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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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Pfrieger FW. The Niemann-Pick type diseases – A synopsis of inborn errors in sphingolipid and cholesterol metabolism. Prog Lipid Res 2023; 90:101225. [PMID: 37003582 DOI: 10.1016/j.plipres.2023.101225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
Disturbances of lipid homeostasis in cells provoke human diseases. The elucidation of the underlying mechanisms and the development of efficient therapies represent formidable challenges for biomedical research. Exemplary cases are two rare, autosomal recessive, and ultimately fatal lysosomal diseases historically named "Niemann-Pick" honoring the physicians, whose pioneering observations led to their discovery. Acid sphingomyelinase deficiency (ASMD) and Niemann-Pick type C disease (NPCD) are caused by specific variants of the sphingomyelin phosphodiesterase 1 (SMPD1) and NPC intracellular cholesterol transporter 1 (NPC1) or NPC intracellular cholesterol transporter 2 (NPC2) genes that perturb homeostasis of two key membrane components, sphingomyelin and cholesterol, respectively. Patients with severe forms of these diseases present visceral and neurologic symptoms and succumb to premature death. This synopsis traces the tortuous discovery of the Niemann-Pick diseases, highlights important advances with respect to genetic culprits and cellular mechanisms, and exposes efforts to improve diagnosis and to explore new therapeutic approaches.
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3
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Armstrong Z, Meek RW, Wu L, Blaza JN, Davies GJ. Cryo-EM structures of human fucosidase FucA1 reveal insight into substrate recognition and catalysis. Structure 2022; 30:1443-1451.e5. [PMID: 35907402 PMCID: PMC9548408 DOI: 10.1016/j.str.2022.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 06/10/2022] [Accepted: 07/04/2022] [Indexed: 01/08/2023]
Abstract
Enzymatic hydrolysis of α-L-fucose from fucosylated glycoconjugates is consequential in bacterial infections and the neurodegenerative lysosomal storage disorder fucosidosis. Understanding human α-L-fucosidase catalysis, in an effort toward drug design, has been hindered by the absence of three-dimensional structural data for any animal fucosidase. Here, we have used cryoelectron microscopy (cryo-EM) to determine the structure of human lysosomal α-L-fucosidase (FucA1) in both an unliganded state and in complex with the inhibitor deoxyfuconojirimycin. These structures, determined at 2.49 Å resolution, reveal the homotetrameric structure of FucA1, the architecture of the catalytic center, and the location of both natural population variations and disease-causing mutations. Furthermore, this work has conclusively identified the hitherto contentious identity of the catalytic acid/base as aspartate-276, representing a shift from both the canonical glutamate acid/base residue and a previously proposed glutamate residue. These findings have furthered our understanding of how FucA1 functions in both health and disease.
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Affiliation(s)
- Zachary Armstrong
- Department of Chemistry, Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, UK
| | - Richard W Meek
- Department of Chemistry, Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, UK
| | - Liang Wu
- Department of Chemistry, Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, UK; The Rosalind Franklin Institute, Harwell Campus, Didcot OX11 0FA, UK
| | - James N Blaza
- Department of Chemistry, Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, UK
| | - Gideon J Davies
- Department of Chemistry, Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, UK.
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4
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Splicing Modulation as a Promising Therapeutic Strategy for Lysosomal Storage Disorders: The Mucopolysaccharidoses Example. Life (Basel) 2022; 12:life12050608. [PMID: 35629276 PMCID: PMC9146820 DOI: 10.3390/life12050608] [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: 03/16/2022] [Revised: 04/07/2022] [Accepted: 04/15/2022] [Indexed: 11/17/2022] Open
Abstract
Over recent decades, the many functions of RNA have become more evident. This molecule has been recognized not only as a carrier of genetic information, but also as a specific and essential regulator of gene expression. Different RNA species have been identified and novel and exciting roles have been unveiled. Quite remarkably, this explosion of novel RNA classes has increased the possibility for new therapeutic strategies that tap into RNA biology. Most of these drugs use nucleic acid analogues and take advantage of complementary base pairing to either mimic or antagonize the function of RNAs. Among the most successful RNA-based drugs are those that act at the pre-mRNA level to modulate or correct aberrant splicing patterns, which are caused by specific pathogenic variants. This approach is particularly tempting for monogenic disorders with associated splicing defects, especially when they are highly frequent among affected patients worldwide or within a specific population. With more than 600 mutations that cause disease affecting the pre-mRNA splicing process, we consider lysosomal storage diseases (LSDs) to be perfect candidates for this type of approach. Here, we introduce the overall rationale and general mechanisms of splicing modulation approaches and highlight the currently marketed formulations, which have been developed for non-lysosomal genetic disorders. We also extensively reviewed the existing preclinical studies on the potential of this sort of therapeutic strategy to recover aberrant splicing and increase enzyme activity in our diseases of interest: the LSDs. Special attention was paid to a particular subgroup of LSDs: the mucopolysaccharidoses (MPSs). By doing this, we hoped to unveil the unique therapeutic potential of the use of this sort of approach for LSDs as a whole.
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Molina Romero M, Yoldi Chaure A, Gañán Parra M, Navas Bastida P, del Pico Sánchez JL, Vaquero Argüelles Á, de la Fuente Vaquero P, Ramírez López JP, Castilla Alcalá JA. Probability of high-risk genetic matching with oocyte and semen donors: complete gene analysis or genotyping test? J Assist Reprod Genet 2022; 39:341-355. [PMID: 35091964 PMCID: PMC8956772 DOI: 10.1007/s10815-021-02381-0] [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: 03/29/2021] [Accepted: 12/17/2021] [Indexed: 02/03/2023] Open
Abstract
PURPOSE To estimate the probability of high-risk genetic matching when assisted reproductive techniques (ART) are applied with double gamete donation, following an NGS carrier test based on a complete study of the genes concerned. We then determine the results that would have been obtained if the genotyping tests most widely used in Spanish gamete banks had been applied. METHODS In this descriptive observational study, 1818 gamete donors were characterised by NGS. The pathogenic variants detected were analysed to estimate the probability of high-risk genetic matching and to determine the results that would have been obtained if the three most commonly used genotyping tests in ART had been applied. RESULTS The probability of high-risk genetic matching with gamete donation, screened by NGS and complete gene analysis, was 5.5%, versus the 0.6-2.7% that would have been obtained with the genotyping test. A total of 1741 variants were detected, including 607 different variants, of which only 22.6% would have been detected by all three genotyping tests considered and 44.7% of which would not have been detected by any of these tests. CONCLUSION Our study highlights the considerable heterogeneity of the genotyping tests, which present significant differences in their ability to detect pathogenic variants. The complete study of the genes by NGS considerably reduces reproductive risks when genetic matching is performed with gamete donors. Accordingly, we recommend that carrier screening in gamete donors be carried out using NGS and a complete study with nontargeted analysis of the variants of the screened genes.
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Affiliation(s)
- Marta Molina Romero
- CEIFER Biobanco - NextClinics, Calle Maestro Bretón, 1, 18004 Granada, Spain
| | | | | | | | | | | | | | | | - José Antonio Castilla Alcalá
- CEIFER Biobanco - NextClinics, Calle Maestro Bretón, 1, 18004 Granada, Spain ,U. Reproducción, UGC Obstetricia y Ginecología, HU Virgen de Las Nieves, Granada, Spain ,Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain
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6
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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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7
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A Comprehensive, Targeted NGS Approach to Assessing Molecular Diagnosis of Lysosomal Storage Diseases. Genes (Basel) 2021; 12:genes12111750. [PMID: 34828358 PMCID: PMC8617937 DOI: 10.3390/genes12111750] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 01/20/2023] Open
Abstract
With over 60 different disorders and a combined incidence occurring in 1:5000-7000 live births, lysosomal storage diseases (LSDs) represent a major public health problem and constitute an enormous burden for affected individuals and their families. Several reasons make the diagnosis of LSDs an arduous task for clinicians, including the phenotype and penetrance variability, the shared signs and symptoms, and the uncertainties related to biochemical enzymatic assay results. Developing a powerful diagnostic tool based on next generation sequencing (NGS) technology may help reduce the delayed diagnostic process for these families, leading to better outcomes for current therapies and providing the basis for more appropriate genetic counseling. Herein, we employed a targeted NGS-based panel to scan the coding regions of 65 LSD-causative genes. A reference group sample (n = 26) with previously known genetic mutations was used to test and validate the entire workflow. Our approach demonstrated elevated analytical accuracy, sensitivity, and specificity. We believe the adoption of comprehensive targeted sequencing strategies into a routine diagnostic route may accelerate both the identification and management of LSDs with overlapping clinical profiles, producing a significant reduction in delayed diagnostic response with beneficial results in the treatment outcome.
