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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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Faller KME, Ridyard AE, Gutierrez-Quintana R, Rupp A, Kun-Rodrigues C, Orme T, Tylee KL, Church HJ, Guerreiro R, Bras J. A deletion of IDUA exon 10 in a family of Golden Retriever dogs with an attenuated form of mucopolysaccharidosis type I. J Vet Intern Med 2020; 34:1813-1824. [PMID: 32785987 PMCID: PMC7517864 DOI: 10.1111/jvim.15868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/11/2020] [Accepted: 07/22/2020] [Indexed: 01/07/2023] Open
Abstract
Background Mucopolysaccharidosis type I (MPS‐I) is a lysosomal storage disorder caused by a deficiency of the enzyme α‐l‐iduronidase, leading to accumulation of undegraded dermatan and heparan sulfates in the cells and secondary multiorgan dysfunction. In humans, depending upon the nature of the underlying mutation(s) in the IDUA gene, the condition presents with a spectrum of clinical severity. Objectives To characterize the clinical and biochemical phenotypes, and the genotype of a family of Golden Retriever dogs. Animals Two affected siblings and 11 related dogs. Methods Family study. Urine metabolic screening and leucocyte lysosomal enzyme activity assays were performed for biochemical characterization. Whole genome sequencing was used to identify the causal mutation. Results The clinical signs shown by the proband resemble the human attenuated form of the disease, with a dysmorphic appearance, musculoskeletal, ocular and cardiac defects, and survival to adulthood. Urinary metabolic studies identified high levels of dermatan sulfate, heparan sulfate, and heparin. Lysosomal enzyme activities demonstrated deficiency in α‐l‐iduronidase activity in leucocytes. Genome sequencing revealed a novel homozygous deletion of 287 bp resulting in full deletion of exon 10 of the IDUA gene (NC_006585.3(NM_001313883.1):c.1400‐76_1521+89del). Treatment with pentosan polyphosphate improved the clinical signs until euthanasia at 4.5 years. Conclusion and Clinical Importance Analysis of the genotype/phenotype correlation in this dog family suggests that dogs with MPS‐I could have a less severe phenotype than humans, even in the presence of severe mutations. Treatment with pentosan polyphosphate should be considered in dogs with MPS‐I.
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Affiliation(s)
- Kiterie M E Faller
- School of Veterinary Medicine, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom.,Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, United Kingdom
| | - Alison E Ridyard
- School of Veterinary Medicine, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Rodrigo Gutierrez-Quintana
- School of Veterinary Medicine, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Angie Rupp
- School of Veterinary Medicine, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Celia Kun-Rodrigues
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, United Kingdom.,Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan, USA
| | - Tatiana Orme
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, United Kingdom
| | - Karen L Tylee
- Willink Biochemical Genetics Unit, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, St Mary's Hospital, Manchester, United Kingdom
| | - Heather J Church
- Willink Biochemical Genetics Unit, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, St Mary's Hospital, Manchester, United Kingdom
| | - Rita Guerreiro
- Department of Neurodegenerative Diseases, Institute of Neurology, University College London, London, United Kingdom.,UK Dementia Research Institute at UCL (UK DRI), London, United Kingdom.,Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan, USA
| | - Jose Bras
- Department of Neurodegenerative Diseases, Institute of Neurology, University College London, London, United Kingdom.,UK Dementia Research Institute at UCL (UK DRI), London, United Kingdom.,Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan, USA
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Kubaski F, de Oliveira Poswar F, Michelin-Tirelli K, Matte UDS, Horovitz DD, Barth AL, Baldo G, Vairo F, Giugliani R. Mucopolysaccharidosis Type I. Diagnostics (Basel) 2020; 10:E161. [PMID: 32188113 PMCID: PMC7151028 DOI: 10.3390/diagnostics10030161] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 12/31/2022] Open
Abstract
Mucopolysaccharidosis type I (MPS I) is caused by the deficiency of α-l-iduronidase, leading to the storage of dermatan and heparan sulfate. There is a broad phenotypical spectrum with the presence or absence of neurological impairment. The classical form is known as Hurler syndrome, the intermediate form as Hurler-Scheie, and the most attenuated form is known as Scheie syndrome. Phenotype seems to be largely influenced by genotype. Patients usually develop several somatic symptoms such as abdominal hernias, extensive dermal melanocytosis, thoracolumbar kyphosis odontoid dysplasia, arthropathy, coxa valga and genu valgum, coarse facial features, respiratory and cardiac impairment. The diagnosis is based on the quantification of α-l-iduronidase coupled with glycosaminoglycan analysis and gene sequencing. Guidelines for treatment recommend hematopoietic stem cell transplantation for young Hurler patients (usually at less than 30 months of age). Intravenous enzyme replacement is approved and is the standard of care for attenuated-Hurler-Scheie and Scheie-forms (without cognitive impairment) and for the late-diagnosed severe-Hurler-cases. Intrathecal enzyme replacement therapy is under evaluation, but it seems to be safe and effective. Other therapeutic approaches such as gene therapy, gene editing, stop codon read through, and therapy with small molecules are under development. Newborn screening is now allowing the early identification of MPS I patients, who can then be treated within their first days of life, potentially leading to a dramatic change in the disease's progression. Supportive care is very important to improve quality of life and might include several surgeries throughout the life course.
