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Prior-de Castro C, Gómez-González C, Rodríguez-López R, Macher HC. Prenatal genetic diagnosis of monogenic diseases. ADVANCES IN LABORATORY MEDICINE 2023; 4:28-51. [PMID: 37359899 PMCID: PMC10197187 DOI: 10.1515/almed-2023-0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/04/2023] [Indexed: 06/28/2023]
Abstract
Prenatal genetic diagnosis of monogenic diseases is a process involving the use of a variety of molecular techniques for the molecular characterization of a potential monogenic disease in the fetus during pregnancy. Prenatal genetic diagnosis can be performed through invasive and non-invasive methods. A distinction must be made between "NIPD" (non-invasive prenatal diagnosis), which is considered to be diagnostic, from "NIPT" (non-invasive prenatal test), which is a screening test that requires subsequent confirmation by invasive methods. The different techniques currently available aim at detecting either, previously characterized pathogenic mutations in the family, the risk haplotype associated with the familial mutation, or potential pathogenic mutation(s) in a gene associated with a diagnostic suspicion. An overview is provided of relevant aspects of prenatal genetic diagnosis of monogenic diseases. The objective of this paper is to describe the main molecular techniques currently available and used in clinical practice. A description is provided of the indications, limitations and analytical recommendations regarding these techniques, and the standards governing genetic counseling. Continuous rapid advances in the clinical applications of genomics have provided increased access to comprehensive molecular characterization. Laboratories are struggling to keep in pace with technology developments.
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Affiliation(s)
| | | | - Raquel Rodríguez-López
- Laboratorio de Genética, Servicio Análisis Clínicos, Consorcio Hospital General Universitario, Valencia, Spain
| | - Hada C. Macher
- Departamento de Bioquímica Clínica, Hospital Universitario Virgen del Rocío de Sevilla, Sevilla, Spain
- Instituto de Investigaciones Biomédicas de Sevilla, IBIS, Universidad de Sevilla, Sevilla, Spain
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Chang YT, Hong SY, Lin WD, Lin CH, Lin SS, Tsai FJ, Chou IC. Genetic Testing in Children with Developmental and Epileptic Encephalopathies: A Review of Advances in Epilepsy Genomics. CHILDREN 2023; 10:children10030556. [PMID: 36980114 PMCID: PMC10047509 DOI: 10.3390/children10030556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023]
Abstract
Advances in disease-related gene discovery have led to tremendous innovations in the field of epilepsy genetics. Identification of genetic mutations that cause epileptic encephalopathies has opened new avenues for the development of targeted therapies. Clinical testing using extensive gene panels, exomes, and genomes is currently accessible and has resulted in higher rates of diagnosis and better comprehension of the disease mechanisms underlying the condition. Children with developmental disabilities have a higher risk of developing epilepsy. As our understanding of the mechanisms underlying encephalopathies and epilepsies improves, there may be greater potential to develop innovative therapies tailored to an individual’s genotype. This article provides an overview of the significant progress in epilepsy genomics in recent years, with a focus on developmental and epileptic encephalopathies in children. The aim of this review is to enhance comprehension of the clinical utilization of genetic testing in this particular patient population. The development of effective and precise therapeutic strategies for epileptic encephalopathies may be facilitated by a comprehensive understanding of their molecular pathogenesis.
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Affiliation(s)
- Yu-Tzu Chang
- School of Post Baccalaureate Chinese Medicine, China Medical University, Taichung 40447, Taiwan; (Y.-T.C.)
- Division of Pediatric Neurology, China Medical University Children’s Hospital, Taichung 40447, Taiwan
| | - Syuan-Yu Hong
- Division of Pediatric Neurology, China Medical University Children’s Hospital, Taichung 40447, Taiwan
- Department of Medicine, School of Medicine, China Medical University, Taichung 40447, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40447, Taiwan
| | - Wei-De Lin
- School of Post Baccalaureate Chinese Medicine, China Medical University, Taichung 40447, Taiwan; (Y.-T.C.)
- Department of Medical Research, China Medical University Hospital, Taichung 40447, Taiwan
| | - Chien-Heng Lin
- Division of Pediatric Pulmonology, China Medical University Children’s Hospital, Taichung 40447, Taiwan
- Department of Biomedical Imaging and Radiological Science, College of Medicine, China Medial University, Taichung 40447, Taiwan
| | - Sheng-Shing Lin
- School of Post Baccalaureate Chinese Medicine, China Medical University, Taichung 40447, Taiwan; (Y.-T.C.)
- Division of Pediatric Neurology, China Medical University Children’s Hospital, Taichung 40447, Taiwan
| | - Fuu-Jen Tsai
- Department of Medical Research, China Medical University Hospital, Taichung 40447, Taiwan
- Division of Genetics and Metabolism, China Medical University Children’s Hospital, Taichung 40447, Taiwan
- Department of Medical Genetics, China Medical University Hospital, Taichung 40447, Taiwan
- School of Chinese Medicine, China Medical University, Taichung 40447, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 40447, Taiwan
| | - I-Ching Chou
- Division of Pediatric Neurology, China Medical University Children’s Hospital, Taichung 40447, Taiwan
- Graduate Institute of Integrated Medicine, China Medical University, Taichung 40447, Taiwan
- Correspondence: ; Tel.: +886-4-22052121
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Touhami R, Foddha H, Alix E, Jalloul A, Mougou-Zerelli S, Saad A, Sanlaville D, Haj Khelil A. Case report: 7p22.3 deletion and 8q24.3 duplication in a patient with epilepsy and psychomotor delay-Does both possibly act to modulate a candidate gene region for the patient's phenotype? Front Genet 2023; 13:1061539. [PMID: 36778913 PMCID: PMC9909830 DOI: 10.3389/fgene.2022.1061539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/20/2022] [Indexed: 01/12/2023] Open
Abstract
Background: Psychomotor delay, epilepsy and dysmorphic features are clinical signs which are described in multiple syndromes due to chromosomal imbalances or mutations involving key genes implicated in the stages of Early Embryonic Development. In this context, we report a 10 years old Tunisian patient with these three signs. Our objective is to determine the cause of developmental, behavioral and facial abnormalities in this patient. Methods: We used banding cytogenetics (karyotype) and Array Comparative Genomic Hybridization (Array CGH) to this purpose. Results: The karyotype was in favor of a derivative of chromosome 7 in the patient and Array CGH analysis revealed a loss of genetic material in 7p22.3-p22.1 (4,56 Mb) with a gain at 8q24.23-q24 (9.20 Mb) resulting from maternal 7/8 reciprocal translocation. An in silico analysis of the unbalanced region was carried out and showed that the 7p22.3-p22.1 deletion contains eight genes. Among them, BRAT1 gene, previously described in several neurodevelopmental diseases, may be a candidate gene which absence could be correlated to the patient's phenotype. However, the 8q24.23-q24 duplication could be involved in the phenotype of this patient. Conclusion: In this study, we report for the first time a 7p deletion/8q duplication in a patient with psychomoteur delay, epilepsy and facial dysmorphism. Our study showed that Array CGH still useful for delivering a conclusive genetic diagnosis for patients having neurodevelopmental abnormalities in the era of next-generation sequencing.
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Affiliation(s)
- Rahma Touhami
- Laboratory of human genome and multifactorial diseases, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia,Department of Cellular and Molecular Biology, Superior Institute of Biotechnology, University of Monastir, Monastir, Tunisia,Laboratory of Cytogenetics, Hôpital Mère-enfant, CHU Lyon, Lyon, France
| | - Hajer Foddha
- Laboratory of human genome and multifactorial diseases, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Eudeline Alix
- Laboratory of Cytogenetics, Hôpital Mère-enfant, CHU Lyon, Lyon, France
| | - Afef Jalloul
- Laboratory of Cytogenetics, Hôpital Mère-enfant, CHU Lyon, Lyon, France
| | - Soumaya Mougou-Zerelli
- Laboratory of Cytogenetics, molecular genetics, and human reproduction biology, CHU Farhat Hached, Sousse, Tunisia
| | - Ali Saad
- Laboratory of Cytogenetics, molecular genetics, and human reproduction biology, CHU Farhat Hached, Sousse, Tunisia
| | - Damien Sanlaville
- Laboratory of Cytogenetics, Hôpital Mère-enfant, CHU Lyon, Lyon, France
| | - Amel Haj Khelil
- Laboratory of human genome and multifactorial diseases, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia,Department of Cellular and Molecular Biology, Superior Institute of Biotechnology, University of Monastir, Monastir, Tunisia,*Correspondence: Amel Haj Khelil,
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Streață I, Caramizaru A, Riza AL, Șerban-Sosoi S, Pîrvu A, Cara ML, Cucu MG, Dobrescu AM, Shelby ES, Albeanu A, Burada F, Ioana M. Pathogenic Copy Number Variations Involved in the Genetic Etiology of Syndromic and Non-Syndromic Intellectual Disability-Data from a Romanian Cohort. Diagnostics (Basel) 2022; 12:diagnostics12123137. [PMID: 36553144 PMCID: PMC9777762 DOI: 10.3390/diagnostics12123137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/29/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
The investigation of unexplained global developmental delay (GDD)/intellectual disability (ID) is challenging. In low resource settings, patients may not follow a standardized diagnostic process that makes use of the benefits of advanced technologies. Our study aims to explore the contribution of chromosome microarray analysis (CMA) in identifying the genetic etiology of GDD/ID. A total of 371 Romanian patients with syndromic or non-syndromic GDD/ID, without epilepsy, were routinely evaluated in tertiary clinics. A total of 234 males (63.07%) and 137 (36.93%) females, with ages ranging from 6 months to 40 years (median age of 5.5 years), were referred for genetic diagnosis between 2015 and 2022; testing options included CMA and/or karyotyping. Agilent Technologies and Oxford Gene Technology CMA workflows were used. Pathogenic/likely pathogenic copy number variations (pCNVs) were identified in 79 patients (21.29%). Diagnosis yield was comparable between mild ID (17.05%, 22/129) and moderate/severe ID 23.55% (57/242). Higher rates were found in cases where facial dysmorphism (22.97%, 71/309), autism spectrum disorder (ASD) (19.11%, 26/136) and finger anomalies (20%, 27/96) were associated with GDD/ID. GDD/ID plus multiple congenital anomalies (MCA) account for the highest detection rates at 27.42% (17/62). pCNVs represent a significant proportion of the genetic causes of GDD/ID. Our study confirms the utility of CMA in assessing GDD/ID with an uncertain etiology, especially in patients with associated comorbidities.
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Affiliation(s)
- Ioana Streață
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Alexandru Caramizaru
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
- Doctoral School, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Anca-Lelia Riza
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
- Correspondence: (A.-L.R.); (F.B.)
| | - Simona Șerban-Sosoi
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Andrei Pîrvu
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Monica-Laura Cara
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Department of Public Health, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Mihai-Gabriel Cucu
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Amelia Mihaela Dobrescu
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Ro-NMCA-ID Group
- The Ro-NMCA-ID (RoNetwork Multiple Congenital Abnormalities with ID) Member of European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability (ERN-ITHACA) [EU Framework Partnership Agreement ID: 3HP-HP-FPA ERN-01-2016/739516], 400011 Timisoara, Romania
| | | | | | - Elena-Silvia Shelby
- National University Center for Children’s Neurorehabilitation “Dr. Nicolae Robănescu”, 44 Dumitru Mincă Street, District 4, 041408 Bucharest, Romania
| | - Adriana Albeanu
- Department of Pediatric Neurology, Clinical Emergency Children Hospital Brasov, Nicopole Street No. 45, 500063 Brasov, Romania
| | - Florin Burada
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
- Correspondence: (A.-L.R.); (F.B.)
| | - Mihai Ioana
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
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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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The Emerging Roles of Long Non-Coding RNAs in Intellectual Disability and Related Neurodevelopmental Disorders. Int J Mol Sci 2022; 23:ijms23116118. [PMID: 35682796 PMCID: PMC9181295 DOI: 10.3390/ijms23116118] [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: 04/30/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 02/05/2023] Open
Abstract
In the human brain, long non-coding RNAs (lncRNAs) are widely expressed in an exquisitely temporally and spatially regulated manner, thus suggesting their contribution to normal brain development and their probable involvement in the molecular pathology of neurodevelopmental disorders (NDD). Bypassing the classic protein-centric conception of disease mechanisms, some studies have been conducted to identify and characterize the putative roles of non-coding sequences in the genetic pathogenesis and diagnosis of complex diseases. However, their involvement in NDD, and more specifically in intellectual disability (ID), is still poorly documented and only a few genomic alterations affecting the lncRNAs function and/or expression have been causally linked to the disease endophenotype. Considering that a significant fraction of patients still lacks a genetic or molecular explanation, we expect that a deeper investigation of the non-coding genome will unravel novel pathogenic mechanisms, opening new translational opportunities. Here, we present evidence of the possible involvement of many lncRNAs in the etiology of different forms of ID and NDD, grouping the candidate disease-genes in the most frequently affected cellular processes in which ID-risk genes were previously collected. We also illustrate new approaches for the identification and prioritization of NDD-risk lncRNAs, together with the current strategies to exploit them in diagnosis.
