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Porubsky D, Eichler EE. A 25-year odyssey of genomic technology advances and structural variant discovery. Cell 2024; 187:1024-1037. [PMID: 38290514 DOI: 10.1016/j.cell.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 02/01/2024]
Abstract
This perspective focuses on advances in genome technology over the last 25 years and their impact on germline variant discovery within the field of human genetics. The field has witnessed tremendous technological advances from microarrays to short-read sequencing and now long-read sequencing. Each technology has provided genome-wide access to different classes of human genetic variation. We are now on the verge of comprehensive variant detection of all forms of variation for the first time with a single assay. We predict that this transition will further transform our understanding of human health and biology and, more importantly, provide novel insights into the dynamic mutational processes shaping our genomes.
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Affiliation(s)
- David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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2
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Martins M, Oliveira AR, Martins S, Vieira JP, Perdigão P, Fernandes AR, de Almeida LP, Palma PJ, Sequeira DB, Santos JMM, Duque F, Oliveira G, Cardoso AL, Peça J, Seabra CM. A Novel Genetic Variant in MBD5 Associated with Severe Epilepsy and Intellectual Disability: Potential Implications on Neural Primary Cilia. Int J Mol Sci 2023; 24:12603. [PMID: 37628781 PMCID: PMC10454663 DOI: 10.3390/ijms241612603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/04/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023] Open
Abstract
Disruptions in the MBD5 gene have been linked with an array of clinical features such as global developmental delay, intellectual disability, autistic-like symptoms, and seizures, through unclear mechanisms. MBD5 haploinsufficiency has been associated with the disruption of primary cilium-related processes during early cortical development, and this has been reported in many neurodevelopmental disorders. In this study, we describe the clinical history of a 12-year-old child harboring a novel MBD5 rare variant and presenting psychomotor delay and seizures. To investigate the impact of MBD5 haploinsufficiency on neural primary cilia, we established a novel patient-derived cell line and used CRISPR-Cas9 technology to create an isogenic control. The patient-derived neural progenitor cells revealed a decrease in the length of primary cilia and in the total number of ciliated cells. This study paves the way to understanding the impact of MBD5 haploinsufficiency in brain development through its potential impact on neural primary cilia.
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Affiliation(s)
- Mariana Martins
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Ana Rafaela Oliveira
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Solange Martins
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - José Pedro Vieira
- Neuropediatrics Unit, Central Lisbon Hospital Center, 1169-045 Lisbon, Portugal
| | - Pedro Perdigão
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Ana Rita Fernandes
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Luís Pereira de Almeida
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Paulo Jorge Palma
- Institute of Endodontics, Faculty of Medicine, University of Coimbra, 3000-075 Coimbra, Portugal
- Center for Innovation and Research in Oral Sciences (CIROS), Faculty of Medicine, University of Coimbra, 3000-075 Coimbra, Portugal
| | - Diana Bela Sequeira
- Institute of Endodontics, Faculty of Medicine, University of Coimbra, 3000-075 Coimbra, Portugal
- Center for Innovation and Research in Oral Sciences (CIROS), Faculty of Medicine, University of Coimbra, 3000-075 Coimbra, Portugal
| | - João Miguel Marques Santos
- Institute of Endodontics, Faculty of Medicine, University of Coimbra, 3000-075 Coimbra, Portugal
- Center for Innovation and Research in Oral Sciences (CIROS), Faculty of Medicine, University of Coimbra, 3000-075 Coimbra, Portugal
| | - Frederico Duque
- University Clinic of Pediatrics, Faculty of Medicine, University of Coimbra, 3000-602 Coimbra, Portugal
- Child Developmental Center and Research and Clinical Training Center, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra (CHUC), 3000-602 Coimbra, Portugal
| | - Guiomar Oliveira
- University Clinic of Pediatrics, Faculty of Medicine, University of Coimbra, 3000-602 Coimbra, Portugal
- Child Developmental Center and Research and Clinical Training Center, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra (CHUC), 3000-602 Coimbra, Portugal
| | - Ana Luísa Cardoso
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - João Peça
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Catarina Morais Seabra
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
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Gómez-Martín A, Fuentes JM, Jordán J, Galindo MF, Fernández-García JL. Detection of rare Genetic Variations in the promoter regions of the ATG16L gene in Parkinson's patients. Neurosci Lett 2023; 804:137195. [PMID: 36958426 DOI: 10.1016/j.neulet.2023.137195] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/07/2023] [Accepted: 03/18/2023] [Indexed: 03/25/2023]
Abstract
Mutations in the ATG genes have been related to impair autophagic function, contributing to the sporadic onset of Parkinsońs Disease (PD). However, scarce studies have been performed about ins/del within the regulatory domains of the autophagy genes in sporadic PD patients. This study was aimed to found ins/del within part of the crucial core autophagy promotor gene region of the ATG16L1 in a groups of sporadic PD patients. After developing a genetic marker to find ins/del using fragment size analysis, a rare mutation by insertion (0.45%) was reported in the patients. This mutation was characterized by sequencing. No others ins/del were found. As a results, the frequency of this insertion should be considered as a rare genetic variant. An in silico analysis also highlighting the usefulness of a search GDV which revealed multiples ins/del within ATG16L1 promoter. Furthermore, these genetic insertions could be found in patients with sporadic PD in the ATG161L promoter gene. When a breakpoint as deletions, insertions or tandem duplication are located within a functional gene interruption of the gene and a loss of function was expected but removing or altering in the regulatory sequence can influence the expression or the regulation of a nearby gene which may impair healthy due to dosage effects in sporadic diseases.
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Affiliation(s)
- A Gómez-Martín
- Universidad de Extremadura, Departamento de Enfermería, Facultad de Enfermería y Terapia Ocupacional, Avda. de la Universidad s/n, 10003, Cáceres, España; Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE), Cáceres, España.
| | - José M Fuentes
- Universidad de Extremadura, Departamento de Bioquímica y Biología Molecular y Genética. Facultad de Enfermería y Terapia Ocupacional, Avda de la Universidad s/n, 10003, Cáceres, España; Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas-Instituto de Salud Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain; Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE), Cáceres, España.
| | - J Jordán
- Departamento de Farmacología. Facultad de Medicina de Albacete. Universidad de Castilla-La Mancha, Albacete, España.
| | - M F Galindo
- Universidad de Castilla-La Mancha, Área de Farmacia y Tecnología Farmacéutica. Departamento de Farmacología, Facultad de Farmacia de Albacete, Albacete, España.
| | - José L Fernández-García
- Universidad Extremadura, Departamento de Producción animal y ciencias de los alimentos, Facultad de Veterinaria, Avda. de la Universidad, s/n, 10003, Cáceres, España
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Mishra R, Kapoor S. Genetic Counselling for Global Developmental Delay/Intellectual Disability (GDD/ID) — Changing Landscapes and Persisting Challenges. Indian Pediatr 2023. [DOI: 10.1007/s13312-023-2813-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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5
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The Genetics of Intellectual Disability. Brain Sci 2023; 13:brainsci13020231. [PMID: 36831774 PMCID: PMC9953898 DOI: 10.3390/brainsci13020231] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/23/2022] [Accepted: 01/16/2023] [Indexed: 02/03/2023] Open
Abstract
Intellectual disability (ID) has a prevalence of ~2-3% in the general population, having a large societal impact. The underlying cause of ID is largely of genetic origin; however, identifying this genetic cause has in the past often led to long diagnostic Odysseys. Over the past decades, improvements in genetic diagnostic technologies and strategies have led to these causes being more and more detectable: from cytogenetic analysis in 1959, we moved in the first decade of the 21st century from genomic microarrays with a diagnostic yield of ~20% to next-generation sequencing platforms with a yield of up to 60%. In this review, we discuss these various developments, as well as their associated challenges and implications for the field of ID, which highlight the revolutionizing shift in clinical practice from a phenotype-first into genotype-first approach.
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6
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Mohiuddin M, Kooy RF, Pearson CE. De novo mutations, genetic mosaicism and human disease. Front Genet 2022; 13:983668. [PMID: 36226191 PMCID: PMC9550265 DOI: 10.3389/fgene.2022.983668] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/08/2022] [Indexed: 11/23/2022] Open
Abstract
Mosaicism—the existence of genetically distinct populations of cells in a particular organism—is an important cause of genetic disease. Mosaicism can appear as de novo DNA mutations, epigenetic alterations of DNA, and chromosomal abnormalities. Neurodevelopmental or neuropsychiatric diseases, including autism—often arise by de novo mutations that usually not present in either of the parents. De novo mutations might occur as early as in the parental germline, during embryonic, fetal development, and/or post-natally, through ageing and life. Mutation timing could lead to mutation burden of less than heterozygosity to approaching homozygosity. Developmental timing of somatic mutation attainment will affect the mutation load and distribution throughout the body. In this review, we discuss the timing of de novo mutations, spanning from mutations in the germ lineage (all ages), to post-zygotic, embryonic, fetal, and post-natal events, through aging to death. These factors can determine the tissue specific distribution and load of de novo mutations, which can affect disease. The disease threshold burden of somatic de novo mutations of a particular gene in any tissue will be important to define.
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Affiliation(s)
- Mohiuddin Mohiuddin
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- *Correspondence: Mohiuddin Mohiuddin, ; Christopher E. Pearson,
| | - R. Frank Kooy
- Department of Medical Genetics, University of Antwerp, Edegem, Belgium
| | - Christopher E. Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- *Correspondence: Mohiuddin Mohiuddin, ; Christopher E. Pearson,
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7
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DuBose CO, Daum JR, Sansam CL, Gorbsky GJ. Dynamic Features of Chromosomal Instability during Culture of Induced Pluripotent Stem Cells. Genes (Basel) 2022; 13:genes13071157. [PMID: 35885940 PMCID: PMC9318709 DOI: 10.3390/genes13071157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 02/04/2023] Open
Abstract
Induced pluripotent stem cells (iPSCs) hold great potential for regenerative medicine. By reprogramming a patient′s own cells, immunological rejection can be avoided during transplantation. For expansion and gene editing, iPSCs are grown in artificial culture for extended times. Culture affords potential danger for the accumulation of genetic aberrations. To study these, two induced pluripotent stem (iPS) cell lines were cultured and periodically analyzed using advanced optical mapping to detect and classify chromosome numerical and segmental changes that included deletions, insertions, balanced translocations and inversions. In one of the lines, a population trisomic for chromosome 12 gained dominance over a small number of passages. This appearance and dominance of the culture by chromosome 12 trisomic cells was tracked through intermediate passages by the analysis of chromosome spreads. Mathematical modeling suggested that the proliferation rates of diploid versus trisomic cells could not account for the rapid dominance of the trisomic population. In addition, optical mapping revealed hundreds of structural variations distinct from those generally found within the human population. Many of these structural variants were detected in samples obtained early in the culturing process and were maintained in late passage samples, while others were acquired over the course of culturing.
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Affiliation(s)
- Casey O. DuBose
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; (C.O.D.); (J.R.D.)
| | - John R. Daum
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; (C.O.D.); (J.R.D.)
| | - Christopher L. Sansam
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; (C.O.D.); (J.R.D.)
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Gary J. Gorbsky
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; (C.O.D.); (J.R.D.)