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Affiliation(s)
- Francyne Kubaski
- Postgraduate Program in Genetics and Molecular Biology, UFRGS, Porto Alegre 91501970, Brazil; (F.K.); (F.d.O.P.); (U.d.S.M.); (G.B.)
- Medical Genetics Service, HCPA, Porto Alegre 90035903, Brazil;
- INAGEMP, Porto Alegre 90035903, Brazil
- Biodiscovery Research Group, Experimental Research Center, HCPA, Porto Alegre 90035903, Brazil
| | - Fabiano de Oliveira Poswar
- Postgraduate Program in Genetics and Molecular Biology, UFRGS, Porto Alegre 91501970, Brazil; (F.K.); (F.d.O.P.); (U.d.S.M.); (G.B.)
- Medical Genetics Service, HCPA, Porto Alegre 90035903, Brazil;
| | - Kristiane Michelin-Tirelli
- Medical Genetics Service, HCPA, Porto Alegre 90035903, Brazil;
- Biodiscovery Research Group, Experimental Research Center, HCPA, Porto Alegre 90035903, Brazil
| | - Ursula da Silveira Matte
- Postgraduate Program in Genetics and Molecular Biology, UFRGS, Porto Alegre 91501970, Brazil; (F.K.); (F.d.O.P.); (U.d.S.M.); (G.B.)
- INAGEMP, Porto Alegre 90035903, Brazil
- Biodiscovery Research Group, Experimental Research Center, HCPA, Porto Alegre 90035903, Brazil
- Gene Therapy Center, HCPA, Porto Alegre 90035903, Brazil
- Department of Genetics, UFRGS, Porto Alegre 91501970, Brazil
| | - Dafne D. Horovitz
- Medical Genetics Department, National Institute of Women, Children, and Adolescent Health, Oswaldo Cruz Foundation, Rio de Janeiro 21040900, Brazil; (D.D.H.); (A.L.B.)
| | - Anneliese Lopes Barth
- Medical Genetics Department, National Institute of Women, Children, and Adolescent Health, Oswaldo Cruz Foundation, Rio de Janeiro 21040900, Brazil; (D.D.H.); (A.L.B.)
| | - Guilherme Baldo
- Postgraduate Program in Genetics and Molecular Biology, UFRGS, Porto Alegre 91501970, Brazil; (F.K.); (F.d.O.P.); (U.d.S.M.); (G.B.)
- INAGEMP, Porto Alegre 90035903, Brazil
- Biodiscovery Research Group, Experimental Research Center, HCPA, Porto Alegre 90035903, Brazil
- Gene Therapy Center, HCPA, Porto Alegre 90035903, Brazil
- Department of Physiology, UFRGS, Porto Alegre 90050170, Brazil
| | - Filippo Vairo
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA;
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Roberto Giugliani
- Postgraduate Program in Genetics and Molecular Biology, UFRGS, Porto Alegre 91501970, Brazil; (F.K.); (F.d.O.P.); (U.d.S.M.); (G.B.)
- Medical Genetics Service, HCPA, Porto Alegre 90035903, Brazil;
- INAGEMP, Porto Alegre 90035903, Brazil
- Biodiscovery Research Group, Experimental Research Center, HCPA, Porto Alegre 90035903, Brazil
- Gene Therapy Center, HCPA, Porto Alegre 90035903, Brazil
- Department of Genetics, UFRGS, Porto Alegre 91501970, Brazil
- Postgraduation Program in Medicine, Clinical Sciences, UFRGS, Porto Alegre 90035003, Brazil
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Jahic A, Günther S, Muschol N, Fossøy Stadheim B, Braaten Ø, Kjensli Hyldebrandt H, Kuiper GA, Tylee K, Wijburg FA, Beetz C. "Missing mutations" in MPS I: Identification of two novel copy number variations by an IDUA-specific in house MLPA assay. Mol Genet Genomic Med 2019; 7:e00615. [PMID: 31319022 PMCID: PMC6732313 DOI: 10.1002/mgg3.615] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/06/2019] [Accepted: 02/11/2019] [Indexed: 11/10/2022] Open
Abstract
Background Mucopolysaccharidosis type I (MPS I) is a rare, recessively inherited lysosomal storage disorder, characterized by progressive multi‐systemic disease. It is caused by a reduced or absent alpha‐l iduronidase (IDUA) enzyme activity secondary to biallelic loss‐of‐function variants in the IDUA. Over 200 causative variants in IDUA have been identified. Nevertheless, there is a fraction of MPS I patients with only a single mutated IDUA allele detectable. Methods As genetic testing of MPS I is usually based on sequencing methods, copy number variations (CNVs) in IDUA can be missed and therefore presumably remain underdiagnosed. The aim of this study was the detection of CNVs using an IDUA‐specific in house multiplex ligation‐dependent probe amplification (MLPA) assay. Results A total of five unrelated MPS I patient samples were re‐analyzed after only a single heterozygous IDUA mutation c.979G>C (p.A327P), c.1469T>C (p.L490P), c.1598C>G (p.P533R), c.1205G>A (p.W402X), c.973‐7C>G (p.?) could be identified. We detected a novel splice site variant c.973‐7C>G (p.?), as well as two novel CNVs, a large deletion of IDUA exon 14 and 3’UTR c.(1828 + 1_1829‐1)_(*1963_?)del, and a large duplication extending from IDUA exon 2 to intron 12 c.(157 + 1_158‐1)_(1727 + 1_1728‐1)dup. Conclusion Together with the CNVs we previously identified, a total of four pathogenic IDUACNVs have now been reported.
