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Hiraoka M, Urakawa Y, Kawai K, Yoshida A, Hosakawa J, Takazawa M, Inaba A, Yokota S, Hirami Y, Takahashi M, Ohara O, Kurimoto Y, Maeda A. Copy number variant detection using next-generation sequencing in EYS-associated retinitis pigmentosa. PLoS One 2024; 19:e0305812. [PMID: 38913662 PMCID: PMC11195993 DOI: 10.1371/journal.pone.0305812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/05/2024] [Indexed: 06/26/2024] Open
Abstract
Retinitis pigmentosa (RP) is the most common inherited retinal dystrophy and a major cause of blindness. RP is caused by several variants of multiple genes, and genetic diagnosis by identifying these variants is important for optimizing treatment and estimating patient prognosis. Next-generation sequencing (NGS), which is currently widely used for diagnosis, is considered useful but is known to have limitations in detecting copy number variations (CNVs). In this study, we re-evaluated CNVs in EYS, the main causative gene of RP, identified via NGS using multiplex ligation-dependent probe amplification (MLPA). CNVs were identified in NGS samples of eight patients. To identify potential CNVs, MLPA was also performed on samples from 42 patients who were undiagnosed by NGS but carried one of the five major pathogenic variants reported in Japanese EYS-RP cases. All suspected CNVs based on NGS data in the eight patients were confirmed via MLPA. CNVs were found in 2 of the 42 NGS-undiagnosed RP cases. Furthermore, results showed that 121 of the 661 patients with RP had EYS as the causative gene, and 8.3% (10/121 patients with EYS-RP) had CNVs. Although NGS using the CNV calling criteria utilized in this study failed to identify CNVs in two cases, no false-positive results were detected. Collectively, these findings suggest that NGS is useful for CNV detection during clinical diagnosis of RP.
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Affiliation(s)
- Masakazu Hiraoka
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe, Japan
- Department of Ophthalmology, Kawasaki Medical School, Kurashiki, Okayama, Japan
| | - Yusaku Urakawa
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe, Japan
- Department of Ophthalmology, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Kanako Kawai
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe, Japan
| | - Akiko Yoshida
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe, Japan
| | - Junichi Hosakawa
- Department of Frontier Research and Development, Laboratory of Medical Omics Research, Kazusa DNA Research Institute, Chiba, Japan
| | - Masaki Takazawa
- Department of Frontier Research and Development, Laboratory of Medical Omics Research, Kazusa DNA Research Institute, Chiba, Japan
| | - Akira Inaba
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe, Japan
| | - Satoshi Yokota
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe, Japan
- Department of Ophthalmology, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Yasuhiko Hirami
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe, Japan
- Department of Ophthalmology, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Masayo Takahashi
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe, Japan
- Vision Care Inc., Kobe, Japan
- Research Organization of Science and Technology SR Center, Ritsumeikan University, Shiga, Japan
| | - Osamu Ohara
- Department of Frontier Research and Development, Laboratory of Medical Omics Research, Kazusa DNA Research Institute, Chiba, Japan
| | - Yasuo Kurimoto
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe, Japan
- Department of Ophthalmology, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Akiko Maeda
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe, Japan
- Department of Ophthalmology, Kobe City Medical Center General Hospital, Kobe, Japan
- Research Organization of Science and Technology SR Center, Ritsumeikan University, Shiga, Japan
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Daher A, Banjak M, Noureldine J, Nehme J, El Shamieh S. Genotype-phenotype associations in CRB1 bi-allelic patients: a novel mutation, a systematic review and meta-analysis. BMC Ophthalmol 2024; 24:167. [PMID: 38622537 PMCID: PMC11017593 DOI: 10.1186/s12886-024-03419-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 03/29/2024] [Indexed: 04/17/2024] Open
Abstract
PURPOSE The goal of the study was to search for novel bi-allelic CRB1 mutations, and then to analyze the CRB1 literature at the genotypic and phenotypic levels. APPROACH We screened various variables such as the CRB1 mutation types, domains, exons, and genotypes and their relation with specific ocular phenotypes. An emphasis was given to the bi-allelic missense and nonsense mutations because of their high prevalence compared to other mutation types. Finally, we quantified the effect of various non-modifiable factors over the best-corrected visual acuity oculus uterque (BCVA OU) using multivariate linear regression models and identified genetic interactions. RESULTS A novel bi-allelic missense in the exon 9 of CRB1; c.2936G > A; p.(Gly979Asp) was found to be associated with rod-cone dystrophy (RCD). CRB1 mutation type, exons, domains, and genotype distribution varied significantly according to fundus characteristics, such as peripheral pigmentation and condition, optic disc, vessels, macular condition, and pigmentation (P < 0.05). Of the 154 articles retrieved from PubMed, 96 studies with 439 bi-allelic CRB1 patients were included. Missense mutations were significantly associated with an absence of macular pigments, pale optic disc, and periphery pigmentation, resulting in a higher risk of RCD (P < 0.05). In contrast, homozygous nonsense mutations were associated with macular pigments, periphery pigments, and a high risk of LCA (P < 0.05) and increased BCVA OU levels. We found that age, mutation types, and inherited retinal diseases were critical determinants of BCVA OU as they significantly increased it by 33% 26%, and 38%, respectively (P < 0.05). Loss of function alleles additively increased the risk of LCA, with nonsense having a more profound effect than indels. Finally, our analysis showed that p.(Cys948Tyr) and p.(Lys801Ter) and p.(Lys801Ter); p.(Cys896Ter) might interact to modify BCVA OU levels. CONCLUSION This meta-analysis updated the literature and identified genotype-phenotype associations in bi-allelic CRB1 patients.