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Correspondence:
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8
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AYAZ A, GEZDIRICI A, YILMAZ GULEC E, OZALP Ö, KOSEOGLU AH, DOGRU Z, YALCINTEPE S. Diagnostic Value of Microarray Method in Autism Spectrum Disorder, Intellectual Disability, and Multiple Congenital Anomalies and Some Candidate Genes for Autism: Experience of Two Centers. Medeni Med J 2022; 37:180-193. [PMID: 35735171 PMCID: PMC9234369 DOI: 10.4274/mmj.galenos.2022.70962] [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: 12/02/2022] Open
Abstract
Objective: This study aimed to demonstrate the diagnostic value of microarray testing in autism spectrum disorder, intellectual disability, and multiple congenital anomalies of unknown etiology, as well as to report some potential candidate genes for autism. Methods: Microarray analysis records between January 2016 and December 2017 from two Genetic Diagnostic Centers in Turkey, Kanuni Sultan Suleyman and Adana Numune Training and Research Hospital, were compiled. Detected copy number variations (CNVs) were classified as benign, likely benign, variants of uncertain significance (VUS), likely pathogenic, and pathogenic according to American College of Medical Genetics and Genomics guidelines. The clinical findings of the some patients and the literature data were compared. Results: In 109 (24.5%) of 445 patients, a total of 163 CNVs with reporting criterion feature were detected. Sixty-nine (42%) and 8 (5%) of these were evaluated as pathogenic and likely pathogenic, respectively. Fifteen (9%) CNVs were also evaluated as VUS. Pathogenic or likely pathogenic CNVs were detected in 61 (13.6%) of 445 patients. Conclusions: We found that the probability of elucidating the etiology of microarray method in autism spectrum disorder, intellectual disability, and multiple congenital anomalies is 13.6% with a percentage similar to the literature. We suggest that the MYT1L, PXDN, TPO, and AUTS2 genes are all strong candidate genes for autism spectrum disorders. We detailed the clinical findings of the cases and reported that some CNV regions in the genome may be associated with autism.
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Avdeyev P, Zhou J. Computational Approaches for Understanding Sequence Variation Effects on the 3D Genome Architecture. Annu Rev Biomed Data Sci 2022; 5:183-204. [PMID: 35537461 DOI: 10.1146/annurev-biodatasci-102521-012018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Decoding how genomic sequence and its variations affect 3D genome architecture is indispensable for understanding the genetic architecture of various traits and diseases. The 3D genome organization can be significantly altered by genome variations and in turn impact the function of the genomic sequence. Techniques for measuring the 3D genome architecture across spatial scales have opened up new possibilities for understanding how the 3D genome depends upon the genomic sequence and how it can be altered by sequence variations. Computational methods have become instrumental in analyzing and modeling the sequence effects on 3D genome architecture, and recent development in deep learning sequence models have opened up new opportunities for studying the interplay between sequence variations and the 3D genome. In this review, we focus on computational approaches for both the detection and modeling of sequence variation effects on the 3D genome, and we discuss the opportunities presented by these approaches. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 5 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Pavel Avdeyev
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, USA;
| | - Jian Zhou
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, USA;
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10
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Wen X, Xing H, Qi K, Wang H, Li X, Zhu J, Chen W, Cui L, Zhang J, Qi H. Analysis of 17 Prenatal Cases with the Chromosomal 1q21.1 Copy Number Variation. DISEASE MARKERS 2022; 2022:5487452. [PMID: 37284664 PMCID: PMC10241571 DOI: 10.1155/2022/5487452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/12/2022] [Indexed: 10/10/2023]
Abstract
Copy number variations (CNVs) at the chromosomal 1q21.1 region represent a group of hot-spot recurrent rearrangements in human genome, which have been detected in hundreds of patients with variable clinical manifestations. Yet, report of such CNVs in prenatal scenario was relatively scattered. In this study, 17 prenatal cases involving the 1q21.1 microdeletion or duplication were recruited. The clinical survey and imaging examination were performed; and genetic detection with karyotyping and CNV analysis using chromosomal microarray (CMA) or CNVseq were subsequently carried out. These cases were all positive with 1q21.1 CNV, yet presented with exceedingly various clinical and utrasonographic indications. Among them, 12 pregnancies carried 1q21.1 deletions, while the other 5 carried 1q21.1 duplications, all of which were within the previously defined breaking point (BP) regions. According to the verification results, 9 CNVs were de novo, 7 were familial, and the other 1 was not certain. We summarized the clinical information of these cases, and the size and distribution of CNVs, and attempted to analyze the association between these two aspects. The findings in our study may provide important basis for the prenatal diagnosis and genetic counseling on such conditions in the future.
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Affiliation(s)
- Xiaohui Wen
- Prenatal Diagnosis Center, Haidian Maternal and Child Health Care Hospital, Beijing, China
| | - Huanxia Xing
- Prenatal Diagnosis Center, Langfang Maternal and Child Health Care Hospital, Langfang, Hebei, China
| | - Keyan Qi
- Prenatal Diagnosis Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Hao Wang
- Prenatal Diagnosis Center, Hangzhou Women's Hospital, Hangzhou, Zhejiang, China
- Department of Cell Biology and Medical Genetics, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaojun Li
- Prenatal Diagnosis Center, Haidian Maternal and Child Health Care Hospital, Beijing, China
| | - Jianjiang Zhu
- Prenatal Diagnosis Center, Haidian Maternal and Child Health Care Hospital, Beijing, China
| | - Wenqi Chen
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Shijiazhuang, Hebei, China
| | - Limin Cui
- Prenatal Diagnosis Center, Langfang Maternal and Child Health Care Hospital, Langfang, Hebei, China
| | - Jing Zhang
- Prenatal Diagnosis Center, Shijiazhuang Obstetrics and Gynecology Hospital, Shijiazhuang, Hebei, China
| | - Hong Qi
- Prenatal Diagnosis Center, Haidian Maternal and Child Health Care Hospital, Beijing, China
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11
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Gordeeva V, Sharova E, Arapidi G. Progress in Methods for Copy Number Variation Profiling. Int J Mol Sci 2022; 23:ijms23042143. [PMID: 35216262 PMCID: PMC8879278 DOI: 10.3390/ijms23042143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 02/04/2023] Open
Abstract
Copy number variations (CNVs) are the predominant class of structural genomic variations involved in the processes of evolutionary adaptation, genomic disorders, and disease progression. Compared with single-nucleotide variants, there have been challenges associated with the detection of CNVs owing to their diverse sizes. However, the field has seen significant progress in the past 20–30 years. This has been made possible due to the rapid development of molecular diagnostic methods which ensure a more detailed view of the genome structure, further complemented by recent advances in computational methods. Here, we review the major approaches that have been used to routinely detect CNVs, ranging from cytogenetics to the latest sequencing technologies, and then cover their specific features.
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Affiliation(s)
- Veronika Gordeeva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.S.); (G.A.)
- Moscow Institute of Physics and Technology, National Research University, Moscow Oblast, 141701 Moscow, Russia
- Correspondence:
| | - Elena Sharova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.S.); (G.A.)
| | - Georgij Arapidi
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.S.); (G.A.)
- Moscow Institute of Physics and Technology, National Research University, Moscow Oblast, 141701 Moscow, Russia
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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12
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Maia N, Nabais Sá MJ, Melo-Pires M, de Brouwer APM, Jorge P. Intellectual disability genomics: current state, pitfalls and future challenges. BMC Genomics 2021; 22:909. [PMID: 34930158 PMCID: PMC8686650 DOI: 10.1186/s12864-021-08227-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 12/02/2021] [Indexed: 12/18/2022] Open
Abstract
Intellectual disability (ID) can be caused by non-genetic and genetic factors, the latter being responsible for more than 1700 ID-related disorders. The broad ID phenotypic and genetic heterogeneity, as well as the difficulty in the establishment of the inheritance pattern, often result in a delay in the diagnosis. It has become apparent that massive parallel sequencing can overcome these difficulties. In this review we address: (i) ID genetic aetiology, (ii) clinical/medical settings testing, (iii) massive parallel sequencing, (iv) variant filtering and prioritization, (v) variant classification guidelines and functional studies, and (vi) ID diagnostic yield. Furthermore, the need for a constant update of the methodologies and functional tests, is essential. Thus, international collaborations, to gather expertise, data and resources through multidisciplinary contributions, are fundamental to keep track of the fast progress in ID gene discovery.
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Affiliation(s)
- Nuno Maia
- Centro de Genética Médica Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), Porto, Portugal. .,Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal.
| | - Maria João Nabais Sá
- Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal
| | - Manuel Melo-Pires
- Serviço de Neuropatologia, Centro Hospitalar e Universitário do Porto (CHUPorto), Porto, Portugal
| | - Arjan P M de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Paula Jorge
- Centro de Genética Médica Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), Porto, Portugal.,Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal
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13
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Ali Khan I. Do second generation sequencing techniques identify documented genetic markers for neonatal diabetes mellitus? Heliyon 2021; 7:e07903. [PMID: 34584998 PMCID: PMC8455689 DOI: 10.1016/j.heliyon.2021.e07903] [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: 05/06/2020] [Revised: 01/15/2021] [Accepted: 08/27/2021] [Indexed: 12/24/2022] Open
Abstract
Neonatal diabetes mellitus (NDM) is noted as a genetic, heterogeneous, and rare disease in infants. NDM occurs due to a single-gene mutation in neonates. A common source for developing NDM in an infant is the existence of mutations/variants in the KCNJ11 and ABCC8 genes, encoding the subunits of the voltage-dependent potassium channel. Both KCNJ11 and ABCC8 genes are useful in diagnosing monogenic diabetes during infancy. Genetic analysis was previously performed using first-generation sequencing techniques, such as DNA-Sanger sequencing, which uses chain-terminating inhibitors. Sanger sequencing has certain limitations; it can screen a limited region of exons in one gene, but it cannot screen large regions of the human genome. In the last decade, first generation sequencing techniques have been replaced with second-generation sequencing techniques, such as next-generation sequencing (NGS), which sequences nucleic-acids more rapidly and economically than Sanger sequencing. NGS applications are involved in whole exome sequencing (WES), whole genome sequencing (WGS), and targeted gene panels. WES characterizes a substantial breakthrough in human genetics. Genetic testing for custom genes allows the screening of the complete gene, including introns and exons. The aim of this review was to confirm if the 22 genetic variations previously documented to cause NDM by Sanger sequencing could be detected using second generation sequencing techniques. The author has cross-checked global studies performed in NDM using NGS, ES/WES, WGS, and targeted gene panels as second-generation sequencing techniques; WES confirmed the similar variants, which have been previously documented with Sanger sequencing. WES is documented as a powerful tool and WGS as the most comprehensive test for verified the documented variants, as well as novel enhancers. This review recommends for the future studies should be performed with second generation sequencing techniques to identify the verified 22 genetic and novel variants by screening in NDM (PNDM or TNMD) children.
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Affiliation(s)
- Imran Ali Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, PO Box-10219, Riyadh, 11433, Saudi Arabia
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14
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Mechanisms Underlying the Suppression of Chromosome Rearrangements by Ataxia-Telangiectasia Mutated. Genes (Basel) 2021; 12:genes12081232. [PMID: 34440406 PMCID: PMC8392746 DOI: 10.3390/genes12081232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 02/07/2023] Open
Abstract
Chromosome rearrangements are structural variations in chromosomes, such as inversions and translocations. Chromosome rearrangements have been implicated in a variety of human diseases. Ataxia-telangiectasia (A-T) is an autosomal recessive disorder characterized by a broad range of clinical and cellular phenotypes. At the cellular level, one of the most prominent features of A-T cells is chromosome rearrangement, especially that in T lymphocytes. The gene that is defective in A-T is ataxia-telangiectasia mutated (ATM). The ATM protein is a serine/threonine kinase and plays a central role in the cellular response to DNA damage, particularly DNA double-strand breaks. In this review, the mechanisms by which ATM suppresses chromosome rearrangements are discussed.
