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Zeuli R, Karali M, de Bruijn SE, Rodenburg K, Scarpato M, Capasso D, Astuti GDN, Gilissen C, Rodríguez-Hidalgo M, Ruiz-Ederra J, Testa F, Simonelli F, Cremers FPM, Banfi S, Roosing S. Whole genome sequencing identifies elusive variants in genetically unsolved Italian inherited retinal disease patients. HGG ADVANCES 2024; 5:100314. [PMID: 38816995 PMCID: PMC11225895 DOI: 10.1016/j.xhgg.2024.100314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/01/2024] Open
Abstract
Inherited retinal diseases (IRDs) are a group of rare monogenic diseases with high genetic heterogeneity (pathogenic variants identified in over 280 causative genes). The genetic diagnostic rate for IRDs is around 60%, mainly thanks to the routine application of next-generation sequencing (NGS) approaches such as extensive gene panels or whole exome analyses. Whole-genome sequencing (WGS) has been reported to improve this diagnostic rate by revealing elusive variants, such as structural variants (SVs) and deep intronic variants (DIVs). We performed WGS on 33 unsolved cases with suspected autosomal recessive IRD, aiming to identify causative genetic variants in non-coding regions or to detect SVs that were unexplored in the initial screening. Most of the selected cases (30 of 33, 90.9%) carried monoallelic pathogenic variants in genes associated with their clinical presentation, hence we first analyzed the non-coding regions of these candidate genes. Whenever additional pathogenic variants were not identified with this approach, we extended the search for SVs and DIVs to all IRD-associated genes. Overall, we identified the missing causative variants in 11 patients (11 of 33, 33.3%). These included three DIVs in ABCA4, CEP290 and RPGRIP1; one non-canonical splice site (NCSS) variant in PROM1 and three SVs (large deletions) in EYS, PCDH15 and USH2A. For the previously unreported DIV in CEP290 and for the NCCS variant in PROM1, we confirmed the effect on splicing by reverse transcription (RT)-PCR on patient-derived RNA. This study demonstrates the power and clinical utility of WGS as an all-in-one test to identify disease-causing variants missed by standard NGS diagnostic methodologies.
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Affiliation(s)
- Roberta Zeuli
- Medical Genetics, Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Marianthi Karali
- Medical Genetics, Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy; Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Suzanne E de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Kim Rodenburg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Margherita Scarpato
- Medical Genetics, Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Dalila Capasso
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomic and Experimental Medicine Program, Naples, Italy
| | - Galuh D N Astuti
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - María Rodríguez-Hidalgo
- Department of Neuroscience, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Department of Dermatology, Ophthalmology, and Otorhinolaryngology, University of the Basque Country (UPV/EHU), Donostia-San Sebastián, Spain
| | - Javier Ruiz-Ederra
- Department of Neuroscience, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Department of Dermatology, Ophthalmology, and Otorhinolaryngology, University of the Basque Country (UPV/EHU), Donostia-San Sebastián, Spain
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sandro Banfi
- Medical Genetics, Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
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Torii K, Nishina S, Morikawa H, Mizobuchi K, Takayama M, Tachibana N, Kurata K, Hikoya A, Sato M, Nakano T, Fukami M, Azuma N, Hayashi T, Saitsu H, Hotta Y. The Structural Abnormalities Are Deeply Involved in the Cause of RPGRIP1-Related Retinal Dystrophy in Japanese Patients. Int J Mol Sci 2023; 24:13678. [PMID: 37761981 PMCID: PMC10531429 DOI: 10.3390/ijms241813678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 08/31/2023] [Accepted: 09/02/2023] [Indexed: 09/29/2023] Open
Abstract
Leber congenital amaurosis (LCA) is the most severe form of inherited retinal dystrophy. RPGRIP1-related LCA accounts for 5-6% of LCA. We performed whole-exome sequencing and whole-genome sequencing (WGS) on 29 patients with clinically suspected LCA and examined ophthalmic findings in patients with biallelic pathogenic variants of RPGRIP1. In addition to five previously reported cases, we identified five cases from four families with compound heterozygous RPGRIP1 variants using WGS. Five patients had null variants comprising frameshift variants, an Alu insertion, and microdeletions. A previously reported 1339 bp deletion involving exon 18 was found in four cases, and the deletion was relatively prevalent in the Japanese population (allele frequency: 0.002). Microdeletions involving exon 1 were detected in four cases. In patients with RPGRIP1 variants, visual acuity remained low, ranging from light perception to 0.2, and showed no correlation with age. In optical coherence tomography images, the ellipsoid zone (EZ) length decreased with age in all but one case of unimpaired EZ. The retinal structure was relatively preserved in all cases; however, there were cases with great differences in visual function compared to their siblings and a 56-year-old patient who still had a faint EZ line. Structural abnormalities may be important genetic causes of RPGRIP1-related retinal dystrophy in Japanese patients, and WGS was useful for detecting them.
