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Quinodoz M, Kaminska K, Cancellieri F, Han JH, Peter VG, Celik E, Janeschitz-Kriegl L, Schärer N, Hauenstein D, György B, Calzetti G, Hahaut V, Custódio S, Sousa AC, Wada Y, Murakami Y, Fernández AA, Hernández CR, Minguez P, Ayuso C, Nishiguchi KM, Santos C, Santos LC, Tran VH, Vaclavik V, Scholl HPN, Rivolta C. Detection of elusive DNA copy-number variations in hereditary disease and cancer through the use of noncoding and off-target sequencing reads. Am J Hum Genet 2024; 111:701-713. [PMID: 38531366 PMCID: PMC11023916 DOI: 10.1016/j.ajhg.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 03/28/2024] Open
Abstract
Copy-number variants (CNVs) play a substantial role in the molecular pathogenesis of hereditary disease and cancer, as well as in normal human interindividual variation. However, they are still rather difficult to identify in mainstream sequencing projects, especially involving exome sequencing, because they often occur in DNA regions that are not targeted for analysis. To overcome this problem, we developed OFF-PEAK, a user-friendly CNV detection tool that builds on a denoising approach and the use of "off-target" DNA reads, which are usually discarded by sequencing pipelines. We benchmarked OFF-PEAK on data from targeted sequencing of 96 cancer samples, as well as 130 exomes of individuals with inherited retinal disease from three different populations. For both sets of data, OFF-PEAK demonstrated excellent performance (>95% sensitivity and >80% specificity vs. experimental validation) in detecting CNVs from in silico data alone, indicating its immediate applicability to molecular diagnosis and genetic research.
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Affiliation(s)
- Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Ji Hoon Han
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Virginie G Peter
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Department of Ophthalmology, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Elifnaz Celik
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Lucas Janeschitz-Kriegl
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Nils Schärer
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Daniela Hauenstein
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Bence György
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Giacomo Calzetti
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Vincent Hahaut
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Sónia Custódio
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon, Portugal
| | - Ana Cristina Sousa
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon, Portugal
| | | | - Yusuke Murakami
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Almudena Avila Fernández
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain; Centre for Biomedical Network Research On Rare Diseases (CIBERER), Madrid, Spain
| | - Cristina Rodilla Hernández
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain; Centre for Biomedical Network Research On Rare Diseases (CIBERER), Madrid, Spain
| | - Pablo Minguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain; Centre for Biomedical Network Research On Rare Diseases (CIBERER), Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain; Centre for Biomedical Network Research On Rare Diseases (CIBERER), Madrid, Spain
| | - Koji M Nishiguchi
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Cristina Santos
- NOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisbon, Portugal; Instituto de Oftalmologia Dr Gama Pinto (IOGP), Lisbon, Portugal
| | | | - Viet H Tran
- Unité d'oculogénétique, Jules Gonin Eye Hospital, University of Lausanne, Lausanne, Switzerland; Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
| | - Veronika Vaclavik
- Unité d'oculogénétique, Jules Gonin Eye Hospital, University of Lausanne, Lausanne, Switzerland
| | - Hendrik P N Scholl
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
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2
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Arsenijevic Y, Chang N, Mercey O, El Fersioui Y, Koskiniemi-Kuendig H, Joubert C, Bemelmans AP, Rivolta C, Banin E, Sharon D, Guichard P, Hamel V, Kostic C. Fine-tuning FAM161A gene augmentation therapy to restore retinal function. EMBO Mol Med 2024; 16:805-822. [PMID: 38504136 PMCID: PMC11018783 DOI: 10.1038/s44321-024-00053-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 03/21/2024] Open
Abstract
For 15 years, gene therapy has been viewed as a beacon of hope for inherited retinal diseases. Many preclinical investigations have centered around vectors with maximal gene expression capabilities, yet despite efficient gene transfer, minimal physiological improvements have been observed in various ciliopathies. Retinitis pigmentosa-type 28 (RP28) is the consequence of bi-allelic null mutations in the FAM161A, an essential protein for the structure of the photoreceptor connecting cilium (CC). In its absence, cilia become disorganized, leading to outer segment collapses and vision impairment. Within the human retina, FAM161A has two isoforms: the long one with exon 4, and the short one without it. To restore CC in Fam161a-deficient mice shortly after the onset of cilium disorganization, we compared AAV vectors with varying promoter activities, doses, and human isoforms. While all vectors improved cell survival, only the combination of both isoforms using the weak FCBR1-F0.4 promoter enabled precise FAM161A expression in the CC and enhanced retinal function. Our investigation into FAM161A gene replacement for RP28 emphasizes the importance of precise therapeutic gene regulation, appropriate vector dosing, and delivery of both isoforms. This precision is pivotal for secure gene therapy involving structural proteins like FAM161A.
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Affiliation(s)
- Yvan Arsenijevic
- Unit of Retinal Degeneration and Regeneration, Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland.
| | - Ning Chang
- Unit of Retinal Degeneration and Regeneration, Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
- Group for Retinal Disorder Research, Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
| | - Olivier Mercey
- University of Geneva, Department of Molecular and Cellular Biology, Sciences III, Geneva, Switzerland
| | - Younes El Fersioui
- Unit of Retinal Degeneration and Regeneration, Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
- Group for Retinal Disorder Research, Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
| | - Hanna Koskiniemi-Kuendig
- Unit of Retinal Degeneration and Regeneration, Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
| | - Caroline Joubert
- Unit of Retinal Degeneration and Regeneration, Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
| | - Alexis-Pierre Bemelmans
- Université Paris-Saclay, CEA, CNRS, Laboratoire des Maladies Neurodégénératives: mécanismes, thérapies, imagerie, Fontenay-aux-Roses, France
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Eyal Banin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Faculty of Medicine, The Hebrew of Jerusalem, Jerusalem, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Faculty of Medicine, The Hebrew of Jerusalem, Jerusalem, Israel
| | - Paul Guichard
- University of Geneva, Department of Molecular and Cellular Biology, Sciences III, Geneva, Switzerland
| | - Virginie Hamel
- University of Geneva, Department of Molecular and Cellular Biology, Sciences III, Geneva, Switzerland
| | - Corinne Kostic
- Group for Retinal Disorder Research, Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland.
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3
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Han JH, Rodenburg K, Hayman T, Calzetti G, Kaminska K, Quinodoz M, Marra M, Wallerich S, Allon G, Nagy ZZ, Knézy K, Li Y, Chen R, Barboni MTS, Yang P, Pennesi ME, van den Born LI, Varsányi B, Szabó V, Sharon D, Banin E, Ben-Yosef T, Roosing S, Koenekoop RK, Rivolta C. Loss-of-function variants in UBAP1L cause autosomal recessive retinal degeneration. Genet Med 2024:101106. [PMID: 38420906 DOI: 10.1016/j.gim.2024.101106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/23/2024] [Accepted: 02/23/2024] [Indexed: 03/02/2024] Open
Abstract
PURPOSE Inherited retinal diseases (IRDs) are a group of monogenic conditions that can lead to progressive blindness. Their missing heritability is still considerable, due in part to the presence of disease genes that await molecular identification. The purpose of this work was to identify novel genetic associations with IRDs. METHODS Patients underwent a comprehensive ophthalmological evaluation using standard-of-care tests, such as detailed retinal imaging (macular optical coherence tomography and short-wavelength fundus autofluorescence) and electrophysiological testing. Exome and genome sequencing, as well as computer-assisted data analysis were used for genotyping and detection of DNA variants. A minigene-driven splicing assay was performed to validate the deleterious effects of 1 of such variants. RESULTS We identified 8 unrelated families from Hungary, the United States, Israel, and The Netherlands with members presenting with a form of autosomal recessive and nonsyndromic retinal degeneration, predominantly described as rod-cone dystrophy but also including cases of cone/cone-rod dystrophy. Age of disease onset was very variable, with some patients experiencing first symptoms during their fourth decade of life or later. Myopia greater than 5 diopters was present in 5 of 7 cases with available refractive data, and retinal detachment was reported in 2 cases. All ascertained patients carried biallelic loss-of-function variants in UBAP1L (HGNC: 40028), a gene with unknown function and with homologies to UBAP1, encoding a protein involved in ubiquitin metabolism. One of these pathogenic variants, the intronic NM_001163692.2:c.910-7G>A substitution, was identified in 5 unrelated families. Minigene-driven splicing assays in HEK293T cells confirmed that this DNA change is responsible for the creation of a new acceptor splice site, resulting in aberrant splicing. CONCLUSION We identified UBAP1L as a novel IRD gene. Although its function is currently unknown, UBAP1L is almost exclusively expressed in photoreceptors and the retinal pigment epithelium, hence possibly explaining the link between pathogenic variants in this gene and an ocular phenotype.
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Affiliation(s)
- Ji Hoon Han
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Kim Rodenburg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tamar Hayman
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Giacomo Calzetti
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Molly Marra
- Casey Eye Institute, Oregon Health and Science University, Portland, OR
| | - Sandrine Wallerich
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Gilad Allon
- Department of Ophthalmology, Meir Medical Center, Kfar Saba, Israel
| | - Zoltán Z Nagy
- Department of Ophthalmology, Semmelweis University, Budapest, Hungary
| | - Krisztina Knézy
- Department of Ophthalmology, Semmelweis University, Budapest, Hungary
| | - Yumei Li
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Rui Chen
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | | | - Paul Yang
- Casey Eye Institute, Oregon Health and Science University, Portland, OR
| | - Mark E Pennesi
- Casey Eye Institute, Oregon Health and Science University, Portland, OR
| | | | - Balázs Varsányi
- Department of Ophthalmology, Semmelweis University, Budapest, Hungary
| | - Viktória Szabó
- Department of Ophthalmology, Semmelweis University, Budapest, Hungary
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tamar Ben-Yosef
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Robert K Koenekoop
- Departments of Pediatric Surgery, Human Genetics and Ophthalmology, Montreal Children's Hospital, McGill University and McGill University Health Center Research Institute, Montreal, QC, Canada
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom.
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4
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Bauwens M, Celik E, Zur D, Lin S, Quinodoz M, Michaelides M, Webster AR, Van Den Broeck F, Leroy BP, Rizel L, Moye AR, Meunier A, Tran HV, Moulin AP, Mahieu Q, Van Heetvelde M, Arno G, Rivolta C, De Baere E, Ben-Yosef T. Mutations in SAMD7 cause autosomal-recessive macular dystrophy with or without cone dysfunction. Am J Hum Genet 2024; 111:393-402. [PMID: 38272031 PMCID: PMC10870129 DOI: 10.1016/j.ajhg.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 01/27/2024] Open
Abstract
Sterile alpha motif domain containing 7 (SAMD7) is a component of the Polycomb repressive complex 1, which inhibits transcription of many genes, including those activated by the transcription factor Cone-Rod Homeobox (CRX). Here we report bi-allelic mutations in SAMD7 as a cause of autosomal-recessive macular dystrophy with or without cone dysfunction. Four of these mutations affect splicing, while another mutation is a missense variant that alters the repressive effect of SAMD7 on CRX-dependent promoter activity, as shown by in vitro assays. Immunostaining of human retinal sections revealed that SAMD7 is localized in the nuclei of both rods and cones, as well as in those of cells belonging to the inner nuclear layer. These results place SAMD7 as a gene crucial for human retinal function and demonstrate a significant difference in the role of SAMD7 between the human and the mouse retina.
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Affiliation(s)
- Miriam Bauwens
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Elifnaz Celik
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, 4031 Basel, Switzerland
| | - Dinah Zur
- Ophthalmology Division, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel; Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Siying Lin
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the Institute of Ophthalmology, London, UK; Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, 4031 Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Michel Michaelides
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the Institute of Ophthalmology, London, UK; Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Andrew R Webster
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the Institute of Ophthalmology, London, UK; Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Filip Van Den Broeck
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Head & Skin, Ghent University, 9000 Ghent, Belgium
| | - Bart P Leroy
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Head & Skin, Ghent University, 9000 Ghent, Belgium; Department of Ophthalmology, Ghent University Hospital, 9000 Ghent, Belgium; The Division of Ophthalmology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leah Rizel
- The Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Abigail R Moye
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, 4031 Basel, Switzerland
| | - Audrey Meunier
- Department of Ophthalmology, Centre Hospitalier Universitaire Saint-Pierre, 1000 Brussels, Belgium
| | - Hoai Viet Tran
- Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, University of Lausanne, 1004 Lausanne, Switzerland; Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
| | - Alexandre P Moulin
- Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, University of Lausanne, 1004 Lausanne, Switzerland
| | - Quinten Mahieu
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Mattias Van Heetvelde
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Gavin Arno
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the Institute of Ophthalmology, London, UK; Institute of Ophthalmology, University College London, London EC1V 9EL, UK; North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3BH, UK
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, 4031 Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Elfride De Baere
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Tamar Ben-Yosef
- The Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel.
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5
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Cortinhal T, Santos C, Vaz-Pereira S, Marta A, Duarte L, Miranda V, Costa J, Sousa AB, Peter VG, Kaminska K, Rivolta C, Carvalho AL, Saraiva J, Soares CA, Silva R, Murta J, Santos LC, Marques JP. Genetic profile of syndromic retinitis pigmentosa in Portugal. Graefes Arch Clin Exp Ophthalmol 2024:10.1007/s00417-023-06360-2. [PMID: 38189974 DOI: 10.1007/s00417-023-06360-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 12/11/2023] [Accepted: 12/28/2023] [Indexed: 01/09/2024] Open
Abstract
PURPOSE Retinitis pigmentosa (RP) comprises a genetically and clinically heterogeneous group of inherited retinal degenerations, where 20-30% of patients exhibit extra-ocular manifestations (syndromic RP). Understanding the genetic profile of RP has important implications for disease prognosis and genetic counseling. This study aimed to characterize the genetic profile of syndromic RP in Portugal. METHODS Multicenter, retrospective cohort study. Six Portuguese healthcare providers identified patients with a clinical diagnosis of syndromic RP and available genetic testing results. All patients had been previously subjected to a detailed ophthalmologic examination and clinically oriented genetic testing. Genetic variants were classified according to the American College of Medical Genetics and Genomics; only likely pathogenic or pathogenic variants were considered relevant for disease etiology. RESULTS One hundred and twenty-two patients (53.3% males) from 100 families were included. Usher syndrome was the most frequent diagnosis (62.0%), followed by Bardet-Biedl (19.0%) and Senior-Løken syndromes (7.0%). Deleterious variants were identified in 86/100 families for a diagnostic yield of 86.0% (87.1% for Usher and 94.7% for Bardet-Biedl). A total of 81 genetic variants were identified in 25 different genes, 22 of which are novel. USH2A and MYO7A were responsible for most type II and type I Usher syndrome cases, respectively. BBS1 variants were the cause of Bardet-Biedl syndrome in 52.6% of families. Best-corrected visual acuity (BCVA) records were available at baseline and last visit for 99 patients (198 eyes), with a median follow-up of 62.0 months. The mean BCVA was 56.5 ETDRS letters at baseline (Snellen equivalent ~ 20/80), declining to 44.9 ETDRS letters (Snellen equivalent ~ 20/125) at the last available follow-up (p < 0.001). CONCLUSION This is the first multicenter study depicting the genetic profile of syndromic RP in Portugal, thus contributing toward a better understanding of this heterogeneous disease group. Usher and Bardet-Biedl syndromes were found to be the most common types of syndromic RP in this large Portuguese cohort. A high diagnostic yield was obtained, highlighting current genetic testing capabilities in providing a molecular diagnosis to most affected individuals. This has major implications in determining disease-related prognosis and providing targeted genetic counseling for syndromic RP patients in Portugal.
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Affiliation(s)
- Telmo Cortinhal
- Department of Ophthalmology, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
| | - Cristina Santos
- Instituto de Oftalmologia Dr. Gama Pinto (IOGP), Lisboa, Portugal
- iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Sara Vaz-Pereira
- Department of Ophthalmology, Centro Hospitalar Universitário de Lisboa Norte (CHULN), Lisboa, Portugal
- Department of Ophthalmology, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Ana Marta
- Department of Ophthalmology, Centro Hospitalar e Universitário de Santo António (CHUdSA), Porto, Portugal
- Instituto Ciências Biomédicas Abel Salazar (ICBAS), Porto, Portugal
| | - Lilianne Duarte
- Department of Ophthalmology, Centro Hospitalar de Entre Douro e Vouga (CHEDV), Santa Maria da Feira, Portugal
| | - Vitor Miranda
- Department of Ophthalmology, Centro Hospitalar de Entre Douro e Vouga (CHEDV), Santa Maria da Feira, Portugal
| | - José Costa
- Department of Ophthalmology, Hospital de Braga (HB), Braga, Portugal
| | - Ana Berta Sousa
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Lisboa Norte (CHULN), Lisboa, Portugal
| | - Virginie G Peter
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031, Basel, Switzerland
- Department of Ophthalmology, University of Basel, 4031, Basel, Switzerland
- Department of Ophthalmology, Inselspital, Bern University Hospital, 3010, Bern, Switzerland
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031, Basel, Switzerland
- Department of Ophthalmology, University of Basel, 4031, Basel, Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031, Basel, Switzerland
- Department of Ophthalmology, University of Basel, 4031, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Ana Luísa Carvalho
- Medical Genetics Unit, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
- University Clinic of Medical Genetics, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal
| | - Jorge Saraiva
- Medical Genetics Unit, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
- University Clinic of Pediatrics, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal
| | - Célia Azevedo Soares
- Medical Genetics Department, Centro de Genética Médica Jacinto Magalhães, Centro Hospitalar e Universitário do Porto (CHUP), Porto, Portugal
- Unit for Multidisciplinary Research in Biomedicine, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
- Medical Science Department, Universidade de Aveiro, Aveiro, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Rufino Silva
- Department of Ophthalmology, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
- University Clinic of Ophthalmology, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal
| | - Joaquim Murta
- Department of Ophthalmology, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal
- University Clinic of Ophthalmology, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal
| | | | - João Pedro Marques
- Department of Ophthalmology, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal.
- Clinical Academic Center of Coimbra (CACC), Coimbra, Portugal.
- University Clinic of Ophthalmology, Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal.
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6
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Dueñas Rey A, Del Pozo Valero M, Bouckaert M, Wood KA, Van den Broeck F, Daich Varela M, Thomas HB, Van Heetvelde M, De Bruyne M, Van de Sompele S, Bauwens M, Lenaerts H, Mahieu Q, Josifova D, Rivolta C, O'Keefe RT, Ellingford J, Webster AR, Arno G, Ayuso C, De Zaeytijd J, Leroy BP, De Baere E, Coppieters F. Combining a prioritization strategy and functional studies nominates 5'UTR variants underlying inherited retinal disease. Genome Med 2024; 16:7. [PMID: 38184646 PMCID: PMC10771650 DOI: 10.1186/s13073-023-01277-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/15/2023] [Indexed: 01/08/2024] Open
Abstract
BACKGROUND 5' untranslated regions (5'UTRs) are essential modulators of protein translation. Predicting the impact of 5'UTR variants is challenging and rarely performed in routine diagnostics. Here, we present a combined approach of a comprehensive prioritization strategy and functional assays to evaluate 5'UTR variation in two large cohorts of patients with inherited retinal diseases (IRDs). METHODS We performed an isoform-level re-analysis of retinal RNA-seq data to identify the protein-coding transcripts of 378 IRD genes with highest expression in retina. We evaluated the coverage of their 5'UTRs by different whole exome sequencing (WES) kits. The selected 5'UTRs were analyzed in whole genome sequencing (WGS) and WES data from IRD sub-cohorts from the 100,000 Genomes Project (n = 2397 WGS) and an in-house database (n = 1682 WES), respectively. Identified variants were annotated for 5'UTR-relevant features and classified into seven categories based on their predicted functional consequence. We developed a variant prioritization strategy by integrating population frequency, specific criteria for each category, and family and phenotypic data. A selection of candidate variants underwent functional validation using diverse approaches. RESULTS Isoform-level re-quantification of retinal gene expression revealed 76 IRD genes with a non-canonical retina-enriched isoform, of which 20 display a fully distinct 5'UTR compared to that of their canonical isoform. Depending on the probe design, 3-20% of IRD genes have 5'UTRs fully captured by WES. After analyzing these regions in both cohorts, we prioritized 11 (likely) pathogenic variants in 10 genes (ARL3, MERTK, NDP, NMNAT1, NPHP4, PAX6, PRPF31, PRPF4, RDH12, RD3), of which 7 were novel. Functional analyses further supported the pathogenicity of three variants. Mis-splicing was demonstrated for the PRPF31:c.-9+1G>T variant. The MERTK:c.-125G>A variant, overlapping a transcriptional start site, was shown to significantly reduce both luciferase mRNA levels and activity. The RDH12:c.-123C>T variant was found in cis with the hypomorphic RDH12:c.701G>A (p.Arg234His) variant in 11 patients. This 5'UTR variant, predicted to introduce an upstream open reading frame, was shown to result in reduced RDH12 protein but unaltered mRNA levels. CONCLUSIONS This study demonstrates the importance of 5'UTR variants implicated in IRDs and provides a systematic approach for 5'UTR annotation and validation that is applicable to other inherited diseases.
