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Zhou C, Zhu J, Tang P, Zhu J, Zhu X, Yang L, Bian W, Zhao W, Liu X. Compound heterozygous variants in SLC45A1 might cause syndromic intellectual disability by localization failure and activity attenuation in cells. Clin Genet 2024. [PMID: 39003656 DOI: 10.1111/cge.14588] [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: 04/04/2024] [Revised: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 07/15/2024]
Abstract
Intellectual disability (ID) is a kind of nervous developmental disorder and affects more than 1% of people worldwide. SLC45A1 as a transmembrane protein is implicated in the regulation of glucose homoeostasis. Through trio-based exome sequencing, the missense mutations of SLC45A1 c.103G>A (p.V35M) and c.1211T>G (p.F404C) were identified in the proband with syndromic ID. The distribution, expression and activity of SLC45A1 wild-type (WT) and variants were assayed in transfected COS7 cells. In SLC45A1 variants, the hydrogen bonds surrounding the 35th and 404th amino acid were changed, location on the cytomembrane was failed, their activity to transport glucose was also significantly decreased to contrast with SLC45A1-WT. No difference was observed at the mRNA and protein level. In conclusion, the compound heterozygous variants of SLC45A1 might be the genetic etiology for syndromic ID. These novel mutations probably attenuated its activity to transport glucose by the alteration of tertiary structure and failure of intracellular location.
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Affiliation(s)
- Chiyan Zhou
- Center for Fetal Medicine, Affiliated Women and Children's Hospital of Jiaxing University, Jiaxing, China
| | - Jianjun Zhu
- Center for Fetal Medicine, Affiliated Women and Children's Hospital of Jiaxing University, Jiaxing, China
| | - Ping Tang
- Center for Fetal Medicine, Affiliated Women and Children's Hospital of Jiaxing University, Jiaxing, China
| | - Jingkang Zhu
- Department of Critical Care Medicine, First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xinyi Zhu
- Center for Fetal Medicine, Affiliated Women and Children's Hospital of Jiaxing University, Jiaxing, China
| | - Li Yang
- Center for Fetal Medicine, Affiliated Women and Children's Hospital of Jiaxing University, Jiaxing, China
| | - Wei Bian
- Department of Radiology, Affiliated Women and Children's Hospital of Jiaxing University, Jiaxing, China
| | - Wei Zhao
- Center for Fetal Medicine, Affiliated Women and Children's Hospital of Jiaxing University, Jiaxing, China
| | - Xiaodan Liu
- Center for Fetal Medicine, Affiliated Women and Children's Hospital of Jiaxing University, Jiaxing, China
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Weymann D, Buckell J, Fahr P, Loewen R, Ehman M, Pollard S, Friedman JM, Stockler-Ipsiroglu S, Elliott AM, Wordsworth S, Buchanan J, Regier DA. Health Care Costs After Genome-Wide Sequencing for Children With Rare Diseases in England and Canada. JAMA Netw Open 2024; 7:e2420842. [PMID: 38985473 PMCID: PMC11238031 DOI: 10.1001/jamanetworkopen.2024.20842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/07/2024] [Indexed: 07/11/2024] Open
Abstract
Importance Etiologic diagnoses for rare diseases can involve a diagnostic odyssey, with repeated health care interactions and inconclusive diagnostics. Prior studies reported cost savings associated with genome-wide sequencing (GWS) compared with cytogenetic or molecular testing through rapid genetic diagnosis, but there is limited evidence on whether diagnosis from GWS is associated with reduced health care costs. Objective To measure changes in health care costs after diagnosis from GWS for Canadian and English children with suspected rare diseases. Design, Setting, and Participants This cohort study was a quasiexperimental retrospective analysis across 3 distinct English and Canadian cohorts, completed in 2023. Mixed-effects generalized linear regression was used to estimate associations between GWS and costs in the 2 years before and after GWS. Difference-in-differences regression was used to estimate associations of genetic diagnosis and costs. Costs are in 2019 US dollars. GWS was conducted in a research setting (Genomics England 100 000 Genomes Project [100KGP] and Clinical Assessment of the Utility of Sequencing and Evaluation as a Service [CAUSES] Research Clinic) or clinical outpatient setting (publicly reimbursed GWS in British Columbia [BC], Canada). Participants were children with developmental disorders, seizure disorders, or both undergoing GWS between 2014 and 2019. Data were analyzed from April 2021 to September 2023. Exposures GWS and genetic diagnosis. Main Outcomes and Measures Annual health care costs and diagnostic costs per child. Results Study cohorts included 7775 patients in 100KGP, among whom 788 children had epilepsy (mean [SD] age at GWS, 11.6 [11.1] years; 400 female [50.8%]) and 6987 children had an intellectual disability (mean [SD] age at GWS, 8.2 [8.4] years; 2750 female [39.4%]); 77 patients in CAUSES (mean [SD] age at GWS, 8.5 [4.4] years; 33 female [42.9%]); and 118 publicly reimbursed GWS recipients from BC (mean [SD] age at GWS, 5.5 [5.2] years; 58 female [49.2%]). GWS diagnostic yield was 143 children (18.1%) for those with epilepsy and 1323 children (18.9%) for those with an intellectual disability in 100KGP, 47 children (39.8%) in the BC publicly reimbursed setting, and 42 children (54.5%) in CAUSES. Mean annual per-patient spending over the study period was $5283 (95% CI, $5121-$5427) for epilepsy and $3373 (95% CI, $3322-$3424) for intellectual disability in the 100KGP, $724 (95% CI, $563-$886) in CAUSES, and $1573 (95% CI, $1372-$1773) in the BC reimbursed setting. Receiving a genetic diagnosis from GWS was not associated with changed costs in any cohort. Conclusions and Relevance In this study, receiving a genetic diagnosis was not associated with cost savings. This finding suggests that patient benefit and cost-effectiveness should instead drive GWS implementation.
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Affiliation(s)
- Deirdre Weymann
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - John Buckell
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Primary Health Care Sciences, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom
| | - Patrick Fahr
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Rosalie Loewen
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Morgan Ehman
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Samantha Pollard
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Jan M. Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Sylvia Stockler-Ipsiroglu
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
- Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Division of Biochemical Genetics, BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Alison M. Elliott
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Sarah Wordsworth
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom
| | - James Buchanan
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom
| | - Dean A. Regier
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- School of Population and Public Health, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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Garg P, Jamal F, Srivastava P. RNA-Seq data analysis reveals novel nonsense mutations in the NPR3 gene leading to the progression of intellectual disability disorder. Heliyon 2024; 10:e30755. [PMID: 38765165 PMCID: PMC11101858 DOI: 10.1016/j.heliyon.2024.e30755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/21/2024] Open
Abstract
Intellectual disability (ID) is a progressive disorder that affects around 1-3% of the world's population. The heterogeneity of intellectual disability makes it difficult to diagnose as a complete disease. Genetic factors and major mutations play a noticeable role in the development and progression of ID. There is a high need to explore novel variants that may lead to new insights into the progressive aspects of ID. In the current course of study, 31 samples of ID from different studies available on GEO (GSE77742, GSE74263, GSE90682, GSE98476, GSE108887, GSE145710, and PRJEB21964) datasets were taken for the study. These datasets were analyzed for differential gene expression and single nucleotide polymorphism (SNPs). The SNPs of high impact were compared with the differentially expressed genes. Comparison leads to the identification of the priority gene ie NPR3 gene. The identified priority gene further was evaluated for the effect of the mutation using a Mutation Taster. Structure comparison analysis of the wild and mutated proteins of the NPR3 gene was further carried out by UCSF Chimera. Structural analysis reveals the anomalies in protein expression affecting the regulations of the NPR3 gene. These findings identified a novel nonsense mutation (E222*) in the downregulated NPR3 gene that leads to anomalies in the regulation of its protein expression. This missense mutation reveals a major role in causing ID. Our study concludes that the decrease in the expression of the NPR3 gene causes delayed sensory, motor, and physiological functions of the human brain leading to neurodevelopmental delay that causes ID.
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Affiliation(s)
- Prekshi Garg
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, 226028, India
| | - Farrukh Jamal
- Department of Biochemistry, Dr. Rammanohar Lohia Avadh University, Ayodhya, 224001, UP, India
| | - Prachi Srivastava
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, 226028, India
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Ghorashi T, Darvish H, Bakhtiari S, Tafakhori A, Kruer MC, Mozdarani H. A biallelic loss-of-function variant in TMEM147 causes profound intellectual disability and spasticity. Neurogenetics 2023; 24:311-316. [PMID: 37668766 DOI: 10.1007/s10048-023-00734-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/27/2023] [Indexed: 09/06/2023]
Abstract
Intellectual disability (ID), occurring in syndromic or non-syndromic forms, is the most common neurodevelopmental disorder. Although many cases are caused by single gene defects, ID is highly genetically heterogeneous. Biallelic variants in the transmembrane protein TMEM147 have recently been linked to intellectual disability with dysmorphic facial features. TMEM147 is believed to localize to the endoplasmic reticulum membrane and nuclear envelope and also involved in biogenesis of multi-pass membrane proteins. Here, we report two patients born to a consanguineous family with a novel loss-of-function variant; (NM_001242597.2:c.193-197del) in TMEM147 causing intellectual disability and spasticity. Whole exome sequencing and validating Sanger sequencing were utilized to confirm the identified causal variant. Our findings were in line with the previously described patients with TMEM147 variants manifesting intellectual disability as a major clinical sign but also featured spasticity as a phenotypic expansion. This study provides additional evidence for the pathogenicity of TMEM147 mutations in intellectual disability and expands the phenotypic and variant spectrum linked to this gene.
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Affiliation(s)
- Tahereh Ghorashi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hossein Darvish
- Neuroscience Research Center, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Somayeh Bakhtiari
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, USA
- Departments of Child Health, Neurology, and Cellular & Molecular Medicine, and Program in Genetics, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA
| | - Abbas Tafakhori
- Iranian Center of Neurological Research, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Michael C Kruer
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, USA.
