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Li XY, Wang Z, Yang Y, Lin R, Wang C. Domain-specific phenotypes in LINS1-related disorder-A Chinese family with the Q92X variant and literature review. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2024:e32085. [PMID: 38563234 DOI: 10.1002/ajmg.c.32085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/12/2024] [Accepted: 03/20/2024] [Indexed: 04/04/2024]
Abstract
LINS1 is the human homolog of the Drosophila segment polarity gene that encodes an essential regulator of the wingless/Wnt signaling. By 2011, only seven pedigrees (16 patients) with eight causative variants in LINS1 gene have been reported. These cases mainly presented with infancy-/child-onset neurodevelopmental disorders, facial dysmorphia, and other clinical features, and a wide spectrum of clinically distinct phenotypes were also manifested. In our study, two brothers in a family were admitted and diagnosed with child-onset movement disorders, slight intellectual disability, psychological symptoms, eye problems, urinary and bowel dysfunction, mitral value prolapse, and Q-T prolongation. By exome sequencing, we identified a nonsense homozygous pathogenic variant (LINS1: c.274C > T (p.Q92X)), which had been reported in a case diagnosed with intellectual disability and psychiatric disorders (such as schizophrenia and anxiety). Compared with this case, the clinical features of our cases were distinct. In particular, our cases displayed unusual features of heart and blood system. Furthermore, the genotype-phenotype relationship analysis suggested that distinct phenotypes presented in cases carrying variants in different domains of the LINS1 gene. In conclusions, our findings suggest the high clinical variations in the LINS1 variants-related disorders. Moreover, the Q92X might be a recurrent variant in Hans of Southern China.
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Affiliation(s)
- Xu-Ying Li
- Department of Neurology and Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, China
| | - Zhanjun Wang
- Department of Neurology and Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, China
| | - Yanping Yang
- Department of Neurology, Shuozhou People's Hospital, Shanxi, China
| | - Ruichai Lin
- Shenzhen Clabee Biotechnology Incorporation, Shenzhen, China
| | - Chaodong Wang
- Department of Neurology and Neurobiology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing, China
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2
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Magrassi L, Brambilla F, Viganò R, Di Silvestre D, Benazzi L, Bellantoni G, Danesino GM, Comincini S, Mauri P. Proteomic Analysis on Sequential Samples of Cystic Fluid Obtained from Human Brain Tumors. Cancers (Basel) 2023; 15:4070. [PMID: 37627098 PMCID: PMC10452907 DOI: 10.3390/cancers15164070] [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: 06/06/2023] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Cystic formation in human primary brain tumors is a relatively rare event whose incidence varies widely according to the histotype of the tumor. Composition of the cystic fluid has mostly been characterized in samples collected at the time of tumor resection and no indications of the evolution of cystic content are available. We characterized the evolution of the proteome of cystic fluid using a bottom-up proteomic approach on sequential samples obtained from secretory meningioma (SM), cystic schwannoma (CS) and cystic high-grade glioma (CG). We identified 1008 different proteins; 74 of these proteins were found at least once in the cystic fluid of all tumors. The most abundant proteins common to all tumors studied derived from plasma, with the exception of prostaglandin D2 synthase, which is a marker of cerebrospinal fluid origin. Overall, the protein composition of cystic fluid obtained at different times from the same tumor remained stable. After the identification of differentially expressed proteins (DEPs) and the protein-protein interaction network analysis, we identified the presence of tumor-specific pathways that may help to characterize tumor-host interactions. Our results suggest that plasma proteins leaking from local blood-brain barrier disruption are important contributors to cyst fluid formation, but cerebrospinal fluid (CSF) and the tumor itself also contribute to the cystic fluid proteome and, in some cases, as with immunoglobulin G, shows tumor-specific variations that cannot be simply explained by differences in vessel permeability or blood contamination.
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Affiliation(s)
- Lorenzo Magrassi
- Neurosurgery, Dipartimento di Scienze Clinico-Chirurgiche e Pediatriche, Università degli Studi di Pavia, Fondazione IRCCS Policlinico S. Matteo, 27100 Pavia, Italy
- Istituto di Genetica Molecolare—CNR, 27100 Pavia, Italy
| | - Francesca Brambilla
- Proteomics and Metabolomics Institute for Biomedical Technologies (ITB-CNR), Segrate, 20090 Milan, Italy; (F.B.); (R.V.); (D.D.S.); (L.B.); (P.M.)
| | - Raffaello Viganò
- Proteomics and Metabolomics Institute for Biomedical Technologies (ITB-CNR), Segrate, 20090 Milan, Italy; (F.B.); (R.V.); (D.D.S.); (L.B.); (P.M.)
| | - Dario Di Silvestre
- Proteomics and Metabolomics Institute for Biomedical Technologies (ITB-CNR), Segrate, 20090 Milan, Italy; (F.B.); (R.V.); (D.D.S.); (L.B.); (P.M.)
| | - Louise Benazzi
- Proteomics and Metabolomics Institute for Biomedical Technologies (ITB-CNR), Segrate, 20090 Milan, Italy; (F.B.); (R.V.); (D.D.S.); (L.B.); (P.M.)
| | - Giuseppe Bellantoni
- Struttura Complessa di Neurochirurgia, Fondazione IRCCS Policlinico S. Matteo, 27100 Pavia, Italy;
| | - Gian Marco Danesino
- Struttura Complessa di Radiologia Diagnostica per Immagini 2—Neuroradiologia, Fondazione IRCCS Policlinico S. Matteo, 27100 Pavia, Italy;
| | - Sergio Comincini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, 27100 Pavia, Italy;
| | - Pierluigi Mauri
- Proteomics and Metabolomics Institute for Biomedical Technologies (ITB-CNR), Segrate, 20090 Milan, Italy; (F.B.); (R.V.); (D.D.S.); (L.B.); (P.M.)
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3
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Cheng Y, Xu SM, Takenaka K, Lindner G, Curry-Hyde A, Janitz M. A Unique Circular RNA Expression Pattern in the Peripheral Blood of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Patients. Gene 2023:147568. [PMID: 37328077 DOI: 10.1016/j.gene.2023.147568] [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: 02/20/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/18/2023]
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating disease with obscure aetiology. The underdiagnosis rate of ME/CFS is high due to the lack of diagnostic criteria based on objective markers. In recent years, circRNAs have emerged as potential genetic biomarkers for neurological diseases, including Parkinson's disease and Alzheimer's disease, making them likely to have the same prospect of being biomarkers in ME/CFS. However, despite the extensive amount of research that has been performed on the transcriptomes of ME/CFS patients, all of them are solely focused on linear RNAs, and the profiling of circRNAs in ME/CFS has been completely omitted. In this study, we investigated the expression profiles of circRNAs, comparing ME/CFS patients and controls before and after two sessions of cardiopulmonary exercise longitudinally. In patients with ME/CFS, the number of detected circRNAs was higher compared to healthy controls, indicating potential differences in circRNA expression associated with the disease. Additionally, healthy controls showed an increase in the number of circRNAs following exercise testing, while no similar pattern was evident in ME/CFS patients, further highlighting physiological differences between the two groups. A lack of correlation was observed between differentially expressed circRNAs and their corresponding coding genes in terms of expression and function, suggesting the potential of circRNAs as independent biomarkers in ME/CFS. Specifically, 14 circRNAs were highly expressed in ME/CFS patients but absent in controls throughout the exercise study, indicating a unique molecular signature specific to ME/CFS patients and providing potential diagnostic biomarkers for the disease. Significant enrichment of protein and gene regulative pathways were detected in relation to five of these 14 circRNAs based on their predicted miRNA target genes. Overall, this is the first study to describe the circRNA expression profile in peripheral blood of ME/CFS patients, providing valuable insights into the molecular mechanisms underlying the disease.
