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Matczyńska E, Beć-Gajowniczek M, Sivitskaya L, Gregorczyk E, Łyszkiewicz P, Szymańczak R, Jędrzejowska M, Wylęgała E, Krawczyński MR, Teper S, Boguszewska-Chachulska A. Optimised, Broad NGS Panel for Inherited Eye Diseases to Diagnose 1000 Patients in Poland. Biomedicines 2024; 12:1355. [PMID: 38927562 PMCID: PMC11202224 DOI: 10.3390/biomedicines12061355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/10/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Advances in gene therapy and genome editing give hope that new treatments will soon be available for inherited eye diseases that together affect a significant proportion of the adult population. New solutions are needed to make genetic diagnosis fast and affordable. This is the first study of such a large group of patients with inherited retinal dystrophies (IRD) and inherited optic neuropathies (ION) in the Polish population. It is based on four years of diagnostic analysis using a broad, targeted NGS approach. The results include the most common pathogenic variants, as well as 91 novel causative variants, including frameshifts in the cumbersome RPGR ORF15 region. The high frequency of the ABCA4 complex haplotype p.(Leu541Pro;Ala1038Val) was confirmed. Additionally, a deletion of exons 22-24 in USH2A, probably specific to the Polish population, was uncovered as the most frequent copy number variation. The diagnostic yield of the broad NGS panel reached 64.3% and is comparable to the results reported for genetic studies of IRD and ION performed for other populations with more extensive WES or WGS methods. A combined approach to identify genetic causes of all known diseases manifesting in the posterior eye segment appears to be the optimal choice given the currently available treatment options and advanced clinical trials.
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Affiliation(s)
- Ewa Matczyńska
- Genomed S.A., 02-971 Warsaw, Poland
- Chair and Clinical Department of Ophthalmology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland
| | | | | | | | | | | | | | - Edward Wylęgała
- Chair and Clinical Department of Ophthalmology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland
| | - Maciej R. Krawczyński
- Chair and Department of Medical Genetics, Poznań University of Medical Sciences, 61-701 Poznań, Poland
- Centers for Medical Genetics Genesis, 60-529 Poznań, Poland
| | - Sławomir Teper
- Chair and Clinical Department of Ophthalmology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland
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Molina Romero M, Yoldi Chaure A, Gañán Parra M, Navas Bastida P, del Pico Sánchez JL, Vaquero Argüelles Á, de la Fuente Vaquero P, Ramírez López JP, Castilla Alcalá JA. Probability of high-risk genetic matching with oocyte and semen donors: complete gene analysis or genotyping test? J Assist Reprod Genet 2022; 39:341-355. [PMID: 35091964 PMCID: PMC8956772 DOI: 10.1007/s10815-021-02381-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 12/17/2021] [Indexed: 02/03/2023] Open
Abstract
PURPOSE To estimate the probability of high-risk genetic matching when assisted reproductive techniques (ART) are applied with double gamete donation, following an NGS carrier test based on a complete study of the genes concerned. We then determine the results that would have been obtained if the genotyping tests most widely used in Spanish gamete banks had been applied. METHODS In this descriptive observational study, 1818 gamete donors were characterised by NGS. The pathogenic variants detected were analysed to estimate the probability of high-risk genetic matching and to determine the results that would have been obtained if the three most commonly used genotyping tests in ART had been applied. RESULTS The probability of high-risk genetic matching with gamete donation, screened by NGS and complete gene analysis, was 5.5%, versus the 0.6-2.7% that would have been obtained with the genotyping test. A total of 1741 variants were detected, including 607 different variants, of which only 22.6% would have been detected by all three genotyping tests considered and 44.7% of which would not have been detected by any of these tests. CONCLUSION Our study highlights the considerable heterogeneity of the genotyping tests, which present significant differences in their ability to detect pathogenic variants. The complete study of the genes by NGS considerably reduces reproductive risks when genetic matching is performed with gamete donors. Accordingly, we recommend that carrier screening in gamete donors be carried out using NGS and a complete study with nontargeted analysis of the variants of the screened genes.
