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Akahoshi K, Nakagawa E, Goto YI, Inoue K. Duplication within two regions distal to MECP2: clinical similarity with MECP2 duplication syndrome. BMC Med Genomics 2023; 16:43. [PMID: 36879246 PMCID: PMC9987063 DOI: 10.1186/s12920-023-01465-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/21/2023] [Indexed: 03/08/2023] Open
Abstract
BACKGROUND X-linked methyl-CpG-binding protein 2 (MECP2) duplication syndrome is prevalent in approximately 1% of X-linked intellectual disabilities. Accumulating evidence has suggested that MECP2 is the causative gene of MECP2 duplication syndrome. We report a case of a 17-year-old boy with a 1.2 Mb duplication distal to MECP2 on chromosome Xq28. Although this region does not contain MECP2, the clinical features and course of the boy are remarkably similar to those observed in MECP2 duplication syndrome. Recently, case reports have described duplication in the region distal to, and not containing, MECP2. These regions have been classified as the K/L-mediated Xq28 duplication region and int22h1/int22h2-mediated Xq28 duplication region. The case reports also described signs similar to those of MECP2 duplication syndrome. To the best of our knowledge, ours is the first case to include these two regions. CASE PRESENTATION The boy presented with a mild to moderate regressive intellectual disability and progressive neurological disorder. He developed epilepsy at the age of 6 years and underwent a bilateral equinus foot surgery at 14 years of age because of the increasing spasticity in lower extremities since the age of 11. Intracranial findings showed hypoplasia of the corpus callosum, cerebellum, and brain stem; linear hyperintensity in the deep white matter; and decreased white matter capacity. During his childhood, he suffered from recurrent infection. However, genital problems, skin abnormalities and gastrointestinal manifestations (gastroesophageal reflux) were not observed. CONCLUSIONS Cases in which duplication was observed in the region of Xq28 that does not include MECP2 also showed symptoms similar to those of MECP2 duplication syndrome. We compared four pathologies: MECP2 duplication syndrome with minimal regions, duplication within the two distal regions without MECP2, and our case including both regions. Our results suggest that MECP2 alone may not explain all symptoms of duplication in the distal part of Xq28.
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Affiliation(s)
- Keiko Akahoshi
- Department of Pediatrics, Tokyo Children's Rehabilitation Hospital, 4-10-1 Gakuen, Musashi-Murayama, Tokyo, 208-0011, Japan.
| | - Eiji Nakagawa
- Department of Child Neurology, National Center of Neurology and Psychiatry, Tokyo, 187-8551, Japan
| | - Yu-Ichi Goto
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, Tokyo, 187-8502, Japan.,Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo, 187-8551, Japan
| | - Ken Inoue
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, Tokyo, 187-8502, Japan
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Gottschalk I, Kölsch U, Wagner DL, Kath J, Martini S, Krüger R, Puel A, Casanova JL, Jezela-Stanek A, Rossi R, Chehadeh SE, Van Esch H, von Bernuth H. IRAK1 Duplication in MECP2 Duplication Syndrome Does Not Increase Canonical NF-κB-Induced Inflammation. J Clin Immunol 2023; 43:421-439. [PMID: 36319802 PMCID: PMC9628328 DOI: 10.1007/s10875-022-01390-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 10/20/2022] [Indexed: 01/24/2023]
Abstract
PURPOSE Besides their developmental and neurological phenotype, most patients with MECP2/IRAK1 duplication syndrome present with recurrent and severe infections, accompanied by strong inflammation. Respiratory infections are the most common cause of death. Standardized pneumological diagnostics, targeted anti-infectious treatment, and knowledge of the underlying pathomechanism that triggers strong inflammation are unmet clinical needs. We investigated the influence of IRAK1 overexpression on the canonical NF-κB signaling as a possible cause for excessive inflammation in these patients. METHODS NF-κB signaling was examined by measuring the production of proinflammatory cytokines and evaluating the IRAK1 phosphorylation and degradation as well as the IκBα degradation upon stimulation with IL-1β and TLR agonists in SV40-immortalized fibroblasts, PBMCs, and whole blood of 9 patients with MECP2/IRAK1 duplication syndrome, respectively. RESULTS Both, MECP2/IRAK1-duplicated patients and healthy controls, showed similar production of IL-6 and IL-8 upon activation with IL-1β and TLR2/6 agonists in immortalized fibroblasts. In PBMCs and whole blood, both patients and controls had a similar response of cytokine production after stimulation with IL-1β and TLR4/2/6 agonists. Patients and controls had equivalent patterns of IRAK1 phosphorylation and degradation as well as IκBα degradation upon stimulation with IL-1β. CONCLUSION Patients with MECP2/IRAK1 duplication syndrome do not show increased canonical NF-κB signaling in immortalized fibroblasts, PBMCs, and whole blood. Therefore, we assume that these patients do not benefit from a therapeutic suppression of this pathway.
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Affiliation(s)
- Ilona Gottschalk
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH), Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Uwe Kölsch
- Labor Berlin GmbH, Department of Immunology, Berlin, Germany
| | - Dimitrios L Wagner
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH), Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Berlin Center for Advanced Therapies (BeCAT), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität, Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
- Institute of Transfusion Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
- Institute of Medical Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Campus Virchow-Klinikum, Berlin, Germany
| | - Jonas Kath
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH), Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Berlin Center for Advanced Therapies (BeCAT), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität, Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Stefania Martini
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH), Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Renate Krüger
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris, Paris, France
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
- Pediatric Hematology and Immunology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Aleksandra Jezela-Stanek
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, Warsaw, Poland
| | - Rainer Rossi
- Childrens' Hospital Neukölln, Vivantes GmbH, Berlin, Germany
| | | | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, Louvain, Belgium
| | - Horst von Bernuth
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Berlin Institute of Health (BIH), Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany.
- Labor Berlin GmbH, Department of Immunology, Berlin, Germany.
- Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Berlin, Germany.
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Xing L, Shen Y, Wei X, Luo Y, Yang Y, Liu H, Liu H. Long-read Oxford nanopore sequencing reveals a de novo case of complex chromosomal rearrangement involving chromosomes 2, 7, and 13. Mol Genet Genomic Med 2022; 10:e2011. [PMID: 35758276 PMCID: PMC9482406 DOI: 10.1002/mgg3.2011] [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: 03/17/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 12/21/2022] Open
Abstract
Background Complex chromosomal rearrangements (CCRs) are associated with high reproductive risk, infertility, abnormalities in offspring, and recurrent miscarriage in women. It is essential to accurately characterize apparently balanced chromosome rearrangements in unaffected individuals. Methods A CCR young couple who suffered two spontaneous abortions and underwent labor induction due to fetal chromosomal abnormalities was studied using long‐read sequencing(LRS), single‐nucleotide polymorphism (SNP) array, G‐banding karyotype analysis (550‐band resolution), and Sanger sequencing. Results SNP analysis of the amniotic fluid cells during the third pregnancy revealed a 9.9‐Mb duplication at 7q21.11q21.2 and a 24.8‐Mb heterozygous deletion at 13q21.1q31.1. The unaffected female partner was a carrier of a three‐way CCR [46,XX,? ins(7;13)(q21.1;q21.1q22)t(2;13)(p23;q22)]. Subsequent LRS analysis revealed the exact breakpoint locations on the derivative chromosomes and the specific method of chromosome rearrangement, indicating that the CCR carrier was a more complex structural rearrangement comprising five breakpoints. Furthermore, LRS detected an inserted fragment of chromosome 13 in chromosome 7. Conclusions LRS is effective for analyzing the complex structural variations of the human genome and may be used to clarify the specific CCRs for effective genetic counseling and appropriate intervention.
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Affiliation(s)
- Lingling Xing
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Ying Shen
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Xiang Wei
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Yuan Luo
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Yan Yang
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Haipeng Liu
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Hongqian Liu
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
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Collins BE, Neul JL. Rett Syndrome and MECP2 Duplication Syndrome: Disorders of MeCP2 Dosage. Neuropsychiatr Dis Treat 2022; 18:2813-2835. [PMID: 36471747 PMCID: PMC9719276 DOI: 10.2147/ndt.s371483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/14/2022] [Indexed: 11/30/2022] Open
Abstract
Rett syndrome (RTT) is a neurodevelopmental disorder caused predominantly by loss-of-function mutations in the gene Methyl-CpG-binding protein 2 (MECP2), which encodes the MeCP2 protein. RTT is a MECP2-related disorder, along with MECP2 duplication syndrome (MDS), caused by gain-of-function duplications of MECP2. Nearly two decades of research have advanced our knowledge of MeCP2 function in health and disease. The following review will discuss MeCP2 protein function and its dysregulation in the MECP2-related disorders RTT and MDS. This will include a discussion of the genetic underpinnings of these disorders, specifically how sporadic X-chromosome mutations arise and manifest in specific populations. We will then review current diagnostic guidelines and clinical manifestations of RTT and MDS. Next, we will delve into MeCP2 biology, describing the dual landscapes of methylated DNA and its reader MeCP2 across the neuronal genome as well as the function of MeCP2 as a transcriptional modulator. Following this, we will outline common MECP2 mutations and genotype-phenotype correlations in both diseases, with particular focus on mutations associated with relatively mild disease in RTT. We will also summarize decades of disease modeling and resulting molecular, synaptic, and behavioral phenotypes associated with RTT and MDS. Finally, we list several therapeutics in the development pipeline for RTT and MDS and available evidence of their safety and efficacy.
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Affiliation(s)
- Bridget E Collins
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, USA
| | - Jeffrey L Neul
- Vanderbilt Kennedy Center, Departments of Pediatrics, Pharmacology, and Special Education, Vanderbilt University Medical Center and Vanderbilt University, Nashville, TN, USA
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Qi M, Stenson PD, Ball EV, Tainer JA, Bacolla A, Kehrer-Sawatzki H, Cooper DN, Zhao H. Distinct sequence features underlie microdeletions and gross deletions in the human genome. Hum Mutat 2021; 43:328-346. [PMID: 34918412 PMCID: PMC9069542 DOI: 10.1002/humu.24314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/02/2021] [Accepted: 12/14/2021] [Indexed: 11/18/2022]
Abstract
Microdeletions and gross deletions are important causes (~20%) of human inherited disease and their genomic locations are strongly influenced by the local DNA sequence environment. This notwithstanding, no study has systematically examined their underlying generative mechanisms. Here, we obtained 42,098 pathogenic microdeletions and gross deletions from the Human Gene Mutation Database (HGMD) that together form a continuum of germline deletions ranging in size from 1 to 28,394,429 bp. We analyzed the DNA sequence within 1 kb of the breakpoint junctions and found that the frequencies of non‐B DNA‐forming repeats, GC‐content, and the presence of seven of 78 specific sequence motifs in the vicinity of pathogenic deletions correlated with deletion length for deletions of length ≤30 bp. Further, we found that the presence of DR, GQ, and STR repeats is important for the formation of longer deletions (>30 bp) but not for the formation of shorter deletions (≤30 bp) while significantly (χ2, p < 2E−16) more microhomologies were identified flanking short deletions than long deletions (length >30 bp). We provide evidence to support a functional distinction between microdeletions and gross deletions. Finally, we propose that a deletion length cut‐off of 25–30 bp may serve as an objective means to functionally distinguish microdeletions from gross deletions.
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Affiliation(s)
- Mengling Qi
- Department of Medical Research Center, Sun Yat-sen Memorial Hospital; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, China
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Edward V Ball
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - John A Tainer
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Albino Bacolla
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | | | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Huiying Zhao
- Department of Medical Research Center, Sun Yat-sen Memorial Hospital; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, China
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Abdala BB, Gonçalves AP, Dos Santos JM, Boy R, de Carvalho CMB, Grochowski CM, Krepischi ACV, Rosenberg C, Gusmão L, Pehlivan D, Pimentel MMG, Santos-Rebouças CB. Molecular and clinical insights into complex genomic rearrangements related to MECP2 duplication syndrome. Eur J Med Genet 2021; 64:104367. [PMID: 34678473 DOI: 10.1016/j.ejmg.2021.104367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 10/04/2021] [Accepted: 10/16/2021] [Indexed: 10/20/2022]
Abstract
MECP2 duplication syndrome (MDS) is caused by copy number variation (CNV) spanning the MECP2 gene at Xq28 and is a major cause of intellectual disability (ID) in males. Herein, we describe two unrelated males harboring non-recurrent complex Xq28 rearrangements associated with MDS. Copy number gains were initially detected by quantitative real-time polymerase chain reaction and further delineated by high-resolution array comparative genomic hybridization, familial segregation, expression analysis and X-chromosome inactivation (XCI) evaluation in a carrier mother. SNVs within the rearrangements and/or fluorescent in situ hybridization (FISH) were used to assess the parental origin of the rearrangements. Patient 1 exhibited an intrachromosomal rearrangement, whose structure is consistent with a triplicated segment presumably embedded in an inverted orientation between two duplicated sequences (DUP-TRP/INV-DUP). The rearrangement was inherited from the carrier mother, who exhibits extreme XCI skewing and subtle psychiatric symptoms. Patient 2 presented a de novo (X;Y) unbalanced translocation resulting in duplication of Xq28 and deletion of Yp, originated in the paternal gametogenesis. Neurodevelopmental trajectory and non-neurological symptoms were consistent with previous reports, with the exception of cerebellar vermis hypoplasia in patient 2. Although both patients share the core MDS phenotype, patient 1 showed MECP2 transcript levels in blood similar to controls. Understanding the molecular mechanisms related to MDS is essential for designing targeted therapeutic strategies.
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Affiliation(s)
- Bianca Barbosa Abdala
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andressa Pereira Gonçalves
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jussara Mendonça Dos Santos
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raquel Boy
- Pedro Ernesto University Hospital, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Texas, USA; Section of Neurology, Department of Pediatrics, Baylor College of Medicine, Texas, USA
| | - Márcia Mattos Gonçalves Pimentel
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cíntia Barros Santos-Rebouças
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil.