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Affiliation(s)
- Amir Jahic
- Institute of Clinical Chemistry and Laboratory Diagnostics, Jena University Hospital, Jena, Germany.,Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Sven Günther
- Institute of Clinical Chemistry and Laboratory Diagnostics, Jena University Hospital, Jena, Germany
| | - Nicole Muschol
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Øivind Braaten
- Department of Clinical Genetics, Oslo University Hospital, Oslo, Norway
| | | | - Gé-Ann Kuiper
- Pediatric Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Academic Medical Center (AMC), Amsterdam, Netherlands
| | - Karen Tylee
- Manchester Center for Genomic Medicine, St Mary's Hospital, Manchester, UK
| | - Frits A Wijburg
- Pediatric Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Academic Medical Center (AMC), Amsterdam, Netherlands
| | - Christian Beetz
- Institute of Clinical Chemistry and Laboratory Diagnostics, Jena University Hospital, Jena, Germany.,Centogene AG, Rostock, Germany
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Brusius-Facchin AC, Rojas Malaga D, Leistner-Segal S, Giugliani R. Recent advances in molecular testing to improve early diagnosis in children with mucopolysaccharidoses. Expert Rev Mol Diagn 2018; 18:855-866. [DOI: 10.1080/14737159.2018.1523722] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
| | - Diana Rojas Malaga
- Medical Genetics Service, HCPA, Porto Alegre, RS, Brazil
- Postgraduate Program of Genetics and Molecular Biology, UFRGS, Porto Alegre, RS, Brazil
| | - Sandra Leistner-Segal
- Medical Genetics Service, HCPA, Porto Alegre, RS, Brazil
- Postgraduate Program in Medical Science, UFRGS, Porto Alegre, RS, Brazil
| | - Roberto Giugliani
- Medical Genetics Service, HCPA, Porto Alegre, RS, Brazil
- Postgraduate Program of Genetics and Molecular Biology, UFRGS, Porto Alegre, RS, Brazil
- Postgraduate Program in Medical Science, UFRGS, Porto Alegre, RS, Brazil
- Department of Genetics, UFRGS, Porto Alegre, RS, Brazil
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Ghosh A, Mercer J, Mackinnon S, Yue WW, Church H, Beesley CE, Broomfield A, Jones SA, Tylee K. IDUA mutational profile and genotype-phenotype relationships in UK patients with Mucopolysaccharidosis Type I. Hum Mutat 2017; 38:1555-1568. [PMID: 28752568 DOI: 10.1002/humu.23301] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/14/2017] [Accepted: 07/24/2017] [Indexed: 01/01/2023]
Abstract
Mucopolysaccharidosis Type I (MPS I) is a lysosomal storage disorder with varying degrees of phenotypic severity caused by mutations in IDUA. Over 200 disease-causing variants in IDUA have been reported. We describe the profile of disease-causing variants in 291 individuals with MPS I for whom IDUA sequencing was performed, focusing on the UK subset of the cohort. A total of 63 variants were identified, of which 20 were novel, and the functional significance of the novel variants is explored. The severe form of MPS I is treated with hematopoietic stem cell transplantation, known to have improved outcomes with earlier age at treatment. Developing genotype-phenotype relationships would therefore have considerable clinical utility, especially in the light of the development of newborn screening programs for MPS I. Associations between genotype and phenotype are examined in this cohort, particularly in the context of the profile of variants identified in UK individuals. Relevant associations can be made for the majority of UK individuals based on the presence of nonsense or truncating variants as well as other associations described in this report.
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Affiliation(s)
- Arunabha Ghosh
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre (MAHSC), Manchester, UK.,School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Jean Mercer
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre (MAHSC), Manchester, UK
| | - Sabrina Mackinnon
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, London, UK
| | - Wyatt W Yue
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, London, UK
| | - Heather Church
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre (MAHSC), Manchester, UK
| | - Clare E Beesley
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Alex Broomfield
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre (MAHSC), Manchester, UK
| | - Simon A Jones
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre (MAHSC), Manchester, UK
| | - Karen Tylee
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester Academic Health Science Centre (MAHSC), Manchester, UK
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