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La Cognata V, Cavallaro S. Detection of Structural Variants by NGS: Revealing Missing Alleles in Lysosomal Storage Diseases. Biomedicines 2022; 10:biomedicines10081836. [PMID: 36009380 PMCID: PMC9405548 DOI: 10.3390/biomedicines10081836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
Lysosomal storage diseases (LSDs) are a heterogeneous group of rare multisystem metabolic disorders occurring mostly in infancy and childhood, characterized by a gradual accumulation of non-degraded substrates inside the cells. Although biochemical enzymatic assays are considered the gold standard for diagnosis of symptomatic patients, genotyping is a requirement for inclusion in enzyme replacement programs and is a prerequisite for carrier tests in relatives and DNA-based prenatal diagnosis. The emerging next-generation sequencing (NGS) technologies are now offering a powerful diagnostic tool for genotyping LSDs patients by providing faster, cheaper, and higher-resolution testing options, and are allowing to unravel, in a single integrated workflow SNVs, small insertions and deletions (indels), as well as major structural variations (SVs) responsible for the pathology. Here, we summarize the current knowledge about the most recurrent and private SVs involving LSDs-related genes, review advantages and drawbacks related to the use of the NGS in the SVs detection, and discuss the challenges to bring this type of analysis in clinical diagnostics.
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Josahkian JA, Brusius-Facchin AC, Netto ABO, Leistner-Segal S, Málaga DR, Burin MG, Michelin-Tirelli K, Trapp FB, Cardoso-Dos-Santos AC, Ribeiro EM, Kim CA, de Siqueira ACM, Santos ML, do Valle DA, da Silva RTB, Horovitz DDG, de Medeiros PFV, de Souza CFM, Giuliani LDR, Miguel DSCG, Santana-da-Silva LC, Galera MF, Giugliani R. Genotype-phenotype studies in a large cohort of Brazilian patients with Hunter syndrome. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2021; 187:349-356. [PMID: 33960103 DOI: 10.1002/ajmg.c.31915] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/25/2021] [Accepted: 04/18/2021] [Indexed: 11/05/2022]
Abstract
Mucopolysaccharidosis type II (MPS II) is an X-linked inherited disease caused by pathogenic variants in the IDS gene, leading to deficiency of the lysosomal enzyme iduronate-2-sulfatase and consequent widespread storage of glycosaminoglycans, leading to several clinical consequences, with progressive manifestations which most times includes cognitive decline. MPS II has wide allelic and clinical heterogeneity and a complex genotype-phenotype correlation. We evaluated data from 501 Brazilian patients diagnosed with MPS II from 1982 to 2020. We genotyped 280 of these patients (55.9%), which were assigned to 206 different families. Point mutations were present in 70% of our patients, being missense variants the most frequent. We correlated the IDS pathogenic variants identified with the phenotype (neuronophatic or non-neuronopathic). Except for two half-brothers, there was no discordance in the genotype-phenotype correlation among family members, nor among MPS II patients from different families with the same single base-pair substitution variant. Mothers were carriers in 82.0% of the cases. This comprehensive study of the molecular profile of the MPS II cases in Brazil sheds light on the genotype-phenotype correlation and helps the better understanding of the disease and the prediction of its clinical course, enabling the provision of a more refined genetic counseling to the affected families.