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Pascual-Alonso A, Martínez-Monseny AF, Xiol C, Armstrong J. MECP2-Related Disorders in Males. Int J Mol Sci 2021; 22:9610. [PMID: 34502518 PMCID: PMC8431762 DOI: 10.3390/ijms22179610] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/25/2021] [Accepted: 09/01/2021] [Indexed: 12/23/2022] Open
Abstract
Methyl CpG binding protein 2 (MECP2) is located at Xq28 and is a multifunctional gene with ubiquitous expression. Loss-of-function mutations in MECP2 are associated with Rett syndrome (RTT), which is a well-characterized disorder that affects mainly females. In boys, however, mutations in MECP2 can generate a wide spectrum of clinical presentations that range from mild intellectual impairment to severe neonatal encephalopathy and premature death. Thus, males can be more difficult to classify and diagnose than classical RTT females. In addition, there are some variants of unknown significance in MECP2, which further complicate the diagnosis of these children. Conversely, the entire duplication of the MECP2 gene is related to MECP2 duplication syndrome (MDS). Unlike in RTT, in MDS, males are predominantly affected. Usually, the duplication is inherited from an apparently asymptomatic carrier mother. Both syndromes share some characteristics, but also differ in some aspects regarding the clinical picture and evolution. In the following review, we present a thorough description of the different types of MECP2 variants and alterations that can be found in males, and explore several genotype-phenotype correlations, although there is still a lot to understand.
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Affiliation(s)
- Ainhoa Pascual-Alonso
- Fundació Per la Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain; (A.P.-A.); (C.X.)
- Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain;
| | - Antonio F. Martínez-Monseny
- Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain;
- Clinical Genetics, Molecular and Genetic Medicine Section, Hospital Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain
| | - Clara Xiol
- Fundació Per la Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain; (A.P.-A.); (C.X.)
- Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain;
| | - Judith Armstrong
- Institut de Recerca Sant Joan de Déu, Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain;
- Clinical Genetics, Molecular and Genetic Medicine Section, Hospital Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain
- CIBER-ER (Biomedical Network Research Center for Rare Diseases), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
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Study of complex structural variations of X-linked deafness-2 based on single-molecule sequencing. Biosci Rep 2021; 41:228372. [PMID: 33860785 PMCID: PMC8193640 DOI: 10.1042/bsr20203740] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 03/21/2021] [Accepted: 03/31/2021] [Indexed: 12/16/2022] Open
Abstract
X-linked deafness-2 (DFNX2) is cochlear incomplete partition type III (IP-III), one of inner ear malformations characterized by an abnormally wide opening in the bone separating the basal turn of the cochlea from the internal auditory canal, fixation of the stapes and cerebrospinal fluid (CSF) gusher upon stapedectomy or cochleostomy. The causative gene of DFNX2 was POU3F4. To investigate the genetic causes of DFNX2 and compare the efficiency of different sequencing methods, 12 unrelated patients were enrolled in the present study. Targeted next-generation sequencing (NGS) and long-read sequencing were used to analyze the genetic etiology of DFNX2. Six variants of POU3F4 were identified in this cohort by NGS. Three patients with a negative diagnosis based on NGS were enrolled in further long-read sequencing. Two of them were all found to carry structural variations (SVs) on chromosome X, consisting of an 870-kb deletion (DEL) at upstream of POU3F4 and an 8-Mb inversion (INV). The 870-kb DEL may have been due to non-homologous end joining (NHEJ), while non-allelic homologous recombination (NAHR) within a single chromatid may have accounted for the 8-Mb INV. Common POU3F4 mutations in DFNX2 included point mutations, small insertions and deletions (INDELs), and exon mutations, which can be detected by Sanger sequencing and NGS. Single-molecule long-read sequencing constitutes an additional and valuable method for accurate detection of pathogenic SVs in IP-III patients with negative NGS results.
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Zhang Z, Yang P, He P, Xu J, Lyu S, Liu X, Cai C, Li H, Li Z, Ru B, Xie J, Lei C, Chen H, Wang E, Huang Y. Distribution and association study of PLAG1 gene between copy number variation and Chinese cattle populations. Anim Biotechnol 2020; 33:273-278. [PMID: 32723213 DOI: 10.1080/10495398.2020.1793769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Copy number variation mainly refers to the copy number change of DNA fragments from 1 to 5 Mb. The deletion, duplication, inversion and ectopic of these fragments are collectively referred to as CNV. Numerous studies have shown that transfer factors play a vital role in regulating the growth and development of the body, for example the pleomorphic adenoma gene (PLAG). However, there is no study of CNV in PLAG1 gene. We qualified copy numbers within PLAG1 gene in 8 cattle breeds (Qinchuan, Qaidamu, Jinjiang, Guangfeng, Ji'an, Jiaxian, Pinan and Xianan cattle) by quantitative PCR, and explored their impacts on CNV of PLAG1 gene and phenotypic traits in Xianan cattle. We defined Deletion into CN = 0, Normal into CN = 1 and Duplication into CN = 2. The results showed that the individual with type of CN = 1 has a significant better effect on heart girth in JA cattle population (p < 0.01); the individual with type of CN = 1 and CN = 0 has a better effect on Rump length in JX cattle population (p < 0.05); the individual with type of CN = 0 has a better effect on cannon bone circumference in XN cattle population (p < 0.05). Association analysis showed that in JA cattle, the number of CN = 2 is great in JA cattle population, and the performance of CN = 2 in heart girth is better than CN = 1; in JX cattle, the rump length of CN = 2 is less than individual with CN = 0 and CN = 1; in XN cattle, individuals with CN = 0 have a better performance on cannon bone circumference than others. The results can provide a theoretical basis for molecular breeding of Chinese cattle, molecular mark-assist selection (MAS) of growth traits of Chinese cattle, and rapidly establish a Chinese cattle population with excellent genetic resources. Simple summaryWith the living standards rising, people's demand for beef is getting higher and higher, and there is a great significance to improve the growth performance of cattle. We measured body size data and detected copy number type of different cattle breeds (Xianan cattle, Ji'an cattle and Jiaxian cattle), and analyzed the correlation between the two object. We found that copy number variation of PLAG1 gene significantly affected some growth traits of XN cattle, JA cattle, and JX cattle. This may provide the basic material for molecular marker-assisted selection breeding of Chinese cattle breeds.
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Affiliation(s)
- Zijing Zhang
- Henan Academy of Agricultural Sciences, Institute of Animal Husbandry and Veterinary Science, Zhengzhou, Henan, People's Republic of China
| | - Peng Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, People's Republic of China
| | - Pan He
- College of Animal Science and Technology, Northwest A&F University, Yangling, People's Republic of China
| | - Jiawei Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling, People's Republic of China
| | - Shijie Lyu
- Henan Academy of Agricultural Sciences, Institute of Animal Husbandry and Veterinary Science, Zhengzhou, Henan, People's Republic of China
| | - Xian Liu
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Cuicui Cai
- Guyuan Branch of Ningxia Academy of Agriculture and Forestry Sciences, Guyuan, Ningxia, People's Republic of China
| | - Huimin Li
- Agricultural and Rural Work Committee of Huiji District, Zhengzhou, People's Republic of China
| | - Zhiming Li
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Baorui Ru
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Jianliang Xie
- Guyuan Branch of Ningxia Academy of Agriculture and Forestry Sciences, Guyuan, Ningxia, People's Republic of China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, People's Republic of China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, People's Republic of China
| | - Eryao Wang
- Henan Academy of Agricultural Sciences, Institute of Animal Husbandry and Veterinary Science, Zhengzhou, Henan, People's Republic of China
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, People's Republic of China
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10
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Deciphering the complexity of simple chromosomal insertions by genome sequencing. Hum Genet 2020; 140:361-380. [PMID: 32728808 DOI: 10.1007/s00439-020-02210-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/22/2020] [Indexed: 10/23/2022]
Abstract
Chromosomal insertions are thought to be rare structural rearrangements. The current understanding of the underlying mechanisms of their origin is still limited. In this study, we sequenced 16 cases with apparent simple insertions previously identified by karyotyping and/or chromosomal microarray analysis. Using mate-pair genome sequencing (GS), we identified all 16 insertions and revised previously designated karyotypes in 75.0% (12/16) of the cases. Additional cryptic rearrangements were identified in 68.8% of the cases (11/16). The incidence of additional cryptic rearrangements in chromosomal insertions was significantly higher compared to balanced translocations and inversions reported in other studies by GS. We characterized and classified the cryptic insertion rearrangements into four groups, which were not mutually exclusive: (1) insertion segments were fragmented and their subsegments rearranged and clustered at the insertion site (10/16, 62.5%); (2) one or more cryptic subsegments were not inserted into the insertion site (5/16, 31.3%); (3) segments of the acceptor chromosome were scattered and rejoined with the insertion segments (2/16, 12.5%); and (4) copy number gains were identified in the flanking regions of the insertion site (2/16, 12.5%). In addition to the observation of these chromothripsis- or chromoanasynthesis-like events, breakpoint sequence analysis revealed microhomology to be the predominant feature. However, no significant correlation was found between the number of cryptic rearrangements and the size of the insertion. Overall, our study provide molecular characterization of karyotypically apparent simple insertions, demonstrate previously underappreciated complexities, and evidence that chromosomal insertions are likely formed by nonhomologous end joining and/or microhomology-mediated replication-based DNA repair.
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11
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Peters SU, Fu C, Suter B, Marsh E, Benke TA, Skinner SA, Lieberman DN, Standridge S, Jones M, Beisang A, Feyma T, Heydeman P, Ryther R, Kaufmann WE, Glaze DG, Neul JL, Percy AK. Characterizing the phenotypic effect of Xq28 duplication size in MECP2 duplication syndrome. Clin Genet 2019; 95:575-581. [PMID: 30788845 DOI: 10.1111/cge.13521] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 02/01/2019] [Accepted: 02/05/2019] [Indexed: 12/11/2022]
Abstract
Individuals with methyl CpG binding protein 2 (MECP2) duplication syndrome (MDS) have varying degrees of severity in their mobility, hand use, developmental skills, and susceptibility to infections. In the present study, we examine the relationship between duplication size, gene content, and overall phenotype in MDS using a clinical severity scale. Other genes typically duplicated within Xq28 (eg, GDI1, RAB39B, FLNA) are associated with distinct clinical features independent of MECP2. We additionally compare the phenotype of this cohort (n = 48) to other reported cohorts with MDS. Utilizing existing indices of clinical severity in Rett syndrome, we found that larger duplication size correlates with higher severity in total clinical severity scores (r = 0.36; P = 0.02), and in total motor behavioral assessment inventory scores (r = 0.31; P = 0.05). Greater severity was associated with having the RAB39B gene duplicated, although most of these participants also had large duplications. Results suggest that developmental delays in the first 6 months of life, hypotonia, vasomotor disturbances, constipation, drooling, and bruxism are common in MDS. This is the first study to show that duplication size is related to clinical severity. Future studies should examine whether large duplications which do not encompass RAB39B also contribute to clinical severity. Results also suggest the need for creating an MDS specific severity scale.
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Affiliation(s)
- Sarika U Peters
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Cary Fu
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Bernhard Suter
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Eric Marsh
- Division of Neurology and Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Timothy A Benke
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado
| | | | - David N Lieberman
- Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts
| | - Shannon Standridge
- Department of Pediatrics, Cincinnati Children's Hospital, Cincinnati, Ohio
| | - Mary Jones
- Department of Pediatrics, UCSF Benioff Children's Hospital, Oakland, California
| | - Arthur Beisang
- Department of Pediatrics, Gilette Children's Specialty Healthcare, Saint Paul, Minnesota
| | - Timothy Feyma
- Department of Pediatrics, Gilette Children's Specialty Healthcare, Saint Paul, Minnesota
| | - Peter Heydeman
- Department of Pediatrics, Rush University Medical Center, Chicago, Illinois
| | - Robin Ryther
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri
| | | | - Daniel G Glaze
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Jeffrey L Neul
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Alan K Percy
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
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12
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Miguet M, Faivre L, Amiel J, Nizon M, Touraine R, Prieur F, Pasquier L, Lefebvre M, Thevenon J, Dubourg C, Julia S, Sarret C, Remerand G, Francannet C, Laffargue F, Boespflug-Tanguy O, David A, Isidor B, Vigneron J, Leheup B, Lambert L, Philippe C, Béri-Dexheimer M, Cuisset JM, Andrieux J, Plessis G, Toutain A, Guibaud L, Cormier-Daire V, Rio M, Bonnefont JP, Echenne B, Journel H, Burglen L, Chantot-Bastaraud S, Bienvenu T, Baumann C, Perrin L, Drunat S, Jouk PS, Dieterich K, Devillard F, Lacombe D, Philip N, Sigaudy S, Moncla A, Missirian C, Badens C, Perreton N, Thauvin-Robinet C, AChro-Puce R, Pedespan JM, Rooryck C, Goizet C, Vincent-Delorme C, Duban-Bedu B, Bahi-Buisson N, Afenjar A, Maincent K, Héron D, Alessandri JL, Martin-Coignard D, Lesca G, Rossi M, Raynaud M, Callier P, Mosca-Boidron AL, Marle N, Coutton C, Satre V, Caignec CL, Malan V, Romana S, Keren B, Tabet AC, Kremer V, Scheidecker S, Vigouroux A, Lackmy-Port-Lis M, Sanlaville D, Till M, Carneiro M, Gilbert-Dussardier B, Willems M, Van Esch H, Portes VD, El Chehadeh S. Further delineation of the MECP2 duplication syndrome phenotype in 59 French male patients, with a particular focus on morphological and neurological features. J Med Genet 2018; 55:359-371. [PMID: 29618507 DOI: 10.1136/jmedgenet-2017-104956] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 02/04/2018] [Accepted: 02/15/2018] [Indexed: 12/22/2022]
Abstract
The Xq28 duplication involving the MECP2 gene (MECP2 duplication) has been mainly described in male patients with severe developmental delay (DD) associated with spasticity, stereotypic movements and recurrent infections. Nevertheless, only a few series have been published. We aimed to better describe the phenotype of this condition, with a focus on morphological and neurological features. Through a national collaborative study, we report a large French series of 59 affected males with interstitial MECP2 duplication. Most of the patients (93%) shared similar facial features, which evolved with age (midface hypoplasia, narrow and prominent nasal bridge, thick lower lip, large prominent ears), thick hair, livedo of the limbs, tapered fingers, small feet and vasomotor troubles. Early hypotonia and global DD were constant, with 21% of patients unable to walk. In patients able to stand, lower limbs weakness and spasticity led to a singular standing habitus: flexion of the knees, broad-based stance with pseudo-ataxic gait. Scoliosis was frequent (53%), such as divergent strabismus (76%) and hypermetropia (54%), stereotypic movements (89%), without obvious social withdrawal and decreased pain sensitivity (78%). Most of the patients did not develop expressive language, 35% saying few words. Epilepsy was frequent (59%), with a mean onset around 7.4 years of age, and often (62%) drug-resistant. Other medical issues were frequent: constipation (78%), and recurrent infections (89%), mainly lung. We delineate the clinical phenotype of MECP2 duplication syndrome in a large series of 59 males. Pulmonary hypertension appeared as a cause of early death in these patients, advocating its screening early in life.
