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Xu P, Wang L, Li J, Huang S, Gao M, Kang R, Li J, Xie H, Liu X, Yan J, Gao X, Gao Y. OGM and WES identifies translocation breakpoints in PKD1 gene in an polycystic kidney patient and healthy baby delivered using PGT. BMC Med Genomics 2023; 16:285. [PMID: 37953234 PMCID: PMC10642002 DOI: 10.1186/s12920-023-01725-2] [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: 06/10/2023] [Accepted: 11/02/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common autosomal dominant genetic diseases. Whole exome sequencing (WES) is a routine tool for diagnostic confirmation of genetic diseases, and it is usually performed to confirm the clinical diagnosis in ADPKD. Reciprocal translocation is the most common chromosomal structural abnormalities and most of its carriers have normal phenotypes until they are encountered infertility problems in adulthood. However, for the polycystic kidney disease caused by abnormal chromosome structure, WES is difficult to achieve the purpose of gene diagnosis. METHODS ADPKD-related genes were detected by WES; Chromosomal karyotyping and Optical Genome Mapping (OGM) were used to detect structural variant; The genomic break-point locations and the abnormal splicing were detected by reverse transcription-PCR and Sanger sequencing; The karyomapping gene chip and Next-Generation Sequencing (NGS) were performed to screen aneuploidy and to distinguish the non-carrier embryos from the carrier embryos. RESULTS No pathogenic variant was found after the first round of WES analysis. Karyotyping data showed 46, XX, t (16; 17) (p13.3; q21.3). With the help of OGM, the translocation breakpoint on chromosome 16 was located within the PKD1 gene. With re-analysis of WES raw data, the breakpoint of translocation was verified to be located at the c.10618 + 3 of PKD1 gene. Based on this molecular diagnosis, a non-carrier embryo was selected out from three blastocysts. With preimplantation genetic testing (PGT) after in vitro fertilization (IVF), it was then transferred into uterus. With confirmation by prenatal and postnatal testing, the pedigree delivered a healthy baby. CONCLUSION We identified a case of ADPKD caused by balanced translocation and assisted the patient to have a healthy child. When the phenotype was closely related with a monogenic disease and the WES analysis was negative, chromosomal structural analysis would be recommended for further genetic diagnosis. Based on the precision diagnosis, preventing the recurrence of hereditary diseases in offspring would be reachable.
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Affiliation(s)
- Peiwen Xu
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
- Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China
| | - Lijuan Wang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
- Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China
| | - Jing Li
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
- Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China
| | - Sexin Huang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
- Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China
| | - Ming Gao
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
- Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China
| | - Ranran Kang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
- Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China
| | - Jie Li
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
- Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China
| | - Hongqiang Xie
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
- Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China
| | - Xiaowei Liu
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
- Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China
| | - Junhao Yan
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
- Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China
| | - Xuan Gao
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
- Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China
| | - Yuan Gao
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China.
- Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.
- Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China.
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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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Demirhan O, Hergüner Ö, Tunç E. A Cytogenetic Study of Turkish Children with Global Developmental Delay. J Pediatr Genet 2022. [DOI: 10.1055/s-0042-1758872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
AbstractGlobal developmental delay (GDD)/intellectual disability (ID) is common in children and its etiology is unknown in many cases. Chromosomal abnormalities are predominant genetic causes of GDD/ID. The aim of this study is to determine the genetic risk factors that may be involved in the etiology of GDD/ID. In this study, 810 children with moderate to severe, clinically unexplained GDD/ID for whom cytogenetic analysis were performed were retrospectively rescreened. The results showed that GDD/ID affected more females than males (2 girls:1 boy). A total of 54 children (6.7%) with GDD showed chromosomal aberrations (CAs): 59.3% of these CAs were structural aberrations, and the rest were numerical aberrations (40.7%). Specifically, inversions, deletions, and reciprocal and robertsonian translocations, which were detected in 1, 0.7, 0.8, and 0.4% of the children, respectively, constituted important categories of structural CAs. Among numerical CAs, classic Turner and mosaics were detected in 1.2% of all children. Trisomy 21 and mosaic trisomy 21 were detected in 1% of the children. Marker chromosomes and 47,XXY karyotypes were found in two children each. Our results suggest that female sex is more affected by CAs among GDD/ID cases, and cytogenetic analysis is useful in the etiological diagnosis of GDD/ID.
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Affiliation(s)
- Osman Demirhan
- Department of Medical Biology and Genetics, Faculty of Medicine, Çukurova University, Balcali-Adana, Turkey
| | - Özlem Hergüner
- Department of Child Neurology, Faculty of Medicine, Çukurova University, Balcali-Adana, Turkey
| | - Erdal Tunç
- Department of Medical Biology and Genetics, Faculty of Medicine, Çukurova University, Balcali-Adana, Turkey
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Lengyel A, Pinti É, Pikó H, Kristóf Á, Abonyi T, Némethi Z, Fekete G, Haltrich I. Clinical evaluation of rare copy number variations identified by chromosomal microarray in a Hungarian neurodevelopmental disorder patient cohort. Mol Cytogenet 2022; 15:47. [PMID: 36320065 PMCID: PMC9623912 DOI: 10.1186/s13039-022-00623-z] [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: 08/08/2022] [Revised: 09/22/2022] [Accepted: 09/30/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Neurodevelopmental disorders are genetically heterogeneous pediatric conditions. The first tier diagnostic method for uncovering copy number variations (CNVs), one of the most common genetic etiologies in affected individuals, is chromosomal microarray (CMA). However, this methodology is not yet a routine molecular cytogenetic test in many parts of the world, including Hungary. Here we report clinical and genetic data of the first, relatively large Hungarian cohort of patients whose genetic testing included CMA. METHODS Clinical data were retrospectively collected for 78 children who were analyzed using various CMA platforms. Phenotypes of patients with disease-causing variants were compared to patients with negative results using the chi squared/Fisher exact tests. RESULTS A total of 30 pathogenic CNVs were identified in 29 patients (37.2%). Postnatal growth delay (p = 0.05564), pectus excavatum (p = 0.07484), brain imaging abnormalities (p = 0.07848), global developmental delay (p = 0.08070) and macrocephaly (p = 0.08919) were more likely to be associated with disease-causing CNVs. CONCLUSION Our results allow phenotypic expansion of 14q11.2 microdeletions encompassing SUPT16H and CHD8 genes. Variants of unknown significance (n = 24) were found in 17 patients. We provide detailed phenotypic and genetic data of these individuals to facilitate future classification efforts, and spotlight two patients with potentially pathogenic alterations. Our results contribute to unraveling the diagnostic value of rare CNVs.
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Affiliation(s)
- Anna Lengyel
- grid.11804.3c0000 0001 0942 9821II. Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Éva Pinti
- grid.11804.3c0000 0001 0942 9821II. Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Henriett Pikó
- grid.11804.3c0000 0001 0942 9821Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Árvai Kristóf
- grid.11804.3c0000 0001 0942 9821Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Tünde Abonyi
- grid.11804.3c0000 0001 0942 9821II. Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Zaránd Némethi
- grid.11804.3c0000 0001 0942 9821II. Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - György Fekete
- grid.11804.3c0000 0001 0942 9821II. Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Irén Haltrich
- grid.11804.3c0000 0001 0942 9821II. Department of Pediatrics, Semmelweis University, Budapest, Hungary
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Atherton M, Hart AR. How paediatricians investigate early developmental impairment in the UK: a qualitative descriptive study. BMC Pediatr 2022; 22:285. [PMID: 35578214 PMCID: PMC9109194 DOI: 10.1186/s12887-022-03233-1] [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: 09/29/2021] [Accepted: 03/22/2022] [Indexed: 11/24/2022] Open
Abstract
Background Early developmental impairment (EDI) is common and has many aetiologies and, therefore, potential investigations. There are several published guidelines recommending aetiological investigations, and paediatricians’ views of them varies. Little is known on the thought processes underlying clinical decisions in investigating EDI. This study aimed to describe the thought processes affecting clinical decisions on the investigation of EDI within a nationalised health care system. Methods A qualitative descriptive study using semi-structured qualitative interviews performed in person or via video link with paediatricians who see children with EDI in England. As part of the interview, a case study of a fictional disease, Cavorite deficiency, modelled on biotinidase deficiency, was given to participants with the cost of testing, incidence and likelihood it would respond to treatment. This allowed exploration of cost without encumbrance from predisposing views and training on the condition. Thematic analysis was performed by iterative approach. Where participants stated they wanted to redirect money from investigations to treatment, were that even possible, we asked which services they would like to be better funded in their area. Results Interviews were conducted with 14 consultant paediatricians: 9 Community / Neurodisability, 2 General paediatricians, and 3 Paediatric Neurologists. Two themes were identified: the value of an aetiological diagnosis to families and managing risk and probability when investigating EDI. The latter contained 4 subthemes: ‘circumspection’ involved blanket investigations chosen irrespective of phenotype and high regard for guidelines; ‘accepting appropriate risk’ involved participants choosing investigations based on clinical phenotype, recognising some aetiologies would be missed; consultants found they ‘transitioned between practices’ during their career; and ‘improved practice’ was thought possible with better evidence on how to stratify investigations based on phenotype. Services that were most frequently reported to need additional funding were therapy services, early community developmental services, management of behaviour, sleep and mental health, and educational support. Conclusions There are many factors that influence paediatricians’ choice of aetiological investigation in EDI, but clinical factors are the most important. Paediatricians want better evidence to allow them to select the right investigations for each child without a significant risk of missing an important diagnosis. Supplementary Information The online version contains supplementary material available at 10.1186/s12887-022-03233-1.
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Affiliation(s)
- Mark Atherton
- Department of Paediatric Neurology, Sheffield Children's NHS Foundation Trust, Ryegate Children's Centre, Tapton Crescent Road, Sheffield, S10 5DD, UK
| | - Anthony R Hart
- Department of Paediatric Neurology, Sheffield Children's NHS Foundation Trust, Ryegate Children's Centre, Tapton Crescent Road, Sheffield, S10 5DD, UK.
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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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Su M, Page S, Haag M, Swisshelm K, Hennerich D, Graw S, LeRoux J, Brzeskiewicz P, Svihovec S, Bao L. Clinical utility and cost-effectiveness analysis of chromosome testing concomitant with chromosomal microarray of patients with constitutional disorders in a U.S. academic medical center. J Genet Couns 2021; 31:364-374. [PMID: 34397147 DOI: 10.1002/jgc4.1496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 12/11/2022]
Abstract
Chromosomal microarray (CMA) is now widely used as first-tier testing for the detection of copy number variants (CNVs) and absence of heterozygosity (AOH) in patients with multiple congenital anomalies (MCA), autism spectrum disorder (ASD), developmental delay (DD), and/or intellectual disability (ID). Chromosome analysis is commonly used to complement CMA in the detection of balanced genomic aberrations. However, the cost-effectiveness and the impact on clinical management of chromosome analysis concomitant with CMA were not well studied, and there is no consensus on how to best utilize these two tests. To assess the clinical utility and cost-effectiveness of chromosome analysis concomitant with CMA in patients with MCA, ASD, DD, and/or ID, we retrospectively analyzed 3,360 postnatal cases for which CMA and concomitant chromosome analysis were performed in the Colorado Genetic Laboratory (CGL) at the University Of Colorado School Of Medicine. Chromosome analysis alone yielded a genetic diagnosis in two patients (0.06%) and contributed additional information to CMA results in 199 (5.92%) cases. The impact of abnormal chromosome results on patient management was primarily related to counseling for reproductive and recurrence risks assessment (101 cases, 3.01%) while a few (5 cases, 0.15%) led to changes in laboratory testing and specialist referral (25 cases, 0.74%). The incremental cost-effectiveness ratio (ICER) of combined testing demonstrated the cost of each informative chromosome finding was significantly higher for patients with clinically insignificant (CI) CMA findings versus clinically significant (CS) CMA results. Our results suggest that a stepwise approach with CMA testing with reflex to chromosome analysis on cases with CS CMA findings is a more cost-effective testing algorithm for patients with MCA, ASD, and/or DD/ID.
