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Sheth H, Nair A, Bhavsar R, Kamate M, Gowda VK, Bavdekar A, Kadam S, Nampoothiri S, Panigrahi I, Kaur A, Shah S, Mehta S, Jagadeesan S, Suresh I, Kapoor S, Bajaj S, Devi RR, Prajapati A, Godbole K, Patel H, Luhar Z, Shah RC, Iyer A, Bijarnia S, Puri R, Muranjan M, Shah A, Magar S, Gupta N, Tayade N, Gandhi A, Sowani A, Kale S, Jalan A, Solanki D, Dalal A, Mane S, Prabha CR, Sheth F, Joshi CG, Joshi M, Sheth J. Development, validation and application of single molecule molecular inversion probe based novel integrated genetic screening method for 29 common lysosomal storage disorders in India. Hum Genomics 2024; 18:46. [PMID: 38730490 PMCID: PMC11088154 DOI: 10.1186/s40246-024-00613-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Current clinical diagnosis pathway for lysosomal storage disorders (LSDs) involves sequential biochemical enzymatic tests followed by DNA sequencing, which is iterative, has low diagnostic yield and is costly due to overlapping clinical presentations. Here, we describe a novel low-cost and high-throughput sequencing assay using single-molecule molecular inversion probes (smMIPs) to screen for causative single nucleotide variants (SNVs) and copy number variants (CNVs) in genes associated with 29 common LSDs in India. RESULTS 903 smMIPs were designed to target exon and exon-intron boundaries of targeted genes (n = 23; 53.7 kb of the human genome) and were equimolarly pooled to create a sequencing library. After extensive validation in a cohort of 50 patients, we screened 300 patients with either biochemical diagnosis (n = 187) or clinical suspicion (n = 113) of LSDs. A diagnostic yield of 83.4% was observed in patients with prior biochemical diagnosis of LSD. Furthermore, diagnostic yield of 73.9% (n = 54/73) was observed in patients with high clinical suspicion of LSD in contrast with 2.4% (n = 1/40) in patients with low clinical suspicion of LSD. In addition to detecting SNVs, the assay could detect single and multi-exon copy number variants with high confidence. Critically, Niemann-Pick disease type C and neuronal ceroid lipofuscinosis-6 diseases for which biochemical testing is unavailable, could be diagnosed using our assay. Lastly, we observed a non-inferior performance of the assay in DNA extracted from dried blood spots in comparison with whole blood. CONCLUSION We developed a flexible and scalable assay to reliably detect genetic causes of 29 common LSDs in India. The assay consolidates the detection of multiple variant types in multiple sample types while having improved diagnostic yield at same or lower cost compared to current clinical paradigm.
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Affiliation(s)
- Harsh Sheth
- FRIGE Institute of Human Genetics, FRIGE House, Jodhpur Village Road, Satellite, Ahmedabad, India, 380015.
| | - Aadhira Nair
- FRIGE Institute of Human Genetics, FRIGE House, Jodhpur Village Road, Satellite, Ahmedabad, India, 380015
| | - Riddhi Bhavsar
- FRIGE Institute of Human Genetics, FRIGE House, Jodhpur Village Road, Satellite, Ahmedabad, India, 380015
| | - Mahesh Kamate
- KLES Prabhakar Kore Hospital, Belgaum, Karnataka, India
| | - Vykuntaraju K Gowda
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, India
| | | | - Sandeep Kadam
- Department of Pediatrics, K.E.M Hospital, Pune, India
| | | | - Inusha Panigrahi
- Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Anupriya Kaur
- Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Siddharth Shah
- Royal Institute of Child Neurosciences, Vastrapur, Ahmedabad, India
| | - Sanjeev Mehta
- Royal Institute of Child Neurosciences, Vastrapur, Ahmedabad, India
| | - Sujatha Jagadeesan
- Department of Clinical Genetics and Genetic Counselling, Mediscan Systems, Chennai, India
| | - Indrani Suresh
- Department of Clinical Genetics and Genetic Counselling, Mediscan Systems, Chennai, India
| | - Seema Kapoor
- Division of Genetics and Metabolism Department of Pediatrics, Lok Nayak Hospital and Maulana Azad Medical College, New Delhi, India
| | - Shruti Bajaj
- The Purple Gene Clinic, Simplex Khushaangan, SV Road, Malad West, Mumbai, India
| | | | | | - Koumudi Godbole
- Deenanath Mangeshkar Hospital &Amp; Research Centre, Pune, India
| | - Harsh Patel
- Zydus Hospital & Healthcare Research Pvt Ltd, Ahmedabad, India
| | | | - Raju C Shah
- Ankur Institute of Child Health, Ahmedabad, India
| | | | - Sunita Bijarnia
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Ratna Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Mamta Muranjan
- Department of Paediatrics, KEM Hospital, Parel, Mumbai, India
| | - Ami Shah
- BJ Wadia Hospital for Children, Parel, Mumbai, India
| | | | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Naresh Tayade
- Department of Pediatrics, Dr. Panjabrao Deshmukh Memorial Medical College, Amravati, India
| | | | - Ajit Sowani
- Zydus Hospital & Healthcare Research Pvt Ltd, Ahmedabad, India
| | - Shrutikaa Kale
- FRIGE Institute of Human Genetics, FRIGE House, Jodhpur Village Road, Satellite, Ahmedabad, India, 380015
| | | | - Dhaval Solanki
- Mantra Child Neurology and Epilepsy Hospital, Bhavnagar, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Shrikant Mane
- Department of Genetics, Yale School of Medicine, Yale Center for Genome Analysis, West Haven, CT, USA
| | - C Ratna Prabha
- Department of Biochemistry, Faculty of Science, The M. S. University of Baroda, Vadodara, India
| | - Frenny Sheth
- FRIGE Institute of Human Genetics, FRIGE House, Jodhpur Village Road, Satellite, Ahmedabad, India, 380015
| | | | - Madhvi Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Jayesh Sheth
- FRIGE Institute of Human Genetics, FRIGE House, Jodhpur Village Road, Satellite, Ahmedabad, India, 380015.