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Affiliation(s)
- Marguerite Miguet
- Service de génétique médicale, Institut de Génétique Médicale d'Alsace (IGMA), Centre de Référence Maladies Rares "Anomalies du développement et syndromes malformatifs", Centre de Référence Maladies Rares "Des déficiences intellectuelles de causes rares", Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Laurence Faivre
- FHU TRANSLAD, Centre de Référence Maladies Rares «Anomalies du développement et syndromes malformatifs», Centre de Génétique, CHU de Dijon, Dijon, France
| | - Jeanne Amiel
- Service de Génétique Clinique, Hôpital Necker Enfants Malades, APHP, Paris, France
| | - Mathilde Nizon
- Service de Génétique Clinique, Hôpital Necker Enfants Malades, APHP, Paris, France
| | - Renaud Touraine
- Service de Génétique Clinique, CHU de Saint-Etienne, Saint-Etienne, France
| | - Fabienne Prieur
- Service de Génétique Clinique, CHU de Saint-Etienne, Saint-Etienne, France
| | - Laurent Pasquier
- Service de Génétique Clinique, CLAD Ouest, CHU de Rennes, Rennes, France
| | - Mathilde Lefebvre
- FHU TRANSLAD, Centre de Référence Maladies Rares «Anomalies du développement et syndromes malformatifs», Centre de Génétique, CHU de Dijon, Dijon, France
| | - Julien Thevenon
- FHU TRANSLAD, Centre de Référence Maladies Rares «Anomalies du développement et syndromes malformatifs», Centre de Génétique, CHU de Dijon, Dijon, France
| | | | - Sophie Julia
- Service de Génétique Médicale, CHU de Toulouse, Toulouse, France
| | - Catherine Sarret
- Service de Neuropédiatrie, CHU de Clermont-Ferrand, Clermont-Ferrand, France
| | - Ganaëlle Remerand
- Service de Neuropédiatrie, CHU de Clermont-Ferrand, Clermont-Ferrand, France
| | - Christine Francannet
- Service de Génétique Médicale, CHU de Clermont-Ferrand, Clermont-Ferrand, France
| | - Fanny Laffargue
- Service de Génétique Médicale, CHU de Clermont-Ferrand, Clermont-Ferrand, France
| | - Odile Boespflug-Tanguy
- Service de Neuropédiatrie et Maladies Métaboliques, Hôpital Robert Debré, APHP, Paris, France
| | - Albert David
- Service de Génétique Médicale, CHU de Nantes, Nantes, France
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, Nantes, France
| | | | - Bruno Leheup
- Service de Génétique Médicale, CHU de Nancy, Nancy, France
| | | | | | | | | | - Joris Andrieux
- Laboratoire de Génétique Médicale, Hôpital Jeanne de Flandre, CHRU de Lille, Lille, France
| | | | | | - Laurent Guibaud
- Service de Radiologie, Hôpital Femme Mère Enfant, Bron, France
| | | | - Marlene Rio
- Service de Génétique Clinique, Hôpital Necker Enfants Malades, APHP, Paris, France
| | - Jean-Paul Bonnefont
- Laboratoire de Biologie Moléculaire, Hôpital Necker Enfants Malades, APHP, Paris, France
| | - Bernard Echenne
- Service de Neurologie pédiatrique, CHU de Montpellier, Montpellier, France
| | - Hubert Journel
- Service de Génétique, Centre Hospitalier de Vannes, Vannes, France
| | - Lydie Burglen
- Service de Génétique, Hôpital Armand Trousseau, APHP, Paris, France
| | | | - Thierry Bienvenu
- Laboratoire de Génétique Moléculaire, GH Cochin-Broca Hôtel Dieu, APHP, Paris, France
| | - Clarisse Baumann
- Service de Génétique Clinique, Hôpital Robert Debré, APHP, Paris, France
| | - Laurence Perrin
- Service de Génétique Clinique, Hôpital Robert Debré, APHP, Paris, France
| | - Séverine Drunat
- Laboratoire de Biologie Moléculaire, Hôpital Robert Debré, APHP, Paris, France
| | - Pierre-Simon Jouk
- Département de Génétique et Procréation - UMR CNRS 5525 TIMC-IMAG - équipe DYCTIM, CHU Grenoble, Grenoble, France
| | - Klaus Dieterich
- Département de Génétique et Procréation - UMR CNRS 5525 TIMC-IMAG - équipe DYCTIM, CHU Grenoble, Grenoble, France
| | - Françoise Devillard
- Département de Génétique et Procréation - UMR CNRS 5525 TIMC-IMAG - équipe DYCTIM, CHU Grenoble, Grenoble, France
| | - Didier Lacombe
- Université de Bordeaux, Laboratoire MRGM, INSERM U1211 and Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | - Nicole Philip
- Département de Génétique Médicale, Hôpital de la Timone, Marseille, France
| | - Sabine Sigaudy
- Département de Génétique Médicale, Hôpital de la Timone, Marseille, France
| | - Anne Moncla
- Laboratoire de Génétique Chromosomique, Hôpital de la Timone, Marseille, France
| | - Chantal Missirian
- Laboratoire de Génétique Chromosomique, Hôpital de la Timone, Marseille, France
| | - Catherine Badens
- Laboratoire de Biologie Moléculaire, Hôpital de la Timone, Marseille, France
| | | | - Christel Thauvin-Robinet
- FHU TRANSLAD, Centre de Référence Maladies Rares «Anomalies du développement et syndromes malformatifs», Centre de Génétique, CHU de Dijon, Dijon, France
| | | | | | - Caroline Rooryck
- Université de Bordeaux, Laboratoire MRGM, INSERM U1211 and Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | - Cyril Goizet
- Université de Bordeaux, Laboratoire MRGM, INSERM U1211 and Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | | | - Bénédicte Duban-Bedu
- Centre de Génétique Chromosomique, GH de l'Institut Catholique de Lille, Hôpital Saint-Vincent-de-Paul, Lille, France
| | - Nadia Bahi-Buisson
- Service de Neuropédiatrie, Hôpital Necker Enfants Malades, APHP, Paris, France
| | - Alexandra Afenjar
- Département de Génétique Médicale, Centre de Référence "Malformations et maladies congénitales du cervelet", APHP, Hôpital Armand Trousseau, APHP, Paris, France
| | - Kim Maincent
- Département de Génétique Médicale, Centre de Référence "Malformations et maladies congénitales du cervelet", APHP, Hôpital Armand Trousseau, APHP, Paris, France
| | - Delphine Héron
- Service de Génétique Clinique, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | | | | | - Gaëtan Lesca
- Service de génétique, Hospices Civils de Lyon, Lyon, France.,INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, GENDEV Team, Université Claude Bernard Lyon 1, Lyon, France
| | - Massimiliano Rossi
- Service de génétique, Hospices Civils de Lyon, Lyon, France.,INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, GENDEV Team, Université Claude Bernard Lyon 1, Lyon, France
| | - Martine Raynaud
- Laboratoire de Génétique Moléculaire, CHRU de Tours, Tours, France
| | | | | | - Nathalie Marle
- Laboratoire de Cytogénétique, CHU de Dijon, Dijon, France
| | - Charles Coutton
- Laboratoire de Cytogénétique, CHU de Grenoble, Grenoble, France
| | - Véronique Satre
- Laboratoire de Cytogénétique, CHU de Grenoble, Grenoble, France
| | - Cédric Le Caignec
- Laboratoire de Cytogénétique, CHU de Nantes, Nantes, France.,Sarcomes osseux et remodelage des tissus calcifiés, Université Bretagne Loire, INSERM, UMR1238, Nantes, France
| | - Valérie Malan
- Laboratoire de Cytogénétique, Hôpital Necker Enfants Malades, APHP, Paris, France
| | - Serge Romana
- Laboratoire de Cytogénétique, Hôpital Necker Enfants Malades, APHP, Paris, France
| | - Boris Keren
- Laboratoire de Cytogénétique, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - Anne-Claude Tabet
- Laboratoire de Cytogénétique, Hôpital Robert Debré, APHP, Paris, France
| | - Valérie Kremer
- Laboratoire de Cytogénétique, CHU de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Sophie Scheidecker
- Laboratoire de Cytogénétique, CHU de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | | | | | | | - Marianne Till
- Laboratoire de Cytogénétique, CHU de Lyon, Lyon, France
| | - Maryline Carneiro
- Service de Neuropédiatrie, CHU de Lyon, Hôpital Femme-Mère-Enfant, Lyon, France
| | | | | | - Hilde Van Esch
- Laboratory for Genetics of Cognition, Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Vincent Des Portes
- Centre de Référence Maladies Rares «Des déficiences intellectuelles de causes rares», HFME, Hospices Civils de Lyon and Université de Lyon, Lyon, France.,Institut des Sciences Cognitives, CNRS UMR 5304, Bron, France
| | - Salima El Chehadeh
- Service de génétique médicale, Institut de Génétique Médicale d'Alsace (IGMA), Centre de Référence Maladies Rares "Anomalies du développement et syndromes malformatifs", Centre de Référence Maladies Rares "Des déficiences intellectuelles de causes rares", Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, Strasbourg, France.,FHU TRANSLAD, Centre de Référence Maladies Rares «Anomalies du développement et syndromes malformatifs», Centre de Génétique, CHU de Dijon, Dijon, France
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13
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Ward DI, Buckley BA, Leon E, Diaz J, Galegos MF, Hofherr S, Lewanda AF. Intellectual disability and epilepsy due to the K/L-mediated Xq28 duplication: Further evidence of a distinct, dosage-dependent phenotype. Am J Med Genet A 2018; 176:551-559. [PMID: 29341460 DOI: 10.1002/ajmg.a.38524] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 09/27/2017] [Accepted: 10/08/2017] [Indexed: 12/30/2022]
Abstract
Copy number variants of the X-chromosome are a common cause of X-linked intellectual disability in males. Duplication of the Xq28 band has been known for over a decade to be the cause of the Lubs X-linked Mental Retardation Syndrome (OMIM 300620) in males and this duplication has been narrowed to a critical region containing only the genes MECP2 and IRAK1. In 2009, four families with a distal duplication of Xq28 not including MECP2 and mediated by low-copy repeats (LCRs) designated "K" and "L" were reported with intellectual disability and epilepsy. Duplication of a second more distal region has been described as the cause of the Int22h-1/Int22h-2 Mediated Xq28 Duplication Syndrome, characterized by intellectual disability, psychiatric problems, and recurrent infections. We report two additional families possessing the K/L-mediated Xq28 duplication with affected males having intellectual disability and epilepsy similar to the previously reported phenotype. To our knowledge, this is the second cohort of individuals to be reported with this duplication and therefore supports K/L-mediated Xq28 duplications as a distinct syndrome.