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Affiliation(s)
- Meng Su
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Stephanie Page
- Genetics Counseling Program, Department of Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Mary Haag
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Karen Swisshelm
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Deborrah Hennerich
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sharon Graw
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jamie LeRoux
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Peter Brzeskiewicz
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Shayna Svihovec
- Clinical Genetics and Metabolism, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Liming Bao
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
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Mantere T, Neveling K, Pebrel-Richard C, Benoist M, van der Zande G, Kater-Baats E, Baatout I, van Beek R, Yammine T, Oorsprong M, Hsoumi F, Olde-Weghuis D, Majdali W, Vermeulen S, Pauper M, Lebbar A, Stevens-Kroef M, Sanlaville D, Dupont JM, Smeets D, Hoischen A, Schluth-Bolard C, El Khattabi L. Optical genome mapping enables constitutional chromosomal aberration detection. Am J Hum Genet 2021; 108:1409-1422. [PMID: 34237280 PMCID: PMC8387289 DOI: 10.1016/j.ajhg.2021.05.012] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 05/28/2021] [Indexed: 01/02/2023] Open
Abstract
Chromosomal aberrations including structural variations (SVs) are a major cause of human genetic diseases. Their detection in clinical routine still relies on standard cytogenetics. Drawbacks of these tests are a very low resolution (karyotyping) and the inability to detect balanced SVs or indicate the genomic localization and orientation of duplicated segments or insertions (copy number variant [CNV] microarrays). Here, we investigated the ability of optical genome mapping (OGM) to detect known constitutional chromosomal aberrations. Ultra-high-molecular-weight DNA was isolated from 85 blood or cultured cells and processed via OGM. A de novo genome assembly was performed followed by structural variant and CNV calling and annotation, and results were compared to known aberrations from standard-of-care tests (karyotype, FISH, and/or CNV microarray). In total, we analyzed 99 chromosomal aberrations, including seven aneuploidies, 19 deletions, 20 duplications, 34 translocations, six inversions, two insertions, six isochromosomes, one ring chromosome, and four complex rearrangements. Several of these variants encompass complex regions of the human genome involved in repeat-mediated microdeletion/microduplication syndromes. High-resolution OGM reached 100% concordance compared to standard assays for all aberrations with non-centromeric breakpoints. This proof-of-principle study demonstrates the ability of OGM to detect nearly all types of chromosomal aberrations. We also suggest suited filtering strategies to prioritize clinically relevant aberrations and discuss future improvements. These results highlight the potential for OGM to provide a cost-effective and easy-to-use alternative that would allow comprehensive detection of chromosomal aberrations and structural variants, which could give rise to an era of "next-generation cytogenetics."
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Affiliation(s)
- Tuomo Mantere
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Radboud Institute of Medical Life Sciences, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Radboud Institute of Health Sciences, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Céline Pebrel-Richard
- Department of Chromosomal and Molecular Genetics, University Hospital of Clermont-Ferrand, 63003 Clermont-Ferrand, France
| | - Marion Benoist
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Guillaume van der Zande
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Ellen Kater-Baats
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Imane Baatout
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Ronald van Beek
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Tony Yammine
- Institut Neuromyogène, CNRS UMR 5310, INSERM U1217, Lyon 1 University, 69008 Lyon, France; Unit of Medical Genetics, Saint-Joseph University, 1107 2180 Beyrouth, Lebanon
| | - Michiel Oorsprong
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Faten Hsoumi
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Daniel Olde-Weghuis
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Wed Majdali
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Susan Vermeulen
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Marc Pauper
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Aziza Lebbar
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Marian Stevens-Kroef
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Damien Sanlaville
- Institut Neuromyogène, CNRS UMR 5310, INSERM U1217, Lyon 1 University, 69008 Lyon, France; Department of Genetics, Hospices Civils de Lyon, 69677 Bron, France
| | - Jean Michel Dupont
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France; Université de Paris, Cochin Institute U1016, INSERM, 75014 Paris, France
| | - Dominique Smeets
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Radboud Institute of Medical Life Sciences, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands.
| | - Caroline Schluth-Bolard
- Institut Neuromyogène, CNRS UMR 5310, INSERM U1217, Lyon 1 University, 69008 Lyon, France; Department of Genetics, Hospices Civils de Lyon, 69677 Bron, France
| | - Laïla El Khattabi
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France; Université de Paris, Cochin Institute U1016, INSERM, 75014 Paris, France.
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Fitzgerald J, Gallagher L. Parental stress and adjustment in the context of rare genetic syndromes: A scoping review. JOURNAL OF INTELLECTUAL DISABILITIES : JOID 2021; 26:1744629521995378. [PMID: 33866895 PMCID: PMC9168905 DOI: 10.1177/1744629521995378] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/24/2021] [Indexed: 06/10/2023]
Abstract
Chromosomal abnormalities are now considered a common cause of intellectual disability. With increased genetic testing, phenotyping and technological advancements, many new syndromes have been identified. This review sought to explore parental stress and adjustment in the context of rare genetic syndromes to evaluate their clinical impact. A systematic review of English peer-reviewed literature across three databases (PsycINFO, Medline, CINAHL) was completed and 69 articles were included. Parents of children with rare genetic syndromes experienced greater distress relative to other disabilities. Differences in parental wellbeing were syndrome-specific relative to ASD thus demonstrating the need to consider the contribution of syndrome-specific phenotypes. Child emotional and behavioural difficulties were the most consistent predictor of parental distress. Research reflecting other factors such as physical health, syndrome-specific behaviours, benefit finding and, parental appraisal in the context of a rare genetic aetiology is required in order to support parental adjustment in these conditions.
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Affiliation(s)
| | - Louise Gallagher
- Trinity College Dublin, Ireland; Children Health Ireland at Tallaght Hospital, Ireland;
Cherry Orchard Hospital, Ireland
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10
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Jussila MP, Olsén P, Niinimäki J, Suo-Palosaari M. Is Brain MRI Needed in Diagnostic Evaluation of Mild Intellectual Disability? Neuropediatrics 2021; 52:27-33. [PMID: 33111301 DOI: 10.1055/s-0040-1716902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AIM The purpose of our study was to suggest an imaging strategy and guidelines for the selection of the children with mild intellectual disability (ID) for magnetic resonance imaging (MRI), to avoid unnecessary imaging. METHODS The brain MRIs and patient reports of 471 children were reviewed for the imaging findings and ID severity. The correlation between the clinical and brain MRI findings was analyzed in the 305 children with mild ID. RESULTS Thirty-eight (12.5%) of the children with mild ID had significant abnormal brain MRI findings. Thirty-five of these had other neurological symptoms or diseases in addition to ID, which were an indication for brain MRI. In the logistic regression analysis, seizures (in patients without an epilepsy diagnosis), epilepsy, movement disorders, dysmorphia, encephalitis, traumatic brain injury, and abnormal head size were statistically significant symptoms or comorbidities associated with abnormal MRI findings. Only three children (1.0%) with mild ID had a significant MRI finding without any other clinical symptoms or disease. CONCLUSION Routine MRI in children with mild ID without specific neurological symptoms, dysmorphic features, or related diseases is not suggested for revealing an etiology of mild ID. Since children with ID usually need to be sedated for MRI, routine imaging in the diagnostic evaluation of mild ID should be carefully considered. Clinical examination, other symptoms, and related diseases should be carefully assessed to decide the need for MRI.
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Affiliation(s)
- Miro Pekka Jussila
- Department of Diagnostic Radiology, Oulu University Hospital and Research Unit of Medical Imaging, Physics and Technology, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Päivi Olsén
- Department of Pediatrics and Adolescence, Oulu University Hospital and PEDEGO Research Unit, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Jaakko Niinimäki
- Department of Diagnostic Radiology, Oulu University Hospital and Research Unit of Medical Imaging, Physics and Technology, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Maria Suo-Palosaari
- Department of Diagnostic Radiology, Oulu University Hospital and Research Unit of Medical Imaging, Physics and Technology, Oulu University Hospital and University of Oulu, Oulu, Finland
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11
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Tang X, Zhang H, Zhou J, Kang H, Yang S, Cui H, Peng Y. Brain development in children with developmental delay using amide proton transfer-weighted imaging and magnetization transfer imaging. Pediatr Investig 2020; 4:250-256. [PMID: 33376952 PMCID: PMC7768295 DOI: 10.1002/ped4.12237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 06/02/2020] [Indexed: 11/09/2022] Open
Abstract
IMPORTANCE The process of brain development in children with developmental delay is not well known. Amide proton transfer-weighted (APTw) imaging is a novel molecular magnetic resonance imaging (MRI) technique that can noninvasively detect cytosolic endogenous mobile proteins and peptides involved in the myelination process, and may be useful for providing insights into brain development. OBJECTIVE To assess the contribution of amide proton transfer-weighted (APTw) imaging and magnetization transfer (MT) imaging to the evaluation of children with developmental delay (DD). METHODS Fifty-one patients with DD were recruited to this study. The patients were divided into two groups according to the state of myelination assessed on conventional magnetic resonance imaging (MRI). Thirty patients (10 girls, 20 boys; age range: 1-8 months; median age: 4 months) in group A showed delayed myelination on MRI, while 21 patients (3 girls, 18 boys; age range: 12-36months; median age: 25months) in group B showed normal myelination on MRI. Fifty-one age- and sex-matched children with normal developmental quotient (DQ) and normal MRI appearance were recruited as normal controls. Three-slice APTw/MT axial imaging was performed at the level of the centrum semiovale, the basal ganglia and the pons. Quantitative data of the MT ratio (MTR) and APTw were analyzed for multiple brain regions. Independent-sample t-tests were used to compare differences in APTw and MTR signals between the two DD groups and normal controls. Analysis of Covariance was conducted to correct the statistical results. The level of statistical significance was set to P < 0.05. RESULTS For group A, the MTR values were lower in all regions (P = 0.004-0.033) compared with the normal controls, while the APTw values were higher in the pons, middle cerebellar peduncle, corpus callosum, frontal white matter, occipital white matter and centrum semiovale (P = 0.004-0.040 ). For Group B, the MTR values were slightly reduced, and the APTw values were slightly increased compared with the normal controls, but the differences were not statistically significant (P > 0.05). INTERPRETATION For DD patients showing signs of delayed myelination on MRI, MTR and APTw imaging can help to diagnose myelination delay by quantifying semi-solid macromolecules and cytosolic endogenous mobile proteins and peptides at a molecular level, providing a new method for comprehensive evaluation of DD. For DD patients with normal myelination on MRI, the clinical values of MTR and APTw imaging remain to be explored.
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Affiliation(s)
- Xiaolu Tang
- Imaging CenterBeijing Children's HospitalCapital Medical UniversityNational Center for Children's HealthBeijingChina
| | - Hong Zhang
- Imaging CenterBeijing Children's HospitalCapital Medical UniversityNational Center for Children's HealthBeijingChina
| | - Jinyuan Zhou
- Division of MR ResearchDepartment of RadiologyJohns Hopkins UniversityBaltimoreMDUSA
| | - Huiying Kang
- Imaging CenterBeijing Children's HospitalCapital Medical UniversityNational Center for Children's HealthBeijingChina
| | - Shuangfeng Yang
- Imaging CenterBeijing Children's HospitalCapital Medical UniversityNational Center for Children's HealthBeijingChina
| | - Haijing Cui
- Rehabilitation DepartmentBeijing Children's HospitalCapital Medical UniversityNational Center for Children's HealthBeijingChina
| | - Yun Peng
- Imaging CenterBeijing Children's HospitalCapital Medical UniversityNational Center for Children's HealthBeijingChina
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12
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The diagnosis of inborn errors of metabolism in previously undiagnosed adults referred for medical genetics evaluation. Mol Genet Metab Rep 2020; 25:100653. [PMID: 33072517 PMCID: PMC7549142 DOI: 10.1016/j.ymgmr.2020.100653] [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: 08/13/2020] [Revised: 09/15/2020] [Accepted: 09/19/2020] [Indexed: 11/21/2022] Open
Abstract
Traditionally thought of as a pediatric diagnostic and therapeutic dilemma, the diagnostic rate and spectrum of inborn errors of metabolism (IEM) in the adult population is largely unknown. A retrospective chart review of patients seen by the Michigan Medicine Adult Medical Genetics Clinic for clinical evaluation from 2014 to 2018 was conducted. Patients referred for a primary indication possibly consistent with an IEM were considered. Variables included age at genetic evaluation, symptom onset age, sex, clinical course, organ systems involved, developmental history, family history and prior genetic testing. Of patients evaluated during the study period, 112 were referred for an indication possibly consistent with an IEM and underwent a complete biochemical workup with an IEM diagnostic rate of 9.8% achieved. An additional 9.8% were diagnosed with a non-IEM genetic diagnosis. Management changes were implemented in all IEM diagnoses. Metabolic disorders in the adult population are under-recognized and under-diagnosed. This report demonstrates the need for clinicians to consider these diagnoses in adults and either refer to a genetics clinic or initiate a biochemical workup. As advances in diagnosis, treatment, and life expectancy of patients with IEMs increases, recognizing and diagnosing these conditions can significantly impact care.
