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Li Y, Ding B, Mao Y, Zhang H, Wang X, Ding Q. Tandem and inverted duplications in haemophilia A: Breakpoint characterisation provides insight into possible rearrangement mechanisms. Haemophilia 2023. [PMID: 37192522 DOI: 10.1111/hae.14799] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 05/18/2023]
Abstract
INTRODUCTION Approximately half of patients with severe haemophilia A are caused by structural variants in the F8 gene. Unlike inversions or deletions directly impairing the integrity of F8, some duplications do not completely disrupt the open reading frame or even retain an intact F8 copy. Currently, only a few duplication breakpoints were precisely characterized, and the corresponding rearrangement mechanisms and clinical outcomes remain to be further investigated. AIM Establishing an effective strategy for breakpoint characterization of duplications and revealing their rearrangement mechanisms. METHODS AccuCopy is used for the detection of duplications, long-distance PCR for the characterization of tandem duplications, genome walking technique and whole genome sequencing for the characterization of inverted duplications. RESULTS Four F8 duplication rearrangements were successfully characterized at the nucleotide level: one tandem duplication (exons 7-11) and three inverted duplications (exons 7-22, exons 2-26, and exons 15-22). Two shared features of inverted duplication were found after carefully analysing our results and breakpoint information in the literature: 1, an inverted fragment was inserted into the original chromosome via two junctions; 2, one junction is mediated by a pair of inverted repetitive elements, while the other consists of two breakpoints with microhomology. CONCLUSION Similar breakpoint features motivated us to propose a DNA replication-based model to explain the formation of duplication rearrangements. Based on our model, we further divide the inverted duplications into three basic types: type I with a DEL-NOR/INV-DUP pattern, type II with a DUP-NOR/INV-DUP pattern and type III with a DUP-TRP/INV-DUP pattern.
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Affiliation(s)
- Yang Li
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Biying Ding
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yinqi Mao
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Huayang Zhang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xuefeng Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qiulan Ding
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Tang J, Chang G, Wei M, Li X, Chen H, Qin Y, Wang J, Wang X, Chen R, Li N. Diagnosis of patients with mucopolysaccharidosis type II via RNA sequencing. Clin Chim Acta 2022; 537:38-45. [DOI: 10.1016/j.cca.2022.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/29/2022] [Accepted: 10/10/2022] [Indexed: 11/03/2022]
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La Cognata V, Cavallaro S. Detection of Structural Variants by NGS: Revealing Missing Alleles in Lysosomal Storage Diseases. Biomedicines 2022; 10:biomedicines10081836. [PMID: 36009380 PMCID: PMC9405548 DOI: 10.3390/biomedicines10081836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
Lysosomal storage diseases (LSDs) are a heterogeneous group of rare multisystem metabolic disorders occurring mostly in infancy and childhood, characterized by a gradual accumulation of non-degraded substrates inside the cells. Although biochemical enzymatic assays are considered the gold standard for diagnosis of symptomatic patients, genotyping is a requirement for inclusion in enzyme replacement programs and is a prerequisite for carrier tests in relatives and DNA-based prenatal diagnosis. The emerging next-generation sequencing (NGS) technologies are now offering a powerful diagnostic tool for genotyping LSDs patients by providing faster, cheaper, and higher-resolution testing options, and are allowing to unravel, in a single integrated workflow SNVs, small insertions and deletions (indels), as well as major structural variations (SVs) responsible for the pathology. Here, we summarize the current knowledge about the most recurrent and private SVs involving LSDs-related genes, review advantages and drawbacks related to the use of the NGS in the SVs detection, and discuss the challenges to bring this type of analysis in clinical diagnostics.