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Affiliation(s)
- Marta Molina Romero
- CEIFER Biobanco - NextClinics, Calle Maestro Bretón, 1, 18004 Granada, Spain
| | | | | | | | | | | | | | | | - José Antonio Castilla Alcalá
- CEIFER Biobanco - NextClinics, Calle Maestro Bretón, 1, 18004 Granada, Spain ,U. Reproducción, UGC Obstetricia y Ginecología, HU Virgen de Las Nieves, Granada, Spain ,Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain
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Toms M, Pagarkar W, Moosajee M. Usher syndrome: clinical features, molecular genetics and advancing therapeutics. Ther Adv Ophthalmol 2020; 12:2515841420952194. [PMID: 32995707 PMCID: PMC7502997 DOI: 10.1177/2515841420952194] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/27/2020] [Indexed: 01/12/2023] Open
Abstract
Usher syndrome has three subtypes, each being clinically and genetically heterogeneous characterised by sensorineural hearing loss and retinitis pigmentosa (RP), with or without vestibular dysfunction. It is the most common cause of deaf–blindness worldwide with a prevalence of between 4 and 17 in 100 000. To date, 10 causative genes have been identified for Usher syndrome, with MYO7A accounting for >50% of type 1 and USH2A contributing to approximately 80% of type 2 Usher syndrome. Variants in these genes can also cause non-syndromic RP and deafness. Genotype–phenotype correlations have been described for several of the Usher genes. Hearing loss is managed with hearing aids and cochlear implants, which has made a significant improvement in quality of life for patients. While there is currently no available approved treatment for the RP, various therapeutic strategies are in development or in clinical trials for Usher syndrome, including gene replacement, gene editing, antisense oligonucleotides and small molecule drugs.
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Affiliation(s)
- Maria Toms
- UCL Institute of Ophthalmology, London, UK; The Francis Crick Institute, London, UK
| | - Waheeda Pagarkar
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK; University College London Hospitals NHS Foundation Trust, London, UK
| | - Mariya Moosajee
- Development, Ageing and Disease, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
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4
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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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5
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Abstract
OBJECTIVE To describe the genetic and phenotypic spectrum of Usher syndrome after 6 years of studies by next-generation sequencing, and propose an up-to-date classification of Usher genes in patients with both visual and hearing impairments suggesting Usher syndrome, and in patients with seemingly isolated deafness. STUDY DESIGN The systematic review and meta-analysis protocol was based on Cochrane and Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We performed 1) a meta-analysis of data from 11 next-generation sequencing studies in 684 patients with Usher syndrome; 2) a meta-analysis of data from 21 next-generation studies in 2,476 patients with seemingly isolated deafness, to assess the involvement of Usher genes in seemingly nonsyndromic hearing loss, and thus the proportion of patients at high risk of subsequent retinitis pigmentosa (RP); 3) a statistical analysis of differences between parts 1) and 2). RESULTS In patients with both visual and hearing impairments, the biallelic disease-causing mutation rate was assessed for each Usher gene to propose a classification by frequency: USH2A: 50% (341/684) of patients, MYO7A: 21% (144/684), CDH23: 6% (39/684), ADGRV1: 5% (35/684), PCDH15: 3% (21/684), USH1C: 2% (17/684), CLRN1: 2% (14/684), USH1G: 1% (9/684), WHRN: 0.4% (3/684), PDZD7 0.1% (1/684), CIB2 (0/684). In patients with seemingly isolated sensorineural deafness, 7.5% had disease-causing mutations in Usher genes, and are therefore at high risk of developing RP. These new findings provide evidence that usherome dysfunction is the second cause of genetic sensorineural hearing loss after connexin dysfunction. CONCLUSION These results promote generalization of early molecular screening for Usher syndrome in deaf children.
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Karali M, Testa F, Brunetti-Pierri R, Di Iorio V, Pizzo M, Melillo P, Barillari MR, Torella A, Musacchia F, D’Angelo L, Banfi S, Simonelli F. Clinical and Genetic Analysis of a European Cohort with Pericentral Retinitis Pigmentosa. Int J Mol Sci 2019; 21:ijms21010086. [PMID: 31877679 PMCID: PMC6982348 DOI: 10.3390/ijms21010086] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/12/2019] [Accepted: 12/19/2019] [Indexed: 12/28/2022] Open
Abstract
Retinitis pigmentosa (RP) is a clinically heterogenous disease that comprises a wide range of phenotypic and genetic subtypes. Pericentral RP is an atypical form of RP characterized by bone-spicule pigmentation and/or atrophy confined in the near mid-periphery of the retina. In contrast to classic RP, the far periphery is better preserved in pericentral RP. The aim of this study was to perform the first detailed clinical and genetic analysis of a cohort of European subjects with pericentral RP to determine the phenotypic features and the genetic bases of the disease. A total of 54 subjects from 48 independent families with pericentral RP, non-syndromic and syndromic, were evaluated through a full ophthalmological examination and underwent clinical exome or retinopathy gene panel sequencing. Disease-causative variants were identified in 22 of the 35 families (63%) in 10 different genes, four of which are also responsible for syndromic RP. Thirteen of the 34 likely pathogenic variants were novel. Intra-familiar variability was also observed. The current study confirms the mild phenotype of pericentral RP and extends the spectrum of genes associated with this condition.
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Affiliation(s)
- Marianthi Karali
- Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, via Luigi De Crecchio 7, 80138 Naples, Italy; (M.K.); (A.T.)
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli, Italy; (M.P.); (F.M.)
