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Abstract
Hypomyelinating leukodystrophies constitute a subset of genetic white matter disorders characterized by a primary lack of myelin deposition. Most patients with severe hypomyelination present in infancy or early childhood and develop severe neurological deficits, but the clinical presentation can also be mild with onset of symptoms in adolescence or adulthood. MRI can be used to visualize the process of myelination in detail, and MRI pattern recognition can provide a clinical diagnosis in many patients. Next-generation sequencing provides a definitive diagnosis in 80-90% of patients. Genes associated with hypomyelination include those that encode structural myelin proteins but also many that encode proteins involved in RNA translation and some lysosomal proteins. The precise pathomechanisms remain to be elucidated. Improved understanding of the process of myelination, the metabolic axonal support functions of myelin and the proposed contribution of myelin to CNS plasticity provide possible explanations as to why almost all patients with hypomyelination experience slow clinical decline after a long phase of stability. In this Review, we provide an overview of the hypomyelinating leukodystrophies, the advances in our understanding of myelin biology and of the genes involved in these disorders, and the insights these advances have provided into their clinical presentations and evolution.
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Lammert DB, Miedema D, Ochotorena J, Dosa N, Petropoulou K, Lebel RR, Sakonju A. Central and peripheral dysmyelination in a 3-year-old girl with ring chromosome 18. Clin Case Rep 2019; 7:2087-2091. [PMID: 31788257 PMCID: PMC6878035 DOI: 10.1002/ccr3.2426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 08/03/2019] [Accepted: 08/12/2019] [Indexed: 11/22/2022] Open
Abstract
Myelin basic protein (MBP) contributes to peripheral and central nervous system myelin. Developmental myelinopathies exist on a clinical spectrum, but MBP is not included on leukodystrophy or CMT gene panels. This ring chromosome 18 case presents serial MRI and EMG/NCS, shedding light on the early clinical course of the disorder.
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Affiliation(s)
- Dawn Brianna Lammert
- Department of PediatricsJohns Hopkins HospitalBaltimoreMaryland
- Present address:
Department of PediatricsJohns Hopkins HospitalBaltimoreMaryland
| | | | - Josiree Ochotorena
- Child and Adolescent Health AssociatesSamaritan Health SystemsWatertownNew York
| | - Nienke Dosa
- Center for Development, Behavior, and GeneticsSUNY Upstate Medical UniversitySyracuseNew York
| | | | - Roger Robert Lebel
- Center for Development, Behavior, and GeneticsSUNY Upstate Medical UniversitySyracuseNew York
| | - Ai Sakonju
- Department of NeurologySUNY Upstate Medical UniversitySyracuseNew York
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Jávorszky E, Morinière V, Kerti A, Balogh E, Pikó H, Saunier S, Karcagi V, Antignac C, Tory K. QMPSF is sensitive and specific in the detection of NPHP1 heterozygous deletions. ACTA ACUST UNITED AC 2017; 55:809-816. [DOI: 10.1515/cclm-2016-0819] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/08/2016] [Indexed: 11/15/2022]
Abstract
Abstract
Background:
Nephronophthisis, an autosomal recessive nephropathy, is responsible for 10% of childhood chronic renal failure. The deletion of its major gene, NPHP1, with a minor allele frequency of 0.24% in the general population, is the most common mutation leading to a monogenic form of childhood chronic renal failure. It is challenging to detect it in the heterozygous state. We aimed to evaluate the sensitivity and the specificity of the quantitative multiplex PCR of short fluorescent fragments (QMPSF) in its detection.
Methods:
After setting up the protocol of QMPSF, we validated it on 39 individuals diagnosed by multiplex ligation-dependent probe amplification (MLPA) with normal NPHP1 copy number (n=17), with heterozygous deletion (n=13, seven parents and six patients), or with homozygous deletion (n=9). To assess the rate of the deletions that arise from independent events, deleted alleles were haplotyped.
