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Abedini SS, Akhavantabasi S, Liang Y, Heng JIT, Alizadehsani R, Dehzangi I, Bauer DC, Alinejad-Rokny H. A critical review of the impact of candidate copy number variants on autism spectrum disorder. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2024; 794:108509. [PMID: 38977176 DOI: 10.1016/j.mrrev.2024.108509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/14/2024] [Accepted: 07/02/2024] [Indexed: 07/10/2024]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder (NDD) influenced by genetic, epigenetic, and environmental factors. Recent advancements in genomic analysis have shed light on numerous genes associated with ASD, highlighting the significant role of both common and rare genetic mutations, as well as copy number variations (CNVs), single nucleotide polymorphisms (SNPs) and unique de novo variants. These genetic variations disrupt neurodevelopmental pathways, contributing to the disorder's complexity. Notably, CNVs are present in 10 %-20 % of individuals with autism, with 3 %-7 % detectable through cytogenetic methods. While the role of submicroscopic CNVs in ASD has been recently studied, their association with genomic loci and genes has not been thoroughly explored. In this review, we focus on 47 CNV regions linked to ASD, encompassing 1632 genes, including protein-coding genes and long non-coding RNAs (lncRNAs), of which 659 show significant brain expression. Using a list of ASD-associated genes from SFARI, we detect 17 regions harboring at least one known ASD-related protein-coding gene. Of the remaining 30 regions, we identify 24 regions containing at least one protein-coding gene with brain-enriched expression and a nervous system phenotype in mouse mutants, and one lncRNA with both brain-enriched expression and upregulation in iPSC to neuron differentiation. This review not only expands our understanding of the genetic diversity associated with ASD but also underscores the potential of lncRNAs in contributing to its etiology. Additionally, the discovered CNVs will be a valuable resource for future diagnostic, therapeutic, and research endeavors aimed at prioritizing genetic variations in ASD.
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Affiliation(s)
- Seyedeh Sedigheh Abedini
- UNSW BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia; School of Biotechnology & Biomolecular Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Shiva Akhavantabasi
- Department of Molecular Biology and Genetics, Yeni Yuzyil University, Istanbul, Turkey; Ghiaseddin Jamshid Kashani University, Andisheh University Town, Danesh Blvd, 3441356611, Abyek, Qazvin, Iran
| | - Yuheng Liang
- UNSW BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Julian Ik-Tsen Heng
- Curtin Health Innovation Research Institute, Curtin University, Bentley 6845, Australia
| | - Roohallah Alizadehsani
- Institute for Intelligent Systems Research and Innovation (IISRI), Deakin University, Victoria, Australia
| | - Iman Dehzangi
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA; Department of Computer Science, Rutgers University, Camden, NJ 08102, USA
| | - Denis C Bauer
- Transformational Bioinformatics, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney, Australia; Applied BioSciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, Australia
| | - Hamid Alinejad-Rokny
- UNSW BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia; Tyree Institute of Health Engineering (IHealthE), UNSW Sydney, Sydney, NSW 2052, Australia.
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Shimojima Yamamoto K, Shimomura R, Shoji H, Yamamoto T. Glass syndrome derived from chromosomal breakage downstream region of SATB2. Brain Dev 2024:S0387-7604(24)00095-0. [PMID: 38972777 DOI: 10.1016/j.braindev.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/16/2024] [Accepted: 06/20/2024] [Indexed: 07/09/2024]
Abstract
BACKGROUND Glass syndrome, derived from chromosomal 2q33.1 microdeletions, manifests with intellectual disability, microcephaly, epilepsy, and distinctive features, including micrognathia, down-slanting palpebral fissures, cleft palate, and crowded teeth. Recently, SATB2 located within the deletion region, was identified as the causative gene responsible for Glass syndrome. Numerous disease-causing variants within the SATB2 coding region have been reported. OBJECTIVE Given the presentation of intellectual disability and multiple congenital anomalies in a patient with a de novo reciprocal translocation between chromosomes 1 and 2, disruption of the causative gene(s) was suspected. This study sought to identify the causative gene in the patient. METHODS Long-read whole-genome sequencing was performed, and the expression level of the candidate gene was analyzed. RESULTS The detection of breakpoints was successful. While the breakpoint on chromosome 1 disrupted RNF220, it was not deemed to be a genetic cause. Conversely, SATB2 is located in the approximately 100-kb telomeric region of the breakpoint on chromosome 2. The patient's clinical features resembled those of previously reported cases of Glass syndrome, despite the lack of confirmed reduced SATB2 expression. CONCLUSION The patient was diagnosed with Glass syndrome due to the similarity in clinical features. This led us to hypothesize that disruption in the downstream region of SATB2 could result in Glass syndrome. The microhomologies identified in the breakpoint junctions indicate a potential molecular mechanism involving microhomology-mediated break-induced repair mechanism or template switching.
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Affiliation(s)
- Keiko Shimojima Yamamoto
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan; Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan; Division of Gene Medicine, Graduate School of Medicine, Tokyo Women's Medical University, Tokyo, Japan
| | - Rina Shimomura
- Division of Gene Medicine, Graduate School of Medicine, Tokyo Women's Medical University, Tokyo, Japan; Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Hiromichi Shoji
- Department of Pediatrics and Adolescent Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan; Division of Gene Medicine, Graduate School of Medicine, Tokyo Women's Medical University, Tokyo, Japan.
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Chida‐Nagai A, Akagawa H, Sawai S, Ma Y, Yakuwa S, Muneuchi J, Yasuda K, Yamazawa H, Yamamoto T, Takakuwa E, Tomaru U, Furutani Y, Kato T, Harada G, Inai K, Nakanishi T, Manabe A, Takeda A, Jing Z. Identification of Prostaglandin I2 Synthase Rare Variants in Patients With Williams Syndrome and Severe Peripheral Pulmonary Stenosis. J Am Heart Assoc 2024; 13:e032872. [PMID: 38639351 PMCID: PMC11179920 DOI: 10.1161/jaha.123.032872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/18/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND Peripheral pulmonary stenosis (PPS) is a condition characterized by the narrowing of the pulmonary arteries, which impairs blood flow to the lung. The mechanisms underlying PPS pathogenesis remain unclear. Thus, the aim of this study was to investigate the genetic background of patients with severe PPS to elucidate the pathogenesis of this condition. METHODS AND RESULTS We performed genetic testing and functional analyses on a pediatric patient with PPS and Williams syndrome (WS), followed by genetic testing on 12 patients with WS and mild-to-severe PPS, 50 patients with WS but not PPS, and 21 patients with severe PPS but not WS. Whole-exome sequencing identified a rare PTGIS nonsense variant (p.E314X) in a patient with WS and severe PPS. Prostaglandin I2 synthase (PTGIS) expression was significantly downregulated and cell proliferation and migration rates were significantly increased in cells transfected with the PTGIS p.E314X variant-encoding construct when compared with that in cells transfected with the wild-type PTGIS-encoding construct. p.E314X reduced the tube formation ability in human pulmonary artery endothelial cells and caspase 3/7 activity in both human pulmonary artery endothelial cells and human pulmonary artery smooth muscle cells. Compared with healthy controls, patients with PPS exhibited downregulated pulmonary artery endothelial prostaglandin I2 synthase levels and urinary prostaglandin I metabolite levels. We identified another PTGIS rare splice-site variant (c.1358+2T>C) in another pediatric patient with WS and severe PPS. CONCLUSIONS In total, 2 rare nonsense/splice-site PTGIS variants were identified in 2 pediatric patients with WS and severe PPS. PTGIS variants may be involved in PPS pathogenesis, and PTGIS represents an effective therapeutic target.