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13
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Milone R, Cesario C, Goldoni M, Pasquariello R, Fusilli C, Giovannetti A, Giglio S, Novelli A, Caputo V, Cioni G, Mazza T, Battaglia A, Bernardini L, Battini R. Correlating Neuroimaging and CNVs Data: 7 Years of Cytogenomic Microarray Analysis on Patients Affected by Neurodevelopmental Disorders. J Pediatr Genet 2020; 10:292-299. [PMID: 34849274 DOI: 10.1055/s-0040-1716398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/27/2020] [Indexed: 11/08/2022]
Abstract
The aim of this study was to evaluate the relationship between neurodevelopmental disorders, brain anomalies, and copy number variations (CNVs) and to estimate the diagnostic potential of cytogenomical microarray analysis (CMA) in individuals neuroradiologically characterized with intellectual developmental disorders (IDDs) isolated or associated with autism spectrum disorders (ASDs) and epilepsy (EPI), all of which were identified as a "synaptopathies." We selected patients who received CMA and brain magnetic resonance imaging (MRI) over a 7-year period. We divided them into four subgroups: IDD, IDD + ASD, IDD + EPI, and IDD + ASD + EPI. The diagnostic threshold of CMA was 16%. The lowest detection rate for both CMA and brain anomalies was found in IDD + ASD, while MRI was significantly higher in IDD and IDD + EPI subgroups. CMA detection rate was significantly higher in patients with brain anomalies, so CMA may be even more appropriate in patients with pathological MRI, increasing the diagnostic value of the test. Conversely, positive CMA in IDD patients should require an MRI assessment, which is more often associated with brain anomalies. Posterior fossa anomalies, both isolated and associated with other brain anomalies, showed a significantly higher rate of CMA positive results and of pathogenic CNVs. In the next-generation sequencing era, our study confirms once again the relevant diagnostic output of CMA in patients with IDD, either isolated or associated with other comorbidities. Since more than half of the patients presented brain anomalies in this study, we propose that neuroimaging should be performed in such cases, particularly in the presence of genomic imbalances.
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Affiliation(s)
- Roberta Milone
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Claudia Cesario
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Marina Goldoni
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, Italy
| | - Rosa Pasquariello
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Caterina Fusilli
- Bioinformatics Unit, IRCCS Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, Italy
| | - Agnese Giovannetti
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, Italy
| | - Sabrina Giglio
- Medical Genetics Unit, Meyer Children's University Hospital, Florence, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Viviana Caputo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Giovanni Cioni
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Pisa, Italy.,Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Tommaso Mazza
- Bioinformatics Unit, IRCCS Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, Italy
| | - Agatino Battaglia
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Laura Bernardini
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, Italy
| | - Roberta Battini
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Pisa, Italy.,Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
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Biallelic ZNF407 mutations in a neurodevelopmental disorder with ID, short stature and variable microcephaly, hypotonia, ocular anomalies and facial dysmorphism. J Hum Genet 2020; 65:1115-1123. [PMID: 32737394 DOI: 10.1038/s10038-020-0812-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/25/2020] [Accepted: 07/19/2020] [Indexed: 12/28/2022]
Abstract
We describe five members of a consanguineous Pakistani family (Family I) plus two affected children from families of different ethnic origins presenting with neurodevelopmental disorders with overlapping features. All affected individuals from families have intellectual disability (ID), ranging from mild to profound, and reduced motor and cognitive skills plus variable features including short stature, microcephaly, developmental delay, hypotonia, dysarthria, deafness, visual problems, enuresis, encopresis, behavioural anomalies, delayed pubertal onset and facial dysmorphism. We first mapped the disease locus in the large family (Family I), and by exome sequencing identified homozygous ZNF407 c.2814_2816dup (p.Val939dup) in four affected members where DNA samples were available. By exome sequencing we detected homozygous c.2405G>T (p.Gly802Val) in the affected member of Family II and compound heterozygous variants c.2884C>G (p.Arg962Gly) and c.3642G>C (p.Lys1214Asn) in the affected member of Family III. Homozygous c.5054C>G (p.Ser1685Trp) has been reported in two brothers with an ID syndrome. Affected individuals we present did not exhibit synophrys, midface hypoplasia, kyphosis, 5th finger camptodactyly, short 4th metatarsals or limited knee mobility observed in the reported family.
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15
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Abstract
Developmental diagnosis is based on an understanding of basic concepts of typical and atypical developmental progression. Child development is influenced by multiple factors, including the development of the nervous system and other organ systems, and the child's physical and social environment. Different factors interplay with each other in influencing the overall development of the child. Development and behavior of the child are intricately associated. Typical child development follows certain basic principles. Some of the more commonly reported developmental concerns include global developmental delay, intellectual disability, cerebral palsy, delayed speech and language, attention deficits, autism, and specific learning disabilities. The clinical presentation of atypical development varies, depending up on the age of the child; with motor delay in early infancy, and learning difficulties in school age child. Regular surveillance and periodic screening help identify specific areas of developmental and behavioral concerns and suggest a need for further appropriate psychological, medical and laboratory evaluation. The principles of management of a child with developmental concerns include early intervention and response to treatment approach, remediation, accommodation, and specific behavioral and pharmacological interventions when indicated.
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Affiliation(s)
- Kelly A Brown
- Department of Pediatric and Adolescent Medicine, Western Michigan University Homer Stryker MD School of Medicine, Kalamazoo, Michigan, USA
| | - Sonia Parikh
- Department of Pediatric and Adolescent Medicine, Western Michigan University Homer Stryker MD School of Medicine, Kalamazoo, Michigan, USA
| | - Dilip R Patel
- Department of Pediatric and Adolescent Medicine, Western Michigan University Homer Stryker MD School of Medicine, Kalamazoo, Michigan, USA
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16
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Abstract
Between 1% and 3% of persons in general population are estimated to have some degree of intellectual disability. A diagnosis of intellectual disability is based on clinical history, level of intellectual ability and level of adaptive function. Both, the intellectual and adaptive functioning are measured using individually administered standardized tests. More than 75% of persons who have intellectual disability have mild intellectual disability and an underlying specific etiology is less likely to be identified; whereas, in a small percentage of persons with severe intellectual disability, an underlying specific biologic cause is highly likely to be identified. Genetic abnormalities, inborn errors of metabolism and brain malformations are major categories of causes identified in severe to profound intellectual disability. The initial clinical presentation and recognition depends on the severity and underlying cause of intellectual disability. The etiology, severity, cognitive abilities, and adaptive function, vary among persons with intellectual disability and need consideration in developing a treatment plan. The physician plays an essential role in the evaluation, treatment of associated medical conditions and preventive care, and in facilitating and coordinating consultative services and community based care.
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Affiliation(s)
- Dilip R Patel
- Western Michigan University Homer Stryker MD School of Medicine, Kalamazoo, Michigan, USA
| | - Maria Demma Cabral
- Western Michigan University Homer Stryker MD School of Medicine, Kalamazoo, Michigan, USA
| | - Arlene Ho
- Western Michigan University Homer Stryker MD School of Medicine, Kalamazoo, Michigan, USA
| | - Joav Merrick
- Hadassah Hebrew University Medical Center, Jarusalem, Israel.,University of Kentucky, Lexington, USA.,School of Public Health, Georgia State University, Atlanta, USA
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17
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Diagnosis of intellectual disability/global developmental delay via genetic analysis in a central region of China. Chin Med J (Engl) 2020; 132:1533-1540. [PMID: 31205075 PMCID: PMC6616229 DOI: 10.1097/cm9.0000000000000295] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Supplemental Digital Content is available in the text Background: Advanced technology has become a valuable tool in etiological studies of intellectual disability/global developmental delay (ID/GDD). The present study investigated the role of genetic analysis to confirm the etiology in ID/GDD patients where the cause of the disease was uncertain in central China. Methods: We evaluated 1051 ID/GDD children aged 6 months to 18 years from March 2009 to April 2017. Data concerning basic clinical manifestations were collected, and the method of etiology confirmation was recorded. Genome-wide copy number variations (CNVs) detection and high-throughput sequencing of exons in the targeted regions was performed to identify genetically-based etiologies. We compared the incidence of different methods used to confirm ID/GDD etiology among groups with differing degrees of ID/GDD using the Chi-square or Fisher exact probability test. Results: We recruited 1051 children with mild (367, 34.9%), moderate (301, 28.6%), severe (310, 29.5%), and profoundly severe (73, 6.9%) ID/GDD. The main causes of ID/GDD in the children assessed were perinatal factors, such as acquired brain injury, as well as single gene imbalance and chromosomal gene mutation. We identified karyotype and/or CNVs variation in 46/96 (47.9%) of cases in severe ID/GDD patients, which was significantly higher than those with mild and moderate ID/GDD of 34/96 (35.4%) and 15/96 (15.6%), respectively. A total of 331/536 (61.8%) patients with clear etiology have undergone genetic analysis while 262/515 (50.9%) patients with unclear etiology have undergone genetic analysis (χ2 = 12.645, P < 0.001). Gene structure variation via karyotype analysis and CNV detection increased the proportion of children with confirmed etiology from 51.0% to 56.3%, and second-generation high-throughput sequencing dramatically increased this to 78.9%. Ten novel mutations were detected, recessive mutations in X-linked genes (ATPase copper transporting alpha and bromodomain and WD repeat domain containing 3) and dominant de novo heterozygous mutations in X-linked genes (cyclin-dependent kinase like 5, protocadherin 19, IQ motif and Sec7 domain 2, and methyl-CpG binding protein 2) were reported in the study. Conclusions: The present study indicates that genetic analysis is an effective method to increase the proportion of confirmed etiology in ID/GDD children and is highly recommended, especially in ID/GDD children with uncertain etiology.
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Proband-Only Clinical Exome Sequencing for Neurodevelopmental Disabilities. Pediatr Neurol 2019; 99:47-54. [PMID: 30952489 DOI: 10.1016/j.pediatrneurol.2019.02.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/16/2019] [Accepted: 02/20/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Whole exome sequencing on family trios gives the highest diagnostic yield, but high cost limits its application. Here, we performed proband-only clinical exome sequencing in a population of patients with neurodevelopmental disabilities and tested the diagnostic yield. METHODS This observational, retrospective study included 108 unrelated patients with neurodevelopmental disabilities who underwent clinical exome sequencing at the outpatient clinics of the Severance Children's Hospital, Seoul, South Korea, between March 2017 and May 2018. Clinical exome sequencing targeted 4503 disease-causing genes. RESULTS The overall diagnostic rate was 38.0% (41 of 108) when proband-only clinical exome sequencing was performed without additional parental testing. Four sequence variants were reclassified as likely pathogenic after parental testing, representing an additional 3.7% of the diagnostic yield. The final diagnostic rate was 41.7% (45 of 108). Of 45 patients with genetic abnormalities, a total of 38 sequence variations were detected in 33 (30.6%) patients with five homozygous cases, and 13 chromosomal copy number variants were detected in 12 (11.1%) patients. Novel variants of known causal genes for neurodevelopmental disabilities were detected in 18 (16.7%) patients. These were variants that could be reclassified as likely pathogenic if the de novo nature of the mutation was confirmed after testing of parental samples. CONCLUSIONS Proband-only clinical exome sequencing is a practical diagnostic tool that may be implemented in the clinical setting for patients with neurodevelopmental disabilities. A cost-effective approach to neurodevelopmental disabilities would be a proband-only clinical exome sequencing followed by parental testing of selective candidate variants.
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Çaksen H, Aktar F, Yıldırım G, Ceylaner S. Importance of pedigree in patients with familial epilepsy and intellectual disability. Sudan J Paediatr 2019; 19:52-56. [PMID: 31384089 DOI: 10.24911/sjp.106-1536222362] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In this study, we prospectively evaluated demographic characteristics, clinical findings and pedigree patterns in 70 patients with familial epilepsy and/or intellectual disability (ID)/global developmental delay (GDD) and/or motor retardation but without specific etiologic diagnosis to determine genetic inheritance patterns by using at least a three-generation pedigree analysis. Mean age of the patients was 6.85 ± 3.93 years and male/female ratio was 1.50. There was consanguinity between the parents of 47 (67.1%) patients. Only epilepsy was diagnosed in 14 patients; only ID/GDD in 22; epilepsy and ID/GDD in 9 and epilepsy and ID/GDD and motor retardation in 25 patients. Genetic inheritance pattern was definitely determined in 60 (85.7%) patients, and most of the patients (61.4%) displayed autosomal recessive inheritance. Based on our findings, we suggest that a three-generation pedigree analysis should be obtained in all patients with familial neurological disorders, including epilepsy, ID/GDD and motor retardation, to optimise counselling, screening and diagnostic testing.