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8
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Mak J, Cowan TM. Detecting lysosomal storage disorders by glycomic profiling using liquid chromatography mass spectrometry. Mol Genet Metab 2021; 134:43-52. [PMID: 34474962 PMCID: PMC9069563 DOI: 10.1016/j.ymgme.2021.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 08/14/2021] [Accepted: 08/15/2021] [Indexed: 01/15/2023]
Abstract
BACKGROUND Urine and plasma biomarker testing for lysosomal storage disorders by liquid chromatography mass spectrometry (LC-MS) currently requires multiple analytical methods to detect the abnormal accumulation of oligosaccharides, mucopolysaccharides, and glycolipids. To improve clinical testing efficiency, we developed a single LC-MS method to simultaneously identify disorders of oligosaccharide, mucopolysaccharide, and glycolipid metabolism with minimal sample preparation. METHODS We created a single chromatographic method for separating free glycans and glycolipids in their native form, using an amide column and high pH conditions. We used this glycomic profiling method both in untargeted analyses of patient and control urines using LC ion-mobility high-resolution MS (biomarker discovery), and targeted analyses of urine, serum, and dried blood spot samples by LC-MS/MS (clinical validation). RESULTS Untargeted glycomic profiling revealed twenty biomarkers that could identify and subtype mucopolysaccharidoses. We incorporated these with known oligosaccharide and glycolipid biomarkers into a rapid test that identifies at least 27 lysosomal storage disorders, including oligosaccharidoses, mucopolysaccharidoses, sphingolipidoses, glycogen storage disorders, and congenital disorders of glycosylation and de-glycosylation. In a validation set containing 115 urine samples from patients with lysosomal storage disorders, all were unambiguously distinguished from normal controls, with correct disease subtyping for 88% (101/115) of cases. Glucosylsphingosine was reliably elevated in dried blood spots from Gaucher disease patients with baseline resolution from galactosylsphingosine. CONCLUSION Glycomic profiling by liquid chromatography mass spectrometry identifies a range of lysosomal storage disorders. This test can be used in clinical evaluations to rapidly focus a diagnosis, as well as to clarify or support additional gene sequencing and enzyme studies.
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Affiliation(s)
- Justin Mak
- Clinical Biochemical Genetics Laboratory, Stanford Health Care, United States of America.
| | - Tina M Cowan
- Clinical Biochemical Genetics Laboratory, Stanford Health Care, United States of America; Department of Pathology, Stanford University Medical Center, United States of America
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Ludwig NF, Sperb-Ludwig F, Randon DN, Bernardi P, Giuliani LR, Moreno CA, Cavalcanti DP, Silva LCSD, Schwartz IVD. A decade of molecular diagnosis of Mucolipidosis II and III in Brazil: a pooled analysis of 32 patients. JOURNAL OF INBORN ERRORS OF METABOLISM AND SCREENING 2021. [DOI: 10.1590/2326-4594-jiems-2020-0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Nataniel F Ludwig
- Hospital de Clínicas de Porto Alegre, Brazil; Universidade Federal do Rio Grande do Sul, Porto Alegre, Brasil, Brazil
| | - Fernanda Sperb-Ludwig
- Hospital de Clínicas de Porto Alegre, Brazil; Universidade Federal do Rio Grande do Sul, Porto Alegre, Brasil, Brazil
| | - Dévora N Randon
- Hospital de Clínicas de Porto Alegre, Brazil; Universidade Federal do Rio Grande do Sul, Porto Alegre, Brasil, Brazil
| | | | | | | | | | | | - Ida V D Schwartz
- Hospital de Clínicas de Porto Alegre, Brazil; Universidade Federal do Rio Grande do Sul, Porto Alegre, Brasil, Brazil; Hospital de Clínicas de Porto Alegre, Brazil
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10
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Fucosidosis-Clinical Manifestation, Long-Term Outcomes, and Genetic Profile-Review and Case Series. Genes (Basel) 2020; 11:genes11111383. [PMID: 33266441 PMCID: PMC7700486 DOI: 10.3390/genes11111383] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/10/2020] [Accepted: 11/19/2020] [Indexed: 12/21/2022] Open
Abstract
Fucosidosis is a neurodegenerative disorder which progresses inexorably. Clinical features include coarse facial features, growth retardation, recurrent upper respiratory infections, dysostosis multiplex, and angiokeratoma corporis diffusum. Fucosidosis is caused by mutations in the FUCA1 gene resulting in α-L-fucosidase deficiency. Only 36 pathogenic variants in the FUCA1 gene are related to fucosidosis. Most of them are missense/nonsense substitutions; six missense and 11 nonsense mutations. Among deletions there were eight small and five gross changes. So far, only three splice site variants have been described—one small deletion, one complete deletion and one stop-loss mutation. The disease has a significant clinical variability, the cause of which is not well understood. The genotype–phenotype correlation has not been well defined. This review describes the genetic profile and clinical manifestations of fucosidosis in pediatric and adult cases.
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11
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Encarnação M, Coutinho MF, Silva L, Ribeiro D, Ouesleti S, Campos T, Santos H, Martins E, Cardoso MT, Vilarinho L, Alves S. Assessing Lysosomal Disorders in the NGS Era: Identification of Novel Rare Variants. Int J Mol Sci 2020; 21:E6355. [PMID: 32883051 PMCID: PMC7503609 DOI: 10.3390/ijms21176355] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/25/2020] [Accepted: 08/28/2020] [Indexed: 11/16/2022] Open
Abstract
Lysosomal storage diseases (LSDs) are a heterogeneous group of genetic disorders with variable degrees of severity and a broad phenotypic spectrum, which may overlap with a number of other conditions. While individually rare, as a group LSDs affect a significant number of patients, placing an important burden on affected individuals and their families but also on national health care systems worldwide. Here, we present our results on the use of an in-house customized next-generation sequencing (NGS) panel of genes related to lysosome function as a first-line molecular test for the diagnosis of LSDs. Ultimately, our goal is to provide a fast and effective tool to screen for virtually all LSDs in a single run, thus contributing to decrease the diagnostic odyssey, accelerating the time to diagnosis. Our study enrolled a group of 23 patients with variable degrees of clinical and/or biochemical suspicion of LSD. Briefly, NGS analysis data workflow, followed by segregation analysis allowed the characterization of approximately 41% of the analyzed patients and the identification of 10 different pathogenic variants, underlying nine LSDs. Importantly, four of those variants were novel, and, when applicable, their effect over protein structure was evaluated through in silico analysis. One of the novel pathogenic variants was identified in the GM2A gene, which is associated with an ultra-rare (or misdiagnosed) LSD, the AB variant of GM2 Gangliosidosis. Overall, this case series highlights not only the major advantages of NGS-based diagnostic approaches but also, to some extent, its limitations ultimately promoting a reflection on the role of targeted panels as a primary tool for the prompt characterization of LSD patients.
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Affiliation(s)
- Marisa Encarnação
- Research and Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, 4000-055 Porto, Portugal; (M.E.); (M.F.C.); (L.S.); (D.R.); (L.V.)
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, 4000-055 Porto, Portugal
- Center for the Study of Animal Science, CECA-ICETA, University of Porto, 4051-401 Porto, Portugal
| | - Maria Francisca Coutinho
- Research and Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, 4000-055 Porto, Portugal; (M.E.); (M.F.C.); (L.S.); (D.R.); (L.V.)
- Center for the Study of Animal Science, CECA-ICETA, University of Porto, 4051-401 Porto, Portugal
| | - Lisbeth Silva
- Research and Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, 4000-055 Porto, Portugal; (M.E.); (M.F.C.); (L.S.); (D.R.); (L.V.)
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, 4000-055 Porto, Portugal
| | - Diogo Ribeiro
- Research and Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, 4000-055 Porto, Portugal; (M.E.); (M.F.C.); (L.S.); (D.R.); (L.V.)
| | - Souad Ouesleti
- Biochemical Service, CHU Farhat Hached, 4000 Sousse, Tunisia;
| | - Teresa Campos
- Reference Center for Inherited Metabolic Disorders, University Hospital Centre S. João, 4202-451 Porto, Portugal; (T.C.); (M.T.C.)
| | - Helena Santos
- Department of Pediatrics, Hospital Centre, EPE, 4434-502 V.N. Gaia, Portugal;
| | - Esmeralda Martins
- Oporto Hospital Centre, University of Porto, 4099-001 Porto, Portugal;
| | - Maria Teresa Cardoso
- Reference Center for Inherited Metabolic Disorders, University Hospital Centre S. João, 4202-451 Porto, Portugal; (T.C.); (M.T.C.)
| | - Laura Vilarinho
- Research and Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, 4000-055 Porto, Portugal; (M.E.); (M.F.C.); (L.S.); (D.R.); (L.V.)
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, 4000-055 Porto, Portugal
- Center for the Study of Animal Science, CECA-ICETA, University of Porto, 4051-401 Porto, Portugal
| | - Sandra Alves
- Research and Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, 4000-055 Porto, Portugal; (M.E.); (M.F.C.); (L.S.); (D.R.); (L.V.)
