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Yunisova G, Ceylaner S, Oflazer P, Deymeer F, Parman YG, Durmus H. Clinical and genetic characteristics of Emery-Dreifuss muscular dystrophy patients from Turkey: 30 years longitudinal follow-up study. Neuromuscul Disord 2022; 32:718-727. [DOI: 10.1016/j.nmd.2022.07.397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 06/29/2022] [Accepted: 07/11/2022] [Indexed: 10/17/2022]
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2
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Song D, Li X, Wei W, Liu X, Wu L, Xiong H. Microhomology-Mediated Nonhomologous End Joining Caused Rearrangement of EMD and FLNA in Emery-Dreifuss Muscular Dystrophy. Front Genet 2022; 12:786294. [PMID: 34976019 PMCID: PMC8719250 DOI: 10.3389/fgene.2021.786294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/15/2021] [Indexed: 12/01/2022] Open
Abstract
Background: Emery–Dreifuss muscular dystrophy (EDMD) is a rare disease characterized by early joint contractures, slowly progressive muscular dystrophy, and cardiac involvement, which includes arrhythmia, dilated cardiomyopathy, hypertrophic cardiomyopathy, heart failure, and sudden death. Methods: Clinical data of the proband and family members were collected. The next-generation sequencing technology was used to analyze the pathogenic variants and copy number variations. Polymerase chain reaction was used to sequence the breakpoints of gene locus rearrangements. Results: Here, we report two siblings with EDMD in a family. The proband, a 17-year-old boy, manifested a dilated right heart, bradycardia, mild muscle weakness, and joint contractures. His younger brother only showed a mild bowing limitation with elevated creatine kinase. Next-generation sequencing revealed the complete deletion of EMD and a rearrangement in FLNA (exon29_48dup) in these two patients. The EMD deletion and partial FLNA duplication were accompanied by a 5 bp overlap (GTCCC) on the background of the FLNA-EMD inversion. These findings support the pathogenic mechanism of microhomology-mediated nonhomologous end joining. Conclusion: We report two siblings with complete EMD deletion and FLNA duplication in a family. A microhomology-mediated nonhomologous end joining event involving EMD and FLNA acts as the underlying mechanism.
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Affiliation(s)
- Danyu Song
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xiaomei Li
- Department of Pediatric Cardiology, The First Hospital of Tsinghua University (Beijing Huaxin Hospital), Beijing, China
| | - Wei Wei
- Beijing Kangso Medical Inspection Co., Ltd., Beijing, China
| | - Xueqin Liu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Lin Wu
- Department of Cardiology, Peking University First Hospital, Beijing, China
| | - Hui Xiong
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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3
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Budisteanu M, Papuc S, Erbescu A, Iliescu C, Dobre M, Barca D, Tarta‑arsene O, Motoescu C, Dica A, Sandu C, Anghelescu C, Craiu D, Arghir A. Clinical and genomic findings in brain heterotopia: Report of a pediatric patient cohort from Romania. Exp Ther Med 2021; 23:101. [PMID: 34976143 PMCID: PMC8674960 DOI: 10.3892/etm.2021.11024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/09/2021] [Indexed: 11/08/2022] Open
Abstract
Brain heterotopia is a group of rare malformations with a heterogeneous phenotype, ranging from asymptomatic to a severe clinical picture (drug-resistant epilepsy, severe developmental delay). The etiology is multifactorial, including both genetic and environmental factors. In the present study, a cohort of 15 pediatric patients with brain heterotopia were investigated by clinical examination, electroencephalographic studies, brain imaging, and genomic tests. Most of the patients had epileptic seizures, often difficult to control with one antiepileptic drug; another frequent characteristic in the cohort was developmental delay or intellectual disability, in some cases associated with behavioral problems. The genomic studies revealed an interstitial 22q11.2 microduplication, an anomaly not reported previously in heterotopia patients. Comparing the cohort of the present study with that of a previous series of heterotopia patients, both adult and pediatric, similar aspects, such as the high frequency of drug-resistant epilepsy were observed as well as some differences, such as no systemic malformations and no cases with fatal evolution. The current findings add new data to existing knowledge on a rare heterogeneous disorder. The detailed clinical description, including the epilepsy phenotypes, and genomic profiles bring new insights into a group of disorders, yet to be fully understood.