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Affiliation(s)
- Alfredo Dueñas Rey
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Marta Del Pozo Valero
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Manon Bouckaert
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Katherine A Wood
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Filip Van den Broeck
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Malena Daich Varela
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Huw B Thomas
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Mattias Van Heetvelde
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Marieke De Bruyne
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Stijn Van de Sompele
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Miriam Bauwens
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Hanne Lenaerts
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Quinten Mahieu
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | | | - Carlo Rivolta
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Raymond T O'Keefe
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Jamie Ellingford
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
- Genomics England, London, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Andrew R Webster
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Gavin Arno
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Bart P Leroy
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
- Division of Ophthalmology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elfride De Baere
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Frauke Coppieters
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium.
- Department of Pharmaceutics, Ghent University, Ghent, Belgium.
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Conti GM, Cancellieri F, Quinodoz M, Kaminska K, Vaclavik V, Rivolta C, Tran HV. GNB1-Related Rod-Cone Dystrophy: A Case Report. Case Rep Ophthalmol 2024; 15:230-237. [PMID: 38500542 PMCID: PMC10948171 DOI: 10.1159/000537997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 02/19/2024] [Indexed: 03/20/2024] Open
Abstract
Introduction The GNB1 (guanine nucleotide-binding protein, β1) gene encodes for the ubiquitous β1 subunit of heterotrimeric G proteins, which are associated with G-protein-coupled receptors (GPCRs). GNB1 mutations cause a neurodevelopmental disorder characterized by a broad clinical spectrum. A novel variant has recently been confirmed in a case of rod-cone dystrophy. Case Presentation We describe the second confirmed case of a classical rod-cone dystrophy associated with a mutation located in exon 6 of GNB1 [NM_002074.5:c.217G>C, p.(Ala73Pro)] in a 56-year-old patient also presenting mild intellectual disability, attention deficit/hyperactivity disorder, and truncal obesity. Conclusion This paper confirms the role of GNB1 in the pathogenesis of a classic rod-cone dystrophy and highlights the importance of including this gene in the genetic analysis panel for inherited retinal diseases.
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Affiliation(s)
- Giovanni Marco Conti
- Genetic Ophthalmic Department, Hôpital Ophtalmique Jules-Gonin, University of Lausanne and Faculty of Life Sciences, Lausanne, Switzerland
- Institut D’Ophtalmologie de Vevey (INOV), Vevey, Switzerland
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Veronika Vaclavik
- Genetic Ophthalmic Department, Hôpital Ophtalmique Jules-Gonin, University of Lausanne and Faculty of Life Sciences, Lausanne, Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Hoai Viet Tran
- Genetic Ophthalmic Department, Hôpital Ophtalmique Jules-Gonin, University of Lausanne and Faculty of Life Sciences, Lausanne, Switzerland
- Institut D’Ophtalmologie de Vevey (INOV), Vevey, Switzerland
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, London, UK
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8
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Conti GM, Vaclavik V, Rivolta C, Escher P, Schorderet DF, Munier FL, Tran HV. Genetics of Retinitis Pigmentosa and Other Hereditary Retinal Disorders in Western Switzerland. Ophthalmic Res 2023; 67:172-182. [PMID: 38160664 DOI: 10.1159/000536036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
INTRODUCTION Mutational screening of inherited retinal disorders is prerequisite for gene targeted therapy. Our aim was to report and analyze the proportions of mutations in inherited retinal disease (IRD)-causing genes from a single center in Switzerland in order to describe the distribution of IRDs in Western Switzerland. METHODS We conducted a retrospective study of patient records. Criteria for inclusion were residence in Western Switzerland for patients and relatives presenting a clinical diagnosis of IRDs and an established molecular diagnosis managed by the genetics service of the Jules-Gonin Eye Hospital (JGEH) of Lausanne between January 2002 and December 2022. We initially investigated the IRD phenotypes in all patients (full cohort) with a clinical diagnosis, then calculated the distribution of IRD gene mutations in the entire cohort (genetically determined cohort). We analyzed a sub-group that comprised pediatric patients (≤18 years of age). In addition, we calculated the distribution of gene mutations within the most represented IRDs. Comprehensive gene screening was performed using a combined approach of different generation of DNA microarray analysis, direct sequencing, and Sanger sequencing. RESULTS The full cohort comprised 899 individuals from 690 families with a clinical diagnosis of IRDs. We identified 400 individuals from 285 families with an elucidated molecular diagnosis (variants in 84 genes) in the genetically determined cohort. The pediatric cohort included 89 individuals from 65 families with an elucidated molecular diagnosis. The molecular diagnosis rate for the genetically determined cohort was 58.2% (family ratio) and the 5 most frequently implicated genes per family were ABCA4 (11.6%), USH2A (7.4%), EYS (6.7%), PRPH2 (6.3%), and BEST1 (4.6%). The pediatric cohort had a family molecular diagnosis rate of 64.4% and the 5 most common mutated genes per family were RS1 (9.2%), ABCA4 (7.7%), CNGB3 (7.7%), CACNA1F (6.2%), CEP290 (4.6%). CONCLUSIONS This study describes the genetic mutation landscape of IRDs in Western Switzerland in order to quantify their disease burden and contribute to a better orientation of the development of future gene targeted therapies.
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Affiliation(s)
- Giovanni Marco Conti
- Genetic Ophthalmic Department, Hôpital Ophtalmique Jules-Gonin, University of Lausanne and Faculty of Life Sciences, Lausanne, Switzerland,
- Institut d'ophtalmologie de Vevey (INOV), Vevey, Switzerland,
| | - Veronika Vaclavik
- Genetic Ophthalmic Department, Hôpital Ophtalmique Jules-Gonin, University of Lausanne and Faculty of Life Sciences, Lausanne, Switzerland
| | - Carlo Rivolta
- Department, Institute of Molecular and Clinical Ophthalmology Basel (IOB), University of Basel, Basel, Switzerland
| | - Pascal Escher
- Department of Ophthalmology, Inselspital, Bern University Hospital and Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Daniel Francis Schorderet
- Faculty of Biology and Medicine, University of Lausanne and School of Life Sciences, Ecole polytechnique fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Francis L Munier
- Genetic Ophthalmic Department, Hôpital Ophtalmique Jules-Gonin, University of Lausanne and Faculty of Life Sciences, Lausanne, Switzerland
| | - Hoai Viet Tran
- Genetic Ophthalmic Department, Hôpital Ophtalmique Jules-Gonin, University of Lausanne and Faculty of Life Sciences, Lausanne, Switzerland
- Institut d'ophtalmologie de Vevey (INOV), Vevey, Switzerland
- Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
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9
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Han JH, Cancellieri F, Perea-Romero I, Ayuso C, Quinodoz M, Rivolta C. The p.C759F Variant in USH2A Is a Pathogenic Mutation: Systematic Literature Review and Meta-Analysis of 667 Genotypes. Ophthalmic Res 2023; 67:107-114. [PMID: 38016437 DOI: 10.1159/000535545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 11/14/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND Although the p.C759F (c.2276G>T, p.Cys759Phe) variant in the USH2A gene has been identified in association with retinal degeneration by several authors, its pathogenicity has been questioned once by the publication of two unaffected homozygotes from a single family. OBJECTIVES The objective of the study was to ascertain the role of p.C759F in hereditary retinal disease. METHODS We examined 87 research articles reporting on patients carrying this variant and then used this information as primary data for a series of meta-analytical tests. RESULTS Independent statistical analyses showed that p.C759F (i) is highly enriched in patients with respect to healthy individuals, (ii) represents a clear-cut recessive allele causing disease when it is in trans with other mutations, (iii) is pathogenic in homozygotes. CONCLUSIONS Our results confirm that p.C759F is a bona fide mutation, leading to retinal blindness according to a recessive pattern of inheritance.
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Affiliation(s)
- Ji Hoon Han
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Irene Perea-Romero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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10
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Bocquet B, Borday C, Erkilic N, Mamaeva D, Donval A, Masson C, Parain K, Kaminska K, Quinodoz M, Perea-Romero I, Garcia-Garcia G, Jimenez-Medina C, Boukhaddaoui H, Coget A, Leboucq N, Calzetti G, Gandolfi S, Percesepe A, Barili V, Uliana V, Delsante M, Bozzetti F, Scholl HP, Corton M, Ayuso C, Millan JM, Rivolta C, Meunier I, Perron M, Kalatzis V. TBC1D32 variants disrupt retinal ciliogenesis and cause retinitis pigmentosa. JCI Insight 2023; 8:e169426. [PMID: 37768732 PMCID: PMC10721274 DOI: 10.1172/jci.insight.169426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023] Open
Abstract
Retinitis pigmentosa (RP) is the most common inherited retinal disease (IRD) and is characterized by photoreceptor degeneration and progressive vision loss. We report 4 patients presenting with RP from 3 unrelated families with variants in TBC1D32, which to date has never been associated with an IRD. To validate TBC1D32 as a putative RP causative gene, we combined Xenopus in vivo approaches and human induced pluripotent stem cell-derived (iPSC-derived) retinal models. Our data showed that TBC1D32 was expressed during retinal development and that it played an important role in retinal pigment epithelium (RPE) differentiation. Furthermore, we identified a role for TBC1D32 in ciliogenesis of the RPE. We demonstrated elongated ciliary defects that resulted in disrupted apical tight junctions, loss of functionality (delayed retinoid cycling and altered secretion balance), and the onset of an epithelial-mesenchymal transition-like phenotype. Last, our results suggested photoreceptor differentiation defects, including connecting cilium anomalies, that resulted in impaired trafficking to the outer segment in cones and rods in TBC1D32 iPSC-derived retinal organoids. Overall, our data highlight a critical role for TBC1D32 in the retina and demonstrate that TBC1D32 mutations lead to RP. We thus identify TBC1D32 as an IRD-causative gene.
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Affiliation(s)
- Béatrice Bocquet
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, CHU, Montpellier, France
| | - Caroline Borday
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Nejla Erkilic
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, CHU, Montpellier, France
| | - Daria Mamaeva
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
| | - Alicia Donval
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Christel Masson
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Karine Parain
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Irene Perea-Romero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Gema Garcia-Garcia
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
- Joint Unit of Rare Diseases, IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Carla Jimenez-Medina
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
| | - Hassan Boukhaddaoui
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
| | - Arthur Coget
- Department of Neuroradiology and
- Institute for Human Functional Imaging (I2FH), University of Montpellier, CHU, Montpellier, France
| | | | - Giacomo Calzetti
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Medicine and Surgery
| | | | | | | | | | | | - Francesca Bozzetti
- Neuroradiology Unit, Diagnostic Department, University Hospital of Parma, Parma, Italy
| | - Hendrik P.N. Scholl
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Marta Corton
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Jose M. Millan
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
- Joint Unit of Rare Diseases, IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Isabelle Meunier
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, CHU, Montpellier, France
| | - Muriel Perron
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Vasiliki Kalatzis
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
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Grosso A, Yannuzzi LA, Tsang SH, Ceruti P, Sarraf D, Zamir E, Kaminska K, Quinodoz M, Amoroso A, Deaglio S, Francis JH, Fioretto M, Rivolta C, Calzetti G. A Unique Presentation of Bilateral Chorioretinal Atrophy. Asia Pac J Ophthalmol (Phila) 2023; 12:500-501. [PMID: 36650090 DOI: 10.1097/apo.0000000000000563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Andrea Grosso
- Santo Spirito Hospital, Casale Monferrato, Italy
- Centre for Macular Research, San Mauro Torinese, Italy
| | | | - Stephen H Tsang
- Jonas Children's Vision Care, and Bernard and Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia Stem Cell Initiative, Columbia University, New York, NY
| | - Piero Ceruti
- Ophthalmic Unit, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - David Sarraf
- Jules Stein Eye Institute, University of California Los Angeles School of Medicine, Los Angeles, CA
| | - Ehud Zamir
- Centre for Eye Research Australia, Melbourne, Australia
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Antonio Amoroso
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Silvia Deaglio
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Jasmine H Francis
- Ophthalmic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Giacomo Calzetti
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
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12
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Ullah M, Rehman AU, Folcher M, Ullah A, Usman F, Rashid A, Khan B, Quinodoz M, Ansar M, Rivolta C. A Novel Intronic Deletion in PDE6B Causes Autosomal Recessive Retinitis Pigmentosa by Interfering with RNA Splicing. Ophthalmic Res 2023; 66:878-884. [PMID: 37094557 DOI: 10.1159/000530800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/17/2023] [Indexed: 04/26/2023]
Abstract
INTRODUCTION Retinitis pigmentosa (RP) is a rare degenerative retinal disease caused by mutations in approximately seventy genes. Currently, despite the availability of large-scale DNA sequencing technologies, ∼30-40% of patients still cannot be diagnosed at the molecular level. In this study, we investigated a novel intronic deletion of PDE6B, encoding the beta subunit of phosphodiesterase 6 in association with recessive RP. METHODS Three unrelated consanguineous families were recruited from the northwestern part of Pakistan. Whole exome sequencing was performed for the proband of each family, and the data were analyzed according to an in-house computer pipeline. Relevant DNA variants in all available members of these families were assessed through Sanger sequencing. A minigene-based splicing assay was also performed. RESULTS The clinical phenotype for all patients was compatible with rod cone degeneration, with the onset during childhood. Whole exome sequencing revealed a homozygous 18 bp intronic deletion (NM_000283.3:c.1921-20_1921-3del) in PDE6B, which co-segregated with disease in 10 affected individuals. In vitro splicing tests showed that this deletion causes aberrant RNA splicing of the gene, leading to the in-frame deletion of 6 codons and, likely, to disease. CONCLUSION Our findings further expand the mutational spectrum of the PDE6B gene.
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Affiliation(s)
- Mukhtar Ullah
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Atta Ur Rehman
- Department of Zoology, Faculty of Biological and Health Sciences, Hazara University Mansehra, Mansehra, Pakistan
| | - Marc Folcher
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Adnan Ullah
- Department of Zoology, Islamia College Peshawar, Peshawar, Pakistan
| | - Faisal Usman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological and Health Sciences, Hazara University Mansehra, Mansehra, Pakistan
| | - Abdur Rashid
- Department of Higher Education, Archives and Libraries Peshawar, Peshawar, Pakistan
| | - Bilal Khan
- Medical Teaching Institution Khyber Teaching Hospital Peshawar, Peshawar, Pakistan
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Muhammad Ansar
- Department of Ophthalmology, Jules Gonin Eye Hospital, Fondation Asile Des Aveugles, University of Lausanne, Lausanne, Switzerland
- Advanced Molecular Genetics and Genomics Disease Research and Treatment Centre, Dow University of Health Sciences, Karachi, Pakistan
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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13
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Yahya F, Escher P, Rivolta C, Scholl HP, Roulez F. SPATA7-Associated Juvenile Retinitis Pigmentosa in Two Brothers from a Consanguineous Iraqi Family in Switzerland. Klin Monbl Augenheilkd 2023; 240:544-548. [PMID: 37164434 DOI: 10.1055/a-2009-0498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Affiliation(s)
- Faady Yahya
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- University Hospital Basel Eye Clinic, Basel, Switzerland
| | - Pascal Escher
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Carlo Rivolta
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Hendrik Pn Scholl
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- University Hospital Basel Eye Clinic, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Francoise Roulez
- Department of Ophthalmology, University of Basel, Basel, Switzerland
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14
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Koval A, Larasati YA, Savitsky M, Solis GP, Good JM, Quinodoz M, Rivolta C, Superti-Furga A, Katanaev VL. In-depth molecular profiling of an intronic GNAO1 mutant as the basis for personalized high-throughput drug screening. Med 2023; 4:311-325.e7. [PMID: 37001522 DOI: 10.1016/j.medj.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 04/03/2023]
Abstract
BACKGROUND The GNAO1 gene, encoding the major neuronal G protein Gαo, is mutated in a subset of pediatric encephalopathies. Most such mutations consist of missense variants. METHODS In this study, we present a precision medicine workflow combining next-generation sequencing (NGS) diagnostics, molecular etiology analysis, and personalized drug discovery. FINDINGS We describe a patient carrying a de novo intronic mutation (NM_020988.3:c.724-8G>A), leading to epilepsy-negative encephalopathy with motor dysfunction from the second decade. Our data show that this mutation creates a novel splice acceptor site that in turn causes an in-frame insertion of two amino acid residues, Pro-Gln, within the regulatory switch III region of Gαo. This insertion misconfigures the switch III loop and creates novel interactions with the catalytic switch II region, resulting in increased GTP uptake, defective GTP hydrolysis, and aberrant interactions with effector proteins. In contrast, intracellular localization, Gβγ interactions, and G protein-coupled receptor (GPCR) coupling of the Gαo[insPQ] mutant protein remain unchanged. CONCLUSIONS This in-depth analysis characterizes the heterozygous c.724-8G>A mutation as partially dominant negative, providing clues to the molecular etiology of this specific pathology. Further, this analysis allows us to establish and validate a high-throughput screening platform aiming at identifying molecules that could correct the aberrant biochemical functions of the mutant Gαo. FUNDING This work was supported by the Joint Seed Money Funding scheme between the University of Geneva and the Hebrew University of Jerusalem.
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Affiliation(s)
- Alexey Koval
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Yonika A Larasati
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Mikhail Savitsky
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Gonzalo P Solis
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Jean-Marc Good
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Vladimir L Katanaev
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland; Institute of Life Sciences and Biomedicine, Far Eastern Federal University, 690090 Vladivostok, Russia.
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15
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Peter VG, Kaminska K, Santos C, Quinodoz M, Cancellieri F, Cisarova K, Pescini Gobert R, Rodrigues R, Custódio S, Paris LP, Sousa AB, Coutinho Santos L, Rivolta C. The first genetic landscape of inherited retinal dystrophies in Portuguese patients identifies recurrent homozygous mutations as a frequent cause of pathogenesis. PNAS Nexus 2023; 2:pgad043. [PMID: 36909829 PMCID: PMC10003751 DOI: 10.1093/pnasnexus/pgad043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/15/2023]
Abstract
Inherited retinal diseases (IRDs) are a group of ocular conditions characterized by an elevated genetic and clinical heterogeneity. They are transmitted almost invariantly as monogenic traits. However, with more than 280 disease genes identified so far, association of clinical phenotypes with genotypes can be very challenging, and molecular diagnosis is essential for genetic counseling and correct management of the disease. In addition, the prevalence and the assortment of IRD mutations are often population-specific. In this work, we examined 230 families from Portugal, with individuals suffering from a variety of IRD diagnostic classes (270 subjects in total). Overall, we identified 157 unique mutations (34 previously unreported) in 57 distinct genes, with a diagnostic rate of 76%. The IRD mutational landscape was, to some extent, different from those reported in other European populations, including Spanish cohorts. For instance, the EYS gene appeared to be the most frequently mutated, with a prevalence of 10% among all IRD cases. This was, in part, due to the presence of a recurrent and seemingly founder mutation involving the deletion of exons 13 and 14 of this gene. Moreover, our analysis highlighted that as many as 51% of our cases had mutations in a homozygous state. To our knowledge, this is the first study assessing a cross-sectional genotype-phenotype landscape of IRDs in Portugal. Our data reveal a rather unique distribution of mutations, possibly shaped by a small number of rare ancestral events that have now become prevalent alleles in patients.