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Perovic D, Damnjanovic T, Jekic B, Dusanovic-Pjevic M, Grk M, Djuranovic A, Rasic M, Novakovic I, Maksimovic N. Chromosomal microarray in postnatal diagnosis of congenital anomalies and neurodevelopmental disorders in Serbian patients. J Clin Lab Anal 2022; 36:e24441. [PMID: 35441737 PMCID: PMC9169173 DOI: 10.1002/jcla.24441] [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: 03/03/2022] [Revised: 04/04/2022] [Accepted: 04/07/2022] [Indexed: 11/27/2022] Open
Abstract
Background Array‐based genomic analysis is a gold standard for the detection of copy number variations (CNVs) as an important source of benign as well as pathogenic variations in humans. The introduction of chromosomal microarray (CMA) has led to a significant leap in diagnostics of genetically caused congenital malformations and neurodevelopmental disorders, with an average diagnostic yield of 15%. Here, we present our experience from a single laboratory perspective in four years’ postnatal clinical CMA application. Methods DNA samples of 430 patients with congenital anomalies and/or neurodevelopmental disorders were analyzed by comparative genome hybridization using oligonucleotide‐based microarray platforms. Interpretation of detected CNVs was performed according to current guidelines. The detection rate (DR) of clinically significant findings (pathogenic/likely pathogenic CNVs) was calculated for the whole cohort and isolated or combined phenotypic categories. Results A total of 140 non‐benign CNVs were detected in 113/430 patients (26.5%). In 70 patients at least one CNV was considered clinically significant thus reaching a diagnostic yield of 16.3%. The more complex the phenotype, including developmental delay/intellectual disability (DD/ID) as a prevailing feature, the higher the DR of clinically significant CNVs is obtained. Isolated congenital anomalies had the lowest, while the “dysmorphism plus” category had the highest diagnostic yield. Conclusion In our study, CMA proved to be a very useful method in the diagnosis of genetically caused congenital anomalies and neurodevelopmental disorders. DD/ID and dysmorphism stand out as important phenotypic features that significantly increase the diagnostic yield of the analysis.
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Affiliation(s)
- Dijana Perovic
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | - Tatjana Damnjanovic
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | - Biljana Jekic
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | | | - Milka Grk
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | - Ana Djuranovic
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | - Milica Rasic
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | - Ivana Novakovic
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | - Nela Maksimovic
- Faculty of Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
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Kamath V, Yoganathan S, Thomas MM, Gowri M, Chacko MP. Utility of Chromosomal Microarray in Children with Unexplained Developmental Delay/Intellectual Disability. Fetal Pediatr Pathol 2022; 41:208-218. [PMID: 32701375 DOI: 10.1080/15513815.2020.1791292] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
ObjectiveTo evaluate the chromosomal microarray (CMA) yield among children who presented with global developmental delay/intellectual disability (GDD/ID) with/without co-occurring conditions. Methods: The pathogenic copy number variation (pCNVs) findings on CMA of all children who presented with unexplained GDD/ID were categorized based on the clinical features. The karyotype results were compared with CMA. Results: The overall pCNV yield in children presenting with GDD/ID with or without comorbid conditions constituted 20.9%. Among the 17 pCNVs, 13 were losses and four were gains. Cardiac defect was the only co-morbidity in our study that demonstrated statistically significant prediction for pCNV (odds ratio 6.13, p value- 0.031). Six children who were karyotyped prior to CMA testing showed a structural abnormality. Conclusions: In our study, 20.9% of children with GDD/ID showed pCNVs on CMA. Cardiac defect alongside GDD/ID, emerged as the single strongest phenotype associated with pCNVs. CMA also provided vital information in previously karyotyped patients.
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Affiliation(s)
- Vandana Kamath
- Department of Cytogenetics, Christian Medical College and Hospital, Vellore, India
| | - Sangeetha Yoganathan
- Department of Neurological Sciences, Christian Medical College and Hospital, Vellore, India
| | - Maya Mary Thomas
- Department of Neurological Sciences, Christian Medical College and Hospital, Vellore, India
| | - Mahasampath Gowri
- Department of Biostatistics, Christian Medical College and Hospital, Vellore, India
| | - Mary Purna Chacko
- Department of Cytogenetics, Christian Medical College and Hospital, Vellore, India
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Palka Bayard de Volo C, Alfonsi M, Morizio E, Guaciali-Franchi P, Mohn A, Chiarelli F. A 343 Italian cohort of patients analysed with array-comparative genomic hybridization: unsolved problems and genetic counselling difficulties. JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2021; 65:863-869. [PMID: 34338393 DOI: 10.1111/jir.12867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 06/11/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The recent introduction of microarrays for genetic analyses has allowed higher etiological diagnostic rates in patient with intellectual disability (ID), autism spectrum disorders (ASD), epilepsy and multiple congenital anomalies (MCA), because of its resolution. This approach still results of high complexity and some limitations have been reported. In fact, it discloses several variants of unknown significance (VOUS) or incidental findings. In all cases, a massive amount of data is generated, because of this, the analysis and the interpretation is very difficult and often without a definitive conclusion. METHOD We analysed an Italian cohort of 343 patients with ID, MCA and ASD by array-comparative genomic hybridization. The purpose of this work was to consider the proportion of the chromosomal abnormalities in such cohort and to assess the distribution of the different type of the chromosomal abnormalities concerning their pathogenic significance, their origin and their correlation to these clinical phenotypes. RESULTS Array-comparative genomic hybridization analysis revealed 76 positive results. Abnormalities were detected in 27.8% of patients with ID, 11.1% with ASD, 10.7% with epilepsy and 19.4% with multiple congenital anomalies. The anomalies were classified in three major groups: group 1 (27 patients) with pathogenic alterations (P group); group 2 (34 patients) with VOUS potentially pathogenic (PP group); and group 3 (13 patients) with VOUS potentially benign (PB group). As expected, comparing the diagnostic groups, we observed a greater number of deletions in the P group and that all the abnormalities of the PB group were inherited. CONCLUSIONS Our retrospective study resulted in confirming the high detection rate of microarrays. CNV classification remains a complex procedure. The difficulty in CNV classification points out the importance of the patient selection, helping the interpretation of the molecular cytogenetic results.
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Affiliation(s)
| | - M Alfonsi
- Medical Genetics Unit, Ss Annunziata Hospital, Chieti, Italy
| | - E Morizio
- Department of Medical Genetics, G. d'Annunzio University, Chieti, Italy
| | - P Guaciali-Franchi
- Medical Genetics Unit, Ss Annunziata Hospital, Chieti, Italy
- Department of Medical Genetics, G. d'Annunzio University, Chieti, Italy
| | - A Mohn
- Department of Pediatrics, G. d'Annunzio University, Chieti, Italy
| | - F Chiarelli
- Department of Pediatrics, G. d'Annunzio University, Chieti, Italy
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Pattern of cytogenetic abnormalities in syndromic mental retardation/intellectual disability in Kashmir region of Jammu and Kashmir. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Chromosomal Microarray Analysis Has a Poor Diagnostic Yield in Children with Developmental Delay/Intellectual Disability When Concurrent Cerebellar Anomalies Are Present. THE CEREBELLUM 2021; 19:629-635. [PMID: 32472476 DOI: 10.1007/s12311-020-01145-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Chromosomal microarray analysis is commonly used as screening test for children with neurodevelopmental issues, also in case of complex neurological phenotypes. Developmental delay/intellectual disability is a common presentation sign in pediatric ataxias, diseases with high clinical and genetic heterogeneity. In order to determine the diagnostic yield of Array-CGH in such conditions, all the tests performed in the last 10-year activity of a single referral center in children who present, besides the neurodevelopmental impairment, cerebellar abnormalities have been systematically gathered. The study demonstrates that, except for Dandy-Walker malformation or poly-malformative phenotypes, chromosomal microarray analysis should be discouraged as first-line diagnostic test in pediatric ataxias with neurodevelopmental disability.
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Abstract
Neurodevelopmental disorders are the most prevalent chronic medical conditions encountered in pediatric primary care. In addition to identifying appropriate descriptive diagnoses and guiding families to evidence-based treatments and supports, comprehensive care for individuals with neurodevelopmental disorders includes a search for an underlying etiologic diagnosis, primarily through a genetic evaluation. Identification of an underlying genetic etiology can inform prognosis, clarify recurrence risk, shape clinical management, and direct patients and families to condition-specific resources and supports. Here we review the utility of genetic testing in patients with neurodevelopmental disorders and describe the three major testing modalities and their yields - chromosomal microarray, exome sequencing (with/without copy number variant calling), and FMR1 CGG repeat analysis for fragile X syndrome. Given the diagnostic yield of genetic testing and the potential for clinical and personal utility, there is consensus that genetic testing should be offered to all patients with global developmental delay, intellectual disability, and/or autism spectrum disorder. Despite this recommendation, data suggest that a minority of children with autism spectrum disorder and intellectual disability have undergone genetic testing. To address this gap in care, we describe a structured but flexible approach to facilitate integration of genetic testing into clinical practice across pediatric specialties and discuss future considerations for genetic testing in neurodevelopmental disorders to prepare pediatric providers to care for patients with such diagnoses today and tomorrow.
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Affiliation(s)
- Juliann M. Savatt
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, United States
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13
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Lee J, Park JE, Lee C, Kim AR, Kim BJ, Park WY, Ki CS, Lee J. Genomic Analysis of Korean Patient With Microcephaly. Front Genet 2021; 11:543528. [PMID: 33584783 PMCID: PMC7876370 DOI: 10.3389/fgene.2020.543528] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 12/30/2020] [Indexed: 12/17/2022] Open
Abstract
Microcephaly is a prevalent phenotype in patients with neurodevelopmental problems, often with genetic causes. We comprehensively investigated the clinical phenotypes and genetic background of microcephaly in 40 Korean patients. We analyzed their clinical phenotypes and radiologic images and conducted whole exome sequencing (WES) and analysis of copy number variation (CNV). Infantile hypotonia and developmental delay were present in all patients. Thirty-four patients (85%) showed primary microcephaly. The diagnostic yield from the WES and CNV analyses was 47.5%. With WES, we detected pathogenic or likely pathogenic variants that were previously associated with microcephaly in 12 patients (30%); nine of these were de novo variants with autosomal dominant inheritance. Two unrelated patients had mutations in the KMT2A gene. In 10 other patients, we found mutations in the GNB1, GNAO1, TCF4, ASXL1, SMC1A, VPS13B, ACTG1, EP300, and KMT2D genes. Seven patients (17.5%) were diagnosed with pathogenic CNVs. Korean patients with microcephaly show a genetic spectrum that is different from that of patients with microcephaly of other ethnicities. WES along with CNV analysis represents an effective approach for diagnosis of the underlying causes of microcephaly.
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Affiliation(s)
- Jiwon Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Jong Eun Park
- Department of Laboratory Medicine and Genetics, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, South Korea
| | - Chung Lee
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Ah Reum Kim
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Byung Joon Kim
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | | | - Jeehun Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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Yang EH, Shin YB, Choi SH, Yoo HW, Kim HY, Kwak MJ, Park KH, Bae MH, Kong JH, Lee YJ, Nam SO, Kim YM. Chromosomal Microarray in Children With Developmental Delay: The Experience of a Tertiary Center in Korea. Front Pediatr 2021; 9:690493. [PMID: 34604135 PMCID: PMC8480257 DOI: 10.3389/fped.2021.690493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 08/13/2021] [Indexed: 11/20/2022] Open
Abstract
Background and Objectives: Chromosomal microarray (CMA) is a first-tier genetic test for children with developmental delay (DD), intellectual disability (ID), autism spectrum disorders (ASDs), and multiple congenital anomalies (MCA). In this study, we report our experiences with the use of CMA in Korean children with unexplained DD/ID. Methods: We performed CMA in a cohort of 308 children with DD/ID between January 2010 and September 2020. We also retrospectively reviewed their medical records. The Affymetrix CytoScan 750 K array with an average resolution of 100 kb was used to perform CMA. Results: Comorbid neurodevelopmental disorders were ASD (37 patients; 12.0%), epilepsy (34 patients; 11.0%), and attention deficit hyperactivity disorders (12 patients; 3.9%). The diagnostic yield was 18.5%. Among the 221 copy number variants (CNVs) identified, 70 CNVs (57 patients; 18.5%) were pathogenic. Deletion CNVs were more common among pathogenic CNVs (PCNVs) than in non-PCNVs (P < 0.001). The size difference between PCNVs and non-PCNVs was not significant (P = 0.023). The number of included genes within CNV intervals was significantly higher in PCNVs (average 8.6; 0-347) than in non-PCNVs (average 47.5; 1-386) (P < 0.001). Short stature and hearing difficulty were also more common in the PCNV group than in the non-PCNV group (P = 0.010 and 0.070, respectively). Conclusion: This study provides additional evidence for the usefulness of CMA in genetic testing of children with DD/ID in Korea. The pathogenicity of CNVs correlated with the number of included genes within the CNV interval and deletion type of the CNVs, but not with CNV size.
