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Parra A, Tenorio-Castano J, Nevado J, Cazalla M, Miranda-Alcaraz L, Gallego-Zazo N, Silván C, Arias P, Pozo-Román J, Ballesta-Martínez MJ, Guillén-Navarro E, Arroyo I, Lotersztein V, Cosentino V, González-Meneses A, Galán E, Rosell J, Ramos F, Lapunzina P. Identification of copy-number variants in patients with overgrowth disorders. Clin Genet 2024; 106:614-624. [PMID: 39091142 DOI: 10.1111/cge.14596] [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: 06/17/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 08/04/2024]
Abstract
Overgrowth syndromes (OGS) comprise a heterogeneous group of disorders whose main characteristic is that the weight, height or the head circumference are above the 97th centile or 2-3 standard deviations above the mean for age, gender, and ethnic group. Several copy-number variants (CNVs) have been associated with the development of OGS, such as the 5q35 microdeletion or the duplication of the 15q26.1-qter, among many others. In this study, we have applied 850K SNP-arrays to 112 patients and relatives with OGS from the Spanish OverGrowth Registry Initiative. We have identified CNVs associated with the disorder in nine individuals (8%). Subsequently, whole genome sequencing (WGS) analysis was performed in these nine samples in order to better understand these genomic imbalances. All the CNVs were detected by both techniques, settling that WGS is a useful tool for CNV detection. We have found six patients with genomic abnormalities associated with previously well-established disorders and three patients with CNVs of unknown significance, which may be related to OGS, based on scientific literature. In this report, we describe these findings and comment on genes associated with OGS that are located within the CNV regions.
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Affiliation(s)
- Alejandro Parra
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- INGEMM-Idipaz, Institute of Medical and Molecular Genetics, Madrid, Spain
- ITHACA, European Reference Network, Hospital Universitario La Paz, Madrid, Spain
| | - Jair Tenorio-Castano
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- INGEMM-Idipaz, Institute of Medical and Molecular Genetics, Madrid, Spain
- ITHACA, European Reference Network, Hospital Universitario La Paz, Madrid, Spain
| | - Julián Nevado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- INGEMM-Idipaz, Institute of Medical and Molecular Genetics, Madrid, Spain
- ITHACA, European Reference Network, Hospital Universitario La Paz, Madrid, Spain
| | - Mario Cazalla
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- INGEMM-Idipaz, Institute of Medical and Molecular Genetics, Madrid, Spain
- ITHACA, European Reference Network, Hospital Universitario La Paz, Madrid, Spain
| | - Lucía Miranda-Alcaraz
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- INGEMM-Idipaz, Institute of Medical and Molecular Genetics, Madrid, Spain
- ITHACA, European Reference Network, Hospital Universitario La Paz, Madrid, Spain
| | - Natalia Gallego-Zazo
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- INGEMM-Idipaz, Institute of Medical and Molecular Genetics, Madrid, Spain
- ITHACA, European Reference Network, Hospital Universitario La Paz, Madrid, Spain
| | - Cristina Silván
- INGEMM-Idipaz, Institute of Medical and Molecular Genetics, Madrid, Spain
| | - Pedro Arias
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- INGEMM-Idipaz, Institute of Medical and Molecular Genetics, Madrid, Spain
- ITHACA, European Reference Network, Hospital Universitario La Paz, Madrid, Spain
| | - Jesús Pozo-Román
- Unit of Pediatric Endocrinology, Department of Pediatrics, Hospital Universitario Infantil Niño Jesús, Madrid, Spain
- Department of Pediatrics, Medical School, Autonomous University of Madrid, Madrid, Spain
| | - María Juliana Ballesta-Martínez
- Sección de Genética Médica, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain
| | - Encarna Guillén-Navarro
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain
| | - Ignacio Arroyo
- Pediatrics Department, San Pedro de Alcántara Hospital, Cáceres, Spain
| | - Vanesa Lotersztein
- Department of Genetics, Centro Nacional de Genética, Buenos Aires, Argentina
| | | | | | - Enrique Galán
- Pediatrics Department, Hospital Materno-Infantil, Badajoz, Spain
| | - Jordi Rosell
- Department of Genetics, Hospital Son Espases, Palma de Mallorca, Spain
| | - Feliciano Ramos
- Pediatrics Department, Hospital Lozano Blesa, Zaragoza, Spain
| | - Pablo Lapunzina
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- INGEMM-Idipaz, Institute of Medical and Molecular Genetics, Madrid, Spain
- ITHACA, European Reference Network, Hospital Universitario La Paz, Madrid, Spain