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Affiliation(s)
- David Isum Ward
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Bethany A Buckley
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Eyby Leon
- Rare Disease Institute Genetics and Metabolism, Children's National Health System, Washington, District of Columbia
| | - Jullianne Diaz
- Rare Disease Institute Genetics and Metabolism, Children's National Health System, Washington, District of Columbia
| | - Margaret Faust Galegos
- Rare Disease Institute Genetics and Metabolism, Children's National Health System, Washington, District of Columbia
| | - Sean Hofherr
- Rare Disease Institute Genetics and Metabolism, Children's National Health System, Washington, District of Columbia
| | - Amy Feldman Lewanda
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland.,Rare Disease Institute Genetics and Metabolism, Children's National Health System, Washington, District of Columbia
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14
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El Chehadeh S, Touraine R, Prieur F, Reardon W, Bienvenu T, Chantot-Bastaraud S, Doco-Fenzy M, Landais E, Philippe C, Marle N, Callier P, Mosca-Boidron AL, Mugneret F, Le Meur N, Goldenberg A, Guerrot AM, Chambon P, Satre V, Coutton C, Jouk PS, Devillard F, Dieterich K, Afenjar A, Burglen L, Moutard ML, Addor MC, Lebon S, Martinet D, Alessandri JL, Doray B, Miguet M, Devys D, Saugier-Veber P, Drunat S, Aral B, Kremer V, Rondeau S, Tabet AC, Thevenon J, Thauvin-Robinet C, Perreton N, Des Portes V, Faivre L. Xq28 duplication includingMECP2in six unreported affected females: what can we learn for diagnosis and genetic counselling? Clin Genet 2017; 91:576-588. [DOI: 10.1111/cge.12898] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/14/2016] [Accepted: 10/17/2016] [Indexed: 11/27/2022]
Affiliation(s)
- S. El Chehadeh
- FHU TRANSLAD, Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs» de l'Est; Centre de Génétique, CHU de Dijon; Dijon France
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs» de l'Est; Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre; Strasbourg France
| | - R. Touraine
- Service de Génétique Clinique Chromosomique et Moléculaire; CHU de Saint-Etienne; Saint-Étienne France
| | - F. Prieur
- Service de Génétique Clinique Chromosomique et Moléculaire; CHU de Saint-Etienne; Saint-Étienne France
| | - W. Reardon
- Clinical Genetics, Division National Centre for Medical Genetics; Our Lady's Children's Hospital; Dublin Ireland
| | - T. Bienvenu
- AP-HP, Laboratoire de Génétique et Biologie Moléculaires, HU Paris Centre, Site Cochin, France; Université Paris Descartes; Institut Cochin, INSERM U1016; Paris France
| | - S. Chantot-Bastaraud
- Service de Génétique et Embryologie Médicales; CHU Paris Est - Hôpital d'Enfants Armand-Trousseau; Paris France
| | - M. Doco-Fenzy
- Service de Génétique, EA3801; SFR-CAP Santé, CHU de Reims; Reims France
| | - E. Landais
- PRBI, Pôle de Biologie Médicale; CHU de Reims; Reims France
| | - C. Philippe
- Laboratoire de Génétique Médicale; Hôpitaux de Brabois CHRU; Vandoeuvre les Nancy France
| | - N. Marle
- Service de Cytogénétique; CHU de Dijon; Dijon France
| | - P. Callier
- Service de Cytogénétique; CHU de Dijon; Dijon France
| | | | - F. Mugneret
- Service de Cytogénétique; CHU de Dijon; Dijon France
| | - N. Le Meur
- Etablissement Français du Sang; CHU de Rouen; Rouen France
| | - A. Goldenberg
- Service de Génétique et Inserm U1079, Centre Normand de Génomique Médicale et Médecine Personnalisée, CHU de Rouen; Inserm et Université de Rouen; Rouen France
| | - A.-M. Guerrot
- Service de Génétique et Inserm U1079, Centre Normand de Génomique Médicale et Médecine Personnalisée, CHU de Rouen; Inserm et Université de Rouen; Rouen France
| | - P. Chambon
- Laboratoire D'histologie, Cytogénétique et Biologie de la Reproduction; CHU de Rouen; Rouen France
| | - V. Satre
- Département de Génétique et Procréation, CHU Grenoble Alpes; Université Grenoble Alpes; Grenoble France
| | - C. Coutton
- Département de Génétique et Procréation, CHU Grenoble Alpes; Université Grenoble Alpes; Grenoble France
| | - P.-S. Jouk
- Département de Génétique et Procréation, CHU Grenoble Alpes; Université Grenoble Alpes; Grenoble France
| | - F. Devillard
- Département de Génétique et Procréation, CHU Grenoble Alpes; Université Grenoble Alpes; Grenoble France
| | - K. Dieterich
- Département de Génétique et Procréation, CHU Grenoble Alpes; Université Grenoble Alpes; Grenoble France
| | - A. Afenjar
- Service de Génétique; CHU Paris Est - Hôpital d'Enfants Armand-Trousseau; Paris France
| | - L. Burglen
- Service de Génétique; CHU Paris Est - Hôpital d'Enfants Armand-Trousseau; Paris France
| | - M.-L. Moutard
- Unité de neuropédiatrie et pathologie du développement; CHU Paris Est - Hôpital d'Enfants Armand-Trousseau; Paris France
| | - M.-C. Addor
- Service de Génétique Médicale; Centre Hospitalier Universitaire Vaudois CHUV; Lausanne Switzerland
| | - S. Lebon
- Unité de Neuropédiatrie; Centre Hospitalier Universitaire Vaudois CHUV; Lausanne Switzerland
| | - D. Martinet
- Laboratoire de Cytogénétique Constitutionnelle et Prénatale; Centre Hospitalier Universitaire Vaudois CHUV; Lausanne Switzerland
| | - J.-L. Alessandri
- Pôle Enfants; CHU de la Réunion - Hôpital Félix Guyon; Saint-Denis France
| | - B. Doray
- Service de Génétique; CHU de la Réunion - Hôpital Félix Guyon; Saint-Denis France
| | - M. Miguet
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs» de l'Est; Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre; Strasbourg France
| | - D. Devys
- Laboratoire de Diagnostic Génétique; CHU de Strasbourg - Hôpital Civil; Strasbourg France
| | - P. Saugier-Veber
- Laboratoire de Génétique Moléculaire; Faculté de Médecine et de Pharmacie; Rouen France
| | - S. Drunat
- Laboratoire de Biologie Moléculaire; Hôpital Robert Debré; Paris France
| | - B. Aral
- Service de Biologie Moléculaire; CHU de Dijon; Dijon France
| | - V. Kremer
- Laboratoire de Cytogénétique, Hôpitaux Universitaires de Strasbourg; Hôpital de Hautepierre; Strasbourg France
| | - S. Rondeau
- Service de Pédiatrie Néonatale et Réanimation; CHU de Rouen; Rouen France
| | - A.-C. Tabet
- Laboratoire de Cytogénétique; Hôpital Robert Debré; Paris France
| | - J. Thevenon
- FHU TRANSLAD, Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs» de l'Est; Centre de Génétique, CHU de Dijon; Dijon France
- GAD, EA4271, Génétique et Anomalies du Développement; Université de Bourgogne; Dijon France
| | - C. Thauvin-Robinet
- FHU TRANSLAD, Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs» de l'Est; Centre de Génétique, CHU de Dijon; Dijon France
- GAD, EA4271, Génétique et Anomalies du Développement; Université de Bourgogne; Dijon France
| | - N. Perreton
- EPICIME-CIC 1407 de Lyon, Inserm; Service de Pharmacologie Clinique, CHU-Lyon; Bron France
| | - V. Des Portes
- Service de Neurologie Pédiatrique; CHU de Lyon-GH Est; Bron France
| | - L. Faivre
- FHU TRANSLAD, Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs» de l'Est; Centre de Génétique, CHU de Dijon; Dijon France
- GAD, EA4271, Génétique et Anomalies du Développement; Université de Bourgogne; Dijon France
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15
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Clifton BD, Librado P, Yeh SD, Solares ES, Real DA, Jayasekera SU, Zhang W, Shi M, Park RV, Magie RD, Ma HC, Xia XQ, Marco A, Rozas J, Ranz JM. Rapid Functional and Sequence Differentiation of a Tandemly Repeated Species-Specific Multigene Family in Drosophila. Mol Biol Evol 2016; 34:51-65. [PMID: 27702774 DOI: 10.1093/molbev/msw212] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Gene clusters of recently duplicated genes are hotbeds for evolutionary change. However, our understanding of how mutational mechanisms and evolutionary forces shape the structural and functional evolution of these clusters is hindered by the high sequence identity among the copies, which typically results in their inaccurate representation in genome assemblies. The presumed testis-specific, chimeric gene Sdic originated, and tandemly expanded in Drosophila melanogaster, contributing to increased male-male competition. Using various types of massively parallel sequencing data, we studied the organization, sequence evolution, and functional attributes of the different Sdic copies. By leveraging long-read sequencing data, we uncovered both copy number and order differences from the currently accepted annotation for the Sdic region. Despite evidence for pervasive gene conversion affecting the Sdic copies, we also detected signatures of two episodes of diversifying selection, which have contributed to the evolution of a variety of C-termini and miRNA binding site compositions. Expression analyses involving RNA-seq datasets from 59 different biological conditions revealed distinctive expression breadths among the copies, with three copies being transcribed in females, opening the possibility to a sexually antagonistic effect. Phenotypic assays using Sdic knock-out strains indicated that should this antagonistic effect exist, it does not compromise female fertility. Our results strongly suggest that the genome consolidation of the Sdic gene cluster is more the result of a quick exploration of different paths of molecular tinkering by different copies than a mere dosage increase, which could be a recurrent evolutionary outcome in the presence of persistent sexual selection.
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Affiliation(s)
- Bryan D Clifton
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Shu-Dan Yeh
- Department of Life Sciences, National Central University, Taoyuan City, Zhongli District, Taiwan
| | - Edwin S Solares
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - Daphne A Real
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - Suvini U Jayasekera
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - Wanting Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Mijuan Shi
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Ronni V Park
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - Robert D Magie
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - Hsiu-Ching Ma
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - Xiao-Qin Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Antonio Marco
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadistica, and Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - José M Ranz
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
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16
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Cardoso AR, Oliveira M, Amorim A, Azevedo L. Major influence of repetitive elements on disease-associated copy number variants (CNVs). Hum Genomics 2016; 10:30. [PMID: 27663310 PMCID: PMC5035501 DOI: 10.1186/s40246-016-0088-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/16/2016] [Indexed: 01/13/2023] Open
Abstract
Copy number variants (CNVs) are important contributors to the human pathogenic genetic diversity as demonstrated by a number of cases reported in the literature. The high homology between repetitive elements may guide genomic stability which will give rise to CNVs either by non-allelic homologous recombination (NAHR) or non-homologous end joining (NHEJ). Here, we present a short guide based on previously documented cases of disease-associated CNVs in order to provide a general view on the impact of repeated elements on the stability of the genomic sequence and consequently in the origin of the human pathogenic variome.
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Affiliation(s)
- Ana R Cardoso
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Manuela Oliveira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Antonio Amorim
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007, Porto, Portugal
| | - Luisa Azevedo
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal. .,IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal. .,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007, Porto, Portugal.
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17
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Zhang LN, Meng Z, He ZW, Li DF, Luo XY, Liang LY. [Clinical phenotypes and copy number variations in children with microdeletion and microduplication syndromes: an analysis of 50 cases]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2016; 18:840-845. [PMID: 27655541 PMCID: PMC7389961 DOI: 10.7499/j.issn.1008-8830.2016.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/14/2016] [Indexed: 06/06/2023]
Abstract
OBJECTIVE To investigate the association between genotype and phenotype of microdeletion and microduplication syndromes (MMSs) and the pathogenesis of pathogenic copy number variations (CNVs). METHODS A total of 50 children with MMSs diagnosed by chromosomal microarray analysis (CMA) from June 2013 to September 2015 were enrolled, and the clinical manifestations and features of pathogenic CNVs were analyzed. RESULTS The main clinical manifestations of children with MMSs included mental retardation, developmental delay, short stature, and unusual facies, with the presence of abnormalities in multiple systems. There were 54 pathogenic CNVs in total, consisting of 36 microdeletion segments and 18 microduplication segments, with sizes ranging from 28 kb to 48.5 Mb (mean 13.86 Mb). Pathogenic CNVs often occurred in chromosomes X, 15, and 1. CONCLUSIONS The clinical manifestations of MMSs are not specific, and a genotype-first approach can be used for diagnosis. Mode of inheritance, type of recombination (deletion or duplication), size of segment, and functional genes included helps with the interpretation of CNVs of de novo mutations, and in-depth research on rare pathogenesis may become breakthrough points for the identification of new MMSs.
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Affiliation(s)
- Li-Na Zhang
- Department of Pediatric Endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510260, China.
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18
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Yi Z, Pan H, Li L, Wu H, Wang S, Ma Y, Qi Y. Chromosome Xq28 duplication encompassing MECP2: Clinical and molecular analysis of 16 new patients from 10 families in China. Eur J Med Genet 2016; 59:347-53. [PMID: 27180140 DOI: 10.1016/j.ejmg.2016.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/08/2016] [Accepted: 05/09/2016] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Chromosome Xq28 duplications encompassing methyl-CpG-binding protein 2 gene (MECP2) are observed most in males with a severe neurodevelopmental disorder associated with hypotonia, spasticity, severe learning disability, delayed psychomotor development, and recurrent pulmonary infections. Most female carriers are asymptomatic due to extremely or completely skewed X-inactivation. METHODS A retrospective clinical and molecular study was conducted to examine 16 patients and two fetuses from 10 families who were identified among patients with Xq28 duplications who presented at genetic clinics. RESULTS Of all 16 patients, 10 had a family history. Only one patient was female. All of the patients had no relevant pre-natal history. All of the patients exhibited severe psychomotor developmental delay, infantile hypotonia and recurrent infections. Some of the patients exhibited cardiac abnormalities, gastrointestinal mobility problems, hydrocele of tunica vaginalis, cryptorchidism, and autistic phenotypes. Additionally, neonatal kidney calculus, premature closure of the fontanel and pulmonary sequestration were found in the patients. Duplication sizes in these patients range from 0.21 to 14.391 Mb (most were smaller than 1 Mb), and all the duplications included host cell factor C1 (HCFC1), interleukin-1 receptor-associated kinase 1 (IRAK1), and MECP2. Bioinformatics analysis revealed that approximately half of the distal breakpoints were located within the low-copy repeats (LCRs), which may be involved in the recombination. The two fetuses were found to be healthy in the prenatal diagnosis. CONCLUSION This is the first large cohort of patients with MECP2 duplication syndrome, including a female, reported in China. Interestingly, neonatal kidney calculus, premature closure of the fontanel and pulmonary sequestration were first reported in this syndrome. However, it was difficult to distinguish if these patients represented unique cases or if these phenotypes can be considered as part of the syndrome. The correlation between the infrequent phenotypes and duplications/genes in the duplication region needs further systematic delineation. In conclusion, our study suggested that it is important to emphasize molecular genetic analysis in patients with developmental delay/intellectual disability and recurrent infections and that it is especially important for familial female carriers to accept prenatal diagnosis.
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Affiliation(s)
- Zhi Yi
- Department of Central Laboratory, Peking University First Hospital, Beijing, China
| | - Hong Pan
- Department of Central Laboratory, Peking University First Hospital, Beijing, China.
| | - Lin Li
- Department of Central Laboratory, Peking University First Hospital, Beijing, China
| | - Hairong Wu
- Department of Central Laboratory, Peking University First Hospital, Beijing, China
| | - Songtao Wang
- Department of Central Laboratory, Peking University First Hospital, Beijing, China
| | - Yinan Ma
- Department of Central Laboratory, Peking University First Hospital, Beijing, China
| | - Yu Qi
- Department of Central Laboratory, Peking University First Hospital, Beijing, China
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19
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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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20
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San Antonio-Arce V, Fenollar-Cortés M, Oancea Ionescu R, DeSantos-Moreno T, Gallego-Merlo J, Illana Cámara FJ, Cotarelo Pérez MC. MECP2 Duplications in Symptomatic Females: Report on 3 Patients Showing the Broad Phenotypic Spectrum. Child Neurol Open 2016; 3:2329048X16630673. [PMID: 28503606 PMCID: PMC5417292 DOI: 10.1177/2329048x16630673] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 11/28/2015] [Accepted: 01/11/2016] [Indexed: 12/22/2022] Open
Abstract
Xq28 microduplications including the MECP2 gene constitute a 100% penetrant X-linked syndrome in males caused by overexpression of normal MeCP2 protein. A small number of cases of affected females have been reported. This can be due to the location of the duplicated material into an autosome, but it can also be due to the location of the duplicated material into one of the X chromosomes and random or unfavorable skewed X chromosome inactivation, which is much more likely to occur but may be underdiagnosed because of the resulting broad phenotypic spectrum. In order to contribute to the phenotypic delineation of Xq28 microduplications including MECP2 in symptomatic females, the authors present clinical and molecular data on 3 patients illustrating the broad phenotypic spectrum. Our finding underlines the importance of quantitative analysis of MECP2 in females with intellectual disability and raises the question of the indication in females with borderline intellectual performances or learning difficulties.