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Affiliation(s)
- Hüseyin Çaksen
- Department of Pediatric Neurology, Necmettin Erbakan University Meram Medical Faculty, Konya, Turkey
| | - Fesih Aktar
- Department of Pediatrics, Dicle University Faculty of Medicine, Diyarbakır, Turkey
| | - Gökçen Yıldırım
- Department of Pediatric Neurology, Necmettin Erbakan University Meram Medical Faculty, Konya, Turkey
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Wang W, Corominas R, Lin GN. De novo Mutations From Whole Exome Sequencing in Neurodevelopmental and Psychiatric Disorders: From Discovery to Application. Front Genet 2019; 10:258. [PMID: 31001316 PMCID: PMC6456656 DOI: 10.3389/fgene.2019.00258] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 03/08/2019] [Indexed: 12/13/2022] Open
Abstract
Neurodevelopmental and psychiatric disorders are a highly disabling and heterogeneous group of developmental and mental disorders, resulting from complex interactions of genetic and environmental risk factors. The nature of multifactorial traits and the presence of comorbidity and polygenicity in these disorders present challenges in both disease risk identification and clinical diagnoses. The genetic component has been firmly established, but the identification of all the causative variants remains elusive. The development of next-generation sequencing, especially whole exome sequencing (WES), has greatly enriched our knowledge of the precise genetic alterations of human diseases, including brain-related disorders. In particular, the extensive usage of WES in research studies has uncovered the important contribution of de novo mutations (DNMs) to these disorders. Trio and quad familial WES are a particularly useful approach to discover DNMs. Here, we review the major WES studies in neurodevelopmental and psychiatric disorders and summarize how genes hit by discovered DNMs are shared among different disorders. Next, we discuss different integrative approaches utilized to interrogate DNMs and to identify biological pathways that may disrupt brain development and shed light on our understanding of the genetic architecture underlying these disorders. Lastly, we discuss the current state of the transition from WES research to its routine clinical application. This review will assist researchers and clinicians in the interpretation of variants obtained from WES studies, and highlights the need to develop consensus analytical protocols and validated lists of genes appropriate for clinical laboratory analysis, in order to reach the growing demands.
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Affiliation(s)
- Weidi Wang
- Shanghai Mental Health Center, School of Biomedical Engineering, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai, China
- Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Roser Corominas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain
- Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Guan Ning Lin
- Shanghai Mental Health Center, School of Biomedical Engineering, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai, China
- Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
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21
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Mir YR, Kuchay RAH. Advances in identification of genes involved in autosomal recessive intellectual disability: a brief review. J Med Genet 2019; 56:567-573. [PMID: 30842223 DOI: 10.1136/jmedgenet-2018-105821] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 02/01/2019] [Accepted: 02/11/2019] [Indexed: 12/28/2022]
Abstract
Intellectual disability (ID) is a clinically and genetically heterogeneous disorder, affecting 1%-3% of the general population. The number of ID-causing genes is high. Many X-linked genes have been implicated in ID. Autosomal dominant genes have recently been the focus of several large-scale studies. The total number of autosomal recessive ID (ARID) genes is estimated to be very high, and most are still unknown. Although research into the genetic causes of ID has recently gained momentum, identification of pathogenic mutations that cause ARID has lagged behind, predominantly due to non-availability of sizeable families. A commonly used approach to identify genetic loci for recessive disorders in consanguineous families is autozygosity mapping and whole-exome sequencing. Combination of these two approaches has recently led to identification of many genes involved in ID. These genes have diverse function and control various biological processes. In this review, we will present an update regarding genes that have been recently implicated in ID with focus on ARID.
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Affiliation(s)
- Yaser Rafiq Mir
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, India
| | - Raja Amir Hassan Kuchay
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, India
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22
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Chen X, Li H, Chen C, Zhou L, Xu X, Xiang Y, Tang S. Genome-Wide Array Analysis Reveals Novel Genomic Regions and Candidate Gene for Intellectual Disability. Mol Diagn Ther 2019; 22:749-757. [PMID: 30259421 DOI: 10.1007/s40291-018-0358-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Intellectual disability (ID) is often sporadic, and its complex etiology makes clinical diagnosis extremely difficult. OBJECTIVE The aims of this study were to detect copy number variations (CNVs) in patients with ID and to analyze the correlation between pathogenic CNVs and clinical phenotype. METHODS After cases of ID caused by metabolic dysfunction or environmental factors were excluded, 64 patients with moderate to severe ID were enrolled. Karyotype and single nucleotide polymorphism (SNP) array analyses were performed for all patients. The relationship between CNVs and phenotype was identified with genotype-phenotype comparisons and by searching CNV databases. RESULTS Karyotype analysis showed four patients with chromosomal aneuploidy and seven with chromosomal structural abnormality. After excluding the four cases with chromosomal aneuploidy, the remaining 60 cases were analyzed using SNP array. The results revealed 87 CNVs in 45 cases, including 16 pathogenic CNVs in 12 individuals, with a diagnostic yield of 20.0% (12/60). We found large deletions at 16q22.2q23.1 and 3q24q25.32 in two patients, respectively, in whom specific syndromes had not been defined. Our array analysis showed one case carried a 210 kb deletion at 1p21.2p21.3, which included only one coding gene LPPR4, which might be a candidate gene for ID phenotype. CONCLUSIONS Use of the genome-wide array method can improve the detection rate of CNVs, reveal chromosomal abnormalities that have not been well-characterized by cytology, and provide a new way to locate genes for patients with the ID phenotype. Interpretation of CNVs remains a major challenge. Sharing of CNVs and phenotype information from different laboratories in public databases is important.
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Affiliation(s)
- Xiangnan Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Huanzheng Li
- The Center of Wenzhou Prenatal Diagnostics, Key Laboratory of Birth Defects, Wenzhou Central Hospital, Wenzhou, Zhejiang, China
| | - Chong Chen
- The Center of Wenzhou Prenatal Diagnostics, Key Laboratory of Birth Defects, Wenzhou Central Hospital, Wenzhou, Zhejiang, China
| | - Lili Zhou
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- The Center of Wenzhou Prenatal Diagnostics, Key Laboratory of Birth Defects, Wenzhou Central Hospital, Wenzhou, Zhejiang, China
| | - Xueqin Xu
- The Center of Wenzhou Prenatal Diagnostics, Key Laboratory of Birth Defects, Wenzhou Central Hospital, Wenzhou, Zhejiang, China
| | - Yanbao Xiang
- The Center of Wenzhou Prenatal Diagnostics, Key Laboratory of Birth Defects, Wenzhou Central Hospital, Wenzhou, Zhejiang, China
| | - Shaohua Tang
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
- The Center of Wenzhou Prenatal Diagnostics, Key Laboratory of Birth Defects, Wenzhou Central Hospital, Wenzhou, Zhejiang, China.
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Kishore MT, Udipi GA, Seshadri SP. Clinical Practice Guidelines for Assessment and Management of intellectual disability. Indian J Psychiatry 2019; 61:194-210. [PMID: 30745696 PMCID: PMC6345136 DOI: 10.4103/psychiatry.indianjpsychiatry_507_18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- M Thomas Kishore
- Clinical Psychology, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Gautham Arunachal Udipi
- Human Genetics, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Shekhar P Seshadri
- Child and Adolescent Psychiatry, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
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Abstract
In the last few years, next-generation sequencing has led to enormous progress in deciphering monogenic forms of intellectual disability. Autosomal dominant intellectual disability (ADID) and X chromosomal intellectual disability (XLID) have been the focus of research. Apart from metabolic disorders, autosomal recessive intellectual disability (ARID) is still behind, probably because it is more heterogeneous and less prevalent in industrial populations. The prevalence of ARID in a cohort of affected children of an outbred population is estimated to be about 10%, with an upward tendency in still unclarified cases. The risk for ARID in children of first cousins or closer is a magnitude higher than for children of unrelated parents. Taken together, it seems that children of related parents are at a 2 to 3 times higher risk for ID. There are no prevalent ARID genes, pathways, or protein complexes and the functions of the affected proteins are very diverse and limited not only to neurological aspects. Thus, in a regular case, there is no reasoning for picking a few genes for a first diagnostic step, and a genetic diagnosis of ID in general, and ARID specifically, is better made using large panels or exome sequencing. In addition, in the last few months, evidence has been growing that many ARID genes are pleiotropic and that the resulting phenotypes may have a broad spectrum. For an exhaustive deciphering of the genetics of ARID, we suggest research at the level of single genes rather than large meta-analyses.
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Affiliation(s)
- Rami Jamra
- Institute of Human Genetics, University Medical Center, Philipp-Rosenthal-Str. 55, Leipzig, Germany
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25
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Al-Nabhani M, Al-Rashdi S, Al-Murshedi F, Al-Kindi A, Al-Thihli K, Al-Saegh A, Al-Futaisi A, Al-Mamari W, Zadjali F, Al-Maawali A. Reanalysis of exome sequencing data of intellectual disability samples: Yields and benefits. Clin Genet 2018; 94:495-501. [PMID: 30125339 DOI: 10.1111/cge.13438] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/08/2018] [Accepted: 08/15/2018] [Indexed: 01/07/2023]
Abstract
Recently, with the advancement in next generation sequencing (NGS) along with the improvement of bioinformatics tools, whole exome sequencing (WES) has become the most efficient diagnostic test for patients with intellectual disability (ID). This study aims to estimate the yield of a reanalysis of ID negative exome cases after data reannotation. Total of 50 data files of exome sequencing, representing 50 samples were collected. The inclusion criteria include ID phenotype, and previous analysis indicated a negative result (no abnormality detected). These files were pre-processed and reannotated using ANNOVAR tool. Prioritized variants in the 50 cases studied were classified into three groups, (1) disease-causative variants (2) possible disease-causing variants and (3) variants in novel genes. Reanalysis resulted in the identification of pathogenic/likely pathogenic variants in six cases (12%). Thirteen cases (26%) were classified as having possible disease-causing variants. Candidate genes requiring future functional studies were detected in seven cases (14%). Improvement in bioinformatics tools, update in the genetic databases and literature, and patients' clinical phenotype update were the main reasons for identification of these variants in this study.
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Affiliation(s)
- Maryam Al-Nabhani
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Samiya Al-Rashdi
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Fathiya Al-Murshedi
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.,Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Adila Al-Kindi
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.,Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Khalid Al-Thihli
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.,Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Abeer Al-Saegh
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.,Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Amna Al-Futaisi
- Department of Child Health, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Watfa Al-Mamari
- Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman.,Department of Child Health, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Fahad Zadjali
- Department of Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Almundher Al-Maawali
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman.,Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
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26
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Ceroni JRM, Dutra RL, Honjo RS, Llerena JC, Acosta AX, Medeiros PFV, Galera MF, Zanardo ÉA, Piazzon FB, Dias AT, Novo-Filho GM, Montenegro MM, Madia FAR, Bertola DR, de Melo JB, Kulikowski LD, Kim CA. A Multicentric Brazilian Investigative Study of Copy Number Variations in Patients with Congenital Anomalies and Intellectual Disability. Sci Rep 2018; 8:13382. [PMID: 30190605 PMCID: PMC6127201 DOI: 10.1038/s41598-018-31754-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/21/2018] [Indexed: 12/13/2022] Open
Abstract
Genomic imbalances are the most common cause of congenital anomalies (CA) and intellectual disability (ID). The aims of this study were to identify copy number variations (CNVs) in 416 patients with CA and ID from 5 different genetics centers within 4 different states by using the Multiplex Ligation-dependent Probe Amplification (MLPA) technique and to apply the chromosomal microarray (CMA) methodology in selected cases. The samples were analyzed by MLPA kits P064, P036, P070 and P250. Positive results were found in 97/416 (23.3%) patients. CMA was applied in 14 selected cases. In 6/14 (42.85%) patients, CMA detected other copy number variations not detected by the MLPA studies. Although CMA is indispensable for genotype refinement, the technique is still unfeasible in some countries as a routine analysis due to economic and technical limitations. In these cases, clinical evaluation followed by karyotyping and MLPA analysis is a helpful and affordable solution for diagnostic purposes.
