information that underscores the most probable candidates, ii) the invaluable clues in cases of shared haplotypes, which are indicative of a common founder effect, and iii) the detection of extended haplotypes over closely mapping genes, which substantiates cosegregation, although the assumptions in which the genetic analysis is based could exceptionally lead astray. The combination of the genetic approach with whole exome sequencing (WES) greatly increases the diagnosis efficiency, and revealed novel mutations in USH2A and GUCY2D. Overall, the RD-chip diagnosis efficiency ranges from 16% in dominant, to 80% in consanguineous recessive pedigrees, with an average of 47%, well within the upper range of massive sequencing approaches, highlighting the validity of this time- and cost-effective approach whilst high-throughput methodologies become amenable for routine diagnosis in medium sized labs.
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Affiliation(s)
- Marta de Castro-Miró
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Esther Pomares
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Laura Lorés-Motta
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Raul Tonda
- Centre Nacional d’Anàlisi Genòmica, PCB, Barcelona, Spain
| | - Joaquín Dopazo
- Department of Computational Genomics, Centro de Investigación Príncipe Felipe, Valencia, Spain
- BIER, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Gemma Marfany
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Roser Gonzàlez-Duarte
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
- * E-mail:
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Analysis of the Ush2a gene in medaka fish (Oryzias latipes). PLoS One 2013; 8:e74995. [PMID: 24086419 PMCID: PMC3781144 DOI: 10.1371/journal.pone.0074995] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 08/13/2013] [Indexed: 11/19/2022] Open
Abstract
Patients suffering from Usher syndrome (USH) exhibit sensorineural hearing loss, retinitis pigmentosa (RP) and, in some cases, vestibular dysfunction. USH is the most common genetic disorder affecting hearing and vision and is included in a group of hereditary pathologies associated with defects in ciliary function known as ciliopathies. This syndrome is clinically classified into three types: USH1, USH2 and USH3. USH2 accounts for well over one-half of all Usher cases and mutations in the USH2A gene are responsible for the majority of USH2 cases, but also for atypical Usher syndrome and recessive non-syndromic RP. Because medaka fish (Oryzias latypes) is an attractive model organism for genetic-based studies in biomedical research, we investigated the expression and function of the USH2A ortholog in this teleost species. Ol-Ush2a encodes a protein of 5.445 aa codons, containing the same motif arrangement as the human USH2A. Ol-Ush2a is expressed during early stages of medaka fish development and persists into adulthood. Temporal Ol-Ush2a expression analysis using whole mount in situ hybridization (WMISH) on embryos at different embryonic stages showed restricted expression to otoliths and retina, suggesting that Ol-Ush2a might play a conserved role in the development and/or maintenance of retinal photoreceptors and cochlear hair cells. Knockdown of Ol-Ush2a in medaka fish caused embryonic developmental defects (small eyes and heads, otolith malformations and shortened bodies with curved tails) resulting in late embryo lethality. These embryonic defects, observed in our study and in other ciliary disorders, are associated with defective cell movement specifically implicated in left-right (LR) axis determination and planar cell polarity (PCP).