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21
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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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22
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Altered neuronal network and rescue in a human MECP2 duplication model. Mol Psychiatry 2016; 21:178-88. [PMID: 26347316 PMCID: PMC4720528 DOI: 10.1038/mp.2015.128] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 06/30/2015] [Accepted: 07/28/2015] [Indexed: 01/07/2023]
Abstract
Increased dosage of methyl-CpG-binding protein-2 (MeCP2) results in a dramatic neurodevelopmental phenotype with onset at birth. We generated induced pluripotent stem cells (iPSCs) from patients with the MECP2 duplication syndrome (MECP2dup), carrying different duplication sizes, to study the impact of increased MeCP2 dosage in human neurons. We show that cortical neurons derived from these different MECP2dup iPSC lines have increased synaptogenesis and dendritic complexity. In addition, using multi-electrodes arrays, we show that neuronal network synchronization was altered in MECP2dup-derived neurons. Given MeCP2 functions at the epigenetic level, we tested whether these alterations were reversible using a library of compounds with defined activity on epigenetic pathways. One histone deacetylase inhibitor, NCH-51, was validated as a potential clinical candidate. Interestingly, this compound has never been considered before as a therapeutic alternative for neurological disorders. Our model recapitulates early stages of the human MECP2 duplication syndrome and represents a promising cellular tool to facilitate therapeutic drug screening for severe neurodevelopmental disorders.
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23
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Zhang Q, Zhao Y, Yang Y, Bao X. MECP2 duplication syndrome in a Chinese family. BMC MEDICAL GENETICS 2015; 16:112. [PMID: 26672597 PMCID: PMC4682232 DOI: 10.1186/s12881-015-0264-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Accepted: 12/14/2015] [Indexed: 01/28/2023]
Abstract
Background Methyl-CpG-binding protein 2 (MeCP2) is a key transcriptional regulator of gene expression in the maintenance and development of the central nervous system. Loss- or gain-function of this gene may contribute to neurodevelopmental disorders. The aim of this study is to delineate the clinical characteristics of MECP2 duplication syndrome and the hereditary mechanism in a Chinese family. Case presentation We identified a Chinese family with three persons carry MECP2 gene duplication: a boy, his mother and his grandmother. The duplication segment which was detected by multiplex ligation-dependent probe amplification (MLPA) included gene MECP2, interleukin-1 receptor-associated kinase 1 (IRAK1), filamin A (FLNA), and L1 cell adhesion molecule (L1CAM). Furthermore, array comparative genomic hybridization (aCGH) was performed on the mother, showed that MECP2 containing duplication was 510 Kb (153,113,885-153,624,154), including 16 other genes except MECP2. The boy showed most symptoms of MECP2 duplication syndrome. His mother and maternal grandmother were asymptomatic. Both female carriers had a skewed X chromosome inactivation (XCI), which were 80:20 and 74:26 respectively. Conclusion To our knowledge, this is the second reported Chinese Han family with MECP2-containing duplications. And this patient had recurrent respiratory infections which was different from the first two Chinese-brother cases. MECP2 is the core gene responsible for MECP2 duplication syndrome. XCI may play an important role in modulating the clinical manifestation.
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Affiliation(s)
- Qingping Zhang
- Department of Pediatrics, Peking University First Hospital, No.1, Xi An Men Street, Xicheng District, Beijing, 100034, China.
| | - Ying Zhao
- Department of Pediatrics, Peking University First Hospital, No.1, Xi An Men Street, Xicheng District, Beijing, 100034, China.
| | - Yanling Yang
- Department of Pediatrics, Peking University First Hospital, No.1, Xi An Men Street, Xicheng District, Beijing, 100034, China.
| | - Xinhua Bao
- Department of Pediatrics, Peking University First Hospital, No.1, Xi An Men Street, Xicheng District, Beijing, 100034, China.
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24
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Lannoy N, Ravoet M, Grisart B, Fretigny M, Vikkula M, Hermans C. Five int22h homologous copies at the Xq28 locus identified in intron22 inversion type 3 of the Factor VIII gene. Thromb Res 2015; 137:224-227. [PMID: 26653368 DOI: 10.1016/j.thromres.2015.11.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 11/03/2015] [Accepted: 11/14/2015] [Indexed: 10/22/2022]
Affiliation(s)
- N Lannoy
- Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, Brussels, Belgium.
| | - M Ravoet
- Center of Human Genetics, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - B Grisart
- Center of Human Genetics IPG, Gosselies, Belgium
| | - M Fretigny
- Service d'Hématologie Biologique, Hôpital Edouard Herriot, Hospices Civils de Lyon, France
| | - M Vikkula
- Laboratory of Human Molecular Genetics de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - C Hermans
- Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, Brussels, Belgium; Haemostasis and Thrombosis Unit, Haemophilia Clinic, Division of Haematology, UCL, Cliniques Universitaires Saint-Luc, Brussels, Belgium
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25
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El Chehadeh S, Faivre L, Mosca-Boidron AL, Malan V, Amiel J, Nizon M, Touraine R, Prieur F, Pasquier L, Callier P, Lefebvre M, Marle N, Dubourg C, Julia S, Sarret C, Francannet C, Laffargue F, Boespflug-Tanguy O, David A, Isidor B, Le Caignec C, Vigneron J, Leheup B, Lambert L, Philippe C, Cuisset JM, Andrieux J, Plessis G, Toutain A, Goldenberg A, Cormier-Daire V, Rio M, Bonnefont JP, Thevenon J, Echenne B, Journel H, Afenjar A, Burglen L, Bienvenu T, Addor MC, Lebon S, Martinet D, Baumann C, Perrin L, Drunat S, Jouk PS, Devillard F, Coutton C, Lacombe D, Delrue MA, Philip N, Moncla A, Badens C, Perreton N, Masurel A, Thauvin-Robinet C, Portes VD, Guibaud L. Large national series of patients with Xq28 duplication involvingMECP2: Delineation of brain MRI abnormalities in 30 affected patients. Am J Med Genet A 2015; 170A:116-29. [DOI: 10.1002/ajmg.a.37384] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 09/07/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Salima El Chehadeh
- FHU TRANSLAD, Centre de Référence Maladies Rares “Anomalies du Développement et Syndromes Malformatifs” de l'Est; Centre de Génétique; CHU de Dijon France
- GAD, EA4271, Génétique et Anomalies du Développement; Université de Bourgogne; Dijon France
| | - Laurence Faivre
- FHU TRANSLAD, Centre de Référence Maladies Rares “Anomalies du Développement et Syndromes Malformatifs” de l'Est; Centre de Génétique; CHU de Dijon France
- GAD, EA4271, Génétique et Anomalies du Développement; Université de Bourgogne; Dijon France
| | - Anne-Laure Mosca-Boidron
- GAD, EA4271, Génétique et Anomalies du Développement; Université de Bourgogne; Dijon France
- Service de Cytogénétique; CHU de Dijon France
| | - Valérie Malan
- Service de Cytogénétique; Hôpital Necker Enfants Malades; Paris France
| | - Jeanne Amiel
- Service de Génétique Clinique; Hôpital Necker Enfants Malades; Paris France
| | - Mathilde Nizon
- Service de Génétique Clinique; Hôpital Necker Enfants Malades; Paris France
| | - Renaud Touraine
- Service de Génétique Clinique Chromosomique et Moléculaire; CHU de Saint-Etienne France
| | - Fabienne Prieur
- Service de Génétique Clinique Chromosomique et Moléculaire; CHU de Saint-Etienne France
| | | | - Patrick Callier
- GAD, EA4271, Génétique et Anomalies du Développement; Université de Bourgogne; Dijon France
- Service de Cytogénétique; CHU de Dijon France
| | - Mathilde Lefebvre
- FHU TRANSLAD, Centre de Référence Maladies Rares “Anomalies du Développement et Syndromes Malformatifs” de l'Est; Centre de Génétique; CHU de Dijon France
- GAD, EA4271, Génétique et Anomalies du Développement; Université de Bourgogne; Dijon France
| | - Nathalie Marle
- GAD, EA4271, Génétique et Anomalies du Développement; Université de Bourgogne; Dijon France
- Service de Cytogénétique; CHU de Dijon France
| | | | - Sophie Julia
- Service de Génétique Médicale; CHU de Toulouse France
| | | | | | - Fanny Laffargue
- Service de Génétique Médicale; CHU de Clermont-Ferrand France
| | | | - Albert David
- Service de Génétique Médicale; CHU de Nantes France
| | | | | | | | - Bruno Leheup
- Service de Génétique Médicale; CHU de Nancy France
| | | | | | | | - Joris Andrieux
- Laboratoire de Génétique Médicale; Hôpital Jeanne de Flandre; CHRU de Lille France
| | | | | | | | | | - Marlène Rio
- Service de Génétique Clinique; Hôpital Necker Enfants Malades; Paris France
| | - Jean-Paul Bonnefont
- Laboratoire de Biologie Moléculaire; Hôpital Necker Enfants Malades; Paris France
| | - Julien Thevenon
- FHU TRANSLAD, Centre de Référence Maladies Rares “Anomalies du Développement et Syndromes Malformatifs” de l'Est; Centre de Génétique; CHU de Dijon France
- GAD, EA4271, Génétique et Anomalies du Développement; Université de Bourgogne; Dijon France
| | - Bernard Echenne
- Service de Neurologie Pédiatrique; CHU de Montpellier France
| | - Hubert Journel
- Service de Génétique; Centre Hospitalier de Vannes; Vannes France
| | | | - Lydie Burglen
- Service de Génétique; Hôpital Armand Trousseau; Paris France
| | - Thierry Bienvenu
- Laboratoire de Biochimie et Génétique Moléculaire; GH Cochin-Broca-Hôtel Dieu; Paris France
| | | | | | - Danièle Martinet
- Laboratoire de Cytogénétique Constitutionnelle et Prénatale; CHUV de Lausanne; Lausanne, Suisse
| | - Clarisse Baumann
- Service de Génétique Clinique; Hôpital Robert Debré; Paris France
| | - Laurence Perrin
- Service de Génétique Clinique; Hôpital Robert Debré; Paris France
| | - Séverine Drunat
- Laboratoire de Biologie Moléculaire; Hôpital Robert Debré; Paris France
| | - Pierre-Simon Jouk
- Département de Génétique et Procréation-UMR CNRS 5525 TIMC-IMAG équipe DYCTIM; CHU Grenoble France
| | - Françoise Devillard
- Département de Génétique et Procréation-UMR CNRS 5525 TIMC-IMAG équipe DYCTIM; CHU Grenoble France
| | - Charles Coutton
- Département de Génétique et Procréation-UMR CNRS 5525 TIMC-IMAG équipe DYCTIM; CHU Grenoble France
| | | | | | - Nicole Philip
- Département de Génétique Médicale; Hôpital de la Timone; Marseille France
| | - Anne Moncla
- Laboratoire de Génétique Chromosomique; Hôpital de la Timone; Marseille France
| | - Catherine Badens
- Laboratoire de Biologie Moléculaire; Hôpital de la Timone; Marseille France
| | - Nathalie Perreton
- EPICIME-CIC 1407 de Lyon, Inserm, Service de Pharmacologie Clinique; CHU de Lyon Bron France
| | - Alice Masurel
- FHU TRANSLAD, Centre de Référence Maladies Rares “Anomalies du Développement et Syndromes Malformatifs” de l'Est; Centre de Génétique; CHU de Dijon France
| | - Christel Thauvin-Robinet
- FHU TRANSLAD, Centre de Référence Maladies Rares “Anomalies du Développement et Syndromes Malformatifs” de l'Est; Centre de Génétique; CHU de Dijon France
- GAD, EA4271, Génétique et Anomalies du Développement; Université de Bourgogne; Dijon France
| | | | - Laurent Guibaud
- Service de Radiologie; Hôpital Femme Mère Enfant; Bron France
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Abstract
Two severe, progressive neurological disorders characterized by intellectual disability, autism, and developmental regression, Rett syndrome and MECP2 duplication syndrome, result from loss and gain of function, respectively, of the same critical gene, methyl-CpG-binding protein 2 (MECP2). Neurons acutely require the appropriate dose of MECP2 to function properly but do not die in its absence or overexpression. Instead, neuronal dysfunction can be reversed in a Rett syndrome mouse model if MeCP2 function is restored. Thus, MECP2 disorders provide a unique window into the delicate balance of neuronal health, the power of mouse models, and the importance of chromatin regulation in mature neurons. In this Review, we will discuss the clinical profiles of MECP2 disorders, the knowledge acquired from mouse models of the syndromes, and how that knowledge is informing current and future clinical studies.
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Lannoy N, Bandelier C, Grisart B, Reginster M, Ronge-Collard E, Vikkula M, Hermans C. Tandem inversion duplication withinF8Intron 1 associated with mild haemophilia A. Haemophilia 2015; 21:516-22. [DOI: 10.1111/hae.12675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2015] [Indexed: 12/16/2022]
Affiliation(s)
- N. Lannoy
- Center of Human Genetics UCLouvain; Cliniques Universitaires Saint-Luc; Bruxelles Belgium
- Institut de Recherche Expérimentale et Clinique (IREC); Université Catholique de Louvain; Bruxelles Belgium
| | - C. Bandelier
- Center of Human Genetics UCLouvain; Cliniques Universitaires Saint-Luc; Bruxelles Belgium
| | - B. Grisart
- Center of Human Genetics; Institut de Pathologie et de Génétique (IPG); Charleroi (Gosselies) Belgium
| | - M. Reginster
- Department of Hemato-oncology; Centre Hospitalier Regional de Huy; Huy Belgium
| | - E. Ronge-Collard
- Hemostasis Laboratory; Department of Biological Chemistry; Centre Hospitalier Regional de Liège; Liege Belgium
| | - M. Vikkula
- Laboratory of Human Molecular Genetics de Duve Institute; Université Catholique de Louvain; Bruxelles Belgium
| | - C. Hermans
- Institut de Recherche Expérimentale et Clinique (IREC); Université Catholique de Louvain; Bruxelles Belgium
- Haemostasis and Thrombosis Unit; Haemophilia Clinic; Division of Haematology; Cliniques Universitaires Saint-Luc; Bruxelles Belgium
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Hardy-Weinberg equilibrium revisited for inferences on genotypes featuring allele and copy-number variations. Sci Rep 2015; 5:9066. [PMID: 25765626 PMCID: PMC4357990 DOI: 10.1038/srep09066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 02/11/2015] [Indexed: 12/22/2022] Open
Abstract
Copy number variations represent a substantial source of genetic variation and are associated with a plethora of physiological and pathophysiological conditions. Joint copy number and allelic variations (CNAVs) are difficult to analyze and require new strategies to unravel the properties of genotype distributions. We developed a Bayesian hidden Markov model (HMM) approach that allows dissecting intrinsic properties and metastructures of the distribution of CNAVs within populations, in particular haplotype phases of genes with varying copy numbers. As a key feature, this approach incorporates an extension of the Hardy-Weinberg equilibrium, allowing both a comprehensive and parsimonious model design. We demonstrate the quality of performance and applicability of the HMM approach with a real data set describing the Fcγ receptor (FcγR) gene region. Our concept, using a dynamic process to analyze a static distribution, establishes the basis for a novel understanding of complex genomic data sets.