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Uribe-Carretero E, Rey V, Fuentes JM, Tamargo-Gómez I. Lysosomal Dysfunction: Connecting the Dots in the Landscape of Human Diseases. BIOLOGY 2024; 13:34. [PMID: 38248465 PMCID: PMC10813815 DOI: 10.3390/biology13010034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/22/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
Lysosomes are the main organelles responsible for the degradation of macromolecules in eukaryotic cells. Beyond their fundamental role in degradation, lysosomes are involved in different physiological processes such as autophagy, nutrient sensing, and intracellular signaling. In some circumstances, lysosomal abnormalities underlie several human pathologies with different etiologies known as known as lysosomal storage disorders (LSDs). These disorders can result from deficiencies in primary lysosomal enzymes, dysfunction of lysosomal enzyme activators, alterations in modifiers that impact lysosomal function, or changes in membrane-associated proteins, among other factors. The clinical phenotype observed in affected patients hinges on the type and location of the accumulating substrate, influenced by genetic mutations and residual enzyme activity. In this context, the scientific community is dedicated to exploring potential therapeutic approaches, striving not only to extend lifespan but also to enhance the overall quality of life for individuals afflicted with LSDs. This review provides insights into lysosomal dysfunction from a molecular perspective, particularly in the context of human diseases, and highlights recent advancements and breakthroughs in this field.
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Affiliation(s)
- Elisabet Uribe-Carretero
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Caceres, Spain; (E.U.-C.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salud Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE), 10003 Caceres, Spain
| | - Verónica Rey
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Jose Manuel Fuentes
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Caceres, Spain; (E.U.-C.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salud Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE), 10003 Caceres, Spain
| | - Isaac Tamargo-Gómez
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
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Tang J, Chang G, Wei M, Li X, Chen H, Qin Y, Wang J, Wang X, Chen R, Li N. Diagnosis of patients with mucopolysaccharidosis type II via RNA sequencing. Clin Chim Acta 2022; 537:38-45. [DOI: 10.1016/j.cca.2022.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/29/2022] [Accepted: 10/10/2022] [Indexed: 11/03/2022]
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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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Stepien KM, Bentley A, Chen C, Dhemech MW, Gee E, Orton P, Pringle C, Rajan J, Saxena A, Tol G, Gadepalli C. Non-cardiac Manifestations in Adult Patients With Mucopolysaccharidosis. Front Cardiovasc Med 2022; 9:839391. [PMID: 35321113 PMCID: PMC8935042 DOI: 10.3389/fcvm.2022.839391] [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: 12/19/2021] [Accepted: 02/10/2022] [Indexed: 12/12/2022] Open
Abstract
Mucopolysaccharidoses (MPS) are a heterogeneous group of disorders that results in the absence or deficiency of lysosomal enzymes, leading to an inappropriate storage of glycosaminoglycans (GAGs) in various tissues of the body such as bones, cartilage, heart valves, arteries, upper airways, cornea, teeth, liver and nervous system. Clinical manifestations can become progressively exacerbated with age and affect their quality of life. Developments in advanced supportive treatment options such as enzyme replacement therapy (ERT), hematopoietic stem cell transplantation (HSCT) may have improved patients' life span. Adult MPS patients require specialist clinical surveillance long-term. In many cases, in addition to the MPS-related health problems, they may develop age-related complications. Considering the complexity of their clinical manifestations and lack of guidelines on the management of adult MPS disorders, multispecialty and multidisciplinary teams' care is essential to diagnose and treat health problems that are likely to be encountered. This review presents non-cardiac clinical manifestations, their pathophysiology, management and long-term outcomes in adult MPS patients.