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Affiliation(s)
- J R M Ceroni
- Unidade de Genética, Departamento de Pediatria, Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da USP, HCFMUSP, São Paulo, SP, Brazil.
| | - R L Dutra
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - R S Honjo
- Unidade de Genética, Departamento de Pediatria, Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da USP, HCFMUSP, São Paulo, SP, Brazil
| | - J C Llerena
- Instituto Nacional de Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira - Fiocruz, Rio de Janeiro, RJ, Brazil
| | - A X Acosta
- Universidade Federal da Bahia, Salvador, BA, Brazil
| | - P F V Medeiros
- Universidade Federal de Campina Grande, Campina Grande, PB, Brazil
| | - M F Galera
- Universidade Federal do Mato Grosso, Cuiabá, MT, Brazil
| | - É A Zanardo
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - F B Piazzon
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - A T Dias
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - G M Novo-Filho
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - M M Montenegro
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - F A R Madia
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - D R Bertola
- Unidade de Genética, Departamento de Pediatria, Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da USP, HCFMUSP, São Paulo, SP, Brazil.,Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil., São Paulo, SP, Brazil
| | - J B de Melo
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, CIMAGO - Centro de Investigação em Meio Ambiente, Genética e Oncobiologia, Faculdade de Medicina, Universidade de Coimbra, Faculdade de Medicina, Universidade de Coimbra, CNC, IBILI - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - L D Kulikowski
- Laboratorio de Citogenômica, Departamento de Patologia, Faculdade de Medicina da USP, FMUSP, São Paulo, SP, Brazil
| | - C A Kim
- Unidade de Genética, Departamento de Pediatria, Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da USP, HCFMUSP, São Paulo, SP, Brazil
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Abstract
PURPOSE OF REVIEW This article discusses the diagnostic evaluation of intellectual developmental disorder, comprising global developmental delay and intellectual disability in children. RECENT FINDINGS With a prevalence of 1% to 3% and substantial comorbidity, high lifetime costs, and emotional burden, intellectual developmental disorder is characterized by limitations in both intellectual functioning (IQ less than 70) and adaptive behavior starting before 18 years of age. Pinpointing the precise genetic cause is important, as it allows for accurate genetic counseling, avoidance of unnecessary testing, prognostication, and tailored management, which, for an increasing number of genetic conditions, targets the pathophysiology and improves outcomes. SUMMARY The etiology of intellectual developmental disorder is heterogeneous, which mandates a structured approach that considers family situation, test costs, yield, and potential therapeutic tractability of the identified condition. Diagnosis of an underlying genetic cause is increasingly important with the advent of new treatments. Still, in many cases, the cause remains unknown, and research is needed to elucidate its complex molecular basis.
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28
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Tremblay I, Janvier A, Laberge AM. Paediatricians underuse recommended genetic tests in children with global developmental delay. Paediatr Child Health 2018; 23:e156-e162. [PMID: 30842697 DOI: 10.1093/pch/pxy033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Objectives To assess paediatricians' use of genetic testing for children with global developmental delay (GDD). Study Design We developed and piloted a questionnaire assessing the use of genetic tests in children with GDD and awareness of relevant guidelines. All practicing Quebec paediatricians were contacted. Paediatricians who did not evaluate children with GDD in their practice were excluded. Descriptive and statistical analyses were performed with SPSS. Results Of the 651 paediatricians, 225 answered (34.5%) and 141 were eligible. Only 31.9% were familiar with at least one guideline about genetic tests for the investigation of children with GDD, but 93.6% had ordered genetic testing for children with GDD (Fragile X testing [92.9%], karyotype [87.2%] and chromosomal microarray [63.8%]). Based on vignettes, 20.6% of participants would order genetic tests for isolated GDD and 95.0% for GDD with dysmorphic features and microcephaly. Only 56.7% ordered Fragile X testing for a girl with GDD and a known family history of Fragile X syndrome. Use of tests for isolated GDD was increased in presence of maternal pregnancy, compared with absence of pregnancy (44.7% and 27.7%, respectively). More participants would order genetic tests for a child with GDD and fetal exposure to alcohol (69.5%) than isolated GDD (20.6%). Conclusions Even though paediatricians often order genetic testing for children with GDD, practices and knowledge regarding testing are not optimal. As new and more complex genetic tests are developed, up-to-date training about the use of genetic tests for children with GDD needs to be integrated into paediatrics residency programs and continuous medical education.
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Affiliation(s)
- Isabelle Tremblay
- Research Center, CHU Sainte-Justine, Montréal, Quebec.,Division of Psychology, CHU Sainte-Justine, Montreal, Quebec.,Unité d'éthique Clinique, CHU Sainte-Justine, Montreal, Quebec
| | - Annie Janvier
- Research Center, CHU Sainte-Justine, Montréal, Quebec.,Unité d'éthique Clinique, CHU Sainte-Justine, Montreal, Quebec.,Division of Neonatology, Unité de soins palliatifs, Unité de recherche en éthique clinique et partenariat famille, CHU Sainte-Justine, Montréal, Quebec.,Bureau de l'Éthique Clinique, Université de Montreal, Montreal, Quebec.,Department of Pediatrics, Université de Montréal, Montreal, Quebec
| | - Anne-Marie Laberge
- Research Center, CHU Sainte-Justine, Montréal, Quebec.,Department of Pediatrics, Université de Montréal, Montreal, Quebec.,Division of Medical Genetics, CHU Sainte-Justine, Montreal, Quebec
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Craig F, Lorenzo A, Lucarelli E, Russo L, Fanizza I, Trabacca A. Motor competency and social communication skills in preschool children with autism spectrum disorder. Autism Res 2018; 11:893-902. [PMID: 29493892 DOI: 10.1002/aur.1939] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 01/12/2018] [Accepted: 02/12/2018] [Indexed: 12/25/2022]
Abstract
This study aimed to investigate the association between motor competency and social communication in children with Autism Spectrum Disorder (ASD) compared with children with Intellectual Disabilities (ID) and typically developing (TD) children. Motor competency, ASD symptoms, and nonverbal Intelligent Quotient (IQ) were investigated through the following tests: Movement Assessment Battery for Children, second edition (MABC-2), Social Communication Questionnaire (SCQ), Autism Classification System of Functioning: Social Communication (ACSF:SC) and Leiter International Performances Scale Revised (Leiter-R). The ASD + ID and ID groups had lower MABC-2-manual dexterity mean scores, MABC-2-aiming and catching mean scores, MABC-2-static and dynamic balance mean scores and MABC-2-TTS compared with the TD group (P < 0.05). In addition, the ASD + ID group had lower MABC-2-aiming and catching mean scores compared with the ID group. In the ASD + ID group, we found a significant negative correlation (P < 0.001) between MABC-2-aiming and catching scores with SCQ scores, nonverbal IQ and ACSF:SC levels. Our findings provide new insight into the common neuropsychological mechanisms underlying social communication and motor deficits in ASD. Multiple deficits in motor functioning may be present in ASD and ID, however deficits involving the ability to integrate motor and social cues are somewhat specific to ASD. Autism Res 2018, 11: 893-902. © 2018 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY This study highlighted the specificity of motor impairment in ASD comparing performances on a frequently used measure of motor impairment between clinical groups (ASD + ID and ID) and a non-clinical group. While previous research has suggested that multiple deficits in motor functioning may be present in ASD, our findings suggest that deficits in tasks involving the ability to integrate visual and motor cues (aiming and catching task) are somewhat specific to ASD.
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Affiliation(s)
- Francesco Craig
- Scientific Institute I.R.C.C.S. "Eugenio Medea"- "La Nostra Famiglia", Unit for Severe disabilities in developmental age and young adults, Developmental Neurology and Neurorehabilitation, Brindisi Research Centre, Brindisi, Italy
| | - Alessandro Lorenzo
- Scientific Institute I.R.C.C.S. "Eugenio Medea"- "La Nostra Famiglia", Unit for Severe disabilities in developmental age and young adults, Developmental Neurology and Neurorehabilitation, Brindisi Research Centre, Brindisi, Italy
| | - Elisabetta Lucarelli
- Scientific Institute I.R.C.C.S. "Eugenio Medea"- "La Nostra Famiglia", Unit for Severe disabilities in developmental age and young adults, Developmental Neurology and Neurorehabilitation, Brindisi Research Centre, Brindisi, Italy
| | - Luigi Russo
- Scientific Institute I.R.C.C.S. "Eugenio Medea"- "La Nostra Famiglia", Unit for Severe disabilities in developmental age and young adults, Developmental Neurology and Neurorehabilitation, Brindisi Research Centre, Brindisi, Italy
| | - Isabella Fanizza
- Scientific Institute I.R.C.C.S. "Eugenio Medea"- "La Nostra Famiglia", Unit for Severe disabilities in developmental age and young adults, Developmental Neurology and Neurorehabilitation, Brindisi Research Centre, Brindisi, Italy
| | - Antonio Trabacca
- Scientific Institute I.R.C.C.S. "Eugenio Medea"- "La Nostra Famiglia", Unit for Severe disabilities in developmental age and young adults, Developmental Neurology and Neurorehabilitation, Brindisi Research Centre, Brindisi, Italy
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30
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Mohan S, Koshy T, Vekatachalam P, Nampoothiri S, Yesodharan D, Gowrishankar K, Kumar J, Ravichandran L, Joseph S, Chandrasekaran A, Paul SFD. Subtelomeric rearrangements in Indian children with idiopathic intellectual disability/developmental delay: Frequency estimation & clinical correlation using fluorescence in situ hybridization (FISH). Indian J Med Res 2017; 144:206-214. [PMID: 27934799 PMCID: PMC5206871 DOI: 10.4103/0971-5916.195031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022] Open
Abstract
Background & objectives: Subtelomeres are prone to deleterious rearrangements owing to their proximity to unique sequences on the one end and telomeric repetitive sequences, which increase their tendency to recombine, on the other end. These subtelomeric rearrangements resulting in segmental aneusomy are reported to contribute to the aetiology of idiopathic intellectual disability/developmental delay (ID/DD). We undertook this study to estimate the frequency of subtelomeric rearrangements in children with ID/DD. Methods: One hundred and twenty seven children with idiopathic ID/DD were tested for subtelomeric rearrangements using karyotyping and FISH. Blood samples were cultured, harvested, fixed and GTG-banded using the standard protocols. Results: Rearrangements involving the subtelomeres were observed in 7.8 per cent of the tested samples. Detection of rearrangements visible at the resolution of the karyotype constituted 2.3 per cent, while those rearrangements detected only with FISH constituted 5.5 per cent. Five deletions and five unbalanced translocations were detected. Analysis of parental samples wherever possible was informative regarding the inheritance of the rearrangement. Interpretation & conclusions: The frequency of subtelomeric rearrangements observed in this study was within the reported range of 0-35 per cent. All abnormal genotypes were clinically correlated. Further analysis with array technologies presents a future prospect. Our results suggest the need to test individuals with ID/DD for subtelomeric rearrangements using sensitive methods such as FISH.
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Affiliation(s)
- Shruthi Mohan
- Department of Human Genetics, Sri Ramachandra University, Porur, India
| | - Teena Koshy
- Department of Human Genetics, Sri Ramachandra University, Porur, India
| | | | - Sheela Nampoothiri
- Department of Paediatric Genetics, Amrita Institute of Medical Sciences, Kochi, India
| | - Dhanya Yesodharan
- Department of Paediatric Genetics, Amrita Institute of Medical Sciences, Kochi, India
| | - Kalpana Gowrishankar
- Department of Medical Genetics, CHILDS Trust Medical Research Foundation, Kanchi Kamakoti CHILDS Trust Hospital, Chennai, India
| | - Jeevan Kumar
- Department of Medical Genetics, CHILDS Trust Medical Research Foundation, Kanchi Kamakoti CHILDS Trust Hospital, Chennai, India
| | | | - Santhosh Joseph
- Department of Radiology, Sri Ramachandra University, Porur, India
| | | | - Solomon F D Paul
- Department of Human Genetics, Sri Ramachandra University, Porur, India
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Puri RD, Tuteja M, Verma IC. Genetic Approach to Diagnosis of Intellectual Disability. Indian J Pediatr 2016; 83:1141-9. [PMID: 27619815 DOI: 10.1007/s12098-016-2205-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 07/20/2016] [Indexed: 01/29/2023]
Abstract
Intellectual disability is a non-specific phenotype present in a genetically heterogeneous group of disorders. It is characterized by deficits in intellectual and adaptive functioning, presenting before 18 y of age. Identifying the cause of ID is important to provide treatment where available, genetic counseling, recurrence risks and reproductive options for subsequent pregnancies. Advances in technology, especially next generation sequencing and microarrays, have greatly increased the diagnostic yield of evaluation in cases of ID. This paper describes the points in history taking and examination in the evaluation of a proband, and discusses the proper use of newer diagnostic technologies.