Results:
The results of QMPSF and MLPA correlated perfectly in the identification of 76 heterozygously deleted and 56 homozygously deleted exons. The inter-experimental variability of the dosage quotient obtained by QMPSF was low: control, 1.05 (median; range, 0.86−1.33, n = 102 exons); heterozygous deletion, 0.51 (0.42−0.67, n = 76 exons); homozygous deletion, 0 (0−0, n = 56 exons). All patients harboring a heterozygous deletion were found to carry a hemizygous mutation. At least 15 out of 18 deletions appeared on different haplotypes and one deletion appeared de novo.
Conclusions:
The cost- and time-effective QMPSF has a 100% sensitivity and specificity in the detection of NPHP1 deletion. The potential de novo appearance of NPHP1 deletions makes its segregation analysis highly recommended in clinical practice.
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Ferreira MC, Dorboz I, Rodriguez D, Boespflug Tanguy O. Screening for GFAP rearrangements in a cohort of Alexander disease and undetermined leukoencephalopathy patients. Eur J Med Genet 2015. [DOI: 10.1016/j.ejmg.2015.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Boespflug-Tanguy O. Inborn errors of brain myelin formation. HANDBOOK OF CLINICAL NEUROLOGY 2013; 113:1581-92. [PMID: 23622380 DOI: 10.1016/b978-0-444-59565-2.00027-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Inborn errors of brain myelin formation or hypomyelinating leukodystrophies (HLD) represent a heterogeneous group of white matter diseases related to a primitive impairment of oligodendrocytes to produce myelin in the central nervous system (CNS). Cerebral magnetic resonance imaging (MRI) allows an assessment of the myelination pattern. The clinical presentation is related to the degree of hypomyelination and its consequences on axonal functions. When the gene defect interferes with the active infantile phase of myelination, the consequences might be severe, with delayed and loss of psychomotor development, absence of myelin signal on cerebral MRI and of identifiable waves on cerebral evoked potentials, as described by Pelizaeus and Merzbacher (PMD). When the pathophysiological mechanism is less severe, myelin production is maintained, although signs of progressive axonopathy are observed, related to progressive spastic paraplegia (SPG) associated with cognitive or behavioral disturbances. HLDs have been classified according to gene defects or associated signs. The X-linked HDL1 (PMD and SPG2) is related to the gene that controls the production of the major CNS myelin proteins, the proteolipid proteins (PLP). The gap junction protein, gamma 2 gene (GJC2) encoding oligodendrocyte-specific connexin, has been shown to be involved in the autosomal recessive HLD2 (PMLD1 and SPG44).
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Affiliation(s)
- Odile Boespflug-Tanguy
- National Reference Center for Rare Diseases "leukodystrophies", INSERM U676, Université Paris Diderot, Sorbonne Paris Cité Université and Pediatric Neurology and Metabolic Disease Service, Hôpital Robert Debré, Paris, France.