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Affiliation(s)
- Karolina M. Stepien
- Adult Inherited Metabolic Diseases, Salford Royal National Health Service Foundation Trust, Salford, United Kingdom
| | - Andrew Bentley
- Northwest Ventilation Unit and Sleep Department, Wythenshawe Hospital, Manchester University National Health Service Foundation Trust, Manchester, United Kingdom
- Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
- Intensive Care & Respiratory Medicine, Manchester University National Health Service Foundation Trust, Manchester, United Kingdom
| | - Cliff Chen
- Clinical Neuropsychology, Salford Royal National Health Service Foundation Trust, Salford, United Kingdom
| | - M. Wahab Dhemech
- Northwest Ventilation Unit and Sleep Department, Wythenshawe Hospital, Manchester University National Health Service Foundation Trust, Manchester, United Kingdom
| | - Edward Gee
- Trauma and Orthopaedic Surgery, Salford Royal National Health Service Foundation Trust, Salford, United Kingdom
| | - Peter Orton
- Trauma and Orthopaedic Surgery, Salford Royal National Health Service Foundation Trust, Salford, United Kingdom
| | - Catherine Pringle
- Neurosurgery, Salford Royal National Health Service Foundation Trust, Salford, United Kingdom
| | - Jonathan Rajan
- Manchester and Salford Pain Centre, Salford Royal National Health Service Foundation Trust, Salford, United Kingdom
| | - Ankur Saxena
- Neurosurgery, Salford Royal National Health Service Foundation Trust, Salford, United Kingdom
| | - Govind Tol
- Anaesthetics Department, Salford Royal National Health Service Foundation Trust, Salford, United Kingdom
| | - Chaitanya Gadepalli
- Ear, Nose and Throat, Salford Royal National Health Service Foundation Trust, Salford, United Kingdom
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Genotype-phenotype spectrum of 130 unrelated Indian families with Mucopolysaccharidosis type II. Eur J Med Genet 2022; 65:104447. [PMID: 35144014 DOI: 10.1016/j.ejmg.2022.104447] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 12/20/2021] [Accepted: 02/06/2022] [Indexed: 11/22/2022]
Abstract
MPS II is an X linked recessive lysosomal storage disorder with multi-system involvement and marked molecular heterogeneity. In this study, we explored the clinical and molecular spectrum of 144 Indian patients with MPS II from 130 unrelated families. Clinical information was collected on a predesigned clinical proforma. Sanger method was employed to sequence all the exons and exon/intron boundaries of the IDS gene. In cases where causative variation was not detected by Sanger sequencing, MLPA and RFLP were performed to identify large deletions/duplications and complex rearrangements. Cytogenetic microarray was done in one patient to see the breakpoints and extent of deletion. In one patient with no detectable likely pathogenic or pathogenic variation, whole-genome sequencing was also performed. Novel variants were systematically assessed by in silico prediction software and protein modelling. The pathogenicity of variants was established based on ACMG criteria. An attempt was also made to establish a genotype-phenotype correlation. Positive family history was present in 31% (41/130) of patients. Developmental delay and intellectual disability were the main reasons for referral. Macrocephaly, coarse facies and dysostosis were present in almost all patients. Hepatosplenomegaly, joint contractures and short stature were the characteristic features, seen in 87% (101/116), 67.8% (74/109) and 41.4% (41/99) patients respectively. Attenuated phenotype was seen in 32.6% (47/144) patients, while severe phenotype was seen in 63% (91/144) patients. The detection rate for likely pathogenic or pathogenic variants in our cohort is 95.5% (107/112) by Sanger sequencing, MLPA and RFLP. We also found two variants of unknown significance, one each by Sanger sequencing and WGS. Total of 71 variants were identified by Sanger sequencing and 29 of these variants were found to be novel. Amongst the novel variants, there was a considerable proportion (51%) of frameshift variants (15/29). Almost half of the causative variants were located in exon 3,8 and 9. A significant genotype-phenotype correlation was also noted for both known and novel variants. This information about the genotype spectrum and phenotype will be helpful for diagnostic and prognostic purposes.