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Affiliation(s)
- Ratna Dua Puri
- Ganga Ram Institute of Postgraduate Medical Research and Education, Institute of Medical Genetics & Genomics, Sir Ganga Ram Hospital, New Delhi, 110060, India.
| | - Moni Tuteja
- Ganga Ram Institute of Postgraduate Medical Research and Education, Institute of Medical Genetics & Genomics, Sir Ganga Ram Hospital, New Delhi, 110060, India
| | - I C Verma
- Ganga Ram Institute of Postgraduate Medical Research and Education, Institute of Medical Genetics & Genomics, Sir Ganga Ram Hospital, New Delhi, 110060, India
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Affiliation(s)
- Donatella Milani
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Luisa Ronzoni
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Susanna Esposito
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
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Ruiz-Botero F, Pachajoa H. Deletion 21q22.3 and duplication 7q35q36.3 in a Colombian girl: a case report. J Med Case Rep 2016; 10:204. [PMID: 27459995 PMCID: PMC4962380 DOI: 10.1186/s13256-016-0988-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 06/16/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic disorders are a major cause in the etiology of cases with intellectual disability; however, analysis by a conventional technique such as cytogenetic karyotyping only allows the detection of chromosomal alterations in approximately 9.5 % of cases. The inclusion of new technologies such as high resolution microarray analysis has allowed the study of alterations in chromosomal segments that are less than 5 Mb in length; this has led to an increase in the diagnosis of these patients of up to 25 %. CASE PRESENTATION We report the first case of an 8-year-old Colombian girl of mixed race ancestry (Mestizo), with clinical features that include: delayed psychomotor and language development, intellectual disability, upward slanting palpebral fissures, divergent strabismus, low-set and rotated ears, tall and broad nasal bridge, flat philtrum, bifid uvula, posterior cleft palate, increased anteroposterior diameter of her chest, congenital heart defect type interventricular communication, scoliosis, and umbilical hernia. Genetic analysis was performed using comparative genomic hybridization array, which evidenced the deletion of a region of approximately 3.608 Mb on chromosome 21q22.3, and a duplication of 12.326 Mb on chromosome 7q35q36.3, these alterations affect approximately 112 and 186 genes, respectively. CONCLUSIONS To date, this is the first report of an associated terminal deletion of 21q and 7q duplication in a patient with delayed psychomotor development and intellectual disability. We consider that future implementation of exome and RNA sequencing techniques, and analysis of their proteomic expression in a clinical context could lead to better analysis and interpretation of the genotype-phenotype correlation in cases similar to that described.
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Affiliation(s)
- Felipe Ruiz-Botero
- Faculty of Health, Universidad Icesi, Research Centre on Congenital Anomalies and Rare Diseases (CIACER), Calle 18 No. 122-135, bloque L, Oficina: 5025A Pance, Cali, Colombia
| | - Harry Pachajoa
- Faculty of Health, Universidad Icesi, Research Centre on Congenital Anomalies and Rare Diseases (CIACER), Calle 18 No. 122-135, bloque L, Oficina: 5025A Pance, Cali, Colombia.
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Houwen S, Visser L, van der Putten A, Vlaskamp C. The interrelationships between motor, cognitive, and language development in children with and without intellectual and developmental disabilities. RESEARCH IN DEVELOPMENTAL DISABILITIES 2016; 53-54:19-31. [PMID: 26851384 DOI: 10.1016/j.ridd.2016.01.012] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 10/30/2015] [Accepted: 01/18/2016] [Indexed: 06/05/2023]
Abstract
It is generally agreed that cognitive and language development are dependent on the emergence of motor skills. As the literature on this issue concerning children with developmental disabilities is scarce, we examined the interrelationships between motor, cognitive, and language development in children with intellectual and developmental disabilities (IDD) and compared them to those in children without IDD. In addition, we investigated whether these relationships differ between children with different levels of cognitive delay. Seventy-seven children with IDD (calendar age between 1;0 and 9;10 years; mean developmental age: 1;8 years) and 130 typically developing children (calendar age between 0;3 and 3;6 years; mean developmental age: 1;10 years) were tested with the Dutch Bayley Scales of Infant and Toddler Development, Third Edition, which assesses development across three domains using five subscales: fine motor development, gross motor development (motor), cognition (cognitive), receptive communication, and expressive communication (language). Results showed that correlations between the motor, cognitive, and language domains were strong, namely .61 to .94 in children with IDD and weak to strong, namely .24 to .56 in children without IDD. Furthermore, the correlations showed a tendency to increase with the severity of IDD. It can be concluded that both fine and gross motor development are more strongly associated with cognition, and consequently language, in children with IDD than in children without IDD. The findings of this study emphasize the importance of early interventions that boost both motor and cognitive development, and suggest that such interventions will also enhance language development.
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Affiliation(s)
- Suzanne Houwen
- University of Groningen, Department of Special Needs Education and Youth Care, Grote Rozenstraat 38, 9712 TJ Groningen, The Netherlands.
| | - Linda Visser
- University of Groningen, Department of Special Needs Education and Youth Care, Grote Rozenstraat 38, 9712 TJ Groningen, The Netherlands.
| | - Annette van der Putten
- University of Groningen, Department of Special Needs Education and Youth Care, Grote Rozenstraat 38, 9712 TJ Groningen, The Netherlands.
| | - Carla Vlaskamp
- University of Groningen, Department of Special Needs Education and Youth Care, Grote Rozenstraat 38, 9712 TJ Groningen, The Netherlands.
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Mansoori Derakhshan S, Shekari Khaniani M. Cytogenetic findings in patients with intellectual disability and/or multiple congenital anomalies. JOURNAL OF ANALYTICAL RESEARCH IN CLINICAL MEDICINE 2016. [DOI: 10.15171/jarcm.2016.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Abstract
Developmental delay occurs in 1-3% of the population, with unknown etiology in approximately 50% of cases. Initial genetic work up for developmental delay previously included chromosome analysis and subtelomeric FISH (fluorescent in situ hybridization). Array Comparative Genomic Hybridization (aCGH) has emerged as a tool to detect genetic copy number changes and uniparental disomy and is the most sensitive test in providing etiological diagnosis in developmental delay. aCGH allows for the provision of prognosis and recurrence risks, improves access to resources, helps limit further investigations and may alter medical management in many cases. aCGH has led to the delineation of novel genetic syndromes associated with developmental delay. An illustrative case of a 31-year-old man with long standing global developmental delay and recently diagnosed 4q21 deletion syndrome with a deletion of 20.8 Mb genomic interval is provided. aCGH is now recommended as a first line test in children and adults with undiagnosed developmental delay and congenital anomalies. Puce d'hybridation génomique comparative et retard de développement : un outil diagnostic pour les neurologues. Le retard de développement survient chez 1 à 3% de la population et son étiologie est inconnue chez à peu près 50% des cas. L'évaluation génétique initiale pour un retard de développement incluait antérieurement une analyse chromosomique et une analyse par FISH (hybridation in situ en fluorescence) de régions subtélomériques. La puce d'hybridation génomique comparative (CGHa) est devenue un outil de détection des changements du nombre de copies géniques ainsi que de la disomie uniparentale et elle est le test le plus sensible pour fournir un diagnostic étiologique dans le retard de développement. Le CGHa permet d'offrir un pronostic et un risque de récurrence, améliore l'accès aux ressources, aide à limiter les évaluations et peut modifier le traitement médical dans bien des cas. Le CGHa a mené à la définition de nouveaux syndromes génétiques associés à un retard de développement. À titre d'exemple, nous décrivons le cas d'un homme âgé de 31 ans qui présentait un retard de développement global depuis longtemps et chez qui un syndrome associé à une délétion 4q21 a été diagnostiqué récemment, soit une délétion de 20,8 Mb. Le CGHa est maintenant recommandé comme test de première ligne chez les enfants et les adultes présentant un retard de développement et des anomalies congénitales.
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Beale S, Sanderson D, Sanniti A, Dundar Y, Boland A. A scoping study to explore the cost-effectiveness of next-generation sequencing compared with traditional genetic testing for the diagnosis of learning disabilities in children. Health Technol Assess 2016; 19:1-90. [PMID: 26132578 DOI: 10.3310/hta19460] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Learning disability (LD) is a serious and lifelong condition characterised by the impairment of cognitive and adaptive skills. Some cases of LD with unidentified causes may be linked to genetic factors. Next-generation sequencing (NGS) techniques are new approaches to genetic testing that are expected to increase diagnostic yield. OBJECTIVES This scoping study focused on the diagnosis of LD in children and the objectives were to describe current pathways that involve the use of genetic testing; collect stakeholder views on the changes in service provision that would need to be put in place before NGS could be used in clinical practice; describe the new systems and safeguards that would need to be put in place before NGS could be used in clinical practice; and explore the cost-effectiveness of using NGS compared with conventional genetic testing. METHODS A research advisory group was established. This group provided ongoing support by e-mail and telephone through the lifetime of the study and also contributed face-to-face through a workshop. A detailed review of published studies and reports was undertaken. In addition, information was collected through 33 semistructured interviews with key stakeholders. RESULTS NGS techniques consist of targeted gene sequencing, whole-exome sequencing (WES) and whole-genome sequencing (WGS). Targeted gene panels, which are the least complex, are in their infancy in clinical settings. Some interviewees thought that during the next 3-5 years targeted gene panels would be superseded by WES. If NGS technologies were to be fully introduced into clinical practice in the future a number of factors would need to be overcome. The main resource-related issues pertaining to service provision are the need for additional computing capacity, more bioinformaticians, more genetic counsellors and also genetics-related training for the public and a wide range of staff. It is also considered that, as the number of children undergoing genetic testing increases, there will be an increase in demand for information and support for families. The main issues relating to systems and safeguards are giving informed consent, sharing unanticipated findings, developing ethical and other frameworks, equity of access, data protection, data storage and data sharing. There is little published evidence on the cost-effectiveness of NGS technologies. The major barriers to determining cost-effectiveness are the uncertainty around diagnostic yield, the heterogeneity of diagnostic pathways and the lack of information on the impact of a diagnosis on health care, social care, educational support needs and the wider family. Furthermore, as NGS techniques are currently being used only in research, costs and benefits to the NHS are unclear. CONCLUSIONS NGS technologies are at an early stage of development and it is too soon to say whether they can offer value for money to the NHS as part of the LD diagnostic process. Substantial organisational changes, as well as new systems and safeguards, would be required if NGS technologies were to be introduced into NHS clinical practice. Considerable further research is required to establish whether using NGS technologies to diagnose learning disabilities is clinically effective and cost-effective. FUNDING The National Institute for Health Research Health Technology Assessment programme.
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Affiliation(s)
- Sophie Beale
- Liverpool Reviews and Implementation Group (LRiG), University of Liverpool, Liverpool, UK
| | | | - Anna Sanniti
- Liverpool Reviews and Implementation Group (LRiG), University of Liverpool, Liverpool, UK
| | - Yenal Dundar
- Liverpool Reviews and Implementation Group (LRiG), University of Liverpool, Liverpool, UK
| | - Angela Boland
- Liverpool Reviews and Implementation Group (LRiG), University of Liverpool, Liverpool, UK
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Abstract
Genetic factors play a major part in intellectual disability (ID), but genetic studies have been complicated for a long time by the extreme clinical and genetic heterogeneity. Recently, progress has been made using different next-generation sequencing approaches in combination with new functional readout systems. This approach has provided novel insights into the biological pathways underlying ID, improved the diagnostic process and offered new targets for therapy. In this Review, we highlight the insights obtained from recent studies on the role of genetics in ID and its impact on diagnosis, prognosis and therapy. We also discuss the future directions of genetics research for ID and related neurodevelopmental disorders.
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Erbetta A, Bulgheroni S, Contarino VE, Chiapparini L, Esposito S, Annunziata S, Riva D. Low-Functioning Autism and Nonsyndromic Intellectual Disability: Magnetic Resonance Imaging (MRI) Findings. J Child Neurol 2015; 30:1658-63. [PMID: 25895913 DOI: 10.1177/0883073815578523] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 02/16/2015] [Indexed: 01/25/2023]
Abstract
Previous neuroradiologic studies reported a high incidence of abnormalities in low-functioning autistic children. In this population, it is difficult to know which abnormality depends on autism itself and which is related to intellectual disability associated with autism. The aim of this study was to evaluate the frequency of neuroradiologic abnormalities in low-functioning autistic children compared to Intellectual Quotient and age-matched nonsyndromic children, using the same set of magnetic resonance imaging (MRI) sequences. MRI was rated as abnormal in 44% of autistic and 54% of children with intellectual disability. The main results were mega cisterna magna in autism and hypoplastic corpus callosum in intellectual disability. These abnormalities are morphologically visible signs of altered brain development. These findings, more frequent than expected, are not specific to the 2 conditions. Although MRI cannot be considered mandatory, it allows an in-depth clinical assessment in nonsyndromic intellectual-disabled and autistic children.