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15
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Mantere T, Neveling K, Pebrel-Richard C, Benoist M, van der Zande G, Kater-Baats E, Baatout I, van Beek R, Yammine T, Oorsprong M, Hsoumi F, Olde-Weghuis D, Majdali W, Vermeulen S, Pauper M, Lebbar A, Stevens-Kroef M, Sanlaville D, Dupont JM, Smeets D, Hoischen A, Schluth-Bolard C, El Khattabi L. Optical genome mapping enables constitutional chromosomal aberration detection. Am J Hum Genet 2021; 108:1409-1422. [PMID: 34237280 PMCID: PMC8387289 DOI: 10.1016/j.ajhg.2021.05.012] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 05/28/2021] [Indexed: 01/02/2023] Open
Abstract
Chromosomal aberrations including structural variations (SVs) are a major cause of human genetic diseases. Their detection in clinical routine still relies on standard cytogenetics. Drawbacks of these tests are a very low resolution (karyotyping) and the inability to detect balanced SVs or indicate the genomic localization and orientation of duplicated segments or insertions (copy number variant [CNV] microarrays). Here, we investigated the ability of optical genome mapping (OGM) to detect known constitutional chromosomal aberrations. Ultra-high-molecular-weight DNA was isolated from 85 blood or cultured cells and processed via OGM. A de novo genome assembly was performed followed by structural variant and CNV calling and annotation, and results were compared to known aberrations from standard-of-care tests (karyotype, FISH, and/or CNV microarray). In total, we analyzed 99 chromosomal aberrations, including seven aneuploidies, 19 deletions, 20 duplications, 34 translocations, six inversions, two insertions, six isochromosomes, one ring chromosome, and four complex rearrangements. Several of these variants encompass complex regions of the human genome involved in repeat-mediated microdeletion/microduplication syndromes. High-resolution OGM reached 100% concordance compared to standard assays for all aberrations with non-centromeric breakpoints. This proof-of-principle study demonstrates the ability of OGM to detect nearly all types of chromosomal aberrations. We also suggest suited filtering strategies to prioritize clinically relevant aberrations and discuss future improvements. These results highlight the potential for OGM to provide a cost-effective and easy-to-use alternative that would allow comprehensive detection of chromosomal aberrations and structural variants, which could give rise to an era of "next-generation cytogenetics."
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Affiliation(s)
- Tuomo Mantere
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Radboud Institute of Medical Life Sciences, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Radboud Institute of Health Sciences, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Céline Pebrel-Richard
- Department of Chromosomal and Molecular Genetics, University Hospital of Clermont-Ferrand, 63003 Clermont-Ferrand, France
| | - Marion Benoist
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Guillaume van der Zande
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Ellen Kater-Baats
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Imane Baatout
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Ronald van Beek
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Tony Yammine
- Institut Neuromyogène, CNRS UMR 5310, INSERM U1217, Lyon 1 University, 69008 Lyon, France; Unit of Medical Genetics, Saint-Joseph University, 1107 2180 Beyrouth, Lebanon
| | - Michiel Oorsprong
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Faten Hsoumi
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Daniel Olde-Weghuis
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Wed Majdali
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Susan Vermeulen
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Marc Pauper
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Aziza Lebbar
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France
| | - Marian Stevens-Kroef
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Damien Sanlaville
- Institut Neuromyogène, CNRS UMR 5310, INSERM U1217, Lyon 1 University, 69008 Lyon, France; Department of Genetics, Hospices Civils de Lyon, 69677 Bron, France
| | - Jean Michel Dupont
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France; Université de Paris, Cochin Institute U1016, INSERM, 75014 Paris, France
| | - Dominique Smeets
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Radboud Institute of Medical Life Sciences, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands.
| | - Caroline Schluth-Bolard
- Institut Neuromyogène, CNRS UMR 5310, INSERM U1217, Lyon 1 University, 69008 Lyon, France; Department of Genetics, Hospices Civils de Lyon, 69677 Bron, France
| | - Laïla El Khattabi
- Department of Cytogenetics, APHP.centre - Université de Paris, Hôpital Cochin, 75014 Paris, France; Université de Paris, Cochin Institute U1016, INSERM, 75014 Paris, France.
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16
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Mishra RS, Mohanty SK, Cordes J, Sahoo U, Singh RR, Subramanian SV. Economic gradient of onset of disability in India. BMC Public Health 2021; 21:769. [PMID: 33882902 PMCID: PMC8061006 DOI: 10.1186/s12889-021-10826-5] [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: 01/12/2021] [Accepted: 04/12/2021] [Indexed: 12/02/2022] Open
Abstract
Background Disability in India is associated with increasing non-communicable diseases, rising longevity, and increasing accidents and injuries. Though studies have examined prevalence, patterns, and socioeconomic correlates of disability, no attempt has been made in estimating age of onset of disability in India. Objective This paper investigates the economic gradient of age of onset of locomotor, visual, hearing, speech, mental retardation, mental illness, and other disabilities in India. Method We use nationally representative data of 106,894 disabled individuals from the 76th round of National Sample Survey (NSS), 2018. Descriptive statistics, kernel density, Kaplan-Meier survival curves, and linear regression models are used in the analysis. Result The disability rate in India was 2184 per 100,000 persons. The disability rate was highest for locomotor (1353) followed by hearing (296), visual (234), speech (228), mental retardation (158), and mental illness (131). Over 85% of mental retardation and 80% of speech disabilities occur at birth, while 82% of locomotor and 81% of visual disabilities occur after birth. Among those who had disability after birth, the median age for mental retardation was 2 years followed by mental illness (28 years), speech (29 years), locomotor (42 years), visual (55 years), and 56 years for hearing disability. Adjusting for socioeconomic covariates, the age of onset of locomotor and speech disabilities among the poorest individuals were 7 and 11 years earlier than the richest, respectively. Conclusion The economic gradient of onset of locomotive and speech disabilities are strong. The age of onset of disability was earliest for mental retardation followed by mental illness and speech disability. Supplementary Information The online version contains supplementary material available at 10.1186/s12889-021-10826-5.
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Affiliation(s)
- Radhe Shyam Mishra
- International Institute for Population Sciences, Govandi station road Deonar, Mumbai, 400088, India.
| | - Sanjay K Mohanty
- Department of Fertility Studies, International Institute for Population Sciences, Mumbai, India.
| | - Jack Cordes
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Umakanta Sahoo
- International Institute for Population Sciences, Govandi station road Deonar, Mumbai, 400088, India
| | - Rajeev R Singh
- International Institute for Population Sciences, Govandi station road Deonar, Mumbai, 400088, India
| | - S V Subramanian
- Harvard Centre for Population and Development Studies, Harvard University, Cambridge, MA, USA
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17
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Sun Y, Liu F, Fan C, Wang Y, Song L, Fang Z, Han R, Wang Z, Wang X, Yang Z, Xu Z, Peng J, Shi C, Zhang H, Dong W, Huang H, Li Y, Le Y, Sun J, Peng Z. Characterizing sensitivity and coverage of clinical WGS as a diagnostic test for genetic disorders. BMC Med Genomics 2021; 14:102. [PMID: 33849535 PMCID: PMC8045368 DOI: 10.1186/s12920-021-00948-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 03/31/2021] [Indexed: 12/30/2022] Open
Abstract
Background Due to its reduced cost and incomparable advantages, WGS is likely to lead to changes in clinical diagnosis of rare and undiagnosed diseases. However, the sensitivity and breadth of coverage of clinical WGS as a diagnostic test for genetic disorders has not been fully evaluated. Methods Here, the performance of WGS in NA12878, the YH cell line, and the Chinese trios were measured by assessing their sensitivity, PPV, depth and breadth of coverage using MGISEQ-2000. We also compared the performance of WES and WGS using NA12878. The sensitivity and PPV were tested using the family-based trio design for the Chinese trios. We further developed a systematic WGS pipeline for the analysis of 8 clinical cases. Results In general, the sensitivity and PPV for SNV/indel detection increased with mean depth and reached a plateau at an ~ 40X mean depth using down-sampling samples of NA12878. With a mean depth of 40X, the sensitivity of homozygous and heterozygous SNPs of NA12878 was > 99.25% and > 99.50%, respectively, and the PPV was 99.97% and 98.96%. Homozygous and heterozygous indels showed lower sensitivity and PPV. The sensitivity and PPV were still not 100% even with a mean depth of ~ 150X. We also observed a substantial variation in the sensitivity of CNV detection across different tools, especially in CNVs with a size less than 1 kb. In general, the breadth of coverage for disease-associated genes and CNVs increased with mean depth. The sensitivity and coverage of WGS (~ 40X) was better than WES (~ 120X). Among the Chinese trios with an ~ 40X mean depth, the sensitivity among offspring was > 99.48% and > 96.36% for SNP and indel detection, and the PPVs were 99.86% and 97.93%. All 12 previously validated variants in the 8 clinical cases were successfully detected using our WGS pipeline. Conclusions The current standard of a mean depth of 40X may be sufficient for SNV/indel detection and identification of most CNVs. It would be advisable for clinical scientists to determine the range of sensitivity and PPV for different classes of variants for a particular WGS pipeline, which would be useful when interpreting and delivering clinical reports. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-00948-5.
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Affiliation(s)
- Yan Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Fengxia Liu
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Chunna Fan
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Yaoshen Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Lijie Song
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Zhonghai Fang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Rui Han
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Zhonghua Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Xiaodan Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Ziying Yang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Zhenpeng Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jiguang Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Chaonan Shi
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | | | - Wei Dong
- BGI-Beijing Clinical Laboratories, BGI-Shenzhen, Beijing, 101300, China
| | - Hui Huang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yun Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yanqun Le
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Jun Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China. .,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
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18
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Kang JU. Medical Implementation of Microarray Technology. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2020. [DOI: 10.15324/kjcls.2020.52.4.310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Ji Un Kang
- Department of Biomedical Laboratory Science, Korea Nazarene University, Cheonan, Korea
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19
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Yang J, Liu A, He I, Bai Y. Bioinformatics Analysis Revealed Novel 3'UTR Variants Associated with Intellectual Disability. Genes (Basel) 2020; 11:genes11090998. [PMID: 32858868 PMCID: PMC7563394 DOI: 10.3390/genes11090998] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/15/2020] [Accepted: 08/24/2020] [Indexed: 01/03/2023] Open
Abstract
MicroRNAs (or miRNAs) are short nucleotide sequences (~17–22 bp long) that play important roles in gene regulation through targeting genes in the 3′untranslated regions (UTRs). Variants located in genomic regions might have different biological consequences in changing gene expression. Exonic variants (e.g., coding variant and 3′UTR variant) are often causative of diseases due to their influence on gene product. Variants harbored in the 3′UTR region where miRNAs perform their targeting function could potentially alter the binding relationships for target pairs, which could relate to disease causation. We gathered miRNA–mRNA targeting pairs from published studies and then employed the database of microRNA Target Site single nucleotide variants (SNVs) (dbMTS) to discover novel SNVs within the selected pairs. We identified a total of 183 SNVs for the 114 pairs of accurate miRNA–mRNA targeting pairs selected. Detailed bioinformatics analysis of the three genes with identified variants that were exclusively located in the 3′UTR section indicated their association with intellectual disability (ID). Our result showed an exceptionally high expression of GPR88 in brain tissues based on GTEx gene expression data, while WNT7A expression data were relatively high in brain tissues when compared to other tissues. Motif analysis for the 3′UTR region of WNT7A showed that five identified variants were well-conserved across three species (human, mouse, and rat); the motif that contains the variant identified in GPR88 is significant at the level of the 3′UTR of the human genome. Studies of pathways, protein–protein interactions, and relations to diseases further suggest potential association with intellectual disability of our discovered SNVs. Our results demonstrated that 3′UTR variants could change target interactions of miRNA–mRNA pairs in the context of their association with ID. We plan to automate the methods through developing a bioinformatics pipeline for identifying novel 3′UTR SNVs harbored by miRNA-targeted genes in the future.
