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Fernández-Suárez E, González-del Pozo M, García-Núñez A, Méndez-Vidal C, Martín-Sánchez M, Mejías-Carrasco JM, Ramos-Jiménez M, Morillo-Sánchez MJ, Rodríguez-de la Rúa E, Borrego S, Antiñolo G. Expanding the phenotype of THRB: a range of macular dystrophies as the major clinical manifestations in patients with a dominant splicing variant. Front Cell Dev Biol 2023; 11:1197744. [PMID: 37547476 PMCID: PMC10401274 DOI: 10.3389/fcell.2023.1197744] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/27/2023] [Indexed: 08/08/2023] Open
Abstract
Inherited retinal dystrophies (IRDs) are a clinically and genetically heterogeneous group of disorders that often severely impair vision. Some patients manifest poor central vision as the first symptom due to cone-dysfunction, which is consistent with cone dystrophy (COD), Stargardt disease (STGD), or macular dystrophy (MD) among others. Here, we aimed to identify the genetic cause of autosomal dominant COD in one family. WGS was performed in 3 affected and 1 unaffected individual using the TruSeq Nano DNA library kit and the NovaSeq 6,000 platform (Illumina). Data analysis identified a novel spliceogenic variant (c.283 + 1G>A) in the thyroid hormone receptor beta gene (THRB) as the candidate disease-associated variant. Further genetic analysis revealed the presence of the same heterozygous variant segregating in two additional unrelated dominant pedigrees including 9 affected individuals with a diagnosis of COD (1), STGD (4), MD (3) and unclear phenotype (1). THRB has been previously reported as a causal gene for autosomal dominant and recessive thyroid hormone resistance syndrome beta (RTHβ); however, none of the IRD patients exhibited RTHβ. Genotype-phenotype correlations showed that RTHβ can be caused by both truncating and missense variants, which are mainly located at the 3' (C-terminal/ligand-binding) region, which is common to both THRB isoforms (TRβ1 and TRβ2). In contrast, the c.283 + 1G>A variant is predicted to disrupt a splice site in the 5'-region of the gene that encodes the N-terminal domain of the TRβ1 isoform protein, leaving the TRβ2 isoform intact, which would explain the phenotypic variability observed between RTHβ and IRD patients. Interestingly, although monochromacy or cone response alterations have already been described in a few RTHβ patients, herein we report the first genetic association between a pathogenic variant in THRB and non-syndromic IRDs. We thereby expand the phenotype of THRB pathogenic variants including COD, STGD, or MD as the main clinical manifestation, which also reflects the extraordinary complexity of retinal functions mediated by the different THRB isoforms.
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Affiliation(s)
- Elena Fernández-Suárez
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - María González-del Pozo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Alejandro García-Núñez
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
| | - Cristina Méndez-Vidal
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Marta Martín-Sánchez
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - José Manuel Mejías-Carrasco
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
| | - Manuel Ramos-Jiménez
- Department of Clinical Neurophysiology, University Hospital Virgen Macarena, Seville, Spain
| | | | - Enrique Rodríguez-de la Rúa
- Department of Ophthalmology, University Hospital Virgen Macarena, Seville, Spain
- RETICS Patología Ocular, OFTARED, Instituto de Salud Carlos III, Madrid, Spain
| | - Salud Borrego
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Guillermo Antiñolo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/Spanish National Research Council (CSIC)/University of Seville, Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
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de Borja Domínguez-Serrano F, Soto-Sierra M, González-del Pozo M, Morillo-Sánchez MJ, Ramos-Jiménez M, López-Domínguez M, Ponte-Zuñiga B, Antiñolo-Gil G, Rodríguez de la Rúa-Franch E. X-linked Retinoschisis Associated with Retinitis Punctata Albescens Caused by a Mutation in the RS1 Gene: A Family Study. Open Ophthalmol J 2021. [DOI: 10.2174/1874364102115010201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Purpose:
To describe the clinical and genetic characteristics (mutation in RS1 gene) of a Spanish family with X-linked retinoschisis (XLRS) associated with retinitis punctata albescens (RPA).