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Affiliation(s)
- Virginie G Peter
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland.,Department of Ophthalmology, Inselspital, Bern University Hospital, Bern 3010, Switzerland
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Cristina Santos
- Department of Ophthalmology, Instituto de Oftalmologia Dr Gama Pinto (IOGP), Lisbon 1169-019, Portugal.,iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisbon 1169-056, Portugal
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Katarina Cisarova
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | | | - Raquel Rodrigues
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon 1649-035, Portugal
| | - Sónia Custódio
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon 1649-035, Portugal
| | - Liliana P Paris
- Department of Ophthalmology, Instituto de Oftalmologia Dr Gama Pinto (IOGP), Lisbon 1169-019, Portugal
| | - Ana Berta Sousa
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon 1649-035, Portugal.,Laboratory of Basic Immunology, Faculty of Medicine, University of Lisbon, Lisbon 1649-028, Portugal
| | - Luisa Coutinho Santos
- Department of Ophthalmology, Instituto de Oftalmologia Dr Gama Pinto (IOGP), Lisbon 1169-019, Portugal
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
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16
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Panneman DM, Hitti-Malin RJ, Holtes LK, de Bruijn SE, Reurink J, Boonen EGM, Khan MI, Ali M, Andréasson S, De Baere E, Banfi S, Bauwens M, Ben-Yosef T, Bocquet B, De Bruyne M, de la Cerda B, Coppieters F, Farinelli P, Guignard T, Inglehearn CF, Karali M, Kjellström U, Koenekoop R, de Koning B, Leroy BP, McKibbin M, Meunier I, Nikopoulos K, Nishiguchi KM, Poulter JA, Rivolta C, Rodríguez de la Rúa E, Saunders P, Simonelli F, Tatour Y, Testa F, Thiadens AAHJ, Toomes C, Tracewska AM, Tran HV, Ushida H, Vaclavik V, Verhoeven VJM, van de Vorst M, Gilissen C, Hoischen A, Cremers FPM, Roosing S. Cost-effective sequence analysis of 113 genes in 1,192 probands with retinitis pigmentosa and Leber congenital amaurosis. Front Cell Dev Biol 2023; 11:1112270. [PMID: 36819107 PMCID: PMC9936074 DOI: 10.3389/fcell.2023.1112270] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/20/2023] [Indexed: 02/05/2023] Open
Abstract
Introduction: Retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA) are two groups of inherited retinal diseases (IRDs) where the rod photoreceptors degenerate followed by the cone photoreceptors of the retina. A genetic diagnosis for IRDs is challenging since >280 genes are associated with these conditions. While whole exome sequencing (WES) is commonly used by diagnostic facilities, the costs and required infrastructure prevent its global applicability. Previous studies have shown the cost-effectiveness of sequence analysis using single molecule Molecular Inversion Probes (smMIPs) in a cohort of patients diagnosed with Stargardt disease and other maculopathies. Methods: Here, we introduce a smMIPs panel that targets the exons and splice sites of all currently known genes associated with RP and LCA, the entire RPE65 gene, known causative deep-intronic variants leading to pseudo-exons, and part of the RP17 region associated with autosomal dominant RP, by using a total of 16,812 smMIPs. The RP-LCA smMIPs panel was used to screen 1,192 probands from an international cohort of predominantly RP and LCA cases. Results and discussion: After genetic analysis, a diagnostic yield of 56% was obtained which is on par with results from WES analysis. The effectiveness and the reduced costs compared to WES renders the RP-LCA smMIPs panel a competitive approach to provide IRD patients with a genetic diagnosis, especially in countries with restricted access to genetic testing.
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Affiliation(s)
- Daan M. Panneman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands,*Correspondence: Daan M. Panneman,
| | - Rebekkah J. Hitti-Malin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Lara K. Holtes
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Suzanne E. de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Janine Reurink
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Erica G. M. Boonen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Muhammad Imran Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Manir Ali
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom
| | - Sten Andréasson
- Department of Ophthalmology and Clinical Sciences Lund, Lund University, Skane University Hospital, Lund, Sweden
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy,Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Miriam Bauwens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Tamar Ben-Yosef
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Béatrice Bocquet
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, Montpellier University Hospital, Sensgene Care Network, ERN-EYE Network, Montpellier, France,Institute for Neurosciences of Montpellier (INM), L’Institut National de la Santé et de la Recherche Médicale, University of Montpellier, L’Institut National de la Santé et de la Recherche Médicale, Montpellier, France
| | - Marieke De Bruyne
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Berta de la Cerda
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), Seville, Spain
| | - Frauke Coppieters
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium,Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Pietro Farinelli
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Thomas Guignard
- Chromosomal Genetics Unit, University Hospital of Montpellier, Montpellier, France
| | - Chris F. Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom
| | - Marianthi Karali
- 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
| | - Ulrika Kjellström
- Department of Ophthalmology and Clinical Sciences Lund, Lund University, Skane University Hospital, Lund, Sweden
| | - Robert Koenekoop
- McGill University Health Center (MUHC) Research Institute, Montreal, QC, Canada,Departments of Paediatric Surgery, Human Genetics, and Adult Ophthalmology, McGill University Health Center, Montreal, QC, Canada
| | - Bart de Koning
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, Netherlands
| | - Bart P. Leroy
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium,Department of Head & Skin, Ghent University, Ghent, Belgium,Division of Ophthalmology & Center for Cellular & Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Martin McKibbin
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom,Department of Ophthalmology, St. James’s University Hospital, Leeds, United Kingdom
| | - Isabelle Meunier
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, Montpellier University Hospital, Sensgene Care Network, ERN-EYE Network, Montpellier, France,Institute for Neurosciences of Montpellier (INM), L’Institut National de la Santé et de la Recherche Médicale, University of Montpellier, L’Institut National de la Santé et de la Recherche Médicale, Montpellier, France
| | | | - Koji M. Nishiguchi
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - James A. Poulter
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland,Department of Ophthalmology, University of Basel, Basel, Switzerland,Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Enrique Rodríguez de la Rúa
- Department of Ophthalmology, Retics Patologia Ocular, OFTARED, Instituto de Salud Carlos III, University Hospital Virgen Macarena, Madrid, Spain
| | | | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Yasmin Tatour
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | | | - Carmel Toomes
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom
| | - Anna M. Tracewska
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Hoai Viet Tran
- Oculogenetic Unit, University Eye Hospital Jules Gonin, Geneva, Switzerland
| | - Hiroaki Ushida
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Veronika Vaclavik
- Oculogenetic Unit, University Eye Hospital Jules Gonin, Geneva, Switzerland
| | - Virginie J. M. Verhoeven
- Department of Ophthalmology, Erasmus, Rotterdam, Netherlands,Department of Clinical Genetics, Erasmus, Rotterdam, Netherlands
| | - Maartje van de Vorst
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
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17
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Peter VG, Quinodoz M, Sadio S, Held S, Rodrigues M, Soares M, Sousa AB, Santos LC, Damme M, Rivolta C. New clinical and molecular evidence linking mutations in ARSG to Usher syndrome type IV. Hum Mutat 2022; 43:2326-2327. [PMID: 36317447 DOI: 10.1002/humu.24496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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18
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Rivolta C. genetic dynamics and global clinical features of inherited retinal diseases. Acta Ophthalmol 2022. [DOI: 10.1111/j.1755-3768.2022.15625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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19
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Butler-Laporte G, Povysil G, Kosmicki JA, Cirulli ET, Drivas T, Furini S, Saad C, Schmidt A, Olszewski P, Korotko U, Quinodoz M, Çelik E, Kundu K, Walter K, Jung J, Stockwell AD, Sloofman LG, Jordan DM, Thompson RC, Del Valle D, Simons N, Cheng E, Sebra R, Schadt EE, Kim-Schulze S, Gnjatic S, Merad M, Buxbaum JD, Beckmann ND, Charney AW, Przychodzen B, Chang T, Pottinger TD, Shang N, Brand F, Fava F, Mari F, Chwialkowska K, Niemira M, Pula S, Baillie JK, Stuckey A, Salas A, Bello X, Pardo-Seco J, Gómez-Carballa A, Rivero-Calle I, Martinón-Torres F, Ganna A, Karczewski KJ, Veerapen K, Bourgey M, Bourque G, Eveleigh RJM, Forgetta V, Morrison D, Langlais D, Lathrop M, Mooser V, Nakanishi T, Frithiof R, Hultström M, Lipcsey M, Marincevic-Zuniga Y, Nordlund J, Schiabor Barrett KM, Lee W, Bolze A, White S, Riffle S, Tanudjaja F, Sandoval E, Neveux I, Dabe S, Casadei N, Motameny S, Alaamery M, Massadeh S, Aljawini N, Almutairi MS, Arabi YM, Alqahtani SA, Al Harthi FS, Almutairi A, Alqubaishi F, Alotaibi S, Binowayn A, Alsolm EA, El Bardisy H, Fawzy M, Cai F, Soranzo N, Butterworth A, Geschwind DH, Arteaga S, Stephens A, Butte MJ, Boutros PC, Yamaguchi TN, Tao S, Eng S, Sanders T, Tung PJ, Broudy ME, Pan Y, Gonzalez A, Chavan N, Johnson R, Pasaniuc B, Yaspan B, Smieszek S, Rivolta C, Bibert S, Bochud PY, Dabrowski M, Zawadzki P, Sypniewski M, Kaja E, Chariyavilaskul P, Nilaratanakul V, Hirankarn N, Shotelersuk V, Pongpanich M, Phokaew C, Chetruengchai W, Tokunaga K, Sugiyama M, Kawai Y, Hasegawa T, Naito T, Namkoong H, Edahiro R, Kimura A, Ogawa S, Kanai T, Fukunaga K, Okada Y, Imoto S, Miyano S, Mangul S, Abedalthagafi MS, Zeberg H, Grzymski JJ, Washington NL, Ossowski S, Ludwig KU, Schulte EC, Riess O, Moniuszko M, Kwasniewski M, Mbarek H, Ismail SI, Verma A, Goldstein DB, Kiryluk K, Renieri A, Ferreira MAR, Richards JB. Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative. PLoS Genet 2022; 18:e1010367. [PMID: 36327219 PMCID: PMC9632827 DOI: 10.1371/journal.pgen.1010367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/29/2022] [Indexed: 11/05/2022] Open
Abstract
Host genetics is a key determinant of COVID-19 outcomes. Previously, the COVID-19 Host Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with COVID-19 outcomes. However, variants with the largest impact on COVID-19 outcomes are expected to be rare in the population. Hence, studying rare variants may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome and whole-genome sequencing from 21 cohorts across 12 countries and performed rare variant exome-wide burden analyses for COVID-19 outcomes. In an analysis of 5,085 severe disease cases and 571,737 controls, we observed that carrying a rare deleterious variant in the SARS-CoV-2 sensor toll-like receptor TLR7 (on chromosome X) was associated with a 5.3-fold increase in severe disease (95% CI: 2.75-10.05, p = 5.41x10-7). This association was consistent across sexes. These results further support TLR7 as a genetic determinant of severe disease and suggest that larger studies on rare variants influencing COVID-19 outcomes could provide additional insights.
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Grants
- 409511 CIHR
- RG/13/13/30194 British Heart Foundation
- C18281/A29019 Cancer Research UK
- 100558 CIHR
- MC_PC_20004 Medical Research Council
- 365825 CIHR
- UL1 TR001873 NCATS NIH HHS
- RG/18/13/33946 British Heart Foundation
- CH/12/2/29428 British Heart Foundation
- CanCOGeN HostSeq
- Fonds de Recherche Québec Santé (FRQS)
- Génome Québec
- Public Health Agency of Canada
- Canadian Institutes of Health Research (CIHR)
- Lady Davis Institute of the Jewish General Hospital
- Canadian Foundation for Innovation
- NIH Foundation
- McGill Interdisciplinary Initiative in Infection and Immunity (MI4)
- Jewish General Hospital Foundation
- McGill University
- Calcul Québec and Compute Canada
- Compute Canada
- Vagelos College of Physicians & Surgeons Office for Research
- Biomedical Informatics Resource of the Columbia University Irving Institute for Clinical and Translational Research (CTSA)
- National Center for Advancing Translational Sciences, National Institutes of Health
- German Research Foundation
- NGS Competence Center Tübingen
- West German Genome Center
- Stiftung Universitätsmedizin Essen
- Technical University of Munich
- BONFOR program of the Medical Faculty, University of Bonn
- Emmy-Noether programm of the German Research Foundation
- State of Saarland
- Dr. Rolf M. Schwiete Foundation
- Munich Clinician Scientist Programm
- Netzwerk-Universitaetsmedizin-COVIM
- Federal Ministry of Education and Research
- Swiss National Science Foundation
- Leenaards Foundation
- Santos-Suarez Foundation
- Carigest
- MIUR project “Dipartimenti di Eccellenza 2018-2020”
- Bando Ricerca COVID-19 Toscana
- charity fund 2020 from Intesa San Paolo
- Italian Ministry of University and Research
- Istituto Buddista Italiano Soka Gakkai
- Instituto de Salud Carlos III
- GePEM
- DIAVIR
- Resvi-Omics
- ReSVinext
- Enterogen
- Agencia Gallega para la Gestión del Conocimiento en Salud
- BI-BACVIR
- CovidPhy
- Agencia Gallega de Innovación (GAIN):
- GEN-COVID
- Framework Partnership Agreement between the Consellería de Sanidad de la XUNTA de Galicia
- GENVIP-IDIS
- consorcio Centro de Investigación Biomédica en Red de Enfermedades Respiratorias
- F. Hoffmann-La Roche Ltd
- U.S. Department of Health and Human Services, Office of the Assistant Secretary for Preparedness and Response, and Biomedical Advanced Research and Development Authority
- Nevada Governor's Office of Economic Development
- Renown Health and the Renown Health Foundation
- Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University
- Healthcare-associated Infection Research Group STAR (Special Task Force for Activating Research)
- Grant for Development of New Faculty Staff, Ratchadaphiseksomphot Endowment Fund
- e-ASIA Joint Research Program (National Science and Technology Development Agency)
- Health Systems Research Institute, TSRI Fund
- Thailand Research Fund
- Ratchadapiseksompotch Fund
- Ratchadapiseksompotch Fund, Faculty of Medicine,Chulalongkorn University, Bangkok, Thailand
- Health Systems Research Institute
- Ratchadapisek Sompoch Endowment Fund, Chulalongkorn University
- NHS Blood and Transplant
- National Institute for Health Research
- UK Medical Research Council
- Japan Agency for Medical Research and Development
- Japan Science and Technology Agency
- National Center for Global Health and Medicine
- Agency for Medical Research and Development
- Polish National Science Centre
- Medical Research Agency
- Perelman School of Medicine at University of Pennsylvania
- Smilow family
- National Center for Advancing Translational Sciences of the National Institutes of Health
- Polish Medical Research Agency
- Qatar Foundation for Education, Science and Community Development
- Saudi Ministry of Health
- King Abdulaziz City for Science and Technology
- European Union’s Horizon 2020 research and innovation program
- Science for Life Laboratory
- Swedish Research Council
- Knut and Alice Wallenberg Foundation
- OCRC
- Microsoft COVID Compute Funding
- Illumina
- UCLA David Geffen School of Medicine - Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research Award Program
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Affiliation(s)
- Guillaume Butler-Laporte
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Gundula Povysil
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
| | - Jack A. Kosmicki
- Regeneron Genetics Center, Tarrytown, New York, United States of America
| | | | - Theodore Drivas
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Simone Furini
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
| | - Chadi Saad
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Axel Schmidt
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | | | - Urszula Korotko
- IMAGENE.ME SA, Bialystok, Poland
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Elifnaz Çelik
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Kousik Kundu
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Klaudia Walter
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Junghyun Jung
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, United States of America
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Amy D. Stockwell
- Genentech Inc, South San Francisco, California, United States of America
| | - Laura G. Sloofman
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Daniel M. Jordan
- Mount Sinai Clnical Intelligence Center, Charles Bronfman Institute for Personalized Medicine, Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Ryan C. Thompson
- Icahn Institute of Data Science and Genomics Technology, New York city, New York, United States of America
| | - Diane Del Valle
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Nicole Simons
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Esther Cheng
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city,New York, United States of America
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city,New York, United States of America
| | - Seunghee Kim-Schulze
- Department of Oncological Science, Human Immune Monitoring Center, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Sacha Gnjatic
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Miriam Merad
- Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Joseph D. Buxbaum
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Noam D. Beckmann
- Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Alexander W. Charney
- Mount Sinai Clinical Intelligence Center; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | | | - Timothy Chang
- Department of Neurology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Tess D. Pottinger
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
| | - Ning Shang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York city, New York, United States of America
| | - Fabian Brand
- Institute of Genomic Statistics and Bioinformatics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Francesca Fava
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | - Francesca Mari
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | - Karolina Chwialkowska
- IMAGENE.ME SA, Bialystok, Poland
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Magdalena Niemira
- Centre for Clinical Research, Medical University of Bialystok, Bialystok, Poland
| | | | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
- Centre for Inflammation Research, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | | | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Xabier Bello
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Jacobo Pardo-Seco
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Irene Rivero-Calle
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Federico Martinón-Torres
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachussets, United States of America
| | - Konrad J. Karczewski
- Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Kumar Veerapen
- Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Mathieu Bourgey
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
| | - Guillaume Bourque
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Robert JM Eveleigh
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
| | - Vincenzo Forgetta
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - David Morrison
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - David Langlais
- McGill Genome Center, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Mark Lathrop
- McGill Genome Center, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Vincent Mooser
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Tomoko Nakanishi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Research Fellow, Japan Society for the Promotion of Science, Tokyo, Japan
| | - Robert Frithiof
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Michael Hultström
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Integrative Physiology, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Miklos Lipcsey
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Hedenstierna Laboratory, CIRRUS, Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Yanara Marincevic-Zuniga
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - William Lee
- Helix, San Mateo, California, United States of America
| | | | - Simon White
- Helix, San Mateo, California, United States of America
| | | | | | | | - Iva Neveux
- Center for Genomic Medicine, Desert Research Institute, Reno, Nevada United States of America
| | - Shaun Dabe
- Renown Health, Reno, Nevada, United States of America
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- NGS Competence Center Tuebingen, Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Susanne Motameny
- West German Genome Center, site Cologne, University of Cologne, Cologne, Germany
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Manal Alaamery
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Salam Massadeh
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Nora Aljawini
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Mansour S. Almutairi
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Yaseen M. Arabi
- Ministry of the National Guard Health Affairs, King Abdullah International Medical Research Center and King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Saleh A. Alqahtani
- Liver Transplant Unit, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Fawz S. Al Harthi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Amal Almutairi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Fatima Alqubaishi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Sarah Alotaibi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Albandari Binowayn
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Ebtehal A. Alsolm
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hadeel El Bardisy
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Mohammad Fawzy
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Fang Cai
- Genentech Inc, South San Francisco, California, United States of America
| | - Nicole Soranzo
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Adam Butterworth
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | | | | | | | | | | | | | | | - Daniel H. Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Stephanie Arteaga
- Department of Neurology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Alexis Stephens
- Department of Pediatrics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Manish J. Butte
- Department of Pediatrics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
- Department of Microbiology, Immunology, and Molecular Genetics (MIMG), David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Paul C. Boutros
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Takafumi N. Yamaguchi
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Shu Tao
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Stefan Eng
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Timothy Sanders
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Paul J. Tung
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Michael E. Broudy
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Yu Pan
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Alfredo Gonzalez
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Nikhil Chavan
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Ruth Johnson
- Department of Computer Science, McGill University, Montréal, Québec, Canada
| | - Bogdan Pasaniuc
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
- Department of Computational Medicine, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
- Department of Pathology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Brian Yaspan
- Genentech Inc, South San Francisco, California, United States of America
| | - Sandra Smieszek
- Vanda Pharmaceuticals, Washington, District of Columbia, United States of America
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Stephanie Bibert
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Pierre-Yves Bochud
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Maciej Dabrowski
- MNM Bioscience Inc., Cambridge, Massachusetts, United States of America
| | - Pawel Zawadzki
- MNM Bioscience Inc., Cambridge, Massachusetts, United States of America
- Faculty of Physics, Adam Mickiewicz University, Poznan, Poland
| | | | - Elżbieta Kaja
- MNM Bioscience Inc., Cambridge, Massachusetts, United States of America
- Department of Medical Chemistry and Laboratory Medicine, Poznań University of Medical Sciences, Poznań, Poland
| | - Pajaree Chariyavilaskul
- Clinical Pharmacokinetics and Pharmacogenomics Research Unit, Department of Pharmacology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Voraphoj Nilaratanakul
- Healthcare-associated Infection Research Group STAR (Special Task Force for Activating Research) and Division of Infectious Diseases, Department of Medicine,Chulalongkorn University, Bangkok, Thailand
| | - Nattiya Hirankarn
- Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, and Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Chureerat Phokaew
- Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Wanna Chetruengchai
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Katsushi Tokunaga
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Masaya Sugiyama
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Takanori Hasegawa
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tatsuhiko Naito
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ho Namkoong
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
| | - Ryuya Edahiro
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Akinori Kimura
- Institute of Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Koichi Fukunaga
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, United States of America
| | - Malak S. Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hugo Zeberg
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Joseph J. Grzymski
- Center for Genomic Medicine, Desert Research Institute, Reno, Nevada United States of America
| | | | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- NGS Competence Center Tuebingen, Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Kerstin U. Ludwig
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
- West German Genome Center, site Bonn, University of Bonn, Bonn, Germany
| | - Eva C. Schulte
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
- Institute of Virology, Technical University Munich/Helmholtz Zentrum München, Munich, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- NGS Competence Center Tuebingen, Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Marcin Moniuszko
- Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, Bialystok, Poland
- Department of Allergology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
| | - Miroslaw Kwasniewski
- IMAGENE.ME SA, Bialystok, Poland
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Hamdi Mbarek
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Said I. Ismail
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Anurag Verma
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America
| | - David B. Goldstein
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
- Department of Genetics & Development, Columbia University, New York city, New York, United States of America
| | - Krzysztof Kiryluk
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York city, New York, United States of America
| | - Alessandra Renieri
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | | | - J Brent Richards
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- Department of Twin Research, King’s College London, London, United Kingdom
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
- * E-mail:
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20
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Jurkute N, Cancellieri F, Pohl L, Li CHZ, Heaton RA, Reurink J, Bellingham J, Quinodoz M, Yioti G, Stefaniotou M, Weener M, Zuleger T, Haack TB, Stingl K, Hoyng CB, Mahroo OA, Hargreaves I, Raymond FL, Michaelides M, Rivolta C, Kohl S, Roosing S, Webster AR, Arno G. Biallelic variants in coenzyme Q10 biosynthesis pathway genes cause a retinitis pigmentosa phenotype. NPJ Genom Med 2022; 7:60. [PMID: 36266294 PMCID: PMC9581764 DOI: 10.1038/s41525-022-00330-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/29/2022] [Indexed: 11/21/2022] Open
Abstract
The aim of this study was to investigate coenzyme Q10 (CoQ10) biosynthesis pathway defects in inherited retinal dystrophy. Individuals affected by inherited retinal dystrophy (IRD) underwent exome or genome sequencing for molecular diagnosis of their condition. Following negative IRD gene panel analysis, patients carrying biallelic variants in CoQ10 biosynthesis pathway genes were identified. Clinical data were collected from the medical records. Haplotypes harbouring the same missense variant were characterised from family genome sequencing (GS) data and direct Sanger sequencing. Candidate splice variants were characterised using Oxford Nanopore Technologies single molecule sequencing. The CoQ10 status of the human plasma was determined in some of the study patients. 13 individuals from 12 unrelated families harboured candidate pathogenic genotypes in the genes: PDSS1, COQ2, COQ4 and COQ5. The PDSS1 variant c.589 A > G was identified in three affected individuals from three unrelated families on a possible ancestral haplotype. Three variants (PDSS1 c.468-25 A > G, PDSS1 c.722-2 A > G, COQ5 c.682-7 T > G) were shown to lead to cryptic splicing. 6 affected individuals were diagnosed with non-syndromic retinitis pigmentosa and 7 had additional clinical findings. This study provides evidence of CoQ10 biosynthesis pathway gene defects leading to non-syndromic retinitis pigmentosa in some cases. Intronic variants outside of the canonical splice-sites represent an important cause of disease. RT-PCR nanopore sequencing is effective in characterising these splice defects.