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Affiliation(s)
- Junmeng Yang
- Shanghai Starriver Bilingual School, Shanghai 201100, China;
| | - Anna Liu
- Appleby College, Oakville, ON L6L3V7, Canada;
| | - Isabella He
- Pittsford Mendon High School, 472 Mendon Road, Pittsford, NY 14534, USA;
| | - Yongsheng Bai
- Department of Biology, Eastern Michigan University, 441 Mark Jefferson Hall, Ypsilanti, MI 48197, USA
- Next-Gen Intelligent Science Training, Ann Arbor, MI 48105, USA
- Correspondence:
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20
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Pang H, Yu X, Kim YM, Wang X, Jinkins JK, Yin J, Li S, Gu H. Disorders Associated With Diverse, Recurrent Deletions and Duplications at 1q21.1. Front Genet 2020; 11:577. [PMID: 32655619 PMCID: PMC7325322 DOI: 10.3389/fgene.2020.00577] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 05/11/2020] [Indexed: 01/22/2023] Open
Abstract
The subchromosomal region 1q21.1 is one of the hotspots in the human genome for deletions and reciprocal duplications, owing to the existence of hundreds of segmental duplications. Recurrent deletions and duplications in this region are thought to be causative in patients with variable clinical manifestations. Based on the genomic locations, deletions and duplications at the 1q21.1 locus have been associated with distinguishable syndromes: chromosome 1q21.1 deletion syndrome, chromosome 1q21.1 duplication syndrome, and thrombocytopenia-absent radius (TAR) syndrome, which is partially due to deletions at the proximal 1q21.1 region. We report here diverse, recurrent deletions and duplications at the 1q21.1 locus in 36 patients from a cohort of 5,200 individuals. Among the 36 patients, 18 patients carry 1q21.1 deletions, nine individuals have reciprocal duplications at 1q21.1, two patients share an identical short deletion, and the remaining seven possess variable sizes of duplications at the proximal 1q21.1 region. Furthermore, we provide cytogenetic characterization and detailed clinical features for each patient. Notably, duplications at the proximal 1q21.1 region have not been associated with a defined disorder in publications. However, recurrent duplications at the proximal 1q21.1 region among the seven patients strongly suggested that the variants are likely pathogenic. The common phenotypical features of those disorders are also summarized to facilitate clinical diagnoses and genetic counseling.
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Affiliation(s)
- Hui Pang
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Xiaowei Yu
- The First Affiliated Hospital of Jilin University, Changchun, China
| | - Young Mi Kim
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Xianfu Wang
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Jeremy K Jinkins
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Jianing Yin
- The First Affiliated Hospital of Jilin University, Changchun, China
| | - Shibo Li
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Hongcang Gu
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma, OK, United States.,Broad Institute of MIT and Harvard, Cambridge, MA, United States
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21
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Labonne JDJ, Driessen TM, Harris ME, Kong IK, Brakta S, Theisen J, Sangare M, Layman LC, Kim CH, Lim J, Kim HG. Comparative Genomic Mapping Implicates LRRK2 for Intellectual Disability and Autism at 12q12, and HDHD1, as Well as PNPLA4, for X-Linked Intellectual Disability at Xp22.31. J Clin Med 2020; 9:jcm9010274. [PMID: 31963867 PMCID: PMC7019335 DOI: 10.3390/jcm9010274] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/28/2019] [Accepted: 12/06/2019] [Indexed: 01/01/2023] Open
Abstract
We report a genomic and phenotypic delineation for two chromosome regions with candidate genes for syndromic intellectual disability at 12q12 and Xp22.31, segregating independently in one family with four affected members. Fine mapping of three affected members, along with six unreported small informative CNVs, narrowed down the candidate chromosomal interval to one gene LRRK2 at 12q12. Expression studies revealed high levels of LRRK2 transcripts in the whole human brain, cerebral cortex and hippocampus. RT-qPCR assays revealed that LRRK2 transcripts were dramatically reduced in our microdeletion patient DGDP289A compared to his healthy grandfather with no deletion. The decreased expression of LRRK2 may affect protein–protein interactions between LRRK2 and its binding partners, of which eight have previously been linked to intellectual disability. These findings corroborate with a role for LRRK2 in cognitive development, and, thus, we propose that intellectual disability and autism, displayed in the 12q12 microdeletions, are likely caused by LRRK2. Using another affected member, DGDP289B, with a microdeletion at Xp22.31, in this family, we performed the genomic and clinical delineation with six published and nine unreported cases. We propose HDHD1 and PNPLA4 for X-linked intellectual disability in this region, since their high transcript levels in the human brain substantiate their role in intellectual functioning.
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Affiliation(s)
- Jonathan D. J. Labonne
- Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA 30912, USA (M.E.H.); (S.B.); (J.T.); (L.C.L.)
| | - Terri M. Driessen
- Department of Genetics, Yale University, New Haven, CT 06510, USA; (T.M.D.); (J.L.)
| | - Marvin E. Harris
- Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA 30912, USA (M.E.H.); (S.B.); (J.T.); (L.C.L.)
| | - Il-Keun Kong
- Department of Animal Science, Division of Applied Life Science (BK21plus), Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Korea;
| | - Soumia Brakta
- Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA 30912, USA (M.E.H.); (S.B.); (J.T.); (L.C.L.)
| | - John Theisen
- Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA 30912, USA (M.E.H.); (S.B.); (J.T.); (L.C.L.)
| | - Modibo Sangare
- Faculty of Medicine and Odontostomatology (FMOS), University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali;
| | - Lawrence C. Layman
- Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA 30912, USA (M.E.H.); (S.B.); (J.T.); (L.C.L.)
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, GA 30912, USA
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon 34134, Korea;
| | - Janghoo Lim
- Department of Genetics, Yale University, New Haven, CT 06510, USA; (T.M.D.); (J.L.)
- Department of Neuroscience, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale Stem Cell Center, Yale University, New Haven, CT 06510, USA
| | - Hyung-Goo Kim
- Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA 30912, USA (M.E.H.); (S.B.); (J.T.); (L.C.L.)
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha P.O. Box 34110, Qatar
- Correspondence:
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Markovic-Jovanovic SR, Milovanovic JD, Jovanovic AN, Zivkovic JB, Balovic AD, Nickovic V, Vasic MZ, Ristic MZ. Comorbidities in children with intellectual disabilities. Birth Defects Res 2020; 112:54-61. [PMID: 31502761 DOI: 10.1002/bdr2.1587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 11/08/2022]
Abstract
BACKGROUND Intellectual disability (ID) is registered in 2%-3% of newborns. In most cases, the causes are not identifiable. OBJECTIVE We explored the correlation between the intellectual disability and gestational age, birth weight, Apgar score, familial diseases, congenital anomalies, and acquired medical disorders, with the aim to estimate the prevalence and severity of comorbidities in the affected children. METHODS Our study included 22 children with ID, and 24 with proper psychomotor development, aged 5-10 who were not considered to have ID. RESULTS The presence of familial disorders and CNS congenital anomalies increased the risk of ID 4.147 and 2.59 times, respectively. The risk for other congenital and noncongenital diseases was higher (7.38 and 1.4 times, respectively) in children with intellectual disability. CONCLUSIONS Children with intellectual disabilities have higher incidence of congenital diseases, family disorders and a higher frequency of acquired disorders during childhood. Apgar score is a sensitive predictor of morbidity regarding congenital as well as noncongenital medical conditions.
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Affiliation(s)
| | | | | | - Jovan B Zivkovic
- Department of Pediatrics, Medical Faculty, University of Pristina, K. Mitrovica
| | | | - Vanja Nickovic
- Department of Infectology, Clinical Hospital Center of Gracanica
| | - Maja Z Vasic
- Department of Pediatrics, Medical Faculty, University of Pristina, K. Mitrovica
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Savory K, Manivannan S, Zaben M, Uzun O, Syed YA. Impact of copy number variation on human neurocognitive deficits and congenital heart defects: A systematic review. Neurosci Biobehav Rev 2019; 108:83-93. [PMID: 31682886 DOI: 10.1016/j.neubiorev.2019.10.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/26/2019] [Indexed: 12/16/2022]
Abstract
Copy number variant (CNV) syndromes are often associated with both neurocognitive deficits (NCDs) and congenital heart defects (CHDs). Children and adults with cardiac developmental defects likely to have NCDs leading to increased risk of hospitalisation and reduced level of independence. To date, the association between these two phenotypes have not been explored in relation to CNV syndromes. In order to address this question, we systematically reviewed the prevalence of CHDs in a range of CNV syndromes associated with NCDs. A meta-analysis showed a relationship with the size of CNV and its association with both NCDs and CHDs, and also inheritance pattern. To our knowledge, this is the first review to establish association between NCD and CHDs in CNV patients, specifically in relation to the severity of NCD. Importantly, we also found specific types of CHDs were associated with severe neurocognitive deficits. Finally, we discuss the implications of these results for patients in the clinical setting which warrants further exploration of this association in order to lead an improvement in the quality of patient's life.
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Affiliation(s)
- Katrina Savory
- Neuroscience and Mental Health Research Institute (NMHRI), Hadyn Ellis Building, Cathays, CF24 4HQ, Cardiff, UK; School of Bioscience, The Sir Martin Evans Building, Museum Ave, Cardiff, CF10 3AX, UK
| | - Susruta Manivannan
- Neuroscience and Mental Health Research Institute (NMHRI), Hadyn Ellis Building, Cathays, CF24 4HQ, Cardiff, UK
| | - Malik Zaben
- Neuroscience and Mental Health Research Institute (NMHRI), Hadyn Ellis Building, Cathays, CF24 4HQ, Cardiff, UK
| | - Orhan Uzun
- University Hospital of Wales, Heath Park, Cardiff, CF10 3AX, UK
| | - Yasir Ahmed Syed
- Neuroscience and Mental Health Research Institute (NMHRI), Hadyn Ellis Building, Cathays, CF24 4HQ, Cardiff, UK; School of Bioscience, The Sir Martin Evans Building, Museum Ave, Cardiff, CF10 3AX, UK.
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24
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Misra S, Peters G, Barnes E, Ardern-Holmes S, Webster R, Troedson C, Mohammad SS, Gill D, Menezes M, Gupta S, Procopis P, Antony J, Kurian MA, Dale RC. Yield of comparative genomic hybridization microarray in pediatric neurology practice. NEUROLOGY-GENETICS 2019; 5:e367. [PMID: 31872051 PMCID: PMC6878849 DOI: 10.1212/nxg.0000000000000367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/28/2019] [Indexed: 12/14/2022]
Abstract
Objective The present study investigated the diagnostic yield of array comparative genomic hybridization (aCGH) in a large cohort of children with diverse neurologic disorders as seen in child neurology practice to test whether pathogenic copy number variants (CNVs) were more likely to be detected in specific neurologic phenotypes. Methods A retrospective cross-sectional analysis was performed on 555 children in whom a genetic etiology was suspected and who underwent whole-genome aCGH testing between 2006 and 2012. Neurologic phenotyping was performed using hospital medical records. An assessment of pathogenicity was made for each CNV, based on recent developments in the literature. Results Forty-seven patients were found to carry a pathogenic CNV, giving an overall diagnostic yield of 8.59%. Certain phenotypes predicted for the presence of a pathogenic CNV, including developmental delay (odds ratio [OR] 3.69 [1.30-10.51]), cortical visual impairment (OR 2.73 [1.18-6.28]), dysmorphism (OR 2.75 [1.38-5.50]), and microcephaly (OR 2.16 [1.01-4.61]). The combination of developmental delay/intellectual disability with dysmorphism and abnormal head circumference was also predictive for a pathogenic CNV (OR 2.86 [1.02-8.00]). For every additional clinical feature, there was an increased likelihood of detecting a pathogenic CNV (OR 1.18 [1.01-1.38]). Conclusions The use of aCGH led to a pathogenic finding in 8.59% of patients. The results support the use of aCGH as a first tier investigation in children with diverse neurologic disorders, although whole-genome sequencing may replace aCGH as the detection method in the future. In particular, the yield was increased in children with developmental delay, dysmorphism, cortical visual impairment, and microcephaly.