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Affiliation(s)
- Yuning Cheng
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Si-Mei Xu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Konii Takenaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Grace Lindner
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Ashton Curry-Hyde
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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4
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Identification of a novel nonsense homozygous mutation of LINS1 gene in two sisters with intellectual disability, schizophrenia, and anxiety. Biomed J 2021; 44:748-751. [PMID: 34450347 PMCID: PMC8847845 DOI: 10.1016/j.bj.2021.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 08/15/2021] [Accepted: 08/18/2021] [Indexed: 11/23/2022] Open
Abstract
Background LINS1 encodes the lines homolog 1 protein that contains the Drosophila lines homologous domain. LINS1 mutations cause a rare recessive form of intellectual disability. So far, eight LINS1 mutations were reported in the literature. Methods We conducted a whole-genome sequencing analysis for a family with two sisters diagnosed with moderate intellectual disability, schizophrenia, and anxiety. Results We identified a novel homozygous nonsense mutation in the LINS1 in these two sisters. The mutation was a C-to-T substitution at the cDNA nucleotide position 274 that changed the amino acid glutamine at the codon 92 to stop codon (Gln92X). The mutation was transmitted from their unrelated parents, who were heterozygous carriers. Conclusions We identified the first case of LINS1-associated neurodevelopmental disorder in Taiwan. Our findings suggest that besides intellectual disability, psychiatric diagnoses such as schizophrenia and anxiety disorder may also be part of clinical phenotypes of LINS1 mutations.
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Taşkıran EZ, Karaosmanoğlu B, Koşukcu C, Ürel-Demir G, Akgün-Doğan Ö, Şimşek-Kiper PÖ, Alikaşifoğlu M, Boduroğlu K, Utine GE. Diagnostic yield of whole-exome sequencing in non-syndromic intellectual disability. JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2021; 65:577-588. [PMID: 33739554 DOI: 10.1111/jir.12835] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 02/23/2021] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Aetiological diagnosis in non-syndromic intellectual disability (NSID) still poses a diagnostic challenge to clinicians. METHODS Screening is currently achieved by chromosomal microarrays followed by whole-exome sequencing (WES). In search for the aetiological yield of WES in patients with NSID, 59 unrelated patients were studied. RESULTS Among the 59 patients, 44 (74.6%) were from consanguineous unions. Epilepsy was present in 11 (37.9%), behavioural problems in 12 (41.4%) and autistic features in 14 (48.3%). WES analysis resulted in molecular diagnosis in 29 patients (49.2%). Some of the genes were specific for nervous system functioning, like HERC1, TBC1D7, LINS, HECW2, DEAF1, HNMT, DLG3, NRXN1 and HUWE1. Others were ubiquitously expressed genes involved in fundamental cellular processes, like IARS, UBE3A, COQ4, TAF1, SETBP1, ARV1, ZC4H2, KAT6A, ASXL3, THOC6, HNRNPH2, TUBA8 and KIF1A. Twenty-two (75.8%) were consanguineously married; however, only 12 (41.4%) of the detected genes caused autosomal recessive phenotypes. CONCLUSIONS This cohort suggests that recessive genes probably represent an actually smaller subgroup of NSID, even among families with consanguinity. Although in societies with high consanguinity rates, considering the recessive inheritance first seems to be an advantageous strategy, de novo mutations in autosomal dominantly expressed genes represent the major aetiological group in patients with NSID, even among those patients from consanguineous families.
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Affiliation(s)
- E Z Taşkıran
- Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - B Karaosmanoğlu
- Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - C Koşukcu
- Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - G Ürel-Demir
- Department of Pediatrics, Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Ö Akgün-Doğan
- Department of Pediatrics, Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - P Ö Şimşek-Kiper
- Department of Pediatrics, Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - M Alikaşifoğlu
- Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - K Boduroğlu
- Department of Pediatrics, Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - G E Utine
- Department of Pediatrics, Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
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6
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Neuhofer CM, Catarino CB, Schmidt H, Seelos K, Alhaddad B, Haack TB, Klopstock T. LINS1-associated neurodevelopmental disorder: Family with novel mutation expands the phenotypic spectrum. NEUROLOGY-GENETICS 2020; 6:e500. [PMID: 32802957 PMCID: PMC7413627 DOI: 10.1212/nxg.0000000000000500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/29/2020] [Indexed: 11/18/2022]
Abstract
Objective Clinical, neuroimaging, and genetic characterization of 3 patients with LINS1-associated developmental regression, intellectual disability, dysmorphism, and further neurologic deficits. Methods Three affected brothers from a consanguineous family from Afghanistan, their 2 healthy siblings, and both parents were all assessed in the clinic. General and neurologic examination, expert dysmorphology examination, and 3T brain MRI were performed. Whole-exome sequencing was performed for the 3 affected brothers, followed by Sanger sequencing in all available family members. Results The index patient and his 2 affected brothers presented a complex neurologic syndrome with similar features but marked intrafamilial phenotypical variability, including varying degrees of cognitive impairment, speech impairment, dystonia, abnormal eye movements, and dysmorphic features. All 3 affected brothers are homozygous for a novel, pathogenic frameshift mutation in LINS1, c.1672_1679del, and p.Gly558Profs*22, whereas both parents and healthy siblings are heterozygous for the mutation. No major brain malformations were evident in 3T brain MRI of the affected brothers. Conclusion This consanguineous family with a novel mutation expands the spectrum of LINS1-associated disorder to include developmental regression, oculomotor signs, and dystonia, previously not described in the published 9 cases of this rare disorder. The 3T-MRI data from our 3 patients and review of the neuroimaging data in the literature showed unspecific brain MRI changes. LINS1 protein is a known modulating factor of the Wnt signaling pathway, with important roles in organogenesis including of the cerebral cortex. More research is warranted to disentangle the underlying pathophysiologic mechanisms, leading to cognitive impairment and the complex phenotype of LINS1-associated disorder.