- Center for the Study of Animal Science, CECA-ICETA, University of Porto, 4051-401 Porto, Portugal
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12
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Schiff ER, Daich Varela M, Robson AG, Pierpoint K, Ba-Abbad R, Nutan S, Zein WM, Ullah E, Huryn LA, Tuupanen S, Mahroo OA, Michaelides M, Burke D, Harvey K, Arno G, Hufnagel RB, Webster AR. A genetic and clinical study of individuals with nonsyndromic retinopathy consequent upon sequence variants in HGSNAT, the gene associated with Sanfilippo C mucopolysaccharidosis. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:631-643. [PMID: 32770643 PMCID: PMC8125330 DOI: 10.1002/ajmg.c.31822] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/02/2020] [Accepted: 07/21/2020] [Indexed: 11/06/2022]
Abstract
Pathogenic variants in the gene HGSNAT (heparan-α-glucosaminide N-acetyltransferase) have been reported to underlie two distinct recessive conditions, depending on the specific genotype, mucopolysaccharidosis type IIIC (MPSIIIC)-a severe childhood-onset lysosomal storage disorder, and adult-onset nonsyndromic retinitis pigmentosa (RP). Here we describe the largest cohort to-date of HGSNAT-associated nonsyndromic RP patients, and describe their retinal phenotype, leukocyte enzymatic activity, and likely pathogenic genotypes. We identified biallelic HGSNAT variants in 17 individuals (15 families) as the likely cause of their RP. None showed any other symptoms of MPSIIIC. All had a mild but significant reduction of HGSNAT enzyme activity in leukocytes. The retinal condition was generally of late-onset, showing progressive degeneration of a concentric area of paramacular retina, with preservation but reduced electroretinogram responses. Symptoms, electrophysiology, and imaging suggest the rod photoreceptor to be the cell initially compromised. HGSNAT enzymatic testing was useful in resolving diagnostic dilemmas in compatible patients. We identified seven novel sequence variants [p.(Arg239Cys); p.(Ser296Leu); p.(Phe428Cys); p.(Gly248Ala); p.(Gly418Arg), c.1543-2A>C; c.1708delA], three of which were considered to be retina-disease-specific alleles. The most prevalent retina-disease-specific allele p.(Ala615Thr) was observed heterozygously or homozygously in 8 and 5 individuals respectively (7 and 4 families). Two siblings in one family, while identical for the HGSNAT locus, but discordant for retinal disease, suggest the influence of trans-acting genetic or environmental modifying factors.
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Affiliation(s)
- Elena R Schiff
- Genetics Service, Moorfields Eye Hospital, London, UK.,UCL Institute of Ophthalmology, London, UK
| | - Malena Daich Varela
- Ophthalmic Genetics and Visual Function branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Anthony G Robson
- UCL Institute of Ophthalmology, London, UK.,Department of Electrophysiology, Moorfields Eye Hospital, London, UK
| | | | - Rola Ba-Abbad
- Genetics Service, Moorfields Eye Hospital, London, UK.,UCL Institute of Ophthalmology, London, UK
| | - Savita Nutan
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Wadih M Zein
- Ophthalmic Genetics and Visual Function branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Ehsan Ullah
- Ophthalmic Genetics and Visual Function branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Laryssa A Huryn
- Ophthalmic Genetics and Visual Function branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Omar A Mahroo
- Genetics Service, Moorfields Eye Hospital, London, UK.,UCL Institute of Ophthalmology, London, UK.,Section of Ophthalmology, King's College London, London, UK
| | - Michel Michaelides
- Genetics Service, Moorfields Eye Hospital, London, UK.,UCL Institute of Ophthalmology, London, UK
| | - Derek Burke
- Enzyme Unit, Chemical Pathology, Paediatric Laboratory Medicine, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Katie Harvey
- Enzyme Unit, Chemical Pathology, Paediatric Laboratory Medicine, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Gavin Arno
- Genetics Service, Moorfields Eye Hospital, London, UK.,UCL Institute of Ophthalmology, London, UK.,North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrew R Webster
- Genetics Service, Moorfields Eye Hospital, London, UK.,UCL Institute of Ophthalmology, London, UK
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13
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Lv RJ, Li TR, Zhang YD, Shao XQ, Wang Q, Jin LR. Clinical and genetic characteristics of type I sialidosis patients in mainland China. Ann Clin Transl Neurol 2020; 7:911-923. [PMID: 32472645 PMCID: PMC7318099 DOI: 10.1002/acn3.51058] [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: 02/05/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 11/23/2022] Open
Abstract
Objective Type I sialidosis (ST‐1) is a rare autosomal recessive inherited disorder. To date, there has been no study on ST‐1 patients in mainland China. Methods We reported in detail the cases of five Chinese ST‐1 patients from two centers, and summarized all worldwide cases. Then, we compared the differences between Chinese and foreign patients. Results A total of 77 genetically confirmed ST‐1 patients were identified: 12 from mainland China, 23 from Taiwan, 10 from other Asian regions, and 32 from European and American regions. The mean age of onset was 16.0 ± 6.7 years; the most common symptoms were myoclonus seizures (96.0%), followed by ataxia (94.3%), and blurred vision (67.2%). Compared to other groups, the onset age of patients from mainland China was much younger (10.8 ± 2.7 years). The incidence of visual impairment was lower in patients from other Asian regions than in patients from mainland China and Taiwan (28.6% vs. 81.8%–100%). Cherry‐red spots were less frequent in the Taiwanese patients than in patients from other regions (27.3% vs. 55.2%–90.0%). Furthermore, 48 different mutation types were identified. Chinese mainland and Taiwanese patients were more likely to carry the c.544A > G mutation (75% and 100%, respectively) than the patients from other regions (only 0%–10.0%). Approximately 50% of Chinese mainland patients carried the c.239C > T mutation, a much higher proportion than that found in the other populations. In addition, although the brain MRI of most patients was normal, 18F‐FDG‐PET analysis could reveal cerebellar and occipital lobe hypometabolism. Interpretation ST‐1 patients in different regions are likely to have different mutation types; environmental factors may influence clinical manifestations. Larger studies enrolling more patients are required.
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Affiliation(s)
- Rui-Juan Lv
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University; China National Clinical Research Center for Neurological Diseases, 119 South Fourth Ring West Road, Fengtai District, Beijing, 100070, PR. China
| | - Tao-Ran Li
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University; China National Clinical Research Center for Neurological Diseases, 119 South Fourth Ring West Road, Fengtai District, Beijing, 100070, PR. China.,Department of Neurology, Xuanwu Hospital of Capital Medical University, 45 Chang Chun Road, Xicheng District, Beijing, 100053, PR. China
| | - Yu-Di Zhang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University; China National Clinical Research Center for Neurological Diseases, 119 South Fourth Ring West Road, Fengtai District, Beijing, 100070, PR. China.,Department of Neurology, the Second Hospital of Hebei Medical University, Hebei Medical University, 215 Heping West Road, Xinhua District, Hebei, 050000, Shijiazhuang, PR. China
| | - Xiao-Qiu Shao
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University; China National Clinical Research Center for Neurological Diseases, 119 South Fourth Ring West Road, Fengtai District, Beijing, 100070, PR. China
| | - Qun Wang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University; China National Clinical Research Center for Neurological Diseases, 119 South Fourth Ring West Road, Fengtai District, Beijing, 100070, PR. China
| | - Li-Ri Jin
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, PR. China
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14
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Roca I, González-Castro L, Maynou J, Palacios L, Fernández H, Couce ML, Fernández-Marmiesse A. PattRec: An easy-to-use CNV detection tool optimized for targeted NGS assays with diagnostic purposes. Genomics 2020; 112:1245-1256. [DOI: 10.1016/j.ygeno.2019.07.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/25/2019] [Accepted: 07/21/2019] [Indexed: 12/17/2022]
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15
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D’Avanzo F, Rigon L, Zanetti A, Tomanin R. Mucopolysaccharidosis Type II: One Hundred Years of Research, Diagnosis, and Treatment. Int J Mol Sci 2020; 21:E1258. [PMID: 32070051 PMCID: PMC7072947 DOI: 10.3390/ijms21041258] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 12/11/2022] Open
Abstract
Mucopolysaccharidosis type II (MPS II, Hunter syndrome) was first described by Dr. Charles Hunter in 1917. Since then, about one hundred years have passed and Hunter syndrome, although at first neglected for a few decades and afterwards mistaken for a long time for the similar disorder Hurler syndrome, has been clearly distinguished as a specific disease since 1978, when the distinct genetic causes of the two disorders were finally identified. MPS II is a rare genetic disorder, recently described as presenting an incidence rate ranging from 0.38 to 1.09 per 100,000 live male births, and it is the only X-linked-inherited mucopolysaccharidosis. The complex disease is due to a deficit of the lysosomal hydrolase iduronate 2-sulphatase, which is a crucial enzyme in the stepwise degradation of heparan and dermatan sulphate. This contributes to a heavy clinical phenotype involving most organ-systems, including the brain, in at least two-thirds of cases. In this review, we will summarize the history of the disease during this century through clinical and laboratory evaluations that allowed its definition, its correct diagnosis, a partial comprehension of its pathogenesis, and the proposition of therapeutic protocols. We will also highlight the main open issues related to the possible inclusion of MPS II in newborn screenings, the comprehension of brain pathogenesis, and treatment of the neurological compartment.