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Bauer M, Kölsch U, Krüger R, Unterwalder N, Hameister K, Kaiser FM, Vignoli A, Rossi R, Botella MP, Budisteanu M, Rosello M, Orellana C, Tejada MI, Papuc SM, Patat O, Julia S, Touraine R, Gomes T, Wenner K, Xu X, Afenjar A, Toutain A, Philip N, Jezela-Stanek A, Gortner L, Martinez F, Echenne B, Wahn V, Meisel C, Wieczorek D, El-Chehadeh S, Van Esch H, von Bernuth H. Infectious and immunologic phenotype of MECP2 duplication syndrome. J Clin Immunol 2015; 35:168-81. [PMID: 25721700 PMCID: PMC7101860 DOI: 10.1007/s10875-015-0129-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Accepted: 01/12/2015] [Indexed: 12/02/2022]
Abstract
MECP2 (methyl CpG binding protein 2) duplication causes syndromic intellectual disability. Patients often suffer from life-threatening infections, suggesting an additional immunodeficiency. We describe for the first time the detailed infectious and immunological phenotype of MECP2 duplication syndrome. 17/27 analyzed patients suffered from pneumonia, 5/27 from at least one episode of sepsis. Encapsulated bacteria (S.pneumoniae, H.influenzae) were frequently isolated. T-cell immunity showed no gross abnormalities in 14/14 patients and IFNy-secretion upon ConA-stimulation was not decreased in 6/7 patients. In 6/21 patients IgG2-deficiency was detected – in 4/21 patients accompanied by IgA-deficiency, 10/21 patients showed low antibody titers against pneumococci. Supra-normal IgG1-levels were detected in 11/21 patients and supra-normal IgG3-levels were seen in 8/21 patients – in 6 of the patients as combined elevation of IgG1 and IgG3. Three of the four patients with IgA/IgG2-deficiency developed multiple severe infections. Upon infections pronounced acute-phase responses were common: 7/10 patients showed CRP values above 200 mg/l. Our data for the first time show systematically that increased susceptibility to infections in MECP2 duplication syndrome is associated with IgA/IgG2-deficiency, low antibody titers against pneumococci and elevated acute-phase responses. So patients with MECP2 duplication syndrome and low IgA/IgG2 may benefit from prophylactic substitution of sIgA and IgG.
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Affiliation(s)
- Michael Bauer
- Pediatric Pneumology and Immunology, Charité University Medicine, Berlin, Germany,
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30
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Vanmarsenille L, Giannandrea M, Fieremans N, Verbeeck J, Belet S, Raynaud M, Vogels A, Männik K, Õunap K, Jacqueline V, Briault S, Van Esch H, D'Adamo P, Froyen G. Increased dosage of RAB39B affects neuronal development and could explain the cognitive impairment in male patients with distal Xq28 copy number gains. Hum Mutat 2014; 35:377-83. [PMID: 24357492 DOI: 10.1002/humu.22497] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 12/16/2013] [Indexed: 12/21/2022]
Abstract
Copy number gains at Xq28 are a frequent cause of X-linked intellectual disability (XLID). Here, we report on a recurrent 0.5 Mb tandem copy number gain at distal Xq28 not including MECP2, in four male patients with nonsyndromic mild ID and behavioral problems. The genomic region is duplicated in two families and triplicated in a third reflected by more distinctive clinical features. The X-inactivation patterns in carrier females correspond well with their clinical symptoms. Our mapping data confirm that this recurrent gain is likely mediated by nonallelic homologous recombination between two directly oriented Int22h repeats. The affected region harbors eight genes of which RAB39B encoding a small GTPase, was the prime candidate since loss-of-function mutations had been linked to ID. RAB39B is expressed at stable levels in lymphocytes from control individuals, suggesting a tight regulation. mRNA levels in our patients were almost two-fold increased. Overexpression of Rab39b in mouse primary hippocampal neurons demonstrated a significant decrease in neuronal branching as well as in the number of synapses when compared with the control neurons. Taken together, we provide evidence that the increased dosage of RAB39B causes a disturbed neuronal development leading to cognitive impairment in patients with this recurrent copy number gain.
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Chen C, Ma H, Zhang F, Chen L, Xing X, Wang S, Zhang X, Luo Y. Screening of Duchenne muscular dystrophy (DMD) mutations and investigating its mutational mechanism in Chinese patients. PLoS One 2014; 9:e108038. [PMID: 25244321 PMCID: PMC4171529 DOI: 10.1371/journal.pone.0108038] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 08/25/2014] [Indexed: 11/18/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a common X-linked recessive disease of muscle degeneration and death. In order to provide accurate and reliable genetic counseling and prenatal diagnosis, we screened DMD mutations in a cohort of 119 Chinese patients using multiplex ligation-dependent probe amplification (MLPA) and denaturing high performance liquid chromatography (DHPLC) followed by Sanger sequencing. In these unrelated DMD patients, we identified 11 patients with DMD small mutations (9.2%) and 81 patients with DMD deletions/duplications (del/dup) (68.1%), of which 64 (79.0%) were deletions, 16 (19.8%) were duplications, and one (1.2%) was both deletion and duplication. Furthermore, we analyzed the frequency of DMD breakpoint in the 64 deletion cases by calculating exon-deletion events of certain exon interval that revealed a novel mutation hotspot boundary. To explore why DMD rearrangement breakpoints were predisposed to specific regions (hotspot), we precisely characterized junction sequences of breakpoints at the nucleotide level in 21 patients with exon deleted/duplicated in DMD with a high-resolution SNP microarray assay. There were no exactly recurrent breakpoints and there was also no significant difference between single-exon del/dup and multiple-exon del/dup cases. The data from the current study provided a comprehensive strategy to detect DMD mutations for clinical practice, and identified two deletion hotspots at exon 43–55 and exon 10–23 by calculating exon-deletion events of certain exon interval. Furthermore, this is the first study to characterize DMD breakpoint at the nucleotide level in a Chinese population. Our observations provide better understanding of the mechanism for DMD gene rearrangements.
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Affiliation(s)
- Chen Chen
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Chinese Ministry of Education, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Hongwei Ma
- Department of Developing Pediatrics, Shengjing Hospital, China Medical University, Shenyang, China
| | - Feng Zhang
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Lu Chen
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xuesha Xing
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Chinese Ministry of Education, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Shusen Wang
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Chinese Ministry of Education, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Luo
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Chinese Ministry of Education, College of Basic Medical Science, China Medical University, Shenyang, China
- * E-mail:
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Fieremans N, Bauters M, Belet S, Verbeeck J, Jansen AC, Seneca S, Roelens F, De Baere E, Marynen P, Froyen G. De novo MECP2 duplications in two females with intellectual disability and unfavorable complete skewed X-inactivation. Hum Genet 2014; 133:1359-67. [DOI: 10.1007/s00439-014-1469-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 07/09/2014] [Indexed: 12/11/2022]
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Popovici C, Busa T, Boute O, Thuresson AC, Perret O, Sigaudy S, Södergren T, Andrieux J, Moncla A, Philip N. Whole ARX gene duplication is compatible with normal intellectual development. Am J Med Genet A 2014; 164A:2324-7. [PMID: 25044608 DOI: 10.1002/ajmg.a.36564] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 03/12/2014] [Indexed: 12/24/2022]
Abstract
We report here on four males from three families carrying de novo or inherited small Xp22.13 duplications including the ARX gene detected by chromosomal microarray analysis (CMA). Two of these males had normal intelligence. Our report suggests that, unlike other XLMR genes like MECP2 and FMR1, the presence of an extra copy of the ARX gene may not be sufficient to perturb its developmental functions. ARX duplication does not inevitably have detrimental effects on brain development, in contrast with the effects of ARX haploinsufficiency. The abnormal phenotype ascribed to the presence of an extra copy in some male patients may have resulted from the effect of another, not yet identified, chromosomal or molecular anomaly, alone or in association with ARX duplication.
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Affiliation(s)
- Cornel Popovici
- APHM, Hôpital Timone-Enfants, Département de Génétique Médicale, Marseille, France; Aix-Marseille Université, Inserm, GMGF UMR_S 910, Marseille, France
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Vogt J, Bengesser K, Claes KBM, Wimmer K, Mautner VF, van Minkelen R, Legius E, Brems H, Upadhyaya M, Högel J, Lazaro C, Rosenbaum T, Bammert S, Messiaen L, Cooper DN, Kehrer-Sawatzki H. SVA retrotransposon insertion-associated deletion represents a novel mutational mechanism underlying large genomic copy number changes with non-recurrent breakpoints. Genome Biol 2014; 15:R80. [PMID: 24958239 PMCID: PMC4229983 DOI: 10.1186/gb-2014-15-6-r80] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 06/02/2014] [Indexed: 01/06/2023] Open
Abstract
Background Genomic disorders are caused by copy number changes that may exhibit recurrent breakpoints processed by nonallelic homologous recombination. However, region-specific disease-associated copy number changes have also been observed which exhibit non-recurrent breakpoints. The mechanisms underlying these non-recurrent copy number changes have not yet been fully elucidated. Results We analyze large NF1 deletions with non-recurrent breakpoints as a model to investigate the full spectrum of causative mechanisms, and observe that they are mediated by various DNA double strand break repair mechanisms, as well as aberrant replication. Further, two of the 17 NF1 deletions with non-recurrent breakpoints, identified in unrelated patients, occur in association with the concomitant insertion of SINE/variable number of tandem repeats/Alu (SVA) retrotransposons at the deletion breakpoints. The respective breakpoints are refractory to analysis by standard breakpoint-spanning PCRs and are only identified by means of optimized PCR protocols designed to amplify across GC-rich sequences. The SVA elements are integrated within SUZ12P intron 8 in both patients, and were mediated by target-primed reverse transcription of SVA mRNA intermediates derived from retrotranspositionally active source elements. Both SVA insertions occurred during early postzygotic development and are uniquely associated with large deletions of 1 Mb and 867 kb, respectively, at the insertion sites. Conclusions Since active SVA elements are abundant in the human genome and the retrotranspositional activity of many SVA source elements is high, SVA insertion-associated large genomic deletions encompassing many hundreds of kilobases could constitute a novel and as yet under-appreciated mechanism underlying large-scale copy number changes in the human genome.
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35
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Fukushi D, Yamada K, Nomura N, Naiki M, Kimura R, Yamada Y, Kumagai T, Yamaguchi K, Miyake Y, Wakamatsu N. Clinical characterization and identification of duplication breakpoints in a Japanese family with Xq28 duplication syndrome including MECP2. Am J Med Genet A 2014; 164A:924-33. [PMID: 24478188 DOI: 10.1002/ajmg.a.36373] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 11/03/2013] [Indexed: 11/05/2022]
Abstract
Xq28 duplication syndrome including MECP2 is a neurodevelopmental disorder characterized by axial hypotonia at infancy, severe intellectual disability, developmental delay, mild characteristic facial appearance, epilepsy, regression, and recurrent infections in males. We identified a Japanese family of Xq28 duplications, in which the patients presented with cerebellar ataxia, severe constipation, and small feet, in addition to the common clinical features. The 488-kb duplication spanned from L1CAM to EMD and contained 17 genes, two pseudo genes, and three microRNA-coding genes. FISH and nucleotide sequence analyses demonstrated that the duplication was tandem and in a forward orientation, and the duplication breakpoints were located in AluSc at the EMD side, with a 32-bp deletion, and LTR50 at the L1CAM side, with "tc" and "gc" microhomologies at the duplication breakpoints, respectively. The duplicated segment was completely segregated from the grandmother to the patients. These results suggest that the duplication was generated by fork-stalling and template-switching at the AluSc and LTR50 sites. This is the first report to determine the size and nucleotide sequences of the duplicated segments at Xq28 of three generations of a family and provides the genotype-phenotype correlation of the patients harboring the specific duplicated segment.
