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Alvarez-Mora MI, Rodríguez-Revenga L, Jodar M, Potrony M, Sanchez A, Badenas C, Oriola J, Villanueva-Cañas JL, Muñoz E, Valldeoriola F, Cámara A, Compta Y, Carreño M, Martí MJ, Sánchez-Valle R, Madrigal I. Implementation of Exome Sequencing in Clinical Practice for Neurological Disorders. Genes (Basel) 2023; 14:genes14040813. [PMID: 37107571 PMCID: PMC10137364 DOI: 10.3390/genes14040813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/21/2023] [Accepted: 03/25/2023] [Indexed: 03/30/2023] Open
Abstract
Neurological disorders (ND) are diseases that affect the brain and the central and autonomic nervous systems, such as neurodevelopmental disorders, cerebellar ataxias, Parkinson’s disease, or epilepsies. Nowadays, recommendations of the American College of Medical Genetics and Genomics strongly recommend applying next generation sequencing (NGS) as a first-line test in patients with these disorders. Whole exome sequencing (WES) is widely regarded as the current technology of choice for diagnosing monogenic ND. The introduction of NGS allows for rapid and inexpensive large-scale genomic analysis and has led to enormous progress in deciphering monogenic forms of various genetic diseases. The simultaneous analysis of several potentially mutated genes improves the diagnostic process, making it faster and more efficient. The main aim of this report is to discuss the impact and advantages of the implementation of WES into the clinical diagnosis and management of ND. Therefore, we have performed a retrospective evaluation of WES application in 209 cases referred to the Department of Biochemistry and Molecular Genetics of the Hospital Clinic of Barcelona for WES sequencing derived from neurologists or clinical geneticists. In addition, we have further discussed some important facts regarding classification criteria for pathogenicity of rare variants, variants of unknown significance, deleterious variants, different clinical phenotypes, or frequency of actionable secondary findings. Different studies have shown that WES implementation establish diagnostic rate around 32% in ND and the continuous molecular diagnosis is essential to solve the remaining cases.
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2
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Meng T, Chen X, He Z, Huang H, Lin S, Liu K, Bai G, Liu H, Xu M, Zhuang H, Zhang Y, Waqas A, Liu Q, Zhang C, Sun XD, Huang H, Umair M, Yan Y, Feng D. ATP9A deficiency causes ADHD and aberrant endosomal recycling via modulating RAB5 and RAB11 activity. Mol Psychiatry 2023; 28:1219-1231. [PMID: 36604604 PMCID: PMC9816018 DOI: 10.1038/s41380-022-01940-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 12/10/2022] [Accepted: 12/22/2022] [Indexed: 01/07/2023]
Abstract
ATP9A, a lipid flippase of the class II P4-ATPases, is involved in cellular vesicle trafficking. Its homozygous variants are linked to neurodevelopmental disorders in humans. However, its physiological function, the underlying mechanism as well as its pathophysiological relevance in humans and animals are still largely unknown. Here, we report two independent families in which the nonsense mutations c.433C>T/c.658C>T/c.983G>A (p. Arg145*/p. Arg220*/p. Trp328*) in ATP9A (NM_006045.3) cause autosomal recessive hypotonia, intellectual disability (ID) and attention deficit hyperactivity disorder (ADHD). Atp9a null mice show decreased muscle strength, memory deficits and hyperkinetic movement disorder, recapitulating the symptoms observed in patients. Abnormal neurite morphology and impaired synaptic transmission are found in the primary motor cortex and hippocampus of the Atp9a null mice. ATP9A is also required for maintaining neuronal neurite morphology and the viability of neural cells in vitro. It mainly localizes to endosomes and plays a pivotal role in endosomal recycling pathway by modulating small GTPase RAB5 and RAB11 activation. However, ATP9A pathogenic mutants have aberrant subcellular localization and cause abnormal endosomal recycling. These findings provide strong evidence that ATP9A deficiency leads to neurodevelopmental disorders and synaptic dysfunctions in both humans and mice, and establishes novel regulatory roles for ATP9A in RAB5 and RAB11 activity-dependent endosomal recycling pathway and neurological diseases.
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Affiliation(s)
- Tian Meng
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, 510095, China.,Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, 511436, Guangzhou, China.,State Key Laboratory of Respiratory Disease, Guangzhou Medical University, 511436, Guangzhou, China
| | - Xiaoting Chen
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, 510095, China
| | - Zhengjie He
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, 510095, China.,Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, 511436, Guangzhou, China
| | - Haofeng Huang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, 510095, China
| | - Shiyin Lin
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, 510095, China
| | - Kunru Liu
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, 510095, China
| | - Guo Bai
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, 510095, China
| | - Hao Liu
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, 511436, Guangzhou, China.,State Key Laboratory of Respiratory Disease, Guangzhou Medical University, 511436, Guangzhou, China.,Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, 511500, China
| | - Mindong Xu
- Key Laboratory of Neuroscience, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Haixia Zhuang
- Department of Anesthesiology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Yunlong Zhang
- Key Laboratory of Neuroscience, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Ahmed Waqas
- Department of Zoology, Division of Science and Technology, University of Education, Lahore, 54000, Pakistan
| | - Qian Liu
- Department of Cerebrovascular Disease Center, Gansu Provincial Hospital, Lanzhou, 730000, China
| | - Chuan Zhang
- Medical Genetics Center, Gansu Provincial Maternity and Child-care Hospital; Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Lanzhou, 730050, China
| | - Xiang-Dong Sun
- Key Laboratory of Neuroscience, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Huansen Huang
- Department of Anesthesiology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, 11481, Saudi Arabia. .,Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, 22209, Pakistan.
| | - Yousheng Yan
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, 100026, China.
| | - Du Feng
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, 510095, China. .,Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, 511436, Guangzhou, China. .,State Key Laboratory of Respiratory Disease, Guangzhou Medical University, 511436, Guangzhou, China.