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Steele-Stallard HB, Le Quesne Stabej P, Lenassi E, Luxon LM, Claustres M, Roux AF, Webster AR, Bitner-Glindzicz M. Screening for duplications, deletions and a common intronic mutation detects 35% of second mutations in patients with USH2A monoallelic mutations on Sanger sequencing. Orphanet J Rare Dis 2013; 8:122. [PMID: 23924366 PMCID: PMC3751126 DOI: 10.1186/1750-1172-8-122] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 08/04/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Usher Syndrome is the leading cause of inherited deaf-blindness. It is divided into three subtypes, of which the most common is Usher type 2, and the USH2A gene accounts for 75-80% of cases. Despite recent sequencing strategies, in our cohort a significant proportion of individuals with Usher type 2 have just one heterozygous disease-causing mutation in USH2A, or no convincing disease-causing mutations across nine Usher genes. The purpose of this study was to improve the molecular diagnosis in these families by screening USH2A for duplications, heterozygous deletions and a common pathogenic deep intronic variant USH2A: c.7595-2144A>G. METHODS Forty-nine Usher type 2 or atypical Usher families who had missing mutations (mono-allelic USH2A or no mutations following Sanger sequencing of nine Usher genes) were screened for duplications/deletions using the USH2A SALSA MLPA reagent kit (MRC-Holland). Identification of USH2A: c.7595-2144A>G was achieved by Sanger sequencing. Mutations were confirmed by a combination of reverse transcription PCR using RNA extracted from nasal epithelial cells or fibroblasts, and by array comparative genomic hybridisation with sequencing across the genomic breakpoints. RESULTS Eight mutations were identified in 23 Usher type 2 families (35%) with one previously identified heterozygous disease-causing mutation in USH2A. These consisted of five heterozygous deletions, one duplication, and two heterozygous instances of the pathogenic variant USH2A: c.7595-2144A>G. No variants were found in the 15 Usher type 2 families with no previously identified disease-causing mutations. In 11 atypical families, none of whom had any previously identified convincing disease-causing mutations, the mutation USH2A: c.7595-2144A>G was identified in a heterozygous state in one family. All five deletions and the heterozygous duplication we report here are novel. This is the first time that a duplication in USH2A has been reported as a cause of Usher syndrome. CONCLUSIONS We found that 8 of 23 (35%) of 'missing' mutations in Usher type 2 probands with only a single heterozygous USH2A mutation detected with Sanger sequencing could be attributed to deletions, duplications or a pathogenic deep intronic variant. Future mutation detection strategies and genetic counselling will need to take into account the prevalence of these types of mutations in order to provide a more comprehensive diagnostic service.
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Besnard T, García-García G, Baux D, Vaché C, Faugère V, Larrieu L, Léonard S, Millan JM, Malcolm S, Claustres M, Roux AF. Experience of targeted Usher exome sequencing as a clinical test. Mol Genet Genomic Med 2013; 2:30-43. [PMID: 24498627 PMCID: PMC3907913 DOI: 10.1002/mgg3.25] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 06/06/2013] [Indexed: 12/15/2022] Open
Abstract
We show that massively parallel targeted sequencing of 19 genes provides a new and reliable strategy for molecular diagnosis of Usher syndrome (USH) and nonsyndromic deafness, particularly appropriate for these disorders characterized by a high clinical and genetic heterogeneity and a complex structure of several of the genes involved. A series of 71 patients including Usher patients previously screened by Sanger sequencing plus newly referred patients was studied. Ninety-eight percent of the variants previously identified by Sanger sequencing were found by next-generation sequencing (NGS). NGS proved to be efficient as it offers analysis of all relevant genes which is laborious to reach with Sanger sequencing. Among the 13 newly referred Usher patients, both mutations in the same gene were identified in 77% of cases (10 patients) and one candidate pathogenic variant in two additional patients. This work can be considered as pilot for implementing NGS for genetically heterogeneous diseases in clinical service.
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Affiliation(s)
- Thomas Besnard
- U827, Inserm Montpellier, F-34000, France ; Univ, Montpellier I Montpellier, F-34000, France
| | - Gema García-García
- U827, Inserm Montpellier, F-34000, France ; Grupo de Investigación en Enfermedades Neurosensoriales, Instituto de Investigación Sanitaria IIS-La Fe and CIBERER Valencia, Spain
| | - David Baux
- Laboratoire de Génétique Moléculaire, CHU Montpellier Montpellier, F-34000, France
| | - Christel Vaché
- Laboratoire de Génétique Moléculaire, CHU Montpellier Montpellier, F-34000, France
| | - Valérie Faugère
- Laboratoire de Génétique Moléculaire, CHU Montpellier Montpellier, F-34000, France
| | - Lise Larrieu
- Laboratoire de Génétique Moléculaire, CHU Montpellier Montpellier, F-34000, France
| | - Susana Léonard
- Laboratoire de Génétique Moléculaire, CHU Montpellier Montpellier, F-34000, France
| | - Jose M Millan
- Grupo de Investigación en Enfermedades Neurosensoriales, Instituto de Investigación Sanitaria IIS-La Fe and CIBERER Valencia, Spain
| | - Sue Malcolm
- Clinical and Molecular Genetics, Institute of Child Health, University College London London, United Kingdom
| | - Mireille Claustres
- U827, Inserm Montpellier, F-34000, France ; Univ, Montpellier I Montpellier, F-34000, France ; Laboratoire de Génétique Moléculaire, CHU Montpellier Montpellier, F-34000, France