- Departments of Child Health, Neurology, and Cellular & Molecular Medicine, and Program in Genetics, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA.
| | - Hossein Mozdarani
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
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Bogue D, Ryan G, Wassmer E, Research Consortium GE, Naik S. VAMP2 Gene-Related Neurodevelopmental Disorder: A Differential Diagnosis for Rett/Angelman-Type Spectrum of Disorders. Mol Syndromol 2023; 14:449-456. [PMID: 37901860 PMCID: PMC10601795 DOI: 10.1159/000530150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/08/2023] [Indexed: 10/31/2023] Open
Abstract
Introduction VAMP2 is an instrumental protein in neuronal synaptic transmission in the brain, facilitating neurotransmitter release. It is encoded by the VAMP2 gene, and pathogenic variants in this gene cause neurodevelopmental features including early onset axial hypotonia, intellectual disability, and features of autism spectrum disorder. To date, only three types of allelic variants (loss of function, in-frame deletions, and missense variants) in the VAMP2 gene have been previously reported in 11 patients with learning difficulties. Here, we describe a patient in whom a novel de novo pathogenic variant in the VAMP2 gene was identified. Case Presentation A 15-month-old girl presented with early onset hypotonia, global developmental delay, learning difficulties, microcephaly, nystagmus, strabismus, and stereotypies. Later, she developed a sleep disorder, challenging behaviour with self-injury, and scoliosis. Gene agnostic analysis of whole genome sequencing data identified a novel de novo heterozygous missense variant c.197G>C (p.Arg66Pro) in the VAMP2 gene SNARE motif region. Discussion This is the fourth report describing VAMP2 gene-related neurodevelopmental disorder. This report adds to the genotype-phenotype correlation and highlights this condition as an important differential diagnosis of Rett/Angelman-type spectrum of disorders. Patients presenting with features of either Rett syndrome or Angelman syndrome, in whom genetic testing is not suggestive, should be evaluated for variants in the VAMP2 gene, given the significant overlap in clinical presentation of these disorders.
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Affiliation(s)
- Danielle Bogue
- West Midlands Clinical Genetics Unit, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, UK
| | - Gavin Ryan
- West Midlands Regional Genetics Laboratory, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, UK
| | - Evangeline Wassmer
- Department of Neurology, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, UK
- Institute of Health and Neurodevelopment, Aston University, Birmingham, UK
| | | | - Swati Naik
- West Midlands Clinical Genetics Unit, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, UK
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Ballesta-Martínez MJ, Pérez-Fernández V, López-González V, Sánchez-Soler MJ, Serrano-Antón AT, Rodríguez-Peña LI, Barreda-Sánchez M, Armengol-Dulcet L, Guillén-Navarro E. Validation of clinical exome sequencing in the diagnostic procedure of patients with intellectual disability in clinical practice. Orphanet J Rare Dis 2023; 18:201. [PMID: 37480025 PMCID: PMC10362575 DOI: 10.1186/s13023-023-02809-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/05/2023] [Indexed: 07/23/2023] Open
Abstract
Intellectual disability (ID) has a prevalence of 1-3% and aproximately 30-50% of ID cases have a genetic cause. Development of next-generation sequencing has shown a high diagnostic potential. The aim of this work was to evaluate the diagnostic yield of clinical exome sequencing in 188 ID patients and the economic impact of its introduction in clinical practice. An analysis of diagnostic yield according to the different clinical variables was performed in order to establish an efficient diagnostic protocol for ID patients. Diagnostic yield of clinical exome sequencing was significant (34%) supporting its utility in diagnosis of ID patients. Wide genetic heterogeneity and predominance of autosomal dominant de novo variants in ID patients were observed. Time to diagnosis was shortened and diagnostic study costs decreased by 62% after implementation of clinical exome sequencing. No association was found between any of the variables analyzed and a higher diagnostic yield; added to the fact that many of the diagnoses weren't clinically detectable, the reduction of time to diagnosis and the economic savings with respect to classical diagnostic studies, strengthen the clinical and economical convenience of early implementation of clinical exome sequencing in the diagnostic workup of ID patients in clinical practice.
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Affiliation(s)
- María Juliana Ballesta-Martínez
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain.
- Instituto Murciano de Investigación Biomédica (IMIB), Murcia, Spain.
- Centro de Investigación Biomédica en Red-Enfermedades Raras (CIBERER-Instituto de Salud Carlos III), Madrid, Spain.
| | - Virginia Pérez-Fernández
- Departamento de Ciencias Sociosanitarias-Área de Bioestadística, Facultad de Medicina, Universidad de Murcia, Murcia, Spain
| | - Vanesa López-González
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
- Instituto Murciano de Investigación Biomédica (IMIB), Murcia, Spain
- Centro de Investigación Biomédica en Red-Enfermedades Raras (CIBERER-Instituto de Salud Carlos III), Madrid, Spain
| | - María José Sánchez-Soler
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
- Instituto Murciano de Investigación Biomédica (IMIB), Murcia, Spain
| | - Ana Teresa Serrano-Antón
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
- Instituto Murciano de Investigación Biomédica (IMIB), Murcia, Spain
| | - Lidia Isolina Rodríguez-Peña
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
| | | | - Lluís Armengol-Dulcet
- Quantitative Genomic Medicine Laboratories (qGenomics), Esplugues del Llobregat, Catalonia, Spain
| | - Encarna Guillén-Navarro
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain.
- Instituto Murciano de Investigación Biomédica (IMIB), Murcia, Spain.
- Centro de Investigación Biomédica en Red-Enfermedades Raras (CIBERER-Instituto de Salud Carlos III), Madrid, Spain.
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7
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Chander V, Mahmoud M, Hu J, Dardas Z, Grochowski CM, Dawood M, Khayat MM, Li H, Li S, Jhangiani S, Korchina V, Shen H, Weissenberger G, Meng Q, Gingras MC, Muzny DM, Doddapaneni H, Posey JE, Lupski JR, Sabo A, Murdock DR, Sedlazeck FJ, Gibbs RA. Long read sequencing and expression studies of AHDC1 deletions in Xia-Gibbs syndrome reveal a novel genetic regulatory mechanism. Hum Mutat 2022; 43:2033-2053. [PMID: 36054313 PMCID: PMC10167679 DOI: 10.1002/humu.24461] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 01/25/2023]
Abstract
Xia-Gibbs syndrome (XGS; MIM# 615829) is a rare mendelian disorder characterized by Development Delay (DD), intellectual disability (ID), and hypotonia. Individuals with XGS typically harbor de novo protein-truncating mutations in the AT-Hook DNA binding motif containing 1 (AHDC1) gene, although some missense mutations can also cause XGS. Large de novo heterozygous deletions that encompass the AHDC1 gene have also been ascribed as diagnostic for the disorder, without substantial evidence to support their pathogenicity. We analyzed 19 individuals with large contiguous deletions involving AHDC1, along with other genes. One individual bore the smallest known contiguous AHDC1 deletion (∼350 Kb), encompassing eight other genes within chr1p36.11 (Feline Gardner-Rasheed, IFI6, FAM76A, STX12, PPP1R8, THEMIS2, RPA2, SMPDL3B) and terminating within the first intron of AHDC1. The breakpoint junctions and phase of the deletion were identified using both short and long read sequencing (Oxford Nanopore). Quantification of RNA expression patterns in whole blood revealed that AHDC1 exhibited a mono-allelic expression pattern with no deficiency in overall AHDC1 expression levels, in contrast to the other deleted genes, which exhibited a 50% reduction in mRNA expression. These results suggest that AHDC1 expression in this individual is compensated by a novel regulatory mechanism and advances understanding of mutational and regulatory mechanisms in neurodevelopmental disorders.
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Affiliation(s)
- Varuna Chander
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jianhong Hu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Zain Dardas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Moez Dawood
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Michael M. Khayat
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - He Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Shoudong Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Shalini Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Viktoriya Korchina
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Hua Shen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | | | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Marie-Claude Gingras
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - James R. Lupski
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Hospital, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - David R. Murdock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Computer Science, Rice University, Houston, Texas, USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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8
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Sánchez-Luquez KY, Carpena MX, Karam SM, Tovo-Rodrigues L. The contribution of whole-exome sequencing to intellectual disability diagnosis and knowledge of underlying molecular mechanisms: A systematic review and meta-analysis. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108428. [PMID: 35905832 DOI: 10.1016/j.mrrev.2022.108428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 01/01/2023]
Abstract
Whole-exome sequencing (WES) is useful for molecular diagnosis, family genetic counseling, and prognosis of intellectual disability (ID). However, ID molecular diagnosis ascertainment based on WES is highly dependent on de novo mutations (DNMs) and variants of uncertain significance (VUS). The quantification of DNM frequency in ID molecular diagnosis ascertainment and the biological mechanisms common to genes with VUS may provide objective information about WES use in ID diagnosis and etiology. We aimed to investigate and estimate the rate of ID molecular diagnostic assessment by WES, quantify the contribution of DNMs to this rate, and biologically and functionally characterize the genes whose mutations were identified through WES. A PubMed/Medline, Web of Science, Scopus, Science Direct, BIREME, and PsycINFO systematic review and meta-analysis was performed, including studies published between 2010 and 2022. Thirty-seven articles with data on ID molecular diagnostic yield using the WES approach were included in the review. WES testing accounted for an overall diagnostic rate of 42% (Confidence interval (CI): 35-50%), while the estimate restricted to DNMs was 11% (CI: 6-18%). Genetic information on mutations and genes was extracted and split into two groups: (1) genes whose mutation was used for positive molecular diagnosis, and (2) genes whose mutation led to uncertain molecular diagnosis. After functional enrichment analysis, in addition to their expected roles in neurodevelopment, genes from the first group were enriched in epigenetic regulatory mechanisms, immune system regulation, and circadian rhythm control. Genes from uncertain diagnosis cases were enriched in the renin angiotensin pathway. Taken together, our results support WES as an important approach to the molecular diagnosis of ID. The results also indicated relevant pathways that may underlie the pathogenesis of ID with the renin-angiotensin pathway being suggested to be a potential pathway underlying the pathogenesis of ID.
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Affiliation(s)
| | - Marina Xavier Carpena
- Postgraduate Program in Epidemiology, Universidade Federal de Pelotas, Pelotas, Brazil.
| | - Simone M Karam
- Postgraduate Program in Public Health, Universidade Federal do Rio Grande, Rio Grande, Brazil.
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9
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Brea-Fernández AJ, Álvarez-Barona M, Amigo J, Tubío-Fungueiriño M, Caamaño P, Fernández-Prieto M, Barros F, De Rubeis S, Buxbaum J, Carracedo Á. Trio-based exome sequencing reveals a high rate of the de novo variants in intellectual disability. Eur J Hum Genet 2022; 30:938-945. [PMID: 35322241 PMCID: PMC9349217 DOI: 10.1038/s41431-022-01087-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/15/2022] [Accepted: 03/08/2022] [Indexed: 12/16/2022] Open
Abstract
Intellectual disability (ID), a neurodevelopmental disorder affecting 1-3% of the general population, is characterized by limitations in both intellectual function and adaptive skills. The high number of conditions associated with ID underlines its heterogeneous origin and reveals the difficulty of obtaining a rapid and accurate genetic diagnosis. However, the Next Generation Sequencing, and the whole exome sequencing (WES) in particular, has boosted the diagnosis rate associated with ID. In this study, WES performed on 244 trios of patients clinically diagnosed with isolated or syndromic ID and their respective unaffected parents has allowed the identification of the underlying genetic basis of ID in 64 patients, yielding a diagnosis rate of 25.2%. Our results suggest that trio-based WES facilitates ID's genetic diagnosis, particularly in patients who have been extensively waiting for a definitive molecular diagnosis. Moreover, genotypic information from parents provided by trio-based WES enabled the detection of a high percentage (61.5%) of de novo variants inside our cohort. Establishing a quick genetic diagnosis of ID would allow early intervention and better clinical management, thus improving the quality of life of these patients and their families.