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Oliveira Netto AB, Brusius-Facchin AC, Leistner-Segal S, Kubaski F, Josahkian J, Giugliani R. Detection of Mosaic Variants in Mothers of MPS II Patients by Next Generation Sequencing. Front Mol Biosci 2021; 8:789350. [PMID: 34805285 PMCID: PMC8602069 DOI: 10.3389/fmolb.2021.789350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 10/22/2021] [Indexed: 11/13/2022] Open
Abstract
Mucopolysaccharidosis type II is an X-linked lysosomal storage disorder caused by mutations in the IDS gene that encodes the iduronate-2-sulfatase enzyme. The IDS gene is located on the long arm of the X-chromosome, comprising 9 exons, spanning approximately 24 kb. The analysis of carriers, in addition to detecting mutations in patients, is essential for genetic counseling, since the risk of recurrence for male children is 50%. Mosaicism is a well-known phenomenon described in many genetic disorders caused by a variety of mechanisms that occur when a mutation arises in the early development of an embryo. Sanger sequencing is limited in detecting somatic mosaicism and sequence change levels of less than 20% may be missed. The Next Generation Sequencing (NGS) has been increasingly used in diagnosis. It is a sensitive and fast method for the detection of somatic mosaicism. Compared to Sanger sequencing, which represents a cumulative signal, NGS technology analyzes the sequence of each DNA read in a sample. NGS might therefore facilitate the detection of mosaicism in mothers of MPS II patients. The aim of this study was to reanalyze, by NGS, all MPS II mothers that showed to be non-carriers by Sanger analysis. Twelve non-carriers were selected for the reanalysis on the Ion PGM and Ion Torrent S5 platform, using a custom panel that includes the IDS gene. Results were visualized in the Integrative Genomics Viewer (IGV). We were able to detected the presence of the variant previously found in the index case in three of the mothers, with frequencies ranging between 13 and 49% of the reads. These results suggest the possibility of mosaicism in the mothers. The use of a more sensitive technology for detecting low-level mosaic mutations is essential for accurate recurrence-risk estimates. In our study, the NGS analysis showed to be an effective methodology to detect the mosaic event.
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Affiliation(s)
- Alice Brinckmann Oliveira Netto
- Laboratory of Molecular Genetics, Medical Genetics Service, HCPA, Porto Alegre, Brazil.,Postgraduate Program in Genetics and Molecular Biology, UFRGS, Porto Alegre, Brazil
| | - Ana Carolina Brusius-Facchin
- Laboratory of Molecular Genetics, Medical Genetics Service, HCPA, Porto Alegre, Brazil.,National Institute on Population Medical Genetics, INAGEMP, Porto Alegre, Brazil.,BioDiscovery Laboratory, Experimental Research Center, HCPA, Porto Alegre, Brazil
| | - Sandra Leistner-Segal
- Laboratory of Molecular Genetics, Medical Genetics Service, HCPA, Porto Alegre, Brazil
| | - Francyne Kubaski
- Laboratory of Molecular Genetics, Medical Genetics Service, HCPA, Porto Alegre, Brazil.,Postgraduate Program in Genetics and Molecular Biology, UFRGS, Porto Alegre, Brazil.,National Institute on Population Medical Genetics, INAGEMP, Porto Alegre, Brazil.,BioDiscovery Laboratory, Experimental Research Center, HCPA, Porto Alegre, Brazil
| | - Juliana Josahkian
- Postgraduate Program in Genetics and Molecular Biology, UFRGS, Porto Alegre, Brazil.,Department of Clinical Medicine, Hospital Universitario de Santa Maria (HUSM), Santa Maria, Brazil
| | - Roberto Giugliani
- Laboratory of Molecular Genetics, Medical Genetics Service, HCPA, Porto Alegre, Brazil.,National Institute on Population Medical Genetics, INAGEMP, Porto Alegre, Brazil.,BioDiscovery Laboratory, Experimental Research Center, HCPA, Porto Alegre, Brazil.,Department of Genetics, UFRGS, Porto Alegre, Brazil
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Differences in MPS I and MPS II Disease Manifestations. Int J Mol Sci 2021; 22:ijms22157888. [PMID: 34360653 PMCID: PMC8345985 DOI: 10.3390/ijms22157888] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 02/06/2023] Open
Abstract
Mucopolysaccharidosis (MPS) type I and II are two closely related lysosomal storage diseases associated with disrupted glycosaminoglycan catabolism. In MPS II, the first step of degradation of heparan sulfate (HS) and dermatan sulfate (DS) is blocked by a deficiency in the lysosomal enzyme iduronate 2-sulfatase (IDS), while, in MPS I, blockage of the second step is caused by a deficiency in iduronidase (IDUA). The subsequent accumulation of HS and DS causes lysosomal hypertrophy and an increase in the number of lysosomes in cells, and impacts cellular functions, like cell adhesion, endocytosis, intracellular trafficking of different molecules, intracellular ionic balance, and inflammation. Characteristic phenotypical manifestations of both MPS I and II include skeletal disease, reflected in short stature, inguinal and umbilical hernias, hydrocephalus, hearing loss, coarse facial features, protruded abdomen with hepatosplenomegaly, and neurological involvement with varying functional concerns. However, a few manifestations are disease-specific, including corneal clouding in MPS I, epidermal manifestations in MPS II, and differences in the severity and nature of behavioral concerns. These phenotypic differences appear to be related to different ratios between DS and HS, and their sulfation levels. MPS I is characterized by higher DS/HS levels and lower sulfation levels, while HS levels dominate over DS levels in MPS II and sulfation levels are higher. The high presence of DS in the cornea and its involvement in the arrangement of collagen fibrils potentially causes corneal clouding to be prevalent in MPS I, but not in MPS II. The differences in neurological involvement may be due to the increased HS levels in MPS II, because of the involvement of HS in neuronal development. Current treatment options for patients with MPS II are often restricted to enzyme replacement therapy (ERT). While ERT has beneficial effects on respiratory and cardiopulmonary function and extends the lifespan of the patients, it does not significantly affect CNS manifestations, probably because the enzyme cannot pass the blood-brain barrier at sufficient levels. Many experimental therapies, therefore, aim at delivery of IDS to the CNS in an attempt to prevent neurocognitive decline in the patients.