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Genotype-phenotype spectrum of 130 unrelated Indian families with Mucopolysaccharidosis type II. Eur J Med Genet 2022; 65:104447. [PMID: 35144014 DOI: 10.1016/j.ejmg.2022.104447] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 12/20/2021] [Accepted: 02/06/2022] [Indexed: 11/22/2022]
Abstract
MPS II is an X linked recessive lysosomal storage disorder with multi-system involvement and marked molecular heterogeneity. In this study, we explored the clinical and molecular spectrum of 144 Indian patients with MPS II from 130 unrelated families. Clinical information was collected on a predesigned clinical proforma. Sanger method was employed to sequence all the exons and exon/intron boundaries of the IDS gene. In cases where causative variation was not detected by Sanger sequencing, MLPA and RFLP were performed to identify large deletions/duplications and complex rearrangements. Cytogenetic microarray was done in one patient to see the breakpoints and extent of deletion. In one patient with no detectable likely pathogenic or pathogenic variation, whole-genome sequencing was also performed. Novel variants were systematically assessed by in silico prediction software and protein modelling. The pathogenicity of variants was established based on ACMG criteria. An attempt was also made to establish a genotype-phenotype correlation. Positive family history was present in 31% (41/130) of patients. Developmental delay and intellectual disability were the main reasons for referral. Macrocephaly, coarse facies and dysostosis were present in almost all patients. Hepatosplenomegaly, joint contractures and short stature were the characteristic features, seen in 87% (101/116), 67.8% (74/109) and 41.4% (41/99) patients respectively. Attenuated phenotype was seen in 32.6% (47/144) patients, while severe phenotype was seen in 63% (91/144) patients. The detection rate for likely pathogenic or pathogenic variants in our cohort is 95.5% (107/112) by Sanger sequencing, MLPA and RFLP. We also found two variants of unknown significance, one each by Sanger sequencing and WGS. Total of 71 variants were identified by Sanger sequencing and 29 of these variants were found to be novel. Amongst the novel variants, there was a considerable proportion (51%) of frameshift variants (15/29). Almost half of the causative variants were located in exon 3,8 and 9. A significant genotype-phenotype correlation was also noted for both known and novel variants. This information about the genotype spectrum and phenotype will be helpful for diagnostic and prognostic purposes.
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Gomes CP, Marins MM, Motta FL, Kyosen SO, Curiati MA, D'Almeida V, Martins AM, Pesquero JB. A New Mutation in IDS Gene Causing Hunter Syndrome: A Case Report. Front Genet 2020; 10:1383. [PMID: 32256517 PMCID: PMC7093562 DOI: 10.3389/fgene.2019.01383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/18/2019] [Indexed: 12/02/2022] Open
Abstract
Rationale Mucopolysaccharidosis type II (Hunter syndrome) is an X-linked multisystem disorder, caused by deficiency of the lysosomal enzyme iduronate-2-sulfatase (I2S). The clinical manifestations of this disease are severe skeletal deformities, airway obstruction, cardiomyopathy, and neurologic deterioration. Patient The patient was 5 years and 6 months boy, with developmental delay, hearing loss, hepatosplenomegaly, and skeletal dysplasia. He was diagnosed with mucopolysaccharidosis type II based on clinical manifestations, biochemical and genetic analysis. Outcomes The patient carries a new mutation (c.879-1210_1007-218del) in hemizygosis in the IDS gene, which was defined as pathogenic according to the 2015 American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines and as responsible for the mucopolysaccharidosis type II phenotype in the patient.