- Spanish OverGrowth Registry Initiative, La Paz University Hospital, Madrid, Spain
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Chan ER, Benchek P, Miller G, Brustoski K, Schaffer A, Truitt B, Tag J, Freebairn L, Lewis BA, Stein CM, Iyengar SK. Importance of copy number variants in childhood apraxia of speech and other speech sound disorders. Commun Biol 2024; 7:1273. [PMID: 39369109 PMCID: PMC11455877 DOI: 10.1038/s42003-024-06968-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 09/25/2024] [Indexed: 10/07/2024] Open
Abstract
Childhood apraxia of speech (CAS) is a severe and rare form of speech sound disorder (SSD). CAS is typically sporadic, but may segregate in families with broader speech and language deficits. We hypothesize that genetic changes may be involved in the etiology of CAS. We conduct whole-genome sequencing in 27 families with CAS, 101 individuals in all. We identify 17 genomic regions including 19 unique copy number variants (CNVs). Three variants are shared across families, but the rest are unique; three events are de novo. In four families, siblings with milder phenotypes co-inherited the same CNVs, demonstrating variable expressivity. We independently validate eight CNVs using microarray technology and find many of these CNVs are present in children with milder forms of SSD. Bioinformatic investigation reveal four CNVs with substantial functional consequences (cytobands 2q24.3, 6p12.3-6p12.2, 11q23.2-11q23.3, and 16p11.2). These discoveries show that CNVs are a heterogeneous, but prevalent, cause of CAS.
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Affiliation(s)
- E Ricky Chan
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Penelope Benchek
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Gabrielle Miller
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Kim Brustoski
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Ashleigh Schaffer
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Barbara Truitt
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Jessica Tag
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Lisa Freebairn
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Barbara A Lewis
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Catherine M Stein
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
| | - Sudha K Iyengar
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA.
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Crippa V, Fina E, Ramazzotti D, Piazza R. Control-FREEC viewer: a tool for the visualization and exploration of copy number variation data. BMC Bioinformatics 2024; 25:72. [PMID: 38355453 PMCID: PMC10868011 DOI: 10.1186/s12859-024-05694-w] [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: 07/26/2023] [Accepted: 02/09/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Copy number alterations (CNAs) are genetic changes commonly found in cancer that involve different regions of the genome and impact cancer progression by affecting gene expression and genomic stability. Computational techniques can analyze copy number data obtained from high-throughput sequencing platforms, and various tools visualize and analyze CNAs in cancer genomes, providing insights into genetic mechanisms driving cancer development and progression. However, tools for visualizing copy number data in cancer research have some limitations. In fact, they can be complex to use and require expertise in bioinformatics or computational biology. While copy number data analysis and visualization provide insights into cancer biology, interpreting results can be challenging, and there may be multiple explanations for observed patterns of copy number alterations. RESULTS We created Control-FREEC Viewer, a tool that facilitates effective visualization and exploration of copy number data. With Control-FREEC Viewer, experimental data can be easily loaded by the user. After choosing the reference genome, copy number data are displayed in whole genome or single chromosome view. Gain or loss on a specific gene can be found and visualized on each chromosome. Analysis parameters for subsequent sessions can be stored and images can be exported in raster and vector formats. CONCLUSIONS Control-FREEC Viewer enables users to import and visualize data analyzed by the Control-FREEC tool, as well as by other tools sharing a similar tabular output, providing a comprehensive and intuitive graphical user interface for data visualization.
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Affiliation(s)
- Valentina Crippa
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy.
| | - Emanuela Fina
- Department of Thoracic Surgery, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniele Ramazzotti
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy.
- Fondazione IRCCS San Gerardo Dei Tintori, Monza, Italy.