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Zubaida B, Batool H, Cheema HA, Waheed N, Naeem M. Novel IDS Variants Identified in Three Unrelated Pakistani Patients Affected with Mucopolysaccharidosis Type II (Hunter Syndrome). Hum Hered 2020; 84:279-286. [PMID: 33075783 DOI: 10.1159/000510065] [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: 02/20/2020] [Accepted: 07/09/2020] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Mucopolysaccharidosis type II (MPS-II) or Hunter syndrome is a rare X-linked recessive disorder caused by genetic lesions in the IDS gene, encoding the iduronate-2-sulfatase (IDS) enzyme, disrupting the metabolism of certain sulfate components of the extracellular matrix. Thus, the undegraded components, also known as glycosaminoglycans, accumulate in multiple tissues resulting in multisystemic abnormalities. OBJECTIVE To uncover causative genetic lesions in probands of three unrelated Pakistani families affected with rare X-linked recessive Hunter syndrome. METHODS Screening of the IDS gene was performed in six individuals (three patients and their mothers) through whole genomic DNA extraction from peripheral blood followed by PCR and Sanger sequencing. MutationTaster, PROVEAN, Human Splicing Finder, Swiss-Model, and SwissPdbViewer were used for in silico analysis of identified variants. RESULTS All probands were presented with coarse facies, recurrent respiratory tract infection, and reduced IDS activity. Molecular screening of IDS identified three different pathogenic variants including a novel duplication variant c.114_117dupCGTT, a novel splice site variant c.1006 + 1G>C, and a nonsense variant c.1165C>T. In silico analysis unanimously revealed the pathogenic nature of the variants due to their deleterious effects upon the encoded enzyme. CONCLUSION Identified variants predictably lead to either the expression of a nonfunctional enzyme due to partial loss of SD1 and complete loss of SD2 subdomains or a complete lack of the IDS enzyme as a result of nonsense-mediated mRNA decay. Our study provides the first genetic depiction of MPS-II in Pakistan, expands the global IDS mutation spectrum, may provide insights into the three-dimensional structure of IDS, and should benefit the affected families in genetic counseling and prenatal diagnosis.
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Affiliation(s)
- Bibi Zubaida
- Medical Genetics Research Laboratory, Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Hajira Batool
- Medical Genetics Research Laboratory, Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Huma Arshad Cheema
- Department of Gastroenterology, The Children's Hospital and The Institute of Child Health, Lahore, Pakistan
| | - Nadia Waheed
- Department of Gastroenterology, The Children's Hospital and The Institute of Child Health, Lahore, Pakistan
| | - Muhammad Naeem
- Medical Genetics Research Laboratory, Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan,
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Sampayo-Cordero M, Miguel-Huguet B, Malfettone A, Pérez-García JM, Llombart-Cussac A, Cortés J, Pardo A, Pérez-López J. The Value of Case Reports in Systematic Reviews from Rare Diseases. The Example of Enzyme Replacement Therapy (ERT) in Patients with Mucopolysaccharidosis Type II (MPS-II). INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E6590. [PMID: 32927819 PMCID: PMC7558586 DOI: 10.3390/ijerph17186590] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/04/2020] [Accepted: 09/07/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND Case reports are usually excluded from systematic reviews. Patients with rare diseases are more dependent on novel individualized strategies than patients with common diseases. We reviewed and summarized the novelties reported by case reports in mucopolysaccharidosis type II (MPS-II) patients treated with enzyme replacement therapy (ERT). METHODS We selected the case reports included in a previous meta-analysis of patients with MPS-II treated with ERT. Later clinical studies evaluating the same topic of those case reports were reported. Our primary aim was to summarize novelties reported in previous case reports. Secondary objectives analyzed the number of novelties evaluated in subsequent clinical studies and the time elapsed between the publication of the case report to the publication of the clinical study. RESULTS We identified 11 innovative proposals in case reports that had not been previously considered in clinical studies. Only two (18.2%) were analyzed in subsequent nonrandomized cohort studies. The other nine novelties (81.8%) were analyzed in later case reports (five) or were not included in ulterior studies (four) after more than five years from their first publication. CONCLUSIONS Case reports should be included in systematic reviews of rare disease to obtain a comprehensive summary of the state of research and offer valuable information for healthcare practitioners.