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Affiliation(s)
- Eun Hye Yang
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, South Korea
| | - Yong Beom Shin
- Department of Rehabilitation, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, South Korea, Busan, South Korea
| | - Soo Han Choi
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, South Korea
| | - Hye Won Yoo
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, South Korea
| | - Hye Young Kim
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, South Korea
| | - Min Jung Kwak
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, South Korea
| | - Kyung Hee Park
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, South Korea
| | - Mi Hye Bae
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, South Korea
| | - Ju Hyun Kong
- Department of Pediatrics, Pusan National University Children's Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Yangsan, South Korea
| | - Yun-Jin Lee
- Department of Pediatrics, Pusan National University Children's Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Yangsan, South Korea
| | - Sang Ook Nam
- Department of Pediatrics, Pusan National University Children's Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Yangsan, South Korea
| | - Young Mi Kim
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, South Korea
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15
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Espeche LD, Solari AP, Mori MÁ, Arenas RM, Palomares M, Pérez M, Martínez C, Lotersztein V, Segovia M, Armando R, Dain LB, Nevado J, Lapunzina P, Rozental S. Implementation of chromosomal microarrays in a cohort of patients with intellectual disability at the Argentinean public health system. Mol Biol Rep 2020; 47:6863-6878. [PMID: 32920771 DOI: 10.1007/s11033-020-05743-6] [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: 02/03/2020] [Accepted: 08/28/2020] [Indexed: 01/03/2023]
Abstract
Intellectual disability is a neurodevelopmental disorder in which genetic, epigenetic and environmental factors are involved. In consequence, the determination of its etiology is usually complex. Though many countries have migrated from conventional cytogenetic analysis to chromosomal microarrays as the first-tier genetic test for patients with this condition, this last technique was implemented in our country a few years ago. We report on the results of the implementation of chromosomal microarrays in a cohort of 133 patients with intellectual disability and dysmorphic features, normal karyotype and normal subtelomeric MLPA results in an Argentinean public health institution. Clinically relevant copy number variants were found in 12% of the patients and one or more copy number variants classified as variants of uncertain significance were found in 5.3% of them. Although the diagnostic yield of chromosomal microarrays is greater than conventional cytogenetics for these patients, there are financial limitations to adopt this technique as a first-tier test in our country, especially in the public health system.
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Affiliation(s)
- Lucía Daniela Espeche
- Centro Nacional de Genética Médica "Dr. Eduardo Castilla"- ANLIS "Dr. Carlos G. Malbrán", Ministerio de Salud, Buenos Aires, Argentina
| | - Andrea Paula Solari
- Centro Nacional de Genética Médica "Dr. Eduardo Castilla"- ANLIS "Dr. Carlos G. Malbrán", Ministerio de Salud, Buenos Aires, Argentina
| | - María Ángeles Mori
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid, Spain.,CIBERER (Centro de Investigación Biomédica en Red de Enfermedades Raras), ISCIII, Madrid, Spain.,ITHACA European Reference Network, Madrid, Spain
| | - Rubén Martín Arenas
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid, Spain.,CIBERER (Centro de Investigación Biomédica en Red de Enfermedades Raras), ISCIII, Madrid, Spain.,ITHACA European Reference Network, Madrid, Spain
| | - María Palomares
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid, Spain.,CIBERER (Centro de Investigación Biomédica en Red de Enfermedades Raras), ISCIII, Madrid, Spain.,ITHACA European Reference Network, Madrid, Spain
| | - Myriam Pérez
- Centro Nacional de Genética Médica "Dr. Eduardo Castilla"- ANLIS "Dr. Carlos G. Malbrán", Ministerio de Salud, Buenos Aires, Argentina
| | - Cinthia Martínez
- Centro Nacional de Genética Médica "Dr. Eduardo Castilla"- ANLIS "Dr. Carlos G. Malbrán", Ministerio de Salud, Buenos Aires, Argentina
| | - Vanesa Lotersztein
- Centro Nacional de Genética Médica "Dr. Eduardo Castilla"- ANLIS "Dr. Carlos G. Malbrán", Ministerio de Salud, Buenos Aires, Argentina
| | - Mabel Segovia
- Centro Nacional de Genética Médica "Dr. Eduardo Castilla"- ANLIS "Dr. Carlos G. Malbrán", Ministerio de Salud, Buenos Aires, Argentina
| | - Romina Armando
- Servicio de Genética, Hospital de Niños "Dr. Ricardo Gutiérrez", Buenos Aires, Argentina
| | - Liliana Beatriz Dain
- Centro Nacional de Genética Médica "Dr. Eduardo Castilla"- ANLIS "Dr. Carlos G. Malbrán", Ministerio de Salud, Buenos Aires, Argentina
| | - Julián Nevado
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid, Spain.,CIBERER (Centro de Investigación Biomédica en Red de Enfermedades Raras), ISCIII, Madrid, Spain.,ITHACA European Reference Network, Madrid, Spain
| | - Pablo Lapunzina
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid, Spain.,CIBERER (Centro de Investigación Biomédica en Red de Enfermedades Raras), ISCIII, Madrid, Spain.,ITHACA European Reference Network, Madrid, Spain
| | - Sandra Rozental
- Centro Nacional de Genética Médica "Dr. Eduardo Castilla"- ANLIS "Dr. Carlos G. Malbrán", Ministerio de Salud, Buenos Aires, Argentina.
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16
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Ilyas M, Mir A, Efthymiou S, Houlden H. The genetics of intellectual disability: advancing technology and gene editing. F1000Res 2020; 9. [PMID: 31984132 PMCID: PMC6966773 DOI: 10.12688/f1000research.16315.1] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/10/2020] [Indexed: 12/22/2022] Open
Abstract
Intellectual disability (ID) is a neurodevelopmental condition affecting 1–3% of the world’s population. Genetic factors play a key role causing the congenital limitations in intellectual functioning and adaptive behavior. The heterogeneity of ID makes it more challenging for genetic and clinical diagnosis, but the advent of large-scale genome sequencing projects in a trio approach has proven very effective. However, many variants are still difficult to interpret. A combined approach of next-generation sequencing and functional, electrophysiological, and bioinformatics analysis has identified new ways to understand the causes of ID and help to interpret novel ID-causing genes. This approach offers new targets for ID therapy and increases the efficiency of ID diagnosis. The most recent functional advancements and new gene editing techniques involving the use of CRISPR–Cas9 allow for targeted editing of DNA in
in vitro and more effective mammalian and human tissue-derived disease models. The expansion of genomic analysis of ID patients in diverse and ancient populations can reveal rare novel disease-causing genes.
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Affiliation(s)
- Muhammad Ilyas
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan.,Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Asif Mir
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
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17
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de Souza LC, Dos Santos AP, Sgardioli IC, Viguetti-Campos NL, Marques Prota JR, de Oliveira-Sobrinho RP, Vieira TP, Gil-da-Silva-Lopes VL. Phenotype comparison among individuals with developmental delay/intellectual disability with or without genomic imbalances. JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2019; 63:1379-1389. [PMID: 30900361 DOI: 10.1111/jir.12615] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/18/2019] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The chromosomal microarray analysis (CMA) is recommended as a first-tier test for individuals with developmental delay (DD)/intellectual disability (ID) and/or multiple congenital anomalies. However, owing to high costs, this technique is not widely performed for diagnostic purposes in several countries. The aim of this study was to identify clinical features that could favour the hypothesis of genomic imbalances (GIs) in individuals with DD/ID. METHODS The sample consisted of 63 individuals, and all of them underwent a detailed evaluation by a clinical geneticist and were investigated by the CMA. They were divided into two groups. Group A composed of 20 individuals with pathogenic copy number variants (CNVs); and group B composed of 43 individuals with normal CMA results or variants of uncertain clinical significance (VUS). RESULTS Pathogenic GIs were found in 20 cases (32%), including 11 individuals with an abnormal karyotype, VUS was found in five individuals (8%) and the results were normal in 38 individuals (60%). Major anomalies were found in 15/20 (75%) individuals in group A against 35/43 (81%) in group B. Dysmorphisms (≥5) were found in 17/20 (85%) in group A and 41/43 (95%) in group B. The most frequent major anomalies detected in group A were congenital heart disease, epilepsy and renal malformation; and in group B, they were malformations of central nervous system, congenital heart disease, microcephaly, epilepsy and hearing impairment. There was no significant statistical difference among the frequencies in groups A and B. CONCLUSIONS Evidences point that every individual with DD/ID, with no specific clinical suspicion, should have screening for GIs as a first-tier test, regardless of the presence or absence of additional major anomalies or dysmorphisms. Future studies with a similar design would be helpful, especially in countries where the access to new technologies is still limited.
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Affiliation(s)
- L C de Souza
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - A P Dos Santos
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - I C Sgardioli
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - N L Viguetti-Campos
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - J R Marques Prota
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - R P de Oliveira-Sobrinho
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - T P Vieira
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - V L Gil-da-Silva-Lopes
- Department of Medical Genetics, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
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18
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Additive Diagnostic Yield of Homozygosity Regions Identified During Chromosomal microarray Testing in Children with Developmental Delay, Dysmorphic Features or Congenital Anomalies. Biochem Genet 2019; 58:74-101. [PMID: 31273557 DOI: 10.1007/s10528-019-09931-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 06/27/2019] [Indexed: 11/26/2022]
Abstract
Chromosomal microarray (CMA) has emerged as a robust tool for identifying microdeletions and microduplications, termed copy number variants (CNVs). Nevertheless, data regarding its utility in different patient populations with developmental delay (DD), dysmorphic features (DF) and congenital anomalies (CA), is a matter of dense debate. Although regions of homozygosity (ROH) are not diagnostic of a specific condition, they may have pathogenic implications. Certain CNVs and ROH have ethnically specific occurrences and frequencies. We aimed to determine whether CMA testing offers additional diagnostic information over classical cytogenetics for identifying genomic imbalances in a pediatric cohort with idiopathic DD, DF, or CA. One hundred sixty-nine patients were offered cytogenetics and CMA simultaneously for etiological diagnosis of DD (n = 67), DF (n = 52) and CA (n = 50). CMA could identify additional, clinically significant anomalies as compared with cytogenetics. CMA detected 61 CNVs [21 (34.4%) pathogenic CNVs, 37 (60.7%) variants of uncertain clinical significance and 3 (4.9%) benign CNVs] in 44 patients. CMA identified one or more ROH in 116/169 (68.6%) patients. When considering pathogenic CNVs and aneuploidies as positive findings, 9/169 (5.3%) received a genetic diagnosis from cytogenetics, while 25/169 (14.8%) could have a genetic diagnosis from CMA. The identification of ROH was clinically significant in two cases (2/169), thereby, adding 1.2% to the diagnostic yield of CMA (16% vs. 5.3%, p < 0.001). CMA uncovers additional genetic diagnoses over cytogenetics, thereby, offering a much higher diagnostic yield. Our findings convincingly demonstrate the additive diagnostic value of clinically significant ROH identified during CMA testing, highlighting the need for careful clinical interpretation of these ROH.
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19
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Altıner Ş, Yürür Kutlay N. Importance of patient selection criteria in determining diagnostic copy number variations in patients with multiple congenital anomaly/mental retardation. Mol Cytogenet 2019; 12:23. [PMID: 31149029 PMCID: PMC6537423 DOI: 10.1186/s13039-019-0436-2] [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: 04/04/2019] [Accepted: 05/17/2019] [Indexed: 11/10/2022] Open
Abstract
Background Etiology of developmental delay/intellectual disability is very heterogeneous. In recent years, genetic causes have been defined through the use of chromosomal microarray analysis as a first step genetic test. Results Samples from 30 patients with multiple congenital anomaly and/or mental retardation were analyzed with array comparative genomic hybridization in the context of this study. Before this analysis, karyotyping, subtelomeric fluorescence in situ hybridization and additionally fragment analysis for fragile X in males, had been routinely made all of which were reported to be normal. The purpose of our study was to determine the copy number variations as well as to investigate methods to increase diagnostic yield of array comparative genomic hybridization and forming a suitable flow chart decision pipeline for test indication especially for developing countries. Genomic changes were identified at a rate of about 27% in our series. Although this ratio is higher than the literature data, it could be due to the patient selection criteria. Conclusion Chromosomal microarray analysis is not easily utilized for all patients because of its high-cost. Thus, for increasing cost-effectiveness, it may be used step by step for defined targets. Along with discussing the patients with copy number variations relevant with the phenotype, we suggest a flow chart for selection of diagnostic test with the highest diagnostic rate and the lowest expenditure which is quite important for developing countries.