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Università degli Studi della Campania ‘Luigi Vanvitelli’, via Pansini 5, 80131 Naples, Italy; (F.T.); (R.B.-P.); (V.D.I.); (P.M.); (M.R.B.); (L.D.A.)
| | - Raffaella Brunetti-Pierri
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Università degli Studi della Campania ‘Luigi Vanvitelli’, via Pansini 5, 80131 Naples, Italy; (F.T.); (R.B.-P.); (V.D.I.); (P.M.); (M.R.B.); (L.D.A.)
| | - Valentina Di Iorio
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Università degli Studi della Campania ‘Luigi Vanvitelli’, via Pansini 5, 80131 Naples, Italy; (F.T.); (R.B.-P.); (V.D.I.); (P.M.); (M.R.B.); (L.D.A.)
| | - Mariateresa Pizzo
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli, Italy; (M.P.); (F.M.)
| | - Paolo Melillo
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Università degli Studi della Campania ‘Luigi Vanvitelli’, via Pansini 5, 80131 Naples, Italy; (F.T.); (R.B.-P.); (V.D.I.); (P.M.); (M.R.B.); (L.D.A.)
| | - Maria Rosaria Barillari
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Università degli Studi della Campania ‘Luigi Vanvitelli’, via Pansini 5, 80131 Naples, Italy; (F.T.); (R.B.-P.); (V.D.I.); (P.M.); (M.R.B.); (L.D.A.)
| | - Annalaura Torella
- Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, via Luigi De Crecchio 7, 80138 Naples, Italy; (M.K.); (A.T.)
| | - Francesco Musacchia
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli, Italy; (M.P.); (F.M.)
| | - Luigi D’Angelo
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Università degli Studi della Campania ‘Luigi Vanvitelli’, via Pansini 5, 80131 Naples, Italy; (F.T.); (R.B.-P.); (V.D.I.); (P.M.); (M.R.B.); (L.D.A.)
| | - Sandro Banfi
- Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, via Luigi De Crecchio 7, 80138 Naples, Italy; (M.K.); (A.T.)
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli, Italy; (M.P.); (F.M.)
- Correspondence: (S.B.); (F.S.); Tel.: +39-081-19230628 (S.B.); +39-081-7704501 (F.S.)
| | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Università degli Studi della Campania ‘Luigi Vanvitelli’, via Pansini 5, 80131 Naples, Italy; (F.T.); (R.B.-P.); (V.D.I.); (P.M.); (M.R.B.); (L.D.A.)
- Correspondence: (S.B.); (F.S.); Tel.: +39-081-19230628 (S.B.); +39-081-7704501 (F.S.)
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Ataluren for the Treatment of Usher Syndrome 2A Caused by Nonsense Mutations. Int J Mol Sci 2019; 20:ijms20246274. [PMID: 31842393 PMCID: PMC6940777 DOI: 10.3390/ijms20246274] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/05/2019] [Accepted: 12/10/2019] [Indexed: 12/18/2022] Open
Abstract
The identification of genetic defects that underlie inherited retinal diseases (IRDs) paves the way for the development of therapeutic strategies. Nonsense mutations caused approximately 12% of all IRD cases, resulting in a premature termination codon (PTC). Therefore, an approach that targets nonsense mutations could be a promising pharmacogenetic strategy for the treatment of IRDs. Small molecules (translational read-through inducing drugs; TRIDs) have the potential to mediate the read-through of nonsense mutations by inducing expression of the full-length protein. We provide novel data on the read-through efficacy of Ataluren on a nonsense mutation in the Usher syndrome gene USH2A that causes deaf-blindness in humans. We demonstrate Ataluren´s efficacy in both transiently USH2AG3142*-transfected HEK293T cells and patient-derived fibroblasts by restoring USH2A protein expression. Furthermore, we observed enhanced ciliogenesis in patient-derived fibroblasts after treatment with TRIDs, thereby restoring a phenotype that is similar to that found in healthy donors. In light of recent findings, we validated Ataluren´s efficacy to induce read-through on a nonsense mutation in USH2A-related IRD. In line with published data, our findings support the use of patient-derived fibroblasts as a platform for the validation of preclinical therapies. The excellent biocompatibility combined with sustained read-through efficacy makes Ataluren an ideal TRID for treating nonsense mutations based IRDs.