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Affiliation(s)
- Miguel Sampayo-Cordero
- Medica Scientia Innovation Research (MedSIR), Ridgewood, NJ 07450, USA; (A.M.); (J.M.P.-G.); (A.L.-C.); (J.C.)
- Medica Scientia Innovation Research (MedSIR), 08018 Barcelona, Spain
| | - Bernat Miguel-Huguet
- Department of Surgery, Hospital de Bellvitge, L’Hospitalet de Llobregat, 08907 Barcelona, Spain;
| | - Andrea Malfettone
- Medica Scientia Innovation Research (MedSIR), Ridgewood, NJ 07450, USA; (A.M.); (J.M.P.-G.); (A.L.-C.); (J.C.)
- Medica Scientia Innovation Research (MedSIR), 08018 Barcelona, Spain
| | - José Manuel Pérez-García
- Medica Scientia Innovation Research (MedSIR), Ridgewood, NJ 07450, USA; (A.M.); (J.M.P.-G.); (A.L.-C.); (J.C.)
- Medica Scientia Innovation Research (MedSIR), 08018 Barcelona, Spain
- Institute of Breast Cancer, Quiron Group, 08023 Barcelona, Spain
| | - Antonio Llombart-Cussac
- Medica Scientia Innovation Research (MedSIR), Ridgewood, NJ 07450, USA; (A.M.); (J.M.P.-G.); (A.L.-C.); (J.C.)
- Medica Scientia Innovation Research (MedSIR), 08018 Barcelona, Spain
- Hospital Arnau de Vilanova, Universidad Católica de Valencia “San Vicente Mártir”, 46015 Valencia, Spain
| | - Javier Cortés
- Medica Scientia Innovation Research (MedSIR), Ridgewood, NJ 07450, USA; (A.M.); (J.M.P.-G.); (A.L.-C.); (J.C.)
- Medica Scientia Innovation Research (MedSIR), 08018 Barcelona, Spain
- Institute of Breast Cancer, Quiron Group, 08023 Barcelona, Spain
- Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Almudena Pardo
- Albiotech Consultores y Redacción Científica S.L., 28035 Madrid, Spain;
| | - Jordi Pérez-López
- Department of Internal Medicine, Hospital Vall d’Hebron, 08035 Barcelona, Spain;
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11
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Seo JH, Okuyama T, Shapiro E, Fukuhara Y, Kosuga M. Natural history of cognitive development in neuronopathic mucopolysaccharidosis type II (Hunter syndrome): Contribution of genotype to cognitive developmental course. Mol Genet Metab Rep 2020; 24:100630. [PMID: 32775211 PMCID: PMC7394748 DOI: 10.1016/j.ymgmr.2020.100630] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 12/20/2022] Open
Abstract
The natural history of cognitive growth in the neuronopathic form of Mucopolysaccharidosis type II (MPS II) is not well defined especially their patterns of development and decline. The ability to predict the developmental course of the neurologically impaired patient is necessary to assess treatment outcomes aimed at the brain. Thirteen intravenous enzyme replacement therapy-treated Japanese patients with neuronopathic MPSII who had mutation analysis were followed on one standard measure of cognitive development over time. Six children in Group MS had missense mutations and 7 children in Group NT had null type mutations such as deletions, recombination with the pseudogene, and nonsense mutations. The patients as a whole demonstrated cognitive growth until about 36-42 months of age, followed by a plateau in development. The mean age equivalent score at age 3 was similar to that at age 6. While the decline was slow for the entire group, the patients in Group NT showed a more rapid decline than those in Group MS. Two patients with deletions showed decline to a very low level by age 5. The long plateau in cognitive development in patents with MPS II was substantiated and was consistent with other studies. This is the first demonstration that different mutation types within the neuronopathic MPS II patients are associated with different rates of decline. We also were able to identify the chronological age before which a trial would need to start in order to maintain cognitive growth and a ceiling beyond which a relatively normal outcome would not be likely.