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Affiliation(s)
- Ahmad Daher
- Medical Testing Laboratory, Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
| | - Malak Banjak
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Jinane Noureldine
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Joseph Nehme
- Faculty of Medicine, Holy Spirit University of Kaslik (USEK), Jounieh, Lebanon
| | - Said El Shamieh
- Medical Testing Laboratory, Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon.
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Jaffal L, Joumaa H, Noureldine J, Banjak M, Ibrahim M, Mrad Z, Salami A, Shamieh SE. The genetic landscape of inherited retinal dystrophies in Arabs. BMC Med Genomics 2023; 16:89. [PMID: 37127645 PMCID: PMC10150479 DOI: 10.1186/s12920-023-01518-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 04/13/2023] [Indexed: 05/03/2023] Open
Abstract
Inherited retinal dystrophies (IRDs) are a major cause of vision loss. Altogether are highly heterogeneous genotypically and phenotypically, exhibiting substantial differences worldwide. To shed more light on these conditions, we investigated the genetic and phenotypic landscape of IRDs in the Arabs globally and per country.We analyzed 1,621 affected individuals from 16 Arabic countries reported in 198 articles. At the phenotypic level, rod-cone dystrophy (RCD) and Usher syndrome were the most prevalent conditions among non-syndromic and syndromic IRDs. At the gene level, TULP1, ABCA4, RP1, CRB1, MYO7A, RPE65, KCNV2, and IMPG2 were the most mutated genes. Interestingly, all except CRB1 were highly prevalent because they harbored founder mutations, implying that consanguinity is a major determinant in Arab countries. Of note, ~ 93% of the investigated individuals carried homozygous mutations. The country analysis for the IRDs conditions and their associated genotypes revealed that whereas Leber Congenital Amaurosis, RCD, and USHER syndrome were widely distributed, bestrophinopathies and non-syndromic hearing loss were restricted to specific countries (till now).This study could be a starting point for initiating suitable health policies towards IRDs in the Arab world. The high degree of homozygosity urges the need for genetic counsellors to provide personalized information and support the affected individuals.
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Affiliation(s)
- Lama Jaffal
- Department of Biological and Chemical Sciences, School of Arts and Sciences, Lebanese International University, Beirut, Lebanon
| | - Hawraa Joumaa
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Jinane Noureldine
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Malak Banjak
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Mariam Ibrahim
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Zamzam Mrad
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Ali Salami
- Department of Mathematics, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Said El Shamieh
- Molecular Testing Laboratory, Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon.