Methods:
The detailed ophthalmological examination included best corrected visual acuity (BCVA), colour and autofluorescence photography, fluorescein angiography, optical coherence tomography and electrophysiology tests. A next-generation sequencing (NGS) strategy was applied to the index patient, and then sequenced in an Illumina NextSeq500 system. Candidate variants considered to be disease-causing in the patient were confirmed and segregated in the family by Sanger sequencing.
Results:
We have studied three siblings of 54, 59 and 50 years old. Two of them presented with macular foveoschisis and a whitish mottling of the pigment epithelium in the peripheral and equatorial retina, while the other had macular atrophy. Electroretinography revealed a reduced b-wave, while a-wave remained unchanged. Mutation in RS1 (c.98G>A; p.Trp33*) was identified as the cause of the disease.
Conclusion:
XLRS is a genetic disease that leads to irreversible visual loss. We describe an unusual phenotype manifestation of a known mutation.
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Martín-Sánchez M, Bravo-Gil N, González-del Pozo M, Méndez-Vidal C, Fernández-Suárez E, Rodríguez-de la Rúa E, Borrego S, Antiñolo G. A Multi-Strategy Sequencing Workflow in Inherited Retinal Dystrophies: Routine Diagnosis, Addressing Unsolved Cases and Candidate Genes Identification. Int J Mol Sci 2020; 21:E9355. [PMID: 33302505 PMCID: PMC7763277 DOI: 10.3390/ijms21249355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 11/18/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 01/17/2023] Open
Abstract
The management of unsolved inherited retinal dystrophies (IRD) cases is challenging since no standard pipelines have been established. This study aimed to define a diagnostic algorithm useful for the diagnostic routine and to address unsolved cases. Here, we applied a Next-Generation Sequencing-based workflow, including a first step of panel sequencing (PS) followed by clinical-exome sequencing (CES) and whole-exome sequencing (WES), in 46 IRD patients belonging to 42 families. Twenty-six likely causal variants in retinal genes were found by PS and CES. CES and WES allowed proposing two novel candidate loci (WDFY3 and a X-linked region including CITED1), both abundantly expressed in human retina according to RT-PCR and immunohistochemistry. After comparison studies, PS showed the best quality and cost values, CES and WES involved similar analytical efforts and WES presented the highest diagnostic yield. These results reinforce the relevance of panels as a first step in the diagnostic routine and suggest WES as the next strategy for unsolved cases, reserving CES for the simultaneous study of multiple conditions. Standardizing this algorithm would enhance the efficiency and equity of clinical genetics practice. Furthermore, the identified candidate genes could contribute to increase the diagnostic yield and expand the mutational spectrum in these disorders.
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Affiliation(s)
- Marta Martín-Sánchez
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (M.M.-S.); (N.B.-G.); (M.G.-d.P.); (C.M.-V.); (E.F.-S.); (S.B.)
| | - Nereida Bravo-Gil
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (M.M.-S.); (N.B.-G.); (M.G.-d.P.); (C.M.-V.); (E.F.-S.); (S.B.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 41013 Seville, Spain
| | - María González-del Pozo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (M.M.-S.); (N.B.-G.); (M.G.-d.P.); (C.M.-V.); (E.F.-S.); (S.B.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 41013 Seville, Spain
| | - Cristina Méndez-Vidal
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (M.M.-S.); (N.B.-G.); (M.G.-d.P.); (C.M.-V.); (E.F.-S.); (S.B.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 41013 Seville, Spain
| | - Elena Fernández-Suárez
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (M.M.-S.); (N.B.-G.); (M.G.-d.P.); (C.M.-V.); (E.F.-S.); (S.B.)
