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Zhang J, Xu Y, Liu Y, Yue L, Jin H, Chen Y, Wang D, Wang M, Chen G, Yang L, Zhang G, Zhang X, Li S, Zhao H, Zhao Y, Niu G, Gao Y, Cai Z, Yang F, Zhu C, Zhu D. Genetic Testing for Global Developmental Delay in Early Childhood. JAMA Netw Open 2024; 7:e2415084. [PMID: 38837156 PMCID: PMC11154162 DOI: 10.1001/jamanetworkopen.2024.15084] [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: 01/27/2024] [Accepted: 04/03/2024] [Indexed: 06/06/2024] Open
Abstract
Importance Global developmental delay (GDD) is characterized by a complex etiology, diverse phenotypes, and high individual heterogeneity, presenting challenges for early clinical etiologic diagnosis. Cognitive impairment is the core symptom, and despite the pivotal role of genetic factors in GDD development, the understanding of them remains limited. Objectives To assess the utility of genetic detection in patients with GDD and to examine the potential molecular pathogenesis of GDD to identify targets for early intervention. Design, Setting, and Participants This multicenter, prospective cohort study enrolled patients aged 12 to 60 months with GDD from 6 centers in China from July 4, 2020, to August 31, 2023. Participants underwent trio whole exome sequencing (trio-WES) coupled with copy number variation sequencing (CNV-seq). Bioinformatics analysis was used to unravel pathogenesis and identify therapeutic targets. Main Outcomes and Measures The main outcomes of this study involved enhancing the rate of positive genetic diagnosis for GDD, broadening the scope of genetic testing indications, and investigating the underlying pathogenesis. The classification of children into levels of cognitive impairment was based on the developmental quotient assessed using the Gesell scale. Results The study encompassed 434 patients with GDD (262 [60%] male; mean [SD] age, 25.75 [13.24] months) with diverse degrees of cognitive impairment: mild (98 [23%]), moderate (141 [32%]), severe (122 [28%]), and profound (73 [17%]). The combined use of trio-WES and CNV-seq resulted in a 61% positive detection rate. Craniofacial abnormalities (odds ratio [OR], 2.27; 95% CI, 1.45-3.56), moderate or severe cognitive impairment (OR, 1.69; 95% CI, 1.05-2.70), and age between 12 and 24 months (OR, 1.57; 95% CI, 1.05-2.35) were associated with a higher risk of carrying genetic variants. Additionally, bioinformatics analysis suggested that genetic variants may induce alterations in brain development and function, which may give rise to cognitive impairment. Moreover, an association was found between the dopaminergic pathway and cognitive impairment. Conclusions and Relevance In this cohort study of patients with GDD, combining trio-WES with CNV-seq was a demonstrable, instrumental strategy for advancing the diagnosis of GDD. The close association among genetic variations, brain development, and clinical phenotypes contributed valuable insights into the pathogenesis of GDD. Notably, the dopaminergic pathway emerged as a promising focal point for potential targets in future precision medical interventions for GDD.
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Affiliation(s)
- Jiamei Zhang
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yiran Xu
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yun Liu
- Kunming Children’s Hospital, Kunming, China
| | - Ling Yue
- Department of Neurological Rehabilitation, Children’s Hospital of Hebei Province, Shijiazhuang, China
| | - Hongfang Jin
- Qinghai Provincial Women and Children’s Hospital, Xining, China
| | | | - Dong Wang
- Department of Pediatric Neurology, Xi’an Children’s Hospital, Xi’an, China
| | - Mingmei Wang
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Gongxun Chen
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lei Yang
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guangyu Zhang
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoli Zhang
- Department of Pediatric Neurology, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Sansong Li
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huiling Zhao
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yunxia Zhao
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guohui Niu
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yongqiang Gao
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhijun Cai
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | | | - Changlian Zhu
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Center for Brain Repair and Rehabilitation, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Dengna Zhu
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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2
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Calame DG, Emrick LT. Functional genomics and small molecules in mitochondrial neurodevelopmental disorders. Neurotherapeutics 2024; 21:e00316. [PMID: 38244259 PMCID: PMC10903096 DOI: 10.1016/j.neurot.2024.e00316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/16/2023] [Accepted: 01/02/2024] [Indexed: 01/22/2024] Open
Abstract
Mitochondria are critical for brain development and homeostasis. Therefore, pathogenic variation in the mitochondrial or nuclear genome which disrupts mitochondrial function frequently results in developmental disorders and neurodegeneration at the organismal level. Large-scale application of genome-wide technologies to individuals with mitochondrial diseases has dramatically accelerated identification of mitochondrial disease-gene associations in humans. Multi-omic and high-throughput studies involving transcriptomics, proteomics, metabolomics, and saturation genome editing are providing deeper insights into the functional consequence of mitochondrial genomic variation. Integration of deep phenotypic and genomic data through allelic series continues to uncover novel mitochondrial functions and permit mitochondrial gene function dissection on an unprecedented scale. Finally, mitochondrial disease-gene associations illuminate disease mechanisms and thereby direct therapeutic strategies involving small molecules and RNA-DNA therapeutics. This review summarizes progress in functional genomics and small molecule therapeutics in mitochondrial neurodevelopmental disorders.