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Affiliation(s)
- Alejandro J Brea-Fernández
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain.
| | - Miriam Álvarez-Barona
- Grupo de Medicina Xenómica, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jorge Amigo
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain.,Fundación Pública Galega de Medicina Xenómica (FPGMX), Santiago de Compostela, Spain
| | - María Tubío-Fungueiriño
- Grupo de Medicina Xenómica, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Genomics and Bioinformatics Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Pilar Caamaño
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Santiago de Compostela, Spain
| | - Montserrat Fernández-Prieto
- Genetics Group, GC05, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Grupo de Medicina Xenómica, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - Francisco Barros
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain.,Grupo de Medicina Xenómica, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Fundación Pública Galega de Medicina Xenómica (FPGMX), Santiago de Compostela, Spain
| | | | - Joseph Buxbaum
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ángel Carracedo
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain.,Grupo de Medicina Xenómica, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Fundación Pública Galega de Medicina Xenómica (FPGMX), Santiago de Compostela, Spain.,Genomics and Bioinformatics Group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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10
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Yahia A, Ayed IB, Hamed AA, Mohammed IN, Elseed MA, Bakhiet AM, Guillot-Noel L, Abozar F, Adil R, Emad S, Abubaker R, Musallam MA, Eltazi IZM, Omer Z, Maaroof OM, Soussi A, Bouzid A, Kmiha S, Kamoun H, Salih MA, Ahmed AE, Elsayed L, Masmoudi S, Stevanin G. Genetic diagnosis in Sudanese and Tunisian families with syndromic intellectual disability through exome sequencing. Ann Hum Genet 2022; 86:181-194. [PMID: 35118659 DOI: 10.1111/ahg.12460] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 11/24/2021] [Accepted: 01/17/2022] [Indexed: 12/20/2022]
Abstract
BACKGROUND Intellectual disability is a form of neurodevelopmental disorders that begin in childhood and is characterized by substantial intellectual difficulties as well as difficulties in conceptual, social, and practical areas of living. Several genetic and nongenetic factors contribute to its development; however, its most severe forms are generally attributed to single-gene defects. High-throughput technologies and data sharing contributed to the diagnosis of hundreds of single-gene intellectual disability subtypes. METHOD We applied exome sequencing to identify potential variants causing syndromic intellectual disability in six Sudanese patients from four unrelated families. Data sharing through the Varsome portal corroborated the diagnosis of one of these patients and a Tunisian patient investigated through exome sequencing. Sanger sequencing validated the identified variants and their segregation with the phenotypes in the five studied families. RESULT We identified three pathogenic/likely pathogenic variants in CCDC82, ADAT3, and HUWE1 and variants of uncertain significance in HERC2 and ATP2B3. The patients with the CCDC82 variants had microcephaly and spasticity, two signs absent in the two previously reported families with CCDC82-related intellectual disability. CONCLUSION In conclusion, we report new patients with pathogenic mutations in the genes CCDC82, ADAT3, and HUWE1. We also highlight the possibility of extending the CCDC82-linked phenotype to include spastic paraplegia and microcephaly.
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Affiliation(s)
- Ashraf Yahia
- Department of Biochemistry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan.,Department of Biochemistry, Faculty of Medicine, National University, Khartoum, Sudan.,Institut du Cerveau - Paris Brain Institute, ICM, Sorbonne Université, INSERM, CNRS, APHP, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
| | - Ikhlas Ben Ayed
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), LR15CBS07, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia.,Medical Genetic Department, Hedi Chaker Hospital, Sfax, Tunisia
| | - Ahlam A Hamed
- Department of Pediatrics, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Inaam N Mohammed
- Department of Pediatrics, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Maha A Elseed
- Department of Pediatrics, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Aisha M Bakhiet
- Department of Psychiatry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Lena Guillot-Noel
- Institut du Cerveau - Paris Brain Institute, ICM, Sorbonne Université, INSERM, CNRS, APHP, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
| | - Fatima Abozar
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Rawaa Adil
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Sara Emad
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Rayan Abubaker
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan.,National University Biomedical Research Institute (NUBRI), National University, Khartoum, Sudan
| | | | - Isra Z M Eltazi
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Zulfa Omer
- Department of Hematology and Medical Oncology, University of Cincinnati Medical Center, Cincinnati, Ohio, USA
| | - Omer M Maaroof
- Council of Diagnostic Radiology, Sudan Medical Specialization Board, Khartoum, Sudan
| | - Amal Soussi
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), LR15CBS07, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Amal Bouzid
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), LR15CBS07, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Sana Kmiha
- Laboratory of Human Molecular Genetics, LR33ES99, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia.,Department of pediatrics, Hedi Chaker Hospital, Sfax, Tunisia
| | - Hassen Kamoun
- Medical Genetic Department, Hedi Chaker Hospital, Sfax, Tunisia.,Laboratory of Human Molecular Genetics, LR33ES99, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Mustafa A Salih
- Division of Pediatric Neurology, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Pediatrics, College of Medicine, AlMughtaribeen University, Khartoum, Sudan
| | - Ammar E Ahmed
- Department of Physiology, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Liena Elsayed
- Department of Biochemistry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan.,Department of Basic Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, 11671, Saudi Arabia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), LR15CBS07, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Giovanni Stevanin
- Institut du Cerveau - Paris Brain Institute, ICM, Sorbonne Université, INSERM, CNRS, APHP, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
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11
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Zhang W, Li D, Pang N, Jiang L, Li B, Ye F, He F, Chen S, Liu F, Peng J, Yin J, Yin F. The second-tier status of fragile X syndrome testing for unexplained intellectual disability/global developmental delay in the era of next-generation sequencing. Front Pediatr 2022; 10:911805. [PMID: 35935362 PMCID: PMC9353215 DOI: 10.3389/fped.2022.911805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE Although many unexplained intellectual disability/global developmental delay (ID/GDD) individuals have benefited from the excellent detection yield of copy number variations and next-generation sequencing testing, many individuals still who suffer from ID/GDD of unexplained etiology. In this study, we investigated the applicability of fragile X syndrome (FXS) testing in unexplained ID/GDD individuals with negative or absent genetic testing. METHODS In this study, we used the triplet repeat primed polymerase chain reaction to evaluate the value and application of fragile X testing in unexplained ID/GDD individuals with negative or absent genetic testing (n = 681) from three hospitals. RESULTS Of the 681 ID/GDD individuals with negative or absent genetic testing results detected by FXS testing, 12 men and one woman were positive. This corresponded to a diagnostic yield of 1.9% for FXS testing in our cohort. All FXS individuals had either a family history of ID/GDD or suggestive clinical features. The detection yield of FXS testing in ID/GDD individuals who completed genetic testing (2.70%, 12/438) was significantly higher than in individuals without any genetic testing (0.40%, 1/243). CONCLUSIONS This is the first report of FXS testing in ID/GDD individuals who lacked previous genetic testing, which promotes standardization of the FXS diagnostic process. These results highlight the utility of FXS testing of unexplained ID/GDD individuals with negative results from standard genetic testing. In the era of next-generation sequencing, FXS testing is more suitable as a second-tier choice and provides clinicians and geneticists with auxiliary references for tracing the etiology of ID/GDD.
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Affiliation(s)
- Wen Zhang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Dong Li
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Nan Pang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Li Jiang
- Department of Neurology, Children's Hospital Affiliated to Chongqing Medical University, Chongqing, China
| | - Baomin Li
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Fanghua Ye
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Fang He
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Shimeng Chen
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Fangyun Liu
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Jinghua Yin
- Department of Pathophysiology, Xiangya Hospital, Central South University, Changsha, China
| | - Fei Yin
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
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12
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Maia N, Nabais Sá MJ, Melo-Pires M, de Brouwer APM, Jorge P. Intellectual disability genomics: current state, pitfalls and future challenges. BMC Genomics 2021; 22:909. [PMID: 34930158 PMCID: PMC8686650 DOI: 10.1186/s12864-021-08227-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 12/02/2021] [Indexed: 12/18/2022] Open
Abstract
Intellectual disability (ID) can be caused by non-genetic and genetic factors, the latter being responsible for more than 1700 ID-related disorders. The broad ID phenotypic and genetic heterogeneity, as well as the difficulty in the establishment of the inheritance pattern, often result in a delay in the diagnosis. It has become apparent that massive parallel sequencing can overcome these difficulties. In this review we address: (i) ID genetic aetiology, (ii) clinical/medical settings testing, (iii) massive parallel sequencing, (iv) variant filtering and prioritization, (v) variant classification guidelines and functional studies, and (vi) ID diagnostic yield. Furthermore, the need for a constant update of the methodologies and functional tests, is essential. Thus, international collaborations, to gather expertise, data and resources through multidisciplinary contributions, are fundamental to keep track of the fast progress in ID gene discovery.
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Affiliation(s)
- Nuno Maia
- Centro de Genética Médica Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), Porto, Portugal. .,Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal.
| | - Maria João Nabais Sá
- Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal
| | - Manuel Melo-Pires
- Serviço de Neuropatologia, Centro Hospitalar e Universitário do Porto (CHUPorto), Porto, Portugal
| | - Arjan P M de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Paula Jorge
- Centro de Genética Médica Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), Porto, Portugal.,Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal
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13
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Bruno LP, Doddato G, Valentino F, Baldassarri M, Tita R, Fallerini C, Bruttini M, Lo Rizzo C, Mencarelli MA, Mari F, Pinto AM, Fava F, Fabbiani A, Lamacchia V, Carrer A, Caputo V, Granata S, Benetti E, Zguro K, Furini S, Renieri A, Ariani F. New Candidates for Autism/Intellectual Disability Identified by Whole-Exome Sequencing. Int J Mol Sci 2021; 22:ijms222413439. [PMID: 34948243 PMCID: PMC8707363 DOI: 10.3390/ijms222413439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 12/27/2022] Open
Abstract
Intellectual disability (ID) is characterized by impairments in the cognitive processes and in the tasks of daily life. It encompasses a clinically and genetically heterogeneous group of neurodevelopmental disorders often associated with autism spectrum disorder (ASD). Social and communication abilities are strongly compromised in ASD. The prevalence of ID/ASD is 1–3%, and approximately 30% of the patients remain without a molecular diagnosis. Considering the extreme genetic locus heterogeneity, next-generation sequencing approaches have provided powerful tools for candidate gene identification. Molecular diagnosis is crucial to improve outcome, prevent complications, and hopefully start a therapeutic approach. Here, we performed parent–offspring trio whole-exome sequencing (WES) in a cohort of 60 mostly syndromic ID/ASD patients and we detected 8 pathogenic variants in genes already known to be associated with ID/ASD (SYNGAP1, SMAD6, PACS1, SHANK3, KMT2A, KCNQ2, ACTB, and POGZ). We found four de novo disruptive variants of four novel candidate ASD/ID genes: MBP, PCDHA1, PCDH15, PDPR. We additionally selected via bioinformatic tools many variants in unknown genes that alone or in combination can contribute to the phenotype. In conclusion, our data confirm the efficacy of WES in detecting pathogenic variants of known and novel ID/ASD genes.