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3
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Li JM, Li X, Chan LWC, Hu R, Yang S. A high fat diet in glutamate 3-/Y mice causes changes in behavior that resemble human intellectual disability. Physiol Behav 2023; 259:114050. [PMID: 36476780 DOI: 10.1016/j.physbeh.2022.114050] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/20/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Cognitive impairment in individuals with intellectual disability (ID) is characterized by developmental delay and deficits in language and memory. Ionotropic AMPA mediate the majority of excitatory synaptic transmission in the central nervous system and are essential for the induction and maintenances of long-term potentiation (LTP) and long-term depression (LTD), two cellular models of learning and memory underlie many the symptoms of ID. Clinical research has found obese male patients with GluA3 interrupted underlie the symptom of ID. We tested GluA3-/Y mice under high fat diet (HFD) stress on a series of behavioral paradigms associated with symptoms of ID: wild type mice showed significant levels of sociability, while GluA3-/Y mice did not. Wild type mice showed significant preference for social novelty, while GluA3-/Y mice did not. Normal scores on relevant control measures confirmed general health and physical abilities in both GluA3-/Y and wild type mice (WT), ruling out artifactual explanations for social deficits. GluA3-/Y mice also showed working spatial memory behavior impairment in Y-maze test and abnormal anxiety in open-field test, compared to wild-type littermate controls. GluA3-/Y mice had a significantly reduced spontaneous activities tested by elevated plus maze, display both low social approach and resistance to change in routine on the T-maze, consistent with an ID-like phenotype. These findings demonstrate that selective gene deletion of GluA3 receptor in male mice under oxidative stress induced phenotypic abnormalities related to ID-like symptoms.
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Affiliation(s)
- Jian-Ming Li
- Department of Anatomy, School of Basic Medical Sciences, Changsha Medical University, Changsha, 410219, China; Department of Rehabilitation, Xiangya Boai Rehabilitation Hospital, Changsha, 410151, China
| | - Xianyu Li
- Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hong Kong, 99077, Hong Kong
| | - Lawrence W C Chan
- School of Life Science, Wuchang University of Technology, Wuhan, 430070, China
| | - Ruinian Hu
- Department of Pathophysiology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, 442000, China
| | - Sijun Yang
- Department of Anatomy, School of Basic Medical Sciences, Changsha Medical University, Changsha, 410219, China; Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hong Kong, 99077, Hong Kong; School of life science, Shaoxing University, Shaoxing, 312000, China; School of Public Health, He University, No.66 Sishui Street, Hunnan New District, Shenyang, 110163, China.
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4
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Álvarez-Mora MI, Sánchez A, Rodríguez-Revenga L, Corominas J, Rabionet R, Puig S, Madrigal I. Diagnostic yield of next-generation sequencing in 87 families with neurodevelopmental disorders. Orphanet J Rare Dis 2022; 17:60. [PMID: 35183220 PMCID: PMC8858550 DOI: 10.1186/s13023-022-02213-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 02/06/2022] [Indexed: 01/14/2023] Open
Abstract
Abstract
Background
Neurodevelopmental disorders (NDDs) are a group of heterogeneous conditions, which include mainly intellectual disability, developmental delay (DD) and autism spectrum disorder (ASD), among others. These diseases are highly heterogeneous and both genetic and environmental factors play an important role in many of them. The introduction of next generation sequencing (NGS) has lead to the detection of genetic variants in several genetic diseases. The main aim of this report is to discuss the impact and advantages of the implementation of NGS in the diagnosis of NDDs. Herein, we report diagnostic yields of applying whole exome sequencing in 87 families affected by NDDs and additional data of whole genome sequencing (WGS) from 12 of these families.
Results
The use of NGS technologies allowed identifying the causative gene alteration in approximately 36% (31/87) of the families. Among them, de novo mutation represented the most common cause of genetic alteration found in 48% (15/31) of the patients with diagnostic mutations. The majority of variants were located in known neurodevelopmental disorders genes. Nevertheless, some of the diagnoses were made after the use of GeneMatcher tools which allow the identification of additional patients carrying mutations in THOC2, SETD1B and CHD9 genes. Finally the use of WGS only allowed the identification of disease causing variants in 8% (1/12) of the patients in which previous WES failed to identify a genetic aetiology.
Conclusion
NGS is more powerful in identifying causative pathogenic variant than conventional algorithms based on chromosomal microarray as first-tier test. Our results reinforce the implementation of NGS as a first-test in genetic diagnosis of NDDs.
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5
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The importance of long non-coding RNAs in neuropsychiatric disorders. Mol Aspects Med 2019; 70:127-140. [DOI: 10.1016/j.mam.2019.07.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 06/10/2019] [Accepted: 07/14/2019] [Indexed: 12/20/2022]
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Identification and In Silico Characterization of a Novel Point Mutation within the Phosphatidylinositol Glycan Anchor Biosynthesis Class G Gene in an Iranian Family with Intellectual Disability. J Mol Neurosci 2019; 69:538-545. [PMID: 31414351 DOI: 10.1007/s12031-019-01376-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 07/08/2019] [Indexed: 10/26/2022]
Abstract
Intellectual disability (ID) is characterized by limited mental ability and adaptive behavior that imposes a heavy burden on the patients' families and the health care system. This study was aimed at determining the molecular aspect of nonsyndromic ID, in a family from South Khorasan Province in Iran. Exome sequencing was performed, as well as complete clinical examinations of the family. Afterward, in silico studies have been done to examine the changes that occurred in the protein structure, in association with the ID phenotype. The PIGG (NC_000004.12) mutation was found on Chr 4:517639G>A, and this chromosomal location was proposed as the disorder-causing variant. This Arg658Gln alteration was confirmed by Sanger sequencing, using specific primers for PIGG. In conclusion, our study indicated a novel mutation in the PIGG in the affected family. This mutation is a novel variant (p. R658Q) with an autosomal recessive inheritance pattern. These findings could improve genetic counseling in the future.
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7
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Mir YR, Kuchay RAH. Advances in identification of genes involved in autosomal recessive intellectual disability: a brief review. J Med Genet 2019; 56:567-573. [PMID: 30842223 DOI: 10.1136/jmedgenet-2018-105821] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 02/01/2019] [Accepted: 02/11/2019] [Indexed: 12/28/2022]
Abstract
Intellectual disability (ID) is a clinically and genetically heterogeneous disorder, affecting 1%-3% of the general population. The number of ID-causing genes is high. Many X-linked genes have been implicated in ID. Autosomal dominant genes have recently been the focus of several large-scale studies. The total number of autosomal recessive ID (ARID) genes is estimated to be very high, and most are still unknown. Although research into the genetic causes of ID has recently gained momentum, identification of pathogenic mutations that cause ARID has lagged behind, predominantly due to non-availability of sizeable families. A commonly used approach to identify genetic loci for recessive disorders in consanguineous families is autozygosity mapping and whole-exome sequencing. Combination of these two approaches has recently led to identification of many genes involved in ID. These genes have diverse function and control various biological processes. In this review, we will present an update regarding genes that have been recently implicated in ID with focus on ARID.