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Affiliation(s)
- Shibalik Misra
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Greg Peters
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Elizabeth Barnes
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Simone Ardern-Holmes
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Richard Webster
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Christopher Troedson
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Shekeeb S Mohammad
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Deepak Gill
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Manoj Menezes
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Sachin Gupta
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Peter Procopis
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Jayne Antony
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Manju A Kurian
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
| | - Russell C Dale
- Kids Neuroscience Centre (S.M., R.D.), the Children's Hospital at Westmead, Faculty of Medicine and Health, the University of Sydney; Department of Clinical Genetics (G.P.) at the Children's Hospital at Westmead; Kids Research Institute at Westmead (E.B.); TY Nelson Department of Neurology and Neurosurgery at the Children's Hospital at Westmead Sydney (S.A.-H., R.W., C.T., S.S.M., D.G., M.M., S.G., P.P., J.A., R.C.D.), New South Wales, Australia; and Institute of Child Health (M.K.), University College London, UK
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Proband-Only Clinical Exome Sequencing for Neurodevelopmental Disabilities. Pediatr Neurol 2019; 99:47-54. [PMID: 30952489 DOI: 10.1016/j.pediatrneurol.2019.02.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/16/2019] [Accepted: 02/20/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Whole exome sequencing on family trios gives the highest diagnostic yield, but high cost limits its application. Here, we performed proband-only clinical exome sequencing in a population of patients with neurodevelopmental disabilities and tested the diagnostic yield. METHODS This observational, retrospective study included 108 unrelated patients with neurodevelopmental disabilities who underwent clinical exome sequencing at the outpatient clinics of the Severance Children's Hospital, Seoul, South Korea, between March 2017 and May 2018. Clinical exome sequencing targeted 4503 disease-causing genes. RESULTS The overall diagnostic rate was 38.0% (41 of 108) when proband-only clinical exome sequencing was performed without additional parental testing. Four sequence variants were reclassified as likely pathogenic after parental testing, representing an additional 3.7% of the diagnostic yield. The final diagnostic rate was 41.7% (45 of 108). Of 45 patients with genetic abnormalities, a total of 38 sequence variations were detected in 33 (30.6%) patients with five homozygous cases, and 13 chromosomal copy number variants were detected in 12 (11.1%) patients. Novel variants of known causal genes for neurodevelopmental disabilities were detected in 18 (16.7%) patients. These were variants that could be reclassified as likely pathogenic if the de novo nature of the mutation was confirmed after testing of parental samples. CONCLUSIONS Proband-only clinical exome sequencing is a practical diagnostic tool that may be implemented in the clinical setting for patients with neurodevelopmental disabilities. A cost-effective approach to neurodevelopmental disabilities would be a proband-only clinical exome sequencing followed by parental testing of selective candidate variants.
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The clinical benefit of array-based comparative genomic hybridization for detection of copy number variants in Czech children with intellectual disability and developmental delay. BMC Med Genomics 2019; 12:111. [PMID: 31337399 PMCID: PMC6651926 DOI: 10.1186/s12920-019-0559-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 07/16/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Chromosomal microarray analysis has been shown to be a valuable and cost effective assay for elucidating copy number variants (CNVs) in children with intellectual disability and developmental delay (ID/DD). METHODS In our study, we performed array-based comparative genomic hybridization (array-CGH) analysis using oligonucleotide-based platforms in 542 Czech patients with ID/DD, autism spectrum disorders and multiple congenital abnormalities. Prior to the array-CGH analysis, all the patients were first examined karyotypically using G-banding. The presence of CNVs and their putative derivation was confirmed using fluorescence in situ hybridization (FISH), multiplex ligation-dependent probe amplification (MLPA) and predominantly relative quantitative polymerase chain reaction (qPCR). RESULTS In total, 5.9% (32/542) patients were positive for karyotypic abnormalities. Pathogenic/likely pathogenic CNVs were identified in 17.7% of them (96/542), variants of uncertain significance (VOUS) were detected in 4.8% (26/542) and likely benign CNVs in 9.2% of cases (50/542). We identified 6.6% (36/542) patients with known recurrent microdeletion (24 cases) and microduplication (12 cases) syndromes, as well as 4.8% (26/542) patients with non-recurrent rare microdeletions (21 cases) and microduplications (5 cases). In the group of patients with submicroscopic pathogenic/likely pathogenic CNVs (13.3%; 68/510) we identified 91.2% (62/68) patients with one CNV, 5.9% (4/68) patients with two likely independent CNVs and 2.9% (2/68) patients with two CNVs resulting from cryptic unbalanced translocations. Of all detected CNVs, 21% (31/147) had a de novo origin, 51% (75/147) were inherited and 28% (41/147) of unknown origin. In our cohort pathogenic/likely pathogenic microdeletions were more frequent than microduplications (69%; 51/74 vs. 31%; 23/74) ranging in size from 0.395 Mb to 10.676 Mb (microdeletions) and 0.544 Mb to 8.156 Mb (microduplications), but their sizes were not significantly different (P = 0.83). The pathogenic/likely pathogenic CNVs (median 2.663 Mb) were significantly larger than benign CNVs (median 0.394 Mb) (P < 0.00001) and likewise the pathogenic/likely pathogenic CNVs (median 2.663 Mb) were significantly larger in size than VOUS (median 0.469 Mb) (P < 0.00001). CONCLUSIONS Our results confirm the benefit of array-CGH in the current clinical genetic diagnostics leading to identification of the genetic cause of ID/DD in affected children.
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Dong HQ, Du YX. The study of copy number variations in the regions of PRKAB2 and PPM1K among congenital heart defects patients. ACTA ACUST UNITED AC 2019; 65:786-790. [PMID: 31340305 DOI: 10.1590/1806-9282.65.6.786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 08/27/2018] [Indexed: 11/22/2022]
Abstract
OBJECTIVE This study was to assess the genetic association of copy number variations in two genes (PRKAB2 and PPM1K) located in two regions (tetralogy of Fallot and ventricular septal defect) in a Chinese Han population. METHODS A total of 200 congenital heart disease patients (100 tetralogy of Fallot patients and 100 ventricular septal defect patients) and 100 congenital heart defect-free controls were recruited, and quantitative real-time PCR analysis was used to replicate the association of two copy number variations with congenital heart defects in a Chinese Han population. RESULTS One deletion at PRKAB2 and one duplication at PPM1K were found in two of the tetralogy of Fallot patients, respectively; while all these regions were duplicated in both ventricular septal defect patients and in the 100 congenital heart defects-free controls. CONCLUSIONS We replicated the copy number variations at the disease-candidate genes of PRKAB2 and PPM1K with tetralogy of Fallot in a Chinese Han population, and in patients with ventricular septal defect mutations in these two genes were not found. These results indicate the same molecular population genetics exist in these two genes with different ethnicity. This shows that these two genes are possibly specific pf tetralogy of Fallot candidates.
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Affiliation(s)
- Han-Quan Dong
- Department of Pneumology, Tianjin Children's Hospital, Tianjin, 300074-China
| | - Yue-Xin Du
- Department of Child Healthcare, Tianjin Municipal Women and Children health care center, Tianjin, 300070, China
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Abstract
Structural and quantitative chromosomal rearrangements, collectively referred to as structural variation (SV), contribute to a large extent to the genetic diversity of the human genome and thus are of high relevance for cancer genetics, rare diseases and evolutionary genetics. Recent studies have shown that SVs can not only affect gene dosage but also modulate basic mechanisms of gene regulation. SVs can alter the copy number of regulatory elements or modify the 3D genome by disrupting higher-order chromatin organization such as topologically associating domains. As a result of these position effects, SVs can influence the expression of genes distant from the SV breakpoints, thereby causing disease. The impact of SVs on the 3D genome and on gene expression regulation has to be considered when interpreting the pathogenic potential of these variant types.
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Affiliation(s)
- Malte Spielmann
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Darío G Lupiáñez
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, Germany. .,Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany.
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Ceylan AC, Sahin I, Erdem HB, Kayhan G, Simsek-Kiper PO, Utine GE, Percin F, Boduroglu K, Alikasifoglu M. An eight-case 1q21 region series: novel aberrations and clinical variability with new features. JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2019; 63:548-557. [PMID: 30773728 DOI: 10.1111/jir.12592] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/04/2018] [Accepted: 12/31/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Rearrangement of the 1q21 region of chromosome 1 manifests as multiple phenotypes, including microcephaly, intellectual disability, dysmorphic facial features, eye abnormalities, cardiac defects, genitourinary anomalies, autism spectrum disorder, psychiatric conditions and seizures. Herein, we describe eight patients with 1q21 deletion and duplication syndromes, and novel deletions and findings. METHODS Chromosomal microarray analysis was performed to identify the existence of copy number variation. Quantitative polymerase chain reaction was applied using specific primers for the control and 1q21 region of chromosome 1. Mutational analysis was performed in case 5 using direct genomic sequencing for exons 1-6 in RBM8A. RESULTS Copy number variation analysis identified seven deletions and one duplication of the 1q21 region in the eight patients. In addition, four variations were de novo, and two deletions are reported here for the first time. One of the cases (case 7) presents moderate intellectual disability and dysmorphic facial findings, whereas chromosomal microarray analysis showed that case 7 had an 889-kb deletion in the 1q21 proximal region (GPR89A, PDZK1, CD160, POLR3C and NBPF12). CONCLUSION Although the deletion in case 5 did not include the thrombocytopenia-absent radius syndrome critical region or the RBM8A gene, he had pectoral muscle hypoplasia, radius and humerus hypoplasia and short curved ribs, which are indicative of a potential thrombocytopenia-absent radius region modifier. The findings in case 7 suggest that the proximal part of the 1q21 microdeletion syndrome region might be very important for the onset of clinical manifestations. Some novel findings were observed in the presented cases, such as radius and humerus hypoplasia and brain stem hypoplasia. The presented findings expand the spectrum of 1q21 aberrations and provide evidence of genotype-phenotype correlations for this region.