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8
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Soares de Lima Y, Chiabai M, Shen J, Córdoba MS, Versiani BR, Benício ROA, Pogue R, Mingroni-Netto RC, Lezirovitz K, Pic-Taylor A, Mazzeu JF, Oliveira SF. Syndromic hearing loss molecular diagnosis: Application of massive parallel sequencing. Hear Res 2018; 370:181-188. [PMID: 30390570 DOI: 10.1016/j.heares.2018.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/19/2018] [Accepted: 10/14/2018] [Indexed: 12/17/2022]
Abstract
Syndromic hearing loss accounts for approximately 30% of all cases of hearing loss due to genetic causes. Mutation screening in known genes is important because it potentially sheds light on the genetic etiology of hearing loss and helps in genetic counseling of families. In this study, we describe a customized Ion AmpliSeq Panel, specifically designed for the investigation of syndromic hearing loss. The Ion AmpliSeq Panel was customized to cover the coding sequences of 52 genes. Twenty-four patients were recruited: 17 patients with a clinical diagnosis of a known syndrome, and seven whose clinical signs did not allow identification of a syndrome. Of 24 patients sequenced, potentially causative mutations were found in nine, all of which belonged to the group with a previous clinical diagnostic and none in the group not clinically diagnosed. We were able to provide conclusive molecular diagnosis to six patients, constituting a diagnostic rate of 25% (6/24). In the group of patients with a suspected clinical diagnosis, the diagnostic rate was 35% (6/17). Of the nine different mutations identified, three are novel, and were found in patients with Waardenburg, Treacher Collins and CHARGE syndromes. Since all patients with a conclusive molecular diagnosis through this panel had a previous suspected clinical diagnosis, our results suggest that this panel was more effective in diagnosing this group of patients. Therefore, the panel demonstrated effectiveness in molecular diagnosis when compared to others in the literature, especially for patients with a defined clinical diagnosis.
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Affiliation(s)
- Yasmin Soares de Lima
- Departamento de Genética e Morfologia, Universidade de Brasília, Brasília, Brazil; Programa de Pós-graduação em Biologia Animal, Universidade de Brasília, Brasília, Brazil.
| | - Marcela Chiabai
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, Brasília, Brazil.
| | - Jun Shen
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Mara S Córdoba
- Hospital Universitário de Brasília, Universidade de Brasília, Brasília, Brazil.
| | - Beatriz R Versiani
- Hospital Universitário de Brasília, Universidade de Brasília, Brasília, Brazil.
| | | | - Robert Pogue
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, Brasília, Brazil.
| | - Regina Célia Mingroni-Netto
- Centro de Estudos do Genoma Humano, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
| | - Karina Lezirovitz
- Laboratório de Otorrinolaringologia - LIM32, Hospital das Clínicas, Universidade de São Paulo, São Paulo, Brazil.
| | - Aline Pic-Taylor
- Departamento de Genética e Morfologia, Universidade de Brasília, Brasília, Brazil; Programa de Pós-graduação em Biologia Animal, Universidade de Brasília, Brasília, Brazil.
| | - Juliana F Mazzeu
- Hospital Universitário de Brasília, Universidade de Brasília, Brasília, Brazil; Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil.
| | - Silviene F Oliveira
- Departamento de Genética e Morfologia, Universidade de Brasília, Brasília, Brazil; Programa de Pós-graduação em Biologia Animal, Universidade de Brasília, Brasília, Brazil.
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9
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Analysis of intragenic USH2A copy number variation unveils broad spectrum of unique and recurrent variants. Eur J Med Genet 2018; 61:621-626. [DOI: 10.1016/j.ejmg.2018.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 04/09/2018] [Accepted: 04/11/2018] [Indexed: 11/21/2022]
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10
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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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11
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Kletke S, Batmanabane V, Dai T, Vincent A, Li S, Gordon KA, Papsin BC, Cushing SL, Héon E. The combination of vestibular impairment and congenital sensorineural hearing loss predisposes patients to ocular anomalies, including Usher syndrome. Clin Genet 2017; 92:26-33. [PMID: 27743452 DOI: 10.1111/cge.12895] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/05/2016] [Accepted: 10/12/2016] [Indexed: 11/29/2022]
Abstract
The co-occurrence of hearing impairment and visual dysfunction is devastating. Most deaf-blind etiologies are genetically determined, the commonest being Usher syndrome (USH). While studies of the congenitally deaf population reveal a variable degree of visual problems, there are no effective ophthalmic screening guidelines. We hypothesized that children with congenital sensorineural hearing loss (SNHL) and vestibular impairment were at an increased risk of having USH. A retrospective chart review of 33 cochlear implants recipients for severe to profound SNHL and measured vestibular dysfunction was performed to determine the ocular phenotype. All the cases had undergone ocular examination and electroretinogram (ERG). Patients with an abnormal ERG underwent genetic testing for USH. We found an underlying ocular abnormality in 81.81% (27/33) of cases; of which 75% had refractive errors, and 50% of those patients showed visual improvement with refractive correction. A total of 14 cases (42.42%; 14/33) had generalized rod-cone dysfunction on ERG suggestive of Usher syndrome type 1, confirmed by mutational analysis. This work shows that adding vestibular impairment as a criterion for requesting an eye exam and adding the ERG to detect USH increases the chances of detecting ocular anomalies, when compared with previous literature focusing only on congenital SNHL.