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Jeon JP, Shim SM, Nam HY, Ryu GM, Hong EJ, Kim HL, Han BG. Copy number variation at leptin receptor gene locus associated with metabolic traits and the risk of type 2 diabetes mellitus. BMC Genomics 2010; 11:426. [PMID: 20624279 PMCID: PMC2996954 DOI: 10.1186/1471-2164-11-426] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 07/12/2010] [Indexed: 12/26/2022] Open
Abstract
Background Recent efforts have been made to link complex human traits and disease susceptibility to DNA copy numbers. The leptin receptor (LEPR) has been implicated in obesity and diabetes. Mutations and genetic variations of LEPR gene have been discovered in rodents and humans. However, the association of DNA copy number variations at the LEPR gene locus with human complex diseases has not been reported. In an attempt to study DNA copy number variations associated with metabolic traits and type 2 diabetes mellitus (T2DM), we targeted the LEPR gene locus in DNA copy number analyses. Results We identified DNA copy number variations at the LEPR gene locus among a Korean population using genome-wide SNP chip data, and then quantified copy numbers of the E2 DNA sequence in the first two exons overlapped between LEPR and LEPROT genes by the quantitative multiplex PCR of short fluorescent fragment (QMPSF) method. Among the non-diabetic subjects (n = 1,067), lower E2 DNA copy numbers were associated with higher fasting glucose levels in men (p = 1.24 × 10-7) and women (p = 9.45 × 10-5), as well as higher total cholesterol levels in men (p = 9.96 × 10-7). In addition, the significant association between lower E2 DNA copy numbers and lower level of postprandial 2hr insulin was evident only in non-diabetic women, whereas some obesity-related phenotypes and total cholesterol level exhibited significant associations only in non-diabetic men. Logistic regression analysis indicated that lower E2 DNA copy numbers were associated with T2DM (odds ratio, 1.92; 95% CI, 1.26~2.96; p < 0.003) in our nested case-control study. Interestingly, the E2 DNA copy number exhibited a negative correlation with LEPR gene expression, but a positive correlation with LEPROT gene expression. Conclusions This work suggests that a structural variation at the LEPR gene locus is functionally associated with complex metabolic traits and the risk of T2DM.
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Affiliation(s)
- Jae-Pil Jeon
- Division of Biobank for Health Sciences, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, 194 Tongil Ro, Seoul, 122-701, Korea.
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Jeon JP, Shim SM, Jung JS, Nam HY, Lee HJ, Oh BS, Kim K, Kim HL, Han BG. A comprehensive profile of DNA copy number variations in a Korean population: identification of copy number invariant regions among Koreans. Exp Mol Med 2010; 41:618-28. [PMID: 19478558 DOI: 10.3858/emm.2009.41.9.068] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
To examine copy number variations among the Korean population, we compared individual genomes with the Korean reference genome assembly using the publicly available Korean HapMap SNP 50 k chip data from 90 individuals. Korean individuals exhibited 123 copy number variation regions (CNVRs) covering 27.2 mb, equivalent to 1.0% of the genome in the copy number variation (CNV) analysis using the combined criteria of P value (P<0.01) and standard deviation of copy numbers (SD>or= 0.25) among study subjects. In contrast, when compared to the Affymetrix reference genome assembly from multiple ethnic groups, considerably more CNVRs (n=643) were detected in larger proportions (5.0%) of the genome covering 135.1 mb even by more stringent criteria (P<0.001 and SD>or=0.25), reflecting ethnic diversity of structural variations between Korean and other populations. Some CNVRs were validated by the quantitative multiplex PCR of short fluorescent fragment (QMPSF) method, and then copy number invariant regions were detected among the study subjects. These copy number invariant regions would be used as good internal controls for further CNV studies. Lastly, we demonstrated that the CNV information could stratify even a single ethnic population with a proper reference genome assembly from multiple heterogeneous populations.
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Affiliation(s)
- Jae Pil Jeon
- Division of Biobank for Health Sciences, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Seoul 122-701, Korea
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Cody JD, Heard PL, Crandall AC, Carter EM, Li J, Hardies LJ, Lancaster J, Perry B, Stratton RF, Sebold C, Schaub RL, Soileau B, Hill A, Hasi M, Fox PT, Hale DE. Narrowing critical regions and determining penetrance for selected 18q- phenotypes. Am J Med Genet A 2009; 149A:1421-30. [PMID: 19533771 DOI: 10.1002/ajmg.a.32899] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
One of our primary goals is to help families who have a child with an 18q deletion anticipate medical issues in order to optimize their child's medical care. To this end we have narrowed the critical regions for four phenotypic features and determined the penetrance for each of those phenotypes when the critical region for that feature is hemizygous. We completed molecular analysis using oligo-array CGH and clinical assessments on 151 individuals with deletions of 18q and made genotype-phenotype correlations defining or narrowing critical regions. These nested regions, all within 18q22.3 to q23, were for kidney malformations, dysmyelination of the brain, growth hormone stimulation response failure, and aural atresia. The region for dysmyelination and growth hormone stimulation response failure were identical and was narrowed to 1.62 Mb, a region containing five known genes. The region for aural atresia was 2.3 Mb and includes an additional three genes. The region for kidney malformations was 3.21 Mb and includes an additional four genes. Penetrance rates were calculated by comparing the number of individuals hemizygous for a critical region with the phenotype to those without the phenotype. The kidney malformations region was 25% penetrant, the dysmyelination region was 100% penetrant, the growth hormone stimulant response failure region was 90% penetrant with variable expressivity, and the aural atresia region was 78% penetrant. Identification of these critical regions suggest possible candidate genes, while penetrance calculations begin to create a predictive phenotypic description based on genotype.