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Affiliation(s)
- Francesca D’Avanzo
- Laboratory of Diagnosis and Therapy of Lysosomal Disorders, Department of Women’s and Children ‘s Health, University of Padova, Via Giustiniani 3, 35128 Padova, Italy; (F.D.); (A.Z.)
- Fondazione Istituto di Ricerca Pediatrica “Città della Speranza”, Corso Stati Uniti 4, 35127 Padova, Italy;
| | - Laura Rigon
- Fondazione Istituto di Ricerca Pediatrica “Città della Speranza”, Corso Stati Uniti 4, 35127 Padova, Italy;
- Molecular Developmental Biology, Life & Medical Science Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | - Alessandra Zanetti
- Laboratory of Diagnosis and Therapy of Lysosomal Disorders, Department of Women’s and Children ‘s Health, University of Padova, Via Giustiniani 3, 35128 Padova, Italy; (F.D.); (A.Z.)
- Fondazione Istituto di Ricerca Pediatrica “Città della Speranza”, Corso Stati Uniti 4, 35127 Padova, Italy;
| | - Rosella Tomanin
- Laboratory of Diagnosis and Therapy of Lysosomal Disorders, Department of Women’s and Children ‘s Health, University of Padova, Via Giustiniani 3, 35128 Padova, Italy; (F.D.); (A.Z.)
- Fondazione Istituto di Ricerca Pediatrica “Città della Speranza”, Corso Stati Uniti 4, 35127 Padova, Italy;
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16
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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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17
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Molecular Characterization of a Novel Splicing Mutation underlying Mucopolysaccharidosis (MPS) type VI-Indirect Proof of Principle on Its Pathogenicity. Diagnostics (Basel) 2020; 10:diagnostics10020058. [PMID: 31973102 PMCID: PMC7168280 DOI: 10.3390/diagnostics10020058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 12/24/2022] Open
Abstract
Here, we present the molecular diagnosis of a patient with a general clinical suspicion of Mucopolysaccharidosis, highlighting the different tools used to perform its molecular characterization. In order to decrease the turnaround time for the final report and contribute to reduce the “diagnostic odyssey”, which frequently afflicts affected families, the proband’s sample was simultaneously screened for mutations in a number of lysosomal function-related genes with targeted next-generation sequencing (NGS) protocol. After variant calling, the most probable cause for disease was a novel ARSB intronic variant, c.1213+5G>T [IVS6+5G>T], detected in homozygosity. In general, homozygous or compound heterozygous mutations in the ARSB gene, underlie MPS type VI or Maroteaux-Lamy syndrome. Still, even though the novel c.1213+5G>T variant was easy to detect by both NGS and Sanger sequencing, only through indirect studies and functional analyses could we present proof of principle on its pathogenicity. Globally, this case reminds us that whenever a novel variant is detected, its pathogenicity must be carefully assessed before a definitive diagnosis is established, while highlighting alternative approaches that may be used to assess its effect in the absence RNA/cDNA sample(s) from the proband. This is particularly relevant for intronic variants such as the one here reported. Special attention will be given to the use of reporter minigene systems, which may be constructed/designed to dissect the effect of this sort of alterations, providing an insight into their consequences over the normal pre-mRNA splicing process of the affected gene.
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18
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Velho RV, Harms FL, Danyukova T, Ludwig NF, Friez MJ, Cathey SS, Filocamo M, Tappino B, Güneş N, Tüysüz B, Tylee KL, Brammeier KL, Heptinstall L, Oussoren E, van der Ploeg AT, Petersen C, Alves S, Saavedra GD, Schwartz IV, Muschol N, Kutsche K, Pohl S. The lysosomal storage disorders mucolipidosis type II, type III alpha/beta, and type III gamma: Update on GNPTAB and GNPTG mutations. Hum Mutat 2019; 40:842-864. [PMID: 30882951 DOI: 10.1002/humu.23748] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/19/2019] [Accepted: 03/14/2019] [Indexed: 01/04/2023]
Abstract
Mutations in the GNPTAB and GNPTG genes cause mucolipidosis (ML) type II, type III alpha/beta, and type III gamma, which are autosomal recessively inherited lysosomal storage disorders. GNPTAB and GNPTG encode the α/β-precursor and the γ-subunit of N-acetylglucosamine (GlcNAc)-1-phosphotransferase, respectively, the key enzyme for the generation of mannose 6-phosphate targeting signals on lysosomal enzymes. Defective GlcNAc-1-phosphotransferase results in missorting of lysosomal enzymes and accumulation of non-degradable macromolecules in lysosomes, strongly impairing cellular function. MLII-affected patients have coarse facial features, cessation of statural growth and neuromotor development, severe skeletal abnormalities, organomegaly, and cardiorespiratory insufficiency leading to death in early childhood. MLIII alpha/beta and MLIII gamma are attenuated forms of the disease. Since the identification of the GNPTAB and GNPTG genes, 564 individuals affected by MLII or MLIII have been described in the literature. In this report, we provide an overview on 258 and 50 mutations in GNPTAB and GNPTG, respectively, including 58 novel GNPTAB and seven novel GNPTG variants. Comprehensive functional studies of GNPTAB missense mutations did not only gain insights into the composition and function of the GlcNAc-1-phosphotransferase, but also helped to define genotype-phenotype correlations to predict the clinical outcome in patients.
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Affiliation(s)
- Renata Voltolini Velho
- Section Cell Biology of Rare Diseases, Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Frederike L Harms
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tatyana Danyukova
- Section Cell Biology of Rare Diseases, Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nataniel F Ludwig
- Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Post-Graduation Program in Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | | | | | - Mirella Filocamo
- Laboratorio di Genetica Molecolare e Biobanche, Istituto Giannina Gaslini, Genova, Italy
| | - Barbara Tappino
- Laboratorio di Genetica Molecolare e Biobanche, Istituto Giannina Gaslini, Genova, Italy
| | - Nilay Güneş
- Department of Pediatric Genetics, Istanbul University Cerrahpasa, Medicine School, Istanbul, Turkey
| | - Beyhan Tüysüz
- Department of Pediatric Genetics, Istanbul University Cerrahpasa, Medicine School, Istanbul, Turkey
| | - Karen L Tylee
- Willink Biochemical Genetics Unit, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Saint Mary's Hospital, Manchester, UK
| | - Kathryn L Brammeier
- Willink Biochemical Genetics Unit, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Saint Mary's Hospital, Manchester, UK
| | - Lesley Heptinstall
- Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Saint Mary's Hospital, Manchester, UK
| | - Esmee Oussoren
- Department of Pediatrics, Center for LyMannose phosphorylation in health and diseasesosomal and Metabolic Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Ans T van der Ploeg
- Department of Pediatrics, Center for LyMannose phosphorylation in health and diseasesosomal and Metabolic Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Christine Petersen
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sandra Alves
- Department of Human Genetics, INSA, National Health Institute Doutor Ricardo Jorge, Porto, Portugal
| | - Gloria Durán Saavedra
- División de Pediatría, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ida V Schwartz
- Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Post-Graduation Program in Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Nicole Muschol
- International Center for Lysosomal Disorders, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sandra Pohl
- Section Cell Biology of Rare Diseases, Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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19
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Brusius-Facchin AC, Siebert M, Leão D, Malaga DR, Pasqualim G, Trapp F, Matte U, Giugliani R, Leistner-Segal S. Phenotype-oriented NGS panels for mucopolysaccharidoses: Validation and potential use in the diagnostic flowchart. Genet Mol Biol 2019; 42:207-214. [PMID: 30985855 PMCID: PMC6687349 DOI: 10.1590/1678-4685-gmb-2018-0102] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 10/24/2018] [Indexed: 11/21/2022] Open
Abstract
Mucopolysaccharidosis (MPS) are a group of rare genetic disorders caused by deficiency in the activity of specific lysosomal enzymes required for the degradation of glycosaminoglycans (GAGs). A defect in the activity of these enzymes will result in the abnormal accumulation of GAGs inside the lysosomes of most cells, inducing progressive cellular damage and multiple organ failure. DNA samples from 70 patients with biochemical diagnosis of different MPSs genotypes confirmed by Sanger sequencing were used to evaluate a Next Generation Sequencing (NGS) protocol. Eleven genes related to MPSs were divided into three different panels according to the clinical phenotype. This strategy led to the identification of several pathogenic mutations distributed across all exons of MPSs-related genes. We were able to identify 96% of all gene variants previously identified by Sanger sequencing, showing high sensitivity in detecting different types of mutations. Furthermore, new variants were not identified, representing 100% specificity of the NGS protocol. The use of this NGS approach for genotype identification in MPSs is an attractive option for diagnosis of patients. In addition, the MPS diagnosis workflow could be divided in a two-tier approach: NGS as a first-tier followed by biochemical confirmation as a second-tier.