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Affiliation(s)
- S Kletke
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Ontario, Canada
| | - V Batmanabane
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - T Dai
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Ontario, Canada
| | - A Vincent
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Ontario, Canada.,Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - S Li
- Program of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - K A Gordon
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Ontario, Canada.,Department of Otolaryngology - Head & Neck Surgery, The Hospital for Sick Children, Toronto, Ontario, Canada.,Archie's Cochlear Implant Laboratory, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - B C Papsin
- Department of Otolaryngology - Head & Neck Surgery, The Hospital for Sick Children, Toronto, Ontario, Canada.,Archie's Cochlear Implant Laboratory, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - S L Cushing
- Department of Otolaryngology - Head & Neck Surgery, The Hospital for Sick Children, Toronto, Ontario, Canada.,Archie's Cochlear Implant Laboratory, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - E Héon
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Ontario, Canada.,Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
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12
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Antisense Oligonucleotide-based Splice Correction for USH2A-associated Retinal Degeneration Caused by a Frequent Deep-intronic Mutation. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 5:e381. [PMID: 27802265 DOI: 10.1038/mtna.2016.89] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 09/07/2016] [Indexed: 12/21/2022]
Abstract
Usher syndrome (USH) is the most common cause of combined deaf-blindness in man. The hearing loss can be partly compensated by providing patients with hearing aids or cochlear implants, but the loss of vision is currently untreatable. In general, mutations in the USH2A gene are the most frequent cause of USH explaining up to 50% of all patients worldwide. The first deep-intronic mutation in the USH2A gene (c.7595-2144A>G) was reported in 2012, leading to the insertion of a pseudoexon (PE40) into the mature USH2A transcript. When translated, this PE40-containing transcript is predicted to result in a truncated non-functional USH2A protein. In this study, we explored the potential of antisense oligonucleotides (AONs) to prevent aberrant splicing of USH2A pre-mRNA as a consequence of the c.7595-2144A>G mutation. Engineered 2'-O-methylphosphorothioate AONs targeting the PE40 splice acceptor site and/or exonic splice enhancer regions displayed significant splice correction potential in both patient derived fibroblasts and a minigene splice assay for USH2A c.7595-2144A>G, whereas a non-binding sense oligonucleotide had no effect on splicing. Altogether, AON-based splice correction could be a promising approach for the development of a future treatment for USH2A-associated retinitis pigmentosa caused by the deep-intronic c.7595-2144A>G mutation.
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13
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Ellingford JM, Barton S, Bhaskar S, O'Sullivan J, Williams SG, Lamb JA, Panda B, Sergouniotis PI, Gillespie RL, Daiger SP, Hall G, Gale T, Lloyd IC, Bishop PN, Ramsden SC, Black GCM. Molecular findings from 537 individuals with inherited retinal disease. J Med Genet 2016; 53:761-767. [PMID: 27208204 PMCID: PMC5106339 DOI: 10.1136/jmedgenet-2016-103837] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/14/2016] [Indexed: 01/12/2023]
Abstract
BACKGROUND Inherited retinal diseases (IRDs) are a clinically and genetically heterogeneous set of disorders, for which diagnostic second-generation sequencing (next-generation sequencing, NGS) services have been developed worldwide. METHODS We present the molecular findings of 537 individuals referred to a 105-gene diagnostic NGS test for IRDs. We assess the diagnostic yield, the spectrum of clinical referrals, the variant analysis burden and the genetic heterogeneity of IRD. We retrospectively analyse disease-causing variants, including an assessment of variant frequency in Exome Aggregation Consortium (ExAC). RESULTS Individuals were referred from 10 clinically distinct classifications of IRD. Of the 4542 variants clinically analysed, we have reported 402 mutations as a cause or a potential cause of disease in 62 of the 105 genes surveyed. These variants account or likely account for the clinical diagnosis of IRD in 51% of the 537 referred individuals. 144 potentially disease-causing mutations were identified as novel at the time of clinical analysis, and we further demonstrate the segregation of known disease-causing variants among individuals with IRD. We show that clinically analysed variants indicated as rare in dbSNP and the Exome Variant Server remain rare in ExAC, and that genes discovered as a cause of IRD in the post-NGS era are rare causes of IRD in a population of clinically surveyed individuals. CONCLUSIONS Our findings illustrate the continued powerful utility of custom-gene panel diagnostic NGS tests for IRD in the clinic, but suggest clear future avenues for increasing diagnostic yields.