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Affiliation(s)
- Magdalena Budisteanu
- Medical Genetics Laboratory, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania
| | - Sorina Papuc
- Medical Genetics Laboratory, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania
| | - Alina Erbescu
- Medical Genetics Laboratory, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania
| | - Catrinel Iliescu
- Department of Pediatric Neurology, Expertise Centre for Rare Diseases in Pediatric Neurology, Member of The EpiCARE European Reference Network, ‘Prof. Dr. Alex. Obregia’ Clinical Hospital, 041914 Bucharest, Romania
| | - Maria Dobre
- Medical Genetics Laboratory, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania
| | - Diana Barca
- Department of Pediatric Neurology, Expertise Centre for Rare Diseases in Pediatric Neurology, Member of The EpiCARE European Reference Network, ‘Prof. Dr. Alex. Obregia’ Clinical Hospital, 041914 Bucharest, Romania
| | - Oana Tarta‑arsene
- Department of Pediatric Neurology, Expertise Centre for Rare Diseases in Pediatric Neurology, Member of The EpiCARE European Reference Network, ‘Prof. Dr. Alex. Obregia’ Clinical Hospital, 041914 Bucharest, Romania
| | - Cristina Motoescu
- Department of Pediatric Neurology, Expertise Centre for Rare Diseases in Pediatric Neurology, Member of The EpiCARE European Reference Network, ‘Prof. Dr. Alex. Obregia’ Clinical Hospital, 041914 Bucharest, Romania
| | - Alice Dica
- Department of Pediatric Neurology, Expertise Centre for Rare Diseases in Pediatric Neurology, Member of The EpiCARE European Reference Network, ‘Prof. Dr. Alex. Obregia’ Clinical Hospital, 041914 Bucharest, Romania
| | - Carmen Sandu
- Department of Pediatric Neurology, Expertise Centre for Rare Diseases in Pediatric Neurology, Member of The EpiCARE European Reference Network, ‘Prof. Dr. Alex. Obregia’ Clinical Hospital, 041914 Bucharest, Romania
| | - Cristina Anghelescu
- Department of Pediatric Neurology, Expertise Centre for Rare Diseases in Pediatric Neurology, Member of The EpiCARE European Reference Network, ‘Prof. Dr. Alex. Obregia’ Clinical Hospital, 041914 Bucharest, Romania
| | - Dana Craiu
- Department of Pediatric Neurology, Expertise Centre for Rare Diseases in Pediatric Neurology, Member of The EpiCARE European Reference Network, ‘Prof. Dr. Alex. Obregia’ Clinical Hospital, 041914 Bucharest, Romania
| | - Aurora Arghir
- Medical Genetics Laboratory, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania
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4
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A Novel EMD Mutation Identified by Whole-Exome Sequencing in Twins with Emery-Dreifuss Muscular Dystrophy. Case Rep Genet 2020; 2020:2071738. [PMID: 32908726 PMCID: PMC7463389 DOI: 10.1155/2020/2071738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 08/04/2020] [Accepted: 08/13/2020] [Indexed: 01/17/2023] Open
Abstract
This case reports a novel hemizygous frameshift EMD mutation (c.487delA, p.Ser163fs) in twins of an Emery–Dreifuss muscular dystrophy family with severe cardiac involvement and mild muscle weakness. Their mother carried the same heterozygous mutation.
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5
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Dai X, Zheng C, Chen X, Tang Y, Zhang H, Yan C, Ma H, Li X. Targeted next-generation sequencing identified a known EMD mutation in a Chinese patient with Emery-Dreifuss muscular dystrophy. Hum Genome Var 2019; 6:42. [PMID: 31645980 PMCID: PMC6804839 DOI: 10.1038/s41439-019-0072-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/22/2019] [Accepted: 07/22/2019] [Indexed: 02/07/2023] Open
Abstract
Emery-Dreifuss muscular dystrophy (EDMD) is a rare X-linked recessive disease characterized by the clinical triad of early childhood joint contractures, progressive weakness in muscles and cardiac involvement and can result in sudden death. Targeted next-generation sequencing was performed for a Chinese patient with EDMD and the previously reported mutation [NM_000117.2: c.251_255del (p.Leu84Profs*7)] in exon 3 of the emerin gene (EMD) was identified.