| | - Enrique Rodríguez-de la Rúa
- Department of Ophthalmology, University Hospital Virgen Macarena, 41013 Seville, Spain;
- Retics Patologia Ocular, OFTARED, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Salud Borrego
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (M.M.-S.); (N.B.-G.); (M.G.-d.P.); (C.M.-V.); (E.F.-S.); (S.B.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 41013 Seville, Spain
| | - Guillermo Antiñolo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (M.M.-S.); (N.B.-G.); (M.G.-d.P.); (C.M.-V.); (E.F.-S.); (S.B.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 41013 Seville, Spain
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González-del Pozo M, Bravo-Gil N, Méndez-Vidal C, Montero-de-Espinosa I, Millán JM, Dopazo J, Borrego S, Antiñolo G. Re-evaluation casts doubt on the pathogenicity of homozygousUSH2Ap.C759F. Am J Med Genet A 2015; 167:1597-600. [DOI: 10.1002/ajmg.a.37003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 01/19/2015] [Indexed: 11/06/2022]
Affiliation(s)
- María González-del Pozo
- Department of Genetics; Reproduction and Fetal Medicine; Institute of Biomedicine of Seville; University Hospital Virgen del Rocío/CSIC/University of Seville; Seville Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER); Spain
| | - Nereida Bravo-Gil
- Department of Genetics; Reproduction and Fetal Medicine; Institute of Biomedicine of Seville; University Hospital Virgen del Rocío/CSIC/University of Seville; Seville Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER); Spain
| | - Cristina Méndez-Vidal
- Department of Genetics; Reproduction and Fetal Medicine; Institute of Biomedicine of Seville; University Hospital Virgen del Rocío/CSIC/University of Seville; Seville Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER); Spain
| | | | - José M Millán
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER); Spain
- Grupo de Investigación en Enfermedades Neurosensoriales; IIS-La Fe; Valencia Spain
- Unidad de Genética y Diagnóstico Prenatal; Hospital Universitario La Fé; Valencia Spain
| | - Joaquín Dopazo
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER); Spain
- Genomics and Bioinformatics Platform of Andalusia (GBPA); Seville; Spain
- Computational Genomics Department; Centro de Investigación Príncipe Felipe (CIPF); Valencia Spain
| | - Salud Borrego
- Department of Genetics; Reproduction and Fetal Medicine; Institute of Biomedicine of Seville; University Hospital Virgen del Rocío/CSIC/University of Seville; Seville Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER); Spain
| | - Guillermo Antiñolo
- Department of Genetics; Reproduction and Fetal Medicine; Institute of Biomedicine of Seville; University Hospital Virgen del Rocío/CSIC/University of Seville; Seville Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER); Spain
- Genomics and Bioinformatics Platform of Andalusia (GBPA); Seville; Spain
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Pozo MGD, Méndez-Vidal C, Bravo-Gil N, Vela-Boza A, Dopazo J, Borrego S, Antiñolo G. Exome sequencing reveals novel and recurrent mutations with clinical significance in inherited retinal dystrophies. PLoS One 2014; 9:e116176. [PMID: 25544989 PMCID: PMC4278866 DOI: 10.1371/journal.pone.0116176] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 12/02/2014] [Indexed: 12/02/2022] Open
Abstract
This study aimed to identify the underlying molecular genetic cause in four Spanish families clinically diagnosed of Retinitis Pigmentosa (RP), comprising one autosomal dominant RP (adRP), two autosomal recessive RP (arRP) and one with two possible modes of inheritance: arRP or X-Linked RP (XLRP). We performed whole exome sequencing (WES) using NimbleGen SeqCap EZ Exome V3 sample preparation kit and SOLID 5500xl platform. All variants passing filter criteria were validated by Sanger sequencing to confirm familial segregation and the absence in local control population. This strategy allowed the detection of: (i) one novel heterozygous splice-site deletion in RHO, c.937-2_944del, (ii) one rare homozygous mutation in C2orf71, c.1795T>C; p.Cys599Arg, not previously associated with the disease, (iii) two heterozygous null mutations in ABCA4, c.2041C>T; p.R681* and c.6088C>T; p.R2030*, and (iv) one mutation, c.2405-2406delAG; p.Glu802Glyfs*31 in the ORF15 of RPGR. The molecular findings for RHO and C2orf71 confirmed the initial diagnosis of adRP and arRP, respectively, while patients with the two ABCA4 mutations, both previously associated with Stargardt disease, presented symptoms of RP with early macular involvement. Finally, the X-Linked inheritance was confirmed for the family with the RPGR mutation. This latter finding allowed the inclusion of carrier sisters in our preimplantational genetic diagnosis program.