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Lee BJH, Tham YC, Tan TE, Bylstra Y, Lim WK, Jain K, Chan CM, Mathur R, Cheung CMG, Fenner BJ. Characterizing the genotypic spectrum of retinitis pigmentosa in East Asian populations: a systematic review. Ophthalmic Genet 2023; 44:109-118. [PMID: 36856324 DOI: 10.1080/13816810.2023.2182329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
BACKGROUND Ongoing trials for retinitis pigmentosa (RP) are genotype-specific, with most trials conducted on European cohorts. Due to genetic differences across diverse ancestries and populations, these therapies may not be efficacious in East Asians. MATERIALS AND METHODS A literature search was conducted from 1966 to September 2022 for cohort studies on East Asian populations reporting on non-syndromic RP genotypes and variants. Population-weighted prevalence was used to determine the genotypes and individual variants across the entire cohort. The carrier prevalence of common variants was compared against those in Europe. RESULTS A total of 12 articles describing 2,932 clinically diagnosed East Asian RP probands were included. We identified 876 variants across 54 genes. The most common genotypes included USH2A, EYS, RPGR, ABCA4, PRPF31, RHO, RP1, RP2, PDE6B and SNRNP200, with USH2A as the most common (17.1%). Overall, 60.5% of probands with clinically relevant variants were found to have one of the genotypes above, with 543/876 (62.0%) of the variants occurring in these genes. The most frequently reported variant was USH2A missense variant c.2802T>G/p.C934W (4.9%). Carrier prevalence of these variants was significantly different (p < 0.0001) than in Europe. CONCLUSIONS USH2A was the most commonly affected RP gene in this East Asian cohort, although sub-population analysis revealed distinct genotype prevalence patterns. While the genotypes are similar between East Asia and European cohorts, variants are specific to East Asia. The identification of several prevalent variants in USH2A and EYS provides an opportunity for the development of therapeutics that are relevant for East Asia patients.
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Affiliation(s)
- Brian Juin Hsien Lee
- Department of Medical Retina, Singapore National Eye Centre, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Yih-Chung Tham
- Retina Research Group Singapore Eye Research Institute, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Medical School, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Centre for Innovation & Precision Eye Health, Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore
| | - Tien-En Tan
- Department of Medical Retina, Singapore National Eye Centre, Singapore
- Retina Research Group Singapore Eye Research Institute, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Medical School, Singapore
| | - Yasmin Bylstra
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore
| | - Kanika Jain
- POLARIS, Genome Institute of Singapore, Singapore
| | - Choi Mun Chan
- Department of Medical Retina, Singapore National Eye Centre, Singapore
- Retina Research Group Singapore Eye Research Institute, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Medical School, Singapore
| | - Ranjana Mathur
- Department of Medical Retina, Singapore National Eye Centre, Singapore
- Retina Research Group Singapore Eye Research Institute, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Medical School, Singapore
| | - Chui Ming Gemmy Cheung
- Department of Medical Retina, Singapore National Eye Centre, Singapore
- Retina Research Group Singapore Eye Research Institute, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Medical School, Singapore
| | - Beau J Fenner
- Department of Medical Retina, Singapore National Eye Centre, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Retina Research Group Singapore Eye Research Institute, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Medical School, Singapore
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Bodenbender JP, Marino V, Bethge L, Stingl K, Haack TB, Biskup S, Kohl S, Kühlewein L, Dell’Orco D, Weisschuh N. Biallelic Variants in TULP1 Are Associated with Heterogeneous Phenotypes of Retinal Dystrophy. Int J Mol Sci 2023; 24:ijms24032709. [PMID: 36769033 PMCID: PMC9916573 DOI: 10.3390/ijms24032709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
Biallelic pathogenic variants in TULP1 are mostly associated with severe rod-driven inherited retinal degeneration. In this study, we analyzed clinical heterogeneity in 17 patients and characterized the underlying biallelic variants in TULP1. All patients underwent thorough ophthalmological examinations. Minigene assays and structural analyses were performed to assess the consequences of splice variants and missense variants. Three patients were diagnosed with Leber congenital amaurosis, nine with early onset retinitis pigmentosa, two with retinitis pigmentosa with an onset in adulthood, one with cone dystrophy, and two with cone-rod dystrophy. Seventeen different alleles were identified, namely eight missense variants, six nonsense variants, one in-frame deletion variant, and two splice site variants. For the latter two, minigene assays revealed aberrant transcripts containing frameshifts and premature termination codons. Structural analysis and molecular modeling suggested different degrees of structural destabilization for the missense variants. In conclusion, we report the largest cohort of patients with TULP1-associated IRD published to date. Most of the patients exhibited rod-driven disease, yet a fraction of the patients exhibited cone-driven disease. Our data support the hypothesis that TULP1 variants do not fold properly and thus trigger unfolded protein response, resulting in photoreceptor death.