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Affiliation(s)
- Xiafei Dai
- 1School of Medicine, University of Electronic Science and Technology of China, 610072 Chengdu, Sichuan China.,2Department of Cardiology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, 610072 Chengdu, Sichuan China
| | - Chenqing Zheng
- Shenzhen RealOmics (Biotech) Co., Ltd., 518081 Shenzhen, China
| | - Xuepin Chen
- 2Department of Cardiology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, 610072 Chengdu, Sichuan China.,4ZunYi Medical University, 563000 Zunyi, Guizhou China
| | - Yibin Tang
- 2Department of Cardiology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, 610072 Chengdu, Sichuan China
| | - Hongmei Zhang
- 2Department of Cardiology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, 610072 Chengdu, Sichuan China
| | - Chao Yan
- 1School of Medicine, University of Electronic Science and Technology of China, 610072 Chengdu, Sichuan China.,2Department of Cardiology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, 610072 Chengdu, Sichuan China
| | - Huihui Ma
- 1School of Medicine, University of Electronic Science and Technology of China, 610072 Chengdu, Sichuan China.,2Department of Cardiology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, 610072 Chengdu, Sichuan China
| | - Xiaoping Li
- 1School of Medicine, University of Electronic Science and Technology of China, 610072 Chengdu, Sichuan China.,2Department of Cardiology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, 610072 Chengdu, Sichuan China
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6
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Lannoy N, Hermans C. Principles of genetic variations and molecular diseases: applications in hemophilia A. Crit Rev Oncol Hematol 2016; 104:1-8. [PMID: 27296059 DOI: 10.1016/j.critrevonc.2016.04.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 03/07/2016] [Accepted: 04/14/2016] [Indexed: 11/24/2022] Open
Abstract
DNA structure alterations are the ultimate source of genetic variations. Without them, evolution would be impossible. While they are essential for DNA diversity, defects in DNA synthesis can lead to numerous genetic diseases. Due to increasingly innovative technologies, our knowledge of the human genome and genetic diseases has grown considerably over the last few years, allowing us to detect another class of variants affecting the chromosomal structure. DNA sequence can be altered in multiple ways: DNA sequence changes by substitution, deletion, or duplication of some nucleotides; chromosomal structure alterations by deletion, duplication, translocation, and inversion, ranging in size from kilobases to mega bases; changes in the cell's genome size. If the alteration is located within a gene and sufficiently deleterious, it can cause genetic disorders. Due to the F8 gene's high rate of new small mutations and its location at the tip of X chromosome, containing high repetitive sequences, a wide variety of genetic variants has been described as the cause of hemophilia A (HA). In addition to the F8 intron 22 repeat inversion, HA can also result from point mutations, other inversions, complex rearrangements, such as duplications or deletions, and transposon insertions causing phenotypes of variable severity characterized by complete or partial deficiency of circulating FVIII. This review aims to present the origins, mechanisms, and consequences of F8 alterations. A sound understanding of the multiple genetic mechanisms responsible for HA is essential to determine the appropriate strategy for molecular diagnosis and detected each type of genetic variant.
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Affiliation(s)
- N Lannoy
- Hemostasis and Thrombosis Unit, Hemophilia Clinic, Division of Hematology, Cliniques Universitaires Saint-Luc, Brussels, Belgium; Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, Brussels, Belgium.
| | - C Hermans
- Hemostasis and Thrombosis Unit, Hemophilia Clinic, Division of Hematology, Cliniques Universitaires Saint-Luc, Brussels, Belgium
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7
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Carvalho CMB, Lupski JR. Mechanisms underlying structural variant formation in genomic disorders. Nat Rev Genet 2016; 17:224-38. [PMID: 26924765 DOI: 10.1038/nrg.2015.25] [Citation(s) in RCA: 410] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
With the recent burst of technological developments in genomics, and the clinical implementation of genome-wide assays, our understanding of the molecular basis of genomic disorders, specifically the contribution of structural variation to disease burden, is evolving quickly. Ongoing studies have revealed a ubiquitous role for genome architecture in the formation of structural variants at a given locus, both in DNA recombination-based processes and in replication-based processes. These reports showcase the influence of repeat sequences on genomic stability and structural variant complexity and also highlight the tremendous plasticity and dynamic nature of our genome in evolution, health and disease susceptibility.