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Affiliation(s)
- Christiane M Neuhofer
- Friedrich-Baur-Institute (C.M.N., C.B.C., T.K.), Department of Neurology, University Hospital, LMU Munich, Germany; Institute of Human Genetics (C.M.N.), University Medical Center Göttingen, Germany; Department of Pediatrics (H.S.), Medical Genetics, Dr. von Haunersches Kinderspital, University Hospital, LMU Munich, Germany; Department of Neuroradiology (K.S.), University Hospital, LMU Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technical University Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Helmholtz Zentrum München, Neuherberg, Germany; German Center for Neurodegenerative Diseases (DZNE) (T.K.), Munich, Germany; and Munich Cluster for Systems Neurology (SyNergy) (T.K.), Munich, Germany
| | - Claudia B Catarino
- Friedrich-Baur-Institute (C.M.N., C.B.C., T.K.), Department of Neurology, University Hospital, LMU Munich, Germany; Institute of Human Genetics (C.M.N.), University Medical Center Göttingen, Germany; Department of Pediatrics (H.S.), Medical Genetics, Dr. von Haunersches Kinderspital, University Hospital, LMU Munich, Germany; Department of Neuroradiology (K.S.), University Hospital, LMU Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technical University Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Helmholtz Zentrum München, Neuherberg, Germany; German Center for Neurodegenerative Diseases (DZNE) (T.K.), Munich, Germany; and Munich Cluster for Systems Neurology (SyNergy) (T.K.), Munich, Germany
| | - Heinrich Schmidt
- Friedrich-Baur-Institute (C.M.N., C.B.C., T.K.), Department of Neurology, University Hospital, LMU Munich, Germany; Institute of Human Genetics (C.M.N.), University Medical Center Göttingen, Germany; Department of Pediatrics (H.S.), Medical Genetics, Dr. von Haunersches Kinderspital, University Hospital, LMU Munich, Germany; Department of Neuroradiology (K.S.), University Hospital, LMU Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technical University Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Helmholtz Zentrum München, Neuherberg, Germany; German Center for Neurodegenerative Diseases (DZNE) (T.K.), Munich, Germany; and Munich Cluster for Systems Neurology (SyNergy) (T.K.), Munich, Germany
| | - Klaus Seelos
- Friedrich-Baur-Institute (C.M.N., C.B.C., T.K.), Department of Neurology, University Hospital, LMU Munich, Germany; Institute of Human Genetics (C.M.N.), University Medical Center Göttingen, Germany; Department of Pediatrics (H.S.), Medical Genetics, Dr. von Haunersches Kinderspital, University Hospital, LMU Munich, Germany; Department of Neuroradiology (K.S.), University Hospital, LMU Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technical University Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Helmholtz Zentrum München, Neuherberg, Germany; German Center for Neurodegenerative Diseases (DZNE) (T.K.), Munich, Germany; and Munich Cluster for Systems Neurology (SyNergy) (T.K.), Munich, Germany
| | - Bader Alhaddad
- Friedrich-Baur-Institute (C.M.N., C.B.C., T.K.), Department of Neurology, University Hospital, LMU Munich, Germany; Institute of Human Genetics (C.M.N.), University Medical Center Göttingen, Germany; Department of Pediatrics (H.S.), Medical Genetics, Dr. von Haunersches Kinderspital, University Hospital, LMU Munich, Germany; Department of Neuroradiology (K.S.), University Hospital, LMU Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technical University Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Helmholtz Zentrum München, Neuherberg, Germany; German Center for Neurodegenerative Diseases (DZNE) (T.K.), Munich, Germany; and Munich Cluster for Systems Neurology (SyNergy) (T.K.), Munich, Germany
| | - Tobias B Haack
- Friedrich-Baur-Institute (C.M.N., C.B.C., T.K.), Department of Neurology, University Hospital, LMU Munich, Germany; Institute of Human Genetics (C.M.N.), University Medical Center Göttingen, Germany; Department of Pediatrics (H.S.), Medical Genetics, Dr. von Haunersches Kinderspital, University Hospital, LMU Munich, Germany; Department of Neuroradiology (K.S.), University Hospital, LMU Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technical University Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Helmholtz Zentrum München, Neuherberg, Germany; German Center for Neurodegenerative Diseases (DZNE) (T.K.), Munich, Germany; and Munich Cluster for Systems Neurology (SyNergy) (T.K.), Munich, Germany
| | - Thomas Klopstock
- Friedrich-Baur-Institute (C.M.N., C.B.C., T.K.), Department of Neurology, University Hospital, LMU Munich, Germany; Institute of Human Genetics (C.M.N.), University Medical Center Göttingen, Germany; Department of Pediatrics (H.S.), Medical Genetics, Dr. von Haunersches Kinderspital, University Hospital, LMU Munich, Germany; Department of Neuroradiology (K.S.), University Hospital, LMU Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Technical University Munich, Germany; Institute of Human Genetics (B.A., T.B.H.), Helmholtz Zentrum München, Neuherberg, Germany; German Center for Neurodegenerative Diseases (DZNE) (T.K.), Munich, Germany; and Munich Cluster for Systems Neurology (SyNergy) (T.K.), Munich, Germany
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7
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Muthusamy B, Bellad A, Prasad P, Bandari AK, Bhuvanalakshmi G, Kiragasur RM, Girimaj SC, Pandey A. A Novel LINS1 Truncating Mutation in Autosomal Recessive Nonsyndromic Intellectual Disability. Front Psychiatry 2020; 11:354. [PMID: 32499722 PMCID: PMC7247441 DOI: 10.3389/fpsyt.2020.00354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The large majority of cases with intellectual disability are syndromic (i.e. occur with other well-defined clinical phenotypes) and have been studied extensively. Autosomal recessive nonsyndromic intellectual disability is a group of genetically heterogeneous disorders for which a number of potentially causative genes have been identified although the molecular basis of most of them remains unexplored. Here, we report the clinical characteristics and genetic findings of a family with two male siblings affected with autosomal recessive nonsyndromic intellectual disability. Whole exome sequencing was carried out on two affected male siblings and unaffected parents. A potentially pathogenic variant identified in this study was confirmed by Sanger sequencing to be inherited in an autosomal recessive fashion. We identified a novel nonsense mutation (p.Gln368Ter) in the LINS1 gene which leads to loss of 389 amino acids in the C-terminus of the encoded protein. The truncation mutation causes a complete loss of LINES_C domain along with loss of three known phosphorylation sites and a known ubiquitylation site in addition to other evolutionarily conserved regions of LINS1. LINS1 has been reported to cause MRT27 (mental retardation, autosomal recessive 27), a rare autosomal recessive nonsyndromic intellectual disability, with limited characterization of the phenotype. Identification of a potentially pathogenic truncating mutation in LINS1 in two profoundly intellectually impaired patients also confirms its role in cognition.