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Affiliation(s)
- Jannine D Cody
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA.
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Bonnet-Dupeyron MN, Combes P, Boespflug-Tanguy O, Vaurs-Barrière C. Absence of OLIG2 mutations in patients presenting with a severe Pelizaeus-Merzbacher-like leukodystrophy associated with motor neuron dysfunction. Am J Med Genet B Neuropsychiatr Genet 2008; 147B:538-9. [PMID: 17918228 DOI: 10.1002/ajmg.b.30613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Carson AR, Feuk L, Mohammed M, Scherer SW. Strategies for the detection of copy number and other structural variants in the human genome. Hum Genomics 2006; 2:403-14. [PMID: 16848978 PMCID: PMC3525157 DOI: 10.1186/1479-7364-2-6-403] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022] Open
Abstract
Advances in genome scanning technologies are revealing that copy number variants (CNVs) and polymorphisms, ranging from a few kilobases to several megabases in size, are present in genomes at frequencies much greater than previously known. Discoveries of additional forms of genomic variation, including inversions, insertions, deletions and complex rearrangements, are also occurring at an increased rate. Along with CNVs, these sequence alterations are collectively known as structural variants, and their discovery has had an immediate impact on the interpretation of basic research and clinical diagnostic data. This paper discusses different methods, experimental strategies and technologies that are currently available to study copy number variation and other structural variants in the human genome.
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Affiliation(s)
- Andrew R Carson
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children and Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Lars Feuk
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children and Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Stephen W Scherer
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children and Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada
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Armour JAL, Palla R, Zeeuwen PLJM, den Heijer M, Schalkwijk J, Hollox EJ. Accurate, high-throughput typing of copy number variation using paralogue ratios from dispersed repeats. Nucleic Acids Res 2006; 35:e19. [PMID: 17175532 PMCID: PMC1807953 DOI: 10.1093/nar/gkl1089] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recent work has demonstrated an unexpected prevalence of copy number variation in the human genome, and has highlighted the part this variation may play in predisposition to common phenotypes. Some important genes vary in number over a high range (e.g. DEFB4, which commonly varies between two and seven copies), and have posed formidable technical challenges for accurate copy number typing, so that there are no simple, cheap, high-throughput approaches suitable for large-scale screening. We have developed a simple comparative PCR method based on dispersed repeat sequences, using a single pair of precisely designed primers to amplify products simultaneously from both test and reference loci, which are subsequently distinguished and quantified via internal sequence differences. We have validated the method for the measurement of copy number at DEFB4 by comparison of results from >800 DNA samples with copy number measurements by MAPH/REDVR, MLPA and array-CGH. The new Paralogue Ratio Test (PRT) method can require as little as 10 ng genomic DNA, appears to be comparable in accuracy to the other methods, and for the first time provides a rapid, simple and inexpensive method for copy number analysis, suitable for application to typing thousands of samples in large case-control association studies.
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Affiliation(s)
- John A L Armour
- Institute of Genetics, University of Nottingham, Nottingham, NG7 2UH, UK.