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Affiliation(s)
- Lucia Pia Bruno
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
| | - Gabriella Doddato
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
| | - Floriana Valentino
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
| | - Margherita Baldassarri
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
| | - Rossella Tita
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Chiara Fallerini
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
| | - Mirella Bruttini
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Caterina Lo Rizzo
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Maria Antonietta Mencarelli
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Francesca Mari
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Anna Maria Pinto
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Francesca Fava
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Alessandra Fabbiani
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Vittoria Lamacchia
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Anna Carrer
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Valentina Caputo
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Stefania Granata
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Elisa Benetti
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
| | - Kristina Zguro
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
| | - Simone Furini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
| | - Alessandra Renieri
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
| | - Francesca Ariani
- Medical Genetics, University of Siena, 53100 Siena, Italy; (L.P.B.); (G.D.); (F.V.); (M.B.); (C.F.); (M.B.); (F.M.); (F.F.); (A.F.); (V.L.); (A.C.); (V.C.); (S.G.); (A.R.)
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (K.Z.); (S.F.)
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy; (R.T.); (C.L.R.); (M.A.M.); (A.M.P.)
- Correspondence: ; Tel.: +39-0577-233303
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Nouri N, Bahreini A, Nasiri J, Salehi M. Clinical and genetic profile of children with unexplained intellectual disability/developmental delay and epilepsy. Epilepsy Res 2021; 177:106782. [PMID: 34695666 DOI: 10.1016/j.eplepsyres.2021.106782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 09/28/2021] [Accepted: 10/01/2021] [Indexed: 10/20/2022]
Abstract
OBJECTIVE This study was conducted to evaluate the validity of performing whole exome sequencing in children with unexplained intellectual disability (ID), developmental delay (DD), and epilepsy. METHODS We enrolled 61 Iranian children with unexplained DD/ID, and epilepsy with no etiologic diagnosis. 64 % of cases were male and 36 % were female, with a mean age of 6.2 years (range, 38 days to 15 years). Approximately 79 % of patients were born to consanguineous parents or had non-related parents from a highly inbred local region. Whole-exome sequencing analysis followed by Sanger sequencing was performed in all patients. RESULTS Pathogenic/likely pathogenic variants were identified in 59% (36/61) of patients, consisting of 26 novel and 14 known alterations. Variants of unknown significance were observed in 6.5 % (4/61) of patients. Variants in 28 genes have not been previously reported in Iranian patients with ID. Several additional phenotypes, mostly microcephaly, were common in 57.4 % of cases. Additionally, epilepsy was refractory in 40 % of patients. Three groups of brain anomalies consisting of brain dysgenesis, brain atrophy, and leukodystrophy were identified in our cohort. Mutations in genes implicated in cellular metabolic pathways were the most common, followed by ion channel/ion transporter and transcription pathways. DISCUSSION High-throughput DNA sequencing of the Iranian population with a high rate of parental consanguinity is a valuable strategy for identifying genetic etiology in children with unexplained ID/DD and epilepsy. Determining the genetic basis and most commonly involved pathways may help to identify novel genes and targeted antiepileptic treatments.
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Affiliation(s)
- Nayereh Nouri
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Amir Bahreini
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, PA, USA; KaryoGen, Isfahan, Iran
| | - Jafar Nasiri
- Child Growth and Development Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mansoor Salehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran; Cellular, Molecular and Genetics Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
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15
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Dai L, Zhang D, Wu Z, Guan X, Ma M, Li L, Zhang Y, Bai Y, Guo H. A Tiered Genetic Screening Strategy for the Molecular Diagnosis of Intellectual Disability in Chinese Patients. Front Genet 2021; 12:669217. [PMID: 34630504 PMCID: PMC8495063 DOI: 10.3389/fgene.2021.669217] [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: 02/18/2021] [Accepted: 09/10/2021] [Indexed: 01/02/2023] Open
Abstract
Objective: Intellectual disability (ID) is one of the most common developmental disabilities. To identify the genetic etiology of IDs in Chongqing, we conducted a multistage study in Chinese Han patients. Methods: We collected the clinical and etiological data of 1665 ID patients, including 1,604 from the disabled children evaluation center and 61 from the pediatric rehabilitation unit. Routine genetic screening results were obtained, including karyotype and candidate gene analysis. Then 105 idiopathic cases with syndromic and severe ID/developmental delay (DD) were selected and tested by chromosomal microarray (CMA) and whole exome sequencing (WES) sequentially. The pathogenicity of the CNVs and SNVs were evaluated according to ACMG guidelines. Results: Molecular diagnosis was made by routine genetic screening in 216 patients, including 196 chromosomal syndromes. Among the 105 idiopathic patients, 49 patients with pathogenic/likely pathogenic CNVs and 21 patients with VUS were identified by CMA. Twenty-six pathogenic CNVs underlying well-known syndromic cases, such as Williams-Beuren syndrome, were confirmed by multiplex ligation-dependent probe amplification (MLPA). Nine novel mutations were identified by WES in thirty-fix CNV-negative ID cases. Conclusions: The study illustrated the genetic aberrations distribution of a large ID cohort in Chongqing. Compared with conventional or single methods, a tiered high-throughput diagnostic strategy was developed to greatly improve the diagnostic yields and extend the variation spectrum for idiopathic syndromic ID cases.
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Affiliation(s)
- Limeng Dai
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Danyan Zhang
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China.,Chongqing Population and Family Planning Science and Technology Research Institute/NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing, China
| | - Zhifeng Wu
- Department of Pediatrics, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Xingying Guan
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Mingfu Ma
- Chongqing Population and Family Planning Science and Technology Research Institute/NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing, China
| | - Lianbing Li
- Chongqing Population and Family Planning Science and Technology Research Institute/NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing, China
| | - Yuping Zhang
- Department of Pediatrics, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Yun Bai
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Hong Guo
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China
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16
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Milone R, Scalise R, Pasquariello R, Berloffa S, Ricca I, Battini R. De Novo 1q21.3q22 Duplication Revaluation in a "Cold" Complex Neuropsychiatric Case with Syndromic Intellectual Disability. Genes (Basel) 2021; 12:genes12040511. [PMID: 33807234 PMCID: PMC8066010 DOI: 10.3390/genes12040511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/24/2021] [Accepted: 03/28/2021] [Indexed: 11/26/2022] Open
Abstract
Syndromic intellectual disability often obtains a genetic diagnosis due to the combination of first and next generation sequencing techniques, although their interpretation may require revaluation over the years. Here we report on a composite neuropsychiatric case whose phenotype includes moderate intellectual disability, spastic paraparesis, movement disorder, and bipolar disorder, harboring a 1.802 Mb de novo 1q21.3q22 duplication. The role of this duplication has been reconsidered in the light of negativity of many other genetic exams, and of the possible pathogenic role of many genes included in this duplication, potentially configuring a contiguous gene-duplication syndrome.
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Affiliation(s)
- Roberta Milone
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, 56128 Pisa, Italy; (R.M.); (R.S.); (R.P.); (S.B.)
| | - Roberta Scalise
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, 56128 Pisa, Italy; (R.M.); (R.S.); (R.P.); (S.B.)
- Tuscan PhD Program of Neuroscience, University of Florence, Pisa and Siena, 50139 Florence, Italy
| | - Rosa Pasquariello
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, 56128 Pisa, Italy; (R.M.); (R.S.); (R.P.); (S.B.)
| | - Stefano Berloffa
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, 56128 Pisa, Italy; (R.M.); (R.S.); (R.P.); (S.B.)
| | - Ivana Ricca
- Molecular Medicine, IRCCS Stella Maris Foundation, 56128 Pisa, Italy;
| | - Roberta Battini
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Calambrone, 56128 Pisa, Italy; (R.M.); (R.S.); (R.P.); (S.B.)
- Department of Clinical and Experimental Medicine, University of Pisa, 56125 Pisa, Italy
- Correspondence: ; Tel.: +39-050886229; Fax: +39-050886247
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17
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Barros II, Leão V, Santis JO, Rosa RCA, Brotto DB, Storti CB, Siena ÁDD, Molfetta GA, Silva WA. Non-Syndromic Intellectual Disability and Its Pathways: A Long Noncoding RNA Perspective. Noncoding RNA 2021; 7:ncrna7010022. [PMID: 33799572 PMCID: PMC8005948 DOI: 10.3390/ncrna7010022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/05/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023] Open
Abstract
Non-syndromic intellectual disability (NS-ID or idiopathic) is a complex neurodevelopmental disorder that represents a global health issue. Although many efforts have been made to characterize it and distinguish it from syndromic intellectual disability (S-ID), the highly heterogeneous aspect of this disorder makes it difficult to understand its etiology. Long noncoding RNAs (lncRNAs) comprise a large group of transcripts that can act through various mechanisms and be involved in important neurodevelopmental processes. In this sense, comprehending the roles they play in this intricate context is a valuable way of getting new insights about how NS-ID can arise and develop. In this review, we attempt to bring together knowledge available in the literature about lncRNAs involved with molecular and cellular pathways already described in intellectual disability and neural function, to better understand their relevance in NS-ID and the regulatory complexity of this disorder.