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Affiliation(s)
- Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Centro de Pesquisas René Rachou - FIOCRUZ, Belo Horizonte, MG 30190-002, Brazil
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Texas Children's Hospital, Houston, Texas 77030, USA
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8
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Aguado C, Gayà-Vidal M, Villatoro S, Oliva M, Izquierdo D, Giner-Delgado C, Montalvo V, García-González J, Martínez-Fundichely A, Capilla L, Ruiz-Herrera A, Estivill X, Puig M, Cáceres M. Validation and genotyping of multiple human polymorphic inversions mediated by inverted repeats reveals a high degree of recurrence. PLoS Genet 2014; 10:e1004208. [PMID: 24651690 PMCID: PMC3961182 DOI: 10.1371/journal.pgen.1004208] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 01/14/2014] [Indexed: 01/17/2023] Open
Abstract
In recent years different types of structural variants (SVs) have been discovered in the human genome and their functional impact has become increasingly clear. Inversions, however, are poorly characterized and more difficult to study, especially those mediated by inverted repeats or segmental duplications. Here, we describe the results of a simple and fast inverse PCR (iPCR) protocol for high-throughput genotyping of a wide variety of inversions using a small amount of DNA. In particular, we analyzed 22 inversions predicted in humans ranging from 5.1 kb to 226 kb and mediated by inverted repeat sequences of 1.6-24 kb. First, we validated 17 of the 22 inversions in a panel of nine HapMap individuals from different populations, and we genotyped them in 68 additional individuals of European origin, with correct genetic transmission in ∼ 12 mother-father-child trios. Global inversion minor allele frequency varied between 1% and 49% and inversion genotypes were consistent with Hardy-Weinberg equilibrium. By analyzing the nucleotide variation and the haplotypes in these regions, we found that only four inversions have linked tag-SNPs and that in many cases there are multiple shared SNPs between standard and inverted chromosomes, suggesting an unexpected high degree of inversion recurrence during human evolution. iPCR was also used to check 16 of these inversions in four chimpanzees and two gorillas, and 10 showed both orientations either within or between species, providing additional support for their multiple origin. Finally, we have identified several inversions that include genes in the inverted or breakpoint regions, and at least one disrupts a potential coding gene. Thus, these results represent a significant advance in our understanding of inversion polymorphism in human populations and challenge the common view of a single origin of inversions, with important implications for inversion analysis in SNP-based studies.
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Affiliation(s)
- Cristina Aguado
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Magdalena Gayà-Vidal
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Sergi Villatoro
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Meritxell Oliva
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - David Izquierdo
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Carla Giner-Delgado
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Víctor Montalvo
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Judit García-González
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | | | - Laia Capilla
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Aurora Ruiz-Herrera
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
- Departament de Biologia Celular, Fisiologia i Immunologia. Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Xavier Estivill
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marta Puig
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Mario Cáceres
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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9
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Chardon JW, Mignot C, Aradhya S, Keren B, Afenjar A, Kaminska A, Beldjord C, Héron D, Boycott KM. Deletion of filamin A in two female patients with periventricular nodular heterotopia. Am J Med Genet A 2012; 158A:1512-6. [DOI: 10.1002/ajmg.a.35409] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Accepted: 03/14/2012] [Indexed: 11/09/2022]
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10
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Clapham KR, Yu TW, Ganesh VS, Barry B, Chan Y, Mei D, Parrini E, Funalot B, Dupuis L, Nezarati MM, du Souich C, van Karnebeek C, Guerrini R, Walsh CA. FLNA genomic rearrangements cause periventricular nodular heterotopia. Neurology 2012; 78:269-78. [PMID: 22238415 DOI: 10.1212/wnl.0b013e31824365e4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To identify copy number variant (CNV) causes of periventricular nodular heterotopia (PNH) in patients for whom FLNA sequencing is negative. METHODS Screening of 35 patients from 33 pedigrees on an Affymetrix 6.0 microarray led to the identification of one individual bearing a CNV that disrupted FLNA. FLNA-disrupting CNVs were also isolated in 2 other individuals by multiplex ligation probe amplification. These 3 cases were further characterized by high-resolution oligo array comparative genomic hybridization (CGH), and the precise junctional breakpoints of the rearrangements were identified by PCR amplification and sequencing. RESULTS We report 3 cases of PNH caused by nonrecurrent genomic rearrangements that disrupt one copy of FLNA. The first individual carried a 113-kb deletion that removes all but the first exon of FLNA. A second patient harbored a complex rearrangement including a deletion of the 3' end of FLNA accompanied by a partial duplication event. A third patient bore a 39-kb deletion encompassing all of FLNA and the neighboring gene EMD. High-resolution oligo array CGH of the FLNA locus suggests distinct molecular mechanisms for each of these rearrangements, and implicates nearby low copy repeats in their pathogenesis. CONCLUSIONS These results demonstrate that FLNA is prone to pathogenic rearrangements, and highlight the importance of screening for CNVs in individuals with PNH lacking FLNA point mutations.