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Affiliation(s)
- Ayako Chida‐Nagai
- Department of PediatricsHokkaido University HospitalSapporoJapan
- Department of Pediatric Cardiology and Adult Congenital CardiologyTokyo Women’s Medical UniversityTokyoJapan
| | - Hiroyuki Akagawa
- Institute for Comprehensive Medical SciencesTokyo Women’s Medical UniversityTokyoJapan
| | - Saori Sawai
- Department of PediatricsHokkaido University HospitalSapporoJapan
| | - Yue‐Jiao Ma
- Department of Cardiology, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
| | - Satoshi Yakuwa
- Department of PediatricsObihiro Kosei HospitalObihiroJapan
| | - Jun Muneuchi
- Department of Pediatrics, Kyushu HospitalJapan Community Healthcare OrganizationKitakyusyuJapan
| | - Kazushi Yasuda
- Department of Pediatric CardiologyAichi Children’s Health and Medical CenterObuJapan
| | | | - Toshiyuki Yamamoto
- Division of Gene Medicine, Graduate School of Medical ScienceTokyo Women’s Medical UniversityTokyoJapan
| | - Emi Takakuwa
- Department of Surgical PathologyHokkaido University HospitalSapporoJapan
| | - Utano Tomaru
- Department of Surgical PathologyHokkaido University HospitalSapporoJapan
| | - Yoshiyuki Furutani
- Department of Pediatric Cardiology and Adult Congenital CardiologyTokyo Women’s Medical UniversityTokyoJapan
| | - Tatsuya Kato
- Department of Thoracic SurgeryHokkaido University HospitalSapporoJapan
| | - Gen Harada
- Department of Pediatric Cardiology and Adult Congenital CardiologyTokyo Women’s Medical UniversityTokyoJapan
| | - Kei Inai
- Department of Pediatric Cardiology and Adult Congenital CardiologyTokyo Women’s Medical UniversityTokyoJapan
| | - Toshio Nakanishi
- Department of Pediatric Cardiology and Adult Congenital CardiologyTokyo Women’s Medical UniversityTokyoJapan
| | - Atsushi Manabe
- Department of PediatricsHokkaido University HospitalSapporoJapan
| | - Atsuhito Takeda
- Department of PediatricsHokkaido University HospitalSapporoJapan
| | - Zhi‐Cheng Jing
- Department of Cardiology, Guangdong Cardiovascular Institute, Guangdong Provincial People’s HospitalGuangdong Academy of Medical Sciences Southern Medical UniversityGuangzhouChina
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Allison K, Maletic-Savatic M, Pehlivan D. MECP2-related disorders while gene-based therapies are on the horizon. Front Genet 2024; 15:1332469. [PMID: 38410154 PMCID: PMC10895005 DOI: 10.3389/fgene.2024.1332469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/23/2024] [Indexed: 02/28/2024] Open
Abstract
The emergence of new genetic tools has led to the discovery of the genetic bases of many intellectual and developmental disabilities. This creates exciting opportunities for research and treatment development, and a few genetic disorders (e.g., spinal muscular atrophy) have recently been treated with gene-based therapies. MECP2 is found on the X chromosome and regulates the transcription of thousands of genes. Loss of MECP2 gene product leads to Rett Syndrome, a disease found primarily in females, and is characterized by developmental regression, motor dysfunction, midline hand stereotypies, autonomic nervous system dysfunction, epilepsy, scoliosis, and autistic-like behavior. Duplication of MECP2 causes MECP2 Duplication Syndrome (MDS). MDS is found mostly in males and presents with developmental delay, hypotonia, autistic features, refractory epilepsy, and recurrent respiratory infections. While these two disorders share several characteristics, their differences (e.g., affected sex, age of onset, genotype/phenotype correlations) are important to distinguish in the light of gene-based therapy because they require opposite solutions. This review explores the clinical features of both disorders and highlights these important clinical differences.
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Affiliation(s)
- Katherine Allison
- Royal College of Surgeons in Ireland, School of Medicine, Dublin, Ireland
| | - Mirjana Maletic-Savatic
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, United States
| | - Davut Pehlivan
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, United States
- Blue Bird Circle Rett Center, Texas Children's Hospital, Houston, TX, United States
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Wang Z, Niu M, Zheng N, Meng J, Jiang Y, Yang D, Yao P, Yao T, Luo H, Xu H, Ge Y, Zhang YW, Zhang X. Increased level of RAB39B leads to neuronal dysfunction and behavioural changes in mice. J Cell Mol Med 2023; 27:1214-1226. [PMID: 36977207 PMCID: PMC10148058 DOI: 10.1111/jcmm.17704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 01/22/2023] [Accepted: 02/22/2023] [Indexed: 03/30/2023] Open
Abstract
Duplications of the Xq28 region are a common cause of X-linked intellectual disability (XLID). The RAB39B gene locates in Xq28 and has been implicated in disease pathogenesis. However, whether increased dosage of RAB39B leads to cognitive impairment and synaptic dysfunction remains elusive. Herein, we overexpressed RAB39B in mouse brain by injecting AAVs into bilateral ventricles of neonatal animals. We found that at 2 months of age, neuronal overexpression of RAB39B impaired the recognition memory and the short-term working memory in mice and resulted in certain autism-like behaviours, including social novelty defect and repetitive grooming behaviour in female mice. Moreover, overexpression of RAB39B decreased dendritic arborization of primary neurons in vitro and reduced synaptic transmission in female mice. Neuronal overexpression of RAB39B also altered autophagy without affecting levels and PSD distribution of synaptic proteins. Our results demonstrate that overexpression of RAB39B compromises normal neuronal development, thereby resulting in dysfunctional synaptic transmission and certain intellectual disability and behavioural abnormalities in mice. These findings identify a molecular mechanism underlying XLID with increased copy numbers of Xq28 and provide potential strategies for disease intervention.
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Affiliation(s)
- Zijie Wang
- Center for Brain Sciences, the First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, China
- Department of Neurosurgery, Xiang'an Hospital of Xiamen University, Xiamen, China
| | - Mengxi Niu
- Center for Brain Sciences, the First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, China
| | - Naizhen Zheng
- Center for Brain Sciences, the First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, China
| | - Jian Meng
- Center for Brain Sciences, the First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, China
| | - Yiru Jiang
- Center for Brain Sciences, the First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, China
| | - Dingting Yang
- Center for Brain Sciences, the First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, China
| | - Peijie Yao
- Center for Brain Sciences, the First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, China
| | - Tingting Yao
- Center for Brain Sciences, the First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, China
| | - Hong Luo
- Center for Brain Sciences, the First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, China
| | - Huaxi Xu
- Center for Brain Sciences, the First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, China
| | - Yunlong Ge
- Department of Neurosurgery, Xiang'an Hospital of Xiamen University, Xiamen, China
| | - Yun-Wu Zhang
- Center for Brain Sciences, the First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, China
| | - Xian Zhang
- Center for Brain Sciences, the First Affiliated Hospital of Xiamen University, Institute of Neuroscience, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, School of Medicine, Xiamen University, Xiamen, China
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Tamura T, Shimojima Yamamoto K, Imaizumi T, Yamamoto H, Miyamoto Y, Yagasaki H, Morioka I, Kanno H, Yamamoto T. Breakpoint analysis for cytogenetically balanced translocation revealed unexpected complex structural abnormalities and suggested the position effect for MEF2C. Am J Med Genet A 2023; 191:1632-1638. [PMID: 36916329 DOI: 10.1002/ajmg.a.63182] [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: 11/08/2022] [Revised: 01/27/2023] [Accepted: 03/02/2023] [Indexed: 03/15/2023]
Abstract
Many disease-causing genes have been identified by determining the breakpoints of balanced chromosomal translocations. Recent progress in genomic analysis has accelerated the analysis of chromosomal translocation-breakpoints at the nucleotide level. Using a long-read whole-genome sequence, we analyzed the breakpoints of the cytogenetically balanced chromosomal translocation t(5;15)(q21;26.3), which was confirmed to be of de novo origin, in a patient with a neurodevelopmental disorder. The results showed complex rearrangements with seven fragments consisting of five breakpoint-junctions (BJs). Four of the five BJs showed microhomologies of 1-3-bp, and only one BJ displayed a signature of blunt-end ligation, indicating chromothripsis as the underlying mechanism. Although the BJs did not disrupt any disease-causing gene, the clinical features of the patient were compatible with MEF2C haploinsufficiency syndrome. Complex rearrangements were located approximately 2.5-Mb downstream of MEF2C. Therefore, position effects were considered the mechanism of the occurrence of MEF2C haploinsufficiency syndrome.