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Affiliation(s)
- Daniel G Calame
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Lisa T Emrick
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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3
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Jurcău MC, Andronie-Cioara FL, Jurcău A, Marcu F, Ţiț DM, Pașcalău N, Nistor-Cseppentö DC. The Link between Oxidative Stress, Mitochondrial Dysfunction and Neuroinflammation in the Pathophysiology of Alzheimer's Disease: Therapeutic Implications and Future Perspectives. Antioxidants (Basel) 2022; 11:2167. [PMID: 36358538 PMCID: PMC9686795 DOI: 10.3390/antiox11112167] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 10/28/2022] [Accepted: 10/29/2022] [Indexed: 08/26/2023] Open
Abstract
Alzheimer's disease (AD), the most common form of dementia, has increasing incidence, increasing mortality rates, and poses a huge burden on healthcare. None of the currently approved drugs for the treatment of AD influence disease progression. Many clinical trials aiming at inhibiting amyloid plaque formation, increasing amyloid beta clearance, or inhibiting neurofibrillary tangle pathology yielded inconclusive results or failed. Meanwhile, research has identified many interlinked vicious cascades implicating oxidative stress, mitochondrial dysfunction, and chronic neuroinflammation, and has pointed to novel therapeutic targets such as improving mitochondrial bioenergetics and quality control, diminishing oxidative stress, or modulating the neuroinflammatory pathways. Many novel molecules tested in vitro or in animal models have proven efficient, but their translation into clinic needs further research regarding appropriate doses, delivery routes, and possible side effects. Cell-based therapies and extracellular vesicle-mediated delivery of messenger RNAs and microRNAs seem also promising strategies allowing to target specific signaling pathways, but need further research regarding the most appropriate harvesting and culture methods as well as control of the possible tumorigenic side effects. The rapidly developing area of nanotechnology could improve drug delivery and also be used in early diagnosis.
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Affiliation(s)
| | - Felicia Liana Andronie-Cioara
- Department of Psycho-Neuroscience and Rehabilitation, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania
| | - Anamaria Jurcău
- Department of Psycho-Neuroscience and Rehabilitation, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania
| | - Florin Marcu
- Department of Psycho-Neuroscience and Rehabilitation, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania
| | - Delia Mirela Ţiț
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410028 Oradea, Romania
| | - Nicoleta Pașcalău
- Department of Psycho-Neuroscience and Rehabilitation, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania
| | - Delia Carmen Nistor-Cseppentö
- Department of Psycho-Neuroscience and Rehabilitation, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania
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4
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Fell CW, Hagelkruys A, Cicvaric A, Horrer M, Liu L, Li JSS, Stadlmann J, Polyansky AA, Mereiter S, Tejada MA, Kokotović T, Achuta VS, Scaramuzza A, Twyman KA, Morrow MM, Juusola J, Yan H, Wang J, Burmeister M, Choudhury B, Andersen TL, Wirnsberger G, Holmskov U, Perrimon N, Žagrović B, Monje FJ, Moeller JB, Penninger JM, Nagy V. FIBCD1 is an endocytic GAG receptor associated with a novel neurodevelopmental disorder. EMBO Mol Med 2022; 14:e15829. [PMID: 35916241 PMCID: PMC9449597 DOI: 10.15252/emmm.202215829] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 11/21/2022] Open
Abstract
Whole-exome sequencing of two patients with idiopathic complex neurodevelopmental disorder (NDD) identified biallelic variants of unknown significance within FIBCD1, encoding an endocytic acetyl group-binding transmembrane receptor with no known function in the central nervous system. We found that FIBCD1 preferentially binds and endocytoses glycosaminoglycan (GAG) chondroitin sulphate-4S (CS-4S) and regulates GAG content of the brain extracellular matrix (ECM). In silico molecular simulation studies and GAG binding analyses of patient variants determined that such variants are loss-of-function by disrupting FIBCD1-CS-4S association. Gene knockdown in flies resulted in morphological disruption of the neuromuscular junction and motor-related behavioural deficits. In humans and mice, FIBCD1 is expressed in discrete brain regions, including the hippocampus. Fibcd1 KO mice exhibited normal hippocampal neuronal morphology but impaired hippocampal-dependent learning. Further, hippocampal synaptic remodelling in acute slices from Fibcd1 KO mice was deficient but restored upon enzymatically modulating the ECM. Together, we identified FIBCD1 as an endocytic receptor for GAGs in the brain ECM and a novel gene associated with an NDD, revealing a critical role in nervous system structure, function and plasticity.