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Affiliation(s)
- Kaoruko Torii
- Department of Ophthalmology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
| | - Sachiko Nishina
- Division of Ophthalmology, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan
| | - Hazuki Morikawa
- Division of Ophthalmology, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan
| | - Kei Mizobuchi
- Department of Ophthalmology, The Jikei University School of Medicine, 3-25-8 Nishi-shimbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Masakazu Takayama
- Department of Ophthalmology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
| | - Nobutaka Tachibana
- Department of Ophthalmology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
| | - Kentaro Kurata
- Department of Ophthalmology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
| | - Akiko Hikoya
- Department of Ophthalmology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
| | - Miho Sato
- Department of Ophthalmology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
| | - Tadashi Nakano
- Department of Ophthalmology, The Jikei University School of Medicine, 3-25-8 Nishi-shimbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan
| | - Noriyuki Azuma
- Division of Ophthalmology, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan
- Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Takaaki Hayashi
- Department of Ophthalmology, The Jikei University School of Medicine, 3-25-8 Nishi-shimbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
| | - Yoshihiro Hotta
- Department of Ophthalmology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
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Synofzik M, van Roon-Mom WMC, Marckmann G, van Duyvenvoorde HA, Graessner H, Schüle R, Aartsma-Rus A. Preparing n-of-1 Antisense Oligonucleotide Treatments for Rare Neurological Diseases in Europe: Genetic, Regulatory, and Ethical Perspectives. Nucleic Acid Ther 2021; 32:83-94. [PMID: 34591693 PMCID: PMC9058873 DOI: 10.1089/nat.2021.0039] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Antisense oligonucleotide (ASO) therapies present a promising disease-modifying treatment approach for rare neurological diseases (RNDs). However, the current focus is on "more common" RNDs, leaving a large share of RND patients still without prospect of disease-modifying treatments. In response to this gap, n-of-1 ASO treatment approaches are targeting ultrarare or even private variants. While highly attractive, this emerging, academia-driven field of ultimately individualized precision medicine is in need of systematic guidance and standards, which will allow global scaling of this approach. We provide here genetic, regulatory, and ethical perspectives for preparing n-of-1 ASO treatments and research programs, with a specific focus on the European context. By example of splice modulating ASOs, we outline genetic criteria for variant prioritization, chart the regulatory field of n-of-1 ASO treatment development in Europe, and propose an ethically informed classification for n-of-1 ASO treatment strategies and level of outcome assessments. To accommodate the ethical requirements of both individual patient benefit and knowledge gain, we propose a stronger integration of patient care and clinical research when developing novel n-of-1 ASO treatments: each single trial of therapy should inherently be driven to generate generalizable knowledge, be registered in a ASO treatment registry, and include assessment of generic outcomes, which allow aggregated analysis across n-of-1 trials of therapy.
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Affiliation(s)
- Matthis Synofzik
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany.,Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | | | - Georg Marckmann
- Institute of Ethics, History and Theory of Medicine, Ludwig Maximilians University Munich, Munich, Germany
| | | | - Holm Graessner
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Center for Rare Diseases, Tübingen, Germany
| | - Rebecca Schüle
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany.,Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
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