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Affiliation(s)
- María González-del Pozo
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
| | - Cristina Méndez-Vidal
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
| | - Nereida Bravo-Gil
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
| | - Alicia Vela-Boza
- Genomics and Bioinformatics Platform of Andalusia (GBPA), Seville, Spain
| | - Joaquin Dopazo
- Genomics and Bioinformatics Platform of Andalusia (GBPA), Seville, Spain
- Department of Bioinformatics, Prince Felipe Research Centre (CIPF), Valencia, Spain
- Functional Genomics Node (INB), Prince Felipe Research Centre (CIPF), Valencia, Spain
| | - Salud Borrego
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
| | - Guillermo Antiñolo
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
- Genomics and Bioinformatics Platform of Andalusia (GBPA), Seville, Spain
- * E-mail:
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Méndez-Vidal C, González-del Pozo M, Vela-Boza A, Santoyo-López J, López-Domingo FJ, Vázquez-Marouschek C, Dopazo J, Borrego S, Antiñolo G. Whole-exome sequencing identifies novel compound heterozygous mutations in USH2A in Spanish patients with autosomal recessive retinitis pigmentosa. Mol Vis 2013; 19:2187-95. [PMID: 24227914 PMCID: PMC3820429] [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: 05/21/2013] [Accepted: 11/05/2013] [Indexed: 10/25/2022] Open
Abstract
PURPOSE Retinitis pigmentosa (RP) is an inherited retinal dystrophy characterized by extreme genetic and clinical heterogeneity. Thus, the diagnosis is not always easily performed due to phenotypic and genetic overlap. Current clinical practices have focused on the systematic evaluation of a set of known genes for each phenotype, but this approach may fail in patients with inaccurate diagnosis or infrequent genetic cause. In the present study, we investigated the genetic cause of autosomal recessive RP (arRP) in a Spanish family in which the causal mutation has not yet been identified with primer extension technology and resequencing. METHODS We designed a whole-exome sequencing (WES)-based approach using NimbleGen SeqCap EZ Exome V3 sample preparation kit and the SOLiD 5500×l next-generation sequencing platform. We sequenced the exomes of both unaffected parents and two affected siblings. Exome analysis resulted in the identification of 43,204 variants in the index patient. All variants passing filter criteria were validated with Sanger sequencing to confirm familial segregation and absence in the control population. In silico prediction tools were used to determine mutational impact on protein function and the structure of the identified variants. RESULTS Novel Usher syndrome type 2A (USH2A) compound heterozygous mutations, c.4325T>C (p.F1442S) and c.15188T>G (p.L5063R), located in exons 20 and 70, respectively, were identified as probable causative mutations for RP in this family. Family segregation of the variants showed the presence of both mutations in all affected members and in two siblings who were apparently asymptomatic at the time of family ascertainment. Clinical reassessment confirmed the diagnosis of RP in these patients. CONCLUSIONS Using WES, we identified two heterozygous novel mutations in USH2A as the most likely disease-causing variants in a Spanish family diagnosed with arRP in which the cause of the disease had not yet been identified with commonly used techniques. Our data reinforce the clinical role of WES in the molecular diagnosis of highly heterogeneous genetic diseases where conventional genetic approaches have previously failed in achieving a proper diagnosis.