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Affiliation(s)
- Şule Altıner
- Department of Medical Genetics, Trabzon Kanuni Training and Research Hospital, University of Health Sciences, Topal Osman Street 7, 61290 Trabzon, Turkey.,2Department of Medical Genetics, School of Medicine, Ankara University, Ankara, Turkey
| | - Nüket Yürür Kutlay
- 2Department of Medical Genetics, School of Medicine, Ankara University, Ankara, Turkey
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Belkady B, Elkhattabi L, Elkarhat Z, Zarouf L, Razoki L, Aboulfaraj J, Nassereddine S, Cadi R, Rouba H, Barakat A. Chromosomal Abnormalities in Patients with Intellectual Disability: A 21-Year Retrospective Study. Hum Hered 2019; 83:274-282. [PMID: 31064002 DOI: 10.1159/000499710] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/19/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Intellectual disability (ID) has been defined as a considerably reduced ability to understand new or complex information and to learn new skills. It is associated with life-long intellectual and adaptive functioning impairments that have a profound impact on individuals, families, and society. It affects about 3% of the general population. ID often comes out with other mental conditions like attention deficit, hyperactivity, and autism spectrum disorders (ASD), and it can be part of a malformation syndrome that affects other organs. It may be syndromic (S-ID) or non-syndromic (NS-ID). OBJECTIVE The aims of this study were to identify the profile of intellectually disable patients being referred for cytogenetic analysis in Morocco, to determine the prevalence of chromosomal abnormalities in a Moroccan group, and to compare the results with those of analogous studies from other countries. PARTICIPANTS We included data from Moroccan patients with NS-ID and others with S-ID (mostly Down syndrome cases) who have been referred between 1996 and 2016. 1,626 patients were involved in this study, 1,200 were referred with a clinical diagnosis of Down syndrome, 37 were clinically diagnosed for ASD with ID, and 389 were suspected of NS-ID. RESULTS We identified 1,200 cases of Down syndrome. In 1,096 analyses (91.3%), a cytogenetic variant of trisomy 21 was identified: standard trisomy 21 in 1,037 cases (94.6%), a translocation in 34 cases (3.10%), and mosaicism in 25 cases (2.3%). The cytogenetic analysis among ASD with ID cases did not reveal any specific chromosomal abnormalities. The present study also shows that chromosomal abnormalities were present in 6.43% of the patients with NS-ID (25 abnormal karyotypes out of 389 NS-ID cases). Autosomal structural abnormalities were the largest proportion of chromosomal aberrations. CONCLUSION The high rate of chromosomal abnormalities found in the Moroccan patients studied demonstrates the capital importance of cytogenetic evaluation in patients who show ID or any clinical development abnormality.
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Affiliation(s)
- Boutaina Belkady
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc, Casablanca, Morocco.,Laboratory of Molecular Genetics and Biotechnology, Faculty of Science Ain Chock, Casablanca, Morocco
| | - Lamiae Elkhattabi
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Zouhair Elkarhat
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Latifa Zarouf
- Laboratory of Cytogenetics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Lunda Razoki
- Laboratory of Cytogenetics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Jamila Aboulfaraj
- Laboratory of Cytogenetics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Sanaa Nassereddine
- Laboratory of Cytogenetics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Rachida Cadi
- Laboratory of Molecular Genetics and Biotechnology, Faculty of Science Ain Chock, Casablanca, Morocco
| | - Hassan Rouba
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Abdelhamid Barakat
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc, Casablanca, Morocco,
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Jang W, Kim Y, Han E, Park J, Chae H, Kwon A, Choi H, Kim J, Son JO, Lee SJ, Hong BY, Jang DH, Han JY, Lee JH, Kim SY, Lee IG, Sung IK, Moon Y, Kim M, Park JH. Chromosomal Microarray Analysis as a First-Tier Clinical Diagnostic Test in Patients With Developmental Delay/Intellectual Disability, Autism Spectrum Disorders, and Multiple Congenital Anomalies: A Prospective Multicenter Study in Korea. Ann Lab Med 2019; 39:299-310. [PMID: 30623622 PMCID: PMC6340852 DOI: 10.3343/alm.2019.39.3.299] [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: 05/27/2018] [Revised: 08/06/2018] [Accepted: 11/07/2018] [Indexed: 11/20/2022] Open
Abstract
Background To validate the clinical application of chromosomal microarray analysis (CMA) as a first-tier clinical diagnostic test and to determine the impact of CMA results on patient clinical management, we conducted a multicenter prospective study in Korean patients diagnosed as having developmental delay/intellectual disability (DD/ID), autism spectrum disorders (ASD), and multiple congenital anomalies (MCA). Methods We performed both CMA and G-banding cytogenetics as the first-tier tests in 617 patients. To determine whether the CMA results directly influenced treatment recommendations, the referring clinicians were asked to complete a 39-item questionnaire for each patient separately after receiving the CMA results. Results A total of 122 patients (19.8%) had abnormal CMA results, with either pathogenic variants (N=65) or variants of possible significance (VPS, N=57). Thirty-five well-known diseases were detected: 16p11.2 microdeletion syndrome was the most common, followed by Prader-Willi syndrome, 15q11-q13 duplication, Down syndrome, and Duchenne muscular dystrophy. Variants of unknown significance (VUS) were discovered in 51 patients (8.3%). VUS of genes putatively associated with developmental disorders were found in five patients: IMMP2L deletion, PTCH1 duplication, and ATRNL1 deletion. CMA results influenced clinical management, such as imaging studies, specialist referral, and laboratory testing in 71.4% of patients overall, and in 86.0%, 83.3%, 75.0%, and 67.3% of patients with VPS, pathogenic variants, VUS, and benign variants, respectively. Conclusions Clinical application of CMA as a first-tier test improves diagnostic yields and the quality of clinical management in patients with DD/ID, ASD, and MCA.
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Affiliation(s)
- Woori Jang
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Eunhee Han
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Joonhong Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hyojin Chae
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ahlm Kwon
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hayoung Choi
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jiyeon Kim
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jung Ok Son
- Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sang Jee Lee
- Department of Rehabilitation Medicine, Daejeon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Daejeon, Korea
| | - Bo Young Hong
- Department of Rehabilitation Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Suwon, Korea
| | - Dae Hyun Jang
- Department of Rehabilitation Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, Korea
| | - Ji Yoon Han
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jung Hyun Lee
- Department of Pediatrics, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Suwon, Korea
| | - So Young Kim
- Department of Pediatrics, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - In Goo Lee
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - In Kyung Sung
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yeonsook Moon
- Department of Laboratory Medicine, Inha University School of Medicine, Incheon, Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea.
| | - Joo Hyun Park
- Department of Rehabilitation Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
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22
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Kessi M, Xiong J, Wu L, Yang L, He F, Chen C, Pang N, Duan H, Zhang W, Arafat A, Yin F, Peng J. Rare Copy Number Variations and Predictors in Children With Intellectual Disability and Epilepsy. Front Neurol 2018; 9:947. [PMID: 30510536 PMCID: PMC6252327 DOI: 10.3389/fneur.2018.00947] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/23/2018] [Indexed: 11/19/2022] Open
Abstract
Introduction: The concurrence of intellectual disability/global developmental delay and epilepsy (ID/GDD-EP) is very common in the pediatric population. The etiologies for both conditions are complex and largely unknown. The predictors of significant copy number variations (CNVs) are known for the cases with ID/GDD, but unknown for those with exclusive ID/GDD-EP. Importantly, the known predictors are largely from the same ethnic group; hence, they lack replication. Purpose: We aimed to determine and investigate the diagnostic yield of CNV tests, new causative CNVs, and the independent predictors of significant CNVs in Chinese children with unexplained ID/GDD-EP. Materials and methods: A total of 100 pediatric patients with unexplained ID/GDD-EP and 1,000 healthy controls were recruited. The American College of Medical Genetics guideline was used to classify the CNVs. Additionally, clinical information was collected and compared between those with significant and non-significant CNVs. Results: Twenty-eight percent of the patients had significant CNVs, 16% had variants of unknown significance, and 56% had non-significant CNVs. In total, 31 CNVs were identified in 28% (28/100) of cases: 25 pathogenic and 6 likely pathogenic. Eighteen known syndromes were diagnosed in 17 cases. Thirteen rare CNVs (8 novel and 5 reported in literature) were identified, of which three spanned dosage-sensitive genes: 19q13.2 deletion (ATP1A3), Xp11.4-p11.3 deletion (CASK), and 6q25.3-q25.3 deletion (ARID1B). By comparing clinical features in patients with significant CNVs against those with non-significant CNVs, a statistically significant association was found between the presence of significant CNVs and speech and language delay for those aged above 2 years and for those with facial malformations, microcephaly, congenital heart disease, fair skin, eye malformations, and mega cisterna magna. Multivariate logistic regression analysis allowed the identification of two independent significant CNV predictors, which are eye malformations and facial malformations. Conclusion: Our study supports the performance of CNV tests in pediatric patients with unexplained ID/GDD-EP, as there is high diagnostic yield, which informs genetic counseling. It adds 13 rare CNVs (8 novel), which can be accountable for both conditions. Moreover, congenital eye and facial malformations are clinical markers that can aid clinicians to understand which patients can benefit from the CNV testing and which will not, thus helping patients to avoid unnecessary and expensive tests.
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Affiliation(s)
- Miriam Kessi
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Juan Xiong
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Liwen Wu
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Lifen Yang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fang He
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Chen Chen
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Nan Pang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Haolin Duan
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Wen Zhang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Ahmed Arafat
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fei Yin
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
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23
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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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24
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García-Acero M, Suárez-Obando F, Gómez-Gutiérrez A. CGH analysis in Colombian patients: findings of 1374 arrays in a seven-year study. Mol Cytogenet 2018; 11:46. [PMID: 30166995 PMCID: PMC6104019 DOI: 10.1186/s13039-018-0398-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 08/14/2018] [Indexed: 11/22/2022] Open
Abstract
Background Array-based comparative genome hybridization (array CGH) is a first-line test used in the genetic evaluation of individuals with multiple anomalies, developmental delays, and cognitive deficits. In this study, we analyzed clinical indications and findings of array CGH tests of Colombian individuals forwarded to a reference laboratory over a period of seven years in order to evaluate the diagnostic performance of the test in our population. Results The results of 1374 array CGH analyses of Colombian individuals were referred to the Andean Reference Institute in Colombia (Instituto de Referencia Andino) during a 7-year period (2009–2015). Chromosomal imbalances were detected in 488 cases (35%), whereas 121 cases were classified as nonpathogenic variants, 65 cases (4.7%) were classified as variants of uncertain significance, and 302 cases (22%) were classified as abnormal or pathogenic. The most common findings in the abnormal and/or pathogenic set were deletions, followed by duplications and complex rearrangements. Variants in the carrier status of autosomal recessive diseases were identified as incidental findings in 29 subjects (2%). Conclusions Clinical indications preceding the referral of aCGH in Colombian patients are not standardized and result in unexpected pathogenic variants as well as secondary findings that need careful interpretation. Development of local infrastructure will probably improve the communication between all stakeholders, to ensure accurate clinical diagnoses.
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Affiliation(s)
- Mary García-Acero
- 1Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Fernando Suárez-Obando
- 1Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia.,2Servicio de Genética, Hospital Universitario San Ignacio, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Alberto Gómez-Gutiérrez
- 1Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia
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25
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Lee JS, Hwang H, Kim SY, Kim KJ, Choi JS, Woo MJ, Choi YM, Jun JK, Lim BC, Chae JH. Chromosomal Microarray With Clinical Diagnostic Utility in Children With Developmental Delay or Intellectual Disability. Ann Lab Med 2018; 38:473-480. [PMID: 29797819 PMCID: PMC5973923 DOI: 10.3343/alm.2018.38.5.473] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 12/01/2017] [Accepted: 05/10/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Chromosomal microarray (CMA) testing is a first-tier test for patients with developmental delay, autism, or congenital anomalies. It increases diagnostic yield for patients with developmental delay or intellectual disability. In some countries, including Korea, CMA testing is not yet implemented in clinical practice. We assessed the diagnostic utility of CMA testing in a large cohort of patients with developmental delay or intellectual disability in Korea. METHODS We conducted a genome-wide microarray analysis of 649 consecutive patients with developmental delay or intellectual disability at the Seoul National University Children's Hospital. Medical records were reviewed retrospectively. Pathogenicity of detected copy number variations (CNVs) was evaluated by referencing previous reports or parental testing using FISH or quantitative PCR. RESULTS We found 110 patients to have pathogenic CNVs, which included 100 deletions and 31 duplications of 270 kb to 30 Mb. The diagnostic yield was 16.9%, demonstrating the diagnostic utility of CMA testing in clinic. Parental testing was performed in 66 patients, 86.4% of which carried de novo CNVs. In eight patients, pathogenic CNVs were inherited from healthy parents with a balanced translocation, and genetic counseling was provided to these families. We verified five rarely reported deletions on 2p21p16.3, 3p21.31, 10p11.22, 14q24.2, and 21q22.13. CONCLUSIONS This study demonstrated the clinical utility of CMA testing in the genetic diagnosis of patients with developmental delay or intellectual disability. CMA testing should be included as a clinical diagnostic test for all children with developmental delay or intellectual disability.