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Affiliation(s)
- Juliana Alves Josahkian
- Department of Clinical Medicine, Hospital Universitário de Santa Maria (HUSM), Santa Maria, Rio Grande do Sul, Brazil.,Postgraduate Program in Genetics and Molecular Biology, UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Alice Brinckmann Oliveira Netto
- Medical Genetics Service, HCPA, Porto Alegre, Rio Grande do Sul, Brazil.,National Institute on Population Medical Genetics, INAGEMP, Porto Alegre, Rio Grande do Sul, Brazil.,Graduate in Biological Sciences, UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Sandra Leistner-Segal
- Medical Genetics Service, HCPA, Porto Alegre, Rio Grande do Sul, Brazil.,National Institute on Population Medical Genetics, INAGEMP, Porto Alegre, Rio Grande do Sul, Brazil
| | - Diana Rojas Málaga
- Medical Genetics Service, HCPA, Porto Alegre, Rio Grande do Sul, Brazil.,Research and Development, Grupo Fleury, São Paulo, São Paulo, Brazil
| | | | | | | | - Augusto César Cardoso-Dos-Santos
- Postgraduate Program in Genetics and Molecular Biology, UFRGS, Porto Alegre, Rio Grande do Sul, Brazil.,National Institute on Population Medical Genetics, INAGEMP, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Chong Ae Kim
- Genetic Unit, Pediatric Department, HC-FMUSP, São Paulo University, São Paulo, São Paulo, Brazil
| | | | - Mara Lucia Santos
- Neuropediatric Division, Hospital Pequeno Príncipe, Curitiba, Paraná, Brazil
| | | | | | - Dafne Dain Gandelman Horovitz
- Medical Genetics Department, National Institute of Women, Children and Adolescents Health Fernandes Figueira-Fiocruz/Reference Center for Rare Diseases, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Liane de Rosso Giuliani
- Hospital Universitário Maria Aparecida Pedrossian (HUMAP), UFMS, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Luiz Carlos Santana-da-Silva
- Laboratory of Innate Errors of Metabolism, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Marcial Francis Galera
- Department of Pediatrics, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Roberto Giugliani
- Medical Genetics Service, HCPA, Porto Alegre, Rio Grande do Sul, Brazil.,National Institute on Population Medical Genetics, INAGEMP, Porto Alegre, Rio Grande do Sul, Brazil.,Department of Genetics, UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
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Zanetti A, D'Avanzo F, Bertoldi L, Zampieri G, Feltrin E, De Pascale F, Rampazzo A, Forzan M, Valle G, Tomanin R. Setup and Validation of a Targeted Next-Generation Sequencing Approach for the Diagnosis of Lysosomal Storage Disorders. J Mol Diagn 2020; 22:488-502. [PMID: 32036093 DOI: 10.1016/j.jmoldx.2020.01.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 11/07/2019] [Accepted: 01/11/2020] [Indexed: 12/14/2022] Open
Abstract
Lysosomal storage disorders (LSDs) are monogenic diseases, due to accumulation of specific undegraded substrates into lysosomes. LSD diagnosis could take several years because of both poor knowledge of these diseases and shared clinical features. The diagnostic approach includes clinical evaluations, biochemical tests, and genetic analysis of the suspected gene. In this study, we evaluated an LSD targeted sequencing panel as a tool capable to potentially reverse this classic diagnostic route. The panel includes 50 LSD genes and 230 intronic sequences conserved among 33 placental mammals. For the validation phase, 56 positive controls, 13 biochemically diagnosed patients, and nine undiagnosed patients were analyzed. Disease-causing variants were identified in 66% of the positive control alleles and in 62% of the biochemically diagnosed patients. Three undiagnosed patients were diagnosed. Eight patients undiagnosed by the panel were analyzed by whole exome sequencing: for two of them, the disease-causing variants were identified. Five patients, undiagnosed by both panel and exome analyses, were investigated through array comparative genomic hybridization: one of them was diagnosed. Conserved intronic fragment analysis, performed in cases unresolved by the first-level analysis, evidenced no candidate intronic variants. Targeted sequencing has low sequencing costs and short sequencing time. However, a coverage >60× to 80× must be ensured and/or Sanger validation should be performed. Moreover, it must be supported by a thorough clinical phenotyping.
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Affiliation(s)
- Alessandra Zanetti
- Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova, Padova, Italy; Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
| | - Francesca D'Avanzo
- Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova, Padova, Italy; Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
| | - Loris Bertoldi
- Department of Biology and CRIBI Biotechnology Centre, University of Padova, Padova, Italy
| | - Guido Zampieri
- Department of Biology and CRIBI Biotechnology Centre, University of Padova, Padova, Italy
| | - Erika Feltrin
- Department of Biology and CRIBI Biotechnology Centre, University of Padova, Padova, Italy
| | - Fabio De Pascale
- Department of Biology and CRIBI Biotechnology Centre, University of Padova, Padova, Italy
| | - Angelica Rampazzo
- Infantile Neuropsychiatric Unit, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Monica Forzan
- Clinical Genetics Unit, University Hospital of Padua, Padua, Italy
| | - Giorgio Valle
- Department of Biology and CRIBI Biotechnology Centre, University of Padova, Padova, Italy
| | - Rosella Tomanin
- Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova, Padova, Italy; Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy.