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Affiliation(s)
- Takeaki Tamura
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan.,Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan.,Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
| | - Keiko Shimojima Yamamoto
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Taichi Imaizumi
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Hisako Yamamoto
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yusaku Miyamoto
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Hiroshi Yagasaki
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Ichiro Morioka
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Hitoshi Kanno
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Toshiyuki Yamamoto
- Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
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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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9
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Tamura T, Yamamoto Shimojima K, Okamoto N, Yagasaki H, Morioka I, Kanno H, Minakuchi Y, Toyoda A, Yamamoto T. Long-read sequence analysis for clustered genomic copy number aberrations revealed architectures of intricately intertwined rearrangements. Am J Med Genet A 2023; 191:112-119. [PMID: 36282026 DOI: 10.1002/ajmg.a.62997] [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: 05/22/2022] [Revised: 07/13/2022] [Accepted: 08/24/2022] [Indexed: 12/14/2022]
Abstract
Most chromosomal aberrations revealed by chromosomal microarray testing (CMA) are simple; however, very complex chromosomal structural rearrangements can also be found. Although the mechanism of structural rearrangements has been gradually revealed, not all mechanisms have been elucidated. We analyzed the breakpoint-junctions (BJs) of two or more clustered copy number variations (CNVs) in the same chromosome arms to understand their conformation and the mechanism of complex structural rearrangements. Combining CMA with long-read whole-genome sequencing (WGS) analysis, we successfully determined all BJs for the clustered CNVs identified in four patients. Multiple CNVs were intricately intertwined with each other, and clustered CNVs in four patients were involved in global complex chromosomal rearrangements. The BJs of two clustered deletions identified in two patients showed microhomologies, and their characteristics were explained by chromothripsis. In contrast, the BJs in the other two patients, who showed clustered deletions and duplications, consisted of blunt-end and nontemplated insertions. These findings could be explained only by alternative nonhomologous end-joining, a mechanism related to polymerase theta. All the patients had at least one inverted segment. Three patients showed cryptic aberrations involving a disruption and a deletion/duplication, which were not detected by CMA but were first identified by WGS. This result suggested that complex rearrangements should be considered if clustered CNVs are observed in the same chromosome arms. Because CMA has potential limitations in genotype-phenotype correlation analysis, a more detailed analysis by whole genome examination is recommended in cases of suspected complex structural aberrations.
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Affiliation(s)
- Takeaki Tamura
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan.,Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan.,Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
| | - Keiko Yamamoto Shimojima
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Hiroshi Yagasaki
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Ichiro Morioka
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Hitoshi Kanno
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Yohei Minakuchi
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Toshiyuki Yamamoto
- Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
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10
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Hara-Isono K, Nakamura A, Fuke T, Inoue T, Kawashima S, Matsubara K, Sano S, Yamazawa K, Fukami M, Ogata T, Kagami M. Pathogenic Copy Number and Sequence Variants in Children Born SGA With Short Stature Without Imprinting Disorders. J Clin Endocrinol Metab 2022; 107:e3121-e3133. [PMID: 35583390 DOI: 10.1210/clinem/dgac319] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Indexed: 11/19/2022]
Abstract
CONTEXT Children born small-for-gestational-age with short stature (SGA-SS) is associated with (epi)genetic defects, including imprinting disorders (IDs), pathogenic copy number variants (PCNVs), and pathogenic variants of genes involved in growth. However, comprehensive studies evaluating these 3 factors are very limited. OBJECTIVE To clarify the contribution of PCNVs and candidate pathogenic variants to SGA-SS. DESIGN Comprehensive molecular analyses consisting of methylation analysis, copy number analysis, and multigene sequencing. METHODS We enrolled 140 patients referred to us for genetic testing for SGA-SS. Among them, we excluded 42 patients meeting Netchine-Harbison clinical scoring system criteria for Silver-Russell syndrome and 4 patients with abnormal methylation levels of the IDs-related differentially methylated regions. Consequently, we conducted copy number analysis and multigene sequencing for 86 SGA-SS patients with sufficient sample volume. We also evaluated clinical phenotypes of patients with PCNVs or candidate pathogenic variants. RESULTS We identified 8 (9.3%) and 11 (12.8%) patients with PCNVs and candidate pathogenic variants, respectively. According to the American College of Medical Genetics standards and guidelines, 5 variants were classified as pathogenic and the remaining 6 variants were classified as variants of unknown significance. Genetic diagnosis was made in 12 patients. All patients with PCNVs or candidate pathogenic variants did not correspond perfectly to characteristic clinical features of each specific genetic cause. CONCLUSION We clarified the contribution of PCNVs and pathogenic variants to SGA-SS without IDs. Comprehensive molecular analyses, including copy number analysis and multigene sequencing, should be considered for patients with unknown SGA-SS etiology.
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Affiliation(s)
- Kaori Hara-Isono
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
- Department of Pediatrics, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Akie Nakamura
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
- Department of Pediatrics, Hokkaido University Graduate School of Medicine, Sapporo 060-8648, Japan
| | - Tomoko Fuke
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Takanobu Inoue
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Sayaka Kawashima
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Shinichiro Sano
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
- Department of Endocrinology and Metabolism, Shizuoka Children's Hospital, Shizuoka 420-8660, Japan
| | - Kazuki Yamazawa
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
- Medical Genetics Center, National Hospital Organization Tokyo Medical Center, Tokyo 152-8902, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Tsutomu Ogata
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
- Department of Pediatrics, Hamamatsu Medical Center, Hamamatsu 432-8580, Japan
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
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11
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Chien YC, Chen JS, Shiao YM, Hsiao CH. Prenatal diagnosis of de novo int22h1/int22h2-mediated Xq28 duplication syndrome involving RAB39B following a previous ambiguous genitalia pregnancy. Taiwan J Obstet Gynecol 2022; 61:501-503. [PMID: 35595445 DOI: 10.1016/j.tjog.2022.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2021] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVE To report a prenatal diagnosis of int22h1/int22h2-mediated Xq28 duplication syndrome. CASE REPORT Herein, we present the case of a 28-year-old female who had a previous ambiguous genitalia pregnancy without genetic abnormality that was terminated at 23+2 weeks of gestation. The fetus of the current pregnancy harbored a de novo copy number variation at the Xq recurrent region (int22h1/int22h2-flanked; including the RAB39B gene) with a 0.397 Mb microduplication. The literature suggests the clinical manifestation of int22h1/int22h2-mediated Xq28 duplication syndrome tends to show a milder clinical phenotype in females than males. Although the fetus in this case was female, taking into consideration the parents' age and culture, the family decided to terminate this pregnancy due to the genetic abnormality. CONCLUSION Prenatally diagnosed de novo int22h-1/int22h-2-mediated Xq28 duplication syndrome exhibits variable phenotypic traits in female fetuses.
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Affiliation(s)
- Yung Chen Chien
- Department of Medical Education, Taipei Medical University Hospital, Taiwan
| | - Jia Shing Chen
- School of Medicine for International Students, I-Shou University, Kaohsiung, Taiwan
| | - Yu Ming Shiao
- Department of Bioscience Technology, Chung Yuan Christian University, Taiwan
| | - Ching Hua Hsiao
- Department of Obstetrics and Gynecology, Taipei City Hospital, Women and Children Campus, Taiwan; Department of Biomedical Engineering, National Yang Ming Chiao Tung University, Yang Ming Campus, Taiwan.
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12
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A brief history of MECP2 duplication syndrome: 20-years of clinical understanding. Orphanet J Rare Dis 2022; 17:131. [PMID: 35313898 PMCID: PMC8939085 DOI: 10.1186/s13023-022-02278-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 03/07/2022] [Indexed: 11/10/2022] Open
Abstract
MECP2 duplication syndrome (MDS) is a rare, X-linked, neurodevelopmental disorder caused by a duplication of the methyl-CpG-binding protein 2 (MECP2) gene-a gene in which loss-of-function mutations lead to Rett syndrome (RTT). MDS has an estimated live birth prevalence in males of 1/150,000. The key features of MDS include intellectual disability, developmental delay, hypotonia, seizures, recurrent respiratory infections, gastrointestinal problems, behavioural features of autism and dysmorphic features-although these comorbidities are not yet understood with sufficient granularity. This review has covered the past two decades of MDS case studies and series since the discovery of the disorder in 1999. After comprehensively reviewing the reported characteristics, this review has identified areas of limited knowledge that we recommend may be addressed by better phenotyping this disorder through an international data collection. This endeavour would also serve to delineate the clinical overlap between MDS and RTT.