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Affiliation(s)
- Babylakshmi Muthusamy
- Institute of Bioinformatics, Bangalore, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India.,Manipal Academy of Higher Education, Manipal, India
| | - Anikha Bellad
- Institute of Bioinformatics, Bangalore, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India.,Manipal Academy of Higher Education, Manipal, India
| | - Pramada Prasad
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Aravind K Bandari
- Institute of Bioinformatics, Bangalore, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India.,Manipal Academy of Higher Education, Manipal, India
| | | | - R M Kiragasur
- Department of Child and Adolescent Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Satish Chandra Girimaj
- Department of Child and Adolescent Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Akhilesh Pandey
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India.,Manipal Academy of Higher Education, Manipal, India.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
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8
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Hu H, Kahrizi K, Musante L, Fattahi Z, Herwig R, Hosseini M, Oppitz C, Abedini SS, Suckow V, Larti F, Beheshtian M, Lipkowitz B, Akhtarkhavari T, Mehvari S, Otto S, Mohseni M, Arzhangi S, Jamali P, Mojahedi F, Taghdiri M, Papari E, Soltani Banavandi MJ, Akbari S, Tonekaboni SH, Dehghani H, Ebrahimpour MR, Bader I, Davarnia B, Cohen M, Khodaei H, Albrecht B, Azimi S, Zirn B, Bastami M, Wieczorek D, Bahrami G, Keleman K, Vahid LN, Tzschach A, Gärtner J, Gillessen-Kaesbach G, Varaghchi JR, Timmermann B, Pourfatemi F, Jankhah A, Chen W, Nikuei P, Kalscheuer VM, Oladnabi M, Wienker TF, Ropers HH, Najmabadi H. Genetics of intellectual disability in consanguineous families. Mol Psychiatry 2019; 24:1027-1039. [PMID: 29302074 DOI: 10.1038/s41380-017-0012-2] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 10/19/2017] [Accepted: 10/30/2017] [Indexed: 01/17/2023]
Abstract
Autosomal recessive (AR) gene defects are the leading genetic cause of intellectual disability (ID) in countries with frequent parental consanguinity, which account for about 1/7th of the world population. Yet, compared to autosomal dominant de novo mutations, which are the predominant cause of ID in Western countries, the identification of AR-ID genes has lagged behind. Here, we report on whole exome and whole genome sequencing in 404 consanguineous predominantly Iranian families with two or more affected offspring. In 219 of these, we found likely causative variants, involving 77 known and 77 novel AR-ID (candidate) genes, 21 X-linked genes, as well as 9 genes previously implicated in diseases other than ID. This study, the largest of its kind published to date, illustrates that high-throughput DNA sequencing in consanguineous families is a superior strategy for elucidating the thousands of hitherto unknown gene defects underlying AR-ID, and it sheds light on their prevalence.
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Affiliation(s)
- Hao Hu
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany.,Guangzhou Women and Children's Medical Center, 510623, Guangzhou, China
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Luciana Musante
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Ralf Herwig
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Masoumeh Hosseini
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Cornelia Oppitz
- IMP-Research Institute of Molecular Pathology, 1030, Vienna, Austria
| | - Seyedeh Sedigheh Abedini
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Vanessa Suckow
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Farzaneh Larti
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | | | - Tara Akhtarkhavari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Sepideh Mehvari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Sabine Otto
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Payman Jamali
- Shahrood Genetic Counseling Center, Welfare Office, Semnan, 36156, Iran
| | - Faezeh Mojahedi
- Mashhad Medical Genetic Counseling Center, Mashhad, 91767, Iran
| | - Maryam Taghdiri
- Shiraz Genetic Counseling Center, Welfare Office, Shiraz, Iran
| | - Elaheh Papari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | | | - Saeide Akbari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Seyed Hassan Tonekaboni
- Pediatric Neurology Research Center, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, 15468, Iran
| | - Hossein Dehghani
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Mohammad Reza Ebrahimpour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Ingrid Bader
- Kinderzentrum München, Technische Universität München, 81377, München, Germany
| | - Behzad Davarnia
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Monika Cohen
- Children's Center Munich, 81377, Munich, Germany
| | - Hossein Khodaei
- Meybod Genetics Research Center, Welfare Organization, Yazd, 89651, Iran
| | - Beate Albrecht
- Institute of Human Genetics, University Hospital Essen, 45122, Essen, Germany
| | - Sarah Azimi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Birgit Zirn
- Genetikum Counseling Center, 70173, Stuttgart, Germany
| | - Milad Bastami
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Dagmar Wieczorek
- Institute of Human Genetics and Anthropology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Gholamreza Bahrami
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Krystyna Keleman
- IMP-Research Institute of Molecular Pathology, 1030, Vienna, Austria.,Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Leila Nouri Vahid
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Andreas Tzschach
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany.,Institute of Clinical Genetics, Technische Universität Dresden, Dresden, Germany
| | - Jutta Gärtner
- University Medical Center, Georg August University Göttingen, 37075, Göttingen, Germany
| | | | | | - Bernd Timmermann
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | | | - Aria Jankhah
- Shiraz Genetic Counseling Center, Shiraz, 71346, Iran
| | - Wei Chen
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, 13125, Berlin, Germany
| | - Pooneh Nikuei
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | | | - Morteza Oladnabi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Thomas F Wienker
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Hans-Hilger Ropers
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany. .,Institute of Human Genetics, University Medicine, Mainz, Germany.
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran. .,Kariminejad - Najmabadi Pathology & Genetics Centre, Tehran, 14667-13713, Iran.
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9
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Martin HC, Jones WD, McIntyre R, Sanchez-Andrade G, Sanderson M, Stephenson JD, Jones CP, Handsaker J, Gallone G, Bruntraeger M, McRae JF, Prigmore E, Short P, Niemi M, Kaplanis J, Radford EJ, Akawi N, Balasubramanian M, Dean J, Horton R, Hulbert A, Johnson DS, Johnson K, Kumar D, Lynch SA, Mehta SG, Morton J, Parker MJ, Splitt M, Turnpenny PD, Vasudevan PC, Wright M, Bassett A, Gerety SS, Wright CF, FitzPatrick DR, Firth HV, Hurles ME, Barrett JC. Quantifying the contribution of recessive coding variation to developmental disorders. Science 2018; 362:1161-1164. [PMID: 30409806 DOI: 10.1126/science.aar6731] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 08/10/2018] [Accepted: 10/29/2018] [Indexed: 12/13/2022]
Abstract
We estimated the genome-wide contribution of recessive coding variation in 6040 families from the Deciphering Developmental Disorders study. The proportion of cases attributable to recessive coding variants was 3.6% in patients of European ancestry, compared with 50% explained by de novo coding mutations. It was higher (31%) in patients with Pakistani ancestry, owing to elevated autozygosity. Half of this recessive burden is attributable to known genes. We identified two genes not previously associated with recessive developmental disorders, KDM5B and EIF3F, and functionally validated them with mouse and cellular models. Our results suggest that recessive coding variants account for a small fraction of currently undiagnosed nonconsanguineous individuals, and that the role of noncoding variants, incomplete penetrance, and polygenic mechanisms need further exploration.