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Affiliation(s)
- Joo-Hyun Seo
- Clinical Laboratory Medicine, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan
| | - Torayuki Okuyama
- Clinical Laboratory Medicine, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan
- Center for Lysosomal Storage Diseases, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan
| | - Elsa Shapiro
- Department of Pediatrics, University of Minnesota Twin Cities, Minneapolis, MN 55455, United States of America
| | - Yasuyuki Fukuhara
- Division of Medical Genetics, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan
| | - Motomichi Kosuga
- Division of Medical Genetics, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535, Japan
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12
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Li D, Lin Y, Huang Y, Zhang W, Jiang M, Li X, Zhao X, Sheng H, Yin X, Su X, Shao Y, Liu Z, Li D, Li F, Liao C, Liu L. Early prenatal diagnosis of lysosomal storage disorders by enzymatic and molecular analysis. Prenat Diagn 2018; 38:779-787. [PMID: 29966168 DOI: 10.1002/pd.5329] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 06/10/2018] [Accepted: 06/27/2018] [Indexed: 01/28/2023]
Abstract
OBJECTIVE To report the 4-year experience of early prenatal diagnosis of lysosomal storage disorders (LSDs) at a center in mainland China. METHOD Forty-seven pregnancies affected with LSDs were assed using enzymes and/or molecular studies. Prenatal studies were performed on 43 uncultured chorionic villi (CV) samples, two amniotic fluid samples, and two umbilical cord blood samples. RESULTS Of the 47 fetuses, 23 (48.9%) were determined to normal, 13 (27.7%) to be carriers, and 11 (23.4%) diagnosed as affected. In this cohort, mucopolysaccharidoses (MPS) type II was the most common LSD, followed by Pompe disease and then metachromatic leucodystrophy. In the 17 MPS II cases, the four affected fetuses showed MPS II enzyme activity expression levels of 1.4% to 6.7%, while the enzyme activity levels of the 13 normal fetuses ranged from 72% to 240.4%. In the seven Pompe cases, three fetuses were normal with Pompe enzyme activity expression levels of 20%, 38.8%, and 77.3%, while four carrier pregnancies showed enzyme activity levels of 17.5%, 17.5%, 33.4%, and 13.8%, respectively. CONCLUSION Based on different enzyme properties in uncultured CV, different prenatal diagnostic strategies should be adopted for MPS II and Pompe disease. Combining enzyme assay and molecular studies in uncultured CV improves the reliability of prenatal diagnosis of LSDs.
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Affiliation(s)
- Duan Li
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Yunting Lin
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Yonglan Huang
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Wen Zhang
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Minyan Jiang
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Xiuzhen Li
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Xiaoyuan Zhao
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Huiying Sheng
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Xi Yin
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Xueying Su
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Yongxian Shao
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Zongcai Liu
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Dongzhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Fatao Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Can Liao
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Li Liu
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou, China
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13
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Dvorakova L, Vlaskova H, Sarajlija A, Ramadza DP, Poupetova H, Hruba E, Hlavata A, Bzduch V, Peskova K, Storkanova G, Kecman B, Djordjevic M, Baric I, Fumic K, Barisic I, Reboun M, Kulhanek J, Zeman J, Magner M. Genotype-phenotype correlation in 44 Czech, Slovak, Croatian and Serbian patients with mucopolysaccharidosis type II. Clin Genet 2017; 91:787-796. [PMID: 27883178 DOI: 10.1111/cge.12927] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/07/2016] [Accepted: 11/17/2016] [Indexed: 11/26/2022]
Abstract
Mucopolysaccharidosis type II (Hunter syndrome, MPS II, OMIM 309900) is an X-linked lysosomal storage disorder caused by deficiency of iduronate-2-sulfatase (IDS). We analyzed clinical and laboratory data from 44 Slavic patients with this disease. In total, 21 Czech, 7 Slovak, 9 Croatian and 7 Serbian patients (43 M/1 F) were included in the study (median age 11.0 years, range 1.2-43 years). Birth prevalence ranged from 1:69,223 (Serbia) to 1:192,626 (Czech Rep.). In the majority of patients (71%), the disease manifested in infancy. Cognitive functions were normal in 10 patients. Four, six and 24 patients had mild, moderate, and severe developmental delay, respectively, typically subsequent to developmental regression (59%). Residual enzyme activity showed no predictive value, and estimation of glycosaminoglycans (GAGs) had only limited importance for prognosis. Mutation analysis performed in 36 families led to the identification of 12 novel mutations, eight of which were small deletions/insertions. Large deletions/rearrangements and all but one small deletion/insertion led to a severe phenotype. This genotype-phenotype correlation was also identified in six cases with recurrent missense mutations. Based on patient genotype, the severity of the disease may be predicted with high probability in approximately half of MPS II patients.
