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3. Cost-effective sequence analysis of 113 genes in 1,192 probands with retinitis pigmentosa and Leber congenital amaurosis

Author

Panneman, Daan M., primary, Hitti-Malin, Rebekkah J., additional, Holtes, Lara K., additional, de Bruijn, Suzanne E., additional, Reurink, Janine, additional, Boonen, Erica G. M., additional, Khan, Muhammad Imran, additional, Ali, Manir, additional, Andréasson, Sten, additional, De Baere, Elfride, additional, Banfi, Sandro, additional, Bauwens, Miriam, additional, Ben-Yosef, Tamar, additional, Bocquet, Béatrice, additional, De Bruyne, Marieke, additional, Cerda, Berta de la, additional, Coppieters, Frauke, additional, Farinelli, Pietro, additional, Guignard, Thomas, additional, Inglehearn, Chris F., additional, Karali, Marianthi, additional, Kjellström, Ulrika, additional, Koenekoop, Robert, additional, de Koning, Bart, additional, Leroy, Bart P., additional, McKibbin, Martin, additional, Meunier, Isabelle, additional, Nikopoulos, Konstantinos, additional, Nishiguchi, Koji M., additional, Poulter, James A., additional, Rivolta, Carlo, additional, Rodríguez de la Rúa, Enrique, additional, Saunders, Patrick, additional, Simonelli, Francesca, additional, Tatour, Yasmin, additional, Testa, Francesco, additional, Thiadens, Alberta A. H. J., additional, Toomes, Carmel, additional, Tracewska, Anna M., additional, Tran, Hoai Viet, additional, Ushida, Hiroaki, additional, Vaclavik, Veronika, additional, Verhoeven, Virginie J. M., additional, van de Vorst, Maartje, additional, Gilissen, Christian, additional, Hoischen, Alexander, additional, Cremers, Frans P. M., additional, and Roosing, Susanne, additional

Published
2023
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4. Cost-effective sequence analysis of 113 genes in 1,192 probands with retinitis pigmentosa and Leber congenital amaurosis

Author

Panneman, Daan M., primary, Hitti-Malin, Rebekkah J., additional, Holtes, Lara K., additional, de Bruijn, Suzanne E., additional, Reurink, Janine, additional, Boonen, Erica G.M., additional, Khan, Muhammad Imran, additional, Ali, Manir, additional, Andréasson, Sten, additional, De Baere, Elfride, additional, Banfi, Sandro, additional, Bauwens, Miriam, additional, Ben-Yosef, Tamar, additional, Bocquet, Béatrice, additional, De Bruyne, Marieke, additional, de la Cerda, Berta, additional, Coppieters, Frauke, additional, Farinelli, Pietro, additional, Guignard, Thomas, additional, Inglehearn, Chris F., additional, Karali, Marianthi, additional, Kjellström, Ulrika, additional, Koenekoop, Robert, additional, de Koning, Bart, additional, Leroy, Bart P., additional, McKibbin, Martin, additional, Meunier, Isabelle, additional, Nikopoulos, Konstantinos, additional, Nishiguchi, Koji M., additional, Poulter, James A., additional, Rivolta, Carlo, additional, Rodríguez de la Rúa, Enrique, additional, Saunders, Patrick, additional, Simonelli, Francesca, additional, Tatour, Yasmin, additional, Testa, Francesco, additional, Thiadens, Alberta A.H.J., additional, Toomes, Carmel, additional, Tracewska, Anna M., additional, Viet Tran, Hoai, additional, Ushida, Hiroaki, additional, Vaclavik, Veronika, additional, Verhoeven, Virginie J.M., additional, van de Vorst, Maartje, additional, Gilissen, Christian, additional, Hoischen, Alexander, additional, Cremers, Frans P.M., additional, and Roosing, Susanne, additional

Published
2022
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8. A novel intronic mutation of PDE6B is a major cause of autosomal recessive retinitis pigmentosa among Caucasus Jews

Author

Tatour, Yasmin, Tamaiev, Jonathan, Shamaly, Shamaly, Colombo, Roberto, Bril, Ephrat, Rabinowitz, Tom, Yaakobi, Alona, Mezer, Eedy, Leibu, Rina, Tiosano, Beatrice, Shomron, Noam, Chowers, Itay, Banin, Eyal, Dror Sharon, and Ben-Yosef, Tamar