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Affiliation(s)
- Jamie M Ellingford
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
- Institute of Human Development, University of Manchester, Manchester, UK
| | - Stephanie Barton
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
| | - Sanjeev Bhaskar
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
| | - James O'Sullivan
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
- Institute of Human Development, University of Manchester, Manchester, UK
| | - Simon G Williams
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
| | - Janine A Lamb
- Institute of Population Health, University of Manchester, Manchester, UK
| | - Binay Panda
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Panagiotis I Sergouniotis
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
- Institute of Human Development, University of Manchester, Manchester, UK
- Manchester Royal Eye Hospital, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Rachel L Gillespie
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
- Institute of Human Development, University of Manchester, Manchester, UK
| | - Stephen P Daiger
- School of Public Health, University of Texas Health Science Center, Houston, Texas, USA
| | - Georgina Hall
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
| | - Theodora Gale
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
| | - I Christopher Lloyd
- Institute of Human Development, University of Manchester, Manchester, UK
- Manchester Royal Eye Hospital, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Paul N Bishop
- Institute of Human Development, University of Manchester, Manchester, UK
- Manchester Royal Eye Hospital, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Simon C Ramsden
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
| | - Graeme C M Black
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
- Institute of Human Development, University of Manchester, Manchester, UK
- Manchester Royal Eye Hospital, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
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14
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An innovative strategy for the molecular diagnosis of Usher syndrome identifies causal biallelic mutations in 93% of European patients. Eur J Hum Genet 2016; 24:1730-1738. [PMID: 27460420 PMCID: PMC5117943 DOI: 10.1038/ejhg.2016.99] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/23/2016] [Accepted: 06/04/2016] [Indexed: 11/08/2022] Open
Abstract
Usher syndrome (USH), the most prevalent cause of hereditary deafness–blindness, is an autosomal recessive and genetically heterogeneous disorder. Three clinical subtypes (USH1–3) are distinguishable based on the severity of the sensorineural hearing impairment, the presence or absence of vestibular dysfunction, and the age of onset of the retinitis pigmentosa. A total of 10 causal genes, 6 for USH1, 3 for USH2, and 1 for USH3, and an USH2 modifier gene, have been identified. A robust molecular diagnosis is required not only to improve genetic counseling, but also to advance gene therapy in USH patients. Here, we present an improved diagnostic strategy that is both cost- and time-effective. It relies on the sequential use of three different techniques to analyze selected genomic regions: targeted exome sequencing, comparative genome hybridization, and quantitative exon amplification. We screened a large cohort of 427 patients (139 USH1, 282 USH2, and six of undefined clinical subtype) from various European medical centers for mutations in all USH genes and the modifier gene. We identified a total of 421 different sequence variants predicted to be pathogenic, about half of which had not been previously reported. Remarkably, we detected large genomic rearrangements, most of which were novel and unique, in 9% of the patients. Thus, our strategy led to the identification of biallelic and monoallelic mutations in 92.7% and 5.8% of the USH patients, respectively. With an overall 98.5% mutation characterization rate, the diagnosis efficiency was substantially improved compared with previously reported methods.
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15
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Genomic screening of ABCA4 and array CGH analysis underline the genetic variability of Greek patients with inherited retinal diseases. Meta Gene 2016; 8:37-43. [PMID: 27014590 PMCID: PMC4792891 DOI: 10.1016/j.mgene.2016.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 01/12/2016] [Accepted: 02/10/2016] [Indexed: 11/22/2022] Open
Abstract
Background Retinal dystrophies are a clinically and genetically heterogeneous group of disorders which affect more than two million people worldwide. The present study focused on the role of the ABCA4 gene in the pathogenesis of hereditary retinal dystrophies (autosomal recessive Stargardt disease, autosomal recessive cone-rod dystrophy, and autosomal recessive retinitis pigmentosa) in patients of Greek origin. Materials and methods Our cohort included 26 unrelated patients and their first degree healthy relatives. The ABCA4 mutation screening involved Sanger sequencing of all exons and flanking regions. Evaluation of novel variants included sequencing of control samples, family segregation analysis and characterization by in silico prediction tools. Twenty five patients were also screened for copy number variations by array-comparative genomic hybridization. Results Excluding known disease-causing mutations and polymorphisms, two novel variants were identified in coding and non-coding regions of ABCA4. Array-CGH analysis revealed two partial deletions of USH2A and MYO3A in two patients with nonsyndromic autosomal recessive retinitis pigmentosa. Conclusions The ABCA4 mutation spectrum in Greek patients differs from other populations. Bioinformatic tools, segregation analysis along with clinical data from the patients seemed to be crucial for the evaluation of genetic variants and particularly for the discrimination between causative and non-causative variants. Sixteen known pathological genetic variants were identified in ABCA4 gene in Greek patients with retinal dystrophies. Two novel variants were found in patients with Stargardt’s disease and cone-rod dystrophy respectively. Two reported mutations in Stargardt's patients were identified in retinitis pigmentosa and cone-rod dystrophy patients. The mutations p.Gly1961Glu and p.Ala1038Val, which are common in other populations, where also found in our cohort consisted of 26 Greek patients. Array-comparative genome hybridization revealed large deletions in two out of the 25 cases studied.