| | - Anne-Françoise Roux
- U827, Inserm Montpellier, F-34000, France ; Laboratoire de Génétique Moléculaire, CHU Montpellier Montpellier, F-34000, France
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García-García G, Besnard T, Baux D, Vaché C, Aller E, Malcolm S, Claustres M, Millan JM, Roux AF. The contribution of GPR98 and DFNB31 genes to a Spanish Usher syndrome type 2 cohort. Mol Vis 2013; 19:367-73. [PMID: 23441107 PMCID: PMC3580968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 02/11/2013] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Usher syndrome type 2 (USH2) is an autosomal recessive disease characterized by moderate to severe hearing loss and retinitis pigmentosa. To date, three disease-causing genes have been identified, USH2A, GPR98, and DFNB31, of which USH2A is clearly the major contributor. The aim of this work was to determine the contribution of GPR98 and DFNB31 genes in a Spanish cohort of USH2A negative patients using exhaustive molecular analysis, including sequencing, dosage, and splicing analysis. METHODS Linkage analysis was performed to prioritize the gene to study, followed by sequencing of exons and intron-exon boundaries of the selected gene, GPR98 (90 exons) or DFNB31 (12 exons). Functional splicing analyses and comparative genomic hybridization array to detect large rearrangements were performed when appropriate. RESULTS We confirmed that mutations in GPR98 contribute a significant but minor role to Usher syndrome type 2. In a group of patients referred for molecular diagnosis, 43 had been found to be positive for USH2A mutations, the remaining 19 without USH2A alterations were screened, and seven different mutations were identified in the GPR98 gene in seven patients (five in the homozygous state), of which six were novel. All detected mutations result in a truncated protein; deleterious missense mutations were not found. No pathological mutations were identified in the DFNB31 gene. CONCLUSIONS In Spain, USH2A and GPR98 are responsible for 95.8% and 5.2% of USH2 mutated cases, respectively. DFNB31 plays a minor role in the Spanish population. There was a group of patients in whom no mutation was found. These findings confirm the importance of including at least GPR98 analysis for comprehensive USH2 molecular diagnosis.
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Affiliation(s)
- Gema García-García
- INSERM, U827, Montpellier, F-34000, France,Grupo de Investigación en Enfermedades Neurosensoriales, Instituto de Investigación Sanitaria IIS-La Fe and Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain
| | - Thomas Besnard
- INSERM, U827, Montpellier, F-34000, France,Centre Hospitalier Universitaire, Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, F-34000, France,Université Montpellier 1, UFR de Médecine, Montpellier, France
| | - David Baux
- Centre Hospitalier Universitaire, Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, F-34000, France
| | - Christel Vaché
- Centre Hospitalier Universitaire, Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, F-34000, France
| | - Elena Aller
- Grupo de Investigación en Enfermedades Neurosensoriales, Instituto de Investigación Sanitaria IIS-La Fe and Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain
| | - Sue Malcolm
- Clinical and Molecular Genetics, Institute of Child Health, University College London, London, United Kingdom
| | - Mireille Claustres
- INSERM, U827, Montpellier, F-34000, France,Centre Hospitalier Universitaire, Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, F-34000, France,Université Montpellier 1, UFR de Médecine, Montpellier, France
| | - Jose M. Millan
- Grupo de Investigación en Enfermedades Neurosensoriales, Instituto de Investigación Sanitaria IIS-La Fe and Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain
| | - Anne-Françoise Roux
- INSERM, U827, Montpellier, F-34000, France,Centre Hospitalier Universitaire, Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, F-34000, France
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Anasagasti A, Irigoyen C, Barandika O, López de Munain A, Ruiz-Ederra J. Current mutation discovery approaches in Retinitis Pigmentosa. Vision Res 2012; 75:117-29. [PMID: 23022136 DOI: 10.1016/j.visres.2012.09.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 09/08/2012] [Accepted: 09/13/2012] [Indexed: 12/22/2022]
Abstract
With a worldwide prevalence of about 1 in 3500-5000 individuals, Retinitis Pigmentosa (RP) is the most common form of hereditary retinal degeneration. It is an extremely heterogeneous group of genetically determined retinal diseases leading to progressive loss of vision due to impairment of rod and cone photoreceptors. RP can be inherited as an autosomal-recessive, autosomal-dominant, or X-linked trait. Non-Mendelian inheritance patterns such as digenic, maternal (mitochondrial) or compound heterozygosity have also been reported. To date, more than 65 genes have been implicated in syndromic and non-syndromic forms of RP, which account for only about 60% of all RP cases. Due to this high heterogeneity and diversity of inheritance patterns, the molecular diagnosis of syndromic and non-syndromic RP is very challenging, and the heritability of 40% of total RP cases worldwide remains unknown. However new sequencing methodologies, boosted by the human genome project, have contributed to exponential plummeting in sequencing costs, thereby making it feasible to include molecular testing for RP patients in routine clinical practice within the coming years. Here, we summarize the most widely used state-of-the-art technologies currently applied for the molecular diagnosis of RP, and address their strengths and weaknesses for the molecular diagnosis of such a complex genetic disease.