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Affiliation(s)
- Jin Sook Lee
- Department of Pediatrics, Department of Genome Medicine and Science, Gil Medical Center, Gachon University College of Medicine, Incheon, Korea
| | - Hee Hwang
- Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Soo Yeon Kim
- Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Ki Joong Kim
- Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jin Sun Choi
- The Institute of Reproductive Medicine and Population, Medical Research Center, Seoul National University College of Medicine, Seoul, Korea
| | - Mi Jung Woo
- The Institute of Reproductive Medicine and Population, Medical Research Center, Seoul National University College of Medicine, Seoul, Korea
| | - Young Min Choi
- The Institute of Reproductive Medicine and Population, Medical Research Center, Seoul National University College of Medicine, Seoul, Korea
- Department of Obstetrics and Gynecology, Seoul National University Hospital, Seoul, Korea
| | - Jong Kwan Jun
- The Institute of Reproductive Medicine and Population, Medical Research Center, Seoul National University College of Medicine, Seoul, Korea
- Department of Obstetrics and Gynecology, Seoul National University Hospital, Seoul, Korea
| | - Byung Chan Lim
- Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
- The Institute of Reproductive Medicine and Population, Medical Research Center, Seoul National University College of Medicine, Seoul, Korea.
| | - Jong Hee Chae
- Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
- The Institute of Reproductive Medicine and Population, Medical Research Center, Seoul National University College of Medicine, Seoul, Korea
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26
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Chromosomal microarray analysis in developmental delay and intellectual disability with comorbid conditions. BMC Med Genomics 2018; 11:49. [PMID: 29793483 PMCID: PMC5968608 DOI: 10.1186/s12920-018-0368-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 05/15/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Developmental delay (DD) and intellectual disability (ID) are frequently associated with a broad spectrum of additional phenotypes. Chromosomal microarray analysis (CMA) has been recommended as a first-tier test for DD/ID in general, whereas the diagnostic yield differs significantly among DD/ID patients with different comorbid conditions. METHODS To investigate the genotype-phenotype correlation, we examined the characteristics of identified pathogenic copy number variations (pCNVs) and compared the diagnostic yields among patient subgroups with different co-occurring conditions. RESULTS This study is a retrospective review of CMA results generated from a mixed cohort of 710 Chinese patients with DD/ID. A total of 247 pCNVs were identified in 201 patients (28%). A large portion of these pCNVs were copy number losses, and the size of copy number losses was generally smaller than gains. The diagnostic yields were significantly higher in subgroups with co-occurring congenital heart defects (55%), facial dysmorphism (39%), microcephaly (34%) or hypotonia (35%), whereas co-occurring conditions of skeletal malformation (26%), brain malformation (24%) or epilepsy (24%) did not alter the yield. In addition, the diagnostic yield nominally correlated with ID severity. CONCLUSION Varied yields exist in DD/ID patients with different phenotypic presentation. The presence of comorbid conditions can be among factors to consider when planning CMA.
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27
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Kim HJ, Park CI, Lim JW, Lee GM, Cho E, Kim HJ. Phenotypic Analysis of Korean Patients with Abnormal Chromosomal Microarray in Patients with Unexplained Developmental Delay/Intellectual Disability. Yonsei Med J 2018; 59:431-437. [PMID: 29611406 PMCID: PMC5889996 DOI: 10.3349/ymj.2018.59.3.431] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 12/13/2017] [Accepted: 01/19/2018] [Indexed: 01/18/2023] Open
Abstract
PURPOSE The present study aimed to investigate chromosomal microarray (CMA) and clinical data in patients with unexplained developmental delay/intellectual disability (DD/ID) accompanying dysmorphism, congenital anomalies, or epilepsy. We also aimed to evaluate phenotypic clues in patients with pathogenic copy number variants (CNVs). MATERIALS AND METHODS We collected clinical and CMA data from patients at Konyang University Hospital between September 2013 and October 2014. We included patients who had taken the CMA test to evaluate the etiology of unexplained DD/ID. RESULTS All of the 50 patients identified had DD/ID. Thirty-nine patients had dysmorphism, 19 patients suffered from epilepsy, and 12 patients had congenital anomalies. Twenty-nine of the 50 patients (58%) showed abnormal results. Eighteen (36%) were considered to have pathogenic CNVs. Dysmorphism (p=0.028) was significantly higher in patients with pathogenic CNVs than in those with normal CMA. Two or more clinical features were presented by 61.9% (13/21) of the patients with normal CMA and by 83.3% (15/18) of the patients with pathogenic CMA. CONCLUSION Dysmorphism can be a phenotypic clue to pathogenic CNVs. Furthermore, pathogenic CNV might be more frequently found if patients have two or more clinical features in addition to DD/ID.
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Affiliation(s)
- Hyo Jeong Kim
- Department of Pediatrics, Gachon University Gil Medical Center, Incheon, Korea
| | - Chang Il Park
- Department of Rehabilitation Medicine, Konyang University College of Medicine, Daejeon, Korea
| | - Jae Woo Lim
- Department of Pediatrics, Konyang University College of Medicine, Daejeon, Korea
| | - Gyung Min Lee
- Department of Pediatrics, Konyang University College of Medicine, Daejeon, Korea
| | | | - Hyon J Kim
- Department of Medical Genetics, Konyang University College of Medicine, Daejeon, Korea.
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28
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Maini I, Ivanovski I, Djuric O, Caraffi SG, Errichiello E, Marinelli M, Franchi F, Bizzarri V, Rosato S, Pollazzon M, Gelmini C, Malacarne M, Fusco C, Gargano G, Bernasconi S, Zuffardi O, Garavelli L. Prematurity, ventricular septal defect and dysmorphisms are independent predictors of pathogenic copy number variants: a retrospective study on array-CGH results and phenotypical features of 293 children with neurodevelopmental disorders and/or multiple congenital anomalies. Ital J Pediatr 2018; 44:34. [PMID: 29523172 PMCID: PMC5845186 DOI: 10.1186/s13052-018-0467-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 02/21/2018] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Since 2010, array-CGH (aCGH) has been the first-tier test in the diagnostic approach of children with neurodevelopmental disorders (NDD) or multiple congenital anomalies (MCA) of unknown origin. Its broad application led to the detection of numerous variants of uncertain clinical significance (VOUS). How to appropriately interpret aCGH results represents a challenge for the clinician. METHOD We present a retrospective study on 293 patients with age range 1 month - 29 years (median 7 years) with NDD and/or MCA and/or dysmorphisms, investigated through aCGH between 2005 and 2016. The aim of the study was to analyze clinical and molecular cytogenetic data in order to identify what elements could be useful to interpret unknown or poorly described aberrations. Comparison of phenotype and cytogenetic characteristics through univariate analysis and multivariate logistic regression was performed. RESULTS Copy number variations (CNVs) with a frequency < 1% were detected in 225 patients of the total sample, while 68 patients presented only variants with higher frequency (heterozygous deletions or amplification) and were considered to have negative aCGH. Proved pathogenic CNVs were detected in 70 patients (20.6%). Delayed psychomotor development, intellectual disability, intrauterine growth retardation (IUGR), prematurity, congenital heart disease, cerebral malformations and dysmorphisms correlated to reported pathogenic CNVs. Prematurity, ventricular septal defect and dysmorphisms remained significant predictors of pathogenic CNVs in the multivariate logistic model whereas abnormal EEG and limb dysmorphisms were mainly detected in the group with likely pathogenic VOUS. A flow-chart regarding the care for patients with NDD and/or MCA and/or dysmorphisms and the interpretation of aCGH has been made on the basis of the data inferred from this study and literature. CONCLUSION Our work contributes to make the investigative process of CNVs more informative and suggests possible directions in aCGH interpretation and phenotype correlation.
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MESH Headings
- Abnormalities, Multiple/diagnosis
- Abnormalities, Multiple/genetics
- Adolescent
- Adult
- Child
- Child, Preschool
- Comparative Genomic Hybridization/methods
- DNA Copy Number Variations
- Facies
- Female
- Genetic Testing
- Heart Septal Defects, Ventricular/diagnosis
- Heart Septal Defects, Ventricular/genetics
- Humans
- Infant
- Infant, Newborn
- Infant, Premature, Diseases/diagnosis
- Infant, Premature, Diseases/genetics
- Male
- Muscular Atrophy/diagnosis
- Muscular Atrophy/genetics
- Neurodevelopmental Disorders/diagnosis
- Neurodevelopmental Disorders/genetics
- Phenotype
- Retrospective Studies
- Young Adult
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Affiliation(s)
- I. Maini
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- Child Neuropsychiatry Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - I. Ivanovski
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - O. Djuric
- Institute of Epidemiology, School of Medicine, University of Belgrade, Belgrade, Serbia
| | - S. G. Caraffi
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - E. Errichiello
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - M. Marinelli
- Laboratory of Genetics, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - F. Franchi
- Laboratory of Genetics, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - V. Bizzarri
- Laboratory of Genetics, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - S. Rosato
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - M. Pollazzon
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - C. Gelmini
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - M. Malacarne
- Division of Medical Genetics, Galliera Hospital, Genoa, Italy
| | - C. Fusco
- Child Neuropsychiatry Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - G. Gargano
- Neonatal Intensive Care Unit (NICU), Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
| | - S. Bernasconi
- Former Director Pediatric Department, University of Parma, Parma, Italy
| | - O. Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - L. Garavelli
- Clinical Genetics Unit, Maternal and Child Health Department, AUSL-IRCCS of Reggio Emilia, Reggio Emilia, Italy
- Santa Maria Nuova Hospital, viale Risorgimento 80, 42123 Reggio Emilia, Italy
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29
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d’Orsi G, Martino T, Palumbo O, Pascarella MG, Palumbo P, Di Claudio MT, Avolio C, Carella M. The epilepsy phenotype in adult patients with intellectual disability and pathogenic copy number variants. Seizure 2017; 53:86-93. [PMID: 29156220 DOI: 10.1016/j.seizure.2017.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/10/2017] [Accepted: 11/13/2017] [Indexed: 12/30/2022] Open
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Caballero Pérez V, López Pisón F, Miramar Gallart M, González Álvarez A, García Jiménez M, García Iñiguez J, Orden Rueda C, Gil Hernández I, Fuertes Rodrigo C, Fernando Martínez R, Rodríguez Valle A, Alcaine Villarroya M. Phenotype in patients with intellectual disability and pathological results in array CGH. NEUROLOGÍA (ENGLISH EDITION) 2017. [DOI: 10.1016/j.nrleng.2016.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Quintela I, Eirís J, Gómez-Lado C, Pérez-Gay L, Dacruz D, Cruz R, Castro-Gago M, Míguez L, Carracedo Á, Barros F. Copy number variation analysis of patients with intellectual disability from North-West Spain. Gene 2017; 626:189-199. [PMID: 28506748 DOI: 10.1016/j.gene.2017.05.032] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/07/2017] [Accepted: 05/11/2017] [Indexed: 10/19/2022]
Abstract
Intellectual disability (ID) is a complex and phenotypically heterogeneous neurodevelopmental disorder characterized by significant deficits in cognitive and adaptive skills, debuting during the developmental period. In the last decade, microarray-based copy number variation (CNV) analysis has been proved as a strategy particularly useful in the discovery of loci and candidate genes associated with these phenotypes and is widely used in the clinics with a diagnostic purpose. In this study, we evaluated the usefulness of two genome-wide high density SNP microarrays -Cytogenetics Whole-Genome 2.7M SNP array (n=126 patients; Group 1) and CytoScan High-Density SNP array (n=447 patients; Group 2)- in the detection of clinically relevant CNVs in a cohort of ID patients from Galicia (NW Spain). In 159 (27.7%) patients, we detected 186 rare exonic chromosomal imbalances, that were grouped into the following classes: Clinically relevant (67/186; 36.0%), of unknown clinical significance (93/186; 50.0%) and benign (26/186; 14.0%). The 67 pathogenic CNVs were identified in 64 patients, which means an overall diagnostic yield of 11.2%. Overall, we confirmed that ID is a genetically heterogeneous condition and emphasized the importance of using genome-wide high density SNP microarrays in the detection of its genetic causes. Additionally, we provided clinical and molecular data of patients with pathogenic or likely pathogenic CNVs and discussed the potential implication in neurodevelopmental disorders of genes located within these variants.
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Affiliation(s)
- Inés Quintela
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro Nacional de Genotipado - Plataforma de Recursos Biomoleculares y Bioinformáticos - Instituto de Salud Carlos III (CeGen-PRB2-ISCIII), Santiago de Compostela, Spain
| | - Jesús Eirís
- Complexo Hospitalario Universitario de Santiago de Compostela, Unidad de Neurología Pediátrica, Departamento de Pediatría, Santiago de Compostela, Spain
| | - Carmen Gómez-Lado
- Complexo Hospitalario Universitario de Santiago de Compostela, Unidad de Neurología Pediátrica, Departamento de Pediatría, Santiago de Compostela, Spain
| | - Laura Pérez-Gay
- Hospital Universitario Lucus Augusti, Unidad de Neurología Pediátrica, Departamento de Pediatría, Lugo, Spain
| | - David Dacruz
- Complexo Hospitalario Universitario de Santiago de Compostela, Unidad de Neurología Pediátrica, Departamento de Pediatría, Santiago de Compostela, Spain
| | - Raquel Cruz
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, CIBER de Enfermedades Raras (CIBERER)-Instituto de Salud Carlos III, Santiago de Compostela, Spain
| | - Manuel Castro-Gago
- Complexo Hospitalario Universitario de Santiago de Compostela, Unidad de Neurología Pediátrica, Departamento de Pediatría, Santiago de Compostela, Spain
| | - Luz Míguez
- Grupo de Medicina Xenómica, CIBERER, Fundación Pública Galega de Medicina Xenómica - SERGAS, Santiago de Compostela, Spain
| | - Ángel Carracedo
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro Nacional de Genotipado - Plataforma de Recursos Biomoleculares y Bioinformáticos - Instituto de Salud Carlos III (CeGen-PRB2-ISCIII), Santiago de Compostela, Spain; Grupo de Medicina Xenómica, CIBERER, Fundación Pública Galega de Medicina Xenómica - SERGAS, Santiago de Compostela, Spain; King Abdulaziz University, Center of Excellence in Genomic Medicine Research, Jeddah, Saudi Arabia
| | - Francisco Barros
- Grupo de Medicina Xenómica, CIBERER, Fundación Pública Galega de Medicina Xenómica - SERGAS, Santiago de Compostela, Spain.