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Affiliation(s)
- Alessandra Erbetta
- Neuroradiology Division, Fondazione IRCCS Istituto Neurologico C. Besta, Milano, Italy
| | - Sara Bulgheroni
- Developmental Neurology Division, Fondazione IRCCS Istituto Neurologico C. Besta, Milano, Italy
| | | | - Luisa Chiapparini
- Neuroradiology Division, Fondazione IRCCS Istituto Neurologico C. Besta, Milano, Italy
| | - Silvia Esposito
- Developmental Neurology Division, Fondazione IRCCS Istituto Neurologico C. Besta, Milano, Italy
| | - Silvia Annunziata
- Developmental Neurology Division, Fondazione IRCCS Istituto Neurologico C. Besta, Milano, Italy
| | - Daria Riva
- Developmental Neurology Division, Fondazione IRCCS Istituto Neurologico C. Besta, Milano, Italy
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Chen X, Wang J, Xie H, Zhou W, Wu Y, Wang J, Qin J, Guo J, Gu Q, Zhang X, Ji T, Zhang Y, Xiong Z, Wang L, Wu X, Latham GJ, Jiang Y. Fragile X syndrome screening in Chinese children with unknown intellectual developmental disorder. BMC Pediatr 2015; 15:77. [PMID: 26174701 PMCID: PMC4502947 DOI: 10.1186/s12887-015-0394-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 06/25/2015] [Indexed: 11/18/2022] Open
Abstract
Background Fragile X syndrome is the most common genetic disorder of intellectual developmental disorder/mental retardation (IDD/MR). The prevalence of FXS in a Chinese IDD children seeking diagnosis/treatment in mainland China is unknown. Methods Patients with unknown moderate to severe IDD were recruited from two children’s hospitals. Informed consent was obtained from the children's parents. The size of the CGG repeat was identified using a commercial TP-PCR assay. The influence of AGG interruptions on the CGG expansion during maternal transmission was analyzed in 24 mother-son pairs (10 pairs with 1 AGG and 14 pairs with 2 AGGs). Results 553 unrelated patients between six months and eighteen years of age were recruited. Specimens from 540 patients (male:female = 5.2:1) produced high-quality TP-PCR data, resulting in the determination of the FMR1 CGG repeat number for each. The most common repeat numbers were 29 and 30, and the most frequent interruption pattern was 2 or 3 AGGs. Five full mutations were identified (1 familial and 4 sporadic IDD patients), and size mosaicism was apparent in 4 of these FXS patients (4/5 = 80 %). The overall yield of FXS in the IDD cohort was 0.93 % (5/540). Neither the mean size of CGG expansion (0.20 vs. 0.79, p > 0.05) nor the frequency of CGG expansion (2/10 vs. 9/14, p > 0.05) was significantly different between the 1 and 2 AGG groups following maternal transmission. Conclusions The FMR1 TP-PCR assay generates reliable and sensitive results across a large number of patient specimens, and is suitable for clinical genetic diagnosis. Using this assay, the prevalence of FXS was 0.93 % in Chinese children with unknown IDD. Electronic supplementary material The online version of this article (doi:10.1186/s12887-015-0394-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaoli Chen
- Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China.
| | - Jingmin Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China.
| | - Hua Xie
- Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China.
| | - Wenjuan Zhou
- Department of Pediatrics, Peking University First Hospital, Beijing, China.
| | - Ye Wu
- Department of Pediatrics, Peking University First Hospital, Beijing, China.
| | - Jun Wang
- Department of Neurology, Affiliated Children's Hospital of Capital Institute of Pediatrics, Beijing, China.
| | - Jian Qin
- Beijing Microread Genetech Co., Ltd, Beijing, China.
| | - Jin Guo
- Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China.
| | - Qiang Gu
- Department of Pediatrics, Peking University First Hospital, Beijing, China.
| | - Xiaozhen Zhang
- Department of Genetics, Jiangxi Previncial Children's Hospital, Jiangxi, China.
| | - Taoyun Ji
- Department of Pediatrics, Peking University First Hospital, Beijing, China.
| | - Yu Zhang
- Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China.
| | - Zhiming Xiong
- State Key Lab of Medical Genetics, Central South University, Changsha, China.
| | - Liwen Wang
- Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China.
| | - Xiru Wu
- Department of Pediatrics, Peking University First Hospital, Beijing, China.
| | - Gary J Latham
- Research & Technology Development, Asuragen, Inc., Austin, TX, USA.
| | - Yuwu Jiang
- Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China. .,Department of Pediatrics, Peking University First Hospital, Beijing, China.
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Sayson B, Popurs MAM, Lafek M, Berkow R, Stockler-Ipsiroglu S, van Karnebeek CDM. Retrospective analysis supports algorithm as efficient diagnostic approach to treatable intellectual developmental disabilities. Mol Genet Metab 2015; 115:1-9. [PMID: 25801009 DOI: 10.1016/j.ymgme.2015.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/02/2015] [Accepted: 03/02/2015] [Indexed: 10/23/2022]
Abstract
BACKGROUND Intellectual developmental disorders (IDD(1)), characterized by a significant impairment in cognitive function and behavior, affect 2.5% of the population and are associated with considerable morbidity and healthcare costs. Inborn errors of metabolism (IEM) currently constitute the largest group of genetic defects presenting with IDD, which are amenable to causal therapy. Recently, we created an evidence-based 2-tiered diagnostic protocol (TIDE protocol); the first tier is a 'screening step' applied in all patients, comprising routinely performed, wide available metabolic tests in blood and urine, while second-tier tests are more specific and based on the patient's phenotype. The protocol is supported by an app (www.treatable-ID.org). OBJECTIVE To retrospectively examine the cost- and time-effectiveness of the TIDE protocol in patients identified with a treatable IEM at the British Columbia Children's Hospital. METHODS We searched the database for all IDD patients diagnosed with a treatable IEM, during the period 2000-2009 in our academic institution. Data regarding the patient's clinical phenotype, IEM, diagnostic tests and interval were collected. Total costs and time intervals associated with all testing and physician consultations actually performed were calculated and compared to the model of the TIDE protocol. RESULTS Thirty-one patients (16 males) were diagnosed with treatable IDD during the period 2000-2009. For those identifiable via the 1st tier (n=20), the average cost savings would have been $311.17 CAD, and for those diagnosed via a second-tier test (n=11) $340.14 CAD. Significant diagnostic delay (mean 9 months; range 1-29 months) could have been avoided in 9 patients with first-tier diagnoses, had the TIDE protocol been used. For those with second-tier treatable IDD, diagnoses could have been more rapidly achieved with the use of the Treatable IDD app allowing for specific searches based on signs and symptoms. CONCLUSION The TIDE protocol for treatable forms of IDD appears effective reducing diagnostic delay and unnecessary costs. Larger prospective studies, currently underway, are needed to prove that standard screening for treatable conditions in patients with IDD is time- and cost-effective, and most importantly will preserve brain function by timely diagnosis enabling initiation of causal therapy.
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Affiliation(s)
- Bryan Sayson
- Division of Pediatric Neurology, BC Children's Hospital, Vancouver, Canada; Department of Pediatrics, BC Children's Hospital, Vancouver, Canada; Treatable Intellectual Disability Endeavour in British Columbia, Vancouver, Canada; University of British Columbia, Vancouver, Canada
| | - Marioara Angela Moisa Popurs
- Department of Pediatrics, BC Children's Hospital, Vancouver, Canada; Treatable Intellectual Disability Endeavour in British Columbia, Vancouver, Canada; Division of Biochemical Diseases, BC Children's Hospital, Vancouver, Canada
| | - Mirafe Lafek
- Department of Pediatrics, BC Children's Hospital, Vancouver, Canada; Treatable Intellectual Disability Endeavour in British Columbia, Vancouver, Canada; Division of Biochemical Diseases, BC Children's Hospital, Vancouver, Canada
| | - Ruth Berkow
- Treatable Intellectual Disability Endeavour in British Columbia, Vancouver, Canada
| | - Sylvia Stockler-Ipsiroglu
- Department of Pediatrics, BC Children's Hospital, Vancouver, Canada; Treatable Intellectual Disability Endeavour in British Columbia, Vancouver, Canada; Division of Biochemical Diseases, BC Children's Hospital, Vancouver, Canada; Child and Family Research Institute, Vancouver, Canada; University of British Columbia, Vancouver, Canada
| | - Clara D M van Karnebeek
- Department of Pediatrics, BC Children's Hospital, Vancouver, Canada; Treatable Intellectual Disability Endeavour in British Columbia, Vancouver, Canada; Division of Biochemical Diseases, BC Children's Hospital, Vancouver, Canada; Child and Family Research Institute, Vancouver, Canada; University of British Columbia, Vancouver, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, Canada.
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Eun SH, Hahn SH. Metabolic evaluation of children with global developmental delay. KOREAN JOURNAL OF PEDIATRICS 2015; 58:117-22. [PMID: 25932032 PMCID: PMC4414625 DOI: 10.3345/kjp.2015.58.4.117] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/04/2015] [Indexed: 12/05/2022]
Abstract
Global developmental delay (GDD) is a relatively common early-onset chronic neurological condition, which may have prenatal, perinatal, postnatal, or undetermined causes. Family history, physical and neurological examinations, and detailed history of environmental risk factors might suggest a specific disease. However, diagnostic laboratory tests, brain imaging, and other evidence-based evaluations are necessary in most cases to elucidate the causes. Diagnosis of GDD has recently improved because of remarkable advances in genetic technology, but this is an exhaustive and expensive evaluation that may not lead to therapeutic benefits in the majority of GDD patients. Inborn metabolic errors are one of the main targets for the treatment of GDD, although only a small proportion of GDD patients have this type of error. Nevertheless, diagnosis is often challenging because the phenotypes of many genetic or metabolic diseases often overlap, and their clinical spectra are much broader than currently known. Appropriate and cost-effective strategies including up-to-date information for the early identification of the "treatable" causes of GDD are needed for the development of well-timed therapeutic applications with the potential to improve neurodevelopmental outcomes.
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Affiliation(s)
- So-Hee Eun
- Department of Pediatrics, Korea University College of Medicine, Seoul, Korea
| | - Si Houn Hahn
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
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O’Byrne JJ, Lynch SA, Treacy EP, King MD, Betts DR, Mayne PD, Sharif F. Unexplained developmental delay/learning disability: guidelines for best practice protocol for first line assessment and genetic/metabolic/radiological investigations. Ir J Med Sci 2015; 185:241-8. [DOI: 10.1007/s11845-015-1284-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 03/07/2015] [Indexed: 11/30/2022]
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Gergev G, Máté A, Zimmermann A, Rárosi F, Sztriha L. Spectrum of neurodevelopmental disabilities: a cohort study in hungary. J Child Neurol 2015; 30:344-56. [PMID: 24868008 DOI: 10.1177/0883073814532543] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The spectrum of neurodevelopmental disabilities was studied in a cohort of patients in Hungary. A search for etiologies and assessment of the degree of intellectual disability were carried out. The study included 241 (131 boys) patients. Disability occurred without any prenatal, perinatal, and/or neonatal adverse events in 167 patients. They were classified into the following subgroups: genetic syndromes with recognized etiology, global developmental delay/intellectual disability in association with dysmorphic features but unknown etiology, global developmental delay/intellectual disability without dysmorphic features and recognized etiology, brain malformations, inborn errors of metabolism, leukoencephalopathies, epileptic syndromes, developmental language impairment, and neuromuscular disorders. Adverse events occurred in 74 children classified into subgroups such as cerebral palsy after delivery preterm or at term, and disabilities without cerebral palsy. The etiology was identified in 66.4%, and genetic diagnosis was found in 19.5%. Classification of neurodevelopmental disorders contribute to etiological diagnosis, proper rehabilitation, and genetic counseling.