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Mikesová E, Baránková L, Sakmaryová I, Tatarková I, Seeman P. Quantitative Multiplex Real-Time PCR for Detection of PLP1 Gene Duplications in Pelizaeus–Merzbacher Patients. ACTA ACUST UNITED AC 2006; 10:215-20. [PMID: 17020474 DOI: 10.1089/gte.2006.10.215] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Pelizaeus-Merzbacher disease (PMD) is an X-linked recessive disorder of central nervous system (CNS) myelination typically affecting males. A genomic duplication of variable size at Xq22.2, containing the entire proteolipid protein 1 gene (PLP1), is responsible for approximately 60-70% of PMD cases. The aim of this study was to develop a rapid and robust method for determination of PLP1 gene dosage. We optimized two multiplex real-time quantitative PCR (Q-PCR) assays targeting exons 3 and 6 of the PLP1 gene, and then validated these assays by retrospective analysis of a set of genomic DNAs from 67 previously tested patients and 43 normal controls. Samples were analyzed in multiplex PCR reactions using TaqMan chemistry and the ABI Prism 7000 Sequence Detection System. PLP1 dosage was determined by the relative quantitative comparative threshold cycle method (DeltaDeltaCt) using the human serum albumin gene as the endogenous reference gene. Three clearly non-overlapping ranges of results, corresponding to the presence of one, two, or three PLP1 copies, were detected in both assays. The results were completely concordant with gender and previous PLP1 gene dosage testing based on quantitative fluorescent multiplex PCR and analysis of a dinucleotide polymorphism in the first intron of the PLP1 gene. We conclude that multiplex real-time Q-PCR represents a fast and reliable tool for PLP1 duplication testing in PMD families.
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Affiliation(s)
- Emilie Mikesová
- Department of Child Neurology, DNA Laboratory, 2nd School of Medicine, Charles University Prague, Prague, Czech Republic.
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Combes P, Bonnet-Dupeyron MN, Gauthier-Barichard F, Schiffmann R, Bertini E, Rodriguez D, Armour JAL, Boespflug-Tanguy O, Vaurs-Barrière C. PLP1 and GPM6B intragenic copy number analysis by MAPH in 262 patients with hypomyelinating leukodystrophies: identification of one partial triplication and two partial deletions of PLP1. Neurogenetics 2006; 7:31-7. [PMID: 16416265 DOI: 10.1007/s10048-005-0021-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Accepted: 09/15/2005] [Indexed: 02/03/2023]
Abstract
The proteolipid protein 1 (PLP1) gene is known to be mutated in the X-linked disorders of myelin formation Pelizaeus-Merzbacher disease (PMD) and spastic paraplegia type 2. The most commonly found PLP1 mutations are gene duplications (60-70%) and point mutations (20%). About 20% of patients with a PMD phenotype do not present identified PLP1 mutation, thus suggesting genetic heterogeneity and/or undetected PLP1 abnormalities. Except the recently described MLPA screening the seven exonic regions, the currently used techniques to quantify PLP1 gene copy number do not investigate small intragenic PLP1 rearrangements. Using the multiplex amplifiable probe hybridization (MAPH) technique, we looked simultaneously for intragenic rearrangements along the PLP1 gene (exonic and regulatory regions) and for rearrangements in the GPM6B candidate gene (a member of the proteolipid protein family). We tested 262 hypomyelinating patients: 56 PLP1 duplicated patients, 1 PLP1 triplicated patient, and 205 patients presenting a leukodystrophy of undetermined origin with brain MRI suggesting a defect in myelin formation. Our results show that MAPH is an alternative reliable technique for diagnosis of PLP1 gene copy number. It allows us (1) to demonstrate that all PLP1 duplications previously found encompass the whole gene, (2) to establish that copy number changes in GPM6B and intragenic duplications of PLP1 are very unlikely to be involved in the etiology of UHL, and (3) to identify one partial triplication and two partial deletions of PLP1 in patients presenting with a PMD phenotype.
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Affiliation(s)
- Patricia Combes
- INSERM U 384, Faculté de Médecine, Place Henri Dunant, 63000 Clermont-Ferrand, France
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