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13
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Bastos PAD, Barbosa R. A Newly Identified Int22h1/Int22h2‐Mediated Xq28 Duplication Syndrome Case Misdiagnosed as Cerebral Palsy. JOURNAL OF PEDIATRIC NEUROLOGY 2022. [DOI: 10.1055/s-0042-1743435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
AbstractCerebral palsy (CP) is a nonprogressive, early-onset neurodevelopmental disorder affecting ∼2 to 3/1,000 children worldwide. It is characterized by movement/postural disabilities accompanied by sensitive, perceptual, cognitive, communicational, behavioral, and musculoskeletal perturbations. Many CP patients are thought to have genetic etiologies overlapping those of other neurodevelopmental conditions. Herein, we reported a newly discovered case (the 36th case to date) of a female patient (misdiagnosed with CP until age 19) with the rare X-linked intellectual disability syndrome resulting from an int22h1/int22h2-mediated Xq28 duplication. A microarray analysis revealed a ∼0.4 Mb duplication within the 154.1 to 154.6 Mb subregion of Xq28 (hg19, CRCh37), confirming a diagnosis of the rare int22h1/int22h2-mediated Xq28 duplication intellectual disability syndrome. Atypical T2 hyperintensities were also observed. This case report builds upon the limited cohort of X-linked intellectual disability syndrome patients and reiterates the growing observations pertaining to the phenotypic overlap between genetic CP cases and other neurodevelopmental disorders.
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Affiliation(s)
- Paulo André Dias Bastos
- Chronic Diseases Research Centre, NOVA Medical School, Faculty of Medical Sciences, Universidade Nova de Lisboa, Lisbon, Portugal
- Department of Neurology, Hospital de Egas Moniz, Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - Raquel Barbosa
- Chronic Diseases Research Centre, NOVA Medical School, Faculty of Medical Sciences, Universidade Nova de Lisboa, Lisbon, Portugal
- Department of Neurology, Hospital de Egas Moniz, Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
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14
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Genomic Aberrations Associated with the Pathophysiological Mechanisms of Neurodevelopmental Disorders. Cells 2021; 10:cells10092317. [PMID: 34571966 PMCID: PMC8470284 DOI: 10.3390/cells10092317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/30/2021] [Accepted: 09/03/2021] [Indexed: 12/27/2022] Open
Abstract
Genomic studies are increasingly revealing that neurodevelopmental disorders are caused by underlying genomic alterations. Chromosomal microarray testing has been used to reliably detect minute changes in genomic copy numbers. The genes located in the aberrated regions identified in patients with neurodevelopmental disorders may be associated with the phenotypic features. In such cases, haploinsufficiency is considered to be the mechanism, when the deletion of a gene is related to neurodevelopmental delay. The loss-of-function mutation in such genes may be evaluated using next-generation sequencing. On the other hand, the patients with increased copy numbers of the genes may exhibit different clinical symptoms compared to those with loss-of-function mutation in the genes. In such cases, the additional copies of the genes are considered to have a dominant negative effect, inducing cell stress. In other cases, not the copy number changes, but mutations of the genes are responsible for causing the clinical symptoms. This can be explained by the dominant negative effects of the gene mutations. Currently, the diagnostic yield of genomic alterations using comprehensive analysis is less than 50%, indicating the existence of more subtle alterations or genomic changes in the untranslated regions. Copy-neutral inversions and insertions may be related. Hence, better analytical algorithms specialized for the detection of such alterations are required for higher diagnostic yields.
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15
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The int22h1/int22h2-Mediated Xq28 Duplication Syndrome: An Intersection between Neurodevelopment, Immunology, and Cancer. Genes (Basel) 2021; 12:genes12060860. [PMID: 34199727 PMCID: PMC8229372 DOI: 10.3390/genes12060860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/30/2021] [Accepted: 06/02/2021] [Indexed: 11/23/2022] Open
Abstract
The int22h1/int22h2-mediated Xq28 duplication syndrome is a rare X-linked intellectual disability syndrome (XLIDS) arising from a duplication of the segment between intron 22 homologous regions 1 and 2, on the q28 subregion of the X chromosome. The main clinical features of the syndrome include intellectual disability, neurobehavioral abnormalities, and dysmorphic facial features. Due to the X-linked nature of the syndrome, affected males exhibit more severe phenotypes compared with heterozygous females. A unique distinguishing feature of the syndrome across the sexes, however, is a peculiar combination of recurrent sinopulmonary infections and atopy exclusively seen in a subset of affected males. In addition to the ‘typical’ 0.5 Mb duplication detected in most cases reported to date with the syndrome, a shortened centromeric version, and another 0.2 Mb telomerically shifted one, have been recently identified, with most detected duplications being maternally inherited, except for three recent cases found to have de novo duplications. Interestingly, a recently reported case of an affected male suggests a possible association of the syndrome with multiple malignancies, an observation that has been recently replicated in two pediatric patients. As a result, a better understanding of the pathogenesis of int22h1/int22h2-mediated Xq28 duplication syndrome may grant us a better understanding of the sex-specific differences in immunological responses, as well as the potential role of the genes involved by the duplication, in oncogenesis.
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16
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MECP2-Related Disorders and Epilepsy Phenotypes. JOURNAL OF PEDIATRIC NEUROLOGY 2021. [DOI: 10.1055/s-0041-1728643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Abstract
MECP2 (methyl-CpG binding protein-2) gene, located on chromosome Xq28, encodes for a protein particularly abundant in the brain that is required for maturation of astrocytes and neurons and is developmentally regulated. A defective homeostasis of MECP2 expression, either by haploinsufficiency or overexpression, leads to a neurodevelopmental phenotype. As MECP2 is located on chromosome X, the clinical presentation varies in males and females ranging from mild learning disabilities to severe encephalopathies and early death. Typical Rett syndrome (RTT), the most frequent phenotype associated with MECP2 mutations, primarily affects girls and it was previously thought to be lethal in males; however, MECP2 duplication syndrome, resulting from a duplication of the Xq28 region including MECP2, leads to a severe neurodevelopmental disorder in males. RTT and MECP2 duplication syndrome share overlapping clinical phenotypes including intellectual disabilities, motor deficits, hypotonia, progressive spasticity, and epilepsy. In this manuscript we reviewed literature on epilepsy related to MECP2 disorders, focusing on clinical presentation, genotype–phenotype correlation, and treatment.
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17
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Tang BL. RAB39B's role in membrane traffic, autophagy, and associated neuropathology. J Cell Physiol 2020; 236:1579-1592. [PMID: 32761840 DOI: 10.1002/jcp.29962] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/19/2020] [Accepted: 07/13/2020] [Indexed: 12/14/2022]
Abstract
Neuropathological disorders are increasingly associated with dysfunctions in neuronal membrane traffic and autophagy, with defects among members of the Rab family of small GTPases implicated. Mutations in the human Xq28 localized gene RAB39B have been associated with X-linked neurodevelopmental defects including macrocephaly, intellectual disability, autism spectrum disorder (ASD), as well as rare cases of early-onset Parkinson's disease (PD). Despite the finding that RAB39B regulates GluA2 trafficking and could thus influence synaptic α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor subunit composition, reasons for the wide-ranging neuropathological consequences associated with RAB39B defects have been unclear. Recent studies have now unraveled possible mechanisms underlying the neuropathological roles of this brain-enriched small GTPase. Studies in RAB39B knockout mice showed that RAB39B interacts with components of Class I phosphatidylinositol-3-kinase (PI3K) signaling. In its absence, the PI3K-AKT-mechanistic target of rapamycin signaling pathway in neural progenitor cells (NPCs) is hyperactivated, which promotes NPC proliferation, leading to macrocephaly and ASD. Pertaining to early-onset PD, a complex of C9orf72, Smith-Magenis syndrome chromosome region candidate 8 and WD repeat domain 41 that functions in autophagy has been identified as a guanine nucleotide exchange factor of RAB39B. Here, recent findings that have shed light on our mechanistic understanding of RAB39B's role in neurodevelopmental and neurodegenerative pathologies are reviewed. Caveats and unanswered questions are also discussed, and future perspectives outlined.