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Affiliation(s)
- Hilary C Martin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
| | - Wendy D Jones
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Great Ormond Street Hospital for Children, National Health Service (NHS) Foundation Trust, Great Ormond Street Hospital, Great Ormond Street, London WC1N 3JH, UK
| | - Rebecca McIntyre
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Mark Sanderson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - James D Stephenson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Carla P Jones
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Juliet Handsaker
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Giuseppe Gallone
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Jeremy F McRae
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Elena Prigmore
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Patrick Short
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Mari Niemi
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Joanna Kaplanis
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Elizabeth J Radford
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Department of Paediatrics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Nadia Akawi
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, OPD2, Northern General Hospital, Herries Rd., Sheffield, S5 7AU, UK
| | - John Dean
- Department of Genetics, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Rachel Horton
- Wessex Clinical Genetics Service, G Level, Princess Anne Hospital, Coxford Road, Southampton SO16 5YA, UK
| | - Alice Hulbert
- Cheshire and Merseyside Clinical Genetic Service, Liverpool Women's NHS Foundation Trust, Crown Street, Liverpool L8 7SS, UK
| | - Diana S Johnson
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, OPD2, Northern General Hospital, Herries Rd., Sheffield, S5 7AU, UK
| | - Katie Johnson
- Department of Clinical Genetics, City Hospital Campus, Hucknall Road, Nottingham NG5 1PB, UK
| | - Dhavendra Kumar
- Institute of Cancer and Genetics, University Hospital of Wales, Cardiff, UK
| | | | - Sarju G Mehta
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jenny Morton
- Clinical Genetics Unit, Birmingham Women's Hospital, Edgbaston, Birmingham B15 2TG, UK
| | - Michael J Parker
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Western Bank, Sheffield S10 2TH, UK
| | - Miranda Splitt
- Northern Genetics Service, Newcastle upon Tyne Hospitals, NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Peter D Turnpenny
- Clinical Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Pradeep C Vasudevan
- Department of Clinical Genetics, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester LE1 5WW, UK
| | - Michael Wright
- Northern Genetics Service, Newcastle upon Tyne Hospitals, NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Andrew Bassett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Sebastian S Gerety
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Caroline F Wright
- University of Exeter Medical School, Institute of Biomedical and Clinical Science, Research, Innovation, Learning and Development (RILD), Royal Devon and Exeter Hospital, Barrack Road, Exeter, EX2 5DW, UK
| | - David R FitzPatrick
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Helen V Firth
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Jeffrey C Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
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10
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McMillan HJ, Holahan AL, Richer J. Worster-Drought Syndrome Associated With LINS Mutations. Child Neurol Open 2018; 5:2329048X18791083. [PMID: 30090841 PMCID: PMC6077897 DOI: 10.1177/2329048x18791083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 05/28/2018] [Accepted: 06/30/2018] [Indexed: 11/25/2022] Open
Abstract
Worster-Drought syndrome is a congenital, pseudobulbar paresis. There is no identified molecular etiology despite familial cases reported. The authors report a boy who was diagnosed with Worster-Drought syndrome due to longstanding drooling, dysphagia, and impaired tongue movement. Magnetic resonance imaging of the brain was unrevealing. At 14 years old, he remains aphonic with normal facial and extraocular movements. Nonsense mutations in the LINS gene, p.Glu366X and p.Lys393X, were found. Results from neuropsychological testing at 14 years old were consistent with a diagnosis of intellectual disability and revealed nonverbal reasoning skills at a 5-year-old level with relative sparing of his receptive vocabulary and visual attention. Compared to prior testing at 9 years old, his receptive language improved from a 6-year-old to an 8.5-year-old level. The authors report LINS mutations associated with Worster-Drought syndrome. This highlights that despite severe and persistent aphonia, receptive language improvements can be observed within the context of intellectual disability.
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Affiliation(s)
- Hugh J McMillan
- Department of Pediatrics, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Anne-Lise Holahan
- Department of Pediatrics, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Julie Richer
- Department of Genetics, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
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11
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Cannarella R, Mattina T, Condorelli RA, Mongioì LM, Pandini G, La Vignera S, Calogero AE. Chromosome 15 structural abnormalities: effect on IGF1R gene expression and function. Endocr Connect 2017; 6:528-539. [PMID: 28899882 PMCID: PMC5597972 DOI: 10.1530/ec-17-0158] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 12/27/2022]
Abstract
Insulin-like growth factor 1 receptor (IGF1R), mapping on the 15q26.3 chromosome, is required for normal embryonic and postnatal growth. The aim of the present study was to evaluate the IGF1R gene expression and function in three unrelated patients with chromosome 15 structural abnormalities. We report two male patients with the smallest 15q26.3 chromosome duplication described so far, and a female patient with ring chromosome 15 syndrome. Patient one, with a 568 kb pure duplication, had overgrowth, developmental delay, mental and psychomotor retardation, obesity, cryptorchidism, borderline low testis volume, severe oligoasthenoteratozoospermia and gynecomastia. We found a 1.8-fold increase in the IGF1R mRNA and a 1.3-fold increase in the IGF1R protein expression (P < 0.05). Patient two, with a 650 kb impure duplication, showed overgrowth, developmental delay, mild mental retardation, precocious puberty, low testicular volume and severe oligoasthenoteratozoospermia. The IGF1R mRNA and protein expression was similar to that of the control. Patient three, with a 46,XX r(15) (p10q26.2) karyotype, displayed intrauterine growth retardation, developmental delay, mental and psychomotor retardation. We found a <0.5-fold decrease in the IGF1R mRNA expression and an undetectable IGF1R activity. After reviewing the previously 96 published cases of chromosome 15q duplication, we found that neurological disorders, congenital cardiac defects, typical facial traits and gonadal abnormalities are the prominent features in patients with chromosome 15q duplication. Interestingly, patients with 15q deletion syndrome display similar features. We speculate that both the increased and decreased IGF1R gene expression may play a role in the etiology of neurological and gonadal disorders.