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Affiliation(s)
- Isabela I. Barros
- Department of Genetics at the Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto, São Paulo 14049-900, Brazil; (I.I.B.); (V.L.); (J.O.S.); (R.C.A.R.); (D.B.B.); (C.B.S.); (Á.D.D.S.); (G.A.M.)
| | - Vitor Leão
- Department of Genetics at the Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto, São Paulo 14049-900, Brazil; (I.I.B.); (V.L.); (J.O.S.); (R.C.A.R.); (D.B.B.); (C.B.S.); (Á.D.D.S.); (G.A.M.)
| | - Jessica O. Santis
- Department of Genetics at the Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto, São Paulo 14049-900, Brazil; (I.I.B.); (V.L.); (J.O.S.); (R.C.A.R.); (D.B.B.); (C.B.S.); (Á.D.D.S.); (G.A.M.)
| | - Reginaldo C. A. Rosa
- Department of Genetics at the Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto, São Paulo 14049-900, Brazil; (I.I.B.); (V.L.); (J.O.S.); (R.C.A.R.); (D.B.B.); (C.B.S.); (Á.D.D.S.); (G.A.M.)
| | - Danielle B. Brotto
- Department of Genetics at the Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto, São Paulo 14049-900, Brazil; (I.I.B.); (V.L.); (J.O.S.); (R.C.A.R.); (D.B.B.); (C.B.S.); (Á.D.D.S.); (G.A.M.)
| | - Camila B. Storti
- Department of Genetics at the Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto, São Paulo 14049-900, Brazil; (I.I.B.); (V.L.); (J.O.S.); (R.C.A.R.); (D.B.B.); (C.B.S.); (Á.D.D.S.); (G.A.M.)
| | - Ádamo D. D. Siena
- Department of Genetics at the Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto, São Paulo 14049-900, Brazil; (I.I.B.); (V.L.); (J.O.S.); (R.C.A.R.); (D.B.B.); (C.B.S.); (Á.D.D.S.); (G.A.M.)
| | - Greice A. Molfetta
- Department of Genetics at the Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto, São Paulo 14049-900, Brazil; (I.I.B.); (V.L.); (J.O.S.); (R.C.A.R.); (D.B.B.); (C.B.S.); (Á.D.D.S.); (G.A.M.)
| | - Wilson A. Silva
- Department of Genetics at the Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Monte Alegre, Ribeirão Preto, São Paulo 14049-900, Brazil; (I.I.B.); (V.L.); (J.O.S.); (R.C.A.R.); (D.B.B.); (C.B.S.); (Á.D.D.S.); (G.A.M.)
- National Institute of Science and Technology in Stem Cell and Cell Therapy and Center for Cell Based Therapy, Ribeirão Preto Medical School, University of São Paulo, Rua Tenente Catão Roxo, 2501, Monte Alegre, Ribeirão Preto 14051-140, Brazil
- Center for Integrative Systems Biology-CISBi, NAP/USP, Ribeirão Preto Medical School, University of São Paulo, Rua Catão Roxo, 2501, Monte Alegre, Ribeirão Preto 14051-140, Brazil
- Department of Medicine at the Midwest State University of Paraná-UNICENTRO, and Guarapuava Institute for Cancer Research, Rua Fortim Atalaia, 1900, Cidade dos Lagos, Guarapuava 85100-000, Brazil
- Correspondence: ; Tel.: +55-16-3315-3293
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Quach TT, Stratton HJ, Khanna R, Kolattukudy PE, Honnorat J, Meyer K, Duchemin AM. Intellectual disability: dendritic anomalies and emerging genetic perspectives. Acta Neuropathol 2021; 141:139-158. [PMID: 33226471 PMCID: PMC7855540 DOI: 10.1007/s00401-020-02244-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022]
Abstract
Intellectual disability (ID) corresponds to several neurodevelopmental disorders of heterogeneous origin in which cognitive deficits are commonly associated with abnormalities of dendrites and dendritic spines. These histological changes in the brain serve as a proxy for underlying deficits in neuronal network connectivity, mostly a result of genetic factors. Historically, chromosomal abnormalities have been reported by conventional karyotyping, targeted fluorescence in situ hybridization (FISH), and chromosomal microarray analysis. More recently, cytogenomic mapping, whole-exome sequencing, and bioinformatic mining have led to the identification of novel candidate genes, including genes involved in neuritogenesis, dendrite maintenance, and synaptic plasticity. Greater understanding of the roles of these putative ID genes and their functional interactions might boost investigations into determining the plausible link between cellular and behavioral alterations as well as the mechanisms contributing to the cognitive impairment observed in ID. Genetic data combined with histological abnormalities, clinical presentation, and transgenic animal models provide support for the primacy of dysregulation in dendrite structure and function as the basis for the cognitive deficits observed in ID. In this review, we highlight the importance of dendrite pathophysiology in the etiologies of four prototypical ID syndromes, namely Down Syndrome (DS), Rett Syndrome (RTT), Digeorge Syndrome (DGS) and Fragile X Syndrome (FXS). Clinical characteristics of ID have also been reported in individuals with deletions in the long arm of chromosome 10 (the q26.2/q26.3), a region containing the gene for the collapsin response mediator protein 3 (CRMP3), also known as dihydropyrimidinase-related protein-4 (DRP-4, DPYSL4), which is involved in dendritogenesis. Following a discussion of clinical and genetic findings in these syndromes and their preclinical animal models, we lionize CRMP3/DPYSL4 as a novel candidate gene for ID that may be ripe for therapeutic intervention.
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Affiliation(s)
- Tam T Quach
- Institute for Behavioral Medicine Research, Wexner Medical Center, The Ohio State University, Columbus, OH, 43210, USA
- INSERM U1217/CNRS, UMR5310, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | | | - Rajesh Khanna
- Department of Pharmacology, University of Arizona, Tucson, AZ, 85724, USA
| | | | - Jérome Honnorat
- INSERM U1217/CNRS, UMR5310, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
- French Reference Center on Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon, Lyon, France
- SynatAc Team, Institut NeuroMyoGène, Lyon, France
| | - Kathrin Meyer
- The Research Institute of Nationwide Children Hospital, Columbus, OH, 43205, USA
- Department of Pediatric, The Ohio State University, Columbus, OH, 43210, USA
| | - Anne-Marie Duchemin
- Department of Psychiatry and Behavioral Health, The Ohio State University, Columbus, OH, 43210, USA.
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Novel exon-skipping variant disrupting the basic domain of HCFC1 causes intellectual disability without metabolic abnormalities in both male and female patients. J Hum Genet 2021; 66:717-724. [PMID: 33517344 DOI: 10.1038/s10038-020-00892-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 11/09/2022]
Abstract
HCFC1, a global transcriptional regulator, has been shown to associate with MMACHC expression. Pathogenic variants in HCFC1 cause X-linked combined methylmalonic acidemia and hyperhomocysteinemia, CblX type (MIM# 309541). Recent studies showed that certain variants in HCFC1 are associated with X-linked intellectual disability with mild or absent metabolic abnormalities. Here, we report five subjects (three males, two females) from the same family with a novel predicted loss of function HCFC1 variant. All five patients exhibit developmental delay or intellectual disability/learning difficulty and some dysmorphic features; findings were milder in the female as compared to male subjects. Biochemical studies in all patients did not show methylmalonic acidemia or hyperhomocysteinemia but revealed elevated vitamin B12 levels. Trio exome sequencing of the proband and his parents revealed a maternally inherited novel variant in HCFC1 designated as c.1781_1803 + 3del26insCA (NM_005334). Targeted testing confirmed the presence of the same variant in two half-siblings and maternal great uncle. In silico analysis showed that the variant is expected to reduce the quality of the splice donor site in intron 10 and causes abnormal splicing. Sequencing of proband's cDNA revealed exon 10 skipping. Further molecular studies in the two manifesting females revealed moderate and high skewing of X inactivation. Our results support previous observation that HCFC1 variants located outside the Kelch domain exhibit dissociation of the clinical and biochemical phenotype and cause milder or no metabolic changes. We also show that this novel variant can be associated with a phenotype in females, although with milder severity, but further studies are needed to understand the role of skewed X inactivation among females in this rare disorder. Our work expands the genotypes and phenotypes associated with HCFC1-related disorder.
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Lin L, Zhang Y, Pan H, Wang J, Qi Y, Ma Y. Clinical and genetic characteristics and prenatal diagnosis of patients presented GDD/ID with rare monogenic causes. Orphanet J Rare Dis 2020; 15:317. [PMID: 33176815 PMCID: PMC7656751 DOI: 10.1186/s13023-020-01599-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/26/2020] [Indexed: 12/18/2022] Open
Abstract
Background Global developmental delay/intellectual disability (GDD/ID), used to be named as mental retardation (MR), is one of the most common phenotypes in neurogenetic diseases. In this study, we described the diagnostic courses, clinical and genetic characteristics and prenatal diagnosis of a cohort with patients presented GDD/ID with monogenic causes, from the perspective of a tertiary genetic counseling and prenatal diagnostic center. Method We retrospectively analyzed the diagnostic courses, clinical characteristics, and genetic spectrum of patients presented GDD/ID with rare monogenic causes. We also conducted a follow-up study on prenatal diagnosis in these families. Pathogenicity of variants was interpreted by molecular geneticists and clinicians according to the guidelines of the American College of Medical Genetics and Genomics (ACMG). Results Among 81 patients with GDD/ID caused by rare monogenic variants it often took 0.5–4.5 years and 2–8 referrals to obtain genetic diagnoses. Devlopmental delay typically occurred before 3 years of age, and patients usually presented severe to profound GDD/ID. The most common co-existing conditions were epilepsy (58%), microcephaly (21%) and facial anomalies (17%). In total, 111 pathogenic variants were found in 62 different genes among the 81 pedigrees, and 56 variants were novel. The most common inheritance patterns in this outbred Chinese population were autosomal dominant (AD; 47%), following autosomal recessive (AR; 37%), and X-linked (XL; 16%). SCN2A, SHANK3 and STXBP1 were important causal genes. Hot-spot variants were rarely found. By the follow-up, 33 affected families, including 15, 13 and 5 families inherited in AR, AD and XL modes respectively, had undergone prenatal diagnosis. And the recurrence rates are 26.7%, 15.4% and 20% for families inherited in AR, AD, and XL patterns. Conclusion Patients presented with GDD/ID caused by rare single gene variants are characterized by early onset, relatively severe symptoms and great clinical variability and genetic heterogeneity. Timely referrals to genetic counseling and prenatal diagnostic laboratories are important for affected families planning to have additional children.
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Affiliation(s)
- Liling Lin
- Department of Central Laboratory, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China
| | - Ying Zhang
- Department of Central Laboratory, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China
| | - Hong Pan
- Department of Central Laboratory, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China
| | - Jingmin Wang
- Department of Pediatrics, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China
| | - Yu Qi
- Department of Central Laboratory, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China
| | - Yinan Ma
- Department of Central Laboratory, Peking University First Hospital, No. 8, Xishiku Street, Xicheng District, Beijing, 100034, China.