Subjects
Adult, Male, PDE6B, lcsh:QH426-470, Gene Expression, Genes, Recessive, Linkage Disequilibrium, Retina, whole exome sequencing, retinitis pigmentosa, Exome Sequencing, Electroretinography, Humans, Frameshift Mutation, lcsh:QH301-705.5, Aged, Cyclic Nucleotide Phosphodiesterases, Type 6, Homozygote, Computational Biology, Exons, Middle Aged, Founder Effect, Introns, Siberia, lcsh:Genetics, lcsh:Biology (General), Jews, Evoked Potentials, Visual, Female, RNA Splice Sites, Tomography, Optical Coherence, Research Article
Abstract

Purpose: To identify the genetic basis for retinitis pigmentosa (RP) in a cohort of Jewish patients from Caucasia. Methods: Patients underwent a detailed ophthalmic evaluation, including funduscopic examination, visual field testing, optical coherence tomography (OCT), and electrophysiological tests, electroretinography (ERG) and visual evoked potentials (VEP). Genetic analysis was performed with a combination of whole exome sequencing (WES) and Sanger sequencing. Bioinformatic analysis of the WES results was performed via a customized pipeline. Pathogenicity of the identified intronic variant was evaluated in silico using the web tool Human Splicing Finder, and in vitro, using a minigene-based splicing assay. Linkage disequilibrium (LD) analysis was used to demonstrate a founder effect, and the decay of LD over generations around the mutation in Caucasus Jewish chromosomes was modeled to estimate the age of the most recent common ancestor. Results: In eight patients with RP from six unrelated families, all of Caucasus Jewish ancestry, we identified a novel homozygous intronic variant, located at position −9 of PDE6B intron 15. The c.1921–9C>G variant was predicted to generate a novel acceptor splice site, nine bases upstream of the original splice site of intron 15. In vitro splicing assay demonstrated that this novel acceptor splice site is used instead of the wild-type site, leading to an 8-bp insertion into exon 16, which is predicted to cause a frameshift. The presence of a common ancestral haplotype in mutation-bearing chromosomes was compatible with a founder effect. Conclusions: The PDE6B c.1921–9C>G intronic mutation is a founder mutation that accounts for at least 40% (6/15 families) of autosomal recessive RP among Caucasus Jews. This result is highly important for molecular diagnosis, carrier screening, and genetic counseling in this population.

Published
2019

10. Parental mosaic cutaneous‐gonadal GJB2 mutation: From epidermal nevus to inherited ichthyosis‐deafness syndrome.

Author

Cohen‐Barak, Eran, Mwassi, Bannan, Zagairy, Fadia, Danial‐Farran, Nada, Khayat, Morad, Tatour, Yasmin, and Ziv, Michael

Abstract

Ichthyosis and deafness syndrome is a group of devastating genodermatoses caused by heterozygous mutations in GJB2, encoding the gap junction protein connexin 26. These syndromes are characterized by severe skin disease, hearing loss, recurrent infections, and cutaneous neoplasms. Cutaneous somatic mutations in the same gene are associated with porokeratotic eccrine ostial dermal duct nevus. Here we report a family in which a parent presented with localized epidermal nevus and his child suffered with hystrix‐like ichthyosis with deafness. Histologic examination of the parent's cutaneous lesion revealed verrucous epidermal nevus without features of porokeratotic eccrine ostial dermal duct nevus. Genetic analysis identified the same pathogenic variant, GJB2 c.148G>A (p.D50N), in DNA extracted from the parent's cutaneous lesion and the child's leukocytes, but not in the parent's leukocytes. This study expands the phenotypic heterogeneity of GJB2 mosaic variants in addition to porokeratotic eccrine ostial dermal duct nevus, and emphasizes the importance of molecular diagnosis of mosaic skin diseases considering the risk of severe inherited diseases in the offspring. [ABSTRACT FROM AUTHOR]

Published
2022
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13. Mutations in SCAPERcause autosomal recessive retinitis pigmentosa with intellectual disability

Author

Tatour, Yasmin, Sanchez-Navarro, Iker, Chervinsky, Elana, Hakonarson, Hakon, Gawi, Haithum, Tahsin-Swafiri, Saoud, Leibu, Rina, Lopez-Molina, Maria Isabel, Fernandez-Sanz, Guillermo, Ayuso, Carmen, and Ben-Yosef, Tamar