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Sharma P, Gupta N, Chowdhury MR, Sapra S, Ghosh M, Gulati S, Kabra M. Application of chromosomal microarrays in the evaluation of intellectual disability/global developmental delay patients – A study from a tertiary care genetic centre in India. Gene 2016; 590:109-19. [DOI: 10.1016/j.gene.2016.06.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Revised: 06/07/2016] [Accepted: 06/08/2016] [Indexed: 01/21/2023]
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Rosenfeld JA, Patel A. Chromosomal Microarrays: Understanding Genetics of Neurodevelopmental Disorders and Congenital Anomalies. J Pediatr Genet 2016; 6:42-50. [PMID: 28180026 DOI: 10.1055/s-0036-1584306] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 04/23/2016] [Indexed: 01/09/2023]
Abstract
Chromosomal microarray (CMA) testing, used to identify DNA copy number variations (CNVs), has helped advance knowledge about genetics of human neurodevelopmental disease and congenital anomalies. It has aided in discovering new CNV syndromes and uncovering disease genes. It has discovered CNVs that are not fully penetrant and/or cause a spectrum of phenotypes, including intellectual disability, autism, schizophrenia, and dysmorphisms. Such CNVs can pose challenges to genetic counseling. They also have helped increase knowledge of genetic risk factors for neurodevelopmental disease and raised awareness of possible shared etiologies among these variable phenotypes. Advances in CMA technology allow CNV identification at increasingly finer scales, improving detection of pathogenic changes, although these sometimes are difficult to distinguish from normal population variation. This paper confronts some of the challenges uncovered by CMA testing while reviewing advances in genetics and the clinical use of this test that has replaced standard karyotyping in most genetic evaluations.
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Affiliation(s)
- Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States; Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, Texas, United States
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States; Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, Texas, United States
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Phenotype in patients with intellectual disability and pathological results in array CGH. Neurologia 2016; 32:568-578. [PMID: 27157524 DOI: 10.1016/j.nrl.2016.03.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 03/07/2016] [Accepted: 03/08/2016] [Indexed: 02/04/2023] Open
Abstract
INTRODUCTION Global developmental delay (GDD) and intellectual disability (ID) are frequent reasons for consultation in paediatric neurology departments. Nowadays, array comparative genomic hybridisation (array-CGH) is one of the most widely used techniques for diagnosing these disorders. Our purpose was to determine the phenotypic features associated with pathological results in this genetic test. METHODS We conducted a blind study of the epidemiological, clinical, anthropometric, and morphological features of 80 patients with unexplained ID to determine which features were associated with pathological results in array-CGH. RESULTS Pathological results were found in 27.5% of the patients. Factors associated with pathological results in array-CGH were a family history of GDD/ID (OR = 12.1), congenital malformations (OR = 5.33), having more than 3 facial dysmorphic features (OR = 20.9), and hypotonia (OR = 3.25). CONCLUSIONS Our findings are consistent with those reported by other published series. We therefore conclude that the probability of having pathological results in array-CGH increases with the presence of any of the features mentioned above in patients with ID/GDD.
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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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Cappuccio G, Vitiello F, Casertano A, Fontana P, Genesio R, Bruzzese D, Ginocchio VM, Mormile A, Nitsch L, Andria G, Melis D. New insights in the interpretation of array-CGH: autism spectrum disorder and positive family history for intellectual disability predict the detection of pathogenic variants. Ital J Pediatr 2016; 42:39. [PMID: 27072107 PMCID: PMC4830019 DOI: 10.1186/s13052-016-0246-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 03/15/2016] [Indexed: 12/08/2022] Open
Abstract
BACKGROUND Array-CGH (aCGH) is presently used into routine clinical practice for diagnosis of patients with intellectual disability (ID), multiple congenital anomalies (MCA), and autism spectrum disorder (ASD). ACGH could detect small chromosomal imbalances, copy number variations (CNVs), and closely define their size and gene content. ACGH detects pathogenic imbalances in 14-20 % of patients with ID. The aims of this study were: to establish clinical clues potentially associated with pathogenic CNVs and to identify cytogenetic indicators to predict the pathogenicity of the variants of uncertain significance (VOUS) in a large cohort of paediatric patients. METHODS We enrolled 214 patients referred for either: ID, and/or ASD and/or MCA to genetic services at the Federico II University of Naples, Department of Translational Medicine. For each patient we collected clinical and imaging data. All the patients were tested with aCGH or as first-tier test or as part of a wider diagnostic work-up. RESULTS Pathologic data were detected in 65 individuals (30 %) and 46 CNVs revealed a known syndrome. The pathological CNVs were usually deletions showing the highest gene-dosage content. The positive family history for ID/ASD/MCA and ASD were good indicators for detecting pathological chromosomal rearrangements. Other clinical features as eyes anomalies, hearing loss, neurological signs, cutaneous dyscromia and endocrinological problems seem to be potential predictors of pathological CNVs. Among patients carrying VOUS we analyzed genetic features including CNVs size, presence of deletion or duplication, genic density, multiple CNVs, to clinical features. Higher gene density was found in patients affected by ID. This result suggest that higher gene content has more chances to include pathogenic gene involved and causing ID in these patients. CONCLUSION Our study suggest the use of aCGH as first-tier test in patients with neurdevelopmental phenotypes. The inferred results have been used for building a flow-chart to be applied for children with ID.
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Affiliation(s)
- Gerarda Cappuccio
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Via Sergio Pansini 5, 80131, Naples, Italy
| | - Francesco Vitiello
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Via Sergio Pansini 5, 80131, Naples, Italy
| | - Alberto Casertano
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Via Sergio Pansini 5, 80131, Naples, Italy
| | - Paolo Fontana
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Via Sergio Pansini 5, 80131, Naples, Italy
| | - Rita Genesio
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, Naples, Italy
| | - Dario Bruzzese
- Preventive Medical Sciences, Federico II University, Naples, Italy
| | | | - Angela Mormile
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, Naples, Italy
| | - Lucio Nitsch
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, Naples, Italy
| | - Generoso Andria
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Via Sergio Pansini 5, 80131, Naples, Italy
| | - Daniela Melis
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Via Sergio Pansini 5, 80131, Naples, Italy.
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Neuropädiatrische Differenzialdiagnostik der Mikrozephalie im Kindesalter. MED GENET-BERLIN 2016. [DOI: 10.1007/s11825-016-0081-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Zusammenfassung
Eine Mikrozephalie betrifft 2–3 % der Bevölkerung und geht oftmals mit einer Intelligenzminderung einher. Die zugrunde liegende Reduktion des Gehirnvolumens kann sowohl durch exogene Faktoren als auch durch genetische Ursachen bedingt sein. Problematisch sind sowohl die uneinheitliche Klassifikation als auch die große Heterogenität der hinter dem klinischen Zeichen Mikrozephalie stehenden Erkrankungen. Im vorliegenden Artikel stellen wir unseren Vorschlag für die diagnostische Herangehensweise an ein Kind mit Mikrozephalie aus neuropädiatrischer Sicht vor.
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Hang XY, Shang AJ, Zhao QJ, Bai SC, Cheng C, Tao BZ, Wang LK, Liang S, Yin L. Association between chromosomal aberration of COX8C and tethered spinal cord syndrome: array-based comparative genomic hybridization analysis. Neural Regen Res 2016; 11:1333-8. [PMID: 27651783 PMCID: PMC5020834 DOI: 10.4103/1673-5374.189200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Copy number variations have been found in patients with neural tube abnormalities. In this study, we performed genome-wide screening using high-resolution array-based comparative genomic hybridization in three children with tethered spinal cord syndrome and two healthy parents. Of eight copy number variations, four were non-polymorphic. These non-polymorphic copy number variations were associated with Angelman and Prader-Willi syndromes, and microcephaly. Gene function enrichment analysis revealed that COX8C, a gene associated with metabolic disorders of the nervous system, was located in the copy number variation region of Patient 1. Our results indicate that array-based comparative genomic hybridization can be used to diagnose tethered spinal cord syndrome. Our results may help determine the pathogenesis of tethered spinal cord syndrome and prevent occurrence of this disease.
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Edwards M, Brescianini S, Allgood C, Freelander M, Dunstan R, Patradoon-Ho P, Chin R, Morgan L, Pervez T, Legendre M, Burgess T, Amselem S, Whitehall J. Syndrome diagnosis with single-nucleotide polymorphism (SNP) microarray. J Paediatr Child Health 2016; 52:85-9. [PMID: 26228624 DOI: 10.1111/jpc.12981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/28/2015] [Indexed: 11/26/2022]
Affiliation(s)
- Matthew Edwards
- Department of Clinical Genetics, Campbelltown Hospital, Campbelltown, New South Wales, Australia.,Department of Paediatrics, University of Western Sydney School of Medicine, Sydney, New South Wales, Australia
| | - Sally Brescianini
- Department of Clinical Genetics, Campbelltown Hospital, Campbelltown, New South Wales, Australia
| | - Catherine Allgood
- Department of Paediatrics, University of Western Sydney School of Medicine, Sydney, New South Wales, Australia
| | - Michael Freelander
- Department of Paediatrics, University of Western Sydney School of Medicine, Sydney, New South Wales, Australia
| | - Richard Dunstan
- Department of Paediatrics, University of Western Sydney School of Medicine, Sydney, New South Wales, Australia
| | - Patrick Patradoon-Ho
- Department of Paediatrics, University of Western Sydney School of Medicine, Sydney, New South Wales, Australia.,Department of Paediatrics, Mount Druitt Hospital, Mount Druitt, New South Wales, Australia
| | - Raymond Chin
- Department of Paediatrics, University of Western Sydney School of Medicine, Sydney, New South Wales, Australia
| | - Lucy Morgan
- Department of Respiratory Medicine, Concord Hospital, Sydney, New South Wales, Australia
| | - Tasnuba Pervez
- Department of Paediatrics, University of Western Sydney School of Medicine, Sydney, New South Wales, Australia
| | - Marie Legendre
- U.F. de Génétique Moléculaire, Hôpital Armand Trousseau, Paris, France
| | - Trent Burgess
- Molecular Cytogenetics, Victorian Clinical Genetics Services, Melbourne, Victoria, Australia
| | - Serge Amselem
- Service de Génétique et d'Embryologie Médicales, UMR_S933 INSERM/UPMC, Paris, France
| | - John Whitehall
- Department of Paediatrics, University of Western Sydney School of Medicine, Sydney, New South Wales, Australia
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Carreira IM, Ferreira SI, Matoso E, Pires LM, Ferrão J, Jardim A, Mascarenhas A, Pinto M, Lavoura N, Pais C, Paiva P, Simões L, Caramelo F, Ramos L, Venâncio M, Ramos F, Beleza A, Sá J, Saraiva J, de Melo JB. Copy number variants prioritization after array-CGH analysis - a cohort of 1000 patients. Mol Cytogenet 2015; 8:103. [PMID: 26719768 PMCID: PMC4696247 DOI: 10.1186/s13039-015-0202-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 12/17/2015] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Array-based comparative genomic hybridization has been assumed to be the first genetic test offered to detect genomic imbalances in patients with unexplained intellectual disability with or without dysmorphisms, multiple congenital anomalies, learning difficulties and autism spectrum disorders. Our study contributes to the genotype/phenotype correlation with the delineation of laboratory criteria which help to classify the different copy number variants (CNVs) detected. We clustered our findings into five classes ranging from an imbalance detected in a microdeletion/duplication syndrome region (class I) to imbalances that had previously been reported in normal subjects in the Database of Genomic Variants (DGV) and thus considered common variants (class IV). RESULTS All the analyzed 1000 patients had at least one CNV independently of its clinical significance. Most of them, as expected, were alterations already reported in the DGV for normal individuals (class IV) or without known coding genes (class III-B). In approximately 14 % of the patients an imbalance involving known coding genes, but with partially overlapping or low frequency of CNVs described in the DGV was identified (class IIIA). In 10.4 % of the patients a pathogenic CNV that explained the phenotype was identified consisting of: 40 class I imbalances, 44 class II de novo imbalances and 21 class II X-chromosome imbalances in male patients. In 20 % of the patients a familial pathogenic or potentially pathogenic CNV, consisting of inherited class II imbalances, was identified that implied a family evaluation by the clinical geneticists. CONCLUSIONS As this interpretation can be sometimes difficult, particularly if it is not possible to study the parents, using the proposed classification we were able to prioritize the multiple imbalances that are identified in each patient without immediately having to classify them as pathogenic or benign.