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Affiliation(s)
- Neringa Jurkute
- Moorfields Eye Hospital NHS Foundation Trust, London, UK. .,Institute of Ophthalmology, University College London, London, UK.
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Lisa Pohl
- University Eye Hospital, Centre for Ophthalmology, University Hospital Tübingen, Tübingen, Germany
| | - Catherina H Z Li
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Robert A Heaton
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores, Liverpool, UK
| | - Janine Reurink
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - James Bellingham
- Institute of Ophthalmology, University College London, London, UK
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Georgia Yioti
- University of Ioannina Medical School, Ioannina, Greece
| | | | | | - Theresia Zuleger
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Katarina Stingl
- University Eye Hospital, Centre for Ophthalmology, University Hospital Tübingen, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | | | - Carel B Hoyng
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Omar A Mahroo
- Moorfields Eye Hospital NHS Foundation Trust, London, UK.,Institute of Ophthalmology, University College London, London, UK
| | - Iain Hargreaves
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores, Liverpool, UK
| | - F Lucy Raymond
- NIHR BioResource-Rare Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK.,Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Michel Michaelides
- Moorfields Eye Hospital NHS Foundation Trust, London, UK.,Institute of Ophthalmology, University College London, London, UK
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Susanne Kohl
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Susanne Roosing
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Andrew R Webster
- Moorfields Eye Hospital NHS Foundation Trust, London, UK.,Institute of Ophthalmology, University College London, London, UK
| | - Gavin Arno
- Moorfields Eye Hospital NHS Foundation Trust, London, UK. .,Institute of Ophthalmology, University College London, London, UK. .,North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children, London, UK.
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21
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Daich Varela M, Bellingham J, Motta F, Jurkute N, Ellingford JM, Quinodoz M, Oprych K, Niblock M, Janeschitz-Kriegl L, Kaminska K, Cancellieri F, Scholl HPN, Lenassi E, Schiff E, Knight H, Black G, Rivolta C, Cheetham ME, Michaelides M, Mahroo OA, Moore AT, Webster AR, Arno G. Multidisciplinary team directed analysis of whole genome sequencing reveals pathogenic non-coding variants in molecularly undiagnosed inherited retinal dystrophies. Hum Mol Genet 2022; 32:595-607. [PMID: 36084042 PMCID: PMC9896476 DOI: 10.1093/hmg/ddac227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/23/2022] [Accepted: 09/04/2022] [Indexed: 02/07/2023] Open
Abstract
The purpose of this paper is to identify likely pathogenic non-coding variants in inherited retinal dystrophy (IRD) genes, using genome sequencing (GS). Patients with IRD were recruited to the study and underwent comprehensive ophthalmological evaluation and GS. The results of GS were investigated through virtual gene panel analysis, and plausible pathogenic variants and clinical phenotype evaluated by the multidisciplinary team (MDT) discussion. For unsolved patients in whom a specific gene was suspected to harbor a missed pathogenic variant, targeted re-analysis of non-coding regions was performed on GS data. Candidate variants were functionally tested by messenger RNA analysis, minigene or luciferase reporter assays. Previously unreported, likely pathogenic, non-coding variants in 7 genes (PRPF31, NDP, IFT140, CRB1, USH2A, BBS10 and GUCY2D), were identified in 11 patients. These were shown to lead to mis-splicing (PRPF31, IFT140, CRB1 and USH2A) or altered transcription levels (BBS10 and GUCY2D). MDT-led, phenotype-driven, non-coding variant re-analysis of GS is effective in identifying the missing causative alleles.
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Affiliation(s)
- Malena Daich Varela
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | | | - Fabiana Motta
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Department of Ophthalmology, Universidade Federal de Sao Paulo, Sao Paulo 04021001, Brazil
| | - Neringa Jurkute
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Jamie M Ellingford
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WL, UK,Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | | | | | - Lucas Janeschitz-Kriegl
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Hendrik P N Scholl
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Eva Lenassi
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WL, UK,Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | | | | | - Graeme Black
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WL, UK,Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | | | - Michel Michaelides
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Omar A Mahroo
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Anthony T Moore
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK,University of California, San Francisco, CA 94607, USA
| | - Andrew R Webster
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Gavin Arno
- To whom correspondence should be addressed at: UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1 9EL, UK. Tel: +44 2076086971;
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22
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Ansar M, Javed S, Baig HMA, Quinodoz M, Ullah M, Han JH, Rahim MU, Kausar H, Calzetti G, Rivolta C. A new nonsense mutation in HMX1 in two siblings with oculoauricular syndrome. Ophthalmic Genet 2022; 43:720-723. [PMID: 35946463 DOI: 10.1080/13816810.2022.2096242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Muhammad Ansar
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Advanced Molecular Genetics and Genomics Disease Research and Treatment Centre, Dow University of Health Sciences, Karachi, Pakistan
| | - Samra Javed
- Department of Biotechnology, Kinnaird College for Women, Lahore, Pakistan
| | - Hafiz Muhammad Azhar Baig
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Mukhtar Ullah
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Ji Hoon Han
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | | | - Humera Kausar
- Department of Biotechnology, Kinnaird College for Women, Lahore, Pakistan
| | - Giacomo Calzetti
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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23
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Pathak GA, Karjalainen J, Stevens C, Neale BM, Daly M, Ganna A, Andrews SJ, Kanai M, Cordioli M, Polimanti R, Harerimana N, Pirinen M, Liao RG, Chwialkowska K, Trankiem A, Balaconis MK, Nguyen H, Solomonson M, Veerapen K, Wolford B, Roberts G, Park D, Ball CA, Coignet M, McCurdy S, Knight S, Partha R, Rhead B, Zhang M, Berkowitz N, Gaddis M, Noto K, Ruiz L, Pavlovic M, Hong EL, Rand K, Girshick A, Guturu H, Baltzell AH, Niemi MEK, Rahmouni S, Guntz J, Beguin Y, Cordioli M, Pigazzini S, Nkambule L, Georges M, Moutschen M, Misset B, Darcis G, Guiot J, Azarzar S, Gofflot S, Claassen S, Malaise O, Huynen P, Meuris C, Thys M, Jacques J, Léonard P, Frippiat F, Giot JB, Sauvage AS, Frenckell CV, Belhaj Y, Lambermont B, Nakanishi T, Morrison DR, Mooser V, Richards JB, Butler-Laporte G, Forgetta V, Li R, Ghosh B, Laurent L, Belisle A, Henry D, Abdullah T, Adeleye O, Mamlouk N, Kimchi N, Afrasiabi Z, Rezk N, Vulesevic B, Bouab M, Guzman C, Petitjean L, Tselios C, Xue X, Afilalo J, Afilalo M, Oliveira M, Brenner B, Brassard N, Durand M, Schurr E, Lepage P, Ragoussis J, Auld D, Chassé M, Kaufmann DE, Lathrop GM, Adra D, Hayward C, Glessner JT, Shaw DM, Campbell A, Morris M, Hakonarson H, Porteous DJ, Below J, Richmond A, Chang X, Polikowski H, Lauren PE, Chen HH, Wanying Z, Fawns-Ritchie C, North K, McCormick JB, Chang X, Glessner JR, Hakonarson H, Gignoux CR, Wicks SJ, Crooks K, Barnes KC, Daya M, Shortt J, Rafaels N, Chavan S, Timmers PRHJ, Wilson JF, Tenesa A, Kerr SM, D’Mellow K, Shahin D, El-Sherbiny YM, von Hohenstaufen KA, Sobh A, Eltoukhy MM, Nkambul L, Elhadidy TA, Abd Elghafar MS, El-Jawhari JJ, Mohamed AAS, Elnagdy MH, Samir A, Abdel-Aziz M, Khafaga WT, El-Lawaty WM, Torky MS, El-shanshory MR, Yassen AM, Hegazy MAF, Okasha K, Eid MA, Moahmed HS, Medina-Gomez C, Ikram MA, Uitterlinden AG, Mägi R, Milani L, Metspalu A, Laisk T, Läll K, Lepamets M, Esko T, Reimann E, Naaber P, Laane E, Pesukova J, Peterson P, Kisand K, Tabri J, Allos R, Hensen K, Starkopf J, Ringmets I, Tamm A, Kallaste A, Alavere H, Metsalu K, Puusepp M, Batini C, Tobin MD, Venn LD, Lee PH, Shrine N, Williams AT, Guyatt AL, John C, Packer RJ, Ali A, Free RC, Wang X, Wain LV, Hollox EJ, Bee CE, Adams EL, Palotie A, Ripatti S, Ruotsalainen S, Kristiansson K, Koskelainen S, Perola M, Donner K, Kivinen K, Palotie A, Kaunisto M, Rivolta C, Bochud PY, Bibert S, Boillat N, Nussle SG, Albrich W, Quinodoz M, Kamdar D, Suh N, Neofytos D, Erard V, Voide C, Bochud PY, Rivolta C, Bibert S, Quinodoz M, Kamdar D, Neofytos D, Erard V, Voide C, Friolet R, Vollenweider P, Pagani JL, Oddo M, zu Bentrup FM, Conen A, Clerc O, Marchetti O, Guillet A, Guyat-Jacques C, Foucras S, Rime M, Chassot J, Jaquet M, Viollet RM, Lannepoudenx Y, Portopena L, Bochud PY, Vollenweider P, Pagani JL, Desgranges F, Filippidis P, Guéry B, Haefliger D, Kampouri EE, Manuel O, Munting A, Papadimitriou-Olivgeris M, Regina J, Rochat-Stettler L, Suttels V, Tadini E, Tschopp J, Van Singer M, Viala B, Boillat-Blanco N, Brahier T, Hügli O, Meuwly JY, Pantet O, Gonseth Nussle S, Bochud M, D’Acremont V, Estoppey Younes S, Albrich WC, Suh N, Cerny A, O’Mahony L, von Mering C, Bochud PY, Frischknecht M, Kleger GR, Filipovic M, Kahlert CR, Wozniak H, Negro TR, Pugin J, Bouras K, Knapp C, Egger T, Perret A, Montillier P, di Bartolomeo C, Barda B, de Cid R, Carreras A, Moreno V, Kogevinas M, Galván-Femenía I, Blay N, Farré X, Sumoy L, Cortés B, Mercader JM, Guindo-Martinez M, Torrents D, Garcia-Aymerich J, Castaño-Vinyals G, Dobaño C, Gori M, Renieri A, Mari F, Mondelli MU, Castelli F, Vaghi M, Rusconi S, Montagnani F, Bargagli E, Franchi F, Mazzei MA, Cantarini L, Tacconi D, Feri M, Scala R, Spargi G, Nencioni C, Bandini M, Caldarelli GP, Canaccini A, Ognibene A, D’Arminio Monforte A, Girardis M, Antinori A, Francisci D, Schiaroli E, Scotton PG, Panese S, Scaggiante R, Monica MD, Capasso M, Fiorentino G, Castori M, Aucella F, Biagio AD, Masucci L, Valente S, Mandalà M, Zucchi P, Giannattasio F, Coviello DA, Mussini C, Tavecchia L, Crotti L, Rizzi M, Rovere MTL, Sarzi-Braga S, Bussotti M, Ravaglia S, Artuso R, Perrella A, Romani D, Bergomi P, Catena E, Vincenti A, Ferri C, Grassi D, Pessina G, Tumbarello M, Pietro MD, Sabrina R, Luchi S, Furini S, Dei S, Benetti E, Picchiotti N, Sanarico M, Ceri S, Pinoli P, Raimondi F, Biscarini F, Stella A, Zguro K, Capitani K, Nkambule L, Tanfoni M, Fallerini C, Daga S, Baldassarri M, Fava F, Frullanti E, Valentino F, Doddato G, Giliberti A, Tita R, Amitrano S, Bruttini M, Croci S, Meloni I, Mencarelli MA, Rizzo CL, Pinto AM, Beligni G, Tommasi A, Sarno LD, Palmieri M, Carriero ML, Alaverdian D, Busani S, Bruno R, Vecchia M, Belli MA, Mantovani S, Ludovisi S, Quiros-Roldan E, Antoni MD, Zanella I, Siano M, Emiliozzi A, Fabbiani M, Rossetti B, Bergantini L, D’Alessandro M, Cameli P, Bennett D, Anedda F, Marcantonio S, Scolletta S, Guerrini S, Conticini E, Frediani B, Spertilli C, Donati A, Guidelli L, Corridi M, Croci L, Piacentini P, Desanctis E, Cappelli S, Verzuri A, Anemoli V, Pancrazzi A, Lorubbio M, Miraglia FG, Venturelli S, Cossarizza A, Vergori A, Gabrieli A, Riva A, Paciosi F, Andretta F, Gatti F, Parisi SG, Baratti S, Piscopo C, Russo R, Andolfo I, Iolascon A, Carella M, Merla G, Squeo GM, Raggi P, Marciano C, Perna R, Bassetti M, Sanguinetti M, Giorli A, Salerni L, Parravicini P, Menatti E, Trotta T, Coiro G, Lena F, Martinelli E, Mancarella S, Gabbi C, Maggiolo F, Ripamonti D, Bachetti T, Suardi C, Parati G, Bottà G, Domenico PD, Rancan I, Bianchi F, Colombo R, Barbieri C, Acquilini D, Andreucci E, Segala FV, Tiseo G, Falcone M, Lista M, Poscente M, Vivo OD, Petrocelli P, Guarnaccia A, Baroni S, Hayward C, Porteous DJ, Fawns-Ritchie C, Richmond A, Campbell A, van Heel DA, Hunt KA, Trembath RC, Huang QQ, Martin HC, Mason D, Trivedi B, Wright J, Finer S, Akhtar S, Anwar M, Arciero E, Ashraf S, Breen G, Chung R, Curtis CJ, Chowdhury M, Colligan G, Deloukas P, Durham C, Finer S, Griffiths C, Huang QQ, Hurles M, Hunt KA, Hussain S, Islam K, Khan A, Khan A, Lavery C, Lee SH, Lerner R, MacArthur D, MacLaughlin B, Martin H, Mason D, Miah S, Newman B, Safa N, Tahmasebi F, Trembath RC, Trivedi B, van Heel DA, Wright J, Griffiths CJ, Smith AV, Boughton AP, Li KW, LeFaive J, Annis A, Niavarani A, Aliannejad R, Sharififard B, Amirsavadkouhi A, Naderpour Z, Tadi HA, Aleagha AE, Ahmadi S, Moghaddam SBM, Adamsara A, Saeedi M, Abdollahi H, Hosseini A, Chariyavilaskul P, Jantarabenjakul W, Hirankarn N, Chamnanphon M, Suttichet TB, Shotelersuk V, Pongpanich M, Phokaew C, Chetruengchai W, Putchareon O, Torvorapanit P, Puthanakit T, Suchartlikitwong P, Nilaratanakul V, Sodsai P, Brumpton BM, Hveem K, Willer C, Wolford B, Zhou W, Rogne T, Solligard E, Åsvold BO, Franke L, Boezen M, Deelen P, Claringbould A, Lopera E, Warmerdam R, Vonk JM, van Blokland I, Lanting P, Ori APS, Feng YCA, Mercader J, Weiss ST, Karlson EW, Smoller JW, Murphy SN, Meigs JB, Woolley AE, Green RC, Perez EF, Wolford B, Zöllner S, Wang J, Beck A, Sloofman LG, Ascolillo S, Sebra RP, Collins BL, Levy T, Buxbaum JD, Sealfon SC, Jordan DM, Thompson RC, Gettler K, Chaudhary K, Belbin GM, Preuss M, Hoggart C, Choi S, Underwood SJ, Salib I, Britvan B, Keller K, Tang L, Peruggia M, Hiester LL, Niblo K, Aksentijevich A, Labkowsky A, Karp A, Zlatopolsky M, Zyndorf M, Charney AW, Beckmann ND, Schadt EE, Abul-Husn NS, Cho JH, Itan Y, Kenny EE, Loos RJF, Nadkarni GN, Do R, O’Reilly P, Huckins LM, Ferreira MAR, Abecasis GR, Leader JB, Cantor MN, Justice AE, Carey DJ, Chittoor G, Josyula NS, Kosmicki JA, Horowitz JE, Baras A, Gass MC, Yadav A, Mirshahi T, Hottenga JJ, Bartels M, de geus EEJC, Nivard MMG, Verma A, Ritchie MD, Rader D, Li B, Verma SS, Lucas A, Bradford Y, Abedalthagafi M, Alaamery M, Alshareef A, Sawaji M, Massadeh S, AlMalik A, Alqahtani S, Baraka D, Harthi FA, Alsolm E, Safieh LA, Alowayn AM, Alqubaishi F, Mutairi AA, Mangul S, Almutairi M, Aljawini N, Albesher N, Arabi YM, Mahmoud ES, Khattab AK, Halawani RT, Alahmadey ZZ, Albakri JK, Felemban WA, Suliman BA, Hasanato R, Al-Awdah L, Alghamdi J, AlZahrani D, AlJohani S, Al-Afghani H, AlDhawi N, AlBardis H, Alkwai S, Alswailm M, Almalki F, Albeladi M, Almohammed I, Barhoush E, Albader A, Alotaibi S, Alghamdi B, Jung J, fawzy MS, Alrashed M, Zeberg H, Nkambul L, Frithiof R, Hultström M, Lipcsey M, Tardif N, Rooyackers O, Grip J, Maricic T, Helgeland Ø, Magnus P, Trogstad LIS, Lee Y, Harris JR, Mangino M, Spector TD, Emma D, Moutsianas L, Caulfield MJ, Scott RH, Kousathanas A, Pasko D, Walker S, Stuckey A, Odhams CA, Rhodes D, Fowler T, Rendon A, Chan G, Arumugam P, Karczewski KJ, Martin AR, Wilson DJ, Spencer CCA, Crook DW, Wyllie DH, O’Connell AM, Atkinson EG, Kanai M, Tsuo K, Baya N, Turley P, Gupta R, Walters RK, Palmer DS, Sarma G, Solomonson M, Cheng N, Lu W, Churchhouse C, Goldstein JI, King D, Zhou W, Seed C, Daly MJ, Neale BM, Finucane H, Bryant S, Satterstrom FK, Band G, Earle SG, Lin SK, Arning N, Koelling N, Armstrong J, Rudkin JK, Callier S, Bryant S, Cusick C, Soranzo N, Zhao JH, Danesh J, Angelantonio ED, Butterworth AS, Sun YV, Huffman JE, Cho K, O’Donnell CJ, Tsao P, Gaziano JM, Peloso G, Ho YL, Smieszek SP, Polymeropoulos C, Polymeropoulos V, Polymeropoulos MH, Przychodzen BP, Fernandez-Cadenas I, Planas AM, Perez-Tur J, Llucià-Carol L, Cullell N, Muiño E, Cárcel-Márquez J, DeDiego ML, Iglesias LL, Soriano A, Rico V, Agüero D, Bedini JL, Lozano F, Domingo C, Robles V, Ruiz-Jaén F, Márquez L, Gomez J, Coto E, Albaiceta GM, García-Clemente M, Dalmau D, Arranz MJ, Dietl B, Serra-Llovich A, Soler P, Colobrán R, Martín-Nalda A, Martínez AP, Bernardo D, Rojo S, Fiz-López A, Arribas E, de la Cal-Sabater P, Segura T, González-Villa E, Serrano-Heras G, Martí-Fàbregas J, Jiménez-Xarrié E, de Felipe Mimbrera A, Masjuan J, García-Madrona S, Domínguez-Mayoral A, Villalonga JM, Menéndez-Valladares P, Chasman DI, Sesso HD, Manson JE, Buring JE, Ridker PM, Franco G, Davis L, Lee S, Priest J, Sankaran VG, van Heel D, Biesecker L, Kerchberger VE, Baillie JK. A first update on mapping the human genetic architecture of COVID-19. Nature 2022; 608:E1-E10. [PMID: 35922517 PMCID: PMC9352569 DOI: 10.1038/s41586-022-04826-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/29/2022] [Indexed: 01/04/2023]
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Santos C, Almeida A, Pinto R, Kaminska K, Peter VG, Sousa AB, Rivolta C, Coutinho-Santos L. Anisometropia and asymmetric ABCA4-related cone-rod dystrophy. Ophthalmic Genet 2022; 43:576-580. [PMID: 35903041 DOI: 10.1080/13816810.2022.2103834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
| | | | - Rita Pinto
- Instituto Dr. Gama Pinto, Lisbon, Portugal
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Virginie G Peter