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Affiliation(s)
- Bor Luen Tang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Graduate School of Integrative Sciences and Engineering, National University of Singapore, Singapore
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18
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Gao Y, Wilson GR, Salce N, Romano A, Mellick GD, Stephenson SEM, Lockhart PJ. Genetic Analysis of RAB39B in an Early-Onset Parkinson's Disease Cohort. Front Neurol 2020; 11:523. [PMID: 32670181 PMCID: PMC7332711 DOI: 10.3389/fneur.2020.00523] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 05/12/2020] [Indexed: 12/12/2022] Open
Abstract
Pathogenic variants in the gene encoding RAB39B, resulting in the loss of protein function, lead to the development of X-linked early-onset parkinsonism. The gene is located within a chromosomal region that is susceptible to genomic rearrangement, and while an increased dosage of RAB39B was previously associated with cognitive impairment, the potential role of dosage alterations in Parkinson's disease (PD) remains to be determined. This study aimed to investigate the contribution of the genetic variation in RAB39B to the development of early-onset PD. We performed gene dosage studies and sequence analysis in a cohort of 176 individuals with early-onset PD (age of onset ≤ 50 years) of unknown genetic etiology. An assessment of the copy number variation over both coding exons and the 3' untranslated region (UTR) of RAB39B did not identify any alterations in gene dosage. An analysis of the UTRs identified two male individuals carrying single, likely benign, nucleotide variants in the 3'UTR (chrX:154489749-A-G and chrX:154489197-T-G). Furthermore, one novel variant of uncertain significance was identified in the 5'UTR, 229 bp upstream of the start codon (chrX:154493802-C-T). In silico analyses predicted that this variant disrupts a highly conserved transcription factor binding site and could impact RAB39B expression. The results of this study do not support a significant role for genetic variation in RAB39B as contributing to early-onset PD but do highlight that additional molecular studies are required to determine the mechanisms regulating RAB39B expression and their association with the disease. Genetic investigations in larger parkinsonism/PD cohorts and longitudinal studies of individuals with cognitive impairment due to an altered dosage of RAB39B will be required to fully delineate the contribution of RAB39B to parkinsonism.
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Affiliation(s)
- Yujing Gao
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Gabrielle R Wilson
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Nicholas Salce
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Alexandra Romano
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - George D Mellick
- Griffith Institute for Drug Discovery (GRIDD), Griffith University, Nathan, QLD, Australia
| | - Sarah E M Stephenson
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
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19
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Ballout RA, Dickerson C, Wick MJ, Al-Sweel N, Openshaw AS, Srivastava S, Swanson LC, Bramswig NC, Kuechler A, Hong B, Fleming LR, Curry K, Robertson SP, Andersen EF, El-Hattab AW. Int22h1/Int22h2-mediated Xq28 duplication syndrome: de novo duplications, prenatal diagnoses, and additional phenotypic features. Hum Mutat 2020; 41:1238-1249. [PMID: 32112660 DOI: 10.1002/humu.24009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/25/2020] [Accepted: 02/27/2020] [Indexed: 12/11/2022]
Abstract
Int22h1/Int22h2-mediated Xq28 duplication syndrome is a relatively new X-linked intellectual disability syndrome, arising from duplications of the subregion flanked by intron 22 homologous regions 1 and 2 on the q arm of chromosome X. Its primary manifestations include variable cognitive deficits, distinct facial dysmorphia, and neurobehavioral abnormalities that mainly include hyperactivity, irritability, and autistic behavior. Affected males are hemizygous for the duplication, which explains their often more severe manifestations compared with heterozygous females. In this report, we describe the cases of nine individuals recently identified having the syndrome, highlighting unique and previously unreported findings of this syndrome. Specifically, we report for the first time in this syndrome, two cases with de novo duplications, three receiving prenatal diagnosis with the syndrome, and three others having atypical versions of the duplication. Among the latter, one proband has a shortened version spanning only the centromeric half of the typical duplication, while the other two cases have a nearly identical length duplication as the classical duplication, with the exception that their duplication's breakpoints are telomerically shifted by about 0.2 Mb. Finally, we shed light on two new manifestations in this syndrome, vertebral anomalies and multiple malignancies, which possibly expand the phenotypic spectrum of the syndrome.
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Affiliation(s)
- Rami A Ballout
- Lipoprotein Metabolism Section, Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland.,Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Cheryl Dickerson
- WakeMed Physician Practices, Maternal-Fetal Medicine, Raleigh, North Carolina
| | - Myra J Wick
- Departments of Obstetrics and Gynecology and Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Najla Al-Sweel
- Department of Pathology, University of Utah, Salt Lake City, Utah.,ARUP Laboratories, Cytogenetics and Genomic Microarray, Salt Lake City, Utah
| | - Amanda S Openshaw
- ARUP Laboratories, Cytogenetics and Genomic Microarray, Salt Lake City, Utah
| | | | - Lindsay C Swanson
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts
| | - Nuria C Bramswig
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Alma Kuechler
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Bo Hong
- Department of Pathology, University of Utah, Salt Lake City, Utah.,ARUP Laboratories, Cytogenetics and Genomic Microarray, Salt Lake City, Utah
| | - Leah R Fleming
- St. Luke's Children's Genetics and Metabolic Clinic, Boise, Idaho
| | - Kathryn Curry
- St. Luke's Children's Genetics and Metabolic Clinic, Boise, Idaho
| | - Stephen P Robertson
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Erica F Andersen
- Department of Pathology, University of Utah, Salt Lake City, Utah.,ARUP Laboratories, Cytogenetics and Genomic Microarray, Salt Lake City, Utah
| | - Ayman W El-Hattab
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, UAE
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20
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Imaizumi T, Yamamoto-Shimojima K, Yamamoto H, Yamamoto T. Establishment of a simple and rapid method to detect MECP2 duplications using digital polymerase chain reaction. Congenit Anom (Kyoto) 2020; 60:10-14. [PMID: 30684281 DOI: 10.1111/cga.12325] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 11/30/2022]
Abstract
Genomic copy number variations (CNVs) can be detected by chromosomal microarray testing. However, upon final diagnosis, other methods may be recommended for a validation method to confirm CNVs. Trio analyses or carrier detection in family members are also frequently required. Previously, fluorescence in situ hybridization and/or quantitative PCR have been used; however, these methods present limitations. The purpose of this study was to establish a simple and rapid method to detect genomic copy numbers. We utilized droplet digital PCR (dPCR) with an intercalation method. Thirteen patients, who were diagnosed with MECP2 duplications via chromosomal microarray testing, were enrolled in this study. Four of their female relatives, who were verified as carriers of MECP2 duplications, were also included. Genomic copy numbers of MECP2 and IRAK1 were analyzed in comparison with reference genes: XIST and AR on the X-chromosome, and RPP30 and RPPH1 on the autosomal chromosomes. As a result, genomic copy numbers of MECP2 were rapidly and precisely detected by the dPCR system established in this study. This method can be widely applied as a diagnostic method to confirm CNVs on other chromosomal regions.