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Chiurazzi P, Kiani AK, Miertus J, Paolacci S, Barati S, Manara E, Stuppia L, Gurrieri F, Bertelli M. Genetic analysis of intellectual disability and autism. ACTA BIO-MEDICA : ATENEI PARMENSIS 2020; 91:e2020003. [PMID: 33170170 PMCID: PMC8023126 DOI: 10.23750/abm.v91i13-s.10684] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 10/23/2020] [Indexed: 12/16/2022]
Abstract
Background and aim: Intellectual disability (ID) and autism spectrum disorders (ASD) are neurodevelopmental conditions that often co-exist and affect children from birth, impacting on their cognition and adaptive behaviour. Social interaction and communication ability are also severely impaired in ASD. Almost 1-3% of the population is affected and it has been estimated that approximately 30% of intellectual disability and autism is caused by genetic factors. The aim of this review is to summarize monogenic conditions characterized by intellectual disability and/or autism for which the causative genes have been identified. Methods and Results: We identified monogenic ID/ASD conditions through PubMed and other NCBI databases. Many such genes are located on the X chromosome (>150 out of 900 X-linked protein-coding genes), but at least 2000 human genes are estimated to be involved in ID/ASD. We selected 174 genes (64 X-linked and 110 autosomal) for an NGS panel in order to screen patients with ID and/or ASD, after fragile X syndrome and significant Copy Number Variants have been excluded. Conclusions: Accurate clinical and genetic diagnosis is required for precise treatment of these disorders, but due to their genetic heterogeneity, most cases remain undiagnosed. Next generation sequencing technologies have greatly enhanced the identification of new genes associated with intellectual disability and autism, ultimately leading to the development of better treatment options. (www.actabiomedica.it)
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Affiliation(s)
- Pietro Chiurazzi
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Rome, Italy; Fondazione Policlinico Universitario "A. Gemelli" IRCCS, UOC Genetica Medica, Rome, Italy.
| | | | - Jan Miertus
- Génius n.o., Mestská Poliklinika, Trnava, Slovakia; MAGI´'S LAB, Rovereto (TN), Italy.
| | | | | | | | - Liborio Stuppia
- Dipartimento di Scienze Psicologiche della Salute e del Territorio, Università degli Studi "G. D'Annunzio", Chieti, Italy.
| | | | - Matteo Bertelli
- MAGI EUREGIO, Bolzano, Italy; MAGI'S LAB, Rovereto (TN), Italy; EBTNA-LAB, Rovereto (TN), Italy.
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Pathogenic 12-kb copy-neutral inversion in syndromic intellectual disability identified by high-fidelity long-read sequencing. Genomics 2020; 113:1044-1053. [PMID: 33157260 DOI: 10.1016/j.ygeno.2020.10.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/08/2020] [Accepted: 10/31/2020] [Indexed: 01/07/2023]
Abstract
We report monozygotic twin girls with syndromic intellectual disability who underwent exome sequencing but with negative pathogenic variants. To search for variants that are unrecognized by exome sequencing, high-fidelity long-read genome sequencing (HiFi LR-GS) was applied. A 12-kb copy-neutral inversion was precisely identified by HiFi LR-GS after trio-based variant filtering. This inversion directly disrupted two genes, CPNE9 and BRPF1, the latter of which attracted our attention because pathogenic BRPF1 variants have been identified in autosomal dominant intellectual developmental disorder with dysmorphic facies and ptosis (IDDDFP), which later turned out to be clinically found in the twins. Trio-based HiFi LR-GS together with haplotype phasing revealed that the 12-kb inversion occurred de novo on the maternally transmitted chromosome. This study clearly indicates that submicroscopic copy-neutral inversions are important but often uncharacterized culprits in monogenic disorders and that long-read sequencing is highly advantageous for detecting such inversions involved in genetic diseases.
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23
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Bodnar B, DeGruttola A, Zhu Y, Lin Y, Zhang Y, Mo X, Hu W. Emerging role of NIK/IKK2-binding protein (NIBP)/trafficking protein particle complex 9 (TRAPPC9) in nervous system diseases. Transl Res 2020; 224:55-70. [PMID: 32434006 PMCID: PMC7442628 DOI: 10.1016/j.trsl.2020.05.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 05/02/2020] [Accepted: 05/05/2020] [Indexed: 02/05/2023]
Abstract
NFκB signaling and protein trafficking network play important roles in various biological and pathological processes. NIK-and-IKK2-binding protein (NIBP), also known as trafficking protein particle complex 9 (TRAPPC9), is a prototype member of a novel protein family, and has been shown to regulate both NFκB signaling pathway and protein transport/trafficking. NIBP is extensively expressed in the nervous system and plays an important role in regulating neurogenesis and neuronal differentiation. NIBP/TRAPPC9 mutations have been linked to an autosomal recessive intellectual disability syndrome, called NIBP Syndrome, which is characterized by nonsyndromic autosomal recessive intellectual disability along with other symptoms such as obesity, microcephaly, and facial dysmorphia. As more cases of NIBP Syndrome are identified, new light is being shed on the role of NIBP/TRAPPC9 in the central nervous system developments and diseases. NIBP is also involved in the enteric nervous system. This review will highlight the importance of NIBP/TRAPPC9 in central and enteric nervous system diseases, and the established possible mechanisms for developing a potential therapeutic.
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Affiliation(s)
- Brittany Bodnar
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania; MD/PhD and Biomedical Sciences Graduate Program, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Arianna DeGruttola
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania; MD/PhD and Biomedical Sciences Graduate Program, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Yuanjun Zhu
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania; Department of Molecular and Cellular Pharmacology, Peking University School of Pharmaceutical Sciences, Beijing, China
| | - Yuan Lin
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Yonggang Zhang
- Center for Stem Cell Research and Application, Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS & PUMC), Chengdu, China
| | - Xianming Mo
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Wenhui Hu
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania; MD/PhD and Biomedical Sciences Graduate Program, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania.
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24
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Mariano V, Achsel T, Bagni C, Kanellopoulos AK. Modelling Learning and Memory in Drosophila to Understand Intellectual Disabilities. Neuroscience 2020; 445:12-30. [PMID: 32730949 DOI: 10.1016/j.neuroscience.2020.07.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 07/19/2020] [Accepted: 07/20/2020] [Indexed: 12/24/2022]
Abstract
Neurodevelopmental disorders (NDDs) include a large number of conditions such as Fragile X syndrome, autism spectrum disorders and Down syndrome, among others. They are characterized by limitations in adaptive and social behaviors, as well as intellectual disability (ID). Whole-exome and whole-genome sequencing studies have highlighted a large number of NDD/ID risk genes. To dissect the genetic causes and underlying biological pathways, in vivo experimental validation of the effects of these mutations is needed. The fruit fly, Drosophila melanogaster, is an ideal model to study NDDs, with highly tractable genetics, combined with simple behavioral and circuit assays, permitting rapid medium-throughput screening of NDD/ID risk genes. Here, we review studies where the use of well-established assays to study mechanisms of learning and memory in Drosophila has permitted insights into molecular mechanisms underlying IDs. We discuss how technologies in the fly model, combined with a high degree of molecular and physiological conservation between flies and mammals, highlight the Drosophila system as an ideal model to study neurodevelopmental disorders, from genetics to behavior.
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Affiliation(s)
- Vittoria Mariano
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne 1005, Switzerland; Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Tilmann Achsel
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne 1005, Switzerland
| | - Claudia Bagni
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne 1005, Switzerland; Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome 00133, Italy.
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Dai Y, Wei Y, Chen Y, Guo H, Zhong M. Intellectual disability in two Chinese sisters caused by a 3p26.3p25.3 microdeletion and a 14q32.13q32.33 microduplication inherited from the mother with 46, XX, t (3, 14) (p25; q32). Mol Genet Genomic Med 2020; 8:e1335. [PMID: 32489010 PMCID: PMC7434598 DOI: 10.1002/mgg3.1335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/09/2020] [Accepted: 05/12/2020] [Indexed: 11/20/2022] Open
Abstract
Background Genetic factors associated with intellectual disability (ID) include chromosomal aberrations, copy number variations (CNVs), and pathogenic variants. Identifying the genetic etiologies is beneficial for patient classification, therapy, management, and prognostic evaluation. Emerging genetic tests are helpful in identifying these genetic causes. Methods We enrolled two girl siblings with ID. Trio whole‐exome sequencing (WES) and Copy number variation sequencing (CNV‐Seq) were performed for genetic molecular analysis in these probands and their parents. The parents also accepted high‐resolution G‐banded karyotype studies. Results No significant homozygous or heterozygous variants were identified through WES. By CNV‐seq, we identified an abnormal 3p26.3p25.3 microdeletion and 14q32.13q32.33 microduplication in the two girl siblings but not in their parents. A balanced translocation 46, XX, t (3, 14) (p25; q32) was found in their mother. Conclusion The affected siblings have similar phenotype, including ID, short stature, and microcephaly. Their mother had a history of seven first‐trimester miscarriages and one elective termination because of multiple malformations. This abnormal karyotype was also thought to be responsible for the mother's recurrent miscarriage. WES in combination with CNV‐seq analysis is very helpful for identification of the genetic causes of ID without positive karyotype findings.
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Affiliation(s)
- Ying Dai
- Department of Primary Child Health Care, Children's Hospital of Chongqing Medical University, Chongqing, China.,Pediatric Research Institute, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Engineering Research Center of Stem Cell Therapy, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,National Clinical Research Center for Child Health and Disorders, Chongqing, China
| | - Yongjuan Wei
- Pediatric Research Institute, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Engineering Research Center of Stem Cell Therapy, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,National Clinical Research Center for Child Health and Disorders, Chongqing, China.,Department of Neurology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yuanyuan Chen
- Pediatric Research Institute, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Engineering Research Center of Stem Cell Therapy, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,National Clinical Research Center for Child Health and Disorders, Chongqing, China.,Center for Clinical Molecular Medicine, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Hui Guo
- Department of Pediatric, Qianjiang Central Hospital of Chongqing, Chongqing, China
| | - Min Zhong
- Pediatric Research Institute, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Engineering Research Center of Stem Cell Therapy, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,National Clinical Research Center for Child Health and Disorders, Chongqing, China.,Department of Neurology, Children's Hospital of Chongqing Medical University, Chongqing, China.,Department of Pediatric, Qianjiang Central Hospital of Chongqing, Chongqing, China
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26
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Kim JS. Next-generation sequencing is a powerful method to enhance diagnostic yield in global developmental delay/intellectual disability. Clin Exp Pediatr 2020; 63:211-212. [PMID: 32536047 PMCID: PMC7303427 DOI: 10.3345/cep.2019.01683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 02/18/2020] [Indexed: 12/25/2022] Open
Affiliation(s)
- Jon Soo Kim
- Department of Pediatrics, Chungbuk National University Hospital, Cheongju, Korea
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Ilyas M, Mir A, Efthymiou S, Houlden H. The genetics of intellectual disability: advancing technology and gene editing. F1000Res 2020; 9. [PMID: 31984132 PMCID: PMC6966773 DOI: 10.12688/f1000research.16315.1] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/10/2020] [Indexed: 12/22/2022] Open
Abstract
Intellectual disability (ID) is a neurodevelopmental condition affecting 1–3% of the world’s population. Genetic factors play a key role causing the congenital limitations in intellectual functioning and adaptive behavior. The heterogeneity of ID makes it more challenging for genetic and clinical diagnosis, but the advent of large-scale genome sequencing projects in a trio approach has proven very effective. However, many variants are still difficult to interpret. A combined approach of next-generation sequencing and functional, electrophysiological, and bioinformatics analysis has identified new ways to understand the causes of ID and help to interpret novel ID-causing genes. This approach offers new targets for ID therapy and increases the efficiency of ID diagnosis. The most recent functional advancements and new gene editing techniques involving the use of CRISPR–Cas9 allow for targeted editing of DNA in
in vitro and more effective mammalian and human tissue-derived disease models. The expansion of genomic analysis of ID patients in diverse and ancient populations can reveal rare novel disease-causing genes.