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Landoulsi Z, Pachchek S, Bobbili DR, Pavelka L, May P, Krüger R. Genetic landscape of Parkinson's disease and related diseases in Luxembourg. Front Aging Neurosci 2023; 15:1282174. [PMID: 38173558 PMCID: PMC10761438 DOI: 10.3389/fnagi.2023.1282174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Objectives To explore the genetic architecture of PD in the Luxembourg Parkinson's Study including cohorts of healthy people and patients with Parkinson's disease (PD) and atypical parkinsonism (AP). Methods 809 healthy controls, 680 PD and 103 AP were genotyped using the Neurochip array. We screened and validated rare single nucleotide variants (SNVs) and copy number variants (CNVs) within seven PD-causing genes (LRRK2, SNCA, VPS35, PRKN, PARK7, PINK1 and ATP13A2). Polygenic risk scores (PRSs) were generated using the latest genome-wide association study for PD. We then estimated the role of common variants in PD risk by applying gene-set-specific PRSs. Results We identified 60 rare SNVs in seven PD-causing genes, nine of which were pathogenic in LRRK2, PINK1 and PRKN. Eleven rare CNVs were detected in PRKN including seven duplications and four deletions. The majority of PRKN SNVs and CNVs carriers were heterozygous and not differentially distributed between cases and controls. The PRSs were significantly associated with PD and identified specific molecular pathways related to protein metabolism and signal transduction as drivers of PD risk. Conclusion We performed a comprehensive genetic characterization of the deep-phenotyped individuals of the Luxembourgish Parkinson's Study. Heterozygous SNVs and CNVs in PRKN were not associated with higher PD risk. In particular, we reported novel digenic variants in PD related genes and rare LRRK2 SNVs in AP patients. Our findings will help future studies to unravel the genetic complexity of PD.
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Affiliation(s)
- Zied Landoulsi
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Sinthuja Pachchek
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Dheeraj Reddy Bobbili
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Lukas Pavelka
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Patrick May
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rejko Krüger
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
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Moschella A, Capra AP, Corica D, Pepe G, Di Tommaso S, Sallicandro E, Wasniewska MG, Briuglia S, Aversa T. A novel case of 16q22.3 duplication syndrome in a child with overgrowth: case report and literature review. BMC Med Genomics 2023; 16:315. [PMID: 38049856 PMCID: PMC10696707 DOI: 10.1186/s12920-023-01716-3] [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: 07/24/2023] [Accepted: 10/25/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Distal chromosome 16 duplication syndrome (also known as 16q partial trisomy) is a very rare genetic disorder recently described in few clinical reports. 16q trisomy is generally associated with a multisystemic phenotype including intrauterine growth restriction (IUGR), brain and cardiac defects, intellectual disability (ID) and an increased risk of both prenatal and postnatal lethality. Smaller copy number variants (CNV) within the 16q region create partial trisomies, which occur less frequently than full trisomy 16q. CASE PRESENTATION We present the clinical case of a 12-years-old male with a 16q22.3q24.1 de novo heterozygous duplication whose phenotype was characterized by ID, facial dysmorphisms, stature and weight overgrowth. To date, only five other cases of this syndrome have been reported in scientific literature, and none of them comprised overgrowth. CONCLUSIONS Our case report highlights the great heterogeneity in clinical manifestations and provides new evidence for better defining the phenotypic picture for smaller 16q distal CNVs, suggesting unusual features.
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Affiliation(s)
- Antonino Moschella
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, "BIOMORF", Unit of Genetics and Pharmacogenetics, University of Messina, Messina, Italy
| | - Anna Paola Capra
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Domenico Corica
- Department of Human Pathology of Adulthood and Childhood "G. Barresi", Unit of Paediatrics, University of Messina, Messina, Italy
| | - Giorgia Pepe
- Department of Human Pathology of Adulthood and Childhood "G. Barresi", Unit of Paediatrics, University of Messina, Messina, Italy
| | - Silvia Di Tommaso
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, "Bambino Gesù" Children Hospital, IRCCS, Rome, Italy
| | - Ester Sallicandro
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, "Bambino Gesù" Children Hospital, IRCCS, Rome, Italy
| | - Malgorzata G Wasniewska
- Department of Human Pathology of Adulthood and Childhood "G. Barresi", Unit of Paediatrics, University of Messina, Messina, Italy
| | - Silvana Briuglia
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, "BIOMORF", Unit of Genetics and Pharmacogenetics, University of Messina, Messina, Italy.