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Affiliation(s)
- Yaser Rafiq Mir
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, India
| | - Raja Amir Hassan Kuchay
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, India
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8
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Duan Y, Lin S, Xie L, Zheng K, Chen S, Song H, Zeng X, Gu X, Wang H, Zhang L, Shao H, Hong W, Zhang L, Duan S. Exome sequencing identifies a novel mutation of the GDI1 gene in a Chinese non-syndromic X-linked intellectual disability family. Genet Mol Biol 2017; 40:591-596. [PMID: 28863211 PMCID: PMC5596370 DOI: 10.1590/1678-4685-gmb-2016-0249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 03/18/2017] [Indexed: 12/29/2022] Open
Abstract
X-linked intellectual disability (XLID) has been associated with various genes.
Diagnosis of XLID, especially for non-syndromic ones (NS-XLID), is often hampered by
the heterogeneity of this disease. Here we report the case of a Chinese family in
which three males suffer from intellectual disability (ID). The three patients shared
the same phenotype: no typical clinical manifestation other than IQ score ≤ 70. For a
genetic diagnosis for this family we carried out whole exome sequencing on the
proband, and validated 16 variants of interest in the genomic DNA of all the family
members. A missense mutation (c.710G > T), which mapped to exon 6 of the Rab
GDP-Dissociation Inhibitor 1 (GDI1) gene, was found segregating with
the ID phenotype, and this mutation changes the 237th position in the guanosine
diphosphate dissociation inhibitor (GDI) protein from glycine to valine (p.
Gly237Val). Through molecular dynamics simulations we found that this substitution
results in a conformational change of GDI, possibly affecting the Rab-binding
capacity of this protein. In conclusion, our study identified a novel
GDI1 mutation that is possibly NS-XLID causative, and showed that
whole exome sequencing provides advantages for detecting novel ID-associated variants
and can greatly facilitate the genetic diagnosis of the disease.
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Affiliation(s)
- Yongheng Duan
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Sheng Lin
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Lichun Xie
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Kaifeng Zheng
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Shiguo Chen
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Hui Song
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Xuchun Zeng
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Xueying Gu
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Heyun Wang
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Linghua Zhang
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Hao Shao
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Wenxu Hong
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
| | - Lijie Zhang
- College of Pharmacy, Nankai University, Tianjin City, People's Republic of China
| | - Shan Duan
- Laboratory of Medical Genetics, Center for Birth Defect Research and Prevention, Shenzhen Research Institute of Population and Family Planning, Shenzhen City, People's Republic of China
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9
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Intellectual Disability & Rare Disorders: A Diagnostic Challenge. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1031:39-54. [PMID: 29214565 DOI: 10.1007/978-3-319-67144-4_3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Rare disorders constitute a large and heterogeneous group of diagnoses of which many cause chronic disabilities with significant impact on the lives of affected individuals and their families as well as on the health-care system. Each individual disorder is rare, but when considered as a group, rare disorders are common with a total prevalence of approximately 6-8%. The clinical presentation of these disorders includes a broad diversity of symptoms and signs, often involving the nervous system and resulting in symptoms such as intellectual disability, neuropsychiatric disorders, epilepsy and motor dysfunction. The methods for establishing an etiological diagnosis in patients with rare disorders have improved dramatically during recent years. With the introduction of genomic screening methods, it has been shown that the cause is genetic in the majority of the patients and many will receive an etiological diagnosis in a clinical setting. However, there are a lot of challenges in diagnosing these disorders and despite recent years' advances, a large number of patients with rare disorders still go without an etiological diagnosis. In this chapter we will review the etiology of rare disorders with focus on intellectual disability and what has been learned from massive parallel sequencing studies in deciphering the genetic basis. Furthermore, we will discuss challenges in the etiological diagnostics of these disorders including issues that regard interpretation of the numerous genetic variants detected by genomic screening methods and challenges in the translation of massive parallel sequencing technologies into clinical practice.
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10
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D'haene E, Jacobs EZ, Volders PJ, De Meyer T, Menten B, Vergult S. Identification of long non-coding RNAs involved in neuronal development and intellectual disability. Sci Rep 2016; 6:28396. [PMID: 27319317 PMCID: PMC4913242 DOI: 10.1038/srep28396] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/01/2016] [Indexed: 12/15/2022] Open
Abstract
Recently, exome sequencing led to the identification of causal mutations in 16–31% of patients with intellectual disability (ID), leaving the underlying cause for many patients unidentified. In this context, the noncoding part of the human genome remains largely unexplored. For many long non-coding RNAs (lncRNAs) a crucial role in neurodevelopment and hence the human brain is anticipated. Here we aimed at identifying lncRNAs associated with neuronal development and ID. Therefore, we applied an integrated genomics approach, harnessing several public epigenetic datasets. We found that the presence of neuron-specific H3K4me3 confers the highest specificity for genes involved in neurodevelopment and ID. Based on the presence of this feature and GWAS hits for CNS disorders, we identified 53 candidate lncRNA genes. Extensive expression profiling on human brain samples and other tissues, followed by Gene Set Enrichment Analysis indicates that at least 24 of these lncRNAs are indeed implicated in processes such as synaptic transmission, nervous system development and neurogenesis. The bidirectional or antisense overlapping orientation relative to multiple coding genes involved in neuronal processes supports these results. In conclusion, we identified several lncRNA genes putatively involved in neurodevelopment and CNS disorders, providing a resource for functional studies.
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Affiliation(s)
- Eva D'haene
- Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Eva Z Jacobs
- Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Pieter-Jan Volders
- Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Tim De Meyer
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.,Dept. of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
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11
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Armanet N, Metay C, Brisset S, Deschenes G, Pineau D, Petit FM, Di Rocco F, Goossens M, Tachdjian G, Labrune P, Tosca L. Double Xp11.22 deletion including SHROOM4 and CLCN5 associated with severe psychomotor retardation and Dent disease. Mol Cytogenet 2015; 8:8. [PMID: 25670966 PMCID: PMC4322561 DOI: 10.1186/s13039-015-0107-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/08/2015] [Indexed: 11/23/2022] Open
Abstract
Background Here we report the clinical and molecular characterization of two Xp11.22 deletions including SHROOM4 and CLCN5 genes. These deletions appeared in the same X chromosome of the same patient. Results The patient is a six-year-old boy who presented hydrocephalus, severe psychomotor and growth retardation, facial dysmorphism and renal proximal tubulopathy associated with low-molecular-weight proteinuria, hypercalciuria, hyperaminoaciduria, hypophosphatemia and hyperuricemia. Standard and high resolution karyotypes showed a 46,XY formula. Array-CGH revealed two consecutive cryptic deletions in the region Xp11.22, measuring respectively 148 Kb and 2.6 Mb. The two deletions were inherited from the asymptomatic mother. Conclusions Array-CGH allowed us to determine candidate genes in the deleted region. The disruption and partial loss of CLCN5 confirmed the diagnostic of Dent disease for this patient. Moreover, the previously described involvement of SHROOM4 in neuronal development is discussed.