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Affiliation(s)
- Muhammad Ilyas
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan.,Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Asif Mir
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
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28
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Capkova Z, Capkova P, Srovnal J, Staffova K, Becvarova V, Trkova M, Adamova K, Santava A, Curtisova V, Hajduch M, Prochazka M. Differences in the importance of microcephaly, dysmorphism, and epilepsy in the detection of pathogenic CNVs in ID and ASD patients. PeerJ 2019; 7:e7979. [PMID: 31741789 PMCID: PMC6859875 DOI: 10.7717/peerj.7979] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 10/02/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Autism spectrum disorders (ASD) and intellectual disabilities (ID) are heterogeneous and complex developmental diseases with significant genetic backgrounds and overlaps of genetic susceptibility loci. Copy number variants (CNVs) are known to be frequent causes of these impairments. However, the clinical heterogeneity of both disorders causes the diagnostic efficacy of CNV analysis to be modest. This could be resolved by stratifying patients according to their clinical features. AIM First, we sought to assess the significance of particular clinical features for the detection of pathogenic CNVs in separate groups of ID and ASD patients and determine whether and how these groups differ from each other in the significance of these variables. Second, we aimed to create a statistical model showing how particular clinical features affect the probability of pathogenic CNV findings. METHOD We tested a cohort of 204 patients with ID (N = 90) and ASD (N = 114) for the presence of pathogenic CNVs. We stratified both groups according to their clinical features. Fisher's exact test was used to determine the significance of these variables for pathogenic CNV findings. Logistic regression was used to create a statistical model of pathogenic CNV findings. RESULTS The frequency of pathogenic CNV was significantly higher in the ID group than in the ASD group: 18 (19.78%) versus 8 (7%) (p < 0.004). Microcephaly showed a significant association with pathogenic findings in ID patients (p < 0.01) according to Fisher's exact test, whereas epilepsy showed a significant association with pathogenic findings in ASD patients (p < 0.01). The probability of pathogenic CNV findings when epilepsy occurred in ASD patients was more than two times higher than if epilepsy co-occurred with ID (29.6%/14.0%). Facial dysmorphism was a significant variable for detecting pathogenic CNVs in both groups (ID p = 0.05, ASD p = 0.01). However, dysmorphism increased the probability of pathogenic CNV detection in the ID group nearly twofold compared to the ASD group (44.4%/23.7%). The presence of macrocephaly in the ASD group showed a 25% probability of pathogenic CNV findings by logistic regression, but this was insignificant according to Fisher's exact test. The probability of detecting pathogenic CNVs decreases up to 1% in the absence of dysmorphism, macrocephaly, and epilepsy in the ASD group. CONCLUSION Dysmorphism, microcephaly, and epilepsy increase the probability of pathogenic CNV findings in ID and ASD patients. The significance of each feature as a predictor for pathogenic CNV detection differs depending on whether the patient has only ASD or ID. The probability of pathogenic CNV findings without dysmorphism, macrocephaly, or epilepsy in ASD patients is low. Therefore the efficacy of CNV analysis is limited in these patients.
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Affiliation(s)
- Zuzana Capkova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
- Department of Medical Genetics/Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Pavlina Capkova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
- Department of Medical Genetics/Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Josef Srovnal
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
- Institute of Molecular and Translational Medicine/Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Katerina Staffova
- Institute of Molecular and Translational Medicine/Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | | | | | - Katerina Adamova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
- Department of Medical Genetics/Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Alena Santava
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
- Department of Medical Genetics/Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Vaclava Curtisova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
- Department of Medical Genetics/Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine/Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Martin Prochazka
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
- Department of Medical Genetics/Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
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29
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Wang R, Han S, Liu H, Khan A, Xiaerbati H, Yu X, Huang J, Zhang X. Novel Compound Heterozygous Mutations in TTI2 Cause Syndromic Intellectual Disability in a Chinese Family. Front Genet 2019; 10:1060. [PMID: 31737043 PMCID: PMC6830114 DOI: 10.3389/fgene.2019.01060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 10/03/2019] [Indexed: 11/13/2022] Open
Abstract
Telomere maintenance 2 (TELO2)-interacting protein 2 (TTI2) interacts with TTI1 and TELO2 to form the Triple T complex, which is required for various cellular processes, including the double-strand DNA break response, nonsense-mediated mRNA decay, and telomerase assembly. Herein, we identified compound heterozygous mutations in TTI2 using whole-exome sequencing (WES) in a Chinese family with a recessive inheritance pattern of syndromic intellectual disability. The patients displayed intellectual disability, aggressive and self-injurious behaviors, facial dysmorphic features, microcephaly, and skeletal anomalies. In addition, one patient showed cerebral white matter abnormality. Maternal novel indel mutation resulted in a premature termination codon and nonsense-mediated mRNA decay. Paternal reported c.1100C > T mutation changed the highly conserved proline to leucine that located in the DUF2454 domain. Immunoblotting experiments showed significantly decreased TTI2, TTI1, and TELO2 in the patients' lymphocytes. These results indicated that TTI2 loss-of-function mutations might cause an autosomal-recessive syndromic intellectual disability by affecting the Triple T complex. Our report expands the genetic causes of syndromic intellectual disability in the Chinese population.
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Affiliation(s)
- Rongrong Wang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Shirui Han
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.,The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Hongyan Liu
- Medical Genetics Institute, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, China
| | - Amjad Khan
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.,The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Habulieti Xiaerbati
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Xue Yu
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.,Department of Pediatrics, the First Affiliated Hospital of Guangxi Medical University, Guangxi, China
| | - Jia Huang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.,The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
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30
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Bi-allelic Variants in METTL5 Cause Autosomal-Recessive Intellectual Disability and Microcephaly. Am J Hum Genet 2019; 105:869-878. [PMID: 31564433 DOI: 10.1016/j.ajhg.2019.09.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/04/2019] [Indexed: 02/01/2023] Open
Abstract
Intellectual disability (ID) is a genetically and clinically heterogeneous disorder, characterized by limited cognitive abilities and impaired adaptive behaviors. In recent years, exome sequencing (ES) has been instrumental in deciphering the genetic etiology of ID. Here, through ES of a large cohort of individuals with ID, we identified two bi-allelic frameshift variants in METTL5, c.344_345delGA (p.Arg115Asnfs∗19) and c.571_572delAA (p.Lys191Valfs∗10), in families of Pakistani and Yemenite origin. Both of these variants were segregating with moderate to severe ID, microcephaly, and various facial dysmorphisms, in an autosomal-recessive fashion. METTL5 is a member of the methyltransferase-like protein family, which encompasses proteins with a seven-beta-strand methyltransferase domain. We found METTL5 expression in various substructures of rodent and human brains and METTL5 protein to be enriched in the nucleus and synapses of the hippocampal neurons. Functional studies of these truncating variants in transiently transfected orthologous cells and cultured hippocampal rat neurons revealed no effect on the localization of METTL5 but alter its level of expression. Our in silico analysis and 3D modeling simulation predict disruption of METTL5 function by both variants. Finally, mettl5 knockdown in zebrafish resulted in microcephaly, recapitulating the human phenotype. This study provides evidence that biallelic variants in METTL5 cause ID and microcephaly in humans and highlights the essential role of METTL5 in brain development and neuronal function.
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Aspromonte MC, Bellini M, Gasparini A, Carraro M, Bettella E, Polli R, Cesca F, Bigoni S, Boni S, Carlet O, Negrin S, Mammi I, Milani D, Peron A, Sartori S, Toldo I, Soli F, Turolla L, Stanzial F, Benedicenti F, Marino-Buslje C, Tosatto SCE, Murgia A, Leonardi E. Characterization of intellectual disability and autism comorbidity through gene panel sequencing. Hum Mutat 2019; 40:1346-1363. [PMID: 31209962 DOI: 10.1002/humu.23822] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/18/2019] [Accepted: 05/27/2019] [Indexed: 12/22/2022]
Abstract
Intellectual disability (ID) and autism spectrum disorder (ASD) are clinically and genetically heterogeneous diseases. Recent whole exome sequencing studies indicated that genes associated with different neurological diseases are shared across disorders and converge on common functional pathways. Using the Ion Torrent platform, we developed a low-cost next-generation sequencing gene panel that has been transferred into clinical practice, replacing single disease-gene analyses for the early diagnosis of individuals with ID/ASD. The gene panel was designed using an innovative in silico approach based on disease networks and mining data from public resources to score disease-gene associations. We analyzed 150 unrelated individuals with ID and/or ASD and a confident diagnosis has been reached in 26 cases (17%). Likely pathogenic mutations have been identified in another 15 patients, reaching a total diagnostic yield of 27%. Our data also support the pathogenic role of genes recently proposed to be involved in ASD. Although many of the identified variants need further investigation to be considered disease-causing, our results indicate the efficiency of the targeted gene panel on the identification of novel and rare variants in patients with ID and ASD.