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Affiliation(s)
- L Dvorakova
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - H Vlaskova
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - A Sarajlija
- Department of Metabolism and Clinical Genetics, Mother and Child Health Care Institute of Serbia, Belgrade, Serbia.,School of Medicine, University of Belgrade, Belgrade, Serbia
| | - D P Ramadza
- Department of Pediatrics, University Hospital Center, Zagreb, Croatia
| | - H Poupetova
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - E Hruba
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - A Hlavata
- 2nd Department of Pediatrics, Comenius University Medical School in Bratislava University Children's Hospital, Bratislava, Slovakia
| | - V Bzduch
- 1st Department of Pediatrics, Comenius University Medical School in Bratislava University Children's Hospital, Bratislava, Slovakia
| | - K Peskova
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - G Storkanova
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - B Kecman
- Department of Metabolism and Clinical Genetics, Mother and Child Health Care Institute of Serbia, Belgrade, Serbia
| | - M Djordjevic
- Department of Metabolism and Clinical Genetics, Mother and Child Health Care Institute of Serbia, Belgrade, Serbia.,School of Medicine, University of Belgrade, Belgrade, Serbia
| | - I Baric
- Department of Pediatrics, University Hospital Center and University of Zagreb, School of Medicine, Zagreb, Croatia
| | - K Fumic
- Department of Laboratory Diagnostics, University Hospital Centre Zagreb and School of Medicine, Zagreb, Croatia
| | - I Barisic
- Department of Paediatrics, Children's Hospital Zagreb, School of Medicine, Zagreb, Croatia
| | - M Reboun
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - J Kulhanek
- Department of Paediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - J Zeman
- Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic.,Department of Paediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - M Magner
- Department of Paediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
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14
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Cervera-Gaviria M, Alcántara-Ortigoza MA, González-Del Angel A, Moyers-Pérez P, Legorreta-Ramírez BGL, Barrera-Carmona N, Cervera-Gaviria J. An uncommon inheritance pattern in Niemann-Pick disease type C: identification of probable paternal germline mosaicism in a Mexican family. BMC Neurol 2016; 16:147. [PMID: 27549128 PMCID: PMC4994172 DOI: 10.1186/s12883-016-0649-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 07/26/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Niemann-Pick disease type C (NP-C) is a fatal lysosomal neurodegenerative and neurovisceral disease. It is caused by defects in intracellular lipid trafficking, which lead to the accumulation of lipids and glycosphingolipids within the endosomes and lysosomes of affected individuals. Pathogenic variants of the NPC1 or NPC2 genes yield highly variable phenotypes with a time course that ranges from fetal onset (i.e., hydrops fetalis) to progressive dementia in adults. NP-C is typically inherited in an autosomal-recessive manner. To our knowledge, no previous report has identified germline mosaicism as an inheritance mechanism in NP-C. CASE PRESENTATION We report the case of a male Mexican patient with "variant" filipin staining and a juvenile form of NP-C attributed to compound heterozygosity for two previously reported pathogenic variants of NPC1: c.[1042C>T];[2780C>T] or p.[Arg348*];[Ala927Val]. The proband's mother and healthy sister were heterozygous carriers of the c.2780C > T (exon 18) and c.1042C > T (exon 8) variants, respectively. However, direct sequencing of exons 8 and 18 of NPC1 revealed no mutation in genomic DNA obtained from the father's peripheral blood. DNA profiling ruled out the possibility of non-paternity. We were unable to obtain a sperm sample to demonstrate paternal gonadal mosaicism. NPC1 haplotype analysis using 20 linked single nucleotide variants failed to yield sufficient information to document a p.(Arg348*) NPC1 pathogenic variant-associated haplotype in the family. CONCLUSIONS We propose that this case of NP-C involves paternal germline mosaicism. To the best of our knowledge, this has not previously been reported in NP-C.
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Affiliation(s)
- Marivi Cervera-Gaviria
- Departamento de Genética Médica, Centro de Rehabilitación e Inclusión Infantil Teletón, Vía Gustavo Baz No. 219, Colonia San Pedro Barrientos, Tlalnepantla, Estado de México, 54960, México.
| | - Miguel Angel Alcántara-Ortigoza
- Laboratorio de Biología Molecular, Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de México, México.,DNA-GEN, S.C. Centro de Alta Especialidad en Genética Humana, Ciudad de México, México
| | - Ariadna González-Del Angel
- Laboratorio de Biología Molecular, Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de México, México.,DNA-GEN, S.C. Centro de Alta Especialidad en Genética Humana, Ciudad de México, México
| | - Paola Moyers-Pérez
- Departamento de Genética Médica, Centro de Rehabilitación e Inclusión Infantil Teletón, Vía Gustavo Baz No. 219, Colonia San Pedro Barrientos, Tlalnepantla, Estado de México, 54960, México
| | | | - Nancy Barrera-Carmona
- Departamento de Neuropediatría, Centro de Rehabilitación e Inclusión Infantil Teletón, Estado de México, México
| | - Jaime Cervera-Gaviria
- Servicio de Medicina Interna, Sociedad de Beneficencia Española, Ciudad de México, México
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