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Ana-Berta Sousa
- Serviço de Genética Médica, Departamento de Pediatria, Hospital Santa Maria/CHULN, Lisbon, Portugal
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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Han JH, Ryan G, Guy A, Liu L, Quinodoz M, Helbling I, Lai-Cheong JE, Barwell J, Folcher M, McGrath JA, Moss C, Rivolta C. Mutations in the ribosome biogenesis factor gene LTV1 are linked to LIPHAK syndrome, a novel poikiloderma-like disorder. Hum Mol Genet 2022; 31:1970-1978. [PMID: 34999892 PMCID: PMC9239743 DOI: 10.1093/hmg/ddab368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/18/2021] [Accepted: 12/13/2021] [Indexed: 11/12/2022] Open
Abstract
In the framework of the UK 100 000 Genomes Project, we investigated the genetic origin of a previously undescribed recessive dermatological condition, which we named LIPHAK (LTV1-associated Inflammatory Poikiloderma with Hair abnormalities and Acral Keratoses), in four affected individuals from two UK families of Pakistani and Indian origins, respectively. Our analysis showed that only one gene, LTV1, carried rare biallelic variants that were shared in all affected individuals, and specifically they bore the NM_032860.5:c.503A > G, p.(Asn168Ser) change, found homozygously in all of them. In addition, high-resolution homozygosity mapping revealed the presence of a small 652-kb stretch on chromosome 6, encompassing LTV1, that was haploidentical and common to all affected individuals. The c.503A > G variant was predicted by in silico tools to affect the correct splicing of LTV1's exon 5. Minigene-driven splicing assays in HEK293T cells and in a skin sample from one of the patients confirmed that this variant was indeed responsible for the creation of a new donor splice site, resulting in aberrant splicing and in a premature termination codon in exon 6 of this gene. LTV1 encodes one of the ribosome biogenesis factors that promote the assembly of the small (40S) ribosomal subunit. In yeast, defects in LTV1 alter the export of nascent ribosomal subunits to the cytoplasm; however, the role of this gene in human pathology is unknown to date. Our data suggest that LIPHAK could be a previously unrecognized ribosomopathy.
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Affiliation(s)
- Ji Hoon Han
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland
- Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
| | - Gavin Ryan
- West Midlands Regional Genetics Laboratory, Central and South Genomic Laboratory Hub, Birmingham B15 2TG, UK
| | - Alyson Guy
- Viapath, St Thomas' Hospital, London SE1 7EH, UK
| | - Lu Liu
- Viapath, St Thomas' Hospital, London SE1 7EH, UK
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland
- Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Ingrid Helbling
- Department of Dermatology, University Hospitals of Leicester NHS Trust, Leicester LE1 5WW, UK
| | | | | | - Julian Barwell
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Department of Clinical Genetics, University Hospitals of Leicester NHS Trust, Leicester LE1 5WW, UK
| | - Marc Folcher
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland
- Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
| | - John A McGrath
- NIHR Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust and King's College London, London SE1 9RT, UK
- St John's Institute of Dermatology, King's College London (Guy's campus), London SE1 9RT, UK
| | - Celia Moss
- Department of Paediatric Dermatology, Birmingham Women’s and Children’s Hospital NHS FT, Birmingham B4 6NH, UK
- College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland
- Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
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Schroeder M, Peter VG, Gränse L, Andréasson S, Rivolta C, Kjellström U. A novel phenotype associated with the R162W variant in the KCNJ13 gene. Ophthalmic Genet 2022; 43:500-507. [PMID: 35477418 DOI: 10.1080/13816810.2022.2068041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Pathogenic variants in KCNJ13 have been associated with both autosomal dominant Snowflake vitreoretinal degeneration (SVD) and autosomal recessive Leber congenital amaurosis. SVD is characterized by aberrant vitreoretinal interface leading to increased risk of retinal detachment, crystalline retinal snowflake deposits, optic disc abnormalities, early-onset cataract, and cornea guttae. Reduced dark adaptation and reduced scotopic rod b-waves have also been described. We report a novel phenotype associated with the R162W variant in KCNJ13. METHODS Four affected members of a Swedish family were included. Three of them were examined with best corrected visual acuity, Goldmann perimetry, full-field-and multifocal electroretinography, optical coherence tomography, fundus color photographs, fundus autofluorescence images, slit lamp inspection, and genetic testing. The fourth subject only managed genetic testing. RESULTS All subjects carry the pathogenic missense variant; c.484C>T (NM_002242.4), R162W, in KCNJ13. ERG measurements revealed reduced macular-as well as general retinal function. Two of the subjects had a history of retinal detachment and the two younger subjects demonstrated early onset cataract. They all had structural macular changes and slightly gliotic optic discs. CONCLUSION In this family, the R162W variant in KCNJ13, previously described in association with SVD, causes a somewhat novel phenotype including macular dystrophy and moderate reduction of general retinal function as the main features combined with disc abnormalities, retinal detachment, and presenile cataract that has been described before. In times of up-coming gene-based therapies, it is important to report new genotype-phenotype associations to improve the possibilities to identify future treatment candidates.
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Affiliation(s)
- Marion Schroeder
- Department of Ophthalmology and Clinical Sciences Lund, Lund University, Skane University Hospital, Lund, Sweden
| | - Virginie G Peter
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Lotta Gränse
- Department of Ophthalmology and Clinical Sciences Lund, Lund University, Skane University Hospital, Lund, Sweden
| | - Sten Andréasson
- Department of Ophthalmology and Clinical Sciences Lund, Lund University, Skane University Hospital, Lund, Sweden
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Ulrika Kjellström
- Department of Ophthalmology and Clinical Sciences Lund, Lund University, Skane University Hospital, Lund, Sweden
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Nardou K, Nicolas M, Kuttler F, Cisarova K, Celik E, Quinodoz M, Riggi N, Michielin O, Rivolta C, Turcatti G, Moulin AP. Identification of New Vulnerabilities in Conjunctival Melanoma Using Image-Based High Content Drug Screening. Cancers (Basel) 2022; 14:cancers14061575. [PMID: 35326726 PMCID: PMC8946509 DOI: 10.3390/cancers14061575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 02/05/2023] Open
Abstract
Recent evidence suggests that numerous similarities exist between the genomic landscapes of both conjunctival and cutaneous melanoma. Since alterations of several components of the MAP kinases, PI3K/mTOR, and cell cycle pathways have been reported in conjunctival melanoma, we decided to assess the sensitivity of conjunctival melanoma to targeted inhibition mostly of kinase inhibitors. A high content drug screening assay based on automated fluorescence microscopy was performed in three conjunctival melanoma cell lines with different genomic backgrounds with 489 kinase inhibitors and 53 other inhibitors. IC50 and apoptosis induction were respectively assessed for 53 and 48 compounds. The genomic background influenced the response to MAK and PI3K/mTOR inhibition, more specifically cell lines with BRAF V600E mutations were more sensitive to BRAF/MEK inhibition, while CRMM2 bearing the NRASQ61L mutation was more sensitive to PI3k/mTOR inhibition. All cell lines demonstrated sensitivity to cell cycle inhibition, being more pronounced in CRMM2, especially with polo-like inhibitors. Our data also revealed new vulnerabilities to Hsp90 and Src inhibition. This study demonstrates that the genomic background partially influences the response to targeted therapy and uncovers a large panel of potential vulnerabilities in conjunctival melanoma that may expand available options for the management of this tumor.
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Affiliation(s)
- Katya Nardou
- Jules-Gonin Eye Hospital, University of Lausanne, 1004 Lausanne, Switzerland; (K.N.); (M.N.)
| | - Michael Nicolas
- Jules-Gonin Eye Hospital, University of Lausanne, 1004 Lausanne, Switzerland; (K.N.); (M.N.)
| | - Fabien Kuttler
- Biomolecular Screening Facility, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (F.K.); (G.T.)
| | - Katarina Cisarova
- Medical Genetics Unit, Centre Hospitalier Universitaire Vaudois (CHUV), 1011 Lausanne, Switzerland;
| | - Elifnaz Celik
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; (E.C.); (M.Q.); (C.R.)
- Department of Ophthalmology, University of Basel, 4056 Basel, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; (E.C.); (M.Q.); (C.R.)
- Department of Ophthalmology, University of Basel, 4056 Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Nicolo Riggi
- Experimental Pathology, Institute of Pathology, Lausanne University, 1011 Lausanne, Switzerland;
| | - Olivier Michielin
- Oncology Department, Centre Hospitalier Universitaire Vaudois (CHUV), 1011 Lausanne, Switzerland;
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; (E.C.); (M.Q.); (C.R.)
- Department of Ophthalmology, University of Basel, 4056 Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Gerardo Turcatti
- Biomolecular Screening Facility, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (F.K.); (G.T.)
| | - Alexandre Pierre Moulin
- Jules-Gonin Eye Hospital, University of Lausanne, 1004 Lausanne, Switzerland; (K.N.); (M.N.)
- Correspondence:
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Azhar Baig HM, Ansar M, Iqbal A, Naeem MA, Quinodoz M, Calzetti G, Iqbal M, Rivolta C. Genetic analysis of consanguineous Pakistani families with congenital stationary night blindness. Ophthalmic Res 2021; 65:104-110. [PMID: 34781300 DOI: 10.1159/000520895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/28/2021] [Indexed: 11/19/2022]
Abstract
AIM Congenital stationary night blindness (CSNB) is a rare, largely non progressive, inherited retinal disorder that can be clinically classified on the basis of fundus and electroretinogram (ERG) abnormalities. METHODS We analyzed four large consanguineous families from the Southern Punjab region of Pakistan including multiple individuals affected with CSNB. Exome sequencing (ES) was performed in probands of all four families; Sanger sequencing was performed in additional members to test co-segregation of the variants identified. RESULTS We identified two novel and likely pathogenic variants in two pedigrees, namely NM_002905.4:c.668A>C (p.Gln223Pro) in RDH5, and NM_022567.2:c.908del (p.Gly303ValfsTer45) in NYX. In the two other families, the variants NM_002905.4:c.319G>C (p.Gly107Arg) in RDH5 and NM_000541.5:c.874C>T (p.Arg292Ter) in SAG were identified. These variants have been reported previously, but not in the Pakistani population. CONCLUSIONS Our findings expand the mutational spectrum of CSNB, in particular within the population of Southern Punjab.
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Affiliation(s)
- Hafiz Muhammad Azhar Baig
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Muhammad Ansar
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Afia Iqbal
- Department of Zoology, Lahore College for Women University, Lahore, Pakistan
| | - Muhammad Asif Naeem
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Giacomo Calzetti
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Muhammad Iqbal
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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Rehman AU, Sepahi N, Bedoni N, Ravesh Z, Salmaninejad A, Cancellieri F, Peter VG, Quinodoz M, Mojarrad M, Pasdar A, Asad AG, Ghalamkari S, Piran M, Piran M, Superti-Furga A, Rivolta C. Whole exome sequencing in 17 consanguineous Iranian pedigrees expands the mutational spectrum of inherited retinal dystrophies. Sci Rep 2021; 11:19332. [PMID: 34588515 PMCID: PMC8481312 DOI: 10.1038/s41598-021-98677-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 09/06/2021] [Indexed: 11/24/2022] Open
Abstract
Inherited retinal dystrophies (IRDs) constitute one of the most heterogeneous groups of Mendelian human disorders. Using autozygome-guided next-generation sequencing methods in 17 consanguineous pedigrees of Iranian descent with isolated or syndromic IRD, we identified 17 distinct genomic variants in 11 previously-reported disease genes. Consistent with a recessive inheritance pattern, as suggested by pedigrees, variants discovered in our study were exclusively bi-allelic and mostly in a homozygous state (in 15 families out of 17, or 88%). Out of the 17 variants identified, 5 (29%) were never reported before. Interestingly, two mutations (GUCY2D:c.564dup, p.Ala189ArgfsTer130 and TULP1:c.1199G > A, p.Arg400Gln) were also identified in four separate pedigrees (two pedigrees each). In addition to expanding the mutational spectrum of IRDs, our findings confirm that the traditional practice of endogamy in the Iranian population is a prime cause for the appearance of IRDs.
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Affiliation(s)
- Atta Ur Rehman
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Neda Sepahi
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Nicola Bedoni
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Zeinab Ravesh
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Arash Salmaninejad
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Virginie G Peter
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Institute of Experimental Pathology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Mathieu Quinodoz
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Majid Mojarrad
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Pasdar
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Medical Genetics Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Division of Applied Medicine, Medical School, University of Aberdeen, Aberdeen, UK
| | - Ali Ghanbari Asad
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | | | - Mehran Piran
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Mehrdad Piran
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Carlo Rivolta
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK. .,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland. .,Department of Ophthalmology, University of Basel, Basel, Switzerland.
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30
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Perea-Romero I, Blanco-Kelly F, Sanchez-Navarro I, Lorda-Sanchez I, Tahsin-Swafiri S, Avila-Fernandez A, Martin-Merida I, Trujillo-Tiebas MJ, Lopez-Rodriguez R, Rodriguez de Alba M, Iancu IF, Romero R, Quinodoz M, Hakonarson H, Garcia-Sandova B, Minguez P, Corton M, Rivolta C, Ayuso C. NGS and phenotypic ontology-based approaches increase the diagnostic yield in syndromic retinal diseases. Hum Genet 2021; 140:1665-1678. [PMID: 34448047 PMCID: PMC8553673 DOI: 10.1007/s00439-021-02343-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/10/2021] [Indexed: 02/08/2023]
Abstract
Syndromic retinal diseases (SRDs) are a group of complex inherited systemic disorders, with challenging molecular underpinnings and clinical management. Our main goal is to improve clinical and molecular SRDs diagnosis, by applying a structured phenotypic ontology and next-generation sequencing (NGS)-based pipelines. A prospective and retrospective cohort study was performed on 100 probands with an a priori diagnosis of non-Usher SRDs, using available clinical data, including Human Phenotype Ontology annotation, and further classification into seven clinical categories (ciliopathies, specific syndromes and five others). Retrospective molecular diagnosis was assessed using different molecular and bioinformatic methods depending on availability. Subsequently, uncharacterized probands were prospectively screened using other NGS approaches to extend the number of analyzed genes. After phenotypic classification, ciliopathies were the most common SRD (35%). A global characterization rate of 52% was obtained, with six cases incompletely characterized for a gene that partially explained the phenotype. An improved characterization rate was achieved addressing prospective cases (83%) and well-recognizable syndrome (62%) subgroups. The 27% of the fully characterized cases were reclassified into a different clinical category after identification of the disease-causing gene. Clinical-exome sequencing is the most appropriate first-tier approach for prospective cases, whereas whole-exome sequencing and bioinformatic reanalysis increases the diagnosis of uncharacterized retrospective cases to 45%, mostly those with unspecific symptoms. Our study describes a comprehensive approach to SRDs in daily clinical practice and the importance of thorough clinical assessment and selection of the most appropriate molecular test to be used to solve these complex cases and elucidate novel associations.