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Affiliation(s)
- Ana Carolina Brusius-Facchin
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.,Post-Graduation Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Marina Siebert
- Molecular and Protein Analysis Unit, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.,Gene Therapy Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Delva Leão
- Molecular and Protein Analysis Unit, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Diana Rojas Malaga
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.,Post-Graduation Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Gabriela Pasqualim
- Post-Graduation Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Molecular and Protein Analysis Unit, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.,Genetics Departament, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Franciele Trapp
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Ursula Matte
- Post-Graduation Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Molecular and Protein Analysis Unit, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.,Gene Therapy Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.,Genetics Departament, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Post-Graduation Program in Medicine, Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Roberto Giugliani
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.,Post-Graduation Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Genetics Departament, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Post-Graduation Program in Medicine, Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Sandra Leistner-Segal
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.,Post-Graduation Program in Medicine, Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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20
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Málaga DR, Brusius-Facchin AC, Siebert M, Pasqualim G, Saraiva-Pereira ML, Souza CFMD, Schwartz IVD, Matte U, Giugliani R. Sensitivity, advantages, limitations, and clinical utility of targeted next-generation sequencing panels for the diagnosis of selected lysosomal storage disorders. Genet Mol Biol 2019; 42:197-206. [PMID: 30985853 PMCID: PMC6687342 DOI: 10.1590/1678-4685-gmb-2018-0092] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 10/18/2018] [Indexed: 01/22/2023] Open
Abstract
Lysosomal storage disorders (LSDs) constitute a heterogeneous group of
approximately 50 genetic disorders. LSDs diagnosis is challenging due to
variability in phenotype penetrance, similar clinical manifestations, and a high
allelic heterogeneity. A powerful tool for the diagnosis of the disease could
reduce the “diagnostic odyssey” for affected families, leading to an appropriate
genetic counseling and a better outcome for current therapies, since enzyme
replacement therapies have been approved in Brazil for Gaucher, Fabry, and Pompe
diseases, and are under development for Niemann-Pick Type B. However,
application of next-generation sequencing (NGS) technology in the clinical
diagnostic setting requires a previous validation phase. Here, we assessed the
application of this technology as a fast, accurate, and cost-effective method to
determine genetic diagnosis in selected LSDs. We have designed two panels for
testing simultaneously 11 genes known to harbor casual mutations of LSDs. A
cohort of 58 patients was used to validate those two panels, and the clinical
utility of these gene panels was tested in four novel cases. We report the
assessment of a NGS approach as a new tool in the diagnosis of LSDs in our
service.
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Affiliation(s)
- Diana Rojas Málaga
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Porto Alegre, RS, Brazil
| | | | - Marina Siebert
- Experimental Research Center, Hospital de Clinicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Gabriela Pasqualim
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Experimental Research Center, Hospital de Clinicas de Porto Alegre, Porto Alegre, RS, Brazil.,Gene Therapy Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Maria Luiza Saraiva-Pereira
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Porto Alegre, RS, Brazil.,Department of Biochemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Carolina F M de Souza
- Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Ida V D Schwartz
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Porto Alegre, RS, Brazil.,Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Ursula Matte
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Experimental Research Center, Hospital de Clinicas de Porto Alegre, Porto Alegre, RS, Brazil.,Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Roberto Giugliani
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre, Porto Alegre, RS, Brazil.,Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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21
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Wang P, Mazrier H, Caverly Rae J, Raj K, Giger U. A GNPTAB nonsense variant is associated with feline mucolipidosis II (I-cell disease). BMC Vet Res 2018; 14:416. [PMID: 30591066 PMCID: PMC6307278 DOI: 10.1186/s12917-018-1728-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/30/2018] [Indexed: 11/15/2022] Open
Abstract
Background Mucolipidosis II (ML II; I-cell disease) is caused by a deficiency of N-acetylglucosamine-1-phosphotransferase (GNPTAB; EC 2.7.8.17), which leads to a failure to internalize acid hydrolases into lysosomes for proper catabolism of various substances. This is an autosomal recessive lysosomal storage disease and causes severe progressive neuropathy and oculoskeletal dysfunction in humans (OMIM 252500). A naturally occurring disease model has been reported in juvenile domestic cats (OMIA 001248–9685) with clinical signs similar to human patients. We investigated the molecular genetic basis of ML II in a colony of affected cats by sequencing the coding and regulatory regions of GNPTAB from affected and clinically healthy related and unrelated domestic cats and compared the sequences to the published feline genome sequence (NCBI-RefSeq accession no. XM_003989173.4, Gene ID: 101100231). Results All affected cats were homozygous for a single base substitution (c.2644C > T) in exon 13 of GNPTAB. This variant results in a premature stop codon (p.Gln882*) which predicts severe truncation and complete dysfunction of the GNPTAB enzyme. About 140 GNPTAB variants have been described in human ML II patients, with 41.3% nonsense/missense mutations, nine occurring in the same gene region as in this feline model. Restriction fragment length polymorphism and allelic discrimination real-time polymerase chain reaction assays accurately differentiated between clear, asymptomatic carriers and homozygous affected cats. Conclusion Molecular genetic characterization advances this large animal model of ML II for use to further define the pathophysiology of the disease and evaluate novel therapeutic approaches for this fatal lysosomal storage disease in humans. Electronic supplementary material The online version of this article (10.1186/s12917-018-1728-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ping Wang
- Section of Medical Genetics, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Hamutal Mazrier
- Section of Medical Genetics, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jessica Caverly Rae
- Section of Medical Genetics, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Karthik Raj
- Section of Medical Genetics, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Urs Giger
- Section of Medical Genetics, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
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22
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Filocamo M, Tomanin R, Bertola F, Morrone A. Biochemical and molecular analysis in mucopolysaccharidoses: what a paediatrician must know. Ital J Pediatr 2018; 44:129. [PMID: 30442161 PMCID: PMC6238298 DOI: 10.1186/s13052-018-0553-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mucopolysaccharidoses (MPS) are rare inherited disorders caused by a deficit of the lysosomal hydrolases involved in the degradation of mucopolysaccharides, also known as glycosaminoglycans (GAGs). They are all monogenic defects, transmitted in an autosomal recessive way, except for MPS type II which is X-linked. The enzymatic deficit causes a pathologic accumulation of undegraded or partially degraded substrates inside lysosomes as well as in the extracellular compartment. MPS generally present with recognizable signs and symptoms to raise a clinical suspicion. However, although they have individual peculiarities, often signs and symptoms may overlap between different MPS types. Therefore, a deeper evaluation of specific disease biomarkers becomes necessary to reach an appropriate diagnosis. This paper stresses the central role of the laboratory in completing and confirming the clinical suspicion of MPS according to a standardized procedure: first, a biochemical evaluation of the patient samples, including qualitative/quantitative urinary GAG analysis and a determination of enzyme activities, and then the molecular diagnosis. We also encourage a constant and close communication between clinicians and laboratory personnel to address a correct and early MPS diagnosis.
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Affiliation(s)
- Mirella Filocamo
- Laboratorio di Genetica Molecolare e Biobanche, Istituto G. Gaslini, Genova, Italy
| | - Rosella Tomanin
- Laboratory of Diagnosis and Therapy of Lysosomal Disorders, Department of Women’s and Children’s Health, University of Padova, Padova, Italy
| | - Francesca Bertola
- School of Medicine and Surgery, University of Milano Bicocca, Monza, Italy
| | - Amelia Morrone
- Neuroscience Department, Molecular and Cell Biology Laboratory of Neurometabolic Diseases, Meyer Children’s Hospital, University of Florence, Florence, Italy
- Department of Neurofarba, University of Florence, Florence, Italy
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23
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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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24
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Tomanin R, Karageorgos L, Zanetti A, Al-Sayed M, Bailey M, Miller N, Sakuraba H, Hopwood JJ. Mucopolysaccharidosis type VI (MPS VI) and molecular analysis: Review and classification of published variants in the ARSB gene. Hum Mutat 2018; 39:1788-1802. [PMID: 30118150 PMCID: PMC6282714 DOI: 10.1002/humu.23613] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/10/2018] [Accepted: 08/13/2018] [Indexed: 01/26/2023]
Abstract
Maroteaux–Lamy syndrome (MPS VI) is an autosomal recessive lysosomal storage disorder caused by pathogenic ARSB gene variants, commonly diagnosed through clinical findings and deficiency of the arylsulfatase B (ASB) enzyme. Detection of ARSB pathogenic variants can independently confirm diagnosis and render genetic counseling possible. In this review, we collect and summarize 908 alleles (201 distinct variants, including 3 polymorphisms previously considered as disease‐causing variants) from 478 individuals diagnosed with MPS VI, identified from literature and public databases. Each variant is further analyzed for clinical classification according to American College of Medical Genetics and Genomics (ACMG) guidelines. Results highlight the heterogeneity of ARSB alleles, with most unique variants (59.5%) identified as missense and 31.7% of unique alleles appearing once. Only 18% of distinct variants were previously recorded in public databases with supporting evidence and clinical significance. ACMG recommends publishing clinical and biochemical data that accurately characterize pathogenicity of new variants in association with reporting specific alleles. Variants analyzed were sent to ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/), and MPS VI locus‐specific database (http://mps6-database.org) where they will be available. High clinical suspicion coupled with diagnostic testing for deficient ASB activity and timely submission and classification of ARSB variants with biochemical and clinical data in public databases is essential for timely diagnosis of MPS VI.