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Affiliation(s)
- Taichi Imaizumi
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Keiko Yamamoto-Shimojima
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan.,Tokyo Women's Medical University, Institute of Integrated Medical Sciences, Tokyo, Japan
| | - Hitoshi Yamamoto
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan.,Tokyo Women's Medical University, Institute of Integrated Medical Sciences, Tokyo, Japan
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21
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Yamamoto T, Imaizumi T, Yamamoto-Shimojima K, Lu Y, Yanagishita T, Shimada S, Chong PF, Kira R, Ueda R, Ishiyama A, Takeshita E, Momosaki K, Ozasa S, Akiyama T, Kobayashi K, Oomatsu H, Kitahara H, Yamaguchi T, Imai K, Kurahashi H, Okumura A, Oguni H, Seto T, Okamoto N. Genomic backgrounds of Japanese patients with undiagnosed neurodevelopmental disorders. Brain Dev 2019; 41:776-782. [PMID: 31171384 DOI: 10.1016/j.braindev.2019.05.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 05/08/2019] [Accepted: 05/21/2019] [Indexed: 01/07/2023]
Abstract
BACKGROUND Recently, many genes related to neurodevelopmental disorders have been identified by high-throughput genomic analysis; however, a comprehensive understanding of the mechanism underlying neurodevelopmental disorders remains to be established. To further understand these underlying mechanisms, we performed a comprehensive genomic analysis of patients with undiagnosed neurodevelopmental disorders. METHODS Genomic analysis using next-generation sequencing with a targeted panel was performed for a total of 133 Japanese patients (male/female, 81/52) with previously undiagnosed neurodevelopmental disorders, including developmental delay (DD), intellectual disability (ID), autism spectrum disorder (ASD), and epilepsy. Genomic copy numbers were also analyzed using the eXome Hidden Markov Model (XHMM). RESULTS Thirty-nine patients (29.3%) exhibited pathogenic or likely pathogenic findings with single-gene variants or chromosomal aberrations. Among them, 20 patients were presented here. Pathogenic or likely pathogenic variants were identified in 18 genes, including ACTG1, CACNA1A, CHD2, CDKL5, DNMT3A, EHMT1, GABRB3, GABRG2, GRIN2B, KCNQ3, KDM5C, MED13L, SCN2A, SHANK3, SMARCA2, STXBP1, SYNGAP1, and TBL1XR1. CONCLUSION A diagnostic yield of 29.3% in this study was nearly the same as that previously reported from other countries. Thus, we suggest that there is no difference in genomic backgrounds in Japanese patients with undiagnosed neurodevelopmental disabilities. Although most of the patients possessed de novo variants, one of the patients showed an X-linked inheritance pattern. As X-linked recessive disorders exhibit the possibility of recurrent occurrence in the family, comprehensive molecular diagnosis is important for genetic counseling.
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Affiliation(s)
- Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan; Tokyo Women's Medical University Institute of Integrated Medical Sciences, Tokyo, Japan.
| | - Taichi Imaizumi
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan; Department of Pediatrics, St. Mariannna University School of Medicine, Kawasaki, Japan
| | - Keiko Yamamoto-Shimojima
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan; Tokyo Women's Medical University Institute of Integrated Medical Sciences, Tokyo, Japan
| | - Yongping Lu
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Tomoe Yanagishita
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan; Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Shino Shimada
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Pin Fee Chong
- Department of Pediatric Neurology, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Ryutaro Kira
- Department of Pediatric Neurology, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Riyo Ueda
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Akihiko Ishiyama
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Eri Takeshita
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Ken Momosaki
- Department of Pediatrics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Shiro Ozasa
- Department of Pediatrics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Tomoyuki Akiyama
- Department of Child Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Katsuhiro Kobayashi
- Department of Child Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Hiroo Oomatsu
- Department of Pediatrics, National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Japan
| | - Hikaru Kitahara
- Department of Pediatrics, National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Japan
| | - Tokito Yamaguchi
- Department of Pediatrics, National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Japan
| | - Katsumi Imai
- Department of Pediatrics, National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Japan
| | | | - Akihisa Okumura
- Department of Pediatrics, Aichi Medical University, Nagakute, Japan
| | - Hirokazu Oguni
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Toshiyuki Seto
- Department of Pediatrics, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Japan
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22
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Marafi D, Suter B, Schultz R, Glaze D, Pavlik VN, Goldman AM. Spectrum and time course of epilepsy and the associated cognitive decline in MECP2 duplication syndrome. Neurology 2018; 92:e108-e114. [PMID: 30552298 DOI: 10.1212/wnl.0000000000006742] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/12/2018] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE We characterized the epilepsy features and contribution to cognitive regression in 47 patients with MECP2 duplication syndrome (MDS) and reviewed these characteristics in over 280 MDS published cases. METHODS The institutional review board approved this retrospective review of medical records and case histories of patients with MDS. RESULTS The average age at enrollment was 10 ± 7 years. Patients with epilepsy were older (13 ± 7 years vs 8 ± 5 years, p = 0.004) and followed for a longer time (11.8 ± 6.5 years vs 6.3 ± 4.2 years, p = 0.003) than patients without a seizure disorder. Epilepsy affected 22/47 (47%) patients with MDS. It was treatment-refractory and consistent with epileptic encephalopathy in 18/22 (82%) cases. Lennox-Gastaut syndrome (LGS) was present in 12/22 (55%) patients and manifested between late childhood and adulthood in 83% of cases. The emergence of neurologic regression coincided with the onset of epilepsy. The MECP2 duplication size and gene content did not correlate with epilepsy presence, type, age at onset, or treatment responsiveness. CONCLUSION Epilepsy in MDS is common, often severe, and medically refractory. LGS occurs frequently and may have a late onset. Developmental regression often follows the onset of epilepsy. The MECP2 duplication extent and gene content do not discriminate between patients with or without epilepsy. Our findings inform clinical care and family counseling with respect to early epilepsy recognition, diagnosis, specialty referral, and implementation of aggressive seizure therapy to minimize detrimental effect of uncontrolled seizures on cognitive functions or preexisting neurologic deficits.
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Affiliation(s)
- Dana Marafi
- From the Departments of Neurology (D.M., B.S., R.S., D.G., V.N.P., A.M.G.) and Pediatrics (R.S., D.G.), Baylor College of Medicine, Houston, TX
| | - Bernhard Suter
- From the Departments of Neurology (D.M., B.S., R.S., D.G., V.N.P., A.M.G.) and Pediatrics (R.S., D.G.), Baylor College of Medicine, Houston, TX
| | - Rebecca Schultz
- From the Departments of Neurology (D.M., B.S., R.S., D.G., V.N.P., A.M.G.) and Pediatrics (R.S., D.G.), Baylor College of Medicine, Houston, TX
| | - Daniel Glaze
- From the Departments of Neurology (D.M., B.S., R.S., D.G., V.N.P., A.M.G.) and Pediatrics (R.S., D.G.), Baylor College of Medicine, Houston, TX
| | - Valory N Pavlik
- From the Departments of Neurology (D.M., B.S., R.S., D.G., V.N.P., A.M.G.) and Pediatrics (R.S., D.G.), Baylor College of Medicine, Houston, TX
| | - Alica M Goldman
- From the Departments of Neurology (D.M., B.S., R.S., D.G., V.N.P., A.M.G.) and Pediatrics (R.S., D.G.), Baylor College of Medicine, Houston, TX.
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23
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Yao R, Yu T, Qing Y, Wang J, Shen Y. Evaluation of copy number variant detection from panel-based next-generation sequencing data. Mol Genet Genomic Med 2018; 7:e00513. [PMID: 30565893 PMCID: PMC6382442 DOI: 10.1002/mgg3.513] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/21/2018] [Accepted: 10/26/2018] [Indexed: 12/23/2022] Open
Abstract
Background Targeted gene capture and next‐generation sequencing (NGS) has been widely utilized as a robust and cost‐effective approach for detecting small variants among a group of disease genes. Copy number variations (CNV) can also be inferred from the read‐depth information but the accuracy of CNVs called from panel‐based NGS data has not been well evaluated. Methods Sequencing data were acquired from patients underwent routine clinical targeted panel sequencing testing. Pathogenic CNVs detected from targeted panel sequencing data were evaluated using CNVs generated by two clinical accepted platforms, namely chromosome microarray analysis (CMA) and multiple ligation‐dependent probe amplification (MLPA) as benchmarks. CNVkit was used in our study to call CNVs from sequencing data using read‐depth information. CMA and MLPA tests were used to confirm and further assess the size and breakpoints of CNVs. Results The size of CNVs detected using panel‐based NGS data are over 300 kb. The sizes of CNVs detected are slightly larger (102.3% on average) using the NGS platform than using the CMA platform, and the size accuracy improved as the size of variants increases. The breakpoints of CNVs detected using NGS data are quite close (within 2.3% of margin) to the breakpoints detected by CMA. CNVs on sex chromosomes, however, are less concordant between NGS and CMA platforms. Conclusion Copy number variations covering adequate exons on autosomes can be accurately detected using targeted panel sequencing data as using CMA. CNVs detected from sex chromosomes need further evaluation and validation. Except for exon‐level deletion/duplication and CNV on sex chromosome, our data support the use of panel‐based NGS data for routine clinical detection of pathogenic CNVs.