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Affiliation(s)
- I Perea-Romero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - F Blanco-Kelly
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - I Sanchez-Navarro
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - I Lorda-Sanchez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - S Tahsin-Swafiri
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - A Avila-Fernandez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - I Martin-Merida
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - M J Trujillo-Tiebas
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - R Lopez-Rodriguez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - M Rodriguez de Alba
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - I F Iancu
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - R Romero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - M Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - H Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Blanca Garcia-Sandova
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Department of Ophthalmology, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - P Minguez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - M Corton
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - C Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - C Ayuso
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain. .,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
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31
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Bedoni N, Quinodoz M, Pinelli M, Cappuccio G, Torella A, Nigro V, Testa F, Simonelli F, Corton M, Lualdi S, Lanza F, Morana G, Ayuso C, Di Rocco M, Filocamo M, Banfi S, Brunetti-Pierri N, Superti-Furga A, Rivolta C. An Alu-mediated duplication in NMNAT1, involved in NAD biosynthesis, causes a novel syndrome, SHILCA, affecting multiple tissues and organs. Hum Mol Genet 2021; 29:2250-2260. [PMID: 32533184 DOI: 10.1093/hmg/ddaa112] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/30/2020] [Accepted: 06/01/2020] [Indexed: 12/22/2022] Open
Abstract
We investigated the genetic origin of the phenotype displayed by three children from two unrelated Italian families, presenting with a previously unrecognized autosomal recessive disorder that included a severe form of spondylo-epiphyseal dysplasia, sensorineural hearing loss, intellectual disability and Leber congenital amaurosis (SHILCA), as well as some brain anomalies that were visible at the MRI. Autozygome-based analysis showed that these children shared a 4.76 Mb region of homozygosity on chromosome 1, with an identical haplotype. Nonetheless, whole-exome sequencing failed to identify any shared rare coding variants, in this region or elsewhere. We then determined the transcriptome of patients' fibroblasts by RNA sequencing, followed by additional whole-genome sequencing experiments. Gene expression analysis revealed a 4-fold downregulation of the gene NMNAT1, residing indeed in the shared autozygous interval. Short- and long-read whole-genome sequencing highlighted a duplication involving 2 out of the 5 exons of NMNAT1 main isoform (NM_022787.3), leading to the production of aberrant mRNAs. Pathogenic variants in NMNAT1 have been previously shown to cause non-syndromic Leber congenital amaurosis (LCA). However, no patient with null biallelic mutations has ever been described, and murine Nmnat1 knockouts show embryonic lethality, indicating that complete absence of NMNAT1 activity is probably not compatible with life. The rearrangement found in our cases, presumably causing a strong but not complete reduction of enzymatic activity, may therefore result in an intermediate syndromic phenotype with respect to LCA and lethality.
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Affiliation(s)
- Nicola Bedoni
- Department of Computational Biology, University of Lausanne, 1011 Lausanne, Switzerland.,Division of Genetic Medicine, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Mathieu Quinodoz
- Department of Computational Biology, University of Lausanne, 1011 Lausanne, Switzerland.,Department of Genetics and Genome Biology, University of LE1 7RH Leicester, Leicester, UK.,Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland.,Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
| | - Michele Pinelli
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Department of Translational Medicine, Section of Pediatrics, Federico II University, 80131 Naples, Italy
| | - Gerarda Cappuccio
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Department of Translational Medicine, Section of Pediatrics, Federico II University, 80131 Naples, Italy
| | - Annalaura Torella
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Medical Genetics, Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Medical Genetics, Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania "Luigi Vanvitelli", 80131 Naples, Italy
| | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania "Luigi Vanvitelli", 80131 Naples, Italy
| | | | - Marta Corton
- Department of Genetics, Instituto de Investigación Sanitaria - Fundación Jiménez Díaz, University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28029 Madrid, Spain
| | - Susanna Lualdi
- Laboratorio di Genetica Molecolare e Biobanche, Istituto G. Gaslini, 16147 Genoa, Italy
| | - Federica Lanza
- Laboratorio di Genetica Molecolare e Biobanche, Istituto G. Gaslini, 16147 Genoa, Italy
| | - Giovanni Morana
- Neuroradiology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria - Fundación Jiménez Díaz, University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28029 Madrid, Spain
| | - Maja Di Rocco
- Laboratorio di Genetica Molecolare e Biobanche, Istituto G. Gaslini, 16147 Genoa, Italy
| | - Mirella Filocamo
- Laboratorio di Genetica Molecolare e Biobanche, Istituto G. Gaslini, 16147 Genoa, Italy
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Medical Genetics, Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Department of Translational Medicine, Section of Pediatrics, Federico II University, 80131 Naples, Italy
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Carlo Rivolta
- Department of Genetics and Genome Biology, University of LE1 7RH Leicester, Leicester, UK.,Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland.,Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
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32
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Gonçalves AB, Hasselbalch SK, Joensen BB, Patzke S, Martens P, Ohlsen SK, Quinodoz M, Nikopoulos K, Suleiman R, Damsø Jeppesen MP, Weiss C, Christensen ST, Rivolta C, Andersen JS, Farinelli P, Pedersen LB. CEP78 functions downstream of CEP350 to control biogenesis of primary cilia by negatively regulating CP110 levels. eLife 2021; 10:63731. [PMID: 34259627 PMCID: PMC8354638 DOI: 10.7554/elife.63731] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 07/13/2021] [Indexed: 12/12/2022] Open
Abstract
CEP78 is a centrosomal protein implicated in ciliogenesis and ciliary length control, and mutations in the CEP78 gene cause retinal cone-rod dystrophy associated with hearing loss. However, the mechanism by which CEP78 affects cilia formation is unknown. Based on a recently discovered disease-causing CEP78 p.L150S mutation, we identified the disease-relevant interactome of CEP78. We confirmed that CEP78 interacts with the EDD1-DYRK2-DDB1VPRBP E3 ubiquitin ligase complex, which is involved in CP110 ubiquitination and degradation, and identified a novel interaction between CEP78 and CEP350 that is weakened by the CEP78L150S mutation. We show that CEP350 promotes centrosomal recruitment and stability of CEP78, which in turn leads to centrosomal recruitment of EDD1. Consistently, cells lacking CEP78 display significantly increased cellular and centrosomal levels of CP110, and depletion of CP110 in CEP78-deficient cells restored ciliation frequency to normal. We propose that CEP78 functions downstream of CEP350 to promote ciliogenesis by negatively regulating CP110 levels via an EDD1-dependent mechanism.
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Affiliation(s)
- André Brás Gonçalves
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Sarah Kirstine Hasselbalch
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Beinta Biskopstø Joensen
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Sebastian Patzke
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Pernille Martens
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Signe Krogh Ohlsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | | | - Reem Suleiman
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Magnus Per Damsø Jeppesen
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Catja Weiss
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Søren Tvorup Christensen
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Pietro Farinelli
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Lotte Bang Pedersen
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
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33
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Ansar M, Ranza E, Shetty M, Paracha SA, Azam M, Kern I, Iwaszkiewicz J, Farooq O, Pournaras CJ, Malcles A, Kecik M, Rivolta C, Muzaffar W, Qurban A, Ali L, Aggoun Y, Santoni FA, Makrythanasis P, Ahmed J, Qamar R, Sarwar MT, Henry LK, Antonarakis SE. Taurine treatment of retinal degeneration and cardiomyopathy in a consanguineous family with SLC6A6 taurine transporter deficiency. Hum Mol Genet 2021; 29:618-623. [PMID: 31903486 DOI: 10.1093/hmg/ddz303] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/03/2019] [Accepted: 12/05/2019] [Indexed: 01/05/2023] Open
Abstract
In a consanguineous Pakistani family with two affected individuals, a homozygous variant Gly399Val in the eighth transmembrane domain of the taurine transporter SLC6A6 was identified resulting in a hypomorph transporting capacity of ~15% compared with normal. Three-dimensional modeling of this variant has indicated that it likely causes displacement of the Tyr138 (TM3) side chain, important for transport of taurine. The affected individuals presented with rapidly progressive childhood retinal degeneration, cardiomyopathy and almost undetectable plasma taurine levels. Oral taurine supplementation of 100 mg/kg/day resulted in maintenance of normal blood taurine levels. Following approval by the ethics committee, a long-term supplementation treatment was introduced. Remarkably, after 24-months, the cardiomyopathy was corrected in both affected siblings, and in the 6-years-old, the retinal degeneration was arrested, and the vision was clinically improved. Similar therapeutic approaches could be employed in Mendelian phenotypes caused by the dysfunction of the hundreds of other molecular transporters.
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Affiliation(s)
- Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Emmanuelle Ranza
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Madhur Shetty
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, USA
| | - Sohail A Paracha
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Maleeha Azam
- Department of Biosciences, Faculty of Science, COMSATS University, Islamabad, Pakistan
| | - Ilse Kern
- Pediatric Nephrology and Metabolism Unit, Pediatric Subspecialties Service, Children's Hospital, Geneva University Hospitals, Geneva, Switzerland
| | - Justyna Iwaszkiewicz
- Swiss Institute of Bioinformatics, Molecular Modeling Group, University of Lausanne, Lausanne, Switzerland
| | - Omer Farooq
- Bahria University Medical and Dental College, Karachi, Pakistan
| | | | - Ariane Malcles
- Department of Ophthalmology, University Hospitals of Geneva, Geneva, Switzerland
| | - Mateusz Kecik
- Department of Ophthalmology, University Hospitals of Geneva, Geneva, Switzerland
| | - Carlo Rivolta
- Clinical Research Center, Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University Hospital Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Waqar Muzaffar
- Armed Forces Institute of Ophthalmology, Rawalpindi, Pakistan
| | - Aziz Qurban
- Armed Forces Institute of Ophthalmology, Rawalpindi, Pakistan
| | - Liaqat Ali
- Department of Biosciences, Faculty of Science, COMSATS University, Islamabad, Pakistan
| | - Yacine Aggoun
- Pediatric Cardiology, Geneva University Hospitals, Geneva, Switzerland
| | - Federico A Santoni
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Jawad Ahmed
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Raheel Qamar
- Department of Biosciences, Faculty of Science, COMSATS University, Islamabad, Pakistan
| | - Muhammad T Sarwar
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - L Keith Henry
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, USA
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
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34
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Bibert S, Guex N, Lourenco J, Brahier T, Papadimitriou-Olivgeris M, Damonti L, Manuel O, Liechti R, Götz L, Tschopp J, Quinodoz M, Vollenweider P, Pagani JL, Oddo M, Hügli O, Lamoth F, Erard V, Voide C, Delorenzi M, Rufer N, Candotti F, Rivolta C, Boillat-Blanco N, Bochud PY. Transcriptomic Signature Differences Between SARS-CoV-2 and Influenza Virus Infected Patients. Front Immunol 2021; 12:666163. [PMID: 34135895 PMCID: PMC8202013 DOI: 10.3389/fimmu.2021.666163] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/10/2021] [Indexed: 12/19/2022] Open
Abstract
The reason why most individuals with COVID-19 have relatively limited symptoms while other develop respiratory distress with life-threatening complications remains unknown. Increasing evidence suggests that COVID-19 associated adverse outcomes mainly rely on dysregulated immunity. Here, we compared transcriptomic profiles of blood cells from 103 patients with different severity levels of COVID-19 with that of 27 healthy and 22 influenza-infected individuals. Data provided a complete overview of SARS-CoV-2-induced immune signature, including a dramatic defect in IFN responses, a reduction of toxicity-related molecules in NK cells, an increased degranulation of neutrophils, a dysregulation of T cells, a dramatic increase in B cell function and immunoglobulin production, as well as an important over-expression of genes involved in metabolism and cell cycle in patients infected with SARS-CoV-2 compared to those infected with influenza viruses. These features also differed according to COVID-19 severity. Overall and specific gene expression patterns across groups can be visualized on an interactive website (https://bix.unil.ch/covid/). Collectively, these transcriptomic host responses to SARS-CoV-2 infection are discussed in the context of current studies, thereby improving our understanding of COVID-19 pathogenesis and shaping the severity level of COVID-19.
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Affiliation(s)
- Stéphanie Bibert
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
| | - Joao Lourenco
- SIB Swiss Institute of Bioinformatics and Department of Fundamenal Oncology, University of Lausanne, Lausanne, Switzerland
| | - Thomas Brahier
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - Lauro Damonti
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
- Department of Infectious Diseases, Bern University Hospital, Bern, Switzerland
| | - Oriol Manuel
- Infectious Diseases Service and Transplantation Center, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Robin Liechti
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics and Department of Fundamenal Oncology, University of Lausanne, Lausanne, Switzerland
| | - Lou Götz
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics and Department of Fundamenal Oncology, University of Lausanne, Lausanne, Switzerland
| | - Jonathan Tschopp
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Peter Vollenweider
- Internal Medicine Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Jean-Luc Pagani
- Department of Adult Intensive Care Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Mauro Oddo
- Department of Adult Intensive Care Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Olivier Hügli
- Emergency Department, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Frédéric Lamoth
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
- Department of Laboratory Medicine, Institute of Microbiology, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Véronique Erard
- Clinique de Médecine et spécialités, Infectiologie, Hôpital Fribourgeois-Fribourg, Fribourg, Switzerland
| | - Cathy Voide
- Department of Infectious Diseases, Central Institute, Valais Hospital, Sion, Switzerland
| | - Mauro Delorenzi
- SIB Swiss Institute of Bioinformatics and Department of Fundamenal Oncology, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, University Hospital and University of Lausanne, Epalinges, Switzerland
| | - Nathalie Rufer
- Department of Oncology, University Hospital and University of Lausanne, Epalinges, Switzerland
| | - Fabio Candotti
- Division of Immunology and Allergy, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Noémie Boillat-Blanco
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Pierre-Yves Bochud
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
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Ruberto FP, Balzano S, Namburi P, Kimchi A, Pescini-Gobert R, Obolensky A, Banin E, Ben-Yosef T, Sharon D, Rivolta C. Heterozygous deletions of noncoding parts of the PRPF31 gene cause retinitis pigmentosa via reduced gene expression. Mol Vis 2021; 27:107-116. [PMID: 33907366 PMCID: PMC8056469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 03/16/2021] [Indexed: 11/18/2022] Open
Abstract
Purpose Heterozygous mutations in the gene PRPF31, encoding a pre-mRNA splicing factor, cause autosomal dominant retinitis pigmentosa (adRP) with reduced penetrance. At the molecular level, pathogenicity results from haploinsufficiency, as the largest majority of such mutations trigger nonsense-mediated mRNA decay or involve large deletions of coding exons. We investigated genetically two families with a history of adRP, one of whom showed incomplete penetrance. Methods All patients underwent thorough ophthalmological examination, including electroretinography (ERG) and Goldmann perimetry. Array-based comparative genomic hybridization (aCGH) and multiplex ligation-dependent probe amplification (MLPA) were used to map heterozygous deletions, while real-time PCR on genomic DNA and long-range PCR allowed resolving the mutations at the base-pair level. PRPF31 transcripts were quantified with real-time PCR on patient-derived lymphoblastoid cell lines. Results We identified two independent deletions affecting the promoter and the 5' untranslated region (UTR) of PRPF31 but leaving its coding sequence completely unaltered. Analysis of PRPF31 mRNA from lymphoblastoid cell lines from one of these families showed reduced levels of expression in patients versus controls, probably due to the heterozygous ablation of its promoter sequences. Conclusions In addition to reporting the identification of two novel noncoding deletions in PRPF31, this study provides strong additional evidence that mRNA-mediated haploinsufficiency is the primary cause of pathogenesis for PRPF31-linked adRP.
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Affiliation(s)
- Francesco Paolo Ruberto
- Experimental Cardiology Unit, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
| | - Sara Balzano
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Prasanthi Namburi
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Adva Kimchi
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Alexey Obolensky
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tamar Ben-Yosef
- Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland,Department of Ophthalmology, University of Basel, Basel, Switzerland,Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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36
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Atallah I, Quinodoz M, Campos-Xavier B, Peter VG, Fouriki A, Bonvin C, Bottani A, Kumps C, Angelini F, Bellutti Enders F, Christen-Zaech S, Rizzi M, Renella R, Beck-Popovic M, Poloni C, Frossard V, Blouin JL, Rivolta C, Riccio O, Candotti F, Hofer M, Unger S, Superti-Furga A. Immune deficiency, autoimmune disease and intellectual disability: A pleiotropic disorder caused by biallelic variants in the TPP2 gene. Clin Genet 2021; 99:780-788. [PMID: 33586135 DOI: 10.1111/cge.13942] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 12/16/2022]
Abstract
Four individuals from two families presented with a multisystemic condition of suspected genetic origin that was diagnosed only after genome analysis. The main phenotypic features were immune system dysregulation (severe immunodeficiency with autoimmunity) and intellectual disability. The four individuals were found to be homozygous for a 4.4 Kb deletion removing exons 20-23 (NM_003291.4) of the TPP2 gene, predicting a frameshift with premature termination of the protein. The deletion was located on a shared chromosome 13 haplotype indicating a Swiss founder mutation. Tripeptidyl peptidase 2 (TPP2) is a protease involved in HLA/antigen complex processing and amino acid homeostasis. Biallelic variants in TPP2 have been described in 10 individuals with variable features including immune deficiency, autoimmune cytopenias, and intellectual disability or chronic sterile brain inflammation mimicking multiple sclerosis. Our observations further delineate this severe condition not yet included in the OMIM catalog. Timely recognition of TPP2 deficiency is crucial since (1) immune surveillance is needed and hematopoietic stem cell transplantation may be necessary, and (2) for provision of genetic counselling. Additionally, enzyme replacement therapy, as already established for TPP1 deficiency, might be an option in the future.