Abstract

BackgroundRetinitis pigmentosa (RP) is the most common form of inherited retinal dystrophy, with a worldwide prevalence of 1 in 4000 persons. While in most cases of RP, the disease is limited to the eye (non-syndromic), over 40 forms of syndromic RP have been described.ObjectivesTo identify the genetic basis for syndromic RP in three unrelated families from Israel and Spain.MethodsWhole exome sequencing was conducted in one Israeli and two Spanish families segregating autosomal recessive RP with intellectual disability. Complete ophthalmic examination included best-corrected visual acuity, funduscopy, optical coherence tomography, fluorescein angiography, flash visual evoked potentials, and electroretinography. Reverse transcription (RT)-PCR and immunostaining were used to examine the spatial and temporal expression pattern of SCAPER.ResultsIn all patients, biallelic SCAPERmutations were observed. Clinically, patients with SCAPERmutations show signs of typical RP. In addition, they have mild to moderate intellectual disability and attention-deficit/hyperactivity disorder. SCAPERwas found to be ubiquitously expressed in a wide range of human tissues, including retina and brain. Furthermore, RT-PCR analysis revealed that in both mouse eye and brain, Scaperis expressed as early as embryonic day 14. In the mouse retina, SCAPER is located in multiple layers, including the retinal pigment epithelium, photoreceptor outer and inner segments, the inner plexiform layer and the ganglion cell layer.ConclusionsDeleterious SCAPERmutations were identified in four patients from three unrelated families of different ethnic backgrounds, thereby confirming the involvement of this gene in the aetiology of autosomal recessive syndromic RP.

Published
2017
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14. Cost-effective sequence analysis of 113 genes in 1,192 probands with retinitis pigmentosa and Leber congenital amaurosis

Author

Daan M. Panneman, Rebekkah J. Hitti-Malin, Lara K. Holtes, Suzanne E. de Bruijn, Janine Reurink, Erica G.M. Boonen, Muhammad Imran Khan, Manir Ali, Sten Andréasson, Elfride De Baere, Sandro Banfi, Miriam Bauwens, Tamar Ben-Yosef, Béatrice Bocquet, Marieke De Bruyne, Berta de la Cerda, Frauke Coppieters, Pietro Farinelli, Thomas Guignard, Chris F. Inglehearn, Marianthi Karali, Ulrika Kjellström, Robert Koenekoop, Bart de Koning, Bart P. Leroy, Martin McKibbin, Isabelle Meunier, Konstantinos Nikopoulos, Koji M. Nishiguchi, James A. Poulter, Carlo Rivolta, Enrique Rodríguez de la Rúa, Patrick Saunders, Francesca Simonelli, Yasmin Tatour, Francesco Testa, Alberta A.H.J. Thiadens, Carmel Toomes, Anna M. Tracewska, Hoai Viet Tran, Hiroaki Ushida, Veronika Vaclavik, Virginie J.M. Verhoeven, Maartje van de Vorst, Christian Gilissen, Alexander Hoischen, Frans P.M. Cremers, Susanne Roosing, MUMC+: DA KG Lab Informatica en BIO (9), RS: FHML non-thematic output, Panneman, Daan M., Hitti-Malin, Rebekkah J., Holtes, Lara K., de Bruijn, Suzanne E., Reurink, Janine, Boonen, Erica G. M., Khan, Muhammad Imran, Ali, Manir, Andréasson, Sten, De Baere, Elfride, Banfi, Sandro, Bauwens, Miriam, Ben-Yosef, Tamar, Bocquet, Béatrice, De Bruyne, Marieke, Cerda, Berta de la, Coppieters, Frauke, Farinelli, Pietro, Guignard, Thoma, Inglehearn, Chris F., Karali, Marianthi, Kjellström, Ulrika, Koenekoop, Robert, de Koning, Bart, Leroy, Bart P., Mckibbin, Martin, Meunier, Isabelle, Nikopoulos, Konstantino, Nishiguchi, Koji M., Poulter, James A., Rivolta, Carlo, Rodríguez de la Rúa, Enrique, Saunders, Patrick, Simonelli, Francesca, Tatour, Yasmin, Testa, Francesco, Thiadens, Alberta A. H. J., Toomes, Carmel, Tracewska, Anna M., Tran, Hoai Viet, Ushida, Hiroaki, Vaclavik, Veronika, Verhoeven, Virginie J. M., van de Vorst, Maartje, Gilissen, Christian, Hoischen, Alexander, Cremers, Frans P. M., and Roosing, Susanne

Subjects
Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], targeted gene sequencing, MUTATIONS, cost-effective, inherited retinal diseases, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Biology and Life Sciences, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], Cell Biology, VARIANTS, RETINAL DYSTROPHY, Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12], All institutes and research themes of the Radboud University Medical Center, smMIPs, high-throughput, Developmental Biology
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.

Published
2023

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