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Affiliation(s)
- Maria C Aspromonte
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, C.so Stati Uniti, 4, Padova, Italy.,Fondazione Istituto di Ricerca Pediatrica, Città della Speranza, Padova, Italy
| | - Mariagrazia Bellini
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, C.so Stati Uniti, 4, Padova, Italy.,Fondazione Istituto di Ricerca Pediatrica, Città della Speranza, Padova, Italy
| | | | - Marco Carraro
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Elisa Bettella
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, C.so Stati Uniti, 4, Padova, Italy.,Fondazione Istituto di Ricerca Pediatrica, Città della Speranza, Padova, Italy
| | - Roberta Polli
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, C.so Stati Uniti, 4, Padova, Italy.,Fondazione Istituto di Ricerca Pediatrica, Città della Speranza, Padova, Italy
| | - Federica Cesca
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, C.so Stati Uniti, 4, Padova, Italy.,Fondazione Istituto di Ricerca Pediatrica, Città della Speranza, Padova, Italy
| | - Stefania Bigoni
- Medical Genetics Unit, Ospedale Universitario S. Anna, Ferrara, Italy
| | - Stefania Boni
- Medical Genetics Unit, San Martino Hospital, Belluno, Italy
| | - Ombretta Carlet
- Epilepsy and Child Neurophysiology Unit, Scientific Institute IRCCS E. Medea, Treviso, Italy
| | - Susanna Negrin
- Epilepsy and Child Neurophysiology Unit, Scientific Institute IRCCS E. Medea, Treviso, Italy
| | - Isabella Mammi
- Medical Genetics Unit, Dolo General Hospital, Venezia, Italy
| | - Donatella Milani
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, University of Milano, Milan, Italy
| | - Angela Peron
- Child Neuropsychiatry Unit, Epilepsy Center, Department of Health Sciences, Santi Paolo-Carlo Hospital, University of Milano, Milano, Italy.,Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah
| | - Stefano Sartori
- Paediatric Neurology Unit, Department of Woman and Child Health, University Hospital of Padova, Padova, Italy
| | - Irene Toldo
- Paediatric Neurology Unit, Department of Woman and Child Health, University Hospital of Padova, Padova, Italy
| | - Fiorenza Soli
- Medical Genetics Department, APSS Trento, Trento, Italy
| | - Licia Turolla
- Medical Genetics Unit, Local Health Authority, Treviso, Italy
| | - Franco Stanzial
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Francesco Benedicenti
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | | | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Institute of Neuroscience, National Research Council, Padova, Italy
| | - Alessandra Murgia
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, C.so Stati Uniti, 4, Padova, Italy.,Fondazione Istituto di Ricerca Pediatrica, Città della Speranza, Padova, Italy
| | - Emanuela Leonardi
- Molecular Genetics of Neurodevelopment, Department of Woman and Child Health, University of Padova, C.so Stati Uniti, 4, Padova, Italy.,Fondazione Istituto di Ricerca Pediatrica, Città della Speranza, Padova, Italy
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Pekeles H, Accogli A, Boudrahem-Addour N, Russell L, Parente F, Srour M. Diagnostic Yield of Intellectual Disability Gene Panels. Pediatr Neurol 2019; 92:32-36. [PMID: 30581057 DOI: 10.1016/j.pediatrneurol.2018.11.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 11/06/2018] [Accepted: 11/07/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Recent technological advances have improved the understanding and identification of the genetic basis of intellectual disability (ID) and global developmental delay (GDD). Next-generation sequencing panels of ID genes are now available for clinical testing; however, their overall yield in clinical practice has not yet been investigated. AIM We determined the diagnostic yield of ID gene panels in a clinical setting and explored whether any clinical features are associated with an increased diagnostic yield. METHODS We performed a systematic retrospective chart review of all patients with ID/GDD who underwent an ID gene panel between April 2014 and July 2017 at our institution. Chi-square analysis assessed whether any specific clinical features were significantly associated with a positive diagnostic yield. RESULTS Forty-eight subjects (18 females, 30 males; median age: 7.5 years) were included. Consanguinity was present in 17%, autism in 38%, seizures in 42%, nonspecific dysmorphic features in 67%, and abnormalities on neurological examination in 56%; furthermore, 29% of the cohort was nonverbal and 4% was nonambulatory. Four different gene panels were used. The diagnostic yield was 21% (10/48) overall, and 38% with the more recent trio-based panel. Eight of 10 patients had de novo pathogenic dominant mutations, one had an inherited pathogenic autosomal dominant mutation, and one had compound heterozygous pathogenic recessive mutations. No clinical feature was significantly associated with an increased diagnostic yield. CONCLUSIONS Our study suggests that ID gene panels have a high yield and are a valuable diagnostic tool in the evaluation of children with ID/GDD.
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Affiliation(s)
| | - Andrea Accogli
- Division of Pediatric Neurology, Departments of Pediatrics and Neurology & Neurosurgery, McGill University, Montreal, Canada; Scientific Institute for Research and Healthcare, Istituto Giannina Gaslini, Genova, Italy; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, and Maternal and Children's Sciences, Università degli Studi di Genova, Italy
| | - Nassima Boudrahem-Addour
- Child Health and Human Development Program, McGill University Health Center (MUHC) Research Institute, Montreal, Canada
| | - Laura Russell
- Division of Medical Genetics, Department of Medicine, McGill University, Montreal, Canada
| | - Fabienne Parente
- Division of Medical Genetics, Department of Medicine, McGill University, Montreal, Canada
| | - Myriam Srour
- Division of Pediatric Neurology, Departments of Pediatrics and Neurology & Neurosurgery, McGill University, Montreal, Canada.
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Levchenko OA, Lavrov AV. [Massive parallel sequencing for molecular-genetic diagnosis of mental retardation]. Zh Nevrol Psikhiatr Im S S Korsakova 2019; 118:65-71. [PMID: 30698565 DOI: 10.17116/jnevro201811812165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Gene mutations occur with high frequency in children with mental retardation. Standard diagnostic methods, such as TMS, Sanger's sequencing of individual genes, MLPA analysis of deletions, and investigation of methylation status in Martin-Bell syndrome are not informative in the majority of cases that hampered further diagnostic efforts. Massive parallel sequencing (MPS) allowed physicians to continue diagnostic search in previously undiagnosed cases and to find molecular causes of disease. MPS permits to discover a large number of new genes and understand the pathogenesis of mental retardation and brain development more deeply. It became possible to perform prenatal and pre-implantation diagnostics. However, big data generate big problems with their interpretation the genetic counselor faces with. This review reflects the advantages and disadvantages of MPS. Different variants of MPS, including gene panels, whole exome and whole genome sequencing as well as sequencing of trios, are described. In addition, the authors discuss the difficulties of interpretation of the results and recommendations for obtaining the most accurate results.
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Affiliation(s)
- O A Levchenko
- Research Centre for Medical Genetics, Moscow, Russia
| | - A V Lavrov
- Research Centre for Medical Genetics, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
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Elmas M, Yıldız H, Erdoğan M, Gogus B, Avcı K, Solak M. Comparison of clinical parameters with whole exome sequencing analysis results of autosomal recessive patients; a center experience. Mol Biol Rep 2018; 46:287-299. [PMID: 30426380 DOI: 10.1007/s11033-018-4470-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/02/2018] [Indexed: 11/24/2022]
Abstract
Whole-exome sequencing (WES) is an ideal method for the diagnosis of autosomal recessive diseases. The aim of this study was to evaluate the diagnostic power of WES in patients with autosomal recessive inheritance and to determine the relationship between genotype and phenotype. Retrospective screenings of 24 patients analysed with WES were performed and clinical and genetic data were evaluated. Any pathogenic mutation that could explain the suspected disease in 4 patients was not identified. A homozygous pathogenic mutation was detected in 18 patients. 2 patients had heterozygous mutations. According to this study results, WES is a successful technique to be used at the stage of diagnosis in patients who are accompanied by various degrees of intellectual disability matching the inheritance of the autosomal recessive.
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Affiliation(s)
- M Elmas
- Medical Genetics Department, Afyon Kocatepe University, Afyonkarahisar, Turkey.
| | - H Yıldız
- Medical Genetics Department, Afyon Kocatepe University, Afyonkarahisar, Turkey
| | - M Erdoğan
- Medical Biology and Genetics Department, Afyon Kocatepe University, Afyonkarahisar, Turkey
| | - B Gogus
- Medical Genetics Department, Afyon Kocatepe University, Afyonkarahisar, Turkey
| | - K Avcı
- Medical Genetics Department, Afyon Kocatepe University, Afyonkarahisar, Turkey
| | - M Solak
- Medical Genetics Department, Afyon Kocatepe University, Afyonkarahisar, Turkey
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Liu Z, Zhang N, Zhang Y, Du Y, Zhang T, Li Z, Wu J, Wang X. Prioritized High-Confidence Risk Genes for Intellectual Disability Reveal Molecular Convergence During Brain Development. Front Genet 2018; 9:349. [PMID: 30279698 PMCID: PMC6153320 DOI: 10.3389/fgene.2018.00349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/09/2018] [Indexed: 01/09/2023] Open
Abstract
Dissecting the genetic susceptibility to intellectual disability (ID) based on de novo mutations (DNMs) will aid our understanding of the neurobiological and genetic basis of ID. In this study, we identify 63 high-confidence ID genes with q-values < 0.1 based on four background DNM rates and coding DNM data sets from multiple sequencing cohorts. Bioinformatic annotations revealed a higher burden of these 63 ID genes in FMRP targets and CHD8 targets, and these genes show evolutionary constraint against functional genetic variation. Moreover, these ID risk genes were preferentially expressed in the cortical regions from the early fetal to late mid-fetal stages. In particular, a genome-wide weighted co-expression network analysis suggested that ID genes tightly converge onto two biological modules (M1 and M2) during human brain development. Functional annotations showed specific enrichment of chromatin modification and transcriptional regulation for M1 and synaptic function for M2, implying the divergent etiology of the two modules. In addition, we curated 12 additional strong ID risk genes whose molecular interconnectivity with known ID genes (q-values < 0.3) was greater than random. These findings further highlight the biological convergence of ID risk genes and help improve our understanding of the genetic architecture of ID.
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Affiliation(s)
- Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Na Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Yu Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Yaoqiang Du
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Tao Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xiaobing Wang
- Department of Rheumatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Di Resta C, Galbiati S, Carrera P, Ferrari M. Next-generation sequencing approach for the diagnosis of human diseases: open challenges and new opportunities. EJIFCC 2018; 29:4-14. [PMID: 29765282 PMCID: PMC5949614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The rapid evolution and widespread use of next generation sequencing (NGS) in clinical laboratories has allowed an incredible progress in the genetic diagnostics of several inherited disorders. However, the new technologies have brought new challenges. In this review we consider the important issue of NGS data analysis, as well as the interpretation of unknown genetic variants and the management of the incidental findings. Moreover, we focus the attention on the new professional figure of bioinformatics and the new role of medical geneticists in clinical management of patients. Furthermore, we consider some of the main clinical applications of NGS, taking into consideration that there will be a growing progress in this field in the forthcoming future.
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Affiliation(s)
- Chiara Di Resta
- Vita-Salute San Raffaele University, Milan, Italy
- Genomic Unit for the Diagnosis of Human Disorders, Division of Genetics and Cell Biology, IRCCS San Raffaele Hospital, Milan, Italy
| | - Silvia Galbiati
- Genomic Unit for the Diagnosis of Human Disorders, Division of Genetics and Cell Biology, IRCCS San Raffaele Hospital, Milan, Italy
| | - Paola Carrera
- Genomic Unit for the Diagnosis of Human Disorders, Division of Genetics and Cell Biology, IRCCS San Raffaele Hospital, Milan, Italy
- Laboratory of Clinical Molecular Biology and Cytogenetics, IRCCS San Raffaele Hospital, Milan, Italy
| | - Maurizio Ferrari
- Vita-Salute San Raffaele University, Milan, Italy
- Genomic Unit for the Diagnosis of Human Disorders, Division of Genetics and Cell Biology, IRCCS San Raffaele Hospital, Milan, Italy
- Laboratory of Clinical Molecular Biology and Cytogenetics, IRCCS San Raffaele Hospital, Milan, Italy
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