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Affiliation(s)
- Narjes Armanet
- Service d'Histologie, Embryologie et Cytogénétique, Hôpitaux Universitaires Paris-Sud. Hôpital Antoine Béclère, 157 rue de la Porte de Trivaux, 92141, Clamart, F-92140 France.,Université Paris-Sud, Le Kremlin-Bicêtre, F-94276 France
| | - Corinne Metay
- Plateforme de Génomique IMRB 955, Hôpital Henri Mondor, Créteil, F-94010 France
| | - Sophie Brisset
- Service d'Histologie, Embryologie et Cytogénétique, Hôpitaux Universitaires Paris-Sud. Hôpital Antoine Béclère, 157 rue de la Porte de Trivaux, 92141, Clamart, F-92140 France.,Université Paris-Sud, Le Kremlin-Bicêtre, F-94276 France
| | - Georges Deschenes
- Service de Néphrologie pédiatrique, Hôpital Robert Debré, Paris, F-75935 France
| | - Dominique Pineau
- Service d'Histologie, Embryologie et Cytogénétique, Hôpitaux Universitaires Paris-Sud. Hôpital Antoine Béclère, 157 rue de la Porte de Trivaux, 92141, Clamart, F-92140 France
| | - François M Petit
- Laboratoire de Génétique Moléculaire, Hôpitaux Universitaires Paris-Sud. Hôpital Antoine Béclère, Clamart, F-92140 France
| | - Federico Di Rocco
- Service de Neurochirurgie pédiatrique, Hôpital Necker Enfants Malades, Clamart, F-75015 France
| | - Michel Goossens
- Plateforme de Génomique IMRB 955, Hôpital Henri Mondor, Créteil, F-94010 France.,Université Paris Est, Créteil, F-94010 France
| | - Gérard Tachdjian
- Service d'Histologie, Embryologie et Cytogénétique, Hôpitaux Universitaires Paris-Sud. Hôpital Antoine Béclère, 157 rue de la Porte de Trivaux, 92141, Clamart, F-92140 France.,Université Paris-Sud, Le Kremlin-Bicêtre, F-94276 France
| | - Philippe Labrune
- Université Paris-Sud, Le Kremlin-Bicêtre, F-94276 France.,Service de Pédiatrie, Hôpitaux Universitaires Paris-Sud. Hôpital Antoine Béclère, Clamart, F-92140 France
| | - Lucie Tosca
- Service d'Histologie, Embryologie et Cytogénétique, Hôpitaux Universitaires Paris-Sud. Hôpital Antoine Béclère, 157 rue de la Porte de Trivaux, 92141, Clamart, F-92140 France.,Université Paris-Sud, Le Kremlin-Bicêtre, F-94276 France
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12
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Helsmoortel C, Vandeweyer G, Ordoukhanian P, Van Nieuwerburgh F, Van der Aa N, Kooy RF. Challenges and opportunities in the investigation of unexplained intellectual disability using family-based whole-exome sequencing. Clin Genet 2014; 88:140-8. [PMID: 25081361 DOI: 10.1111/cge.12470] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 07/22/2014] [Accepted: 07/25/2014] [Indexed: 12/25/2022]
Abstract
Intellectual disability (ID), characterized by an intellectual performance of at least 2 SD (standard deviations) below average is a frequent, lifelong disorder with a prevalence of 2-3%. Today, only for at most half of patients a diagnosis is made. Knowing the cause of the ID is important for patients and their relatives, as it allows for appropriate medical care, prognosis on further development of the disorder, familial counselling or access to support groups. Whole-exome sequencing (WES) now offers the possibility to identify the genetic cause for patients for which all previously available genetic tests, including karyotyping, specific gene analysis, or microarray analysis did not reveal causative abnormalities. However, data analysis of WES experiments is challenging. Here we present an analysis workflow implementable in any laboratory, requiring no bioinformatics knowledge. We demonstrated its feasibility on a cohort of 10 patients, in which we found a conclusive diagnosis in 3 and a likely diagnosis in 2 more patients. Of the three conclusive diagnoses, one was a clinically suspected mutation missed by Sanger sequencing, and one was an atypical presentation of a known monogenic disorder, highlighting two essential strengths of WES-based diagnostics.
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Affiliation(s)
- C Helsmoortel
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - G Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Biomedical Informatics Research Center Antwerpen (Biomina), Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - P Ordoukhanian
- Next Generation Sequencing Core, The Scripps Research Institute, La Jolla, CA, USA
| | - F Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - N Van der Aa
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Department of Medical Genetics, University Hospital Antwerp, Antwerp, Belgium
| | - R F Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
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Willemsen M, Kleefstra T. Making headway with genetic diagnostics of intellectual disabilities. Clin Genet 2013; 85:101-10. [DOI: 10.1111/cge.12244] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 07/24/2013] [Accepted: 07/24/2013] [Indexed: 01/31/2023]
Affiliation(s)
- M.H. Willemsen
- Department of Human Genetics; Radboud University Medical Centre; Nijmegen The Netherlands
| | - T. Kleefstra
- Department of Human Genetics; Radboud University Medical Centre; Nijmegen The Netherlands
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14
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Iqbal Z, Vandeweyer G, van der Voet M, Waryah AM, Zahoor MY, Besseling JA, Roca LT, Vulto-van Silfhout AT, Nijhof B, Kramer JM, Van der Aa N, Ansar M, Peeters H, Helsmoortel C, Gilissen C, Vissers LELM, Veltman JA, de Brouwer APM, Frank Kooy R, Riazuddin S, Schenck A, van Bokhoven H, Rooms L. Homozygous and heterozygous disruptions of ANK3: at the crossroads of neurodevelopmental and psychiatric disorders. Hum Mol Genet 2013; 22:1960-70. [PMID: 23390136 DOI: 10.1093/hmg/ddt043] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
AnkyrinG, encoded by the ANK3 gene, is involved in neuronal development and signaling. It has previously been implicated in bipolar disorder and schizophrenia by association studies. Most recently, de novo missense mutations in this gene were identified in autistic patients. However, the causative nature of these mutations remained controversial. Here, we report inactivating mutations in the Ankyrin 3 (ANK3) gene in patients with severe cognitive deficits. In a patient with a borderline intelligence, severe attention deficit hyperactivity disorder (ADHD), autism and sleeping problems, all isoforms of the ANK3 gene, were disrupted by a balanced translocation. Furthermore, in a consanguineous family with moderate intellectual disability (ID), an ADHD-like phenotype and behavioral problems, we identified a homozygous truncating frameshift mutation in the longest isoform of the same gene, which represents the first reported familial mutation in the ANK3 gene. The causality of ANK3 mutations in the two families and the role of the gene in cognitive function were supported by memory defects in a Drosophila knockdown model. Thus we demonstrated that ANK3 plays a role in intellectual functioning. In addition, our findings support the suggested association of ANK3 with various neuropsychiatric disorders and illustrate the genetic and molecular relation between a wide range of neurodevelopmental disorders.