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Affiliation(s)
- A C Ceylan
- Faculty of Medicine, Department of Medical Genetics, Hacettepe University, Ankara, Turkey
- Department of Medical Genetics, Ankara Ataturk Training and Research Hospital, Yildirim Beyazit University, Ankara, Turkey
| | - I Sahin
- Faculty of Medicine, Department of Medical Genetics, Ataturk University, Erzurum, Turkey
- Department of Medical Genetics, Ankara Diskapi Yildirim Beyazit Training and Research Hospital, Ankara, Turkey
| | - H B Erdem
- Faculty of Medicine, Department of Medical Genetics, Ataturk University, Erzurum, Turkey
- Department of Medical Genetics, Ankara Diskapi Yildirim Beyazit Training and Research Hospital, Ankara, Turkey
| | - G Kayhan
- Faculty of Medicine, Department of Medical Genetics, Gazi University, Ankara, Turkey
| | - P O Simsek-Kiper
- Faculty of Medicine, Department of Pediatric Genetics, Hacettepe University, Ankara, Turkey
| | - G E Utine
- Faculty of Medicine, Department of Pediatric Genetics, Hacettepe University, Ankara, Turkey
| | - F Percin
- Faculty of Medicine, Department of Medical Genetics, Gazi University, Ankara, Turkey
| | - K Boduroglu
- Faculty of Medicine, Department of Medical Genetics, Hacettepe University, Ankara, Turkey
- Faculty of Medicine, Department of Pediatric Genetics, Hacettepe University, Ankara, Turkey
| | - M Alikasifoglu
- Faculty of Medicine, Department of Medical Genetics, Hacettepe University, Ankara, Turkey
- Faculty of Medicine, Department of Pediatric Genetics, Hacettepe University, Ankara, Turkey
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Jurko T, Jurko A, Jurko A, Krsiakova J, Minarik M, Mestanik M, Tonhajzerova I. Pulmonary artery sling – A novel cardiovascular finding in a patient with distal 18q deletion. PROGRESS IN PEDIATRIC CARDIOLOGY 2019. [DOI: 10.1016/j.ppedcard.2018.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Park KB, Nam KE, Cho AR, Jang W, Kim M, Park JH. Effects of Copy Number Variations on Developmental Aspects of Children With Delayed Development. Ann Rehabil Med 2019; 43:215-223. [PMID: 31072088 PMCID: PMC6509583 DOI: 10.5535/arm.2019.43.2.215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/19/2018] [Indexed: 11/06/2022] Open
Abstract
Objective To determine effects of copy number variations (CNV) on developmental aspects of children suspected of having delayed development. Methods A retrospective chart review was done for 65 children who underwent array-comparative genomic hybridization after visiting physical medicine & rehabilitation department of outpatient clinic with delayed development as chief complaints. Children were evaluated with Denver Developmental Screening Test II (DDST-II), Sequenced Language Scale for Infants (SELSI), or Preschool Receptive-Expressive Language Scale (PRES). A Mann-Whitney U test was conducted to determine statistical differences of developmental quotient (DQ), receptive language quotient (RLQ), and expressive language quotient (ELQ) between children with CNV (CNV(+) group, n=16) and children without CNV (CNV(–) group, n=37). Results Of these subjects, the average age was 35.1 months (mean age, 35.1±24.2 months). Sixteen (30.2%) patients had copy number variations. In the CNV(+) group, 14 children underwent DDST-II. In the CNV(–) group, 29 children underwent DDST-II. Among variables, gross motor scale was significantly (p=0.038) lower in the CNV(+) group compared with the CNV(–) group. In the CNV(+) group, 5 children underwent either SELSI or PRES. In the CNV(–) group, 27 children underwent above language assessment examination. Both RLQ and ELQ were similar between the two groups. Conclusion The gross motor domain in DQ was significantly lower in children with CNV compared to that in children without CNV. This result suggests that additional genetic factors contribute to this variability. Active detection of genomic imbalance could play a vital role when prominent gross motor delay is presented in children with delayed development.
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Affiliation(s)
- Kee-Boem Park
- Department of Rehabilitation Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kyung Eun Nam
- Department of Rehabilitation Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ah-Ra Cho
- Department of Rehabilitation Medicine, St. Paul's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Woori Jang
- Department of Laboratory Medicine College of Medicine, The Catholic University of Korea, Seoul, Korea.,Department of Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Myungshin Kim
- Department of Laboratory Medicine College of Medicine, The Catholic University of Korea, Seoul, Korea.,Department of Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Joo Hyun Park
- Department of Rehabilitation Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Mir YR, Kuchay RAH. Advances in identification of genes involved in autosomal recessive intellectual disability: a brief review. J Med Genet 2019; 56:567-573. [PMID: 30842223 DOI: 10.1136/jmedgenet-2018-105821] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 02/01/2019] [Accepted: 02/11/2019] [Indexed: 12/28/2022]
Abstract
Intellectual disability (ID) is a clinically and genetically heterogeneous disorder, affecting 1%-3% of the general population. The number of ID-causing genes is high. Many X-linked genes have been implicated in ID. Autosomal dominant genes have recently been the focus of several large-scale studies. The total number of autosomal recessive ID (ARID) genes is estimated to be very high, and most are still unknown. Although research into the genetic causes of ID has recently gained momentum, identification of pathogenic mutations that cause ARID has lagged behind, predominantly due to non-availability of sizeable families. A commonly used approach to identify genetic loci for recessive disorders in consanguineous families is autozygosity mapping and whole-exome sequencing. Combination of these two approaches has recently led to identification of many genes involved in ID. These genes have diverse function and control various biological processes. In this review, we will present an update regarding genes that have been recently implicated in ID with focus on ARID.
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Affiliation(s)
- Yaser Rafiq Mir
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, India
| | - Raja Amir Hassan Kuchay
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, India
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Chen X, Li H, Chen C, Zhou L, Xu X, Xiang Y, Tang S. Genome-Wide Array Analysis Reveals Novel Genomic Regions and Candidate Gene for Intellectual Disability. Mol Diagn Ther 2019; 22:749-757. [PMID: 30259421 DOI: 10.1007/s40291-018-0358-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Intellectual disability (ID) is often sporadic, and its complex etiology makes clinical diagnosis extremely difficult. OBJECTIVE The aims of this study were to detect copy number variations (CNVs) in patients with ID and to analyze the correlation between pathogenic CNVs and clinical phenotype. METHODS After cases of ID caused by metabolic dysfunction or environmental factors were excluded, 64 patients with moderate to severe ID were enrolled. Karyotype and single nucleotide polymorphism (SNP) array analyses were performed for all patients. The relationship between CNVs and phenotype was identified with genotype-phenotype comparisons and by searching CNV databases. RESULTS Karyotype analysis showed four patients with chromosomal aneuploidy and seven with chromosomal structural abnormality. After excluding the four cases with chromosomal aneuploidy, the remaining 60 cases were analyzed using SNP array. The results revealed 87 CNVs in 45 cases, including 16 pathogenic CNVs in 12 individuals, with a diagnostic yield of 20.0% (12/60). We found large deletions at 16q22.2q23.1 and 3q24q25.32 in two patients, respectively, in whom specific syndromes had not been defined. Our array analysis showed one case carried a 210 kb deletion at 1p21.2p21.3, which included only one coding gene LPPR4, which might be a candidate gene for ID phenotype. CONCLUSIONS Use of the genome-wide array method can improve the detection rate of CNVs, reveal chromosomal abnormalities that have not been well-characterized by cytology, and provide a new way to locate genes for patients with the ID phenotype. Interpretation of CNVs remains a major challenge. Sharing of CNVs and phenotype information from different laboratories in public databases is important.
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Affiliation(s)
- Xiangnan Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Huanzheng Li
- The Center of Wenzhou Prenatal Diagnostics, Key Laboratory of Birth Defects, Wenzhou Central Hospital, Wenzhou, Zhejiang, China
| | - Chong Chen
- The Center of Wenzhou Prenatal Diagnostics, Key Laboratory of Birth Defects, Wenzhou Central Hospital, Wenzhou, Zhejiang, China
| | - Lili Zhou
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- The Center of Wenzhou Prenatal Diagnostics, Key Laboratory of Birth Defects, Wenzhou Central Hospital, Wenzhou, Zhejiang, China
| | - Xueqin Xu
- The Center of Wenzhou Prenatal Diagnostics, Key Laboratory of Birth Defects, Wenzhou Central Hospital, Wenzhou, Zhejiang, China
| | - Yanbao Xiang
- The Center of Wenzhou Prenatal Diagnostics, Key Laboratory of Birth Defects, Wenzhou Central Hospital, Wenzhou, Zhejiang, China
| | - Shaohua Tang
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
- The Center of Wenzhou Prenatal Diagnostics, Key Laboratory of Birth Defects, Wenzhou Central Hospital, Wenzhou, Zhejiang, China.
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Chromosome 2p15-p16.1 microduplication in a boy with congenital anomalies: Is it a distinctive syndrome? Eur J Med Genet 2019; 62:47-54. [PMID: 29864511 DOI: 10.1016/j.ejmg.2018.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 04/30/2018] [Accepted: 05/03/2018] [Indexed: 11/17/2022]
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Affiliation(s)
- Ji-Un Kang
- Department of Biomedical Laboratory Science, Korea Nazarene University, Cheonan, Korea
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36
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Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity. Nat Genet 2018; 51:106-116. [PMID: 30559488 PMCID: PMC6309590 DOI: 10.1038/s41588-018-0288-4] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 10/23/2018] [Indexed: 12/11/2022]
Abstract
We combined de novo mutation (DNM) data from 10,927 individuals with developmental delay and autism to identify 253 candidate neurodevelopmental disease genes with an excess of missense and/or likely gene-disruptive (LGD) mutations. Of these genes, 124 reach exome-wide significance (P < 5 × 10-7) for DNM. Intersecting these results with copy number variation (CNV) morbidity data shows an enrichment for genomic disorder regions (30/253, likelihood ratio (LR) +1.85, P = 0.0017). We identify genes with an excess of missense DNMs overlapping deletion syndromes (for example, KIF1A and the 2q37 deletion) as well as duplication syndromes, such as recurrent MAPK3 missense mutations within the chromosome 16p11.2 duplication, recurrent CHD4 missense DNMs in the 12p13 duplication region, and recurrent WDFY4 missense DNMs in the 10q11.23 duplication region. Network analyses of genes showing an excess of DNMs highlights functional networks, including cell-specific enrichments in the D1+ and D2+ spiny neurons of the striatum.
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Zhou B, Ho SS, Zhang X, Pattni R, Haraksingh RR, Urban AE. Whole-genome sequencing analysis of CNV using low-coverage and paired-end strategies is efficient and outperforms array-based CNV analysis. J Med Genet 2018; 55:735-743. [PMID: 30061371 DOI: 10.1136/jmedgenet-2018-105272] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 05/16/2018] [Accepted: 06/26/2018] [Indexed: 11/03/2022]
Abstract
BACKGROUND Copy number variation (CNV) analysis is an integral component of the study of human genomes in both research and clinical settings. Array-based CNV analysis is the current first-tier approach in clinical cytogenetics. Decreasing costs in high-throughput sequencing and cloud computing have opened doors for the development of sequencing-based CNV analysis pipelines with fast turnaround times. We carry out a systematic and quantitative comparative analysis for several low-coverage whole-genome sequencing (WGS) strategies to detect CNV in the human genome. METHODS We compared the CNV detection capabilities of WGS strategies (short insert, 3 kb insert mate pair and 5 kb insert mate pair) each at 1×, 3× and 5× coverages relative to each other and to 17 currently used high-density oligonucleotide arrays. For benchmarking, we used a set of gold standard (GS) CNVs generated for the 1000 Genomes Project CEU subject NA12878. RESULTS Overall, low-coverage WGS strategies detect drastically more GS CNVs compared with arrays and are accompanied with smaller percentages of CNV calls without validation. Furthermore, we show that WGS (at ≥1× coverage) is able to detect all seven GS deletion CNVs >100 kb in NA12878, whereas only one is detected by most arrays. Lastly, we show that the much larger 15 Mbp Cri du chat deletion can be readily detected with short-insert paired-end WGS at even just 1× coverage. CONCLUSIONS CNV analysis using low-coverage WGS is efficient and outperforms the array-based analysis that is currently used for clinical cytogenetics.