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Affiliation(s)
- Rossella Cannarella
- Department of Clinical and Experimental MedicineUniversity of Catania, Catania, Italy
| | | | - Rosita A Condorelli
- Department of Clinical and Experimental MedicineUniversity of Catania, Catania, Italy
| | - Laura M Mongioì
- Department of Clinical and Experimental MedicineUniversity of Catania, Catania, Italy
| | - Giuseppe Pandini
- Department of Clinical and Experimental MedicineUniversity of Catania, Catania, Italy
| | - Sandro La Vignera
- Department of Clinical and Experimental MedicineUniversity of Catania, Catania, Italy
| | - Aldo E Calogero
- Department of Clinical and Experimental MedicineUniversity of Catania, Catania, Italy
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12
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Khan MA, Khan S, Windpassinger C, Badar M, Nawaz Z, Mohammad RM. The Molecular Genetics of Autosomal Recessive Nonsyndromic Intellectual Disability: a Mutational Continuum and Future Recommendations. Ann Hum Genet 2017; 80:342-368. [PMID: 27870114 DOI: 10.1111/ahg.12176] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 10/03/2016] [Indexed: 12/19/2022]
Abstract
Intellectual disability (ID) is a clinical manifestation of the central nervous system without any major dysmorphologies of the brain. Biologically it affects learning capabilities, memory, and cognitive functioning. The basic defining features of ID are characterized by IQ<70, age of onset before 18 years, and impairment of at least two of the adaptive skills. Clinically it is classified in a syndromic (with additional abnormalities) and a nonsyndromic form (with only cognitive impairment). The study of nonsyndromic intellectual disability (NSID) can best explain the pathophysiology of cognition, intelligence and memory. Genetic analysis in autosomal recessive nonsyndrmic ID (ARNSID) has mapped 51 disease loci, 34 of which have revealed their defective genes. These genes play diverse physiological roles in various molecular processes, including methylation, proteolysis, glycosylation, signal transduction, transcription regulation, lipid metabolism, ion homeostasis, tRNA modification, ubiquitination and neuromorphogenesis. High-density SNP array and whole exome sequencing has increased the pace of gene discoveries and many new mutations are being published every month. The lack of uniform criteria has assigned multiple identifiers (or accession numbers) to the same MRT locus (e.g. MRT7 and MRT22). Here in this review we describe the molecular genetics of ARNSID, prioritize the candidate genes in uncharacterized loci, and propose a new nomenclature to reorganize the mutation data that will avoid the confusion of assigning duplicate accession numbers to the same ID locus and to make the data manageable in the future as well.
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Affiliation(s)
- Muzammil Ahmad Khan
- Genomic Core Facility, Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar.,Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I.Khan, 29050 KPK, Pakistan
| | - Saadullah Khan
- Genomic Core Facility, Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar.,Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, KPK, Pakistan
| | | | - Muhammad Badar
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I.Khan, 29050 KPK, Pakistan
| | - Zafar Nawaz
- Genomic Core Facility, Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar
| | - Ramzi M Mohammad
- Genomic Core Facility, Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar
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13
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Sheth J, Ranjan G, Shah K, Bhavsar R, Sheth F. NovelLINS1missense mutation in a family with non-syndromic intellectual disability. Am J Med Genet A 2017; 173:1041-1046. [DOI: 10.1002/ajmg.a.38089] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 11/23/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Jayesh Sheth
- FRIGE's Institute of Human Genetics; Ahmedabad Gujarat India
| | - Gyan Ranjan
- Department of Genetic Engineering; SRM University; Kattankulathur Tamil Nadu India
| | - Krati Shah
- FRIGE's Institute of Human Genetics; Ahmedabad Gujarat India
| | - Riddhi Bhavsar
- FRIGE's Institute of Human Genetics; Ahmedabad Gujarat India
| | - Frenny Sheth
- FRIGE's Institute of Human Genetics; Ahmedabad Gujarat India
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14
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Akawi NA, Ben-Salem S, Hertecant J, John A, Pramathan T, Kizhakkedath P, Ali BR, Al-Gazali L. A homozygous splicing mutation in ELAC2 suggests phenotypic variability including intellectual disability with minimal cardiac involvement. Orphanet J Rare Dis 2016; 11:139. [PMID: 27769300 PMCID: PMC5073853 DOI: 10.1186/s13023-016-0526-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 10/14/2016] [Indexed: 02/08/2023] Open
Abstract
Background The group of ELAC2-related encephalomyopathies is a recent addition to the rapidly growing heterogeneous mitochondrial disorders. Results We describe a highly inbred consanguineous Pakistani family with multiple affected children in 2 branches exhibiting moderately severe global developmental delay. Using homozygosity mapping, we mapped the phenotype in this family to a single locus on chromosome 17. In addition, whole-exome sequencing identified a homozygous splicing mutation (c.1423 + 2 T > A) in ELAC2 gene that disrupted the canonical donor splice site of intron 15 of all known isoforms. A noticeable reduction in ELAC2 expression was observed in patients compared to controls. In addition, patients exhibited significantly increased levels of 5′ end unprocessed mt-RNAs compared to the control fibroblast cells. Conclusions The only three previously reported families with defects in ELAC2 gene exhibited infantile hypertrophic cardiomyopathy and complex I deficiency. In contrast, our patients exhibited intellectual disability as the main feature with minimal cardiac involvement. Therefore our findings expand the phenotypic spectrum of ELAC2- associated disorders illustrating clinical heterogeneity of mutations in this gene. In addition, ELAC2 mutations should be considered when evaluating patient with mainly intellectual disability phenotypes. Electronic supplementary material The online version of this article (doi:10.1186/s13023-016-0526-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nadia A Akawi
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.,Present address: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Salma Ben-Salem
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Jozef Hertecant
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.,Department of Paediatrics, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Anne John
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Thachillath Pramathan
- Department of Paediatrics, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666, Al-Ain, United Arab Emirates
| | - Praseetha Kizhakkedath
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Lihadh Al-Gazali
- Department of Paediatrics, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666, Al-Ain, United Arab Emirates.
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15
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Akawi N, Ben-Salem S, Lahti L, Partanen J, Ali BR, Al-Gazali L. A recessive syndrome of intellectual disability, moderate overgrowth, and renal dysplasia predisposing to Wilms tumor is caused by a mutation in FIBP gene. Am J Med Genet A 2016; 170:2111-8. [PMID: 27183861 DOI: 10.1002/ajmg.a.37741] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/27/2016] [Indexed: 02/05/2023]
Abstract
Clinical classification of overgrowth syndromes represents a challenge since a wide spectrum of disorders result in marked overgrowth. Therefore, there is a continuous effort to identify the genetic basis of these disorders that will eventually facilitate their molecular classification. Here, we have identified the genetic etiology and the pathogenetic mechanism underlying a rare autosomal recessive overgrowth syndrome in three affected siblings. The overgrowth phenotype in the patients was accompanied by developmental delay, learning disabilities, and variable congenital abnormalities. To elucidate the genetic etiology of the disorder, whole-genome genotyping and whole-exome sequencing were used. The disease was mapped to 3p21.1-p14.2 and 11q13.1-q13.4, where an in-frame insertion (c.175_176insTAA) in FIBP gene was revealed. The resulting indel (p.H59LN) was predicted to change the protein conformation with likely deleterious effect on its function as one of the fibroblast growth factor signaling mediators. In vitro cellular proliferation assay and in situ hypridization in vivo were then performed to understand the pathophysiology of the disease. The patients' skin fibroblasts showed an increased proliferation capacity compared to the controls' explaining the observed overgrowth phenotype. In addition, we detected Fibp expression most notably in the brains of mice embryos suggesting a possible effect on cognitive functions early in development. To date, only one patient has been reported with a homozygous nonsense mutation in FIBP exhibiting an overgrowth syndrome with multiple congenital abnormalities. Taken all together, these findings provide convincing evidence implicating FIBP aberrations in the newly recognized overgrowth syndrome and expand the associated phenotypes to include possible Wilms tumor predisposition. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Nadia Akawi
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Salma Ben-Salem
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Laura Lahti
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Juha Partanen
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Bassam R Ali
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Lihadh Al-Gazali
- Department of Paediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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16
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Discovery of four recessive developmental disorders using probabilistic genotype and phenotype matching among 4,125 families. Nat Genet 2015; 47:1363-9. [PMID: 26437029 PMCID: PMC5988033 DOI: 10.1038/ng.3410] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 08/31/2015] [Indexed: 12/29/2022]
Abstract
Discovery of most autosomal recessive disease genes has involved analysis of large, often consanguineous, multiplex families or small cohorts of unrelated individuals with a well-defined clinical condition. Discovery of novel dominant causes of rare, genetically heterogenous developmental disorders has been revolutionized by exome analysis of large cohorts of phenotypically diverse parent-offspring trios 1,2. Here we analysed 4,125 families with diverse, rare, genetically heterogeneous developmental disorders and identified four novel autosomal recessive disorders. These four disorders were identified by integrating Mendelian filtering (identifying probands with rare biallelic putatively damaging variants in the same gene) with statistical assessments of (i) the likelihood of sampling the observed genotypes from the general population, and (ii) the phenotypic similarity of patients with the same recessive candidate gene. This new paradigm promises to catalyse discovery of novel recessive disorders, especially those with less consistent or nonspecific clinical presentations, and those caused predominantly by compound heterozygous genotypes.