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Affiliation(s)
- Zafar Iqbal
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Donders Institute for Brain, Cognitionand Behaviour, Radboud University Medical Centre, Nijmegen, TheNetherlands
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15
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Dheedene A, Maes M, Vergult S, Menten B. A de novo POU3F3 Deletion in a Boy with Intellectual Disability and Dysmorphic Features. Mol Syndromol 2013; 5:32-5. [DOI: 10.1159/000356060] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2013] [Indexed: 11/19/2022] Open
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16
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Mundhofir FE, Winarni TI, van Bon BW, Aminah S, Nillesen WM, Merkx G, Smeets D, Hamel BC, Faradz SM, Yntema HG. A Cytogenetic Study in a Large Population of Intellectually Disabled Indonesians. Genet Test Mol Biomarkers 2012; 16:412-7. [DOI: 10.1089/gtmb.2011.0157] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Farmaditya E.P. Mundhofir
- Division of Human Genetics, Center for Biomedical Research (CEBIOR), Faculty of Medicine, Diponegoro University GSG, Semarang, Indonesia
- Department of Human Genetics, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Tri Indah Winarni
- Division of Human Genetics, Center for Biomedical Research (CEBIOR), Faculty of Medicine, Diponegoro University GSG, Semarang, Indonesia
| | - Bregje W. van Bon
- Department of Human Genetics, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Siti Aminah
- Department of Neurology, Hasan Sadikin Central General Hospital, Bandung, Indonesia
| | - Willy M. Nillesen
- Department of Human Genetics, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Gerard Merkx
- Department of Human Genetics, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Dominique Smeets
- Department of Human Genetics, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Ben C.J. Hamel
- Department of Human Genetics, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Sultana M.H. Faradz
- Division of Human Genetics, Center for Biomedical Research (CEBIOR), Faculty of Medicine, Diponegoro University GSG, Semarang, Indonesia
| | - Helger G. Yntema
- Department of Human Genetics, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
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17
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Verloes A, Héron D, Billette de Villemeur T, Afenjar A, Baumann C, Bahi-Buisson N, Charles P, Faudet A, Jacquette A, Mignot C, Moutard ML, Passemard S, Rio M, Robel L, Rougeot C, Ville D, Burglen L, des Portes V. Stratégie d’exploration d’une déficience intellectuelle inexpliquée. Arch Pediatr 2012; 19:194-207. [DOI: 10.1016/j.arcped.2011.11.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 11/22/2011] [Accepted: 11/25/2011] [Indexed: 02/07/2023]
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Wong VCN, Chung B. Value of clinical assessment in the diagnostic evaluation of Global Developmental Delay (GDD) using a Likelihood Ratio Model. Brain Dev 2011; 33:548-57. [PMID: 20965674 DOI: 10.1016/j.braindev.2010.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 09/26/2010] [Accepted: 09/27/2010] [Indexed: 12/08/2022]
Abstract
OBJECTIVE A selective approach is recommended for investigating children with GDD. Our objective is to identify clinical markers to improve the diagnostic yield of evaluation of children with GDD. METHOD Children with GDD (delay>2 S.D. in>1 domain) followed up in our centre were reviewed retrospectively. We selected nine clinical markers (sex, severity of GDD, parental consanguinity, family history, behavioral problems, head size, facial dysmorphism, non-facial anomalies and neurological deficits) and looked into the likelihood of finding an underlying etiology during follow-up. RESULTS There were 577 children with 63%, 33% and 4% having mild, moderate and severe grade GDD. An identifiable etiology is detected in 53%. Genetic disease (25%) was the commonest cause identified. We have found that severity of GDD (severe and moderate versus mild grade [LR+=1.92 (95% C.I.=1.49-2.48); LR-=0.72(0.64-0.81)], behavioral problems [LR+=0.24 (95% C.I.=0.17-0.34); LR-=1.67 (1.48-1.88)], facial dysmorphism [LR+=2.66 (95% C.I.=1.10-3.54); LR-=0.65 (0.58-0.73)] and neurological deficits [LR+=2.85 (95% C.I.=2.32-3.50); LR-=0.31(0.25-0.39)] were clinical markers associated with increased chance of identifying an underlying etiology by multivariate analysis. CONCLUSION These four clinical markers are useful in selecting patients with GDD for further diagnostic tests. Using the LR model, clinical markers in the first clinical evaluation of any child with GDD can potentially improve the etiological yield using targeted investigations.
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Affiliation(s)
- Virginia C N Wong
- Division of Child Neurology/Developmental Paediatrics/Neurohabilitation, Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong.
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Abstract
Autosomal recessive mental retardation (AR-MR) may account for up to 25% of genetic mental retardation (MR). So far, mapping of AR-MR genes in consanguineous families has resulted in six nonsyndromic genes, whereas more than 2000 genes might contribute to AR-MR. We propose to use outbred families with multiple affected siblings for AR-MR gene identification. Homozygosity mapping in ten outbred families with affected brother-sister pairs using a 250 K single nucleotide polymorphism array revealed on average 57 homozygous regions over 1 Mb in size per affected individual (range 20-74). Of these, 21 homozygous regions were shared between siblings on average (range 8-36). None of the shared regions of homozygosity (SROHs) overlapped with the nonsyndromic genes. A total of 13 SROHs had an overlap with previously reported loci for AR-MR, namely with MRT8, MRT9, MRT10 and MRT11. Among these was the longest observed SROH of 11.0 Mb in family ARMR1 on chromosome 19q13, which had 2.9 Mb (98 genes) in common with the 5.4 Mb MRT11 locus (195 genes). These data support that homozygosity mapping in outbred families may contribute to identification of novel AR-MR genes.