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Affiliation(s)
- Cristina Méndez-Vidal
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
| | - María González-del Pozo
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
| | - Alicia Vela-Boza
- Medical Genome Project, Genomics and Bioinformatics Platform of Andalusia (GBPA), Seville, Spain
| | - Javier Santoyo-López
- Medical Genome Project, Genomics and Bioinformatics Platform of Andalusia (GBPA), Seville, Spain
| | | | | | - Joaquin Dopazo
- Medical Genome Project, Genomics and Bioinformatics Platform of Andalusia (GBPA), Seville, Spain,Department of Bioinformatics, Centro de Investigación Príncipe Felipe, Valencia, Spain,Functional Genomics Node (INB), Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Salud Borrego
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
| | - Guillermo Antiñolo
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain,Medical Genome Project, Genomics and Bioinformatics Platform of Andalusia (GBPA), Seville, Spain
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Carbonell J, Alloza E, Arce P, Borrego S, Santoyo J, Ruiz-Ferrer M, Medina I, Jiménez-Almazán J, Méndez-Vidal C, González-del Pozo M, Vela A, Bhattacharya SS, Antiñolo G, Dopazo J. A map of human microRNA variation uncovers unexpectedly high levels of variability. Genome Med 2012; 4:62. [PMID: 22906193 PMCID: PMC4064319 DOI: 10.1186/gm363] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [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: 06/19/2012] [Revised: 06/27/2012] [Accepted: 08/24/2012] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are key components of the gene regulatory network in many species. During the past few years, these regulatory elements have been shown to be involved in an increasing number and range of diseases. Consequently, the compilation of a comprehensive map of natural variability in a healthy population seems an obvious requirement for future research on miRNA-related pathologies. METHODS Data on 14 populations from the 1000 Genomes Project were analyzed, along with new data extracted from 60 exomes of healthy individuals from a population from southern Spain, sequenced in the context of the Medical Genome Project, to derive an accurate map of miRNA variability. RESULTS Despite the common belief that miRNAs are highly conserved elements, analysis of the sequences of the 1,152 individuals indicated that the observed level of variability is double what was expected. A total of 527 variants were found. Among these, 45 variants affected the recognition region of the corresponding miRNA and were found in 43 different miRNAs, 26 of which are known to be involved in 57 diseases. Different parts of the mature structure of the miRNA were affected to different degrees by variants, which suggests the existence of a selective pressure related to the relative functional impact of the change. Moreover, 41 variants showed a significant deviation from the Hardy-Weinberg equilibrium, which supports the existence of a selective process against some alleles. The average number of variants per individual in miRNAs was 28. CONCLUSIONS Despite an expectation that miRNAs would be highly conserved genomic elements, our study reports a level of variability comparable to that observed for coding genes.
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Affiliation(s)
- José Carbonell
- Institute of Computational Genomics, Centro de Investigación Príncipe Felipe (CIPF), C/ Eduardo Primo Yufera 3, Valencia, 46012, Spain
| | - Eva Alloza
- Institute of Computational Genomics, Centro de Investigación Príncipe Felipe (CIPF), C/ Eduardo Primo Yufera 3, Valencia, 46012, Spain
| | - Pablo Arce
- Medical Genome Project, Andalusian Center for Human Genomic Sequencing, c/ Albert Einstein s/n. Plta. Baja, Sevilla, 41092, Spain
| | - Salud Borrego
- Unidad de Gestión Clínica de Genética, Reproducción y Medicina Fetal. Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/CSIC/ Universidad de Sevilla, Avda. Manuel Siurot s/n, Sevilla, 41013, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Avda. Manuel Siurot s/n, Sevilla, 41013, Spain
| | - Javier Santoyo
- Medical Genome Project, Andalusian Center for Human Genomic Sequencing, c/ Albert Einstein s/n. Plta. Baja, Sevilla, 41092, Spain
| | - Macarena Ruiz-Ferrer
- Medical Genome Project, Andalusian Center for Human Genomic Sequencing, c/ Albert Einstein s/n. Plta. Baja, Sevilla, 41092, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Avda. Manuel Siurot s/n, Sevilla, 41013, Spain