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Marshall LS, Simon J, Wood T, Peng M, Owen R, Feldman GS, Zaragoza MV. Deletion Xq27.3q28 in female patient with global developmental delays and skewed X-inactivation. BMC MEDICAL GENETICS 2013; 14:49. [PMID: 23634718 PMCID: PMC3643848 DOI: 10.1186/1471-2350-14-49] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 04/25/2013] [Indexed: 01/28/2023]
Abstract
BACKGROUND Global developmental delay and mental retardation are associated with X-linked disorders including Hunter syndrome (mucopolysaccharidosis type II) and Fragile X syndrome (FXS). Single nucleotide mutations in the iduronate 2-sulfatase (IDS) gene at Xq28 most commonly cause Hunter syndrome while a CGG expansion in the FMR1 gene at Xq27.3 is associated with Fragile X syndrome. Gene deletions of the Xq27-28 region are less frequently found in either condition with rare reports in females. Additionally, an association between Xq27-28 deletions and skewed X-inactivation of the normal X chromosome observed in previous studies suggested a primary role of the Xq27-28 region in X-inactivation. CASE PRESENTATION We describe the clinical, molecular and biochemical evaluations of a four year-old female patient with global developmental delay and a hemizygous deletion of Xq27.3q28 (144,270,614-154,845,961 bp), a 10.6 Mb region that contains >100 genes including IDS and FMR1. A literature review revealed rare cases with similar deletions that included IDS and FMR1 in females with developmental delay, variable features of Hunter syndrome, and skewed X-inactivation of the normal X chromosome. In contrast, our patient exhibited skewed X-inactivation of the deleted X chromosome and tested negative for Hunter syndrome. CONCLUSIONS This is a report of a female with a 10.6 Mb Xq27-28 deletion with skewed inactivation of the deleted X chromosome. Contrary to previous reports, our observations do not support a primary role of the Xq27-28 region in X-inactivation. A review of the genes in the deletion region revealed several potential genes that may contribute to the patient's developmental delays, and sequencing of the active X chromosome may provide insight into the etiology of this clinical presentation.
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Froissart R, Moreira da Silva I, Guffon N, Bozon D, Maire I. Mucopolysaccharidosis type II--genotype/phenotype aspects. ACTA PAEDIATRICA (OSLO, NORWAY : 1992). SUPPLEMENT 2003; 91:82-7. [PMID: 12572848 DOI: 10.1111/j.1651-2227.2002.tb03116.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
UNLABELLED Establishing correlations between a patient's genotype and clinical phenotype is based on the assumption that the same clinical consequences will be observed in individuals with the same residual function of a specific metabolic step. In mucopolysaccharidosis type II (MPS II; Hunter disease), patients present with a wide clinical spectrum. Furthermore, current methods for measuring the activity of the deficient enzyme in MPS II--iduronate-2-sulphatase (IDS)--are insufficiently sensitive to differentiate between complete absence of activity and the presence of residual activity. Attempts have therefore been made to establish genotype-phenotype correlations in order to explain the large degree of heterogeneity and to serve as a better guide to prognosis on which to base genetic counselling and treatment options. Using MPS II as an example, this paper illustrates the difficulties and potential advantages of determining genotype-phenotype correlations in lysosomal storage diseases. The response of patients with MPS II to allogenic bone marrow transplantation provides some insight into the likely influence of certain genotypes on therapeutic efficacy. CONCLUSIONS Evaluation of residual activity of IDS in MPS II using gene analysis, expression studies and transcript analysis does not always allow prediction of a patient's phenotype. The variable response to bone marrow transplantation, however, illustrates the potential importance of determining the genotype for selecting the most appropriate therapy for individual patients.
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Affiliation(s)
- R Froissart
- Paediatric Biochemistry Department, Debrousse Hospital, Lyon, France
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