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van Bon BWM, Balciuniene J, Fruhman G, Nagamani SCS, Broome DL, Cameron E, Martinet D, Roulet E, Jacquemont S, Beckmann JS, Irons M, Potocki L, Lee B, Cheung SW, Patel A, Bellini M, Selicorni A, Ciccone R, Silengo M, Vetro A, Knoers NV, de Leeuw N, Pfundt R, Wolf B, Jira P, Aradhya S, Stankiewicz P, Brunner HG, Zuffardi O, Selleck SB, Lupski JR, de Vries BBA. The phenotype of recurrent 10q22q23 deletions and duplications. Eur J Hum Genet 2011; 19:400-8. [PMID: 21248748 DOI: 10.1038/ejhg.2010.211] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The genomic architecture of the 10q22q23 region is characterised by two low-copy repeats (LCRs3 and 4), and deletions in this region appear to be rare. We report the clinical and molecular characterisation of eight novel deletions and six duplications within the 10q22.3q23.3 region. Five deletions and three duplications occur between LCRs3 and 4, whereas three deletions and three duplications have unique breakpoints. Most of the individuals with the LCR3-4 deletion had developmental delay, mainly affecting speech. In addition, macrocephaly, mild facial dysmorphisms, cerebellar anomalies, cardiac defects and congenital breast aplasia were observed. For congenital breast aplasia, the NRG3 gene, known to be involved in early mammary gland development in mice, is a putative candidate gene. For cardiac defects, BMPR1A and GRID1 are putative candidate genes because of their association with cardiac structure and function. Duplications between LCRs3 and 4 are associated with variable phenotypic penetrance. Probands had speech and/or motor delays and dysmorphisms including a broad forehead, deep-set eyes, upslanting palpebral fissures, a smooth philtrum and a thin upper lip. In conclusion, duplications between LCRs3 and 4 on 10q22.3q23.2 may lead to a distinct facial appearance and delays in speech and motor development. However, the phenotypic spectrum is broad, and duplications have also been found in healthy family members of a proband. Reciprocal deletions lead to speech and language delay, mild facial dysmorphisms and, in some individuals, to cerebellar, breast developmental and cardiac defects.
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Affiliation(s)
- Bregje W M van Bon
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
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22
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Balanced translocations in mental retardation. Hum Genet 2009; 126:133-47. [PMID: 19347365 DOI: 10.1007/s00439-009-0661-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2009] [Accepted: 03/23/2009] [Indexed: 12/13/2022]
Abstract
Over the past few decades, the knowledge on genetic defects causing mental retardation has dramatically increased. In this review, we discuss the importance of balanced chromosomal translocations in the identification of genes responsible for mental retardation. We present a database-search guided overview of balanced translocations identified in patients with mental retardation. We divide those in four categories: (1) balanced translocations that helped to identify a causative gene within a contiguous gene syndrome, (2) balanced translocations that led to the identification of a mental retardation gene confirmed by independent methods, (3) balanced translocations disrupting candidate genes that have not been confirmed by independent methods and (4) balanced translocations not reported to disrupt protein coding sequences. It can safely be concluded that balanced translocations have been instrumental in the identification of multiple genes that are involved in mental retardation. In addition, many more candidate genes were identified with a suspected but (as yet?) unconfirmed role in mental retardation. Some balanced translocations do not disrupt a protein coding gene and it can be speculated that in the light of recent findings concerning ncRNA's and ultra-conserved regions, such findings are worth further investigation as these potentially may lead us to the discovery of novel disease mechanisms.
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23
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Dysmorphic features, simplified gyral pattern and 7q11.23 duplication reciprocal to the Williams-Beuren deletion. Eur J Hum Genet 2008; 16:880-7. [DOI: 10.1038/ejhg.2008.42] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Sharp AJ, Mefford HC, Li K, Baker C, Skinner C, Stevenson RE, Schroer RJ, Novara F, De Gregori M, Ciccone R, Broomer A, Casuga I, Wang Y, Xiao C, Barbacioru C, Gimelli G, Bernardina BD, Torniero C, Giorda R, Regan R, Murday V, Mansour S, Fichera M, Castiglia L, Failla P, Ventura M, Jiang Z, Cooper GM, Knight SJL, Romano C, Zuffardi O, Chen C, Schwartz CE, Eichler EE. A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizures. Nat Genet 2008; 40:322-8. [PMID: 18278044 PMCID: PMC2365467 DOI: 10.1038/ng.93] [Citation(s) in RCA: 412] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2007] [Accepted: 01/07/2008] [Indexed: 11/09/2022]
Abstract
We report a recurrent microdeletion syndrome causing mental retardation, epilepsy and variable facial and digital dysmorphisms. We describe nine affected individuals, including six probands: two with de novo deletions, two who inherited the deletion from an affected parent and two with unknown inheritance. The proximal breakpoint of the largest deletion is contiguous with breakpoint 3 (BP3) of the Prader-Willi and Angelman syndrome region, extending 3.95 Mb distally to BP5. A smaller 1.5-Mb deletion has a proximal breakpoint within the larger deletion (BP4) and shares the same distal BP5. This recurrent 1.5-Mb deletion contains six genes, including a candidate gene for epilepsy (CHRNA7) that is probably responsible for the observed seizure phenotype. The BP4-BP5 region undergoes frequent inversion, suggesting a possible link between this inversion polymorphism and recurrent deletion. The frequency of these microdeletions in mental retardation cases is approximately 0.3% (6/2,082 tested), a prevalence comparable to that of Williams, Angelman and Prader-Willi syndromes.
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Affiliation(s)
- Andrew J Sharp
- Department of Genome Sciences, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, Washington 98195, USA
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Rogers RC, Stevenson RE, Simensen RJ, Holden KR, Schwartz CE. Finding new etiologies of mental retardation and hypotonia: X marks the spot. Dev Med Child Neurol 2008; 50:104-11. [PMID: 18190539 DOI: 10.1111/j.1469-8749.2007.02022.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Mental retardation (MR) and hypotonia occur together frequently and have a heterogeneous etiology. Molecular and clinical studies have led to the recent discovery of genes on the X chromosome that may be associated with syndromal forms of X-linked MR (XLMR). These disorders manifest additional neurological and somatic features that are helpful in establishing a specific diagnosis and etiology. This article provides an overview of MR and its association with hypotonia, with a review of five 'new' XLMR-hypotonia syndromes.