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Affiliation(s)
- K R Clapham
- Harvard-MIT Division of Health Sciences and Technology, Boston, MA, USA
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11
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Carvalho CMB, Zhang F, Liu P, Patel A, Sahoo T, Bacino CA, Shaw C, Peacock S, Pursley A, Tavyev YJ, Ramocki MB, Nawara M, Obersztyn E, Vianna-Morgante AM, Stankiewicz P, Zoghbi HY, Cheung SW, Lupski JR. Complex rearrangements in patients with duplications of MECP2 can occur by fork stalling and template switching. Hum Mol Genet 2009; 18:2188-203. [PMID: 19324899 DOI: 10.1093/hmg/ddp151] [Citation(s) in RCA: 156] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Duplication at the Xq28 band including the MECP2 gene is one of the most common genomic rearrangements identified in neurodevelopmentally delayed males. Such duplications are non-recurrent and can be generated by a non-homologous end joining (NHEJ) mechanism. We investigated the potential mechanisms for MECP2 duplication and examined whether genomic architectural features may play a role in their origin using a custom designed 4-Mb tiling-path oligonucleotide array CGH assay. Each of the 30 patients analyzed showed a unique duplication varying in size from approximately 250 kb to approximately 2.6 Mb. Interestingly, in 77% of these non-recurrent duplications, the distal breakpoints grouped within a 215 kb genomic interval, located 47 kb telomeric to the MECP2 gene. The genomic architecture of this region contains both direct and inverted low-copy repeat (LCR) sequences; this same region undergoes polymorphic structural variation in the general population. Array CGH revealed complex rearrangements in eight patients; in six patients the duplication contained an embedded triplicated segment, and in the other two, stretches of non-duplicated sequences occurred within the duplicated region. Breakpoint junction sequencing was achieved in four duplications and identified an inversion in one patient, demonstrating further complexity. We propose that the presence of LCRs in the vicinity of the MECP2 gene may generate an unstable DNA structure that can induce DNA strand lesions, such as a collapsed fork, and facilitate a Fork Stalling and Template Switching event producing the complex rearrangements involving MECP2.
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Affiliation(s)
- Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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12
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Bauters M, Van Esch H, Friez MJ, Boespflug-Tanguy O, Zenker M, Vianna-Morgante AM, Rosenberg C, Ignatius J, Raynaud M, Hollanders K, Govaerts K, Vandenreijt K, Niel F, Blanc P, Stevenson RE, Fryns JP, Marynen P, Schwartz CE, Froyen G. Nonrecurrent MECP2 duplications mediated by genomic architecture-driven DNA breaks and break-induced replication repair. Genome Res 2008; 18:847-58. [PMID: 18385275 DOI: 10.1101/gr.075903.107] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Recurrent submicroscopic genomic copy number changes are the result of nonallelic homologous recombination (NAHR). Nonrecurrent aberrations, however, can result from different nonexclusive recombination-repair mechanisms. We previously described small microduplications at Xq28 containing MECP2 in four male patients with a severe neurological phenotype. Here, we report on the fine-mapping and breakpoint analysis of 16 unique microduplications. The size of the overlapping copy number changes varies between 0.3 and 2.3 Mb, and FISH analysis on three patients demonstrated a tandem orientation. Although eight of the 32 breakpoint regions coincide with low-copy repeats, none of the duplications are the result of NAHR. Bioinformatics analysis of the breakpoint regions demonstrated a 2.5-fold higher frequency of Alu interspersed repeats as compared with control regions, as well as a very high GC content (53%). Unexpectedly, we obtained the junction in only one patient by long-range PCR, which revealed nonhomologous end joining as the mechanism. Breakpoint analysis in two other patients by inverse PCR and subsequent array comparative genomic hybridization analysis demonstrated the presence of a second duplicated region more telomeric at Xq28, of which one copy was inserted in between the duplicated MECP2 regions. These data suggest a two-step mechanism in which part of Xq28 is first inserted near the MECP2 locus, followed by breakage-induced replication with strand invasion of the normal sister chromatid. Our results indicate that the mechanism by which copy number changes occur in regions with a complex genomic architecture can yield complex rearrangements.