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Affiliation(s)
- Bo Zhou
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Steve S Ho
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Xianglong Zhang
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Rajini R Haraksingh
- Department of Life Sciences, The University of the West Indies, Saint Augustine, Trinidad and Tobago
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.,Program on Genetics of Brain Function, Stanford Center for Genomics and Personalized Medicine, Tasha and John Morgridge Faculty Scholar, Stanford Child Health Research Institute, Stanford University, Stanford, California, USA
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38
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Kalnak N, Stamouli S, Peyrard-Janvid M, Rabkina I, Becker M, Klingberg T, Kere J, Forssberg H, Tammimies K. Enrichment of rare copy number variation in children with developmental language disorder. Clin Genet 2018; 94:313-320. [PMID: 29851021 DOI: 10.1111/cge.13389] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/23/2018] [Accepted: 05/27/2018] [Indexed: 02/04/2023]
Abstract
Developmental language disorder (DLD) is a common neurodevelopmental disorder with largely unknown etiology. Rare copy number variants (CNVs) have been implicated in the genetic architecture of other neurodevelopmental disorders (NDDs), which have led to clinical genetic testing recommendations for these disorders; however, the evidence is still lacking for DLD. We analyzed rare and de novo CNVs in 58 probands with severe DLD, their 159 family members and 76 Swedish typically developing children using high-resolution microarray. DLD probands had larger rare CNVs as measured by total length (P = .05), and average length (P = .04). In addition, the rate of rare CNVs overlapping coding genes was increased (P = .03 and P = .01) and in average more genes were affected (P = .006 and P = .03) in the probands and their siblings, respectively. De novo CNVs were found in 4.8% DLD probands (2/42) and 2.4% (1/42) siblings. Clinically significant CNVs or chromosomal anomalies were found in 6.9% (4/58) of the probands of which 2 carried 16p11.2 deletions. We provide further evidence that rare CNVs contribute to the etiology of DLD in loci that overlap with other NDDs. Based on our results and earlier literature, families with DLD should be offered molecular genetic testing as a routine in their clinical follow-up.
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Affiliation(s)
- N Kalnak
- Department of Women and Children's Health, Neuropediatric Unit, Karolinska Institutet, Astrid Lindgren Children's Hospital, Solna, Sweden.,Department of Clinical Sciences Lund, Child, and Adolescent Psychiatry Unit, Faculty of Medicine, Lund University, Lund, Sweden
| | - S Stamouli
- Department of Women and Children's Health, Center of Neurodevelopmental Disorders, Karolinska Institutet, Sweden and Centre for Psychiatry Research, Stockholm County Council, Stockholm, Sweden
| | - M Peyrard-Janvid
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - I Rabkina
- Department of Women and Children's Health, Center of Neurodevelopmental Disorders, Karolinska Institutet, Sweden and Centre for Psychiatry Research, Stockholm County Council, Stockholm, Sweden
| | - M Becker
- Department of Women and Children's Health, Center of Neurodevelopmental Disorders, Karolinska Institutet, Sweden and Centre for Psychiatry Research, Stockholm County Council, Stockholm, Sweden
| | - T Klingberg
- Department of Clinical Neuroscience, Karolinska Institutet, Solna, Sweden
| | - J Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,School of Basic and Medical Biosciences, King's College London, London, UK.,Molecular Neurology Research Program, University of Helsinki, and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - H Forssberg
- Department of Women and Children's Health, Neuropediatric Unit, Karolinska Institutet, Astrid Lindgren Children's Hospital, Solna, Sweden
| | - K Tammimies
- Department of Women and Children's Health, Center of Neurodevelopmental Disorders, Karolinska Institutet, Sweden and Centre for Psychiatry Research, Stockholm County Council, Stockholm, Sweden
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40
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Wang W, Mao B, Wei X, Yin D, Li H, Mao L, Guo X, Sun Y, Yang Y. Application of an improved targeted next generation sequencing method to diagnose non‑syndromic mental retardation in one step: A case report. Mol Med Rep 2018; 18:981-986. [PMID: 29845227 DOI: 10.3892/mmr.2018.9031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/01/2018] [Indexed: 11/06/2022] Open
Abstract
The genetic basis of congenital mental retardation includes chromosomal anomalies and single gene mutations. In addition to chromosome microarray analysis, next‑generation sequencing (NGS) and Sanger sequencing have additionally been applied to identify single gene mutations. However, no methods exist to identify the cause of an anomaly in one step. The present study applied an improved targeted NGS method to diagnose an 8‑year‑old Chinese Han female with mental retardation in one step. The microdeletion 17p11.2 was successfully detected by the improved targeted NGS and no single gene mutations were identified. The same microdeletion was verified using low coverage whole‑genome sequencing. Fertility guidance was also given to the patient's parents. In the present study, an improved targeted NGS method was applied to diagnose non‑syndromic mental retardation of unknown cause in one step. This improved method has the potential to be developed into a screening panel for the effective diagnosis of genetic abnormalities in non‑syndromic mental retardation and other congenital anomalies.
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Affiliation(s)
- Weipeng Wang
- Prenatal Diagnosis Center, Hubei Maternal and Child Health Hospital, Wuhan, Hubei 430070, P.R. China
| | - Bing Mao
- Department of Neurology, Wuhan Medical and Health Center for Women and Children, Wuhan, Hubei 430016, P.R. China
| | - Xiaoming Wei
- BGI‑Wuhan, BGI‑Shenzhen, Wuhan, Hubei 430074, P.R. China
| | - Dan Yin
- BGI‑Wuhan, BGI‑Shenzhen, Wuhan, Hubei 430074, P.R. China
| | - Hui Li
- Prenatal Diagnosis Center, Hubei Maternal and Child Health Hospital, Wuhan, Hubei 430070, P.R. China
| | - Liangwei Mao
- BGI‑Wuhan, BGI‑Shenzhen, Wuhan, Hubei 430074, P.R. China
| | - Xueqin Guo
- BGI‑Wuhan, BGI‑Shenzhen, Wuhan, Hubei 430074, P.R. China
| | - Yan Sun
- BGI‑Wuhan, BGI‑Shenzhen, Wuhan, Hubei 430074, P.R. China
| | - Yun Yang
- BGI‑Wuhan, BGI‑Shenzhen, Wuhan, Hubei 430074, P.R. China
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Zhao JJ, Halvardson J, Zander CS, Zaghlool A, Georgii‐Hemming P, Månsson E, Brandberg G, Sävmarker HE, Frykholm C, Kuchinskaya E, Thuresson A, Feuk L. Exome sequencing reveals NAA15 and PUF60 as candidate genes associated with intellectual disability. Am J Med Genet B Neuropsychiatr Genet 2018; 177:10-20. [PMID: 28990276 PMCID: PMC5765476 DOI: 10.1002/ajmg.b.32574] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 05/09/2017] [Accepted: 07/05/2017] [Indexed: 11/07/2022]
Abstract
Intellectual Disability (ID) is a clinically heterogeneous condition that affects 2-3% of population worldwide. In recent years, exome sequencing has been a successful strategy for studies of genetic causes of ID, providing a growing list of both candidate and validated ID genes. In this study, exome sequencing was performed on 28 ID patients in 27 patient-parent trios with the aim to identify de novo variants (DNVs) in known and novel ID associated genes. We report the identification of 25 DNVs out of which five were classified as pathogenic or likely pathogenic. Among these, a two base pair deletion was identified in the PUF60 gene, which is one of three genes in the critical region of the 8q24.3 microdeletion syndrome (Verheij syndrome). Our result adds to the growing evidence that PUF60 is responsible for the majority of the symptoms reported for carriers of a microdeletion across this region. We also report variants in several genes previously not associated with ID, including a de novo missense variant in NAA15. We highlight NAA15 as a novel candidate ID gene based on the vital role of NAA15 in the generation and differentiation of neurons in neonatal brain, the fact that the gene is highly intolerant to loss of function and coding variation, and previously reported DNVs in neurodevelopmental disorders.
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Affiliation(s)
- Jin J. Zhao
- Department of ImmunologyGenetics and PathologyScience for Life Laboratory UppsalaUppsala UniversityUppsalaSweden
| | - Jonatan Halvardson
- Department of ImmunologyGenetics and PathologyScience for Life Laboratory UppsalaUppsala UniversityUppsalaSweden
| | - Cecilia S. Zander
- Department of ImmunologyGenetics and PathologyScience for Life Laboratory UppsalaUppsala UniversityUppsalaSweden
| | - Ammar Zaghlool
- Department of ImmunologyGenetics and PathologyScience for Life Laboratory UppsalaUppsala UniversityUppsalaSweden
| | - Patrik Georgii‐Hemming
- Department of ImmunologyGenetics and PathologyScience for Life Laboratory UppsalaUppsala UniversityUppsalaSweden,Department of Molecular Medicine and SurgeryKarolinska InstituteKarolinska University Hospital SolnaStockholmSweden
| | - Else Månsson
- Department of PediatricsÖrebro University HospitalÖrebroSweden
| | | | | | - Carina Frykholm
- Department of ImmunologyGenetics and PathologyScience for Life Laboratory UppsalaUppsala UniversityUppsalaSweden
| | - Ekaterina Kuchinskaya
- Department of Clinical Genetics, and Department of Clinical MedicineLinköping UniversityLinköpingSweden
| | - Ann‐Charlotte Thuresson
- Department of ImmunologyGenetics and PathologyScience for Life Laboratory UppsalaUppsala UniversityUppsalaSweden
| | - Lars Feuk
- Department of ImmunologyGenetics and PathologyScience for Life Laboratory UppsalaUppsala UniversityUppsalaSweden
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Pinchefsky E, Laneuville L, Srour M. Distal 22q11.2 Microduplication: Case Report and Review of the Literature. Child Neurol Open 2017; 4:2329048X17737651. [PMID: 29147671 PMCID: PMC5673001 DOI: 10.1177/2329048x17737651] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/24/2017] [Accepted: 08/19/2017] [Indexed: 12/20/2022] Open
Abstract
Distal chromosome 22q11.2 microduplications are associated with a wide range of phenotypes and unclear pathogenicity. The authors report on a 3-year-old girl with global developmental delay harboring a de novo 1.24 Mb distal chromosome 22q11.2 microduplication and a paternally inherited 0.25 Mb chromosome 4p14 microduplication. The authors review clinical features of 30 reported cases of distal 22q11.2 duplications. Common features include developmental delay (93%), neuropsychiatric features (26%), and nonspecific facial dysmorphisms (74%). In 70% of cases, the distal 22q11.2 duplications were inherited, and the majority of the carrier parents were phenotypically normal. Furthermore, 30% of probands carried an additional copy number variant. Review of the phenotype in individuals carrying microduplications involving similar low copy repeats (LCR) failed to establish any clear genotype–phenotype correlations. Distal 22q11.2 duplications represent a major challenge for genetic counseling and prediction of clinical consequences. Our report suggests a pathogenic role of distal 22q11.2 duplications and supports a “multiple hit” hypothesis underlying its variable expressivity and phenotypic severity.
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Affiliation(s)
- Elana Pinchefsky
- Division of Pediatric Neurology, Department of Pediatrics, Montreal Children's Hospital, McGill University Health Centre (MUHC), Montreal, Québec, Canada
| | | | - Myriam Srour
- Division of Pediatric Neurology, Department of Pediatrics, Montreal Children's Hospital, McGill University Health Centre (MUHC), Montreal, Québec, Canada
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Lee KY, Shin E. Application of array comparative genomic hybridization in Korean children under 6 years old with global developmental delay. KOREAN JOURNAL OF PEDIATRICS 2017; 60:282-289. [PMID: 29042871 PMCID: PMC5638834 DOI: 10.3345/kjp.2017.60.9.282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 07/11/2017] [Accepted: 07/27/2017] [Indexed: 11/30/2022]
Abstract
Purpose Recent advancements in molecular techniques have greatly contributed to the discovery of genetic causes of unexplained developmental delay. Here, we describe the results of array comparative genomic hybridization (CGH) and the clinical features of 27 patients with global developmental delay. Methods We included 27 children who fulfilled the following criteria: Korean children under 6 years with global developmental delay; children who had at least one or more physical or neurological problem other than global developmental delay; and patients in whom both array CGH and G-banded karyotyping tests were performed. Results Fifteen male and 12 female patients with a mean age of 29.3±17.6 months were included. The most common physical and neurological abnormalities were facial dysmorphism (n=16), epilepsy (n=7), and hypotonia (n=7). Pathogenic copy number variation results were observed in 4 patients (14.8%): 18.73 Mb dup(2)(p24.2p25.3) and 1.62 Mb del(20p13) (patient 1); 22.31 Mb dup(2) (p22.3p25.1) and 4.01 Mb dup(2)(p21p22.1) (patient 2); 12.08 Mb del(4)(q22.1q24) (patient 3); and 1.19 Mb del(1)(q21.1) (patient 4). One patient (3.7%) displayed a variant of uncertain significance. Four patients (14.8%) displayed discordance between G-banded karyotyping and array CGH results. Among patients with normal array CGH results, 4 (16%) revealed brain anomalies such as schizencephaly and hydranencephaly. One patient was diagnosed with Rett syndrome and one with Möbius syndrome. Conclusion As chromosomal microarray can elucidate the cause of previously unexplained developmental delay, it should be considered as a first-tier cytogenetic diagnostic test for children with unexplained developmental delay.