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Wu Y, Arai AC, Rumbaugh G, Srivastava AK, Turner G, Hayashi T, Suzuki E, Jiang Y, Zhang L, Rodriguez J, Boyle J, Tarpey P, Raymond FL, Nevelsteen J, Froyen G, Stratton M, Futreal A, Gecz J, Stevenson R, Schwartz CE, Valle D, Huganir RL, Wang T. Mutations in ionotropic AMPA receptor 3 alter channel properties and are associated with moderate cognitive impairment in humans. Proc Natl Acad Sci U S A 2007; 104:18163-8. [PMID: 17989220 PMCID: PMC2084314 DOI: 10.1073/pnas.0708699104] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Indexed: 11/18/2022] Open
Abstract
Ionotropic alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors (iGluRs) mediate the majority of excitatory synaptic transmission in the CNS and are essential for the induction and maintenance of long-term potentiation and long-term depression, two cellular models of learning and memory. We identified a genomic deletion (0.4 Mb) involving the entire GRIA3 (encoding iGluR3) by using an X-array comparative genomic hybridization (CGH) and four missense variants (G833R, M706T, R631S, and R450Q) in functional domains of iGluR3 by sequencing 400 males with X-linked mental retardation (XLMR). Three variants were found in males with moderate MR and were absent in 500 control males. Expression studies in HEK293 cells showed that G833R resulted in a 78% reduction of iGluR3 due to protein misfolding. Whole-cell recording studies of iGluR3 homomers in HEK293 cells revealed that neither iGluR3-M706T (S2 domain) nor iGluR3-R631S (near channel core) had substantial channel function, whereas R450Q (S1 domain) was associated with accelerated receptor desensitization. When forming heteromeric receptors with iGluR2 in HEK293 cells, all four iGluR3 variants had altered desensitization kinetics. Our study provides the genetic and functional evidence that mutant iGluR3 with altered kinetic properties is associated with moderate cognitive impairment in humans.
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Affiliation(s)
- Ye Wu
- Institute of Genetic Medicine and Department of Pediatrics
- Department of Pediatrics, Beijing University First Hospital, Beijing 100034, People's Republic of China
| | - Amy C. Arai
- Department of Pharmacology, Southern Illinois University School of Medicine, Springfield, IL 62794
| | - Gavin Rumbaugh
- Department of Neuroscience, and
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | | | - Gillian Turner
- Hunter Genetics and Genetics of Learning Disability (GOLD) Service, University of Newcastle, Callaghan NSW 2308, Australia
| | - Takashi Hayashi
- Department of Neuroscience, and
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Erika Suzuki
- Department of Pharmacology, Southern Illinois University School of Medicine, Springfield, IL 62794
| | - Yuwu Jiang
- Institute of Genetic Medicine and Department of Pediatrics
- Department of Pediatrics, Beijing University First Hospital, Beijing 100034, People's Republic of China
| | - Lilei Zhang
- Institute of Genetic Medicine and Department of Pediatrics
| | | | - Jackie Boyle
- Hunter Genetics and Genetics of Learning Disability (GOLD) Service, University of Newcastle, Callaghan NSW 2308, Australia
| | - Patrick Tarpey
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
| | - F. Lucy Raymond
- Department of Medical Genetics, Cambridge Institute of Medical Research, University of Cambridge, Cambridge CB2 2XY, United Kingdom
| | - Joke Nevelsteen
- Human Genome Laboratory, Department of Human Genetics, Vlaams Instituut voor Biotechnologie, University of Leuven, 3000 Leuven, Belgium
| | - Guy Froyen
- Human Genome Laboratory, Department of Human Genetics, Vlaams Instituut voor Biotechnologie, University of Leuven, 3000 Leuven, Belgium
| | - Mike Stratton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
| | - Andy Futreal
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
| | - Jozef Gecz
- Department of Genetic Medicine, Women's and Children's Hospital, and Departments of Pediatrics and Molecular Biosciences, University of Adelaide, Adelaide SA 5005, Australia; and
| | | | | | - David Valle
- Institute of Genetic Medicine and Department of Pediatrics
| | - Richard L. Huganir
- Department of Neuroscience, and
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Tao Wang
- Institute of Genetic Medicine and Department of Pediatrics
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Abstract
PURPOSE OF REVIEW Mutations in genes on the X chromosome rival chromosome aberrations as a cause of mental retardation. Progress in the clinical and molecular delineation of X-linked mental retardation has outpaced progress in understanding autosomal mental retardation. This is a result in large part of the identification of large families in which mental retardation has segregated in an X-linked pattern and the greater ease with which molecular technologies can be applied to hemizygosity in males. RECENT FINDINGS About one-third of the estimated 165 genes associated with syndromal mutations of genes on the X chromosome and one-fourth of the estimated 100 genes associated with nonsyndromal mutations of genes on the X chromosome have been identified. In a number of instances, the same gene is responsible for syndromal and nonsyndromal mutations of genes on the X chromosome. The molecular delineation of mutations of genes on the X chromosome has allowed certain conditions to be lumped together on the basis of allelism and has caused others that appear clinical similar to remain separate. SUMMARY The clinical and molecular advances have allowed X-linked mental retardation to be more clearly delineated, have provided the means of confirmatory laboratory testing, and have ushered in an era of carrier testing, prenatal diagnosis, and prevention strategies.
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Hagens O, Dubos A, Abidi F, Barbi G, Van Zutven L, Hoeltzenbein M, Tommerup N, Moraine C, Fryns JP, Chelly J, van Bokhoven H, Gécz J, Dollfus H, Ropers HH, Schwartz CE, de Cassia Stocco Dos Santos R, Kalscheuer V, Hanauer A. Disruptions of the novel KIAA1202 gene are associated with X-linked mental retardation. Hum Genet 2005; 118:578-90. [PMID: 16249884 DOI: 10.1007/s00439-005-0072-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2005] [Accepted: 08/30/2005] [Indexed: 12/14/2022]
Abstract
The extensive heterogeneity underlying the genetic component of mental retardation (MR) is the main cause for our limited understanding of the aetiology of this highly prevalent condition. Hence we set out to identify genes involved in MR. We investigated the breakpoints of two balanced X;autosome translocations in two unrelated female patients with mild/moderate MR and found that the Xp11.2 breakpoints disrupt the novel human KIAA1202 (hKIAA1202) gene in both cases. We also identified a missense exchange in this gene, segregating with the Stocco dos Santos XLMR syndrome in a large four-generation pedigree but absent in >1,000 control X-chromosomes. Among other phenotypic characteristics, the affected males in this family present with severe MR, delayed or no speech, seizures and hyperactivity. Molecular studies of hKIAA1202 determined its genomic organisation, its expression throughout the brain and the regulation of expression of its mouse homologue during development. Transient expression of the wild-type KIAA1202 protein in HeLa cells showed partial colocalisation with the F-actin based cytoskeleton. On the basis of its domain structure, we argue that hKIAA1202 is a new member of the APX/Shroom protein family. Members of this family contain a PDZ and two ASD domains of unknown function and have been shown to localise at the cytoskeleton, and play a role in neurulation, cellular architecture, actin remodelling and ion channel function. Our results suggest that hKIAA1202 may be important in cognitive function and/or development.