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Affiliation(s)
- Marijke Bauters
- Human Genome Laboratory, Department for Molecular and Developmental Genetics, VIB, B-3000 Leuven, Belgium
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13
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de Visser M. Myopathies with early contractures. HANDBOOK OF CLINICAL NEUROLOGY 2007; 86:35-59. [PMID: 18808994 DOI: 10.1016/s0072-9752(07)86002-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
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14
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Abstract
Genomic rearrangements play a major role in the pathogenesis of human genetic diseases. Nonallelic homologous recombination (NAHR) between low-copy repeats (LCRs) that flank unique genomic segments results in changes of genome organization and can cause a loss or gain of genomic segments. These LCRs appear to have arisen recently during primate speciation via paralogous segmental duplication, thus making the human species particularly susceptible to genomic rearrangements. Genomic disorders are defined as a group of diseases that result from genomic rearrangements, mostly mediated by NAHR. Molecular investigations of genomic disorders have revealed genome architectural features associated with susceptibility to rearrangements and the recombination mechanisms responsible for such rearrangements. The human genome sequence project reveals that LCRs may account for 5% of the genome, suggesting that many novel genomic disorders might still remain to be recognized.
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Affiliation(s)
- Ken Inoue
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.
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15
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van der Flier A, Sonnenberg A. Structural and functional aspects of filamins. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1538:99-117. [PMID: 11336782 DOI: 10.1016/s0167-4889(01)00072-6] [Citation(s) in RCA: 321] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Filamins are a family of high molecular mass cytoskeletal proteins that organize filamentous actin in networks and stress fibers. Over the past few years it has become clear that filamins anchor various transmembrane proteins to the actin cytoskeleton and provide a scaffold for a wide range of cytoplasmic signaling proteins. The recent cloning of three human filamins and studies on filamin orthologues from chicken and Drosophila revealed unexpected complexity of the filamin family, the biological implications of which have just started to be addressed. Expression of dysfunctional filamin-A leads to the genetic disorder of ventricular heterotopia and gives reason to expect that abnormalities in the other isogenes may also be connected with human disease. In this review aspects of filamin structure, its splice variants, binding partners and biological function will be discussed.
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Affiliation(s)
- A van der Flier
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
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16
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Abstract
Emery-Dreifuss muscular dystrophy (EDMD) was delineated as a separate form of muscular dystrophy nearly 40 years ago, based on the distinctive clinical features of early contractures and humero-peroneal weakness, and cardiac conduction defects. The gene, STA at Xq28, for the commoner X-linked EDMD encodes a 34 kD nuclear membrane protein designated 'emerin', and in almost all cases on immunostaining is absent in muscle, skin fibroblasts, leucocytes and even exfoliative buccal cells, and a mosaic pattern in female carriers. The gene, LMNA at 1q21, for the autosomal dominant Emery-Dreifuss muscular dystrophy encodes other nuclear membrane proteins, lamins A/C. The diagnosis (at present) depends on mutation analysis rather than protein immunohistochemistry. It is still not at all clear how defects in these nuclear membrane proteins are related to the phenotype, even less clear that LMNA mutations can also be associated with familial dilated cardiomyopathy with no weakness, and even familial partial lipodystrophy with diabetes mellitus and coronary heart disease! What began as clinical studies in a relatively rare form of dystrophy has progressed to detailed research into the functions of nuclear membrane proteins particularly in regard to various forms of heart disease.