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17
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Ben-Salem S, Gleeson JG, Al-Shamsi AM, Islam B, Hertecant J, Ali BR, Al-Gazali L. Asparagine synthetase deficiency detected by whole exome sequencing causes congenital microcephaly, epileptic encephalopathy and psychomotor delay. Metab Brain Dis 2015; 30:687-94. [PMID: 25227173 PMCID: PMC4915861 DOI: 10.1007/s11011-014-9618-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 09/08/2014] [Indexed: 02/05/2023]
Abstract
Deficiency of Asparagine Synthetase (ASNSD, MIM 615574) is a very rare autosomal recessive disorder presenting with some brain abnormalities. Affected individuals have congenital microcephaly and progressive encephalopathy associated with severe intellectual disability and intractable seizures. The loss of function of the asparagine synthetase (ASNS, EC 6.3.5.4), particularly in the brain, is the major cause of this particular congenital microcephaly. In this study, we clinically evaluated an affected child from a consanguineous Emirati family presenting with congenital microcephaly and epileptic encephalopathy. In addition, whole-exome sequencing revealed a novel homozygous substitution mutation (c.1193A > C) in the ASNS gene. This mutation resulted in the substitution of highly conserved tyrosine residue by cysteine (p.Y398C). Molecular modeling analysis predicts hypomorphic and damaging effects of this mutation on the protein structure and altering its enzymatic activity. Therefore, we conclude that the loss of ASNS function is most likely the cause of this condition in the studied family. This report brings the number of reported families with this very rare disorder to five and the number of pathogenic mutations in the ASNS gene to four. This finding extends the ASNS pathogenic mutations spectrum and highlights the utility of whole-exome sequencing in elucidation the causes of rare recessive disorders that are heterogeneous and/or overlap with other conditions.
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Affiliation(s)
- Salma Ben-Salem
- Department of Pathology, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Joseph G. Gleeson
- Department of Neuroscience and Pediatrics, Neurogenetics Laboratory, Howard Hughes Medical Institute, University of California, San Diego, CA, USA
| | - Aisha M. Al-Shamsi
- Department of Pediatrics, Tawam Hospital, Al-Ain, United Arab Emirates, Al-Ain, United Arab Emirates
| | - Barira Islam
- Department of Pediatrics, College of Medicine and Heath Sciences, United Arab Emirates University, P.O. Box 17666, Al-Ain, United Arab Emirates
| | - Jozef Hertecant
- Department of Pediatrics, Tawam Hospital, Al-Ain, United Arab Emirates, Al-Ain, United Arab Emirates
- Department of Pediatrics, College of Medicine and Heath Sciences, United Arab Emirates University, P.O. Box 17666, Al-Ain, United Arab Emirates
| | - Bassam R. Ali
- Department of Pathology, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Lihadh Al-Gazali
- Department of Pediatrics, College of Medicine and Heath Sciences, United Arab Emirates University, P.O. Box 17666, Al-Ain, United Arab Emirates
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Cox DM, Butler MG. Distal Partial Trisomy 15q26 and Partial Monosomy 16p13.3 in a 36-Year-Old Male with Clinical Features of Both Chromosomal Abnormalities. Cytogenet Genome Res 2015; 145:29-34. [PMID: 25871641 DOI: 10.1159/000381293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2015] [Indexed: 11/19/2022] Open
Abstract
We report a 36-year-old Caucasian male identified with distal partial trisomy 15q and partial monosomy 16p from an unbalanced chromosome translocation detected by microarray and FISH analysis. He had a history of developmental delay and intellectual disability, chronic anemia, tall and slender stature, thoracic scoliosis and lumbar lordosis, and dysmorphic features. The distal partial trisomy 15q included the insulin-like growth factor 1 receptor gene involved with growth, while genes in the distal partial monosomy 16p region are involved with alpha hemoglobin production, intellectual disability, dysmorphic features, and acromegaly. The chromosome derivative found in our patient contains genes known to play a role in his phenotype.
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Affiliation(s)
- Devin M Cox
- Department of Psychiatry, University of Kansas Medical Center, Kansas City, Kans., USA
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19
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Ben-Salem S, Al-Shamsi AM, John A, Ali BR, Al-Gazali L. A novel whole exon deletion in WWOX gene causes early epilepsy, intellectual disability and optic atrophy. J Mol Neurosci 2014; 56:17-23. [PMID: 25403906 DOI: 10.1007/s12031-014-0463-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 11/06/2014] [Indexed: 02/05/2023]
Abstract
Recent studies have implicated the WW domain-containing oxidoreductase encoding gene (WWOX) in a severe form of autosomal recessive neurological disorder. This condition showed an overlapping spectrum of clinical features including spinocerebellar ataxia associated with generalized seizures and delayed psychomotor development to growth retardation, spasticity, and microcephaly. We evaluated a child from a consanguineous Emirati family that presented at birth with growth retardation, microcephaly, epileptic seizures, and later developed spasticity and delayed psychomotor development. Screening for deletions and duplications using whole-chromosomal microarray analysis identified a novel homozygous microdeletion encompassing exon 5 of the WWOX gene. Analysis of parental DNA indicated that this deletion was inherited from both parents and lies within a large region of homozygosity. Sanger sequencing of the cDNA showed that the deletion resulted in exon 5 skipping leading to a frame-shift and creating a premature stop codon at amino acid position 212. Quantification of mRNA revealed striking low level of WWOX expression in the child and moderate level of expression in the mother compared to a healthy control. To the best of our knowledge, this is the first homozygous germline structural variation in WWOX gene resulting in truncated transcripts that were presumably subject to NMD pathway. Our findings extend the clinical and genetic spectrum of WWOX mutations and support a crucial role of this gene in neurological development.