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Affiliation(s)
- Gyurgyinka Gergev
- Department of Pediatrics, Faculty of Medicine, University of Szeged, Szeged, Hungary 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Adrienn Máté
- Department of Neurosurgery, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Alíz Zimmermann
- Department of Pediatrics, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Ferenc Rárosi
- Department of Medical Physics and Informatics, Faculty of Medicine, University of Szeged, Szeged, Hungary Bolyai Institute, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - László Sztriha
- Department of Pediatrics, Faculty of Medicine, University of Szeged, Szeged, Hungary
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van Karnebeek CD, Stockler-Ipsiroglu S. Early identification of treatable inborn errors of metabolism in children with intellectual disability: The Treatable Intellectual Disability Endeavor protocol in British Columbia. Paediatr Child Health 2014; 19:469-71. [PMID: 25414581 DOI: 10.1093/pch/19.9.469] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2014] [Indexed: 12/25/2022] Open
Affiliation(s)
- Clara Dm van Karnebeek
- Division of Biochemical Diseases, Department of Pediatrics, BC Children's Hospital, Child & Family Research Institute, University of British Columbia; ; Treatable Intellectual Disability Endeavor in British Columbia (TIDE-BC); ; Centre for Molecular Medicine & Therapeutics, Vancouver, British Columbia
| | - Sylvia Stockler-Ipsiroglu
- Division of Biochemical Diseases, Department of Pediatrics, BC Children's Hospital, Child & Family Research Institute, University of British Columbia; ; Treatable Intellectual Disability Endeavor in British Columbia (TIDE-BC)
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Alfei E, Raviglione F, Franceschetti S, D'Arrigo S, Milani D, Selicorni A, Riva D, Zuffardi O, Pantaleoni C, Binelli S. Seizures and EEG features in 74 patients with genetic-dysmorphic syndromes. Am J Med Genet A 2014; 164A:3154-61. [PMID: 25257908 DOI: 10.1002/ajmg.a.36746] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 07/31/2014] [Indexed: 12/27/2022]
Abstract
Epilepsy is one of the most common findings in chromosome aberrations. Types of seizures and severity may significantly vary both between different conditions and within the same aberration. Hitherto specific seizures and EEG patterns are identified for only few syndromes. We studied 74 patients with defined genetic-dysmorphic syndromes with and without epilepsy in order to assess clinical and electroencephalographic features, to compare our observation with already described electro-clinical phenotypes, and to identify putative electroencephalographic and/or seizure characteristics useful to address the diagnosis. In our population, 10 patients had chromosomal disorders, 19 microdeletion or microduplication syndromes, and 32 monogenic syndromes. In the remaining 13, syndrome diagnosis was assessed on clinical grounds. Our study confirmed the high incidence of epilepsy in genetic-dysmorphic syndromes. Moreover, febrile seizures and neonatal seizures had a higher incidence compared to general population. In addition, more than one third of epileptic patients had drug-resistant epilepsy. EEG study revealed poor background organization in 42 patients, an excess of diffuse rhythmic activities in beta, alpha or theta frequency bands in 34, and epileptiform patterns in 36. EEG was completely normal only in 20 patients. No specific electro-clinical pattern was identified, except for inv-dup15, Angelman, and Rett syndromes. Nevertheless some specific conditions are described in detail, because of notable differences from what previously reported. Regarding the diagnostic role of EEG, we found that--even without any epileptiform pattern--the generation of excessive rhythmic activities in different frequency bandwidths might support the diagnosis of a genetic syndrome.
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Affiliation(s)
- Enrico Alfei
- Developmental Neurology Division, Carlo Besta Neurological Institute, I.R.C.C.S. Foundation, Milan, Italy
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López-Pisón J, García-Jiménez M, Monge-Galindo L, Lafuente-Hidalgo M, Pérez-Delgado R, García-Oguiza A, Peña-Segura J. Our experience with the aetiological diagnosis of global developmental delay and intellectual disability: 2006–2010. NEUROLOGÍA (ENGLISH EDITION) 2014. [DOI: 10.1016/j.nrleng.2013.10.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Moeschler JB, Shevell M. Comprehensive evaluation of the child with intellectual disability or global developmental delays. Pediatrics 2014; 134:e903-18. [PMID: 25157020 PMCID: PMC9923626 DOI: 10.1542/peds.2014-1839] [Citation(s) in RCA: 333] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Global developmental delay and intellectual disability are relatively common pediatric conditions. This report describes the recommended clinical genetics diagnostic approach. The report is based on a review of published reports, most consisting of medium to large case series of diagnostic tests used, and the proportion of those that led to a diagnosis in such patients. Chromosome microarray is designated as a first-line test and replaces the standard karyotype and fluorescent in situ hybridization subtelomere tests for the child with intellectual disability of unknown etiology. Fragile X testing remains an important first-line test. The importance of considering testing for inborn errors of metabolism in this population is supported by a recent systematic review of the literature and several case series recently published. The role of brain MRI remains important in certain patients. There is also a discussion of the emerging literature on the use of whole-exome sequencing as a diagnostic test in this population. Finally, the importance of intentional comanagement among families, the medical home, and the clinical genetics specialty clinic is discussed.
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Redin C, Gérard B, Lauer J, Herenger Y, Muller J, Quartier A, Masurel-Paulet A, Willems M, Lesca G, El-Chehadeh S, Le Gras S, Vicaire S, Philipps M, Dumas M, Geoffroy V, Feger C, Haumesser N, Alembik Y, Barth M, Bonneau D, Colin E, Dollfus H, Doray B, Delrue MA, Drouin-Garraud V, Flori E, Fradin M, Francannet C, Goldenberg A, Lumbroso S, Mathieu-Dramard M, Martin-Coignard D, Lacombe D, Morin G, Polge A, Sukno S, Thauvin-Robinet C, Thevenon J, Doco-Fenzy M, Genevieve D, Sarda P, Edery P, Isidor B, Jost B, Olivier-Faivre L, Mandel JL, Piton A. Efficient strategy for the molecular diagnosis of intellectual disability using targeted high-throughput sequencing. J Med Genet 2014; 51:724-36. [PMID: 25167861 PMCID: PMC4215287 DOI: 10.1136/jmedgenet-2014-102554] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background Intellectual disability (ID) is characterised by an extreme genetic heterogeneity. Several hundred genes have been associated to monogenic forms of ID, considerably complicating molecular diagnostics. Trio-exome sequencing was recently proposed as a diagnostic approach, yet remains costly for a general implementation. Methods We report the alternative strategy of targeted high-throughput sequencing of 217 genes in which mutations had been reported in patients with ID or autism as the major clinical concern. We analysed 106 patients with ID of unknown aetiology following array-CGH analysis and other genetic investigations. Ninety per cent of these patients were males, and 75% sporadic cases. Results We identified 26 causative mutations: 16 in X-linked genes (ATRX, CUL4B, DMD, FMR1, HCFC1, IL1RAPL1, IQSEC2, KDM5C, MAOA, MECP2, SLC9A6, SLC16A2, PHF8) and 10 de novo in autosomal-dominant genes (DYRK1A, GRIN1, MED13L, TCF4, RAI1, SHANK3, SLC2A1, SYNGAP1). We also detected four possibly causative mutations (eg, in NLGN3) requiring further investigations. We present detailed reasoning for assigning causality for each mutation, and associated patients’ clinical information. Some genes were hit more than once in our cohort, suggesting they correspond to more frequent ID-associated conditions (KDM5C, MECP2, DYRK1A, TCF4). We highlight some unexpected genotype to phenotype correlations, with causative mutations being identified in genes associated to defined syndromes in patients deviating from the classic phenotype (DMD, TCF4, MECP2). We also bring additional supportive (HCFC1, MED13L) or unsupportive (SHROOM4, SRPX2) evidences for the implication of previous candidate genes or mutations in cognitive disorders. Conclusions With a diagnostic yield of 25% targeted sequencing appears relevant as a first intention test for the diagnosis of ID, but importantly will also contribute to a better understanding regarding the specific contribution of the many genes implicated in ID and autism.
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Affiliation(s)
- Claire Redin
- Département de Médicine translationnelle et Neurogénétique, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France Chaire de Génétique Humaine, Collège de France, Illkirch, France
| | - Bénédicte Gérard
- Laboratoire de diagnostic génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Julia Lauer
- Laboratoire de diagnostic génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Yvan Herenger
- Laboratoire de diagnostic génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Jean Muller
- Département de Médicine translationnelle et Neurogénétique, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France Laboratoire de diagnostic génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Angélique Quartier
- Département de Médicine translationnelle et Neurogénétique, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France Chaire de Génétique Humaine, Collège de France, Illkirch, France
| | - Alice Masurel-Paulet
- Centre de Génétique et Centre de Référence Anomalies du développement et Syndromes malformatifs, Hôpital d'Enfants, CHU de Dijon, Dijon, France
| | - Marjolaine Willems
- Département de Génétique Médicale, Centre de Référence Maladies Rares Anomalies du Développement et Syndromes Malformatifs Sud-Languedoc Roussillon, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - Gaétan Lesca
- Département de Génétique Médicale, Hospices Civils de Lyon, Bron, France
| | - Salima El-Chehadeh
- Centre de Génétique et Centre de Référence Anomalies du développement et Syndromes malformatifs, Hôpital d'Enfants, CHU de Dijon, Dijon, France
| | - Stéphanie Le Gras
- Plateforme de Biopuces et Séquençage, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Serge Vicaire
- Plateforme de Biopuces et Séquençage, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Muriel Philipps
- Plateforme de Biopuces et Séquençage, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Michaël Dumas
- Plateforme de Biopuces et Séquençage, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Véronique Geoffroy
- Plateforme de Bioinformatique de Strasbourg (BIPS), IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Claire Feger
- Plateforme de Biopuces et Séquençage, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Nicolas Haumesser
- Département de Médicine translationnelle et Neurogénétique, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France Chaire de Génétique Humaine, Collège de France, Illkirch, France
| | - Yves Alembik
- Département de Génétique, CHU de Hautepierre, Strasbourg, France
| | - Magalie Barth
- Départment de Biochimie et de Génétique, CHU d'Angers, Angers, France
| | - Dominique Bonneau
- Départment de Biochimie et de Génétique, CHU d'Angers, Angers, France
| | - Estelle Colin
- Départment de Biochimie et de Génétique, CHU d'Angers, Angers, France
| | - Hélène Dollfus
- Laboratoire de Génétique Médicale, INSERM U1112, Faculté de Médecine de Strasbourg, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Bérénice Doray
- Département de Génétique, CHU de Hautepierre, Strasbourg, France
| | - Marie-Ange Delrue
- CHU de Bordeaux, Génétique Médicale, Université de Bordeaux, Laboratoire MRGM, Bordeaux, France
| | | | - Elisabeth Flori
- Département de Génétique, CHU de Hautepierre, Strasbourg, France
| | - Mélanie Fradin
- Service de Génétique Médicale, Centre De Référence Anomalies du Développement, CHU de Rennes, Rennes, France
| | | | | | | | | | | | - Didier Lacombe
- CHU de Bordeaux, Génétique Médicale, Université de Bordeaux, Laboratoire MRGM, Bordeaux, France
| | - Gilles Morin
- Unité de Génétique Clinique, CHU d'Amiens, Amiens, France
| | - Anne Polge
- Laboratoire de Biochimie, CHU de Nîmes, Nîmes, France
| | - Sylvie Sukno
- Service de Neuropédiatrie, Hôpital Saint Vincent de Paul, Groupe Hospitalier de l'Institut Catholique Lillois, Faculté Libre de Médecine, Lille, France
| | - Christel Thauvin-Robinet
- Centre de Génétique et Centre de Référence Anomalies du développement et Syndromes malformatifs, Hôpital d'Enfants, CHU de Dijon, Dijon, France
| | - Julien Thevenon
- Centre de Génétique et Centre de Référence Anomalies du développement et Syndromes malformatifs, Hôpital d'Enfants, CHU de Dijon, Dijon, France
| | | | - David Genevieve
- Département de Génétique Médicale, Centre de Référence Maladies Rares Anomalies du Développement et Syndromes Malformatifs Sud-Languedoc Roussillon, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - Pierre Sarda
- Département de Génétique Médicale, Centre de Référence Maladies Rares Anomalies du Développement et Syndromes Malformatifs Sud-Languedoc Roussillon, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - Patrick Edery
- Département de Génétique Médicale, Hospices Civils de Lyon, Bron, France
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, Nantes, France
| | - Bernard Jost
- Plateforme de Biopuces et Séquençage, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Laurence Olivier-Faivre
- Centre de Génétique et Centre de Référence Anomalies du développement et Syndromes malformatifs, Hôpital d'Enfants, CHU de Dijon, Dijon, France
| | - Jean-Louis Mandel
- Département de Médicine translationnelle et Neurogénétique, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France Chaire de Génétique Humaine, Collège de France, Illkirch, France Laboratoire de diagnostic génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Amélie Piton
- Département de Médicine translationnelle et Neurogénétique, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France Chaire de Génétique Humaine, Collège de France, Illkirch, France
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Jimenez-Gomez A, Standridge SM. A refined approach to evaluating global developmental delay for the international medical community. Pediatr Neurol 2014; 51:198-206. [PMID: 25079568 DOI: 10.1016/j.pediatrneurol.2013.12.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 11/18/2013] [Accepted: 12/21/2013] [Indexed: 12/08/2022]
Abstract
BACKGROUND Global developmental delay is usually defined as significant delay in two or more domains of development. Etiologic diagnosis generally proves difficult and the etiology remains undetermined in up to 62% of these children. Those in whom an etiology is established generally undergo an exhaustive and costly diagnostic evaluation, even though this may not change the medical or therapeutic management of the delay. The history and physical examination may provide up to 40% of etiologic diagnoses if adequately conducted. METHODS We performed a critical review of the literature on global developmental delay via PubMed. RESULTS Five major etiologic categories for global developmental delay were identified and traits of the history and physical examination suggestive for their diagnosis were described. Additionally, current diagnostic tools and their benefits and limitations were appraised. CONCLUSIONS We propose an improved approach to enhance clinical diagnosis in both resource-rich and resource-limited settings favoring early intervention and management.
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Affiliation(s)
- Andres Jimenez-Gomez
- Cincinnati Children's Hospital Medical Center Pediatric Residency Program, Cincinnati, Ohio
| | - Shannon M Standridge
- Department of Child Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.
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