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Affiliation(s)
- Isabel Marques Carreira
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal ; CIMAGO - Centro de Investigação em Meio Ambiente, Genética e Oncobiologia, Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; CNC, IBILI - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - Susana Isabel Ferreira
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Eunice Matoso
- CIMAGO - Centro de Investigação em Meio Ambiente, Genética e Oncobiologia, Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Laboratório de Citogenética, Hospital Pediátrico de Coimbra, Coimbra, Portugal
| | - Luís Miguel Pires
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - José Ferrão
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Ana Jardim
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Alexandra Mascarenhas
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Marta Pinto
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Nuno Lavoura
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Cláudia Pais
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Patrícia Paiva
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Lúcia Simões
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal
| | - Francisco Caramelo
- Laboratório de Bioestatística e Informática Médica, IBILI - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - Lina Ramos
- Laboratório de Bioestatística e Informática Médica, IBILI - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - Margarida Venâncio
- Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Serviço de Genética Médica, Hospital Pediátrico - Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Fabiana Ramos
- Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Serviço de Genética Médica, Hospital Pediátrico - Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Ana Beleza
- Serviço de Genética Médica, Hospital Pediátrico - Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Joaquim Sá
- Serviço de Genética Médica, Hospital Pediátrico - Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Jorge Saraiva
- Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Serviço de Genética Médica, Hospital Pediátrico - Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Joana Barbosa de Melo
- Laboratório de Citogenética e Genómica - Faculdade de Medicina, Universidade de Coimbra, Pólo Ciências da Saúde, Sub-Unidade 1 - Piso 2, Azinhaga de Santa Comba, 3000-354 Coimbra, Portugal ; CIMAGO - Centro de Investigação em Meio Ambiente, Genética e Oncobiologia, Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal ; CNC, IBILI - Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
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Kumar R, Corbett MA, Van Bon BWM, Gardner A, Woenig JA, Jolly LA, Douglas E, Friend K, Tan C, Van Esch H, Holvoet M, Raynaud M, Field M, Leffler M, Budny B, Wisniewska M, Badura-Stronka M, Latos-Bieleńska A, Batanian J, Rosenfeld JA, Basel-Vanagaite L, Jensen C, Bienek M, Froyen G, Ullmann R, Hu H, Love MI, Haas SA, Stankiewicz P, Cheung SW, Baxendale A, Nicholl J, Thompson EM, Haan E, Kalscheuer VM, Gecz J. Increased STAG2 dosage defines a novel cohesinopathy with intellectual disability and behavioral problems. Hum Mol Genet 2015; 24:7171-81. [PMID: 26443594 DOI: 10.1093/hmg/ddv414] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/28/2015] [Indexed: 11/13/2022] Open
Abstract
Next generation genomic technologies have made a significant contribution to the understanding of the genetic architecture of human neurodevelopmental disorders. Copy number variants (CNVs) play an important role in the genetics of intellectual disability (ID). For many CNVs, and copy number gains in particular, the responsible dosage-sensitive gene(s) have been hard to identify. We have collected 18 different interstitial microduplications and 1 microtriplication of Xq25. There were 15 affected individuals from 6 different families and 13 singleton cases, 28 affected males in total. The critical overlapping region involved the STAG2 gene, which codes for a subunit of the cohesin complex that regulates cohesion of sister chromatids and gene transcription. We demonstrate that STAG2 is the dosage-sensitive gene within these CNVs, as gains of STAG2 mRNA and protein dysregulate disease-relevant neuronal gene networks in cells derived from affected individuals. We also show that STAG2 gains result in increased expression of OPHN1, a known X-chromosome ID gene. Overall, we define a novel cohesinopathy due to copy number gain of Xq25 and STAG2 in particular.
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Affiliation(s)
- Raman Kumar
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Mark A Corbett
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | | | - Alison Gardner
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Joshua A Woenig
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Lachlan A Jolly
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Evelyn Douglas
- Genetics and Molecular Pathology, SA Pathology, North Adelaide, SA 5006, Australia
| | - Kathryn Friend
- Genetics and Molecular Pathology, SA Pathology, North Adelaide, SA 5006, Australia
| | - Chuan Tan
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Maureen Holvoet
- Center for Human Genetics, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Martine Raynaud
- Centre Hospitalier Régional Universitaire, Service de Génétique, 37000 Tours, France
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Melanie Leffler
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Bartłomiej Budny
- Department of Endocrinology, Metabolism and Internal Diseases and
| | - Marzena Wisniewska
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan 60-355, Poland
| | | | - Anna Latos-Bieleńska
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan 60-355, Poland
| | | | - Jill A Rosenfeld
- Signature Genomic Laboratories, Spokane, WA 99207, USA, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lina Basel-Vanagaite
- Raphael Recanati Genetic Institute and Felsenstein Medical Research Center, Rabin Medical Center, Beilinson Campus, Petah Tikva 49100, Israel
| | | | | | - Guy Froyen
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium and
| | - Reinhard Ullmann
- Department of Human Molecular Genetics and, Bundeswehr Institute of Radiobiology, 80937 Munich, Germany
| | - Hao Hu
- Department of Human Molecular Genetics and
| | - Michael I Love
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anne Baxendale
- South Australian Clinical Genetics Service, SA Pathology, North Adelaide, SA 5006, Australia
| | - Jillian Nicholl
- Genetics and Molecular Pathology, SA Pathology, North Adelaide, SA 5006, Australia
| | - Elizabeth M Thompson
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia, South Australian Clinical Genetics Service, SA Pathology, North Adelaide, SA 5006, Australia
| | - Eric Haan
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia, South Australian Clinical Genetics Service, SA Pathology, North Adelaide, SA 5006, Australia
| | | | - Jozef Gecz
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia,
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Lingen M, Albers L, Borchers M, Haass S, Gärtner J, Schröder S, Goldbeck L, von Kries R, Brockmann K, Zirn B. Obtaining a genetic diagnosis in a child with disability: impact on parental quality of life. Clin Genet 2015; 89:258-66. [PMID: 26084449 DOI: 10.1111/cge.12629] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/16/2015] [Accepted: 06/16/2015] [Indexed: 12/14/2022]
Abstract
Recent progress in genetic testing has facilitated obtaining an etiologic diagnosis in children with developmental delay/intellectual disability (DD/ID) or multiple congenital anomalies (MCA) or both. Little is known about the benefits of diagnostic elucidation for affected families. We studied the impact of a genetic diagnosis on parental quality of life (QoL) using a validated semiquantitative questionnaire in families with a disabled child investigated by array-based comparative genomic hybridization (aCGH). We received completed questionnaires from 95 mothers and 76 fathers of 99 families. We used multivariate analysis for adjustment of potential confounders. Taken all 99 families together, maternal QoL score (percentile rank scale 51.05) was significantly lower than fathers' QoL (61.83, p = 0.01). Maternal QoL score was 20.17 [95% CI (5.49; 34.82)] percentile rank scales higher in mothers of children with diagnostic (n = 34) aCGH as opposed to mothers of children with inconclusive (n = 65) aCGH (Hedges' g = 0.71). Comparison of these QoL scores with retrospectively recalled QoL before aCGH revealed an increase of maternal QoL after diagnostic clarification. Our results indicate a benefit for maternal QoL if a genetic test, here aCGH, succeeds to clarify the etiologic diagnosis in a disabled child.
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Affiliation(s)
- M Lingen
- Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Paediatrics and Adolescent Medicine, University of Göttingen, Göttingen, Germany
| | - L Albers
- Institute of Social Paediatrics and Adolescent Medicine, Division of Epidemiology, Ludwig Maximilians University Munich, Munich, Germany
| | - M Borchers
- Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Paediatrics and Adolescent Medicine, University of Göttingen, Göttingen, Germany
| | - S Haass
- Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Paediatrics and Adolescent Medicine, University of Göttingen, Göttingen, Germany
| | - J Gärtner
- Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Paediatrics and Adolescent Medicine, University of Göttingen, Göttingen, Germany
| | - S Schröder
- Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Paediatrics and Adolescent Medicine, University of Göttingen, Göttingen, Germany
| | - L Goldbeck
- Department of Child and Adolescent Psychiatry/Psychotherapy, University Ulm, Ulm, Germany
| | - R von Kries
- Institute of Social Paediatrics and Adolescent Medicine, Division of Epidemiology, Ludwig Maximilians University Munich, Munich, Germany
| | - K Brockmann
- Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Paediatrics and Adolescent Medicine, University of Göttingen, Göttingen, Germany
| | - B Zirn
- Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Paediatrics and Adolescent Medicine, University of Göttingen, Göttingen, Germany.,Genetikum, Genetic Counselling and Diagnostics, Stuttgart, Germany
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Contribution of copy number variants (CNVs) to congenital, unexplained intellectual and developmental disabilities in Lebanese patients. Mol Cytogenet 2015; 8:26. [PMID: 25922617 PMCID: PMC4411788 DOI: 10.1186/s13039-015-0130-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/23/2015] [Indexed: 11/10/2022] Open
Abstract
Background Chromosomal microarray analysis (CMA) is currently the most widely adopted clinical test for patients with unexplained intellectual disability (ID), developmental delay (DD), and congenital anomalies. Its use has revealed the capacity to detect copy number variants (CNVs), as well as regions of homozygosity, that, based on their distribution on chromosomes, indicate uniparental disomy or parental consanguinity that is suggestive of an increased probability of recessive disease. Results We screened 149 Lebanese probands with ID/DD and 99 healthy controls using the Affymetrix Cyto 2.7 M and SNP6.0 arrays. We report all identified CNVs, which we divided into groups. Pathogenic CNVs were identified in 12.1% of the patients. We review the genotype/phenotype correlation in a patient with a 1q44 microdeletion and refine the minimal critical regions responsible for the 10q26 and 16q monosomy syndromes. Several likely causative CNVs were also detected, including new homozygous microdeletions (9p23p24.1, 10q25.2, and 8p23.1) in 3 patients born to consanguineous parents, involving potential candidate genes. However, the clinical interpretation of several other CNVs remains uncertain, including a microdeletion affecting ATRNL1. This CNV of unknown significance was inherited from the patient’s unaffected-mother; therefore, additional ethnically matched controls must be screened to obtain enough evidence for classification of this CNV. Conclusion This study has provided supporting evidence that whole-genome analysis is a powerful method for uncovering chromosomal imbalances, regardless of consanguinity in the parents of patients and despite the challenge presented by analyzing some CNVs. Electronic supplementary material The online version of this article (doi:10.1186/s13039-015-0130-y) contains supplementary material, which is available to authorized users.
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Al-Qattan SM, Wakil SM, Anazi S, Alazami AM, Patel N, Shaheen R, Shamseldin HE, Hagos ST, AlDossari HM, Salih MA, El Khashab HY, Kentab AY, AlNasser MN, Bashiri FA, Kaya N, Hashem MO, Alkuraya FS. The clinical utility of molecular karyotyping for neurocognitive phenotypes in a consanguineous population. Genet Med 2014; 17:719-25. [PMID: 25503496 DOI: 10.1038/gim.2014.184] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 11/11/2014] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Molecular karyotyping has rapidly become the test of choice in patients with neurocognitive phenotypes, but studies of its clinical utility have largely been limited to outbred populations. In consanguineous populations, single-gene recessive causes of neurocognitive phenotypes are expected to account for a relatively high percentage of cases, thus diminishing the yield of molecular karyotyping. The aim of this study was to test the clinical yield of molecular karyotyping in the highly consanguineous population of Saudi Arabia. METHODS We have reviewed the data of 584 patients with neurocognitive phenotypes (mainly referred from pediatric neurology clinics), all evaluated by a single clinical geneticist. RESULTS At least 21% of tested cases had chromosomal aberrations that are likely disease-causing. These changes include both known and novel deletion syndromes. The higher yield of molecular karyotyping in this study as compared with the commonly cited 11% can be explained by our ability to efficiently identify single-gene disorders, thus enriching the samples that underwent molecular karyotyping for de novo chromosomal aberrations. We show that we were able to identify a causal mutation in 37% of cases on a clinical basis with the help of autozygome analysis, thus bypassing the need for molecular karyotyping. CONCLUSION Our study confirms the clinical utility of molecular karyotyping even in highly consanguineous populations.