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Affiliation(s)
- Jan-Philipp Bodenbender
- Department for Ophthalmology, University Eye Hospital, University of Tübingen, 72076 Tübingen, Germany
- Correspondence: (J.-P.B.); (N.W.)
| | - Valerio Marino
- Section of Biological Chemistry, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37124 Verona, Italy
| | - Leon Bethge
- Department for Ophthalmology, University Eye Hospital, University of Tübingen, 72076 Tübingen, Germany
| | - Katarina Stingl
- Department for Ophthalmology, University Eye Hospital, University of Tübingen, 72076 Tübingen, Germany
| | - Tobias B. Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, 72076 Tübingen, Germany
| | - Saskia Biskup
- Praxis für Humangenetik, 72076 Tübingen, Germany
- CeGaT GmbH, 72076 Tübingen, Germany
| | - Susanne Kohl
- Department for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, 72076 Tübingen, Germany
| | - Laura Kühlewein
- Department for Ophthalmology, University Eye Hospital, University of Tübingen, 72076 Tübingen, Germany
| | - Daniele Dell’Orco
- Section of Biological Chemistry, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37124 Verona, Italy
| | - Nicole Weisschuh
- Department for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, 72076 Tübingen, Germany
- Correspondence: (J.-P.B.); (N.W.)
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Jaffal L, Ibrahim M, El Shamieh S. Analysis of rod-cone dystrophy genes reveals unique mutational patterns. BMJ OPEN SCIENCE 2022; 6:e100291. [PMID: 36618607 PMCID: PMC9812813 DOI: 10.1136/bmjos-2022-100291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Background Rod-cone dystrophy (RCD) is the most common inherited retinal disease that is characterised by the progressive degeneration of retinal photoreceptors. RCD genes classification is based exclusively on gene mutations' prevalence and does not consider the implication of the same gene in different phenotypes. Therefore, we first investigated the mutations occurrence in autosomal recessive RCD (arRCD) and non-arRCD conditions. Then, finally, we identified arRCD enriched mutational patterns in specific genes and coding exons. Methods and results The mutations patterns differed according to arRCD (p=0.001). Specifically, When compared with missense; insertions/deletions (OR=1.2, p=0.007), nonsense (OR=1.2, p=0.014) and splice-site mutations (OR=1.6, p=0.038) increased the OR of arRCD by 20%-60% versus non-arRCD conditions. The gene-based analysis identified that EYS, IMPG2, RP1L1 and USH2A mutations were enriched in arRCD (p<0.05). The exon-based analysis revealed specific mutation patterns in exons of CRB1, RP1L1 and exons 12, 60 and 62 coding for Lamin EGF and FTIII domains of USH2A. Conclusion The current analysis showed that many aRCD genes have unique mutational patterns.
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Affiliation(s)
- Lama Jaffal
- Department of Biological and Chemical Sciences, School of Arts and Sciences, Lebanese International University, Nabatyeh, Lebanon,Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatyeh, Lebanon
| | - Mariam Ibrahim
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatyeh, Lebanon
| | - Said El Shamieh
- Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
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El Shamieh S, Maltese PE. Editorial: The genetics of inherited retinal diseases in understudied ethnic groups: Novel associations, challenges, and perspectives. Front Genet 2022; 13:990782. [PMID: 36081992 PMCID: PMC9445133 DOI: 10.3389/fgene.2022.990782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Said El Shamieh
- Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
- *Correspondence: Said El Shamieh, ; Paolo Enrico Maltese,
| | - Paolo Enrico Maltese
- Magi’s Lab SRL, Rovereto, Italy
- *Correspondence: Said El Shamieh, ; Paolo Enrico Maltese,
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Bouzidi A, Charoute H, Charif M, Amalou G, Kandil M, Barakat A, Lenaers G. Clinical and genetic spectrums of 413 North African families with inherited retinal dystrophies and optic neuropathies. Orphanet J Rare Dis 2022; 17:197. [PMID: 35551639 PMCID: PMC9097391 DOI: 10.1186/s13023-022-02340-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/26/2022] [Indexed: 11/26/2022] Open
Abstract
Background Inherited retinal dystrophies (IRD) and optic neuropathies (ION) are the two major causes world-wide of early visual impairment, frequently leading to legal blindness. These two groups of pathologies are highly heterogeneous and require combined clinical and molecular diagnoses to be securely identified. Exact epidemiological studies are lacking in North Africa, and genetic studies of IRD and ION individuals are often limited to case reports or to some families that migrated to the rest of the world. In order to improve the knowledge of their clinical and genetic spectrums in North Africa, we reviewed published data, to illustrate the most prevalent pathologies, genes and mutations encountered in this geographical region, extending from Morocco to Egypt, comprising 200 million inhabitants. Main body We compiled data from 413 families with IRD or ION together with their available molecular diagnosis. The proportion of IRD represents 82.8% of index cases, while ION accounted for 17.8%. Non-syndromic IRD were more frequent than syndromic ones, with photoreceptor alterations being the main cause of non-syndromic IRD, represented by retinitis pigmentosa, Leber congenital amaurosis, and cone-rod dystrophies, while ciliopathies constitute the major part of syndromic-IRD, in which the Usher and Bardet Biedl syndromes occupy 41.2% and 31.1%, respectively. We identified 71 ION families, 84.5% with a syndromic presentation, while surprisingly, non-syndromic ION are scarcely reported, with only 11 families with autosomal recessive optic atrophies related to OPA7 and OPA10 variants, or with the mitochondrial related Leber ION. Overall, consanguinity is a major cause of these diseases within North African countries, as 76.1% of IRD and 78.8% of ION investigated families were consanguineous, explaining the high rate of autosomal recessive inheritance pattern compared to the dominant one. In addition, we identified many founder mutations in small endogamous communities. Short conclusion As both IRD and ION diseases constitute a real public health burden, their under-diagnosis in North Africa due to the absence of physicians trained to the identification of inherited ophthalmologic presentations, together with the scarcity of tools for the molecular diagnosis represent major political, economic and health challenges for the future, to first establish accurate clinical diagnoses and then treat patients with the emergent therapies. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02340-7.