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Affiliation(s)
- Salma Ben-Salem
- Department of Pathology, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates,
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Roberts JL, Hovanes K, Dasouki M, Manzardo AM, Butler MG. Chromosomal microarray analysis of consecutive individuals with autism spectrum disorders or learning disability presenting for genetic services. Gene 2014; 535:70-8. [PMID: 24188901 PMCID: PMC4423794 DOI: 10.1016/j.gene.2013.10.020] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 09/26/2013] [Accepted: 10/10/2013] [Indexed: 01/15/2023]
Abstract
Chromosomal microarray analysis is now commonly used in clinical practice to identify copy number variants (CNVs) in the human genome. We report our experience with the use of the 105 K and 180K oligonucleotide microarrays in 215 consecutive patients referred with either autism or autism spectrum disorders (ASD) or developmental delay/learning disability for genetic services at the University of Kansas Medical Center during the past 4 years (2009-2012). Of the 215 patients [140 males and 75 females (male/female ratio=1.87); 65 with ASD and 150 with learning disability], abnormal microarray results were seen in 45 individuals (21%) with a total of 49 CNVs. Of these findings, 32 represented a known diagnostic CNV contributing to the clinical presentation and 17 represented non-diagnostic CNVs (variants of unknown significance). Thirteen patients with ASD had a total of 14 CNVs, 6 CNVs recognized as diagnostic and 8 as non-diagnostic. The most common chromosome involved in the ASD group was chromosome 15. For those with a learning disability, 32 patients had a total of 35 CNVs. Twenty-six of the 35 CNVs were classified as a known diagnostic CNV, usually a deletion (n=20). Nine CNVs were classified as an unknown non-diagnostic CNV, usually a duplication (n=8). For the learning disability subgroup, chromosomes 2 and 22 were most involved. Thirteen out of 65 patients (20%) with ASD had a CNV compared with 32 out of 150 patients (21%) with a learning disability. The frequency of chromosomal microarray abnormalities compared by subject group or gender was not statistically different. A higher percentage of individuals with a learning disability had clinical findings of seizures, dysmorphic features and microcephaly, but not statistically significant. While both groups contained more males than females, a significantly higher percentage of males were present in the ASD group.
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Key Words
- A2BP1
- ACADL
- ACOXL
- ADIPOQ
- ALS2 chromosome region gene 8
- ALS2CR8
- ANKRD11
- ANOVA
- ASD
- Autism spectrum disorders (ASD)
- BAC
- BCL2-like 11 gene
- BCL2L11
- CACNA1C
- CHRNA7
- CNV
- COBL
- CT
- Chromosomal microarray analysis
- Copy number variant (CNV)
- DLG1
- DLG4
- DNA
- Developmental delay
- EEF1B2
- EEG
- F-box only 45 gene
- FAM117B
- FAT tumor suppressor 1 gene
- FAT1
- FBXO45
- FISH
- FXR2
- FZD5
- GALR1
- GATA zinc finger domain-containing protein 2B gene
- GATAD2B
- GDNF-inducible zinc finger protein 1 gene
- GZF1
- HAX1
- HCLS1-associated protein X1 gene
- HDAC
- IDH1
- IL1RAPL1
- ITPR1
- KLF7
- KNG1
- LINS
- LMNA
- Learning disability
- MAP2
- MBP
- MRPL19
- MYL1
- NADH-ubiquinone oxidoreductase Fe-S protein 1 gene
- NDUFS1
- NLGN2
- NPHP1
- NRXN1
- PAK2
- PARK2
- PMP22
- POLG
- PRPF8
- PTEN
- PTH2R
- RPE
- SACS
- SD
- SH2B adaptor protein 1 gene
- SH2B1
- SH3 and multiple ankyrin repeat domains 3 gene
- SHANK3
- SHOX
- SMARCA4
- STAG2
- SUMF1
- SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member gene
- TRAPPC2
- UCSC
- USP6
- University of California, Santa Cruz
- X-linked inhibitor of apoptosis gene
- XIAP
- YWHAE
- ZNF407
- aCGH
- acyl-coA dehydrogenase, long chain gene
- acyl-coA oxidase-like gene
- adipocyte-, C1q-, and collagen domain containing gene
- analysis of variance
- ankyrin repeat domain-containing protein 11 gene
- array comparative genomic hybridization
- ataxin 2-binding protein 1 gene
- autism spectrum disorder
- bacterial artificial chromosome
- calcium channel, voltage dependent, L-type, alpha 1C subunit gene
- cholinergic receptor, neuronal nicotinic, alpha polypeptide 7 gene
- computed tomography
- copy number variant
- cordon-bleu gene
- deoxyribonucleic acid
- discs, large homolog 1 gene
- discs, large homolog 4 gene
- electroencephalogram
- eukaryotic translation elongation factor 1, beta-2 gene
- family with sequence similarity 117, member B gene
- fluorescence in situ hybridization
- fragile X mental retardation, autosomal homolog 2 gene
- frizzled 5 gene
- galanin receptor 1 gene
- histone deacetylase gene
- inositol 1,4,5-triphosphate receptor, type 1 gene
- interleukin 1 receptor accessory protein-like 1 gene
- isocitrate dehydrogenase 1 gene
- kininogen 1 gene
- kruppel-like factor 7 gene
- lamin A gene
- lines homolog gene
- microtubule-associated protein 2 gene
- mitochondrial ribosomal protein L19 gene
- myelin basic protein gene
- myosin, light peptide 1 gene
- nephrocystin 1 gene
- neurexin 1 gene
- neuroligin 2 gene
- parathyroid hormone receptor 2 gene
- parkin gene
- peripheral myelin protein 22 gene
- phosphatase and tensin homolog gene
- polymerase gamma gene
- precursor mRNA-processing factor 8 gene
- protein-activated kinase 2 gene
- ribulose 5-phosphate 3-epimerase gene
- sacsin gene
- short stature homeobox gene
- standard deviation
- stromal antigen 2 gene
- sulfatase-modifying factor 1 gene
- tracking protein particle complex, subunit 2 gene
- tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon isoform gene
- ubiquitin-specific protease 6 gene
- zinc finger protein 407 gene
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Affiliation(s)
- Jennifer L Roberts
- Departments of Psychiatry, Behavioral Sciences and Pediatrics, The University of Kansas, Medical Center, Kansas City, KS, USA
| | | | - Majed Dasouki
- Department of Neurology, The University of Kansas Medical Center, Kansas City, KS, USA; King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ann M Manzardo
- Departments of Psychiatry, Behavioral Sciences and Pediatrics, The University of Kansas, Medical Center, Kansas City, KS, USA
| | - Merlin G Butler
- Departments of Psychiatry, Behavioral Sciences and Pediatrics, The University of Kansas, Medical Center, Kansas City, KS, USA.
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