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Affiliation(s)
- Sarah M Al-Qattan
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Salma M Wakil
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Shamsa Anazi
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Anas M Alazami
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nisha Patel
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ranad Shaheen
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Samya T Hagos
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Haya M AlDossari
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mustafa A Salih
- Division of Pediatric Neurology, Department of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Heba Y El Khashab
- Division of Pediatric Neurology, Department of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Pediatrics, Children Hospital, Ain Shams University, Cairo, Egypt
| | - Amal Y Kentab
- Division of Pediatric Neurology, Department of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed N AlNasser
- Division of Pediatric Neurology, Department of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Fahad A Bashiri
- Division of Pediatric Neurology, Department of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Namik Kaya
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais O Hashem
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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45
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Asadollahi R, Oneda B, Joset P, Azzarello-Burri S, Bartholdi D, Steindl K, Vincent M, Cobilanschi J, Sticht H, Baldinger R, Reissmann R, Sudholt I, Thiel CT, Ekici AB, Reis A, Bijlsma EK, Andrieux J, Dieux A, FitzPatrick D, Ritter S, Baumer A, Latal B, Plecko B, Jenni OG, Rauch A. The clinical significance of small copy number variants in neurodevelopmental disorders. J Med Genet 2014; 51:677-88. [PMID: 25106414 PMCID: PMC4173859 DOI: 10.1136/jmedgenet-2014-102588] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
BACKGROUND Despite abundant evidence for pathogenicity of large copy number variants (CNVs) in neurodevelopmental disorders (NDDs), the individual significance of genome-wide rare CNVs <500 kb has not been well elucidated in a clinical context. METHODS By high-resolution chromosomal microarray analysis, we investigated the clinical significance of all rare non-polymorphic exonic CNVs sizing 1-500 kb in a cohort of 714 patients with undiagnosed NDDs. RESULTS We detected 96 rare CNVs <500 kb affecting coding regions, of which 58 (60.4%) were confirmed. 6 of 14 confirmed de novo, one of two homozygous and four heterozygous inherited CNVs affected the known microdeletion regions 17q21.31, 16p11.2 and 2p21 or OMIM morbid genes (CASK, CREBBP, PAFAH1B1, SATB2; AUTS2, NRXN3, GRM8). Two further de novo CNVs affecting single genes (MED13L, CTNND2) were instrumental in delineating novel recurrent conditions. For the first time, we here report exonic deletions of CTNND2 causing low normal IQ with learning difficulties with or without autism spectrum disorder. Additionally, we discovered a homozygous out-of-frame deletion of ACOT7 associated with features comparable to the published mouse model. In total, 24.1% of the confirmed small CNVs were categorised as pathogenic or likely pathogenic (median size 130 kb), 17.2% as likely benign, 3.4% represented incidental findings and 55.2% remained unclear. CONCLUSIONS These results verify the diagnostic relevance of genome-wide rare CNVs <500 kb, which were found pathogenic in ∼2% (14/714) of cases (1.1% de novo, 0.3% homozygous, 0.6% inherited) and highlight their inherent potential for discovery of new conditions.
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Affiliation(s)
- Reza Asadollahi
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | | | - Deborah Bartholdi
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Marie Vincent
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Joana Cobilanschi
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Heinrich Sticht
- Institute of Biochemistry, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Rosa Baldinger
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Regina Reissmann
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Irene Sudholt
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Christian T Thiel
- Institute of Human Genetics, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, University of Erlangen-Nuremberg, Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Joris Andrieux
- Institut de Génétique Médicale, Hôpital Jeanne de Flandre, CHRU de Lille, Lille, France
| | - Anne Dieux
- Clinique de Génétique Guy Fontaine, Hôpital Jeanne de Flandre, CHRU de Lille, Lille, France
| | - David FitzPatrick
- MRC Human Genetics Unit, MRC Institute for Genetic and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Susanne Ritter
- Child Development Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Alessandra Baumer
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Beatrice Latal
- Child Development Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Barbara Plecko
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, Switzerland
| | - Oskar G Jenni
- Child Development Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
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von der Hagen M, Pivarcsi M, Liebe J, von Bernuth H, Didonato N, Hennermann JB, Bührer C, Wieczorek D, Kaindl AM. Diagnostic approach to microcephaly in childhood: a two-center study and review of the literature. Dev Med Child Neurol 2014; 56:732-41. [PMID: 24617602 DOI: 10.1111/dmcn.12425] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/15/2014] [Indexed: 12/12/2022]
Abstract
AIM The aim of this study was to assess the diagnostic approach to microcephaly in childhood and to identify the prevalence of the various underlying causes/disease entities. METHOD We conducted a retrospective study on a cohort of 680 children with microcephaly (399 males, 281 females; mean age at presentation 7-8mo, range 1mo-5y) from patients presenting to Charité - University Medicine Berlin (n=474) and University Hospital Dresden (n=206). Patient discharge letters were searched electronically to identify cases of microcephaly, and then the medical records of these patients were used to analyze parameters for distribution. RESULTS The putative aetiology for microcephaly was ascertained in 59% of all patients, leaving 41% without a definite diagnosis. In the cohort of pathogenetically defined microcephaly, genetic causes were identified in about half of the patients, perinatal brain damage accounted for 45%, and postnatal brain damage for 3% of the cases. Microcephaly was associated with intellectual impairment in 65% of participants, epilepsy was diagnosed in 43%, and ophthalmological disorders were found in 30%. Brain magnetic resonance imaging revealed abnormalities in 76% of participants. INTERPRETATION Microcephaly remains a poorly defined condition, and a uniform diagnostic approach is urgently needed. A definite aetiological diagnosis is important in order to predict the prognosis and offer genetic counselling. Identifying gene mutations as causes of microcephaly increases our knowledge of brain development and the clinical spectrum of microcephaly. We therefore propose a standardized initial diagnostic approach to microcephaly.
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Affiliation(s)
- Maja von der Hagen
- Abteilung Neuropaediatrie, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
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Qiao Y, Mercier E, Dastan J, Hurlburt J, McGillivray B, Chudley AE, Farrell S, Bernier FP, Lewis MS, Pavlidis P, Rajcan-Separovic E. Copy number variants (CNVs) analysis in a deeply phenotyped cohort of individuals with intellectual disability (ID). BMC MEDICAL GENETICS 2014; 15:82. [PMID: 25030379 PMCID: PMC4107469 DOI: 10.1186/1471-2350-15-82] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 07/03/2014] [Indexed: 01/13/2023]
Abstract
Background DNA copy number variants (CNVs) are found in 15% of subjects with ID but their association with phenotypic abnormalities has been predominantly studied in smaller cohorts of subjects with detailed yet non-systematically categorized phenotypes, or larger cohorts (thousands of cases) with smaller number of generalized phenotypes. Methods We evaluated the association of de novo, familial and common CNVs detected in 78 ID subjects with phenotypic abnormalities classified using the Winter-Baraitser Dysmorphology Database (WBDD) (formerly the London Dysmorphology Database). Terminology for 34 primary (coarse) and 169 secondary (fine) phenotype features were used to categorize the abnormal phenotypes and determine the prevalence of each phenotype in patients grouped by the type of CNV they had. Results In our cohort more than 50% of cases had abnormalities in primary categories related to head (cranium, forehead, ears, eye globes, eye associated structures, nose) as well as hands and feet. The median number of primary and secondary abnormalities was 12 and 18 per subject, respectively, indicating that the cohort consisted of subjects with a high number of phenotypic abnormalities (median De Vries score for the cohort was 5). The prevalence of each phenotypic abnormality was comparable in patients with de novo or familial CNVs in comparison to those with only common CNVs, although a trend for increased frequency of cranial and forehead abnormalities was noted in subjects with rare de novo and familial CNVs. Two clusters of subjects were identified based on the prevalence of each fine phenotypic feature, with an average of 28.3 and 13.5 abnormal phenotypes/subject in the two clusters respectively (P < 0.05). Conclusions Our study is a rare example of using standardized, deep morphologic phenotype clustering with phenotype/CNV correlation in a cohort of subjects with ID. The composition of the cohort inevitably influences the phenotype/genotype association, and our studies show that the influence of the de novo CNVs on the phenotype is less obvious in cohorts consisting of subjects with a high number of phenotypic abnormalities. The outcome of phenotype/genotype analysis also depends on the choice of phenotypes assessed and standardized phenotyping is required to minimize variability.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Me Suzanne Lewis
- Department of Pathology (Cytogenetics), BC Child and Family Research Institute, University of British Columbia (UBC), 950 West 28th, Room 3060, Vancouver, BC V5Z 4H4, Canada.
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Caramaschi E, Stanghellini I, Magini P, Giuffrida MG, Scullin S, Giuva T, Bergonzini P, Guerra A, Paolucci P, Percesepe A. Predictive diagnostic value for the clinical features accompanying intellectual disability in children with pathogenic copy number variations: a multivariate analysis. Ital J Pediatr 2014; 40:39. [PMID: 24775911 PMCID: PMC4014206 DOI: 10.1186/1824-7288-40-39] [Citation(s) in RCA: 9] [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: 11/21/2013] [Accepted: 04/14/2014] [Indexed: 11/10/2022] Open
Abstract
Background Array comparative genomic hybridization (a-CGH) has become the first-tier investigation in patients with unexplained developmental delay/intellectual disability (DD/ID). Although the costs are progressively decreasing, a-CGH is still an expensive and labour-intensive technique: for this reason a definition of the categories of patients that can benefit the most of the analysis is needed. Aim of the study was to retrospectively analyze the clinical features of children with DD/ID attending the outpatient clinic of the Mother & Child Department of the University Hospital of Modena subjected to a-CGH, to verify by uni- and multivariate analysis the independent predictors of pathogenic CNVs. Methods 116 patients were included in the study. Data relative to the CNVs and to the patients’ clinical features were analyzed for genotype/phenotype correlations. Results and conclusions 27 patients (23.3%) presented pathogenic CNVs (21 deletions, 3 duplications and 3 cases with both duplications and deletions). Univariate analysis showed a significant association of the pathogenic CNVs with the early onset of symptoms (before 1 yr of age) and the presence of malformations and dysmorphisms. Logistic regression analysis showed a significant independent predictive value for diagnosing a pathogenic CNV for malformations (P = 0.002) and dysmorphisms (P = 0.023), suggesting that those features should address a-CGH analysis as a high-priority test for diagnosis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Antonio Percesepe
- Medical Genetics Unit, Department of Mother & Child, University Hospital of Modena, Via del Pozzo, 71, 41124 Modena, Italy.
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Duga B, Czakó M, Hadzsiev K, Komlósi K, Sümegi K, Kisfali P, Kosztolányi G, Melegh B. [Identifying rare genomic disorders with array comparative genomic hybridization in Hungary]. Orv Hetil 2014; 155:358-61. [PMID: 24566700 DOI: 10.1556/oh.2014.29825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
INTRODUCTION In the past decade the study of genomic disorders has received more interest. Array comparative genome hybridization is a widely spread diagnostic method in the research of genomic disorders. This method was implemented in the laboratory of the authors in 2012. AIM This molecular cytogenetic method was first used to examine patients with complex developmental disorders in whom no genetic background was identified by traditional methods. METHOD The authors complemented traditional diagnostic methods with array comparative genome hybridization, which has not been used in routine diagnostics in Hungary so far. RESULTS Using this novel method the authors were able to identify genomic alterations in 7 out of 18 patients with complex developmental disorders. They found de novo alterations in 6 out of 7 patients, which were most likely causative in the development of the phenotype, while in one case they detected a familial genomic alteration. This method helped the authors to determine the breakpoint of genomic variation in their patients and delineate the affected genes contributing to the phenotype. CONCLUSIONS These results call attention to the usefulness of next generation diagnostic methods available in the laboratory of the authors.
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Affiliation(s)
- Balázs Duga
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
| | - Márta Czakó
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
| | - Kinga Hadzsiev
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
| | - Katalin Komlósi
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
| | - Katalin Sümegi
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
| | - Péter Kisfali
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
| | - György Kosztolányi
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
| | - Béla Melegh
- Pécsi Tudományegyetem, Általános Orvostudományi Kar, Klinikai Központ Orvosi Genetikai Intézet Pécs Szigeti út 12. 7624 Pécsi Tudományegyetem Szentágothai János Kutatóközpont Pécs
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Considering specific clinical features as evidence of pathogenic copy number variants. J Appl Genet 2014; 55:189-96. [PMID: 24535828 DOI: 10.1007/s13353-014-0197-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 01/24/2014] [Accepted: 01/29/2014] [Indexed: 01/29/2023]
Abstract
Since the introduction of high-resolution microarray technologies, it has become apparent that structural chromosomal rearrangements can lead to a wide variety of clinical manifestations, including developmental delay/intellectual disability (DD/ID). It has been shown previously that the diagnostic yield of genome-wide array-based identification of submicroscopic alterations in patients with ID varies widely and depends on the patient selection criteria. More attempts have recently been made to define the phenotypic clues of pathogenic copy number variants (CNVs). The aim of this study was to investigate a well-phenotyped cohort of patients with DD/ID and determine whether certain clinical features may serve as indicators for pathogenic CNVs. A retrospective analysis was conducted for patients with DD/ID (n = 211) who were tested using genome-wide chromosomal microarray technologies and a review of the clinical data was performed. Pathogenic CNVs were detected in 29 patients. In comparison with individuals who had normal molecular karyotyping results (n = 182), malformations of the musculoskeletal system; congenital malformations of the CNS (particularly hydrocephalus and congenital malformations of the corpus callosum); minor anomalies of the eye, face, and neck subgroup (particularly downward-slanting palpebral fissures, minor anomalies of the ear, and micrognathia); brachydactyly; and umbilical hernia were more common in patients with chromosomal alterations. A multivariate logistic regression analysis allowed the identification of three independent pathogenic CNV predictors: congenital malformations of the corpus callosum, minor anomalies of the ear, and brachydactyly. Insights into the chromosomal phenotype may help to increase the diagnostic yield of microarray technologies and sharpen the distinction between chromosomal alterations and other conditions.
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