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Affiliation(s)
- Caio Perez Gomes
- Center for Research and Molecular Diagnosis of Genetic Diseases, Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Maryana Mara Marins
- Center for Research and Molecular Diagnosis of Genetic Diseases, Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Fabiana Louise Motta
- Center for Research and Molecular Diagnosis of Genetic Diseases, Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Sandra Obikawa Kyosen
- Inborn Errors of Metabolism Reference Center, Department of Pediatrics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Marco Antonio Curiati
- Inborn Errors of Metabolism Reference Center, Department of Pediatrics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Vânia D'Almeida
- Inborn Errors of Metabolism Laboratory, Department of Psychobiology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ana Maria Martins
- Inborn Errors of Metabolism Reference Center, Department of Pediatrics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - João Bosco Pesquero
- Center for Research and Molecular Diagnosis of Genetic Diseases, Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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Purizaca-Rosillo N, Mori T, Benites-Cóndor Y, Hisama FM, Martin GM, Oshima J. High incidence of BSCL2 intragenic recombinational mutation in Peruvian type 2 Berardinelli-Seip syndrome. Am J Med Genet A 2016; 173:471-478. [PMID: 27868354 DOI: 10.1002/ajmg.a.38053] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/27/2016] [Indexed: 11/06/2022]
Abstract
Congenital generalized lipodystrophy (CGL) is a genetically heterogeneous group of disorders characterized by the absence of functional adipose tissue. We identified two pedigrees with CGL in the community of the Mestizo tribe in the northern region of Peru. Five cases, ranging from 15 months to 7 years of age, presented with generalized lipodystrophy, muscular prominence, mild intellectual disability, and a striking aged appearance. Sequencing of the BSCL2 gene, known to be mutated in type 2 CGL (CGL2; Berardinelli-Seip syndrome), revealed a homozygous deletion of exon 3 in all five patients examined, suggesting the presence of a founder mutation. This intragenic deletion appeared to be mediated by recombination between Alu sequences in introns 2 and 3. CGL2 in this population is likely underdiagnosed and undertreated because of its geographical, socio-economic, and cultural isolation.© 2016 Wiley Periodicals, Inc.
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Affiliation(s)
| | - Takayasu Mori
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington
| | | | - Fuki M Hisama
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington
| | - George M Martin
- Department of Pathology, University of Washington, Seattle, Washington
| | - Junko Oshima
- Department of Pathology, University of Washington, Seattle, Washington
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Hemmat M, Hemmat O, Anguiano A, Boyar FZ, El Naggar M, Wang JC, Wang BT, Sahoo T, Owen R, Haddadin M. Genotype-phenotype analysis of recombinant chromosome 4 syndrome: an array-CGH study and literature review. Mol Cytogenet 2013; 6:17. [PMID: 23639048 PMCID: PMC3648413 DOI: 10.1186/1755-8166-6-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Accepted: 03/01/2013] [Indexed: 11/14/2022] Open
Abstract
Background Recombinant chromosome 4, a rare constitutional rearrangement arising from pericentric inversion, comprises a duplicated segment of 4p13~p15→4pter and a deleted segment of 4q35→4qter. To date, 10 cases of recombinant chromosome 4 have been reported. Result We describe the second case in which array-CGH was used to characterize recombinant chromosome 4 syndrome. The patient was a one-year old boy with consistent clinical features. Conventional cytogenetics and FISH documented a recombinant chromosome 4, derived from a paternal pericentric inversion, leading to partial trisomy 4p and partial monosomy of 4q. Array-CGH, performed to further characterize the rearranged chromosome 4 and delineate the breakpoints, documented a small (4.36 Mb) 4q35.1 terminal deletion and a large (23.81 Mb) 4p15.1 terminal duplication. Genotype-phenotype analysis of 10 previously reported cases and the present case indicated relatively consistent clinical features and breakpoints. This consistency was more evident in our case and another characterized by array-CGH, where both showed the common breakpoints of p15.1 and q35.1. A genotype-phenotype correlation study between rec(4), dup(4p), and del(4q) syndromes revealed that urogenital and cardiac defects are probably due to the deletion of 4q whereas the other clinical features are likely due to 4p duplication. Conclusion Our findings support that the clinical features of patients with rec(4) are relatively consistent and specific to the regions of duplication or deletion. Recombinant chromosome 4 syndrome thus appears to be a discrete entity that can be suspected on the basis of clinical features or specific deleted and duplicated chromosomal regions.
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Affiliation(s)
- Morteza Hemmat
- Cytogenetics Department, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA.,Cytogenetics Department, Quest Diagnostics Nichols Institute, 33608 Ortega Highway, San Juan Capistrano, CA, 92690, USA
| | - Omid Hemmat
- Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
| | - Arturo Anguiano
- Cytogenetics Department, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Fatih Z Boyar
- Cytogenetics Department, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Mohammed El Naggar
- Cytogenetics Department, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Jia-Chi Wang
- Cytogenetics Department, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Borris T Wang
- Cytogenetics Department, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Trilochan Sahoo
- Cytogenetics Department, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Renius Owen
- Cytogenetics Department, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Mary Haddadin
- Cytogenetics Department, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
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