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Affiliation(s)
- Olivier Hagens
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195, Berlin, Germany
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29
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Chiurazzi P, Tabolacci E, Neri G. X-linked mental retardation (XLMR): from clinical conditions to cloned genes. Crit Rev Clin Lab Sci 2004; 41:117-58. [PMID: 15270552 DOI: 10.1080/10408360490443013] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
X-linked mental retardation (XLMR) is a heterogenous set of conditions responsible for a large proportion of inherited mental retardation. Approximately 200 XLMR conditions and 45 cloned genes are now listed in our catalogue on the Internet at http://xlmr.interfree.it/home.htm. Traditionally, XLMR conditions were subdivided into specific (MRXS) and nonspecific (MRX) forms, depending on their clinical presentation. Now that a growing number of candidate genes have become available for screening XLMR families and patients, this distinction is becoming less useful and similar conditions that had been previously listed as separate can now be grouped together because different mutations in the same gene have been identified. Furthermore, different mutations in the same XLMR gene may account for diseases of increasing severity, but can also cause different phenotypes. As the functions of proteins corresponding to these genes are characterized, biological networks involved in causing mental retardation and conversely in supporting normal intellectual functioning will be discovered. Molecular biologists and neurobiologists will need to cooperate in order to verify the effects of XLMR gene mutations in the context of neuronal circuitry. Eventually, DNA and protein microarray technologies will assist researchers and physicians in reaching a diagnosis even in small families or in individual patients with XLMR.
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Affiliation(s)
- Pietro Chiurazzi
- Institute of Medical Genetics, A. Gemelli School of Medicine, Catholic University, Rome, Italy
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Lenski C, Abidi F, Meindl A, Gibson A, Platzer M, Frank Kooy R, Lubs HA, Stevenson RE, Ramser J, Schwartz CE. Novel truncating mutations in the polyglutamine tract binding protein 1 gene (PQBP1) cause Renpenning syndrome and X-linked mental retardation in another family with microcephaly. Am J Hum Genet 2004; 74:777-80. [PMID: 15024694 PMCID: PMC1181956 DOI: 10.1086/383205] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Affiliation(s)
- Claus Lenski
- Department of Medical Genetics at the Ludwig-Maximilians-University, Munich; J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC; Royal University Hospital, Saskatoon, Canada; Institute for Molecular Biotechnology, Jena, Germany; Department of Medical Genetics, University of Antwerp, Antwerp, Belgium; and Mailman Center for Child Development, University of Miami School of Medicine, Miami, FL
| | - Fatima Abidi
- Department of Medical Genetics at the Ludwig-Maximilians-University, Munich; J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC; Royal University Hospital, Saskatoon, Canada; Institute for Molecular Biotechnology, Jena, Germany; Department of Medical Genetics, University of Antwerp, Antwerp, Belgium; and Mailman Center for Child Development, University of Miami School of Medicine, Miami, FL
| | - Alfons Meindl
- Department of Medical Genetics at the Ludwig-Maximilians-University, Munich; J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC; Royal University Hospital, Saskatoon, Canada; Institute for Molecular Biotechnology, Jena, Germany; Department of Medical Genetics, University of Antwerp, Antwerp, Belgium; and Mailman Center for Child Development, University of Miami School of Medicine, Miami, FL
| | - Alice Gibson
- Department of Medical Genetics at the Ludwig-Maximilians-University, Munich; J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC; Royal University Hospital, Saskatoon, Canada; Institute for Molecular Biotechnology, Jena, Germany; Department of Medical Genetics, University of Antwerp, Antwerp, Belgium; and Mailman Center for Child Development, University of Miami School of Medicine, Miami, FL
| | - Matthias Platzer
- Department of Medical Genetics at the Ludwig-Maximilians-University, Munich; J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC; Royal University Hospital, Saskatoon, Canada; Institute for Molecular Biotechnology, Jena, Germany; Department of Medical Genetics, University of Antwerp, Antwerp, Belgium; and Mailman Center for Child Development, University of Miami School of Medicine, Miami, FL
| | - R. Frank Kooy
- Department of Medical Genetics at the Ludwig-Maximilians-University, Munich; J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC; Royal University Hospital, Saskatoon, Canada; Institute for Molecular Biotechnology, Jena, Germany; Department of Medical Genetics, University of Antwerp, Antwerp, Belgium; and Mailman Center for Child Development, University of Miami School of Medicine, Miami, FL
| | - Herbert A. Lubs
- Department of Medical Genetics at the Ludwig-Maximilians-University, Munich; J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC; Royal University Hospital, Saskatoon, Canada; Institute for Molecular Biotechnology, Jena, Germany; Department of Medical Genetics, University of Antwerp, Antwerp, Belgium; and Mailman Center for Child Development, University of Miami School of Medicine, Miami, FL
| | - Roger E. Stevenson
- Department of Medical Genetics at the Ludwig-Maximilians-University, Munich; J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC; Royal University Hospital, Saskatoon, Canada; Institute for Molecular Biotechnology, Jena, Germany; Department of Medical Genetics, University of Antwerp, Antwerp, Belgium; and Mailman Center for Child Development, University of Miami School of Medicine, Miami, FL
| | - Juliane Ramser
- Department of Medical Genetics at the Ludwig-Maximilians-University, Munich; J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC; Royal University Hospital, Saskatoon, Canada; Institute for Molecular Biotechnology, Jena, Germany; Department of Medical Genetics, University of Antwerp, Antwerp, Belgium; and Mailman Center for Child Development, University of Miami School of Medicine, Miami, FL
| | - Charles E. Schwartz
- Department of Medical Genetics at the Ludwig-Maximilians-University, Munich; J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC; Royal University Hospital, Saskatoon, Canada; Institute for Molecular Biotechnology, Jena, Germany; Department of Medical Genetics, University of Antwerp, Antwerp, Belgium; and Mailman Center for Child Development, University of Miami School of Medicine, Miami, FL
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