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Affiliation(s)
- Christopher W Fell
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
- Department of NeurologyMedical University of ViennaViennaAustria
| | - Astrid Hagelkruys
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
| | - Ana Cicvaric
- Department of Neurophysiology and Neuropharmacology, Centre for Physiology and PharmacologyMedical University of ViennaViennaAustria
- Department of Psychiatry and Behavioral Sciences, Feinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Marion Horrer
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
| | - Lucy Liu
- Department of Genetics, Harvard Medical SchoolHoward Hughes Medical InstituteBostonMAUSA
| | - Joshua Shing Shun Li
- Department of Genetics, Harvard Medical SchoolHoward Hughes Medical InstituteBostonMAUSA
| | - Johannes Stadlmann
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
- Institute of BiochemistryUniversity of Natural Resource and Life SciencesViennaAustria
| | - Anton A Polyansky
- Department of Structural and Computational Biology, Max Perutz LabsUniversity of ViennaViennaAustria
- MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussia
| | - Stefan Mereiter
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
| | - Miguel Angel Tejada
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
- Research Unit on Women's Health‐Institute of Health Research INCLIVAValenciaSpain
| | - Tomislav Kokotović
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
- Department of NeurologyMedical University of ViennaViennaAustria
| | - Venkat Swaroop Achuta
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- Department of NeurologyMedical University of ViennaViennaAustria
| | - Angelica Scaramuzza
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- Department of NeurologyMedical University of ViennaViennaAustria
| | | | | | | | - Huifang Yan
- Department of PediatricsPeking University First HospitalBeijingChina
- Joint International Research Center of Translational and Clinical ResearchBeijingChina
| | - Jingmin Wang
- Department of PediatricsPeking University First HospitalBeijingChina
- Joint International Research Center of Translational and Clinical ResearchBeijingChina
| | - Margit Burmeister
- Michigan Neuroscience InstituteUniversity of MichiganAnn ArborMIUSA
- Departments of Computational Medicine & Bioinformatics, Psychiatry and Human GeneticsUniversity of MichiganAnn ArborMIUSA
| | - Biswa Choudhury
- Department of Cellular and Molecular MedicineUCSDLa JollaCAUSA
| | - Thomas Levin Andersen
- Clinical Cell Biology, Department of PathologyOdense University HospitalOdenseDenmark
- Pathology Research Unit, Department of Clinical Research and Department of Molecular MedicineUniversity of Southern DenmarkOdenseDenmark
| | - Gerald Wirnsberger
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
- Apeiron Biologics AG, Vienna BioCenter CampusViennaAustria
| | - Uffe Holmskov
- Cancer and Inflammation Research, Department of Molecular MedicineUniversity of Southern DenmarkOdenseDenmark
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical SchoolHoward Hughes Medical InstituteBostonMAUSA
| | - Bojan Žagrović
- Department of Structural and Computational Biology, Max Perutz LabsUniversity of ViennaViennaAustria
| | - Francisco J Monje
- Department of Neurophysiology and Neuropharmacology, Centre for Physiology and PharmacologyMedical University of ViennaViennaAustria
| | - Jesper Bonnet Moeller
- Cancer and Inflammation Research, Department of Molecular MedicineUniversity of Southern DenmarkOdenseDenmark
- Danish Institute for Advanced StudyUniversity of Southern DenmarkOdenseDenmark
| | - Josef M Penninger
- VBC – Vienna BioCenter CampusIMBA, Institute of Molecular Biotechnology of the Austrian Academy of SciencesViennaAustria
- Department of Medical Genetics, Life Science InstituteUniversity of British ColumbiaVancouverBCCanada
| | - Vanja Nagy
- Ludwig Boltzmann Institute for Rare and Undiagnosed DiseasesViennaAustria
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
- Department of NeurologyMedical University of ViennaViennaAustria
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5
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Zhu D, Wang M, Xu Y, Zhang J, Yang F, Yang Z. Identification of a 5 bp duplicate in the AP1S2 gene of an individual with X-linked intellectual disability. Neurogenetics 2022; 23:179-185. [DOI: 10.1007/s10048-022-00691-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 03/25/2022] [Indexed: 11/28/2022]
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6
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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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7
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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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8
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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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