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Affiliation(s)
- Ruen Yao
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute for Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Tingting Yu
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute for Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yanrong Qing
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute for Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute for Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yiping Shen
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
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24
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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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25
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Characteristics of rare and private deletions identified in phenotypically normal individuals. Hum Genome Var 2017; 4:17037. [PMID: 28912957 PMCID: PMC5597573 DOI: 10.1038/hgv.2017.37] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 07/10/2017] [Accepted: 07/10/2017] [Indexed: 11/13/2022] Open
Abstract
Genomic copy number variations (CNVs) identified through chromosomal microarray testing must be validated to confirm whether they are pathogenically and functionally relevant to their respective clinical features. Although larger deletions have a higher probability to be pathogenic, this is not always true. Phenotypically normal individuals showed five CNV deletions larger than 1.5 Mb. The genes related to autosomal dominant trait were absent within these CNV deletions.
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26
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Yon DK, Park JE, Kim SJ, Shim SH, Chae KY. A sibship with duplication of Xq28 inherited from the mother; genomic characterization and clinical outcomes. BMC MEDICAL GENETICS 2017; 18:30. [PMID: 28302064 PMCID: PMC5356410 DOI: 10.1186/s12881-017-0394-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 03/07/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND Loss-of-function mutations in methyl-CpG-binding protein 2 (MECP2; MIM *300005) results in the Rett syndrome, whereas gain-of-function mutations are associated with the MECP2 duplication syndrome. METHODS We did research on a family with two brothers showing Xq28 duplication syndrome using various molecular cytogenetic techniques such as multiplex ligation-dependent probe amplification and array-based genomic hybridization. RESULTS The duplicated region had several genes including MECP2 and interleukin-1 receptor associated kinase 1 (IRAK1; MIM *300283). MECP2 and IRAK1 were associated with the neurological phenotypes in dose-sensitive and dose-critical manner. The brothers demonstrated severe intellectual disability, autistic features, generalized hypotonia, recurrent infections, epilepsy, choreiform movements such as hand-wringing movement, and moderate increased spasticity with the lower limbs. The X-inactivation test showed a complete skewed X inactivation pattern of mother. In this reason, the mother had the same loci duplication but showed significantly little neurological manifestation compared to the two sons. CONCLUSIONS MECP2/IRAK1 duplication at Xq28 is inherited as an X-linked recessive trait and male-specific disorder associated with severe intellectual disability. We tried to analyze the information of the relationship between neuropsychiatric phenotype and the extent of duplication at Xq28 by comparing with previous reports.
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Affiliation(s)
- Dong Keon Yon
- Department of Pediatrics, CHA Bundang Medical Center, School of Medicine, CHA University, 351 Yatap-dong, Bundang-gu, Seongnam, 463-712 Republic of Korea
| | - Ji Eun Park
- Genetics Laboratory, Fertility Center, CHA Gangnam Medical Center, School of Medicine, CHA University, 606-13 Yeoksam-dong, Gangnam-gu, Seoul, 06135 Republic of Korea
| | - Seung Jun Kim
- GenoLifeCare Division, BioCore, Seoul, Republic of Korea
| | - Sung Han Shim
- Genetics Laboratory, Fertility Center, CHA Gangnam Medical Center, School of Medicine, CHA University, 606-13 Yeoksam-dong, Gangnam-gu, Seoul, 06135 Republic of Korea
- Department of Biomedical Science, College of Life Science, CHA University, 335 Pankyo-ro, Bundang-gu, Seongnam, 13488 Republic of Korea
| | - Kyu Young Chae
- Department of Pediatrics, CHA Bundang Medical Center, School of Medicine, CHA University, 351 Yatap-dong, Bundang-gu, Seongnam, 463-712 Republic of Korea
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27
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Yamamoto T, Shimojima K, Ondo Y, Imai K, Chong PF, Kira R, Amemiya M, Saito A, Okamoto N. Challenges in detecting genomic copy number aberrations using next-generation sequencing data and the eXome Hidden Markov Model: a clinical exome-first diagnostic approach. Hum Genome Var 2016; 3:16025. [PMID: 27579173 PMCID: PMC4989049 DOI: 10.1038/hgv.2016.25] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/13/2016] [Accepted: 06/17/2016] [Indexed: 01/22/2023] Open
Abstract
Next-generation sequencing (NGS) is widely used for the detection of disease-causing nucleotide variants. The challenges associated with detecting copy number variants (CNVs) using NGS analysis have been reported previously. Disease-related exome panels such as Illumina TruSight One are more cost-effective than whole-exome sequencing (WES) because of their selective target regions (~21% of the WES). In this study, CNVs were analyzed using data extracted through a disease-related exome panel analysis and the eXome Hidden Markov Model (XHMM). Samples from 61 patients with undiagnosed developmental delays and 52 healthy parents were included in this study. In the preliminary study to validate the constructed XHMM system (microarray-first approach), 34 patients who had previously been analyzed by chromosomal microarray testing were used. Among the five CNVs larger than 200 kb that were considered as non-pathogenic CNVs and were used as positive controls, four CNVs was successfully detected. The system was subsequently used to analyze different samples from 27 patients (NGS-first approach); 2 of these patients were successfully diagnosed as having pathogenic CNVs (an unbalanced translocation der(5)t(5;14) and a 16p11.2 duplication). These diagnoses were re-confirmed by chromosomal microarray testing and/or fluorescence in situ hybridization. The NGS-first approach generated no false-negative or false-positive results for pathogenic CNVs, indicating its high sensitivity and specificity in detecting pathogenic CNVs. The results of this study show the possible clinical utility of pathogenic CNV screening using disease-related exome panel analysis and XHMM.
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Affiliation(s)
- Toshiyuki Yamamoto
- Tokyo Women's Medical University Institute for Integrated Medical Sciences , Tokyo, Japan
| | - Keiko Shimojima
- Tokyo Women's Medical University Institute for Integrated Medical Sciences , Tokyo, Japan
| | - Yumiko Ondo
- Tokyo Women's Medical University Institute for Integrated Medical Sciences , Tokyo, Japan
| | - Katsumi Imai
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders , Shizuoka, Japan
| | - Pin Fee Chong
- Department of Pediatric Neurology, Fukuoka Children's Hospital , Fukuoka, Japan
| | - Ryutaro Kira
- Department of Pediatric Neurology, Fukuoka Children's Hospital , Fukuoka, Japan
| | | | - Akira Saito
- Division of Biomedical Informatics, StaGen Co., Ltd. , Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Medical Center and Research Institute for Maternal and Child Health , Osaka, Japan
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28
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Lim Z, Downs J, Wong K, Ellaway C, Leonard H. Expanding the clinical picture of the MECP2 Duplication syndrome. Clin Genet 2016; 91:557-563. [PMID: 27247049 DOI: 10.1111/cge.12814] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/26/2016] [Accepted: 05/27/2016] [Indexed: 12/15/2022]
Abstract
Individuals with two or more copies of the MECP2 gene, located at Xq28, share clinical features and a distinct facial phenotype known as MECP2 Duplication syndrome. We have examined perinatal characteristics, early childhood development and medical co-morbidities in this disorder. The International Rett Syndrome Phenotype Database (InterRett), which collects information from caregivers and clinicians on individuals with Rett syndrome and MECP2 associated disorders, was used as the data source. Data were available on 56 cases (49 males and 7 females) with MECP2 Duplication syndrome. Median age at ascertainment was 7.9 years (range: 1.2-37.6 years) and at diagnosis 3.0 years (range: 3 weeks-37 years). Less than a third (29%) learned to walk. Speech deterioration was reported in 34% and only 20% used word approximations or better at ascertainment. Over half (55%) had been hospitalised for respiratory infections in the first 2 years of life. Just under half (44%) had seizures, occurring daily in nearly half of this group. The majority (89%) had gastrointestinal problems and a third had a gastrostomy. Following the recent demonstration of phenotype reversal in a mouse model of MECP2 Duplication, a clear understanding of the natural history is crucial to the design and implementation of future therapeutic strategies.