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Affiliation(s)
- Daisuke Fukushi
- Department of Genetics, Institute for Developmental Research, Aichi Human Service Center, Kasugai, Aichi, Japan
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36
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Lin DS, Chuang TP, Chiang MF, Ho CS, Hsiao CD, Huang YW, Wu TY, Wu JY, Chen YT, Chen TC, Li LH. De novo MECP2 duplication derived from paternal germ line result in dysmorphism and developmental delay. Gene 2014; 533:78-85. [DOI: 10.1016/j.gene.2013.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 09/26/2013] [Accepted: 10/01/2013] [Indexed: 02/02/2023]
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37
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Enggaard Hoeffding LK, Hansen T, Ingason A, Doung L, Thygesen JH, Møller RS, Tommerup N, Kirov G, Rujescu D, Larsen LA, Werge T. Sequence analysis of 17 NRXN1 deletions. Am J Med Genet B Neuropsychiatr Genet 2014; 165B:52-61. [PMID: 24339137 DOI: 10.1002/ajmg.b.32204] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 08/27/2013] [Indexed: 11/06/2022]
Abstract
BACKGROUND Genome instability plays fundamental roles in human evolution and phenotypic variation within our population. This instability leads to genomic rearrangements that are involved in a wide variety of human disorders, including congenital and neurodevelopmental disorders, and cancers. Insight into the molecular mechanisms governing such genomic rearrangements may increase our understanding of disease pathology and evolutionary processes. Here we analyse 17 carriers of non-recurrent deletions in the NRXN1 gene, which have been associated with neurodevelopmental disorders, e.g. schizophrenia, autism and epilepsies. METHODS 17 non-recurrent NRXN1 deletions identified by GWA were sequenced to map the breakpoints of each. Meme … etc. was used to identify shared patterns between the deletions and compare these were previously studies on non-recurrent deletions. RESULTS We discovered two novel sequence motifs shared between all 17 NRXN1 deletions and a significantly higher AT nucleotide content at the breakpoints, compared to the overall nucleotide content on chromosome 2. We found different alteration of sequence at the breakpoint; small insertions and duplications giving rise to short microhomology sequences. CONCLUSIONS No single mechanism seems to be implicated in the deletion events, but the results suggest that NHEJ, FoSTeS or MMBIR is implicated. The two novel sequence motifs together with a high AT content in all in NRXN1 deletions may lead to increased instability leading to a increase susceptibility to a single stranded structures. This favours potentially repaired by NHEJ mechanism of double strand breaks or may leading to replication errors. © 2013 Wiley Periodicals, Inc.
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Møller RS, Jensen LR, Maas SM, Filmus J, Capurro M, Hansen C, Marcelis CLM, Ravn K, Andrieux J, Mathieu M, Kirchhoff M, Rødningen OK, de Leeuw N, Yntema HG, Froyen G, Vandewalle J, Ballon K, Klopocki E, Joss S, Tolmie J, Knegt AC, Lund AM, Hjalgrim H, Kuss AW, Tommerup N, Ullmann R, de Brouwer APM, Strømme P, Kjaergaard S, Tümer Z, Kleefstra T. X-linked congenital ptosis and associated intellectual disability, short stature, microcephaly, cleft palate, digital and genital abnormalities define novel Xq25q26 duplication syndrome. Hum Genet 2013; 133:625-38. [PMID: 24326587 DOI: 10.1007/s00439-013-1403-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 11/21/2013] [Indexed: 12/12/2022]
Abstract
Submicroscopic duplications along the long arm of the X-chromosome with known phenotypic consequences are relatively rare events. The clinical features resulting from such duplications are various, though they often include intellectual disability, microcephaly, short stature, hypotonia, hypogonadism and feeding difficulties. Female carriers are often phenotypically normal or show a similar but milder phenotype, as in most cases the X-chromosome harbouring the duplication is subject to inactivation. Xq28, which includes MECP2 is the major locus for submicroscopic X-chromosome duplications, whereas duplications in Xq25 and Xq26 have been reported in only a few cases. Using genome-wide array platforms we identified overlapping interstitial Xq25q26 duplications ranging from 0.2 to 4.76 Mb in eight unrelated families with in total five affected males and seven affected females. All affected males shared a common phenotype with intrauterine- and postnatal growth retardation and feeding difficulties in childhood. Three had microcephaly and two out of five suffered from epilepsy. In addition, three males had a distinct facial appearance with congenital bilateral ptosis and large protruding ears and two of them showed a cleft palate. The affected females had various clinical symptoms similar to that of the males with congenital bilateral ptosis in three families as most remarkable feature. Comparison of the gene content of the individual duplications with the respective phenotypes suggested three critical regions with candidate genes (AIFM1, RAB33A, GPC3 and IGSF1) for the common phenotypes, including candidate loci for congenital bilateral ptosis, small head circumference, short stature, genital and digital defects.
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Affiliation(s)
- R S Møller
- Danish Epilepsy Centre, Dianalund, Kolonivej 7, 4293, Dianalund, Denmark,
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Xq28 (MECP2) microdeletions are common in mutation-negative females with Rett syndrome and cause mild subtypes of the disease. Mol Cytogenet 2013; 6:53. [PMID: 24283533 PMCID: PMC4176196 DOI: 10.1186/1755-8166-6-53] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 11/19/2013] [Indexed: 01/13/2023] Open
Abstract
Background Rett syndrome (RTT) is an X-linked neurodevelopmental disease affecting predominantly females caused by MECP2 mutations. Although RTT is classically considered a monogenic disease, a stable proportion of patients, who do not exhibit MECP2 sequence variations, does exist. Here, we have attempted at uncovering genetic causes underlying the disorder in mutation-negative cases by whole genome analysis using array comparative genomic hybridization (CGH) and a bioinformatic approach. Results Using BAC and oligonucleotide array CGH, 39 patients from RTT Russian cohort (in total, 354 RTT patients), who did not bear intragenic MECP2 mutations, were studied. Among the individuals studied, 12 patients were those with classic RTT and 27 were those with atypical RTT. We have detected five 99.4 kb deletions in chromosome Xq28 affecting MECP2 associated with mild manifestations of classic RTT and five deletions encompassing MECP2 spanning 502.428 kb (three cases), 539.545 kb (one case) and 877.444 kb (one case) associated with mild atypical RTT. A case has demonstrated somatic mosaicism. Regardless of RTT type and deletion size, all the cases exhibited mild phenotypes. Conclusions Our data indicate for the first time that no fewer than 25% of RTT cases without detectable MECP2 mutations are caused by Xq28 microdeletions. Furthermore, Xq28 (MECP2) deletions are likely to cause mild subtypes of the disease, which can manifest as both classical and atypical RTT.
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A novel in-frame deletion affecting the BAR domain of OPHN1 in a family with intellectual disability and hippocampal alterations. Eur J Hum Genet 2013; 22:644-51. [PMID: 24105372 DOI: 10.1038/ejhg.2013.216] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 08/12/2013] [Accepted: 08/16/2013] [Indexed: 12/13/2022] Open
Abstract
Oligophrenin-1 (OPHN1) is one of at least seven genes located on chromosome X that take part in Rho GTPase-dependent signaling pathways involved in X-linked intellectual disability (XLID). Mutations in OPHN1 were primarily described as an exclusive cause of non-syndromic XLID, but the re-evaluation of the affected individuals using brain imaging displayed fronto-temporal atrophy and cerebellar hypoplasia as neuroanatomical marks. In this study, we describe clinical, genetic and neuroimaging data of a three generation Brazilian XLID family co-segregating a novel intragenic deletion in OPHN1. This deletion results in an in-frame loss of exon 7 at transcription level (c.781_891del; r.487_597del), which is predicted to abolish 37 amino acids from the highly conserved N-terminal BAR domain of OPHN1. cDNA expression analysis demonstrated that the mutant OPHN1 transcript is stable and no abnormal splicing was observed. Features shared by the affected males of this family include neonatal hypotonia, strabismus, prominent root of the nose, deep set eyes, hyperactivity and instability/intolerance to frustration. Cranial MRI scans showed large lateral ventricles, vermis hypoplasia and cystic dilatation of the cisterna magna in all affected males. Interestingly, hippocampal alterations that have not been reported in patients with loss-of-function OPHN1 mutations were found in three affected individuals, suggesting an important function for the BAR domain in the hippocampus. This is the first description of an in-frame deletion within the BAR domain of OPHN1 and could provide new insights into the role of this domain in relation to brain and cognitive development or function.
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Replicative mechanisms for CNV formation are error prone. Nat Genet 2013; 45:1319-26. [PMID: 24056715 PMCID: PMC3821386 DOI: 10.1038/ng.2768] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 08/27/2013] [Indexed: 01/20/2023]
Abstract
We investigated 67 breakpoint junctions of gene copy number gains (CNVs) in 31 unrelated subjects. We observed a strikingly high frequency of small deletions and insertions (29%) apparently originating from polymerase-slippage events, in addition to frameshifts and point mutations in homonucleotide runs (13%), at or flanking the breakpoint junctions of complex CNVs. These simple nucleotide variants (SNV) were generated concomitantly with the de novo complex genomic rearrangement (CGR) event. Our findings implicate a low fidelity error-prone DNA polymerase in synthesis associated with DNA repair mechanisms that leads to a local increase in point mutation burden associated with human CGR.
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Giorgio E, Rolyan H, Kropp L, Chakka AB, Yatsenko S, Gregorio ED, Lacerenza D, Vaula G, Talarico F, Mandich P, Toro C, Pierre EE, Labauge P, Capellari S, Cortelli P, Vairo FP, Miguel D, Stubbolo D, Marques LC, Gahl W, Boespflug-Tanguy O, Melberg A, Hassin-Baer S, Cohen OS, Pjontek R, Grau A, Klopstock T, Fogel B, Meijer I, Rouleau G, Bouchard JPL, Ganapathiraju M, Vanderver A, Dahl N, Hobson G, Brusco A, Brussino A, Padiath QS. Analysis of LMNB1 duplications in autosomal dominant leukodystrophy provides insights into duplication mechanisms and allele-specific expression. Hum Mutat 2013; 34:1160-71. [PMID: 23649844 PMCID: PMC3714349 DOI: 10.1002/humu.22348] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 04/19/2013] [Indexed: 02/05/2023]
Abstract
Autosomal dominant leukodystrophy (ADLD) is an adult onset demyelinating disorder that is caused by duplications of the lamin B1 (LMNB1) gene. However, as only a few cases have been analyzed in detail, the mechanisms underlying LMNB1 duplications are unclear. We report the detailed molecular analysis of the largest collection of ADLD families studied, to date. We have identified the minimal duplicated region necessary for the disease, defined all the duplication junctions at the nucleotide level and identified the first inverted LMNB1 duplication. We have demonstrated that the duplications are not recurrent; patients with identical duplications share the same haplotype, likely inherited from a common founder and that the duplications originated from intrachromosomal events. The duplication junction sequences indicated that nonhomologous end joining or replication-based mechanisms such fork stalling and template switching or microhomology-mediated break induced repair are likely to be involved. LMNB1 expression was increased in patients' fibroblasts both at mRNA and protein levels and the three LMNB1 alleles in ADLD patients show equal expression, suggesting that regulatory regions are maintained within the rearranged segment. These results have allowed us to elucidate duplication mechanisms and provide insights into allele-specific LMNB1 expression levels.
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Affiliation(s)
- Elisa Giorgio
- University of Torino, Department of Medical SciencesTorino, Italy
| | - Harshvardhan Rolyan
- Department of Human Genetics Graduate School of Public Health, University of PittsburghPittsburgh, Pennsylvania
| | - Laura Kropp
- Department of Human Genetics Graduate School of Public Health, University of PittsburghPittsburgh, Pennsylvania
| | - Anish Baswanth Chakka
- Department of Biomedical Informatics School of Medicine, University of PittsburghPittsburgh, Pennsylvania
| | - Svetlana Yatsenko
- Department of Obstetrics Gynecology and Reproductive Sciences, University of PittsburghPittsburgh, Pennsylvania
- Department of Pathology University of Pittsburgh, School of MedicinePittsburgh, Pennsylvania
| | - Eleonora Di Gregorio
- University of Torino, Department of Medical SciencesTorino, Italy
- S.C.D.U. Medical Genetics, Az. Osp. Città della Salute e della ScienzaTorino, Italy
| | | | - Giovanna Vaula
- Department of Neuroscience, Az. Osp. Città della Salute e della ScienzaTorino, Italy
| | - Flavia Talarico
- S.C.D.U. Medical Genetics, Az. Osp. Città della Salute e della ScienzaTorino, Italy
| | - Paola Mandich
- Department of Neurology, Ophthalmology and Genetics, di Bologna, Department of Biomedical and NeuroMotor Sciences (DIBINEM) Alma Mater StudiorumBologna, Italy
| | - Camilo Toro
- NIH Undiagnosed Diseases Program NIH Office of Rare Disease, Research and NHGRIBethesda, Maryland
| | | | - Pierre Labauge
- Neurologie Hopital Caremeau, Centre Hospitalo-Universitaire de NimesNimes, France
| | - Sabina Capellari
- University of Bologna IRCCS Istituto delle Scienze Neurologiche di Bologna Department of Biomedical and NeuroMotor Sciences (DIBINEM), Alma Mater StudiorumItaly
| | - Pietro Cortelli
- University of Bologna IRCCS Istituto delle Scienze Neurologiche di Bologna Department of Biomedical and NeuroMotor Sciences (DIBINEM), Alma Mater StudiorumItaly
| | - Filippo Pinto Vairo
- Hospital de Clínicas de Porto Alegre … Universidade Federal do Rio Grande do SulPorto Alegre, Brazil
| | - Diego Miguel
- Hospital de Clínicas de Porto Alegre … Universidade Federal do Rio Grande do SulPorto Alegre, Brazil
| | - Danielle Stubbolo
- Nemours Biomedical Research, Alfred I. duPont Hospital for ChildrenWilmington, Delaware
| | - Lourenco Charles Marques
- Department of Medical Genetics Clinics Hospital of Ribeirao Preto, University of Sao PauloSao Paulo, Brazil
| | - William Gahl
- NIH Undiagnosed Diseases Program NIH Office of Rare Disease, Research and NHGRIBethesda, Maryland
| | - Odile Boespflug-Tanguy
- Institut National de la Santé et de la Recherche Médicale (INSERM) – Paris Diderot Sorbonne Paris Cité University, Robert Debré HospitalParis, France
- Assistance Publique des Hopitaux de Paris Reference Center for Rare Diseases “Leukodystrophies”, Child Neurology and Metabolic Disorders DepartmentParis, France
| | - Atle Melberg
- Department of Neuroscience Neurology, Uppsala UniversityUppsala, Sweden
| | - Sharon Hassin-Baer
- Parkinson’s disease and Movement Disorders Clinic Department of Neurology, Chaim Sheba Medical CenterTel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv UniversityTel Aviv, Israel
| | - Oren S Cohen
- Parkinson’s disease and Movement Disorders Clinic Department of Neurology, Chaim Sheba Medical CenterTel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv UniversityTel Aviv, Israel
| | - Rastislav Pjontek
- Department of Neurology, University of HeidelbergHeidelberg, Germany
| | - Armin Grau
- Dept. of Neurology, Klinikum LudwigshafenLudwigshafen, Germany
| | - Thomas Klopstock
- Dept. of Neurology Friedrich-Baur-Institute, Ludwig-Maximilians-UniversityMunich, Germany
- German Center for Vertigo and Balance DisordersMunich, Germany
- DZNE – German Center for Neurodegenerative DiseasesMunich, Germany
- German Network for Mitochondrial Disorders(mitoNET), Germany
| | - Brent Fogel
- Department of Neurology David Geffen School of Medicine, University of CaliforniaLos Angeles, California
| | - Inge Meijer
- Montreal Neurological Institute, McGill UniversityMontreal, Canada
| | - Guy Rouleau
- Montreal Neurological Institute, McGill UniversityMontreal, Canada
| | | | - Madhavi Ganapathiraju
- Department of Biomedical Informatics School of Medicine, University of PittsburghPittsburgh, Pennsylvania
| | - Adeline Vanderver
- Department of Neurology, Childrens National Medical CenterWashington, District of Columbia
| | - Niklas Dahl
- Dept. of Immunology Genetics and Pathology Section of Clinical Genetics The Rudbeck laboratory, Uppsala University Children’s HospitalUppsala, Sweden
| | - Grace Hobson
- Nemours Biomedical Research, Alfred I. duPont Hospital for ChildrenWilmington, Delaware
- University of Delaware, Department of BiologyNewark, Delaware
- Thomas Jefferson University, Jefferson Medical CollegePhiladelphia, Pennsylvania
| | - Alfredo Brusco
- University of Torino, Department of Medical SciencesTorino, Italy
- S.C.D.U. Medical Genetics, Az. Osp. Città della Salute e della ScienzaTorino, Italy
| | | | - Quasar Saleem Padiath
- Department of Human Genetics Graduate School of Public Health, University of PittsburghPittsburgh, Pennsylvania
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Neira VA, Romero-Espinoza P, Rojas-Martínez A, Ortiz-López R, Córdova-Fletes C, Plaja A, Barros-Núñez P. De novo MECP2 disomy in a Mexican male carrying a supernumerary marker chromosome and no typical Lubs syndrome features. Gene 2013; 524:381-5. [PMID: 23639959 DOI: 10.1016/j.gene.2013.04.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 04/02/2013] [Accepted: 04/03/2013] [Indexed: 10/26/2022]
Abstract
Xq28 duplication, including the MECP2 gene, is among the most frequently identified Xq subtelomeric rearrangements. The resulting clinical phenotype is named Lubs syndrome and mainly consists of intellectual disability, congenital hypotonia, absent speech, recurrent infections, and seizures. Here we report a Mexican male patient carrying a supernumerary marker chromosome with de novo Xq28 gain. By MLPA, duplication of MECP2, GDI1, and SLC6A8 was found and a subsequent a-CGH analysis demonstrated that the gain spanned ~2.1Mb. Despite gain of the MECP2 gene, the features of this patient do not evoke Lubs syndrome. Probably the mosaicism of the supernumerary marker chromosome is modifying the phenotype in this patient.