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16
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Pugh TJ, Amr SS, Bowser MJ, Gowrisankar S, Hynes E, Mahanta LM, Rehm HL, Funke B, Lebo MS. VisCap: inference and visualization of germ-line copy-number variants from targeted clinical sequencing data. Genet Med 2015; 18:712-9. [PMID: 26681316 PMCID: PMC4940431 DOI: 10.1038/gim.2015.156] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 09/15/2015] [Indexed: 01/10/2023] Open
Abstract
Purpose: To develop and validate VisCap, a software program targeted to clinical laboratories for inference and visualization of germ-line copy-number variants (CNVs) from targeted next-generation sequencing data. Genet Med18 7, 712–719. Methods: VisCap calculates the fraction of overall sequence coverage assigned to genomic intervals and computes log2 ratios of these values to the median of reference samples profiled using the same test configuration. Candidate CNVs are called when log2 ratios exceed user-defined thresholds. Genet Med18 7, 712–719. Results: We optimized VisCap using 14 cases with known CNVs, followed by prospective analysis of 1,104 cases referred for diagnostic DNA sequencing. To verify calls in the prospective cohort, we used droplet digital polymerase chain reaction (PCR) to confirm 10/27 candidate CNVs and 72/72 copy-neutral genomic regions scored by VisCap. We also used a genome-wide bead array to confirm the absence of CNV calls across panels applied to 10 cases. To improve specificity, we instituted a visual scoring system that enabled experienced reviewers to differentiate true-positive from false-positive calls with minimal impact on laboratory workflow. Genet Med18 7, 712–719. Conclusions: VisCap is a sensitive method for inferring CNVs from targeted sequence data from targeted gene panels. Visual scoring of data underlying CNV calls is a critical step to reduce false-positive calls for follow-up testing. Genet Med18 7, 712–719.
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Affiliation(s)
- Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Sami S Amr
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Boston, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital and Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Mark J Bowser
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Boston, Massachusetts, USA
| | - Sivakumar Gowrisankar
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Boston, Massachusetts, USA
| | - Elizabeth Hynes
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Boston, Massachusetts, USA
| | - Lisa M Mahanta
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Boston, Massachusetts, USA
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Boston, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital and Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Birgit Funke
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Boston, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital and Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Matthew S Lebo
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Boston, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital and Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
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17
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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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18
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Grotta S, D'Elia G, Scavelli R, Genovese S, Surace C, Sirleto P, Cozza R, Romanzo A, De Ioris MA, Valente P, Tomaiuolo AC, Lepri FR, Franchin T, Ciocca L, Russo S, Locatelli F, Angioni A. Advantages of a next generation sequencing targeted approach for the molecular diagnosis of retinoblastoma. BMC Cancer 2015; 15:841. [PMID: 26530098 PMCID: PMC4632486 DOI: 10.1186/s12885-015-1854-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 10/27/2015] [Indexed: 11/10/2022] Open
Abstract
Background Retinoblastoma (RB) is the most common malignant childhood tumor of the eye and results from inactivation of both alleles of the RB1 gene. Nowadays RB genetic diagnosis requires classical chromosome investigations, Multiplex Ligation-dependent Probe Amplification analysis (MLPA) and Sanger sequencing. Nevertheless, these techniques show some limitations. We report our experience on a cohort of RB patients using a combined approach of Next-Generation Sequencing (NGS) and RB1 custom array-Comparative Genomic Hybridization (aCGH). Methods A total of 65 patients with retinoblastoma were studied: 29 cases of bilateral RB and 36 cases of unilateral RB. All patients were previously tested with conventional cytogenetics and MLPA techniques. Fifty-three samples were then analysed using NGS. Eleven cases were analysed by RB1 custom aCGH. One last case was studied only by classic cytogenetics. Finally, it has been tested, in a lab sensitivity assay, the capability of NGS to detect artificial mosaicism series in previously recognized samples prepared at 3 different mosaicism frequencies: 10, 5, 1 %. Results Of the 29 cases of bilateral RB, 28 resulted positive (96.5 %) to the genetic investigation: 22 point mutations and 6 genomic rearrangements (four intragenic and two macrodeletion). A novel germline intragenic duplication, from exon18 to exon 23, was identified in a proband with bilateral RB. Of the 36 available cases of unilateral RB, 8 patients resulted positive (22 %) to the genetic investigation: 3 patients showed point mutations while 5 carried large deletion. Finally, we successfully validated, in a lab sensitivity assay, the capability of NGS to accurately measure level of artificial mosaicism down to 1 %. Conclusions NGS and RB1-custom aCGH have demonstrated to be an effective combined approach in order to optimize the overall diagnostic procedures of RB. Custom aCGH is able to accurately detect genomic rearrangements allowing the characterization of their extension. NGS is extremely accurate in detecting single nucleotide variants, relatively simple to perform, cost savings and efficient and has confirmed a high sensitivity and accuracy in identifying low levels of artificial mosaicisms.