| | - Tommaso Aversa
- Department of Human Pathology of Adulthood and Childhood "G. Barresi", Unit of Paediatrics, University of Messina, Messina, Italy
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Tenorio-Castano J, Gómez ÁSA, Coronado M, Rodríguez-Martín P, Parra A, Pascual P, Cazalla M, Gallego N, Arias P, Morales AV, Nevado J, Lapunzina P. Lamb-Shaffer syndrome: 20 Spanish patients and literature review expands the view of neurodevelopmental disorders caused by SOX5 haploinsufficiency. Clin Genet 2023; 104:637-647. [PMID: 37702321 DOI: 10.1111/cge.14423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/24/2023] [Accepted: 08/27/2023] [Indexed: 09/14/2023]
Abstract
Lamb-Shaffer Syndrome (LSS; OMIM #616803; ORPHA #313892; ORPHA #313884) is an infrequent genetic disorder that affects multiple aspects of human development especially those related to the development of the nervous system. LSS is caused by variants in the SOX5 gene. At the molecular level, SOX5 gene encodes for a transcription factor containing a High Mobility Group (HMG) DNA-Binding domain with relevant functions in brain development in different vertebrate species. Clinical features of Lamb-Shaffer syndrome may include intellectual disability, delayed speech and language development, attention deficits, hyperactivity, autism spectrum disorder, visual problems and seizures. Additionally, patients with the syndrome may present distinct facial dimorphism such as a wide mouth with full lips, small chin, broad nasal bridge, and deep-set eyes. Other physical features that have been reported in some patients include short stature, scoliosis, and joint hypermobility. Here, we report the clinical and molecular characterization of a Spanish LSS cohort of new 20 patients and review all the patients published so far which amount for 111 patients. The most frequent features included developmental delay, intellectual disability, visual problems, poor speech development and facial dysmorphic features. Strikingly, pain insensitivity and hypermetropia seems to be more frequent than previously reported, based on the frequency seen in the Spanish cohort. Eighty-three variants have been reported so far, single nucleotide variants (SNV) and copy number variants represent 47% and 53%, respectively, from the total of variants reported. Similarly to previous reports, the majority of the SNVs variants of the novel patients reported herein fall in the HMG domain of the protein. However, new variants, affecting other functional domains, were also detected. In conclusion, LLS is a rare genetic disorder mostly characterized by a wide range of developmental and neurological symptoms. Early diagnosis would allow to start of care programs, clinical follow up, prospective studies and appropriate genetic counseling, to promote clinical and social improvement to have profound lifelong benefits for patients and their families. Further research is needed to better understand the underlying mechanisms of the syndrome related to SOX5 haploinsufficiency.
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Affiliation(s)
- Jair Tenorio-Castano
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- INGEMM-IdIPAZ, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, Madrid, Spain
- ITHACA, European Reference Network, Brussels, Belgium
| | | | - Mónica Coronado
- Department of Radiology, Hospital Universitario La Paz, Madrid, Spain
| | | | - Alejandro Parra
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- INGEMM-IdIPAZ, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, Madrid, Spain
- ITHACA, European Reference Network, Brussels, Belgium
| | - Patricia Pascual
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- INGEMM-IdIPAZ, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, Madrid, Spain
- ITHACA, European Reference Network, Brussels, Belgium
| | - Mario Cazalla
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- INGEMM-IdIPAZ, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, Madrid, Spain
- ITHACA, European Reference Network, Brussels, Belgium
| | - Natalia Gallego
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- INGEMM-IdIPAZ, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, Madrid, Spain
- ITHACA, European Reference Network, Brussels, Belgium
| | - Pedro Arias
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- INGEMM-IdIPAZ, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, Madrid, Spain
- ITHACA, European Reference Network, Brussels, Belgium
| | - Aixa V Morales
- Instituto Cajal, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Julián Nevado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- INGEMM-IdIPAZ, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, Madrid, Spain
- ITHACA, European Reference Network, Brussels, Belgium
| | - Pablo Lapunzina
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- INGEMM-IdIPAZ, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, Madrid, Spain
- ITHACA, European Reference Network, Brussels, Belgium
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