| | - Ignacio Medina
- Institute of Computational Genomics, Centro de Investigación Príncipe Felipe (CIPF), C/ Eduardo Primo Yufera 3, Valencia, 46012, Spain
| | - Jorge Jiménez-Almazán
- Institute of Computational Genomics, Centro de Investigación Príncipe Felipe (CIPF), C/ Eduardo Primo Yufera 3, Valencia, 46012, Spain
- BIER, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), CIPF, C/ Eduardo Primo Yufera 3, Valencia, 46012, Spain
| | - Cristina Méndez-Vidal
- Unidad de Gestión Clínica de Genética, Reproducción y Medicina Fetal. Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/CSIC/ Universidad de Sevilla, Avda. Manuel Siurot s/n, Sevilla, 41013, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Avda. Manuel Siurot s/n, Sevilla, 41013, Spain
| | - María González-del Pozo
- Unidad de Gestión Clínica de Genética, Reproducción y Medicina Fetal. Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/CSIC/ Universidad de Sevilla, Avda. Manuel Siurot s/n, Sevilla, 41013, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Avda. Manuel Siurot s/n, Sevilla, 41013, Spain
| | - Alicia Vela
- Medical Genome Project, Andalusian Center for Human Genomic Sequencing, c/ Albert Einstein s/n. Plta. Baja, Sevilla, 41092, Spain
| | - Shomi S Bhattacharya
- Medical Genome Project, Andalusian Center for Human Genomic Sequencing, c/ Albert Einstein s/n. Plta. Baja, Sevilla, 41092, Spain
- Andalusian Molecular Biology and Regenerative Medicine Centre (CABIMER), Avda. Americo Vespucio s/n, Sevilla, 41092, Spain
| | - Guillermo Antiñolo
- Medical Genome Project, Andalusian Center for Human Genomic Sequencing, c/ Albert Einstein s/n. Plta. Baja, Sevilla, 41092, Spain
- Unidad de Gestión Clínica de Genética, Reproducción y Medicina Fetal. Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/CSIC/ Universidad de Sevilla, Avda. Manuel Siurot s/n, Sevilla, 41013, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Avda. Manuel Siurot s/n, Sevilla, 41013, Spain
| | - Joaquín Dopazo
- Institute of Computational Genomics, Centro de Investigación Príncipe Felipe (CIPF), C/ Eduardo Primo Yufera 3, Valencia, 46012, Spain
- Medical Genome Project, Andalusian Center for Human Genomic Sequencing, c/ Albert Einstein s/n. Plta. Baja, Sevilla, 41092, Spain
- BIER, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), CIPF, C/ Eduardo Primo Yufera 3, Valencia, 46012, Spain
- Functional Genomics Node (INB), CIPF, C/ Eduardo Primo Yufera 3, Valencia, 46012, Spain
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8
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González-del Pozo M, Borrego S, Barragán I, Pieras JI, Santoyo J, Matamala N, Naranjo B, Dopazo J, Antiñolo G. Mutation screening of multiple genes in Spanish patients with autosomal recessive retinitis pigmentosa by targeted resequencing. PLoS One 2011; 6:e27894. [PMID: 22164218 PMCID: PMC3229495 DOI: 10.1371/journal.pone.0027894] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 10/27/2011] [Indexed: 01/22/2023] Open
Abstract
Retinitis Pigmentosa (RP) is a heterogeneous group of inherited retinal dystrophies characterised ultimately by the loss of photoreceptor cells. RP is the leading cause of visual loss in individuals younger than 60 years, with a prevalence of about 1 in 4000. The molecular genetic diagnosis of autosomal recessive RP (arRP) is challenging due to the large genetic and clinical heterogeneity. Traditional methods for sequencing arRP genes are often laborious and not easily available and a screening technique that enables the rapid detection of the genetic cause would be very helpful in the clinical practice. The goal of this study was to develop and apply microarray-based resequencing technology capable of detecting both known and novel mutations on a single high-throughput platform. Hence, the coding regions and exon/intron boundaries of 16 arRP genes were resequenced using microarrays in 102 Spanish patients with clinical diagnosis of arRP. All the detected variations were confirmed by direct sequencing and potential pathogenicity was assessed by functional predictions and frequency in controls. For validation purposes 4 positive controls for variants consisting of previously identified changes were hybridized on the array. As a result of the screening, we detected 44 variants, of which 15 are very likely pathogenic detected in 14 arRP families (14%). Finally, the design of this array can easily be transformed in an equivalent diagnostic system based on targeted enrichment followed by next generation sequencing.