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Affiliation(s)
- Ander Anasagasti
- Division of Neurosciences, Instituto Biodonostia, San Sebastián, Gipuzkoa, Spain
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Paterson RL, De Roach JN, McLaren TL, Hewitt AW, Hoffmann L, Lamey TM. Application of a high-throughput genotyping method for loci exclusion in non-consanguineous Australian pedigrees with autosomal recessive retinitis pigmentosa. Mol Vis 2012; 18:2043-52. [PMID: 22876132 PMCID: PMC3413434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 07/20/2012] [Indexed: 11/03/2022] Open
Abstract
PURPOSE Retinitis pigmentosa (RP) is the most common form of inherited blindness, caused by progressive degeneration of photoreceptor cells in the retina, and affects approximately 1 in 3,000 people. Over the past decade, significant progress has been made in gene therapy for RP and related diseases, making genetic characterization increasingly important. Recently, high-throughput technologies have provided an option for reasonably fast, cost-effective genetic characterization of autosomal recessive RP (arRP). The current study used a single nucleotide polymorphism (SNP) genotyping method to exclude up to 28 possible disease-causing genes in 31 non-consanguineous Australian families affected by arRP. METHODS DNA samples were collected from 59 individuals affected with arRP and 74 unaffected family members from 31 Australian families. Five to six SNPs were genotyped for 28 genes known to cause arRP or the related disease Leber congenital amaurosis (LCA). Cosegregation analyses were used to exclude possible causative genes from each of the 31 families. Bidirectional sequencing was used to identify disease-causing mutations in prioritized genes that were not excluded with cosegregation analyses. RESULTS Two families were excluded from analysis due to identification of false paternity. An average of 28.9% of genes were excluded per family when only one affected individual was available, in contrast to an average of 71.4% or 89.8% of genes when either two, or three or more affected individuals were analyzed, respectively. A statistically significant relationship between the proportion of genes excluded and the number of affected individuals analyzed was identified using a multivariate regression model (p<0.0001). Subsequent DNA sequencing resulted in identification of the likely disease-causing gene as CRB1 in one family (c.2548 G>A) and USH2A in two families (c.2276 G>T). CONCLUSIONS This study has shown that SNP genotyping cosegregation analysis can be successfully used to refine and expedite the genetic characterization of arRP in a non-consanguineous population; however, this method is effective only when DNA samples are available from more than one affected individual.
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Affiliation(s)
- Rachel L. Paterson
- Australian Inherited Retinal Disease Register & DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - John N. De Roach
- Australian Inherited Retinal Disease Register & DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Terri L. McLaren
- Australian Inherited Retinal Disease Register & DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Alex W. Hewitt
- Lions Eye Institute, Centre for Ophthalmology and Visual Science, University of Western Australia, Perth, Western Australia, Australia
| | - Ling Hoffmann
- Australian Inherited Retinal Disease Register & DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Tina M. Lamey
- Australian Inherited Retinal Disease Register & DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
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