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Affiliation(s)
- Isis Atallah
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Belinda Campos-Xavier
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Virginie G Peter
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Athina Fouriki
- Pediatric Immunology Unit, Division of Pediatrics, Lausanne University Hospital, Lausanne, Switzerland
| | - Christophe Bonvin
- Division of Neurology, Lausanne University Hospital, Lausanne, Switzerland
| | - Armand Bottani
- Division of Genetic Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Camille Kumps
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Federica Angelini
- Pediatric Immunology Unit, Division of Pediatrics, Lausanne University Hospital, Lausanne, Switzerland
| | - Felicitas Bellutti Enders
- Pediatric Immunology Unit, Division of Pediatrics, Lausanne University Hospital, Lausanne, Switzerland
| | | | - Mattia Rizzi
- Pediatric Hemato-Oncology Unit, Lausanne University Hospital, Lausanne, Switzerland
| | - Raffaele Renella
- Pediatric Hemato-Oncology Unit, Lausanne University Hospital, Lausanne, Switzerland
| | - Maja Beck-Popovic
- Pediatric Hemato-Oncology Unit, Lausanne University Hospital, Lausanne, Switzerland
| | - Claudia Poloni
- Pediatric Neurology Unit, Sion Hospital, Sion, Switzerland
| | | | - Jean-Louis Blouin
- Division of Genetic Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Orbicia Riccio
- Division of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Fabio Candotti
- Division of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Michael Hofer
- Pediatric Immunology Unit, Division of Pediatrics, Lausanne University Hospital, Lausanne, Switzerland
| | - Sheila Unger
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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37
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Allou L, Balzano S, Magg A, Quinodoz M, Royer-Bertrand B, Schöpflin R, Chan WL, Speck-Martins CE, Carvalho DR, Farage L, Lourenço CM, Albuquerque R, Rajagopal S, Nampoothiri S, Campos-Xavier B, Chiesa C, Niel-Bütschi F, Wittler L, Timmermann B, Spielmann M, Robson MI, Ringel A, Heinrich V, Cova G, Andrey G, Prada-Medina CA, Pescini-Gobert R, Unger S, Bonafé L, Grote P, Rivolta C, Mundlos S, Superti-Furga A. Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator. Nature 2021; 592:93-98. [DOI: 10.1038/s41586-021-03208-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 01/07/2021] [Indexed: 11/09/2022]
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38
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Poulter JA, Gravett MSC, Taylor RL, Fujinami K, De Zaeytijd J, Bellingham J, Rehman AU, Hayashi T, Kondo M, Rehman A, Ansar M, Donnelly D, Toomes C, Ali M, De Baere E, Leroy BP, Davies NP, Henderson RH, Webster AR, Rivolta C, Zeitz C, Mahroo OA, Arno G, Black GCM, McKibbin M, Harris SA, Khan KN, Inglehearn CF. New variants and in silico analyses in GRK1 associated Oguchi disease. Hum Mutat 2021; 42:164-176. [PMID: 33252155 PMCID: PMC7898643 DOI: 10.1002/humu.24140] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 09/15/2020] [Accepted: 11/05/2020] [Indexed: 12/16/2022]
Abstract
Biallelic mutations in G-Protein coupled receptor kinase 1 (GRK1) cause Oguchi disease, a rare subtype of congenital stationary night blindness (CSNB). The purpose of this study was to identify disease causing GRK1 variants and use in-depth bioinformatic analyses to evaluate how their impact on protein structure could lead to pathogenicity. Patients' genomic DNA was sequenced by whole genome, whole exome or focused exome sequencing. Disease associated variants, published and novel, were compared to nondisease associated missense variants. The impact of GRK1 missense variants at the protein level were then predicted using a series of computational tools. We identified twelve previously unpublished cases with biallelic disease associated GRK1 variants, including eight novel variants, and reviewed all GRK1 disease associated variants. Further structure-based scoring revealed a hotspot for missense variants in the kinase domain. In addition, to aid future clinical interpretation, we identified the bioinformatics tools best able to differentiate disease associated from nondisease associated variants. We identified GRK1 variants in Oguchi disease patients and investigated how disease-causing variants may impede protein function in-silico.
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Affiliation(s)
- James A. Poulter
- Division of Molecular Medicine, Leeds Institute of Medical ResearchUniversity of LeedsLeedsUK
| | | | - Rachel L. Taylor
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and HealthUniversity of ManchesterManchesterUK
| | - Kaoru Fujinami
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical CentreTokyoJapan
- Moorfields Eye HospitalLondonUK
- UCL Institute of OphthalmologyLondonUK
- Keio University School of MedicineTokyoJapan
| | | | | | - Atta Ur Rehman
- Division of Genetic Medicine, Centre Hospitalier Universitaire Vaudois (CHUV)University of LausanneLausanneSwitzerland
| | | | - Mineo Kondo
- Mie University Graduate School of MedicineMieJapan
| | - Abdur Rehman
- Department of Genetics, Faculty of ScienceHazara University MansehraDhodialPakistan
| | - Muhammad Ansar
- Clinical Research Center, Institute of Molecular and Clinical Ophthalmology Basel (IOB)BaselSwitzerland
| | - Dan Donnelly
- School of Biomedical Sciences, University of LeedsLeedsUK
| | - Carmel Toomes
- Division of Molecular Medicine, Leeds Institute of Medical ResearchUniversity of LeedsLeedsUK
| | - Manir Ali
- Division of Molecular Medicine, Leeds Institute of Medical ResearchUniversity of LeedsLeedsUK
| | | | | | - Bart P. Leroy
- Ghent UniversityGhentBelgium
- Children's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
| | | | | | - Andrew R. Webster
- Moorfields Eye HospitalLondonUK
- UCL Institute of OphthalmologyLondonUK
| | - Carlo Rivolta
- Department of Genetics and Genome BiologyUniversity of LeicesterLeicesterUK
- Clinical Research Center, Institute of Molecular and Clinical Ophthalmology Basel (IOB)BaselSwitzerland
- Department of OphthalmologyUniversity Hospital BaselBaselSwitzerland
| | - Christina Zeitz
- Sorbonne UniversitéINSERM, CNRS, Institut de la VisionParisFrance
| | - Omar A. Mahroo
- Moorfields Eye HospitalLondonUK
- UCL Institute of OphthalmologyLondonUK
| | - Gavin Arno
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical CentreTokyoJapan
- Moorfields Eye HospitalLondonUK
- UCL Institute of OphthalmologyLondonUK
| | - Graeme C. M. Black
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and HealthUniversity of ManchesterManchesterUK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation TrustManchesterUK
| | - Martin McKibbin
- Division of Molecular Medicine, Leeds Institute of Medical ResearchUniversity of LeedsLeedsUK
- Leeds Teaching Hospitals NHS Trust, St James’ University HospitalLeedsUK
| | | | - Kamron N. Khan
- Division of Molecular Medicine, Leeds Institute of Medical ResearchUniversity of LeedsLeedsUK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation TrustManchesterUK
| | - Chris F. Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical ResearchUniversity of LeedsLeedsUK
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39
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Poulter JA, Gravett MSC, Taylor RL, Fujinami K, De Zaeytijd J, Bellingham J, Rehman AU, Hayashi T, Kondo M, Rehman A, Ansar M, Donnelly D, Toomes C, Ali M, De Baere E, Leroy BP, Davies NP, Henderson RH, Webster AR, Rivolta C, Zeitz C, Mahroo OA, Arno G, Black GCM, McKibbin M, Harris SA, Khan KN, Inglehearn CF. Cover, Volume 42, Issue 2. Hum Mutat 2021. [DOI: 10.1002/humu.24169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- James A. Poulter
- Division of Molecular Medicine, Leeds Institute of Medical Research University of Leeds Leeds UK
| | | | - Rachel L. Taylor
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
| | - Kaoru Fujinami
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Centre Tokyo Japan
- Moorfields Eye Hospital London UK
- UCL Institute of Ophthalmology London UK
- Keio University School of Medicine Tokyo Japan
| | | | | | - Atta Ur Rehman
- Division of Genetic Medicine, Centre Hospitalier Universitaire Vaudois (CHUV) University of Lausanne Lausanne Switzerland
| | | | - Mineo Kondo
- Mie University Graduate School of Medicine Mie Japan
| | - Abdur Rehman
- Department of Genetics, Faculty of Science Hazara University Mansehra Dhodial Pakistan
| | - Muhammad Ansar
- Clinical Research Center, Institute of Molecular and Clinical Ophthalmology Basel (IOB) Basel Switzerland
| | - Dan Donnelly
- School of Biomedical Sciences, University of Leeds Leeds UK
| | - Carmel Toomes
- Division of Molecular Medicine, Leeds Institute of Medical Research University of Leeds Leeds UK
| | - Manir Ali
- Division of Molecular Medicine, Leeds Institute of Medical Research University of Leeds Leeds UK
| | | | - Bart P. Leroy
- Ghent University Ghent Belgium
- Children's Hospital of Philadelphia Philadelphia Pennsylvania USA
| | | | | | - Andrew R. Webster
- Moorfields Eye Hospital London UK
- UCL Institute of Ophthalmology London UK
| | - Carlo Rivolta
- Department of Genetics and Genome Biology University of Leicester Leicester UK
- Clinical Research Center, Institute of Molecular and Clinical Ophthalmology Basel (IOB) Basel Switzerland
- Department of Ophthalmology University Hospital Basel Basel Switzerland
| | - Christina Zeitz
- Sorbonne Université INSERM, CNRS, Institut de la Vision Paris France
| | - Omar A. Mahroo
- Moorfields Eye Hospital London UK
- UCL Institute of Ophthalmology London UK
| | - Gavin Arno
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Centre Tokyo Japan
- Moorfields Eye Hospital London UK
- UCL Institute of Ophthalmology London UK
| | - Graeme C. M. Black
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust Manchester UK
| | - Martin McKibbin
- Division of Molecular Medicine, Leeds Institute of Medical Research University of Leeds Leeds UK
- Leeds Teaching Hospitals NHS Trust, St James’ University Hospital Leeds UK
| | - Sarah A. Harris
- School of Physics and Astronomy, University of Leeds Leeds UK
| | - Kamron N. Khan
- Division of Molecular Medicine, Leeds Institute of Medical Research University of Leeds Leeds UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust Manchester UK
| | - Chris F. Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical Research University of Leeds Leeds UK
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40
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Quinodoz M, Peter VG, Bedoni N, Royer Bertrand B, Cisarova K, Salmaninejad A, Sepahi N, Rodrigues R, Piran M, Mojarrad M, Pasdar A, Ghanbari Asad A, Sousa AB, Coutinho Santos L, Superti-Furga A, Rivolta C. AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data. Nat Commun 2021; 12:518. [PMID: 33483490 PMCID: PMC7822856 DOI: 10.1038/s41467-020-20584-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 12/09/2020] [Indexed: 12/11/2022] Open
Abstract
Homozygosity mapping is a powerful method for identifying mutations in patients with recessive conditions, especially in consanguineous families or isolated populations. Historically, it has been used in conjunction with genotypes from highly polymorphic markers, such as DNA microsatellites or common SNPs. Traditional software performs rather poorly with data from Whole Exome Sequencing (WES) and Whole Genome Sequencing (WGS), which are now extensively used in medical genetics. We develop AutoMap, a tool that is both web-based or downloadable, to allow performing homozygosity mapping directly on VCF (Variant Call Format) calls from WES or WGS projects. Following a training step on WES data from 26 consanguineous families and a validation procedure on a matched cohort, our method shows higher overall performances when compared with eight existing tools. Most importantly, when tested on real cases with negative molecular diagnosis from an internal set, AutoMap detects three gene-disease and multiple variant-disease associations that were previously unrecognized, projecting clear benefits for both molecular diagnosis and research activities in medical genetics. Homozygosity mapping is a useful tool for identifying candidate mutations in recessive conditions, however application to next generation sequencing data has been sub-optimal. Here, the authors present AutoMap, which efficiently identifies runs of homozygosity in whole exome/genome sequencing data.
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Affiliation(s)
- Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Virginie G Peter
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.,Institute of Experimental Pathology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Nicola Bedoni
- Service of Medical Genetics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Béryl Royer Bertrand
- Service of Medical Genetics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Katarina Cisarova
- Service of Medical Genetics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Arash Salmaninejad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Neda Sepahi
- Noncommunicable Diseases Research Center, Fasa University of Sciences, Fasa, Iran
| | - Raquel Rodrigues
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon Academic Medical Center (CAML), Lisbon, Portugal
| | - Mehran Piran
- Noncommunicable Diseases Research Center, Fasa University of Sciences, Fasa, Iran.,Bioinformatics and Computational Biology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Majid Mojarrad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Pasdar
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Division of Applied Medicine, Medical School, University of Aberdeen, Aberdeen, UK
| | - Ali Ghanbari Asad
- Noncommunicable Diseases Research Center, Fasa University of Sciences, Fasa, Iran
| | - Ana Berta Sousa
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon Academic Medical Center (CAML), Lisbon, Portugal.,Medical Faculty, Lisbon University, Lisbon, Portugal
| | | | - Andrea Superti-Furga
- Service of Medical Genetics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland. .,Department of Ophthalmology, University of Basel, Basel, Switzerland. .,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
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41
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Janeschitz‐Kriegl L, Rivolta C, György B, Quinodoz M, Meyer P, Wild A, Escher P, Scholl H, Goldblum D. c.‐61G>A in OVOL2 is a pathogenic variant in posterior polymorphous corneal dystrophy 1—a case report. Acta Ophthalmol 2021. [DOI: 10.1111/j.1755-3768.2020.0178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Lucas Janeschitz‐Kriegl
- Eye Clinic University Hospital Basel Basel Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel (IOB) Basel Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB) Basel Switzerland
| | - Bence György
- Eye Clinic University Hospital Basel Basel Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel (IOB) Basel Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB) Basel Switzerland
| | - Peter Meyer
- Eye Clinic University Hospital Basel Basel Switzerland
| | | | - Pascal Escher
- Inselspital Universitätsklinik für Augenheilkunde Bern Switzerland
| | - Hendrik Scholl
- Eye Clinic University Hospital Basel Basel Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel (IOB) Basel Switzerland
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42
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Peter VG, Quinodoz M, Sadio S, Held S, Rodrigues M, Soares M, Sousa AB, Coutinho Santos L, Damme M, Rivolta C. New clinical and molecular evidence linking mutations in ARSG to Usher syndrome type IV. Hum Mutat 2020; 42:261-271. [PMID: 33300174 DOI: 10.1002/humu.24150] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 11/11/2020] [Accepted: 12/06/2020] [Indexed: 11/11/2022]
Abstract
In murine and canine animal models, mutations in the Arylsulfatase G gene (ARSG) cause a particular lysosomal storage disorder characterized by neurological phenotypes. Recently, two variants in the same gene were found to be associated with an atypical form of Usher syndrome in humans, leading to visual and auditory impairment without the involvement of the central nervous system. In this study, we identified three novel pathogenic variants in ARSG, which segregated recessively with the disease in two families from Portugal. The probands were affected with retinitis pigmentosa and sensorineural hearing loss, generally with an onset of symptoms in their fourth decade of life. Functional experiments showed that these pathogenic variants abolish the sulfatase activity of the Arylsulfatase G enzyme and impede the appropriate lysosomal localization of the protein product, which appears to be retained in the endoplasmic reticulum. Our data enable to definitely confirm that different biallelic variants in ARSG cause a specific deaf-blindness syndrome, by abolishing the activity of the enzyme it encodes.
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Affiliation(s)
- Virginie G Peter
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Institute of Experimental Pathology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Silvia Sadio
- Department of Ophthalmology, Instituto de Oftalmologia Dr. Gama Pinto, Lisbon, Portugal
| | - Sebastian Held
- Department of Biochemistry, University of Kiel, Kiel, Germany
| | - Márcia Rodrigues
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon Academic Medical Center (CAML), Lisbon, Portugal
| | - Marta Soares
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon Academic Medical Center (CAML), Lisbon, Portugal
| | - Ana Berta Sousa
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon Academic Medical Center (CAML), Lisbon, Portugal.,Department of Basic Immunology, Medical Faculty, University of Lisbon, Lisbon, Portugal
| | - Luisa Coutinho Santos
- Department of Ophthalmology, Instituto de Oftalmologia Dr. Gama Pinto, Lisbon, Portugal
| | - Markus Damme
- Department of Biochemistry, University of Kiel, Kiel, Germany
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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43
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de Bruijn SE, Fiorentino A, Ottaviani D, Fanucchi S, Melo US, Corral-Serrano JC, Mulders T, Georgiou M, Rivolta C, Pontikos N, Arno G, Roberts L, Greenberg J, Albert S, Gilissen C, Aben M, Rebello G, Mead S, Raymond FL, Corominas J, Smith CEL, Kremer H, Downes S, Black GC, Webster AR, Inglehearn CF, van den Born LI, Koenekoop RK, Michaelides M, Ramesar RS, Hoyng CB, Mundlos S, Mhlanga MM, Cremers FPM, Cheetham ME, Roosing S, Hardcastle AJ. Structural Variants Create New Topological-Associated Domains and Ectopic Retinal Enhancer-Gene Contact in Dominant Retinitis Pigmentosa. Am J Hum Genet 2020; 107:802-814. [PMID: 33022222 PMCID: PMC7675008 DOI: 10.1016/j.ajhg.2020.09.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 09/02/2020] [Indexed: 01/07/2023] Open
Abstract
The cause of autosomal-dominant retinitis pigmentosa (adRP), which leads to loss of vision and blindness, was investigated in families lacking a molecular diagnosis. A refined locus for adRP on Chr17q22 (RP17) was delineated through genotyping and genome sequencing, leading to the identification of structural variants (SVs) that segregate with disease. Eight different complex SVs were characterized in 22 adRP-affected families with >300 affected individuals. All RP17 SVs had breakpoints within a genomic region spanning YPEL2 to LINC01476. To investigate the mechanism of disease, we reprogrammed fibroblasts from affected individuals and controls into induced pluripotent stem cells (iPSCs) and differentiated them into photoreceptor precursor cells (PPCs) or retinal organoids (ROs). Hi-C was performed on ROs, and differential expression of regional genes and a retinal enhancer RNA at this locus was assessed by qPCR. The epigenetic landscape of the region, and Hi-C RO data, showed that YPEL2 sits within its own topologically associating domain (TAD), rich in enhancers with binding sites for retinal transcription factors. The Hi-C map of RP17 ROs revealed creation of a neo-TAD with ectopic contacts between GDPD1 and retinal enhancers, and modeling of all RP17 SVs was consistent with neo-TADs leading to ectopic retinal-specific enhancer-GDPD1 accessibility. qPCR confirmed increased expression of GDPD1 and increased expression of the retinal enhancer that enters the neo-TAD. Altered TAD structure resulting in increased retinal expression of GDPD1 is the likely convergent mechanism of disease, consistent with a dominant gain of function. Our study highlights the importance of SVs as a genomic mechanism in unsolved Mendelian diseases.
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Affiliation(s)
- Suzanne E de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Alessia Fiorentino
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership
| | | | - Stephanie Fanucchi
- Gene Expression and Biophysics Group, Division of Chemical, Systems and Synthetic Biology, Department of Integrative Biomedical Science, Institute for Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, 7935, South Africa
| | - Uirá S Melo
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany; Institute for Medical and Human Genetics, Charité - Universitätsmedizin, Berlin, 10117, Germany
| | | | - Timo Mulders
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Michalis Georgiou
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; Moorfields Eye Hospital, London, EC1V 2PD, UK
| | - Carlo Rivolta
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK; Clinical Research Center, Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, 4031, Switzerland; Department of Ophthalmology, University Hospital Basel, Basel, 4001, Switzerland
| | - Nikolas Pontikos
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership
| | - Gavin Arno
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership; Moorfields Eye Hospital, London, EC1V 2PD, UK
| | - Lisa Roberts
- University of Cape Town/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, 7935, South Africa
| | - Jacquie Greenberg
- University of Cape Town/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, 7935, South Africa
| | - Silvia Albert
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Marco Aben
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - George Rebello
- University of Cape Town/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, 7935, South Africa
| | - Simon Mead
- MRC Prion Unit at UCL, UCL Institute of Prion Disease, London, W1W 7FF, UK
| | - F Lucy Raymond
- NIHR BioResource, Cambridge University Hospitals, Cambridge, CB2 0QQ, UK; Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 OXY, UK
| | - Jordi Corominas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Claire E L Smith
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, LS2 9JT, UK
| | - Hannie Kremer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Susan Downes
- UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership; Oxford Eye Hospital, Oxford University Hospitals NHS Trust and Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford, OX3 9DU, UK
| | - Graeme C Black
- UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership; Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester, M13 9WL, UK
| | - Andrew R Webster
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership; Moorfields Eye Hospital, London, EC1V 2PD, UK
| | - Chris F Inglehearn
- UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership; Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, LS2 9JT, UK
| | | | - Robert K Koenekoop
- Department of Paediatric Surgery, Human Genetics and Ophthalmology, McGill University, Montréal, QC H4A 3J1, Canada
| | - Michel Michaelides
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership; Moorfields Eye Hospital, London, EC1V 2PD, UK
| | - Raj S Ramesar
- University of Cape Town/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, 7935, South Africa
| | - Carel B Hoyng
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany; Institute for Medical and Human Genetics, Charité - Universitätsmedizin, Berlin, 10117, Germany
| | - Musa M Mhlanga
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Gene Expression and Biophysics Group, Division of Chemical, Systems and Synthetic Biology, Department of Integrative Biomedical Science, Institute for Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, 7935, South Africa; Gene Expression and Biophysics Unit, Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, Lisbon, 1649-028, Portugal; Epigenomics & Single Cell Biophysics Group, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, 6525 GA, the Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Michael E Cheetham
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands.
| | - Alison J Hardcastle
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership
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Del Pozo-Valero M, Riveiro-Alvarez R, Blanco-Kelly F, Aguirre-Lamban J, Martin-Merida I, Iancu IF, Swafiri S, Lorda-Sanchez I, Rodriguez-Pinilla E, Trujillo-Tiebas MJ, Jimenez-Rolando B, Carreño E, Mahillo-Fernandez I, Rivolta C, Corton M, Avila-Fernandez A, Garcia-Sandoval B, Ayuso C. Genotype-Phenotype Correlations in a Spanish Cohort of 506 Families With Biallelic ABCA4 Pathogenic Variants. Am J Ophthalmol 2020; 219:195-204. [PMID: 32619608 DOI: 10.1016/j.ajo.2020.06.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/19/2020] [Accepted: 06/21/2020] [Indexed: 01/28/2023]
Abstract
PURPOSE To define genotype-phenotype correlations in the largest cohort study worldwide of patients with biallelic ABCA4 variants, including 434 patients with Stargardt disease (STGD1) and 72 with cone-rod dystrophy (CRD). DESIGN Cohort study. METHODS We characterized 506 patients with ABCA4 variants using conventional genetic tools and next-generation sequencing technologies. Medical history and ophthalmologic data were obtained from 372 patients. Genotype-phenotype correlation studies were carried out for the following variables: variant type, age at symptom onset (AO), and clinical phenotype. RESULTS A total of 228 different pathogenic variants were identified in 506 ABCA4 patients, 50 of which were novel. Genotype-phenotype correlations showed that most of the patients with biallelic truncating variants presented with CRD and that these cases had a significantly earlier AO than patients with STGD1. Three missense variants are associated with CRD for the first time (c.1804C>T; p.[Arg602Trp], c.3056C>T; p.[Thr1019Met], and c.6320G>C; p.[Arg2107Pro]). Analysis of the most prevalent ABCA4 variant in Spain, c.3386G>T; p.(Arg1129Leu), revealed that is correlated to STGD1, later AO, and foveal sparing. CONCLUSIONS Our study, conducted in the largest ABCA4-associated disease cohort reported to date, updates the genotype-phenotype model established for ABCA4 variants and broadens the mutational spectrum of the gene. According to our observations, patients with ABCA4 presenting with 2 truncating variants may first present features of STGD1 but eventually develop rod dysfunction, and specific missense variants may be associated with a different phenotype, underscoring the importance of an accurate genetic diagnosis. Also, it is a prerequisite for enrollment in clinical trials, and to date, no other treatment has been approved for STGD1.