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Affiliation(s)
- María González-del Pozo
- Unidad de Gestión Clínica de Genética, Reproducción y Medicina Fetal, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Sevilla, Spain
| | - Salud Borrego
- Unidad de Gestión Clínica de Genética, Reproducción y Medicina Fetal, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Sevilla, Spain
| | - Isabel Barragán
- Unidad de Gestión Clínica de Genética, Reproducción y Medicina Fetal, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Sevilla, Spain
| | - Juan I. Pieras
- Unidad de Gestión Clínica de Genética, Reproducción y Medicina Fetal, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Sevilla, Spain
| | - Javier Santoyo
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Sevilla, Spain
- Medical Genome Project, Andalusian Center for Human Genomic Sequencing, Sevilla, Spain
- Departamento de Bioinformática y Genómica, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Nerea Matamala
- Unidad de Gestión Clínica de Genética, Reproducción y Medicina Fetal, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
- Medical Genome Project, Andalusian Center for Human Genomic Sequencing, Sevilla, Spain
| | - Belén Naranjo
- Unidad de Gestión Clínica de Genética, Reproducción y Medicina Fetal, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - Joaquín Dopazo
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Sevilla, Spain
- Medical Genome Project, Andalusian Center for Human Genomic Sequencing, Sevilla, Spain
- Departamento de Bioinformática y Genómica, Centro de Investigación Príncipe Felipe, Valencia, Spain
- Functional Genomics Node (INB), Valencia, Spain
- * E-mail: (JD); (GA)
| | - Guillermo Antiñolo
- Unidad de Gestión Clínica de Genética, Reproducción y Medicina Fetal, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Sevilla, Spain
- Medical Genome Project, Andalusian Center for Human Genomic Sequencing, Sevilla, Spain
- * E-mail: (JD); (GA)
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9
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Barragán I, Borrego S, Pieras JI, González-del Pozo M, Santoyo J, Ayuso C, Baiget M, Millan JM, Mena M, Abd El-Aziz MM, Audo I, Zeitz C, Littink KW, Dopazo J, Bhattacharya SS, Antiñolo G. Mutation spectrum of EYS in Spanish patients with autosomal recessive retinitis pigmentosa. Hum Mutat 2010; 31:E1772-800. [PMID: 21069908 PMCID: PMC3045506 DOI: 10.1002/humu.21334] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [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] [Indexed: 11/09/2022]
Abstract
Retinitis pigmentosa (RP) is a heterogeneous group of inherited retinal dystrophies characterised ultimately by the loss of photoreceptor cells. We have recently identified a new gene(EYS) encoding an ortholog of Drosophila space maker (spam) as a commonly mutated gene in autosomal recessive RP. In the present study, we report the identification of 73 sequence variations in EYS, of which 28 are novel. Of these, 42.9% (12/28) are very likely pathogenic, 17.9% (5/28)are possibly pathogenic, whereas 39.3% (11/28) are SNPs. In addition, we have detected 3 pathogenic changes previously reported in other populations. We are also presenting the characterisation of EYS homologues in different species, and a detailed analysis of the EYS domains, with the identification of an interesting novel feature: a putative coiled-coil domain.Majority of the mutations in the arRP patients have been found within the domain structures of EYS. The minimum observed prevalence of distinct EYS mutations in our group of patients is of 15.9% (15/94), confirming a major involvement of EYS in the pathogenesis of arRP in the Spanish population. Along with the detection of three recurrent mutations in Caucasian population, our hypothesis of EYS being the first prevalent gene in arRP has been reinforced in the present study.
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Affiliation(s)
- Isabel Barragán
- Unidad de Gestión Clínica de Genética, Reproducción y Medicina Fetal, Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío/CSIC/ Universidad de Sevilla, Sevilla, Spain
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