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Affiliation(s)
- Aymane Bouzidi
- Equipe MitoLab, Unité MitoVasc, INSERM U1083, CHU d'Angers, CNRS 6015, Université d'Angers, 49933, Angers, France.,Genomics and Human Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco.,Team of Anthropogenetics and Biotechnologies, Faculty of Sciences, Chouaïb Doukkali University, Eljadida, Morocco
| | - Hicham Charoute
- Research Unit of Epidemiology, Biostatistics and Bioinformatics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Majida Charif
- Genetics, and Immuno-Cell Therapy Team, Mohamed First University, Oujda, Morocco
| | - Ghita Amalou
- Equipe MitoLab, Unité MitoVasc, INSERM U1083, CHU d'Angers, CNRS 6015, Université d'Angers, 49933, Angers, France.,Genomics and Human Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco.,Team of Anthropogenetics and Biotechnologies, Faculty of Sciences, Chouaïb Doukkali University, Eljadida, Morocco
| | - Mostafa Kandil
- Team of Anthropogenetics and Biotechnologies, Faculty of Sciences, Chouaïb Doukkali University, Eljadida, Morocco
| | - Abdelhamid Barakat
- Genomics and Human Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Guy Lenaers
- Equipe MitoLab, Unité MitoVasc, INSERM U1083, CHU d'Angers, CNRS 6015, Université d'Angers, 49933, Angers, France. .,Service de Neurologie, CHU d'Angers, Angers, France.
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Jaffal L, Mrad Z, Ibrahim M, Salami A, Audo I, Zeitz C, El Shamieh S. The research output of rod-cone dystrophy genetics. Orphanet J Rare Dis 2022; 17:175. [PMID: 35461258 PMCID: PMC9034540 DOI: 10.1186/s13023-022-02318-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 04/09/2022] [Indexed: 11/10/2022] Open
Abstract
Non-syndromic rod-cone dystrophy (RCD) is the most common condition in inherited retinal diseases. The aim of this study was to evaluate the research output and productivity related to RCD genetics per countries as classified by the human development index (HDI), by analyzing publication frequency and citations, the choice of journals and publishers, since 2000 to date. We have also analyzed the use of next-generation sequencing (NGS) in publications originating from countries with different HDIs. One thousand four hundred articles focusing on non-syndromic RCD were downloaded and analyzed. Citations and published articles were adjusted per one million individuals. The research output is significantly higher in very high HDI countries (86% of the total publications and 95% of the citations) than countries with lower HDIs in all aspects. High and medium HDI countries published together 13.6% of the total articles worldwide and received 4.6% of the citations. On the publication level, the USA (26%), United Kingdom (10%), and Japan (7%) were the top 3 among very high HDI countries, while China (6%) and India (2%) ranked first in high and medium HDI countries respectively. On the citation level, similar profiles were found. Following adjustment for population size, Switzerland (~14%), Jordan (~ 1%) and Morocco (<0.2%) showed the highest rates of publications in very high, high and medium HDI countries respectively. Very high HDI countries published 71% of their papers in first quartile journals (first quartile in Scimago journal rank; Q1), and 23% in Q2 journals. High and medium HDI countries showed a similar profile in quartiles with ~ 40% of their papers published in Q1 journals and ~ 30% in Q2 journals. The first publication using NGS was issued in 2009 in very high HDI countries, while it appeared in 2012 in high HDI countries, and in 2017 in medium HDI countries, with a respective lag of 3 to 8 years compared to very high HDI countries. A profound gap exists between very high HDI countries and the rest of the world. To fill it in, we propose implementing NGS, supporting international collaborations, building capacities and infrastructures, improving accessibility of patients to services, and increasing national and international funding.