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Affiliation(s)
- Simona Grotta
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy. .,Present address: S. Pietro Fatebenefratelli Hospital, UOSD Medical Genetics, Rome, Italy.
| | - Gemma D'Elia
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy.
| | | | - Silvia Genovese
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy.
| | - Cecilia Surace
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy.
| | - Pietro Sirleto
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy.
| | - Raffaele Cozza
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, Rome, Italy.
| | - Antonino Romanzo
- Ophtalmology Unit, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, Rome, Italy.
| | - Maria Antonietta De Ioris
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, Rome, Italy.
| | - Paola Valente
- Ophtalmology Unit, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, Rome, Italy.
| | - Anna Cristina Tomaiuolo
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy.
| | - Francesca Romana Lepri
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy.
| | - Tiziana Franchin
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy.
| | - Laura Ciocca
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy.
| | - Serena Russo
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy.
| | - Franco Locatelli
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, Rome, Italy. .,University of Pavia, Pavia, Italy.
| | - Adriano Angioni
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy.
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19
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Vona B, Nanda I, Hofrichter MAH, Shehata-Dieler W, Haaf T. Non-syndromic hearing loss gene identification: A brief history and glimpse into the future. Mol Cell Probes 2015; 29:260-70. [PMID: 25845345 DOI: 10.1016/j.mcp.2015.03.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/19/2015] [Accepted: 03/23/2015] [Indexed: 11/27/2022]
Abstract
From the first identified non-syndromic hearing loss gene in 1995, to those discovered in present day, the field of human genetics has witnessed an unparalleled revolution that includes the completion of the Human Genome Project in 2003 to the $1000 genome in 2014. This review highlights the classical and cutting-edge strategies for non-syndromic hearing loss gene identification that have been used throughout the twenty year history with a special emphasis on how the innovative breakthroughs in next generation sequencing technology have forever changed candidate gene approaches. The simplified approach afforded by next generation sequencing technology provides a second chance for the many linked loci in large and well characterized families that have been identified by linkage analysis but have presently failed to identify a causative gene. It also discusses some complexities that may restrict eventual candidate gene discovery and calls for novel approaches to answer some of the questions that make this simple Mendelian disorder so intriguing.
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Affiliation(s)
- Barbara Vona
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany.
| | - Indrajit Nanda
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | | | - Wafaa Shehata-Dieler
- Comprehensive Hearing Center, Department of Otorhinolaryngology, Plastic, Aesthetic and Reconstructive Surgery, University Hospital, Würzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
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20
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Zein WM, Falsini B, Tsilou ET, Turriff AE, Schultz JM, Friedman TB, Brewer CC, Zalewski CK, King KA, Muskett JA, Rehman AU, Morell RJ, Griffith AJ, Sieving PA. Cone responses in Usher syndrome types 1 and 2 by microvolt electroretinography. Invest Ophthalmol Vis Sci 2014; 56:107-14. [PMID: 25425308 DOI: 10.1167/iovs.14-15355] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Progressive decline of psychophysical cone-mediated measures has been reported in type 1 (USH1) and type 2 (USH2) Usher syndrome. Conventional cone electroretinogram (ERG) responses in USH demonstrate poor signal-to-noise ratio. We evaluated cone signals in USH1 and USH2 by recording microvolt level cycle-by-cycle (CxC) ERG. METHODS Responses of molecularly genotyped USH1 (n = 18) and USH2 (n = 24) subjects (age range, 15-69 years) were compared with those of controls (n = 12). A subset of USH1 (n = 9) and USH2 (n = 9) subjects was examined two to four times over 2 to 8 years. Photopic CxC ERG and conventional 30-Hz flicker ERG were recorded on the same visits. RESULTS Usher syndrome subjects showed considerable cone flicker ERG amplitude losses and timing phase delays (P < 0.01) compared with controls. USH1 and USH2 had similar rates of progressive logarithmic ERG amplitude decline with disease duration (-0.012 log μV/y). Of interest, ERG phase delays did not progress over time. Two USH1C subjects retained normal response timing despite reduced amplitudes. The CxC ERG method provided reliable responses in all subjects, whereas conventional ERG was undetectable in 7 of 42 subjects. CONCLUSIONS Cycle-by-cycle ERG showed progressive loss of amplitude in both USH1 and USH2 subjects, comparable to that reported with psychophysical measures. Usher subjects showed abnormal ERG response latency, but this changed less than amplitude with time. In USH syndrome, CxC ERG is more sensitive than conventional ERG and warrants consideration as an outcome measure in USH treatment trials.
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Affiliation(s)
- Wadih M Zein
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Benedetto Falsini
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Ekaterina T Tsilou
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Amy E Turriff
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Julie M Schultz
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, United States
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, United States
| | - Carmen C Brewer
- Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, United States
| | - Christopher K Zalewski
- Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, United States
| | - Kelly A King
- Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, United States
| | - Julie A Muskett
- Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, United States
| | - Atteeq U Rehman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, United States
| | - Robert J Morell
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, United States
| | - Andrew J Griffith
- Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, United States
| | - Paul A Sieving
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland, United States
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