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Affiliation(s)
- Z Lim
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - J Downs
- Telethon Kids Institute, University of Western Australia, Perth, Australia.,School of Physiotherapy and Exercise Science, Curtin University, Perth, Australia
| | - K Wong
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - C Ellaway
- Discipline of Genetic Medicine, The University of Sydney, Sydney, Australia.,Discipline of Child and Adolescent Health, The University of Sydney, The Children's Hospital at Westmead, Sydney, Australia.,Western Sydney Genetic Program, Sydney Children's Hospitals Network (Westmead), Sydney, NSW, Australia
| | - H Leonard
- Telethon Kids Institute, University of Western Australia, Perth, Australia
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29
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Iwasaki N, Tsurumi M, Asai K, Shimuzu W, Watanabe A, Ogata M, Takizawa M, Ide R, Yamamoto T, Saito K. Pancreatic developmental defect evaluated by celiac artery angiography in a patient with MODY5. Hum Genome Var 2016; 3:16022. [PMID: 27468355 PMCID: PMC4944010 DOI: 10.1038/hgv.2016.22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 06/01/2016] [Accepted: 06/06/2016] [Indexed: 11/09/2022] Open
Abstract
The hepatocyte nuclear factor 1β gene (HNF1B) is responsible for maturity-onset diabetes of the young type 5 (MODY5), which is characterized by early-onset diabetes mellitus and urogenital malformations. HNF1B is expressed during visceral endoderm formation. We identified a disruption of the great pancreatic artery in a patient with MODY5 with no pancreatic body or tail. Our finding supports the significance of HNF1B in the development of the pancreas.
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Affiliation(s)
- Naoko Iwasaki
- Diabetes Center, Tokyo Women's Medical University, Tokyo, Japan; Tokyo Women's Medical University Institute of Medical Genetics, Tokyo, Japan; Tokyo Women's Medical University Institute of Integrated Medical Science, Tokyo, Japan
| | - Masashi Tsurumi
- Department of Cardiovascular Medicine, Nippon Medical School , Tokyo, Japan
| | - Kuniya Asai
- Department of Cardiovascular Medicine, Nippon Medical School , Tokyo, Japan
| | - Wataru Shimuzu
- Department of Cardiovascular Medicine, Nippon Medical School , Tokyo, Japan
| | - Atsushi Watanabe
- Division of Clinical Genetics, Nippon Medical School , Tokyo, Japan
| | - Makiko Ogata
- Diabetes Center, Tokyo Women's Medical University , Tokyo, Japan
| | - Miho Takizawa
- Diabetes Center, Tokyo Women's Medical University , Tokyo, Japan
| | - Risa Ide
- Diabetes Center, Tokyo Women's Medical University , Tokyo, Japan
| | - Toshiyuki Yamamoto
- Tokyo Women's Medical University Institute of Medical Genetics, Tokyo, Japan; Tokyo Women's Medical University Institute of Integrated Medical Science, Tokyo, Japan
| | - Kayoko Saito
- Tokyo Women's Medical University Institute of Medical Genetics, Tokyo, Japan; Tokyo Women's Medical University Institute of Integrated Medical Science, Tokyo, Japan
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30
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Kumar R, Corbett MA, Van Bon BWM, Gardner A, Woenig JA, Jolly LA, Douglas E, Friend K, Tan C, Van Esch H, Holvoet M, Raynaud M, Field M, Leffler M, Budny B, Wisniewska M, Badura-Stronka M, Latos-Bieleńska A, Batanian J, Rosenfeld JA, Basel-Vanagaite L, Jensen C, Bienek M, Froyen G, Ullmann R, Hu H, Love MI, Haas SA, Stankiewicz P, Cheung SW, Baxendale A, Nicholl J, Thompson EM, Haan E, Kalscheuer VM, Gecz J. Increased STAG2 dosage defines a novel cohesinopathy with intellectual disability and behavioral problems. Hum Mol Genet 2015; 24:7171-81. [PMID: 26443594 DOI: 10.1093/hmg/ddv414] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/28/2015] [Indexed: 11/13/2022] Open
Abstract
Next generation genomic technologies have made a significant contribution to the understanding of the genetic architecture of human neurodevelopmental disorders. Copy number variants (CNVs) play an important role in the genetics of intellectual disability (ID). For many CNVs, and copy number gains in particular, the responsible dosage-sensitive gene(s) have been hard to identify. We have collected 18 different interstitial microduplications and 1 microtriplication of Xq25. There were 15 affected individuals from 6 different families and 13 singleton cases, 28 affected males in total. The critical overlapping region involved the STAG2 gene, which codes for a subunit of the cohesin complex that regulates cohesion of sister chromatids and gene transcription. We demonstrate that STAG2 is the dosage-sensitive gene within these CNVs, as gains of STAG2 mRNA and protein dysregulate disease-relevant neuronal gene networks in cells derived from affected individuals. We also show that STAG2 gains result in increased expression of OPHN1, a known X-chromosome ID gene. Overall, we define a novel cohesinopathy due to copy number gain of Xq25 and STAG2 in particular.
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Affiliation(s)
- Raman Kumar
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Mark A Corbett
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | | | - Alison Gardner
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Joshua A Woenig
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Lachlan A Jolly
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Evelyn Douglas
- Genetics and Molecular Pathology, SA Pathology, North Adelaide, SA 5006, Australia
| | - Kathryn Friend
- Genetics and Molecular Pathology, SA Pathology, North Adelaide, SA 5006, Australia
| | - Chuan Tan
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Maureen Holvoet
- Center for Human Genetics, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Martine Raynaud
- Centre Hospitalier Régional Universitaire, Service de Génétique, 37000 Tours, France
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Melanie Leffler
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Bartłomiej Budny
- Department of Endocrinology, Metabolism and Internal Diseases and
| | - Marzena Wisniewska
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan 60-355, Poland
| | | | - Anna Latos-Bieleńska
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan 60-355, Poland
| | | | - Jill A Rosenfeld
- Signature Genomic Laboratories, Spokane, WA 99207, USA, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lina Basel-Vanagaite
- Raphael Recanati Genetic Institute and Felsenstein Medical Research Center, Rabin Medical Center, Beilinson Campus, Petah Tikva 49100, Israel
| | | | | | - Guy Froyen
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium and
| | - Reinhard Ullmann
- Department of Human Molecular Genetics and, Bundeswehr Institute of Radiobiology, 80937 Munich, Germany
| | - Hao Hu
- Department of Human Molecular Genetics and
| | - Michael I Love
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anne Baxendale
- South Australian Clinical Genetics Service, SA Pathology, North Adelaide, SA 5006, Australia
| | - Jillian Nicholl
- Genetics and Molecular Pathology, SA Pathology, North Adelaide, SA 5006, Australia
| | - Elizabeth M Thompson
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia, South Australian Clinical Genetics Service, SA Pathology, North Adelaide, SA 5006, Australia
| | - Eric Haan
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia, South Australian Clinical Genetics Service, SA Pathology, North Adelaide, SA 5006, Australia
| | | | - Jozef Gecz
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia,
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31
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Yamamoto T, Shimojima K. A novel MED12 mutation associated with non-specific X-linked intellectual disability. Hum Genome Var 2015; 2:15018. [PMID: 27081531 PMCID: PMC4785543 DOI: 10.1038/hgv.2015.18] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 04/24/2015] [Accepted: 04/24/2015] [Indexed: 11/18/2022] Open
Abstract
The mediator complex subunit 12 gene (MED12) is responsible for an X-linked recessive intellectual disability syndrome that is characterized by dysmorphic features such as a long, narrow face and blepharophimosis, which is now recognized as an MED12-related syndrome. We identified a novel non-synonymous single-nucleotide variant, p.Ile1023Val, in a male patient with non-specific X-linked intellectual disability (XLID). Our results, together with the existence of similar reports, suggest a relationship between MED12 variants and XLID.
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Affiliation(s)
- Toshiyuki Yamamoto
- Tokyo Women's Medical University Institute for Integrated Medical Sciences , Tokyo, Japan
| | - Keiko Shimojima
- Tokyo Women's Medical University Institute for Integrated Medical Sciences , Tokyo, Japan
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