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Affiliation(s)
- Marta Del Pozo-Valero
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Rosa Riveiro-Alvarez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Jana Aguirre-Lamban
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Inmaculada Martin-Merida
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Ionut-Florin Iancu
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Saoud Swafiri
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Isabel Lorda-Sanchez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Elvira Rodriguez-Pinilla
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Maria José Trujillo-Tiebas
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Belen Jimenez-Rolando
- Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ester Carreño
- Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ignacio Mahillo-Fernandez
- Department of Epidemiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Marta Corton
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Almudena Avila-Fernandez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Blanca Garcia-Sandoval
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain; Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain.
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Gallay C, Meylan P, Mermoud S, Johannsen A, Lang C, Rivolta C, Christen-Zaech S. Genetic predisposition and environmental factors associated with the development of atopic dermatitis in infancy: a prospective birth cohort study. Eur J Pediatr 2020; 179:1367-1377. [PMID: 32144501 DOI: 10.1007/s00431-020-03616-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 02/07/2020] [Accepted: 02/18/2020] [Indexed: 11/30/2022]
Abstract
The influence of environmental factors on atopic dermatitis (AD) has been investigated in many cross-sectional studies. It remains however unclear if they could influence AD development early in life. This prospective birth cohort study aimed to monitor aspects of family lifestyle and child's nutrition within a Caucasian population and to assess its association with AD development over the first 2 years of life. Genetic predisposition was evaluated based on family history and profilaggrin genotyping. Of 149 included children, 36 developed AD. Infants with a family history of atopy developed AD 2.6 times more frequently (30 of 97) than infants without atopic predisposition (6 of 52). Genotyping was carried out on 50% of the children included. Profilaggrin mutations (R501X, 2282del4, R2447X, and S3247X) were infrequent in our population. Lower incidence of AD was observed in infants exposed to a damp housing environment, lower household income, and smoking mothers with a higher but not with a lower education level.Conclusion: Family history of atopy was a significant risk factor for AD regardless of the most common, currently defined, FLG mutations. Humidity at home and passive smoking seem associated with AD development in infancy. What is Known: • Atopic dermatitis (AD) is associated with mutations in various genes of the immune system and the epidermal barrier complex in particular filaggrin (FLG) mutation. • Inherited factors alone cannot explain the rising AD; environmental factors are therefore likely to play a decisive role in this rise but the exact role that these factors may play in increasing AD risk in infancy remains unclear. Moreover, the relationship between environmental factors and AD has been the focus of mostly cross-sectional studies and not prospective studies. What is New: • This prospective birth cohort study demonstrates that family history of atopy is a significant risk factor for AD regardless of the most common, currently defined, FLG mutations. • A lower incidence of AD was observed in infants exposed to a moist housing environment, lower household income, and smoking of mothers with a higher but not with a lower education level.
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Affiliation(s)
- Caroline Gallay
- Pediatric Dermatology Unit, Departments of Dermatology & Venereology, and Pediatrics, University Hospital Lausanne, University of Lausanne, Chemin de Montétan 16, 1004, Lausanne, Switzerland
| | - Patrick Meylan
- Pediatric Dermatology Unit, Departments of Dermatology & Venereology, and Pediatrics, University Hospital Lausanne, University of Lausanne, Chemin de Montétan 16, 1004, Lausanne, Switzerland
| | - Sophie Mermoud
- Pediatric Dermatology Unit, Departments of Dermatology & Venereology, and Pediatrics, University Hospital Lausanne, University of Lausanne, Chemin de Montétan 16, 1004, Lausanne, Switzerland
| | - Alexandre Johannsen
- Pediatric Dermatology Unit, Departments of Dermatology & Venereology, and Pediatrics, University Hospital Lausanne, University of Lausanne, Chemin de Montétan 16, 1004, Lausanne, Switzerland
| | - Caroline Lang
- Pediatric Dermatology Unit, Departments of Dermatology & Venereology, and Pediatrics, University Hospital Lausanne, University of Lausanne, Chemin de Montétan 16, 1004, Lausanne, Switzerland
| | - Carlo Rivolta
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Stephanie Christen-Zaech
- Pediatric Dermatology Unit, Departments of Dermatology & Venereology, and Pediatrics, University Hospital Lausanne, University of Lausanne, Chemin de Montétan 16, 1004, Lausanne, Switzerland.
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Panagiotou ES, Papathomas T, Nikopoulos K, Koukoula S, Quinodoz M, Rehman AU, Giannopoulos T, Rivolta C, Konstas AG. Management of Full-Thickness Macular Hole in A Genetically Confirmed Case with Usher Syndrome. Ophthalmol Ther 2020; 9:677-684. [PMID: 32566994 PMCID: PMC7406580 DOI: 10.1007/s40123-020-00276-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Indexed: 11/12/2022] Open
Abstract
INTRODUCTION Full-thickness macular hole (FTMH) formation is rarely seen in patients with retinitis pigmentosa (RP) and can have an adverse impact on their residual visual function. The underlying mechanisms are unknown, and clinical experience is limited regarding surgical outcomes. Here, we describe the surgical management of FTMH in a young patient with genetically confirmed Usher syndrome, the most common form of syndromic RP. CASE REPORT A 28-year-old woman presented with blurred vision in her right eye (RE). She had a history of RP and bilateral hearing impairment since childhood. Fundoscopy and spectral-domain optical coherence tomography revealed a FTMH in the RE along with typical RP features bilaterally. After pars plana vitrectomy (PPV) with internal limiting membrane peel and gas tamponade, the FTMH closed. Six months after PPV the patient underwent cataract surgery in the affected eye, and the visual acuity remained stable compared to baseline. The clinical diagnosis of Usher syndrome was genetically confirmed by whole exome sequencing (WES), which revealed the presence of two pathogenic nucleotide variants in trans (compound heterozygosity) in the gene USH2A. CONCLUSION We report a rare case of successful closure of a FTMH in a patient with Usher syndrome. Surgical treatment of FTMH can help preserve the central vision in RP patients, whose peripheral vision is severely affected.
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Affiliation(s)
- Evangelia S Panagiotou
- 1st Department of Ophthalmology, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece
| | - Thomas Papathomas
- 1st Department of Ophthalmology, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece
| | - Konstantinos Nikopoulos
- Laboratory of Oncogenomics, Department of Hematology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | | | - Mathieu Quinodoz
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Atta Ur Rehman
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Theodoros Giannopoulos
- 1st Department of Ophthalmology, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece
| | - Carlo Rivolta
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Anastasios G Konstas
- 1st Department of Ophthalmology, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece.
- 3rd Department of Ophthalmology, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece.
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Ueno S, Koyanagi Y, Kominami T, Ito Y, Kawano K, Nishiguchi KM, Rivolta C, Nakazawa T, Sonoda KH, Terasaki H. Clinical characteristics and high resolution retinal imaging of retinitis pigmentosa caused by RP1 gene variants. Jpn J Ophthalmol 2020; 64:485-496. [PMID: 32627106 DOI: 10.1007/s10384-020-00752-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 05/14/2020] [Indexed: 11/27/2022]
Abstract
PURPOSE To report the clinical course and high resolution images of autosomal recessive retinitis pigmentosa (RP) associated with a variant of the RP1 gene (c.4052_4053ins328/p.Tyr1352Alafs*9; m1), a high frequency founder variant in Japanese RP patients. STUDY DESIGN Retrospective case series. METHODS Nine patients from 5 unrelated Japanese families were studied. Five patients had the m1 variant homozygously, and 4 patients had the m1 variant compound heterozygously with another frameshift variant (c.4196delG/p.Cys1399Leufs*5). Ophthalmic examinations including adaptive optics (AO) fundus imaging were performed periodically. RESULTS The fundus photographs, fundus autofluorescence (FAF) images, and optical coherence tomographic (OCT) images indicated severe retinal degeneration in all the patients involving the macula even at a young age (20 s). The areas of surviving photoreceptors in the central macula were seen as hyper-autofluorescent regions in the FAF images and preserved outer retinal structure in the OCT images; they were identifiable in the AO fundus images in 8 eyes. The borders of the surviving photoreceptor areas were surrounded by hyporeflective clumps, presumably containing melanin, and the size of these areas decreased progressively during the 4-year follow-up period. The disappearance of the surviving photoreceptor areas was associated with complete blindness. CONCLUSION Patients with RP associated with the m1 variant have a progressive and severe retinal degeneration that begins at an early age. Monitoring the surviving photoreceptor areas by AO fundus imaging can provide a more precise pathological record of retinal degeneration.
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Affiliation(s)
- Shinji Ueno
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya, 466-8550, Japan.
| | - Yoshito Koyanagi
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya, 466-8550, Japan.,Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Taro Kominami
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yasuki Ito
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Kenichi Kawano
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Koji M Nishiguchi
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Toru Nakazawa
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Koh-Hei Sonoda
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroko Terasaki
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya, 466-8550, Japan
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48
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Henry LK, Ansar M, Ranza E, Shetty M, Paracha SA, Azam M, Kern I, Iwaszkiewicz J, Farooq O, Pournaras CJ, Malcles A, Kecik M, Muzaffar W, Qurban A, Ali L, Aggoun Y, Santoni FA, Makrythanasis P, Ahmed J, Qamar R, Rivolta C, Sarwar MT, Antonarakis SE. Identification, Characterization, and Treatment for a Taurine Transporter (SLC6A6) Variant Resulting in Taurine Deficiency and Pathologies in a Consanguineous Family. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.06466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- L. Keith Henry
- University of North Dakota School of Medicine and Health Sciences
| | | | | | - Madhur Shetty
- University of North Dakota School of Medicine and Health Sciences
| | | | | | - Ilse Kern
- Geneva University Childrens Hospitals
| | | | - Omer Farooq
- Bahria University Medical and Dental College
| | | | | | | | | | | | | | | | | | | | | | | | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel
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Ascari G, Peelman F, Farinelli P, Rosseel T, Lambrechts N, Wunderlich KA, Wagner M, Nikopoulos K, Martens P, Balikova I, Derycke L, Holtappels G, Krysko O, Van Laethem T, De Jaegere S, Guillemyn B, De Rycke R, De Bleecker J, Creytens D, Van Dorpe J, Gerris J, Bachert C, Neuhofer C, Walraedt S, Bischoff A, Pedersen LB, Klopstock T, Rivolta C, Leroy BP, De Baere E, Coppieters F. Functional characterization of the first missense variant in CEP78, a founder allele associated with cone-rod dystrophy, hearing loss, and reduced male fertility. Hum Mutat 2020; 41:998-1011. [PMID: 31999394 PMCID: PMC7187288 DOI: 10.1002/humu.23993] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/27/2019] [Accepted: 01/16/2020] [Indexed: 12/19/2022]
Abstract
Inactivating variants in the centrosomal CEP78 gene have been found in cone-rod dystrophy with hearing loss (CRDHL), a particular phenotype distinct from Usher syndrome. Here, we identified and functionally characterized the first CEP78 missense variant c.449T>C, p.(Leu150Ser) in three CRDHL families. The variant was found in a biallelic state in two Belgian families and in a compound heterozygous state-in trans with c.1462-1G>T-in a third German family. Haplotype reconstruction showed a founder effect. Homology modeling revealed a detrimental effect of p.(Leu150Ser) on protein stability, which was corroborated in patients' fibroblasts. Elongated primary cilia without clear ultrastructural abnormalities in sperm or nasal brushes suggest impaired cilia assembly. Two affected males from different families displayed sperm abnormalities causing infertility. One of these is a heterozygous carrier of a complex allele in SPAG17, a ciliary gene previously associated with autosomal recessive male infertility. Taken together, our data indicate that a missense founder allele in CEP78 underlies the same sensorineural CRDHL phenotype previously associated with inactivating variants. Interestingly, the CEP78 phenotype has been possibly expanded with male infertility. Finally, CEP78 loss-of-function variants may have an underestimated role in misdiagnosed Usher syndrome, with or without sperm abnormalities.
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Affiliation(s)
- Giulia Ascari
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Frank Peelman
- Department of Medical Protein Research, Faculty of Medicine and Health Sciences, Flanders Institute for Biotechnology (VIB), Ghent University, Ghent, Belgium
| | - Pietro Farinelli
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Toon Rosseel
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Nina Lambrechts
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Kirsten A Wunderlich
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland.,Department of Physiological Genomics, BMC, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Matias Wagner
- Institute of Human Genetics, Faculty of Medicine, Technical University of Munich, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.,Institut für Neurogenomik, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Konstantinos Nikopoulos
- Oncogenomics laboratory, Department of Hematology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Pernille Martens
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Irina Balikova
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium.,Department of Ophthalmology, University Hospital Leuven, Leuven, Belgium
| | - Lara Derycke
- Upper Airways Research Laboratory, Department Otorhinolaryngology, Ghent University Hospital, Ghent, Belgium
| | - Gabriële Holtappels
- Upper Airways Research Laboratory, Department Otorhinolaryngology, Ghent University Hospital, Ghent, Belgium
| | - Olga Krysko
- Upper Airways Research Laboratory, Department Otorhinolaryngology, Ghent University Hospital, Ghent, Belgium
| | - Thalia Van Laethem
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Sarah De Jaegere
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Brecht Guillemyn
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Riet De Rycke
- Department of Biomedical Molecular Biology and Expertise Centre for Transmission Electron Microscopy, Ghent University, Ghent, Belgium.,VIB Center for Inflammation Research and BioImaging Core, VIB, Ghent, Belgium
| | - Jan De Bleecker
- Department of Neurology, Ghent University Hospital, Ghent, Belgium
| | - David Creytens
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Jan Gerris
- Department of Human Structure and Repair, Ghent University Hospital, Ghent, Belgium
| | - Claus Bachert
- Upper Airways Research Laboratory, Department Otorhinolaryngology, Ghent University Hospital, Ghent, Belgium
| | - Christiane Neuhofer
- Institute of Human Genetics, University Medical Center Göttingen (UMG), Göttingen, Germany
| | - Sophie Walraedt
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
| | - Almut Bischoff
- Department of Neurology, Friedrich-Baur-Institute, Ludwig-Maximilians-University, Munich, Germany
| | - Lotte B Pedersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institute, Ludwig-Maximilians-University, Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Carlo Rivolta
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland.,Clinical Research Center, Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University Hospital Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Bart P Leroy
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium.,Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium.,Division of Ophthalmology and Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elfride De Baere
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Frauke Coppieters
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
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50
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Bastos F, Quinodoz M, Addor MC, Royer-Bertrand B, Fodstad H, Rivolta C, Poloni C, Superti-Furga A, Roulet-Perez E, Lebon S. Childhood neurodegeneration associated with a specific UBTF variant: a new case report and review of the literature. BMC Neurol 2020; 20:17. [PMID: 31931739 PMCID: PMC6958716 DOI: 10.1186/s12883-019-1586-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 12/22/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND A new monogenic neurodegenerative disease affecting ribosomal metabolism has recently been identified in association with a monoallelic UBTF putative gain of function variant (NM_001076683.1:c.628G>A, hg19). Phenotype is consistent among these probands with progressive motor, cognitive, and behavioural regression in early to middle childhood. CASE PRESENTATION We report on a child with this monoallelic UBTF variant who presented with progressive disease including regression, episodes of subacute deterioration during febrile illnesses and a remarkable EEG pattern with a transient pattern of semi-periodic slow waves. CONCLUSIONS This case further supports the phenotype-genotype correlation of neurodegeneration associated with UBTF c.628G>A. Moreover, it brings new insights into the clinical features and EEG that could possibly serve as diagnostic markers of this otherwise nonspecific phenotype.
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Affiliation(s)
- Filipa Bastos
- Department woman-mother-child, Unit of Paediatric Neurology and Neurorehabilitation, Lausanne University Hospital (CHUV), Rue du Bugnon 21, 1011, Lausanne, Switzerland. .,Great Ormond Street Hospital Institute of Child Health, University College London, 30 Guilford Steet, London, WC1N 1EH, United Kingdom.
| | - Mathieu Quinodoz
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Rue du Bugnon 27, 1011, Lausanne, Switzerland
| | - Marie-Claude Addor
- Department of Medecine, Division of Genetic Medicine, Lausanne University Hospital (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Beryl Royer-Bertrand
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Rue du Bugnon 27, 1011, Lausanne, Switzerland.,Department of Medecine, Division of Genetic Medicine, Lausanne University Hospital (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Heidi Fodstad
- Department of Medecine, Division of Genetic Medicine, Lausanne University Hospital (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Carlo Rivolta
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Rue du Bugnon 27, 1011, Lausanne, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, United Kingdom
| | - Claudia Poloni
- Department woman-mother-child, Unit of Paediatric Neurology and Neurorehabilitation, Lausanne University Hospital (CHUV), Rue du Bugnon 21, 1011, Lausanne, Switzerland.,Department of Paediatrics, Sion Hospital, Avenue Grand-Champsec 80, 1950, Sion, Switzerland
| | - Andrea Superti-Furga
- Department of Medecine, Division of Genetic Medicine, Lausanne University Hospital (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Eliane Roulet-Perez
- Department woman-mother-child, Unit of Paediatric Neurology and Neurorehabilitation, Lausanne University Hospital (CHUV), Rue du Bugnon 21, 1011, Lausanne, Switzerland
| | - Sebastien Lebon
- Department woman-mother-child, Unit of Paediatric Neurology and Neurorehabilitation, Lausanne University Hospital (CHUV), Rue du Bugnon 21, 1011, Lausanne, Switzerland
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