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Affiliation(s)
- Kyung Yeon Lee
- Department of Pediatrics, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan, Korea
| | - Eunsim Shin
- Korea Clinical Laboratory, Molecular Diagnostics Team, Seoul, Korea
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Zahir FR, Tucker T, Mayo S, Brown CJ, Lim EL, Taylor J, Marra MA, Hamdan FF, Michaud JL, Friedman JM. Intragenic CNVs for epigenetic regulatory genes in intellectual disability: Survey identifies pathogenic and benign single exon changes. Am J Med Genet A 2017; 170:2916-2926. [PMID: 27748065 DOI: 10.1002/ajmg.a.37669] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 04/07/2016] [Indexed: 02/05/2023]
Abstract
The disruption of genes involved in epigenetic regulation is well known to cause Intellectual Disability (ID). We reported a custom microarray study that interrogated among others, the epigenetic regulatory gene-class, at single exon resolution. Here we elaborate on identified intragenic CNVs involving epigenetic regulatory genes; specifically discussing those in three genes previously unreported in ID etiology-ARID2, KDM3A, and ARID4B. The changes in ARID2 and KDM3A are likely pathogenic while the ARID4B variant is uncertain. Previously, we found a CNV involving only exon 6 of the JARID2 gene occurred apparently de novo in seven patients. JARID2 is known to cause ID and other neurodevelopmental conditions. However, exon 6 of this gene encodes one of a series of repeated motifs. We therefore, investigated the impact of this variant in two cohorts and present a genotype-phenotype assessment. We find the JARID2 exon 6 CNV is benign, with a high population frequency (>14%), but nevertheless could have a contributory effect. We also present results from an interrogation of the exomes of 2,044 patients with neurocognitive phenotypes for the incidence of potentially damaging mutation in the epigenetic regulatory gene-class. This paper provides a survey of the fine-scale CNV landscape for epigenetic regulatory genes in the context of ID, describing likely pathogenic as well as benign single exon imbalances. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Farah R Zahir
- Canada's Michael Smith Genome Sciences Center, Vancouver, British Columbia, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Tracy Tucker
- Provincial Medical Genetics Programme, Children's and Women's Health Centre of British Columbia, Vancouver, British Columbia, Canada
| | - Sonia Mayo
- Unidad de Genética y Diagnóstico Prenatal, Hospital Universitario y Politécnico La Fe. Valencia, Valencia, Spain
| | - Carolyn J Brown
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Emilia L Lim
- Canada's Michael Smith Genome Sciences Center, Vancouver, British Columbia, Canada
| | - Jonathan Taylor
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Center, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Fadi F Hamdan
- CHU Sainte-Justine Research Center, Montréal, Quebec, Canada
| | | | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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45
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Chari R, Lockwood WW, Lam WL. Computational Methods for the Analysis of Array Comparative Genomic Hybridization. Cancer Inform 2017. [DOI: 10.1177/117693510600200007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Array comparative genomic hybridization (array CGH) is a technique for assaying the copy number status of cancer genomes. The widespread use of this technology has lead to a rapid accumulation of high throughput data, which in turn has prompted the development of computational strategies for the analysis of array CGH data. Here we explain the principles behind array image processing, data visualization and genomic profile analysis, review currently available software packages, and raise considerations for future software development.
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Affiliation(s)
- Raj Chari
- Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, Vancouver BC, Canada V5Z 1L3
- These authors contributed equally to this work
| | - William W. Lockwood
- Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, Vancouver BC, Canada V5Z 1L3
- These authors contributed equally to this work
| | - Wan L. Lam
- Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, Vancouver BC, Canada V5Z 1L3
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46
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Tadros S, Wang R, Waters JJ, Waterman C, Collins AL, Collinson MN, Ahn JW, Josifova D, Chetan R, Kumar A. Inherited 2q23.1 microdeletions involving the MBD5 locus. Mol Genet Genomic Med 2017; 5:608-613. [PMID: 28944244 PMCID: PMC5606852 DOI: 10.1002/mgg3.316] [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: 02/01/2017] [Revised: 05/31/2017] [Accepted: 06/02/2017] [Indexed: 02/06/2023] Open
Abstract
Background Microdeletions of 2q23.1 disrupting MBD5 and loss of function mutations of MBD5 cause MBD5‐Associated Neurodevelopmental disorders (MAND). Nearly all reported patients have been isolated cases of de novo origin. Methods This study investigates three families with inherited MBD5 mutations from three different Regional Genetics Centres in the UK. Results Two of the parents in the study had MBD5 deletions in a mosaic form. The parent with an MBD5 deletion in an apparently nonmosaic form has a psychiatric disorder in the absence of developmental delay or dysmorphism. Conclusions Inherited forms of MBD5 deletions are rare, but do occur, especially in a mosaic form. The phenotypic spectrum of MAND may be wider than previously thought.
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Affiliation(s)
- Shereen Tadros
- North East Thames Regional Genetics ServiceGreat Ormond Street HospitalLondonWC1N 3JHUK
| | - Rubin Wang
- North East Thames Regional Genetics ServiceGreat Ormond Street HospitalLondonWC1N 3JHUK
| | - Jonathan J Waters
- North East Thames Regional Genetics ServiceGreat Ormond Street HospitalLondonWC1N 3JHUK
| | - Christine Waterman
- Wessex Regional Genetics LaboratorySalisbury NHS Foundation TrustOdstock RoadSalisburySP2 8BJUK
| | - Amanda L Collins
- Wessex Clinical Genetics ServicePrincess Anne HospitalMailpoint 627SouthamptonSO16 5YAUK
| | - Morag N Collinson
- Wessex Regional Genetics LaboratorySalisbury NHS Foundation TrustOdstock RoadSalisburySP2 8BJUK
| | - Joo W Ahn
- South East Thames Regional Genetics ServiceGuy's HospitalGreat Maze PondLondonSE1 9RTUK
| | - Dragana Josifova
- South East Thames Regional Genetics ServiceGuy's HospitalGreat Maze PondLondonSE1 9RTUK
| | - Ravi Chetan
- Department of PaediatricsSouthend University HospitalWestcliff on SeaSS0 0RYUK
| | - Ajith Kumar
- North East Thames Regional Genetics ServiceGreat Ormond Street HospitalLondonWC1N 3JHUK
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Wu Y, Wang Y, Tao J, Han X, Zhao X, Liu C, Gao L, Cheng W. The clinical use of chromosomal microarray analysis in detection of fetal chromosomal rearrangements: a study from China Mainland. Eur J Obstet Gynecol Reprod Biol 2017; 212:44-50. [DOI: 10.1016/j.ejogrb.2017.03.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 02/19/2017] [Accepted: 03/04/2017] [Indexed: 10/20/2022]
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48
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Lei TY, Wang HT, Li F, Cui YQ, Fu F, Li R, Liao C. Application of high resolution SNP arrays in patients with congenital oral clefts in south China. J Genet 2017; 95:801-809. [PMID: 27994178 DOI: 10.1007/s12041-016-0696-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Chromosome microarray analysis (CMA) has proven to be a powerful tool in postnatal patients with intellectual disabilities. However, the diagnostic capability of CMA in patients with congenital oral clefts remain mysterious. Here, we present our clinical experience in implementing whole-genome high-resolution SNP arrays to investigate 33 patients with syndromic and nonsyndromic oral clefts in whom standard karyotyping analyses showed normal karyotypes. We aim to identify the genomic aetiology and candidate genes in patients with congenital oral clefts. CMA revealed copy number variants (CNVs) in every patient, which ranged from 2 to 9 per sample. The size of detected CNVs varied from 100 to 3.2 Mb. In 33 patients, we identified six clinically significant CNVs. The incidence of clinically significant CNVs was 18.2% (6/33). Three of these six CNVs were detected in patients with nonsyndromic clefts, including one who presented with isolated cleft lip with cleft palate (CLP) and two with cleft palate only (CPO). The remaining three CNVs were detected in patients with syndromic clefts. However, no CNV was detected in patients with cleft lip only (CLO). The six clinically significant CNVs were as follows: 8p23.1 microduplication (198 kb); 10q22.2-q22.3 microdeletion (1766 kb); 18q12.3 microduplication (638 kb); 20p12.1 microdeletion (184 kb); 6q26 microdeletion (389 kb); and 22q11.21-q11.23 microdeletion (3163 kb). In addition, two novel candidate genes for oral clefts, KAT6B and MACROD2, were putatively identified. We also found a CNV of unknown clinical significance with a detection rate of 3.0% (1/33). Our results further support the notion that CNVs significantly contributed to the genetic aetiology of oral clefts and emphasize the efficacy of whole-genome high-resolution SNP arrays to detect novel candidate genes in patients with syndromic and nonsyndromic clefts.
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Affiliation(s)
- Ting-Ying Lei
- Department of Prenatal Diagnostic Center Guangzhou Medical University, Guangdong, 510623, People's Republic of China.
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49
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O'Mahony EF, Hutchinson DP, McGillivray G, Nisbet DL, Palma-Dias R. Right-sided aortic arch in the age of microarray. Prenat Diagn 2017; 37:440-445. [DOI: 10.1002/pd.5029] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/20/2017] [Accepted: 02/12/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Edward F. O'Mahony
- Royal Women's Hospital; Parkville Victoria Australia
- University of Melbourne; Department of Obstetrics & Gynaecology, Royal Womens Hospital; Parkville VIC 3052 Australia
| | - Darren P. Hutchinson
- Royal Women's Hospital; Parkville Victoria Australia
- Royal Children's Hospital; Parkville Victoria Australia
| | - George McGillivray
- Royal Women's Hospital; Parkville Victoria Australia
- Victorian Clinical Genetics Services; Murdoch Children's Research Institute; Melbourne Australia
| | | | - Ricardo Palma-Dias
- Royal Women's Hospital; Parkville Victoria Australia
- University of Melbourne; Department of Obstetrics & Gynaecology, Royal Womens Hospital; Parkville VIC 3052 Australia
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50
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Copy-number variation of housekeeping gene rpl13a in rat strains selected for nervous system excitability. Mol Cell Probes 2017; 33:11-15. [PMID: 28192165 DOI: 10.1016/j.mcp.2017.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 02/07/2017] [Accepted: 02/07/2017] [Indexed: 11/20/2022]
Abstract
We evaluated copy number variation (CNV) for four genes in rat strains differing in nervous system excitability. rpl13a copy number is significantly reduced in hippocampus and bone marrow in rats with a high excitability threshold and stress. The observed phenomenon may be associated with a role for rpl13a in lipid metabolism.
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