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Affiliation(s)
- Rosella Tomanin
- Laboratory of Diagnosis and Therapy of Lysosomal Disorders, Department of Women's and Children's Health, University of Padova and "Fondazione Istituto di Ricerca Pediatrica Città della Speranza", Padova, Italy
| | - Litsa Karageorgos
- Hopwood Centre for Neurobiology, South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Alessandra Zanetti
- Laboratory of Diagnosis and Therapy of Lysosomal Disorders, Department of Women's and Children's Health, University of Padova and "Fondazione Istituto di Ricerca Pediatrica Città della Speranza", Padova, Italy
| | | | - Mitch Bailey
- BioMarin Pharmaceutical Inc., Novato, CA, United States
| | - Nicole Miller
- BioMarin Pharmaceutical Inc., Novato, CA, United States
| | - Hitoshi Sakuraba
- Department of Clinical Genetics, Meiji Pharmaceutical University, Tokyo, Japan
| | - John J Hopwood
- Hopwood Centre for Neurobiology, South Australian Health and Medical Research Institute, Adelaide, Australia
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25
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Fernández-Marmiesse A, Gouveia S, Couce ML. NGS Technologies as a Turning Point in Rare Disease Research , Diagnosis and Treatment. Curr Med Chem 2018; 25:404-432. [PMID: 28721829 PMCID: PMC5815091 DOI: 10.2174/0929867324666170718101946] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/19/2017] [Accepted: 07/14/2017] [Indexed: 01/17/2023]
Abstract
Approximately 25-50 million Americans, 30 million Europeans, and 8% of the Australian population have a rare disease. Rare diseases are thus a common problem for clinicians and account for enormous healthcare costs worldwide due to the difficulty of establishing a specific diagnosis. In this article, we review the milestones achieved in our understanding of rare diseases since the emergence of next-generation sequencing (NGS) technologies and analyze how these advances have influenced research and diagnosis. The first half of this review describes how NGS has changed diagnostic workflows and provided an unprecedented, simple way of discovering novel disease-associated genes. We focus particularly on metabolic and neurodevelopmental disorders. NGS has enabled cheap and rapid genetic diagnosis, highlighted the relevance of mosaic and de novo mutations, brought to light the wide phenotypic spectrum of most genes, detected digenic inheritance or the presence of more than one rare disease in the same patient, and paved the way for promising new therapies. In the second part of the review, we look at the limitations and challenges of NGS, including determination of variant causality, the loss of variants in coding and non-coding regions, and the detection of somatic mosaicism variants and epigenetic mutations, and discuss how these can be overcome in the near future.
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Affiliation(s)
- Ana Fernández-Marmiesse
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Sofía Gouveia
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - María L. Couce
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
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26
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Wang N, Zhang Y, Gedvilaite E, Loh JW, Lin T, Liu X, Liu CG, Kumar D, Donnelly R, Raymond K, Schuchman EH, Sleat DE, Lobel P, Xing J. Using whole-exome sequencing to investigate the genetic bases of lysosomal storage diseases of unknown etiology. Hum Mutat 2017; 38:1491-1499. [PMID: 28703315 DOI: 10.1002/humu.23291] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 07/04/2017] [Accepted: 07/08/2017] [Indexed: 12/17/2022]
Abstract
Lysosomes are membrane-bound, acidic eukaryotic cellular organelles that play important roles in the degradation of macromolecules. Mutations that cause the loss of lysosomal protein function can lead to a group of disorders categorized as the lysosomal storage diseases (LSDs). Suspicion of LSD is frequently based on clinical and pathologic findings, but in some cases, the underlying genetic and biochemical defects remain unknown. Here, we performed whole-exome sequencing (WES) on 14 suspected LSD cases to evaluate the feasibility of using WES for identifying causal mutations. By examining 2,157 candidate genes potentially associated with lysosomal function, we identified eight variants in five genes as candidate disease-causing variants in four individuals. These included both known and novel mutations. Variants were corroborated by targeted sequencing and, when possible, functional assays. In addition, we identified nonsense mutations in two individuals in genes that are not known to have lysosomal function. However, mutations in these genes could have resulted in phenotypes that were diagnosed as LSDs. This study demonstrates that WES can be used to identify causal mutations in suspected LSD cases. We also demonstrate cases where a confounding clinical phenotype may potentially reflect more than one lysosomal protein defect.
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Affiliation(s)
- Nan Wang
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey
| | - Yeting Zhang
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey.,Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, New Jersey
| | - Erika Gedvilaite
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey
| | - Jui Wan Loh
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey
| | - Timothy Lin
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey
| | - Xiuping Liu
- Sequencing and ncRNA Program, Department of Experimental Therapeutics, The University of Texas-MD Anderson Cancer Center, Houston, Texas
| | - Chang-Gong Liu
- Sequencing and ncRNA Program, Department of Experimental Therapeutics, The University of Texas-MD Anderson Cancer Center, Houston, Texas
| | - Dibyendu Kumar
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, New Jersey
| | - Robert Donnelly
- Molecular Resource Facility at Rutgers, New Jersey Medical School, Newark, New Jersey
| | - Kimiyo Raymond
- Department of Laboratory Medicine and Pathology, Biochemical Genetics Laboratory, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Edward H Schuchman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - David E Sleat
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, New Jersey.,Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, Piscataway, New Jersey
| | - Peter Lobel
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, New Jersey.,Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, Piscataway, New Jersey
| | - Jinchuan Xing
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey.,Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, New Jersey
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27
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Next-generation sequencing corroborates a probable de novo GNPTG variation previously detected by Sanger sequencing. Mol Genet Metab Rep 2017. [PMID: 28649512 PMCID: PMC5470938 DOI: 10.1016/j.ymgmr.2017.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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28
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Park KJ, Park S, Lee E, Park JH, Park JH, Park HD, Lee SY, Kim JW. A Population-Based Genomic Study of Inherited Metabolic Diseases Detected Through Newborn Screening. Ann Lab Med 2017; 36:561-72. [PMID: 27578510 PMCID: PMC5011110 DOI: 10.3343/alm.2016.36.6.561] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 05/11/2016] [Accepted: 06/27/2016] [Indexed: 01/29/2023] Open
Abstract
Background A newborn screening (NBS) program has been utilized to detect asymptomatic newborns with inherited metabolic diseases (IMDs). There have been some bottlenecks such as false-positives and imprecision in the current NBS tests. To overcome these issues, we developed a multigene panel for IMD testing and investigated the utility of our integrated screening model in a routine NBS environment. We also evaluated the genetic epidemiologic characteristics of IMDs in a Korean population. Methods In total, 269 dried blood spots with positive results from current NBS tests were collected from 120,700 consecutive newborns. We screened 97 genes related to NBS in Korea and detected IMDs, using an integrated screening model based on biochemical tests and next-generation sequencing (NGS) called NewbornSeq. Haplotype analysis was conducted to detect founder effects. Results The overall positive rate of IMDs was 20%. We identified 10 additional newborns with preventable IMDs that would not have been detected prior to the implementation of our NGS-based platform NewbornSeq. The incidence of IMDs was approximately 1 in 2,235 births. Haplotype analysis demonstrated founder effects in p.Y138X in DUOXA2, p.R885Q in DUOX2, p.Y439C in PCCB, p.R285Pfs*2 in SLC25A13, and p.R224Q in GALT. Conclusions Through a population-based study in the NBS environment, we highlight the screening and epidemiological implications of NGS. The integrated screening model will effectively contribute to public health by enabling faster and more accurate IMD detection through NBS. This study suggested founder mutations as an explanation for recurrent IMD-causing mutations in the Korean population.