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Affiliation(s)
- Vivian Alejandra Neira
- División de Genética, Centro de Investigación Biomédica de Occidente, CMNO-IMSS, Guadalajara, Jalisco, Mexico
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You GL, Ding QL, Lu YL, Dai J, Xi XD, Wang XF, Wang HL. Characterization of large deletions in the F8 gene using multiple competitive amplification and the genome walking technique. J Thromb Haemost 2013; 11:1103-10. [PMID: 23551875 DOI: 10.1111/jth.12205] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 03/15/2013] [Indexed: 11/29/2022]
Abstract
BACKGROUND Large deletions in the F8 gene are responsible for approximately 3% of severe hemophilia A (HA) cases. However, only a few breakpoints in large deletions have been characterized. OBJECTIVES To identify large deletions in the F8 gene and to characterize the molecular mechanisms leading to these deletions. PATIENTS AND METHODS We used AccuCopy technology, a copy number variation (CNV) genotyping method based on multiplex competitive amplification, to confirm deletions in index patients and to screen potential female carriers in 10 HA families. Also, breakpoints of these large deletions were characterized by a primer walking strategy and genome walking technique. RESULTS Ten large deletions and four female carriers were identified by AccuCopy. The extents of deleted regions ranged from 1.3 to 68.5 kb. Exact breakpoints of these deletions were successfully characterized. Eight of them presented microhomologies at breakpoint junctions and several recombination-associated elements (repetitive elements, non-B conformation forming motifs and sequence motifs) were also observed in close proximity to the junctions. CONCLUSIONS AccuCopy technology is a reliable and efficient tool for detecting large deletions in the F8 gene and identifying HA female carriers. The genome walking technique is a highly specific, efficient and versatile method for characterizing the deletion breakpoints. Molecular characterization of deletion breakpoints revealed that non-homologous end joining and microhomology-mediated replication-dependent recombination were the major causative mechanisms of the 10 large deletions in the F8 gene.
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Affiliation(s)
- G L You
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Vanmarsenille L, Verbeeck J, Belet S, Roebroek AJ, Van de Putte T, Nevelsteen J, Callaerts-Vegh Z, D’Hooge R, Marynen P, Froyen G. Generation and characterization of an Nxf7 knockout mouse to study NXF5 deficiency in a patient with intellectual disability. PLoS One 2013; 8:e64144. [PMID: 23675524 PMCID: PMC3652825 DOI: 10.1371/journal.pone.0064144] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/09/2013] [Indexed: 12/11/2022] Open
Abstract
Members of the Nuclear eXport Factor (NXF) family are involved in the export of mRNA from the nucleus to the cytoplasm, or hypothesized to play a role in transport of cytoplasmic mRNA. We previously reported on the loss of NXF5 in a male patient with a syndromic form of intellectual disability. To study the functional role of NXF5 we identified the mouse counterpart. Based on synteny, mouse Nxf2 is the ortholog of human NXF5. However, we provide several lines of evidence that mouse Nxf7 is the actual functional equivalent of NXF5. Both Nxf7 and NXF5 are predominantly expressed in the brain, show cytoplasmic localization, and present as granules in neuronal dendrites suggesting a role in cytoplasmic mRNA metabolism in neurons. Nxf7 was primarily detected in the pyramidal cells of the hippocampus and in layer V of the cortex. Similar to human NXF2, mouse Nxf2 is highly expressed in testis and shows a nuclear localization. Interestingly, these findings point to a different evolutionary path for both NXF genes in human and mouse. We thus generated and validated Nxf7 knockout mice, which were fertile and did not present any gross anatomical or morphological abnormalities. Expression profiling in the hippocampus and the cortex did not reveal significant changes between wild-type and Nxf7 knockout mice. However, impaired spatial memory was observed in these KO mice when evaluated in the Morris water maze test. In conclusion, our findings provide strong evidence that mouse Nxf7 is the functional counterpart of human NXF5, which might play a critical role in mRNA metabolism in the brain.
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Affiliation(s)
- Lieselot Vanmarsenille
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Jelle Verbeeck
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Stefanie Belet
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Anton J. Roebroek
- Experimental Mouse Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Tom Van de Putte
- Laboratory of Molecular Biology (Celgen), Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Joke Nevelsteen
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Rudi D’Hooge
- Laboratory of Biological Psychology, KU Leuven, Leuven, Belgium
- Leuven Institute for Neuroscience and Disease (LIND), KU Leuven, Leuven, Belgium
| | - Peter Marynen
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Guy Froyen
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, Belgium
- * E-mail:
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Shimada S, Okamoto N, Ito M, Arai Y, Momosaki K, Togawa M, Maegaki Y, Sugawara M, Shimojima K, Osawa M, Yamamoto T. MECP2 duplication syndrome in both genders. Brain Dev 2013; 35:411-9. [PMID: 22877836 DOI: 10.1016/j.braindev.2012.07.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Revised: 07/07/2012] [Accepted: 07/15/2012] [Indexed: 12/21/2022]
Abstract
BACKGROUND Duplications involving the methyl-CpG-binding protein 2 gene (MECP2) locus at Xq28 have been frequently identified in male patients who exhibit a phenotype unique from that of Rett syndrome, which is mainly characterized by severe mental retardation, recurrent infections, and epilepsy. This combination of features is recognized as MECP2 duplication syndrome. METHODS Genomic copy number was investigated for patients with unexplained mental retardation, and phenotypic features of the patients having interstitial duplications including MECP2 were analyzed. RESULTS Three male and one female patients with MECP2 duplication were identified. The phenotypic features of all the four patients were compatible with MECP2 duplication syndrome. The X-chromosome inactivation (XCI) pattern was analyzed in the female patient, identifying a skewed XCI that activated the X-chromosome containing the MECP2 duplication. Her mother possessed the same MECP2 duplication and a random XCI pattern but exhibited no phenotypic features, indicating a nonsymptomatic carrier. The brain magnetic resonance imaging revealed periventricular cystic lesions in all four patients, including the female patient. CONCLUSION This study suggested clinical implications of the MECP2 duplication syndrome not only in the male but also in female patients with unexplained mental retardation.
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Affiliation(s)
- Shino Shimada
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo, Japan
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Simple, rapid and inexpensive quantitative fluorescent PCR method for detection of microdeletion and microduplication syndromes. PLoS One 2013; 8:e61328. [PMID: 23620743 PMCID: PMC3631209 DOI: 10.1371/journal.pone.0061328] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 03/08/2013] [Indexed: 12/14/2022] Open
Abstract
Because of economic limitations, the cost-effective diagnosis of patients affected with rare microdeletion or microduplication syndromes is a challenge in developing countries. Here we report a sensitive, rapid, and affordable detection method that we have called Microdeletion/Microduplication Quantitative Fluorescent PCR (MQF-PCR). Our procedure is based on the finding of genomic regions with high homology to segments of the critical microdeletion/microduplication region. PCR amplification of both using the same primer pair, establishes competitive kinetics and relative quantification of amplicons, as happens in microsatellite-based Quantitative Fluorescence PCR. We used patients with two common microdeletion syndromes, the Williams-Beuren syndrome (7q11.23 microdeletion) and the 22q11.2 microdeletion syndromes and discovered that MQF-PCR could detect both with 100% sensitivity and 100% specificity. Additionally, we demonstrated that the same principle could be reliably used for detection of microduplication syndromes, by using patients with the Lubs (MECP2 duplication) syndrome and the 17q11.2 microduplication involving the NF1 gene. We propose that MQF-PCR is a useful procedure for laboratory confirmation of the clinical diagnosis of microdeletion/microduplication syndromes, ideally suited for use in developing countries, but having general applicability as well.
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Intron 22 homologous regions are implicated in exons 1-22 duplications of the F8 gene. Eur J Hum Genet 2013; 21:970-6. [PMID: 23299923 DOI: 10.1038/ejhg.2012.275] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 11/05/2012] [Accepted: 11/15/2012] [Indexed: 02/02/2023] Open
Abstract
The intron 22 inversion found in up to 50% of severe hemophilia A patients results from a recombination between three intron 22 homologous copies (int22h). This study evaluated the implication of these copies in the formation of extended duplications comprising exons 1-22 of the factor 8 (F8) gene and their association with hemophilia and mental retardation. Two hemophilic patients with moderate and severe phenotypes and a third nonhemophilic patient with developmental delay were studied. All exhibited a duplication of F8 gene exons 1-22 identified by multiplex ligation-dependent probe amplification along with abnormal patterns on Southern blotting and unexpected long-range PCR amplification. Breakpoint analysis using array comparative genomic hybridization was performed to delimit the extent of these rearrangements. These duplications were bounded on one side by the F8 intragenic int22h-1 repeat and on the other side by extragenic int22h-2 or int22h-3 copies. However, the simultaneous identification of a second duplication containing F8 gene exons 2-14 for the moderate patient and the classical intron 22 inversion for the severe patient are considered in this study as the genetic causal defects of hemophilia. This study shows that the well-known int22h copies are involved in extended duplications comprising F8 gene exons 1-22. These specific duplications are probably not responsible for hemophilia and intellectual disability, but should be carefully considered in genetic counseling, while continuing to investigate the causal mutation of hemophilia.
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Robberecht C, Voet T, Zamani Esteki M, Nowakowska BA, Vermeesch JR. Nonallelic homologous recombination between retrotransposable elements is a driver of de novo unbalanced translocations. Genome Res 2012; 23:411-8. [PMID: 23212949 PMCID: PMC3589530 DOI: 10.1101/gr.145631.112] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Large-scale analysis of balanced chromosomal translocation breakpoints has shown nonhomologous end joining and microhomology-mediated repair to be the main drivers of interchromosomal structural aberrations. Breakpoint sequences of de novo unbalanced translocations have not yet been investigated systematically. We analyzed 12 de novo unbalanced translocations and mapped the breakpoints in nine. Surprisingly, in contrast to balanced translocations, we identify nonallelic homologous recombination (NAHR) between (retro)transposable elements and especially long interspersed elements (LINEs) as the main mutational mechanism. This finding shows yet another involvement of (retro)transposons in genomic rearrangements and exposes a profoundly different mutational mechanism compared with balanced chromosomal translocations. Furthermore, we show the existence of compound maternal/paternal derivative chromosomes, reinforcing the hypothesis that human cleavage stage embryogenesis is a cradle of chromosomal rearrangements.
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Affiliation(s)
- Caroline Robberecht
- Laboratory for Molecular Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
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Helsmoortel C, Vandeweyer G, Kooy RF. On the spot: very local chromosomal rearrangements. F1000 BIOLOGY REPORTS 2012. [PMID: 23189093 PMCID: PMC3505860 DOI: 10.3410/b4-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Over the last decade, the detection of chromosomal abnormalities has shifted from conventional karyotyping under a light microscope to molecular detection using microarrays. The latter technology identified copy number variation as a major source of variation in the human genome; moreover, copy number variants were found responsible for 10-20% of cases of intellectual disability. Recent technological advances in microarray technology have also enabled the detection of very small local chromosomal rearrangements, sometimes affecting the function of only a single gene. Here, we illustrate how high resolution microarray analysis has led to increased insights into the contribution of specific genes in disease.
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Affiliation(s)
- Céline Helsmoortel
- Cognitive Genetics, Department of Medical Genetics, University of Antwerp Prins Boudewijnlaan 43, B-2650 Edegem, Belgium
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