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Affiliation(s)
- A E Emery
- Department of Neurology, Royal Devon & Exeter Hospital, EX2 5DW, Exeter, UK
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17
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Funakoshi M, Tsuchiya Y, Arahata K. Emerin and cardiomyopathy in Emery-Dreifuss muscular dystrophy. Neuromuscul Disord 1999; 9:108-14. [PMID: 10220866 DOI: 10.1016/s0960-8966(98)00097-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Emery-Dreifuss muscular dystrophy (EDMD) is an inherited disorder characterized by the clinical triad of life-threatening progressive cardiomyopathy with conduction defect, early onset joint contractures and slow progressive muscle weakness in scapulo-humero-peroneal distribution. Cardiomyopathy in EDMD is usually noticed after the second to third decade of life, and becomes worse with age. Permanent auricular paralysis occurs frequently and is considered a hallmark of EDMD cardiomyopathy. Cardiac involvement may also occur in female carriers. In autopsy cases, enlargement of the atria with remarkable thinning have been observed. Identification of the gene responsible for X-linked EDMD (X-EDMD) and the protein product, emerin, provided a diagnostic clue for EDMD. Since the emerin gene is rather small, the entire sequence can easily be surveyed. Western blot and immunohistochemistry show an absence of emerin in muscle and skin tissues and oral exfoliating cells in male patients with X-EDMD, and a reduction of the protein content with a mosaic expression pattern in female carriers. Emerin anchors at the inner nuclear membrane of cardiac, skeletal and smooth muscles, and interacts with lamins and nucleoplasm, thereby possibly maintaining the mechanical stability of the nuclear membrane of muscle cells that shows rigorous contraction/relaxation. More recently, positive emerin staining at the cardiac demosomes and fasciae adherentes was noticed in addition to the specific localization at the inner nuclear membrane. This localization implies a physiological role for the protein in cardiac conduction.
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Affiliation(s)
- M Funakoshi
- Department of Neuromuscular Research, National Institute of Neuroscience, Tokyo, Japan
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18
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Fox JW, Lamperti ED, Ekşioğlu YZ, Hong SE, Feng Y, Graham DA, Scheffer IE, Dobyns WB, Hirsch BA, Radtke RA, Berkovic SF, Huttenlocher PR, Walsh CA. Mutations in filamin 1 prevent migration of cerebral cortical neurons in human periventricular heterotopia. Neuron 1998; 21:1315-25. [PMID: 9883725 DOI: 10.1016/s0896-6273(00)80651-0] [Citation(s) in RCA: 683] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Long-range, directed migration is particularly dramatic in the cerebral cortex, where postmitotic neurons generated deep in the brain migrate to form layers with distinct form and function. In the X-linked dominant human disorder periventricular heterotopia (PH), many neurons fail to migrate and persist as nodules lining the ventricular surface. Females with PH present with epilepsy and other signs, including patent ductus arteriosus and coagulopathy, while hemizygous males die embryonically. We have identified the PH gene as filamin 1 (FLN1), which encodes an actin-cross-linking phosphoprotein that transduces ligand-receptor binding into actin reorganization, and which is required for locomotion of many cell types. FLN1 shows previously unrecognized, high-level expression in the developing cortex, is required for neuronal migration to the cortex, and is essential for embryogenesis.
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Affiliation(s)
- J W Fox
- Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Institutes of Medicine, Boston, Massachusetts 02115, USA
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Lupski JR. Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet 1998; 14:417-22. [PMID: 9820031 DOI: 10.1016/s0168-9525(98)01555-8] [Citation(s) in RCA: 594] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Molecular medicine began with Pauling's seminal work, which recognized sickle-cell anemia as a molecular disease, and with Ingram's demonstration of a specific chemical difference between the hemoglobins of normal and sickled human red blood cells. During the four decades that followed, investigations have focused on the gene--how mutations specifically alter DNA and how these changes affect the structure and expression of encoded proteins. Recently, however, the advances of the human genome project and the completion of total genome sequences for yeast and many bacterial species, have enabled investigators to view genetic information in the context of the entire genome. As a result, we recognize that the mechanisms for some genetic diseases are best understood at a genomic level. The evolution of the mammalian genome has resulted in the duplication of genes, gene segments and repeat gene clusters. This genome architecture provides substrates for homologous recombination between nonsyntenic regions of chromosomes. Such events can result in DNA rearrangements that cause disease.
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Affiliation(s)
- J R Lupski
- Department of Molecular and Human Genetics, Texas Children's Hospital, Baylor College of Medicine, Houston 77030, USA.
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