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Affiliation(s)
- Kyoung Jin Park
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
| | | | | | - Jong Ho Park
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
| | - June Hee Park
- Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | - Hyung Doo Park
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Soo Youn Lee
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong Won Kim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea.,Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
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29
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Richard E, Brasil S, Leal F, Navarrete R, Vega A, Ecay MJ, Desviat LR, Pérez-Cerda C, Ugarte M, Merinero B, Pérez B. Isolated and Combined Remethylation Disorders. JOURNAL OF INBORN ERRORS OF METABOLISM AND SCREENING 2017. [DOI: 10.1177/2326409816685732] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Eva Richard
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- IdiPAZ, Madrid, Spain
| | - Sandra Brasil
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- IdiPAZ, Madrid, Spain
| | - Fátima Leal
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- IdiPAZ, Madrid, Spain
| | - Rosa Navarrete
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- IdiPAZ, Madrid, Spain
| | - Ana Vega
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- IdiPAZ, Madrid, Spain
| | - María Jesús Ecay
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- IdiPAZ, Madrid, Spain
| | - Lourdes R. Desviat
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- IdiPAZ, Madrid, Spain
| | - Celia Pérez-Cerda
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- IdiPAZ, Madrid, Spain
| | - Magdalena Ugarte
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- IdiPAZ, Madrid, Spain
| | - Begoña Merinero
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- IdiPAZ, Madrid, Spain
| | - Belén Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- IdiPAZ, Madrid, Spain
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30
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Komlosi K, Sólyom A, Beck M. The Role of Next-Generation Sequencing in the Diagnosis of Lysosomal Storage Disorders. JOURNAL OF INBORN ERRORS OF METABOLISM AND SCREENING 2016. [DOI: 10.1177/2326409816669376] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Katalin Komlosi
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
- Institute of Medical Genetics, University of Pecs, Hungary
| | | | - Michael Beck
- Institute of Human Genetics, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
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31
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Vega AI, Medrano C, Navarrete R, Desviat LR, Merinero B, Rodríguez-Pombo P, Vitoria I, Ugarte M, Pérez-Cerdá C, Pérez B. Molecular diagnosis of glycogen storage disease and disorders with overlapping clinical symptoms by massive parallel sequencing. Genet Med 2016; 18:1037-43. [PMID: 26913919 DOI: 10.1038/gim.2015.217] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 12/17/2015] [Indexed: 12/30/2022] Open
Abstract
PURPOSE Glycogen storage disease (GSD) is an umbrella term for a group of genetic disorders that involve the abnormal metabolism of glycogen; to date, 23 types of GSD have been identified. The nonspecific clinical presentation of GSD and the lack of specific biomarkers mean that Sanger sequencing is now widely relied on for making a diagnosis. However, this gene-by-gene sequencing technique is both laborious and costly, which is a consequence of the number of genes to be sequenced and the large size of some genes. METHODS This work reports the use of massive parallel sequencing to diagnose patients at our laboratory in Spain using either a customized gene panel (targeted exome sequencing) or the Illumina Clinical-Exome TruSight One Gene Panel (clinical exome sequencing (CES)). Sequence variants were matched against biochemical and clinical hallmarks. RESULTS Pathogenic mutations were detected in 23 patients. Twenty-two mutations were recognized (mostly loss-of-function mutations), including 11 that were novel in GSD-associated genes. In addition, CES detected five patients with mutations in ALDOB, LIPA, NKX2-5, CPT2, or ANO5. Although these genes are not involved in GSD, they are associated with overlapping phenotypic characteristics such as hepatic, muscular, and cardiac dysfunction. CONCLUSIONS These results show that next-generation sequencing, in combination with the detection of biochemical and clinical hallmarks, provides an accurate, high-throughput means of making genetic diagnoses of GSD and related diseases.Genet Med 18 10, 1037-1043.
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Affiliation(s)
- Ana I Vega
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Instituto de Investigación La Paz (IdiPAZ), Madrid, Spain
| | - Celia Medrano
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Instituto de Investigación La Paz (IdiPAZ), Madrid, Spain
| | - Rosa Navarrete
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Instituto de Investigación La Paz (IdiPAZ), Madrid, Spain
| | - Lourdes R Desviat
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Instituto de Investigación La Paz (IdiPAZ), Madrid, Spain
| | - Begoña Merinero
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Instituto de Investigación La Paz (IdiPAZ), Madrid, Spain
| | - Pilar Rodríguez-Pombo
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Instituto de Investigación La Paz (IdiPAZ), Madrid, Spain
| | - Isidro Vitoria
- Unidad de Nutrición y Metabolopatías, Hospital La Fe, Valencia, Spain
| | - Magdalena Ugarte
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Instituto de Investigación La Paz (IdiPAZ), Madrid, Spain
| | - Celia Pérez-Cerdá
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Instituto de Investigación La Paz (IdiPAZ), Madrid, Spain
| | - Belen Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Instituto de Investigación La Paz (IdiPAZ), Madrid, Spain
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Giraldo GA, Ayala-Ramírez P, Prieto JC, García-Robles R, Acosta JC. Molecular findings of Colombian patients with type VI mucopolysaccharidosis (Maroteaux-Lamy syndrome). Meta Gene 2015; 7:83-9. [PMID: 26909334 PMCID: PMC4733218 DOI: 10.1016/j.mgene.2015.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 12/15/2015] [Accepted: 12/21/2015] [Indexed: 11/24/2022] Open
Abstract
Introduction Maroteaux–Lamy syndrome, or mucopolysaccharidosis (MPS) type VI, is an autosomal recessive lysosomal storage disease caused by a deficient activity of the enzyme arylsulfatase B (ARSB), required to degrade dermatan sulfate. The onset and progression of the disease vary, producing a spectrum of clinical presentation. So far, 133 mutations have been reported. The aim of this study is to determine the mutations in the ARSB gene that are responsible for this disease in Colombian patients. Results Fourteen patients with clinical manifestations and biochemical diagnosis of MPS VI were studied, including two siblings. The 8 exons of the gene were directly sequenced from patients' DNA, and 14 mutations were found. 57% of these mutations had not been previously reported (p.H111P, p.C121R, p.G446S, p.*534W, p.S334I, p.H147P, c.900T > G, and c.1531_1553del) and 43% had been previously reported (p.G144R, p.W322*, p.G302R, p.C447F, p.L128del, and c.1143-1G > C). Of the previously reported mutations, 80% have been associated with severe phenotypes and 20% with intermediate-severe phenotypes. Bioinformatic predictions indicate that the new mutations reported in this paper are also highly deleterious. Conclusions Most of the Colombian patients in this study had private mutations.
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Affiliation(s)
| | - Paola Ayala-Ramírez
- Instituto de Genética Humana, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Juan Carlos Prieto
- Instituto de Genética Humana, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Reggie García-Robles
- Instituto de Investigación en Nutrición, Genética y Metabolismo, Universidad El Bosque, Bogotá, Colombia
| | - Johanna Carolina Acosta
- Instituto de Investigación en Nutrición, Genética y Metabolismo, Universidad El Bosque, Bogotá, Colombia
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Giugliani R, Brusius-Facchin AC, Pasqualim G, Leistner-Segal S, Riegel M, Matte U. Current molecular genetics strategies for the diagnosis of lysosomal storage disorders. Expert Rev Mol Diagn 2015; 16:113-23. [DOI: 10.1586/14737159.2016.1121101] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Cracking the Code of Human Diseases Using Next-Generation Sequencing: Applications, Challenges, and Perspectives. BIOMED RESEARCH INTERNATIONAL 2015; 2015:161648. [PMID: 26665001 PMCID: PMC4668301 DOI: 10.1155/2015/161648] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 09/30/2015] [Accepted: 10/18/2015] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) technologies have greatly impacted on every field of molecular research mainly because they reduce costs and increase throughput of DNA sequencing. These features, together with the technology's flexibility, have opened the way to a variety of applications including the study of the molecular basis of human diseases. Several analytical approaches have been developed to selectively enrich regions of interest from the whole genome in order to identify germinal and/or somatic sequence variants and to study DNA methylation. These approaches are now widely used in research, and they are already being used in routine molecular diagnostics. However, some issues are still controversial, namely, standardization of methods, data analysis and storage, and ethical aspects. Besides providing an overview of the NGS-based approaches most frequently used to study the molecular basis of human diseases at DNA level, we discuss the principal challenges and applications of NGS in the field of human genomics.