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Affiliation(s)
- Lama Jaffal
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon.,Department of Biological and Chemical Sciences, School of Arts and Sciences, Lebanese International University, Beirut, Lebanon
| | - Zamzam Mrad
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Mariam Ibrahim
- Rammal Hassan Rammal Research Laboratory, PhyToxE Research Group, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Ali Salami
- Department of Mathematics, Faculty of Sciences, Lebanese University, Nabatieh, Lebanon
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de La Vision, Paris, France.,CHNO Des Quinze-Vingts, INSERM-DGOS CIC1423, Paris, France.,University College London Institute of Ophthalmology, London, UK
| | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de La Vision, Paris, France
| | - Said El Shamieh
- Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon.
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Shen-Sampas JH, Duret S, Duncan JL. Retinal Degeneration Secondary to MERTK Mutations: Potential Candidate for Gene Therapy. Int Ophthalmol Clin 2021; 61:143-148. [PMID: 34584051 PMCID: PMC8486302 DOI: 10.1097/iio.0000000000000374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Perea-Romero I, Gordo G, Iancu IF, Del Pozo-Valero M, Almoguera B, Blanco-Kelly F, Carreño E, Jimenez-Rolando B, Lopez-Rodriguez R, Lorda-Sanchez I, Martin-Merida I, Pérez de Ayala L, Riveiro-Alvarez R, Rodriguez-Pinilla E, Tahsin-Swafiri S, Trujillo-Tiebas MJ, Garcia-Sandoval B, Minguez P, Avila-Fernandez A, Corton M, Ayuso C. Genetic landscape of 6089 inherited retinal dystrophies affected cases in Spain and their therapeutic and extended epidemiological implications. Sci Rep 2021; 11:1526. [PMID: 33452396 PMCID: PMC7810997 DOI: 10.1038/s41598-021-81093-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/31/2020] [Indexed: 02/08/2023] Open
Abstract
Inherited retinal diseases (IRDs), defined by dysfunction or progressive loss of photoreceptors, are disorders characterized by elevated heterogeneity, both at the clinical and genetic levels. Our main goal was to address the genetic landscape of IRD in the largest cohort of Spanish patients reported to date. A retrospective hospital-based cross-sectional study was carried out on 6089 IRD affected individuals (from 4403 unrelated families), referred for genetic testing from all the Spanish autonomous communities. Clinical, demographic and familiar data were collected from each patient, including family pedigree, age of appearance of visual symptoms, presence of any systemic findings and geographical origin. Genetic studies were performed to the 3951 families with available DNA using different molecular techniques. Overall, 53.2% (2100/3951) of the studied families were genetically characterized, and 1549 different likely causative variants in 142 genes were identified. The most common phenotype encountered is retinitis pigmentosa (RP) (55.6% of families, 2447/4403). The most recurrently mutated genes were PRPH2, ABCA4 and RS1 in autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL) NON-RP cases, respectively; RHO, USH2A and RPGR in AD, AR and XL for non-syndromic RP; and USH2A and MYO7A in syndromic IRD. Pathogenic variants c.3386G > T (p.Arg1129Leu) in ABCA4 and c.2276G > T (p.Cys759Phe) in USH2A were the most frequent variants identified. Our study provides the general landscape for IRD in Spain, reporting the largest cohort ever presented. Our results have important implications for genetic diagnosis, counselling and new therapeutic strategies to both the Spanish population and other related populations.
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Affiliation(s)
- 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 Gordo
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Ionut 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
| | - Marta Del Pozo-Valero
- 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
| | - Berta Almoguera
- 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
| | - Fiona 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
| | - Ester Carreño
- Department of Ophthalmology, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Belen Jimenez-Rolando
- Department of Ophthalmology, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Rosario Lopez-Rodriguez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Isabel 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
| | - Inmaculada 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
| | - Lucia Pérez de Ayala
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Rosa Riveiro-Alvarez
- 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
| | - Elvira Rodriguez-Pinilla
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Saoud 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
| | - Maria 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
| | | | | | | | - Blanca Garcia-Sandoval
- 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
| | - Pablo 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
| | - Almudena 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
| | - 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.
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