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Wu CC, Lin YH, Liu TC, Lin KN, Yang WS, Hsu CJ, Chen PL, Wu CM. Identifying Children With Poor Cochlear Implantation Outcomes Using Massively Parallel Sequencing. Medicine (Baltimore) 2015; 94:e1073. [PMID: 26166082 PMCID: PMC4504554 DOI: 10.1097/md.0000000000001073] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cochlear implantation is currently the treatment of choice for children with severe to profound hearing impairment. However, the outcomes with cochlear implants (CIs) vary significantly among recipients. The purpose of the present study is to identify the genetic determinants of poor CI outcomes. Twelve children with poor CI outcomes (the "cases") and 30 "matched controls" with good CI outcomes were subjected to comprehensive genetic analyses using massively parallel sequencing, which targeted 129 known deafness genes. Audiological features, imaging findings, and auditory/speech performance with CIs were then correlated to the genetic diagnoses. We identified genetic variants which are associated with poor CI outcomes in 7 (58%) of the 12 cases; 4 cases had bi-allelic PCDH15 pathogenic mutations and 3 cases were homozygous for the DFNB59 p.G292R variant. Mutations in the WFS1, GJB3, ESRRB, LRTOMT, MYO3A, and POU3F4 genes were detected in 7 (23%) of the 30 matched controls. The allele frequencies of PCDH15 and DFNB59 variants were significantly higher in the cases than in the matched controls (both P < 0.001). In the 7 CI recipients with PCDH15 or DFNB59 variants, otoacoustic emissions were absent in both ears, and imaging findings were normal in all 7 implanted ears. PCDH15 or DFNB59 variants are associated with poor CI performance, yet children with PCDH15 or DFNB59 variants might show clinical features indistinguishable from those of other typical pediatric CI recipients. Accordingly, genetic examination is indicated in all CI candidates before operation.
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Affiliation(s)
- Chen-Chi Wu
- From Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan (C-CW, Y-HL, T-CL, K-NL, C-JH); Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan (C-CW, W-SY, P-LC); Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan (Y-HL, P-LC); Department of Otolaryngology, Cardinal Tien Hospital, New Taipei, Taiwan (K-NL); Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan (W-SY, P-LC); Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan (W-SY, P-LC); Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan (W-SY, P-LC); Department of Otolaryngology, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, Taiwan (C-JH); and Department of Otolaryngology, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan, Taiwan (C-MW)
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Kohan R, Pesaola F, Guelbert N, Pons P, Oller-Ramírez AM, Rautenberg G, Becerra A, Sims K, Xin W, Cismondi IA, Noher de Halac I. The neuronal ceroid lipofuscinoses program: A translational research experience in Argentina. Biochim Biophys Acta Mol Basis Dis 2015; 1852:2301-11. [PMID: 25976102 DOI: 10.1016/j.bbadis.2015.05.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 04/29/2015] [Accepted: 05/05/2015] [Indexed: 10/23/2022]
Abstract
BACKGROUND The Argentinean program was initiated more than a decade ago as the first experience of systematic translational research focused on NCL in Latin America. The aim was to overcome misdiagnoses and underdiagnoses in the region. SUBJECTS 216 NCL suspected individuals from 8 different countries and their direct family members. METHODS Clinical assessment, enzyme testing, electron microscopy, and DNA screening. RESULTS AND DISCUSSION 1) The study confirmed NCL disease in 122 subjects. Phenotypic studies comprised epileptic seizures and movement disorders, ophthalmology, neurophysiology, image analysis, rating scales, enzyme testing, and electron microscopy, carried out under a consensus algorithm; 2) DNA screening and validation of mutations in genes PPT1 (CLN1), TPP1 (CLN2), CLN3, CLN5, CLN6, MFSD8 (CLN7), and CLN8: characterization of variant types, novel/known mutations and polymorphisms; 3) Progress of the epidemiological picture in Latin America; and 4) NCL-like pathology studies in progress. The Translational Research Program was highly efficient in addressing the misdiagnosis/underdiagnosis in the NCL disorders. The study of "orphan diseases" in a public administrated hospital should be adopted by the health systems, as it positively impacts upon the family's quality of life, the collection of epidemiological data, and triggers research advances. This article is part of a Special Issue entitled: "Current Research on the Neuronal Ceroid Lipofuscinoses (Batten Disease)".
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Affiliation(s)
- Romina Kohan
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Ferroviarios 1250, 5014 Córdoba, Argentina; Facultad de Odontología, Universidad Nacional de Córdoba, Haya de la Torre s/n, 5000 Córdoba, Argentina.
| | - Favio Pesaola
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Ferroviarios 1250, 5014 Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917, C1033AAJ CABA, Argentina.
| | - Norberto Guelbert
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Ferroviarios 1250, 5014 Córdoba, Argentina.
| | - Patricia Pons
- Centro de Microscopía Electrónica, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Haya de la Torre esq. Enrique Barros, 1º piso, 5000 Córdoba, Argentina.
| | - Ana María Oller-Ramírez
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Ferroviarios 1250, 5014 Córdoba, Argentina.
| | - Gisela Rautenberg
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Ferroviarios 1250, 5014 Córdoba, Argentina.
| | - Adriana Becerra
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Ferroviarios 1250, 5014 Córdoba, Argentina.
| | - Katherine Sims
- Massachussets General Hospital, Neurology Department, Center for Genetic Research [CHGR], Boston, MA 02114, USA.
| | - Winnie Xin
- Massachussets General Hospital, Neurology Department, Center for Genetic Research [CHGR], Boston, MA 02114, USA.
| | - Inés Adriana Cismondi
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Ferroviarios 1250, 5014 Córdoba, Argentina; Facultad de Odontología, Universidad Nacional de Córdoba, Haya de la Torre s/n, 5000 Córdoba, Argentina.
| | - Inés Noher de Halac
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Ferroviarios 1250, 5014 Córdoba, Argentina; Facultad de Odontología, Universidad Nacional de Córdoba, Haya de la Torre s/n, 5000 Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917, C1033AAJ CABA, Argentina.
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Qian Y, van Meel E, Flanagan-Steet H, Yox A, Steet R, Kornfeld S. Analysis of mucolipidosis II/III GNPTAB missense mutations identifies domains of UDP-GlcNAc:lysosomal enzyme GlcNAc-1-phosphotransferase involved in catalytic function and lysosomal enzyme recognition. J Biol Chem 2014; 290:3045-56. [PMID: 25505245 DOI: 10.1074/jbc.m114.612507] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
UDP-GlcNAc:lysosomal enzyme GlcNAc-1-phosphotransferase tags newly synthesized lysosomal enzymes with mannose 6-phosphate recognition markers, which are required for their targeting to the endolysosomal system. GNPTAB encodes the α and β subunits of GlcNAc-1-phosphotransferase, and mutations in this gene cause the lysosomal storage disorders mucolipidosis II and III αβ. Prior investigation of missense mutations in GNPTAB uncovered amino acids in the N-terminal region and within the DMAP domain involved in Golgi retention of GlcNAc-1-phosphotransferase and its ability to specifically recognize lysosomal hydrolases, respectively. Here, we undertook a comprehensive analysis of the remaining missense mutations in GNPTAB reported in mucolipidosis II and III αβ patients using cell- and zebrafish-based approaches. We show that the Stealth domain harbors the catalytic site, as some mutations in these regions greatly impaired the activity of the enzyme without affecting its Golgi localization and proteolytic processing. We also demonstrate a role for the Notch repeat 1 in lysosomal hydrolase recognition, as missense mutations in conserved cysteine residues in this domain do not affect the catalytic activity but impair mannose phosphorylation of certain lysosomal hydrolases. Rescue experiments using mRNA bearing Notch repeat 1 mutations in GNPTAB-deficient zebrafish revealed selective effects on hydrolase recognition that differ from the DMAP mutation. Finally, the mutant R587P, located in the spacer between Notch 2 and DMAP, was partially rescued by overexpression of the γ subunit, suggesting a role for this region in γ subunit binding. These studies provide new insight into the functions of the different domains of the α and β subunits.
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Affiliation(s)
- Yi Qian
- From the Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri 63110 and
| | - Eline van Meel
- From the Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri 63110 and
| | | | - Alex Yox
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Richard Steet
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Stuart Kornfeld
- From the Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri 63110 and
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Sobral I, Cachulo MDL, Figueira J, Silva R. Sialidosis type I: ophthalmological findings. BMJ Case Rep 2014; 2014:bcr-2014-205871. [PMID: 25323282 DOI: 10.1136/bcr-2014-205871] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Sialidosis is a lysosomal storage disease caused by deficit of neuraminidase. It is an autosomal recessive disease, heterogeneous in its onset, presentation and prognosis. We report a case of a male patient with molecular and enzymatic confirmation of the diagnosis. Symptoms began at age 26 with reduced visual acuity, bilateral cherry-red spots and later myoclonus. A brother, now deceased, had the same confirmed disease. We describe the symptoms and clinical findings of the patient, as well review the current knowledge on the topic. With this report, we highlight the importance of a clinical history integrating all the patient's symptoms in order to achieve the diagnosis. In the presence of a cherry-red spot, a comprehensive study is mandatory. Despite being a rare disease, sialidosis carries a significant burden for its patients and its diagnosis should always be considered in the appropriate setting.
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Affiliation(s)
- Isa Sobral
- Department of Ophthalmology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Maria da Luz Cachulo
- Department of Ophthalmology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - João Figueira
- Department of Ophthalmology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Rufino Silva
- Department of Ophthalmology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
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